title: MYC-OE rep 2

first: Kevin Fongching

last: Chau

address: Enders Building. Room 1150, 300 Longwood Avenue

institute: Boston Children's Hospital

description:
WTvsOE_Cuffdiff_gene_exp.xlsx
Sample 9

data_processing:
Mapping to mouse reference genome using TopHat v2
fragments per kilobase per million reads (FPKM) values were estimated using cufflinks v2
differentially expressed genes (DEG) were identified using cuffdiff v2
Genome_build: Samples 1-4: mm9; samples 5-10: mm10
Supplementary_files_format_and_content: Excel, Cuffdiff output showing FPKM values, fold change and differential expression analysis

source_name: Sorted Pax6+ cortical neural progenitors

extract_protocol:
Samples 1 - 4: The forebrain epithelium from E8.5 and E10.5 embryos was dissected as described (Chau et al.,2015). Samples 5 - 10: E13.5 brains were bisected in half, and the dorsal telencephalon was then microdissected, avoiding the lateral ganglionic eminence and structures ventral to it. The cortex was then separatedfrom the meninges. Pax6+ neural progenitors were isolated by FACS
Samples 1 - 4: Total RNA was isolated using the RNeasy Micro Kit (Qiagen) and converted to cDNA and preamplified using the Ovation RNA-seq System V2 (NuGEN) following the manufacturer’s instructions. cDNA was converted to Illumina paired-end sequencing libraries following the standard protocol (TruSeq v2). Samples 5 - 10: RNA was extracted from sorted neural progenitors using RecoverAll Total Nucleic Acid Isolation Kit (Ambion), then reverse transcribed into cDNA and preamplified using Ovation RNA-Seq System V2 (Nugen 7102). Library was prepared using Ovation Ultralow System V2 1-16 (Nugen 0344)

value: Embryonic Day 13.5

value: Nes-cre + / StopFLMYC +/-

value: Pax6+ cortical neural progenitors

tag: overexpression

value: MYC


title: MYC-OE rep 3

status: Public on May 10 2018

type: SRA

city: Boston

state: MA

country: USA

description:
WTvsOE_Cuffdiff_gene_exp.xlsx
Sample 10

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: age

tag: strain

tag: genotype/variation

tag: cell type


title: WT rep 3

description:
WTvsOE_Cuffdiff_gene_exp.xlsx
Sample 7

value: Nes-cre - / StopFLMYC +/-

value: control


title: K4KO_peritoneal macrophage 2

city: Cleveland

first: Mukesh

last: Jain

state: OH

address: 2103 Cornell Rd

institute: Case Western Reserve University

data_processing:
Software for the Illumina HiSeq 2500 was used for basecalling. 100bp paired-end sequencing performed
Reads from each sample were aligned to the mouse genome (UCSC mm10) using TopHat2 (Kim et al., 2013).
Macrophage gene expression was quantitated as fragments per kilobase of transcript per million mapped reads (FPKM) using Cufflinks (Trapnell et al., 2010). A total of 1,465 differentially expressed genes (DEGs) were identified and were defined as genes having FPKM>2, absolute log2 fold change >0.35, and an adjusted p-value cutoff q <0.05
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes table of FPKM values for each sample

source_name: KO_peritoneal macrophage

growth_protocol: Mice were injected intraperitoneally with thioglycolate. 72 hours later, cells were isolated from the peritoneum. Cells were then plated in DMEM media containing 10% fetal bovine serum and 1% PenStrep + Glutamine. Cells were incubated for 24 hours at 5% CO2 and 37 degrees until harvesting cells for RNA.

extract_protocol:
RNA isolation was performed using the RNeasy kit (Qiagen, Hilden, Germany). cDNA sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA kit (poly A selection)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: myeloid-specific KLF4 knockout (K4KO)

value: peritoneal macrophage


title: WT rep 1

description:
WTvsOE_Cuffdiff_gene_exp.xlsx
Sample 5


title: WT rep 2

description:
WTvsOE_Cuffdiff_gene_exp.xlsx
Sample 6


title: Vian-2018-HIC233

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

library_source: genomic

data_processing:
The paired end reads were aligned separately using BWA against the mm9 mouse build or the b37 human build
PCR duplicates, low mapping quality and unligated reads were removed using Juicer (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
Contact matrices were constructed at various resolutions and normalized using Juicer (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
loops were annotated using HiCCUPS (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016), domains were annotated using Arrowhead (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
Genome_build: mm9 (mouse), b37 (human)
Supplementary_files_format_and_content: .hic file (contains contact matrices at various resolutions in an easy to visualize and access format) (see Durand, Robinson, et al Cell Systems 2016)

molecule: genomic DNA

organism: Homo sapiens

source_name: Colorectal carcinoma

extract_protocol:
Cells were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads.
standard Illumina library construction protocol, Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeqX Ten, NextSeq 500, or HiSeq 2500 following the manufacturer's protocols

