title: p_150909_CX

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
Reads adaptor trimming with cutapdapt (v1.2.1). Proton 5’ adapter sequence (--front = TTCTACAGTCCGACGATC). Proton 3’ adapter sequence (--adapter = TGGAATTCTCGGGTGCCAAGG) and SOLiD 3' adapter sequence(--adapter=33020103).
Trimmed reads with a length under 20 bases were discarded.
Remaining reads were aligned with bowtie (version 0.12.7) directly to refseq transcriptome downloaded from NCBI ftp server (release 20161019) with “--best --strata --norc”.
Reads mapped to more than one unique gene were discard with a custom java class based on Picard java API.
Alignment files were filtered to discards PCR duplicates by keeping only one read per alignment start position taking into account possible stretch of soft clipped bases at the 5’ of the reads.
Resulting reads are called fragments and represent the signal of our CLIP experiments aiming at the detection of the FMRP binding sites.
Genome_build: mm10
Supplementary_files_format_and_content: Fragments counts per sample and per gene.

source_name: cortex  from PND13 mice

extract_protocol:
FMRP-IP, proteinase K, phenol:chloroform extraction
CleanTag Ligation Kit for Small RNA Library Prep (trilink)

treatment_protocol: tissue grinded in liquid nitrogen and crosslinked 3 x 400mJ, 254nm

value: cortex


title: p_150909_HC2

status: Public on Mar 28 2018

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: hippocampus  from PND13 mice

tag: tissue

value: hippocampus


title: NMR_NM_6074_LVR [re-used]

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

description:
This is duplicated sample record of GSM2609153 for the convenient retrieval of the complete raw data from SRA
140912_nmr_6074_Leber

data_processing:
Extraction of read information in FastQ format was done using the tool bcl2astq v1.8.4 (provided by Illumina).
Reads were mapped using STAR (v2.4.1d) with a maximum mismatch of 6% and a minimum aligned length of 90%. Reads mapped to multiple loci were discarded.
Reads per gene were counted using HTSeq framework (0.6.1p1)
Genome_build: genome (hetgla2, GCA_000247695.1) can be download from UCSC (ftp://hgdownload.cse.ucsc.edu/goldenPath/hetGla2/bigZips/)
Supplementary_files_format_and_content: The Excel sheet includes raw counts for all genes and each sample.

molecule: polyA RNA

organism: Heterocephalus glaber

extract_protocol:
Extraction was done as described in Bens et al. 2016. (PMID:26763976)
Library preparation was done using Illumina's TruSeq RNA Library Prep Kit v2 kit following the manufacturer's description.

tag: Sex

value: male

tag: age

value: 3.8 years

value: liver


title: Exonic_amplicon_E5F-E6R

city: Newcastle Upon Tybe

first: Michael

last: Jackson

address: International Centre for Life

country: United Kingdom

institute: Institute of Genetic Medicine

description:
FIRRE_amplicon_junctions_identified.xlsx
Amplicons generated using FIRRE exonic primers to verify splice junctions

library_source: genomic

data_processing:
Library strategy: Amplicon sequencing
Base calling and demultiplexing were performed using Illumina's CASAVA software
For amplicon sequences only, splice sites were mapped to human genome using MapSplice
Genome_build: HG19
Supplementary_files_format_and_content: Excel spreadsheet with amplicon junctions

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Human embryonic stem cells (H9 line, passage 34-45), were plated in triplicate, expanded and differentiated for a minimum of 90 days according to the protocol of Mellough et al., 2012 (PMID: 22267304), with minor modifications outlined in Mellough et al., 2015 (PMID: 25827910).

extract_protocol:
Cells were harvested at three time points (days 0, 45 & 90) and RNA was extracted using the RNAeasy micro extraction kit with genomic DNA elimination columns (Qiagen), according to manufacturer’s recommendations. RNA quantitation was performed using the NanoDrop ND-1000 spectrophotometer (Thermo Scientific), and quality was assessed using the Agilent 2100 Bioanalyser (Agilent Technologies). RIN values indicated some reduction in RNA quality over time, with day 0 sample RIN values ranging from 9.8-10, day 45 samples ranging from 7.6-9.1 and day 90 samples ranging from 7.1-8.9
Amplicons were generated using a total RNA template extracted from an independent H9 day 0 replicate extracted as per extract protocol. Primers from FIRRE exons with illumina Nextera linkers attached were used in all cases, with sequencing primers and Illumina indexes being attached in a 2nd amplification using the Nextera DNA library preparation kit. These were then sequenced as paired ends using an Illumina nano DNA kit on the Illumina MiSeq platform according to manufacturers recommendations to target depths ranging from 1500-6000 reads per amplicon.

treatment_protocol: Cultures were supplemented with recombinant human IGF-1 (Sigma-Aldrich) at a concentration of 5ng/ml (to day 37) followed by 10ng/ml (after day 37).

tag: cell line

tag: cell type

value: human embryonic stem cells

tag: treatment

value: No treatment


title: p_150909_CXT1


title: Exonic_amplicon_E1F-E5R


title: s_140729_CB

source_name: cerebellum from PND13 mice

value: cerebellum


title: Exonic_amplicon_E6F-E7R


title: s_140408_HC


title: p_150909_HC1


title: p_150723_CX


title: s_140729_HC


title: s_140408_HCH


title: s_140408_CX


title: NMR_NM_1449_LVR [re-used]

description:
This is duplicated sample record of GSM2609145 for the convenient retrieval of the complete raw data from SRA
140912_nmr_1449_Leber

value: 2.7 years


title: Exonic_amplicon_E8F-E5R

description:
FIRRE_amplicon_junctions_identified.xlsx
Amplicons generated using FIRRE exonic primers in divergent orientation to verify splice junctions within circRNAs


title: s_140408_CB


title: Exonic_amplicon_E5BF-E5R


title: day90 control replicate 3

data_processing:
Base calling and demultiplexing were performed using Illumina's CASAVA software
Inner distance metrics computation and quality control analysis were performed using Piccard v 1.85 (http://broadinstitute.github.io/picard/) and FastQC v 0.10 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) respectively
Sequence reads were aligned to the human genome (hg19) using tophat v. 2.0.10 (Trapnell, Pachter, & Salzberg, 2009). GENCODE v. 19 annotations were supplied using – GTF option along with options: -b2-sensitive, -r, --mate-std-dev, --library-type, as required for each sample. Read counts were generated using HTSEQ v. 0.6.1 (Anders, Pyl, & Huber, 2014), exonic nucleotide sequence coverage data were generated using Bedtools v 2.17 (Quinlan & Hall, 2010).
Identification of circRNAs was perfomed using PTESFinder Pipeline v. 1 (Izuogu et al., 2016). Briefly, this pipeline identifies all RNAseq reads mapping in inverted order and the same orientiation to the same GENCODE entry as putative back-splice exon junction reads, generates exon models of these junctions, and re-maps all reads under analysis to improve mapping efficiency for back-splice exon junction reads with exon junctions close the the read termini. It then eliminates false positives through removal of reads which do not utilise known exon junctions and reads which map equally well or better to the genomic or transcriptome reference. Parameters used were: JSpan 10 (to ensure no mismatches within 5bp either side of the back-splice exon junction, PID 0.85 to endure high mapping identity to both exons, and -m 7 to allow mapping to multiple isoforms within GENCODE annotations.
Genome_build: HG19
Supplementary_files_format_and_content: Bed file containing all identified circRNA and suitable for UCSC custom track upload.

extract_protocol:
Cells were harvested at three time points (days 0, 45 & 90) and RNA was extracted using the RNAeasy micro extraction kit with genomic DNA elimination columns (Qiagen), according to manufacturer’s recommendations. RNA quantitation was performed using the NanoDrop ND-1000 spectrophotometer (Thermo Scientific), and quality was assessed using the Agilent 2100 Bioanalyser (Agilent Technologies). RIN values indicated some reduction in RNA quality over time, with day 0 sample RIN values ranging from 9.8-10, day 45 samples ranging from 7.6-9.1 and day 90 samples ranging from 7.1-8.9
400ng of total RNA was used in library preparation and sequencing. Libraries were prepared according to Illumina's guidelines for TruSeq RiboZero stranded mRNA LT sample prep kit, following the alternative fragmentation protocol. Paired-end reads were sequenced using a paired end 100 base pair protocol on an Illumina HiSeq2000.

tag: time point (day)


title: day90 igf1 replicate 3

value: + recombinant human IGF-1


title: day90 igf1 replicate 2


title: day45 igf1 replicate 2


title: day45 igf1 replicate 1


title: day90 igf1 replicate 1


title: day90 control replicate 2


title: day0 replicate 1


title: day45 control replicate 3


title: day0 replicate 2


title: day45 control replicate 1


title: 5105 Braf/Pten/Dnmt3bWT

city: New Haven

first: Goran

last: Micevic

state: CT

address: 200 S Frontage Road NSB287

department: Dermatology

country: USA

institute: Yale University School of Medicine

data_processing:
Filtering by quality (phred 33) using TrimGalore! V.0.37. Default parameters.
Alignment to NCBI37 mm10 using bsmap V 2.74 . Parameters: -a genome.fa -p 8
Methylation calling using methratio.py script from the bsmap V 2.74 package. Default parameters.
Differential methylation identification using MetkylKit V 0.92 package for R according to https://code.google.com/p/methylkit/#Documentation
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited; methylation calls

source_name: Cutaneous melanoma

growth_protocol: Genetically induced murine melanomas.

extract_protocol:
Genomic DNA extraction from macrodissected tumors using Qiagen blood and tissue easy kit according to manufacturer's instructions.
MspI digestion, bisulfite modification using Qiagen's EpiTect kit and protocol, size selection by DNA electrophoresis.

tag: strain

tag: genotype/variation

value: BrafV600E Ptenlox

value: melanoma tumor


title: d5co-f-f_K27ac-1

status: Public on Mar 27 2018

city: RTP

first: Wendy

last: Jefferson

state: NC

address: 105 T. W. Alexander Drive

institute: NIEHS

data_processing:
The raw ChIP-Seq reads were initially processed by filtering with average quality scores greater than 20.
Then the reads were aligned to the mouse reference genome (mm10; Genome Reference Consortium Mouse Build 38 from December 2011) using Bowtie version 1.1.2 with unique mapping and up to 2 mismatches for each read (-m 1 -v 2)
The duplicated reads with the same sequence were discarded
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated from normalized bedgraph files using bedGraphToBigWig; Scores represent normalized mapped read coverage

source_name: uterus

extract_protocol:
ChIP-Seq samples
True Seq RNA kit

treatment_protocol: Mice were treated neonatally on days 1-5 with vehicle (corn oil) or DES (1 mg/kg/day).

value: uterus

tag: ChIP

tag: genotype

value: Wild type

value: Control


title: d5DES-f-fcre_K27ac-2

value: Uterine conditional knock out

value: DES


title: d5co-f-fcre_K27ac-1


title: d5DESH3K4me1-2


title: d5DES-f-f_K27ac-1


title: d5co-f-fcre_K27ac-2


title: d5DES-f-fcre_K27ac-1


title: 6491 Braf/Pten/Dnmt3bKO

value: BrafV600E Ptenlox Dnmt3blox


title: 5196 Braf/Pten/Dnmt3bWT


title: d5DESH3K4me1-1


title: 6883 Braf/Pten/Dnmt3bKO


title: d5coH3K4me1-2


title: d5DES-f-f_K27ac-2


title: day90 control replicate 1


title: day45 igf1 replicate 3


title: day45 control replicate 2


title: day0 replicate 3


title: d5coH3K4me1-1


title: d5co-f-f_K27ac-2


title: d5coH3K27ac-1


title: d5DESH3K27ac-2


title: d5DESH3K27ac-1


title: d5coH3K27ac-2


title: PND5-DES-rep2

data_processing:
The raw RNA-Seq reads were initially processed by filtering with average quality scores greater than 20.
The reads passing the initial processing were aligned to the mouse reference genome (mm10; Genome Reference Consortium Mouse Build 38 from December 2011) using TopHat version 2.0.4 and assembled using Cufflinks version 2.0.2
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated from normalized bedgraph files using bedGraphToBigWig; Scores represent normalized mapped read coverage

extract_protocol:
Total RNA was isolated using RNeasy kit and DNase was applied on the column.
Tru seq RNA kit

tag: developmental stage


title: PND5-DES-rep3


title: d5coH3K4me3


title: PND5-DES-rep4


title: d5DESH3K4me3


title: d5coH3K27me3


title: d5DESH3K27me3


title: PND5-DES-rep1


title: PND5-CO-rep3

value: control


title: PND5-CO-rep1


title: PND5-CO-rep4


title: PND5-CO-rep2


title: week 10 WT-DES4 U_RNA-seq

first: Yin

last: Li

address: 111 TW alexander Drive

source_name: week 10 WT mouse uterus DES group

growth_protocol: The mouse SV or uterus tissues were colleclted from WT and aERKO mice in the control and DES groups.

