Project Achilles Copy Number Paper by Robin Meyers (2819002)

“…</div><div><br></div><div><br></div><div><br></div><div>Analysis steps v3.3.8a:</div><div><br></div><div>1. QC and identify reps with reproducibility <0.8 or are outliers on PCA or fail FP</div><div>2. remove sgRNAs(guides) with low counts in DNA samples:</div><div>completely remove shRNAs with median <=1 </div><div>3. remove replicates that fail QC measures </div><div>4. fold change(FC) with DNA pool samples </div><div>5. zero-center median of negative controls</div><div>6. collapse replicates per line </div><div>7. sgRNAs are mapped to genes using(Achilles_v3.3.8a.gct)</div><div><br></div><div>Analysis steps v3.3.8:</div><div><br></div><div>1. …”

<strong>Drought re-routes soil microbial carbon metabolism towards emission of volatile metabolites in an artificial tropical rainforest</strong> by Linnea Honeker (13113813)

“…After gas fluxes were expected to equilibrate, approximately 8 hr post pyruvate labeling (~ 6 PM), measurement intervals were decreased to low frequency (50 minutes) and remained at this frequency until measurements were stopped at 48 hr post labeling. …”

Image_5_Multi-omics analysis identifies IgG2b class-switching with ALCAM-CD6 co-stimulation in joint-draining lymph nodes during advanced inflammatory-erosive arthritis.tif by H. Mark Kenney (10320665)

“…Integration of single-cell and spatial transcriptomics revealed the increased IgG2b⁺ plasma cells localized in MARCO⁺ peri-follicular medullary sinuses. A concomitant decreased Fth1 expression (Early 2.5 ± 0.74 vs Advanced 1.0 ± 0.50 counts, p<0.001) within Advanced PLN sinuses was associated with accumulation of iron-laden Prussian blue positive macrophages in lymph nodes and synovium of Advanced TNF-Tg mice, and further validated in RA clinical samples. …”

Cic controls ISC proliferation by regulating <i>pnt</i> transcription. by Yinhua Jin (838896)

“…<p>(A–E) Effects caused by <i>pntP1</i> overexpression and RNAi’s. …”

Table_2_Multi-omics analysis identifies IgG2b class-switching with ALCAM-CD6 co-stimulation in joint-draining lymph nodes during advanced inflammatory-erosive arthritis.docx by H. Mark Kenney (10320665)

“…Integration of single-cell and spatial transcriptomics revealed the increased IgG2b⁺ plasma cells localized in MARCO⁺ peri-follicular medullary sinuses. A concomitant decreased Fth1 expression (Early 2.5 ± 0.74 vs Advanced 1.0 ± 0.50 counts, p<0.001) within Advanced PLN sinuses was associated with accumulation of iron-laden Prussian blue positive macrophages in lymph nodes and synovium of Advanced TNF-Tg mice, and further validated in RA clinical samples. …”

Table_1_Multi-omics analysis identifies IgG2b class-switching with ALCAM-CD6 co-stimulation in joint-draining lymph nodes during advanced inflammatory-erosive arthritis.docx by H. Mark Kenney (10320665)

“…Integration of single-cell and spatial transcriptomics revealed the increased IgG2b⁺ plasma cells localized in MARCO⁺ peri-follicular medullary sinuses. A concomitant decreased Fth1 expression (Early 2.5 ± 0.74 vs Advanced 1.0 ± 0.50 counts, p<0.001) within Advanced PLN sinuses was associated with accumulation of iron-laden Prussian blue positive macrophages in lymph nodes and synovium of Advanced TNF-Tg mice, and further validated in RA clinical samples. …”

Image_7_Multi-omics analysis identifies IgG2b class-switching with ALCAM-CD6 co-stimulation in joint-draining lymph nodes during advanced inflammatory-erosive arthritis.tif by H. Mark Kenney (10320665)

“…Integration of single-cell and spatial transcriptomics revealed the increased IgG2b⁺ plasma cells localized in MARCO⁺ peri-follicular medullary sinuses. A concomitant decreased Fth1 expression (Early 2.5 ± 0.74 vs Advanced 1.0 ± 0.50 counts, p<0.001) within Advanced PLN sinuses was associated with accumulation of iron-laden Prussian blue positive macrophages in lymph nodes and synovium of Advanced TNF-Tg mice, and further validated in RA clinical samples. …”

