title: Dengue 1 ribosome profiling footprint REP2

status: Public on Feb 28 2019

city: Singapore

first: Roland

middle: G

last: Huber

address: 30 Biopolis Street

department: Bioinformatics Institute (BII)

country: Singapore

institute: Agency for Science, Technology and Research (A*STAR)

description:
ribosome profiling- ribosome footprints
DEN1_RIBO_PROFILE_REP2.txt.gz

data_processing:
Library strategy: Ribo-Seq
NAI-Map files are processed using the ShapeMapper v1.2 script by the Kevin M. Weeks lab (www.chem.unc.edu/rna/software.html) with default settings to generate reactivity profiles (ShapeMapper called local bowtie2 2.3.3 for alignment)
SPLASH data is aligned using bowtie2 2.3.3 against the reference genome; all reads that align to two distinct sites along the reference genome are filtered and included as a bam and csv file;
Ribosome footprinting reads (footprints and mRNA sets) were aligned to the reference genome using bowtie2 (2.3.3) with the options "--local -D 20 -R 3 - N 1 -L 15 -i S,1,0.50 --score-min G,20,8 --ma 2 --mp 6,2 --rdg 5,1 --rfg 5,1"; relative intensities were calculated by dividng read number of the footprint set by the read number of the mRNA set at each nucleotide position along the reference genome
Genome_build: Dengue 1 EU081230.1; Dengue 2 EU081177.1; Dengue 3 EU081190.1; Dengue 4 GQ398256.1; Zika MR766 AY632535.1; Zika BeH815744 KU365780.1; Zika H/PF/2013 KJ776791.2; Zika ZIKV-SG-032 KY241702.1
Supplementary_files_format_and_content: processed NAI-Map files are tar.gz archives and contain 2 pdf files showing shape reactivity and quality scores and 3 text files containing the raw shape reactivity numbers; Processed SPLASH files are tar.gz archives and contain paired read alignments and location summaries as bam and csv respectively; Processed RIBO_PROFILE files are gzipped text files that contain a list of FP/mRNA calculated for each position;

source_name: Dengue 1 infected Huh7 cells

growth_protocol: Dengue 1-4 are amplified from african green monkey kidney (Vero) cells.  Zika strains are amplified by mosquito C6/36 cells. Huh7 cells were grown in DMEM, supplemented with 10% FBS and 1% Pen-Strep.

extract_protocol:
NAI or biotinylated treated RNA was extracted from virus particles using Trizol extraction.  RNA from Dengue1 infected Huh7 cells were extracted using Trizol.
Local secondary structure mapping was performed using SHAPE-map strategy, and long-range interactome mapping was performed using SPLASH.  Ribsome profiling was performed using the Artseq ribosome profiling kit (Epicenter).

treatment_protocol: Fresh virus particles are treated with NAI for secondary structure mapping, and with biotinylated psoralen for interactome mapping, at 37C for 10 min. Virions treated with biotinylated psoralen were then crosslinked using UV.

tag: assembly

value: Huh7 cells

tag: agent

value: Dengue 1


title: Dev2D

status: Public on Mar 01 2019

type: SRA

city: Botucatu

first: Danillo

last: Pinhal

state: SP

address: R. Prof. Dr. Antonio C. W. Zanin s/n

department: Genetics

country: Brazil

institute: Sao Paulo State University

description: microRNA sequencing

library_source: transcriptomic

data_processing:
Base-calling was performed using Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70).
Adaptor sequences were trimmed. FASTQ files were converted into FASTA with a custom Perl script. Reads were counted, collapsed to unique reads and filtered using the UEA small RNA Workbench. Reads were exactly matched to tilapia genome (Orenil1.1v) with PatMaN
Precursors from miRBase were searched against the tilapia genome using BLAST. Novel tilapia miRNA loci were predicted with both miRCat 79 and miRDeep2
An in-house Python pipeline selected matched reads from each precursor locus and estimated the read counts by weight count (raw read count divided by number of precursor locus aligned).
Reads were normalized by DESeq method for miRNA 5p and 3p using Bioconductor package in R
Genome_build: Orenil 1.1
Supplementary_files_format_and_content: counts

molecule: total RNA

organism: Oreochromis niloticus

extract_protocol:
Tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Illumina TruseqTM Small RNA Preparation kit was used for the construction of small RNA sequencing libraries, following manufacture's protocol.

tag: developmental period

value: Embryo

tag: Stage

value: Gastrula segmentation

tag: strain

value: Chitralada


title: Dev10D

description: microRNA sequencing

value: Larva

value: Late larva


title: Dev3D

description: microRNA sequencing


title: FTH3_rna

city: Athens

first: Kristen

middle: Jean

last: Navara

state: GA

address: 203 Poultry Science Building

department: Poultry Science

country: USA

institute: The University of Georgia

description:
Processed data file: all_genes_fpkm.tsv.gz
Processed data file: gene_exp.diff.gz

data_processing:
RNA-seq data: Reads were trimmed using Cutadapt v1.9.1, and PRINSEQ v0.20.4, reads were then mapped to the T. guttata genome using Tophat2 v2.1.1. Gene expression was quantified and differentially expressed genes called using Cuffquant, followed by Cuffdiff2 from Cufflinks v2.2.1.
MethylC-seq data: Read trimming, alignment, and methylation calling were performed using the methylpy pipeline from Schultz et al. Human body epigenome maps reveal noncanonical DNA methylation variation Nature 523, 212–216 (2015).
Genome_build: Taeniopygia guttata v3.2.4
Supplementary_files_format_and_content: RNA-seq data: all_genes_fpkm.tsv.gz, gene_exp.diff.gz.
Supplementary_files_format_and_content: MethylC-seq data (marked as “allc_total.tsv”): column 1 = chr = chromosome; column 2 = pos = coordinate for the cytosine position on the chromosome; column 3 = strand = + or - strand; column 4 = mc_class = context of the cytosine and the two following bases from the same strand; column 5 = mc_count = number of reads supporting a methylated cytosine; column 6 = total = total number of reads at that position; column 7 = methylated = cytosine is considered methylated if there is a 1 or unmethylated if there is a 0.

organism: Taeniopygia guttata

source_name: hypothalamus

extract_protocol:
Brains were flash frozen in liquid nitrogen, embedded in optimal cutting temperature compound, and 50um sections were cut with a cryostat until 1mm biopsy punch was used to make vertical punches to obtain the hypothalamus and nucleus taenia of the amygdala. Tissue was homogenized with a Mini-BeadBeater-16 (BioSpec Products) using 0.2g of 1mm beads for 10s in TRIzol/TRI Reagent to extract total RNA with a Direct-zol RNA MicroPrep kit (Zymo Research) with a DNase treatment step to remove DNA contamination or in Genomic Lysis Buffer to extract genomic DNA with a Quick-gDNA MicroPrep kit (Zymo Research).
Stranded mRNA-Seq libraries were made using KAPA Stranded mRNA-Seq Kit (Kapa Biosystems).
Methyl-Seq libraries were prepared according to Urich et al. (2015) Nature protocols 10:475-483.

treatment_protocol: Testosterone: 500pg of testosterone dissolved in 5ul peanut oil injected into egg the morning it was laid; Control: 5ul of peanut oil injected into egg the morning it was laid.

tag: tissue

value: brain

tag: brain region

value: hypothalamus

tag: developmental stage

value: adult

tag: Sex

value: female

tag: treatment

value: testosterone


title: Dengue 1 ribosome profiling mRNA REP2

description:
ribosome profiling- mRNA
DEN1_RIBO_PROFILE_REP2.txt.gz

organism: Homo sapiens

tag: cell type


title: FTH1_rna


title: Dengue 4 SPLASH REP2

description:
long range interaction mapping
DEN4_REP3-SPALSH.tar.gz

data_processing:
Library strategy: SHAPE-map
NAI-Map files are processed using the ShapeMapper v1.2 script by the Kevin M. Weeks lab (www.chem.unc.edu/rna/software.html) with default settings to generate reactivity profiles (ShapeMapper called local bowtie2 2.3.3 for alignment)
SPLASH data is aligned using bowtie2 2.3.3 against the reference genome; all reads that align to two distinct sites along the reference genome are filtered and included as a bam and csv file;
Ribosome footprinting reads (footprints and mRNA sets) were aligned to the reference genome using bowtie2 (2.3.3) with the options "--local -D 20 -R 3 - N 1 -L 15 -i S,1,0.50 --score-min G,20,8 --ma 2 --mp 6,2 --rdg 5,1 --rfg 5,1"; relative intensities were calculated by dividng read number of the footprint set by the read number of the mRNA set at each nucleotide position along the reference genome
Genome_build: Dengue 1 EU081230.1; Dengue 2 EU081177.1; Dengue 3 EU081190.1; Dengue 4 GQ398256.1; Zika MR766 AY632535.1; Zika BeH815744 KU365780.1; Zika H/PF/2013 KJ776791.2; Zika ZIKV-SG-032 KY241702.1
Supplementary_files_format_and_content: processed NAI-Map files are tar.gz archives and contain 2 pdf files showing shape reactivity and quality scores and 3 text files containing the raw shape reactivity numbers; Processed SPLASH files are tar.gz archives and contain paired read alignments and location summaries as bam and csv respectively; Processed RIBO_PROFILE files are gzipped text files that contain a list of FP/mRNA calculated for each position;

organism: dengue virus type 4

source_name: Virus particle

value: Virus particle


title: MTH2_rna

value: male


title: MTH3_rna


title: Dengue 4 SPLASH REP1

description:
long range interaction mapping
DEN4_REP2-SPALSH.tar.gz


title: Dengue 1 ribosome profiling footprint REP1

description:
ribosome profiling- ribosome footprints
DEN1_RIBO_PROFILE_REP1.txt.gz


title: Dengue 4 IN VITRO NAI-Map - DENATURED+NAI

description:
local secondary structure mapping
DEN4_INVITRO-NAI-Map.tar.gz


title: FIG2

description: microRNA sequencing

source_name: Liver

value: Adult


title: Dengue 4 IN VITRO NAI-Map - DMSO


title: Ep1

description: microRNA sequencing

source_name: Eye


title: Dengue 1 ribosome profiling mRNA REP1

description:
ribosome profiling- mRNA
DEN1_RIBO_PROFILE_REP1.txt.gz


title: Dengue 4 IN VITRO NAI-Map - NAI


title: Zika Singapore ZIKV-SG-032 SPLASH REP2

description:
long range interaction mapping
ZSIN_REP2-SPLASH.tar.gz

data_processing:
Library strategy: SPLASH
NAI-Map files are processed using the ShapeMapper v1.2 script by the Kevin M. Weeks lab (www.chem.unc.edu/rna/software.html) with default settings to generate reactivity profiles (ShapeMapper called local bowtie2 2.3.3 for alignment)
SPLASH data is aligned using bowtie2 2.3.3 against the reference genome; all reads that align to two distinct sites along the reference genome are filtered and included as a bam and csv file;
Ribosome footprinting reads (footprints and mRNA sets) were aligned to the reference genome using bowtie2 (2.3.3) with the options "--local -D 20 -R 3 - N 1 -L 15 -i S,1,0.50 --score-min G,20,8 --ma 2 --mp 6,2 --rdg 5,1 --rfg 5,1"; relative intensities were calculated by dividng read number of the footprint set by the read number of the mRNA set at each nucleotide position along the reference genome
Genome_build: Dengue 1 EU081230.1; Dengue 2 EU081177.1; Dengue 3 EU081190.1; Dengue 4 GQ398256.1; Zika MR766 AY632535.1; Zika BeH815744 KU365780.1; Zika H/PF/2013 KJ776791.2; Zika ZIKV-SG-032 KY241702.1
Supplementary_files_format_and_content: processed NAI-Map files are tar.gz archives and contain 2 pdf files showing shape reactivity and quality scores and 3 text files containing the raw shape reactivity numbers; Processed SPLASH files are tar.gz archives and contain paired read alignments and location summaries as bam and csv respectively; Processed RIBO_PROFILE files are gzipped text files that contain a list of FP/mRNA calculated for each position;

