title: Macaca mulatta with SARS-CoV2 detected in different parts. (K.BAM)

description:
"K" represents the rhesus macaques lung-dpi 5-3
N2002260_YFP_80-440791514.xlsx


title: KP1 spheroid 10-cell sample 6

status: Public on Jan 19 2021

type: SRA

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

country: USA

institute: University of Virginia

library_source: transcriptomic

data_processing:
Adapters were trimmed using fastq-mcf with the following options:  -q 10 -t 0.01 -k 0 (quality threshold 10, 0.01% occurrence frequency, no nucleotide skew causing cycle removal).
Datasets were aligned to the human (GRCh38.p12)  transcriptome using RSEM. Reference ERCC sequences were also provided for the alignment.
RSEM options  for 10c samples  --bowtie2 --single-cell-prior --paired-end (Bowtie2 transcriptome aligner, single-cell prior to account for dropouts)
Genome_build: GRCm38.82
Supplementary_files_format_and_content: Comma separated file includes read counts from RSEM

molecule: polyA RNA

organism: Mus musculus

source_name: Explanted small cell lung cancer

extract_protocol:
All samples were cryoembedded and sectioned on to glass slides (8µm sections). Cell samples were isolated with laser capture microdissection and poly(A) RNA extracted, reverse transcribed and poly(A) PCR amplified prior to library preparation
Amplified cDNA samples were diluted to 0.2 µg/ml for tagmentation with the Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s earlier recommendation to purify libraries with 180% (vol/vol) SPRI beads

tag: sample name

value: mSCLC1 spheroid 10-cell sample 6

tag: genotype

tag: sample type

value: 10-cell sample


title: Macaca mulatta with SARS-CoV2 detected in different parts. (J.BAM)

city: Beijing

first: Xuefei

last: Guo

state: Bejing

address: Xueyuan road, haidian district

department: Institute of Systems Biomedicine

country: China

institute: Peking university health science center

description:
"J" represents the rhesus macaques lung-dpi 5-2
N2002260_YFP_80-440791514.xlsx

data_processing:
fastqc, cutadapt and fastx_trimmer were used for raw data quality control
tophat2 was used for mapping rads to the genome
the R package Rsubread was used for counts the reads
the GFOLD, a Linux program was used for analyzed DEGs
Genome_build: mm10 and rheMac10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Macaca mulatta

source_name: Lung

growth_protocol: All animals were kept and bred in specific pathogen-free conditions.

extract_protocol:
Lungs were removed, flash frozen on dry ice, and RNA was harvested using RNeasy Mini Kit (Qiagen NO. 74104).The transcriptome library for sequencing was generated using VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme Biotech Co.,Ltd, Nanjing, China) following the manufacturer's recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Experiments with live SARS-CoV-2 viruses were carried out in the enhanced biosafety level 3 (P3+) facilities. WT Rhesus macaques were inoculated intranasally with SARS-CoV-2 (10^6 TCID50/ml) after anesthesia and  lungs were harvested at 0 dpi, 3 dpi and 5 dpi. WT and hACE2 mice were inoculated intranasally with IAV (10^5 TCID50) and MHV (MHV-a59)  after anesthesia and  lungs were harvested at 0 hour, 6 hour,24, 48hour, 3day, 5day, 7 day post-infection.

tag: infection

value: WT

tag: time

value: 5 dpi

tag: tissue

value: lung


title: acute_myeloid_leukemia [Cyto114]

type: genomic

city: Meldola

first: Giorgia

last: Simonetti

state: FC

address: Via Piero Maroncelli, 40

country: Italy

institute: IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori"

description: Genomic data from bone marrow cells of AML patients at diagnosis

hyb_protocol: DNA was processed through the following steps: digestion, ligation, amplification and purification, fragmentation, labeling, hybridization in each array according to the manufacturer's instructions. The volume of 10x Fragmentation Buffer and Fragmentation Reagent has been increased compared to the standard protocol in order to improve the quality of the fragmented DNA, according to the  Affymetrix Technical Support’s suggestion.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL files (SNP 6.0 and Cytoscan HD Array) were processed with Genotyping console (GTC) 4.1 and Chromosome Analysis Suite (ChAS) v. 4.1 to obtain CN5.CNCHP and cyhd.cychp files, respectively. CN5.CNCHP and cyhd.cychp were used to check QC, thresholds and MAPD. CEL files were used to produce raw segments files for the analysis as described in the correspective papers.
CEL, CN5.CNCHP and cyhd.cychp files obtained from SNP 6.0 and Cytoscan HD were uploaded.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: mononuclear cells

label_protocol: As per manufacturer (Affymetrix, Thermo Fisher Scientific)

extract_protocol: Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit or the DNA Blood Mini Kit (Qiagen). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: disease

value: acute myeloid leukemia

tag: gender

value: female


title: RRBS_dermalfibroblasts_SSc_12-3A

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

library_source: genomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated MethylSeq pipeline based on Bismark and methylation extractor from Babraham (https://www.bioinformatics.babraham.ac.uk/projects/bismark/)
Bismark aligns reads to the genome via Bowtie2 and maps bisulfite converted sequence reads and determine cytosine methylation states producing coverage files
Coverage files from Bismark were analyzed via the  Biconducotr R package RnBeads
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited .txt files include BISMARK output for each Sample

source_name: cultured dermal fibroblasts

growth_protocol: Primary dermal fibroblasts lines were established from skin biopsies taken from healthy control donors or patients with systemic sclerosis (scleroderma). Fibroblasts were cultured for 3 passages in DMEM + 20% FBS + Antibiotic-Antimycotic , then DNA was isolated.

extract_protocol:
DNA was isolated using DNeasy kit (Qiagen) following the manufacturer’s protocols. RRBS was performed using the Ovation® RRBS Methyl-Seq System 1–16 (NuGEN Technologies) following the manufacture’s procedure.
Library construction was done following Ovation® RRBS Methyl-Seq System (part no. 0353)

tag: disease status

value: systemic sclerosis

tag: disease subtype

value: diffuse

tag: Sex

tag: age at skin biopsy

tag: passage


title: acute_myeloid_leukemia [Cyto115]


title: Macaca mulatta lung with SARS-CoV and SARS-CoV2. (Du-2.BAM)

description:
"Du-2" represents the rhesus macaques lung-control 2
N2003482_YFP_80-461806545.xlsx

value: SARS-CoV and SARS-CoV-2

value: 0 dpi


title: KP1 spheroid 10-cell sample 4

value: mSCLC1 spheroid 10-cell sample 4


title: Macaca mulatta with SARS-CoV2 detected in different parts. (H.BAM)

description:
"H" represents the rhesus macaques lung-dpi 5-1
N2002260_YFP_80-440791514.xlsx


title: Macaca mulatta with SARS-CoV2 detected in different parts. (F.BAM)

description:
"F" represents the rhesus macaques lung-dpi 3-4
N2002260_YFP_80-440791514.xlsx

value: 3 dpi


title: acute_myeloid_leukemia [Cyto105]


title: RRBS_dermalfibroblasts_control_11-12C

value: control


title: KP1 spheroid 10-cell sample 3

value: mSCLC1 spheroid 10-cell sample 3


title: Macaca mulatta with SARS-CoV2 detected in different parts. (D.BAM)

description:
"D" represents the rhesus macaques lung-dpi 3-3
N2002260_YFP_80-440791514.xlsx


title: RRBS_dermalfibroblasts_control_13-8C


title: Macaca mulatta with SARS-CoV2 detected in different parts. (B.BAM)

description:
"B" represents the rhesus macaques lung-dpi 3-2
N2002260_YFP_80-440791514.xlsx


title: acute_myeloid_leukemia [Cyto104]


title: KP1 spheroid 10-cell sample 2

value: mSCLC1 spheroid 10-cell sample 2


title: RRBS_dermalfibroblasts_SSc_10-15A


title: RRBS_dermalfibroblasts_control_10-2C

value: male


title: acute_myeloid_leukemia [Cyto103]


title: acute_myeloid_leukemia [Cyto102]


title: KP1 spheroid 10-cell sample 1

value: mSCLC1 spheroid 10-cell sample 1


title: Macaca mulatta with SARS-CoV2 detected in different parts. (A.BAM)

description:
"A" represents the rhesus macaques lung-dpi 3-1
N2002260_YFP_80-440791514.xlsx


title: KP2 Spheroid bulk

extract_protocol:
Total RNA extracted using RNEasy kit (Qiagen) and oligo dT-purified to obtain mRNA from 500ng of total RNA
NEB Next Ultra RNA library preparation kit (New England Bioloabs)

value: Bulk


title: RRBS_dermalfibroblasts_SSc_9-4A


title: acute_myeloid_leukemia [Cyto112]


title: KP1 spheroid 10-cell sample 5

value: mSCLC1 spheroid 10-cell sample 5

value: 10-cell sample


title: acute_myeloid_leukemia [Cyto101]


title: Macaca mulatta lung with SARS-CoV2 at 0 dpi, 3 dpi, and 5 dpi. (F326)

description:
"F326" represents the  rhesus macaques lung-control
N2001400_YFP_80-429452914.xlsx

value: WT

value: lung


title: Macaca mulatta lung with SARS-CoV2 at 0 dpi, 3 dpi, and 5 dpi. (E202)

description:
"E202" represents the  rhesus macaques lung-dpi 5-6
N2001400_YFP_80-429452914.xlsx

value: 5 dpi


title: RRBS_dermalfibroblasts_control_8-3C


title: acute_myeloid_leukemia [Cyto100]

value: acute myeloid leukemia

value: female


title: RRBS_dermalfibroblasts_SSc_11-9A

value: systemic sclerosis

value: diffuse


title: RRBS_dermalfibroblasts_control_9-10C


title: KP3 Spheroid bulk


title: Macaca mulatta lung with SARS-CoV2 at 0 dpi, 3 dpi, and 5 dpi. (D77)

description:
"D77" represents the  rhesus macaques lung-dpi 5-5
N2001400_YFP_80-429452914.xlsx


title: RRBS_dermalfibroblasts_SSc_8-2A


title: KP1 Spheroid bulk


title: Macaca mulatta lung with SARS-CoV2 at 0 dpi, 3 dpi, and 5 dpi. (C205)

description:
"C205" represents the  rhesus macaques lung-dpi 3-7
N2001400_YFP_80-429452914.xlsx


title: RRBS_dermalfibroblasts_SSc_7-8A


title: L1 line without expression of Mn-superoxide dismutase and deficient production of H2O2. - L1_rep2

city: Irapuato

first: Luis

middle: F.

last: Garcia-Ortega

state: Guanajuato

address: Km 9.6 Libramiento Norte

department: Department of Genetic Engineering

country: Mexico

institute: Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav)

description: Bisulfite-treated genomic DNA

data_processing:
Raw reads were pre-processed with the Fastp v0.20.0 using -c -x -y options for polyX trimming in 3' ends, base correction in overlapped regions and low complexity filtering, respectively.
Clean reads were aligned to the N. tabacum reference genome (Nitab4.5) using Bismark aligner v0.22.3 under the parameters –N 1 -L 20 –bowtie2 --nondirectional.
Differential methylation analysis was performed using Methylkit v1.14.2 in R v4.0.0 as follows: Methylated cytosines were extracted from aligned reads using processBismarkAln function. In order to filter bases above the background expected from inefficiencies in the bisulfite conversion reaction and sequencing errors, filterByCoverage function was used to discards bases that have coverage below 10X and also discards the bases that have more than 99.9th percentile of coverage in each sample. The parameters for calculated DiffMeth function were slim = TRUE, weighted. mean = TRUE. Differential methylated cytosines (DmC) were defined as bases that had q-value < 0.01 and methylation difference > 25 %.
Genome_build: GCA_002210045.1
Supplementary_files_format_and_content: bedGraph files was obtained with bismark_methylation_extractor

organism: Nicotiana tabacum

source_name: L1 transgenic line tobacco

growth_protocol: All plants were kept at room temperature under a 16 h light/8 h dark photoperiod. After three weeks the seedlings were transferred into individual pots with Mixture 3 Peat Moss Sunshine as substrate and kept inside a glass chamber at room temperature with humidity of 70% for three days. They were kept in a greenhouse until sampling. The plants were watered daily.

extract_protocol:
Genomic DNA was extracted from 200 mg of leaf tissue of each sample, which was pulverised with liquid nitrogen. Extractions were carried out by the cetyltrimethylammonium bromide (CTAB) method described by Clarke 2009
The library preparation was done by BGI according to their standard directional WGBS pipeline. The WGBS consisted of a 150 pb paired-end sequencing with coverage of 12X on a NovaSeq 6000 system (Illumina, Inc.).

