title: Rectum_UC_Inflamed [I0286 RSDF00A CosMx1k]

description:
I0286RI0277R1119_exprMat_file.csv
I0286RI0277R1119_fov_positions_file.csv
I0286RI0277R1119_metadata_file.csv
I0286RI0277R1119_tx_file.csv
I0286RI0277R1119-polygons.csv
fov 29-51


title: Rectum_CD_Noninflamed [I0275 RSDF00A CosMx1k]

status: Public on Mar 13 2026

type: RNA

city: Chicago

first: Parambir

last: Dulai

state: IL

address: 259 E Erie St Ste 1600

country: USA

institute: Northwestern University

description:
I0262RI0275R4119_exprMat_file.csv
I0262RI0275R4119_fov_positions_file.csv
I0262RI0275R4119_metadata_file.csv
I0262RI0275R4119_tx_file.csv
I0262RI0275R4119-polygons.csv
fov 1-21

hyb_protocol: CosMx

scan_protocol: CosMx

data_processing: We performed cell quality control (QC) on CosMx multi-tissue, Xenium multi-tissue, Xenium colon-specific, CosMx 6K, and Xenium 5K data. For CosMx multi-tissue, we performed QC by removing the cells with fewer than 20 unique molecular identifiers (UMIs). For Xenium multi-tissue and Xenium colon-specific, we performed QC by removing the cells with fewer than 5 UMIs. For CosMx 6K and Xenium 5K data, we performed QC by excluding the cells with fewer than 50 UMIs. After QC, we normalized and transformed the raw datasets using log normalization (each cell’s gene counts are divided by its total counts, multiplied by 10,000, and log transformed). For CosMx 6K and Xenium 5K data, the top 3,000 highly variable genes were next identified. After further scaling the data, we performed principal component analysis on the normalized data and clustered the cells through a shared nearest neighbor approach.

label: CosMx

molecule: total RNA

organism: Homo sapiens

source_name: human rectum

label_protocol: CosMx

growth_protocol: Colonic biopsies were obtained with informed consent from healthy and IBD patients during routine screening. All procedures were approved by Northwestern University IRB committee (STU00214234) operating under the main biorepository IRB (STU00203172) at the Digestive Health Center. A standardized biopsy collection protocol was used, and biopsies were targeted for the most inflamed portion of each segment, and if no inflammation was present, they were taken from areas adjacent to where routine care biopsies were taken to most closely align with routine care histology assessments.

extract_protocol: Biopsies were immediately placed in formalin jars fixed and transferred to the Northwestern University Pathology Core for automated embedding, cataloging, and H&E imaging. Formalin-fixed, paraffin-embedded blocks were cut into sections on positively charged slides, and full block sections were used for all experiments.

tag: tissue

value: Rectum


title: hPA, gRNA-hit, INPUT, rep 3

type: SRA

city: Durham

first: Samuel

last: Reisman

state: NC

address: 1328 Campus Drive

institute: Duke University

description: Library name: hPA_gRNAhit_INPUT_rep3

library_source: genomic

data_processing:
Reads that aligned to the integrated lentiviral cargo were removed using Bowtie2. Remaining reads were then aligned to the hg38 reference genome, and PCR duplicates were removed using rmdup from SAMtools. Peaks were called in each replicate individually using MACS2. Peaks passing qval < .05 not in hg38 blacklist regions were then input to IDR analysis to identify high-confidence reproducible peaks across replicates. Peaks passing a stringent IDR threshold (IDR < 0.001) in all replicate comparisons within a condition were merged using BEDtools to generate per-gRNA peaksets, then a union peakset was generated by merging across gRNA conditions. BAM files were converted to normalized bigWig tracks using deepTools. For each sample, reads were extended to estimated fragment length and binned at 25 bp resolution. Genome coverage was computed with bamCoverage, applying read-per-genome-coverage (RPGC) normalization to an effective hg38 genome size of 2.91 Gb and masking ENCODE hg38 blacklist regions.
Assembly: hg38
Supplementary files format and content: .bed file of consensus IDR peaks, bigWigs

molecule: genomic DNA

source_name: astrocyte

growth_protocol: Primary human astrocytes derived from the fetal cerebral cortex were purchased (Sciencell 1800) and routine cell culture was performed following the supplier’s protocol. Upon thawing, cells were seeded on plates coated with poly-D-lysine (PDL), and grown in Astrocyte Medium (Sciencell 1801) supplemented to 10% fetal bovine serum (Gibco) to encourage proliferation. Culture medium was replaced every two days until cultures reached 70% confluence, and subsequently every three days until cultures reached 95% confluence. To passage, cells were rinsed with PBS and dissociated using 0.025% trypsin. To eliminate residual potential progenitor cells and non-proliferative neuronal cells, astrocytes expanded for two passages. All experiments were initiated upon replating after the second passage reached confluence. Astrocytes were subjected to freeze/thaw cycles.

extract_protocol:
Supernatant containing sheared chromatin was incubated at 65°C overnight to reverse DNA-protein crosslinks. ChIP DNA was purified with QIAquick PCR Purification kit (Qiagen).
ChIP-seq libraries were constructed with a KAPA HyperPrep kit (Roche). ChIP DNA was quantified and amplified with 7 PCR cycles after KAPA adapter ligation. Libraries were pooled and sequenced with 1% PhiX spike-in on an Illumina NextSeq with a P4 XLEAP-SBS reagent kit.

treatment_protocol: ChIP experiments were performed in triplicate and harvested 8 days after transduction. For each replicate, 2 x 107 astrocytes were resuspended in Astrocyte Medium with 1% formaldehyde (Pierce) and fixed for 10 minutes at room temperature with gentle rocking. Fixation was blocked with 0.125 M glycine for 5 minutes. Cells were then washed twice with ice-cold PBS and resuspended in cell lysis buffer (5 mM HEPES, 85mM KCl, 0.5% NP-40 pH 8.0) with protease inhibitor. To facilitate nuclei extraction, cells were passed 15 times through a Dounce homogenizer before incubation for 15 minutes at 4°C. Nuclei were then resuspended in nuclear lysis buffer (50 mM Tris HCl, 10 mM EDTA, 0.1% SDS pH 8.1) and sonicated to 200-700 bp fragments using a Diagenode Bioruptor Pico for 15 cycles of 30 seconds on and 30 seconds off. Before IP, a sample was collected for input control. For each replicate, we conjugated 5 µg monoclonal Anti-FLAG M2 (Sigma F1804) to 200 µl Dynabeads M-280 Sheep Anti-Mouse IgG (Invitrogen 11201D). Sheared chromatin was then incubated with antibody-conjugated beads on a rotator overnight at 4°C. Beads were washed five times with a LiCl wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate), and remaining ions were removed with a TE wash (10 mM Tris-HCl, pH 7.5, 0.1 mM EDTA). Chromatin fragments were eluted in an IP elution buffer (PBS, 1% SDS, 0.1M NaHCO3) at 65°C for 1 hour.

tag: cell type

value: astrocyte

tag: genotype

value: gRNA-hit

tag: treatment

value: neuronal reprogramming


title: Rectum_UC_Inflamed [I0380 RSDF00A CosMx6k]

description:
Cos1380R387RRNA6K4u2716_exprMat_file.csv
Cos1380R387RRNA6K4u2716_fov_positions_file.csv
Cos1380R387RRNA6K4u2716_metadata_file.csv
Cos1380R387RRNA6K4u2716_tx_file.csv
Cos1380R387RRNA6K4u2716-polygons.csv
fov 18-45


title: hPA, gRNA-hit, INPUT, rep 2

description: Library name: hPA_gRNAhit_INPUT_rep2


title: Rectum_CD_Inflamed [I0262 RSDF00A CosMx1k]

description:
I0262RI0275R4119_exprMat_file.csv
I0262RI0275R4119_fov_positions_file.csv
I0262RI0275R4119_metadata_file.csv
I0262RI0275R4119_tx_file.csv
I0262RI0275R4119-polygons.csv
fov 22-35


title: dHepaRG cells, HDV, rep2

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

country: France

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

description: Library name: HDV_2

library_source: transcriptomic

data_processing:
Paired-end clean reads were aligned to the human reference genome (version hg38) using HISAT2 v2.0.5 (Mortazavi et al., 2008).
The mapped reads for each sample were assembled with StringTie v1.3.3b in a reference-guided approach (Pertea et al., 2015).
FeatureCounts v1.5.0-p3 (Liao et al., 2014) was used to count the number of reads mapped to each gene, and FPKM values were calculated
For samples with biological replicates, differential expression analysis was performed using the DESeq2 R package (v1.20.0) (Love et al., 2014).
The resulting p-values were adjusted using the Benjamini-Hochberg method to control the false discovery rate.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each sample, and differential expression results

molecule: polyA RNA

source_name: dHepaRG cells

extract_protocol:
Total intracellular RNA was purified using the Monarch Nucleic Acid Purification Kit (New England Biolabs)
RNA-seq libraries were prepared with the NEB-Next® Ultra™ II Directional RNA sample preparation kit (New England Biolabs, Inc., Ipswich, MA, USA).Messenger RNA was isolated from total RNA using poly-T oligo-attached magnetic beads. cDNA was synthesized, and libraries were prepared as previously described (Parkhomchuk et al., 2009).

tag: cell line

value: dHepaRG cells

tag: time

value: day 6

value: HDV


title: Ileum_CD_Noninflamed [I0262 ITDF00A CosMx1k]

description:
262I275I3119_exprMat_file.csv
262I275I3119_fov_positions_file.csv
262I275I3119_metadata_file.csv
262I275I3119_tx_file.csv
262I275I3119-polygons.csv
fov 23-31

source_name: human Ileum

value: Ileum


title: Rectum_UC_Inflamed [I0277 RSDF00A CosMx1k]

description:
I0286RI0277R1119_exprMat_file.csv
I0286RI0277R1119_fov_positions_file.csv
I0286RI0277R1119_metadata_file.csv
I0286RI0277R1119_tx_file.csv
I0286RI0277R1119-polygons.csv
fov 1-28


title: dHepaRG cells, SeV, rep2

description: Library name: SeV_2

value: SeV


title: dHepaRG cells, ECMV, rep2

description: Library name: ECMV_2

value: ECMV


title: Rectum_UC_Inflamed [I0284 RSDF00A CosMx1k]

description:
I0284RI0276R2119_exprMat_file.csv
I0284RI0276R2119_fov_positions_file.csv
I0284RI0276R2119_metadata_file.csv
I0284RI0276R2119_tx_file.csv
I0284RI0276R2119-polygons.csv
fov 14-19


title: Ileum_CD_Inflamed [I0294 ITDF00A CosMx1k ]

description:
278I294I2124_exprMat_file.csv
278I294I2124_fov_positions_file.csv
278I294I2124_metadata_file.csv
278I294I2124_tx_file.csv
278I294I2124-polygons.csv
fov 1-14


title: dHepaRG cells, HDV, rep3

description: Library name: HDV_3


title: hPA, non-targeting, ChIP, rep 1

description: Library name: hPA_NT_ChIP_rep1

value: non-targeting


title: Trp53-/-; sgPten; sgArid1a gastric organoid, clone 1

city: Chengdu, China

first: Ailing

last: Zhong

state: Sichuan

address: No.17 Renmin road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sichuan University.

country: China

institute: Sichuan University

description: Library name: monoclonal_TPA_1

data_processing:
Monoclonal mouse organoids were processed for RNA-seq following the standard Illumina RNA library preparation protocol. Libraries were sequenced on an Illumina NovaSeq X Plus platform. Sequencing reads were aligned to the mouse reference genome (mm10) using STAR (v2.6.0, RRID:SCR_004463). Gene-level count matrices were generated from aligned reads and used for downstream normalization and differential expression analysis with DESeq2 (RRID:SCR_015687), yielding log2 fold-change values and adjusted P values.
Assembly: mm10
Supplementary files format and content: csv files include counts and DESeq2 normalized data

organism: Mus musculus

source_name: gastric organoid

extract_protocol:
Total RNA was extracted using TRIzol reagent (Applied Biosystems, Cat# 15596026) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared following manufacturer's protocols.

value: gastric organoid

value: Trp53-/-; sgPten; sgArid1a


title: Cardiomyocytes RRAGD WT Diff 2

city: Nijmegen

first: Sara

last: van Katwijk

address: Geert Grooteplein Zuid 28

department: Medical BioSciences

country: Netherlands

institute: Radboudumc

description:
Library name: CMs-RRAGD-WT-2
Column name in GRCh38.p13-counts.tsv WT_diff_2

data_processing:
seq2science pipeline (https://vanheeringen-lab.github.io/seq2science/content/workflows/rna_seq.html)
Assembly: GRCh38.p14
Supplementary files format and content: tsv file of raw counts

source_name: hiPSC-CMs

growth_protocol: hiPSC-derived cardiomyocytes (hiPSC-CMs) were cultured in cardio culture medium (RPMI-1640 Medium with GlutaMAXTM Supplement with HEPES supplemented with B-27 Supplement 50x-serum free (#17504001, Thermo Fisher Scientific, California, USA) in humidified incubator at 37°C and 5% (v/v) CO2

extract_protocol:
Total RNA was extracted from 80-day old hiPSC-CMs using the Trizol Reagent (Invitrogen, Bleiswijk, The Netherlands) according to the manufacturer’s protocol.
RNA-Seq libraries were prepared from total RNA using the KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems, Massachusetts, USA). Oligo hybridization, rRNA depletion, rRNA depletion cleanup, DNase digestion, DNase digestion cleanup, and RNA elution were performed according to the manufacturer’s protocol.

