title: hrmA-REV∆uge3, rep4

city: Hanover

first: Nicole

last: Kordana

state: NH

address: 74 College Street, Hinman Box 7550

department: Microbiology and Immunology

institute: Dartmouth College

description: Library name: AF293_hrmArev_duge3_4

data_processing:
trimming was performed with cutadapt v 2.4: nextseq-trim=20, minumum length = 1, quality cutoff = 20
Read mapping was performed with STAR v 2.7.2b: output type = BAM SortedByCoordinate, outFilterType = BySJout, genome = A1163 (v  FungiDB-52), gff file = AF293  (v FungiDB-52)
Read counting was performed with htseq-count v 0.11.2: format = BAM, stranded = no, order = pos
Assembly: FungiDB-52_AfumigatusAf293_Genome.fasta
Supplementary files format and content: tab-delimited text file included raw counts for each sample

organism: Aspergillus fumigatus

source_name: Mycelium (submerged biofilm)

growth_protocol: 37 °C, 5% CO2, liquid glucose minimal media, 24 hours of development

extract_protocol:
Tissue was harvested in TRI reagent with bead beating, RNA was purified from the aqueous phase with Qiagen RNAeasy Plus Mini kit. DNA contamination was removed with the TURBO DNA-free kit (Ambion).
RNA samples were prepared for sequencing using the Illumina Stranded mRNA Prep (#20040534) with Illumina Unique Dual Indexes.

value: Mycelium (submerged biofilm)

value: AF293::hrmA (D304G)dUge3


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

status: Public on Jun 02 2026

type: SRA

city: Palo Alto

first: Lattice

last: Data Coordination

state: CA

address: 3165 Porter Drive

department: Genetics

country: USA

institute: Stanford University

description:
Library name: Th1Th2_validation_Diff084_DonorC_NTC1_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorC_bulkRNAseq.csv

library_source: transcriptomic

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

molecule: polyA RNA

organism: Homo sapiens

source_name: blood

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

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.

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 non-targeting control

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

tag: donor ethnicity

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: hiPSC-CMs co-treated with ponatinib and metformin biol rep 2

city: Maastricht

first: Brigitta

middle: Rita

last: Szabo

address: Minderbroedersberg 4-6

department: CARIM

country: Netherlands

institute: Maastricht University

description: Library name: PM_2

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

molecule: total RNA

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

tag: cell type

value: hiPSC-CMs

tag: genotype

value: wild type

tag: treatment

value: Ponatinib 1 µM + Metformin 1 µM


title: hrmA-REV∆uge3, rep3

description: Library name: AF293_hrmArev_duge3_3

tag: tissue

value: Mycelium (submerged biofilm)

value: AF293::hrmA (D304G)dUge3


title: SD_wk12_A_R8

city: South San Francisco

first: ashmita

last: Saigal

state: California

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

institute: Merck & Co., Inc.

description: Library name: 8260

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

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: TA

tag: timepoint (duration_on_diet)

value: C57BL/6J, Male

value: GAN diet


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_NTC1_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorC_bulkRNAseq.csv

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

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi non-targeting control

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

tag: anticoagulant

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


title: hiPSC-CMs co-treated with ponatinib and metformin biol rep 1

description: Library name: PM_1

tag: cell line

value: Ncyte vCardiomyocytes

tag: cell type

value: hiPSC-CMs

tag: genotype

value: wild type

value: Ponatinib 1 µM + Metformin 1 µM


title: SD_wk12_A_R7

description: Library name: 8259

tag: tissue

value: Liver

tag: housing temperature

value: TA

value: C57BL/6J, Male

tag: treatment


title: hrmA-REV∆uge3, rep2

description: Library name: AF293_hrmArev_duge3_2

value: Mycelium (submerged biofilm)

value: AF293::hrmA (D304G)dUge3


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_NKTR_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 knockdown of NKTR

tag: donor id

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

tag: donor ethnicity

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: hiPSC-CMs treated with metformin biol rep 3

description: Library name: Met_3

tag: cell line

value: Ncyte vCardiomyocytes

value: hiPSC-CMs

value: wild type

value: Metformin 1 µM


title: hrmA-REV∆uge3, rep1

description: Library name: AF293_hrmArev_duge3_1


title: SD_wk12_B_R8

description: Library name: 8376

value: Liver

value: TN

tag: timepoint (duration_on_diet)

value: C57BL/6J, Male

value: GAN diet


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_PPP1R7_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorC_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

value: CRISPRi knockdown of PPP1R7

tag: donor age

tag: donor weight

tag: donor height

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


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_PPP1R7_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorE_bulkRNAseq.csv

tag: tissue

tag: treatment

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

tag: experimental perturbation

tag: donor id

value: O+

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: Chromium 10X,RAD EBVST, hTCR

city: Houston

first: Cliona

last: Rooney

state: TX

address: 1102 Bates Ave

institute: Baylor College of Medicine

description:
Library name: 5v3_RAD_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).

