title: HCI_ATAC_DMSO_Rep2

city: Salt Lake City

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

institute: University of Utah

description: Library name: Sample 2

data_processing:
Libraries were sequenced on a NovaSeq X at a depth of ~50 million reads/sample and reads were trimmed to 50 bp.
Reads were aligned to the hg19 build of the human genome using Bowtie: -m1 -t -best -q -S -l 32 -e 80 -n 2
SAMtools was used to sort and convert SAM files to BAM files
MACS2 was used to call peaks with a P-value cutoff of 1x10-10 and mfold parameter between 15 and 100
Assembly: hg19
Supplementary files format and content: BigWig files
Supplementary files format and content: narrowPeak files from MACS2

growth_protocol: Cells were cultured in full serum media: RPMI-1640 with 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were incubated at 37°C with 5% CO2 for the duration of all experiments. 5 days prior to treatment, cells were placed in hormone deprived media: phenol-red free RPMI-1640 media (Thermo Fisher Scientific) with 10% charcoal-dextran stripped fetal bovine serum (Thermo Fisher Scientific) and 1% penicillin-streptomycin.

extract_protocol:
Cells (~100,000/sample) were washed with 250 µL of ice-cold 1X PBS, pH 7.4 (Thermo Scientific; 10010072). The cells were then centrifuged at 500 x g for 5 minutes at 4°C, the supernatant was aspirated, and the resulting cell pellet was resuspended in 50 µL of lysis buffer containing the following: 10 mM Tris-HCl, pH 7.4 (Sigma-Aldrich; T2194), 3 mM MgCl2 (Sigma-Aldrich; M1028), 10 mM NaCl (Sigma-Aldrich; 71386), 0.1% NP-40 (Millipore Sigma; 492016), 0.1% Tween-20 (Bio-Rad; 1610781), and 0.01% digitonin (Invitrogen; BN20061). Samples were then lysed via incubation on ice for 5 minutes and centrifuged at 500 x g for 5 minutes at 4°C.  Following lysis, 1 mL of wash buffer (10 mM Tris-HCl, pH 7.4, 3 mM MgCl2, 10 mM NaCl, and 0.1% Tween-20) was added to each sample, which was then centrifuged at 500 x g for 5 minutes at 4°C. The supernatant was aspirated, and the resulting cell pellet was resuspended a second time in 1 mL of wash buffer. To pellet nuclei, cells were centrifuged at 500 x g for 10 minutes at 4°C. The supernatant was aspirated, and each resulting nuclei pellet was resuspended in transposition buffer containing the following: 10 mM Tris-HCl, pH 8.0, 5 mM MgCl2, 10% Dimethylformamide (Fisher Bioreagents; BP1160), and 1 µL of TDE1 Tagment DNA enzyme per sample (Illumina; 20034197) diluted in PBS, pH 7.4. For the transposition reaction, nuclei were incubated at 37°C for 30 minutes in an Eppendorf ThermoMixer C (EP5382000015) set to rotate at 1000 RPM. Following transposition, DNA was purified using the Zymo DNA Clean & Concentrator-5 kit (D4014) according to the manufacturer’s instructions with a binding buffer to sample ratio of 5:1.
The purified DNA was then amplified by PCR using a final concentration of 1X Phusion Master Mix (New England Biolabs; M0530), and 200 nM each of forward and reverse barcode primers. Amplified libraries were purified using a 1:1 volume ratio of AMPure XP beads (Beckman Coulter; A63882) and fragment size distribution and quality were assessed using a High-Sensitivity D1000 ScreenTape assay.

treatment_protocol: Cells were treated with 0.1% DMSO for one hour

value: endometrial adenocarcinoma

tag: treatment

value: DMSO


title: Input_Ascl1_WT_D2_rep3

status: Public on Jun 02 2026

type: SRA

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 415/420 Clinical Research Building (CRB)

country: USA

institute: University of Pennsylvania

description: Library name: 18_Input_WT_D2_rep3_S1

library_source: genomic

data_processing:
Index creation: human hg19 genome assemblies were used for bowtie2 index with bowtie2-build -f.
Alignment: FASTQs were aligned to the hg19 with bowtie2 v2.3.4.1 -p 16 --local -X 1000.
Filtering: unmapped/unpaired reads were filtered out using samtools v1.1 view -bS -h -f 3
PCR duplicates removal were performed using PICARD: picard.jar MarkDuplicates REMOVE_DUPLICATES=True ASSUME_SORT_ORDER=queryname
Track creation: bigWig files of ChIP and Input samples were created using deeptools 3.5.1: bamCoverage --normalizeUsing RPGC --extendReads
Input Subtracted tracks: Input subtracted ChIP-seq bigWig files were created using deeptools 3.5.1: bigwigCompare --operation subtract
Peak calling: narrow peaks were called using macs2 2.2.7.1 callpeak -f BAMPE -g hs --qvalue 0.01 --keep-dup all
The macs2 narrow peaks for each sample and PCR duplicates removed bam files were used in Differential Peak analysis using R/4.3 DiffBind package.
Assembly: GRCh37/hg19
Supplementary files format and content: BigWig files ending in *.bw were input subtrated as indicated above.
Supplementary files format and content: The table DiffBind_consensus_peaks.Named.bed is the conensus peak sets generated by the DiffBind differential peak analysis.

molecule: genomic DNA

organism: Homo sapiens

source_name: hBJ fibroblast

growth_protocol: The human fibrobalst cells were cultured at 37°C incubator at 5% CO2 in fibroblast medium with DMEM, 10% TET-free FBS, 2mM GlutaMax and 1x Non-essential amino acids. When  reaching 85 - 95% confluency, cells were plated at 1:3 to 1:5, and passaged every 3-5 days.

extract_protocol:
The crosslinked cells were incubated with lysis buffer 1 (50 mM HEPES-KOH, pH7.5, 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1 mM DTT, and 1x complete protease inhibitors cocktail) and lysis buffer 2 (10 mM Tis-HCl, pH8, 200 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 1x complete protease inhibitors cocktail) for 5 minutes each at 4 °C. The nuclei were then washed once in the lysis buffers 3 (10 mM Tis-HCl, pH8, 200 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 1 mM DTT, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1x complete protease inhibitors cocktail) on ice, followed by centrifugation at 1350g for 5 minutes. The nuclei pellets were sonicated in lysis buffer 3 with Covaris (Incident peak power: 140; Duty Cycle: 5; Burst/Cycle: 200) for 10 minutes at 4 °C. The sonicated chromatin was collected and supplemented with 1% Triton before centrifuging at 20,000g for 20 minutes. The soluble chromatin were collected, and 20 μl chromatin was de-crosslinked in 200 μl elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS) at 65 °C over night and the rest was aliquoted, snap frozen in liquid nitrogen and stored in -80 °C freezer. The de-crosslinked chromatin was treated with proteinase K and RNase, followed by ethanol precipitation and DNA was resuspended in nuclease-free H2O. For V5-Ascl1 ChIP-seq, 50 μg of chromatin was combined with 40 μl pre-wahed Protein G Dynabeads and 4 μg of V5 (Thermo Fisher, R960-25) on a rotating wheel at 4 °C overnight. The chromatin-antibody-dynabead slurry was then washed 5 times with RIPA buffer (50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1mM EDTA, 1% NP40, 0.7% Na-Deoxycholate, 1x complete protease inhibitors cocktail) and once with TE (10 mM Tris-HCl, pH 8.0, 1mM EDTA). The chromatin was eluted in the elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA and 1% SDS) and de-crosslinked at 65 °C overnight, followed by proteinase and RNase treatment and ethanol precipitation. The DNA concentration was quantified with Qubit HS DNA kit and stored in -20 °C.
ChIP-seq DNA libraries were prepared with NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645), following the manufacturer’s instructions. Briefly, 10 ng of Input DNA and all ChIP DNA were used for library construction and amplified with 10 and 13 PCR cycles respectively for Input and ChIP samples. The PCR products were purified with Ampure XP beads and the distribution of the library DNA were analyzed using High Sensitivity D1000 DNA ScreenTape (Agilent, 5067-5584) on Agilent Tapestation 4150.

treatment_protocol: For ChIP-seq experiments, cells were plated at 2 million cells per 15cm dish, and induced with 0.5 μg/mL dox for 48 hrs before being fixed with 1% Formaldehyde for 10 minutes at room temperature (RT), followed by quenching with 0.125 M glycine for 5 minutes at RT. Cells were then washed with ice-cold DPBS for 3 times, and incubated with swelling buffer (25 mM HEPES, pH 7.9, 1.5 mM MgCl, 10 mM KCl, 0.1 % NP-40 and 1x Proteinase inhibitor cocktail) at 4 °C for 10 minutes, before being scraped and collected by centrifugation at 3000 g for 5 minutes at 4 degree. The cell pellets were snap frozen in liquid nitrogen, and stored in -80 degree for storage.

tag: cell line

value: hBJ fibroblast

tag: cell type

value: human fribroblast

tag: genotype

value: Doxycycline day2

tag: antibody

tag: replicate

tag: matching input


title: BAT_WT_7538

city: Leipzig

first: Alexander

last: Jais

address: Philipp-Rosenthal-Straße 27

country: Germany

institute: Helmholtz Institute for Metabolic, Obesity, and Vascular Research (HI-MAG)

description: Library name: WT_7538

library_source: transcriptomic

data_processing:
The trimmed reads were aligned to the reference genome using HISAT2 v2.0.5, which generated a database of splice junctions from the gene model annotation file to improve alignment quality.
Gene expression levels were quantified using featureCounts v1.5.0-p3, with results expressed in FPKM (Fragments Per Kilobase of transcript per Million mapped reads) to normalize for gene length and sequencing depth.
For differential gene expression analysis, DESeq2 was employed for groups with biological replicates. Criteria for differential expression included log2 fold change > 0.5 and adjusted p-value < 0.05.
Assembly: GRCm39 (mm39)
Supplementary files format and content: Fully processed data file (tab-delimited csv.file)

molecule: polyA RNA

organism: Mus musculus

source_name: Intrascapular brown adipose tissue

extract_protocol:
RNeasy Lipid Tissue Mini Kit (Qiagen)
Fragmentation was followed by the synthesis of the first strand cDNA using random hexamer primers, and the second strand cDNA was synthesized using dUTP to ensure strand specificity. The resulting cDNA libraries underwent end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Library quality was confirmed using Qubit for quantification, real-time PCR, and bioanalyzer for size distribution.

