title: CRC0404LMX0B02002TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0404LMO0A05024001R01000, LMO_BASALE, bio rep 2, QC ok

status: Public on Mar 01 2023

type: SRA

city: Candiolo

first: Livio

last: Trusolino

state: Turin

address: Strada Provinciale, 142 -KM 3.95

department: Oncology

country: Italy

institute: IRCCS Istituto Candiolo

library_source: transcriptomic

data_processing:
Align with STAR on hybrid mm/hs genome
Assign counts to genes with FeatureCounts
Consider only human genes to normalize with DESeq2
QC based on evidence of lymphomatous infiltration
https://github.com/molinerisLab/StromaDistiller, https://github.com/vodkatad/RNASeq_biod_metadata
Assembly: GRCh38_GRCm38
Supplementary files format and content: merged_hs_mm.tsv.gz: raw counts for human and murine genes
Supplementary files format and content: vsd.tsv.gz: normalized expression values for human genes

molecule: polyA RNA

organism: Homo sapiens

source_name: Colorectal Cancer

growth_protocol: Please check the linked publication

extract_protocol:
total RNA extraction
PolyA enriched
Forward Stranded

treatment_protocol: Please check the linked publication

tag: tissue

value: Colorectal Cancer

tag: cell line

value: O

tag: cell type

value: LM

tag: genotype

value: WT

tag: treatment


title: CRC0427LMX0A02004TUMR02000, LMX_BASALE, bio rep 1, QC failed

value: X


title: CRC0419LMX0B03005TUMR01000, LMX_cetux_h, bio rep 2, QC ok

value: CET


title: CRC0404LMX0B03003TUMR05000, LMX_cetux_h_NT, bio rep 1, QC ok

value: NT


title: CRC0404LMX0B03009TUMR09000, LMX_cetux_h, bio rep 1, QC ok


title: CRC0406LMX0B02003TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0404LMO0A04019001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0438LMH0000000000R05000, LMH, bio rep 1, QC ok

value: H


title: CRC0404LMH0000000000R09000, LMH, bio rep 1, QC ok


title: CRC0403LMX0A02003TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: CRC0419LMX0A03005TUMR01000, LMX_cetux_h, bio rep 1, QC ok


title: CRC0401PRX0A01201TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: CRC0401PRH0000000000R01000, PRH, bio rep 1, QC ok


title: CRC0399LMX0B02001TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0400LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0399LMX0B03008TUMR01000, LMX_cetux_h, bio rep 2, QC ok


title: CRC0399LMX0A03004TUMR01000, LMX_cetux_h_NT, bio rep 1, QC ok


title: CRC0399LMO0A03013007R01000, LMO_cetuxi_h_NT, bio rep 2, QC ok


title: CRC0399LMO0A03013006R01000, LMO_cetuxi_h, bio rep 1, QC ok


title: CRC0396LMX0A02003TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: CRC0395PRX0B01201TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0399LMH0000000000R01000, LMH, bio rep 1, QC ok


title: CRC0399LMO0A02006001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0399LMO0A04010001R01000, LMO_BASALE, bio rep 2, QC ok


title: CRC0399LMO0A03013008R01000, LMO_cetuxi_h, bio rep 2, QC ok


title: CRC0391LMX0A02002TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: CRC0381PRX0B01201TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0399LMO0A03013005R01000, LMO_cetuxi_h_NT, bio rep 1, QC ok


title: CRC0396LMX0A03010TUMR01000, LMX_cetux_h_NT, bio rep 1, QC ok


title: CRC0396LMX0A03004TUMR05000, LMX_cetux_h, bio rep 1, QC ok


title: CRC0381PRH0000000000R01000, PRH, bio rep 1, QC ok


title: CRC0394LMX0A02002TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: CRC0393PRH0000000000R01000, PRH, bio rep 1, QC ok


title: CRC0393PRX0B01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0379LMX0A02201TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: CRC0382LMX0A02002TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0384PRH0000000000R01000, PRH, bio rep 1, QC ok


title: CRC0384PRX0A01201TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0378LMX0A03007TUMR05000, LMX_cetux_h_NT, bio rep 1, QC ok


title: CRC0399LMX0B03001TUMR04000, LMX_cetux_h_NT, bio rep 2, QC ok


title: CRC0378LMX0A03005TUMR05000, LMX_cetux_h, bio rep 1, QC ok


title: CRC0378LMX0A02004TUMR08000, LMX_BASALE, bio rep 1, QC ok


title: CRC0377LMX0A02002TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0370LMX0B02001TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0370LMO0A03017001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0358LMX0B02202TUMR08000, LMX_BASALE, bio rep 1, QC ok


title: CRC0374PRH0000000000R01000, PRH, bio rep 1, QC failed


title: CRC0374PRX0A01201TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0360PRH0000000000R01000, PRH, bio rep 1, QC ok


title: CRC0356LMX0A03006TUMR05000, LMX_cetux_6w, bio rep 2, QC ok


title: CRC0362LMX0B02204TUMR06000, LMX_BASALE, bio rep 1, QC ok


title: CRC0367PRX0B01201TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0373PRX0A01201TUMR02000, PRX_BASALE, bio rep 1, QC ok


title: CRC0368PRX0A01201TUMR05000, PRX_BASALE, bio rep 1, QC ok


title: CRC0356LMH0000000000R01000, LMH, bio rep 1, QC ok


title: CRC0355LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0356LMX0A02004TUMR02000, LMX_BASALE, bio rep 2, QC ok


title: CRC0356LMX0A03001TUMR05000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: CRC0355LMO0B02012001R01000, LMO_BASALE, bio rep 2, QC ok


title: CRC0356LMX0A03005TUMR01000, LMX_cetux_6w, bio rep 1, QC ok


title: CRC0356LMX0A03003TUMR01000, LMX_cetux_6w_NT, bio rep 2, QC ok


title: CRC0360PRX0B01201TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0354LMX0A02003TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0355LMO0B01017001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0349LMX0A03011TUMR01000, LMX_cetux_6w, bio rep 1, QC ok


title: CRC0371LMX0B02004TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: CRC0373PRH0000000000R01000, PRH, bio rep 1, QC ok


title: CRC0356LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0349LMX0A03008TUMR01000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: CRC0349LMX0A02203TUMR08000, LMX_BASALE, bio rep 2, QC ok


title: CRC0357LMX0B02003TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0348LMX0A03012TUMR01000, LMX_cetux_6w, bio rep 2, QC ok


title: CRC0348LMX0A02003TUMR02000, LMX_BASALE, bio rep 2, QC ok


title: CRC0348LMX0A02002TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0340PRH0000000000R01000, PRH, bio rep 1, QC ok


title: CRC0348LMX0A03006TUMR01000, LMX_cetux_6w_NT, bio rep 2, QC ok


title: CRC0343LMX0A02201TUMR07000, LMX_BASALE, bio rep 1, QC ok


title: CRC0340PRX0A01201TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0348LMX0A03009TUMR02000, LMX_cetux_6w, bio rep 1, QC ok


title: CRC0345LMX0A02202TUMR02000, LMX_BASALE, bio rep 1, QC failed


title: CRC0336PRX0A01201TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0344LMX0A02003TUMR12000, LMX_BASALE, bio rep 1, QC ok


title: CRC0333PRX0A01201TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0332LMX0A02002TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0334LMX0B02201TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: CRC0333LMX0B02201TUMR02000, LMX_BASALE, bio rep 2, QC ok


title: CRC0330LMX0A06006TUMR01000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: CRC0330LMX0A02203TUMR01000, LMX_BASALE, bio rep 2, QC ok


title: CRC0333LMX0A02202TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0330LMX0A02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0339LMX0A02201TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0349LMX0A02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0333LMH0000000000R01000, LMH, bio rep 1, QC ok


title: CRC0328LMX0A02002TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: CRC0329LMX0A02201TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0327LMX0B03205TUMR05000, LMX_cetux_h_NT, bio rep 1, QC ok


title: CRC0327LMX0B03202TUMR05000, LMX_cetux_h, bio rep 1, QC ok


title: CRC0327LMX0B02201TUMR07000, LMX_BASALE, bio rep 1, QC ok


title: CRC0348LMX0A03003TUMR05000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: CRC0327LMO0B04044002R01000, LMO_cetuxi_h, bio rep 2, QC ok


title: CRC0327LMO0B04043002R01000, LMO_cetuxi_h, bio rep 1, QC ok


title: CRC0327LMO0B04044001R01000, LMO_cetuxi_h_NT, bio rep 2, QC ok


title: CRC0327LMO0B04043001R01000, LMO_cetuxi_h_NT, bio rep 1, QC ok


title: CRC0327LMO0B04008001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0327LMO0B03049001R01000, LMO_BASALE, bio rep 2, QC ok


title: CRC0323LMX0A02004TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0322LMX0A04114TUMR01000, LMX_cetux_h, bio rep 2, QC ok


title: CRC0330LMX0A06002TUMR05000, LMX_cetux_6w, bio rep 1, QC ok


title: CRC0322LMX0A04094TUMR05000, LMX_cetux_h, bio rep 1, QC ok


title: CRC0322LMX0A04014TUMR02000, LMX_cetux_h_NT, bio rep 2, QC ok


title: CRC0322LMO0A06039002R02000, LMO_BASALE, bio rep 2, QC ok


title: CRC0322LMO0A04013002R01000, LMO_cetuxi_h, bio rep 1, QC ok


title: CRC0322LMO0A04012001R01000, LMO_cetuxi_h_NT, bio rep 2, QC ok


title: CRC0321LMX0A02201TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0322LMO0A04009001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0322LMO0A04013001R01000, LMO_cetuxi_h_NT, bio rep 1, QC ok


title: CRC0318LMX0A02201TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0322LMO0A04012002R01000, LMO_cetuxi_h, bio rep 2, QC ok


title: CRC0320PRX0B01201TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0317PRX0B01201TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0316LMX0A01201TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0316LMO0A03010002R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0316LMO0A04017001R01000, LMO_BASALE, bio rep 2, QC ok


title: CRC0315PRX0A01201TUMR02000, PRX_BASALE, bio rep 1, QC ok


title: CRC0315PRH0000000000R10000, PRH, bio rep 1, QC ok


title: CRC0314LMX0A02202TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0313LMX0B02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0312LMX0B02201TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: CRC0310LMX0B02203TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0324LMX0A02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0322LMX0A04018TUMR02000, LMX_cetux_h_NT, bio rep 1, QC ok


title: CRC0309LMX0B02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0306LMX0B02201TUMR01000, LMX_BASALE, bio rep 2, QC ok


title: CRC0307LMX0A02201TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0399LMX0A03007TUMR09000, LMX_cetux_h, bio rep 1, QC ok


title: CRC0306LMH0000000000R01000, LMH, bio rep 1, QC ok


title: CRC0306LMX0A02201TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0297LMX0A03208TUMR09000, LMX_cetux_h_NT, bio rep 1, QC ok


title: CRC0305LMX0B02203TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: CRC0297LMX0B03210TUMR09000, LMX_cetux_h_NT, bio rep 2, QC ok


title: CRC0291LMX0A02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0292LMX0A02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0291LMO0A04013001R01000, LMO_BASALE, bio rep 2, QC ok


title: CRC0291LMO0A03012001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0290PRX0A01201TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0297LMX0A02201TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0291LMH0000000000R01000, LMH, bio rep 1, QC ok


title: CRC0290PRH0000000000R09000, PRH, bio rep 1, QC ok


title: CRC0322LMX0A02202TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0311PRX0A01201TUMR01000, PRX_BASALE, bio rep 1, QC failed


title: CRC0285LMX0A02204TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0287PRX0A01201TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0297LMX0B03207TUMR02000, LMX_cetux_h, bio rep 2, QC ok


title: CRC0282PRX0B01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0281PRX0B01201TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0297LMX0A03210TUMR17000, LMX_cetux_h, bio rep 1, QC ok


title: CRC0277LMX0A02201TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: CRC0277LMO0A03008001R01000, LMO_BASALE, bio rep 2, QC ok


title: CRC0276LMX0A02001TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0277LMO0A01004001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0274LMX0A01201TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0272PRX0B01201TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0269PRX0A01201TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0269PRH0000000000R01000, PRH, bio rep 1, QC ok


