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

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim48hr_Rep1_ATP2A3
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of ATP2A3

value: No

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor disease

value: Hispanic

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol


title: BS_CMT2-T1h2a.z_3

status: Public on Jun 02 2026

type: SRA

city: Tokyo

first: Shoko

last: Oda

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

country: Japan

institute: The University of Tokyo

description: Library name: Sample 31

library_source: genomic

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

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Leaves

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

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

tag: tissue

value: Leaves

tag: genotype

value: hta8 hta9 hta11 cmt2 cmt3 +CMT2 tg


title: ChIP_suvh_H2A.W_rep2

description: Library name: Sample 93

source_name: seedling

value: seedling

value: suvh4 suvh5 suvh6


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

city: Palo Alto

first: Lattice

last: Data Coordination

state: CA

address: 3165 Porter Drive

department: Genetics

country: USA

institute: Stanford University

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim48hr_Rep1_ATP2A2
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

library_source: transcriptomic

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

organism: Homo sapiens

source_name: blood

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

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

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

value: blood

tag: cell type

tag: treatment

value: CRISPRi knockdown of ATP2A2

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: A+

value: Female

value: adult stage

value: TRUE

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

tag: donor ethnicity

value: CRISPRi

value: Plasmidsaurus RNA-Seq

tag: batch


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

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: pLEX_Vps34INH1_24h_3
clean reads

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

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

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

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

tag: cell line

value: human embryonic kidney

value: WT

value: transfected empty vector, 24h, Vps34IN1


title: BS_CMT2-T1h2a.z_2

description: Library name: Sample 30

value: Leaves

value: hta8 hta9 hta11 cmt2 cmt3 +CMT2 tg


title: ChIP_suvh_H2A.W_rep1

description: Library name: Sample 92

value: seedling

value: suvh4 suvh5 suvh6


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

description:
Library name: pLEX_Vps34INH1_24h_2
clean reads


title: DonorH cells perturbed with SGF29 knockdown by CRISPRi and SGF29-4 gRNA in batch Diff092

description:
Library name: IL10IL21_validation_Diff092_DonorH_SGF29-4
IL10IL21_validation_Diff092_DonorH_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, 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 10 morning, cells were centrifuged and resuspended at 2 x 106 cells/ml with cXVIVO supplemented with 200 IU/mL IL-2 and 12.5 µL/mL ImmunoCult human CD3/CD28/CD2 T cell activator for 8 hours.

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of SGF29 by SGF29-4 gRNA

value: Yes

value: A-

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Male

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor disease

value: Hispanic

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol


title: BS_CMT2-T1h2a.z_1

description: Library name: Sample 29

tag: tissue

tag: genotype


title: ChIP_cmt_H2A.W_rep2

description: Library name: Sample 91

value: cmt2 cmt3


title: DonorH cells perturbed with Non-targeting control 2 by CRISPRi in batch Diff092

description:
Library name: IL10IL21_validation_Diff092_DonorH_NTC2
IL10IL21_validation_Diff092_DonorH_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

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: adult stage

value: TRUE

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

value: CRISPRi

value: Plasmidsaurus RNA-Seq


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

description:
Library name: pLEX_Vps34INH1_24h_1
clean reads

tag: cell line

value: human embryonic kidney

value: WT

value: transfected empty vector, 24h, Vps34IN1

tag: batch


title: BS_CMT3-T1h2a.z_3

description: Library name: Sample 25

value: Leaves

value: hta8 hta9 hta11 cmt2 cmt3 +CMT3 tg


title: DonorH cells perturbed with Non-targeting control 1 by CRISPRi in batch Diff092

description:
Library name: IL10IL21_validation_Diff092_DonorH_NTC1
IL10IL21_validation_Diff092_DonorH_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

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 disease

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy


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

description:
Library name: Methionase_NLS_dmso_24h_3
clean reads

tag: cell type

tag: genotype

tag: treatment

value: transfected MethionaseNLS, 24h, dmso


title: BS_CMT3-T1h2a.z_2

description: Library name: Sample 24

tag: tissue


title: ChIP_Col_H2A.W_rep2

description: Library name: Sample 89

value: seedling

value: Wild-type


title: DonorH cells perturbed with GATA3 knockdown by CRISPRi and GATA3-3 gRNA in batch Diff092

description:
Library name: IL10IL21_validation_Diff092_DonorH_GATA3-3
IL10IL21_validation_Diff092_DonorH_bulkRNAseq.csv

value: CRISPRi knockdown of GATA3 by GATA3-3 gRNA

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

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

value: Hispanic

value: CRISPRi

tag: enriched cell_types

tag: library protocol


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

description:
Library name: Methionase_NLS_dmso_24h_2
clean reads

tag: cell line

value: human embryonic kidney

value: WT

tag: batch


title: BS_CMT3-T1h2a.z_1

description: Library name: Sample 23

value: Leaves

value: hta8 hta9 hta11 cmt2 cmt3 +CMT3 tg


title: ChIP_Col_H2A.W_rep1

description: Library name: Sample 88


title: DonorH cells perturbed with ATP2A2 knockdown by CRISPRi and ATP2A2-3 gRNA in batch Diff092

description:
Library name: IL10IL21_validation_Diff092_DonorH_ATP2A2-3
IL10IL21_validation_Diff092_DonorH_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of ATP2A2 by ATP2A2-3 gRNA

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 disease

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy

value: Plasmidsaurus RNA-Seq


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

description:
Library name: Methionase_NLS_dmso_24h_1
clean reads

tag: cell type

tag: genotype

tag: treatment

value: transfected MethionaseNLS, 24h, dmso


title: BS_cmth2a.z(ccz)_rep2

description: Library name: Sample 22

tag: tissue

value: cmt2 cmt3 hta8 hta9 hta11


title: RNA, HEK293T, pLEX, dmso,24h, rep3

description:
Library name: pLEX_dmso_24h_3
clean reads

value: transfected empty vector, 24h, dmso


title: DonorD cells perturbed with SGF29 knockdown by CRISPRi and SGF29-4 gRNA in batch Diff092

description:
Library name: IL10IL21_validation_Diff092_DonorD_SGF29-4
IL10IL21_validation_Diff092_DonorD_bulkRNAseq.csv

value: CRISPRi knockdown of SGF29 by SGF29-4 gRNA

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

value: Female

value: adult stage

value: TRUE

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

value: Hispanic

value: CRISPRi

tag: enriched cell_types

tag: library protocol


title: ChIP_cmth2a.z(ccz)_H3_for_H2A.W_rep2

description: Library name: Sample 87

value: seedling


title: ChIP_cmt_H2A.W_rep1

description: Library name: Sample 90

value: cmt2 cmt3


title: BS_cmth2a.z(ccz)_rep1

description: Library name: Sample 21

value: Leaves


title: ChIP_cmth2a.z(ccz)_H3_for_H2A.W_rep1

description: Library name: Sample 86


title: DonorD cells perturbed with Non-targeting control 2 by CRISPRi in batch Diff092

description:
Library name: IL10IL21_validation_Diff092_DonorD_NTC2
IL10IL21_validation_Diff092_DonorD_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi non-targeting control

