title: Hair follicles, with polyIC WT_4__ISM

status: Public on Jul 23 2021

city: Bethesda

first: Keisuke

middle: Chris

last: Nagao

state: Maryland

address: 9000 Rockville Pike, Bldg 10, Rm12N240B

institute: National Institute of Arthritis and Musculoskeletal and Skin Diseases

data_processing:
The FASTQ files were aligned to the reference mouse genome (mm10) using STAR software (2.6.1c).
Gene-level count matrix was generated from mapped reads via GenomicFeatures and GenomicAlignments tools on R platform and then used as an input for downstream analysis using DESeq2 or kallisto (ver. 0.44.0), a pseudoalignment tool and sleuth pipeline (Bray et al., 2016).
Genes with lower than 10 read count were filtered out from further analysis.
The differentially expressed genes were based on a threshold of false discovery rate below 0.1.
Genome_build: mm10
Supplementary_files_format_and_content: WT_polyIC_IFD_ISM_TPM.xlsx

source_name: skin

extract_protocol:
Total RNA was extracted using Direct-zol RNA MicroPrep (Zymo Research).
RNA libraries were prepared using a NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs), NEBNext Ultra RNA Library Prep Kit for Illumina (New England BioLabs) and NEBNext Multiplex Oligos for Illumina (Index Primers Set) (New England BioLabs) according to manufacturer protocol.

treatment_protocol: Epidermis from C57BL/6 mice were harvested one day after saline or poly(I:C) i.p. injection and upper hair follicle cells were sorted into Trizol.

value: Hair follicles

tag: tissue subset

value: ISM

value: skin

value: wild type


title: Hair follicles, with polyIC WT_2__ISM

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: strain

tag: treatment

tag: genotype


title: Hair follicles, with polyIC WT_2__IFD

value: IFD


title: Hair follicles, with polyIC WT_3__ISM


title: Hair follicles, no polyIC WT_4__ISM

value: saline


title: Hair follicles, with polyIC WT_4__IFD


title: P28_3

status: Public on Oct 08 2021

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

data_processing:
Raw sequencing data was demultiplexed and converted into FASTQ files using CASAVA (v1.8.2), and quality tested with FASTQC v0.11.2.
Alignment to the mm10 genome was performed using the STAR aligner version 2.5.1b (Dobin et al., 2013). Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read), and a high ratio of uniquely mapped reads (>75%) was confirmed with exonic alignment inspected to ensure that reads were mapped predominantly to annotated exons.
Raw and normalized (FPKM) gene expression was quantified across all genes (RNAseq) using the top-expressed isoform as proxy for gene expression using HOMER v4.10 (Heinz et al.,2010),resulting in 10-55 million uniquely mapped reads in exons.
Principal Component Analysis was carried out with prcomp in R 3.4.3 on normalized counts. Differential gene expression was carried out using the DESeq2[1] package version 1.14.1 using the HOMER getDiffExpression.pl script with default normalization and using replicates to compute within-group dispersion. Significance for differential expression was defined as adjusted P<0.05, calculated using Benjamini-Hochberg's procedure for multiple comparison adjustment.
Genome_build: mm10
Supplementary_files_format_and_content: Excel Table with normalized gene counts

molecule: polyA RNA

source_name: from astrocyte ribome pulldown

growth_protocol: 12 hour light/dark cycle with ad lib access to standard mouse chow

extract_protocol:
1% PFA perfusion then brain microdissection in cold physiological buffer, then RNA extracted (input) or ribosomal pulldown via Ribotag protocol (Sanz et al PNAS 2009): HA-tagged ribosome pulled down with Cst Rb anti-HA antibody, isolated via Pierce IgG beads. All RNA extracted with Qiagen RNeasy Micro kit.
standard Illumina protocol (PolyA beads)

tag: age

value: post natal day 28

value: 73.12 GFAP-cre x RPL22-HA

value: visual cortex


title: Hair follicles, with polyIC WT_3__IFD


title: Hair follicles, with polyIC WT_1__IFD


title: Hair follicles, no polyIC WT_3__ISM


title: Hair follicles, no polyIC WT_2__ISM


title: Hair follicles, no polyIC WT_1__ISM


title: Hair follicles, no polyIC WT_3__IFD


title: Hair follicles, no polyIC WT_1__IFD


title: Hair follicles, no polyIC WT_4__IFD


title: mIMCD3 WT #3

status: Public on Jul 15 2021

city: Freiburg

first: Sebastian

last: Friedrich

address: Hugstetter Str. 55

country: Germany

institute: University Hosptial Freiburg

data_processing:
Illumina Casava1.7 software used for basecalling.
Data analysis was performed on Galaxy Europe platform. Sequenced reads were trimmed for adaptor sequence (Trim Galore, Galaxy Tool Version 0.4.3.1, default settings) and quality checked (FastQC, Galaxy Tool Version 0.72, default settings). Reads were mapped to mm10 whole genome using HISAT2 (Galaxy Tool Version 2.1.0+galaxy3) with spliced alignment options: Penalty for canonical splice sites 0, Penalty for non-canonical splice sites 3, Penalty function for long introns with canonical splice sites  Constant [f(x) = B], Constant term (B) 0.0, Coefficient (A) 0.0, Penalty function for long introns with non-canonical splice sites Natural logarithm [f(x) = B + A * log(x)], Constant term (B)  -8.0, Coefficient (A) 1.0, Minimum intron length 20, Maximum intron length 500000)
Mapped reads were counted with htseq-count (Galaxy Tool Version 0.9.1, default settings) . Differential gene expression was tested using DESeq2 (Galaxy Tool Version 2.11.40.4, default settings for estimateSizeFactors). False discovery rate of DGE was controlled with a p-value < 0.05 adjusted for multiple testing (Benjamini-Hochberg procedure).
The reads processed in the RNA-seq analysis were also aligned to the reference genome and tailored for StringTie tool with HISAT2 (Galaxy Tool Version 2.1.0+galaxy3). De novo transcript reconstruction was conducted with StringTie (Galaxy Tool Version 1.3.6). The transcriptome was assembled using StringTie-merge (Galaxy Tool Version 1.3.6). Assembled transcripts were compared to the reference annotation (Mus musculus, mm9) with GFFCompare (Galaxy Tool Version 0.11.2). Exon abundancies were then estimated using DEXSeq-Count (Galaxy Tool Version 1.28.1.0). Differential exon usage (DEU) was tested with DEXSeq (Galaxy Tool Version 1.28.1+galaxy1). False discovery rate of DEU was controlled with a p-value < 0.05 adjusted for multiple testing (Benjamini-Hochberg procedure).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table (.csv) containing DESeq2 normalized counts for every transcript and every sample

source_name: murine inner medullary collecting duct cells

growth_protocol: Cells were cultured in a mix of Dulbecco’s modified eagle’s and F12 medium (DMEM-F12; Lonza), which was supplemented with 10 % fetal bovine serum and 1 % Penicillin-Streptomycin (10,000 U Penicillin and 10 mg / ml Streptomycin; both Sigma Aldrich). Per genotype, six 10 cm cell culture dishes were grown, starting with 5 × 10^6 cells per dish. Cells were grown at 37 °C and 10 % CO2. PCR-based testing for mycoplasma contamination was performed regularly. New ampules were started after ~25 passages.

extract_protocol:
Per genotype, 6 cell culture dishes were grown to full confluency, starting with 5 × 10^6 cells per dish. RNA Isolation was performed 4 days after full confluency according to manufacturer’s protocol using the RNeasy Plus Mini Kit (Qiagen), harvesting 2 × 10^6 cells per dish. Purification of RNA samples was performed by solvent extraction with 100 % ethanol followed by precipitation with ammonium acetate.10 µl glycogen was added to 100 µl RNA solution. RNA was solved in 10 µl  ammonium acetate (7,5 M) and 250 µl ethanol (100 %). After 30 min at -80 °C RNA was precipitated and separated by centrifugation for 30 min with 13,000 rpm at 4 °C. RNA was then washed twice in 200 µl cold ethanol (80 %) followed by 30 min centrifugation with 13,000 rpm at 4 °C. RNA pellets were dried for 5 min at room temperature and resuspended in 10-15 µl RNAse-free water. Quality of RNA was checked by a Nanodrop photometer (Thermo Fisher). Four of the six samples were chosen for RNA sequencing according to highest ratios for A260/280 (> 2.0) and A260/230 (> 2.0).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were harvested using 0.25 % Trypsin-EDTA (Gibco). Cell counts were performed by Countess II cell counter (Thermo Fisher).

tag: cell type

value: wild-type


title: Xuebin#4

status: Public on Jun 04 2021

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

description: Control

data_processing:
bcl2fast2/2.17.1 and 10x Cellranger-4.0.0 were used to generate Fastq files, perform alignment,filtering,barcode counting,UMI counting and aggregation.
Seurat V.3.0.0 for scRNA QC and further analysis

source_name: Lung

growth_protocol: All mice were obtained from Jax farm and maintained in specific pathogen-free rooms at Tulane University. Experiment were preformed when mice were at age of six to ten weeks.

extract_protocol:
mRNA was extracted from lung single cell suspension using the 10X Genomics Chromium™ Single Cell G Chip Kit
Library construction was performed according to 10x Genomics Chromium™ Single Cell 3' Reagent Kit v3.1 protocol

value: C57BL/6J mice

tag: time point of infection

value: SARS-CoV2_4 days post infection

value: lung


title: mIMCD3 WT #2

value: murine inner medullary collecting duct cells


title: mIMCD3 WT #4


title: mIMCD3 WT #1


title: RNA-Seq of  HEPG2 treated with WORTMANIN at 100nM concentration H_23_02

status: Public on Jul 09 2021

city: Los Angeles

first: Brunilda

last: Balliu

state: CA

address: 621 Charles Young Drive South

department: Computational Medicine

institute: UCLA

data_processing:
Reference genome (hg19) and gene model annotation files were downloaded from the UCSC genome browser website directly.
Indexes of the reference genome were built using STAR3 and paired-end clean reads were aligned to the reference genome using STAR (v2.6.0; with default option mismatch = 10).
Bam files were filtered for uniquely mapped reads, sorted, and indexed using SAMtools4 (v1.4.1).
HTSeq5 (v0.11.0) was used to count the read numbers mapped to each gene (with option -m union).
Genome_build: hg19

organism: Homo sapiens

source_name: liver

growth_protocol: HepG2, terminally differentiated SGBS, and HCML-7304 cells were starved for 6 hours in EMEA with no FBS (HepG2), DMEM/F12 supplemented with pan/bio and penicillin/streptomycin but no FBS (SGBS adipocytes) or HCML growth medium (PromoCell) without supplements. For the glucose condition DMEM no glucose medium (Thermo) was used.

extract_protocol: none provided by the submitter

treatment_protocol: After starvation and washing with PBS, the cells were exposed for 2 hours to the different compounds or the respective control media.

value: liver

value: hepatocyte

tag: cell line

value: WORTMANIN


title: Acne Donor 6

status: Public on May 31 2021

first: Tran

middle: Hue

last: Do

address: 615 Charles E Young Dr

institute: David Geffen School of Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR
Each read was tagged with a 12bp barcode and 8bp unique molecular identifier (UMI)
After alignment, the reads were grouped by the barcodes and deduplicated using the UMIs. The number of UMIs was then counted for each gene in each cell to generate the digital expression matrix (DEM).
Ambient RNA contamination was removed using SoupX (v0.3.1)
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Five metafiles are cell types that we were able to identify from the 6 donors.  Columns from myeloid, lymphocyte, and keratinocyte are identified by the individual cell types that we cited in our manuscript. Columns for the fibroblast and endothelial cell were left as cluster 0, cluster 1, cluster 2, etc because we were unable to assigned specific identities to genes. Instead in our manuscript we cited them as fibroblast 0, fibroblast 1, fibroblast 2, etc and endothelial 0, endothelial 1, etc.

source_name: Human Skin

extract_protocol:
Patients were excluded from the study if they had been using acne medication, hormonal regulation medication, or hormonal-related implants in the past three months. Skin samples were obtained from 3mm punch biopsies in the back. Briefly, skin was digested enzymatically at 2 hours with 0.4% Dispase II at 37°C with agitation. The epidermis was separated from the dermis. Epidermis was then treated with 0.25% Trypsin and 10U/mL of DNAse I for 30 minutes. Dermis was homogenized and treated with 0.4% Collagenase II and 10U/mL DNase I for 2 hours.
Isolated cells were loaded into the Chromium instrument (10X Genomics) according to manufacturer’s protocol, sequenced with NovaSeqS2, and analyzed using Seurat.