organism: Zika virus


title: Dengue 4 NAI-Map REP2 - DMSO

description:
local secondary structure mapping
DEN4-NAI-Map.tar.gz


title: Dengue 4 NAI-Map REP1 - DENATURED+NAI


title: Dengue 4 NAI-Map REP2 - DENATURED+NAI


title: Zika Singapore ZIKV-SG-032 SPLASH REP3

description:
long range interaction mapping
ZSIN_REP3-SPLASH.tar.gz


title: Dengue 4 NAI-Map REP1 - DMSO


title: Zika French Polynesia SPLASH REP2

description:
long range interaction mapping
ZILM_REP2-SPLASH.tar.gz


title: Dengue 4 NAI-Map REP1 - NAI


title: Zika French Polynesia SPLASH REP3

description:
long range interaction mapping
ZILM_REP3-SPLASH.tar.gz


title: Zika Singapore ZIKV-SG-032 SPLASH REP1

description:
long range interaction mapping
ZSIN_REP1-SPLASH.tar.gz


title: Zika French Polynesia SPLASH REP1

description:
long range interaction mapping
ZILM_REP1-SPLASH.tar.gz


title: Dengue 2 SPLASH REP2

description:
long range interaction mapping
DEN2_REP3-SPALSH.tar.gz

organism: dengue virus type 2


title: Dengue 2 SPLASH REP1

description:
long range interaction mapping
DEN2_REP2-SPALSH.tar.gz


title: Dengue 4 NAI-Map REP2 - NAI


title: Zika Brazil BeH815744 SPLASH REP1

description:
long range interaction mapping
ZBRA_REP1-SPLASH.tar.gz


title: Dengue 2 NAI-Map REP2 - DENATURED+NAI

description:
local secondary structure mapping
DEN2-NAI-Map.tar.gz


title: Dengue 2 NAI-Map REP2 - DMSO


title: Dengue 2 NAI-Map REP1 - DENATURED+NAI


title: Zika African MR766 SPLASH REP1

description:
long range interaction mapping
ZAFR_REP1-SPLASH.tar.gz


title: Dengue 2 NAI-Map REP2 - NAI


title: Zika French Polynesia IN VITRO NAI-Map - DENAT+NAI

description:
local secondary structure mapping
ZILM_INVITRO-NAI-Map.tar.gz


title: Zika African MR766 SPLASH REP2

description:
long range interaction mapping
ZAFR_REP2-SPLASH.tar.gz


title: Dengue 2 NAI-Map REP1 - DMSO


title: Zika French Polynesia IN VITRO NAI-Map - NAI


title: Zika French Polynesia IN VITRO NAI-Map - DMSO


title: Zika Singapore ZIKV-SG-032 NAI-Map REP3 - DENAT+NAI

description:
local secondary structure mapping
ZSIN-NAI-Map.tar.gz


title: Zika Singapore ZIKV-SG-032 NAI-Map REP3 - DMSO


title: Dengue 2 SPLASH REP3

description:
long range interaction mapping
DEN2_REP4-SPALSH.tar.gz


title: Zika Singapore ZIKV-SG-032 NAI-Map REP1 - DMSO


title: Zika Singapore ZIKV-SG-032 NAI-Map REP2 - DENAT+NAI


title: Zika Brazil BeH815744 SPLASH REP2

description:
long range interaction mapping
ZBRA_REP2-SPLASH.tar.gz


title: Zika Singapore ZIKV-SG-032 NAI-Map REP3 - NAI


title: Zika French Polynesia NAI-Map REP1 - DMSO

description:
local secondary structure mapping
ZILM-NAI-Map.tar.gz


title: Zika French Polynesia NAI-Map REP2 - DENAT+NAI


title: Zika Singapore ZIKV-SG-032 NAI-Map REP2 - DMSO


title: Zika French Polynesia NAI-Map REP3 - NAI


title: Zika Singapore ZIKV-SG-032 NAI-Map REP1 - DENAT+NAI


title: Zika French Polynesia NAI-Map REP1 - DENAT+NAI


title: Zika Singapore ZIKV-SG-032 NAI-Map REP2 - NAI


title: Zika French Polynesia NAI-Map REP3 - DENAT+NAI


title: Zika French Polynesia NAI-Map REP1 - NAI


title: Zika French Polynesia NAI-Map REP2 - DMSO


title: Zika Brazil BeH815744 NAI-Map REP3 - DENAT+NAI

description:
local secondary structure mapping
ZBRA-NAI-Map.tar.gz


title: Zika French Polynesia NAI-Map REP2 - NAI


title: Dengue 2 NAI-Map REP1 - NAI


title: Zika Brazil BeH815744 NAI-Map REP3 - NAI


title: Zika Brazil BeH815744 NAI-Map REP3 - DMSO


title: Zika Brazil BeH815744 NAI-Map REP2 - NAI


title: Zika Brazil BeH815744 NAI-Map REP2 - DMSO


title: Zika Brazil BeH815744 NAI-Map REP2 - DENAT+NAI


title: Zika Brazil BeH815744 NAI-Map REP1 - DMSO


title: Zika African MR766 NAI-Map REP3 - DENAT+NAI

description:
local secondary structure mapping
ZAFR-NAI-Map.tar.gz


title: Zika Brazil BeH815744 NAI-Map REP1 - NAI


title: Zika African MR766 NAI-Map REP3 - DMSO


title: Zika Singapore ZIKV-SG-032 NAI-Map REP1 - NAI


title: Zika African MR766 NAI-Map REP3 - NAI


title: Zika French Polynesia NAI-Map REP3 - DMSO


title: Zika African MR766 NAI-Map REP2 - NAI


title: Zika African MR766 NAI-Map REP1 - DENAT+NAI


title: Dengue 1 NAI-Map REP1 - NAI

description:
local secondary structure mapping
DEN1-NAI-Map.tar.gz

organism: dengue virus type 1


title: Dengue 1 NAI-Map REP2 - DENATURED+NAI


title: Dengue 1 NAI-Map REP1 - DMSO


title: Dengue 1 NAI-Map REP2 - DMSO


title: Dengue 1 SPLASH REP1

description:
long range interaction mapping
DEN1_REP2-SPALSH.tar.gz


title: Zika African MR766 NAI-Map REP1 - DMSO


title: Zika African MR766 NAI-Map REP2 - DMSO


title: Zika African MR766 NAI-Map REP1 - NAI


title: Dengue 1 NAI-Map REP2 - NAI


title: Dengue 3 NAI-Map REP2 - NAI

description:
local secondary structure mapping
DEN3-NAI-Map.tar.gz

organism: dengue virus type 3


title: Dengue 1 NAI-Map REP1 - DENATURED+NAI


title: Dengue 3 SPLASH REP2

description:
long range interaction mapping
DEN3_REP3-SPALSH.tar.gz


title: Dengue 3 NAI-Map REP1 - DENATURED+NAI


title: Dengue 3 NAI-Map REP2 - DMSO


title: Zika Brazil BeH815744 NAI-Map REP1 - DENAT+NAI


title: Dengue 3 SPLASH REP1

description:
long range interaction mapping
DEN3_REP2-SPALSH.tar.gz


title: Dengue 3 NAI-Map REP1 - DMSO


title: Dengue 3 NAI-Map REP1 - NAI


title: N606

status: Public on Feb 27 2019

city: Los Angeles

first: Ayako

last: Shigeta

state: CALIFORNIA

address: 675 C.E. Young Dr

institute: UCLA

data_processing:
The workflow consists of first-strand synthesis, template switching, adaptor ligation, cleavage of ribosomal cDNA and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Sequencing was performed on an Illumina Nextseq500 a single read 75 run. Data quality check was conducted on Illumina SAV. Demultiplexing was performed with the Illumina Bcl2fastq2 v 2.17 program.
Reads were aligned to the UCSC mm10 reference genome map using TopHat.
DEseq2 on R software version3.2 (R Foundation for statistical computing) was used to identify differentially expressed genes of EcTMs compared to non-EcTMs.
Genome_build: mm10
Supplementary_files_format_and_content: Text file with read counts and normalized read count (CPM) values of all samples

organism: Mus musculus

source_name: non Endocardially-derived Cardiac tissue macrophage

extract_protocol:
Total RNA of sorted EcTMs and non-EcTMs by FACS were extracted using the QIAGEN RNeasy plus micro kit.
Libraries for RNA-Seq were prepared with Clonetech SMARTer Stranded Total RNA-Seq (Pico) Kit.

value: Heart

tag: age

value: Postnatal day 28

tag: genotype

value: Nfatc1Cre/+; Rosa26Tomato reporter/+


title: N592

value: non Endocardially-derived Cardiac tissue macrophage


title: N604


title: N591


title: E606

source_name: Endocardially-derived Cardiac tissue macrophage


title: E604

value: Endocardially-derived Cardiac tissue macrophage


title: Zika African MR766 NAI-Map REP2 - DENAT+NAI


title: E591


title: E592


title: Rec-1_GSI_SMC1a_HiChIP

city: Philadelphia

first: YEQIAO

last: ZHOU

state: PA

address: 421 Curie Boulevard

department: Pathology

institute: University of Pennsylvania

library_source: genomic

data_processing:
Library strategy: HiChIP
Raw reads for each HiChIP sample were processed with HiC-Pro (version v2.5.0) (Servant et al., 2015) to obtain putative interactions with default parameters except LIGATION_SITE = GATCGATC and GENOME_FRAGMENT generated for MboI restriction enzyme.
The valid pairs (allValidPairs file) from HiC-Pro were used to generate .hic file using Juicer tools (version 1.7.6) ‘pre’ command.
Valid pairs (VI), self-circle (SC) and dangling-end (DE) interactions in cis were used as input for significant interaction calling in ‘.bedpe’ format. Mango (version 1.2.0) step 4 identified putative significant interaction anchors by MACS peak calling (Zhang et al., 2008) with MACS_qvalue = 0.05 and MACS_shiftsize = 75. Mango step 5 identified significant interactions with default parameters except maxinteractingdist = 2000000 and MHT = found. Only significant interactions with PETs >= 4 were used in following analyses and visualization.
Genome_build: hg19
Supplementary_files_format_and_content: .hic formatted file for juicebox viewing of contact matrices; .bed.gz for WashU EpiGenome Browser viewing of significant interactions

molecule: genomic DNA

source_name: Rec-1 cell line

growth_protocol: Rec-1 (female) cells were grown in RPMI 1640 (Corning, cat# 10-040-CM) supplemented with 10% fetal bovine serum (Hyclone, cat# SH30070.03), 2 mM L-glutamine (Corning, cat# 25-005-CI), 100 U/mL and 100 μg/mL penicillin/streptomycin (Corning, cat# 30-002-CI), 100 mM nonessential amino acids (Gibco, cat# 11140-050), 1mM sodium pyruvate (Gibco, cat#11360-070) and 0.1mM of 2-mercaptoethanol (Sigma, cat# M6250).

extract_protocol:
HiChIP was performed as described (Mumbach et al., 2016) using antibody against Smc1 (Bethyl, cat# A300-055A). Briefly, 2 x 10^7 cells were crosslinked with 1% formaldehyde (Thermo Scientific, cat# 28908) for 10 min and subsequently quenched with 0.125M glycine (Invitrogen, cat# 15527-013). Chromatin was digested using MboI restriction enzyme (NEB, Cat#R0147), followed by biotin incorporation with Biotin-14-dATP (Invitrogen, 19524-016) in end-repair step, ligation, and sonication. Sheared chromatin was 4-fold diluted with ChIP dilution buffer (16.7mM Tris pH 7.5, 167mM NaCl, 1.2mM EDTA, 0.01% SDS, 1.1% Triton X-100) and cleared and then incubated with anti-Smc1 antibody at 4°C for overnight. Chromatin-antibody complexes were captured by Protein-A magnetic beads (Pierce, cat# 88846) and subsequently washed with Low Salt Wash Buffer, High Salt Wash Buffer, LiCl Wash Buffer and eluted.
DNA was purified with MinElute PCR Purification Kit (Qiagen, cat# 28004) and quantified using Qubit dsDNA HS Assay Kit (Invitrogen, cat# Q32851). 50-150ng was used for capture with Dynabeads MyOne Streptavidin C-1 (Invitrogen, cat# 65001) and an appropriate amount of Tn5 enzyme was added to captured DNA to generate sequencing library. Paired-end sequencing (38 bp+38 bp) was performed on a NextSeq 550.

treatment_protocol: Cells were treated with the GSI compound E (1 μM, Calbiochem cat# 565790) for 72 hours.

tag: cell line

value: Mantle cell lymphoma cell line

tag: chip antibody

tag: drug treatment

value: GSI-treated


title: Rec-1_untreated_SMC1a_HiChIP

growth_protocol: Rec-1 (male) cells were grown in RPMI 1640 (Corning, cat# 10-040-CM) supplemented with 10% fetal bovine serum (Hyclone, cat# SH30070.03), 2 mM L-glutamine (Corning, cat# 25-005-CI), 100 U/mL and 100 μg/mL penicillin/streptomycin (Corning, cat# 30-002-CI), 100 mM nonessential amino acids (Gibco, cat# 11140-050), 1mM sodium pyruvate (Gibco, cat#11360-070) and 0.1mM of 2-mercaptoethanol (Sigma, cat# M6250).

treatment_protocol: Untreated.

