title: Li-2:1


title: Kyoto

status: Public on Mar 07 2013

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: transcriptomic

data_processing:
Bioscope version 1.3 was used to align .csfasta and .qual files to SNP-substituted reference genomes for each accession using default parameters which allows up to 10 locations per sequenced read.
Cufflinks version 1.1 was used to quantify gene expression values using the following parameters: -F 0 –b –N –library-type fr-secondstrand –G TAIR10.gtf.
Genome_build: TAIR10
Supplementary_files_format_and_content: Expression values for all genes in the TAIR10 reference annotation as defined by Cufflinks version 1.1

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
RNA was isolated using the Qiagen Plant RNeasy kit (Qiagen) following the manufacturer’s instructions.
RNA-Seq libraries were prepared according to the described methods in Li, L. et al. Linking photoreceptor excitation to changes in plant architecture. Genes Dev 26, 785-790 (2012).

tag: cultivar

value: Kyoto

tag: tissue

value: leaf


title: Knox-18


title: Kondara

value: Kondara


title: Kro-0


title: Kin-0


title: Kz-9


title: Krot-0


title: Day 14 pregnant, biological replicate 4

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

description: Pool of RNAs from endometrial tissue samples collected from implantation zones located in the distal, medial and proximal part of one uterine horn

data_processing:
Basecalls performed using CASAVA version 1.6
Trimming: 3' ends were trimmed using Galaxy FASTQ Quality Trimmer, window size: 5, step size: 1, maximum number of bases to exclude from the window during aggregation: 0, aggregate action for window: min. score, trim until aggregate score is: >=30
Trimmed sequences were filtered according to a minimal length of 30 bp with Galaxy Filter FASTQ
Mapping to genome assembly Sscrofa10.2 with Tophat 1.4, tophat parameters: Input Parameter  Value  Will you select a reference genome from your history or use a built-in index?  indexed  Select a reference genome  sscrofa_10.2_stefan  Is this library mate-paired?  single  RNA-Seq FASTQ file  224: Filter FASTQ on merged 909_Pr  TopHat settings to use  full  Library Type  FR Unstranded  Anchor length (at least 3)  15  Maximum number of mismatches that can appear in the anchor region of spliced alignment  0  The minimum intron length  50  The maximum intron length  500000  Allow indel search  Yes  Max insertion length.  3  Max deletion length.  3  Maximum number of alignments to be allowed  5  Minimum intron length that may be found during split-segment (default) search  50  Maximum intron length that may be found during split-segment (default) search  500000  Number of mismatches allowed in the initial read mapping  1  Number of mismatches allowed in each segment alignment for reads mapped independently  1  Minimum length of read segments  25  Use Own Junctions  Yes  Use Gene Annotation Model  Yes  Gene Model Annotations  227: Ssc10_2_EntrezGene.gtf  Use Raw Junctions  No  Only look for supplied junctions  No  Use Closure Search  No  Use Coverage Search  Yes  Minimum intron length that may be found during coverage search  50  Maximum intron length that may be found during coverage search  20000  Use Microexon Search  No
Cufflinks 1.3, Max Intron Length  300000  Min Isoform Fraction  0.05  Pre MRNA Fraction  0.05  Perform quartile normalization  No  Use Reference Annotation  Yes  Reference Annotation  227: Ssc10_2_EntrezGene.gtf  Use Reference Annotation for RABT assembly  No  Ignore reads come from this annotation file  No  Perform Multiread correction  Yes  Perform Bias Correction  Yes  Reference sequence data  cached  Set Parameters for Paired-end Reads? (not recommended)  No
Cuffmerge for generation of a GTF file for transcript annotation
RPKM calculator; calculates RPKM (reads per kilobase per exon model) and number of reads mapped for each gene/transcript from a BAM file based on a given GTF annotation file. GTF from Cuffmerge was used as annotation file. Read counts were subsequently used for statistical analysis with DESeq.
Genome_build: Sscrofa10.2/susScr3
Supplementary_files_format_and_content: txt files, containing columns for transcript consensus ID, Entrez Gene ID, original transcript ID (Refseq ID or Cufflinks ID), nearest Refseq ID, number of mapped reads

molecule: total RNA

organism: Sus scrofa

source_name: endometrial tissue sample

growth_protocol: Prepuberal German Landrace gilts obtained a single injection of 750 IU PMSG (Intergonan®, MSD Animal Health Innovation GmbH, Schwabenheim, Germany) and 72 h later 500 IU hCG (Ovogest®, MSD Animal Health Innovation GmbH) to synchronize ovulation. Gilts of the “pregnant” group were inseminated twice (24 h and 36 h after hCG) with a standard dose of Pietrain semen whereas gilts of the “non-pregnant” control group were inseminated with the supernatant of centrifuged (10 min, 3,000 rpm) semen of the same boar. Gilts were slaughtered on day 14 after insemination.

extract_protocol:
Total RNA was isolated from endometrium using TRIzol® (Invitrogen, Carlsbad, CA, USA) according to the manufacturers recommendations. Purity (based on 260nm:280nm and 260nm:230nm ratios) and quantity of the obtained total RNA was measured by use of a NanoDrop ND-1000 (PEQLAB Biotechnologie GmbH, Erlangen, Germany). Integrity of the RNA was assessed by analysis on Agilent RNA Nano 6000 microfluidic chips with an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany). RNA integrity numbers (RIN) ranged from 7.0 to 8.8.
Equal amounts of total RNA from samples derived from proximal, medial and distal endometrial sections of one uterine horn were pooled for each animal. The mRNA-Seq sample preparation kit (Illumina, San Diego, USA) was used for preparation of RNA-Seq libraries. Library preparation followed the manufacturers instructions. Briefly, poly(A)-containing RNA was purified with oligo-dT-coated magnetic beads starting from 5 µg total RNA and fragmented under elevated temperature using divalent cations. The obtained cleaved RNA fragments were reverse transcribed to first strand cDNA using Superscript II reverse transcriptase (Invitrogen, Karlsruhe, Germany) and random primers, followed by second strand cDNA synthesis using DNA polymerase I and RNase H. The cDNA fragments underwent an end-repair process with T4 DNA polymerase, Klenow DNA polymerase and T4 Polynucleotide kinase, addition of a single ´A´-base, and ligation of adapters. Ligation products were subsequently separated on a 2% agarose gel (Biozym Phor Agarose, Biozym Scientific GmbH, Hess. Oldendorf, Germany) and a gel slice was cut out (X-Tracta, Biozym Scientific GmbH) in the 200 bp (±25 bp) range. After isolation of the DNA from the gel slice (QIAquick Gel Extraction Kit, Qiagen, Hilden, Germany), cDNA fragments were amplified through 15 cycles of PCR (Phusion DNA polymerase, New England Biolabs GmbH, Frankfurt a. Main, Germany) to generate the final sequencing libraries. Concentration of the cDNA fragments was estimated on an Agilent DNA 1000 chip (Agilent Technologies) and with the Qubit Fluorometer (Invitrogen).

