title: eIF2A S51A ER mrna, 1 h Tg (rep 1)

description:
S1Mmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx


title: eIF2A S51A cytosol mrna, 2 h Tg (rep 1)

status: Public on Jan 01 2016

type: SRA

city: Durham

first: David

last: Reid

state: NC

address: 436 Nanaline Duke Bldg., Box 3709 DUMC

department: Biochemistry

country: USA

institute: Duke University

description:
S2Cmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

library_source: transcriptomic

data_processing:
Cutadapt: Trim AAGATCGGAAGAGCACACGTCT: cutadapt -a AAGATCGGAAGAGCACACGTCT -m 20 DBA37-P.fastq -o trimDBA37-P.fastq: cutadapt 1.6 with Python 2.7.6.
Bowtie: bowtie -p 7 -v 0 --norc database/chosenTranscripts reads/trimDBA37-P.fastq mapped/DBA37-P.map: Bowtie 1.1.1.
Read counting (Python script): Count reads in coding sequence, output as RPKM.
Genome_build: MGSCv37 (NCBI v37)
Supplementary_files_format_and_content: XLSX; RPKM values for all genes within the coding sequence.

molecule: total RNA

organism: Mus musculus

source_name: eIF2a S51A mouse embryonic fibroblasts, cytosol, 2 h Tg

extract_protocol:
Cells fractionated between cytosol and ER using digitonin and DDM.
Ribosome profiling samples: digested with micrococcal nuclease, pellet ribosomes, end polish with PNK, gel purify ribosome footprint.
mRNA samples: Deplete rRNA using RiboZero, fragment RNA 20 min 95C in Mg-containing buffer, end polish with PNK.
NEB Directional Small RNA kit. Libraries purified by gel electrophoresis.

treatment_protocol: 1 uM Thapsigargin for a timecourse from 30 min to 4h.

tag: cell type

value: mouse embryonic fibroblasts

tag: genotype/variation

value: eIF2a S51A

tag: subcellular compartment

value: cytosol

tag: treatment

value: 2 h Thapsigargin

tag: method

value: mRNA


title: eIF2A S51A cytosol mrna, 1 h Tg (rep 1)

description:
S1Cmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: eIF2a S51A mouse embryonic fibroblasts, cytosol, 1 h Tg

value: 1 h Thapsigargin


title: ATF4-/- ER mrna, untreated (rep 2)

description:
BNMmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: ATF4-/- mouse embryonic fibroblasts, ER, untreated

value: endoplasmic reticulum

value: untreated


title: eIF2A S51A ER mrna, 0.5 h Tg (rep 1)

description:
S05Mmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: eIF2a S51A mouse embryonic fibroblasts, ER, 0.5 h Tg

value: 0.5 h Thapsigargin


title: eIF2A S51A cytosol mrna, 0.5 h Tg (rep 1)

description:
S05Cmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: eIF2a S51A mouse embryonic fibroblasts, cytosol, 0.5 h Tg


title: ATF4-/- ER mrna, 4 h Tg (rep 2)

description:
B4Mmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: ATF4-/- mouse embryonic fibroblasts, ER, 4 h Tg

value: 4 h Thapsigargin


title: ATF4-/- cytosol mrna, untreated (rep 2)

description:
BNCmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: ATF4-/- mouse embryonic fibroblasts, cytosol, untreated


title: ATF4-/- cytosol mrna, 2 h Tg (rep 2)

description:
B2Cmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: ATF4-/- mouse embryonic fibroblasts, cytosol, 2 h Tg


title: ATF4-/- ER mrna, 2 h Tg (rep 2)

description:
B2Mmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: ATF4-/- mouse embryonic fibroblasts, ER, 2 h Tg


title: ATF4-/- ER mrna, 1 h Tg (rep 2)

description:
B1Mmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: ATF4-/- mouse embryonic fibroblasts, ER, 1 h Tg


title: ATF4-/- cytosol mrna, 4 h Tg (rep 2)

description:
B4Cmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: ATF4-/- mouse embryonic fibroblasts, cytosol, 4 h Tg


title: ATF4-/- cytosol mrna, 1 h Tg (rep 2)

description:
B1Cmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: ATF4-/- mouse embryonic fibroblasts, cytosol, 1 h Tg


title: ATF4-/- ER mrna, 0.5 h Tg (rep 2)

description:
B05Mmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: ATF4-/- mouse embryonic fibroblasts, ER, 0.5 h Tg


title: ATF4-/- ER mrna, 4 h Tg (rep 1)

description:
A4Mmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx


title: ATF4-/- cytosol mrna, 2 h Tg (rep 1)

description:
A2Cmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx


title: ATF4-/- cytosol mrna, untreated (rep 1)

description:
ANCmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx


title: ATF4-/- cytosol mrna, 4 h Tg (rep 1)

description:
A4Cmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx


title: ATF4-/- ER mrna, untreated (rep 1)

description:
ANMmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx


title: ATF4-/- ER mrna, 2 h Tg (rep 1)

description:
A2Mmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx


title: ATF4-/- ER mrna, 1 h Tg (rep 1)

description:
A1Mmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx


title: eIF2A S51A cytosol mrna, 4 h Tg (rep 1)

description:
S4Cmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: eIF2a S51A mouse embryonic fibroblasts, cytosol, 4 h Tg


title: ATF4-/- cytosol mrna, 0.5 h Tg (rep 2)

description:
B05Cmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: ATF4-/- mouse embryonic fibroblasts, cytosol, 0.5 h Tg


title: ATF4-/- cytosol mrna, 1 h Tg (rep 1)

description:
A1Cmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx


title: ATF4-/- cytosol mrna, 0.5 h Tg (rep 1)

description:
A05Cmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx


title: eIF2A S51A cytosol ribosome profiling, untreated (rep 2)

description:
TNCfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx

data_processing:
Library strategy: Ribo-Seq
Cutadapt: Trim AAGATCGGAAGAGCACACGTCT: cutadapt -a AAGATCGGAAGAGCACACGTCT -m 20 DBA37-P.fastq -o trimDBA37-P.fastq: cutadapt 1.6 with Python 2.7.6.
Bowtie: bowtie -p 7 -v 0 --norc database/chosenTranscripts reads/trimDBA37-P.fastq mapped/DBA37-P.map: Bowtie 1.1.1.
Read counting (Python script): Count reads in coding sequence, output as RPKM.
Genome_build: MGSCv37 (NCBI v37)
Supplementary_files_format_and_content: XLSX; RPKM values for all genes within the coding sequence.

source_name: eIF2a S51A mouse embryonic fibroblasts, cytosol, untreated

value: ribosome profiling


title: eIF2A S51A ER ribosome profiling, 4 h Tg (rep 2)

description:
T4Mfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx

source_name: eIF2a S51A mouse embryonic fibroblasts, ER, 4 h Tg


title: eIF2A S51A ER ribosome profiling, untreated (rep 2)

description:
TNMfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx

source_name: eIF2a S51A mouse embryonic fibroblasts, ER, untreated


title: eIF2A S51A cytosol ribosome profiling, 4 h Tg (rep 2)

description:
T4Cfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx


title: ATF4-/- ER mrna, 0.5 h Tg (rep 1)

description:
A05Mmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx


title: eIF2A S51A ER ribosome profiling, 2 h Tg (rep 2)

description:
T2Mfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx

source_name: eIF2a S51A mouse embryonic fibroblasts, ER, 2 h Tg


title: eIF2A S51A cytosol ribosome profiling, 2 h Tg (rep 2)

description:
T2Cfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx

source_name: eIF2a S51A mouse embryonic fibroblasts, cytosol, 2 h Tg


title: eIF2A S51A ER ribosome profiling, 4 h Tg (rep 1)

description:
S4Mfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx


title: eIF2A S51A cytosol ribosome profiling, 1 h Tg (rep 2)

description:
T1Cfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx

source_name: eIF2a S51A mouse embryonic fibroblasts, cytosol, 1 h Tg


title: eIF2A S51A ER ribosome profiling, 0.5 h Tg (rep 2)

description:
T05Mfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx

source_name: eIF2a S51A mouse embryonic fibroblasts, ER, 0.5 h Tg


title: eIF2A S51A cytosol ribosome profiling, 0.5 h Tg (rep 2)

description:
T05Cfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx

source_name: eIF2a S51A mouse embryonic fibroblasts, cytosol, 0.5 h Tg


title: eIF2A S51A cytosol ribosome profiling, 4 h Tg (rep 1)

description:
S4Cfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx


title: eIF2A S51A ER ribosome profiling, 2 h Tg (rep 1)

description:
S2Mfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx


title: eIF2A S51A cytosol ribosome profiling, untreated (rep 1)

description:
SNCfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx


title: eIF2A S51A cytosol ribosome profiling, 2 h Tg (rep 1)

description:
S2Cfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx


title: eIF2A S51A cytosol ribosome profiling, 0.5 h Tg (rep 1)

description:
S05Cfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx


title: eIF2A S51A ER ribosome profiling, 1 h Tg (rep 1)

description:
S1Mfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx

source_name: eIF2a S51A mouse embryonic fibroblasts, ER, 1 h Tg


title: ATF4-/- ER ribosome profiling, 2 h Tg (rep 2)

description:
B2Mfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx


title: eIF2A S51A ER ribosome profiling, 1 h Tg (rep 2)

description:
T1Mfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx


title: ATF4-/- ER ribosome profiling, 0.5 h Tg (rep 2)

description:
B05Mfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx


title: eIF2A S51A ER ribosome profiling, 0.5 h Tg (rep 1)

description:
S05Mfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx


title: ATF4-/- cytosol ribosome profiling, untreated (rep 1)

description:
ANCfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx

source_name: ATF4-/- mouse embryonic fibroblasts, cytosol, untreated


title: ATF4-/- cytosol ribosome profiling, 2 h Tg (rep 2)

description:
B2Cfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx

source_name: ATF4-/- mouse embryonic fibroblasts, cytosol, 2 h Tg


title: eIF2A S51A ER ribosome profiling, untreated (rep 1)

description:
SNMfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx


title: ATF4-/- ER ribosome profiling, untreated (rep 2)

description:
BNMfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx

source_name: ATF4-/- mouse embryonic fibroblasts, ER, untreated


title: ATF4-/- cytosol ribosome profiling, 2 h Tg (rep 1)

description:
A2Cfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx


title: ATF4-/- cytosol ribosome profiling, untreated (rep 2)

description:
BNCfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx


title: ATF4-/- ER ribosome profiling, 0.5 h Tg (rep 1)

description:
A05Mfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx


title: ATF4-/- ER ribosome profiling, 1 h Tg (rep 2)

description:
B1Mfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx

source_name: ATF4-/- mouse embryonic fibroblasts, ER, 1 h Tg


title: ATF4-/- cytosol ribosome profiling, 1 h Tg (rep 1)

description:
A1Cfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx

source_name: ATF4-/- mouse embryonic fibroblasts, cytosol, 1 h Tg


title: ATF4-/- ER ribosome profiling, 4 h Tg (rep 2)

description:
B4Mfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx

source_name: ATF4-/- mouse embryonic fibroblasts, ER, 4 h Tg


title: ATF4-/- cytosol ribosome profiling, 4 h Tg (rep 1)

description:
A4Cfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx

source_name: ATF4-/- mouse embryonic fibroblasts, cytosol, 4 h Tg


title: ATF4-/- ER ribosome profiling, untreated (rep 1)

description:
ANMfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx


title: ATF4-/- ER ribosome profiling, 1 h Tg (rep 1)

description:
A1Mfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx


title: mRNAseq from MEF line 129S5E95

city: Cold Spring Harbor

first: Cinthya

middle: J

last: Zepeda-Mendoza

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description:
polyA+ selected mRNA, sequenced in Illumina's GA2X
WT95