tag: subject status

value: Acne Donor


title: Saline_2_Visium

status: Public on Jun 03 2021

city: New York

first: Philip

last: Hasel

address: 435 E 30th St

institute: NYU Langone Medical Centre

data_processing:
NovaSeq 6000 followed by RTA v3.4.4 for basecalling
SpaceRanger was used to align reads to mm10 and generate the barcode.tsv.gz,features.tsv.gz, filtered_feature_bc_matrix.h5 and matrix.mtx.gz files
Tissue_hires_image.png images of brain sections were acquired on a Keyence BZ-X710 microscope
Supplementary_files_format_and_content: barcode.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_feature_bc_matrix.h5, tissue_hires_image.png

extract_protocol:
Tissue was enzymatically permeabelized accroding to the Visium protocol
Visium library kit

treatment_protocol: Female Aldh1l1egfp mice were either injected with 5 mg/kg LPS or saline for 24h and brains sectioned to 10 um

tag: stimulation

tag: transgene

value: Coronal brain section


title: Acne Donor 4

value: skin


title: Saline_3_Visium


title: Saline_1_Visium


title: LPS_3_Visium


title: LPS_1_Visium


title: Acne Donor 3


title: Acne Donor 5


title: Acne Donor 2


title: Pulmonary artery endothelial cells - Control_RepB_for_caMEK5

status: Public on May 28 2021

city: Stanford

first: Jan-Renier

last: Moonen

address: 269 Campus Drive, CCSR 1220

department: Pediatrics

institute: Stanford University

data_processing:
Basecalls were performed using Bcl2fastq.
Reads were aligned to the human genome using STAR v.2.5.4b. Aligned transcripts were quantitated by RSEM v. 1.3.1 (http://deweylab.biostat.wisc.edu/rsem/).
Genome_build: hg19
Supplementary_files_format_and_content: Gene count matrix files

source_name: Pulmonary artery endothelial cells

growth_protocol: PAEC were grown in commercial EC media containing 5% FBS (Sciencell) in a 5% CO2 air atmosphere and used at passages 3–7.

extract_protocol:
RNA was extracted using RNeasy Plus Mini Kit (Qiagen)
Libraries were prepared using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina)

treatment_protocol: PAEC were transduced with adenoviral vectors encoding caMEK5, or GFP as control.

value: Pulmonary artery endothelial cells

value: ad.GFP transduced


title: Acne Donor 1


title: Pulmonary artery endothelial cells - Control_RepC_for_caMEK5


title: Pulmonary artery endothelial cells - caMEK5_RepB

value: ad.caMEK5 transduced


title: Hair follicles, with polyIC WT_1__ISM

value: Hair follicles

value: ISM

value: wild type


title: Pulmonary artery endothelial cells - Control_RepA_for_caMEK5


title: Hair follicles, no polyIC WT_2__IFD

value: IFD

value: saline


title: Pulmonary artery endothelial cells - caMEK5_RepC


title: pSS_09

status: Public on May 19 2021

city: Utrecht

first: Ana

middle: Pinheiro

last: Lopes

state: Utrecht

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

data_processing:
Reads were aligned using STAR aligner using the default parameters to the 65,217 annotated genes obtained from the GrCh38 (v79) built of the human genome.
The read counts per gene were quantified by the Python package HTSeq.
Variance stabilizing transformation (VST) was applied to obtain normalized gene counts.
Genome_build: GrCh38 (v79)
Supplementary_files_format_and_content: Matrix table with normalized gene counts (VST) for every gene across all samples

source_name: peripheral blood

extract_protocol:
CD14+ Monocytes were isolated from peripheral blood mononuclear cells with the CD14+ isolation kit (Miltenyi) according to manufacturer's instruction. Cells were lysed in RLTplus buffer (Qiagen) supplemented with beta-mercaptoethanol (1%). Total RNA was purified using AllPrep Universal Kit (Qiagen), according to the manufacturer’s instructions. RNA integrity was measured by capillary electrophoresis using a Bioanalyzer (Agilent), and the RNA 6000 Nano Kit (Agilent Technologies); all samples had RIN-score >7.0.
RNA libraries were prepared according to the standard Illumina protocols

value: CD14+ monocytes

tag: gender

value: Female

tag: group

value: primary Sjogren's syndrome


title: pSS_11

value: Male


title: pSS_12


title: pSS_10


title: pSS_08


title: pSS_07


title: pSS_06


title: pSS_05


title: pSS_02


title: pSS_01


title: pSS_03


title: pSS_04


title: nSS_06

value: non-Sjogren's sicca


title: nSS_05


title: nSS_03


title: HC_11

value: healthy control


title: Pulmonary artery endothelial cells - caMEK5_RepA


title: nSS_02


title: nSS_01


title: HC_10


title: nSS_08


title: HC_09


title: HC_08


title: HC_05


title: HC_03


title: HC_02


title: HC_04


title: HC_06


title: ANGPTL4_overExpression

description:
ANGPTL4.fpkm.xlsx
ANGPTL4.raw.xlsx
ANGPTL4.DEresult.edgeR.xlsx

data_processing:
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters.
Alignment to the hg19 genome (from illumina iGenome) was performed using the STAR aligner version 2.5.3a using the --outFilterIntronMotifs RemoveNoncanonical parameter
Gene expression was quantified using the HOMER analysis suite version 4.9.1, makeTagDirectory, analyzeRepeats.pl across exons of RefSeq genes.
The differential gene expression (DE) analysis was carried out using edgeR package v3.20.9. A dispersion of 0.05 was used for the test with single replicate. The DE cutoff applied was FDR < 0.1 and absolute log2 fold change greater than 0.5
Genome_build: hg19 (illumina iGenome)
Supplementary_files_format_and_content: ADtotal.fpkm.xlsx contains FPKM normalized gene expression values
Supplementary_files_format_and_content: ADtotal.raw.xlsx contains raw read count
Supplementary_files_format_and_content: ADtotal.Deresult.edgeR.xlsx contains edgeR differential expression outputs
Supplementary_files_format_and_content: ANGPTL4.fpkm.xlsx contains FPKM normalized gene expression values
Supplementary_files_format_and_content: ANGPTL4.raw.xlsx contains raw read count
Supplementary_files_format_and_content: ANGPTL4.DEresult.edgeR.xlsx contains edgeR differential expression outputs

source_name: human brain endothelial cells

growth_protocol: Endothelial cells were co-cultured with fibroblasts or brain pericytes+astrocytes within 3D fibrin scaffolds (Bersini etal., Biomaterials, 2016, doi: 10.1016/j.biomaterials.2015.10.057). Cells were grown in EGM-2MV supplied by Lonza.

extract_protocol:
RNA was extracted following standard procedures based on Trizol and chloroform. The RNeasy Mini kit was used to purify RNA (Qiagen). Samples were incubated with DNAse I for 30 min to degrade genomic DNA. RNA was resuspended in RNAse-free water. The amount of RNA was quantified with Nanodrop.
mRNA-Seq libraries were prepared using the TruSeq RNA Library Preparation Kit according to the manufacturer’s instructions (Illumina).

treatment_protocol: Test conditions: skin endothelial cells were co-cultured with either young or old fibroblasts (1). Skin endothelial cells were co-cultured with young fibroblasts and incubated with young or old serum (2). Brain endothelial cells were co-cultured with brain pericytes and astrocytes and incubated with serum from AD or age-matched healthy donors (3).

value: ANGPTL4 over-expression

value: endothelium


title: normal_rep2

description:
ADtotal.fpkm.xlsx
ADtotal.raw.xlsx
ADtotal.DEresult.edgeR.xlsx

value: cells cultured with serum from age-matched healthy donors

value: 14 days


title: AD_rep2

value: cells cultured with serum from AD patients


title: nSS_04


title: nSS_07


title: OldFibro_rep3

data_processing:
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters.
Alignment to the hg19 genome (from illumina iGenome) was performed using the STAR aligner version 2.5.3a using the --outFilterIntronMotifs RemoveNoncanonical parameter
Gene expression was quantified using the HOMER analysis suite version 4.9.1, makeTagDirectory, analyzeRepeats.pl across exons of RefSeq genes.
The differential gene expression (DE) analysis was carried out using edgeR package v3.20.9. A dispersion of 0.05 was used for the test with single replicate. The DE cutoff applied was FDR < 0.1 and absolute log2 fold change greater than 0.5
Genome_build: hg19 (illumina iGenome)
Supplementary_files_format_and_content: SerumTotal.fpkm.xlsx (FPKM normalized gene expression in Excel spreadsheet)
Supplementary_files_format_and_content: SerumTotal.raw.xlsx (raw count used for differential expression analysis)
Supplementary_files_format_and_content: SerumTotal.DEresult.edgeR.xlsx (Differenital gene expression results in Excel spreadsheet)
Supplementary_files_format_and_content: FibroTotal.fpkm.xlsx (FPKM normalized gene expression in Excel spreadsheet)
Supplementary_files_format_and_content: FibroTotal.raw.xlsx (raw count used for differential expression analysis)
Supplementary_files_format_and_content: FibroTotal.DEresult.edgeR.xlsx (Differenital gene expression results in Excel spreadsheet)

source_name: human endothelial cells

value: treated with old fibroblast

value: 25 days

value: endothelial cells


title: OldFibro_rep4


title: YoungFibro_rep4

value: treated with young fribroblast


title: YoungFibro_rep2


title: YoungFibro_rep1


title: Youngserum_rep3

value: treated with young serum


title: Youngserum_rep2


title: AD_rep3


title: normal_rep1


title: YoungFibro_rep5


title: Youngserum_rep1


title: AD_rep1


title: Oldserum_rep4

value: treated with old serum


title: OldFibro_rep5


title: Oldserum_rep2


title: OldFibro_rep2


title: YoungFibro_rep3


title: HC_07

value: CD14+ monocytes


title: Oldserum_rep3


title: OldFibro_rep1


title: Youngserum_rep4


title: ANGPTL4_control

value: control samples for ANGPTL4 over-expression


title: HC_01


title: SAMP8_old031_rep2

status: Public on Apr 21 2021

data_processing:
FastQC v0.11.5 with default parameter was used for quality test.
Reads were mapped to mm10/rn6 reference genome by STAR v2.5.1 with default parameters. Only uniquely mapped reads were considered for downstream analysis.
RNA-Seq gene expression was quantified by HOMER analyzeRepeats command, summing reads mapped across all gene exons of RefSeq genes.
RNA-Seq differential expression was carried out using edgeR v3.16.1 on the raw counts of replicates. FDR < 0.05 and logFC +/- 1.2 was used as cutoff to identify the DE genes.
Genome_build: mm10; rn6
Supplementary_files_format_and_content: tab delimited text file for RNA-Seq FPKM values.

growth_protocol: All experiments with the SAMP8 animals were performed in accordance with the US Public Health Service Guide for Care and Use of Laboratory Animals and protocols approved by the IACUC at the Salk Institute. Primary cortical neurons were prepared from day seventeen rat embryos and grown in culture as described in Soucek, T. Neuron. 2003 Jul 3;39(1):43-56.

extract_protocol:
RNA from both primary neurons and adult brain hippocampus was isolated using the RNeasy Plus Universal mini kit (Qiagen).
RNA-seq libraries were performed using stranded mRNA kit from Illumina and sequenced in an Illumina HiSeq 2500 device.

treatment_protocol: Mice were fed control diet and diet containing CAD031, CMS 121 and J147 for four months. Primary neurons were treated with 1μM of each compound for 24h.