extract_protocol: Trizol/ extraction of total RNA was perforemd accoding to the manufacture's instructions. RNA-Seq was performed at NISC/NIH for each group which includes four samples. The RNA libraries were sequenced with a HiSeq 2000 system [Illumina]

treatment_protocol: For neonatal treatment, male or female pups were treated by subcutaneous injection with DES (Sigma Aldrich), dissolved in corn oil at 2 µg/pup/day on days 1-5 (day of birth = 1) (DES group) or an equal volume of corn oil (control group).

value: wildtype

value: week 10


title: week 10 WT-DES2 U_RNA-seq


title: week 10 WT-veh4 U_RNA-seq

source_name: week 10 WT mouse uterus control group


title: week 10 WT-veh2 U_RNA-seq


title: week 10 WT-veh1 U_RNA-seq


title: week 10 WT-veh3 U_RNA-seq


title: week 10 WT-DES1 U_RNA-seq


title: week 10 aERKO-DES4 SV_RNA-seq

source_name: week 10 aERKO mouse SVs DES group

value: aERKO

value: seminal vesicle


title: week 10 aERKO-DES3 SV_RNA-seq


title: week 10 aERKO-DES2 SV_RNA-seq


title: week 10 aERKO-DES1 SV_RNA-seq


title: week 10 aERKO-veh3 SV_RNA-seq

source_name: week 10 aERKO mouse SVs control group


title: week 10 WT-DES3 U_RNA-seq


title: week 10 WT-DES U

description: methylated DNA

extract_protocol:
Pooled genomic DNA samples were sonicated with Biorupter (Diogenode) and methylated DNAs were captured with his-tagged recombinant MBD2b along with its binding partner MBD3L1 using MethyColletor Ultra kit (cat# 55005, ACTIVE MOTIF).
The MBD-Seq libraries were prepared using the TruSeq kit (Illumina, San Diego, CA) and the sequencing was conducted in the Epigenetic Core at NIEHS/NIH with a MiSeq system (Illumina).

value: MBD


title: week 10 WT-veh U

description: methylated DNA


title: week 10 aERKO-DES SV

description: methylated DNA


title: week 10 WT-veh3 SV_RNA-seq

source_name: week 10 WT mouse SVs control group


title: week 10 WT-veh1 SV_RNA-seq


title: week 10 WT-veh2 SV_RNA-seq


title: week 10 WT-DES4 SV_RNA-seq

source_name: week 10 WT mouse SVs DES group


title: week 10 aERKO-veh1 SV_RNA-seq


title: week 10 WT-DES1 SV_RNA-seq


title: week 10 aERKO-veh2 SV_RNA-seq


title: w_3

city: Guangzhou

first: Wei

last: Luo

state: Guangdong

address: Wushan Road

department: The College of Animal Science

country: China

institute: South China Agricultural University

data_processing:
Paired-end clean reads were aligned to the chicken reference genome (ftp://ftp.ensembl.org/pub/release-88/fasta/gallus_gallus/) using TopHat v2.0.12 (Trapnell et al., 2012; Kim et al., 2013) after the reference genome index built with Bowtie v2.2.3 (Langmead & Salzberg, 2012; Langmead et al., 2009).
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene.
Gene expression levels were calculated by the number of fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM) (Trapnell et al., 2010).
Differential expression analysis of two groups (3 biological replicates for each) was performed using the DESeq R package (1.18.0) (Anders & Huber, 2010).
Genes that exhibited more than 1.5-fold changes between two groups and an adjusted P-value < 0.05 were assigned as the differentially expressed.
Genome_build: Ensembl genome build 88.
Supplementary_files_format_and_content: Differentially expressed genes list

organism: Gallus gallus

source_name: white_earlobe skin

extract_protocol:
RNA of the earlobe skin was extracted with RNAiso Plus Kit (TaKaRa, Japan) used, in accordance with the manufacturer’s instruction. Both the DNA and RNA concentration were detected on a Nanodrop 2000 spectrophotometer at 260/280 nm ratio.
The obtained RNA was treated with RNase free-DNaseI (Promega, USA) to remove any contaminated genomic DNA. For each sample, a total of 3 μg RNA was used for sequencing library preparation by NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA), according to the manufacturer’s instruction. In order to select cDNA fragments of 150~200 bp in length, the library was purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was added into size-selected, adaptor-ligated cDNA for PCR at 37 °C for 15 min followed by 5 min at 95 °C. At last, PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system. The sample clustering was carrried out on a cBot Cluster Generation System with the use of TruSeq PE Cluster Kit v3-cBot-HS (Illumina, USA) according to the manufacturer’s instruction.

tag: breed

value: Qingyuan Partridge chicken

value: male

value: earlobe skin

tag: earlobe color

value: white


title: week 10 WT-DES2 SV_RNA-seq


title: week 10 WT-veh4 SV_RNA-seq


title: week 10 aERKO-veh SV

description: methylated DNA


title: week 10 WT-DES SV

description: methylated DNA


title: w_2


title: r_3

source_name: red_earlobe skin

value: red


title: week 5 WT-DES SV

description: methylated DNA

source_name: week 5 WT mouse SVs DES group

value: week 5


title: w_1


title: week 10 WT-veh SV

description: methylated DNA


title: week 5 aERKO-veh SV

description: methylated DNA

source_name: week 5 aERKO mouse SVs control group


title: r_2


title: week 10 aERKO-veh4 SV_RNA-seq


title: Mycorrhizaed roots of Nicotiana benthamiana [Nb] biological replicate 2

city: Wageningen

first: Tian

last: Zeng

address: Droevendaalsesteeg 1

department: Plant Sciences

country: Netherlands

institute: Wageningen University

description:
processed data file:
Secretome in different hosts with DESeq results and TPM.xlsx

data_processing:
Sequenced reads were trimmed for adaptor sequence
RNASeq data were then mapped to Rhizophagus irregularis genome (Lin, et al., 2013) with manual corrections for secreted proteins. Mapping was done using CLC genomics workbench 9.5.4
Count tables were analyzed using DESeq2 package in R to find out differential expressed AM fungal secreted proteins in different hosts and developmental stages
Genome_build: Rhizophagus irregularis genome (Lin, et al., 2013) with manual corrections on annotation for some secreted proteins
Supplementary_files_format_and_content: Expression levels were represented using TPM value generated by CLC genomics workbench 9.5.4; differential gene analyses were done using DESeq2 package in R

organism: Rhizophagus irregularis

source_name: Mycorrhizaed Nicotiana roots

extract_protocol:
plants roots were harvested 7 weeks post innoculation
RNA was isolated using the Qiagen RNeasy mini kit according to manufacturers protocol
RNASeq library was made using TruSeq RNA Sample Prep Kit v2 (Illumina)

value: all stages


title: week 5 aERKO-DES SV

description: methylated DNA

source_name: week 5 aERKO mouse SVs DES group


title: r_1


title: Mycorrhizaed roots of Nicotiana benthamiana [Nb] biological replicate 1


title: week 5 WT-veh SV

description: methylated DNA

source_name: week 5 WT mouse SVs control group


title: week 10 WT-DES3 SV_RNA-seq


title: Mycorrhizaed roots of Allium schoenoprasum [As] biological replicate 3

source_name: Mycorrhizaed Chives roots


title: Mycorrhizaed roots of Allium schoenoprasum [As] biological replicate 2


title: Mycorrhizaed roots of Allium schoenoprasum [As] biological replicate 1


title: Mycorrhizaed roots of Medicago truncatula [Mt] biological replicate 1

source_name: Mycorrhizaed Medicago roots


title: Mycorrhizaed roots of Medicago truncatula [Mt] biological replicate 3


title: Mycorrhizaed roots of Nicotiana benthamiana [Nb] biological replicate 3


title: SF2+TEX

city: Leioa

first: Ander

middle: Hernández

last: Plágaro

state: Bizkaia

address: Barrio Sarriena S/N

department: Immunology, Microbiology and Parasitology

country: Spain

institute: University of the Basque Country

data_processing:
Base-calling was performed online during the sequencing procedure with the Real-Time Analysis (RTA) software version 2.4.11 and System Suite Version 2.1.2.1. Illumina sequencing instruments generate per-cycle BCL base call files as primary sequencing output in bcl2 format
Conversion of the bcl2 file to gzipped fastq files was performed using the bcl2fastq script v. 2.18.0.12 provided by Illumina
Quality, polyA and adapter trimming, mapping of reads to reference sequences as well as calculation of expression values was performed using CLC Genomics Workbench v. 9.0 tools
Generation of gtf files with the assigned TSS was performed using programs developed by Laurence Ettwiller (https://github.com/Ettwiller/TSS) using standard settings
Genome_build: GCA_001558435.1
Supplementary_files_format_and_content: gtf files include predicted TSS, tab-delimited text files include RPKM values in separated files for each chromosome
Supplementary_files_format_and_content: gff file includes updated Vibrio harveyi genome annotation including transcription start sites discovered in this study.

organism: Vibrio harveyi NBRC 15634 = ATCC 14126 = KCTC 12724

source_name: Cell pellet

growth_protocol: 20 ml of marine broth (Applichem) in 100 ml flasks, 26 ºC, 90 rpm, darkness, cultured overnight

extract_protocol:
Cell pellets were collected by centrifugation, total RNA was extracted with TRIzol reagent (Ambion) and PureLink RNA Mini Kit (Ambion) and treated with DNAseI (Invitrogen)
Fragmented RNA was poly(A)-tailed using poly(A) polymerase and an RNA adapter was ligated to the 5'-phosphate of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and M-MLV reverse transcriptase. The resulting cDNA was PCR-amplified to about 10-20 ng/µl using a high-fidelity DNA polymerase. PCR cycles performed and barcode sequences, which are attached to the 5' ends of the cDNAs, are as follows: SF1-star AGGATAGG 13 cycles, SF2-star TCAGAGCC 13 cycles, SF3-star CTTCGCCT 13 cycles, SF1-star+TEX CTCCTTAC 15 cycles, SF2-star+TEX TATGCAGT 15 cycles, SF2-star+TEX TACTCCTT 15 cycles. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis. For Illumina NextSeq sequencing, the cDNA preparations were pooled in approximately equimolar amounts and size fractionated in the size range of 200 – 500 bp using a differential clean-up with the Agencourt AMPure kit. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina. The following adapter sequences flank the DNA insert: TruSeq_Sense_primer (N=barcode) AATGATACGGCGACCACCGAGATCTACAC-NNNNNNNN-ACACTCTTTCCCTACACGACGCTCTTCCGATCT, TruSeq_Antisense_primer CAAGCAGAAGACGGCATACGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC(dT)25

treatment_protocol: Not applicable

tag: growth phase

value: Statonary phase

tag: agent

value: TEX


title: Mycorrhizaed roots of Medicago truncatula [Mt] biological replicate 2


title: OG86

city: Manchester

first: Tim

middle: C

last: Somervaille

state: Lancashire

address: Wilmslow Road

institute: Cancer Research UK Manchester Institute

data_processing:
Sequencing reads were quality checked using FASTQ (Andrews, 2010). Any adapter sequences present in the data were removed using Cutadapt (Martin, 2012). The cleaned and trimmed FASTQ files were mapped to the hg38 reference assembly using BWA (Li and Durbin, 2009) and processed using Samtools (Li et al, 2009). The data were cleaned for duplicates, low mapping quality reads (i.e. MAPQ<30), non-uniquely mapped reads, not properly paired reads and reads mapped to non-conventional chromosomes and mitochondrial DNA.
For analyses of reads surrounding MYB, GFI1 or LSD1 binding peaks, the region ±2.5kB surrounding the apex of the binding peak was divided into 50 100 base pair sub-regions. The number of reads mapped to each of the 100 regions was calculated.
Genome_build: hg38
Supplementary_files_format_and_content: ATACseq reads +/-2.5kB surrounding GFI1, MYB or LSD1 binding peaks in the presence of OG86 or DMSO vehicle control.