data_processing:
We used the Ensembl release 72 gene set for the C57BL6/J transcriptome (GRCm38/mm10). The 129S5/SvEvBrd transcriptome was constructed by modifying the C57BL/6J transcriptome using SNPs and indels calls derived from The Sanger Mouse Sequencing Project.
Where multiple transcripts exist for a gene, we selected the longest transcript as the representative transcript for the gene in the transcriptome. We used the GSNAP alignment algorithm with the parameter of no mismatches. Reads were filtered to keep only those with one best mapping location. To obtain estimates of expression values, we only counted those reads aligning at a gene location if both reads of a paired-end set were mapped to the same gene.
To avoid biological interpretation from mapping noise, we excluded genes with less than 10 reads mapping to each allele if this occurs across genotypes. Differential expression analyses were performed using the R Bioconductor package – DESeq, using an FDR cut-off of 0.05.
We performed non-allele-specific differential expression analyses (pairwise between WT and deletion heterozygote) using counts summed from both alleles. Allele-specific analysis were performed only using reads that mapped to the transcriptome of each strain and compared in a pairwise manner, that is, between +129/+Bl6 samples (C57BL/6J x 129S5/SvEvBrd) and Df/+Bl6 samples. To account for the allelic mapping biases that is a result of more reads mapping to the C57BL/6J transcriptome, we tested for changes in the proportion of reads mapping to each allele between treatment and WT groups, on a gene by gene basis, to determine whether similar degree of changes to expression levels occurred between alleles.
Counts were normalized using DESeq and tests were done using the R function, prop.test, using median counts across replicates and p-values were adjusted for multiple testing in R using the fdr method (adjusted p-value cut-off = 0.01).
Genome_build: mm10
Supplementary_files_format_and_content: .txt files with differentially expressed genes are included per combined allelic values, 129S5SvEvBrd allelic comparisons, as well as C57Bl/6J allelic comparisons between the Df/+ Bl6 and +129/+Bl6 genotypes

growth_protocol: Embryos of Df/Dp male chimeras X C57BL6/J crosses were dissected at 13.5 days after plug observation. Heads were removed for DNA extraction and genotyping, and the bodies minced by passing through syringes with 18G1 ½ and 20G 1 ½ needles and plated on 10cm dishes previously coated with 0.1% gelatin and using for culture Dulbecco's Modified Eagle Medium (DMEM) High Glucose (4.5g/L) supplemented with 10% Fetal Bovine Serum (FBS) (v/v), 50U/ml Penicillin G, and 100µg/ml Streptomycin sulfate. Cells were incubated on 5% CO2 at 37°C, and passaged every 2-3 days depending on confluency and growth rate. All experiments were subsequently performed on MEF plates 10 hours after reaching confluency at passage 4.

extract_protocol:
RNA from seven independent primary MEF lines was isolated (+129/+Bl6: 129S5E88, 129S5E90, 129S5E95; Df/+Bl6: 129S5E36, 129S5E56, 129S5E71, 129S5E98) using TRIzol reagent (Ambion), and polyA+ RNA was isolated (Oligotex kit; QIAGEN).
Stranded libraries were prepared using a protocol adapted for paired-end sequencing on the Illumina GA IIx platform.

tag: strain background

value: C57BL/6J & 129S5SvEvBrd

value: +/+ genotype

tag: cell line

value: Mouse Embryonic Fibroblasts (MEFs)

tag: passages

value: confluent passage 4


title: ATF4-/- cytosol ribosome profiling, 0.5 h Tg (rep 1)

description:
A05Cfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx

source_name: ATF4-/- mouse embryonic fibroblasts, cytosol, 0.5 h Tg


title: mRNAseq from MEF line 129S5E90

description:
polyA+ selected mRNA, sequenced in Illumina's GA2X
WT90


title: mRNAseq from MEF line 129S5E56

description:
polyA+ selected mRNA, sequenced in Illumina's GA2X
DF56

value: df/+ genotype


title: eIF2A S51A cytosol ribosome profiling, 1 h Tg (rep 1)

description:
S1Cfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx


title: ATF4-/- ER ribosome profiling, 4 h Tg (rep 1)

description:
A4Mfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx


title: mRNAseq from MEF line 129S5E36

description:
polyA+ selected mRNA, sequenced in Illumina's GA2X
DF36


title: mRNAseq from MEF line 129S5E71

description:
polyA+ selected mRNA, sequenced in Illumina's GA2X
DF71


title: mRNAseq from MEF line 129S5E98

description:
polyA+ selected mRNA, sequenced in Illumina's GA2X
DF98


title: ATF4-/- ER ribosome profiling, 2 h Tg (rep 1)

description:
A2Mfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx

source_name: ATF4-/- mouse embryonic fibroblasts, ER, 2 h Tg


title: ATF4-/- cytosol ribosome profiling, 1 h Tg (rep 2)

description:
B1Cfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx


title: control_4h_2

city: New York

first: Christoph

last: Hafemeister

address: 101 Avenue of the Americas

institute: New York Genome Center

library_source: genomic

data_processing:
Reads aligned to the O. sativa Nipponbare - release 7 of the MSU Rice Genome Annotation Project reference genome - including 12 rice chromosomes, chloroplast, mitochondrion, Syngenta pseudomolecule, and the unanchored BAC pseudomolecule using Bowtie version 2.2.3, discarding low-quality alignments (quality score below 30)
We pooled the reads from all 18 ATAC-seq libraries, and defined open regions. To call bases “open” we counted the number of ATAC cut sites (ATAC cut sites are defined as the first base of an aligned fragment and first base after the fragment) that fell into the 72 bp window centered on each base. We considered a base open if its window contained at least one cut site in more than half of the libraries. If two open bases were less than 72 bp apart, we called all intermediate bases open.
Genome_build: Release 7 of the MSU Rice Genome Annotation Project reference genome
Supplementary_files_format_and_content: tab-delimited text files in gff format specifying the genomic regions we called open

molecule: genomic DNA

organism: Oryza sativa

growth_protocol: The rice plants were grown hydroponically (Peter's solution) in climate controlled growth chambers at 30C, 12h light.

extract_protocol:
Leaf tissue was frozen and ground manually with a mortar and pestle cooled in liquid nitrogen. Intact nuclei were isolated using a protocol from Jiming Jiang - hexylene glycol based method.
ATAC-seq libraries prepared as described in Buenrostro et al. PMID: 25559105
2x50 HiSeq RapidRun v2 - 9 libraries per lane

treatment_protocol: Heat stress: samples were shifted from 30C to 40C; Dehydration stress: samples were removed from liquid media to expose roots to air

tag: replicate

value: Azucena

tag: time point (hr)

tag: treatment group

value: Control

tag: tissue

value: 14 day old leaves (2nd leaf)


title: cm_hey1_-dox_rnaseq

city: Wuerzburg

first: Manfred

last: Gessler

address: Am Hubland

department: Developmental Biochemistry

country: Germany

institute: Biocenter, University of Wuerzburg

data_processing:
sequencing reads were mapped to the mm9 genome using bowtie 1.0
Regulated genes from RNAseq data were identified using Deseq and RPKM values were calculated using custom R scripts
Binding peaks were identified using MACS 1.4.1
Binding peaks were normalized according to the 1000 highest peaks within each sample
Genome_build: mm9
Supplementary_files_format_and_content: wig files generated with MACS 1.4.1, scores represent raw reads

source_name: invitro differentiated murine cardiomyocytes (CM7/1)

extract_protocol:
total RNA was isolated using the Qiagen RNeasy Mini Kit according to manufactures recomendations; Chromatin immuno precipitation was performed as described before in Heisig J, et al. (2012)
NEBNext RNAseq and ChIPseq sample preparation kit according to manufactures recomendation

value: cardiomyocytes

tag: induction

value: control


title: es_hey1_+dox_chipseq

source_name: murine embryonic stem cells (CM7/1)

value: embryonic stem cells

value: 50ng/ml doxycycline for 48h


title: cm_hey2_+dox_chipseq


title: cm_hey1_+dox_chipseq


title: es_hey2_+dox_chipseq


title: es_hey1_-dox_chipseq


title: cm_hey2_-dox_chipseq


title: heat_4h_2

value: Heat


title: ATF4-/- cytosol ribosome profiling, 4 h Tg (rep 2)

description:
B4Cfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx

value: mouse embryonic fibroblasts

value: cytosol


title: cm_hey2_-dox_rnaseq


title: control_30min_3


title: heat_30min_2


title: heat_recovery_4h_1

value: Heat recovery


title: drought_recovery_4h_1

value: Dehydration recovery


title: drought_2h_3

value: Dehydration


title: control_2h_1


title: heat_recovery_4h_2


title: drought_recovery_4h_2


title: control_2h_3


title: cm_hey1_-dox_chipseq


title: drought_2h_2


title: es_hey2_-dox_chipseq


title: ATF4-/- cytosol ribosome profiling, 0.5 h Tg (rep 2)

description:
B05Cfp
ATF4-/- MEFs: Hettmann et al. (PMID 10885750)
Processed data file: translation_expression.xlsx

value: 0.5 h Thapsigargin

value: ribosome profiling


title: control_4h_1


title: heat_4h_3


title: ID115

data_processing:
Reads aligned to the O. sativa Nipponbare - release 7 of the MSU Rice Genome Annotation Project reference genome - including 12 rice chromosomes, chloroplast, mitochondrion, Syngenta pseudomolecule, and the unanchored BAC pseudomolecule using Tophat version 2.0.6, discarding low-quality alignments (quality score below 1)
Counting number of reads that uniquely mapped to genes using HTSeq version 0.6.1 (mode: intersection-strict)
Normalization: compensation for variable sequencing depth between samples using the median-of-ratios method of DESeq2 version 1.6.3 and variance stabilizing transformation provided by the same package. The minimum expression value was subtracted so that zero read counts had an expression value of zero.
Genome_build: Release 7 of the MSU Rice Genome Annotation Project reference genome
Supplementary_files_format_and_content: tab-delimited text file with normalized read counts for each sample

source_name: Rice leaf

growth_protocol: The rice plants were grown hydroponically (Peter's solution) in climate controlled growth chambers at IRRI, 30C, 12h light.

extract_protocol:
Frozen leaf tissue was ground manually with a mortar and pestle cooled in liquid nitrogen. Total RNA was extracted from about 200 to 400 µL of ground tissue using the RNeasy® Plant Mini Kit following manufacturer's instructions.
RNA treated with Baseline-ZERO Dnase, depleted of ribosomal RNA using Epicentre® Ribo-Zero Magnetic Kit for plant leaf tissue. Libraries constructed RNA libraries using the Epicentre® ScriptSeqTM v2 RNA-Seq Library Preparation Kit.
RNA-Seq, using HiSeq® 2000, 51 bp paired-end sequencing, with either 6 or 8 libraries per lane

treatment_protocol: Control (30C, liquid media); Heat (transferred from 30C to 40C; up to 4h); Heat recovery (transferred back to 30C after 2h at 40C; up to 2h); Dehydration (roots exposed to air; up to 2.25h); Dehydration recovery (roots returned to liquid media after 1.5h in air; up to 3.5h)

tag: genotype

value: Tadukan (TD; IRGC#9804, Indica)

tag: time

value: 270 min

value: leaf


title: ID116

value: 300 min


title: ID266

value: 240 min


title: ID267


title: heat_2h_1

value: Azucena

value: 14 day old leaves (2nd leaf)


title: ID113

value: 210 min


title: ID253

value: 165 min


title: heat_30min_3

value: Heat


title: control_30min_2

value: Control


title: ID114


title: ID700


title: ID265


title: R4d rep1

city: NEW YORK

first: Nam-Hai

last: Chua

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Strand-specific single-end RNA-seq reads from replicates were merged and mapped to the Phaeodactylum tricornutum genome (Phatr2) using TopHat (version 2.0.8, specific parameters: --library-type=fr-firststrand -i 40 -I 5000 -g 1 --segment-length=20)
The mapped reads were assembled using Cufflinks (v2.1.1, specific parameters: --library-type=fr-firststrand -I 5000 --min-intron-length=40) with Phatr2 annotation as the reference
The assembled transcripts of each RNA-seq sample were merged and annotated using Cuffcompare (v2.1.1)
The expression levels of each gene were calculated by the fragments per kilobase of exons per million fragments mapped (FPKM) using Cuffdiff (v2.1.1, specific parameters: --library-type=fr-firststrand)
A 2-fold variance in FPKM and a p-value (Fisher’s exact test) less than 0.05 were used as cutoffs to define differentially expressed (DE) genes
Genome_build: Phatr2
Supplementary_files_format_and_content: tab-delimited files include FPKM values and raw read counts for each Sample
Supplementary_files_format_and_content: TranscriptsFPKM.txt:  FPKMs of 10,402 coding genes
Supplementary_files_format_and_content: TranscriptsReadCounts.txt:  Read counts of 10,402 coding genes

