title: SAM24358719 Patient245 Y M Placebo Screen Colon Active 1.34632871642265 GNE

value: GNE


title: SAM24358717 Patient155 N F Etrolizumab Screen Ileum Active 1.37553242956758 GNE

status: Public on Jul 23 2021

type: SRA

city: South San Francisco

first: Jason

middle: A

last: Hackney

state: CA

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

country: USA

institute: Genentech, Inc.

library_source: transcriptomic

data_processing: Reads were aligned to the GRCh38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. We used GENCODE basic (v.27) gene models. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Ensembl Gene IDs, counts and nRPKM statistics.

molecule: total RNA

organism: Homo sapiens

source_name: RNA from human intestinal biopsy

extract_protocol: Biopsies from the etrolizumab clinical study were thawed, removed from RNAlater, homogenized with 0.1 mm glass beads and RNA was purified using Qiagen All-prep 96 kits. Quantity and quality of the RNA was assessed with a NanoDrop 8000 (Thermo Scientific) and Bioanalyzer, respectively. Sequence libraries were prepared from 0.1 ug of RNA using TruSeq Stranded Total RNA Library Prep kit (Illumina) according to the manufacturer's instructions.

value: N

tag: Sex

value: F

tag: treatment

value: Etrolizumab

tag: visit

value: Screen

tag: location

value: Ileum

value: Active

tag: sequencingcenter


title: SAM24358718 Patient237 Y F Etrolizumab Screen Ileum Inactive 1.1565538105919 GNE

value: Y

value: Inactive


title: SAM24358724 Patient55 Y F Etrolizumab Screen Colon Active 1.01194203213715 GNE

value: Colon


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 127]

type: protein

city: Athens

first: Daniel

middle: Roberto

last: Perez

state: GA

address: 953 College Station Road

institute: University of Georgia

description: Fig. 7 and 8

hyb_protocol: Serum and NW samples were diluted 1:100 in a protein array blocking buffer (GVS, Sanford,  ME, USA), supplemented with E. coli lysate (GenScript, Piscataway, NJ, USA) to a final  concentration of 10 mg/mL, and preincubated at room temperature (RT) for 30 min. Concurrently,  arrays were rehydrated in blocking buffer (without lysate) for 30 min. Blocking  buffer was removed, and arrays were probed with preincubated serum samples using  sealed chambers to prevent cross-contamination of samples between the pads. Arrays were  incubated overnight at 4  C with gentle agitation. They were then washed at RT three  times with Tris-buffered saline (TBS) containing 0.05% Tween 20 (T-TBS), biotin-conjugated  goat anti-mouse IgA and Biotin-conjugated anti-mouse IgG (Jackson Immuno Research  Laboratories, Inc., West Grove, PA, USA) were diluted 1:400 in blocking buffer and applied  to separate arrays for 1 h, RT with gentle agitation. Arrays were washed three times  with T-TBS, followed by incubation with streptavidin-conjugated Qdot655 (Thermo Fisher  Scientific, Waltham, MA, USA) diluted 1:200 in blocking buffer for 1 h, RT. Arrays were  washed three times with T-TBS and once with water. Arrays were air dried by centrifugation  at 500 g for 5 min. Images were acquired using the ArrayCAM imaging system from  Grace Bio-Labs (Bend, OR, USA). Spot and background intensities were measured using  an annotated grid (.gal) file. Mean fluorescence across antigens grouped by isotypes were  used for subsequent analysis. The different antigens were acquired from Sino biological  (Wayne, PA, USA).

scan_protocol: Images were acquired using the ArrayCAM imaging system from Grace Bio-Labs (Bend, OR) with gain and exposure times of 50 and 400-1000ms, respectively.

data_processing: Spot and background intensities were measured using an annotated grid (.gal) file.  Signal intensities (SI) for each antigen on the array were first background corrected by subtracting sample-specific T-PBS buffer signals from purified protein spot signals. For statistical analysis,   A two-way ANOVA was performed. A P value below 0.05 was considered significan. All data analyses and graphs were performed using GraphPad Prism software version 9 (GraphPad Software Inc., San Diego, CA, USA). We utilized the raw data for our analyses without any further corrections.

molecule: protein

organism: Mus musculus

source_name: Nasal wash

tag: tissue

value: Nasal wash

tag: strain

tag: vaccine regimen

value: prime/boost challenge

tag: vaccine

value: FluB-RAM

tag: time point

value: d14 dpc

tag: mouse id


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 126]

description: Fig. 7 and 8


title: prime/boost challengePBSd14 dpc [SAMPLE 125]

description: Fig. 7 and 8

value: PBS


title: SAM24358716 Patient175 N M Placebo Screen Colon Inactive 0.882640374381935 GNE

value: M

value: Placebo


title: prime/boost challengePBSd14 dpc [SAMPLE 124]

description: Fig. 7 and 8


title: SAM24358713 Patient229 N F Placebo Screen Colon Active 1.00515069183882 GNE

value: GNE


title: SAM24358714 Patient204 N M Etrolizumab Screen NA NA 1.29849495737973 GNE

value: N


title: SAM24358712 Patient16 Y F Etrolizumab Screen Colon Active 1.24093199396609 GNE

value: F


title: SAM24358710 Patient97 Y F Etrolizumab Screen Ileum Active 1.28807686768066 GNE

value: Etrolizumab


title: SAM24358711 Patient149 N M Placebo Screen Ileum Inactive 1.44730128841206 GNE

value: Screen


title: SAM24358709 Patient97 Y F Etrolizumab Week14 Ileum Active 0.997411359692174 GNE

value: Ileum


title: prime/boost challengePBSd14 dpc [SAMPLE 122]

description: Fig. 7 and 8


title: prime/boost challengePBSd14 dpc [SAMPLE 121]

description: Fig. 7 and 8


title: prime/boost challengeFluB attd14 dpc [SAMPLE 117]

description: Fig. 7 and 8

value: FluB att


title: prime/boost challengePBSd14 dpc [SAMPLE 120]

description: Fig. 7 and 8


title: prime/boost challengeFluB attd14 dpc [SAMPLE 118]

description: Fig. 7 and 8


title: SAM24359473 Patient209 Y M Etrolizumab Week14 Ileum Active 1.14682764423728 GNE

value: Y

value: Active


title: SAM24358708 Patient175 N M Placebo Week14 Colon Inactive 0.862380081072457 GNE

value: Colon

value: Inactive


title: prime/boost challengeFluB attd14 dpc [SAMPLE 116]

description: Fig. 7 and 8

value: Nasal wash

value: prime/boost challenge


title: SAM24358715 Patient23 Y F Etrolizumab Screen Ileum Active 1.51529278552564 GNE


title: SAM24358706 Patient130 Y F Placebo Week14 Colon Active 1.64608258909253 GNE


title: prime/boost challengeFluB attd14 dpc [SAMPLE 115]

description: Fig. 7 and 8

value: d14 dpc


title: prime/boost challengeFluB attd14 dpc [SAMPLE 114]

description: Fig. 7 and 8


title: SAM24358705 Patient94 Y F Etrolizumab Week14 Ileum Active 1.43677136771117 GNE


title: prime/boost challengePBSd14 dpc [SAMPLE 123]

description: Fig. 7 and 8

value: PBS


title: SAM24358701 Patient181 N F Etrolizumab Week14 Colon Active 1.11752861552487 GNE


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 113]

description: Fig. 7 and 8

value: FluB-RANS


title: SAM24358703 Patient149 N M Placebo Week14 Ileum Inactive 1.07126447794775 GNE

value: M

value: Placebo


title: SAM24358702 Patient182 N M Etrolizumab Week14 Ileum Inactive 1.43134273554218 GNE

value: N

value: GNE


title: SAM24358700 Patient25 N F Etrolizumab Week14 Colon Active 1.0852216134374 GNE

value: F

value: Etrolizumab


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 111]

description: Fig. 7 and 8


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 109]

description: Fig. 7 and 8


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 110]

description: Fig. 7 and 8


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 112]

description: Fig. 7 and 8


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 107]

description: Fig. 7 and 8


title: prime/boost challengeFluB attd14 dpc [SAMPLE 119]

description: Fig. 7 and 8


title: SAM24358699 Patient218 Y F Etrolizumab Week14 Ileum Active 1.34173897146323 GNE

value: Ileum


title: SAM24358698 Patient229 N F Placebo Week14 Colon Active 1.0143166169557 GNE


title: SAM24358697 Patient217 Y M Etrolizumab Week14 Ileum Inactive 1.08285527871738 GNE


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 106]

description: Fig. 7 and 8

value: FluB-RAM


title: SAM24329729 CD8 aE+ CD8 AphaE_positive

data_processing: Reads were aligned to the GRCh38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were based on Refseq canonical transcript alignments to GRCh38. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

extract_protocol: Single T cells were sorted into individual wells of 96 well plates. SMART-seq v4 kit was used to generate cDNA from the sorted cells. Samples were assessed by PicoGreen assay at this point, and only wells with detectable DNA were included in the library preparation. Libraries were prepared with the Nextera kits using 1ng of cDNA per cell, according to manufacturer's specifications. Samples in each plate were uniquely barcoded, and pooled. Each plate was pooled individually. Pooled libraries were QC'd by Bioanalyzer and Qubit. Pooled libraries were then sequenced on one lane of an Illumina HiSeq4000 (Illumina) to generating an average of ~260M of paired end 75 base pair reads per pool.

value: CD8 aE+


title: SAM24329835 CD8 aE+ CD8 AphaE_positive


title: SAM24329760 CD4 aE- CD4 AphaE_negative

value: CD4 aE-


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 104]

description: Fig. 7 and 8


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 103]

description: Fig. 7 and 8


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 105]

description: Fig. 7 and 8


title: SAM24329869 CD4 aE+ CD4 AphaE_positive

value: CD4 aE+


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 101]

description: Fig. 7 and 8


title: SAM24329723 CD8 aE- CD8 AphaE_negative

value: CD8 aE-


title: SAM24329815 CD8 aE+ CD8 AphaE_positive


title: prime/boost challengePBSd14 dpc [SAMPLE 100]

description: Fig. 7 and 8

value: Nasal wash


title: prime/boost challengePBSd14 dpc [SAMPLE 99]

description: Fig. 7 and 8

value: prime/boost challenge


title: prime/boost challengePBSd14 dpc [SAMPLE 98]

description: Fig. 7 and 8

value: d14 dpc


title: SAM24329881 CD8 aE- CD8 AphaE_negative


title: SAM24329698 CD4 aE+ CD4 AphaE_positive


title: prime/boost challengePBSd14 dpc [SAMPLE 96]

description: Fig. 7 and 8

value: PBS


title: prime/boost challengePBSd14 dpc [SAMPLE 97]

description: Fig. 7 and 8


title: SAM24329830 CD8 aE+ CD8 AphaE_positive


title: prime/boost challengeFluB attd14 dpc [SAMPLE 93]

description: Fig. 6 and 8

source_name: Serum

value: serum

value: FluB att


title: prime/boost challengeFluB attd14 dpc [SAMPLE 94]

description: Fig. 6 and 8


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 102]

description: Fig. 7 and 8


title: SAM24329878 CD8 aE- CD8 AphaE_negative


title: SAM24329860 CD4 aE+ CD4 AphaE_positive


title: prime/boost challengeFluB attd14 dpc [SAMPLE 92]

description: Fig. 6 and 8


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 108]

description: Fig. 7 and 8

value: FluB-RANS


title: SAM24329897 CD8 aE+ CD8 AphaE_positive


title: prime/boost challengeFluB attd14 dpc [SAMPLE 89]

description: Fig. 6 and 8


title: SAM24329596 CD4 aE+ CD4 AphaE_positive


title: prime/boost challengeFluB attd14 dpc [SAMPLE 90]

description: Fig. 6 and 8


title: SAM24329827 CD8 aE+ CD8 AphaE_positive


title: SAM24329891 CD8 aE- CD8 AphaE_negative


title: prime/boost challengePBSd14 dpc [SAMPLE 95]

description: Fig. 7 and 8


title: SAM24329783 CD4 aE+ CD4 AphaE_positive


title: SAM24329812 CD8 aE- CD8 AphaE_negative


title: prime/boost challengeFluB attd14 dpc [SAMPLE 88]

description: Fig. 6 and 8


title: prime/boost challengeFluB attd14 dpc [SAMPLE 87]

description: Fig. 6 and 8


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 86]

description: Fig. 6 and 8


title: SAM24329915 CD8 aE+ CD8 AphaE_positive


title: SAM24329838 CD4 aE- CD4 AphaE_negative


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 85]