treatment_protocol: Intrascapular subcutaneous BAT depot - harvested one hour after CNO injection

tag: tissue

value: Intrascapular brown adipose tissue

value: Wildtype

value: 1 hour CNO


title: ChIP_Ascl1_allRs_D2_rep2

description: Library name: 25_V5_allRs_D2_rep3_S8

value: V5 (Thermo Fisher, R960-25)


title: DonorE cells perturbed with CD3G knockdown by CRISPRi in batch Rep2 collected 48 hrs after restimulation

city: Palo Alto

first: Lattice

last: Data Coordination

state: CA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim48hr_Rep2_CD3G
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

data_processing:
Quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32. Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file.
Assembly: GRCh38, GENCODE48
Supplementary files format and content: processed data format:csv, processed data content: raw counts, normalized counts (CPM)

source_name: blood

growth_protocol: Naive human CD4+ T cells were isolated isolated with the EasySep Human Naive CD4+ T Cell Isolation Kit (catalog no. #19555, STEMCELL Technologies) according to the manufacturer’s protocol from PBMC-enriched leukapheresis products (Leukopaks, STEMCELL Technologies, catalog no. 70500) from healthy donors, after institutional review board–approved informed written consent (STEMCELL Technologies). At day 0, primary naive human CD4+ T cells were seeded at 1 x 106 cells/ml in cXVIVO and 200 IU/ml IL-2 at 150µL/well in 96-well flat bottom plates. Cells were activated using ImmunoCult human CD3/CD28/CD2 T cell activator at 25 µl/ml. The next morning, cells were transduced with 2% v/v concentrated ZIM3KRAB-dCas9-BlastR lentivirus. In the afternoon, cells in each well were transduced with a distinct, individual single gRNA expressing lentivirus at 2% v/v. On day 3, cells were split to ~5 x 105 cells/mL and Blasticidin was added at 10 µg/mL final concentration. At day 5, cells were centrifuged and resuspended with cXVIVO supplemented with 200 IU/mL IL-2, 5 ng/mL IL-7 and 10 µg/mL blasticidin at ~5 x 105 cells/mL. At day 7, cells were counted and diluted to 1 x 106 cells/mL with cXVIVO supplemented with 200 IU/mL IL-2, 5 ng/mL IL-7 and 10 µg/mL blasticidin. At day 8 and day 10, cells were centrifuged and resuspended at 1 x 106 cells/mL with cXVIVO supplemented with 200 IU/mL IL-2 and 5 ng/mL IL-7. On day 12 morning, cells were centrifuged and resuspended at 2 x 106 cells/ml with cXVIVO supplemented with 200 IU/mL IL-2 and 12.5 µL/mL ImmunoCult human CD3/CD28/CD2 T cell activator for 8 hours or 48 hours.

extract_protocol:
Cells were centrifuged and resuspended in DNA/RNA Shield (Zymo Research) and sent for bulk RNAseq by Plasmidsaurus.
plasmidsaurus library preparation - conversion of mRNA into complementary DNA via reverse transcription and second-strand synthesis, followed by tagmentation, library indexing, and amplification.

treatment_protocol: 200 IU/mL IL-2 and 12.5 µL/mL ImmunoCult human CD3/CD28/CD2 T cell activator for 8 hours and 48 hours.

value: blood

value: CD4-positive, alpha-beta T cells

value: 48 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown of CD3G

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: O+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: HCI_ATAC_DMSO_Rep1

first: Jason

description: Library name: Sample 1

tag: cell line

tag: cell type

value: endometrial adenocarcinoma

tag: treatment

value: DMSO


title: Input_Ascl1_WT_D2_rep2

description: Library name: 31_Input_WT_D2_rep2_S2

value: hBJ fibroblast

value: human fribroblast

tag: genotype

value: Doxycycline day2

tag: antibody

tag: replicate

tag: matching input


title: M20 PD-1 treatment

city: Hirataka

first: Takashi

last: Yamaguchi

state: Osaka

address: Shinmachi 2-3-1

department: Gastroenterology and Hepatology

country: Japan

institute: Kansai Medical University

description: Library name: Sample 4

data_processing:
MGI DNBseq-G400 FAST was used to perform the amplicons deep sequencing following the standard operation protocol. The sequence format was 150bp pair read for all samples.
All sequencing reads were trimmed low-quality bases and adapters with Trimmomatic (v.0.38) .
Raw counts for each gene were estimated in each sample using RSEM version 1.3.0 and Bowtie 2. Calculation of the log fold-change (log FC) and p-value were performed using edgeR.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

molecule: total RNA

source_name: Liver

extract_protocol:
The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using MGIEasy rRNA Depletion Kit and MGIEasy RNA Directional Library Prep Set  according protocols

tag: tissue

value: Liver

tag: disease model

value: HFD/CCl4-induced MASH model

value: Anti-PD-1 antibody


title: DonorE cells perturbed with ATP2A3 knockdown by CRISPRi in batch Rep2 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim48hr_Rep2_ATP2A3
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

value: 48 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown of ATP2A3

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: O+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease


title: ME_SETDB1.SUV39H1.H2-CRISPRi-Dox.3d_MEKi.1d_RNA_A5.R2

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

description:
Library name: ME_MTase.TKD-MEKi.1d_RNA_Rep2
featureCount-SETDB1.xlsx

data_processing:
Sequencing reads were aligned to combined genome of hg38 and dm6. Only uniquely mapped reads were retained for downstream analysis.
Read count mapped to each gene was measured using featureCounts with options ‘-O --fracOverlap 0.8’.
Assembly: hg38 + dm6
Supplementary files format and content: Excel file containing read counts per human genes. Columns names matche with sample titles.

source_name: human induced pluripotent stem cells

growth_protocol: Human induced pluripotent stem cells (72.3, male, RRID: CVCL_A1BW) were obtained from the CCHMC Pluripotent Stem Cell Facility (PSCF) and cultured under feeder-free condition in mTeSR1 medium (85850, StemCell Technologies) on plates coated with either hESC-qualified Matrigel (354277, Corning) or Cultrex Stem Cell Qualified Reduced Growth Factor Basement Membrane Extract (3434-010-02, Biotechne). hPSCs were cultured in a humidified incubator at 37℃ with 5% CO2.

extract_protocol:
1.0x106 cultured cells were dissociated into single cells using Accutase and were mixed with 100,000 Drosophila Schneider 2 (S2) cells for a spike-in control. Cells were lysed with Aurum Total RNA Lysis Solution (7326802, BioRad). Total RNA was extracted using Aurum™ Total RNA Mini Kit (7326820, BioRad).
The sequencing libraries were prepared by Novogene or Plasmidsaurus

treatment_protocol:
For definitive endoderm (DE) differentiation, hPSCs were plated on Matrigel- or Culturex SCQ-coated plates (dilution factor as per hPSC culture) one day before induction. For ME induction, hPSCs were cultured in CDM2 medium supplemented with 100 ng/ml ActivinA, 2 uM CHIR99021, and 50 nM PI103 (SML0559-5MG, Sigma-Aldrich) for 24 hours. For subsequent DE differentiation, ME cells were briefly washed with DMEM/F12 and cultured in CDM2 medium supplemented with 100 ng/ml ActivinA and 250 nM LDN193189 for 24 hours.
For neuroectoderm (NE) differentiation, hPSCs were plated on Matrigel- (1:50 dilution) or Culturex SCQ-coated cell culture plates one day before differentiation. NE was induced by E6 medium (A1516401, Thermo Fisher Scientific) supplemented with 500 nM LDN193189 (SML0559-5MG, Sigma-Aldrich), 10 uM, SB431542 (S4317-5MG, Sigma-Aldrich), and 5 uM XAV931 (X3004-5MG, Sigma-Aldrich). Cells were cultured in this medium for 48 hours with daily media changes.
For inhibiting MEK/ERK signaling, cells were treated with 1 uM of PD0325901 (MEK inhibitor; 72182, STEMCELL Technologies) or DMSO (vehicle control) for one or two days during differentiation from hPSC into NE, ME, and DE.
For inducing MTase-TKD/CRISPRi, cells were cultured with 2 uM doxycycline (D9891-5G, Sigma-Aldrich) for 3 days.

tag: cell line

value: human induced pluripotent stem cells

tag: cell type

value: Mesendoderm

tag: treatment

value: Dox for 3 days for MTase-CRISPRi and MEK inhibitor for 2 day


title: M18 control

description: Library name: Sample 3

tag: tissue

tag: disease model

value: Isotype control

tag: replicate


title: Input_Ascl1_WT_D2_rep1

description: Library name: 30_Input_WT_D2_rep1_S1

value: hBJ fibroblast

value: human fribroblast

tag: genotype

value: Doxycycline day2

tag: antibody

tag: matching input


title: ME_SETDB1.SUV39H1.H2-CRISPRi-Dox.3d_MEKi.1d_RNA_A5.R1

description:
Library name: ME_MTase.TKD-MEKi.1d_RNA_Rep1
featureCount-SETDB1.xlsx


title: M17 control

description: Library name: Sample 2

value: Liver

value: HFD/CCl4-induced MASH model


title: DonorE cells perturbed with ATP2A2 knockdown by CRISPRi in batch Rep2 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim48hr_Rep2_ATP2A2
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi knockdown of ATP2A2