molecule: polyA RNA

organism: Phaeodactylum tricornutum

source_name: P. tricornutum cells, Pi resupply 4 days growth

growth_protocol: Axenic cultures of Phaeodactylum tricornutum strain CCMP632 were obtained from the Center for the Culture of Marine Phytoplankton (Maine, USA) and maintained under continuous shaking (100 rpm) in filtered (0.22 M) steam-sterilized artificial sea water (Sigma) supplemented with f/2 nutrients, elements and vitamins (46) with the exception of silica (f/2-Si). Cultures were kept under agitation (100 rpm) at 20°C, under cool white fluorescent lights at 100 µmol.m-2.s-1 with a 12-h photoperiod

extract_protocol:
Total RNA was extracted from P. tricornutum cells using the Trizol method according to the manufacturer’s instructions (Invitrogen). Extracted RNA was treated with TurboDNAse I (Life Technologies AM2238) according to product instructions and the treated RNA was purified using and RNeasy spin column (Qiagen) with 0.5 volumes of ethanol, washed and then eluted with 50 μL room temperature molecular grade water (Qiagen). The quality of the purified RNA was assessed using the Agilent 2100 Bionanalyzer. cDNA libraries for sequence-specific RNA Sequencing (ssRNA-seq) were prepared using the Illumina TruSeq Stranded mRNA Sample Preparation Kit following the Low Sample (LS) Protocol guidelines. The quality and size of the libraries from each sample was tested using an Agilent High Sensitivity D1K ScreenTape System. Samples were pooled into three wells (three to five samples total per well were used) and sequenced on an Illumina HiSeq 2500 with 100-cycle single reads per multiplexed sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For the Pi fluctuation studies, equal aliquots of early exponentially growing cells from the same batch culture were inoculated in parallel in fresh f/2-Si media (control conditions) and in fresh f/2-Si media without phosphate supplement (Pi depleted) and cultured in the same conditions as described above. Pi re-supplementation was performed on 4 day-old Pi depleted cultures by pelleting (5000 x g, 10 min, 4°C) and ressuspension in fresh f/2-Si media. Culture growth was followed using a hematocytometer (Fisher Scientific, USA). All cultures were started with the approximately the same initial cell density of 4.5x105 cells/mL with the exception of recovery experiments started at 2.5x105 cells/mL. All experiments were repeated at least three times with two biological replicates. Cells (225 mL) were harvested by filtration (0.22 M), flash-frozen in liquid nitrogen and maintained at -80°C until used.

tag: strain


title: ID720

value: 120 min


title: cm_hey1_+dox_rnaseq

value: cardiomyocytes

value: 1000ng/ml doxycycline for 48h


title: ID264

value: 180 min


title: ID261

value: DROUGHT

value: 135 min


title: ID110

value: Tadukan (TD; IRGC#9804, Indica)

value: 150 min


title: ID111

value: leaf


title: ID112


title: cm_hey2_+dox_rnaseq


title: ID262


title: ID108


title: ID008-2

value: 105 min


title: R4d rep2


title: P4d rep1

source_name: P. tricornutum cells, Pi depleted 4 days growth


title: ID259


title: ID230-2

value: 90 min


title: ID107


title: P8d rep2

source_name: P. tricornutum cells, Pi depleted 8 days growth


title: heat_2h_3

value: Azucena


title: ID109


title: P8d rep1


title: P4d rep2


title: C8d rep2

source_name: P. tricornutum cells, control full media 8 days growth


title: C4d rep2

source_name: P. tricornutum cells, control full media 4 days growth


title: C8d rep1


title: ID232_2


title: ID080-2


title: mRNAseq from MEF line 129S5E88

description:
polyA+ selected mRNA, sequenced in Illumina's GA2X
WT88

value: C57BL/6J & 129S5SvEvBrd

value: +/+ genotype

value: Mouse Embryonic Fibroblasts (MEFs)

value: confluent passage 4


title: ID227

value: 45 min


title: ID079


title: ID076-2

value: 60 min


title: ID229

value: 75 min


title: ID751

value: 15 min


title: ID078-2


title: ID074-2

value: 30 min


title: ID077

value: DROUGHT


title: ID228-1


title: ID225


title: ID440

value: 240 min


title: ID075

value: Tadukan (TD; IRGC#9804, Indica)


title: C4d rep1


title: ID569

value: 225 min


title: ID826

value: leaf


title: ID570


title: ID438

value: 210 min


title: ID568


title: ID566

value: 180 min


title: ID437

value: 195 min


title: ID567


title: ID226-2


title: ID565

value: 165 min


title: ID830

value: 135 min


title: ID554

value: HEAT


title: ID563


title: ID391


title: ID434

value: 150 min


title: ID521


title: ID564


title: ID389


title: ID516


title: ID388


title: ID390


title: ID517


title: ID518


title: ID503


title: ID386


title: ID515


title: ID436


title: ID186-2

value: 120 min


title: ID520


title: ID387


title: ID385


title: ID384


title: ID383-2


title: ID513

value: 105 min


title: ID382


title: ID512-2

value: 90 min


title: ID435


title: ID381-2


title: ID511

value: 75 min


title: ID380


title: ID510-2

value: 60 min


title: ID379-2


title: ID827

value: 45 min


title: ID509


title: ID524_1

value: 30 min


title: Dmel_ChIP-seq_v5_IP_rep2

city: Vienna

first: Daria

last: Shlyueva

address: Dr. Bohr-gasse,7

country: Austria

institute: IMP

description: PCR amplified DNA

data_processing:
Basecall where performed using Real-Time Analysis (RTA) version > 1.12.4.2 or CASAVA 1.9.1
Reads were mapped to the dm3 genome using bowtie (bowtie -p 12 -f -X 2000 -v 3 -m 1 --best --strata --quiet INDEX -1 reads_1.fa -2 reads_2.fa) excluding chrU, chrUextra, and chrM.
ChIP-seq peaks were called using peakzilla (Bardet et al. 2013) using default parameters
Genome_build: dm3
Supplementary_files_format_and_content: Processed files are tab-delimited text: chromosome, start, end, name, summit, score, ChIP, control, fold enrichment, distribution score, FDR

organism: Drosophila melanogaster

source_name: embryos

extract_protocol: 1g of forzen embryos were fixed and chromatin was isolated and sheared to the average size of 500 bp (Omni Sonic Ruptor 250 Watt Ultrasonic Homogenizer, for 7 cycles (1 min on [Duty cycle 30%, Output 20%], 1 min off)). 500 ul of chromatin was incubated with 25 ul of anti-V5 agarose affinity gel (Sigma, A7345-1ML) for 2 hr at 4° C. 3 ng of material was used for library generation.  Library was constructed following instructions of NEBNext® DNA Library Prep Reagent Set for Illumina® (NEB; cat. no. E6000L). Library amplifcation was done using KAPA Library Amp Real Time (KAPA biosystems: cat.no. KK2701).

tag: age

tag: developmental stage

value: embryo

tag: chip antibody

value: anti-V5 agarose affinity gel (Sigma, catalog# A7345, lot# 021M4839)


title: Dmel_ChIP-seq_v5_input_rep2

description: PCR amplified DNA


title: ID507

value: Tadukan (TD; IRGC#9804, Indica)

value: 15 min

value: leaf


title: ID706

value: CONTROL

value: 300 min


title: ID376


title: ID702

value: 270 min


title: ID032


title: Dmel_ChIP-seq_v5_input_rep1

description: PCR amplified DNA


title: Dmel_ChIP-seq_wt_IP_rep1

description: PCR amplified DNA

value: wild type


title: Dmel_ChIP-seq_wt_IP_rep2

description: PCR amplified DNA


title: Dmel_ChIP-seq_v5_IP_rep1

description: PCR amplified DNA


title: Dmel_ChIP-seq_wt_input_rep2

description: PCR amplified DNA


title: Dmel_ChIP-seq_wt_input_rep1

description: PCR amplified DNA


title: ID176

value: 240 min


title: ID175

value: 225 min


title: ID031


title: A. duranensis methylC-seq

city: East Lansing

first: Chad

middle: E.

last: Niederhuth

state: M

address: 612 Wilson Road

department: Plant Biology

institute: Michigan State University

description: Whole Genome Bisulphite Sequencing of Arachis duranensis

data_processing:
Reads were trimmed, aligned, and methylation called using the methylpy pipeline Schultz et al. Human body epigenome maps reveal noncanonical DNA methylation variation Nature 523, 212–216 (2015).
Genome_build: Aradu_v1.0_20140908 and Araip_v1.0_20140908
Supplementary_files_format_and_content: column 1 = chr = chromosome; column 2 = pos = coordinate for the cytosine position on the chromosome; column 3 = strand = + or - strand; column 4 = mc_class = context of the cytosine and the two following bases from the same strand; column 5 = mc_count = number of reads supporting a methylated cytosine; column 6 = total = total number of reads at that position; column 7 = methylated = cytosine is considered methylated if there is a 1 or unmethylated if there is a 0

organism: Arachis duranensis

source_name: young unexpanded leaves

extract_protocol:
Leaves were ground in liquid nitrogen and DNA extracted using QIAGEN DNAeasy Plant Mini Kit (Cat. No. 69106).
Libraries were constructed according to Urich et. al. MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nature Protocols 10, 475–483 (2015).

tag: cultivar

value: young unexpanded leaves


title: ID142

tag: treatment


title: wild type post-mature green seeds biological replicate 1

city: Los Angeles

first: Bob

last: Goldberg

state: CA

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Post-mature green seeds from Arabidopsis Col 0 wild type were collected

data_processing:
Basecalls performed using RTA version 1.12.4.2
Original data file from the Illumina sequencing pipeline.  Each lane of sequencing is attached as an individual compressed file.  The sequence data are in the QSEQ format.
Sequenced reads were quality-filtered, reads corresponding to rDNA sequences were removed and the resulting filtered reads were mapped to TAIR gene models (v10) using bowtie v0.12.7 with parameters -v 2 -m 1 --best --strata.
Read counts for each gene models were computed using a custom script. Normalized counts are obtained using the EdgeR package v3.10.5 (Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140).
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text file including the normalized counts for gene models

organism: Arabidopsis thaliana

source_name: Post-mature green seeds from Arabidopsis wild type

growth_protocol: Arabidopsis thaliana (L.) Heynh, ecotype Columbia (Col) wild type and ddcc mutant plants were grown under standard greenhouse conditions (Belmonte et al., PNAS 2013). The whole seeds containing post-mature green stage embryos were collected.

extract_protocol:
Collected seeds were quickly frozen in liquid nitrogen and ground to a fine powder using a mortar and pestle. Total RNA was isolated from the powder using the Concert Plant RNA Reagent (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions. Total RNA was treated with RNase-free DNase I (QIAGEN, Valencia, CA) and quantified with Quant-iT™ RiboGreen® RNA reagent (Thermo Fisher Scientific, Grand Island, NY) on a Nanodrop ND-3300.
Approximately 25 nanogram of total RNA was amplified with Nugen Ovation RNA-Seq system v2 (Nugen, San Carlos, CA) and quantified with Picogreen on the Nanodrop ND-3300 (Nanodrop Technologies).  One microgram of double-stranded cDNA was used to prepare the Illumina library using the Illumina TruSeq DNA Sample prep kit (Illumina, San Diego, CA). Libraries were quantified using Quant-iT PicoGreen dsDNA Reagent (Thermo Fisher Scientific , Grand Island, NY) and a Nanodrop ND-3300 instrument. Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

value: Col 0

value: wildtype

value: seed


title: wild type post-mature green seeds biological replicate 2

source_name: Post-mature green seeds from Arabidopsis ddcc mutant


title: ddcc mutant post-mature green seeds biological replicate 2

description: Post-mature green seeds from Arabidopsis Col 0 ddcc mutant were collected

value: ddcc


title: ddcc mutant post-mature green seeds biological replicate 1


title: ID377-2

value: HEAT

value: 30 min


title: ID174

value: 210 min


title: ID029

value: Tadukan (TD; IRGC#9804, Indica)


title: ID173

value: 195 min


title: ID139

value: leaf


title: NSRab mutant rep1

city: Orsay

first: souiai

last: oussema

address: 15, rue Georges Clémenceau -

department: IGM

country: France

institute: CNRS

data_processing:
Mapping of reads to TAIR10 genome was performed using tophat2.0.9  allowing  segment-mismatches of 2 and segment-length equal to 20.
BigWig files for read mapping were generated by converting the strand-specific coverage of TAIR10 genome computed by bedtools with the UCSC bedGraphToBigWig program
Genome_build: TAIR10.22

source_name: plantlets

growth_protocol: Plants were grown in a long day (16h light/ 8h dark) on solid half-strength MS (Duchefa biochemie, M0222) medium. Plantlets were collected at 15 days.