value: untreated


title: HCC1599_untreated_SMC1a_HiChIP

source_name: HCC1599 cell line

growth_protocol: HCC1599 (female) cells were grown in RPMI 1640 (Corning, cat# 10-040-CM) supplemented with 10% fetal bovine serum (Hyclone, cat# SH30070.03), 2 mM L-glutamine (Corning, cat# 25-005-CI), 100 U/mL and 100 μg/mL penicillin/streptomycin (Corning, cat# 30-002-CI), 100 mM nonessential amino acids (Gibco, cat# 11140-050), 1mM sodium pyruvate (Gibco, cat#11360-070) and 0.1mM of 2-mercaptoethanol (Sigma, cat# M6250).

value: Triple-negative breast cancer cell line


title: MB157_washout_SMC1a_HiChIP

source_name: MB157 cell line

growth_protocol: MB157 (female) cells were grown in DMEM (Corning, cat# 10-013-CV) supplemented with 10% fetal bovine serum (Hyclone, cat# SH30070.03) and 100 U/mL and 100 μg/mL penicillin/streptomycin (Corning, cat# 30-002-CI). When passaged cells were detached with 0.25% trypsin, EDTA-free (Gibco, cat# 15090-046) to avoid activation of Notch signaling.

treatment_protocol: Cells were treated with the GSI compound E (1 μM, Calbiochem cat# 565790) for 72 hours, washed, and then cultured for 3 days in media containing DMSO.

value: GSI-washout


title: LNCaP-Flag_OC2-ChIP-Seq-Hypoxia

city: TORONTO

first: Haiyang

last: Guo

state: Ontario

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

country: Canada

institute: UNIV HEALTH NETWORK

data_processing:
All ChIP-Seq data were aligned using Bowtie2 (version 2.2.1) to the human genome of build version NCBI37/HG19
MACS2 was used for peak calling with the parameter “--SPMR” on and and --keep-dup=1.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated by UCSC bedGraphToBigWig tool from resultant bedgraph files.

growth_protocol: LNCaP and PC3 cell lines were obtained from the American Type Culture Collection (ATCC). All prostate cancer cell lines were cultured as recommended by ATCC. No mycoplasma contamination was detected in these cell lines using MycoAlert™ Mycoplasma Detection Kit (LT07-118, Lonza).

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-enriched DNA was used for library creation with the Rubicon ThruPLEX-FD kit and sequenced (75 bp single-end reads).

treatment_protocol: For hypoxia treatment, cells were incubated in hypoxia chamber at 0.2% O2.

tag: tumor type

value: prostate cancer

value: LNCaP

tag: antibody

tag: protocol

value: Hypoxia


title: LNCaP-Flag_OC2-ChIP-Seq-Normoxia

value: Normoxia


title: PC3-HIF1A-ChIP-Seq-siOC2


title: PC3-HIF1A-ChIP-Seq-siCtrl

value: siCtrl


title: 130514-N1-LO

city: St Louis

first: Winnie

middle: W

last: Pong

state: MO

address: 660 S. Euclid Avenue

department: Department of Neurology

institute: Washington University School of Medicine

description: normal microglia biological replicate 2

data_processing:
Basecalls performed using Illumina Real-Time Analysis (RTA) version 1.17.21.3 followed by demultiplexing of the index sequence using CASAVA 1.8.2.
SPIA adapter sequence aligned and trimmed from raw sequence reads using Flexbar 2.29 with command line parameters : --adapter-min-overlap 7 --adapter-trim-end LEFT --adapter CTTTGTGTTTGA --max-uncalled 150 --min-readlength 25 --no-length-dist --threads 1
Aligned with TopHat 2.0.8, Bowtie 2.1.0 and Ensembl 67 annotation (-G param)
FPKM calculated per sample with Cufflinks 2.0.2 (--num-threads 4 --max-bundle-length 10000000)  and Ensembl 67 annotation with -G param
Genome_build: mm9
Supplementary_files_format_and_content: GBM_gene_fpkm.tsv a tab delimited file with columns for gene ID and the normalized expression values per sample name

source_name: microglia

growth_protocol: not applicable

extract_protocol:
Total RNA was isolated from snap-frozen flow sorted cell pellets using TRIzol-chloroform extraction. RNA was resuspended in 10µl Ambion Nuclease-free water (Life Technologies) and DNAse treated (Ambion TURBO DNA-free Kit)
For cDNA synthesis, we added 5µl of isolated RNA into the Ovation® RNA-Seq method.  500ng cDNA was fragmented using covaris shearing and processed for Illumina library construction with the Illumina paired-end LT indexing protocol as previously published (Mardis et al., 2009; Govindan et al., 2012). Each library was sequenced on the Illumina HiSeq, generating between 15-22Mbp per lane.
RNA-Seq (300-500bp size fractionation): cDNA samples were constructed into Illumina libraries according to the manufacturer’s protocol (Illumina Inc, San Diego, CA) with the following modifications:  1) DNA was fragmented using Covaris S2 DNA Sonicitor using the following condtions: Duty Cycle: 5, Intensity: 4, Cycles/Burst: 200, Time: 90sec (Covaris, Inc. Woburn, MA).  Fragment sizes ranged between 100 and 500bp.  2) Illumina adapter-ligated DNA was amplified in a single 50ml PCR for five cycles.  3) Solid Phase Reversible Immobilization (SPRI) bead cleanup was used to purify the PCR and select for 300-500bp fragments.   We added 0.8 volumes of the AmpureXP solution (preformulated with polyethylene glycol and sodium chloride) to size select DNA molecules greater than 300 bp.  The size-fractioned cDNA was washed three times with 750 µl of 70% ethanol, the beads were dried, and the cDNA library was eluted off the beads by adding 20µl 10 mM Tris-HCl (pH 8.0).  The size-fractioned libraries were assayed using the Agilent BioAnalyzer High Sensitivity DNA chips.

treatment_protocol: Tissue was dissociated, enriched by Percoll gradient, and cells were flow sorted.

value: forebrain

value: 3 months

tag: gender

value: Female

tag: cell population

value: CD11b+ CD45lo


title: 130514-N2-LO

description: normal microglia biological replicate 3


title: 130425-GBM1-L-HI

description: GBM macrophage biological replicate 1

source_name: macrophage

value: tumor

value: CD11b+ CD45hi


title: 130509-GBM1-L-HI

description: GBM macrophage biological replicate 2


title: 130509-GBM1-L-LO

description: GBM microglia biological replicate 2


title: 130514-GBM2-L-LO

description: GBM microglia biological replicate 4


title: 130503-N1-LO

description: normal microglia biological replicate 1


title: 130425-GBM1-L-LO

description: GBM microglia biological replicate 1


title: 130514-GBM1-L-HI

description: GBM macrophage biological replicate 3


title: 130514-GBM2-L-HI

description: GBM macrophage biological replicate 4


status: Public on Feb 26 2019

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

description: Transcriptome profile of ATP7B KO Hep G2 cells treated with Cu, biological rep1

data_processing:
Reads were aligned and assigned to Human Gencode release 19 transcripts and genes by using STAR 2.3.0 with Htseq-count
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: ATP7B KO Hep G2 cells

growth_protocol: ATP7B-KO and control HepG2 cells were incubated with Cu for 24h and their transcriptional responses to the metal were analyzed using QuantSeq 3’ mRNA sequencing

extract_protocol:
Extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit  (Lexogen, Vienna, Austria) according to manufacturer's instructions
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NextSeq500 (Illumina) with a read length of 75 bp

treatment_protocol: Both ATP7B KO Hep G2 cells and control HepG2 cells were incubated with Cu for 24h and then total RNA was extracted

value: Hep G2

tag: genotype/variation

value: ATP7B KO

value: treated with Cu


description: Transcriptome profile of ATP7B KO Hep G2 cells untreated, biological rep3

value: untreated


description: Transcriptome profile of ATP7B KO Hep G2 cells untreated, biological rep2


description: Transcriptome profile of ATP7B KO Hep G2 cells treated with Cu, biological rep3


description: Transcriptome profile of ATP7B KO Hep G2 cells untreated, biological rep1


description: Transcriptome profile of Hep G2 wt cells treated with Cu, biological rep3

source_name: Hep G2 wt cells

value: wild type


title: HCC1599_GSI_SMC1a_HiChIP

value: Triple-negative breast cancer cell line

value: GSI-treated


description: Transcriptome profile of Hep G2 wt cells treated with Cu, biological rep1


title: MB157_GSI_SMC1a_HiChIP


title: MB157_untreated_SMC1a_HiChIP


description: Transcriptome profile of Hep G2 wt cells treated with Cu, biological rep2


description: Transcriptome profile of Hep G2 wt cells untreated, biological rep3


title: 130516-N1-LO

description: normal microglia biological replicate 4

tag: tissue


description: Transcriptome profile of Hep G2 wt cells untreated, biological rep2


description: Transcriptome profile of Hep G2 wt cells untreated, biological rep1


title: 130514-GBM1-L-LO

description: GBM microglia biological replicate 3


title: 19NS-TP53-R248L

city: Seoul

first: Seok Won

last: Ham

address: Anam-ro 145

department: College of Life Sciences & Biotechnology

country: South Korea

institute: Korea University

description: Processed data file: 19NS-control_vs_19NS-TP53-R248L_Processed data.txt

data_processing:
Data were processed using Complete Genomics sequencing instrument.
Briefly, raw reads were filtered through several steps; removing reads with adaptors, removing reads when unknown bases are more than 10%, and have low quality. After filtering, the remaining reads are stored as FASTQ format.
Reads mapping were processed by using Bowtie2 and BWA softwares.
Gene expression was calculated by FPKM method to eliminate the influence of different gene length and sequencing discrepancy.
Finally, a probability value (PA) was calculated to screen differentially expressed genes.
Genome_build: GRCh38.p4
Supplementary_files_format_and_content: 19NS-control_vs_19NS-TP53-R248L_Processed data.txt: Tab-delimited text file includes contents: [1] NCBI gene accession ID, [2] Gene length, [3] Means of FPKM values for each experimental sets, [4] Log2 ratio of gene expression, [5] Probability value (PA), [6] Gene symbol, [7] Gene description, [8] KEGG orthology, [9] GO component, [10] GO function, [11] GO process, [12] Blast nr.

source_name: 19NS glioblastoma cell line, TP53-R248L

growth_protocol: 19NS cell line was cultured in Dulbecco’s Modified Eagle’s Medium/F12 (DMEM/F12) supplemented with B27 (0.2%), epidermal growth factor (EGF; 20 ng/mL), basic fibroblast growth factor (bFGF; 20 ng/mL), penicillin/streptomycin (1%), L-glutamine (2 mmol/L), and gentamicin (50 μg/mL).

extract_protocol:
Total RNA was isolated from 19NS cells using Qiazol reagent (Qiagen) according to the manufacturer's instructions.
Libraries were prepared for RNA-seq by using CG RNA-seq platform. All procedures were proceeded by Beijing Genomics Institute (BGI) corporation.

value: Glioblastoma cells

tag: transfection

value: pLL CMV TP53-R248L puro


title: E12.5_DFB_RNA

city: Wuhan

first: Tian

last: Kuan

state: Hubei

address: Luojiashan

country: China

description: Sample 2

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome using Tophat for Illumina (version 1.5.0) on Galaxy platform
Bam file convert to Bedgraph using BEDTools
Bedgraph convert to bigwig using wig/BedGraph-to-bigwig (version 1.1.0) on Galaxy platform
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files of E10.5 and E12.5 for display read dense of high-throughput sequencing

source_name: dorsal forebrain

growth_protocol: CD-1 Mice were kept under Specific Pathogen Free (SPF) housing conditions and mouse experiments are carried out according to guidelines set by the Animal Care and Ethical Committee of College of Life Sciences at Wuhan University. The noon of the day on which the vaginal plug is found is counted as embryonic (E) day 0.5, and female mice with plugs were separated right away.

extract_protocol:
Total RNAs were extracted twice using Trizol (Invitrogen) and were treated with DNase I (NEB). The integrity of RNAs was analyzed using Agilent Bioanalyzer 2100.
Removal of ribosomal RNAs and construction of libraries for standard strand-specific RNA-seq were performed in BGI Tech. Briefly, first strand was synthesized using normal dNTPs and second strand using dTTP-dUTPs. Illumina PE adapters were ligated to fragments followed by uracil-N-glycosylase (UNG) treatment. Fragment fractioning was carried out using agarose gel electrophoresis. Sequencing was performed using Illumina HiSeq 2000 and around 400 million reads were generated for each developmental stage.

treatment_protocol: Dorsal forebrain (cortex) tissues were resected from E10.5 or E12.5 mouse embryos under dissecting microscopes followed by flash-frozen in liquid nitrogen.

