title: VMCUB1, siTP63_83, rep1 (RNA)

description:
Library name: VMCUB1_siTP63_83_1
3'RNA-seq


title: VMCUB1, ctrl, rep2 (RNA)

status: Public on Jun 02 2026

type: SRA

city: Gif-sur-Yvette

first: Lilia

last: Estrada Virrueta

address: 1, Avenue de la Terrasse

country: France

description:
Library name: VMCUB1_ctrl_2
3'RNA-seq

library_source: transcriptomic

data_processing:
Reads were mapped to the UCSC hg19 genome and then counted using star (v2.7.6a).
Statistically significant differences in gene expression were determined by performing a differential analysis using DESeq2 (v1.30.1)
Assembly: hg19
Supplementary files format and content: csv file includes TPM values for each sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cells were cultured in DMEM (MGHU3, VMCUB1) supplemented with 10% fetal bovine serum at 37°C under a 5% CO2 atmosphere.

extract_protocol:
RNA isolates from siTP63-transfected and control cells were prepared using the Qiagen RNA easy minikit supplemented with DNase treatment.
Library were prepared using the QuantSeq 3’mRNA library prep kit.

treatment_protocol: Cells were transfected for 48h with 5 nM siRNA and Lipofectamine RNAi Max reagent (Invitrogen).

tag: cell line

tag: treatment

value: WT


title: VMCUB1, siTP63_11, rep2 (RNA)

description:
Library name: VMCUB1_siTP63_11_2
3'RNA-seq

value: TP63 knockdown


title: MGHU3, ctrl, rep3 (RNA)

description:
Library name: MGHU3_ctrl_3
3'RNA-seq


title: MGHU3, ctrl, rep2 (RNA)

description:
Library name: MGHU3_ctrl_2
3'RNA-seq


title: VMCUB1, siTP63_11, rep1 (RNA)

description:
Library name: VMCUB1_siTP63_11_1
3'RNA-seq


title: MGHU3, ctrl, rep1 (RNA)

description:
Library name: MGHU3_ctrl_1
3'RNA-seq


title: MGHU3, siTP63, rep3 (RNA)

description:
Library name: MGHU3_siTP63_3
3'RNA-seq


title: MGHU3, siTP63, rep2 (RNA)

description:
Library name: MGHU3_siTP63_2
3'RNA-seq


title: MGHU3, siTP63, rep1 (RNA)

description:
Library name: MGHU3_siTP63_1
3'RNA-seq


title: Donor4_CD14+ mono/PM_20_ug/ml

city: Khlong Luang

first: Naunpun

last: Sangphech

state: Prathumtani

address: Moo 18, Phahon Yothin Rd., Khlong Nueng

department: Medical Technology

country: Thailand

institute: Thammasat University

data_processing:
online platform (useGalaxy, Galaxy version 23.1.rc1)
Sequence reads were trimmed for adaptor sequence using trimmomatic
Trimmed sequence were quantified transcript using Sailfish tool and use GRCh38_lasted_rna.fna.gz as reference transcriptome.
DESeq2 was used to compare the differences between each condition, and GRCh38_lasted_genomic.gff.gz was used to identify gene annotation.
Assembly: GRCh38_lasted_rna.fna.gz/GRCh38_lastest_genomic.gff.gz
Supplementary files format and content: tabular file includes TPM value for each sample
Supplementary files format and content: tab-delimited text includes normalized count from DESeq2 for each sample

source_name: CD14+ monocytes

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from the buffy coat or whole blood of healthy donors and asthma patients by Ficoll gradient centrifugation (GE Healthcare, UK). PBMCs was used as sources for CD14+ monocytes separation by human CD14 microbeads (MACS Miltenyi Biotec, Germany). CD14+ monocytes were maintained in RPMI-1640 supplemented with 5% human serum (Sigma, USA) and antibiotics plus antimycotics (Gibco, USA).

extract_protocol:
RNA was extracted using an RNeasy® Mini kit (QIAGEN, Germany). Total RNA was sent to perform RNA sequencing at the Omics Sciences & Bioinformatics Center, Chulalongkorn University, Thailand.
The sample library was prepared using a TruSeq mRNA library kit (Illumina, USA).

treatment_protocol: CD14+ primary human monocytes were stimulated with Chiang-Mai-PM2.5 at a concentration of 5 or 20 micrograms  per militer for 24 hours.

tag: individual

tag: tissue

value: CD14+ monocytes

tag: cell type

tag: genotype

value: Not specified

value: 20 ug/ml of PM2.5


title: Donor5_CD14+ mono/PM_20_ug/ml


title: Donor5_CD14+ mono/PM_5_ug/ml

value: 5 ug/ml of PM2.5


title: Donor4_CD14+ mono/PM_5_ug/ml


title: Donor4_CD14+ mono/unstim

value: Non-treatment


title: Donor5_CD14+ mono/unstim


title: Donor3_CD14+ mono/unstim


title: Donor3_CD14+ mono/PM_5_ug/ml


title: Donor3_CD14+ mono/PM_20_ug/ml


title: Donor2_CD14+ mono/PM_20_ug/ml


title: Donor2_CD14+ mono/PM_5_ug/ml


title: Donor2_CD14+ mono/unstim


title: Donor1_CD14+ mono/PM_20_ug/ml


title: Donor1_CD14+ mono/PM_5_ug/ml


title: Donor1_CD14+ mono/unstim


title: TvHM2, fungal biomass, high melanin fungal necromass, rep2

city: Saint Paul

first: Jonathan

last: Schilling

state: Minnesota

address: 1445 Gortner Avenue

department: Plant and Microbial Biology

country: USA

institute: University of Minnesota

description: Library name: TvHM2

data_processing:
Raw data were processed with Collection of Hierarchical UMII-RIS Pipelines (CHURP; v0.2.2; Baller et al., 2019).
kallisto version 0.51.1 (Bray et al., 2016; Sullivan et al., 2025) was used for constructing transcriptome index and quantification of transcript abundances
DESeq2 version 1.48.2 (Love et al., 2014) was used for differential expression analysis
Assembly: For Gloeophyllum trabeum: GCF_000344685.1_Glotr1_1_rna_from_genomic.fna.gz from the assembly GCF_000344685.1. For Trametes versicolor: Traver1_GeneCatalog_transcripts_20220719.nt.fasta.gz obtained from Joint Genome Institute (JGI) MycoCosm portal.
Supplementary files format and content: tsv files generated by kallisto for each sample that contain estimated counts and tpm. These files were used for differential gene expression analysis with DESeq2 all downstream visualizations.

organism: Trametes versicolor

source_name: Fungal biomass

growth_protocol: Gloeophyllum trabeum and Trametes versicolor were routinely maintained on malt extract agar plates and malt extract broth

extract_protocol:
RNA was extracted using TRIzol and PureLink RNA mini kit
NEBNext Ultra II RNA Library Prep kit

treatment_protocol: Three treatments were used: 1. Highley’s medium supplemented with 1% (w/v) glucose, 2. Highley’s medium with 0.45% (w/v) low-melanin necromass, 3. Highley’s medium with 0.45% high-melanin necromass

value: Fungal biomass

tag: strain

tag: time

value: 7 days

value: high melanin fungal necromass


title: TvHM1, fungal biomass, high melanin fungal necromass, rep1

description: Library name: TvHM1


title: TvHM3, fungal biomass, high melanin fungal necromass, rep3

description: Library name: TvHM3


title: DS18_E18.5

city: La Jolla

first: Jessica

middle: Xinyun

last: Du

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, and generation of gene counts were done using CellRanger. Reference files for the mouse genome and the viral sequence used for fluorescent labeleing were used to recover and align the transgene.
Assembly: GRCm39
Supplementary files format and content: TSV files and matrix files

molecule: polyA RNA

organism: Mus musculus

source_name: brain, cortex

extract_protocol:
Cortical tissue was dissected from E18.5 mouse embryos in cold Leibovitz’s L15 medium supplemented with 7mM HEPES, pooling embryos from the same litter. Tissue was dissociated into single cell suspensions using reagents from the Worthington Tissue Dissociation Kit; tissue was digested in papain/DNAse for 15 min at 37C with carbogen oxygenation, mechanically triturated in EBSS, and resuspended in an optimem-trehalose media (Optimem supplemented with 50mM of trehalose, 10mMglucose, 0.5 mM kynurenic acid, 0.025 mM APV, 4 mM MgCl2, 0.2 mM HEPES, with osmolarity of 290 ± 10 mOsm/kg). Debris was removed with an 5% optiprep gradient spin and the cell pellet was resuspended in 500 uL of optimem-trehalose media. We sorted for live eYFP+ cells using an Astrios EQ sorting flow cytometer with an 100 um nozzle
Libraries construction was done with 10x genomics Chromium reagents to load single cells, form GEMs, and perform the RT reaction. Sequencing was done on a Illumina Nextseq200 with a P2 flowcell to a depth of approximately 200 million reads.