source_name: THP1 AML cells

growth_protocol: THP1 cells were cultured in RPMI 1640 without supplemental growth factors.

extract_protocol:
Cell pellets were re-suspended in 50μl lysis buffer (10mM Tris-HCL pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630) and nuclei were pelleted by centrifugation for 10 minutes at 500 x g. Supernatant was discarded and the nuclei were re-suspended in 25μl reaction buffer containing 2μl of Tn5 transposase and 12.5ul TD buffer (Nextera Sample preparation kit from Illumina). The reaction was incubated for 30 minutes at 37ºC and 300rpm, and purified using the Qiagen MinElute Kit.
Library fragments were amplified using 1x NEBNext High-Fidelity PCR master mix and 1.25μM of custom PCR primers and conditions (Buenrostro et al., 2013). The PCR reaction was monitored to reduce GC and size bias by amplifying the full libraries for five cycles and taking an aliquot to run for 20 cycles using the same PCR cocktail and 0.6x SYBR Green. The remaining 45ul reaction was amplified for additional cycles as determined by qPCR. Libraries were finally purified using the Qiagen MinElute Kit. Libraries were size selected with AMPure beads (Beckman Coulter) for 200-800 base pair size range and quantified by Q-PCR using Kapa Library Quantification Kit (Kapa Biosystems).

treatment_protocol: The Assay for Transposase Accessible Chromatin (ATACseq) protocol (Buenrostro et al., 2013) was performed using 50,000 THP1 cells cultured for 24 hours in the presence of DMSO or 250nM OG86 at a density of 3x105/ml.

value: AML


title: DMSO


title: SF1+TEX


title: SF3+TEX


title: SF3


title: THP1_DMSO_replicate1

data_processing:
Reads were aligned to the human genome (build hg19) with SHRIMP2 (Langmead et al., 2009; David et al., 2011) using default settings. Reads aligning to multiple loci were discarded. There were 58.5 million and 67.6 million uniquely mapped reads for the DMSO and OG86 treated THP1 cell samples respectively. Data from two technical replicates for each sample were merged. 90.8% and 90.5% of reads mapped to annotated protein coding genes (ENSEMBL v66) using the annmap database, R and Bioconductor (Gentleman et al., 2004; Yates et al., 2007). RPKM (reads per kilobase per million uniquely mapped reads) was computed for each transcript. Gene level expression values were calculated as the mean RPKM expression for all transcripts arising from the same annotated gene. Genes annotated as protein coding in ENSEMBL v66 but not by the Human Genome Consortium (www.genenames.org, access date 31 March 2014) were discarded, as were mitochondrial genes, leaving 18670 for analysis. Once genes with expression levels less than 2 RPKM in both samples were discarded, 10,007 remained for downstream analyses (processed data file).
Genome_build: hg19
Supplementary_files_format_and_content: Processed data file. Gene expression in THP1 AML cells treated with 250nM OG86 or DMSO vehicle. Only expressed genes were considered in the analysis (i.e. the 10,007 Human Genome Consortium annotated protein-coding genes exhibiting expression levels of >2.0 reads per kilobase per million mapped reads (RPKM) in at least one of the samples ).

source_name: THP1 cells

growth_protocol: THP1 cells were cultured in methylcellulose (H4320, Stem Cell Technologies, Vancouver, BC) without supplemental growth factors.

extract_protocol:
Total RNA was extracted from vehicle or OG86-treated THP1 AML cells using QIAshredder spin columns and an RNeasy Plus Micro Kit (Qiagen, Manchester, UK).
PolyA selection using 15µg total RNA was carried out by performing three rounds of selection using a MicroPoly(A)Purist Kit. Barcoded polyA libraries for pooling and sequencing were prepared using 55ng of the polyA selected RNA with a SOLiD Total RNA-seq Kit. Following quantitation of the libraries by Q-PCR using a SOLiD Library TaqMan Quantitation Kit, emulsion PCR was performed using the SOLiD EZBead System prior to sequencing of single-ended strand-specific 50mers using a SOLiD 5500 System (all from Life Technologies, Paisley, UK).

treatment_protocol: THP1 AML cells were treated with 250nM OG86 or DMSO vehicle for 24 hours in semi-solid culture.

value: acute myeloid leukemia (AML)


title: THP1_DMSO_replicate2


title: H3K4Me3_OG86

data_processing:
Reads were aligned to human genome hg19 using SMALT (www.sanger.ac.uk/resources/software/smalt) using default settings. The numbers of uniquely mapped reads were: 75-100 million for the monomethyl- and dimethyl-H3K4 samples and 40-60 million for the trimethyl-H3K4 samples. Reads were mapped relative to annotated genes (ENSEMBL v66) using the annmap database, R and Bioconductor (Gentleman et al., 2004; Yates et al., 2007).
For analysis of histone methylation marks, for each gene the gene body (i.e. from the transcription start site (TSS) to the end of the gene) was divided into ten sub-regions of equal length. The region upstream of the gene was divided into two regions: from 10kb to 2.5kb upstream, and from 2.5kb upstream to the TSS. The region downstream of the gene was similarly divided. Therefore each gene consists of 14 regions covering upstream sequences, the gene body and downstream sequences. The number of reads mapped to each of the 14 regions for each gene was calculated, as were values for reads per kilobase.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files 1 to 6. For analysis of histone methylation marks, for each gene the gene body (i.e. from the transcription start site (TSS) to the end of the gene) was divided into ten sub-regions of equal length. The region upstream of the gene was divided into two regions: from 10kb to 2.5kb upstream, and from 2.5kb upstream to the TSS. The region downstream of the gene was similarly divided. Therefore each gene consists of 14 regions covering upstream sequences, the gene body and downstream sequences. The number of reads mapped to each of the 14 regions for each gene was calculated, as were values for reads per kilobase.

extract_protocol:
ChIP was performed using a HighCell# ChIP kit (Diagenode, Liege, Belgium) according to the manufacturer’s instructions. Prior to ChIPseq, DNA was purified with an iPure kit (Diagenode), according to manufacturer’s instructions.
To prepare samples for sequencing on the Illumina HiSeq 2500 (Illumina, San Diego, CA), a Microplex Library Preparation Kit (Diagenode) was used to generate libraries from 1ng ChIP DNA. Libraries were then size selected (200-800 base pairs) by adding 0.55x volume of AMPure beads (Beckman Coulter, Pasadena, CA) to the sample, followed by 0.3x volume of AMPure beads to the supernatant. The supernatant was then discarded and the beads washed with 70% ethanol before drying and elution of the size selected library. Library quantitation was performed by Q-PCR using a Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Next, 15pM of the library was used for on board cluster generation in the Rapid Mode of a HiSeq 2500 (Illumina) and then paired end 75 or 101 base pair sequencing was performed using a TruSeq Rapid SBS Kit (Illumina).


title: THP1_OG86_replicate2


title: H3K4Me2_DMSO


title: H3K4Me3_DMSO


title: H3K4Me1_OG86


title: MYB DMSO vehicle

data_processing:
Reads were aligned to human genome hg38 using Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/) using default settings. The number of uniquely mapped reads per sample was 50-100 million. Reads were mapped relative to annotated genes (ENSEMBL v66) using the Annmap database, R and Bioconductor (Gentleman et al., 2004; Yates et al., 2007).
MACS2 (Model-based Analysis of ChIP-seq, version 2.1.0) software was used to call peaks (Zhang et al., 2008). DMSO or OG86 treated input samples were respectively used as reference, duplicates at the exact same location were removed and a cutoff of 0.01 False Discovery Rarte (FDR) was used as a threshold. Only those peaks showing pileup values ≥18 and log(qvalue) ≥3 were considered for further analysis.
Using ChIPseeker package (R, Bioconductor) (Yu et al., 2015) peak coordinates were annotated to the nearest genomic features using transcript-related features from UCSC hg38. Transcript start site (TSS) region was defined as ±1kb from the TSS. As some peaks overlap multiple genomic regions, the package adopted the following priority in annotation: promoter, 5’ UTR, 3’ UTR, exon, intron, downstream, intergenic.
A ChIPpeakAnno package (R/Bioconductor) (Yu et al., 2015) was used to find peaks with apices located within 500 bps of one another, and to extract Fastq sequences around the summit of each peak. For motif analysis a window of ±500bp around summit was analyzed using the MEME-ChIP (Machanick & Bailey, 2011) with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data files 1-6: Binding peaks for LSD1, MYB or GFI1 in the presence or absence of OG86.

extract_protocol:
THP1 cells were cultured for 48 hours in the presence of DMSO or OG86 250nM at a density of 3x105/ml. Cells were cross-linked at room temperature using 1% formaldehyde. After 10 minutes the reaction was stopped by incubation for 5 minutes with 0.125M glycine. Cell pellets were washed twice with cold PBS containing protease inhibitors (Complete EDTA-free tablets, Roche, Basel, Switzerland). 100 million cells were used per ChIP, as described in the protocol reported by Lee et al. (2006). Briefly, nuclear lysates were sonicated using a Bioruptor Plus (Diagenode) for 15 min at high, 30 sec ON, 30 sec OFF settings. Immunoprecipiation was performed overnight at 20 rpm and 4°C, with 100ul magnetic beads (Dynabeads (Protein G), Invitrogen, Carlsbad, CA) per 10µg antibody. ChIP-grade antibodies were used as follows: LSD1 (ab17721), GFI1 (ab21061) and MYB (ab45150) (Abcam). After washing six times with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCl), chromatin IP-bound fractions were extracted at 65°C for 30min with elution buffer (50mM TrisHCl pH8, 10mM EDTA, 1% SDS) vortexing frequently. RNAseA (1mg/ml) and proteinase K (20mg/ml) were used to eliminate any RNA or protein from the samples. Finally DNA was extracted using phenol:chloroform:isoamyl alcohol extraction and precipitated with ethanol (adding 2 volumes of ice-cold 100% ethanol, glycogen (20µg/µl) and 200mM NaCl) for at least 1 hour at -80°C. Pellets were washed with 70% ethanol and eluted in 50ul 10mM TrisHCl pH8.0.
ChIP DNA samples were prepared for sequencing using the Microplex Library Preparation Kit (Diagenode) and 1 ng ChIP DNA. Libraries were size selected with AMPure beads (Beckman Coulter) for 200-800 base pair size range and quantified by Q-PCR using Kapa Library Quantification Kit (Kapa Biosystems).