tag: genotype

tag: cell line

tag: protocol

value: in situ Hi-C

tag: treatment

value: 6 hours 500uM IAA, 24 hour withdraw; 1 hour 300nM flavopiridol


title: Vian-2018-HIC047

source_name: B-lymhoblastoids


title: Vian-2018-HIC232


title: Vian-2018-HIC228

value: 6 hours 500uM IAA, 60 min withdraw; 1 hour 300nM flavopiridol


title: Vian-2018-HIC223

value: 6 hours 500uM IAA; 1 hour 300nM flavopiridol


title: Vian-2018-HIC229


title: Vian-2018-HIC230

value: 6 hours 500uM IAA, 180 min withdraw; 1 hour 300nM flavopiridol


title: Vian-2018-HIC224

value: 6 hours 500uM IAA, 20 min withdraw; 1 hour 300nM flavopiridol


title: Vian-2018-HIC222


title: Vian-2018-HIC217

value: 6 hours 500uM IAA, 24 hour withdraw; 6 hours 300nM flavopiridol


title: Vian-2018-HIC221

value: no IAA; 1 hour 300nM flavopiridol


title: Vian-2018-HIC218


title: Vian-2018-HIC231


title: MYC-OE rep 1

description:
WTvsOE_Cuffdiff_gene_exp.xlsx
Sample 8


title: Vian-2018-HIC216


title: Vian-2018-HIC220


title: Vian-2018-HIC212

value: 6 hours 500uM IAA, 180 min withdraw; 6 hours 300nM flavopiridol


title: Vian-2018-HIC211

value: 6 hours 500uM IAA, 60 min withdraw; 6 hours 300nM flavopiridol


title: Vian-2018-HIC214


title: Vian-2018-HIC219


title: Vian-2018-HIC213


title: Vian-2018-HIC210


title: Vian-2018-HIC209


title: Vian-2018-HIC215


title: Vian-2018-HIC208


title: Vian-2018-HIC227

value: 6 hours 500uM IAA, 40 min withdraw; 1 hour 300nM flavopiridol


title: Vian-2018-HIC225


title: Vian-2018-HIC206

value: 6 hours 500uM IAA, 40 min withdraw; 6 hours 300nM flavopiridol


title: Vian-2018-HIC226


title: Vian-2018-HIC203

value: 6 hours 500uM IAA, 20 min withdraw; 6 hours 300nM flavopiridol


title: Vian-2018-HIC204


title: Vian-2018-HIC201


title: Vian-2018-HIC202


title: Vian-2018-HIC198

value: 6 hours 500uM IAA; 6 hours 300nM flavopiridol


title: Vian-2018-HIC197


title: Vian-2018-HIC199


title: Vian-2018-HIC195

value: 6 hours 500uM IAA, 24 hour withdraw; 30 min 5mM 2DG, 0.1uM oligomycin


title: Vian-2018-HIC200


title: Vian-2018-HIC194


title: Vian-2018-HIC193

value: 6 hours 500uM IAA, 180 min withdraw; 30 min 5mM 2DG, 0.1uM oligomycin


title: Vian-2018-HIC186

value: 6 hours 500uM IAA, 20 min withdraw; 30 min 5mM 2DG, 0.1uM oligomycin


title: Vian-2018-HIC191

value: in situ Hi-C

value: 6 hours 500uM IAA, 60 min withdraw; 30 min 5mM 2DG, 0.1uM oligomycin


title: Vian-2018-HIC192


title: Vian-2018-HIC190


title: Vian-2018-HIC189

value: 6 hours 500uM IAA, 40 min withdraw; 30 min 5mM 2DG, 0.1uM oligomycin


title: Vian-2018-HIC181

value: 6 hours 500uM IAA, 17 hour withdraw; 2 hours 5mM 2DG, 0.1uM oligomycin


title: Vian-2018-HIC205


title: Vian-2018-HIC182

value: no IAA; 30 min 5mM 2DG, 0.1uM oligomycin


title: Vian-2018-HIC179


title: Vian-2018-HIC185

value: 6 hours 500uM IAA; 30 min 5mM 2DG, 0.1uM oligomycin


title: Vian-2018-HIC188


title: Vian-2018-HIC180


title: Vian-2018-HIC183


title: Vian-2018-HIC187


title: Vian-2018-HIC176

value: 6 hours 500uM IAA, 180 min withdraw; 2 hours 5mM 2DG, 0.1uM oligomycin


title: Vian-2018-HIC196


title: Vian-2018-HIC175


title: Vian-2018-HIC177


title: Vian-2018-HIC174


title: Vian-2018-HIC170

value: 6 hours 500uM IAA, 60 min withdraw; 2 hours 5mM 2DG, 0.1uM oligomycin


title: Vian-2018-HIC173


title: Vian-2018-HIC168

value: 6 hours 500uM IAA, 40 min withdraw; 2 hours 5mM 2DG, 0.1uM oligomycin


title: Vian-2018-HIC167


title: Vian-2018-HIC184


title: Vian-2018-HIC169


title: Vian-2018-HIC165

value: 6 hours 500uM IAA, 20 min withdraw; 2 hours 5mM 2DG, 0.1uM oligomycin


title: Vian-2018-HIC164


title: Vian-2018-HIC161

value: 6 hours 500uM IAA; 2 hours 5mM 2DG, 0.1uM oligomycin


title: Vian-2018-HIC160


title: Vian-2018-HIC162


title: Vian-2018-HIC159


title: Vian-2018-HIC158


title: Vian-2018-HIC156

value: no IAA; 2 hours 5mM 2DG, 0.1uM oligomycin


title: Vian-2018-HIC154


title: Vian-2018-HIC178


title: Vian-2018-HIC153

value: 6 hours 500uM IAA, 24 hour withdraw; 18hr 2mM thymidine


title: Vian-2018-HIC155


title: Vian-2018-HIC152


title: Vian-2018-HIC172


title: Vian-2018-HIC149

value: 6 hours 500uM IAA, 60 min withdraw; 18hr 2mM thymidine


title: Vian-2018-HIC171


title: Vian-2018-HIC166


title: Vian-2018-HIC148


title: Vian-2018-HIC147

value: 6 hours 500uM IAA, 40 min withdraw; 18hr 2mM thymidine


title: Vian-2018-HIC207

value: 6 hours 500uM IAA, 40 min withdraw; 6 hours 300nM flavopiridol


title: Vian-2018-HIC144

value: 6 hours 500uM IAA, 20 min withdraw; 18hr 2mM thymidine


title: Vian-2018-HIC143

value: in situ Hi-C

value: 6 hours 500uM IAA; 18hr 2mM thymidine


title: Vian-2018-HIC146


title: Vian-2018-HIC142


title: Vian-2018-HIC145


title: Vian-2018-HIC163


title: Vian-2018-HIC141

value: no IAA; 18hr 2mM thymidine


title: Vian-2018-HIC139

value: 6 hours 500uM IAA followed by 24 hours IAA withdrawal


title: Vian-2018-HIC138


title: Vian-2018-HIC140


title: Vian-2018-HIC136


title: Vian-2018-HIC137


title: Vian-2018-HIC157


title: Vian-2018-HIC150

value: 6 hours 500uM IAA, 180 min withdraw; 18hr 2mM thymidine


title: Vian-2018-HIC151


title: Vian-2018-HIC134

value: 6 hours 500uM IAA followed by 20 hours IAA withdrawal


title: Vian-2018-HIC135


title: Vian-2018-HIC133

value: 6 hours 500uM IAA followed by 17 hours IAA withdrawal


title: Vian-2018-HIC132


title: Vian-2018-HIC128

value: 6 hours 500uM IAA followed by 180 min IAA withdrawal


title: Vian-2018-HIC126


title: Vian-2018-HIC127


title: Vian-2018-HIC124


title: Vian-2018-HIC129


title: Vian-2018-HIC123


title: Vian-2018-HIC119

value: 6 hours 500uM IAA followed by 60 min IAA withdrawal


title: Vian-2018-HIC042


title: Vian-2018-HIC122


title: Vian-2018-HIC118


title: Vian-2018-HIC120


title: Vian-2018-HIC121


title: Vian-2018-HIC116


title: Vian-2018-HIC113


title: Vian-2018-HIC114


title: Vian-2018-HIC112


title: Vian-2018-HIC131


title: Vian-2018-HIC117


title: Vian-2018-HIC110


title: Vian-2018-HIC108

value: 6 hours 500uM IAA followed by 40 min IAA withdrawal


title: Vian-2018-HIC111


title: Vian-2018-HIC106


title: Colorectal tissue Cancer 75

city: Rochester

first: Wilson

last: Wu

state: MN

address: 200 First Street SW

department: Gastroenterology and Hepatology

institute: Mayo Clinic

description: small RNA

data_processing:
Initial analysis was performed using the CAP-miRSeq pipeline (http://bioinformaticstools.mayo.edu/research/cap-mirseq/). Briefly, the reads were trimmed of the 3' NEB Next small RNA adapters with Cutadapt. Mature miRNA were quantified using mirdeep2 by aligning reads to the human mirbase v19 mature miRNA sequences.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delemited text file containing raw read counts for each human mirbase v19 mature miRNA.

source_name: Colorectal tissue

extract_protocol:
Total RNA was extracted using RecoverAll Total Nucleic Acid Isolation Kit for FFPE (Thermo Fisher Scientific, MA, USA).
Five hundred nano-gram RNA per sample was used to prepare small RNA libraries using NEBNext® Small RNA Library Prep Set following manufacturer’s guide (New England Biolabs, MA, USA). Number of cycle for PCR enrichment was adjusted based on initial library amount quantified by qPCR. Up to 24 different libraries were indexed and pooled in a single sequencing lane in a randomized fashion. The libraries were sequenced at 50 bp single-read mode on an Illumina HiSeq 2000 sequencing system (Illumina, CA, USA).

tag: pathology

value: Cancer


title: Vian-2018-HIC109


title: Vian-2018-HIC125


title: Vian-2018-HIC104


title: Vian-2018-HIC105


title: Vian-2018-HIC100


title: Vian-2018-HIC099

value: 6 hours 500uM IAA followed by 20 min IAA withdrawal


title: Vian-2018-HIC101


title: Vian-2018-HIC096


title: Vian-2018-HIC098


title: Vian-2018-HIC107


title: Vian-2018-HIC095


title: Vian-2018-HIC094


title: Vian-2018-HIC093


title: Vian-2018-HIC090


title: Vian-2018-HIC092


title: Vian-2018-HIC087

value: 6 hours 500uM IAA


title: Vian-2018-HIC088


title: Vian-2018-HIC089


title: Vian-2018-HIC102


title: Vian-2018-HIC085


title: Vian-2018-HIC084


title: Vian-2018-HIC103


title: Vian-2018-HIC082


title: Vian-2018-HIC083


title: Vian-2018-HIC080


title: Vian-2018-HIC081


title: Vian-2018-HIC078


title: Vian-2018-HIC097


title: Vian-2018-HIC076


title: Vian-2018-HIC074


title: Vian-2018-HIC077


title: Vian-2018-HIC091


title: Vian-2018-HIC075


title: Vian-2018-HIC072


title: Vian-2018-HIC071


title: Vian-2018-HIC069


title: Vian-2018-HIC068


title: Vian-2018-HIC070


title: Vian-2018-HIC115


title: Vian-2018-HIC066


title: Vian-2018-HIC067


title: KO 6h_2

city: Pohang

first: Gi-Cheon

middle: careful

last: Kim

state: Hyoja-dong Namgu

address: POSTECH, postech biotech center Rm 430, Hyoja-dong Namgu, pohang

country: South Korea

institute: IBS

data_processing:
QC/adapter sequence trimming for raw FASTQ sequences  Raw read quality evaluation by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc ) with default options.  Adapter sequence trimming by CutAdapt (https://pypi.python.org/pypi/cutadapt)
Mapping on mouse reference genome  By TopHat2 (http://tophat.cbcb.umd.edu) and bowtie2 (http://bowtie-bio.sourceforge.net)
Expression and DEG analysis  Expression analysis by CuffLinks (http://cufflinks.cbcb.umd.edu) with default options[4].  DEG analysis by CuffDiff (http://cufflinks.cbcb.umd.edu) with significance thresholds as FDR<0.05, p<0.001, and p<0.01. Scatter plot and volcano plot by in-house R scripts. Unsupervised clustering by in-house R scripts
Genome_build: Human hg 19

source_name: MDA-MB-231 cells (CRE deletion)

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with Ribospin II RNA purification kit (GeneAll, Korea)
TruSeq Stranded mRNA Sample Preparation Protocol (Illumina)

value: KO (CRE deleted)

tag: treatment time point

value: 6 hr


title: KO 0h_2

value: 0 hr


title: KO 0h_1


title: KO 24h_2

value: 24 hr


title: KO 6h_1


title: WT 24h_1

source_name: MDA-MB-231 cells

value: wild type


title: Vian-2018-HIC086

value: in situ Hi-C


title: KO 24h_1


title: WT 0h_2


title: WT 24h_2


title: WT 6h_1


title: WT 6h_2


title: Vian-2018-HIC035

source_name: B cells

value: WT

value: splenic B cells isolated from 6-8 weeks old C57BL6/J mouse spleen by negative selection

value: activated for 24 hours with LPS (50 μg/mL; Sigma), IL-4 (2.5 ng/mL; Sigma), and anti-CD180 (RP105) antibody (0.5 μg/mL, BD PharMingen), treated for 4 hours with 1uM flavopiridol


title: Vian-2018-HIC073


title: Vian-2018-HIC034


title: Vian-2018-HIC032


title: 265-95

city: Chicago

first: Sidney

last: Wang

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

data_processing:
Sequencing image analysis and basecalling were performed using CASAVA version 1.7.0
Raw data provided are fastq files after the following processing. FASTX-Toolkit were used to clip the adaptor sequence and trim the 5' most base for each read. Reads that are shorter than 22-nt or that are mapped to rRNA, tRNA, snoRNA using bowtie were removed from the file.
Processed reads are then map to human genome (hg19) or chimpanzee genome (PanTro3) or rhesus macaque gemome (rheMac2) respectively using BWA. Uniquely mapped reads are used to intersect with orthologous gene annotations using BEDTools to get read count per gene for each individual.
Genome_build: hg19 or PanTro3 or rheMac2
Supplementary_files_format_and_content: Processed data file contains read count per orthologous gene for each individual. It is organized with one individual per column and one gene per row. The first two columns are ENSG ID and gene length.

molecule: cytoplasmic RNA

organism: Macaca mulatta

source_name: NEPRC

growth_protocol: Cells were cultured at 37 degree Celsius and 5% CO2 in RPMI 1640 (supplemented with 2mM L-glutamine and 15% fetal bovine serum)

extract_protocol:
Ribosome footprint profiling experiments were performed using ARTseqTM Ribosome Profiling kit for mammalian cells (RPHMR12126) following vendor’s instructions. Cell lysates were prepared from flash frozen pellets of 30 to 50 million live cells by repeat pipetting in 1 ml cold lysis buffer. Sephacryl S400 spin column (GE; 27-5140-01) was used for monosome isolation. For rRNA depletion, Ribo-Zero Magnetic Kit (Epicentre; MRZH11124) was used.
Ribosome footprint cDNA libraries were PCR amplified (12 to 15 thermo-cycles) and barcoded using ScriptMiner Index PCR Primers (Epicentre; SMIP2124). Indexed libraries were pooled to sequence on an Illumina HiSeq 2500.

tag: gender

value: Male

value: Lymphoblastoid Cell

tag: enrichment type

value: ribosome protected fragments


title: R290-96


title: R249-97


title: R181-96


title: 150-99

value: Female


title: Vian-2018-HIC033


title: Vian-2018-HIC031


title: Vian-2018-HIC029


title: Vian-2018-HIC028


title: Pt91

organism: Pan troglodytes

source_name: Arizona State University


title: Vian-2018-HIC026


title: Vian-2018-HIC027


title: WT 0h_1


title: Vian-2018-HIC025


title: GM19147 ribosome protected fragments

data_processing:
Sequencing image analysis and basecalling were performed using CASAVA version 1.7.0
Raw data provided are fastq files after the following processing. FASTX-Toolkit were used to clip the adaptor sequence and trim the 5' most base for each read. Reads that are shorter than 22-nt or that are mapped to rRNA, tRNA, snoRNA using bowtie were removed from the file.
For the supplement count-table, processed reads are then map to human genome (hg19) or chimpanzee genome (PanTro3) or rhesus macaque gemome (rheMac2) respectively using BWA. Uniquely mapped reads are used to intersect with orthologous gene annotations using BEDTools to get read count per gene for each individual.
Genome_build: hg19 or PanTro3 or rheMac2
Supplementary_files_format_and_content: Processed data file contains read count per orthologous gene for each individual. It is organized with one individual per column and one gene per row. The first two columns are ENSG ID and gene length.

source_name: HapMap

value: Lymphoblastoid Cell Line


title: NS04973

source_name: Coriell/IPBIR


title: Vian-2018-HIC024


title: Vian-2018-HIC023


title: NS03659


title: Min18359

source_name: New Iberia Research Center


title: Vian-2018-HIC030


title: Vian-2018-HIC022


title: Min18358


title: Day8 4Factors and SCG

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

description: RNA-seq

data_processing:
Basecalls performed using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
Sequence reads were aligned to the human genome (hg19) using TopHat2 software.
The sequenced short reads were trimmed by Trimmomatic 0.3.3 and mapped to the human reference genome hg19 using TopHat 2.0.14 and Bowtie 2.2.5.
RPKM counts for each gene were obtained using the RPKMforgenes software.
Genome_build: hg19
Supplementary_files_format_and_content: Calculation of gene expression value and normalization were performed by RPKMforgenes (10th, Dec, 2012). The processed data file contains Gene name, Refseq ID, RPKM, and Raw counts columns (from left to right), and the expression level was represented by RPKM.

source_name: differentiated hiPSC-derived PDX1+ PP cells

growth_protocol: 201B7 iPSC cells were grown on feeder layers of mitomycin C-treated SNL cells in media containing Primate ES medium (ReproCELL) supplemented with 500 U/ml penicillin/streptomycin (PS; Life Technologies) and 4 ng/ml recombinant human basic fibroblast growth factor (bFGF; Wako).

extract_protocol:
Total RNA was extracted with the RNeasy kit (Qiagen).
After the depletion of ribosomal RNA by RiboZero Gold (Epicentre), we prepared libraries using the Illumina TruSeq Stranded Total RNA Sample Prep kit. The libraries were sequenced in the HiSeq2500 set in the 101-cycle Single-Read mode.