value: hiPSC-CMs

value: Human induced pluripotent stem cell-derived cardiomyocytes

value: RRAGD WT/WT

value: Cardiomyogenic differentiation

tag: batch


title: dHepaRG cells, mock, rep2

description: Library name: mock_2

value: Mock


title: Colon_HC [302c4]

description:
5um302428_exprMat_file.csv
5um302428_fov_positions_file.csv
5um302428_metadata_file.csv
5um302428_tx_file.csv
5um302428-polygons.csv
fov 1-13

source_name: human colon

value: Colon


title: hPA, gRNA-hit, ChIP, rep 1

description: Library name: hPA_gRNAhit_ChIP_rep1

value: astrocyte

value: gRNA-hit


title: dHepaRG cells, mockPEG, rep3

description: Library name: mockPEG_3

value: dHepaRG cells

value: PEG


title: dHepaRG cells, SeV, rep3

description: Library name: SeV_3


title: hPA, gRNA-hit, INPUT, rep 1

description: Library name: hPA_gRNAhit_INPUT_rep1

value: neuronal reprogramming


title: Trp53-/-; sgPten gastric organoid, clone 2

description: Library name: monoclonal_TP_2

value: Trp53-/-; sgPten


title: Trp53-/-; sgPten gastric organoid, clone 1

description: Library name: monoclonal_TP_1


title: Rectum_UC_Inflamed [I0321 RSDF00A CosMx1k]

description:
310R321R228_exprMat_file.csv
310R321R228_fov_positions_file.csv
310R321R228_metadata_file.csv
310R321R228_tx_file.csv
310R321R228-polygons.csv
fov 1-31

value: Rectum


title: dHepaRG cells, ECMV, rep1

description: Library name: ECMV_1

value: ECMV


title: TM4_miRNA

city: Zhengzhou

first: wanyi

last: zhu

state: Henan

address: No.19,Renmin Road,Jinshui Districtt

institute: The First Affiliated Hospital of Henan University of Chinese Medicine

description:
Library name: sample24
Column name in miRNA_count.txt: TM4

data_processing:
Raw sequencing reads were filtered using Fastp to remove adapter sequences, low-quality bases (Q < 20), reads with >10% N content, and sequences shorter than 20 bp.
Clean reads were aligned to the mouse reference genome using HiSat2.
Gene expression levels (Read counts and FPKM) were quantified using RSEM.
Assembly: Mouse reads were aligned to the Mus musculus reference genome assembly GRCm39 as provided by the sequencing report (section “reference genome information”).
Supplementary files format and content: tab-delimited text file includes raw gene counts for long RNA-seq samples.
Supplementary files format and content: tab-delimited text file includes raw miRNA counts for small RNA-seq samples.

source_name: liver

extract_protocol:
Total RNA was extracted from mouse liver tissue using TRIzol reagent and purified with an RNA purification kit.
For long RNA-seq: Libraries were prepared using Illumina Stranded Total RNA Prep and Ribo-Zero Plus kits. For small RNA-seq: Adapters were ligated to 3’ and 5’ ends, followed by reverse transcription and PCR enrichment.

value: liver

value: WT

value: High-fat diet + HQHF


title: dHepaRG cells, ECMV, rep3

description: Library name: ECMV_3


title: Lx2 cells, HIV-1-Bal infetion for 24hrs,CHIP

city: Bethesda

first: Laurence

last: Zhang

address: 9000 Rockville pike

institute: NIH/Kelly

description:
Library name: sample12
Lx2_CHIP_HIV1

data_processing:
The data was trimmed using fastp
Alignning reads with STAR-samtools;ht-seq to count the reads for RNA-seq
CHIP-seq was analyzed using a pipeline of bowtie2, macs callpeak2, samtools, bedtools, and deeptools
Assembly: hg19
Supplementary files format and content: tab delimited txt including the raw count for all the samples
Supplementary files format and content: bigwig file for chip-seq samples

growth_protocol: Lx2 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) with 10% FBS

extract_protocol:
Total RNA was extracted by using RNeasy spin columns (Qiagen, Cat No:74136). 1ug  RNA was used for RNA-seq.
library construction was prepared by the Genomics Core Facility of Mount Sinai

treatment_protocol: PBS or 0.1MOI HIV-1 Bal infection or 0.1MOI HIV-1 Bal infection pkus LTS treament

value: human stellate cells

value: 0.1MOI HIV-1 infection


title: dHepaRG cells, HDVIL29, rep2

description: Library name: HDVIL29_2

value: day 6

value: HDV + IFN-λ1


title: Rectum_CD_Noninflamed [I0303 RSDF00A CosMx1k ]

description:
294R303R1124_exprMat_file.csv
294R303R1124_fov_positions_file.csv
294R303R1124_metadata_file.csv
294R303R1124_tx_file.csv
294R303R1124-polygons.csv
fov 1-11


title: dHepaRG cells, IFNa, rep1

description: Library name: IFNa_1


title: Ileum_CD_Noninflamed [I0278 ITDF00A CosMx1k ]

description:
278I294I2124_exprMat_file.csv
278I294I2124_fov_positions_file.csv
278I294I2124_metadata_file.csv
278I294I2124_tx_file.csv
278I294I2124-polygons.csv
fov 15-39

value: Ileum


title: TM2_miRNA

description:
Library name: sample22
Column name in miRNA_count.txt: TM2


title: dHepaRG cells, IFNa, rep2

description: Library name: IFNa_2


title: dHepaRG cells, mock, rep1

description: Library name: mock_1

value: Mock


title: dHepaRG cells, mock, rep3

description: Library name: mock_3


title: dHepaRG cells, IL29, rep2

description: Library name: IL29_2


title: TM1_miRNA

description:
Library name: sample21
Column name in miRNA_count.txt: TM1


title: Rectum_UC_Noninflamed [I0310 RSDF00A CosMx1k]

description:
310R321R228_exprMat_file.csv
310R321R228_fov_positions_file.csv
310R321R228_metadata_file.csv
310R321R228_tx_file.csv
310R321R228-polygons.csv
fov 32-61


title: dHepaRG cells, IFNa, rep3

description: Library name: IFNa_3


title: dHepaRG cells, IL29, rep3

description: Library name: IL29_3


title: Ileum_CD_Inflamed [I0275 ITDF00A CosMx1k]

description:
262I275I3119_exprMat_file.csv
262I275I3119_fov_positions_file.csv
262I275I3119_metadata_file.csv
262I275I3119_tx_file.csv
262I275I3119-polygons.csv
fov 1-22


title: Lx2 cells, PBS treatment for 24hrs,CHIP

description:
Library name: sample10
Lx2_CHIP_CTL

value: PBS


title: dHepaRG cells, HDVIFNa, rep2

description: Library name: HDVIFNa_2

value: HDV + IFN-α-2a


title: Trp53-/-; sgPten; sgArid1a gastric organoid, clone 2

description: Library name: monoclonal_TPA_2

value: gastric organoid

value: Trp53-/-; sgPten; sgArid1a


title: ChIP-Rx, U2OS, MYC, IP, rep1

city: Pittsburgh

first: Da

last: Yang

state: PA

address: 3501 Terrace

department: School of Pharmacy

institute: University of Pittsburgh

description: Library name: ChIP_U2OS_MYC_IP_rep1

data_processing:
The adapters were trimmed using Cutadapt with “--match-read-wildcards --trim-n -O 1 -m 25 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT” parameters. Since the library contains reads from both human and mouse samples, we first generated a “genome” concatenated by human (hg19) and mouse (mm10) genome. To distinguish the chromosome names, we added a suffix “__mm10” to all mouse chromosome names. A custom Bowtie2 library was built based on this combined genome sequence using “bowtie2-build” command. Reads were first mapped using bowtie2 with parameters “--local --very-sensitive-local --no-unal --no-mixed --no-discordant -X 800”.
The SAM files were converted to BAM files using samtools. Read pairs with XS tag and MAPQ score >= 30 were retained using samtools. Duplicates were removed using Picard MarkDuplicates. Then the reads were split to two files such that hg38 reads were stored in one file and mm10 reads were stored in the other one. All suffix “__mm10” were removed for the mm10 SAM file. Alignment files were then parsed and converted in a bed format using MACS2 “filterdup” command with “--keep-dup -f BAMPE” parameters.
Next, the peaks were called by MACS2 with “--keep-dup all -f BEDPE” parameters using the similar steps as described in our previous work (PMID: 40378850). Final peaks overlapped with “blacklist” regions were removed.
For visualization in the UCSC genome browser, based on the bed files of aligned and processed reads, bedgraph files were first generated using MACS2 “pileup” command with “-f BEDPE” parameters. Then the counts in the bedgraph were RRPM (reference-adjusted reads per million) normalized using MACS2 “bdgopt” command. Next, the bedgraph files were converted into bigwig files using “bedGraphToBigWig” tool.
Assembly: hg38
Supplementary files format and content: The bw files contain the read distribution across the genome.
Supplementary files format and content: The narrowPeak files contain the peak details.

growth_protocol: U2OS cells were maintained in McCoy's 5A medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin in a humidified atmosphere with 5% CO2 at 37°C. Mouse embryonic fibroblast cell line NIH/3T3 was maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FBS, 1% MEM non-essential amino acids (Gibco), 10 mM HEPES (Gibco), and 1% penicillin/streptomycin.

extract_protocol:
After reverse cross-linking, RNase A, and proteinase K treatment on MYC-DNA adducts enriched with anti-MYC antibodies, DNA was purified with phenol:chloroform:isoamyl alcohol (25:24:1, pH 8.0).
DNA libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). 5 ng of DNA was used as starting material for input and IP samples. Libraries were amplified using 9 cycles on the thermocycler. Post-amplification libraries were size selected at 200 - 500 bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the 1× dsDNA High Sensitivity DNA Kit (Invitrogen).

treatment_protocol: Both NIH3T3 cells at exponential growth phase and U2OS cells were fixed with 1% formaldehyde for 10 min. After quenching by glycine, 10% of NIH3T3 cells were  mixed with U2OS cells, mixed chromatin were sheared to a size of 200 - 500 bp using a Bioruptor Pico (Diagenode) and incubated for overnight with an anti-MYC (Cell Signaling, 13987) antibody at 4°C.

tag: chip antibody


title: Ileum_UC_Noninflamed [I0321 ITDF00A CosMx1k]

description:
321I310I128_exprMat_file.csv
321I310I128_fov_positions_file.csv
321I310I128_metadata_file.csv
321I310I128_tx_file.csv
321I310I128-polygons.csv
fov 29-53


title: dHepaRG cells, HDVIL29, rep1

description: Library name: HDVIL29_1

value: dHepaRG cells


title: dHepaRG cells, mockPEG, rep2

description: Library name: mockPEG_2

value: PEG


title: dHepaRG cells, HDV, rep1

description: Library name: HDV_1

value: HDV


title: dHepaRG cells, SeV, rep1

description: Library name: SeV_1

value: SeV


title: dHepaRG cells, HDVIFNa, rep1

description: Library name: HDVIFNa_1


title: Trophoblast-mesoderm D23 ExM

city: Sendai

first: Shun

last: Shibata

address: 2-1 Seiryo-chou

department: Graduate School of Medicine

country: Japan

institute: Tohoku University

description:
Library name: TSOr_ExM_D23
snRNA-seq of ExM-primed cells at day 23

library_source: transcriptomic single cell

data_processing:
Raw reads were processed using Cell Ranger v8.0.1 (10x Genomics) with the human reference genome GRCh38-2020-A-2.0.0.
Assembly: GRCh38-2020-A-2.0.0 (10x Genomics)
Supplementary files format and content: filtered_feature_bc_matrix.h5 (HDF5 format containing sparse gene expression matrix, including barcodes and feature lists), as generated by Cell Ranger.

growth_protocol: ExM-primed cells (day 8) were dissociated using TrypLE Express for 3 minutes at 37°C, followed by differential adhesion on 0.1% gelatin-coated plates for 30 minutes to remove MEF feeders. Non-adherent cells were collected, filtered through a 70 μm cell strainer, counted, and resuspended in RCL medium with 10 μM Y27632 at 1.6 × 10⁵ cells/mL. hTSCs were prepared by centrifugation (380 × g, 1 minute) and resuspended in ECSY medium at 6.0 × 10⁵ cells/mL. ExM cells and hTSCs were mixed to achieve final concentrations of 1.6 × 10⁵ and 6.0 × 10⁵ cells/mL, respectively (total 7.6 × 10⁵ cells/mL), and seeded in AggreWell 400 24-well plates (2 mL per well). Plates were centrifuged at 100 × g for 3 minutes and incubated overnight at 37°C under 5% CO₂ and 5% O₂ conditions. The following day, formed spheroids were collected by gentle pipetting, filtered through a 200 μm cell strainer, and transferred to a ClinoStar bioreactor containing pre-warmed ECSYFB medium. Rotational culture was initiated at 9.6 rpm, with medium changes performed three times weekly. Rotation speed was gradually increased as assembloids enlarged to prevent contact with the vessel wall during extended culture periods.