extract_protocol:
Plantlets were collected, frozen in liquid nitrogen and grind. RNA was extracted using Qiagen RNeasy® Plant kit according to the supplier’s instructions (QIAGEN S.A, France) including the DNAse treatment. RNA libraries were prepared for sequencing using standard Illumina protocols.
TruSeq Stranded mRNA SamplePrep Guide 15031047_D protocol (Illumina®, California, U.S.A.). The RNA-seq samples have been sequenced in paired-end (PE) with a sizing of 260 bp and a read length of 100.

treatment_protocol: 14 days old plantlets were transfer to a 1μM NAA medium (solid half-strength MS with 1µM NAA) for 24 hours.

value: NSRa/NSRb


title: NSRab mutant rep3


title: NSRab mutant rep2


title: A. ipaensis methylC-seq

description: Whole Genome Bisulphite Sequencing of Arachis ipaensis

organism: Arachis ipaensis


title: ID172

value: CONTROL

value: 180 min


title: ID030


title: WT rep2

value: wild type


title: ID028


title: WT rep1


title: ID170

value: 150 min


title: ID026


title: ID168-2

value: 120 min


title: ID024-2


title: ID025

value: 135 min


title: ID021

value: 75 min


title: ID166-2

value: 90 min


title: ID023

value: 105 min


title: ID022_1


title: ID165


title: ID167


title: ID027

value: 165 min


title: ID171


title: ID169


title: ID164-2

value: 60 min


title: ID163

value: 45 min


title: ID020-2


title: WT rep3


title: ID019


title: ID017

value: 15 min


title: ID018-2

value: Tadukan (TD; IRGC#9804, Indica)

value: 30 min


title: ID126

value: Pandan wangi (PW; IRGC#35834, Japonica)

value: 300 min

value: leaf


title: ID125

value: 270 min


title: ID161

value: CONTROL


title: ID277


title: ID124

value: 240 min


title: ID275

value: 210 min


title: ID276


title: ID123


title: ID121


title: ID273


title: ID272

value: 150 min


title: ID120


title: ID122

value: 180 min


title: ID118

value: 120 min


title: ID240

value: DROUGHT


title: ID270


title: ID239

value: 105 min


title: ID117


title: ID271

value: 135 min


title: ID087


title: ID088


title: ID086

value: 90 min


title: ID237

value: 75 min


title: ID238


title: ID162-2

value: Tadukan (TD; IRGC#9804, Indica)


title: ID085


title: ID236

value: 60 min


title: ID234

value: Pandan wangi (PW; IRGC#35834, Japonica)

value: 30 min


title: ID233

value: 15 min

value: leaf


title: ID082


title: ID083

value: 45 min


title: ID081


title: ID274


title: ID578

value: 240 min


title: ID448


title: ID576

value: 210 min


title: ID446


title: ID447

value: 225 min


title: ID002-2


title: ID445

value: 195 min


title: ID575


title: ID574

value: 180 min


title: ID822

value: 150 min


title: ID444


title: ID119

value: DROUGHT


title: ID573

value: 165 min


title: ID823


title: ID441

value: 135 min


title: ID571


title: ID538

value: HEAT


title: ID407


title: ID235


title: ID537


title: ID406


title: ID084


title: ID405


title: ID536


title: ID534


title: ID404


title: ID403


title: ID533


title: ID532


title: ID531


title: ID402


title: ID400


title: ID572


title: ID528

value: 90 min


title: ID399

value: 120 min


title: ID529

value: Pandan wangi (PW; IRGC#35834, Japonica)

value: 105 min


title: ID527

value: 75 min


title: ID398

value: leaf


title: ID396


title: ID526-1

value: 60 min


title: ID395


title: ID394

value: 45 min


title: ID821

value: 30 min


title: ID397


title: ID525


title: ID393


title: ID523

value: 15 min


title: ID392


title: ID535

value: 195 min


title: ID707

value: CONTROL

value: 300 min


title: ID703

value: 270 min


title: ID046

value: 240 min


title: ID047


title: ID048


title: ID192


title: ID191

value: 225 min


title: ID401

value: HEAT

value: 150 min


title: ID820

value: 120 min


title: ID188

value: Pandan wangi (PW; IRGC#35834, Japonica)


title: ID045

value: 210 min


title: ID514-2

value: 165 min


title: ID143

value: leaf


title: ID044

value: 180 min


title: ID190


title: ID043


title: ID140


title: ID709


title: ID185

value: 135 min


title: ID041


title: ID042


title: ID184


title: THP1_3030_IgG

city: Cambridge

first: Carl

middle: G

last: de Boer

state: MA

address: 415 Main St

institute: The Broad Institute

description:
Used in final analysis: no
ChIP conditions: 2mM EGS (Thermo Scientific) for 30 minutes, 1% of formaldehyde for 30 minutes at room temperature

data_processing:
Aligned to genome; bowtie version 0.12.7 (bowtie -q -n 2 -e 70 --phred33-quals -X 1000 -p 4 -S -m 1[ …])
Merge SAMs from different runs; samtools version 1.2 (samtools merge […])
Sort BAMs by index; samtools version 1.2 (samtools sort […])
Remove PCR duplicates; picard ([…] REMOVE_DUPLICATES=true)
Call peaks using input as background; homer version 4.7.2 (findPeaks -style factor -fdr 0.01 -LP 0.01 -P 0.1 […])
Convert BAMs to BigWigs
Genome_build: hg19
Supplementary_files_format_and_content: *.bw: bigwig files containing genomic coverage; *.gff: GFF files containing peaks called for each factor

organism: Homo sapiens

source_name: THP-1 cells

growth_protocol: Cells were grown in RPMI with addition of 50uM 2-mercaptoethanol and 10% fetal bovine serum.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as previously described (Kowalczyk, 2012) with minor modifications. Specifically, cells were first fixed in 2mM EGS (Thermo Scientific) for 30 minutes or 1 hour, followed by 1% of formaldehyde for 30 or 15 minutes at room temperature respectively. Chromatin was sonicated to a size less than 500bp and then incubated overnight with appropriate antibodies.
 ChIP sequencing (ChIP-Seq) libraries were prepared through the process of DNA end-repair (Epicentre), A-base addition and adaptor ligation using indexed Illumina adaptors followed by enrichment PCR. All enzymatic steps are carried out using enzymes from New England Biolabs. Final libraries were pooled, size selected and sequenced on HiSeq2500 with 25 paired-end reads.

tag: cell type

value: MLL-AF9 leukemia

value: Rabbit IgG, purified (Millipore, PP64B, lot DAM1852692, 1mg/ml)


title: ID183

value: 105 min


title: NOMO1_biotin_HoxA9

description:
Used in final analysis: no
ChIP conditions: 1% formaldehyde for 10 minutes at room temperature

source_name: NOMO-1 cells

value: NOMO-1; BirA; HoxA9-bio

value: Dynabeads MyOne Streptavidin T1 (Invitrogen, cat. no. 65001)


title: ID040

value: CONTROL


title: THP1_3030_Clock

description:
Used in final analysis: yes
ChIP conditions: 2mM EGS (Thermo Scientific) for 30 minutes, 1% of formaldehyde for 30 minutes at room temperature

value: anti-KAT13D/Clock (Abcam, ab3517, lot GR130170-5, 1mg/ml)


title: THP1_3030_Bmal1

value: anti-Bmal1 (Abcam, ab3350, lot GR152555-3, 1mg/ml)


title: THP1_115_Bmal1

description:
Used in final analysis: no
ChIP conditions: 2mM EGS (Thermo Scientific) for 1 hour, followed by 1% of formaldehyde for 15 minutes at room temperature


title: THP1_115_IgG


title: THP1_115_Clock


title: NOMO1_biotin_BirA

value: NOMO-1; BirA


title: ID039


title: NOMO1_3030_IgG


title: NOMO1_3030_Clock


title: NOMO1_3030_input


title: ID038

value: 90 min


title: ID187


title: ID182


title: ID181

value: 75 min


title: NOMO1_3030_Bmal1


title: ID180

value: Pandan wangi (PW; IRGC#35834, Japonica)

value: 60 min


title: NOMO1_115_input


title: ID036


title: NOMO1_115R2_IgG


title: NOMO1_115R2_Clock


title: ID179

value: 45 min


title: ID035

value: leaf


title: NOMO1_115R2_Bmal1


title: NOMO1_115R1_IgG


title: T1-6-2

value: 30 min


title: ID177

value: 15 min


title: ID178


title: NOMO1_115R1_Clock

value: MLL-AF9 leukemia


title: ID136

value: Kinandang puti (KP; IRGC#44513, Indica)

value: 300 min


title: ID288


title: NOMO1_115Ab2_Bmal1

value: anti-Bmal1 (Abcam, ab93806, lot GR8441-9, 1mg/ml)


title: ID135

value: 270 min


title: ID287


title: ID033

value: CONTROL


title: ID037


title: ID286

value: 240 min


title: NOMO1_3030Ab2_Bmal1


title: wdr5_rep1_fRIP-seq

middle: R

last: Kelley

address: 7 Divinity Ave.

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: fRIP-seq/RNA-seq

data_processing:
Basecalls performed using CASAVA version 1.4
We aligned sequencing reads to human genome assembly hg19 and GENCODE v18 reference annotation (Harrow et al. 2012) using TopHat (Trapnell, Pachter, and Salzberg 2009) using the -M option
We estimated transcript and gene abundances per REPLICATE as well as depletion/ enrichment calls using the Cuffdiff 2 cuffNorm option
We made significance calls to date matched input samples per CONDITION  using  Cuffdiff 2 with the -u option
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample at gene and isoform level in addition to CuffDiff 2 generated p and q values with significance calls

source_name: K562 cells

growth_protocol: K562 cells (ATCC cat #CCL-243) were grown in RPMI 1640 (Invitrogen, cat #22400105) with 10% FBS and 1% Antibiotic-Antimycotic 100X (Invitrogen, cat #15240062).