treatment_protocol: In order to generate pancreatic lineage cells, hiPSC/ESC colonies grown on SNL feeder cells at 70% confluence were first dissociated using CTK dissociation solution and subsequently incubated on gelatin-coated plates for 30 minutes to remove SNL cells. The cells were then dissociated into single cells via gentle pipetting after treatment with Accutase (Innovative Cell Technologies, Inc.) for 20 minutes and seeded on Matrigel (BD Biosciences)-coated 24-well plates at a density of 2 × 105 cells/well. The induction protocol was based on a modified version of the previously described method (Hara M, Wang X, Kawamura T et al (2003) ). At Stage 1, the dissociated single hiPSCs/ESCs were treated with 1 μM CHIR99021 (Axon), 100 ng/ml activin A (R&D systems) and 10 μM ROCK inhibitor Y-27632 (Wako) in the Stage 1 medium containing RPMI1640 (Nacalai) supplemented with 2 × B27 supplements (Life Technologies) and 500 U/ml PS for 2 days, after which the medium was changed to the Stage 1 medium containing 1 μM CHIR99021 and 100 ng/ml activin A every day for an additional 3 days. At Stage 2, the cells were treated with 1 μM Dorsomorphin (Merck), 2 μM Retinoic Acid (Sigma) and 10 μM SB431542 (Cayman) in the Stage 2 medium containing Improved MEM Zinc Option medium (Life Technologies) supplemented with 2 × B27 supplements and 500 U/ml PS, after which the medium was changed every 2 days for a total of 6 days. At Stage 3, four chemical compounds (4Fs), 10 μM Forskolin (Wako), 10 μM Dexamethasone (Wako), 5 μM Alk5 inhibitor II (Wako) and 10 mM Nicotinamide (Stemcell Technologies), were used with or without sodium cromoglicate (Sigma) in the Stage 3 medium containing Improved MEM Zinc Option medium supplemented with 2 × B27 supplements and 500 U/ml PS, and the medium was changed every 4 days for a total of 8 days.

tag: agent

value: 4Factors and SCG


title: Day8 4Factors

description: RNA-seq

value: differentiated hiPSC-derived PDX1+ PP cells


title: E10.5 rep 1

description:
E8.5vsE10.5_Cuffdiff_gene_exp.xlsx
Sample 3

source_name: forebrain neuroepithelium

value: Embryonic Day 10.5

value: Wildtype

tag: tissue

value: forebrain neuroepithelium


title: E8.5 rep 2

description:
E8.5vsE10.5_Cuffdiff_gene_exp.xlsx
Sample 2

value: Embryonic Day 8.5


title: Day8 SCG

description: RNA-seq

value: SCG


title: UMSCC47_9_AzaTSA

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Read were aligned with TopHat v1.3.2. Command line options for Tophat were '-r 100' for RNA-Seq.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.0.2. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: UMSCC47, Aza/TSA

growth_protocol: FaDu and UMSCC47 were grown in RPMI-1640 with 10% FBS and penicillin-streptomycin  .

extract_protocol:
Total RNA was collected using RNeasy (Invitrogen, Carlsbad, CA)
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: UMSCC47 was exposed to 3 μM Aza or vehicle (DMSO), and FaDu was exposed to 5μM Aza or vehicle (DMSO), on days 1, 2, and 3. UMSCC47 was exposed to 300 nM TSA or vehicle (ethanol), and FADU was exposed to 100 nM TSA or vehicle (ethanol), on day 3.

value: head and neck cancer

tag: stimulation

value: Aza/TSA


title: FaDu_DMSO

source_name: FaDu, DMSO only

value: DMSO only

value: FaDu


title: FaDu_AzaTSA

source_name: FaDu, Aza/TSA


title: UMSCC47_1_DMSO

source_name: UMSCC47, DMSO only


title: E10.5 rep 2

description:
E8.5vsE10.5_Cuffdiff_gene_exp.xlsx
Sample 4


title: Day8 control

description: RNA-seq

value: control


title: GB1088

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

description: RNA-Seq

data_processing:
Basecalls performed using CASAVA 2.18
Sequence reads were mapped to mouse genome (mm9) by using bowtie 2 with default settings (PMID: 22388286 ). Reads mapped to multiple positions (MAPQ < 10) were discarded.
The mRNA expression level of a gene is quantified by RPKM (reads per kilo-base of exon model per million reads; PMID 18516045) with in-house script.
Genome_build: mm9
Supplementary_files_format_and_content: *rpkm.gz: zipped text file for gene expression. Columns from left to right denote RefSeq ID, RPKM, gene transcript size, number of read mapped to exons, a combination of RefSeq ID, gene symbol, etc, and reserved column for future development.

molecule: polyA RNA

extract_protocol:
The total RNAs were purified using Qiagen's miRNeasy micro kit (Qiagen cat# 217084). PolyA-tailed RNAs were purified from pure total RNA using Dynabeads® mRNA DIRECT™ Kit (ambion life technologies cat# 61012).
Library constructions RNA-Seq follow the protocols described previously in (PMID: 19528076)

value: lymph node

tag: condition

value: WT, stimulated


title: GB1087

description: RNA-Seq


title: E8.5 rep 1

description:
E8.5vsE10.5_Cuffdiff_gene_exp.xlsx
Sample 1

tag: age


title: GB1085

description: RNA-Seq

tag: strain

value: Bhlhe40 KO, stimulated


title: ssMG-02d-34

status: Public on May 09 2018

city: Campobasso

first: Valentino

last: Palombo

address: via Francesco De Sanctis

department: Dipartimento Agricoltura Ambiente e Alimenti

country: Italy

institute: Università degli Studi del Molise

data_processing:
Quality control metrics were performed on raw sequencing reads using the FASTQC (v0.11.15) application.
An index of the reference genome was built and single-end clean reads for each individual were aligned to the reference genome by STAR (v2.5.1b).
Reads aligned were quantified with Subread package (v1.5.0) based on the Refseq gene annotation (Sus scrofa genome v10.2.86).
Genome_build: Sus scrofa genome (v10.2.86).
Supplementary_files_format_and_content: Tab-delimited text files include data matrix containing read counts for each feature in each library obtained by featureCounts (Subread package). The data frame includes six columns:  GeneID, Chr, Start, End and Length.

organism: Sus scrofa

source_name: Sow mammary gland

extract_protocol:
Tissue was harvested and immediately frozen in liquid N2 and preserved at - 80°C until RNA extraction. Total RNA from 0.4 to 1.4 g of tissue was extracted with ice-cold Trizol reagent (Invitrogen, Carlsbad, CA). Tissue was weighed, placed in 10–15 ml of ice-cold TRIzol reagent, homogenized, and RNA extracted according to the manufacturer's protocol. RNA was resuspended in RNA storage buffer (Ambion, Austin, TX) and stored at −80°C until use. Quantity and purity of isolated RNA samples were analyzed with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). The RNA quality was assessed using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). The libraries were quantitated by qPCR and sequenced on two lanes for 101 cycles from one end of the fragments on a HiSeq2500 using a HiSeq SBS sequencing kit version 4. Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina). Adaptors have been trimmed from the reads with Trimmomatic (v0.33).

value: mammary gland

tag: time

value: (-) 2 days to parturition


title: ssMG-01d-43

value: (+) 1 day after parturition


title: Vian-2018-HIC021

value: WT

value: splenic B cells isolated from 6-8 weeks old C57BL6/J mouse spleen by negative selection

value: in situ Hi-C

value: activated for 24 hours with LPS (50 μg/mL; Sigma), IL-4 (2.5 ng/mL; Sigma), and anti-CD180 (RP105) antibody (0.5 μg/mL, BD PharMingen), treated for 4 hours with 1uM flavopiridol


title: ssMG-06d-22

value: (-) 6 days to parturition


title: ssMG-01d-37


title: ssMG-01d-40


title: ssMG-10d-16

value: (-) 10 days to parturition


title: GB1086

description: RNA-Seq

tag: cell type


title: Vian-2018-HIC079

source_name: Colorectal carcinoma


title: ssMG-06d-25


title: ssMG-02d-28


title: ssMG-02d-31


title: ssMG-06d-19


title: ssMG-10d-13


title: ssMG-10d-10


title: ssMG-14d-7

value: (-) 14 days to parturition


title: ssMG-14d-4


title: meis2b+_3

city: Bad Nauheim

first: Almary

middle: Victoria

last: Guerra Rodríguez

state: Hessen

address: Ludwigstrasse 43

department: Dept. III Developmental Genetics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Basecalls with RTA v2 (Illumina)
Trimmomatic version 0.33 was employed to trim reads after a quality drop below a mean of Q18 in a window of 5 nucleotides. Only reads above 30 nucleotides were cleared for further analyses.
Mapping: alignment versus the Ensembl Zebrafish genome version DanRer10 (GRCz10.87) using STAR 2.4.0a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package.  Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.62.  Only genes with a minimum fold change of +- 1.5 (log2 +-0.59), a maximum Benjamini-Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed.
Genome_build: DanRer10
Supplementary_files_format_and_content: library size normalized counts per sample

organism: Danio rerio

source_name: atrium

growth_protocol: Embryos and adult zebrafish were maintained and handled under standard conditions

extract_protocol:
The hearts were extracted and the atria dissected into the meis2b-positive and meis2b-negative halves.  RNA was isolated using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
Truseq Stranded mRNA Kit. Briefly, 50-100ng of RNA were used as input for Library preparation following the low sample protocol (Illumina). Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry, resulting in minimum of 27M reads per library with 2x75bp paired end setup.

value: heart

tag: atrial tissue region

value: meis2b-positive atrial domain

value: 3 mpf

tag: transgenic line

value: AB


title: meis2b+_1


title: meis2b-_3

value: meis2b-negative atrial domain


title: meis2b-_1


title: C3_7dpf_MU

city: Guangzhou

first: Shaoyang

last: Zhao

state: Guangdong

address: 190 Kaiyuan Avenue

country: China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
Illumina bcl2fastq (v1.8.4) software was used for base calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The number of raw reads mapped to genes was calculated by RSEM (rsem-1.2.4) and put all the sample results together and normalized by EDAseq(1.99.1).
Gene expression fold change was calculated using normalized raw reads
The downstream analysis was performed using glbase scripts
Genome_build: danRer10
Supplementary_files_format_and_content: text file with expected count, TPM and FPKM.

source_name: embryos

extract_protocol:
Total RNA from 3-5 embryos at the indicated stages were lysed in trizol and prepared using the RNA Clean & Concentrator Kit (R1019, Zymo Research).
cDNA library was constructed with the TruSeq RNA Sample Prep Kit (RS-122-2001, Illumina) and sequenced with the NextSeq 500/550 High Output Kit V2 (FC-404-2005, Illumina).

value: TU

tag: developmental stage

tag: genotype

value: pik3c3 KO

value: embryo


title: C3_7dpf_WT

value: wild type


title: C3_6dpf_MU


title: C3_6dpf_WT


title: hp_WT_9804

city: Gainesville

first: Kyle

middle: James

last: Lorentsen

state: FL

address: 1345 Center Drive, MSB M350

department: Medicine

institute: University of Florida

description: These cells are Bcl11b sufficient

data_processing:
Fastq files were trimmed using Seqtk
Trimmed fastq files were aligned to the mm10 genome via Hisat2
Raw counts were extracted from bam files using htseq
Differential analysis was performed on raw counts with DESeq2 using a multifactor design to control for sequencing type (single vs paired end)
Normalized counts were calculated with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: *.count files are pre-normalized count values for each sample generated by htseq.  Deseq2_norm_counts.csv is a normalized count matrix generated by DESeq2.  hp_rna.csv is the differential analysis file from DESeq2.

