title: induced astrocyte, shCtrl_3

city: Guangzhou

first: Lu

last: Yang

state: Guangdong

address: No.600 Tianhe Road, Tianhe District, Guangzhou, China

country: China

institute: The Third Affiliated Hospital of Sun Yat sen University

description:
Library name: SAMPLE 6
coloum name in raw-count.txt: shCtrl-2

data_processing:
High-throughput RNA sequencing (RNA-seq) was performed using the Illumina HiSeq 2500 platform (Illumina, San Diego, CA) at CapitalBio (Beijing, China). Raw sequencing data were aligned to the human reference genome (GRCh38). Differentially expressed genes (DEGs) between CLCN2 knockdown and control iASTs, with triplicate biological replicates for each group, were analyzed based on gene fold change on a log2 fold change scale.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: astrocytes defferentiated from induced pluripotent stemm cells

growth_protocol: Induced astrocytes were cultured in TEMdiff™ Astrocyte Maturation Medium with 5% CO2 in 37℃

extract_protocol:
RNA was harvested by TRIZOL and was isolated using the RecoverAll Total Nucleic Acid Isolation kit
RNA libraries for RNA-seg were prepared by CapitalBio (Beijing, China)

treatment_protocol: normal induced astrocytes were transduced with Lenti-shCLCN2 or Lenti-shCtrl, and RNA was extracted 5 days after transfection.

tag: cell line

tag: cell type

value: differentiated astrocytes

value: WT

value: tranfection with lentivirus-shCtrl


title: conservative treatment peripheral blood mononuclear cells 2

status: Public on Jun 02 2026

type: other

city: Valencia

first: Angela

middle: L.

last: Riffo-Campos

state: Valencia

address: Avda. Blasco Ibáñes, 17

department: Department of Biochemistry and Molecular Biology

country: Spain

institute: University of Valencia, and INCLIVA

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

scan_protocol: Standard Illumina Protocol

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

label: Cy3 and Cy5

molecule: other

organism: Homo sapiens

source_name: blood mononuclear cells

label_protocol: Standard Illumina Protocol

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

tag: tissue

value: blood mononuclear cells

tag: genotype

value: Final

tag: treatment

value: conservative treatment


title: AWO organoid scRNA, G90

type: SRA

first: junjie

last: lv

address: haizhu

institute: GZLAB

description: Library name: sample awo 3

library_source: transcriptomic single cell

data_processing:
Raw sequencing data was processed with the DNBelabTM C Series Single-cell RNA Analysis Report V2.1.1 (hAWOs). Reads were mapped to the GRCh38 genome for hAWOs (25,926 cells; 77,778 reads) . Low-quality cells were excluded based on a cutoff of fewer than 500 genes or 1000 UMIs. Doublets were predicted using DoubletFinder (v2.0.4)7, DoubletDetection (v4.2)8, scDblFinder (v1.18.0)9, and Scrublet (v0.2.3)10, and cells flagged by at least two methods were excluded. Gruffi (v1.5.5)11 was used to remove stressed cells of organoids with default parameters. All statistical analysis for violin charts and box charts is performed using 'wilcox.test (alternative=" two-sided ")' in the R package "stats".
Assembly: Human hg38
Supplementary files format and content: gene expression matrices of 10X format

molecule: polyA RNA

source_name: human lung organoid

extract_protocol:
Lung organoids cultured under different stiffness conditions for 49 days were dissociated into single-cell suspensions using TrypLE (Thermo Fisher, Cat#12605028). The suspensions were passed through a 70 µm cell strainer (BD Falcon, Cat#352235) into FACS tubes, ensuring a single-cell yield of over 90%. For hAWOs, epithelial cell-positive populations were pre-sorted using a flow cytometer, following previously described methods. Cell viability and concentration were assessed using Trypan Blue Stain (Invitrogen, Cat#15250061) with the Countess™ 3 Automated Cell Counter (Life Technologies). Final cell concentrations were adjusted to 1000 cells/µL with a viability of ≥80%.
hAWOs were sequenced on the C4 platform by Geneplus Gene Technology. Single-cell suspensions were processed using the DNBelabTM C Series High-throughput scRNA Library Kit (MGI, Cat#940-001818-00). Libraries were constructed following the manufacturer’s instructions, including cDNA synthesis, size selection, end repair, A-tailing, adapter ligation, index library amplification (PCR), and library circularization of the sequencing library to build a library of 3' transcripts. Purification and quantification was performed using the Qubit ssDNA Assay Kit (Thermo Fisher) and Qsep100 (Bioptic). Sequencing was conducted on the DNBelabTM C4/TaiM4 platform with paired-end reads on a DNBSEQ-T7 sequencer.

value: human lung organoid


title: PoA, PNOC neuron ribosome IP RNA, rep3

city: Leipzig

first: Alexander

last: Jais

address: Philipp-Rosenthal-Straße 27

country: Germany

institute: Helmholtz Institute for Metabolic, Obesity, and Vascular Research (HI-MAG)

description: Library name: PoA_IP3

library_source: transcriptomic

data_processing:
Raw sequencing reads were adapter- and quality-trimmed, aligned to the mouse reference genome (mm39) using HISAT2, and quantified at the gene level with featureCounts. Gene expression was normalized and differential expression was analyzed using DESeq2.
Assembly: The mouse reference genome build mm39 (UCSC) was used for read alignment and downstream analysis.

molecule: total RNA

organism: Mus musculus

source_name: Preoptic area (POA) of hypothalamus, mouse brain

extract_protocol:
POA tissue was microdissected from NuTRAP::Pnoc-Cre mice, homogenized in lysis buffer, and EGFP-tagged ribosomes were affinity-purified overnight at 4°C using anti-GFP antibody-coupled magnetic beads. After washing, ribosome-bound RNA was extracted using the RNeasy Micro Kit, quality-checked, and used for Illumina library preparation and sequencing.
Poly(A)+ mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and reverse transcribed. cDNA was end-repaired, A-tailed, ligated to Illumina adapters, PCR-amplified, and quality-checked by Bioanalyzer and Qubit before paired-end sequencing on an Illumina NovaSeq X Plus platform.

treatment_protocol: POA tissue from NuTRAP::Pnoc-Cre mice


title: induced astrocyte, shCtrl_2

description:
Library name: SAMPLE 5
coloum name in raw-count.txt: shCtrl-2

value: astrocytes defferentiated from induced pluripotent stemm cells


title: PoA, PNOC neuron ribosome IP RNA, rep2

description: Library name: PoA_IP2

value: Preoptic area (POA) of hypothalamus, mouse brain


title: conservative treatment peripheral blood mononuclear cells 1

value: Basal


title: induced astrocyte, shCtrl_1

description:
Library name: SAMPLE 4
coloum name in raw-count.txt: shCtrl-1


title: AWO organoid scRNA, G60

description: Library name: sample awo 2


title: AWO organoid scRNA, G30

description: Library name: sample awo 1


title: peritoneal dialysis peripheral blood mononuclear cells 1

value: peritoneal dialysis


title: PoA, PNOC neuron ribosome IP RNA, rep1

description: Library name: PoA_IP1


title: induced astrocyte, shCLCN2_3

description:
Library name: SAMPLE 3
coloum name in raw-count.txt: shCLCN2-3

value: CLCN2 knockdown

value: tranfection with lentivirus-shCLCN2


title: induced astrocyte, shCLCN2_2

description:
Library name: SAMPLE 2
coloum name in raw-count.txt: shCLCN2-2


title: hemodialysis peripheral blood mononuclear cells 2

value: hemodialysis


title: PoA bulk tissue, input RNA, rep3

description: Library name: PoA_Input3


title: PoA bulk tissue, input RNA, rep2

description: Library name: PoA_Input2


title: hemodialysis peripheral blood mononuclear cells 1


title: induced astrocyte, shCLCN2_1

description:
Library name: SAMPLE 1
coloum name in raw-count.txt: shCLCN2-1


title: PoA bulk tissue, input RNA, rep1

description: Library name: PoA_Input1


title: ALV organoid scRNA, G90

description: Library name: sample alv 3

data_processing:
Raw sequencing data was processed with CellRanger v8.0.0 (hALOs) using default parameters. Reads were mapped to the GRCh38 genome for hALOs (8,132 cells; 407,789 reads). Low-quality cells were excluded based on a cutoff of fewer than 500 genes or 1000 UMIs. Doublets were predicted using DoubletFinder (v2.0.4)7, DoubletDetection (v4.2)8, scDblFinder (v1.18.0)9, and Scrublet (v0.2.3)10, and cells flagged by at least two methods were excluded. Gruffi (v1.5.5)11 was used to remove stressed cells of organoids with default parameters. All statistical analysis for violin charts and box charts is performed using 'wilcox.test (alternative=" two-sided ")' in the R package "stats".
Assembly: Human hg38
Supplementary files format and content: gene expression matrices of 10X format

extract_protocol:
Lung organoids cultured under different stiffness conditions for 49 days were dissociated into single-cell suspensions using TrypLE (Thermo Fisher, Cat#12605028). The suspensions were passed through a 70 µm cell strainer (BD Falcon, Cat#352235) into FACS tubes, ensuring a single-cell yield of over 90%. Cell viability and concentration were assessed using Trypan Blue Stain (Invitrogen, Cat#15250061) with the Countess™ 3 Automated Cell Counter (Life Technologies). Final cell concentrations were adjusted to 1000 cells/µL with a viability of ≥80%.
hALOs were sequenced on the 10x Genomics platform by Annoroad Gene Technology. Single-cell suspensions were combined with Gel Beads and oil droplets in separate channels of Chromium Chip G (10x Genomics, Cat#1000121) to generate Gel Bead-In-Emulsions (GEMs) via microfluidics. Following the manufacturer’s protocol, mRNA was reverse-transcribed into complementary DNA (cDNA) and subsequently amplified into double-stranded cDNA. A-tailing was performed, followed by ligation of sequencing adapters, including the Read2 primer. The resulting libraries incorporated P5 and P7 adapters and dual indices, enabling compatibility with Illumina sequencing platforms. The quality-controlled libraries were sequenced on an Illumina platform by Annoroad Gene Technology, ensuring high-quality data acquisition for downstream analysis.


title: ALV organoid scRNA, G30

description: Library name: sample alv 1


title: MetR_overexpression_rep3

status: Public on Jun 01 2026

type: RNA

city: Hachioji

first: Atsushi

last: Kouzuma

state: Tokyo

address: 1432-1 Horinouchi

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

description: Gene expression in MR-1(pBBR-SOmetR) grown under TMAO-reducing conditions

hyb_protocol: For each array, 19 µL of the purified Cy3-labeled cRNA (600 ng) was mixed with 5 µL of 10× Blocking Agent, 1 µL of 25× Fragmentation Buffer, and 25 µL of 2× GE Hybridization Buffer HI-RPM. The resultant mixtures were hybridized to the arrays at 65ºC for 17 h. After hybridization, each microarray slide was washed with Gene Expression wash buffer 1 at room temperature for 1 min, followed by Gene Expression wash buffer 2 at 37ºC for 1min.

scan_protocol: Slides were air dried for 1 min and scanned using an Agilent DNA Microarray Scanner at 5-µm resolution.