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: adult stage

value: TRUE

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: ChIP_Ascl1_WT_D2_rep3

description: Library name: 24_V5_WT_D2_rep3_S7

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: V5 (Thermo Fisher, R960-25)

tag: replicate


title: DonorE cells perturbed with VAV1 knockdown by CRISPRi in batch Rep1 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim48hr_Rep1_VAV1
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

tag: tissue

value: 48 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown of VAV1

tag: donor id

tag: donor age

value: No

value: O+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease


title: ME_SETDB1.SUV39H1.H2-CRISPRi-Dox.3d_DMSO_RNA_A5.R2

description:
Library name: ME_MTase.TKD_RNA_Rep2
featureCount-SETDB1.xlsx

value: human induced pluripotent stem cells

value: Mesendoderm

value: Dox for 3 days for MTase-CRISPRi


title: M16 control

description: Library name: Sample 1

value: Liver

tag: disease model

value: HFD/CCl4-induced MASH model

value: Isotype control


title: ChIP_Ascl1_WT_D2_rep2

description: Library name: 35_V5_WT_D2_rep2_S4

tag: cell line

value: hBJ fibroblast

value: human fribroblast

value: Doxycycline day2

tag: antibody

tag: matching input


title: DonorE cells perturbed with SIK3 knockdown by CRISPRi in batch Rep1 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim48hr_Rep1_SIK3
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: treatment

value: CRISPRi knockdown of SIK3

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: adult stage

value: TRUE

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: ATAC_Ascl1_WT_D4_rep2

description: Library name: 20_ATAC_UAE_WT_D4_rep2_S24

data_processing:
Pipeline overview: data were aligned to human genome assembly hg19 and subsequent analysis was performed with CUT&RUNTools v2.0 (https://github.com/fl-yu/CUT-RUNTools-2.0) using the standard CUT&Tag pipeline.
Read trimming and alignment: reads were trimmed with trimmomatic v0.36 and aligned with bowtie2 v2.4.2.
Read shift: aligned reads were shifted +4bp and -5bp for positive and negative strand reference genome alignments, respectively, to account for the 9-bp duplication created by DNA repair of the nick by Tn5 transposase.
Filtering and peak calling: aligned reads were filtered by size and duplicates were marked; peaks were called using MACS2 v2.2.7.1.
Peak merge: peaks from individual replicates were merged where overlapping.
Track creation: ATACseq bigwig files were generated with deeptools 3.5.1  bamCoverage --normalizeUsing CPM. the nucleosome positioning analysis was performed using NucleoATAC with default settings. Bedgraphs from the smoothed NucleoATAC signals were converted into bigWig format using UCSC Genome Browser's bedGraphToBigWig utility.
Assembly: GRCh37/hg19
Supplementary files format and content: The BED file atac_filtered_clusters.bed contains all ATAC-seq peaks identified through the CUT&RUN Tools pipeline (MACS2 narrow peak calls) which were then merged if overlapping.
Supplementary files format and content: The bigwig files *.bw were generated using deeptools bamCoverage with CPM normalisation.

extract_protocol:
The cells were washed once with DPBS, before incubating directly on the plate with 1 ml of ice-cold ATAC-RSB buffer (10 mM Tris-HCl pH 7.6, 10mM NaCl, 3mM MgCl2) with 0.1% NP40, 0.1% Tween 20, and 0.01% Digitonin for 10 minutes on ice. The nuclei were then scaped and washed once with ATAC-RSB buffer with 0.1% Tween 20, before being pelleted at 500g for 10 minutes at 4°C. The nuclei pellet was incubated with 50 μl transposition mix (25 μl 2x TD buffer, 2.5 μl transposase (120 nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, 5 μl H2O) at 37°C for 30 minutes and mixed in thermomixer at 1000 RPM. The transposition was stopped by adding 250 μl (five volumes) DNA binding buffer to the transposition mix and DNA was purified with Zymo DNA Clean and Concentrator-5 Kit (D4014) and eluted in 21 μl elution buffer.
For library preparation, 5 cycle of pre-amplification was performed, and the DNA concentration was then quantified, followed by an additional 4 cycles of amplifications. The library DNA was purified with Zymo DNA Clean and Concentrator-5 Kit and eluted in 20 μl of H2O, and the library DNA were analyzed using High Sensitivity D1000 DNA ScreenTape (Agilent, 5067-5584) on Agilent Tapestation 4150.

treatment_protocol: For ATAC-seq experiments, cells were plated at 100,000 cells per 6-well, and induced with 0.5 μg/mL dox for 0, 48, 96 and 168 hrs before being colected for ATAC-seq analysis.

value: human fibroblast

tag: genotype

value: WT

tag: time

tag: replicate

value: 0.5μg/ml doxycycline


title: ME_SETDB1.SUV39H1.H2-CRISPRi-Dox.3d_DMSO_RNA_A5.R1

description:
Library name: ME_MTase.TKD_RNA_Rep1
featureCount-SETDB1.xlsx

tag: cell line

value: human induced pluripotent stem cells

value: Mesendoderm

value: Dox for 3 days for MTase-CRISPRi


title: IR-LYC1

city: beijing

first: bio

last: xin

address: Cancer Hospital, No. 17 Nanli, Panjiayuan, Chaoyang District, Beijing

country: China

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description: IR+LYC

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software.
Assembly: Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: intestine

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system
PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: tissue

value: intestine

value: IR-LYC


title: ChIP_Ascl1_WT_D2_rep1

description: Library name: 32_V5_WT_D2_rep1_S3

value: hBJ fibroblast

tag: cell type

value: human fribroblast

tag: treatment

value: Doxycycline day2

tag: antibody

value: V5 (Thermo Fisher, R960-25)

tag: matching input


title: DonorE cells perturbed with Non-targeting control by CRISPRi in batch Rep1 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim48hr_Rep1_NTC
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

value: 48 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi non-targeting control

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: O+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

value: Zymo DNA/RNA Shield


title: ME_SETDB1.SUV39H1.H2-CRISPRi-DMSO.Ctrl_RNA_A5.R2

description:
Library name: ME_Ctrl.DMSO_RNA_Rep2
featureCount-SETDB1.xlsx

tag: cell line

value: human induced pluripotent stem cells

tag: cell type

value: Mesendoderm

tag: treatment

value: Control (DMSO)


title: chr_Dis3_A_3

city: Paris

first: Antonin

last: Morillon

state: Paris

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: Total ribo-depleted RNA from chromatin fraction from CRISPR with DIS3-AID in HCT116 cell line with constitutive expression of TIR1 after 1h with auxin

data_processing:
Reads were mapped on the human genome hg38 with STAR version 2.7.3a, with the following parameters : --outSAMstrandField intronMotif --outSAMattributes All --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 –alignIntronMax 1000000.
New transcripts discovery was performed using Scallop v0.10.5 on each alignment file, with the following parameters : --min_transcript_length_base 200 --library_type "first" --min_splice_bundary_hits 5 --min_transcript_coverage 10 --min_single_exon_coverage 20. The GTF files were merged using the cuffmerge program of cufflinks-2.2.1, then converted in GFF format with gffread, and the 3rd and 9th columns was adapted to gencode format (for further use by featureCounts). Scallop transcripts overlapping gencode v26 were discarded, and the non-overlapping ones were concatenated with gencode v26 in order to obtain an extended annotation.
Read counting for each alignment file was performed using featureCounts version 2.0.0 on the extended annotation (gencode v26 + Scallop transcripts non-overlapping gencode v26), with the following parameters : -F "GTF" -t “gene” -g “gene_id” -p -s 2.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files for each sample, containing the raw read counts for each gene_id

source_name: HCT116 derivative cell line

growth_protocol: HCT116 cell line was grown in McCoy's 5A Modified medium, supplemented with 10% FBS at 37°C, 5% CO2.

extract_protocol:
cells were washed with PBS and scrapped, collected by centrifugation and series of lysis buffers with different salt concentrations were used to isolate subcellular fractions, followed by RNA extraction using Quiazol and miRNase Mini Kit (Quiagen). Obtained RNA was subjected to DNase treatement (Quiagen) and quality control with Bioanalyzer.
Total RNA-seq libraries were prepared with TruSeq Stranded Total RNA Sample Prep Kit (Illumina) and sequenced on NovaSeq - S1

treatment_protocol: auxin was added to cells in concentration 500uM for 1h before RNA extraction

tag: fraction

value: chromatin fraction

value: 1h induction with auxin


title: IR3

description: IR

tag: tissue

value: intestine

value: IR


title: DonorE cells perturbed with MEN1 knockdown by CRISPRi in batch Rep1 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim48hr_Rep1_MEN1
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

value: 48 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown of MEN1

tag: donor id

tag: donor age

tag: sample preservation_method

tag: suspension depletion_factors

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: HuP74A

type: RNA

city: San Francisco

first: Zev

middle: Jordan

last: Gartner

department: PhramChem

institute: UCSF

description:
T2D_merscopeROIinfo.h5ad
MERSCOPE MERFISH spatial transcriptomic profiling of type 2 diabetic adult human pancreatic FFPE tissue using a custom 300-gene panel enriched for extracellular matrix, vascular, endocrine, and stromal-associated genes.

hyb_protocol: Samples were hybridized with the custom MERFISH probe panel followed by sequential rounds of fluorescent readout hybridization and imaging for transcript barcode decoding.

scan_protocol: Samples were imaged using the Vizgen MERSCOPE imaging platform. Images were processed using the Vizgen MERSCOPE pipeline and cell segmentation was performed using Cellpose 2.0.

data_processing:
Detected transcript tables, segmented cell boundaries, cell metadata, and per-sample AnnData (.h5ad) objects were generated using the Vizgen MERSCOPE pipeline and downstream analysis in Scanpy & Squidpy. Integrated annotated AnnData objects containing merged donor datasets, cell-type annotations, dimensionality reduction embeddings, spatial coordinates, and gene program scores were generated following CONCORD integration and downstream clustering analysis. Supplementary series-level files: alldata.h5ad, integrated AnnData object containing all cell types across all ND and T2D donors; ND_merscopeROIinfo.h5ad, all cell types across non-diabetic donors only, with ROI-level annotations and islet area metadata; T2D_merscopeROIinfo.h5ad, all cell types across type 2 diabetic donors only, with ROI-level annotations and islet area metadata; allvascular_cells.h5ad: vascular and stromal-associated populations across all donors used for ECM niche analyses.
Processed files contain transcript spatial coordinates, segmented cell boundaries, annotated cell metadata, normalized expression values, dimensionality reduction embeddings, and cell-type annotations.

