title: RNA-Seq_mm_fc_22mo

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description: RNA-Seq

data_processing:
Data were mapped to the Homo sapiens reference genome (hg18) or the Mus musculus reference genome (mm9).
MethylC-Seq, TAB-Seq, CMS-IP and hmC-gluc-IP-Seq analyses were performed as described in Lister, Mukamel et al. Global epigenomic reconfiguration during mammalian brain development. Science (2013).
RNA-Seq RPKM data were generated using Bowtie2 and Tophat2. Gene expression values were calculated using Cufflinks2.
genome build: mm9

source_name: Frontal cortex from 22 month old male mouse brain

growth_protocol: The mouse lines C57Bl/6 and S100b-eGFP (B6;D2-Tg(S100B-EGFP)1Wjt/J), both from Jackson Laboratories, ME were bred and maintained in our animal facility in 12 h light/dark cycles with food ad libitum. To produce the S100b-eGFP animals used for FACS, animals were crossed to C57BL/6 to produce heterozygotes for eGFP expression. Tet2-/- mice were produced by targeted disruption of the Tet2 gene. Animals were weaned in groups of 3-4 per cage, and used at the postnatal time-points indicated. Three animals obtained from separate litters were processed together for DNA and RNA isolations.

extract_protocol: Total RNA was purified from tissue using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. mRNA-Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA). Strand-specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al., High-Throughput Illumina Strand-Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011, 940-949 (2011)], while non-strand-specific libraries were constructed with the TruSeq RNA Sample prep Kit v2 as per manufacturer’s instructions.

tag: tissue

value: brain (frontal cortex)

tag: cell type(s)

value: all

tag: age

value: 22 months (689 days)

tag: gender

value: male


title: H3K9ac.L3.Solexa ChIP Rep1

status: Public on Jul 03 2013

type: SRA

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

library_source: genomic

data_processing: Bowtie alignment protocol. Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes.Reads that passed default parameters of the Illumina quality filter were mapped with Bowtie 0.12.7. The reference sequence used to built an index for mapping was the Flybase reference r5.22. The reference index was created using the bowtie-build function with default parameters. Reads were mapped using  -n 2 -l 28 -e 70 -k 1 -m 10 --best in Bowtie (-n 2, -l 28, -e 70 default). Parameters-n INT number of allowed mismatch-l INT seed length-e INT maximum permitted total of quality values at all mismatched read positions-m INT suppress all alignments for a particular read or pair if more than INT reportable alignments-k INT report up to INT valid alignments--best report alignments in best-to worst orderReads were converted to SAM formant using the bowtie2sam.pl script provided by the DCC. SPP Peak calling protocol. The aligned reads were called using SPP R package (ver.1.10, Kharchenko et al., Nat.Biotech 2008). The binding characteristics and tag shift were estimated using SPP get.binding.characteristics() function. The reads showing abnormality were removed using SPP remove.local.tag.anomalies() function. The regions of enrichment were identified as continuous blocks of positions that exhibit significant enrichment of IP over input reads. The significance of enrichment was assessed within a 1Kb window around each point using a Poisson model. A position was considered significantly enriched if the number of IP read counts was significantly higher (Z-score > 3) than the number of input read counts, after adjusting for the total number of reads sequenced in IP and input measurements. For each replicate set, if replicates were consistent (>80% agreement for top 40% of peaks/enrichment clusters), reads in each replicates were combined and enrichment regions were called as described above.  Processed data are obtained using following parameters: genome version is FlyBase r5

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: H3K9ac.L3 ChIP expt.2410

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Growth conditions and collection protocol to harvest third instar larvae from bottles.
Drosophila tissues were homogenized, and treated with formaldehyde.  Nuclei were lysed with SDS and sonication in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).
Protocol for making libraries for ChIP-seq with Illumina platform, using the TruSeq DNA Sample Prep Kit.http://www.illumina.com/products/truseq_dna_sample_prep_kit.ilmn

tag: strain

value: Oregon-R(official name :Oregon-R-modENCODE genotype :wild type )

tag: developmental stage

value: 3rd Instar Larvae

tag: genotype

value: wild type


title: RNA-Seq_mm_fc_10wk_rep3

state: CA

country: USA

description: RNA-Seq

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: Frontal cortex from 10 week old male mouse brain, biological replicate 3

value: 10 weeks (P70)


title: Control replicate 2

city: Seattle

first: Slobodan

last: Beronja

address: PO Box 19024, Mailstop D4-100

institute: Fred Hutchinson Cancer Research Center

data_processing:
RNA-seq reads were aligned to the genome using Tophat with defult settings.  Trapnell et al.
Transcript assembly and differential expression were determined using Cufflinks using Refseq mRNAs to guide assembly.  Trapnell et al.
Anaylsis of RNA-seq data was done in R using CummeRbund analysis package.  Trapnell et al.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: epidermal progenitors

extract_protocol:
FACS isolated cells were sorted directly into TrizolLS and RNA was extracted using Direct-Zol RNA Miniprep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols at Weill Cornel Medical School Genomics Core Facility

value: embryonic day 18.5 (E18.5)

value: wild-type


title: RNA-Seq_mm_fc_10wk_rep1b

description: RNA-Seq

source_name: Frontal cortex from 10 week old male mouse brain, biological replicate 1, technical replicate b


title: RNA-Seq_mm_fc_6wk_rep1b

description: RNA-Seq

source_name: Frontal cortex from 6 week old male mouse brain, biological replicate 1, technical replicate b

value: 6 weeks (P39)


title: RNA-Seq_mm_fc_6wk_rep2

description: RNA-Seq

source_name: Frontal cortex from 6 week old male mouse brain, biological replicate 2

value: 6 weeks (P40)


title: RNA-Seq_mm_fc_6wk_rep3

description: RNA-Seq

source_name: Frontal cortex from 6 week old male mouse brain, biological replicate 3

value: 6 weeks (P41)


title: RNA-Seq_mm_fc_4wk_rep2

description: RNA-Seq

source_name: Frontal cortex from 4 week old male mouse brain, biological replicate 2

value: 4 weeks (P27)


title: RNA-Seq_mm_fc_6wk_rep1a

description: RNA-Seq

source_name: Frontal cortex from 6 week old male mouse brain, biological replicate 1, technical replicate a


title: Hras-G12V Ctnnb1KD replicate 2

value: HrasG12V depleted of Ctnnb1


title: RNA-Seq_mm_fc_4wk_rep1

description: RNA-Seq

source_name: Frontal cortex from 4 week old male mouse brain, biological replicate 1

value: 4 weeks (P25)


title: IgG_G73M6

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse mm9 (July 2007) genome using the Illumina Genome Analyzer (Eland mapping software) and HiSeq2000 (Bowtie mapping software) Pipelines. All reads mapping with two or fewer mismatches were retained.
Peaks: For H3K4me1, H3K4me3, and H3K27ac, Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) version 1.4.1 using default parameters. Peaks that met MACS score > 50 were used. For each histone modification in each sex, replicates were combined and all IgG control samples in this series, along with IgG sample in GSE31578, were combined to serve as the background.
Peaks: For H3K9me3, H3K27me3, and H3K36me3, histone mark islands were identified with the SICER algorithm (http://home.gwu.edu/~wpeng/Software.htm), version 1.1. For each histone modification in each sex, replicates were combined and all IgG control samples in this series, along with IgG sample in GSE31578, were combined to serve as the background. Window and gap size parameters are listed above for each sample. Islands meeing FDR <0.001 are listed in the processed data files.
Sex-bias of peaks: for peaks located on autosomes, numbers of reads in male and female liver were normalized by the total numbers of reads in common peaks (peaks present in both male and female liver), peaks that had a >2-fold sex-ratio and that met p<0.001 were considered sex-biased.
Genome_build: mm9 (July 2007)
Supplementary_files_format_and_content: Processed data files consist of MACS or SICER output, along with sex-bias information for peaks on autosomes.

source_name: liver tissue

growth_protocol: Male and female CD-1 mice (Charles River Laboratories), 8 weeks old, were euthanized and their livers extracted.

extract_protocol:
Liver genomic DNA isolated by ChIP was prepared for sequencing using a SPRI-TE Nucleic Acid Extractor for size selection (Beckman Coulter Genomics, Danvers MA) followed by PCR enrichment with barcoding
Multiplexed samples were prepared for Illumina sequencing using standard Illumina methods.

value: CD-1 (Charles River)

tag: Sex

value: 8 weeks old

tag: chip antibody

value: IgG

value: liver

tag: chip antibody manufacturer

value: Santa Cruz

tag: chip antibody catalog #


title: IgG_G73M5

value: female

value: santa Cruz


title: IgG_G72M3

value: male


title: RNA-Seq_mm_fc_2wk_rep2

description: RNA-Seq

source_name: Frontal cortex from 2 week old male mouse brain, biological replicate 2

value: wild type

value: brain (frontal cortex)

value: all

value: 2 weeks (P13)


title: K4me3F_G69M4

tag: sicer window size

tag: sicer gap size

value: Abcam


title: RNA-Seq_mm_fc_2wk_rep3

description: RNA-Seq

source_name: Frontal cortex from 2 week old male mouse brain, biological replicate 3


title: RNA-Seq_mm_fc_2wk_rep1b

description: RNA-Seq

source_name: Frontal cortex from 2 week old male mouse brain, biological replicate 1, technical replicate b


title: K4me3F_G69M3


title: K4me1F_G72M2


title: RNA-Seq_mm_fc_10wk_rep2

description: RNA-Seq

source_name: Frontal cortex from 10 week old male mouse brain, biological replicate 2

value: 10 weeks (P69)


title: K4me3M_G69M2


title: K4me1F_G68M3


title: RNA-Seq_mm_fc_1wk_rep2

description: RNA-Seq

source_name: Frontal cortex from 1 week old male mouse brain, biological replicate 2

value: 1 week (P5)


title: RNA-Seq_mm_fc_1wk_rep1b

description: RNA-Seq

source_name: Frontal cortex from 1 week old male mouse brain, biological replicate 1, technical replicate b


title: RNA-Seq_mm_fc_1wk_rep3

description: RNA-Seq

source_name: Frontal cortex from 1 week old male mouse brain, biological replicate 3


title: RNA-Seq_mm_fc_2wk_rep1a

description: RNA-Seq

source_name: Frontal cortex from 2 week old male mouse brain, biological replicate 1, technical replicate a


title: RNA-Seq_mm_fc_10wk_rep1a

description: RNA-Seq

source_name: Frontal cortex from 10 week old male mouse brain, biological replicate 1, technical replicate a

value: 10 weeks (P70)


title: RNA-Seq_mm_fc_1wk_rep1a

description: RNA-Seq

source_name: Frontal cortex from 1 week old male mouse brain, biological replicate 1, technical replicate a


title: RNA-Seq_mm_fc_fetal_rep2

description: RNA-Seq

source_name: Frontal cortex from fetal mouse brain, biological replicate 2

value: male/female


title: RNA-Seq_mm_fc_fetal_rep1

description: RNA-Seq

source_name: Frontal cortex from fetal mouse brain, biological replicate 1


title: K9me3F_G67M3

value: CD-1 (Charles River)


title: K9me3F_G63M1

value: 8 weeks old


title: hmC-gluc-IP-Seq_mm_fc_6wk

description: Other: hmC-gluc-IP-Seq

source_name: Frontal cortex from 6 week old male mouse brain

extract_protocol: Genomic DNA was purified from cells using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. hmC-gluc-IP-Seq sequenging libraries were generated by biotin-glucosyl tagging and enrichment of hmC according to the following procedure. The Hydroxymethyl Collector Kit (Active Motif, Carlsbad, CA, USA) was used to selectively tag hmC bases within genomic DNA fragments (100-200 bp) with glucose and biotin moieties to form biotin-N3-5-gmC (biotin-gmC), as described previously [Song C.-X. et al., Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine, Nature Biotechnology 29, 68–72 (2011)]. Genomic DNA fragments containing biotin-gmC were then enriched and purified by high-affinity capture using streptavidin magnetic beads. Enriched DNA containing biotin-gmC was used to generate Illumina DNA sequencing libraries with the TruSeq DNA Sample Prep Kit v2 (Illumina, San Diego, CA).