description: Fig. 6 and 8


title: SAM24329604 CD4 aE+ CD4 AphaE_positive


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 84]

description: Fig. 6 and 8


title: prime/boost challengeFluB attd14 dpc [SAMPLE 91]

description: Fig. 6 and 8


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 83]

description: Fig. 6 and 8


title: SAM24329782 CD4 aE+ CD4 AphaE_positive


title: SAM24329643 CD8 aE+ CD8 AphaE_positive


title: SAM24329746 CD8 aE+ CD8 AphaE_positive


title: SAM24329661 CD4 aE- CD4 AphaE_negative


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 81]

description: Fig. 6 and 8


title: SAM24329575 CD4 aE- CD4 AphaE_negative


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 80]

description: Fig. 6 and 8


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 82]

description: Fig. 6 and 8


title: SAM24329863 CD4 aE+ CD4 AphaE_positive


title: SAM24329670 CD4 aE- CD4 AphaE_negative


title: SAM24329745 CD8 aE+ CD8 AphaE_positive


title: SAM24329828 CD8 aE+ CD8 AphaE_positive


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 77]

description: Fig. 6 and 8


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 78]

description: Fig. 6 and 8


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 79]

description: Fig. 6 and 8


title: SAM24329572 CD4 aE- CD4 AphaE_negative


title: SAM24329630 CD8 aE- CD8 AphaE_negative


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 73]

description: Fig. 6 and 8


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 76]

description: Fig. 6 and 8


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 72]

description: Fig. 6 and 8


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 71]

description: Fig. 6 and 8


title: SAM24329709 CD8 aE- CD8 AphaE_negative


title: SAM24329824 CD8 aE+ CD8 AphaE_positive


title: SAM24329690 CD4 aE+ CD4 AphaE_positive


title: prime/boost challengePBSd14 dpc [SAMPLE 70]

description: Fig. 6 and 8


title: prime/boost challengePBSd14 dpc [SAMPLE 69]

description: Fig. 6 and 8


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 74]

description: Fig. 6 and 8


title: SAM24329756 CD4 aE- CD4 AphaE_negative


title: prime/boost challengePBSd14 dpc [SAMPLE 67]

description: Fig. 6 and 8


title: prime/boost challengePBSd14 dpc [SAMPLE 66]

description: Fig. 6 and 8


title: SAM24329667 CD4 aE- CD4 AphaE_negative


title: SAM24329584 CD4 aE- CD4 AphaE_negative


title: SAM24329788 CD4 aE+ CD4 AphaE_positive


title: prime/boost challengePBSd14 dpc [SAMPLE 68]

description: Fig. 6 and 8


title: SAM24329646 CD8 aE+ CD8 AphaE_positive


title: prime/boost challengePBSd14 dpc [SAMPLE 65]

description: Fig. 6 and 8


title: SAM24358752 Patient64 N M Etrolizumab Screen Colon Active 1.56491414695079 GNE

value: N

value: M

value: Screen

value: Colon

value: Active


title: prime/boost challengePBSd14 dpc [SAMPLE 63]

description: Fig. 6 and 8


title: SAM24329733 CD8 aE+ CD8 AphaE_positive


title: prime/boostFluB attd19 dpb [SAMPLE 61]

description: Fig. 3 and 4

value: prime/boost

value: d19 dpb


title: prime/boost challengePBSd14 dpc [SAMPLE 64]

description: Fig. 6 and 8


title: SAM24329871 CD4 aE+ CD4 AphaE_positive


title: SAM24329790 CD4 aE+ CD4 AphaE_positive


title: prime/boostFluB attd19 dpb [SAMPLE 60]

description: Fig. 3 and 4


title: SAM24329870 CD4 aE+ CD4 AphaE_positive


title: SAM24329718 CD8 aE- CD8 AphaE_negative


title: SAM24329597 CD4 aE+ CD4 AphaE_positive


title: SAM24329585 CD4 aE- CD4 AphaE_negative

value: CD4 aE-


title: SAM24329741 CD8 aE+ CD8 AphaE_positive

value: CD8 aE+


title: prime/boostFluB-RANSd19 dpb [SAMPLE 56]

description: Fig. 3 and 4


title: prime/boostFluB-RANSd19 dpb [SAMPLE 57]

description: Fig. 3 and 4


title: SAM24329636 CD8 aE+ CD8 AphaE_positive


title: SAM24329889 CD8 aE- CD8 AphaE_negative

value: CD8 aE-


title: SAM24329628 CD8 aE- CD8 AphaE_negative


title: SAM24329650 CD8 aE+ CD8 AphaE_positive


title: SAM24329732 CD8 aE+ CD8 AphaE_positive


title: prime/boostFluB-RAMd19 dpb [SAMPLE 53]

description: Fig. 3 and 4

value: FluB-RAM


title: prime/boostFluB-RANSd19 dpb [SAMPLE 55]

description: Fig. 3 and 4


title: SAM24329639 CD8 aE+ CD8 AphaE_positive


title: prime/boostFluB attd19 dpb [SAMPLE 62]

description: Fig. 3 and 4


title: SAM24329792 CD4 aE+ CD4 AphaE_positive

value: CD4 aE+


title: prime/boostFluB-RANSd19 dpb [SAMPLE 58]

description: Fig. 3 and 4


title: prime/boostFluB attd19 dpb [SAMPLE 59]

description: Fig. 3 and 4


title: prime/boostPBSd19 dpb [SAMPLE 51]

description: Fig. 3 and 4


title: SAM24329882 CD8 aE- CD8 AphaE_negative


title: prime/boostFluB-RAMd19 dpb [SAMPLE 52]

description: Fig. 3 and 4


title: SAM24329903 CD8 aE+ CD8 AphaE_positive


title: prime/boostPBSd19 dpb [SAMPLE 50]

description: Fig. 3 and 4


title: SAM24329687 CD4 aE+ CD4 AphaE_positive


title: prime/boostPBSd19 dpb [SAMPLE 49]

description: Fig. 3 and 4


title: prime/boost challengeFluB attd14 dpc [SAMPLE 47]

description: Fig. 6 and 8

value: prime/boost challenge

value: d14 dpc


title: prime/boost challengeFluB attd14 dpc [SAMPLE 45]

description: Fig. 6 and 8

value: serum


title: prime/boost challengeFluB attd14 dpc [SAMPLE 46]

description: Fig. 6 and 8

value: FluB att


title: prime/boostPBSd19 dpb [SAMPLE 48]

description: Fig. 3 and 4

value: PBS


title: prime/boost challengeFluB attd14 dpc [SAMPLE 44]

description: Fig. 6 and 8


title: SAM24329797 CD8 aE- CD8 AphaE_negative


title: SAM24329681 CD4 aE+ CD4 AphaE_positive


title: prime/boost challengeFluB attd14 dpc [SAMPLE 43]

description: Fig. 6 and 8


title: SAM24329727 CD8 aE+ CD8 AphaE_positive


title: prime/boost challengeFluB attd14 dpc [SAMPLE 42]

description: Fig. 6 and 8


title: SAM24329573 CD4 aE- CD4 AphaE_negative


title: SAM24329702 CD8 aE- CD8 AphaE_negative


title: SAM24329805 CD8 aE- CD8 AphaE_negative


title: SAM24329818 CD8 aE+ CD8 AphaE_positive


title: SAM24329700 CD4 aE+ CD4 AphaE_positive


title: SAM24329676 CD4 aE- CD4 AphaE_negative


title: prime/boost challengeFluB attd14 dpc [SAMPLE 41]

description: Fig. 6 and 8


title: SAM24329836 CD8 aE+ CD8 AphaE_positive


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 39]

description: Fig. 6 and 8

value: FluB-RANS


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 38]

description: Fig. 6 and 8


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 36]

description: Fig. 6 and 8


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 37]

description: Fig. 6 and 8


title: SAM24329861 CD4 aE+ CD4 AphaE_positive


title: prime/boost challengeFluB attd14 dpc [SAMPLE 40]

description: Fig. 6 and 8


title: SAM24329826 CD8 aE+ CD8 AphaE_positive


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 35]

description: Fig. 6 and 8


title: SAM24329794 CD8 aE- CD8 AphaE_negative


title: SAM24329704 CD8 aE- CD8 AphaE_negative


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 34]

description: Fig. 6 and 8


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 32]

description: Fig. 6 and 8


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 31]

description: Fig. 6 and 8


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 33]

description: Fig. 6 and 8


title: SAM24329906 CD8 aE+ CD8 AphaE_positive


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 30]

description: Fig. 6 and 8


title: SAM24329846 CD4 aE- CD4 AphaE_negative


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 75]

description: Fig. 6 and 8


title: SAM24329660 CD4 aE- CD4 AphaE_negative


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 29]

description: Fig. 6 and 8


title: SAM24329734 CD8 aE+ CD8 AphaE_positive


title: SAM24329651 CD8 aE+ CD8 AphaE_positive


title: SAM24329658 CD4 aE- CD4 AphaE_negative


title: SAM24329832 CD8 aE+ CD8 AphaE_positive


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 26]

description: Fig. 6 and 8


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 27]

description: Fig. 6 and 8


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 28]

description: Fig. 6 and 8


title: SAM24329645 CD8 aE+ CD8 AphaE_positive


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 25]

description: Fig. 6 and 8


title: prime/boostFluB-RAMd19 dpb [SAMPLE 54]

description: Fig. 3 and 4


title: genomic DNA from liver 338

type: genomic

city: Atlanta

first: Karen

last: Conneely

address: 615 Michael Street

institute: Emory University

description:
liver biopsy
sample name:
203991530183_R05C01

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2
MatrixProcessed.csv contains: Average Beta values

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Liver

label_protocol: Standard Illumina Protocol

extract_protocol: Liver genomic DNA was extracted with the ALLprep DNA/RNA Mini Kit (Qiagen; Valencia, CA) and quantified using the Qubit system (ThermoFisher Scientific; Waltham, MA)

value: Liver

value: Male

tag: disease state

tag: age

tag: bmi

tag: t2d medication

value: Yes

tag: chip id

tag: rnaseq-matched srr id

tag: individual id


title: genomic DNA from liver 333

description:
liver biopsy
sample name:
203991530166_R08C01

tag: Sex


title: genomic DNA from liver 339

description:
liver biopsy
sample name:
203991530183_R06C01

value: No


title: genomic DNA from liver 334

description:
liver biopsy
sample name:
203991530183_R01C01


title: genomic DNA from liver 335

description:
liver biopsy
sample name:
203991530183_R02C01


title: genomic DNA from liver 341

description:
liver biopsy
sample name:
203991530183_R08C01

value: Female


title: genomic DNA from liver 340

description:
liver biopsy
sample name:
203991530183_R07C01


title: genomic DNA from liver 336

description:
liver biopsy
sample name:
203991530183_R03C01


title: genomic DNA from liver 330

description:
liver biopsy
sample name:
203991530166_R05C01


title: genomic DNA from liver 331

description:
liver biopsy
sample name:
203991530166_R06C01


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 24]

description: Fig. 6 and 8


title: SAM24329625 CD8 aE- CD8 AphaE_negative


title: prime/boost challengePBSd14 dpc [SAMPLE 23]

description: Fig. 6 and 8


title: genomic DNA from liver 329

description:
liver biopsy
sample name:
203991530166_R04C01


title: genomic DNA from liver 337

description:
liver biopsy
sample name:
203991530183_R04C01


title: SAM24329711 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 328

description:
liver biopsy
sample name:
203991530166_R03C01


title: genomic DNA from liver 326

description:
liver biopsy
sample name:
203991530166_R01C01


title: genomic DNA from liver 332

description:
liver biopsy
sample name:
203991530166_R07C01


title: prime/boost challengePBSd14 dpc [SAMPLE 22]

description: Fig. 6 and 8


title: SAM24329688 CD4 aE+ CD4 AphaE_positive


title: SAM24329752 CD4 aE- CD4 AphaE_negative


title: genomic DNA from liver 327

description:
liver biopsy
sample name:
203991530166_R02C01


title: SAM24329884 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 324

description:
liver biopsy
sample name:
203991530165_R07C01


title: genomic DNA from liver 323

description:
liver biopsy
sample name:
203991530165_R06C01


title: prime/boost challengePBSd14 dpc [SAMPLE 21]

description: Fig. 6 and 8


title: genomic DNA from liver 322

description:
liver biopsy
sample name:
203991530165_R05C01


title: genomic DNA from liver 325

description:
liver biopsy
sample name:
203991530165_R08C01


title: genomic DNA from liver 321

description:
liver biopsy
sample name:
203991530165_R04C01


title: SAM24329721 CD8 aE- CD8 AphaE_negative


title: SAM24329742 CD8 aE+ CD8 AphaE_positive


title: prime/boost challengePBSd14 dpc [SAMPLE 20]

