title: BRD4_96h_rep2_ChIPSeq

description: Chromatin sonication for 16 min with Covaris

data_processing:
Sequencing data preprocessing. Paired-end reads with additional 6 base reads of barcodes were obtained for each of the samples. Reads from TT-seq/RNA-seq or ChIP-seq/ATAC-seq were demultiplexed and mapped with STAR 2.3.0 (Dobin et al., 2013) or Bowtie2.2.5/Bowtie1.0.0 (Langmead and Salzberg, 2012), respectively, to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium). For ATAC-seq, chromosome M was removed. Samtools (Li et al., 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f 163) were selected. Further data processing was carried out using the R/Bioconductor environment.
For ChIP-seq , we used the 'callpeak' function of MACS2.1.1 (Zhang et al., 2008) with ‘--BAMPE’ options. To catalogue all the C/EBPα, BRD4 or H3K4me1 binding sites over all the time points, we merged and reduced all peaks, and removed those falling +/- 4Mb of centromeric heterochromatin regions. Duplicates were removed. To obtain the enriched signal (count matrix), read count within the merged peaks were normalized by library size followed by a normalization with counts in corresponding input.
For ATAC-seq, reads were aligned to GRCh38 genome assembly without mitochondrial chromosome (ChrM) using Bowtie1.0.0 (Langmead et al., 2009). Bigwig files were generated by Deeptools 2.3.4 .
For TT-seq, we used a spike-in (RNAs) as described in (Schwalb et al., 2016) to allow antisense bias determination (ratio of spurious reads originating from the opposite strand introduced by the RT reactions) in TT-seq signal. Read counts for all spike-ins necessary to that end were calculated using HTSeq (Anders et al., 2015).
For Total RNA-seq, reads were aligned to GRCh38 genome assembly with STAR2.4.2 ((Dobin et al., 2013).
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: BRD4allPeaks_reduced.txt:Merged BRD4 peaks from all the time points.; BRD4mat.txt: BRD4 count table for genomic coordinates in BRD4allPeaks_reduced.txt, normalized with size factors and input
Supplementary_files_format_and_content: CEBPallPeaks_reduced.txt:Merged CEBPa peaks from all the time points; CEBPmat.txt: CEBP coverage normalized to size factors and input on the genomic coordinates in CEBPallPeaks_reduced.txt
Supplementary_files_format_and_content: H3K4me1allpeaks_reduced.txt:Merged H3K4me1 peaks from all the time points; H3K4me1mat.txt: H3K4me1 coverage normalized to size factors and input on the genomic coordinates in H3K4me1allPeaks_reduced.txt
Supplementary_files_format_and_content: The bigwig files of ATAC-seq were generated by deepTools2.3.4 (Ramirez et al., 2016) using --normalizeSizefactors1X options.
Supplementary_files_format_and_content: Strand specific bigwig files of TT-seq and RNA-seq were generated by deepTools2.3.4 (Ramirez et al., 2016) using --normalizeSizefactors1X --filterRNAstrand options.

value: NEB Ultra DNA Library kit

value: Beta-estradiol (100nM) treatment 96h

tag: chip antibody

value: anti-BRD4 (Bethyl Laboratories, A301-985A100)


title: 10005839158_R06C01 Sample253

status: Public on Apr 07 2021

type: genomic

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

department: Medical School

country: United Kingdom

institute: University of Exeter

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylation450K BeadChip (Illumina) protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing: Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.

label: hapten-labeled dideoxynucleotides

molecule: genomic DNA

organism: Homo sapiens

source_name: Whole Blood

label_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit (Zymo Research) according to the manufacturer’s standard protocol.

extract_protocol: DNA was extracted using a phenol/chloroform method

tag: status

value: FEP

tag: gender

value: F

tag: ageatbloodcollection


title: 10005839158_R04C01 Sample250

value: CON


title: 1560_P1_CONV_POOR [RNA-seq]

type: SRA

city: New York

first: Nicholas

last: Brady

state: NY

address: 1188 York Ave

department: Pathology and Laboratory Medicine

country: USA

institute: Weill Cornell Medicine

library_source: transcriptomic

data_processing:
Quality control of raw sequencing reads was performed using FastQC
Low-quality reads were removed using Trimmomatic with a sliding window of 4bp and quality threshold of 20
Reads passing QC were aligned to mm10 using STAR
BAM file creation, sorting, and indexing were performed using SAMtools
Transcript abundances in FPKM were caluculated using Cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: Transcript abundances in FPKM calculated using Cufflinks in comma-separated values (CSV) format

molecule: total RNA

organism: Mus musculus

source_name: Mouse tumor

extract_protocol:
RNA extraction from GEM prostate tumors was performed using the Maxwell 16 LEV simplyRNA Tissue Kit (Promega, AS1280). Regions of the cryopreserved tumor samples that were identified by a blinded pathologist were excised with a biopsy punch and processed as described.
Libraries were generated using the TruSeq RNA Library Prep Kit [Non-stranded, polyA+] (Illumina) following the manufacturer's recommended protocol.

tag: genotype

value: PbCre/+ ; Pten f/f; NMYC/+; Rb1 f/+

tag: age

value: 32 weeks

tag: tissue

value: Mouse tumor

value: Intact

tag: pathology

value: Conventional/Poorly Differentiated


title: TT_36h_rep1

city: Göttingen

first: Jinmi

last: Choi

address: Am Fassberg 11

department: Molecular Biology

country: Germany

institute: Max Planck Institute for Biophysical Chemistry

description: 4sU-labeled RNA

data_processing:
Library strategy: TT-seq (Schwalb et al., 2016)
Sequencing data preprocessing. Paired-end reads with additional 6 base reads of barcodes were obtained for each of the samples. Reads from TT-seq/RNA-seq or ChIP-seq/ATAC-seq were demultiplexed and mapped with STAR 2.3.0 (Dobin et al., 2013) or Bowtie2.2.5/Bowtie1.0.0 (Langmead and Salzberg, 2012), respectively, to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium). For ATAC-seq, chromosome M was removed. Samtools (Li et al., 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f 163) were selected. Further data processing was carried out using the R/Bioconductor environment.
For ChIP-seq , we used the 'callpeak' function of MACS2.1.1 (Zhang et al., 2008) with ‘--BAMPE’ options. To catalogue all the C/EBPα, BRD4 or H3K4me1 binding sites over all the time points, we merged and reduced all peaks, and removed those falling +/- 4Mb of centromeric heterochromatin regions. Duplicates were removed. To obtain the enriched signal (count matrix), read count within the merged peaks were normalized by library size followed by a normalization with counts in corresponding input.
For ATAC-seq, reads were aligned to GRCh38 genome assembly without mitochondrial chromosome (ChrM) using Bowtie1.0.0 (Langmead et al., 2009). Bigwig files were generated by Deeptools 2.3.4 .
For TT-seq, we used a spike-in (RNAs) as described in (Schwalb et al., 2016) to allow antisense bias determination (ratio of spurious reads originating from the opposite strand introduced by the RT reactions) in TT-seq signal. Read counts for all spike-ins necessary to that end were calculated using HTSeq (Anders et al., 2015).
For Total RNA-seq, reads were aligned to GRCh38 genome assembly with STAR2.4.2 ((Dobin et al., 2013).
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: BRD4allPeaks_reduced.txt:Merged BRD4 peaks from all the time points.; BRD4mat.txt: BRD4 count table for genomic coordinates in BRD4allPeaks_reduced.txt, normalized with size factors and input
Supplementary_files_format_and_content: CEBPallPeaks_reduced.txt:Merged CEBPa peaks from all the time points; CEBPmat.txt: CEBP coverage normalized to size factors and input on the genomic coordinates in CEBPallPeaks_reduced.txt
Supplementary_files_format_and_content: H3K4me1allpeaks_reduced.txt:Merged H3K4me1 peaks from all the time points; H3K4me1mat.txt: H3K4me1 coverage normalized to size factors and input on the genomic coordinates in H3K4me1allPeaks_reduced.txt
Supplementary_files_format_and_content: The bigwig files of ATAC-seq were generated by deepTools2.3.4 (Ramirez et al., 2016) using --normalizeSizefactors1X options.
Supplementary_files_format_and_content: Strand specific bigwig files of TT-seq and RNA-seq were generated by deepTools2.3.4 (Ramirez et al., 2016) using --normalizeSizefactors1X --filterRNAstrand options.

source_name: BLaER

extract_protocol:
ChIP-seq: At each time point, 3x10^7 cells were harvested and fixed with 1% of formaldehyde for 8 minutes (Thermo Scientific, 28908). Formaldehyde was quenched with 0.2M glycine for 5 min. Chromatin was sheared to 200-500 bp in size using the Covaris S220 ultrasonicator (16min for C/EBPα and BRD4, 18min for H3K4me1). A fraction of the resulting chromatin was used as input control. Sheared chromatin (50ug for C/EBPα and BRD4, 30ul for H3K4me1) was incubated with 5 ug of antibodies - anti-C/EBPα (Santa Cruz, sc-61), anti-H3K4me1 (abcam, ab8895), anti-BRD4 (Bethyl Laboratories, A301–985A100)- bound to protein-A beads (Life Technologies, 9999-01). Samples were incubated at 65ºC overnight to reverse the crosslinks, followed by RNase and proteinase K treatments.
ATAC-seq: ATAC-seq was performed as described (Buenrostro et al., 2013). Briefly, 5 x 10^4 cells were harvested and treated with Nextera Tn5 Transposase (Illumina, FC-121-1030) for 45 min at 37°C.
Total RNA-seq: Total RNA was extracted from the cells labelled with 0.5mM 4-thiouridine (4sU, Carbosynth, 13957-31-8) for 5 min. RNA prepared using QIAzol according to the manufacturer’s instructions was fragmented to 1500 – 5000 bp in size using Covaris S220 Ultrasonicator before the library preparation.
At each time point, 1-2.2 x 10^8 cells were labeled with 0.5mM 4-thiouridine (4sU, Carbosynth, 13957-31-8) for 5 min and harvested by centrifuging at 500g for 2 min. Harvested pellets were lysed with QIAzol (Qiagen, 79306). Following addition of 5ng of spike-in mix per 1 x 10^8 cells, total RNA was purified using QIAzol (Qiagen, 79306) according to the manufacturer’s instructions. Total RNA (300ug) was fragmented to 1500 – 5000 bp in size using Covaris S220 Ultrasonicator. Newly synthesized RNAs were purified as described (Schwalb et al., 2016) with the following modifications. After streptavidin pull down, the resulting RNA was purified with RNeasy Micro Kit (Qiagen, 74004), together with DNase treatment (Qiagen, 79254).
ChIP-seq: NEB Ultra DNA Library kit (NEB, E7370S) ; ATAC-seq:Nextera Tn5 Transposase ((Illumina, FC-121-1030)) 1x NEBNext High-Fidelity 2x PCR Master Mix (NEB, M0541S) ; Total RNA-seq and TT-seq Ovation Universal RNA-seq System (Nugen, 0343)

tag: cell type

value: RCH-ACV stably expressing estrogen inducible C/EBPa

tag: treatment

value: Beta-estradiol (100nM) treatment 12h + 5 min 4sU labeling


title: NMYC_RB_2418_Input

library_source: genomic

data_processing:
Quality control of raw sequencing reads was performed using FastQC
Low-quality reads were removed using Trimmomatic with a sliding window of 4bp and quality threshold of 20
Reads passing QC were aligned to mm10 using Bowtie2
BAM file creation, sorting, removal of PCR duplicates and indexing were performed using samtools
ChIP-seq peaks were called using MACS2 with input chromatin as the control for each set of data.
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq signal (bigWig) called by MACS2 using input chromatin as control

extract_protocol:
Fifteen cryosections were collected and crosslinked with 1% methanol-free formaldehyde for 10 minutes and fixation was quenched using 2.5 M glycine for 5 minutes. The cell pellets were centrifuged and washed twice in cold PBS. Each pellet was resuspended in 1 ml of lysis buffer (50 mM Tris HCl pH 8, 0.5% SDS, 10 mM EDTA with protease and phosphatase inhibitors (Thermo Scientific)) and lysed for 20 minutes at 4°C. The nuclei were collected by centrifugation and resuspended in a second lysis buffer (10 mM Tris HCl pH 7.5, 150 mM NaCl, 0.1% SDS, 1 mM EDTA, 1% NP-40, 1% sodium deoxycholate, with protease and phosphatase inhibitors (Thermo Scientific)). The protein-bound chromatin was sheared by sonication (Diagenode, Bioruptor Pico). Input sheared chromatin was reserved as a control for downstream ChIP-seq analysis. Equal volumes of sheared chromatin were immunoprecipitated with specified antibodies.
Libraries were generated using the Hyper Prep Kit (Kapa Biosystems) following the manufacturer's recommended protocol.

treatment_protocol: Tumors were harvested and frozen in OCT. Frozen tumor blocks were sliced into 30 um thick cryosections.

value: Pb-Cre+; Pten f/f; Rb1 f/f; MYCN+


title: NMYC_RB_2418_NMYC_IP

value: MYCN (Santa Cruz, sc-53993)


title: BRD4_96h_rep1_ChIPSeq


title: 200863770097_R08C01 Sample216

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) using a Illumina iScan System (Illumina).