value: 6 weeks (P40)


title: hmC-gluc-IP-Seq_mm_fc_fetal

description: Other: hmC-gluc-IP-Seq

source_name: Frontal cortex from fetal mouse brain


title: K9me3M_G67M4

value: liver


title: CMS-IP_mm_fc_10wk_IP

description: Other: CMS-IP

source_name: Frontal cortex from 10 week old male mouse brain

extract_protocol: Genomic DNA was purified from cells using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. Cytosine 5-methylenesulphonate immunoprecipitation (CMS-IP) sequencing libraries were made as follows. Genomic DNA was fragmented to 100-200 bp using a Covaris S2 (Covaris, Woburn, MA, USA), end repaired, 3’ adenylated, ligated to methylated Illumina adaptor oligonucleotides, and bisulfite converted as per the MethylC-Seq protocol, descibed previously [Lister R. et al., Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471, 68-73 (2011)]. Bisulfite conversion of hmC to cytosine 5-methylenesulphonate (CMS) was followed by immunoprecipitation of genomic DNA fragments containing CMS with a specific antiserum to CMS. Bisulfite converted genomic DNA was first denatured for 10 minutes at 95°C (0.4 M NaOH, 10 mM EDTA), neutralized by addition of cold 2 M Ammonium Acetate pH 7.0, incubated with anti-CMS antiserum in 1x IP buffer (10 mM sodium phosphate pH 7.0, 140 mM NaCl, 0.05% Triton X-100) for 2 h to overnight at 4°C, and then precipitated with Protein G beads. Precipitated DNA was washed 3 times with 1x IP buffer and eluted with Proteinase K, then purified with Phenol Chloroform. Following immunoprecipitation, sequencing libraries were amplified by 8 cycles of PCR.


title: CMS-IP_mm_fc_10wk_input

description: Other: CMS-IP


title: K27me3F_G44


title: K27me3F_G67M2


title: K27me3F_G67M1


title: CMS-IP_mm_fc_fetal_input

description: Other: CMS-IP


title: K27me3M_G64M1


title: CMS-IP_mm_fc_fetal_IP

description: Other: CMS-IP


title: K27me3M_G64M2


title: K4me1M_G68M2


title: K27me3M_G43


title: TAB-Seq_mm_fc_6wk

description: Other: TAB-Seq

extract_protocol: Genomic DNA was purified from tissue using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. TAB-Seq libraries were generated as descibed previously [Yu M. et al., Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome. Cell 149, 1368-1380 (2012)].


title: TAB-Seq_mm_fc_fetal

description: Other: TAB-Seq


title: MethylC-Seq_mm_fc_female_12mo_neun_pos

description: Bisulfite-Seq

data_processing:
Data were mapped to the Homo sapiens reference genome (hg18) or the Mus musculus reference genome (mm9).
MethylC-Seq, TAB-Seq, CMS-IP and hmC-gluc-IP-Seq analyses were performed as described in Lister, Mukamel et al. Global epigenomic reconfiguration during mammalian brain development. Science (2013).
RNA-Seq RPKM data were generated using Bowtie2 and Tophat2. Gene expression values were calculated using Cufflinks2.
genome build: mm9
Supplementary_files_format_and_content: The processed data for the allC.MethylC-Seq_<sample>.<chr>.txt files contain a row of headers indicating the chromosome, position, strand, methylation class, methylation count, and total coverage. This is a tab-delimited file.

source_name: NeuN+ nuclei isolated from frontal cortex from 12 month old female mouse brain

extract_protocol: Genomic DNA was purified from tissue, sorted cells or nuclei using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. MethylC-Seq libraries were constructed as descibed previously [Lister R. et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells, Nature 471, 68-73 (2011)], except library amplification was performed with either PfuTurboCx Hotstart DNA polymerase (Agilent Technologies, Santa Clara, CA, USA) or KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA, USA).

value: neurons (NeuN+)

value: 12 months


title: MethylC-Seq_mm_fc_female_12mo_neun_neg

description: Bisulfite-Seq

source_name: NeuN- nuclei isolated from frontal cortex from 12 month old female mouse brain

value: non-neurons (NeuN-, predominantly glia)

value: female


title: K9me3M_G63M2

source_name: liver tissue

value: male


title: MethylC-Seq_mm_fc_tet2ko

description: Bisulfite-Seq

source_name: Frontal cortex from 8 week old Tet2-/- mouse brain

value: brain (frontal cortex)

value: 8 weeks


title: MethylC-Seq_mm_fc_female_6wk_neun_pos

description: Bisulfite-Seq

source_name: NeuN+ nuclei isolated from frontal cortex from 6 week old female mouse brain

value: wild type


title: 3TAG Rrp40-1

city: Oxford

first: Aino

middle: Inkeri

last: Järvelin

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing: CAGE: basecalling by CASAVA version 1.8.2. The first 10 nt from 5'end and the last 8nt from 3'end are trimmed off (check sample description).  All the reads are then filtered by fastq_quality_filter (fastx_toolkit) using -q 30 -p 50 and mapped to hg19 by bowtie version 0.12.7 using --strata --best -k 10. Only 5'end of single mapped reads are used in the analysis.

organism: Homo sapiens

source_name: HeLa

growth_protocol: HeLa cells grown in DMEM medium supplemented with 10% fetal bovine serum at 37°C and 5% CO2.

extract_protocol:
Trizol (Invitrogen), MicroPolyA Purist (Ambion) and RiboZero (Epicentre)
3'TAGseq (PMID: 22929774)

treatment_protocol: 22nM siRNA transfection (doule hit)

tag: barcode

value: AAGCTA

tag: cell line

value: HeLa

tag: cell type

value: exosome-depleted


title: RNASeq Rrp40

description: (non-rRNA)

extract_protocol:
Trizol and RiboMinus (Invitrogen)
ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre)

value: CGATGT

tag: sample note

value: Barcode provided after read name in fastq file


title: MethylC-Seq_mm_fc_glia_S100b_pos

description: Bisulfite-Seq

source_name: Glial cells (S100b-eGFP+) isolated from frontal cortex of 7 week old make mouse brain

tag: tissue

value: glia (S100b-eGFP+)

value: 7 weeks


title: RNASeq egfp

description: (non-rRNA)

value: GCCAAT

value: egfp control


title: MethylC-Seq_mm_fc_female_6wk_neun_neg

description: Bisulfite-Seq

source_name: NeuN- nuclei isolated from frontal cortex from 6 week old female mouse brain

tag: cell type(s)

value: 6 weeks (P40)


title: CAGE Rrp40

description: For the 5' end, an extra G in position 10 of the reads, right after the barcode, needs to be trimmed. This is due to an artifact in the reverse transcription of the capped G. For the 3'end, the last 8 nt also needs to be trimmed due to 3' end adaptors.

extract_protocol:
Purelink (Ambion)
CAGE (PMID: 21938627)

value: ATGCAGCAG


title: MethylC-Seq_mm_fc_22mo

description: Bisulfite-Seq

source_name: Frontal cortex from 22 month old male mouse brain

value: all

tag: age

value: 22 months


title: CAGE egfp


title: RNA-Seq_hs_mfg_25yr

description: RNA-Seq

data_processing:
Data were mapped to the Homo sapiens reference genome (hg18) or the Mus musculus reference genome (mm9).
MethylC-Seq, TAB-Seq, CMS-IP and hmC-gluc-IP-Seq analyses were performed as described in Lister, Mukamel et al. Global epigenomic reconfiguration during mammalian brain development. Science (2013).
RNA-Seq RPKM data were generated using Bowtie2 and Tophat2. Gene expression values were calculated using Cufflinks2.
genome build: hg18

source_name: Middle frontal gyrus from 25 year old male human brain (UMB_1829)

value: brain (middle frontal gyrus)

value: 25 years (25 yr 88 d)

tag: gender

value: male


title: FemaleTotal_G78M10

data_processing:
Sequence reads were obtained and mapped to the mouse genome (mm9, July 2007) using Bowtie mapping software. All reads mapping with two or fewer mismatches were retained.
Aligned reads were mapped to MGI genes using Seqmonk (http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/; Babraham Bioinformatics, Cambridge, UK). Genes were considered liver-expressed if log2 RPKM >= 1 in either male or female liver.
Sex-biased genes were identified by differential expression analysis of transcripts identified using Seqmonk by using edgeR (Robinson et al, 2010, Bioinformatics 26:139-140). Genes that had an adjusted p-value < 0.01 were considered sex-biased in expression.
Genome_build: mm9 (July 2007)
Supplementary_files_format_and_content: Processed data files consist of transcripts with log2 RPKM values in male and female liver and sex-specificity log2-ratio and p-value calculated using edgeR.

growth_protocol: Untreated male and female CD-1 mice (Charles River Laboratories), 8 weeks old, were euthanized and their livers were then extracted.

extract_protocol:
Trizol reagent was used to prepare total liver RNA using standard protocols.
Poly-A-enriched RNA was prepared for Illumina sequencing using a strand-specific sample preparation protocol (Parkhomchuk et al, 2009, Nucleic Acids Res 37:e123)

tag: strain

value: CD-1 (Charles River)

value: female

value: 8 weeks old


title: MethylC-Seq_mm_fc_6wk

description: Bisulfite-Seq

value: wild type

value: brain (frontal cortex)


title: RNA-Seq_hs_mfg_12yr

description: RNA-Seq

source_name: Middle frontal gyrus from 12 year old male human brain (UMB_616)


title: FemaleTotal_G78M9


title: RNA-Seq_hs_mfg_5yr

description: RNA-Seq

source_name: Middle frontal gyrus from 5 year old male human brain (UMB_1185)

value: 5 years (4 yr 258 d)


title: RNA-Seq_hs_mfg_16yr

description: RNA-Seq

source_name: Middle frontal gyrus from 16 year old male human brain (UMB_1158)

value: 16 years (16 yr 63 d)


title: MaleTotal_G78M6


title: MaleTotal_G78M5


title: MethylC-Seq_mm_fc_4wk

description: Bisulfite-Seq

source_name: Frontal cortex from 4 week old male mouse brain

value: 4 weeks (P25)


title: RNA-Seq_hs_mfg_2yr

description: RNA-Seq

source_name: Middle frontal gyrus from 2 year old male human brain (UMB_5180)

value: 2 years (1 yr 262 d)


title: MethylC-Seq_mm_fc_1wk

description: Bisulfite-Seq

source_name: Frontal cortex from 1 week old male mouse brain

value: 1 week (P5)


title: 3TAG Rrp40-2

value: GTAGCC

value: HeLa

value: exosome-depleted


title: RNA-Seq_hs_mfg_35do

description: RNA-Seq

source_name: Middle frontal gyrus from 35 day old male human brain (UMB_759)

value: all

value: 35 days


title: MD1.32

city: Brisbane

first: Graham

last: Kay

address: 300 Herston Rd

country: Australia

institute: Queensland Institute of Medical Research

data_processing:
RNA-Seq reads were aligned to mm10 using tophat 2.0.6 (bowtie 2.0.2)
Transcripts were assembled with cufflinks, version 2.0.2 using --frag-bias-correct --multi-read-correct --upper-quartile-norm
Differential expression was assessed with cuffdiff version 2.0.2
SNPs were called in the RNA-seq data using mpileup (Samtools 0.1.18), bcftools and vcfutils (BCFtools 0.1.17)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing FDR corrected p-values for DGE
Supplementary_files_format_and_content: comma-delimited text file containing percentage of reads supporting SNPs

source_name: mouse placenta

extract_protocol:
Placentae were dissected at E14.5 and flash frozen in liquid nitrogen. Genotypes determined using the embryo. RNA prepared using Qiagen RNeasy Mini Kits.
Barcoded RNA-seq libraries were prepared and sequenced by the Australian Genome Research Facility using Illumina reagents

tag: developmental stage

value: E14.5 placenta

tag: background strain

value: C57Bl6/J x FVB/n


title: MD1.7

tag: Sex

value: male

tag: genotype


title: MethylC-Seq_mm_fc_10wk

description: Bisulfite-Seq

source_name: Frontal cortex from 10 week old male mouse brain

value: 10 weeks (P70)


title: MD1.9


title: MD1.3


title: MD1.2


title: RNA-Seq_hs_fc_53yr

description: RNA-Seq

source_name: Dorsal prefrontal cortex from 53 year old female human brain (UMB_579)

value: brain (dorsal prefrontal cortex)

value: 53 years

value: female


title: MD1.18


title: MD1.14


title: MethylC-Seq_hs_hues6

description: Bisulfite-Seq

data_processing:
Data were mapped to the Homo sapiens reference genome (hg18) or the Mus musculus reference genome (mm9).
MethylC-Seq, TAB-Seq, CMS-IP and hmC-gluc-IP-Seq analyses were performed as described in Lister, Mukamel et al. Global epigenomic reconfiguration during mammalian brain development. Science (2013).
RNA-Seq RPKM data were generated using Bowtie2 and Tophat2. Gene expression values were calculated using Cufflinks2.
genome build: hg18
Supplementary_files_format_and_content: The processed data for the allC.MethylC-Seq_<sample>.<chr>.txt files contain a row of headers indicating the chromosome, position, strand, methylation class, methylation count, and total coverage. This is a tab-delimited file.