title: CRC0267PRH0000000000R01000, PRH, bio rep 1, QC ok


title: CRC0264LMX0A05033TUMR02000, LMX_cetux_6w, bio rep 1, QC ok


title: CRC0288PRX0A01201TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0264LMX0A02201TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: CRC0263PRH0000000000R01000, PRH, bio rep 1, QC ok


title: CRC0263PRX0A01201TUMR09000, PRX_BASALE, bio rep 1, QC ok


title: CRC0262LMX0B03211TUMR09000, LMX_cetux_h, bio rep 1, QC ok


title: CRC0265LMX0B02202TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: CRC0264LMX0A05007TUMR03000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: CRC0262LMX0A02202TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0261LMX0A02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0262LMH0000000000R01000, LMH, bio rep 1, QC ok


title: CRC0285LMO0A04008001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0259PRH0000000000R01000, PRH, bio rep 1, QC ok


title: CRC0257LMX0A05006TUMR02000, LMX_cetux_6w, bio rep 1, QC ok


title: CRC0257LMX0A05020TUMR02000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: CRC0257LMX0A02202TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: CRC0256PRX0A01201TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0256PRH0000000000R01000, PRH, bio rep 1, QC ok


title: CRC0254LMX0B02201TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0254LMO0B04021001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0252LMX0A03201TUMR03000, LMX_cetux_6w_NT, bio rep 2, QC ok


title: CRC0252LMX0A02201TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0252LMX0A03206TUMR02000, LMX_cetux_h, bio rep 1, QC ok


title: CRC0253LMX0A02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0262LMX0B03207TUMR21000, LMX_cetux_h_NT, bio rep 1, QC ok


title: CRC0243LMX0A02203TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0238PRX0B01201TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0234PRH0000000000R01000, PRH, bio rep 1, QC ok


title: CRC0234PRX0A01201TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0231LMO0A03010001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0238PRH0000000000R01000, PRH, bio rep 1, QC failed


title: CRC0231LMX0A02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0272PRH0000000000R01000, PRH, bio rep 1, QC failed


title: CRC0221LMX0B02202TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0219LMX0B03205TUMR03000, LMX_cetux_h_NT, bio rep 1, QC ok


title: CRC0226PRX0B01201TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0242LMX0B02204TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0219LMX0B03202TUMR02000, LMX_cetux_h, bio rep 1, QC ok


title: CRC0219LMX0A02201TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: CRC0240PRX0A01201TUMR05000, PRX_BASALE, bio rep 1, QC failed


title: CRC0219LMH0000000000R05000, LMH, bio rep 1, QC ok


title: CRC0218LMX0A02202TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0217LMX0A02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0207LMX0A02202TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0229LMX0B02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0204LMX0A02201TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: CRC0216LMX0A02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0207LMH0000000000R01000, LMH, bio rep 1, QC ok


title: CRC0202LMX0B06034TUMR02000, LMX_cetux_6w, bio rep 1, QC ok


title: CRC0223PRX0A01201TUMR05000, PRX_BASALE, bio rep 1, QC ok


title: CRC0202LMX0B02201TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0197LMX0B02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0202LMX0B06012TUMR02000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: CRC0196LMO0B04008001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0198LMX0B02203TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0190LMX0B02201TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: CRC0188LMO0A02005001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0196LMX0B02201TUMR11000, LMX_BASALE, bio rep 1, QC ok


title: CRC0186LMO0B04025001R01000, LMO_BASALE, bio rep 2, QC ok


title: CRC0186LMX0A02201TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0214LMX0A02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0186LMO0B04024001R01000.2, LMO_BASALE, bio rep 1, QC ok


title: CRC0185LMX0B04077TUMR01000, LMX_cetux_h, bio rep 1, QC ok


title: CRC0188LMO0A04009001R01000, LMO_BASALE, bio rep 2, QC ok


title: CRC0185LMX0B04063TUMR01000, LMX_cetux_h_NT, bio rep 2, QC ok


title: CRC0195PRH0000000000R01000, PRH, bio rep 1, QC ok


title: CRC0204LMO0B04012001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0185LMX0B04054TUMR05000, LMX_cetux_h, bio rep 2, QC ok


title: CRC0185LMX0B04048TUMR01000, LMX_cetux_h_NT, bio rep 1, QC ok


title: CRC0180LMX0A02201TUMR02000, LMX_BASALE, bio rep 1, QC failed


title: CRC0184LMX0B02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0179LMX0A02202TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0199LMX0B02204TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: CRC0185LMX0B01201TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0195PRX0A01201TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0188LMX0A01201TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0177LMO0D04021002R01000, LMO_BASALE, bio rep 2, QC ok


title: CRC0177LMX0A02201TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: CRC0177LMO0D04017001R01000, LMO_BASALE, bio rep 3, QC ok


title: CRC0177LMO0A04008002R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0171LMO0A04008001R01000, LMO_BASALE, bio rep 2, QC ok


title: CRC0187LMX0A02201TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0174LMX0A02202TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0170LMX0A02204TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0169LMX0A02202TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0169LMO0A04014001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0171LMX0B02202TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: CRC0176LMX0B02203TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: CRC0171LMO0A02006001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0168LMX0A02204TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0166LMX0B02204TUMR05000, LMX_BASALE, bio rep 2, QC ok


title: CRC0166LMX0A05027TUMR09000, LMX_cetux_6w_NT, bio rep 2, QC ok


title: CRC0166LMX0A05015TUMR02000, LMX_cetux_6w, bio rep 2, QC ok


title: CRC0178LMX0B02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0166LMX0A05011TUMR05000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: CRC0166LMX0A05009TUMR01000, LMX_cetux_6w, bio rep 1, QC ok


title: CRC0175LMX0A02202TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: CRC0166LMO0B04015001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0166LMH0000000000R02000, LMH, bio rep 1, QC ok


title: CRC0165LMX0A02208TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: CRC0166LMO0B05020001R01000, LMO_BASALE, bio rep 2, QC ok


title: CRC0164LMX0B02202TUMR02000, LMX_BASALE, bio rep 1, QC failed


title: CRC0162LMX0B02204TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0161LMX0A02204TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0165LMH0000000000R01000, LMH, bio rep 1, QC ok


title: CRC0161LMO0C05029001R01000, LMO_cetuxi_h_NT, bio rep 2, QC ok


title: CRC0161LMO0C05029002R01000, LMO_cetuxi_h, bio rep 2, QC ok


title: CRC0167LMX0B02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0161LMO0C04021001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0161LMO0C05026002R01000, LMO_cetuxi_h, bio rep 1, QC ok


title: CRC0159LMX0A02203TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0155LMX0B02204TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0161LMO0C05028001R01000, LMO_BASALE, bio rep 2, QC ok


title: CRC0154LMX0A02204TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0161LMO0C05026001R01000, LMO_cetuxi_h_NT, bio rep 1, QC ok


title: CRC0153LMX0B05026TUMR02000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: CRC0153LMX0B05010TUMR02000, LMX_cetux_6w, bio rep 1, QC ok


title: CRC0153LMX0B02204TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0166LMX0A02206TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: CRC0152LMO0C05021005R01000, LMO_cetuxi_h, bio rep 2, QC ok


title: CRC0152LMX0B02201TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0152LMO0C05021004R01000, LMO_cetuxi_h_NT, bio rep 2, QC ok


title: CRC0152LMO0C05021002R01000, LMO_cetuxi_h, bio rep 1, QC ok


title: CRC0152LMO0C05021001R01000, LMO_cetuxi_h_NT, bio rep 1, QC ok


title: CRC0152LMO0C04010001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0151LMX0A02204TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: CRC0150LMX0A02204TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0151LMO0A04007001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0150LMO0A04016001R01000, LMO_BASALE, bio rep 2, QC ok


title: CRC0150LMO0A04014001R01000.2, LMO_BASALE, bio rep 1, QC ok


title: CRC0160LMX0B02211TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0150LMH0000000000R01000, LMH, bio rep 1, QC failed


title: CRC0148LMO0A04008001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0149LMX0A02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0158LMX0A02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0145LMX0B02203TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0146LMX0B04023TUMR02000, LMX_cetux_6w, bio rep 1, QC ok


title: CRC0147LMX0B02202TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: CRC0146LMX0B04049TUMR02000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: CRC0146LMX0B02204TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0143LMX0B02202TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0140LMX0A02203TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0144LMX0A02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0141LMX0B02204TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0139LMX0A02204TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0138LMX0B02201TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0137LMX0A02201TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0152LMO0C05019001R01000, LMO_BASALE, bio rep 2, QC ok


title: CRC0137LMO0A03009001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0148LMX0A02201TUMR08000, LMX_BASALE, bio rep 1, QC ok


title: CRC0127LMX0A02204TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0134LMX0B02204TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0128LMX0A02201TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: CRC0125LMX0A02201TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: CRC0136LMX0B02201TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0125LMO0A04016001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0134LMO0A04009001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0135LMX0A02204TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0133LMX0B02204TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: CRC0129LMX0A02201TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: CRC0130LMX0A02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0124LMO0B04019001R05000, LMO_BASALE, bio rep 2, QC ok


title: CRC0123LMO0A04015001R01000.2, LMO_BASALE, bio rep 2, QC ok


title: CRC0123LMX0A02204TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0123LMO0A04012001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0124LMX0B02201TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0131LMX0A02204TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: CRC0123LMH0000000000R01000, LMH, bio rep 1, QC ok


title: CRC0124LMO0B04019001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0121LMX0A07210TUMR02000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: CRC0119LMX0B02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0117LMX0A04219TUMR02000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: CRC0117LMX0A04226TUMR02000, LMX_cetux_6w, bio rep 1, QC ok


title: CRC0118LMX0A02204TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0120LMX0A02204TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: CRC0117LMX0A02201TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0121LMX0A02204TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0121LMX0A07208TUMR02000, LMX_cetux_6w, bio rep 1, QC ok


title: CRC0116LMX0B03206TUMR02000, LMX_cetux_h, bio rep 1, QC ok


title: CRC0116LMX0A02201TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: Pep13, HEK293T WT, GFP low

city: New York

first: Xuebing

last: Wu

state: NY

address: 630 West 168th Street, P&S 10-401

country: USA

institute: Columbia University

library_source: genomic

data_processing:
Reads were aligned to a custom index for the Pep30 library generated with the command bowtie-build in bowtie version 1.2.3 and the option -v 3 --best (best alignment with up to 3 mismatches). The counts of each Pep30 sequence were extracted from the alignment with the bash command cut -f 3 | sort | uniq -c.
Pep13: unique 40-nt read sequences were counted directly from fastq files. Sequences do not end with T were removed (encoded by the vector)
Assembly: Custom
Supplementary files format and content: Pep30lib-GFP-high-vs-low.txt: tab-delimited. Columns are: ID, DNA sequence, GFP_high read count, GFP_low read count, Peptide
Supplementary files format and content: Pep30lib-GFP-mCherry-ratio.txt (both replicates): space-delimited. Columns are: ID Seq Peptide KO_high KO_midhigh KO_midlow KO_low WT_high WT_midhigh WT_midlow WT_low
Supplementary files format and content: Pep13.txt: tab-delimited. Columns are: DNA sequence, peptide sequence (stop codon decoded as *), peptide length, followed by read counts in libraries of DNA, RNA, GFP-high, and GFP-low
Library strategy: DNA amplicon sequencing

molecule: genomic DNA

growth_protocol: HEK293T cells used in this study were purchased from ATCC, from which the BAG6 KO cells were derived using CRISPR/Cas9. Cells were cultured in DMEM with 4.5 g/L D-Glucose supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin was added except when producing lentivirus. Low passage number cells were used and maintained under 90% visual confluency. Cells were maintained at 5% CO2 and 37 °C. HEK293T cells used in this study were confirmed to be negative for Mycoplasma Contamination and routinely tested using the MycoAlertTM Mycoplasma Detection Kit (Lonza, LT07-418).