description: Fig. 6 and 8


title: SAM24329833 CD8 aE+ CD8 AphaE_positive


title: prime/boost challengePBSd14 dpc [SAMPLE 18]

description: Fig. 6 and 8


title: genomic DNA from liver 319

description:
liver biopsy
sample name:
203991530165_R02C01


title: prime/boost challengePBSd14 dpc [SAMPLE 19]

description: Fig. 6 and 8


title: genomic DNA from liver 318

description:
liver biopsy
sample name:
203991530165_R01C01


title: prime/boost challengePBSd14 dpc [SAMPLE 17]

description: Fig. 6 and 8


title: SAM24329724 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 316

description:
liver biopsy
sample name:
203293440245_R07C01


title: genomic DNA from liver 315

description:
liver biopsy
sample name:
203293440245_R06C01


title: genomic DNA from liver 320

description:
liver biopsy
sample name:
203991530165_R03C01


title: SAM24329841 CD4 aE- CD4 AphaE_negative


title: prime/boost challengePBSd14 dpc [SAMPLE 16]

description: Fig. 6 and 8


title: genomic DNA from liver 314

description:
liver biopsy
sample name:
203293440245_R05C01


title: genomic DNA from liver 313

description:
liver biopsy
sample name:
203293440245_R04C01


title: genomic DNA from liver 312

description:
liver biopsy
sample name:
203293440245_R03C01


title: genomic DNA from liver 311

description:
liver biopsy
sample name:
203293440245_R02C01


title: prime/boostFluB attd19 dpb [SAMPLE 15]

description: Fig. 3 and 4

value: prime/boost

value: d19 dpb


title: genomic DNA from liver 310

description:
liver biopsy
sample name:
203293440245_R01C01


title: genomic DNA from liver 309

description:
liver biopsy
sample name:
203293440216_R08C01


title: genomic DNA from liver 317

description:
liver biopsy
sample name:
203293440245_R08C01


title: SAM24329722 CD8 aE- CD8 AphaE_negative


title: prime/boostFluB attd19 dpb [SAMPLE 14]

description: Fig. 3 and 4


title: SAM24329652 CD8 aE+ CD8 AphaE_positive

value: CD8 aE+


title: genomic DNA from liver 306

description:
liver biopsy
sample name:
203293440216_R04C01


title: genomic DNA from liver 304

description:
liver biopsy
sample name:
203293440216_R01C01


title: SAM24329626 CD8 aE- CD8 AphaE_negative

value: CD8 aE-


title: prime/boostFluB attd19 dpb [SAMPLE 12]

description: Fig. 3 and 4


title: prime/boostFluB attd19 dpb [SAMPLE 13]

description: Fig. 3 and 4


title: SAM24329850 CD4 aE+ CD4 AphaE_positive


title: genomic DNA from liver 308

description:
liver biopsy
sample name:
203293440216_R06C01


title: prime/boostFluB-RANSd19 dpb [SAMPLE 11]

description: Fig. 3 and 4


title: TGW treated with mock

city: Tokyo

first: Naoko

last: Hattori

address: 5-1-1 Tsukiji, Chuo-ku

department: Research Institute

country: Japan

institute: National Cancer Center

hyb_protocol: Standard Illumina Protocol

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing: The data were analyzed using GenomeStudio Methylation Module Software (v1.9.0). Beta values were obtained after background correction and normalization to internal controls.

source_name: TGW

growth_protocol: TGW cell line was maintained in MEM medium with 10% FBS.

extract_protocol: High-quality DNA was extracted by the phenol/chloroform method.

treatment_protocol: Cells were seeded on Day 0. On Days 1, 2, and 3, the medium was replaced with a medium containing 0.3 µM of 5-aza-dC. On Day 4, the cells were collected for genomic DNA extraction.

tag: cell line

value: TGW

tag: treatment

value: mock


title: SAM24329858 CD4 aE+ CD4 AphaE_positive

value: CD4 aE+


title: genomic DNA from liver 302

description:
liver biopsy
sample name:
203293440207_R07C01


title: TGW treated with 5-aza-dC


title: genomic DNA from liver 307

description:
liver biopsy
sample name:
203293440216_R05C01


title: genomic DNA from liver 303

description:
liver biopsy
sample name:
203293440207_R08C01


title: prime/boostFluB-RANSd19 dpb [SAMPLE 10]

description: Fig. 3 and 4


title: prime/boostFluB-RANSd19 dpb [SAMPLE 9]

description: Fig. 3 and 4


title: genomic DNA from liver 301

description:
liver biopsy
sample name:
203293440207_R05C01


title: SAM24329800 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 305

description:
liver biopsy
sample name:
203293440216_R03C01


title: genomic DNA from liver 300

description:
liver biopsy
sample name:
203293440207_R04C01


title: SAM24329581 CD4 aE- CD4 AphaE_negative

value: CD4 aE-


title: genomic DNA from liver 299

description:
liver biopsy
sample name:
203293440207_R02C01


title: SAM24329808 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 297

description:
liver biopsy
sample name:
203293440204_R08C01


title: SAM24329899 CD8 aE+ CD8 AphaE_positive


title: genomic DNA from liver 298

description:
liver biopsy
sample name:
203293440207_R01C01


title: genomic DNA from liver 295

description:
liver biopsy
sample name:
203293440204_R06C01


title: prime/boostFluB-RAMd19 dpb [SAMPLE 7]

description: Fig. 3 and 4

value: serum

value: FluB-RAM


title: genomic DNA from liver 294

description:
liver biopsy
sample name:
203293440204_R05C01


title: SAM24329847 CD4 aE- CD4 AphaE_negative


title: prime/boostFluB-RANSd19 dpb [SAMPLE 8]

description: Fig. 3 and 4


title: genomic DNA from liver 292

description:
liver biopsy
sample name:
203293440204_R03C01


title: genomic DNA from liver 293

description:
liver biopsy
sample name:
203293440204_R04C01


title: genomic DNA from liver 296

description:
liver biopsy
sample name:
203293440204_R07C01


title: genomic DNA from liver 291

description:
liver biopsy
sample name:
203293440204_R02C01


title: prime/boostPBSd19 dpb [SAMPLE 4]

description: Fig. 3 and 4

value: PBS


title: prime/boostFluB-RAMd19 dpb [SAMPLE 5]

description: Fig. 3 and 4


title: prime/boostFluB-RAMd19 dpb [SAMPLE 6]

description: Fig. 3 and 4


title: genomic DNA from liver 290

description:
liver biopsy
sample name:
203293440204_R01C01


title: SAM24329913 CD8 aE+ CD8 AphaE_positive


title: genomic DNA from liver 288

description:
liver biopsy
sample name:
203293440180_R07C01


title: genomic DNA from liver 289

description:
liver biopsy
sample name:
203293440180_R08C01


title: SAM24329905 CD8 aE+ CD8 AphaE_positive


title: genomic DNA from liver 287

description:
liver biopsy
sample name:
203293440180_R06C01


title: SAM24329894 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 285

description:
liver biopsy
sample name:
203293440180_R04C01


title: prime/boostPBSd19 dpb [SAMPLE 2]

description: Fig. 3 and 4


title: prime/boostPBSd19 dpb [SAMPLE 3]

description: Fig. 3 and 4


title: SAM24329735 CD8 aE+ CD8 AphaE_positive


title: SAM24329656 CD4 aE- CD4 AphaE_negative


title: genomic DNA from liver 284

description:
liver biopsy
sample name:
203293440180_R03C01


title: SAM24329810 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 283

description:
liver biopsy
sample name:
203293440180_R02C01


title: genomic DNA from liver 286

description:
liver biopsy
sample name:
203293440180_R05C01


title: prime/boostPBSd19 dpb [SAMPLE 1]

description: Fig. 3 and 4


title: genomic DNA from liver 281

description:
liver biopsy
sample name:
203293440179_R08C01


title: genomic DNA from liver 282

description:
liver biopsy
sample name:
203293440180_R01C01


title: genomic DNA from liver 280

description:
liver biopsy
sample name:
203293440179_R07C01


title: IP T Naïve 2

city: Gothenburg

first: Xiaoyang

last: Wang

address: Medicinaregatan 11

department: Physiology

country: Sweden

institute: University of Gothenburg

description: Naïve 2

data_processing:
Genome_build: mouse reference genome: mm10_withIgTCRgenes
Genome_build: V(D)J reference: vdj_GRCm38_alts_ensembl
alignment: CellRanger 2.2.0
main software: Seurat 3.027
general filtering: cells with between 200 and 6000 expressed genes and with mitochondrial counts below 7% were kept for downstream analysis
normalization: data were normalized with a scale factor of 10,000 and were log transformed before identify-ing the 2,000 most highly variable genes
scaling: all genes were scaled using the default settings in Seurat (including cell cycle bias) before performing the principal component analysis
Supplementary_files_format_and_content: for all GEX amples, barcodes.tsv, genes.tsv and matrix.mtx are provided; for V(D)J enrichment analysis, the filtered_contig_annotations file is provided
Supplementary_files_format_and_content: MTX files: The top three lines of this file are header lines. The third line contains the total number of rows in all the three files in this folder (genes.tsv, barcodes.tsv, matrix.mtx).  The next lines (line number 4 onwards) have three columns:   - The first column refers to the "gene id" index.   - The second column refers to "cell id" index.

source_name: brain meninges

extract_protocol:
Used 10x Genomics kits - GEX 5' Library & Gel Bead Kit (PN-1000014) and 5’ Library & Gel Bead Kit + Single Cell V(D)J Enrichment Kit (Mouse T cells and B cells)
Manufacturer's instructions
droplet scRNA-seq (10x Genomics)

value: postnatal day 4

tag: pooling

value: 12 mice, 6 males and 6 females


title: SAM24329713 CD8 aE- CD8 AphaE_negative


title: SAM24329793 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 279

description:
liver biopsy
sample name:
203293440179_R06C01

tag: tissue

value: Liver


title: IP T HI 1

description: HI 1

tag: strain

value: postnatal day 4 - 6h after HI


title: genomic DNA from liver 278

description:
liver biopsy
sample name:
203293440179_R05C01

value: No


title: genomic DNA from liver 276

description:
liver biopsy
sample name:
203293440179_R03C01

value: Female

value: Yes


title: genomic DNA from liver 277

description:
liver biopsy
sample name:
203293440179_R04C01


title: SAM24329829 CD8 aE+ CD8 AphaE_positive


title: IP T HI 2

description: HI 2


title: SAM24329763 CD4 aE- CD4 AphaE_negative


title: genomic DNA from liver 273

description:
liver biopsy
sample name:
203293440177_R08C01


title: genomic DNA from liver 274

description:
liver biopsy
sample name:
203293440179_R01C01


title: SAM24329631 CD8 aE- CD8 AphaE_negative


title: IP B HI 1

description: HI 1


title: SAM24329577 CD4 aE- CD4 AphaE_negative


title: genomic DNA from liver 271

description:
liver biopsy
sample name:
203293440177_R06C01


title: genomic DNA from liver 272

description:
liver biopsy
sample name:
203293440177_R07C01


title: genomic DNA from liver 270

description:
liver biopsy
sample name:
203293440177_R05C01


title: genomic DNA from liver 269

description:
liver biopsy
sample name:
203293440177_R04C01


title: SAM24329849 CD4 aE+ CD4 AphaE_positive


title: IP B Naïve 1

description: Naïve 1


title: Y79 rep5 RNA-seq

city: Wenzhou

first: dandan

last: Fan

address: 270 Xueyuan West Road

country: China

institute: Wenzhou Medical University

description: RNA sequencing

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome.
Reads count and Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated.
Genome_build: GRCh38
Supplementary_files_format_and_content: excel files include count and FPKM values for each Sample ...

