title: DonorA cells perturbed with ZMYND8 knockdown by CRISPRi under nonpolarized culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_ZMYND8_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorA_bulkRNAseq.csv

tag: tissue

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

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

value: CRISPRi knockdown of ZMYND8

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: 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: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: Ribo, spaceflight, PGCLCs [Ribo_sPGCLCs_1]

status: Public on Jun 02 2026

type: SRA

city: Fuzhou

first: Ying

last: Li

state: Fujian

address: No. 2, Xueyuan Road, University Town

country: China

institute: Fuzhou University

description:
Library name: Ribo_sPGCLCs_1
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: Ribo_sPGCLCs_1
spaceflight_submission_H9_TTseq_gene_count_matrix.txt
spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv

library_source: transcriptomic

data_processing:
Raw sequencing reads underwent adapter trimming and quality control using Trim Galore (v0.6.4).
Cleaned reads were aligned to the human reference genome via HISAT2 (v2.1.0). Gene-level quantification was performed using featureCounts (v1.6.5).
Transcript abundance was normalized to TPM using an in-house Python script. Differential expression analysis was conducted with DESeq2 (v1.26.0), and translation efficiency (TE) calculated as the translatome-to-transcriptome TPM ratio (excluding genes with TPM ≤1). Functional enrichment (GO, KEGG) used Metascape with thresholds: *minimum overlap=3, P<0.01, enrichment factor≥1.5*.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include TPM values for each Sample
Library strategy: Ribo-Seq

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: The H9 human embryonic stem cell line (WiCell, Inc.) was propagated on γ-irradiated mouse embryonic fibroblast (MEF) feeder layers in KnockOut™ DMEM (Gibco, 10829018) supplemented with 20% KnockOut™ Serum Replacement (Gibco, A3181502), 25 μg/mL recombinant human basic fibroblast growth factor (R&D Systems, 233-FB/CF), 1% penicillin-streptomycin (Gibco, 15140163), 1 mM GlutaMAX (Gibco, 35050061), and 1% Non-Essential Amino Acids (NEAA; Gibco, 11140076). Cultures were maintained at 37°C in a humidified atmosphere with 5% CO₂. The H1 human embryonic stem cell line (WiCell, Inc.) was cultured on Matrigel-coated plates (Corning, 365230) using E8 medium (Gibco, A1517001) containing 1% penicillin-streptomycin. Cultures were incubated at 37°C in a humidified 5% CO₂ environment. For subculturing, H1 hESCs were rinsed twice with DPBS (Yeasen, 60152ES76), detached into single cells using EDTA (Cellapy, CA1023100) incubated at 37°C for 2 minutes, and subsequently replated onto fresh Matrigel-coated plates. The culture medium was replaced daily, and cells were passaged every four days.

extract_protocol:
Based on post-flight processing of germ cell derivatives (PGCLCs, FLCs, SSCLCs) preserved in RNALater: Transcriptome Fraction: Cell pellets were resuspended in 2 μL lysis buffer, mixed with 1 mL TRIzol Reagent, vortexed, and incubated for 5 min at RT. Chloroform (200 μL) was added, followed by centrifugation (12,000 × g, 15 min, 4°C). The aqueous phase underwent isopropanol precipitation (0.5 mL, 10 min RT), 75% ethanol wash, and resuspension in 11 μL nuclease-free water. Translatome Fraction: Cell lysates (8 μL) were subjected to ribosome capture using RiboLace beads with 70-min rotation at 4°C. Beads were washed twice with W-buffer, then dissociated in 1% SDS + Proteinase K (37°C, 30 min). RNA was purified identically to transcriptome fractions (TRIzol/chloroform extraction, overnight precipitation).
For T&T-seq libraries, both transcriptome (2 μL lysate) and translatome (8 μL lysate) fractions underwent identical processing: full-length cDNA synthesis was performed using the Single Cell Full-Length mRNA-Amplification Kit, followed by library construction with the TruePrep DNA Library Prep Kit V2, and final sequencing generated >20 million 150-bp paired-end reads per sample on the Illumina NovaSeq 6000 platform.

treatment_protocol: PGCLC Differentiation Protocol (from H9 hESCs) H9 hESCs were seeded onto Matrigel-coated chambers at 30–40% confluency and propagated for 24 hours. Differentiation was initiated using PGC-specific medium (KnockOut™ DMEM supplemented with 10% FBS, 1 mM GlutaMAX, 1% NEAA, 1% penicillin-streptomycin, and 50 ng/mL recombinant human BMP4. Cultures were maintained at 37℃/5% CO₂ with complete medium replacement every 48 hours for 6 days. FLCs Differentiation Protocol (from H9 hESCs) 5 × 10⁴ undifferentiated H9 hESCs (50% confluency) were seeded onto Matrigel-coated 6-well plates. Cells were treated with induction medium (KnockOut™ DMEM + 10% FBS, 1 mM GlutaMAX, 1% NEAA, 50 ng/mL BMP4, and 50 ng/mL BMP8a for 1 hour at 37°C/5% CO₂. Subsequently, cells were transduced with lentiviral vectors expressing DAZL and BOLL for 24 hours, followed by 24-hour recovery and 72-hour blasticidin selection (2 μg/mL). At day 7, cells were treated with differentiation medium containing 5 ng/mL GDF9:BMP15 heterodimer (purified per established protocol) and 10 ng/mL EGF for 24 hours, followed by medium refresh every 48 hours with 50 ng/mL GDF9 + 25 ng/mL BMP15. SSCLC Differentiation Protocol (from H1 hESCs) H1 hESCs were seeded onto Matrigel-coated vessels at 30–40% confluency and propagated for 48 hours. Differentiation was initiated using SSC-specific medium (MEMα supplemented with 3% KnockOut Serum Replacement, 1 mM GlutaMAX, 1× ITS-X, 0.2 mg/mL vitamin C, 1× Chemically Defined Lipid Concentrate, 1 ng/mL bFGF, and 20 ng/mL recombinant human GDNF). Medium was refreshed every 36 hours for 15 days.

tag: cell line

tag: cell type

value: human embryonic stem cell

tag: treatment

value: PGCLCs differentiaton under spaceflight environment were subjected to ribosome-associated mRNA capture using RiboLace beads


title: WT_CD8_d4_media_002

city: Montreal

first: Judith

last: Mandl

state: QC

address: 3649 Promenade Sir William Osler

country: Canada

institute: McGill University

data_processing:
pre-alignment QC: FastQC, MultiQC
alignment: HISAT2 (-k 1 --rna-strandness RF) ; mapping to GRCm38/mm10
post-alignment processing: QC: Samtools Flagstat, FastQC, Picard Tools, MultiQC
post-alignment QC: Flagstat, FastQC, Picard Tools, MultiQC
read summarization: featureCounts (-t exon -g gene_name -s 0 -p --donotsort)
Assembly: GRCm38/mm10
Supplementary files format and content: comma delimited CSV file including summarized counts per gene (row, gene symbol) for each sample (column)

molecule: total RNA

organism: Mus musculus

source_name: CD8+ activated T cells

growth_protocol: CD8+ T cells were isolated from the spleen and LNs of WT male mice (n=3 per group). A fraction of the naive cells was not activated and directly lysed to extract RNA (fresh). The rest was activated in vitro for 2 days with plate-bound anti-CD3 and soluble CD28, and expanded for an additional day with rmIL-2.