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor disease

tag: suspension depletion_factors

value: Plasmidsaurus RNA-Seq

tag: batch


title: BS_h2a.zcmt(zcc)_rep2

description: Library name: Sample 20

tag: tissue

tag: genotype

value: hta8 hta9 hta11 cmt2 cmt3


title: RNA, HEK293T, pLEX, dmso,24h, rep2

description:
Library name: pLEX_dmso_24h_2
clean reads

tag: cell line

tag: cell type

value: human embryonic kidney

value: WT

tag: treatment

value: transfected empty vector, 24h, dmso


title: ChIP_h2a.zcmt(zcc)_H3_for_H2A.W_rep2

description: Library name: Sample 85


title: DonorD cells perturbed with Non-targeting control 1 by CRISPRi in batch Diff092

description:
Library name: IL10IL21_validation_Diff092_DonorD_NTC1
IL10IL21_validation_Diff092_DonorD_bulkRNAseq.csv

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

value: Female

value: adult stage

value: TRUE

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

tag: donor ethnicity

tag: genetic perturbation_strategy


title: RNA, HEK293T, pLEX, dmso,24h, rep1

description:
Library name: pLEX_dmso_24h_1
clean reads


title: BS_h2a.zcmt(zcc)_rep1

description: Library name: Sample 19

value: Leaves


title: ChIP_h2a.zcmt(zcc)_H3_for_H2A.W_rep1

description: Library name: Sample 84

value: seedling


title: DonorD cells perturbed with GATA3 knockdown by CRISPRi and GATA3-3 gRNA in batch Diff092

description:
Library name: IL10IL21_validation_Diff092_DonorD_GATA3-3
IL10IL21_validation_Diff092_DonorD_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of GATA3 by GATA3-3 gRNA

tag: anticoagulant

value: ACDA

tag: source

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor disease

tag: suspension depletion_factors

value: Hispanic

value: CRISPRi

tag: enriched cell_types

tag: library protocol


title: RNA, HEK293T, MethionaseNLS, dmso,12h, rep3

description:
Library name: Methionase_NLS_dmso_12h_3
clean reads

tag: cell line

tag: cell type

value: human embryonic kidney

tag: genotype

value: WT

tag: treatment

value: transfected MethionaseNLS, 12h, dmso

tag: batch


title: DonorD cells perturbed with ATP2A2 knockdown by CRISPRi and ATP2A2-3 gRNA in batch Diff092

description:
Library name: IL10IL21_validation_Diff092_DonorD_ATP2A2-3
IL10IL21_validation_Diff092_DonorD_bulkRNAseq.csv

tag: tissue

value: CRISPRi knockdown of ATP2A2 by ATP2A2-3 gRNA

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

value: STEMCELL technologies

value: Female

value: adult stage

tag: donor body_mass_index

tag: sample preservation_method

tag: donor ethnicity

value: Plasmidsaurus RNA-Seq


title: ChIP_h2a.z_H3_for_H2A.W_rep2

description: Library name: Sample 83

value: seedling

value: hta8 hta9 hta11


title: BS_h2a.z_rep2

description: Library name: Sample 18

value: Leaves


title: RNA, HEK293T, MethionaseNLS, dmso,12h, rep2

description:
Library name: Methionase_NLS_dmso_12h_2
clean reads


title: BS_h2a.z_rep1

description: Library name: Sample 17


title: ChIP_h2a.z_H3_for_H2A.W_rep1

description: Library name: Sample 82


title: DonorC cells perturbed with SGF29 knockdown by CRISPRi and SGF29-4 gRNA in batch Diff092

description:
Library name: IL10IL21_validation_Diff092_DonorC2_SGF29-4
IL10IL21_validation_Diff092_DonorC2_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of SGF29 by SGF29-4 gRNA

tag: anticoagulant

tag: source

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor disease

value: Normal

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

value: Caucasian

tag: genetic perturbation_strategy

tag: enriched cell_types


title: RNA, HEK293T, MethionaseNLS, dmso,12h, rep1

description:
Library name: Methionase_NLS_dmso_12h_1
clean reads

tag: cell line

tag: cell type

value: human embryonic kidney

tag: genotype

value: WT

tag: treatment

value: transfected MethionaseNLS, 12h, dmso

tag: batch


title: BS_CMT2-T1WT_2

description: Library name: Sample 16

tag: tissue

value: cmt2 cmt3 +CMT2 tg


title: DonorC cells perturbed with Non-targeting control 2 by CRISPRi in batch Diff092

description:
Library name: IL10IL21_validation_Diff092_DonorC2_NTC2
IL10IL21_validation_Diff092_DonorC2_bulkRNAseq.csv

value: CRISPRi non-targeting control

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

value: ACDA

value: STEMCELL technologies

value: Female

value: adult stage

tag: donor body_mass_index

tag: sample preservation_method

tag: donor ethnicity

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: RNA, HEK293T, pLEX, dmso,12h, rep3

description:
Library name: pLEX_dmso_12h_3
clean reads

value: transfected empty vector, 12h, dmso


title: BS_CMT2-T1WT_1

description: Library name: Sample 15

value: Leaves


title: ChIP_F1WT(suvh X cmt)_H3_for_H2A.W_rep4

description: Library name: Sample 81

value: seedling


title: ChIP_F1WT(suvh X cmt)_H3_for_H2A.W_rep3

description: Library name: Sample 80


title: RNA, HEK293T, pLEX, dmso,12h, rep2

description:
Library name: pLEX_dmso_12h_2
clean reads


title: DonorC cells perturbed with Non-targeting control 1 by CRISPRi in batch Diff092

description:
Library name: IL10IL21_validation_Diff092_DonorC2_NTC1
IL10IL21_validation_Diff092_DonorC2_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

tag: anticoagulant

tag: source

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor disease

value: Normal

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

value: Caucasian

tag: genetic perturbation_strategy

tag: enriched cell_types


title: BS_CMT3-T1WT_2

description: Library name: Sample 14

tag: tissue

tag: genotype

value: cmt2 cmt3 +CMT3 tg


title: ChIP_F1WT(cmt X suvh)_H3_for_H2A.W_rep2

description: Library name: Sample 79


title: RNA, HEK293T, pLEX, dmso,12h, rep1

description:
Library name: pLEX_dmso_12h_1
clean reads

tag: cell line

tag: cell type

value: human embryonic kidney

value: WT

tag: treatment

tag: batch


title: DonorB cells perturbed with SGF29 knockdown by CRISPRi and SGF29-4 gRNA in batch Diff092

description:
Library name: IL10IL21_validation_Diff092_DonorB_SGF29-4
IL10IL21_validation_Diff092_DonorB_bulkRNAseq.csv

value: CRISPRi knockdown of SGF29 by SGF29-4 gRNA

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

value: ACDA

value: STEMCELL technologies

value: Male

value: adult stage

tag: donor body_mass_index

tag: sample preservation_method

tag: donor ethnicity

tag: library protocol


title: BS_CMT3-T1WT_1

description: Library name: Sample 13

value: Leaves


title: ChIP_F1WT(cmt X suvh)_H3_for_H2A.W_rep1

description: Library name: Sample 78

value: seedling


title: DonorB cells perturbed with Non-targeting control 2 by CRISPRi in batch Diff092

description:
Library name: IL10IL21_validation_Diff092_DonorB_NTC2
IL10IL21_validation_Diff092_DonorB_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi non-targeting control

tag: anticoagulant

tag: source

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor disease

tag: suspension depletion_factors

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: Input for HEK293 cells overexpressing Vps34

description: Library name: Input_for_RNA_Pol2_S5P_Vps34_overexp

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

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

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

tag: cell line

tag: cell type

value: human embryonic kidney

tag: genotype

value: WT

tag: treatment

value: Vps34 overexpression

tag: chip antibody

value: input


title: BS_F1h2a.w(h2a.wsuvh X h2a.wcmt)_rep4

description: Library name: Sample 12

tag: tissue


title: ChIP_suvh_H3_for_H2A.W_rep2

description: Library name: Sample 77

value: suvh4 suvh5 suvh6


title: DonorB cells perturbed with Non-targeting control 1 by CRISPRi in batch Diff092

description:
Library name: IL10IL21_validation_Diff092_DonorB_NTC1
IL10IL21_validation_Diff092_DonorB_bulkRNAseq.csv