tag: phenotype

value: Case

tag: Sex

value: Male


title: BRD4_24h_rep2_ChIPSeq

value: NEB Ultra DNA Library kit

value: Beta-estradiol (100nM) treatment 24h


title: 10005839158_R03C02 Sample249

value: M


title: 10005839158_R03C01 Sample248

value: SCZ


title: BRD4_24h_rep1_ChIPSeq

value: anti-BRD4 (Bethyl Laboratories, A301-985A100)


title: NMYC_RB_1803_2_NMYC_IP


title: 200863770097_R05C01 Sample214

value: Control


title: BRD4_12h_rep2_ChIPSeq

value: Beta-estradiol (100nM) treatment 12h


title: NMYC_RB_1803_2_Input


title: NMYC_RB_1803_1_NMYC_IP


title: 10005839158_R02C01 Sample246

value: CON

value: F


title: 200863770097_R03C01 Sample213

value: Female


title: TT_30h_rep2

description: 4sU-labeled RNA

value: Ovation Universal RNA-seq System (Nugen, 0343)

value: Beta-estradiol (100nM) treatment 0h + 5 min 4sU labeling


title: 10005839158_R02C02 Sample247


title: 200863770100_R02C01 Sample218


title: 200863770097_R01C01 Sample212


title: BRD4_12h_rep1_ChIPSeq

value: RCH-ACV stably expressing estrogen inducible C/EBPa


title: NMYC_RB_1803_1_Input

value: Pb-Cre+; Pten f/f; Rb1 f/f; MYCN+

value: Mouse tumor


title: 200863770093_R08C01 Sample211


title: NMYC_2444_NMYC_IP

value: Pb-Cre+; Pten f/f; MYCN+

value: MYCN (Santa Cruz, sc-53993)


title: 200863770093_R06C01 Sample210


title: BRD4_0h_rep1_ChIPSeq

value: NEB Ultra DNA Library kit

value: Beta-estradiol (100nM) treatment 0h


title: 10005839151_R06C02 Sample244

value: FEP

value: M


title: 10005839151_R06C01 Sample243

value: SCZ


title: BRD4_0h_rep2_ChIPSeq

value: anti-BRD4 (Bethyl Laboratories, A301-985A100)


title: NMYC_2444_Input


title: BMDC_ + zymosan and ASF519  40h#3

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts (subread 2.0.0) with GENCODE annotation (vM25)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: BMDC

growth_protocol: BMDCs were cultured in cDMEM with 20 ng/ml GM-CSF (2 x 10^6 cells in 10 ml per untreated petri dish 100 mm x 15 mm) at 37℃, 5% CO2.

extract_protocol:
1,000 BMDC Cells were collected directly into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.

treatment_protocol: 1 x 10^5 BMDCs in 140 μl were placed in a 96-well non-tissue culture treated microplate (Corning #351172), mixed with 60 μl of ASF519 SSM for 40 hrs incubation at 37℃, 5% CO2, then supplemented with zymosan at 4 μg/ml for additional 16 hrs incubation under the same condition. The control groups used uninoculated bacterial broth with or without zymosan added. The cDMEM medium was not supplemented with GM-CSF.

tag: strain

value: Bone marrow derived DCs

value: Wild-type

tag: agent

value: zymosan and ASF519


title: 200863770093_R04C01 Sample209

value: Control

value: Female


title: NMYC_2128_NMYC_IP


title: BMDC_ + zymosan and ASF519  40h#2


title: 10005839151_R05C02 Sample242

value: F


title: 10005839151_R05C01 Sample241


title: 10005839158_R01C02 Sample245


title: 200863770093_R02C01 Sample207

value: Case

value: Male


title: NMYC_2128_Input

value: Mouse tumor


title: 200863770093_R03C01 Sample208


title: BMDC_ + zymosan and ASF519  40h#1


title: BMDC_ + ASF519  40h#3


title: 10005839151_R04C02 Sample240

value: CON


title: 10005839151_R04C01 Sample239


title: 200863670090_R07C01 Sample205


title: BMDC_ + ASF519  40h#2


title: BMDC_ + ASF519  40h#1


title: 200863670090_R08C01 Sample206


title: 200863770097_R07C01 Sample215


title: 10005839151_R03C02 Sample238


title: 200863670090_R05C01 Sample203


title: 200863670090_R06C01 Sample204


title: 10005839151_R02C02 Sample236


title: 10005839151_R03C01 Sample237


title: BMDC_ + zymosan  40h#2

value: zymosan


title: BMDC_ + zymosan  40h#1


title: BMDC_ + zymosan  40h#3


title: 200863670090_R03C01 Sample201


title: 10005839150_R06C02 Sample234


title: 200863670090_R02C01 Sample200


title: BMDC_broth only 40h#2


title: 10005839150_R06C01 Sample233


title: 200863670090_R01C01 Sample199


title: BMDC_broth only 40h#3


title: 10005839150_R05C02 Sample232


title: NAdr_3 [ATAC-seq]

city: Houston

first: Brittney

last: Lozzi

state: TX

address: 1 Baylor Plaza

department: Cell & Gene Therapy

institute: Baylor College of Medicine

data_processing:
Quality control was performed on fastq files using fastQC and multiQC. Single end reads were mapped to the mouse genome (mm10) using bowtie2.
BigWig files were constructed using bamCompare from deepTools where each experimental sample was normalized to the control.
Peaks were called using findPeaks from HOMER (v4.11) and differential enrichment was determined using getDifferentialPeaksReplicates.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: BigWig

growth_protocol: The mES_astrocyte cultures were generated from mouse embryonic stem cells grown on feeder layers for 1-2 days, following which the cells were grown as neurospheres to induce formation of neural stem cells for 1 week. These were further differentiated in DMEM/F12 media supplemented with N2/B27 and growth factors EGF/FGF2 to generate astrocytes from 2-10 weeks. ATAC studies were performed on day35 cultures.

extract_protocol:
Cells were washed with PBS and incubated with lysis buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL) to purify nuclei.
Illumina sequencing libraries were constructed by treating ~50,000 nuclei with Tn5 Transposase in TD buffer (Illumina) followed by amplification and purification with Qiagen MinElute PCR Purification Kit.

treatment_protocol: In triplicate, mES_astrocytes were treated with neuroactive chemicals for 30 minutes before harvesting for ATAC library preparation.

value: stem cell induced astrocyte

value: noradrenaline

tag: time point

value: 35 days


title: 5HT_3 [ATAC-seq]

value: serotonin


title: KPC-IL6ko adipose 8

city: Portland

first: Teresa

last: Zimmers

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Cell, Developmental & Cancer Biology

institute: Oregon Health & Science University

description:
ILMN_127
Epididymal fat_mRNAseq_STAR_featurecounts.txt
J30

data_processing:
FastQC/MulitQC ver 0.11.5 (Babraham Bioinformatics) was use for quality control.
Sequenced libraries were mapped  to the UCSC Mm10 genome using STAR RNA-seq Aligner ver 2.5, with the following parameter: -08tSAMmapqUnique 60.
Illumina Real-Time Anlysis (RTA v2) was used for basecalling
Reads distribution across the genome was assessed using NSGUtils/bamutils ver 0.5.9
Uniquely mapped seqeuncing reads were assigned to Mm10 refTenes using subread/featureCounts ver 1.5.1 with the following parameters: -s 2 -p -Q 10.
edgeR v 3.12.1 was used to perform differential expression analysis
Genome_build: UCSC Mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: Epididymal fat pad

extract_protocol:
RNA extraction and purification from tissue snap frozen in liquid nitrogen was done via homogenization in Trizol and the Qiagen miRNeasy Mini Kit (skeletal muscle) and the Qiagen RNeasy Lipid Tissue Mini Kit (adipose tissue).
Adipose: The concentration and quality of total RNA samples was first assessed using Agilent 2100 Bioanalyzer. A RIN (RNA Integrity Number) of five or higher was required to pass the quality control. Then 100 nanograms of RNA (muscle) or 500 nanograms of RNA (adipose) per sample were used to prepared dual-indexed strand-specific cDNA library using TruSeq RNA Access Library Prep Kit (Illumina). The resulting libraries were assessed for its quantity and size distribution using Qubit and Agilent 2100 Bioanalyzer. Two hundred pico molar pooled libraries were utilized per flowcell for clustering amplification on cBot using HiSeq 3000/4000 PE Cluster Kit and sequenced with 2×75bp paired-end configuration on HiSeq4000 (Illumina) using HiSeq 3000/4000 PE SBS Kit. A Phred quality score (Q score) was used to measure the quality of sequencing. Greater than 95% (muscle) or >90% (adipose) of the sequencing reads reached Q30 (99.9% base call accuracy).

treatment_protocol: RNA isolation, sequencing for all quadriceps samples were done at one time. RNA isolation, sequencing of all adipose samples was done separately.

value: Adipose

tag: tumor

value: Orthotopic KPC-IL6ko


title: 200863670090_R04C01 Sample202


title: KPC-IL6ko adipose 6

description:
ILMN_127
Epididymal fat_mRNAseq_STAR_featurecounts.txt
J26


title: 10005839150_R04C02 Sample230

value: SCZ

value: M


title: 10005839150_R05C01 Sample231


title: ACh_3 [ATAC-seq]

value: acetylcholine


title: 200863770078_R05C01 Sample197

value: Control


title: 200863770078_R04C01 Sample196

value: Female


title: 200863770078_R03C01 Sample195


title: 10005839151_R01C01 Sample235


title: 10005839150_R04C01 Sample229


title: 200863770078_R02C01 Sample194


title: 10005839150_R03C02 Sample228

value: FEP


title: KPC adipose 8

description:
ILMN_127
Epididymal fat_mRNAseq_STAR_featurecounts.txt
J15

value: Orthotopic KPC


title: 10005839150_R03C01 Sample227

value: F


title: 200863770077_R08C01 Sample193

value: Case


title: KPC adipose 6

description:
ILMN_127
Epididymal fat_mRNAseq_STAR_featurecounts.txt
J13

value: Male


title: 10005839150_R02C02 Sample226


title: BMDC_broth only 40h#1

value: Bone marrow derived DCs

value: Wild-type


title: Glu_3 [ATAC-seq]

value: stem cell induced astrocyte

value: glutamate


title: 200863770078_R06C01 Sample198


title: KPC adipose 5

description:
ILMN_127
Epididymal fat_mRNAseq_STAR_featurecounts.txt
J12


title: KPC-IL6ko adipose 7

description:
ILMN_127
Epididymal fat_mRNAseq_STAR_featurecounts.txt
J27


title: KPC-IL6ko adipose 5

description:
ILMN_127
Epididymal fat_mRNAseq_STAR_featurecounts.txt
J25


title: 10005839150_R02C01 Sample225


title: 5HT_2 [ATAC-seq]

value: serotonin

value: 35 days


title: 10005839150_R01C02 Sample224


title: 200863770077_R05C01 Sample191


title: NAdr_2 [ATAC-seq]

value: noradrenaline


title: Sham adipose 7

description:
ILMN_127
Epididymal fat_mRNAseq_STAR_featurecounts.txt
J22

value: Adipose


title: 200863770077_R04C01 Sample190


title: 200863770077_R03C01 Sample189


title: ACh_2 [ATAC-seq]


title: GABA_3 [ATAC-seq]

value: gamma-aminobutyric acid


title: GABA_2 [ATAC-seq]


title: KPC adipose 7

description:
ILMN_127
Epididymal fat_mRNAseq_STAR_featurecounts.txt
J14


title: 10005839145_R06C02 Sample222

value: M


title: 10005839150_R01C01 Sample223


title: Sham adipose 6

description:
ILMN_127
Epididymal fat_mRNAseq_STAR_featurecounts.txt
J20


title: Sham adipose 5

description:
ILMN_127
Epididymal fat_mRNAseq_STAR_featurecounts.txt
J18


title: Glu_2 [ATAC-seq]


title: 10005839145_R06C01 Sample221


title: 200863770077_R07C01 Sample192

value: Control


title: 10005839145_R05C01 Sample220

value: SCZ


title: control_3 [ATAC-seq]


title: 200863770077_R01C01 Sample187

value: Female


title: KPC-IL6ko muscle 4

description:
ILMN_016
Quadriceps mRNAseq_STAR_featurecounts.txt
J76

source_name: Quadriceps muscle

value: Muscle

value: Orthotopic KPC-IL6ko


title: control_2 [ATAC-seq]


title: 200863770076_R08C01 Sample186


title: KPC-IL6ko muscle 3

description:
ILMN_016
Quadriceps mRNAseq_STAR_featurecounts.txt
J75


title: 5HT_1 [ATAC-seq]


title: 10005839145_R04C02 Sample219

value: F


title: Sham adipose 8

description:
ILMN_127
Epididymal fat_mRNAseq_STAR_featurecounts.txt
J23

value: Male


title: 200863770076_R07C01 Sample185


title: 10005839145_R04C01 Sample218

value: FEP


title: KPC-IL6ko muscle 2

description:
ILMN_016
Quadriceps mRNAseq_STAR_featurecounts.txt
J74


title: NAdr_1 [ATAC-seq]


title: 200863770076_R06C01 Sample184

value: Case


title: KPC-IL6ko muscle 1

description:
ILMN_016
Quadriceps mRNAseq_STAR_featurecounts.txt
J73


title: ACh_1 [ATAC-seq]

value: stem cell induced astrocyte

value: acetylcholine


title: KPC muscle 4

description:
ILMN_016
Quadriceps mRNAseq_STAR_featurecounts.txt
J62

value: Orthotopic KPC


title: 200863770077_R02C01 Sample188


title: 10005839145_R03C01 Sample216


title: GABA_1 [ATAC-seq]

value: 35 days


title: 200863770076_R05C01 Sample183


title: 10005839145_R03C02 Sample217


title: 200863770076_R04C01 Sample182


title: 10005839145_R02C02 Sample215


title: 200863770076_R03C01 Sample181


title: KPC muscle 2

description:
ILMN_016
Quadriceps mRNAseq_STAR_featurecounts.txt
J53


title: 200863770076_R02C01 Sample180


title: control_1 [ATAC-seq]


title: KPC muscle 1

description:
ILMN_016
Quadriceps mRNAseq_STAR_featurecounts.txt
J50


title: 200863770076_R01C01 Sample179


title: 10005839145_R02C01 Sample214


title: 5HT_3 [RNA-seq]

description:
5HT_3x
mESastrocyte_neurochemical_CPM.csv

data_processing:
Quality control was performed on fastq files using fastQC and multiQC. Paired end reads were mapped to the mouse genome (mm10) using STAR (v2.5.0a). Co-cultured samples were aligned and filtered using Sargasso.
Reads Per Million (RPM) were calculated using GenomicAlignments (v1.16.0) and DESeq2 (v1.20.0) was used for read count normalization and differential gene expression for mES_astrocytes. Transcript abundance estimation (fpkm) values were determined using cufflinks for co-cultured samples.
Genome_build: mm10 (GRCm38), hg38 (GRCh38)
Supplementary_files_format_and_content: *.csv: Comma-separated text files include CPM and FPKM values from ES_astrocytes.

