title: Control group

city: Stanford

first: Xiangqian

last: Guo

address: 300 Pasteur Dr.

department: Department of Pathology

institute: Stanford University

description:
Experiment type: Illumina’s Digital Gene Expression Tag Profiling
TPM-Control
Illumina 1G Genome Analyzer

data_processing:
Low-quality reads and 5'/3' adaptor sequences were filtered out and discarded before mapping with SOAP.
After sequencing, the sequencing reads were aligned against mRNAs and genome sequences of Apis mellifera downloaded from Genbank and UCSC.
The expression level for each gene was measureed by summing all the reads which uniquely mapped to the same gene in the corresponding library.
The Audic and Claverie test was used to test the statistical significance of expression differences for each mRNA gene between the larvae treated by miR-184 (has the phenotype like worker larvae) and larvae treated by water (has the phenotype like queen larvae).
Genome_build: Amel_2.0
Supplementary_files_format_and_content: RNAiandControl.bee.txt is an expressional matrix with sample by column and gene by row

organism: Apis mellifera

source_name: queen larvae, treated by Water

growth_protocol: Eight experimental colonies of Apis mellifera ligustica ZND No.1 were used. Three colonies were used for reproduction of larvae, and the remaining five were prepared for rearing queens. The larvae were prepared for the experiment 2~8 hrs later after hatching by inserting an empty comb into the colony at 7:00, and then transferred the comb with newly-laid eggs to a super box at 13:00 on the same day. After 72 hrs, the hatched larvae were grafted into plastic cells for queen breeding, which were arranged in a line and adhered onto queen cell frames at 15:00. Thereafter the frames were transferred to the queen-breeding colonies. After 24 hrs, we brought the queen cell frames out, and marked the accepted queen cells "1, 2, 3" in sequence, each number denoting an experimental group of 20~25 queen cells. 26~32 hrs later after hatching, the treatment for the larvae was designated as following: Group 1 was as "untreated group", Group 2 was fed with 5µl DEPC-water for each larva as "control group", and Group 3 was fed with 5µl 100ng/µl microRNA as "miRNA-treated group".

extract_protocol:
Total RNAs of Group2 (treated with water) and Group3 (treated with miRNA) were extracted with Trizol (Invitrogen) for sequencing. Group1 (untreated group) was not sequenced for this study.
Sequence tag preparation was done with Illumina’s Digital Gene Expression Tag Profiling Kit according to the manufacturer’s instructions. Briefly, the enriched mRNAs were reverse-transcribed into first strand cDNA with biotin-labelled oligo(dT). The second cDNA strand was synthesized with DNA polymerase I and RNase H, and then was completely digested with restriction enzyme Nla III.  The digested products with 3’ poly(A) end were enriched by streptavidin, and then the 5’ end of digested products were ligated with GEX Adaptor 1 which contains the restriction enzyme digestive site of MmeI. The ligated products were digested with MmeI, and depleted of the fragments with poly(A). And then GEX Adaptor 2 was ligated to 3’end of above enriched fragments. Finally ligated products were amplified by PCR, purified (about 85bp) and sequenced by Illumina/solexa platform.

treatment_protocol: The bee samples were collected in 50ml tubes and immediately transferred to liquid nitrogen and thereafter stored at -80°C until total RNA extraction.

value: control

tag: tissue archive

value: Fresh Frozen

tag: Stage

value: larva

tag: extraction method

value: Trizol


title: miRNA-treated group

status: Public on Jan 06 2014

type: SRA

state: CA

country: USA

description:
Experiment type: Illumina’s Digital Gene Expression Tag Profiling
TPM-RNAi
Illumina 1G Genome Analyzer

library_source: transcriptomic

molecule: total RNA

source_name: queen larvae, treated by miR-184

tag: treatment


title: C02-PBL_Bisulfite-seq

city: Houston

first: Govindarajan

last: Kunde Ramamoorthy

state: Texas

address: 1100 Bates Street

institute: Baylor College of Medicine

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4 followed by adapter trimming by cutadapt program using default parameters. Adapter trimmed reads are mapped to hg19 genome build using BSMAP bisulfite-seq mapping software using default parameters and allowing 7 mismatches and methylation estimates of genome-wide CpG sites were obtained using in-house perl script.
Genome_build: hg19
Supplementary_files_format_and_content: text format with hg19 chromosome coordinates. Column1=chr;Column2=position;Column3=methylated reads;Column4=Total.no. of reads.

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral blood lymphocyte

extract_protocol:
Isolation of genomic DNA by proteinase-k digestion and phenol-chloroform extraction.
Illumina libraries were generated according to the manufacturer’s sample preparation protocol for genomic DNA.  Around 1ug of genomic DNA was fragmented to 200-500bp and end-repaired.  The 5’ ends of DNA fragments were phosphorylated and a single adenine base was added to 3’ end. The Y-shape illumina adaptors were ligated to the genomic DNA. The bisulfite treated DNA was amplified by using adaptor-specific primers and fragments of 200-500 bp were isolated by bead purification.  The quantity and size distribution of sequencing libraries were determined using the Pico Green fluorescence assay and the Agilent 2100 Bioanalyzer, respectively.  The DNA was sequenced on the Illumina HiSeq 2000 as 100-bp paired-end reads, following the manufacturer's protocols.

tag: tissue

value: Peripheral blood lymphocyte


title: C01-HF_Bisulfite-seq

source_name: Hair follicle

value: Hair follicle


title: C02-HF_Bisulfite-seq


title: TET3 ChIP-seq result

status: Public on Jan 04 2014

city: Duarte

first: Xiaochun

last: Yu

address: 1500 E. Duarte Rd, Rm 202, Lippman-Graff Bldg

department: Internal Medicine

institute: city of hope

description: Home-made antibody

data_processing:
The read quality of each sample was determined by FastQC software. After prefiltering the raw data by removing sequenced adapters and low quality reads, the tags were mapped to the human genome (assembly hg19) by Bowtie software. Parameter settings were as follows: -v, 3 (reported alignments with at most 3 mismatches), -5, 3 and -3, 3 (trim3 bases from 5’ and 3’ end to remove low-quality bases). Peak detection was performed using MACS software from Galaxy browser (www.galaxy.psu.edu). Parameters settings were as follows: tag size with 25bp, band width with 300bp, P-value cutoff for peak detection was set to 1e-05. The peaks obtained from ChIP sequencing were matched to the annotated reference genome (hg19) using Cisgenome 2.0
Genome_build: hg19

source_name: HEK 293T cells

growth_protocol: All procedures are to be done under sterile conditions in a laminar flow hood using sterile instruments and detergent-free glassware. Dulbecco’s modified Eagle’s media (DMEM) is used for 293T cell culture

extract_protocol:
293T cells were crosslinked with formaldehyde treatment. The chromatin were isolated from 1 × 108 cells and fragmented to 200 to 400 bp by sonication.
DNA were repaired to blunt ends by T4 DNA polymerase and phosphorylated with T4 polynucleotide kinase using the END-IT kit (Epicentre). A single “A” base was added to 3’ end with Klenow. Double-stranded adaptors were ligated to the fragments with DNA ligase. Ligation products between 200 and 600 bp were gel purified on 2% agarose to remove unligated adaptors and subjected to 20 PCR cycles. Following ligation of a pair of adaptors to the repaired ends, the fragments around 160 bp to 370 bp were isolated from agarose gel.

treatment_protocol: No special treatment

tag: antibody

tag: cell line

value: HEK 293T


title: worker jelly small RNA

description: Experiment type: small RNA sequencing

data_processing:
Low-quality reads and 5’/3’ adaptor sequences were filtered out and discarded before mapping the small RNA reads to the honeybee genome with SOAP. Only perfect matches were accepted and retained for the following analysis.
To identify known miRNAs, we aligned all the small RNA reads to mature miRNAs and miRNA hairpins in miRBase13.0 with blast using an E-value threshold of 0.01. As a miRNA gene could have different isoforms, the sum of all sequence reads corresponding to a miRNA gene was used as a digital measure of the gene expression level.
For other known non-coding RNAs and coding genes, we collected all the non-coding RNAs such as rRNAs, tRNAs, snoRNAs, and snRNAs from NCBI, and Rfam, and all coding genes from UCSC, and aligned the small RNA reads to these sequences with blast using an E-value threshold of 0.01.
All the remaining unannotated distinct small RNAs were tested for their miRNA-encoding potential with “MIREAP” (https://sourceforge.net/projects/mireap/). Given that a miRNA could have different isoforms, we took the predominant small RNA from “MIREAP” as the novel representative miRNA.
The Audic and Claverie test was used to compare small RNA expression differences between worker and royal jelly .
Genome_build: apiMel2
Supplementary_files_format_and_content: expressional matrix with sample by column and gene by row

source_name: worker jelly

growth_protocol: We prepared three healthy colonies of “Zhenongda No.1”- a royal jelly high-yielding breed of Apis mellifera ligustica at the Huajiachi campus, Zhejiang University. In each colony, worker jelly (WJ) and royal jelly (RJ) were collected at 4-days (73~90 hrs after hatch), 5-days (97~114 hrs after hatch) and 6-days (121~138 hrs after hatch).

extract_protocol:
Total RNAs were extracted from the jellies with Trizol (Invitrogen) as per the manual. For small RNA library construction, total RNA was size fractionated on a 15% Tris-Borate-EDTA (TBE) urea polyacrylamide gel and the 18-30nt fraction was excised. Small RNAs were eluted in 0.3 M NaCl by rotating the slice at room temperature for 4 hours. The eluted RNAs were precipitated and washed in ethanol, and resuspended in ultrapure water.
The gel-purified small RNAs were ligated to the 5’ RNA adapter with T4 RNA ligase, and the ligation products were gel fractionated and purified, before ligating to the 3’ RNA adapter. The final ligation products were purified and amplified by RT-PCR. The amplification products were gel fractionated and purified by electrophoresis on a 6% polyacrylamide gel in TBE buffer, and a gel slice corresponding to the amplified library was eluted in 0.3 M NaCl by rotating the mixture at room temperature for 4 hours. The purified PCR products were then precipitated using ethanol, and resuspended in nuclease-free water. The purified PCR products were sequenced on the Solexa sequencing platform.

treatment_protocol: The jelly samples were collected in 50ml tubes and immediately transferred to liquid nitrogen and thereafter stored at -80°C until total RNA extraction.

tag: sample collection

value: pool of day4, day5,day6


title: PGC7 ChIP-seq result

description: Home-made antibody


title: royal jelly small RNA

description: Experiment type: small RNA sequencing

source_name: royal jelly


title: C01-PBL_Bisulfite-seq


title: Control group

city: Qingdao

first: Zhen

last: Sun

state: Shandong

address: No.5 Donghai Middle Road, Qingdao

country: China

institute: Qingdao Municipal Hospital, Taishan Medical University

description: Sample B1

data_processing:
Illumina Hiseq2000 used for basecalling.
The 49nt sequence tags will go through the data cleaning analysis first, which includes getting rid of the low quality tags, 5' adaptor contaminants from the 50nt tags, to get credible clean tags.
The length distribution of the clean tags and common and specific sequences between samples will be summarised.
Map the small RNA tags to genome by SOAP to analyze their expression and distribution on the genome. The parameter is soap -v 0 -r 2 -M 0 -a clean.fa -D ref_genome.fa.index -o match_genome.soap.
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each Sample

organism: Rattus norvegicus

source_name: Rat hippocampus

extract_protocol:
Total RNA isolation was carried out using the mirVana™ miRNA Isolation Kit (Ambion, Austin, TX, US). The quality and quantity of RNA are assessed on the Agilent Bioanalyzer.
Biotinylated cRNA were prepared with the Ambion MessageAmp kit according to the instructions provided by the manufacturer.