tag: tobacco line

tag: cultivar

value: Xanthi

value: CchGLP-

tag: group

value: H2O2 deficient production


title: AB2222

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: 2097 CDHFD + anti-PD1

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: Liver

growth_protocol: All mice were maintained under specific pathogen-free conditions

extract_protocol:
Hepatic CD4+ or CD8+ T-cells  were isolated by liver perfusion, mechanical + enzymatic digestion and percoll gradient enrichment and subsequently single-cell sorted (sorted gate: L/D-,CD11b-,CD11c-,CD19-,CD45+,CD4+ or CD8+ cells) and frozen on dry-ice .
Samples were flow sorted either using AriaII, AriaIII or Aria-Fusion (BD Biosciences, BD Diva Software) cell sorter.
3' end mRNA libraries were prepared for sequencing using a modified MARS-seq protocol (Jaitin et al, Science 2014)

treatment_protocol: 12 months NASH-diet + 8 weeks treatment (IgG, α-PD-1 or α-CD8)

tag: strain

tag: organ

value: Liver

tag: selection marker

tag: treatment

value: CDHFD1 + anti-PD1

tag: mouse age


title: Macaca mulatta lung with SARS-CoV2 at 0 dpi, 3 dpi, and 5 dpi. (A328)

description:
"A328" represents the  rhesus macaques lung-dpi 3-6
N2001400_YFP_80-429452914.xlsx

tag: infection

tag: genotype

tag: time

value: 3 dpi


title: RRBS_dermalfibroblasts_control_7-13C


title: L1 line without expression of Mn-superoxide dismutase and deficient production of H2O2. - L1_rep1

description: Bisulfite-treated genomic DNA


title: RRBS_dermalfibroblasts_control_6-4C

value: control


title: AB2221

description: 2079 ND

value: ND


title: KP5 Spheroid bulk

tag: sample name

value: Rb1-/-Trp53-/- BAT-GAL

tag: sample type

value: Bulk


title: L8 line with a high expression of Mn-superoxide dismutase and overproduction of H2O2. - L8_rep3

description: Bisulfite-treated genomic DNA

source_name: L8 transgenic line tobacco

value: CchGLP+

value: H2O2 overproduction


title: AB2219

description: 2083 ND


title: L1 line without expression of Mn-superoxide dismutase and deficient production of H2O2. - L1_rep3

description: Bisulfite-treated genomic DNA


title: RRBS_dermalfibroblasts_SSc_6-1A

tag: disease status

tag: disease subtype

value: male


title: L8 line with a high expression of Mn-superoxide dismutase and overproduction of H2O2. - L8_rep1

description: Bisulfite-treated genomic DNA


title: RRBS_dermalfibroblasts_control_5-15C

tag: Sex

tag: age at skin biopsy


title: RRBS_dermalfibroblasts_control_4-6C

tag: passage


title: AB2220

description: 2082 ND


title: RRBS_dermalfibroblasts_SSc_5-10A


title: AB2218

description: 2076 ND


title: AB2216

description: 2082 ND


title: AB2217

description: 2076 ND


title: AB2215

description: 2091 CDHFD

value: CDFHD


title: RRBS_dermalfibroblasts_SSc_4-12A

value: female


title: RRBS_dermalfibroblasts_control_3-7C


title: L8 line with a high expression of Mn-superoxide dismutase and overproduction of H2O2. - L8_rep2

description: Bisulfite-treated genomic DNA

tag: tobacco line

tag: cultivar


title: AB2214

description: 2091 CDHFD

tag: strain


title: RRBS_dermalfibroblasts_SSc_3-7A

value: systemic sclerosis


title: RRBS_dermalfibroblasts_control_2-5C


title: AB2213

description: 2085 CDHFD

tag: organ


title: RRBS_dermalfibroblasts_SSc_2-5A

value: diffuse


title: LD10% 3hr S72

type: RNA

city: Saint Louis

first: Bo

last: Zhang

state: MO

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine

description:
LD10% 3hr
RNA was processed using the Ambion WT expression labeling kit and the Porcine Gene 1.0 ST Array (Affymetrix)

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The raw-signal of arrays were induced into R environment and quantile-normalized by using ‘affy’ and ‘oligo’ package. The significantly differentially expressed genes (DEGs) were identified and analyzed by using one regression model in R with package ‘genefilter’, ‘limma’, ‘RUV’, ‘splines’, ‘gplots’ and ‘plotly’at adjusted p-value cutoff 0.05. Then the DEGs were imported into Ingenuity Pathway Analysis (IPA) to perform the pathway enrichment analysis. The DEG heatmap was plotted by using ‘gplots’ in R.

organism: Sus scrofa

source_name: femurs of 12-16w pigs

label_protocol: Total RNA was processed using the Ambion WT expression labeling kit

growth_protocol: Full-thickness porcine articular chondrocytes were enzymatically isolated from the femurs of pigs (~30kg; 12-16 weeks old) using collagenase (Sigma) media. Filtered cells were mixed 1:1 with 4% molten type VII agarose (Sigma) and the cells-agarose mixture was injected into a gel apparatus and allowed to set at room temperature. Chondrocyte-laden disks were punched out yielding engineered cartilage at a final concentration of 2% agarose and 15-20 million cells/mL. All constructs were given 2-3 days to equilibrate and media were changed three times per week during chondrogenic culture using a base media of DMEM-High Glucose (Gibco) supplemented with 10% FBS (Atlas), 0.1 mM nonessential amino acids (Gibco), 15 mM HEPES (Gibco), 40 µg/mL proline (Sigma), 1x-penicillin, streptomycin, and fungizone (Gibco), and fresh 50 µg/mL ascorbyl-2-phosphate (Sigma) and maintained at 37°C and 5% CO2 [1].

extract_protocol: Total RNA was extracted from the constructs using a pestle homogenizer and the Norgen Biotek RNA/protein purification plus kit. RNA quantity and quality were assessed by Nanodrop (Thermoscientific) and the Agilent Bioanalyzer.

treatment_protocol: A custom mechanical compression device was used for sinusoidal compression of 24-individual tissue constructs simultaneously [1] using a closed loop displacement-feedback system. This system allows for compression at 37 C and 5% CO2.

tag: cell type

value: Chondrocyte


title: LD10% 3hr S70


title: LD10% 0hr S12

description:
LD10% 0hr
RNA was processed using the Ambion WT expression labeling kit and the Porcine Gene 1.0 ST Array (Affymetrix)


title: LD10% 0hr S11


title: LD10% 3hr S69


title: CD45lung_LPS-O2_Rep2

city: Philadelphia

first: Sankar

last: Addya

state: PA

address: 233 South 10th Street

department: Kimmel Cancer Center

institute: Thomas Jefferson University Hospital

description: Prenatal lipopolysaccharide and postnatal hyperoxia

hyb_protocol: Mouse Clariom S gene chips were hybridize with 2.5 μg fragmented and biotin-labeled cDNA in 100 μl of hybridization cocktail.

scan_protocol: Chips were scanned on an Affymetrix Gene Chip Scanner 3000 7G, using Command Console Software.

data_processing:
Exp. group was compare with cont. group by using Transcriptome analysis console (TAC 4.0) software.
Rat clariom S
Expression values (Log2 value) of all gene list analyzed by TAC 4.0 software

label: Biotin

organism: Rattus norvegicus

source_name: experimental pulmonary immune cells

label_protocol: cDNA was label with biotin by using WT-Plus kit.

extract_protocol: Cells were directly sorted into aliquots of 500ul of RLT lysis buffer (QIAgen), homogenized in a QIA-shredder (QIAgen), and stored in -80C. Total RNA was extracted using Qiagen All prep kit.

value: Sprague Dawley

tag: tissue

value: lung

value: pulmonary immune cells

tag: age

value: 2-week old

tag: treatment


title: AB2211

description: 2097 CDHFD + anti-PD1

value: Liver

tag: selection marker

value: CDHFD1 + anti-PD1

tag: mouse age


title: CD45lung_LPS-O2_Rep3

value: Prenatal lipopolysaccharide and postnatal hyperoxia


title: CD45lung_LPS-O2_Rep1


title: AB2212

description: 2097 CDHFD + anti-PD1


title: AB2210

description: 2094 CDHFD + anti-PD1


title: LD10% 0hr S9


title: GSK101 72hr S42

description:
GSK101 72hr
RNA was processed using the Ambion WT expression labeling kit and the Porcine Gene 1.0 ST Array (Affymetrix)


title: CD45lung_NS-RA_Rep2

description: Prenatal normal saline and postnatal normoxia

source_name: control pulmonary immune cells


title: RRBS_dermalfibroblasts_SSc_1-6A


title: AB2209

description: 2088 CDHFD


title: PF K115ac input

city: Stellenbosch

first: Hugh

last: Patterton

state: Western Cape

address: Merriman Avenue

department: Biochemistry

country: South Africa

institute: Stellenbosch University

description:
Histone H2AK115ac MNase-ChIP-seq
24A_ACTGAT_L008

data_processing:
Trim_Galore! was used for quality trimming and adapter clipping using default settings with minimum read length set to 115 bp and maximum read length to 125
FASTQ sequence files were analyzed with FastQC, and reads with an average Q>20 retained (other settings default)
Filtered FASTQ files aligned to T. brucei 427 genome (v.37) with Bowtie2 using default settings and -I 115, -X 125
Bowtie 2 alignment files were analyzed for read enrichment using MACS2 with a user‑defined genome size (26,75 Mb); 200 nt fragment size for shifting model; minimum false discovery rate: ≥0.01, composite broad regions: true
Genome_build: T. brucei 427 v.37
Supplementary_files_format_and_content: Two bigwig files for each paired-end sample containing MACS2 results of input DNA and ChIP DNA.

organism: Trypanosoma brucei

source_name: Procyclic form (PF)

growth_protocol: Procyclic form T. brucei 427 cells were cultured anaerobically at 27°C in SDM-79 medium (SDM-79, 2 g/L; NaHCO3, pH 7.3), supplemented with 10% v/v FCS and 5 µg/ml hemin

extract_protocol:
MNase digestion of permeabilised cells:  2.5 x 10^8 ccells/sample were harvested, permeabilised with digitonin and digested with 4U MNase (Worthington). 200 µl input DNA removed and 10 µl antibody added to each sample, incubated and antibody-protein-DNA complex collected using Dynabeads and magnetic pull down.
DNA repair, adapter ligation, and library preparation were performed using the Illumina Truseq Chip-seq kit. The Illumina paired-end adaptor was ligated to the nucleosomal DNA. Indices were added to the DNA during PCR according to Illumina kit instructions. DNA was sequenced with an Illumina HiSeq 2500 platform using one flow cell, producing 2x 125 nt sequences

tag: cell line

value: Procyclic form T. brucei Lister 427 Amsterdam wild-type cell line.

tag: genotype

value: Wild type


title: BF K115ac input

description:
Histone H2AK115ac MNase-ChIP-seq
21A_GTGAAA_L008

source_name: Bloodstream form (BF)

growth_protocol: BF T. brucei (S16 221 Puro) was cultured in HMI‑9 medium supplemented with 15% v/v FCS, 0.1 mM β-mercaptoethanol, and 0.2 µg/ml puromycin at 37°C with 5% CO2.

value: BF T. brucei (S16 221 Puro)

value: Puromycin resistance gene in active VSG221 ES


title: BF K115ac ChIP

description:
Histone H2AK115ac MNase-ChIP-seq
21B_CGTACG_L008


title: PF K115ac ChIP

description:
Histone H2AK115ac MNase-ChIP-seq
24B_ATTCCT_L008


title: GSK101 24hr S32

description:
GSK101 24hr
RNA was processed using the Ambion WT expression labeling kit and the Porcine Gene 1.0 ST Array (Affymetrix)


title: RRBS_dermalfibroblasts_control_1-14C

tag: disease status

value: control


title: PF2 K125ac ChIP

description:
Histone H2AK125ac MNase-ChIP-seq
20B_CCGTCC_L008


title: AB2208_2

description: 2100 CDHFD + anti-PD1


title: CD45lung_NS-RA_Rep3

value: Prenatal normal saline and postnatal normoxia


title: AB2207_2

description: 2085 CDHFD

value: CDFHD


title: GSK101 72hr S41


title: GSK101 72hr S43


title: AB2206

description: 2094 CDHFD + anti-PD1


title: PF2 K125ac input

description:
Histone H2AK125ac MNase-ChIP-seq
20A_ATGTCA_L008


title: GSK101 24hr S30


title: AB2146

description: 2100 CDHFD + anti-PD1


title: PF1 K125ac ChIP

description:
Histone H2AK125ac MNase-ChIP-seq
19B_AGTTCC_L008


title: OE0011: S1PR3OE

city: Toronto

first: Stephanie

middle: Zhi-Juan

last: Xie

state: ON

address: 101 College St. TMDT 8-401

country: Canada

institute: University Health Network

description:
Cell isolation protocol: LT-HSC (CD34+CD38-CD45RA-CD90+CD49f+) and ST-HSC (CD34+CD38-CD45RA-CD90-CD49f-) from 3 pool of CB lin- were FACS-purified on a BD Aria Fusion.
Transduction protocol: HSC subsets were pre-stimulated in gene transfer media in gene transfer media composed of X-VIVO 10 media, 1 % BSA supplemented with 1x Pen/Strep, L-Glutamine and the following cytokines: SCF (100 ng/ml), Flt3L (100 ng/ml), TPO (50 ng/ml) and IL7 (10 ng/ml) for 4 hours. Then mtGP91 or S1PR3OE lentiviral particles were added at matching multiplicity of infection (MOI). Lentiviral vectors were marked with blue fluorescent protein (BFP) to track transduced cells. At day 3 post-transduction, BFP+ cells were FACS-purified. We were able to isolate only 1600-1800 BFP+ cells from LT-HSC control samples as opposed to 4000-5400 BFP+ cells from S1PR3OE samples. Thus, we pooled all control BFP+ LT-HSC cells into one sample for RNA-seq analysis. BFP- LT-HSC from control vector transduction were purified from CB1 as an additional LT-HSC control.