source_name: Adult human pancreas FFPE tissue

label_protocol: Target transcripts were labeled using combinatorial barcoded encoding probes and fluorescent readout probes according to the Vizgen MERSCOPE protocol.

extract_protocol: 4-µm FFPE human pancreatic tissue sections were deparaffinized, rehydrated, decrosslinked, conditioned, and hybridized according to the Vizgen MERSCOPE FFPE protocol using a custom 300-gene MERFISH probe panel enriched for extracellular matrix, vascular, endocrine, and stromal-associated genes.

tag: disease state

value: type 2 diabetic

tag: cohort

value: ProteoGeneX (HuP-)

value: pancreas

tag: histology

value: FFPE

tag: Sex

value: Female

tag: age


title: ME_SETDB1.SUV39H1.H2-CRISPRi-DMSO.Ctrl_RNA_A5.R1

description:
Library name: ME_Ctrl.DMSO_RNA_Rep1
featureCount-SETDB1.xlsx

tag: cell line

value: human induced pluripotent stem cells

tag: cell type

value: Mesendoderm

tag: treatment

value: Control (DMSO)


title: IR2

description: IR

tag: tissue

value: intestine

value: IR


title: HuP97A


title: DonorE cells perturbed with LAT knockdown by CRISPRi in batch Rep1 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim48hr_Rep1_LAT
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi knockdown of LAT

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: O+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

value: Zymo DNA/RNA Shield


title: DE_SETDB1.SUV39H1.H2-CRISPRi-Dox.3d_MEKi.2d_RNA_A5.R2

description:
Library name: DE_MTase.TKD-MEKi.2d_RNA_Rep2
featureCount-SETDB1.xlsx

tag: cell line

tag: cell type

value: Definitive Endoderm

value: Dox for 3 days for MTase-CRISPRi and MEK inhibitor for 2 day


title: IR1

description: IR

tag: tissue

tag: treatment


title: HuP93A

tag: disease state

value: type 2 diabetic

tag: cohort

value: ProteoGeneX (HuP-)

value: pancreas

tag: histology

value: FFPE

tag: Sex

value: Male

tag: age


title: DonorE cells perturbed with HEXDC knockdown by CRISPRi in batch Rep1 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim48hr_Rep1_HEXDC
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

value: 48 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown of HEXDC

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: Female

tag: sample preservation_method

tag: suspension depletion_factors

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: NC3

description: control

tag: tissue

value: intestine

tag: treatment

value: NC


title: DE_SETDB1.SUV39H1.H2-CRISPRi-Dox.3d_MEKi.2d_RNA_A5.R1

description:
Library name: DE_MTase.TKD-MEKi.2d_RNA_Rep1
featureCount-SETDB1.xlsx

tag: cell line

value: human induced pluripotent stem cells

tag: cell type

value: Definitive Endoderm

value: Dox for 3 days for MTase-CRISPRi and MEK inhibitor for 2 day


title: HuP61A

description:
T2D_merscopeROIinfo.h5ad
MERSCOPE MERFISH spatial transcriptomic profiling of type 2 diabetic adult human pancreatic FFPE tissue using a custom 300-gene panel enriched for extracellular matrix, vascular, endocrine, and stromal-associated genes. Four ROIs were profiled for this donor. All ROI data are contained within the sample archive

tag: disease state

value: type 2 diabetic

tag: cohort

value: ProteoGeneX (HuP-)

value: pancreas

tag: histology

tag: Sex

tag: age


title: DonorE cells perturbed with GPI knockdown by CRISPRi in batch Rep1 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim48hr_Rep1_GPI
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

value: blood

tag: experimental perturbation

value: CRISPRi knockdown of GPI

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: O+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

value: Zymo DNA/RNA Shield


title: NC2

description: control

tag: tissue

value: intestine

tag: treatment

value: NC


title: DE_SETDB1.SUV39H1.H2-CRISPRi-Dox.3d_DMSO_RNA_A5.R2

description:
Library name: DE_MTase.TKD_RNA_Rep2
featureCount-SETDB1.xlsx

tag: cell line

value: human induced pluripotent stem cells

tag: cell type

value: Definitive Endoderm

value: Dox for 3 days for MTase-CRISPRi


title: HuP51A

tag: disease state

value: type 2 diabetic

tag: cohort

value: ProteoGeneX (HuP-)

tag: histology

value: FFPE

tag: Sex

value: Female

tag: age


title: DonorE cells perturbed with CD3G knockdown by CRISPRi in batch Rep1 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim48hr_Rep1_CD3G
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

value: 48 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown of CD3G

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

tag: sample preservation_method

tag: suspension depletion_factors

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: NC1

description: control

tag: tissue

value: intestine

tag: treatment

value: NC


title: DE_SETDB1.SUV39H1.H2-CRISPRi-Dox.3d_DMSO_RNA_A5.R1

description:
Library name: DE_MTase.TKD_RNA_Rep1
featureCount-SETDB1.xlsx

tag: cell line

value: human induced pluripotent stem cells

tag: cell type

value: Definitive Endoderm


title: RHIP156

description:
ND_merscopeROIinfo.h5ad
MERSCOPE MERFISH spatial transcriptomic profiling of non-diabetic adult human pancreatic FFPE tissue using a custom 300-gene panel enriched for extracellular matrix, vascular, endocrine, and stromal-associated genes.

tag: disease state

value: non-diabetic

tag: cohort

value: UCSF (RHIP-)

value: pancreas

tag: histology

tag: Sex

tag: age


title: DonorE cells perturbed with ATP2A3 knockdown by CRISPRi in batch Rep1 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim48hr_Rep1_ATP2A3
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi knockdown of ATP2A3

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: O+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

value: Zymo DNA/RNA Shield


title: DE_SETDB1.SUV39H1.H2-CRISPRi-DMSO.Ctrl_RNA_A5.R2

description:
Library name: DE_Ctrl.DMSO_RNA_Rep2
featureCount-SETDB1.xlsx

tag: cell line

tag: cell type

tag: treatment

value: Control (DMSO)


title: HuP71A

tag: disease state

tag: cohort

value: ProteoGeneX (HuP-)

tag: tissue

tag: histology

value: FFPE

tag: Sex

value: Male

tag: age


title: ChIP_F1h2a.w(h2a.wsuvh X h2a.wcmt)_H2A.Z_rep4

city: Tokyo

first: Shoko

last: Oda

address: 7-3-1, Hongo, Bunkyo-ku

institute: The University of Tokyo

description: Library name: Sample 71

data_processing:
(WGBS) Raw sequence data were trimmed and quality-filtered using Trimmomatic version 0.33 (Bolger et al., 2014). The trimmed and quality-filtered sequences were mapped to the reference genome (TAIR10; Lamesch et al., 2012), deduplicated and analyzed to extract methylation data using Bismark version 0.10.1 (Krueger et al., 2011).
(ChIP-seq) Raw sequence data were trimmed and quality-filtered using Trimmomatic version 0.33 (Bolger et al., 2014). The trimmed and quality-filtered sequences were mapped to reference genome (TAIR10) using Bowtie (version 1.1.2) with the option -M 1–best (Langmead et al., 2009).
Assembly: TAIR10
Supplementary files format and content: (WGBS) CX_report file, (ChIP-seq) pergene

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Plants were grown at 22°C on MS media with 1% sucrose and 0.8% agar in 16 h light and 8 h dark conditions for 1-2 weeks, and then grown on soil.

extract_protocol:
(WGBS) Genomic DNA was isolated from rosette leaves using Nucleon PhytoPure (Cytiva). (ChIP-seq) eChIP method (Zhao et al., 2020) was performed as described in Mori et al. (2023).
(WGBS) Genomic DNA was fragmented using S220 Focused Ultrasonicator (Covaris) and the size of 300-500bp was gel-extracted. The libraries were prepared using TruSeq DNA LT Sample Prep Kit (Illumina) and KAPA HyperPrep Kit (Kapa Biosystems) and then bisulfite conversion was performed using MethylCode Bisulfite Conversion Kit (Thermo). The libraries were amplified using KAPA HiFi HotStart Uracil ReadyMix (Kapa Biosystems) and purified using SPRIselect (Beckman Coulter). (ChIP-seq) Cross-linking, chromatin fragmentation were performed as Mori et al. (2023). The chromatin was incubated with the antibody overnight at 4°C and Dynabeads Protein G (invitrogen) for 2 hours at 4°C and washed with the buffers described in Zhao et al., 2020. Then the chromatin was incubated with 150 μl of ChIP Elution buffer for 6-9 hours at 65°C. DNA was extracted from the eluted samples with Monarch PCR & DNA Cleanup Kit (NEB) and libraries were constructed with ThruPLEX DNA-Seq Kit (Takara).

value: seedling

tag: genotype


title: DonorE cells perturbed with ATP2A2 knockdown by CRISPRi in batch Rep1 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim48hr_Rep1_ATP2A2
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

value: 48 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown of ATP2A2

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

tag: anticoagulant

tag: sample preservation_method

tag: suspension depletion_factors

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: DE_SETDB1.SUV39H1.H2-CRISPRi-DMSO.Ctrl_RNA_A5.R1

description:
Library name: DE_Ctrl.DMSO_RNA_Rep1
featureCount-SETDB1.xlsx

tag: cell line

value: human induced pluripotent stem cells

tag: cell type

value: Definitive Endoderm

tag: treatment


title: ChIP_F1h2a.w(h2a.wsuvh X h2a.wcmt)_H2A.Z_rep3

description: Library name: Sample 70

tag: tissue

tag: genotype


title: ATAC_Ascl1_WT_D2_rep1

description: Library name: 4_ATAC_UAE_WT_D2_rep1_S8

value: hBJ fibroblast

value: human fibroblast

value: WT

tag: time

tag: replicate

value: 0.5μg/ml doxycycline


title: HuP67A

tag: disease state

value: non-diabetic

tag: cohort

value: ProteoGeneX (HuP-)

value: pancreas

tag: histology

value: FFPE

tag: Sex

value: Male

tag: age


title: DonorD cells perturbed with VAV1 knockdown by CRISPRi in batch Rep2 collected 8 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim8hr_Rep2_VAV1
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

value: 8 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown of VAV1

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: A+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity


title: ChIP_F1h2a.w(h2a.wcmt X h2a.wsuvh)_H2A.Z_rep2

description: Library name: Sample 69

tag: tissue

value: seedling

tag: genotype


title: ME_MEKi.1d_RNA_Rep2

description:
Library name: ME_MEKi.1d_RNA_Rep2
featureCount-MEKi.xlsx
Lib615

tag: cell line

value: human induced pluripotent stem cells

tag: cell type

value: Mesendoderm

tag: treatment

value: MEK inhibitor for 1 days


title: DonorD cells perturbed with SIK3 knockdown by CRISPRi in batch Rep2 collected 8 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim8hr_Rep2_SIK3
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi knockdown of SIK3