treatment_protocol: Experimental rats were subjected to status epilepticus (induced by stimulating the lateral nucleus of the right amygdala for 20 min), whereas control rats were subjected to sham stimulation.

tag: strain

value: Wistar

tag: age

value: 5 months

value: Hippocampus


title: Experimental group

description: Sample A1

value: status epilepticus induced by amygdala stimulation


title: Patient #3 post RNA-seq

city: Amsterdam

first: Rene

last: Bernards

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description: processed data file = diffexp_3.txt

data_processing:
Sequence reads were mapped to hg19 using tophat version 2.0.6 with parameters --library-type fr-unstranded, --no-coverage-search -M --transcriptome-index, Ensembl GTF version 66
Readcounts were obtained by counting the number of reads per gene using HTSeq-count.
Differential expression was performed using the R package DEGseq. Upon differential expression analysis all values were added with 1. Genes that had no expression in both samples were removed.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files containing the output of the differential expression analysis. These files include the absolute gene expressions, the fold change and the p-value.

growth_protocol: RPMI

extract_protocol:
Trizol for cultured cells and High Pure RNA Paraffin Kit for FFPE samples
TruSeq RNA Sample Prep Kit

treatment_protocol: Vemurafenib/dabrafenib/trametinib

value: 43 yrs

tag: gender

value: female

tag: date of melanoma diagnosis

tag: type of primary melanoma

value: SSM

tag: site of primary melanoma

value: right buttock

tag: treatment (initiation date)

tag: date of biopsy i

tag: site of biopsy i

value: inguinal

tag: response at biopsy i

tag: time to progression i

tag: date of biopsy ii

tag: site of biopsy ii

value: peritoneal

tag: response at biopsy ii

value: PD

tag: time to progression ii

value: 10 months

tag: cell/tissue type

value: tumor biopsy (FFPE) after treatment


title: Patient #2 post RNA-seq

description: processed data file = diffexp_3.txt

value: 66 yrs

value: male

value: left thigh

value: right arm

value: thoracic skin

value: < 7 months


title: Patient #5 post RNA-seq

description: processed data file = diffexp_2.txt

value: 53 yrs

value: unknown

value: right axillary

value: 4 months


title: Patient #5 pre RNA-seq

description: processed data file = diffexp_2.txt

value: female

value: tumor biopsy (FFPE) before treatment


title: shSOX10-2 RNA-seq

description: processed data file = diffexp_1.txt

tag: cell line

value: Human malignant melanoma cells

tag: transfected with


title: After Extinction CI 3

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

description: Sample 6

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Tophat
Differential analysis was conducted with Cuffdiff
Genome_build: mm9
Supplementary_files_format_and_content: cell7298mmc1.xlsx, Table S1. Differentially Expressed Genes after Remote Fear Memory Extinction between CI-994- and VEH-Treated Animals, Related to Experimental Procedures

organism: Mus musculus

source_name: After Extinction_HDAC inhibitor

growth_protocol: Standard animal husbandry

extract_protocol:
Total RNA was extracted using Qiagen's Rneasy Mini Kit precisely as per the manufacturer's instructions, with the exception that the elution volume used was 40 microlitres.
Libraries were prepared according to Illumina's instructions

treatment_protocol: All animals underwent contextual fear conditioning. After recalling the memory (context exposure), animals were split into two groups, both of which underwent the spaced extinction training (as described in Gräff et al., 2014). The first group received daily injections of the HDAC inhibitor CI-994 ("CI") at 30mg/kg, the other group received daily injections of CI-994's vehicle ("VEH"). One hour after the last extinction session, animals were sacrificed by cervical dislocation followed by decapitation and their hippicampi dissected and snap-frozen in liquid nitrogen.

tag: strain

tag: age

tag: injected with

value: HDAC inhibitor CI-994 ('CI') at 30mg/kg

tag: tissue

value: brain

tag: tissue subtype

value: hippocampus


title: After Extinction CI 2

description: Sample 5


title: After Extinction CI 1

description: Sample 4


title: PLKO RNA-seq

description: processed data file = diffexp_1.txt

value: non-target shRNA control plasmid DNA


title: After Extinction VEH 2

description: Sample 2

source_name: After Extinction_vehicle

value: CI-994's vehicle ('VEH')


title: After Extinction VEH 1

description: Sample 1


title: Macrophages miR-155 k.o. +LDL

status: Public on Jan 03 2014

city: Munich

first: Anne

last: Dueck

state: Bavaria

address: Biedersteiner Str.29

department: Institute of Pharmacology and Toxicology

country: Germany

institute: TUM

description: small RNA sequencing data

data_processing:
Basecalls performed using CASAVA version 1.8.2
Adapter trimming was performed using custom scripts. Aggregation of identical sequences resulted in processed TXT-files
Reads were mapped to miRBase 19, Mus musculus using custom scripts
Supplementary_files_format_and_content: tab-delimited TXT-file; trimmed read sequence followed by a tab and the number of reads

source_name: Macrophages miR-155 k.o. +LDL

growth_protocol: Wildtype (C57BL/6) and mir-155-/- (To-Ha Thai et al., Science, 2007, B6.Cg-Mir155tm1.1Rsky/J, JAX) mice used in this study were bred and maintained in a conventional animal facility according to local regulations, and sacrificed at 8 to 12 weeks of age for use in experiments. DCs were generated as described previously (Lutz et al., J Immunol Methods, 1999). In brief, flushed bone marrow from femur and tibia was cultured in R10 culture medium (RPMI 1640 supplemented with 10 % fetal calf serum, L-Glutamine and Penicillin/Streptomycin, all from Life Sciences) supplemented with GM-CSF hybridoma supernatant.Macrophages were differentiated according to the DC culture but using M-CSF hybridoma supernatant instead of GM-CSF (Rutherford et al., J. Leukoc. 1992).

extract_protocol:
Cells were harvested, lysed in Trizol and total RNA was extracted according to the manufacturere's protocol.
Libraries were constructed according to Illumina's TruSeq cloning kit using the following adapters:  5′adapter 5′-GUUCAGAGUUCUACAGUCCGACGAUC-3′; 3′adapter Phospho-TGGAATTCTCGGGTGCCAAGG-Amino-C7. Barcoding was performed on the PCR level.

treatment_protocol: At day 8-9 of culture, DCs were matured by overnight stimulation with either 200 ng/ml LPS (Sigma-Aldrich), 5 µg/ml Pam3Cys (EMC Microcollections), 5 ng/ml TNFα (PeproTech), or 100 µg/ml Curdlan (Sigma-Aldrich), respectively.

tag: cell type

value: bone marrow derived macrophages


title: After Extinction VEH 3

description: Sample 3


title: Macrophages miR-155 k.o. +eLDL

description: small RNA sequencing data

source_name: Macrophages miR-155 k.o. +eLDL


title: Macrophages miR-155 k.o. +LPS

description: small RNA sequencing data

source_name: Macrophages miR-155 k.o. +LPS


title: Macrophages miR-155 k.o. +oxLDL

description: small RNA sequencing data

source_name: Macrophages miR-155 k.o. +oxLDL


title: Patient #2 pre RNA-seq

description: processed data file = diffexp_3.txt

value: 66 yrs

tag: gender

value: male

tag: date of melanoma diagnosis

tag: type of primary melanoma

value: SSM

tag: site of primary melanoma

value: left thigh

tag: treatment (initiation date)

tag: date of biopsy i

value: PD


title: Macrophages miR-155 k.o. unstimulated

description: small RNA sequencing data

source_name: Macrophages miR-155 k.o. unstimulated


title: Patient #3 pre RNA-seq

description: processed data file = diffexp_3.txt

value: 43 yrs

value: right buttock

tag: site of biopsy i

value: inguinal

tag: response at biopsy i

tag: time to progression i

tag: date of biopsy ii

tag: site of biopsy ii

value: peritoneal

tag: response at biopsy ii

value: 10 months


title: Macrophages wild type +oxLDL

description: small RNA sequencing data

source_name: Macrophages wild type +oxLDL

tag: strain


title: Macrophages wild type +eLDL

description: small RNA sequencing data

source_name: Macrophages wild type +eLDL


title: Macrophages wild type unstimulated

description: small RNA sequencing data

source_name: Macrophages wild type unstimulated


title: Dendritic cells miR-155 k.o. +eLDL

description: small RNA sequencing data

source_name: Dendritic cells miR-155 k.o. +eLDL

value: bone marrow derived dendritic cells


title: shSOX10-1 RNA-seq

description: processed data file = diffexp_1.txt

tag: cell line

tag: cell/tissue type

value: Human malignant melanoma cells

tag: transfected with


title: Macrophages wild type +LPS

description: small RNA sequencing data

source_name: Macrophages wild type +LPS

tag: cell type


title: Dendritic cells miR-155 k.o. +LPS

description: small RNA sequencing data

source_name: Dendritic cells miR-155 k.o. +LPS


title: Dendritic cells miR-155 k.o. +LDL

description: small RNA sequencing data

source_name: Dendritic cells miR-155 k.o. +LDL


title: Dendritic cells miR-155 k.o. immature

description: small RNA sequencing data

source_name: Dendritic cells miR-155 k.o. immature


title: Dendritic cells wild type +eLDL

description: small RNA sequencing data

source_name: Dendritic cells wild type +eLDL


title: Dendritic cells wild type immature

description: small RNA sequencing data

source_name: Dendritic cells wild type immature


title: Utf1_KH2_mES_endogenous_ChIP

first: Michael

middle: Johannes

last: Ziller

address: Kraepelinstrasse 2-10

department: Translational Psychiatry

institute: Max Planck Institute of Psychiatry

data_processing:
Base calling was performed with the standard Illumina pipeline 1.83
ChIP-Seq data was aligned to the mm9/NCBI37 reference genome using bwa version  0.5.7 (Li and Durbin, 2009) with default parameter settings. Subsequently, reads were filtered for duplicates and extended by 200bp.
Transcription factor ChIP-Seq data for Utf1 was first analyzed with macs version 1.4 (Zhang et al., 2008) to determine regions of enrichment using the following parameters: -g 1.87e9 --tsize=36 --pvalue=1e-5 --tsize=36 --pvalue=1e-5 --keep-dup=1 and using the KH2_mES_WCE as input control. Data analysis was conducted in R version 2.15.2 (http://www.r-project.org/) and python version 2.6.5 (http://python.org/) using custom scripts.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data reports the macs peak calling output on the two ChIP experiments.

source_name: KH2 mouse embryonic stem cells

growth_protocol: Mouse embryonic stem (ES) cells were cultured in DMEM media containing 15% FBS, 1% PEN/STREP, 1% Glutamine, 1% NEAA and 5x105U LIF. For ES cell maintenance dishes were coated with 0.2% gelantin and irradiated CF1 mouse embryonic fibroblasts (MEFs) were plated as confluent layer of feeder cells. ES cells were seeded in a density of 50000 cells/ 6-well and were passaged every 2-3 days. The 2i media was prepared according to the following protocol (Ying et al., 2008) and was supplemented with 5x105U LIF.

