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

description:
Library name: Th1Th2_validation_Diff081_DonorY_NTC1_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 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

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: IX_56689

status: Public on Jun 02 2026

type: SRA

city: Houston

first: Yang

last: Liu

state: TEXAS

address: 1885 EL Paseo St

country: USA

institute: MD anderson cancer center

description: Library name: IX_56689

library_source: other

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

molecule: other

organism: Homo sapiens

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: H3K4me3, liver, Fast wt, 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_H3K4me3_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.

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/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

molecule: genomic DNA

organism: Mus musculus

source_name: liver

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

value: liver

tag: cell type

value: hepatocyte

tag: genotype

value: WT

tag: treatment

value: Fast 24h, ZT14 sacrifice

tag: chip antibody

value: H3K4me3, Cell Signaling 9751


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

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

library_source: transcriptomic

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.

molecule: total RNA

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

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: H3K4me3, liver, Fed wt, rep2

description:
Library name: ChIP_H3K4me3_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: Ad. Lib Fed, ZT14 sacrifice


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


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

city: Palo Alto

first: Lattice

last: Data Coordination

state: CA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

description:
Library name: Th1Th2_validation_Diff081_DonorY_MED24_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorY_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)

molecule: polyA RNA

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 MED24

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

tag: anticoagulant

value: ACDA

value: STEMCELL technologies

tag: donor 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: low body weight at weaning, female, hypothalamus, replicate 3

source_name: hypothalamus

tag: tissue

value: hypothalamus

tag: strain

value: TallyHo/JngJ

tag: Sex

value: female

tag: age

tag: development stage

value: low body weight at weaning


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

description:
Library name: Th1Th2_validation_Diff081_DonorY_KDM1A_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorY_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

tag: cell type

tag: treatment

tag: experimental perturbation

value: CRISPRi knockdown of KDM1A

tag: donor id

tag: donor age

tag: donor weight

value: O+

tag: source

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, Fed wt, rep1

description:
Library name: ChIP_H3K4me3_Fedwt_1
bigwigs have blacklisted regions removed, duplicates removed, filtered to have mapq scores above 40, and are csaw composition bias normalized within each ChIPd factor.

tag: tissue

value: liver

value: hepatocyte

tag: genotype

value: WT

value: Ad. Lib Fed, ZT14 sacrifice

tag: chip antibody

value: H3K4me3, Cell Signaling 9751


title: cyt_Dis3_A_3_polyA

first: Antonin

last: Morillon

state: Paris

address: 26 rue d'Ulm

institute: Institut Curie

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

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

source_name: HCT116 derivative cell line

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

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

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

tag: cell line

tag: fraction

value: cytoplasmic fraction

value: 1h induction with auxin


title: cyt_Dis3_A_2_polyA


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

value: hypothalamus

tag: strain

tag: Sex

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


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

description:
Library name: Th1Th2_validation_Diff081_DonorY_JAK2_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

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

tag: anticoagulant

value: ACDA

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: cyt_Dis3_A_1_polyA

tag: cell line

tag: fraction

value: cytoplasmic fraction


title: Input for RNA Pol II S5P Fed Vps15LKO

description: Library name: Input_FedKO_6

tag: tissue

value: liver

tag: cell type

value: hepatocyte

tag: genotype

value: Ttr CRE+, Vps15f/f

tag: treatment

value: Ad. Lib Fed, ZT14 sacrifice

tag: chip antibody

value: input


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

value: hypothalamus

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

description:
Library name: Th1Th2_validation_Diff081_DonorY_GATA3_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 GATA3

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

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

tag: donor ethnicity

value: African American

value: CRISPRi


title: cyt_Dis3_3_polyA

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

tag: cell line

tag: fraction

value: cytoplasmic fraction

tag: treatment

value: non induced


title: Input for Vps15 Fast wt

description: Library name: Input_Fastwt_4

tag: tissue

value: liver

tag: cell type

value: hepatocyte

tag: genotype

value: WT

value: Fast 24h, ZT14 sacrifice

tag: chip antibody

value: input


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

description:
Library name: Th1Th2_validation_Diff081_DonorY_FBXO32_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 FBXO32

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: Input for RNA Pol II S5P Fast wt

description: Library name: Input_Fastwt_9

tag: treatment


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

tag: tissue

value: hypothalamus

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


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

description:
Library name: Th1Th2_validation_Diff081_DonorY_FAM120A_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorY_bulkRNAseq.csv

tag: cell type

tag: experimental perturbation

value: CRISPRi knockdown of FAM120A

tag: donor id

tag: donor age

value: No

value: O+

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

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

tag: donor ethnicity

value: African American

value: CRISPRi


title: Input for Vps15 Fed wt

description: Library name: Input_Fedwt_1

tag: tissue

value: liver

value: hepatocyte

tag: genotype

value: WT

tag: treatment

value: Ad. Lib Fed, ZT14 sacrifice

tag: chip antibody

value: input


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

description:
Library name: Th1Th2_validation_Diff081_DonorY_CDKAL1_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorY_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