extract_protocol:
RNA extraction was performed using the PureLink RNA Mini Kit (Invitrogen). A step with DNAse I was included. 150 ng of material was used to generate the sequencing libraries.
RNA libraries prepared using RiboCop rRNA Depletion Kit HMR (Lexogen, kit #037.96), KAPA RNA HyperPrep Kit (Roche, kit #8098107702), and TruSeq DNA UDI 96 Indexes (Illumina, kit #20022370)

treatment_protocol: Activated CD8+ T cells (day 3) were further cultured in media or in collagen gels (2 mg/mL) of bovine or rat origin for 24h. RNA was extracted at the end of the experiment on day 4.

tag: tissue of_origin

value: spleen and LNs

value: CD8+ activated T cells

tag: genotype

value: WT

tag: migratory environment

value: media


title: RNA Pol II S5P, MEFs, basal methionine, rep1

city: Paris

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,

country: France

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

description:
Library name: ChIP_RNA_Pol2_S5P_Basal_1
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

library_source: genomic

data_processing:
Reads were filtered with SAOPnuke to remove adaptor sequences and low quality reads.
Clean reads were aligned to the mm10 genome with Bowtie2 version 2.4.4.
samtools, picard tools, and bedtools  were used to filter reads with mapq score higher than 40, and remove duplicated and blacklisted regions
Composition bias normalization with csaw was performed to generate bigwig files.
Peak calling was performed with MACS2 and differential binding analysis was performed with Diffbind 3.10.0 or the bdgdiff command in MACS2. Peaks were annotated with ChIPseeker and pathway analysis and visualization was performed with clusterProfiler.
Assembly: mm10
Supplementary files format and content: bigwig

molecule: genomic DNA

growth_protocol: For ChIP in liver: 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 ChIP. For ChIP in MEFs: Cells were grown to 90% confluence in 15cm plates in DMEM High Glucose (4.5g/L) + 10% FBS and used for ChIP.

extract_protocol:
Liver powder was fixed for 15min at RT with 1% formaldehyde and then quenched with glycine. Tissue was washed and homogenized, after which was sonicated to acheieve 200-500bp fragments. For MEF experiments, cells were fixed for 10min with 1% formaldehyde in cold PBS, quenced with glycine, and cells scraped, homogenized, and sonicted to acheive 200-500bp fragments.
DNA fragments were subject to end-repair and 3' adenylation. PCR products were enriched using Agencourt AMPure XP-medium kit. dsDNA PCR products were denatured and circularized by the splint oligonucleotide sequence. Single-stranded circular DNA was formatted as the final library, and DNA nanoballs were made from the library and loaded into a patterned nanoarray. Paired-end reads were generated by sequenced combinatorial Probe-Anchor-Synthesis with the DNBSEQ-400 sequencer.

treatment_protocol: For Methionine experiments, MEFs were kept in basal media (DMEM High Glucose, without FBS, methionine-free DMEM, or methionine-free DMEM + methionine replenishment for indicated times.

tag: tissue

value: MEF

value: mouse embryonic fibroblast

value: basal methionine condition

tag: chip antibody

value: RNA Pol II S5P, Abcam ab5408


title: high blood glucose, high body weight at weaning, male, visceral adipose tissue, replicate 1

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

data_processing:
The sequenced reads (raw reads) often contain low quality reads and adapters, which will affect the analysis quality. So it's necessary to filter the raw reads and get the clean reads. The filtering process is as follows: 1. Remove reads containing adapters. 2.  Remove reads containing N > 10% (N represents the base cannot be determined). 3. Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
Sequences of adaptors: 5' Adapter:   5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3'; 3' Adapter(The underlined 6bp bases is Index):  5'-GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG-3'
Mapping with STAR version 2.7.6a
Gene-level read counts were obtained with summarizeOverlaps, mode = ’Union’, package GenomicAlignments v1.30.0
Normalization with DESeq2 (version 1.28.1)
Assembly: GRCm38.101
Supplementary files format and content: tab-delimited file with normalized linear counts. Tissues were normalized separately.

source_name: visceral adipose tissue

growth_protocol: Male and female TallyHo/JngJ mice were housed in ventilated cages (SealsafePlus AERO IVC Greenline, Tecniplast) on a 12-h light/12-h dark cycle with ad libitum access to food and water. Room temperature was kept constant (22 +/- 1°C) and humidity (55%) was controlled. Mouse experiments were conducted in compliance with the Federation of European Laboratory Animal Science Association (FELASA) protocols. All mouse experiments were performed according to European Union directive 2010/63/EU and were approved by the responsible authorities of the government of Upper Bavaria.  Male TallyHo/JngJ mice were mated with one or two female TallyHo/JngJ mice for 5 – 7 days. Litter size adjustment or shifting of litters (pups of the same father were exchanged between mothers to achieve small or large litters) was performed within 48 hours after birth. Unless otherwise indicated, the animals for each experiment were bred in different time-shifted batches.

extract_protocol:
Total RNA (including miRNA and other small RNA molecules) was extracted from tissues (VAT, hypothalamus, liver, SAT, muscle) using the miRNeasy® Mini Kit (Qiagen), following the manufacturer’s instructions.
Directional mRNA library done by Novogene. mRNA from eukaryotic organisms is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: no

value: visceral adipose tissue

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: Ribo, ground, FLCs [Ribo_gFLCs_1]

description:
Library name: Ribo_gFLCs_1
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: Ribo_gFLCs_1
spaceflight_submission_H9_TTseq_gene_count_matrix.txt
spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv

value: FLCs differentiaton under ground condition were subjected to ribosome-associated mRNA capture using RiboLace beads


title: DonorA cells perturbed with ZMYND8 knockdown by CRISPRi under Th2 culture condition in batch Diff084

city: Palo Alto

first: Lattice

last: Data Coordination

state: CA

address: 3165 Porter Drive

department: Genetics

country: USA

institute: Stanford University

description:
Library name: Th1Th2_validation_Diff084_DonorA_ZMYND8_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorA_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.

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.

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 ZMYND8

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: 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

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: Caucasian

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: Input for RNA Pol II S5P Fast wt, rep1

description: Library name: Input_Fastwt_1

source_name: liver

tag: tissue

value: liver

tag: cell line

tag: cell type

value: hepatocyte

tag: genotype

value: WT

tag: treatment

value: Fast 24h, ZT14 sacrifice

tag: chip antibody

value: input


title: Ribo, ground, PGCLCs [Ribo_gPGCLCs_1]

description:
Library name: Ribo_gPGCLCs_1
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: Ribo_gPGCLCs_1
spaceflight_submission_H9_TTseq_gene_count_matrix.txt
spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv

value: human embryonic stem cell

value: PGCLCs differentiaton under ground condition were subjected to ribosome-associated mRNA capture using RiboLace beads


title: DonorA cells perturbed with ZMYND8 knockdown by CRISPRi under Th1 culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_ZMYND8_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorA_bulkRNAseq.csv

treatment_protocol: 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 ZMYND8

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

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy


title: low body weight at weaning, female, subcutaneous adipose tissue, replicate 3

source_name: subcutaneous adipose tissue

tag: tissue

value: subcutaneous adipose tissue

tag: strain

value: TallyHo/JngJ

tag: Sex

value: female

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition

value: low body weight at weaning


title: Input for RNA Pol II S5P Fed wt, rep1

description: Library name: Input_Fedwt_1

value: liver

tag: cell line

tag: cell type

value: hepatocyte

tag: genotype

value: WT

tag: treatment

value: Ad. Lib Fed, ZT14 sacrifice

tag: chip antibody

value: input


title: low body weight at weaning, female, subcutaneous adipose tissue, replicate 2


title: Ribo, H9 [Ribo_hESCs_XX_1]

description:
Library name: Ribo_hESCs_XX_1
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: Ribo_hESCs_XX_1
spaceflight_submission_H9_TTseq_gene_count_matrix.txt
spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv

value: human embryonic stem cell

value: CRISPR-Cas9 edited human ROSA loci VASA-GFP reporter cell line, which was subjected to ribosome-associated mRNA capture using RiboLace beads


title: DonorA cells perturbed with TBX21 knockdown by CRISPRi under nonpolarized culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_TBX21_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorA_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 TBX21

