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

description:
Library name: Th1Th2_validation_Diff084_DonorG_MAMLD1_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorG_bulkRNAseq.csv

tag: tissue

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi knockdown of MAMLD1

tag: donor age

tag: donor weight

tag: donor height

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity

tag: library protocol


title: SD_wk32_B_R2

status: Public on Jun 02 2026

type: SRA

city: South San Francisco

first: ashmita

last: Saigal

state: California

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

country: USA

institute: Merck & Co., Inc.

description: Library name: 8338

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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

city: Palo Alto

first: Lattice

last: Data Coordination

state: CA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

description:
Library name: Th1Th2_validation_Diff084_DonorG_MAMLD1_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorG_bulkRNAseq.csv

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

molecule: polyA RNA

organism: Homo sapiens

source_name: blood

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

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

tag: donor id

tag: donor smoker

value: No

tag: donor blood_type

value: A+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

value: Normal

value: Zymo DNA/RNA Shield

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

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq

tag: batch


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_JAK2_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorG_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

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi knockdown of JAK2

tag: donor age

tag: donor weight

tag: donor height

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity

tag: library protocol


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_MAMLD1_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorG_bulkRNAseq.csv

value: blood

tag: treatment

value: CRISPRi knockdown of MAMLD1

tag: donor id

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

tag: donor dev_stage


title: SD_wk32_A_R6

description: Library name: 8275

tag: tissue

value: Liver

tag: housing temperature

value: TA

tag: timepoint (duration_on_diet)

tag: genotype

value: C57BL/6J, Male

value: GAN diet


title: SD_wk32_B_R1

description: Library name: 8337

value: TN


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_JAK2_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorG_bulkRNAseq.csv

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 height

value: No

value: A+

value: ACDA

value: STEMCELL technologies

value: Female

value: adult stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: batch


title: Microglia, WT, rep2

status: Public on Jun 03 2026

city: Zwijnaarde

first: Roosmarijn

middle: E.

last: Vandenbroucke

state: Gent

address: Technologiepark-Zwijnaarde 71

department: VIB Center for Inflammation Research

country: Belgium

institute: VIB-UGent

description:
Library name: X05_M5_C3WT_3_micro_S17
Bulk_RNA_seq_PieterD_raw_counts_Microglia_no_outliers.txt
Bulk_RNA_seq_PieterD_normalized_counts_Microglia_no_outliers.txt

data_processing:
Element Biosciences software was used for basecalling.
Sequenced reads were inspected with FastQC v0.11.8, trimmed for adaptor sequences with Trimmomatic v0.39, then mapped to mm10 whole genome using STAR v2.7.3a, converted to BAM-files with Samtools v1.9 and finally counted with HTSeqCount v0.11.2
An edgeR (v3.32.1) - limma (v3.46.0) workflow was used to normalize the count data.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample (one file for microglia samples and another file for astrocyte samples)
Supplementary files format and content: Matrix table with log-CPM values for all biologically meaningfully expressed genes for each sample (one file for microglia samples and another file for astrocyte samples)

source_name: Microglia

extract_protocol:
After euthanasia using an overdose of ketamine (87.5 mg/kg) and xylazine (12.5 mg/kg), mice were perfused transcardially using 10 ml 0.2 % heparin in ice-cold D‐PBS per mouse  at a flow rate of 4.50 ml/min. Whole brain samples were isolated from the skull, weighed and collected in 1.5 mL ice-cold 1x HBSS -/- . Brains were cut into pieces using spring scissors and slurry was dissociated into single cell suspensions using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec). Cells were enzymatically dissociated using activated enzyme (P) for 15 min at 37 °C and enzyme (A) for 2x10 min at 37 °C under continuous nutation, with mechanical dissociation by trituration 10 times with a 5 ml serological pipet in between enzymatic dissociation steps. Subsequently, samples were passed through a 70 µM cell strainer. Myelin was removed by centrifugation (300g, 11 min, room temperature, low acceleration/break) of samples in 24 % Percoll PLUS and 75 U/ml DNase. After aspiration of the myelin layer and supernatant, cell pellet was resuspended in 50 µL of FACS buffer (0.5% BSA in D‐PBS). This process was repeated twice. Single cell suspensions were pre-incubated with Fc Block (1/100; BD Biosciences, 553142) for 10 min at 4 °C and stained with appropriate antibodies diluted at 4 °C in the dark for 30 min. After washing and centrifugation (400g, 7min, 4°C), supernatans was removed and pellets were resuspended in FACS buffer and transferred through a 35 µm mesh into a 5 ml Falco®Round‐Bottom Polystyrene Test Tube with Cell Strainer Snap Cap. Cell viability was assessed using DAPI 1/200, added immediately prior to sorting. Cell sorting was performed on the FACSymphony S6 using the 85 µm nozzle.  Cells were sorted into 2 ml Eppendorf tubes containing 450 µL RLT Plus lysis buffer (QIAGEN) containing 1% β-mercaptoethanol. The samples were extensively vortexed and stored at ‐80 °C until RNA isolation. Total RNA from sorted cells was extracted using the RNeasy ®Plus Micro Kit (QIAGEN, 74034) according to the manufacturer’s instructions. The concentration and purity of the RNA was determined using the Nanodrop ND-1000 (Nanodrop Technologies, Thermo Scientific) and the Agilent 2100 Bio-Analyzer.
RNA libraries were prepared for sequencing according to Element Biosciences protocols with the following parameters: AVITI 150 cycles Cloudbreak Freestyle sequencing kit single-end reads (101-10-10-0), 1% PhiX.