value: SAMP8 mice brain hippocampal tissue

value: 13 months


title: SAMP8_old031_rep1


title: SAMP8_old031_rep6


title: PrimaryNeuron_treatment031_rep3

organism: Rattus norvegicus

value: rat primary neuron

value: embryo


title: RNA sequencing Cerebrum-3 biological replicate 3

status: Public on Apr 20 2021

city: Chengdu

first: jin

last: long

address: Hui ming

country: China

institute: Sichuan Agricultural University

description:
pig_PCG.all_exp_tpm_gene.txt
pig_lncRNA.all_exp_tpm_gene.txt
pig_TUCP.all_exp_tpm_gene.txt
pig_circRNA.all_exp_tpm_gene.txt
analysis.gtf
Pig-Cerebrum-3

data_processing:
Sequence reads are aligned to pig reference genome (Sscrofa 11.1, GCA_000003025.6) by alignment tool STAR (version 2.5.3a).
The aligned reads of these samples were assembled using Cufflinks (version 2.1.1).
We developed and employed a previously reported computational methods to filter out library-specific background noise and predict the most likely isoforms from the assemblies of transcript fragments (transfrags).
After these filtering, we got high-quality assemblies containing reliable transcripts. These high-quality transcript assemblies were then subjected to TACO (a meta-assembly method with a robust solution for leveraging the vast RNA-seq data landscape for transcript structure prediction), leading to the construction of transcriptome maps.
We predicted coding potential by integrating two sources of evidence: (i) predictions from the alignment-free Coding Potential Calculator (CPC2)
LncRNAs were classified into locus biotypes based on both transcription localization and transcription direction of proximal PCG loci (5-kb distance cutoff) with FEElnc software
CIRCExplorer was used to retrieve RNA-seq reads that are mapped to back-splicing junction sites for circRNA prediction
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: PCG expression level (TPM) text file
Supplementary_files_format_and_content: lncRNA expression level (TPM) text file
Supplementary_files_format_and_content: TUCP expression level (TPM) text file
Supplementary_files_format_and_content: circRNA expression level (TPM) text file
Supplementary_files_format_and_content: gtf file

organism: Sus scrofa

source_name: Cerebrum

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
We used an rRNA depletion protocol (Ribo-Zero kit, Epicentre) coupled with the Illumina TruSeq stranded RNA-Seq library protocol to construct the RNA-Seq libraries. All libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) and sequenced on HiSeq X Ten (Illumina) platform to produce average ~ 49 million 150-bp paired-end raw reads and ~ 48 million high-quality reads for each library.

tag: breed

value: Rongchang pig

value: Cerebrum

tag: developmental stage

value: Adult

tag: Sex

value: female


title: PrimaryNeuron_treatment031_rep1


title: PrimaryNeuron_treatment031_rep2


title: SAMP8_old031_rep3


title: RNA sequencing Cerebrum-1 biological replicate 1

description:
pig_PCG.all_exp_tpm_gene.txt
pig_lncRNA.all_exp_tpm_gene.txt
pig_TUCP.all_exp_tpm_gene.txt
pig_circRNA.all_exp_tpm_gene.txt
analysis.gtf
Pig-Cerebrum-1


title: RNA sequencing Cerebrum-2 biological replicate 2

description:
pig_PCG.all_exp_tpm_gene.txt
pig_lncRNA.all_exp_tpm_gene.txt
pig_TUCP.all_exp_tpm_gene.txt
pig_circRNA.all_exp_tpm_gene.txt
analysis.gtf
Pig-Cerebrum-2


title: GATA2_ChIP-exo_DHT rep2

status: Public on Apr 14 2021

city: San Antonio

first: Tianbao

last: Li

state: Texas

address: 7703 Floyd Curl

department: Molecular Medicine

institute: University of Texas Health Science Center at San Anotnio

description: Extraction protocol 1

library_source: genomic

data_processing:
Library strategy: ChIP-exo
hIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 version with parameters '-k 2 -v 2' to report up to two valid alignments
Read with multiple valid alignments were removed using a Perl program
Uniquely mapped reads from replicates of the same sample were pooled
Peaks were called using MACS2 with parameters '-m 3,30 -g hs -p 1e-8'
ChIP-exo data were processed using ePEST with parameters '-p 1e-8 -R 25 -c 0.05 -k 2.0'
BigWig file was generated by deeptools for visualization
Genome_build: GRCh37/hg19

molecule: genomic DNA

source_name: GATA2_ChIP-exo_DHT rep2

growth_protocol: LNCaP cells were cultured in 10% FBS RPMI 1640 medium, 1:2.5 split every 2 days. Cells are cultured in 5% charcoal stripped FBS RPMI-1640 medium

extract_protocol:
extract 1: For ChIP-exo, after treatment with 10 nm DHT or vehicle for 4 h, LNCaP cells were crosslinked with 1% formaldehyde for 10 min. Sonicated chromatin was enriched by immunoprecipatation with an anti-GATA2 antibody and T4 DNA polymerase, T4 PNK, and Klenow DNA Polymerase were used together for end polishing. The ligation step was performed with less reducing agent. Protein A Dynal magnetic beads were washed using modified RIPA buffer (50mM Tris-HCL pH 7.8, 1mM EDTA, 0.25% Na Deoxycholate, 1% NP-40, 0.5M LiCl). The library was amplified with only 10 or 12 PCR cycles, and prepared without gel-based size selection.
extract2: For Mnase-ChIP-seq, chromatin was isolated from freshly cultured cells and Mono-nucleosomes with solubilized chromatin was achieved by MNase digestion at 37 °C, then immunoprecipitated with antibody-conjugated magnetic beads. DNA is phenol extracted and ethanol precipitated.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part#15023092). Briefly, DNA was end-repaired, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, the DNA was size selected from an agarose gel and was PCR amplified with Illumina primers for 15 cycles. Libraries were sequenced on the Hi-seq 3000 following the manufacturer's protocols.

treatment_protocol: 10 nM DHT was added before cell collection for MNase-seq/ MNase-ChIP-seq of histone markers assay.

value: LNCap cell line

tag: antibody

tag: vendor

value: Abcam

tag: catalog #

value: DHT


title: Spleen RT rep1

city: Genève

first: Noushin

last: Hadadi

address: 1 rue Michel-Servet

department: Physiology and Cellular Metabolism

country: Switzerland

institute: University of Geneva

description: NEBNext Ultra RNA Library Prep Kit

data_processing:
The reads were mapped with STAR aligner v.2.5.3a to the UCSC Mus musculus mm10
reference. The average mapping rate is 80 %.
The transcriptome metrics were evaluated with the Picard tools v.1.141
The table of counts with the number of reads mapping to each gene feature of the UCSC Mus
Genome_build: musculus mm10 was prepared with HTSeq v0.6p1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Spleen

extract_protocol:
Tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina RNA Kits were used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cold exposure at 10 °C for 2 weeks with an initial acclimatization period of 5 days at 18°C and 5 days at 14°C

tag: strain

tag: tissue

value: Spleen

value: week 11

value: wild type

tag: treatment

value: RT


title: VAT CE rep2

description: NEBNext Ultra RNA Library Prep Kit

source_name: VAT

value: VAT

tag: age

tag: genotype

value: CE


title: VAT RT rep3

description: NEBNext Ultra RNA Library Prep Kit


title: Ba/F3, SPAG9-JAK2(+), rep2

status: Public on May 18 2021

type: RNA

city: Kyoto

first: Azusa

last: Mayumi

address: 465, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

country: Japan

institute: Kyoto Prefectural University of Medicine

description: Gene expression data from SPAG9-JAK2-expressing Ba/F3 cells induced by doxycycline (Ba/F3-SPAG9-JAK2)

hyb_protocol: Biotin-labeled cRNA was hybridized to a GeneChip Mouse Genome 430 2.0 Array (Thermo Fisher Scientific) following the standard protocols.

scan_protocol: Hybridized arrays were stained and scanned with a Genechip 3000 7G Scanner (Thermo Fisher Scientific) at the default settings.

data_processing: Data were analyzed using Affymetrix Expression Console Software 1.4.1.

label: biotin

label_protocol: cRNA target synthesis was carried out using a GeneChip 3’IVT PLUS Reagent Kit (Thermo Fisher Scientific).

growth_protocol: Ba/F3 cells transduced with SPAG9-JAK2 fusion protein by the Retro-X Tet-on Advanced Inducible System (Takara Bio) were washed twice with phosphate-buffered saline and seeded in triplicate with or without 500 ng/ml doxycycline.

extract_protocol: Total RNA was extracted 48 hours later from Ba/F3 cells with or without expression of SPAG9-JAK2 using an RNeasy Mini Kit (Qiagen, Hilden, Germany), and the quality was checked on a NanoDrop 2000 (Thermo Fisher Scientific) and a 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).

treatment_protocol: Ba/F3 cells expressing SPAG9-JAK2 under doxycycline dependent manner were established, and SPAG9-JAK2 protein expression was induced using 500 ng/ml doxycycline.

tag: cell line

tag: cell type

value: interleukin-3-dependent murine pro-B cell line


title: Ba/F3, SPAG9-JAK2(+), rep3

source_name: SPAG9-JAK2-expressing Ba/F3 cells induced by doxycycline (Ba/F3-SPAG9-JAK2)


title: GATA2_ChIP-exo_DHT rep1

description: Extraction protocol 1

source_name: GATA2_ChIP-exo_DHT rep1


title: Spleen CE rep3

description: NEBNext Ultra RNA Library Prep Kit


title: Spleen CE rep2

description: NEBNext Ultra RNA Library Prep Kit


title: GATA2_ChIP-exo_veh rep1

description: Extraction protocol 1

source_name: GATA2_ChIP-exo_veh rep1

value: DMSO


title: VAT CE rep3

description: NEBNext Ultra RNA Library Prep Kit


title: VAT CE rep1

description: NEBNext Ultra RNA Library Prep Kit


title: Spleen RT rep3

description: NEBNext Ultra RNA Library Prep Kit


title: VAT RT rep1

description: NEBNext Ultra RNA Library Prep Kit


title: SAT CE rep3

description: NEBNext Ultra RNA Library Prep Kit

source_name: SAT

value: SAT


title: SAT CE rep1

description: NEBNext Ultra RNA Library Prep Kit


title: Spleen CE rep1

description: NEBNext Ultra RNA Library Prep Kit


title: SAT CE rep2

description: NEBNext Ultra RNA Library Prep Kit


title: SAT RT rep2

description: NEBNext Ultra RNA Library Prep Kit


title: Spleen RT rep2

description: NEBNext Ultra RNA Library Prep Kit


title: Liver RT rep2

description: NEBNext Ultra RNA Library Prep Kit

source_name: Liver

value: Liver


title: Liver CE rep3

description: NEBNext Ultra RNA Library Prep Kit


title: Liver CE rep1

description: NEBNext Ultra RNA Library Prep Kit


title: Ileum RT rep3

description: NEBNext Ultra RNA Library Prep Kit

source_name: Ileum

value: Ileum


title: Ileum RT rep2

description: NEBNext Ultra RNA Library Prep Kit


title: Hypothalamus RT rep2

description: NEBNext Ultra RNA Library Prep Kit

source_name: Hypothalamus

value: Hypothalamus


title: SAT RT rep1

description: NEBNext Ultra RNA Library Prep Kit


title: GATA2_ChIP-exo_veh rep2

description: Extraction protocol 1

source_name: GATA2_ChIP-exo_veh rep2


title: VAT RT rep2

description: NEBNext Ultra RNA Library Prep Kit


title: Hypothalamus CE rep3

description: NEBNext Ultra RNA Library Prep Kit


title: Liver RT rep3

description: NEBNext Ultra RNA Library Prep Kit


title: SAT RT rep3

description: NEBNext Ultra RNA Library Prep Kit


title: Brain RT rep2

description: NEBNext Ultra RNA Library Prep Kit

source_name: Brain

value: Brain


title: Brain RT rep1

description: NEBNext Ultra RNA Library Prep Kit


title: Liver RT rep1

description: NEBNext Ultra RNA Library Prep Kit


title: Liver CE rep2

description: NEBNext Ultra RNA Library Prep Kit


title: Ileum CE rep3

description: NEBNext Ultra RNA Library Prep Kit


title: Ileum CE rep1

description: NEBNext Ultra RNA Library Prep Kit


title: BAT CE rep3

description: NEBNext Ultra RNA Library Prep Kit

source_name: BAT

value: BAT


title: Hypothalamus RT rep3

description: NEBNext Ultra RNA Library Prep Kit


title: Ileum CE rep2

description: NEBNext Ultra RNA Library Prep Kit


title: BAT RT rep3

description: NEBNext Ultra RNA Library Prep Kit


title: BAT CE rep2

description: NEBNext Ultra RNA Library Prep Kit


title: Ileum RT rep1

description: NEBNext Ultra RNA Library Prep Kit


title: H1-ChIP_DHT rep2

description: Extraction protocol 2

data_processing:
hIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 version with parameters '-k 2 -v 2' to report up to two valid alignments
Read with multiple valid alignments were removed using a Perl program
Uniquely mapped reads from replicates of the same sample were pooled
Peaks were called using MACS2 with parameters '-m 3,30 -g hs -p 1e-8'
ChIP-exo data were processed using ePEST with parameters '-p 1e-8 -R 25 -c 0.05 -k 2.0'
BigWig file was generated by deeptools for visualization
Genome_build: GRCh37/hg19