value: brain, cortex

value: cortical inhibitory neuron


title: TvLM3, fungal biomass, low melanin fungal necromass, rep3

description: Library name: TvLM3

value: low melanin fungal necromass


title: TvLM2, fungal biomass, low melanin fungal necromass, rep2

description: Library name: TvLM2


title: TvLM1, fungal biomass, low melanin fungal necromass, rep1

description: Library name: TvLM1


title: TvG3, fungal biomass, glucose, rep3

description: Library name: TvG3

value: Glucose


title: TvG1, fungal biomass, glucose, rep1

description: Library name: TvG1


title: TvG2, fungal biomass, glucose, rep2

description: Library name: TvG2


title: GtHM3, fungal biomass, high melanin fungal necromass, rep3

description: Library name: GtHM3

organism: Gloeophyllum trabeum


title: GtHM2, fungal biomass, high melanin fungal necromass, rep2

description: Library name: GtHM2


title: GtHM1, fungal biomass, high melanin fungal necromass, rep1

description: Library name: GtHM1


title: GtLM1, fungal biomass, low melanin fungal necromass, rep1

description: Library name: GtLM1


title: GtLM2, fungal biomass, low melanin fungal necromass, rep2

description: Library name: GtLM2


title: GtG3, fungal biomass, glucose, rep3

description: Library name: GtG3


title: GtLM3, fungal biomass, low melanin fungal necromass, rep3

description: Library name: GtLM3


title: GtG2, fungal biomass, glucose, rep2

description: Library name: GtG2


title: GtG1, fungal biomass, glucose, rep1

description: Library name: GtG1


title: Injury

city: Philadelphia

first: Jianing

last: Yang

state: Pennsylvania

address: 3400 Civic Blvd

department: Neuroscience

institute: University of Pennsylvania

description: Library name: Injury

data_processing:
We aligned and quantified the sequencing reads using the CellRanger (v7.2.0) count command. We captured an estimated 4546 cells in the control sample, with a mean reads per cell of 54269, and an estimated 4203 cells in the injury sample, with a mean reads per cell of 50309. We then performed downstream analysis on the output filtered feature barcode matrices using the Python package SCANPY (v1.9.6).
For the preprocessing of the data, we first filtered out outlier cells and cells with mitochondrial percentage over 20% (damaged/dying cells). Then we filtered ambient RNA with SoupX (from ~13000 genes to ~8000 genes), and filtered doublet cells with scDblFinder (~6% cells called doublets). We integrated filtered control and injury data sets with scVI, taking into account batch effects for better mixing. The resulting merged data set contains 4201 cells from the control group and 3713 cells from the injury group. We then normalized the read counts using shifted logarithm with Scran estimated size factors. Finally, we performed principal component analysis (PCA) on the top 4000 highly variable genes, and the variance ratio levelled off at around 50 PCs. We created umap and tsne plots to visualize the data set.
We clustered the scVI integrated data using the leiden algorithm (scanpy.tl.leiden), using the top 50 principal components, at various resolutions ranging from 0.5 to 20. For the automated annotation of the cells, we used two methods, scArches (scVI tools v1.0.4) and CellTypist (v1.6.2). With scArches, we integrated our data set with a reference data set (ref. Davie et al 2018), and then used the k-nearest neighbor algorithm to transfer the cell type labels from the reference data set to our data set. Celltypist uses a logistic regression model trained on the reference data set to predict the cell type for each cell in our data set based on its transcriptomic profile. For both methods, we marked cells annotated with less than 80% certainty as unknown. We then took the combined annotation from these two methods, going with CellTypist for the few cells where they disagree since its annotation aligns slightly better with expression of known marker genes. Finally, we manually annotated 13 leiden clusters from resolutions 0.5, 5, 15 and 20 according to the results of this combined automated annotation. Since some of the neuronal clusters are too small for downstream differential expression analysis, we also annotated the nSyb positive cells with more general neuronal cell types. Using the four neuronal markers (Gad1 for gabaergic cells, VGlut for glutamatergic cells, VAChT for cholinergic cells and Vmat for monoaminergic cells), we annotated the neurons with their most highly expressed marker.
Differential Expression analysis on each of the large cell types was performed using the pseudobulk method. We constructed 3 pseudobulk samples for each cell type and each condition by randomly dividing the cells into 3 samples and aggregating the gene counts. We then ran DESeq2 on the pseudobulk data to generate our list of differentially expressed genes for each cell type.
cellranger-7.2.0
Assembly: Drosophila_melanogaster.BDGP6.32.dna.primary_assembly.fa
Supplementary files format and content: control_filtered_feature_bc_matrix.tar.gz: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: injury_filtered_feature_bc_matrix.tar.gz: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

organism: Drosophila melanogaster

source_name: brain

extract_protocol:
100 female CantonS red flies were dissected in ice cold Schneider’s medium. Optic lobes were removed and transferred to a tube with 3mg/ml of dispase. Samples were incubated in a thermoshaker for 15 min at 25C and 1000 rpm. To stop the enzymatic reaction, cells were rinsed three times with Schneider’s with table top spins in between. Cells were resuspended in 60 ul of DPBS with 0.04% BSA. Cell suspensions were FACS sorted using an Aria Cell Sorter (using a 100 um nozzle and 1.25 drop precision) to ensure cell viability and adjust concentration. Cells were kept on ice until processed for 10x Genomics. Single Cell 3’ Library and Gel Bead Kit following the manufacturer’s recommendation protocol
Single Cell 3’ Library and Gel Bead Kit following the manufacturer’s recommendation protocol and the libraries were sequenced on an Illumina NovaSeq 6000 in the Centre for Applied Genomics at the Children’s Hospital of Philadelphia (CHOP).

value: brain

tag: Sex

value: female

value: CantonS

value: sterile injury


title: Control

description: Library name: Control

value: handled control


title: DonorF cells perturbed with STAT6 knockdown by CRISPRi under nonpolarized culture condition in batch Diff089

city: Palo Alto

first: Lattice

last: Data Coordination

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

description:
Library name: Th1Th2_validation_Diff089_DonorF_STAT6_non
nonpolarized
Th1Th2_validation_Diff089_non_DonorF_bulkRNAseq.csv

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

source_name: blood

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

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

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of STAT6

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: AB+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

tag: donor ethnicity

value: Asian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: DonorF cells perturbed with STAT6 knockdown by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorF_STAT6_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorF_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: tissue

value: blood

tag: cell type

tag: treatment

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor weight

tag: donor height


title: DonorF cells perturbed with STAT6 knockdown by CRISPRi under Th1 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorF_STAT6_Th1
Th1 polarized
Th1Th2_validation_Diff089_Th1_DonorF_bulkRNAseq.csv

value: CD4-positive, alpha-beta T cells

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index


title: DonorF cells perturbed with Non-targeting control 2 by CRISPRi under nonpolarized culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorF_NTC2_non
nonpolarized
Th1Th2_validation_Diff089_non_DonorF_bulkRNAseq.csv