treatment_protocol: Not treated

tag: Sex

value: Male

tag: strain

value: Microglia

value: WT


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_JAK2_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorG_bulkRNAseq.csv

tag: tissue

value: blood

value: CD4-positive, alpha-beta T cells

tag: treatment

value: CRISPRi knockdown of JAK2

tag: donor id

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

tag: donor dev_stage

value: TRUE

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

tag: donor ethnicity

value: Hispanic

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: SD_wk32_A_R7

description: Library name: 8276

value: Liver

tag: housing temperature

value: TA

tag: timepoint (duration_on_diet)

tag: genotype

value: C57BL/6J, Male

value: GAN diet


title: primary rat astrocytes, H2O2, MitoCoat-mRNA 2

city: Charlestown

first: Kazuhide

last: Hayakawa

state: Massachusetts

address: MGH149 13th street, Room 2401

department: Radiology

institute: Massachusetts General Hospital

description: Library name: Stress-MRC2

data_processing:
by GENEWIZ (New Jersey, USA).
Assembly: Alignment files (BAM) were generated for downstream analysis. Gene-level counts were quantified using featureCounts from the Subread package (v1.5.2), counting uniquely mapped reads overlapping annotated exons (strand-specific when applicable).

organism: Rattus norvegicus

source_name: Primary

growth_protocol: Astrocytes were plated in poly-D-lysine-coated 75-cm2 flasks, and maintained in Dulbecco’s Modified Eagle’s medium containing 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
Total RNA, including mitochondrial mRNA, was extracted from mitochondria-enriched fractions using the RNeasy Micro Kit (QIAGEN) according to the manufacturer’s protocol.
Library preparation and sequencing were performed by GENEWIZ (New Jersey, USA). Raw reads were trimmed to remove adapter sequences and low-quality bases using Trimmomatic (v0.36) and aligned to the Rattus norvegicus reference genome (Rnor6.0, Ensembl annotation) using the splice-aware aligner STAR aligner (v2.5.2b).

treatment_protocol: Cells were treated with H₂O₂ at a final concentration of 100 µM for 30 min at 37 °C in a humidified 5% CO₂ incubator by adding plate-specific volumes of the 10 mM H₂O₂ stock (1 µL, 10 µL, and 20 µL to 96-well, 12-well, and 6-well plates, respectively), while vehicle control wells received the same volume of sterile distilled water.

value: Primary

tag: cell line

value: astrocyte

tag: cell type

value: ATP restoration

tag: batch

value: polyA RNA


title: SD_wk32_A_R5

description: Library name: 8274

tag: tissue

tag: treatment


title: SD_wk32_A_R4

description: Library name: 8268


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_GATA3_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 knockdown of GATA3

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

value: ACDA

value: STEMCELL technologies

value: Female

value: adult stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: genetic perturbation_strategy

tag: enriched cell_types


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_GATA3_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorG_bulkRNAseq.csv

tag: anticoagulant

tag: source

tag: donor sex

tag: donor dev_stage

value: TRUE

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

tag: donor ethnicity

value: Hispanic

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: SD_wk32_A_R3

description: Library name: 8265

tag: tissue

value: Liver

tag: housing temperature

value: TA

tag: timepoint (duration_on_diet)

tag: genotype

value: C57BL/6J, Male

tag: treatment

value: GAN diet


title: SD_wk32_A_R2

description: Library name: 8222


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

description:
Library name: Th1Th2_validation_Diff084_DonorG_GATA3_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorG_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of GATA3

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: batch


title: SD_wk32_A_R1

description: Library name: 8221


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_ZMYND8_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorF_bulkRNAseq.csv

value: CRISPRi knockdown of ZMYND8

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 disease

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity

value: Asian

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol


title: NC_wk23_B_R8

description: Library name: 8324

tag: tissue

tag: housing temperature

value: TN

tag: timepoint (duration_on_diet)

tag: genotype

tag: treatment

value: Normal Chow


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_ZMYND8_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorF_bulkRNAseq.csv

tag: cell type

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

value: Normal

value: Zymo DNA/RNA Shield

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

value: CRISPRi

value: Plasmidsaurus RNA-Seq

tag: batch


title: NC_wk23_B_R6

description: Library name: 8322

value: Liver

value: C57BL/6J, Male


title: NC_wk23_B_R5

description: Library name: 8321


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_ZMYND8_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorF_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

value: CRISPRi knockdown of ZMYND8

value: No

tag: anticoagulant

tag: source

tag: donor sex

tag: donor dev_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


title: NC_wk23_B_R7

description: Library name: 8323

tag: tissue

tag: housing temperature

tag: timepoint (duration_on_diet)

tag: genotype

tag: treatment


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_TBX21_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorF_bulkRNAseq.csv

tag: cell type

tag: experimental perturbation

value: CRISPRi knockdown of TBX21

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: AB+

value: ACDA

value: STEMCELL technologies

value: Female

value: adult stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: batch


title: NC_wk23_B_R4

description: Library name: 8320

value: TN

value: Normal Chow


title: NC_wk23_B_R3

description: Library name: 8319


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_TBX21_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorF_bulkRNAseq.csv

tag: anticoagulant

tag: source

tag: donor sex

tag: donor dev_stage

value: TRUE

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


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_STYXL1_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorF_bulkRNAseq.csv

tag: tissue

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: treatment

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

tag: experimental perturbation

value: CRISPRi knockdown of STYXL1

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

value: Plasmidsaurus RNA-Seq


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_TBX21_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorF_bulkRNAseq.csv

value: CRISPRi knockdown of TBX21

tag: donor smoker

value: No

tag: donor blood_type

value: AB+

tag: anticoagulant

value: ACDA

tag: source

tag: donor sex

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: batch


title: NC_wk23_B_R2

description: Library name: 8318

value: Liver

tag: housing temperature

value: TN

tag: timepoint (duration_on_diet)

tag: genotype

value: C57BL/6J, Male


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_STYXL1_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorF_bulkRNAseq.csv

tag: tissue

tag: cell type

tag: treatment

value: STEMCELL technologies

value: Female

tag: donor dev_stage

value: adult stage

value: TRUE

tag: donor disease

value: Normal

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol


title: NC_wk23_B_R1

description: Library name: 8317

value: Normal Chow


title: NC_wk23_A_R8

description: Library name: 8208

value: TA


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_STYXL1_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorF_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