extract_protocol:
Cells were crosslinked in 1% formaldehyde for 5 minutes at room temperature, with constant agitation, followed by quenching with 125mM Glycine for 5 minutes at room temperature. Nuclei were isolated and chromatin was sheared using Branson sonifier until the majority of DNA was in the range of 200-700 base pairs. Chromatin was incubated with antibody overnight at 4°C, with constant agitation. Immunoprecipitation of antibody-protein complexes was completed using Protein A or Protein G Dynabeads (Invitrogen) for 2-3 hour at 4°C, with constant agitation. ChIPs were completed using previously reported methods (Mikkelsen et al., 2010). For the bioChIP Streptavidin-coupled Dynabeads (Invitrogen) were incubated with the chromatin for 2-3 hours at 4°C. The SDS concentration in the Low Salt Buffer was raised to 2% and reverse crosslinking was performed on beads overnight at 65°C.
Immunoprecipitated DNA was end repaired using the End-It DNA End-Repair Kit (Epicentre), extended using a Klenow fragment (3’-5’ exo)(NEB), and ligated to sequencing adapter oligos (Illumina). Each library was then PCR-amplified using PFU Ultra II Hotstart Master Mix (Agilent), and a size range of 300-600 was selected for sequencing on the Illumina HiSeq 2000.

treatment_protocol: ChIP was performed using the following antibodies at a final concentration of 1µg/1x106 cells: Utf1 (Abcam, ab24273).

value: mouse embryonic stem cells

tag: type

tag: culture condition

value: Standard Serum

tag: antibody

value: Utf1 (Abcam, ab24273)

tag: antibody tag

value: endogenous


title: Dendritic cells wild type +LPS

description: small RNA sequencing data

source_name: Dendritic cells wild type +LPS


title: Utf1_KH2_mES_Biotin_ChIP

value: biotin


title: Dendritic cells wild type +oxLDL

description: small RNA sequencing data

source_name: Dendritic cells wild type +oxLDL


title: Macrophages wild type +LDL

description: small RNA sequencing data

source_name: Macrophages wild type +LDL

value: bone marrow derived macrophages


title: Input_ChIPseq_ZHBTc4-TSC

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequence reads were aligned to the mouse reference genome (mm9) using Bowtie2 with default parameters.
Sequence reads overlapping with repetitive sequences were removed using BedTools and repeat region data from UCSC Genome Browse.
Peak Calling was performed using MACS2 with input DNA as a control and with a q-value cutoff of 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using MACS2. The signals were normalized by sequencing depth of million mapped reads with the --SPMR option.

source_name: ZHBTc4-TS cells

growth_protocol: TS cells were maintained in GMEM/10% FBS supplemented with 50 ng/ml human FGF4, 2 ug/ml heparin, 10 ng/ml human Activin A and 2 mM L-glutamine on MEF feeders.

extract_protocol:
Chromatin was sheared into fragments with an average size of 300-500 bp using a Covaris S220.
Sequencing libraries were prepared from ChIP DNA using KAPA Library Amplification Kit (KAPA Biosystem). Briefly, ChIP DNA was end-repaired, A-tailed, ligated to the adapters, size selected to 200-500 bp and amplified by PCR. Libraries were sequenced on the HiSeq 1500 (Illumina) as single-end 50-bp reads.


title: Sox2_ChIPseq_EGFP-TS3.5

description: On MEF feeders, with FGF4/heparin/Activin A

source_name: EGFP-TS3.5 TS cells

value: ICR

value: Sox2 raised by ourselves


title: Dendritic cells wild type +LDL

description: small RNA sequencing data

source_name: Dendritic cells wild type +LDL


title: Dendritic cells miR-155 k.o. +oxLDL

description: small RNA sequencing data

source_name: Dendritic cells miR-155 k.o. +oxLDL


title: KH2_mES_WCE

description: Whole cell extract control


title: Sox2_ChIPseq_ZHBTc4-TSC


title: Cdx2_ChIPseq_ZHBTc4-TSC

value: Cdx2 (CDX2-88, BioGenex)


title: Input_Ezh2_TT2_G9a-/-andGLP-/-_0

city: Paris

first: PONTIS

last: Julien

address: 35, rue Hélène BRION

country: France

institute: UMR7216 CNRS

description: Control

data_processing:
Illumina Casava1.7 software used for basecallin
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie v0.12.7 with parameters : -t -q -p 8 -S -n 2 -e 70 -l 50 --maxbts 125 -k 1 - m 1 --phred33-quals
Peaks were call with MACS v1.4 using paramters : --shiftsize 50 --nomodel
Genome_build: mm9
Supplementary_files_format_and_content: Proccessed data files are peaks location files of Ezh2 and G9a binding sites

source_name: TT2 G9a-/-andGLP-/-

growth_protocol: mESCs cells were maintained in DMEM containing 15% FBS, penicillin/streptomycin and sodium pyruvate (PAA), 0.1 mM β-mercaptoethanol (Gibco), Non-Essential Amino acids (PAA) and 1000 U/mL of LIF ESGRO (PAA).

extract_protocol:
Fixed cells were washed and harvested with PBS. Chromatin was prepared by two subsequent extraction steps (10 min at 4°C) with Buffer 1 (50 mM Hepes/KOH pH 7.5; 140 mM NaCl; 1 mM EDTA; 10% Glycerol; 0.5% NP-40; 0.25% Triton) and Buffer 2 (200 mM NaCl; 1mM EDTA; 0.5mM EGTA; 10 mM Tris pH 8). Nuclei were then pelleted by centrifugation, resuspended in Buffer 3 (50 mM Tris pH 8; 0.1% SDS; 1% NP-40; 0.1% Na-Deoxycholate; 10 mM EDTA; 150 mM NaCl) and subjected to sonication with Bioruptor Power-up (Diagenode) yealding genomic DNA fragments with a bulk size of 150-300 bp. Chromatin was precleared with Protein A/G ultralink beads (53133, Pierce) for 2h at 4°C and immunoprecipitation with the specific antibodies carried out overnight at 4°C. Immune complexes were recovered by adding pre-blocked protein A/G ultralink beads and incubated for 2 h at room temperature. Beads were washed twice with Low salt buffer (0.1% SDS; 1% Triton; 2 mM EDTA; 20 mM Tris pH 8; 150 mM NaCl), twice with High salt buffer (0.1% SDS; 1% Triton; 2 mM EDTA; 20 mM Tris pH 8; 500 mM NaCl), once with LiCl wash buffer (10 mM Tris pH 8.0; 1% Na- deoxycholate; 1% NP-40, 250 mM LiCl; 1 mM EDTA) and twice with TE + 50mM NaCl. Beads were eluted in TE + 1% SDS at 65°C and cross-link was reversed O/N at 65°C. The eluted material was phenol/chloroform-extracted and ethanol-precipitated
Five to fifteen nanogramms of ChIP DNA or un- enriched whole cell extract (Input) were prepared for sequencing on Illumina Hiseq 2000. We used library kit (Truseq DNA sample prep kit V2, Illumina) with modifications as follows: DNA fragments were repaired to blunt ends, purified with magnetic beads (Agencourt AMPure XP, beckman coulter) and a step of A tailing was performed before Illumina adapters ligation. Two steps of DNA purification on magnetic beads were carried out to eliminate unligated adaptors and then amplified with 15 PCR cycles. To remove unligated left adapters and un- sequenceable large DNA fragments, DNA libraries were selected on E-Gel (2% SizeSelect, Invitrogen) to obtain 280-330 pb DNA fragments (including 130 pb of adapters). Final library was quality checked by DNA high sensitivity chip (Agilent) and for positive target enrichment by qPCR. Quality-controlled samples were then quantified by qPCR and picogreen (Qubit® 2.0 Fluorometer, Invitrogen). Libraries were pooled thanks to various adaptors and qPCR relative measurements. Cluster amplification and following sequencing steps strictly followed Illumina standard protocol.

treatment_protocol: Formaldehyde (Sigma) was added to the culture medium to a final concentration of 1%. Cross- linking was allowed to proceed for 10 min at room temperature and stopped by addition of glycine at a final concentration of 0.125 M. Only for G9a ChIP we introduced another step of cross-linking before formaldehyde, by adding DSG (Di-Succinimidyl Glutarate; Santa Cruz) at a final concentration of 2 mM for 45 min at room temperature, as described in (Nowak et al., 2005).

value: mES

value: C57BL/ 6 female and a CBA male


title: RNA-seq_G9a_--_rep2

description: RNA from TT2 G9a-/-

data_processing:
Illumina Casava1.7 software used for basecallin
Reads were cleaned from adapter sequences and from sequences of low quality using an in-house program. Only sequences with a minimum length of 30 nucleotides were considered for further analysis. Bowtie  (version 0.12.7) was used to align the reads to the reference genome.
Statistical analyses were performed using R version 2.12.1 and BioConductor (www.bioconductor.org/) package. DEseq2 was used to determine significantly up- and down regulated genes. Genes marked as differentially regulated by both methods (P < 0.05) were kept for further analysis
P values obtained from the statistical test were then adjusted for multiple comparisons according to the Benjamini and Hochberg method implemented in the p.adjust function. The normalized library sizes were used to compute the normalized read counts.
genome build: mm9

extract_protocol:
Total RNA purification was performed according to the manufacturer's instructions of Qiagen kit
Poly-A Library from Illumina Kit

value: C57BL/6 female and CBA male


title: Input_TT2_0

description: Control


title: RNA-seq_TT2_rep3

description: RNA from TT2


title: Input_TT2_1

description: Control


title: RNA-seq_TT2_rep1

description: RNA from TT2


title: Ezh2_TT2_G9a-/-andGLP-/-_0_ChIP-seq

description: ChIP Ezh2 in KO of TT2 G9a-/-andGLP-/-

tag: chip antibody

value: anti-Ezh2 :BD Transduction Laboratories ref :612666


title: RNA-seq_G9a_--_rep3

description: RNA from TT2 G9a-/-


title: G9a_WT_TT2_G9a-/-andGLP-/-_1_ChIP-seq

description: ChIP G9a rescue in KO of TT2 G9a-/-andGLP-/-

source_name: TT2 KO for G9a and GLP rescued with G9a-wt

value: anti-G9a :Cell Signalling Technologies ref :3306S


title: RNA-seq_G9a_--_rep1

description: RNA from TT2 G9a-/-


title: Ezh2_TT2_1_ChIP-seq

description: ChIP Ezh2 in TT2


title: G9a_TT2_1_ChIP-seq

description: ChIP G9a in TT2


title: Input_ChIPseq_EGFP-TS3.5


title: Tfap2c_ChIPseq_ZHBTc4-TSC

value: Tfap2c (sc-8977, Santa Cruz)


title: RNA-seq_TT2_rep2

description: RNA from TT2


title: Ezh2_TT2_0_ChIP-seq

description: ChIP Ezh2 in TT2


title: Myc_FIbro2

city: Boston

first: Frederick

last: Alt

state: MA

address: 1 Blackfan Circle

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital

data_processing:
Library strategy: HTGTS
Standard basecalling formats for  Miseq reads
Paired end reads required trimming and stitching using ea-utilsv1.1.2 (http://code.google.com/p/ea-utils) followed by CD-HITv4.5 (Li & Godzik, Bioinformatics 2006) to remove 100% duplicates
Miseq reads are aligned using Blat (Kent, Genome Research 2002).  Reads containing artifacts or duplicate junctions were removed.
For alignment of reads from IgH  B and T cell libraries, the reference genome was modified to delete the Smu region (chr12:114661018-114664694) and include an I-SceI site target (sequence: TCGAGGTCGAAATAGGGATAACAGGGTAATAATTATTACCCTGTTATCCCTAAATCGACCCTAGTGGGGGCGCCAAGTTAGCTTGGCTGGACGTAAACTCCTCTTCAGACCTAATAACTTCGTATAGCATACATTATACGAAGTTATATTAAGGGTTATTGAATATGATCGGAATTCCTCGACATCGATGCATCGATGCATCGATGCATCGATGTCGAGT) at position chr12:114661018
For alignment of reads from c-myc B cell libraries, the reference genome was modified to  include an I-SceI site target (sequence: GATCGAATTCGTCGACCGCCGCTAATTCCGATCATATTCAATAACCCTTAATATAACTTCGTATAATGTATGCTATACGAAGTTATTAGGTCCCTCGAGGAATTCTGCAGATTAGGGATAACAGGGTAATAATTATTACCCTGTTATCCCTAATCCATCACACTGGCGGCCC) at position chr15:61914629
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text files containing filtered unique junctions and including the following information: sequence ID (Qname); blat score (score); beginning (Qstart) and end (Qend) nucleotide position within the read of alignment; orientation of junction (strand); chromosome (Tname) and position (Tstart and Tend) of alignment to the genome build; the entire read sequence (raw) including stitched paired end reads; and the RefGene feature the alignment is associated with (Genes; NA=no annotation)

source_name: SV40-transformed tail fibroblasts

extract_protocol:
Cells were lysed in the presence of proteinaseK, and genomic DNA was Ethanol-precipitated, then resuspended. Genomic DNA was sonicated to fragment size 200-500bp.
HTGTS libraries were constructed with the adapter-PCR method as described in Chiarle et al., Cell, 2011. Libraries were prepared for sequencing with MiSeq Illumina kit MS-102-2003, according to instructions.