data_processing:
S1PR3OERNA-seq was aligned using STAR 2.5.2b9 against GRCh38 and transcript sequences downloaded from Ensembl build 90. Default parameters were used except for the following: “--chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --chimSegmentReadGapMax parameter 3 --alignSJstitchMismatchNmax 5 -1 5 5”.
Counts were the obtained using HTSeq v0.7.2
HTSeq counts were imported into R (3.4.1) and normalized using RLE
Submitter states that raw data will be submitted separately to the EGA for controlled access
Genome_build: GRCh38
Supplementary_files_format_and_content: normalized counts

source_name: Cord blood 2

extract_protocol:
RNA was isolated with a PicoPure kit (ThermoFisher Scientific, KIT0214).
Nextera libraries generated from 10 ng RNA from 5 LT-HSC samples (2 controls, 3 S1PR3OE) and 6 ST-HSC samples (3 controls, 3 S1PR3OE) were subjected to 125 bp, paired-end RNA-sequencing on the Illumina HiSeq 2500 with an average of 50 million reads/sample at the Center for Applied Genomics, Sick Kids Hospital.

value: lineage depleted human cord blood cells

tag: subpopulation

value: ST-HSC

tag: lentiviral vector


title: CD45lung_NS-RA_Rep1


title: GSK101 20hr S56

description:
GSK101 20hr
RNA was processed using the Ambion WT expression labeling kit and the Porcine Gene 1.0 ST Array (Affymetrix)

value: Chondrocyte


title: GSK101 24hr S29


title: AB2145

description: 2103 CDHFD + anti-CD8

value: CDHFD1 + anti-CD8


title: GSK101 20hr S55


title: BF2 K125ac ChIP

description:
Histone H2AK125ac MNase-ChIP-seq
18B_CTTGTA_L008


title: GSK101 12hr S20

description:
GSK101 12hr
RNA was processed using the Ambion WT expression labeling kit and the Porcine Gene 1.0 ST Array (Affymetrix)


title: AB2144

description: 2088 CDHFD


title: OE0008: S1PR3OE

value: LT-HSC


title: OE0017: S1PR3OE

source_name: Cord blood 3


title: GSK101 20hr S54


title: OE0005: S1PR3OE

source_name: Cord blood 1


title: AB2143

description: 2109 CDHFD + anti-CD8


title: BF2 K125ac input

description:
Histone H2AK125ac MNase-ChIP-seq
18A_GGCTAC_L008


title: OE0002: S1PR3OE


title: OE0014: S1PR3OE


title: OE0016: Control


title: AB2142

description: 2079 ND

value: ND


title: PF1 K125ac input

description:
Histone H2AK125ac MNase-ChIP-seq
19A_AGTCAA_L008


title: BF1 K125ac input

description:
Histone H2AK125ac MNase-ChIP-seq
17A_GATCAG_L008


title: BF1 K125ac ChIP

description:
Histone H2AK125ac MNase-ChIP-seq
17B_TAGCTT_L008


title: AB2141

description: 2076 ND


title: GSK101 12hr S18


title: AB2140

description: 2085 CDHFD


title: PF H3 ChIP

description:
Histone H3 MNase-ChIP-seq
3B_GCCAAT_L008


title: OE0009: Control

source_name: Cord blood 1 BFP-


title: GSK101 3hr S66

description:
GSK101 3hr
RNA was processed using the Ambion WT expression labeling kit and the Porcine Gene 1.0 ST Array (Affymetrix)


title: GSK101 3hr S67


title: PF H3 input

description:
Histone H3 MNase-ChIP-seq
3A_ACAGTG_L008


title: LD10% 12hr S22

description:
LD10% 12hr
RNA was processed using the Ambion WT expression labeling kit and the Porcine Gene 1.0 ST Array (Affymetrix)


title: OE0004: Control


title: OE0001: Control

source_name: 3 cord blood pooled  BFP+


title: AB2138_2

description: 2109 CDHFD + anti-CD8


title: AB2137_2

description: 2076 ND


title: MOLM13 ATAC_rep2

city: New York

first: Hua

last: Zhou

state: NY

address: 550 First Avenue, Smilow 1307

department: PATHOLOGY

institute: NYU SCHOOL OF MEDICINE

data_processing:
Peaks were determined algorithmically using Model-based Analysis of ChIP-Seq 2 algorithm with q < 0.05. Differential peaks were called using the DiffBind package. Differential peaks were subject to ontology analysis using Genomic Regions Enrichment of Annotation Tool with human (hg19) as the background.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files ATAC sites for the samples as well as the bigwig and bed files.

source_name: MOLM13 AML cell line

growth_protocol: MOLM13 AML cells were grown in RPMI-1640 medium supplemented with 10% FBS and 1% PenStrep

extract_protocol:
MOLM-13 cells were subjected to cell lysis in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Following 30 seconds of lysis, cells were centrifuged at 500 ×g for 10 minutes, 4°C. Lysed cell pellets were then subjected to the transposition reaction at 37°C for 30 minutes using Tn5 Transposes (Illumina Cat #FC-121-1030), followed by purification of transposed DNA using the Qiagen MinElute Kit.
Transposed DNA fragment were amplified using NEBNext High-Fidelity 2x PCR Master Mix (New England Labs Cat #M0541) and Customized Nextera PCR primers under the following conditions: (Step 1) 72°C for 5 minutes, (Step 2) 98°C for 30 seconds, (Step 3) 98°C for 30 seconds, (Step 4) 63°C for 30 seconds, (Step 5) 72°C for 1 minute, and (Step 6) 4°C hold, with amplified library purified using Qiagen PCR Cleanup Kit prior to Illumina Sequencing. For PCR steps 3-5, transposed library was amplified with number of cycles based on quantitative PCR in order to stop amplification prior to saturation, thus reducing GC and size bias in PCR.

value: MOLM13 AML cell line


title: THESCBVECT

city: Parkville

first: Sarah

last: Holdsworth-Carson

state: VIC

address: Level 7, University Department, Royal Women's Hospital, Crn Grattan Street and Flemington Rd

country: Australia

institute: University of Melbourne

description: T-HESC transfected with LINC00339 vector

data_processing:
Pooled libraries were sequenced on the Illumina NovaSeq 6000 (100bp single-end reads; ~20 million reads/sample).
Reads were aligned against the human reference genome (Ensembl Homo sapiens GRCh38) using HISAT2 v2.0.5 and transcripts were assembled and quantified using StringTie v1.3.3 and the Ensembl Homo sapiens GRCh38 release 91 reference.
Genome_build: Homo sapiens GRCh38
Supplementary_files_format_and_content: Matrix table with gene counts for every gene and every sample

source_name: endometrial stroma

growth_protocol: All cell cultures were grown in culture media (DMEM/F12 / 10% [v/v] fetal calf serum [FCS] / 1x insulin-transferrin-selenium-ethanolamine [ITS-X] / 1x antibiotic-antimycotic [Thermo Fisher Scientific]), with media changes every 2-3 days, in humidified CO2 incubators at 37C.

extract_protocol:
RNA was extracted from stromal cell cultures for RNA-seq using an RNeasy Mini Kit (Qiagen).  Prior to RNA-seq, RNA concentration and quality were assessed using a Bioanalyzer 2100 (Agilent Technologies) and a NanoDropND-6000 (Thermo Fisher Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A human expression vector (pPM-N-D-C-HA) containing LINC00339 (RefSeq NR_109759) and a blank control vector were transfected into 3 HESC cell lines for 48 hours.

value: endometrium

value: stromal

value: T-HESC

tag: transfection

value: LINC00339 vector


title: OE0010: Control


title: AB2043

description: 2013 CDHFD

value: Liver


title: THESCAVECT


title: MOLM13 ATAC_rep1


title: GSK101 0hr S5

description:
GSK101 0hr
RNA was processed using the Ambion WT expression labeling kit and the Porcine Gene 1.0 ST Array (Affymetrix)


title: THESCBCONT

description: T-HESC transfected with blank control vector

value: Blank control vector


title: AB2042

description: 2079 ND


title: MOLM13_HiC_rep1

data_processing:
Hi-C raw reads were processed using the HiC-bench pipeline. More specifically, alignment was performed against the human reference genome (GRCh37/hg19) using bowtie2 (version 2.3.4.1); mostly default parameters were used (additional parameters: --very-sensitive-local --local). Filtering of aligned reads was performed using the “tools-hic filter” command from Genomic Tools through the HiC-bench pipeline.
More specifically, alignment was performed against the human reference genome (GRCh37/hg19) using bowtie2 (version 2.3.4.1); mostly default parameters were used (additional parameters: --very-sensitive-local --local). Filtering of aligned reads was performed using the “tools-hic filter” command from Genomic Tools through the HiC-bench pipeline. The tool discards multi-mapped reads (“multihit”), read-pairs with only one mappable read (“single sided”), duplicated read-pairs (“ds.duplicate”), read-pairs with a low mapping quality of MAPQ < 20, read-pairs resulting from self-ligated fragments (together called “ds.filtered”) and short-range interactions resulting from read-pairs aligning within 25kb (“ds.too.short”).
The accepted intra-chromosomal read-pairs (“ds.accepted intra”) are used for subsequent analysis. Interaction matrices were generated by the HiC-bench platform at 40kb resolution for each chromosome. The matrices were normalized using “iterative correction and eigenvector decomposition” (ICE) and distance normalization for each chromosome matrix. TAD calling was performed using the hicratio caller, using an insulating window of 500kb.
For visualization of Hi-C data, we created heatmaps for regions of interest using the normalized contact matrices. Heatmaps were generated with the R function “image”, and color scale was set to the highest normalized score seen in any sample for the particular window.
Genome_build: hg19

extract_protocol:
In brief, 2 x 107 MOLM-13 human AML cells were fixed with 1% formaldehyde for 10 minutes at room temperature, followed by immediate addition of 2.5M glycine. The cell pellet in 1 ml of ice-cold lysis buffer (10 mM Tris-HCl, pH = 8.0, 10 mL NaCL, 0.8% NP40) containing protease inhibitor cocktail (Thermo Scientific) and incubated at 15 minutes on ice prior to homogenization with a tight Dounce pestle. To open chromatin, the homogenized lysate was then subjected to 0.1% SDS and incubated for 10 minutes at 65 °C to open chromatin, followed by addition of Triton-X (1 % final concentration. Chromatin was then digested overnight at 65 °C with HindII (Thermo Scientific). Digested DNA ends were then filled in with biotin-14-dCTP, as well as non-biotinylated dATP, dGTP and dTTP using Klenow (Invitrogen). Blunt end proximity ligation was performed using T4 DNA ligase (Invitrogen) for 4 hours at 16 °C, followed by overnight proteinase K treatment to remove DNA-bound proteins. Proximity-ligated DNA was purified using phenol chloroform DNA purification and subjected to the removal of biotin from un-ligated DNA ends. DNA was purified using Amicon Ultra 30K spin columns (Millipore) and sonicated to produce 150-350 DNA fragments using the Covaris instrument (Duty Cycle 10%, Intensity 5, Cycles per Burst 200, Frequency Sweeping mode with contant degassing for 3 cycles and 60 seconds process time). Sonicated DNA was purified using AMP pure XP beads (0.8X large fragment exclusion step followed by 1.1X bead bound purification).
End repair of purified sonicated DNA was performed using T4 polynucleotide kinase and Klenow DNA polymerase, followed by dATP-tailing using Klenow fragment (3’-5’ exo). Biotinylated Hi-C DNA was then enriched using MyOne Streptavidin C1 beads, followed by Illumina paired-end adapter ligation and PCR amplification (Q5 HotStart) under the following conditions: : (Step 1) 98°C for 30 seconds, (Step 2) 98°C for 30 seconds, (Step 3) 63°C for 30 seconds, (Step 4) 72°C for 1 minute, and (Step 5) 4°C hold, with amplified library purified using AMP pure bead cleanup (1.5x bead reaction). For cycling PCR steps 2-4, the number of cycles used ensured PCR amplification remained in the linear range with the expected library size distribution as assessed by agarose gel visualization.


