title: MiSeq_PE_Prep2

description:
Amplicon-seq
C57BL/6J gDNA was sonicated and prepared with Illumina TruSeq kits. Targeted cis-regulome capture was conducted with biotinylated RNA baits. The captured fragments were PCR amplified to add restriction sites, and subsequently cloned into a barcoded vector library. Colonies were harvested to yield capture-and-clone prep #2. The prep was prepared for paired-end sequencing by PCR amplifying the CRE-barcode cassette and ligating sequencing adapters.
Loading concentration of 2 pM with 12% Phi-X

data_processing:
For MiSeq data: FastQC was run to check for sequencing quality. Read pairs were required to perfectly match an index (GCTCGA, TAGACTA, CGCTACCC, or ATAGTGGACA) and adapter sequence (AGACGTGTGCTCTTCCGATCT or TACACGACGCTCTTCCGATCT). The barcode sequence was extracted based on 6 flanking bases on either side (CGGTTT-barcode-GGGACG). The captured-and-cloned fragment was extracted based on the adjacent adapter sequence.
For MiSeq data: Captured-and-cloned fragment portion of reads were aligned to mm9 using Bowtie2 v2.1.0 with -X 1000 setting.
For MiSeq data: SAM file was converted to sorted BAM using samtools v0.1.19, and then to sorted BED using bedtools v2.22.1.
For MiSeq data: Captured-and-cloned fragments were examined for overlap with the 4,000 target regions. Only paired reads were used that mapped concordantly by Bowtie2, and with forward and reverse reads mapping to opposite strands of DNA (since the same fragment of DNA was sequenced from opposite directions for a given pair of reads). The number of reads for a given CRE-barcode association were tabulated. If a fragment overlapped two target regions, the target region with the most bases of overlap with the fragment was assigned.
For MiSeq data: Barcodes were required to be 14-16 bp in length. To account for a barcode being associated with multiple fragments (as a result of either sequencing error, or multiple fragments being cloned onto vectors with the same barcode), the following criteria were imposed. Each barcode was examined for the "top species" (the fragment with the highest number of paired reads for the barcode) and the "2nd species" (the fragment with the second-highest number of paired reads for the barcode). Let read_top = number of paired reads for the top species, read_2nd = number of paired reads for the 2nd species, and top_fraction = read_top/total number of paired reads for the barcode. Barcodes were included only if: (1) read_top ≥ 20 and top_fraction >0.95, or (2) read_top ≥ 10 and read_2nd ≤ 2 and top_fraction > 0.5. Barcodes present in both library preps were excluded.
For MiSeq data: For fragments associated with multiple barcodes (e.g., due to PCR amplification of the fragment), only the barcode with the greatest number of reads was included.
For HiSeq data: FastQC was run to check for sequencing quality. After trimming the first base, reads were required to begin with a perfect 10 bp match to a sample index plus additional bases of flanking sequence (GCTACGGCCG, CTCGATGGCC, AGACTATGGC, ATCGTCATGG, TAGTGGACAG, or CAGACTCAGT). These sample indices corresponded to RNA #1, RNA #2, RNA #3, DNA #1, DNA #2, and DNA #3 for each lane of HiSeq.
For HiSeq data: The barcode sequence was extracted based on 6 flanking bases on either side (CGTCCC-barcode-AAACCG). Barcodes (with known CRE correspondences, based on the MiSeq data) were tabulated for each sample. This gave the "raw counts".
For HiSeq data: For each tissue, barcodes that did not have at least 10 raw DNA counts for all 3 DNA samples were excluded from the subsequent analysis. Let r = the raw RNA count for a given barcoded construct, and let R be the total RNA counts for a given replicate. Let d be the raw DNA counts for a given barcoded construct, and let D be the total DNA counts for a given replicate. The expression (in log2 units) of a given barcoded construct is log base 2 of [0.001 + (r/R)/(d/D)], i.e., the ratio of normalized RNA to normalized DNA, plus a pseudocount of 0.001.
Genome_build: mm9

organism: Synthetic plasmid

source_name: Plasmid

extract_protocol:
MiSeq: maxiprep; HiSeq: TRIzol extraction
PCR amplification and ligation of sequencing adapters

tag: harvest


title: MiSeq_PE_Prep1

status: Public on Oct 15 2015

type: SRA

city: St. Louis

first: Joseph

middle: C

last: Corbo

state: MO

address: 660 S. Euclid Ave.

country: USA

institute: Washington University School of Medicine

description:
Amplicon-seq
C57BL/6J gDNA was sonicated and prepared with Illumina TruSeq kits. Targeted cis-regulome capture was conducted with biotinylated RNA baits. The captured fragments were PCR amplified to add restriction sites, and subsequently cloned into a barcoded vector library. Colonies were harvested to yield capture-and-clone prep #1. The prep was prepared for paired-end sequencing by PCR amplifying the CRE-barcode cassette and ligating sequencing adapters.
Loading concentration of 1.6 pM with 15% Phi-X

library_source: genomic

molecule: other

tag: tissue

tag: strain

tag: treatment


title: MCSF W_Small

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
Sample name: 20140506_04
M-CSF withdrawal_SmallRNA
SOLiD5500 Wildfire, Life Technology. Sequencing of 50b. with 10b. barcoding sequences.
Processed data file: norm1Msignal_mouse.txt

library_source: transcriptomic

data_processing:
Lifescope v2.5.1 smallRNA pipeline. Mapping with mapreads, default parameters.
Bam files were then processed with a java home made class, based on picard java classes to perform identification and produce raw data count of microRNAs (mirbase release 18), tRNAs from  UCSC web server (UCSC tables), yRNAs and ncRNAs from ensembl ncRNAs release 69 and piRNAs from fRNAdb.
Genome_build: mm10
Supplementary_files_format_and_content: [norm1Msignal_mouse.txt] Tabulated text file of raw data counts normalized to 1000000 count in each sample.

molecule: total RNA

organism: Mus musculus

source_name: M-CSF withdrawal_Small

extract_protocol:
RNA extraction with Trizol
2 µg of total RNA were ligated, reverse transcribed and amplified (11 cycles) with the reagents from the NEBNext Small RNA Library Prep Set for SOLiD. Amplified libraries were size-selected from 110 nt to 145 nt with the LabChip XT DNA 300 Assay Kit (Caliper Lifesciences). Libraries were subjected to 4 additional PCR rounds with the primers from the 5500 W Conversion Primers Kit (Life Technologies) and converted with the enzyme kit from the 5500 W Conversion Primers Kit (Life Technologies). Libraries were then quantified with the Bioanalyzer High Sensitivity DNA Kit (Agilent).

treatment_protocol: BMDM upon 36 hr with or without M-CSF withdrawal

tag: strain/background

tag: cell type

value: Bone Marrow Derived Macrophage

value: M-CSF withdrawal

tag: rna extract

value: small RNA

tag: concentration sample (ng/ul)

tag: rin number


title: low shear force 3

status: Public on Oct 14 2015

city: Balice

first: Katarzyna

last: Piorkowska

address: Krakowska 1

department: Animal Genomics and Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

data_processing:
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove Illumina adapters and poly-A sequences
Cleaned sequences were aligned to the Gallus gallus genome (Galgal 4.74 assembly) with a reference annotation containing 17,954 genes listed in the Ensembl database.
The alignment and estimation of gene and isoforms level expression was made using TopHat and RSEM package, both supported by a Bowtie2 aligner.
The differential expression estimation was proceed with utilization of cuffdiff, edgeR and DeSeq2 Bioconductor R-project packages.
Genome_build: galGal4 (Gallus_gallus-4.0; http://www.ncbi.nlm.nih.gov/assembly/GCF_000002315.3)
Supplementary_files_format_and_content: output files from cuffdiff, edgeR and DeSeq2 Bioconductor R-project packages;
raw*.csv.gz containing raw genes or isoforms counts
cuffdiff.*exp.diff.gz containing TopHat results for differential expression analysis (high vs low) for genes or isoforms
edgeR.DeSeq2.results*.csv.gz containing egred and DeSeq2 results for differential expression analysis (high vs low) for genes or isoforms

organism: Gallus gallus

source_name: low shear force of pectoralis musle

extract_protocol:
Pectoralis muscle were stabilized by RNAlater solution  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 300 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hubbard Flex

tag: gender

value: female

tag: age

value: 6 week

tag: sample group

value: low shear force

value: pectoralis muscle


title: Control_Total

description:
Sample name: 20140506_01
Control_TotalRNA
SOLiD5500 Wildfire, Life Technology. Sequencing of 50b. with 10b. barcoding sequences.
Processed data file: norm1Msignal_mouse.txt

value: total RNA


title: Control_Small

description:
Sample name: 20140506_03
Control_SmallRNA
SOLiD5500 Wildfire, Life Technology. Sequencing of 50b. with 10b. barcoding sequences.
Processed data file: norm1Msignal_mouse.txt


title: high shear force 3

source_name: high shear force of pectoralis musle

value: high shear force


title: Multinucleate_3

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

country: United Kingdom

institute: Queen Mary University of London

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to Creolimax  genome using Tophat 2. tophat2 -i 30 -g 1 --library-type=fr-firststrand -r 5 -G
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a Cufflinks2. cuffdiff  --max-bundle-frags 10000000 --library-type=fr-firststrand -N -u -b
Genome_build: Creolimax1
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for all Samples. A FASTA file with the assembled sequences is available on the series record.

organism: Creolimax fragrantissima

source_name: Multinucleate cells

growth_protocol: Marine Broth liquid medium, 12ºC.

extract_protocol:
A culture grown for 3 days was filtered with a 5 um mesh, isolating amoeboid cells. mRNA from Amoebas was extracted immediately. Multinucleate stage was obtained after culturing amoebas for 24 hr. RNA was harvested using Trizol reagent. TruSeq Stranded mRNA Sample Prep kit (Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell stage

value: Coenocyte stage

tag: time after filtering for 5um

value: 24 hr


title: Multinucleate_1


title: Amoeboid_2

source_name: Amoeboid cells

value: Amoeba stage

value: 0 hr


title: Amoeboid_3


title: low shear force 4


title: high shear force 4


title: Multinucleate_2


title: low shear force 1


title: low shear force 2


title: Amoeboid_1


title: high shear force 1


title: CH_3

city: Shanghai

first: Peng

last: Hu

address: Huchenghuan Road 999

country: China

institute: Shanghai Ocean University

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw reads were assessed for their quality using FASTX_toolkit (http://hannonlab.cshl.edu/fastx_toolkit). Reads with a Phred quality score less than 5 over the 95% nt would be removed.
A total of nine head kidney RNA samples from three individuals of each of three Antarctic notothenioid species, including one white-blooded icefish (C. hamatus) and two red-blooded notothenioids (G. acuticeps and T. Bernacchii), were deeply sequenced using the Illumina HiSeq1500 platform.
High-quality reads were assembled to unigenes, annotated, and mapped to a common protein set (~24,000 uni-proteins deduced from the Antarctic notothenioid Dissostichus mawsoni genome).
Genome_build: A total of 17,407 D. mawsoni genes were matched to the assembled unigenes expressed in the head kidney of the three species. After blasting against with the Uniprot proteins and redundancy elimination, a set of 12,653 genes remained for the expression profile comparison.
Supplementary_files_format_and_content: a tab-delimited text file include reads count for all Sample.

organism: Chionodraco hamatus

source_name: C. hamatus_head kidney

extract_protocol:
Tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 6 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: head kidney


title: GA_3

organism: Gymnodraco acuticeps

source_name: G. acuticeps_head kidney


title: CH_1


title: CH_2


title: GA_1


title: Control_RNAseA

city: MARSEILLE CEDEX 09

first: Christelle

last: Cayrou

address: 27 Boulevard Lei Roure

institute: CRCM

description: Replication Nascent strands

data_processing:
Sequenced reads were mapped against the mm9 mouse genome sequence (NCBI Build 37) with the CASAVA software (version 1.8 – Illumina)
After mapping, unique mapping reads of the nascent strand (NS) replicates 1, 2 and 3 (59M, 43M, 10M reads, respectively) were combined (112M unique reads) for further analysis, and genomic DNA (45M reads) and RNAse A (63M reads) samples were recovered.
After a thorough evaluation, we combined two peak-calling programs with complementary properties. We thus retained SWEMBL for the identification of precise peaks in NS reads that we defined as initiation sites, whereas SICER returns wider regions enriched in reads. All SICER regions that overlapped with at least one SWEMBL peak were retained and defined as IZ. Reciprocally, all SWEMBL peaks falling within a SICER region were identified as IS. RNAse A control was used as input.
Genome_build: mm9
Supplementary_files_format_and_content: 50bp binned WIG files generated with a custom R pipeline represent the average local enrichment in the genome of studied feature.