data_processing: Gene expression data (fluorescent intensities) were extracted from the scanned image using the Feature Extraction Software version 8.1 (Agilent Technologies) and normalized and statistically analyzed using the limma software package (version 3.36.2; https://www.bioconductor.org/packages/release/bioc/html/limma.html)

organism: Shewanella oneidensis

source_name: MR-1(pBBR-SOmetR), replicate 3

label_protocol: Cyanine3 (Cy3)-labeled cRNA was synthesized from 50 ng of total RNA using the Low Input Quick Amp WT Labeling Kit (Agilent Technologies) and purified using a RNeasy Mini Kit (Qiagen). The labeled cRNA was quantified using NanoDrop ND-1000 Spectrophotometer (Thermo Scientific).

growth_protocol: Shewanella oneidensis strains were grown in lactate minimal medium under anaerobic TMAO-reducing conditions, and cells  cells were harvested at the logarithmic growth phase.

extract_protocol: Total RNA was extracted using a TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. The extracted RNA was purified using an RNeasy Mini kit and RNase-Free DNase set (Qiagen, Valencia, CA, USA). The quality of purified RNA was evaluated using an Agilent 2100 Bioanalyzer, RNA 6000 Pico reagents, and RNA Pico chips (Agilent Technologies, Inc., Santa Clara, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: The cultures were centrifuged at 13,000 rpm for 1 min to precipitate bacterial cells.

tag: strain


title: MetR_overexpression_rep4

source_name: MR-1(pBBR-SOmetR), replicate 4


title: MetR_overexpression_rep1

source_name: MR-1(pBBR-SOmetR), replicate 1


title: Vector_control_rep4

description: Gene expression in MR-1(pBBR1MCS-5) grown under TMAO-reducing conditions

source_name: MR-1(pBBR1MCS-5), replicate 4


title: Met_supplemented_LMM_rep3

description: Gene expression in MR-1 grown in methionine-supplemented medium

organism: Shewanella oneidensis MR-1

growth_protocol: Shewanella oneidensis MR-1 was cultured in lactate minimal medium with or without the addition of 130 µM methionine, and cells  cells were harvested at the logarithmic growth phase.

tag: medium

value: Methionine-supplemented lactate minimal medium


title: Vector_control_rep2

source_name: MR-1(pBBR1MCS-5), replicate 2


title: Vector_control_rep1

source_name: MR-1(pBBR1MCS-5), replicate 1


title: Vector_control_rep3

source_name: MR-1(pBBR1MCS-5), replicate 3


title: Met_free_LMM_rep2

description: Gene expression in MR-1 grown in methionine-free medium

source_name: MR-1 grown in methionine-free medium

value: Lactate minimal medium


title: Met_supplemented_LMM_rep1

source_name: MR-1 grown in methionine-supplemented medium


title: GNS166_5_n4

city: Donostia

first: Estefania

last: Carrasco-Garcia

state: Guipúzcoa

address: Dr. Begiritsain s/n

department: Oncology

institute: Biodonostia

description:
Library name: Sample 8
n9

data_processing:
This project uses the filtering software SOAPnuke developed by BGI independently for filtering.
Data filtering steps: (1) Remove the reads containing the adaptor(adaptor pollution);  (2) Remove reads whose N content is greater than 5%;  (3) Remove low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).
The filtered "Clean Reads" are saved in FASTQ format. Version v1.5.2. Parameters -l 15 -q 0.2 -n 0.05
Bowtie2 was used to map the clean reads to the reference gene sequence. Version：v2.2.5. Parameters：-q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
RSEM was used to calculate the gene expression level of each sample. Version：v1.2.8. Parameters：-p 8 --forward-prob 0 --paired-end
Assembly: GRCh38.p13
Supplementary files format and content: Normalized and raw counts of all 8 samples
Supplementary files format and content: excel document (xlsx) and csv

source_name: Treated

growth_protocol: Patient-derived glioma stem cell lines (GNS166) were kindly provided by Dr. Steve Pollard and cultured in adhesion in DMEM/F12 media (Gibco) supplemented with 100 U/mL penicillin and streptomycin, 2 mM of L-Glutamine, 1 % N2 (Gibco), 2 % B27 (Gibco), 1.34 % D-(+)-Glucose solution 45 % (Sigma-Aldrich), 20 ng/mL basic Fibroblast Growth Factor (bFGF, Gibco) and 20 ng/mL epidermal growth factor (EGF, Sigma-Aldrich).

extract_protocol:
Total RNA was isolated using trizol (Life Technologies, Carlsbad, CA, USA).
1) mRNA enrichment and purification: Oligo dT Selection (mRNA enrichment): Use oligo dT beads to enrich mRNA with poly A tail. 2) RNA fragment and reverse transcription Fragment the RNA and first-strand cDNA was generated using random N6-primed reverse transcription, followed by a second-strand cDNA synthesis with dUTP instead of dTTP. 3) End repair, add A and adaptor ligation The synthesized cDNA was subjected to end-repair and then was 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 4) PCR amplification. Prior to PCR amplification, the dUTP-marked strand is selectively degraded by Uracil-DNA-Glycosylase(UDG). The remaining strand is amplified to generate a cDNA library suitable for sequencing. Many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer; 5) Single strand separation and cyclization Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase; 6) DNA nanoball synthesis 7) Sequencing on DNBSEQ (DNBSEQ Technology) platform

treatment_protocol: GNS166 cells were cultured with 5 µM of MTP150 for 48 h, and pellets were then taken for RNAseq

value: GNS166 treated with MTP150 (5μM)


title: Met_supplemented_LMM_rep2


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

city: Palo Alto

first: Lattice

last: Data Coordination

state: CA

address: 3165 Porter Drive

department: Genetics

country: USA

institute: Stanford University

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim8hr_Rep2_HEXDC
Tact_cluster_validation_Diff092_Stim8hr_Rep2_bulkRNAseq.csv

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

source_name: blood

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

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

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

value: blood

value: CD4-positive, alpha-beta T cells

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

tag: experimental perturbation

value: CRISPRi knockdown of HEXDC

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: O+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

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

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: NK-92 cells, shscramble-1

status: Public on Jun 03 2026

first: Rukang

last: Liang

address: Shipai Street, Tianhe district

department: Biotherapy Center

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

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

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

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

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

tag: cell line

tag: treatment

value: shscramble


title: GNS166_0_n4

description:
Library name: Sample 7
n9

source_name: Control

value: GNS166 Control


title: GNS166_5_n3

description:
Library name: Sample 6
n8

value: GNS166 treated with MTP150 (5μM)


title: Met_free_LMM_rep3

tag: medium

value: Lactate minimal medium


title: GNS166_5_n2

description:
Library name: Sample 4
n7


title: Met_free_LMM_rep1


title: GNS166_5_n1

description:
Library name: Sample 2
n6


title: GNS166_0_n1

description:
Library name: Sample 1
n6


title: Nuclear DDX6 Input replicate A

city: Singapore

first: jinghe

last: xie

address: 21 Lower Kent Ridge Road

country: Singapore

institute: nuh

data_processing:
Read alignment using STAR
Read counting using featureCounts
Differential gene enrichment analysis using R DESeq2
Assembly: hg19
Supplementary files format and content: Raw gene count matrix of all samples

molecule: nuclear RNA

extract_protocol:
To conduct RIP assays in the nuclear or cytoplasmic fractions, cells were fractionated using the Nuclear Extract Kit (Active Motif, 40010), according to manufacturer’s protocol. After which, DDX6 IP was performed using 500~750µg protein from each fraction, with 5% of lysates set aside as RNA and protein input samples. To ensure IP conditions largely identical across both fractions, the nuclear fraction was supplemented with the cytoplasmic lysis buffer and vice versa, before topping up with 2× RIP lysis buffer in a 1:1 ratio. Next, lysates were supplemented with 1µg of anti-DDX6 antibody or rabbit IgG isotype control, followed by incubation at 4°C on a rotating platform for 4 hours. Subsequently, 30µL of DynabeadsTM Protein A magnetic beads was added into the lysates (Invitrogen, 10002D), followed by incubation at 4°C overnight on a rotating platform. Next, beads were washed thrice in pre-chilled wash buffer (50mM Tris-HCl pH 7.5, 150mM NaCl, 1× cOmplete protease inhibitor cocktail and 0.2U/µL SUPERase InTM RNase inhibitor) for 10 mins each at 4°C on a rotating platform. RNA was eluted in 500µL RLT buffer (Qiagen, 79216) for 20 mins at RT on a rotating platform. The eluted RNA was purified by the RNeasy Mini Kit, according to manufacturer’s instructions.
Input and eluted RNA from both nuclear and cytoplasmic fractions were reverse transcribed using random hexamers from Advantage® RT-for-PCR Kit.

tag: cell type

value: human esophageal squamous carcinoma cells

tag: genotype

value: WT

value: No treatment


title: Nuclear IgG replicate B

description:
Antibody: IgG
Nuclear_IgG_B


title: Nuclear IgG replicate A

description:
Antibody: IgG
Nuclear_IgG_A


title: Nuclear DDX6 Input replicate B


title: Nuclear DDX6 IP replicate B

description:
Antibody: Anti-DDX6
Nuclear_DDX6_B


title: Cytosolic DDX6 Input replicate B

molecule: cytoplasmic RNA


title: Cytosolic IgG replicate B

description:
Antibody: IgG
Cyto_IgG_B


title: Nuclear DDX6 IP replicate A

description:
Antibody: Anti-DDX6
Nuclear_DDX6_A


title: Cytosolic DDX6 IP replicate A

description:
Antibody: Anti-DDX6
Cyto_DDX6_A


title: 2xCRC, 3xGBM, 2xHCC, 1xHD, 3xHNSCC

city: Rostock

first: Brigitte

last: Müller-Hilke

address: Schillingallee 70

department: Core Facility for Cell Sorting and Cell Analysis

institute: Rostock University Medical Center

description: Library name: WTA7

data_processing:
BD Rhapsody™ Sequence Analysis Pipeline 2.2.1
Assembly: GRCh38
Supplementary files format and content: Counts per Cell in h5ad- and MatrixMarket formats.

source_name: PBMC

extract_protocol:
RNA was harvested using the single-cell capture and cDNA synthesis protocol on the BD Rhapsody Single-Cell Analysis System according to the manufacturer's protocol.
RNA libraries for scRNA-seq were prepared using the Library Preparation Protocol for mRNA Whole Transcriptome Analysis and Sample Tag using the BD Rhapsody System according to the manufacturer's instructions.

value: PBMC

value: Spike C7


title: 1xCRC, 2xGBM, 3xHCC, 2xHD, 3xHNSCC

description: Library name: WTA6

value: Spike C6


title: 5xCRC, 1xGBM, 1xHCC, 2xHD, 2xHNSCC

description: Library name: WTA3

value: Spike C3


title: 4xCRC, 1xGBM, 2xHCC, 2xHD, 2xHNSCC

description: Library name: WTA2

value: Spike C2


title: PBMCs, Male, GW, rep1

city: Wageningen

first: Benthe

last: van der Lugt

address: Akkermaalsbos 2

country: Netherlands

institute: Wageningen University & Research

description: Library name: GW_M_1

data_processing:
The RNAseq reads were used to quantify transcript abundances. To this end, the tool Cutadapt (version 1.16) was used to trim adapters from the reads and HISAT2 (version 2.2.1) was used to map the reads to the GRCh38.p13 (release 42)human genome assembly-based transcriptome sequences as annotated by the GENCODE consortium. HISAT2 (version 2.2.1.) output was converted and sorted by chromosomal position using Samtools (version 1.9). RSeQC (v3.0.1) and PRINSEQ (v0.20.4) were used for quality control. HTSeq (version 0.11.2) was used to count reads in transcripts using gene-level quantification. Differential gene expression was determined using the package limma (version 3.50.3) utilizing the obtained scaled gene-level counts. Briefly, before statistical analyses, non-specific filtering of the count table was performed to increase detection power, based on the requirement that a gene should have an expression level greater than around 10 counts in at least three samples. Differences in library size were adjusted by the trimmed mean of M-values normalization method, implemented in the package edgeR (version 3.36.0).
Assembly: GRCh38.p13
Supplementary files format and content: Text file including the normalized counts for each sample.

