title: Yap-Taz, SFFFM, sample 3

city: Nashville

first: Jason

last: Gokey

state: TN

department: Medicine - Allergy, Pulmonary and Critical Care

institute: Vanderbilt University Medical Center

description:
Library name: YTS3
Column name in raw_counts_GEO_YapTaz.csv: YTS3

data_processing:
Trimmomatic v.0.36. was used to remove adaptor sequences
Trimmed reads were mapped and BAM files were generated using STAR aligner v.2.5.2b
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted
DESeq2 was used for comparison between groups. Genes with adjusted P values < 0.05 and absolute log2 fold changes >0.5 were called as differentially expressed genes for each comparison.
Assembly: GRCm38
Supplementary files format and content: csv count files

source_name: lung

growth_protocol: Cells were isolated from WT or Yap/Taz active mice that were injected with 3mg/mouse tamoxifen 2-weeks prior. CD326+ epithelial cells were isolated with Miltenyi beads. Cells were cultuired for 2-weeks in serum-free-feeder free media (SFFFM) as per the Katsura et al (PMID:33128895) protocol. TdTomato+ lineage labeled cells were then flow sorted and cultured again in SFFFM for 10 days and then either continued in SFFFM or switched to alveolar differentiation media for 7-days. Organoids were then imaged and cells extracted via dispase.

extract_protocol:
Once cells were isolated RNA was extracted following Qiagen Rneasy mini-plus kit protocol using RLT.
ERCC RNA Spike-In Mix (Cat: #4456740) from ThermoFisher Scientific, was added to normalized total RNA prior to library preparation following manufacturer’s protocol. The NEBNext Ultra II RNA Library Prep Kit for Illumina & NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA) were used.

treatment_protocol: There were no treatments beyond changing the media

value: lung

tag: cell line

value: primary

tag: cell type

value: alveolar type 2

value: Yap-Taz active

tag: treatment

value: serum-free, feeder-free media


title: cyt_clone1_ad_2

status: Public on Jun 02 2026

type: SRA

city: Paris

first: Antonin

last: Morillon

state: Paris

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: Total ribo-depleted RNA from cytoplasmic fraction from CRISPR clone1 with XRN1-AID in HCT116 cell line with doxycycline inducible expression of TIR1 and with 24h induction of XRN1 depletion with doxycycline and auxin

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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 differenr 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: doxocyline was added to cells in concentration of 2ug/ml and auxin at final concentration of 500uM for 24h

tag: fraction

value: cytoplasmic fraction

value: 24h induction with doxycycline and auxin


title: RNA, Liver, Fed Vps15LKO, rep2

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: FedKO_2
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 mm10 genome with HISAT2 and counts generated from the Subread R package. Read-count normalization and group comparisons were generated by three independent statistical methods: DESeq2, LimmaVoom, and edgeR. Direct comparisons were made between treatment conditions. DOSE Gene Set Enrichment Analysis was performed with the DOSE package, in R.
Assembly: mm10
Supplementary files format and content: raw counts

molecule: polyA RNA

organism: Mus musculus

source_name: liver

growth_protocol: 4 week old male mice were either ad. lib. fed or 24h fasted prior to sacrifice at ZT14 (2h after lights go off in the animal facility). Livers were flash frozen in liquid nitrogen, powdered, and used for total RNA extraction.

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 nanball and sequenced on the DNBSEQ-G400.

tag: tissue

value: liver

value: hepatocyte

tag: genotype

value: Ttr CRE+, Vps15f/f

value: Ad. Lib Fed, ZT14 sacrifice


title: Yap-Taz, SFFFM, sample 2

country: USA

description:
Library name: YTS2
Column name in raw_counts_GEO_YapTaz.csv: YTS2

tag: batch


title: DonorH cells perturbed with VAV1 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_DonorH_Stim48hr_Rep2_VAV1
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 VAV1

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Yes

tag: donor blood_type

value: A-

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Male

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


title: ATAC_Ascl1_allRs_D7_rep1

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 415/420 Clinical Research Building (CRB)

institute: University of Pennsylvania

description: Library name: 2_ATAC_UAE_allRs_D7_rep1_S2

library_source: genomic

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.

molecule: genomic DNA

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 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.

tag: cell line

value: hBJ fibroblast

tag: cell type

value: human fibroblast

tag: genotype

value: allRs

tag: time

tag: replicate

tag: treatment

value: 0.5μg/ml doxycycline


title: RNA, Liver, Fast wt, rep3

description:
Library name: Fastwt_3
clean reads

tag: tissue

value: liver

value: hepatocyte

value: WT

value: Fast 24h, ZT14 sacrifice


title: ATAC_Ascl1_WT_D7_rep1

description: Library name: 1_ATAC_UAE_WT_D7_rep1_S1


title: Yap-Taz, SFFFM, sample 1

description:
Library name: YTS1
Column name in raw_counts_GEO_YapTaz.csv: YTS1

value: lung

value: primary

value: alveolar type 2

value: Yap-Taz active

value: serum-free, feeder-free media

tag: batch


title: cyt_clone1_ad_1

tag: fraction

value: cytoplasmic fraction

value: 24h induction with doxycycline and auxin


title: cyt_wt_ad_3

description: Total ribo-depleted RNA from cytoplasmic fraction from HCT116 cell line with doxycycline inducible expression of TIR1 with 24h induction with doxycycline and auxin


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim48hr_Rep2_SIK3
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 SIK3