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

value: CRISPRi non-targeting control

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: DonorF cells perturbed with Non-targeting control 2 by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorF_NTC2_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorF_bulkRNAseq.csv

tag: tissue

tag: cell type

tag: treatment

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

value: No


title: DonorF cells perturbed with Non-targeting control 2 by CRISPRi under Th1 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorF_NTC2_Th1
Th1 polarized
Th1Th2_validation_Diff089_Th1_DonorF_bulkRNAseq.csv

tag: donor smoker

tag: donor blood_type

value: AB+

tag: anticoagulant

tag: source

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index


title: DonorF cells perturbed with Non-targeting control 1 by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorF_NTC1_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorF_bulkRNAseq.csv

value: ACDA

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: DonorF cells perturbed with Non-targeting control 1 by CRISPRi under nonpolarized culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorF_NTC1_non
nonpolarized
Th1Th2_validation_Diff089_non_DonorF_bulkRNAseq.csv

tag: tissue

tag: cell type

tag: treatment

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

value: STEMCELL technologies


title: DonorF cells perturbed with Non-targeting control 1 by CRISPRi under Th1 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorF_NTC1_Th1
Th1 polarized
Th1Th2_validation_Diff089_Th1_DonorF_bulkRNAseq.csv

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index


title: DonorF cells perturbed with NAB2 knockdown by CRISPRi under nonpolarized culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorF_NAB2_non
nonpolarized
Th1Th2_validation_Diff089_non_DonorF_bulkRNAseq.csv

value: CRISPRi knockdown of NAB2

value: adult stage

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: DonorF cells perturbed with NAB2 knockdown by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorF_NAB2_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorF_bulkRNAseq.csv

tag: tissue

tag: cell type

tag: treatment

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

value: TRUE

value: Normal


title: DonorF cells perturbed with NAB2 knockdown by CRISPRi under Th1 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorF_NAB2_Th1
Th1 polarized
Th1Th2_validation_Diff089_Th1_DonorF_bulkRNAseq.csv

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

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


title: DonorF cells perturbed with MED24 knockdown by CRISPRi under nonpolarized culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorF_MED24_non
nonpolarized
Th1Th2_validation_Diff089_non_DonorF_bulkRNAseq.csv

value: CRISPRi knockdown of MED24

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity

value: Asian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

tag: batch


title: DonorF cells perturbed with MED24 knockdown by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorF_MED24_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorF_bulkRNAseq.csv

tag: tissue

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: treatment

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

value: Plasmidsaurus RNA-Seq


title: KTD2

city: Cambridge

first: Constantine

last: Tzouanas

address: 77 Massachusetts Avenue

institute: Massachusetts Institute of Technology

description: Library name: Sample 4

data_processing:
Counts matrices were generated using CellRanger 2.1.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Small intestine

extract_protocol:
Mice were placed onto control or ketogenic diets, and intestines were dissociated into single cell suspensions for scRNA-seq
Single-cell suspensions were processed with 10x Single Cell 3' v2

value: Small intestine

tag: diet

value: KetoDiet


title: DonorF cells perturbed with MED24 knockdown by CRISPRi under Th1 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorF_MED24_Th1
Th1 polarized
Th1Th2_validation_Diff089_Th1_DonorF_bulkRNAseq.csv

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

tag: donor smoker

value: No

tag: donor blood_type

value: AB+

tag: anticoagulant

value: ACDA

tag: source

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease


title: KTD1

description: Library name: Sample 3

tag: tissue


title: DonorF cells perturbed with KDM1A knockdown by CRISPRi under nonpolarized culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorF_KDM1A_non
nonpolarized
Th1Th2_validation_Diff089_non_DonorF_bulkRNAseq.csv

tag: cell type

tag: treatment

value: CRISPRi knockdown of KDM1A

value: STEMCELL technologies

value: Female

value: adult stage

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: Cont_KTD2

description: Library name: Sample 2

tag: diet

value: ControlDiet


title: DonorF cells perturbed with KDM1A knockdown by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorF_KDM1A_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorF_bulkRNAseq.csv

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

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


title: Cont_KTD1

description: Library name: Sample 1

tag: tissue


title: DonorF cells perturbed with KDM1A knockdown by CRISPRi under Th1 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorF_KDM1A_Th1
Th1 polarized
Th1Th2_validation_Diff089_Th1_DonorF_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: treatment

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

value: Asian

value: CRISPRi


title: DonorC cells perturbed with STAT6 knockdown by CRISPRi under nonpolarized culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorC_STAT6_non
nonpolarized
Th1Th2_validation_Diff089_non_DonorC_bulkRNAseq.csv

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

tag: experimental perturbation

value: CRISPRi knockdown of STAT6

tag: donor id

tag: donor age

value: A+

tag: donor ethnicity

value: Caucasian

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: E16.5 Hes1-lineage traced (TAM E10.5) ovarian cells

city: Research Triangle Park

first: Yu-Ying

last: Chen

address: 111 TW Alexander Dr

institute: National Institute of Environmental Health Sciences

description: Library name: Sample1

data_processing:
For single-cell analysis, FASTQ files were processed using CellRanger (v. 7.0.0) with default setting using a custom mm10 reference genome that incorporated the sfGFP-Myc reporter allele, which contains two copies of superfolder GFP (sfGFP) followed by six Myc epitope sequences.  For RNA-seq analysis, raw paired-end FASTQ files were trimmed using Trim Galore (v. 0.6.10), with the following parameters: --quality 20, --illumina, --stringency 5, --length 20, and --paired. The mm10 reference genome and NCBI RefSeq GTF annotation were downloaded from the UCSC Genome Browser on January 9, 2025 and used to generate a STAR (v. 2.6.0c) genome index. Trimmed reads were aligned to the mm10 reference using STAR, producing coordinate-sorted BAM files, which were indexed with samtools (v. 1.18). Gene-level quantification was performed with featureCounts (Subread, v. 2.0.6) using the RefSeq annotation, specifying paired-end mode (-p) and reverse-stranded orientation (-s 2).
Assembly: mm10
Supplementary files format and content: CellRanger filtered_feature_bc_matrix output files for single-cell analysis and count matrix for RNA-seq analysis