treatment_protocol: The uteri were removed and each uterine horn was subsequently opened longitudinally at the anti-mesometrial side. Hyperemic zones, the sites of embryonic attachment, were visual in the endometrium on the mesometrial side. In pregnant sows, samples of the endometrium (containing the lamina epithelialis, lamina propria and tela submucosa, but not tunica muscularis) were taken from hyperemic zones (see Supplemental Figure 1 for examples of hyperemic zones). Samples were taken from three locations of each uterine horn, proximal (the end, close to the ovaries), medial, and distal (next to the corpus uteri). Samples from the endometrium of the non-pregnant sows were taken from comparable locations. Tissue samples for isolation of RNA were immediately transferred to RNAlater™ (Ambion, Huntingdon, Cambridgeshire, UK), incubated overnight at 4°C and stored at -80°C until further use.

tag: gender

value: female

tag: Stage

value: day 14 of pregnancy

tag: organ/tissue

value: uterus/endometrium

tag: breed

value: German Landrace


title: Kil-0


title: Day 14 pregnant, biological replicate 3


title: Qar-8a


title: Ler-1


title: Kl-5


title: Day 14 pregnant, biological replicate 1


title: Kas-1


title: Day 14 pregnant, biological replicate 2


title: Jl-3


title: Day 14 non-pregnant control, biological replicate 2

description: Pool of RNAs from endometrial tissue samples collected from the distal, medial and proximal part of one uterine horn

value: day 14 of estrous cycle


title: Je-0


title: Is-0


title: Day 14 non-pregnant control, biological replicate 4


title: NOD.Rag1KOWK6.5_RNA-seq

city: Pasadena

first: Mary

last: Yui

email: yui@caltech.edu, jingli@caltech.edu

address: 1200 E California Blvd

department: Biology

institute: California Institute of Technology

data_processing:
Sequence reads from each cDNA library (38 bp, single-read) were trimmed to 32 bp long and mapped onto the mouse genome build NCBI37/mm9 using Bowtie (bowtie-0.12.1, http://bowtie-bio.sourceforge.net/index.shtml) with setting ‘-v 2 -k 11 -m 10 -t --best --strata’. The mappable data were then processed by the ERANGE v. 3.3 RNA-seq analysis program (Mortazavi et al, 2008)
Genome_build: mm9
Supplementary_files_format_and_content: RPKM files containing expression profiling data (gene ID, name, transcript length and normalized read abundance in RPKM)

organism: Mus musculus

source_name: NOD.Rag1KO WK6.5

extract_protocol: Flow cytometry sorted thymocytes were lysed in Trizol. Total RNA was extracted using chloroform. mRNA was then purified by two rounds of selection using Oligo-dT coupled magnetic beads (Dynabeads) according to the manufacturer’s protocol. mRNA was then fragmented to an average length of 200 bp by magnesium-catalyzed hydrolysis and converted into cDNA by random priming. Purified cDNA fragments were end-repaired using a combination of T4 DNA polymerase, Klenow polymerase and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3' 'A' base for ligation of Illumina's adapters  which have a single 3'  overhanging 'T' base. After (paired-end) adapter ligation DNA was purified and size selected for ~300bp by gel electrophoresis and extraction. The purified DNA was treated with Beckman/Coulter Genomics SPRI beads (Agencourt AMPure XP catalog # A63880)  to remove low MW fragments (<100 bp) from the target size population that was selected on the agarose gel. The recovered DNA was enriched by PCR amplification for 15 cycles. PCR product was treated again with SPRI beads to remove extra primer. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