treatment_protocol: No additional treatment


title: H3K4Me1_DMSO


title: SF2


title: GFI1 OG86


title: SF1


title: GFI1 DMSO vehicle


title: LSD1 OG86


title: THP1_OG86_replicate1


title: LSD1 DMSO vehicle


title: Div8+.rep2

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm9 version of the mouse genome using Bowtie-1.1.1
For each sample peaks of accessibility were identified and annotated using MACS2 with the default settings
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files are normalized to reads per peak per million (rppm) using R/Bioconductor

source_name: B cells

extract_protocol:
Three days following LPS stimulation, CD45.1 transferred cells were magnetically enriched and 20,000 cells per sample were FACS sorted based on cellular division and CD138 status
Cells were centrifuged for 10 minutes at 500xg, resuspended in 50 ul of Lysis Buffer (contents), and immediately centrifuged for 30 minutes at 500xg. Tagmentation was performed using the Illumina Nextera Kit by resuspending cells in 25 ul of Tagmentation mix (1x TD Buffer, 2.5 ul Tn5 Transpoase) and incubating for 60 minutes at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

value: female

tag: sorting markers

value: CFSE, CD138

value: B6.SJL-Ptprca Pepcb/BoyJ (CD45.1)

tag: stimulation

value: LPS

tag: division

value: positive

value: adoptively transferred CD43- Splenic B cells


title: H3K4Me2_OG86


title: Extraradical mycelium [ERM] collected from carrot root culture biolocal replicate 3

description:
processed data file:
Secretome in different stages with DESeq results and TPM.xlsx

source_name: Extraradical mycelium collected from carrot root culture

extract_protocol:
Extraradical mycelium were harvested 2-month after growing with carrot hairy root on plate
RNA was isolated using the Qiagen RNeasy micro kit
cDNA was amplified using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech)
library was made using ThruPLEX DNA-seq Kit (Rubicon genomics)

value: extraradical mycelium


title: Extraradical mycelium [ERM] collected from carrot root culture biolocal replicate 2


title: Div5.rep2

tag: Sex

value: negative


title: Div1.rep2


title: Extraradical mycelium [ERM] collected from carrot root culture biolocal replicate 1


title: Cells contain Intraradical mycelium [IRM] collected from Medicago truncatula biological replicate 3

source_name: Intraradical mycelium in mycorrhizaed Medicago roots

extract_protocol:
Medicago roots were harvested 7 weeks post innoculation
Laser microdissection was used to collect cells contain intraradical mycelium
RNA was isolated using the Qiagen RNeasy micro kit
cDNA was amplified using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech)
library was made using ThruPLEX DNA-seq Kit (Rubicon genomics)

value: intraradical mycelium


title: Div3.rep2


title: Cells contain Intraradical mycelium [IRM] collected from Medicago truncatula biological replicate 2


title: Div8+.rep1


title: Cells contain Intraradical mycelium [IRM] collected from Medicago truncatula biological replicate 1


title: Div0.rep2


title: Cells contain arbuscules [ARB] collected from Medicago truncatula biological replicate 2

source_name: Arbuscule cells in mycorrhizaed Medicago roots

extract_protocol:
Medicago roots were harvested 7 weeks post innoculation
Laser microdissection was used to collect arbuscules
RNA was isolated using the Qiagen RNeasy micro kit
cDNA was amplified using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech)
library was made using ThruPLEX DNA-seq Kit (Rubicon genomics)

value: arbuscule


title: Cells contain arbuscules [ARB] collected from Medicago truncatula biological replicate 3


title: Div0.rep1


title: Div5.rep1


title: Div3.rep1


title: Div1.rep1


title: CRY1-Kidney-F-ZT20-WT

status: Public on Mar 26 2018

city: Lausanne

first: Felix

last: Naef

address: AAB 040 Station 15

department: Bioengineering

country: Switzerland

institute: École Polytechnique Fédérale de Lausanne

description:
Cross-linked genomic DNA
4CSeq of Kidney of mice
processed_4Cseq_log10_counts_ZT20_ZT08.txt.gz

data_processing:
mm9
Mapping was done using HTS station (http://htsstation.epfl.ch). See Supplemental methods of paper for detailed processing methods. In brief, read counts were normalized by total counts on the cis chromosome. For each fragment, we fit a weighted linear model with a Gaussian window of 2.5kb in order to incorporate signal from neighboring fragments.
Log10 4CSeq signal (value A with variance Avar). Processed formats show fragments within +/- 2MB of the bait. Zscore and p-value represent differential contacts between liver and kidney

source_name: Crosslinked genomic DNA

extract_protocol: Liver and kidney nuclei were prepared as previously described (Ripperger and Schibler 2006) with some minor changes.         In brief, liver and kidneys from individual animals were homogenized and fixed in 4ml of PBS including 1.5percent formaldehyde for 10 minutes at room temperature.         Cross-linking reaction was stopped by adding 25 ml of ice-cold stop reaction buffer (2.2 M sucrose; 150 mM glycine; 10 mM HEPES pH 7.6; 15 mM KCl; 2 mM EDTA; 0.15 mM spermine; 0.5 mM spermidine; 0.5 mM DTT; 0.5 mM PMSF)         to the homogenates and kept 5 minutes on ice. Homogenates were then loaded on top of 10 ml cushion buffer (2.05 M sucrose; 10 % glycerol; 125 mM glycine; 10 mM HEPES pH 7.6; 15 mM KCl; 2 mM EDTA; 0.15 mM spermine; 0.5 mM spermidine; 0.5 mM DTT; 0.5 mM PMSF)         and centrifuged for 45 minutes at 105g at  4degC. Nuclei were washed twice in PBS and immediately frozen.

tag: tissue

value: Kidney

tag: feeding

value: Ad libitum

tag: age

value: post-natal 8-12 weeks

value: WT


title: Cells contain arbuscules [ARB] collected from Medicago truncatula biological replicate 1


title: CRY1-Liver-F-ZT20-KO

description:
Cross-linked genomic DNA
4CSeq of Liver of mice
processed_4Cseq_log10_counts_ZT20_ZT08.txt.gz

value: Liver

value: KO


title: CRY1-Liver-C-ZT08-WT


title: CRY1-Kidney-A-ZT08-WT


title: CRY1-Liver-A-ZT08-KO


title: Gys2-Kidney-C-ZT08-WT


title: Gys2intron-Liver-F-ZT20-WT


title: Gys2intron-Liver-A-ZT08-WT


title: GYS2-Liver-B-ZT08-KO


title: GYS2-Liver-D-ZT08-WT


title: GYS2-Liver-G-ZT20-WT


title: Cry1intron-Liver-F-ZT20-WT


title: GYS2-Liver-E-ZT20-KO


title: Cry1intron-Liver-A-ZT08-WT


title: GYS2-Liver-F-ZT20-WT


title: Cry1intron-Liver-G-ZT20-WT


title: GYS2-Liver-C-ZT08-KO


title: CRY1-Liver-H-ZT20-WT


title: Gys2intron-Liver-G-ZT20-WT


title: Gys2-Kidney-B-ZT08-WT


title: Gys2-Kidney-E-ZT20-WT


title: Gys2intron-Liver-D-ZT08-WT


title: Gys2-Kidney-H-ZT20-WT


title: CRY1-Kidney-G-ZT20-WT


title: CRY1-Liver-D-ZT20-KO


title: CRY1-Kidney-D-ZT08-WT


title: CRY1-Liver-B-ZT08-WT


title: CRY1-Liver-C-ZT08-KO


title: Cry1intron-Liver-D-ZT08-WT


title: CRY1-Kidney-C-ZT08-WT


title: CRY1-Liver-A-ZT08-WT


title: Gys2-Kidney-A-ZT08-WT


title: CRY1-Liver-F-ZT20-WT


title: Gys2-Kidney-F-ZT20-WT


title: Gys2intron-Liver-C-ZT08-WT


title: GYS2-Liver-H-ZT20-WT


title: Cry1intron-Liver-C-ZT08-WT


title: GYS2-Liver-E-ZT20-WT


title: GYS2-Liver-A-ZT08-WT


title: GYS2-Liver-B-ZT08-WT


title: GYS2-Liver-C-ZT08-WT


title: GYS2-Liver-F-ZT20-KO


title: Cry1intron-Liver-B-ZT08-WT


title: CRY1-Liver-E-ZT20-WT


title: GYS2-Liver-A-ZT08-KO


title: Gys2intron-Liver-H-ZT20-WT


title: Cry1intron-Liver-H-ZT20-WT


title: Gys2-Kidney-G-ZT20-WT


title: CRY1-Liver-E-ZT20-KO


title: CRY1-Liver-D-ZT08-WT


title: Gys2intron-Liver-E-ZT20-WT


title: CRY1-Kidney-B-ZT08-WT


title: CRY1-Kidney-H-ZT20-WT


title: CD8+ MAIT lymph - Patient CHOP39 - rep 2

city: Cape Town

first: Valentin

last: Voillet

state: Western Cape

address: First Floor Wembley Square, 3 McKenzie St, Gardens

country: South Africa

institute: cape town hvtn immunology laboratory

description: sample name: lib12814-R1-final

data_processing:
Single-read sequencing of the pooled libraries was carried out on a HiSeq2500 sequencer (Illumina) with 58-base reads, either using TruSeq v4 or Rapid Run v2 Cluster and SBS kits (Illumina).
The RNA sequencing (RNA-seq) data were aligned to the human genome (UCSC Human Genome Assembly GRCh38 reference) using STAR (v2.4.2a).
Gene expression quantification was performed using RSEM (v1.2.22)
The edgeR Bioconductor package was used to calculate normalization factors to scale the raw library sizes, followed by a normalization using the voom transformation from the limma Bioconductor package.
Genome_build: UCSC Human Genome Assembly GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample; tab-delimited text files include log2CPM for each sample.

source_name: CD8+ MAIT

extract_protocol:
MAIT cells from cryopreserved PBMCs and lymph of 5 patients were sorted and processed with the SMARTseq v4 kit (Clontech).
Sequencing libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina). Barcoded libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies).

tag: cell type

value: CD8+ MAIT

value: Lymph

tag: patient id


title: CRY1-Liver-G-ZT20-WT

tag: strain


title: CRY1-Kidney-E-ZT20-WT


title: ZT46-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT46
RNASeq_Kidney_WT_RPKM.txt.gz

data_processing:
mm10
Reads were mapped using HTSStation (http://htsstation.epfl.ch) on Mus musculus genome build GRCm38 reference.
Estimates of mRNA abundance in RPKM

source_name: PolyA-selected RNA

extract_protocol: RNAs were extracted as previously described (Gachon et al, 2006) with classical methods using guanidium  thiocyanate lysis buffer.

value: Night-restricted feeding


title: CD8+ MAIT blood - Patient CHOP39 - rep 2

description: sample name: lib12813-R1-final

value: Blood


title: CRY1-Liver-B-ZT08-KO


title: ZT12-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT12
RNASeq_Kidney_WT_RPKM.txt.gz


title: GYS2-Liver-G-ZT20-KO


title: CD8+ MAIT lymph - Patient 151214 - rep 1

description: sample name: lib12811-R1-final


title: ZT40-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT40
RNASeq_Kidney_WT_RPKM.txt.gz


title: CD8+ MAIT blood - Patient 151214 - rep 2

description: sample name: lib12812-R1-final


title: CD8+ MAIT blood - Patient 151214 - rep 1

description: sample name: lib12810-R1-final


title: ZT14-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT14
RNASeq_Kidney_WT_RPKM.txt.gz


title: Gys2intron-Liver-B-ZT08-WT


title: ZT10-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT10
RNASeq_Kidney_WT_RPKM.txt.gz


title: Cry1intron-Liver-E-ZT20-WT


title: CD8+ MAIT lymph - Patient CHOP39 - rep 1

description: sample name: lib12809-R1-final


title: CD8+ MAIT blood - Patient CHOP39 - rep 1

description: sample name: lib12808-R1-final


title: Gys2-Kidney-D-ZT08-WT


title: ZT16-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT16
RNASeq_Kidney_WT_RPKM.txt.gz


title: ZT44-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT44
RNASeq_Kidney_WT_RPKM.txt.gz


title: CD8+ MAIT blood - Patient 20151029 - rep 2

description: sample name: lib12805-R1-final


title: ZT42-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT42
RNASeq_Kidney_WT_RPKM.txt.gz


title: CD8+ MAIT lymph - Patient 20151029 - rep 1

description: sample name: lib12806-R1-final


title: ZT06-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT06
RNASeq_Kidney_WT_RPKM.txt.gz


title: CD8+ MAIT blood - Patient 20151029 - rep 1

description: sample name: lib12804-R1-final


title: CD8+ MAIT lymph - Patient 20151013 - rep 2

description: sample name: lib12800-R1-final


title: ZT00-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT00
RNASeq_Kidney_WT_RPKM.txt.gz