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: source

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

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: Caucasian

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: RNA Pol II S5P, liver, Fast wt, rep3

description:
Library name: ChIP_RNA_Pol2_S5P_Fastwt_3
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

tag: tissue

value: liver

tag: cell line

tag: cell type

value: hepatocyte

tag: genotype

value: WT

tag: treatment

value: Ad. Lib Fed, ZT14 sacrifice

tag: chip antibody

value: RNA Pol II S5P, Abcam ab5408


title: low body weight at weaning, female, subcutaneous adipose tissue, replicate 1

value: subcutaneous adipose tissue

tag: strain

value: TallyHo/JngJ

tag: Sex

value: female

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition

value: low body weight at weaning


title: DonorA cells perturbed with TBX21 knockdown by CRISPRi under Th2 culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_TBX21_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorA_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 TBX21

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: Male

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

value: Normal

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy


title: low body weight at weaning, female, visceral adipose tissue, replicate 2

tag: tissue

value: visceral adipose tissue

tag: strain

value: TallyHo/JngJ

tag: Sex

tag: age

tag: development stage

tag: condition


title: SD_wk16_A_R7

city: South San Francisco

first: ashmita

last: Saigal

state: California

address: 213 E Grand Ave, South San Francisco, CA-94080, USA

institute: Merck & Co., Inc.

description: Library name: 8271

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) was generated for following process
Assembly: mm10
Supplementary files format and content: Excel file containing FPKM values and counts for each sample

source_name: Liver

extract_protocol:
Liver tissues were homogenized into RNA STAT-60 (Tel-Test Inc., Friendswood, TX) using a polytron homogenizer, followed by total RNA isolation using the MagMAX mirVana Total RNA isolation kit (Thermo Fisher Scientific Inc., Foster City, CA) according to the manufacturer's instructions. Total RNA samples were qualified and quantified on the Fragment Analyzer (Agilent Technologies, Santa Clara, CA) per manufacturer’s instructions.
For the TruSeq Stranded mRNA protocol, total RNA was utilized as the input for Illumina’s TruSeq Stranded mRNA library preparation kit (Platform: Illumina NovaSeq6000). This method purified polyA-containing mRNA molecules using oligo-dT attached magnetic beads and involved two rounds of purification. During the second elution of the polyA RNA, the RNA was fragmented and primed for complementary DNA (cDNA) synthesis. Subsequently, the cleaved RNA fragments, primed with random hexamers, were reverse transcribed into first-strand cDNA. The RNA template was then removed, and a replacement strand was synthesized, incorporating dUTP in place of dTTP to generate double-stranded cDNA (ds cDNA). An adenine (A) nucleotide was added to the 3ʹ ends of the blunt fragments to prevent them from ligating to one another during the adapter ligation reaction. Multiple indexing adapters were ligated to the ends of the ds cDNA fragments in preparation for hybridization. Polymerase chain reaction (PCR) was employed to selectively enrich those DNA fragments that possessed adapter molecules on both ends and to amplify the quantity of DNA in the library. After amplification, the targeted libraries were quantified using quantitative PCR (qPCR) and pooled into a single lane. The pooled libraries were subsequently prepared for cluster generation and sequencing on high-throughput Illumina NovaSeq instruments. At least 4 gigabases of 50 base pairs of paired-end data were generated by the sequencing machine, in accordance with the project’s raw data requirements.

value: Liver

tag: housing temperature

value: TA

tag: timepoint (duration_on_diet)

tag: genotype

value: C57BL/6J, Male

tag: treatment

value: GAN diet


title: RNA Pol II S5P, liver, Fast wt, rep2

description:
Library name: ChIP_RNA_Pol2_S5P_Fastwt_2
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

value: liver

tag: cell line

tag: cell type

value: hepatocyte

value: WT

value: Ad. Lib Fed, ZT14 sacrifice

tag: chip antibody

value: RNA Pol II S5P, Abcam ab5408


title: low blood glucose, high body weight at weaning, male, subcutaneous adipose tissue, replicate 3

value: subcutaneous adipose tissue

value: male

value: 18 weeks

value: adult


title: DonorA cells perturbed with TBX21 knockdown by CRISPRi under Th1 culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_TBX21_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorA_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 TBX21

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: Male

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

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: Caucasian

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: Nevus and melanoma in a single slide of patient D3 and D20

city: Leiden

first: Roderick

last: Slieker

address: PO Box 9600

department: Medical Oncology

country: Netherlands

institute: Leiden University Medical Center

description:
Library name: D3, D20
FFPE Spatial transcriptomics

data_processing:
Raw sequencing data was processed using 10x SpaceRanger (v2.1.1) based on a probe set provided by the manufacturer (GRCh38-2020-A), a Visium CytAssist image and a H&E image of the slide. Data was further processed with the R-package semla. Spots with more than 500 genes were retained as well as spots with less than 30% mitochondrial counts.
Assembly: hg38
Supplementary files format and content: aligned_fiducials.jpg = aligned fiducials
Supplementary files format and content: features.tsv.gz = list of gene Ids
Supplementary files format and content: barcodes.tsv.gz = list of spatial barcodes
Supplementary files format and content: matrix.mtx.gz = gene expression count data
Supplementary files format and content: scalefactors_json.json = scale factors in json format
Supplementary files format and content: tissue_hires_image.png = high res image of the tissue
Supplementary files format and content: tissue_lowres_image.png = low res image of the tissue
Supplementary files format and content: tissue_positions.csv = list of spatial coordinates
Library strategy: Spatial Transcriptomics

source_name: Skin

extract_protocol:
According to manufacturer's protocol
The sequencing libraries were further prepared as per manufacturer’s instructions (document number CG000495 Rev C, 10X Genomics). In short, this included destaining, decrosslinking, probe hybridization, probe ligation, probe release, probe extension, and library construction.

tag: tissue

value: Skin


title: Nevus and melanoma in a single slide of patient B14, B15 and B38.2

description:
Library name: B14, B15, B38.2
FFPE Spatial transcriptomics


title: RNA Pol II S5P, liver, Fast wt, rep1

description:
Library name: ChIP_RNA_Pol2_S5P_Fastwt_1
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

value: liver

tag: cell line

tag: cell type

value: hepatocyte

tag: genotype

value: WT

tag: treatment

value: Ad. Lib Fed, ZT14 sacrifice

tag: chip antibody

value: RNA Pol II S5P, Abcam ab5408


title: DonorA cells perturbed with STYXL1 knockdown by CRISPRi under nonpolarized culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_STYXL1_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorA_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 STYXL1