growth_protocol: The mES_astrocyte cultures were generated from mouse embryonic stem cells grown on feeder layers for 1-2 days, following which the cells were grown as neurospheres to induce formation of neural stem cells for 1 week. These were further differentiated in DMEM/F12 media supplemented with N2/B27 and growth factors EGF/FGF2 to generate astrocytes from 2-10 weeks. All RNA-Seq studies was performed from day7-day35 cultures.

extract_protocol:
Spheres were washed with PBS and frozen with Trizol. RNA was isolated using Trizol and chloroform and purified using the RNeasy Mini Kit (QIAGEN).
Illumina sequencing libraries were constructed from 300-500ng of total RNA using the TruSeq Stranded mRNA Library preparation kit (Illumina).

treatment_protocol: In triplicate, mES_astrocytes were treated with neuroactive chemicals for 30 minutes before harvesting for RNA isolation.

value: serotonin


title: 10005839145_R01C02 Sample213

value: CON


title: Sham muscle 3

description:
ILMN_016
Quadriceps mRNAseq_STAR_featurecounts.txt
J37


title: Sham muscle 2

description:
ILMN_016
Quadriceps mRNAseq_STAR_featurecounts.txt
J36


title: 5HT_2 [RNA-seq]

description:
5HT_2x
mESastrocyte_neurochemical_CPM.csv


title: 200863770046_R08C01 Sample178


title: 10005839145_R01C01 Sample212


title: 5HT_1 [RNA-seq]

description:
5HT_1x
mESastrocyte_neurochemical_CPM.csv


title: 10005839118_R06C02 Sample211


title: 10005839118_R06C01 Sample210


title: 200863770046_R07C01 Sample177


title: Sham muscle 1

description:
ILMN_016
Quadriceps mRNAseq_STAR_featurecounts.txt
J35


title: Glu_1 [ATAC-seq]

value: glutamate


title: KPC muscle 3

description:
ILMN_016
Quadriceps mRNAseq_STAR_featurecounts.txt
J58


title: 200863770046_R05C01 Sample176


title: NAdr_2 [RNA-seq]

description:
NAdr_2x
mESastrocyte_neurochemical_CPM.csv

value: noradrenaline


title: 200863770046_R04C01 Sample175

value: Control


title: NAdr_3 [RNA-seq]

description:
NAdr_3x
mESastrocyte_neurochemical_CPM.csv


title: 10005839118_R05C01 Sample208

value: M


title: 10005839118_R05C02 Sample209


title: 14269-HTB20-006 8ClAdo 500nM 24H rep1

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
Illumina bcl2fastq v2.18.0.12 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR 2.6.0.a with default parameters
The HTSeq software (v.0.6.0) was applied to generate the count matrix, with default parameters. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR 3.28.1.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: human primary leukemia cells

growth_protocol: American Type Culture Collection (ATCC) and maintained in DMEM (Dulbecco Modified Eagle Medium) supplemented with 10% FBS and 100 units of penicillin/streptomycin at 37C with 5% CO2.

extract_protocol: Total RNA was extracted from cultured cells using the RNeasy Mini kit

treatment_protocol: In a 6 Well plate, place 1 million cells and treatment in 4mL of culture media and incubate for 4, 12, or 24H. Than harvest for RNA extraction.

value: myeloblasts

value: 500nM 8ClAdo 24H


title: 14269-HTB20-006 VEN 10nM 24H rep1

value: 10nM Ven 24H


title: 14269-HTB20-006 Combo 24H rep1

value: 500nM 8ClAdo/10nM Ven 24H


title: 200864580110_R08C01 Sample172

value: Female


title: 200863770046_R02C01 Sample173


title: 14269-HTB20-006 NT 24H rep1

value: No treatment


title: 10005839118_R04C02 Sample207

value: SCZ

value: F


title: 14269-HTB19-005 Combo 24H rep1


title: ACh_2 [RNA-seq]

description:
ACh_2x
mESastrocyte_neurochemical_CPM.csv

value: stem cell induced astrocyte

value: acetylcholine


title: ACh_1 [RNA-seq]

description:
ACh_1x
mESastrocyte_neurochemical_CPM.csv

value: 35 days


title: 10005839118_R04C01 Sample206

value: FEP


title: 200864580110_R07C01 Sample171


title: 14269-HTB19-005 VEN 10nM 24H rep1


title: GABA_3 [RNA-seq]

description:
GABA_3x
mESastrocyte_neurochemical_CPM.csv

value: gamma-aminobutyric acid


title: 10005839118_R03C02 Sample205


title: 200864580110_R06C01 Sample170

value: Male


title: GABA_2 [RNA-seq]

description:
GABA_2x
mESastrocyte_neurochemical_CPM.csv


title: NAdr_1 [RNA-seq]

description:
NAdr_1x
mESastrocyte_neurochemical_CPM.csv

value: noradrenaline


title: 10005839118_R01C02 Sample202


title: 200864580110_R04C01 Sample169

value: Case


title: GABA_1 [RNA-seq]

description:
GABA_1x
mESastrocyte_neurochemical_CPM.csv


title: 10005839118_R02C02 Sample203

value: M


title: 14269-HTB19-005 NT 24H rep1

value: myeloblasts


title: 200863770046_R03C01 Sample174


title: 200864580110_R03C01 Sample168


title: Glu_3 [RNA-seq]

description:
Glu_3x
mESastrocyte_neurochemical_CPM.csv

value: glutamate


title: KG-1a Combo 24H rep2

source_name: human leukemia cell line


title: ACh_3 [RNA-seq]

description:
ACh_3x
mESastrocyte_neurochemical_CPM.csv


title: 200863770081_R08C01 Sample167

value: Control


title: KG-1a Combo 24H rep1

value: 500nM 8ClAdo/10nM Ven 24H


title: 10005839118_R01C01 Sample201


title: 10005839110_R06C02 Sample200

value: CON


title: 200863770081_R07C01 Sample166

value: Female


title: Glu_1 [RNA-seq]

description:
Glu_1x
mESastrocyte_neurochemical_CPM.csv


title: 10005839118_R03C01 Sample204

value: SCZ


title: KG-1a VEN 10nM 24H rep2

value: 10nM Ven 24H


title: Glu_2 [RNA-seq]

description:
Glu_2x
mESastrocyte_neurochemical_CPM.csv

value: stem cell induced astrocyte


title: 10005839110_R05C02 Sample198


title: control_2 [RNA-seq]

description:
control_2x
mESastrocyte_neurochemical_CPM.csv


title: 14269-HTB19-005 8ClAdo 500nM 24H rep1

value: 500nM 8ClAdo 24H


title: 10005839110_R06C01 Sample199

value: F


title: KG-1a VEN 10nM 24H rep1


title: KG-1a 8ClAdo 500nM 24H rep2


title: 200863770081_R06C01 Sample165


title: 200863770081_R05C01 Sample164


title: 10005839110_R04C02 Sample196

value: FEP


title: 200863770081_R04C01 Sample163


title: KG-1a NT 24H rep2

value: No treatment


title: DS40_muAs-2 [RNA-seq]

description:
DS40_muAs-2
coculture_FPKM.csv

value: 35 days


title: 10005839110_R05C01 Sample197


title: KG-1a 8ClAdo 500nM 24H rep1


title: KG-1a NT 24H rep1


title: 200863770081_R02C01 Sample161

value: Male


title: DS57_muAs-1 [RNA-seq]

description:
DS57_muAs-1
coculture_FPKM.csv


title: 200863770081_R03C01 Sample162

value: Case


title: DS110_day35-3 [RNA-seq]

description:
DS110
mESastro_d35vsd21_CPM.csv


title: 200863770081_R01C01 Sample160


title: DS109_day21-3 [RNA-seq]

description:
DS109
mESastro_d35vsd21_CPM.csv

value: 21 days


title: 10005839110_R03C02 Sample195

value: M


title: KG-1a Combo 12H rep2

value: myeloblasts

value: 500nM 8ClAdo/10nM Ven 12H


title: 200863770080_R08C01 Sample159


title: 10005839110_R02C02 Sample193


title: KG-1a Combo 12H rep1


title: DS108_day35-2 [RNA-seq]

description:
DS108
mESastro_d35vsd21_CPM.csv


title: 200863770080_R06C01 Sample158


title: KG-1a VEN 10nM 12H rep2

value: 10nM Ven 12H


title: KG-1a VEN 10nM 12H rep1


title: DS106_day35-1 [RNA-seq]

description:
DS106
mESastro_d35vsd21_CPM.csv


title: 200863770080_R04C01 Sample157


title: DS107_day21-2 [RNA-seq]

description:
DS107
mESastro_d35vsd21_CPM.csv


title: control_1 [RNA-seq]

description:
control_1x
mESastrocyte_neurochemical_CPM.csv


title: 200863770080_R03C01 Sample156

value: Control


title: KG-1a 8ClAdo 500nM 12H rep2

value: 500nM 8ClAdo 12H


title: 10005839096_R06C02 Sample189


title: 10005839110_R01C01 Sample190


title: 10005839110_R03C01 Sample194

value: SCZ


title: 200863770080_R02C01 Sample155

value: Female


title: KG-1a 8ClAdo 500nM 12H rep1


title: DS105_day21-1 [RNA-seq]

description:
DS105
mESastro_d35vsd21_CPM.csv

value: stem cell induced astrocyte


title: 10005839096_R05C02 Sample188


title: 200863770080_R01C01 Sample154


title: DS8_day35-2 [RNA-seq]

description:
DS8_day35-2
d7-d35 mES_astrocyte FPKM.csv


title: KG-1a NT 12H rep2


title: 10005839096_R05C01 Sample187

value: CON


title: DS7_day35-1 [RNA-seq]

description:
DS7_day35-1
d7-d35 mES_astrocyte FPKM.csv


title: 10005839110_R02C01 Sample192


title: 10005839096_R04C02 Sample186


title: 10005839110_R01C02 Sample191


title: KG-1a NT 12H rep1


title: 200863770096_R07C01 Sample152


title: MV4-11 Combo 24H rep2

value: 250nM 8ClAdo/10nM Ven 24H


title: 10005839096_R04C01 Sample185


title: DS6_day21-2 [RNA-seq]

description:
DS6_day21-2
d7-d35 mES_astrocyte FPKM.csv


title: 200863770096_R06C01 Sample151


title: DS5_day21-1 [RNA-seq]

description:
DS5_day21-1
d7-d35 mES_astrocyte FPKM.csv


title: 10005839096_R03C01 Sample184


title: DS4_day14-2 [RNA-seq]

description:
DS4_day14-2
d7-d35 mES_astrocyte FPKM.csv

value: 14 days


title: 200863770096_R05C01 Sample150


title: MV4-11 Combo 24H rep1


title: MV4-11 VEN 10nM 24H rep2

value: 10nM Ven 24H


title: 200863770096_R04C01 Sample149


title: MV4-11 VEN 10nM 24H rep1


title: DS2_day7-2 [RNA-seq]

description:
DS2_day7-2
d7-d35 mES_astrocyte FPKM.csv

value: 7 days


title: 10005839096_R01C02 Sample182


title: DS3_day14-1 [RNA-seq]

description:
DS3_day14-1
d7-d35 mES_astrocyte FPKM.csv


title: 10005839096_R02C01 Sample183

value: F


title: 200863770096_R03C01 Sample148

value: Male


title: MV4-11 8ClAdo 250nM 24H rep2

value: 250nM 8ClAdo 24H


title: 200863770096_R02C01 Sample147

value: Case


title: 200863770096_R08C01 Sample153


title: DS1_day7-1 [RNA-seq]