title: ZT04-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT04
RNASeq_Kidney_WT_RPKM.txt.gz


title: CD8+ MAIT blood - Patient 20151013 - rep 1

description: sample name: lib12797-R1-final


title: CD8+ MAIT lymph - Patient 20151013 - rep 1

description: sample name: lib12799-R1-final


title: ZT02-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT02
RNASeq_Kidney_WT_RPKM.txt.gz


title: WGBS NPF4

city: Darlinghurst

first: Ruth

last: Pidsley

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
Bisulfite reads were aligned to the human genome using version 1.2 of an internally developed pipeline, publicly available for download from http://github.com/astatham/Bisulfite_tools. Briefly, adaptor sequences and poor quality bases were removed using Trimgalore (version 0.2.8, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) in paired-end mode with default parameters. Bismark v0.8.3 [PMID: 21493656] was then used to align reads to hg19 using the parameters “-p 4 –bowtie2 –X 1000 –unmapped –ambiguous –gzip –bam”. PCR duplicates were removed using Picard v1.91 (http://broadinstitute.github.io/picard). Count tables of the number of methylated and unmethylated bases sequenced at each CpG site in the genome were constructed using bismark_methylation_extractor with the parameters “-p –no_overlap –ignore_r2 4 –comprehensive –merge_non_CpG –bedgraph –counts –report –gzip –buffer_size 20G”.
Genome_build: hg19
Supplementary_files_format_and_content: file containing counts of methylated (C) and T unmethylated (T) and coverage (cov) at each CpG site assayed

source_name: NPF

growth_protocol: Prostate tissue was chopped into small pieces, approximately 2 mm3, and digested overnight at 37°C in RPMI containing 10% fetal calf serum (FCS), 25 mM HEPES, 100 U/mL penicillin, 100 mg/mL streptomycin, 0.5 mg/mL fungizone, 100 mg/mL gentamicin, 225 U/mL Collagenase Type I and 125 U/mL Hyaluronidase Type II (Sigma Aldrich) as previously described [PMID: 23558784]. Cell suspensions were seeded in RPMI containing 5% FCS, penicillin/streptomycin, 1 nM testosterone (Sigma Aldrich) and 10 ng/mL bFGF (Millipore), a medium that selects for fibroblasts compared to other prostatic cell types. Cells were grown at 37°C in a humidified incubator with 5% O2 and 5% CO2. The first passage of cells typically reached confluency within 2 weeks. The cells were used between passages 2-6.

extract_protocol:
DNA was extracted from CAF and NPF samples using the DNeasy kit (Qiagen) with on-column RNase A digestion. Eluates were precipitated with 0.1 volume sodium acetate and 2.5 volumes ethanol and then resuspended in nuclease-free water. DNA was quantified using a NanoDrop 2000. , library quality was assessed with the Agilent 2100 Bioanalyzer using the High-sensitivity DNA kit (Agilent, CA, USA). DNA was quantified using the KAPA Library Quantification kit by quantitative PCR (KAPA Biosystems). One lane of paired-end 100bp sequencing was performed for each library on the Illumina HiSeq 2500 platform using Truseq v3 cluster kits and SBS kits.
Whole genome bisulfite sequencing libraries were prepared using the Illumina Paired-end DNA Sample Prep Kit (discontinued, Illumina). Briefly, DNA (1ug), was spiked with 0.5% unmethylated lambda DNA (Promega) in a final volume of 50-65ul.  DNA was sheared to 150-300bp by sonication with a Covaris S2. Library preparation was performed according to the manufacturer’s protocol - fragments were end-repaired and adenylated before ligation of Illumina Truseq adaptors.  Gel size selection (260-330bp) was used to purify and size select the ligated DNA, using Qiagen Gel extraction kit (Qiagen, part #28704) and DNA was eluted in 20ul H2O.  Bisulphite treatment was then carried out as previously described [PMID: 17406479], with the bisuphite reaction being performed for 4 hrs at 55°C. After bisulphite cleanup the DNA pellet was resuspended in 50 ul H2O. The adaptor-ligated bisulfite-treated DNA was enriched by performing 5 independent PCR reactions for 10 cycles using PfuTurboCx Hotstart DNA polymerase (Stratagene) in a volume of 50ul per PCR reaction.  The 5 independent PCRs were pooled together, cleaned up using the MinElute PCR purification kit and eluted in 20ul Qiagen EB buffer.
WGBS

treatment_protocol: Cells were cultured in standard media to approximately 80% confluency before being trypsinised, resuspended in media and then centifuged to create cell pellets. Cells were stored at -80°C until DNA extraction.

tag: patient

value: Prostate

tag: gender

value: Male

value: Normal Prostate Fibroblast


title: ZT34-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT34
RNASeq_Kidney_WT_RPKM.txt.gz

tag: genotype


title: ZT32-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT32
RNASeq_Kidney_WT_RPKM.txt.gz


title: ZT36-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT36
RNASeq_Kidney_WT_RPKM.txt.gz


title: WGBS NPF2


title: WGBS NPF3


title: ZT08-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT08
RNASeq_Kidney_WT_RPKM.txt.gz


title: CD8+ MAIT lymph - Patient 20151029 - rep 2

description: sample name: lib12807-R1-final


title: ZT30-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT30
RNASeq_Kidney_WT_RPKM.txt.gz


title: ZT28-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT28
RNASeq_Kidney_WT_RPKM.txt.gz


title: ZT38-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT38
RNASeq_Kidney_WT_RPKM.txt.gz


title: MYB OG86

value: AML


title: ZT20-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT20
RNASeq_Kidney_WT_RPKM.txt.gz


title: WGBS CAF4

source_name: CAF

value: Cancer Associated Fibroblast


title: ZT18-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT18
RNASeq_Kidney_WT_RPKM.txt.gz


title: ZT22-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT22
RNASeq_Kidney_WT_RPKM.txt.gz


title: ZT26-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT26
RNASeq_Kidney_WT_RPKM.txt.gz


title: WGBS NPF1


title: WGBS CAF2


title: RNA-seq NPF4

data_processing:
75bp paired-end reads for 4 pairs of patient-matched CAF and NPF cells were processed using Trim Galore (version 0.2.8) for adapter trimming, Tophat (version 2.0.10) [PMID: 23618408] for mapping reads and Cufflinks (version 2.0.10) [PMID: 20436464] to assemble transcripts, both guided by GENCODE annotations (version 19) [PMID: 22955987]. Uniquely mapped properly paired reads were unambiguously assigned to exons of GENCODE genes (version 19) and counted using ht-seqcount (version 0.5.4p3) [PMID: 25260700], reads mapping to known rRNA loci were discarded using samtools procedures [PMID: 19505943].
Genome_build: hg19
Supplementary_files_format_and_content: file of counts data generated from Htseq count

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen) with on-column DNase I digestion. RNA concentration and integrity was assessed on an Agilent Bioanalyzer 2100 using the Eukaryote Total RNA Nano Chip (Agilent).  RNA (500 ng) was depleted of ribosomal RNA using RiboZero (Illumina, CA, USA).
Library preparation was performed for each sample using the Illumina TruSeq Stranded Total RNA sample kit (Illumina, CA, USA) according to the manufacturer’s protocol.  TruSeq directional paired-end sequencing with 75bp chemistry was performed with six samples multiplexed per lane.
RiboZero RNA-seq

treatment_protocol: Cells were cultured in standard media to approximately 80% confluency before being trypsinised, resuspended in media and then centifuged to create cell pellets. Cells were stored at -80°C until RNA extraction.


title: RNA-seq NPF2


title: RNA-seq CAF4


title: RNA-seq NPF1


title: RNA-seq NPF3


title: RNA-seq CAF2


title: RNA-seq CAF3


title: WGBS CAF3


title: Pcon12_vegetative mycelium (pool)

city: Bochum

first: Minou

last: Nowrousian

address: Universitaetsstr. 150

department: Molecular and Cellular Botany

institute: Ruhr-University Bochum

description:
Pcon_vegmix_2
One of two technical replicates from Pcon_vegmix_2: SRR593264

data_processing:
Illumina Casava 1.8.2 used for base calling.
reads were trimmed for low quality bases, and reads with undefined bases ("N") were removed as described in Teichert et al. 2012, BMC Genomics 13: 511
read counts and expression ratios for annotated gene models were determined with DESeq (Anders S, Huber W 2010, Genome Biol 11: R106), LOX 1.8 (Zhang et al. 2010, Bioinf 26: 1918-1919), and "classical analysis" as described in Teichert et al. 2012, BMC Genomics 13:511. RNA-seq reads from a previous analysis (Traeger et al. 2013, PLoS Genet 9: e1003820, GEO accession number GSE41631) were also included in the analysis.
a consensus for differential expression was determined from the three analyses (DESeq, LOX, classical) as described in  Teichert et al. 2012, BMC Genomics 13:511. Thresholds for differential expression were 2-fold/0.5-fold and 4-fold/0.25-fold for stringent analysis.
Genome_build: P. confluens genome version 01 (acc. no. CATG01000000, BioProject acc. PRJNA65573)
Supplementary_files_format_and_content: tab-delimited text file includes read counts (also including read counts for RNA-seq data from a previous experiment, samples Pcon7-Pcon12, from Traeger et al. 2013, PLoS Genet 9: e1003820, GEO accession number GSE41631) and expression ratios (from LOX, DESeq, classical) for all annotated genes as well as additional information (e.g. predicted function, length of transcript, peptide etc.)

organism: Pyronema omphalodes CBS 100304

source_name: vegetative mycelium (pool)

growth_protocol: Growth for samples Pcon_sex was in surface cultures in constant light (pool of RNAs from 3, 4, and 5d) in WPC medium, for Pcon_veg samples in surface cultures in WPC in constant darkness (pool of RNAs from 3, 4, and 5d), and for Pcon_vegmix samples, pooled RNA from the following conditions was used: growth in WPC in submerged culture in constant light and constant darkness, and growth in BMM in surface culture in constant darkness, all for 3d

extract_protocol:
Total RNA was extracted with the Qiagen RNeasy lipid tissue mini kit with some modifications as described in Nowrousian and Kück 2006, FEMS Microbiol Lett 257: 328-335
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: vegetative mycelium


title: Pcon11_vegetative mycelium (pool)

description:
Pcon_vegmix_1
One of two technical replicates from Pcon_vegmix_1: SRR593262


title: RNA-seq CAF1


title: WGBS CAF1


title: Pcon8_vegetative mycelium

description:
Pcon_veg_2
One of two technical replicates from Pcon_veg_2: SRR593260

source_name: vegetative mycelium


title: G1

city: Uppsala

first: Minerva

middle: Susana

last: Trejo Arellano

state: Uppsala

address: Almas Allé 5

department: Plant Biology

country: Sweden

institute: SLU

description:
First homozygous generation segregated from a selfed heterozygous parental plant
Bisulphite converted DNA

data_processing:
Quality control was done with an in-house R script
Adapter trimming was done with reaper (EMBL-EBI)
Clean reads were mapped to Arabidopsis TAIR10 genome using bismark. To increase the coverage, mates from the paired-end were mapped as independent single end reads: R1 as directional and R2 and non-directional
Mapping sam files were deduplicated using samtools rmdup
bismark_methylation_extractor was used to do the methylation calling of cytosines covered by 7 or more reads
Methylation status of a cytosines was calculated as #C/(#C+#NC) where #C is the absolute number of reads in which C was converted to T by bisulfite treatment and NC is the absolute number of reads in which C was unaffected by bisulphite treatment
Subsequent analysis were performed in R. The gene models used were from TAIR10 gff annotation file
Genome_build: TAIR10
Supplementary_files_format_and_content: bedgraph converted and non converted cytosines per methylation context; bigwig format

organism: Arabidopsis thaliana

source_name: leaf no. 6

growth_protocol: Plants were grown at 21°C with humidity of 60% under 16/8 h or 8/16 h light-dark cycles corresponding to long day- or short day-conditions, respectively, at 120 µmol m-2 s-1

extract_protocol:
GE Healthcare Nucleon PhytoPure kit according to manufacturer's instructions. Bisulfite treatment by ZYMO EZ DNA Methylation-Gold kit
Tru Seq chemistry

value: leaf

tag: ecotype

value: Columbia

tag: biological replicate


title: Pcon9_sexually developing mycelium

description:
Pcon_sex_1
One of two technical replicates from Pcon_sex_1: SRR593254

source_name: sexually developing mycelium

value: sexually developing mycelium


title: Col

description: Bisulphite converted DNA


title: Pcon10_sexually developing mycelium

description:
Pcon_sex_2
One of two technical replicates from Pcon_sex_2: SRR593256


title: Pcon7_vegetative mycelium

description:
Pcon_veg_1
One of two technical replicates from Pcon_veg_1: SRR593258


title: G6

description:
Sixth selfed generation
Bisulphite converted DNA


title: ZT4-Cry1IntronWT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from Cry1IntronWT mice at ZT4
RNASeq_LiverKidney_WTCry1IntronKO_RPKM.txt.gz

value: Kidney

value: Ad libitum

value: post-natal 8-12 weeks


title: ZT24-WT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT24
RNASeq_Kidney_WT_RPKM.txt.gz

value: WT


title: Pcon21_ProApoC

source_name: protoapothecia

growth_protocol: Samples were grown on microdissection slides with 150 µl WPC medium (+0.8 % agar) for 4d at 25 °C.