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

tag: donor living_at_sample_collection

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: Asian

value: CRISPRi


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_PPP1R7_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorF_bulkRNAseq.csv

tag: tissue

tag: cell type

tag: treatment

value: CRISPRi knockdown of PPP1R7

value: No

value: AB+

value: ACDA

tag: donor dev_stage

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

value: Plasmidsaurus RNA-Seq

tag: batch


title: NC_wk23_A_R7

description: Library name: 8207

value: Liver

tag: housing temperature

tag: timepoint (duration_on_diet)

tag: genotype

value: C57BL/6J, Male


title: NC_wk23_A_R6

description: Library name: 8206


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_PPP1R7_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorF_bulkRNAseq.csv

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: STEMCELL technologies

value: Female

value: adult stage

value: TRUE

value: Normal

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol


title: NC_wk23_A_R5

description: Library name: 8205

tag: tissue

value: TA

tag: treatment

value: Normal Chow


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_PPP1R7_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorF_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: 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

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

tag: batch


title: primary rat astrocytes, H2O2, Mitochondria treatment 2

description: Library name: Stress-mito2

value: Primary

tag: cell line

value: astrocyte

value: WT

tag: genotype

value: ATP restoration

value: polyA RNA


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_NTC2_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorF_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi non-targeting control

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

value: AB+

value: ACDA

value: STEMCELL technologies

tag: suspension depletion_factors

tag: donor ethnicity

value: Asian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: NC_wk23_A_R4

description: Library name: 8204

tag: tissue

value: Liver

tag: housing temperature

value: TA

tag: timepoint (duration_on_diet)

value: C57BL/6J, Male

tag: treatment

value: Normal Chow


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_NTC2_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorF_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: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

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

tag: library protocol

tag: batch


title: NC_wk23_A_R3

description: Library name: 8203

tag: genotype


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_NTC2_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorF_bulkRNAseq.csv

tag: tissue

tag: experimental perturbation

value: CRISPRi non-targeting control

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

value: AB+

value: ACDA

value: STEMCELL technologies

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types


title: NC_wk23_A_R2

description: Library name: 8202

value: Liver

tag: housing temperature

value: TA

tag: timepoint (duration_on_diet)

tag: treatment


title: NC_wk23_A_R1

description: Library name: 8201

value: C57BL/6J, Male

value: Normal Chow


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_NTC1_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorF_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

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

tag: donor disease

tag: sample preservation_method

value: Asian

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_NTC1_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorF_bulkRNAseq.csv

tag: tissue

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

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Female

value: adult stage

value: TRUE

value: Normal

tag: suspension depletion_factors

tag: donor ethnicity

tag: batch


title: SD_wk23_B_R8

description: Library name: 8332

tag: housing temperature

value: TN

tag: timepoint (duration_on_diet)

tag: genotype

tag: treatment

value: GAN diet


title: SD_wk23_B_R7

description: Library name: 8331


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_NKTR_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorF_bulkRNAseq.csv

tag: cell type

value: CRISPRi knockdown of NKTR

value: No

tag: donor blood_type

value: AB+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: 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: SD_wk23_B_R6

description: Library name: 8330

tag: tissue

value: Liver

value: C57BL/6J, Male


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_NTC1_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorF_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi non-targeting control

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity

value: Asian

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_NKTR_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorF_bulkRNAseq.csv

tag: cell type

tag: treatment

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

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

value: Normal


title: SD_wk23_B_R5

description: Library name: 8329

tag: tissue

tag: housing temperature

value: TN

tag: timepoint (duration_on_diet)

tag: genotype

value: GAN diet


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_NKTR_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorF_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi knockdown of NKTR

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

value: AB+

value: ACDA

value: STEMCELL technologies

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: genetic perturbation_strategy

tag: enriched cell_types


title: SD_wk23_B_R4

description: Library name: 8328

value: Liver

value: C57BL/6J, Male

tag: treatment


title: SD_wk23_B_R3

description: Library name: 8327


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_MAMLD1_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorF_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

value: CRISPRi knockdown of MAMLD1

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

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

value: CRISPRi

tag: library protocol

tag: batch


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_MAMLD1_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorF_bulkRNAseq.csv

tag: tissue

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

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Female

value: adult stage

value: TRUE

tag: donor body_mass_index

value: Normal

value: Plasmidsaurus RNA-Seq


title: SD_wk23_B_R1

description: Library name: 8325

tag: housing temperature

value: TN

tag: timepoint (duration_on_diet)

tag: genotype

tag: treatment

value: GAN diet


title: SD_wk23_B_R2

description: Library name: 8326


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_MAMLD1_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorF_bulkRNAseq.csv

tag: cell type

value: No

tag: donor blood_type

value: AB+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor disease

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: genetic perturbation_strategy

tag: enriched cell_types


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_JAK2_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorF_bulkRNAseq.csv

tag: tissue

value: blood

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi knockdown of JAK2

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: suspension depletion_factors

tag: donor ethnicity

tag: library protocol

tag: batch


title: Case3_BLBC

city: Dalian

first: Xuehong

last: Zhang

state: Liaoning

address: No. 9 West Section Lvshun South Road, Dalian 116044, Liaoning, China

department: Institute of Cancer Stem Cell

country: China

institute: Dalian Medical University

description:
Library name: Sample 5
10x Genomics

library_source: transcriptomic single cell

data_processing:
The scRNA-seq data were processed and integrated using Cell Ranger Suite v7.1.0 along with the GRCh38 reference genome, resulting in the generation of unique molecular identifier (UMI) count matrices. Following barcode demultiplexing, the UMI matrices were imported into the R package Seurat (version 5.0.3), which is an R toolkit utilized for quality control, analysis, and exploration of scRNA-seq data. Cells expressing fewer than 200 genes, with total UMI counts below 6000, or with over 10% of total UMI counts in the mitochondrial genome were considered low-quality or indicative of dead or dying cells. Doublets within each sample were identified using DoubletFinder. These identified cells were subsequently excluded from further analyses.
Assembly: human GRCh38
Supplementary files format and content: cell barcodes (barcodes.tsv.gz), genes (genes.tsv.gz), and count matrix (matrix.mtx.gz)

source_name: Bone Marrow

extract_protocol:
scRNA-seq was performed on the BM mononucleated cells (BMMCs) from the chronic phase and B-lymphoblastic crisis samples collected from three patients using the chromium system (10X Genomics).
Single-cell gene expression libraries were prepared according to the Chromium NextGEM Single Cell Gene Expression 3v3.1 kit (10x Genomics). Briefly, single cells, reverse transcription reagents, gel beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single-cell GEMs (Gel Bead-In-Emulsion). Full-length cDNA was synthesized and barcoded within each GEM. Subsequently, GEMs were broken, and cDNA was pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA was amplified by PCR. The amplified product was fragmented prior to end-repair, A-tailing, and adaptor ligation.