DataSheet_1_Multi-omics analysis identifies IgG2b class-switching with ALCAM-CD6 co-stimulation in joint-draining lymph nodes during advanced inflammatory-erosive arthritis.docx by H. Mark Kenney (10320665)

“…Integration of single-cell and spatial transcriptomics revealed the increased IgG2b⁺ plasma cells localized in MARCO⁺ peri-follicular medullary sinuses. A concomitant decreased Fth1 expression (Early 2.5 ± 0.74 vs Advanced 1.0 ± 0.50 counts, p<0.001) within Advanced PLN sinuses was associated with accumulation of iron-laden Prussian blue positive macrophages in lymph nodes and synovium of Advanced TNF-Tg mice, and further validated in RA clinical samples. …”

Video_1_Multi-omics analysis identifies IgG2b class-switching with ALCAM-CD6 co-stimulation in joint-draining lymph nodes during advanced inflammatory-erosive arthritis.mp4 by H. Mark Kenney (10320665)

“…Integration of single-cell and spatial transcriptomics revealed the increased IgG2b⁺ plasma cells localized in MARCO⁺ peri-follicular medullary sinuses. A concomitant decreased Fth1 expression (Early 2.5 ± 0.74 vs Advanced 1.0 ± 0.50 counts, p<0.001) within Advanced PLN sinuses was associated with accumulation of iron-laden Prussian blue positive macrophages in lymph nodes and synovium of Advanced TNF-Tg mice, and further validated in RA clinical samples. …”

Image_6_Multi-omics analysis identifies IgG2b class-switching with ALCAM-CD6 co-stimulation in joint-draining lymph nodes during advanced inflammatory-erosive arthritis.tif by H. Mark Kenney (10320665)

“…Integration of single-cell and spatial transcriptomics revealed the increased IgG2b⁺ plasma cells localized in MARCO⁺ peri-follicular medullary sinuses. A concomitant decreased Fth1 expression (Early 2.5 ± 0.74 vs Advanced 1.0 ± 0.50 counts, p<0.001) within Advanced PLN sinuses was associated with accumulation of iron-laden Prussian blue positive macrophages in lymph nodes and synovium of Advanced TNF-Tg mice, and further validated in RA clinical samples. …”

Video_3_Multi-omics analysis identifies IgG2b class-switching with ALCAM-CD6 co-stimulation in joint-draining lymph nodes during advanced inflammatory-erosive arthritis.mp4 by H. Mark Kenney (10320665)

“…Integration of single-cell and spatial transcriptomics revealed the increased IgG2b⁺ plasma cells localized in MARCO⁺ peri-follicular medullary sinuses. A concomitant decreased Fth1 expression (Early 2.5 ± 0.74 vs Advanced 1.0 ± 0.50 counts, p<0.001) within Advanced PLN sinuses was associated with accumulation of iron-laden Prussian blue positive macrophages in lymph nodes and synovium of Advanced TNF-Tg mice, and further validated in RA clinical samples. …”

Video_2_Multi-omics analysis identifies IgG2b class-switching with ALCAM-CD6 co-stimulation in joint-draining lymph nodes during advanced inflammatory-erosive arthritis.mp4 by H. Mark Kenney (10320665)

“…Integration of single-cell and spatial transcriptomics revealed the increased IgG2b⁺ plasma cells localized in MARCO⁺ peri-follicular medullary sinuses. A concomitant decreased Fth1 expression (Early 2.5 ± 0.74 vs Advanced 1.0 ± 0.50 counts, p<0.001) within Advanced PLN sinuses was associated with accumulation of iron-laden Prussian blue positive macrophages in lymph nodes and synovium of Advanced TNF-Tg mice, and further validated in RA clinical samples. …”

Image_4_Multi-omics analysis identifies IgG2b class-switching with ALCAM-CD6 co-stimulation in joint-draining lymph nodes during advanced inflammatory-erosive arthritis.tif by H. Mark Kenney (10320665)