source_name: male

growth_protocol: PBMCs were isolated from buffy coats obtained from anonymous male and female healthy donors purchased from the Niguarda Hospital (Milan, Italy). PBMCs were isolated by Ficoll gradient centrifugation and subsequently washed five times with PBS. For the experiments, PBMCs were suspended in RPMI 1640 without phenol red containing 2 mM L-glutamine, 100 IU/mL penicillin, 0.1 mg/mL streptomycin, 10 µg/mL gentamycin, 50 µM 2-mercaptoethanol, supplemented with 5% of heat-inactivated human serum (hereafter referred to as complete medium). The aforementioned cell culture medium, serum and all supplements were purchased from Sigma-Aldrich. Cells were incubated in a humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
RNA was extracted using RNeasy Mini spin columns (Qiagen, Hilden, Germany) according to the manufacturer's instructions. RNA concentration and purity were determined by measuring the absorbance of the samples at 230, 260, and 280 nm using a NanoReady F-3100 spectrophotometer (Life Real, Zhejiang, China). The optical density (OD) ratios A260/A280 and A260/A230 were used to assess RNA purity.
After poly(A) selection, library preparation was performed using the NEBNext Ultra II RNA Library Preparation kit.

treatment_protocol: PBMCs were isolated from 5 male and 5 female donors and seeded in 48-wells plates containing 1.26 x 10^6 PBMCs in 1 mL of complete medium. PBMCs were exposed either to PFOA or PFOS (at the concentration of 12.6 µg/mL), DEX (150 µg/mL) or DMSO as vehicle control (final concentration 0.1% (v/v)) and incubated for 24 hours without subsequent stimulation. Following exposure, RNA was extracted and used for RNA sequencing.

tag: tissue

value: male

value: PBMCs


title: PBMCs, Male, GW, rep2

description: Library name: GW_M_2


title: 3xGBM, 3xHCC, 2xHD, 3xHNSCC

description: Library name: WTA1

value: Spike C1


title: PBMCs, Male, GW, rep3

description: Library name: GW_M_3


title: PBMCs, Male, dexamethason, rep3

description: Library name: DEX_M_3

value: 150 μg/mL dexamethason


title: PBMCs, Male, dexamethason, rep2

description: Library name: DEX_M_2


title: PBMCs, Male, dexamethason, rep1

description: Library name: DEX_M_1


title: PBMCs, Male, PFOS, rep5

description: Library name: PFOS_M_5

value: 12.6 μg/mL PFOS


title: PBMCs, Male, PFOS, rep4

description: Library name: PFOS_M_4


title: PBMCs, Male, PFOS, rep3

description: Library name: PFOS_M_3


title: PBMCs, Male, PFOA, rep5

description: Library name: PFOA_M_5

value: 12.6 μg/mL PFOA


title: 4DM6F505LI_S52

city: Durham

first: Scott

last: Auerbach

state: NC

address: 111 TW Alexander Drive

institute: Division of the National Toxicology Program at NIEHS

description: Library name: 4DM6F505LI_S52_R1_001

data_processing:
TempO-Seq sequences were aligned to the rat S1500+ probe sequences using Bowtie version 1.3.1. The Bowtie configuration allowed up to three mismatches and selected the single best alignment for reporting.
The aligned read counts for attenuated probes were properly readjusted to calculate unattenuated equivalent counts using the attenuation factors provided in the platform manifest.
Assembly: BioSpyder TempO-seq mouse S1500+ manifest
Supplementary files format and content: tab-delimited text file includes attenuation-adjusted raw probe counts for each sample

source_name: Liver Left Lobe

extract_protocol:
The majority of all tissues from all animals were collected within approximately 10 minutes of euthanasia. Tissue samples were collected following organ weight measurements in the following order: lung, heart, liver (left lobe), kidney, and ovary (no ovary weights were taken) from all remaining animals on study day 5 for transcriptomic analysis. Two samples of lung, heart, liver, and kidney tissue (approximately 5 mm3) were collected and placed into cryotubes containing RNAlater. The ovaries were collected whole bilaterally (one sample) and placed into cryotubes containing RNAlater. The tissue samples were stored at 2°C to 8°C for approximately 55 hours for rats or up to 48 hours for mice. The RNAlater was then removed and the samples were stored in a −85°C to −60°C freezer until processed for RNA isolation. Tissues were homogenized in QIAzol lysis buffer (Qiagen Inc., Valencia, CA) using the TissueLyser II bead-beating system followed by RNA extraction using the RNeasy 96 QIAcube HT kits (Qiagen Inc., Valencia, CA) with a DNA digestion step.
Isolated RNA was utilized for analysis using either the Mouse S1500+ v1.2 TempO-Seq (BioSpyder, Carlsbad, CA) platform with a minimum of 500 mapped read counts/transcript and approximately 1.5 million counts/sample. Work instructions developed by Battelle using the BioSpyder User Guide (https://www.biospyder.com/s/100802-TempO-Seq-User-Guide-rev-C-r8r7.pdf) were followed.

value: Liver Left Lobe

value: B6D2F1/Crl (BDF-1)

tag: Sex

value: female

tag: age

value: 9 weeks

tag: concentration (ppm)

tag: animal id

tag: sample status

value: Used in Analysis

tag: qc issue


title: 4DM6F505LU_S52

description: Library name: 4DM6F505LU_S52_R1_001

source_name: Lung

value: Lung


title: 4DM6F505KI_S46

description: Library name: 4DM6F505KI_S46_R1_001

source_name: Kidney

value: Kidney


title: 4DM6F505OV_S134

description: Library name: 4DM6F505OV_S134_R1_001

source_name: Ovary

value: Ovary


title: 4DM6F505HE_S46

description: Library name: 4DM6F505HE_S46_R1_001

source_name: Heart

value: Heart


title: PBMCs, Male, PFOA, rep3

description: Library name: PFOA_M_3


title: PBMCs, Male, PFOS, rep1

description: Library name: PFOS_M_1


title: 4DM6F504OV_S139

description: Library name: 4DM6F504OV_S139_R1_001


title: 4DM6F504LU_S57

description: Library name: 4DM6F504LU_S57_R1_001


title: PBMCs, Male, PFOA, rep1

description: Library name: PFOA_M_1


title: 4DM6F504LI_S57

description: Library name: 4DM6F504LI_S57_R1_001


title: 4DM6F504KI_S51

description: Library name: 4DM6F504KI_S51_R1_001


title: PBMCs, Male, Control, rep4

description: Library name: Ctrl_M_4

value: 0.1% DMSO


title: 4DM6F504HE_S51

description: Library name: 4DM6F504HE_S51_R1_001


title: PBMCs, Male, Control, rep3

description: Library name: Ctrl_M_3


title: 4DM6F503OV_S123

description: Library name: 4DM6F503OV_S123_R1_001


title: PBMCs, Male, Control, rep1

description: Library name: Ctrl_M_1


title: 4DM6F503LI_S41

description: Library name: 4DM6F503LI_S41_R1_001


title: PBMCs, Female, GW, rep3

description: Library name: GW_F_3

source_name: female


title: 4DM6F503KI_S70

description: Library name: 4DM6F503KI_S70_R1_001


title: 4DM6F503HE_S70

description: Library name: 4DM6F503HE_S70_R1_001


title: PBMCs, Female, GW, rep2

description: Library name: GW_F_2


title: 4DM6F502OV_S135

description: Library name: 4DM6F502OV_S135_R1_001


title: PBMCs, Female, dexamethason, rep3

description: Library name: DEX_F_3


title: PBMCs, Female, GW, rep1

description: Library name: GW_F_1


title: 4DM6F502LU_S53

description: Library name: 4DM6F502LU_S53_R1_001


title: 4DM6F502LI_S53

description: Library name: 4DM6F502LI_S53_R1_001


title: PBMCs, Female, dexamethason, rep1

description: Library name: DEX_F_1


title: 4DM6F502KI_S47

description: Library name: 4DM6F502KI_S47_R1_001


title: PBMCs, Female, PFOS, rep5

description: Library name: PFOS_F_5


title: PBMCs, Female, PFOS, rep4

description: Library name: PFOS_F_4


title: 4DM6F501OV_S143

description: Library name: 4DM6F501OV_S143_R1_001


title: PBMCs, Female, PFOS, rep3

description: Library name: PFOS_F_3


title: 4DM6F501LU_S61

description: Library name: 4DM6F501LU_S61_R1_001


title: PBMCs, Female, PFOS, rep2

description: Library name: PFOS_F_2


title: 4DM6F501LI_S61

description: Library name: 4DM6F501LI_S61_R1_001


title: 4DM6F501KI_S55

description: Library name: 4DM6F501KI_S55_R1_001


title: PBMCs, Female, PFOA, rep5

description: Library name: PFOA_F_5


title: PBMCs, Female, PFOS, rep1

description: Library name: PFOS_F_1


title: 4DM6F501HE_S55

description: Library name: 4DM6F501HE_S55_R1_001


title: PBMCs, Female, PFOA, rep4

description: Library name: PFOA_F_4


title: 4DM5F405OV_S156

description: Library name: 4DM5F405OV_S156_R1_001


title: 4DM5F405LU_S74

description: Library name: 4DM5F405LU_S74_R1_001


title: PBMCs, Female, PFOA, rep3

description: Library name: PFOA_F_3


title: PBMCs, Female, PFOA, rep2

description: Library name: PFOA_F_2


title: PBMCs, Female, dexamethason, rep2

description: Library name: DEX_F_2


title: 4DM5F405LI_S74

description: Library name: 4DM5F405LI_S74_R1_001


title: PBMCs, Female, PFOA, rep1

description: Library name: PFOA_F_1


title: 4DM5F405KI_S68

description: Library name: 4DM5F405KI_S68_R1_001


title: PBMCs, Female, Control, rep4

description: Library name: Ctrl_F_4


title: PBMCs, Female, Control, rep3

description: Library name: Ctrl_F_3


title: 4DM6F502HE_S47

description: Library name: 4DM6F502HE_S47_R1_001


title: 4DM5F405HE_S68

description: Library name: 4DM5F405HE_S68_R1_001


title: 4DM5F404OV_S152

description: Library name: 4DM5F404OV_S152_R1_001


title: PBMCs, Female, Control, rep2

description: Library name: Ctrl_F_2


title: 4DM5F404LU_S70

description: Library name: 4DM5F404LU_S70_R1_001


title: PBMCs, Female, Control, rep1

description: Library name: Ctrl_F_1


title: 4DM5F404LI_S70

description: Library name: 4DM5F404LI_S70_R1_001


title: Bcells, Male, rapamycin, rep3

description: Library name: RAP_M_3

treatment_protocol: PBMCs were isolated from 5 male and 5 female donors and seeded in 48-wells plates containing 1.26 x 106 PBMCs in 1 mL of complete medium. In the first independent experiment, PBMCs were exposed to PFOA or PFOS (at the concentration of 12.6 µg/mL), rapamycin (2 µg/mL) and DMSO as vehicle control (final concentration 0.1% (v/v)) for 24 hours and subsequently stimulated with 100 IU/mL of rhIL-2 and 1 μg/mL ODN2006 for 6 days to induce B cell differentiation and activation. Following exposure, RNA was extracted and used for RNA sequencing.