source_name: human retinoblastoma cells

growth_protocol: Human retinal and Rb organoids differentiation were performed as previously described with minor modifications. On day 0, RB1Wt/Wt and RB1Mut/Mut hESCs maintained on Matrigel-coated plates were pretreated with 10 μM Y-27632 for 2h, and then carefully dissociated into single-cell suspensions using TrypLE Select (containing 0.05 mg/ml DNase I and 20 μM Y-27632), plated at a density of 12,000 live cells per well in 96-well low-attachment V-bottom plates in retinal differentiation medium I containing 44% Iscove’s modified Dulbecco’s medium, 44% Hams F12, 10% KnockOut Serum Replacement, 1% GlutaMAX-I, 1% Penicillin-Streptomycin (10,000 U/ml), and 20 μM Y-27632. 1.5nM (55 ng/ml) recombinant human BMP4 was added to the culture on day 6, and its concentration was semi-reduced with half medium change every 3 days. Retinal differentiation media Ⅱ [DMEM/F12-Glutamax medium containing 10% Fetal Bovine Serum, 1% N2 supplement, 1% Penicillin-Streptomycin (10,000 U/ml), 0.5 μM retinoic acid and 0.1 mM taurine] was exchanged until day 18 when the aggregate bodies were transferred to 9 cm nonadherent dishes (30 bodies per dish) for further long-term culture in a 37℃, 5% CO2/40% O2 incubator, and half of the volume changed with fresh retinal differentiation media Ⅱ every 5 days. The state and morphology of organoids was monitored in real time using the inverted fluorescence microscope.

extract_protocol:
Total RNA for each sample was isolated with TRIzol reagent and purified using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions, RNA quality and quantity were assessed using NanoDrop 2000, Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano Kit.
RNA library construction and RNA sequencing were performed by the annoroad Gene Technology. Sequencing libraries were generated using NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) and library clustering was performed using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) following the manufacturer’s recommendations. After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated.

tag: organoids

value: human retinoblastoma cells

tag: developmental/tumor stage

tag: genotype


title: genomic DNA from liver 268

description:
liver biopsy
sample name:
203293440177_R03C01


title: IP T Naïve 1

description: Naïve 1


title: genomic DNA from liver 267

description:
liver biopsy
sample name:
203293440177_R02C01


title: genomic DNA from liver 265

description:
liver biopsy
sample name:
203293440154_R08C01


title: Y79 rep4 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 275

description:
liver biopsy
sample name:
203293440179_R02C01


title: IP B HI 2

description: HI 2


title: genomic DNA from liver 264

description:
liver biopsy
sample name:
203293440154_R07C01


title: genomic DNA from liver 266

description:
liver biopsy
sample name:
203293440177_R01C01


title: IP B Naïve 2

description: Naïve 2


title: Y79 rep3 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 263

description:
liver biopsy
sample name:
203293440154_R06C01


title: SAM24329837 CD8 aE+ CD8 AphaE_positive

value: CD8 aE+


title: Y79 rep2 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 262

description:
liver biopsy
sample name:
203293440154_R05C01


title: genomic DNA from liver 261

description:
liver biopsy
sample name:
203293440154_R04C01


title: genomic DNA from liver 260

description:
liver biopsy
sample name:
203293440154_R03C01


title: genomic DNA from liver 259

description:
liver biopsy
sample name:
203293440154_R02C01


title: Y79 rep1 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 258

description:
liver biopsy
sample name:
203293440154_R01C01


title: SAM24329775 CD4 aE+ CD4 AphaE_positive


title: SAM24329885 CD8 aE- CD8 AphaE_negative

value: CD8 aE-


title: SAM24329908 CD8 aE+ CD8 AphaE_positive


title: SAM24329880 CD8 aE- CD8 AphaE_negative


title: D120 RB1-KO hESC-hRBOs rep2 RNA-seq

description: RNA sequencing

source_name: human embryonic stem cells

value: human ES-derived retinoblastoma organoids

value: day 120

value: RB1 knockout hESCs


title: SAM24329730 CD8 aE+ CD8 AphaE_positive


title: genomic DNA from liver 257

description:
liver biopsy
sample name:
203293440137_R08C01


title: D120 RB1-KO hESC-hRBOs rep1 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 255

description:
liver biopsy
sample name:
203293440137_R06C01


title: SAM24329641 CD8 aE+ CD8 AphaE_positive


title: genomic DNA from liver 254

description:
liver biopsy
sample name:
203293440137_R05C01


title: SAM24329622 CD8 aE- CD8 AphaE_negative


title: D120 RB1-Mut hESC (C2)-hRBOs rep3 RNA-seq

description: RNA sequencing

value: RB1 mutation knock-in hESCs


title: genomic DNA from liver 252

description:
liver biopsy
sample name:
203293440137_R03C01


title: genomic DNA from liver 251

description:
liver biopsy
sample name:
203293440137_R02C01


title: D120 RB1-Mut hESC (C2)-hRBOs rep2 RNA-seq

description: RNA sequencing


title: SAM24329893 CD8 aE- CD8 AphaE_negative


title: D120 RB1-Mut hESC (C2)-hRBOs rep1 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 250

description:
liver biopsy
sample name:
203293440137_R01C01


title: genomic DNA from liver 249

description:
liver biopsy
sample name:
203293440135_R08C01

value: Male


title: genomic DNA from liver 253

description:
liver biopsy
sample name:
203293440137_R04C01


title: genomic DNA from liver 248

description:
liver biopsy
sample name:
203293440135_R07C01


title: SAM24329737 CD8 aE+ CD8 AphaE_positive


title: D120 WT hESC-hROs rep3 RNA-seq

description: RNA sequencing

value: human ES-derived retinal organoids

value: WT hESCs


title: genomic DNA from liver 246

description:
liver biopsy
sample name:
203293440135_R05C01


title: D120 WT hESC-hROs rep2 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 247

description:
liver biopsy
sample name:
203293440135_R06C01


title: SAM24329649 CD8 aE+ CD8 AphaE_positive


title: genomic DNA from liver 244

description:
liver biopsy
sample name:
203293440135_R03C01


title: genomic DNA from liver 245

description:
liver biopsy
sample name:
203293440135_R04C01


title: D105 RB1-KO hESC-hRBOs rep3 RNA-seq

description: RNA sequencing

value: day 105


title: D120 WT hESC-hROs rep1 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 242

description:
liver biopsy
sample name:
203293440135_R01C01


title: genomic DNA from liver 243

description:
liver biopsy
sample name:
203293440135_R02C01


title: genomic DNA from liver 256

description:
liver biopsy
sample name:
203293440137_R07C01


title: genomic DNA from liver 241

description:
liver biopsy
sample name:
203293440105_R08C01


title: genomic DNA from liver 240

description:
liver biopsy
sample name:
203293440105_R07C01


title: genomic DNA from liver 238

description:
liver biopsy
sample name:
203293440105_R05C01


title: genomic DNA from liver 239

description:
liver biopsy
sample name:
203293440105_R06C01


title: SAM24329602 CD4 aE+ CD4 AphaE_positive

value: CD4 aE+


title: SAM24329791 CD4 aE+ CD4 AphaE_positive


title: genomic DNA from liver 236

description:
liver biopsy
sample name:
203293440105_R03C01

value: Liver


title: SAM24329728 CD8 aE+ CD8 AphaE_positive


title: genomic DNA from liver 237

description:
liver biopsy
sample name:
203293440105_R04C01


title: genomic DNA from liver 235

description:
liver biopsy
sample name:
203293440105_R02C01


title: SAM24329916 CD8 aE+ CD8 AphaE_positive


title: genomic DNA from liver 234

description:
liver biopsy
sample name:
203293440105_R01C01


title: D105 RB1-KO hESC-hRBOs rep1 RNA-seq

description: RNA sequencing


title: SAM24329857 CD4 aE+ CD4 AphaE_positive


title: D105 RB1-Mut hESC (C3)-hRBOs rep2 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 233

description:
liver biopsy
sample name:
203293440096_R08C01


title: D105 RB1-Mut hESC (C3)-hRBOs rep1 RNA-seq

description: RNA sequencing


title: SAM24329872 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 232

description:
liver biopsy
sample name:
203293440096_R07C01


title: SAM24329852 CD4 aE+ CD4 AphaE_positive


title: genomic DNA from liver 231

description:
liver biopsy
sample name:
203293440096_R06C01


title: genomic DNA from liver 230

description:
liver biopsy
sample name:
203293440096_R05C01


title: D105 RB1-Mut hESC (C3)-hRBOs rep3 RNA-seq

description: RNA sequencing


title: D105 RB1-KO hESC-hRBOs rep2 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 228

description:
liver biopsy
sample name:
203293440096_R03C01


title: SAM24329796 CD8 aE- CD8 AphaE_negative


title: SAM24329605 CD4 aE+ CD4 AphaE_positive


title: D105 RB1-Mut hESC (C2)-hRBOs rep2 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 226

description:
liver biopsy
sample name:
203293440096_R01C01


title: genomic DNA from liver 225

description:
liver biopsy
sample name:
203293440038_R08C01


title: D105 RB1-Mut hESC (C2)-hRBOs rep1 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 223

description:
liver biopsy
sample name:
203293440038_R06C01


title: SAM24329776 CD4 aE+ CD4 AphaE_positive


title: SAM24329618 CD8 aE- CD8 AphaE_negative


title: D105 RB1-Mut hESC (C1)-hRBOs rep3 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 222

description:
liver biopsy
sample name:
203293440038_R05C01


title: genomic DNA from liver 224

description:
liver biopsy
sample name:
203293440038_R07C01


title: D105 RB1-Mut hESC (C1)-hRBOs rep2 RNA-seq

description: RNA sequencing


title: SAM24329825 CD8 aE+ CD8 AphaE_positive


title: D105 RB1-Mut hESC (C2)-hRBOs rep3 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 221

description:
liver biopsy
sample name:
203293440038_R04C01


title: genomic DNA from liver 229

description:
liver biopsy
sample name:
203293440096_R04C01


title: SAM24329754 CD4 aE- CD4 AphaE_negative

value: CD4 aE-


title: genomic DNA from liver 220

description:
liver biopsy
sample name:
203293440038_R03C01


title: genomic DNA from liver 219

description:
liver biopsy
sample name:
203293440038_R02C01


title: SAM24329633 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 217

description:
liver biopsy
sample name:
203293440021_R08C01


title: D105 RB1-Mut hESC (C1)-hRBOs rep1 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 218

description:
liver biopsy
sample name:
203293440038_R01C01


title: D105 WT hESC-hROs rep2 RNA-seq

description: RNA sequencing


title: SAM24329705 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 215

description:
liver biopsy
sample name:
203293440021_R06C01


title: D105 WT hESC-hROs rep1 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 227

description:
liver biopsy
sample name:
203293440096_R02C01


title: SAM24329673 CD4 aE- CD4 AphaE_negative


title: genomic DNA from liver 214

description:
liver biopsy
sample name:
203293440021_R05C01


title: D90 RB1-KO hESC-hRBOs rep2 RNA-seq

description: RNA sequencing

value: day 90


title: genomic DNA from liver 213

description:
liver biopsy
sample name:
203293440021_R04C01

value: Female

value: No


title: SAM24329714 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 211

description:
liver biopsy
sample name:
203293440021_R01C01


title: genomic DNA from liver 210

description:
liver biopsy
sample name:
203293440020_R08C01

value: Yes


title: SAM24329600 CD4 aE+ CD4 AphaE_positive


title: D90 RB1-Mut hESC (C3)-hRBOs rep3 RNA-seq

description: RNA sequencing


title: SAM24329879 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 209

description:
liver biopsy
sample name:
203293440020_R07C01


title: genomic DNA from liver 208

description:
liver biopsy
sample name:
203293440020_R06C01


title: genomic DNA from liver 206

description:
liver biopsy
sample name:
203293440020_R04C01


title: D90 RB1-Mut hESC (C3)-hRBOs rep2 RNA-seq

description: RNA sequencing


title: SAM24329843 CD4 aE- CD4 AphaE_negative


title: genomic DNA from liver 216

description:
liver biopsy
sample name:
203293440021_R07C01


title: genomic DNA from liver 205

description:
liver biopsy
sample name:
203293440020_R03C01


title: genomic DNA from liver 204

description:
liver biopsy
sample name:
203293440020_R02C01


title: genomic DNA from liver 207

description:
liver biopsy
sample name:
203293440020_R05C01


title: SAM24329900 CD8 aE+ CD8 AphaE_positive

value: CD8 aE+


title: D90 RB1-Mut hESC (C2)-hRBOs rep2 RNA-seq

description: RNA sequencing


title: D90 RB1-Mut hESC (C2)-hRBOs rep3 RNA-seq

description: RNA sequencing


title: SAM24329801 CD8 aE- CD8 AphaE_negative

value: CD8 aE-


title: genomic DNA from liver 202

description:
liver biopsy
sample name:
203287590141_R08C01


title: genomic DNA from liver 212

description:
liver biopsy
sample name:
203293440021_R03C01


title: D90 RB1-Mut hESC (C3)-hRBOs rep1 RNA-seq

description: RNA sequencing

value: human ES-derived retinoblastoma organoids


title: genomic DNA from liver 199

description:
liver biopsy
sample name:
203287590141_R05C01


title: genomic DNA from liver 200

description:
liver biopsy
sample name:
203287590141_R06C01


title: D90 RB1-Mut hESC (C2)-hRBOs rep1 RNA-seq

description: RNA sequencing


title: SAM24329834 CD8 aE+ CD8 AphaE_positive


title: D90 RB1-KO hESC-hRBOs rep1 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 198