tag: strain

tag: developmental stage

value: dorsal forebrain (cortex)

tag: molecule subtype

value: ribosomal-depletion RNA


title: E10.5_DFB_RNA

institute: College of Life Sciences at Wuhan University

description: Sample 1


description: Transcriptome profile of ATP7B KO Hep G2 cells treated with Cu, biological rep2

tag: treatment


title: 19NS-control

source_name: 19NS glioblastoma cell line, control

tag: cell type

value: pLL CMV puro


title: hMedip_N_input

status: Public on Feb 25 2019

city: Dresden

first: Federico

last: Calegari

address: Fetscherstr. 105

department: Center for Molecular and Cellular Bioengineering (CMCB)

country: Germany

institute: TU Dresden

data_processing:
Library strategy: hMeDIP-Seq
Basecalls were performed using Illumina bcl2fastq version 1.8.4.
Reads were aligned to the mouse genome assembly (mm10) using BWA (0.7.8-r455); parameters: BWA-backtrack algorithm (ALN) with default parameters
Peaks were called using SICER v1.1(window=25 bp, gap=50 bp, fragment=250 bp, max. redundant reads=2, FDR 0.0001) and those found in all replicates of each cell type were merged to build a reference peak-sets of PP, DP and neurons for 5mC and 5hmC.
Peaks overlap with repetitive sequences (RepeatMasker) were excluded and differential (hydroxy-)methylated regions (50% change, p<0.05) identified by Diffbind. Peaks were annotated using HOMER v4.7.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file which contains differential (hydroxy-)methylated loci (50% change, p<0.05) between PP-DP, DP-N and PP-N (DMR.txt or DhMR.txt, respectively) with the nearest gene and its expression (Aprea et al. 2013). Bigwig files were generated using Deeptools v2.2 (merged triplicates of each cell type and modification, respectively).

source_name: E14.5 mouse cortex

extract_protocol:
E14.5 cortices were dissected and dissociated using the papain-based neural dissociation kit (Milteney Biotec). FAC-sorting was performed at 4ºC in the 4-waypurity mode as previously described (Aprea et al., 2013). DNA was isolated (QIAamp DNA micro kit, Qiagen), sheared (250bp) and ligated to barcoded sequencing adaptors (NEBNext Ultra DNA Library Prep Kit for Illumina, New England Biolabs). 300 ng of DNA from each cell type was pooled and (h)MeDIP performed using the MagMeDIP or hMeDIP kits (Diagnode) according to the manufacturer instructions.
The isolated DNA was sheared (250bp) and ligated to barcoded sequencing adaptors (NEBNext Ultra DNA Library Prep Kit for Illumina, New England Biolabs). 300 ng of DNA from each cell type was pooled and (h)MeDIP performed using the MagMeDIP or hMeDIP kits (Diagnode) according to the manufacturer instructions. The immunoprecipitated DNA and nonantibody treated control was quantified, amplified (15 cycles; NEBNext High-Fidelity 2X PCR Master Mix, New England Biolabs) gel size selected (225-325 bp) using the E-Gel EX system (2%) (Invitrogen) and used for 75 bp single read sequencing on a Illumina HiSeq 2000 platform.

value: neurons (Tubb3+)

value: hMedip (Diagnode hMedip Kit)

tag: antibody treated (output) or non-treated controll (input)

value: input


title: hMedip_DP_output

value: neurogenic progenitors (Btg2+/Tubb3-)

value: output


title: methanol_rep3

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

institute: UNIST

data_processing:
RNA-seq reads were aligned to reference sequence using Bowtie 1.2.1.1
The sequence alignment/map (SAM) files were post-processed using SAMTools 0.1.19
Differentially Expressed Genes (DEG) were analyzed by Cufflinks and Cuffdiff to calculate fragments per kilobase of exon per million fragments (FPKM) and differential expression, respectively, with default options and library type of dUTP RNA-seq
Genome_build: Methylomonas sp. DH-1 plasmid, complete sequence (CP014361.1) and Methylomonas sp. DH-1, complete genome (CP014360.1)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Methylomonas sp. DH-1

source_name: cell culture

growth_protocol: Methylomonas sp. DH-1 was cultured in a nitrate mineral salt (NMS) medium containing 10 µM CuSO4 as described in our previous work. Methylomonas sp. DH-1 cells were cultured in a 500 ml baffled flask sealed with a screw cap containing 50 ml of NMS medium at 30oC and 230 rpm. Methane was supplied to a final concentration of 30% (v/v) by gas substitution using a gas-tight syringe, and the headspace was refreshed every day. Methanol-cultured Methylomonas sp. DH-1 was cultured in the same medium containing 1% (v/v) methanol without added methane. All culture was grown in triplicate for subsequent RNA extraction and sequencing.

extract_protocol:
Total RNA in the cell was stabilized using the bacterial reagent RNAprotect (Qiagen, Hilden, Germany). Cell lysis and total RNA were extracted using a GeneJET RNA Purification Kit (Thermo Fisher Scientific, USA) following the manufacturer’s protocol
Total RNA quality and quantity were measured using an RNA 6000 Nano kit with the Agilent Bioanalyzer (Agilent Technologies, CA, USA). Then rRNA was removed using Ribo-Zero rRNA removal kits (Gram-negative bacteria; Epicentre, Madison, WI, USA) and then RNA was used for sequencing library using TruSeq Stranded Total RNA Sample Prep Kit (Illumina, USA) according to the manufacturer’s instructions. Briefly, transcriptome sequencing was conducted using Illumina/Hiseq-2000 RNA sequencing (Macrogen, Korea).

tag: development stage

value: exponential phase

tag: agent

value: methanol


title: methane_rep3

value: methane


title: hMedip_DP_input

tag: chip antibody


title: methane_rep2


title: methanol_rep1


title: Medip_N_input

data_processing:
Basecalls were performed using Illumina bcl2fastq version 1.8.4.
Reads were aligned to the mouse genome assembly (mm10) using BWA (0.7.8-r455); parameters: BWA-backtrack algorithm (ALN) with default parameters
Peaks were called using SICER v1.1(window=25 bp, gap=50 bp, fragment=250 bp, max. redundant reads=2, FDR 0.0001) and those found in all replicates of each cell type were merged to build a reference peak-sets of PP, DP and neurons for 5mC and 5hmC.
Peaks overlap with repetitive sequences (RepeatMasker) were excluded and differential (hydroxy-)methylated regions (50% change, p<0.05) identified by Diffbind. Peaks were annotated using HOMER v4.7.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file which contains differential (hydroxy-)methylated loci (50% change, p<0.05) between PP-DP, DP-N and PP-N (DMR.txt or DhMR.txt, respectively) with the nearest gene and its expression (Aprea et al. 2013). Bigwig files were generated using Deeptools v2.2 (merged triplicates of each cell type and modification, respectively).

value: Medip (Diagnode Magmedip Kit)


title: Medip_DP_output


title: Medip_DP_input


title: hMedip_N_output


title: hMedip_PP_output

value: neuronal stem cells (Btg2-/Tubb3-)


title: methanol_rep2


title: Medip_N_output


title: Medip_PP_input


title: hMedip_PP_input


title: Cell line 1

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

data_processing:
Trimmomatic was used to crop reads to length 50 and to remove the TruSeq3-PE-2 Illumina adapters
The reads were then aligned using tophat2 and bowtie1 with the no-novel-juncs argument set with mouse genome version mm10 and transcriptome defined by the mm10 genes.gtf table from http://genome.ucsc.edu
Reads that did not align or aligned to multiple locations were discarded.
The FPKM were determined by cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: The FPKM.xls file gives the FPKM for each sample (columns) and gene (rows). The row names are gene symbols.

source_name: Subclonal cell line of PTEN-deficient mouse prostate tumor cell line

growth_protocol: Cell lines were cultured in DMEM medium supplemented with 10% FBS, 100U/ml Penicillin, and 100g/ml Streptomycin.

extract_protocol:
Total RNA was isolated from the cell lines using RNeasy Mini Kit (Qiagen)
TruSeq Stranded Total RNA Library Prep Kit (Illumina) following low sample protocol

tag: cell line


title: Cell line 5

value: Subclonal cell line of PTEN-deficient mouse prostate tumor cell line


title: Cell line 4


title: Cell line P

source_name: PTEN-deficient mouse prostate tumor cell line


title: Cell line 2


title: Cell line 3


title: A-Dapt_IGO_07381_6

city: New York

first: Lorenz

last: Studer

state: NY

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description:
Neurons
AllData_combined_GEO.txt

data_processing:
Illumina Casava1.7 software used for basecalling
RNASeq - FASTQ files were aligned using the STAR aligner to hg38.  BAM files were then processed into a counts table using HTSeq and imported into DESeq2 for further analysis
ATAC-Seq - FASTQ files were aligned using Bowtie2 aligner to hg19.  BAM files were then processed into peak files using MACS2 and partial analysis was performed using the HOMER suite.
Genome_build: hg38 and hg19
Supplementary_files_format_and_content: tab delimited files.  RNA seq - fold change compared to rosette cells, ATACseq - called peak files.
Supplementary_files_format_and_content: RNASeq counts table from HTSeq
Supplementary_files_format_and_content: Fold changes of RNASeq ccompared to H9 derived rosettes

molecule: polyA RNA

source_name: Neural stem cells

growth_protocol: NSCs were maintained in 10ng/ml FGF2 and 10ng/ml EGF in N2 media

extract_protocol:
RNA was isolated from cell pellets resuspended in TRIzol and purified using the RNEasy spin column
RNA and ATAC libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 2ug/ml doxycycline was added as treatment

tag: es cell line

value: H9 ESCs


title: C-d12_IGO_07381_17

description:
d12
AllData_combined_GEO.txt


title: B-d12_IGO_07381_11

description:
d12
AllData_combined_GEO.txt


title: B-Dapt_IGO_07381_12

description:
Neurons
AllData_combined_GEO.txt


title: methane_rep1


title: A-d12_IGO_07381_5

description:
d12
AllData_combined_GEO.txt


title: C-d9_IGO_07381_16

description:
d9
AllData_combined_GEO.txt


title: B-d9_IGO_07381_10

description:
d9
AllData_combined_GEO.txt


title: Medip_PP_output


title: A-d6_IGO_07381_3

description:
d6
AllData_combined_GEO.txt


title: A-d6_R_IGO_07381_B_4

description:
d6
AllData_combined_GEO.txt


title: A-d9_IGO_07381_4

description:
d9
AllData_combined_GEO.txt


title: H9-CD44_IGO_07381_20

description:
d6
AllData_combined_GEO.txt


title: B-d0_IGO_07381_7

description:
d0
AllData_combined_GEO.txt


title: H9-d0_IGO_07381_19

description:
Rosettes
AllData_combined_GEO.txt


title: A-d3_IGO_07381_2

description:
d3
AllData_combined_GEO.txt


title: H9-d6_new_IGO_07381_B_7

description:
d6
AllData_combined_GEO.txt


title: C-d0_IGO_07381_13

description:
d0
AllData_combined_GEO.txt


title: B-d6_R_IGO_07381_B_5

description:
d6
AllData_combined_GEO.txt


title: 305M-9

data_processing:
Trimmomatic was used to crop reads to length 50 and to remove the TruSeq3-PE-2 Illumina adapters
The paired-end reads were then aligned using tophat2 and bowtie1 with the no-novel-juncs argument set with mouse genome version mm10 and transcriptome defined by the mm10 genes.gtf table from http://genome.ucsc.edu
Reads that did not align or aligned to multiple locations were discarded.
The number of reads aligning to each gene was then determined using htseq-count.
Samples that had less than 300,000 reads were discarded.
Genome_build: mm10
Supplementary_files_format_and_content: The readCounts.xls file gives the read counts described above for each sample (columns) and gene (rows). The row names are official gene symbols.