extract_protocol:
Single nuclei were isolated using the Chromium Nuclei Isolation Kit (10x Genomics) according to the manufacturer's instructions. Approximately 10,000 nuclei per sample were used for library generation.
Single-nucleus RNA-seq libraries were prepared using 10x Genomics Chromium Single Cell 3′ Reagent Kits v3.1 with dual indexing. Libraries were sequenced (150 bp paired-end) on Illumina NovaSeq X Plus.

treatment_protocol: Rotational culture under simulated microgravity conditions in ClinoStar bioreactor, day 11 or day 23

value: trophoblast-mesoderm assembloids (ExM)

value: wild-type

value: co-culture assembloids, day 23


title: Trophoblast-mesoderm D11 ExM

description:
Library name: TSOr_ExM_D11
snRNA-seq of ExM-primed cells at day 11

value: co-culture assembloids, day 11


title: Trophoblast-mesoderm D11 Mix

description:
Library name: TSOr_Mix_D11
snRNA-seq of co-cultured cells (Mix) at day 11

value: trophoblast-mesoderm assembloids (Mix)


title: HFD2_miRNA

description:
Library name: sample18
Column name in miRNA_count.txt: HFD2

value: liver

value: WT

value: High-fat diet


title: Huh7-ris-A1

city: Nantong

first: Long

last: Hu

address: Chongchuan DistrictNantong University No.9 Seyuan Rd

institute: nantong university

description:
Library name: Huh7-ris-A1
Lenvatinib - Resistance

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low  quality bases which will affect the following assembly and analysis. Thus, to get high quality clean  reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows:  1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N);  3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Assembly: HG38
Supplementary files format and content: Excel file includes TPM values for each Sample

source_name: cell culture

extract_protocol:
Trizol reagent is a reagent used to directly extract total RNA from cells or tissues. It can maintain the integrity of RNA while lysing and dissolving cells. After lysing the cells and releasing RNA, adding chloroform and centrifuging will separate the sample into an aqueous layer and an organic layer. Under acidic conditions, RNA can be separated from DNA, and RNA is present in the aqueous layer. After collecting the above aqueous layer, RNA can be recovered by isopropanol precipitation.
The extracted mRNA is enriched using mRNA Capture Beads. After purification with beads, the  mRNA is fragmented using high temperatures. The fragmented mRNA is then used as a template  to synthesize the first strand of cDNA in a reverse transcription enzyme mixture system. While  synthesizing the second strand of cDNA, end repair and A tailing are completed. Next, adapters are ligated, and Hieff NGS® DNA Selection Beads are used for purification to select target  fragments. PCR library amplification is then performed, and finally, detection is carried out using  the Illumina Novaseq X Plus.

value: cell culture

value: Lenvatinib - Resistance


title: Lx2 cells, PBS treatment for 24hrs,Repeat1

description:
Library name: sample1
CTL_1

value: human stellate cells

value: PBS


title: dHepaRG cells, IL29, rep1

description: Library name: IL29_1


title: control4_miRNA

description:
Library name: sample16
Column name in miRNA_count.txt: control4

value: Normal diet


title: Day14,763,Mock

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: Day14-763-Mock

data_processing:
RNA-seq data were aligned using the STAR algorithm to a combined reference of the human genome (hg19) and the EBV genome (NC_007605.1). RSEM v.1.2.12 software was used to estimate read counts and reads per kilobase per million mapped reads (RPKM) values using gene information from Ensemble transcriptome (v.GRCh37.p13). DESeq2 was used on raw counts to estimate significance of expression differences between any two experimental groups and generate normalized counts.
Assembly: human genome (hg19) and the EBV genome (NC007605.1)
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

source_name: PBMC

extract_protocol:
RNeasy Kit mini (Qiagen)
Lexogen quantseq mRNA

value: PBMC

value: Control


title: dHepaRG cells, mockPEG, rep1

description: Library name: mockPEG_1

value: dHepaRG cells

value: day 6

value: PEG


title: Lx2 cells, HIV-1-Bal infetion for 24hrs,Repeat3

description:
Library name: sample6
HIV-1_3

value: 0.1MOI HIV-1 infection


title: Hep3B-WplusL-B1

description:
Library name: Hep3B-WplusL-B1
WWL70 20μM+lenvatinib

value: WWL70 20μM+lenvatinib


title: Hep3B-WL-A1

description:
Library name: Hep3B-WL-A1
WWL70 20μM

value: WWL70 20μM


title: Lx2 cells, HIV-1-Bal infetion for 24hrs,Repeat1

description:
Library name: sample4
HIV-1_1


title: Lx2 cells, HIV-1-Bal infetion with LTA stimulation for 24hrs,Repeat3

description:
Library name: sample9
HIV1_LTA3

value: 0.1MOI HIV-1 infection+1ug/ml LTA


title: Day14,757,Mock

description: Library name: Day14-757-Mock


title: Lx2 cells, HIV-1-Bal infetion with LTA stimulation for 24hrs,Repeat1

description:
Library name: sample7
HIV1_LTA1


title: ChIP-Rx, U2OS, MYC, IP, rep2

description: Library name: ChIP_U2OS_MYC_IP_rep2


title: Trophoblast-mesoderm D23 Mix (Rep2)

description:
Library name: TSOr_Mix_D23_New
snRNA-seq of co-cultured cells (Mix) at day 23

value: trophoblast-mesoderm assembloids (Mix)

value: wild-type

value: co-culture assembloids, day 23


title: HFD4_miRNA

description:
Library name: sample20
Column name in miRNA_count.txt: HFD4

value: liver

value: WT

value: High-fat diet


title: Hep3B-Con-B1

description:
Library name: Hep3B-Con-B1
control

value: cell culture

value: control


title: TM3_miRNA

description:
Library name: sample23
Column name in miRNA_count.txt: TM3

value: High-fat diet + HQHF


title: Lx2 cells, HIV-1-Bal infetion with LTA stimulation for 24hrs,Repeat2

description:
Library name: sample8
HIV1_LTA2

value: human stellate cells


title: Huh7-ris-B1

description:
Library name: Huh7-ris-B1
Lenvatinib - Resistance

value: Lenvatinib - Resistance


title: Lx2 cells, PBS treatment for 24hrs,Repeat3

description:
Library name: sample3
CTL_3

value: PBS


title: Lx2 cells, HIV-1-Bal infetion for 24hrs,Repeat2

description:
Library name: sample5
HIV-1_2


title: Day14,732,Mock

description: Library name: Day14-732-Mock

value: PBMC

value: Control


title: TM4

description:
Library name: sample12
Column name in gene_count_matrix.txt: TM4


title: NHDF-n6, dox-induced, replicate 4

city: New York

first: Angus

middle: C

last: Wilson

state: NY

department: Department of Microbiology

institute: NYU Langone Health

description: Library name: 241213_n6

data_processing:
Paired-end sequencing reads (FASTQ format) were subjected to quality control using FastQC to assess read quality metrics(Brown et al., 2017)
Adapter/quality trimming and filtering were conducted with Trim Galore (https://github.com/FelixKrueger/TrimGalore)(Krueger, n.d.) and minimum length and quality parameters adjusted after examining the FastQC report
Reads were aligned with STAR(Dobin et al., 2013) to a modified GRCh38 reference genome that included the ICP4 WT or mutant sequence
STAR was run with default parameters with output in sorted BAM format (--outSAMtype BAM SortedByCoordinate) and gene-level quantification enabled (--quantMode GeneCounts)
Lowly expressed genes were removed by filtering to those where at least 10 reads were mapped in a minimum of 2 or 3 samples, depending on group size
Linear models included a term to account for batch effect, except when not possible (mock conditions)
Differential expression analysis was performed on all samples with a standard DESeq2 pipeline in R(Love et al., 2014)
Assembly: GRCh38 left unmodified or modified to include ICP4 WT or mutant sequence
Supplementary files format and content: .csv files include log counts per million (CPM) for all samples, including the controls
Supplementary files format and content: .csv files include log counts per million (CPM) for all ICP4 WT and mutant samples, not including the controls

source_name: NHDF

growth_protocol: NHDFs were grown in DMEM with 10% FBS and 1% P/S and maintained in a humidified chamber at 37ºC with 5% CO2

extract_protocol:
RNA was extracted at using Ambion PureLink Mini Kit (Invitrogen; 12-183-018A) following manufacturer’s protocol.
Samples were analyzed on Bioanalyzer before automated stranded RNA-Seq library prep with polyA selection on ~1 ug of RNA. Sequencing was performed on NovaSeq X+ 10B 100 Cycle Flowcells

treatment_protocol: Cells were treated with 3 ug/mL doxycycline for 9 h before RNA was extracted

value: NHDF

value: Normal human dermal fibroblasts

value: dox


title: Huh7-Con-B1

description:
Library name: Huh7-Con-B1
control


title: Day14,732,EBV

description: Library name: Day14-732-EBV

value: EBV infected

value: Intected with virus


title: Day14,763,EBV

description: Library name: Day14-763-EBV


title: ChIP-Rx, U2OS, MYC, input

description: Library name: ChIP_U2OS_MYC_input


title: HFD3_miRNA

description:
Library name: sample19
Column name in miRNA_count.txt: HFD3


title: control2_miRNA

description:
Library name: sample14
Column name in miRNA_count.txt: control2

value: Normal diet


title: HFD1_miRNA

description:
Library name: sample17
Column name in miRNA_count.txt: HFD1

value: liver


title: TM2

description:
Library name: sample10
Column name in gene_count_matrix.txt: TM2

value: WT


title: control3_miRNA

description:
Library name: sample15
Column name in miRNA_count.txt: control3


title: Hep3B-len-B1

description:
Library name: Hep3B-len-B1
lenvatinib20μM


title: Hep3B-len-A1

description:
Library name: Hep3B-len-A1
lenvatinib20μM


title: Lx2 cells, PBS treatment for 24hrs,Repeat2

description:
Library name: sample2
CTL_2


title: TM3

description:
Library name: sample11
Column name in gene_count_matrix.txt: TM3


title: NHDF-ICP4, dox-induced, replicate 6

description: Library name: 240926_ICP4

value: WT ICP4


title: TM1

description:
Library name: sample9
Column name in gene_count_matrix.txt: TM1


title: NHDF-ICP4, dox-induced, replicate 7

description: Library name: 241210_ICP4


title: Huh7-Con-A1

description:
Library name: Huh7-Con-A1
control

value: cell culture


title: NHDF-n6, dox-induced, replicate 5

description: Library name: 241217_n6


title: Day14,757,EBV

description: Library name: Day14-757-EBV


title: Trophoblast-mesoderm D23 TS

description:
Library name: TSOr_TS_D23
snRNA-seq of hTSCs at day 23

value: wild-type

value: co-culture assembloids, day 23


title: NHDF-n208, dox-induced, replicate 3

description: Library name: 240905_n208


title: control1_miRNA

description:
Library name: sample13
Column name in miRNA_count.txt: control1


title: HFD3

description:
Library name: sample7
Column name in gene_count_matrix.txt: HFD3

value: High-fat diet


title: Hep3B-WplusL-A1

description:
Library name: Hep3B-WplusL-A1
WWL70 20μM+lenvatinib

value: WWL70 20μM+lenvatinib


title: Hep3B-Con-A1

description:
Library name: Hep3B-Con-A1
control

value: control


title: NHDF-n6, dox-induced, replicate 1

description: Library name: 240905_n6


title: Day14,514,EBV

description: Library name: Day14-514-EBV

value: PBMC


title: HFD2

description:
Library name: sample6
Column name in gene_count_matrix.txt: HFD2


title: NHDF-ICP4, dox-induced, replicate 8

description: Library name: 241213_ICP4


title: Day14,514,Mock

description: Library name: Day14-514-Mock

value: Control


title: NHDF-ICP4, dox-induced, replicate 3

description: Library name: 240814_ICP4

value: NHDF


title: HFD4

description:
Library name: sample8
Column name in gene_count_matrix.txt: HFD4


title: NHDF-mDBD, dox-induced, replicate 3

description: Library name: 240814_RR_LL

value: Normal human dermal fibroblasts

value: mDBD


title: NHDF-n6, dox-induced, replicate 2

description: Library name: 240827_n6

value: dox


title: NHDF-n208, dox-induced, replicate 2

description: Library name: 240904_n208


title: NHDF-mDBD, dox-induced, replicate 1

description: Library name: 240501_RR_LL


title: NHDF-n6, dox-induced, replicate 3

description: Library name: 241210_n6


title: control3

description:
Library name: sample3
Column name in gene_count_matrix.txt: control3


title: Day14,235,EBV

description: Library name: Day14-235-EBV

value: EBV infected

value: Intected with virus


title: Day8,514,Mock

description: Library name: Day8-514-Mock


title: Hep3B-WL-B1

description:
Library name: Hep3B-WL-B1
WWL70 20μM

value: WWL70 20μM


title: NHDF-ICP4, dox-induced, replicate 5

description: Library name: 240905_ICP4


title: HFD1

description:
Library name: sample5
Column name in gene_count_matrix.txt: HFD1

value: liver

value: WT


title: Day8,757,Mock

description: Library name: Day8-757-Mock


title: NHDF-ICP4, dox-induced, replicate 4

description: Library name: 240904_ICP4

value: WT ICP4


title: control1

description:
Library name: sample1
Column name in gene_count_matrix.txt: control1

value: Normal diet


title: NHDF-n208, dox-induced, replicate 1

description: Library name: 240313_n208


title: Day14,235,Mock

description: Library name: Day14-235-Mock


title: NHDF, mock-transduced, replicate 3

description: Library name: siNTC_rep3

value: mock


title: NHDF-mDBD, dox-induced, replicate 2

description: Library name: 240710_RR_LL


title: control4

description:
Library name: sample4
Column name in gene_count_matrix.txt: control4


title: control2

description:
Library name: sample2
Column name in gene_count_matrix.txt: control2


title: NHDF-ICP4, dox-induced, replicate 1

description: Library name: 240313_ICP4


title: NHDF, mock-transduced, replicate 2

description: Library name: siNTC_rep2


title: Day8,514,EBV

description: Library name: Day8-514-EBV


title: p60 Cnpy1-KO VNO biol rep 3

city: Hyderabad

first: Adish

last: Dani

state: Telangana

address: 36/P, Gopanpally

country: India

institute: Tata Institute of Fundamental Research, Hyderabad

description: Library name: p60 KO-3

data_processing:
Raw sequencing data was trimmed for adapter sequence using trim_galore v0.6.6 ,
Salmon v1.9.0 was used to quantify transcripts and DESeq2 was used to perform differential expression analysis.
Assembly: mm10/GRCm38.99
Supplementary files format and content: Tab-separated files contain raw counts and normalized transcript level counts for each sample.