source_name: CD4+ T-cells

extract_protocol:
CD4+ T-cells were isolated from mesenteric lymph nodes by negative isolation (Invitrogen #11415D).  Cells were lysed and RNA was isolated using Qiagen Rneasy Plus Micro Kit (Qiagen #74034). RNA quality was determined on a bioanalyzer (Agilent RNA 6000 Nano #5067-1511)
Libraries were prepared at sequencing facilities by their staff (University of Rochester Medical Center, Genomic Research Center, Rochester, NY and University of Florida, Interdisciplinary Center for Biotechnology Research, Gainesville, NY)

value: Mesenteric Lymph Nodes

value: Wild Type


title: hp_Infected_WT_7677_Bcl11b_ChIP

description: These cells are Bcl11b sufficient

data_processing:
Fastq files prepared using Illumina FASTQ Generation application
Fastq files were trimmed using Trimmomatic
Reads were aligned to the mm10 genome using Bowtie2
Duplicate reads were removed using PicardTools
Peaks were called using Macs2
Genome_build: mm10
Supplementary_files_format_and_content: Wig files were generated from macs2 bedgraph outputfiles using kent bedGraphToBigWig utility.  Scores represent enrichment over CD4cre knock-out samples.

extract_protocol:
Isolated cells were fixed with 1% formaldehyde in PBS for 10 minutes, then quenched with glycine.  After washing, DNA was extracted using the Illumina SimpleChIP Enzymatic ChIP kit (#9003S). Briefly, nuclei were isolated by incubating in 1ml buffer A for 10 min on Ice, followed by centrifugation and resuspension in 1 ml Buffer B.  Chromatin was digested for 20 min at 37oC in 1 ml buffer B with 2 ul 1:10 diluted micrococcal nuclease.  Digestion was stopped with EDTA.  Nuclei were lysed by sonication, centrifuged to clear lysates, and the supernatant containing the DNA was transferred to a fresh tube for overnight antibody complexing.  Next day, protein A dynalbeads were added to each tube, incubated, washed, and isolated with magnet.  DNA complexes were then released from the beads, decrosslinked, and phenol:choloroform:isolamyl alcohol extracted for library prep.
DNA libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina.  Briefly, DNA ends were repaired, followed by ligation of adapter sequences.  DNA was cleaned with AMPure XP beads, and then DNA was PCR amplified with 7-8 cycles.  After final cleaup with AMPure XP Beads, libraries were quantified using Agilent Bioanalyzer high sensitivity DNA kit and were subsequently sequenced.

tag: chip antibody

value: anti-Ctip2 (Bcl11b) (abcam ab18465)

value: Wild type


title: hp_Lck_9813

description: These cells are Bcl11b deficient

value: Bcl11bfl/fl dLck-iCre


title: hp_Lck_9812

description: These cells are Bcl11b deficient


title: hp_Infected_WT_7480_Bcl11b_ChIP

description: These cells are Bcl11b sufficient


title: CD4Cre_8061_Bcl11b_ChIP

description: These cells are Bcl11b deficient - used as negative control

source_name: CD4+CD8+ Thymocytes

value: Bcl11bfl/fl CD4cre+


title: hp_WT_9802

description: These cells are Bcl11b sufficient


title: Vian-2018-HIC130

tag: cell line

tag: protocol

value: in situ Hi-C

tag: treatment

value: 6 hours 500uM IAA followed by 24 hours IAA withdrawal


title: WT-Lung-CD4-9995

description: These cells are Bcl11b sufficient

data_processing:
Library strategy: ATAC-Seq
Fastq files prepared using Illumina FASTQ Generation application
Fastq files were trimmed using Trimmomatic
Reads were aligned to the mm10 genome using Bowtie2
Duplicate reads were removed using PicardTools
Peaks were called using Macs2
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated from macs2 bedgraph outputfiles using kent bedGraphToBigWig utility.  Scores represent enrichment over CD4cre knock-out samples.

extract_protocol:
DNA from 50,000 CD4+ T-cells was prepared as previously described by others (Buenrostro, J.D., Wu, B., Chang, H.Y., and Greenleaf, W.J. (2015). ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol 109, 21.29.21-29.) Briefly, cells were lysed and the nuclei underwent the transposition reaction at 37oC for 30 minutes.
DNA was purified after transposition reaction using Qiagen MinElute PCR Purification Kit and libraries were generated by amplifying DNA with 12-15 cycles. Necessary cycles determined by qPCR. DNA was purified using AMPure XP beads, quality and quantity was determined by Agilent bioanalyzer (high sensitivity DNA kit), and the libraries were subsequently sequenced.

value: Lung Parenchyma


title: WT-Lung-CD4-1207

description: These cells are Bcl11b sufficient


title: Lck-Lung-CD4-1217

description: These cells are Bcl11b deficient


title: ssMG-14d-1

value: mammary gland

value: (-) 14 days to parturition


title: C3_8dpf_MU


title: Lck-Lung-CD4-1205

description: These cells are Bcl11b deficient


title: C3_8dpf_WT


title: shAPT1 1

city: Philadelphia

first: Eric

last: Witze

state: PA

address: 421 Curie Blvd.

department: Cancer Biology

institute: University of Pennsylvania School of Medicine

data_processing:
Library pools were clustered and run on Nextseq500 platform with paired-end reads of 75 bases, according to the manufacturer's recommended protocol (Illumina Inc.). Raw reads passing the Illumina RTA quality filter were pre-processed using FASTQC for sequencing base quality control
Transcripts described in Gencode version 26 (based on GRCh38.p10) were indexed for salmon
Fastq files were processed by salmon quantify transcript expression
Transcrpts were summarized to genes using the Bioconductor module tximport
Genome_build: GRCh38, Ensembl 89 / Gencode v26 for gene models
Supplementary_files_format_and_content: For all samples, depth-scaled gene count matrix (ensembl rel89 gene IDs, calculated in DESeq2 after tximport summarization), and per-sample, salmon transcript quantification (ensembl rel89 transcript IDs)

growth_protocol: Cells were grown in DMEM containing 10% FBS

extract_protocol:
Total RNA was isolated using RNeasy Kit (Invitrogen) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MDA-MB-231 triple receptor negative  breast cancer cells were cultured in DMEM + Glutamax (ThermoFisher) supplemented with 10% (v/v) FBS (Gibco). Stable APT1 knockdown was achieved by short hairpin RNA with lentiviral infection followed by 72 hour puromycin selection. Stable APT1 overexpression was achieved by lentiviral-mediated expression of APT1wt plasmid.

value: breast

value: lentiviral-mediated knockdown APT1 using short hairpin RNA


title: Control 3

value: lentiviral-mediated expression of scramble control RNA


title: shAPT1 2


title: APT1wt 1

value: lentiviral-mediated overexpression of APT1wt


title: APT1wt 2


title: shAPT1 3


title: 418 Nmi ko

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

institute: Univ of Alabama at Birmingham

description: Processed data file: rna-seq_FPKM.txt

data_processing:
QC by fastqc.
Trimming by quality score by trimomonic.
Alignment by TopHat.
Remove duplicates by samtools.
Quantification by Cufflinks.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: rna-seq_FPKM.txt: Tab-delimited text file includes FPKM-normalized counts (Samples in rows).

source_name: Mammary epithelial cells, Nmi KO

extract_protocol:
Total RNA was harvested from mammary epithelial organoids with TRIzol® reagent (Invitrogen, Carlsbad, CA) and purified using the RNeasy kit (Qiagen Inc., Valencia, CA). RNA was quantitated and assessed using spectrophotometry (NanoDropLite, Thermo Scientific, Wilmington, DE).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

value: FVB

tag: genotype/variation

value: Nmi-/-

value: Mammary epithelial cells


title: Control 2

tag: tissue


title: 410 Nmi ko

description: Processed data file: rna-seq_FPKM.txt


title: Control 1


title: 406 Nmi ko

description: Processed data file: rna-seq_FPKM.txt


title: 436 Nmi wt

description: Processed data file: rna-seq_FPKM.txt

source_name: Mammary epithelial cells, WT

value: Wild Type


title: 434 Nmi wt

description: Processed data file: rna-seq_FPKM.txt


title: 414 Nmi wt

description: Processed data file: rna-seq_FPKM.txt


title: APT1wt 3


title: TAI_154

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

institute: Helmholtz Centre for Infection Research

data_processing:
library quality assessment using FastQC
alignment vs. reference genome using Tophat2 (V1.20) with default parametrization
read count quantification using htseq-count (http://www.huber.embl.de/users/anders/HTSeq)
RPKM normalization of raw read counts
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: htseqcounts*.tab files: raw read counts per gene; htseqcounts*.rpkm files: RPKM normalized read counts per gene

source_name: brain tissue_7 dpi

extract_protocol: Animals were euthanized, perfused with PBS and brain tissue was removed immediately, snap frozen on liquid nitrogen and stored at -80°C until further use. RNA was isolated from transversal sections of the brain at the level of the hippocampus using QIAzol Lysis Reagent and RNeasy® Mini Kit (Qiagen).

value: SJL/J

tag: Sex

value: female

value: 5 weeks

tag: infected with

value: TMEV BeAn strain

tag: day post infection

value: brain


title: TAI_157

source_name: brain tissue_14 dpi

tag: strain

tag: age


title: TAI_158


title: TAI_149

source_name: brain tissue_4 dpi


title: TAI_161


title: TAI_155


title: TAI_153


title: TAI_145


title: TAI_147


title: TAI_159


title: TAI_152


title: TAI_150


title: TAI_148


title: TAI_151


title: hp_WT_5319

description: These cells are Bcl11b sufficient

value: Mesenteric Lymph Nodes


title: TAI_160


title: hp_Lck_5320

description: These cells are Bcl11b deficient

value: Bcl11bfl/fl dLck-iCre


title: hp_Lck_5280

description: These cells are Bcl11b deficient


title: hp_WT_5393

description: These cells are Bcl11b sufficient


title: C2C12_SCR_2

city: Rome

first: Mariangela

last: Morlando

address: P.le Aldo Moro, 5

department: Dept. of Biologi and Biotechnology "C. Darwin"

institute: Sapienza Unoversity of Rome

data_processing:
Base-Calling with Casava.
Trimmomatic software was used pre-process mRNA-Seq reads by removing adapter sequences and poor quality bases; the minimum read length after trimming was set to 30. Surviving reads were aligned using Bowtie 2 to a sequence database composed of rRNAs, tRNAs, snRNA and snoRNAs; reads mapping to these sequences were filtered out.
In order to calculate the distribution of the inner distance between mate pairs, reads were aligned to a non-redundant set of murine mRNA sequences derived from Gencode M4 annotation using BWA software. We estimated mean and variance of the inner distance distribution from aligned read pairs whose inner distance was within interval [Q1-2(Q3-Q1),Q3+2(Q3-Q1)] (Q1=first quartile, Q3=third quartile). TopHat2 was employed to align reads to mm10 mouse genome and Gencode M4 transcriptome using parameters -i 50 -r -27 --mate-std-dev 85 --library-type fr-firststrand.
Gene-level expression estimation, as well as differential expression analysis, were performed using Cuffdiff 2 software.
Genome_build: mm10
Supplementary_files_format_and_content: text file containing per sample gene FPKMs

source_name: proliferating C2C12 treated with si-scr

growth_protocol: Mantainance of C2C12 cells is described in Ballarino et al., 2015 (doi: 10.1128/MCB.01394-14)

extract_protocol:
TruSeq Stranded mRNA Library Prep Kit
Total RNA was extracted Qiazol reagent and miRNEasy spin columns according to the manufacturer’s specifications (QIAGEN).