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

value: ACDA

value: STEMCELL technologies

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

tag: donor ethnicity

value: Caucasian

tag: library protocol

tag: batch


title: Input for HEK293 cells overexpressing Vps15

description: Library name: Input_for_RNA_Pol2_S5P_Vps15_overexp

tag: cell line

value: Vps15 overexpression


title: ChIP_suvh_H3_for_H2A.W_rep1

description: Library name: Sample 76

value: seedling


title: DonorG cells perturbed with Non-targeting control 2 by CRISPRi in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorG_NTC2
IL10IL21_validation_Diff087_DonorG_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi non-targeting control

tag: anticoagulant

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor disease

tag: suspension depletion_factors

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types


title: BS_F1h2a.w(h2a.wsuvh X h2a.wcmt)_rep3

description: Library name: Sample 11

tag: tissue

value: Leaves

tag: genotype


title: Input for HEK293 cells overexpressing pcDNA3.1

description: Library name: Input_for_RNA_Pol2_S5P_pcDNA3

value: human embryonic kidney

value: WT

tag: treatment

value: pcDNA3.1 overexpression

tag: chip antibody

value: input


title: ChIP_cmt_H3_for_H2A.W_rep2

description: Library name: Sample 75

value: cmt2 cmt3


title: BS_F1h2a.w(h2a.wcmt X h2a.wsuvh)_rep2

description: Library name: Sample 10


title: DonorG cells perturbed with Non-targeting control 1 by CRISPRi in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorG_NTC1
IL10IL21_validation_Diff087_DonorG_bulkRNAseq.csv

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

value: ACDA

value: STEMCELL technologies

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

tag: donor ethnicity

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: RNA Pol II S5P, HEK293 cells, overexpressing Vps34, rep2

description:
Library name: ChIP_RNA_Pol2_S5P_Vps34_overexp_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 line

tag: cell type

value: Vps34 overexpression

value: RNA Pol II S5P, Abcam ab5408


title: BS_F1h2a.w(h2a.wcmt X h2a.wsuvh)_rep1

description: Library name: Sample 9

tag: tissue


title: DonorG cells perturbed with NFKB2 knockdown by CRISPRi and NFKB2-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorG_NFKB2-3
IL10IL21_validation_Diff087_DonorG_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of NFKB2 by NFKB2-3 gRNA

tag: anticoagulant

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor disease

tag: suspension depletion_factors

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types


title: RNA Pol II S5P, HEK293 cells, overexpressing Vps34, rep1

description:
Library name: ChIP_RNA_Pol2_S5P_Vps34_overexp_1
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

value: human embryonic kidney

tag: genotype

value: WT

tag: treatment

tag: chip antibody


title: BS_h2a.wsuvh_rep2

description: Library name: Sample 8

value: Leaves

value: hta6 hta7 hta12 suvh4 suvh5 suvh6


title: ChIP_cmt_H3_for_H2A.W_rep1

description: Library name: Sample 74

value: seedling

value: cmt2 cmt3


title: DonorG cells perturbed with MEN1 knockdown by CRISPRi and MEN1-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorG_MEN1-3
IL10IL21_validation_Diff087_DonorG_bulkRNAseq.csv

value: CRISPRi knockdown of MEN1 by MEN1-3 gRNA

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

value: ACDA

value: STEMCELL technologies

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

tag: donor ethnicity

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: ChIP_Col_H3_for_H2A.W_rep2

description: Library name: Sample 73

tag: tissue

value: Wild-type


title: RNA Pol II S5P, HEK293 cells, overexpressing Vps15, rep2

description:
Library name: ChIP_RNA_Pol2_S5P_Vps15_overexp_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 line

tag: cell type

value: Vps15 overexpression

value: RNA Pol II S5P, Abcam ab5408


title: BS_h2a.wsuvh_rep1

description: Library name: Sample 7

tag: genotype


title: ChIP_Col_H3_for_H2A.W_rep1

description: Library name: Sample 72


title: DonorG cells perturbed with MED24 knockdown by CRISPRi and MED24-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorG_MED24-3
IL10IL21_validation_Diff087_DonorG_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

tag: treatment

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

tag: experimental perturbation

value: CRISPRi knockdown of MED24 by MED24-3 gRNA

tag: anticoagulant

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor disease

tag: suspension depletion_factors

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types


title: RNA Pol II S5P, HEK293 cells, overexpressing Vps15, rep1

description:
Library name: ChIP_RNA_Pol2_S5P_Vps15_overexp_1
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

value: human embryonic kidney

value: WT

tag: chip antibody


title: BS_h2a.wcmt_rep2

description: Library name: Sample 6

value: Leaves

value: hta6 hta7 hta12 cmt2 cmt3


title: BS_CMT3-T1h2a.z_6

description: Library name: Sample 28

value: cmt2 cmt3 hta8 hta9 hta11 +CMT3 tg


title: DonorG cells perturbed with KDM1A knockdown by CRISPRi and KDM1A-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorG_KDM1A-3
IL10IL21_validation_Diff087_DonorG_bulkRNAseq.csv

value: CRISPRi knockdown of KDM1A by KDM1A-3 gRNA

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

value: ACDA

value: STEMCELL technologies

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

tag: donor ethnicity

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: RNA Pol II S5P, HEK293 cells, overexpressing pcDNA3.1, rep2

description:
Library name: ChIP_RNA_Pol2_S5P_pcDNA3_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 line

tag: cell type

tag: genotype

tag: treatment

value: pcDNA3.1 overexpression

value: RNA Pol II S5P, Abcam ab5408


title: BS_h2a.wcmt_rep1

description: Library name: Sample 5

tag: tissue


title: BS_CMT3-T1h2a.z_5

description: Library name: Sample 27


title: DonorG cells perturbed with GATA3 knockdown by CRISPRi and GATA3-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorG_GATA3-3
IL10IL21_validation_Diff087_DonorG_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of GATA3 by GATA3-3 gRNA

tag: anticoagulant

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor disease

tag: suspension depletion_factors

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types


title: RNA Pol II S5P, HEK293 cells, overexpressing pcDNA3.1, rep1

description:
Library name: ChIP_RNA_Pol2_S5P_pcDNA3_1
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

value: human embryonic kidney

value: WT

tag: chip antibody


title: BS_h2a.w_rep2

description: Library name: Sample 4

value: Leaves

value: hta6 hta7 hta12


title: BS_CMT3-T1h2a.z_4

description: Library name: Sample 26

value: cmt2 cmt3 hta8 hta9 hta11 +CMT3 tg


title: DonorG cells perturbed with ELOB knockdown by CRISPRi and ELOB-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorG_ELOB-3
IL10IL21_validation_Diff087_DonorG_bulkRNAseq.csv

value: CRISPRi knockdown of ELOB by ELOB-3 gRNA

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

value: ACDA

value: STEMCELL technologies

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

tag: donor ethnicity

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: TXMS subcutaneous xenograft mouse tumors from TXMS3 cells injection, biol rep 3

city: Chicago

first: Lobna

last: Elkhadragy

state: Illinois

address: 2201 W Campbell Park Dr,

department: Radiology

institute: University of Illinois at Chicago

description: Library name: TXMS3

data_processing:
Sequence reads were trimmed for adaptor sequence and/or low-quality sequence using Trimmomatic v0.36.
Trimmed sequence reads were mapped to Sscrofa11.1 using STAR v2.7.11b
Read count quantification and normalization were performed using RSEM v1.3.3.
Assembly: Sscrofa11.1
Supplementary files format and content: csv files contain raw counts, FPKM and TPM values for each sample

molecule: total RNA

organism: Sus scrofa

source_name: Subcutaneous xenograft tumor

growth_protocol: Primary hepatocytes were suspended in hepatocyte plating medium. Cells developed by hepatocyte gene alterataion were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and Penicillin-Streptomycin in humidified incubator with 5% CO2 at 37C.