source_name: HUES6 human embryonic stem cell line

value: embryonic stem cells


title: MethylC-Seq_hs_fc_male_55yr_NeuN_neg

description: Bisulfite-Seq

source_name: NeuN- nuclei isolated from dorsal prefrontal cortex from 55 year old male human brain (UMB_797)

value: non-neurons (NeuN-, predominantly glia)

value: 55 years


title: MD1.13


title: MethylC-Seq_hs_fc_male_55yr_tissue

description: Bisulfite-Seq

source_name: Dorsal prefrontal cortex from 55 year old male human brain (UMB_797)


title: MethylC-Seq_mm_fc_2wk

description: Bisulfite-Seq

source_name: Frontal cortex from 2 week old male mouse brain

value: wild type

value: brain (frontal cortex)

value: 2 weeks (P13)


title: MethylC-Seq_hs_fc_male_55yr_NeuN_pos

description: Bisulfite-Seq

source_name: NeuN+ nuclei isolated from dorsal prefrontal cortex from 55 year old male human brain (UMB_797)

value: neurons (NeuN+)


title: MethylC-Seq_hs_fc_female_53yr_NeuN_neg

description: Bisulfite-Seq

source_name: NeuN- nuclei isolated from dorsal prefrontal cortex from 53 year old female human brain (UMB_579)


title: XPS245

data_processing:
RNA-Seq reads were aligned to mm10 using tophat 2.0.6 (bowtie 2.0.2)
Transcripts were assembled with cufflinks, version 2.0.2 using --frag-bias-correct --multi-read-correct --upper-quartile-norm
Differential expression was assessed with cuffdiff version 2.0.2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing FDR corrected p-values for DGE

source_name: mouse embryo

extract_protocol:
Embryos were dissected at E9.5 and flash frozen in liquid nitrogen. Genotypes determined using the yolk sac. RNA prepared using Qiagen RNeasy Mini Kits.
Barcoded RNA-seq libraries were prepared and sequenced by the Australian Genome Research Facility using Illumina reagents

value: embryo


title: MD1.4


title: XPS234


title: MethylC-Seq_hs_fc_female_53yr_NeuN_pos

description: Bisulfite-Seq

source_name: NeuN+ nuclei isolated from dorsal prefrontal cortex from 53 year old female human brain (UMB_579)


title: MethylC-Seq_hs_fc_64yr

description: Bisulfite-Seq

source_name: Frontal cortex from 64 year old female human brain

value: all

value: 64 years


title: MethylC-Seq_hs_mfg_2yr

description: Bisulfite-Seq

value: brain (middle frontal gyrus)

value: 2 years (1 yr 262 d)


title: XPS160

value: male

value: C57Bl6/J x FVB/n


title: MD1.31

value: E14.5 placenta


title: XPS172


title: MethylC-Seq_hs_mfg_25yr

description: Bisulfite-Seq

source_name: Middle frontal gyrus from 25 year old male human brain (UMB_1829)

value: 25 years (25 yr 88 d)


title: XPS170


title: MethylC-Seq_hs_mfg_5yr

description: Bisulfite-Seq

source_name: Middle frontal gyrus from 5 year old male human brain (UMB_1185)

value: 5 years (4 yr 258 d)


title: XPS124


title: Metastatic CRPC 6

city: New York

first: Pei-Chun

last: Lin

state: NY

address: 1300 York Ave

department: Pathology and Laboratory Medicine

institute: Cornell Weill Medical College

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequences using FAR software and then mapped to hg18 whole genome using the bismark alignment software with a maximum of 2 mismatches in a directional manner. Only uniquely aligning reads were retained
Methylation score were determined for cytosines with at least 20 phred quality score and 10× coverage
Percentage of bisulfite converted Cytosines (Cs; representing unmethylated Cs) and non-converted Cs (representing methylated Cs) were recorded for each C position in a CpG context
Percent methylation values for CpG dinucleotides are calculated by dividing the number of methylated Cs by total coverage on that base.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include the number of methylated Cs and Ts per position (or per base)

source_name: prostate

extract_protocol: Genomic DNA was purified from primary human samples, digested with MspI restriction enzyme (200U MspI per reaction), subjected to end repair and adenylation followed by ligation to cytosine methylated paired-end Illumina adaptors (T4 DNA ligase). Fragments of 150-400 bp were isolated after agarose gel electrophoresis and subjected to bisulfite conversion and PCR amplification using paired-end Illumina primers (18 cycles).  Libraries were sequenced using an Illumina HiSeq2000 per manufacturer’s recommended protocol for 50bp single end read runs.

tag: tissue type

value: Castration resistant prostate cancer (CRPC)


title: MethylC-Seq_hs_mfg_12yr

description: Bisulfite-Seq

source_name: Middle frontal gyrus from 12 year old male human brain (UMB_616)


title: K36me3F_G78M4

source_name: liver tissue

value: CD-1 (Charles River)

value: female

value: 8 weeks old

tag: chip antibody

value: liver

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #


title: Metastatic CRPC 5


title: Metastatic CRPC 4


title: MethylC-Seq_hs_mfg_16yr

description: Bisulfite-Seq

source_name: Middle frontal gyrus from 16 year old male human brain (UMB_1158)

value: 16 years (16 yr 63 d)


title: K36me3F_G76M6a

tag: sicer window size

tag: sicer gap size


title: Metastatic CRPC 3


title: Metastatic CRPC 2


title: K36me3M_G78M3


title: MethylC-Seq_hs_mfg_35do

description: Bisulfite-Seq

source_name: Middle frontal gyrus from 35 day old male human brain (UMB_759)

value: 35 days


title: K27acF_G76M4a


title: Metastatic CRPC 1


title: MethylC-Seq_hs_fc_fetal

description: Bisulfite-Seq

source_name: Cerebral cortex from fetal human brain

value: brain (cerebral cortex)

value: all

value: 20 weeks (gestational)


title: K27acF_G78M2


title: PCA7

value: Primary, Prostate cancer, localized


title: PCA6


title: K27acF_G76M3a


title: K27acM_G76M2a

value: male


title: K27acM_G78M1


title: PCA3


title: PCA4


title: PCA1


title: PCA2


title: K27acM_G76M1a


title: K4me3F_G75M8a


title: Benign Prostate Tissue 7

value: Benign, prostate tissue


title: Benign Prostate Tissue 6


title: K4me3M_G75M5a


title: K4me3M_G75M6a


title: K4me3M_G75M4


title: Benign Prostate Tissue 4


title: Benign Prostate Tissue 5


title: K36me3M_G76M5a


title: K4me1F_G75M7a


title: PCA5


title: K4me1M_G75M1


title: K4me1M_G75M2


title: mouse_E13.5_FL_rep1_H3K27ac_ChIP-Seq

status: Public on Jul 02 2013

city: Philadelphia

first: Justin

last: Cotney

state: PA

address: 3501 Civic Center Blvd

department: Surgery

institute: Children's Hospital of Philadelphia

description:
Forelimb and hindlimb samples for a given replicate were combined for signal plots (available on Series Records).

processed data file (ChIP Enriched Regions): e13.5_1_h3k27acEnrichedRegions0.00001.bed
processed data file (Signal Track): e13.5_1_h3k27ac_300_uniq.bw

data_processing:
Basecalls with CASAVA-1.8.2
ChIP-seq and RNA-Seq reads were aligned to the hg19, rheMac2, or mm9 genome assembly using Bowtie (0.12.7) with the -m1 flag.
Aligned ChIP-Seq reads in each sample were scanned along the genome in 500bp windows at 25bp step-size. For each window, the total number of reads from H3K27ac and control experiment were counted respectively. Raw read number in control experiment was then scaled to match the sequencing depth of H3K27ac experiment. The number of expected reads in a window based on uniform distribution of total mapped reads along a specific chromosome was also calculated. Then the significance of enrichment was calculated using a Poisson model where the null model is the larger number of control or expected read counts in the window. Significantly enriched windows (p-value≤10-5) within 1kb of each other were then merged.
Signal plots were generated by extending reads to 300bp and counting number of reads at each position in wiggle format.  Wiggle tracks were then converted to bigwig using wigToBigWig from the Kent utilities.
Genome_build: hg19, rheMac2, or mm9
Supplementary_files_format_and_content: No raw data are provided for human samples.  Human alignments were anonymized by removing sequence information and converting to bed format
Supplementary_files_format_and_content: Enriched Region files are in bed format.
Supplementary_files_format_and_content: Bigwig files were generated with wigToBigWig with the -clip flag.

growth_protocol: Normal Gestatation

extract_protocol:
For each ChIP-Seq, limb bud tissue was crosslinked with 1% formaldehyde at room temperature and stored at -80°C. Chromatin was extracted and sheared by sonication. Soluble chromatin was combined with Protein G Dynabeads prebound with appropriate antibodies at 4C overnight. Beads were collected with magnet and washed 5x. Chromatin was eluted with TE+1%SDS at 65C for 10 minutes. Crosslinks were reversed at 65C overnight, and then chromatin was purified with the PCR cleanup kit (Qiagen).
Standard Paired End Illumina Multiplexing protocols

treatment_protocol: Human samples were obtained from the Human Developmental Biological Resource (HDBR).

value: gestational day E13.5

value: forelimb autopod

tag: chip antibody vendor

tag: chip antibody cat. #

tag: chip antibody lot #


title: mouse_E13.5_FL_rep2_H3K27ac_ChIP-Seq

description:
Forelimb and hindlimb samples for a given replicate were combined for signal plots (available on Series Records).

processed data file (ChIP Enriched Regions): e13.5_2_h3k27acEnrichedRegions0.00001.bed
processed data file (Signal Track): e13.5_2_h3k27ac_300_uniq.bw

tag: tissue


title: Benign Prostate Tissue 1


title: S. cerevisiae and K. lactis direct RNA sequence

first: Zarmik

last: Moqtaderi

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

data_processing:
alignment to genome (Helicos Helisphere)
separation of unambiguous data by yeast species
counting of sequence tags by coordinate on each strand
classification of coordinates by associated ORF on appropriate strand
Saccharomyces cerevisiae genome build 61 (2008/06/05); D. hansenii genome release 2 (2008/09/10); K. lactis version CR382121.1 (2004/07/03)
Genome_build: Saccharomyces cerevisiae genome build 61 (2008/06/05); D. hansenii genome release 2 (2008/09/10); K. lactis version CR382121.1 (2004/07/03)
Genome_build: Genome build: Saccharomyces cerevisiae: SGD genome build 61 (2008/06/05), version S288C_reference_genome_R61-1-1_20080605.tgz; http://downloads.yeastgenome.org/sequence/S288C_reference/genome_releases/.
Genome_build: Genome build: D. hansenii: ASM644v1
Supplementary_files_format_and_content: Tab-delimited text files of tag counts at each coordinate in the 400 nt downstream of each ORF.

organism: Kluyveromyces lactis

source_name: Saccharomyces cerevisiae and Kluyveromyces lactis

growth_protocol: Cells were cultured  to mid-log phase in rich medium (YPD for S. cerevisiae).