value: Bcells

value: 2 μg/mL rapamycin


title: ALV organoid scRNA, G60

description: Library name: sample alv 2

source_name: human lung organoid

value: human lung organoid


title: Bcells, Male, rapamycin, rep2

description: Library name: RAP_M_2

value: male


title: 4DM5F404HE_S64

description: Library name: 4DM5F404HE_S64_R1_001


title: MetR_overexpression_rep2

source_name: MR-1(pBBR-SOmetR), replicate 2

tag: strain


title: Bcells, Male, rapamycin, rep1

description: Library name: RAP_M_1


title: Bcells, Male, PFOS, rep5

description: Library name: PFOS_M_5


title: 4DM5F403OV_S130

description: Library name: 4DM5F403OV_S130_R1_001


title: 4DM5F403LU_S48

description: Library name: 4DM5F403LU_S48_R1_001


title: 4DM5F404KI_S64

description: Library name: 4DM5F404KI_S64_R1_001


title: Bcells, Male, PFOS, rep4

description: Library name: PFOS_M_4


title: GNS166_0_n3

description:
Library name: Sample 5
n8

value: GNS166 Control


title: 4DM5F403LI_S48

description: Library name: 4DM5F403LI_S48_R1_001

value: Not Used in Analysis

value: Outlier based on PCA/correlation


title: 4DM5F403KI_S42

description: Library name: 4DM5F403KI_S42_R1_001


title: Bcells, Male, PFOS, rep3

description: Library name: PFOS_M_3

value: 12.6 μg/mL PFOS


title: GNS166_0_n2

description:
Library name: Sample 3
n7


title: Bcells, Male, PFOS, rep2

description: Library name: PFOS_M_2


title: Bcells, Male, PFOS, rep1

description: Library name: PFOS_M_1


title: Cytosolic DDX6 Input replicate A

value: human esophageal squamous carcinoma cells

value: WT

value: No treatment


title: 4DM5F402OV_S122

description: Library name: 4DM5F402OV_S122_R1_001

value: B6D2F1/Crl (BDF-1)

value: female

value: 9 weeks

value: Used in Analysis


title: 4DM5F402LU_S40

description: Library name: 4DM5F402LU_S40_R1_001

value: Lung


title: Bcells, Male, PFOA, rep5

description: Library name: PFOA_M_5

value: 12.6 μg/mL PFOA


title: Bcells, Male, PFOA, rep4

description: Library name: PFOA_M_4

value: Bcells


title: Cytosolic IgG replicate A

description:
Antibody: IgG
Cyto_IgG_A


title: Bcells, Male, PFOA, rep3

description: Library name: PFOA_M_3


title: 4DM5F402LI_S40

description: Library name: 4DM5F402LI_S40_R1_001

value: Liver Left Lobe


title: Cytosolic DDX6 IP replicate B

description:
Antibody: Anti-DDX6
Cyto_DDX6_B


title: 4DM5F402KI_S69

description: Library name: 4DM5F402KI_S69_R1_001

value: Kidney

value: Potential Tissue Contamination


title: Bcells, Male, PFOA, rep2

description: Library name: PFOA_M_2

value: male


title: 2xCRC, 2xGBM, 2xHCC, 2xHD, 3xHNSCC

description: Library name: WTA8

value: PBMC

value: Spike C8


title: 7xCRC, 1xHCC, 3xHNSCC

description: Library name: WTA4

value: Spike C4


title: 4DM5F402HE_S69

description: Library name: 4DM5F402HE_S69_R1_001

value: Heart


title: Bcells, Male, PFOA, rep1

description: Library name: PFOA_M_1


title: 4DM5F401OV_S144

description: Library name: 4DM5F401OV_S144_R1_001

value: Ovary


title: Bcells, Male, Control, rep5

description: Library name: Ctrl_M_5

value: 0.1% DMSO


title: 4DM5F403HE_S42

description: Library name: 4DM5F403HE_S42_R1_001

value: B6D2F1/Crl (BDF-1)


title: 4DM5F401LU_S62

description: Library name: 4DM5F401LU_S62_R1_001

value: female


title: Bcells, Male, Control, rep4

description: Library name: Ctrl_M_4


title: 4DM5F401LI_S62

description: Library name: 4DM5F401LI_S62_R1_001

value: 9 weeks


title: Bcells, Male, Control, rep3

description: Library name: Ctrl_M_3


title: 4DM5F401KI_S56

description: Library name: 4DM5F401KI_S56_R1_001

value: Used in Analysis


title: 4DM5F401HE_S56

description: Library name: 4DM5F401HE_S56_R1_001


title: Bcells, Male, Control, rep1

description: Library name: Ctrl_M_1


title: Bcells, Male, Control, rep2

description: Library name: Ctrl_M_2


title: 4DM4F305OV_S155

description: Library name: 4DM4F305OV_S155_R1_001


title: Bcells, Female, rapamycin, rep3

description: Library name: RAP_F_3

value: 2 μg/mL rapamycin


title: 4DM4F305LU_S73

description: Library name: 4DM4F305LU_S73_R1_001

value: Lung


title: PBMCs, Male, PFOS, rep2

description: Library name: PFOS_M_2

value: PBMCs

value: 12.6 μg/mL PFOS


title: 4DM4F305LI_S73

description: Library name: 4DM4F305LI_S73_R1_001

value: Liver Left Lobe


title: Bcells, Female, rapamycin, rep2

description: Library name: RAP_F_2

value: Bcells


title: Bcells, Female, rapamycin, rep1

description: Library name: RAP_F_1


title: 4DM4F305HE_S67

description: Library name: 4DM4F305HE_S67_R1_001


title: Bcells, Female, PFOS, rep5

description: Library name: PFOS_F_5


title: 4DM4F305KI_S67

description: Library name: 4DM4F305KI_S67_R1_001

value: Kidney


title: 4DM4F304OV_S151

description: Library name: 4DM4F304OV_S151_R1_001


title: Bcells, Female, PFOS, rep3

description: Library name: PFOS_F_3


title: 4DM4F304LU_S69

description: Library name: 4DM4F304LU_S69_R1_001


title: Bcells, Female, PFOS, rep2

description: Library name: PFOS_F_2


title: Bcells, Female, PFOS, rep1

description: Library name: PFOS_F_1


title: 4DM4F304LI_S69

description: Library name: 4DM4F304LI_S69_R1_001


title: 4DM4F304HE_S63

description: Library name: 4DM4F304HE_S63_R1_001


title: 4DM4F303OV_S153

description: Library name: 4DM4F303OV_S153_R1_001


title: Bcells, Female, PFOA, rep4

description: Library name: PFOA_F_4

value: 12.6 μg/mL PFOA


title: Bcells, Female, PFOA, rep3

description: Library name: PFOA_F_3


title: 4DM4F303LU_S71

description: Library name: 4DM4F303LU_S71_R1_001


title: 4DM4F303LI_S71

description: Library name: 4DM4F303LI_S71_R1_001


title: Bcells, Female, PFOA, rep2

description: Library name: PFOA_F_2


title: Bcells, Female, PFOA, rep1

description: Library name: PFOA_F_1


title: 4DM4F303KI_S65

description: Library name: 4DM4F303KI_S65_R1_001

value: Not Used in Analysis

value: Potential Tissue Contamination


title: Bcells, Female, Control, rep5

description: Library name: Ctrl_F_5


title: 4DM4F303HE_S65

description: Library name: 4DM4F303HE_S65_R1_001

value: Heart


title: 4DM4F302OV_S127

description: Library name: 4DM4F302OV_S127_R1_001

value: Ovary


title: 4DM4F302LU_S45

description: Library name: 4DM4F302LU_S45_R1_001


title: Bcells, Female, Control, rep1

description: Library name: Ctrl_F_1

value: 0.1% DMSO


title: 4DM4F302LI_S45

description: Library name: 4DM4F302LI_S45_R1_001

value: B6D2F1/Crl (BDF-1)


title: 4DM4F302KI_S39

description: Library name: 4DM4F302KI_S39_R1_001

value: female


title: Human pancreatic T cells from donor SW041, ADT, HTO

city: NYC

first: Alexey

last: Koshkin

state: New York

department: Department of Pathology and Cell Biology

institute: Columbia University Medical center, department of Pathology and Cell Biology

description:
Library name: SW041_Pancreas_Tcells_ADT_HTO
10x Genomics Feature Barcode library containing 142 antibody-derived tags (ADT) for protein detection and 5 hashtag oligonucleotides (HTO) for sample demultiplexing

library_source: other

data_processing:
Data Preprocessing Macrophages Raw sequencing data were processed using Cell Ranger, loaded as Seurat objects, and underwent quality control to remove cells with high mitochondrial genes. Each donor sample underwent independent processing with initial dimensionality reduction using buildUMAP and marker identification using findMarkers functions. Multiple rounds of cluster-based sequential selection (2-5 rounds per donor) were performed with comprehensive marker validation, including lineage contamination assessment. Clusters were excluded based on high expression of lymphocyte markers (CD2, CD7, CD8A, CD3E, CD19) and mast and epithelial cell markers (SPINK1, KRT8, TPSAB1). Macrophage confirmation utilized established macrophage markers (CD163, CD14, CD33). Multi-modal validation compared RNA-protein expression pairs (CD14/Hu.CD14-M5E2, CD163/Hu.CD163, CD33/Hu.CD33). Final macrophage populations were exported as donor-specific whitelists and saved as cleaned Seurat objects. T cells:   Raw sequencing data were processed with Cell Ranger (v6.0, 10x Genomics) and underwent quality control removing cells with high mitochondrial transcripts and low unique molecular identifiers (UMIs). Hashtag Oligonucleotide (HTO) Demultiplexing: For this multi-tissue CITE-seq study, T cells and macrophages from different tissue sites were labeled using TotalSeq-C hashtag oligonucleotides (BioLegend).  For demultiplexing, raw antibody capture counts were processed separately using Seurat in R.  HTO counts were normalized using the centered log-ratio (CLR) method, followed by  demultiplexing with the HTODemux function using a threshold at the 99th percentile to remove  doublets. Post-demultiplexing, the Seurat object was filtered to include only singlets and were  exported as CSV files for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: SW038_RNA_counts.csv (CSV): Raw RNA UMI count matrix (genes x cells) for donor SW038, SW038_ADT_counts.csv (CSV): Raw ADT count matrix (proteins x cells) for donor SW038, SW038_HTO_counts.csv (CSV): Raw HTO count matrix (hashtags x cells) for donor SW038, SW038_HTO_classification.csv (CSV): HTO demultiplexing results (cell barcodes with classifications) for donor SW038, SW038_obs.csv (CSV): Cell metadata (QC metrics, clusters, and annotations) for donor SW038, SW038_genes.csv (CSV): Gene metadata (gene IDs and symbols) for donor SW038, barcodes.tsv.gz (TSV.GZ): Filtered cell barcodes for donor SW038, features.tsv.gz (TSV.GZ): Filtered features (genes, ADTs, HTOs with types) for donor SW038, matrix.mtx.gz (MTX.GZ): Filtered count matrix (combined RNA/ADT/HTO) for donor SW038; SW039_RNA_counts.csv (CSV): Raw RNA UMI count matrix (genes x cells) for donor SW039, SW039_ADT_counts.csv (CSV): Raw ADT count matrix (proteins x cells) for donor SW039, SW039_HTO_counts.csv (CSV): Raw HTO count matrix (hashtags x cells) for donor SW039, SW039_HTO_classification.csv (CSV): HTO demultiplexing results (cell barcodes with classifications) for donor SW039, SW039_obs.csv (CSV): Cell metadata (QC metrics, clusters, and annotations) for donor SW039, SW039_genes.csv (CSV): Gene metadata (gene IDs and symbols) for donor SW039, barcodes.tsv.gz (TSV.GZ): Filtered cell barcodes for donor SW039, features.tsv.gz (TSV.GZ): Filtered features (genes, ADTs, HTOs with types) for donor SW039, matrix.mtx.gz (MTX.GZ): Filtered count matrix (combined RNA/ADT/HTO) for donor SW039; SW041_RNA_counts.csv (CSV): Raw RNA UMI count matrix (genes x cells) for donor SW041, SW041_ADT_counts.csv (CSV): Raw ADT count matrix (proteins x cells) for donor SW041, SW041_HTO_counts.csv (CSV): Raw HTO count matrix (hashtags x cells) for donor SW041, SW041_HTO_classification.csv (CSV): HTO demultiplexing results (cell barcodes with classifications) for donor SW041, SW041_obs.csv (CSV): Cell metadata (QC metrics, clusters, and annotations) for donor SW041, SW041_genes.csv (CSV): Gene metadata (gene IDs and symbols) for donor SW041, barcodes.tsv.gz (TSV.GZ): Filtered cell barcodes for donor SW041, features.tsv.gz (TSV.GZ): Filtered features (genes, ADTs, HTOs with types) for donor SW041, matrix.mtx.gz (MTX.GZ): Filtered count matrix (combined RNA/ADT/HTO) for donor SW041.
Library strategy: CITE-seq