source_name: H1-ChIP_DHT rep2

value: LNCap cell line


title: Brain CE rep2

description: NEBNext Ultra RNA Library Prep Kit


title: Oldserum_rep1

value: treated with old serum

value: 25 days

value: endothelial cells


title: Hypothalamus CE rep1

description: NEBNext Ultra RNA Library Prep Kit

value: week 11


title: H3K27me3_DHT rep1

description: Extraction protocol 2

source_name: H3K27me3_DHT rep1

value: Abcam

value: DHT


title: SAMP8_old031_rep4

value: SAMP8 mice brain hippocampal tissue

value: 13 months


title: H3K27me3_DHT rep2

description: Extraction protocol 2

source_name: H3K27me3_DHT rep2


title: Brain CE rep3

description: NEBNext Ultra RNA Library Prep Kit

value: wild type

value: CE


title: BAT CE rep1

description: NEBNext Ultra RNA Library Prep Kit


title: SAMP8_old031_rep5


title: H3K27ac_DHT rep1

description: Extraction protocol 2

source_name: H3K27ac_DHT rep1


title: Brain CE rep1

description: NEBNext Ultra RNA Library Prep Kit


title: Hypothalamus RT rep1

description: NEBNext Ultra RNA Library Prep Kit

value: RT


title: H3K4me2_DHT rep2

description: Extraction protocol 2

source_name: H3K4me2_DHT rep2


title: BAT RT rep1

description: NEBNext Ultra RNA Library Prep Kit


title: H3K4me3_DHT rep1

description: Extraction protocol 2

source_name: H3K4me3_DHT rep1

value: Millipore


title: H3K4me1_DHT rep1

description: Extraction protocol 2

source_name: H3K4me1_DHT rep1


title: MNase_DHT rep2

description: Extraction protocol 2

source_name: MNase_DHT rep2

value: MNase digestion only


title: H1-ChIP_DHT rep1

description: Extraction protocol 2

source_name: H1-ChIP_DHT rep1


title: H3K79me2_DHT rep2

description: Extraction protocol 2

source_name: H3K79me2_DHT rep2


title: Brain RT rep3

description: NEBNext Ultra RNA Library Prep Kit


title: H3K79me2_DHT rep1

description: Extraction protocol 2

source_name: H3K79me2_DHT rep1


title: H3K36me3_DHT rep2

description: Extraction protocol 2

source_name: H3K36me3_DHT rep2


title: MNase_DHT rep1

description: Extraction protocol 2

source_name: MNase_DHT rep1


title: H3K36me3_DHT rep1

description: Extraction protocol 2

source_name: H3K36me3_DHT rep1


title: Hypothalamus CE rep2

description: NEBNext Ultra RNA Library Prep Kit

source_name: Hypothalamus

value: Hypothalamus


title: H3K36me3_veh rep2

description: Extraction protocol 2

source_name: H3K36me3_veh rep2

value: DMSO


title: H3K79me2_veh rep1

description: Extraction protocol 2

source_name: H3K79me2_veh rep1


title: H3K27ac_DHT rep2

description: Extraction protocol 2

source_name: H3K27ac_DHT rep2


title: H3K36me3_veh rep1

description: Extraction protocol 2

source_name: H3K36me3_veh rep1


title: H3K27me3_veh rep1

description: Extraction protocol 2

source_name: H3K27me3_veh rep1


title: H3K27me3_veh rep2

description: Extraction protocol 2

source_name: H3K27me3_veh rep2


title: H3K27ac_veh rep2

description: Extraction protocol 2

source_name: H3K27ac_veh rep2


title: H3K9me3_DHT rep2

description: Extraction protocol 2

source_name: H3K9me3_DHT rep2


title: H3K9me3_DHT rep1

description: Extraction protocol 2

source_name: H3K9me3_DHT rep1


title: H3K4me1_DHT rep2

description: Extraction protocol 2

source_name: H3K4me1_DHT rep2


title: H3K4me3_veh rep2

description: Extraction protocol 2

source_name: H3K4me3_veh rep2


title: H3K4me3_DHT rep2

description: Extraction protocol 2

source_name: H3K4me3_DHT rep2


title: H3K4me3_veh rep1

description: Extraction protocol 2

source_name: H3K4me3_veh rep1


title: H3K4me2_veh rep2

description: Extraction protocol 2

source_name: H3K4me2_veh rep2


title: H3K4me1_veh rep2

description: Extraction protocol 2

source_name: H3K4me1_veh rep2


title: H3K4me1_veh rep1

description: Extraction protocol 2

source_name: H3K4me1_veh rep1


title: MNase_veh rep1

description: Extraction protocol 2

source_name: MNase_veh rep1


title: H1-ChIP_veh rep1

description: Extraction protocol 2

source_name: H1-ChIP_veh rep1


title: H3K79me2_veh rep2

description: Extraction protocol 2

source_name: H3K79me2_veh rep2


title: H3K27ac_veh rep1

description: Extraction protocol 2

source_name: H3K27ac_veh rep1


title: Bonemarrow RT rep6

description:
RNA extraction via RNAeasy mini kit (Qiagen)
TruSeq stranded mRNA kit

source_name: Bone marrow

value: Bone marrow


title: Bonemarrow RT rep5


title: H3K4me2_DHT rep1

description: Extraction protocol 2

source_name: H3K4me2_DHT rep1

value: LNCap cell line


title: BAT RT rep2

description: NEBNext Ultra RNA Library Prep Kit

source_name: BAT

value: BAT


title: Bonemarrow RT rep2


title: Bonemarrow CE rep6


title: Bonemarrow RT rep1


title: MNase_veh rep2

description: Extraction protocol 2

source_name: MNase_veh rep2


title: Bonemarrow CE rep4


title: Bonemarrow CE rep1


title: H1-ChIP_veh rep2

description: Extraction protocol 2

source_name: H1-ChIP_veh rep2


title: Spinalcord RT rep5

description: TruSeq stranded mRNA kit

source_name: spinal cord

value: spinal cord


title: Spinalcord RT rep4

description: TruSeq stranded mRNA kit


title: Bonemarrow RT rep4


title: Bonemarrow RT rep3


title: Bonemarrow CE rep5


title: Bonemarrow CE rep2


title: Spinalcord RT rep3

description: TruSeq stranded mRNA kit


title: Spinalcord RT rep2

description: TruSeq stranded mRNA kit


title: Spinalcord CE rep1

description: TruSeq stranded mRNA kit


title: cyto_STARVE_4

status: Public on Apr 05 2021

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

data_processing:
The alignment (with HISAT2) and quantification (default parameters) of RNAseq reads were performed using the nf-core/rnaseq v1.2 pipeline available at https://github.com/nf-core/rnaseq (Ewels et al, 2019).
Genes with multiple loci were excluded from the analysis and only protein-coding genes were further analyzed.
Replicate 1A was excluded from the downstream analysis (it is from the same biological replicate as 1B ans was used only as a quality check).
For downstream transformation, filtering and normalization, the default methods of the anota2seq R package (Oertlin et al, 2019) were selected (Robinson & Oshlack, 2010; Ritchie et al, 2015).
Analysis of changes in mRNA abundance and changes in translational efficiencies leading to altered protein levels or buffering was carried out with anota2seq using default parameters (biological replicate was used as a batch effect in anota2seq) of the anota2seqRun function (Oertlin et al, 2019). This was implemented for the following contrasts: DMSO (full serum media) vs. starvation, MLN0128 vs. DMSO (full serum media), RMC-4627 vs. MLN0128 and RMC-4745 vs. MLN0128.
Genome_build: GRCh37
Supplementary_files_format_and_content: The processed data files are featureCounts output of the nf-core/rnaseq pipeline

source_name: MCF7 cells

growth_protocol: MCF7 scr cells were cultured in RPMI containing 10% FBS and 1% penicillin/streptomycin at 37 °C and 5% CO2.

extract_protocol:
Polysome-associated mRNA was extracted from fractions corresponding to mRNA associated with more than 3 ribosomes. RNA extraction was performed in parallel for polysome-associated and cytoplasmic RNA using Tri-reagent followed by purification using the RNeasy MinElute Cleanup Kit (Qiagen).
Sequencing libraries were constructed using the smartSeq2 protocol (Picelli et al., 2014).

treatment_protocol: On day 0, cells were seeded in 15-cm plates. On day 2, cells were washed three times in PBS and starved in RPMI with 0.1% FBS media for 16h. This was followed by a 4h stimulation with complete media in presence of vehicle (DMSO), RMC-4627 (3nM), RMC-4745 (35nM) or MLN0128 (40nM). Cell confluence was at 80% upon harvest. Four biological replicates were generated and polysome-profiling was performed as previously described (Gandin et al. 2014).

value: MCF7 cells

value: Cytosolic

value: STARVE


title: poly_MLN0128_4

value: Polysome assoc.


title: Spinalcord CE rep4

description: TruSeq stranded mRNA kit

value: week 11


title: Spinalcord RT rep1

description: TruSeq stranded mRNA kit


title: Spinalcord CE rep5

description: TruSeq stranded mRNA kit


title: Spinalcord CE rep2

description: TruSeq stranded mRNA kit


title: cyto_RMC4627_4


title: poly_RMC4745_4


title: cyto_DMSO_4


title: Spinalcord CE rep3

description: TruSeq stranded mRNA kit


title: cyto_STARVE_3


title: poly_MLN0128_3


title: cyto_MLN0128_4


title: Bonemarrow CE rep3


title: poly_RMC4627_4


title: poly_DMSO_4


title: cyto_MLN0128_3


title: poly_DMSO_3


title: cyto_DMSO_3


title: cyto_RMC4745_3


title: cyto_RMC4745_4


title: poly_MLN0128_2


title: poly_RMC4627_3


title: cyto_DMSO_2


title: poly_STARVE_3


title: cyto_STARVE_2


title: poly_RMC4745_2


title: cyto_RMC4627_3


title: poly_DMSO_2


title: poly_RMC4745_3


title: cyto_MLN0128_2


title: cyto_RMC4745_2


title: cyto_STARVE_1B


title: cyto_DMSO_1B


title: poly_RMC4745_1B


title: cyto_RMC4745_1B


title: cyto_RMC4627_2


title: cyto_MLN0128_1B


title: poly_STARVE_2


title: poly_RMC4627_1B


title: poly_DMSO_1B


title: poly_STARVE_4


title: poly_STARVE_1B


title: cyto_RMC4627_1B


title: poly_MLN0128_1B


title: poly_STARVE_1A


title: cyto_STARVE_1A


title: poly_MLN0128_1A


title: poly_RMC4627_2


title: poly_RMC4745_1A


title: cyto_MLN0128_1A


title: cyto_RMC4745_1A


title: poly_DMSO_1A


title: poly_RMC4627_1A


title: X031-RP1C1W3 Leuokopak control

status: Public on Mar 29 2021

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

data_processing:
Binary Base Call (BCL) files were demultiplexed using the mkfastq function in 10x's cell ranger software (version 3.1.0) producing fastq files.
FASTQs were run through 10x’s cell ranger alignment tool (cell ranger count) with defaults against human reference annotation (Ensembl GRCh38 GRCh38-3.0.0).
HDF5 files (filtered) were then uploaded into R statistical programming language (version 3.6.0) using the Seurat package (version 3.0) where normalization, scaling, integration and reference based label transfer was performed.
Genome_build: Ensembl GRCh38 GRCh38-3.0.0
Supplementary_files_format_and_content: HDF5 file (Hierarchical Data Format )
Genome_build: Ensembl GRCh38-3.0.0
Supplementary_files_format_and_content: HDF5 file (Hierarchical Data Format)

source_name: peripheral blood mononuclear cell

extract_protocol:
Biological specimens were purchased from BioIVT as cryopreserved PBMCs and Bloodworks NW as freshly drawn whole blood. All sample collections were conducted by BioIVT and Bloodworks NW under IRB-approved protocols, and all donors sign informed consent forms.PBMCs were removed from liquid nitrogen storage and immediately thawed in a 37C water bath. Cells were diluted dropwise with 37°C AIM V media up to a final volume of 10 mL. A single wash was performed in 10 mL of PBS+BSA. PBMCs were resuspended 2 mL in PBS+BSA, counted on a ViCell or Cellometer Spectrum, as above, and 1x106 cells were incubated sequentially or together with Human Trustain FcX (BioLegend #422302) and Fixable Viability Stain 510 (BD #564406), on ice according to manufacturer’s instructions. Cell were washed with PBS+BSA and stained with a master mix cocktail of antibodies (STAR*Methods/Antibodies) on ice for 25-30 minutes
Single-cell RNA-seq libraries were generated using the 10X Genomics Chromium 3’ Single Cell Gene Expression assay (#100075 or #1000121) and Chromium Controller Instrument according to the manufacturer’s published protocol. 16,000 cells from each PBMC sample was loaded into a separate Chromium Single Cell Chip B (10X Genomics #1000073) well targeting a recovery of 10,000 cells. Gel Beads-in-emulsion (GEMs) were then generated using the 10X Chromium Controller.