value: Bone Marrow

tag: disease stage

value: B-cell lymphoblastic crisis


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_JAK2_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorF_bulkRNAseq.csv

tag: cell type

tag: treatment

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

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

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: Asian

value: CRISPRi


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_JAK2_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorF_bulkRNAseq.csv

tag: tissue

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor weight

value: adult stage

value: TRUE

tag: donor disease

value: Normal

tag: sample preservation_method

tag: genetic perturbation_strategy

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: SD_wk23_A_R8

description: Library name: 8216

value: Liver

tag: housing temperature

value: TA

tag: timepoint (duration_on_diet)

tag: genotype

value: C57BL/6J, Male

tag: treatment

value: GAN diet


title: Case2_BLBC

description:
Library name: Sample 4
10x Genomics

tag: disease stage


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_GATA3_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorF_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

value: CRISPRi knockdown of GATA3

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

tag: donor dev_stage

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity

tag: library protocol

tag: batch


title: SD_wk23_A_R7

description: Library name: 8215

tag: tissue

tag: housing temperature


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_GATA3_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorF_bulkRNAseq.csv

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

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor weight

value: Female

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: Asian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types


title: Case2_CP

description:
Library name: Sample 3
10x Genomics

value: Bone Marrow

tag: disease stage

value: chronic phase


title: SD_wk23_A_R6

description: Library name: 8214

value: Liver

value: TA

tag: timepoint (duration_on_diet)

tag: genotype

value: C57BL/6J, Male

tag: treatment


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

description:
Library name: Th1Th2_validation_Diff084_DonorF_GATA3_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorF_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

tag: donor dev_stage

value: adult stage

value: TRUE

value: Normal

tag: suspension depletion_factors

tag: donor ethnicity

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: Donor9, SIC, scRNA-seq, T3

city: wuhan

first: Mingjie

last: Li

address: union hospital

institute: Huazhong University of Science and Technology

description: Library name: Donor9, SIC, scRNA-seq, T3

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

source_name: locally advanced rectal cancer

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

tag: tissue

value: locally advanced rectal cancer

value: stromal and immune cells


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_ZMYND8_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorE_bulkRNAseq.csv

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

tag: experimental perturbation

value: CRISPRi knockdown of ZMYND8

tag: donor id

tag: donor age

tag: donor weight

value: No

value: O+

value: ACDA

value: STEMCELL technologies

value: Female

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

value: Zymo DNA/RNA Shield

value: Hispanic

tag: genetic perturbation_strategy

tag: enriched cell_types


title: LC_uninfected_female_rep2

type: RNA

city: Stillwater

first: Clinton

last: Jones

state: Oklahoma

address: 250 McElroy Hall

department: Veterinary Pathobiology

institute: Oklahoma State University

description:
OCJ4140_Female_LC_HSVvsControl.txt
OCJ4140_Female_LC_dLATvsControl.txt

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

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

label: NanoString target-specific fluorescent barcodes

source_name: LC, uninfected

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

tag: Sex

value: female

value: LC

tag: infection

value: uninfected


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_ZMYND8_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorE_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: treatment

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

tag: donor dev_stage

value: adult stage

value: TRUE

tag: suspension depletion_factors

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

value: CRISPRi


title: NK-92 cells, shADAR1-2

city: Guangzhou

first: Rukang

last: Liang

state: Guangdong

address: Shipai Street, Tianhe district

department: Biotherapy Center

institute: The Third Affiliated Hospital of Sun Yat-Sen University

data_processing:
fastp (version 0.18.0)
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0).
Assembly: Ensembl release106
Supplementary files format and content: tab-delimited text fle includes raw counts and FPKM values for each Sample

growth_protocol: NK-92 cells were cultured in RPMI 1640 medium supplemented with 12.5% FBS, 50 μM β-mercaptoethanol, 100 IU/ml recombinant human IL-2 and 1% Penicillin-Streptomycin solution.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA).
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530, New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.     The ligation reaction was purified with the AMPure XP Beads(1.0X).

treatment_protocol: For transduction, lentivirus was added to NK-92 cells in the presence of 8 μg/mL polybrene. Then, the samples were centrifuged at the speed of 1800 g for 60 mins at 32 ℃ and incubated overnight in a humidified incubator at 37 ℃ with 5% CO2 before replacing the medium with a regular growth medium

tag: cell line


title: Case1_BLBC

description:
Library name: Sample 2
10x Genomics

tag: tissue

value: Bone Marrow

tag: disease stage

value: B-cell lymphoblastic crisis


title: SD_wk23_A_R5

description: Library name: 8213

value: Liver

tag: housing temperature

value: TA

tag: timepoint (duration_on_diet)

tag: genotype

value: C57BL/6J, Male

value: GAN diet


title: Case1_CP

description:
Library name: Sample 1
10x Genomics

value: chronic phase


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_TBX21_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorE_bulkRNAseq.csv

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

tag: experimental perturbation

value: CRISPRi knockdown of TBX21

tag: donor id

tag: donor age

tag: donor weight

value: No

value: O+

value: ACDA

value: STEMCELL technologies

value: Female

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_ZMYND8_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorE_bulkRNAseq.csv

tag: tissue

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: treatment

value: CRISPRi knockdown of ZMYND8

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

tag: donor dev_stage

value: adult stage

value: TRUE

tag: suspension depletion_factors

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

value: CRISPRi


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_TBX21_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorE_bulkRNAseq.csv