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Yes

tag: donor blood_type

value: A-

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Male

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

value: Normal

value: Zymo DNA/RNA Shield

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


title: Yap-Taz, ADM, sample 4

description:
Library name: YTA4
Column name in raw_counts_GEO_YapTaz.csv: YTA4

value: lung

tag: cell line

value: primary

tag: cell type

value: alveolar type 2

tag: genotype

value: Yap-Taz active

tag: treatment

value: alveolar differentiation media


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim48hr_Rep2_NTC
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

tag: tissue

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

value: Yes

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: cyt_wt_ad_2

tag: fraction

value: cytoplasmic fraction

value: 24h induction with doxycycline and auxin


title: ATAC_Ascl1_QA_D4_rep3

description: Library name: 27_ATAC_UAE_QA_D4_rep3_S31

value: hBJ fibroblast

value: human fibroblast

value: QA

tag: time

tag: replicate

value: 0.5μg/ml doxycycline


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim48hr_Rep2_MEN1
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

value: CRISPRi knockdown of MEN1

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: Male

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

value: Normal

value: Zymo DNA/RNA Shield

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


title: ATAC_Ascl1_AAA_D4_rep3

description: Library name: 26_ATAC_UAE_AAA_D4_rep3_S30

tag: cell line

tag: cell type

tag: genotype

value: AAA

tag: treatment


title: Yap-Taz, ADM, sample 3

description:
Library name: YTA3
Column name in raw_counts_GEO_YapTaz.csv: YTA3

tag: tissue

value: lung

value: primary

value: alveolar type 2

value: Yap-Taz active

value: alveolar differentiation media

tag: batch


title: cyt_wt_ad_1

tag: fraction

value: cytoplasmic fraction

value: 24h induction with doxycycline and auxin


title: Yap-Taz, ADM, sample 2

description:
Library name: YTA2
Column name in raw_counts_GEO_YapTaz.csv: YTA2


title: Chromium 10X,Control 3hr MVST, hTCR

city: Houston

first: Cliona

last: Rooney

state: TX

address: 1102 Bates Ave

institute: Baylor College of Medicine

description:
Library name: 5v3_Ctrl3hr_hTCR
10x Genomics

data_processing:
Reads from the gene expression library were aligned to the GRCh38 human genome with those from the 10x Genomics V(D)J TCR enriched library, following the 10x Genomics standard, using Cell Ranger multi (v8.0.0).
Before analysis, the raw feature barcode matrices were filtered by removing cells with fewer than 100 genes, cells with greater than 10,000 genes and cells with more than 15% of the feature set being comprised of mitochondrial genes. Quality controls were then conducted by removing the residual cells with more or less than the 95th and 5th percentile of features per cell and the upper 95th percentile of mitochondrial gene counts per cell.
Clonotypes were defined as cells that shared a common CDR3 beta sequence and when possible, each single cell was annotated by the corresponding CDR3 beta sequence using custom software designed for the analysis of the activation of cells and their sequencing (aocseq)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: 10x genomics Cell Ranger multi feature barcode matrices for the reads from the gene expression libraries and corresponding  contig_annotations.csv files for each sample. RDS files containing data processed by the aocsq software are also provided for each experiment.
Library strategy: TCR-Seq

source_name: MVST virus-specific T cells

extract_protocol:
Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) using the 10X Controller with a Chromium Single Cell 5' ver.3, 3' ver.3 and 5' ver.2 GEM Library and Gel Bead kits.
The TCR library was amplified using Chromium single-cell V(D)J enrichment kit (human T cell) (10x Genomics).

value: Peripheral blood

value: T cells

value: virus specific T cells

value: T cell products

value: Donor #1


title: DonorE cells perturbed with GATA3 knockdown by CRISPRi under Th1 culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorE_GATA3_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorE_bulkRNAseq.csv

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.

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 GATA3

tag: donor id

tag: donor age

tag: donor weight

value: No

value: O+

value: ACDA

value: STEMCELL technologies

value: Female

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

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: IWP2_BR_DIV65 n3

status: Public on Jun 03 2026

first: Michela

last: Deleidi

address: 24 boulevard du Montparnasse

institute: Institut Imagine, INSERM UMR1163

description:
Library name: E7
10xGenomics

library_source: transcriptomic single cell

data_processing:
The sequencing data was analyzed with the Cell Ranger software (version 6.0.1) provided by 10x Genomics. Demultiplexing of the sequencing reads was performed with cellranger mkfastq.
For each sample, FASTQ files generated with cellranger mkfastq were subsequently processed with cellranger count. Cellranger count performs alignment, filtering, barcode counting and UMI counting. Using the filtered barcodes, it also generates feature-barcode matrices
Assembly: GRCh38-3.0.0
Supplementary files format and content: cellranger output files for 'filtered_feature_bc_matrix' (barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz)

source_name: iPSC-derived midbrain organoids

growth_protocol: Human induced pluripotent stem cells were used to generate human midbrain organoids (hMOs). iPSCs were dissociated into single cells and seeded at a density of 9,000 cells per well in U-bottom 96-well plates to form embryoid bodies (EBs). The initial neuroinduction medium consisted of a DMEM/F12 and Neurobasal base supplemented with N2, B27, NEAA, and was guided by dual SMAD inhibition (SB431542 and LDN) and Wnt activation (CHIR99021). From day 4, midbrain patterning was promoted by the addition of SHH and FGF8. On day 7, EBs were embedded in Matrigel and transferred to six-well plates. From day 8 onwards, organoids were cultured in a maturation medium containing neurotrophic factors, including BDNF and GDNF, as well as ascorbic acid and db-cAMP. On day 20, the organoids were mechanically freed from the Matrigel and transferred to either an orbital shaker or a spinning bioreactor for long-term dynamic culture.

extract_protocol:
Midbrain organoids were dissociated into single-cell suspension following the Worthington Papain Dissociation System kit instructions (Worthington Biochemical) with intermittent trituration steps. The final solution was centrifuge 300g per 7 min, cell pellet were resuspended in PBS-0,04% BSA and filtered twice (40um, 30um) to obtain single-cell suspensions.
Cells loaded to Chromium Chip (target cell recovery): 10,000 cells. Library Preparation Kit: Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (10x Genomics). Sequencing parameters: NovaSeq X, SP Flow Cell, 100 cycles. Read 1: 28 bp, i7-index: 10 bp, i5-index 10 bp, Read 2: 90 bp.

treatment_protocol: The Wnt-TriP protocol was developed as a modification of the standard growth protocol to investigate the role of temporal Wnt gradients on dopaminergic neuron development. Following the initial neuroinduction and midbrain patterning stages, a key treatment window was introduced between DIV 11 and DIV 18. During this period, the Wnt activator CHIR99021 was removed from the culture medium. Concurrently, the medium was supplemented with the Wnt-signalling inhibitor IWP-2 at a final concentration of 2.2 µM. Organoids in the "Standard" protocol, serving as the control, did not receive IWP-2 and were instead cultured with decreasing concentrations of CHIR99021 during this same timeframe. After DIV 18, the Wnt-TriP organoids were subsequently maintained in the final maturation medium, identical to that used for the standard condition.