extract_protocol:
We re-suspended frozen pellets in 1 mL of RIPA lysis buffer (50mM Tris (pH 8), 150 mM KCl, 0.1% SDS, 1% Triton-X, 5 mM EDTA, 0.5% sodium deoxycholate,0.5 mM DTT (add fresh) + protease inhibitor cocktail (Thermo Scientific, PI-87785) + 100 U/ml RNaseOUTTM  (Life Technologies , 10777-019)). We incubated cells at 4°C for 10 minutes before lysing on a Branson® digital sonifier using 10% amplitude for 0.7 seconds on and 1.3 seconds off at 30 second intervals for a total of 90 seconds. We used chilled tube holders and swapped them out between shearing runs to reduce temperature elevation. After lysis, we spun the lysate at 4°C max speed for 10 minutes.  We collected supernatant and diluted by adding equal volume of fRIP binding/wash buffer (150 mM KCl, 25 mM Tris (pH 7.5), 5 mM EDTA, 0.5% NP-40, 0.5 mM DTT (add fresh), 1X PIC (add fresh), 100 U/mL RNaseOUT  (add fresh)). At this point, we removed 50 μl of lysate for input sample and stored at -20°C for later RNA purification and library construction. After dilution, we clarified the lysate by passage through a 0.45 μM syringe filter. We then “pre-cleared” filtered lysate by incubating with Dynabeads® Protein G (Life Technologies cat#10004D) at a concentration of 25 μl of beads per 5 million cells for 30 minutes at 4°C with slow rotation. We flash froze pre-cleared lysate in 1 mL aliquots of ~5 million cells and stored it at -80 °C. For fRIP, we thawed lysate on ice and added 6 μg of HuR antibody (Santa Cruz, sc-5483). After addition of antibody, we rotated lysate at 4°C for 2 hours before adding 50 μl of Dynabeads® Protein G. We rotated beads and lysate at 4°C for 1 hour before washing 2X with 1 mL of fRIP binding/washing buffer + 1X PIC and 100 U/mL RNaseOUT. After the final wash, we removed the supernatant and froze and stored the beads at -20°C. We re-suspended the frozen beads in 56 μl of RNase-free water and added 33uL of 3X reverse-crosslinking buffer (3X PBS (without Mg or Ca), 6% N-Lauroyl Sarcosine, 30 mM EDTA, 15 mM DTT (add fresh)), 10 μl of Proteinase K (Life Technologies, cat #AM9516), and 1 μl of RNaseOUT to both the re-suspended beads and input sample. We performed protein degradation and reverse-crosslinking for 1 hour at 42°C, then another 1 hour at 55°C. We added beads and reaction buffer to 1 mL of TriZol (Life Technologies, 15596-026). After agitation, we added 200 μl of chloroform followed by ~15 seconds of vigorous agitation and a 20 minute microcentrifuge spin at 4°C max speed. We collected the aqueous layer, added it to 750 μl of ethanol + 1 μl GlycoBlue™, and ran it over a Qiagen RNeasy® min-elute column (Qiagen, cat #74204). We extracted RNA using the buffer RWT/3X isopropanol modification detailed in “Appendix B: Optional On-Column DNAse Digestion…” of the Qiagen miRNeasy® Mini Handbook. We eluted RNA in 15μl of RNase-free water.
to remove ribosomal RNA, we fed ≥ 70 ng of input and fRIP RNA into the Ribo-Zero™ Magnetic Gold Kit (Epicentre, cat #MRZG12324) followed by a cleanup using Agencourt RNAClean XP beads (Beckman Coulter, cat #A63987) and elution with 19.5 uL of Elute, Prime, Fragment mix from the TruSeq RNA Sample Preparation Kit (Illumina, cat #RS-122-2001). We performed library construction per the vendor’s instructions, starting with the “Incubate RFP” step. We pooled the resulting cDNA libraries and subjected them to paired-end sequencing on an Illumina HiSeq 2500 at a depth of 31 base pairs per read.

treatment_protocol: CROSSLINKING: We collected cells with a gentle 5 minute spin 500g and washed with room temperature PBS. We re-suspended at 5e6 cells per ml in room temperature RPMI media sans FBS or Antibiotic-Antimycotic and added formaldehyde to a final concentration of 0.1%. We cross-linked at room temperature for 10 minutes and then halted it by quenching for 5 minutes at room temperature after adding glycine to a final concentration of 125 mM at a medium pace. We spun cells for 5 minutes 500g and washed 2X in 4°C PBS. We flash froze pellets of 10e6 cells and stored them at -80 °C

tag: frip antibody

tag: passage

value: four to seven


title: wdr5_rep3_fRIP-seq

description: fRIP-seq/RNA-seq

tag: cell line


title: suz12_rep2_fRIP-seq

description: fRIP-seq/RNA-seq

value: Cell Signaling,3737S,3


title: suz12_rep3_fRIP-seq

description: fRIP-seq/RNA-seq


title: wdr5_rep2_fRIP-seq

description: fRIP-seq/RNA-seq


title: suz12_rep1_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID134


title: ID133

value: 210 min


title: ID284

value: 180 min


title: rbbp5_rep3_fRIP-seq

description: fRIP-seq/RNA-seq


title: stag2_rep1_fRIP-seq

description: fRIP-seq/RNA-seq

value: Cell Signaling,5882S,1


title: NOMO1_115R1_Bmal1

value: anti-Bmal1 (Abcam, ab3350, lot GR152555-3, 1mg/ml)


title: rbbp5_rep2_fRIP-seq

description: fRIP-seq/RNA-seq


title: phf8_rep3_fRIP-seq

description: fRIP-seq/RNA-seq


title: rbbp5_rep1_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID130

value: 150 min


title: phf8_rep1_fRIP-seq

description: fRIP-seq/RNA-seq


title: phf8_rep2_fRIP-seq

description: fRIP-seq/RNA-seq


title: pcbx_rep3_fRIP-seq

description: fRIP-seq/RNA-seq

value: Cell Signaling,2600S,2


title: ID131

value: 165 min

value: leaf


title: ID280

value: 120 min


title: stag2_rep3_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID282

value: Kinandang puti (KP; IRGC#44513, Indica)


title: pcbx_rep2_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID279

value: 105 min


title: ID127


title: pcbx_rep1_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID128


title: ID285


title: ID132


title: pcaf_rep3_fRIP-seq

description: fRIP-seq/RNA-seq

value: Cell Signaling,3378S,1


title: pcaf_rep1_fRIP-seq

description: fRIP-seq/RNA-seq


title: pcaf_rep2_fRIP-seq

description: fRIP-seq/RNA-seq


title: pabp_rep3_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID248

value: DROUGHT


title: ID281

value: 135 min


title: ID246


title: pabp_rep1_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID095


title: ID283


title: ID094

value: 90 min


title: nup98_rep2_fRIP-seq

description: fRIP-seq/RNA-seq

value: Cell Signaling,2598S,2

value: four to seven


title: nup98_rep1_fRIP-seq

description: fRIP-seq/RNA-seq


title: lsd1_rep3_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID069

value: 75 min


title: ID129


title: lsd1_rep1_fRIP-seq

description: fRIP-seq/RNA-seq


title: lsd1_rep2_fRIP-seq

description: fRIP-seq/RNA-seq


title: input3_rep2_RNA-seq

description: fRIP-seq/RNA-seq


title: input3_rep3_RNA-seq

description: fRIP-seq/RNA-seq


title: ID066-2

value: 45 min


title: ID091


title: ID242

value: 30 min


title: ID092

value: 60 min


title: ID090


title: input3_rep1_RNA-seq

description: fRIP-seq/RNA-seq


title: ID096


title: ID241

value: 15 min


title: pabp_rep2_fRIP-seq

description: fRIP-seq/RNA-seq


title: input2_rep1_RNA-seq

description: fRIP-seq/RNA-seq


title: input2_rep2_RNA-seq

description: fRIP-seq/RNA-seq


title: ID089


title: input2_rep3_RNA-seq

description: fRIP-seq/RNA-seq


title: input1_rep3_RNA-seq

description: fRIP-seq/RNA-seq


title: ID586

value: 240 min


title: nup98_rep3_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID456


title: ID245


title: input1_rep2_RNA-seq

description: fRIP-seq/RNA-seq


title: ID585

value: 225 min


title: ID244

value: leaf


title: ID594

value: 210 min


title: imp1_rep3_fRIP-seq

description: fRIP-seq/RNA-seq

value: Cell Signaling,8482S,1


title: imp1_rep2_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID454

value: Kinandang puti (KP; IRGC#44513, Indica)


title: imp1_rep1_fRIP-seq

description: fRIP-seq/RNA-seq


title: hur_rep3_fRIP-seq

description: fRIP-seq/RNA-seq

value: Santa Cruz,sc-5483,A0814


title: ID583

value: 195 min


title: hur_rep2_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID452

value: 180 min


title: hnrnpu_rep2_fRIP-seq

description: fRIP-seq/RNA-seq


title: hnrnpu_rep3_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID451

value: 165 min


title: ID581


title: ID450

value: 150 min


title: ID453


title: hur_rep1_fRIP-seq

description: fRIP-seq/RNA-seq

value: four to seven


title: ID582


title: ID449

value: 135 min


title: hnrnpu_rep1_fRIP-seq

description: fRIP-seq/RNA-seq


title: hnrnph_rep2_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID580


title: input1_rep1_RNA-seq

description: fRIP-seq/RNA-seq


title: ID424

value: HEAT


title: ID522


title: hdac1_rep3_fRIP-seq

description: fRIP-seq/RNA-seq

value: Cell Signaling,5356S,3


title: hnrnph_rep1_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID455


title: hdac1_rep2_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID553


title: ID422


title: hdac1_rep1_fRIP-seq

description: fRIP-seq/RNA-seq


title: ezh2_rep2_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID552


title: ID421


title: ezh2_rep1_fRIP-seq

description: fRIP-seq/RNA-seq


title: dnmt1_rep3_fRIP-seq

description: fRIP-seq/RNA-seq


title: hnrnph_rep3_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID551


title: ID420


title: ID550


title: dnmt1_rep1_fRIP-seq

description: fRIP-seq/RNA-seq


title: dnmt1_rep2_fRIP-seq

description: fRIP-seq/RNA-seq


title: ctcf_rep2_fRIP-seq

description: fRIP-seq/RNA-seq

value: Cell Signaling,3418S,1


title: ID419


title: ID548


title: ctcf_rep3_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID418


title: ID417


title: chd7_rep3_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID416


title: chd7_rep1_fRIP-seq

description: fRIP-seq/RNA-seq


title: chd4_rep3_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID546

value: 120 min


title: ID549


title: ctcf_rep1_fRIP-seq

description: fRIP-seq/RNA-seq


title: chd4_rep2_fRIP-seq

description: fRIP-seq/RNA-seq


title: chd4_rep1_fRIP-seq

description: fRIP-seq/RNA-seq


title: chd7_rep2_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID545

value: 105 min


title: ID415


title: chd1_rep3_fRIP-seq

description: fRIP-seq/RNA-seq

value: Cell Signaling,4351S,1


title: ID414

value: leaf


title: chd1_rep1_fRIP-seq

description: fRIP-seq/RNA-seq


title: chd1_rep2_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID544

value: 90 min


title: cbx_rep3_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID413


title: ID543

value: 75 min


title: ID412

value: Kinandang puti (KP; IRGC#44513, Indica)


title: cbx_rep2_fRIP-seq

description: fRIP-seq/RNA-seq


title: cbx_rep1_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID547


title: cbp_rep3_fRIP-seq

description: fRIP-seq/RNA-seq

value: Cell Signaling,7389S,1


title: ID411

value: 60 min


title: cbp_rep1_fRIP-seq

description: fRIP-seq/RNA-seq


title: cbp_rep2_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID541

value: 45 min


title: ID410


title: ID540

value: 30 min


title: ID409


title: adar_rep2_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID408

value: 15 min


title: ID539


title: adar_rep1_fRIP-seq

description: fRIP-seq/RNA-seq

value: four to seven


title: ID708

value: CONTROL

value: 300 min


title: ID064


title: ID721

value: 270 min


title: ID063


title: ID208

value: 240 min


title: ID062


title: ID207

value: 225 min


title: ID144


title: ID205

value: 195 min


title: ID061

value: 210 min


title: ID542

value: HEAT

value: leaf


title: ID137


title: ID204

value: 180 min


title: ID060

value: Kinandang puti (KP; IRGC#44513, Indica)


title: ID203

value: 165 min


title: adar_rep3_fRIP-seq

description: fRIP-seq/RNA-seq


title: ID202

value: 150 min


title: ID059


title: ID058


title: ID201

value: 135 min


title: ID057


title: ID056

value: 120 min


title: ID200


title: ID055

value: 105 min


title: ID054

value: 90 min


title: ID199

value: CONTROL


title: ID198


title: ID197

value: 75 min


title: ID195

value: 45 min


title: ID052

value: 60 min


title: ID051


title: ID206


title: ID196


title: ID050

value: 30 min


title: ID193

value: 15 min


title: ID049


title: ID258

value: Azuenca (AZ; IRGC#328, Japonica)

value: 300 min


title: ID106

value: leaf


title: ID257

value: 270 min


title: ID256

value: 240 min


title: ID255

value: 210 min


title: ID105


title: ID104


title: ID103


title: ID102

value: 180 min


title: ID254


title: ID053

value: Kinandang puti (KP; IRGC#44513, Indica)


title: ID100

value: 150 min


title: ID252


title: ID263

value: 165 min


title: ID251

value: DROUGHT

value: 135 min


title: ID097

value: 105 min


title: ID260

value: 120 min


title: ID098


title: ID101


title: ID506-2


title: ID194

value: CONTROL


title: ID099


title: ID223


title: ID071


title: ID070-2

value: 90 min


title: ID249


title: ID221

value: 75 min


title: ID093

value: Azuenca (AZ; IRGC#328, Japonica)