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

tag: experimental perturbation

value: CRISPRi knockdown of TBX21

tag: donor id

tag: donor age

tag: donor weight

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method


title: Chromium 10X,RAD Tetramer EBVST hTCR

city: Houston

first: Cliona

last: Rooney

state: TX

address: 1102 Bates Ave

institute: Baylor College of Medicine

description:
Library name: 5v3_TetRAD_hTCR
10x Genomics

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

source_name: EBV virus-specific T cells

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

tag: tissue

value: Peripheral blood

tag: cell type

value: T cells

tag: genotype

value: virus specific T cells

tag: treatment

value: T cell products

tag: batch

value: Donor #1


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_TBX21_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorE_bulkRNAseq.csv

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: O+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

value: Female

value: Normal

value: Zymo DNA/RNA Shield

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol


title: SD_wk23_A_R4

description: Library name: 8212

value: Liver

tag: housing temperature

value: TA

tag: timepoint (duration_on_diet)

value: C57BL/6J, Male

value: GAN diet


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_STYXL1_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorE_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of STYXL1

tag: donor id

tag: donor age

tag: donor weight

tag: donor sex

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

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

value: Hispanic

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: SD_wk23_A_R3

description: Library name: 8211

tag: tissue

tag: genotype

tag: treatment


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_STYXL1_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorE_bulkRNAseq.csv

tag: cell type

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: O+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

value: Female

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: enriched cell_types

tag: library protocol

tag: batch


title: SD_wk23_A_R2

description: Library name: 8210

value: Liver

tag: housing temperature

value: TA

tag: timepoint (duration_on_diet)

value: C57BL/6J, Male


title: Chromium 10X,Whole Tetramer EBVST, hTCR

description:
Library name: 5v3_TetWhole_hTCR
10x Genomics

value: Peripheral blood

value: T cells

value: virus specific T cells

value: T cell products

value: Donor #1


title: SD_wk23_A_R1

description: Library name: 8209

value: GAN diet


title: Chromium 10X, Whole EBVST, hTCR

description:
Library name: 5v3_Whole_hTCR
10x Genomics


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_PPP1R7_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorE_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 PPP1R7

tag: donor id

tag: donor age

tag: donor weight

tag: donor sex

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

value: Hispanic


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_PPP1R7_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorE_bulkRNAseq.csv

tag: tissue

tag: cell type

tag: treatment

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: O+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

value: Female

tag: donor ethnicity

tag: genetic perturbation_strategy

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: SD_wk16_B_R8

description: Library name: 8388

value: Liver

tag: housing temperature

value: TN

tag: timepoint (duration_on_diet)

tag: genotype

value: C57BL/6J, Male

value: GAN diet


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_NTC2_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorE_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi non-targeting control

tag: donor id

tag: donor age

tag: donor weight

tag: donor sex

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: enriched cell_types

tag: library protocol

tag: batch


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_NTC2_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorE_bulkRNAseq.csv

tag: tissue

tag: cell type

tag: treatment

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

value: TRUE

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

value: Hispanic


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_NTC1_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorE_bulkRNAseq.csv

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor weight

value: No

value: O+

value: ACDA

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

tag: donor ethnicity

tag: genetic perturbation_strategy


title: Chromium 10X,RAD EBVST, GEX

description:
Library name: 5v3_RAD_GEX
10x Genomics

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

tag: tissue

value: Peripheral blood

tag: cell type

value: T cells

tag: genotype

value: virus specific T cells

tag: treatment

value: T cell products

tag: batch

value: Donor #1


title: SD_wk16_B_R7

description: Library name: 8387

value: Liver

tag: housing temperature

value: TN

tag: timepoint (duration_on_diet)

value: C57BL/6J, Male

value: GAN diet


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_NTC1_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorE_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 height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_NTC1_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorE_bulkRNAseq.csv

tag: tissue

tag: cell type

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor weight

value: No

value: O+

value: ACDA

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

tag: suspension depletion_factors

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

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy


title: SD_wk16_B_R6

description: Library name: 8386

value: Liver

tag: housing temperature

value: TN

tag: timepoint (duration_on_diet)

tag: genotype

value: C57BL/6J, Male

tag: treatment

value: GAN diet


title: Chromium 10X,Whole Tetramer EBVST, GEX

description:
Library name: 5v3_TetWhole_GEX
10x Genomics

value: Peripheral blood

value: T cells

value: virus specific T cells

value: T cell products

tag: batch

value: Donor #1


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_NKTR_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorE_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

value: CRISPRi knockdown of NKTR

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: SD_wk16_B_R5

description: Library name: 8385

tag: tissue

value: Liver

value: TN

value: C57BL/6J, Male


title: Chromium 10X,Whole EBVST, GEX

description:
Library name: 5v3_Whole_GEX
10x Genomics

value: Peripheral blood

tag: cell type

value: T cells


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_NKTR_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorE_bulkRNAseq.csv

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor weight

value: No

value: O+

value: ACDA

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

tag: suspension depletion_factors

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

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy


title: SD_wk16_B_R4

description: Library name: 8380

tag: housing temperature

tag: timepoint (duration_on_diet)

tag: genotype

tag: treatment

value: GAN diet


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_MAMLD1_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorE_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

value: CRISPRi knockdown of MAMLD1

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

tag: enriched cell_types

tag: batch


title: SD_wk16_B_R3

description: Library name: 8379

tag: tissue

value: Liver

value: TN

value: C57BL/6J, Male


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_JAK2_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorE_bulkRNAseq.csv

tag: cell type

tag: experimental perturbation

value: CRISPRi knockdown of JAK2

tag: donor id

tag: donor age

tag: donor weight

value: No

value: O+

tag: donor sex

tag: donor dev_stage

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: Chromium 10X,Control 6hr MVST, hTCR

description:
Library name: 5v3_Ctrl6hr_hTCR
10x Genomics

source_name: MVST virus-specific T cells

value: Peripheral blood

value: T cells

tag: genotype

value: virus specific T cells

tag: treatment

value: T cell products

value: Donor #1


title: SD_wk16_B_R1

description: Library name: 8377

tag: housing temperature

tag: timepoint (duration_on_diet)

value: GAN diet


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

description:
Library name: 5v3_EBV3hr_hTCR
10x Genomics

tag: batch


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_GATA3_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorE_bulkRNAseq.csv