value: iPSC-derived midbrain organoids

value: Wnt-TriP

tag: incubation

value: Bioreactor

tag: days in_vitro

value: DIV 65


title: ATAC_Ascl1_allRs_D4_rep3

description: Library name: 25_ATAC_UAE_allRs_D4_rep3_S29

tag: cell line

value: hBJ fibroblast

tag: cell type

value: human fibroblast

tag: genotype

value: allRs

tag: time

tag: replicate

tag: treatment

value: 0.5μg/ml doxycycline


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim48hr_Rep2_LAT
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

tag: tissue

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 LAT

tag: donor id

tag: donor age

tag: donor height

tag: donor smoker

value: Yes

tag: donor blood_type

value: A-

tag: anticoagulant

tag: source

tag: donor sex

value: Male

tag: donor dev_stage

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: batch


title: cyt_clone2_3

description: Total ribo-depleted RNA from cytoplasmic fraction from CRISPR clone2 of XRN1-AID in HCT116 cell line with doxycycline inducible expression of TIR1 without induction

tag: fraction

value: cytoplasmic fraction

value: non induced


title: Yap-Taz, ADM, sample 1

description:
Library name: YTA1
Column name in raw_counts_GEO_YapTaz.csv: YTA1

value: lung

tag: cell line

value: primary

tag: cell type

value: alveolar type 2

tag: genotype

value: Yap-Taz active

value: alveolar differentiation media


title: ATAC_Ascl1_WT_D4_rep3

description: Library name: 24_ATAC_UAE_WT_D4_rep3_S28

value: hBJ fibroblast

value: human fibroblast

value: WT

tag: time

tag: replicate

tag: treatment

value: 0.5μg/ml doxycycline


title: cyt_clone2_2

description: Total ribo-depleted RNA from cytoplasmic fraction from CRISPR clone2 with XRN1-AID in HCT116 cell line with doxycycline inducible expression of TIR1 without induction


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim48hr_Rep2_HEXDC
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

tag: tissue

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

value: Yes

value: ACDA

value: STEMCELL technologies

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

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim48hr_Rep2_GPI
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

tag: cell type

value: CRISPRi knockdown of GPI

tag: donor smoker

tag: donor blood_type

value: A-

tag: anticoagulant

tag: source

tag: donor sex

value: Male

tag: donor dev_stage

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: batch


title: Wild type, SFFFM, sample 3

description:
Library name: WTS3
Column name in raw_counts_GEO_YapTaz.csv: WTS3

tag: tissue

value: lung

tag: cell line

value: primary

value: alveolar type 2

tag: genotype

value: wildtype

tag: treatment

value: serum-free, feeder-free media


title: chr_wt_2

description: Total ribo-depleted RNA from chromatin fraction from HCT116 cell line with doxycycline inducible expression of TIR1 without induction

tag: fraction

value: chromatin fraction

value: non induced


title: Wild type, SFFFM, sample 2

description:
Library name: WTS2
Column name in raw_counts_GEO_YapTaz.csv: WTS2


title: ATAC_Ascl1_QA_D4_rep2

description: Library name: 23_ATAC_UAE_QA_D4_rep2_S27

value: hBJ fibroblast

value: human fibroblast

value: QA

tag: time

tag: replicate

value: 0.5μg/ml doxycycline


title: ATAC_Ascl1_AAA_D4_rep2

description: Library name: 22_ATAC_UAE_AAA_D4_rep2_S26

tag: cell type

value: AAA


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim48hr_Rep2_CD3G
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 CD3G

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Yes

value: A-

value: ACDA

value: STEMCELL technologies

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

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: cyt_clone1_3

tag: fraction

value: cytoplasmic fraction

tag: treatment

value: non induced


title: cyt_clone2_1


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim48hr_Rep2_ATP2A3
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

tag: tissue

value: CRISPRi knockdown of ATP2A3

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

value: Male

tag: donor dev_stage

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: batch


title: ATAC_Ascl1_allRs_D4_rep2

description: Library name: 21_ATAC_UAE_allRs_D4_rep2_S25

tag: cell line

value: hBJ fibroblast

tag: cell type

value: human fibroblast

tag: genotype

value: allRs

tag: time

tag: replicate

value: 0.5μg/ml doxycycline


title: Wild type, SFFFM, sample 1

description:
Library name: WTS1
Column name in raw_counts_GEO_YapTaz.csv: WTS1

value: lung

value: primary

value: alveolar type 2

value: wildtype

value: serum-free, feeder-free media


title: Wild type, ADM, sample 4

description:
Library name: WTA4
Column name in raw_counts_GEO_YapTaz.csv: WTA4

value: alveolar differentiation media


title: cyt_clone1_2

description: Total ribo-depleted RNA from cytoplasmic fraction from CRISPR clone1 with XRN1-AID in HCT116 cell line with doxycycline inducible expression of TIR1 without induction

value: cytoplasmic fraction


title: cyt_clone1_1

value: non induced


title: Wild type, ADM, sample 3

description:
Library name: WTA3
Column name in raw_counts_GEO_YapTaz.csv: WTA3


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim48hr_Rep2_ATP2A2
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 ATP2A2