source_name: Ovary

extract_protocol:
For single cell collection, ovary pairs from E16.5 Hes1+/CreERT2; ROSA+/Sun1-sfGFP animals that were lineage-labeled at E10.5 (1 injection of 1mg/10g body weight tamoxifen (Sigma-Aldrich, T5648) in corn oil ( Sigma-Aldrich, C8267)) were collected in ice-cold 1X PBS containing 0.04% bovine serum albumin (BSA; Sigma, A9576), cut into smaller pieces, and transferred into dissociation buffer: 0.04% BSA, 1.2 U/mL Dispase II (Millipore Sigma, 4942078001), 1 mg/mL collagenase B (Millipore Sigma, 11088807001), and 5 U/mL DNase I (Millipore Sigma; 101041590001) in 1X PBS. Tissue pieces were incubated at 37 °C and gently pipetted every 5 min for 20 – 30 min. To stop the enzymatic reaction, tissues were diluted with an equal volume of cold 0.04% BSA/ PBS, passed through a 40 µm FLOWMI cell strainer (SP Bel-Art, 136800040), and washed by pelleting at 350 rcf for 5 min at 4 °C, before resuspending in 110 µL cold DMEM/F12 (Thermo Fisher, 11330032). Cells were cryopreserved by adding 1:1 filtered cryoprotectant (20% DMSO in heat-inactivated FBS, HI-FBS; Thermo Fisher, 16140071) and frozen at −80°C, with each pair of the ovary in a cryovial, before long-term storage in liquid nitrogen. Once genotypes were further confirmed through PCR (Transnetyx, Inc), two cryovials containing sfGfp+ cells were rapidly thawed at 37°C for 1 min and pooled into one new 1.5 mL tube. This pooled sample contained cells from four ovaries from two animals carrying the sfGfp allele. The cryovial was rinsed three times with 300 µL of 10% HI-FBS/ DMEM/F12 pre-warmed at 37 °C using wide-bore tips, adding each rinse dropwise with gentle agitation. Cells were pelleted at 350 rcf for 5 min at 4 °C, resuspended in 50 µL 0.04% BSA/ PBS.  For bulk RNA-seq, E13.5 Notch-induced (Tg(Nr5a1-cre)+; ROSA+/Notch) and control (Tg(Nr5a1-cre)+; ROSA+/+) ovary pairs were collected. As matings were performed by crossing either male or female Tg(Nr5a1-cre) with ROSA+/Notch, we collected two pairs of Notch-induced ovaries from ROSA+/Notch dams, four pairs of Notch-induced ovaries from Tg(Nr5a1-cre) dams, three pairs of control ovaries from ROSA+/Notch dams, and three pairs of control ovaries from Tg(Nr5a1-cre) dams, yielding six biological replicates for each genotype. Each ovary pair was dissected and snap-frozen in 50 µL of extraction buffer from the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems, 12204-01) and stored at −80°C. For RNA isolation, samples were thawed on ice, vortexed, mixed with an equal volume of 70% ethanol, and applied to pre-conditioned columns. On-column DNA digestion was performed using the RNase-Free DNase Set (Qiagen, 79254), at a final concentration of around 0.34 U/µL for 15 min at RT. After two washes, RNA was eluted in 11 µL of elution buffer. RNA quantity and quality were measured using the Qubit RNA High Sensitivity kit (Invitrogen, Q32852) and the High Sensitivity RNA Screen Tape Analysis (Agilent, 5067-5579) on the Agilent TapeStation 4200.
Library preparation and sequencing were performed at the NIEHS Epigenomics and DNA Sequencing Core Facility. For single-cell RNA-seq, cells were counted and examined for viability with AO/PI staining using a Luna FX7cell counter (Logos Biosystems). Up to 16,000 live cells were loaded into the Single Cell Chip to generate single cell emulsion in Chromium Controller with Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (10x Genomics, 1000268). Reverse transcription of mRNA and cDNA amplification were carried out following the manufacture’s instruction (10x Genomics, 1000268). The amplified cDNA was further fragmented to construct NGS libraries. Sequencing was performed on an Illumina NovaSeq 6000 using a S1 flow cell with i7 index 10bp, i5 index 10bp, achieving a depth of ~20,000 read pairs per cell.  For bulk RNA-seq, Libraries were made using the TruSeq Stranded mRNA (Illumina, 20020594) according to the manufacturer’s protocol. Approximately 250 ng of total RNA from each sample was used for poly(A) mRNA enrichment followed by cDNA synthesis and library construction. Sequencing was performed on an Illumina NextSeq 500 sequencer using a SP flow cell to generate paired-end 150-bp reads. Sequencing yielded ~80 million reads per sample. FASTQ files were generated using bcl2fastq/DRAGEN with default parameters.

tag: tissue

value: Ovary

tag: genotype

value: Hes1+/CreERT2; ROSA+/Sun1-sfGFP

value: Lineage-traced with tamoxifen at E10.5


title: L929 cells, H2O2-SCU, biological replicate 3

city: shanghai

first: Fei

last: Liu

address: No. 1908, Gaoke West Road

country: China

institute: Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

description:
Library name: H2O2-SCU-3
Condition: H2O2-SCU; biological replicate 3; processed data columns: counts_anno.tsv and FPKM_anno.tsv.

data_processing:
Libraries were sequenced on an Illumina NovaSeq 6000 platform to generate 150 bp paired-end reads, with an approximate sequencing depth of 6 Gb per sample. Raw FASTQ reads were processed using fastp to remove low-quality reads, and the resulting clean reads were mapped to the reference genome using HISAT2. Gene expression was calculated as FPKM, and read counts for each gene were obtained using HTSeq-count. Principal component analysis was performed in R to evaluate sample clustering. Differential expression analysis was performed using DESeq2, with q < 0.05 and fold change > 2 or < 0.5 used to define differentially expressed genes.
Assembly: Mus musculus NCBI GRCm39 (NCBI_GRCm39, 2023-09; GCF_000001635.27_GRCm39)
Gene annotation used the NCBI GRCm39 genomic GFF annotation file (NCBI_GRCm39, 2023-09; GCF_000001635.27_GRCm39_genomic.gff.gz). The NCBI GRCm39 mRNA FASTA database, Gene Ontology database, and KEGG database dated 2023-09 were used for annotation/enrichment-related analyses.
Supplementary files format and content: Tab-delimited text files. counts_anno.tsv contains gene-level read counts and annotation; FPKM_anno.tsv contains gene-level FPKM values and annotation for all six samples; gene_stat.tsv contains per-sample detected gene counts.

growth_protocol: Fibroblasts were used to establish an in vitro oxidative stress injury model. L929 fibroblasts were used in the in vitro experiments. L929 cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin and maintained at 37°C in a humidified incubator containing 5% CO2. Hydrogen peroxide (H₂O₂) was used to induce injury and SCU dissolved in DMSO was used as the intervention.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's protocol. RNA purity and concentration were evaluated using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA), and RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA-seq libraries were constructed using the VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer's instructions.

treatment_protocol: Methods: A streptozotocin-induced diabetic mouse cutaneous wound model was used to evaluate the effects of topical SCU treatment on wound closure, epithelial repair, and collagen deposition. In vitro, an H₂O₂-induced oxidative injury model in fibroblasts was employed to assess SCU-mediated protection on migration, viability, redox balance, and mitochondrial structure and function. Transcriptomics (RNA-seq) was performed to identify SCU-responsive molecular pathways, and SCU-P2RX1 molecular docking combined with ATP rescue experiments was used to interrogate a P2RX1–calcium axis.

tag: cell line

tag: cell type

value: fibroblast

tag: treatment

value: H2O2 plus scutellarein

value: biological replicate 3


title: DonorC cells perturbed with STAT6 knockdown by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorC_STAT6_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorC_bulkRNAseq.csv

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

value: Normal

value: Zymo DNA/RNA Shield


title: L929 cells, H2O2-SCU, biological replicate 2

description:
Library name: H2O2-SCU-2
Condition: H2O2-SCU; biological replicate 2; processed data columns: counts_anno.tsv and FPKM_anno.tsv.

value: biological replicate 2


title: DonorC cells perturbed with STAT6 knockdown by CRISPRi under Th1 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorC_STAT6_Th1
Th1 polarized
Th1Th2_validation_Diff089_Th1_DonorC_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of STAT6

tag: donor id

tag: donor age

value: A+

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

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

tag: donor ethnicity

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol


title: L929 cells, H2O2-SCU, biological replicate 1

description:
Library name: H2O2-SCU-1
Condition: H2O2-SCU; biological replicate 1; processed data columns: counts_anno.tsv and FPKM_anno.tsv.

tag: cell line

tag: cell type

value: fibroblast

tag: treatment

value: H2O2 plus scutellarein

tag: batch

value: biological replicate 1


title: DonorC cells perturbed with Non-targeting control 2 by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorC_NTC2_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorC_bulkRNAseq.csv

tag: tissue

value: CRISPRi non-targeting control

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: Plasmidsaurus RNA-Seq


title: DonorC cells perturbed with Non-targeting control 2 by CRISPRi under nonpolarized culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorC_NTC2_non
nonpolarized
Th1Th2_validation_Diff089_non_DonorC_bulkRNAseq.csv

value: blood

tag: experimental perturbation

tag: donor id

tag: donor age

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity


title: L929 cells, H2O2, biological replicate 3

description:
Library name: H2O2-3
Condition: H2O2; biological replicate 3; processed data columns: counts_anno.tsv and FPKM_anno.tsv.

tag: cell line

tag: cell type

tag: treatment

tag: batch

value: biological replicate 3


title: L929 cells, H2O2, biological replicate 2

description:
Library name: H2O2-2
Condition: H2O2; biological replicate 2; processed data columns: counts_anno.tsv and FPKM_anno.tsv.

value: biological replicate 2


title: DonorC cells perturbed with Non-targeting control 1 by CRISPRi under nonpolarized culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorC_NTC1_non
nonpolarized
Th1Th2_validation_Diff089_non_DonorC_bulkRNAseq.csv

tag: tissue

value: CD4-positive, alpha-beta T cells

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

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: A+

tag: anticoagulant

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

value: CRISPRi

tag: enriched cell_types

tag: library protocol


title: L929 cells, H2O2, biological replicate 1

description:
Library name: H2O2-1
Condition: H2O2; biological replicate 1; processed data columns: counts_anno.tsv and FPKM_anno.tsv.