tag: strain

value: NOD

tag: genetic background

tag: cell type

value: thymocyte


title: Kelsterbach-1


title: Jm-0


title: Hs-0


title: NOD.Rag1KOWK4_RNA-Seq

source_name: NOD.Rag1KO WK4


title: B6.Rag1KOWK7_RNA-Seq

source_name: B6.Rag1KO WK7


title: Day 14 non-pregnant control, biological replicate 1


title: B6.Rag1KOWK4_RNA-Seq

source_name: B6.Rag1KO WK4


title: Gu-0


title: Gy-0


title: Hey-1


title: Hh-0


title: Gr-1


title: Gre-0


title: Ha-0


title: Gifu-2


title: Kar-1


title: Day 14 non-pregnant control, biological replicate 3


title: Gie-0


title: Got-7


title: Fr-2


title: Et-0


title: In-0


title: Es-0


title: En-D

value: En-D


title: El-0


title: Est

value: Est


title: Gel-1


title: HR-5


title: Durh-1


title: Dra-0


title: Hau-0


title: Di-G

value: Di-G


title: Dja-1


title: Com-1


title: Cnt-1


title: Ga-0


title: Co-1


title: Col-0


title: Cerv-1


title: Chi-0


title: Fi-0


title: Chat-1


title: Cal-0


title: Er-0


title: Ca-0


title: Bsch_0


title: Etna-2


title: Bu_0


title: Bs_1


title: Boot_1


title: Do-0


title: Ei-2


title: Anholt_1


title: Bik_1


title: Bl_1


title: Ann_1


title: Db-1


title: Da(1)-12


title: Amel_1


title: Altai_5


title: Alst_1


title: Abd_0


title: Ak_1


title: An_1


title: Ang_0


title: Aa_0


title: Whole_Dana_371.13_Male_Rep1

status: Public on Mar 06 2013

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

data_processing:
Basecalls performed using Illumina pipeline version 1.6.47.1 for runs on Illumina GAIIx, or CASAVA version 1.7 for runs on Illumina HiSeq 2000 instrument.
Reads that passed Illumina pipeline quality filtering criteria (those output to s_x_x_sequence.txt fastq files) were mapped to a reference genome.
Reads were trimmed to 75 bp due to low quality on the 3' end of the 101 bp reads. Trimmed 75 bp reads were used for subsequent analyses. Trimmed reads that passed the Illumina filter were mapped with Tophat 1.1.4. The species-specific reference sequence plus ERCC spike-in control sequences (see GEO entry GSE20555 for spike-in control sequences) was used to build a reference index for mapping. The reference index was created using the bowtie-build function with default parameters and reads were mapped to this reference using the Tophat parameters -g 1 -F 0 -r 150 -solexa1.3-quals.
Genome_build: droYak2, droAna3, dp4, droMoj3, droVir3
Supplementary_files_format_and_content: BAM files contain alignments for uniquely-mapped reads, BEDGRAPH contain base-level coverage

organism: Drosophila ananassae

source_name: Whole tissue

growth_protocol: Adult flies were growth 5-7 days post eclosion. See GSE6640 for details.

extract_protocol: See GSE6640 for RNA extraction methods. We fragmented mRNA using alkaline hydrolysis. First, 9 µl of 100 ng of mRNA and 1 µl of 10X fragmentation buffer (Ambion, Austin, Texas.) was incubated at 70°C for 5 minutes to fragment mRNA. One microliter of Stop Buffer (Ambion, Austin, Texas) was added and samples were placed on ice. Fragments were precipitated with 1 µl 3 M NaOAC (pH 5.2), 2 µl glycogen (5 µg/µl , Ambion, Austin, Texas), and 30 µl 100% EtOH and then incubated for 30 minutes at -80 °C. Fragmented RNA was pelleted at 14000 rpm with a microcentrifuge at 4°C. The pellet was washed with 70% EtOH, air dried and resuspended with 10.5 µl RNase free H2O. Fragmented mRNA was reverse transcribed to create cDNA. One microliter of random hexamer primers (3µg/µl, Invitrogen, Carlsbad, California) was placed with 10.5 µl of fragmented mRNA, then samples were incubated at 65°C for 5 minutes and placed on ice. Four microliters 5X first strand buffer, 2 µl 100 mM DTT, 1 µl dNTP, and 0.5 µl RNaseOUT were added to the mRNA and samples were incubated at 25°C for 2 minutes. One microliter of SuperScript II (200 U/µl, Invitrogen, Carlsbad, California) was added and samples were incubated under the following conditions: 25°C-10 minutes, 42°C-50 minutes, 70°C-15 minutes. Samples were then placed on ice. Second strand cDNA was synthesized by adding 61µl H2O to the first strand mix, 10 µl 10X second strand buffer (500 mM Tris-HCl pH 7.8, 50 mM MgCl2, 10 mM DTT), and 3 µl dNTP (10 mM), mixed, incubated on ice for 5 minutes, then 1 µl RNaseH (2U/µl, Invitrogen, Carlsbad, California) and 5 µl DNA Pol I (10 U/µl, Invitrogen, Carlsbad, California) were added. Samples were incubated at 16°C for 2.5 hours and DNA products purified using a QIAquick spin column and following manufacture directions and eluted with 30 µl. cDNA fragment libraries were prepared for sequencing. The ends of cDNA fragments were repaired using 30 µl of DNA, 45 µl H2O, 10 µl T4 DNA ligase buffer with 10 mM ATP, 4 µl dNTP mix (10 mM), 5 µl T4 DNA polymerase (3 U/µl), 1 µl Klenow DNA polymerase (5U/µl), and 5 µl T4 PNK(10 U/µl). Samples were incubated for 30 minutes at 20°C, purified with QIAquick PCR spin columns, and eluted with 32 µl of Buffer EB. A single "A" base was added to the ends of cDNA by using 5 µl Klenow buffer, 10 µl dATP (1 mM) and 3 µl Klenow 3' to 5' exonuclease (5 U/µl). Samples were incubated at 37°C for 30 minutes, purified with a QIAquick MiniElute column, and eluted with 19µl of EB solution. Adaptor oligonucleotdies were ligated to A overhang fragments as follows. Overhang fragments were combined with 25 µl DNA ligase buffer, 1 µl adaptor olio mix, and 5 µl DNA ligase (1U/µl). Samples were incubated at room temperature for 15 minutes, purified with a QIAquick MiniElute column, and eluted with 10 µl of buffer EB. cDNA templates were sized selected by gel purification then amplified by PCR using oligo-specific primers. Samples were loaded into a 2% agarose gel with 1X TAE buffer and run for 50 minutes with a 100 bp ladder. The gel was stained with ethidium bromide and bands were visualized under UV fluorescence. For each sample, a gel slice was cut at the 300 (+/- 25) bp region, purified with a QIAquick gel extraction kit, and eluted with 30 µl buffer EB. Purified cDNA was amplified in a 50 µl reaction using 25 µl Phusion Mix (Phusion polymerase, dNTPs, and buffer), 1 µl primer 1.1, 1 µl primer 2.1, and 23 µl template along with the following cycling conditions: initial denaturation 98°C-30 sec, cycle denaturation 98°C-10 sec, anneal 65°C-30 sec, and extend 72°C -30 sec with 15X cycles and a final extension of 72°C for 5 minutes followed by a hold at 4°C. The amplified product was purified using a QIAquick column and eluted with 30 µl buffer EB.

treatment_protocol: Flies were raised incubators with no photoperiod at 22 C and 60% humidity. See GSE6640 for details.

value: Drosophila Species Stock Center (DSSC) 14024-0371.13. See Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218 for more details about strain origin.

value: Whole flies

tag: developmental stage

value: Adult

tag: Sex

value: Male


title: Whole_Dana_371.13_Male_Rep2


title: Whole_Dvir_1051.87_Male_Rep2

organism: Drosophila virilis

value: Drosophila Species Stock Center (DSSC) 15010-1051.87. See Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218 for more details about strain origin.