source_name: Vomeronasal organ

extract_protocol:
Wildtype and Cnpy1-KO mice were euthanized using carbon dioxide asphyxiation, and the vomeronasal organ was collected. The outer bone was removed, and organs from both sides were used for RNA extraction in each biological replicate. Dissected tissue was transferred into tubes containing RLT buffer from the Qiagen RNeasy Plus Mini Kit with 1.4 mm ceramic beads. Tissue lysis was accomplished using a beadruptor, and subsequent steps were performed according to the manufacturer's instructions for the kit.
A total of 500 ng of RNA was used for each library preparation using the NEB Ultra II Directional RNA-Seq Library Prep Kit (NEB Cat #E7760L) protocol. Poly(A) selection was performed using the NEBNext Poly(A) Magnetic Isolation Module (NEB Cat #E7490L), in accordance with the manufacturer's instructions. The libraries were indexed using NEBNext Multiplex Oligos for Illumina 96 Unique Dual Index Primer 96 rxn Set 3

value: Vomeronasal organ

tag: Sex

value: Female


title: ipt 4h BAP 7d  rep2 (15)

city: Helsinki

first: Tiina

last: Blomster

address: Viikinkaari 1 (P.O. Box 65)

country: Finland

institute: University of Helsinki

description:
Library name: ipt_BAP_15
the same RNA sample (15) was also analysed with microarrays (Agilent)

data_processing:
RNA-seq data analysis was performed with the JAVA-based client-server system Chipster
Quality of sequences was checked with FastQC package
First 13 nucleotides were trimmed with PRINSEQ package, then reads were mapped to wild type Col-0 whole genome using Bowtie2 for single end reads.
Number of reads per each gene was counted with HTSeq package
Assembly: Col-0 TAIR10.23
Supplementary files format and content: Tab-separated files include AGI code, chromosomes, start, end, length, strand and raw count values for each sample

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Plants (ipt1,3,5,7 mutants) were grown on a nylon mesh (SEFAR NITEX 03-100/44) on vertical plates containing 0.8% Plant Agar (Duchefa), 1% sucrose (Duchefa), 0.5× MS medium including vitamins (Duchefa) and pH adjusted to 5.7–5.8 with 20× MES buffer (Mes monohydrate, Duchefa).

extract_protocol:
Total RNA was isolated with Qiagen RNeasy Plant Mini Kit with an on-column DNase treatment.
Libraries were prepared from 100 ng of total RNA with Illumina TruSeq RNA Sample Prep Kit v2 according to the kit manual.

treatment_protocol: 7-day-old plants were transferred with the mesh to plates containing 1 µM BAP or the DMSO control. Samples were harvested after 1h (DMSO and 4h (BAP) post-transfer by cutting primary roots a few millimeters below the hypocotyl, root tips and lateral roots were discarded.

value: root

value: 4h BAP


title: ipt DMSO 7d rep2 (11)

description:
Library name: ipt_DMSO_11
the same RNA sample (11) was also analysed with microarrays (Agilent)

value: 1h DMSO


title: NHDF, mock-transduced, replicate 1

description: Library name: siNTC_rep1

value: NHDF


title: ipt DMSO 7d  rep3 (21)

description:
Library name: ipt_DMSO_21
the same RNA sample (21) was also analysed with microarrays (Agilent)


title: Day7,763,Mock

description: Library name: Day7-763-Mock

value: PBMC

value: Control


title: Day8,235,EBV

description: Library name: Day8-235-EBV


title: NHDF-ICP4, dox-induced, replicate 2

description: Library name: 240501_ICP4

value: Normal human dermal fibroblasts

value: dox


title: ipt 4h BAP 7d rep1 (5)

description:
Library name: ipt_BAP_5
the same RNA sample (5) was also analysed with microarrays (Agilent)


title: Day8,235,Mock

description: Library name: Day8-235-Mock


title: ipt 4h BAP 7d rep3 (25)

description:
Library name: ipt_BAP_25
the same RNA sample (25) was also analysed with microarrays (Agilent)


title: p60 Cnpy1-KO VNO biol rep 1

description: Library name: p60 KO-1

value: Male


title: p60 Cnpy1-KO VNO biol rep 2

description: Library name: p60 KO-2


title: Day8,757,EBV

description: Library name: Day8-757-EBV

value: EBV infected

value: Intected with virus


title: p60 Cnpy1-WT VNO biol rep 2

description: Library name: p60 WT-2


title: ipt DMSO 7d rep1 (1)

description:
Library name: ipt_DMSO_1
the same RNA sample (1) was also analysed with microarrays (Agilent)


title: Day5,763,EBV

description: Library name: Day5-763-EBV


title: Tcell_Control_Malate_2

city: Houston

first: Arun

last: Sreekumar

state: Texas

address: One Baylor Plaza

department: Molecular and Cell Biology

institute: Baylor College of Medicine

description: Library name: Sample_8

data_processing:
Raw RNA-seq reads were first assessed for quality using FastQC (Andrews, 2010), and low-quality bases and adapter sequences were trimmed using Trim Galore (Krueger, 2015)
Cleaned reads were then aligned to the human reference genome (GRCm38/mm38) using HISAT2 (Kim et al., 2019) with default parameters.
The resulting SAM files were converted to BAM format, sorted, and indexed using SAMtools (Li et al., 2009).
Gene-level read counts were quantified using featureCounts (Liao et al., 2014) from Subread. Only uniquely mapped reads overlapping exons were counted toward gene-level expression estimates
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include Feature counts

source_name: CD8+ T cells

growth_protocol: Mouse spleen was isolated after sacrificing a 6–8-week-old female OT-1 mouse obtained from The Jackson Laboratory (C57BL/6-Tg(TcraTcrb)1100Mjb/J, Strain #: 003831). The tissue was immediately washed with 1X PBS supplemented with 2% FBS and 1% Penicillin-Streptomycin (hereafter referred to as FACS buffer). Mechanical disruption of the tissue was performed to obtain a single-cell suspension with FACS buffer. The cell suspension was then filtered through a cell strainer (pluriSelect USA pluriStrainer Mini 10 µm (Cell Strainer), Cat. No. 43-10010-60) and collected in a 5 ml polystyrene tube. The strained cell suspension was centrifuged at 500g for 5 minutes at room temperature. The pelleted cells were incubated in 1X RBC lysis buffer (TONBO biosciences, Cat No. TNB-4300) for 10 minutes at room temperature. After another centrifugation under the same conditions, FCδ receptors were blocked by adding Purified Anti-Mouse CD16 / CD32 (FC shield) from Cytek Biosciences, Cat. No. 70-0161-U500. Negative selection of CD8+ T cells was performed by incubating the cells with a 1:100 dilution of biotin-labeled anti-mouse CD4 (TONBO Biosciences Cat. # 30-0041-U100), CD11c (TONBO Biosciences Cat. # 30-0114-U100), CD11b, CD45R, Ly-6G, and Ly-6C antibodies (BD PharmigenTM, Biotin Mouse Lineage Panel, Cat. No. 559971) at 4°C for 15 minutes. This was followed by centrifugation and resuspension of the pellet in 2 ml of FACS buffer with a 1:40 dilution of Streptavidin Particles Plus-DM (BD IMagTM, Cat. # 557812). Magnetic separation of these beads finally yields a CD8+ T cell population in the cell suspension. The cells were plated with growth media and T cell activation beads (25 µl per 10^6 T cells) (Thermo Fisher Scientific, DynabeadsTM Mouse T-Activator CD3/CD28, Cat. No. 11456D). The T cell growth media consisted of 9 ml RPMI, 1 ml heat-inactivated FBS, 40 µl 1:1000 β-mercaptoethanol, 4 µl of 10 ng/µl IL-2, and 100 µl Penicillin-Streptomycin solution. After 48 hours of activation, activated CD8+ T cells were co-cultured with tumor cells (1:5 ratio) and/or with treatment conditions.

extract_protocol:
The CD8+ T cell pellets were harvested from the 1:5 T cell: tumor cell co-culture. The cells were then washed with Phosphate Buffer Saline (PBS). Three million cells were harvested and counted per replicate (n=3). RNA extraction was performed using the Aurum™ Total RNA Mini Kit (Bio-Rad).
Libraries were prepared using the ABclonal mRNA-seq Library Prep Kit for Illumina (poly (A) selection). RNA integrity and quantification were confirmed on the AATI Fragment Analyzer and quantitative PCR. Quality assessment and sequencing were performed by Novogene Corporation, Sacramento. Sequencing was performed using Illumina NovaSeq X Plus (PE150).

treatment_protocol: The CD8+ T cells are co-cultured with E0771-ova+ cells with or without inducible KD of AADAT. Additionally, we included a co-culture with uninduced E0771-ova+ and CD8+ T cells where the media was supplemented with 2.5 mM malate

value: CD8+ T cells


title: Day7,763,EBV

description: Library name: Day7-763-EBV


title: Day7,732,EBV

description: Library name: Day7-732-EBV


title: Tcell_Control_Malate_1

description: Library name: Sample_7


title: p60 Cnpy1-WT VNO biol rep 1

description: Library name: p60 WT-1


title: Day5,763,Mock

description: Library name: Day5-763-Mock


title: p60 Cnpy1-WT VNO biol rep 3

description: Library name: p60 WT-3


title: Tcell_Dox_2

description: Library name: Sample_5

value: Dox


title: Grandfather

city: Chengdu

first: Lei

last: Chu

state: SICHUAN

address: 37 Guoxue Road

department: Dermatology

institute: West China Hospital

description: YEYE

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 2.0 in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G

data_processing: Expression data were generated by Affymetrix Expression Console software and normalized by the RMA(Robust Multi-chip Average ) method.

label: biotin

source_name: Total White Blood cells

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using GeneChip® WT PLUS Reagent Kit

extract_protocol: none provided by the submitter

tag: sample type

value: Family Normal Control


title: Day5,757,Mock

description: Library name: Day5-757-Mock


title: Tcell_Dox_3

description: Library name: Sample_6


title: Tcell_Control_Malate_3

description: Library name: Sample_9


title: Amplicon_U6_3

city: Beijing

first: Yangming

last: Wang

address: No.5 Yiheyuan Road, Haidian District

department: College of Future Technology

institute: Peking University

description: Library name: Sample 27

data_processing:
The 150-bp paired-end sequencing reads were quality-checked by FastQC (v0.11.9) and processed using Trim Galore (v0.6.7). Processed reads were then aligned to DNA sequence of mCherry-TAG-GFP by Bowtie2 (v2.4.5). The editing rates were quantified by REDItools.
Supplementary files format and content: tab-delimited text files

source_name: HEK293T cell line

growth_protocol: WIBR3 Human ESCs were grown in mTeSRTM (STEMCELL Technologies) on Matrigel-coated dish. HEK293T cells were cultured in high glucose DMEM supplemented with 10% (v/v) FBS and 1% (v/v) PS. All cells were maintained at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted following the standard TRIzol protocol (invitrogen).
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme) following manufacturer’s protocols; RNA libraries for amplicon were prepared by specific RT and PCR amplification.