molecule: protein

source_name: Pancreas

extract_protocol:
Human Tissue Samples Tissues were obtained from 68 deceased adult organ donors (Supplemental information 1) as part of organ acquisition for clinical transplantation through an approved protocol and material transfer agreement with organ procurement organizations as described previously¹⁻⁶. All donors had no reported autoimmune diseases, or cancers, tested seronegative for hepatitis B, C, and HIV and did not have a history of chronic pancreatitis or evidence of acute pancreatitis (peak lipase < 3 times upper limit of normal, non-indurated). Use of organ donor tissues does not qualify as ‘‘human subjects’’ research, as confirmed by the Columbia University IRB as tissue samples were obtained from brain-dead (deceased) individuals. Isolation and preparation of single cell suspensions from tissue samples After procurement in the operating room, tissue samples were maintained in cold saline or CoStorSol® (University of Wisconsin (UW) solution (Preservation Solutions, Elkhorn, WI, Cat# PS004) and transported to the laboratory within 2–4 hours. Pancreas and small intestine were carefully inspected for the presence of lymph nodes, and these were removed and processed separately. Spleen, PLN, and small intestine samples were processed using enzymatic and mechanical digestion, resulting in high yields of live leukocytes, as previously described ¹⁻⁶.  Human pancreatic tissue was processed by the Human Islet Core at Columbia University as described previously⁷. After taking tissue samples for paraffin embedding and image analysis, the body and tail portions of the pancreas were perfused through the pancreatic duct and digested with warmed and circulating enzyme solution in a Ricordi chamber (Biorep Technologies, Inc., Miami Lakes, FL, Cat# RC3–600-MUL) containing Premium Grade Collagenase (SERVA Electrophoresis GmbH, Heidelberg, Germany, Cat#17455.1) and Neutral Protease (SERVA Electrophoresis GmbH, Cat#30301.5) until the majority of the islets were separated from exocrine tissue as examined microscopically by Dithizone-staining (Sigma, Cat#D5130). The pancreas cell suspension, was diluted, washed, and collected using at least 8L of circulating RPMI (Mediatech, Cat# 99–595-CM). Islets were purified using an Optiprep gradient (densities 1.11–1.06) and COBE 2991 blood cell processor, further manually selected to achieve >90% purity by dithizone staining and dispersed using Accutase (Innovative Cell Technologies). Aliquots of the crude pancreas suspension and dispersed islets were immediately cryopreserved in a solution of 90% FBS and 10% dimethyl sulfoxide (DMSO) and stored in a temperature controlled liquid nitrogen freezer for subsequent immune cell recovery. Sorting Pancreas Immune Cells Cryopreserved tissue suspension aliquots were rapidly thawed at 37°C, washed in RPMI with 10% FBS and DNase I (Sigma, Cat# DN25–5G) (50–100 µg/ml). Dead cells were labeled using Zombie-NIR followed by surface staining with antibodies (Supplemental information 2). For the multi-tissue CITE-seq studies, each different tissue site was labeled with distinct TotalSeq barcoded hashtag antibodies (Biolegend). For sorting, samples were resuspended in PBS with 2% human AB serum and 4',6-diamidino-2-phenylindole (DAPI) for added sensitivity in detection of dead and dying cells. Sorting was performed using either the BD Influx or FACS Aria Cell Sorters. For multi-tissue CITE-seq, hash tagged cells were sorted from each tissue site at equal proportions.  Viable pancreas immune cells were detected as Zombie-NIR⁻ DAPI⁻ CD45⁺. Due to the low abundance of T cells relative to macrophages in pancreas⁷, for the multi-tissue T cell CITE-seq studies, the T cells were further selected as CD2⁺ CD19⁻. Cells were sorted into Hanks' Balanced Salt Solution (HBSS) with 5% human albumin and 10mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) buffer. Post-sort viability was confirmed to be >90%. The sorted immune cells were then processed for CITE-seq, bulk RNA-seq and co-culture studies. CITE-seq of Pancreatic Immune Cells After sorting, the pancreas immune cells were pelleted, blocked using human TruStain FcX (Biolegend), and then incubated for 30 minutes at 4°C with the TotalSeq-B (10x Genomics Chromium Single Cell 3' sequencing) or TotalSeq-C (for 10x Genomics Chromium Single Cell 5' sequencing) Universal cocktail per the manufacturer’s instructions. Immediately after staining and washing 3 times, 8,000–10,000 cells were processed by the Columbia Genome Center Single Cell Analysis Core. Briefly, the cells were loaded into the 10X Genomics Chromium controller and cDNA synthesis, amplification, and sequencing libraries were prepared using Next GEM Single Cell 5’ or 3’ Kit (10X Genomics) and sequenced on a NovaSeq X (Illumina). 1. Carpenter, C.B. Safety considerations for working with animal models involving human health hazards. Animal Model Exp Med 1, 91-99 (2018). 2. Gordon, C.L., et al. Tissue reservoirs of antiviral T cell immunity in persistent human CMV infection. J Exp Med 214, 651-667 (2017). 3. Granot, T., et al. Dendritic Cells Display Subset and Tissue-Specific Maturation Dynamics  over Human Life. Immunity 46, 504-515 (2017). 4. Kumar, B.V., et al. Human Tissue-Resident Memory T Cells Are Defined by Core Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites. Cell Rep 20, 2921-2934 (2017) 5. Miron, M., et al. Human Lymph Nodes Maintain TCF-1(hi) Memory T Cells with High Functional Potential and Clonal Diversity throughout Life. J Immunol 201, 2132-2140 (2018). 6. Senda, T., et al. Microanatomical dissection of human intestinal T-cell immunity reveals site specific changes in gut-associated lymphoid tissues over life. Mucosal Immunol 12, 378-389 (2019). 7. Weisberg, S.P., et al. Tissue-Resident Memory T Cells Mediate Immune Homeostasis in the Human Pancreas through the PD-1/PD-L1 Pathway. Cell Rep 29, 3916-3932 e3915 (2019)
library preparation and RNA-seq was performed by the Columbia Genome Center as previously described. In this study the HTO and ADT matrices come from the same fastq batch.

value: Pancreas

value: T cell

tag: library type

value: ADT & HTO

tag: adt

value: 142 antibodies

tag: hto

value: 5 hashtags


title: 4DM4F302HE_S39

description: Library name: 4DM4F302HE_S39_R1_001

value: 9 weeks

value: Used in Analysis


title: Human pancreatic T cells from donor SW041, GEX

description:
Library name: SW041_Pancreas_Tcells_mRNA
10x Genomics 5' v2 Gene Expression library from multiplexed human pancreatic T cells

value: mRNA

tag: batch


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_NTC1_Th2
Th2 polarized
Th1Th2_validation_Diff084_Th2_DonorB_bulkRNAseq.csv

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

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: 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

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: Human pancreatic T cells from donor SW039, ADT, HTO

description:
Library name: SW039_Pancreas_Tcells_ADT_HTO
10x Genomics Feature Barcode library containing 142 antibody-derived tags (ADT) for protein detection and 6 hashtag oligonucleotides (HTO) for sample demultiplexing

tag: tissue

value: Pancreas

tag: cell type

value: T cell

tag: library type

value: ADT & HTO

tag: adt

value: 142 antibodies

tag: hto

value: 6 hashtags

tag: batch


title: 4DM4F301LU_S51

description: Library name: 4DM4F301LU_S51_R1_001

value: Lung

tag: cell line

value: B6D2F1/Crl (BDF-1)

tag: Sex

value: female

tag: age

value: 9 weeks

tag: treatment

tag: concentration (ppm)

tag: animal id

tag: sample status

value: Used in Analysis

tag: qc issue


title: 4DM4F301LI_S51

description: Library name: 4DM4F301LI_S51_R1_001

value: Liver Left Lobe


title: 4DM4F301HE_S45

description: Library name: 4DM4F301HE_S45_R1_001

value: Heart


title: 4DM3F205OV_S128

description: Library name: 4DM3F205OV_S128_R1_001

value: Ovary


title: iMGL-iNSpheroids, iPSC DF6-9-9T.B cell line, rAAV9-mCherry transduced 24hpt

city: Oeiras

first: Catarina

middle: Monteiro

last: Gomes

state: Lisboa

address: Av. República, Qta. do Marquês

country: Portugal

institute: iBET

description:
Library name: Treated-24h-1
10X Genomics

data_processing:
The resultant gene expression matrix was imported into the R statistical environment for further analysis (RStudio 2024.04.2+764 "Chocolate Cosmos" Release). Ambient RNA removal was carried out using the DecontX methodology [104]. Cell filtering, data normalization, and clustering were carried out using the R package Seurat v5.0.1. Filtered feature-barcode matrices were used as input for the initial Seurat object, including only cells with at least 200 genes expressed in at least three cells. Datasets were further filtered to remove low-quality cells based on the following exclusion criteria parameters: (i) ratio of mitochondrial versus endogenous gene expression < 20% (putative dying cells); (ii) < 200 or > 5,000 total genes (putative poorly informative cells and multiplets). Data normalization, scaling, and identification of the top 3,000 most variable genes were performed using SCTransform v2.0 method, using default parameters and regressing out the percentage of genes coding for ribosomal proteins. This normalization method is claimed to outperform the classical log-normalization workflow, allowing the use of a higher principal component (PC) to capture more detailed biological variation for clustering. Principal Component Analysis (PCA) was run on each dataset and the first 30 PCs were selected for downstream analysis, based on their contribution to each PC variability (Elbow Plot). The overall significance of each PC and the corresponding p-value were calculated according to the JackStraw method. The different sample datasets were integrated into a single object using Seurat’s integration standard workflow, using the first 30 PCs, 3,000 variable features, and the SCTransform normalized data. Integration anchors were identified using reciprocal PCA and reference-based integration, with the timepoint 0 hours being used as reference. Dimensionality reduction was then performed with PCA on the batch-corrected data. Uniform Manifold Approximation and Projection (UMAP) dimensionality reduction was performed on the calculated PCs to obtain a 2D representation for data visualization. To find the optimal clustering resolution, the Clustree package was used to compute different resolution values (0.1-1.0); the 0.1 resolution was selected for downstream analysis. Cell clusters were identified using the Louvain algorithm at resolution r = 0.1, implemented by the FindCluster function of Seurat. To characterize each cluster, a comprehensive manual annotation was performed.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files.