title: Bla_1

value: leaf


title: Whole_Dvir_1051.87_Male_Rep1


title: Anz_0


title: Illumina2-GMCSF

city: Liverpool

first: Helen

middle: Louise

last: Wright

address: 6 West Derby Street

department: Institute of Life Course and Medical Sciences

country: United Kingdom

institute: University of Liverpool

data_processing:
Reads were mapped to the human genome (hg19) using TopHat (v1.4.1).
Illumina libraries:default TopHat parameters were used with the addition of the -g / --max-multi-hits option set as 1, to report only uniquely mapping reads.
SOLiD libraries: preliminary analysis of read quality scores showed a decrease in quality of SOLiD reads towards the 3’ end of the read, and consequently reads were trimmed by 10 bases from the 3’ end and first mapped to the human genome using Bowtie (v0.12.7).  Reads not uniquely mapped by Bowtie were then mapped using TopHat and the two datasets merged.
Gene annotation and calculation of RPKM values was carried out using Cufflinks (v1.3.0) with the provision of a GTF annotation file (hg19).
Genome_build: hg19
Supplementary_files_format_and_content: Files were created using cuffdiff applying a 5% false discovery rate and with the provision of a reference GTF (hg19)

organism: Homo sapiens

source_name: Neutrophil

extract_protocol: RNA was isolated using TRIzol-chloroform precipitation, followed by clean-up with the Rneasy kit (Qiagen) including DNA digestion.  RNAseq was carried out using standard SOLiD and Illumina protocols.  mRNA was enriched by ribosomal depletion (SOLiD) or poly-A selection (Illumina).

treatment_protocol: Neutrophils were isolated from peripheral blood and incubated for 1h with TNF-alpha (10 ng/mL) or GM-CSF (5 ng/mL).

value: male

tag: age

tag: treatment

value: incubated for 1h with GM-CSF (5 ng/mL)


title: Solid1-Untreated

description: RNA (ribosome-depleted)


title: Illumina2-TNF

value: incubated for 1h with TNF-alpha (10 ng/mL)


title: Solid1-TNF

description: RNA (ribosome-depleted)


title: Solid1-GMCSF

description: RNA (ribosome-depleted)


title: Illumina2-Untreated


title: Whole_Dyak_261.01_Male_Rep2

organism: Drosophila yakuba

value: Drosophila Species Stock Center (DSSC) 14021-0261.01. See Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218 for more details about strain origin.


title: Illumina1-GMCSF


title: Bor_4


title: Illumina1-TNF


title: Illumina1-Untreated


title: HBERNC

status: Public on Mar 05 2013

city: Guangzhou

first: Gong

last: Zhang

address: Huang-Pu Avenue West 601

department: Institute of Life and Health Engineering

country: China

institute: Jinan University

description: High quality reads which passed Illumina filter were kept. RNC-mRNA was extracted and the polyA+ mRNA was sequenced.

data_processing:
Reads were mapped to RefSeq RNA reference sequence using FANSe v7.2 with the options –L78 –S8 –I0 –E9 –B1.
Splice variants were summed
The reads mapped to splice variants of one gene were summed. The mRNA abundance was calculated using rpkM (reads per kilobase per million reads) normalization (Mortazavi et al. 2008)
Supplementary_files_format_and_content: Text files with RPKMs

source_name: HBE

growth_protocol: Cells were maintained in DMEM  (Invitrogen, Carlsbad, CA), supplemented with 10% fetal bovine serum (FBS) (PAA Australia, Weike Biochemical Reagent, Shanghai, China), 1% penicillin/streptomycin and 10 μg/mL ciprofloxacin.

extract_protocol:
RNC extraction: Esposito AM, Mateyak M, He D, Lewis M, Sasikumar AN, Hutton J, Copeland PR, Kinzy TG. 2010. Eukaryotic polyribosome profile analysis. J Vis Exp(40). RNA extraction: standard Trizol protocol.
Standard Illumina TruSeq mRNA library prep

value: normal human bronchial epithelial (HBE) cells


title: HBERNA

description: High quality reads which passed Illumina filter were kept


title: Whole_Dyak_261.01_Male_Rep1


title: A549RNC

tag: cell line

value: lung cancer


title: Heart_Tbx3_ChIP-seq

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

description: Sample run through SOLiD v3.0

library_source: genomic

data_processing:
Reads were then processed and aligned to the mouse reference genome (NCBI Build 37, mm9) as previously described, allowing a maximum of two mismatches. To generate a WIG file, all tags were extended to the calculated shear length as given by MACS (159bp). The WIG was then converted to a bigWig using the Galaxy Wig-to-bigWig conversion tool. To generate the bed file, peaks were called on the WIG file using the OccuPeak method (submitted for publication).
Genome_build: mm9
Supplementary_files_format_and_content: Tbx3_heart_adult_mouse.bigWig is a bigWig file visualizing the binding profile of Tbx3 in the mouse heart. Tbx3_heart_adult_mouse.bed is a bed file containing peaks called with the OccuPeak method (submitted for publication).

molecule: genomic DNA

extract_protocol: Material was used for library preparation with standard SOLiD library construction kit for SOLiD sequencing (Applied Biosystems, #4443713, #4400413).

tag: strain background

value: FVB/N

tag: genotype/variation

value: adult

value: heart

tag: chip antibody

tag: chip antibody vendor

value: Santa Cruz Biotechnology

tag: chip antibody cat#

tag: chip antibody lot#


title: A549mRNA


title: Trophozoite H2B.Z input

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

data_processing:
Basecalling and quality control was performed by the Illumina pipeline
Reads (76 bp) were aligned to the P.falciparum (3D7) genome (PlasmoDB v6.1) using BWA.
For comparative analysis 10.6M uniquely mapped reads were randomly selected for each dataset
Coverage plots were generated by counting the number of overlapping, uniquely mapped 76bp tags in 10bp windows
Genome_build: PlasmoDB 6.1
Supplementary_files_format_and_content: gff

organism: Plasmodium falciparum 3D7

source_name: parasite nucleus

growth_protocol: Parasites, carrying a Ty1 tagged copy of H2B.Z under the control of crt promoter, were cultured in standard RPMI medium supplemented with 10% human serum and 0.2% NaHCO3 in 20ml per 250ml tissue culture flasks and candle jars. The culture was synchronised with multiple rounds of sorbitol treatments and Percoll gradient centrifugation.