treatment_protocol: siRNA treatment is described in Ballarino et al., 2015 (doi: 10.1128/MCB.01394-14); while the pull down was performed as described in this study.

tag: cell type

value: C2C12 murine myoblasts

value: control


title: C2C12_lnc-31_SI_2

source_name: proliferating C2C12 treated with si-lnc-31

value: lnc31 knockdown


title: C2C12_SCR_1


title: C2C12_INPUT

data_processing:
Base-Calling with Casava.
Raw reads relative to the pull down experiment were subjected to quality trimming using Trimmomatic and adapter sequences were removed using Cutadapt; the minimum read length after trimming was set to 30. Low complexity reads were then removed using the DUST algorithm included in the PRINSEQ suite, setting the complexity score threshold to 7.
Reads mapping to rRNAs, tRNAs, snRNA or snoRNAs, found using the Bowtie 2 aligner, were filtered out. Surviving reads were mapped to mm10 mouse genome and Gencode M4 transcriptome using Tophat2 with parameters -i 50 --library-type fr-unstranded.
Duplicate reads, which could represent PCR artifacts, were removed using MarkDuplicates from Picard. Reads mapping to multiple locations were filtered out using BamTools. Piranha was employed, using the input as a covariate, to find enriched read clusters both for lnc-31 pull down and lacZ experiment; bin size was set to 200.
Genome_build: mm10
Supplementary_files_format_and_content: bed files containing genomic coordinates and p-values of ODD and lacZ enriched read clusters. Since strand information is not available, all the strand fields were set to +.

source_name: INPUT from C2C12 RNA pull down

extract_protocol:
NuGEN Ovation RNA-Seq System V2
Total RNA was extracted Qiazol reagent and miRNEasy spin columns according to the manufacturer’s specifications (QIAGEN).

tag: pull down


title: C2C12_lacZ

source_name: lacZ sample from C2C12 RNA pull down

value: aspecific (lacZ) biotinylated antisense probes


title: C2C12_ODD

source_name: ODD sample from C2C12 RNA pull down

value: specific (ODD) biotinylated antisense probes


title: J1836T1

city: Shanghai

first: Hongbin

last: Ji

address: 320 Yue Yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology

description: Lung tumor

data_processing:
RNA-Seq reads were mapped to the mouse genome (build mm10) using the STAR(2.4.2a) with default parameters
The mapped reads were further analyzed with Cufflinks 2.2.1 to calculate the level of gene expression with FPKM
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: Lung

extract_protocol:
Lung tumors were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung


title: J1967T1

description: Lung tumor

value: KrasG12D/+ UTXL/Y


title: J1985T1

description: Lung tumor


title: C2C12_lnc-31_SI_1


title: J2171T2

description: Lung tumor


title: J2171T1

description: Lung tumor


title: J1988T1

description: Lung tumor

value: KrasG12D/+ UTXL/L


title: RNA_Hep_15wk_Tet2_3DKO_CRE_3wk_rep2

first: Klaus

middle: H

last: Kaestner

address: University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard

department: Department of Genetics and Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine

institute: University of Pennsylvania

description:
polyA RNA
FPKM_all_files_for_paper.txt

data_processing:
One-hundred-base pair paired-end sequencing reads from RRBS were trimmed and quality filtered by trim galore software (v0.3.3) using default parameters for RRBS with the following command:
trim_galore–rrbs–paired sample_R1.fastq.gz sample_R2.fastq.gz
BSMAP v2.74 (Xi and Li, 2009) was used for read alignment (genome build mm9) and extraction of single-base resolution methylation levels using the following commands:
bsmap -a sample_R1_val_1.fq.gz -b sample_R2_val_2.fq.gz -d mm9_AllGenome.fa -o bam_file -R -D C-CGG
python methratio.py -i “no-action” -p -g -z -o sample_trim_galore_mm9.fa.meth -d mm9_AllGenome.fa bam_file
Percent methylation was calculated for one-hundred-base pair tiles with a minimum coverage of 10 CpGs.
Genome_build: mm9
Supplementary_files_format_and_content: bed

extract_protocol:
DNA was isolated from mouse hepatocytes or from snap-frozen mouse tissues and incubated in lysis buffer (25 mM Tris-HCl (pH  8), 2 mM EDTA, 0.2% SDS, 200 mM NaCl) supplemented with 300 μg/ml proteinase K (Roche) followed by phenol:chloroform extraction and ethanol precipitation.
RRBS libraries were prepared as described (Boyle et al., 2012) and run on Hiseq 2500 (Illumina).

value: Hepatocyte

tag: aav injection time


title: RNA_Hep_15wk_Tet2_3DKO_CRE_1d_rep2

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: Chip_Hep_Tet2_3DKO_Input

description:
Chromain
Sample_Chip_586_H3k27Ac_KO.bed


title: Chip_Hep_Tet2_3DKO_H3K4me1

description:
Chromain
Sample_Chip_586_H3k4me1_KO.bed


title: RNA_Hep_15wk_WT_CRE_3wk_rep3

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: RNA_Hep_15wk_Tet2_3DKO_CRE_1d_rep1

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: Chip_Hep_WT_Input

description:
Chromain
Sample_Chip_585_H3k27Ac_WT.bed


title: Chip_Hep_Tet2_3DKO_H3K27ac

description:
Chromain
Sample_Chip_586_H3k27Ac_KO.bed


title: RNA_Hep_15wk_WT_CRE_3wk_rep2

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: Chip_Hep_WT_H3K4me1

description:
Chromain
Sample_Chip_585_H3k4me1_WT.bed


title: RNA_Hep_15wk_WT_CRE_1d_rep1

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: Chip_Hep_WT_H3K27ac

description:
Chromain
Sample_Chip_585_H3k27Ac_WT.bed


title: RNA_Hep_15wk_WT_CRE_3wk_rep1

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: RNA_Hep_17wk_Tet2_3DKO_CRE_13wk_rep4

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: RNA_Hep_15wk_WT_CRE_1d_rep2

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: RNA_Hep_15wk_WT_CRE_1d_rep3

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: WGBS_Hep_Tet2_3DKO

description:
genomic DNA
Big_table_wgbs_200_bp_040516.bed


title: WGBS_Hep_WT


title: RNA_Hep_17wk_Tet2_3DKO_CRE_13wk_rep3

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: WGBS_Hep_newborn


title: RNA_Hep_15wk_Tet2_3DKO_CRE_3wk_rep3

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: RNA_Hep_17wk_Tet2_3DKO_CRE_13wk_rep1

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: RNA_Hep_15wk_Tet2_3DKO_CRE_3wk_rep1

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: RNA_Hep_15wk_Tet2_3DKO_CRE_1d_rep3

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: RNA_Hep_17wk_Tet2_3DKO_CRE_13wk_rep2

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: RNA_Hep_3wk_WT_rep3

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: RNA_Hep_1wk_WT_rep2

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: RNA_Hep_3wk_WT_rep1

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: RNA_Hep_3wk_WT_rep2

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: RNA_Hep_15wk_WT_rep3

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: RNA_Hep_15wk_WT_rep2

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: RRBS_Lung_20wk_WT_rep4

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Colon_36WK_WT

description:
genomic DNA
Big_table_all_samples_RRBS

value: Colon


title: RRBS_Lung_1wk_WT_rep5

description:
genomic DNA
Big_table_all_samples_RRBS


title: RNA_Hep_15wk_WT_rep1

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: RRBS_Lung_20wk_WT_rep3

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Heart_20wk_WT_rep4

description:
genomic DNA
Big_table_all_samples_RRBS

value: Heart


title: RRBS_Neutrophil_36wk_WT

description:
genomic DNA
Big_table_all_samples_RRBS

value: neutrophil


title: RRBS_Heart_1wk_WT_rep7

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Lung_20wk_WT_rep2

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_1wk_invitro_rep8

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Heart_1wk_WT_rep6

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Heart_20wk_WT_rep3

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Lung_1wk_WT_rep4

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_1wk_invitro_rep7

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Heart_20wk_WT_rep1

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hippo_20wk_WT_rep7

description:
genomic DNA
Big_table_all_samples_RRBS

value: Hippocampus


title: RRBS_Lung_20wk_WT_rep1

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hippo_20wk_WT_rep5

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hippo_20wk_WT_rep3

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hippo_20wk_WT_rep1

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hippo_20wk_WT_rep2

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_19wk_Tet2_3DKO_CRE_15wk_rep2

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Fat_25wk_WT

description:
genomic DNA
Big_table_all_samples_RRBS

value: Fat


title: RRBS_Hep_19wk_Tet2_3DKO_CRE_15wk_rep3

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hippo_20wk_WT_rep4

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Heart_20wk_WT_rep2

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_19wk_Tet2_3DKO_CRE_15wk_rep1

description:
genomic DNA
Big_table_all_samples_RRBS


title: RNA_Hep_1wk_WT_rep1

description:
polyA RNA
FPKM_all_files_for_paper.txt


title: RRBS_Hep_6wk_WT_rep2

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_1wk_WT_rep3

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_6wk_WT_rep1

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_15wk_floxTet2_3_rep1

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hippo_20wk_WT_rep6

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_3wk_WT_rep4

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_3wk_WT_rep3

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_15wk_WT_rep4

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_15wk_WT_rep2

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_15wk_WT_rep3

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_15wk_Tet2_3DKO_CRE_1d_rep3

description:
genomic DNA
Big_table_all_samples_RRBS


title: KO5 rna-seq

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

description:
RNA-seq data for PTK7KO Wolffian ducts  sample KO5
genecounts.txt

data_processing:
align to genome with STAR
count reads mapping to genes with featureCounts
Genome_build: grcm38
Supplementary_files_format_and_content: gene counts, txt

source_name: Wolffian ducts

growth_protocol: Mice (Ptk7flox/flox:mT/mG) carrying loxP-flanked Ptk7 allele and mT/mG (membrane-Tomato/membrane-EGFP) allele mated with mice (Ptk7Xst87/+:T-Cretg/tg) carrying a disrupted allele of Ptk7 gene, Xst87 (Lu et al., 2004), and two copies of T-Cre to generate conditional knockout (Ptk7Xst87/ flox:T-Cretg: mT/mG) and control offspring (Ptk7+/ flox:T-Cretg: mT/mG). Mice were bred and genotyped based upon the information provided by The Jackson Laboratory (Bar Harbor, Maine).

extract_protocol:
Epididymal ducts were dissected from E18.5 control and TCre-cKO embryos. Total RNA was extracted using Qiagen RNeasy Plus Mini Kit (Valencia, CA) according to manufacturer's instructions. Quality control of RNA was conducted using TapeStation and qPCR methods at the Genewiz (South Plainfield, NJ).
cDNA synthesis and library construction were performed using Illumina Truseq RNASeq (Illumina Inc. San Diego, CA). Four control and four knockout sample replicates were analyzed on an Illumina HiSeq 2000 instrument at Coulter Genewiz (South Plainfield, NJ).