organism:
Homo sapiens
Dependoparvovirus

source_name: Brain

extract_protocol:
Untransduced and rAAV9-mCherry transduced iMGL-iNSpheroids (derived from the iPSC(IMR90)-4 and iPS DF6-9-9T.B cell lines) were analysed by single nuclei RNA-sequencing (sn-RNAseq). Samples were collected at 0-, 6- and 24-hours post-transduction, and sedimented by centrifugation at 300 xg, for 5 min. Cells were then resuspended and cryopreserved in cell freezing medium, CryoStor CS10 (STEMCELL Technologies, cat. no. 100-1061) and stored at -80 °C until shipment. Samples were sent for nuclei isolation and sequencing at Genewiz laboratories (Leipzig, Germany).
Raw data from snRNAseq was analysed and processed into a transcript count matrix using Cell Ranger (https://www.10xgenomics.com/, v6.1.1) from the Chromium Single Cell Software Suite by 10x Genomics. Fastq files were generated using the Cell Ranger mkfastq command with default parameters. Gene counts for each cell were quantified with the Cell Ranger count command with default parameters. For all analyses, the human (GRCh38) plus the mCherry genes were used as reference.

treatment_protocol: rAAV9 encoded mCherry fluorescence protein under the CAG promoter was used at na MOI of 5 x 10^5 VG/cell. iNSpheroids-iMGL, control and treated, were collected at 0-, 6- and 24h post-transduction.

value: Brain

value: iPSC DF6-9-9T.B

value: rAAV9-mCherry transduced


title: iMGL-iNSpheroids, iPSC DF6-9-9T.B cell line, rAAV9-mCherry transduced 6hpt

description:
Library name: Treated-6h-1
10X Genomics


title: 4DM3F205LU_S46

description: Library name: 4DM3F205LU_S46_R1_001


title: Human pancreatic T cells from donor SW038, GEX

description:
Library name: SW038_Pancreas_Tcells_mRNA
Human pancreas T cells isolated from donor SW038 using 10x Genomics CITE-seq protocol for mRNA modality.

value: mRNA


title: 6.36 Geriatric day 4

city: Columbus

first: Ayse

middle: Selen

last: Yilmaz

state: OH

address: 1800 Cannon Drive

department: Biomedical Informatics

institute: OSU

description:
Library name: Geriatric_D4_6.36
6-36_S45

data_processing:
150 bp paired-end reads were aligned using Hisat2 version 2.1.0 using the Sigmodon hispidus complete DNA reference assembly
Mapped reads are quantified using featureCounts software and the Sigmodon hispidus annotation in gtf format.
The resulting count matrix was annotated with Sigmodon hispidus gene IDs, associated Ensembl gene IDs, and mouse gene orthologs
Assembly: Sigmodon hispidus complete DNA (https://denovo.cnag.cat/cottonrat_data)
Supplementary files format and content: format: Tab separated txt file
Supplementary files format and content: content: Sigmodon hispidus gene IDs, associated Ensembl gene IDs, and mouse (Mus musculus) gene orthologs, raw counts for each sample (quantified by featurecounts)

organism: Sigmodon hispidus

growth_protocol: Inbred cotton rats (Sigmodon hispidus) were purchased from Inotiv (formerly Envigo; West Lafayette, IN). All cotton rats were maintained in NexGen Rat 900 polysulfone microisolator cages (Allentown Inc., Allentown, NJ) in a barrier facility with 12:12 hour light cycles, 22 ± 2 °C, and 20-70% relative humidity. Age ranges were 1-4 months for adult animals and >8 months for geriatric animals.

extract_protocol:
RNA was extracted and isolated with RNeasy Plus Mini extraction kits (QIAGEN) following manufacturer instructions, with a final elution volume of 30 µL. RNA concentrations, 260/280 ratios, and 260/230 ratios were measured using a NanoDrop One spectrophotometer (Thermo Fisher), ensuring a minimum concentration of 100 ng/µL and 260/280 ratios between 1.8 and 2.2 for all extracted RNA samples.
The RNA Integrity Number (RIN) for DNase-treated total RNA were assessed using Agilent BioAnalyzer RNA Nano Kit (Agilent Technologies, Inc., Santa Clara, CA) and the RNA amount was assayed with the Invitrogen Qubit RNA HS Assay Kit (Thermo Fisher Scientific, Waltham, MA). Samples with RIN > 7 were used in mRNA-seq library generation using the QIAseq FastSelect RNA Lib Core Kit (QIAGEN) and the QIAseq Stranded mRNA Enrichment Kit (QIAGEN). Briefly, 100 ng DNase-treated total RNA was used as input for library generation. RNA fragmentation was set for 3 minutes at 94C. 17 PCR cycles were used in final library generation. Library quantification and characterization were assessed with Agilent BioAnalyzer HS DNA Kit and the Invitrogen Qubit DNA HS Assay Kit. Libraries were pooled together with other index – compatible RNA-seq libraries for sequencing on Illumina NovaSeq X Plus 10B (Illumina Technology, Portland, OR) flow cell lane to a minimum depth of 15 - 20 million clusters per sample.

treatment_protocol: At indicated end-points, cotton rats were euthanized by CO2-induced asphyxiation followed by exsanguination. The left lung lobe was collected and placed in 2 mL RNAprotect (QIAGEN, Hilden, Germany) at room temperature. Homogenization of lung was performed the same day as collection, following transportation at room temperature in RNAprotect (QIAGEN). 25-30 µg of each lung sample was removed by sterile dissection and placed in 2 mL Precellys® bead tubes (Bertin Technologies, France) with 600 µL Buffer RLT Plus (QIAGEN) and 6 µL β-mercaptoethanol. Samples were homogenized at room temperature with a Precellys® 24 tissue homogenizer (Bertin) at 6000 RPM, 3 cycles for 30 seconds each with 10-second breaks. The homogenate was passed through QIAshredder tubes (QIAGEN).

value: RSV intranasal 4 days prior to lung collection


title: 4DM3F205LI_S46

description: Library name: 4DM3F205LI_S46_R1_001


title: 6.35 Geriatric day 4

description:
Library name: Geriatric_D4_6.35
6-35_S44


title: 6.34 Geriatric day 4

description:
Library name: Geriatric_D4_6.34
6-34_S43


title: 4DM3F205KI_S40

description: Library name: 4DM3F205KI_S40_R1_001

value: Kidney


title: 6.33 Geriatric day 4

description:
Library name: Geriatric_D4_6.33
6-33_S42


title: 4DM3F205HE_S40

description: Library name: 4DM3F205HE_S40_R1_001


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

description:
Library name: Th1Th2_validation_Diff084_DonorB_NKTR_non
nonpolarized
Th1Th2_validation_Diff084_non_DonorB_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 knockdown of NKTR

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

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

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

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: low body weight at weaning


title: 4DM3F204OV_S148

description: Library name: 4DM3F204OV_S148_R1_001

value: Ovary

tag: cell line

value: B6D2F1/Crl (BDF-1)

value: 9 weeks

tag: treatment

tag: concentration (ppm)