extract_protocol: Sequencing libraries were prepared by the LADS protocol (Hoeijmakers et al., Nature Protocols 2011)

value: Trophozoite (30h post invasion)

tag: sample type

value: mononucleosomal DNA

tag: tissue

value: whole organism


title: Schizont H2B.Z input

value: Schizont (40h post invasion)


title: Ring H2B.Z input

value: Ring (20h post invasion)


title: Trophozoite H2B.Z ChIP-seq

value: anti Ty1 (BB2)

value: ChIPed DNA


title: Ring H2B.Z ChIP-seq


title: Schizont H2B.Z ChIP-seq


title: IgG

city: boston

first: Chris

middle: A

last: French

state: MA

address: 75 francis st.

department: Pathology

institute: BWH

description: control IgG ChIP-Seq in TC-797 cells

data_processing:
Reads were uniquely aligned (--best -k 1 --strata -M 10) to the human genome (hg19 assembly) excluding chromosome Y (to avoid rejecting reads mapping to the pseudo-autosomal region) using the bowtie short read aligner (http://bowtie-bio.sourceforge.net/index.shtml) to report the single best match per read. Replicate reads with identical start and end positions were collapsed before using SPP (http://compbio.med.harvard.edu/Supplements/ChIP-seq/) to generate smoothed density maps of H3K9/K14ac ChIP reads corrected for IgG input.
Genome Build:
TC797_IgG.map.gz: hg19

growth_protocol: DMEM supplemented with 10% fetal bovine serum, pen-strep, and L-glutamine

extract_protocol: ChIP-seq libraries were constructed per the Illumnia ChIP DNA library preparation kit.

value: NUT Midline Carcinoma cell line

value: female

value: IgG control


title: H3K9/14Ac

description: acetylated H3K9/K14 ChIP-Seq in TC-797 cells

data_processing:
Reads were uniquely aligned (--best -k 1 --strata -M 10) to the human genome (hg19 assembly) excluding chromosome Y (to avoid rejecting reads mapping to the pseudo-autosomal region) using the bowtie short read aligner (http://bowtie-bio.sourceforge.net/index.shtml) to report the single best match per read. Replicate reads with identical start and end positions were collapsed before using SPP (http://compbio.med.harvard.edu/Supplements/ChIP-seq/) to generate smoothed density maps of H3K9/K14ac ChIP reads corrected for IgG input.
Genome Build:
TC797_H3K9K14ac.map.gz: hg19
TC797_H3K9K14ac.bw.gz: hg19

value: Histone H3 Lysine 9/14 acetylation


title: H1299RNC

description: translating mRNA (RNC-mRNA) of H1299

value: non-small cell lung carcinoma


title: small RNA profile of rat normal liver tissue

city: Fuzhou

first: Weiqiang

last: Yang

address: Shang Xia Dian 15

department: The Ministry of Education Key Laboratory of Biopesticide and Chemical Biology

institute: Fujian agriculture and forestry  university

description:
C4A
small RNA sequencing

data_processing:
We use software developed by BGI for data processing.
The reference genome used for read alignment is available on rat genome database. Rat Genome V3.4 Assembly.(http://rgd.mcw.edu/).
The data is processed by the following steps:1) Getting rid of low quality reads.2) Getting rid of reads with 5' primer contaminants.3) Getting rid of reads without 3' primer.4) Getting rid of reads without the insert tag.5) Getting rid of reads with poly A.6) Getting rid of reads shorter than 18nt.
Normalized expression of micorRNA were calculated by the following program designed by BGI and parameters: blastall -p blastn -F F -e 0.01.
Genome build: Rat Genome Database, RGD_v3.4
Supplementary_files_format_and_content: miR_count.txt reports abundance measurements.
Supplementary_files_format_and_content: C4A_TB.txt reports differential expression measurements.

organism: Rattus norvegicus

source_name: liver tissue, normal control

extract_protocol:
Livers were collected after surgery,and RNA were extracted using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rats of expremental group were treated with AFB1 at the dose of 1.5mg/kg,and rats of control group were treated with DMSO and equal amount of NS (normal saline). After 3d,Liver tissue were excised and RNA were extracted.

value: normal control

tag: gender

value: male

value: 7 weeks

value: liver


title: H1299mRNA

description: total mRNA of H1299


title: small RNA profile of aflatoxin B1 treated liver

description:
TB
small RNA sequencing

source_name: liver tissue, aflatoxin B1 treated

tag: strain

value: aflatoxin B1


title: HeLa mitochondrial RNA

city: Gandhinagar

first: Rajesh

last: Singh

state: GJ

address: Koba Inst Area

department: Cell Biology

country: India

institute: Indian Institute of Advanced Research

data_processing: The data cleaning of 50nt sequence tags was done to exclude the low quality tags and all contaminants. The 3' adaptor sequences, 5' contaminants and polyA reads were removed using a dynamic programming algorithm. The remaining sequences were mapped to human genome using SOAP with the following options: soap -v 0 -r 2 -s 7 -p 7 -a.

source_name: cervical adenocarcinoma

growth_protocol: Dulbecco's Modified Eagle's Medium (DMEM, Lonza, Switzerland) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (Lonza, Switzerland) and 1% penicillin, streptomycin and amphotericin B (PSA) antibiotic mixture  (Lonza, Switzerland). Maintained cells were used to prepare various plates and disc as per requirement.

extract_protocol: sRNAs ranging from 18 to 30-nt were gel-purified and ligated to the 3' adaptor and 5' adaptor. The ligated products were used for cDNA synthesis, purified by acrylamide gel electrophoresis and then amplified to generate small RNA libraries.

treatment_protocol: Mitochondria were prepared from HEK293 and HeLa cells using Qproteome Mitochondria Isolation Kit (Qaigen, USA). The purity of mitochondria was confirmed by western blotting using different antibodies. RNA was isolated from mitochondria using miRCURYTM RNA Isolation Kit (Exiqon, Germany) according to manufacturer's instructions. RNA integrity was checked by Agilent 2100 Bioanalyzer (Ambion, USA).