value: Wolffian ducts

tag: condition


title: RRBS_Hep_15wk_Tet2_3DKO_CRE_1d_rep1

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_15wk_WT_CRE_3wk_rep4

description:
genomic DNA
Big_table_all_samples_RRBS


title: KO2B rna-seq

description:
RNA-seq data for PTK7KO Wolffian ducts  sample KO2B
genecounts.txt


title: KO1A rna-seq

description:
RNA-seq data for PTK7KO Wolffian ducts  sample KO1A
genecounts.txt


title: con6F rna-seq

description:
RNA-seq data for control Wolffian ducts  sample con6F
genecounts.txt


title: RRBS_Hep_15wk_WT_CRE_3wk_rep2

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_15wk_WT_CRE_3wk_rep3

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_15wk_floxTet2_3_rep2

description:
genomic DNA
Big_table_all_samples_RRBS


title: con3c rna-seq

description:
RNA-seq data for control Wolffian ducts  sample con3c
genecounts.txt


title: RRBS_Hep_15wk_WT_rep1

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_15wk_WT_CRE_1d_rep3

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_15wk_Tet2_3DKO_CRE_1d_rep4

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_15wk_WT_CRE_1d_rep2

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_15wk_Tet2_3DKO_CRE_1d_rep5

description:
genomic DNA
Big_table_all_samples_RRBS


title: con1 rna-seq

description:
RNA-seq data for control Wolffian ducts  sample con1
genecounts.txt


title: RRBS_Hep_15wk_WT_CRE_1d_rep4

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_15wk_WT_CRE_1d_rep1

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_15wk_WT_CRE_3wk_rep1

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_15wk_Tet2_3DKO_CRE_3wk_rep4

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_15wk_Tet2_3DKO_CRE_3wk_rep5

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_15wk_Tet2_3DKO_CRE_3wk_rep3

description:
genomic DNA
Big_table_all_samples_RRBS


title: KO4D rna-seq

description:
RNA-seq data for PTK7KO Wolffian ducts  sample KO4D
genecounts.txt


title: RRBS_Hep_15wk_Tet2_3DKO_CRE_1d_rep2

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_15wk_Tet2_3DKO_CRE_3wk_rep1

description:
genomic DNA
Big_table_all_samples_RRBS


title: W3

city: Pontevedra

first: Victor

middle: M

last: Rodriguez

address: Apartado 28

department: Plant Genetics and Breeding

country: Spain

institute: Mision Biologica de Galicia (CSIC)

data_processing:
library strategy: Massive Analysis of 3′-cDNA Ends (MACE)
HCS from Illumina HiSeq 2000
1) Assembly and annotation to the ENSEMBL maize genome, release 23 (ftp://ftp.ensemblgenomes.org/pub/plants/release-23/fasta/zea_mays/). 2) Annotation to the transcriptome from the same release with those reads for which no information could be retrieved after 1). 3) Assembly of all treads with no annotation after 1) and 2) and BLASTX with the generated contigs to the swissprot DB. 4) BLASTN with the generated contigs after 3) to all plant transcriptomes
Assemblies were performed with NovoAlign v3.00.05; reads mapping to multiple locations were limited to 10
Differential expression analysis was performed with the R package DESeq (Anders and Huber 2010) with the standard parameters
Genome_build: ENSEMBL maize genome, release 23
Supplementary_files_format_and_content: text file containing Gene annotation, logFC,  FDR, raw and normalized counts

organism: Zea mays

growth_protocol: Sixty plants were individually grown in pots under greenhouse conditions (untreated plants)] was applied to 15 plants per genotype.

extract_protocol:
The total RNA from three biological replicates of each treatment was extracted using the SpectrumTM Plant Total RNA kit (Sigma-Aldrich, MO, USA)
Twelve Massive Analysis of 3′-cDNA Ends (MACE) libraries, one from each sample, were constructed by GenXPro GmbH (GenXPro GmbH, Frankfurt am Main, Germany) as described by Zawada et al., (2014).

treatment_protocol: At the VT developmental stage, each treatment (infestation with S. nonagrioides larvae, wounding, wounding + regurgitate, and control) was applied to 15 plants per genotype

value: Wounding

tag: harvesting time

value: 15 dpi

value: Stem


title: con4D rna-seq

description:
RNA-seq data for control Wolffian ducts  sample con4D
genecounts.txt

value: control


title: OS3

source_name: Regurgitate + Wounding_stem

value: Regurgitate + Wounding


title: W1


title: RRBS_Lung_1wk_WT_rep3

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Lung_1wk_WT_rep2

description:
genomic DNA
Big_table_all_samples_RRBS


title: OS2


title: RRBS_Heart_1wk_WT_rep5

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Heart_1wk_WT_rep4

description:
genomic DNA
Big_table_all_samples_RRBS


title: S3

source_name: Sesamia larvae_stem

value: Sesamia larvae


title: W2


title: RRBS_Lung_1wk_WT_rep1

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_20wk_WT_rep1

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_20wk_WT_rep2

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_15wk_Tet2_3DKO_CRE_3wk_rep2

description:
genomic DNA
Big_table_all_samples_RRBS


title: C2

value: Control


title: C3


title: S2


title: RRBS_Hep_12wk_WT_rep4

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Heart_1wk_WT_rep3

description:
genomic DNA
Big_table_all_samples_RRBS


title: C1


title: RRBS_Hep_20wk_WT_rep3

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_12wk_WT_rep1

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_12wk_WT_rep3

description:
genomic DNA
Big_table_all_samples_RRBS


title: AMPKa2WT1

city: Pullman

first: Zhihua

last: Jiang

state: WA

address: Veterinary and Biomedical Research Building, Room 151

department: Animal Science

institute: Washington State University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mouse genome using the aligner TMAP. The ends of mapped reads within 24bp of each other on the same strand were clustered to detect poly(A) sites.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: read counts

source_name: AMPKalpha2 WT_skeletal muscle

extract_protocol:
Total RNA was harvested using Trizol reagent.
WTTS libraries were constructed based on our protocols. The WTTS method includes several major steps: fragmentation, poly(A)+ RNA enrichment, 1st strand cDNA synthesis, Size selection and PCR amplication.

tag: strain background

value: AMPKalpha2 WT

tag: developmental stage

value: Adult

value: skeletal muscle


title: AMPKa2WT2


title: OS1


title: RRBS_Hep_12wk_WT_rep2

description:
genomic DNA
Big_table_all_samples_RRBS

value: Hepatocyte


title: AMPKa2KO2

source_name: AMPKalpha2 KO_skeletal muscle

value: AMPKalpha2 KO


title: RRBS_Hep_3wk_WT_rep1

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_3wk_WT_rep2

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_1wk_WT_rep2

description:
genomic DNA
Big_table_all_samples_RRBS


title: AMPKa2KO1


title: AMPKa1WT1

source_name: AMPKalpha1 WT_skeletal muscle

value: AMPKalpha1 WT


title: AMPKa1WT2


title: RRBS_Hippo_1wk_WT_rep4

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hippo_1wk_WT_rep3

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_1wk_WT_rep1

description:
genomic DNA
Big_table_all_samples_RRBS


title: S1


title: AMPKa1KO2

source_name: AMPKalpha1 KO_skeletal muscle

value: AMPKalpha1 KO


title: RRBS_Hippo_1wk_WT_rep2

description:
genomic DNA
Big_table_all_samples_RRBS

value: Hippocampus


title: RRBS_Hep_1wk_invitro_rep6

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Heart_1wk_WT_rep2

description:
genomic DNA
Big_table_all_samples_RRBS

value: Heart


title: RRBS_Hep_1wk_invitro_rep3

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hep_1wk_invitro_rep4

description:
genomic DNA
Big_table_all_samples_RRBS


title: RRBS_Hippo_20wk_WT_rep8

description:
genomic DNA
Big_table_all_samples_RRBS


title: NCH421k transduced with Chronophin targeting shRNA#2 biological replicate 1

city: Regensburg

first: Markus

last: Schulze

address: Franz-Josef-Strauss Allee 11

department: Neuropathology

institute: University Hospital Regensburg

data_processing:
Image analysis and base calling resulted in .bcl files, which were converted into .fastq files by the CASAVA1.8.2 software
Fastq files were imported to the commercially available Genomatix mining station with the data import and validation tool ver. 2.2.2
Reads were mapped to the human genome version GRCh38 with the commercially available Genomatix mapper ver. 3.7.6.3 allowing one mismatch
Count tables as well as RPKM values were created by the Genomatix Genome Analyzer v3.51106. Genomatix Genome Analyzer v3.51106, which was used to create count tables for all samples. Reads were counted locus-based, i.e. for unions of exons of genes.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited file with counts and RPKM values, columns are column1: Gene_Symbol column2: Chromosome column3: Start_coordinate column 4: End_coordinate 5: Strand 6: Count C column7: RPKM

extract_protocol: Libraries for next-generation sequencing were prepared with total RNA with the TruSeq® RNA Sample Preparation Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer´s instructions. Poly-A RNA was purified from the total RNA preparation with magnetic oligo-dT beads. The RNA-bead mixture was incubated at 65°C for five minutes to denature the RNA. Then, the mixture was incubated for five minutes at RT to allow the RNA to bind to the beads. Afterwards, the beads were washed with bead washing buffer and resuspended in elution buffer for two minutes at 80°C. Bead binding buffer was added to allow rebinding of the eluted RNA. The beads were washed with bead washing buffer and resuspended in elute, prime, fragment mix. The RNA was eluted at 94°C for eight minutes, and first strand cDNA synthesis was performed with SuperScript II (Thermo Fisher Scientific, Waltham, MA, USA) in first strand mix supplied by Illumina. Second strand synthesis was performed with the second strand mix for one hour at 16°C and the resulting double stranded cDNA was purified using AMPure XP beads (Beckman Coulter, Brea, CA, USA). Then, end repair was performed for 30 minutes at 30°C with the provided end repair mix. The end repaired DNA was again cleaned up with AMPure XP beads. A-tailing was performed with the A-tailing mix at 37°C for 30 minutes followed by 70°C for five minutes. Indexed adapters were ligated to the end-repaired A-tailed cDNA at 30°C for ten minutes. Next, stop ligation buffer was added, and the libraries were cleaned up with AMPure XP beads. PCR amplification was performed with the provided PCR reagents and the following cycling conditions: Denaturation at 98°C for 30 seconds and then 15 cycles of1) 98°C for 10 seconds, 2)60°C for 30 seconds and 3)72°C for 30 seconds. Afterwards, a final extension at 72°C for five minutes was performed and the amplified libraries were purified again with AMPure XP beads.

tag: cell line

tag: type

value: tumor cell line


title: NCH421k transduced with Chronophin targeting shRNA#2 biological replicate 2


title: RRBS_Hep_1wk_invitro_rep2

description:
genomic DNA
Big_table_all_samples_RRBS


title: NCH421k transduced with Chronophin targeting shRNA#1 biological replicate 2


title: NCH421k transduced with Chronophin targeting shRNA#2 biological replicate 3


title: RRBS_Hep_1wk_invitro_rep1

description:
genomic DNA
Big_table_all_samples_RRBS


title: hMuStem_hPL_3

city: Nantes

first: Aurélie

last: Lardenois

address: INRA UMR 703 PAnTher, Ecole Nationale Vétérinaire, Agroalimentaire et de l'Alimentation, Nantes-Atlantique (Oniris) Atlanpole- La Chantrerie; CS. 40706

country: France

institute: INRA

data_processing:
library strategy: 3'-DGE-Seq
All sixteen bases of the first read (from the read pairs) must have quality scores of at least 10 and the first six bases must correspond exactly to a designed well-specific barcode.
The second reads were aligned to RefSeq human mRNA sequences (hg19) using bwa version 0.7.4 4
Genome_build: hg19
Supplementary_files_format_and_content: bam alignment files obtained from bwa
Supplementary_files_format_and_content: Expression file in dat format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 14936 genes detected.

growth_protocol: hMuStem cells were cultured under standard conditions (37°C in a humidified atmosphere containing 5% CO2) in growth medium (GM, Macopharma) supplemented with either 10% FBS / 1% PSF / 10 ng/mL human recombinant basic fibroblast growth factor (bFGF; Miltenyi, Bergisch Gladbach, Germany) / 25 ng/mL human recombinant epidermal growth factor (EGF; Miltenyi) (hMuStem cellsFBS), or 10% HS / 1% PSF / 10 ng/mL bFGF / 2 ng/mL EGF (hMuStem cellsHS) or 10% hPL / 1% PSF / 2 ng/mL EGF (hMuStem cellshPL). Heparin (5 UI/mL, Sanofi-Aventis, Frankfurt, Germany) was added in hPL-supplemented media to prevent clot formation. Cells were seeded on CELLstart™ substrate (Invitrogen) at 2.5x103 cells/cm² and GM was renewed twice a week.