value: Peripheral blood

tag: cell type

value: T cells

tag: genotype

value: virus specific T cells

value: T cell products

tag: batch

value: Donor #1


title: SD_wk12_A_R6

description: Library name: 8258

value: Liver

tag: housing temperature

value: TA

tag: timepoint (duration_on_diet)

value: C57BL/6J, Male

value: GAN diet


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_NKTR_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

value: CRISPRi knockdown of NKTR

tag: donor age

tag: donor weight

tag: donor height

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

value: TRUE

value: Caucasian

tag: enriched cell_types

tag: library protocol


title: Chromium 10X,RAD Tetramer EBVST, GEX

description:
Library name: 5v3_TetRAD_GEX
10x Genomics

library_source: transcriptomic single cell

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

value: T cells

value: virus specific T cells

tag: treatment

value: T cell products

value: Donor #1


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_NTC2_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorE_bulkRNAseq.csv

value: blood

tag: cell type

tag: experimental perturbation

value: CRISPRi non-targeting control

tag: donor id

value: O+

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: hrmA-REV, rep4

description: Library name: AF293_hrmArev_4

value: Mycelium (submerged biofilm)

tag: genotype


title: hiPSC-CMs treated with metformin biol rep 2

description: Library name: Met_2

tag: cell line

value: Ncyte vCardiomyocytes

value: hiPSC-CMs

value: wild type

value: Metformin 1 µM


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_NKTR_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorC_bulkRNAseq.csv

value: CD4-positive, alpha-beta T cells

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

value: CRISPRi knockdown of NKTR

tag: donor age

tag: donor weight

tag: donor height

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

value: TRUE

value: Caucasian

tag: batch


title: SD_wk12_A_R5

description: Library name: 8257

tag: tissue

value: Liver

tag: housing temperature

value: TA

tag: timepoint (duration_on_diet)

value: C57BL/6J, Male

tag: treatment

value: GAN diet


title: hiPSC-CMs treated with metformin biol rep 1

description: Library name: Met_1

value: Ncyte vCardiomyocytes

tag: cell type

value: hiPSC-CMs

value: wild type


title: SD_wk12_A_R4

description: Library name: 8256

tag: genotype


title: hrmA-REV, rep3

description: Library name: AF293_hrmArev_3

value: Mycelium (submerged biofilm)


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_MAMLD1_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 knockdown of MAMLD1

tag: donor id

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

tag: donor ethnicity

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: SD_wk12_A_R3

description: Library name: 8255

tag: tissue

value: Liver


title: hrmA-REV, rep2

description: Library name: AF293_hrmArev_2


title: hiPSC-CMs treated with vehicle biol rep 3

description: Library name: Veh_3

tag: cell line

value: Vehicle


title: hiPSC-CMs treated with vehicle biol rep 2

description: Library name: Veh_2


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_MAMLD1_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorC_bulkRNAseq.csv

tag: donor age

tag: donor weight

tag: donor height

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

value: TRUE

value: Caucasian

tag: batch


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_NKTR_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorE_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: treatment

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

tag: experimental perturbation

value: CRISPRi knockdown of NKTR

tag: donor id

value: O+

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

value: Hispanic


title: hrmA-REV, rep1

description: Library name: AF293_hrmArev_1

tag: tissue

value: Mycelium (submerged biofilm)

tag: genotype


title: SD_wk12_A_R2

description: Library name: 8254

value: Liver

tag: housing temperature

value: TA

tag: timepoint (duration_on_diet)

value: C57BL/6J, Male

value: GAN diet


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_MAMLD1_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorC_bulkRNAseq.csv

value: CRISPRi knockdown of MAMLD1

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

tag: anticoagulant

value: ACDA

tag: source

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

tag: donor ethnicity

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: hiPSC-CMs treated with vehicle biol rep 1

description: Library name: Veh_1

tag: cell line

value: Ncyte vCardiomyocytes

tag: cell type

value: hiPSC-CMs

value: wild type

tag: treatment

value: Vehicle


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

description:
Library name: Th1Th2_validation_Diff084_DonorE_MAMLD1_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_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

tag: experimental perturbation

tag: donor id

value: O+

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

value: Hispanic

tag: batch


title: AF293∆uge3, rep4

description: Library name: AF293_duge3_4

value: Mycelium (submerged biofilm)

tag: genotype


title: SD_wk12_A_R1

description: Library name: 8253

value: Liver

tag: housing temperature

value: TA

tag: timepoint (duration_on_diet)

value: C57BL/6J, Male

value: GAN diet


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_JAK2_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorC_bulkRNAseq.csv

value: CRISPRi knockdown of JAK2

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

tag: anticoagulant

value: ACDA

tag: source

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

tag: donor ethnicity

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


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

description:
Library name: 5v3_CMV6hr_hTCR
10x Genomics

source_name: MVST virus-specific T cells

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


title: AF293∆uge3, rep3

description: Library name: AF293_duge3_3

value: Mycelium (submerged biofilm)

tag: genotype


title: hiPSC-CMs treated with ponatinib biol rep 3

description: Library name: Pon_3

tag: cell line

value: Ncyte vCardiomyocytes

value: hiPSC-CMs

value: wild type

value: Ponatinib 1 µM


title: AF293∆uge3, rep2

description: Library name: AF293_duge3_2


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_JAK2_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 JAK2

tag: donor id

value: No

value: A+

value: ACDA

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

tag: batch


title: CD8+ T cells, KO4 (p38α-/-p38β-/-), biol rep 4

city: Xiamen

first: Lichen

last: Hu

state: Fujian

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District

department: School of Life Sciences

country: China

institute: Xiamen University

description:
Library name: Sample 8
L1EJD0303171-KO4

data_processing:
Sequence reads were obtained from image data using Base Calling base discrimination
Sequence reads were trimmed for adaptor sequence/reads with undefined base/low-quality sequence (base with Qphred <= 20 at a proportion greater than 50%)
Trimmed sequence reads were mapped to GRCm38/mm10
New transcripts were predicted
Read count extraction and normalization were performed
Assembly: GRCm38/mm10
Supplementary files format and content: Excel file includes raw counts and FPKM values for each Sample

source_name: spleen

extract_protocol:
RNA was extracted using RNAiso Plus (Takara). 1 μg of total RNA was used for the construction of sequencing libraries.
mRNA was enriched from total RNA using Oligo(dT) magnetic bead, and then fragmented ramdonly. cDNA was synthesized from mRNA fragments using ramdon primers by M-MuLV reverse transcriptase. Thereafter RNA was degraded by RNaseH and the complementary DNA strand was synthesized by DNA polymerase I using dNTPs. After end repairing, polyA elongation and adding sequencing adaptor, around 370-420bp purified double strand cDNA was selected using AMPure XP beads. The cDNA was PCR amplified and further purified using AMPure XP beads to obtain the cDNA library.