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: HuP20A

tag: disease state

value: non-diabetic

tag: cohort

value: ProteoGeneX (HuP-)

value: pancreas

tag: histology

value: FFPE

tag: Sex

value: Male

tag: age


title: ME_MEKi.1d_RNA_Rep1

description:
Library name: ME_MEKi.1d_RNA_Rep1
featureCount-MEKi.xlsx
Lib614

tag: cell line

tag: cell type


title: HuP53A

tag: tissue

value: Female


title: ChIP_F1h2a.w(h2a.wcmt X h2a.wsuvh)_H2A.Z_rep1

description: Library name: Sample 68

tag: genotype


title: DonorD cells perturbed with Non-targeting control by CRISPRi in batch Rep2 collected 8 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim8hr_Rep2_NTC
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

tag: treatment

value: 8 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi non-targeting control

tag: donor id

tag: donor age

tag: donor blood_type

value: A+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity


title: HuP03A

description:
ND_merscopeROIinfo.h5ad
MERSCOPE MERFISH spatial transcriptomic profiling of non-diabetic adult human pancreatic FFPE tissue using a custom 300-gene panel enriched for extracellular matrix, vascular, endocrine, and stromal-associated genes. Two ROIs were profiled for this donor. All ROI data are contained within the sample archive

tag: disease state

value: non-diabetic

tag: cohort

tag: tissue

tag: histology

tag: Sex

tag: age


title: ChIP_h2a.wsuvh_H2A.Z_rep2

description: Library name: Sample 67

value: seedling

tag: genotype

value: hta6 hta7 hta12 suvh4 suvh5 suvh6


title: DE_MEKi.1d_RNA_Rep2

description:
Library name: DE_MEKi.1d_RNA_Rep2
featureCount-MEKi.xlsx
Lib621

tag: cell line

value: human induced pluripotent stem cells

tag: cell type

value: Definitive Endoderm

tag: treatment

value: MEK inhibitor for 1 days


title: DonorD cells perturbed with MEN1 knockdown by CRISPRi in batch Rep2 collected 8 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim8hr_Rep2_MEN1
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

value: blood

tag: experimental perturbation

value: CRISPRi knockdown of MEN1

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: DE_MEKi.1d_RNA_Rep1

description:
Library name: DE_MEKi.1d_RNA_Rep1
featureCount-MEKi.xlsx
Lib620

tag: cell line

tag: cell type


title: ChIP_h2a.wsuvh_H2A.Z_rep1

description: Library name: Sample 66

tag: tissue

tag: genotype


title: HuP31A

tag: disease state

tag: cohort

value: ProteoGeneX (HuP-)

value: pancreas

tag: histology

value: FFPE

tag: Sex

tag: age


title: DonorD cells perturbed with LAT knockdown by CRISPRi in batch Rep2 collected 8 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim8hr_Rep2_LAT
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

value: CD4-positive, alpha-beta T cells

tag: treatment

value: 8 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown of LAT

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: A+

tag: anticoagulant

value: ACDA

value: STEMCELL technologies

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity


title: ME_MEKi.1d_Input_Rep2

description: Library name: ME_MEKi.1d_Input_Rep2

data_processing:
Sequencing reads were aligned to combined genome of hg38 and dm6 using STAR aligner. Only uniquely mapped reads were retained for downstream analysis.
BigWig files were generated using reads aligned to hg38 using bedtools and UCSC toolkit in a RPM scale (*.rpm.bw). For ChIP samples, additional bigwig files were generated by normalizing by spike-in counts, i.e. read per 0.1 million spike-in count (*.rpsm.bw).
Assembly: hg38 + dm6
Supplementary files format and content: bigwig in RPM scale (*.rpm.bw); bigwig in spike-in normalized scale (*.rpsm.bw)

source_name: Mesoendoderm

extract_protocol:
Cells were crosslinked with 1% formaldehyde in 1x PBS for 10 min at room temperature. The crosslinking reaction was quenched by adding 0.125 M glycine for 5 min at room temperature. Crosslinked cells were centrifuged at 600 x g for 5 min at 4°C, and the supernatant was removed. The cell pellet was washed with ice-cold 1x PBS, centrifuged again at 600 x g for 5 min at 4°C, and the supernatant was aspirated. This wash step was repeated once more. The final cell pellet was frozen on dry ice and stored at -80°C until use.  Crosslinked human cells were resuspended in Lysis Buffer1 (10 mM Tris-HCl [pH 8.0], 10 mM NaCl, 0.5% NP-40, and 1x Complete Protease Inhibitor EDTA-free) and incubated on ice for 10 min. For Drosophila S2 spike-in controls, crosslinked S2 cells were resuspended in 100 uL Lysis Buffer1 at a final concentration of 2.0x105 or 4.0x105 cells/uL, and 25% of the S2 cells were mixed with human cells. The mixed cell suspension was centrifuged at 665 x g for 5 min at 4℃, and the supernatant was removed. The cell pellet was then resuspended in Lysis Buffer2 (50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 0.32% SDS, 1x Complete Protease Inhibitor EDTA-free) and incubated on ice for 10 min. The cell lysate was then diluted in IP Dilution Buffer (20 mM Tris-HCl [pH 8.0], 150 mM NaCl, 2 mM EDTA, 1% TritonX-100, 1x Complete Protease Inhibitor EDTA-free) and transferred to a milliTUBE ATA Fiber (Covaris). Chromatin was sonicated using a Covaris S220 (Covaris) for 5.5 min. Insoluble debris was removed by centrifugation at 12,000 x g for 5 min at 4℃. The supernatant containing sonicated chromatin was transferred to a new tube and stored at -80℃ until use.  Dynabeads Protein-G (10004D, Thermo Fisher Scientific) (25 - 80 uL) were washed twice with PBS-T (0.02% Tween-20 in 1x PBS). The desired amounts of H3K9me3 (ab8898, Abcam) antibodies were conjugated to washed Dynabeads by incubating for 2 to 6 hours at 4°C with rotation. Meanwhile, frozen sonicated chromatin was thawed on ice. A desired amount of chromatin (Table S3, based on DNA quantity) was diluted with IP dilution buffer at a 4:1 ratio. Antibody-conjugated Dynabeads were washed twice with IP Dilution Buffer (without protease inhibitor), resuspended in the diluted chromatin, and incubated overnight at 4°C with rotation. The next day, ChIPed beads were washed four times using the following washing buffers: (1) FA Lysis Buffer (50 mM HEPES-KOH [pH 7.5], 150 mM NaCl, 2 mM EDTA, 1% TritonX-100, 0.1% Sodium deoxycholate, 1x Complete protease inhibitor EDTA-free); (2) NaCl Buffer (50 mM HEPES-KOH [pH 7.5], 500 mM NaCl, 2 mM EDTA, 1% TritonX-100, 0.1% Sodium deoxycholate); (3) LiCl Buffer (100 mM Tris-HCl [pH 8.0], 500 mM LiCl, 1% NP-40, 1% Sodium deoxycholate); (4) 10 mM Tris-HCl [pH 8.0]. Following washing steps, chromatin was eluted with TES buffer (50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 1% SDS) for 15 min at 65℃ while shaking at 1,000 rpm in ThermoMixer F1.5 (Eppendorf). The ChIP and Input chromatin were reverse-crosslinked by adding NaCl to a final concentration of 200 mM and incubating for 8 hours at 65°C. Samples were then treated with 50 ng/uL RNaseA (EN0531, ThermoFisher Scientific) for 30 min at 37°C, followed by treatment with 0.2 mg/mL Protease K (03115828001, Roche) for 2 hours at 37°C. DNA was purified using phenol-chloroform extraction, followed by ethanol precipitation. DNA concentration was measured using Quantus fluorometer (Promega).
Multiplexed libraries were prepared from ChIP and Input samples (two replicates) using NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, NEB), following the manufacturer’s protocol with the following modifications. After adaptor ligation, cleanup was performed using AMPure XP Beads (A63880, Beckman Coulter), MagBind Magnetic Beads (M1378-01, Omega), or homemade Sera-mag beads (Rohland et al., Genome Res. 2012) without size selection. After RCR enrichment of the adaptor-ligated library, two rounds of size selection were performed using the AMPure XP Beads or MagBind Magnetic Beads.

treatment_protocol:
For definitive endoderm (DE) differentiation, hPSCs were plated on Matrigel- or Culturex SCQ-coated plates (dilution factor as per hPSC culture) one day before induction. For ME induction, hPSCs were cultured in CDM2 medium supplemented with 100 ng/ml ActivinA, 2 uM CHIR99021, and 50 nM PI103 (SML0559-5MG, Sigma-Aldrich) for 24 hours. For subsequent DE differentiation, ME cells were briefly washed with DMEM/F12 and cultured in CDM2 medium supplemented with 100 ng/ml ActivinA and 250 nM LDN193189 for 24 hours.
For neuroectoderm (NE) differentiation, hPSCs were plated on Matrigel- (1:50 dilution) or Culturex SCQ-coated cell culture plates one day before differentiation. NE was induced by E6 medium (A1516401, Thermo Fisher Scientific) supplemented with 500 nM LDN193189 (SML0559-5MG, Sigma-Aldrich), 10 uM, SB431542 (S4317-5MG, Sigma-Aldrich), and 5 uM XAV931 (X3004-5MG, Sigma-Aldrich). Cells were cultured in this medium for 48 hours with daily media changes.
For inhibiting MEK/ERK signaling, cells were treated with 1 uM of PD0325901 (MEK inhibitor; 72182, STEMCELL Technologies) or DMSO (vehicle control) for one or two days during differentiation from hPSC into NE, ME, and DE.