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: Normal

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy


title: RNA Pol II S5P, liver, Fed wt, rep3

description:
Library name: ChIP_RNA_Pol2_S5P_Fedwt_3
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

tag: tissue


title: low blood glucose, high body weight at weaning, male, subcutaneous adipose tissue, replicate 2

value: subcutaneous adipose tissue

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: Nevus and melanoma in a single slide of patient B8 and B13

description:
Library name: B8, B13
FFPE Spatial transcriptomics

value: Skin


title: DonorA cells perturbed with STYXL1 knockdown by CRISPRi under Th2 culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_STYXL1_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorA_bulkRNAseq.csv

tag: cell type

tag: treatment

tag: experimental perturbation

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

tag: sample preservation_method

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: Caucasian

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: Nevus and melanoma in a single slide of patient B4

description:
Library name: B4
FFPE Spatial transcriptomics

tag: tissue


title: RNA Pol II S5P, liver, Fed wt, rep2

description:
Library name: ChIP_RNA_Pol2_S5P_Fedwt_2
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

value: liver

tag: cell line

value: hepatocyte

tag: genotype

value: WT

value: Ad. Lib Fed, ZT14 sacrifice

tag: chip antibody

value: RNA Pol II S5P, Abcam ab5408


title: low blood glucose, high body weight at weaning, male, subcutaneous adipose tissue, replicate 1

value: subcutaneous adipose tissue

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: high body weight at weaning, female, subcutaneous adipose tissue, replicate 3

value: female

value: high body weight at weaning


title: RNA Pol II S5P, liver, Fed wt, rep1

description:
Library name: ChIP_RNA_Pol2_S5P_Fedwt_1
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

tag: cell type

tag: treatment


title: DonorA cells perturbed with STYXL1 knockdown by CRISPRi under Th1 culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_STYXL1_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorA_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 STYXL1

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: 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

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy


title: high body weight at weaning, female, subcutaneous adipose tissue, replicate 2

tag: tissue

value: subcutaneous adipose tissue

tag: strain

value: TallyHo/JngJ

tag: Sex

tag: age

value: 18 weeks

tag: development stage

tag: condition


title: Nevus and melanoma in a single slide of patient B1 and B38ex

description:
Library name: B1, B38ex
FFPE Spatial transcriptomics

value: Skin


title: DonorA cells perturbed with PPP1R7 knockdown by CRISPRi under nonpolarized culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_PPP1R7_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorA_bulkRNAseq.csv

value: blood

tag: cell type

tag: treatment

tag: experimental perturbation

value: CRISPRi knockdown of PPP1R7

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

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: Caucasian

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: Nevus and melanoma in a single slide of patient A34

description:
Library name: A34
FFPE Spatial transcriptomics

tag: tissue


title: high body weight at weaning, female, subcutaneous adipose tissue, replicate 1

tag: strain

tag: Sex

value: female

tag: age

value: adult

value: high body weight at weaning


title: IgG, HEK293T, Flag-Vps15 overexpression, rep2

description: Library name: CutRun_IgG_Flag-Vps15_2

data_processing:
Reads were filtered with SAOPnuke to remove adaptor sequences and low quality reads.
Clean reads were aligned to the hg38 genome with Bowtie2 version 2.4.4.
samtools, picard tools, and bedtools  were used to filter reads with mapq score higher than 40, and remove duplicated and blacklisted regions
Composition bias normalization with csaw was performed to generate bigwig files.
Peak calling was performed with MACS2 and differential binding analysis was performed with Diffbind 3.10.0 or the bdgdiff command in MACS2. Peaks were annotated with ChIPseeker and pathway analysis and visualization was performed with clusterProfiler.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Run

source_name: HEK293T cells

growth_protocol: HEK293T cells were transfected with either pcDNA3.1 empty vector (ev) or Flag-Vps15 constructs for 24h prior to Cut & Run.

extract_protocol:
Cells were scraped from plates in Cut & Run Wash Buffer with protease and phosphotase inhibitors and briefly fixed with 0.1% formaldehyde in DPBS for 3min. After washing with Wash Buffer, cells were attached to Concavalin A beads, and then incubated with respective antibodies for 1h. Cells attached to beads were then washed twice with Wash Buffer and then incubated with pAG-MNase for 10min, and washed twice again prior to putting on ice and adding Ca2+ to each well to inititate the cutting of pAG-MNase. Ca2+ was quenched with Stop  Buffer and DNA fragments eluted at 37C. DNA was purified with phenol-chloroform extraction prior to library preparation, quality control, and sequencing.
DNA fragments were subject to end-repair and 3' adenylation. PCR products were enriched using Agencourt AMPure XP-medium kit. dsDNA PCR products were denatured and circularized by the splint oligonucleotide sequence. Single-stranded circular DNA was formatted as the final library, and DNA nanoballs were made from the library and loaded into a patterned nanoarray. Paired-end reads were generated by sequenced combinatorial Probe-Anchor-Synthesis with the DNBSEQ-400 sequencer.

tag: cell line

value: HEK293T cells

tag: genotype

value: WT

value: basal growth media, Flag-Vps15 overexpression

tag: chip antibody

value: IgG, Cell Signaling 3900


title: IgG, HEK293T, Flag-Vps15 overexpression, rep1

description: Library name: CutRun_IgG_Flag-Vps15_1

tag: treatment


title: DonorA cells perturbed with PPP1R7 knockdown by CRISPRi under Th2 culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_PPP1R7_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorA_bulkRNAseq.csv

tag: cell type

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

tag: donor id

tag: donor age

value: No

tag: donor blood_type

value: O+

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

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy


title: Nevus and melanoma in a single slide of patient A22 and A24

description:
Library name: A22, A24
FFPE Spatial transcriptomics

tag: tissue

value: Skin


title: high blood glucose, low body weight at weaning, male, subcutaneous adipose tissue, replicate 2

value: subcutaneous adipose tissue

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: DonorA cells perturbed with PPP1R7 knockdown by CRISPRi under Th1 culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_PPP1R7_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorA_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: treatment

tag: experimental perturbation

value: CRISPRi knockdown of PPP1R7

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

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: Caucasian

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: IgG, HEK293T, empty vector overexpression, rep2

description: Library name: CutRun_IgG_ev_2

tag: cell line

value: HEK293T cells

tag: genotype

value: WT

value: basal growth media, empty vector overexpression

tag: chip antibody

value: IgG, Cell Signaling 3900


title: high blood glucose, low body weight at weaning, male, subcutaneous adipose tissue, replicate 1

tag: tissue

tag: strain

tag: Sex

tag: age

tag: development stage

tag: condition


title: Nevus and melanoma in a single slide of patient A16 and A23

description:
Library name: A16, A23
FFPE Spatial transcriptomics

value: Skin


title: DonorA cells perturbed with Non-targeting control 2 by CRISPRi under nonpolarized culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_NTC2_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorA_bulkRNAseq.csv

tag: cell type

tag: treatment

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

tag: experimental perturbation

value: CRISPRi non-targeting control

tag: donor id

tag: donor age

tag: donor weight

value: No

tag: donor blood_type

value: O+

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

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy


title: high blood glucose, high body weight at weaning, male, subcutaneous adipose tissue, replicate 3

tag: tissue

value: subcutaneous adipose tissue

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: DonorA cells perturbed with Non-targeting control 2 by CRISPRi under Th2 culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_NTC2_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorA_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: treatment

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

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: Caucasian

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: high blood glucose, high body weight at weaning, male, subcutaneous adipose tissue, replicate 2

tag: tissue

tag: strain

tag: Sex


title: DonorA cells perturbed with Non-targeting control 2 by CRISPRi under Th1 culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_NTC2_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorA_bulkRNAseq.csv