value: peripheral blood mononuclear cell

tag: disease state

value: normal


title: X019-RP2C3W6-RNA_Aged pbmcs derived from a normal subject D at 18 hours

description:
barcoded libraries were made using a 10x chromium controller  and an Illumina NovaSeq for sequencing
The FASTQS are human subjects going into dbGAP so they are not included here

data_processing:
Binary Base Call (BCL) files were demultiplexed using the mkfastq function in 10x's cell ranger software (version 3.1.0) producing fastq files.
FASTQs were run through 10x’s cell ranger alignment tool (cell ranger count) with defaults against human reference annotation (Ensembl GRCh38 GRCh38-3.0.0).
HDF5 files (filtered) were then uploaded into R statistical programming language (version 3.6.0) using the Seurat package (version 3.0) where normalization, scaling, integration and reference based label transfer was performed.
Genome_build: Ensembl GRCh38 GRCh38-3.0.0
Supplementary_files_format_and_content: HDF5 file (Hierarchical Data Format )

extract_protocol:
PBMCs were removed from liquid nitrogen storage and immediately thawed in a 37C water bath. Cells were diluted dropwise with 37°C AIM V media up to a final volume of 10 mL. A single wash was performed in 10 mL of PBS+BSA. PBMCs were resuspended 2 mL in PBS+BSA, counted on a ViCell or Cellometer Spectrum, as above, and 1x106 cells were incubated sequentially or together with Human Trustain FcX (BioLegend #422302) and Fixable Viability Stain 510 (BD #564406), on ice according to manufacturer’s instructions. Cell were washed with PBS+BSA and stained with a master mix cocktail of antibodies (STAR*Methods/Antibodies) on ice for 25-30 minutes
Single-cell RNA-seq libraries were generated using the 10X Genomics Chromium 3’ Single Cell Gene Expression assay (#100075 or #1000121) and Chromium Controller Instrument according to the manufacturer’s published protocol. 16,000 cells from each PBMC sample was loaded into a separate Chromium Single Cell Chip B (10X Genomics #1000073) well targeting a recovery of 10,000 cells. Gel Beads-in-emulsion (GEMs) were then generated using the 10X Chromium Controller.

treatment_protocol: Blood samples were obtained from healthy (no diagnosis of disease) and non-matched SLE donors through protocols approved by the relevant institutional review boards. Blood was drawn into BD NaHeparin vacutainer tubes for PBMC (BD #367874) and, upon arrival at the processing lab, all NaHeparin tubes for each donor were pooled into a sterile plastic receptacle to establish one common pool for all time points. PBMC isolation was started at 2, 4, 6, 8, and 18 hours post-draw (Experiment 1) or 2, 4, 6, 10, 14, and 18 hours post-draw (Experiment 2). For PBMC isolation, at each time point the pool of blood was gently swirled until fully mixed, about 30 times, and a volume of blood was removed and combined with an equivalent volume of room temperature PBS (ThermoFisher #14190235). PBMC were isolated using one or more Leucosep tubes (Greiner Bio-One #227290) loaded with 15 mL of Ficoll Premium (GE Healthcare #17-5442-03) to which a 3 mL cushion of PBS had been slowly added on top of the Leucosep barrier. The 24-30 mL diluted whole blood was slowly added to the tube and spun at 1000xg for 10 minutes at 20°C with no brake. PBMC were recovered from the Leucosep tube by quickly pouring all volume above the barrier into a sterile 50 mL conical tube. 15 mL cold PBS+0.2% BSA (Sigma #A9576; “PBS+BSA”) was added and the cells were pelleted at 400xg for 5-10 minutes at 4-10°C. The supernatant was quickly decanted, the pellet dispersed by flicking the tube, and the cells washed with 25-50 mL cold PBS+BSA. Cell pellets were combined, if applicable, the cells were pelleted as before, supernatant quickly decanted, and residual volume was carefully aspirated. The PBMC were resuspended in 1 mL cold PBS+BSA per 15 mL whole blood processed and counted with a ViCell (Beckman Coulter) using VersaLyse reagent (Beckman Coulter #A09777) or with a Cellometer Spectrum (Nexcelom) using Acridine Orange/Propidium Iodide solution. PBMC were cryopreserved in Cryostor10 (StemCell Technologies #07930) or 90% FBS (ThermoFisher #10438026) / 10% DMSO (Fisher Scientific #D12345) at 5x106 cells/mL by slow freezing in a Coolcell LX (VWR #75779-720) overnight in a -80°C freezer followed by transfer to liquid nitrogen.

tag: hours after blood draw

value: 18 hours

tag: subject id

value: D


title: cyto_RMC4627_1A


title: X019-RP2C3W5-RNA_Aged pbmcs derived from a normal subject C at 18 hours

value: C


title: X019-RP2C3W4-RNA_Aged pbmcs derived from a normal subject B at 18 hours

value: B


title: X019-RP2C3W3-RNA_Aged pbmcs derived from a normal subject A at 18 hours

value: A


title: X019-RP2C3W2-RNA_Aged pbmcs derived from a normal subject D at 14 hours

value: 14 hours


title: X019-RP2C2W8-RNA_Aged pbmcs derived from a normal subject B at 14 hours


title: X019-RP2C2W7-RNA_Aged pbmcs derived from a normal subject A at 14 hours


title: X019-RP2C2W6-RNA_Aged pbmcs derived from a normal subject D at 10 hours

value: 10 hours


title: X019-RP1C2W4-RNA_Aged pbmcs derived from a normal subject B at 10 hours


title: X019-RP2C2W5-RNA_Aged pbmcs derived from a normal subject C at 10 hours


title: X019-RP1C2W2-RNA_Aged pbmcs derived from a normal subject D at 6 hours

value: 6 hours


title: X019-RP1C2W1-RNA_Aged pbmcs derived from a normal subject C at 6 hours


title: X019-RP1C1W8-RNA_Aged pbmcs derived from a normal subject D at 4 hours

value: 4 hours


title: cyto_DMSO_1A

value: DMSO


title: X019-RP1C1W7-RNA_Aged pbmcs derived from a normal subject C at 4 hours


title: X019-RP1C1W6-RNA_Aged pbmcs derived from a normal subject B at 4 hours


title: X031-RP1C1W2 Leuokopak control


title: H3K9me3_veh rep2

description: Extraction protocol 2

source_name: H3K9me3_veh rep2

value: LNCap cell line

value: Millipore


title: X019-RP1C1W5-RNA_Aged pbmcs derived from a normal subject A at 4 hours


title: X019-RP1C1W4-RNA_Aged pbmcs derived from a normal subject D at 2 hours

value: 2 hours


title: X031-RP1C1W1 Leuokopak control


title: X019-RP1C1W3-RNA_Aged pbmcs derived from a normal subject C at 2 hours


title: NW_TX0011-17_GRCh38_Aged pbmcs derived from a sle subject BRISL7 at 4 hours

value: sle


title: X019-RP1C1W2-RNA_Aged pbmcs derived from a normal subject B at 2 hours


title: X019-RP1C1W1-RNA_Aged pbmcs derived from a normal subject A at 2 hours


title: NW_TX0011-18_GRCh38_Aged pbmcs derived from a sle subject BRISL7 at 6 hours


title: NW_TX0011-20_GRCh38_Aged pbmcs derived from a sle subject BRISL7 at 18 hours


title: NW_TX0011-19_GRCh38_Aged pbmcs derived from a sle subject BRISL7 at 8 hours

value: 8 hours


title: X019-RP2C3W1-RNA_Aged pbmcs derived from a normal subject C at 14 hours

value: peripheral blood mononuclear cell


title: NW_TX0011-16_GRCh38_Aged pbmcs derived from a sle subject BRISL7 at 2 hours


title: X019-RP1C2W3-RNA_Aged pbmcs derived from a normal subject A at 10 hours

value: normal


title: NW_TX0011-13_GRCh38_Aged pbmcs derived from a sle subject BRISL6 at 6 hours


title: NW_TX0011-12_GRCh38_Aged pbmcs derived from a sle subject BRISL6 at 4 hours


title: NW_TX0011-14_GRCh38_Aged pbmcs derived from a sle subject BRISL6 at 8 hours


title: NW_TX0011-15_GRCh38_Aged pbmcs derived from a sle subject BRISL6 at 18 hours

value: 18 hours


title: NW_TX0011-9_GRCh38_Aged pbmcs derived from a sle subject BRISL5 at 8 hours


title: NW_TX0011-11_GRCh38_Aged pbmcs derived from a sle subject BRISL6 at 2 hours


title: H3K4me2_veh rep1

description: Extraction protocol 2

source_name: H3K4me2_veh rep1

value: Abcam


title: H3K9me3_veh rep1

description: Extraction protocol 2

source_name: H3K9me3_veh rep1


title: NW_TX0011-8_GRCh38_Aged pbmcs derived from a sle subject BRISL5 at 6 hours


title: NW_TX0011-10_GRCh38_Aged pbmcs derived from a sle subject BRISL5 at 18 hours


title: NW_TX0005-15_GRCh38_Aged pbmcs derived from a normal subject BRISL4 at 18 hours


title: NW_TX0011-7_GRCh38_Aged pbmcs derived from a sle subject BRISL5 at 4 hours


title: NW_TX0005-14_GRCh38_Aged pbmcs derived from a normal subject BRISL4 at 8 hours


title: NW_TX0005-13_GRCh38_Aged pbmcs derived from a normal subject BRISL4 at 6 hours


title: NW_TX0005-12_GRCh38_Aged pbmcs derived from a normal subject BRISL4 at 4 hours


title: NW_TX0005-11_GRCh38_Aged pbmcs derived from a normal subject BRISL4 at 2 hours


title: NW_TX0005-10_GRCh38_Aged pbmcs derived from a normal subject BRISL3 at 18 hours


title: NW_TX0005-9_GRCh38_Aged pbmcs derived from a normal subject BRISL3 at 8 hours


title: NW_TX0011-6_GRCh38_Aged pbmcs derived from a sle subject BRISL5 at 2 hours


title: NW_TX0005-8_GRCh38_Aged pbmcs derived from a normal subject BRISL3 at 6 hours


title: NW_TX0005-7_GRCh38_Aged pbmcs derived from a normal subject BRISL3 at 4 hours


title: NW_TX0005-4_GRCh38_Aged pbmcs derived from a normal subject BRISL2 at 8 hours


title: NW_TX0005-5_GRCh38_Aged pbmcs derived from a normal subject BRISL2 at 18 hours


title: NW_TX0005-2_GRCh38_Aged pbmcs derived from a normal subject BRISL2 at 4 hours


title: NW_TX0005-1_GRCh38_Aged pbmcs derived from a normal subject BRISL2 at 2 hours


title: Dros96H2WingDisc (scRNA-seq)

status: Public on Mar 23 2021

city: Berkeley

first: Iswar

middle: Krishna

last: Hariharan

address: Weill Hall

department: Molecular & Cell Biology

institute: University of California, Berkeley

description: Replicate 2 for single-cell RNA collected at 96 hours after egg lay

data_processing:
Sequencing reads were aligned to the Drosophila genome using the CellRanger software (v2.2).
Genome_build: Drosophila genome version 6.24
Supplementary_files_format_and_content: *_matrix.mtx: Genes by cells UMI count matrix
*_barcodes.tsv: Cell barcodes for matrix.mtx
*_genes.tsv: Gene names for matrix.mtx
*_raw_gene_bc_matrices_h5.h5: Genes by cells UMI count matrix for all sequenced barcodes, including empty droplets, in h5 compressed format

organism: Drosophila melanogaster

source_name: Drosophila wing-imaginal disc

growth_protocol: Drosophila were raised at 25 degrees Celsius.

extract_protocol:
Each sample was loaded onto and barcoded by the 10x Chromium Single Cell 3' platform (v2 chemistry).
Illumina sequencing adapters were ligated on to cDNA molecules.

treatment_protocol: Wing disc tissue was dissociated in a collagenase-TrypLE cocktail to generate a single-cell suspension.