extract_protocol:
Total RNA was isolated by the hot acidic phenol method and purified with DNase treatment on Qiagen RNeasy columns.
RNA sequenced directly by Helicos (DRS method); purified RNA was not modified

tag: direct rna sequence from

tag: s. cerevisiae strain

tag: k. lactis strain

value: CLIB 209

tag: culture protocol

value: Strains were cultured separately and pooled into one sequencing lane.  AB1380 is the non-YAC-containing S. cerevisiae parental strain for JYAC06 and JYAC07.


title: mouse_E13.5_HL_rep2_H3K27ac_ChIP-Seq

tag: developmental stage

value: hindlimb autopod


title: mouse_E12.5_HL_rep2_H3K27ac_ChIP-Seq

description:
Forelimb and hindlimb samples for a given replicate were combined for signal plots (available on Series Records).

processed data file (ChIP Enriched Regions): e12.5_2_h3k27acEnrichedRegions0.00001.bed
processed data file (Signal Track): e12.5_2_h3k27ac_300_uniq.bw

value: gestational day E12.5


title: Benign Prostate Tissue 2


title: mouse_E12.5_FL_rep2_H3K27ac_ChIP-Seq


title: mouse_E12.5_HL_rep1_H3K27ac_ChIP-Seq

description:
Forelimb and hindlimb samples for a given replicate were combined for signal plots (available on Series Records).

processed data file (ChIP Enriched Regions): e12.5_1_h3k27acEnrichedRegions0.00001.bed
processed data file (Signal Track): e12.5_1_h3k27ac_300_uniq.bw


title: mouse_E13.5_HL_rep1_H3K27ac_ChIP-Seq


title: mouse_E11.5_HL_H3K27ac_ChIP-Seq

description:
Forelimb and hindlimb samples for a given replicate were combined for signal plots (available on Series Records).

processed data file (ChIP Enriched Regions): e11.5_2_h3k27acEnrichedRegions0.00001.bed
processed data file (Signal Track): e11.5_2_h3k27ac_300_uniq.bw

value: gestational day E11.5


title: mouse_E12.5_FL_rep1_H3K27ac_ChIP-Seq


title: mouse_E10.5_FL_H3K27ac_ChIP-Seq

description:
Forelimb and hindlimb samples for a given replicate were combined for signal plots (available on Series Records).

processed data file (ChIP Enriched Regions): e10.5_3_h3k27acEnrichedRegions0.00001.bed
processed data file (Signal Track): e10.5_3_h3k27ac_300_uniq.bw

value: gestational day E10.5

value: forelimb


title: mouse_E11.5_FL_H3K27ac_ChIP-Seq

value: Abcam


title: Benign Prostate Tissue 3


title: K4me1M_G75M3

tag: strain

value: CD-1 (Charles River)

tag: Sex

tag: age

value: 8 weeks old

value: liver


title: mouse_E13.5_HL_rep2_input

description: Signal tracks for input (ie big wigs) were not generated as they were not used in any analysis.


title: mouse_E13.5_HL_rep1_input


title: mouse_E13.5_FL_rep2_input


title: mouse_E12.5_FL_rep1_input


title: mouse_E13.5_FL_rep1_input


title: mouse_E11.5_FL_input


title: mouse_E12.5_FL_rep2_input


title: mouse_E11.5_HL_input


title: mouse_E10.5_HL_input

value: hindlimb


title: mouse_E10.5_FL_input


title: rhesus_E36_H3K27ac_ChIP-Seq

description:
processed data file (ChIP Enriched Regions): rm_e36_h3k27ac_1EnrichedRegions0.00001.bed
processed data file (Signal Track): rm_e36_h3k27ac_300_uniq.bw

organism: Macaca mulatta

value: gestational day E36

value: forelimb and hindlimb autopod

tag: chip antibody


title: Jersey

city: East Lansing

first: Wen

last: Huang

state: MI

address: 474 S Shaw Ln, Anthony Hall 1205F

department: Animal Science

institute: Michigan State University

data_processing:
Alignment: Tophat (v1.0.14) with Bowtie (v0.12.7), maximally 2 mismatches allowed in 25-bp segments.
Transcript assembly: Cufflinks (v0.9.3)
Gene expression estimation: Cufflinks (v0.9.3)
Genome_build: btau4
Supplementary_files_format_and_content: gene.exp.table: tab delimited txt with FPKM for each of the three samples

organism: Bos taurus

source_name: Poly A+ RNA from peripheral white blood cells of Jersey cows

extract_protocol:
Tail vein blood was collected from 40 Holstein cows at the University of Wisconsin Dairy Cattle Center, 7 Jersey cows at the University of Wisconsin Arlington Agricultural Research Station, and 45 Cholistani cows at GujaitPeer Farm, Bahawalpur, Punjab, Pakistan. Immediately following blood sampling, equal volumes of whole blood were pooled before white blood cells were isolated by centrifugation at 3000 g for 15 min. The white blood cells were washed twice with red blood cell lysis buffer, followed by RNA extraction using the Qiagen RNAEasy Mini Kit (Qiagen, Valencia, CA). For the Cholistani breed, RNA was transported in RNAStable (Biomatrica, San Diego, CA), a storage matrix mimicking an anhydrobiotic environment, to preserve its integrity. We quality checked all RNA samples using Agilent Bioanalyzer 2100 (Agilent, Santa Clara CA) before generation of sequencing libraries.
Polyadenylated RNA was selected using magnetic oligo dT beads and subjected to Illumina's mRNA-Seq library generation.

tag: breed

value: Jersey

value: blood


title: Holstein

source_name: Poly A+ RNA from peripheral white blood cells of Holstein cows

value: Holstein


title: rhesus_E32_H3K27ac_ChIP-Seq

description:
processed data file (ChIP Enriched Regions): rm_e32_h3k27ac_1EnrichedRegions0.00001.bed
processed data file (Signal Track): rm_e32_h3k27ac_300_uniq.bw

value: gestational day E32


title: rhesus_E33_H3K27ac_ChIP-Seq

description:
processed data file (ChIP Enriched Regions): rm_e33_h3k27ac_1EnrichedRegions0.00001.bed
processed data file (Signal Track): rm_e33_h3k27ac_300_uniq.bw

value: gestational day E33


title: rhesus_E36_input


title: mouse_E10.5_HL_H3K27ac_ChIP-Seq


title: rhesus_E31_H3K27ac_ChIP-Seq

description:
processed data file (ChIP Enriched Regions): rm_e31_h3k27acEnrichedRegions0.00001.bed
processed data file (Signal Track): rm_e31_h3k27ac_300_uniq.bw

value: gestational day E31


title: rhesus_E31_input


title: rhesus_E32_input


title: mouse_E12.5_HL_rep2_input

value: gestational day E12.5

value: hindlimb autopod


title: mouse_E12.5_HL_rep1_input


title: WT

city: Zurich

first: Antonin

last: Marchais

address: Universitatstrasse 2

department: Department of Biology

country: Switzerland

institute: ETHZ

description: small RNAs

data_processing:
Basecalls performed using HiSeq Control Soft. v. 1.4.8, RTA 1.12.4.2 and CASAVA 1.8.2
sRNAseq reads were aligned to the TAIR9 genome assembly using ncPRO pipeline after filtering out the reads of size lower than 19nt.
Genome_build: TAIR9
Supplementary_files_format_and_content: Sequence count for A. thaliana derived small RNAs

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis thaliana floweres from plants grown on soil under continuous light conditions

extract_protocol:
Total RNA was isolated with Trizol
Libraries construction was contracted out to Fasteris SA. At Fasteris SA, barcoded libraries were prepared such that four samples could be run per lane. Libraries were prepared according to Illumina's instructions accompanying the sequencing Kit TruSeq(TM) SBS v5.

tag: ecotype

tag: line

value: Flower

tag: generation


title: F8

description: small RNAs

source_name: Col0 met1 derived EpiRIL


title: Cholistani

organism: Bos indicus

source_name: Poly A+ RNA from peripheral white blood cells of Cholistani (Parkistan) cows

value: Cholistani


title: F11

description: small RNAs


title: rack1_rep2

status: Public on Jul 01 2013

city: Oldenburg

first: Sascha

last: Laubinger

address: Carl-von-Ossietzky-Str. 9-11

country: Germany

institute: University of Oldenburg

description: rack1abc small RNAs, replicate 2

data_processing:
adaptor trimming (sRNA Toolkit tool=adaptor, minsize=17, maxsize=27)
mapping to TAIR10 (genomemapper, mismatches=0)
read annotation according to TAIR10 (custom perl script)
filtering for rRNA/tRNA (custom perl script)
mapping to known mature miRNA sequences (custom perl script)
differential expression analysis (edgeR, library size = total #reads after filtering for tRNA/sRNA (s.a))
Genome_build: TAIR10
Supplementary_files_format_and_content: fasta, trimmed and filtered reads

source_name: seedlings

growth_protocol: Plants were grown on half-strength MS medium for 10 days

extract_protocol: small RNA libraries were generated with GATC (Konstanz, Germany). Library construction was performed according to the TruSeq Small RNA Kit (Illumina).

treatment_protocol: no special treat was applied

tag: genotype/variation

value: rack1abc mutant

value: 10 day-old seedlings

tag: growth conditions

value: half-strength MS medium for 10 days


title: WT_rep1

description: WT small RNAs, replicate 1

value: wildtype


title: rack1_rep1

description: rack1abc small RNAs, replicate 1


title: Input Afos (Dex + E2)

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

description: Input DNA from cells treated with Dex + E2 - replicate 1

data_processing:
Illumina Casava 1.8 software was used for basecalling.
Areas of enrichment were identified using DNase2Hotspots software(htrceforge.net/projects/dnase2hotspots/) software with FDR 0%.   Peaks with the maximum tag density lower than 10 were eliminated.
Raw signal density graphs were generated by counting tags at each genomic coordinate after extending the length of sequences to 150bp by strands.
Genome_build: mm9 (NCBI 37)
Supplementary_files_format_and_content: comma-delimited (CSV)  text files include genomic locations (Chromosome, start,  end ), z-score, p-value and the maximum density of hotspots.

source_name: 7438 cells + Afos

growth_protocol: For maintenance cells were cultured in DMEM supplemented with 10% calf serum, sodium pyruvate, non-essential amino acids, and 5 ug/ml tetracycline to repress expression of the tet-regulated fusion proteins.

extract_protocol: Lysates were clarified from sonicated nuclei and GR-DNA complexes or ER-DNA complexes were isolated with antibody

treatment_protocol: Cells were plated for experiments in DMEM growth medium supplemented with 10% charcoal-dextran serum with tetracyline 48 hours prior to conducting the experiment.  Twenty-four hours before hormone treatment, cells were washed three times with phosphate-buffered saline and fresh DMEM with 10% charcoal-dextran serum (no tetracyline) was added to the cells to induce expression of GFP-GR and Ch-ER.  Cells were untreated or induced with 100nM dexamethasone, 100nM estradiol, or 100nM dexamethasone plus 100nM estradiol for 30 mins.