molecule: genomic DNA

source_name: Es cells nascent strands

growth_protocol: CGR8 mESCs were cultured in ESC culture medium supplemented with foetal bovine serum (FBS) and leukaemia inhibitory factor (LIF) without feeders.

extract_protocol:
Nascent strands (NS) were purified as previously described in details (Cayrou et al., 2012b). Briefly, after extraction with DNAzol, NS were first separated from genomic DNA by sucrose gradient. Several fractions of interest containing NS DNA (0.5 to 2 Kb range) were phosphorylated by T4 polynucleotide kinase, and digested with L-Exo (100-150 units that correspond to 300-500 L-Exo units/ug of DNA) overnight at 37 °C to eliminate contaminating DNA. A second round of phosphorylation/digestion, using the same conditions, is performed before purification of the samples for library preparation. Three samples were purified from three independent cell cultures. The RNase A controls were obtained by treating NS-containing fractions with 100 ng/ml RNAse A before L-Exo digestion to remove RNA primers at the 5' end of the NS. Another control we also used was genomic DNA sonicated to the same size of the NS DNA and treated by L-Exo in the same conditions used for NS samples. To allow reliable comparison with the NS samples, around 1ug of sonicated DNA was thereby treated.
Libraries were prepared for sequencing using standard Illumina protocols

value: pluripotent embryonic cells

tag: cell line


title: MCSF W_Total

description:
Sample name: 20140506_02
M-CSF withdrawal_TotalRNA
SOLiD5500 Wildfire, Life Technology. Sequencing of 50b. with 10b. barcoding sequences.
Processed data file: norm1Msignal_mouse.txt

source_name: M-CSF withdrawal_Total


title: Replicate_2

description:
Replication Nascent strands
Combined data from the 3 replicates are in Series supplementary files Combination_3replicates.wig, Initiation_Sites.bedGraph, and Initiation_Zones.bed.


title: high shear force 2


title: Replicate_3


title: Control_genomic_DNA

description: Replication Nascent strands


title: Replicate_1


title: GA_2


title: Liver_8mkd-furan_FreshFrozen_41_polyA-RNAseq

city: Ottawa

first: Anna

middle: Francina

last: Jackson

state: Ontario

address: 50 Colombine Drive, Tunney's Pasture

department: Environmental Health Center

country: Canada

institute: Health Canada

description:
RNA from fresh-frozen livers
polyA RNA enrichment

data_processing:
Basecalls performed using RTA version 1.9
Reads were demultiplexed and converted into fastq files using CASAVA version 1.8.2
RNA-seq reads were aligned to the mm9 genome assembly using STAR version 2.3.0 with default parameters
Counts per gene were calculated using a featureCounts version 1.4.4.   In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted for each gene.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited matrix which includes counts per gene for each Sample

source_name: liver

growth_protocol: 5-6 week old female specific pathogen free B6C3F1 mice were purchased from Charles River Breeding Laboratories (Portage, ME) and were allowed to acclimatize for at least 7 days prior to the start of the study. Feed (NIH-07; Zeigler Brothers, Inc., Gardners, PA) and tap water were available ad libitum. Mice were housed five per cage in polycarbonate cages in a specific pathogen free (SPF) and Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC) accredited facility. All procedures were conducted in compliance with the Animal Welfare Act Regulations (9CFR1–4). Mice were handled and treated according to the guidelines provided in the National Institute of Health (NIH) Guide for the Care and Use of Laboratory Animals (ILAR, 1996; http://dels.nas.edu/ilar/).

extract_protocol:
Mice were anaesthetized under carbon dioxide inhalation followed by exsanguination. Livers were removed and divided into three: One piece was frozen, one piece was preserved in formalin for 18 hours, one piece was preserved in formalin for 3 weeks. FROZEN: samples were placed in cryovials and immediately snap frozen in liquid nitrogen, these tissues were stored at -80oC until RNA extraction was performed.  Total RNA was extracted from ~100mg frozen tissue using the RNeasy Midi Kit (Qiagen) according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  Fresh-frozen RNA samples had A260/280 ratios > 1.83 and RINs > 8.9. FFPE: samples were preserved in formalin for 18 hours or 3 weeks and then stored in paraffin blocks at room temperature. RNA was extracted from 1x10uM section (18 hours samples) and 2x10uM sections (3 weeks samples) using the RNeasy FFPE RNA extraction kit (Qiagen). Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  FFPE RNA samples had A260/280 ratios > 1.74 and RINs 1.3-2.4.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Kit v2 (Part# RS-122-2001). Briefly, poly(A)+ mRNA was selected via oligo(dT) beads, fragmented, and converted into ds-cDNA.   The resultant cDNAs were barcoded and ligated to Illumina adapters.  After adapter ligation, the cDNA was PCR amplified. The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2000 following the manufacturer's protocols.

treatment_protocol: Mice were dosed via oral gavage for 21 days. Treated animals were exposed to 8 mg/kg bw/day furan in corn oil.  Control animals were gavaged with cornoil oil only.   Tissues were collected 4 hours following the final dose.

value: 5-6 weeks

value: liver


title: Liver_Control_FreshFrozen_06_polyA-RNAseq


title: Liver_8mkd-furan_FreshFrozen_44_polyA-RNAseq


title: Liver_8mkd-furan_FreshFrozen_42_polyA-RNAseq


title: Liver_Control_FreshFrozen_04_polyA-RNAseq


title: Liver_Control_FreshFrozen_02_polyA-RNAseq


title: Liver_8mkd-furan_FreshFrozen_43_polyA-RNAseq


title: Liver_Control_FFPE3wk_04_polyA-RNAseq

description:
RNA from FFPE livers
polyA RNA enrichment


title: Liver_8mkd-furan_FFPE3wk_42_polyA-RNAseq


title: Liver_8mkd-furan_FFPE3wk_41_polyA-RNAseq


title: Liver_Control_FFPE3wk_06_polyA-RNAseq


title: Liver_Control_FreshFrozen_03_polyA-RNAseq


title: Liver_Control_FFPE3wk_03_polyA-RNAseq


title: Liver_8mkd-furan_FFPE3wk_43_polyA-RNAseq


title: Liver_Control_FFPE3wk_02_polyA-RNAseq


title: Liver_8mkd-furan_FFPE18h_42_polyA-RNAseq


title: Liver_8mkd-furan_FFPE18h_41_polyA-RNAseq


title: Liver_Control_FFPE18h_04_polyA-RNAseq


title: Liver_8mkd-furan_FFPE18h_44_polyA-RNAseq


title: Liver_Control_FFPE18h_03_polyA-RNAseq


title: Liver_Control_FFPE18h_02_polyA-RNAseq


title: Liver_8mkd-furan_FreshFrozen_44_riboRNAseq

description:
RNA from fresh-frozen livers
ribo-depleted RNA

extract_protocol:
Mice were anaesthetized under carbon dioxide inhalation followed by exsanguination. Livers were removed and divided into three: One piece was frozen, one piece was preserved in formalin for 18 hours, one piece was preserved in formalin for 3 weeks. FROZEN: samples were placed in cryovials and immediately snap frozen in liquid nitrogen, these tissues were stored at -80oC until RNA extraction was performed.  Total RNA was extracted from ~100mg frozen tissue using the RNeasy Midi Kit (Qiagen) according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  Fresh-frozen RNA samples had A260/280 ratios > 1.83 and RINs > 8.9. FFPE: samples were preserved in formalin for 18 hours or 3 weeks and then stored in paraffin blocks at room temperature. RNA was extracted from 1x10uM section (18 hours samples) and 2x10uM sections (3 weeks samples) using the RNeasy FFPE RNA extraction kit (Qiagen). Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  FFPE RNA samples had A260/280 ratios > 1.74 and RINs 1.3-2.4.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Total RNA Sample Kit (Part# RS-122-2201). Briefly, RNA was depleted of ribosomal RNA via beads, fragmented, and converted into ds-cDNA.   The resultant cDNAs were barcoded and ligated to Illumina adapters.  After adapter ligation, the cDNA was PCR amplified. The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2000 following the manufacturer's protocols.


title: Liver_8mkd-furan_FreshFrozen_43_riboRNAseq


title: Liver_8mkd-furan_FFPE3wk_44_polyA-RNAseq


title: Liver_8mkd-furan_FFPE18h_43_polyA-RNAseq


title: Liver_8mkd-furan_FreshFrozen_42_riboRNAseq


title: Liver_8mkd-furan_FreshFrozen_41_riboRNAseq


title: Liver_Control_FreshFrozen_03_riboRNAseq


title: K562 genomic rep2

city: Memphis

first: Daniel

last: Savic

state: Tennessee

address: 262 Danny Thomas Place

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

description: Sequence barcode counts from DNA and RNA (cDNA) is tabulated for two independent replicate transfection experiments

data_processing:
Library strategy: Cre-seq
Imaging and basecalls from Illumina RTA
Cutadapt adaptor sequences and split file by inline barcodes
Align sequenced reads to plasmid sequence, requiring perfect match
Calculate counts per barcode sequence
Genome_build: hg19 (for CEBPB binding site locations)
Supplementary_files_format_and_content: TXT file contains (in order as columns): binding site location/name, barcode sequence, site category, site type, cell type, read type, replicate, counts

organism: Homo sapiens

source_name: Plasmid DNA

growth_protocol: HepG2 and K562 cells were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell)

extract_protocol:
Next generation sequencing library preparation was performed as previously described (Kwasnieski et al. 2012; White et al. 2013; Kwasnieski et al. 2014).  Nucleic acids were purified from cell lysates using Norgen Total RNA Purification Kit (Norgen Biotek Corporation) and DNeasy Blood and Tissue Kit (Qiagen) for RNA and DNA, respectively.  RNA was treated with DNaseI (Turbo DNase, Life Technologies) and reverse transcription was performed using Superscript II reverse transcriptase (Life Technologies).  The 3’ UTR of the luciferase gene containing barcode sequences was amplified (Phusion high fidelity master mix, New England Biolabs) from cellular RNA (cDNA) or DNA prior to next-generation sequencing.  Each replicate experiment was sequenced as a pool on one lane on an Illumina HiSeq 2000 sequencer.
Illumina Single End

treatment_protocol: HepG2 and K562 cells were transfected at ~75% confluence using FUGENE reagent (Promega, E2311).

tag: experiment type

value: Plasmid transfection

value: Acute Myelogenous Leukemia (K562)


title: HepG2 genomic rep1

value: Hepatocellular Carcinoma (HepG2)


title: K562 rna rep1


title: K562 genomic rep1


title: young set1_RRBS

city: Bronx

first: Bo

last: Yu

state: NY

address: 1300 Morris Park Ave, Block 621

institute: Albert Einstein College of Medicine

description: young set1

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 MethylCap reads were mapped to hg19 whole genome using bowtie
Bismark was used for read mapping and methylation calling in RRBS datasets.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include peak values (in MethylCap-seq datasets) or methylation levels (in RRBS datasets) for each set of samples (young versus old).  MethylCap-seq data: used sliding window of 2000bp and 1000bp step.

source_name: young set_RRBS

extract_protocol:
ovarian granulosa cells were purified from follicular fluids obtained at the time of oocyte retrieval.  DNA was extracted QIAamp DNA mini kits (Qiagen).
MethylCap-seq (PMID:20852634; 20542119) and RRBS libraries (PMID: 21412275; 23325432) were prepared according to protocols previously published.