value: fibroblast

value: biological replicate 1


title: DonorC cells perturbed with Non-targeting control 2 by CRISPRi under Th1 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorC_NTC2_Th1
Th1 polarized
Th1Th2_validation_Diff089_Th1_DonorC_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi non-targeting control

tag: donor id

tag: donor age

value: No

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease


title: DonorC cells perturbed with Non-targeting control 1 by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorC_NTC1_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorC_bulkRNAseq.csv

tag: tissue

value: blood

tag: cell type

tag: treatment

tag: donor weight

value: adult stage

value: TRUE

value: Normal

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity

value: Plasmidsaurus RNA-Seq

tag: batch


title: Renca,Triplet

city: NEW HAVEN

first: Dijana

last: Djureinovic

state: CT

address: 333 Cedar street

institute: Yale University

description:
Library name: Sample 5
10X Genomics Chromium

data_processing:
Cellranger was used to align reads to the mouse reference transcriptome (mm9) and to generate cell-by-gene matrices for each sample library
Assembly: mm9
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

growth_protocol: Renca cells were cultured in RPMI-1640 plus 10% FBS, 1× MEM nonessential amino acids, sodium pyruvate (1 mM), L-glutamine (2 mM), and 1× antibiotic-antimycotic.Cells were cultured in a humidified incubator containing 5% CO2 at 37°C. All cells were injected at passage <10 and tested negative for mycoplasma.

extract_protocol:
Tumors were dissociated in RPMI + 2% FBS supplemented with 0.1 mg/ml collagenase and DNase I for 30 min at 37ºC, and filtered through a 70 μM filter to obtain a single cell suspension. Cells were washed with RPMI+10% FBS and resuspended in RPMI+20% FBS. For sorting, cells were incubated for 30 min at 4ºC with fluorophore-conjugated antibodies using the following antibodies: anti-CD45 (clone 30-F11, BD Biosciences) and anti-CD3 (clone 17A2, BD Bioscience). Samples were sorted using a BD FACSAriaII into three populations: T cells (CD45+ CD3+);  immune cells non-T-cells(CD45+ CD3-); and tumor and stromal cells (CD45- CD3-). AmCyan Kit (Thermo Fisher Scientific) was used for live/dead stain. Sorted cells for each subset were counted manually and then combined in a 2:1:1 ratio of T cells:non-T immune cells:tumor and stromal cells, with an equal contribution from each biologic replicate from an experimental condition. Ten thousand cells from each of the mixed sorted samples for each condition were loaded onto the 10x Genomics Chromium System.
Library preparation for scRNA-seq and scTCR-seq was performed using the 5’ Reagent Kit from 10x Genomics according to the manufacturer’s instructions by the Yale Center for Genome Analysis (YCGA) and passed quality control.

treatment_protocol: Treatment started at day 10 post tumor cell injection and was administered intraperitoneally twice  the following antibodies and doses: 200 μg αPD-1 (Bio X Cell, Clone RMP1-14), 200 μg αCD40 (Bio X Cell, Clone: FGK4.5/FGK45), 200 μg αCTLA-4 ( BioXCell, clone 9H10).

value: tumor

tag: cell line

value: Renca

value: renal cortical adenocarcinoma.

tag: genotype

value: WT

value: immunotherapy


title: Renca,CD40plusCTLA4

description:
Library name: Sample 4
10X Genomics Chromium


title: DonorC cells perturbed with Non-targeting control 1 by CRISPRi under Th1 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorC_NTC1_Th1
Th1 polarized
Th1Th2_validation_Diff089_Th1_DonorC_bulkRNAseq.csv

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor height

tag: donor smoker

tag: donor blood_type

value: A+

tag: anticoagulant

value: Zymo DNA/RNA Shield

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

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol


title: Renca,PD1plusCD40

description:
Library name: Sample 3
10X Genomics Chromium

tag: tissue

tag: cell type

tag: treatment


title: DonorC cells perturbed with NAB2 knockdown by CRISPRi under nonpolarized culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorC_NAB2_non
nonpolarized
Th1Th2_validation_Diff089_non_DonorC_bulkRNAseq.csv

value: blood

value: CRISPRi knockdown of NAB2

tag: donor weight

value: No

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity


title: DonorC cells perturbed with NAB2 knockdown by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorC_NAB2_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorC_bulkRNAseq.csv

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

value: adult stage

value: TRUE

value: Normal

value: Plasmidsaurus RNA-Seq

tag: batch


title: Renca,PD1plusCTLA4

description:
Library name: Sample 2
10X Genomics Chromium

tag: tissue

value: tumor

tag: cell line

value: Renca

tag: cell type

value: renal cortical adenocarcinoma.

tag: genotype

value: WT

tag: treatment

value: immunotherapy


title: DonorC cells perturbed with NAB2 knockdown by CRISPRi under Th1 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorC_NAB2_Th1
Th1 polarized
Th1Th2_validation_Diff089_Th1_DonorC_bulkRNAseq.csv

value: CD4-positive, alpha-beta T cells

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

tag: donor weight

value: A+

tag: source

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

value: Zymo DNA/RNA Shield

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

value: Caucasian

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol


title: YapTaz active, bleomycin, RNA

city: Nashville

first: Jason

last: Gokey

state: TN

department: Medicine - Allergy, Pulmonary and Critical Care

institute: Vanderbilt University Medical Center

description:
Library name: 8765-CT-1_RNA
YapTaz active, bleomycin, RNA gene expression

data_processing:
SoupX and scDoublet were used to remove ambient DNA and detect doublets
Seurat/Signac used for Multi-resolution clustering, normalization and dimension reduction
Harmony was used to map the scATAC-seq data onto these clusters by identifying open chromatin regions associated with specific marker genes and integrated with the scRNA-Seq
MACS2 was used for peak calling with 2kbp of transcriptional start site
Promoter associated TF factor enrichment was assessed using Chromvar
Assembly: GRcm39 reference genome
Supplementary files format and content: h5 files

source_name: lung

growth_protocol: Primary cells directly after mouse sacrifice.

extract_protocol:
Lungs were excised, incubated in DNAse, Disapse and collagenase in a C-Tube and single cells were generated using an octomacs. Cell suspensions were passed through 100um then 40um filter.
10X multiome protocol-10x Genomics Chromium sequencing targeting 10,000 nuclei per sample and 50,000 reads per nuclei

treatment_protocol: Mice were given 3mg/mouse of tamoxifen, 3 weeks later they were injured with 0.08iU bleomycin or saline, then mice were sacrificed 4-weeks after bleomycin injury.

value: lung

value: primary

value: whole lung

value: YapTaz active

value: bleomycin

tag: library type

value: RNA


title: Renca,PBS

description:
Library name: Sample 1
10X Genomics Chromium

value: tumor

value: untreated


title: YapTaz active, bleomycin, ATAC

description:
Library name: 8765-CT-1_ATAC
YapTaz active, bleomycin, ATAC sequences

library_source: genomic single cell

molecule: genomic DNA

tag: batch

value: ATAC


title: DonorC cells perturbed with MED24 knockdown by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorC_MED24_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorC_bulkRNAseq.csv

tag: tissue

value: blood

tag: experimental perturbation

value: CRISPRi knockdown of MED24

tag: donor id

tag: donor age

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

tag: anticoagulant

value: ACDA

value: STEMCELL technologies

value: Female

value: adult stage

value: TRUE

value: Normal

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: DonorC cells perturbed with MED24 knockdown by CRISPRi under nonpolarized culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorC_MED24_non
nonpolarized
Th1Th2_validation_Diff089_non_DonorC_bulkRNAseq.csv