title: THESCACONT


title: MOLM13_HiC_rep2


title: AB2139

description: 2085 CDHFD


title: AB2041

description: 2079 ND


title: GSK101 0hr S6


title: Control 72hr S39

description:
Control 72hr
RNA was processed using the Ambion WT expression labeling kit and the Porcine Gene 1.0 ST Array (Affymetrix)


title: Control 72hr S38


title: GSK101 3hr S65


title: Control 72hr S37


title: 1458BVECT

description: M-HESC (1458) transfected with LINC00339 vector


title: BF H3 ChIP

description:
Histone H3 MNase-ChIP-seq
1B_CGATGT_L008

value: BF T. brucei (S16 221 Puro)

value: Puromycin resistance gene in active VSG221 ES


title: BF H3 input

description:
Histone H3 MNase-ChIP-seq
1A_ATCACG_L008


title: GSK101 0hr S7


title: 24.CSVM34_No_Nitrate

first: Bareket

last: Dassa

department: Life Sciences Core Facilities

data_processing:
Raw reads were quality trimmed using Cutadapt in addition to removal of sequencing adapters.
In order to deplete rRNA genes in silico, reads were mapped to the 5S, 16S, 28S rRNA genes of strain PCC 7120 using Bowtie2 in end-to-end mode. Reads which did not map to rRNA genes were further used for the analysis of gene expression, and were aligned to the bacterial genome (GCA_000009705.1_ASM970v1) using Bowtie2 in end-to-end mode.
Gene quantification was done using HTseq (in union mode).
Normalization and analysis of differentially expressed genes was done using DESeq2 package, using a model combining genotype and treatment into a single factor.
Genome_build: GCA_000009705.1_ASM970v1
Supplementary_files_format_and_content: DESeq_results.txt

organism: Nostoc sp. PCC 7120 = FACHB-418

source_name: Anabaena

growth_protocol: Strains were cultured in 100 ml of BG11 liquid medium in 250-ml flasks with cotton plugs until a concentration of 3-5 μg Chl . ml-1 was reached, then these cultures were collected, washed 3 times with BG110 medium and used to set 50 ml cultures (at 2 μg Chl · ml-1) in nitrate conditions (BG11) and under nitrogen deprivation (BG110). Strains under these conditions were incubated for 18 hours under standard growth conditions.

extract_protocol:
Ribosomal RNA from the 700 ng of total RNA we used Ribozero rRNA removal kit Bacteria (Illumina) according to the manufacturer’s instructions.
reverse transcription was done with random hexamers on 70ng RNA followed by fragmentation and synthesis of double‑stranded cDNA. Then, end repair, adenosine base addition, adapter ligation aand TapeStation (Agilent). Sequencing libraries were constructed with barcodes to allow multiplexing of 24 samples in 1 lanes.  About 9.3 to 13M single-end 60-bp reads were sequenced per sample on Illumina HiSeq 2500 V4 instrument.nd PCR amplification steps were performed. Libraries were evaluated by Qubit (Thermo Fisher scientific)

treatment_protocol: For each sample, cells were rapidly collected by filtration and washed with buffer TE50 (50 mM Tris-HCl [pH 8.0], 100 mM EDTA). Cells were resuspended in 2 ml of buffer TE50 and transferred to 2-ml tubes, and then they were collected by centrifugation at 11.500 x g for 2 minutes at 4°C. Supernatant was removed and cell pellets were flasTotal RNA was isolated by using hot phenol as described (Mohamed and Jansson, 1989)  with modifications.h frozen in nitrogen liquid for storage at ‑80°C. All samples were treated with DNase I (Turbo DNA‑free kit; Invitrogen).

value: nitrogen-poor

tag: time

value: 18 hrs.


title: AB2044

description: 2100 CDHFD + anti-PD1

value: CDHFD1 + anti-PD1


title: Control 24hr S26

description:
Control 24hr
RNA was processed using the Ambion WT expression labeling kit and the Porcine Gene 1.0 ST Array (Affymetrix)


title: AB2040

description: 2088 CDHFD

value: CDFHD


title: 1458AVECT


title: 23.CSVM34_Nitrate

value: nitrogen-replete


title: 1458BCONT

description: M-HESC (1458) transfected with blank control vector


title: Control 24hr S25

value: Chondrocyte


title: AB2038

description: 2106 CDHFD + anti-CD8

value: CDHFD1 + anti-CD8


title: AB2039

description: 2106 CDHFD + anti-CD8


title: 22.CSVM141_No_Nitrate


title: 21.CSVM141_Nitrate


title: Control 24hr S27


title: 1458ACONT


title: AB2037

description: 2082 ND


title: 20.WT_No_Nitrate


title: Control 20hr S52

description:
Control 20hr
RNA was processed using the Ambion WT expression labeling kit and the Porcine Gene 1.0 ST Array (Affymetrix)


title: GSK101 12hr S17

description:
GSK101 12hr
RNA was processed using the Ambion WT expression labeling kit and the Porcine Gene 1.0 ST Array (Affymetrix)


title: 1455BVECT

description: L-HESC (1455) transfected with LINC00339 vector


title: AB2036

description: 2091 CDHFD


title: 1455BCONT

description: L-HESC (1455) transfected with blank control vector


title: AB2035

description: 2094 CDHFD1 + anti-PD1


title: 1455AVECT


title: 19.WT_Nitrate


title: 18.CSVM34_No_Nitrate


title: 17.CSVM34_Nitrate


title: ChIPseq-GRKO-GFP-GRmon_abGFP_DEX_rep2

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
RTA 2.4.11 was used for Basecalling and Bcl2fastq 2.17 was used for demultiplexing allowing 1 mismatch.
Trimmomatic 0.36 was used for adapter and quality control
ChIP- and ATAC-seq alignment was performed by Bowtie2 (2.1.0) with Bowtie2 –p 8 –x bowtie2_ref/genome_prefix –U read1.fastq –S result.sam.
RNA-seq alignment was performed by STAR (2.7) with STAR --sjdbOverhang 50  --readFilesIn INPUT_R1.pair.fastq.gz INPUT_R2_R2.pair.fastq.gz --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outTmpDir --outFileNamePrefix bam/rnaseq_STAR/OUTPUT . Dex regulated genes were defined with DESeq2 through HOMER program version 4.9.
Peaks were called using HOMER program version 4.9 with findPeaks with following parameters; FDR<0.001, 4x fold enrichment over control, 4x fold enrichment over local background, and >75 tags per site. In addition, untreated GR ChIP sample was used to further filter out noise from GR samples using default parameters on getDifferentialPeaks.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph (HOMER makeUCSCfile command) from alignment file.

source_name: 3617-KOGR cells, stably integrated A465T/I634A GFP-GRmon, Dex-treated, GFP ChIP

growth_protocol: Mouse adenocarcinoma and MEF cells were grown in Dulbecco's Modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 25 U/ml penicillin and 25 µg/ml streptomycin, and 2mM L-Glutamine, and kept at 37 °C in a humidified 95% air/ 5% CO2 incubator. Mouse adenocarcinoma cells were also supplemented with 5 µg/ml of tetracycline to supress GFP-GR expression.

extract_protocol:
For ChIP-seq, lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with specified antibody. For ATAC-seq, 100 000 isolated nuclei were treated with 2.5 µl Nextera Tn5 Transposase from Nextera kit. For RNA-seq, RNA was extracted using the PureLink RNA mini kit.
Libraries were prepared for sequencing using standard Illumina protocols.
For ChIP-seq, Illumina TruSeq Chip Sample Prep Kit; for ATAC-seq, Illumina Nextera DNA Library Prep Kit; for RNA-seq, Illumina Stranded Total RNA.

treatment_protocol: Mouse adenocarcinoma and MEF cells were grow in steroid-depleted medium (10% charcoal stripped FBS in DMEM) for 24 h, and the cells were subsequently left untreated or treated 100 nM of dexamethasone for 1 h in ChIP-seq and ATAC-seq, and for 2 h in RNA-seq, prior extraction.

value: mouse adenocarcinoma

tag: stably expressing

value: A465T/I634A GFP-GRmon

value: Dexamethasone

tag: concentration

value: 1 h

tag: chip antibody


title: 1455ACONT

value: endometrium

value: stromal


title: 16.CSVM141_No_Nitrate

tag: strain


title: ChIPseq-GRKO-GFP-GRmon_abGFP_DEX_rep1

tag: cell type


title: Control 12hr S14

description:
Control 12hr
RNA was processed using the Ambion WT expression labeling kit and the Porcine Gene 1.0 ST Array (Affymetrix)


title: Control 20hr S49


title: ChIPseq-GRKO-GFP-GRmon_abGFP_NT_rep2

source_name: 3617-KOGR cells, stably integrated A465T/I634A GFP-GRmon, non-treated, GFP ChIP

value: no treatment


title: 25D

city: Chicago

first: Larisa

last: Nonn

state: IL

address: 840 S. Wood St, MC847

department: Pathology

institute: University of Illinois at Chicago

data_processing:
SpaceRanger demultimplexed raw base cal (BCL) files into FASTQ files
SpaceRanger demultimplexed raw base cal (BCL) files into FASTQ files
Genome_build: Ensembl_GRCh38
Supplementary_files_format_and_content: SpaceRanger gene expression matrix for import into R

source_name: Prostate tissue

extract_protocol:
Tissue slices were dried and embedded in OCT then flash flozen. 10 micron sections were sliced and hydridized to the Visium slide
Visium Spatial Gene Expression Library Construction. For selected spots, spots corresponding to epithelial markers were chosen to minimze stromal influence and spots on tissue folds were excluded

treatment_protocol:
ETOH: 300micron prostate tissue slice cultured in EtOH in a 37 degree celcius incubator for 8 hours. Tissue was frozen, sectioned, and placed on an array
25D: 300micron prostate tissue slice cultured in 25D in a 37 degree celcius incubator for 8 hours. Tissue was frozen, sectioned, and placed on an array

tag: sample type

value: heterogenous

value: 2D culture in 50nM 25D


title: ChIPseq-GRKO-GFP-GRmon_abGFP_NT_rep1


title: 15.CSVM141_Nitrate


title: Control 12hr S16


title: Control 12hr S13


title: iBlastoids scRNA-seq

city: Clayton

first: Jan

last: Schroeder

address: Building 75 Innovation Walk

department: Anatomy & Developmental Biology

institute: Monash University

description: 10x genomics single cell RNA-seq v3

data_processing:
Cellranger count function
Genome_build: Ensembl GRCh37.87 + custom sequences
Supplementary_files_format_and_content: tsv/mtx files for transcript counts per cell

source_name: 32F and 38F

growth_protocol: Human somatic cell reprogramming was performed as previously described to obtain the d21 reprogramming intermediates. Briefly, reprogramming of human fibroblasts was conducted using CytoTune-iPS 2.0 Sendai reprogramming kit according to the manufacturer’s instructions (ThermoFisher). Primary HDFa were seeded at a density of ~5-10×104 cells in fibroblast medium. As shown in Fig. 1a, cells were transduced with Sendai viruses in FM at the multiplicity of infection (MOI) as follows, KOS MOI=5, c-MYC MOI=5, KLF4 MOI=6. Media replacement was done every other day starting from day 1 following transduction and every day from day 8 onwards. On day 21 of reprogramming, cells were dissociated and seeded at a density of 1.2 x 105 cells per well onto a 24-well Aggrewell plate  (Stem Cell Technologies) in Human iBlastoid Medium supplemented with 10μM Y-27632 (ROCK inhibitors) (Selleckchem) according to the manufacturer’s instructions. The cells were cultured at 37 °C, 5% O2 and 5% CO2 incubators. After 24 hours, the cells were replenished with fresh Human iBlastoid Medium without ROCK inhibitors. On day 6 of iBlastoid formation, the iBlastoids were collected for subsequent analysis.

extract_protocol:
Sample preparation followed by 10x Genomics scRNA-seq v3 chemistry protocol.
Samples were processed as described on the Chromium Single Cell 3' Reagent Kits User Guide (v3 Chemistry).

value: Dermal fibroblasts

value: iBlastoid medium

tag: Sex

value: Female


title: 14.WT_No_Nitrate

tag: treatment

value: nitrogen-poor

value: 18 hrs.


title: Control 3hr S64

description:
Control 3hr
RNA was processed using the Ambion WT expression labeling kit and the Porcine Gene 1.0 ST Array (Affymetrix)

source_name: femurs of 12-16w pigs


title: 13.WT_Nitrate

value: nitrogen-replete


title: Control 20hr S51

value: Chondrocyte


title: U2OS WDR5-FKBP(F36V) RNA-seq dTAG rep4 [dTAG_4]

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

description:
4489-AG-8_S1
processed data file: U2OS-WDR5-count.txt

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include raw counts for each Sample

source_name: U2OS WDR5-FKBP(F36V) RNA-seq dTAG

growth_protocol: All cells were grown in DMEM with 10% FBS and 10 U/ml Penicillin-Streptomycin. All cells were cultured at 37˚C and 5% CO2.