description:
liver biopsy
sample name:
203287590141_R04C01


title: SAM24329696 CD4 aE+ CD4 AphaE_positive


title: SAM24329608 CD4 aE+ CD4 AphaE_positive


title: D90 RB1-Mut hESC (C1)-hRBOs rep3 RNA-seq

description: RNA sequencing


title: SAM24329901 CD8 aE+ CD8 AphaE_positive


title: D90 RB1-Mut hESC (C1)-hRBOs rep2 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 195

description:
liver biopsy
sample name:
203287590141_R01C01


title: genomic DNA from liver 194

description:
liver biopsy
sample name:
203282450029_R08C01


title: D90 RB1-Mut hESC (C1)-hRBOs rep1 RNA-seq

description: RNA sequencing


title: SAM24329773 CD4 aE+ CD4 AphaE_positive


title: genomic DNA from liver 203

description:
liver biopsy
sample name:
203293440020_R01C01


title: genomic DNA from liver 193

description:
liver biopsy
sample name:
203282450029_R07C01


title: genomic DNA from liver 192

description:
liver biopsy
sample name:
203282450029_R06C01


title: SAM24329864 CD4 aE+ CD4 AphaE_positive


title: genomic DNA from liver 190

description:
liver biopsy
sample name:
203282450029_R04C01


title: genomic DNA from liver 188

description:
liver biopsy
sample name:
203282450029_R01C01


title: D90 WT hESC-hROs rep2 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 187

description:
liver biopsy
sample name:
203271750151_R08C01


title: D90 WT hESC-hROs rep3 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 201

description:
liver biopsy
sample name:
203287590141_R07C01


title: genomic DNA from liver 197

description:
liver biopsy
sample name:
203287590141_R03C01


title: genomic DNA from liver 186

description:
liver biopsy
sample name:
203271750151_R07C01


title: SAM24329892 CD8 aE- CD8 AphaE_negative


title: D90 WT hESC-hROs rep1 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 185

description:
liver biopsy
sample name:
203271750151_R06C01


title: D75 RB1-Mut hESC (C3)-hRBOs rep2 RNA-seq

description: RNA sequencing

value: day 75


title: SAM24329740 CD8 aE+ CD8 AphaE_positive


title: D75 RB1-Mut hESC (C3)-hRBOs rep1 RNA-seq

description: RNA sequencing


title: SAM24329762 CD4 aE- CD4 AphaE_negative


title: genomic DNA from liver 196

description:
liver biopsy
sample name:
203287590141_R02C01


title: genomic DNA from liver 183

description:
liver biopsy
sample name:
203271750151_R04C01


title: SAM24329588 CD4 aE- CD4 AphaE_negative


title: SAM24329813 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 180

description:
liver biopsy
sample name:
203271750151_R01C01


title: genomic DNA from liver 191

description:
liver biopsy
sample name:
203282450029_R05C01


title: D75 RB1-Mut hESC (C2)-hRBOs rep2 RNA-seq

description: RNA sequencing


title: SAM24329739 CD8 aE+ CD8 AphaE_positive


title: genomic DNA from liver 189

description:
liver biopsy
sample name:
203282450029_R03C01


title: genomic DNA from liver 179

description:
liver biopsy
sample name:
203271750121_R08C01


title: genomic DNA from liver 178

description:
liver biopsy
sample name:
203271750121_R07C01


title: D75 RB1-Mut hESC (C2)-hRBOs rep1 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 177

description:
liver biopsy
sample name:
203271750121_R06C01


title: genomic DNA from liver 174

description:
liver biopsy
sample name:
203271750121_R03C01


title: genomic DNA from liver 184

description:
liver biopsy
sample name:
203271750151_R05C01


title: SAM24329767 CD4 aE- CD4 AphaE_negative


title: genomic DNA from liver 175

description:
liver biopsy
sample name:
203271750121_R04C01


title: SAM24329844 CD4 aE- CD4 AphaE_negative


title: D75 RB1-Mut hESC (C1)-hRBOs rep3 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 176

description:
liver biopsy
sample name:
203271750121_R05C01


title: D75 RB1-Mut hESC (C1)-hRBOs rep2 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 173

description:
liver biopsy
sample name:
203271750121_R02C01


title: D75 RB1-Mut hESC (C1)-hRBOs rep1 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 170

description:
liver biopsy
sample name:
203271750078_R06C01


title: genomic DNA from liver 171

description:
liver biopsy
sample name:
203271750078_R07C01


title: genomic DNA from liver 172

description:
liver biopsy
sample name:
203271750121_R01C01


title: D75 RB1-Mut hESC (C2)-hRBOs rep3 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 181

description:
liver biopsy
sample name:
203271750151_R02C01


title: SAM24329662 CD4 aE- CD4 AphaE_negative


title: D75 WT hESC-hROs rep3 RNA-seq

description: RNA sequencing


title: SAM24329717 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 169

description:
liver biopsy
sample name:
203271750078_R05C01


title: genomic DNA from liver 168

description:
liver biopsy
sample name:
203271750078_R04C01


title: genomic DNA from liver 166

description:
liver biopsy
sample name:
203271750078_R02C01


title: D75 WT hESC-hROs rep2 RNA-seq

description: RNA sequencing


title: D75 WT hESC-hROs rep1 RNA-seq

description: RNA sequencing


title: SAM24329726 CD8 aE+ CD8 AphaE_positive


title: genomic DNA from liver 165

description:
liver biopsy
sample name:
203271750078_R01C01


title: genomic DNA from liver 164

description:
liver biopsy
sample name:
203271750076_R07C01


title: D60 RB1-Mut hESC (C3)-hRBOs rep2 RNA-seq

description: RNA sequencing

value: day 60


title: genomic DNA from liver 162

description:
liver biopsy
sample name:
203271750076_R05C01


title: genomic DNA from liver 161

description:
liver biopsy
sample name:
203271750076_R04C01


title: SAM24329778 CD4 aE+ CD4 AphaE_positive


title: D60 RB1-Mut hESC (C3)-hRBOs rep1 RNA-seq

description: RNA sequencing

value: RB1 mutation knock-in hESCs


title: genomic DNA from liver 167

description:
liver biopsy
sample name:
203271750078_R03C01

value: Male


title: genomic DNA from liver 160

description:
liver biopsy
sample name:
203271750076_R03C01


title: SAM24329917 CD8 aE+ CD8 AphaE_positive


title: D60 RB1-Mut hESC (C2)-hRBOs rep3 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 158

description:
liver biopsy
sample name:
203271750076_R01C01


title: D60 RB1-Mut hESC (C2)-hRBOs rep2 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 157

description:
liver biopsy
sample name:
203271750063_R08C01


title: genomic DNA from liver 156

description:
liver biopsy
sample name:
203271750063_R07C01


title: SAM24329619 CD8 aE- CD8 AphaE_negative


title: SAM24329694 CD4 aE+ CD4 AphaE_positive


title: SAM24329799 CD8 aE- CD8 AphaE_negative


title: D60 RB1-Mut hESC (C2)-hRBOs rep1 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 163

description:
liver biopsy
sample name:
203271750076_R06C01


title: genomic DNA from liver 155

description:
liver biopsy
sample name:
203271750063_R06C01


title: genomic DNA from liver 154

description:
liver biopsy
sample name:
203271750063_R05C01


title: genomic DNA from liver 153

description:
liver biopsy
sample name:
203271750063_R04C01


title: SAM24329804 CD8 aE- CD8 AphaE_negative


title: SAM24329693 CD4 aE+ CD4 AphaE_positive


title: D60 RB1-Mut hESC (C1)-hRBOs rep3 RNA-seq

description: RNA sequencing


title: D60 RB1-Mut hESC (C1)-hRBOs rep2 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 152

description:
liver biopsy
sample name:
203271750063_R03C01


title: genomic DNA from liver 151

description:
liver biopsy
sample name:
203271750063_R02C01


title: SAM24329683 CD4 aE+ CD4 AphaE_positive


title: SAM24329807 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 148

description:
liver biopsy
sample name:
203271750061_R07C01


title: genomic DNA from liver 159

description:
liver biopsy
sample name:
203271750076_R02C01


title: genomic DNA from liver 149

description:
liver biopsy
sample name:
203271750061_R08C01


title: genomic DNA from liver 147

description:
liver biopsy
sample name:
203271750061_R06C01


title: D60 WT hESC-hROs rep3 RNA-seq

description: RNA sequencing

value: human ES-derived retinal organoids


title: D60 RB1-Mut hESC (C1)-hRBOs rep1 RNA-seq

description: RNA sequencing


title: SAM24329895 CD8 aE- CD8 AphaE_negative


title: SAM24329699 CD4 aE+ CD4 AphaE_positive


title: genomic DNA from liver 144

description:
liver biopsy
sample name:
203271750061_R03C01


title: D60 WT hESC-hROs rep2 RNA-seq

description: RNA sequencing

value: WT hESCs


title: genomic DNA from liver 145

description:
liver biopsy
sample name:
203271750061_R04C01


title: SAM24329595 CD4 aE+ CD4 AphaE_positive


title: genomic DNA from liver 142

description:
liver biopsy
sample name:
203271750061_R01C01


title: genomic DNA from liver 143

description:
liver biopsy
sample name:
203271750061_R02C01


title: D60 WT hESC-hROs rep1 RNA-seq

description: RNA sequencing


title: SAM24329677 CD4 aE- CD4 AphaE_negative


title: genomic DNA from liver 146

description:
liver biopsy
sample name:
203271750061_R05C01


title: D45 RB1-Mut hESC (C2)-hRBOs rep3 RNA-seq

description: RNA sequencing

value: day 45


title: SAM24329655 CD8 aE+ CD8 AphaE_positive


title: genomic DNA from liver 141

description:
liver biopsy
sample name:
203271750015_R08C01


title: genomic DNA from liver 140

description:
liver biopsy
sample name:
203271750015_R07C01


title: D45 RB1-Mut hESC (C2)-hRBOs rep2 RNA-seq

description: RNA sequencing


title: SAM24329777 CD4 aE+ CD4 AphaE_positive

value: CD4 aE+


title: genomic DNA from liver 150

description:
liver biopsy
sample name:
203271750063_R01C01

value: Liver


title: D45 RB1-Mut hESC (C2)-hRBOs rep1 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 139

description:
liver biopsy
sample name:
203271750015_R04C01


title: genomic DNA from liver 138

description:
liver biopsy
sample name:
203271750015_R03C01


title: genomic DNA from liver 137

description:
liver biopsy
sample name:
203271750015_R02C01


title: SAM24329712 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 136

description:
liver biopsy
sample name:
203271750015_R01C01


title: SAM24329627 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 135

description:
liver biopsy
sample name:
203271750013_R08C01


title: genomic DNA from liver 134

description:
liver biopsy
sample name:
203271750013_R07C01


title: D45 WT hESC-hROs rep2 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 133

description:
liver biopsy
sample name:
203271750013_R06C01


title: SAM24329751 CD4 aE- CD4 AphaE_negative

value: CD4 aE-


title: D45 WT hESC-hROs rep1 RNA-seq

description: RNA sequencing


title: D30 RB1-Mut hESC (C2)-hRBOs rep3 RNA-seq

description: RNA sequencing

value: day 30


title: genomic DNA from liver 132

description:
liver biopsy
sample name:
203271750013_R05C01

value: Female


title: genomic DNA from liver 128

description:
liver biopsy
sample name:
203271750013_R01C01


title: genomic DNA from liver 131

description:
liver biopsy
sample name:
203271750013_R04C01

value: No


title: D30 RB1-Mut hESC (C2)-hRBOs rep2 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 130

description:
liver biopsy
sample name:
203271750013_R03C01


title: genomic DNA from liver 129

description:
liver biopsy
sample name:
203271750013_R02C01


title: genomic DNA from liver 127

description:
liver biopsy
sample name:
203259190148_R08C01

value: Yes


title: genomic DNA from liver 126

description:
liver biopsy
sample name:
203259190148_R07C01


title: D30 RB1-Mut hESC (C2)-hRBOs rep1 RNA-seq

description: RNA sequencing


title: D45 WT hESC-hROs rep3 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 125

description:
liver biopsy
sample name:
203259190148_R06C01


title: SAM24329798 CD8 aE- CD8 AphaE_negative


title: D30 WT hESC-hROs rep3 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 124