extract_protocol:
Genomic DNA was isolated from the cell populations using QIAGEN QIAamp DNA mini kit or Machery Nagel Nucleospin Tissue kit. For Pep13, genomic DNA from unsorted input cells was also extracted. In addition, RNA was also isolated using Trizol for Pep13 cells.
Genomic DNA was eluted in 50 uL of elution buffer. Libraries were then amplified using PCR with custom Illumina adapters, using Q5 high-fidelity PCR mix with 1000 ng input gDNA per sample. Libraries were amplified for a total of 24-27 cycles. After amplification, libraries were cleanup up using SPRISelect beads at a ratio of 0.7x. Purified library size was confirmed via gel and libraries were quantified using the KAPA qPCR Illumina library quantification kit. Libraries were subsequently pooled in a ratio based on the number of total cells collected from each sample. Pep13 RNA was reverse transcribed into cDNA and then preped using the same protocol described above.

treatment_protocol: Sorting based on EGFP alone in HEK293T cells: cells were transduced with Pep30 lentivirus at low MOI, grown for 6 days, then FACS sort top and bottom 20% GFP cells. Sorting based on mCherry/EGFP ratio of WT and BAG6 KO cells: HEK293T as well as a clonal BAG6 knockout cell line were reverse transduced with the Pep30 library such that less than 30% of cells were transduced (thus are most likely a single integration per cell). The virus-containing media was removed after 24 hours and fresh media with 10% FBS and 1% PenStrep was added to the plates. After another 24 hours, transduced cells were purified based on their expression of mCherry. The transduced populations were returned to culture and allowed to grow out for an additional 6 days, with passaging as necessary to maintain confluence below 80%. After 6 days, both populations were sorted into 4 bins based on the ratio of EGFP/mCherry expression (High, mid-high, mid-low, and low) using a FACSAria cell sorter. The same mCherry/EGFP ratio gates were used for both WT and BAG6 KO cells. Sorted cells were spun down at 500 RCF for 5 minutes, washed once with 1000 uL PBS, spun down again, then frozen at -20 as a cell pellet.

value: Human embryonic kidney

value: wild-type


title: CRC0116LMO0B04025007R01000, LMO_cetuxi_h, bio rep 2, QC ok


title: CRC0116LMX0B03204TUMR03000, LMX_cetux_h_NT, bio rep 1, QC ok


title: CRC0116LMO0B04021001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0116LMO0B04025006R01000, LMO_cetuxi_h_NT, bio rep 2, QC ok


title: CRC0116LMO0B04020001R01000, LMO_BASALE, bio rep 2, QC ok


title: Pep13, HEK293T WT, DNA from unsorted cells


title: CRC0115LMX0A02202TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0116LMO0B04025004R01000, LMO_cetuxi_h, bio rep 1, QC ok


title: Pep13, HEK293T WT, RNA from unsorted cells

molecule: total RNA


title: CRC0115LMH0000000000R01000, LMH, bio rep 1, QC ok


title: CRC0116LMO0B04025003R01000, LMO_cetuxi_h_NT, bio rep 1, QC ok


title: SLE043

city: Billerica

first: Andrew

last: Bender

state: MA

address: 45A Middlesex Turnpike

institute: EMD Serono

data_processing:
Gene expression level was quantified using Kallisto v 0.46.1 by mapping to Homo sapiens (GRCh38 v91) primary transcript sequences.
Supplementary files format and content: GRCh38
Supplementary files format and content: tab-delimited text files include abundance values for each sample

source_name: blood

extract_protocol:
RNA was harvested using PAXgene Blood RNA Kit.
RNA libraries for RNA-seq were prepared using NEB Next Ultra II RNA Library Kit following manufacturer's protocols.

value: blood

tag: disease state

value: SLE


title: CRC0113LMX0B02201TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: SLE041


title: Pep13, HEK293T WT, GFP high


title: CRC0110LMX0A02204TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0112LMX0A02202TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: SLE040


title: SLE042


title: SLE037


title: CRC0109LMX0A02204TUMR06000, LMX_BASALE, bio rep 1, QC ok


title: SLE035


title: CRC0231LMO0A04014001R01000, LMO_BASALE, bio rep 2, QC ok


title: SLE039


title: CRC0108LMX0B02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: SLE034


title: CRC0114LMX0B02202TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0104LMX0B02201TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0103LMX0B02201TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: SLE033


title: CRC0103LMO0A04010001R01000, LMO_BASALE, bio rep 2, QC ok


title: SLE032


title: CRC0103LMO0A02007002R01000, LMO_BASALE, bio rep 1, QC ok


title: SLE031


title: CRC0105LMX0A02204TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0106LMX0B02202TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0102LMX0B03201TUMR12000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: SLE029


title: SLE028


title: SLE036


title: CRC0102LMX0B02204TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: SLE024


title: SLE025


title: CRC0101LMX0A02201TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: SLE030


title: CRC0102LMX0B03205TUMR12000, LMX_cetux_6w, bio rep 1, QC ok


title: CRC0102LMH0000000000R06000, LMH, bio rep 1, QC ok


title: CRC0099LMX0B05102TUMR03000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: CRC0100LMX0A02201TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: SLE019


title: SLE018


title: SLE026


title: SLE022


title: SLE016


title: CRC0099LMX0B02204TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: CRC0099LMX0A02204TUMR04000, LMX_BASALE, bio rep 2, QC ok


title: SLE015


title: SLE010


title: SLE012


title: CRC0098LMX0B04220TUMR09000, LMX_cetux_6w, bio rep 1, QC ok


title: CRC0099LMO0A02005001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0098LMX0B04201TUMR09000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: SLE017


title: SLE014


title: SLE009


title: CRC0098LMX0A02202TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: SLE007


title: CRC0098LMH0000000000R01000, LMH, bio rep 1, QC ok


title: CRC0099LMX0B05099TUMR02000, LMX_cetux_6w, bio rep 1, QC ok


title: SjS029

value: SjS


title: CRC0097LMO0A04028001R01000, LMO_BASALE, bio rep 1, QC ok


title: SjS025


title: SLE004


title: CRC0096LMX0A03206TUMR05000, LMX_cetux_6w, bio rep 1, QC ok


title: SjS028


title: CRC0097LMX0B02201TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0096LMX0A02201TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: SLE006


title: CRC0096LMX0A03206TUMR09000, LMX_cetux_6w, bio rep 2, QC ok


title: SLE008


title: CRC0097LMO0A05032001R01000, LMO_BASALE, bio rep 2, QC ok


title: SjS024


title: SjS026


title: CRC0096LMO0C04020001R02000, LMO_BASALE, bio rep 2, QC ok


title: CRC0096LMO0C04018001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0095LMX0B02204TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: SjS021


title: SjS023


title: SjS020


title: CRC0095LMO0A04019001R01000, LMO_BASALE, bio rep 2, QC ok


title: SjS019


title: SjS018


title: CRC0095LMH0000000000R01000, LMH, bio rep 1, QC ok


title: CRC0094PRH0000000000R01000, PRH, bio rep 1, QC ok


title: CRC0095LMO0A04020001R01000, LMO_BASALE, bio rep 1, QC ok


title: SjS013


title: SjS011


title: CRC0094LMX0B02203TUMR01000, LMX_BASALE, bio rep 2, QC ok


title: CRC0094LMX0A02202TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0094LMH0000000000R01000, LMH, bio rep 1, QC ok


title: SjS010


title: CRC0086LMX0A02204TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0085LMX0B02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: SjS006


title: SjS004


title: CRC0082LMX0A02202TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: SjS005


title: HC019

value: healthy control


title: CRC0081LMO0A04012001R01000, LMO_BASALE, bio rep 1, QC ok


title: HC018


title: CRC0081LMH0000000000R03000, LMH, bio rep 1, QC ok


title: HC010


title: HC009


title: CRC0080LMX0B02204TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: CRC0080LMO0A04019001R02000, LMO_BASALE, bio rep 1, QC ok


title: SjS016


title: HC008


title: CRC0079LMO0A04018002R01000, LMO_BASALE, bio rep 2, QC ok


title: CRC0079LMX0A02204TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: SjS007


title: CRC0081LMX0B02204TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: HC006


title: CRC0079LMO0A04012001R01000, LMO_BASALE, bio rep 1, QC ok


title: HC005


title: CRC0078LMX0B02204TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: HC004


title: HC003


title: C35

city: 南京

first: Enkang

last: Lu

address: 江苏省南京市鼓楼区江东北路368号

country: China

institute: Nanjing medicine university

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: condition

value: Control


title: HC002


title: CRC0078LMX0A04057TUMR02000, LMX_cetux_h_NT, bio rep 2, QC ok


title: CRC0078LMX0A04033TUMR01000, LMX_cetux_h, bio rep 2, QC ok


title: Proximal colon on plenish + coconut oil 3

city: Riverside

first: Frances

last: Sladek

state: CA

address: 900 University Avenue

institute: University of California

description:
50 bp paired-end
PC PL+CO 3

data_processing:
Reads were de-multiplexed and had adapters trimmed by Genomics Core at UCR.
Reads were aligned to the mouse reference genome, mm10, with Illumina’s iGenome genes.gtf file using STAR v2.7.10a using default parameters with the exception of allowing only 1 unique alignment for a given read
Raw read counts were calculated at the gene level for each sample using HTSeq v0.6.1
Library normalization was performed with EDASeq; within-lane normalization on GC content was performed with the LOESS method and between-lane normalization was performed with non-linear full quantile method
Normalization factors from EDASeq were used for differential expression analysis with DESeq2. Normalized read counts, FPKM (fragments per kilobase per million), and rlog (regularized log transformation) results were generated for downstream analysis
Assembly: mm10
Supplementary files format and content: FPKM output from DESeq2 split into each sample.

organism: Mus musculus

source_name: Proximal colon

growth_protocol: Male C57BL/6N mice were weaned at three weeks of age and assigned randomly to one of the four diets used in the study (see Table 1 for dietary composition). The animals were maintained on a 12:12 h light-dark cycle in a non-specific pathogen free vivarium at the University of California, Riverside (UCR). Twelve mice were placed on each diet with three to four animals per cage. The animals had ad libitum access to food and water. Individual mouse weights were recorded once a week while food was changed twice a week. Mice were kept on the assigned diets for upto 24 weeks.

extract_protocol:
At the end of the study animals were euthanized by CO2  inhalation followed by cervical dislocation. Intestinal tissue was excised immediately and put in RNALater for 24 hours at room temperature and then stored at -80°C. Total RNA was isolated using miRNeasy kit (Qiagen, Inc., Valencia, CA) and evaluated for purity and concentration by NanoDrop (Wilmington, DE) and Agilent 2100 Bioanalyzer (Santa Clara, CA). 4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Long RNA Sample Prep Kit following manufacturer's protocols.