value: Drosophila wing-imaginal disc

value: Oregon R

value: 96 hours after egg lay (mid 3rd instar)


title: SOL_D8.5_Control_rep2

status: Public on Mar 22 2021

description:
SOL_D8p5_control_rep2
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt

data_processing:
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters.
Alignment to the mm10 genome (from Illumina iGenome) was performed using the STAR aligner version 2.5.3a using the --outFilterIntronMotifs RemoveNoncanonical parameter.
Gene expression was quantified using the HOMER analysis suite version 4.9.1, makeTagDirectory, analyzeRepeats.pl across exons of RefSeq genes.
Genome_build: mm10 (Illumina iGenome)
Supplementary_files_format_and_content: TimeCourse4F.raw.txt: Tab-delimited text file with raw count gene expression values.

source_name: mouse soleus muscle

growth_protocol: Mice were all fed on regular chow diet.

extract_protocol:
Total RNA of muscles was extracted using Trizol Reagent (Ambion).
mRNA-Seq libraries were prepared using the TruSeq RNA Library Preparation Kit according to the manufacturer’s instructions (Illumina).

treatment_protocol: Mice were fed with water containing Dox (1 mg/ml) for 2.5, 5.5 or 8.5-days to induce 4F overexpression.

tag: genotype/variation

value: 2 months

tag: dox treatment time

value: 8.5 days

value: soleus muscle


title: Dros120H1WingDisc (scRNA-seq)

description: Replicate 1 for single-cell RNA collected at 120 hours after egg lay

tag: developmental stage

value: 120 hours after egg lay (late 3rd instar)


title: Dros120H2WingDisc (scRNA-seq)

description:
Replicate 2 for single-cell RNA collected at 120 hours after egg lay
Raw files in SRR12368433 contains 117 reads. The small file size does not represent file corruption.


title: EDL_D8.5_Control_rep2

description:
EDL_D8p5_control_rep2
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt

source_name: mouse extensor digitorum longus muscle

value: extensor digitorum longus muscle


title: EDL_D8.5_Treatment_rep2

description:
EDL_D8p5_treatment_rep2
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt


title: SOL_D8.5_Treatment_rep1

description:
SOL_D8p5_treatment_rep1
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt


title: SOL_D5.5_Treatment_rep2

description:
SOL_D5p5_treatment_rep2
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt

value: 5.5 days


title: EDL_D8.5_Treatment_rep1

description:
EDL_D8p5_treatment_rep1
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt


title: SOL_D8.5_Treatment_rep2

description:
SOL_D8p5_treatment_rep2
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt


title: SOL_D5.5_Control_rep2

description:
SOL_D5p5_control_rep2
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt


title: EDL_D8.5_Control_rep1

description:
EDL_D8p5_control_rep1
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt


title: EDL_D5.5_Treatment_rep2

description:
EDL_D5p5_treatment_rep2
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt


title: SOL_D5.5_Treatment_rep1

description:
SOL_D5p5_treatment_rep1
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt


title: SOL_D8.5_Control_rep1

description:
SOL_D8p5_control_rep1
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt


title: EDL_D5.5_Control_rep2

description:
EDL_D5p5_control_rep2
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt


title: EDL_D5.5_Treatment_rep1

description:
EDL_D5p5_treatment_rep1
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt


title: EDL_D5.5_Control_rep1

description:
EDL_D5p5_control_rep1
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt


title: SOL_D2.5_Control_rep2

description:
SOL_D2p5_control_rep2
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt

value: 2.5 days


title: EDL_D2.5_Control_rep2

description:
EDL_D2p5_control_rep2
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt


title: SOL_D2.5_Treatment_rep2

description:
SOL_D2p5_treatment_rep2
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt


title: SOL_D5.5_Control_rep1

description:
SOL_D5p5_control_rep1
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt


title: NW_TX0005-6_GRCh38_Aged pbmcs derived from a normal subject BRISL3 at 2 hours

description:
barcoded libraries were made using a 10x chromium controller  and an Illumina NovaSeq for sequencing
The FASTQS are human subjects going into dbGAP so they are not included here

value: 2 hours


title: EDL_D2.5_Treatment_rep2

description:
EDL_D2p5_treatment_rep2
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt


title: SOL_D2.5_Control_rep1

description:
SOL_D2p5_control_rep1
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt


title: EDL_D2.5_Control_rep1

description:
EDL_D2p5_control_rep1
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt


title: NW_TX0005-3_GRCh38_Aged pbmcs derived from a normal subject BRISL2 at 6 hours

value: 6 hours


title: EDL_D2.5_Treatment_rep1

description:
EDL_D2p5_treatment_rep1
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt


title: Dros96H1WingDisc (scRNA-seq)

description: Replicate 1 for single-cell RNA collected at 96 hours after egg lay


title: SOL_D2.5_Treatment_rep1

description:
SOL_D2p5_treatment_rep1
PolyA RNA
Stranded single-end mRNA-seq
processed data file: TimeCourse4F.raw.txt


title: Bipolar disorder 5a BD5a_NA

status: Public on Mar 19 2021

description:
Bipolar disorder 5a
bipolar disorder; PBS vehicle stimulated

data_processing:
Sequenced reads were quality-tested using FASTQC.
Reads were aligned to the hg19 human genome using STAR aligner version 2.4.0k. Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read). The genome index was constructed using the gene annotation supplied with the hg19 Illumina iGenomes collection[4] and sjdbOverhang value of 100.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Raw gene expression was quantified across all gene exons (RNA-Seq) using the top-expressed isoform as proxy for gene expression.
Differential expression was performed using DESeq2 package version 1.20.0. Differentially expressed genes were defined as having a false discovery rate (FDR) <0.05 and a log2  fold change >1.
Enrichment analysis was performed using WebGestaltR package version 0.1.1.Hierarchical clustering was performed using the R language (v.3.3.2) with Ward’s hierarchical agglomerative clustering method and 1-correlation as a distance metric.Principal Component  Analysis (PCA) was performed on the normalized filtered gene counts using the R prcomp function.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited raw gene counts and differential expression tables

source_name: ipsc-derived astrocytes

growth_protocol: Astrocyte differentiation protocol details have been described in our study (Vadodaria et al.)

extract_protocol:
in vitro derivation from human iPSC
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The growth protocols of treatmennt with IL1b for 5 hours have been described in our study (Vadodarial et al)

value: fibroblast derived induced pluripotent stem cells

value: bipolar disorder


title: Bipolar disorder 5b BD5b_Il1b

description:
Bipolar disorder 5b
bipolar disorder; IL1b stimulated


title: Bipolar disorder 5a BD5a_Il1b

description:
Bipolar disorder 5a
bipolar disorder; IL1b stimulated


title: Bipolar disorder 5b BD5b_NA

description:
Bipolar disorder 5b
bipolar disorder; PBS vehicle stimulated


title: Bipolar disorder 3b BD3b_NA

description:
Bipolar disorder 3b
bipolar disorder; PBS vehicle stimulated


title: Bipolar disorder 4b BD4b_Il1b

description:
Bipolar disorder 4b
bipolar disorder; IL1b stimulated


title: Bipolar disorder 3a BD3a_Il1b

description:
Bipolar disorder 3a
bipolar disorder; IL1b stimulated


title: Bipolar disorder 4b BD4b_NA

description:
Bipolar disorder 4b
bipolar disorder; PBS vehicle stimulated


title: Bipolar disorder 4a BD4a_Il1b

description:
Bipolar disorder 4a
bipolar disorder; IL1b stimulated


title: Bipolar disorder 2a BD2a_NA2

description:
Bipolar disorder 2a
bipolar disorder; PBS vehicle stimulated


title: Bipolar disorder 2a BD2a_NA


title: Bipolar disorder 4a BD4a_NA

description:
Bipolar disorder 4a
bipolar disorder; PBS vehicle stimulated


title: Bipolar disorder 2a BD2a_Il1b

description:
Bipolar disorder 2a
bipolar disorder; IL1b stimulated


title: Bipolar disorder 1a BD1a_Il1b

description:
Bipolar disorder 1a
bipolar disorder; IL1b stimulated


title: Bipolar disorder 1b BD1b_Il1b

description:
Bipolar disorder 1b
bipolar disorder; IL1b stimulated


title: Bipolar disorder 1b BD1b_NA

description:
Bipolar disorder 1b
bipolar disorder; PBS vehicle stimulated


title: Control 4a C4a_NA

description:
Control 4a
neurotypical; PBS vehicle stimulated

value: neurotypical


title: Control 4a C4a_Il1b

description:
Control 4a
neurotypical; IL1b stimulated


title: Control 3b C3b_NA

description:
Control 3b
neurotypical; PBS vehicle stimulated


title: Control 2b C2b_Il1b

description:
Control 2b
neurotypical; IL1b stimulated


title: Control 3a C3a_Il1b

description:
Control 3a
neurotypical; IL1b stimulated


title: Control 3b C3b_Il1b

description:
Control 3b
neurotypical; IL1b stimulated


title: Control 3a C3a_NA

description:
Control 3a
neurotypical; PBS vehicle stimulated


title: Control 2b C2B_NA

description:
Control 2b
neurotypical; PBS vehicle stimulated


title: Control 2a C2A_NA

description:
Control 2a
neurotypical; PBS vehicle stimulated


title: Control 1b C1b_Il1b

description:
Control 1b
neurotypical; IL1b stimulated


title: Control 1b C1B_NA

description:
Control 1b
neurotypical; PBS vehicle stimulated


title: NOK1508p5_RES12_S5

status: Public on Mar 18 2021

data_processing:
Image analysis and base calling was done with Illumina CASAVA-1.8.2.
Sequenced reads were quality-tested using FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) v0.11.8.
Reads were aligned to the hg19  human genome using the STAR aligner version 2.5.3a. Mapping was carried out using default parameters, filtering non-canonical introns and allowing up to 10 mismatches per read and only keeping uniquely mapped reads. The genome index was constructed using the gene annotation supplied with the hg19 Illumina iGenomes collection (iGenomes online. Illumina. 2015. http://support.illumina.com/sequencing/sequencing_software/igenome.html) and sjdbOverhang value of 100.
Raw or FPKM (fragments per kilobase per million mapped reads) gene expression was quantified across all gene exons with HOMER v4.10.4 analyzeRepeats.pl with hg19 annotation v6.4 and parameters -strand + -count exons -condenseGenes (top-expressed isoform as proxy for gene expression) -normMatrix 1000000. Since ChrM genes are not part of the RefSeq annation, the Ensembl annotation was used.
Differential gene expression was carried out on the raw counts with HOMER getDiffExpression.pl that runs DESeq2  v1.14.1 using replicates to compute within-group dispersion and experimental batch modeled as a separate variable.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized expression (FPKMs) as a text table

source_name: Normal human oral keratinocytes

growth_protocol: Cells were grown in defined keratinocyte serum-free medium on collagen-coated plates and were passaged every 4 days through passage 11 and every 5 days thereafter

extract_protocol:
Cells were collected in TRIzol and RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo Research)
RNA-Seq libraries were prepared using the TruSeq Total mRNA Sample Preparation Kit (Illumina).
RNA-seq libraries were multiplexed, normalized, pooled for sequencing, and sequenced on the HiSeq system (Illumina) at single read 50.