treatment_protocol: 8 weeks old male mice were sacrificed, splenic CD44-CD62L+ CD8+ T cells were purified through negative selection.

value: spleen

value: CD8+ T cell

value: CD44-CD62L+ CD8+ T cell


title: hiPSC-CMs treated with ponatinib biol rep 2

description: Library name: Pon_2

value: Ncyte vCardiomyocytes

value: hiPSC-CMs


title: CD8+ T cells, KO3 (p38α-/-p38β-/-), biol rep 3

description:
Library name: Sample 7
L1EJD0303170-KO3


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_JAK2_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorC_bulkRNAseq.csv

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

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

tag: donor ethnicity

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: CD8+ T cells, KO2 (p38α-/-p38β-/-), biol rep 2

description:
Library name: Sample 6
L1EJD0303169-KO2

tag: tissue

tag: cell line

tag: cell type

tag: genotype


title: hiPSC-CMs treated with ponatinib biol rep 1

description: Library name: Pon_1

value: wild type

tag: treatment

value: Ponatinib 1 µM


title: PCa5_NEPC_Lymph node

city: Taipei

first: Pei-Ching

last: Chang

address: No. 155, Sec. 2, Linong Street, Beitou District

department: Institute of Microbiology and Immunology

country: Taiwan

institute: National Yang Ming Chiao Tung University

description:
Library name: PCa5
10x Genomics

data_processing:
Raw sequencing data were processed using Cell Ranger (10x Genomics) and analyzed using Partek Flow software (Partek, Cat. No. 4485102).
Assembly: Homo sapiens Hg38
Supplementary files format and content: Tab-seperated matrix files

source_name: Lymph node

extract_protocol:
Single-cell suspensions with viability greater than 90% were resuspended at a density of 1,000 cells/μL. Approximately 8,000–10,000 cells per sample were encapsulated into individual droplets using the 10x Genomics Chromium Single Cell-A Chip platform. Single-cell RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) following the manufacturer's protocol.
Sequencing was performed on an Illumina NovaSeq 6000 platform, generating 150 bp paired-end reads with a target sequencing depth of ~150 million reads per sample.

value: Lymph node

value: Prostate cancer cell


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_GATA3_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 knockdown of GATA3

tag: donor id

value: No

value: A+

value: ACDA

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

tag: library protocol


title: AF293, rep 4

description: Library name: AF293_4

value: Mycelium (submerged biofilm)


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_GATA3_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorC_bulkRNAseq.csv

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

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

tag: donor ethnicity

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: batch


title: PCa4_CRPC_Prostate

description:
Library name: PCa4
10x Genomics

source_name: Prostate gland

tag: tissue

value: Prostate gland

tag: cell type

value: Prostate cancer cell


title: CD8+ T cells, KO1 (p38α-/-p38β-/-), biol rep 1

description:
Library name: Sample 5
L1EJD0303168-KO1

value: spleen

tag: cell line

value: CD8+ T cell

value: CD44-CD62L+ CD8+ T cell

tag: genotype


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

description:
Library name: Th1Th2_validation_Diff084_DonorC_GATA3_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorC_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

tag: treatment

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

tag: experimental perturbation

value: CRISPRi knockdown of GATA3

tag: donor id

value: No

value: A+

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: CD8+ T cells, WT4 (p38α+/+p38β+/+), biol rep 4

description:
Library name: Sample 4
L1EJD0303167-WT4


title: AF293, rep 3

description: Library name: AF293_3

value: Mycelium (submerged biofilm)


title: PCa3_HSPC_Prostate

description:
Library name: PCa3
10x Genomics


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_ZMYND8_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorB_bulkRNAseq.csv

value: CRISPRi knockdown of ZMYND8

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

value: Male

value: adult stage

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: donor ethnicity

tag: library protocol


title: CD8+ T cells, WT3 (p38α+/+p38β+/+), biol rep 3

description:
Library name: Sample 3
L1EJD0303166-WT3

tag: tissue

value: spleen

tag: cell line

value: CD8+ T cell

tag: cell type

value: CD44-CD62L+ CD8+ T cell

tag: genotype


title: PCa2_CRPC_Adrenal

description:
Library name: PCa2
10x Genomics

source_name: Adrenal

value: Adrenal

value: Prostate cancer cell


title: CD8+ T cells, WT2 (p38α+/+p38β+/+), biol rep 2

description:
Library name: Sample 2
L1EJD0303165-WT2


title: AF293, rep1

description: Library name: AF293_1


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_ZMYND8_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorB_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

tag: treatment

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

tag: experimental perturbation

tag: donor id

value: No

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

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

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: batch


title: RNA, spaceflight, SSCLCs [RNA_sSSCLCs_2]

city: Fuzhou

first: Ying

last: Li

address: No. 2, Xueyuan Road, University Town

institute: Fuzhou University

description:
Library name: RNA_sSSCLCs_2
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: RNA_sSSCLCs_2
spaceflight_submission_H1_TTseq_gene_count_matrix.txt
spaceflight_submission_H1_TTseq_gene_TPM_matrix.csv