title: ID222-2


title: ID502-2

value: 60 min


title: ID220-2

value: leaf


title: ID218-2

value: 30 min


title: ID243-2


title: ID217

value: 15 min


title: ID065


title: ID562

value: 240 min


title: ID432


title: ID560

value: 210 min


title: ID431

value: 225 min


title: ID561


title: ID430


title: ID828

value: 195 min


title: ID559


title: ID224-2


title: ID558

value: 180 min


title: ID427

value: 165 min


title: ID556

value: 150 min


title: ID425

value: 135 min


title: ID072-2

value: HEAT


title: ID505


title: ID426


title: ID374


title: ID067

value: DROUGHT

value: 45 min


title: ID469


title: ID470


title: ID504


title: ID371


title: ID803


title: ID501


title: ID370


title: ID499


title: ID428


title: ID498-2

value: 120 min


title: ID500

value: Azuenca (AZ; IRGC#328, Japonica)


title: ID368


title: ID433


title: ID367-2


title: ID557


title: ID375


title: ID496-2

value: 90 min


title: ID365-2

value: leaf


title: ID495

value: 75 min


title: ID366

value: 105 min


title: ID497


title: ID364


title: ID494-2

value: 60 min


title: ID068-2


title: ID362


title: ID492-2

value: 30 min


title: ID363-2


title: ID493-2


title: ID361-2


title: ID360

value: 15 min


title: ID705

value: CONTROL

value: 300 min


title: ID016


title: ID752

value: 270 min


title: ID219


title: ID141_1

value: 225 min


title: ID701


title: ID141


title: ID158

value: 210 min


title: ID159


title: ID160

value: 240 min


title: ID138

value: 195 min


title: ID157


title: ID156

value: 180 min


title: ID153

value: 135 min


title: ID010

value: Azuenca (AZ; IRGC#328, Japonica)

value: 150 min


title: ID009

value: leaf


title: ID155

value: 165 min


title: ID012


title: ID011


title: ID013


title: ID231-2

value: 120 min


title: ID491

value: HEAT


title: ID152-2


title: ID150-2

value: 90 min


title: ID007

value: 105 min


title: ID006-2

value: CONTROL


title: ID005

value: 75 min


title: ID004

value: 60 min


title: ID148-2


title: ID369


title: ID003

value: 45 min


title: ID147


title: ID577-2

value: 30 min


title: ID001

value: 15 min


title: ID146-2


title: J1018_treated

first: Andreas

last: Schlattl

address: Dr. Boehringer-Gasse 5-11

institute: Boehringer Ingelheim RCV GmbH & Co KG

description: test sample

data_processing:
Read sequence alignment using STAR aligner v2.3.0.1 against hybrid human(GRCh37/hg19)/mouse genome(GRCm38/mm10)
Retaining only reads that map uniquely to human chromosomes
Realignment of retained reads using GNAP aligner version 2012-12-20 to human reference genome (GRCh37/hg19)
HTSeq version 0.5.3 on Ensembl v70 annotation
GC-content correction using EDASeq
Differential gene expression analysis using DESeq version 1.18.0
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited format for differential gene expression analysis results; matrix for raw read counts after GSNAP alignment

source_name: A375 melanoma bearing mouse

extract_protocol:
Five slides (5 µm each) from frozen xenografts were used for total RNA extraction using TRIzol reagent (Invitrogen). RNA was purified using a miRNeasy kit (Qiagen) according to the manufacturer's instructions. RNA-seq transcriptome libraries were prepared following the TruSeq RNA Sample Preparation v2 (Illumina, Part# 15026495 Rev. A), using 2 μg of total RNA. PolyA+ RNA was isolated using Sera-Mag oligo(dT) beads (Thermo Scientific) and fragmented with the Ambion Fragmentation Reagents kit. cDNA synthesis, end repair, A-base addition and ligation of the Illumina-indexed adaptors were performed according to Illumina's protocol. Libraries were then PCR amplified using Phusion DNA polymerase (NEB) for 14 PCR cycles before quantification and multiplexing. 10 pmol of multiplexed (n=4) paired-end libraries were sequenced with the Illumina HiSeq1000 (2 × 50-nt read length). Reads that passed the chastity filter of Illumina BaseCall software were used for subsequent analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A375 bearing mice were treated with 120 mg/kg vemurafenib until day 39 (n=5) when tumors became resistant to vemurfenib treatment. For comparison control untreated A375 tumors (n=4) were taken and frozen (liquid nitrogen). For RNA extraction see extract protocol.

value: A375 tumor

tag: phenotype

value: vemurafenib-resistant

tag: host mouse treatment

value: vemurafenib


title: J1017_treated

description: test sample


title: J1019_treated

description: test sample


title: J1015_treated

description: test sample


title: J1013_untreated

description: control sample

value: vemurafenib-sensitive


title: J1016_treated

description: test sample


title: Med20/Rrp6 C

city: Göteborg

first: Jonas

last: Carlsten

address: Medicinaregatan 9A

department: Biomedicin

country: Sweden

institute: University of Gothenburg

description: med20:natMX rrp6∆::KanMx6 leu1-32 ura4-D20

data_processing:
Qualitycontrolled, filtered and trimmed using FASTX-Toolkit Hannon Lab
Aligment against S. Pombe genome EF2 using Bowtie 0.12.7
Differential Expression using DEseq
Genome_build: S. Pombe EF2
Supplementary_files_format_and_content: Microsoft Excel, Differential expression data with baseMeanA as wt control and baseMeanB as corresponding mutant strain.

organism: Schizosaccharomyces pombe

growth_protocol: YEA liquid medium - Yeast Extract + Casaminacids + Adenine + Glucose

extract_protocol:
Hot Phenol RNA extraction, Qiagen RNA-easy clean up
Poly-A enrichment using oligo(dT) beads. cDNA synthesis using Invitrogen Supercript III. Incorporation of dUTP on second strand. Standard Illumina library preparation protocol.

treatment_protocol: 30 degrees, harvested during logaritmic phase, O.D. 0,5 - 1

tag: genotype/variation

value: knockout of med20 and rrp6 gene


title: J1011_untreated

description: control sample

tag: tissue


title: Med20/Rrp6 A

description: med20:natMX rrp6∆::KanMx6 leu1-32 ura4-D18


title: J1014_untreated

description: control sample


title: ID151

value: Azuenca (AZ; IRGC#328, Japonica)

value: leaf


title: Med20/Rrp6 B

description: med20:natMX rrp6∆::KanMx6 leu1-32 ura4-D19


title: Rrp6 B

description: h- Leu1-32 His2 Ura4 DS/E  216 rrp6∆::KanMx6 Otr1R(Sph1)::ura+

value: knock out of rrp6 gene


title: Med20 C

description: h+ leu1-32 ura4-D18 med20:NAT

value: knock out of med20 gene


title: Med20 A

description: h+ leu1-32 ura4-D18 med20:NAT


title: WT C

description: h- L974

source_name: wild type

value: wild type


title: J1012_untreated

description: control sample


title: Med20 B

description: h+ leu1-32 ura4-D18 med20:NAT


title: WT B

description: h- L973


title: Rrp6 A


title: ID149


title: H3K4me3 Smyd3KO ChIPseq_replicate 2

city: Vassilika Vouton, Herakleion

first: Iannis

last: Talianidis

state: Crete

address: 100 N. Plastira Str

department: Institute of Molecular Biology and Biotechnology

country: Greece

institute: Foundation for Research and Technology - Hellas

description:
H3K4me3 ChIP DNA from liver extract from 8.5mo C57BL6/CBA DEN treated Smyd3KO mouse 2
H3K4me3_Smyd3KO_ChIP_enriched_regions.bed.gz

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer.
Sequenced reads were trimmed for adaptor sequence using cutadapt software and mapped to mm9 whole genome using: for RNA-Seq tophat 2.0.9 with default settings and using additional transcript annotation data for the mm9 genome from Illumina iGenomes (http://cufflinks.cbcb.umd.edu/igenomes.html), for ChIP-Seq, using Bowtie2 with default parameters.
Tags overlapping the Ensembl build 67 mouse exons were counted and filtered for artifacts as follows: if an annotated gene had up to five exons, tag presence was required in at least two exons. If an annotated gene had E >5 exons, tag presence was required in at least E/5 exons. The final gene counts were calculated as the sums of their exon tags. The counts table was normalized using EDASeq and analyzed for differential expression using DESeq. The final list of differentially expressed genes was derived by the genes demonstrating a binomial test p-value less than 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: [RNA-Seq] Tab-delimited files containing DESeq normalized counts for each Ensembl gene. [ChIP-Seq] bigWig and bed files.

source_name: Liver

growth_protocol: C57Bl6 mice were maintained in grouped cages in a temperature controlled, pathogen-free facility on a 12-h light/dark cycle and fed by a standard chow diet (Altromin 1324; 19% protein, 5% fat) and water ad libitum.

extract_protocol:
Approximately 20 µg of total RNAs were used for mRNA isolation using the Dynabeads® mRNA DIRECT™ Micro Kit (Life Technologies, Carlsbad, CA, USA)
For RNA-Seq experiments, the isolated mRNA was digested with RNaseIII, hybridized and ligated to Ion Adaptors, reverse transcribed, barcoded and amplified, using the Ion Total RNA-Seq Kit v2 (Life Technologies, Carlsbad, CA, USA). Samples were processed on an OneTouch 2 instrument and enriched on a One Touch ES station. Templating was performed using the Ion PI™ Template OT2 200 Kit (Life Technologies, Carlsbad, CA, USA) and sequencing with the Ion PI™ Sequencing 200 Kit on Ion Proton PI™ chips (Life Technologies, Carlsbad, CA, USA) according to commercially available protocols. For ChIP-Seq experiments, chromatin immunoprecipitation was performed as described in (Schmidt et al., 2009) http://www.ncbi.nlm.nih.gov/pubmed/19275939 except the first step of crosslinking, which was performed as follows. Liver tissue was minced to small pieces in PBS and after addition of formaldehyde to a 1% final concentration immediately was subjected to 10 strokes of dounce homogenization. Cross-linking was continued for 10 min and stopped by the addition of glycine at 0.125 M final concentration. Immunoprecipitations were performed with antibodies against RNA Pol-II (Euromedex 1PB-7G5 LOT number 072105), H3K4Me3 (Abcam ab8580 - LOT number GR164534-1) and Smyd3 antiserum raised in-house in rabbits injected with full length recombinant Smyd3 protein.

treatment_protocol: Mice were left untreated or treated by a single intraperitoneal injection of 25mg/kg diethylnitrosamine (N0756 Sigma) and sacrificed at 8.5 months of age. DEN (diethylnitrosamine) is a hepatotoxic agent whose administration triggers late onset hepatocellular carcinoma (HCC). DEN treatment is commonly used to model HCC in mice. Livers were dissected and divided for the preparation of RNA and crosslinked chromatin.

value: 8.5 months

value: liver

value: H3K4Me3 (Abcam, catalog# ab8580, lot# GR164534-1)


title: H3K4me3 Smyd3KO DNA Input replicate 1

description: H3K4me3 Input DNA from liver extract from 8.5mo C57BL6/CBA DEN treated Smyd3KO mouse 1

value: none (input)


title: H3K4me3 Smyd3KO ChIPseq_replicate 1

description:
H3K4me3 ChIP DNA from liver extract from 8.5mo C57BL6/CBA DEN treated Smyd3KO mouse 1
H3K4me3_Smyd3KO_ChIP_enriched_regions.bed.gz


title: H3K4me3 WT DNA Input replicate 1

description: H3K4me3 Input DNA from liver extract from 8.5mo C57BL6/CBA DEN treated WT mouse 1

value: WT


title: CD4 SP oxBS-seq replicate 2

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

institute: Flatiron Institute

data_processing:
First the sequencing adapters were removed from the reads when encountered.
Bismark v0.7.12 (Krueger and Andrews 2011) was used to align the BS and oxBS reads against the mm9 reference genome and lambda phage DNA simultaneously. The alignment was done using the paired-end Bowtie 2 (Langmead and Salzberg 2012) backend with the following parameters ”-I 0 -X 2000 -N 0”.
The “bismark_methylation_extractor” script distributed with the Bismark aligner was used to extract the number of unconverted and converted read-outs for each cytosine with the following parameters “--paired-end --CX --cutoff 10 --no_overlap --bedGraph --counts”. The cytosines having at least 10 read-outs across all six samples were taken into account.
Genome_build: mm9
Supplementary_files_format_and_content: The processed data files have been generated by the bismark_methylation_extractor script, which is part of the Bismark software package.
The column headers are:<chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>
as described in http://www.bioinformatics.babraham.ac.uk/projects/bismark/Bismark_User_Guide.pdf.