description:
liver biopsy
sample name:
203259190148_R05C01


title: genomic DNA from liver 123

description:
liver biopsy
sample name:
203259190148_R04C01


title: SAM24329612 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 122

description:
liver biopsy
sample name:
203259190148_R03C01


title: SAM24329665 CD4 aE- CD4 AphaE_negative


title: genomic DNA from liver 121

description:
liver biopsy
sample name:
203259190148_R02C01


title: genomic DNA from liver 119

description:
liver biopsy
sample name:
203259190121_R08C01


title: SAM24329822 CD8 aE+ CD8 AphaE_positive

value: CD8 aE+


title: D30 WT hESC-hROs rep1 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 120

description:
liver biopsy
sample name:
203259190148_R01C01


title: SAM24329753 CD4 aE- CD4 AphaE_negative


title: SAM24329621 CD8 aE- CD8 AphaE_negative

value: CD8 aE-


title: SAM24329716 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 116

description:
liver biopsy
sample name:
203259190121_R05C01


title: SAM24329731 CD8 aE+ CD8 AphaE_positive


title: genomic DNA from liver 115

description:
liver biopsy
sample name:
203259190121_R04C01


title: D0 RB1-KO hESC rep1 RNA-seq

description: RNA sequencing

value: human ES-derived retinoblastoma organoids

value: day 0

value: RB1 knockout hESCs


title: D0 RB1-Mut hESC (C3) rep2 RNA-seq

description: RNA sequencing

value: RB1 mutation knock-in hESCs


title: genomic DNA from liver 114

description:
liver biopsy
sample name:
203259190121_R03C01


title: genomic DNA from liver 117

description:
liver biopsy
sample name:
203259190121_R06C01


title: genomic DNA from liver 113

description:
liver biopsy
sample name:
203259190121_R02C01


title: SAM24329657 CD4 aE- CD4 AphaE_negative


title: genomic DNA from liver 112

description:
liver biopsy
sample name:
203259190121_R01C01


title: SAM24329579 CD4 aE- CD4 AphaE_negative


title: genomic DNA from liver 111

description:
liver biopsy
sample name:
203259190033_R08C01


title: D30 WT hESC-hROs rep2 RNA-seq

description: RNA sequencing


title: D0 RB1-Mut hESC (C3) rep1 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 110

description:
liver biopsy
sample name:
203259190033_R07C01


title: D0 RB1-Mut hESC (C2) rep2 RNA-seq

description: RNA sequencing


title: SAM24329632 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 109

description:
liver biopsy
sample name:
203259190033_R06C01


title: genomic DNA from liver 108

description:
liver biopsy
sample name:
203259190033_R05C01


title: D0 RB1-KO hESC rep2 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 118

description:
liver biopsy
sample name:
203259190121_R07C01


title: SAM24329695 CD4 aE+ CD4 AphaE_positive


title: SAM24329785 CD4 aE+ CD4 AphaE_positive


title: genomic DNA from liver 106

description:
liver biopsy
sample name:
203259190033_R03C01


title: D0 RB1-Mut hESC (C1) rep2 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 107

description:
liver biopsy
sample name:
203259190033_R04C01


title: D0 RB1-Mut hESC (C2) rep1 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 105

description:
liver biopsy
sample name:
203259190033_R02C01


title: SAM24329831 CD8 aE+ CD8 AphaE_positive


title: D0 RB1-Mut hESC (C1) rep1 RNA-seq

description: RNA sequencing


title: genomic DNA from liver 103

description:
liver biopsy
sample name:
203259190032_R08C01


title: genomic DNA from liver 101

description:
liver biopsy
sample name:
203259190032_R06C01


title: genomic DNA from liver 102

description:
liver biopsy
sample name:
203259190032_R07C01


title: D0 WT hESC rep1 RNA-seq

description: RNA sequencing


title: D0 WT hESC rep2 RNA-seq

description: RNA sequencing


title: SAM24329811 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 100

description:
liver biopsy
sample name:
203259190032_R05C01


title: SAM24329710 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 98

description:
liver biopsy
sample name:
203259190032_R03C01


title: genomic DNA from liver 99

description:
liver biopsy
sample name:
203259190032_R04C01


title: genomic DNA from liver 97

description:
liver biopsy
sample name:
203259190032_R02C01


title: genomic DNA from liver 96

description:
liver biopsy
sample name:
203259190032_R01C01


title: SAM24329914 CD8 aE+ CD8 AphaE_positive


title: SAM24329684 CD4 aE+ CD4 AphaE_positive


title: genomic DNA from liver 94

description:
liver biopsy
sample name:
203257030076_R07C01


title: genomic DNA from liver 93

description:
liver biopsy
sample name:
203257030076_R06C01


title: genomic DNA from liver 104

description:
liver biopsy
sample name:
203259190033_R01C01


title: SAM24329614 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 92

description:
liver biopsy
sample name:
203257030076_R05C01


title: genomic DNA from liver 91

description:
liver biopsy
sample name:
203257030076_R04C01


title: SAM24329642 CD8 aE+ CD8 AphaE_positive


title: Post-YBLI Patient4 Rep2

city: Hyderabad

first: Divya Tej

last: Sowpati

state: Telangana

address: Habsiguda

country: India

institute: CSIR Centre for Cellular and Molecular biology

library_source: genomic

data_processing:
Base-calling was performed using bcl2fastq of Illumina
Quality control was performed on the FASTQ read files using FastQC v0.11.7.
The genome was first bisulfite converted using bismark_genome_preparation --bowtie2 Genome/hg38.fasta. The reads were in-silico converted and aligned to the reference genome using bismark --bowtie2 --parallel 1 -N 1 -L 20 --temp_dir temp Genome/ Pre_YBLI1_Rep1.fastq.gz
Generation of Percent methylation scores using MethylKit
Differential expression analysis using MethylKit
Genome_build: hg38
Supplementary_files_format_and_content: Processed methylation data

extract_protocol:
Semen samples were obtained from each of the participants after 4 days of abstinence at baseline and post-YBLI (0 and 21 days respectively) and analysed as per WHO 2010 guidelines
Libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: Post-YBLI

value: Sperm


title: Post-YBLI Patient5 Rep1


title: Post-YBLI Patient4 Rep1


title: genomic DNA from liver 90

description:
liver biopsy
sample name:
203257030076_R03C01

tag: disease state


title: SAM24329890 CD8 aE- CD8 AphaE_negative


title: Post-YBLI Patient5 Rep2


title: Post-YBLI Patient3 Rep1


title: genomic DNA from liver 182

description:
liver biopsy
sample name:
203271750151_R03C01

tag: age


title: genomic DNA from liver 87

description:
liver biopsy
sample name:
203257030066_R08C01

tag: bmi


title: genomic DNA from liver 88

description:
liver biopsy
sample name:
203257030076_R01C01

tag: t2d medication


title: SAM24329593 CD4 aE+ CD4 AphaE_positive


title: SAM24329675 CD4 aE- CD4 AphaE_negative


title: genomic DNA from liver 86

description:
liver biopsy
sample name:
203257030066_R07C01

tag: chip id


title: genomic DNA from liver 84

description:
liver biopsy
sample name:
203257030066_R05C01

tag: rnaseq-matched srr id


title: SAM24329738 CD8 aE+ CD8 AphaE_positive


title: Post-YBLI Patient2 Rep2


title: Post-YBLI Patient2 Rep1


title: genomic DNA from liver 95

description:
liver biopsy
sample name:
203257030076_R08C01

tag: individual id


title: genomic DNA from liver 85

description:
liver biopsy
sample name:
203257030066_R06C01

tag: Sex


title: genomic DNA from liver 81

description:
liver biopsy
sample name:
203257030066_R02C01


title: genomic DNA from liver 82

description:
liver biopsy
sample name:
203257030066_R03C01


title: SAM24329840 CD4 aE- CD4 AphaE_negative


title: Post-YBLI Patient1 Rep2


title: Post-YBLI Patient3 Rep2


title: genomic DNA from liver 79

description:
liver biopsy
sample name:
203257030044_R08C01


title: genomic DNA from liver 89

description:
liver biopsy
sample name:
203257030076_R02C01


title: Pre-YBLI Patient5 Rep2

value: Pre-YBLI


title: genomic DNA from liver 78

description:
liver biopsy
sample name:
203257030044_R07C01


title: Pre-YBLI Patient5 Rep1


title: genomic DNA from liver 83

description:
liver biopsy
sample name:
203257030066_R04C01


title: Pre-YBLI Patient4 Rep2


title: genomic DNA from liver 77

description:
liver biopsy
sample name:
203257030044_R06C01


title: SAM24329888 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 75

description:
liver biopsy
sample name:
203257030044_R04C01


title: SAM24329587 CD4 aE- CD4 AphaE_negative


title: genomic DNA from liver 76

description:
liver biopsy
sample name:
203257030044_R05C01


title: genomic DNA from liver 74

description:
liver biopsy
sample name:
203257030044_R03C01


title: Pre-YBLI Patient4 Rep1


title: SAM24329623 CD8 aE- CD8 AphaE_negative


title: Pre-YBLI Patient3 Rep2


title: SAM24329887 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 71

description:
liver biopsy
sample name:
203257030011_R08C01


title: Pre-YBLI Patient3 Rep1


title: genomic DNA from liver 80

description:
liver biopsy
sample name:
203257030066_R01C01


title: genomic DNA from liver 70

description:
liver biopsy
sample name:
203257030011_R07C01


title: SAM24329817 CD8 aE+ CD8 AphaE_positive


title: genomic DNA from liver 68

description:
liver biopsy
sample name:
203257030011_R05C01


title: genomic DNA from liver 69

description:
liver biopsy
sample name:
203257030011_R06C01


title: Pre-YBLI Patient2 Rep2


title: genomic DNA from liver 66

description:
liver biopsy
sample name:
203257030011_R03C01


title: SAM24329802 CD8 aE- CD8 AphaE_negative


title: SAM24329765 CD4 aE- CD4 AphaE_negative


title: Pre-YBLI Patient2 Rep1


title: SAM24329855 CD4 aE+ CD4 AphaE_positive


title: genomic DNA from liver 67

description:
liver biopsy
sample name:
203257030011_R04C01


title: genomic DNA from liver 64

description:
liver biopsy
sample name:
203257030011_R01C01


title: genomic DNA from liver 65

description:
liver biopsy
sample name:
203257030011_R02C01


title: SAM24329672 CD4 aE- CD4 AphaE_negative


title: genomic DNA from liver 62

description:
liver biopsy
sample name:
203257030009_R07C01


title: Pre-YBLI Patient1 Rep2


title: genomic DNA from liver 73

description:
liver biopsy
sample name:
203257030044_R02C01


title: genomic DNA from liver 63

description:
liver biopsy
sample name:
203257030009_R08C01


title: genomic DNA from liver 61

description:
liver biopsy
sample name:
203257030009_R06C01


title: SAM24329867 CD4 aE+ CD4 AphaE_positive


title: genomic DNA from liver 72

description:
liver biopsy
sample name:
203257030044_R01C01


title: genomic DNA from liver 60

description:
liver biopsy
sample name:
203257030009_R05C01


title: genomic DNA from liver 59

description:
liver biopsy
sample name:
203257030009_R04C01


title: genomic DNA from liver 58

description:
liver biopsy
sample name:
203257030009_R03C01


title: SAM24329766 CD4 aE- CD4 AphaE_negative


title: SAM24329744 CD8 aE+ CD8 AphaE_positive


title: genomic DNA from liver 57

description:
liver biopsy
sample name:
203257030009_R02C01


title: genomic DNA from liver 56

description:
liver biopsy
sample name:
203257030009_R01C01


title: genomic DNA from liver 55

description:
liver biopsy
sample name:
203257020249_R08C01


title: genomic DNA from liver 54

description:
liver biopsy
sample name:
203257020249_R07C01


title: SAM24329758 CD4 aE- CD4 AphaE_negative


title: genomic DNA from liver 52

description:
liver biopsy
sample name:
203257020249_R05C01


title: genomic DNA from liver 51

description:
liver biopsy
sample name:
203257020249_R04C01


title: SAM24329589 CD4 aE+ CD4 AphaE_positive


title: SAM24329706 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 53

description:
liver biopsy
sample name:
203257020249_R06C01


title: genomic DNA from liver 50

description:
liver biopsy
sample name:
203257020249_R03C01


title: SAM24329772 CD4 aE+ CD4 AphaE_positive


title: SAM24329809 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 48

description:
liver biopsy
sample name:
203257020249_R01C01


title: genomic DNA from liver 49

description:
liver biopsy
sample name:
203257020249_R02C01


title: genomic DNA from liver 46

description:
liver biopsy
sample name:
203257020247_R06C01


title: genomic DNA from liver 47

description:
liver biopsy
sample name:
203257020247_R07C01


title: HCT116p53-/- cells, 8h Isoginkgetin 2 (gene-level)

type: RNA

city: Ottawa

first: Bruce

last: McKay

state: Ontario

address: 1125 Colonel By Dr, Ottawa

department: Biology

country: Canada

institute: Carleton University

hyb_protocol: Samples were hybridized to Affymetrix Human Transcriptome 2.0 oligonucleotide microarrays and scanned at the Affymetrix Core Facility, Stemcore Laboratories, Ottawa Hospital Research Institute.