description:
DS1_day7-1
d7-d35 mES_astrocyte FPKM.csv


title: 10005833142_R06C02 Sample181

value: FEP

value: M


title: 10005833142_R05C02 Sample180


title: 200863670076_R08C01 Sample146


title: 10005833142_R05C01 Sample179


title: 200863670076_R07C01 Sample145


title: 10005833142_R04C02 Sample178


title: MV4-11 NT 24H rep2

value: myeloblasts

value: No treatment


title: MV4-11 NT 24H rep1


title: scRNA_JM001_Control

city: Hangzhou

first: Ming

last: Jiang

state: Zhejiang

address: 866 Yuhangtang Road

country: China

institute: Zhejiang University

data_processing:
Reads were aligned to mm10 mouse genome and quantified using Cell Ranger Single-Cell Software.The matrix outputs were generated with barcodes (cell IDs), genes (gene names).
Genome_build: mm10
Supplementary_files_format_and_content: 10X genomics cellranger output

source_name: Lung epithelium

extract_protocol:
Single cells were isolated via flow cytometry
Libraries were constructed using the Chromium Single-Cell 3' library kit (10X Genomics)

value: Lung

value: Epithelium


title: MV4-11 Combo 12H rep1

value: 250nM 8ClAdo/10nM Ven 12H


title: MV4-11 Combo 12H rep2


title: P4_RNA_Ctrl_2

city: st. louis

first: Naveen

last: Reddy

state: MO

address: 660 S Euclid Ave

institute: Washington University In St. Louis

data_processing:
ChIP-seq reads were aligned to the mm10 and hg38 genome assemblies using Bowtie2
Data were filtered using a map quality score of >10
Peaks were called using MACS2 on each dataset. Bandwidth = 200; q-value 0.05
RNA-seq reads were aligned to mm10 genome assembly using RNA STAR 2.6
Genome_build: mm10, hg38
Supplementary_files_format_and_content: Text or excel workbooks containing raw read counts or CPM, histone enrichment, or fold change

source_name: Anterior Mouse Cerebellum

growth_protocol: Brain tissue was taken from CHD7 conditional knockout and control mice maintained under standard housing conditions.

extract_protocol:
RNA was extracted from the anterior cerebella of P4 mice using Trizol (Invitrogen) according to the manufacturer’s instructions. ChIP lysates clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.

value: Anterior Mouse Cerebellum

value: CHD7 Ctrl

value: pooled male and female

value: None (RNA-seq)


title: P4_RNA_Ctrl_1


title: P4_ATAC_cKO_3

value: CHD7 cKO

value: None (ATAC)


title: 10005833142_R03C02 Sample176

value: CON


title: 200863670076_R04C01 Sample142

value: Control

value: Female


title: MV4-11 VEN 10nM 12H rep2

value: 10nM Ven 12H


title: 200863670076_R03C01 Sample141

value: Case

value: Male


title: P4_ATAC_cKO_2


title: MV4-11 8ClAdo 250nM 24H rep1

value: myeloblasts

value: 250nM 8ClAdo 24H


title: 10005833142_R03C01 Sample175

value: FEP

value: M


title: P4_ATAC_cKO_1


title: MV4-11 VEN 10nM 12H rep1


title: 10005833142_R02C02 Sample174

value: SCZ

value: F


title: scRNA_JM002_NAPH

value: Lung

value: Epithelium


title: 200863670076_R02C01 Sample140


title: 10005833142_R02C01 Sample173


title: MV4-11 8ClAdo 250nM 12H rep2

value: 250nM 8ClAdo 12H


title: P4_ATAC_Ctrl_3

value: Anterior Mouse Cerebellum

value: CHD7 Ctrl

value: pooled male and female


title: 200863670076_R01C01 Sample139

value: Control


title: P4_ATAC_Ctrl_2

value: None (ATAC)


title: 10005833142_R04C01 Sample177


title: 10005833142_R01C02 Sample172


title: 200863670076_R05C01 Sample143

value: Female


title: MV4-11 8ClAdo 250nM 12H rep1


title: 200863670077_R08C01 Sample138


title: MV4-11 NT 12H rep2

value: No treatment


title: P4_ATAC_Ctrl_1


title: 10005833137_R06C02 Sample171


title: 200863670077_R07C01 Sample137

value: Case

value: Male


title: MV4-11 NT 12H rep1

value: myeloblasts


title: P4_CHD7_Input_Ctrl

value: None (Input)


title: MV4-11 Combo 4H rep2

value: 250nM 8ClAdo/10nM Ven 4H


title: 10005833137_R05C02 Sample169

value: FEP

value: M


title: P4_CHD7_Input_cKO

value: CHD7 cKO


title: 200863670077_R04C01 Sample135


title: 200863670077_R05C01 Sample136


title: 10005833137_R06C01 Sample170

value: SCZ


title: 200863670077_R02C01 Sample134


title: MV4-11 VEN 10nM 4H rep2

value: 10nM Ven 4H


title: MV4-11 Combo 4H rep1


title: P4_ChIP_CHD7_cKO

value: Anterior Mouse Cerebellum

value: CHD7 (Cell Signaling, 6505)


title: 200863670077_R01C01 Sample133


title: P4_ChIP_CHD7_Ctrl_2

value: CHD7 Ctrl

value: pooled male and female


title: MV4-11 VEN 10nM 4H rep1


title: P4_ChIP_CHD7_Ctrl_1


title: 10005833137_R04C01 Sample166

value: CON


title: 200863670088_R08C01 Sample132

value: Control

value: Female


title: P4_Input_Ctrl


title: 10005833137_R03C02 Sample165


title: 200863670088_R07C01 Sample131

value: Case


title: 10005833137_R03C01 Sample164


title: MV4-11 8ClAdo 250nM 4H rep1

value: 250nM 8ClAdo 4H


title: MV4-11 8ClAdo 250nM 4H rep2

value: myeloblasts


title: P4_Input_cKO

value: None (Input)


title: 200863670076_R06C01 Sample144


title: 200863670088_R06C01 Sample130


title: MV4-11 NT 4H rep2

value: No treatment


title: 10005833137_R02C02 Sample163

value: FEP


title: 10005833137_R05C01 Sample168

value: F


title: P4_ChIP_H3K4me3_Ctrl

value: H3K4me1 (Active Motif, #39297)


title: MV4-11 NT 4H rep1


title: P4_ChIP_H3K4me1_Ctrl


title: 200863670088_R04C01 Sample128

value: Male


title: 10005833137_R04C02 Sample167

value: SCZ


title: 10005833137_R02C01 Sample162


title: 10005833137_R01C02 Sample161


title: 200863670088_R05C01 Sample129


title: 22w_ChIP_Human_H3K27ac

source_name: Anterior Human Cerebellum

value: Anterior Human Cerebellum

value: Human Ctrl

value: missing

value: H3K27ac (Abcam ab4729)


title: 22w_Human_Input


title: P4_ChIP_H3K27ac_Ctrl_3

value: Anterior Mouse Cerebellum

value: CHD7 Ctrl

value: pooled male and female

value: H3K27ac (Active Motif, #39133)


title: P4_ChIP_H3K27ac_Ctrl_2


title: 10005833136_R06C02 Sample160


title: 200863670088_R02C01 Sample126

value: Control

value: Female


title: 200863670088_R03C01 Sample127


title: P4_ChIP_H3K27ac_Ctrl_1


title: 10005833136_R06C01 Sample159

value: M


title: 22w_ChIP_Human_CHD7

value: CHD7 (Cell Signaling, 6505)


title: P4_ChIP_H3K27ac_cKO_3

value: CHD7 cKO


title: 200863770072_R08C01 Sample124


title: 10005833136_R05C01 Sample157


title: P4_ChIP_H3K27ac_cKO_2


title: 200863670088_R01C01 Sample125


title: 200863770072_R07C01 Sample123

value: Case


title: Normal6

city: Fuzhou

first: Ye

middle: wang

last: zhong

state: Fujian

address: No.420, Fuma Road

department: Department of Radiation Oncology

institute: Fujian Medical University Cancer Hospital & Fujian Cancer Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas (clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. Q20, Q30, and GC-content of the raw datas were calculated.
miRBase20.0 was used as reference, software mirDeep_star_v38 was used to obtain the potential miRNA and the miRNA counts.
MiRNA expression levels were estimated by TPM (transcript per million) through the following criteria: Normalization formula: Normalized expression = mapped readcount/Total reads*1000000.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file include count and TPM values for each Sample

source_name: Normal plasma

extract_protocol:
The ExoQuick kit (System Biosciences, Mountain View, CA) was applied to isolate exosomes as according to the manufacturer’s protocol. Frozen plasma was thawed and centrifuged at 21,000 g for fifteen min at 4°C to purify them. The supernatant was later moved to a clean tube, and quarter of EXOQ5A-1 solution was added and mixed lightly. After 2 hours incubating at 4°C, the mix was centrifuged at 1,500 g for 30 min, and the supernatant was removed using aspiration. The residual supernatant was removed after centrifugation for 5 minutes; exosome containing pellets were resuspended in water free of nuclease or relevant buffer for RNA and protein extraction.
The entire 3 mg total RNA of each sample was divided into aliquots and a small RNA (sRNA) library prepared. The NEBNext Multiplex sRNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA, USA) was applied to generate the sequencing library. The index code was added to assign a sequence to every specimen. TruSeq SR Cluster Kit v3-cBot-HS (Illumina, San Diego, CA, USA) was applied to cluster index-coded specimens. The libraries were sequenced on an Illumina Hiseq 2500 machine to generate the 50 bp single-end reads.

treatment_protocol: The plasma was isolated from the blood after centrifugation for 10 minutes at 2000 RPM.

tag: subject status

value: healthy volunteer

value: plasma

tag: molecule subtype

value: miRNA


title: Normal5


title: Normal4


title: 10005833136_R04C02 Sample156

tag: status

value: FEP

value: F


title: 10005833136_R04C01 Sample155

value: SCZ

tag: gender


title: 200863770072_R05C01 Sample121


title: Normal3


title: P4_ChIP_RNAP2_Ctrl_3

tag: chip antibody

value: RNAP2 (Santa Cruz, #sc-47701 X)


title: Normal1


title: 10005833136_R03C02 Sample154

tag: ageatbloodcollection


title: Normal2


title: P4_ChIP_RNAP2_Ctrl_2

value: Anterior Mouse Cerebellum

tag: genotype


title: 200863770072_R04C01 Sample120

tag: age


title: 200863770072_R06C01 Sample122

value: Male


title: 200863770072_R03C01 Sample119


title: P4_ChIP_RNAP2_Ctrl_1

tag: tissue

value: CHD7 Ctrl

value: pooled male and female


title: 10005833136_R05C02 Sample158

value: CON


title: NPC5

source_name: Early NPC plasma

value: nasopharyngeal carcinoma (NPC)


title: 200863770072_R02C01 Sample118

value: Control


title: 10005833136_R01C02 Sample150


title: 10005833136_R03C01 Sample153

value: M


title: NPC6


title: P4_ChIP_RNAP2_cKO_1

value: CHD7 cKO


title: 10005833136_R02C01 Sample151


title: NPC3


title: 200863770071_R07C01 Sample116

value: Female


title: 200863770071_R08C01 Sample117


title: NPC4


title: P4_ChIP_H3K27ac_cKO_1

value: H3K27ac (Active Motif, #39133)


title: 10005833136_R02C02 Sample152


title: 10005833136_R01C01 Sample149


title: P4_ChIP_RNAP2_cKO_3


title: P4_ChIP_RNAP2_cKO_2


title: 10005833128_R06C02 Sample148


title: 200863770071_R05C01 Sample114


title: 200863770071_R06C01 Sample115

value: Case


title: NPC2

value: plasma

value: miRNA


title: 10005833128_R05C02 Sample146


title: NPC1


title: P4_ChIP_RAD21_Ctrl_2

value: RAD21 (Abcam, #ab992)


title: 200863770071_R03C01 Sample112


title: P4_ChIP_RAD21_Ctrl_1


title: P4_ChIP_RAD21_cKO_3


title: P4_ChIP_RAD21_Ctrl_3


title: 200863770071_R02C01 Sample111


title: P4_ChIP_RAD21_cKO_2


title: 200863770071_R01C01 Sample110


title: 10005833128_R04C01 Sample143

value: F


title: P4_ChIP_RAD21_cKO_1


title: 10005833128_R03C02 Sample142


title: 10005833128_R05C01 Sample145

value: FEP


title: P4_ChIP_CTCF_Ctrl_3

value: Anterior Mouse Cerebellum

value: CTCF (Millipore, #07-729)


title: P4_ChIP_CTCF_Ctrl_2

value: CHD7 Ctrl


title: 200863770070_R08C01 Sample109


title: 10005833128_R06C01 Sample147


title: Adipocytes on medium with OA + poly-IC, 96 h, replicate 3

type: RNA

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol for 4x44k microarrays

scan_protocol: Arrays were scanned with Agilent microarray scanner

data_processing: Global normalization was performed by equalizing the mean intensities of all microarrays. The individual values for each feature were divided to the mean value of all samples and expression ratios (ER) were calculated. Log2-ER were normalized with the locally weighted non-linear regression (Lowess)

organism: Salmo salar

source_name: Adipocyte culture

label_protocol: Amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Salmon was fed with commercial feed