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Yes

value: A-

value: ACDA

value: STEMCELL technologies

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

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: ATAC_Ascl1_QA_D4_rep1

description: Library name: 19_ATAC_UAE_QA_D4_rep1_S23

tag: cell line

value: hBJ fibroblast

tag: cell type

value: human fibroblast

value: QA

tag: treatment

value: 0.5μg/ml doxycycline


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim48hr_Rep1_VAV1
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

tag: tissue

value: blood

value: CRISPRi knockdown of VAV1

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

value: Male

tag: donor dev_stage

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: batch


title: cyt_wt_3

description: Total ribo-depleted RNA from cytoplasmic fraction from HCT116 cell line with doxycycline inducible expression of TIR1 without induction

tag: fraction

value: cytoplasmic fraction

value: non induced


title: Wild type, ADM, sample 2

description:
Library name: WTA2
Column name in raw_counts_GEO_YapTaz.csv: WTA2

value: lung

value: primary

value: alveolar type 2

tag: genotype

value: wildtype

value: alveolar differentiation media


title: ATAC_Ascl1_AAA_D4_rep1

description: Library name: 18_ATAC_UAE_AAA_D4_rep1_S22

value: hBJ fibroblast

value: AAA

tag: time

tag: replicate


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim48hr_Rep1_SIK3
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

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 SIK3

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Yes

value: A-

value: ACDA

value: STEMCELL technologies

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

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: cyt_wt_2

tag: fraction

value: cytoplasmic fraction

tag: treatment

value: non induced


title: Wild type, ADM, sample 1

description:
Library name: WTA1
Column name in raw_counts_GEO_YapTaz.csv: WTA1

tag: tissue

value: lung

tag: cell line

value: primary

tag: cell type

value: alveolar type 2

tag: genotype

value: wildtype

value: alveolar differentiation media

tag: batch


title: ATAC_Ascl1_allRs_D4_rep1

description: Library name: 17_ATAC_UAE_allRs_D4_rep1_S21

value: hBJ fibroblast

value: human fibroblast

value: allRs

tag: time

tag: replicate

value: 0.5μg/ml doxycycline


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_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: Yes

tag: donor blood_type

value: A-

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Male

tag: donor dev_stage

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


title: Female, KO, rep6

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: F_KO_6

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.

source_name: Liver

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

tag: tissue

value: Liver

tag: Sex

value: Female

tag: genotype

value: AADAC KO

tag: treatment

value: One week western-type diet, fed state


title: ATAC_Ascl1_WT_D4_rep1

description: Library name: 16_ATAC_UAE_WT_D4_rep1_S20

tag: cell line

value: hBJ fibroblast

tag: cell type

value: human fibroblast

value: WT

tag: time

tag: replicate

value: 0.5μg/ml doxycycline


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_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: donor weight

tag: donor height

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

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: Female, KO, rep5

description: Library name: F_KO_5

tag: tissue

value: Liver

tag: Sex

tag: genotype

tag: treatment


title: chr_Dis3_A_2

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

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: ATAC_Ascl1_QA_D2_rep3

description: Library name: 15_ATAC_UAE_QA_D2_rep3_S19

tag: cell line

tag: cell type

value: QA

tag: time

tag: replicate


title: chr_Dis3_A_1


title: Female, KO, rep4

description: Library name: F_KO_4

value: Female

value: AADAC KO

value: One week western-type diet, fed state


title: Female, KO, rep3

description: Library name: F_KO_3


title: ATAC_Ascl1_allRs_D2_rep3

description: Library name: 13_ATAC_UAE_allRs_D2_rep3_S17

value: hBJ fibroblast

value: human fibroblast

value: allRs

value: 0.5μg/ml doxycycline


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim48hr_Rep1_GPI
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 GPI

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Yes

tag: donor blood_type

value: A-

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Male

tag: donor dev_stage

tag: donor living_at_sample_collection

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

value: Hispanic

value: CRISPRi


title: Female, KO, rep2

description: Library name: F_KO_2

tag: tissue

value: Liver

tag: Sex

value: Female

tag: genotype

value: AADAC KO

tag: treatment

value: One week western-type diet, fed state


title: chr_Dis3_3

description: Total ribo-depleted RNA from chromatin fraction from CRISPR with DIS3-AID in HCT116 cell line with constitutive expression of TIR1 without induction

tag: fraction

value: chromatin fraction

value: non induced


title: ATAC_Ascl1_WT_D2_rep3

description: Library name: 12_ATAC_UAE_WT_D2_rep3_S16

tag: cell line

value: hBJ fibroblast

tag: cell type

value: human fibroblast

value: WT

tag: time

tag: replicate

value: 0.5μg/ml doxycycline


title: ATAC_Ascl1_QA_D2_rep2

description: Library name: 11_ATAC_UAE_QA_D2_rep2_S15

value: QA


title: Female, KO, rep1

description: Library name: F_KO_1


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim48hr_Rep1_ATP2A3
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 ATP2A3

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Yes

tag: donor blood_type

value: A-

value: ACDA

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

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: Female, WT, rep6

description: Library name: F_WT_6

tag: tissue

value: Liver

tag: Sex

value: Female

tag: genotype

value: AADAC WT

tag: treatment

value: One week western-type diet, fed state


title: ATAC_Ascl1_AAA_D2_rep2

description: Library name: 10_ATAC_UAE_AAA_D2_rep2_S14

tag: cell line

value: hBJ fibroblast

tag: cell type

value: human fibroblast

value: AAA

tag: time

tag: replicate

value: 0.5μg/ml doxycycline


title: chr_Dis3_1

tag: fraction

value: chromatin fraction

value: non induced


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_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: Yes

tag: donor blood_type

value: A-

tag: anticoagulant

tag: source

value: STEMCELL technologies

tag: donor sex

value: Male

tag: donor dev_stage

tag: donor living_at_sample_collection

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

value: Hispanic

value: CRISPRi


title: Female, WT, rep5

description: Library name: F_WT_5

tag: tissue

value: Liver

tag: Sex

value: Female

tag: genotype

value: AADAC WT

tag: treatment

value: One week western-type diet, fed state


title: ATAC_Ascl1_allRs_D2_rep2

description: Library name: 9_ATAC_UAE_allRs_D2_rep2_S13

tag: cell line

value: hBJ fibroblast

tag: cell type

value: human fibroblast

value: allRs

tag: time

tag: replicate

value: 0.5μg/ml doxycycline


title: chr_ctrl_A_3

description: Total ribo-depleted RNA from chromatin fraction from HCT116 cell line expressing TIR1 after 1h treatement with auxin

tag: fraction

value: chromatin fraction

value: 1h induction with auxin


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_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

value: No

tag: donor blood_type

value: O+

value: ACDA

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

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: chr_ctrl_A_2

tag: treatment


title: Female, WT, rep4

description: Library name: F_WT_4

tag: tissue

value: Liver

tag: Sex

value: Female

tag: genotype

value: AADAC WT

value: One week western-type diet, fed state


title: ATAC_Ascl1_QA_D2_rep1

description: Library name: 7_ATAC_UAE_QA_D2_rep1_S11

tag: cell line

value: hBJ fibroblast

tag: cell type

value: human fibroblast

value: QA

tag: time

tag: replicate

value: 0.5μg/ml doxycycline


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim8hr_Rep2_SIK3
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 SIK3