tag: cell type

value: mouse mammary cells (express GFP-GR, Cherry-ER, and Afos under a tet regulated promoter)

tag: treatment

value: Dexamethasone + Estradiol for 30 minutes

tag: cell line

value: 7438 cells

tag: replicate

value: replicate 1


title: ER ChIP-Seq Afos (+E2) r2

description: ER-ChIP in cells treated with E2 - replicate 2

value: Estradiol for 30 minutes

value: replicate 2

tag: chip antibodies

value: cocktail of Ab-10 from Labvision and sc-543 from Santa Cruz


title: ER ChIP-Seq Afos (+Dex) r2

description: ER-ChIP in cells treated with Dex - replicate 2

value: Dexamethasone for 30 minutes


title: ER ChIP-Seq Afos (Dex + E2) r2

description: ER-ChIP in cells treated with Dex + E2 - replicate 2


title: ER ChIP-Seq Afos (+Dex) r1

description: ER-ChIP in cells treated with Dex - replicate 1


title: ER ChIP-Seq Afos (untreated) r2

description: ER-ChIP in untreated cells - replicate 2

value: untreated


title: GR ChIP-Seq Afos (Dex + E2) r2

description: GR-ChIP in cells treated with Dex + E2 - replicate 2

value: cocktail of PA-510A and PA-511A from Affinity BioReagents and sc-1004 from Santa Cruz


title: ER ChIP-Seq Afos (untreated) r1

description: ER-ChIP in untreated cells - replicate 1


title: F14

description: small RNAs

tag: tissue


title: GR ChIP-Seq Afos (+Dex) r2

description: GR-ChIP in cells treated with Dex - replicate 2


title: GR ChIP-Seq Afos (+E2) r2

description: GR-ChIP in cells treated with E2 - replicate 2


title: ER ChIP-Seq Afos (Dex + E2) r1

description: ER-ChIP in cells treated with Dex + E2 - replicate 1


title: GR ChIP-Seq Afos (+Dex) r1

description: GR-ChIP in cells treated with Dex - replicate 1


title: GR ChIP-Seq Afos (Dex + E2) r1

description: GR-ChIP in cells treated with Dex + E2 - replicate 1


title: GR ChIP-Seq Afos (+E2) r1

description: GR-ChIP in cells treated with E2 - replicate 1


title: WT_rep2

description: WT small RNAs, replicate 2

tag: developmental stage


title: GR ChIP-Seq Afos (untreated) r1

description: GR-ChIP in untreated cells - replicate 1


title: ER DBD mut ChIP-Seq (+E2) r2

description: ER(DBDmut)-ChIP in cells treated with E2 - replicate 2

source_name: 3617 cells expressing ER DBD mutant

value: mouse mammary cells (express GFP-GR and Cherry-ER which has been mutated in its DNA binding domain - under a tet regulated promoter)


title: ER ChIP-Seq Afos (+E2) r1

description: ER-ChIP in cells treated with E2 - replicate 1


title: ER DBD mut ChIP-Seq (+E2) r1

description: ER(DBDmut)-ChIP in cells treated with E2 - replicate 1


title: Input (Dex + E2) r1

description: Input DNA from cells treated with Dex + E2 - replicate 1

source_name: 7438 cells

value: mouse mammary cells (express GFP-GR and Cherry-ER under a tet regulated promoter)


title: Input (Dex + E2) r2

description: Input DNA from cells treated with Dex + E2 - replicate 2


title: ER DBD mut ChIP-Seq (Dex + E2) r1

description: ER(DBDmut)-ChIP in cells treated with Dex + E2 - replicate 1


title: ER DBD mut ChIP-Seq (Dex + E2) r2

description: ER(DBDmut)-ChIP in cells treated with Dex + E2 - replicate 2


title: ER ChIP-Seq (Dex + E2) r2

description: ER-ChIP in cells treated with Dex + E2 - replicate 2


title: ER ChIP-Seq (+E2) r2

description: ER-ChIP in cells treated with E2 - replicate 2


title: ER ChIP-Seq (Dex + E2) r1


title: ER ChIP-Seq (+Dex) r2

description: ER-ChIP in cells treated with Dex - replicate 2


title: ER ChIP-Seq (+E2) r1


title: ER ChIP-Seq (+Dex) r1

description: ER-ChIP in cells treated with Dex - replicate 1


title: ER ChIP-Seq (untreated) r1

description: ER-ChIP in untreated cells - replicate 1


title: ER ChIP-Seq (untreated) r2

description: ER-ChIP in untreated cells - replicate 2


title: GR ChIP-Seq (Dex + E2) r2

description: GR-ChIP in cells treated with Dex + E2 - replicate 2


title: GR ChIP-Seq Afos (untreated) r2

description: GR-ChIP in untreated cells - replicate 2


title: GR ChIP-Seq (Dex + E2) r1

description: GR-ChIP in cells treated with Dex + E2 - replicate 1


title: GR ChIP-Seq (+E2) r2

description: GR-ChIP in cells treated with E2 - replicate 2


title: GR ChIP-Seq (+E2) r1

description: GR-ChIP in cells treated with E2 - replicate 1


title: GR ChIP-Seq (+Dex) r1

description: GR-ChIP in cells treated with Dex - replicate 1


title: GR ChIP-Seq (+Dex) r2

description: GR-ChIP in cells treated with Dex - replicate 2


title: GR ChIP-Seq (untreated) r1

description: GR-ChIP in untreated cells - replicate 1


title: GR ChIP-Seq (untreated) r2


title: DNase-Seq (+E2)

description: DNase-Seq in cells treated with E2

data_processing:
Illumina Casava 1.8 software was used for basecalling.
Areas of enrichment were identified using DNase2Hotspots software(https://sourceforge.net/projects/dnase2hotspots) software with FDR 0%.   Hotspots with the maximum tag density lower than 10 were eliminated.
Raw signal density graphs were generated by counting tags at each genomic coordinate after extending the length of sequences to 150bp by strands.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph and z-scores

extract_protocol: Lysates were clarified from sonicated nuclei


title: DNase-Seq (untreated)

description: DNase-Seq in untreated cells


title: DNase-Seq (Dex + E2)

description: DNase-Seq in cells treated with Dex + E2


title: WT 20min Rep2

city: Tianjin

first: Huifeng

last: Jiang

address: #32XiQiDao Tianjin airport economic park

country: China

institute: Tianjin Institute of Industrial Biotechnology

description: Ribosome-protected mRNA

data_processing:
Prior to alignment, polyA tails were removed from the 3' end of reads.
SOAP2 were used to map reads onto genome allowing two or less mismatches.
RPKM of each gene was calculated by summing the number of reads on the gene location
Genome_build: n/a (e. coli and phage genes)
Supplementary_files_format_and_content: rpkm

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli WT heatshock 20min

growth_protocol: MG1655 and MG1655 (λcI857)  incubated with shaking at 32°C to an optical density at 600 nm (OD600) of 0.4 to 0.5.

extract_protocol:
RNA was extracted from monosomes by the hot acid phenol method.
RNA dephosphorylated by T4 polynucleotide kinase (M0236, NEB) for 1 h at 37 °C. RNA was loaded onto a 15% Mini-PROTEAN® TBE-Urea Precast Gel (BIO-RAD) and run until the ~30 nt region was resolved.  The region from 28nt to 42nt was excised, based on the mobility of defined RNA oligonucleotides and a 10bp DNA ladder. The gel fraction was eluted overnight in 300 mM NaOAc pH 5.5, 1 mM EDTA, and 0.1U/ul SUPERas In (Ambion #AM2694), followed by ethanol precipitation. PolyA tails were added to the purified RNA fragments by E. coli polyA polymerase (NEB) at 37 °C for 20 min in the buffer provided.  The tailed RNA molecules were reverse transcribed using barcoded primers and SuperScript III (Invitrogen) to generate the first-strand cDNA. After reverse transcription RNA was removed from RNA-DNA duplexes by incubation for 15 min at 98° in 0.1M NaOH, followed by addition of an equal concentration of HCl.  Reverse-transcription products were loaded onto a 10% polyacrylamide TBE-urea gel. The band of the first-strand cDNA synthesis was excised and recovered using DNA gel elution buffer (300mM NaCl, 1mM EDTA). Purified first-strand cDNA was circularized by 50U CircLigase (Epicentre). Circularized ribosomal footprint cDNA was amplified by PCR using the Phusion High-Fidelity enzyme (New England Biolabs) according to the manufacturer’s instructions. The PCR products were separated on a non-denaturing 8% polyacrylamide TBE gel.  Mixed DNA samples from different barcoded samples typically were used for cluster generation. Deep sequencing was performed with the Illumina HiSEQ2000.

treatment_protocol: Cultures were transferred to a 42 °C water bath and incubated with shaking; samples were taken at 2, 5, 10, and 20 min. Chloramphenicol was added to 0.1 mg/ml 2 minutes before harvesting the cells in order to freeze the translating ribosomes. The cell culture was mixed with an equal mass of ice in centrifuge tubes and centrifuged at 8,000 rpm (10,000 X g) for 10 min at 4°C to harvest the cells. The cell pellet was resuspended in 0.5 ml ice-cold lysis buffer (20 mM Tris-Cl, pH 7.5, 100 mM NH4Cl, 10 mM MgCl2, 0.1 mg/ml chloramphenicol), supplemented with 50 μl of lysozyme solution (10 mg/ml?; Sigma), mixed by pipetting, and frozen for 5 min in liquid nitrogen.  The suspension was thawed, refrozen, thawed again, and supplemented with 15µl of 10% deoxycholate to complete the cell lysis. Cell debris was removed by centrifugation at 10,000 rpm for 10 min at 4 °C. 100 OD260 units of the ribosome preparation was digested with 20,000 gel units of micrococcal nuclease (M0247, NEB) and 20 units of DNase I (M0303S, NEB) at 25°C for 1 hour, followed by gentle layering onto a sucrose gradient consisting of 2.5 ml layers of 10%, 20%, 30%, and 40% sucrose solutions in polysome buffer (20 mM Tris-Cl, pH 7.5, 100 mM NH4Cl, 10 mM MgCl2, 2 mM 2-mercaptoethanol, 0.1 mg/ml chloramphenicol) that had equilibrated overnight at 4°C.  The gradient was centrifuged in an SW41 Ti rotor at 35,000 rpm (151,000 X g) for 3 hours at 4°C and monosome fractions were collected.

tag: strain

tag: sample type

value: E. coli

tag: time

value: heat shock


title: WT 10min Rep1

description: Ribosome-protected mRNA

source_name: E. coli WT heatshock 10min


title: WT 10min Rep2

description: Ribosome-protected mRNA


title: WT 5min Rep2

description: Ribosome-protected mRNA

source_name: E. coli WT heatshock 5min


title: WT 2min Rep2

description: Ribosome-protected mRNA

source_name: E. coli WT heatshock 2min


title: WT 5min Rep1

description: Ribosome-protected mRNA


title: WT 20min Rep1

description: Ribosome-protected mRNA


title: WT 0min Rep1

description: Ribosome-protected mRNA

source_name: E. coli WT heatshock 0min


title: WT 0min Rep2

description: Ribosome-protected mRNA


title: Induction 20min Rep1

description: Ribosome-protected mRNA

source_name: E. coli lambda phage lysogen heatshock 20min

value: λcI857 lysogen of MG1655 and E. coli

tag: infection

value: Bacteriophage lambda


title: Induction 10min Rep2

description: Ribosome-protected mRNA

source_name: E. coli lambda phage lysogen heatshock 10min


title: Induction 20min Rep2

description: Ribosome-protected mRNA


title: Induction 10min Rep1

description: Ribosome-protected mRNA


title: Induction 5min Rep2

description: Ribosome-protected mRNA

source_name: E. coli lambda phage lysogen heatshock 5min


title: Induction 5min Rep1

description: Ribosome-protected mRNA


title: Induction 2min Rep1

description: Ribosome-protected mRNA

source_name: E. coli lambda phage lysogen heatshock 2min


title: Induction 2min Rep2

description: Ribosome-protected mRNA


title: Induction 0min Rep1

description: Ribosome-protected mRNA

source_name: E. coli lambda phage lysogen heatshock 0min


title: Induction 0min Rep2

description: Ribosome-protected mRNA


title: DNase-Seq (+Dex)

description: DNase-Seq in cells treated with Dex


title: picogram 2

first: Sarah

middle: Keating

last: Bowman

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital

description: K27me3 chromatin

data_processing:
Base calling: Illumina
Alignment: Bowtie
Genome_build: dm3
Supplementary_files_format_and_content: The processed files give the counts of the aligned and filtered tags at the corresponding genomic positions in the following format:
Supplementary_files_format_and_content: chromosome, strand, coordinate of the tag 5'-end, tag count

source_name: H3K27me3 chromatin from embryonic nuclei

extract_protocol:
crosslinked nuclei were isolated from Drosophila embryos. 100 000 nuclei were treated with micrococcal nuclease to fragment the chromatin, and subjected to K27me3 ChIP by standard methods.
crosslinked nuclei were isolated from Drosophila embryos. 100 000 nuclei were treated with micrococcal nuclease to fragment the chromatin, and subjected to K27me3 ChIP by standard method (described in Bowman et al., BMC Genomics 2013)

tag: chip antibody

value: embryo


title: WT 2min Rep1

description: Ribosome-protected mRNA


title: Root_polyA_KNO3_Treatment_rep2

city: Santiago

first: Elena

middle: A

last: Vidal

address: Avenida Libertador Bernardo O'Higgins 340

department: Genetica Molecular y Microbiologia

country: Chile

institute: Pontificia Universidad Catolica de Chile

data_processing:
Basecalls performed using Bustard version 1.3.2
Low quality reads were extracted with fastq quality filter by FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). The Phred quality score was set to 20, a probability of incorrect base call of 1 in 100.
Sequence reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Sequences of ≥ 18 nt (polyA libraries) or ≥ 18 nt and ≤ 28 nt (sRNA libraries) were mapped to the Arabidopsis thaliana genome (TAIR10) using Novoalign 2.05.17 with default configurations.
For sRNA data, the number of different sequences were counted (raw sRNA expression) and normalized using the edgeR package for R (Robinson et al., 2010, Bioinformatics 26(1): 139–140)
For polyA data, sequences were mapped to the genome and sequences corresponding to annotated elements of the TAIR10 genome were counted (raw gene expression). Data was normalized using the edgeR package for R (Robinson et al., 2010, Bioinformatics 26(1): 139–140).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each Sample, using the edgeR package for R (Robinson et al., 2010, Bioinformatics 26(1): 139–140).