tag: animal id

tag: sample status

value: Used in Analysis

tag: qc issue


title: 4DM3F204LU_S66

description: Library name: 4DM3F204LU_S66_R1_001

value: Lung


title: 4DM3F204LI_S66

description: Library name: 4DM3F204LI_S66_R1_001

value: Liver Left Lobe

value: Not Used in Analysis

value: SEQ DEPTH < 300000


title: 6.31 Geriatric day 4

description:
Library name: Geriatric_D4_6.31
6-31_S40

value: RSV intranasal 4 days prior to lung collection


title: 4DM3F204KI_S60

description: Library name: 4DM3F204KI_S60_R1_001

value: Kidney


title: 5.30 Geriatric day 1

description:
Library name: Geriatric_D1_5.30
5-30_S39

value: RSV intranasal 1 day prior to lung collection


title: 5.29 Geriatric day 1

description:
Library name: Geriatric_D1_5.29
5-29_S38


title: 4DM3F204HE_S60

description: Library name: 4DM3F204HE_S60_R1_001

value: Heart


title: 5.27 Geriatric day 1

description:
Library name: Geriatric_D1_5.27
5-27_S36


title: 4DM3F203OV_S142

description: Library name: 4DM3F203OV_S142_R1_001


title: 4DM3F203LU_S60

description: Library name: 4DM3F203LU_S60_R1_001


title: 5.26 Geriatric day 1

description:
Library name: Geriatric_D1_5.26
5-26_S35


title: 4DM3F203LI_S60

description: Library name: 4DM3F203LI_S60_R1_001


title: 5.25 Geriatric day 1

description:
Library name: Geriatric_D1_5.25
5-25_S34


title: 4DM3F203KI_S54

description: Library name: 4DM3F203KI_S54_R1_001


title: 4.23 Geriatric day 0

description:
Library name: Geriatric_D0_4.23
4-23_S32

value: PBS intranasal 1 day prior to lung collection


title: 4DM3F202OV_S136

description: Library name: 4DM3F202OV_S136_R1_001

value: female


title: 4.22 Geriatric day 0

description:
Library name: Geriatric_D0_4.22
4-22_S31


title: 4DM3F202LU_S54

description: Library name: 4DM3F202LU_S54_R1_001


title: 4.21 Geriatric day 0

description:
Library name: Geriatric_D0_4.21
4-21_S30


title: 4DM3F202LI_S54

description: Library name: 4DM3F202LI_S54_R1_001


title: 4.20 Geriatric day 0

description:
Library name: Geriatric_D0_4.20
4-20_S29


title: 4.19 Geriatric day 0

description:
Library name: Geriatric_D0_4.19
4-19_S28


title: 4DM3F202HE_S48

description: Library name: 4DM3F202HE_S48_R1_001


title: 3.18 Adult day 4

description:
Library name: Adult_D4_3.18
3-18_S27


title: 4DM3F201OV_S137

description: Library name: 4DM3F201OV_S137_R1_001


title: 3.17 Adult day 4

description:
Library name: Adult_D4_3.17
3-17_S26


title: 4DM3F201LU_S55

description: Library name: 4DM3F201LU_S55_R1_001


title: 3.16 Adult day 4

description:
Library name: Adult_D4_3.16
3-16_S25


title: 4DM3F201LI_S55

description: Library name: 4DM3F201LI_S55_R1_001


title: 4DM3F201KI_S49

description: Library name: 4DM3F201KI_S49_R1_001


title: 3.14 Adult day 4

description:
Library name: Adult_D4_3.14
3-14_S23


title: 4DM3F201HE_S49

description: Library name: 4DM3F201HE_S49_R1_001


title: 3.13 Adult day 4

description:
Library name: Adult_D4_3.13
3-13_S22


title: 4DM2F105OV_S126

description: Library name: 4DM2F105OV_S126_R1_001


title: 4DM3F203HE_S54

description: Library name: 4DM3F203HE_S54_R1_001


title: 4.24 Geriatric day 0

description:
Library name: Geriatric_D0_4.24
4-24_S33


title: 2.12 Adult day 1

description:
Library name: Adult_D1_2.12
2-12_S21


title: 4DM2F105LU_S44

description: Library name: 4DM2F105LU_S44_R1_001


title: 2.11 Adult day 1

description:
Library name: Adult_D1_2.11
2-11_S20


title: 2.10 Adult day 1

description:
Library name: Adult_D1_2.10
2-10_S19


title: 4DM2F105KI_S38

description: Library name: 4DM2F105KI_S38_R1_001

value: Potential Tissue Contamination


title: 4DM2F105LI_S44

description: Library name: 4DM2F105LI_S44_R1_001


title: 4DM3F202KI_S48

description: Library name: 4DM3F202KI_S48_R1_001


title: 4DM2F105HE_S38

description: Library name: 4DM2F105HE_S38_R1_001


title: 2.9 Adult day 1

description:
Library name: Adult_D1_2.9
2-9_S18


title: 2.8 Adult day 1

description:
Library name: Adult_D1_2.8
2-8_S17


title: 2.7 Adult day 1

description:
Library name: Adult_D1_2.7
2-7_S16


title: 4DM2F104OV_S132

description: Library name: 4DM2F104OV_S132_R1_001


title: 4DM2F104LU_S50

description: Library name: 4DM2F104LU_S50_R1_001


title: Bcells, Female, PFOS, rep4

description: Library name: PFOS_F_4

tag: cell type

value: Bcells

value: 12.6 μg/mL PFOS


title: 1.6 Adult day 0

description:
Library name: Adult_D0_1.6
1-6_S15


title: 4DM2F104LI_S50

description: Library name: 4DM2F104LI_S50_R1_001


title: 4DM4F304KI_S63

description: Library name: 4DM4F304KI_S63_R1_001


title: 1.5 Adult day 0

description:
Library name: Adult_D0_1.5
1-5_S14


title: 4DM2F104KI_S44

description: Library name: 4DM2F104KI_S44_R1_001


title: 1.4 Adult day 0

description:
Library name: Adult_D0_1.4
1-4_S13


title: 4DM2F104HE_S44

description: Library name: 4DM2F104HE_S44_R1_001


title: 3.15 Adult day 4

description:
Library name: Adult_D4_3.15
3-15_S24


title: Bcells, Female, PFOA, rep5

description: Library name: PFOA_F_5

value: 12.6 μg/mL PFOA


title: 1.3 Adult day 0

description:
Library name: Adult_D0_1.3
1-3_S12


title: 4DM2F103OV_S150

description: Library name: 4DM2F103OV_S150_R1_001

value: Ovary

value: B6D2F1/Crl (BDF-1)


title: 1.2 Adult day 0

description:
Library name: Adult_D0_1.2
1-2_S11


title: Bcells, Female, Control, rep4

description: Library name: Ctrl_F_4

value: 0.1% DMSO


title: 1.1 Adult day 0

description:
Library name: Adult_D0_1.1
1-1_S10

value: Lung


title: 4DM2F103LI_S68

description: Library name: 4DM2F103LI_S68_R1_001

value: Liver Left Lobe

value: 9 weeks

value: Used in Analysis


title: 4DM2F103LU_S68

description: Library name: 4DM2F103LU_S68_R1_001


title: CpG methylation - SD12 aposymbiotic H. viridissima

city: Baltimore

first: Alex

last: Bortvin

state: MD

address: 3520 San Martin Dr

department: Embryology

institute: Carnegie Institution

description:
Library name: SD12_meth
ONT ultralong run SD12, R10.4.1, Dorado sup 5mCG_5hmCG

library_source: genomic

data_processing:
Basecalled with Dorado 1.0.2 (sup,5mCG_5hmCG model) producing unaligned BAM with MM/ML modification tags.
Reads aligned to Carnegie v1 with minimap2 2.28 (-x map-ont -a -y --secondary=no).
CpG methylation quantified with modkit 0.6.1 (pileup --cpg --combine-strands --modified-bases 5mC).
BigWig signal tracks generated with bedGraphToBigWig (UCSC kent utils 482).
Assembly: Carnegie v1 (JBWVZK010000000), 111 scaffolds, 315.1 Mb
Supplementary files format and content: BED files: tab-delimited, columns: chrom, start, end, modified_base, score, strand, n_valid, n_mod, pct_modified. One row per CpG site.
Supplementary files format and content: BigWig files: CpG methylation percentage (_pct.bw) and coverage (_cov.bw) signal tracks.

molecule: genomic DNA

organism: Hydra viridissima

source_name: whole organism

growth_protocol: Hydra viridissima clone 2 cultured at room temperature (+24C) in hydra medium, fed freshly hatched brine shrimp 3-4 times per week. Large polyps harvested 2-3 days after last feeding.

extract_protocol:
Genomic DNA extracted from ~800-1000 pooled animals (with buds and testes) using Monarch HMW DNA extraction kit for tissue (NEB).
ONT ultralong library preparation, R10.4.1 chemistry. Each library represents one MinION flow cell run.

value: whole organism

value: aposymbiotic

value: aposymbiotic clone 2


title: 4DM2F103KI_S62

description: Library name: 4DM2F103KI_S62_R1_001

value: Kidney


title: Bcells, Female, Control, rep3

description: Library name: Ctrl_F_3


title: CpG methylation - SD11 aposymbiotic H. viridissima

description:
Library name: SD11_meth
ONT ultralong run SD11, R10.4.1, Dorado sup 5mCG_5hmCG


title: 4DM2F103HE_S62

description: Library name: 4DM2F103HE_S62_R1_001

value: Heart


title: Bcells, Female, Control, rep2

description: Library name: Ctrl_F_2

value: female


title: CpG methylation - SD10 aposymbiotic H. viridissima

description:
Library name: SD10_meth
ONT ultralong run SD10, R10.4.1, Dorado sup 5mCG_5hmCG


title: 4DM2F102OV_S140

description: Library name: 4DM2F102OV_S140_R1_001


title: CpG methylation - SD9 aposymbiotic H. viridissima

description:
Library name: SD9_meth
ONT ultralong run SD9, R10.4.1, Dorado sup 5mCG_5hmCG


title: 4DM4F301OV_S133

description: Library name: 4DM4F301OV_S133_R1_001


title: 4DM2F102LU_S58

description: Library name: 4DM2F102LU_S58_R1_001


title: CpG methylation - SD8 symbiotic H. viridissima

description:
Library name: SD8_meth
ONT ultralong run SD8, R10.4.1, Dorado sup 5mCG_5hmCG

value: symbiotic

value: symbiotic clone 2


title: 4DM2F102LI_S58

description: Library name: 4DM2F102LI_S58_R1_001


title: Cortex, NeuN neg. Nuclei, SPNT, 4

city: Hamburg

first: Manuel

middle: Alexander

last: Friese

state: Hamburg

address: Falkenried 94

department: ZMNH

institute: UKE

description: Library name: Sample 26

data_processing:
Reads were aligned to the Ensembl mouse reference genome (GRCm39) using STAR v.2.4 with default parameters, as previously applied to transcriptomic studies in the Djungarian hamster. Differential expression analysis was performed with DESeq2 (v.3.12), identifying differentially expressed genes as those showing ≥ 2-fold change with a false discovery rate (FDR)-adjusted P < 0.05. Overlaps with annotated gene loci were counted using featureCounts v.1.5.1.
Assembly: GRCm39
Supplementary files format and content: gene_counts_all_samples.txt contains raw counts of all samples for all detected genes

organism: Cricetiscus sungorus

source_name: Cortex

extract_protocol:
RNA was isolated by lysing samples in RLT buffer (RNeasy Mini Kit, Qiagen) supplemented with β-mercaptoethanol (1:100) and homogenised using QIAshredder columns (Qiagen), followed by additional homogenisation with a glass douncer. RNA was purified from the flow-through using silica membrane spin columns (RNeasy Mini Kit) according to the manufacturer’s protocol. The RNA was eluted in 30 µl RNase-free H₂O and stored at −80 °C.
RNA sequencing libraries were prepared using the TruSeq stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

value: Cortex

value: Non-neuronal nuclei (other CNS cells)


title: 4DM2F102KI_S52

description: Library name: 4DM2F102KI_S52_R1_001


title: 4DM2F102HE_S52

description: Library name: 4DM2F102HE_S52_R1_001


title: Cortex, NeuN neg. Nuclei, SPNT, 2

description: Library name: Sample 24


title: Cortex, NeuN neg. Nuclei, SPNT, 3

description: Library name: Sample 25


title: 4DM2F101OV_S138

description: Library name: 4DM2F101OV_S138_R1_001

value: Ovary


title: 4DM4F301KI_S45

description: Library name: 4DM4F301KI_S45_R1_001

value: B6D2F1/Crl (BDF-1)


title: Human pancreatic T cells from donor SW038, ADT, HTO

description:
Library name: SW038_Pancreas_Tcells_ADT_HTO
10x Genomics Feature Barcode library containing 137 antibody-derived tags (ADT) for protein detection and 7 hashtag oligonucleotides (HTO) for sample demultiplexing

value: Pancreas

value: T cell

tag: library type

value: ADT & HTO

tag: adt

value: 137 antibodies

tag: hto

value: 7 hashtags

tag: batch


title: Human pancreatic T cells from donor SW039, GEX

description:
Library name: SW039_Pancreas_Tcells_mRNA
Human pancreas T cells isolated from donor SW039 using CITE-seq protocol for mRNA modality.

tag: tissue

value: mRNA


title: Cortex, NeuN neg. Nuclei, SPNT, 1

description: Library name: Sample 23


title: 4DM2F101LI_S56

description: Library name: 4DM2F101LI_S56_R1_001

value: Liver Left Lobe

value: 9 weeks

value: Used in Analysis


title: Cortex, NeuN neg. Nuclei, SPHT, 4

description: Library name: Sample 22


title: 4DM2F101LU_S56

description: Library name: 4DM2F101LU_S56_R1_001

value: Lung


title: 4DM2F101KI_S50

description: Library name: 4DM2F101KI_S50_R1_001

value: Kidney

value: female


title: 4DM2F101HE_S50

description: Library name: 4DM2F101HE_S50_R1_001

value: Heart


title: Cortex, NeuN neg. Nuclei, SPHT, 1

description: Library name: Sample 19

value: Cortex


title: 4DM1F9OV_S145

description: Library name: 4DM1F9OV_S145_R1_001


title: Cortex, NeuN neg. Nuclei, SPHT, 2

description: Library name: Sample 20

value: Non-neuronal nuclei (other CNS cells)


title: 4DM1F9LU_S63

description: Library name: 4DM1F9LU_S63_R1_001


title: Cortex, NeuN neg. Nuclei, LPNT, 5

description: Library name: Sample 18


title: Cortex, NeuN neg. Nuclei, LPNT, 4

description: Library name: Sample 17


title: Cortex, NeuN neg. Nuclei, LPNT, 2

description: Library name: Sample 15


title: Cortex, NeuN neg. Nuclei, LPNT, 3

description: Library name: Sample 16


title: 4DM1F9HE_S57

description: Library name: 4DM1F9HE_S57_R1_001


title: Cortex, NeuN neg. Nuclei, LPNT, 1

description: Library name: Sample 14


title: 4DM1F9KI_S57

description: Library name: 4DM1F9KI_S57_R1_001

value: Not Used in Analysis

value: SEQ DEPTH < 300000


title: 4DM1F8OV_S147

description: Library name: 4DM1F8OV_S147_R1_001

value: Ovary

value: B6D2F1/Crl (BDF-1)