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

value: on medium with OA + poly-IC, 96 h


title: 200863770071_R04C01 Sample113


title: Adipocytes on medium with OA + poly-IC, 96 h, replicate 4


title: 10005833128_R03C01 Sample141

value: SCZ


title: 10005833128_R04C02 Sample144


title: P4_ChIP_CTCF_Ctrl_1

value: pooled male and female


title: Adipocytes on medium with OA + poly-IC, 96 h, replicate 2


title: 200863770070_R05C01 Sample106

value: Control

value: Male


title: 200863770070_R06C01 Sample107


title: Adipocytes on medium with OA + poly-IC, 24 h, replicate 4

value: on medium with OA + poly-IC, 24 h


title: Adipocytes on medium with OA + poly-IC, 24 h, replicate 3


title: P4_ChIP_CTCF_cKO_3

value: CHD7 cKO


title: 200863770070_R04C01 Sample105


title: P4_ChIP_CTCF_cKO_2


title: 10005833128_R01C01 Sample138

value: M


title: P4_ChIP_CTCF_cKO_1


title: 200863770070_R03C01 Sample104

value: Case


title: 10005833128_R02C01 Sample139


title: Adipocytes on medium with OA + poly-IC, 96 h, replicate 1


title: Adipocytes on medium with OA + poly-IC, 24 h, replicate 2


title: 10005833086_R06C02 Sample137

value: CON


title: 200863770070_R02C01 Sample103

value: Female


title: EmyoPBS3

city: Adelaide

first: Susan

last: Woods

state: Select State

address: Level 5 South, SAHMRI building, North Terrace

department: School of Medicine

country: Australia

institute: The University of Adelaide

data_processing:
KAPA adapters were trimmed off using cutadapt19,20 (V1.16; minimum-length 18, error-rate 0.2, overlap=5) and reads were mapped to the mouse genome (mm10) using the STAR aligner2 (V2.6.1b; default parameters, read counts quantified by GeneCounts).  97%+ of reads mapped to the genome for each sequenced sample.
Genome_build: mm10
Supplementary_files_format_and_content: count table .tsv files row names are gene id. Each file contain one sample

molecule: polyA RNA

source_name: E14.5 myofibroblast exposed to PBS

growth_protocol: Adult mouse small intestine (SI) was removed, opened longitudinally, and the villi was mechanically scraped off. Embryonic mouse SI was collected under dissection microscope and cut into 2 mm pieces. The intestine was incubated with chelation buffer (3mM EDTA, 0.05mM DTT (Sigma) in PBS) for 30 minutes at room temperature. The epithelial layer was removed with shaking in PBS. The remaining intestine was digested using 3.8mg/ml Collagenase XI (Sigma) and 0.1mg/ml Dispase II (Roche) for 15 minutes at 37℃. The resulting supernatant was passed through a 70 µm strainer and single cells were pelleted by centrifugation at 300g for 5 minutes and plated in RPMI1640, supplemented with 5% FBS, 2 mM L-glutamine (GIBCO), 10 mM HEPES, 1mM sodium pyruvate, 100 U/ml penicillin and 100 mg/ml streptomycin (GIBCO), 50µM β-mercaptoethanol, and 1µM Y27632 until confluent.

extract_protocol:
RNeasy mini kits (Qiagen) were used to isolate RNA from cultured cells. RNA quality and quantity were analyzed using a NanoDrop and TapeStation.
PolyA+ stranded RNA-seq libraries were prepared using the KAPA RNA Hyper Prep kit (Roche). The multiplexed libraries were sequenced on an Illumina NextSeq 500 to obtain a single-end 75 bp read.

treatment_protocol: Cells were used at passages 2-3. Lipopolysaccharides (LPS) from Eschericia coli O111:B4 (Sigma) at the final concentration of 10µg/µl was added to the culture medium and cultured at 37℃ in 5%CO2 for 6 hours.

tag: cell type

value: intestinal myofibroblast

value: PBS


title: 200863770070_R07C01 Sample108


title: 10005833128_R02C02 Sample140

value: F


title: Adipocytes on medium with OA + poly-IC, 24 h, replicate 1

tag: treatment


title: Adipocytes on medium with OA, 96 h, replicate 2

value: on medium with OA, 96 h


title: 10005833086_R05C02 Sample135

value: FEP


title: 200863770070_R01C01 Sample102

tag: phenotype


title: 200863770109_R08C01 Sample101

tag: Sex


title: 10005833086_R06C01 Sample136


title: EmyoPBS2


title: Adipocytes on medium with OA, 96 h, replicate 4


title: Adipocytes on medium with OA, 96 h, replicate 3


title: EmyoPBS1


title: 200863770109_R07C01 Sample100


title: EmyoLPS3

source_name: E14.5 myofibroblast exposed to LPS

value: LPS


title: 10005833086_R05C01 Sample134


title: 10005833086_R04C01 Sample132


title: EmyoLPS2


title: 10005833086_R04C02 Sample133


title: 200863770109_R02C01 Sample98


title: EmyoLPS1


title: Adipocytes on medium with OA, 96 h, replicate 1


title: 10005833086_R03C02 Sample131


title: AdultmyoPBS3

source_name: Adult myofibroblast exposed to PBS

value: Adult


title: Adipocytes on medium with OA, 24 h, replicate 3

value: on medium with OA, 24 h


title: 200863770109_R01C01 Sample97

source_name: Whole Blood


title: AdultmyoPBS2


title: 10005833086_R03C01 Sample130


title: Adipocytes on medium with OA, 24 h, replicate 1


title: 200863770120_R08C01 Sample96


title: Adipocytes on medium with OA, 24 h, replicate 4


title: AdultmyoPBS1


title: 200863770120_R07C01 Sample95


title: 10005833086_R02C02 Sample129

value: SCZ


title: 10005833086_R02C01 Sample128


title: Adipocytes on medium with EPA + poly-IC, 96 h, replicate 4

value: on medium with EPA + poly-IC, 96 h


title: AdultmyoLPS3

source_name: Adult myofibroblast exposed to LPS


title: 200863770109_R04C01 Sample99

value: Control


title: Adipocytes on medium with EPA + poly-IC, 96 h, replicate 3


title: 200863770120_R06C01 Sample94


title: Adipocytes on medium with EPA + poly-IC, 96 h, replicate 2


title: 200863770120_R05C01 Sample93


title: AdultmyoLPS2


title: 10005833086_R01C02 Sample127


title: 10005833054_R06C01 Sample125


title: Adipocytes on medium with OA, 24 h, replicate 2


title: Treated 3

city: Lyon

first: Michelina

last: Plateroti

address: 28 rue Laennec

country: France

institute: Cancer Research Center of Lyon

data_processing:
1. Read Mapping: Standard RNA-sequencing generates 42-nt sequence reads using Illumina NextSeq 500. The reads are mapped to the genome using the STAR algorithm with default settings (Dobin et al., 2013). Alignment information for each read is stored in the BAM format.
2. Fragment Assignment: This process step is to count the number of reads (for single-end library) or fragments (for paired-end library) overlapping predefined genomic features of interest (e.g. genes). Only read pairs that have both ends aligned were counted. Read pairs that have their two ends mapping to different chromosomes or mapping to the same chromosome but on different strands were discarded. We also require that at least 25 bp overlapping bases in a fragment for read assignment. The gene annotations we used were obtained from Subread package (Liao et al., 2014). These annotations were originally from NCBI RefSeq database and then adapted by merging overlapping exons from the same gene to form a set of disjoint exons for each gene. Genes with the same Entrez gene identifiers were also merged into one gene (Liao et al., 2014).
3. Differential Analysis: After obtaining the gene table containing the fragment (or read) counts of genes, differential analysis was performed to identify statistically significant differential genes using DESeq2 (Love et al., 2014).
4: Filtering criteria. DE genes were filters for shrunkenLog2FC >0.5 and adjusted p-value 0.05. The adjusted p-value was generated by Benjamini and Hochberg’s FDR (False Discovery Rate) procedure and it is commonly used to evaluate statistical significance after multiple testing adjustment.
Genome_build: Mus musculus
Supplementary_files_format_and_content: The CSV file reports useful information for each gene along with DESeq2’s results. The table was ranked by adjusted p-values (i.e. False Discovery Rate - FDR) of the differential test and thus the most significant differential genes will be at the top of the list.

growth_protocol: Organoids were grown in a drop of Matrigel in Intesticult

extract_protocol:
RNA was extracted by Active Motif company
Directional library generation and QC of NGS library

treatment_protocol: Organoids were treated with 10-7M T3 or with the vehicle for 17 hours before recovery and RNA extraction

value: intestinal organoids

tag: tissue source

value: small intestine

value: WT


title: 200864580115_R08C01 Sample91


title: 10005833054_R05C02 Sample124

value: M


title: Adipocytes on medium with EPA + poly-IC, 24 h, replicate 3

value: on medium with EPA + poly-IC, 24 h


title: Treated 2


title: Adipocytes on medium with EPA + poly-IC, 96 h, replicate 1


title: Adipocytes on medium with EPA + poly-IC, 24 h, replicate 2


title: Control 3


title: Treated 1


title: 10005833054_R05C01 Sample123


title: 10005833054_R04C02 Sample122


title: 200864580115_R07C01 Sample90

value: Case

value: Male


title: 200864580115_R06C01 Sample89


title: 10005833086_R01C01 Sample126


title: 10005833054_R04C01 Sample121


title: 200863770120_R01C01 Sample92


title: 200864580115_R05C01 Sample88


title: Adipocytes on medium with EPA + poly-IC, 24 h, replicate 1


title: Adipocytes on medium with EPA + poly-IC, 24 h, replicate 4


title: Control 2


title: AdultmyoLPS1

value: intestinal myofibroblast


title: Control 1


title: 10005833054_R03C02 Sample120

value: F


title: 200864580115_R02C01 Sample87

value: Female


title: Adipocytes on medium with EPA, 96 h, replicate 4

value: on medium with EPA, 96 h


title: 200864580026_R08C01 Sample86


title: Ak4 shRNA KD M1 rep3

city: Taipei

first: Shi-Chuen

last: Miaw

address: No.1 Jen Ai road section 1

department: Immunology

country: Taiwan

institute: National Taiwan University, College of Medicine

data_processing:
Total RNA extracted from M1 cells was digested to 180 bp fragments after removing rRNAs with a Ribo-Zero Gold kit (Illumina, San Diego, USA). A sequencing library was created by reverse-transcribing RNA fragments to cDNA, and ligating specific adapters at both ends of these cDNA fragments.
The sequencing libraries were loaded to the surface of flow cells, and amplified into clonal clusters through bridge amplification. All of the clusters on the flow cell were sequenced by NextSeq 500 (Illumina).
The FastQC (v0.11.8) program (http://www.bioinformatics. babraham.ac.uk/projects/fastqc/) was used to examine the quality of sequencing reads, and HISAT2 (v2.1.0) was used to align sequencing reads to mouse genome references (GRCm38).
The output SAM files were normalized and quantified with R packages Rsubread (v 2.0.0)and edgeR (v 3.28.0) from Bioconductor. A robust normalization approach, the trimmed mean of M value, was applied and log2-transformation was used to obtain the final expression values.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw and normalized counts

source_name: Bone marrow

growth_protocol: BMDMs were cultured in complete DMEM containing 20%L929 supernatant for 7 days

extract_protocol:
cell lyses RNA was harvested using Trizol reagent. Direct-zol RNA miniPrep (Zymo Research) was used for  total RNA isolation for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lentiviral transduction was conducted in serum free medium containing 20% L929 supernatant with 8 μg/ml polybrene at day 3 (MOI = 30). For BMDMs were stimulated with 1000 ng/ml LPS and 20 ng/ml IFNγfor 6 hours.

tag: strain

value: M1 macrophages

value: Ak4 shRNA


title: 10005833054_R03C01 Sample119


title: 200864580026_R07C01 Sample85


title: Ak4 shRNA KD M1 rep2


title: Adipocytes on medium with EPA, 96 h, replicate 3


title: Adipocytes on medium with EPA, 96 h, replicate 1


title: Adipocytes on medium with EPA, 24 h, replicate 4

value: on medium with EPA, 24 h


title: 10005833054_R01C02 Sample116

value: SCZ


title: Scramble M1 rep3

value: scramble shRNA


title: 200864580026_R05C01 Sample83

value: Control


title: Adipocytes on medium with EPA, 24 h, replicate 3


title: Ak4 shRNA KD M1 rep1


title: 200864580026_R04C01 Sample82


title: Adipocytes on medium with EPA, 96 h, replicate 2


title: 10005833054_R01C01 Sample115

value: CON


title: Scramble M1 rep2


title: 10005833019_R06C02 Sample114

value: FEP


title: Adipocytes on medium with EPA, 24 h, replicate 2


title: sc_m4_10

city: Rehovot

first: Keren

last: Bahar-Halpern

address: Herzl St 234

country: Israel

institute: Weizmann Institute

description:
2onlyEpcam10_S2
processed data file: Clumps_Seq_sc_umitab.txt

data_processing:
bcl2fastq/2.15.0.4. Plate demultiplexing was provided to obtain plate specific reads in two fastq files (read 1 (R1) and read 2 (R2)); single (cell_BC (1-7), UMI (8-15))
Pooled data of scRNAseq were demultiplexed using plate specific barcode. Specific sequences for each cell were demultiplexed using well specific barcode (attached).
Genome_build: GRCm38.84
Supplementary_files_format_and_content: Clumps_Seq_clumps_umitab.txt: single cell expression matrix
Supplementary_files_format_and_content: Clumps_Seq_sc_umitab.txt: expression matrix of clumps
Supplementary_files_format_and_content: readme.txt: text file explaining formating of cell names in umitab files and how to extract meta-data such as mouse and plate number
Supplementary_files_format_and_content: marsseq_cell_barcodes.txt: list of barcods used for demultiplexing the cells in the single cell RNAseq experiment

source_name: Jejunum single cells

growth_protocol: C57bl6 male mice were fed regular chow ad libitum

extract_protocol:
Isolation of clumps was performed incubated 20min the Jejunum in a 10mM EDTA solution. Afterwards, the tissue was cut in 1cm pieces , moved in a pre-warmed 10 mM EDTA solution for 5 min and shacked vigorously at the end of the incubation time. – To obtain single cell suspension, differently from the clumps protocol, the tissue was incubated for 10 min on ice in a 10mM EDTA solution, before to be cut in small pieces and moved for other 10 min in a pre-warmed 10 mM EDTA solution. The tissue was shacked vigorously every 2 min.
for scRNAseq, 3' end mRNA libraries were prepared for sequencing using MARS-seq 2.0 (Keren-Shaul et al, Nature Protocol 2019).