value: CRISPRi knockdown of CDKAL1

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: cyt_ctrl_A_3_polyA

description: polyA enriched RNA from cytoplasmic fraction from HCT116 cell line expressing TIR1 after 1h treatement with auxin

tag: cell line

tag: fraction

value: cytoplasmic fraction

value: 1h induction with auxin


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

value: hypothalamus

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


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

description:
Library name: Th1Th2_validation_Diff081_DonorY_APPBP2_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorY_bulkRNAseq.csv

tag: tissue

tag: cell type

tag: treatment

tag: experimental perturbation

value: CRISPRi knockdown of APPBP2

tag: donor id

tag: donor age

value: No

value: O+

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

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

tag: donor ethnicity

value: African American

value: CRISPRi


title: cyt_ctrl_A_2_polyA

tag: cell line

tag: fraction

value: cytoplasmic fraction


title: Vps15, liver, Fast wt, rep3

description:
Library name: ChIP_Vps15_Fastwt_7
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

value: hepatocyte

tag: genotype

value: WT

value: Fast 24h, ZT14 sacrifice

tag: chip antibody


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

value: hypothalamus

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

tag: condition


title: cyt_ctrl_A_1_polyA

tag: treatment

value: 1h induction with auxin


title: Vps15, liver, Fast wt, rep2

description:
Library name: ChIP_Vps15_Fastwt_5
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


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

description:
Library name: Th1Th2_validation_Diff081_DonorX_STAT6_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorX_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

value: No

tag: donor blood_type

value: B+

tag: anticoagulant

value: ACDA

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

value: Normal

value: Zymo DNA/RNA Shield

value: Hispanic

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: cyt_ctrl_3_polyA

description: polyA enriched RNA from cytoplasmic fraction from HCT116 cell line expressing TIR1 without induction

tag: cell line

tag: fraction

value: cytoplasmic fraction

tag: treatment

value: non induced


title: Vps15, liver, Fast wt, rep1

description:
Library name: ChIP_Vps15_Fastwt_4
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 type

value: hepatocyte

tag: genotype

value: WT

value: Fast 24h, ZT14 sacrifice

tag: chip antibody


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

value: hypothalamus

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


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

description:
Library name: Th1Th2_validation_Diff081_DonorX_PTPN2_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorX_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 PTPN2

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: B+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

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: CRISPRi


title: cyt_ctrl_2_polyA

tag: cell line

tag: fraction

value: cytoplasmic fraction

tag: treatment

value: non induced


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

tag: tissue

value: hypothalamus

tag: strain

value: TallyHo/JngJ

tag: Sex

value: female

tag: age

tag: development stage

tag: condition

value: high body weight at weaning


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

description:
Library name: Th1Th2_validation_Diff081_DonorX_NTC3_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorX_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

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 sex

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

value: Hispanic

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: cyt_ctrl_1_polyA

tag: cell line

tag: fraction

tag: treatment


title: Vps15, liver, Fed wt, rep1

description:
Library name: ChIP_Vps15_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.

tag: tissue

value: liver

tag: cell type

value: hepatocyte

tag: genotype

value: WT

value: Ad. Lib Fed, ZT14 sacrifice

tag: chip antibody


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

tag: strain

tag: Sex

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


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

description:
Library name: Th1Th2_validation_Diff081_DonorX_NTC2_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorX_bulkRNAseq.csv

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: B+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

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: CRISPRi


title: Dis3_A_2

description: Ribosome protected RNA fragments after ribosomal RNA depletion from CRISPR with DIS3-AID in HCT116 cell line with constitutive expression of TIR1 1h treatement with auxin

data_processing:
Reads were trimmed with cutadapt 2.8, with the following options as suggested by Diagenode kit’s manual : --trim-n --match-read-wildcards -u 16 -n 4 -m 15 -e 0.2 --nextseq-trim 20 -a AGATCGGAAGAGCACACGTCTG -a AAAAAAAA -a GAACTCCAGTCAC.
Trimmed Reads were mapped on the human genome hg38 with STAR version 2.7.3a, with the following parameters : --outSAMstrandField intronMotif --outSAMattributes All --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 –alignIntronMax 1000000.
Only unique mapped reads of length 25 to 34 nucleotides not falling on rRNAs were kept for downstream analysis.
The alignment files were converted in tdf of coverages (IGV visualization files) in RPM normalization (reads per million of mapped reads), using UCSC tools.
Assembly: hg38
Supplementary files format and content: for each sample, tdf (IGV visualization files) of read coverage in RPM (reads per million of mapped reads) normalization.
Library strategy: Ribo-seq