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

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

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

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

value: human embryonic stem cell

value: SSCLCs differentiaton under spaceflight environment were subjected to RNA-seq


title: MEF Vps15KO, EBSS2h, rep3

city: Paris

first: Ganna

last: Panasyuk

address: 156-160 Rue Vaugirard, Faculté de Médecine Paris Descartes,, 4th Floor - Lab-408/Office-404,, 4th Floor - Lab-408/Office-404,

country: France

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

description:
Library name: EBSS_pLEX_CRE_3
RNA, MEF Vps15KO, EBSS2h, rep3

data_processing:
Adapter sequences and low-quality reads were filtered with SOAPnuke. Clean reads were obtained with an output read quality of Phred+33.
Clean reads were aligned to the mm10 genome with STAR-2.7.10b and counts generated uing featurecounts. Variance stabilized transformation was used to generate vst normalized count table. Deseq2 and limma were used for differential expression analysis. Direct comparisons were made between treatment conditions. DOSE Gene Set Enrichment Analysis was performed with the DOSE package, in R.
Assembly: mm10
Supplementary files format and content: variance stabilized transformation counts table

source_name: MEF Vps15f/f

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

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

treatment_protocol: MEFs were kept in basal medium or treated with EBSS medium for 2h following 5 days of adeno-GFP/CRE transduction.

value: MEF Vps15f/f

value: mouse embryonic fibroblast

value: EBSS media 2h


title: CD8+ T cells, WT1 (p38α+/+p38β+/+), biol rep 1

description:
Library name: Sample 1
L1EJD0303164-WT1

value: spleen


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_ZMYND8_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorB_bulkRNAseq.csv

value: CRISPRi knockdown of ZMYND8

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: A+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

value: Male

value: adult stage

value: TRUE

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: MEF Vps15KO, EBSS2h, rep2

description:
Library name: EBSS_pLEX_CRE_2
RNA, MEF Vps15KO, EBSS2h, rep2

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: WT_CD8_d4_RatCol2mgmL_003

city: Montreal

first: Judith

last: Mandl

state: QC

address: 3649 Promenade Sir William Osler

country: Canada

institute: McGill University

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

source_name: CD8+ activated T cells

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

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

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

tag: tissue of_origin

value: spleen and LNs

value: CD8+ activated T cells

value: WT

tag: migratory environment

value: RatCol 2 mg/mL


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_TBX21_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorB_bulkRNAseq.csv

tag: tissue

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of TBX21

tag: donor id

value: No

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

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

tag: batch


title: RNA, H1 [RNA_hESCs_XY_2]

description:
Library name: RNA_hESCs_XY_2
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: RNA_hESCs_XY_2
spaceflight_submission_H1_TTseq_gene_count_matrix.txt
spaceflight_submission_H1_TTseq_gene_TPM_matrix.csv

tag: cell line

tag: cell type

value: human embryonic stem cell

value: hESCs (XY) was subjected to RNA-seq


title: MEF Vps15KO, EBSS2h, rep1

description:
Library name: EBSS_pLEX_CRE_1
RNA, MEF Vps15KO, EBSS2h, rep1

value: MEF Vps15f/f

value: mouse embryonic fibroblast

tag: genotype

tag: treatment

value: EBSS media 2h


title: WT_CD8_d4_RatCol2mgmL_002

tag: tissue of_origin

value: spleen and LNs

tag: migratory environment


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_TBX21_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorB_bulkRNAseq.csv

tag: tissue

tag: experimental perturbation

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: A+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

value: Male

value: adult stage

value: TRUE

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: Ribo, spaceflight, SSCLCs [Ribo_sSSCLCs_2]

description:
Library name: Ribo_sSSCLCs_2
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: Ribo_sSSCLCs_2
spaceflight_submission_H1_TTseq_gene_count_matrix.txt
spaceflight_submission_H1_TTseq_gene_TPM_matrix.csv

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

tag: cell line

tag: cell type

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


title: MEF WT, EBSS2h, rep3

description:
Library name: EBSS_pLEX_GFP_3
RNA, MEF WT, EBSS2h, rep3

tag: genotype

value: WT

tag: treatment

tag: batch


title: Ribo, ground, SSCLCs [Ribo_gSSCLCs_2]

description:
Library name: Ribo_gSSCLCs_2
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: Ribo_gSSCLCs_2
spaceflight_submission_H1_TTseq_gene_count_matrix.txt
spaceflight_submission_H1_TTseq_gene_TPM_matrix.csv

value: human embryonic stem cell

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


title: MEF WT, EBSS2h, rep2

description:
Library name: EBSS_pLEX_GFP_2
RNA, MEF WT, EBSS2h, rep2

value: MEF Vps15f/f


title: WT_CD8_d4_RatCol2mgmL_001

tag: tissue of_origin

value: CD8+ activated T cells

tag: migratory environment

value: RatCol 2 mg/mL


title: WT_CD8_d4_Nutragen2mgmL_003

value: spleen and LNs

value: Nutragen 2 mg/mL


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_STYXL1_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorB_bulkRNAseq.csv

tag: tissue

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of STYXL1

tag: donor id

tag: donor age

value: No

value: A+

value: ACDA

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

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


title: Ribo, H1 [Ribo_hESCs_XY_2]

description:
Library name: Ribo_hESCs_XY_2
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: Ribo_hESCs_XY_2
spaceflight_submission_H1_TTseq_gene_count_matrix.txt
spaceflight_submission_H1_TTseq_gene_TPM_matrix.csv