treatment_protocol: Mice were sacrificed by cervical dislocation

value: post natal three months

tag: tissue/cell type

value: Jejunum single cells


title: 200864580026_R01C01 Sample80

data_processing: Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.

extract_protocol: DNA was extracted using a phenol/chloroform method


title: Scramble M1 rep1


title: 200864580026_R03C01 Sample81


title: sc_m4_9

description:
2onlyEpcam9_S19
processed data file: Clumps_Seq_sc_umitab.txt


title: Adipocytes on medium with EPA, 24 h, replicate 1


title: 10005833019_R06C01 Sample113

value: M


title: 10005833054_R02C02 Sample118


title: 10005833019_R05C02 Sample112


title: sc_m4_8

description:
2onlyEpcam8_S18
processed data file: Clumps_Seq_sc_umitab.txt


title: sc_m4_7

description:
2onlyEpcam7_S1
processed data file: Clumps_Seq_sc_umitab.txt


title: 200864580043_R07C01 Sample78


title: 200864580026_R06C01 Sample84


title: 10005833019_R05C01 Sample111


title: 10005833054_R02C01 Sample117


title: 10005833019_R04C02 Sample110


title: 200864580043_R06C01 Sample77

value: Case


title: 200864580043_R05C01 Sample76


title: sc_m4_6

description:
2onlyEpcam6_S16
processed data file: Clumps_Seq_sc_umitab.txt


title: 10005833019_R04C01 Sample109


title: sc_m4_5

description:
2onlyEpcam5_S15
processed data file: Clumps_Seq_sc_umitab.txt


title: 10005833019_R03C01 Sample108


title: 10005833019_R02C02 Sample107


title: 200864580043_R03C01 Sample74

value: Male


title: sc_m4_3

description:
2CD54Epcam3_S13
processed data file: Clumps_Seq_sc_umitab.txt


title: 200864580043_R02C01 Sample73


title: 10005833019_R02C01 Sample106


title: sc_m4_2

description:
2CD54Epcam2_S12
processed data file: Clumps_Seq_sc_umitab.txt


title: 200864580043_R08C01 Sample79


title: 200864580043_R01C01 Sample72


title: sc_m4_1

description:
2CD54Epcam1_S11
processed data file: Clumps_Seq_sc_umitab.txt


title: 200864580034_R08C01 Sample71


title: 10005833019_R01C02 Sample105


title: 200864580043_R04C01 Sample75


title: 10005771153_R06C02 Sample104


title: sc_m3_10

description:
1onlyEpcam10_S10
processed data file: Clumps_Seq_sc_umitab.txt


title: 200864580034_R06C01 Sample70


title: 10005771153_R06C01 Sample103


title: sc_m3_9

description:
1onlyEpcam9_S9
processed data file: Clumps_Seq_sc_umitab.txt


title: 200864580034_R05C01 Sample69


title: 200864580034_R04C01 Sample68


title: sc_m3_8

description:
1onlyEpcam8_S8
processed data file: Clumps_Seq_sc_umitab.txt


title: WT_Glt1_12mo_35

city: Rochester

first: John

last: Mariani

address: 601 Elmwood Avenue

department: Neurology

institute: University of Rochester

description: Gene expression from FACS isolated mouse striatum

hyb_protocol: Hybridization was processed according ot manufacturer instructions

scan_protocol: GeneChips were scanned according to manufacturer instructions

data_processing: Following import of raw data into R with the affy package (Gautier et al. 2004; R Core Team 2017) robust multiarray analysis (RMA) was utilized for pre-processing and normalization (Irizarry et al., 2003).  Probe annotations were fetched using biomaRt (Durinck et al. 2009) and probes targeting multiple ensembl IDs were removed.  Glt1 and Cd11b sample intensities were individually subset and analyzed for between timepoint differential expression using limma (Ritchie et al. 2015). An adjusted p-value of < 0.05 was deemed significant.

label: biotin

source_name: 12mo Glt1 WT

label_protocol: Total RNA was labeled with biotin according to manufacturer instructions

extract_protocol:
[dissociation protocol]  The mice were euthanized with carbon dioxide, transcardially perfused with sterile Hank’s Balanced Salt Solution (HBSS), and the brain removed. The brains were immersed in ice-cold sterile HBSS for about 5 minutes to facilitate the microdissection. Under a dissecting microscope, the sub-ventricular zone was removed and discarded and the striata from each mouse was dissected and placed in sterile HBSS on ice. The striata from all the mice of the litter were pooled together as per genotype. The striatal tissues were transferred to a petri dish containing sterile HBSS then chopped into small pieces using sterile disposable scalpels, transferred into a sterile tube and then incubated in a papain/DNase dissociation solution at 37oC for 50 minutes. Minimum essential media plus 0.5% BSA (MEM-BSA) containing 5% serum was then added to inactivate the papain. The tissue was triturated by repeated pipetting in order to achieve a single cell suspension. The cells were then pelleted, resuspended into MEM-BSA and overlaid first onto a 90% Percoll gradient followed by a second 30% Percoll gradient and the solution centrifuged. The myelin and debris were removed from the tube and then the cells were resuspended into MEM-BSA plus donkey serum for flow cytometry analysis.
[facs protocol]  Flow cytometry analysis for astrocyte surface markers was performed on freshly dissociated striatal cells from wild-type or R6/2 mice. Cells were stained with primary antibodies against the astrocyte marker, GLT1 and the microglial marker, CD11b-PE (BD Biosciences). The primary antibodies, directly conjugated antibodies or their corresponding isotype controls were added to the cells and then incubated on ice for 15 minutes. 5 ml of MEM-BSA wash buffer was added to the cells and the cells were spun down. For the non-conjugated antibodies, the pelleted cells were resuspended in MEM-BSA plus 5% donkey serum and the appropriate secondary antibody, APC conjugated donkey anti-rabbit IgG, was added at a 1:200 dilution (Jackson ImmunoResearch). The samples were incubated on ice for 15 minutes and then washed with 5 ml of MEM-BSA wash buffer for 10 minutes. All samples were resuspended in MEM-BSA containing 20U/ml DNase to a concentration of 1-1.5x106 cells/ml and then passed over a 35 µm tube top cell strainer prior to flow cytometry. DAPI was added at 1 µg/ml. Flow cytometry analysis and FACS was performed on a BD FACSAria IIIU (Becton Dickinson, San Jose, CA). The cells were analyzed by forward and side scatter, for PE fluorescence through a 582 ± 15 nm band-pass filter, for APC fluorescence through a 660 ± 20 nm band-pass, and for DAPI fluorescence through a 450 ± 50 nm band-pass. Unstained cells were used to set the background fluorescence; a false positive rate of 0.5% was accepted. The GLT1+, CD11b+ and the GLT1-/CD11b- striatal cells isolated by FACS were pelleted, frozen on dry ice and stored at -80oC until the time of RNA extraction.
RNA was extracted from the pelleted/frozen cells using the Qiagen RNeasy Mini kit. An on column DNase treatment was performed and the RNA concentration was determined using a Nanodrop. A portion of the RNA was then used for bioanalysis to confirm the integrity of the RNA.