treatment_protocol: Mice were on a HFD or Vivarium chow for 24 weeks

tag: strain

value: Proximal colon

value: Plenish + coconut oil

tag: time

value: 24 weeks


title: Proximal colon on plenish + coconut oil 4

description:
50 bp paired-end
PC PL+CO 4


title: C31

address: 江苏省南京市鼓楼区江东北路368号


title: CRC0078LMO0D04029001R01000, LMO_BASALE, bio rep 2, QC ok

value: Colorectal Cancer

value: O

value: LM


title: HC007


title: CRC0079LMH0000000000R02000, LMH, bio rep 1, QC ok

value: WT


title: Proximal colon on plenish + coconut oil 2

description:
50 bp paired-end
PC PL+CO 2


title: Proximal colon on coconut oil 4

description:
50 bp paired-end
PC CO 4

value: Coconut oil


title: C30

address: 江苏省南京市鼓楼区江东北路368号


title: CRC0078LMX0A05004TUMR01000, LMX_cetux_h, bio rep 1, QC ok

value: X

value: CET


title: Proximal colon on coconut oil 3

description:
50 bp paired-end
PC CO 3


title: CRC0077LMX0B02201TUMR02000, LMX_BASALE, bio rep 2, QC ok


title: CRC0078LMX0A05007TUMR02000, LMX_cetux_h_NT, bio rep 1, QC ok

value: NT


title: CRC0078LMO0D03033001R01000, LMO_BASALE, bio rep 1, QC ok


title: Proximal colon on coconut oil 2

description:
50 bp paired-end
PC CO 2


title: CRC0099LMO0A04010001R01000, LMO_BASALE, bio rep 2, QC ok


title: C29

address: 江苏省南京市鼓楼区江东北路368号


title: Proximal colon on soybean + coconut oil 4

description:
50 bp paired-end
PC SO+CO 4

value: Soybean + coconut oil


title: CRC0077LMX0A02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: C28

address: 江苏省南京市鼓楼区江东北路368号

value: blood


title: Proximal colon on soybean + coconut oil 1

description:
50 bp paired-end
PC SO+CO 1


title: D40

address: 江苏省南京市鼓楼区江东北路368号

value: CHD


title: Proximal colon on soybean + coconut oil 3

description:
50 bp paired-end
PC SO+CO 3


title: Proximal colon on plenish + coconut oil 1

description:
50 bp paired-end
PC PL+CO 1


title: Proximal colon on Vivarium Chow 2

description:
50 bp paired-end
PC VIV 2

value: Vivarium Chow


title: CRC0077LMH0000000000R01000, LMH, bio rep 1, QC ok

value: H


title: D27

address: 江苏省南京市鼓楼区江东北路368号


title: Proximal colon on Vivarium Chow 1

description:
50 bp paired-end
PC VIV 1


title: CRC0076LMX0B04205TUMR12000, LMX_cetux_h_NT, bio rep 1, QC ok


title: Terminal ileum on plenish + coconut oil 4

description:
50 bp paired-end
TI PL+CO 4

source_name: Terminal ileum

value: Terminal ileum


title: D24

address: 江苏省南京市鼓楼区江东北路368号


title: CRC0076LMX0B04201TUMR24000, LMX_cetux_h, bio rep 1, QC ok


title: Terminal ileum on plenish + coconut oil 3

description:
50 bp paired-end
TI PL+CO 3


title: D26

address: 江苏省南京市鼓楼区江东北路368号


title: Proximal colon on coconut oil 1

description:
50 bp paired-end
PC CO 1

value: Proximal colon


title: D25

address: 江苏省南京市鼓楼区江东北路368号


title: CRC0076LMO0B04014001R02000, LMO_BASALE, bio rep 1, QC ok


title: Terminal ileum on plenish + coconut oil 1

description:
50 bp paired-end
TI PL+CO 1

value: Plenish + coconut oil


title: Terminal ileum on coconut oil 4

description:
50 bp paired-end
TI CO 4

value: 24 weeks


title: Terminal ileum on plenish + coconut oil 2

description:
50 bp paired-end
TI PL+CO 2


title: Terminal ileum on coconut oil 2

description:
50 bp paired-end
TI CO 2


title: D5

address: 江苏省南京市鼓楼区江东北路368号


title: CRC0076LMO0B04013001R01000, LMO_BASALE, bio rep 2, QC ok

value: Colorectal Cancer


title: Proximal colon on Vivarium Chow 3

description:
50 bp paired-end
PC VIV 3


title: Terminal ileum on coconut oil 3

description:
50 bp paired-end
TI CO 3


title: human liver sample A2016259

city: Durham

first: Anna Mae

last: Diehl

address: 905 S LaSalle St

institute: Duke University

data_processing:
Sequencing reads were trimmed using TrimGalore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned to the mm10 reference genome using STAR
Gene expression counts were generated using HTSeq and DEseq2 was used to perform differential expression analyses (absolute log2FC >= 1 and q <0.05)
Assembly: hg39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: liver cells

extract_protocol:
Total RNAs were isolated from liver tissues or hepatocytes as previously described
Libraries were made with NEBNext Ultra RNA Library Prep Kit from Illumina. Sample qualities were assessed by Agilent RNA Bioanalyzer chip traces before pooled and sequenced with an Illumina HiSeq 2500

value: liver cells

tag: fibrotic stage


title: Terminal ileum on coconut oil 1

description:
50 bp paired-end
TI CO 1


title: Terminal ileum on soybean + coconut oil 2

description:
50 bp paired-end
TI SO+CO 2


title: human liver sample A2016258


title: Terminal ileum on soybean + coconut oil 4

description:
50 bp paired-end
TI SO+CO 4


title: Terminal ileum on soybean + coconut oil 3

description:
50 bp paired-end
TI SO+CO 3


title: human liver sample A2016287


title: CRC0076LMO0B03016003R01000, LMO_cetuxi_h_NT, bio rep 2, QC ok

value: O

value: LM


title: Terminal ileum on Vivarium Chow 3

description:
50 bp paired-end
TI VIV 3

value: WT


title: CRC0076LMO0B03013004R01000, LMO_cetuxi_h, bio rep 1, QC ok


title: CRC0076LMX0B02204TUMR08000, LMX_BASALE, bio rep 1, QC ok

value: X


title: Proximal colon on soybean + coconut oil 2

description:
50 bp paired-end
PC SO+CO 2


title: human liver sample A2016292


title: Terminal ileum on Vivarium Chow 1

description:
50 bp paired-end
TI VIV 1


title: Jejunum on plenish + coconut oil 4

description:
50 bp paired-end
JEJ PL+CO 4

source_name: Jejunum

value: Jejunum


title: CRC0076LMO0B03013003R01000, LMO_cetuxi_h_NT, bio rep 1, QC ok

value: NT


title: CRC0076LMH0000000000R02000, LMH, bio rep 1, QC ok


title: Jejunum on plenish + coconut oil 3

description:
50 bp paired-end
JEJ PL+CO 3


title: CRC0073LMX0A02202TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: Jejunum on plenish + coconut oil 2

description:
50 bp paired-end
JEJ PL+CO 2


title: Jejunum on coconut oil 3

description:
50 bp paired-end
JEJ CO 3

value: Coconut oil


title: Jejunum on coconut oil 4

description:
50 bp paired-end
JEJ CO 4


title: Jejunum on plenish + coconut oil 1

description:
50 bp paired-end
JEJ PL+CO 1


title: CRC0072LMX0B02204TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: human liver sample A2013134


title: human liver sample A2013147


title: human liver sample A2010462


title: human liver sample A2016296


title: Jejunum on coconut oil 1

description:
50 bp paired-end
JEJ CO 1


title: Terminal ileum on soybean + coconut oil 1

description:
50 bp paired-end
TI SO+CO 1

value: Soybean + coconut oil


title: Jejunum on soybean + coconut oil 3

description:
50 bp paired-end
JEJ SO+CO 3


title: CRC0076LMO0B03016004R01000, LMO_cetuxi_h, bio rep 2, QC ok

value: CET


title: Terminal ileum on Vivarium Chow 2

description:
50 bp paired-end
TI VIV 2

value: Vivarium Chow


title: CRC0071PRX0A01201TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: human liver sample A2013174


title: Jejunum on soybean + coconut oil 2

description:
50 bp paired-end
JEJ SO+CO 2


title: Jejunum on soybean + coconut oil 1

description:
50 bp paired-end
JEJ SO+CO 1


title: human liver sample A2010430


title: Jejunum on Vivarium Chow 3

description:
50 bp paired-end
JEJ VIV 3


title: human liver sample A2010482


title: Jejunum on Vivarium Chow 2

description:
50 bp paired-end
JEJ VIV 2


title: CRC0071LMX0B02204TUMR02000, LMX_BASALE, bio rep 2, QC ok


title: Jejunum on coconut oil 2

description:
50 bp paired-end
JEJ CO 2


title: CRC0072LMH0000000000R01000, LMH, bio rep 1, QC ok

value: H


title: CRC0071LMX0A02204TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: Duodenum on plenish + coconut oil 4

description:
50 bp paired-end
DUO PL+CO 4

source_name: Duodenum

value: Duodenum


title: Jejunum on Vivarium Chow 1

description:
50 bp paired-end
JEJ VIV 1


title: Jejunum on soybean + coconut oil 4

description:
50 bp paired-end
JEJ SO+CO 4


title: human liver sample A2008221


title: human liver sample A2010466


title: CRC0071LMH0000000000R01000, LMH, bio rep 1, QC ok


title: Duodenum on plenish + coconut oil 3

description:
50 bp paired-end
DUO PL+CO 3

value: Plenish + coconut oil


title: CRC0070LMX0B02204TUMR14000, LMX_BASALE, bio rep 1, QC ok


title: Duodenum on plenish + coconut oil 2

description:
50 bp paired-end
DUO PL+CO 2

value: 24 weeks


title: Duodenum on coconut oil 4

description:
50 bp paired-end
DUO CO 4


title: Duodenum on coconut oil 3

description:
50 bp paired-end
DUO CO 3


title: CRC0069LMX0B02201TUMR02000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer


title: human liver sample A2008231

value: liver cells


title: CRC0071PRH0000000000R06000, PRH, bio rep 1, QC ok


title: human liver sample A2008229


title: C32

address: 江苏省南京市鼓楼区江东北路368号

value: blood

value: Control


title: Duodenum on coconut oil 1

description:
50 bp paired-end
DUO CO 1

value: WT


title: CRC0069LMX0A07045TUMR09000, LMX_cetux_h, bio rep 1, QC ok

value: X

value: LM


title: Duodenum on soybean + coconut oil 3

description:
50 bp paired-end
DUO SO+CO 3


title: human liver sample A2008226


title: Duodenum on soybean + coconut oil 2

description:
50 bp paired-end
DUO SO+CO 2


title: Duodenum on soybean + coconut oil 1

description:
50 bp paired-end
DUO SO+CO 1


title: CRC0069LMX0A07018TUMR13000, LMX_cetux_h_NT, bio rep 1, QC failed

value: NT


title: Duodenum on plenish + coconut oil 1

description:
50 bp paired-end
DUO PL+CO 1


title: Duodenum on Vivarium Chow 3

description:
50 bp paired-end
DUO VIV 3


title: human liver sample A2008220


title: Duodenum on Vivarium Chow 2

description:
50 bp paired-end
DUO VIV 2


title: CRC0069LMX0A03201TUMR20000, LMX_cetux_h_NT, bio rep 2, QC ok


title: Duodenum on Vivarium Chow 1

description:
50 bp paired-end
DUO VIV 1


title: human liver sample A2008210


title: Duodenum on coconut oil 2

description:
50 bp paired-end
DUO CO 2

value: Coconut oil


title: CRC0069LMX0A03204TUMR13000, LMX_cetux_h, bio rep 2, QC ok


title: The integration sites of N-Myc 2

city: Tianjin

first: Haitao

last: Bai

state: Tianjin

address: 288 Nanjing Road

department: Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using BWA (Li H et al.) and Samblaster
The alignment of BAM file was performed by Samblaster
The multiple hits for SNP, INDEL, CNV and integration site of N-Myc
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files  for each Sample

extract_protocol:
Whole genome sequencing (WGS) analysis was performed on B-ALL, T-ALL, AML, AUL, MPAL and empty control samples to detect mutations and integration sites of retroviral N-Myc. 2x106 GFP+ leukemia cells collected from B-ALL, T-ALL, AML, AUL mice, 1x106 GFP+Mac1/Gr1+B220-CD3/4/8- and GFP+Mac1/Gr1-B220-CD3/4/8+ leukemia cells from MPAL as well as 1x106 GFP+ cells from empty control  mice, and stocked at -80℃. Genomic DNAs were extracted from samples. DNA concentration ≥20 ng/µL, and DNA mass≥0.2 µg were used for the quality control (Qubit 2.0 software).
350 bp of DNA fragments were produced by Covaris ultrasonicator, followed by end-repair, phosphorylation, and adding A-tailing to DNA fragments. P5 adaptor (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’) and P7 adaptor (5’-GATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG-3’) were used for library construction. The quality of DNA library was tested by Agilent 2100 and Q-PCR. The DNA library was sequenced under 30x sequencing depth by Illumina HiSeq PE150 (Pair End 150 bp) at Novogene.