tag: tissue

value: blood

value: CD4-positive, alpha-beta T cells

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

value: CRISPRi knockdown of GATA3

tag: donor height

tag: donor smoker

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: TRUE

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

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

value: Hispanic

tag: enriched cell_types


title: SD_wk16_A_R8

description: Library name: 8272

value: Liver

value: TA

value: C57BL/6J, Male


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

description:
Library name: 5v3_CMV3hr_hTCR
10x Genomics

value: Peripheral blood

tag: cell type

value: T cells

value: virus specific T cells

value: T cell products


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_ZMYND8_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorC_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi knockdown of ZMYND8

tag: donor id

tag: donor age

tag: donor weight

value: No

value: A+

tag: donor sex

tag: donor dev_stage

value: Normal

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_ZMYND8_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorC_bulkRNAseq.csv

tag: tissue

tag: treatment

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

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

value: Female

value: adult stage

value: TRUE

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: batch


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_TBX21_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorC_bulkRNAseq.csv

value: blood

tag: cell type

tag: experimental perturbation

value: CRISPRi knockdown of TBX21

tag: donor id

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

tag: enriched cell_types


title: C42B Abi 5 A

city: Sacramento

first: Alan

last: Lombard

address: 4500 2nd Avenue, Rm 4674

institute: University of California, Davis

description: Library name: LLG040

data_processing:
Raw sequencing data were processed using the nf-core/rnaseq pipeline (version 3.14.0, DOI 10.5281/zenodo.10471647), which includes quality control, alignment, and quantification steps
Reads were trimmed using Trim Galore
reads were mapped to the Homo sapiens reference genome (GRCh38) using STAR (Dobin et al., 2013). Gene-level quantification was performed using Salmon (Patro et al., 2017) against the GENCODE v45 gene annotation
Raw counts were extracted from the Salmon file outputs
Assembly: GRCh38 and GENCODE v45 gene annotation
Supplementary files format and content: tab-delimited text file contains raw counts for each sample and associated Ensembl gene id from the GENCODE v45 gene annotation.

growth_protocol: Cells are maintained in RPMI 1640 supplemented with 10% FBS and 1% pen/strep in humidified incubator at 5% CO2.

extract_protocol:
RNA was isolated from cultured cells using Trizol reagent (Thermofisher) following manufacturer’s instructions and further purified using the RNeasy kit (Qiagen) with the optional on-column DNase step according to the manufacturer’s protocols. Total RNA was eluted from the columns in nuclease-free water and stored at -80°C
Indexed, stranded mRNA-seq libraries were prepared from total RNA (1000 ng) using the KAPA Stranded mRNA-Seq Kit (Roche) according to the manufacturer’s standard protocol for mRNA capture, fragmentation, random-primed first strand synthesis, second strand synthesis with dUTP marking, A-tailing, adaptor ligation, and library amplification. Libraries were pooled and multiplex sequenced on an Illumina NovaSeqX Plus System

treatment_protocol: Cells were plated in 60mm and treated as indicated the following day. For LLG001-LLG018, treatment duration is indicated. For LLG037-LLG057, treatment was for 5-days.

tag: cell line

value: Abiraterone Acetate 5μM


title: Chromium 10X,EBV 6hr MVST, GEX

description:
Library name: 5v3_EBV6hr_GEX
10x Genomics

tag: tissue

value: Peripheral blood

value: T cells

tag: genotype

value: virus specific T cells

value: T cell products

value: Donor #1


title: C42B DMSO C

description: Library name: LLG039

tag: treatment

value: DMSO


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_MAMLD1_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorE_bulkRNAseq.csv

value: CD4-positive, alpha-beta T cells

value: CRISPRi knockdown of MAMLD1

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

value: O+

tag: donor sex

tag: donor dev_stage

value: Normal

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: Chromium 10X,BV 6hr MVST, hTCR

description:
Library name: 5v3_EBV6hr_hTCR
10x Genomics

tag: cell type

tag: batch


title: SD_wk16_A_R5

description: Library name: 8269

value: Liver

tag: housing temperature

value: TA

tag: timepoint (duration_on_diet)

value: C57BL/6J, Male

value: GAN diet


title: WT_E9.5

city: Chengdu

first: chao

last: yang

state: Sichuan

address: No.20, Section 3, Renmin South Road

department: West China Second University Hospital

institute: Sichuan University

description: scRNAseq sample 1

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

molecule: nuclear RNA

source_name: whole embryo

extract_protocol:
Embryos were dissociated into single-cell suspension, loaded into Chromium microfluidic chips with 3’ reagent kit (v3.1 chemistry), and barcoded with a 10X Chromium Controller (10X Genomics).
Libraries were performed according to the manufacturer’s instructions (single cell 3’ V3.1, 10X Genomics).

tag: tissue

value: whole embryo

tag: developmental stage

value: WT


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_JAK2_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorE_bulkRNAseq.csv

value: blood

tag: treatment

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

tag: experimental perturbation

value: CRISPRi knockdown of JAK2

tag: donor id

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

value: Female

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

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

tag: enriched cell_types


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_JAK2_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorE_bulkRNAseq.csv

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

value: O+

tag: donor sex

tag: donor dev_stage

value: Normal

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: library protocol


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_GATA3_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorE_bulkRNAseq.csv

tag: tissue

tag: treatment

tag: experimental perturbation

value: CRISPRi knockdown of GATA3

tag: donor id

tag: donor blood_type

tag: anticoagulant

tag: source

value: Plasmidsaurus RNA-Seq

tag: batch


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_TBX21_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorC_bulkRNAseq.csv