value: HEK293T cell line

value: mCherry-TAG-GFP + U6-ART RNA


title: Tcell_Dox_1

description: Library name: Sample_4


title: Day5,732,Mock

description: Library name: Day5-732-Mock


title: Papillon-Lefèvre Syndrome Proband 40 Days after Treatment

description: LFGZHILIAOHOU

value: 40days After Treatment


title: Day7,732,Mock

description: Library name: Day7-732-Mock


title: Amplicon_U6_2

description: Library name: Sample 26


title: Mother


title: Day5,757,EBV

description: Library name: Day5-757-EBV


title: Young Brother

description: DIDI


title: Papillon-Lefèvre Syndrome Proband Before Treatment

description: LFGZHILIAOQIAN

value: Patient Before Treatment


title: Day5,732,EBV

description: Library name: Day5-732-EBV


title: Tcell_Control_3

description: Library name: Sample_3


title: Tcell_Control_2

description: Library name: Sample_2


title: Amplicon_TGT_2

description: Library name: Sample 23

value: mCherry-TAG-GFP + CAG-tRNA-ART RNA-tRNA


title: WT_NALM-6_500_000_cells

city: Toronto

first: Micheal

middle: D

last: Tyers

state: Ontario

address: 555 University Avenue

country: Canada

institute: The Hospital for Sick Children

description:
Library name: WT_NALM-6_500_000_cells
500K cells colllected and ERCC spike-in RNA added

data_processing:
Reads were aligned using Bowtie2.2.5, with default parameters, to all RefSeq transcripts (retrieved in january 2016) for most samples, combined with ERCC spike-in sequences for samples represented in read_counts_ERCC_spike-in.txt and to Gencode (V23) transcripts for samples represented in read_counts2.txt. Alignments with fewer than 2 inserted or deleted bases and a maximum edit distance of 5 (i.e. the sum of inserted, deleted, or mismatched bases) were counted to generate read counts per transcript. For samples represented in read_counts1.txt, read counts for transcripts of the same gene wre summed to produce gene-specific read counts.
Assembly: RefSeq transcripts from January 2016 , ERCC spike-in sequences or Gencode V23 transcripts
Supplementary files format and content: All processed data files are tab-delimited text files with each row corresponding to genes, transcripts or ERCC spike-in RNAs and each column to a sample. All contain row and column headers.

growth_protocol: Nalm-6 cells were grown in 10% FBS (v/v) (Wisent) RPMI 1640 medium (Wisent) at 5% (v/v) CO2 and 37°C. 1 million NALM-6 cells (unless otherwise noted) were collected from an exponentially growing culture (800,000 cells per mL).

extract_protocol:
Cell were centrifugated for 5 min at 2,300 x g at 4°C, resuspended in 1 mL TRIzol (Ambion, Life Technologies) and samples processed by the IRIC Genomic platform. In the case of PABIR1 knockout versus wild type cells, cell concentration was measured using a Beckman Z2 Coulter counter in triplicate. ERCC RNA loading control Spike-in mix (Ambion Ref. 4456740) was diluted 1:20 in water and 20 µL per mL spiked in Trizol prior to addition of 1 mL over each cell pellet. Total RNA was isolated using RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
RNA was quantified using Qubit (Thermo Scientific) and quality was assessed with the 2100 Bioanalyzer (Agilent Technologies). Transcriptome libraries were generated using the KAPA RNA HyperPrep (Roche) using poly-A selection (Thermo Scientific).

treatment_protocol: Specified samples were treated with DMSO 0.1% or 5uM FK-506. Knockout populations were infected with lentivirus infection plus selection,

value: pre-B lymphoid cell line

value: wild type

value: No treatment


title: FAM122a_KO_3B03_11_500_000_cells

description:
Library name: FAM122a_KO_3B03_11_500_000_cells
500K cells colllected and ERCC spike-in RNA added

value: PABIR1 knockout


title: Tcell_Control_1

description: Library name: Sample_1

value: Control


title: Amplicon_U6_1

description: Library name: Sample 25


title: Day5,514,EBV

description: Library name: Day5-514-EBV

value: PBMC


title: Day5,235,Mock

description: Library name: Day5-235-Mock


title: Amplicon_TGT_3

description: Library name: Sample 24


title: Day5,514,Mock

description: Library name: Day5-514-Mock


title: Amplicon_PGP_3

description: Library name: Sample 21

value: mCherry-TAG-GFP + CAG-P1 twister-ART RNA-P3


title: FAM122a_KO_3B03_11_400_000_cells

description:
Library name: FAM122a_KO_3B03_11_400_000_cells
400K cells colllected and ERCC spike-in RNA added


title: Amplicon_PGP_1

description: Library name: Sample 19


title: Amplicon_TGT_1

description: Library name: Sample 22


title: WT_NALM-6_600_000_cells

description:
Library name: WT_NALM-6_600_000_cells
600K cells colllected and ERCC spike-in RNA added


title: FAM122a_KO_500000_cells_DMSO

description:
Library name: FAM122a_KO_500000_cells_DMSO
500K cells colllected and ERCC spike-in RNA added

value: DMSO 0.1%


title: Day1,763,Mock

description: Library name: Day1-763-Mock


title: FAM122a_KO_800000_cells_DMSO

description:
Library name: FAM122a_KO_800000_cells_DMSO
800K cells colllected and ERCC spike-in RNA added


title: WT_NALM-6_600000_cells_DMSO

description:
Library name: WT_NALM-6_600000_cells_DMSO
600K cells colllected and ERCC spike-in RNA added


title: Amplicon_Ctrl_3

description: Library name: Sample 18

value: mCherry-TAG-GFP


title: WT_NALM-6_900000_cells_DMSO

description:
Library name: WT_NALM-6_900000_cells_DMSO
900K cells colllected and ERCC spike-in RNA added


title: Amplicon_PGP_2

description: Library name: Sample 20


title: Amplicon_Ctrl_1

description: Library name: Sample 16


title: WT_NALM-6_400_000_cells

description:
Library name: WT_NALM-6_400_000_cells
400K cells colllected and ERCC spike-in RNA added


title: PPP3R1_KO_5D11

description: Library name: PPP3R1_KO_5D11

value: PPP3R1 knockout


title: Day5,235,EBV

description: Library name: Day5-235-EBV

value: EBV infected

value: Intected with virus


title: WT_NALM-6_500000_cells_DMSO

description:
Library name: WT_NALM-6_500000_cells_DMSO
500K cells colllected and ERCC spike-in RNA added


title: FAM122a_KO_3B03_11_600_000_cells

description:
Library name: FAM122a_KO_3B03_11_600_000_cells
600K cells colllected and ERCC spike-in RNA added


title: FAM122a_KO_900000_cells_DMSO

description:
Library name: FAM122a_KO_900000_cells_DMSO
900K cells colllected and ERCC spike-in RNA added


title: FAM122a_KO_700000_cells_DMSO

description:
Library name: FAM122a_KO_700000_cells_DMSO
700K cells colllected and ERCC spike-in RNA added


title: FAM122a_KO_600000_cells_DMSO

description:
Library name: FAM122a_KO_600000_cells_DMSO
600K cells colllected and ERCC spike-in RNA added


title: PPP3R1_KO_5D10

description: Library name: PPP3R1_KO_5D10


title: Day1,763,EBV

description: Library name: Day1-763-EBV


title: WT_NALM-6_700000_cells_DMSO

description:
Library name: WT_NALM-6_700000_cells_DMSO
700K cells colllected and ERCC spike-in RNA added


title: PPP3CA_KO_5D01

description: Library name: PPP3CA_KO_5D01

value: PPP3CA knockout


title: Day1,757,Mock

description: Library name: Day1-757-Mock


title: Amplicon_CAG_3

description: Library name: Sample 15

value: HEK293T cell line

value: mCherry-TAG-GFP + CAG-ART RNA


title: Amplicon_Ctrl_2

description: Library name: Sample 17


title: Amplicon_CAG_1

description: Library name: Sample 13


title: Day1,514,EBV

description: Library name: Day1-514-EBV


title: Day1,732,EBV

description: Library name: Day1-732-EBV


title: Nalm6_WT

description: Library name: Nalm6_WT


title: DMSO

description: Library name: DMSO


title: NANOG_Dif_D5_rep3

description: Library name: Sample 12

value: NANOG-REDDIT

value: neural induction


title: NANOG_Dif_D5_rep2

description: Library name: Sample 11


title: UM0129480 7uM Round-02 (exp85)

description:
Library name: UM0129480 7uM_Round-02 (exp85)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA

data_processing:
Reads were aligned using Bowtie2.2.5 in the forward direction only (--norc option) with otherwise default parameters and total read counts per sgRNA were tabulated.
For each round (batch of simultaneously-run screens), read counts for all control samples (untreated, DMSO 0.1%-0.3% or ethanol 0.1%-0.3% treated) were summed together. Read counts for samples that were grown together for part of the 8 days of the screen were also summed together so that each sample represented in the processed data files is independent in terms of genetic drift.
Assembly: sgRNAs from the Extended knock-out (EKO) library (Bertomeu et al. 2017).
Supplementary files format and content: sgrna_read_counts_refseq_genes.txt : sgRNA read counts for controls and each independent screen  (sequenced sample experiment numbers are indicated in the colunm headers), targeted refSeq gene symbols (January 2016) and updated HGNC gene symbols (2020).
Supplementary files format and content: sgrna_read_counts_exons_and_hypothetical_genes.txt : sgRNA read counts for controls and each independent screen  (sequenced sample experiment numbers are indicated in the colunm headers), targeted exons (hg19 coordinates) and hypothetical genes (AceView or Gencode symbols).
Library strategy: CRISPR Screen

growth_protocol: Nalm-6 cells were grown in 10% FBS (v/v) (Wisent) RPMI 1640 medium (Wisent) at 5% (v/v) CO2 and 37°C. Media was changed every two days and cells diluted to 400,000 cells/ml.

extract_protocol:
genomic DNA extracted using the Gentra Puregene kit according to the manufacturer’s instructions (QIAGEN), and sgRNA sequences were PCR-amplified
sgRNA libraries were prepared by PCR amplification to add sequencing adapters and indices followed by SPRI beads purification of sequencing-ready amplicons.

treatment_protocol: A Nalm-6 clone with inducible expression of Cas9 was thawed, and Cas9 expression induced with doxycycline at 2 µg/mL for 8 days (see Bertomeu et al., 2017 for details). The pooled EKO library was split in different T-75 flasks, compounds added, and propagated for 8 days. Fresh media and compound was added at each cell passage. The untreated control sample with multiple collected time-points was grown in T-175 spinner flasks.

value: pre-B lymphoid cell line


title: WT_NALM-6_800000_cells_DMSO

description:
Library name: WT_NALM-6_800000_cells_DMSO
800K cells colllected and ERCC spike-in RNA added

value: wild type


title: Amplicon_CAG_2

description: Library name: Sample 14


title: NANOG_Dif_D5_rep1

description: Library name: Sample 10


title: FK-506_5_uM

description: Library name: FK-506_5_uM


title: Azami_KO_2D12

description: Library name: Azami_KO_2D12

value: No treatment


title: PPP3CA_KO_5D03

description: Library name: PPP3CA_KO_5D03


title: AAVS1_KO_2D11

description: Library name: AAVS1_KO_2D11


title: Day1,235,Mock

description: Library name: Day1-235-Mock


title: I-BRD9 4uM Round-07 (exp365)

description:
Library name: I-BRD9 4uM_Round-07 (exp365)
sgRNAs PCR-amplified from genomic DNA

value: I-BRD9 4uM


title: Citral 75uM Round-06 (exp275)

description:
Library name: Citral 75uM_Round-06 (exp275)
sgRNAs PCR-amplified from genomic DNA

value: Citral 75uM


title: PPP3R1_KO_5D12

description: Library name: PPP3R1_KO_5D12


title: Lead acetate 2000uM Round-08 (exp497)

description:
Library name: Lead acetate 2000uM_Round-08 (exp497)
sgRNAs PCR-amplified from genomic DNA

value: Lead acetate 2000uM


title: Day1,514,Mock

description: Library name: Day1-514-Mock

value: PBMC

value: Control


title: Staurosporine 20nM Round-08 (exp524)

description:
Library name: Staurosporine 20nM_Round-08 (exp524)
sgRNAs PCR-amplified from genomic DNA

value: Staurosporine 20nM


title: PPP3CA_KO_5D02

description: Library name: PPP3CA_KO_5D02


title: Day1,757,EBV

description: Library name: Day1-757-EBV


title: NANOG_Dif_D4_rep3

description: Library name: Sample 9


title: Day1,235,EBV

description: Library name: Day1-235-EBV


title: Day7,728,2,EBVc

description: Library name: Day7-728-2-EBVc

extract_protocol:
RNeasy Kit mini (Qiagen)
Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: EBV enriched

value: EBV probe capture


title: Day7,728,1,EBVc

description: Library name: Day7-728-1-EBVc


title: Day7,728,2

description: Library name: Day7-728-2


title: GSK2606414 1uM Round-05 (exp236)

description:
Library name: GSK2606414 1uM_Round-05 (exp236)
sgRNAs PCR-amplified from genomic DNA


title: AICAR 240uM Round-05 (exp211)

description:
Library name: AICAR 240uM_Round-05 (exp211)
sgRNAs PCR-amplified from genomic DNA

value: AICAR 240uM


title: Hippuristanol 120nM Round-08 (exp488)

description:
Library name: Hippuristanol 120nM_Round-08 (exp488)
sgRNAs PCR-amplified from genomic DNA