extract_protocol:
Total RNA was extracted using RNeasy mini or micro kit following manufacturer’s instructions.
Libraries were prepared from 10 ng of total RNA. The mRNA poly(A) tail was tagged with universal adapters, well-specific barcodes and unique molecular identifiers (UMIs) during template-switching reverse transcriptase. Barcoded cDNAs from multiple samples were then pooled, amplified and tagmented using a transposon-fragmentation approach that enriches for 3’ends of cDNA. A library of 350-800 bp was run on an Illumina HiSeq 2500 using a TruSeq Rapid SBS Kit (Illumina, San Diego, CA, USA).

value: Muscle-derived stem (hMuStem) cells

tag: cpd

tag: xeno-free blood derivatives

value: Human platelet lysate (hPL)


title: hMuStem_HS_3

value: Human serum (HS)


title: NCH421k transduced with Control shRNA biological replicate 3


title: NCH421k transduced with Control shRNA biological replicate 2


title: NCH421k transduced with Chronophin targeting shRNA#1 biological replicate 1


title: hMuStem_HS_2


title: NCH644 transduced with Chronophin targeting shRNA#2 biological replicate 2


title: NCH644 transduced with Chronophin targeting shRNA#2 biological replicate 3


title: NCH421k transduced with Control shRNA biological replicate 1


title: hMuStem_hPL_1


title: NCH644 transduced with Chronophin targeting shRNA#1 biological replicate 3


title: NCH644 transduced with Chronophin targeting shRNA#2 biological replicate 1


title: RRBS_Hippo_1wk_WT_rep1

description:
genomic DNA
Big_table_all_samples_RRBS

tag: tissue


title: AMPKa1KO1

tag: genotype/variation


title: hMuStem_HS_1


title: NCH644 transduced with Chronophin targeting shRNA#1 biological replicate 1


title: NCH644 transduced with Chronophin targeting shRNA#1 biological replicate 2


title: RRBS_Hep_1wk_invitro_rep5

description:
genomic DNA
Big_table_all_samples_RRBS


title: NCH644 transduced with Control shRNA biological replicate 3


title: hMuStem_hPL_2


title: NCH644 transduced with Control shRNA biological replicate 1


title: NCH644 transduced with Control shRNA biological replicate 2


title: input_3

city: Halle

first: Claus

last: Weinholdt

address: Von-Seckendorff-Platz 1

department: Institute of Computer Science

institute: Martin Luther University Halle-Wittenberg

data_processing:
adapter trimming by cutadapt
quality filtering by sickle  -q 20 -l 15
maping by bowtie-1.1.2 to rRNA.fa
mapping of unmapped reads by bowtie-1.1.2 to HAIRPIN_SNORNA.fa
counting of mapped reads by Rsamtools
testing for differenial expression and normalisation by edgeR
Genome_build: miRBase v21
Supplementary_files_format_and_content: tab-delimited text files include raw counts and tmm normalized counts for each Sample.

organism: Nicotiana tabacum

source_name: input

growth_protocol: Nicotiana tabacum BY2 cells were grown in Murashige-Skoog liquid medium at 23°C.

extract_protocol:
Evacuolated BY2 protoplasts were obtained by percoll gradient centrifugation and extracts were prepared from cells disrupted by a dounce homogenizer. Small RNAs were precipitated by the p19 siRNA binding protein.
RNA libraries were prepared using illumina protocolls.

value: BY2 lysate (BYL)

tag: cultivar

value: bright yellow 2 (BY2)


title: input_1


title: p19_1

source_name: p19-pull down (p19 siRNA Binding Protein (NEB))


title: p19_2


title: H067

status: Public on May 08 2018

city: Nedlands

first: Abraham

middle: Neelankal

last: John

address: 6, verdun st

department: Islets cell development

country: Australia

institute: Harry Perkins Institute of Medical Research

data_processing:
primary sequence data was generated using the Illumina bcl2fastq 2.20.0.422 pipeline
Sequenced reads were trimmed for adaptor sequence. The reads were also screened for the presence of any Illumina adaptor/overrepresented sequences and cross-species contamination.
The cleaned sequence reads were then aligned against the Mus musculus genome (Build version mm10). The Tophat aligner (v2.0.14) was used to map reads to the genomic sequences.
Genome_build: m6 and reference annotation based assembly option (RABT)
Supplementary_files_format_and_content: tab-delimited text files

source_name: Islets of Langerhans

extract_protocol:
Islets were purified, washed and RNA was harvested using Trizol reagent. Illumina ribo zero gold protocol were used to construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BKS.Cg-Dock7m +/+ Leprdb/J

value: Islets of Langerhans

value: 12 weeks

tag: genotype

value: Wild type (+/+)


title: H069

tag: strain


title: p19_3


title: input_2


title: H075

tag: age


title: G004

value: Heterozygous (+/-)


title: G003


title: G119


title: G037


title: G002


title: Va14dP_4SP_2

city: Novato

last: Verdin

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

data_processing:
FASTQ files of single raw reads were generated using the Illumina HiSeq 4000 NGS system with its native control software, running 6 barcoded samples/lane
~60 million raw reads per sample were trimmed and aligned to the UCSC mm9 genome build using Bowtie 2.0, and outputted in .SAM format
~40 million  mapped reads per sample from  .SAM files were tabulated at the gene level, and normalized  transcript abundance levels calculated using SeqMonk 0.33 (http://www.bioinformatics.babraham.ac.uk/projects).
Genome_build: mm9
Supplementary_files_format_and_content: Processed data for all samples are provided as a tab-delimited text table of normalized transcript abundance measurements, with each row representing one gene and each column representing either data for one sample or one annotation field for each gene.

source_name: Thymus

extract_protocol:
Total RNA was extracted from 0.5-5X10^6 flow-sorted thymocytes or splenocytes using the RNEasy Plus Mini RNA purification kit (Qiagen)
Libraries for high-throughput sequencing were generated from 20ng of input RNA using The Nugen Ovation RNA-Seq System V2 and Ovation Rapid Library System

value: Thymus

value: 6-8 weeks

tag: cell type

value: CD1D-{alpha}GalCer tetramer-reactive CD4 SP thymocytes

tag: isolation method

value: Flow cytometric cell sorting, BD FACS ARIA II

tag: transgenes expressed

value: TCRa V{alpha}14/J{alpha}18 + HDAC7{delta}P


title: Va14dP_4SP_1


title: Va14dP_4SP_3


title: Va14dP_Spl_3

source_name: Spleen

value: Spleen

value: CD1D-{alpha}GalCer tetramer-reactive CD4 T cells


title: Va14_4SP_2

value: TCRa V{alpha}14/J{alpha}18


title: Mock TEpi untreated 6 h rep4

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

institute: Australian Institute for Bioengineering and Nanotechnology

description:
gene_count_frags.txt
gene_count_frags_TMM_RPKM_log2_batch_adjusted.txt
Mock_4_S4

data_processing:
Base calls performed using RTA v2.
Reads were pooled into a single fastq file representative of one individual biological sample (originally the reads for a single sample were split across 4 lanes of the sequencer).
Two trailing nucleotides were trimmed from all reads with fastx_trimmer version 0.0.14.
Trimmed reads were mapped to hg19 (ENSEMBL 69) whole genome using R version 3.2.1 with package Rsubread version 1.18.0 with default parameters.
Batch correction applied to TMM-adjusted RPKM log2 data using R version 3.2.2 with package limma version 3.26.8 with [5448_1_S9, JRS4_1_S5, Mock_1_S1] [5448_2_S10, JRS4_2_S6, Mock_2_S2] [5448_3_S11, JRS4_3_S7, Mock_3_S3] [5448_4_S12, JRS4_4_S8, Mock_4_S4] as batch groups specified.
Genome_build: hg19, ENSEMBL version 69.
Supplementary_files_format_and_content: tab delimited text file containing raw counts, tab delimited text file containing TMM-RPKM log2 abundance measurements which were subsequently batch adjusted with limma's removeBatchEffect() function.

source_name: tonsil

growth_protocol: TEpi cells were seeded at a density of approximately 120,000 viable cells per well in 6 well plates were coated with poly-L-lysine. Cells were grown at 37°C under a 5% CO2/20% O2 until they formed a confluent monolayer. Immediately prior to infection, the TEpi medium was removed, and replaced with fresh TEpi medium.

extract_protocol:
Medium was aspirated and RNA lysis buffer (Buffer RLT (Qiagen) plus 0.1 M -mercaptoethanol) added to each well. Cells were scraped into the buffer using a cell-scraper. Cell lysate was then loaded onto a QIAshredder homogenizer column (Qiagen, Cat. #79654) and homogenized by centrifugation. RNA was then isolated using the RNeasy Mini Kit (Qiagen, Cat. #74104), according to the manufacturer’s instructions. Absorbance of RNA samples was measured at 260 nm using a ND1000 Nanodrop (Biolab), and RNA concentration (µg/ml) was determined by the A260 reading: A260 = 1.0 is equivalent to 40 µg/ml RNA. A260/A280 ratios were measured to determine RNA purity, and an A260/280 ratio of 2.0 – 2.2 was deemed acceptable for subsequent use.
Confluent 6-well plates of TEpi cells were infected with JRS4 or 5448 as described above, at an MOI of 5 for 6 h. Mock cells were included as a control. RNA from four biological replicates was extracted as described above. RNA sequencing was performed by The University of Queensland, Institute of Molecular Biosciences (IMB) sequencing facility. Total RNA was deemed as passing quality control tests (2100 bioanalyzer), with a RIN score of >7.0.  For each sample, the mRNA library was prepared using TruSeq stranded mRNA library prep kit (Illumina) and sequenced using 1 x NextSeq 500, 75 cycle (1 x 75bp) Illumina High Output single-end run.

treatment_protocol: GAS strains were grown to early stationary phase (OD600 = 1.2 for 5448 and OD600 = 1.6 for JRS4), re-suspended in cell culture medium, and then added to cell monolayers at the multiplicity of infection (MOI) of 5. The control included for each experiment were cells not exposed to bacteria (Mock). At 2 h post-infection, the media was aspirated and cells were washed twice with fresh media, before TEpi media containing 100µg/ml of gentamicin was added to each well for the duration of the experiment.

value: TEpi

tag: infection

value: Mock

tag: treatment length

value: 6 hours

value: 12 years

tag: Sex

value: male


title: Va14_4SP_3


title: Va14dP_Spl_2


title: Va14_4SP_1


title: H064

value: BKS.Cg-Dock7m +/+ Leprdb/J

value: Islets of Langerhans


title: input rep1

city: Madrid

first: Oscar

last: Fernandez-Capetillo

address: MFA 3

department: Genomic Instability Group

institute: CNIO

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software. Conversion of Illumina BCL files to bam format was performed with the Illumina2bam tool (Wellcome Trust Sanger Institute - NPG).
ChIP-seq reads were aligned to the mouse genome assembly using Bowtie 1.1.2 with -m 1 and otherwise default options.
Enriched peaks were called with MACS2 version 2.1.0, with --extsize as estimated with macs2 predictd module on the WT-OHT sample and the --nomodel option, --bw obtained from the library fragment sizes mentioned in 'library construction protocol,' --qvalue=0.15 and otherwise default parameters.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Sequencing reads aligned as described are presented in bam format. Called peaks in bedGraph format, which can be readily imported to UCSC genome browser, were created by macs2 callpeak module with the --bdg option.