value: 31 year adult female

value: cervix

tag: disease/cell type

value: transformed with adenovirus 5 DNA

value: HeLa


title: HEK293 mitochondrial RNA

source_name: embryonic kidney

value: fetus

value: kidney

value: adenocarcinoma


title: C57BLmj

city: Seattle

first: Wonjong

last: Moon

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle BioMed

data_processing:
Illumina Genome Analyzer II GA2 HiSeq and CASAVA 1.8.2 for base calling
Additional quality control was applied to the datasets by clipping or removing poor quality reads and N's by ea-utils toolkit (http://code.google.com/p/ea-utils/), with -p 10 and -q 7 settings, then mapped to P. yoelii YM strain reference  genome using tophat version 1.4.1 with default parameters
The differential transcript abundances between samples were measured in Fragments per kilobase of transcript per million mapped fragments (FPKM) using  Cufflinks and Cuffdiff by a protocol from Trapnell C. et al. (2012) Nature.
RNA-Seq differential analysis was visualized by CummeRbund
Transcripts with P values of less than 0.01 and at least 4-fold difference in expression (i.e., log fold > 2) were selected to identify the most differentially regulated genes.
Coverage plots were generated to examine the RNA distribution of reads across selected genes-of-interest by comparing the number of unique reads present at each nucleotide position
Genome_build: Mus musculus UCSC version mm10
Supplementary_files_format_and_content: tab-delimited text files (cuffdiff gene_exp.diff) include gene differential FPKM values for each Sample

source_name: perfused mouse liver

extract_protocol:
RNA was isolated by the Qiagen RNeasy Miniprep Kit with an added DNaseI treatment module.
Library was constructed by Expression Analysis, Inc using the Illumina TruSeq RNA sample preparation kit using standard methods.

treatment_protocol: Mice were infected intravenously with 100,000 transgenic P. yoelii fabb/f- salivary gland sporozoites or with debris from uninfected mosquito salivary glands. Three days post infection mouse livers were perfused with HBSS.  Livers were then flash frozen in liquid nitrogen until extraction.

value: mouse liver

tag: infection

value: 3 days post mock infection with debris from mosquito salivary glands


title: C57BLfab

value: 3 days post infection with Py fabb/f-knock out transgenic  P. yoelii sporozoite infection


title: BmAGO2RIPseq

city: Hangzhou

first: Nie

last: Zuoming

state: Zhejiang

address: Xiasha high Education Zone, No.2 Road

department: School of Life Science

institute: Zhejiang Sci-Tech University

data_processing:
Base calls were obtained using HCS1.5.15.1 and RTA1.13.48
Sequencing file performed using BclConverter-1.9.0-11-03-08, then got rid of the low quality tags and several kinds of contaminants. The clean reads mapped to silkworm integretedseq.txt.gz and BmNPV genome (NC_001962.1; http://www.ncbi.nlm.nih.gov/nuccore/9630816)  using soap -v 0 -r 2 -m 0 -a clean.fa -D ref_genome.fa.index -o match_genome.soap. BmNPV derived small RNAs were regarded as BmNPV-encoded small RNAs.
Align small RNA tags to miRNA precursor/mature miRNA of bombxy mori in miRBase 18 using blastall -p blastn -F F -e 0.01 and show the miRNA families (no specific) which can be found in the samples by BGI- tag2miRNA; Annotate the small RNA tags with TE(transposable element)-, tRNA-, snRNA-, snoRNA- and rRNA-derived small RNAs from Genbank and get rid of matched tags from unnnotated tags using blastall -p blastn -F F -e 0.01.
The >25nt TE-derived small RNAs and the remaining unannotated reads were selected for probing piRNAs using piRNApredicter program and Perl script developed.
Genome_build: silkworm integretedseq; BmNPV genome (http://sgp.dna.affrc.go.jp/pubdata/genomicsequences.html; Apr-2008)
Supplementary_files_format_and_content: The .fa files report abundance counts for several kinds of small RNAs.

organism: Bombyx mori

source_name: BmN cell

extract_protocol:
The harvested cells were disrupted using lysis buffer (50mM Tris, pH 8.0, 150mM NaCl, 5mM EDTA, 0.5% Nonidet P-40) and co-immunoprecipitated HIS-BmAGO2-bound RNA were isolated with HIS monoclonal antibody(Anti-His6(2).Roche). RNA was prepared using TRIzol reagent(Invitrogen) according to the manufacturer's protocal. Illumina Truseq RNA sample Prep kit was used with 2.8ug of RNA for the construction of sequencing libraries.
Libaries were prepared for sequencing according to Illumina's protocol.

value: BmN

tag: cell type

value: ovarian cell

tag: rip antibody

value: HIS  monoclonal antibody [Anti-His6(2), catalog number 04905318001, lot number 70012033, Roche]


title: BALBfab

description: BALB/cJ-fabb/f-

value: BALB/cJ


title: BALBmj

description: BALB/cJ-mock


title: WT rep1

city: Beijing

first: qing

middle: hong

last: zhao

address: changbai road 155

institute: china cdc

description: total RNA

data_processing:
All RNA data were mapped to the reference genome Xuzhou21 using SOAP2.
The distribution of reads was plotted by its location in the reference genome, and then divided into gene region and intergenic region. Genome and gene coverage was calculated by counting the number of reads mapped to the genome and individual genes respectively.
The gene expression was calculated using the RPKM method
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Escherichia coli O157:H7

source_name: Isolated from feces of a HUS patient from an outbreak in China in 1999

growth_protocol: The bacteria were routinely grown in Luria-Bertani (LB) broth or on LB agar plates (pH 7.2).

extract_protocol:
Total RNA were then isolated according to the standard protocol using an RNeasy mini kit (Qiagen). Genomic DNA were extracted from both Xuzhou21 and Xuzhou21m using Wizard Genomic DNA purification kit (Promega, Madison, WI, USA) according to the manufacturer’s protocols.
The total RNA extracted from Xuzhou21 and Xuzhou21m were first treated with Ribo-Zero™ rRNA Removal kit to remove rRNA. The mRNA was fragmented and produced cDNA libraries primed with random hexamers. cDNA was selected by size, amplificated using PCR and and then sent to sequencing using Illumina HiseqTM 2000 commercially.