value: Hippuristanol 120nM


title: NANOG_Dif_D2_rep3

description: Library name: Sample 6


title: NANOG_Dif_D4_rep2

description: Library name: Sample 8


title: Ethanol 0.1% from SF2 Round-08 (exp543)

description:
Library name: Ctl Ethanol 0.1_ D8_SF2_Round-08 (exp543)
sgRNAs PCR-amplified from genomic DNA

value: Ethanol 0.1%


title: Ammonium tetrathiomolybdate 10uM Round-08 (exp448)

description:
Library name: Ammonium tetrathiomolybdate 10uM_Round-08 (exp448)
sgRNAs PCR-amplified from genomic DNA

value: Ammonium tetrathiomolybdate 10uM


title: Day7,728,1

description: Library name: Day7-728-1


title: Day1,732,Mock

description: Library name: Day1-732-Mock


title: Apcin 25uM proTAME 2uM Round-04 (exp177)

description:
Library name: Apcin 25uM_proTAME 2uM_Round-04 (exp177)
sgRNAs PCR-amplified from genomic DNA

value: Apcin 25uM and proTAME 2uM


title: Day7,235,2,EBVc

description: Library name: Day7-235-2-EBVc


title: NANOG_Dif_D0_rep2

description: Library name: Sample 2

value: NANOG-REDDIT

value: neural induction


title: Day7,235,1,EBVc

description: Library name: Day7-235-1-EBVc


title: Lead acetate 2000uM No dilution on Day 6 Round-08 (exp498)

description:
Library name: Lead acetate 2000uM_No dilution D6_Round-08 (exp498)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line


title: QNZ 10nM Round-08 (exp439)

description:
Library name: QNZ 10nM_Round-08 (exp439)
sgRNAs PCR-amplified from genomic DNA

value: QNZ 10nM


title: NANOG_Dif_D0_rep3

description: Library name: Sample 3


title: Quinacrine 2.5uM Round-03 (exp146)

description:
Library name: Quinacrine 2.5uM_Round-03 (exp146)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA

value: Quinacrine 2.5uM


title: NANOG_Dif_D2_rep1

description: Library name: Sample 4


title: NANOG_Dif_D0_rep1

description: Library name: Sample 1


title: HMS-I1 10uM Round-06 (exp256)

description:
Library name: HMS-I1 10uM_Round-06 (exp256)
sgRNAs PCR-amplified from genomic DNA

value: HMS-I1 10uM


title: Day7,235,2

description: Library name: Day7-235-2


title: Rapamycin 2uM FK-506 5uM Round-07 (exp308)

description:
Library name: Rapamycin 2uM_FK-506 5uM_Round-07 (exp308)
sgRNAs PCR-amplified from genomic DNA

value: Rapamycin 2uM and FK-506 5uM


title: Spinner flask No treatment Day 8 Round-06 (exp598)

description:
Library name: SF No treatment D8_Round-06 (exp598)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: WT_hESC_RepSox_rep2

description: Library name: Sample 40

data_processing:
The 150-bp paired-end sequencing reads were quality-checked by FastQC (v0.11.9) and processed using Trim Galore (v0.6.7). Processed reads were then aligned to the human genome (hg38) or mouse genome (mm10) by STAR (v2.7.10a) or Bowtie2 (v2.4.5). The raw counts aligned to exonic regions were quantified by Subread featureCounts (v2.0.1).
Assembly: GRCh38; mm10
Supplementary files format and content: tab-delimited text files include rawcounts and bigWig files for GRO-seq

growth_protocol: WIBR3 Human ESCs were grown in mTeSRTM (STEMCELL Technologies) on Matrigel-coated dish at 37°C under 5% CO2. V6.5 mouse ESCs were grown on gelatin-coated dish at 37°C under 5% CO2, in KnockOutTM DMEM (Gibco) supplemented with 15% FBS (Hyclone), nonessential amino acids, 2-mercaptoethanol, and 1,000 units/ml lymphocyte inhibitory factor.

extract_protocol:
For bulk RNA library construction, total RNA was extracted following the standard TRIzol protocol (invitrogen); For GRO-seq library construction, RNAs are hydrolyzed and purified using beads coated with antibodies to 5-bromo-2-deoxyuridine (BrdU).
RNA libraries for RNA-seq were prepared using AHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme) following manufacturer’s protocols; RNA libraries for GRO-seq using AccuNext Small RNA-seq Library Kit for Illumina (Accurate Biology) following manufacturer’s protocols.

value: human embryonic stem cell

value: WT

value: 10 μM RepSox


title: Rifampicin 30uM Round-08 (exp430)

description:
Library name: Rifampicin 30uM_Round-08 (exp430)
sgRNAs PCR-amplified from genomic DNA

value: Rifampicin 30uM


title: WT_hESC_RepSox_rep1

description: Library name: Sample 39


title: Mubritinib 200nM Round-02 (exp65)

description:
Library name: Mubritinib 200nM_Round-02 (exp65)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA

value: Mubritinib 200nM


title: SNS-032 15uM Round-08 (exp443)

description:
Library name: SNS-032 15uM_Round-08 (exp443)
sgRNAs PCR-amplified from genomic DNA


title: Cadmium 60uM Round-08 (exp462)

description:
Library name: Cadmium 60uM_Round-08 (exp462)
sgRNAs PCR-amplified from genomic DNA

value: Cadmium 60uM


title: Vinorelbine 1nM Round-05 (exp249)

description:
Library name: Vinorelbine 1nM_Round-05 (exp249)
sgRNAs PCR-amplified from genomic DNA

value: Vinorelbine 1nM


title: Day1,728,2,EBVc

description: Library name: Day1-728-2-EBVc

value: PBMC

value: EBV enriched

value: EBV probe capture


title: Day1,728,2

description: Library name: Day1-728-2

value: Control


title: NANOG_Dif_D4_rep1

description: Library name: Sample 7

value: NANOG-REDDIT

value: neural induction


title: NANOG_Dif_D2_rep2

description: Library name: Sample 5


title: Aphidicolin 40nM Round-06 (exp263)

description:
Library name: Aphidicolin 40nM_Round-06 (exp263)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Aphidicolin 40nM


title: Day7,235,1

description: Library name: Day7-235-1


title: Ethanol 1% Round-05 (exp234)

description:
Library name: Ethanol 1__Round-05 (exp234)
sgRNAs PCR-amplified from genomic DNA

value: Ethanol 1%


title: WT_hESC_DMSO_rep2

description: Library name: Sample 38

value: DMSO


title: Day1,728,1,EBVc

description: Library name: Day1-728-1-EBVc


title: VHL Ligand 1 20uM Round-07 (exp421)

description:
Library name: VHL Ligand 1 20uM_Round-07 (exp421)
sgRNAs PCR-amplified from genomic DNA

value: VHL Ligand 1 20uM


title: Day1,235,2,EBVc

description: Library name: Day1-235-2-EBVc


title: REDDIT_SOX2_polyA_rep2

description: Library name: Sample 12

value: human embryonic stem cell

value: SOX2 polyA-REDDIT


title: iCRT14 30uM Round-08 (exp492)

description:
Library name: iCRT14 30uM_Round-08 (exp492)
sgRNAs PCR-amplified from genomic DNA

value: iCRT14 30uM


title: Day1,235,1,EBVc

description: Library name: Day1-235-1-EBVc


title: Day1,728,1

description: Library name: Day1-728-1


title: ABT-702 100nM Round-06 (exp260)

description:
Library name: ABT-702 100nM_Round-06 (exp260)
sgRNAs PCR-amplified from genomic DNA


title: Celastrol 120nM Round-05 (exp225)

description:
Library name: Celastrol 120nM_Round-05 (exp225)
sgRNAs PCR-amplified from genomic DNA

value: Celastrol 120nM


title: Day1,235,1

description: Library name: Day1-235-1


title: Tubastatin A 2.5uM Round-07 (exp417)

description:
Library name: Tubastatin A 2.5uM_Round-07 (exp417)
sgRNAs PCR-amplified from genomic DNA

value: Tubastatin A 2.5uM


title: Docetaxel 0.001-0.002uM Round-04 (exp159)

description:
Library name: Docetaxel 0.001-0.002uM_Round-04 (exp159)
sgRNAs PCR-amplified from genomic DNA

value: Docetaxel 0.001uM, then 0.002uM


title: EPZ-5676 30uM Round-05 (exp233)

description:
Library name: EPZ-5676 30uM_Round-05 (exp233)
sgRNAs PCR-amplified from genomic DNA


title: CHIR-124 142nM Round-09 (exp622)

description:
Library name: CHIR-124 142nM_Round-09 (exp622)
sgRNAs PCR-amplified from genomic DNA


title: FBS Sub-Optimal Growth 10% Round-07 (exp426)

description:
Library name: FBS Sub-Optimal Growth 10__Round-07 (exp426)
sgRNAs PCR-amplified from genomic DNA

value: Sub-Optimal FBS 10%


title: REDDIT_ACTB_polyA_rep1

description: Library name: Sample 9

value: ACTB polyA-REDDIT


title: Day0,728

description: Library name: Day0-728

value: PBMC


title: REDDIT_ACTB_polyA_rep2

description: Library name: Sample 10


title: Day1,235,2

description: Library name: Day1-235-2

value: Control


title: LY2090314 3nM No dilution on Day 6 Round-08 (exp500)

description:
Library name: LY2090314 3nM_No dilution D6_Round-08 (exp500)
sgRNAs PCR-amplified from genomic DNA


title: Day0,728,EBVc

description: Library name: Day0-728-EBVc

value: EBV enriched

value: EBV probe capture


title: FK-506 30uM Round-07 (exp359)

description:
Library name: FK-506 30uM_Round-07 (exp359)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line


title: WT_hESC_DMSO_rep1

description: Library name: Sample 37

value: WT


title: CB-5083 400nM Round-08 (exp468)

description:
Library name: CB-5083 400nM_Round-08 (exp468)
sgRNAs PCR-amplified from genomic DNA


title: THZ531 225nM Round-08 (exp444)

description:
Library name: THZ531 225nM_Round-08 (exp444)
sgRNAs PCR-amplified from genomic DNA


title: REDDIT_ACTB_intron1_rep2

description: Library name: Sample 8

value: ACTB intron1-REDDIT


title: REDDIT_ACTB_intron1_rep1

description: Library name: Sample 7


title: Chlorpromazine 10uM Round-07 (exp344)

description:
Library name: Chlorpromazine 10uM_Round-07 (exp344)
sgRNAs PCR-amplified from genomic DNA

value: Chlorpromazine 10uM


title: REDDIT_SOX2_polyA_rep1

description: Library name: Sample 11


title: S-Trityl-L-cysteine 500nM Round-05 (exp243)

description:
Library name: S-Trityl-L-cysteine 500nM_Round-05 (exp243)
sgRNAs PCR-amplified from genomic DNA

value: S-Trityl-L-cysteine 500nM


title: Day0,235,EBVc

description: Library name: Day0-235-EBVc


title: Sucrose 20000uM Round-06 (exp298)

description:
Library name: Sucrose 20000uM_Round-06 (exp298)
sgRNAs PCR-amplified from genomic DNA

value: Sucrose 20000uM


title: REDDIT_MIR302_rep1

description: Library name: Sample 5

value: human embryonic stem cell


title: Day0,235

description: Library name: Day0-235


title: REDDIT_MIR302_rep2

description: Library name: Sample 6


title: Pyrazinamide 100uM Round-08 (exp516)

description:
Library name: Pyrazinamide 100uM_Round-08 (exp516)
sgRNAs PCR-amplified from genomic DNA

value: Pyrazinamide 100uM


title: Nontransduced, baseline, rep 1

city: Seattle

first: Andras

last: Heczey

state: WA

address: 4800 Sand Point Way NE

institute: Seattle Children's Hospital

description: Library name: N1

data_processing:
Raw fastq files were trimmed of adapters using Trimmomatic v0.39 under the default settings using adapters from TruSeq2-PE.fa
Trimmed read were aligned to the hg38 build of the human genome using the STAR v2.7 aligner
featureCounts v2.0.3 was used to quantify aligned reads and generate count matrix
Assembly: hg38
Supplementary files format and content: Raw count table with genes as rows and samples as columns
Supplementary files format and content: csv file contains raw count values for each sample

source_name: Donor T cells

extract_protocol:
RNA was extracted from pellets frozen at the end of manufacturing (baseline) and at the end of round 2 co-culture in one batch using a Qiagen RNeasy Mini extraction kit (Hilden, Germany)
Samples were then sent for Illumina-based sequencing at Novogene (Sacramento, CA) for construction of polyA RNA libraries

value: Donor T cells

value: T cell

value: Nontransduced T cell

tag: donor


title: ABT-702 5uM Dimethyloxaloylglycine 11uM Round-07 (exp319)

description:
Library name: ABT-702 5uM_Dimethyloxaloylglycine 11uM_Round-07 (exp319)
sgRNAs PCR-amplified from genomic DNA

value: ABT-702 5uM_Dimethyloxaloylglycine 11uM


title: Spinner flask No treatment Day 6 Round-07 (exp603)

description:
Library name: SF No treatment D6_Round-07 (exp603)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: Cannabidiol 13uM Round-08 (exp465)

description:
Library name: Cannabidiol 13uM_Round-08 (exp465)
sgRNAs PCR-amplified from genomic DNA