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

value: CRISPRi non-targeting control

value: No

tag: donor blood_type

value: O+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy


title: DonorA cells perturbed with Non-targeting control 1 by CRISPRi under nonpolarized culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_NTC1_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorA_bulkRNAseq.csv

tag: cell type

tag: treatment

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Male

value: adult stage

value: TRUE

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield


title: H3K4me3, HEK293T, Flag-Vps15 overexpression, rep1

description:
Library name: CutRun_H3K4me3_Flag-Vps15_1
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

tag: cell line

value: HEK293T cells

tag: genotype

value: WT

value: basal growth media, Flag-Vps15 overexpression

tag: chip antibody

value: H3K4me3, Cell Signaling 9751


title: Nevus and melanoma in a single slide of patient A2 and A17

description:
Library name: A2, A17
FFPE Spatial transcriptomics

tag: tissue

value: Skin


title: high blood glucose, high body weight at weaning, male, subcutaneous adipose tissue, replicate 1

value: subcutaneous adipose tissue

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: H3K4me3, HEK293T, empty vector overexpression, rep2

description:
Library name: CutRun_H3K4me3_ev_2
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

tag: treatment

value: basal growth media, empty vector overexpression


title: low body weight at weaning, female, muscle, replicate 3

source_name: muscle

value: muscle

value: female

value: low body weight at weaning


title: DonorA cells perturbed with Non-targeting control 1 by CRISPRi under Th2 culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_NTC1_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorA_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

value: No

tag: donor blood_type

value: O+

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: 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: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: M-ST-37

city: Houston

first: Yang

last: Liu

state: TEXAS

address: 1885 EL Paseo St

institute: MD anderson cancer center

description: Library name: M-ST-37

library_source: other

data_processing:
Spaceranger
Assembly: GRCh38
Supplementary files format and content: Spaceranger output
Library strategy: Spatial Transcriptomics

molecule: other

source_name: Colorectal cancer metastasis

extract_protocol:
formalin-fixed paraffin-embedded (FFPE) biopsy sections were prepared from 37 colorectal cancer metastasis samples
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent

tag: tissue

value: Colorectal cancer metastasis


title: low body weight at weaning, female, muscle, replicate 2

value: muscle

tag: strain

value: TallyHo/JngJ

tag: Sex

value: female

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition

value: low body weight at weaning


title: DonorA cells perturbed with Non-targeting control 1 by CRISPRi under Th1 culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_NTC1_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorA_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: treatment

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

tag: experimental perturbation

value: CRISPRi 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

tag: source

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield


title: M-ST-36

description: Library name: M-ST-36

tag: tissue


title: M-ST-35

description: Library name: M-ST-35


title: DonorA cells perturbed with NKTR knockdown by CRISPRi under nonpolarized culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_NKTR_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorA_bulkRNAseq.csv

value: CRISPRi knockdown of NKTR

value: ACDA

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: 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: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

tag: batch


title: RNA, MEF Vps15KO, -4h+4h_Methionine, rep3

description:
Library name: Methionine_-4h+4h_Methionine_Vps15KO_24
clean reads
vst_normalized_counts.csv

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 STAR-2.7.10b and counts generated uing featurecounts. Variance stabilized transformation was used to generate vst normalized count table. Deseq2 and limma were used for differential expression analysis. Direct comparisons were made between treatment conditions. DOSE Gene Set Enrichment Analysis was performed with the DOSE package, in R.
Assembly: mm10
Supplementary files format and content: variance stabilized transformation counts table

source_name: MEF Vps15f/f

growth_protocol: Cells were grown to 90% confluence in 15cm plates in DMEM High Glucose (4.5g/L) + 10% FBS prior to cell treatments.

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

treatment_protocol: MEFs were kept in basal media (DMEM High Glucose, without FBS, methionine-free DMEM, or methionine-free DMEM + methionine replenishment for indicated times.

tag: cell line

value: MEF Vps15f/f

tag: cell type

value: mouse embryonic fibroblast

tag: genotype

tag: treatment

value: Methionine -4h+4h


title: RNA, MEF Vps15KO, -4h+4h_Methionine, rep2

description:
Library name: Methionine_-4h+4h_Methionine_Vps15KO_23
clean reads
vst_normalized_counts.csv


title: low blood glucose, low body weight at weaning, male, muscle, replicate 3

value: muscle

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: RNA, MEF Vps15KO, -4h+4h_Methionine, rep1

description:
Library name: Methionine_-4h+4h_Methionine_Vps15KO_22
clean reads
vst_normalized_counts.csv


title: low blood glucose, low body weight at weaning, male, muscle, replicate 2

tag: tissue


title: DonorA cells perturbed with NKTR knockdown by CRISPRi under Th1 culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_NKTR_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorA_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 NKTR

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

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

value: Plasmidsaurus RNA-Seq


title: M-ST-33

description: Library name: M-ST-33

value: Colorectal cancer metastasis


title: low blood glucose, low body weight at weaning, male, muscle, replicate 1

tag: strain

tag: Sex

tag: age

tag: development stage

tag: condition


title: RNA, MEF WT, -4h+4h_Methionine, rep3

description:
Library name: Methionine_-4h+4h_Methionine_WT_21
clean reads
vst_normalized_counts.csv

tag: cell line

value: MEF Vps15f/f

tag: cell type

value: mouse embryonic fibroblast

tag: genotype

value: WT

tag: treatment


title: M-ST-32

description: Library name: M-ST-32

tag: tissue


title: DonorA cells perturbed with MAMLD1 knockdown by CRISPRi under nonpolarized culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_MAMLD1_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorA_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi knockdown of MAMLD1

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

value: Male

value: adult stage

value: TRUE

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: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

tag: batch


title: low blood glucose, high body weight at weaning, male, muscle, replicate 3

value: muscle

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: RNA, MEF WT, -4h+4h_Methionine, rep2

description:
Library name: Methionine_-4h+4h_Methionine_WT_20
clean reads
vst_normalized_counts.csv

tag: cell line

value: MEF Vps15f/f

tag: cell type

tag: genotype

tag: treatment

value: Methionine -4h+4h


title: DonorA cells perturbed with MAMLD1 knockdown by CRISPRi under Th2 culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_MAMLD1_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorA_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

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: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

value: Plasmidsaurus RNA-Seq


title: M-ST-31

description: Library name: M-ST-31

value: Colorectal cancer metastasis


title: DonorA cells perturbed with MAMLD1 knockdown by CRISPRi under Th1 culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_MAMLD1_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorA_bulkRNAseq.csv

tag: cell type

value: CRISPRi knockdown of MAMLD1

value: ACDA

tag: source

value: STEMCELL technologies

value: Male

value: adult stage

value: TRUE

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: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

tag: batch


title: M-ST-30

description: Library name: M-ST-30

tag: tissue


title: low blood glucose, high body weight at weaning, male, muscle, replicate 2

value: muscle

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: low blood glucose, high body weight at weaning, male, muscle, replicate 1


title: DonorA cells perturbed with JAK2 knockdown by CRISPRi under nonpolarized culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_JAK2_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorA_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

tag: treatment

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

tag: experimental perturbation

value: CRISPRi knockdown of JAK2

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: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

value: Normal

value: Zymo DNA/RNA Shield


title: RNA, MEF Vps15KO, -4h+1h_Methionine, rep3

description:
Library name: Methionine_-4h+1h_Methionine_Vps15KO_18
clean reads
vst_normalized_counts.csv

tag: cell line

value: MEF Vps15f/f

tag: cell type

value: mouse embryonic fibroblast

tag: genotype

value: Methionine -4h+!h


title: M-ST-29

description: Library name: M-ST-29

tag: tissue

value: Colorectal cancer metastasis


title: RNA, MEF Vps15KO, -4h+1h_Methionine, rep2

description:
Library name: Methionine_-4h+1h_Methionine_Vps15KO_17
clean reads
vst_normalized_counts.csv

tag: treatment


title: DonorA cells perturbed with JAK2 knockdown by CRISPRi under Th2 culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_JAK2_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorA_bulkRNAseq.csv

tag: experimental perturbation

value: ACDA

tag: source

value: STEMCELL technologies

value: Male

value: adult stage

value: TRUE

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

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

tag: donor ethnicity

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: IgG, HEK293T, empty vector overexpression, rep1