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: anticoagulant

tag: source

value: STEMCELL technologies

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

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

value: Hispanic

value: CRISPRi


title: chr_ctrl_3

description: Total ribo-depleted RNA from chromatin fraction from HCT116 cell line expressing TIR1 without induction

tag: fraction

value: chromatin fraction

tag: treatment

value: non induced


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim8hr_Rep2_NTC
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

tag: tissue

tag: cell type

value: CRISPRi non-targeting control

value: No

tag: donor blood_type

value: O+

value: ACDA

value: Female

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

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: Female, WT, rep2

description: Library name: F_WT_2

value: Liver

tag: Sex

tag: genotype

value: AADAC WT

value: One week western-type diet, fed state


title: ATAC_Ascl1_AAA_D2_rep1

description: Library name: 6_ATAC_UAE_AAA_D2_rep1_S10

tag: cell line

value: hBJ fibroblast

value: human fibroblast

value: AAA

tag: time

tag: replicate

value: 0.5μg/ml doxycycline


title: chr_ctrl_2

tag: fraction

value: chromatin fraction

value: non induced


title: ATAC_Ascl1_allRs_D2_rep1

description: Library name: 5_ATAC_UAE_allRs_D2_rep1_S9

value: allRs

tag: treatment


title: chr_ctrl_1


title: JEG-3_Vehicle_rep5

city: Atlanta

first: Erica

middle: L

last: Johnson

state: GA

address: 720 Westview Dr SW

department: Department of Microbiology, Biochemistry, and Immunology

institute: Morehouse School of Medicine

description:
Library name: J18
Trophoblast-like cell (JEG-3) with vehicle control, biological replicate 5.

data_processing:
Raw reads were provided in FASTQ format. Adapter sequences and low-quality bases were removed using vendor quality-control pipelines. Clean reads were aligned to the human reference genome GRCh38 (NCBI GCF_000001405.39, GRCh38.p13) using STAR (v2.7). Only uniquely mapped, properly paired reads were retained. Gene-level counts were generated using featureCounts. Downstream differential expression analysis was performed in DESeq2 using the median-ratio normalization method and a negative binomial model. Wald tests were used to estimate log₂ fold changes and Benjamini–Hochberg adjusted p-values. Log₂ fold changes were shrunk with the apeglm method. Variance-stabilizing transformation (VST) was applied for clustering and visualization. Gene set enrichment used fgsea with MSigDB Hallmark gene sets.
Assembly: Homo sapiens GRCh38 (NCBI GCF_000001405.39, GRCh38.p13)
Supplementary files format and content: Processed data are provided as a gene-by-sample matrix text file (melatonin_counts_raw.txt). Rows correspond to individual genes (gene identifiers), and columns correspond to RNA-seq libraries (JEG-3 and decidual macrophage samples across all treatments). Each cell contains the raw count of reads assigned to that gene in that sample, as generated by featureCounts after alignment to GRCh38.

growth_protocol: Term placentas (>37 weeks’ gestation) were obtained from healthy pregnant individuals (>18 years old, HIV-1 and hepatitis B seronegative) undergoing cesarean delivery at Grady Memorial Hospital (Atlanta, GA, USA) after written informed consent. Maternal decidua basalis was dissected, washed extensively in ice-cold PBS, and enzymatically digested. Mononuclear cells were isolated by Ficoll-Paque density gradient centrifugation and CD14⁺ decidual macrophages were enriched using magnetic microbeads and cultured in complete RPMI (10% FBS, 1% penicillin–streptomycin, 2 mM L-glutamine, HEPES) at 37 °C, 5% CO₂. The human JEG-3 trophoblast-like cell line (ATCC HTB-36) was maintained in EMEM supplemented with 10% FBS and 1% penicillin–streptomycin at 37 °C with 5% CO₂.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions, including on-column DNase digestion when applicable. RNA concentration and purity were assessed by NanoDrop spectrophotometry, and RNA integrity was evaluated using an Agilent Bioanalyzer. Only samples with RNA integrity number (RIN) ≥ 7 were used for library preparation.
mRNA libraries were prepared using the MGIEasy RNA Directional Library Prep Kit (MGI/BGI). Briefly, polyadenylated RNA was enriched using oligo(dT) beads, fragmented, and reverse-transcribed to generate first-strand cDNA. Second-strand synthesis incorporated dUTP for strand specificity, followed by end repair, A-tailing, adapter ligation, and PCR amplification. Libraries were quantified and pooled according to manufacturer’s recommendations and sequenced on a BGISEQ/DNBSEQ platform with paired-end reads.

treatment_protocol: Decidual macrophages and JEG-3 cells were seeded at defined densities and allowed to adhere. Cells were assigned to one of four conditions: No Treatment, Vehicle (diluent control), 1 nM melatonin, or 1000 nM melatonin. For these RNA-seq samples, cells were incubated for 24 h under the indicated melatonin or vehicle conditions. In the broader experimental study, additional conditions included LPS stimulation and melatonin pretreatment or post-treatment, but only the basal melatonin conditions are included in this dataset.

tag: tissue

value: trophoblast-like cell

value: vehicle control


title: JEG-3_Vehicle_rep4

description:
Library name: J14
Trophoblast-like cell (JEG-3) with vehicle control, biological replicate 4.

tag: cell type


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim8hr_Rep2_LAT
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 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