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: treatment

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

tag: donor weight

value: A+

tag: source

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

value: Zymo DNA/RNA Shield

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

value: Caucasian


title: DonorC cells perturbed with MED24 knockdown by CRISPRi under Th1 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorC_MED24_Th1
Th1 polarized
Th1Th2_validation_Diff089_Th1_DonorC_bulkRNAseq.csv

tag: tissue

value: blood

tag: experimental perturbation

tag: donor id

tag: donor age

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: YapTaz active, saline, ATAC

description:
Library name: 9719-CT-1_ATAC
YapTaz active, saline, ATAC sequences

value: lung

tag: cell line

value: primary

tag: cell type

value: whole lung

tag: genotype

value: YapTaz active

value: saline

tag: library type

value: ATAC


title: YapTaz active, saline, RNA

description:
Library name: 9719-CT-1_RNA
YapTaz active, saline, RNA gene expression

tag: treatment

value: RNA


title: DonorC cells perturbed with KDM1A knockdown by CRISPRi under nonpolarized culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorC_KDM1A_non
nonpolarized
Th1Th2_validation_Diff089_non_DonorC_bulkRNAseq.csv

value: CRISPRi knockdown of KDM1A

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

value: TRUE

value: Normal

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity


title: Wild type, bleomycin, ATAC

description:
Library name: 9412-CT-1_ATAC
Wild type, bleomycin, ATAC sequences

tag: tissue

value: wild type

value: bleomycin

tag: batch


title: DonorC cells perturbed with KDM1A knockdown by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorC_KDM1A_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorC_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

tag: donor id

tag: donor age

value: A+

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

value: Zymo DNA/RNA Shield

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

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: Wild type, bleomycin, RNA

description:
Library name: 9412-CT-1_RNA
Wild type, bleomycin, RNA gene expression

value: lung

tag: cell line

value: primary

value: whole lung

tag: genotype

tag: treatment

tag: library type

value: RNA


title: DonorB cells perturbed with STAT6 knockdown by CRISPRi under nonpolarized culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorB_STAT6_non
nonpolarized
Th1Th2_validation_Diff089_non_DonorB_bulkRNAseq.csv

value: CRISPRi knockdown of STAT6

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Male

tag: donor dev_stage

value: adult stage

value: TRUE

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity


title: DonorC cells perturbed with KDM1A knockdown by CRISPRi under Th1 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorC_KDM1A_Th1
Th1 polarized
Th1Th2_validation_Diff089_Th1_DonorC_bulkRNAseq.csv

tag: tissue

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of KDM1A

tag: donor id

tag: donor age

value: A+

value: Female

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: batch


title: Wild type, saline, ATAC

description:
Library name: 9164-CT-1_ATAC
Wild type, saline, ATAC sequences

value: lung

tag: cell line

value: primary

tag: genotype

value: wild type

tag: treatment

value: saline

tag: library type

value: ATAC


title: Wild type, saline, RNA

description:
Library name: 9164-CT-1_RNA
Wild type, saline, RNA gene expression

value: whole lung

value: RNA


title: DonorB cells perturbed with STAT6 knockdown by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorB_STAT6_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorB_bulkRNAseq.csv

value: CRISPRi knockdown of STAT6

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Male

tag: donor dev_stage

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

value: Caucasian

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: Heart , R502W, mavacamten, sample 4

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

description: Library name: KI_1260_MAVA

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 DESeq2
Assembly: GRCm38.99
Supplementary files format and content: Raw counts for each gene in each sampe as estimated by RSEM.

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.

tag: tissue

value: Heart

tag: cell type

value: whole heart tissue

value: mavacamten 2.5 mg/kg/day


title: DonorB cells perturbed with STAT6 knockdown by CRISPRi under Th1 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorB_STAT6_Th1
Th1 polarized
Th1Th2_validation_Diff089_Th1_DonorB_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

tag: donor id

tag: donor age

value: A+

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: batch


title: Heart , R502W, mavacamten, sample 3

description: Library name: KI_1258_MAVA

tag: genotype

tag: treatment


title: DonorB cells perturbed with Non-targeting control 2 by CRISPRi under nonpolarized culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorB_NTC2_non
nonpolarized
Th1Th2_validation_Diff089_non_DonorB_bulkRNAseq.csv

value: CRISPRi non-targeting control

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

tag: donor dev_stage

tag: sample preservation_method


title: Heart , R502W, mavacamten, sample 2

description: Library name: KI_1257_MAVA

tag: tissue

tag: cell type


title: DonorB cells perturbed with Non-targeting control 2 by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorB_NTC2_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorB_bulkRNAseq.csv

tag: experimental perturbation

tag: donor id

tag: donor age

value: Male

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

tag: donor ethnicity

value: Caucasian

tag: library protocol


title: Heart , R502W, mavacamten, sample 1

description: Library name: KI_1256_MAVA

value: Heart

value: whole heart tissue

tag: genotype

tag: treatment


title: DonorB cells perturbed with Non-targeting control 2 by CRISPRi under Th1 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorB_NTC2_Th1
Th1 polarized
Th1Th2_validation_Diff089_Th1_DonorB_bulkRNAseq.csv

value: blood

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq

tag: batch


title: Heart , R502W, control, sample 4

description: Library name: KI_1265_CTRL

tag: tissue

tag: cell type

value: control


title: DonorB cells perturbed with Non-targeting control 1 by CRISPRi under nonpolarized culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorB_NTC1_non
nonpolarized
Th1Th2_validation_Diff089_non_DonorB_bulkRNAseq.csv

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

tag: donor id

tag: donor age

value: A+

tag: donor sex

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method


title: DonorB cells perturbed with Non-targeting control 1 by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorB_NTC1_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorB_bulkRNAseq.csv

tag: treatment

value: CRISPRi non-targeting control

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: TRUE

value: Normal

tag: suspension depletion_factors

tag: donor ethnicity

tag: library protocol


title: DonorB cells perturbed with Non-targeting control 1 by CRISPRi under Th1 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorB_NTC1_Th1
Th1 polarized
Th1Th2_validation_Diff089_Th1_DonorB_bulkRNAseq.csv

tag: tissue

tag: cell type

tag: experimental perturbation

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

value: Male

value: Zymo DNA/RNA Shield

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: batch


title: Heart , R502W, control, sample 2

description: Library name: KI_1253_CTRL

value: Heart

value: whole heart tissue

tag: genotype


title: Heart , R502W, control, sample 3

description: Library name: KI_1264_CTRL

tag: treatment


title: Heart , R502W, control, sample 1

description: Library name: KI_1252_CTRL


title: DonorB cells perturbed with NAB2 knockdown by CRISPRi under nonpolarized culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorB_NAB2_non
nonpolarized
Th1Th2_validation_Diff089_non_DonorB_bulkRNAseq.csv

value: blood

value: CRISPRi knockdown of NAB2

tag: donor id

tag: donor age

tag: donor weight

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

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

value: Caucasian

value: CRISPRi


title: Heart , WT, control, sample 5

description: Library name: WT_1270_CTRL

tag: tissue

tag: cell type

value: WT

value: control


title: DonorB cells perturbed with NAB2 knockdown by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorB_NAB2_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorB_bulkRNAseq.csv

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

tag: donor height

tag: donor smoker

tag: donor blood_type

value: A+

tag: anticoagulant

tag: source

value: adult stage

tag: suspension depletion_factors

tag: donor ethnicity

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: Heart , WT, control, sample 4

description: Library name: WT_1269_CTRL

tag: genotype

tag: treatment


title: DonorB cells perturbed with NAB2 knockdown by CRISPRi under Th1 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorB_NAB2_Th1
Th1 polarized
Th1Th2_validation_Diff089_Th1_DonorB_bulkRNAseq.csv

tag: donor id

tag: donor age

tag: donor weight

value: No

value: ACDA

value: STEMCELL technologies

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

value: TRUE

value: Normal

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: batch


title: Heart , WT, control, sample 3

description: Library name: WT_1235_CTRL

tag: tissue

value: Heart

tag: cell type

value: whole heart tissue


title: Heart , WT, control, sample 2

description: Library name: WT_1234_CTRL


title: DonorB cells perturbed with MED24 knockdown by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorB_MED24_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorB_bulkRNAseq.csv

value: blood

tag: experimental perturbation

value: CRISPRi knockdown of MED24

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

value: Male

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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


title: DonorB cells perturbed with MED24 knockdown by CRISPRi under Th1 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorB_MED24_Th1
Th1 polarized
Th1Th2_validation_Diff089_Th1_DonorB_bulkRNAseq.csv