extract_protocol:
RNA extraction was performed using Direct-zol RNA Miniprep Plus kit (Zymo).
RNAseq libraries were prepared with the Kapa Hyper Stranded mRNA library kit (Roche). Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand. The libraries were pooled; quantitated by qPCR and sequenced on one 10B lane for 151 cycles from both ends of the fragments on a NovaSeq X Plus with V1.0 sequencing kits. Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina). The quality-scores line in fastq files use an ASCII offset of 33 known as Sanger scores

tag: tissue

value: Subcutaneous xenograft tumor

tag: genotype

value: sgTP53; sgAXIN1; c-myc overexpression


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

description:
Library name: Tact_cluster_validation_Diff092_DonorD_Stim48hr_Rep1_VAV1
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: treatment

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

tag: experimental perturbation

value: CRISPRi knockdown of VAV1

tag: anticoagulant

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor disease

tag: suspension depletion_factors

value: Hispanic

value: CRISPRi


title: BS_h2a.w_rep1

description: Library name: Sample 3

value: Leaves

value: hta6 hta7 hta12


title: Rapamycin_70_male_head

city: Houston

first: Hongjie

last: Li

state: TX

address: One Baylor Plaza

department: Huffington Center on Aging

institute: Baylor College of Medicine

description:
Library name: Rapamycin_70_male_head
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw snRNA-seq reads (FASTQ format) were aligned to the Drosophila melanogaster reference genome (FlyBase release 6.31) using Cell Ranger v6.1.2, with a pre-mRNA GTF annotation generated by the FCA algorithm (Li et al., 2022). Ambient RNA contamination was then mitigated with CellBender (Fleming et al., 2023), and putative doublets were detected and removed using scDblFinder (Germain et al., 2022). For quality control, nuclei with <200 detected genes or <400 UMIs were excluded, and genes expressed in fewer than three nuclei were filtered out. We additionally removed nuclei with gene or UMI counts greater than ten median absolute deviations from the median, as well as nuclei in which mitochondrial transcripts comprised >5% of total counts. Downstream analyses were performed primarily in Scanpy v1.8.2 (Wolf et al., 2018).
Assembly: FlyBase release 6.31
Supplementary files format and content: H5ad files containing all cell-type annotations were generated using Scanpy. Matrix files were generated using Cell Ranger count.

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: head

extract_protocol:
Nuclei were isolated following a previously published protocol (McLaughlin et al., 2022). Hoechst-stained nuclei—including polyploid populations—were purified using a BD FACSAria III cell sorter. For each 10x Genomics run, approximately 150,000–200,000 nuclei were sorted and pelleted by centrifugation at 1,000 × g for 10 min at 4 °C. The pellet was resuspended in 80 µL of 1× PBS supplemented with 0.5% BSA and RNase inhibitors. Nuclei were quantified using a hemocytometer, and 45,000–55,000 nuclei were loaded to recover ~20,000 nuclei per sample. Single-nucleus 3′ gene expression libraries were prepared with the Chromium Next GEM Single Cell 3′ HT Reagent Kits v3.1 (Dual Index) according to the manufacturer’s protocol (10x Genomics). Libraries were sequenced on an Illumina NovaSeq X Plus platform (paired-end 150 bp; Novogene Co., Ltd.) to a depth of ~30,000–50,000 reads per nucleus.
snRNA-seq

value: head

value: Rapamycin

tag: Sex

value: male

tag: age


title: DonorG cells perturbed with CYB5R4 knockdown by CRISPRi and CYB5R4-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorG_CYB5R4-3
IL10IL21_validation_Diff087_DonorG_bulkRNAseq.csv

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

value: CRISPRi knockdown of CYB5R4 by CYB5R4-3 gRNA

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

value: ACDA

value: STEMCELL technologies

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: TXMS subcutaneous xenograft mouse tumors from TXMS2 cells injection, biol rep 2

description: Library name: TXMS2

tag: tissue

value: Subcutaneous xenograft tumor

tag: genotype

value: sgTP53; sgAXIN1; c-myc overexpression


title: BS_Col_for_h2a.w_rep2

description: Library name: Sample 2

value: Leaves

value: Wild-type


title: Rapamycin_50_male_head

description:
Library name: Rapamycin_50_male_head
10x Genomics

value: head

tag: treatment


title: DonorG cells perturbed with ATP2A2 knockdown by CRISPRi and ATP2A2-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorG_ATP2A2-3
IL10IL21_validation_Diff087_DonorG_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi knockdown of ATP2A2 by ATP2A2-3 gRNA

tag: anticoagulant

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor disease

tag: suspension depletion_factors

value: Hispanic

value: CRISPRi

tag: library protocol

tag: batch


title: TXMS subcutaneous xenograft mouse tumors from TXMS1 cells injection, biol rep 1

description: Library name: TXMS1


title: BS_Col_for_h2a.w_rep1

description: Library name: Sample 1


title: Rapamycin_30_male_head

description:
Library name: Rapamycin_30_male_head
10x Genomics

value: Rapamycin

tag: Sex

value: male

tag: age


title: DonorF cells perturbed with Non-targeting control by CRISPRi in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorF_NTC2
IL10IL21_validation_Diff087_DonorF_bulkRNAseq.csv

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

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: AB+

value: ACDA

value: STEMCELL technologies

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

tag: donor ethnicity

value: Asian

tag: genetic perturbation_strategy

tag: enriched cell_types


title: peritoneal dialysis peripheral blood mononuclear cells 8

type: other

city: Valencia

first: Angela

middle: L.

last: Riffo-Campos

state: Valencia

address: Avda. Blasco Ibáñes, 17

department: Department of Biochemistry and Molecular Biology

country: Spain

institute: University of Valencia, and INCLIVA

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented, and hybridized to the human Illumina Infinium MethylationEPIC BeadChip, using a standard protocol.

scan_protocol: Standard Illumina Protocol

data_processing: Genome-wide DNA methylation analysis was performed using R statistical software (R version 4.3.2). Probes that missed one or more samples, probes on sex chromosomes, probes with SNPs at the CpG site, and poor quality samples were removed. Raw data were normalized using the preprocessQuantile method in the minfi package.

label: Cy3 and Cy5

molecule: other

source_name: blood mononuclear cells

label_protocol: Standard Illumina Protocol

extract_protocol: DNA extraction was performed with the commercial kit "QIAamp® DNA Mini Kit" (QIAGEN® ref. 51304).