tag: genotype

tag: activation protocol

value: SV40-transformed tail fibroblasts


title: Myc_Bcells37

source_name: activated splenic B cells

value: activated splenic B cells


title: Myc_FIbro1


title: IgH_Tcells23

source_name: activated splenic T cells

value: activated splenic T cells


title: Myc_FIbro3


title: Myc_Bcells14


title: IgH_Tcells21


title: IgH_Tcells19


title: Myc_Bcells36


title: IgH_Bcells23


title: IgH_Bcells21


title: Myc_FIbro4


title: IgH_Bcells19


title: CingGyr_68yo_Male_lower

city: Iowa City

first: Ryan

middle: L

last: Boudreau

state: IA

address: 500 Newton Rd

institute: University of Iowa

description: Isolated from lower band on autoradiogram, corresponding to Ago2-miRNA complexes.

data_processing:
HITS-CLIP, CLIP-seq
Basecalls performed using CASAVA version 1.8  (ASCII offset = 33)
Adapter trimming (removed first 5 nts and trimmed remaining sequence based on alignment to 3' linker sequence, GTTACGCTCGCCGTAGAGG, allowing up to 2 mistmates)
Retained reads of 17-25 nts in length (i.e. short reads)
Determined unique short read counts on a per sample basis
Genome_build: hg19
Supplementary_files_format_and_content: Unique short read counts per sample provided in tab-delimited text file

source_name: Cingulate gyrus (grey matter)

extract_protocol:
Phenol-chloroform extraction of Ago2-bound RNAs recovered from human brain tissues by  crosslinked immunoprecipiation with anti-Ago2 antibody.
Ago2 HITS-CLIP performed as previously described by Chi et al Nature. 2009 Jul 23;460(7254):479-86 using an anti-Ago2 polyclonal antibody and some additional modifications

tag: age (yrs)

tag: gender

value: male

tag: post-mortem delay (hours)

tag: tissue

value: Cingulate gyrus (grey matter)

tag: clip antibody

value: anti-Ago2 polyclonal antibody

tag: clip antibody info.

tag: molecule subtype

value: Ago2-bound RNA


title: CingGyr_66yo_Male(2)_lower


title: BA4_68yo_Male_lower

source_name: BA4 (motor cortex; grey matter)

value: motor cortex (grey matter)


title: CingGyr_44yo_Male_lower


title: BA4_44yo_Male_lower


title: BA4_59yo_Male_lower


title: CingGyr_66yo_Male(1)_lower


title: BA4_66yo_Male(2)_lower


title: CingGyr_59yo_Male_lower


title: BA4_68yo_Male_upper

description: Isolated from upper band on autoradiogram, corresponding to Ago2-miRNA-target mRNA complexes.

data_processing:
HITS-CLIP, CLIP-seq
Basecalls performed using CASAVA version 1.8  (ASCII offset = 33)
Adapter trimming (removed first 5 nts and trimmed remaining sequence based on alignment to 3' linker sequence, GTTACGCTCGCCGTAGAGG, allowing up to 2 mistmates)
Removed reads which align to mature human microRNAs annotated in miRBase (allowing up to 1 mismatch)
Aligned remaining trimmed reads to the human genome (hg19) using Bowtie (allowing up to 2 mismatches)
Peak-calling: 1) determine positional read coverage per sample using zero-truncated negative binomial model, 2) combine p-values across samples using Fisher's method, 3) calculate Bonferroni adjusted p-values.
Genome_build: hg19
Supplementary_files_format_and_content: BED file of significant Ago2 binding clusters (ie. peaks having Bonferroni corrected p-value < 0.05).


title: CingGyr_54yo_Male_lower


title: CingGyr_54yo_Male_upper


title: CingGyr_66yo_Male(2)_upper


title: AX2 5H, rep1rep2

city: Oxfors

first: James

last: Platt

address: Roosevelt Drive

country: United Kingdom

institute: University of Oxford

description:
mRNA
This Sample represents 2 replicates.

data_processing:
Basecalls performed using CASAVA version 1.7.
RNA-seq reads were aligned using Tophat version 1.3.0 and Bowtie version 0.12.7 to the chromosomes 1-6 of the AX4 Dictyostelium genome masking the duplicated region on chromosome 2 (nucleotides 3,015,984 to 3,768,555) and gene models from dictybase.org.
FPKM counts were calculated with HTseq and normalized and DEseq.
Genome_build: Ax4_May2009
Supplementary_files_format_and_content: Tab-delimited text files contain FPKM values for each sample.

organism: Dictyostelium discoideum

source_name: 5H cAMP pulsed, WT

growth_protocol: Cells were grown axenically in HL5 + glucose media (Formedium).

extract_protocol:
Total RNA was extracted with TRIzol. mRNA was enriched using manufacturer's protocol.
The sequencing library was constructed using the Illumina TruSeq low throughput protocol according to the manufacturer's protocol.

treatment_protocol: 5H pulsed cells were pulsed with cAMP every 6 min for 5 hours.

tag: strain/background

value: wild type

tag: development stage

value: 5H cAMP pulsed


title: chdB-null 5H, rep1rep2

source_name: 5H cAMP pulsed, chdB-null

value: chdB-null


title: chdA-null 5H, rep1rep2

source_name: 5H cAMP pulsed, chdA-null

value: chdA-null


title: CingGyr_59yo_Male_upper


title: BA4_66yo_Male(1)_lower


title: chdC-null 0H, rep1rep2

source_name: Growing, chdC-null

value: chdC-null

value: growing (0h)


title: CingGyr_66yo_Male(1)_upper


title: chdB-null 0H, rep1rep2

source_name: Growing, chdB-null


title: BA4_66yo_Male(1)_upper


title: CingGyr_68yo_Male_upper


title: chdA-null 0H, rep1rep2

source_name: Growing, chdA-null


title: CingGyr_44yo_Male_upper


title: BA4_44yo_Male_upper


title: BA4_59yo_Male_upper


title: AX2 0H, rep1rep2

source_name: Growing, WT


title: chdC-null 5H, rep1rep2

source_name: 5H cAMP pulsed, chdC-null


title: BA4_66yo_Male(2)_upper


title: zygote4 - ribozero

status: Public on Jan 02 2014

city: Aurora

first: Jianbin

last: Wang

state: CO

address: 12801 East 17th Ave

department: Biochemistry and Molecular Genetics

institute: University of Colorado Denver

description: ribozero RNA

data_processing:
Following removal of the adaptor sequences from the sequence reads, high quality reads with >= 36 nt in length were selected as previous (PMID: 21685128).
For each predicted Ascaris gene (mRNA), their expression level (RPKM) was calculated using bowtie (v.0.12.7)
The RPKM values for polysome fraction samples were further normalized based on the spike-in RNA reads (see PMID: 21685128)
Genome_build: Ascaris suum (Davis) germline genome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Ascaris suum

source_name: zygotes from region 4 of uterus

growth_protocol: Ascaris fertilized eggs were harvested from female uteri by treatment with 0.5 N NaOH, followed by extensive washing in water, and then stored at 4 °C with 5 volumes of PBS (pH 2.0). For embryonation, the fertilized eggs from final proximal region of the uterus (Zygote-4 = 0 hr embryos) were incubated at 30 °C in PBS (pH 2.0) with constant (100 rpm) shaking for the desired time. The outer shell/membranes were de-coated with 0.4 N KOH/1.4% sodium hypochlorite at 4 °C (zygotes from regions 1-4) or 30°C (developing embryos and larvae) for 180 or 90 minutes, respectively, prior to RNA preparation.

extract_protocol:
RNA from early embryos were extracted directly with Trizol (Invitrogen). Frozen testis, ovary, oocyte, larvae, intestine, muscle, male carcass and female carcass samples were first ground with a mortar and pestle in liquid nitrogen and then extracted with Trizol.
For each sample, 200 µg of total RNA was used for poly(A) selection and 200 ng of poly(A)+ RNA was used to make the cDNA libraries. RNA was treated for 75-150 sec with RNA fragmentation buffer (Ambion) at 70°C to generate RNA fragments 150-400 nt in length. First stand cDNA was prepared by random priming (3-6 µg random hexamers/1 µg of A+ RNA) and second stranded cDNA synthesis was carried out using a SuperScript® Double-Stranded cDNA Synthesis Kit (Invitrogen).  Solexa paired-end adaptors were added to the blunt cDNA as described by Illumina, cDNA fragments of 300-400 bp in length were gel purified, the fragments amplified using 17 PCR cycles, and sequencing reads were generated as described on the Illumina GAII, HiSeq2000, or MiSeq. For total and ribozero RNA (Ribo-Zero™ rRNA Removal Kits, Human/Mouse/Rat, Epicentre MRZH116), TotalScript RNA-seq kit (Epicentre, TSRNA1296) was used to generate the libraries.