source_name: Lung micro-metastases

extract_protocol:
Single CTCs were isolated from fresh whole blood following leukocyte depletion using the microfluidic CTC-iChip as described in PMID 23552373. Macro-metastases were dissected out from the lung under fluorescence dissection microscope. The rest of the lung tissue was digested into single cells by collagenase and hyaluronidase (Stemcell Technologies), which were then sorted by FACS to enrich GFP-positive DTCs. Primary tumor and lung macro-metastases were also digested into single cells using the same procedure. Last, GFP-positive tumor cells from each category (CTC, DTC, Primary, Mets) were individually micromanipulated using a 10um transfer tip on an Eppendorf TransferMan NK 2 micromanipulator, transferred into PCR tubes containing RNA protective lysis buffer, and flash frozen in liquid nitrogen.
Clontech SMARTer Ultra Low Input Kit for RNA v3 for cDNA synthesis and the Nextera XT kit for library construction

tag: mouse

tag: sample type

value: single cell in lysis buffer


title: 305M-6


title: C-d3_IGO_07381_14

description:
d3
AllData_combined_GEO.txt


title: 305M-7


title: 305M-4


title: B-d3_IGO_07381_8

description:
d3
AllData_combined_GEO.txt


title: A-d0_IGO_07381_1

description:
d0
AllData_combined_GEO.txt


title: 305M-1


title: 303M1-6


title: 303M1-8


title: 305M-8


title: 305M-5


title: 305M-2


title: 303M2-4


title: 303M2-6


title: 303M1-4


title: 303M1-5


title: 303M1-3


title: 305M-3


title: 303M2-1


title: 299-Met-9


title: 303M2-3


title: 299-Met-10


title: 303M1-1


title: 303M2-2


title: 299-Met-8


title: 299-Met-7


title: 299-Met-6


title: 303M1-2


title: 299-Met-2


title: 299-Met-1


title: 299-Met-4


title: 299-Met-3


title: 303M1-7


title: 305L-9

source_name: DTC-II


title: 299-Met-11


title: 305L-8


title: 305L-6


title: 305L-7


title: 305L-2


title: 305L-4


title: 305L-3


title: 303L-17


title: 305L-1


title: 305L-5


title: 303L-16


title: 299-Met-5


title: 303L-14


title: 303L-11


title: 303L-10


title: 303L-9


title: 303L-15


title: 303L-13


title: 303L-12


title: 303L-5


title: 303L-8


title: 303L-6


title: 303L-1


title: 303L-4


title: 303L-3


title: 303L-7


title: 300-DTC-10


title: 300-DTC-12


title: 300-DTC-11


title: 300-DTC-15


title: 300-DTC-14


title: 300-DTC-9


title: 300-DTC-13


title: 299-DTC-13


title: 300-DTC-1


title: 299-DTC-14


title: 300-DTC-4


title: 300-DTC-5


title: 300-DTC-8


title: 300-DTC-7


title: 300-DTC-2


title: 299-DTC-15


title: 300-DTC-6


title: 300-DTC-3


title: 299-DTC-11


title: 299-DTC-12


title: 299-DTC-9


title: 299-DTC-4


title: 299-DTC-10


title: LTNSC_NFIA_plus_dox_ATAC


title: 299-DTC-5


title: hESC-astrocytes_d200_ATAC


title: LTNSC_NFIA_reverse_ATAC


title: 299-DTC-7


title: 299-DTC-8


title: 299-DTC-6


title: LTNSC_NFIA_no_dox_ATAC


title: 299-DTC-1


title: 304L-10

source_name: DTC-I


title: 299-DTC-2


title: 304L-14


title: 304L-9


title: 304L-11


title: 299-DTC-3


title: 304L-12


title: 304L-5


title: 303CTC-10

source_name: CTC


title: 303CTC-7


title: 304L-3


title: 301L-1


title: 301L-6


title: 303CTC-1


title: 304L-8


title: 304L-1


title: 303CTC-3


title: 301L-4


title: 301L-3


title: 304L-4


title: 303CTC-8


title: 303CTC-11


title: 303CTC-14


title: 301L-2


title: 303CTC-6


title: 304L-6


title: 301L-7


title: 301L-5


title: 303CTC-13


title: 304L-2


title: 304L-7


title: 303CTC-2


title: 305.3-PT

source_name: Single cells from primary tumor


title: 305.4-PT


title: 305.5-PT


title: 303CTC-12


title: 303CTC-9


title: 305.2-PT


title: 304.1-PT


title: 300-PT-1


title: 303.5-PT


title: 301.1-PT


title: 300-PT-5


title: 304.5-PT


title: 303.3-PT


title: 300-PT-2


title: 305.1-PT


title: 304.2-PT


title: 300-PT-4


title: 299-PT-4


title: 303.2-PT


title: 301.2-PT


title: 304.4-PT


title: 303.4-PT


title: 299-PT-5


title: 299-PT-3


title: Dunaliella salina RNA-seq

status: Public on Feb 23 2019

city: TEDA

first: Hexin

last: Lv

state: Tianjin

address: 29 13th street

institute: Tianjin University of Science and Technology

data_processing:
Sequencing reads were de novo assembled by using Trinity (2013-02-25) under default parameters choice. Assembly quality was assessed by length distribution analysis by common perl scripts.
BLASTX 2.2.22 with an E-value threshold of 10-5 was used for annotation.
RSEM (1.2.3) was used for caculating RPKM of gene expression level
Supplementary_files_format_and_content: Transcripts sequencs of Dunaliella salina under nitrogen deprivation condition in fasta format. Transcrition levels and function annotations of of Dunaliella salina under nitrogen deprivation condition in table format.

organism: Dunaliella salina

source_name: Dunaliella salina cells under nitrogen deprivation condition

growth_protocol: KNO3 in culture media was replaced by equimolar KCl, The algae were grown at 30°C in 0.5-L Erlenmeyer flasks containing 250 mL of medium under continuous illumination (60 μmol m-2 s-1, fluorescent lamp, 400-700 nm). The cultures were shaken manually on a day-to-day basis. Cells were inoculated at 2.0× 105/ml. All the cells were cultured for two 16/8 hour light/dark cycles to synchronize the growth phases before inoculation and transfer to continuous light conditions.

extract_protocol:
Trizol reagent (Invitrogen, CA, USA) was used to extract total RNA as manufacturer's instructions. RNA quantity and purity were determined by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 5 ug of total RNA for each sample was used to isolate mRNA by magnetic beads with poly-T oligo attached (Invitrogen). The purified mRNA was fragmented into small pieces by divalent cations under elevated temperature.
The cDNA library was prepared by reverse-transcription in accordance with instructions of the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). The paired-end sequencing was performed on an Illumina HiseqTM2000 platform (LC Sciences, USA) following the vendor's instruction.

treatment_protocol: Dunaliella salina cells cultured under nitrogen deprivation conditions were harvested for Illumina HiseqTM2000 RNA-sequencing

value: nitrogen-depleted Dunaliella salina


title: 303.1-PT


title: 304.3-PT


title: 299-PT-1


title: 299-PT-2


title: 301.3-PT


title: 301.5-PT


title: Neu-D3_HiC_rep2

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

description:
neuroday3_rep2
Formaldehyde crosslinking, cell lysis, digesion with HindIII, biotin-14-CTP labeling, blunt-end ligation, crosslink reversal, DNA isolation, size-fractionation, DNA pulldown, Ilumina adapter ligation and library preparation

data_processing:
ChIP-seq reads were aligned to the hg19 reference genome using bowtie2 version 2.1.0
Hi-C reads were aligned and processed using hiclib
RNA-seq was processed using the tuxedo protocol. 30 bp was trimmed from the read ends
Duplicate reads were removed using picard MarkDuplicates
ChIP and Input experiments were ensured to have equal read depth per chromosome by downsampling the deeper sequenced experiment
Peak calling was done using EDD version 1.1.7
Genome_build: hg19
Supplementary_files_format_and_content: bed files with four columns: chromosome, start position, end position, score; fpkm_tracking files with 13 columns tracking_id, class_code, nearest_ref_id, gene_id, gene_short_name, tss_id, locus, length, coverage, FPKM, FPKM_conf_lo, FPKM_conf_hi, FPKM_status

source_name: Human primary adipose stem cells

growth_protocol: Human normal adipose tissue-derived mesenchymal stem cells were prepared from subcutaneous liposuction material. Cells were cultured under proliferative conditions in DMEM/F12 containing 10% fetal calf serum, 10 ng/ml epidermal growth factor (Sigma-Aldrich E9644) and 20 ng/ml basic fibroblast growth factor (FGF2; Sigma-Aldrich F5392). Cells at passage 5-7 were used in two independent differentiation experiments, each towards adipose or neuronal lineages.

extract_protocol:
For RNA-seq, total mRNA was isolated from Neu-D1 and Neu-D3 cells using the Qiagen RNeasy kit and processed for Illumina library preparation and sequencing. For ChIP-seq of lamin B1, cells at each differentiation time point were fixed with 1% formaldehyde for 10 min, lysed for 10 min in ChIP lysis buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 1% SDS, protease inhibitors and 1 mM PMSF) and sonicated 4 times 10 min in a Bioruptor (Diagenode) to generate 200 base-pair DNA fragments. After sedimentation, the supernatant was collected and diluted 10-fold in RIPA (140 mM NaCl, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, protease inhibitors, 1 mM PMSF). Chromatin was incubated overnight at 4oC with the anti-lamin B1 antibody coupled to Dynabeads Protein A/G (Invitrogen). ChIP samples were washed 4 times in ice-cold RIPA, crosslinks reversed and DNA eluted for 6 h at 68oC in 50 mM NaCl, 20 mM Tris-HCl pH 7.5, 5 mM EDTA, 1% SDS and 50 ng/µl Proteinase K. DNA was purified using phenol-chloroform isoamylalcohol and dissolved in H2O prior to processing for Illumina library preparation and sequencing. For Hi-C, 25 million cells per time point and differentiation replicate were cross-linked with fresh 1% formaldehyde (Pierce) for 12 min at room temperature on a rocker. Excess formaldehyde was quenched with 0.125 M glycine for 5 min and cells washed 3 times 5 min in ice-cold PBS. Crosslinked cells were lysed in lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA-630 and protease inhibitors) on ice for 15 min and homogenised by Douncing with a B-pestle (tight) in lysis buffer until nuclei were released, as assessed by microscopy. The lysate was sedimented, the pellet was resuspended in NEBuffer 2 (10 mM Tris-HCl pH 7.9, 50 mM NaCl, 10 mM MgCl2, 1 mM dithiothreitol) containing 0.1% SDS, and incubated at 65oC for 10 min. SDS was quenched on ice with 1% Triton X-100 and the sample digested with HindIII overnight at 37oC. Digested fragments were labelled with biotin-14-dCTP and blunt-end ligated. Crosslinks were reversed at 65oC overnight, the ligated DNA was purified by phenol-chloroform:isoamylalcohol (Ambion), desalted and RNAse-treated. DNA was sheared to ~100-300 base-pairs by Covaris sonication and size-fractionated on AMpure XP magnetic beads (Beckman Coulter). Biotinylated DNA fragments were pulled-down with Streptavidin beads and processed for Illumina adapter ligation and library preparation.
Illumina sequencing libraries were generated as per Illumina protocols.

treatment_protocol: Two days before induction of differentiation, proliferating cells (hereafter, ‘Pro’ stage) were harvested and processed for Hi-C or ChIP. For adipogenic differentiation, harvested ‘Pro’ cells were reseeded in DMEM/F12/10% serum without growth factors. Adipogenesis was induced 48 h later (D0) by addition of 10 µg/ml insulin, 200 µM indomethacin, 0.5 µM 1-methyl-3 isobutylxanthine and 1 µM dexamethasone. Medium was left with the cells for the 3 days of differentiation. Cells were collected on D1 and D3 (Ad-D1 and Ad-D3) and processed for Hi-C or ChIP. Neuronal differentiation was initiated on D0. In brief, medium was removed on D0 and cells were washed twice 4 min in pre-warmed Gibco serum-free DMEM (Thermo Fisher Scientific). Washing medium was removed and differentiation was induced by adding Gibco Neurobasal medium (Thermo Fisher Scientific) supplemented with 1% fetal calf serum, 1x B27 (Thermo Fisher Scientific), 0.5 mM IBMX, 1 µm dexamethasone, 10 µm forskolin, 200 µm 8CTP-cAMP and 10 mM valproic acid. Medium was left with the cells for the 3 days of differentiation. Cells were collected on D1 and D3 (Neu-D1 and Neu-D3) and processed for Hi-C or RNA isolation for RNA-seq.