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

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

value: Hispanic

value: CRISPRi


title: Female, WT, rep1

description: Library name: F_WT_1

value: Liver

tag: Sex

tag: genotype

value: AADAC WT

tag: treatment

value: One week western-type diet, fed state


title: LC_wtHSV1_female_rep1

type: RNA

city: Stillwater

first: Clinton

last: Jones

state: Oklahoma

address: 250 McElroy Hall

department: Veterinary Pathobiology

institute: Oklahoma State University

hyb_protocol: Samples were submitted to NanoString Technologies for RNA isolation and subsequent sample processing

data_processing: Quality control, normalization, and between-group comparisons for differential gene expression were done using the nSolver Analysis Software from NanoString Technologies

label: NanoString target-specific fluorescent barcodes

source_name: LC, wt HSV-1

extract_protocol: Serial coronal sections (60 µm thick) of brainstem were obtained on super frost plus slides using a cryostat (Leica CM3050S). The principal sensory nucleus (Pr5) of the spinal trigeminal tract and locus coeruleus (LC) were microdissected by Palkovit’s punch technique, using a mouse brain stereotaxic atlas as a reference (Paxinos and Franklin, 2019). Bilateral micropunches were collected from 60-µm thick coronal sections based on stereotaxic coordinates. Punches collected from Pr5 and LC were preserved in RNAlater at -20°C until shipped.

value: female

tag: tissue

value: LC

tag: infection


title: cyt_Dis3_A_3

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

tag: fraction

value: cytoplasmic fraction

value: 1h induction with auxin


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim8hr_Rep2_GPI
Tact_cluster_validation_Diff092_Stim8hr_Rep2_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 GPI

tag: donor id

tag: donor age

tag: donor weight

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

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: cyt_Dis3_A_2


title: Male, KO, rep3

description: Library name: M_KO_3

tag: Sex

value: Male

tag: genotype

value: AADAC KO


title: JEG-3_MEL_1000nM_rep3

description:
Library name: J12
Trophoblast-like cell (JEG-3) with 1000 nM melatonin, biological replicate 3.

tag: tissue

tag: cell line

value: trophoblast-like cell

tag: treatment

value: 1000 nM melatonin


title: ATAC_Ascl1_AAA_D0_rep1

description: Library name: 2_ATAC_UAE_AAA_D0_rep1_S6

value: hBJ fibroblast

tag: cell type

value: human fibroblast

value: AAA

tag: time

tag: replicate


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim8hr_Rep2_CD3G
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi knockdown of CD3G

tag: donor id

tag: donor age

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

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

value: Hispanic

value: CRISPRi


title: Male, KO, rep2

description: Library name: M_KO_2

tag: tissue

value: Liver

tag: Sex

value: Male

tag: genotype

tag: treatment

value: One week western-type diet, fed state


title: cyt_Dis3_A_1

tag: fraction

value: cytoplasmic fraction

value: 1h induction with auxin


title: ATAC_Ascl1_WT_D0_rep1

description: Library name: 1_ATAC_UAE_WT_D0_rep1_S5

tag: cell line

value: hBJ fibroblast

tag: cell type

value: human fibroblast

value: WT

tag: time

tag: replicate


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_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: Yes

tag: donor blood_type

value: A-

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

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim8hr_Rep2_ATP2A3
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

tag: tissue

tag: cell type

tag: treatment

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

value: CRISPRi knockdown of ATP2A3

value: No

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

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

value: Hispanic

value: CRISPRi


title: Donor6, SIC, scRNA-seq, T1

city: wuhan

first: Mingjie

last: Li

address: union hospital

country: China

institute: Huazhong University of Science and Technology

description: Library name: Donor6, SIC, scRNA-seq, T1

data_processing:
Raw reads were demultiplexed and mapped to the reference genome by 10x Genomics CellRanger pipeline (https://support.10xgenomics.com/ single-cell-geneexpression/ software/ pipelines/latest/what-is-cell-ranger) using default parameters. For each gene and each cell barcode filtered by CellRanger, unique molecule identifiers (UMIs) were counted to construct digital expression matrices.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: locally advanced rectal cancer

extract_protocol:
Single-cell suspensions were generated using the Tumor Dissociation Kit (Miltenyi Biotec) according to the manufacturer’s protocol. A Dead Cell Removal Kit (Miltenyi Biotec) was applied to eliminate dead cells from the single-cell suspensions. Cell viability in single-cell suspensions was >90%. The concentration of single-cell suspension was adjusted to 700-1200 cells/uL. The cell suspension was loaded into Chromium microfluidic chips to establish single-cell gel beads in emulsion (GEMs) for the directed retrieval of approximately 5000 cells and barcoded with the Chromium Controller (10x Genomics).
RNA from the barcoded cells was subsequently reverse transcribed, and sequencing libraries were constructed with reagents from a Chromium Single Cell 3’ Reagent Kit v3 (10x Genomics) according to the manufacturer’s instructions. Sequencing was performed with the Illumina sequencing platform (NovaSeq) in Novogene.

value: locally advanced rectal cancer

value: stromal and immune cells


title: cyt_Dis3_3

description: Total ribo-depleted RNA from cytoplasmic fraction from CRISPR with DIS3-AID in HCT116 cell line with constitutive expression of TIR1 without induction

tag: fraction

value: cytoplasmic fraction

value: non induced


title: Input_Ascl1_QA_D2_rep3

description: Library name: 23_Input_QA_D2_rep3_S6

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.