tag: cell line

tag: cell type

value: human embryonic stem cell

value: hESCs (XY) was subjected to ribosome-associated mRNA capture using RiboLace beads


title: MEF WT, EBSS2h, rep1

description:
Library name: EBSS_pLEX_GFP_1
RNA, MEF WT, EBSS2h, rep1

value: MEF Vps15f/f

value: mouse embryonic fibroblast

tag: genotype

value: WT

tag: treatment

value: EBSS media 2h

tag: batch


title: WT_CD8_d4_Nutragen2mgmL_002

tag: tissue of_origin

value: spleen and LNs

value: CD8+ activated T cells

tag: migratory environment

value: Nutragen 2 mg/mL


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_STYXL1_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorB_bulkRNAseq.csv

tag: tissue

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

tag: donor id

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

value: STEMCELL technologies

value: Male

value: adult stage

value: TRUE

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: MEF Vps15KO, basal, rep3

description:
Library name: pLEX_CRE_3
RNA, MEF Vps15KO, basal, rep3

tag: cell line

value: MEF Vps15f/f

tag: cell type

tag: genotype

value: basal media


title: WT_CD8_d4_Nutragen2mgmL_001

tag: tissue of_origin

value: WT


title: WT_CD8_d4_media_003

tag: migratory environment

value: media


title: RNA, spaceflight, PGCLCs [RNA_sPGCLCs_2]

description:
Library name: RNA_sPGCLCs_2
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: RNA_sPGCLCs_2
spaceflight_submission_H9_TTseq_gene_count_matrix.txt
spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv

value: human embryonic stem cell

tag: treatment

value: PGCLCs differentiaton under spaceflight environment were subjected to RNA-seq


title: RNA, ground, FLCs [RNA_gFLCs_2]

description:
Library name: RNA_gFLCs_2
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: RNA_gFLCs_2
spaceflight_submission_H9_TTseq_gene_count_matrix.txt
spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv

value: FLCs differentiaton under ground condition were subjected to RNA-seq


title: MEF Vps15KO, basal, rep2

description:
Library name: pLEX_CRE_2
RNA, MEF Vps15KO, basal, rep2

value: mouse embryonic fibroblast

tag: batch


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_PPP1R7_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorB_bulkRNAseq.csv

tag: tissue

value: blood

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi knockdown of PPP1R7

tag: donor id

tag: donor age

value: No

value: A+

value: ACDA

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

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


title: MEF Vps15KO, basal, rep1

description:
Library name: pLEX_CRE_1
RNA, MEF Vps15KO, basal, rep1

tag: cell line

value: MEF Vps15f/f

tag: cell type

tag: genotype


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_PPP1R7_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorB_bulkRNAseq.csv

tag: treatment

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

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

value: STEMCELL technologies

value: Male

value: adult stage

value: TRUE

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

tag: enriched cell_types

value: Plasmidsaurus RNA-Seq


title: MEF WT, basal, rep3

description:
Library name: pLEX_GFP_3
RNA, MEF WT, basal, rep3

value: mouse embryonic fibroblast

value: WT

value: basal media

tag: batch


title: RNA, H9 [RNA_hESCs_XX_2]

description:
Library name: RNA_hESCs_XX_2
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: RNA_hESCs_XX_2
spaceflight_submission_H9_TTseq_gene_count_matrix.txt
spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv

value: human embryonic stem cell

value: CRISPR-Cas9 edited human ROSA loci VASA-GFP reporter cell line, which was subjected to RNA-seq


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_NTC2_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorB_bulkRNAseq.csv

tag: tissue

value: blood

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi non-targeting control

tag: donor id

tag: donor age

value: No

value: A+

value: ACDA

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

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

tag: donor ethnicity


title: MEF WT, basal, rep2

description:
Library name: pLEX_GFP_2
RNA, MEF WT, basal, rep2

tag: cell line

value: MEF Vps15f/f

tag: cell type

tag: genotype

tag: treatment


title: WT_CD8_d0_naive_003

source_name: CD8+ naive T cells

tag: tissue of_origin

value: spleen and LNs

value: CD8+ naive T cells

tag: migratory environment


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_NTC2_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorB_bulkRNAseq.csv

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

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

value: STEMCELL technologies

value: Male

value: adult stage

value: TRUE

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

tag: batch


title: MEF WT, basal, rep1

description:
Library name: pLEX_GFP_1
RNA, MEF WT, basal, rep1

tag: cell line

tag: cell type

value: mouse embryonic fibroblast

value: WT

value: basal media


title: WT_CD8_d0_naive_002

tag: genotype


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_NTC2_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorB_bulkRNAseq.csv

tag: tissue

value: blood

value: CD4-positive, alpha-beta T cells

tag: treatment

tag: experimental perturbation

value: CRISPRi non-targeting control

tag: donor id

tag: donor age

value: No

value: A+

value: ACDA

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: donor ethnicity

value: Plasmidsaurus RNA-Seq


title: Ribo, spaceflight, PGCLCs [Ribo_sPGCLCs_2]

description:
Library name: Ribo_sPGCLCs_2
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: Ribo_sPGCLCs_2
spaceflight_submission_H9_TTseq_gene_count_matrix.txt
spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv

value: human embryonic stem cell

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


title: Input for MEFs, basal growth, rep1

description: Library name: Input_1

library_source: genomic

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

molecule: genomic DNA

growth_protocol: For ChIP in liver: 4 week old male mice were either ad. lib. fed or 24h fasted prior to sacrifice at ZT14 (2h after lights go off in the animal facility). Livers were flash frozen in liquid nitrogen, powdered, and used for ChIP. For ChIP in MEFs: Cells were grown to 90% confluence in 15cm plates in DMEM High Glucose (4.5g/L) + 10% FBS and used for ChIP.