scan_protocol: Hybridized microarrays were scanned according to the manufacturer's instructions (Affymetrix)

data_processing: Data was analyzed using the Transcriptome Analysis Console (TAC) 4.0 software.

label: biotin

source_name: Cell culture

label_protocol: Single-stranded cDNA was generated with the WT cDNA Synthesis Kit (Affymetrix), fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix) at the Affymetrix Core Facility, Stemcore Labs, Ottawa Hospital Research Institute.

growth_protocol: HCT116 cells and the p53 null subline (provided by Dr. Bert Vogelstein: Science 282, 1497 – 1501) were grown in McCoys media (Hyclone, San Angelo) supplemented with a 12% mixture of Newborn to Fetal Calf Serum (3:1 ratio) (Gibco, ThermoFisher Scientific, Ottawa), and antibiotic (90 units/ml penicillin, 90 ug/ml streptomycin, Hyclone).

extract_protocol: Total RNA was collected using the QIAGEN RNeasy mini kit according to the manufacturers instractions.

treatment_protocol: Cells were seeded at 1.0 x 10^6 cells per 10 cm dish at least 24 hours before treatment. Cells were left untreated or they exposed to 30 µM IGG or an equivalent volume of DMSO in growth media for 8 hours.

tag: cell line

value: Isoginkgetin


title: SAM24329769 CD4 aE+ CD4 AphaE_positive

value: CD4 aE+


title: genomic DNA from liver 44

description:
liver biopsy
sample name:
203257020247_R04C01

value: Liver


title: genomic DNA from liver 43

description:
liver biopsy
sample name:
203257020247_R03C01


title: SAM24329856 CD4 aE+ CD4 AphaE_positive


title: HCT116p53-/- cells, 8h DMSO 2 (gene-level)

tag: treatment

value: DMSO


title: genomic DNA from liver 42

description:
liver biopsy
sample name:
203257020247_R02C01


title: genomic DNA from liver 41

description:
liver biopsy
sample name:
203257020247_R01C01


title: genomic DNA from liver 39

description:
liver biopsy
sample name:
203257020211_R07C01


title: SAM24329839 CD4 aE- CD4 AphaE_negative

value: CD4 aE-


title: SAM24329848 CD4 aE+ CD4 AphaE_positive


title: genomic DNA from liver 40

description:
liver biopsy
sample name:
203257020211_R08C01

value: Female


title: 503_sparsecont_3

city: Berlin

first: Anna-Marie

last: Finger

address: Virchowweg 6

country: Germany

institute: Charité Universitätsmedizin Berlin

data_processing:
Quality of raw reads was assessed with FastQC and sequence reads were mapped to the human genome index generated with STAR (GRC38.all.fa/GRCh38.93.gft, outFilterMultimap Nmax = 1, twopassMode = Basic).
Quality of aligned reads was assessed with MultiQC, RseQC, Anaconda3 (geneBody_coverage, read_distribution) and samtools.
Read quantification was performed with featureCounts and used to generate a DESeq data set (design = ~density + medium, remove rows with a mean read count ?10) for differential gene expression analysis with DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content:
Excel table with featureCounts results (read counts and alignment information) for every gene and sample
Excel table with DESeq data set (read counts) for every gene and sample
Excel table with DESeq2 DEG results for conditioned medium versus control medium

source_name: whole transcriptome (RNA-seq)

growth_protocol: U-2 OS cells were maintained in T-75 culture flasks in complete culture medium (DMEM supplemented with 10% FBS, 1% Pen/Strep, and 25mM HEPES buffer) and in standard tissue culture incubators (humidified, 5% CO2, 37°C). For the experiment U2OS cells were plated at high (3x10^5 cells) or low (0.3x10^5cells) density into standard tissue culture 6-well plates and incubated in complete culture medium and in standard tissue culture incubators overnight.

extract_protocol:
Total RNA was extracted using the Pure Link RNA Mini Kit (ThermoFisher) according to the manufacturer?s instructions with an additional on-column DNase I digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols. NEBNext Poly(A) mRNA Magnetic Isolation Modules (NEB) were used to enrich poly(A)+ mRNA, which was fragmented. NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) was used for cDNA synthesis and sequencing library preparation. Single read RNAseq was performed using the NextSeq 500/550 High Output Kit v2 (Illumnia; 75 cycles).

treatment_protocol: U-2 OS cells were synchronized with 1µM dexamethasone. Cells were washed twice with 1X PBS and once with serum-free, phenolred-free DMEM supplemented with 1% Pen/Strep. Cells were supplemented with 2mL/well serum-free, phenolred-free DMEM with 1% Pen/Strep and inbcubated for 16-18 hs in a standard tissue culture incubator. Medium was aspirated, cells were stimulated with 300µM conditioned medium or control medium, and incubated for 2 hs in a standard tissue culture incubator prior to RNA isolation.

value: U-2 OS

tag: tissue of origin

value: bone osteosarcoma

value: wild type

value: control medium

tag: cell density

value: sparse

tag: treatment time

value: 16-18 hs post-sync


title: genomic DNA from liver 38

description:
liver biopsy
sample name:
203257020211_R06C01

tag: tissue

value: Yes


title: SAM24329725 CD8 aE- CD8 AphaE_negative

value: CD8 aE-


title: genomic DNA from liver 37

description:
liver biopsy
sample name:
203257020211_R05C01

value: No


title: HCT116p53-/- cells, 8h untreated 2 (gene-level)

value: untreated


title: genomic DNA from liver 45

description:
liver biopsy
sample name:
203257020247_R05C01


title: genomic DNA from liver 36

description:
liver biopsy
sample name:
203257020211_R04C01


title: genomic DNA from liver 35

description:
liver biopsy
sample name:
203257020211_R03C01


title: HCT116p53-/- cells, 8h Isoginkgetin 1 (gene-level)


title: genomic DNA from liver 34

description:
liver biopsy
sample name:
203257020211_R02C01


title: genomic DNA from liver 33

description:
liver biopsy
sample name:
203257020211_R01C01


title: SAM24329666 CD4 aE- CD4 AphaE_negative


title: genomic DNA from liver 32

description:
liver biopsy
sample name:
203239810148_R08C01

value: Male


title: HCT116 cells, 8h Isoginkgetin 2 (gene-level)

value: Isoginkgetin


title: HCT116 cells, 8h untreated 2 (gene-level)


title: genomic DNA from liver 31

description:
liver biopsy
sample name:
203239810148_R07C01


title: SAM24329771 CD4 aE+ CD4 AphaE_positive

value: CD4 aE+


title: 499_sparsecond_3

value: U-2 OS conditioned medium


title: 498_densecond_3

value: dense


title: 496_densecont_2


title: SAM24329902 CD8 aE+ CD8 AphaE_positive

value: CD8 aE+


title: HCT116p53-/- cells, 8h untreated 1 (gene-level)


title: genomic DNA from liver 30

description:
liver biopsy
sample name:
203239810148_R06C01

value: Liver


title: 502_densecont_3

value: U-2 OS


title: genomic DNA from liver 29

description:
liver biopsy
sample name:
203239810148_R05C01


title: SAM24329637 CD8 aE+ CD8 AphaE_positive


title: genomic DNA from liver 28

description:
liver biopsy
sample name:
203239810148_R04C01


title: SAM24329703 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 27

description:
liver biopsy
sample name:
203239810148_R03C01


title: SAM24329898 CD8 aE+ CD8 AphaE_positive


title: genomic DNA from liver 26

description:
liver biopsy
sample name:
203239810148_R02C01


title: SAM24329750 CD4 aE- CD4 AphaE_negative

value: CD4 aE-


title: HCT116p53-/- cells, 8h DMSO 1 (gene-level)

value: DMSO


title: genomic DNA from liver 25

description:
liver biopsy
sample name:
203239810148_R01C01


title: genomic DNA from liver 24

description:
liver biopsy
sample name:
203239810138_R08C01


title: 490_densecont_1

value: bone osteosarcoma

value: wild type

value: control medium


title: 492_densecond_2

value: 16-18 hs post-sync


title: 491_sparsecont_1

value: sparse


title: SAM24329821 CD8 aE+ CD8 AphaE_positive


title: genomic DNA from liver 23

description:
liver biopsy
sample name:
203239810138_R07C01

value: Yes


title: HCT116 cells, 8h DMSO 1 (gene-level)


title: genomic DNA from liver 22

description:
liver biopsy
sample name:
203239810138_R06C01


title: HCT116 cells, 8h Isoginkgetin 1 (gene-level)


title: 487_sparsecond_1


title: HCT116 cells, 8h DMSO 2 (gene-level)


title: SAM24329715 CD8 aE- CD8 AphaE_negative

value: CD8 aE-


title: genomic DNA from liver 18

description:
liver biopsy
sample name:
203239810138_R02C01

value: Female

value: No


title: genomic DNA from liver 19

description:
liver biopsy
sample name:
203239810138_R03C01

value: Male


title: SAM24329653 CD8 aE+ CD8 AphaE_positive


title: SAM24329659 CD4 aE- CD4 AphaE_negative


title: genomic DNA from liver 17

description:
liver biopsy
sample name:
203239810138_R01C01


title: genomic DNA from liver 20

description:
liver biopsy
sample name:
203239810138_R04C01


title: genomic DNA from liver 16

description:
liver biopsy
sample name:
203239810116_R08C01


title: 486_densecond_1

value: U-2 OS conditioned medium


title: MEL_4day_rep1

city: Philadelphia

first: Mengge

last: Shan

state: PA

address: 433 South University Avenue

institute: University of Pennylsvania

data_processing:
Adapters were trimmed with cutadapt -f fastq -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACnnnnnnATCTCGTATGCCGTCTTCTGCTTG -e 0.06 -O 6 -m 14 -
Reads were mapped with tophat --library-type fr-secondstrand --read-mismatches 2 --read-edit-dist 2 --max-multihits 10 --b2-very-sensitive  --no-coverage-search  -p 4 -o
HTSeq was used to create read counts from the aligned BAM files
Genome_build: mm10
Supplementary_files_format_and_content: Read counts are presented in tab-delimited format (*mRNA_read_counts.txt) with transcript ID in the first column and the number of reads in the second column; variance stabilize transformed values are calculated by DESeq2 and found in allDays_VSTvalues.txt

source_name: MEL cells

growth_protocol: MEL cells were grown under standard conditions in minimal essential medium (MEM) and supplemented with 10% (vol/vol) fetal bovine serum (FBS) and 1x antibiotic antimycotic (Invitrogen). MEL cells in suspension culture at the log phase of growth at a density of 2 x 105/ml were supplemented with 2% DMSO (Sigma) to induce differentiation, and cells were collected at various time points for further analysis.