tag: age group

value: young

value: ovarian granulosa cells

tag: molecule subtype

value: Bisulfite treated DNA


title: HepG2 rna rep2


title: HepG2 rna rep1


title: Liver_Control_FreshFrozen_04_riboRNAseq

value: female

tag: tissue


title: K562 rna rep2


title: young set2_RRBS

description: young set2


title: Liver_Control_FFPE18h_06_polyA-RNAseq

tag: strain


title: Liver_8mkd-furan_FFPE3wk_44_riboRNAseq

description:
RNA from FFPE livers
ribo-depleted RNA


title: old set1_MethylCap-seq

description:
old set1
processed data file: czcrOut_hsChr.Bo_DNAmet_Exp1.high_input_low.2000_1000.txt

source_name: old set_MethylCap-seq

value: old


title: Liver_Control_FreshFrozen_06_riboRNAseq


title: old set2_MethylCap-seq

description:
old set2
processed data file: czcrOut_hsChr.Bo_DNAmet_Exp2.high_input_low.2000_1000.txt


title: Liver_8mkd-furan_FFPE3wk_43_riboRNAseq

description:
RNA from FFPE livers
ribo-depleted RNA


title: old set2_RRBS

description: old set2

source_name: old set_RRBS


title: young set2_MethylCap-seq

description:
young set2
processed data file: czcrOut_hsChr.Bo_DNAmet_Exp2.high_input_low.2000_1000.txt

source_name: young set_MethylCap-seq


title: HepG2 genomic rep2


title: Liver_8mkd-furan_FFPE3wk_42_riboRNAseq

description:
RNA from FFPE livers
ribo-depleted RNA


title: Sample 12

description: mRNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
BAM files were aligned to hg18 using ELAND for quality control purposes
BAM files were converted to FASTQ
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR software
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample ...

molecule: polyA RNA

source_name: ovarian granulosa cells

extract_protocol:
ovarian granulosa cells were purified from follicular fluids obtained at the time of oocyte retrieval.  RNA were extracted using Qiagen Rneasy micro kit
mRNA-seq libraries were prepared according to standard Illumina protocol


title: Sample 11

description: mRNA-seq


title: Sample 10

description: mRNA-seq


title: Sample 9

description: mRNA-seq


title: Liver_Control_FreshFrozen_02_riboRNAseq


title: Liver_8mkd-furan_FFPE3wk_41_riboRNAseq

description:
RNA from FFPE livers
ribo-depleted RNA


title: old set1_RRBS

description: old set1


title: Sample 7

description: mRNA-seq


title: Sample 4

description: mRNA-seq


title: young set1_MethylCap-seq

description:
young set1
processed data file: czcrOut_hsChr.Bo_DNAmet_Exp1.high_input_low.2000_1000.txt


title: Sample 2

description: mRNA-seq


title: Liver_Control_FFPE3wk_04_riboRNAseq

description:
RNA from FFPE livers
ribo-depleted RNA


title: Sample 3

description: mRNA-seq


title: Liver_Control_FFPE3wk_02_riboRNAseq

description:
RNA from FFPE livers
ribo-depleted RNA


title: Liver_8mkd-furan_FFPE18h_44_riboRNAseq

description:
RNA from FFPE livers
ribo-depleted RNA


title: Liver_Control_FFPE3wk_03_riboRNAseq

description:
RNA from FFPE livers
ribo-depleted RNA


title: Liver_Control_FFPE3wk_06_riboRNAseq

description:
RNA from FFPE livers
ribo-depleted RNA


title: TRZT22_2; ZT22, total RNA, rep2

city: Lasuanne

first: David

last: Gatfield

address: UNIL CIG

department: CIG

country: Switzerland

institute: University of Lausanne

data_processing:
Base-calling: Casava 1.82
Adapter trimming: Adapter sequences were removed using cutadapt utility with following options: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --match-read-wildcards -m 6
Insert size filtering: Trimmed read sequences were filtered by their size using an in-house Python script with following inclusive ranges: [26,35] for footprints, [21,60] for total RNA
Alignment: Trimmed and filtered insert sequences were mapped sequentially to following databases: mouse rRNA, human rRNA, mt-tRNA, mouse tRNA, mouse cDNA (Ensembl.v.75) and mouse genome (GRCm38.p2). All but last one were mapped using bowtie (version 2.2.1) using following parameters: -p 2 -L 15 -k 20 –no-unal. Mapping against genomic sequence was performed using tophat (v2.0.11) with following parameters: --transcriptome-index=Mmusculus.GRCm38.75.dna.ensembl_data -p 2. After each alignment, only reads that were not aligned were used in the following mapping. For further analysis (processed data files), only alignments against mouse cDNA were used. Separately from this alignment strategy, each query set was also directly aligned against mouse genome using tophat with similar parameters (“global tophat”).
Post-alignment filtering: For each query sequence, only alignments with maximum score were kept. The output of “global tophat” alignment was used to estimate expressed transcript models using cufflinks (v2.2.1) with following parameters: --GTF Mus_musculus.GRCm38.75.gtf --frag-len-mean 37 --frag-len-std-dev 8 --compatible-hits-norm --multi-read-correct --upper-quartile-norm --frag-bias-correct Mmusculus.GRCm38.75.dna.ensembl.fa -p 3. Transcript FPKM estimates from all samples were merged using cuffcompare with following parameters: -r Mus_musculus.GRCm38.75.gtf -R -V. Resulting FPKM tracking information was parsed with an in-house Python script to filter out transcripts which were not found to have an FPKM > 0.1, a LOW95 > 0.05 and a FMI > 2.0 in at least 3 samples. A database of expressed transcripts was used in further analysis.
Abundance measurement: mRNA and RPF (ribosome protected fragment) levels were estimated per locus. An in-house Python script was used to count uniquely (by gene) mapped reads within each annotation feature (5'UTR, CDS, 3'UTR). For multi-isoform loci, preference order used was CDS, 5'UTR, 3'UTR.
Pre-normalization: Mappable and countable feature lengths (in bps) for each locus were calculated by means of generating all possible 21-, 30-, 45-, and 60-bp long reads in silico (faux reads) for each expressed transcript in the database and counting the faux reads through identical mapping and counting work flow used for real experimental reads. Weigthed averages of these mappable and countable lengths were later used in RPKM calculations.
Normalization: Read counts of total RNA and RPF were normalized with upper quantile method of R package edgeR. Prior to normalization, transcripts which did not have at least 10 counts in at least one third of the samples were removed from the datasets.
Normalization: RPKM values were calculated as the number of counted reads per 1000 mappable and countable bases per geometric mean of normalized read counts per million.
Genome_build: Genome Reference Consortium GRCm38.p2 (mm10)
Supplementary_files_format_and_content: rpkm files were generated with R; gene IDs are ENSEMBL-IDS

source_name: TRZT22_2; ZT22, total RNA

extract_protocol:
Livers were homogenized in 3 volumes of lysis buffer (150 mM NaCl, 20 mM Tris-HCl pH7.4, 5 mM MgCl2, 5 mM DTT, 100 μg ml-1 cycloheximide, 1% Triton X-100, 0.5% Sodium deoxycholate, complete EDTA-free protease inhibitors (Roche) and 40 U ml-1 RNasin plus (Promega)) using a Teflon homogenizer. Lysates were incubated for 10 min on ice and cleared by centrifugation at 1000 x g, 4°C for 3 min in a tabletop centrifuge. Supernatants were flash-frozen and stored in liquid nitrogen. Lysates of two mice per timepoint were pooled. Total RNA-seq libraries were generated from the lysate pool. For ribosome profiling libraries, lysate pools (15 OD260) were digested with 650 U RNase I (Ambion) for 45 min at room temperature and passed over size exclusion columns for ribosome purification prior to RNA extraction and library preparation.
Sequencing libraries for total RNA and ribosome protected RNA were generated using Ribo-Zero (Epicentre) and ARTseq ribosome profiling kits (Epicentre).