extract_protocol:
Total RNA was extracted and linearly amplified as described in Teichert et al. 2012, BMC Genomics 13: 511
RNA libraries were prepared for sequencing using standard Illumina protocols (TrueSeq Chemistry)

treatment_protocol: Samples were fixated in ethanol at 4°C, and protoapothecia were harvested by laser microdissection as described in Teichert et al. 2012, BMC Genomics 13: 511

tag: isolation

value: laser microdissected sample

value: protoapothecia


title: Pcon19_ProApoA


title: Pcon20_ProApoB


title: ZT0-Cry1IntronKO-Liver

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from Cry1IntronKO mice at ZT0
RNASeq_LiverKidney_WTCry1IntronKO_RPKM.txt.gz

value: Liver


title: zed1-D 48h R1

city: Beijing

first: Wang

last: Zhicai

address: No.20 Nanxincun, Xiangshan

institute: Institute of Botany, Chinese Academy of Sciences

description: 18oC grown seedlings were transferred to 28oC for 48h, repeat 1.

data_processing:
Casava1.7 software was used for base calling.
Remove low quality readsreads, and reads with adaptor sequences, as well as reads in which the percentage of unknown bases (N) is greater than 10%.
Clean reads were mapped to reference sequences using SOAP2.21 aligner according to  Li R, Yu C, Li Y, et al., Bioinformatics, 2009.  No more than 2 mismatches were allowed in the alignment.
Genome_build: TAIR10
Supplementary_files_format_and_content: txt text files were generated including RPKM values for each Sample

source_name: inflorescences with juvenile leaves

growth_protocol: Plants were grown in growth chamber with an illumination intensity of 80-90 µmol m-2 s-1 and a 16-h light/8-h dark photoperiod.

extract_protocol:
0.5-1.0 cm of inflorescences with juvenile leaves were collected and flash frozen on dry ice, and total RNA was extracted using Trizol reagent.
The mRNA was purified with magnetic (dT) beads, and fragmented to a size of ~200 bp. The resulting fragments were synthesized as double-stranded cDNA molecules, and the ends were modified by adding an adenine to the 3’ terminus.

treatment_protocol: The WT and zed1-D plants were grown at 18oC until the primary inflorescence stem bolted to 0.5-1.0 cm, and then transferred into 28oC.

value: inflorescences with juvenile leaves

value: inflorescence stem bolted to 0.5-1.0 cm

tag: treatment

value: 18oC seedlings were transferred to 28oC for 48h


title: zed1-D 12h R2

description: 18oC seedlings were transferred to 28oC for 12h, repeat 2.


title: zed1-D 48h R2

description: 18oC seedlings were transferred to 28oC for 48h, repeat 2.


title: zed1-D 12h R1

description: 18oC grown seedlings were transferred to 28oC for 12h, repeat 1.

value: 18oC seedlings were transferred to 28oC for 12h


title: ZT12-Cry1IntronKO-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from Cry1IntronKO mice at ZT12
RNASeq_LiverKidney_WTCry1IntronKO_RPKM.txt.gz


title: ZT8-Cry1IntronWT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from Cry1IntronWT mice at ZT8
RNASeq_LiverKidney_WTCry1IntronKO_RPKM.txt.gz


title: zed1-D 3h R1

description: 18oC grown seedlings were transferred to 28oC for 3h, repeat 1.

value: 18oC seedlings were transferred to 28oC for 3h


title: zed1-D 3h R2

description: 18oC seedlings were transferred to 28oC for 3h, repeat 2.


title: ZT20-Cry1IntronWT-Liver

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from Cry1IntronWT mice at ZT20
RNASeq_LiverKidney_WTCry1IntronKO_RPKM.txt.gz


title: ZT4-Cry1IntronKO-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from Cry1IntronKO mice at ZT4
RNASeq_LiverKidney_WTCry1IntronKO_RPKM.txt.gz


title: zed1-D 0h R1

description: 18oC grown seedlings were transferred to 28oC for 0h, repeat 1.

value: 18oC seedlings were transferred to 28oC for 0h


title: ZT8-Cry1IntronWT-Liver


title: ZT12-Cry1IntronWT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from Cry1IntronWT mice at ZT12
RNASeq_LiverKidney_WTCry1IntronKO_RPKM.txt.gz


title: ZT12-Cry1IntronWT-Liver


title: WT 48h R2

value: wild type


title: WT 48h R1


title: ZT8-Cry1IntronKO-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from Cry1IntronKO mice at ZT8
RNASeq_LiverKidney_WTCry1IntronKO_RPKM.txt.gz


title: WT 12h R2


title: ZT4-Cry1IntronWT-Liver


title: WT 12h R1


title: ZT4-Cry1IntronKO-Liver


title: WT 3h R1


title: WT 0h R2

description: 18oC seedlings were transferred to 28oC for 0h, repeat 2.


title: ZT20-Cry1IntronKO-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from Cry1IntronKO mice at ZT20
RNASeq_LiverKidney_WTCry1IntronKO_RPKM.txt.gz


title: WT 0h R1


title: ZT16-Cry1IntronWT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from Cry1IntronWT mice at ZT16
RNASeq_LiverKidney_WTCry1IntronKO_RPKM.txt.gz


title: exp1_CEBPB_dDAVP_input

city: Baltimore

first: Hyun Jun

last: Jung

state: MD

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

institute: Johns Hopkins University School of Medicine

data_processing:
Align and transform the .fastq to .sam files using BWA program and mm10 mouse genome:  bwa samse mm10.fa sample.sai sample.fastq > sample.sam bwa aln -t 8 mm10.fa  sample.fastq > sample.sai.
Convert format from Sam to Bam and index the files using Samtools: Samtools view –bhS sample.sam > sample.bam, samtools sort sample.bam sample.sorted; samtools index sample.sorted.bam.
Create bedgraph files using macs2, macs2 callpeak -t sample_filename.sorted.bam -c input_filename.sorted.bam -f BAM -g mm -n output_filename -B --bw 300 –q 0.01 –SPMR
Create a peak bed file from macs2 peak files using a 'bedtools intersection'
Create a bedGraph file from pile up file of macs2 output
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph (on sample records) and bed files (on series record).

source_name: mpkCCD cells

growth_protocol: Cultured mouse mpkCCD (clone 11) cells were grown and maintained in complete medium, DMEM/F12 containing 2% dialyzed serum and supplements (5 μg/mL insulin, 50 nM dexamethasone, 1 nM triiodothyronine, 10 ng/mL epidermal growth factor, 60 nM sodium selenite, 5 μg/mL transferrin), as previously described (Yu MJ, Proc Natl Acad Sci U S A 106:2441-2446, 2009).

extract_protocol:
Shearing of chromatin was carried out by the manufacturer's protocol of truChIP kit (PN 520075, Covaris, Woburn, Massachusetts). All Covaris buffers were provided in kit. Confluent monolayers mpkCCD cells cultured on 100 mm permeable supports of transwell system were treated with dDAVP (0.1 nM) or vehicle for 30 minutes and then washed in ice-cold PBS followed by cross-linking in 1.1% formaldehyde in Covaris Fixing Buffer (5.5 ml) for 5 minutes at room temperature. Cross-linking was terminated by the addition of 0.3 ml of 1X Covaris Quenching Buffer with rocking. The buffer solution was aspirated and ice-cold PBS was added to each plate. Cells were scraped, spun down (200xg, 5 minutes), and washed twice with ice-cold PBS. Cell pellets were resuspended in 1 ml of 1X Covaris Lysis Buffer for 10 minutes at 4°C with rocking.  Nuclei were pelleted by spinning at 1,700xg for 5 minutes at 4°C. Nuclear pellets was resuspended in 1 ml of 1X Covaris Wash Buffer and incubated for 10 minutes at 4°C with rocking. Samples were spun at 1,700xg for 5 minutes at 4°C. Nuclear pellets were washed twice with 1 ml of Covaris Non-ionic Shearing Buffer and spun at 1,700xg for 5 minutes at 4°C. Nuclei were resuspended in 1 ml of Covaris Non-ionic Shearing Buffer. Two 20 ul aliquots of the resuspended pellets were removed prior to shearing to be used as subsequent unsheared controls for immunoblotting and agarose gel electrophoresis. The remaining samples were transferred to AFA tubes (TC12 x 12 mm). Samples were sheared using a Covaris S2 SonoLAB Single system for 6 minutes (Duty cycle: 5%; Intensity: 4; cycle: 200). Total nuclear protein concentration of each sample in mg/ml was determined with the BCA Protein Assay Kit (Thermo Scientific, Rockford, IL).  To test shearing efficiency, a 20 ul aliquot from each sample was obtained after shearing. The aliquots from the unsheared sample and the sheared sample, were incubated with 100 ul 1X TE buffer, 10 ul 10% SDS, and RNAse A (10 ug/ul, Cell Signaling Technology, Danvers, Massachusetts) for 30 minutes at 37°C. After adding proteinase K (2 ug), the samples were incubated overnight at 65°C. The DNA was purified using DNA Clean & Concentrator columns (Catalog #: D4013, Zymo Research, Irvine, CA) and ran on an E-gel EX 2% agarose (Invitrogen, Carlsbad, CA). Target fragment sizes for chromatin immunoprecipitation were in the range of 150-300 bp.  Immunoprecipitaiton was performed by the manufacturer's instruction (SimpleChIP protocol #9003, Cell Signaling Technology). 'Input' sample (10 ul) was obtained prior to immunoprecipitation.  Chromatin Immunoprecipitation was performed using 700-800 ug of sheared chromatin in 800 uL of 1X Covaris Non-ionic Shearing Buffer with 4 μg of anti-CREB1, anti-CEBPB or anti-rabbit IgG antibodies (as negative control). The mixtures were incubated overnight at 4°C with gentle rotation, followed by incubation with ChIP Grade Protein G Magnet Beads (Catalog #: 9006, Cell Signaling Technology) for 2 hours at 4°C with rotation. The beads were washed a total of four times, including three low salt washes followed by one high salt wash for 5 minutes each at 4°C. Immunoprecipitated chromatin was eluted from the beads with 150 ul of 1X ChIP Elution Buffer for 30 minutes at 65°C in a thermomixer. To reverse crosslinks, 6 ul of 5 M NaCl and 2 ul of 20 ug/ul  Proteinase K were added to the chromatin followed by incubation at 65°C overnight. DNA was purified according to the manufacturer's instruction.
Sequencing libraries were prepared according to the manufacturer's instruction (NuGEN Ovation SP Ultralow library system kit). Adaptor-conjugated iibraries were amplified by PCR. The amplified libararies were measured.  A fixed amount of the total measured DNA was used for sequencing in an Illumina Hiseq2000 instrument to obtain single read data.  Libraries were sequenced using an Illumina HiSeq2000, obtaining 1- by 50-bp reads.