extract_protocol:
After removing media cells were flash freezed in liquid nitrogen. Cells were gently thawed on ice and 250µl of lysis buffer (10mM Tris pH7.5; 10mM (CH3COO)2Mg; 100mM KCl; 1% Triton; 2mM DTT) containing complete protease inhibitor cocktail (Roche) and 2U of RNase Murine Inhibitor (NEB) was added to each dish. Cells were collected with scrapper and then centrifuged for 3 minutes at maximum speed at 4℃ an aliquot of each lysate was collected for RNA extraction and the rest was flash frozen and stored at -80℃. Cell lysates were loaded onto a 24% sucrose cushion centrifugated 90 min at 110 krpm on a TLA110 rotor at +4°C. Next polysomes were rinsed 2 times with 500µl of lysis buffer then resuspended with 500µl of lysis buffer and digested using 5U/UA260nm RNase I (Ambion) for 1h at 25℃ followed by addition of 500U of SUPErasin RNase inhibitor (Invitrogen). RNA was extracted by acid phenol at 65°C, chloroform and precipitated by ethanol with 0.3 M sodium acetate pH5.2. Resuspended RNA was loaded on 17% polyacrylamide (19:1) gel with 7M urea and run in 1xTAE buffer for 6h at 100V. RNA fragments corresponding to 28-34nt were retrieved from gel and precipitated in ethanol with 0.3 M sodium acetate pH5.2 in presence of 100µg glycogen. rRNA was depleted using riboPool (siTools), adjusting initial volume to 40µl reaction and adding 1µl of Murine RNase inhibitor (NEB) to each sample before and after hybridization step. RNA was precipitated and concentration was measured by Qubit (Thermo Fisher Scientific).
10 ng of each sample was engaged in library preparation using D-plex Small RNA-seq Kit (Diagenode) following manufacturer’s instructions with 10 cycles of PCR amplification in the last step followed by DNA purification with Monarch PCR DNA cleanup kit (NEB) and AMPpure XP beads final cleanup. Library molarity was analyzed using Tape Station and an equimolar pool of libraries was sequenced on a NovaSeq 6000 system (Illumina) with 10% PhiX.
D-plex Small RNA-seq Kit (Ribo-seq)

tag: cell line

value: HCT116 derivative cell line

tag: fraction

value: Polysome fraction

tag: treatment

value: 1h induction with auxin


title: RNA Pol II S5P, liver, Fast Vps15LKO, rep3

description:
Library name: ChIP_RNA_Pol2_S5P_FastKO_15
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 type

value: hepatocyte

tag: genotype

value: Ttr CRE+, Vps15f/f

value: Fast 24h, ZT14 sacrifice

tag: chip antibody

value: RNA Pol II S5P, Abcam ab5408


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

value: hypothalamus

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

description:
Library name: Th1Th2_validation_Diff081_DonorX_NTC1_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorX_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: No

tag: donor blood_type

value: B+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

value: Normal

value: Zymo DNA/RNA Shield

value: Hispanic

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: Dis3_A_1

tag: cell line

value: HCT116 derivative cell line

tag: fraction

value: Polysome fraction

tag: treatment

value: 1h induction with auxin


title: RNA Pol II S5P, liver, Fast Vps15LKO, rep2

description:
Library name: ChIP_RNA_Pol2_S5P_FastKO_14
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 type

value: hepatocyte

tag: genotype

value: Ttr CRE+, Vps15f/f

value: Fast 24h, ZT14 sacrifice

tag: chip antibody

value: RNA Pol II S5P, Abcam ab5408


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

value: hypothalamus

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


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

description:
Library name: Th1Th2_validation_Diff081_DonorX_MTA2_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorX_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: No

tag: donor blood_type

value: B+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

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: CRISPRi


title: Dis3_2

description: Ribosome protected RNA fragments after ribosomal RNA depletion from CRISPR with DIS3-AID in HCT116 cell line with constitutive expression of TIR1 without induction

tag: cell line

value: HCT116 derivative cell line

tag: fraction

value: Polysome fraction

tag: treatment

value: non induced


title: Vps15, liver, Fed wt, rep2

description:
Library name: ChIP_Vps15_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

value: liver

tag: cell type

value: hepatocyte

tag: genotype

value: WT

value: Ad. Lib Fed, ZT14 sacrifice

tag: chip antibody


title: RNA Pol II S5P, liver, Fast Vps15LKO, rep1

description:
Library name: ChIP_RNA_Pol2_S5P_FastKO_12
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: Ttr CRE+, Vps15f/f

value: Fast 24h, ZT14 sacrifice

value: RNA Pol II S5P, Abcam ab5408


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

value: hypothalamus

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


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

description:
Library name: Th1Th2_validation_Diff081_DonorX_MED24_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorX_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: No

tag: donor blood_type

value: B+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

value: Normal

value: Zymo DNA/RNA Shield

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

value: Hispanic

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: Dis3_1

tag: cell line

value: HCT116 derivative cell line

tag: fraction

value: Polysome fraction

tag: treatment

value: non induced


title: RNA Pol II S5P, liver, Fed Vps15LKO, rep3

description:
Library name: ChIP_RNA_Pol2_S5P_FedKO_7
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 type

value: hepatocyte

tag: genotype

value: Ttr CRE+, Vps15f/f

value: Ad. Lib Fed, ZT14 sacrifice

tag: chip antibody

value: RNA Pol II S5P, Abcam ab5408


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

value: hypothalamus

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


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

description:
Library name: Th1Th2_validation_Diff081_DonorX_KDM1A_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorX_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 KDM1A