treatment_protocol: For total RNA isolation, the bacteria were inoculated in 5 ml LB broth at 37℃with shaking for 16 h. 50 µl of the above culture was inoculated in 5 ml fresh LB broth and the culture was shaken at 37°C for about 2.5 h until the OD600 reached 0.6. 500 µl of the culture were mixed with 1 ml RNA protect bacterial reagent (Qiagen, Hilden, Germany) to stabilize RNA according to the manufacturer’s instructions.

tag: genotype

value: wild type


title: plasmid cured rep2

description: total RNA

source_name: Xuzhou21 cured of the pO157_Sal plasmid

value: plasmid cured strain


title: plasmid cured rep1

description: total RNA


title: GCB_INPUT

status: Public on Mar 03 2013

city: New York

first: Katerina

last: Hatzi

state: NY

address: 413 E 69th Street, BB-1462

department: Hematology/Oncology

institute: WCMC

description: INPUT-seq for GC B cell datasets

data_processing:
Raw images generated went through primary image analysis and basecalling (RTA v1.6) that was followed by Illumina Genome Analyzer Off-Line Basecaller (OLB v1.6) analysis, where reads were aligned to the human genome (UCSC hg18) using ELAND. Only sequences mapped uniquely to the genome with not more than 2 mismatches were used for downstream analysis. Several reads mapping to the same exact location (clonal reads) were considered amplification artifact and were excluded from the analysis. Read density tracks were generated using ChIPseeqer and visualized using the UCSC browser.
Genome_build: hg18
Supplementary_files_format_and_content: "Read_density-wig" files are wig tracks generated using ChIPseeqerMakeReadDensityTrack of the ChIPseqer package. (http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqerMakeReadDensityTrack).They represent the average ChIPseq read density, normalized to the total number of reads.

source_name: Primary cells

growth_protocol: Germinal center B-cells were isolated from fresh deidentified human tonsils derived from surgery waste with the approval of the Human Research Protections Programs, Division of Research Integrity of the Weill Cornell Medical College in accordance with the Declaration of Helsinki. Purifications were based on the expression of CD77 (GC). Separation was performed using a magnetic beads cell separation system with double positive selection settings (MACS, Miltenyi Biotec). Purity of the isolated cells was confirmed by FACS and always exceeded 95%.

extract_protocol: ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture's instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. A' bases were added to the 3'ends of the DNA fragments and Illumina adapters (1:30 dilution) were ligated to the ends of ChIP fragments. After adapter ligation DNA was separated by electrophoresis and size selected by isolating a gel band of 250±25bp. This fragment range corresponds to a ChIP fragment range of about 158±25bp. Size selected fragments were PCR amplified for 15cycles using Illumina genomic DNA primers 1.1 and 1.2 with the following program (30s at 98oC, 15cycles of 10 at 98oC, 30s at 65oC,30s at 72oC and 5min extension at 75oC). Libraries were quantified and validated using Agilent Technologies 2100 Bioanalyser for size, concentration and purity. Q-PCR was repeated to confirm retention of relative enrichment.

value: Germinal center B cells

value: none (INPUT)


title: GCB_SMRT_ChIP

description: ChIP-seq in GC B cells against SMRT

value: SMRT


title: WT rep2

description: total RNA


title: G9a Input

status: Public on Mar 04 2013

city: new york

first: Rui

last: Wang

state: new york

address: 1275 York Avenue

institute: MSKCC

description: G9a Y1154A input

data_processing:
Basecalls performed using CASAVA version 1.8.1
CliEn-seq reads were aligned to the hg19 genome assembly using BWA with default parameters
Data were filtered using the following specifications: only uniquely mapping reads were conserved.
Genome_build: hg19

source_name: Epithelial cells

growth_protocol: HEK293T cells were routinely seeded into CellBIND surface T75 flask (Corning) and cultured in DMEM medium supplimented with 10% FBS and maintained in a humidified incubator at 37 °C and 5% CO2.

extract_protocol:
The cells were harvested and lysed in ice-cold RIPA buffer (Sigma) containing 1×Complete EDTA-free protease inhibitor cocktail (Roche).
Libraries were prepared using Illumina TruSeq DNA Sample Preparation Kit according to the standard preparation protocol (http://www.illumina.com/) with some modifications. In brief, after adding a single adenine nucleotide overhang to the ChIP/CliEn DNA or ~5ng of the input DNA, a 1:10 dilution of the DNA adapters were ligated. DNA fragments were then amplified with PCR Primer Cocktail (8 cycles) and 1/10 of the PCR product was checked on the Agilent Bioanalyzer. The purified DNA libraries were diluted to 10 nM for loading on the flow cell. Sequencing service was performed on an Illumina Hiseq 2000 sequencer according to the standard Illumina protocol resulting in ~ 15 million quality-filtered sequences of length 75/75 per sample.

value: Embryonic epithelial kidney cell

tag: passage

tag: enrichment


title: G9a

description: G9a Y1154A mediated H3K9 (E)-hex-2-en-5-ynylation

tag: cell line


title: GLP1

description: GLP1 Y1211A mediated H3K9 (E)-hex-2-en-5-ynylation


title: GCB_BCL6_ChIP

description: ChIP-seq in GC B cells against BCL6


title: GCB_BCOR_ChIP

description: ChIP-seq in GC B cells against BCOR

value: BCOR


title: GLP1 Input

description: GLP1 Y1211A input


title: Mg_H3K4Me2_rep2

status: Public on Mar 02 2013

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

data_processing:
Alignment: Sequence reads were obtained and mapped to the Mouse (July, 2007) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: mammary gland