description: Library name: CutRun_IgG_ev_1

value: HEK293T cells

value: WT

value: basal growth media, empty vector overexpression

tag: chip antibody

value: IgG, Cell Signaling 3900


title: H3K4me3, HEK293T, Flag-Vps15 overexpression, rep2

description:
Library name: CutRun_H3K4me3_Flag-Vps15_2
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

value: basal growth media, Flag-Vps15 overexpression

value: H3K4me3, Cell Signaling 9751


title: Nevus and melanoma in a single slide of patient A21

description:
Library name: A21
FFPE Spatial transcriptomics

value: Skin


title: Nevus and melanoma in a single slide of patient A7

description:
Library name: A7
FFPE Spatial transcriptomics


title: high body weight at weaning, female, muscle, replicate 2

value: muscle

tag: strain

value: TallyHo/JngJ

tag: Sex

value: female

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition

value: high body weight at weaning


title: M-ST-28

description: Library name: M-ST-28

tag: tissue

value: Colorectal cancer metastasis


title: RNA, MEF Vps15KO, -4h+1h_Methionine, rep1

description:
Library name: Methionine_-4h+1h_Methionine_Vps15KO_16
clean reads
vst_normalized_counts.csv

tag: cell line

value: MEF Vps15f/f

tag: cell type

value: mouse embryonic fibroblast

tag: genotype

tag: treatment

value: Methionine -4h+!h


title: DonorA cells perturbed with JAK2 knockdown by CRISPRi under Th1 culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_JAK2_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorA_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 JAK2

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: 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

value: Caucasian

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: M-ST-27

description: Library name: M-ST-27

tag: tissue

value: Colorectal cancer metastasis


title: RNA, MEF WT, -4h+1h_Methionine, rep3

description:
Library name: Methionine_-4h+1h_Methionine_WT_15
clean reads
vst_normalized_counts.csv

tag: cell line

value: MEF Vps15f/f

tag: cell type

value: mouse embryonic fibroblast

tag: genotype

value: WT

tag: treatment

value: Methionine -4h+!h


title: M-ST-38

description: Library name: M-ST-38


title: H3K4me3, HEK293T, empty vector overexpression, rep1

description:
Library name: CutRun_H3K4me3_ev_1
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

value: HEK293T cells

value: basal growth media, empty vector overexpression

tag: chip antibody

value: H3K4me3, Cell Signaling 9751


title: DonorA cells perturbed with GATA3 knockdown by CRISPRi under nonpolarized culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_GATA3_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorA_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 GATA3

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

value: O+

value: ACDA

value: STEMCELL technologies

value: Male

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: high body weight at weaning, female, muscle, replicate 1

tag: tissue

value: muscle

tag: strain

value: TallyHo/JngJ

tag: Sex

value: female

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition

value: high body weight at weaning


title: M-ST-26

description: Library name: M-ST-26

value: Colorectal cancer metastasis


title: high blood glucose, low body weight at weaning, male, muscle, replicate 3

value: male


title: DonorA cells perturbed with GATA3 knockdown by CRISPRi under Th2 culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_GATA3_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorA_bulkRNAseq.csv

value: blood

tag: cell type

tag: treatment

tag: experimental perturbation

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: 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

value: Caucasian

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: RNA, MEF WT, -4h+1h_Methionine, rep2

description:
Library name: Methionine_-4h+1h_Methionine_WT_14
clean reads
vst_normalized_counts.csv

tag: cell line

value: MEF Vps15f/f

value: mouse embryonic fibroblast

tag: genotype

value: WT

value: Methionine -4h+!h


title: M-ST-25

description: Library name: M-ST-25

tag: tissue


title: low body weight at weaning, female, muscle, replicate 1

value: muscle

tag: strain

value: TallyHo/JngJ

tag: Sex

value: female

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition

value: low body weight at weaning


title: RNA, MEF WT, -4h+1h_Methionine, rep1

description:
Library name: Methionine_-4h+1h_Methionine_WT_13
clean reads
vst_normalized_counts.csv

tag: cell type

tag: treatment


title: DonorA cells perturbed with NKTR knockdown by CRISPRi under Th2 culture condition in batch Diff084

description:
Library name: Th1Th2_validation_Diff084_DonorA_NKTR_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorA_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 NKTR

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: Male

value: adult stage

value: TRUE

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


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

description:
Library name: Th1Th2_validation_Diff084_DonorA_GATA3_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorA_bulkRNAseq.csv

tag: tissue

tag: cell type

value: CRISPRi knockdown of GATA3

tag: donor dev_stage

tag: donor living_at_sample_collection

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

value: Caucasian

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: high blood glucose, low body weight at weaning, male, muscle, replicate 2

value: muscle

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: M-ST-24

description: Library name: M-ST-24

value: Colorectal cancer metastasis


title: M-ST-34

description: Library name: M-ST-34


title: RNA, MEF Vps15KO, -4h_Methionine, rep3

description:
Library name: Methionine_-4h_Methionine_Vps15KO_12
clean reads
vst_normalized_counts.csv

tag: cell line

value: MEF Vps15f/f

value: mouse embryonic fibroblast

tag: genotype

tag: treatment

value: Methionine -4h


title: M-ST-23

description: Library name: M-ST-23


title: DonorZ cells perturbed with TBX21 knockdown by CRISPRi under nonpolarized culture condition in batch Diff081

description:
Library name: Th1Th2_validation_Diff081_DonorZ_TBX21_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorZ_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 TBX21

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Yes

tag: donor blood_type

value: AB+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

value: adult stage

value: TRUE

tag: donor ethnicity

value: Mixed

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: high blood glucose, low body weight at weaning, male, muscle, replicate 1

tag: tissue

value: muscle

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: high blood glucose, high body weight at weaning, male, muscle, replicate 4


title: RNA, MEF Vps15KO, -4h_Methionine, rep2

description:
Library name: Methionine_-4h_Methionine_Vps15KO_11
clean reads
vst_normalized_counts.csv

tag: cell line

value: MEF Vps15f/f

tag: cell type

value: mouse embryonic fibroblast

tag: genotype

tag: treatment

value: Methionine -4h


title: DonorZ cells perturbed with STAT6 knockdown by CRISPRi under nonpolarized culture condition in batch Diff081

description:
Library name: Th1Th2_validation_Diff081_DonorZ_STAT6_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorZ_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 STAT6

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor dev_stage

tag: donor living_at_sample_collection

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

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: M-ST-22

description: Library name: M-ST-22

tag: tissue

value: Colorectal cancer metastasis


title: RNA, MEF Vps15KO, -4h_Methionine, rep1

description:
Library name: Methionine_-4h_Methionine_Vps15KO_10
clean reads
vst_normalized_counts.csv

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: high blood glucose, high body weight at weaning, male, muscle, replicate 3

value: muscle

tag: strain

value: TallyHo/JngJ

tag: Sex

tag: age

tag: development stage

tag: condition


title: DonorZ cells perturbed with PTPN2 knockdown by CRISPRi under nonpolarized culture condition in batch Diff081

description:
Library name: Th1Th2_validation_Diff081_DonorZ_PTPN2_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorZ_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi knockdown of PTPN2

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Yes

tag: donor blood_type

value: AB+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

value: adult stage

value: TRUE

tag: donor ethnicity

value: Mixed

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: M-ST-21

description: Library name: M-ST-21

tag: tissue


title: high blood glucose, high body weight at weaning, male, muscle, replicate 2

tag: strain

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: RNA, MEF WT, -4h_Methionine, rep3

description:
Library name: Methionine_-4h_Methionine_WT_9
clean reads
vst_normalized_counts.csv

tag: cell line

value: MEF Vps15f/f

tag: cell type

value: mouse embryonic fibroblast

tag: genotype

value: WT

tag: treatment

value: Methionine -4h


title: DonorZ cells perturbed with Non-targeting control 3 by CRISPRi under nonpolarized culture condition in batch Diff081

description:
Library name: Th1Th2_validation_Diff081_DonorZ_NTC3_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorZ_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 non-targeting control