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: B+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity

value: CRISPRi


title: ctrl_A_2

description: Ribosome protected RNA fragments after ribosomal RNA depletion from HCT116 cell line expressing TIR1 1h treatement with auxin

tag: cell line

value: HCT116 derivative cell line

tag: fraction

value: Polysome fraction

tag: treatment

value: 1h induction with auxin


title: RNA Pol II S5P, liver, Fed Vps15LKO, rep2

description:
Library name: ChIP_RNA_Pol2_S5P_FedKO_5
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 type

value: hepatocyte

tag: genotype

value: Ttr CRE+, Vps15f/f

value: Ad. Lib Fed, ZT14 sacrifice

tag: chip antibody

value: RNA Pol II S5P, Abcam ab5408


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

value: hypothalamus

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


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

description:
Library name: Th1Th2_validation_Diff081_DonorX_JAK2_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorX_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: B+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

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

value: Hispanic

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: ctrl_A_1

tag: cell line

value: HCT116 derivative cell line

tag: fraction

value: Polysome fraction

tag: treatment

value: 1h induction with auxin


title: RNA Pol II S5P, liver, Fed Vps15LKO, rep1

description:
Library name: ChIP_RNA_Pol2_S5P_FedKO_4
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 type

value: hepatocyte

tag: genotype

value: Ttr CRE+, Vps15f/f

value: Ad. Lib Fed, ZT14 sacrifice

tag: chip antibody

value: RNA Pol II S5P, Abcam ab5408


title: H3K4me3, liver, Fed Vps15LKO, rep2

description:
Library name: ChIP_H3K4me3_FedKO_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: H3K4me3, Cell Signaling 9751


title: high blood glucose, low 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: DonorY cells perturbed with Non-targeting control 3 by CRISPRi under nonpolarized culture condition in batch Diff081

description:
Library name: Th1Th2_validation_Diff081_DonorY_NTC3_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 non-targeting control

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: O+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: 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

tag: donor ethnicity

value: African American

value: CRISPRi


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

tag: tissue

value: hypothalamus

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

tag: condition


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

description:
Library name: Th1Th2_validation_Diff081_DonorX_GATA3_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorX_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 GATA3

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: B+

value: Female

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

value: Hispanic

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: ctrl_2

description: Ribosome protected RNA fragments after ribosomal RNA depletion from HCT116 cell line expressing TIR1 without induction

tag: cell line

value: HCT116 derivative cell line

tag: fraction

value: Polysome fraction

value: non induced


title: IX_56688

description: Library name: IX_56688

tag: tissue

value: Colorectal cancer metastasis


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

description:
Library name: Th1Th2_validation_Diff081_DonorY_MTA2_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorY_bulkRNAseq.csv

value: CRISPRi knockdown of MTA2

value: No

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

tag: donor ethnicity

value: African American

value: CRISPRi


title: IgG, mouse embryonic fibroblasts, 4h methionine stimulation

description: Library name: CutRun_IgG_methionine_stim

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
Library strategy: CUT&Run

source_name: mouse embryonic fibroblasts

growth_protocol: MEFs were kept in basal DMEM media conditions, or starved of methionine for 4h, or starved of methionine for 4h followed by 1h methionine stimulation.

extract_protocol:
Cells were scraped from plates in Cut and 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 type

value: embryonic fibroblasts

tag: genotype

value: WT

tag: treatment

value: 4h methionine starvation followed by 1h methionine stimulation media conditions

tag: chip antibody

value: IgG, Cell Signaling 3900


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

value: hypothalamus

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


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

description:
Library name: Th1Th2_validation_Diff081_DonorX_FBXO32_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorX_bulkRNAseq.csv

tag: tissue

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of FBXO32

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: B+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

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

value: Hispanic

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: ctrl_1

tag: cell line

value: HCT116 derivative cell line

tag: fraction

value: Polysome fraction

tag: treatment

value: non induced


title: IgG, mouse embryonic fibroblasts, 4h methionine starvation

description: Library name: CutRun_IgG_methionine_starve

tag: cell type

value: embryonic fibroblasts

tag: genotype

value: WT

value: 4h methionine starvation media conditions

tag: chip antibody

value: IgG, Cell Signaling 3900


title: Input for RNA Pol II S5P Fast Vps15LKO

description: Library name: Input_FastKO_12

tag: tissue

value: liver

value: hepatocyte

value: Ttr CRE+, Vps15f/f

value: Fast 24h, ZT14 sacrifice

value: input


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

value: hypothalamus

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


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

description:
Library name: Th1Th2_validation_Diff081_DonorX_FAM120A_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorX_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 height

tag: donor smoker

value: No

tag: donor blood_type

value: B+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

tag: donor ethnicity

value: Hispanic

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: IgG, mouse embryonic fibroblasts, basal methionine

description: Library name: CutRun_IgG_methionine_basal

tag: cell type

value: embryonic fibroblasts

tag: genotype

value: WT

tag: treatment

value: basal growth media conditions

tag: chip antibody

value: IgG, Cell Signaling 3900


title: chr_clone2_ad_3

description: Total ribo-depleted RNA from chromatin fraction from CRISPR clone2 with XRN1-AID in HCT116 cell line with doxycycline inducible expression of TIR1 with 24h induction of XRN1 depletion with doxycycline and auxin