title: Cortex, NeuN pos. Nuclei, SPNT, 4

description: Library name: Sample 13

value: Neuronal nuclei


title: Cortex, NeuN pos. Nuclei, SPNT, 3

description: Library name: Sample 12


title: 4DM1F8LI_S65

description: Library name: 4DM1F8LI_S65_R1_001


title: Cortex, NeuN pos. Nuclei, SPNT, 2

description: Library name: Sample 11


title: Cortex, NeuN pos. Nuclei, SPNT, 1

description: Library name: Sample 10


title: 4DM1F8KI_S59

description: Library name: 4DM1F8KI_S59_R1_001


title: 4DM1F8HE_S59

description: Library name: 4DM1F8HE_S59_R1_001


title: Cortex, NeuN pos. Nuclei, SPHT, 4

description: Library name: Sample 9


title: 4DM1F7OV_S124

description: Library name: 4DM1F7OV_S124_R1_001


title: Cortex, NeuN pos. Nuclei, SPHT, 3

description: Library name: Sample 8


title: Cortex, NeuN pos. Nuclei, SPHT, 2

description: Library name: Sample 7


title: 4DM1F7LU_S42

description: Library name: 4DM1F7LU_S42_R1_001


title: 4DM1F7LI_S42

description: Library name: 4DM1F7LI_S42_R1_001


title: Cortex, NeuN pos. Nuclei, SPHT, 1

description: Library name: Sample 6


title: 4DM1F7KI_S71

description: Library name: 4DM1F7KI_S71_R1_001


title: 4DM1F7HE_S71

description: Library name: 4DM1F7HE_S71_R1_001


title: Cortex, NeuN pos. Nuclei, LPNT, 5

description: Library name: Sample 5


title: Cortex, NeuN pos. Nuclei, LPNT, 4

description: Library name: Sample 4


title: 4DM1F6OV_S146

description: Library name: 4DM1F6OV_S146_R1_001


title: Cortex, NeuN pos. Nuclei, LPNT, 3

description: Library name: Sample 3


title: 4DM1F6LU_S64

description: Library name: 4DM1F6LU_S64_R1_001


title: Cortex, NeuN pos. Nuclei, LPNT, 2

description: Library name: Sample 2


title: 4DM1F6LI_S64

description: Library name: 4DM1F6LI_S64_R1_001


title: Cortex, NeuN pos. Nuclei, LPNT, 1

description: Library name: Sample 1


title: 4DM1F6KI_S58

description: Library name: 4DM1F6KI_S58_R1_001


title: P. putida KT2440, RNA-seq, S3HB, replicate 1

city: Ulsan

first: Nandakumar

last: Arumugam

address: UNIST-gil 50

department: School of Energy and Chemical Engineering

country: South Korea

institute: Ulsan National Institute of Science and Technology

description: Library name: RNA_Seq_KT2440_S3HB_rep1

data_processing:
Sequenced reads of P. putida KT 2440 samples were mapped onto NC_002947.4 reference genome sequence using bowtie v1.0.0. Transcript Per Million (TPM) were calculated using featureCounts in R. Differentially expressed genes were identifiec using DEseq2 in R.
Assembly: NC_002947.4
Supplementary files format and content: csv files include TPM values for each sample

organism: Pseudomonas putida KT2440

source_name: bacteria

growth_protocol: Pseudomonas putida KT2440 wild-type strain was grown in modified M9 minimal medium supplemented with 35 mM of each carbon source ((S)-1,3-BDO], or (S)-3-HB) as the sole carbon source at 30°C with shaking at 200 rpm until mid-exponential phase was reached.

extract_protocol:
Total RNA was isolated from harvested cell pellets using the RNeasy Plus Mini Kit (Qiagen Inc., Valencia, CA, USA) according to the manufacturer's instructions. Genomic DNA contamination was eliminated using the gDNA Eliminator spin column incorporated in the RNeasy Plus Mini Kit. RNA purity and concentration were assessed spectrophotometrically using a NanoDrop 1000 spectrophotometer (Thermo Scientific).
RNA libraries were prepared using KAPA RNA Hyper Prep kit for sequencing using standard Illumina protocols

treatment_protocol: The cell culture was treated with the RNAprotect reagent (Qiagen).

value: bacteria

tag: genotype

value: WT


title: 4DM1F5OV_S149

description: Library name: 4DM1F5OV_S149_R1_001

tag: Sex


title: P. putida KT2440, RNA-seq, S3HB, replicate 2

description: Library name: RNA_Seq_KT2440_S3HB_rep2


title: 4DM1F6HE_S58

description: Library name: 4DM1F6HE_S58_R1_001

tag: age


title: 5.28 Geriatric day 1

description:
Library name: Geriatric_D1_5.28
5-28_S37

value: RSV intranasal 1 day prior to lung collection


title: P. putida KT2440, RNA-seq, SBDO, replicate 2

description: Library name: RNA_Seq_KT2440_SBDO_rep2


title: 4DM1F5LU_S67

description: Library name: 4DM1F5LU_S67_R1_001


title: P. putida KT2440, RNA-seq,SBDO, replicate 1

description: Library name: RNA_Seq_KT2440_SBDO_rep1


title: 4DM1F5LI_S67

description: Library name: 4DM1F5LI_S67_R1_001

value: Liver Left Lobe


title: 4DM1F5KI_S61

description: Library name: 4DM1F5KI_S61_R1_001

value: 9 weeks

value: Potential Tissue Contamination


title: BPAN2_DIFF G HA590

city: Munich

first: Lena

last: Burbulla

address: Feodor-Lynen-Straße 17

institute: LMU

description: iPSC-derived microglia generated from a BPAN patient carrying a WDR45 mutation, analyzed under basal conditions using NanoString neuroinflammation panel.

hyb_protocol: For each sample, 100 ng of total RNA was hybridized with NanoString capture and reporter probes from the Human Neuroinflammation Panel v1.0 overnight at 65 °C for 16 hours, according to the manufacturer’s protocol.

scan_protocol: Following hybridization, samples were processed and scanned using the NanoString nCounter Analysis System at the German Cancer Consortium (DKTK) core facility, in accordance with the manufacturer’s instructions.

data_processing: Raw digital count (RCC) files were processed using NanoString nSolver Analysis Software (v4.0) with the Advanced Analysis module. Background correction was performed using negative control probes, and normalization was carried out using NanoString’s automated reference gene selection method based on stable housekeeping genes. All samples passed quality control metrics. Differential expression analysis was performed using linear modeling with Benjamini–Hochberg adjustment for multiple testing.

source_name: iPSC-derived microglia

label_protocol: Not applicable. NanoString nCounter technology does not require enzymatic labeling or amplification.

growth_protocol: iPSC-derived microglia (iMG) were generated from BPAN patient and control iPSC lines using a modified version of an established differentiation protocol (McQuade et al., 2018). Briefly, iPSCs were differentiated into hematopoietic progenitor cells, which were subsequently matured into microglia in defined differentiation media supplemented with microglia lineage–promoting factors. Cells were maintained under standard culture conditions until reaching a mature microglial state prior to analysis.

extract_protocol: Total RNA was extracted from frozen iPSC-derived microglia pellets using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: iPSC-derived microglia were analyzed under basal conditions

tag: sample type

value: BPAN - WDR45 mutation


title: 4DM1F5HE_S61

description: Library name: 4DM1F5HE_S61_R1_001

value: Used in Analysis


title: BPAN1_DIFF G 8172


title: 4DM1F4OV_S141

description: Library name: 4DM1F4OV_S141_R1_001

value: female


title: Ctrl2_DIFF G SFC

description: iPSC-derived microglia generated from a healthy control, analyzed under basal conditions using NanoString neuroinflammation panel.

value: healthy control


title: 4DM1F4LI_S59

description: Library name: 4DM1F4LI_S59_R1_001


title: 4DM1F4LU_S59

description: Library name: 4DM1F4LU_S59_R1_001

value: Lung


title: Ctrl1_DIFF G 156


title: BPAN1_DIFF F2 8172


title: BPAN2_DIFF F2 HA590


title: 4DM1F4KI_S53

description: Library name: 4DM1F4KI_S53_R1_001

value: Kidney


title: 4DM1F4HE_S53

description: Library name: 4DM1F4HE_S53_R1_001

value: Heart


title: Ctrl2_DIFF F2 SFC


title: Ctrl1_DIFF F2 156


title: 4DM1F3OV_S129

description: Library name: 4DM1F3OV_S129_R1_001


title: 4DM1F3LI_S47

description: Library name: 4DM1F3LI_S47_R1_001


title: Ctrl2_DIFF E SFC


title: 4DM1F3KI_S41

description: Library name: 4DM1F3KI_S41_R1_001


title: Ctrl1_DIFF E 156


title: 4DM1F3HE_S41

description: Library name: 4DM1F3HE_S41_R1_001


title: 4DM1F3LU_S47

description: Library name: 4DM1F3LU_S47_R1_001


title: scRNA-seq_Phf6 Tg_rep2

city: San Antonio

first: Ying

last: Guo

state: Texas

address: 8403 Floyd Curl Dr

institute: UT Health Science Center at San Antonio

data_processing:
Sequencing results from 10x Genomics were demultiplexed and converted to FASTQ format by cellranger  with a parameter of mkfastq
The FASTQ data was aligned to mouse reference genome and quantified using cellranger with default parameters
Assembly: mm10
Supplementary files format and content: h5 files of filtered counts for all genes in each cell

source_name: Bone marrow

extract_protocol:
The libraries for each single cell sample were prepared using the Chromium Single Cell Gene Expression 3’ Version 3.1 Kit (10X Genomics) with the Chromium Controller.
single-cell RNA-seq

treatment_protocol: The Lineage-cKit+ cells were purified from mouse bone marrow cells using BD FACSAria II

value: Lin-cKit+ bone marrow cells

tag: strain

value: Phf6R274X Tg


title: Cortex, NeuN neg. Nuclei, SPHT, 3

description: Library name: Sample 21

value: Cortex

value: Non-neuronal nuclei (other CNS cells)


title: BPAN1_DIFF E 8172


title: BPAN2_DIFF E HA590


title: 4DM1F2LU_S72

description: Library name: 4DM1F2LU_S72_R1_001

tag: cell line

value: B6D2F1/Crl (BDF-1)


title: 4DM1F2KI_S66

description: Library name: 4DM1F2KI_S66_R1_001

tag: treatment


title: 4DM1F9LI_S63

description: Library name: 4DM1F9LI_S63_R1_001

tag: concentration (ppm)

value: Not Used in Analysis

value: SEQ DEPTH < 300000


title: scRNA-seq_WT_rep2

value: wild type


title: 4DM1F2LI_S72

description: Library name: 4DM1F2LI_S72_R1_001

value: Liver Left Lobe

value: 9 weeks

tag: animal id


title: 4DM1F8LU_S65

description: Library name: 4DM1F8LU_S65_R1_001

tag: sample status


title: 4DM1F1OV_S131

description: Library name: 4DM1F1OV_S131_R1_001

value: Ovary

tag: qc issue


title: 4DM1F2HE_S66

description: Library name: 4DM1F2HE_S66_R1_001

value: Used in Analysis


title: 4DM1F1LI_S49

description: Library name: 4DM1F1LI_S49_R1_001

value: female