source_name: CD4 SP cells_oxBS-seq

growth_protocol: 4-6 weeks old female C57/BL6 mice obtained from Jackson labs were used for cell isolation. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee.

extract_protocol:
Genomic DNA were extracted using Qiagen DNeasy Blood and tissue kit by following manufacture’s instruction.
Purified genomic DNA were equally split into two. One part were treated with KRuO4 following the protocol from PMID: 24008380. Then both genomic DNA were parallelly treated with sodium bisulfite using MethylCode bisulfite conversion kit (Life Technologies). Targeted regions were amplified using PyroMark PCR kit and cleaned up with MinElute reaction cleanup kit (Qiagen).  Amplified fragments were multiplexed using Illumina TrueSeq DNA library preparation kit. Pooled libraries were sequenced using MiSeq sequencing instrument (Illumina).

treatment_protocol: Subsets of thymocytes were isolated by cell sorting after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145-2C11), CD24 (M1/69). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo. Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo was obtained by sorting (BD FACS Aria).

value: thymus

value: CD4 SP cells


title: CD4 SP oxBS-seq replicate 1


title: H3K4me3 WT ChIPseq_replicate 2

description:
H3K4me3 ChIP DNA from liver extract from 8.5mo C57BL6/CBA DEN treated WT mouse 2
H3K4me3_WT_ChIP_enriched_regions.bed.gz


title: CD4 SP oxBS-seq replicate 3


title: H3K4me3 WT ChIPseq_replicate 1

description:
H3K4me3 ChIP DNA from liver extract from 8.5mo C57BL6/CBA DEN treated WT mouse 1
H3K4me3_WT_ChIP_enriched_regions.bed.gz


title: CD4 SP BS-seq replicate 1

source_name: CD4 SP cells_BS-seq


title: CD4 SP BS-seq replicate 3


title: Rrp6 C


title: ID145

source_name: Rice leaf

value: CONTROL

value: 15 min


title: CD4 SP BS-seq replicate 2


title: CD4 naïve oxBS-seq replicate 3

source_name: naïve CD4 cells_oxBS-seq

value: spleen and lymph nodes

value: naive CD4 cells


title: Smyd3 DNA Input replicate 2

description: Input DNA from liver extract from 8.5mo C57BL6/CBA DEN treated WT mouse 2


title: WT A

description: h- L972


title: CD4 naïve oxBS-seq replicate 2


title: CD4 naïve oxBS-seq replicate 1


title: Smyd3 ChIPseq_replicate 1

description:
Smyd3 ChIP DNA from liver extract from 8.5mo C57BL6/CBA DEN treated WT mouse 1
Smyd3_ChIP_peaks.bed.gz

value: Smyd3 antiserum (raised in-house in rabbits injected with full length recombinant Smyd3 protein)


title: CD4 naïve BS-seq replicate 2

source_name: naïve CD4 cells_BS-seq


title: Smyd3 ChIPseq_replicate 2

description:
Smyd3 ChIP DNA from liver extract from 8.5mo C57BL6/CBA DEN treated WT mouse 2
Smyd3_ChIP_peaks.bed.gz


title: CD4 naïve BS-seq replicate 3


title: DEN treated Smyd3KO RNAseq_replicate 3

description:
mRNA from liver extract from 8.5mo C57BL6/CBA DEN treated Smyd3KO mouse 3
WT_DEN-WT_Smyd3KO_DEN-Smyd3KO_norm_counts.txt.gz

tag: agent

value: diethylnitrosamine (DEN)


title: Smyd3 DNA Input replicate 1

description: Smyd3 Input DNA from liver extract from 8.5mo C57BL6/CBA DEN treated WT mouse 1


title: DEN treated Smyd3KO RNAseq_replicate 1

description:
mRNA from liver extract from 8.5mo C57BL6/CBA DEN treated Smyd3KO mouse 1
WT_DEN-WT_Smyd3KO_DEN-Smyd3KO_norm_counts.txt.gz


title: CD4 naïve BS-seq replicate 1


title: DP oxBS-seq replicate 3

source_name: DP T cells_oxBS-seq

value: DP T cells


title: RNA PolII ChIPseq_replicate 2

description: PolII ChIP DNA from liver extract from 8.5mo C57BL6/CBA DEN treated WT mouse 2

value: RNA Pol-II (Euromedex, catalog# IPB-7G5, lot# 072105)


title: DP oxBS-seq replicate 1


title: DEN treated WT RNAseq_replicate 1

description:
mRNA from liver extract from 8.5mo C57BL6/CBA DEN treated WT mouse 1
WT_DEN-WT_Smyd3KO_DEN-Smyd3KO_norm_counts.txt.gz


title: DEN treated WT RNAseq_replicate 2

description:
mRNA from liver extract from 8.5mo C57BL6/CBA DEN treated WT mouse 2
WT_DEN-WT_Smyd3KO_DEN-Smyd3KO_norm_counts.txt.gz


title: RNA PolII ChIPseq_replicate 1

description: PolII ChIP DNA from liver extract from 8.5mo C57BL6/CBA DEN treated WT mouse 1


title: DP BS-seq replicate 2

source_name: DP T cells_BS-seq


title: Smyd3KO RNAseq_replicate 3

description:
mRNA from liver extract from 8.5mo C57BL6/CBA Smyd3KO mouse 3
WT_DEN-WT_Smyd3KO_DEN-Smyd3KO_norm_counts.txt.gz


title: DP BS-seq replicate 1


title: WT RNAseq_replicate 3

description:
mRNA from liver extract from 8.5mo C57BL6/CBA WT mouse 3
WT_DEN-WT_Smyd3KO_DEN-Smyd3KO_norm_counts.txt.gz


title: v6.5 knock-down oxBS-seq replicate 3

source_name: parental V6.5 mES cells_oxBS-seq

growth_protocol: Mouse embryonic stem cells were cultured in Knockout D-MEM with 15% ES-qualified FBS (Gemini Bio-products), 2 mM L-glutamine with 0.1 mM 2-mercaptoethanol, 0.1 mM nonessential amino acids, 50 units/ml penicillin/streptomycin and 1000 U/ml ESGRO® (LIF; Chemicon).

treatment_protocol: Cells stably depleted of Tet2 was obtained by electroporating V6.5 mESC with pSUPER-puro-Tet1shRNA or pSUPER-puro-Tet2shRNA (320V, 250F). Cells were selected by 1.5 mg/ml puromycin for 7-10 days on puromycin-resistant mitomycine C-inactivated SNL76/7-4 feeder cells.  Individual clones were picked and propagated in the absence of puromycin if the passage number was less than 10, or maintained in 1 mg/ml puromycin if the passage number was longer than 10. Tet2 mRNA expression in individual clones was evaluated by qPCR.

value: embryonic stem cells

value: wild-type


title: Smyd3KO RNAseq_replicate 1

description:
mRNA from liver extract from 8.5mo C57BL6/CBA Smyd3KO mouse 1
WT_DEN-WT_Smyd3KO_DEN-Smyd3KO_norm_counts.txt.gz

value: 8.5 months


title: Smyd3KO RNAseq_replicate 2

description:
mRNA from liver extract from 8.5mo C57BL6/CBA Smyd3KO mouse 2
WT_DEN-WT_Smyd3KO_DEN-Smyd3KO_norm_counts.txt.gz

value: liver


title: v6.5 knock-down oxBS-seq replicate 2


title: DEN treated Smyd3KO RNAseq_replicate 2

description:
mRNA from liver extract from 8.5mo C57BL6/CBA DEN treated Smyd3KO mouse 2
WT_DEN-WT_Smyd3KO_DEN-Smyd3KO_norm_counts.txt.gz


title: WT RNAseq_replicate 2

description:
mRNA from liver extract from 8.5mo C57BL6/CBA WT mouse 2
WT_DEN-WT_Smyd3KO_DEN-Smyd3KO_norm_counts.txt.gz


title: Tet2 knock-down oxBS-seq replicate 3

source_name: Tet2kd mES cells_oxBS-seq

value: Tet2 knock-down


title: DP oxBS-seq replicate 2


title: v6.5 knock-down BS-seq replicate 3

source_name: parental V6.5 mES cells_BS-seq


title: DEN treated WT RNAseq_replicate 3

description:
mRNA from liver extract from 8.5mo C57BL6/CBA DEN treated WT mouse 3
WT_DEN-WT_Smyd3KO_DEN-Smyd3KO_norm_counts.txt.gz


title: v6.5 knock-down BS-seq replicate 1


title: 7DPA grain

city: Beijing

first: Tian

last: Li

address: Chinese Academy of Agricultural Sciences

country: China

institute: Institute of Crop Science

data_processing:
Illumina Casava1.5 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality reads and other contaminants were removed.
Supplementary_files_format_and_content: tab-delimited text files include read counts and length for each sequence

organism: Triticum aestivum

source_name: Grain

extract_protocol:
Total RNA was extracted from the frozen 7, 14, 21 and 28 DPA grains using the ConcertTM Plant RNA Reagent (Invitrogen) according to the manufacturer’s instructions.
Small RNA libraries were prepared for sequencing according to illumina TruSeq Small RNA Sample Preparation Guide.

tag: variety

value: Chinese spring

value: grain

value: 7 days post anthesis


title: 21DPA grain

value: 21 days post anthesis


title: DP BS-seq replicate 3

value: thymus


title: 28DPA grain

value: 28 days post anthesis


title: 14DPA grain

value: 14 days post anthesis


title: Tet2 knock-down oxBS-seq replicate 2


title: Tet2 knock-down BS-seq replicate 2

source_name: Tet2kd mES cells_BS-seq


title: Tet2 knock-down BS-seq replicate 3


title: Tet2 knock-down BS-seq replicate 1


title: v6.5 knock-down oxBS-seq replicate 1


title: v6.5 knock-down BS-seq replicate 2


title: WT RNAseq_replicate 1

description:
mRNA from liver extract from 8.5mo C57BL6/CBA WT mouse 1
WT_DEN-WT_Smyd3KO_DEN-Smyd3KO_norm_counts.txt.gz

value: WT


title: Asia II 3 on Cotton (AC)

city: Hangzhou

first: Xiaowei

last: Wang

address: 866 Yuhangtang Road

department: Insect Sciences

institute: Zhejiang University

description: ZHJ1 biotype

data_processing:
Basecalls performed using BclConverter-1.9.0
Clean tags were generated after removing adaptor sequences, low quality sequences, empty reads and tags with a copy number of <2 using a custom written Perl program developed by Beijing Genome Institute (BGI, Shenzhen, China).
The common tags were filtered out using a custom written Perl program developed by Beijing Genome Institute (BGI, Shenzhen, China).
To get the orthologous genes, all common tags were mapped to the transcriptome reference database of MEAM1and Asia II 3 and allowed no mismatch using a custom written Perl program developed by Beijing Genome Institute (BGI, Shenzhen, China).
The number of unambiguous clean tags for each gene was calculated for gene expression analysis and TPM (number of transcripts per million tags) were used to normalize the data according to the method described by t' Hoen et al (Nucleic Acids Res. 36, e141).
Genome_build: Read alignment was performed against the MEAM1 and Asia II 3 whitefly transcriptome reference database (BMC Genomics, 12:458; BMC Genomics, 13:529).
Supplementary_files_format_and_content: Tab-delimited text files include TPM (number of transcripts per million tags) values for each tag.

organism: Bemisia tabaci

source_name: Asia II 3 on Cotton (AC)

growth_protocol: The stock cultures of invasive B.tabaci MEAM1 (mitochondrial cytochrome oxidase I, mtCOI GenBank accession no.GQ332577) and indigenous Asia II 3 (mtCOI GenBank accession no. DQ309076) were separately maintained on cotton at 27±1°C, a photoperiod of 14 h light: 10 h darkness and 70±10% relative humidity.