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

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

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

tag: fraction

value: chromatin fraction

value: 24h induction with doxycycline and auxin


title: mock, vero, 48 hpi, 3

city: Madrid

first: Miguel A.

last: Martín-Acebes

state: Madrid

address: Ctra. de La Coruña, km 7, 5

country: Spain

institute: INIA-CSIC

description: Library name: control_3

data_processing:
Average base quality was determined by Fastqc. Sequence reads were trimmed using trimmomatic to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Trimmed sequence reads were mapped to mm10 using HISAT2 version 2.1.0 and Bowtie2 2.3.4.1
Known genes and transcripts were assembled with StringTie based on reference genome model. After assembly, abundance of gene/transcript was calculated in the read count and normalized values as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million) for a sample.
Read count data was normalized with Relative Log Expression (RLE) method in DESeq2 R library. RLE normalized count was adopted for negative binomial Wald Test(nbinomWaldTest) in DESeq2.
Statistical analysis is performed using Fold Change, nbinomWaldTest using DESeq2 per comparison pair. Significant results are selected on conditions of |fc|>=2 & nbinomWaldTest raw p-value<0.05.
Assembly: Vero_WHO_p1.0
Supplementary files format and content: tab-delimited text files including gene ID, gene symbol, log2 fold change (FC), raw pvalue, bh corrected pvalue (benjamini hochberg), expression level (normalized value), raw reads counts, FPKM and TMP values for each group comparison

organism: Chlorocebus sabaeus

source_name: Cell culture

growth_protocol: Experimental infections in cell cultures were performed in the biosafety level 3 (BSL-3) facilities at Centro de Investigación en Sanidad Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (CISA, INIA-CSIC).

extract_protocol:
Total cell RNA was extracted using Ribopure following manufacturer's protocols
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were infected with of USUV SAAR (MOI 10PFU/cell) in Minimum Essential Medium Eagle (Corning) and mock-infected cells were also inoculated with of culture media and collected at 48 hours post-infection (hpi)

tag: tissue

value: Cell culture

tag: cell line

value: Vero CCL-81

value: Epithelial

value: mock


title: chr_clone2_ad_2


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

description:
Library name: Th1Th2_validation_Diff081_DonorX_CDKAL1_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorX_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 CDKAL1

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: B+

tag: anticoagulant

value: ACDA

value: STEMCELL technologies

value: Female

value: adult stage

value: TRUE

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: Vps15, mouse embryonic fibroblasts, 1h methionine stimulation, rep2

description:
Library name: CutRun_Vps15_methionine_stim_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: cell type

value: embryonic fibroblasts

tag: genotype

value: WT

tag: treatment

value: 4h methionine starvation followed by 1h methionine stimulation media conditions


title: mock, vero, 48 hpi, 2

description: Library name: control_2

tag: tissue

value: Cell culture

value: Vero CCL-81


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

value: hypothalamus

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


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

description:
Library name: Th1Th2_validation_Diff081_DonorX_APPBP2_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorX_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 APPBP2

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

value: No

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

tag: suspension depletion_factors

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

tag: donor ethnicity

value: Hispanic

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: chr_clone2_ad_1

tag: fraction

value: chromatin fraction

tag: treatment

value: 24h induction with doxycycline and auxin


title: Vps15, mouse embryonic fibroblasts, 1h methionine stimulation, rep1

description:
Library name: CutRun_Vps15_methionine_stim_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

value: embryonic fibroblasts

tag: genotype

value: WT

value: 4h methionine starvation followed by 1h methionine stimulation media conditions

tag: chip antibody


title: cyt_Dis3_2_polyA

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

tag: cell line

value: cytoplasmic fraction

value: non induced


title: mock, vero, 48 hpi, 1

description: Library name: control_1

tag: tissue

value: Cell culture

value: Vero CCL-81

value: Epithelial

value: mock


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim8hr_Rep2_VAV1
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

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

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

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of VAV1

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Yes

tag: donor blood_type

value: A-

tag: anticoagulant

value: ACDA

value: STEMCELL technologies

value: Male

value: adult stage

value: TRUE

value: Normal

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: chr_clone1_ad_3

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

tag: fraction

value: chromatin fraction

tag: treatment

value: 24h induction with doxycycline and auxin


title: cyt_Dis3_1_polyA

value: cytoplasmic fraction

value: non induced


title: USUV, vero, 48 hpi, 3

description: Library name: tratado_3

value: Cell culture

value: Vero CCL-81

tag: cell type

value: Epithelial

value: infected


title: Vps15, mouse embryonic fibroblasts, 4h methionine starvation, rep2

description:
Library name: CutRun_Vps15_methionine_starvel_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: embryonic fibroblasts

tag: genotype

value: WT

value: 4h methionine starvation media conditions

tag: chip antibody


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

tag: tissue

value: hypothalamus

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: Input for RNA Pol II S5P Fed wt

description: Library name: Input_Fedwt_3

value: liver

value: hepatocyte

value: Ad. Lib Fed, ZT14 sacrifice

value: input


title: chr_clone1_ad_2

value: chromatin fraction

value: 24h induction with doxycycline and auxin


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim8hr_Rep2_SIK3
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of SIK3