tag: time point

value: Day 3

value: ASCs on day 3 after adipogenic induction

tag: replicate


title: Ad-D3_HiC_rep1

description: Formaldehyde crosslinking, cell lysis, digesion with HindIII, biotin-14-CTP labeling, blunt-end ligation, crosslink reversal, DNA isolation, size-fractionation, DNA pulldown, Ilumina adapter ligation and library preparation

data_processing:
ChIP-seq reads were aligned to the hg19 reference genome using bowtie2 version 2.1.0
Hi-C reads were aligned and processed using hiclib
Duplicate reads were removed using picard MarkDuplicates
ChIP and Input experiments were ensured to have equal read depth per chromosome by downsampling the deeper sequenced experiment
Peak calling was done using EDD version 1.1.7
bigWig files generated using deepTools 2.0
Genome_build: hg19
Supplementary_files_format_and_content: bed files with four columns: chromosome, start position, end position, score;bigwig files


title: Neu-D1_HiC_rep2

description:
neuroday1_rep2
Formaldehyde crosslinking, cell lysis, digesion with HindIII, biotin-14-CTP labeling, blunt-end ligation, crosslink reversal, DNA isolation, size-fractionation, DNA pulldown, Ilumina adapter ligation and library preparation

value: Day 1

value: ASCs on day 1 after neuronal induction


title: Neu-D3_HiC_rep1

description:
neuroday3_rep1
Formaldehyde crosslinking, cell lysis, digesion with HindIII, biotin-14-CTP labeling, blunt-end ligation, crosslink reversal, DNA isolation, size-fractionation, DNA pulldown, Ilumina adapter ligation and library preparation


title: Neu-D1_HiC_rep1

description:
neuroday1_rep1
Formaldehyde crosslinking, cell lysis, digesion with HindIII, biotin-14-CTP labeling, blunt-end ligation, crosslink reversal, DNA isolation, size-fractionation, DNA pulldown, Ilumina adapter ligation and library preparation


title: Ad-Pro_HiC_rep2

description:
day2_rep2
Formaldehyde crosslinking, cell lysis, digesion with HindIII, biotin-14-CTP labeling, blunt-end ligation, crosslink reversal, DNA isolation, size-fractionation, DNA pulldown, Ilumina adapter ligation and library preparation

value: Day -2 (proliferative; "Pro")

value: Proliferating adipose stem cells (ASCs) in growth medium


title: stroke_Sample_3049

status: Public on Feb 22 2019

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Library strategy: ribosome profiling
Illumina Casava v1.8 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with HiSat2 (v2.0.11) against the mm10 reference genome
Gene and transcript information was extracted with Partek Genomics Suite (v6.6). Annotated data was normalized using statistical software R (v3.3.1) including DESeq2 package. Normalized read counts lower than 1 were set to the floor value 1.Genes were defined as expressed with normalized RNA-seq values ≥ 10.
Processed DeSeq2 normalized RNA-seq tag counts annotated to the mm10 reference genome
Genome_build: mm10
Supplementary_files_format_and_content: norm_data_ribo.txt

source_name: Mouse brain hemisphere middle section

growth_protocol: MCAO for 1h or control group without MCAO, killing after 3 days

extract_protocol:
Cells were lysed in TRIZOL (Invitrogen) and total RNA was extracted according to the manufacturers’ protocol
1µg of total RNA was converted to RNA-seq libraries according to manufacturers' protocol with Illumina TruSeq RNA Sample Preparation Kit.

treatment_protocol: Dissection of brain hemispheres, RiboTag IP of the brain hemishere middle sections, RNA isolation

tag: tissue

value: Brain

tag: mcao

value: MCAO

tag: hemisphere

value: Left MCAO hemisphere


title: Ad-D1_HiC_rep1

description:
day1_rep1
Formaldehyde crosslinking, cell lysis, digesion with HindIII, biotin-14-CTP labeling, blunt-end ligation, crosslink reversal, DNA isolation, size-fractionation, DNA pulldown, Ilumina adapter ligation and library preparation

value: ASCs on day 1 after adipogenic induction


title: Ad-Pro_HiC_rep1

description:
day2_rep1
Formaldehyde crosslinking, cell lysis, digesion with HindIII, biotin-14-CTP labeling, blunt-end ligation, crosslink reversal, DNA isolation, size-fractionation, DNA pulldown, Ilumina adapter ligation and library preparation


title: Ad-D1_HiC_rep2

description:
day1_rep2
Formaldehyde crosslinking, cell lysis, digesion with HindIII, biotin-14-CTP labeling, blunt-end ligation, crosslink reversal, DNA isolation, size-fractionation, DNA pulldown, Ilumina adapter ligation and library preparation


title: Ad-D0_HiC_rep2

description:
day0_rep2
Formaldehyde crosslinking, cell lysis, digesion with HindIII, biotin-14-CTP labeling, blunt-end ligation, crosslink reversal, DNA isolation, size-fractionation, DNA pulldown, Ilumina adapter ligation and library preparation

value: Day 0

value: ASCs on the day of differentiation induction


title: Ad-D0_HiC_rep1

description:
day0_rep1
Formaldehyde crosslinking, cell lysis, digesion with HindIII, biotin-14-CTP labeling, blunt-end ligation, crosslink reversal, DNA isolation, size-fractionation, DNA pulldown, Ilumina adapter ligation and library preparation


title: Ad-D3_HiC_rep2

description:
day3_rep2
Formaldehyde crosslinking, cell lysis, digesion with HindIII, biotin-14-CTP labeling, blunt-end ligation, crosslink reversal, DNA isolation, size-fractionation, DNA pulldown, Ilumina adapter ligation and library preparation


title: stroke_Sample_3051


title: Ctrl_Sample_3047

value: No MCAO

value: Left control hemisphere


title: Ctrl_Sample_3046


title: Ctrl_Sample_3048


title: MCAO LH 3d

data_processing:
Library strategy: Ribosome profiling
Illumina Casava v1.8 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with HiSat2 (v2.0.11) against the mm10 reference genome
Gene and transcript information was extracted with Partek Genomics Suite (v6.6). Annotated data was normalized using statistical software R (v3.3.1) including DESeq2 package. Normalized read counts lower than 1 were set to the floor value 1.Genes were defined as expressed with normalized RNA-seq values ≥ 10.
mm10
Processed DeSeq2 normalized RNA-seq tag counts annotated to the mm10 reference genome
Genome_build: mm10
Supplementary_files_format_and_content: norm_data_pooled.txt

extract_protocol:
Dissection of brain hemispheres, RiboTag IP of the brain hemishere middle sections, RNA isolation
mRNA converting into cDNA with Transcriptor High Fidelity cDNA synthesis Kit, libraray preperation with TruSeq RNA Sample Preparation 2 Kit

treatment_protocol: MCAO for 1h or control group without MCAO, killing after 3 days


title: Control RH 3d

value: Right control hemisphere


title: 2198-_wt

city: Stockholm

first: Daniel

last: Ramsköld

address: Nobels väg 3

country: Sweden

institute: Karolinska Institutet

description: Brain endothelial cells with wildtype Axin1 expression, biol repl 3

data_processing:
Reads were aligned using Bowtie to genome and ensembl transcriptome
Expression values were calculated using rpkmforgenes.py (http://sandberg.cmb.ki.se/rnaseq) with RefSeq annotation from 16 May 2011
Genome_build: mm9
Supplementary_files_format_and_content: RPKM expression values (tab-delimited text format)

source_name: brain endothelial cells

extract_protocol:
RNeasy Micro Kit (#74004, Qiagen)
SMARTer Ultra Low Input RNA for Illumina Sequencing kit (#634820, Clontech)

treatment_protocol: Tamoxifen at E9.5 to mother

tag: cell sorting

value: CD31+, PECAM1+

tag: developmental stage

tag: genetic modification

tag: strain

value: brain endothelial cells


title: 1814+_Axin1overexpression

description: Brain endothelial cells overexpressing Axin1, biol repl 2

tag: cell type


title: 1814-_wt

description: Brain endothelial cells with wildtype Axin1 expression, biol repl 2


title: 300-PT-3

value: single cell in lysis buffer


title: 1813+_Axin1overexpression

description: Brain endothelial cells overexpressing Axin1, biol repl 1


title: stroke_Sample_3050


title: 1813-_wt

description: Brain endothelial cells with wildtype Axin1 expression, biol repl 1


title: 3A_PbAgo2_A_plus_scr_I

city: Nijmegen

first: Sabine

last: Fraschka

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen

description:
Ago2-expressing P. berghei line, generated by integrating a 5’hsp70-hAgo2 expression cassette into the genome of the P. berghei strain PbGFPcon, clone 1
raw_counts.txt

data_processing:
Data were mapped with BWA samse (Version: 0.7.12-r1039) to the annotated P. berghei ANKA transcriptome from PlasmoDB version 26 and the GFP coding sequence encoded by the PbGFPcon parasite line
Using samtools (version 1.2) sam files were converted to bam files, q15 filtered and filtered for unique reads aligned to the sense strand
Tags were counted for all transcript (excluding mitchochondrial and apicoplast RNA)
Genome_build: P. berghei ANKA transcriptome (PlasmoDB version 26)
Supplementary_files_format_and_content: text file containing tag counts for all transcripts (excluding mitochondrial and apicoplast RNA) for all samples (1A - 4B) in tab-delimited format

organism: Plasmodium berghei

source_name: red blood cell stage

growth_protocol: Schizont-enriched parasite samples were prepared by bleeding Plasmodium-infected mice (parasitemia 1-3 %) via the inferior vena cava using a heparinized needle. Leukocytes were removed from samples by filtering blood over cellulose powder (CF11) columns. Blood cells were eluted in 15 ml pre-warmed RPMI medium supplemented with 20 % (v/v) fetal calf serum of US-origin (FCS-US) and 2 % (v/v) Gentamycin. Cells were pelleted by centrifugation for 8 min, 400x g. The pellet was resuspended in 15 ml pre-warmed transfection medium, transferred to a 25 cm2 cell-culture flask and parasites were cultured for 16 to 18 h at 37 °C and 3 % CO2, 5% O2. After 19 h incubation, cells were pelleted for 8 min, 400x g and resuspended in 6 ml RLT buffer (QIAGEN) supplemented with 1 % (v/v) b-mercaptoethanol.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, #74106; including on-column DNase treatment and RNA clean-up) and PolyA-selected using the Oligotex mRNA Mini Kit (Qiagen, #70022) according to manufacturer’s instructions. PolyA-selected RNA was checked for genomic DNA contamination via qPCR and additionally treated twice with TURBO DNase (Ambion, #AM2238) to eliminate remaining genomic DNA. 2 µg of PolyA-selected total RNA equivalent were fragmented by alkaline hydrolysis as described in (Hoeijmakers, Bártfai and Stunnenberg 2013), precipitated and further processed for strand-specific RNA-seq as described in (Kensche et al. 2015). In short, first strand cDNA synthesis was performed using AT-corrected Random N9 primers and in presence of 0.2µg Actinomycin D to prevent unwanted DNA-dependent second strand cDNA synthesis, and during second strand synthesis dTTPs were replaced with dUTPs.
For each sequencing library 5 ng of double stranded cDNA were end repaired, extended with 3’ A-overhangs, ligated to barcoded NextFlex adapters (Bio Scientific, #514122) and treated with USER enzyme (NEB, #M5505L) to induce dUTP-dependent second strand-specific degradation. Subsequently, libraries were amplified using KAPA HiFi HotStart ready mix (KAPA Biosystems, #KM2602), NEXTflex primer mix (Bio Scientific, #514122) and the following PCR program: 98°C for 2min; 4 cycles of 98°C for 20sec, 62°C for 3min; 62°C for 5 min. Amplified libraries were gel size-selected for 300 - 400 bp using 2% E-Gel Size Select agarose gels (Invitrogen, #G6610-02) and amplified for additional 8 cycles as described above. Adapter dimer depletion and DNA clean-up were performed using Agencourt AMPure XP beads (Beckman Coulter, #A63880) in a 1:1 library beads ratio.

value: PbGFPcon

tag: genomic modification

value: Ago2-expressing P. berghei line

tag: treatment

value: scrambled AgoshRNA from a plasmid


title: MCAO C RH 3d


title: 4A_PbAgo2_A_plus_aGFP_I

value: anti-GFP-AgoshRNA aGFP from a plasmid


title: 3B_PbAgo2_A_plus_scr_III

value: scrambled AgoshRNA from a plasmid, second independent transfection


title: 4B_PbAgo2_A_plus_aGFP_II

value: anti-GFP-AgoshRNA aGFP from a plasmid, second independent transfection


title: 1A_PbGFPcon_WT_I


title: 2B_PbAgo2_clone_B

description:
Ago2-expressing P. berghei line, generated by integrating a 5’hsp70-hAgo2 expression cassette into the genome of the P. berghei strain PbGFPcon, clone 2
raw_counts.txt


title: U2O2_siCont

status: Public on Feb 20 2019

city: Sapporo

first: Masashi

last: Idogawa

country: Japan

institute: Sapporo Medical University

data_processing:
Illumina bcl2fastq v1.8.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v2.0.12
Each gene and lncRNA expression was quantified by Cuffquant v2.2.1 with hg19 and LNCipediaV4 as a reference of transcripts and normalized by Cuffnorm v2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized read count values for each sample

source_name: Osteosarcoma U2OS cells

growth_protocol: U2OS cells were cultured in DMEM with 10% FCS.