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

value: human fribroblast

tag: genotype

value: Doxycycline day2

tag: antibody

tag: replicate

tag: matching input


title: Male, KO, rep1

description: Library name: M_KO_1

value: Liver

tag: Sex

value: Male

value: AADAC KO

value: One week western-type diet, fed state


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim8hr_Rep2_ATP2A2
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

tag: tissue

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 ATP2A2

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: O+

value: ACDA

value: STEMCELL technologies

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

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: cyt_Dis3_2

tag: fraction

value: cytoplasmic fraction

tag: treatment

value: non induced


title: Male, WT, rep6

description: Library name: M_WT_6

tag: tissue

value: Liver

tag: Sex

value: Male

tag: genotype

value: AADAC WT


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim8hr_Rep1_VAV1
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

value: blood

tag: cell type

tag: experimental perturbation

value: CRISPRi knockdown of VAV1

tag: donor id

tag: donor age

tag: anticoagulant

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: 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

value: Hispanic

value: CRISPRi


title: ATAC_Ascl1_WT_D2_rep2

description: Library name: 8_ATAC_UAE_WT_D2_rep2_S12

tag: cell line

value: hBJ fibroblast

value: human fibroblast

value: WT

tag: time

tag: replicate

value: 0.5μg/ml doxycycline


title: cyt_Dis3_1

tag: fraction

tag: treatment


title: Input_Ascl1_QA_D2_rep1

description: Library name: 21_Input_QA_D2_rep1_S4

value: human fribroblast

tag: genotype

value: Doxycycline day2

tag: antibody

tag: matching input


title: cyt_ctrl_A_3

description: Total ribo-depleted RNA from cytoplasmic fraction from HCT116 cell line expressing TIR1 after 1h treatement with auxin

value: cytoplasmic fraction

value: 1h induction with auxin


title: Male, WT, rep4

description: Library name: M_WT_4

tag: tissue

value: Liver

tag: Sex

value: Male

value: One week western-type diet, fed state


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim8hr_Rep1_NTC
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 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

value: STEMCELL technologies

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

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: ChIP_Ascl1_QA_D2_rep3

description: Library name: 29_V5_QA_D2_rep3_S12

tag: cell line

value: hBJ fibroblast

value: human fribroblast

tag: genotype

tag: treatment

value: Doxycycline day2

tag: antibody

value: V5 (Thermo Fisher, R960-25)

tag: replicate

tag: matching input


title: cyt_ctrl_A_2

tag: fraction

value: cytoplasmic fraction

value: 1h induction with auxin


title: Male, WT, rep3

description: Library name: M_WT_3

tag: tissue

value: Liver

tag: Sex

value: Male

value: AADAC WT

value: One week western-type diet, fed state


title: ChIP_Ascl1_QA_D2_rep2

description: Library name: 28_V5_QA_D2_rep2_S11

tag: cell type


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim8hr_Rep1_MEN1
Tact_cluster_validation_Diff092_Stim8hr_Rep1_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 MEN1

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

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: 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


title: cyt_ctrl_A_1

tag: fraction

value: cytoplasmic fraction

tag: treatment


title: ChIP_Ascl1_QA_D2_rep1

description: Library name: 27_V5_QA_D2_rep1_S10

tag: cell line

value: hBJ fibroblast

tag: cell type

value: human fribroblast

tag: genotype

value: Doxycycline day2

tag: antibody

value: V5 (Thermo Fisher, R960-25)

tag: replicate

tag: matching input


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim8hr_Rep1_LAT
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

tag: tissue

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: ACDA

value: STEMCELL technologies

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: Male, WT, rep1

description: Library name: M_WT_1

value: Liver

tag: Sex

value: Male

tag: genotype

value: AADAC WT

tag: treatment

value: One week western-type diet, fed state


title: Input_Ascl1_AAA_D2_rep3

description: Library name: 8_Input_AAA_D2_rep4_S8

tag: cell line

tag: cell type

tag: antibody

tag: replicate

tag: matching input


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim8hr_Rep1_HEXDC
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

tag: tissue

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 HEXDC

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

value: No

value: O+

tag: anticoagulant

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: 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


title: cyt_ctrl_2

description: Total ribo-depleted RNA from cytoplasmic fraction from HCT116 cell line expressing TIR1 without induction

tag: fraction

value: cytoplasmic fraction

tag: treatment

value: non induced


title: BAT_WT_7964

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_7964

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)

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

value: Intrascapular brown adipose tissue

tag: genotype

value: Wildtype

value: 1 hour CNO


title: Input_Ascl1_AAA_D2_rep2

description: Library name: 7_Input_AAA_D2_rep3_S7

tag: cell line

value: hBJ fibroblast

tag: cell type

value: human fribroblast

value: Doxycycline day2

tag: antibody

tag: replicate

tag: matching input


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim8hr_Rep1_GPI
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

tag: tissue

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 GPI

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: ACDA

value: STEMCELL technologies

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: cyt_ctrl_1

tag: fraction

value: cytoplasmic fraction

tag: treatment

value: non induced


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim8hr_Rep1_CD3G
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

tag: cell type

value: CRISPRi knockdown of CD3G

value: No

value: O+

tag: anticoagulant

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: 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


title: Input_Ascl1_AAA_D2_rep1

description: Library name: 5_Input_AAA_D2_rep1_S5

tag: cell line

value: hBJ fibroblast

value: human fribroblast

tag: genotype

value: Doxycycline day2

tag: antibody

tag: replicate

tag: matching input


title: BAT_WT_7131

description: Library name: WT_7131

tag: tissue

value: Intrascapular brown adipose tissue

value: Wildtype

value: 1 hour CNO


title: stem_3.fq.gz

city: Beijing

first: Feifan

last: Lin

address: Tsinghua University,beijing,China

institute: 清华大学

description: Library name: stem_3.fq.gz

data_processing:
Raw reads were preprocessed with fastp v0.23.2 (default parameters) to remove adapters and low-quality bases. Transcript abundance was then estimated with Salmon v1.10.0 in alignment-free mode, using a de novo assembled transcriptome as the reference index.
Assembly: De novo transcriptome assembly (no reference genome was used).
Supplementary files format and content: transcript_counts_matrix.txt: Tab-delimited text file containing estimated read counts for all transcripts, summarized from Salmon output.

organism: Cephalotaxus fortunei

source_name: stem

extract_protocol:
Total RNA was extracted from 100 mg of frozen, ground tissue using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. RNA was treated with DNase I (Ambion) and purified with the RNeasy MinElute Cleanup Kit (Qiagen). RNA integrity was checked on an Agilent 2100 Bioanalyzer (RIN ≥ 7).
Sequencing libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit (NEB) using 1 µg of total RNA. Poly(A) mRNA was enriched with NEBNext Poly(A) mRNA Magnetic Isolation Module.