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor dev_stage

tag: donor living_at_sample_collection

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

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: M-ST-20

description: Library name: M-ST-20

tag: tissue

value: Colorectal cancer metastasis


title: RNA, MEF WT, -4h_Methionine, rep2

description:
Library name: Methionine_-4h_Methionine_WT_8
clean reads
vst_normalized_counts.csv

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: DonorZ cells perturbed with Non-targeting control 2 by CRISPRi under nonpolarized culture condition in batch Diff081

description:
Library name: Th1Th2_validation_Diff081_DonorZ_NTC2_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorZ_bulkRNAseq.csv

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor weight

value: Yes

value: AB+

value: ACDA

value: STEMCELL technologies

tag: donor sex

value: Female

value: adult stage

value: TRUE

tag: donor ethnicity

value: Mixed

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: high blood glucose, high body weight at weaning, male, muscle, replicate 1

value: muscle

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: M-ST-19

description: Library name: M-ST-19

tag: tissue


title: RNA, MEF WT, -4h_Methionine, rep1

description:
Library name: Methionine_-4h_Methionine_WT_7
clean reads
vst_normalized_counts.csv

tag: cell line

value: MEF Vps15f/f

tag: cell type

value: mouse embryonic fibroblast

tag: genotype

value: WT

tag: treatment

value: Methionine -4h


title: low body weight at weaning, female, liver, replicate 2

value: liver

value: female

value: low body weight at weaning


title: DonorZ cells perturbed with Non-targeting control 1 by CRISPRi under nonpolarized culture condition in batch Diff081

description:
Library name: Th1Th2_validation_Diff081_DonorZ_NTC1_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorZ_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 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: AB+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor dev_stage

tag: donor living_at_sample_collection

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

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: M-ST-18

description: Library name: M-ST-18

tag: tissue

value: Colorectal cancer metastasis


title: RNA, MEF WT, -4h+4h_Methionine, rep1

description:
Library name: Methionine_-4h+4h_Methionine_WT_19
clean reads
vst_normalized_counts.csv

tag: cell line

value: MEF Vps15f/f

tag: cell type

value: mouse embryonic fibroblast

tag: genotype

value: WT

tag: treatment

value: Methionine -4h+4h


title: low body weight at weaning, female, liver, replicate 1

value: liver

tag: strain

value: TallyHo/JngJ

tag: Sex

value: female

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition

value: low body weight at weaning


title: DonorZ cells perturbed with MTA2 knockdown by CRISPRi under nonpolarized culture condition in batch Diff081

description:
Library name: Th1Th2_validation_Diff081_DonorZ_MTA2_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorZ_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 MTA2

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Yes

tag: donor blood_type

value: AB+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

value: adult stage

value: TRUE

tag: donor ethnicity

value: Mixed

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: M-ST-17

description: Library name: M-ST-17

tag: tissue

value: Colorectal cancer metastasis


title: RNA, MEF Vps15KO, basal, rep2

description:
Library name: Methionine_basal_Vps15KO_5
clean reads
vst_normalized_counts.csv

tag: cell line

value: MEF Vps15f/f

tag: cell type

value: mouse embryonic fibroblast

tag: genotype

tag: treatment

value: Basal methionine


title: low blood glucose, low body weight at weaning, male, liver, replicate 3

value: liver

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: DonorZ cells perturbed with MED24 knockdown by CRISPRi under nonpolarized culture condition in batch Diff081

description:
Library name: Th1Th2_validation_Diff081_DonorZ_MED24_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorZ_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 MED24

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Yes

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor dev_stage

tag: donor living_at_sample_collection

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

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: M-ST-16

description: Library name: M-ST-16

tag: tissue

value: Colorectal cancer metastasis


title: RNA, MEF Vps15KO, basal, rep1

description:
Library name: Methionine_basal_Vps15KO_4
clean reads
vst_normalized_counts.csv

tag: cell line

value: MEF Vps15f/f

tag: cell type

value: mouse embryonic fibroblast

tag: genotype

tag: treatment

value: Basal methionine


title: low blood glucose, low body weight at weaning, male, liver, replicate 2

value: liver

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

tag: development stage

tag: condition


title: RNA, MEF Vps15KO, basal, rep3

description:
Library name: Methionine_basal_Vps15KO_6
clean reads
vst_normalized_counts.csv


title: M-ST-15

description: Library name: M-ST-15


title: RNA, MEF WT, basal, rep3

description:
Library name: Methionine_basal_WT_3
clean reads
vst_normalized_counts.csv

value: WT


title: low blood glucose, low body weight at weaning, male, liver, replicate 1

value: 18 weeks

value: adult


title: DonorZ cells perturbed with JAK2 knockdown by CRISPRi under nonpolarized culture condition in batch Diff081

description:
Library name: Th1Th2_validation_Diff081_DonorZ_JAK2_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorZ_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 JAK2

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: AB+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

value: adult stage

value: TRUE

tag: donor ethnicity

value: Mixed

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: RNA, MEF WT, basal, rep2

description:
Library name: Methionine_basal_WT_2
clean reads
vst_normalized_counts.csv

tag: cell line

value: MEF Vps15f/f

tag: cell type

value: mouse embryonic fibroblast

tag: genotype

tag: treatment

value: Basal methionine


title: low blood glucose, high body weight at weaning, male, liver, replicate 4

tag: tissue

value: liver

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

tag: development stage

tag: condition


title: M-ST-14

description: Library name: M-ST-14

value: Colorectal cancer metastasis


title: DonorZ cells perturbed with GATA3 knockdown by CRISPRi under nonpolarized culture condition in batch Diff081

description:
Library name: Th1Th2_validation_Diff081_DonorZ_GATA3_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorZ_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi knockdown of GATA3

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Yes

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor dev_stage

tag: donor living_at_sample_collection

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

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: high body weight at weaning, female, muscle, replicate 3

tag: tissue

value: muscle

tag: strain

tag: Sex

value: female

tag: age

value: 18 weeks

tag: development stage

value: adult

value: high body weight at weaning


title: RNA, MEF WT, basal, rep1

description:
Library name: Methionine_basal_WT_1
clean reads
vst_normalized_counts.csv

tag: cell line

value: MEF Vps15f/f

tag: cell type

value: mouse embryonic fibroblast

tag: genotype

value: WT

tag: treatment

value: Basal methionine


title: low blood glucose, high body weight at weaning, male, liver, replicate 3

value: liver

value: TallyHo/JngJ

value: male

tag: condition


title: M-ST-12

description: Library name: M-ST-12

value: Colorectal cancer metastasis


title: M-ST-13

description: Library name: M-ST-13


title: DonorZ cells perturbed with FBXO32 knockdown by CRISPRi under nonpolarized culture condition in batch Diff081

description:
Library name: Th1Th2_validation_Diff081_DonorZ_FBXO32_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorZ_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 FBXO32