value: blood

tag: cell type

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

value: CRISPRi knockdown of TBX21

tag: donor age

tag: donor weight

value: A+

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

value: Caucasian

tag: enriched cell_types


title: Chromium 10X,CMV 6hr MVST, GEX

description:
Library name: 5v3_CMV6hr_GEX
10x Genomics

value: Peripheral blood

value: T cells

tag: genotype

value: virus specific T cells

value: T cell products

value: Donor #1


title: K_marx_P8_5

city: Zapopan

first: Lorena

last: Amaya Delgado

state: Jalisco

address: Camino arenero 1227

department: Industrial Biotechnology

country: Mexico

institute: CIATEJ

description:
P8_c-tx_GEO_NCBI.txt
treatment

data_processing:
Illumina bcl2fastq software used for basecalling.
Paired-end library, reads length 100 bp
Quality control of each sample was analyzed with FASTQC
Reads were mapped to the genome of Kluyveromyces marxianus DMKU3 with SALMON
Transcriptome assembly of reads were performed with SPADES v3.15.3
ORF’s were predicted with TransDecoder v5.5.0 with default settings
ORF’s annotation was performed with the annotate module from funannotate v1.6.0
Genome_build: NCBI ID 10898
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Kluyveromyces marxianus

source_name: Kluyveromyces marxianus

growth_protocol: A defined mineral culture medium was used, containing 20.0 g L-1 glucose as the only carbon source; a mixture of salts composed of (g L-1) 1.49 Na2HPO4·2H2O, 3.0 K2HPO4, 3.0 (NH4)·2SO4 and 1.0 glutamic acid; 2.5 mL L-1 vitamin solution composed of (mg L-1) 1.0 aminobenzoic acid, 125.0 mesoinositol, 5.0 nicotinic acid, 5.0 pantothenic acid, 5.0 pyridoxine, 5.0 thiamine HCl, and 0.012 biotin; and 1 mL L-1 oligoelement solution containing (mg L-1) 410.0 MgCl2·6H2O, 19.2 ZnCl2, 0.61 CuCl2·2H2O, 4.45 MnCl2·4H2O, 0.5 CoCl2·6H2O, 17.37 CaCl2, 11.66 FeCl2·4H2O, 0.36 (NH4)6Mo7O24·4H2O, and 3.0 H3BO3. Glucose was prepared in a 700 g L-1 stock. Glucose and salts were sterilized by autoclave (121 °C for 15 min). Oligoelements and vitamins were sterilized by filtration (0.20 μm). The fermentations were carried out in a 250mL bioreactor at 150 rpm, 30 °C.

extract_protocol:
The samples for transcriptome analysis were collected in the first 3 h of fermentation and subsequent total RNA extraction was performed using an extraction protocol using Tri-Reagen (Sigma Aldrich) and the extraction kit (Promega).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A defined mineral culture medium was used (see growth protocol), and adittionally 1 g/L of furfural was added. The fermentations were carried out in a 250mL bioreactor at 150 rpm, 30 °C.

tag: strain

value: yeast

value: Adapted


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_TBX21_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorC_bulkRNAseq.csv

tag: tissue

value: CD4-positive, alpha-beta T cells

tag: treatment

tag: donor height

tag: donor smoker

value: No

value: ACDA

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: library protocol


title: Chromium 10X,Control 6hr MVST, GEX

description:
Library name: 5v3_Ctrl6hr_GEX
10x Genomics

value: Peripheral blood

tag: cell type

tag: batch


title: K_marx_P8_4

description:
P8_c-tx_GEO_NCBI.txt
treatment


title: SD_wk16_A_R3

description: Library name: 8263

value: Liver

tag: housing temperature

value: TA

tag: timepoint (duration_on_diet)

value: C57BL/6J, Male

value: GAN diet


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_STYXL1_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorC_bulkRNAseq.csv

value: blood

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

tag: experimental perturbation

value: CRISPRi knockdown of STYXL1

tag: donor id

tag: donor age

tag: donor weight

tag: donor blood_type

value: A+

tag: anticoagulant

tag: source

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

value: Caucasian

value: CRISPRi

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: C42B DMSO B

description: Library name: LLG038

tag: cell line

tag: treatment

value: DMSO


title: K_marx_SLP1_6

tag: strain

tag: cell type

value: yeast

value: Parental


title: SD_wk16_A_R2

description: Library name: 8262

tag: tissue

tag: housing temperature

tag: timepoint (duration_on_diet)

tag: genotype


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_ZMYND8_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorC_bulkRNAseq.csv

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi knockdown of ZMYND8

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

value: ACDA

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: library protocol

tag: batch


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_STYXL1_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorC_bulkRNAseq.csv

tag: tissue

value: blood

tag: cell type

tag: treatment

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

value: CRISPRi knockdown of STYXL1

tag: donor blood_type

value: A+

tag: anticoagulant

tag: source

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

tag: enriched cell_types


title: SD_wk16_A_R6

description: Library name: 8270

value: Liver

tag: housing temperature

value: TA

tag: timepoint (duration_on_diet)

tag: genotype

value: C57BL/6J, Male

value: GAN diet


title: Chromium 10X,CMV 3hr MVST, GEX

description:
Library name: 5v3_CMV3hr_GEX
10x Genomics

value: Peripheral blood

value: T cells

value: virus specific T cells

value: T cell products

value: Donor #1


title: K_marx_SLP1_5

tag: strain

value: yeast

value: Parental


title: SD_wk16_A_R1

description: Library name: 8261


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_STYXL1_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorC_bulkRNAseq.csv

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

value: ACDA

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq


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

description:
Library name: 5v3_Ctrl3hr_GEX
10x Genomics

tag: tissue

value: Peripheral blood

tag: cell type

value: T cells

value: virus specific T cells

tag: treatment

tag: batch


title: K_marx_SLP1_4

tag: strain

value: yeast


title: SG-5 mM Lidocaine

city: Taipei

first: Zih-Syuan

last: Wu

address: No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City 114201, Taiwan

country: Taiwan

institute: National defense medical center

description: Library name: SG-5 mM Lidocaine

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data. Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1). In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts for each sample
Supplementary files format and content: tab-delimited text file include FPKM values for each sample

source_name: gingival epithelial cell line

extract_protocol:
RNA was extracted using RNeasy Mini Kit_QIAGEN.
Libraries for polyA+ RNA-Sequencing were prepared from 1 μg RNA per sample using NovaSeq 6000 (Illumina)

value: gingival epithelial cell line

tag: cell line

value: SG


title: K_marx_P8_3

description: control

data_processing:
Illumina bcl2fastq software used for basecalling.
Paired-end library, reads length 100 bp
Quality control of each sample was analyzed with FASTQC
Reads were mapped to the genome of Kluyveromyces marxianus DMKU3 with SALMON
Transcriptome assembly of reads were performed with SPADES v3.15.3
ORFs were predicted with TransDecoder v5.5.0 with default settings
ORF's annotation was performed with the annotate module from funannotate v1.6.0
Genome_build: NCBI ID 10898
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

value: Adapted


title: SD_wk12_B_R7

description: Library name: 8375

value: Liver

tag: housing temperature

value: TN

tag: timepoint (duration_on_diet)

tag: genotype

value: C57BL/6J, Male

value: GAN diet


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_PPP1R7_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_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 PPP1R7