tag: cell line

value: Mesoendoderm

value: MEKi inhibitor


title: ChIP_h2a.wcmt_H2A.Z_rep2

description: Library name: Sample 65

tag: tissue

value: seedling

tag: genotype

value: hta6 hta7 hta12 cmt2 cmt3


title: DonorD cells perturbed with HEXDC knockdown by CRISPRi in batch Rep2 collected 8 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim8hr_Rep2_HEXDC
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

value: blood

tag: cell type

tag: treatment

tag: experimental perturbation

value: CRISPRi knockdown of HEXDC

value: No

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: ME_MEKi.1d_Input_Rep1

description: Library name: ME_MEKi.1d_Input_Rep1


title: ChIP_h2a.wcmt_H2A.Z_rep1

description: Library name: Sample 64


title: DonorD cells perturbed with GPI knockdown by CRISPRi in batch Rep2 collected 8 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim8hr_Rep2_GPI
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

value: CD4-positive, alpha-beta T cells

value: 8 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

value: CRISPRi knockdown of GPI

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: A+

tag: anticoagulant

value: ACDA

value: STEMCELL technologies

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease


title: ChIP_F1met1(met1cmt X met1suvh)_H2A.W_rep1

description: Library name: Sample 126

tag: tissue

tag: genotype


title: ME_Ctrl.DMSOl_Input_Rep2

description: Library name: ME_Ctrl.DMSOl_Input_Rep2

tag: cell line

value: Mesoendoderm

tag: treatment

value: Ctrl


title: ChIP_h2a.w_H2A.Z_rep2

description: Library name: Sample 63

value: seedling

value: hta6 hta7 hta12


title: ChIP_met1suvh_H2A.W_rep2

description: Library name: Sample 125

value: met1-1 suvh4 suvh5 suvh6


title: DonorD cells perturbed with CD3G knockdown by CRISPRi in batch Rep2 collected 8 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim8hr_Rep2_CD3G
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

value: blood

tag: cell type

tag: experimental perturbation

value: CRISPRi knockdown of CD3G

value: No

tag: source

tag: donor sex

tag: donor dev_stage

value: adult stage

value: TRUE

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types


title: ME_Ctrl.DMSO_Input_Rep1

description: Library name: ME_Ctrl.DMSO_Input_Rep1


title: ChIP_h2a.w_H2A.Z_rep1

description: Library name: Sample 62


title: ChIP_F1met1(met1cmt X met1suvh)_H2A.W_rep2

description: Library name: Sample 127


title: Male, WT, rep5

city: Edmonton

first: Richard

last: Lehner

state: Alberta

address: 315 Heritage Medical Research Centre, 11207 - 87 Ave

department: Pediatrics

country: Canada

institute: University of Alberta

description: Library name: M_WT_5

data_processing:
STAR (version 2.5.2b) was used to align RNA-Seq data to the genome reference; RSEM (version 1.3.0) was used to quantify gene and isoform expression; Ensembl 100 gene annotation GTF was used to build the RSEM reference and to add gene and transcript specific information to the output files.
Differential expression (DE) analysis was performed using R (version 4.4.1) and DESeq2 package (version 1.46.0) with raw counts (gene-level abundances) as input data.
Assembly: mm10
Supplementary files format and content: Raw_counts_matrix.txt is a tab-delimited text file contains unnormalized gene-level read counts for all samples, rows = genes, columns = samples. Sample IDs match the library name field in the metadata.
Supplementary files format and content: TPM_matrix.txt is a tab-delimited text file contains TPM-normalized values for all samples, rows = genes, columns = samples. Sample IDs match the library name field in the metadata.
Supplementary files format and content: DESeq2 differential expression results are provided in three files: DESeq2_male_KO_vs_WT.txt, DESeq2_female_KO_vs_WT.txt, and DESeq2_female_vs_male_WT.txt, each containing Gene_Symbol, baseMean, log2FoldChange, lfcSE, stat, p-value, and adjusted p-value (padj). All files are tab-delimited text.

growth_protocol: 10-week old AADAC KO and WT mice were fed with western-type diet for one week, livers were harvested at fed state.

extract_protocol:
Total RNA was extracted using Trizol, and cleaned up with a RNeasy Mini Kit (Qiagen). Messenger RNA was purified from 700ng-1000ng total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
First-strand cDNA was synthesized from heat-denatured purified mRNA using a Maxima H Minus First Strand cDNA Synthesis kit (Thermo-Fisher) and random hexamer primers, followed by PCR Clean DX (Aline Biosciences) bead purification on a Microlab NIMBUS robot (Hamilton Robotics). The second strand cDNA was synthesized following the NEBNext Ultra Directional Second Strand cDNA Synthesis protocol (NEB) with dUTP incorporation. cDNA fragmented to 250-300bp using Covaris LE220, followed by end-repair, A-tailing, and Illumina adapter ligation. Products digested with USER enzyme and immediately amplified with 10 cycles of indexed PCR using NEBNext Ultra II Q5 polymerase (NEB) and Illumina’s dual index primer set. Final libraries purified, size-selected with PCR Clean DX beads, and QC performed using Agilent DNA 1000 and Qubit quantification before pooling for paired-end 150 bp sequencing.

treatment_protocol: Livers were harvested and snap frozen

value: Liver

tag: Sex

value: Male

value: AADAC WT

value: One week western-type diet, fed state


title: ChIP_met1suvh_H2A.W_rep1

description: Library name: Sample 124


title: ME_MEKi.1d_ChIP_P-ERK_Rep2

description: Library name: ME_MEKi.1d_ChIP_P-ERK_Rep2

value: MEKi inhibitor


title: DonorD cells perturbed with ATP2A3 knockdown by CRISPRi in batch Rep2 collected 8 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim8hr_Rep2_ATP2A3
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

value: CD4-positive, alpha-beta T cells

value: 8 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

value: CRISPRi knockdown of ATP2A3

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: A+

tag: anticoagulant

value: ACDA

value: STEMCELL technologies

value: Female

tag: donor living_at_sample_collection

tag: donor body_mass_index

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: Hispanic

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: ChIP_F1WT(suvh X cmt)_H2A.Z_rep4

description: Library name: Sample 61

tag: tissue

value: seedling

tag: genotype


title: ChIP_met1cmt_H2A.W_rep2

description: Library name: Sample 123

value: met1-1 cmt2 cmt3


title: DonorD cells perturbed with ATP2A2 knockdown by CRISPRi in batch Rep2 collected 8 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim8hr_Rep2_ATP2A2
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

value: blood

tag: cell type

tag: treatment

tag: experimental perturbation

value: CRISPRi knockdown of ATP2A2

value: No

tag: source

tag: donor sex

tag: donor dev_stage

value: adult stage

value: TRUE

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity


title: ME_MEKi.1d_ChIP_P-ERK_Rep1

description: Library name: ME_MEKi.1d_ChIP_P-ERK_Rep1

tag: cell line

value: Mesoendoderm

value: MEKi inhibitor


title: ChIP_F1WT(suvh X cmt)_H2A.Z_rep3

description: Library name: Sample 60


title: ChIP_met1cmt_H2A.W_rep1

description: Library name: Sample 122


title: DonorD cells perturbed with VAV1 knockdown by CRISPRi in batch Rep1 collected 8 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim8hr_Rep1_VAV1
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

value: CD4-positive, alpha-beta T cells

value: 8 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

value: CRISPRi knockdown of VAV1

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: A+

tag: anticoagulant

value: ACDA

value: STEMCELL technologies

tag: donor living_at_sample_collection

tag: genetic perturbation_strategy

tag: enriched cell_types


title: ME_Ctrl.DMSO_ChIP_P-ERK_Rep2

description: Library name: ME_Ctrl.DMSO_ChIP_P-ERK_Rep2

tag: treatment

value: Ctrl


title: ChIP_F1WT(cmt X suvh)_H2A.Z_rep2

description: Library name: Sample 59

tag: tissue

value: seedling

tag: genotype


title: ChIP_met1-1_H2A.W_rep2

description: Library name: Sample 121


title: DonorD cells perturbed with SIK3 knockdown by CRISPRi in batch Rep1 collected 8 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim8hr_Rep1_SIK3
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

value: blood

tag: cell type

tag: experimental perturbation

value: CRISPRi knockdown of SIK3

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: Hispanic

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: ME_Ctrl.DMSO_ChIP_P-ERK_Rep1

description: Library name: ME_Ctrl.DMSO_ChIP_P-ERK_Rep1

tag: cell line

value: Mesoendoderm


title: ChIP_F1WT(cmt X suvh)_H2A.Z_rep1

description: Library name: Sample 58


title: DonorD cells perturbed with Non-targeting control by CRISPRi in batch Rep1 collected 8 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim8hr_Rep1_NTC
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

value: CRISPRi non-targeting control

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

tag: anticoagulant

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity


title: ChIP_met1-1_H2A.W_rep1

description: Library name: Sample 120

tag: tissue

tag: genotype


title: DE_MEKi.2d_ChIP_input_Rep2

description: Library name: DE_MEKi.2d_ChIP_input_Rep2

source_name: Definitive endoderm

value: Definitive endoderm

tag: treatment

value: MEKi inhibitor


title: ChIP_suvh_H2A.Z_rep2

description: Library name: Sample 57

value: seedling

value: suvh4 suvh5 suvh6


title: DE_MEKi.2d_ChIP_input_Rep1

description: Library name: DE_MEKi.2d_ChIP_input_Rep1


title: ChIP_F1met1(met1cmt X met1suvh)_H2A.Z_rep2

description: Library name: Sample 119


title: DonorD cells perturbed with MEN1 knockdown by CRISPRi in batch Rep1 collected 8 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim8hr_Rep1_MEN1
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