extract_protocol:
Cells were collected in Trizol and RNA was purified with Direct-Zol RNA Miniprep kit (Zymo) with on-column DNaseI treatment. RNA was submitted to GENEWIZ or the Vanderbilt Technologies for Advanced Genomics Core Laboratory for rRNA reduction, library preparation, and deep sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: engineered genotype

value: endogenous C-terminal tag on WDR5, FKBP(F36V)-2xHA

value: 500 nM dTAG47 for 24 hours


title: ChIPseq-GRKO-GFP-GRdim_abSMARCA4_DEX_rep1

source_name: 3617-KOGR cells, stably integrated A465T GFP-GRdim, Dex-treated, SMARCA4 ChIP

value: mouse adenocarcinoma

value: A465T GFP-GRdim

value: SMARCA4 (BRG1, Epitomics, EPNCIR11A, made in collaboration with Epitomics, PMID:24317492)


title: Control 3hr S63


title: ChIPseq-GRKO-GFP-GRdim_abSMARCA4_NT_rep1

source_name: 3617-KOGR cells, stably integrated A465T GFP-GRdim, non-treated, SMARCA4 ChIP


title: Control 3hr S61


title: U2OS WDR5-FKBP(F36V) RNA-seq dTAG rep3 [dTAG_3]

description:
4489-AG-7_S1
processed data file: U2OS-WDR5-count.txt


title: 11.CSVM34_Nitrate


title: Control 0hr S4

description:
Control 0hr
RNA was processed using the Ambion WT expression labeling kit and the Porcine Gene 1.0 ST Array (Affymetrix)


title: U2OS WDR5-FKBP(F36V) RNA-seq dTAG rep2 [dTAG_2]

description:
4489-AG-6_S1
processed data file: U2OS-WDR5-count.txt


title: ChIPseq-GRKO-GFP-GRdim_abH3K4me1_DEX_rep1

source_name: 3617-KOGR cells, stably integrated A465T GFP-GRdim, Dex-treated, H3K4me1 ChIP

value: Dexamethasone

value: 1 h


title: ChIPseq-GRKO-GFP-GRdim_abH3K4me1_NT_rep2

source_name: 3617-KOGR cells, stably integrated A465T GFP-GRdim, non-treated, H3K4me1 ChIP

value: no treatment


title: 10.CSVM141_No_Nitrate


title: ETOH

value: heterogenous

value: 2D culture in EtOH


title: U2OS WDR5-FKBP(F36V) RNA-seq dTAG rep1 [dTAG_1]

description:
4489-AG-5_S1
processed data file: U2OS-WDR5-count.txt


title: 9.CSVM141_Nitrate


title: Control 0hr S2


title: ChIPseq-GRKO-GFP-GRdim_abH3K4me1_DEX_rep2


title: ChIPseq-GRKO-GFP-GRdim_abH3K4me1_NT_rep1


title: U2OS WDR5-FKBP(F36V) RNA-seq DMSO rep4 [DMSO_4]

description:
4489-AG-4_S1
processed data file: U2OS-WDR5-count.txt

source_name: U2OS WDR5-FKBP(F36V) RNA-seq DMSO

value: 0.01% DMSO for 24 hours


title: U2OS WDR5-FKBP(F36V) RNA-seq DMSO rep2 [DMSO_2]

description:
4489-AG-2_S1
processed data file: U2OS-WDR5-count.txt


title: 7.WT_Nitrate


title: 12.CSVM34_No_Nitrate


title: LD10% 72hr S47

description:
LD10% 72hr
RNA was processed using the Ambion WT expression labeling kit and the Porcine Gene 1.0 ST Array (Affymetrix)


title: ChIPseq-GRKO-GFP-GRdim_abH3K27ac_DEX_rep2

source_name: 3617-KOGR cells, stably integrated A465T GFP-GRdim, Dex-treated, H3K27ac ChIP


title: LD10% 72hr S46


title: ChIPseq-GRKO-GFP-GRdim_abH3K27ac_DEX_rep1


title: LD10% 72hr S45


title: Control 0hr S1


title: U2OS WDR5-FKBP(F36V) RNA-seq DMSO rep1 [DMSO_1]

description:
4489-AG-1_S1
processed data file: U2OS-WDR5-count.txt


title: 6.CSVM34_No_Nitrate


title: ChIPseq-GRKO-GFP-GRdim_abH3K27ac_NT_rep2

source_name: 3617-KOGR cells, stably integrated A465T GFP-GRdim, non-treated, H3K27ac ChIP


title: LD10% 24hr S36

description:
LD10% 24hr
RNA was processed using the Ambion WT expression labeling kit and the Porcine Gene 1.0 ST Array (Affymetrix)


title: THP1_sgRNA_S11

data_processing:
Library strategy: ECCITE-seq (Expanded CRISPR-compatible CITE-seq)
Raw reads were demultiplexed and aligned to GRCh38 (version 3.0.0) using the Cell Ranger Single Cell Gene Expression Software (version 3.1.0, 10x Genomics). Downstream analysis of RNA, antibody derived tags (ADTs) and CRISPR Guide Capture (CGC) data was performed using the Seurat R package (version 3.1.3)56, which enables processing of multi-modal single-cell data. We included cells with more than 400, and less than 6000 unique feature counts, and only kept cells with less than 15% of their transcripts originating from mitochondrial genes to exclude low-quality cells and multiple cells captured in droplets. After quality filtering, we normalized the RNA expression data by total expression, multiplied by a scaling factor of 10,000 and log-transformed the results.
For the ADTs and CGC counts, we divided the counts by the geometric mean of each corresponding feature across cells and log-transformed the results (centered log-ratio transformation). To demultiplex CGC counts, we used the MULTIseqDemux() function, as described57, with default parameters from within Seurat. To visualize RNA expression similarities between cells in two-dimensional space, we first performed principal component analysis (PCA) on the 2,000 most variable genes, and used the first 20 principal components as an input to uniform manifold approximation and projection (UMAP)58. UMAP representation of CGC expression data was based on Euclidean distance between CGC features instead, due to comparably low number of features. All analysis was performed using R, version 3.5.1.

source_name: THP1 human AML cell line

growth_protocol: THP1 AML cells were grown in RPMI-1640 medium supplemented with 10% FBS and 1% PenStrep

extract_protocol:
THP-1 Cas9-expressing cells were transduced with pooled sgRNA lentivirus at a low MOI (~0.3). At day 12 post-transduction, cells were stained with DAPI (Sigma Aldrich #D9542-1MG) and sorted for live GFP positive cells. Subsequently, sorted cells were stained with human Fcblock for 10 mins. at room temperature and then incubated with TotalSeq-C antibodies, CD11B (BioLegends #301359) and CD16 (BioLegends #302065) for 30 mins. on ice.
Samples were processed according to Chromium Next GEM Single Cell V(D)J v1.1 kit with modified steps referenced in ECCITE-seq protocol29. Libraries were pooled consisting of 85% cDNA, 10% guide-tag and 5% protein-tag and sequenced on Nova-Seq SP100 (Recipe 26 cycles read 1, 8 cycles index, and 91 cycles read 2). Oligonucleotide sequences of sgRNAs used for the library and primers for ECCITE-seq can be found in Supplementary Table 1

tag: tissue

value: THP1 human AML cell line

tag: single cell feature

value: sgRNA


title: 5.CSVM34_Nitrate

tag: genotype


title: ChIPseq-GRKO-GFP-GRdim_abH3K27ac_NT_rep1

tag: cell line


title: LD10% 24hr S34


title: ChIPseq-GRKO-GFP-GRdim_abGFP_DEX_rep2

source_name: 3617-KOGR cells, stably integrated A465T GFP-GRdim, Dex-treated, GFP ChIP


title: 4.CSVM141_No_Nitrate

value: nitrogen-poor


title: LD10% 20hr S60

description:
LD10% 20hr
RNA was processed using the Ambion WT expression labeling kit and the Porcine Gene 1.0 ST Array (Affymetrix)


title: 3.CSVM141_Nitrate

value: 18 hrs.


title: LD10% 24hr S35


title: 8.WT_No_Nitrate


title: THP1_cDNA_S10

value: cDNA


title: THP1_cDNA_S8


title: ChIPseq-GRKO-GFP-GRdim_abGFP_DEX_rep1


title: 2.WT_No_Nitrate


title: 1.WT_Nitrate

value: nitrogen-replete


title: LD10% 20hr S59

value: Chondrocyte


title: ChIPseq-GRKO-GFP-GRdim_abGFP_NT_rep2

source_name: 3617-KOGR cells, stably integrated A465T GFP-GRdim, non-treated, GFP ChIP


title: ChIPseq-GRKO-GFP-GRdim_abGFP_NT_rep1


title: THP1_cDNA_S7


title: KRAS-PI3K_CD44v6neg_3

status: Public on Jan 18 2021

city: Trento

first: CIBIO

last: Zippo

state: Not Applicable

address: via sommarive 9

department: Cellular, Computation and Integrative Biology (CIBIO)

institute: University of Trento

data_processing:
Sequenced reads quality was assessed using fastQC
Reads were trimmed using Trimmomatic v0.39.
Reads were aligned to the human genome (GRCh37/hg19) using TopHat2 with the following command: tophat --library-type fr-firststrand --no-coverage-search -g 1 hg19
reads per Kilobase per Megabase of library size (RPKM)  were calculated using HOMER v4.10 with the command analyzeRepeats.pl rna hg19 -count exon  -rpkm -condenseGenes
raw gene counts were retrieved using HOMER v4.10 with the command analyzeRepeats.pl rna hg19 -count exon  -noadj -condenseGenes
RPKM normalized bigwig files created using DeepTools3.1.2 with the following command: bamCoverage -b "$i" -o "$i"_RPKM.bw --effectiveGenomeSize 2685511504 --normalizeUsing RPKM
Genome_build: hg19
Supplementary_files_format_and_content: BigWig track files of RNA-seq data, RPKM normalized. Table with gene raw read counts.

source_name: colon resection

growth_protocol: Sphere cells were cultured in serum-free stem cell medium supplemented with EGF and b-FGF.

extract_protocol:
Cellular pellets were resuspended with TRIzol (Thermo Fisher cat. #15596026Ambion #15596018), and total RNA was extracted according to the manufacturer’s instructions. Contaminating genomic DNA was removed by DNase (Qiagen cat. #79254) digestion. RNA quality and concentration were assed with the 2100 Bioanalyzer (Agilent cat. #G2939BA) and the Qubit fluorometer (Thermo Fisher cat. # Q33226), respectively.
Total RNA-seq libraries were prepared using the Illumina TruSeq library kit (20020597). Libraries were sequenced as single reads of 50 bp with the Illumina HiSeq2500.

treatment_protocol: Purification and propagation of sphere cells was assessed  from primary tumor specimens from colorectal cancer patients undergoing colon resection. Enrichment of CD44v6+ and CD44v6- populations  in 3 different BRAF-mutant sphere cultures was accomplished by FACSMelody cell sorter using a CD44v6-APC antibody. Prior to sorting, cells were washed with PBS containing 2% BSA and 2 mM EDTA and filtered with a 70 µM mesh to prevent clogging. Post-sorting acquisition was performed in order to verify the population purity. Dead cells were excluded on the basis of the uptake of 7-AAD.

value: primary tumor

tag: cd44v6 status

value: negative

tag: disease state

value: colorectal cancer


title: KRAS-PI3K_CD44v6neg_2


title: THP1_ADT_S12

value: ADT


title: LD10% 12hr S24

description:
LD10% 12hr
RNA was processed using the Ambion WT expression labeling kit and the Porcine Gene 1.0 ST Array (Affymetrix)


title: KRAS-PI3K_CD44v6neg_1


title: LD10% 20hr S57


title: KRAS-PI3K_CD44v6pos_3

value: positive


title: M5_Rep2

city: Salt Lake City

first: Jingtao

last: Guo

state: UT

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

institute: University of Utah School of Medicine

data_processing:
Samples were sequenced as paired end sequencing. Raw data were firstly demultiplexed using mkfastq application (Cell Ranger v2.2.0). Three types of fastq files were generated: I1 contains 8 bp sample index; R1 contains 26 bp (10 cell + 16 UMI) index and R2 contains 100 bp cDNA sequence. Fastq files were then run with count application (Cell Ranger v2.2.0) using default settings, which performs alignment (using STAR aligner), filtering and UMI counting. The UMI count table was used for further analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include UMI numbers for all genes and single cells

source_name: Testicular cells

extract_protocol:
Testicular tissues were firstly minced into small pieces mechanically, and subject to trypsin digestion for ~25 min at 37 C. Cell suspension was centrifuged and resuspended in cold PBS buffer with 0.4% of BSA at the concentration of ~1000/ul, which then was loaded onto the 10X Chromium Controller using Chromium Single Cell 3’ v2 reagents.
Sequencing library was prepared following the manufacturer’s instructions (10X Genomics), with 13 cycles used for cDNA amplification and 12 cycles for library amplification, which was then sequenced on a 26 X 100 cycle paired-end run via a Illumina 2500 instrument. Each sample was sequenced in one separate sequencing lane.
10X Genomics single cell RNA sequencing

value: Testicle

tag: age

value: 5 months old


title: M5_Rep1


title: KRAS-PI3K_CD44v6pos_2


title: KRAS-PI3K_CD44v6pos_1


title: BRAF-PI3K_CD44v6neg_3


title: LD10% 12hr S23


title: BRAF-PI3K_CD44v6neg_2


title: RNA_BrainE15_Baf53a_KO_3

city: Geneva

first: Simon

last: Braun

address: rue Michel Servet 1

country: Switzerland

institute: University of Geneva

data_processing:
Reads were trimmed with cutadapt 1.16 using -u 3 option. Transcripts were quantified using Kallisto against UCSC mm10 reference.
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: Kallisto abundance estimates

source_name: Mouse forebrains E15.5

growth_protocol: Forebrains were disected from E15.5 embryos and dissociated into a single cell suspension.