tag: tissue

value: blood mononuclear cells

tag: genotype

value: Final

tag: treatment

value: peritoneal dialysis


title: AF, cardiomyocyte10, DOCA + JK07

city: Leuven

first: Hywel

middle: Llewelyn

last: Roderick

address: Gasthuisberg

department: Cardiovascular Sciences

country: Belgium

institute: KULeuven

data_processing:
Quality and adapter trimming of sequencing reads was performed prior to mapping to remove low-quality reads and adapter contaminations
PCR duplicates were removed using SAMtools
Owing to the high number of intronic reads arising from unspliced RNAs in nuclear RNA-seq data, intronic and exonic regions of coding genes for gene expression analysis were used
Mapped RNA fragments were further processed using StringTie to calculate CPM values as an estimate of transcript expression
edgeR was used for differential gene expression. A q-value of < 0.05 was considered as significant. Genes with expression values of < 3 CPM in all the compared groups were excluded from the differential gene expression analysis
Assembly: Sscrofa11.1
Supplementary files format and content: tab-delimited text file includes raw count for each sample.
Supplementary files format and content: tab-delimited text file includes CPM values for each sample.

source_name: heart

extract_protocol:
The nuclear RNA was extracted from sorted cardiomyocytes by using TRIzol method.  1 ug of nuclear RNA was used for construction of library.
RNA-seq library were prepared with TruSeq RNA Sample Preparation Kit following manufacturer's manual

value: heart

tag: cell type

value: cardiomyocyte

value: WT

value: deoxycorticosterone acetate + JK07


title: Control_70_male_head

description:
Library name: Control_70_male_head
10x Genomics

value: head

value: Control

tag: Sex

value: male


title: peritoneal dialysis peripheral blood mononuclear cells 7

value: Basal


title: DonorF cells perturbed with NFKB2 knockdown by CRISPRi and NFKB2-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorF_NFKB2-3
IL10IL21_validation_Diff087_DonorF_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of NFKB2 by NFKB2-3 gRNA

value: No

value: AB+

tag: anticoagulant

value: ACDA

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor disease

tag: suspension depletion_factors

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: AF, cardiomyocyte9, DOCA + JK07

value: heart

value: cardiomyocyte

value: WT

value: deoxycorticosterone acetate + JK07


title: Control_50_male_head

description:
Library name: Control_50_male_head
10x Genomics

value: head

value: Control

value: male

tag: age


title: DonorF cells perturbed with KDM1A knockdown by CRISPRi and KDM1A-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorF_KDM1A-3
IL10IL21_validation_Diff087_DonorF_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

value: CRISPRi knockdown of KDM1A by KDM1A-3 gRNA

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: STEMCELL technologies

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

tag: donor ethnicity

value: Asian

tag: genetic perturbation_strategy

tag: enriched cell_types


title: not kidney disease peripheral blood mononuclear cells 4

tag: tissue

value: blood mononuclear cells

tag: genotype

value: Final

tag: treatment

value: not kidney disease


title: AF, cardiomyocyte8, DOCA + JK07

value: heart

tag: cell type

value: cardiomyocyte

value: WT


title: Control_30_male_head

description:
Library name: Control_30_male_head
10x Genomics

value: head

value: Control

tag: Sex


title: DonorC cells perturbed with Non-targeting control 2 by CRISPRi in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorC_NTC2
IL10IL21_validation_Diff087_DonorC_bulkRNAseq.csv

value: blood

tag: experimental perturbation

value: CRISPRi non-targeting control

value: No

value: A+

tag: anticoagulant

value: ACDA

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor disease

tag: suspension depletion_factors

value: Caucasian

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: not kidney disease peripheral blood mononuclear cells 3

value: blood mononuclear cells

value: Basal

value: not kidney disease


title: AF, cardiomyocyte7, DOCA

value: heart

value: cardiomyocyte

value: WT

value: deoxycorticosterone acetate


title: DonorC cells perturbed with Non-targeting control 1 by CRISPRi in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorC_NTC1
IL10IL21_validation_Diff087_DonorC_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

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: STEMCELL technologies

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

tag: donor ethnicity

tag: genetic perturbation_strategy


title: Control_7_male_head

description:
Library name: Control_7_male_head
10x Genomics

tag: tissue

value: head

tag: treatment

value: Control

tag: Sex

value: male

tag: genotype

tag: age


title: peritoneal dialysis peripheral blood mononuclear cells 6

value: blood mononuclear cells

value: Final

value: peritoneal dialysis


title: AF, cardiomyocyte6, DOCA

value: heart

tag: cell type

value: cardiomyocyte


title: Rapamycin_70_female_head

description:
Library name: Rapamycin_70_female_head
10x Genomics

value: Rapamycin

value: female


title: DonorC cells perturbed with NFKB2 knockdown by CRISPRi and NFKB2-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorC_NFKB2-3
IL10IL21_validation_Diff087_DonorC_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi knockdown of NFKB2 by NFKB2-3 gRNA

value: No

value: A+

tag: anticoagulant

value: ACDA

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor disease

tag: suspension depletion_factors

value: Caucasian

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: peritoneal dialysis peripheral blood mononuclear cells 5

tag: tissue

value: blood mononuclear cells

value: Basal

value: peritoneal dialysis


title: AF, cardiomyocyte5, Control

value: heart

value: cardiomyocyte

value: WT

tag: treatment

value: PBS


title: Rapamycin_50_female_head

description:
Library name: Rapamycin_50_female_head
10x Genomics

value: head

value: Rapamycin

tag: Sex

value: female


title: DonorC cells perturbed with MEN1 knockdown by CRISPRi and MEN1-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorC_MEN1-3
IL10IL21_validation_Diff087_DonorC_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

value: CRISPRi knockdown of MEN1 by MEN1-3 gRNA

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

value: ACDA

value: STEMCELL technologies

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

tag: donor ethnicity

tag: genetic perturbation_strategy


title: AF, cardiomyocyte4, Control

value: heart

tag: cell type

value: cardiomyocyte

tag: genotype


title: peritoneal dialysis peripheral blood mononuclear cells 4

value: blood mononuclear cells

value: Final

value: peritoneal dialysis


title: DonorC cells perturbed with MED24 knockdown by CRISPRi and MED24-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorC_MED24-3
IL10IL21_validation_Diff087_DonorC_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi knockdown of MED24 by MED24-3 gRNA

tag: anticoagulant

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor disease

tag: suspension depletion_factors

value: Caucasian

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: Rapamycin_30_female_head

description:
Library name: Rapamycin_30_female_head
10x Genomics

tag: tissue

value: head

tag: treatment

value: Rapamycin

tag: Sex

value: female

tag: age


title: AF, cardiomyocyte3, Control

value: WT

value: PBS


title: hemodialysis peripheral blood mononuclear cells 12

value: hemodialysis


title: Control_70_female_head

description:
Library name: Control_70_female_head
10x Genomics

value: Control


title: DonorC cells perturbed with KDM1A knockdown by CRISPRi and KDM1A-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorC_KDM1A-3
IL10IL21_validation_Diff087_DonorC_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

value: CRISPRi knockdown of KDM1A by KDM1A-3 gRNA

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

value: ACDA

value: STEMCELL technologies

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: batch


title: hemodialysis peripheral blood mononuclear cells 11

value: blood mononuclear cells

tag: genotype

value: Basal


title: Control_50_female_head

description:
Library name: Control_50_female_head
10x Genomics

value: head

value: female


title: DonorC cells perturbed with GATA3 knockdown by CRISPRi and GATA3-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorC_GATA3-3
IL10IL21_validation_Diff087_DonorC_bulkRNAseq.csv