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Yes

tag: donor blood_type

value: AB+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

value: adult stage

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

tag: donor ethnicity

value: Mixed

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: Input for H3K4me3 Fast Vps15LKO

description: Library name: Input_for_H3K4me3_FastKO

data_processing:
Reads were filtered with SAOPnuke to remove adaptor sequences and low quality reads.
Clean reads were aligned to the mm10/hg38 genome with Bowtie2 version 2.4.4.
samtools, picard tools, and bedtools  were used to filter reads with mapq score higher than 40, and remove duplicated and blacklisted regions
Composition bias normalization with csaw was performed to generate bigwig files.
Peak calling was performed with MACS2 and differential binding analysis was performed with Diffbind 3.10.0 or the bdgdiff command in MACS2. Peaks were annotated with ChIPseeker and pathway analysis and visualization was performed with clusterProfiler.
Assembly: mm10, hg38
Supplementary files format and content: bigwig

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 ChIP.

extract_protocol:
Liver powder was fixed for 15min at RT with 1% formaldehyde and then quenched with glycine. Tissue was washed and homogenized, after which was soncated to acheieve 200-500bp fragments.
DNA fragments were subject to end-repair and 3' adenylation. PCR products were enriched using Agencourt AMPure XP-medium kit. dsDNA PCR products were denatured and circularized by the splint oligonucleotide sequence. Single-stranded circular DNA was formatted as the final library, and DNA nanoballs were made from the library and loaded into a patterned nanoarray. Paired-end reads were generated by sequenced combinatorial Probe-Anchor-Synthesis with the DNBSEQ-400 sequencer.

tag: tissue

value: liver

tag: cell type

value: hepatocyte

tag: genotype

value: Ttr CRE+, Vps15f/f

tag: treatment

value: Fast 24h, ZT14 sacrifice

tag: chip antibody

value: input


title: DonorZ cells perturbed with FAM120A knockdown by CRISPRi under nonpolarized culture condition in batch Diff081

description:
Library name: Th1Th2_validation_Diff081_DonorZ_FAM120A_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorZ_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 FAM120A

tag: donor id

tag: donor age

tag: donor weight

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

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

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: M-ST-11

description: Library name: M-ST-11

value: Colorectal cancer metastasis


title: low blood glucose, high body weight at weaning, male, liver, replicate 1

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: Input for H3K4me3 Fed Vps15LKO

description: Library name: Input_for_H3K4me3_FedKO

tag: tissue

value: liver

tag: cell type

tag: genotype

tag: treatment

value: Ad. Lib Fed, ZT14 sacrifice


title: Input for H3K4me3 Fast wt

description: Library name: Input_for_H3K4me3_Fastwt

value: hepatocyte

value: WT

tag: chip antibody


title: M-ST-10

description: Library name: M-ST-10


title: DonorZ cells perturbed with CDKAL1 knockdown by CRISPRi under nonpolarized culture condition in batch Diff081

description:
Library name: Th1Th2_validation_Diff081_DonorZ_CDKAL1_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorZ_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi knockdown of CDKAL1

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Yes

tag: donor blood_type

value: AB+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

value: adult stage

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

tag: donor ethnicity

value: Mixed

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: high body weight at weaning, female, liver, replicate 2

tag: tissue

tag: strain

value: TallyHo/JngJ

tag: Sex

value: female

tag: age

value: 18 weeks

tag: development stage

tag: condition

value: high body weight at weaning


title: low blood glucose, high body weight at weaning, male, liver, replicate 2

value: liver

value: male

value: adult


title: DonorZ cells perturbed with APPBP2 knockdown by CRISPRi under nonpolarized culture condition in batch Diff081

description:
Library name: Th1Th2_validation_Diff081_DonorZ_APPBP2_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorZ_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: treatment

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

tag: experimental perturbation

value: CRISPRi knockdown of APPBP2

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

value: Yes

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

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

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: DonorZ cells perturbed with KDM1A knockdown by CRISPRi under nonpolarized culture condition in batch Diff081

description:
Library name: Th1Th2_validation_Diff081_DonorZ_KDM1A_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorZ_bulkRNAseq.csv

tag: tissue

value: CRISPRi knockdown of KDM1A

tag: donor smoker

tag: donor blood_type

value: AB+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

value: adult stage

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: M-ST-09

description: Library name: M-ST-09

value: Colorectal cancer metastasis


title: Input for H3K4me3 Fed wt

description: Library name: Input_for_H3K4me3_Fedwt

value: liver

tag: cell type

value: hepatocyte

tag: genotype

value: WT

tag: treatment

value: Ad. Lib Fed, ZT14 sacrifice

tag: chip antibody

value: input


title: DonorY cells perturbed with TBX21 knockdown by CRISPRi under nonpolarized culture condition in batch Diff081

description:
Library name: Th1Th2_validation_Diff081_DonorY_TBX21_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorY_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 TBX21

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

value: No

value: O+

value: Male

tag: donor dev_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: African American

value: CRISPRi


title: H3K4me3, liver, Fast Vps15LKO, rep2

description:
Library name: ChIP_H3K4me3_FastKO_2
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

tag: tissue

value: Ttr CRE+, Vps15f/f

value: Fast 24h, ZT14 sacrifice

value: H3K4me3, Cell Signaling 9751


title: high body weight at weaning, female, liver, replicate 1

value: liver

tag: strain

value: TallyHo/JngJ

tag: Sex

value: female

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition

value: high body weight at weaning


title: M-ST-08

description: Library name: M-ST-08

value: Colorectal cancer metastasis


title: high blood glucose, low body weight at weaning, male, liver, replicate 3

value: male


title: DonorY cells perturbed with STAT6 knockdown by CRISPRi under nonpolarized culture condition in batch Diff081

description:
Library name: Th1Th2_validation_Diff081_DonorY_STAT6_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorY_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: treatment

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

value: CRISPRi knockdown of STAT6

tag: donor smoker

value: No

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: adult stage

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: M-ST-07

description: Library name: M-ST-07

tag: tissue


title: H3K4me3, liver, Fast Vps15LKO, rep1

description:
Library name: ChIP_H3K4me3_FastKO_1
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

value: liver

value: hepatocyte

tag: genotype

value: Ttr CRE+, Vps15f/f

value: Fast 24h, ZT14 sacrifice

tag: chip antibody

value: H3K4me3, Cell Signaling 9751


title: DonorY cells perturbed with PTPN2 knockdown by CRISPRi under nonpolarized culture condition in batch Diff081

description:
Library name: Th1Th2_validation_Diff081_DonorY_PTPN2_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorY_bulkRNAseq.csv

value: blood

tag: experimental perturbation

value: CRISPRi knockdown of PTPN2

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

value: O+

value: Male

tag: donor dev_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: African American

value: CRISPRi


title: high blood glucose, low body weight at weaning, male, liver, replicate 2

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: M-ST-06

description: Library name: M-ST-06

tag: tissue

value: Colorectal cancer metastasis


title: M-ST-05

description: Library name: M-ST-05


title: H3K4me3, liver, Fed Vps15LKO, rep1

description:
Library name: ChIP_H3K4me3_FedKO_1
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

value: liver

tag: cell type

tag: genotype

tag: treatment

value: Ad. Lib Fed, ZT14 sacrifice

tag: chip antibody


title: IX_56690

description: Library name: IX_56690


title: DonorY cells perturbed with Non-targeting control 2 by CRISPRi under nonpolarized culture condition in batch Diff081

description:
Library name: Th1Th2_validation_Diff081_DonorY_NTC2_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorY_bulkRNAseq.csv

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 smoker

value: No

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: adult stage

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: H3K4me3, liver, Fast wt, rep2

description:
Library name: ChIP_H3K4me3_Fastwt_2
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

tag: tissue

tag: cell type

value: hepatocyte

tag: genotype

value: WT

tag: treatment

value: Fast 24h, ZT14 sacrifice

value: H3K4me3, Cell Signaling 9751


title: high blood glucose, high body weight at weaning, male, liver, replicate 4

value: liver

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: high blood glucose, high body weight at weaning, male, liver, replicate 3