growth_protocol: Wild-type seedlings (Col-0 ecotype) were grown on sterile hydroponic medium containing 1X MS salts without Nitrogen, supplemented with 0.5 mM ammonium succinate as Nitrogen source and 3 mM sucrose on a Percival chamber under a photoperiod of 16 hours of light (100 μE/m2/sec) and 8 hours of dark at 22°C for 14 days.

extract_protocol:
Total RNA was extracted using the TriZol reagent as indicated by the manufacturer. For poly-A+ libraries, poly-A+ RNA was enriched using the Poly(A)Purist™ MAG Kit.  (Ambion, cat, number AM1922M). Poly-A+ RNA was decapped using tobacco acid pyrophosphatase and fragmented using RNA Fragmentation Reagents (Ambion, cat. Number AM8740). Low molecular weight RNA (<40 nt) was isolated from 100 μg of total RNA by Poly Acrylamide Gel Electrophoresis on a FlashPAGE™ fractionator (Ambion, cat. Number AM13100).
For construction of the libraries, cloning linker (AMP-5’p=5’pCTG TAG GCA CCA TCA ATdideoxyC-3’) was ligated to the 3' end of the RNA followed by purification of the ligation product on a 15 % polyacrilamide/urea gel. The 3’-ligated product was ligated to the 5’ Solexa linker (5’-rArCrA rCrUrC rUrUrU rCrCrC rUrArC rArCrG rArCrG rCrUrC rUrUrC rCrGrA rUrC-3’). RNA with ligated adaptors was reverse transcribed into DNA using Illumina specific primer (5’- CAA GCA GAA GAC GGC ATA CGA TTG ATG GTG CCT ACA G-3’) and cDNA was then PCR amplified using  this primer and a specific primer (5’- AAT GAT ACG GCG ACC ACC GAA CAC TGT TTC CCT ACA CGA CG-3’). The libraries were gel purified using the QIAquick gel extraction kit (QIAGEN, cat. Number 28704).

treatment_protocol: Plants were treated at the onset of the light period on day 15 with 5 mM KNO3 or 5 mM KCl as control for 2 hours. Roots were cut and frozen on liquid nitrogen.

tag: ecotype

value: Columbia (Col-0)

value: Whole roots

tag: age

value: 15-day old seedling

value: 2 hours of 5 mM KNO3


title: Root_polyA_KNO3_Treatment_rep1


title: Root_sRNA_KCl_Control_rep1

value: 2 hours of 5 mM KCl


title: rhesus_E33_input

description: Signal tracks for input (ie big wigs) were not generated as they were not used in any analysis.

value: gestational day E33

value: forelimb and hindlimb autopod


title: Root_sRNA_KNO3_Treatment_rep1


title: Root_sRNA_KCl_Control_rep2


title: Chlamydomonas reinhardtii crr1 - Dark anoxic 6 hours

city: Los Angeles

first: Sabeeha

last: Merchant

state: California

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

institute: University of California Los Angeles

description: Illumina's RNA-Seq whole transcriptome analysis

data_processing:
Illumina's proprietary software was used for basecalling.
The reads were aligned using bowtie  in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome.
Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates.
Genome_build: version 4.0 assembly of the Chlamydomonas genome
Supplementary_files_format_and_content: Processed files correpond to expression estimates per lane, in units of RPKMs.

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas cultured cells

growth_protocol: Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 700 ml TAP-medium in 2 l flasks in the light (100 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 2.2 to 2.7 cells ∙ ml-1.

extract_protocol: Total RNA was isolated at time-points indicated in the text according to a method described before (Hill et al., 1991, PMID: 1714451) with the following modifications: 100 ml of cell suspension was harvested by centrifugation (3,440 g) at 4°C and resuspended in 1.6 ml ice-cold lysis buffer (Schmidt et al., 1984; PMID: 6202701) without SDS. After addition of 0.4 ml 10 % (w/v) SDS, cells were vigorously vortexed and RNA was extracted and precipitated according to (Hill et al., 1991, PMID: 1714451). RNA integrity was checked by formaldehyde gel electrophoresis and ethidium bromide staining, by Agilent 2100 Bioanalyzer analysis. DNA was removed from total RNA using TURBO™ DNase from Ambion/Applied Biosystems (www.ambion.com) according to the manufacturer’s recommendations. For quantitative transcriptomes, RNAs were sequenced at JGI by Illumina's whole transcriptome analysis.

treatment_protocol: Cells were grown to the early-logarithmic growth phase (ca. 3 ∙ 106 cells ∙ ml-1). 100 ml culture aliquots were then transferred to squared glass bottles sealed with Red Rubber Suba Seals 37 ), which had a total volume of 118 ml after insertion of the Suba Seals. The flasks were subsequently incubated in a dark-room on magnetic stirrers. Reference cultures were 100 ml culture aliquots removed from the main cultures, transferred to 500 ml Erlenmeyer flasks and placed back to growth conditions in order to prevent the establishment of microaerobic conditions. RNA of the reference cells was isolated when the other incubation flasks had been placed in the dark room, thus 10 min after their removal from the main culture.

value: dark-anoxic


title: Root_sRNA_KNO3_Treatment_rep2


title: picogram 1

description: K27me3 chromatin


title: Chlamydomonas reinhardtii crr1:CRR1 - Dark anoxic 6 hours


title: Chlamydomonas reinhardtii crr1:CRR1 - Light oxic

value: light-oxic


title: Chlamydomonas reinhardtii crr1:CRR1 - Dark anoxic 0.5 hours


title: oocyte chromatin fragmented by endogenous nuclease 50-130 bp

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: NJ

address: Nelson Labs A125, 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

description: C. elegans oocyte chromatin fragments generated by endogenous nuclease activity

data_processing:
Remove barcode if necessary. Use 25 nt tags for alignment
Genome alignment using Bowtie, version 0.12.7
Only perfect matches are considered
Genome_build: WS190 (ce6)
Supplementary_files_format_and_content: UCSC bed format. For pair-end reads, the chromosome is indicated by the first column; the start and end positions of DNA fragments are indicated by column 2 and 3, respectively; the number of identical tags with the same alignment is indicated by column 4. For single-end reads, the position of the sequenced end is indicated by column 2 or 3 for plus strand alignment or minus strand alignment, respectively; strand is indicated by column 5, the number of identical   tags with the same alignment is indicated by column 4.

organism: Caenorhabditis elegans

source_name: purified oocytes

growth_protocol: C. elegans oocytes were purified from the fer-1(b232) mutant worms grown at the restrictive temperature of 25-26°C

extract_protocol:
Oocytes were flash frozen upon harvest. Frozen oocytes were ground to a fine powder in liquid nitrogen. For direct lysis (i.e., no micrococcal nuclease treatment), DNA was isolated by incubating the worm sample with 400 l lysis buffer (100 mM Tris-Cl, pH 7.5, 0.1 M NaCl, 1% SDS, 50 mM EDTA, 0.2 mg/ml protease K) at 65C for 1 hour, followed by extraction with an equal volume of Phenol/Chloroform (1:1), extraction with an equal volume of chloroform, and by precipitation with ethanol (1ml). Approximately 5-20 micrograms of DNA was obtained from this procedure.  In cases where micrococcal nuclease (MNase) treatment was applied, liquid-nitrogen-ground oocytes (or similar samples from other stages) were directly resuspended in buffer A (15 mM Hepes-Na, pH 7.5, 60 mM KCl, 15 mM NaCl, 0.15 mM beta-mercaptoethanol, 0.15 mM spermine, 0.15 mM spermidine, 0.34 M sucrose) containing 0.5 mM PMSF, 1/100 dilution of HALT protease and phosphatase inhibitor cocktail (Thermo Scientific), 1 mM DTT, and 2 mM CaCl2. For micrococcal nuclease (MNase) digestion, 0.1 ml oocyte crude lysate was first pre-warmed to 37°C for one minute, then treated with 0.002, 0.02, or 0.1 U/l MNase (Roche). The reaction mix was incubated at 37°C for two minutes and digestion was then stopped by adding EGTA to a final concentration of 20 mM. DNA was isolated by incubating the worm sample with 400 l lysis buffer (100 mM Tris-Cl, pH 7.5, 0.1 M NaCl, 1% SDS, 50 mM EDTA, 0.2 mg/ml protease K) at 65 C for 1 hour, followed by organic extraction and DNA precipitation as above.
DNA was treated with 0.5 U T4 polynucleotide kinase (NEB) in 1x T4 DNA ligase buffer (NEB, containing 1 mM ATP) at 37°C for 1 hour to phosphorylate 5’ ends and dephosphorylate 3’ ends. Ends were then blunted in a reaction containing 0.75 U of T4 DNA polymerase (NEB), dNTP (100 micro M each, Roche), and 1x NEB buffer 1 at 12°C for 15 min. DNA was then ligated to previously annealed DNA oligonucleotides AF-SG-133 (5’ Pi-AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG-OH 3’) and AF-SG-134 (5’ OH-CCCTACACGACGCTCTTCCGATCT-OH 3’) (NEB Quick Ligation Kit). DNA captured by linker oligonucleotides was resolved using 6 % polyacrylamide (acrylamide:bis-acrylamide = 19:1) gels containing 8 M urea, followed by PCR amplification with primers AF-SG-135 (5’ OH-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-OH 3’) and AF-SG-137 (5’ OH-CAAGCAGAAGACGGCATACGAGCT-OH 3’). We carefully selected cycle numbers for which product levels have not saturated (i.e. product levels were still able to increase substantially with additional cycles); this protocol ensures that the majority of amplified segments are still annealed to a true complement, avoiding reannealing-distortion in the resulting sequence libraries After separating PCR products on 2% agarose gels, DNA bands of the expected size were extracted (QIAchange® Gel Extraction Kit (Invitrogen); omitting the 50°C heating step), followed by massively parallel DNA sequencing (Illumina GAII).
Linker-based library construction for Illumina platform

value: chromatin

value: oocyte

tag: size of dna fragments

tag: sequencing platform

value: Illumina Hiseq, paired-end, 25 nt each end


title: Chlamydomonas reinhardtii crr1 - Dark anoxic 0.5 hours


title: oocyte chromatin fragmented by endogenous nuclease 20-80 bp


title: oocyte chromatin fragmented by endogenous nuclease 80-230 bp


title: oocyte chromatin fragmented by endogenous nuclease 130-430 bp


title: Root_polyA_KCl_Control_rep1


title: Chlamydomonas reinhardtii crr1 - Light oxic


title: Chlamydomonas reinhardtii crr1dCys - Dark anoxic 6 hours


title: Chlamydomonas reinhardtii CC-124 - Dark anoxic 6 hours


title: Chlamydomonas reinhardtii crr1dCys - Light oxic


title: Chlamydomonas reinhardtii crr1dCys - Dark anoxic 0.5 hours


title: U2OS_DXR_input

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: U2OS cells treated with 0.6 ug/ml Doxorubicin for 24 hr

data_processing:
Base-calling performed with CASAVA (Illumina).
Reads were aligned against the hg18 reference genome via Bowtie (v0.12.2), requiring mapping to unique genomic locations and allowing up to 2 mismatches.
Peaks were called via SISSRs using default settings, with input DNA used as a control (p<0.0001).
Genome_build: hg18
Supplementary_files_format_and_content: Mapped read coverage is represented in wig format; scores respresent uniquely-mapped non-redundant reads in 200bp bins, normalized by 10,000,000 divided by total uniquely-mapped non-redundant read counts per sample.
Supplementary_files_format_and_content: Peak calls from SISSRs were converted to coordinate ranges in standard BED format.