tag: cell type

tag: experimental perturbation

value: CRISPRi knockdown of GATA3 by GATA3-3 gRNA

tag: anticoagulant

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor disease

tag: suspension depletion_factors

value: Caucasian

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: AF, cardiomyocyte2, Control

tag: tissue

value: heart

value: cardiomyocyte

value: WT

tag: treatment

value: PBS


title: hemodialysis peripheral blood mononuclear cells 10

value: Final

value: hemodialysis


title: AF, cardiomyocyte1, Control


title: DonorC cells perturbed with ELOB knockdown by CRISPRi and ELOB-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorC_ELOB-3
IL10IL21_validation_Diff087_DonorC_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

value: CRISPRi knockdown of ELOB by ELOB-3 gRNA

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

value: ACDA

value: STEMCELL technologies

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

tag: donor ethnicity


title: Control_30_female_head

description:
Library name: Control_30_female_head
10x Genomics

value: head

value: Control

tag: Sex

value: female

tag: genotype

tag: age


title: hemodialysis peripheral blood mononuclear cells 9

value: blood mononuclear cells

value: Basal


title: Heart , WT, 3 weeks, sample 4

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

institute: CNIC

description: Library name: WT43

data_processing:
Raw data were pre-processed with a pipeline using cutadapt to remove Illumina adapter and FastQC to perform quality control. RSEM was used to align processed reads against a reference transcriptome derived from GRCm38.99, and to obtain gene‑expression levels. The percentage of successfully mapped reads was 87% on average. Differentially expressed genes (DEG, adjusted p-value < 0.05), were estimated using limma analysis of raw counts on a collection of 14,109 genes showing at least 1 count per million in no less than 4 samples.
Assembly: GRCm38.99
Supplementary files format and content: Normalized counts (CPM) for each gene in each sample

organism: Mus musculus

source_name: Heart

extract_protocol:
Cardiac RNA was isolated from 3- and 18-week-old hearts that were stored at -80ºC in 500 μL of RNAlater™ Stabilization Solution (Invitrogen, Cat. No. AM7020). Total RNA was isolated by homogenization with T10 basic ULTRA-TURRAX® (IKA), using TRI reagent followed by chloroform precipitation and a purification step using Rneasy micro-Kit (Qiagen, Cat. No. 74004) following the indications of the provider.
RNA was extracted and libraries were prepared using a strand-specific RNA-seq protocol. mRNA was enriched (polyA selection) and converted to cDNA. Libraries were sequenced on an Illumina platform.

value: Heart

tag: cell type

value: whole heart tissue

value: WT

value: 3 weeks


title: Control_7_female_head

description:
Library name: Control_7_female_head
10x Genomics


title: DonorC cells perturbed with CYB5R4 knockdown by CRISPRi and CYB5R4-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorC_CYB5R4-3
IL10IL21_validation_Diff087_DonorC_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of CYB5R4 by CYB5R4-3 gRNA

tag: anticoagulant

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor disease

tag: suspension depletion_factors

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq

tag: batch


title: Heart , WT, 18 weeks, sample 4

description: Library name: WT418

tag: tissue

tag: treatment

value: 18 weeks


title: Rapamycin_70_male_body

description:
Library name: Rapamycin_70_male_body
10x Genomics

source_name: body

value: body

value: Rapamycin

tag: Sex

value: male


title: conservative treatment peripheral blood mononuclear cells 7

value: blood mononuclear cells

tag: genotype

value: Basal

value: conservative treatment


title: Heart , WT, 3 weeks, sample 3

description: Library name: WT33

value: Heart

value: whole heart tissue

value: WT

value: 3 weeks


title: DonorC cells perturbed with ATP2A2 knockdown by CRISPRi and ATP2A2-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorC_ATP2A2-3
IL10IL21_validation_Diff087_DonorC_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

value: CRISPRi knockdown of ATP2A2 by ATP2A2-3 gRNA

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

value: ACDA

value: STEMCELL technologies

value: Female

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

tag: donor ethnicity

tag: library protocol


title: Rapamycin_50_male_body

description:
Library name: Rapamycin_50_male_body
10x Genomics

value: body

value: Rapamycin

value: male

tag: age


title: DonorA cells perturbed with Non-targeting control 2 by CRISPRi in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorA_NTC2
IL10IL21_validation_Diff087_DonorA_bulkRNAseq.csv

tag: cell type

tag: experimental perturbation

value: CRISPRi non-targeting control

value: O+

tag: anticoagulant

tag: source

tag: donor sex

value: Male

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor disease

tag: suspension depletion_factors

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: conservative treatment peripheral blood mononuclear cells 6

tag: tissue

value: blood mononuclear cells

tag: genotype

value: Final

tag: treatment

value: conservative treatment


title: Heart , WT, 18 weeks, sample 3

description: Library name: WT318

value: Heart

value: whole heart tissue

value: WT

value: 18 weeks


title: Rapamycin_30_male_body

description:
Library name: Rapamycin_30_male_body
10x Genomics

value: body

value: Rapamycin

tag: Sex


title: DonorA cells perturbed with Non-targeting control 1 by CRISPRi in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorA_NTC1
IL10IL21_validation_Diff087_DonorA_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

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: ACDA

value: STEMCELL technologies

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

tag: donor ethnicity

tag: library protocol

tag: batch


title: conservative treatment peripheral blood mononuclear cells 5

value: blood mononuclear cells

value: Basal

value: conservative treatment


title: Control_70_male_body

description:
Library name: Control_70_male_body
10x Genomics

value: Control

value: male

tag: age


title: not kidney disease peripheral blood mononuclear cells 2

value: Final

value: not kidney disease


title: DonorA cells perturbed with NFKB2 knockdown by CRISPRi and NFKB2-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorA_NFKB2-3
IL10IL21_validation_Diff087_DonorA_bulkRNAseq.csv

value: blood

tag: cell type

tag: experimental perturbation

value: CRISPRi knockdown of NFKB2 by NFKB2-3 gRNA

value: O+

tag: anticoagulant

tag: source

tag: donor sex

value: Male

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor disease

tag: suspension depletion_factors

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: Heart , WT, 3 weeks, sample 2

description: Library name: WT23

tag: tissue

value: Heart

value: whole heart tissue

tag: genotype

value: WT

tag: treatment

value: 3 weeks


title: Heart , WT, 18 weeks, sample 2

description: Library name: WT218

value: 18 weeks


title: conservative treatment peripheral blood mononuclear cells 8

value: blood mononuclear cells

value: conservative treatment


title: Control_50_male_body

description:
Library name: Control_50_male_body
10x Genomics

value: body

value: Control

tag: Sex

value: male


title: DonorA cells perturbed with MEN1 knockdown by CRISPRi and MEN1-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorA_MEN1-3
IL10IL21_validation_Diff087_DonorA_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

value: CRISPRi knockdown of MEN1 by MEN1-3 gRNA

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: O+

value: ACDA

value: STEMCELL technologies

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

tag: donor ethnicity

tag: library protocol

tag: batch


title: Heart , WT, 3 weeks, sample 1

description: Library name: WT13

value: Heart

tag: cell type

value: whole heart tissue

value: WT

value: 3 weeks


title: Control_30_male_body

description:
Library name: Control_30_male_body
10x Genomics

value: body

value: Control

tag: age


title: conservative treatment peripheral blood mononuclear cells 4

tag: tissue

value: blood mononuclear cells

value: Final

value: conservative treatment


title: not kidney disease peripheral blood mononuclear cells 1

tag: genotype

value: Basal

value: not kidney disease


title: DonorA cells perturbed with MED24 knockdown by CRISPRi and MED24-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorA_MED24-3
IL10IL21_validation_Diff087_DonorA_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