extract_protocol:
Total RNA extracted using¬†Trizol¬†Reagent per the manufacturer's protocol
TruSeq Stranded mRNA-seq

tag: time

value: 4 days


title: SAM24329904 CD8 aE+ CD8 AphaE_positive

value: CD8 aE+


title: MEL_4day_rep2


title: SAM24329629 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 13

description:
liver biopsy
sample name:
203239810116_R05C01

value: Liver


title: genomic DNA from liver 12

description:
liver biopsy
sample name:
203239810116_R04C01


title: genomic DNA from liver 11

description:
liver biopsy
sample name:
203239810116_R03C01


title: MEL_2day_rep2

value: 2 days


title: SAM24329701 CD4 aE+ CD4 AphaE_positive

value: CD4 aE+


title: MEL_2day_rep1


title: HCT116 cells, 8h untreated 1 (gene-level)

value: untreated


title: genomic DNA from liver 10

description:
liver biopsy
sample name:
203239810116_R02C01


title: genomic DNA from liver 21

description:
liver biopsy
sample name:
203239810138_R05C01


title: SAM24329786 CD4 aE+ CD4 AphaE_positive


title: genomic DNA from liver 9

description:
liver biopsy
sample name:
203239810116_R01C01


title: genomic DNA from liver 8

description:
liver biopsy
sample name:
203239810042_R08C01


title: MEL_0day_rep1

value: 0 days


title: genomic DNA from liver 15

description:
liver biopsy
sample name:
203239810116_R07C01


title: genomic DNA from liver 14

description:
liver biopsy
sample name:
203239810116_R06C01


title: genomic DNA from liver 7

description:
liver biopsy
sample name:
203239810042_R07C01


title: SAM24329594 CD4 aE+ CD4 AphaE_positive


title: genomic DNA from liver 6

description:
liver biopsy
sample name:
203239810042_R06C01


title: SAM24329586 CD4 aE- CD4 AphaE_negative

value: CD4 aE-


title: 4days_rep2_dsRNase_noprotein

data_processing:
Library strategy: PIP-seq
PIP-seq reads were trimmed using cutadapt to remove 3’ sequencing adapters (cutadapt version 1.2.1 with parameters –e 0.006 –O 6 –m 14). Resulting trimmed reads were then collapsed into unique reads and aligned to the mm10 mouse genome sequence using TopHat (version 2.0.10 with parameters – library-type fr-secondstrand –read-mismatches 2 –read-edit-dist 2 –max-multihits 10 –b2-very-sensitive –transcriptome-max-hits 10 –no-coverage-search –no-novel juncs). Any PCR duplicates were collapsed to single reads for all downstream analysis.
PPSs were identified using a modified version of the R package CSAR (Muino et al., 2011). Read coverage values were calculated for each base in the genome and a Poisson test was used to determine an enrichment score for footprint as compared to structure only libraries. PPSs were then called with a false discovery rate of 5% as previously described (Silverman et al., 2014).
Structure scores for each transcript are based on the coverage for dsRNA-seq and ssRNA-seq coverages for each base in detectable transcripts from structure-only samples in each replicate. The structure score for each base was calculated as previously described (Gosai et al., 2015; Silverman et al., 2014).
Genome_build: mm10

source_name: MEL cells 4 days post differentiation, dsRNase treated, without proteinase K

extract_protocol:
Homogenized samples were divided into 2 subsamples one for interrogation of protein binding, the other for interrogation of secondary structure. For protein binding samples, each subsample were then was further divided and half was incubated in either 100 U/ml of a single-stranded RNase (ssRNase) (RNaseONE (Promega; Madison, WI, USA)) with 200 μg/ml BSA in 1X RNaseONE buffer for 1 hour at room temperature (RT), or 2.5 U/ml of a double-stranded RNase (dsRNase) (RNaseV1 (Ambion; Austin, TX, USA)) 1X RNA structure buffer for 1 hour at 37°C as previously described (Anderson et al., 2016). Following RNAse treatment, proteins were denatured and digested by treatment with 1% SDS and 0.1 mg/ml Proteinase K (Roche; Basel, Switzerland) for 15 minutes at RT. Finally, RNAse crosslinks were reversed by incubation at 65°C for 2 hours. For structure only samples, we performed the identical treat-ments as described for protein bound samples, except that the cross-linked homogenate was treated with 1% SDS and 0.1 mg/ml Proteinase K (Roche;Basel,Switzerland)and ethanol precipitated before treatment with the structure specific RNAses. Post digestion, RNA was then isolated using Qiagen miRNeasy RNA isolation kit as described in the manual.
Strand specific libraries were constructed as previously described (Silverman et al, 2014).

treatment_protocol: Undifferentiated and differentiated samples were treated with formaldehyde to induce crosslinking of RNA binding proteins to RNA molecules.

value: MEL cells

tag: differentiation stage


title: genomic DNA from liver 4

description:
liver biopsy
sample name:
203239810042_R04C01


title: 4days_rep1_dsRNase_noprotein


title: SAM24329620 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 3

description:
liver biopsy
sample name:
203239810042_R03C01


title: genomic DNA from liver 1

description:
liver biopsy
sample name:
203239810042_R01C01


title: SAM24329720 CD8 aE- CD8 AphaE_negative


title: genomic DNA from liver 2

description:
liver biopsy
sample name:
203239810042_R02C01


title: SAM24329647 CD8 aE+ CD8 AphaE_positive


title: 4days_rep2_ssRNase_noprotein

source_name: MEL cells 4 days post differentiation, ssRNase treated, without proteinase K


title: 4days_rep1_ssRNase_noprotein


title: MEL_0day_rep2


title: 4days_rep2_dsRNase_protein

source_name: MEL cells 4 days post differentiation, dsRNAse treated, proteinase K treated


title: SAM24329638 CD8 aE+ CD8 AphaE_positive


title: SAM24329883 CD8 aE- CD8 AphaE_negative


title: 4days_rep1_dsRNase_protein


title: 4days_rep2_ssRNase_protein

source_name: MEL cells 4 days post differentiation, ssRNase treated, protein kinase treated


title: genomic DNA from liver 5

description:
liver biopsy
sample name:
203239810042_R05C01


title: SAM24329607 CD4 aE+ CD4 AphaE_positive


title: 4days_rep1_ssRNase_protein


title: 2days_rep2_dsRNase_noprotein

source_name: MEL cells 2 days post differentiation, dsRNase treated, without proteinase K


title: xpf-6

city: PITTSBURGH

first: Aditi

last: Gurkar

address: 100 Technology Drive, Room # 414, Bridge side point

department: Department of Medicine

institute: UNIVERSITY OF PITTSBURGH

data_processing:
Original image data file from high-throughput sequencing (like Illumina) is transformed into sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Index of the reference genome was built using hisat2 2.1.0 and paired-end clean reads were aligned to the reference genome using HISAT2
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Genome_build: reference genome: WBcel235
genome-date 2012-12
genome-build-accession NCBI:GCA_000002985.3
genebuild-last-updated 2014-02
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM  for every gene and every sample

organism: Caenorhabditis elegans

source_name: Whole body

growth_protocol: At least 500 age-synchronized worms in biological triplicate for each condition were grown on NGM plates seeded with E.coli OP50. Whole worms were harvested, washed three times with M9 and resuspended in 500 μl Trizol.

extract_protocol:
To extract total RNA, worm or tissue pellets in Trizol underwent six freeze-thaw cycles in a dry ice-ethanol bath. RNA was extracted according to the Trizol procedure, and resuspended in RNase- and DNase-free water. RNA from whole worms was quantified using the Qubit 2.0 fluorometer (Invitrogen)
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

tag: strain

tag: genotype

value: DNA-repair mutant TG1660 (xpf-1(tm2842))

value: whole body


title: xpf-5

tag: age


title: xpf-4


title: SAM24329851 CD4 aE+ CD4 AphaE_positive

source_name: RNA from human intestinal biopsy


title: SAM24329842 CD4 aE- CD4 AphaE_negative


title: 2days_rep1_dsRNase_noprotein


title: SAM24329853 CD4 aE+ CD4 AphaE_positive


title: xpf-3


title: 2days_rep2_ssRNase_noprotein

source_name: MEL cells 2 days post differentiation, ssRNase treated, without proteinase K


title: 2days_rep1_ssRNase_noprotein


title: 2days_rep2_dsRNase_protein

source_name: MEL cells 2 days post differentiation, dsRNAse treated, proteinase K treated


title: SAM24329875 CD8 aE- CD8 AphaE_negative


title: N2-5

value: Wildtype


title: xpf-1


title: N2-4


title: N2-6


title: xpf-2


title: N2-3


title: SAM24329779 CD4 aE+ CD4 AphaE_positive


title: 2days_rep1_dsRNase_protein


title: NB-1 treated with combination

description: Gene expression in combination-treated cells

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1xAgilent fragmentation buffer and 2xAgilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2xAgilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: NB-1 cell line was maintained in McCoy's 5A medium with 10% FBS.

extract_protocol: Total RNA was extracted using the ReliaPrep™ RNA Cell Miniprep System (Promega, Madison, WI).

treatment_protocol: Cells were treated with 0.3 µM 5-aza-dC for three days, and then treated with 1 µM TBT for an additional four days.

value: combination


title: NB-1 treated with TBT

description: Gene expression in TBT-treated cells

value: TBT


title: SAM24329868 CD4 aE+ CD4 AphaE_positive


title: SAM24329603 CD4 aE+ CD4 AphaE_positive


title: N2-2


title: 2days_rep2_ssRNase_protein

source_name: MEL cells 2 days post differentiation, ssRNase treated, protein kinase treated


title: SAM24329707 CD8 aE- CD8 AphaE_negative

value: CD8 aE-


title: A31-HEART

city: Columbus

first: Michael

last: Tranter

state: OH

address: 2255 Kenny Road

department: Molecular Medicine and Therapeutics

institute: The Ohio State University

data_processing:
All read mapping and analysis was performed using the CLC Genomics Workbench v20.0.2 (CLC Bio-Qiagen).
Reads were mapped using the following parameters:  min. read length fraction = 0.8, min. read similarity fraction = 0.8. mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=10, Expression value= Total counts.
Supplementary_files_format_and_content: TPM

source_name: Heart - left ventricle

extract_protocol:
Tissues were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Heart - left ventricle

value: 28 weeks

value: Adipo-HuR KO


title: A30-HEART


title: 0days_rep2_dsRNase_noprotein

source_name: undifferentiated MEL cells,dsRNase treated, without proteinase K


title: RNA-seq_bisphenol A

city: Yokohama

first: Xian-Yang

last: Qin

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

institute: RIKEN Center for Integrative Medical Sciences

data_processing:
MiSeq Control Software was used for basecalling.
Sequenced reads were mapped to hg19.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: hg19
Supplementary_files_format_and_content: Text files include RPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: pluripotent stem cell

growth_protocol: The iPSCs were maintained under feeder-free condition using mTeSR1 (STEMCELL Technologies, Vancouver, Canada) in a dish coated with 0.5 μg/cm2 of Laminin511-E8 (iMatrix-511, Nippi, Tokyo, Japan).

extract_protocol:
Total RNA was isolated using RNeasy Micro Kit (QIAGEN) from human iPSCs treated with various chemical substances.
RNA libraries were prepared using TruSeq Targeted RNA Expression Kit (Stem Cell Panel, Illumina) for 100 stemness-related genes.

treatment_protocol: Human iPSCs were exposed to DMSO (control), 1 μM biotin, 1 nM etoposide, 1 μM propyl gallate, 1 μM theophylline, and 30 nM bisphenol A for 48 hours.

tag: cell type

value: pluripotent stem cell

value: HPS0063 (Riken BRC, 201B7)

value: bisphenol A


title: 2days_rep1_ssRNase_protein

value: 2 days


title: RNA-seq_theophylline

value: theophylline


title: SAM24329774 CD4 aE+ CD4 AphaE_positive

value: CD4 aE+


title: SAM24329748 CD8 aE+ CD8 AphaE_positive

value: CD8 aE+


title: 0days_rep1_dsRNase_noprotein

source_name: undifferentiated MEL cells, dsRNase treated, without proteinase K

value: MEL cells

value: 0 days


title: SAM24329609 CD4 aE+ CD4 AphaE_positive


title: N2-1

value: whole body


title: RNA-seq_propyl gallate

value: propyl gallate


title: 0days_rep2_ssRNase_noprotein

source_name: undifferentiated MEL cells, ssRNase treated, without proteinase K


title: NB-1 treated with 5-aza-dC

description: Gene expression in 5-aza-dC-treated cells


title: A29-HEART


title: SAM24329669 CD4 aE- CD4 AphaE_negative

value: CD4 aE-


title: A25-HEART


title: 0days_rep2_dsRNase_protein

source_name: undifferentiated MEL cells, dsRNAse treated, proteinase K treated


title: SAM24329708 CD8 aE- CD8 AphaE_negative


title: RNA-seq_control-1

value: control


title: RNA-seq_control-2


title: SAM24329780 CD4 aE+ CD4 AphaE_positive


title: RNA-seq_etoposide

value: etoposide


title: A14-HEART

value: Heart - left ventricle

value: wild-type


title: 0days_rep1_ssRNase_noprotein


title: A7-HEART

value: 28 weeks


title: SAM24329854 CD4 aE+ CD4 AphaE_positive


title: RNA-seq_biotin

value: pluripotent stem cell

value: biotin


title: A5-HEART


title: 0days_rep2_ssRNase_protein

source_name: undifferentiated MEL cells, ssRNase treated, protein kinase treated


title: 0days_rep1_dsRNase_protein


title: SAM24329682 CD4 aE+ CD4 AphaE_positive


title: 0days_rep1_ssRNase_protein


title: A8-HEART