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

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

value: MEF

value: basal growth media

tag: chip antibody

value: input


title: WT_CD8_d0_naive_001

tag: tissue of_origin

value: spleen and LNs

value: CD8+ naive T cells

tag: migratory environment


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_NTC1_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorB_bulkRNAseq.csv

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

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

value: STEMCELL technologies

value: Male

value: adult 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

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

tag: batch


title: Vps15, MEFs, basal growth, rep2

description:
Library name: ChIP_Vps15_2
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

tag: tissue

tag: cell line

tag: cell type

value: mouse embryonic fibroblast

tag: genotype

value: WT

tag: treatment


title: Ribo, ground, FLCs [Ribo_gFLCs_2]

description:
Library name: Ribo_gFLCs_2
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: Ribo_gFLCs_2
spaceflight_submission_H9_TTseq_gene_count_matrix.txt
spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv

value: human embryonic stem cell

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


title: Ribo, ground, PGCLCs [Ribo_gPGCLCs_2]

description:
Library name: Ribo_gPGCLCs_2
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: Ribo_gPGCLCs_2
spaceflight_submission_H9_TTseq_gene_count_matrix.txt
spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv

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


title: Vps15, MEFs, basal growth, rep1

description:
Library name: ChIP_Vps15_1
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

value: MEF

value: basal growth media

tag: chip antibody


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_NTC1_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorB_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi non-targeting control

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

value: No

value: A+

value: ACDA

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: donor ethnicity

value: Plasmidsaurus RNA-Seq


title: Ribo, H9 [Ribo_hESCs_XX_2]

description:
Library name: Ribo_hESCs_XX_2
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: Ribo_hESCs_XX_2
spaceflight_submission_H9_TTseq_gene_count_matrix.txt
spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv

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


title: RNA Pol II S5P, MEFs, basal growth, rep2

description:
Library name: ChIP_RNA_Pol2_S5P_2
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

tag: tissue

value: RNA Pol II S5P, Abcam ab5408


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

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

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

source_name: visceral adipose tissue

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

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

treatment_protocol: no

value: visceral adipose tissue

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: RNA, spaceflight, SSCLCs [RNA_sSSCLCs_1]

description:
Library name: RNA_sSSCLCs_1
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: RNA_sSSCLCs_1
spaceflight_submission_H1_TTseq_gene_count_matrix.txt
spaceflight_submission_H1_TTseq_gene_TPM_matrix.csv

tag: cell line

tag: cell type

value: human embryonic stem cell

tag: treatment

value: SSCLCs differentiaton under spaceflight environment were subjected to RNA-seq


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

description:
Library name: ChIP_RNA_Pol2_S5P_1
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

value: MEF

value: mouse embryonic fibroblast

tag: genotype

value: WT

value: basal growth media

tag: chip antibody


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


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_NKTR_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorB_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of NKTR

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

tag: anticoagulant

tag: source

value: STEMCELL technologies

tag: donor sex

value: Male

value: adult 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

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

tag: batch


title: Input for RNA Pol II S5P in MEFs -4h+1h methionine condition

description: Library name: Input_-4h_+1h_methionine_20

tag: tissue

tag: cell line

value: MEF

tag: cell type

value: mouse embryonic fibroblast

tag: genotype

tag: treatment

value: (-4h+1h) methionine condition

tag: chip antibody

value: input


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_NKTR_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorB_bulkRNAseq.csv

value: blood

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: A+

value: ACDA

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: donor ethnicity

value: Plasmidsaurus RNA-Seq


title: RNA, H1 [RNA_hESCs_XY_1]

description:
Library name: RNA_hESCs_XY_1
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: RNA_hESCs_XY_1
spaceflight_submission_H1_TTseq_gene_count_matrix.txt
spaceflight_submission_H1_TTseq_gene_TPM_matrix.csv

value: human embryonic stem cell

value: hESCs (XY) was subjected to RNA-seq


title: Input for RNA Pol II S5P in MEFs -4h methionine condition

description: Library name: Input_-4h_methionine_9

tag: tissue

value: WT

value: (-4h) methionine condition


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

value: visceral adipose tissue

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_MAMLD1_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorB_bulkRNAseq.csv

tag: cell type

tag: treatment

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

tag: experimental perturbation

value: CRISPRi knockdown of MAMLD1

value: No

tag: donor blood_type

tag: anticoagulant

tag: source

value: STEMCELL technologies

tag: donor sex

value: Male

value: adult 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

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

tag: batch


title: Ribo, spaceflight, SSCLCs [Ribo_sSSCLCs_1]

description:
Library name: Ribo_sSSCLCs_1
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: Ribo_sSSCLCs_1
spaceflight_submission_H1_TTseq_gene_count_matrix.txt
spaceflight_submission_H1_TTseq_gene_TPM_matrix.csv

tag: cell line

value: human embryonic stem cell

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


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

tag: tissue

value: visceral adipose tissue

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age


title: RNA, ground, SSCLCs [RNA_gSSCLCs_1]

description:
Library name: RNA_gSSCLCs_1
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: RNA_gSSCLCs_1
spaceflight_submission_H1_TTseq_gene_count_matrix.txt
spaceflight_submission_H1_TTseq_gene_TPM_matrix.csv

tag: cell type

tag: treatment

value: SSCLCs differentiaton under ground condition were subjected to RNA-seq


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_MAMLD1_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorB_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of MAMLD1