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Yes

tag: donor blood_type

value: A-

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Male

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

tag: donor ethnicity

value: Hispanic

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: Vps15, mouse embryonic fibroblasts, 4h methionine starvation, rep1

description:
Library name: CutRun_Vps15_methionine_starve_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

value: embryonic fibroblasts

tag: genotype

value: WT

tag: treatment

value: 4h methionine starvation media conditions

tag: chip antibody


title: USUV, vero, 48 hpi, 2

description: Library name: tratado_2

tag: tissue

value: Cell culture

tag: cell line

value: Vero CCL-81

value: Epithelial

value: infected


title: chr_clone1_ad_1

tag: fraction

value: chromatin fraction

value: 24h induction with doxycycline and auxin


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim8hr_Rep2_NTC
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi non-targeting control

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Yes

tag: donor blood_type

value: A-

tag: anticoagulant

value: ACDA

value: STEMCELL technologies

value: Male

value: adult stage

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: Vps15, mouse embryonic fibroblasts, basal methionine, rep2

description:
Library name: CutRun_Vps15_methionine_basal_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: cell type

value: embryonic fibroblasts

tag: genotype

value: WT

tag: treatment

value: basal growth media conditions


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim8hr_Rep2_MEN1
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

tag: tissue

value: CRISPRi knockdown of MEN1

tag: source

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

tag: donor ethnicity

value: Hispanic

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: USUV, vero, 48 hpi, 1

description: Library name: tratado_1

value: Cell culture

tag: cell line

value: Vero CCL-81

value: Epithelial

value: infected


title: chr_wt_ad_3

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

tag: fraction

value: chromatin fraction


title: Vps15, mouse embryonic fibroblasts, basal methionine, rep1

description:
Library name: CutRun_Vps15_methionine_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.

tag: chip antibody


title: Peripheral blood mononuclear cell, METTL1 knock down3

city: Hefei

first: Chao

last: Hou

state: Anhui province

address: 81 Meishan Road

country: China

institute: Anhui Medical University

description: Library name: F

data_processing:
The original image data obtained by high-throughput sequencing is transformed into sequence data, namely the FASTQ format, through Base Calling.Data quality control was carried out using fastp(version 0.23.0) software. The first step is to remove the connector sequences in the reads and filter out reads with a length shorter than 15bp. The second step is to filter low-quality reads (discard them when the proportion of bases with a quality value lower than Q20 is greater than 0.08);The third step is to filter and sequence the reads that read N (discard them when the reads read N have more than five bases).
Sequencing quality distribution.
Base content distribution map.
Statistically analyze and plot the distribution maps of clean reads with different GC contents.
Summary of sequencing data quality.
Assembly: GRCh38
Supplementary files format and content: All_reads_counts.txt

source_name: Peripheral blood mononuclear cell

growth_protocol: cells were maintained in medium 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Vezol Reagent  kit.
RNA libraries for RNA-seq were prepared using DNBSEQ-T7 following manufacturer's protocols.

treatment_protocol: Macrophage was induced by treatment of 7 day peripheral blood mononuclear cells  with 1ug/ml macrophage colony stimulating factor.

value: Peripheral blood mononuclear cell

value: METTL1 knock down


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim8hr_Rep2_LAT
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of LAT

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Yes

tag: donor blood_type

value: A-

tag: anticoagulant

value: ACDA

value: STEMCELL technologies

value: Male

value: adult stage

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: RNA, Liver, Fast Vps15LKO, rep3

description:
Library name: FastKO_3
clean reads

data_processing:
Adapter sequences and low-quality reads were filtered with SOAPnuke. Clean reads were obtained with an output read quality of Phred+33.
Clean reads were aligned to the mm10 genome with HISAT2 and counts generated from the Subread R package. Read-count normalization and group comparisons were generated by three independent statistical methods: DESeq2, LimmaVoom, and edgeR. Direct comparisons were made between treatment conditions. DOSE Gene Set Enrichment Analysis was performed with the DOSE package, in R.
Assembly: mm10
Supplementary files format and content: raw counts

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

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

tag: tissue

value: liver

tag: cell type

value: hepatocyte

tag: genotype

value: Ttr CRE+, Vps15f/f

tag: treatment

value: Fast 24h, ZT14 sacrifice


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

description:
Library name: Th1Th2_validation_Diff081_DonorX_TBX21_non
nonpolarized
Th1Th2_validation_Diff081_non_DonorX_bulkRNAseq.csv

value: CRISPRi knockdown of TBX21

value: No

value: B+

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

tag: donor ethnicity

value: Hispanic

value: CRISPRi

value: Plasmidsaurus RNA-Seq


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim8hr_Rep2_HEXDC
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of HEXDC