treatment_protocol: Culture at atmospheric O2

value: normal oral keratinocytes

tag: passage

tag: Sex

value: female

value: 20 years


title: Control 1a C1a_Il1b

description:
Control 1a
neurotypical; IL1b stimulated


title: Control 2a C2a_Il1b

description:
Control 2a
neurotypical; IL1b stimulated


title: NOK1508p5_RES11_S4


title: Bipolar disorder 3a BD3a_NA

description:
Bipolar disorder 3a
bipolar disorder; PBS vehicle stimulated


title: Bipolar disorder 3b BD3b_Il1b

description:
Bipolar disorder 3b
bipolar disorder; IL1b stimulated


title: Bipolar disorder 1a BD1a_NA

description:
Bipolar disorder 1a
bipolar disorder; PBS vehicle stimulated


title: NOK1508p10_RES13_S6


title: NOK1508p10_RES14_S7


title: NOK1508p13_RES15_S8

value: last


title: NOK1508p13_RES16_S9


title: NOK1408p5_RES1_S44

value: 18 years


title: NOK1408p5_RES1_S7


title: NOK1408p16_RES10_S70


title: NOK1415p13_RES22_S33

value: male

value: 35 years


title: NOK1408p10_RES4_S10


title: NOK1408p10_RES4_S47


title: NOK1415p5_RES18_S29


title: NOK1415p5_RES17_S28


title: NOK1415p13_RES21_S32


title: NOK1415p10_RES20_S31


title: HemaCare-D205220 (10X)

status: Public on Mar 15 2021

city: La Jolla

first: Kyle

last: Gaulton

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Note: Barcodes for combinatorial barcoding snATAC-seq experiments are integrated into the original read names.
Alignment: Trimmed Nextera adapter sequences using trim_galore v.0.4.4 and aligned reads to hg19 using bwa mem v.0.7.17-r1188.
Filtering: Low mapping quality (MAPQ<30), mitochondrial reads, duplicate reads on a per-barcode basis with MarkDuplicates from picard.
Clustering: Custom code for processing snATAC-seq datasets is available at https://github.com/kjgaulton/pipelines/tree/master/T1D_snATAC_pipeline.
Peak calling: MACS2 (v.2.1.2) with --nomodel --keep-dup all on aggregate chromatin accessibility profiles for each cluster.
Genome_build: hg19
Supplementary_files_format_and_content: merged peaks
Supplementary_files_format_and_content: single cell cluster labels

source_name: peripheral blood mononuclear cells

extract_protocol:
Nuclei were isolated from fresh pancreatic islets using a glass dounce homogenizer with a tight-fitting pestle, frozen whole pancreas using a mortar and pestle, and PBMCs using a lysis buffer.
(CB; combinatorial barcoding) Permeabilized nuclei were distributed to 96 wells and tagmentation was carried out to introduce a first barcode combination. After pooling, 20 nuclei were sorted into each well of a 96 well plate and a second barcode was introduced by PCR. Libraries were purified according to the MinElute PCR Purification Kit manual using a vacuum manifold and size selection was performed with SPRI Beads. (10X; 10X Genomics) Libraries were generated using the 10X Genomics Chromium Chip E Single Cell ATAC kit following the manufacturers instructions.

value: peripheral blood mononuclear cells

tag: bmi

tag: donor id


title: HemaCare-D182364 (10X)


title: HemaCare-D273097 (10X)


title: Sciatic_3_day_rep1

status: Public on Mar 17 2021

city: Ann Arbor

first: Michigan

middle: CDB

last: Bioinformatics

state: MI

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

institute: University of Michigan

data_processing:
NovaSeq control software 1.6.0, RTA v3.4.4
Cellranger version 3.1.0 used with mm10 genome to align and count reads and generate filtered_feature_bc_matrix with default settings
filtered_feature_bc_matrix imported with R 3.6.2 and Seurat 3.1.2; cells with more than 7500 features, fewer than 200 features, more than 25% mitochondrial removed
Seurat SCTIntegration used to normalize and merge datasets
PCA dimension reduction
UMAP visualization
Clustering with KNN graph, Louvain optimization with resolution .5 (Sciatic_Nerve_MetaData_ClusterAssignment.tsv.gz)
Genome_build: mm10
Supplementary_files_format_and_content: From 10X cellranger count (for each sample): barcode.tsv, features.tsv, and matrix.mtx from "filtered_feature_bc_matrix" folder as well as the position sorted BAM file. From Seurat: "Seurat_Raw_Counts.tsv.gz" contains the initial imported matrix; "Seurat_Integrated_Counts.tsv.gz" contains the SCTransform integration pipeline results for the 3000 most variable genes (This data used for clustering); "Sciatic_Nerve_MetaData_ClusterAssignment.tsv.gz" matches the count file cell identifiers with their cluster assignment.

source_name: sciatic nerve trunk

extract_protocol:
sciatic nerve trunks were disected, enzymatically digested, and purified in a Percol gradient. Myelin debris were removed with myelin depletion beads. The cell isolation procedure was carried out in the presence of actinomycin D to block transcription.
10X Genomics Chromium Single Cell 3' v3 reagent kit following manufacturers directions. RNA was isolated and processed using the Chromium Controller (10X Genomics). Libraries were prepared using standard Illumina protocols.

treatment_protocol: mid-thigh sciatic nerve crush

tag: strain

value: sciatic nerve trunk

tag: procedure

value: mid-thigh sciatic nerve crush

tag: sampletype


title: HemaCare-D270271 (10X)

tag: tissue

tag: age


title: HemaCare-D147558 (10X)


title: Sciatic_3_day_rep2


title: Sciatic_3_day_rep3


title: ADAM1

status: Public on Feb 25 2021

first: April

last: Williams

institute: Salk Institute for Biological Studies

data_processing:
Reads were aligned by 10X cell ranger pipeline (v3.1.0) with default setting
Default filtered gene expression matrix was further processed by Seurat (v3.2.1.9002)
Cells with <10% mitochondrial reads and 200-10000 expressed genes were kept in the analysis.
Genome_build: mm10; Ensembl release-93
Supplementary_files_format_and_content: rawCount.tsv contains gene by cell expression raw count matrix
meta_data.tsv contains annotated cell identities and UMAP coordinates

source_name: brain immune cells FACS sorted CD45+

extract_protocol:
Microglia were isolated from 18mo APP/PS1 (AD) and APP/PS1 Axl-/-Mertk-/- (ADAM) cortices, 2 pooled cortices per sample, 2 biological replicates. Briefly, cortices were digested using a combination of enzymatic digestion and mechanical dissociation followed by removal of debris on a Percoll gradient. Single cell preparations were subjected to FACS sorting based on CD45 positivity.
Libraries were prepared according to Illumina's instructions on gene expression library constrcution (CG000204_ChromiumNextGEMSingleCell3_v3.1_Rev_D)
10X Single-Cell RNA-Seq

value: APP/PS1 Axl-/- Mertk-/-

value: brain

value: immune cells


title: Control 1a C1A_NA

description:
Control 1a
neurotypical; PBS vehicle stimulated

tag: genotype


title: AD2

tag: cell type


title: 177B-pri-all

status: Public on Feb 11 2021

city: Houston

first: Yang

last: Chen

address: 1881 East Road

department: Cancer Biology

institute: UT-MD Anderson Cancer Center

data_processing:
Fastq files from the Illumina platform were aligned to the reference genome mm10 using the 10X Genomics Cell Ranger Pipeline
After the alignment, a matrix file containing the cell barcode identity and gene values was exported by the 10X Genomics Cell Ranger Pipeline
Matrix files for the samples were then processed and analyzed by Seurat R software
Genome_build: Raw sequencing data from the Illumina platform were converted into Fastq files and aligned to the reference genome mm10
Supplementary_files_format_and_content: Processed data are in the CSV matrix format. All samples combined matrix CSV file as processed data was provided, while individual mouse/sample can be identified by the barcode.

source_name: KPC primary tumor live sorted

growth_protocol: KPC;YFP (LSL-KrasG12D;LSL-P53R172H;Pdx1-Cre;LSL-YFP) and KPCST;YFP (LSL-KrasG12D;LSL-P53R172H;Pdx1-Cre;Snail(loxP/loxP);Twist(loxP/loxP);LSL-YFP) mice were housed under standard housing conditions.

extract_protocol:
Single-cell barcoding and library preparation were performed using the 10X Genomics’ Chromium controller and Single Cell 3’ Reagent Kits v2 according to the manufacturer’s instructions.
Following capture and lysis, cDNA was synthesized and amplified to construct Illumina sequencing libraries using the 10X Chromium v2 according to the manufacturer’s instructions.

treatment_protocol: All mice were housed under standard housing conditions at MDACC animal facilities, without any treatment.

value: KPC primary tumor live sorted

value: KPC;YFP

tag: detailed genotype


title: HemaCare-D105 (10X)


title: ADAM2

city: San Diego

address: 10010 N Torrey Pines Rd


title: AD1


title: FlipFlop CD4 LN T cells - rep3

status: Public on Feb 07 2021

city: Frederick

first: Jack

state: MD

address: SAIC-Frederick Miller Dr

institute: NIH

data_processing:
Illumina RTA 1.18.61 software used for basecalling.
Twelve mRNA samples were pooled and sequenced on total 2 lanes on HiSeq2500 with Illumina TruSeq v4 chemistry. All the samples have excellent yield with yield above 61 million bases. Pass filtered reads have Q30 or above values about 93%. Both reads of each sample was trimmed for adapters and low quality bases using Trimmomatic software and aligned with reference mouse mm10 genome and ensemble v80 transcripts using Tophat software as stranded libraries.
CPM filtered by 0.5, TMM was calculated for the comparision
Genome_build: mm10
Supplementary_files_format_and_content: CPM_TMM_genes_filtered.txt

source_name: FlipFlop CD4 LN T cells

extract_protocol:
CD4 and CD8 T cells were sorted from lymph nodes of B6 and FlipFlop mice. Total RNA was prepared from sorted cells using RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: FlipFlop

value: Female

value: 14 wk-old

value: CD4 LN T cells


title: 739-PriTumor-all


title: NOK1408p14_RES8_S14

value: normal oral keratinocytes

value: female


title: FlipFlop CD4 LN T cells - rep2


title: FlipFlop CD8 LN T cells - rep2

source_name: FlipFlop CD8 LN T cells

value: CD8 LN T cells


title: B6 CD4 LN T cells - rep2

source_name: B6 CD4 LN T cells

value: 10 wk-old


title: B6 CD8 LN T cells - rep3

source_name: B6 CD8 LN T cells


title: B6 CD4 LN T cells - rep3


title: B6 CD8 LN T cells - rep1


title: FlipFlop CD8 LN T cells - rep3


title: B6 CD8 LN T cells - rep2


title: NOK1415p10_RES19_S30

value: male

value: 35 years


title: FlipFlop CD4 LN T cells - rep1


title: Sample_1087

status: Public on Jan 28 2021

city: Berlin

first: Il-Kang

address: Augustenburger Platz 1

institute: Charité- Universitätsmedizin Berlin

data_processing:
sequenced reads were mapped to the genome (mm10) with STAR. Gene counts were computed with featureCounts, using the Gencode M12 annotation
Genome_build: mm10
Supplementary_files_format_and_content: gene abundances (read counts) per sample

source_name: CD4 T cells

growth_protocol: T cells were harvested from spleen and inguinal lymph nodes and enriched, using a CD4+ or CD8+ isolation kit (Miltenyi Biotec). T cells were cultured in T cell medium (TCM) consisting of RPMI and 10% fetal bovine serum (FBS; both from Life Technologies) supplemented with 100 U/mL penicillin, 100 mg/mL streptomycin, 1 mmol/L sodium pyruvate, 1x nonessential amino acids, 50 mmol/L beta-mercaptoethanol, and 2 mmol/L L-glutamine (all from Sigma-Aldrich).

extract_protocol:
ST and LT cultured CD8+ or CD4+ T cells were sorted for CD44+CD62L+ (>97%) using a FACS Aria II or Aria III (BD Biosciences). Afterwards, RNA was isolated with the RNeasy Mini Kit (QIAGEN).
The RNA library was generated by using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB). Illumina sequencing was performed with NextSeq® 500/550 High Output Kit v2 (Illumina).

treatment_protocol: For activation, T cells were stimulated in vitro for 72 hours (polyclonal T cells from albino B6 mice) or 24 hours (transgenic T cells from Marilyn-BLITC and MataHari-BLITC) in TCM plus 1 ng/mL recombinant human IL-2 (PeproTech) in 6-well culture plates coated over night at 4°C with anti-CD3/CD28 (3 mg/mL anti-CD3, clone 145-2C11; 2 mg/mL anti-CD28, clone 37.51; both BD Biosciences). Afterwards, T cells were expanded using TCM containing 50 ng/mL recombinant human IL-15 and 10 ng/mL recombinant human IL-7 (both Peprotech) for further 4 days (short-term culture, ST) or 18 days (CD4+) and 25 days (CD8+) (long-term culture, LT).

value: CD4 T cells

tag: condition

tag: time


title: B6 CD4 LN T cells - rep1


title: Sample_1075


title: Sample_1081


title: Sample_1084


title: Sample_1063


title: Sample_1066


title: Sample_603

source_name: CD8 T cells

value: CD8 T cells


title: Sample_599


title: FlipFlop CD8 LN T cells - rep1


title: Sample_1072


title: Sample_595


title: Sample_1060


title: Sample_477


title: Sample_459


title: Sample_474


title: Sample_456


title: Arid2wt_MxCre_LSK_3

status: Public on Jan 08 2021

city: Milwaukee

last: Zhu

state: WI

address: 8733 W Watertown Plank Rd

institute: Versiti Blood Research Institute Milwaukee

data_processing:
Samples were demultiplexed via Illumina BaseSpace
Raw fastq reads were aligned to the mm10 genome using STAR via basepairtech.com
Genome_build: mm10
Supplementary_files_format_and_content: Number of reads aligned to each gene, per sample.  The data are not normalized.