tag: strain

value: North American wild population

tag: developmental stage

value: zygote


title: 64hr - total

source_name: 64hr (2-4-cell) embryos

value: embryo


title: oocyte with wall - ribozero

description: ribozero RNA

source_name: oocyte with wall

value: female germline


title: oocyte - ribozero

description: ribozero RNA

source_name: oocyte


title: A_blood_preLPS_technical_replicate

city: New York

first: Chenyi

last: Xue

state: NY

institute: Columbia University

description:
polyA RNA
Processed data file: lincRNA_A_blood_replicate_gene_exp.diff

data_processing:
Generate lincRNA expression by Cufflinks v1.3.0. For linc-RNAs, we obtained the locations of 4,662 pre-defined linc-RNAs based on RNA-seq data from 24 different human tissues and that also met the following criteria: at least one isoform of the linc-RNA was reconstructed in at least two different tissues or by two assemblers in the same tissue. For consistency across tissues, we included linc-RNAs that were expressed at either time point at FPKM >0. For each linc-RNA, we compared the estimated expression level pre- and post-LPS within the same tissue for a given individual using the cuffdiff option in Cufflinks version 1.3.0. Our analysis of differential expression (DE) involves only one sample in each group.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Standard Cufflink outputs, tab-delimited text files including FPKM values and FDR adjusted p-values.
Supplementary_files_format_and_content: lincRNA_A_adipose_exp.diff contains the expressed lincRNA for adipose tissue of subject A (900M reads). sample_1 = pre-LPS, sample_2 = post-LPS.
Supplementary_files_format_and_content: lincRNA_A_blood_exp.diff contains the expressed lincRNA for blood tissue of subject A (900M reads). sample_1 = pre-LPS, sample_2 = post-LPS.
Supplementary_files_format_and_content: lincRNA_A_adipose_replicate_exp.diff contains the expressed lincRNA for adipose tissue of technical replicate of subject A in much lower depth (67M reads). sample_1 = pre-LPS, sample_2 = post-LPS.
Supplementary_files_format_and_content: lincRNA_A_blood_replicate_exp.diff contains the expressed lincRNA for blood tissue of technical replicate of subject A in much lower depth (67M reads). sample_1 = pre-LPS, sample_2 = post-LPS.

source_name: blood, pre-LPS

extract_protocol: RNA samples were extracted using the RNeasy Lipid Tissue total RNA mini kit (Qiagen, Valencia, CA). Extracted RNA samples underwent quality control (QC) assessment using the Agilent Bioanalyzer (Agilent, Santa Clara, CA) and all RNA samples submitted for sequencing had an RNA Integrity Number (RIN) >6, with a minimum of 1µg input RNA. Poly-A library preparation and sequencing were performed at the Penn Genome Frontiers Institute's High-Throughput Sequencing Facility per standard protocols. Briefly, we generated first-strand cDNA using random hexamer-primed reverse transcription, followed by second-strand cDNA synthesis using RNase H and DNA polymerase, and ligation of sequencing adapters using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA). Fragments of ~350 bp were selected by gel electrophoresis, followed by 15 cycles of PCR amplification. The prepared libraries were then sequenced using Illumina's HiSeq 2000 with four lanes per sample which generated 2×101 bp paired-end reads generating ~1,000 million reads for adipose and blood samples. We also performed RNA-seq of replicate samples from subject A at lower sequencing depth (~50 million reads/sample) for comparison of findings at different RNA-seq depths.

treatment_protocol: Each clinical study was performed with approval of the University of Pennsylvania (U.Penn) Institutional Review Board after written informed consent was obtained from all research participants. The Genetics of Evoked-responses to Niacin and Endotoxemia (GENE) study is a single-center U.Penn-based National Institute of Health-sponsored experimental endotoxemia protocol (NIH.gov clinical trial NCT00953667). Briefly, the GENE study recruited healthy African-American or Caucasian individuals (N = 284, 33% African Americans, age 18-45) to an inpatient protocol that included a pre-LPS acclimatization phase, administration of intravenous LPS bolus (1ng/kg U.S. standard reference endotoxin), and a 30 hour post-LPS phase. Multiple clinical and biochemical variables were recorded. Whole blood RNA samples were collected in Qiagen PAX gene tubes at baseline, 1, 2, 4, 6, 12, and 24 hours post-LPS. Samples of gluteal subcutaneous fat tissue were obtained at baseline, 4, 12 and 24 hours following LPS as previously described and snap-frozen for subsequent RNA extraction. In this report, we focus initially on a self-reported European Ancestry (EA) individual (subject A) for deep RNA-seq. To enrich discovery of evoked transcriptome responses, subject A was chosen from those with above median inflammatory response to LPS. Selective findings in subject A were assessed for replication in additional GENE study participants (n=6) chosen also from those with above average inflammatory response. Based on previous mRNA profiling, we selected baseline and 2-hr blood samples, and baseline and 4-hr adipose samples for RNA-seq.

tag: disease state

value: healthy

value: blood

tag: treatment

tag: time point

value: baseline

tag: subject

value: individual A


title: A_blood_postLPS_technical_replicate

source_name: blood, post-LPS

value: LPS

value: 2 hr post-LPS


title: A_blood_postLPS

description:
polyA RNA
Processed data file: lincRNA_A_blood_gene_exp.diff


title: 1day

description: RNA from fractions of polysome gradient

source_name: 1day (1-cell) embryos

extract_protocol:
RNA from early embryos were extracted directly with Trizol (Invitrogen). Frozen testis, ovary, oocyte, larvae, intestine, muscle, male carcass and female carcass samples were first ground with a mortar and pestle in liquid nitrogen and then extracted with Trizol.
For each sample, 200 µg of total RNA was used for poly(A) selection and 200 ng of poly(A)+ RNA was used to make the cDNA libraries. RNA was treated for 75-150 sec with RNA fragmentation buffer (Ambion) at 70°C to generate RNA fragments 150-400 nt in length. First stand cDNA was prepared by random priming (3-6 µg random hexamers/1 µg of A+ RNA) and second stranded cDNA synthesis was carried out using a SuperScript® Double-Stranded cDNA Synthesis Kit (Invitrogen).  Solexa paired-end adaptors were added to the blunt cDNA as described by Illumina, cDNA fragments of 300-400 bp in length were gel purified, the fragments amplified using 17 PCR cycles, and sequencing reads were generated as described on the Illumina GAII, HiSeq2000, or MiSeq.


title: 7day

description: RNA from fractions of polysome gradient

source_name: 7day (~256-cell) embryos


title: 5day

description: RNA from fractions of polysome gradient

source_name: 5day (32-64-cell) embryos


title: A_adipose_postLPS

description:
polyA RNA
Processed data file: lincRNA_A_adipose_gene_exp.diff

source_name: adipose, post-LPS

value: adipose

value: 4 hr post-LPS


title: L2

source_name: L2 larvae

value: larvae


title: 3day

description: RNA from fractions of polysome gradient

source_name: 3day (4-8-cell) embryos


title: A_blood_preLPS


title: 0day

description: RNA from fractions of polysome gradient


title: A_adipose_preLPS

source_name: adipose, pre-LPS


title: 64hr - ribozero

description: ribozero RNA


title: zygote4 - total


title: MCF7-RON/MSP-shMBD4_3b

city: Salt Lake City

first: Stephanie

last: Cunha

state: Utah

address: 2000 Circle of Hope

department: Oncological Science

institute: Huntsman Cancer Institute, University of Utah

description:
breast cancer cell line
3

data_processing:
SAM alignments were generated from Illumina Fastq files aligned to the human hg19 genome using Novocraft’s novoalign aligner (http://www.novocraft.com) in bisulfite mode with the following parameters: -r Random –t 240 –h 120 –b 2 –p bisulfite.
An in silico chrLambda sequence was used to align the fully methylated lambda sequence that was spiked into the samples in order to measure the bisulfite conversion efficiency and displayed very low non-conversion/ sequencing error rates of 0.00348 (MCF7) and 0.00245 (MCF7-RON/MSP). These rates were used for scoring individual cytosines for significant methylation with a binomial test. A chrPhiX sequence was added to estimate the read quality and a chrAdapter sequence containing all permutations of the adapter sequences was used to remove these artifacts from the data.
Differentially-methylated regions (DMRs) were determined by comparing methylation levels in each cell line using a sliding window of 150 base pairs.  Overlapping windows passing two thresholds, a Benjamini–Hochberg corrected a chi-square test of independence FDR of < 0.01, and fold difference in methylation of > 2, were merged into continuous DMRs and assigned the best window scores (See http://useq.sourceforge.net/ usageBisSeq.html for details). Next, DMRs were used to score mean fraction methylation in every sample.
NovoalignBisulfiteParser(http://useq.sourceforge.net/cmdLnMenus.html#NovoalignBisulfiteParser) was used to parse the text based novoalignments into four binary “PointData” sets containing the number of observed converted Cs (Ts - non methylCs) and non-converted Cs (methylCs) at each reference C sequenced in the genome for both the plus and minus strands.
The PointData was then parsed into mCG context using the ParsePointDataContexts (http://useq.sourceforge.net/cmdLnMenus.html#ParsePointDataContexts) application.
Mean fraction methylation at each DMR was scored using the ScoreMethylatedRegions(http://useq.sourceforge.net/cmdLnMenus.html#ScoreMethylatedRegions) application. Only regions with a minimum of 5Cs and a minimum read coverage of 5 in all samples were used in further analysis.
Differentially methylated regions were identified using the BisSeq (http://useq.sourceforge.net/cmdLnMenus.html#BisSeq) application. Overlapping 150bp windows that met or exceeded an FDR of 0.01 and a 2-fold difference were merged and included in a spread sheet output of differentially methylated regions. This list was further filtered in excel for including regions with sample having > 0.25 fraction methylation difference
Genome_build: hg19
Supplementary_files_format_and_content: bar file converted and non-converted

source_name: breast cancer cell line

growth_protocol: MCF-7 cells were cultured in Dulbecco's modified Eagle's medium (DME/F-12, Thermo Scientific) supplemented with 1% penicillin/streptomycin (Thermo Scientific), 10 µg/ml insulin (Gibco), and 10% heat inactivated fetal bovine serum (Thermo Scientific) at 37°C in 5% CO2. T47D cells were cultured in the same conditions in RPMI1640 (RPMI1640, Thermo Scientific) supplemented with 1% penicillin/streptomycin (Thermo Scientific) and 10% heat inactivated fetal bovine serum. RON and MSP were stably expressed in MCF7 cells by retroviral infection (Liu et al., 2011). MCF7-RON/MSP cells were maintained in MCF7 medium supplemented with 0.2 µg/ml puromycin and 50 µg/ml hygromycin. MCF7 and T47D cell lines were infected with lentiviral constructs that direct the synthesis of shRNA (based on PLKO.1 but with a neo resistant cassette substituted for the puromycin resistant cassette) and selected by the addition of 1 mg/mL G418 48 hours later.