source_name: U2OS cell line

growth_protocol: U2OS expressing endogenous wild-type p53 was maintained in McCoy's 5A medium supplemented with 10% fetal calf serum and 1% Penicillin/Streptomycin at 37ºC in 5% CO2.

extract_protocol:
Treated cells were crosslinked with 1% formaldehyde then cells were lysed and nuclei were collected.  Chromatin was sheared and immunoprecipitated with p53 DO-1 Ab overnight. Input DNA and p53 ChIP-DNA were reverse crosslinked and purified.
Libraries were prepared the using the Illumina ChIP-seq DNA Sample Prep Kit as per manufacturer's instructions

treatment_protocol: for No Treatment: none; Doxorubicin: 0.6 ug/ml Doxorubicin for 24 hrs; DMSO; 0.1% DMSO for 24 hrs; Nutlin: 10 uM Nutlin-3 for 24 hrs

value: osteosarcoma

value: 0.6 ug/ml Doxorubicin for 24 hr


title: U2OS_NT_input

description: U2OS No Treatment control 24 hr, control for Doxorubicin-treated cells

value: no treatment control 24 hr, control for Doxorubicin-treated cells


title: Chlamydomonas reinhardtii CC-124 - Light oxic


title: U2OS_Nutlin_input

description: U2OS cells treated with 10 uM Nutlin-3 for 24 hr

value: 10 uM Nutlin-3 for 24 hr


title: U2OS_DXR_p53chip

description: U2OS cells treated with 0.6 ug/ml Doxorubicin for 24 hr and ChIP with p53

value: p53 DO-1 (Santa Cruz, sc-126)


title: Root_polyA_KCl_Control_rep2

value: Columbia (Col-0)


title: U2OS_NT_p53chip

description: U2OS No Treatment control 24 hr and ChIP with p53 (control for Doxorubicin-treated cells)

value: no treatment control 24 hr and ChIP with p53 (control for Doxorubicin-treated cells)


title: Chlamydomonas reinhardtii CC-124 - Dark anoxic 0.5 hours


title: U2OS_Nutlin_p53chip

description: U2OS cells treated with 10 uM Nutlin-3 for 24 hr and ChIP with p53


title: U2OS_DMSO_input

description: U2OS cells treated with 0.1% DMSO for 24 hr (control for Nutlin-treated cells)


title: U2OS_DMSO_p53chip

description: U2OS cells treated with 0.1% DMSO for 24 hr and ChIP with p53 (control for Nutlin-treated cells)


title: Control_S20

city: Novato

first: Simon

last: Melov

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

data_processing:
RNA-Seq (50 bp paired-end sequencing) was carried out on a HiSeq 2000 according to the manufacturer's protocols (Illumina).
Average Quality scores for the completed run across all 20 samples was >30, with an average of 10 million reads per sample.
The completed sequencing reads were then input into CLCBio Genomics Workbench 5 (ClCBio, Cambridge, MA), and mapped to the MGSCv37 C57BL/6J mouse genome (maximum paired distance=300 and minimum=130, minimum number of reads per mapping = 5, maximum number of mismatches= 2, with the reads being mapped to unique sites in the genome).
Using these parameters, 34,293 genes were mapped and used in subsequent differential expression analysis in Bioconductor.
To identify significantly differentially expressed genes in total heart RNA for the comparisons between the rapamycin-treated group (N=10) versus untreated controls (N=10), we used the freely available edgeR package in Bioconductor.
To allow for the comparatively large group size comparisons, a prior of n=1/18 was set in edgeR. We then used an FDR of 5% to detect significantly differentially expressed genes between the two groups that resulted in a list of 700 genes.
Genome_build: MGSCv37
Supplementary_files_format_and_content: 'DE_genes_processed.txt': Tab-separated value file containing the counts per million reads for each individual sample across the 700 differentially expressed genes.
Supplementary_files_format_and_content: 'All_genes.txt': Tab-separated value file containing all of the genes mapped from each sample and counts per million.

source_name: Adult mouse heart, control diet

extract_protocol:
Whole frozen heart tissue was crushed to a powder in liquid nitrogen. The powdered tissue was then treated with Qiasol lysis buffer and extracted for total RNA on a Qiacube robot using the RNeasy mini kit (Invitrogen). The extracted RNA was quantitated using a NanoDrop and RNA quality was measured via BioAnalyzer chip (Agilent).
Oligo-dT purification of polyadenylated RNA, and reverse transcription to create cDNA. The cDNA is fragmented, blunt-ended, and ligated to indexed (barcoded) adaptors. The library is size selected (in the case of paired-end RNA-Seq), size distribution validated using capillary electrophoresis, and quantified using fluorimetry (PicoGreen) and via Q-PCR.

treatment_protocol: 24-month-old C57BL/6 mice were fed a diet containing 14 ppm Rapamycin or a control diet for 3 months at which point the heart was removed and frozen at -80C.

tag: strain/background

value: heart

value: adult

value: 27 months old

value: control diet


title: Control_S16


title: Control_S11


title: RNAPII 12h

city: new york

first: ivan

last: marazzi

state: ny

address: 1230 York Avenue

institute: rockefeller univeristy

data_processing:
ChIP-Seq libraries were aligned to hg18 using bowtie, allowing 2 mismatches to the reference and no ambiguously mapping reads. RNA-Seq libraries were processed using TopHat/Cufflinks against hg18, allowing 20 max hits to the reference per read.
GRO-Seq libraries were aligned to hg18 after being trimmed of 5' and 3' adapters, using bowtie, allowing 2 mismatches for trimmed reads and 3 for untrimmed reads. These were merged and processed in a strand-specific manner for integrated profiling
Genome Build:
Ivan_PolII_total_T12_fastq.bowtie.bam.bed: hg18

source_name: A549 cells

growth_protocol: Standard culture techniques

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions

treatment_protocol: For siRNA treatments, cells were transfected using Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen) according to the manufacturer’s instructions. siRNA pools targeted to either human PAF1 (L-020349-01, Dharmacon), CHD1 (L-008529-00, Dharmacon) or a control non-targeting pool (D-001810-10-05, Dharmacon) were transfected at a final siRNA concentration of 50 nM. Transfected cells were stimulated with the appropriate stimuli 48 hours post transfection. Gene knockdown efficiency was determined by quantitative PCR and/or Western blotting. For infections, the Flag-NS1 or Flag-∆PAF influenza virus was used at MOI 3.

tag: infected with

value: Flag-NS1 virus

tag: time post infection

tag: antibody

value: anti-RNAP II ctd

tag: antibody vendor

value: Abcam

tag: antibody cat. #

tag: molecule type

value: crosslinked-DNA


title: K4me3 0h

data_processing:
ChIP-Seq libraries were aligned to hg18 using bowtie, allowing 2 mismatches to the reference and no ambiguously mapping reads. RNA-Seq libraries were processed using TopHat/Cufflinks against hg18, allowing 20 max hits to the reference per read.
GRO-Seq libraries were aligned to hg18 after being trimmed of 5' and 3' adapters, using bowtie, allowing 2 mismatches for trimmed reads and 3 for untrimmed reads. These were merged and processed in a strand-specific manner for integrated profiling
Genome Build:
Ivan_H3K4me3_T0_fastq.bowtie.bam.bed: hg18

tag: cell line

value: none (uninfected)

value: Millipore


title: RNAPII 0h

data_processing:
ChIP-Seq libraries were aligned to hg18 using bowtie, allowing 2 mismatches to the reference and no ambiguously mapping reads. RNA-Seq libraries were processed using TopHat/Cufflinks against hg18, allowing 20 max hits to the reference per read.
GRO-Seq libraries were aligned to hg18 after being trimmed of 5' and 3' adapters, using bowtie, allowing 2 mismatches for trimmed reads and 3 for untrimmed reads. These were merged and processed in a strand-specific manner for integrated profiling
Genome Build:
Ivan_PolII_total_T0_fastq.bowtie.bam.bed: hg18


title: NS1 0h

data_processing:
ChIP-Seq libraries were aligned to hg18 using bowtie, allowing 2 mismatches to the reference and no ambiguously mapping reads. RNA-Seq libraries were processed using TopHat/Cufflinks against hg18, allowing 20 max hits to the reference per read.
GRO-Seq libraries were aligned to hg18 after being trimmed of 5' and 3' adapters, using bowtie, allowing 2 mismatches for trimmed reads and 3 for untrimmed reads. These were merged and processed in a strand-specific manner for integrated profiling
Genome Build:
Flag_T0_fastq.bowtie.bam.bed: hg18

value: anti-Flag

value: Sigma


title: Control_S1

tag: tissue

tag: developmental stage

tag: treatment


title: K4me3 12h

data_processing:
ChIP-Seq libraries were aligned to hg18 using bowtie, allowing 2 mismatches to the reference and no ambiguously mapping reads. RNA-Seq libraries were processed using TopHat/Cufflinks against hg18, allowing 20 max hits to the reference per read.
GRO-Seq libraries were aligned to hg18 after being trimmed of 5' and 3' adapters, using bowtie, allowing 2 mismatches for trimmed reads and 3 for untrimmed reads. These were merged and processed in a strand-specific manner for integrated profiling
Genome Build:
Ivan_H3K4me3_T12_fastq.bowtie.bam.bed: hg18


title: Control_S17


title: RNA-Seq 12h (read 1/2)

data_processing:
ChIP-Seq libraries were aligned to hg18 using bowtie, allowing 2 mismatches to the reference and no ambiguously mapping reads. RNA-Seq libraries were processed using TopHat/Cufflinks against hg18, allowing 20 max hits to the reference per read.
GRO-Seq libraries were aligned to hg18 after being trimmed of 5' and 3' adapters, using bowtie, allowing 2 mismatches for trimmed reads and 3 for untrimmed reads. These were merged and processed in a strand-specific manner for integrated profiling
Genome Build:
ribo_minus_WT_12H_accepted_hits.bam.bed: hg18

value: Ribosomal RNA-depleted total RNA


title: NS1 012h

data_processing:
ChIP-Seq libraries were aligned to hg18 using bowtie, allowing 2 mismatches to the reference and no ambiguously mapping reads. RNA-Seq libraries were processed using TopHat/Cufflinks against hg18, allowing 20 max hits to the reference per read.
GRO-Seq libraries were aligned to hg18 after being trimmed of 5' and 3' adapters, using bowtie, allowing 2 mismatches for trimmed reads and 3 for untrimmed reads. These were merged and processed in a strand-specific manner for integrated profiling
Genome Build:
Flag_WT_NS1_T12_fastq.bowtie.bam.bed: hg18


title: Control_S7


title: Control_S13


title: Control_S19


title: Rapa_S18

source_name: Adult mouse heart, rapamycin diet

value: 14 ppm Rapamycin diet (3 month treatment)


title: Rapa_S9


title: Control_S10


title: Rapa_S6


title: RNA-Seq 0h (read 1/2)

data_processing:
ChIP-Seq libraries were aligned to hg18 using bowtie, allowing 2 mismatches to the reference and no ambiguously mapping reads. RNA-Seq libraries were processed using TopHat/Cufflinks against hg18, allowing 20 max hits to the reference per read.
GRO-Seq libraries were aligned to hg18 after being trimmed of 5' and 3' adapters, using bowtie, allowing 2 mismatches for trimmed reads and 3 for untrimmed reads. These were merged and processed in a strand-specific manner for integrated profiling
Genome Build:
ribo_minus_WT_0H_accepted_hits.bam.bed: hg18