“…Integration of single-cell and spatial transcriptomics revealed the increased IgG2b⁺ plasma cells localized in MARCO⁺ peri-follicular medullary sinuses. A concomitant decreased Fth1 expression (Early 2.5 ± 0.74 vs Advanced 1.0 ± 0.50 counts, p<0.001) within Advanced PLN sinuses was associated with accumulation of iron-laden Prussian blue positive macrophages in lymph nodes and synovium of Advanced TNF-Tg mice, and further validated in RA clinical samples. …”

Image_1_Multi-omics analysis identifies IgG2b class-switching with ALCAM-CD6 co-stimulation in joint-draining lymph nodes during advanced inflammatory-erosive arthritis.tif by H. Mark Kenney (10320665)

“…Integration of single-cell and spatial transcriptomics revealed the increased IgG2b⁺ plasma cells localized in MARCO⁺ peri-follicular medullary sinuses. A concomitant decreased Fth1 expression (Early 2.5 ± 0.74 vs Advanced 1.0 ± 0.50 counts, p<0.001) within Advanced PLN sinuses was associated with accumulation of iron-laden Prussian blue positive macrophages in lymph nodes and synovium of Advanced TNF-Tg mice, and further validated in RA clinical samples. …”

Image_2_Multi-omics analysis identifies IgG2b class-switching with ALCAM-CD6 co-stimulation in joint-draining lymph nodes during advanced inflammatory-erosive arthritis.tif by H. Mark Kenney (10320665)

“…Integration of single-cell and spatial transcriptomics revealed the increased IgG2b⁺ plasma cells localized in MARCO⁺ peri-follicular medullary sinuses. A concomitant decreased Fth1 expression (Early 2.5 ± 0.74 vs Advanced 1.0 ± 0.50 counts, p<0.001) within Advanced PLN sinuses was associated with accumulation of iron-laden Prussian blue positive macrophages in lymph nodes and synovium of Advanced TNF-Tg mice, and further validated in RA clinical samples. …”

Image_3_Multi-omics analysis identifies IgG2b class-switching with ALCAM-CD6 co-stimulation in joint-draining lymph nodes during advanced inflammatory-erosive arthritis.tif by H. Mark Kenney (10320665)

“…Integration of single-cell and spatial transcriptomics revealed the increased IgG2b⁺ plasma cells localized in MARCO⁺ peri-follicular medullary sinuses. A concomitant decreased Fth1 expression (Early 2.5 ± 0.74 vs Advanced 1.0 ± 0.50 counts, p<0.001) within Advanced PLN sinuses was associated with accumulation of iron-laden Prussian blue positive macrophages in lymph nodes and synovium of Advanced TNF-Tg mice, and further validated in RA clinical samples. …”

MiR-29b-2-5p, through repression of UNC5C expression, increases filopodia formation and <i>Shigella</i> capture by host cells. by Ushasree Sunkavalli (3916721)

“…Internalization and replication of <i>Shigella</i> within host cells lead to decreased levels of miR-29b-2-5p, which contributes to a balanced intracellular replication, avoiding premature cell death and favoring the efficient dissemination of <i>Shigella</i> to neighboring cells.…”

Sustained activation of β-catenin in the somatic cells leads to the induction of p53-mediated senescence in <i>Amhr2-Cre;Ctnnb1^Δ(ex3)/+</i> ovaries. by Pradeep S. Tanwar (143924)

“…Analyses also showed increased expression of pAKT and pS6K, and decreased expression of p21 and p27kip1 in <i>Amhr2-Cre;Ctnnb1^Δ(ex3)/+;Pten^Δ/Δ</i> ovaries. β-actin was used as a loading control. …”

Optical Activity and Dehydration-Driven Switching of Magnetic Properties in Enantiopure Cyanido-Bridged Co^II₃W^V₂ Trigonal Bipyramids by Szymon Chorazy (1396666)

“…The reversible removal of weakly bonded H₂O above 50 °C induces the structural phase transition <b>1</b> ⇄ <b>1deh</b> and strongly affects the magnetic characteristics. …”

Optical Activity and Dehydration-Driven Switching of Magnetic Properties in Enantiopure Cyanido-Bridged Co^II₃W^V₂ Trigonal Bipyramids by Szymon Chorazy (1396666)

“…The reversible removal of weakly bonded H₂O above 50 °C induces the structural phase transition <b>1</b> ⇄ <b>1deh</b> and strongly affects the magnetic characteristics. …”