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

value: No

tag: donor blood_type

value: A+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

value: Female

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

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

tag: enriched cell_types


title: K_marx_P8_2

description: control

tag: strain

tag: cell type

value: yeast

tag: treatment

value: Adapted


title: SG-3 mM Lidocaine

description: Library name: SG-3 mM Lidocaine

tag: tissue

value: gingival epithelial cell line

tag: cell line

value: SG


title: SD_wk12_B_R6

description: Library name: 8374

value: Liver

tag: housing temperature

value: TN

tag: timepoint (duration_on_diet)

tag: genotype

value: C57BL/6J, Male

value: GAN diet


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_PPP1R7_Th1
Th1 polarized
Th1Th2_validation_Diff084_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 PPP1R7

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor sex

tag: donor dev_stage

value: Normal

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: SG-vehicle

description: Library name: SG-vehicle

tag: tissue

tag: cell line

tag: cell type


title: SD_wk12_B_R5

description: Library name: 8373

tag: housing temperature

tag: timepoint (duration_on_diet)

tag: genotype

tag: treatment


title: K_marx_P8_1

description: control

tag: strain

value: yeast


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_NTC2_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorC_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi non-targeting control

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

value: No

tag: donor blood_type

value: A+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

value: Female

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

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

tag: enriched cell_types


title: OECM1-5 mM Lidocaine

description: Library name: OECM1-5 mM Lidocaine

source_name: Oral Squamous Carcinoma Cell Line

tag: tissue

value: Oral Squamous Carcinoma Cell Line

tag: cell line

tag: cell type


title: K_marx_SLP1_3

tag: strain

tag: treatment

value: Parental


title: SD_wk12_B_R4

description: Library name: 8372

value: Liver

tag: housing temperature

value: TN

tag: timepoint (duration_on_diet)

tag: genotype

value: C57BL/6J, Male

value: GAN diet


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_NTC2_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_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

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor sex

tag: donor dev_stage

value: Normal

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: K_marx_SLP1_2

tag: strain

tag: cell type

value: yeast

tag: treatment


title: OECM1-3 mM Lidocaine

description: Library name: OECM1-3 mM Lidocaine

tag: tissue

tag: cell line


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_NTC2_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorC_bulkRNAseq.csv

tag: experimental perturbation

value: CRISPRi non-targeting control

tag: donor id

value: No

tag: donor blood_type

value: A+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

value: Female

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

tag: enriched cell_types


title: SD_wk12_B_R3

description: Library name: 8371

value: Liver

tag: housing temperature

value: TN

tag: timepoint (duration_on_diet)

tag: genotype

value: C57BL/6J, Male

value: GAN diet


title: SD_wk16_A_R4

description: Library name: 8264

value: TA


title: OECM1-vehicle

description: Library name: OECM1-vehicle

value: Oral Squamous Carcinoma Cell Line

tag: cell type


title: K_marx_SLP1_1

tag: strain

tag: treatment

value: Parental


title: SD_wk12_B_R2

description: Library name: 8370

tag: tissue


title: hiPSC-CMs co-treated with ponatinib and metformin biol rep 3

city: Maastricht

first: Brigitta

middle: Rita

last: Szabo

address: Minderbroedersberg 4-6

department: CARIM

country: Netherlands

institute: Maastricht University

description: Library name: PM_3

data_processing:
Raw reads were processed using the Galaxy platform (galaxy.org), where quality control and adapter trimming were performed with FASTP.
The trimmed reads were aligned to the human genome (GRCh38.112) using the STAR aligner.
Gene-level count tables were subsequently generated with featureCounts.
Assembly: GRCh38.112
Supplementary files format and content: files include raw counts for each sample

source_name: Ncyte vCardiomyocytes

growth_protocol: hiPSC-CMs were maintained in serum-free medium at 37°C and 5% CO2 with regular medium changes every 48 hours.

extract_protocol:
RNA-seq was performed by GenomeScan BV. Briefly, the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the samples. The sample preparation was performed according to the protocol "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760S/L). mRNA was isolated from total RNA using oligo-dT magnetic beads.
After mRNA fragmentation, cDNA synthesis was performed. This was used for ligation with sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp).Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. DNA was diluted to 0.8 nM. NovaSeq control software NCS v1.8 was used.

treatment_protocol: On day 7 post seeding, 3 replicates were exposed to one concentration of a single compound or to vehicle control (0.1% DMSO) for 24 hours. Compound solutions were administered at final concentration of 0.1% DMSO.

tag: cell line

value: Ncyte vCardiomyocytes

value: hiPSC-CMs

value: wild type

value: Ponatinib 1 µM + Metformin 1 µM


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_NTC1_non
nonpolarized
Th1Th2_validation_Diff084_non_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 non-targeting control

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

value: A+

tag: donor sex

tag: donor dev_stage

value: Normal

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

tag: donor ethnicity

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: SD_wk12_B_R1

description: Library name: 8369

value: Liver

tag: housing temperature

value: TN

tag: timepoint (duration_on_diet)

tag: genotype

value: C57BL/6J, Male

value: GAN diet


title: Chromium 10X, EBV 3hr MVST, GEX

description:
Library name: 5v3_EBV3hr_GEX
10x Genomics

tag: tissue

value: Peripheral blood

tag: cell type

value: T cells

value: virus specific T cells

tag: treatment

value: T cell products

value: Donor #1