extract_protocol:
Genomic DNA for  bisulfite modification was isolated using the DNeasy Blood Kit (Qiagen).
Library construction was performed using the Illumina TruSeq.
DNA Sample Preparation Kit (cat# FC-121-2001, FC-121-2002) using the following methods:  Genomic DNA (approximately  50 ng to 2 µg) was sheared to an average size range of 275 bp in a volume of 52.5 µl using a Covaris S2 Focused-ultrasonicator with the following settings: Intensity 5.0; Duty cycle 10%; 25 cycles per Burst 200; Treatment Time 60 seconds.  Sheared DNA was converted to blunt-ended fragments with 5'-phosphates and 3'-hydroxyl groups using a combination of enzymes that perform fill-in reactions and exhibit exonuclease activity.  Size selection of the blunt-ended DNA (200-450 bp average) was accomplished using bead-based methodologies.  An A-base was added to the blunt ends as a means to prepare the fragments for adapter ligation and block concatamer formation during the ligation step.  Adapters containing a T-base overhang were ligated to the A-tailed DNA fragments. Adapter-ligated molecules were purified by bead based methodologies and were bisulfite converted using the Qiagen EpiTect Bisulfite Kit (cat# 59104).  Bisulfite treated DNA was PCR amplified for 12 cycles using Agilent Pfu Turbo Cx (Agilent cat# 600410) to enrich those fragments that have adapter molecules ligated to both ends.  The concentration of the amplified library was measured using the Invitrogen Qubit dsDNA HS Assay (Q32851) and an aliquot of the library was resolved on an Agilent 2200 Tape Station using a D1K (cat# 5067-5361 and 5067-5362) or a High Sensitivity D1K (cat# 5067-5363 and 5067-5364) assay to define the size range.  Libraries were adjusted to a concentration of approximately 10 nM and quantitative PCR was performed using the KapaBiosystems Kapa Library Quant Kit (cat# KK4824) to quantify adapter-ligated library molecules.  The concentration was further adjusted following qPCR to prepare the library for Illumina sequence analysis

tag: cell type

value: breast cancer cell line

tag: passages

tag: cell line

value: RON and MSP and shMBD4


title: MCF7-RON/MSP-shMBD4_2b

description:
breast cancer cell line
3


title: MCF7-RON/MSP-shMBD4_3a

description:
breast cancer cell line
3


title: MCF7-RON/MSP_3b

description:
breast cancer cell line
2

value: RON and MSP


title: MCF7-RON/MSP-shMBD4_2a

description:
breast cancer cell line
3


title: oocyte - total


title: MCF7-RON/MSP-shMBD4_1b

description:
breast cancer cell line
3


title: oocyte with wall - total


title: MCF7-RON/MSP_3a

description:
breast cancer cell line
2


title: A_adipose_preLPS_technical_replicate

description:
polyA RNA
Processed data file: lincRNA_A_adipose_replicate_gene_exp.diff


title: A_adipose_postLPS_technical_replicate


title: MCF7-RON/MSP-shMBD4_1a

description:
breast cancer cell line
3


title: MCF7-RON/MSP_1b

description:
breast cancer cell line
2


title: MCF7-RON/MSP_1a

description:
breast cancer cell line
2


title: mix (paired-end)

source_name: pooled sample from testis, ovary, zygotes, embryos, larvae, intestine, muscle and whole worm

value: mixed stages


title: mix

value: North American wild population


title: MCF7_3a

description:
breast cancer cell line
1


title: MCF7_2b

description:
breast cancer cell line
1


title: MCF7_3b

description:
breast cancer cell line
1


title: MCF7_2a

description:
breast cancer cell line
1


title: MCF7_1a

description:
breast cancer cell line
1


title: L1

source_name: L1 larvae


title: MCF7-RON/MSP_2a

description:
breast cancer cell line
2


title: MCF7-RON/MSP-shMBD4_2

description:
breast cancer cell line
comp3

data_processing:
Alignments were generated from Illumina Fastq files to the hg19 human genome with all known and theorical splice junctions using Novocraft’s novoalign aligner
NovoalignParser (http://useq.sourceforge.net/cmdLnMenus.html#NovoalignParser) application was used to parse the alignment files into binary point data. DefineRegionScanSeqs (http://useq.sourceforge.net/cmdLnMenus.html#DefinedRegionScanSeqs) application was used to define differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: DefineRegionScanSeqs (http://useq.sourceforge.net/cmdLnMenus.html#DefinedRegionScanSeqs) application was used to define differentially expressed genes.

extract_protocol:
Total RNA for gene expression analysis was isolated with the RNeasy Kit (Qiagen) and tested for integrity on RNA 6000 NanoChips using an Agilent 2100 Bioanalyzer.
Illumina TruSeq Stranded RNA Sample Prep with RiboZero treatment


title: 116hr (32-64-cell) embryos

source_name: 116hr (32-64-cell) embryos


title: MCF7-RON/MSP_1

description:
breast cancer cell line
comp1


title: MCF7_3

description:
breast cancer cell line
comp1


title: MCF7-RON/MSP_2

description:
breast cancer cell line
comp1


title: 96hr (10-26-cell) embryos

source_name: 96hr (10-26-cell) embryos


title: MCF7-RON/MSP_2b

description:
breast cancer cell line
2


title: MCF7_1

description:
breast cancer cell line
comp1


title: MCF7-RON/MSP-shMBD4_1

description:
breast cancer cell line
comp3


title: 64hr (2-4-cell) embryos

source_name: 64hr (2-4-cell) embryos


title: MCF7-RON/MSP_3

description:
breast cancer cell line
comp1


title: zygote4

source_name: zygotes from region 4 of uterus

value: zygote


title: 24hr (1-cell) embryos

source_name: 24hr (1-cell) embryos

value: embryo


title: MCF7_2

description:
breast cancer cell line
comp1


title: zygote3

source_name: zygotes from region 3 of uterus


title: MCF7_1b

description:
breast cancer cell line
1


title: SNU216_Input

city: Daejeon

first: Byungho

last: Lim

address: Medical Genomics Research Center, KRIBB, 125 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

data_processing:
Basecalls performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 version 2.0.0 with default options.
Peaks were called using MACS ver 1.4.2 with BAM format input and default options (--pvalue=1e-5 --mfold=10,30 --format=BAM --gsize=hs --tsize=70).
Genome_build: hg19
Supplementary_files_format_and_content: BED files containing MACS peak-calling by comparing TEAD4 ChIP to Input samples

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: gastric cancer cell

tag: chip antibody


title: zygote1

source_name: zygotes from region 1 of uterus


title: MKN28_Input


title: SNU216_TEAD4 ChIP


title: MCF7-RON/MSP-shMBD4_3

description:
breast cancer cell line
comp3


title: oocyte with wall

source_name: oocyte with wall

value: female germline


title: ALHF2 mRNA

city: Auburn

first: Nannan

last: Liu

state: AL

address: 301 Funchess Hall

department: Entomology

institute: Auburn University

description: Highly insecticide-resistant strain obtained in Alabama

data_processing:
Differential expression: The reference transcriptome was generated de novo using Trinity. Contigs were then compressed using CAP3 and the resulting contigs and singletons files were then annotated for coding regions using the Fly model in Augustus. Gene annotation was then conducted using HMM Scan against the PFam database (version 26.0) and Blastx homology to Drosophila melanogaster (version r5.44) using BLOSUM64 and an e-value cut off of 10-10. The coding trimmed sequences from Augustus were then used as the mapping reference for the individual FASTQ files from each strain. trace reads were mapped using RSEM to generate FPKM estimates. Gene expression levels were compared to the ALHF strain using EdgeR.
Genome_build: NCBI_TSA#KA644422-KA650580
Supplementary_files_format_and_content: FPKM expression comparison

organism: Musca domestica

source_name: Whole insect- adult Musca domestica; strain ALHF

growth_protocol: M. domestica were reared at 27C (12:12 L:D) on a diet of Calf manna, Brewer's yeast, powdered skim milk, wheat bran, and sugar.

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the mRNA Seq 8-sample kit by the Hudson Alpha Institute of Biotechnology, Huntsville, AL. Libraries were then sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.

value: ALHF


title: CS mRNA

description: Insecticide susceptible strain for additional comparison

source_name: Whole insect- adult Musca domestica; strain CS

value: CS


title: aabys mRNA

description: Insecticide susceptible strain with five distinct morphological recessive markers- one on each of the five autosomes

source_name: Whole insect- adult Musca domestica; strain aabys

value: aabys


title: WT MEFs -1

status: Public on Jan 01 2014

first: Brandi

middle: Nicole

last: Davis-Dusenbery

address: 7 Divinity Ave

department: SCRB

institute: Harvard University

data_processing:
Basecalls performed using CASAVA
Reads were aligned to the genome using the split read aligner TopHat (v2.0.7) and Bowtie2 (v2.0.5) using default parameters. Reference files of the murine genome build mm10, as well as ensembl transcript annotations, were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn, March 2013 build).
Differential expression was performed using Cuffdiff (v2.1.1) using default parameters and flags  —min-reps-for-js-test 2, GTF from iGenomes was supplied for transcript assembly.
Genome_build: mm10 : ensembl compatible from igenomes (NCBIM37) March 2013 update
Supplementary_files_format_and_content: The FPKM values calculated by cuffdiff are reported as tab-delimited files for each sample (FPKM.txt).  FPKMs calculated across replicates as well as confidence intervals are provided in the FPKM_matrix.txt file.

source_name: embyronic fibroblasts

growth_protocol: Parental Nanog-/- mESCs were obtained from I. Chambers and were cultured on feeders in 2i + LIF conditions as previously described(Chambers et al., 2007;  Silva et al., 2008).  To obtain Nanog-/- MEFs, Nanog-/- mESCs were injected into blastocyst stage embryos.  At E12.5 MEFs were dissected out and sorted for constitutive GFP expression, indicating Nanog-/- genotype (Chambers et al., 2007).   For reprogramming, MEFs were transduced with retroviruses carrying murine Oct4, Sox2, Klf4, +/- c-Myc exactly as described by Ichida et al (Ichida et al., 2009).   On day 20 post-transduction with reprogramming transgenes, iPS colonies were picked and passaged onto feeders and cultured in 2i+LIF conditions with passaging every 5 days (Silva et al., 2008).  MEFs were grown in 10% FBS.

extract_protocol:
RNA was harvested using Trizol (Invitrogen) according to the manufacturers’ directions. RNA quality was determined using BioAnalyzer (Aligent). RNA integrity numbers above 7.5 were deemed sufficiently high quality to proceed with library preparation
RNA sequencing libraries were generated from ~250 ng total RNA using the illumina TruSeq RNA kit v2, according to the manufacturers' directions. Libraries were sequenced at the Broad Institute genomics platform on a HiSeq 2500 or at the Harvard Northwest labs sequencing facility on a HiSeq 2000.

tag: genotype

value: WT

value: MEF

tag: passage


title: WT iPSC -3

source_name: induced pluripotent stem cell

value: iPSC


title: WT ESC -3

source_name: embryonic stem cells

value: ESC


title: WT ESC -4


title: WT iPSC -2


title: Cxcr5+_H3K27me3

city: Bethesda

first: Lai

last: Wei

state: MD

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

description: sorted Cxcr5 (GFP) positive cells

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm9 genome assembly using CASAVA
peaks were called using SICER with the default setting
Genome_build: mm9
Supplementary_files_format_and_content: bed format with peaks

source_name: CD4+ T cells

growth_protocol: Bcl6-RFP reporter mice were subcutaneously immunized with KLH emulsified in CFA. Seven days later, activated CD44+ CD4+ T cell from draining LNs were gated and sorted for CXCR5hiBcl6-RFPhi cells.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA or protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions. Sorted T cells were fixed by 1% paraformaldehyde, and followed with digestion with Mnase cocktail (Active motif). Chromatin from 5x106 cells was used for each ChIP experiment. Antibodies against H3K4me3 (Cat# 07-473, Millipore), H3K27me3 (Cat# 07-449, Millipore), and Ascl2 mAb (clone, 7E2, Millipore) were used. The pull-down DNA fragments were blunt-ended ligated with Solexa adaptors, and amplified for sequencing. The DNA fragments were sequenced with Illumina 1G Analyzer at the Institute for System Biology.

value: CD4+ T cells

tag: genotype/variation

value: Cxcr5 positive


title: zygote2

source_name: zygotes from region 2 of uterus


title: ramA overexpresser

city: Belfast

first: Amy Jayne

last: McKnight

address: Lisburn Road

institute: Queen's University of Belfast

data_processing:
Alignment: Sequence reads were obtained and mapped to the Klebsiella pneumoniae genome sequences using the MAQ (maq.sourceforge.net/maq-man.shtml) to do the alignments, with a score cut of 30.  Their output was a read start position (all on the + strand) and number of tags starting at that position. The alignment locations were then taken, and put into the "bins" under coding or intergenic regions based on the alignment start position, hence bin sizes were biological, rather than some arbitrary size.
ajmcknight_annotated_alignment.txt, NC_009648, MGH 78578 chromosome

organism: Klebsiella pneumoniae

growth_protocol: LB Broth to mid log phase prior to extraction

extract_protocol: RNA treated as described above was subjected to cDNA synthesis .  Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Adapter ligated cDNA was then run on a 2% agarose gel and bands at 100 bp intervals spanning 200-600bp were excised and purified using the Qiagen gel extraction kit (Qiagen, Germany). Each size fragment was amplified individually using Illumina primers, and then quantified and checked by gel electrophoresis for correct product size. These samples were ultimately pooled and sequence using Illumina Genome Analyser GA2x.