value: 8 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown of MEN1

value: A+

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

tag: donor dev_stage

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

tag: genetic perturbation_strategy

tag: enriched cell_types


title: DE_Ctrl.DMSO.2d_ChIP_input_Rep2

description: Library name: DE_Ctrl.DMSO.2d_ChIP_input_Rep2

tag: cell line

value: Ctrl


title: ChIP_suvh_H2A.Z_rep1

description: Library name: Sample 56


title: ChIP_cmt_H2A.Z_rep2

description: Library name: Sample 55

value: cmt2 cmt3


title: ChIP_F1met1(met1cmt X met1suvh)_H2A.Z_rep1

description: Library name: Sample 118


title: DonorD cells perturbed with LAT knockdown by CRISPRi in batch Rep1 collected 8 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim8hr_Rep1_LAT
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

value: CRISPRi knockdown of LAT

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

tag: anticoagulant

value: Female

value: adult stage

tag: donor living_at_sample_collection

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: Hispanic

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: ChIP_met1suvh_H2A.Z_rep2

description: Library name: Sample 117

tag: tissue

value: seedling

tag: genotype

value: met1-1 suvh4 suvh5 suvh6


title: DonorD cells perturbed with HEXDC knockdown by CRISPRi in batch Rep1 collected 8 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim8hr_Rep1_HEXDC
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: treatment

value: 8 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown of HEXDC

tag: source

tag: donor sex

tag: donor dev_stage

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity


title: ChIP_cmt_H2A.Z_rep1

description: Library name: Sample 54

value: cmt2 cmt3


title: ChIP_met1suvh_H2A.Z_rep1

description: Library name: Sample 116


title: DE_Ctrl.DMSO.2d_ChIP_input_Rep1

description: Library name: DE_Ctrl.DMSO.2d_ChIP_input_Rep1

tag: cell line

value: Definitive endoderm

value: Ctrl


title: ChIP_Col_H2A.Z_rep2

description: Library name: Sample 53

value: Wild-type


title: DonorD cells perturbed with GPI knockdown by CRISPRi in batch Rep1 collected 8 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim8hr_Rep1_GPI
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

value: CRISPRi knockdown of GPI

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

tag: anticoagulant

value: ACDA

value: STEMCELL technologies

value: Female

value: adult stage

tag: sample preservation_method

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

tag: genetic perturbation_strategy

tag: enriched cell_types


title: DE_MEKi.2d_ChIP_P-ERK_Rep2

description: Library name: DE_MEKi.2d_ChIP_P-ERK_Rep2

tag: treatment

value: MEKi inhibitor


title: ChIP_met1cmt_H2A.Z_rep2

description: Library name: Sample 115

tag: tissue

value: seedling

tag: genotype

value: met1-1 cmt2 cmt3


title: DonorD cells perturbed with CD3G knockdown by CRISPRi in batch Rep1 collected 8 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim8hr_Rep1_CD3G
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

value: 8 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown of CD3G

tag: source

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

value: Hispanic

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: DE_MEKi.2d_ChIP_P-ERK_Rep1

description: Library name: DE_MEKi.2d_ChIP_P-ERK_Rep1

tag: cell line

value: Definitive endoderm


title: ChIP_Col_H2A.Z_rep1

description: Library name: Sample 52

value: Wild-type


title: DonorD cells perturbed with ATP2A3 knockdown by CRISPRi in batch Rep1 collected 8 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim8hr_Rep1_ATP2A3
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

value: CRISPRi knockdown of ATP2A3

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

tag: anticoagulant

value: ACDA

value: STEMCELL technologies

value: Female

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity


title: ChIP_met1cmt_H2A.Z_rep1

description: Library name: Sample 114

tag: tissue

value: seedling

tag: genotype

value: met1-1 cmt2 cmt3


title: DE_Ctrl.DMSO.2d_ChIP_P-ERK_Rep2

description: Library name: DE_Ctrl.DMSO.2d_ChIP_P-ERK_Rep2

tag: treatment

value: Ctrl


title: DonorD cells perturbed with ATP2A2 knockdown by CRISPRi in batch Rep1 collected 8 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim8hr_Rep1_ATP2A2
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

value: 8 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown of ATP2A2

tag: source

tag: donor sex

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

tag: genetic perturbation_strategy

tag: enriched cell_types


title: DE_Ctrl.DMSO.2d_ChIP_P-ERK_Rep1

description: Library name: DE_Ctrl.DMSO.2d_ChIP_P-ERK_Rep1

tag: cell line

value: Definitive endoderm


title: ChIP_F1h2a.w(h2a.wsuvh X h2a.wcmt)_H3_for_H2A.Z_rep4

description: Library name: Sample 51


title: ChIP_F1h2a.w(h2a.wsuvh X h2a.wcmt)_H3_for_H2A.Z_rep3

description: Library name: Sample 50


title: ChIP_met1-1_H2A.Z_rep2

description: Library name: Sample 113


title: ChIP_met1-1_H2A.Z_rep1

description: Library name: Sample 112


title: DonorD cells perturbed with VAV1 knockdown by CRISPRi in batch Rep2 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim48hr_Rep2_VAV1
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

value: 48 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

value: CRISPRi knockdown of VAV1

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

tag: anticoagulant

value: Normal

tag: sample preservation_method

value: Hispanic

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: DE_MEKi.1d_ChIP_Input_Rep2

description: Library name: DE_MEKi.1d_ChIP_Input_Rep2

tag: treatment

value: MEKi inhibitor


title: ChIP_F1h2a.w(h2a.wcmt X h2a.wsuvh)_H3_for_H2A.Z_rep2

description: Library name: Sample 49

tag: tissue

value: seedling

tag: genotype


title: ChIP_F1met1(met1cmt X met1suvh)_H3_rep2

description: Library name: Sample 111


title: DE_MEKi.1d_ChIP_Input_Rep1

description: Library name: DE_MEKi.1d_ChIP_Input_Rep1


title: DonorD cells perturbed with SIK3 knockdown by CRISPRi in batch Rep2 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim48hr_Rep2_SIK3
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

value: blood

tag: cell type

tag: experimental perturbation

value: CRISPRi knockdown of SIK3

value: A+

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity


title: ChIP_F1h2a.w(h2a.wcmt X h2a.wsuvh)_H3_for_H2A.Z_rep1

description: Library name: Sample 48


title: ChIP_F1met1(met1cmt X met1suvh)_H3_rep1

description: Library name: Sample 110


title: DonorD cells perturbed with Non-targeting control by CRISPRi in batch Rep2 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim48hr_Rep2_NTC
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

value: CD4-positive, alpha-beta T cells

value: CRISPRi non-targeting control

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

value: adult stage

value: TRUE

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

tag: genetic perturbation_strategy

tag: enriched cell_types


title: DE_Ctrl.DMSO.1d_ChIP_Input_Rep2

description: Library name: DE_Ctrl.DMSO_ChIP_Input_Rep2

tag: cell line

value: Definitive endoderm

tag: treatment

value: Ctrl


title: ChIP_met1suvh_H3_rep2

description: Library name: Sample 109

tag: tissue

tag: genotype

value: met1-1 suvh4 suvh5 suvh6


title: ChIP_h2a.wsuvh_H3_for_H2A.Z_rep2

description: Library name: Sample 47

value: hta6 hta7 hta12 suvh4 suvh5 suvh6


title: DonorD cells perturbed with MEN1 knockdown by CRISPRi in batch Rep2 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim48hr_Rep2_MEN1
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

tag: cell type

value: 48 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown of MEN1

value: No

tag: source

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Hispanic

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: DE_Ctrl.DMSO.1d_ChIP_Input_Rep1

description: Library name: DE_Ctrl.DMSO_ChIP_Input_Rep1


title: ChIP_met1suvh_H3_rep1

description: Library name: Sample 108

value: seedling


title: DonorD cells perturbed with LAT knockdown by CRISPRi in batch Rep2 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim48hr_Rep2_LAT
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

value: CRISPRi knockdown of LAT

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: A+

tag: anticoagulant

value: ACDA

value: STEMCELL technologies

value: Female

tag: donor disease

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity


title: ChIP_h2a.wcmt_H3_for_H2A.Z_rep2

description: Library name: Sample 45

tag: tissue

tag: genotype

value: hta6 hta7 hta12 cmt2 cmt3


title: ChIP_h2a.wsuvh_H3_for_H2A.Z_rep1

description: Library name: Sample 46

value: hta6 hta7 hta12 suvh4 suvh5 suvh6


title: ME_MEKi.1d_ChIP_Input_Rep2

description: Library name: ME_MEKi.1d_ChIP_Input_Rep2

tag: cell line

value: Mesoendoderm

tag: treatment

value: MEKi inhibitor


title: ChIP_met1cmt_H3_rep2

description: Library name: Sample 107

value: met1-1 cmt2 cmt3


title: ChIP_h2a.wcmt_H3_for_H2A.Z_rep1

description: Library name: Sample 44


title: DonorD cells perturbed with HEXDC knockdown by CRISPRi in batch Rep2 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim48hr_Rep2_HEXDC
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

tag: cell type

value: 48 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown of HEXDC

value: No

tag: source

tag: donor sex

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: Hispanic

tag: genetic perturbation_strategy

tag: enriched cell_types


title: ChIP_met1cmt_H3_rep1

description: Library name: Sample 106

value: seedling


title: ME_MEKi.1d_ChIP_Input_Rep1

description: Library name: ME_MEKi.1d_ChIP_Input_Rep1


title: DonorD cells perturbed with GPI knockdown by CRISPRi in batch Rep2 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim48hr_Rep2_GPI
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

value: CRISPRi knockdown of GPI

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: A+

tag: anticoagulant

value: ACDA

value: STEMCELL technologies

tag: donor disease

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: ME_Ctrl.DMSO.1d_ChIP_Input_Rep2