extract_protocol:
total RNA
Libraries were prepared using the SMARTer kit (Takara Bio # 634874), which produces stranded libraries from rRNA depleted total RNA.

value: forebrain E15.5

value: KO


title: RNA_BrainE15_Baf53a_KO_4


title: BRAF-PI3K_CD44v6neg_1


title: RNA_BrainE15_Baf53a_KO_2


title: RNA_BrainE15_Baf53a_KO_1


title: BRAF-PI3K_CD44v6pos_3


title: BRAF-PI3K_CD44v6pos_2


title: RNA_BrainE15_Baf53a_Het_4

value: Het


title: KRAS_CD44v6neg_3

value: KRAS


title: RNA_BrainE15_Baf53a_Het_2


title: KRAS_CD44v6neg_2


title: ATAC_BrainE15_Baf53a_KO_4

data_processing:
Basecalls performed using Illumina CASAVA version 1.8.2
Reads were trimmed to remove adapters, then aligned to the mm10 genome assembly using bowtie version 2.1.0. Duplicate reads were discarded.
Peaks were called using MACS 2.1.0 with with default settings.
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated by creating fragments of l150 bp centered over all ATAC-seq read fragments, then calculating the basepair coverage for each replicate using Bedtools. bigWig files represent the mean values across replicates from each condition.

extract_protocol:
Genomic DNA
ATAC-seq was performed as previously described (PMID: 24097267)


title: ATAC_BrainE15_Baf53a_KO_3


title: KRAS_CD44v6neg_1


title: KRAS_CD44v6pos_3


title: BRAF-PI3K_CD44v6pos_1


title: ATAC_BrainE15_Baf53a_KO_1


title: RNA_BrainE15_Baf53a_Het_3


title: KRAS_CD44v6pos_1


title: BRAF_CD44v6neg_3

value: BRAF


title: KRAS_CD44v6pos_2


title: ATAC_BrainE15_Baf53a_KO_2


title: ATAC_BrainE15_Baf53a_Het_3


title: BRAF_CD44v6neg_2


title: ATAC_BrainE15_Baf53a_Het_4


title: ATAC_BrainE15_Baf53a_Het_2


title: BRAF_CD44v6neg_1


title: ATAC_BrainE15_Baf53a_Het_1


title: BRAF_CD44v6pos_2


title: BRAF_CD44v6pos_1


title: WT_CD44v6neg_2

value: WT


title: RNA_BrainE15_Baf53a_Het_1


title: WT_CD44v6neg_1


title: TR2

city: Kitakyushu

first: Kaori

last: Kato

address: 1-1 Iseigaoka, Yahatanishiku, Kitakyushu city, Fukuoka 807-8555 Japan

country: Japan

institute: University of Occupational and Environmental Health, Japan

data_processing:
The sequenced CAGE reads were mapped to the mouse mm9 genome using the BWA software program (version 0.7.12-r1039). The unmapped reads were then mapped by HISAT2 (version 2.0.5). The 5' coordinates of CAGE-tags were input for RECLU clustering, with a maximum irreproducible discovery rate (IDR) was 0.1 and minimum count per million (CPM) value was 0.1. The R program edgeR in the RECLU pipeline was used to perform the differential analysis of the genes.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include CPM calue for each sample.

source_name: Unexposed lung tissue of triply n/i/eNOSs-/- mice

extract_protocol:
RNA extraction and sequencing were performed by DNAFORM (Yokohama, Japan).  The qualities and quantities of total RNA were checked by a Bioanalyzer (Agilent, CA, USA) to ensure that the RINs (RNA integrity number) were above 7.0 and the A260/280 and 260/230 ratios were above 1.7.
First-strand cDNAs were reverse-transcribed from the RNAs, then second-stranded cDNAs were synthesized and selected by the Cap trapping method. After “bar code” tags were attached, CAGE libraries were constructed. Multiplexed 8 CAGE libraries were sequenced using single end reads of 75nt on an Illumina NextSeq 500 sequencer.

tag: strain background

tag: genotype/variation

value: Triply n/i/eNOSs-/-

value: 4 weeks

value: lung


title: TR4


title: WT_CD44v6pos_3


title: WT4

source_name: Unexposed lung tissue of wild type mice

value: wild type


title: WT3


title: WT_CD44v6pos_2

value: primary tumor


title: WT_CD44v6pos_1


title: WT1


title: AK005F: HeLa wt, 10 µM tetramer 2-5A, 4.5 h

city: Bethesda

first: Nicholas

middle: R

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

data_processing:
Library strategy: ribosome profiling
Samples were sequenced on the HiSeq2500 or HiSeq3000. Reads in samples starting with "AK" are demultiplexed and trimmed but contain UMIs (Unique Molecular Identifier). Reads in samples starting with "GJ" have linker sequences but no UMIs (samples prepared as in Ingolia et al., 2009) .
Reads were aligned to a library of human non-coding RNA genes (rRNAs and tRNAs) with bowtie 1 and those not matching were retained.
Samples had PCR duplicates removed (except "GJ" files).
Reads were then aligned to hg38 human transcriptome tophat.  The aligned reads  were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files.
Genome_build: hg38
Supplementary_files_format_and_content: Wig files were created by Plastid. All reads are 5' end aligned.

source_name: whole cell

growth_protocol: cell line appropriate media + 10% FBS, 37˚C, 5% CO2

extract_protocol:
Ribosome profiling lysates were clarified, Rnase I treated, and separated over sucrose cushion. RNA was then extracted using trizol and footprints of the specified size were retained by gel purification.
Samples starting with "GJ" were prepared accoring to Ingolia et al, 2009. Samples starting with "AK" were prepared using the protocol published in McGlincy and Ingolia, 2017. Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription. rRNA was subtracted using Ribo-Zero Illumina kit after ligation. cDNAs were then circularized and PCR amplified.

treatment_protocol: 2-5A and poly I:C were transfected by Lipofectamine 3000. Transfection controls were only treated with Lipofectamine 3000. Cells were washed with ice cold DPBS and flash frozen in liquid nitrogen. Then cells were lysed in lysis buffer.

value: HeLa

value: 10 µM tetramer 2-5A, 4.5 h

tag: molecule subtype

value: 80S ribosome protected RNA (25-34 nt)


title: AK003F: HeLa wt, 10 µM trimer 2-5A, 4.5 h

value: 10 µM trimer 2-5A, 4.5 h


title: AK004F: HeLa wt, 1 µM tetramer 2-5A. 4.5 h

value: 1 µM tetramer 2-5A. 4.5 h


title: HoxB8 transfected Replicate 1

city: Marseille

first: Andrew

middle: J

last: Saurin

address: Campus de Luminy

country: France

institute: IBDM / CNRS

description:
RNA-seq of Hoxb8 GFP+ cells Rep1
Hoxb8-pCIG plasmid
Neural tube in ovo electroporations were performed at HH11. Eggs were windowed, and the DNA solution (1 to 2µg/µl) was injected in neural tube lumen. Needle L-shape platinum electrodes were place on both sides of the embryo at trunk level (5 mm apart), with the cathode always at its right. Five 50 ms pulses of 25 volts were given bilateral at 50 ms intervals with an electroporator NEPA21 (Nepagene). Plasmids DNA concentrations were for the control mix: pCIG 2µg/µl and for the HoxB8 mix : Hoxb8-pCIG 1 µg/µl + pCIG 1µg/µl . Part of the neural tube expressing the GFP were dissected 18 hours after electroporation and dissociated (Trypsin-EDTA 0,25%). A highly enriched population of GFP-expressing cells was isolated by FACS with the use of a dead cell exclusion (DCE)/discrimination dye (DAPI) to eliminate dying cells.

data_processing:
Basecalls performed using RTA (Illumina)
RNA-seq reads were aligned to the galgal4 genome assembly using subread-align
Gene exon counts were made using featureCounts
RNA-Seq differentially expressed genes were called using DESeq2 using a false discovery rate (FDR;padj) cut-off of 0.01
Genome_build: gg4
Supplementary_files_format_and_content: DGE files show the DESeq output of differentially expressed genes (Log2Fold Change, p-value, p-adjusted) of Hoxb8 vs Control

organism: Gallus gallus

source_name: Hoxb8 transfection, GFP positive cells

extract_protocol:
RNA was extracted (RNeasy Mini Kit) and reverse transcribed and cDNA was amplified using a linear amplification system and used for sequencing library building
mRNA libraries were prepared for sequencing using standard Illumina protocols

value: Hoxb8 GFP expressing cells


title: AK001F: HeLa wt, transfection control, 4.5 h

value: untreated


title: GJ102F: WT Hap1 transfection control, 3h


title: Ech_SC_A_6 [S31_S62]

city: Groningen

first: Bart

last: Eggen

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences

country: Netherlands

institute: UMCG Groningen

description:
processed data file: counts_eae.txt
S31_S62_R1_001

data_processing:
After trimming of bad quality bases, FASTQ files were aligned to build Mus_musculus.GRCm38.82 reference genome using HISAT (hisat/0.1.5-beta-goolf-1.7.20) with default settings.
Aligned reads were sorted using SAMtools (SAMtools/1.-goolf-1.7.20) and gene level quantification was done by HTSeq-count (HTSeq/0.6.1p1) using –mode=union.
Genome_build: Mus_musculus.GRCm38.82
Supplementary_files_format_and_content: tab-delimited txt files with HTSeq counts

extract_protocol:
Forebrain, hindbrain, and spinal cord were dissected and astrocytes were isolated using FACS. Cells were lysed in RLT+ lysis buffer and RNA was extracted using the Rneasy Plus Micro Kit (Qiagen, 74034). Primary neonatal astrocytes were lysed in TRIzol (Invitrogen, 15596018) and RNA was isolated according to manufacturers instructions.
Total RNA concentration and quality were measured using the Experion Automated Electrophoresis System (Bio-Rad) in combination with the RNA HighSens Analysis Kit (Bio-Rad, 7007105) according to manufacturer’s protocol. Non-degraded RNA-samples were selected for subsequent sequencing analysis.  Sequencing libraries were manually generated using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, 015.96). The obtained cDNA fragment libraries were sequenced on an Illumina Illumina HiSeq 2500 using default parameters (single read 1x50bp) in pools of multiple samples.

tag: disease

tag: region

value: Astrocytes


title: Ech_SC_A_3 [S27_S70]

description:
processed data file: counts_eae.txt
S27_S70_R1_001

tag: strain

tag: cell type


title: TR1


title: TR3


title: Ech_SC_A_4 [S28_S47]

description:
processed data file: counts_eae.txt
S28_S47_R1_001


title: Ech_SC_A_5 [S29_S52]

description:
processed data file: counts_eae.txt
S29_S52_R1_001


title: ZR-75-1 xenograft DHT 4

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

institute: Flinders University

description:
Xeno_DHT_Tum4_025
processed data file:
Xeno_genes.tpm.filtered.txt
Xeno_genes.fpkm.txt
Xeno_genes.fpkm.filtered.txt
Xeno_genes.counts.txt
Xeno_genes.counts.filtered.txt

data_processing:
Basecalls performed using Illumina bcl2fastq.
Fastq files were quality checked (FastQC v0.11.4; fastq-screen v0.5.2). Sequence adapters were trimmed using cutadapt v1.9.1 (Martin, 2011).
Host reads were removed with Xenome v1.0.1 (Conway et al., 2012) and human sequences were aligned to hg38 using STAR v2.4.2a (Dobin et al., 2013).
Sequences identified as originating from the graft were then aligned to the hg38 reference genome using STAR, version 2.4.2a (Dobin et al., 2013).
Gene feature counting was performed with RSEM v1.2.21 (Li & Dewey, 2011).
Transcripts with expression counts of 0 across all samples were removed and then normalized using TMM (Robinson & Oshlack, 2010).
Transcripts with zero expression counts across all samples were removed. TMM normalized counts (Robinson & Oshlack, 2010) were log transformed using voom (Law et al., 2014) and differential expression was performed with limma (Smyth, 2004).
Moderated F-statistics were calculated and genes that were significantly differentially regulated (with a Benjamini-Hochberg adjusted p-value (BH) <0.05) between the treatment groups were identified.
Genome_build: hg38
Supplementary_files_format_and_content: Differential expression of vehicle, enzalutamide, DHT, and enobosarm-treated ZR-75-1 tumors.

source_name: ZR-75-1 xenograft DHT tumor

growth_protocol: Athymic nude mice were subcutaneously implanted with an E2 pellet and injected with 5x10^6 (20 µL) ZR-75-1 cells into the fourth inguinal mammary fat pad. Tumors were allowed to grow until reaching ~200 mm^3 size before beginning treatment.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit, according to the manufacturer's instructions. Libraries were generated using the TruSeq Stranded mRNA Library Prep Kit and sequenced on the Illumina HiSeq 2500 (v4.0) with 125 bp paired-end reads.