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Yes

tag: donor blood_type

value: A-

tag: anticoagulant

value: ACDA

value: STEMCELL technologies

value: Male

tag: genetic perturbation_strategy


title: chr_wt_ad_1

tag: fraction

value: chromatin fraction

tag: treatment

value: 24h induction with doxycycline and auxin


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim8hr_Rep2_GPI
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

tag: tissue

tag: cell type

value: CRISPRi knockdown of GPI

tag: source

tag: donor sex

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

value: Normal

tag: enriched cell_types

tag: library protocol

tag: batch


title: chr_clone2_3

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

value: non induced


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim8hr_Rep2_CD3G
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi knockdown of CD3G

tag: donor id

tag: donor age

tag: donor weight

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

tag: donor ethnicity

value: Hispanic

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: Peripheral blood mononuclear cell, Normal Control2

description: Library name: B

tag: cell type

value: Peripheral blood mononuclear cell

tag: genotype

value: Normal Control


title: chr_clone2_2

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

tag: fraction

tag: treatment


title: RNA, Liver, Fed Vps15LKO, rep3

description:
Library name: FedKO_3
clean reads

tag: tissue

value: liver

value: hepatocyte

value: Ttr CRE+, Vps15f/f

value: Ad. Lib Fed, ZT14 sacrifice


title: Peripheral blood mononuclear cell, Normal Control3

description: Library name: C


title: chr_clone2_1

value: chromatin fraction


title: Peripheral blood mononuclear cell, Normal Control1

description: Library name: A


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim8hr_Rep2_ATP2A2
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

value: CRISPRi knockdown of ATP2A2

tag: donor height

tag: donor smoker

value: Yes

tag: donor blood_type

value: A-

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Male

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

tag: genetic perturbation_strategy

tag: enriched cell_types


title: chr_clone1_3

value: non induced


title: RNA, Liver, Fed Vps15LKO, rep1

description:
Library name: FedKO_1
clean reads


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim8hr_Rep1_VAV1
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi knockdown of VAV1

tag: donor id

tag: donor age

tag: donor weight

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: Hispanic

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: chr_clone1_2

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

tag: fraction

value: chromatin fraction

tag: treatment


title: ATAC_Ascl1_QA_D7_rep3

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 415/420 Clinical Research Building (CRB)

institute: University of Pennsylvania

description: Library name: 12_ATAC_UAE_QA_D7_rep3_S12

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

source_name: hBJ fibroblast

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

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

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

tag: cell line

value: hBJ fibroblast

tag: cell type

value: human fibroblast

tag: genotype

value: QA

tag: time

tag: replicate

value: 0.5μg/ml doxycycline


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim8hr_Rep1_SIK3
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

tag: tissue

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of SIK3

tag: donor height

tag: donor smoker

value: Yes

tag: donor blood_type

value: A-

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types


title: ATAC_Ascl1_AAA_D7_rep3

description: Library name: 11_ATAC_UAE_AAA_D7_rep3_S11

tag: cell line

tag: cell type

value: AAA

tag: treatment


title: chr_clone1_1

tag: fraction

value: non induced


title: ATAC_Ascl1_allRs_D7_rep3

description: Library name: 10_ATAC_UAE_allRs_D7_rep3_S10

tag: genotype

value: allRs

tag: time

tag: replicate


title: RNA, Liver, Fast wt, rep2

description:
Library name: Fastwt_2
clean reads

tag: tissue

value: liver

value: hepatocyte

value: WT

value: Fast 24h, ZT14 sacrifice


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim8hr_Rep1_NTC
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

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

value: Male

value: adult stage

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: Hispanic

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: RNA, Liver, Fast wt, rep1

description:
Library name: Fastwt_1
clean reads

tag: cell type

tag: genotype

tag: treatment


title: chr_wt_3

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

tag: fraction

value: chromatin fraction


title: ATAC_Ascl1_WT_D7_rep3

description: Library name: 9_ATAC_UAE_WT_D7_rep3_S9

tag: cell line

value: hBJ fibroblast

value: human fibroblast

tag: time

tag: replicate

value: 0.5μg/ml doxycycline


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim8hr_Rep1_MEN1
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

tag: tissue

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of MEN1

tag: donor id

tag: donor age

tag: donor weight

value: Yes

value: A-

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types


title: ATAC_Ascl1_QA_D7_rep2

description: Library name: 8_ATAC_UAE_QA_D7_rep2_S8

tag: cell type

tag: genotype

value: QA

tag: treatment


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim8hr_Rep1_LAT
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