extract_protocol:
24h after the treatment, total RNA was extracted by RNeasy mini kit (QIAGEN) according to manufacturer's protocol. RNA was quantified using the NanoDrop spectrophotometer and Agilent Bioanalyzer 2100.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: U2OS cells were transfected with siRNA targeting NEAT1 or negative control siRNA with Lipofectamin RNAiMAX. 24h after transfection, these cells were treated with or without nutlin-3a (10 uM)

value: Osteosarcoma cells

tag: transfected with

value: negative control siRNA


title: U2O2_siCont+Nutlin

tag: cell line

tag: treated with

value: 10uM nutlin-3a


title: 2A_PbAgo2_clone_A


title: 1B_PbGFPcon_WT_II


title: Whole_6-8h_1

status: Public on Feb 19 2019

city: Berlin

first: Alexandra

middle: Louise

last: McCorkindale

address: Robert Roessle-Strasse 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrueck Center for Molecular Medicine

data_processing:
A reference index was generated with RSEM (v1.3.0) using BDGP genome build (Release 6/dm6) and Flybase transcriptome annotation (Release 6.15)
RNA-Seq reads were pseudo-aligned to the reference index with Salmon (Release 0.8.1)
Gene-level counts were prepared for differential expression analysis with tximport as part of the Bioconductor package (Release 3.5)
Differential expression was measured using DESeq2 default parameters as part of the Bioconductor package (Release 3.5)
Genome_build: dm6
Supplementary_files_format_and_content: *.sf.gz is the quantification file output of Salmon (quasi-mapping and transcript quantification tool for RNA-seq data, doi:10.1038/nmeth.4197). This is a plain text, tab-separated file. The columns have the following interpretation:
Name:  the name of the target transcript provided in the input transcript database (FASTA file).
Length:  the length of the target transcript in nucleotides.
EffectiveLength:  the computed effective length of the target transcript. It takes into account all factors being modeled that will effect the probability of sampling fragments from this transcript, including the fragment length distribution and sequence-specific and gc-fragment bias (if they are being modeled).
TPM:  salmon's estimate of the relative abundance of this transcript in units of Transcripts Per Million (TPM). TPM is the recommended relative abundance measure to use for downstream analysis.
NumReads: salmon's estimate of the number of reads mapping to each transcript that was quantified. It is an    estimate    insofar as it is the expected number of reads that have originated from each transcript given the structure of the uniquely mapping and multi-mapping reads and the relative abundance estimates for each transcript.

organism: Drosophila melanogaster

growth_protocol: Flies were maintained at 25ºC and 65% humidity on apple juice agar plates

extract_protocol:
Cells from dissociated embryos were subjected to hypotonic swelling and detergent lysis to separate cytoplasmic and nuclear fractions for RNA isolation
Ribodepleted RNA-Seq libraries were constructed using NuGEN Ovation Drosophila RNA-Seq System

treatment_protocol: Embryos were collected for 2-4 hour windows and aged appropriately at 25ºC

tag: fly line

tag: genetic background

value: yellow-white

tag: genotype

value: y1 w1118 ; M{3x rho-lexA:Cit}ZH-51C ; P{vnd:FNLDD}

value: 6-8h AEL

tag: fraction

value: Whole embryo


title: 1961+_Axin1overexpression

description: Brain endothelial cells overexpressing Axin1, biol repl 3


title: Nuc_6-8h_2

value: Embryonic nuclear fraction


title: U2O2_siNEAT1+Nutlin

value: siRNA targeting NEAT1


title: siLIMA1

data_processing:
Illumina bcl2fastq v1.8.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v2.0.12
Each gene and lncRNA expression was quantified by Cuffquant v2.2.1 with hg19 and LNCipediaV2 as a reference of transcripts and normalized by Cuffnorm v2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized read count values for each sample

source_name: Lung cancer A549 cells

growth_protocol: A549 cells were cultured in RPMI with 10% FCS.

treatment_protocol: A549 cells were stably infected with lentivrus expressing shRNA-LIMA1 or negative control shRNA. These cells were treated with or without nutlin-3a (10 uM)


title: siLIMA1+Nutlin


title: siCont


title: Whole_18-22h_2


title: Nuc_6-8h_1


title: Cyto_18-22h_2

value: Embryonic cytoplasmic fraction


title: siCont+Nutlin


title: Whole_18-22h_1


title: Nuc_18-22h_2


title: Nuc_18-22h_1


title: 18-22h_Repo-pos_1

description:
processed data file:
DESeq2_18-22h_Repo.csv.gz

data_processing:
A reference index was generated with RSEM (v1.3.0) using BDGP genome build (Release 6/dm6) and Flybase transcriptome annotation (Release 6.15)
RNA-Seq reads were pseudo-aligned to the reference index with Salmon (Release 0.8.1)
Gene-level counts were prepared for differential expression analysis with tximport as part of the Bioconductor package (Release 3.5)
Differential expression was measured using DESeq2 default parameters as part of the Bioconductor package (Release 3.5)
Genome_build: dm6
Supplementary_files_format_and_content:
*.sf.gz is the quantification file output of Salmon (quasi-mapping and transcript quantification tool for RNA-seq data, doi:10.1038/nmeth.4197). This is a plain text, tab-separated file. The columns have the following interpretation:
Name:  the name of the target transcript provided in the input transcript database (FASTA file).
Length:  the length of the target transcript in nucleotides.
EffectiveLength:  the computed effective length of the target transcript. It takes into account all factors being modeled that will effect the probability of sampling fragments from this transcript, including the fragment length distribution and sequence-specific and gc-fragment bias (if they are being modeled).
TPM:  salmon's estimate of the relative abundance of this transcript in units of Transcripts Per Million (TPM). TPM is the recommended relative abundance measure to use for downstream analysis.
NumReads: salmon's estimate of the number of reads mapping to each transcript that was quantified. It is an    estimate    insofar as it is the expected number of reads that have originated from each transcript given the structure of the uniquely mapping and multi-mapping reads and the relative abundance estimates for each transcript.

*.csv.gz are the results extracted from differential expression analysis by DESeq2 (ref. doi: 10.1186/s13059-014-0550-8). For each analysis, the output file is the result of contrasting marker-positive (   treated    condition) versus marker-negative samples (   untreated    condition) for each cell type and time point. The columns have the following interpretation:
baseMean: mean of normalized counts of all samples
log2FoldChange: log2 fold change (MAP) of marker-positive relative to marker-negative samples
lfcSE: standard error of marker-positive relative to marker-negative samples
stat: Wald statistic of marker-positive relative to marker-negative samples
pvalue: Wald p-value of marker-positive relative to marker-negative samples
padj: Benjamin-Hochberg (BH) adjusted p-values

extract_protocol:
Cells from dissociated embryos were subjected to immunostaining and marker-based FACS sorting prior to RNA isolation and library preparation
Ribodepleted RNA-Seq libraries were constructed using NuGEN Ovation Drosophila RNA-Seq System

treatment_protocol: Embryos were collected for two hour windows and aged appropriately at 25ºC

value: y1 w1118 ; M{3x vnd-lexA:Cit}ZH-51C ; P{vnd:FNLDD}

tag: marker

value: Repo

tag: marker enriched/depleted

value: Enriched

tag: tissue/cell type

value: Embryonic glia


title: 18-22h_Repo-neg_2

value: Depleted


title: 8-10h_Repo-pos_2

description:
processed data file:
DESeq2_8-10h_Repo.csv.gz

value: 8-10h AEL


title: 18-22h_Elav-pos_2

description:
processed data file:
DESeq2_18-22h_Elav.csv.gz

value: Elav

value: Embryonic neurons


title: Cyto_18-22h_1


title: Cyto_6-8h_1


title: 18-22h_Repo-pos_2


title: 8-10h_Repo-neg_2


title: 8-10h_Repo-neg_1


title: U2O2_siNEAT1

value: Osteosarcoma cells


title: Whole_6-8h_2


title: 18-22h_Repo-neg_1


title: 8-10h_Elav-pos_2

description:
processed data file:
DESeq2_8-10h_Elav.csv.gz

value: yw


title: 8-10h_Elav-neg_1

value: yellow-white


title: Cyto_6-8h_2

value: y1 w1118 ; M{3x rho-lexA:Cit}ZH-51C ; P{vnd:FNLDD}


title: 6-8h_Repo-neg_1

description:
processed data file:
DESeq2_6-8h_Repo.csv.gz

value: 6-8h AEL


title: 18-22h_Elav-neg_2


title: 18-22h_Elav-pos_1


title: 6-8h_Elav-neg_2

description:
processed data file:
DESeq2_6-8h_Elav.csv.gz


title: 18-22h_Elav-neg_1


title: 8-10h_Repo-pos_1


title: 6-8h_Pros-pos_1

description:
processed data file:
DESeq2_6-8h_Pros.csv.gz

value: Prospero

value: Embryonic neuroblasts


title: 6-8h_Pros-pos_2


title: 6-8h_Repo_pos_2


title: 6-8h_Repo_pos_1


title: 8-10h_Elav-neg_2


title: 6-8h_Vnd-pos_2

description:
processed data file:
DESeq2_6-8h_Vnd.csv.gz

value: Ventral column


title: 6-8h_Repo-neg_2


title: 6-8h_Elav-pos_2


title: 6-8h_Ind-neg_1

description:
processed data file:
DESeq2_6-8h_Ind.csv.gz

value: Intermediate column


title: 6-8h_Elav-pos_1


title: 6-8h_Elav-neg_1


title: 6-8h_Pros-neg_2

value: y1 w1118 ; M{3x vnd-lexA:Cit}ZH-51C ; P{vnd:FNLDD}


title: 4-6h_Pros-neg_2

description:
processed data file:
DESeq2_4-6h_Pros.csv.gz

value: 4-6h AEL


title: 6-8h_Vnd-neg_2


title: 6-8h_Pros-neg_1


title: 6-8h_Ind-neg_2


title: 8-10h_Elav-pos_1

value: Enriched


title: 4-6h_Pros-pos_1


title: 6-8h_Vnd-neg_1


title: 4-6h_Pros-neg_1


title: 4-6h_Vnd-pos_2

description:
processed data file:
DESeq2_4-6h_Vnd.csv.gz


title: JARID2 KO rep1 Day 0

city: Liverpool

first: Aditi

last: Kanhere

address: Institute of Systems, Molecular and Integrative Biology

country: United Kingdom

institute: University of Liverpool

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat v2.0.9 with parameters -p 8  -q 2
Reads Per Kilobase of exon per Megabase of library size (RPKM) and differential expression were calculated against ensemble gene annotations using cuffdiff program with default options and masking repeats.
Genome_build: hg19
Supplementary_files_format_and_content: Cuffdiff output; Differential expression

source_name: JARID2 KO_Day 0

extract_protocol:
At harvesting time, total RNA was extracted from cultured cells using RNeasy Mini Kit (Qiagen, Germany), treated with Amplification Grade DNase I (sigma) to remove genomic DNA and quantified by NanoDrop. The quality of RNA was checked using Agilent's Tapestation.
RNA libraries were prepared for sequencing using standard Illumina protocols using TruSeq®  Stranded mRNA Library Prep Kit for NeoPrep™

value: HaCaT

value: keratinocytes

tag: genotype/variation

value: JARID2 -/-

tag: day of differentiation

value: Day 0


title: JARID2 KO rep2 Day 0


title: Adv-EV

city: Shanghai

first: Daping

last: Yang

address: No.320 Yueyang Road, Xuhui District

institute: SIBS

description: total RNA

data_processing:
Bowtie2 was used to  map clean reads to reference gene. Bowtie2 parameters forPE reads:-q--phred64--sensitive--dpad0--gbar99999999--mp1,1--np1--score-minL,0,-0.1-I1-X1000--no-mixed--no-discordant -p  16-k 200  Bowtie2 parameters forSE reads:-q--phred64--sensitive--dpad0--gbar99999999--mp1,1--np1--score-minL,0,-0.1-p16-k 200
HISAT was used to map clean reads to reference genome.HISAT parameters forPE reads:-p8--phred64--sensitive--no-discordant--no-mixed-I1-X1000  HISTAparameters forSE reads:-p8--phred64--sensitive-I1-X 1000
FPKM method is used in calculated expression level.
Genome_build: mm10

source_name: Lung

growth_protocol: All mice were maintained in specific-pathogen-free (SPF) facility without cohousing

extract_protocol:
Mice were euthanized and lung tissues were removed for RNA collection
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Two groups of mice were intranasally injected with adenovirus Adv-EV or Adv-IL-17B for three days.