treatment_protocol: Mice were randomly assigned to treatment groups and treated for 5 days with either a vehicle, enzalutamide (Enza), DHT, or enobosarm (SARM). Enza (20 mg/kg/day) and SARM (10 mg/kg/day) was dissolved in 10% Tween 80 and delivered daily by oral gavage. DHT pellets were surgically implanted subcutaneously. After 5 days, tumors were excised and snap-frozen.

value: ZR-75-1 cell line xenograft tumor

value: DHT

tag: time point

value: Short-term (5 days treatment)

tag: replicate


title: ZR-75-1 xenograft DHT 2

description:
Xeno_DHT_Tum2_017
processed data file:
Xeno_genes.tpm.filtered.txt
Xeno_genes.fpkm.txt
Xeno_genes.fpkm.filtered.txt
Xeno_genes.counts.txt
Xeno_genes.counts.filtered.txt

tag: treatment


title: ZR-75-1 xenograft DHT 5

description:
Xeno_DHT_Tum5_026
processed data file:
Xeno_genes.tpm.filtered.txt
Xeno_genes.fpkm.txt
Xeno_genes.fpkm.filtered.txt
Xeno_genes.counts.txt
Xeno_genes.counts.filtered.txt

tag: tissue


title: Ech_SC_A_2 [S24_S63]

description:
processed data file: counts_eae.txt
S24_S63_R1_001


title: WT2


title: ZR-75-1 xenograft DHT 3

description:
Xeno_DHT_Tum3_018
processed data file:
Xeno_genes.tpm.filtered.txt
Xeno_genes.fpkm.txt
Xeno_genes.fpkm.filtered.txt
Xeno_genes.counts.txt
Xeno_genes.counts.filtered.txt


title: Ech_SC_A_1 [S20_S59]

description:
processed data file: counts_eae.txt
S20_S59_R1_001


title: ZR-75-1 xenograft DHT 1

description:
Xeno_DHT_Tum1_012
processed data file:
Xeno_genes.tpm.filtered.txt
Xeno_genes.fpkm.txt
Xeno_genes.fpkm.filtered.txt
Xeno_genes.counts.txt
Xeno_genes.counts.filtered.txt


title: ZR-75-1 xenograft SARM 4

description:
Xeno_Sarm_Tum4_022
processed data file:
Xeno_genes.tpm.filtered.txt
Xeno_genes.fpkm.txt
Xeno_genes.fpkm.filtered.txt
Xeno_genes.counts.txt
Xeno_genes.counts.filtered.txt

source_name: ZR-75-1 xenograft SARM tumor

value: Enobosarm


title: Ech_HB_AG_2 [H29_S94]

description:
processed data file: counts_eae.txt
H29_S94_R1_001

value: Hindbrain


title: HoxB8 transfected Replicate 2

description:
RNA-seq of Hoxb8 GFP+ cells Rep2
Hoxb8-pCIG plasmid
Neural tube in ovo electroporations were performed at HH11. Eggs were windowed, and the DNA solution (1 to 2µg/µl) was injected in neural tube lumen. Needle L-shape platinum electrodes were place on both sides of the embryo at trunk level (5 mm apart), with the cathode always at its right. Five 50 ms pulses of 25 volts were given bilateral at 50 ms intervals with an electroporator NEPA21 (Nepagene). Plasmids DNA concentrations were for the control mix: pCIG 2µg/µl and for the HoxB8 mix : Hoxb8-pCIG 1 µg/µl + pCIG 1µg/µl . Part of the neural tube expressing the GFP were dissected 18 hours after electroporation and dissociated (Trypsin-EDTA 0,25%). A highly enriched population of GFP-expressing cells was isolated by FACS with the use of a dead cell exclusion (DCE)/discrimination dye (DAPI) to eliminate dying cells.


title: Ech_HB_AG_3 [H31_24_S82]

description:
processed data file: counts_eae.txt
H31_24_S82_R1_001


title: AK002F: HeLa wt, 1 µM trimer 2-5A, 4.5 h

value: 1 µM trimer 2-5A, 4.5 h


title: GJ103F: WT Hap1, 10 µM 2-5A treated, 3 h

value: 10 µM 2-5A treated, 3 h


title: Ech_HB_A_6 [46_S42]

description:
processed data file: counts_eae.txt
46_S42_R1_001


title: Ech_HB_AG_1 [H28_S76]

description:
processed data file: counts_eae.txt
H28_S76_R1_001


title: Ech_HB_A_5 [31_S40]

description:
processed data file: counts_eae.txt
31_S40_R1_001


title: ZR-75-1 xenograft SARM 1

description:
Xeno_Sarm_Tum1_011
processed data file:
Xeno_genes.tpm.filtered.txt
Xeno_genes.fpkm.txt
Xeno_genes.fpkm.filtered.txt
Xeno_genes.counts.txt
Xeno_genes.counts.filtered.txt


title: ZR-75-1 xenograft Enza 3

description:
Xeno_Enz_Tum3_019
processed data file:
Xeno_genes.tpm.filtered.txt
Xeno_genes.fpkm.txt
Xeno_genes.fpkm.filtered.txt
Xeno_genes.counts.txt
Xeno_genes.counts.filtered.txt

source_name: ZR-75-1 xenograft Enza tumor

value: Enzalutamide


title: ZR-75-1 xenograft Enza 4

description:
Xeno_Enz_Tum4_021
processed data file:
Xeno_genes.tpm.filtered.txt
Xeno_genes.fpkm.txt
Xeno_genes.fpkm.filtered.txt
Xeno_genes.counts.txt
Xeno_genes.counts.filtered.txt


title: Ech_HB_A_4 [29_S53]

description:
processed data file: counts_eae.txt
29_S53_R1_001


title: ZR-75-1 xenograft Enza 1

description:
Xeno_Enz_Tum1_010
processed data file:
Xeno_genes.tpm.filtered.txt
Xeno_genes.fpkm.txt
Xeno_genes.fpkm.filtered.txt
Xeno_genes.counts.txt
Xeno_genes.counts.filtered.txt


title: ZR-75-1 xenograft Enza 2

description:
Xeno_Enz_Tum2_013
processed data file:
Xeno_genes.tpm.filtered.txt
Xeno_genes.fpkm.txt
Xeno_genes.fpkm.filtered.txt
Xeno_genes.counts.txt
Xeno_genes.counts.filtered.txt


title: Ech_HB_A_3 [27_S39]

description:
processed data file: counts_eae.txt
27_S39_R1_001


title: Ech_HB_A_1 [20_S25]

description:
processed data file: counts_eae.txt
20_S25_R1_001


title: ZR-75-1 xenograft Vehicle 4

description:
Xeno_Veh_Tum4_024
processed data file:
Xeno_genes.tpm.filtered.txt
Xeno_genes.fpkm.txt
Xeno_genes.fpkm.filtered.txt
Xeno_genes.counts.txt
Xeno_genes.counts.filtered.txt

source_name: ZR-75-1 xenograft Vehicle tumor

value: Vehicle


title: ZR-75-1 xenograft Vehicle 3

description:
Xeno_Veh_Tum3_023
processed data file:
Xeno_genes.tpm.filtered.txt
Xeno_genes.fpkm.txt
Xeno_genes.fpkm.filtered.txt
Xeno_genes.counts.txt
Xeno_genes.counts.filtered.txt


title: ZR-75-1 xenograft SARM 3

description:
Xeno_Sarm_Tum3_020
processed data file:
Xeno_genes.tpm.filtered.txt
Xeno_genes.fpkm.txt
Xeno_genes.fpkm.filtered.txt
Xeno_genes.counts.txt
Xeno_genes.counts.filtered.txt


title: E4_SC_A_5 [S42_S50]

description:
processed data file: counts_eae.txt
S42_S50_R1_001


title: ZR-75-1 xenograft Vehicle 2

description:
Xeno_Veh_Tum2_016
processed data file:
Xeno_genes.tpm.filtered.txt
Xeno_genes.fpkm.txt
Xeno_genes.fpkm.filtered.txt
Xeno_genes.counts.txt
Xeno_genes.counts.filtered.txt


title: ZR-75-1 xenograft Vehicle 1

description:
Xeno_Veh_Tum1_015
processed data file:
Xeno_genes.tpm.filtered.txt
Xeno_genes.fpkm.txt
Xeno_genes.fpkm.filtered.txt
Xeno_genes.counts.txt
Xeno_genes.counts.filtered.txt


title: E4_SC_A_4 [S30_S48]

description:
processed data file: counts_eae.txt
S30_S48_R1_001


title: ZR-75-1 xenograft SARM 2

description:
Xeno_Sarm_Tum2_014
processed data file:
Xeno_genes.tpm.filtered.txt
Xeno_genes.fpkm.txt
Xeno_genes.fpkm.filtered.txt
Xeno_genes.counts.txt
Xeno_genes.counts.filtered.txt


title: E4_SC_A_3 [S23_S69]

description:
processed data file: counts_eae.txt
S23_S69_R1_001


title: Ech_HB_AG_4 [H46_34_S93]

description:
processed data file: counts_eae.txt
H46_34_S93_R1_001


title: E4_SC_A_2 [S19_S26]

description:
processed data file: counts_eae.txt
S19_S26_R1_001


title: TH-107 ED

description:
TH-107 ED
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx

data_processing:
Basecalls performed using Illumina software
hg19 alignment was performed using CLC Genomics Workbench 11 (QIAGEN) using the following mapping parameters: Mismatch cost 2; Insertion cost 3; Deletion cost 3; Length fraction 0.8; Similarity fraction 0.8.
Treatment comparisons were performed on samples individually due to tissue heterogeneity. Genes common between both Kahl's Z-test (FDR <0.01; Kal et al., 1999) and Baggerley's test (FDR <0.01; Baggerly et al., 2003) were determined to be significantly differentially regulated.
Expression was measured based on the total counts of mapped short reads and normalised based on RPKM (CLC Genomics Workbench).
Genome_build: hg19
Supplementary_files_format_and_content: Processed data presented as RPKM

source_name: Normal breast_E2+DHT

growth_protocol: Patient tissue specimens were cut into small pieces, randomly allocated to a gelatin sponge (3-4 per sponge), pre-soaked in culture media, and incubated at 37°C with 5% CO2 for ~ 36 hours as 'patient-derived explants' (PDEs).

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit, according to the manufacturer's instructions.
Libraries were generated using the TruSeq Stranded Mrna Library Prep Kit
RNA-Seq; Illumina HiSeq 2500 40bp single-end reads

treatment_protocol: PDEs were treated for 24h with either 10nM E2 or 10nM E2 + 10nM DHT.

tag: patient id

tag: tissue type

value: Normal breast


title: TH-108 ED

description:
TH-108 ED
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: TH-106 ED

description:
TH-106 ED
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: E4_SC_A_1 [S15_S31]

description:
processed data file: counts_eae.txt
S15_S31_R1_001


title: TH-105 ED

description:
TH-105 ED
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: TH-103 ED

description:
TH-103 ED
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: TH-104 ED

description:
TH-104 ED
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: E4_HB_AG_4 [H39_S61]

description:
processed data file: counts_eae.txt
H39_S61_R1_001


title: TH-102 ED

description:
TH-102 ED
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: Ech_HB_A_2 [24_S34]

description:
processed data file: counts_eae.txt
24_S34_R1_001


title: E4_HB_AG_6 [H45_S65]

description:
processed data file: counts_eae.txt
H45_S65_R1_001


title: E4_HB_AG_5 [H42_S71]

description:
processed data file: counts_eae.txt
H42_S71_R1_001


title: E4_HB_AG_3 [H30_S90]

description:
processed data file: counts_eae.txt
H30_S90_R1_001


title: E4_HB_AG_2 [H21_S81]

description:
processed data file: counts_eae.txt
H21_S81_R1_001


title: TH-101 ED

description:
TH-101 ED
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: E4_HB_AG_1 [H19_23_S73]

description:
processed data file: counts_eae.txt
H19_23_S73_R1_001


title: TH-89 ED

description:
TH-89 ED
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: TH-88 ED

description:
TH-88 ED
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: E4_SC_A_6 [S53_S37]

description:
processed data file: counts_eae.txt
S53_S37_R1_001


title: E4_HB_A_6 [53_S44]

description:
processed data file: counts_eae.txt
53_S44_R1_001


title: E4_HB_A_5 [45_S46]

description:
processed data file: counts_eae.txt
45_S46_R1_001


title: TH-85 ED

description:
TH-85 ED
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: TH-86 ED

description:
TH-86 ED
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: TH-83 ED

description:
TH-83 ED
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: E4_HB_A_4 [39_S33]

description:
processed data file: counts_eae.txt
39_S33_R1_001


title: TH-87 ED

description:
TH-87 ED
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: E4_HB_A_3 [30_S45]

description:
processed data file: counts_eae.txt
30_S45_R1_001


title: E4_HB_A_1 [15_S28]