extract_protocol:
Total RNA was isolated using SV total RNA isolation system (Promega) and mRNA was purified from 6 µg of the total RNA from each of the samples with magnetic oligobeads.
For each sample, approximately 6 mg mRNA was purified with magnetic oligo (dT) and double strand cDNA were synthesized. The bead bound cDNA was subsequently digested with NlaIII which recognizes the CATG sites. Magnetic beads were used to purify the 3' end cDNA fragments and Illumina adapter 1 was added to their 5' ends. The purified cDNA fragments were digested using MmeI which cuts 17bp downstream of the CATG site thus producing tags with adapter 1. Then, Illumina adaptor 2 was added to the 3’ ends of the tag. After 15 cycles of PCR amplification, 6% TBE polyacrylamide gel electrophoresis was used to purify the tags. After digestion, single strand molecules were added to the Illumina sequencing flowcell and fixed.

treatment_protocol: Four treatments were conducted including MEAM1 from cotton to cotton (MC), MEAM1 from cotton to tobacco (MT), Asia II 3 from cotton to cotton (AC) and Asia II 3 from cotton to tobacco (AT). For each treatment, approximately 1,000 adult whiteflies (24 h after emergence) were shifted respectively. After host shift for 24 h, all the whiteflies were collected for RNA isolation.

value: Whole body

value: Transferred from cotton to cotton

value: Adult


title: Asia II 3 on Tobacco (AT)

description: ZHJ1 biotype

source_name: Asia II 3 on Tobacco (AT)

value: Transferred from cotton to tobacco


title: Intersex

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

description: Sample 2

data_processing:
alignment; bowtie(0.12.7), tophat(1.3.3.Linux_x86_64), tophat -r 20 --mate-std-dev 20 --coverage-search --microexon-search --max-intron-length 500000 -m 1
Transcript assembly; cufflinks(1.1.0.Linux_x86_64)  -I 500000
The reference 'Swamp eel genome' is the result of our assembly, and the contigs sequences of swamp were submitted  to NCBI (pending).
Genome_build: Swamp eel genome (NCBI accession AONE00000000 to be released on Jan  1, 2015)
Supplementary_files_format_and_content: The gtf format annotations file of transcriptome data

organism: Monopterus albus

source_name: swamp eel_intersex

extract_protocol:
Total RNA was extracted using trizol method
Beads with oligo(dT) were used to isolate poly(A) mRNA after total RNA was collected from eukaryote . Fragmentation buffer was added for interrupting mRNA to short fragments. Taking these short fragments as templates, Random hexamer-primer were used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I, respectively. Short fragments were purified with QiaQuick PCR extraction kit and resolved with EB buffer for end reparation and adding poly(A). After that, the short fragments were connected with sequencing adaptors. And, for amplification with PCR, we selected suitable fragments, as templates, with respect to the result of agarose gel electrophoresis. At last, the library could be sequencing using Illumina HiSeqTM 2000.

tag: gender

value: Hermaphrodite

value: ovotestis


title: Male

description: Sample 3

source_name: swamp eel_male

value: male

value: testis


title: Female

description: Sample 1

source_name: swamp eel_female

value: female

value: ovary


title: MEAM1 on Tobacco (MT)

description: B biotype

source_name: MEAM1 on Tobacco (MT)


title: THP1_3030_input

description:
Used in final analysis: yes
ChIP conditions: 2mM EGS (Thermo Scientific) for 30 minutes, 1% of formaldehyde for 30 minutes at room temperature

source_name: THP-1 cells

value: MLL-AF9 leukemia


title: C1 -type cell (rep 1)

city: Jerusalem

first: Jussi

last: Leinonen

address: Kiryat Hadassah p.o.b 12000

department: Cardiovascular Research Center, Heart Institute

country: Israel

institute: Hadassah-Hebrew University Medical Center

description: 6th passage (B -type cells)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were converted to Sanger FASTQ -files by FASTQ Groomer (version 1.0.4) using basic options in Galaxy interface.
Alignment of reads to mm10 genome was done by Tophat for Illumina (version 1.5.0) using default settings.
Bam -files were imported to Genespring 12 software (Agilent).
Data was normalized using Deseq algorithm (S. Anders and W. Huber (2010): Differential expression analysis for sequence count data, Genome Biology, 11:R106). Baseline was assigned to median of all samples and threshold normalized counts to 1.
Genome_build: mm10
Supplementary_files_format_and_content: Text file includes normalized gene expression values calculated by Genespring 12 software (Agilent).

source_name: Cell culture

growth_protocol: Adult (8-12 weeks old) C57BL/6 mice were deeply anesthetized with isoflurane and left atrial appendages were removed. The explants were then digested three times (5min) with trypsin & collagenase D. Strong enzyme digestion was performed with trypsin 0.25% and collagenase D 0.1% and alternatively, weak enzyme digestion with trypsin 0.05% and collagenase D 0.1%. After digestion the explants were placed on 24 –well plates (tissue culture treated) in culture medium (CEM: Isocove’s modified Dulbecco’s Medium with 25mM HEPES, supplemented with 10% FBS (fetal bovine serum), 1% L-glutamine, 1% penicillin-streptomycin & 0.1mM 2 -mercaptoethanol).

extract_protocol:
Total RNA of cultured cells was extracted with High Pure RNA isolation kit (Roche) according to the manufacturer’s instructions. RNA -sample quality and integrity was tested with Bioanalyzer 2100 (Agilent Technologies). RNA from control tissue samples was isolated using Tri-reagent.
Libraries were prepared with Illumina TruSeq RNA sample preparation kit v2 according to the manufacturer's instructions.

tag: strain

value: Left atrial appendage/heart

tag: animal age

value: 8-12 weeks

tag: cell markers


title: B -type cell (rep 2)

description:
Primary cells
weak enzyme digestion

source_name: Tissue culture


title: C3 -type cell (rep 2)

description: 10th passage (B -type cells)


title: C1 -type cell (rep 2)

description: 6th passage (B -type cells)


title: C2 -type cell (rep 1)

description: 8th passage (B -type cells)


title: B -type cell (rep 1)

description:
Primary cells
weak enzyme digestion


title: C2 -type cell (rep 2)

description: 8th passage (B -type cells)


title: MEAM1 on Cotton (MC)

description: B biotype

source_name: MEAM1 on Cotton (MC)

tag: age


title: Tet2 knock-down oxBS-seq replicate 1

value: embryonic stem cells

value: Tet2 knock-down


title: mixed sample of 21 and 28DPA grain

data_processing:
Library strategy: Degradome sequencing
Illumina Casava1.5 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality reads and other contaminants were removed.
Supplementary_files_format_and_content: processed data is the clean data by trimming adaptors and removing low-quality reads and other contaminants

extract_protocol:
Total RNA was extracted from the frozen 7, 14, 21 and 28 DPA grains using the ConcertTM Plant RNA Reagent (Invitrogen) according to the manufacturer’s instructions.
Equal quantities (20 μg) of total RNA isolated from 7 and 14 DPA grains were mixed together to construct the degradome library I, and equal quantities of total RNA from 21 and 28 DPA grains were mixed together to construct the degradome library II. Degradome cDNA libraries using sliced ends of polyadenylated transcripts were constructed based on the method described previously (Addo-Quaye et al., 2008; Ma et al., 2010).

value: Chinese spring

value: grain

tag: developmental stage

value: 21 and 28 days post anthesis


title: mixed sample of 7 and 14DPA grain

value: 7 and 14 days post anthesis


title: sih2

status: Public on Dec 31 2015

city: Illkirch

first: Julien

last: Vermot

address: 1 rue Laurent Fries

institute: IGBMC

data_processing:
Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6
Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4,1
Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69
Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package
Genome_build: Zv9
Supplementary_files_format_and_content: The processed data file is a tabulated text with the following columns : Ensembl gene id, Gene name and one column for each sample containing the normalized read counts

organism: Danio rerio

source_name: tail derived cells

growth_protocol: Embryos were grown in normal conditions

extract_protocol:
RNA was extracted using TRIzol (Invitrogen) according to the manufacturer's instructions
The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” (part #1004898 Rev.D) with some modifications. Briefly, mRNA was purified from 2 µg total RNA using oligo-dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers, then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA-Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit (ref A84801, Beckman Coulter, Inc) with the SPRI-TE instrument (Beckman Coulter, Inc). Briefly, in this system, double stranded cDNA fragments were blunted, phosphorylated and ligated to indexed adapter dimers, and fragments in the range of ~200-400 bp were size selected. The automated steps were followed by PCR amplification (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 13 cycles; 5 min at 72°C), then surplus PCR primers were removed by purification using AMPure XP beads (Agencourt Biosciences Corporation). DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent).

treatment_protocol: sih embryos lack heart contraction

value: sih

tag: embryonic stage

value: 28 hours post fertilisation

value: AB


title: WT2

value: WT


title: sih3


title: C3 -type cell (rep 1)

description: 10th passage (B -type cells)


title: WT1


title: sih1


title: WT3


title: AF

city: YANGLING

first: JIAJIE

last: SUN

state: SHANNXI

address: Taicheng Rd.

department: College of Animal Science and Technology

institute: Northwest A&F University

description: Small RNA

data_processing:
After clearing away the 3' adaptor sequence and removing redundancies and reads smaller than 18nt, the clean reads were screened against and mapped to the latest bovine genome assembly [bosTau6; http://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/bigZips/bosTau6.fa.gz] using the program SOAP.
Then, the reads were searched against the Sanger miRBase (version 19.0) to identify the miRNAs.
Genome_build: Bos_taurus_UMD_3.1, miRBase v19.0
Supplementary_files_format_and_content: Tab-delimited text files include count values for each identified miRNA.

organism: Bos taurus

source_name: Adult bovine backfat

extract_protocol:
On day 200 (d200), bovine embryos (gestation period 280 days) were collected into sterile physiological saline immediately after removal from the reproductive tract of slaughtered cows at a local abattoir. These tissues were snap-frozen in liquid nitrogen and stored at -80°C until use. RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols. Low molecular weight RNAs were separated by 15% polyacrylamide gel electrophoresis (PAGE), and RNA molecules in the range of 18–30nt were enriched and ligated with proprietary adapters to the 5' and 3' termini. A reverse transcription reaction followed by low-cycle PCR was performed to obtain sufficient product for Solexa technology.

tag: breed

value: Chinese Qinchuan cattle

value: backfat

value: 2 years


title: SULB RNA #2

city: Lincoln

first: Paul

last: Blum

state: NE

address: 1901 Vine St.

department: School of Biological Sciences

institute: University of Nebraska-Lincoln

data_processing:
Alignment of reads to genome using TopHat
Gene counts generated using HTSeq
Gene expression analysis and normalization using DESeq2
Genome_build: ASM2474v1
Supplementary_files_format_and_content: the read counts per ORF calculated by RPKM.

organism: Saccharolobus solfataricus

source_name: SULB RNA

growth_protocol: Sulfolobus solfataricus 98/2 and its derivatives were grown in basal salts medium as modified by Brock. Complex medium contained tryptone 0.2% (w/v) and the medium was adjusted to the desired pH using sulfuric acid. All cultures were incubated at 80°C in glass screw-capped flasks with aeration in orbital baths. Planktonic growth was monitored by light absorption at a wavelength of 540 nanometers using a Cary 50 spectrophotometer.

extract_protocol:
Total RNA was isolated by phenol-chloroform extraction
Libraries were prepared according to Illumina's instructions

tag: strain background

value: super acid resistant crenarchaeota (SARC) strain


title: FF

description: Small RNA

source_name: Fetal bovine backfat

value: day 200 embryos


title: SULB RNA


title: A -type cell (rep 2)

description:
Primary cells
strong enzyme digestion

value: Left atrial appendage/heart


title: SULA RNA #2

source_name: SULA RNA

value: wild-type parental strain


title: AM

description: Small RNA

source_name: Adult bovine longissimus thoracis

value: longissimus thoracis


title: SULC RNA #2

source_name: SULC RNA


title: A -type cell (rep 1)

description:
Primary cells
strong enzyme digestion

value: 8-12 weeks


title: SULC RNA