value: CD4-positive, alpha-beta T cells

tag: treatment

tag: donor id

tag: donor age

tag: donor weight

tag: donor sex

tag: suspension depletion_factors

tag: donor ethnicity

value: Caucasian

value: CRISPRi

tag: library protocol


title: DonorB cells perturbed with MED24 knockdown by CRISPRi under nonpolarized culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorB_MED24_non
nonpolarized
Th1Th2_validation_Diff089_non_DonorB_bulkRNAseq.csv

tag: tissue

tag: cell type

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

tag: experimental perturbation

value: A+

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: batch


title: Heart , WT, control, sample 1

description: Library name: WT_1233_CTRL

tag: genotype

value: WT

value: control


title: dam-fed WT 7

city: Portland

first: Sarah

last: Andres

state: Oregon

address: 3181 S.W. Sam Jackson Park Road

department: Department of Pediatrics

institute: Oregon Health and Science University

description: Library name: animal_546

data_processing:
Initial quality assessment of raw FASTQ files was performed using FastQC.
Trimmed reads were aligned to the human reference genome using STAR with default parameters for stranded paired-end data
Transcript-level quantification was performed using Salmon
Downstream analyses were carried out in R using the DESeq2 package. Raw counts were normalized, accounting for sex and experiment number as covariates. Batch correction was applied using the limma package’s removeBatchEffect function for sex and experiment number. Differential expression analysis was then performed using negative binomial generalized linear models as implemented in DESeq2.
Assembly: GRCh38
Supplementary files format and content: csv with normalized reads of each gene

source_name: Terminal Illium

extract_protocol:
Whole-thickness intestinal segments (0.5 cm) were lysed with 1.0 mm zirconia/silica beads  in a mini-bead beater and RNA was extracted using GeneJet RNA purification system.
Illumina stranded Total RNA-seq library preparation protocol with ribosomal RNA (rRNA) depletion .

value: Terminal Illium

value: Whole-thickness

tag: treatment

value: dam-fed


title: DonorB cells perturbed with KDM1A knockdown by CRISPRi under nonpolarized culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorB_KDM1A_non
nonpolarized
Th1Th2_validation_Diff089_non_DonorB_bulkRNAseq.csv

value: CRISPRi knockdown of KDM1A

tag: donor id

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Plasmidsaurus RNA-Seq


title: dam-fed WT 8

description: Library name: animal_552

tag: tissue

tag: cell type


title: DonorB cells perturbed with KDM1A knockdown by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorB_KDM1A_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorB_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

tag: donor age

tag: donor weight

tag: donor sex

value: Male

tag: donor dev_stage

tag: donor living_at_sample_collection

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

tag: donor ethnicity

value: Caucasian

tag: library protocol


title: dam-fed KO 4

description: Library name: animal_545

tag: genotype

value: KO

tag: treatment

tag: batch


title: DonorB cells perturbed with KDM1A knockdown by CRISPRi under Th1 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorB_KDM1A_Th1
Th1 polarized
Th1Th2_validation_Diff089_Th1_DonorB_bulkRNAseq.csv

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

tag: donor id

tag: donor height

tag: donor smoker

tag: donor blood_type

value: A+

tag: anticoagulant

tag: source

value: adult stage

tag: donor body_mass_index

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types


title: formula-fed OE 4

description: Library name: animal_534

tag: tissue

value: Terminal Illium

tag: cell type

value: Whole-thickness

value: OE

value: formula-fed


title: DonorA cells perturbed with STAT6 knockdown by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorA_STAT6_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorA_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi knockdown of STAT6

tag: donor age

tag: donor weight

value: No

value: O+

value: ACDA

value: STEMCELL technologies

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor disease

value: Normal

tag: sample preservation_method

tag: suspension depletion_factors


title: formula-fed WT 8

description: Library name: animal_533

tag: genotype

value: WT

tag: treatment

tag: batch


title: DonorA cells perturbed with Non-targeting control 2 by CRISPRi under nonpolarized culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorA_NTC2_non
nonpolarized
Th1Th2_validation_Diff089_non_DonorA_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

value: CRISPRi non-targeting control

tag: donor id

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

value: Male

tag: donor body_mass_index

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

value: Plasmidsaurus RNA-Seq


title: DonorA cells perturbed with Non-targeting control 2 by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorA_NTC2_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorA_bulkRNAseq.csv

tag: tissue

tag: cell type

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

tag: experimental perturbation

tag: donor age

tag: donor weight

tag: donor sex

tag: donor dev_stage

value: adult stage

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types


title: formula-fed OE 3

description: Library name: animal_532

value: Terminal Illium

value: Whole-thickness

tag: genotype

value: OE

tag: treatment

value: formula-fed

tag: batch


title: dam-fed OE 4

description: Library name: animal_530

value: dam-fed


title: DonorA cells perturbed with Non-targeting control 1 by CRISPRi under nonpolarized culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorA_NTC1_non
nonpolarized
Th1Th2_validation_Diff089_non_DonorA_bulkRNAseq.csv

tag: donor id

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: O+

tag: anticoagulant

value: ACDA

value: STEMCELL technologies

tag: donor living_at_sample_collection

value: TRUE

tag: donor disease

value: Normal

tag: sample preservation_method

tag: suspension depletion_factors


title: dam-fed OE 3

description: Library name: animal_529

tag: tissue

tag: cell type


title: DonorA cells perturbed with Non-targeting control 1 by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorA_NTC1_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorA_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi non-targeting control

tag: donor age

tag: donor weight

tag: source

tag: donor sex

value: Male

tag: donor dev_stage

tag: donor body_mass_index

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: formula-fed WT 7

description: Library name: animal_526

value: Terminal Illium

tag: genotype

value: WT

tag: treatment

tag: batch


title: DonorA cells perturbed with Non-targeting control by CRISPRi under Th1 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorA_NTC1_Th1
Th1 polarized
Th1Th2_validation_Diff089_Th1_DonorA_bulkRNAseq.csv

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

tag: donor id

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

value: adult stage

tag: donor living_at_sample_collection

tag: donor disease

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: dam-fed OE 2

description: Library name: animal_523

tag: tissue

tag: cell type

value: Whole-thickness

value: OE

value: dam-fed


title: DonorA cells perturbed with MED24 knockdown by CRISPRi under nonpolarized culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorA_MED24_non
nonpolarized
Th1Th2_validation_Diff089_non_DonorA_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi knockdown of MED24

tag: donor age

tag: donor weight

value: No

value: O+

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

tag: donor dev_stage

value: TRUE

tag: donor body_mass_index

value: Normal

tag: sample preservation_method

tag: suspension depletion_factors


title: formula-fed WT 6

description: Library name: animal_487

value: Terminal Illium

tag: genotype

tag: treatment

value: formula-fed

tag: batch


title: DonorA cells perturbed with MED24 knockdown by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorA_MED24_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorA_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: donor id

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

value: Male

tag: donor living_at_sample_collection

tag: donor disease

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: dam-fed WT 6

description: Library name: animal_481

tag: tissue

tag: cell type

value: Whole-thickness

value: WT


title: dam-fed WT 5

description: Library name: animal_474

value: dam-fed


title: DonorA cells perturbed with KDM1A knockdown by CRISPRi under nonpolarized culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorA_KDM1A_non
nonpolarized
Th1Th2_validation_Diff089_non_DonorA_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi knockdown of KDM1A

tag: donor age

tag: donor weight

value: No

tag: source

tag: donor sex

tag: donor dev_stage

value: adult stage

tag: donor body_mass_index

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: DonorA cells perturbed with MED24 knockdown by CRISPRi under Th1 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorA_MED24_Th1
Th1 polarized
Th1Th2_validation_Diff089_Th1_DonorA_bulkRNAseq.csv

tag: treatment

value: CRISPRi knockdown of MED24

tag: donor id

tag: donor height

tag: donor smoker

tag: donor blood_type

value: O+

value: ACDA

value: STEMCELL technologies

value: TRUE

value: Normal

tag: sample preservation_method

tag: suspension depletion_factors

tag: batch


title: dam-fed WT 4

description: Library name: animal_473

tag: tissue

value: Terminal Illium

tag: cell type

tag: genotype


title: DonorA cells perturbed with KDM1A knockdown by CRISPRi under Th2 culture condition in batch Diff089