tag: treatment

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

tag: experimental perturbation

value: CRISPRi knockdown of MED24 by MED24-3 gRNA

value: No

value: O+

tag: anticoagulant

tag: source

tag: donor sex

value: Male

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor disease

tag: suspension depletion_factors

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: Heart , WT, 18 weeks, sample 1

description: Library name: WT118

value: Heart

value: whole heart tissue

value: WT

value: 18 weeks


title: Control_7_male_body

description:
Library name: Control_7_male_body
10x Genomics

value: body

value: Control

tag: Sex

value: male


title: chr_Dis3_2

first: Antonin

last: Morillon

state: Paris

address: 26 rue d'Ulm

institute: Institut Curie

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

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

source_name: HCT116 derivative cell line

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

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

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

tag: fraction

value: chromatin fraction

value: non induced


title: ATAC_Ascl1_AAA_D2_rep3

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 415/420 Clinical Research Building (CRB)

institute: University of Pennsylvania

description: Library name: 14_ATAC_UAE_AAA_D2_rep3_S18

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

value: AAA

tag: time

tag: replicate

value: 0.5μg/ml doxycycline


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim48hr_Rep1_HEXDC
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

tag: tissue

value: blood

value: CD4-positive, alpha-beta T cells

tag: treatment

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

value: CRISPRi knockdown of HEXDC

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Yes

tag: donor blood_type

value: A-

value: ACDA

value: STEMCELL technologies

value: Male

value: adult stage

value: TRUE

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

tag: donor ethnicity

value: Hispanic

tag: library protocol

tag: batch


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

description:
Library name: Tact_cluster_validation_Diff092_DonorH_Stim48hr_Rep1_LAT
Tact_cluster_validation_Diff092_Stim48hr_Rep1_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi knockdown of LAT

tag: anticoagulant

tag: source

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor disease

tag: suspension depletion_factors

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: DonorA cells perturbed with KDM1A knockdown by CRISPRi and KDM1A-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorA_KDM1A-3
IL10IL21_validation_Diff087_DonorA_bulkRNAseq.csv

tag: tissue

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: treatment

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

value: CRISPRi knockdown of KDM1A by KDM1A-3 gRNA

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

value: O+

value: Caucasian


title: cyt_wt_1

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

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

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

tag: fraction

value: cytoplasmic fraction

value: non induced


title: conservative treatment peripheral blood mononuclear cells 3

value: blood mononuclear cells

tag: genotype

value: Basal

value: conservative treatment


title: Heart , R502W, 3 weeks, sample 4

description: Library name: KI43

value: Heart

value: whole heart tissue

value: 3 weeks


title: DonorA cells perturbed with GATA3 knockdown by CRISPRi and GATA3-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorA_GATA3-3
IL10IL21_validation_Diff087_DonorA_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi knockdown of GATA3 by GATA3-3 gRNA

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Male

value: adult stage

value: TRUE

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

tag: donor ethnicity

value: CRISPRi

tag: library protocol

tag: batch


title: Rapamycin_70_female_body

description:
Library name: Rapamycin_70_female_body
10x Genomics

tag: tissue

value: body

tag: treatment

value: Rapamycin

tag: Sex

value: female

tag: age


title: Rapamycin_50_female_body

description:
Library name: Rapamycin_50_female_body
10x Genomics


title: Heart , R502W, 18 weeks, sample 4

description: Library name: KI418

tag: cell type

value: 18 weeks


title: hemodialysis peripheral blood mononuclear cells 8

value: blood mononuclear cells

value: Final

value: hemodialysis


title: hemodialysis peripheral blood mononuclear cells 7

value: Basal


title: Heart , R502W, 3 weeks, sample 3

description: Library name: KI33

value: Heart

value: whole heart tissue

value: 3 weeks


title: DonorA cells perturbed with CYB5R4 knockdown by CRISPRi and CYB5R4-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorA_CYB5R4-3
IL10IL21_validation_Diff087_DonorA_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

value: CRISPRi knockdown of CYB5R4 by CYB5R4-3 gRNA

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

value: O+

value: ACDA

value: STEMCELL technologies

value: Male

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

tag: donor disease

tag: suspension depletion_factors

value: Caucasian

tag: genetic perturbation_strategy

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: hemodialysis peripheral blood mononuclear cells 6

value: blood mononuclear cells

tag: genotype

value: Final

value: hemodialysis


title: Heart , R502W, 18 weeks, sample 3

description: Library name: KI318

tag: tissue

value: Heart

value: whole heart tissue

value: 18 weeks


title: Rapamycin_30_female_body

description:
Library name: Rapamycin_30_female_body
10x Genomics

value: body

tag: treatment

value: Rapamycin

value: female


title: DonorA cells perturbed with ELOB knockdown by CRISPRi and ELOB-3 gRNA in batch Diff087

description:
Library name: IL10IL21_validation_Diff087_DonorA_ELOB-3
IL10IL21_validation_Diff087_DonorA_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of ELOB by ELOB-3 gRNA

value: No

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

value: TRUE

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

tag: donor ethnicity

value: CRISPRi

tag: library protocol

tag: batch


title: Control_70_female_body

description:
Library name: Control_70_female_body
10x Genomics

value: Control

tag: Sex

tag: age


title: transverse colon PRO-cap

city: Ithaca

first: Haiyuan

last: Yu

state: NY

address: 10 East Ave.

institute: Cornell University

description: Library name: GT25b

library_source: other

data_processing:
Raw reads were preprocessed with fastp (v0.23.4) for adapter trimming and unique molecular index (UMI) processing, retaining only reads ≥18 bp for downstream analyses.
Processed reads were aligned to the human reference genome hg38 (GCA_000001405.15) and ribosomal DNA (U13369.1) using STAR (v2.7.11a).
Uniquely mapped reads were filtered with samtools (v1.18) and deduplicated using umi_tools (v1.1.5).
The resulting PCR-free, uniquely mapped reads were converted to bigwig format with pints_visualizer (v1.1.15).
Assembly: hg38
Supplementary files format and content: BigWig: plus and minus strand signal of unique reads

source_name: transverse colon

extract_protocol:
Ten million cells were processed per biological replicate. Cells were permeabilized and nuclei were isolated as described previously (PMID: 27442863), prior to downstream PRO-cap library preparation.
PRO-cap libraries were prepared using a previously described protocol (PMID: 27442863) with modifications (PMID: 41040139). Briefly, permeabilized cells/isolated nuclei were subjected to nuclear run-on reactions to capture nascent RNA. Total RNA was isolated and split into two rounds of adaptor ligation (i.e. VRA3 and VRA5) using T4 RNA Ligase 1 (NEB; M0204), followed by reverse transcription using SuperScript III (Invitrogen; 18080044) with custom adapters. Between adaptor ligation steps, cap-stable selection was performed using CIP (NEB; M0290) to dephosphorylate uncapped RNAs, thereby preventing ligation to the 5′ adaptor, and Cap-Clip (CellScript; C-CC15011H) to remove 5′ caps from guanylated transcripts, enabling incorporation into the library through 5′ adaptor ligation. RNA washes, phenol-chloroform extraction, and ethanol precipitation were performed between reactions under RNase-free conditions following manufacturer protocols. Following PCR amplification using RP1 and RPI-n primers and library cleanup, sequencing was performed on an Illumina HiSeq 3000 platform.