tag: tissue

value: Lung

tag: age

value: 6-8 weeks

value: wild type


title: 6-8h_Ind-pos_2

value: yellow-white

tag: developmental stage


title: WT rep1 Day 3

source_name: WT_Day 3

tag: cell type

value: Day 3


title: 4-6h_Vnd-neg_2

value: Depleted


title: 4-6h_Ind-pos_2

description:
processed data file:
DESeq2_4-6h_Ind.csv.gz


title: 4-6h_Ind-pos_1


title: WT rep1 Day 0

source_name: WT_Day 0


title: 6-8h_Vnd-pos_1

value: 6-8h AEL


title: 4-6h_Vnd-pos_1


title: Adv-IL-17B

description: total RNA

tag: strain


title: 4-6h_Ind-neg_2


title: JARID2 KO rep1 Day 3

source_name: JARID2 KO_Day 3


title: BB608-STAT3

city: Cambridge

first: Harry

last: Rogoff

address: 640 Memorial Dr.

institute: Boston Biomedical, Inc.

description: STAT3 Analysis.txt

data_processing:
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq  500) are mapped to the genome using the BWA algorithm with default settings
Only reads that pass Illumina’s purity filter,  align with no more than 2 mismatches, and map uniquely to the genome are used in the  subsequent analysis
Intervals (Peaks) were determined using the MACS peak finding algorithm (see Zhang et al., Genome Biology  2008, 9:R137). Using our default cutoff of p-value = 1e-7,
the tag number of all samples is reduced (by random  sampling) to the number of tags present in the smallest sample.
Genome_build: hg19
Supplementary_files_format_and_content: STAT1 Analysis.txt, STAT3 Analysis.txt

source_name: FaDu Cells

growth_protocol: FaDu cells were maintained in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum and 1% pennicillyn/streptomycin.

extract_protocol:
ChIP-IT® ChIP-Seq Kit (Active Motif) was used for chromatin preparation and ChIP using antibodies for STAT1 (Santa Cruz sc-345) or STAT3 (Santa Cruz sc-482).
ChIP-IT® ChIP-Seq Kit (Active Motif) was used for library construction.

treatment_protocol: FaDu cells were treated with DMSO or 1 uM BB608 for 2 hours. 15 min prior to harvest, cells were stimulated with 20 ng/ml OSM for the STAT3 ChIP samples, or with 20 ng/ml IFN-gamma for the STAT1 samples.

value: HNSCC cell line FaDu

tag: treatment

tag: chip antibody

value: STAT3 (Santa Cruz sc-482)


title: 6-8h_Ind-pos_1

value: Intermediate column


title: BB608-3

data_processing:
RNA-Seq reads were mapped and aligned using Tophat (v2.0.11)
Aligned results were assambled using Cufflinks (v2.2.1) and fragment bias correction performed (Kasper et al,2010 and Adam et al., 2011)
Cuffdiff was used for group comparison and to calculate the FPKM
Post processing of Cufflinks and Cuffdiff was performed by using CummeRbund for data visualization
Genome_build: hg19

extract_protocol:
Trizol
library preparation was done using Illumina TruSeq Stranded Total RNA (with Ribo-Zero Gold) preparation kit

tag: cell line

value: HNSCC


title: BB608-1


title: BB608-2


title: Pooled Input

value: none (input)


title: WT rep2 Day 3


title: WT rep2 Day 0


title: BB608-STAT1

description: STAT1 Analysis.txt

value: STAT1 (Santa Cruz sc-345)


title: 4-6h_Pros-pos_2

tag: fly line

value: y1 w1118 ; M{3x vnd-lexA:Cit}ZH-51C ; P{vnd:FNLDD}

value: 4-6h AEL

value: Prospero

value: Enriched

value: Embryonic neuroblasts


title: DMSO-STAT3

description: STAT3 Analysis.txt

value: DMSO


title: JARID2 KO rep2 Day 3

value: HaCaT

value: keratinocytes

value: JARID2 -/-


title: DMSO-3


title: DMSO-1


title: HEK293T cells transfected with hCLE-TAP plasmid REP2

status: Public on Feb 18 2019

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description:
CLE-2 norm
Processed data file: normalized_counts.txt

data_processing:
Quality checking: Raw reads, in FASTQ format, were quality checked with FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). No additional filters were needed.
Alignment: Single-end reads were aligned against human genome (primary_assembly, Ensembl release 84) with Bowtie2 with default parameters for single-end reads.
Gene quantification: Aligned reads were assigned to human genes with function htseq-count of HTSeq package using default parameters for single-end, strand specific sequences (reverse), and using full genes as features (Ensembl annotation version GRCh84.p5).
Data normalization: As part of the differential expression analysis procedure, read counts were normalized using the function stimateSizeFactors of DESeq2 bioconductor package.
Genome_build: GRCh38.p5
Supplementary_files_format_and_content: normalized_counts.txt: Normalized read gene counts as generated by DESeq2 package (linear scale). One column per sample and replicate. Text-tabulated file.

source_name: HEK293T cells, hCLE-TAP

extract_protocol:
After treatment, phenol-chloroform extraction was performed, followed by isopropanol precipitation. Precipitated RNAs were resuspended in DEPC-treated water before incubation with DNase I (Ambion) following supplier’s recommendations. Another phenol-chloroform extraction was performed for eliminating DNase I and isopropanol-precipitated RNAs were resuspended as before.
A similar number of hCLE-TAP or TAP expressing cells was used for HT-Sequencing, performed with TruSeq v3 chemistry and 50 bp single reads on an Illumina HiSeq 2000.

treatment_protocol: HEK293T cells were transfected with hCLE-TAP plasmid (pC-hCLE-TAP) or empty TAP (pC-TAP) as a control. TAP purification procedure was performed as explained before (Perez-Gonzalez et al., 2014) in RNA preserving conditions until the tobacco etch virus protease (TEV) cleavage step. After TEV (Invitrogen) treatment, eluted proteins were treated with Proteinase K (Sigma) following supplier's indications.

tag: plasmid

value: hCLE-TAP


title: DMSO-2


title: 3206-CJS-1

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

data_processing:
quality trimming with Trimmomatic v0.33, resulting in read length of 25-51bp
alignment with STAR v 2.4.0, controlling for unannotated, non-canonical and rare junctions
raw counts generated using count function from GFOLDv1.1.4, using default parameters
Genome_build: Bos taurus genome build UMD3.1
Supplementary_files_format_and_content: txt files, raw counts from GFold v 1.1.4 count function

organism: Bos taurus

source_name: seminiferous tubule

extract_protocol:
Testes were removed, sections of seminiferous tubules removed and flash frozen. RNA was harvested using a Qiagen RNEasy kit with 1 ug of total RNA used for the construction of the sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 3 month

value: seminiferous tubule


title: 3206-CJS-3

value: 9 month


title: HEK293T cells transfected with empty TAP (pC-TAP) as control REP2

description:
TAP-2 norm
Processed data file: normalized_counts.txt

source_name: HEK293T cells, empty TAP

value: pC-TAP


title: HEK293T cells transfected with hCLE-TAP plasmid REP1

description:
CLE-1 norm
Processed data file: normalized_counts.txt


title: DMSO-STAT1

description: STAT1 Analysis.txt

value: HNSCC cell line FaDu


title: dSG KO-ifetroban_1

description: sample name: 3686-JW-8

data_processing:
alignment with STAR v 2.5.2b, controlling for unannotated, non-canonical and rare junctions
read count generation during STAR alignment using –quantmode GeneCounts option that works like HTSeq-Count in default mode
Genome_build: GRCm38
Supplementary_files_format_and_content: txt files, raw read counts output from STAR alignment using option -–quantmode GeneCounts

source_name: Left ventricle

extract_protocol:
RNA was extracted from mice left ventricle with a Qiagen RNEasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: dSG Knockout Mutant

tag: drug treatment status

value: Ifetroban treated

value: Left ventricle


title: dSG KO-ifetroban_3

description: sample name: 3686-JW-10


title: HEK293T cells transfected with empty TAP (pC-TAP) as control REP1

description:
TAP-1 norm
Processed data file: normalized_counts.txt


title: dSG KO-vehicle_1

description: sample name: 3686-JW-6

value: Vehicle treated


title: WT-ifetroban_2

description: sample name: 3686-JW-4

value: Wild type


title: WT-ifetroban_1

description: sample name: 3686-JW-3


title: WT-vehicle _2

description: sample name: 3686-JW-2


title: dSG KO-ifetroban_2

description: sample name: 3686-JW-9


title: WT-vehicle_1

description: sample name: 3686-JW-1


title: ROSA 4

source_name: adipocytes

extract_protocol:
RNA was extracted from mice adipocytes with a Qiagen RNEasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ROSA


title: BMPR2 DELX 4

value: BMPR2 DELX


title: ROSA 2


title: BMPR2 DELX 3


title: BMPR2 DELX 2


title: ROSA 3


title: KCNK3 KO (UBC) [3441-SG7]

description: gender: F,F,M

data_processing:
alignment with STAR v 2.5.1b, controlling for unannotated, non-canonical and rare junctions
read count generation during STAR alignment using –quantmode GeneCounts option that works like HTSeq-Count in default mode
Genome_build: Mus musculus GRCm38.p4
Supplementary_files_format_and_content: txt files, raw read counts output from STAR alignment using option -–quantmode GeneCounts

extract_protocol:
RNA was extracted from mice kidneys with a Qiagen RNEasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: pooled male and female

value: KCNK3 KO (UBC)

value: Hypoxic


title: KCNK3 KO (UBC) [3441-SG8]

description: gender: M,M,F


title: KCNK3 [3441-SG6]

description: gender: M,M,F

value: Control (no UBC, but floxed KCNK3)


title: ROSA 1


title: dSG KO-vehicle_2

description: sample name: 3686-JW-7


title: BMPR2 DELX 1


title: KCNK3 [3441-SG5]

description: gender: M,M,F


title: 4-6h_Vnd-neg_1

tag: genetic background

value: yellow-white

value: 4-6h AEL

tag: marker

tag: marker enriched/depleted

value: Depleted

value: Ventral column


title: MSX1 HYP [3441-SG4]

description: gender: M, M

value: male

value: Control (Rosa)

value: Sugen-Hypoxic


title: MSX1 NOR [3441-SG2]

description: gender: F, M, M

value: Normoxic


title: MSX1 HYP [3441-SG3]

description: gender: M, M


title: MSX1 NOR [3441-SG1]

description: gender: F, F, F

value: female


title: 4-6h_Ind-neg_1

tag: tissue/cell type

value: Intermediate column


title: Delx4 males

description: flash frozen kidney from 3 mice pooled

data_processing:
alignment with STAR v 2.5.1b, controlling for unannotated, non-canonical and rare junctions
read count generation during STAR alignment using –quantmode GeneCounts option that works like HTSeq-Count in default mode
Genome_build: Bos taurus genome build UMD3.1
Supplementary_files_format_and_content: txt files, raw read counts output from STAR alignment using option -–quantmode GeneCounts

source_name: Kidney

extract_protocol:
RNA was harvested using a Qiagen RNEasy kit with 1 ug of total RNA used for the construction of the sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols for stranded libraries

tag: bmpr2 mutationtype

value: Control


title: R899X + 16OHE females

description: flash frozen kidney from 3 mice pooled

value: Estrogen


title: R899X males

description: flash frozen kidney from 3 mice pooled


title: Rosa + 16OHE males

description: flash frozen kidney from 3 mice pooled

value: Rosa


title: Rosa females

description: flash frozen kidney from 3 mice pooled


title: Rosa + 16OHE females

description: flash frozen kidney from 3 mice pooled


title: Delx4 females

description: flash frozen kidney from 3 mice pooled


title: 3413-ARH-30

data_processing:
alignment with STAR v 2.5.1b, controlling for unannotated, non-canonical and rare junctions
read count generation during STAR alignment using –quantmode GeneCounts option that works like HTSeq-Count in default mode
Genome_build: GRCh38.84
Supplementary_files_format_and_content: txt files, raw read counts output from STAR alignment using option -–quantmode GeneCounts

source_name: aorta

tag: sample type

value: Aorta


title: 3413-ARH-23

source_name: pulmonary artery

value: PAH


title: 3413-ARH-20


title: 3413-ARH-27

value: CTEPH


title: 3413-ARH-26


title: R899X females

description: flash frozen kidney from 3 mice pooled


title: 3413-ARH-15


title: 3413-ARH-16


title: 3413-ARH-18


title: 3413-ARH-13


title: 3413-ARH-21


title: R899X + 16OHE males

description: flash frozen kidney from 3 mice pooled


title: Copper supplementation 4

description: blood pooled from three individuals

source_name: Blood

tag: copper levels in blood (avg for 3 individuals)


title: Control 5

description: blood pooled from three individuals


title: Copper supplementation 5

description: blood pooled from three individuals


title: Copper supplementation 2

description: blood pooled from three individuals


title: Copper supplementation 1

description: blood pooled from three individuals


title: Control 4

description: blood pooled from three individuals


title: 3413-ARH-25


title: Control 2

description: blood pooled from three individuals


title: Control 3

description: blood pooled from three individuals


title: Control 1

description: blood pooled from three individuals