treatment_protocol: For dDAVP treatment, cells were transferred to permeable supports (75mm, 0.4um pore, Corning #3419), and grown until confluency as documented transepithelial resistance measurements (Epithelial Volt ohmmeter; WPI). At that point, the complet medium was changed to serum- and hormone-free medium, and cells were maintained for 24 hr. Cells were incubated with the V2 receptor-selective vasopressin analog dDAVP (0.1 nM) or its vehicle and harvested after 30 minutes.

tag: cell line

value: mpkCCD (clone 11)

value: cultured mouse cortical collecting duct cells (mpkCCD)

tag: passages

tag: chip antibody

value: none (input)


title: 84K  SIM8 RNA-seq [Ptr_34]

city: Fuzhou

first: Bobin

last: Liu

address: No.15 Shangxiadian Road, Cangshan District

data_processing:
The RNA-seq reads were aligned to the Populus genome (version 3.0, https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa) using TopHat (version 2.0.13) (Kim et al., 2013). Only uniquely mapped reads were retained for subsequent analysis.
Genome_build: Populus trichocarpa v3.0 (Poplar)
Supplementary_files_format_and_content: bigWig

organism: Populus alba x Populus glandulosa

source_name: callus

growth_protocol: The leaf, CIM8, SIM4 and SIM8 from 84K and PtWOX11ox plants were harvested in Fujian Agriculture and Forestry University in 2016.

extract_protocol:
The total RNA was extracted using RNAprep pure plant kit (Tiangen, Beijing, China).
Strand-specific RNA-Seq libraries generated from samples above were constructed using SMART method and sequenced on Illumina Hiseq 2500.

treatment_protocol: No treatment

tag: tissue

value: callus growth on shoot inducing medium 8 days after culture

value: P. alba X P. glandulosa (84K)


title: ZT8-Cry1IntronKO-Liver

tag: feeding

value: Ad libitum

value: post-natal 8-12 weeks


title: 84K  SIM8 RNA-seq [Ptr_35]

institute: Fujian Agriculture and Forestry University


title: ZT20-Cry1IntronKO-Liver

tag: age


title: 84K  SIM8 RNA-seq [Ptr_36]


title: zed1-D 0h R2


title: exp1_CEBPB_vehicle_input

tag: cell type


title: ZT16-Cry1IntronWT-Liver


title: ZT20-Cry1IntronWT-Kidney

value: Kidney


title: exp4_CREB1_dDAVP_input


title: ZT0-Cry1IntronWT-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from Cry1IntronWT mice at ZT0
RNASeq_LiverKidney_WTCry1IntronKO_RPKM.txt.gz


title: ZT12-Cry1IntronKO-Liver


title: ZT0-Cry1IntronKO-Kidney

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from Cry1IntronKO mice at ZT0
RNASeq_LiverKidney_WTCry1IntronKO_RPKM.txt.gz


title: ZT0-Cry1IntronWT-Liver


title: exp3_CREB1_exp2_CEBPB_dDAVP_input

description: This sample serves as input for exp3_CREB1_dDAVP (GSM2586796) and exp2_CEBPB_dDAVP (GSM2586801).


title: exp1_CREB1_dDAVP_input


title: 84K  CIM8 RNA-seq [Ptr_28]

value: callus growth on callus inducing medium 8 days after culture


title: WT 3h R2


title: ZT16-Cry1IntronKO-Liver

description:
PolyA-selected RNA
RNA-Seq of Kidney extracted from Cry1IntronKO mice at ZT16
RNASeq_LiverKidney_WTCry1IntronKO_RPKM.txt.gz

value: Liver


title: exp2_CREB1_dDAVP_input


title: 84K  SIM4 RNA-seq [Ptr_31]

value: callus growth on shoot inducing medium 4 days after culture


title: exp3_CREB1_exp2_CEBPB_vehicle_input

description: This sample serves as input for exp3_CREB1_vehicle (GSM2586792) and exp2_CEBPB_vehicle (GSM2586799).


title: ZT16-Cry1IntronKO-Kidney


title: 84K  CIM8 RNA-seq [Ptr_30]


title: 84K  SIM4 RNA-seq [Ptr_32]


title: 84K  SIM4 RNA-seq [Ptr_33]


title: exp4_CREB1_vehicle_input


title: 84K  leaf RNA-seq [Ptr_27]

source_name: leaf

value: 3th-5th leaf


title: 84K leaf RNA-seq [Ptr_25]


title: WT-LN-Treg-Biological-Replicate1

city: Boston

first: Ramesh

last: Shivdasani

state: MA

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

description:
CD45+CD3+CD4+YFP+ Tregs isolated from skin draining LNs
WT-LN-Treg-Replicate1

data_processing:
Alignment: RNA-seq: Tophat, version 2.0.6
RNA-Seq - Read counts were normalized using Deseq2 with defalut parameters and further used for calculating differntial expression (q<0.05).
Genome_build: mm9
Supplementary_files_format_and_content: Read_Counts_All_Cell_Types.txt, Differential_Expression_WT_LN_Treg_vs_WT_Skin_Treg.txt

source_name: Foxp3 cre-eyfp LN Treg RNA-seq

extract_protocol:
Superficial and deep axillary LNs were isolated and homogenized in complete DMEM followed by FACS staining for sorting of Tregs
Total RNA was extracted with Pico pure kit (Life technologies) followed by DNase treatment with the RNeasy kit (Qiagen).
The SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: LN

value: Adult FOXP3+ Tregulatory cells (immune)

value: Foxp3 cre-eyfp


title: exp1_CREB1_vehicle_input


title: Rora cKO-Skin-MC-Treg-Biological-Replicate3

description:
CD45+CD3+CD4+YFP+ Tregs isolated from ears treated with MC903
Rora cKO-Skin-MC-Treg-Replicate3

source_name: Foxp3 cre-eyfp Rora fl/fl MC skin Treg RNA-seq

extract_protocol:
Ears were split into dorsal and ventral halves. Skin was minced finely and digested for 90 minutes in complete DMEM with Liberase TL and DNAse with vigorous shaking. Skin digests were filtered and immediately stained for FACS.
Total RNA was extracted with Pico pure kit (Life technologies) followed by DNase treatment with the RNeasy kit (Qiagen).
The SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: Mice were treated with MC903, dissolved in ethanol which was applied topically on their ears, every other day for total 4 applications.

value: Skin

value: Foxp3 cre-eyfp Rora fl/fl

tag: agent


title: exp2_CEBPB_dDAVP

description: input sample = GSM2586808

value: mpkCCD (clone 11)

value: anti-C/EBPb antibody (Santa Cruz Biotechnology, sc-150X)


title: Rora cKO-Skin-MC-Treg-Biological-Replicate2

description:
CD45+CD3+CD4+YFP+ Tregs isolated from ears treated with MC903
Rora cKO-Skin-MC-Treg-Replicate2

tag: strain


title: PtWOX11ox SIM8 RNA-seq [Ptr_12]

value: P. alba X P. glandulosa (84K) overexpressed PtWOX11


title: 84K  CIM8 RNA-seq [Ptr_29]


title: Rora cKO-Skin-MC-Treg-Biological-Replicate1

description:
CD45+CD3+CD4+YFP+ Tregs isolated from ears treated with MC903
Rora cKO-Skin-MC-Treg-Replicate1


title: exp1_CEBPB_dDAVP

description: input sample = GSM2586811

value: cultured mouse cortical collecting duct cells (mpkCCD)


title: PtWOX11ox SIM8 RNA-seq [Ptr_11]

value: callus growth on shoot inducing medium 8 days after culture


title: WT-Skin-MC-Treg-Biological-Replicate3

description:
CD45+CD3+CD4+YFP+ Tregs isolated from ears treated with MC903
WT-Skin-MC-Treg-Replicate3

source_name: Foxp3 cre-eyfp MC skin Treg RNA-seq


title: exp2_CEBPB_vehicle

description: input sample = GSM2586804


title: exp1_CEBPB_vehicle

description: input sample = GSM2586810


title: PtWOX11ox SIM4 RNA-seq [Ptr_8]


title: WT-Skin-MC-Treg-Biological-Replicate2

description:
CD45+CD3+CD4+YFP+ Tregs isolated from ears treated with MC903
WT-Skin-MC-Treg-Replicate2


title: PtWOX11ox SIM4 RNA-seq [Ptr_9]


title: WT-Skin-MC-Treg-Biological-Replicate1

description:
CD45+CD3+CD4+YFP+ Tregs isolated from ears treated with MC903
WT-Skin-MC-Treg-Replicate1


title: exp4_CREB1_dDAVP

description: input sample = GSM2586809

value: anti-CREB1 antibody (Millipore, 17-600)


title: WT-LN-Treg-Biological-Replicate2

description:
CD45+CD3+CD4+YFP+ Tregs isolated from skin draining LNs
WT-LN-Treg-Replicate2


title: exp3_CREB1_dDAVP

description: input sample = GSM2586808


title: 84K  leaf RNA-seq [Ptr_26]

value: P. alba X P. glandulosa (84K)


title: exp2_CREB1_dDAVP

description: input sample = GSM2586807


title: PtWOX11ox CIM8 RNA-seq [Ptr_6]


title: Rora cKO-Skin-Treg-Biological-Replicate2

description:
CD45+CD3+CD4+YFP+ Tregs isolated from dorsal skin and ears
Rora cKO-Skin-Treg-Replicate2

source_name: Foxp3 cre-eyfp Rora fl/fl skin Treg RNA-seq

extract_protocol:
Mice were shaved and dorsal skin and ears were separated. Dorsal skin was cut into 2cm2 pieces, and ears were split into dorsal and ventral halves. All the fat was removed and skin was minced finely and digested for 90 minutes in complete DMEM with Liberase TL and DNAse with vigorous shaking. Skin digests were filtered and immediately stained for FACS.
Total RNA was extracted with Pico pure kit (Life technologies) followed by DNase treatment with the RNeasy kit (Qiagen).
The SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: exp1_CREB1_dDAVP

description: input sample = GSM2586806


title: exp2_CREB1_vehicle_input

value: none (input)


title: PtWOX11ox SIM8 RNA-seq [Ptr_10]


title: ko2

city: Nanjing

first: Xiaoming

last: Wang

address: 101 Longmian Road

institute: Nanjing Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v2.
Fragments Per Kilobase per Million mapped fragments (FPKM) were calculated using Cufflinks software.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: germinal center b cell

extract_protocol:
Splenic germinal center B cells were FACS sorted, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: germinal center b cell

value: 6-10 weeks

tag: genotype/variation

value: Uhrf1 fl/fl x AID-Cre+


title: PtWOX11ox CIM8 RNA-seq [Ptr_4]

value: callus growth on callus inducing medium 8 days after culture


title: WT-Skin-Treg-Biological-Replicate2

description:
CD45+CD3+CD4+YFP+ Tregs isolated from dorsal skin and ears
WT-Skin-Treg-Replicate2

source_name: Foxp3 cre-eyfp skin Treg RNA-seq


title: wt2

value: Uhrf1 wt


title: exp4_CREB1_vehicle

description: input sample = GSM2586805


title: PtWOX11ox leaf RNA-seq [Ptr_3]

value: 3th-5th leaf


title: ko1


title: WT-Skin-Treg-Biological-Replicate3

description:
CD45+CD3+CD4+YFP+ Tregs isolated from dorsal skin and ears
WT-Skin-Treg-Replicate3

value: Adult FOXP3+ Tregulatory cells (immune)

value: Foxp3 cre-eyfp


title: PtWOX11ox SIM4 RNA-seq [Ptr_7]

value: callus growth on shoot inducing medium 4 days after culture


title: exp3_CREB1_vehicle

description: input sample = GSM2586804

value: mpkCCD (clone 11)


title: exp2_CREB1_vehicle

description: input sample = GSM2586803


title: PtWOX11ox CIM8 RNA-seq [Ptr_5]


title: Rora cKO-Skin-Treg-Biological-Replicate3

description:
CD45+CD3+CD4+YFP+ Tregs isolated from dorsal skin and ears
Rora cKO-Skin-Treg-Replicate3

value: Skin

value: Foxp3 cre-eyfp Rora fl/fl


title: exp1_CREB1_vehicle

description: input sample = GSM2586802

value: cultured mouse cortical collecting duct cells (mpkCCD)


title: wt1


title: PtWOX11ox leaf RNA-seq [Ptr_1]

value: P. alba X P. glandulosa (84K) overexpressed PtWOX11


title: PtWOX11ox leaf RNA-seq [Ptr_2]


title: OCEAN-C GM12878 rep2

status: Public on Mar 25 2018

first: lumeng

last: Jia

address: Yiheyuan road

institute: Peking university

description:
No treatment
Processed data for combined replicates is available on GSM2694185.