value: transverse colon


title: hemodialysis peripheral blood mononuclear cells 5

value: blood mononuclear cells

value: Basal

value: hemodialysis


title: Heart , R502W, 3 weeks, sample 2

description: Library name: KI23

value: Heart

tag: cell type

value: whole heart tissue

value: 3 weeks


title: t2iLGo

city: Ann Arbor

first: Duo

last: Wang

state: MI

address: 2800 Plymouth Road

department: Center for Advanced Models Translational Sciences and Therapeutics

institute: University of Michigan

description:
Library name: t2iLGo
NEBNext Enzymatic Methyl-seq kit

data_processing:
Raw reads were quality assessed using FastQC (v0.11.8).
Adapter trimming and quality filtering were performed using Trim Galore (v0.4.5) with parameters: --adapter AGATCGGAAGAGC -e 0.1 --stringency 6 --length 20 --nextseq 20.
Trimmed reads were aligned to the hg38 reference genome using Bismark (v0.22.1) with Bowtie2 (v2.3.4) under default settings.
Duplicate reads were marked and removed using Picard (v2.20.2), and low-quality alignments were filtered using samtools (v1.2) with MAPQ < 10 removed.
CpG methylation rates were called using MethylDackel (v0.4.0) with parameters -d 5 -D 2000 --mergeContext.
Assembly: hg38
Supplementary files format and content: Pseudo-bedGraph files containing chromosome, start, end, methylation rate, number of methylated reads, and number of unmethylated reads for each CpG site.
Supplementary files format and content: bigWig files containing per-CpG methylation rates for visualization in genome browsers.
Library strategy: EM-seq

source_name: embryonic stem cell

growth_protocol: 6iL-hiPSCs were cultured on feeder cells in 6iL/E4 medium. hESCs were cultured on feeder cells under t2iL/Go conditions. hiPSCs were cultured on Matrigel in mTeSR1 medium.

extract_protocol:
Genomic DNA extraction were performed using the Qiagen Genomic DNA Extraction Kit.  A total of 100 ng for each sample was used as input for the NEBNext Enzymatic Methyl-seq kit
Library PCR amplification was done for 5 cycles using NEBNext Multiplex Oligos for Enzymatic Methyl-seq. The final libraries were quantified with the Qubit dsDNA HS Assay kit. Quality of the libraries was assessed on Agilent’s 4200 TapeStation, using the High Sensitivity D1000 kit. Quantification by qPCR was performed using the KAPA Illumina Library Quantification Kit. Equimolar amounts of each library were pooled and quantified by qPCR before PE-150 sequencing on a 10B 300 cycle shared flow cell on the NovaSeq X Plus.

value: embryonic stem cell

tag: cell line

value: hESC

value: pluripotent stem cell

value: hESC carrying a doxycycline-inducible KLF2/NANOG cassette

value: t2iLGo culture


title: hemodialysis peripheral blood mononuclear cells 4

tag: genotype

value: Final


title: Control_50_female_body

description:
Library name: Control_50_female_body
10x Genomics

tag: tissue

value: body

value: female


title: Heart , R502W, 18 weeks, sample 2

description: Library name: KI218

tag: treatment

value: 18 weeks


title: Control_30_female_body

description:
Library name: Control_30_female_body
10x Genomics

value: Control


title: hemodialysis peripheral blood mononuclear cells 3


title: mTeSR1

description:
Library name: mTeSR1
NEBNext Enzymatic Methyl-seq kit

source_name: induced pluripotent stem cell

treatment_protocol: 6iL-hiPSCs were cultured on feeder cells in 6iL/E4 medium. hESCs were cultured on feeder cells under t2iL/Go conditions. hiPSCs were cultured on Matrigel in mTeSR1 medium.

value: induced pluripotent stem cell

value: hiPSC

value: wild type

value: mTeSR1 culture


title: 6iL

description:
Library name: 6iL
NEBNext Enzymatic Methyl-seq kit

value: 6iL culture


title: Heart , R502W, 3 weeks, sample 1

description: Library name: KI13

value: Heart

value: whole heart tissue


title: Control_7_female_body

description:
Library name: Control_7_female_body
10x Genomics


title: Heart , R502W, 18 weeks, sample 1

description: Library name: KI118


title: peritoneal dialysis peripheral blood mononuclear cells 3

value: blood mononuclear cells

value: peritoneal dialysis


title: 6iL-mESC

description:
Library name: 6iL-mESC
Illumina Single Cell 3′ RNA Prep T2

data_processing:
Raw sequencing reads (FASTQ files) were aligned to the human or mouse reference genome using pipseeker. Human reads were aligned to GRCh38.p13 (GENCODE v40, Ensembl 106) and mouse reads were aligned to GRCm39 (GENCODE vM29, Ensembl 106). Alignment was performed with the following options: full --chemistry V --fastq --remove-bam --star-index-path --output-path --max-sensitivity 5.
Gene expression count matrices generated from sensitivity_3 were selected for downstream analysis.
Count matrices from all samples were integrated using the R package Seurat (v4.3.0) using canonical correlation analysis (CCA) with default parameters.
Assembly: Human: GRCh38.p13 (GENCODE v40, Ensembl 106); Mouse: GRCm39 (GENCODE vM29, Ensembl 106)
Supplementary files format and content: Processed data are provided as gene expression matrices in Matrix Market (.mtx) format. Associated gene annotation files (genes.tsv/features.tsv) and cell barcode files (barcodes.tsv) are included for each sample.

growth_protocol: 6iL-mESC and 6iL-hiPSC cultured in 6iL/E4 medium on feeder.

extract_protocol:
RNA extraction and single-cell capture were performed using the Single Cell 3′ RNA Prep, T2 kit (Illumina) according to the manufacturer's instructions.
Single-cell RNA-seq libraries were prepared using the Single Cell 3′ RNA Prep, T2 kit (Illumina). For indexing, the Mix 7 index set was used for 6iL-hiPSC samples and the Mix 8 index set was used for 6iL-mESC samples. Sequencing was performed on an Illumina NovaSeq X Plus platform using paired-end sequencing (2 × 150 bp), generating approximately 200 million reads per sample.

treatment_protocol: mESC and hiPSC treated with 6iL

value: embryonic stem cell

value: mESC

value: pluripotent stem cell


title: Male, KO, rep5

city: Edmonton

first: Richard

last: Lehner

state: Alberta

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

department: Pediatrics

country: Canada

institute: University of Alberta

description: Library name: M_KO_5

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

source_name: Liver

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

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

treatment_protocol: Livers were harvested and snap frozen

value: Liver

value: Male

value: AADAC KO

value: One week western-type diet, fed state


title: 6iL-hiPSC

description:
Library name: 6iL-hiPSC
Illumina Single Cell 3′ RNA Prep T2


title: chr_ctrl_A_1

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

tag: fraction

value: chromatin fraction

value: 1h induction with auxin


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

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim8hr_Rep2_MEN1
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 MEN1

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: O+

value: ACDA

value: STEMCELL technologies

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor disease

value: Normal

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

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: Female, WT, rep3

description: Library name: F_WT_3

value: Liver

tag: Sex

tag: genotype

value: AADAC WT

value: One week western-type diet, fed state


title: peritoneal dialysis peripheral blood mononuclear cells 2

tag: tissue

value: blood mononuclear cells

value: Basal

tag: treatment

value: peritoneal dialysis