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: A+

value: ACDA

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: donor ethnicity

value: Plasmidsaurus RNA-Seq


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

tag: tissue

tag: strain

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: Ribo, ground, SSCLCs [Ribo_gSSCLCs_1]

description:
Library name: Ribo_gSSCLCs_1
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: Ribo_gSSCLCs_1
spaceflight_submission_H1_TTseq_gene_count_matrix.txt
spaceflight_submission_H1_TTseq_gene_TPM_matrix.csv

tag: cell line

tag: cell type

tag: treatment

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


title: RNA Pol II S5P, MEFs, -4h+1h methionine, rep3

description:
Library name: ChIP_RNA_Pol2_S5P_-4h+1h_methionine_3
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

value: MEF

value: mouse embryonic fibroblast

tag: genotype

value: WT

value: (-4h+1h) methionine condition

tag: chip antibody

value: RNA Pol II S5P, Abcam ab5408


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

value: visceral adipose tissue

value: TallyHo/JngJ

tag: Sex

value: male

tag: age


title: AF293∆uge3, rep1

description: Library name: AF293_duge3_1

value: Mycelium (submerged biofilm)


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_MAMLD1_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorB_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

tag: anticoagulant

tag: source

value: STEMCELL technologies

tag: donor sex

value: Male

value: adult 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

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

tag: batch


title: AF293, rep 2

description: Library name: AF293_2

tag: tissue

tag: genotype


title: RNA Pol II S5P, MEFs, -4h+1h methionine, rep2

description:
Library name: ChIP_RNA_Pol2_S5P_-4h+1h_methionine_2
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

tag: cell line

value: MEF

tag: cell type

value: mouse embryonic fibroblast

value: WT

tag: treatment

value: (-4h+1h) methionine condition

tag: chip antibody

value: RNA Pol II S5P, Abcam ab5408


title: Ribo, H1 [Ribo_hESCs_XY_1]

description:
Library name: Ribo_hESCs_XY_1
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: Ribo_hESCs_XY_1
spaceflight_submission_H1_TTseq_gene_count_matrix.txt
spaceflight_submission_H1_TTseq_gene_TPM_matrix.csv

value: human embryonic stem cell

value: hESCs (XY) was subjected to ribosome-associated mRNA capture using RiboLace beads


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

value: visceral adipose tissue

tag: strain

value: TallyHo/JngJ

tag: Sex

value: female

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition

value: high body weight at weaning


title: RNA, ground, SSCLCs [RNA_gSSCLCs_2]

description:
Library name: RNA_gSSCLCs_2
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: RNA_gSSCLCs_2
spaceflight_submission_H1_TTseq_gene_count_matrix.txt
spaceflight_submission_H1_TTseq_gene_TPM_matrix.csv

value: SSCLCs differentiaton under ground condition were subjected to RNA-seq


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_JAK2_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorB_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of JAK2

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Male

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

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: donor ethnicity

value: Plasmidsaurus RNA-Seq


title: RNA Pol II S5P, MEFs, -4h+1h methionine, rep1

description:
Library name: ChIP_RNA_Pol2_S5P_-4h+1h_methionine_1
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

tag: tissue

tag: cell line

value: MEF

tag: cell type

value: mouse embryonic fibroblast

tag: genotype

value: WT

tag: treatment

value: (-4h+1h) methionine condition

tag: chip antibody

value: RNA Pol II S5P, Abcam ab5408


title: RNA, spaceflight, FLCs [RNA_sFLCs_1]

description:
Library name: RNA_sFLCs_1
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: RNA_sFLCs_1
spaceflight_submission_H9_TTseq_gene_count_matrix.txt
spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv

value: human embryonic stem cell

value: FLCs differentiaton under spaceflight environment were subjected to RNA-seq


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_TBX21_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorB_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of TBX21

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

value: A+

tag: suspension depletion_factors

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

tag: batch


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

tag: tissue

value: visceral adipose tissue

tag: strain

value: TallyHo/JngJ

tag: Sex

value: female

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition

value: high body weight at weaning


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_JAK2_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorB_bulkRNAseq.csv

tag: cell type

tag: treatment

tag: experimental perturbation

value: CRISPRi knockdown of JAK2

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Male

tag: donor dev_stage

value: adult stage

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: donor ethnicity

value: Plasmidsaurus RNA-Seq


title: Input for RNA Pol II S5P in MEFs basal methionine condition

description: Library name: Input_basal_1

tag: tissue

tag: cell line

value: MEF

value: mouse embryonic fibroblast

tag: genotype

value: WT

value: basal methionine condition

tag: chip antibody

value: input


title: RNA, spaceflight, PGCLCs [RNA_sPGCLCs_1]

description:
Library name: RNA_sPGCLCs_1
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: RNA_sPGCLCs_1
spaceflight_submission_H9_TTseq_gene_count_matrix.txt
spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv

tag: cell type

value: human embryonic stem cell

value: PGCLCs differentiaton under spaceflight environment were subjected to RNA-seq


title: RNA Pol II S5P, MEFs, -4h methionine, rep3

description:
Library name: ChIP_RNA_Pol2_S5P_-4h_methionine_3
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

tag: treatment

value: (-4h) methionine condition

value: RNA Pol II S5P, Abcam ab5408


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_STYXL1_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorB_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of STYXL1