treatment_protocol: RNA extraction was perfromed using the Trizol Reagent (Invitrogen), total RNA was DNAse 1 digested and the ribosomal RNA depletion using the mRNA-only kit (Epicentre)

value: TS68 delta ramR

tag: parental isolate

value: ECL 8


title: Cxcr5+_H3K4me3

description: sorted Cxcr5 (GFP) positive cells


title: Ascl2

description: Ascl2 transfected

growth_protocol: Naïve CD4+CD25-CD44lowCD62Lhigh T cells from C57BL6 mice were FACS-sorted and activated with plate-bound anti-CD3e (clone, 2C11) and anti-CD28 (clone, 37.51) under neutral conditions. 24 hours after activation, cells were infected by retroviruses Ascl2 vector (Ascl2-RV-GFP). One days after infection, GFP cells were FACS sorted.

value: Ascl2 vector transfected

value: Ascl2 mAb (clone, 7E2, Millipore, lot# 2066321)


title: Cxcr5-_H3K4me3

description: sorted Cxcr5 (GFP) negative cells

growth_protocol: Bcl6-RFP reporter mice were subcutaneously immunized with KLH emulsified in CFA. Seven days later, activated CD44+ CD4+ T cell from draining LNs were gated and sorted CXCR5-Bcl6-RFP- cells.

value: Cxcr5 negative


title: 01_VZ1

city: Tokyo

first: Itsuki

last: Ajioka

address: 1-5-45 Yushima, Bunkyo-ku

department: Center for Brain Integration Research

institute: Tokyo Medical and Dental University

description:
manually dissected E16 V/SVZ tissue
The ventricular zone (VZ) is enriched in neuronal progenitor, while the cortical plate (CP) is enriched in differentiating neurons.

data_processing:
Basecalls performed using CASAVA version 1.8
Sequence reads were mapped on the mouse genome assembly (NCBI37/mm9) with Bowtie mapping software
Enriched area was detected with Model-based analysis of ChIP-Seq (MACS)
gsize=1870000000 and mfold=10,30 were used for MACS parameter
Genome_build: mm9
Supplementary_files_format_and_content: xls file contains the following information: Region_name, Position, Length, Fold enrichment, Gene ID, and distance from gene body
"VZ-cont" was analyzed from the peak of the VZ subtracted from that of the control DNA (non IP with MBD) of the VZ, while "VZ-CP" was analyzed from the peak of the VZ subtracted from that of CP. Biologically, "VZ-cont" means the methylated region of neuronal progenitor, while "VZ-CP" means the region methylated during neuronal differentiation.

source_name: manually dissected E16 V/SVZ tissue

extract_protocol: Methylated DNA was purified with Methylated DNA Enrichment Kit (Clontech) and was subjected to library construction by ChIP-Seq Sample Prep Kit (Illumina) and Multiplexing Sample Preparation Oligonucleotide Kit (Illumina)

value: ICR

tag: tissue

value: V/SVZ


title: non-ramA expresser

value: TS67 delta ramA


title: RV

description: empty vector transfected

growth_protocol: Naïve CD4+CD25-CD44lowCD62Lhigh T cells from C57BL6 mice were FACS-sorted and activated with plate-bound anti-CD3e (clone, 2C11) and anti-CD28 (clone, 37.51) under neutral conditions. 24 hours after activation, cells were infected by retroviruses control empty vector (Empty-RV-GFP). One days after infection, GFP cells were FACS sorted.

value: empty vector transfected


title: Cxcr5-_H3K27me3

description: sorted Cxcr5 (GFP) negative cells

growth_protocol: Bcl6-RFP reporter mice were subcutaneously immunized with KLH emulsified in CFA. Seven days later, activated CD44+ CD4+ T cell from draining LNs were gated and sorted for CXCR5-Bcl6-RFP- cells.


title: ALHF mRNA

value: ALHF


title: 02_CP1

description:
manually dissected E16 CP tissue
The ventricular zone (VZ) is enriched in neuronal progenitor, while the cortical plate (CP) is enriched in differentiating neurons.

data_processing:
Basecalls performed using CASAVA version 1.8
Sequence reads were mapped on the mouse genome assembly (NCBI37/mm9) with Bowtie mapping software
Enriched area was detected with Model-based analysis of ChIP-Seq (MACS)
gsize=1870000000 and mfold=10,30 were used for MACS parameter
Genome_build: mm9
Supplementary_files_format_and_content: xls file contains the following information: Region_name, Position, Length, Fold enrichment, Gene ID, and distance from gene body
"CP-cont" was analyzed from the peak of the CP subtracted from that of the control DNA (non IP with MBD) of the CP, while "CP-VZ" was analyzed from the peak of the CP subtracted from that of VZ. Biologically, "CP-cont" means the methylated region of differentiating neurons, while "CP-VZ" means the region methylated during neuronal differentiation.

source_name: manually dissected E16 CP tissue

value: CP


title: DRag Total RNA-seq

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

institute: TAGC INSERM U1090

description: total RNA (ribosomal depleted)

data_processing:
Sequencing read were trimmed using sickle (-se  -l  25 -t sanger -q 10). Selected reads were then aligned to mm9 genome using TopHat (version 2.0.4) and multireads were discarded. Gene annotations (gtf files) and index files were obtained from TopHat website (Illumina iGenome). Cufflinks was subsequently used to discover new isoforms and transcripts (using known transcript list as guide) and perform assembly.
Genome_build: Mouse samples : MM9
Supplementary_files_format_and_content: bigwig files (bw) using BEDTtools (bedGraphToBigWig v.4)

source_name: DRag2 thymocytes

extract_protocol: For strand-specific sequencing of RNA, total RNA was extracted using TRIzol (Invitrogen, USA) and DNA was digested. Poly(A) RNA was purified from 8µg of total RNA using the Illumina poly(A) purification kit. Poly(A) purification was verified using RNA Pico chips on a 2100 Bioanalyzer. The RNA sample was fragmented to ~150bp using RNase H (Ambion, USA) at 37°C for 10 minutes. The size distribution of fragmented RNA was again validated using RNA Pico chips on a 2100 Bioanalyzer. Library preparation using the Illumina small RNA kit was essentially carried out as per manufacturer's instructions. In brief, 5’ adapters were ligated and the reaction was separated on a 10% polyacrylamide gel for 2 hours. All RNA above 30bp was recovered by gel cutting, eluted using 300mM NaCl at room temperature under rotation and purified using the RNeasy kit (Qiagen, Germany) with the addition of 1.5 volumes of Ethanol to ensure recovery of all RNAs. These steps were repeated after the ligation of 3’ adapters. The library was reverse-transcribed, PCR amplified, size selected (corresponding to ~20-100 bp without adapters) from an agarose gel and sequenced according to the manufacturer's small RNA kit instructions, except that 36bp tags were sequenced instead of 75bp.

value: Thymus

value: Rag2 KO

value: CD4-, CD8- double negative (DN) Thymocytes


title: H3K79me2

data_processing:
All DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the mouse 2007 (mm9, build 37)  genome. As pre-filtering steps, only non-ambiguously mapped tags were used for further processing. A threshold based on the number of sequenced tags (Nseq) has been set up as Nseq/7,000,000. All regions with a number of repeated tags (with identical sequences/coordinates) above this threshold were filtered out to remove possible sequencing and/or alignment artefacts. Remaining tags were processed using a custom R pipeline, employing the ShortRead library. Briefly, inserts size has been estimated in-silico and tags were elongated before piling and bining steps.
Genome_build: Mouse samples : MM9
Supplementary_files_format_and_content: wig file using custom pipeline

source_name: DP thymocytes

extract_protocol: Chromatin Preparation (ChIP):  EDTA-free protease inhibitors (Roche, France) were added to all washing buffers to a final  concentration of 1x together with 0.2mM PMSF and 1μg/ml pepstatin. Aliquots of 5x107 cells  were lysed after resuspension in 2.5ml LB1 (50mM Hepes pH 7.5, 140mM NaCl, 1mM EDTA  pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) for 20 minutes on a rotating wheel at  4°C. Chromatin was collected by centrifugation for 5 minutes at 4°C and 1.350g in a tabletop  centrifuge, and washed in 2.5ml LB2 (200mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8,  10mM Tris pH 8) on a rotating wheel for 10 minutes at 4°C. Chromatin was collected,  resuspended in 1.5ml of LB3 (1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8, 100mM  NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using a Misonix 4000  (Misonix Inc, USA) sonicator for 10 cycles in the case of thymocytes, 12 cycles for ES cells and  14 cycles in the case of Raji cells (30 seconds on, 30 seconds off, amplitude 40) with the tubes  submerged in ice-cold sonication solution (500mM NaCl, 20% ethanol). After the addition of  Triton X-100 to a final concentration of 1%, particulates were collected through centrifugation at  20.000g and 4°C for 20 minutes. For batch processing, supernatants were combined, mixed  thoroughly and subsequently aliquoted and snap-frozen in liquid nitrogen. Extracts were kept at  -80°C until use and 50μl aliquots were taken to serve as input controls.  Inputs were combined with an equal volume of 2x elution buffer (100mM Tris pH 8, 20mM EDTA  pH 8, 2% SDS) and incubated overnight in a water bath at 65°C for 13-15 hours. SDS was then  diluted by the addition of an equal volume of TE (10mM Tris pH 8, 1mM EDTA pH 8) and RNA  was digested by RNase A at a final concentration of 0.2μg/ml at 37°C for 2 hours. Samples  were subsequently Proteinase K treated at 55°C for two hours at a final concentration of  0.2μg/ml. DNA was purified by two subsequent phenol:chloroform:isoamylalcohol (25:24:1, pH  8) extractions and followed by a Qiaquick purification (PCR purification columns, Qiagen,  Germany). To ensure greater DNA purity, columns were washed twice with PE buffer and eluted  in 50μl H2O. DNA concentration was measured using a Nanodrop 1000 (Thermo Scientific,  France) and 500ng were run on 2% agarose gels to verify sonication efficiencies or alternatively  2ng using High Sensitivity DNA chips on a 2100 Bioanalyzer.  ChIP-Seq:  All experiments were performed using Dynabeads (Invitrogen, USA) coated with Protein-G. For  biological replicates, all steps were repeated using a biologically independent sample as  described above. Beads were washed 3x with 1ml and subsequently resuspended in 250μl of  blocking solution (0.5% BSA in 1x DPBS). After the addition of the antibody, the beads were  incubated at 4°C overnight on a rotating wheel. Unbound antibodies were removed through  three further washes with 1ml of blocking solution. Beads were resuspended in 100μl of  blocking solution, extracts were added and the mix was incubated overnight at 4°C on a rotating  wheel.  EDTA-free protease inhibitors (Roche) were added to all washing buffers to a final concentration  of 1x together with 0.2mM PMSF and 1μg/ml pepstatin. Beads were washed 8 times in RIPA  buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA pH 8, 1% NP-40, 0.7% Na-  Deoxycholate) and once in TE+ (10mM Tris pH 8, 1mM EDTA pH 8, 50mM NaCl).  Immunoprecipitated chromatin was recovered from the beads with two subsequent elution steps  at 65°C for 15 and 10 minutes in 110μl and 100μl of elution buffer (50mM Tris pH 8, 10mM  EDTA pH 8, 1% SDS) respectively. The two eluates were combined and incubated at 65°C  overnight (13-15 hours) for crosslink reversal. DNA was purified as described for the input (see  Supplemental Table 1 for a summary of ChIP conditions for each experiment).  Prior to sequencing, ChIP DNA was quantified using the picogreen method (Invitrogen, USA)  using input dilutions as standards, or by running 20% of the ChIP material on a High Sensitivity  DNA chip on a 2100 Bioanalyzer. At least 1ng of ChIP or input DNA was used for library  preparation according to the Illumina ChIP-seq protocol (see Supplemental Table 1 for  quantities obtained for each experiment). After end-repair and adapter ligation, fragments were  size-selected (cut) on an agarose gel prior to preamplification and clustering. The size-selected  and preamplified fragments were verified on a 2100 Bioanalyzer (Agilent, USA) before  clustering and 36 cycle sequencing on a Genome Analyzer II (Illumina, USA) according to  manufacturer’s instructions.