extract_protocol:
Total RNA was extracted with TRIzol reagent. mRNA was further extracted using NEBNext Poly(a) mRNA Magnetic Isolation Module.
cDNA Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit from Illumina.

treatment_protocol: 6-8 week old mice were injected with pIpC. Bone marrow from mice was isolated 6 weeks post pIpC injection and LSK cell were isolated by FACS sorting.

tag: strain background

value: 6-8 weeks

tag: genotype/variation

value: MxCre+ (control)

tag: treatment/time point

value: 6 weeks post pIpC injection

value: mouse bone marrow

value: lineage negative, cKit+, Sca1+


title: Arid2wt_MxCre_LSK_1


title: Sample_591


title: Arid2wt_MxCre_LSK_2


title: Sample_462


title: Sample_1078


title: MC65_plusAb_plus121_rep4

status: Public on Oct 22 2020

data_processing:
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters.
Alignment to the hg19 genome (from illumina iGenome) was performed using the STAR aligner version 2.5.3a using the --outFilterIntronMotifs RemoveNoncanonical parameter. Reads mapped to mitochondiral-encoded genes were quantified by STAR using "--quantMode GeneCounts" parameter on the 10X cell ranger hg19 1.2.0 star index because Homer doesn't report mitochondrial genes.
Gene expression was quantified using the HOMER analysis suite version 4.9.1, makeTagDirectory, analyzeRepeats.pl across exons of RefSeq genes.
Genome_build: hg19 (illumina iGenome)
Supplementary_files_format_and_content: MC65_exons_raw_count.xlsx is an excel spreadsheet that contains the gene raw count summarized from exons.

source_name: human MC65 nerve cells

growth_protocol: The MC65 nerve cells were grown in Dulbecco's Modified Medium plus 10% fetal calf serum and 2 μg/ml tetracycline.

extract_protocol:
RNA was extracted from cells using the RNeasy Plus Universal Mini kit (Qiagen).
mRNA-Seq libraries were prepared using the TruSeq RNA Library Preparation Kit according to the manufacturer’s instructions (Illumina).

treatment_protocol: Aβ accumulation was induced by the removal of tetracycline from the growth medium. 1 uM CMS121 was added to MC65 cell lines with and without Aβ induction.

value: human MC65 nerve cells

value: plusAb


title: Arid2flfl_MxCre_LSK_2

value: Arid2fl/fl:MxCre+ (knockout)


title: MC65_plusAb_plus121_rep3


title: MC65_plusAb_plus121_rep5


title: MC65_plusAb_plus121_rep2


title: Sample_1069


title: MC65_plusAb_minus121_rep5


title: MC65_plusAb_minus121_rep4


title: MC65_plusAb_minus121_rep3


title: MC65_plusAb_plus121_rep1


title: MC65_minusAb_plus121_rep5

value: minusAb


title: MC65_minusAb_plus121_rep3


title: MC65_plusAb_minus121_rep2


title: MC65_minusAb_plus121_rep4


title: MC65_minusAb_plus121_rep1


title: Sample_465


title: MC65_minusAb_minus121_rep3


title: MC65_plusAb_minus121_rep1


title: MC65_minusAb_plus121_rep2


title: MC65_minusAb_minus121_rep5


title: MC65_minusAb_minus121_rep2


title: MC65_minusAb_minus121_rep1


title: MC65_minusAb_minus121_rep4


title: Arid2flfl_MxCre_LSK_3


title: Arid2flfl_MxCre_LSK_1


title: normal_iSM_rep2

status: Public on Sep 03 2020

data_processing:
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters.
Alignment to the hg19 genome (from illumina iGenome) was performed using the STAR aligner version 2.5.3a using the --outFilterIntronMotifs RemoveNoncanonical parameter
Gene expression was quantified using the HOMER analysis suite version 4.9.1, makeTagDirectory, analyzeRepeats.pl across exons of RefSeq genes.
Genome_build: hg19 (illumina iGenome)
Supplementary_files_format_and_content: iVEC_exons.raw.xlsx (raw count table for the induced vescular endothelial cells dataset)
Supplementary_files_format_and_content: iSM_exons.raw.xlsx(raw count table for the induced smooth muscle cells dataset, including three controls samples from published GEO accessions)
Supplementary_files_format_and_content: iSM_HGPS_exons.raw.txt (raw count table for the induced smooth muscle cells progeria dataset)

source_name: human induced smooth muscle cells

growth_protocol: iVECs were obtained from skin fibroblasts by expressing the master regulator ETV2 while iSM cells were obtained from fibroblasts by expressing MYOCD. iVECs were cultured on collagen-coated dishes in EGM-2MV (Lonza), while iSM cells were cultured in EGM-2 (Lonza).

extract_protocol:
RNA was extracted following standard procedures based on Trizol and chloroform. The RNeasy Mini kit was used to purify RNA (Qiagen). Samples were incubated with DNAse I for 30 min to degrade genomic DNA. RNA was resuspended in RNAse-free water. The amount of RNA was quantified with Nanodrop.
mRNA-Seq libraries were prepared using the TruSeq RNA Library Preparation Kit according to the manufacturer’s instructions (Illumina).

treatment_protocol: Both iVECs and iSM cells were selected with antibiotic treatment during reprogramming. iVECs were FACS sorted for CD31 before analyses.

tag: treatment

value: induced cells

value: normal

value: human induced smooth muscle cells


title: normal_iSM_rep1


title: normal_iSM_rep3


title: HGPS_iSM_rep8

value: HGPS


title: HGPS_iSM_rep5


title: HGPS_iSM_rep7


title: HGPS_iSM_rep6


title: HGPS_iSM_rep3


title: HGPS_iSM_rep2


title: HGPS_iSM_rep1


title: RS14_iSM_young_rep3

value: young


title: HT11_iSM_old_rep3

value: old


title: HT15_iSM_old_rep2


title: RS15_iSM_old_rep1


title: RS17_iSM_young_rep1


title: HT8_Fibro_rep6

source_name: human fibroblast cells

value: non-induced cells from donors

value: human fibroblast cells


title: HT14_Fibro_rep5


title: RS12_Fibro_rep4


title: SB_16_Endo_Prog_rep2

source_name: human endothelial cells

value: human endothelial cells


title: RS7_Fibro_rep1


title: RS2_Fibro_rep3


title: SB_15_Fibro_Prog_rep2


title: SB_14_Endo_Prog_rep1


title: SB_12_Endo_rep6


title: SB_11_Fibro_rep6


title: SB_10_Endo_rep5


title: SB_04_Endo_rep2


title: SB_13_Fibro_Prog_rep1


title: SB_09_Fibro_rep5


title: SB_07_Fibro_rep4


title: SB_05_Fibro_rep3


title: SB_03_Fibro_rep2


title: HGPS_iSM_rep4


title: SB_08_Endo_rep4


title: SB_06_Endo_rep3


title: SB_02_Endo_rep1


title: iVEC_young_rep1

source_name: human induced vascular endothelial cells

value: human induced endothelial cells


title: iVEC_old_rep3


title: iVEC_young_rep2


title: SB_01_Fibro_rep1


title: iVEC_young_rep3


title: Stag2-KO siStag1 Rep3

status: Public on Aug 10 2020

city: Chapel Hill

first: Jill

last: Dowen

state: NC

address: 250 Bell Tower Drive

institute: University of North Carolina at Chapel Hill

data_processing:
Reads Per Gene: Reads per gene were analyzed using STAR --runThreadN 24 -c SortedByCoordinate
Differentially expressed genes were identified using DESeq2 from Bioconductor (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: For each sample, a text file with reads per gene (gene count) is given.

source_name: mESC v6.5_Stag2-KO siStag1

growth_protocol: Murine embryonic stem cells (v6.5, male) were grown on gelatinized tissue culture dishes under standard ESC conditions as previously described (Whyte et al., 2012).

extract_protocol:
Cells were resuspended in Trizol (Invitrogen, Carlsbad CA) and Chloroform (Sigma Aldrich, St. Louis, MO) was added for phase separation. After collection, RNA was purified using the Zymo RNA Clean and Concentrator Kit (Zymo, Irvine, CA).
Libraries were prepared by Novogene, with poly-A transcript enrichment and sequenced by Novogene (Beijing, China).

treatment_protocol: Cells were counted and 5 x 10^5 were plated per well in 6-well plates. Each well was treated with 50nM of siRNA or siGLO transfection control using DharmaFECT (Dharmacon, Lafayette, CO) transfection reagent following manufacturer’s instructions: siGLO (D-001630-01-0) and siStag1 (M-041989-01-0005). Cell were harvested after 48 hours for RNA collection.

tag: cell line

value: Mouse embryonic stem cells

value: Stag2 knockout

tag: sirna treatment


title: iVEC_old_rep1


title: iVEC_old_rep2


title: RS1_Fibro_rep2


title: RS13_iSM_young_rep2


title: Stag2-KO siStag1 Rep1


title: Stag2-KO siStag1 Rep2


title: WT siStag1 Rep3

source_name: mESC v6.5_WT siStag1

value: Wildtype


title: WT siStag1 Rep2


title: Stag2-KO siGLO Rep3

source_name: mESC v6.5_Stag2-KO siGLO

value: siGLO control


title: Stag2-KO siGLO Rep2


title: Stag1-KO siGLO Rep 3

source_name: mESC v6.5_Stag1-KO siGLO

value: Stag1 knockout


title: Stag1-KO siGLO Rep 1


title: Stag2-KO siGLO Rep1


title: Stag1-KO siGLO Rep 2


title: WT siGLO Rep 2

source_name: mESC v6.5_WT siGLO


title: WT siStag1 Rep1


title: EVV23_K4_3

status: Public on Jul 30 2020

description: fpkm.txt

data_processing:
Sequenced reads were quality-tested using FASTQC and aligned to the hg19 human genome using the STAR version 2.5.3a.
Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read).
Gene expression counts were quantified with HOMER v4.10.4 analyzeRepeats.pl using the parameters -fpkm -count exons -condenseGenes -strand + -normMatrix 1000000
Genome_build: hg19 Illumina iGenomes
Supplementary_files_format_and_content: fpkm.txt contains FPKM quantification for all RNA-Seq samples.

source_name: naïve T cells

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated over Lymphoprep (STEMCELL Technologies) gradient . T cells were isolated from fresh PBMCs using EasySep Human T Cell Isolation Kit (STEMCELL Technologies, negative selection) and re-suspended in RPMI media supplemented with 10% FBS, L-glutamine (2 mM), penicillin (100 U/mL), and streptomycin (100 µg/mL) at 2 x 10^6 cells/mL.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) and RNAse free DNAse set (Qiagen) for on column DNA digestion.
RNA-Seq libraries were prepared using the TruSeq stranded mRNA Sample Preparation Kit v2 according to Illumina protocols.

treatment_protocol: The compounds were added to cells as 1000x DMSO stocks and mixed well by pipetting up and down after addition. The cells were kept at 37 °C in 5% CO2 containing incubators for 24 h, then pelleted by centrifugation (524 g, 5 min, 4 °C), washed with cold PBS (10 mL) and

tag: concentration

value: 20 µM

value: T cells


title: EVV22_L4_3

description: fpkm.txt

value: 10 µM


title: EVV21_DMSO_3

description: fpkm.txt

value: DMSO


title: EVV14_L4_1

description: fpkm.txt


title: EVV16_tript_1

description: fpkm.txt

value: triptolide


title: EVV13_DMSO_1

description: fpkm.txt


title: EVV20_tript_2

description: fpkm.txt


title: EVV15_K4_1

description: fpkm.txt


title: EVV11_AT406_3

description: fpkm.txt

value: 1 µM


title: EVV9_DMSO_3

description: fpkm.txt


title: EVV19_K4_2

description: fpkm.txt


title: EVV10_B9_3

description: fpkm.txt


title: EVV2_B9_1

description: fpkm.txt


title: EVV8_DMF_2

description: fpkm.txt

value: dimethylfumarate

value: 50 µM


title: EVV12_DMF_3

description: fpkm.txt


title: EVV7_AT406_2

description: fpkm.txt


title: EVV3_AT406_1

description: fpkm.txt


title: EVV6_B9_2

description: fpkm.txt


title: EVV24_tript_3

description: fpkm.txt


title: WT siGLO Rep 3


title: EVV1_DMSO_1

description: fpkm.txt


title: EVV4_DMF_1

description: fpkm.txt