value: Cannabidiol 13uM


title: REDDIT_NANOG_rep2

description: Library name: Sample 4

value: NANOG-REDDIT


title: RO 3306 3-4uM Round-04 (exp165)

description:
Library name: RO 3306 3-4uM_Round-04 (exp165)
sgRNAs PCR-amplified from genomic DNA


title: Spinner flask No treatment Day 0 Round-09 (exp751)

description:
Library name: SF No treatment D0_Round-09 (exp751)
sgRNAs PCR-amplified from genomic DNA


title: Parthenolide 2.5uM Round-05 (exp238)

description:
Library name: Parthenolide 2.5uM_Round-05 (exp238)
sgRNAs PCR-amplified from genomic DNA

value: Parthenolide 2.5uM


title: Bisphenol A 100uM Round-06 (exp269)

description:
Library name: Bisphenol A 100uM_Round-06 (exp269)
sgRNAs PCR-amplified from genomic DNA

value: Bisphenol A 100uM


title: REDDIT_NANOG_rep1

description: Library name: Sample 3


title: ABBz baseline, rep 4

description: Library name: A7

value: ABBz


title: REDDIT_hESC_ctrl_rep2

description: Library name: Sample 2

value: mCherry-TAG-GFP


title: FK-506 5uM Round-07 (exp358)

description:
Library name: FK-506 5uM_Round-07 (exp358)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line


title: WNT3A 44ng/mL Round-08 (exp537)

description:
Library name: WNT3A 44ng/mL_Round-08 (exp537)
sgRNAs PCR-amplified from genomic DNA

value: WNT3A 44ng/mL


title: Lead acetate 990uM Round-08 (exp496)

description:
Library name: Lead acetate 990uM_Round-08 (exp496)
sgRNAs PCR-amplified from genomic DNA

value: Lead acetate 990uM


title: HCT116 wild-type cells, EHMT2 siRNA, rep1

city: Daejeon

first: In Hwan

last: Tae

address: 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description: Library name: HCT116WT-SiEHMT2

data_processing:
Sequence reads were assessed for quality using FastQC (v0.12.1)
Sequence reads were trimmed for adapter sequences and low-quality bases using cutadapt (v4.9)
Trimmed sequence reads were mapped to GRCh38 using HISAT2(v2.2.1)(default parameters)
Transcript assembly and expression quantification were performed using StringTie(v2.1.1) with the reference annotation.
Assembly: GRCh38(Genome Reference Consortium Human Build 38)
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

source_name: Colon

extract_protocol:
RNA was harvested using Rneasy mini plus kit (250) 1 ug of total RNA was used for the construction of sequencing
RNA libraries ofr RNA-seq were prepared using TruSeq RNA sample prep kit v2 following manufacture's protocols

value: Colon

value: Colorectal carcinoma cell line


title: ABBz round2, rep 1

description: Library name: A9


title: Disulfiram 4.3uM Round-06 (exp281)

description:
Library name: Disulfiram 4.3uM_Round-06 (exp281)
sgRNAs PCR-amplified from genomic DNA

value: Disulfiram 4.3uM


title: Ethanol 0.3% Round-08 (exp437)

description:
Library name: Ethanol 0.3__Round-08 (exp437)
sgRNAs PCR-amplified from genomic DNA

value: Ethanol 0.3%


title: 15.ABBz baseline, rep 4

description: Library name: A8

value: Donor T cells

value: T cell


title: Monensin 300nM Round-08 (exp507)

description:
Library name: Monensin 300nM_Round-08 (exp507)
sgRNAs PCR-amplified from genomic DNA

value: Monensin 300nM


title: Capan1, baseline, rep 1

description: Library name: C1

value: PDAC tumor


title: HCT116 wild-type cells, siRNA control, rep1

description: Library name: HCT116WT-SicONT


title: 15.ABBz baseline, rep 3

description: Library name: A6


title: Spinner flask No treatment Day 2 Round-09 (exp752)

description:
Library name: SF No treatment D2_Round-09 (exp752)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: QNZ 10nM Round-05 (exp241)

description:
Library name: QNZ 10nM_Round-05 (exp241)
sgRNAs PCR-amplified from genomic DNA

value: QNZ 10nM


title: 15.ABBz baseline, rep 2

description: Library name: A4


title: UMK57 600nM Round-03 (exp107)

description:
Library name: UMK57 600nM_Round-03 (exp107)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA

value: UMK57 600nM


title: HCT116 5-FU resistant cells, EHMT2 siRNA, rep1

description: Library name: HCT1165fuR-SiEHMT2


title: DMSO 0.1% Round-07 (exp427)

description:
Library name: Ctl DMSO 0.1_ D8_Round-07 (exp427)
sgRNAs PCR-amplified from genomic DNA

value: DMSO 0.1%


title: ABBz baseline, rep 2

description: Library name: A3

value: ABBz


title: Colchicine 9nM Round-05 (exp215)

description:
Library name: Colchicine 9nM_Round-05 (exp215)
sgRNAs PCR-amplified from genomic DNA

value: Colchicine 9nM


title: Trichostatin A 60nM Round-07 (exp415)

description:
Library name: Trichostatin A 60nM_Round-07 (exp415)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Trichostatin A 60nM


title: HCT116 colorectal cancer cells, wild-type, rep1

description: Library name: HCT116-WT


title: REDDIT_hESC_ctrl_rep1

description: Library name: Sample 1

value: human embryonic stem cell

value: mCherry-TAG-GFP


title: A-395N 10uM Round-05 (exp219)

description:
Library name: A-395N 10uM_Round-05 (exp219)
sgRNAs PCR-amplified from genomic DNA


title: 42oC Round-08 (exp539)

description:
Library name: 42oC_Round-08 (exp539)
sgRNAs PCR-amplified from genomic DNA

value: 42 degrees C


title: Vincristine 0.5nM Round-04 (exp190)

description:
Library name: Vincristine 0.5nM_Round-04 (exp190)
sgRNAs PCR-amplified from genomic DNA

value: Vincristine 0.5nM


title: Patski cells, Day 5, Target 8-9, 30 nM gRNA

city: Pasadena

first: Michael

last: Elowitz

state: CA

address: 1200 E California Blvd

institute: Caltech

description: Library name: D84

data_processing:
hiPSC and Patski samples were aligned with bwa-mem version 0.7.17-rl188 using default settings.
hiPSC and Patski samples were further processed with custom R scripts to retain bases only at base editor target positions and quantify allele frequencies, as well as filter reads with any target base having quality score less than 10.
Samples D1-6, 13-16, 35, 37-45, 56-65, and 76-85 were processed using Crispresso2 version 2.3.3 using default settings.
Assembly: Custom reference sequences were prepared for each sample based on the expected amplicon(s) for each sample.
Supplementary files format and content: "agg*.txt" processed files contain allele frequency information with columns corresponding to each of the 70 A-to-G base editor targets per read, the total number of reads with that pattern in the "freq" column, and the fractional representation of that read in the sample in the "frac_reads" column.
Supplementary files format and content: "*_Alleles_frequency_table.txt" processed files are the Alleles_frequency_table.txt files output by Crispresso2 by default, containing columns for the aligned read sequence for each allele, the reference sequence, the read frequency, the fractional abundance of the allele, and additional columns as described at https://crispresso2.pinellolab.org/help.

organism:
Mus musculus
Mus spretus

source_name: Patski

extract_protocol:
Genomic DNA was extracted using the Qiagen DNeasy Blood and Tissue kit forllowing manufacturer instructions.
Libraries were constructed using PCR to generate amplicons of the desired base editable target including Illumina adapter overhangs.

value: Patski

value: Day 5

value: 30 nM target 8-9 gRNA


title: CHIR-124 40nM Round-06 (exp272)

description:
Library name: CHIR-124 40nM_Round-06 (exp272)
sgRNAs PCR-amplified from genomic DNA

value: CHIR-124 40nM


title: ABBz baseline, rep 3

description: Library name: A5

value: Donor T cells

value: T cell


title: HCT116 5-FU resistant cells, siRNA control, rep1

description: Library name: HCT1165fuR-SicONT

value: Colon

value: Colorectal carcinoma cell line


title: ETC-159 50uM Round-08 (exp480)

description:
Library name: ETC-159 50uM_Round-08 (exp480)
sgRNAs PCR-amplified from genomic DNA


title: Menadione 5uM Round-06 (exp292)

description:
Library name: Menadione 5uM_Round-06 (exp292)
sgRNAs PCR-amplified from genomic DNA

value: Menadione 5uM


title: CI-1040 9.5uM Round-08 (exp472)

description:
Library name: CI-1040 9.5uM_Round-08 (exp472)
sgRNAs PCR-amplified from genomic DNA


title: 15.ABBz round 2, rep 4

description: Library name: A15


title: Patski cells, Day 5, Target 8-10, 30 nM gRNA

description: Library name: D85

value: 30 nM target 8-10 gRNA


title: 15.ABBz baseline, rep 1

description: Library name: A2


title: GSK 626616 14uM Round-08 (exp485)

description:
Library name: GSK 626616 14uM_Round-08 (exp485)
sgRNAs PCR-amplified from genomic DNA


title: Fas-L 44ng/mL Round-08 (exp482)

description:
Library name: Fas-L 44ng/mL_Round-08 (exp482)
sgRNAs PCR-amplified from genomic DNA

value: Fas-L 44ng/mL


title: 15.ABBz round 2, rep 1

description: Library name: A10


title: HCT116 colorectal cancer cells, 5-FU resistant, rep1

description: Library name: HCT116-5fu


title: Spinner flask No treatment D3 Round-04 (exp581)

description:
Library name: SF No treatment D3_Round-04 (exp581)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: No treatment


title: 15.ABBz round 2, rep 3

description: Library name: A13


title: ABBz round 2, rep 4

description: Library name: A16

value: ABBz


title: ABBz round 2, rep 3

description: Library name: A14


title: Spinner flask No treatment Day 2 SF1 Round-08 (exp610)

description:
Library name: SF No treatment D2_SF1_Round-08 (exp610)
sgRNAs PCR-amplified from genomic DNA


title: Bafilomycin A1 9nM Round-08 (exp454)

description:
Library name: Bafilomycin A1 9nM_Round-08 (exp454)
sgRNAs PCR-amplified from genomic DNA

value: Bafilomycin A1 9nM


title: ABBz baseline, rep 1

description: Library name: A1


title: Mdivi-1 15uM Round-05 (exp217)

description:
Library name: Mdivi-1 15uM_Round-05 (exp217)
sgRNAs PCR-amplified from genomic DNA

value: Mdivi-1 15uM


title: Epothilone D 4-6nM Round-05 (exp232)

description:
Library name: Epothilone D 4-6nM_Round-05 (exp232)
sgRNAs PCR-amplified from genomic DNA

value: Epothilone D 4uM, then 6nM


title: Patski cells, Day 5, Target 8-7, 30 nM gRNA

description: Library name: D82

value: Patski

value: 30 nM target 8-7 gRNA


title: ABBz round 2, rep 2

description: Library name: A11


title: Arsenate 40uM Round-06 (exp264)

description:
Library name: Arsenate 40uM_Round-06 (exp264)
sgRNAs PCR-amplified from genomic DNA

value: Arsenate 40uM


title: 15.ABBz round 2, rep 2

description: Library name: A12


title: Patski cells, Day 5, Target 8-6, 30 nM gRNA

description: Library name: D81

value: Day 5

value: 30 nM target 8-6 gRNA


title: Patski cells, Day 5, Target 8-4, 30 nM gRNA

description: Library name: D79

value: 30 nM target 8-4 gRNA


title: Pyridostatin 4uM Round-05 (exp240)

description:
Library name: Pyridostatin 4uM_Round-05 (exp240)
sgRNAs PCR-amplified from genomic DNA

value: Pyridostatin 4uM


title: Patski cells, Day 3, Target 8-10, 30 nM gRNA

description: Library name: D65

value: Day 3


title: Spinner flask No treatment Day 0 Round-04 (exp578)

description:
Library name: SF No treatment D0_Round-04 (exp578)
sgRNAs PCR-amplified from genomic DNA


title: Patski cells, Day 5, Target 8-5, 30 nM gRNA

description: Library name: D80

value: 30 nM target 8-5 gRNA


title: ZLN024 50uM Round-08 (exp538)

description:
Library name: ZLN024 50uM_Round-08 (exp538)
sgRNAs PCR-amplified from genomic DNA

value: ZLN024 50uM


title: GCT_N_300

type: genomic

city: Utrecht

first: Leendert

last: Looijenga

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center

description: Tumor DNA from patient GCT_N_300 with YST

hyb_protocol: Bisulphite converted DNA was amplified, fragmented, and hybridized to human Infinium MethylationEPIC Beadchip (Illumina) using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting.

data_processing:
minfi package in R environment (v4.4.2).
Average beta.