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

value: A+

value: ACDA

value: STEMCELL technologies

tag: suspension depletion_factors

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

tag: batch


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

tag: tissue

value: visceral adipose tissue

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_JAK2_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorB_bulkRNAseq.csv

tag: cell type

tag: treatment

tag: experimental perturbation

value: CRISPRi knockdown of JAK2

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

value: Male

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor 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: donor ethnicity

value: Plasmidsaurus RNA-Seq


title: RNA, spaceflight, FLCs [RNA_sFLCs_2]

description:
Library name: RNA_sFLCs_2
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: RNA_sFLCs_2
spaceflight_submission_H9_TTseq_gene_count_matrix.txt
spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv

tag: cell line

value: human embryonic stem cell

value: FLCs differentiaton under spaceflight environment were subjected to RNA-seq


title: RNA, ground, FLCs [RNA_gFLCs_1]

description:
Library name: RNA_gFLCs_1
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: RNA_gFLCs_1
spaceflight_submission_H9_TTseq_gene_count_matrix.txt
spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv

value: FLCs differentiaton under ground condition were subjected to RNA-seq


title: RNA Pol II S5P, MEFs, -4h methionine, rep2

description:
Library name: ChIP_RNA_Pol2_S5P_-4h_methionine_2
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

tag: tissue

value: MEF

value: mouse embryonic fibroblast

tag: genotype

value: WT

value: (-4h) methionine condition

tag: chip antibody

value: RNA Pol II S5P, Abcam ab5408


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

value: visceral adipose tissue

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_GATA3_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorB_bulkRNAseq.csv

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: treatment

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

tag: experimental perturbation

value: CRISPRi knockdown of GATA3

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

value: Male

value: adult stage

value: TRUE

value: Normal

tag: suspension depletion_factors

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

tag: batch


title: RNA, ground, PGCLCs [RNA_gPGCLCs_1]

description:
Library name: RNA_gPGCLCs_1
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: RNA_gPGCLCs_1
spaceflight_submission_H9_TTseq_gene_count_matrix.txt
spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv

tag: cell line

value: human embryonic stem cell

value: PGCLCs differentiaton under ground condition were subjected to RNA-seq


title: RNA Pol II S5P, MEFs, -4h methionine, rep1

description:
Library name: ChIP_RNA_Pol2_S5P_-4h_methionine_1
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

tag: tissue

value: MEF

tag: cell type

value: mouse embryonic fibroblast

tag: genotype

value: WT

value: (-4h) methionine condition

tag: chip antibody

value: RNA Pol II S5P, Abcam ab5408


title: high blood glucose, high body weight at weaning, male, visceral adipose tissue, replicate 4

value: visceral adipose tissue

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: WT_CD8_d4_media_001

tag: tissue of_origin

value: spleen and LNs

value: CD8+ activated T cells

tag: migratory environment

value: media


title: RNA, ground, PGCLCs [RNA_gPGCLCs_2]

description:
Library name: RNA_gPGCLCs_2
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: RNA_gPGCLCs_2
spaceflight_submission_H9_TTseq_gene_count_matrix.txt
spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv

tag: treatment


title: RNA Pol II S5P, MEFs, basal methionine, rep3

description:
Library name: ChIP_RNA_Pol2_S5P_Basal_3
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

value: basal methionine condition


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


title: RNA, H9 [RNA_hESCs_XX_1]

description:
Library name: RNA_hESCs_XX_1
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: RNA_hESCs_XX_1
spaceflight_submission_H9_TTseq_gene_count_matrix.txt
spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv

value: CRISPR-Cas9 edited human ROSA loci VASA-GFP reporter cell line, which was subjected to RNA-seq


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_GATA3_Th1
Th1 polarized
Th1Th2_validation_Diff084_Th1_DonorB_bulkRNAseq.csv

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

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+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Male

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

tag: donor ethnicity

value: Caucasian

tag: genetic perturbation_strategy

value: CRISPRi

value: Plasmidsaurus RNA-Seq


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_GATA3_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorB_bulkRNAseq.csv

tag: tissue

value: blood

tag: cell type

tag: treatment

tag: experimental perturbation

tag: donor id

tag: enriched cell_types

tag: library protocol

tag: batch


title: Ribo, spaceflight, FLCs [Ribo_sFLCs_1]

description:
Library name: Ribo_sFLCs_1
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: Ribo_sFLCs_1
spaceflight_submission_H9_TTseq_gene_count_matrix.txt
spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv

tag: cell line

value: human embryonic stem cell

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


title: RNA Pol II S5P, MEFs, basal methionine, rep2

description:
Library name: ChIP_RNA_Pol2_S5P_Basal_2
bigwigs have blacklisted regions removed, duplicates removed, filtered to have read scores above 40, and are csaw composition bias normalized within each ChIPd factor.

value: MEF

value: mouse embryonic fibroblast

tag: genotype

value: WT

value: basal methionine condition

tag: chip antibody

value: RNA Pol II S5P, Abcam ab5408


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

value: visceral adipose tissue

tag: strain

value: TallyHo/JngJ

tag: Sex

value: male

tag: age

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: Ribo, spaceflight, FLCs [Ribo_sFLCs_2]

description:
Library name: Ribo_sFLCs_2
Column name in spaceflight_submission_H9_TTseq_gene_count_matrix.txt and spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv: Ribo_sFLCs_2
spaceflight_submission_H9_TTseq_gene_count_matrix.txt
spaceflight_submission_H9_TTseq_gene_TPM_matrix.csv


title: SD_wk16_B_R2

description: Library name: 8378

value: Liver

tag: housing temperature

value: TN

tag: timepoint (duration_on_diet)

value: C57BL/6J, Male

value: GAN diet