value: Striatum

value: WT

value: astrocytes

tag: facs markers


title: sc_m4_4

description:
2onlyEpcam4_S14
processed data file: Clumps_Seq_sc_umitab.txt


title: 10005771153_R05C01 Sample101

value: F


title: 200864580034_R03C01 Sample67


title: sc_m3_6

description:
1onlyEpcam6_S6
processed data file: Clumps_Seq_sc_umitab.txt


title: sc_m3_7

description:
1onlyEpcam7_S7
processed data file: Clumps_Seq_sc_umitab.txt


title: Q175_Glt1_12mo_32

source_name: 12mo Glt1 Q175


title: 200864580062_R06C01 Sample62

value: Female


title: 200864580034_R02C01 Sample66


title: sc_m3_3

description:
1CD45Epcam3_S3
processed data file: Clumps_Seq_sc_umitab.txt


title: 200864580062_R08C01 Sample64


title: sc_m3_4

description:
1onlyEpcam4_S4
processed data file: Clumps_Seq_sc_umitab.txt


title: 200864580034_R01C01 Sample65


title: 10005771153_R02C02 Sample96


title: 10005771153_R03C01 Sample97


title: 200864580062_R07C01 Sample63


title: 10005771153_R04C01 Sample99


title: sc_m3_2

description:
1CD45Epcam2_S2
processed data file: Clumps_Seq_sc_umitab.txt


title: 10005771153_R02C01 Sample95


title: 10005771153_R04C02 Sample100


title: 10005771153_R03C02 Sample98


title: 10005771153_R01C02 Sample94


title: 10003886240_R06C02 Sample93


title: sc_m3_5

description:
1onlyEpcam5_S5
processed data file: Clumps_Seq_sc_umitab.txt


title: 10005771153_R05C02 Sample102


title: sc_m2_16

description:
5_S10
processed data file: Clumps_Seq_sc_umitab.txt


title: sc_m2_15

description:
4_S3
processed data file: Clumps_Seq_sc_umitab.txt


title: 200864580062_R02C01 Sample59


title: 200864580062_R03C01 Sample60


title: 10003886240_R06C01 Sample92


title: sc_m2_14

description:
3_S9
processed data file: Clumps_Seq_sc_umitab.txt

value: post natal four months


title: WT_CD11b_12mo_35

source_name: 12mo CD11b WT

value: microglia


title: sc_m3_1

description:
1CD45Epcam1_S1
processed data file: Clumps_Seq_sc_umitab.txt


title: Q175_CD11b_12mo_32


title: WT_Neg_12mo_35

source_name: 12mo Neg WT

value: negative cells


title: 10003886240_R05C02 Sample91


title: 200864580062_R01C01 Sample58


title: 200864580070_R06C01 Sample56


title: 10003886240_R05C01 Sample90


title: 200864580070_R08C01 Sample57


title: 200864580070_R05C01 Sample55


title: sc_m2_12

description:
1_S7
processed data file: Clumps_Seq_sc_umitab.txt


title: 10003886240_R04C01 Sample88

value: SCZ


title: sc_m2_13

description:
2_S8
processed data file: Clumps_Seq_sc_umitab.txt


title: sc_m2_10

description:
Epcam_5_S4
processed data file: Clumps_Seq_sc_umitab.txt


title: sc_m2_11

description:
Epcam_6_S16
processed data file: Clumps_Seq_sc_umitab.txt


title: 200864580070_R04C01 Sample54


title: 200864580070_R03C01 Sample53


title: 10003886240_R04C02 Sample89


title: 10003886240_R03C01 Sample87


title: 200864580062_R05C01 Sample61


title: sc_m2_8

description:
Epcam_3_S15
processed data file: Clumps_Seq_sc_umitab.txt


title: sc_m2_9

description:
Epcam_4_S6
processed data file: Clumps_Seq_sc_umitab.txt


title: Q175_Neg_12mo_32

description: Gene expression from FACS isolated mouse striatum

source_name: 12mo Neg Q175


title: 10003886240_R02C02 Sample86


title: sc_m2_6

description:
Epcam_1_S2
processed data file: Clumps_Seq_sc_umitab.txt


title: 200864580070_R02C01 Sample52


title: 200864580070_R01C01 Sample51

value: Control


title: 10003886240_R01C02 Sample84


title: 200864580076_R08C01 Sample50


title: 10003886240_R01C01 Sample83


title: 200864580076_R07C01 Sample49


title: 10003886140_R06C02 Sample82


title: sc_m2_5

description:
CD24_5_S13
processed data file: Clumps_Seq_sc_umitab.txt


title: sc_m2_3

description:
CD24_3_S12
processed data file: Clumps_Seq_sc_umitab.txt


title: 10003886140_R06C01 Sample81


title: Q175_Neg_6mo_26

source_name: 6mo Neg Q175


title: sc_m2_4

description:
CD24_4_S1
processed data file: Clumps_Seq_sc_umitab.txt


title: 200864580076_R04C01 Sample46


title: 10003886140_R05C02 Sample80


title: 200864580076_R06C01 Sample48


title: sc_m2_1

description:
CD24_1_S11
processed data file: Clumps_Seq_sc_umitab.txt


title: 10003886140_R04C02 Sample78


title: 10003886240_R02C01 Sample85

value: CON


title: sc_m1_7

description:
4_S12
processed data file: Clumps_Seq_sc_umitab.txt


title: sc_m2_2

description:
CD24_2_S5
processed data file: Clumps_Seq_sc_umitab.txt


title: 200864580076_R05C01 Sample47


title: sc_m2_7

description:
Epcam_2_S14
processed data file: Clumps_Seq_sc_umitab.txt


title: 200864580076_R02C01 Sample44


title: 10003886140_R03C02 Sample77


title: 200864580076_R03C01 Sample45


title: Q175_Neg_6mo_29


title: sc_m1_6

description:
3_S11
processed data file: Clumps_Seq_sc_umitab.txt


title: 10003886140_R03C01 Sample76


title: 200874540093_R08C01 Sample42


title: sc_m1_5

description:
2_S10
processed data file: Clumps_Seq_sc_umitab.txt


title: 10003886140_R02C02 Sample75


title: 10003886140_R05C01 Sample79


title: 200874540093_R07C01 Sample41


title: 10003886140_R01C01 Sample73

value: FEP


title: 10003886140_R02C01 Sample74


title: 200874540093_R05C01 Sample39


title: 200874540093_R06C01 Sample40


title: Q175_CD11b_6mo_27

source_name: 6mo CD11b Q175


title: 10003886128_R06C01 Sample71


title: 10003886128_R05C02 Sample70


title: 200874540093_R04C01 Sample38


title: 10003886128_R05C01 Sample69


title: sc_m1_8

description:
5_S13
processed data file: Clumps_Seq_sc_umitab.txt

value: post natal three months


title: 200874540093_R03C01 Sample37


title: clumps_m6_h2n_4

description:
4_int_clumps_S4
processed data file: Clumps_Seq_clumps_umitab.txt


title: clumps_m6_h2n_3

description:
3_int_clumps_S3
processed data file: Clumps_Seq_clumps_umitab.txt


title: sc_m1_1

description:
Epcam_Cd24low_1_S14
processed data file: Clumps_Seq_sc_umitab.txt

value: Jejunum single cells


title: 10003886128_R04C02 Sample68


title: clumps_m6_h2n_2

description:
2_int_clumps_S2
processed data file: Clumps_Seq_clumps_umitab.txt


title: 200874540091_R08C01 Sample35


title: WT_CD11b_6mo_24

source_name: 6mo CD11b WT


title: 200874540091_R06C01 Sample34


title: 10003886128_R06C02 Sample72


title: sc_m1_3

description:
EpcamLow_Cd24high_2_S17
processed data file: Clumps_Seq_sc_umitab.txt


title: 10003886128_R04C01 Sample67

value: M


title: clumps_m6_h2n_1

description:
1_int_clumps_S1
processed data file: Clumps_Seq_clumps_umitab.txt


title: 200864580076_R01C01 Sample43

value: Case


title: 200874540091_R05C01 Sample33


title: clumps_m5_h4n_5

description:
18_sort_20200109_12_h4n_S18
processed data file: Clumps_Seq_clumps_umitab.txt


title: 10003886128_R03C02 Sample66


title: 200874540091_R04C01 Sample32

value: Male


title: WT_Glt1_6mo_25

description: Gene expression from FACS isolated mouse striatum

source_name: 6mo Glt1 WT

value: Striatum


title: Q175_Glt1_6mo_28

source_name: 6mo Glt1 Q175


title: clumps_m5_h4n_4

description:
14_sort_20200109_8_h4n_S14
processed data file: Clumps_Seq_clumps_umitab.txt


title: 200874540091_R03C01 Sample31


title: clumps_m5_h4n_3

description:
13_sort_20200109_7_h4n_S13
processed data file: Clumps_Seq_clumps_umitab.txt


title: sc_m1_2

description:
EpcamLow_Cd24high_1_S16
processed data file: Clumps_Seq_sc_umitab.txt


title: 10003886128_R03C01 Sample65


title: 10003886128_R02C01 Sample64


title: 10003886128_R01C02 Sample63


title: 200874540091_R02C01 Sample30


title: 200874540091_R01C01 Sample29


title: clumps_m5_h4n_1

description:
11_sort_20200109_3_h4n_S11
processed data file: Clumps_Seq_clumps_umitab.txt


title: 10003886121_R06C02 Sample61


title: sc_m1_4

description:
1_S9
processed data file: Clumps_Seq_sc_umitab.txt


title: clumps_m5_4n_2

description:
15_sort_20200109_9_4n_S15
processed data file: Clumps_Seq_clumps_umitab.txt


title: clumps_m5_4n_1

description:
10_sort_20200109_2_4n_S10
processed data file: Clumps_Seq_clumps_umitab.txt


title: 200874540092_R07C01 Sample27


title: WT_Neg_6mo_23

source_name: 6mo Neg WT

value: WT


title: clumps_m4_h4n_6

description:
9_sort_20200113_12_h4n_S9
processed data file: Clumps_Seq_clumps_umitab.txt


title: 10003886121_R05C02 Sample59


title: clumps_m5_h4n_2

description:
12_sort_20200109_4_h4n_S12
processed data file: Clumps_Seq_clumps_umitab.txt


title: 10003886128_R01C01 Sample62


title: clumps_m4_h4n_5

description:
8_sort_20200113_11_h4n_S8
processed data file: Clumps_Seq_clumps_umitab.txt


title: 200874540092_R05C01 Sample25


title: 200874540092_R08C01 Sample28


title: 200874540092_R04C01 Sample24


title: clumps_m4_h4n_4

description:
7_sort_20200113_10_h4n_S7
processed data file: Clumps_Seq_clumps_umitab.txt


title: 10003886121_R04C02 Sample58


title: 10003886121_R03C02 Sample56


title: 10003886121_R06C01 Sample60


title: 200874540092_R03C01 Sample23


title: 200874540092_R06C01 Sample26


title: 10003886121_R03C01 Sample55


title: 10003886121_R02C02 Sample54


title: 200874540092_R01C01 Sample21


title: 10003886121_R04C01 Sample57


title: 200889820113_R08C01 Sample20


title: R62_Neg_12wk_21

source_name: 12wk Neg R62


title: 10003886121_R02C01 Sample53


title: 200874540092_R02C01 Sample22


title: clumps_m4_h4n_1

description:
4_sort_20200113_7_h4n_S4
processed data file: Clumps_Seq_clumps_umitab.txt


title: clumps_m4_h4n_3

description:
6_sort_20200113_9_h4n_S6
processed data file: Clumps_Seq_clumps_umitab.txt


title: clumps_m4_h4n_2

description:
5_sort_20200113_8_h4n_S5
processed data file: Clumps_Seq_clumps_umitab.txt


title: clumps_m4_4n_3

description:
3_sort_20200113_6_4n_S3
processed data file: Clumps_Seq_clumps_umitab.txt


title: 200889820113_R07C01 Sample19


title: 10003886121_R01C02 Sample52


title: clumps_m4_4n_1

description:
1_sort_20200113_3_4n_S1
processed data file: Clumps_Seq_clumps_umitab.txt


title: 200889820113_R06C01 Sample18


title: R62_Glt1_12wk_21

description: Gene expression from FACS isolated mouse striatum

source_name: 12wk Glt1 R62

value: astrocytes


title: WT_Glt1_6mo_22


title: R62_Neg_12wk_17


title: WT_Glt1_12wk_18

source_name: 12wk Glt1 WT


title: clumps_m3_4n_10

description:
3_10_S18
processed data file: Clumps_Seq_clumps_umitab.txt


title: 200889820113_R05C01 Sample17

source_name: Whole Blood


title: R62_CD11b_12wk_19

source_name: 12wk CD11b R62


title: WT_Neg_12wk_18

source_name: 12wk Neg WT


title: R62_Glt1_12wk_19


title: WT_Glt1_12wk_20


title: WT_CD11b_12wk_20

source_name: 12wk CD11b WT


title: R62_Neg_12wk_19


title: 10003886072_R06C01 Sample50


title: 200889820113_R04C01 Sample16


title: R62_CD11b_12wk_17


title: R62_Glt1_12wk_17


title: 10003886072_R05C02 Sample49


title: clumps_m3_4n_8.rds

description:
3_8_S16
processed data file: Clumps_Seq_clumps_umitab.txt


title: WT_Neg_12wk_20


title: WT_CD11b_12wk_18


title: clumps_m3_4n_6.rds

description:
3_6_S15
processed data file: Clumps_Seq_clumps_umitab.txt


title: clumps_m4_4n_2

description:
2_sort_20200113_4_4n_S2
processed data file: Clumps_Seq_clumps_umitab.txt


title: 200889820113_R01C01 Sample14


title: R62_CD11b_12wk_21


title: 10003886121_R01C01 Sample51


title: 10003886072_R04C02 Sample47


title: 200889820113_R03C01 Sample15


title: WT_CD11b_12wk_16


title: WT_Glt1_12wk_16


title: WT_Neg_12wk_16


title: 10003886072_R05C01 Sample48


title: 200889820117_R06C01 Sample12


title: 10003886072_R04C01 Sample46


title: 10003886072_R03C01 Sample44

value: F


title: clumps_m3_4n_3.rds

description:
3_4_S13
processed data file: Clumps_Seq_clumps_umitab.txt


title: 10003886072_R03C02 Sample45


title: clumps_m3_4n_2.rds

description:
3_2_S12
processed data file: Clumps_Seq_clumps_umitab.txt


title: clumps_m3_4n_5.rds

description:
3_5_S14
processed data file: Clumps_Seq_clumps_umitab.txt


title: 200889820117_R04C01 Sample10

value: Female


title: clumps_m3_4n_1.rds

description:
3_1_S11
processed data file: Clumps_Seq_clumps_umitab.txt


title: 10003886072_R02C02 Sample43


title: clumps_m2_4n_10.rds

description:
2_10_S10
processed data file: Clumps_Seq_clumps_umitab.txt


title: 200889820117_R03C01 Sample9


title: 10003886072_R02C01 Sample42


title: clumps_m2_4n_9.rds

description:
2_9_S9
processed data file: Clumps_Seq_clumps_umitab.txt


title: 200889820117_R02C01 Sample8


title: R62_Glt1_12wk_15


title: R62_Neg_12wk_15


title: 200889820117_R08C01 Sample13


title: R62_CD11b_12wk_15


title: WT_CD11b_12wk_14


title: 200889820117_R05C01 Sample11


title: 10003886072_R01C02 Sample41


title: 200889820112_R08C01 Sample6


title: 10003885082_R05C01 Sample38


title: 10003885082_R06C01 Sample40


title: 10003885082_R05C02 Sample39


title: clumps_m2_4n_5.rds

description:
2_5_S5
processed data file: Clumps_Seq_clumps_umitab.txt


title: clumps_m2_4n_6.rds

description:
2_6_S6
processed data file: Clumps_Seq_clumps_umitab.txt


title: clumps_m2_4n_8.rds

description:
2_8_S8
processed data file: Clumps_Seq_clumps_umitab.txt


title: clumps_m2_4n_7.rds

description:
2_7_S7
processed data file: Clumps_Seq_clumps_umitab.txt


title: WT_Neg_12wk_14


title: WT_Glt1_12wk_14


title: 200889820112_R07C01 Sample5


title: 10003885082_R04C02 Sample37


title: 200889820112_R03C01 Sample3


title: clumps_m2_4n_4.rds

description:
2_4_S4
processed data file: Clumps_Seq_clumps_umitab.txt


title: R62_CD11b_12wk_13


title: WT_Neg_12wk_12


title: R62_Neg_12wk_13


title: R62_Glt1_12wk_13


title: 200889820112_R02C01 Sample2


title: clumps_m3_4n_9

description:
3_9_S17
processed data file: Clumps_Seq_clumps_umitab.txt


title: 200874540093_R01C01 Sample36


title: 200889820117_R01C01 Sample7


title: clumps_m2_4n_3.rds

description:
2_3_S3
processed data file: Clumps_Seq_clumps_umitab.txt


title: 10003885082_R04C01 Sample36


title: 10003885082_R03C02 Sample35


title: clumps_m2_4n_2.rds

description:
2_2_S2
processed data file: Clumps_Seq_clumps_umitab.txt


title: 200889820112_R01C01 Sample1


title: 200889820112_R05C01 Sample4


title: 10003885082_R03C01 Sample34


title: clumps_m2_4n_1.rds

description:
2_1_S1
processed data file: Clumps_Seq_clumps_umitab.txt


title: clumps_m1_h4n_3.rds

description:
RM8_S8
processed data file: Clumps_Seq_clumps_umitab.txt


title: 10003885082_R02C02 Sample33


title: 10003885082_R02C01 Sample32


title: clumps_m1_h4n_2.rds

description:
RM7_S7
processed data file: Clumps_Seq_clumps_umitab.txt


title: 10003885082_R01C01 Sample30


title: 10003885069_R06C02 Sample29


title: clumps_m1_4n_4.rds

description:
RM5_S5
processed data file: Clumps_Seq_clumps_umitab.txt


title: 10003885082_R01C02 Sample31


title: clumps_m1_h4n_1.rds

description:
RM6_S6
processed data file: Clumps_Seq_clumps_umitab.txt


title: R62_Neg_12wk_11

description: Gene expression from FACS isolated mouse striatum


title: clumps_m1_4n_2.rds

description:
RM3_S3
processed data file: Clumps_Seq_clumps_umitab.txt


title: R62_CD11b_12wk_11


title: R62_Glt1_12wk_11


title: adrenal-BMAH-III-3-1

city: ADELAIDE

first: Lucia

last: Gagliardi

state: SA

address: Wayfinding 8G480, 1 Port Road

department: Endocrine and Metabolic Unit

institute: Royal Adelaide Hospital

hyb_protocol: According to manufacturer's instructions (Affymetrix GeneChip® Human Gene 1.0 ST array)

data_processing: The raw expression data were normalised with the RMA function using the aroma.affymetrix package.  Array quality was examined using normalised unscaled standardized box plots and higher weighting was given to better quality arrays.  Tumour samples from the same individual were considered biological replicates.  The analysis was performed in the R statistical environment.  The moderated t-test, using empirical Bayes linear modelling was performed.  The two comparisons were (i) all BMAH vs normal and (ii) advanced vs early BMAH.  A multiple test correction using the Benjamini-Hochberg method was performed to control the false-discovery rate.