data_processing:
Library strategy: OCEAN-C
Hi-C and OCEAN-C  reads were aligned to hg19 using Bowtie2
genome build: hg19
processed data files format and content: bed files for Hi-C OCEAN-C sample with HOCIs

source_name: Normal

growth_protocol: Cells were cultured in RPMI-1640 medium (ATCC, Catalog No. 30-2001) with 15% fetal bovine serum and air, 95%, carbon dioxide (CO2), 5% at 37℃.

extract_protocol:
For OCEAN-C, about 5M cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Formaldehyde was quenched  by 0.2M glycine. Nuclear lysates were incubated with MboI. Fragment ends were filled with biotinylated nucleotides, then ligated with T4. Nuclei were then isolated and sonicated. Sonicate was extracted with phenol–chloroform–isoamyl alcohol (25:24:1) and reverse crosslinked. DNA were purified and size selected before Illumina libraries generation
Sequencing libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645, NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: peripheral blood

value: B lymphocyte

value: No data

tag: disease state

value: Normal

tag: gender

value: female


title: WT-Skin-Treg-Biological-Replicate1

description:
CD45+CD3+CD4+YFP+ Tregs isolated from dorsal skin and ears
WT-Skin-Treg-Replicate1

tag: genotype


title: OCEAN-C GM12878 rep1

description:
No treatment
Processed data for combined replicates is available at foot of this sample.

data_processing:
Library strategy: OCEAN-C
Hi-C and OCEAN-C reads were aligned to hg19 using Bowtie2
genome build: hg19
processed data files format and content: bed files for Hi-C OCEAN-C sample with HOCIs


title: Rora cKO-Skin-Treg-Biological-Replicate1

description:
CD45+CD3+CD4+YFP+ Tregs isolated from dorsal skin and ears
Rora cKO-Skin-Treg-Replicate1


title: OCEAN-C RPMI-8226

description: No treatment

source_name: Multiple myeloma

value: Multiple myeloma

value: male


title: FAIRE-seq U266

description: No treatment

data_processing:
FAIRE-seq reads were aligned to hg19 using BWA-MEM
FAIRE-seq peaks and OCEAN-seq HOCIs were defined using ZINBA
genome build: hg19
processed data files format and content: bed files for FAIRE-seq samples with peaks

extract_protocol:
For FAIRE-seq, about 5M cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Formaldehyde was quenched  by 0.2M glycine. Nuclei were isolated and sonicated. Sonicate was extracted with phenol–chloroform–isoamyl alcohol (25:24:1) and reverse crosslinked. DNA were purified and size selected before Illumina libraries generation.
Sequencing libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645, NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.


title: OCEAN-C U266

description: No treatment

extract_protocol:
For OCEAN-C about 5M cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Formaldehyde was quenched  by 0.2M glycine. Nuclear lysates were incubated with MboI. Fragment ends were filled with biotinylated nucleotides, then ligated with T4. Nuclei were then isolated and sonicated. Sonicate was extracted with phenol–chloroform–isoamyl alcohol (25:24:1) and reverse crosslinked. DNA were purified and size selected before Illumina libraries generation
Sequencing libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645, NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.


title: FAIRE-seq GM12878

description: No treatment


title: 93-114, 1 h cold treatment (B1)

city: Danzhou

first: Wei-Min

last: Tian

state: Hainan

address: Baodao Village

department: Chinese Academy of Tropical Agricultural Sciences

institute: Rubber Research Institute

description:
B1
Two extension units stages of one-year-old with three independent repeat plants

data_processing:
Filter Dirty Raw Reads: Raw reads that only have 3' adaptor fragments should be removed before data analysis
Clean Reads:Reads after filtering dirty raw reads, on which all following analysis are based
Assembly:The methods of the data filtering and de novo assembly of the present Hevea transcriptome were performed in the BGI (Beijing Genomics Institute, Shenzhen, China) and were highly similar with the previous research paper(Wei et al.,2011).The raw reads generated by the Illumina HiSeq2000 genome analyzer was cleaned by removing adaptor sequences and the low-quality sequences including the empty reads, reads with unknown bases 'N' or with more than 10% Q < 20 bases). Then de novo assembly of the filtered clean reads was carried out by using SOAPdenovo (http://soap.genomics.org.cn/soapdenovo.html) with the default settings and an adjusted K-mer value (K =25) to generate the best assembled contigs. The scaffolds were generated by connecting the contigs between each pair of contigs using ‘N’ to represent unknown bases with the SOAPdenovo method. Paired-end reads were used again for scaffold gap filling to generate the unigenes with the sequences containing the least Ns and could not be further extended at either end. Moreover, the overlapping unigenes from six libraries were assembled into a continuous sequence using the overlapping ends of the clustered homologous unigenes, and redundant sequences were removed to yield nonredundant unigenes with the maximum length using the TGICL (TIGR Gene Indices Clustering) tools. The parameters of the TIGR tools were set at a sequence similarity of 94% and an overlap length of 100 bp among the clustered homologous unigenes.The sets of unigenes from the six distinct samples were further integrated as a reference transcriptome. To obtain a global overview of the reference Heave transcriptome, all the assembled unigenes were used for BLASTx searches against the public available databases including NR (non-redundant protein sequences in NCBI), NT and Swiss-Prot protein database with a cut-off E-value of 10-5. In addition, to get the functional annotation of the above sequences, Blast2GO software  was used to get the GO (gene ontology) terms (http://www.geneontology.org). Also, the COG (Clusters of Orthologous Groups) (http://www.ncbi.nlm.nih.gov/COG) and KEGG (Kyoto Encyclopedia of Gene and Genomones Pathyway) (http://www.genome.jp/kegg) annotation was performed respectively against these databases using BLASTx program (E-value threshold 10-5).
Supplementary_files_format_and_content: difference expression unigenes between two clones in distinct stages, with excel format

organism: Hevea brasiliensis

growth_protocol: Hevea cultivated variety ‘Reken501’ and ‘93-114’ were grown at the experimental station of the Rubber Research Institute, Chinese Tropical Academy of Agricultural Sciences, Danzhou, China.

extract_protocol:
Total RNA was extracted from the collected mixed leaves using the CTAB extraction and LiCl precipitation methods according to previous reports with slight modification (Chang et al.,1993;Reid et al.,2006).Total RNA concentration was quantified using a NanoDrop ND-1000 spectrophotometer. The quality of RNA was analyzed using an Agilent 2100 Bioanalyzer and further verified on 1.0% denaturing agarose gels.
Approximately 20 ug of total RNA from each sample pool of the two clones ‘Reken501’ and ‘93-114’  were used for the cDNA library construction via the standard protocols. The detailed process was described at the previous research paper(Wei et al.,2011).

treatment_protocol: These two cultivals in two extension units stages with three independent repeat plants were treated without cold stress as controls or subjected to 4°C treatment for 1 h and 24 h respectively.

tag: clone

value: 1 h cold treatment (B1)


title: 93-114, 24 h cold treatment (B2)

description:
B2
Two extension units stages of one-year-old with three independent repeat plants

value: 24 h cold treatment (B2)


title: 93-114, control (B0)

description:
B0
Two extension units stages of one-year-old with three independent repeat plants

value: control (B0)


title: Reken501, 24 h cold treatment (A2)

description:
A2
Two extension units stages of one-year-old with three independent repeat plants

value: 24 h cold treatment (A2)


title: FAIRE-seq RPMI-8226

description: No treatment


title: Hi-C GM12878

description: No treatment

data_processing:
Hi-C and OCEAN-seq  reads were aligned to hg19 using Bowtie2
genome build: hg19
processed data files format and content: bed file for Hi-C

extract_protocol:
For Hi-C, about 5M cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Formaldehyde was quenched  by 0.2M glycine. Nuclear lysates were incubated with MboI. Fragment ends were filled with biotinylated nucleotides, then ligated with T4. Ligated fragments were reverse crosslinked, purified, sonicated and size selected before Illumina libraries generation.
Sequencing libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645, NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.


title: Reken501, 1 h cold treatment (A1)

description:
A1
Two extension units stages of one-year-old with three independent repeat plants

value: 1 h cold treatment (A1)


title: WcreCSCs2 (B2_rep1)

status: Public on Mar 23 2018

city: Catanzaro

first: Daniele

last: Torella

address: Viale Europa

department: Medical and Surgical Sciences

country: Italy

institute: Magna Graecia University

data_processing:
All libraries were sequenced on the Illumina HiSeq 1000 generating 100 bp paired end reads.
RNA-seq has been performed by using StrandNGS with its default parameters
Raw data sequences have been pre-processed and then related to mus musculus genome. Alignment parameters have been set as it follows: minimum percentage identity = 90 %; maximum percentage gaps = 5 %; maximum number of novel splices = 1; minimum match length = 25.
Reads with less than 5 valid matches have been filtered out, finally obtaining expression values for reads (quantification phase). To detect novel genes and exons we set the parameters, in term of percentile, as it follows: minimum exon length equals to 10.0; minimum intron length equals to 10.0; maximum intron length equals to 90.0; minimum gene length equals to 10.0; minimum exon RPKM equals to 50.0.
Differential expressions were performed using DESeq algorithm. We performed fold change (FC) analysis on filtered expression values using normalized signal values in log-scale. We considered a fold change cut off equals to 2.5 to identify up and down regulated genes.
Gene Ontology, DAVID and Ingenuity Pathways Analysis (IPA) have been used to functional enrich the data.
Genome_build: mm10
Supplementary_files_format_and_content: The .xls file includes read counts and normalized values for the wtCSCs (indicated as A1, A2, A3) and WcreCSCs (indicated as B1, B2, B3).

source_name: Cardiac Stem Cells

growth_protocol: CSCs were plated in gelatin-coated dishes in CSC growth medium supplemented with 10% ESQ-FBS. Cells were maintained at 37 °C in ambient O2 (21%) and 5% CO2.

extract_protocol:
RNA was extracted using TRIzol Reagent. The extracted RNA integrity was measured with an Agilent 2100 Bioanalyzer, and a sample with an RNA Integrity Number greater than or equal to 8 was considered acceptable.
The libraries were generated using depleted RNA obtained from 1μg total RNA by TruSeq Sample Preparation RNA Kit according to the manufacturer’s without further modifications. The first step involves the removal of ribosomal RNA rRNA using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads that depletes samples of both cytoplasmic and mitochondrial rRNA. Following purification, the RNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter  (Multiple indexing adapters were ligate to the ends of the ds cDNA). The products are purified and enriched with PCR to create the final cDNA library.
All libraries were sequenced on the Illumina HiSeq 1000 generating 100 bp paired end reads.

value: Cardiac Stem Cells


title: WcreCSCs3 (B3_rep2)


title: Reken501, control (A0)

description:
A0
Two extension units stages of one-year-old with three independent repeat plants

value: control (A0)


title: WcreCSCs2 (B2_rep2)


title: WcreCSCs3 (B3_rep1)


title: WtCSCs3 (A3_rep2)


title: WcreCSCs1 (B1_rep1)


title: wtCSCs2 (A2_rep2)


title: WcreCSCs1 (B1_rep2)


title: wtCSCs2 (A2_rep1)


title: wtCSCs1 (A1_rep1)