value: stem


title: BAT_WT_7223

description: Library name: WT_7223


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim8hr_Rep1_ATP2A3
Tact_cluster_validation_Diff092_Stim8hr_Rep1_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 ATP2A3

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: ACDA

value: STEMCELL technologies

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: BAT_WT_7224

description: Library name: WT_7224

tag: genotype

tag: treatment


title: ChIP_Ascl1_AAA_D2_rep2

description: Library name: 15_ChIP_AAA_D2_rep3_S15

tag: cell line

value: hBJ fibroblast

tag: cell type

tag: antibody

value: V5 (Thermo Fisher, R960-25)

tag: replicate

tag: matching input


title: cyt_ctrl_3

tag: fraction

value: cytoplasmic fraction

value: non induced


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim8hr_Rep1_ATP2A2
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

tag: tissue

tag: experimental perturbation

value: CRISPRi knockdown of ATP2A2

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

value: No

value: O+

tag: anticoagulant

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: 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


title: stem_1.fq.gz

description: Library name: stem_1.fq.gz

value: stem


title: ChIP_Ascl1_AAA_D2_rep1

description: Library name: 13_ChIP_AAA_D2_rep1_S13

tag: cell line

tag: cell type

value: human fribroblast

tag: genotype

tag: treatment

value: Doxycycline day2

tag: antibody

tag: replicate


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim48hr_Rep2_VAV1
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

tag: tissue

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 VAV1

tag: donor id

tag: donor age

tag: donor smoker

tag: donor blood_type

value: ACDA

value: STEMCELL technologies

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: root_3.fq.gz

description: Library name: root_3.fq.gz

source_name: root

value: root


title: BAT_CRE_7130

description: Library name: CRE_7130

value: Intrascapular brown adipose tissue

value: PnocCre

value: 1 hour CNO


title: Input_Ascl1_allRs_D2_rep3

description: Library name: 20_Input_allRs_D2_rep4_S3

tag: cell line

value: hBJ fibroblast

tag: cell type

tag: matching input


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim48hr_Rep2_SIK3
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

tag: treatment

value: CRISPRi knockdown of SIK3

tag: donor weight

tag: donor height

value: No

value: O+

tag: anticoagulant

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: 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

value: Plasmidsaurus RNA-Seq


title: root_2.fq.gz

description: Library name: root_2.fq.gz

tag: tissue


title: BAT_CRE_8670

description: Library name: CRE_8670

tag: genotype


title: Male, WT, rep2

description: Library name: M_WT_2

value: Liver

tag: Sex

value: Male

value: AADAC WT

value: One week western-type diet, fed state


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim48hr_Rep2_NTC
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 non-targeting control

tag: donor id

tag: donor age

tag: donor smoker

tag: donor blood_type

value: ACDA

value: STEMCELL technologies

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: root_1.fq.gz

description: Library name: root_1.fq.gz

value: root


title: Input_Ascl1_allRs_D2_rep2

description: Library name: 19_Input_allRs_D2_rep3_S2

tag: cell line

value: hBJ fibroblast

tag: cell type

value: human fribroblast

tag: treatment

value: Doxycycline day2

tag: antibody

tag: replicate

tag: matching input


title: Input_Ascl1_allRs_D2_rep1

description: Library name: 4_Input_allRs_D2_rep2_S4

tag: genotype


title: BAT_CRE_7221

description: Library name: CRE_7221

tag: tissue

value: Intrascapular brown adipose tissue

value: PnocCre

value: 1 hour CNO


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim48hr_Rep2_MEN1
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi knockdown of MEN1

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

value: No

value: O+

tag: anticoagulant

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: 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

value: Plasmidsaurus RNA-Seq


title: leaf_3.fq.gz

description: Library name: leaf_3.fq.gz

source_name: leaf

value: leaf


title: BAT_CRE_7536

description: Library name: CRE_7536

tag: treatment


title: ChIP_Ascl1_allRs_D2_rep3

description: Library name: 26_V5_allRs_D2_rep4_S9

tag: cell line

tag: cell type

tag: antibody

value: V5 (Thermo Fisher, R960-25)

tag: replicate

tag: matching input


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim48hr_Rep2_LAT
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

tag: tissue

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 LAT

tag: donor id

tag: donor age

tag: donor smoker

tag: donor blood_type

value: ACDA

value: STEMCELL technologies

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: leaf_2.fq.gz

description: Library name: leaf_2.fq.gz


title: BAT_CRE_7639

description: Library name: CRE_7639

value: Intrascapular brown adipose tissue

tag: genotype

value: PnocCre

tag: treatment

value: 1 hour CNO


title: ChIP_Ascl1_AAA_D2_rep3

description: Library name: 16_ChIP_AAA_D2_rep4_S16

tag: cell line

value: hBJ fibroblast

tag: cell type

value: human fribroblast

value: Doxycycline day2

tag: antibody


title: stem_2.fq.gz

description: Library name: stem_2.fq.gz

tag: tissue

value: stem


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim48hr_Rep2_HEXDC
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi knockdown of HEXDC

tag: donor weight

tag: donor height

value: No

value: O+

tag: anticoagulant

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: 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

value: Plasmidsaurus RNA-Seq


title: M22 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 6

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.

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

value: Liver

tag: disease model

value: HFD/CCl4-induced MASH model

value: Anti-PD-3 antibody

tag: replicate


title: leaf_1.fq.gz

description: Library name: leaf_1.fq.gz

value: leaf


title: ChIP_Ascl1_allRs_D2_rep1

description: Library name: 12_ChIP_allRs_D2_rep2_S12

tag: cell line

value: hBJ fibroblast

tag: genotype

tag: treatment

value: V5 (Thermo Fisher, R960-25)

tag: matching input


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim48hr_Rep2_GPI
Tact_cluster_validation_Diff092_Stim48hr_Rep2_bulkRNAseq.csv

tag: tissue

value: blood

tag: cell type

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 GPI

tag: donor id

tag: donor age

tag: donor smoker

tag: donor blood_type

value: ACDA

value: STEMCELL technologies

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: M21 PD-1 treatment

description: Library name: Sample 5

tag: cell line

tag: disease model

value: Anti-PD-2 antibody

tag: replicate