value: male

value: 11-12 weeks

tag: timepoint

tag: insert type

value: total RNA


title: TRZT22_1; ZT22, total RNA, rep1

source_name: TRZT22_1; ZT22, total RNA


title: Sample 1

description: mRNA-seq

tag: cell type


title: Liver_8mkd-furan_FFPE18h_43_riboRNAseq

description:
RNA from FFPE livers
ribo-depleted RNA


title: TRZT20_2; ZT20, total RNA, rep2

source_name: TRZT20_2; ZT20, total RNA


title: TRZT18_2; ZT18, total RNA, rep2

source_name: TRZT18_2; ZT18, total RNA


title: TRZT20_1; ZT20, total RNA, rep1

source_name: TRZT20_1; ZT20, total RNA


title: Liver_8mkd-furan_FFPE18h_42_riboRNAseq

description:
RNA from FFPE livers
ribo-depleted RNA


title: TRZT18_1; ZT18, total RNA, rep1

source_name: TRZT18_1; ZT18, total RNA


title: TRZT16_2; ZT16, total RNA, rep2

source_name: TRZT16_2; ZT16, total RNA


title: Sample 8

description: mRNA-seq


title: TRZT14_2; ZT14, total RNA, rep2

source_name: TRZT14_2; ZT14, total RNA


title: Liver_8mkd-furan_FFPE18h_41_riboRNAseq

description:
RNA from FFPE livers
ribo-depleted RNA


title: TRZT12_1; ZT12, total RNA, rep1

source_name: TRZT12_1; ZT12, total RNA


title: Liver_Control_FFPE18h_06_riboRNAseq

description:
RNA from FFPE livers
ribo-depleted RNA


title: TRZT16_1; ZT16, total RNA, rep1

source_name: TRZT16_1; ZT16, total RNA


title: Liver_Control_FFPE18h_04_riboRNAseq

description:
RNA from FFPE livers
ribo-depleted RNA

source_name: liver


title: TRZT12_2; ZT12, total RNA, rep2

source_name: TRZT12_2; ZT12, total RNA


title: TRZT14_1; ZT14, total RNA, rep1

source_name: TRZT14_1; ZT14, total RNA


title: Sample 6

description: mRNA-seq


title: Liver_Control_FFPE18h_03_riboRNAseq

description:
RNA from FFPE livers
ribo-depleted RNA


title: TRZT10_1; ZT10, total RNA, rep1

source_name: TRZT10_1; ZT10, total RNA


title: TRZT10_2; ZT10, total RNA, rep2

source_name: TRZT10_2; ZT10, total RNA


title: TR_ZT8_2; ZT8, total RNA, rep2

source_name: TR_ZT8_2; ZT8, total RNA


title: TR_ZT6_1; ZT6, total RNA, rep1

source_name: TR_ZT6_1; ZT6, total RNA


title: TR_ZT4_1; ZT4, total RNA, rep1

source_name: TR_ZT4_1; ZT4, total RNA


title: Sample 5

description: mRNA-seq

source_name: ovarian granulosa cells


title: TR_ZT6_2; ZT6, total RNA, rep2

source_name: TR_ZT6_2; ZT6, total RNA


title: TR_ZT8_1; ZT8, total RNA, rep1

source_name: TR_ZT8_1; ZT8, total RNA


title: TR_ZT0_2; ZT0, total RNA, rep2

source_name: TR_ZT0_2; ZT0, total RNA


title: TR_ZT4_2; ZT4, total RNA, rep2

source_name: TR_ZT4_2; ZT4, total RNA


title: TR_ZT0_1; ZT0, total RNA, rep1

source_name: TR_ZT0_1; ZT0, total RNA


title: RPZT22_2; ZT22, ribosome footprint, rep2

source_name: RPZT22_2; ZT22, ribosome footprint

value: ribosome footprint

value: ribosome protected RNA


title: TR_ZT2_1; ZT2, total RNA, rep1

source_name: TR_ZT2_1; ZT2, total RNA


title: TR_ZT2_2; ZT2, total RNA, rep2

source_name: TR_ZT2_2; ZT2, total RNA


title: RPZT22_1; ZT22, ribosome footprint, rep1

source_name: RPZT22_1; ZT22, ribosome footprint


title: RPZT20_2; ZT20, ribosome footprint, rep2

source_name: RPZT20_2; ZT20, ribosome footprint


title: RPZT18_2; ZT18, ribosome footprint, rep2

source_name: RPZT18_2; ZT18, ribosome footprint


title: RPZT20_1; ZT20, ribosome footprint, rep1

source_name: RPZT20_1; ZT20, ribosome footprint


title: RPZT16_2; ZT16, ribosome footprint, rep2

source_name: RPZT16_2; ZT16, ribosome footprint


title: RPZT18_1; ZT18, ribosome footprint, rep1

source_name: RPZT18_1; ZT18, ribosome footprint


title: RPZT16_1; ZT16, ribosome footprint, rep1

source_name: RPZT16_1; ZT16, ribosome footprint


title: RPZT14_2; ZT14, ribosome footprint, rep2

source_name: RPZT14_2; ZT14, ribosome footprint


title: Liver_Control_FFPE18h_02_riboRNAseq

description:
RNA from FFPE livers
ribo-depleted RNA

source_name: liver


title: RPZT10_1; ZT10, ribosome footprint, rep1

source_name: RPZT10_1; ZT10, ribosome footprint


title: RPZT10_2; ZT10, ribosome footprint, rep2

source_name: RPZT10_2; ZT10, ribosome footprint


title: RP_ZT8_1; ZT8, ribosome footprint, rep1

source_name: RP_ZT8_1; ZT8, ribosome footprint


title: RPZT14_1; ZT14, ribosome footprint, rep1

source_name: RPZT14_1; ZT14, ribosome footprint


title: RP_ZT6_2; ZT6, ribosome footprint, rep2

source_name: RP_ZT6_2; ZT6, ribosome footprint


title: RP_ZT8_2; ZT8, ribosome footprint, rep2

source_name: RP_ZT8_2; ZT8, ribosome footprint


title: RP_ZT6_1; ZT6, ribosome footprint, rep1

source_name: RP_ZT6_1; ZT6, ribosome footprint


title: RP_ZT4_2; ZT4, ribosome footprint, rep2

source_name: RP_ZT4_2; ZT4, ribosome footprint


title: TB_3

organism: Trematomus bernacchii

source_name: T. bernacchii_head kidney

value: head kidney


title: Pb_DHA_rep1

city: Pathumthani

first: Philip

middle: James

last: Shaw

state: Pathumthani

address: 113 Phahonyothin Road

department: National Center for Genetic Engineering and Biotechnology

country: Thailand

institute: National Science and Technology Development Agency

description: ex-vivo parasite from treated mice

data_processing:
Basecalls performed using Illumina RTA 1.18.42
The raw reads from fastq files were first filtered to remove matches to rRNA by BLAST alignment using ncbi-blast-2.2.25+ with parameters:evalue 1e-4, perc_identity 90, outfmt 6, num_threads 8. Pre-processing was performed by trimming low-quality base-calls (N) from reads, followed by removal of exact duplicates and reads of low overall quality using the prinseq-lite-0.20.3 program with parameters: trim_ns_left 2, trim_ns_right 2, min_qual_mean 20, derep 1
The pre-processed reads were mapped mapped to the P. berghei ANKA 2013-3-1 reference genome using Bowtie2 and TopHat2 programs with parameters: max-insertion-length 0, max-deletion-length 0, read-mismatches 10, read-gap-length 0, read-edit-dist 10, i 1, I 2432 , g 1, p 8.
Potential duplicate and inaccurately mapped reads were removed using samtools with parameters: sort, rmdup -s, calmd. Gene expression counts were determined from counts of sense-strand reads (read 1 only) mapping within (complete and partial overlap) annotated genes using a custom Perl script.
Genome_build: P. berghei ANKA 2013-3-1
Supplementary_files_format_and_content: Tab-delimited text files of read counts to annotated sense strand of gene models

organism: Plasmodium berghei

source_name: DHA-treated mixed-stage rep1

growth_protocol: 8-week old female ICR mice (approx. 30 g each) were infected with 1x10E7 P. berghei parasites each and 24 h post-infection, animals were injected i.p. with either drug or vehicle

extract_protocol:
White cells were separated from infected red cells using home-made CF-11 columns (approx. 4 ml packed resin). The parasitized red cells were then collected by centrifugation from the filtered blood. Parasites were liberated from host cells by treatment with 0.15% (w/v) saponin for 5 min on ice. The liberated parasites were washed three times with 1xPBS (137 mM NaCl, 8 mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4, pH 7.4) to remove host cell debris and drug. Total RNA was extracted from parasites using Trizol reagent (Invitrogen) following the manufacturers’ recommendations. Genomic DNA was removed from total RNA using a Turbo DNA freeTM kit (Ambion, Applied Biosystems).
0.7-4 μg of total RNA from each treatment condition was converted to a strand-specific RNA-seq sequencing library using a TruSeq Stranded mRNA LT Sample Prep kit following the manufacturers’ recommendations (Illumina). A different TruSeq adapter was used for each RNA-seq library to allow pooling of samples for Illumina sequencing on the same flow cell. The RNA-seq libraries were quantified by QuantIT dsDNA High Sensitivity kit (Invitrogen) and by qPCR using a library quantification kit (Kapa Biosystems). Libraries were pooled in equimolar ratios and applied to a MiSeq flow cell at 12 pM with 1% phiX174 control library (Illumina). Paired-end sequencing was performed on two MiSeq v2 2x150 bp flow cells according to the manufacturers’ recommendations (Illumina). The raw data from the MiSeq instrument were de-multiplexed and fastq files generated for each RNA-seq library.

treatment_protocol: Infected animals were injected with DHA (10 mg/kg) or an equal volume of vehicle control (30% DMSO in distilled water). Parasites were obtained by cardiac puncture 2 h post-injection of drug or vehicle and harvested in heparinized tubes

value: ANKA

tag: developmental stage

value: mixed

tag: treatment

value: 10 mg/kg DHA injected ip


title: Pf_ring_vehicle_rep2

description: In vitro cultured malaria parasite

data_processing:
Basecalls performed using Illumina RTA 1.18.42
The raw reads from fastq files were first filtered to remove matches to rRNA by BLAST alignment using ncbi-blast-2.2.25+ with parameters:evalue 1e-4, perc_identity 90, outfmt 6, num_threads 8. Pre-processing was performed by trimming low-quality base-calls (N) from reads, followed by removal of exact duplicates and reads of low overall quality using the prinseq-lite-0.20.3 program with parameters: trim_ns_left 2, trim_ns_right 2, min_qual_mean 20, derep 1
The pre-processed reads were mapped mapped to the P. falciparum 3D7 2013-3-1 reference genome using Bowtie2 and TopHat2 programs with parameters: max-insertion-length 0, max-deletion-length 0, read-mismatches 10, read-gap-length 0, read-edit-dist 10, i 1, I 1360, g 1, p 8.
Potential duplicate and inaccurately mapped reads were removed using samtools with parameters: sort, rmdup -s, calmd. Gene expression counts were determined from counts of sense-strand reads (read 1 only) mapping within (complete and partial overlap) annotated genes using a custom Perl script.
Genome_build: P. falciparum 3D7 2013-3-1
Supplementary_files_format_and_content: tab-delimited text files of read counts to annotated sense strand of gene models

organism: Plasmodium falciparum

source_name: Vehicle-treated ring parasites rep no.2

growth_protocol: P. falciparum K1 strain was cultured in vitro according to standard procedures (Trager & Jensen (1976) Science 193:673-5). Parasites cultures were synchronized to ring stages by two consecutive sorbitol treatment cycles (Lambros & Vanderberg (1979) J Parasitol. 65:418-20). 48 h after the second synchronization, the parasite culture was divided equally into new culture plates for drug treatment.

extract_protocol:
Parasites were harvested from culture and liberated from host cells by treatment with 0.15% (w/v) saponin for 5 min on ice. The liberated parasites were washed three times with 1xPBS (137 mM NaCl, 8 mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4, pH 7.4) to remove host cell debris and drug. Total RNA was extracted from parasites using Trizol reagent (Invitrogen) following the manufacturers’ recommendations. Genomic DNA was removed from total RNA using a Turbo DNA freeTM kit (Ambion, Applied Biosystems).
0.7-4 μg of total RNA from each treatment condition was converted to a strand-specific RNA-seq sequencing library using a TruSeq Stranded mRNA LT Sample Prep kit following the manufacturers’ recommendations (Illumina). A different TruSeq adapter was used for each RNA-seq library to allow pooling of samples for Illumina sequencing on the same flow cell. ). The RNA-seq libraries were quantified by QuantIT dsDNA High Sensitivity kit (Invitrogen) and by qPCR using a library quantification kit (Kapa Biosystems). Libraries were pooled in equimolar ratios and applied to a MiSeq flow cell at 12 pM with 1% phiX174 control library (Illumina). Paired-end sequencing was performed on two MiSeq v2 2x150 bp flow cells according to the manufacturers’ recommendations (Illumina). The raw data from the MiSeq instrument were de-multiplexed and fastq files generated for each RNA-seq library.

treatment_protocol: Parasites were treated with 500 nM Dihydroartemisinin (DHA) or vehicle control (0.1% DMSO), immediately, 18 or 36 h after the second synchronization, corresponding to ring, trophozoite or schizont populations, respectively. Parallel plates of parasites from the same synchronized culture were left untreated as controls. Parasites were harvested from culture after 1 h of treatment and processed immediately for RNA extraction.

value: ring

value: vehicle (0.1% DMSO)


title: Pb_vehicle_rep2

description: ex-vivo parasite from treated mice

source_name: Vehicle-treated mixed-stage rep2

value: vehicle (30% DMSO injected ip)


title: Pf_troph_vehicle_rep2

description: In vitro cultured malaria parasite

source_name: Vehicle-treated trophozoite parasites rep no.2

value: trophozoite


title: Pf_schiz_vehicle_rep2

description: In vitro cultured malaria parasite

source_name: Vehicle-treated schizont parasites rep no.2

value: schizont


title: Pf_schiz_DHA_rep1

description: In vitro cultured malaria parasite

source_name: DHA-treated schizont parasites rep no.1

value: 500 nM DHA


title: Pb_vehicle_rep1

description: ex-vivo parasite from treated mice

source_name: Vehicle-treated mixed-stage rep1


title: Pf_troph_vehicle_rep1

description: In vitro cultured malaria parasite

source_name: Vehicle-treated trophozoite parasites rep no.1


title: Pf_ring_DHA_rep1

description: In vitro cultured malaria parasite

source_name: DHA-treated ring parasites rep no.1


title: Pf_troph_DHA_rep1

description: In vitro cultured malaria parasite

source_name: DHA-treated trophozoite parasites rep no.1


title: Pf_ring_DHA_rep2

description: In vitro cultured malaria parasite

source_name: DHA-treated ring parasites rep no.2


title: TB_2


title: Pf_ring_vehicle_rep1

description: In vitro cultured malaria parasite

source_name: Vehicle-treated ring parasites rep no.1


title: Pf_schiz_vehicle_rep1

description: In vitro cultured malaria parasite

source_name: Vehicle-treated schizont parasites rep no.1


title: Pf_troph_DHA_rep2

description: In vitro cultured malaria parasite

source_name: DHA-treated trophozoite parasites rep no.2


title: Pf_schiz_un_rep2

description: In vitro cultured malaria parasite

source_name: Untreated schizont parasites rep no.2


title: TB_1


title: Pf_troph_un_rep2

description: In vitro cultured malaria parasite

source_name: Untreated trophozoite parasites rep no.2


title: Pf_troph_un_rep1

description: In vitro cultured malaria parasite

source_name: Untreated trophozoite parasites rep no.1


title: Pf_ring_un_rep2

description: In vitro cultured malaria parasite

source_name: Untreated ring parasites rep no.2


title: Pf_schiz_un_rep1

description: In vitro cultured malaria parasite

source_name: Untreated schizont parasites rep no.1


title: Pf_schiz_DHA_rep2

description: In vitro cultured malaria parasite

source_name: DHA-treated schizont parasites rep no.2


title: Pf_ring_un_rep1

description: In vitro cultured malaria parasite

source_name: Untreated ring parasites rep no.1


title: RP_ZT4_1; ZT4, ribosome footprint, rep1

source_name: RP_ZT4_1; ZT4, ribosome footprint

value: liver


title: Pb_DHA_rep2

description: ex-vivo parasite from treated mice

source_name: DHA-treated mixed-stage rep2


title: AM13_10MPa_rep1

status: Public on Oct 13 2015

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

institute: TAGC INSERM U1090

data_processing:
The obtained reads were mapped to the D. hydrothermalis AM13T genome sequences (MicroScope accession number: DESAMv2_DESAMv2) using the Life Technologies Bioscope™ Genomic Analysis Software.
Genome_build: Desulfovibrio hydrothermalis AM13T (MicroScope accession number: DESAMv2_DESAMv2; ASM33102v1)
Supplementary_files_format_and_content: bedgraph coverage files were obtained using the UCSC genomeCoverageBed tools.

organism: Maridesulfovibrio hydrothermalis AM13 = DSM 14728

growth_protocol: Desulfovibrio hydrothermalis AM13T was grown anaerobically at the optimal temperature of 30 °C, under either 0.1 MPa (atmospheric pressure, low hydrostatic pressure), 26 or 10 MPa (high hydrostatic pressures), for 40 h in 20 mL of the medium described by Alazard et al. (2003). These cultures were used to inoculate fresh medium (100 mL) for RNA preparation and biochemical experiments at each corresponding hydrostatic pressure. These large-scale cultures were inoculated at a 1:20 ratio and the cells were grown until the OD600 nm = 0.6. All cultures were carried out in duplicate. Cells were treated as indicated below for either RNA preparation or intracellular metabolites extractions.

extract_protocol:
For mRNA enrichment, 23S and 16S rRNA were depleted using a Ribo-ZeroTM Magnetic Kit (Gram-Negative Bacteria by Epicentre, Illumina®, Cat. No. MRZGN126), according to the manufacturer’s instructions. Briefly, 5 µg of total RNA of each sample was treated by Ribo-Zero rRNA Removal Solution; rRNA was then removed using magnetic beads from Ribo-ZeroTM Magnetic Core Kit (Cat. No. MRZ116C). The ribo-depleted samples were purified by ethanol precipitation and eluted in 13 µl of RNase Free water. The concentration of resulted RNA was determined using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA), between 8-16 % of the input RNA was recovered after purification. RNA integrity was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico chip Kit.
Strand-specific libraries constructions were carried out using the SOLiD Total RNA-Seq Kit (Life Technologies) as describes in the manufacturer’s instructions. About 0.35 µg of ribo-depleted RNA was subjected to the enzymatic mRNA fragmentation using RNaseIII from the SOLiD Total RNA-Seq Kit. The fragmented RNA was then concentrated using the Invitrogen RiboMinusTM Concentration Module according to the manufacturer’s protocol. The quantity and quality of resulted RNA were assessed using a Qubit Fluorometer (Life Technologies) and Agilent 2100 Bioanalyzer with the RNA 6000 Pico chip Kit.  Fragmented RNA (0.1 µg) was subjected to cDNA synthesis. After hybridization, ligation of the SOLiDTM Adaptator, RNA was reversed transcripted at 42 °C for 30 min. The resulted cDNA was purified using the Agencourt AMPure XP Reagent performing two rounds. The eluted cDNA was then amplified by PCR reaction (10 cycles: 95 °C 5 min, 95 °C 30 sec, 62 °C 30 sec, 72 °C 30 sec, 72 °C 7 min) using a SOLiDTM 5’ primer and a SOLiDTM 3’ primer specific for each sample (barcode allowing us to pool the samples for sequencing), the resulted product was then purified using the same technique used for the cDNA purification (Agencourt AMPure XP Reagent). The quality and integrity of this DNA was confirmed using a NanoDrop ND-1000 Spectrophotometer and Agilent 2100 Bioanalyzer with DNA 1000 Kit. cDNA libraries were constructed from two independent experiments, for each pressure growth condition. The libraries were amplified with the SOLiD EZ Bead Amplifier, before that the samples were prepared using the SOLiD EZ Bead Emulsifier that allow mixing the aqueous phase containing the SOLiD EZ Bead, library template and primers with the oil phase (Oil Master Mix). The preparation was then amplified by PCR reaction (amplifier software scale E80). After the run was complete, the samples were purified using the SOLiD EZ Bead Enricher according to the manufacturer’s instructions. The P2-enriched beads were then concentrated and the 3’ends were modified as described in the manufacturer’s protocol. Paired-end stranded RNA-Seq with ribo-depleted total RNA was performed using a 5500xl SOLiD high-throughput sequencer (Life Technologies).

treatment_protocol: For total RNA isolation, cells from each hydrostatic pressure condition were harvested by centrifugation at 6000 xg for 20 min at 4 °C and washed once with 20 mL of 0.1 M Tris-HCl 0.15 M NaCl buffer (pH 7.6). The pellets were rinsed three times with 10 mM Tris-HCl (pH 8.0) RNAse-free buffer and finally resuspended in 200 μL of 10 mM Tris-HCl, 1 mM EDTA (pH 8.0) RNase-free buffer. Total RNA was isolated by using the High Pure RNA Isolation Kit (Roche Diagnostics) according to the manufacturer’s instructions with an extra DNase I digestion step in order to eliminate contaminating DNA. RNAs quality was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNAs were quantified to the spectrophotometer at 260 nm (Nanodrop 2000c ThermoScientific). RNAs were prepared from two independent cultures, for each pressure condition (two RNA pools for each condition)

tag: hydrostatic pressure

value: 10 Mpa (high hydrostatic pressures)


title: AM13_26MPa_rep2

value: 26 Mpa (high hydrostatic pressures)


title: AM13_10MPa_rep2


title: AM13_26MPa_rep1


title: AM13_0.1MPa_rep2

value: 0.1 MPa (atmospheric pressure, low hydrostatic pressure)


title: LHSAR_HOXB13_FOXA1_rep2

status: Public on Oct 12 2015

city: Boston

first: Fugen

last: Li

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
Sequence reads were aligned to the hg19 genome using STAR
Gene expression levels were called using Cufflinks
Differential expressed genes were called using LIMMA
Genome_build: hg19
Supplementary_files_format_and_content: FPKM expression level table

growth_protocol: Cells were grown in PrEGM medium.  Cells were passaged every 3-4 days.

extract_protocol:
Extraction was performed using a Qiagen RNA preparation kit per standard protocol
Libraries were constructed using purified total RNA as above.  Polyadenylated mRNA was purified, and the library for RNAseq was constructed using the Truseq v2 kit (Illumina).  Quality control was assessed by BioA analysis (Agilent Technologies) prior to library construction and again prior to sequencing

treatment_protocol: Cells were plated 1 day prior to infection with appropriate lentivirus and medium was replaced 24 hours later with medium with R1881.   Cells were harvested 48 hours after addition of R1881.

value: LHSAR

value: LHSAR overexpressed with HOXB13 and FOXA1


title: LHSAR_HOXB13_FOXA1_rep3


title: LHSAR_LacZ_rep2

value: LHSAR overexpressed with LacZ


title: LHSAR_HOXB13_rep2

value: LHSAR overexpressed with HOXB13


title: AR Chip-seq_LHSAR_HOXB13

data_processing:
Basecalls performed using CASAVA version 1.7
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.7 with default settings. Only uniquely aligned tags were retained
Peaks were called using MACS2 with the following settings: Q value <= 0.01, shiftsize = 100 for AR ChIP
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were converted from wig files generated using unique reads from MACS2

source_name: LHSAR overexpressed HOXB13 cells

growth_protocol: LHSAR cells were grown in PrEGM medium.  LNCaP cells were grown in RPMI supplemented with 10% fetal calf serum.  Cells were passaged every 3-4 days.

extract_protocol:
Fresh-frozen radical prostatectomy specimens were chosen from the Dana-Farber Cancer Institute/Harvard Cancer Center SPORE biobank and database. A genitourinary pathologist (M.L.) reviewed HE stained slides from each case and isolated areas enriched >70% for prostate tumor tissue or normal prostate epithelium. Using a 2mm2 core needle, approximately four cores were extracted from the areas circled on the slide. The frozen cores were pulverized using the Covaris CryoPrep system (Covaris, Woburn, MA). The tissue was then fixed using 1% formaldehyde buffer for 18 minutes and quenched with glycerine. Chromatin was sheared to 300–500 base pairs using the Covaris E220 ultra-sonicator. The resulting chromatin was incubated overnight with 6ug antibody to AR (N-20, Santa Cruz Biotechnology, Dallas, TX) bound to protein A and protein G beads (Life Technologies, Carlsbad, CA). A fraction of the sample was not exposed to antibody to be used as control (input). The samples were de-crosslinked, treated with RNase and proteinase K, and DNA was extracted. The samples were then re-sheared to 50-100 base pairs using the Covaris ultra-sonicator, and concentrations of the ChIP DNA were quantified by Qubit Fluorometer (Life Technologies).  For cell line experiments, cells were fixed with 1 % formaldehyde for 10 minutes and quenched with glycine.  Isolated chromatin from 1 x 10^7 fixed cells was sonicated to 200-300 bp and subjected to immunoprecipitation with the appropriate antibodies as described above.
DNA was amplified using ThruPLEX-FD kit (Rubicon Genomics).

treatment_protocol: LHSAR cells were plated 1 day prior to infection with appropriate lentivirus and medium was replaced 24 hours later with medium with R1881.   Cells were harvested 48 hours after addition of R1881.

tag: antibodies

value: AR


title: AR Chip-seq_LHSAR_LacZ_1

source_name: LHSAR LacZ cells


title: AM13_0.1MPa_rep1


title: LHSAR_HOXB13_rep3


title: HOXB13 Chip-seq_LNCaP

source_name: LNCaP cells

value: LNCaP


title: AR Chip-seq_LHSAR_FOXA1_HOXB13_2

source_name: LHSAR overexpressed HOXB13 and FOXA1 cells


title: AR Chip-seq_LHSAR_FOXA1_HOXB13_1


title: LHSAR_LacZ_rep3


title: FOXA1 Chip-seq_tumor

source_name: Patient prostate tumor tissue

value: prostate tumor


title: LHSAR_FOXA1_rep2

value: LHSAR overexpressed with FOXA1


title: Control_4

city: Berkeley

first: Abraham

last: Morales-Cruz

state: California

address: 1 Cyclotron Road

institute: Joint Genome Institute

description:
Sample 16
Vitis vinifera cv. Sémillon berries
Berries naturally infected with B. cinerea, samples could include other environmental organisms.

data_processing:
Quality trimming of raw reads was done with Sickle v.1.210 with a threshold of 20 (Q>20).
Quality filtering was done with Scythe v.0.991 with a prior of 0.4
A non-redundant B. cinerea mapping reference was obtained by combining B05.10 transcripts (http://www.broadinstitute.org/annotation/genome/botrytis_cinerea) with BcDW1 (http://www.ncbi.nlm.nih.gov/nuccore/AORW00000000.1) transcript using CD-HIT (v. 4.5.4)
Botrytis transcripts were combined to the predicted transcriptome of Vitis vinifera cv. PN40024 (http://www.genoscope.cns.fr/externe/Download/Projets/Projet_ML/data/12X/annotation/)
Bowtie2 v.2.1.0  was used to map the processed reads to the combined references with the following options: -q --end-to-end --sensitive --no-unal -p20.
Read counts were extracted from the bowtie2 alignments using the script sam2counts.py v.0.91
Supplementary_files_format_and_content: raw_counts_noble_rot.txt: tab delimited text file, raw read counts determined by mapping the sequencing reads

organism: Vitis vinifera

source_name: Berries

extract_protocol:
Total RNA was extracted using a CTAB based protocol with a chloroform denaturation step. RNA was cleaned with RNeasy kit (Qiagen, US) including the DNAse treatment on column.
Illumina TruSeq RNA Sample Prep Kit v2 protocol

tag: host cultivar

value: Semillon

tag: host tissue

value: berries

tag: host stage

value: post-veraison (ripe)

tag: enviromental conditions

value: Field

tag: infection

value: Control

tag: stage of noble rot


title: Control_3

description:
Sample 15
Vitis vinifera cv. Sémillon berries
Berries naturally infected with B. cinerea, samples could include other environmental organisms.


title: AR Chip-seq_LHSAR_LacZ_2

tag: cell line


title: AR Chip-seq_LHSAR_FOXA1

source_name: LHSAR overexpressed FOXA1 cells


title: PLCb1b17_S18

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

description: rRNA-depleted total RNA

data_processing:
Illumina Casava1.8 software was used for basecalling. All 76 nt reads use phred33 quality scores.
Sequence reads were mapped to the transcriptome, defined by annotation based on the UCSC mm10 genes.gtf but with mitochondrial RNAs added, and associated bowtie2 index provided by Illumina iGenomes (incorporating the additional mitochondrial RNAs), using tophat v2.0.10 (fr-firststrand)
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the supplied gtf, based on UCSC mm10 genes.gtf but with mitochondrial RNAs added.
htseq-count data allows each user maximum flexibility in performing sample (library) depth normalization and differential gene expression using software such as DESeq or edgeR.
Additionally, we used Cufflinks v2.1 to calculate FPKM for each gene entry in each library.  However, this was merely done for later graph display.  Actual calculations of differential gene expression used htseq-count data as input to DESeq.
Genome_build: mm10
Supplementary_files_format_and_content: single tab-delimited text files include htseq-count values for each gene, or FPKM values for each gene.

source_name: heart, biventricle_PLCb1b

extract_protocol:
Hearts were removed and ventricles were flash frozen in liquid nitrogen.  RNA was harvested using Trizol reagent.
Ribosomal RNA depletion along with RNA fragmentation and conversion to paired-end, strand-specific Illumina sequencing libraries were performed with Illumina TruSeq preparation kits for strand-specific, paired-end RNA-Seq.

tag: gender

value: male

value: heart, biventricle

tag: age

value: 17 weeks


title: PLCb1b16_S17

description: rRNA-depleted total RNA

tag: strain

tag: tissue


title: HOXB13 Chip-seq_tumor


title: Control_2

description:
Sample 14
Vitis vinifera cv. Sémillon berries
Berries naturally infected with B. cinerea, samples could include other environmental organisms.


title: Control_1

description:
Sample 13
Vitis vinifera cv. Sémillon berries
Berries naturally infected with B. cinerea, samples could include other environmental organisms.


title: PLCb1b6_S14

description: rRNA-depleted total RNA


title: PLCb1b8_S15

description: rRNA-depleted total RNA


title: PLCb1b10_S16

description: rRNA-depleted total RNA


title: PLCb1a21_S12

description: rRNA-depleted total RNA

source_name: heart, biventricle_PLCb1a


title: PLCb1a14_S11

description: rRNA-depleted total RNA


title: PLCb1a11_S9

description: rRNA-depleted total RNA


title: LHSAR_FOXA1_rep3


title: PLCb1a13_S10

description: rRNA-depleted total RNA


title: blank36_S6

description: rRNA-depleted total RNA

source_name: heart, biventricle_blank


title: PLCb1a9_S8

description: rRNA-depleted total RNA


title: blank30_S2

description: rRNA-depleted total RNA


title: Term sample 6

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description:
G2
Patients at any gestational age who were delivering by Cesarean section consented to the collection of 10 mL of AF after the uterine incision, and prior to rupture of the amniotic sac.

data_processing:
The raw sequenced reads were aligned from FASTQ files to the human genome build GRCh37/hg19 and the UCSC reference transcriptome (http://tophat.cbcb.umd.edu/igenomes.shtml) using TopHat 2.0.9 and Bowtie2 with default parameters to identify both known and novel exons and junctions. Samples were further processed via Trimmed Mean normalization. For differential expression analyses, an analysis of variance (ANOVA) was performed on AF RNA samples from each of the gestational stages, for genes with an RPKM>1 in at least one sample. Comparison of specific preterm morbidities was performed using an moderated empirical Bayes t-test for gene expression and the percent spliced in method in AltAnalyze (http://www.altanalyze.org).
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes RPKM values

source_name: Amniotic Fluid

extract_protocol:
All AF was immediately placed in AssayAssure tubes with standardized buffer. Samples were stored at -80˚C until they were ready to be processed for RNA isolation. Approximately 6 mL of AF was used from each patient, and cell-free RNA was isolated from the supernatant of the fluid using the QIAamp Circulating Nucleic Acid Kit (QIAGEN), as has been previously described (doi: 10.1002/pd.2732).
RNA-sequencing was performed by the Cincinnati Children’s Hospital Sequencing Core on an Illumina HiSeq, with an average read-depth of 10-20 million reads per sample for 50nt unstranded single-end reads.

tag: gestational age

value: 39-40 weeks

tag: gavage feeding

value: FALSE

tag: respiratory assistance

tag: fetal gender


title: blank32_S3

description: rRNA-depleted total RNA


title: Term sample 4

description:
T4
Patients at any gestational age who were delivering by Cesarean section consented to the collection of 10 mL of AF after the uterine incision, and prior to rupture of the amniotic sac.

value: female


title: Term sample 2

description:
F2
Patients at any gestational age who were delivering by Cesarean section consented to the collection of 10 mL of AF after the uterine incision, and prior to rupture of the amniotic sac.


title: Term sample 5

description:
1-5
Patients at any gestational age who were delivering by Cesarean section consented to the collection of 10 mL of AF after the uterine incision, and prior to rupture of the amniotic sac.


title: blank26_S1

description: rRNA-depleted total RNA


title: Term sample 3

description:
T3
Patients at any gestational age who were delivering by Cesarean section consented to the collection of 10 mL of AF after the uterine incision, and prior to rupture of the amniotic sac.


title: Stage3_4

description:
Sample 12
Vitis vinifera cv. Sémillon berries infected with Botrytis cinerea
Berries naturally infected with B. cinerea, samples could include other environmental organisms.

organism:
Vitis vinifera
Botrytis cinerea

value: Botrytis cinerea


title: Term sample 1

description:
E2
Patients at any gestational age who were delivering by Cesarean section consented to the collection of 10 mL of AF after the uterine incision, and prior to rupture of the amniotic sac.


title: PLCb1b4_S13

description: rRNA-depleted total RNA


title: Late Preterm sample 5

description:
PT9
Patients at any gestational age who were delivering by Cesarean section consented to the collection of 10 mL of AF after the uterine incision, and prior to rupture of the amniotic sac.

value: 36.6 weeks

value: TRUE


title: Late Preterm sample 4

description:
PT8
Patients at any gestational age who were delivering by Cesarean section consented to the collection of 10 mL of AF after the uterine incision, and prior to rupture of the amniotic sac.

value: 34 weeks


title: Late Preterm sample 1

description:
PT5
Patients at any gestational age who were delivering by Cesarean section consented to the collection of 10 mL of AF after the uterine incision, and prior to rupture of the amniotic sac.

value: 35 weeks


title: Late Preterm sample 3

description:
PT7
Patients at any gestational age who were delivering by Cesarean section consented to the collection of 10 mL of AF after the uterine incision, and prior to rupture of the amniotic sac.

value: 35.2 weeks


title: Stage3_2

description:
Sample 10
Vitis vinifera cv. Sémillon berries infected with Botrytis cinerea
Berries naturally infected with B. cinerea, samples could include other environmental organisms.

value: Semillon


title: Stage3_1

description:
Sample 9
Vitis vinifera cv. Sémillon berries infected with Botrytis cinerea
Berries naturally infected with B. cinerea, samples could include other environmental organisms.

value: berries


title: blank33_S4

description: rRNA-depleted total RNA


title: blank34_S5

description: rRNA-depleted total RNA


title: PLCb1a7_S7

description: rRNA-depleted total RNA


title: Stage2_3

description:
Sample 7
Vitis vinifera cv. Sémillon berries infected with Botrytis cinerea
Berries naturally infected with B. cinerea, samples could include other environmental organisms.

value: post-veraison (ripe)


title: Prenatal sample 3

description:
PN3
Patients undergoing amniocentesis for prenatal diagnosis purposes consented to the acquisition of 10 mL of additional fluid to be banked and analyzed for our study.

value: 24.3 weeks

value: UNK


title: Stage2_2

description:
Sample 6
Vitis vinifera cv. Sémillon berries infected with Botrytis cinerea
Berries naturally infected with B. cinerea, samples could include other environmental organisms.

value: Field


title: Late Preterm sample 6

description:
PT10
Patients at any gestational age who were delivering by Cesarean section consented to the collection of 10 mL of AF after the uterine incision, and prior to rupture of the amniotic sac.

value: 35.6 weeks

value: male


title: Prenatal sample 1

description:
PN1
Patients undergoing amniocentesis for prenatal diagnosis purposes consented to the acquisition of 10 mL of additional fluid to be banked and analyzed for our study.

value: 19.3 weeks


title: Stage1_4

description:
Sample 4
Vitis vinifera cv. Sémillon berries infected with Botrytis cinerea
Berries naturally infected with B. cinerea, samples could include other environmental organisms.


title: Stage3_3

description:
Sample 11
Vitis vinifera cv. Sémillon berries infected with Botrytis cinerea
Berries naturally infected with B. cinerea, samples could include other environmental organisms.


title: Stage1_2

description:
Sample 2
Vitis vinifera cv. Sémillon berries infected with Botrytis cinerea
Berries naturally infected with B. cinerea, samples could include other environmental organisms.


title: Patient AR prostate tumor tissue 19

source_name: Patient AR prostate tumor tissue

extract_protocol:
Fresh-frozen radical prostatectomy specimens were chosen from the Dana-Farber Cancer Institute/Harvard Cancer Center SPORE biobank and database. A genitourinary pathologist (M.L.) reviewed HE stained slides from each case and isolated areas enriched >70% for prostate tumor tissue or normal prostate epithelium. Using a 2mm2 core needle, approximately four cores were extracted from the areas circled on the slide. The frozen cores were pulverized using the Covaris CryoPrep system (Covaris, Woburn, MA). The tissue was then fixed using 1% formaldehyde buffer for 18 minutes and quenched with glycerine. Chromatin was sheared to 300–500 base pairs using the Covaris E220 ultra-sonicator. The resulting chromatin was incubated overnight with 6ug antibody to AR (N-20, Santa Cruz Biotechnology, Dallas, TX) bound to protein A and protein G beads (Life Technologies, Carlsbad, CA). A fraction of the sample was not exposed to antibody to be used as control (input). The samples were de-crosslinked, treated with RNase and proteinase K, and DNA was extracted. The samples were then re-sheared to 50-100 base pairs using the Covaris ultra-sonicator, and concentrations of the ChIP DNA were quantified by Qubit Fluorometer (Life Technologies).
DNA was amplified using ThruPLEX-FD kit (Rubicon Genomics).
ChIP-seq libraries were sequenced using Hi-seq 2000 or Miseq (Illumina).

value: prostate tumor tissue

tag: chip antibody

value: AR


title: Patient AR prostate tumor tissue 18


title: Patient AR prostate tumor tissue 20


title: Patient prostate normal tissue 15

source_name: Patient prostate normal tissue

value: prostate normal tissue


title: Patient AR prostate tumor tissue 16


title: Patient AR prostate tumor tissue 13


title: Patient AR prostate tumor tissue 17


title: Patient AR prostate tumor tissue 14


title: Patient AR prostate tumor tissue 12


title: Patient prostate normal tissue 11


title: Patient AR prostate tumor tissue 9


title: Patient AR prostate tumor tissue 10


title: Stage2_4

description:
Sample 8
Vitis vinifera cv. Sémillon berries infected with Botrytis cinerea
Berries naturally infected with B. cinerea, samples could include other environmental organisms.

value: Botrytis cinerea


title: Prenatal sample 4

description:
PN4
Patients undergoing amniocentesis for prenatal diagnosis purposes consented to the acquisition of 10 mL of additional fluid to be banked and analyzed for our study.

value: 23 weeks


title: Patient prostate normal tissue 8


title: Patient AR prostate tumor tissue 6


title: Prenatal sample 2

description:
PN2
Patients undergoing amniocentesis for prenatal diagnosis purposes consented to the acquisition of 10 mL of additional fluid to be banked and analyzed for our study.

value: 18.5 weeks


title: Stage2_1

description:
Sample 5
Vitis vinifera cv. Sémillon berries infected with Botrytis cinerea
Berries naturally infected with B. cinerea, samples could include other environmental organisms.


title: Patient prostate normal tissue 7


title: Patient prostate normal tissue 5


title: Patient AR prostate tumor tissue 4


title: Patient prostate normal tissue 1


title: Patient AR prostate tumor tissue 2


title: Stage1_3

description:
Sample 3
Vitis vinifera cv. Sémillon berries infected with Botrytis cinerea
Berries naturally infected with B. cinerea, samples could include other environmental organisms.


title: Stage1_1

description:
Sample 1
Vitis vinifera cv. Sémillon berries infected with Botrytis cinerea
Berries naturally infected with B. cinerea, samples could include other environmental organisms.


title: Patient prostate normal tissue 3


title: P9_sample3

city: Los Angeles

first: Ksenia

last: Gnedeva

state: CA

address: 1501 San Pablo St

department: USC Caruso Department of Otolaryngology – Head and Neck Surgery

institute: USC

data_processing:
RNA-seq flow in Partek software was used to calculate Reads Per Kilobase of exon per Megabase of library size (RPKM) per each gene per sample
RNA-seq flow in Partek software was used to compare gene expression changes between samples
RNA-seq flow in Partek software was used to identify differentially expressed transcription factors
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for all Samples. Only the genes with RPKM greater than 5 were scored as expressed and included into the output file.

source_name: sensory epithelium of the utricle

extract_protocol:
Utricles were removed, sensory epithelia were isolated, and RNA was harvested using Qiagen RNeasy Micro kit.
RNA libraries were prepared from 250-400 ng of total RNA using standard Illumina protocols

value: Swiss Webster

value: postnatal day 9

value: sensory epithelium of the utricle


title: Late Preterm sample 2

description:
PT6
Patients at any gestational age who were delivering by Cesarean section consented to the collection of 10 mL of AF after the uterine incision, and prior to rupture of the amniotic sac.

value: 34.5 weeks

value: TRUE

value: FALSE


title: P0_sample2

value: postnatal day 0


title: P0_sample1


title: P9_sample2


title: E17_sample2

value: embryonic day 17.5


title: E17_sample3


title: E17_sample1


title: P0_sample3


title: 140226_H3K4me2_28

city: cambridge

first: oren

last: ram

state: MASSACHUSETTS

address: 415 Main Street

department: epigenomics

institute: Broad institute

description:
83_GACCTAAC
antibody: Millipore 07-030

data_processing:
Extracting single cell by barcodes. "Forward_Adapters.xlsx" includes a list of all 1152 barcoded adapters
alignment with Bowtie
filtering duplicates
find mESC clusters using ChIP seq signatures
aggregating mESC clusters
Peak calling
Genome_build: mm9
Supplementary_files_format_and_content: bed

growth_protocol:
mESCs were grown using Knockout DMEM: ~410mL (Gibco)  15% Fetal Bovine serum: 75mL (lot# F12101121)  1% Pen/Strep: 5mL (Gibco)  1% Non-essential amino acids: 5mL (Gibco)  1% Glutamax: 5mL (Gibco)  .01% LIF: 50ul (Millipore: ESG1107)  .0004% BME: 2ul    mEFs were grown using Knockout DMEM: ~410mL (Gibco)  15% Fetal Bovine serum: 75mL (lot# F12101121)  1% Pen/Strep: 5mL (Gibco)  1% Non-essential amino acids: 5mL (Gibco)  1% Glutamax: 5mL (Gibco)
The mEFs were grown:using Knockout DMEM: ~410mL (Gibco)  15% Fetal Bovine serum: 75mL (lot# F12101121)  1% Pen/Strep: 5mL (Gibco)  1% Non-essential amino acids: 5mL (Gibco)  1% Glutamax: 5mL (Gibco)
EML were grown as in Hannah H. Chang et. al."Transcriptome-wide noise controls lineage choice in  mammalian progenitor cells"

extract_protocol:
The cells were trypsinized and washed prior to encapsulation
To minimize the abundance of barcode adaptors concatemers we use PacI restriction enzyme (R0547L, NEB, USA) immediately after ChIP washing steps and while the chromatin is still bound to the ChIP beads. PacI digest in between bound concatemers and in the middle of each adapter to form 30bp DNA fragments that can be easily filter out using simple size selection. Next, we elute the chromatin by adding 2X elution buffer, digesting RNA contaminates with Rnase (11119915001, Roche Diagnostics, USA) and removing the nucleosomes with ProtenaseK (P8102S, NEB, USA). To purify the DNA we use AMPure XP beads (A63880, Beckman Coulter, USA) and follow with 14 rounds of Single-Cell-PCR to amplify the labeled DNA. To reduce unspecific Illumina adapter ligation we first dephosphorylate all 5’ ends with Antarctic Phosphatase (M0289L, NEB, USA) and then use BciVi enzyme (R0596L, NEB, USA) to specifically cleave the labeled DNA, leaving an A overhang at the 5’ end of all DNA fragments with single cell adapters. After ligating Illumina adapters, we digest concatemers again using PacI and perform 14 additional rounds of Illumina-PCR (PfuUltra II Hotstart PCR Master Mix, 600850, Agilent Technologies, USA) before sequencing the library of reads.
Size selected for 200bp-1000bp

tag: cells pointed by barcodes

tag: mescs strain

value: V6.5 strain

tag: mefs source

tag: eml source


title: 140226_H3K4me2_32

description:
87_GATATCCA
antibody: Millipore 07-030


title: 140226_H3K4me2_34

description:
89_AGGTCGCA
antibody: Millipore 07-030


title: 140226_H3K4me2_33

description:
88_TTATATCT
antibody: Millipore 07-030


title: 140226_H3K4me2_31

description:
86_CTGTGGCG
antibody: Millipore 07-030


title: 140226_H3K4me2_26

description:
81_ACTGTATC
antibody: Millipore 07-030


title: 140226_H3K4me2_25

description:
80_TTGTCTAT
antibody: Millipore 07-030


title: 140226_H3K4me2_29

description:
84_TTAATCAG
antibody: Millipore 07-030


title: 140226_H3K4me2_35

description:
91_ACCAACTG
antibody: Millipore 07-030


title: 140226_H3K4me2_27

description:
82_CTGCGGAT
antibody: Millipore 07-030


title: 140226_H3K4me2_36

description:
92_TGCAAGTA
antibody: Millipore 07-030


title: 140226_H3K4me2_23

description:
78_CTATGCGT
antibody: Millipore 07-030


title: 140226_H3K4me2_37

description:
96_TGTAACTC
antibody: Millipore 07-030


title: 140226_H3K4me2_22

description:
77_ACAGTTGA
antibody: Millipore 07-030


title: 140226_H3K4me2_21

description:
76_TGTAATCA
antibody: Millipore 07-030


title: 140226_H3K4me2_19

description:
74_CTAACTCG
antibody: Millipore 07-030


title: 140226_H3K4me2_18

description:
72_TCTGCAAG
antibody: Millipore 07-030


title: 140226_H3K4me2_17

description:
70_CAATAGTC
antibody: Millipore 07-030


title: P9_sample1


title: 140226_H3K4me2_20

description:
75_GAAGGAAG
antibody: Millipore 07-030


title: 140226_H3K4me2_15

description:
68_TCGCTAGA
antibody: Millipore 07-030


title: 140226_H3K4me2_13

description:
66_ATTCCTCT
antibody: Millipore 07-030


title: 140226_H3K4me2_16

description:
69_ATTATCAA
antibody: Millipore 07-030


title: 140226_H3K4me2_11

description:
63_GCCTAGCC
antibody: Millipore 07-030


title: 140226_H3K4me2_10

description:
62_CAGCGGTA
antibody: Millipore 07-030


title: 140226_H3K4me2_12

description:
65_AGGTAAGG
antibody: Millipore 07-030


title: 140226_H3K4me2_9

description:
61_ACTAAGAC
antibody: Millipore 07-030


title: 140226_H3K4me2_24

description:
79_GACCGTTG
antibody: Millipore 07-030


title: 140226_H3K4me2_7

description:
59_GCCGTCGA
antibody: Millipore 07-030


title: 140226_H3K4me2_3

description:
55_GACCAGGA
antibody: Millipore 07-030


title: 140226_H3K4me2_4

description:
56_TGCTGCTG
antibody: Millipore 07-030


title: 140226_H3K4me2_5

description:
57_ACAGGTAT
antibody: Millipore 07-030


title: 140226_H3K4me2_1

description:
52_TATCTGCC
antibody: Millipore 07-030


title: 20130911_H3K4me2_5

description:
40_CCAGAGCT
antibody: Millipore 07-030


title: 20130911_H3K4me2_3

description:
38_CAGCAAGG
antibody: Millipore 07-030


title: 20130620_H3K4me2_12

description:
30_ATAGCGTC
antibody: Millipore 07-030


title: 20130620_H3K4me2_11

description:
29_TCGCCTTG
antibody: Millipore 07-030


title: 20130911_H3K4me2_4

description:
39_TCCAGCAA
antibody: Millipore 07-030


title: 20130911_H3K4me2_2

description:
35_TTACGCAC
antibody: Millipore 07-030


title: 20130620_H3K4me2_13

description:
32_ATTCTAGG
antibody: Millipore 07-030


title: 140226_H3K4me2_30

description:
85_AGCATGGA
antibody: Millipore 07-030


title: 140226_H3K4me2_6

description:
58_CAACTCTC
antibody: Millipore 07-030


title: 20130620_H3K4me2_10

description:
28_CCTATGCC
antibody: Millipore 07-030


title: 20130620_H3K4me2_9

description:
27_GACAGTAA
antibody: Millipore 07-030


title: 20130911_H3K4me2_1

description:
33_CGTTACCA
antibody: Millipore 07-030


title: 20130620_H3K4me2_5

description:
22_ATTATGTT
antibody: Millipore 07-030


title: 20130620_H3K4me2_6

description:
23_CCTACCAT
antibody: Millipore 07-030


title: 20130620_H3K4me2_3

description:
20_CAGGAGCC
antibody: Millipore 07-030


title: 20130620_H3K4me2_7

description:
24_TACTTAGC
antibody: Millipore 07-030


title: 20130620_H3K4me2_8

description:
26_AGGATCTA
antibody: Millipore 07-030


title: 140226_H3K4me2_2

description:
54_CGCCTTCC
antibody: Millipore 07-030


title: 20130620_H3K4me2_4

description:
21_TGTCGGAT
antibody: Millipore 07-030


title: 140226_H3K4me2_14

description:
67_GTAACATC
antibody: Millipore 07-030


title: 20130620_H3K4me2_1

description:
17_GCACACGA
antibody: Millipore 07-030


title: 20130423_H3K4me2_19

description:
44_CCTTCGCA
antibody: Millipore 07-030


title: 20130423_H3K4me2_17

description:
41_TCCTTGGT
antibody: Millipore 07-030


title: 20130423_H3K4me2_18

description:
42_AGGTTATC
antibody: Millipore 07-030


title: 20130423_H3K4me2_15

description:
39_TCCAGCAA
antibody: Millipore 07-030


title: 20130423_H3K4me2_14

description:
38_CAGCAAGG
antibody: Millipore 07-030


title: 20130423_H3K4me2_12

description:
36_TTGAATAG
antibody: Millipore 07-030


title: 20130423_H3K4me2_13

description:
37_AAGACACT
antibody: Millipore 07-030


title: 20130423_H3K4me2_5

description:
29_TCGCCTTG
antibody: Millipore 07-030


title: 20130423_H3K4me2_6

description:
30_ATAGCGTC
antibody: Millipore 07-030


title: 20130423_H3K4me2_9

description:
33_CGTTACCA
antibody: Millipore 07-030


title: 20130423_H3K4me2_16

description:
40_CCAGAGCT
antibody: Millipore 07-030


title: 20130423_H3K4me2_10

description:
34_GTCTGATG
antibody: Millipore 07-030


title: 20130423_H3K4me2_11

description:
35_TTACGCAC
antibody: Millipore 07-030


title: 20130423_H3K4me2_7

description:
31_GTCGCCTT
antibody: Millipore 07-030


title: 20130423_H3K4me2_3

description:
27_GACAGTAA
antibody: Millipore 07-030


title: 20130423_H3K4me2_2

description:
26_AGGATCTA
antibody: Millipore 07-030


title: 140226_H3K4me2_8

description:
60_TAAGCACA
antibody: Millipore 07-030


title: 20130423_H3K4me2_1

description:
25_GAAGAAGT
antibody: Millipore 07-030


title: 20130423_H3K4me2_8

description:
32_ATTCTAGG
antibody: Millipore 07-030


title: 20130306_H3K4me2_7

description:
24_TACTTAGC
antibody: Millipore 07-030


title: 20130306_H3K4me2_6

description:
23_CCTACCAT
antibody: Millipore 07-030


title: 20130306_H3K4me2_10

description:
7_CCAGTTAG
antibody: Millipore 07-030


title: 20130306_H3K4me2_9

description:
6_AGGTGCGA
antibody: Millipore 07-030


title: 20130423_H3K4me2_20

description:
45_TCTCGGTC
antibody: Millipore 07-030


title: 20130306_H3K4me2_5

description:
22_ATTATGTT
antibody: Millipore 07-030


title: 20130306_H3K4me2_8

description:
5_AGCAATTC
antibody: Millipore 07-030


title: 20130306_H3K4me2_3

description:
15_TCGGAATG
antibody: Millipore 07-030


title: 20130306_H3K4me2_1

description:
13_AACTTGAC
antibody: Millipore 07-030


title: 20130423_H3K4me3_23

description:
9_ACCAACTG
antibody: Millipore 07-473


title: 20130620_H3K4me2_2

description:
18_TCTGGCGA
antibody: Millipore 07-030


title: 20130306_H3K4me2_2

description:
14_CACATCCT
antibody: Millipore 07-030


title: 20130423_H3K4me2_4

description:
28_CCTATGCC
antibody: Millipore 07-030


title: 20130423_H3K4me3_19

description:
71_GTCCACAG
antibody: Millipore 07-473

value: MIX:mESC and MEF


title: 20130423_H3K4me3_15

description:
68_TGTAATCA
antibody: Millipore 07-473


title: 20130423_H3K4me3_11

description:
55_GACCAGGA
antibody: Millipore 07-473


title: 20130423_H3K4me3_21

description:
88_TGTAACTC
antibody: Millipore 07-473


title: 20130423_H3K4me3_17

description:
6_AGGTGCGA
antibody: Millipore 07-473


title: 20130423_H3K4me3_22

description:
8_TTGAGCCT
antibody: Millipore 07-473


title: 20130423_H3K4me3_12

description:
5_AGCAATTC
antibody: Millipore 07-473


title: 20130423_H3K4me3_16

description:
69_ATTATCAA
antibody: Millipore 07-473


title: 20130423_H3K4me3_14

description:
67_GTAACATC
antibody: Millipore 07-473


title: 20130423_H3K4me3_7

description:
19_CATAGCGA
antibody: Millipore 07-473


title: 20130423_H3K4me3_9

description:
21_TGTCGGAT
antibody: Millipore 07-473


title: 20130306_H3K4me2_11

description:
8_TTGAGCCT
antibody: Millipore 07-030


title: 20130423_H3K4me3_20

description:
72_TTGTCTAT
antibody: Millipore 07-473


title: 20130423_H3K4me3_10

description:
49_AACGCATT
antibody: Millipore 07-473


title: 20130423_H3K4me3_1

description:
10_GGTCCAGA
antibody: Millipore 07-473


title: 20130306_H3K4me2_4

description:
21_TGTCGGAT
antibody: Millipore 07-030


title: 20130423_H3K4me3_2

description:
11_GTATAACA
antibody: Millipore 07-473


title: 20130423_H3K4me3_8

description:
20_CAGGAGCC
antibody: Millipore 07-473


title: 20130423_H3K4me3_4

description:
16_AAGGATGT
antibody: Millipore 07-473


title: 20130423_H3K4me3_3

description:
12_TTCGCTGA
antibody: Millipore 07-473


title: 20130423_H3K4me3_13

description:
66_CTAACTCG
antibody: Millipore 07-473


title: 20130423_H3K4me3_6

description:
18_TCTGGCGA
antibody: Millipore 07-473


title: 20130306_H3K4me3_12

description:
9_ACCAACTG
antibody: Millipore 07-473

value: CRL-11691, ATCC, USA


title: BSseq_TME7_rep1

first: Steve

last: Jacobsen

address: 4045 Terasaki Life Sciences Building

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

data_processing:
In general, qseq files received from the sequencing core were demultiplexed with an in-house Perl script and converted to fastq files for downstream analysis.
BS-seq reads were aligned to the cassava reference genome (v6.1) using BSMAP 2.87. Only unique mapping reads were used to estimate methylation ratios. Methylation ratios were calculated as the number of Cs divided by Cs plus Ts (#C/#C+#T).
Genome_build: Cassava v6.1
Supplementary_files_format_and_content: CG/CHG/CHH.wig files: Tab-delimited methylation level files with cytosine_locations and methylation_levels.
Supplementary_files_format_and_content: C_coverage.wig file: Tab-delimited read coverage file with cytosine_locations and reads_numbers.

organism: Manihot esculenta

source_name: leaves

extract_protocol: BS-seq libraries were prepared using the TruSeq DNA LT kit (Illumina) as described previously, except that EZ DNA Methylation-Lightning Kit (Qiagen) was used for bisulfite conversion of the DNA. BS-Seq libraries were sequenced on a HiSeq 2000 system (Illumina) to obtain single-end 100bp reads per manufacturer instructions.

tag: cultivar

value: TME 7

value: leaves


title: 20130306_H3K4me3_9

description:
2_CATGCTTA
antibody: Millipore 07-473


title: 20130423_H3K4me3_18

description:
70_CTATGCGT
antibody: Millipore 07-473


title: 20130306_H3K4me3_5

description:
18_TCTGGCGA
antibody: Millipore 07-473


title: RNAseq_TME7_rep3

description:
cassava mRNA
Processed data file: mRNA_abundance_three_replicates.txt

data_processing:
In general, qseq files received from the sequencing core were demultiplexed with an in-house Perl script and converted to fastq files for downstream analysis.
For mRNA-seq, total reads were aligned to the cassava reference genome (v6.1) by using Tophat 2.0.11 using default parameters, then quantified using Cufflinks (v2.2.1). Expression values were expressed in FPKM. To estimate the correlation between replicates, we used the expression levels of individual genes, estimated by FPKM. Genes with values under 0.5 FPKM were discarded and the remaining genes were used to calculate Pearson correlation coefficient.
Genome_build: Cassava v6.1
Supplementary_files_format_and_content: mRNA_abundance_three_replicates.txt: Tab-delimited text file. The format is "gene_id, expression level (FPKM) of replicate1, replicate2, and replicate3". The gene_ids are searchable in the Phytozome database with cassava reference genome version 6.1 (http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Mesculenta_er).

extract_protocol:
Total RNA was extracted from the 3rd or 4th fully expanded leaf of seven and a half week-old TME 7 plants following the cetyltrimethylammonium bromide (CTAB) protocol (Doyl and Doyl 1990). Genomic DNA was removed by TURBO DNA-free™ Kit (Ambion) and RNA quality and quantity were assessed, respectively, by Agilent 2100 BioAnalyzer (Agilent Technologies, Inc., Santa Clara, CA) and NanoDrop 2000c (Thermo Scientific).
One microgram of total RNA per sample was utilized for library preparation using the Illumina TruSeq sample preparation kit (v2) with polyA mRNA selection as per manufacturer's instructions (Illumina, San Diego, CA). Three libraries were pooled and sequenced using an Illumina HiSeq 2000 with paired-end reads of 101 bp at Genome Technology Access Center (GTAC) of Washington University at St. Louis, Missouri.

value: 7-1/2 weeks


title: 20130306_H3K4me3_4

description:
17_GCACACGA
antibody: Millipore 07-473


title: 20130306_H3K4me3_11

description:
4_TGCTCGAC
antibody: Millipore 07-473


title: 20130423_H3K4me3_5

description:
17_GCACACGA
antibody: Millipore 07-473


title: 20130306_H3K4me3_8

description:
20_CAGGAGCC
antibody: Millipore 07-473


title: BSseq_TME7_rep2


title: 20130306_H3K4me3_7

description:
1_CTACCAGG
antibody: Millipore 07-473


title: 20130306_H3K4me3_1

description:
10_GGTCCAGA
antibody: Millipore 07-473


title: BSseq_TME7_rep3


title: 20130306_H3K4me3_2

description:
11_GTATAACA
antibody: Millipore 07-473


title: 011013_H3K4me3_1

description:
1_CTACCAGG
antibody: Millipore 07-473


title: RNAseq_TME7_rep2


title: RNAseq_TME7_rep1


title: 20130306_H3K4me3_10

description:
3_GCACATCT
antibody: Millipore 07-473


title: MII_KO-15

city: Cambridge

first: Gavin

last: Kelsey

address: Babraham Research Campus

institute: The Babraham Institute

description: scBS-Seq was performed according to Smallwood et al (Nat Methods. 2014 Aug;11(8):817-20. doi: 10.1038/nmeth.3035.)

data_processing:
Raw Bisulfite-Seq reads were trimmed to remove both poor quality calls and adapters using Trim Galore (v0.3.7, default parameters; www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Trimmed reads were aligned to the mouse genome in single-end mode (to maximise the number of hits) to be able to count overlapping parts of the reads only once while writing out unmapped singleton reads. Alignments were carried out with Bismark v0.13.1 (Krueger and Andrews, 2011) with the following set of parameters: --bowtie2 --bam --non_directional.
Reads were then deduplicated with deduplicate_bismark selecting a random alignment for position that were covered more than once. CpG methylation calls were extracted from the deduplicated mapping output using the Bismark methylation extractor (v0.13.1) with the following parameters: --bedGraph --counts --gzip -s --report.
Genome_build: NCBIM37
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

source_name: MII oocytes

extract_protocol:
cell lysate; MII oocytes were individually collected by mouth pipetting and lysed in a buffer containing 10mM Tris-Cl (pH 7.4), 1% SDS and 4U of Proteinase K. Bisulfite treatment was performed directly on the lysate using the Imprint DNA Modification kit (Sigma) (two-step protocol, incubation at 65 °C for 90 min, 95 °C for 3 min and 65 °C for 20 min), followed by depurination and purification of converted DNA using the PureLink PCR Micro kit (Life Technologies)
First complementary strand synthesis was performed using Klenow exo- (50U, Sigma) and a biotinylated Illumina-based adapter with 9 random nucleotides for priming (biotin-CTACACGACGCTCTTCCGATCTNNNNNNNNN). This step was repeated an additional 4 times, with DNA denaturation (95 °C, 1min) in between. After capture of the neo-synthesised strands using streptavidin magnetic beads, second strand synthesis was performed using an Illumina-based adapter with 9 random nucleotides (TGCTGAACCGCTCTTCCGATCTNNNNNNNNN). Libraries were then amplified for 13 cycles using KAPA HiFi HotStart DNA Polymerase (KAPA Biosystems), Illumina PE1.0 oligo, and iPCR tag reverse oligos for indexing [Seb Nat Methods]. Libraries were purified using 0.8x AMPure XP beads (Agencourt) according to the manufacturer’s guideline.

tag: background strain

value: oocyte

tag: developmental stage

value: MII oocytes

tag: genotype

value: Hira fl/fl * Gdf9-iCre


title: MII_KO-14


title: MII_KO-13


title: MII_KO-7


title: MII_KO-6


title: 011013_H3K4me3_2

description:
3_GCACATCT
antibody: Millipore 07-473


title: MII_KO-12


title: MII_KO-11


title: MII_KO-10


title: MII_KO-4


title: MII_KO-9


title: 20130306_H3K4me3_3

description:
12_TTCGCTGA
antibody: Millipore 07-473


title: 20130306_H3K4me3_6

description:
19_CATAGCGA
antibody: Millipore 07-473


title: MII_KO-3


title: MII_WT-15

value: Hira fl/fl


title: MII_WT-14


title: MII_KO-1


title: MII_KO-2


title: MII_WT-13


title: MII_KO-5


title: MII_WT-10


title: MII_WT-11


title: MII_WT-7


title: MII_WT-12


title: MII_WT-9


title: MII_WT-6


title: MII_WT-5


title: MII_WT-4


title: MII_WT-2


title: MII_WT-3


title: MII_WT-1


title: P_merged_HTT

status: Public on Oct 10 2015

first: Adam

last: Labadorf

address: 72 East Concord Street E301

department: Neurology

institute: Boston University Medical School

description: Parkinson sample reads aligning to HTT

data_processing:
Bases were called with the Illumina CASAVA 1.7 pipeline
mRNA-Seq reads were trimmed to remove low-quality sequenced bases using the sickle program (https://github.com/najoshi/sickle)
mRNA-Seq reads were aligned to hg38 with the STAR aligner with parameters --readFilesCommand /bin/zcat --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterMultimapNmax 200 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000
aligned reads for samples within each condition were merged together using samtools
reads were analyzed for splicing patterns and visualized using custom python scripts
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text files containing intron/exon counts
Supplementary_files_format_and_content: all_merged_HTT.bed contains all splicing events detected in the      concatenated read dataset. The columns are chromosome, beginning of splice      junction hg38 coordinate, end of splice junction hg38 coordinate, internal      name of feature, and the number of reads supporting the splice junction.

source_name: post-mortem prefrontal cortex (Brodman Area 9)

extract_protocol:
QIAzol, Qiagen miRNeasy kit
Illumina TruSeq RNA Sample Prep Kit, mRNA

tag: disease state

value: Parkinson's Disease

value: prefrontal cortex (Brodman Area 9)


title: H_merged_HTT

description: Huntington sample reads aligning to HTT

value: Huntington's Disease