description:
Library name: Th1Th2_validation_Diff089_DonorA_KDM1A_Th2
Th2 polarized
Th1Th2_validation_Diff089_Th2_DonorA_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

tag: donor age

tag: donor weight

tag: anticoagulant

tag: source

value: Male

tag: donor living_at_sample_collection

tag: donor disease

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

description:
Library name: Th1Th2_validation_Diff084_DonorG_ZMYND8_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorG_bulkRNAseq.csv

tag: treatment

value: CRISPRi knockdown of ZMYND8

tag: donor id

tag: donor height

tag: donor smoker

value: No

value: A+

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor body_mass_index

value: Hispanic

tag: genetic perturbation_strategy

tag: enriched cell_types


title: dam-fed KO 3

description: Library name: animal_465

tag: tissue

tag: cell type

value: Whole-thickness

tag: genotype

value: KO

value: dam-fed

tag: batch


title: formula-fed WT 5

description: Library name: animal_422

value: WT

value: formula-fed


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_ZMYND8_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorG_bulkRNAseq.csv

value: blood

tag: experimental perturbation

tag: donor age

tag: donor weight

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor living_at_sample_collection

value: TRUE

value: Normal

tag: sample preservation_method

tag: suspension depletion_factors

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: formula-fed WT 4

description: Library name: animal_421

value: Terminal Illium

tag: treatment


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_ZMYND8_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorG_bulkRNAseq.csv

value: CD4-positive, alpha-beta T cells

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

value: CRISPRi knockdown of ZMYND8

tag: donor id

tag: donor height

tag: donor smoker

value: No

value: A+

tag: donor sex

tag: donor dev_stage

tag: donor body_mass_index

tag: donor disease

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: dam-fed OE 1

description: Library name: animal_417

tag: tissue

tag: cell type

value: Whole-thickness

tag: genotype

value: OE

value: dam-fed

tag: batch


title: dam-fed WT 3

description: Library name: animal_416

value: WT


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_TBX21_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorG_bulkRNAseq.csv

value: blood

tag: experimental perturbation

value: CRISPRi knockdown of TBX21

tag: donor age

tag: donor weight

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

value: Female

value: adult stage

tag: donor living_at_sample_collection

value: Hispanic

tag: genetic perturbation_strategy

tag: enriched cell_types


title: formula-fed KO 4

description: Library name: animal_415

value: Terminal Illium

value: KO

tag: treatment

value: formula-fed


title: formula-fed KO 3

description: Library name: animal_413


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_STYXL1_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorG_bulkRNAseq.csv

value: CD4-positive, alpha-beta T cells

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

value: CRISPRi knockdown of STYXL1

tag: donor id

tag: donor height

tag: donor smoker

value: No

value: A+

tag: donor sex

tag: donor dev_stage

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

tag: suspension depletion_factors

value: CRISPRi

value: Plasmidsaurus RNA-Seq


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_TBX21_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorG_bulkRNAseq.csv

tag: tissue

value: blood

tag: cell type

tag: experimental perturbation

value: CRISPRi knockdown of TBX21

tag: donor age

tag: donor weight

value: ACDA

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: formula-fed KO 2

description: Library name: animal_412

value: Terminal Illium

value: Whole-thickness

tag: genotype

tag: treatment


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_TBX21_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorG_bulkRNAseq.csv

tag: donor id

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

value: STEMCELL technologies

value: Female

value: adult stage

tag: donor living_at_sample_collection

value: Hispanic

tag: genetic perturbation_strategy

tag: enriched cell_types


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_STYXL1_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorG_bulkRNAseq.csv

tag: tissue

tag: cell type

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of STYXL1

value: No

tag: donor sex

tag: donor dev_stage

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors


title: formula-fed WT 3

description: Library name: animal_410

tag: genotype

value: WT

tag: treatment

value: formula-fed

tag: batch


title: formula-fed WT 2

description: Library name: animal_409


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_STYXL1_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorG_bulkRNAseq.csv

value: blood

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: A+

tag: anticoagulant

value: TRUE

value: Normal

tag: donor ethnicity

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: formula-fed OE 2

description: Library name: animal_384

tag: tissue

value: Terminal Illium

tag: cell type

value: Whole-thickness

value: OE


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_PPP1R7_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorG_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi knockdown of PPP1R7

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

value: 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: genetic perturbation_strategy

tag: enriched cell_types


title: formula-fed WT 1

description: Library name: animal_366

tag: genotype

value: WT

tag: treatment

value: formula-fed

tag: batch


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_NTC2_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorG_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

value: 8 hour 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: A+

tag: anticoagulant

tag: sample preservation_method

tag: suspension depletion_factors

value: Hispanic


title: dam-fed KO 2

description: Library name: animal_408

tag: tissue

value: Terminal Illium

tag: cell type

value: Whole-thickness

value: KO

value: dam-fed


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_PPP1R7_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorG_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi knockdown of PPP1R7

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: donor ethnicity

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_PPP1R7_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorG_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

tag: treatment

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

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

value: adult stage

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: genetic perturbation_strategy

tag: enriched cell_types

tag: batch


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_NTC2_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorG_bulkRNAseq.csv

tag: tissue

tag: cell type

tag: experimental perturbation

value: CRISPRi non-targeting control

tag: donor smoker

value: No

tag: donor blood_type

value: A+

tag: anticoagulant

tag: sample preservation_method

tag: suspension depletion_factors

value: Hispanic


title: formula-fed OE 1

description: Library name: animal_383

value: Terminal Illium

value: Whole-thickness

tag: genotype

value: OE

value: formula-fed


title: formula-fed KO 1

description: Library name: animal_365

value: KO

tag: treatment


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_NTC2_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorG_bulkRNAseq.csv

tag: donor id

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: donor ethnicity

value: CRISPRi

tag: library protocol


title: dam-fed WT 2

description: Library name: animal_359

tag: tissue

tag: cell type

value: WT

value: dam-fed

tag: batch


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_NTC1_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorG_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi non-targeting control

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

value: adult stage

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: genetic perturbation_strategy

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: dam-fed KO 1

description: Library name: animal_358

value: Terminal Illium

value: Whole-thickness

tag: genotype

value: KO

tag: treatment


title: dam-fed WT 1

description: Library name: animal_357


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_NTC1_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorG_bulkRNAseq.csv

tag: donor id

value: No

value: A+

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

value: Hispanic


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_NTC1_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorG_bulkRNAseq.csv

tag: tissue

value: blood

tag: cell type

tag: experimental perturbation

tag: donor age

tag: donor weight

tag: donor height

value: TRUE

value: Normal

tag: donor ethnicity

value: CRISPRi

tag: library protocol

tag: batch


title: SD_wk32_B_R6

city: South San Francisco

first: ashmita

last: Saigal

state: California

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

institute: Merck & Co., Inc.

description: Library name: 8392

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

source_name: Liver

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

value: Liver

tag: housing temperature

value: TN

tag: timepoint (duration_on_diet)

tag: genotype

value: C57BL/6J, Male

tag: treatment

value: GAN diet


title: SD_wk32_B_R5

description: Library name: 8391


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_NKTR_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorG_bulkRNAseq.csv

value: CD4-positive, alpha-beta T cells

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

value: CRISPRi knockdown of NKTR

tag: donor id

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

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: genetic perturbation_strategy

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: SD_wk32_B_R4

description: Library name: 8390

tag: tissue


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_NKTR_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorG_bulkRNAseq.csv

tag: cell type

tag: experimental perturbation

tag: donor age

tag: donor weight

tag: donor height

value: No

value: A+

value: ACDA

value: STEMCELL technologies

value: Female

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity

tag: library protocol

tag: batch


title: SD_wk32_B_R3

description: Library name: 8339

tag: housing temperature

tag: timepoint (duration_on_diet)

tag: genotype

tag: treatment


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_NKTR_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorG_bulkRNAseq.csv

value: blood

tag: donor id

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

value: Normal

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types