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #

tag: chip antibody lot#

value: CD4+, CD8+ double positive (DP) Thymocytes


title: DRag PolyA RNA-seq

description: PolyA RNA (ribosomal depleted)

molecule: polyA RNA

tag: strain


title: H3K4me3_RC04 ChIP seq

first: Przemyslaw

middle: Aleksander

last: Stempor

state: United Kingdom

address: Tennis Court Road

department: The Gurdon Institute

institute: University of Cambridge

data_processing:
ChIP-seq reads were aligned to the WS220 assembly of the C. elegans genome using BWA (Li and Durbin, 2010) with default settings.
Data were normalized using BEADS algorithm (Cheung et al, 2011).
Signals were exported to bigWig tracks at native resolution.
Peaks ware called with MACS 2.0.10 using aligned files (BAM) as input.
Genome_build: WS220
We used 'Oct. 2010 (WS220/ce10)' reference genome assembly provided by USCS Genome Bioinformatics (http://hgdownload.soe.ucsc.edu/goldenPath/ce10/bigZips/)
The WormBase archive: http://ws220.wormbase.org/
Supplementary_files_format_and_content: bigWig track files were generated using BEADS pipeline in R; Scores represent BEADS normalized values;
Supplementary_files_format_and_content: Bed files represents the signal peaks called with MACS 2.0.10;

organism: Caenorhabditis elegans

source_name: late embryos_H3K4me3 ChIP seq

growth_protocol: About 2-7 million of adult worms are bleached to collect embryos.  Late embryos were obtained by aging embryos 3.5 hrs at room teperature prior to flash freezing in liquid nitrogen.

extract_protocol: Libraries were made using the Truseq DNA sample prep kit (Illumina). 1-10ng of ChIP or 10ng of input are blunted (T4 polymerase), an A-overhang is added (Klenow), DNA is ligated to adaptors, amplified by PCR, and the library size-selected to a 250-400 bp range using Agencourt AMPure XP beads.

treatment_protocol: Late embryos are frozen, ground and crosslinked for 10 minutes in 1% formaldehyde. Formaldehyde is quenched and cross-linked tissue washed, then resuspended in FA buffer and sonicated to an average size of 200bp using a Bioruptor. Extracts are then spun down and the soluble fraction is used for ChIP.

value: whole embryo

tag: Stage

value: Late embryo

tag: chip antibody vendor

tag: chip antibody cat.#


title: H3K4me3_RC03 ChIP seq


title: WT MEFs -2

source_name: embryonic fibroblasts

value: WT

value: MEF


title: CFP-1::GFP_RC04 ChIP seq

source_name: late embryos_CFP-1::GFP ChIP seq

value: anti-GFP


title: CFP-1::GFP_RC03  ChIP seq


title: T. circumcincta Texel Day 21 ALNL49

city: Dublin

first: Albin

middle: Mostaque

last: Ahmed

address: Veterinary Science Centre, UCD, Belfield

department: Veterinary Medicines

country: Ireland

institute: University College Dublin

description: Sample 49 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag CTTGTA

data_processing:
Alignment with Bos Taurus genome (UMD 3.1) using Bowtie
conversion from BAM to SAM, sorting, removal of PCR duplicates using SAMTools
SAM to BAM and sorting using SAMtools
Raw counts per gene using HT-seq
Differential gene expression using edgeR
Genome_build: UMD 3.1
Supplementary_files_format_and_content: frequency counts

organism: Ovis aries

source_name: Abomasal lymph nodes

growth_protocol: Lambs were born indoors and then moved to pasture for a 6-week period.  Lambs were weaned at 6 weeks of age and moved indoors.  Animals were maintained on a concentrate-based diet with free access to water for the remained of the experiment.  Upon housing faecal sampling per rectum was attempted on all lambs, but sufficient material was obtained from only 33 individuals (13 Texel and 20 Suffolk).  All lambs were then treated with Ivermectin (Oramec, Merial Animal Health Limited) according to the manufacturer’s instructions. Mean (±s.e.) Nematodirus sp. faecal egg counts (FECNEM) for Texel and Suffolk were 391 (±154.4) and 508 (±123.1), respectively. Mean values for other trichostrongyle FEC (FECOT) (excluding Strongyloides papillosus) were 11 (±4.6) and 106 (±37.0), respectively.  Animals were quarantined in a slatted pen for a period of 48 h prior to being penned as one group on straw. Five weeks post-housing and anthelmintic treatment, faecal samples were collected on 3 consecutive days to determine GIN infection status.  Lambs with a positive FEC (n = 7) for other trichostrongyles (FECOT) or Strongyloides papillosus  (FECSPAP) on any of these days were treated with Ivermectin (Noromectin Drench, Norbrook Laboratories Limited) according to the manufacturer’s instructions and re-sampled to establish the GIN infection status. All lambs were subsequently observed to be GIN negative. Approximately 1 week prior to administration of the challenge bolus, lambs were weighed, and faecal sampled to confirm the trichostrongyle infection-free status.

extract_protocol:
RNA was extracted uning TRIzol method
The standard Illumina protocol for generating single read RNAseq data was followed. Version 2 illumina sequencing kits were used. Library was prepared from all the samples except 2 from day 21 post infection due to available resources. Two library on day 7 post infection (23 and 24) did not work and excluded from the study.

treatment_protocol: At approximately 20 weeks of age the lambs were randomly assigned, within breed, to one of 5 slaughter time points (0, 3, 7, 14 or 21  days post-infection). The slaughter days were chosen based on the expected developmental stages of T. circumcincta in the sheep abomasum; day 3 and day 7 (L4), day 14 (immature adult), days 21  (mature adult). Animals assigned to the day 0 time point (6 Texel and 4 Suffolk) did not receive an experimental challenge, while all other lambs (5 per breed per time point) received a single oral dose of 3×104 infective T. circumcincta larvae (L3).

value: Lymph nodes

tag: breed

value: Texel

tag: time point

value: Day 21

tag: infection

value: T. circumcincta

tag: animal id


title: T. circumcincta Texel Day 21 ALNL47

description: Sample 47 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag GCCAAT


title: T. circumcincta Texel Day 21 ALNL48

description: Sample 48 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag CAGATC


title: T. circumcincta Suffolk Day 21 ALNL45

description: Sample 45 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag TGACCA

value: Suffolk


title: 7D (~256-cell) embryos

source_name: 7day (~256-cell) embryos

value: North American wild population

tag: developmental stage

value: embryo


title: T. circumcincta Suffolk Day 21 ALNL42

description: Sample 42 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag CTTGTA


title: T. circumcincta Suffolk Day 21 ALNL43

description: Sample 43 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag CGATGT


title: T. circumcincta Suffolk Day 21 ALNL46

description: Sample 46 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag ACAGTG


title: T. circumcincta Texel Day 14 ALNL40

description: Sample 40 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag GCCAAT

value: Day 14


title: T. circumcincta Suffolk Day 14 ALNL37

description: Sample 37 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag CGATGT


title: T. circumcincta Suffolk Day 14 ALNL35

description: Sample 35 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag CAGATC


title: T. circumcincta Suffolk Day 14 ALNL34

description: Sample 34 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag GCCAAT


title: T. circumcincta Suffolk Day 14 ALNL39

description: Sample 39 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag ACAGTG


title: T. circumcincta Texel Day 7 ALNL30

description: Sample 30 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag CTTGTA

value: Day 7


title: T. circumcincta Texel Day 14 ALNL33

description: Sample 33 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag ACAGTG


title: T. circumcincta Suffolk Day 14 ALNL32

description: Sample 32 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag TGACCA


title: T. circumcincta Texel Day 14 ALNL31

description: Sample 31 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag CGATGT


title: T. circumcincta Suffolk Day 7 ALNL26

description: Sample 26 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag TGACCA


title: T. circumcincta Suffolk Day 7 ALNL27

description: Sample 27 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag ACAGTG


title: T. circumcincta Texel Day 7 ALNL29

description: Sample 29 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag CAGATC


title: T. circumcincta Suffolk Day 7 ALNL28

description: Sample 28 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag GCCAAT


title: T. circumcincta Texel Day 7 ALNL22

description: Sample 22 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag GCCAAT


title: T. circumcincta Texel Day 7 ALNL25

description: Sample 25 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag CGATGT


title: T. circumcincta Texel Day 3 ALNL20

description: Sample 20 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag TGACCA

value: Day 3


title: MKN28_TEAD4 ChIP

tag: cell line

tag: cell type

value: gastric cancer cell

tag: chip antibody


title: T. circumcincta Texel Day 21 ALNL41

description: Sample 41 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag CAGATC


title: T. circumcincta Texel Day 3 ALNL16

description: Sample 16 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag GCCAAT


title: T. circumcincta Texel Day 3 ALNL12

description: Sample 12 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag CTTGTA


title: T. circumcincta Suffolk Day 3 ALNL15

description: Sample 15 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag ACAGTG


title: T. circumcincta Suffolk Day 3 ALNL13

description: Sample 13 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag CGATGT


title: T. circumcincta Suffolk Day 3 ALNL17

description: Sample 17 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag CAGATC


title: T. circumcincta Suffolk Day 3 ALNL11

description: Sample 11 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag CAGATC


title: T. circumcincta Texel Day 14 ALNL38

description: Sample 38 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag TGACCA


title: control Suffolk Day 0 ALNL10

description: Sample 10 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag GCCAAT

value: Day 0

value: control


title: control Texel Day 0 ALNL9

description: Sample 9 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag ACAGTG


title: control Texel Day 0 ALNL8

description: Sample 8 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag TGACCA


title: control Texel Day 0 ALNL6

description: Sample 6 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag CAGATC


title: control Texel Day 0 ALNL7

description: Sample 7 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag CTTGTA


title: control Suffolk Day 0 ALNL3

description: Sample 3 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag TGACCA


title: control Texel Day 0 ALNL4

description: Sample 4 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag ACAGTG


title: control Suffolk Day 0 ALNL2

description: Sample 2 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag CGATGT


title: 46hr (1-2-cell) embryos

source_name: 46hr (1-2-cell) embryos


title: T. circumcincta Texel Day 14 ALNL36

description: Sample 36 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag CTTGTA