title: Rapa_S14


title: Rapa_S5


title: Rapa_S4


title: Rapa_S8


title: Rapa_S3


title: macrophages control (IFNAR wt/wt) #3

city: Dresden

first: Tina

last: Schumann

address: Fetscherstraße 74

department: Medical Faculty "Carl Gustav Carus"

institute: Institute of Immunology

description:
S1897_mp_Kontrolle_wt_3
Strand specific RNA-Seq

data_processing:
Read Alignment: pBWA version 0.5.9-r32-MPI-patch2 against mm9 (UCSC)
Counts per feature: Reads per exon were computed using bedtools version 2.11, summarized per gene based on Ensembl Gene 61 annotation.
Normalization of reads per gene: The raw counts (absolute number of reads) were normalized with the DESeq R package (v.1.8.1) and sample to sample correlation (Pearson's correlation coefficient) was computed based on the normalized counts.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited 'counts' file with sample size normalized counts per gene (rows) and sample (columns)

source_name: mouse peritoneal macrophages

extract_protocol:
Cells were lysed immediately in µMACS™ mRNA Isolation Kit lysis buffer and cleaned with with LysateClear Columns (Miltenyi Biotec). mRNA was enriched using Oligo(dT) beads.
Poly-dT-enrichment, DNAse treatment, chemical fragmentation, ss-Synthesis, strand specific library prep according to: Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 2009 Jul 20. doi:10.1093/nar/gkp596

tag: strain

value: 18 weeks

tag: gender

value: female

tag: cell type

value: peritoneal macrophage


title: macrophages control (IFNAR wt/ko) #4

description:
S1898_mp_Kontrolle_4
Strand specific RNA-Seq

tag: age


title: Control_S2

value: heart


title: macrophages control (IFNAR wt/ko) #7

description:
S1901_mp_Kontrolle_7
Strand specific RNA-Seq

value: 11 weeks

value: male


title: oocyte chromatin fragmented by endogenous nuclease 140-240 bp

tag: sample type

value: chromatin

value: oocyte

tag: size of dna fragments

value: Illumina GAIIx single-end, 36 nt


title: macrophages control (IFNAR wt/wt) #2

description:
S1896_mp_Kontrolle_wt_2
Strand specific RNA-Seq


title: oocyte chromatin fragmented by endogenous nuclease 90-140 bp

tag: sequencing platform


title: macrophages control (IFNAR wt/ko) #1

description:
S1895_mp_Kontrolle_1
Strand specific RNA-Seq


title: macrophages double-KOs #10

description:
S1894_mp_doppel-Kos_10
Strand specific RNA-Seq


title: macrophages double-KOs #9

description:
S1893_mp_doppel-Kos_9
Strand specific RNA-Seq


title: oocyte chromatin fragmented by endogenous nuclease 40-90 bp


title: macrophages double-KOs #8

description:
S1892_mp_doppel-Kos_8
Strand specific RNA-Seq

value: 14 weeks


title: oocyte mononucleosome 150 bp

description: C. elegans oocyte mononucleosome core DNA generated by Mnase digestion

value: mononucleosome


title: macrophages double-KOs #6

description:
S1890_mp_doppel-Kos_6
Strand specific RNA-Seq


title: macrophages double-KOs #5

description:
S1889_mp_doppel-Kos_5
Strand specific RNA-Seq


title: negative control (AP1-GR ap1 cal) replicate 2

city: Dublin

first: Pat

last: Ryan

address: College Green

country: Ireland

institute: TCD

description: Second ChIP-Seq replicate generated on an Illumina GAIIx machine running data collection SCS2.9/RTA1.9 software used as negative control with second AG replicate (sample 2)

data_processing:
For each dataset, alignment was performed using the SOAPv2 short read alignment program and subsequent peak calling using the CSAR package as implemented in the Bioconductor project.
Main method: Arabidopsis genomic sequences were downloaded from TAIR (www.arabidopsis.org; files ‘TAIR10_chr1.fas’ - ‘TAIR10_chr5.fas’). Short read alignments were performed using the SOAP2 software with default settings. Data were read into R using the CSAR package. and functionality provided by various Bioconductor packages (including the IRanges v1.12.5 and GenomicRanges v1.6.4 packages) was used for data handling operations.
Peak calling was performed using the CSAR package that included a normalization and a test based on the Poisson distribution, and enriched regions were identified at a False Discovery Rate (FDR)<0.001 (with five rounds of permutations for each dataset, resulting in >600,000 permutations). Default parameters were used. Only peak regions with stretches of >50 bp were retained.
Peaks were associated with genes located in the vicinity using CSAR functionality, whereby a peak had to reside in a genomic region ranging from 3 kb upstream of a gene’s transcriptional start position to 1 kb downstream of its transcriptional end position. Gene range definitions were downloaded from TAIR (file TAIR10_GFF3_genes.gff).
Genome_build: TAIR10
Supplementary_files_format_and_content: csv formatted files, 1) file containing peak definitions (chromosome, peak start, peak end, peak position and maximal Poisson-based enrichment score) and putative direct target genes and 2) lists of putative direct target genes according to TAIR v10 genome build. The position of significantly enriched region(s) with respect to the corresponding gene is indicated by dividing the gene region into different segments (as indicated) and the maximum peak scores within these segments are shown. A value of 0 indicates that no significantly enriched peak region was detected within a given segment.

source_name: Inflorescence

growth_protocol: Plants were grown on a soil:vermiculite:perlite (3:1:1) mixture at 20 degrees under constant illumination with cool white fluorescent light

extract_protocol: ChIP was performed using a modified version of previously described protocols (Gomez-Mena C, de Folter S, Costa MM, Angenent GC, & Sablowski R (2005); Development 132(3):429-438 + Kaufmann K, et al. (2010), Nat Protoc 5(3):457-472.) Library preparation was performed as described in the instructions of the Illumina ChIP-Seq DNA Sample Prep Kit (IP-102-1001), whereby the adapter-oligo dilution used was 1:30 in water, the gel for DNA purification was run at low voltage (20V for > 6hrs) and gel-extraction step performed twice.

treatment_protocol: For all experiments,  ~4 week-old plants were used. For the experiments using the FIS (35S:AP1-GR ap1-1 cal-1 plants), flower development was induced using a solution containing 10 μM dexamethasone (Sigma-Aldrich), 0.01% (v/v) ethanol and 0.015% (v/v) Silwet L-77 (De Sangosse) – as described in  Wellmer F, et al. (2006) Genome-Wide Analysis of Gene Expression during Early Arabidopsis Flower Development. PLoS Genetics 2(7):e117.

tag: genotype

value: AP1-GR ap1 cal

value: 4 days after Dexamethasone treatment (early-intermediate floral stage ~ stage 4-5 flowers)

tag: chip antibody

value: Anti-GFP AB290 (Abcam)

tag: chip antibody manufacturer

value: Abcam

value: Inflorescence

tag: genetic background


title: negative control (AP1-GR ap1 cal) replicate 1

description: First ChIP-Seq replicate generated on an Illumina GAIIx machine running data collection SCS2.9/RTA1.9 software used as negative control with first AG replicate (sample 1) also used as negative control for ChIP-Seq experiments in GEO series GSE38358


title: AG-GFP (AP1-GR ap1 cal) ChIPseq replicate 2

description: Second ChIP-Seq replicate generated on an Illumina GAIIx machine running data collection SCS2.9/RTA1.9 software

value: AG-GFP AP1-GR ap1 cal


title: Rapa_S15

tag: strain/background

value: adult

value: 27 months old

value: 14 ppm Rapamycin diet (3 month treatment)


title: AG-GFP (AP1-GR ap1 cal) ChIPseq replicate 1

description: First ChIP-Seq replicate generated on an Illumina GAIIx machine running data collection SCS2.9/RTA1.9 software


title: macrophages double-KOs #4

description:
S1888_mp_doppel-Kos_4
Strand specific RNA-Seq

value: 17 weeks

value: female

value: peritoneal macrophage


title: macrophages double-KOs #2

description:
S1886_mp_doppel-Kos_2
Strand specific RNA-Seq

value: 18 weeks

value: male


title: macrophages double-KOs #3

description:
S1887_mp_doppel-Kos_3
Strand specific RNA-Seq


title: macrophages double-KOs #7

description:
S1891_mp_doppel-Kos_7
Strand specific RNA-Seq


title: GRO-Seq 12h delta-PAF

description: Global Run-On (GRO) Sequencing

data_processing:
ChIP-Seq libraries were aligned to hg18 using bowtie, allowing 2 mismatches to the reference and no ambiguously mapping reads. RNA-Seq libraries were processed using TopHat/Cufflinks against hg18, allowing 20 max hits to the reference per read.
GRO-Seq libraries were aligned to hg18 after being trimmed of 5' and 3' adapters, using bowtie, allowing 2 mismatches for trimmed reads and 3 for untrimmed reads. These were merged and processed in a strand-specific manner for integrated profiling
Genome Build:
GroSeq_sample5_rmdup_merged.bam.bed: hg18

tag: infected with

value: Flag-∆PAF virus

tag: time post infection

tag: antibody

value: anti-deoxyBrU

tag: molecule type

value: Nuclear-Run On RNA


title: GRO-Seq 12h WT

description: Global Run-On (GRO) Sequencing

data_processing:
ChIP-Seq libraries were aligned to hg18 using bowtie, allowing 2 mismatches to the reference and no ambiguously mapping reads. RNA-Seq libraries were processed using TopHat/Cufflinks against hg18, allowing 20 max hits to the reference per read.
GRO-Seq libraries were aligned to hg18 after being trimmed of 5' and 3' adapters, using bowtie, allowing 2 mismatches for trimmed reads and 3 for untrimmed reads. These were merged and processed in a strand-specific manner for integrated profiling
Genome Build:
GroSeq_sample4_rmdup_merged.bam.bed: hg18

tag: cell line

value: Flag-NS1 virus


title: GRO-Seq 0h

description: Global Run-On (GRO) Sequencing

data_processing:
ChIP-Seq libraries were aligned to hg18 using bowtie, allowing 2 mismatches to the reference and no ambiguously mapping reads. RNA-Seq libraries were processed using TopHat/Cufflinks against hg18, allowing 20 max hits to the reference per read.
GRO-Seq libraries were aligned to hg18 after being trimmed of 5' and 3' adapters, using bowtie, allowing 2 mismatches for trimmed reads and 3 for untrimmed reads. These were merged and processed in a strand-specific manner for integrated profiling
Genome Build:
GroSeq_sample1_rmdup_merged.bam.bed: hg18

value: none (uninfected)


title: Normal Brain 1

first: Paul

last: Ryvkin

address: 423 Guardian Dr, 1404 Blockley Hall

department: Pathology

institute: University of Pennsylvania

description: rRNA-depleted RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adapter sequence using cutadapt v0.9 with options "-e 0.06 -O 6 -m 14 -n 2"
Reads were mapped to the genome (hg19) using bowtie with options "--best --strata -v 2 -k 100" and non-unique mappers were removed. Reads with a mismatch rate > 6% were discarded.
Reads mapping to known ribosomal RNA sequences via Bowtie were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files containing read counts for each trimmed, rRNA-masked sequence

source_name: Dorsolateral prefrontal cortex

extract_protocol:
RNA was harvested from frozen brain tissue using Trizol reagent.
Illumina small RNA Sample Prep kit (#FC-102-1009) was used to construct libraries from 30ug total RNA. Instead of initial size fractionation, rRNAs were depleted by one round of Ribominus (Invitrogen).

tag: tissue

value: brain

tag: Sex

tag: pathology

value: normal


title: macrophages double-KOs #1

description:
S1885_mp_doppel-Kos_1
Strand specific RNA-Seq

tag: strain

tag: age

value: 21 weeks

tag: gender

tag: cell type


title: Normal Brain 5

description: rRNA-depleted RNA


title: Normal Brain 3

description: rRNA-depleted RNA


title: Rapa_S12

value: heart

tag: developmental stage

tag: treatment


title: Normal Brain 4

description: rRNA-depleted RNA