description: Library name: ME_Ctrl.DMSO_ChIP_Input_Rep2

tag: cell line

value: Mesoendoderm

tag: treatment

value: Ctrl


title: ChIP_h2a.w_H3_for_H2A.Z_rep2

description: Library name: Sample 43

tag: tissue

tag: genotype

value: hta6 hta7 hta12


title: ChIP_met1-1_H3_rep2

description: Library name: Sample 105


title: DonorD cells perturbed with CD3G knockdown by CRISPRi in batch Rep2 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim48hr_Rep2_CD3G
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

tag: cell type

value: 48 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown of CD3G

value: No

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity


title: ME_Ctrl.DMSO.1d_ChIP_Input_Rep1

description: Library name: ME_Ctrl.DMSO_ChIP_Input_Rep1


title: DonorD cells perturbed with ATP2A3 knockdown by CRISPRi in batch Rep2 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim48hr_Rep2_ATP2A3
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

value: blood

value: CRISPRi knockdown of ATP2A3

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

value: TRUE

tag: donor disease

value: Normal

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: Hispanic

tag: genetic perturbation_strategy

tag: enriched cell_types


title: ChIP_met1-1_H3_rep1

description: Library name: Sample 104

tag: tissue

value: seedling

tag: genotype


title: DE_MEKi.1d_ChIP_H3K9me3_Rep2

description: Library name: DE_MEKi.1d_ChIP_H3K9me3_Rep2

tag: cell line

value: Definitive endoderm

tag: treatment

value: MEKi inhibitor


title: ChIP_h2a.w_H3_for_H2A.Z_rep1

description: Library name: Sample 42


title: ChIP_F1WT(suvh X cmt)_H3_for_H2A.Z_rep4

description: Library name: Sample 41


title: DonorD cells perturbed with ATP2A2 knockdown by CRISPRi in batch Rep2 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim48hr_Rep2_ATP2A2
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi knockdown of ATP2A2

value: A+

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: sample preservation_method

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: ChIP_cmth2a.z(ccz)_H2A.W_rep2

description: Library name: Sample 103

value: cmt2 cmt3 hta8 hta9 hta11


title: ChIP_F1WT(suvh X cmt)_H3_for_H2A.Z_rep3

description: Library name: Sample 40


title: DE_MEKi.1d_ChIP_H3K9me3_Rep1

description: Library name: DE_MEKi.1d_ChIP_H3K9me3_Rep1


title: ChIP_cmth2a.z(ccz)_H2A.W_rep1

description: Library name: Sample 102


title: ChIP_F1WT(cmt X suvh)_H3_for_H2A.Z_rep2

description: Library name: Sample 39


title: ChIP_h2a.zcmt(zcc)_H2A.W_rep2

description: Library name: Sample 101

value: hta8 hta9 hta11 cmt2 cmt3


title: DonorD cells perturbed with SIK3 knockdown by CRISPRi in batch Rep1 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim48hr_Rep1_SIK3
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

value: blood

value: 48 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

value: CRISPRi knockdown of SIK3

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

tag: anticoagulant

value: Female

value: adult stage

tag: donor disease

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity


title: DE_Ctrl.DMSO.1d_ChIP_H3K9me3_Rep2

description: Library name: DE_Ctrl.DMSO_ChIP_H3K9me3_Rep2

tag: cell line

value: Definitive endoderm

tag: treatment

value: Ctrl


title: DE_Ctrl.DMSO.1d_ChIP_H3K9me3_Rep1

description: Library name: DE_Ctrl.DMSO_ChIP_H3K9me3_Rep1


title: ChIP_F1WT(cmt X suvh)_H3_for_H2A.Z_rep1

description: Library name: Sample 38

tag: tissue

value: seedling

tag: genotype


title: DonorD cells perturbed with Non-targeting control by CRISPRi in batch Rep1 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim48hr_Rep1_NTC
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi non-targeting control

value: A+

tag: source

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: Hispanic

tag: genetic perturbation_strategy

tag: enriched cell_types


title: ChIP_h2a.zcmt(zcc)_H2A.W_rep1

description: Library name: Sample 100

value: hta8 hta9 hta11 cmt2 cmt3


title: ME_MEKi.1d_ChIP_H3K9me3_Rep2

description: Library name: ME_MEKi.1d_ChIP_H3K9me3_Rep2

value: Mesoendoderm

value: MEKi inhibitor


title: ChIP_h2a.z_H2A.W_rep2

description: Library name: Sample 99

value: hta8 hta9 hta11


title: DonorD cells perturbed with MEN1 knockdown by CRISPRi in batch Rep1 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim48hr_Rep1_MEN1
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

value: blood

value: 48 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

value: CRISPRi knockdown of MEN1

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

tag: anticoagulant

value: ACDA

value: STEMCELL technologies

value: Female

tag: donor disease

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: ChIP_suvh_H3_for_H2A.Z_rep2

description: Library name: Sample 37

tag: tissue

value: seedling

tag: genotype

value: suvh4 suvh5 suvh6


title: ChIP_suvh_H3_for_H2A.Z_rep1

description: Library name: Sample 36


title: ME_MEKi.1d_ChIP_H3K9me3_Rep1

description: Library name: ME_MEKi.1d_ChIP_H3K9me3_Rep1

tag: cell line

tag: treatment


title: ChIP_h2a.z_H2A.W_rep1

description: Library name: Sample 98


title: DonorD cells perturbed with LAT knockdown by CRISPRi in batch Rep1 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim48hr_Rep1_LAT
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi knockdown of LAT

value: A+

tag: source

tag: donor sex

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

tag: donor ethnicity


title: ME_Ctrl.DMSO.1d_ChIP_H3K9me3_Rep2

description: Library name: ME_Ctrl.DMSO_ChIP_H3K9me3_Rep2

value: Mesoendoderm

value: Ctrl


title: ChIP_cmt_H3_for_H2A.Z_rep2

description: Library name: Sample 35

value: cmt2 cmt3


title: ChIP_F1WT(suvh X cmt)_H2A.W_rep4

description: Library name: Sample 97


title: DonorD cells perturbed with HEXDC knockdown by CRISPRi in batch Rep1 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim48hr_Rep1_HEXDC
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

value: blood

value: 48 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

value: CRISPRi knockdown of HEXDC

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

tag: anticoagulant

value: ACDA

value: STEMCELL technologies

tag: donor disease

value: Hispanic

tag: genetic perturbation_strategy

tag: enriched cell_types


title: ME_Ctrl.DMSO.1d_ChIP_H3K9me3_Rep1

description: Library name: ME_Ctrl.DMSO_ChIP_H3K9me3_Rep1

tag: cell line

tag: treatment


title: DonorD cells perturbed with GPI knockdown by CRISPRi in batch Rep1 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim48hr_Rep1_GPI
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

tag: tissue

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi knockdown of GPI

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

tag: donor living_at_sample_collection

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: ChIP_cmt_H3_for_H2A.Z_rep1

description: Library name: Sample 34

value: seedling

tag: genotype


title: ChIP_F1WT(suvh X cmt)_H2A.W_rep3

description: Library name: Sample 96


title: RNA, HEK293T, MethionaseNLS, Vps34IN1,24h, rep3

first: Ganna

last: Panasyuk

address: 156-160 Rue Vaugirard, Faculté de Médecine Paris Descartes,, 4th Floor - Lab-408/Office-404,, 4th Floor - Lab-408/Office-404,

institute: Inserm U1151/CNRS UMR 8253, Necker Enfants Malades Institute (INEM)

description:
Library name: Methionase_NLS_Vps34INH1_24h_3
clean reads

data_processing:
Adapter sequences and low-quality reads were filtered with SOAPnuke. Clean reads were obtained with an output read quality of Phred+33.
Clean reads were aligned to the hg38 genome with STAR-2.7.10b and counts generated uing featurecounts. Variance stabilized transformation was used to generate vst normalized count table. Deseq2 and limma were used for differential expression analysis. Direct comparisons were made between treatment conditions. DOSE Gene Set Enrichment Analysis was performed with the DOSE package, in R.
Assembly: hg38
Supplementary files format and content: variance stabilized transformation counts table

growth_protocol: Cells were grown to 90% confluence in 15cm plates in DMEM High Glucose (4.5g/L) + 10%  FBS prior to being split into 6 well plates for transfection and treatment.

extract_protocol:
Total RNA was extracted with RNAseasy lipid tissue kit.
mRNA was enriched with oligo dT beads that target the poly A tail. mRNA molecules were fragmented and synthesized into first strand cDNA using random primers. The second strand was synthesized with dUTP instead of dTTP and cDNA was subject to end-repair and 3' adenylation. Adaptors were then ligated to the 3' adenylated cDNA fragments after which were PCR amplified. Libraries were then circularized and amplified to make a DNA nanoball and sequenced on the DNBSEQ-G400.

treatment_protocol: HEK293T cells were transfected for indicated times, with either pLEX (empty vector) or MethionaseNLS, and treated with either dmso (vehicle) or Vps34IN1 at 5uM for 12h.

value: human embryonic kidney

value: WT

value: transfected MethionaseNLS, 24h, Vps34IN1


title: ChIP_Col_H3_for_H2A.Z_rep2

description: Library name: Sample 33

value: Wild-type


title: ChIP_F1WT(cmt X suvh)_H2A.W_rep2

description: Library name: Sample 95


title: DonorD cells perturbed with CD3G knockdown by CRISPRi in batch Rep1 collected 48 hrs after restimulation

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim48hr_Rep1_CD3G
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

value: blood

value: CRISPRi knockdown of CD3G

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: A+

value: adult stage

value: TRUE

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

tag: donor ethnicity


title: RNA, HEK293T, MethionaseNLS, Vps34IN1,24h, rep2

description:
Library name: Methionase_NLS_Vps34INH1_24h_2
clean reads

tag: cell line

tag: cell type

tag: treatment


title: ChIP_Col_H3_for_H2A.Z_rep1

description: Library name: Sample 32

tag: tissue


title: ChIP_F1WT(cmt X suvh)_H2A.W_rep1

description: Library name: Sample 94


title: RNA, HEK293T, MethionaseNLS, Vps34IN1,24h, rep1

description:
Library name: Methionase_NLS_Vps34INH1_24h_1
clean reads