value: Bone marrow

tag: cell stage

value: 8-10 weeks


title: The integration sites of N-Myc 1


title: Empty control

source_name: GFP+


title: Duodenum on soybean + coconut oil 4

description:
50 bp paired-end
DUO SO+CO 4

value: Soybean + coconut oil


title: human liver sample A2008205


title: human liver sample A2008228


title: CRC0069LMO0A04011001R01000, LMO_BASALE, bio rep 1, QC ok

value: O


title: T-MPAL


title: M-MPAL


title: CRC0069LMO0A03023002R01000, LMO_cetuxi_h, bio rep 2, QC ok

value: CET


title: human liver sample A2008244


title: human liver sample A2008246


title: human liver sample A2008247


title: CRC0069LMO0A03023001R01000, LMO_cetuxi_h_NT, bio rep 2, QC ok


title: human liver sample A2008252


title: The integration sites of N-Myc , AUL

data_processing:
Library strategy: WGS
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using BWA (Li H et al.) and Samblaster
The alignment of BAM file was performed by Samblaster
The multiple hits for SNP, INDEL, CNV and integration site of N-Myc
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files  for each Sample

extract_protocol:
Whole genome sequencing (WGS) analysis was performed on B-ALL, T-ALL, AML and AUL samples to detect mutations and integration sites of retroviral N-Myc. 2x106 GFP+ leukemia cells collected from B-ALL, T-ALL, AML, and AUL mice, and stocked at -80℃. Genomic DNAs were extracted from samples. DNA concentration ≥20 ng/µL, and DNA mass≥0.2 µg were used for the quality control (Qubit 2.0 software).
350 bp of DNA fragments were produced by Covaris ultrasonicator, followed by end-repair, phosphorylation, and adding A-tailing to DNA fragments. P5 adaptor (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’) and P7 adaptor (5’-GATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG-3’) were used for library construction. The quality of DNA library was tested by Agilent 2100 and Q-PCR. The DNA library was sequenced under 30x sequencing depth by Illumina HiSeq PE150 (Pair End 150 bp) at Novogene.


title: The integration sites of N-Myc , T-ALL


title: The integration sites of N-Myc , AML


title: The integration sites of N-Myc , B-ALL


title: SNV, INDEL, CNV of WGS, AML


title: SNV, INDEL, CNV of WGS, AUL


title: SNV, INDEL, CNV of WGS, T-ALL


title: human liver sample A2008236


title: CRC0069LMO0A03017001R01000, LMO_cetuxi_h_NT, bio rep 1, QC ok


title: CRC0069LMO0A05068001R02000, LMO_BASALE, bio rep 2, QC ok


title: lineage_cell

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR
Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using HTSeq (http://htseq.readthedocs.io/en/release_0.9.1; Anders S et al., 2015). Then DEGs was analyzed by edgeR (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html; Robinson MD et al., 2010)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
2x106 GFP+ leukemia cells were isolated from B-ALL, T-ALL, AML, and AUL mice. After staining with anti-B220-PerCP-Cyanine 5.5, anti-CD3e-PE-Cy7, anti-CD11b-APC-eFluor 780/anti-Gr1-APC-eFluor 780, and the 7 lineage cocktail antibodies, 2x106 B cells, T cells, myeloid cells, and lineage-negative cells were isolated from normal bone marrow as controls. Sorted cells were washed with 1 ml PBS, and re-suspended by 1ml Trizol reagent (Thermo Fisher). After total RNA extraction, mRNA was enriched by magnetic beads linked with Oligo (dT)
The first-strand cDNA was synthesized by random oligonucleotide primer, and the second cDNA was synthesized by DNA polymerase I. The double strand cDNA was modified by index primers, and sequenced by Illumina HiSeq 2000 at Novogene company (Tianjin Novogene Bioinformatics Technology Co., Ltd. Building B07, Venture Headquarter Base, Tianjin Wuqing Development Area, China). The sequenced strategy of Illumina PE150 (Pair end 150 bp) was taken in this project. Reads containing adaptors and uncertain bases were removed (quality control) before analysis. After filtration of unqualified reads, reads were compared with the public reference sequence of mouse UCSC mm10 (http://genome-asia.ucsc.edu/cgi-bin/hgGateway?redirect=manual&source=genome.ucsc.edu ). The expression level of RNA was quantified with fragments per kilo base of transcript per million mapped reads (FPKM).
Illumina PE150 (Pair end 150 bp) RNA-Seq

tag: age


title: CRC0069LMO0A03017002R01000, LMO_cetuxi_h, bio rep 1, QC ok


title: SNV, INDEL, CNV of WGS, B-ALL


title: CRC0068LMX0A02204TUMR19000, LMX_BASALE, bio rep 1, QC ok


title: human liver sample A2008253


title: CRC0067LMX0B02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: Myeloid_cell


title: CRC0066LMX0A05033TUMR02000, LMX_cetux_6w, bio rep 1, QC ok


title: B-ALL


title: B_cell


title: AML


title: T-ALL


title: T_cell


title: human liver sample A2008237


title: human liver sample A2008257


title: AUL


title: CRC0066LMX0A05006TUMR02000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: human liver sample A2008238


title: human liver sample A2008263


title: human liver sample A2008280


title: CRC0066LMO0A04015001R01000, LMO_BASALE, bio rep 1, QC ok


title: human liver sample A2008279


title: human liver sample A2008265


title: CRC0065PRX0A02201TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: CRC0065LMX0B02202TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: MSCs_DMSO_3

city: Kyoto

first: Makoto

last: Ikeya

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

country: Japan

institute: Kyoto University

description:
iMSCs-BRQ.normalized.data.csv
IonCode_0122

data_processing:
Total reads were aligned to hg19 AmpliSeq Transcriptome ERCCv1
Aligned reads raw count data were analyzed
The count data analyses were performed using R studio with the ‘DESeq2’ package and by filtering the lowly expressed genes
Normalized count data were used for the detection of differentially expressed genes and gene set enrichment
Assembly: hg19
Supplementary files format and content: tab-delimited csv files include normalized data count

growth_protocol: iPS cells were cultured in plastic dishes coated with iMatrix-511 silk (Nippi, 892021) fed with StemFit AK03N (Ajinomoto) under xeno-free culture conditions. Cells were dissociated into a cell suspension using Accutase® (Sigma Aldrich, A6964) and passaged when they reached more than 70% confluence.

extract_protocol:
iPSCs were treated with 100 nM BRQ for 24h or 48h then RNA samples were extracted. iMSCs were cultured with 100 nM BRQ for 7 days then RNA samples were extracted.
RNA samples were extracted using the RNeasy® Mini kit (Qiagen)
Libraries were prepared using the Ion AmpliSeq Transcriptome Human Gene Expression Panel, Chef-Ready Kit (A31446),and Ion Torrent Ion Chef Instrument (4484177) (Thermo Fisher Scientific, Tokyo, Japan)

treatment_protocol: iMSCs were generated by inducing hiPSCs into neural crest cells (NCCs), and then into iMSCs (23), which were then maintained in a plastic dish coated with Fibronectin (Chemicon, FC010-10MG) and fed with PRIME-XV®MSC Expansion XSFM (IrvineScientific, 91149).

value: induced mesenchymal stem cells

value: Day 7


title: MSCs_DMSO_2

description:
iMSCs-BRQ.normalized.data.csv
IonCode_0121


title: MSCs_BRQ_3

description:
iMSCs-BRQ.normalized.data.csv
IonCode_0124


title: MSCs_BRQ_2

description:
iMSCs-BRQ.normalized.data.csv
IonCode_0123


title: human liver sample A2008206


title: MSCs_BRQ_1

description:
iMSCs-BRQ.normalized.data.csv
IonCode_0129


title: MSCs_DMSO_1

description:
iMSCs-BRQ.normalized.data.csv
IonCode_0130


title: CRC0065LMO0A05017001R01000, LMO_BASALE, bio rep 2, QC ok

value: Colorectal Cancer


title: 9234549016_E

type: RNA

city: Los Angeles

first: Vasu

last: Punj

address: Biggy Street

institute: USC

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: Data was background corrected Illumina Genome studio as recommended by manufacturer

label: biotin

source_name: DU154 cells

label_protocol: Biotinylated cRNA was prepared with the Ambion MessageAmp kit for Illumina array.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Prostate cancer cell line DU154

tag: genotype/variation

value: Wild type

tag: replicate


title: CRC0065LMO0A05014001R01000, LMO_BASALE, bio rep 1, QC ok


title: hiPSCs 48h DMSO

description:
hiPSCs-BRQ.normalized.data.csv
IonCode_0128

value: induced pluripotent stem cells

value: Day 2


title: human liver sample A2013185

value: liver cells


title: hiPSCs 24h BRQ

description:
hiPSCs-BRQ.normalized.data.csv
IonCode_0125

value: WT

value: Day 1


title: CRC0066LMX0A02204TUMR08000, LMX_BASALE, bio rep 1, QC ok

value: X

value: LM


title: human liver sample A2006804


title: hiPSCs 24h DMSO

description:
hiPSCs-BRQ.normalized.data.csv
IonCode_0126


title: LN18 glioma cell line ATACseq seq

city: Warsaw

first: Adria-Jaume

last: Roura

address: Ludwika Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology, Polish Academy of Sciences

data_processing:
Trimmomatic was used to remove Illumina-specific adapters, low-quality 5' and 3' bases, and short reads from FASTQ files in the RNAseq primary analysis.
The STAR aligner was used to align RNA sequencing reads to a reference human genome sequence (hg38).
The resulting RNAseq mapped reads were summarized and counted by gene using FeatureCounts, in paired-end mode, reverse-stranded mode, and only taking into account reads with MAPQ values of 255 or higher and primary aligment. Duplicates were found and marked using Picard Tools.
The FastQC tool was employed in the ATACseq quality assessment of the raw data. After trimming ATAC-seq reads with the FASTQ trimmer, only reads with a quality of 10 or higher were taken into account.
Incorrectly paired reads were eliminated if they were less than 20 bp in length. Using the default parameters, the Bowtie2 aligner (59) was used to map the reads to the human genome (hg38).
Only high-quality reads (MAPQ > 30), correctly paired read mates, and uniquely mapped reads were considered for downstream analysis. PicardTools was also used to find and eliminate PCR duplicates.
The following parameters in MACS2 were used to center a 200 bp window on the Tn5 binding site (5' ends of reads represent the cut sites), which is more accurate for ATAC-seq peaks: --broad --nomodel --shift -100 --extsize 200.
Assembly: hg38
Supplementary files format and content: FeatureCounts gene quantification.
Supplementary files format and content: MACS2 broad peaks files

source_name: LN18 ATACseq

extract_protocol:
RNA libraries were prepared using KAPA Stranded mRNA-seq protocol
ATAC-seq transposition reaction was performed using Nextera DNA Library Preparation kit by Illumina

value: LN18 human glioma cell line

value: brain


title: CRC0063LMX0A02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: LN229 glioma cell line ATACseq seq

source_name: LN229 ATACseq

value: LN229 human glioma cell line


title: human liver sample A2008266


title: LN229 glioma cell line RNAseq rep2

description:
DESeq2_LN18_LN229_RNAseq_raw.counts
SAR_F17_0007_P01_V11.bam

source_name: LN229 RNAseq


title: human liver sample A2006799


title: CRC0062LMX0A02201TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: LN18 glioma cell line RNAseq rep2

description:
DESeq2_LN18_LN229_RNAseq_raw.counts
SAR_F09_0003_P01_V11.bam

source_name: LN18 RNAseq


title: LN229 glioma cell line RNAseq rep1

description:
DESeq2_LN18_LN229_RNAseq_raw.counts
SAR_F17_0005_P01_V11.bam


title: CRC0061LMX0A02202TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: CRC0064LMX0A02204TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: 9234549016_H


title: 9234549016_F


title: human liver sample A2006798


title: hiPSCs 48h BRQ

description:
hiPSCs-BRQ.normalized.data.csv
IonCode_0127


title: LN18 glioma cell line RNAseq rep1

description:
DESeq2_LN18_LN229_RNAseq_raw.counts
SAR_F09_0001_P01_V11.bam


title: human liver sample A2006795


title: CRC0059LMX0B04204TUMR05000, LMX_cetux_h, bio rep 1, QC ok

value: CET


title: CRC0059LMX0B04201TUMR05000, LMX_cetux_h_NT, bio rep 1, QC ok

value: NT


title: human liver sample A2006784


title: human liver sample A2006781


title: human liver sample A2008276


title: CRC0059LMX0B02202TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: human liver sample A2006779


title: CRC0059LMO0A05015003R01000, LMO_BASALE, bio rep 2, QC ok

value: O


title: CRC0059LMO0A04013001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0059LMO0A03017002R01000, LMO_cetuxi_h, bio rep 2, QC ok


title: human liver sample A2006773


title: CRC0059LMO0A03017001R01000, LMO_cetuxi_h_NT, bio rep 2, QC ok


title: human liver sample A2006777


title: CRC0059LMO0A03009002R01000, LMO_cetuxi_h, bio rep 1, QC ok


title: 9234549016_G


title: BEAS_PBS_UFP_4h

city: Munich

first: Elias

middle: Josef

last: Zimmermann

state: Bavaria

address: Gmunder Str. 37

department: Comprehensive Molecular Analytics

country: Germany

institute: Helmholtz Zentrum Munich

description: Gene expression after PBS and UFP rich combustion aerosol exposure with 4h pre-incubation in between

hyb_protocol: The Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes with Agilent fragmentation mix, according to the manufacturers instructions. After that, 25uL of 2x Agilent hybridization buffer was added to the fragmentation mixture and 40uL of the samples was hybridized to One-Color SurePrint G3 8x60K Human gene expression arrays (Agilent Technologies, Inc, Waldbronn, Germany) for 17 hours at 65°C in a rotating Agilent hybridization oven. After incubation time, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1, at 500rpm and 1 minute with 32°C GE Wash buffer 2 (Agilent), at 500rpm. Slide was placed in a array gasket chamber for scan procedure.

scan_protocol: Slides were scanned using the Agilent DNA Microarray Scanner using one color scan setting for 8x60k G3 array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green).

data_processing: Scanned images were analyzed with Feature Extraction Software Version 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 072363_D_F_20200924) to obtain background and Processed Signal intensities.

source_name: Bronchial epithelial cells

label_protocol: RNA samples (input of 100ng) were spiked (One-Color RNA Spike-in Kit, Agilent Technologies, Waldbronn, Germany), Cy3-labelled (Low Input Quick Amp Labeling Kit, one-color, Agilent Technologies, Waldbronn, Germany) and purified on RNeasy mini spin columns (QIAGEN). Generated Cy3-labelled cRNA was quantified with NanoPhotometer® N60, IMPLEN, Munich, Germany.

extract_protocol: total RNA

treatment_protocol: BEAS-2B cells were cultured in 6-well Transwells with BEGM Medium. After 24h, basal medium was changed, apical medium was removed and cells were kept in air-liquid interface for 48h, before UFP exposure. 4 h or 24 h before UFP exposure cells were exposed either to 250 µl nebulized (for 6 Transwells) birch pollen extract (30mg/ml), house dust mite extract (25µl/ml) or PBS solvent control as negative control. UFP rich combustion aerosol was generated with a standard combustion aerosol generator and cells were exposed for 2 h to generated aerosol (or clean air) following 2 h post exposure at 37°C and 5% CO2. Both exposures were performed with in vitro exposure systems.

value: PBS

value: Combustion Aerosol

tag: pre-exposure time


title: BEAS_PBS_UFP_24h

description: Gene expression after PBS and UFP rich combustion aerosol exposure with 24h pre-incubation in between


title: CRC0059LMO0A03009001R01000, LMO_cetuxi_h_NT, bio rep 1, QC ok

value: Colorectal Cancer


title: human liver sample A2006770


title: BEAS_HDME_UFP_24h

description: Gene expression after house dust mite extract and UFP rich combustion aerosol exposure with 24h pre-incubation in between

value: HDME


title: BEAS_HDME_CA_24h_rep2

description: Gene expression after house dust mite extract and clean air exposure with 24h pre-incubation in between

value: Clean Air


title: human liver sample A2008282


title: BEAS_HDME_CA_24h_rep1


title: BEAS_BPE_UFP_4h

description: Gene expression after birch pollen extract and UFP rich combustion aerosol exposure with 4h pre-incubation in between

value: BPE


title: BEAS_BPE_UFP_24h

description: Gene expression after birch pollen extract and UFP rich combustion aerosol exposure with 24h pre-incubation in between


title: BEAS_HDME_UFP_4h

description: Gene expression after house dust mite extract and UFP rich combustion aerosol exposure with 4h pre-incubation in between

value: HMDE


title: BEAS_BPE_CA_24h_rep1

description: Gene expression after birch pollen extract and clean air exposure with 24h pre-incubation in between


title: human liver sample A2006769

value: liver cells


title: human liver sample A2006771


title: BEAS_PBS_CA_24h_rep2

description: Gene expression after PBS and clean air exposure with 24h pre-incubation in between


title: BEAS_PBS_CA_24h_rep1


title: BEAS_HDME_CA_4h_rep1

description: Gene expression after house dust mite extract and clean air exposure with 4h pre-incubation in between


title: BEAS_HDME_CA_4h_rep2


title: BEAS_PBS_CA_4h_rep1

description: Gene expression after PBS and clean air exposure with 4h pre-incubation in between


title: CRC0057LMX0A02202TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: WT


title: CRC0058LMX0A02201TUMR04000, LMX_BASALE, bio rep 1, QC ok

value: X


title: sple_mutant_biol_rep2_tech_rep4

city: Iowa City

first: Krishna Madhav

last: Nukala

state: Iowa

address: 129 E Jefferson

department: Department of Biology

institute: University of Iowa

description: Adult prickle-spiny legs mutant brains. Fourth technical replicate of the second biological replicate

hyb_protocol: Hybridization was performed following their standard protocol. See www.roche.com.

scan_protocol: Scanning was performed following their standard protocol. See www.roche.com.

data_processing: Raw data (.pair files) were normalized in ArrayStar software version 16.0.0 (DNASTAR, Inc, Madison, WI). The robust multichip analysis (RMA) algorithm was used for background correction, quantile normalization, and median polish summarization. A Student's t test corrected for multiple testing with the Benjamini and Hochberg false discovery rate (FDR) method was calculated for each experiment.

organism: Drosophila melanogaster

source_name: Brains of prickle-spiny legs adults

label_protocol: Labeling was performed following their standard protocol. See www.roche.com.

growth_protocol: Flies were maintained at 25°C in malt-based media (Archon Scientific).

extract_protocol: RNA was extracted using TRIzol (Invitrogen) and purified with RNeasy Mini Kit (Qiagen). Double-stranded cDNA was generated using Double-Stranded cDNA Synthesis Kit with random hexamer (Invitrogen). RNA and cDNA quality were analyzed using Experion RNA and DNA analysis kits (Bio-Rad), respectively.

treatment_protocol: Adult brains were dissected in 1X PBS (pH 7.4)

value: prickle-spiny legs (pk^sple1):spontaneous mutation

tag: phenotype

value: Bang sensitive

tag: developmental stage

value: Adult

value: Brain


title: BEAS_BPE_CA_24h_rep2


title: BEAS_BPE_CA_4h_rep2

description: Gene expression after birch pollen extract and clean air exposure with 4h pre-incubation in between


title: BEAS_PBS_CA_4h_rep2


title: sple_mutant_biol_rep2_tech_rep3

description: Adult prickle-spiny legs mutant brains. Third technical replicate of the second biological replicate

tag: tissue


title: human liver sample A2006768

value: Control


title: human liver sample A2006746


title: CRC0057LMH0000000000R02000, LMH, bio rep 1, QC ok

tag: cell line

value: H

value: LM


title: CRC0056LMX0A02204TUMR03000, LMX_BASALE, bio rep 1, QC ok

tag: cell type


title: human liver sample A2006766


title: CRC0055LMX0A02201TUMR02000, LMX_BASALE, bio rep 1, QC ok

tag: genotype


title: sple_mutant_biol_rep1_tech_rep4

description: Adult prickle-spiny legs mutant brains. Fourth technical replicate of the first biological replicate


title: human liver sample A2006737


title: CRC0055LMO0A02006001R01000, LMO_BASALE, bio rep 1, QC ok

value: O

tag: treatment


title: sple_mutant_biol_rep2_tech_rep1

description: Adult prickle-spiny legs mutant brains. First technical replicate of the second biological replicate


title: CRC0054LMX0B02201TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: human liver sample A2006734


title: BEAS_BPE_CA_4h_rep1


title: human liver sample A2006731


title: sple_mutant_biol_rep2_tech_rep2

description: Adult prickle-spiny legs mutant brains. Second technical replicate of the second biological replicate


title: sple_mutant_biol_rep1_tech_rep3

description: Adult prickle-spiny legs mutant brains. Third technical replicate of the first biological replicate


title: sple_mutant_biol_rep1_tech_rep2

description: Adult prickle-spiny legs mutant brains. Second technical replicate of the first biological replicate


title: sple_mutant_biol_rep1_tech_rep1

description: Adult prickle-spiny legs mutant brains. First technical replicate of the first biological replicate


title: OR_control_biol_rep2_tech_rep3

description: Adult control brains. Third technical replicate of the second biological replicate

source_name: Brains of control adults

value: Oregon-R (OR)

value: Brown body and red eyes


title: OR_control_biol_rep2_tech_rep4

description: Adult control brains. Fourth technical replicate of the second biological replicate


title: CRC0053PRX0A02201TUMR03000, PRX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: PR


title: OR_control_biol_rep2_tech_rep1

description: Adult control brains. First technical replicate of the second biological replicate


title: OR_control_biol_rep2_tech_rep2

description: Adult control brains. Second technical replicate of the second biological replicate


title: human liver sample A2006728


title: donor 3 2016 D7 Plasmablast

city: Birmingham

first: Alexander

last: Rosenberg

state: AL

address: 1720 2nd Avenue South, Suite 276/11

institute: University of Alabama at Birmingham

description:
20
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_3_HD46.txt.gz

data_processing:
Join forward and reverse reads with FastqJoin: Aronesty E (2011) eaUtils: Command line tools for processing biological sequencing data. https://expressionanalysis.github.io/ea-utils/
Apply quality filtering to joined reads: sequences with <= 200bp were omitted, as were those with low quality bases, >0bp with scores < 10, >=5bp with scores < 20 or >=15bp with quality scores < 30.
Determine isotypes of each sequence by searching against list of IgA, IgG and IgM sequences.
Submitting sequences to IMGT/High V-QUEST for V(D)J gene annotation and mutation statistics (Alamyar et al., 2012; PMID 22665256).
Clustering annotated sequences into lineages - sequences with same V annotation, J annotation, CDR3 length and >= 85% CDR3 nucleotide sequence similarity (see Tipton et al., 2015; PMID 26006014).
Write IMGT output tables with isotypes and lineage assignments into SQLite databases for in-house developed downstream analysis tools.
Supplementary files format and content: Nellore23_annotated_Ig_sequences_Donor_1_HD52.txt - tabular output of IMGT-annotated sequences, populations, isotypes, lineageIDs (table does not include day 120 IgD- memory).
Supplementary files format and content: Nellore23_annotated_Ig_sequences_Donor_2_HD54.txt - tabular output of IMGT-annotated sequences, populations, isotypes, lineageIDs (table does not include day 120 IgD- memory).
Supplementary files format and content: Nellore23_annotated_Ig_sequences_Donor_3_HD46.txt - tabular output of IMGT-annotated sequences, populations, isotypes, lineageIDs (table does not include day 120 IgD- memory).
Supplementary files format and content: Nellore23_annotated_Ig_sequences_Donor_1_HD52_day_120_1FG.txt - tabular output of IMGT-annotated sequences, populations, isotypes, lineageIDs; this table only includes early HA-specific memory and day 120 IgD- memory.
Supplementary files format and content: Nellore23_annotated_Ig_sequences_Donor_2_HD54_day_120_1FG.txt - tabular output of IMGT-annotated sequences, populations, isotypes, lineageIDs; this table only includes early HA-specific memory and day 120 IgD- memory.
Supplementary files format and content: Nellore23_annotated_Ig_sequences_Donor_3_HD46_day_120_1FG.txt - tabular output of IMGT-annotated sequences, populations, isotypes, lineageIDs; this table only includes early HA-specific memory and day 120 IgD- memory.
Library strategy: Rep-Seq

extract_protocol:
Qiagen RNA-micro kit was used to extract RNA from all samples.
Amplification of BCR using primers specific for VH1-7 and constant region as per PMID 26006614.
Amplification using Illumina MiSeq v3 600 cycle reagents and tags.

tag: donor

value: blood

value: Plasmablast

value: influenza vaccine

tag: vaccine year

tag: days post vaccine

tag: number of_cells


title: donor 3 2016 D120 MBC

description:
22
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_3_HD46_day_120_1FG.txt.gz

value: IgD- B Cell


title: donor 3 2017 D7 Plasmablast

description:
23
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_3_HD46.txt.gz


title: donor 3 2016 D14 Naive B Cell

description:
19
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_3_HD46.txt.gz

value: Naive B Cell


title: donor 3 2016 D28 FcRL5neg H1+ MBC

description:
18
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_3_HD46.txt.gz

value: H1 Tetramer+ FcRL5- IgD- B Cell


title: donor 3 2016 D14 Plasmablast

description:
21
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_3_HD46.txt.gz


title: OR_control_biol_rep1_tech_rep2

description: Adult control brains. Second technical replicate of the first biological replicate


title: CRC0053PRX0A02203TUMR01000, PRX_BASALE, bio rep 2, QC ok

value: X

value: WT


title: OR_control_biol_rep1_tech_rep4

description: Adult control brains. Fourth technical replicate of the first biological replicate

value: Adult

value: Brain


title: CRC0053LMX0B02202TUMR02000, LMX_BASALE, bio rep 2, QC ok


title: human liver sample A2006730

value: liver cells

tag: fibrotic stage


title: donor 3 2016 D28 FcRL5+ H1+ MBC

description:
17
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_3_HD46.txt.gz

value: H1 Tetramer+ FcRL5+ IgD- B Cell


title: human liver sample A2006725


title: donor 3 2016 D14 FcRL5+ H1+ MBC

description:
15
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_3_HD46.txt.gz
Nellore23_annotated_Ig_sequences_Donor_3_HD46_day_120_1FG.txt.gz


title: donor 3 2016 D14 FcRL5neg H1+ MBC

description:
16
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_3_HD46.txt.gz
Nellore23_annotated_Ig_sequences_Donor_3_HD46_day_120_1FG.txt.gz


title: donor 2 2017 D7 Plasmablast

description:
14
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_2_HD54.txt.gz


title: CRC0053LMX0A02204TUMR02000, LMX_BASALE, bio rep 1, QC ok

value: LM


title: OR_control_biol_rep1_tech_rep1

description: Adult control brains. First technical replicate of the first biological replicate

value: Oregon-R (OR)


title: human liver sample A2006722


title: donor 2 2016 D14 Naive B Cell

description:
12
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_2_HD54.txt.gz


title: donor 2 2016 D120 MBC

description:
13
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_2_HD54_day_120_1FG.txt.gz


title: CRC0053LMH0000000000R02000, LMH, bio rep 1, QC ok

value: H


title: donor 2 2016 D7 Plasmablast

description:
11
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_2_HD54.txt.gz


title: CRC0051LMX0B01001TUMR01000, LMX_BASALE, bio rep 2, QC ok

value: Colorectal Cancer


title: CRC0051LMX0A02201TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: human liver sample A2006713


title: CRC0053PRH0000000000R04000, PRH, bio rep 1, QC ok

value: PR


title: human liver sample A2006727

value: Control


title: donor 2 2016 D7 FcRL5+ H3+ MBC

description:
9
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_2_HD54.txt.gz
Nellore23_annotated_Ig_sequences_Donor_2_HD54_day_120_1FG.txt.gz

value: blood

value: H3 Tetramer+ FcRL5+ IgD- B Cell


title: donor 1 2016 D120 MBC

description:
7
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_1_HD52_day_120_1FG.txt.gz

value: IgD- B Cell

value: influenza vaccine


title: donor 1 2017 D7 Plasmablast

description:
8
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_1_HD52.txt.gz

value: Plasmablast


title: CRC0051LMO0A04009001R01000, LMO_BASALE, bio rep 2, QC ok

value: O


title: human liver sample A2006729


title: donor 1 2016 D7 Naive B Cell

description:
5
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_1_HD52.txt.gz

value: Naive B Cell


title: human liver sample A2006710


title: human liver sample A2002761


title: CRC0051LMO0A02006001R01000, LMO_BASALE, bio rep 1, QC ok

value: WT


title: donor 1 2016 D14 FcRL5neg H3+ MBC

description:
4
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_1_HD52.txt.gz

value: H3 Tetramer+ FcRL5- IgD- B Cell


title: donor 1 2016 D14 FcRL5+ H3+ MBC

description:
3
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_1_HD52.txt.gz


title: donor 1 2016 D7 FcRL5+ H3+ MBC

description:
1
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_1_HD52.txt.gz
Nellore23_annotated_Ig_sequences_Donor_1_HD52_day_120_1FG.txt.gz


title: human liver sample A2002759

value: liver cells


title: human liver sample A2006715


title: X66.2

city: Stanford

first: Michelle

last: Monje

address: 265 campus drive, SIM1 G3035

department: Neurology

institute: Stanford University

data_processing:
Fastq files were aligned to the human genome (hg38) using STAR 2.5.4b and expression values were computed using RSEM. The resulting expression matrix was fed into Seurat and analyzed.
Supplementary files format and content: final_patch_tpm_matrix_no_CD1.txt: Transcript counts for each cell in a gene x cell matrix.
Supplementary files format and content: TB_ephys_calls.txt is a supplementary table containing electrophysiological recordings from cells that were subsequently profiled by RNA-seq
Supplementary files format and content: Note: All of the cells in final_patch_tpm_matrix_no_CD1.txt were first subjected to whole cell patch clamp and then their cell contents were sucked out to be analyzed by RNA-seq. We only observed responses to neuronal firing in the smaller subset of 25 cells that are in TB_ephys_calls.txt.

source_name: diffuse midline glioma

extract_protocol:
Freshly isolated brains were sliced to 350 micron thickness using a vibratome. Individual GFP-positive glioma cells were targeted for whole cell patch clamp. Subsequent to electrophysiological recordings, the contents of each cell were aspirated into the patch pipet and ejected into PCR tubes for downstream transcriptome amplification.
Full-length cDNA profiles of cells were generated using the Smart-seq2 method, Nextera XT library prep kit and IDT® for Illumina® DNA/RNA UD Indexes

value: diffuse midline glioma


title: CRC0050PRX0A02203TUMR01000, PRX_BASALE, bio rep 2, QC ok

source_name: Colorectal Cancer

value: X


title: donor 2 2016 D7 FcRL5neg H3+ MBC

description:
10
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_2_HD54.txt.gz
Nellore23_annotated_Ig_sequences_Donor_2_HD54_day_120_1FG.txt.gz

source_name: blood


title: X66.1


title: X65.1


title: human liver sample A2002758


title: CRC0050PRX0A02201TUMR03000, PRX_BASALE, bio rep 1, QC ok


title: x64.4


title: human liver sample A2002757


title: X64.3


title: human liver sample A2002756


title: X64.2


title: CRC0050LMX0A03210TUMR01000, LMX_BASALE, bio rep 2, QC ok

value: LM


title: human liver sample A2002752


title: human liver sample A2002760


title: CRC0050LMX0A02201TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: X64.1


title: donor 1 2016 D7 FcRL5neg H3+ MBC

description:
2
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_1_HD52.txt.gz
Nellore23_annotated_Ig_sequences_Donor_1_HD52_day_120_1FG.txt.gz


title: X63.6


title: X63.5


title: X63.4


title: human liver sample A2002751


title: CRC0051LMH0000000000R02000, LMH, bio rep 1, QC ok

value: H


title: X63.3


title: CRC0032LMX0A04037TUMR02000, LMX_cetux_6w, bio rep 1, QC ok

value: Colorectal Cancer

value: CET


title: X65.2


title: CRC0050LMH0000000000R02000, LMH, bio rep 1, QC ok


title: CRC0050PRH0000000000R04000, PRH, bio rep 1, QC ok

value: PR


title: X63.1


title: human liver sample A2002671


title: X62.6


title: human liver sample A2002733


title: X62.5


title: CRC0032LMX0A04020TUMR02000, LMX_cetux_6w_NT, bio rep 1, QC ok

value: NT


title: X62.4


title: CRC0032LMX0A02204TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: X62.3


title: human liver sample A2002672


title: X62.1


title: human liver sample A2002729


title: X61.6


title: X61.5


title: CRC0031LMX0A05012TUMR01000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: X61.4


title: human liver sample A2002727


title: X63.2


title: CRC0031LMX0A02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: human liver sample A2002668


title: human liver sample A2002736


title: X61.3


title: X61.1


title: X61.2


title: donor 1 2016 D7 Plasmablast

description:
6
immunoglobulin RNA
Nellore23_annotated_Ig_sequences_Donor_1_HD52.txt.gz

value: blood


title: CRC0031LMO0A04012001R01000, LMO_BASALE, bio rep 1, QC ok


title: X60.5


title: CRC0031LMH0000000000R02000, LMH, bio rep 1, QC ok


title: X60.6


title: human liver sample A2002720


title: human liver sample A2002718


title: CRC0031LMX0B02201TUMR04000, LMX_BASALE, bio rep 2, QC ok


title: CRC0030LMX0B05346TUMR02000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: human liver sample A2002717


title: X60.1


title: X62.2


title: CRC0030LMX0B05310TUMR02000, LMX_cetux_6w, bio rep 1, QC ok


title: X87.4


title: CRC0031LMX0A05005TUMR05000, LMX_cetux_6w, bio rep 1, QC ok


title: X60.4


title: human liver sample A2002713


title: human liver sample A2002723


title: X87.3


title: CRC0030LMX0B02204TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0030LMO0A04010001R03000, LMO_BASALE, bio rep 2, QC ok


title: X87.1


title: human liver sample A2010449


title: X86.6


title: CRC0030LMO0A04009001R02000, LMO_BASALE, bio rep 1, QC ok


title: human liver sample A2002712


title: X86.5


title: X86.4


title: X86.3


title: x60.3


title: human liver sample A2002709


title: x60.2


title: X86.2


title: X87.5


title: X87.2


title: human liver sample A2002704


title: CRC0028LMX0B02204TUMR02000, LMX_BASALE, bio rep 2, QC ok


title: X86.1


title: X85.7


title: X85.5


title: X85.4


title: human liver sample A2002702


title: CRC0028LMX0A02201TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: human liver sample A2002703


title: CRC0028LMH0000000000R02000, LMH, bio rep 1, QC ok


title: human liver sample A2002696


title: CRC0029LMX0A02204TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: X85.2


title: human liver sample A2002694


title: X84.1


title: CRC0025LMX0B02201TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: X7.5


title: X7.4


title: CRC0027LMX0B02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: X7.1


title: X59.1


title: human liver sample A2002693


title: X85.6


title: CRC0024LMX0A02201TUMR07000, LMX_BASALE, bio rep 1, QC ok


title: X58.6


title: X58.5


title: X7.2


title: CRC0024LMH0000000000R10000, LMH, bio rep 1, QC ok


title: X58.4


title: human liver sample A2002690


title: CRC0022LMX0B02204TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: X85.3


title: CRC0054LMH0000000000R02000, LMH, bio rep 1, QC ok


title: human liver sample A2002688


title: X58.1


title: CRC0022LMO0A04013001R01000, LMO_BASALE, bio rep 2, QC ok


title: CRC0022LMO0A04012002R01000, LMO_BASALE, bio rep 1, QC ok


title: X57.1


title: human liver sample A2002687


title: CRC0024LMX0B02201TUMR01000, LMX_BASALE, bio rep 2, QC failed


title: X54.1


title: human liver sample A2002685

value: Control


title: X54.2


title: X58.7


title: CRC0021LMX0B02201TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: X53.3


title: X53.2


title: OR_control_biol_rep1_tech_rep3

description: Adult control brains. Third technical replicate of the first biological replicate

value: Oregon-R (OR)

value: Brown body and red eyes

value: Adult

value: Brain


title: human liver sample A2002684


title: X51.2


title: X53.1


title: CRC0019LMX0B02202TUMR02000, LMX_BASALE, bio rep 1, QC ok

value: WT


title: X58.3


title: CRC0018LMX0B02204TUMR14000, LMX_BASALE, bio rep 1, QC ok


title: human liver sample A2002691


title: X51.1


title: X50.3


title: X50.2


title: CRC0018LMO0B02004001R01000, LMO_BASALE, bio rep 1, QC ok

value: O


title: X58.2


title: human liver sample A2001366

value: liver cells


title: human liver sample A2002695


title: X49.5

value: diffuse midline glioma


title: human liver sample A2001365


title: X49.4


title: human liver sample A2010426


title: CRC0014LMX0B02202TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X


title: CRC0017LMX0A02204TUMR02000, LMX_BASALE, bio rep 1, QC ok

value: LM


title: X49.3


title: human liver sample A2001351


title: X50.1


title: human liver sample A2002683


title: X49.1


title: X49.2


title: ATAC_p70_D14_H1_T_bet_lo

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the hg38 version of the human genome using Bowtie.
For each sample peaks of accessibility were identified and annotated using MACS2.
Assembly: hg38
Supplementary files format and content: MBC.ASC.ATAC.rppm.txt: Reads per peak per million normalized count file for all peaks.

source_name: FCRL5 negative HSA+ IgD neg B cell

extract_protocol: Cells were centrifuged for 10 minutes at 500xg, and tagmentation was performed by resuspending cells in 25 ul of Tagmentation mix (1X TD buffer (10 mM TAPS-NaOH pH 8.1, 5 mM MgCl2, 10% DMF), 2.5 μl Tn5 transposase, 0.1% Tween 20 and 0.02% Digitonin) and then incubated for 1 h at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

tag: donor id

tag: sorting markers

value: IgDneg CD38 lo/med CD19+ CD3 neg CD4 neg

tag: h1 tetramer

value: positive

value: PBMC

value: FCRL5 negative HSA+ IgD neg B cell

tag: days post influenza pr8 infection


title: X48.1


title: human liver sample A2008275


title: human liver sample A2001349


title: ATAC_p69_D14_H1_T_bet_lo


title: X48.2


title: X48.3


title: ATAC_p67_D14_H1_T_bet_lo


title: X47.2


title: X40.6


title: TbetLow_H1_d14_p64


title: human liver sample A2001346


title: X40.5


title: human liver sample A2001370


title: X45.1


title: ATAC_p70_D7_H1_T_bet_lo


title: human liver sample A2001343


title: X40.4


title: X40.2


title: ATAC_p69_d7_H1Tbet_lo


title: human liver sample A2001342


title: X37.1


title: X35.3


title: ATAC_p67_d7_H1Tbet_lo


title: X25.2


title: X22.1


title: TbetLow_H1_d7_p65


title: X20.4


title: X20.2


title: human liver sample A2001339


title: TbetLow_H1_d7_p64


title: human liver sample A2001334


title: X20.1


title: human liver sample A2001335


title: ATAC_p70_D14_H1_T_bet_hi

source_name: FCRL5 positive HSA+ IgD neg B cell

value: FCRL5 positive HSA+ IgD neg B cell


title: ATAC_p69_D14_H1_T_bet_hi


title: X19.6


title: X18.4


title: X18.6


title: X19.3


title: X19.2


title: X18.3


title: TbetHi_H1_d14_p66


title: human liver sample A2001340

source_name: liver cells


title: human liver sample A1034917


title: X18.1


title: human liver sample A2006772


title: ATAC_p70_D7_H1_Tbet_hi


title: X17.9


title: human liver sample A2002670


title: human liver sample A2001317


title: X17.8


title: X17.7


title: human liver sample A2001312


title: X17.6


title: TbetHi_H1_d7_p64


title: TbetHi_agg_d14_p66

source_name: FCRL5 positive HA- IgD neg B cell

value: negative

value: FCRL5 positive HA- IgD neg B cell


title: X17.5


title: ATAC_p67_D14_H1_T_bet_hi


title: human liver sample A2013186


title: X23.1


title: TbetHi_agg_d14_p64


title: X17.3


title: human liver sample A2006758


title: X17.2


title: X18.2


title: ATAC_p69_d7_Tbet_agg


title: TbetHi_agg_d7_p65


title: X17.1


title: X15.4


title: human liver sample A2001307


title: X15.3


title: X15.2


title: human liver sample A2001306

value: Control


title: ASC_d14_p66

source_name: ASC

value: IgDneg CD27+ CD38 hi CD19+ CD3 neg CD4 neg

value: ASC


title: human liver sample A2001303


title: TbetHi_agg_d7_p64


title: X14.5


title: X14.4


title: X14.6


title: X17.4


title: X12.1


title: ASC_d14_p64


title: X11.9


title: X11.7


title: human liver sample A2001284


title: X11.8


title: X11.4


title: ATAC_p69_D7_ASCs


title: human liver sample A2001282


title: ATAC_p67_d7_ASCs


title: human liver sample A1034994


title: X11.10


title: ASC_d7_p66


title: X11.1


title: human liver sample A1034993


title: X10.7


title: X10.6


title: X10.5


title: human liver sample A1034990


title: human liver sample A1034988


title: X10.4


title: ASC_d7_p64


title: X10.3


title: X10.2


title: human liver sample A2001323


title: X.6


title: X10.1


title: human liver sample A1034975


title: ROS-EXO

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

description: processed data file: all.Counts.Rattusnorvegicus.txt

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Mapsplice v2.1.8 mapping to reference genome
count counting
Genome_build: GRCh38; Rnor_6.0
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Rattus norvegicus

source_name: cell

growth_protocol: 10%FBS high-glucose DMEM were used as culture medium for primary cell culture. When cells reach 80% confluent, the cell were lysed with trypsin for passage.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
Ion  Proton Sequencing Protocol

treatment_protocol: 100ng/ml uMSC derived exosomes were added to the indicated sample for 48h before total RNA extraction. All samples were treated with 1% exosome-free FBS/DMEM 48h before RNA extraction.

value: rat osteoblast cell line

value: 100ng/ml uMSC-derived exosomes


title: Cytosolic fraction 2, replicate [Ribo-seq]

city: Houston

first: Tattym

last: Shaiken

state: TX

address: One Baylor Plaza

department: Medicine

institute: Baylor College of Medicine

data_processing:
Library strategy: Ribo-seq
Fastqc (v0.11.8) was used for quality control and fastq files were trimmed using Trimmomatic (v0.38)
Bowtie aligner (v1.3.0) was used to remove rRNA sequences from the trimmed fastq files for only the Ribo-seq experiment
rRNA sequences used in the rRNA depletion step were downloaded from ensembl biomart
STAR aligner (v2.7.6a) was used to align and quantify gene expression for the trimmed and rRNA depleted Ribo-seq fastq files and the trimmed bulk RNA-seq fastq files
Features were quantified using featureCounts and the Gencode gene model
Assembly: GRCh38 p13 v35
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: HCT-15 cell

growth_protocol: HCT-15 cells were grown in DMEM enriched with 10% FBS

extract_protocol:
We extracted the cytosol with Buffer A (40 mM HEPES pH 7.4, 120 mM KCl, 0.5% Glycerol, and 0.5% NP-40. The CMX was isolated with buffer B (10 mM Tris-HCl pH 7.5, 1.5 mM KCl, 0.5% Triton X-100, 0.5% sodium deoxycholate, 2.5 mM MgCl2, 0.2 M LiCl) . Total RNA was isolated from the cytosol and CMX using RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HCT-15 cells were  treated with 500 nM of pp242 for 24 hours

value: No treatment

tag: treatment time

tag: extraction buffer

value: Buffer A


title: ROS-NC


title: human liver sample A1034949

value: liver cells


title: ROS-Free

value: Exosome-free supernatent


title: Cytosolic fraction 4, replicate [Ribo-seq]

value: TOR-KI, pp242

value: 24 hours


title: X10.8

value: diffuse midline glioma


title: Cytomatrix fraction 2, replicate [Ribo-seq]

value: Buffer B


title: 689_R60_rep3

city: Daejeon

first: hanim

last: kim

address: Daehak-ro 291

department: biological science

country: South Korea

institute: KAIST

description: Supplementary Data Set2_DSG. Xlsx

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to TAIR10 Arabidopsis whole genome using Tophat v2.1.1 with parameters -p 8.
Mapped BAM files were processed with Aspli1.9 R package for the expression and the splicing analysis
Assembly: TAIR10
Supplementary files format and content: DEG analysis result including |log2(Fold-change)| value and FDR value for each genes.
Supplementary files format and content: DSG analysis result including |delta(PSI/PIR)| value and FDR value for each genes.

organism: Arabidopsis thaliana

source_name: Whole Seedling

growth_protocol: Seeds were spotted on 1/2MS plate and cold stratified for 2 days. After 6hr of white light (50 μmol/m2s, 4°C) treatment for germination induction, seeds were kept in either darkness (4°C) or under red-light (19 μmol/m2s, 4°C) for 60hr.

extract_protocol:
Total RNAs were extracted using the Spectrum Plant Total RNA Extraction Kit (Sigma-Aldrich).
RNA libraries were generated and sequenced on the Illumina NextSeq 500 platform.

tag: ecotype background

tag: age

value: Whole Seedling

value: grown in continuous red light (19 μmol/m2s) for 60hr


title: Cytosolic fraction 3 [Ribo-seq]


title: 689_R60_rep1

description: Supplementary Data Set2_DSG. Xlsx

tag: tissue


title: 689_R60_rep2

description: Supplementary Data Set2_DSG. Xlsx


title: human liver sample A1034946

tag: cell type


title: human liver sample A1034948


title: ASC_d7_p65

value: PBMC


title: 689_D60_rep3

description: Supplementary Data Set2_DSG. Xlsx

tag: genotype

value: grown in continuous darkness for 60hr


title: human liver sample A2008196


title: human liver sample A1034972


title: Cytosolic fraction 1 [Ribo-seq]

tag: treatment


title: Col-0_R60_rep3

description: Supplementary Data Set2_DSG. Xlsx


title: 689_D60_rep2

description: Supplementary Data Set2_DSG. Xlsx


title: human liver sample A1034931


title: Cytomatrix fraction 3 [Ribo-seq]


title: Col-0_R60_rep2

description: Supplementary Data Set2_DSG. Xlsx


title: Cytomatrix fraction 1 [Ribo-seq]


title: Col-0_R60_rep1

description: Supplementary Data Set2_DSG. Xlsx


title: human liver sample A2008190


title: Col-0_D60_rep3

description: Supplementary Data Set2_DSG. Xlsx


title: Cytomatrix fraction 4, replicate [RNA-seq]

data_processing:
Fastqc (v0.11.8) was used for quality control and fastq files were trimmed using Trimmomatic (v0.38)
Bowtie aligner (v1.3.0) was used to remove rRNA sequences from the trimmed fastq files for only the Ribo-seq experiment
rRNA sequences used in the rRNA depletion step were downloaded from ensembl biomart
STAR aligner (v2.7.6a) was used to align and quantify gene expression for the trimmed and rRNA depleted Ribo-seq fastq files and the trimmed bulk RNA-seq fastq files
Features were quantified using featureCounts and the Gencode gene model
Assembly: GRCh38 p13 v35
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample


title: Col-0_D60_rep2

description: Supplementary Data Set2_DSG. Xlsx


title: human liver sample A1034925


title: Col-0_D60_rep1

description: Supplementary Data Set2_DSG. Xlsx


title: human liver sample A1034924


title: Cytomatrix fraction 2, replicate [RNA-seq]


title: EMS27_R60_rep3

description:
Supplementary Data Set1_DEG. Xlsx
Supplementary Data Set2_DSG. Xlsx


title: EMS27_R60_rep1


title: human liver sample A1034923

value: Control


title: EMS27_D60_rep3


title: human liver sample A1034963


title: Cytomatrix fraction 1 [RNA-seq]


title: EMS27_D60_rep2


title: 689_D60_rep1

description: Supplementary Data Set2_DSG. Xlsx


title: Cytosolic fraction 4, replicate [RNA-seq]


title: MLB_R60_rep3

value: MLB


title: human liver sample A2008225


title: MLB_R60_rep2


title: Cytosolic fraction 3 [RNA-seq]


title: EMS27_D60_rep1


title: MLB_D60_rep3


title: MLB_D60_rep2


title: Cytomatrix fraction 3 [RNA-seq]


title: human liver sample A1034905


title: EMS27_R60_rep2


title: Cytosolic fraction 1 [RNA-seq]


title: MLB_D60_rep1


title: Cytosolic fraction 2, replicate [RNA-seq]


title: human liver sample A1034913