label: Cy3 and Cy5

source_name: Tumor DNA

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using the DNeasy Blood & Tissue Kit (69504, Qiagen)

tag: histology

value: YST

value: Female

tag: location

value: Sacrum

tag: age

tag: gct type

value: Unknown

tag: material

value: Frozen

tag: disease state

value: Germ cell tumor

value: Tumor DNA


title: Patski cells, Day 5, Target 8-8, 30 nM gRNA

description: Library name: D83

value: Patski

value: 30 nM target 8-8 gRNA


title: Beta-Estradiol 550nM Round-07 (exp425)

description:
Library name: Beta-Estradiol 550nM_Round-07 (exp425)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Beta-Estradiol 550nM


title: Rotenone 70nM Round-08 (exp431)

description:
Library name: Rotenone 70nM_Round-08 (exp431)
sgRNAs PCR-amplified from genomic DNA

value: Rotenone 70nM


title: GCT_N_248

description: Tumor DNA from patient GCT_N_248 with DG

value: DG

value: Ovary

value: II

tag: tissue


title: Olaparib 4uM Round-08 (exp512)

description:
Library name: Olaparib 4uM_Round-08 (exp512)
sgRNAs PCR-amplified from genomic DNA

tag: cell type

value: Olaparib 4uM


title: Glyphosate 1000uM Round-06 (exp283)

description:
Library name: Glyphosate 1000uM_Round-06 (exp283)
sgRNAs PCR-amplified from genomic DNA

value: Glyphosate 1000uM


title: BVD-523 15uM Round-02 (exp67)

description:
Library name: BVD-523 15uM_Round-02 (exp67)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA


title: GCT_N_302

description: Tumor DNA from patient GCT_N_302 with TE

value: TE


title: Patski cells, Day 5, Target 8-2, 30 nM gRNA

description: Library name: D77

value: Day 5

value: 30 nM target 8-2 gRNA


title: Patski cells, Day 5, Target 8-3, 30 nM gRNA

description: Library name: D78

value: 30 nM target 8-3 gRNA


title: Patski cells, Day 5, Target 8-1, 30 nM gRNA

description: Library name: D76

value: 30 nM target 8-1 gRNA


title: Epothilone B 1.5nM Round-05 (exp231)

description:
Library name: Epothilone B 1.5nM_Round-05 (exp231)
sgRNAs PCR-amplified from genomic DNA

value: Epothilone B 1.5nM


title: THZ531 0.11-0.175uM Round-07 (exp413)

description:
Library name: THZ531 0.11-0.175uM_Round-07 (exp413)
sgRNAs PCR-amplified from genomic DNA


title: GCT_N_059

description: Tumor DNA from patient GCT_N_059 with TE

value: Male

value: Testis

value: I

value: Frozen

value: Germ cell tumor

value: Tumor DNA


title: Spinner flask No treatment Day 4 Round-09 (exp753)

description:
Library name: SF No treatment D4_Round-09 (exp753)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: No treatment


title: Patski cells, Day 3, Target 8-7, 30 nM gRNA

description: Library name: D62

value: Patski

value: Day 3

value: 30 nM target 8-7 gRNA


title: Rapamycin 2uM Cyclosporin A 3uM Round-07 (exp307)

description:
Library name: Rapamycin 2uM_Cyclosporin A 3uM_Round-07 (exp307)
sgRNAs PCR-amplified from genomic DNA

value: Rapamycin 2uM and Cyclosporin A 3uM


title: GCT_N_249

description: Tumor DNA from patient GCT_N_249 with GER

value: GER

value: Female

value: CNS

value: II


title: Geldanamycin 10nM Round-05 (exp235)

description:
Library name: Geldanamycin 10nM_Round-05 (exp235)
sgRNAs PCR-amplified from genomic DNA

value: Geldanamycin 10nM


title: Vemurafenib 6.6uM Round-08 (exp434)

description:
Library name: Vemurafenib 6.6uM_Round-08 (exp434)
sgRNAs PCR-amplified from genomic DNA

value: Vemurafenib 6.6uM


title: GCT_N_247

description: Tumor DNA from patient GCT_N_247 with DG

value: DG

value: Ovary


title: HMS-I2 10uM Round-06 (exp288)

description:
Library name: HMS-I2 10uM_Round-06 (exp288)
sgRNAs PCR-amplified from genomic DNA

value: HMS-I2 10uM


title: Phenformin 20uM Round-05 (exp212)

description:
Library name: Phenformin 20uM_Round-05 (exp212)
sgRNAs PCR-amplified from genomic DNA

value: Phenformin 20uM


title: Patski cells, Day 3, Target 8-5, 30 nM gRNA

description: Library name: D60

value: 30 nM target 8-5 gRNA


title: Patski cells, Day 3, Target 8-9, 30 nM gRNA

description: Library name: D64

value: 30 nM target 8-9 gRNA


title: LLY-283 2.6uM Round-06 (exp290)

description:
Library name: LLY-283 2.6uM_Round-06 (exp290)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line


title: 5-Azacytidine 2uM Round-07 (exp330)

description:
Library name: 5-Azacytidine 2uM_Round-07 (exp330)
sgRNAs PCR-amplified from genomic DNA

value: 5-Azacytidine 2uM


title: PT 1 25uM Round-07 (exp392)

description:
Library name: PT 1 25uM_Round-07 (exp392)
sgRNAs PCR-amplified from genomic DNA

value: PT 1 25uM


title: No treatment Round-04 (exp195)

description:
Library name: Ctl No treatment D8_Round-04 (exp195)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: Patski cells, Day 3, Target 8-3, 30 nM gRNA

description: Library name: D58

value: Patski

value: Day 3

value: 30 nM target 8-3 gRNA


title: Patski cells, Day 3, Target 8-8, 30 nM gRNA

description: Library name: D63

value: 30 nM target 8-8 gRNA


title: Patski cells, Day 3, Target 8-6, 30 nM gRNA

description: Library name: D61

value: 30 nM target 8-6 gRNA


title: 35oC Round-06 (exp302)

description:
Library name: 35oC_Round-06 (exp302)
sgRNAs PCR-amplified from genomic DNA

value: 35 degrees C


title: GCT_N_056

description: Tumor DNA from patient GCT_N_056 with TE

value: TE

value: Female

value: I

value: Frozen

value: Germ cell tumor

value: Tumor DNA


title: Patski cells, Day 3, Target 8-2, 30 nM gRNA

description: Library name: D57

value: 30 nM target 8-2 gRNA


title: ABT-702 5uM Cobalt 18uM Round-07 (exp320)

description:
Library name: ABT-702 5uM_Cobalt 18uM_Round-07 (exp320)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: ABT-702 5uM and Cobalt 18uM


title: Patski cells, Day 3, Target 8-1, 30 nM gRNA

description: Library name: D56

value: 30 nM target 8-1 gRNA


title: GCT_N_053

description: Tumor DNA from patient GCT_N_053 with TE

value: Ovary


title: LLY-284 2.6uM Round-06 (exp291)

description:
Library name: LLY-284 2.6uM_Round-06 (exp291)
sgRNAs PCR-amplified from genomic DNA


title: GCT_N_057

description: Tumor DNA from patient GCT_N_057 with YST

value: YST

value: Retroperitoneum


title: Demecolcine 30nM Round-05 (exp228)

description:
Library name: Demecolcine 30nM_Round-05 (exp228)
sgRNAs PCR-amplified from genomic DNA

value: Demecolcine 30nM


title: Patski cells, Day 3, Target 8-4, 30 nM gRNA

description: Library name: D59

value: Patski

value: Day 3

value: 30 nM target 8-4 gRNA


title: GCT_N_058

description: Tumor DNA from patient GCT_N_058 with TE

value: TE

value: Male

value: CNS


title: PFI-2 4uM Round-05 (exp239)

description:
Library name: PFI-2 4uM_Round-05 (exp239)
sgRNAs PCR-amplified from genomic DNA

value: PFI-2 4uM


title: GCT_N_055

description: Tumor DNA from patient GCT_N_055 with YST

value: Female

value: Sacrum

value: I

value: Frozen

value: Germ cell tumor


title: GCT_N_246

description: Tumor DNA from patient GCT_N_246 with GER

value: GER

value: II

value: Tumor DNA


title: Patski cells, Day 1, Target 8-10, 30 nM gRNA

description: Library name: D45

value: Day 1

value: 30 nM target 8-10 gRNA


title: Fluvastatin 2.2uM Round-06 (exp282)

description:
Library name: Fluvastatin 2.2uM_Round-06 (exp282)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Fluvastatin 2.2uM


title: Tanespimycin 14uM Round-08 (exp527)

description:
Library name: Tanespimycin 14uM_Round-08 (exp527)
sgRNAs PCR-amplified from genomic DNA

value: Tanespimycin 14uM


title: Benzoate 10000uM Round-08 (exp455)

description:
Library name: Benzoate 10000uM_Round-08 (exp455)
sgRNAs PCR-amplified from genomic DNA

value: Benzoate 10000uM


title: Spinner flask No treatment Day 8 Round-09 (exp755)

description:
Library name: SF No treatment D8_Round-09 (exp755)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: Spinner flask No treatment Day 4 Round-05 (exp590)

description:
Library name: SF No treatment D4_Round-05 (exp590)
sgRNAs PCR-amplified from genomic DNA


title: Apcin 50-100uM Round-04 (exp176)

description:
Library name: Apcin 50-100uM_Round-04 (exp176)
sgRNAs PCR-amplified from genomic DNA

value: Apcin 50uM, then 100uM


title: GCT_N_051

description: Tumor DNA from patient GCT_N_051 with TE

value: TE

value: Ovary


title: GCT_N_052

description: Tumor DNA from patient GCT_N_052 with TE

value: Female


title: Patski cells, Day 1, Target 8-9, 30 nM gRNA

description: Library name: D44

value: Patski

value: 30 nM target 8-9 gRNA


title: GCT_N_054

description: Tumor DNA from patient GCT_N_054 with TE

value: I

value: Frozen

value: Germ cell tumor


title: GCT_N_301

description: Tumor DNA from patient GCT_N_301 with TE

value: Unknown

value: Tumor DNA


title: Thimerosal 850nM Round-08 (exp529)

description:
Library name: Thimerosal 850nM_Round-08 (exp529)
sgRNAs PCR-amplified from genomic DNA

value: Thimerosal 850nM


title: Vemurafenib 6.6uM Round-02 (exp89)

description:
Library name: Vemurafenib 6.6uM_Round-02 (exp89)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Vemurafenib 6.6uM


title: GCT_N_050

description: Tumor DNA from patient GCT_N_050 with TE

value: Mediastinum


title: Tenofovir 10uM Round-07 (exp405)

description:
Library name: Tenofovir 10uM_Round-07 (exp405)
sgRNAs PCR-amplified from genomic DNA

value: Tenofovir 10uM


title: Dorsomorphin 5uM Round-07 (exp357)

description:
Library name: Dorsomorphin 5uM_Round-07 (exp357)
sgRNAs PCR-amplified from genomic DNA

value: Dorsomorphin 5uM


title: Patski cells, Day 1, Target 8-8, 30 nM gRNA

description: Library name: D43

value: Day 1

value: 30 nM target 8-8 gRNA


title: GCT_N_001

description: Tumor DNA from GCT patient: GCT_N_001

value: MIX

value: Male

value: Testis

value: II


title: GCT_N_321

description: Tumor DNA from GCT patient: GCT_N_321


title: Spinner flask No treatment Day 8 Round-04 (exp584)

description:
Library name: SF No treatment D8_Round-04 (exp584)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: Caffeine 2600uM Round-08 (exp463)

description:
Library name: Caffeine 2600uM_Round-08 (exp463)
sgRNAs PCR-amplified from genomic DNA

value: Caffeine 2600uM


title: GCT_N_236

description: Tumor DNA from GCT patient: GCT_N_236

value: YST

value: Female

value: Ovary

value: FFPE

value: Germ cell tumor


title: Patski cells, Day 1, Target 8-7, 30 nM gRNA

description: Library name: D42

value: Patski

value: 30 nM target 8-7 gRNA


title: Patski cells, Day 1, Target 8-2, 30 nM gRNA

description: Library name: D37

value: 30 nM target 8-2 gRNA


title: Patski cells, Day 1, Target 8-4, 30 nM gRNA

description: Library name: D39

value: 30 nM target 8-4 gRNA


title: Spinner flask No treatment Day 8 SF1 Round-08 (exp616)

description:
Library name: SF No treatment D8_SF1_Round-08 (exp616)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line


title: Aphidicolin 400nM Round-08 (exp440)

description:
Library name: Aphidicolin 400nM_Round-08 (exp440)
sgRNAs PCR-amplified from genomic DNA

value: Aphidicolin 400nM


title: Genistein 15uM Round-07 (exp360)

description:
Library name: Genistein 15uM_Round-07 (exp360)
sgRNAs PCR-amplified from genomic DNA

value: Genistein 15uM


title: Combretastatin A4 0.002-0.003uM Round-04 (exp179)

description:
Library name: Combretastatin A4 0.002-0.003uM_Round-04 (exp179)
sgRNAs PCR-amplified from genomic DNA

value: Combretastatin A4 0.002uM, then 0.003uM


title: DMSO 0.1% Round-09 (exp747)

description:
Library name: Ctl DMSO 0.1_ D8_Round-09 (exp747)
sgRNAs PCR-amplified from genomic DNA

value: DMSO 0.1%


title: INK128 200nM Round-02 (exp70)

description:
Library name: INK128 200nM_Round-02 (exp70)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA