title: HUVEC_NFATc1_VEGF 1h

city: Mitaka

first: Jun-ichi

last: Suehiro

state: Tokyo

address: 6-20-2, Shinkawa

department: Department of Pharmacology and Toxicology

country: Japan

institute: Kyorin University School of Medicine

data_processing:
Basecalls performed using Illumina pipeline CASAVA version 1.7.1
Alignment: Sequence reads were obtained and mapped to the human (UCSC human genome hg18, March, 2006) genomes using the Illumina Genome Analyzer Pipeline (ELAND). All reads mapping with two or fewer mismatches were retained.
Genome_build: hg18
Supplementary_files_format_and_content: Peak files (.wig) were generated using QuEST 2.4 according with the following parameters: Positive region size: 300 (NFATc1), 1000 (H3K4me3 and H4ac); KDE bandwidth: 30 (NFATc1), 100 (H3K4me3 and H4ac); ChIP threshold : 0.163942607142857; Enrichment fold: 3; Rescue fold: 3.

source_name: HUVEC_NFATc1_VEGF plus

growth_protocol: Human umbilical vein endothelial cells (HUVEC) were purchased from Ronza and cultured in EGM-2 MV complete medium (Ronza).

extract_protocol:
Lysates were extracted from fixed cells with paraformaldehyde and sonicated protein-DNA complexes were isolated with antibody.
Libraries were prepared using ChIP-Seq DNA Sample Prep Kit  (Illumina) according to the instruction manuals.

treatment_protocol: HUVEC were serum-starved overnight and then stimulated by 50ng/mL VEGF (R&D systems) for 1 hour.

value: human umbilical vein endothelial cells

tag: stimulation

value: VEGF

tag: chip antibody

value: NFATc1 (generated by our laboratories)


title: HUVEC_NFATc1_0h

status: Public on Sep 01 2013

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type


title: Skin

city: Aarhus

first: Morten

middle: Muhlig

last: Nielsen

address: Palle Juul-Jensens Bouleward 99

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University

description: Normal tissue provided by Biochain

library_source: transcriptomic

data_processing:
Illumina Casava software used for basecalling, and Tophat and Cufflinks used for transcript FPKM estiamtes.
Genome_build: hg18
Supplementary_files_format_and_content: Total transcript FPKM values in the GTF file format

molecule: total RNA

extract_protocol:
Normal tissue provided by Biochain. Total RNA was isolated by a modified guanidine thiocyanate technique according to BioCahin certificate of analysis F-753-1-6 revA.
Using 500 ng of total-RNA from each of the samples, RNA-Seq libraries were constructed by depletion of rRNA followed by synthesis of directional, paired-end and indexed RNA-Seq libraries. The rRNA depleted RNA was purified using the RNA Clean & Concentrator™-5 columns (Zymo Research). Speed-vac was used to reduce the remaining sample volume to 9.5μL followed by synthesis of directional, paired-end and indexed RNA-Seq libraries using the ScriptSeq kit (Epicentre). Briefly, rRNA depleted RNA was chemically fragmented and cDNA was synthesized from a tagged random hexamer. The cDNA was terminal tagged using a 3’-end blocked and tagged oligo followed by MiniElute (Qiagen) purification. The di-tagged cDNA was then used as template in a 10 cycle PCR reaction. Libraries were purified by agarose gel electrophoresis selecting elements of 200-600 bp in size. The RNA-Seq libraries were denaturated and diluted to 10 pM with pre-chilled Hybridization buffer (Illumina) and loaded into TruSeq PE v3 flowcells (Illumina) on an Illumina cBot followed by indexed paired-end sequencing (101+7+101 bp) on a Illumina HiSeq 2000 using TruSeq SBS Kit v3 chemistry.

tag: tissue

value: skin


title: 747_MDA-MB-231

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E Duarte Rd

department: Molecular and Cellular Biology

country: USA

institute: Beckman Research Institute

data_processing:
Sequenced reads from Solexa were first mapped onto human genome version hg18 using novoalign software and the expression level of mature miRNAs in the miRBase human miRNA database v15 was summarized.
Normalization and identification of differentially expressed miRNAs between groups were carried out using Bioconductor package “edgeR”.
genome build: hg18
Log2 transformed Quantile Normlaized counts

source_name: exosome

growth_protocol: MDA-MB-231 cells were grown in DMEM plus 10% FBS.  MCF-10A cells were grown in DMEM/F12 (1:1) supplemented with 5% horse serum, 10 ug/ml insulin, 20 ng/ml EGF, 0.1 ug/ml Cholera Toxin and 0.5 ug/ml Hydrocortisone.

extract_protocol:
TRIZOL reagent (Invitrogen) and TRIZOL LS reagent (Invitrogen) were used to extract total RNA from cells and exosomes, respectively, following the manufacturer’s protocols.  RNA pellet was dissolved in RNase-free water, and subjected to library construction and deep sequencing.
Each sample was independently subjected to library preparation and deep sequencing. All small RNAs of 15–52 nts were selected and sequenced using the Solexa system, following the manufacturer’s protocol (Illumina Inc., San Diego, CA). Library preparation, as well as cluster generation and deep sequencing, was performed according to the 5' ligation-dependent (5′ monophosphate-dependent) manufacturer’s protocol (Digital Gene Expression for small RNA; Illumina). Small RNAs were size-selected between 17 and 52 nt according to the single-stranded DNA marker in the small RNA sequencing kit (Illumina). The library was quantified using picoGreen and qPCR. Sequencing was performed on a Genome Analyzer IIx (Illumina), and image processing and base calling were conducted using Illumina’s pipeline.

tag: cell line


title: Breast

description: Normal tissue provided by Biochain

value: breast


title: Liver

description: Normal tissue provided by Biochain

value: liver


title: Bladder

description: Normal tissue provided by Biochain

value: bladder


title: HUVEC_acetylated H4_0h

source_name: HUVEC_acetylated H4_minus

value: H4ac (06-866; Upstate)


title: HUVEC_H3K4me3 VEGF_1h

source_name: HUVEC_H3K4me3 VEGF plus

value: H3K4me3 (kindly provided by Dr. Kimura, Osaka University)


title: Lung

description: Normal tissue provided by Biochain

value: lung


title: Colon

description: Normal tissue provided by Biochain

value: colon


title: 3 day old heads spermidine food 2

city: Nijmegen

first: Jamie

middle: M

last: Kramer

address: Geert Grootplein 10

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

data_processing:
Raw data was processed using the default Illumina CASAVA pipeline, with mapping to the dm3 genome using ELAND with 0 or 1 mismatches.
Normalized expression values were generated using the Genomatix Genome Analyser v2. 40901.
Genome_build: BDGP R5 / dm3
Supplementary_files_format_and_content: bed files contain one line for each mapped read; wig files are standard

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Drosophila heads

growth_protocol: Flies were cultures according to standard methods at 25 degrees with a 12 hour light dark cycle

extract_protocol: Spd- and Spd+ flies were frozen in liquid nitrogen and heads were collected after vortexing by mechanical separation. Poly A+ RNA was extracted from approximately 50 ul of heads per sample using the RNeasy Lipid tissue Mini kit (Qiagen) and the Oligotex mRNA mini kit (Quiagen). RNA was reverse transcribed into a cDNA using the Superscript III Reverse Transcriptase Kit (Invitrogen) for first strand synthesis. Second strand synthesis was performed with E.coli and T4 DNA polymerases (New England Biolabs). DNA end repair was performed on 9-20 ng of cDNA followed by ligation of adaptors, and size selection for 300 bp fragments using the E-gel Size Select gel (Invitrogen). Fragments were amplified using 14 PCR cycles and linear amplification was validated by qPCR.

treatment_protocol: Flies were cultured either in the presence or absence of 5mM spermidine

tag: food

value: standard Drosophila media with 5mM spermidine

tag: age

value: 3 days after eclosion

value: heads


title: 3 day old heads spermidine food 1


title: 3 day old heads normal food 1

value: standard Drosophila media


title: 10 day old heads spermidine food 1

treatment_protocol: /flies were cultured either in the presence or absence of 5mM spermidine

value: 10 days after eclosion


title: HUVEC_acetylated H4_VEGF_1h

source_name: HUVEC_acetylated H4_VEGF plus


title: Axolotl limb blastemal 28d

city: Rochester

first: Jeff

last: Nie

state: MN

address: 200 First St. SW

institute: Mayo Clinic

data_processing: For data analysis, paired-end reads were treated as two separate single-end reads. After the sequencing was complete, the data were processed by Illumina Pipeline software for quality analysis. For transcript quantification and differential analyses, we used an axolotl contig set assembled with MIRA (Chevreux et al., 2004) from a combination of Sanger and 454 EST sequences. Details of the assembly process are provided in Supplemental Experimental Procedures. We used BLAST to align the contigs against human RefSeq (Pruitt et al., 2009) RNA and protein sequences, taking the best BLAST hit with e-value less than 10-5 as the most closely related human homolog for each contig. RSEM (Li and Dewey, 2011) was used to estimate the relative abundances and expected read counts for the contigs. Contigs mapping to rRNA transcripts were removed and abundances were renormalized. The expected read counts for contigs mapping to the same homologous human transcript were summed to give abundances. Read counts for transcripts belonging to the same gene were summed to give human gene-level abundances.

organism: Ambystoma mexicanum

source_name: axolotl juvenile blastema

growth_protocol:
For Mouse: Mice were housed at the animal facility at the University of Pittsburgh
For Axolotl: The animals were housed in 40% Holtfreter’s salts, kept at 16-18O C with a pH range of 7.0-7.4.

extract_protocol: We linearly amplified axolotl polyA+ RNAs using a modified T7 amplification method (Sengupta et al., 2010) resulting in cDNA. Subsequent steps followed the Illumina Paired End (PE) preparation kit (PE-102-1001, Illumina, San Diego, CA). After the Illumina PE adapters were ligated, 150-250 bp DNA fragments were isolated via gel electrophoresis. Then ten cycles of polymerase chain reaction (PCR) were performed to amplify the selected fragments using the Illumina supplied PCR primers and protocol. The sample was quantitated with the Invitrogen Qubit fluorometer (Q32857).  Samples were loaded on the flowcell cluster station at a concentration of 8pM. The Genome Analyzer II Paired End recipe was used. Some runs were single-read runs, while some runs were paired-end.

treatment_protocol:
For Mouse: Following induction of surgical plane anesthesia with 1-2% inhaled isoflurane (assessed by intact breathing, intact femoral pulses bilaterally, and lack of response to tail and foot stimulus), adult, 6 to 8 week old C57/BL6 mice (Jackson Laboratories, Bar Harbor, ME) were subjected to aseptic, mid-second phalanx amputation of the third digit of each hindfoot. Post surgical buprenorphine and baytril were administered for 3 days post-surgery for analgesia and antibiotic prophylaxis, respectively. Animals were sacrificed and the distal portion of each amputated digit (distal to the proximal joint) was harvested into RNAlater solution (Ambion, Austin, TX) and immediately flash frozen in liquid nitrogen. Time points of harvest included 0 hours, 3 hours, 6 hours, 12 hours, 1 day, 5 days, 10 days, and 14 days. Following transfer of each sample overnight on dry ice to the Morgridge Institute for Research  (Madison, WI), RNA from each sample was isolated using Trizol (Invitrogen, Carlsbad, CA) and treated with Dnase I. Then the RNA was purified by extraction with phenol:chloroform.
For Axolotl: For all surgical procedures, the animals were anesthetized with 0.5-1 g/L Tricaine (MS-222, Sigma, St. Louis, MO) until they were unresponsive to a tail pinch stimulus.We amputated juvenile limbs at the mid-stylopod level. Tissue was harvested as described in Figure 1 at 0 hours, 3 hours, 6 hours, 12 hours, 1 day, 3 days, 5 days, 7 days, 10 days, 14 days, 21 days, and 28 days. Note that for the early time points, some tissue was harvested proximal to the original amputation plane owing to the small amount of regenerative tissue distal to the amputation plane at the time of harvesting. In all cases the harvested tissues were stored in RNAlater (Qiagen, Valencia, CA) at 4OC until the RNA was purified using the RNeasy purification kit from Qiagen.

value: blastema

tag: time course


title: 10 day old heads spermidine food 2


title: Axolotl limb blastemal 21d


title: Axolotl limb blastemal 5d


title: Axolotl limb blastemal 12hr


title: Axolotl limb blastemal 1d


title: Axolotl limb blastemal 7d


title: Axolotl limb blastemal 14d


title: Axolotl limb blastemal 0hr


title: Axolotl limb blastemal 10d


title: Axolotl limb blastemal 3hr


title: HUVEC_H3K4me3 0h

source_name: HUVEC_H3K4me3 minus

value: human umbilical vein endothelial cells


title: An WT Avicel #2

city: Berkeley

first: N

middle: Louise

last: Glass

address: 341 Koshland Hall, Univerisity of California

department: Plant and Microbial Biology

institute: UC Berkeley

description:
multiplexed: yes
multiplexed: NAGATC

data_processing:
Illumina CASAVA_v1.8.0 software used for basecalling.
Reads were mapped to known transcripts with Tophat v2.0.4 (options: --GTF)
Fragments Per exon Kilobase per Megabase read (FPKM) were calculated with Cufflinks v2.0.2 (options: -u -b -G --compatible-hits-norm --max-bundle-frags=10000000)
Rawcounts were calculated with Htseq Count (options: -m intersection-strict --stranded=no)
Differential Expression was estimated with DESeq (method="per-condition")
Genome_build: N. crassa: OR74A version 10 from the Broad Institute.
Genome_build: A. nidulans: FGSC A4 version s09-m01-r04 from the Aspergillus Genome Database (AspGD.org)
Supplementary_files_format_and_content: .fpkm_tracking: tab-delimited output from cufflinks
Supplementary_files_format_and_content: .txt: tab-delimied output from DEseq
Supplementary_files_format_and_content: 2489_DESeq_AvN.txt: differential expression analysis for FGSC 2489 on Avicel versus No Carbon media
Supplementary_files_format_and_content: A4_DESeq_AvN.txt: differential expression analysis for FGSC A4 on Avicel versus No Carbon media

organism: Aspergillus nidulans FGSC A4

source_name: hyphae

growth_protocol: N. crassa strains were innoculated in 100mL Liquid media with 2% sucrose, grown 16 hours at 25C 200rpm and constant light.  Mycelia were washed once in media with no carbon sourse and resuspended in fresh media with 2% Avicel PH-101, 2% sucrose or no added carbon source, then grown and additional 4hrs at 25C.  A. nidulans strains were innuculated in 100mL Liquid media with 1% glucose, grown 16 hours at 37C 200rpm and constant light.  Mycelia were washed once in media with no carbon sourse and resuspended in fresh media with 2% Avicel PH-101 or no added carbon source, then grown and additional 6hrs at 37C.

extract_protocol:
Mycelia were harvested by filtration and flash frozen in liquid nitrogen.  RNA was extracted by bead-beating in TRIZOL reagent and purified with Rneasy columns from Qiagen.
mRNA was enriched with oligo-dT magnetic beads, fragmented and reverse transcribed with Superscript II reverse polymerase from Invitrogen.  Illumina adapters were added to the cDNA library with the TruSeq DNA kit v2, SetA

tag: genotype

value: wildtype

tag: carbon source

value: Avicel


title: An ∆clrB Avicel #1

description:
multiplexed: yes
multiplexed: CCGTCC

value: delta-clrB (deletion of AN3369)


title: An WT No Carbon #1

description:
multiplexed: yes
multiplexed: CGATGT

value: No Carbon


title: An WT Avicel #3

description:
multiplexed: yes
multiplexed: GTCCGC


title: An ∆clrB Avicel #2

description:
multiplexed: yes
multiplexed: GTGAAA


title: An ∆clrB Avicel #3

description:
multiplexed: yes
multiplexed: GTGAAA


title: An WT Avicel #1

description:
multiplexed: yes
multiplexed: GCCAAT


title: An WT No Carbon #3

description:
multiplexed: yes
multiplexed: ACAGTG


title: Nc Pc2 Sucrose

description: multiplexed: no

organism: Neurospora crassa OR74A

value: Pc2 (delta-clr-2 native locus, clr-2 under ccg-1 promoter at the his-3 locus)

value: Sucrose


title: 10 day old heads normal food 2


title: 10 day old heads normal food 1

treatment_protocol: Adult flies were cultured either in the presence or absence of 5mM spermidine


title: Nc Pc2 No Carbon #3

description:
multiplexed: yes
multiplexed: TGACCA


title: Nc Pc2 No Carbon #1

description: multiplexed: no


title: Nc Pc2 No Carbon #2

description:
multiplexed: yes
multiplexed: CGATGT


title: Axolotl limb blastemal 3d


title: Axolotl limb blastemal 6hr


title: Nc ∆clr-2 Avicel #2

description:
multiplexed: yes
multiplexed: CAGATC

value: FGSC 15834, delta-clr-2 (deletion of NCU08042)


title: Nc ∆clr-2 Avicel #3

description:
multiplexed: yes
multiplexed: CTTGTA


title: Nc WT No Carbon #3

description: multiplexed: no


title: Nc ∆clr-2 Avicel #1

description: multiplexed: no


title: Nc WT Avicel #3

description: multiplexed: no


title: Nc WT Avicel #1

description: multiplexed: no


title: Nc WT Avicel #2

description: multiplexed: no


title: Nc WT No Carbon #2

description: multiplexed: no


title: An WT No Carbon #2

description:
multiplexed: yes
multiplexed: CCGTCC


title: small RNA from tdrkh+/- testis cells

city: New Haven

first: Mengjie

last: Chen

address: 13 Pleasant St

institute: Yale University

data_processing:
Counts: Linker sequences were removed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).  Degradation products were removed by mapping with Bowtie, allowing two mismatches to a library consisting of tRNA, rRNA, scRNA, scpRNA, and snoRNA with 25bp extensions on both 5’ and 3’ ends.  Remaining sequences were mapped to the genome (mm9) and allowing for up to two mismatches.
Genome Build:
tdrkh+-.counts.txt: mm9

organism: Mus musculus

source_name: tdrkh+/- testis cells

extract_protocol: Five pairs of testis from each age and genotype were used for small RNA library construction.  Small RNAs were purified using a miRVana RNA isolation kit (Ambion), and 15-40nt RNAs were gel-purified on a TBE-urea gel.  Libraries were prepared using an Illumina Small RNA sample preparation kit and sequenced on a Genome Analyzer II (Illumina).

value: tdrkh+/-

tag: developmental stage

value: testis


title: Nc WT No Carbon #1

description: multiplexed: no


title: small RNA from tdrkh-/- testis cells

data_processing:
Counts: Linker sequences were removed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).  Degradation products were removed by mapping with Bowtie, allowing two mismatches to a library consisting of tRNA, rRNA, scRNA, scpRNA, and snoRNA with 25bp extensions on both 5’ and 3’ ends.  Remaining sequences were mapped to the genome (mm9) and allowing for up to two mismatches.
Genome Build:
tdrkh--.counts.txt: mm9

source_name: tdrkh-/- testis cells

value: tdrkh-/-


title: hMSC-replicate-3

city: Aurora

first: Manoj

last: Pillai

address: Building 500 - 13001 E. 17th Place, Campus Box C290, Room E1354

institute: University of Colorado

description: Barcoded sample: TCGA at 5' end

data_processing:
Library strategy: HITS-CLIP or CLIP-Seq
Basecalling was performed using CASAVA.
Aligned using Novoalign V2.07.18, utilizing iterative 5' trimming until mapped or the length was less than 16 bp.
For peak calling, duplicate aligned read entries were removed using Samtools 0.1.18 rmdup function.
The resultant bam files were converted to bed using bedtools v2.16.2 bamtobed.
The aligned reads in bed format were then converted to strand specific bedgraphs bedItemOverlapCount.
Coverage information contained in the bedgraphs were inserted into a genome data archive (Genomedata 1.3.2).
Peaks were called using the Genomedata archive to pull rolling window sizes of 30 bp, calculating poisson p-values for observations pulled from sample specific tracks.
Q-values were calculated using shuffled data across the same rolling windows as the peak calling step.
Overlapping peaks (q-value < 0.001) from replicates, where the peak was observed in at least 2 samples, were combined into a consensus peak file.
The center of the consensus peaks were set to the peak summit position and the peak was expanded 30 bp up and downstream.
Genome_build: hg18
Supplementary_files_format_and_content: *.peaks.trimmed.bed; name is the case; region represents a significant (q-value < 0.001) peak.

source_name: hMSC

growth_protocol: Cells were cultured in the following Media: HS5, HS27a and hMSC: RPMI with 10% Fetal Calf Serum; HUVEC in ATCC HUVEC growth media (http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-2873&Template=cellBiology); trHBMEC in gelatin-coated plasticware in Dulbecco's modified Eagle's medium (DMEM) with 5% fetal calf serum (FCS), 1% glucose, 3 mmol/L glutamine, 10 mmol/L HEPES, vitamins, 50 μg/mL penicillin, and 50 μg/mL streptomycin.

extract_protocol: HITS-CLIP performed as per Dr. Darnell's protocol (http://ago.rockefeller.edu/Ago_HITS_CLIP_Protocol_June_2009.pdf)

treatment_protocol: Cells were suspended in Hanks Balanced Buffer Solution and cross-linked with 400 mJ/cm2 in a stratalinker 1800 per Dr. Darnell's protocol (http://ago.rockefeller.edu/Ago_HITS_CLIP_Protocol_June_2009.pdf)

value: n/a (primary)

value: Primary human marrow stromal cells (MSS)

tag: passage number

value: 2 to 3

tag: antibody for clip

value: anti-AGO monoclonal antibody 2A8


title: TrHBMEC-replicate-3

description: Barcoded sample: TCGA at 5' end

source_name: TrHBMEC

value: TrHBMEC

value: Bone Marrow Endothelial Cell Line

value: Unknown


title: HS5-replicate-3

value: Stromal Cell line

value: 5 to 8


title: hMSC-replicate-2

description: Barcoded sample: ACTG at 5' end


title: TrHBMEC-replicate-1

description: Barcoded sample: ACTG at 5' end


title: hMSC-replicate-4

description: Barcoded sample: ACTG at 5' end


title: HS27a-replicate-3


title: hMSC-replicate-1


title: HUVEC-replicate-2

source_name: HUVEC

value: Primary human umbilical vein endothelium

value: 1 to 2


title: hMSC-replicate-5

description: Barcoded sample: TCGA at 5' end


title: TrHBMEC-replicate-2

description: Barcoded sample: ACTG at 5' end


title: HS27a-replicate-2


title: HUVEC-replicate-1


title: HS5-replicate-2


title: HS5-replicate-1


title: HS27a-replicate-1


title: Testicular_cancer_02_C_miRNA

city: Shenzhen

first: Jiahao

state: Guangdong

address: Beishan road, Yantian district

department: Cancer Research Group

country: China

institute: Beijing Genomics Institute

data_processing: Low quality reads were trimmed and adapter sequences were accurately clipped with the aid of a dynamic programming algorithm before subsequent statistical analysis. After elimination of the duplicated reads, the remaining reads no shorter than 18nt were mapped to human reference genome (hg18) using SOAP V2.0. To remove tags originating from protein coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, we also mapped the short read tags to UCSC RefGene, RepeatMasker and NCBI Refseq, as well as our in-house ncRNA annotation data sets compiled from the NCBI Genbank database (http://www.ncbi.nih.gov). The similar pipeline used for DGE mRNA differential expression analysis was also applied to miRNAs study. We investigated the biological relevance of miRNA through their regulation of target genes. First, pearson correlation analysis was perform to identify potential targets. Meanwhile, another target gene set was generated according to the intersect result of any two predicted algorithms of DIANA-microT 3.0, TargetScan 5.1, and PicTar. Next, those potential targets defined by the predicted target gene set above were subjected to further analysis.

source_name: testicular, cancer

extract_protocol: 5Î¼g of total RNA extracted from each sample was ligated with both 5âadapter and 3âadapter for reverse transcription by Superscript II, and the reverse transcribed products were amplified subsequently. After collection of ~92bp DNA band on the 6% PAGE gels, PCR products were ethanol precipitated and purified by Spin-X filter columns. Finally, miRNA libraries were sequenced on the Illumina Cluster Station and Genome Analyzer â¡ sequence system following the manufacturerâs protocol.

value: testicular germ

tag: cancer or normal

value: cancer


title: Testicular_cancer_05_N_miRNA

source_name: testicular, normal

value: normal


title: Testicular_cancer_05_C_miRNA


title: Testicular_cancer_07_C_miRNA


title: Testicular_cancer_02_N_miRNA


title: Testicular_cancer_04_C_miRNA


title: Testicular_cancer_01_C_miRNA


title: Testicular_cancer_06_C_miRNA


title: Testicular_cancer_07_N_miRNA


title: Testicular_cancer_03_N_miRNA


title: Testicular_cancer_04_N_miRNA


title: Testicular_cancer_01_N_miRNA


title: Bladder_cancer_03_C_miRNA

source_name: bladder, cancer

value: transitional


title: Bladder_cancer_03_N_miRNA

source_name: bladder, normal


title: Bladder_cancer_02_C_miRNA


title: Bladder_cancer_02_N_miRNA


title: Bladder_cancer_01_C_miRNA


title: Bladder_cancer_10_C_miRNA


title: Bladder_cancer_09_N_miRNA


title: Bladder_cancer_01_N_miRNA


title: Testicular_cancer_03_C_miRNA


title: Bladder_cancer_08_N_miRNA


title: Bladder_cancer_08_C_miRNA


title: Bladder_cancer_09_C_miRNA


title: Bladder_cancer_07_N_miRNA


title: Bladder_cancer_07_C_miRNA


title: Testicular_cancer_06_N_miRNA


title: Bladder_cancer_06_N_miRNA


title: Bladder_cancer_06_C_miRNA


title: Bladder_cancer_05_C_miRNA


title: Bladder_cancer_05_N_miRNA


title: Testicular_cancer_02_N_mRNA

data_processing: Potentially erroneous tags (single copy tags and tags consisting of adaptor sequences or containing unknown sequences 'N') were filtered out. All 17 bp sequences next to the possible Nlaâ¢ restriction sites in human reference genome (hg18) plus the 4 bp CATG restriction enzyme digested site were extracted and created as a new reference. Tags were mapped to the constructed reference using SOAP V2.0 allowing no more than one base mismatch. Only unique mapping tags were used for gene expression analysis. Standardized TPM (transcripts per million clean tags) values were applied for comparing gene expression between tumors and normal adjacent tissues. Expression fold change (tumor versus normal) for each gene was calculated as log2Ratio using TPM values. Next, we performed a rigorous significance test to determine the differentially expressed genes. The resulting P-values for all genes were corrected for multiple tests using FDR (False Discovery Rate) adjustment.

extract_protocol: Total RNA was extracted from normal adjacent tissues and tumor tissues of 7 and 10 patients of testicular germ cell tumor (TGCT) and transitional cell carcinoma of bladder (TCC) respectively by TRIZOL reagent (Invitrogen, US) according to the manufactureâs protocol. The RNA integrity was evaluated by Agilent 2100 Bioanalyzer (Agilent Technologies, US).4Î¼g total RNA extracted from each sample was used in digital gene expression (DGE) sequencing. In brief, reverse transcription reaction was performed after mRNA isolation using oligo(dT)18 beads. 5âadapter was ligated after NlaIII enzyme digestion, and subsequently 3âadapter was ligated after MmeI enzyme digestion. The PCR amplification of double-adapters flanked tags was run and the resulting ~85bp PCR products were ethanol precipitated and purified from the electrophoresis gels by Spin-X filter columns. Finally, mRNA libraries were sequenced on the Illumina Cluster Station and Genome Analyzer â¡ (Illumina Inc, USA) sequence system following manufacturerâs protocol.


title: Testicular_cancer_02_C_mRNA


title: Testicular_cancer_01_N_mRNA


title: Bladder_cancer_10_N_miRNA


title: Testicular_cancer_06_N_mRNA


title: Testicular_cancer_05_C_mRNA


title: Testicular_cancer_05_N_mRNA


title: Testicular_cancer_06_C_mRNA


title: Testicular_cancer_04_N_mRNA


title: Testicular_cancer_07_N_mRNA


title: Bladder_cancer_04_N_miRNA


title: Bladder_cancer_04_C_miRNA


title: Bladder_cancer_02_N_mRNA


title: Testicular_cancer_07_C_mRNA


title: Bladder_cancer_03_C_mRNA


title: Bladder_cancer_02_C_mRNA


title: 14R

city: Jinan

first: Xiuxia

last: Liu

address: 27 Shanda South Road

institute: Shandong University

description: We take all CATG*** tags in a gene, not only the 3' end one, as its reference tags.

data_processing: Unique tag consolidation: Raw sequences were extracted from the resulting image files using the open source Firecrest and Bustard applications (Illumina). Data were consolidated by read counts for unique sequences. The consolidated, unfiltered sequence tags and raw read counts are provided as processed data files for each sample (lane of sequence).All downstream analyses are performed by BGI. Co., Ltd (Shenzhen, China).

organism: Zea mays

source_name: maize root

extract_protocol: Extract 6ug total RNA, use Oligo(dT) magnetic beads adsorption to purify mRNA, and then use Oligo(dT) as primer to synthesize the first and second-strand cDNA. The 5' ends of tags can be generated by two types of Endonuclease: NlaIII or DpnII (see table 1 for recognition sites). Usually, the bead-bound cDNA is subsequently digested with restriction enzyme NlaIII, which recognizes and cuts off the CATG sites. The fragments apart from the 3' cDNA fragments connected to Oligo(dT) beads are washed away and the Illumina adaptor 1 is ligated to the sticky 5' end of the digested bead-bound cDNA fragments. The junction of Illumina adaptor 1 and CATG site is the recognition site of MmeI, which is a type of Endonuclease with separated recognition sites and digestion sites. It cuts at 17bp downstream of the CATG site, producing tags with adaptor 1. After removing 3' fragments with magnetic beads precipitation, Illumina adaptor 2 is ligated to the 3' ends of tags, acquiring tags with different adaptors of both ends to form a tag library. After 15 cycles of linear PCR amplification, 95bp fragments are purified by 6% TBE PAGE Gel electrophoresis. After denaturation, the single-chain molecules are fixed onto the Illumina Sequencing Chip (flowcell). Each molecule grows into a single-molecule cluster sequencing template through Situ amplification. Then add in four types of nucleotides which are labeled by four colors, and perform sequencing with the method of sequencing by synthesis (SBS). Each tunnel will generate millions of raw reads with sequencing length of 35bp.

value: ZmPIS sense transgenic maize DH4866

value: Three-leaf stage

tag: growth condition

value: osmotic stress treatment with 18% (w/v) polyethyleneglycol-6000 (PEG-6000) for 72 hours


title: 10R

value: wide type DH4866

value: osmotic stress treatment with 18% (w/v) polyethyleneglycol-6000 (PEG-6000) for 24 hours


title: 11R


title: Testicular_cancer_01_C_mRNA


title: Bladder_cancer_09_N_mRNA


title: 9R

value: normal condition


title: 8R


title: Testicular_cancer_03_N_mRNA


title: 7L

source_name: maize leaf


title: 13R


title: Bladder_cancer_03_N_mRNA


title: 12R

value: ZmPIS antisense transgenic maize DH4866


title: Bladder_cancer_01_C_mRNA


title: Testicular_cancer_04_C_mRNA


title: Bladder_cancer_01_N_mRNA


title: Bladder_cancer_09_C_mRNA


title: Testicular_cancer_03_C_mRNA


title: Bladder_cancer_10_N_mRNA


title: 5L


title: Bladder_cancer_10_C_mRNA


title: Bladder_cancer_08_C_mRNA


title: Bladder_cancer_08_N_mRNA


title: 2L


title: 3L


title: Bladder_cancer_07_C_mRNA


title: Bladder_cancer_07_N_mRNA


title: Bladder_cancer_06_N_mRNA


title: Bladder_cancer_05_N_mRNA


title: Bladder_cancer_06_C_mRNA


title: Bladder_cancer_05_C_mRNA


title: 1L


title: 6L


title: Bladder_cancer_04_N_mRNA


title: 4L


title: Promoter library

city: Cambridge

first: Carl

middle: G

last: de Boer

state: MA

address: 415 Main St

institute: The Broad Institute

description: Sample 1

library_source: other

data_processing:
Divide reads by barcode into different fluorescent bins
Map reads to possible promoters using bowtie and paired end reads
Tally reads for each promoter and each fluorescent bin
Filter out promoters with fewer than 50 reads
Calculate the expected expression level of each promoter given the frequencies of each promoter in each fluorescent bin.
Genome_build: custom - available as a Series supplementary file
Supplementary_files_format_and_content: 20110823_tagPromoterMatrix.4ml.txt containing the number of each promoter in each fluorescent bin (read counts for the different GFP bins and the unsorted library)
20130228_ExpectedExpressionLevel.txt containing the promoter names and corresponding expected expression levels for promoters with enough reads.

molecule: other

organism: Saccharomyces cerevisiae

source_name: plasmids containing reporter construct

growth_protocol: SC-Leu overnight

extract_protocol:
yeast miniprep from overnight culture
Barcoding via multiplex PCR using common priming sites

treatment_protocol: Flow cytometry, sorting by fluorescence.

tag: transformed with

value: plasmids containing reporter construct

tag: molecule subtype

value: plasmid DNA


title: Bladder_cancer_04_C_mRNA


title: OMA9.41 CenH3 ChIP-seq

city: Madison

first: Yufeng

state: WI

address: 1575 Linden Drive

institute: UW-Madison

data_processing:
ChIP-seq reads were mapped to reference genome of maize B73 version 2 using MAQ alignment program. ChIP-seq reads generated from OMA8.05, OMA9.41 and OMA10.26 lines were mapped to chromosomes 8, 9 and 10 of B73, respectively. We allowed 1 bp mismatch between each sequence read and the reference genome, then kept only reads that mapped to a unique position in the reference genome for further analysis. Here we only released the reads mapped to maize chromosomes.
Genome_build: The gene annotation of maize genome (version 2) and reference genome were downloaded from http://www.maizesequence.org/ (B73 RefGen_v2)
Supplementary_files_format_and_content: In addtition to the raw data of fastq, we released the distribution of ChIP-seq reads along chromosomes. We used the reads number in 10kb window to represent the density of CenH3 signals and released the gff files.

organism: Avena sativa/Zea mays addition line

source_name: OMA9.41 CenH3 ChIP-seq

growth_protocol: All plants were grown in greenhouses

extract_protocol:
Leaves were collected and ground into fine powder in liquid nitrogen.  The resulting powder was suspended in nuclear isolation buffer (NIB: 20mM Tris-HCl, 50mM EDTA, 5mM Spermidine, 0.15mM Spermine, 0.1% mercaptoethanol, 40% Glycerol, pH 7.5) and followed the standard protocol for nuclei isolation.
Construction of ChIP-seq libraries was according to the protocol of “preparing samples for ChIP sequencing of DNA” provided by Illumina.  Briefly, ChIPed DNA was end repaired using ‘End-It DNA End Repair Kit’ (Epicentre, ER0720).  The ‘dA’ base was then added to the 3’ ends of the blunt-ended DNA fragments using Klenow fragment (3’-5’exo-) (NEB, M0212S).  Linker for single read was ligated to the DNA molecules with ‘dA’ overhang using LigaFast kit (Promega, M8221).  After 2% agarose gel running with TAE buffer, the gel region containing about 150-300 bp DNA was excised for adapter ligated DNA size selection.  The adapter modified DNA fragments were enriched by PCR and purified by running 2% agarose gel in TAE buffer for isolation of DNA fragments in the range of 200-300 bp.  The purified DNA sample was ready for Illumina sequencing after quality validation. RNA-seq libraries were constructed using barcode method and then was sequenced by an Illumina Genome Analyzer II platform.

tag: line

value: young leaf tissues

tag: chip antibody manufacturer

value: Biosource International


title: OMA8.05 CenH3 ChIP-seq rep2

source_name: OMA8.05 CenH3 ChIP-seq

tag: chip antibody


title: OMA10.26 CenH3 ChIP-seq

source_name: OMA10.26 CenH3 ChIP-seq

tag: tissue


title: OMA8.05 CenH3 ChIP-seq rep1


title: OMA3.01 RNA-seq replicate 2

data_processing:
ChIP-seq reads were mapped to reference genome of maize B73 version 2 using MAQ alignment program. ChIP-seq reads generated from neoM3, OMA3.01, OMA2.51, OMA1.36, OMA5.60, and OMA6.34 lines were mapped to chromosomes 3, 3, 2, 1, 5 and 6 of B73, respectively. We allowed 1 bp mismatch between each sequence read and the reference genome, then kept only reads that mapped to a unique position in the reference genome for further analysis. Here we only released the reads mapped to maize chromosomes.
We used TopHat to map sequence reads from RNA-seq to the same reference genome and employed Cufflink to measure the difference of gene expression level between OMA3.01 and neoM3.
Genome_build: The gene annotation of maize genome (version 2) and reference genome were downloaded from http://www.maizesequence.org/ (B73 RefGen_v2)
Supplementary_files_format_and_content: In addtition to the raw data of fastq, we released the distribution of ChIP-seq reads along chromosomes. We used the reads number in 10kb window to represent the density of CenH3 signals and released the gff files.

source_name: young leaf tissues

extract_protocol:
Leaves were collected and ground into fine powder in liquid nitrogen.  The resulting powder was suspended in nuclear isolation buffer (NIB: 20mM Tris-HCl, 50mM EDTA, 5mM Spermidine, 0.15mM Spermine, 0.1% mercaptoethanol, 40% Glycerol, pH 7.5) and followed the standard protocol for nuclei isolation.  Total RNA was extracted using a RNeasy plant kit (Qiagen catalog no. 74904). Approximately 40 μg total RNA was converted to cDNA using the mRNA-seq kit from Illumina.
Construction of ChIP-seq libraries was according to the protocol of “preparing samples for ChIP sequencing of DNA” provided by Illumina.  Briefly, ChIPed DNA was end repaired using ‘End-It DNA End Repair Kit’ (Epicentre, ER0720).  The ‘dA’ base was then added to the 3’ ends of the blunt-ended DNA fragments using Klenow fragment (3’-5’exo-) (NEB, M0212S).  Linker for single read was ligated to the DNA molecules with ‘dA’ overhang using LigaFast kit (Promega, M8221).  After 2% agarose gel running with TAE buffer, the gel region containing about 150-300 bp DNA was excised for adapter ligated DNA size selection.  The adapter modified DNA fragments were enriched by PCR and purified by running 2% agarose gel in TAE buffer for isolation of DNA fragments in the range of 200-300 bp.  The purified DNA sample was ready for Illumina sequencing after quality validation. RNA-seq libraries were constructed using barcode method and then was sequenced by an Illumina Genome Analyzer II platform.


title: OMA3.01 RNA-seq replicate 1


title: OMA3.01 CenH3 ChIP-seq

value: anti-CenH3 (Biosource International)


title: neoM3 CenH3 ChIP-seq

data_processing:
ChIP-seq reads were mapped to reference genome of maize B73 version 2 using MAQ alignment program. ChIP-seq reads generated from neoM3, OMA3.01, OMA2.51, OMA1.36, OMA5.60, OMA6.34, OMA8.05, OMA9.41 and OMA10.26 lines were mapped to chromosomes 3, 3, 2, 1, 5, 6, 8, 9, and 10 of B73, respectively. We allowed 1 bp mismatch between each sequence read and the reference genome, then kept only reads that mapped to a unique position in the reference genome for further analysis. Here we only released the reads mapped to maize chromosomes.
We used TopHat to map sequence reads from RNA-seq to the same reference genome and employed Cufflink to measure the difference of gene expression level between OMA3.01 and neoM3.
Genome_build: The gene annotation of maize genome (version 2) and reference genome were downloaded from http://www.maizesequence.org/ (B73 RefGen_v2)
Supplementary_files_format_and_content: In addtition to the raw data of fastq, we released the distribution of ChIP-seq reads along chromosomes. We used the reads number in 10kb window to represent the density of CenH3 signals and released the gff files.


title: OMA6.34 CenH3 ChIP-seq


title: OMA2.51 CenH3 ChIP-seq


title: H3K9me3ES_ChIPSeq

status: Public on Aug 31 2013

city: Munich

first: Miriam

last: Gagliardi

state: Bayern

address: Kraepelinstrasse 2-10

country: Germany

institute: Max Planck Institute of Psychiatry

data_processing:
Base-calling was performed using The SOLiD Experiment Tracking System (SETS) software. This analysis involved image alignment, color assignment, color calls and quality value assignments.
Short reads of 50 bp were first analysed by the Applied’s pipeline software for quality filtering and aligned to the mouse reference genome (mm9) by using Bioscope
Data were filtered by uniquely aligned reads and a single read for each starting position was considered
The SICER peak-finding algorithm (version 1.1 http://home.gwu.edu/~wpeng/Softw are.htm) was used to identify the H3K9me3- and H3K36me3-enriched sites throughout the genome. SICER’s parameter settings were false discovery rate (FDR): 1e-7, window size: 200 bp, expected fragment size: 350 bp and gap size: 3 (600 bp) and 5 (1000 bp) for H3K9me3 and H3K36me3, respectively.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files were generated by the SICER software. Scores represent the enrichment values normalized to the input

source_name: untreated ESCs

growth_protocol: Wild-type mouse TBV2 (129/SvP) embryonic stem cells (ESCs) were cultured in complete medium containing leukemia inhibitory factor (LIF) without non essential aminoacids.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Solid System 4.0 Applied's instructions accompanying the Kit Fragment Library Construction kit . Briefly, sheared DNA was end-repaired and P1 and P2 Adaptors were ligated to the DNA ends. After purification with Agencourt AMPure XP beads, the DNA fragments were used for nick translation and PCR amplification (10–15 cycles). The prepared libraries were subsequently purified with Agencourt AMPure XP beads and then sequenced on the Solid System 4 following the manufacturer's protocols.

treatment_protocol: ESCs were seeded at low density on gelatin-coated feeder-free plates and incubated for 5 days in complete medium without (Control ESCs) or with L-Proline (500 μM) (L-Pro -induced cells; PiCs)

tag: cell type

value: TBV2 Embryonic stem cells

tag: strain

value: H3K9me3 (Abcam, ab8898)


title: Input


title: H3K9me3PiCs_ChIPSeq

source_name: L-Pro treated ESCs


title: H3K36me3PiCs_ChIPSeq

value: H3K36me3 (Abcam, ab9050)


title: H3K36me3ES_ChIPSeq


title: MS2 + let-7d-5p

city: Bangalore

first: Aishwarya

last: Narayanan

address: 5th Floor, KBP, Bellary Road

country: India

institute: Strand Life Sciences

data_processing:
Basecalls performed using CASAVA version 1.8
Quality control, alignment and quantification were performed using the Avadis NGS Software (v 1.4) from Strand Life Sciences
3' adapter was trimmed allowing for 2 mismatches in the adapter sequence
Trimmed reads were aligned against the hg19 reference sequence allowing for 1 mismatch
Reads matching more than 10 locations in the genome were discarded
For all other reads, upto 5 best matches were considered
A read was assigned to a miRNA only if the 5' end of the read matched the 5' end of the miRNA
Genome_build: hg19, miRBase (version 18)  annotations were used to assign reads to miRNA genes
Supplementary_files_format_and_content: tab-delimited file containing the miRNA name and number of reads assigned to it by the Avadis NGS quantification method

organism: Escherichia phage MS2

source_name: MS2 + let-7d-5p

extract_protocol: Illumina TruSeq Small RNA Kit with TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCC as the 3' adapter. 3' then 5' Adapter Ligation, RT, followed by PCR.

tag: biomaterial

value: Synthetic miRNA templates for let-7d-5p were spiked into MS2 phage total RNA (Roche, #10165948001) at 5 x 10^6 copies / ug RNA


title: MS2 + let-7c

source_name: MS2 + let-7c

value: Synthetic miRNA templates for let-7c were spiked into MS2 phage total RNA (Roche, #10165948001) at 5 x 10^6 copies / ug RNA


title: serum + spiked miRs constant concentration repeat

value: Synthetic miRNA templates for miR-10a-5p, let-7a-5p, miR-302a-3p and miR-133a were spiked in serum RNA at 6000 copies per ul serum RNA


title: serum + spiked miRs variable concentration

value: Synthetic miRNA templates for miR-10a-5p, let-7a-5p, miR-302a-3p and miR-133a were spiked in serum RNA at 30,000 copies, 12,000 copies, 3,000 copies, or 600 copies respectively per ul serum RNA


title: serum + spiked miRs variable concentration repeat


title: MS2 + let-7b-5p

source_name: MS2 + let-7b-5p

value: Synthetic miRNA templates for let-7b-5p were spiked into MS2 phage total RNA (Roche, #10165948001) at 5 x 10^6 copies / ug RNA


title: neoM3 RNA-seq replicate 1


title: neoM3 RNA-seq replicate 2


title: serum + spiked miRs constant concentration


title: OMA5.60 CenH3 ChIP-seq


title: liver + miR-302d

source_name: liver + miR-302d

value: Synthetic miRNA templates miR-302d-3p were spiked into human liver total RNA (Life Technologies, # AM7960) at 5 x 10^6 copies / ug RNA


title: liver + miR-302c

source_name: liver + miR-302c

value: Synthetic miRNA templates miR-302c-3p were spiked into human liver total RNA (Life Technologies, # AM7960) at 5 x 10^6 copies / ug RNA


title: MS2 + let-7a-5p

source_name: MS2 + let-7a-5p

value: Synthetic miRNA templates for let-7a-5p were spiked into MS2 phage total RNA (Roche, #10165948001) at 5 x 10^6 copies / ug RNA


title: liver + miR-302a

source_name: liver + miR-302a

value: Synthetic miRNA templates miR-302a-3p were spiked into human liver total RNA (Life Technologies, # AM7960) at 5 x 10^6 copies / ug RNA


title: miRQC D repeat

source_name: miRQC D repeat

value: Mixture of 75% UHRR and 25% HuBr Total RNA


title: miRQC D

source_name: miRQC D


title: miRQC C

source_name: miRQC C

value: Mixture of 25% UHRR and 75% HuBr Total RNA


title: miRQC B

source_name: miRQC B

value: HuBr - human brain total RNA (Life Technologies, #AM6050)


title: miRQC A

source_name: miRQC A

value: UHRR -Universal Human Reference RNA (Agilent Technologies, #750700)


title: miRQC C repeat

source_name: miRQC C repeat


title: miRQC A repeat

source_name: miRQC A repeat


title: miRQC B repeat

source_name: miRQC B repeat


title: scRRBS_Female_Pronucleus5

city: Hangzhou

first: Hongshan

last: Guo

state: Zhejiang Province

address: No.1369, Wenyixi Road

department: School of Medicine, Zhejiang University

institute: Liangzhu Laboratory

description: MspI digested and bisulfite treated genomic DNA

data_processing:
Raw pair-end fastq reads were firstly trimmed to remove the adapter sequences and low quality bases, then the remaining truncated reads were aligned to the mm9 mouse reference genome (downloaded from UCSC Genome browser) using the Bismark tool with the default parameter. And the methylation level of each single CpG site was estimated as the number of reported C (methylated), divided by the total number of reported C (methylated) or T (unmethylated) at the same position of the reference genome. The processed methylation_calling files (.bed) were generated after alignment against mm9 genome applying a customized Perl script, which including methylation status of cytosines existing in CpG, CHH and CHG context.
genome build: mm9

source_name: female pronucleus

growth_protocol: Mouse embryonic stem cells were maintained without feeders on gelatinlized dishes in the presence of 1,000U/ml leukemia inhibitory factor (LIF, Millipore) in Dulbecco's Modification of Eagle's Medium (DMEM/F-12, Gibco) containing 20% fetal calf serum (FCS, Gibco) for routine passage. Metaphse II oocytes or male and female pronuclei from zygotes (after mating with 129S2/Sv male mice) were recovered from the oviduct ampulla of super-ovulated mice of C57BL/6N strain, while the spermatozoa were obtained from the caudal epididymides of adult 129S2/Sv male mice.

extract_protocol: Cells were picked into the lysis buffer to release naked DNA, then the released DNAs were digested with MspI, then filled-in and tailed with an extra "A" , and ligated with Illumina indexed adaptors. Bisulfite conversion was performed under the manufacturer’s instructions of the MethyCode DNA Methylation Kit (Invitrogen) with minor modification, and the converted DNAs were enriched by two rounds of PCR amplifications and size-selected after running 12% native polyacrylamide TBE gel. The quality-ensured libraries were used for pair-ended deep sequencing on Illumina HiSeq2000 Sequencer.

value: female pronucleus

value: zygote

tag: passage


title: Control 2 Replicate 2

city: Seattle

first: Kyle

last: Siebenthall

state: Washington

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

description: With typical paired-end sequencing data, both reads map near each other in the genome within the distance expected by insert size; however, in my case the first read of a pair maps to a single position in the genome, while the second read of a pair maps elsewhere in the genome, even on a different chromosome from the first. Thus, insert size is not relevant.

data_processing:
Prey reads (read2) that passed the Illumina quality filter were scanned for the presence of DpnII sites; sequence after the DpnII site was trimmed and all reads of at least 20bp were kept
Trimmed prey reads were aligned to the reference human genome (hg19, standard chromosomes only) using BWA with default paramaters that allowed up to two mismatches in the seed region and retained only uniquely-aligning reads
Aligned prey reads and their paired SSLP reads were subsequently analyzed using a custom R script (v2.15) and the Bioconductor (v2.10) software packages
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files represent processed prey reads that were aligned to the hg19 reference genome; Columns indicate: chromosome (chr), alignment start (start), alignment end (end), strand, flowcell number and lane (flowcell), read name (readID), BWA mapping quality (mapq), genotype of paired bait read (SSLP)

growth_protocol: Myoblasts grown at 37degC,5% CO2 in F-10 medium with 20% FBS, 1% Pen/strep, 10ng/ml bFGF, 1 uM dexamethasone

extract_protocol: Circular chromosome conformation capture (4C) was performed on 10e7 cells; inverse PCR with primers recognizing a HindIII-DpnII fragment containing the SSLP of the FSHD locus amplified prey fragments captured by this bait in the assay; inverse PCR products were prepared for Illumina sequencing using a custom library preparation method that involved Covaris fragmentation, adapter ligation and amplification to add attachment sequences; the library was subjected to paired-end sequecing, with the first read yielding the SSLP sequence and the second read yielding sequence from the bait fragment captured by each SSLP

value: primary myoblast

tag: disease state

value: Control

tag: Sex

value: Female

tag: age (y)


title: FSHD1 Replicate 1

value: Male


title: FSHD1 Replicate 2


title: FSHD2 Replicate 1


title: scRRBS_Female_Pronucleus4

tag: developmental stage


title: liver + miR-302b

source_name: liver + miR-302b

value: Synthetic miRNA templates miR-302b-3p were spiked into human liver total RNA (Life Technologies, # AM7960) at 5 x 10^6 copies / ug RNA


title: scRRBS_Male_Pronucleus5

source_name: male pronucleus

value: male pronucleus


title: scRRBS_Sperm6

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
Bisulfite-converted reads were aligned to the mouse refference genome (mm9) using Bismark software
CpG methylation level was estimated using comstomized Perl scripts.
Genome_build: mm9
Supplementary_files_format_and_content: bed files which include the methylation level of cytosines in CpG, CHH and CHG context.

source_name: sperm

extract_protocol:
Single cells were picked into the lysis buffer which contained protease to release the naked DNAs
Cells were picked into the lysis buffer to release naked DNA; then the released DNAs were digested with MspI, then filled-in and tailed with an extra "A" , then ligated with Illumina indexed adaptors. Bisulfite conversion was performed under the manufacturer’s instructions of the MethyCode DNA Methylation Kit (Invitrogen) with minor modification, the converted DNAs were enriched by two rounds of PCR amplifications and size-selected after running 12% native polyacrylamide TBE gel. The quality-ensured libraries were used for pair-ended deep sequencing on Illumina HiSeq2000 Sequencer.

value: sperm


title: Control 2 Replicate 1


title: Control 1 Replicate 1


title: Control 1 Replicate 2


title: FSHD2 Replicate 2


title: scRRBS_Sperm7


title: scRRBS_Female_Pronucleus3


title: scRRBS_Female_Pronucleus2


title: scRRBS_Male_Pronucleus3


title: scRRBS_Male_Pronucleus2


title: scRRBS_Female_Pronucleus1


title: OMA1.36 CenH3 ChIP-seq

source_name: young leaf tissues

value: young leaf tissues

value: anti-CenH3 (Biosource International)

value: Biosource International


title: scRRBS_Sperm5


title: scRRBS_Sperm4


title: scRRBS_Male_Pronucleus1


title: scRRBS_Sperm3


title: scRRBS_Sperm2


title: scRRBS_Polar_Body2

source_name: polar body

value: polar body

value: the first polar body


title: scRRBS_Sperm1


title: scRRBS_Polar_Body1


title: scRRBS_MII_Oocyte1

source_name: MII oocyte

value: MII oocyte

value: oocyte


title: RRBS_mESC_Pooled_20Cell

source_name: embryonic stem cell

value: embryonic stem cell


title: scRRBS_MII_Oocyte2


title: RRBS_mESC_Bulk


title: scRRBS_mESC_Single_Cell7


title: RRBS_mESC_Pooled_5Cell


title: scRRBS_mESC_Single_Cell3


title: scRRBS_mESC_Single_Cell1


title: scRRBS_mESC_Single_Cell8


title: scRRBS_mESC_Single_Cell2


title: scRRBS_mESC_Single_Cell5


title: scRRBS_mESC_Single_Cell4


title: mycelia_incubated_30C_24h

city: Beijing

first: Jiang

last: Zhengqiang

address: Qinghua East Road, Haidian Distric

department: Department of Biotechnology

institute: College of Food Science and Nutritional Engineering, China Agricultural University

description: polyA RNA from mycelia of R. miehei CAU432 after incubation at 30C

data_processing: High quality SOLiD reads with median QV (quality value) over 13 were, using Corona_Lite_Plus_4.2.1 (Applied Biosystems), mapped to the R. miehei genome and splice junction database on the base of the predicted gene models. The splice junction database were constructed with the 45 bp length sequences extracted from the termini of each exon. The 50 bp length RNA-seq reads were mapped to R. miehei assembled genome at 5 mismatch, the unmapped reads were mapped to artificial splice junction database. Iteratively, the first 45 bp (at 4 mismatches), 40 bp (at 4 mismatches), 35 bp (at 3 mismatches) and 30 bp (at 3 mismatches) sequences extracted from unmapped reads were mapped to genome and splice junction database in the order.

organism: Rhizomucor miehei

extract_protocol: Total RNA was extracted from mycelia of R. miehei CAU432 after incubation at 30C and 50C for 1 day according to the previous report (Cloonan et al. 2008), and poly(A) mRNA was purified on oligo d(T) conjugated magnetic beads using FastTrack MAG mRNA Isolation Kits (Invitrogen, USA) according to the manufacturer's protocol. The purified mRNA was fragmented, ligated with SOLiD adaptor mix and reversely transcribed by using SOLiD Total RNA-Seq Kit according to the manufacturer's protocol.

value: mycelia

tag: development stage


title: FSHD3 Replicate 1


title: mycelia_incubated_50C_24h

description: polyA RNA from mycelia of R. miehei CAU432 after incubation at 50C

growth_protocol: R. miehei CAU432 after incubation at 30C and 50C for 1 day


title: FSHD3 Replicate 2


title: scRRBS_Negative_Control1

description: MspI digested and bisulfite treated lambda DNA

organism: Lambdavirus lambda

source_name: lambda DNA

tag: sample type

value: control


title: Topotecan_RNAseq [human]

status: Public on Aug 30 2013

city: Carrboro

first: Chandri

last: Yandava

state: NC

address: 101 Renee Lynne Court

department: Carolina Institute for Developmental Disabilities

institute: University of North Carolina at Chapel Hill

data_processing:
Basecalls performed using Illumina CASAVA version 1.3 for single-end reads and CASAVA version 1.8 for paired-end reads
Reads were mapped to hg19 genome using bowtie  version 0.12.7 with default parameters for RNA-seq
Reads Per Kilobase of exon per million of reads mapped (RPKM) were calculated using R package DEGSeq (Wang et al., Bioinformatics, 2010) for RNA-seq
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files containing RPKM values for each sample.

source_name: iPSCs were differentiated into forebrain cortical neurons and treated with 10µM topotecan for 6 days.

growth_protocol: iPSCs derived from an Angelman Syndrome patient were cultured on irradiated mouse embryonic fibroblasts as described in Chamberlain et al. (PMID 20876107)

extract_protocol:
RNA was extracted using Trizol reagent.
Sranded libraries were constructed with Illumina kits for Stranded RNAseq.

treatment_protocol: iPSCs were differentiated into forebrain cortical neurons and treated with 10µM topotecan or vehicle for 6 days.

value: forebrain cortical neurons

tag: agent

value: Topotecan


title: scRRBS_Negative_Control2


title: Vehicle_RNAseq [human]

source_name: iPSCs were differentiated into forebrain cortical neurons and treated with vehicle for 6 days.

value: Vehicle


title: Bisulfite-Seq analysis of WGBS_Lib 66 derived from human fMuscle_Leg  cells; WGBS_Lib 66

first: BROAD

last: INSTITUTE

institute: Broad Institute

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 66
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.16319
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.16321
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1172596_BI.Fetal_Muscle_Leg.Bisulfite-Seq.UW_H24996.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: WGBS_Lib 66.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Fetal Muscle Leg Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Fetal Muscle Leg, Donor UW H24996 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18741
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FML BS 96 66
BROWSER_TRACK_DESCRIPTION: BI Fetal Muscle Leg Bisulfite-Seq Donor UW H24996 Library WGBS_Lib 66 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 453,448,191
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.64
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: Primary fetal leg muscle tissue; WGBS_Lib 66

extract_protocol: Library construction protocol: Genomic DNA (1.5~5µg) was fragmented to 100-500 bp using a Covaris S2. Purified DNA fragments were end-repaired. After A-tailing, the DNA fragments were ligated with methylated paired-end adapters. Adapter-attached DNA fragments of 300-400 bp, which contain 150-250 bp genomic DNA inserts, were gel-purified. The purified DNA fragments were subjected to two cycles of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen). Adapter-attached, bisulfite-converted DNA molecules were enriched by PCR using PfuTurboCx Hotstart DNA polymerase (Stratagene). The PCR amplified DNA fragments were subjected to a second gel size selection to remove PCR primers and adapter dimers. The enriched library was quantified using a Qubit fluorometer and Quant-iT dsDNA HS Assay Kit. Library sequencing was performed using 101 BP PE Illumina technology.

tag: sample alias

value: BioSam 1243

tag: sample common name

value: Fetal Muscle, Leg

value: Post-Mortem

value: presumed normal

tag: disease

value: Unknown

value: Female

value: Primary Tissue

value: Leg

value: University of Washington

value: 2x5hrs Epitect Kit

value: 5 ug

value: Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes

value: T4 Ligase (2,000U/ul) 16C o/n

value: Illumina paired end adapter

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: SPRI Beads

value: Pfu Turbo Cx hot start

value: Covaris S2 (TM)


title: Bisulfite-Seq analysis of WGBS_Lib 65 derived from human fThymus cells; WGBS_Lib 65

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 65
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.16318
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.16320
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1172595_BI.Fetal_Thymus.Bisulfite-Seq.UW_H24943.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: WGBS_Lib 65.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Fetal Thymus Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Fetal Thymus, Donor UW H24943 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18736
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FT BS 43 65
BROWSER_TRACK_DESCRIPTION: BI Fetal Thymus Bisulfite-Seq Donor UW H24943 Library WGBS_Lib 65 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 416,572,769
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.45
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: Primary fetal thymus tissue; WGBS_Lib 65

value: BioSam 1238

value: Fetal Thymus

value: Post-Mortem

value: presumed normal

value: Thymus


title: scRRBS_Male_Pronucleus4

value: male pronucleus

value: zygote


title: RRBS_mESC_Pooled_10Cell

value: embryonic stem cell


title: scRRBS_mESC_Single_Cell6


title: Bisulfite-Seq analysis of WGBS_Lib 23 derived from human CD56+ ectoderm cells; WGBS_Lib 23

description:
sample_term_id: CL_0000221
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 23
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15804
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13314
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1112850_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.Bisulfite-Seq.WGBS_Lib_23.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: WGBS_Lib 23.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of hESC Derived CD56+ Ectoderm Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from hESC Derived CD56+ Ectoderm Cultured Cells, Donor WGBS_Lib 23 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18740
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCEcto BS 23
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Ectoderm Cultured Cells Bisulfite-Seq Library WGBS_Lib 23 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 260,862,074
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.12
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: 0.99

**********************************************************************

source_name: CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; WGBS_Lib 23

tag: sra sample accession

tag: lineage

value: ectoderm

tag: medium

value: Days 0-5:DMEM F12, 15% KSR, Dorsomorphin (2um), A83-01 (2um), PNU 74654 (2um)

tag: line

value: CD56+ ectoderm

value: adherence

tag: batch

value: BioSAli 877

value: Cell Line

value: Male

value: Harvard

value: 2x5hrs Epitect Kit

value: 5 ug

value: Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes


title: Bisulfite-Seq analysis of WGBS_Lib 22 derived from human CD56+ ectoderm cells; WGBS_Lib 22

description:
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 22
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15803
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13314
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1112849_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.Bisulfite-Seq.WGBS_Lib_22.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: WGBS_Lib 22.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of hESC Derived CD56+ Ectoderm Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from hESC Derived CD56+ Ectoderm Cultured Cells, Donor WGBS_Lib 22 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18739
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCEcto BS 22
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Ectoderm Cultured Cells Bisulfite-Seq Library WGBS_Lib 22 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 433,580,444
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.24
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.99

**********************************************************************

source_name: CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; WGBS_Lib 22

value: T4 Ligase (2,000U/ul) 16C o/n

value: Illumina paired end adapter

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: SPRI Beads

value: Pfu Turbo Cx hot start

value: Covaris S2 (TM)


title: Bisulfite-Seq analysis of WGBS_Lib 37 derived from human hippocampus middle cells; WGBS_Lib 37

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 37
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15544
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9441
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1112838_BI.Brain_Hippocampus_Middle.Bisulfite-Seq.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: WGBS_Lib 37.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Brain Hippocampus Middle Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Brain Hippocampus Middle, Donor 149 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18731
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: BHM BS 49 37
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Bisulfite-Seq Donor 149 Library WGBS_Lib 37 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 694,854,894
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.32
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 12
MAXIMUM_REPLICATE_CORRELATION: 0.99

**********************************************************************

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; WGBS_Lib 37

value: Brain, Hippocampus Middle

value: Post-Mortem

value: no AD evident at demise

value: Hippocampus Middle

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years


title: E7

city: Edinburgh

first: Grzegorz

last: Kudla

address: Crewe Road

department: MRC HGU

country: United Kingdom

institute: University of Edinburgh

description: control experiment for background determination - protocol E4

data_processing:
Demultiplexing: Illumina reads were assigned to experimental and control samples using their 5' barcode sequences, and barcodes were clipped
Collapsing reads: Identical sequencing reads were treated in the analysis as one, information on the actual numbers of reads is maintained in the sequence IDs: for E1-E4: X_Y and for E5-E6: X-Z_Y where X is frequency rank of the sequence, Y is a number of identical reads and Z  corresponds to the number of random barcodes associated with identical reads
Reads alignment: Collapsed reads were aligned to a custom transcriptome database by BLAST, version 2.2.24; the components of the BLAST database come from BioMart, NCBI, genomic tRNA database and MirBase; more details in Helwak et. al. Cell 2013
Chimeras identification: We identified as chimeras those reads where: (1) the read yielded at least two blast hits with e-value < 0.1 against the human transcriptome database; (2) the hits were either directly adjacent in the read, or with up to 4 nucleotides gap or overlap between hits; and (3) the hits were in sense orientation with respect to the blast database. We rejected reads with more than ten hits in the database. A custom script was used for the purpose.
The energy of identified interactions was determined by scripts from UnaFold suite (by Markham and Zucker)
Supplementary_files_format_and_content: all processed data files are in the custom .hyb format

source_name: Flp-in T-REx 293-PTH-AGO1

growth_protocol: Flp-In T-REx 293 cells were stably transfected with a plasmid encoding AGO1 N-terminally tagged with ProteinA-TEV protease cleavage site-Hisx6. Expression of tagged AGO1 is tetracycline inducible. Cells were grown in Dulbecco’s modified Eagle medium (DMEM) with high glucose, supplemented with 10% fetal bovine serum at 37°C under humidified air with 5% CO2.

extract_protocol:
UV stabilized protein-RNA interactions were purified under denaturing conditions. RNAs associated with AGO1 were partially truncated, and the ends of RNA-duplexes formed within AGO1 RNA binding pocket were ligated together.
Sequencing 3' adapter was ligated while AGO1-RNA complexes were bound to Ni-NTA agarose, 5' adapter (barcoded for samples E2-E10) was ligated in solution after RNA isolation. RNA library was reverse transcribed and PCR amplified.

treatment_protocol: Cells were induced for PTH-AGO1 expression with Doxycycline for 36 hrs. Then existing protein-RNA complexes were stabilized by UV irradiation  of living cells.

tag: cell type

value: Flp-In T-REx 293

value: PTH-AGO1 bound RNAs

tag: barcode

value: NNNACTCAGC


title: scRRBS_Negative_Control3

value: control


title: E9

description: control experiment for background determination - protocol E6

value: NNNGCGCAGC


title: E8

organism:
Saccharomyces cerevisiae
Homo sapiens

source_name: Flp-in T-REx 293-PTH-AGO1 + BY4741

value: NNNGACTTAGC


title: E10

value: NNNATTAGC


title: Formaldehyde Females

city: Moscow

first: Anna

last: Kudravsteva

address: Vavilova, 32

country: Russia

institute: EIMB RAS

data_processing:
We used the R package DESeq (Anders & Huber 2010) to conduct multiple comparisons of the top 500 expressed genes for all experimental groups,  using principal component analysis.
Genome_build: The transcriptome was assembled using Novoalign software and BDGP5 as a reference. The number of reads per transcript was counted by the coverageBed application. Each of the libraries yielded approximately 50  million or more high-quality filtered sequences.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and p-values for each Sample

source_name: Drosophila melanogaster

extract_protocol:
Total RNA was extracted from 10 Drosophila images with ZR RNA MiniPrep Research; Irvine, CA, USA) per the manufacturer's instructions. The RNA quantity was determined using a Qubit® 2.0 Fluorometer (Invitrogen; NY, USA) and the RNA integrity (RNA Integrity Score ≥ 8) was determined using an Agilent 2100 Bioanalyzer (Agilent; Palo  Alto, CA, USA) per each manufacturer’s instructions.
To prepare samples for the mRNA sequencing libraries, we used the Illumina TruSeq Sample Preparation Kit (Low-Throughput protocol) (Illumina 2012).

tag: strain

value: Canton-S

tag: age

value: 5 days

tag: treatment

value: formaldehyde


title: Toluene Females

value: toluene


title: Formaldehyde Males


title: Radiation Males

value: radiation


title: Dioxine Females

value: dioxine


title: IgG_TgERG_leukemia_2

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

institute: University of Cambridge

description: Transgenic GATA1s

data_processing:
Reads aligned to mm9 using Bowtie
BedGraphs (wigs) created in-house
Peak calling performed using MACS
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph – read density profiles
Supplementary_files_format_and_content: bed – peaks

extract_protocol:
Spleen cells were fixed with 1% formaldehyde and ChIP assays were performed as previously described (Wilson NK et al., 2010 Cell Stem Cell) using polyclonal antibodies against ERG-1/2/3 (clone C-17, Sc354X, Santa Cruz) and control nonspecific rabbit IgG (I5006, Sigma).
Each sample was amplified and sequenced using the Illumina 2G Genome Analyzer, following manufacturer's instructions.

tag: antibody

value: rabbit IgG (I5006, Sigma)


title: ERG_TgERG_leukemia_2

description: Transgenic GATA1s

value: ERG-1/2/3 (clone C-17, Sc354X, Santa Cruz)


title: Toluene Males


title: IgG_TgERG_leukemia_1

description: Transgenic


title: Control Males


title: Radiation Females


title: ERG_TgERG_leukemia_1

description: Transgenic


title: Control Females


title: Vehicle_Chipseq [mouse]

data_processing:
Basecalls performed using Illumina CASAVA version 1.3 for single-end reads and CASAVA version 1.8 for paired-end reads
Reads were mapped to mm9 genome using bowtie  version 0.12.7 with default parameters for RNA-seq, m-1 was used for Chip-seq mapping
Traveling ratios (TR) were calculated after removing duplicate reads, as the ratios between reads mapped (Reads per million) to promoter region and the gene body.
Reads Per Kilobase of exon per million of reads mapped (RPKM) were calculated using R package DEGSeq (Wang et al., Bioinformatics, 2010) for RNA-seq.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq: Tab-delimited text files containing traveling ratio for each sample.
Supplementary_files_format_and_content: RNA-Seq: Tab-delimited text files containing RPKM values for each sample.

source_name: cultured cortical neurons

growth_protocol: Cortical neurons were cultured from E13-15 mouse embryos for 7 days in vitro.

extract_protocol:
Cells for ChIP were fixed, nuclei isolated, and chromatin sheared by sonication. Pol2 DNA complexes were isolated by immunoprecipitation.
Libraries were constructed with Illumina TruSeq kits for RNA or ChIPseq.

treatment_protocol: After 7 days in vitro, neurons were treated with 300 nM topotecan or vehicle. After 72 hrs drug treatement, cells were harvested for RNAseq or ChIPseq.

value: 10 days in vitro

value: cultured cortical neurons

value: Vehicle

value: Anti-PolII N20 (Santa Cruz, sc-899)


title: Topotecan_RNAseq_rep5 [mouse]

extract_protocol:
RNA was extracted using Trizol reagent.
Libraries were constructed with Illumina TruSeq kits for RNA or ChIPseq.

value: C57BL/6J x CASTEi/J

value: Topotecan


title: Topotecan_Chipseq [mouse]


title: Topotecan_RNAseq_rep3 [mouse]


title: Topotecan_RNAseq_rep4 [mouse]


title: Topotecan_RNAseq_rep2 [mouse]


title: Topotecan_RNAseq_rep1 [mouse]


title: Vehicle_RNAseq_rep3 [mouse]


title: Dioxine Males


title: Vehicle_RNAseq_rep4 [mouse]


title: Vehicle_RNAseq_rep2 [mouse]


title: Vehicle_RNAseq_rep1 [mouse]


title: E6_TAON

value: Flp-In T-REx 293

value: PTH-AGO1 bound RNAs


title: E4_L2 and E4_L2HS

value: CACAGC


title: E3_L1 and E3_L1HS

value: GA


title: E2_0727 and E2_0727HS

value: AC


title: E1_A12

value: NO BARCODE


title: Yukon cauline

city: Hamilton

first: Elizabeth

middle: A

last: Weretilnyk

state: Ontario

address: 1280 Main Street West

department: Biology

country: Canada

institute: McMaster University

description: Three repeats were sequenced for each experimental condition

data_processing:
Sequences were trimmed using GS De Novo Assembler v2.6 using default parameters and SeqTrim with minimum quality 20, window size 10, minimum length 80 bp, no contamination removal.
GMAP v2011-11-30 (http://research-pub.gene.com/gmap/src/gmap-gsnap-2011-11-30.tar.gz) was used to map reads to reference genome (ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v7.0/Thalophila/assembly/Thalophila_173_RM.fa.gz).
Reads were counted using htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) with genome annotation file (ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v7.0/Thalophila/annotation/Thalophila_173_gene.gff3.gz).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by dividing number of mapped reads by the median mRNA length and library size.
The expression for genes Thhalv10002723m and Thhalv10002628m were manually adjusted; please refer to the associated publication.
Genome_build: Phytozome v7.0, available at ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v7.0/Thalophila/.
Supplementary_files_format_and_content: Two column tab-delimited text files including gene names from GFF3 file and associated RPKM values for a given Sample.

organism: Eutrema salsugineum

source_name: Yukon cabinet cauline leaves

growth_protocol: Cabinets: Seeds in pots were stratified for 2 d at 4°C before transfer to growth chambers set with a 21 h day and irradiance of 250 μmol m-2s-1 and 22°C/10°C day/night temperature regime. Plants were watered daily as needed and fertilized one time per week with 1 g L-1 20-20-20 (NPK) fertilizer

extract_protocol:
Extractions of nucleic acids from Eutrema proved to be unsatisfactory using methods commonly employed for Arabidopsis. These issues were circumvented using a modification of the method described for cotton leaves in Wan and Wilkins (1994). Briefly, approximately 0.5 g of frozen leaf tissue in liquid nitrogen was ground to fine powder in a mortar and pestle and RNA was extracted according to the manufacturer's recommendation with 8 mL Tri Reagent (Sigma). This first crude preparation of total RNA was resuspended in 1 mL nuclease-free water and purified of polyphenolics and carbohydrates using a "hot borate" step (200 mM sodium borate decahydrate, 30 mM Na-EGTA, 1% (w/v) SDS, 1% (w/v) sodium deoxycholate, 2% (w/v) polyvinylpyrrolidone (PVP 40000), 0.1% (w/v) DEPC, pH 9.0) followed by sequential RNA precipitations with 2 M lithium chloride then ethanol. From approximately 150 μg of this high quality total RNA, mRNAs were purified in 3-4 repeated rounds of oligo-dT selection using a Sigma mRNA miniprep kit (MRN-10). Abundance and quality of RNA following total RNA extraction was assessed using RNA 6000 Nano chips (Agilent) on a Bioanalyzer 2100 instrument and mRNA selections were continued until no rRNA peaks were visible on Bioanalyzer electropherograms.
Procedures for RNA fragmentation, cDNA synthesis, sequencing adaptor ligation andsize selection closely followed the Roche cDNA Rapid Library Preparation Manual,December 2010. Briefly, 200 ng of mRNA was chemically fragmented with ZnCl2 andused as a template to synthesize double-stranded cDNA using Roche Primer "random". The product of each cDNA synthesis was end-repaired and indexed with the regularRapid Library Adaptor with one exception: Libraries Shandong-2 and Shandong-3 wereindexed by ligation of Roche MID Adaptors 2 and Adaptors 3, respectively. Each cDNAlibrary was quantified by fluorometry on a Biotek Synergy 2 fluorometric plate reader.Size selection of each library in the 600-1200 bp range was verified by running a smallaliquot on a High Sensitivity DNA chip (Agilent) on the Bioanalyzer 2100. All sequencing libraries were in the range of 108 to 109 molecules/mL and stored in this concentrated form in TE buffer at -80 °C for several days to approximately 1 month until further analysis. Quantitative real-time RT-PCR was conducted on a Bio-Rad CFX96 instrument using primers specific for Eutrema ACTIN1 (F -ACAGGGTGCTCTTCAGGAGCGAT; R - GCATGGTGTTGTGAGCAACTGGG), whose product spans an intron. Contaminating genomic DNA was not detected in any sequencing library.

tag: accession

value: Yukon

tag: tissue

value: cauline leaf tissue


title: Yukon Field 2005 3

source_name: Yukon field 2005 cauline leaves

growth_protocol: Field.  From field site near Whitehorse, Yukon (location: 60° 55.9280N, 135° 10.2490 W; elevation 647 on June 23,2005.  At time of harvest the soil temperature was 18°C, the daytime air temperature was 24°C, and the light intensity was 1433 μmoles m–2 s–1 Average high and low temperatures for the ten-day period before harvest were 18°C and 7°C, respectively.


title: Δpp-1 5h

first: Abby

last: Leeder

address: 111 Koshland Hall

institute: UC Berkeley

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome with Tophat.
Transcript abundance (FPKM) was estimated with Cufflinks using upper quartile normalization and mapping against reference isoforms.
Fisher's exact test was used to briefly measure the statistical significance of change in gene expression between the samples.
Genome_build: N. crassa OR74A (NC10)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Δpp-1 conidia, 30 degree incubation

growth_protocol: Innoculated at 10^6 conidia / ml and grown for 5 hours

extract_protocol:
mycelia were harvested, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
mRNA was purified with Dynabeads® Oligo dT magnetic beads (Illumina). Purified mRNA was fragmented with buffered zinc solution from Ambion (Cat # AM8740). First and second strand cDNA synthesis was carried out using Superscript II Reverse Transcriptase (Invitrogen) and DNA pol I (Invitrogen) and random primers. Illumina sequencing adapters were then ligated to the cDNA, 200bp fragments were purified by gel electrophoresis, and PCR enriched with Pfx DNA polymerase (Invitrogen).

tag: developmental stage

value: 5 hours growth

tag: genotype

value: delta pp-1


title: Yukon Cabinet 2

source_name: Yukon cabinet rosette leaves

value: rosette leaf tissue


title: Yukon Cabinet 1


title: Shandong Cabinet 3

source_name: Shandong cabinet rosette leaves

value: Shandong


title: Vehicle_RNAseq_rep5 [mouse]

value: 10 days in vitro

value: cultured cortical neurons

tag: agent


title: Yukon Field 2005 1


title: Shandong Cabinet 2


title: Pab1_1

status: Public on Aug 29 2013

city: Basel

first: Alex

middle: Charles

last: Tuck

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description:
Sample 28
All sequences start with the barcode NNNCACTAGC

data_processing:
Reads were pre-processed using the fastx toolkit: fastx_clipper -a TGGAATTCTCGGGTGCCAAGGC -l 15 | fastq_quality_trimmer -t 30 | fastq_quality_filter -q 23 -p 100 | fastx_artifacts_filter
Reads with identical sequence were collapsed, then barcodes removed (between 2 and 11 nt long)
Reads were mapped to the S. cerevisiae genome (SGDv64) using Novoalign with the following settings: -r Random -s 1
Subsequent analyses were performed using custom python and AWK scripts, and the pyCRAC package (Granneman, Webb and Kudla, submitted)
Genome_build: SGDv64 (GenBank Assembly ID: GCA_000146045.2)
Supplementary_files_format_and_content: SGR files generated using pyCRAC (Granneman, Webb and Kudla, submitted); these are pileups of all mapped reads across the genome; these are not normalised to the total number of reads in each library

growth_protocol: Yeast cultures were grown in SD (-TRP, or -TRP -LEU -URA) medium at 30C to OD=0.5

extract_protocol:
Cell lysate
Extracts from UV-crosslinked yeast cells were used to isolate RNAs cross-linked to a tagged protein in a 2-step purification protocol. Recovered RNAs are subjected to limited RNAse digest, linker ligation and cDNA amplification, and identified by Illumina sequencing (according to Granneman et al., PNAS, 2009).

treatment_protocol: Yeast cultures were irradiated with UV light, to fix protein:RNA interactions

value: BY4741 (MATa; his3-delta-1; leu2-delta-0; lys2-delta-0; ura3-delta-0)

tag: tagged protein

tag: growth medium

value: SD (-TRP)


title: Shandong Cabinet 1


title: Nab2_6delta

description:
Sample 25
All sequences start with the barcode NNNCGCTTAGC

value: BY4741 (MATa; his3-delta-1; leu2-delta-0; lys2-delta-0; ura3-delta-0) with RRP6 deleted


title: WT 5h

city: Berkeley

source_name: WT (FGSC 2489) conidia, 30 degree incubation

value: wt


title: Yukon Field 2005 2


title: Yukon Cabinet 3


title: E5_TA1

value: Flp-In T-REx 293

tag: sample type

value: PTH-AGO1 bound RNAs

value: NNNTAAGC


title: Nab2_2

description:
Sample 22
All sequences start with the barcode NNNCACTAGC


title: Ski2_1

description:
Sample 21
All sequences start with the barcode NNNGTGAGC


title: Gbp2_1

description:
Sample 19
All sequences start with the barcode NNNTAAGC


title: Tho2_1

description:
Sample 20
All sequences start with the barcode NNNCGCTTAGC


title: Hek2_1

description:
Sample 17
All sequences start with the barcode NNNGTGAGC


title: Mtr4_3

description:
Sample 13
All sequences start with the barcode NNNCACTAGC

value: BY4741 (MATa; his3-delta-1; leu2-delta-0; lys2-delta-0; ura3-delta-0) with pAT3

value: SD (-TRP -LEU -URA)


title: Mtr4_1

description:
Sample 12
All sequences start with the barcode NNNATTAGC

value: BY4741 (MATa; his3-delta-1; leu2-delta-0; lys2-delta-0; ura3-delta-0) with pAT2


title: BY_3

description:
Sample 16
All sequences start with the barcode NNNTAAGC

source_name: BY4741_No tagged protein

value: No tagged protein


title: Mtr4_2

description:
Sample 11
All sequences start with the barcode NNNTAAGC

value: BY4741 (MATa; his3-delta-1; leu2-delta-0; lys2-delta-0; ura3-delta-0) with pAT1


title: Xrn1_2

description:
Sample 10
All sequences start with the barcode CACAGC


title: BY_2

description:
Sample 9
All sequences start with the barcode GCGAGC

source_name: BY4741_negative control

value: none (negative control)


title: Tif1_1

description:
Sample 8
All sequences start with the barcode AC


title: Mex67_3

description:
Sample 29
All sequences start with the barcode NNNACTCAGC


title: Ski2_4

description:
Sample 31
All sequences start with the barcode NNNTGGAGC

data_processing:
Reads were pre-processed using the fastx toolkit: fastx_clipper -a TGGAATTCTCGGGTGCCAAGGC -l 15 | fastq_quality_trimmer -t 30 | fastq_quality_filter -q 23 -p 100 | fastx_artifacts_filter
Reads with identical sequence were collapsed, then barcodes removed (between 2 and 11 nt long)
Reads were mapped to the S. cerevisiae genome (SGDv64) using Novoalign with the following settings: -r Random -s 1
Subsequent analyses were performed using custom python and AWK scripts, and the pyCRAC package (Granneman, Webb and Kudla, submitted)
Genome_build: SGDv64 (GenBank Assembly ID: GCA_000146045.2)
Supplementary_files_format_and_content: SGR files generated using pyCRAC (Granneman, Webb and Kudla, submitted); these are pileups of all mapped reads across the genome; these are not normalised to the total number of reads in each library.

extract_protocol:
Cell lysate
Extracts from UV-crosslinked yeast cells were used to isolate RNAs cross-linked to a tagged protein in a 2-step purification protocol. Recovered RNAs are subjected to limited RNAse digest, linker ligation and cDNA amplification, and identified by Illumina sequencing (according to Granneman et al., PNAS, 2009). The 5' linkers are (mostly) barcoded - see sample description field for the sequence of the barcode for each sample.

tag: media


title: Cbc1_3

description:
Sample 24
All sequences start with the barcode NNNACTCAGC


title: Mex67_2

description:
Sample 7
All sequences start with the barcode GA


title: Ski2_2

description:
Sample 23
All sequences start with the barcode NNNTAAGC


title: BY_4

description:
Sample 27
All sequences start with the barcode NNNTAAGC


title: Ski2_3

description:
Sample 30
All sequences start with the barcode NNNCTAGC


title: Nab2_3

description:
Sample 26
All sequences start with the barcode NNNGCGCAGC


title: Nab2_1

description:
Sample 14
All sequences start with the barcode NNNGTGAGC


title: Cbc1_2

description:
Sample 15
All sequences start with the barcode NNNACTCAGC


title: Striatum Day 60 Male 4

city: Taipei

first: Pao-Yang

last: Chen

state: Taiwan

address: 128 Sec. 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

data_processing:
BS-seq reads were aligned to the mouse mm9 genome assembly using BS Seeker, allowing up to 10 mismatches.
Alignments with three consecutive methylated non-CG sites are removed.
If multiple alignments mapped to the same location only one is kept.
Genome_build: mouse mm9
Supplementary_files_format_and_content: Processed data (CGmap) is in text format.  column 1=chromosome id (see mouse_mm9_chromosomes.txt); column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.

organism: Mus musculus domesticus

source_name: Striatum

extract_protocol:
Genomic DNA was isolated from the BNST/POA using Qiagen AllPrep DNA/RNA Mini Kit (catalog no. 80204).
Genomic DNA was digested with MspI. They were then ligated with Illumina adaptors, and size selected. Fragments from 100 to 200 bases were selected. These fragments were denatured and treated with sodium bisulfite. Libraries were sequenced using the Solexa sequencing technology (Illumna Hiseq 2000 sequencers). The reads were aligned to the reference genome (mouse mm9) using the modified bisulfite aligner, BS Seeker.

treatment_protocol: Animals were given either 15 ul of peanut oil or 100 ug testosterone on the day of birth depending on their group membership. At 21 days of age, all animals were gonadectomized. 5 mm-long Silastic capsules of testosterone were implanted in all animals at day 45.

tag: gender

value: Male

value: 60 days

value: Striatum


title: Cbc1_1

description:
Sample 18
All sequences start with the barcode NNNCACTAGC


title: Striatum Day 60 Female 5

value: Female


title: Striatum Day 60 Female+T 1

value: testosterone


title: Striatum Day 60 Female+T 3


title: Striatum Day 60 Female 1


title: Striatum Day 4 Female+T 4

value: 4 days


title: Striatum Day 4 Female+T 3


title: Striatum Day 4 Female 3


title: Hrp1_2

description:
Sample 6
All sequences start with the barcode ACAAGC

value: BY4741 (MATa; his3-delta-1; leu2-delta-0; lys2-delta-0; ura3-delta-0)

value: SD (-TRP)


title: Striatum Day 4 Female 2


title: Striatum Day 4 Male 1


title: BNST/POA Day 60 Female+T 3

source_name: BNST/POA

value: BNST/POA


title: BNST/POA Day 60 Male 4


title: BNST/POA Day 60 Female+T 1


title: BNST/POA Day 60 Female 1


title: BNST/POA Day 60 Male 3


title: BNST/POA Day 4 Male 1


title: Xrn1_1

description:
Sample 5
All sequences start with the barcode CACAGC


title: Striatum Day 60 Male 3


title: Hrp1_1

description:
Sample 3
Sequences do not have any barcode at the start


title: BNST/POA Day 4 Female+T 4


title: Mex67_1

description:
Sample 4
All sequences start with the barcode GA


title: Trf4_1

description:
Sample 2
Sequences do not have any barcode at the start


title: BNST/POA Day 4 Male 4


title: Striatum Day 4 Male 4


title: BY_1

description:
Sample 1
Sequences do not have any barcode at the start


title: BNST/POA Day 4 Female 2