description:
processed data file: counts_eae.txt
15_S28_R1_001


title: TH-82 ED

description:
TH-82 ED
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: E1_SC_A_5 [S52_S64]

description:
processed data file: counts_eae.txt
S52_S64_R1_001


title: TH-81 ED

description:
TH-81 ED
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: TH-108 E

description:
TH-108 E
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx

source_name: Normal breast_E2


title: TH-107 E

description:
TH-107 E
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: TH-105 E

description:
TH-105 E
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: E1_SC_A_2 [S35_33_S79]

description:
processed data file: counts_eae.txt
S35_33_S79_R1_001


title: E1_SC_A_4 [S49_S74]

description:
processed data file: counts_eae.txt
S49_S74_R1_001


title: TH-106 E

description:
TH-106 E
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: E1_SC_A_1 [S14_S57]

description:
processed data file: counts_eae.txt
S14_S57_R1_001


title: E1_HB_AG_6 [H52_14_S80]

description:
processed data file: counts_eae.txt
H52_14_S80_R1_001


title: E1_HB_AG_4 [H49_S85]

description:
processed data file: counts_eae.txt
H49_S85_R1_001


title: E1_HB_AG_5 [H50_S78]

description:
processed data file: counts_eae.txt
H50_S78_R1_001


title: E1_HB_AG_3 [H44_S87]

description:
processed data file: counts_eae.txt
H44_S87_R1_001


title: TH-102 E

description:
TH-102 E
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: TH-103 E

description:
TH-103 E
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: TH-101 E

description:
TH-101 E
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: TH-84 ED

description:
TH-84 ED
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: E4_HB_A_2 [21_S36]

description:
processed data file: counts_eae.txt
21_S36_R1_001


title: TH-89 E

description:
TH-89 E
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: E1_HB_AG_2 [H40_35_S86]

description:
processed data file: counts_eae.txt
H40_35_S86_R1_001


title: E1_HB_AG_1 [H16_17_S91]

description:
processed data file: counts_eae.txt
H16_17_S91_R1_001


title: E1_HB_A_6 [52_S49]

description:
processed data file: counts_eae.txt
52_S49_R1_001


title: TH-87 E

description:
TH-87 E
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: E1_HB_A_5 [50_S56]

description:
processed data file: counts_eae.txt
50_S56_R1_001


title: TH-88 E

description:
TH-88 E
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: TH-85 E

description:
TH-85 E
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: E1_HB_A_4 [49_S29]

description:
processed data file: counts_eae.txt
49_S29_R1_001


title: E1_SC_A_3 [S44_S27]

description:
processed data file: counts_eae.txt
S44_S27_R1_001


title: E1_HB_A_3 [40_S55]

description:
processed data file: counts_eae.txt
40_S55_R1_001


title: TH-84 E

description:
TH-84 E
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: TH-104 E

description:
TH-104 E
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: TH-82 E

description:
TH-82 E
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: TH-83 E

description:
TH-83 E
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: E1_HB_A_1 [33_S38]

description:
processed data file: counts_eae.txt
33_S38_R1_001


title: C_SC_A_5 [S8_S67]

description:
processed data file: counts_eae.txt
S8_S67_R1_001

value: Control


title: C_SC_A_4 [S5_S60]

description:
processed data file: counts_eae.txt
S5_S60_R1_001


title: C_SC_A_3 [S4_S66]

description:
processed data file: counts_eae.txt
S4_S66_R1_001


title: C_SC_A_2 [S3_S83]

description:
processed data file: counts_eae.txt
S3_S83_R1_001


title: C_SC_A_1 [S13_S75]

description:
processed data file: counts_eae.txt
S13_S75_R1_001


title: TH8-ED

description:
TH8-ED
processed data file:
Invasive_breast_cancer_E_v_ED_normalised_expression_RPKM.xlsx

source_name: ER+ invasive breast cancer_E2+DHT

value: ER+ invasive breast cancer


title: TH6-ED

description:
TH6-ED
processed data file:
Invasive_breast_cancer_E_v_ED_normalised_expression_RPKM.xlsx


title: TH7-ED

description:
TH7-ED
processed data file:
Invasive_breast_cancer_E_v_ED_normalised_expression_RPKM.xlsx


title: C_HB_AG_5 [H9_S88]

description:
processed data file: counts_eae.txt
H9_S88_R1_001


title: TH4-ED

description:
TH4-ED
processed data file:
Invasive_breast_cancer_E_v_ED_normalised_expression_RPKM.xlsx


title: C_HB_AG_4 [H8_S84]

description:
processed data file: counts_eae.txt
H8_S84_R1_001


title: TH5-ED

description:
TH5-ED
processed data file:
Invasive_breast_cancer_E_v_ED_normalised_expression_RPKM.xlsx


title: TH1-ED

description:
TH1-ED
processed data file:
Invasive_breast_cancer_E_v_ED_normalised_expression_RPKM.xlsx


title: TH-86 E

description:
TH-86 E
processed data file:
Normal_breast_E_v_ED_combined_expression_RPKM.xlsx


title: TH3-ED

description:
TH3-ED
processed data file:
Invasive_breast_cancer_E_v_ED_normalised_expression_RPKM.xlsx


title: C_HB_AG_2 [H4_S95]

description:
processed data file: counts_eae.txt
H4_S95_R1_001


title: C_HB_AG_3 [H5_1_S77]

description:
processed data file: counts_eae.txt
H5_1_S77_R1_001


title: C_HB_A_5 [13_S41]

description:
processed data file: counts_eae.txt
13_S41_R1_001


title: C_HB_AG_1 [H13_10_S68]

description:
processed data file: counts_eae.txt
H13_10_S68_R1_001


title: E1_HB_A_2 [35_S30]

description:
processed data file: counts_eae.txt
35_S30_R1_001


title: TH8-E

description:
TH8-E
processed data file:
Invasive_breast_cancer_E_v_ED_normalised_expression_RPKM.xlsx

source_name: ER+ invasive breast cancer_E2


title: TH7-E

description:
TH7-E
processed data file:
Invasive_breast_cancer_E_v_ED_normalised_expression_RPKM.xlsx


title: TH-81 E

description:
TH-81 E
processed data file:
Invasive_breast_cancer_E_v_ED_normalised_expression_RPKM.xlsx


title: TH2-ED

description:
TH2-ED
processed data file:
Invasive_breast_cancer_E_v_ED_normalised_expression_RPKM.xlsx


title: C_HB_A_3 [9_S43]

description:
processed data file: counts_eae.txt
9_S43_R1_001


title: TH4-E

description:
TH4-E
processed data file:
Invasive_breast_cancer_E_v_ED_normalised_expression_RPKM.xlsx


title: C_HB_A_2 [5_S35]

description:
processed data file: counts_eae.txt
5_S35_R1_001


title: TH6-E

description:
TH6-E
processed data file:
Invasive_breast_cancer_E_v_ED_normalised_expression_RPKM.xlsx


title: TH5-E

description:
TH5-E
processed data file:
Invasive_breast_cancer_E_v_ED_normalised_expression_RPKM.xlsx


title: TH3-E

description:
TH3-E
processed data file:
Invasive_breast_cancer_E_v_ED_normalised_expression_RPKM.xlsx


title: SC_ACSA_pos_glast_neg_2 [B5]

description:
processed data file: counts_subtypes.txt
160114_SN163_0692_BHHHHWBCXX_L1_GATCAC

value: FVB/N


title: SC_ACSA_pos_glast_neg_1 [E1]

description:
processed data file: counts_subtypes.txt
160114_SN163_0692_BHHHHWBCXX_L1_AGGCAT


title: HB_ACSA_pos_glast_pos_3 [H4]

description:
processed data file: counts_subtypes.txt
160114_SN163_0692_BHHHHWBCXX_L1_GGAGGT


title: TH1-E

description:
TH1-E
processed data file:
Invasive_breast_cancer_E_v_ED_normalised_expression_RPKM.xlsx


title: HB_ACSA_pos_glast_pos_1 [F5]

description:
processed data file: counts_subtypes.txt
160114_SN163_0692_BHHHHWBCXX_L1_CATCTA


title: HB_ACSA_pos_glast_neg_3 [B2]

description:
processed data file: counts_subtypes.txt
160114_SN163_0692_BHHHHWBCXX_L1_CGGTTA


title: HB_ACSA_pos_glast_neg_2 [C1]

description:
processed data file: counts_subtypes.txt
160114_SN163_0692_BHHHHWBCXX_L1_ACAACG


title: HB_ACSA_pos_glast_pos_2 [E4]

description:
processed data file: counts_subtypes.txt
160114_SN163_0692_BHHHHWBCXX_L1_GCAGCC


title: FB_ACSA_pos_glast_pos_3 [C2]

description:
processed data file: counts_subtypes.txt
160114_SN163_0692_BHHHHWBCXX_L1_GCGCTG

value: Forebrain


title: C_HB_A_4 [10_S32]

description:
processed data file: counts_eae.txt
10_S32_R1_001


title: FB_ACSA_pos_glast_pos_2 [E5]

description:
processed data file: counts_subtypes.txt
160114_SN163_0692_BHHHHWBCXX_L1_CGCCTG


title: C_HB_A_1 [1_S51]

description:
processed data file: counts_eae.txt
1_S51_R1_001


title: HB_ACSA_pos_glast_neg_1 [B3]

description:
processed data file: counts_subtypes.txt
160114_SN163_0692_BHHHHWBCXX_L1_AACGCC


title: FB_ACSA_pos_glast_pos_1 [F4]

description:
processed data file: counts_subtypes.txt
160114_SN163_0692_BHHHHWBCXX_L1_CGATCT


title: SC_ACSA_pos_glast_neg_3 [C4]

description:
processed data file: counts_subtypes.txt
160114_SN163_0692_BHHHHWBCXX_L1_GTTACC


title: TH2-E

description:
TH2-E
processed data file:
Invasive_breast_cancer_E_v_ED_normalised_expression_RPKM.xlsx


title: FB_ACSA_pos_glast_neg_3 [H2]

description:
processed data file: counts_subtypes.txt
160114_SN163_0692_BHHHHWBCXX_L1_CAACAG


title: FB_ACSA_pos_glast_neg_2 [F2]

description:
processed data file: counts_subtypes.txt
160114_SN163_0692_BHHHHWBCXX_L1_AGAATC


title: FB_ACSA_pos_glast_neg_1 [E2]

description:
processed data file: counts_subtypes.txt
160114_SN163_0692_BHHHHWBCXX_L1_ACCTAC


title: Cultured_astro_3 [H3]

description:
processed data file: counts_subtypes.txt
160114_SN163_0692_BHHHHWBCXX_L1_GAAGTG

value: Primary neonatal astrocytes


title: Cultured_astro_2 [G2]

description:
processed data file: counts_subtypes.txt
160114_SN163_0692_BHHHHWBCXX_L1_CAATGC


title: Cultured_astro_1 [F1]

description:
processed data file: counts_subtypes.txt
160114_SN163_0692_BHHHHWBCXX_L1_AACCGA


title: H69, replicate 3

city: Hospitalet d'Llobregat

first: manuel

last: torres diz

state: Barcelona

address: Gran Via de l’Hospitalet, 199

department: PEBC

country: Spain

institute: IDIBELL

description: Gene expression analysis on parental cell line

hyb_protocol: Hibridaded on the Agilent-072363 SurePrint G3 Human GE v3 8x60K Microarray 039494

scan_protocol: G2505B DNA microarray scanner

data_processing: Data was procesed with limma R Bioconductor

source_name: cell line

label_protocol: 100 ng of total RNA were labeled with Cy3

growth_protocol: All cell lines were growth acording to ATTC recommendations

extract_protocol: RNA was extracted using Maxwell® RSC simplyRNA Tissue Kit (Ref. AS1340) and following

treatment_protocol: None of the cells were treated

tag: cell line


title: HCC33, replicate 2


title: H1963, replicate 2


title: H1963, replicate 3


title: Fs-2

city: Nagoya

first: Kousuke

last: Okimura

address: Furocho

institute: Nagoya University

description: Gene expression under LW condition at 22 hrs later from midnight

data_processing:
RNA-seq reads were aligned to mouse reference genome and annotation (Mus musculus (GRCm38.p6), index and annotation packages) using HISAT2 (version 2.0.4).
Gene expression levels were calculated by RNA-seq by Expectation-Maximization (RSEM)
Genome_build: Mus musculus (GRCm38.p6)
Supplementary_files_format_and_content: Excel file include Gene expression for each sample.

source_name: LW eyes collected at 22 hrs later from midnight

growth_protocol: Mouse (Mus musculus) were obtained from a local dealer and kept under SC or LW conditions.

extract_protocol:
Total RNA of eyes were isolated with elimination of DNA contamination using DNase.
According to TruSeq Stranded mRNA Sample Preparation Guide (Illumina), the cDNA libraries were prepared using TruSeq stranded mRNA LT sample prep kit (Illumina).

treatment_protocol: Mouse were kept under SC or LW conditions for 4 weeks. After that, mouse eyes were collected every 4 hours from middnight.

value: CBA/N

value: eye

tag: gender

value: male