source_name: mouse ES cells_input

growth_protocol: ES cells were grown on gelatin at 37°C, 5% CO2, in high glucose DMEM (Invitrogen) supplemented with 15% fetal bovine serum (FBS), LIF (1000 U/ml), 0.1 mM non-essential aminoacids, 1% glutamax, 55 mM b-mercaptoethanol and 1% Penicillin/Streptomycin

extract_protocol:
Lysates were clarified from sonicated nuclei and ERF-DNA complexes were isolated with antibody.
Fragmented immunoprecipitated DNA samples, in the range <0.1 to 5ng, were processed with "NEBNext Ultra II DNA Library Prep Kit for Illumina" from New England BioLabs (catalog # E7645). Briefly, samples went through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters. Adapter-ligated libraries were completed by limited-cycle PCR and extracted with a [single] double-sided SPRI size selection. Median fragment sizes were 600 and 480 bp for samples "rep1" and "rep2", respectively, from which 120 bp correspond to adaptor sequences. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina HiSeq2500 instrument by following manufacturer's protocols.

treatment_protocol: WT-OHT samples were treated with 4-hydroxy-tamoxifen for at least 7days

tag: cell line background

value: RASlox/lox

value: ERF WT+KO mix; (H-Ras-/-;N-Ras-/-;K-Raslox/lox;RERTert/ert)

tag: treated with

tag: chip antibody


title: input rep2


title: WT rep1

source_name: mouse ES cells_WT

value: anti-ERF (Santa Cruz, #sc-15435)


title: ERF rep1

source_name: mouse ES cells_ERF


title: ERF rep2


title: WT-OHT rep2

source_name: mouse ES cells_WT-OHT


title: WT-OHT rep1


title: Va14_spl_2

value: 6-8 weeks


title: WT rep2


title: WT_CD4SP_3

value: Thymus

value: CD4 Single-positive thymocytes


title: Va14_spl_1

value: Flow cytometric cell sorting, BD FACS ARIA II


title: Mock TEpi untreated 6 h rep2

description:
gene_count_frags.txt
gene_count_frags_TMM_RPKM_log2_batch_adjusted.txt
Mock_2_S2


title: Mock TEpi untreated 6 h rep3

description:
gene_count_frags.txt
gene_count_frags_TMM_RPKM_log2_batch_adjusted.txt
Mock_3_S3


title: Mock TEpi untreated 6 h rep1

description:
gene_count_frags.txt
gene_count_frags_TMM_RPKM_log2_batch_adjusted.txt
Mock_1_S1


title: WT_CD4SP_2


title: WT_CD4SP_1


title: JRS4 TEpi MOI 5 infected 6 h rep3

description:
gene_count_frags.txt
gene_count_frags_TMM_RPKM_log2_batch_adjusted.txt
JRS4_3_S7


title: Va14dP_Spl_1

value: Spleen

value: TCRa V{alpha}14/J{alpha}18 + HDAC7{delta}P


title: WT_naive_2

value: CD4+, CD44- {alpha}{beta}T cells


title: JRS4 TEpi MOI 5 infected 6 h rep2

description:
gene_count_frags.txt
gene_count_frags_TMM_RPKM_log2_batch_adjusted.txt
JRS4_2_S6

value: TEpi


title: WT_naive_3


title: Va14_spl_3

value: CD1D-{alpha}GalCer tetramer-reactive CD4 T cells

value: TCRa V{alpha}14/J{alpha}18


title: JRS4 TEpi MOI 5 infected 6 h rep1

description:
gene_count_frags.txt
gene_count_frags_TMM_RPKM_log2_batch_adjusted.txt
JRS4_1_S5

value: 6 hours

value: 12 years


title: WT_naive_1


title: 5448 TEpi MOI 5 infected 6 h rep3

description:
gene_count_frags.txt
gene_count_frags_TMM_RPKM_log2_batch_adjusted.txt
5448_3_S11

value: male


title: shDdx1_UNS (Rep 2)

city: Oxford

first: Nicholas

last: Proudfoot

address: South Parks Road

country: United Kingdom

institute: Sir William Dunn School of Pathology,  University of Oxford

data_processing:
75-bp paired-end HiSeq 4000 sequencing reads were aligned to the mouse genome (mm10) using BWA with default parameters.
Prior to alignment, adaptor sequences were trimmed using Cutadapt retaining reads longer than 10 bases.
Uniquely aligned reads with no more than two mismatches were kept for further analysis.
Data were scaled to library size. Bigwig track files were generated using UCSC bedGraphToBigWig tool.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig file containing read densities from RNA-seq experiments.

source_name: shDdx1_UNS, CH12

growth_protocol: CH12 cells were stably depleted of Ddx1 using lentivirus expressing short-hairpin RNA (shDdx1). CH12 cells transduced with a shRNA sequence that does not target any known mammalian mRNA (shCtrl) were used as a control.

extract_protocol:
Nuclear RNA was fractionated in nucleoplasmic and chromatin fractions.
Chromatin-associated RNA was depleted for rRNA using the Ribo-Zero Magnetic kit (Illumina). Libraries were prepared using the NEBNext Ultra Directional RNA Library Prep kit and NEBnext multiplex Oligos (Index Primers Set 2) for Illumina (NEB).
RNA-Seq on a HiSeq 4000 sequencer (Illumina) with 75 bp paired-end reads.

treatment_protocol: Cells were cultured in unstimulated (UNS) or anti-CD40, IL-4 and TGF-β (CIT) stimulation conditions for 24h.

tag: cell line

value: B-cell lymphoma

value: depleted for Ddx1

tag: culture condition

value: UNS


title: shDdx1_UNS (Rep 1)


title: shDdx1_CIT (Rep 2)

source_name: shDdx1_CIT, CH12

value: CIT


title: 5448 TEpi MOI 5 infected 6 h rep2

description:
gene_count_frags.txt
gene_count_frags_TMM_RPKM_log2_batch_adjusted.txt
5448_2_S10


title: 5448 TEpi MOI 5 infected 6 h rep1

description:
gene_count_frags.txt
gene_count_frags_TMM_RPKM_log2_batch_adjusted.txt
5448_1_S9


title: shDdx1_CIT (Rep 1)


title: shctr_UNS (Rep 2)

source_name: shctr_UNS, CH12

value: control


title: shctr_CIT (Rep 1)

source_name: shctr_CIT, CH12


title: shctr_UNS (Rep 1)


title: WT-1-2

city: Ann Arbor

first: Anthony

last: Antonellis

state: MI

address: 1241 E Catherine St.

institute: University of Michigan

description: WT-1-2 is a technical replicate of WT-1-1; WT-1-2 is Sample 44048

data_processing:
Quality Control: Reads were analyzed using FastQC to ensure sequencing quality.
Alignment: Reads were uniquely aligned to the rat (rn5) RefSeq genome using STAR RNA-Seq alignment.
Read Counts: Number of reads per gene was determined using HT-Seq.
Gene Length: The length of each transcript was determined from the RefSeq database using a custom Perl script.
RPKM Value: The RPKM values were calculated for each gene by dividing the number of reads per gene, by the kilobase length of the gene, by the millions of total reads.
Genome_build: rn5 (RefSeq)
Supplementary_files_format_and_content: RPKM values

organism: Rattus norvegicus

source_name: Myelinating Schwann Cell

growth_protocol: S16 cells were cultured using standard growth media supplemented with L-glutamine. The cells were cultured in a T-75 flask and passaged every 2-3 days.

extract_protocol:
Total RNA was isolated from a confluent T75 flask using a standard TRIzol protocol. The mRNA was isolated using poly dT magnetic beads.
RNA libraries were prepared for sequencing using standard Illumina protocols and TruSeq RNA Library Preparation Kit V2 (RS-122-2001)

tag: passage

value: Passage 9


title: WT-2-2

description: WT-2-2 is a technical replicate of WT-2-1; WT-2-2 is Sample 44053

value: Passage 39


title: Bulk sequencing of trophospheres stimulated with Bmp4 / Nodal NR-bulkrescue7

status: Public on May 07 2018

city: Utrecht

first: Jean-Charles

last: Boisset

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases).
Genome_build: mm10
Supplementary_files_format_and_content: *.gene.coutt.csv or *.gene.coutc.csv: Tab separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicate the cell number of the experiment, separated by a space. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

source_name: embryo

extract_protocol:
Cells were directly placed into Trizol (Life Technologies) and total RNA was isolated according to the manufacturer’s instructions, with the following alterations. RNA was precipitated overnight at -20 °C, with 2.5µg GlycoBlue (Life Technologies).
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

value: Bulk trophospheres stimulated with Bmp4 / Nodal


title: Bulk sequencing of trophospheres stimulated with Bmp4 / Nodal NR-bulkrescue4


title: Bulk sequencing of trophospheres stimulated with Bmp4 / Nodal NR-bulkrescue6


title: JRS4 TEpi MOI 5 infected 6 h rep4

description:
gene_count_frags.txt
gene_count_frags_TMM_RPKM_log2_batch_adjusted.txt
JRS4_4_S8


title: WT-2-1

description: WT-2-1 is a technical replicate of WT-2-2; WT-2-1 is Sample 44052


title: Bulk sequencing of trophospheres stimulated with Bmp4 / Nodal NR-bulkrescue8


title: shctr_CIT (Rep 2)

tag: genotype/variation


title: Bulk sequencing of trophospheres stimulated with Bmp4 / Nodal NR-bulkrescue5


title: WT-1-1

description: WT-1-1 is a technical replicate of WT-1-2; WT-1-1 is Sample 44047


title: Bulk sequencing of trophospheres stimulated with Bmp4 / Nodal NR-bulkrescue3


title: Bulk sequencing of trophospheres stimulated with Bmp4 / Nodal NR-bulkrescue2


title: Bulk sequencing of trophospheres stimulated with Bmp4 / Nodal NR-bulkrescue1


title: Bulk mouse blastocyst, blastoid JCNG1

value: Bulk mouse blastocyst, blastoid


title: MI_3dMI_2

city: Honolulu

first: Allison

middle: Lesher

last: Williams

state: HI - Hawaii

address: 651 Ilalo St BSB 311

institute: University of Hawaii

data_processing:
FASTQ files were explored using FastQC and cleaned by filtering out reads having mean Phred quality score less than 20 using Prinseq.
Mus musculus UCSC mm10 reference genome was indexed by Bowtie2 v2.2.5 and filtered high quality reads were mapped against the reference genome using Tophat v2.0.14.
Mapped BAM files for Sham and MI samples were sorted and converted to SAM files using SAMtools v0.1.2, and then used to generate count reads mapped to mouse gene models using htseq-count script on HTSeq package.
Differential gene expression from the count data was identified using DESeq2 bioconductor package.
CLC Genomic Workbench v9 software (CLC Bio) along with empirical analysis of DGE algorithm implemented in it was used for the transcript-level expression analysis. The genes and transcripts with Benjamini and Hochberg q-value <0.05 were called differentially expressed between sham and MI.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-delimited text files

source_name: heart tissue

extract_protocol:
RNA was extracted using a Qiagen miRNeasy mini kit according to manufacturer’s instructions.
Total RNA samples were sent to Genewiz (South Plainfield, NJ) for rRNA depletion and paired-end sequencing on an Illumina HiSeq2500.

tag: tissue

value: heart left ventricle (free wall)

tag: gender

value: 8-12 weeks

tag: surgery

value: LAD ligation


title: sham_3dMI_2

tag: strain

tag: age

value: sham


title: Bulk mouse embryonic and trophectoderm stem cells JCNG2

tag: cell type


title: sham_3dMI_1


title: MI_1dMI_2


title: MI_1dMI_1


title: sham_1dMI_1


title: sham_1dMI_2