source_name: resected adrenal

growth_protocol: adrenal tissue was flash frozen in liquid nitrogen, then stored at -80degC until RNA extraction

extract_protocol: Qiagen RNeasy lipid tissue midi kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions

tag: tumour stage

value: early

tag: disease state

value: familial bilateral macronodular adrenal hyperplasia

value: resected adrenal


title: adrenal-BMAH-III-3-2

scan_protocol: According to manufacturer's instructions (Affymetrix GeneChip® Human Gene 1.0 ST array)


title: 10003885069_R04C01 Sample27

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

institute: University of Exeter

tag: status

value: SCZ


title: R62_Neg_6wk_10

source_name: 6wk Neg R62

value: negative cells


title: WT_Glt1_12wk_12


title: clumps_m1_4n_1.rds

description:
RM2_S2
processed data file: Clumps_Seq_clumps_umitab.txt


title: 10003885069_R03C02 Sample26

value: CON

tag: gender


title: R62_CD11b_6wk_10

source_name: 6wk CD11b R62

value: microglia


title: clumps_m1_4n_3.rds

description:
RM4_S4
processed data file: Clumps_Seq_clumps_umitab.txt

value: post natal three months


title: adrenal-BMAH-III-1-2

label_protocol: According to manufacturer's instructions (Affymetrix GeneChip® Human Gene 1.0 ST array)

value: advanced


title: R62_Glt1_6wk_10

source_name: 6wk Glt1 R62


title: adrenal-BMAH-III-2-1


title: 10003885069_R04C02 Sample28

value: FEP


title: 10003885069_R03C01 Sample25


title: R62_CD11b_6wk_9


title: R62_Glt1_6wk_9


title: R62_Neg_6wk_9


title: adrenal-BMAH-III-1-1


title: y5000exp3: young_3_of_3

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

institute: University of Ulm

description: Lt-HSC

data_processing:
Following the removal of adaptors by autodectection, raw reads were  aligned to mm10 using bowtie2.
We removed unmapped reads,  duplicates, non-primary alignments, and multi-mapped reads Multi-mappers, duplicates and lowquality  reads were removed using samtools and picard.
After Tn5 shifting of tagaligns, peak calling was performed  using MACS2.
Genome_build: mouse genome build 10 (mm10)
Supplementary_files_format_and_content: ATAC-seq Peak files (excel format)

source_name: bone marrow-derived cells

growth_protocol: primary cells cultured overnight at 3%O2 in HBSS+10%FBS

extract_protocol:
cells we sorted from bone marrow as Lin-ckit+sca1+Flk2-Cd34-
according to protocol in Grigoryan A. et al (2018)

value: long-term Hematopoietic stem cells (Lt-HSCs)


title: adrenal-BMAH-III-2-2


title: y2500exp5: young_2_of_3

description: Lt-HSC


title: adrenal-normal-1

value: normal


title: R62_Neg_6wk_8

value: Striatum


title: 10003885069_R02C01 Sample24

value: M


title: y2385exp2: young_1_of_3

description: Lt-HSC


title: Donor13low

city: Amsterdam

first: Manon

last: Wildenberg

address: Meibergdreef 9

department: Gastroenterology

country: Netherlands

institute: Amsterdam UMC

hyb_protocol: Fragmented cDNA was hybridized on human Clariom S HTassay platform following standard hybridisation protocol (Thermofisher)

scan_protocol: Gene Titan instrument

data_processing: Data were analysed using Affimetrix expression console, RMA as normalization method [gene-level data]

label: Biotin

source_name: Blood, monocyte, TREM-1 low

label_protocol: Samples were labeled using 3′ IVT Pico Kit (Affymetrix) and RNA Amplification Kit (Nugene) according to manufacturer's protocols

extract_protocol: Bioline Isolate II RNA mini kit

treatment_protocol: Monocytes were isolated from buffy coat samples by density gradient centrifugation. Cells were stained for TREM-1 expression, and the highest and lowest 30% expression range were sorted by flow cytometric cell sorting.

tag: trem1 expression

value: Low


title: Donor13high

source_name: Blood, monocyte, TREM-1 high

value: High


title: a5000exp3: aged_3_of_3

description: Lt-HSC


title: R62_CD11b_6wk_8


title: WT_CD11b_12wk_12

value: WT


title: 10003885069_R01C01 Sample22

tag: ageatbloodcollection


title: adrenal-normal-2


title: a2500exp5: aged_2_of_3

description: Lt-HSC


title: 10003885063_R06C02 Sample21


title: R62_Neg_6wk_7

tag: genotype


title: 10003885063_R06C01 Sample20


title: a10000exp2: aged_1_of_3

description: Lt-HSC


title: 10003885063_R05C02 Sample19


title: Donor12low


title: Donor12high


title: 10003885069_R01C02 Sample23


title: 10003885063_R05C01 Sample18

value: F


title: R62_Glt1_6wk_8

tag: age

value: astrocytes


title: Donor11high


title: YMS 1077_12

first: Selva

last: Baltan

address: 3181 S.W. Sam Jackson Park Rd.

department: Anesthesia and Perioperative Medicine (APOM)

institute: Oregon Health and Science University

data_processing: Raw expression data was normalized using nSolver application software.

source_name: Optic nerve

extract_protocol: small size RNA was isolated and processed for miRNA profiling using nCounter miRNA expression panel.

treatment_protocol: Isolated optic nerves were treated with OGD, OGD+CX-4945 and OGD+MS-275.

value: male

tag: agent


title: YMS 1075_10


title: YMS 1132_11


title: Donor10high


title: Donor11low


title: Donor10low


title: 10003885063_R04C01 Sample16

value: SCZ


title: R62_CD11b_6wk_7

tag: tissue

tag: cell type


title: R62_Glt1_6wk_7


title: YCX 1140_09


title: R62_Glt1_6wk_6


title: 10003885063_R03C02 Sample15


title: 10003885063_R03C01 Sample14


title: YCX 1133_08


title: 10003885063_R04C02 Sample17


title: YCX 1074_07


title: Donor9high


title: 10003885063_R02C02 Sample13


title: WT_Neg_6wk_5

source_name: 6wk Neg WT

value: negative cells


title: Donor9low


title: Donor8low


title: Donor8high


title: R62_CD11b_6wk_6


title: 10003885063_R02C01 Sample12

value: CON


title: R62_Neg_6wk_6


title: YO1 1136_05

value: OGD


title: WT_Glt1_6wk_5

source_name: 6wk Glt1 WT


title: WT_CD11b_6wk_5

source_name: 6wk CD11b WT

value: microglia


title: YO1 1144_06


title: Donor7low


title: 10003885063_R01C02 Sample11


title: WT_Neg_6wk_4


title: YO1 1071_04


title: WT_CD11b_6wk_4


title: Donor6low


title: WT_Glt1_6wk_4


title: 10003885063_R01C01 Sample10


title: YC1 1145_03

value: Control


title: 10003885059_R06C02 Sample9

value: FEP


title: WT_CD11b_6wk_3


title: Donor6high


title: YC1 1137_02


title: 10003885059_R06C01 Sample8


title: Donor5low


title: YC1 1070_01


title: 10003885059_R05C01 Sample7


title: 10003885059_R04C01 Sample6


title: WT_Neg_6wk_3


title: Donor5high


title: 10003885059_R03C02 Sample5


title: Donor7high


title: 10003885059_R03C01 Sample4


title: 10003885059_R02C01 Sample3


title: WT_Glt1_6wk_3


title: 10003885059_R01C02 Sample2


title: WT_Neg_6wk_2


title: YWHAG-si2

city: Gothenburg

first: Subazini

last: TK

address: Medicineragatan 9A

country: Sweden

institute: Gothenburg university

description: siRNA YWHAG knockdown sample2

data_processing:
Sequenced reads were mapped to hg38 whole genome using STAR Aligner with default parameters
The reads are quantified using featureCounts from Subread package
Picard tools is used to determine the average insert size and standard deviation
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample analyzed

source_name: Lung adenocarcinoma cells

growth_protocol: Cells were grown in DMEM medium supplemented with 10% FBS and 1% pen+strep antibiotics

extract_protocol:
RNA was extracted from 100000 cells using reliaprep rna cell miniprep system
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected either with 25 pmol control LNA-GapmeRs or 25 pmol LY6k-AS targeting LNA GapmeRs. For siRNA experiments, Sigma siRNAs were transcfted at 40 pmol concentration. The RNA-iMAX transfection reagent was used in all experiments.

tag: cell line

value: A549 cell line


title: Donor4high


title: Donor4low


title: WT_CD11b_6wk_2


title: 10003885059_R01C01 Sample1


title: Donor3low


title: Donor3high


title: WT_Neg_6wk_1


title: Donor2low


title: si_Ctr2

description: Control sample2 transfected with scramble siRNA


title: YWHAG-si1

description: siRNA YWHAG knockdown sample1


title: Donor1low


title: WT_CD11b_6wk_1


title: Donor2high


title: WT_Glt1_6wk_1


title: Donor1high


title: LNA1_LY6K-AS

description: LNA-GapmeR LY6K-AS knockdown sample 1


title: LNA_Ctr2

description: Control sample2 transfected with scramble LNA-GapmeR


title: WT_Glt1_6wk_2


title: HuPV_042616H_WL18_H1975 6hr #3

city: Vancouver

first: William

last: Lockwood

state: British Columbia

address: 675 West 10th Avenue

department: Integrative Oncology

country: Canada

institute: BC Cancer

hyb_protocol: cDNA was hybridized according to manufacturer's instructions at The Centre for Applied Genomics

scan_protocol: GeneChips were scanned according to manufacturer's instructions at The Centre for Applied Genomics

data_processing: Experssion data was RMA normalized by The Centre for Applied Genomics

label_protocol: 500ng of RNA was converted to cDNA according to manufacturer's instructions and labelled at The Centre for Applied Genomics

growth_protocol: NCI-H23 (H23) and NCI-H1975 (H1975) were cultured in RPMI-1640 medium (Gibco, cat. #11875119) supplemented with 5% (vol/vol) FBS (Sigma), 1% penicillin-streptomycin solution (Gibco), and 1% Glutamax (Gibco) (standard growth media). Cultured cells were incubated in a humidified incubator at 37°C with 5% (vol/vol) CO2 and 95% (vol/vol) air. JQ1 resistant lines were generated by treating parental H23 and H1975 cells with increasing concentrations of JQ1 over a period of 6 months until cells could grow in 10μM JQ1. In parallel, cells were cultured in standard growth media plus 0.1% (vol/vol) DMSO as a control. Resistant lines were maintained in 10μM JQ1 media and the control lines in 0.1% DMSO media. Both resistant and control lines were tested for mycoplasma contamination and authenticated by STR profiling through Genetica.

extract_protocol: Total RNA was extracted from biological triplicates using a RNeasy Mini Kit (Qiagen). Sample quality was assessed using an Agilent Bioanalyzer and subsequent sample preparation, array hybridization, and data acquisition was performed by the Centre for Applied Genomics Microarray Facility (Toronto, Ontario).

treatment_protocol: H23 and H1975 resistant lines were grown in standard growth media with 10μM JQ1 media, control lines were grown in standard growth media with 0.1% DMSO media and control lines were grown in standrd growth media and treated with 10μM JQ1 for 6 hours. All treatments were performed in 6-well plates.

tag: jq1 status

value: Control Treated

tag: treatment


title: HCC70 IL-26 3hr

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: HCC70 cells were grown in RPMI1640 supplemented with 10% FBS. Cells were cultured at 37°C  in a humidified 5 % CO2 incubator.

extract_protocol: Cell pellets were harvested and treated with RLT buffer and RNA isolated with Qiagen RNeasy Mini kit following the standard protocol.

treatment_protocol: HCC70 cells were stimulated with IL-26 (30 ng /ml) in the presence or absence of Gefitinib (40μM) for 3 hr.

value: IL-26 3hr


title: HCC70 Gefitinib+IL-26 3hr

value: Gefitinib+IL-26 3hr


title: HuPV_042616H_WL17_H1975 6hr #2


title: LNA3_LY6K-AS

description: LNA-GapmeR LY6K-AS knockdown sample 2


title: LNA_Ctr1

description: Control sample1 transfected with scramble LNA-GapmeR


title: HuPV_042616H_WL16_H1975 6hr #1