value: CRISPRi knockdown of LAT

tag: donor height

tag: donor smoker

tag: donor blood_type

value: Male

value: adult stage

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: library protocol

tag: batch


title: RNA, Liver, Fed wt, rep3

description:
Library name: Fedwt_3
clean reads

tag: tissue

value: liver

value: hepatocyte

value: WT

value: Ad. Lib Fed, ZT14 sacrifice


title: chr_wt_1

tag: fraction

value: chromatin fraction

value: non induced


title: RNA, Liver, Fed wt, rep2

description:
Library name: Fedwt_2
clean reads


title: ATAC_Ascl1_AAA_D7_rep2

description: Library name: 7_ATAC_UAE_AAA_D7_rep2_S7

tag: cell line

value: hBJ fibroblast

value: human fibroblast

value: AAA

tag: time

tag: replicate

value: 0.5μg/ml doxycycline


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim8hr_Rep1_HEXDC
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of HEXDC

tag: donor id

tag: donor age

tag: donor weight

value: Yes

value: A-

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: cyt_clone2_ad_3

description: Total ribo-depleted RNA from cytoplasmic fraction from CRISPR clone2 with XRN1-AID in HCT116 cell line with doxycycline inducible expression of TIR1 with 24h induction of XRN1 depletion with doxycycline and auxin

tag: fraction

value: cytoplasmic fraction

tag: treatment

value: 24h induction with doxycycline and auxin


title: ATAC_Ascl1_allRs_D7_rep2

description: Library name: 6_ATAC_UAE_allRs_D7_rep2_S6

tag: cell line

value: hBJ fibroblast

tag: genotype

value: allRs

tag: time


title: RNA, Liver, Fed wt, rep1

description:
Library name: Fedwt_1
clean reads

tag: tissue

value: liver

tag: cell type

value: hepatocyte

value: WT

value: Ad. Lib Fed, ZT14 sacrifice


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim8hr_Rep1_GPI
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of GPI

tag: donor id

tag: donor age

tag: donor height

tag: donor smoker

tag: donor blood_type

value: Male

value: adult stage

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: library protocol

tag: batch


title: cyt_clone2_ad_2

tag: fraction

value: cytoplasmic fraction

tag: treatment

value: 24h induction with doxycycline and auxin


title: Peripheral blood mononuclear cell, METTL1 knock down2

description: Library name: E

value: Peripheral blood mononuclear cell

tag: genotype

value: METTL1 knock down


title: chr_wt_ad_2

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

value: chromatin fraction


title: IR-LYC3

city: beijing

first: bio

last: xin

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

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

description: IR+LYC

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

source_name: intestine

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

tag: tissue

value: intestine

value: IR-LYC


title: ATAC_Ascl1_WT_D7_rep2

description: Library name: 5_ATAC_UAE_WT_D7_rep2_S5

tag: cell line

value: hBJ fibroblast

tag: cell type

value: human fibroblast

value: WT

tag: time

tag: replicate

value: 0.5μg/ml doxycycline


title: Peripheral blood mononuclear cell, METTL1 knock down1

description: Library name: D


title: RNA, Liver, Fast Vps15LKO, rep2

description:
Library name: FastKO_2
clean reads

value: liver

value: hepatocyte

value: Ttr CRE+, Vps15f/f

value: Fast 24h, ZT14 sacrifice


title: RNA, Liver, Fast Vps15LKO, rep1

description:
Library name: FastKO_1
clean reads


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim8hr_Rep1_CD3G
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of CD3G

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

value: Yes

value: A-

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Male

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: cyt_clone2_ad_1

tag: fraction

value: cytoplasmic fraction

tag: treatment

value: 24h induction with doxycycline and auxin


title: ATAC_Ascl1_QA_D7_rep1

description: Library name: 4_ATAC_UAE_QA_D7_rep1_S4

tag: cell line

value: hBJ fibroblast

tag: cell type

value: human fibroblast

tag: genotype

value: QA

tag: time

value: 0.5μg/ml doxycycline


title: IR-LYC2

description: IR+LYC

tag: tissue

value: intestine

value: IR-LYC


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim8hr_Rep2_ATP2A3
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of ATP2A3

tag: donor id

tag: donor age

tag: donor weight

tag: donor smoker

value: Yes

tag: donor blood_type

value: A-

value: ACDA

value: STEMCELL technologies

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

tag: library protocol

tag: batch


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim8hr_Rep1_ATP2A3
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

tag: treatment

tag: donor height

tag: anticoagulant

tag: source

tag: donor sex

value: Male

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: cyt_clone1_ad_3

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

tag: fraction

value: cytoplasmic fraction

value: 24h induction with doxycycline and auxin


title: ATAC_Ascl1_AAA_D7_rep1

description: Library name: 3_ATAC_UAE_AAA_D7_rep1_S3

tag: cell line

value: hBJ fibroblast

tag: cell type

value: human fibroblast

tag: genotype

value: AAA

tag: time

tag: replicate

value: 0.5μg/ml doxycycline


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim8hr_Rep1_ATP2A2
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

tag: tissue

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of ATP2A2

tag: donor id

tag: donor age

tag: donor weight

tag: donor smoker

value: Yes

tag: donor blood_type

value: A-

value: ACDA

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

tag: library protocol

tag: batch