extract_protocol: Illumina standard protocol

tag: tissue type

value: mammary gland

tag: developmental stage

value: lactation day 8

value: female

tag: antibody

tag: antibody vendor

value: millipore

tag: antibody catalog #

tag: antibody lot #


title: Mg_H3K4Me2_rep1


title: Mg_K4K9_input


title: Mg_H3K4Me2_rep3


title: Mec_H3K4Me2

source_name: mammary epithelial cells

value: mammary epithelial cell

value: 12 week virgin-diestrus


title: Lvr_H3K4K9_input

source_name: liver

value: liver


title: Lvr_H3K4Me2_rep3


title: Lvr_H3K4Me2_rep2


title: Mec_input


title: Lvr_H3K4Me2_rep1


title: PS

city: Tai'an

first: Xiaoming

last: Li

state: Shandong

address: 61st ,Daizong Street

institute: Shandong Agriculutural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Unique reads were mapped onto the genome using the program SOAP3
The perfectly matched reads were searched against the Metazoa mature micorRNA of Sanger miRBase4 (Release 18) using the software Patscan12.
The inverted repeats (step loops or hairpin structure) were found using software Einverted of Emboss9, with the parameters threshold = 30, match score = 3, mismatch score = 3, gap penalty = 6, and maximum repeat length = 240
Secondary structure of the inverted repeat was predicted by RNAfold
Inverted repeats of secondary structure were evaluated by MirCheck10 using modified parameter
Genome_build: Sanger miRBase 18.0
Supplementary_files_format_and_content: excel file includes miRNA name, length, reads number, TPM(RPKM), significance analysis and target genes prediction for each sample.

organism: Zea mays

source_name: pollinated silks

extract_protocol:
Mature pollens (MP) were collected by shaking tassels at 9:00-10:00 a.m. To ensure the viability of collected pollens, we tested the percentage of in vitro germination. Only pollen grains with germination percentage greater than 90% were used. Germinated pollens (GP) were obtained after culturing 30 min in liquid media, with a germinated percentage greater than 90%. Silks with approximately 5 cm out of the bracts were harvested as mature silks (MS). To obtain pollinated silks (PS), mature silks were pollinated by an overdose of active pollens. Thirty min later, most pollen grains germinated and their tubes penetrated into silk tissues. Then, the pollinated silks were harvested after shaking off un-adhered pollen grains.
Briefly, total RNA was isolated using Trizol reagent. Small RNAs ranging from 18-30 nt were gel-purified and ligated to proprietary adapters at the 5' and 3' termini. RT-PCR was performed with 18 cycles, and the products were purified and used for Solexa sequencing.

tag: inbred line

tag: tissue

value: pollinated silks


title: MS

source_name: mature silks

value: mature silks


title: GP

source_name: in-vitro germinated pollens

value: in-vitro germinated pollens


title: TAF3_PHD_WT

city: Frederick

first: Xiaolin

last: Wu

address: 8560 Progress Drive, C3001

department: Cancer Research Technology Program

institute: Frederick National Laboratory for Cancer Research/SAIC-Frederick Inc

data_processing:
Library strategy: HIT-Seq
Basecalls performed using Illumina RTA 1.8.70.0
Paired-end reads were first filtered for HIV-LTR end. We require that one of the paired reads contains sequence of the 3' HIV-LTR end from the HIV vector used.
Integration junction site sequences were trimmed for LTR and linker sequences and mapped to the mouse genome mm9 using BLAT.  Integration sites were considered to be authentic if the sequence (i) began with 3 bp of the end of the HIV-1 LTR, (ii) had a match to the mouse genome with at least 20 bp in length and 95% identity, (iii) had a unique best hit to the mouse genome, and (iv) the paired end must be within 1kb distance and on different strand on the same chromosome.  Because PCR amplification can produce multiple copies of the same integration site, only tags with unique paired end alignments were used for further analysis.
To facilitate comparisons of datasets compiled for WT and mutant TAF3, the datasets were normalized to 10,000 integration sites, or similarly to the RPKM value (reads per kilobase per million). HITseq TAF3 binding peaks were called using MACS 1.4.2. A p-value cutoff of 1x10^5 was used.
Genome_build: mm9
Supplementary_files_format_and_content: bed files representing protein binding sites identified by HIV integration sites.  Each tag represents the genomic junction DNA fragment after the 3' HIV-LTR. If on "+" strand, the integration site is the left position.  If on "-" strand, the integration site is the right position.

source_name: MEF cells

growth_protocol: The Psip1 (−/−) E2 MEF-KO cells were maintained in DMEM supplemented with 5% FBS, 5% newborn calf serum, and penicillin (50 U/mL) plus streptomycin (50 μg/mL).

extract_protocol:
Genomic DNA was isolated from transduced MEF-KO cells using a QIAamp DNA Blood Mini Kit (Qiagen).
TAF3 binding sites were identified by amplifying HIV integration sites using linker-mediated PCR.  Briefly, 10 ug of genomic DNA was sheared to average size of 500 bp, end-repaired with Endit kit.  A protruding 3’-A base was added to the blunt ends of the end-repaired DNA and ligated to an asymmetric linker which has a 3’-T base overhang.  HIV integration junctions were amplified with nested PCR using two primer pairs specific for the HIV-LTR and the linker.  Then the PCR products were subjected again to Illumina library construction protocol for the DNA Sample Kit (Part# 0801-0303). Briefly, DNA of the PCR products was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and purified with Qiagen column.  The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx for 108 bp x 2 following the manufacturer's protocols.

treatment_protocol: Plasmid DNAs encoding TAF3-LEDGF-IBD fusion proteins were introduced into MEF-KO cells by nucleofection (Amaxa). The cells were allowed to recover for 24–36 h and were sorted for GFP expression using a Becton Dickinson FACS Aria 1 cell sorter to enrich for cells that express fusion proteins. Approximately 1-2 million GFP-positive cells were plated on a 100-mm dish and infected with 500 ng VSV-G pseudotyped pNLNgoMIVR-Emod Luc and 8 μg/mL polybrene. After 48–72 h, cells were harvested for titer and HIT-seq analyses.

value: MEF cells

tag: genotype/variation

tag: strain

tag: taf3 status


title: TAF3_PHD_Mut

tag: cell type


title: mix7-rep2

status: Public on Mar 01 2013

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

description: fmol of spiked oligos per 1mg of total RNA

data_processing:
Basecalls performed using CASAVA version 1.8.1
Adaptors were removed and then collapsed into tags and quantified.
Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).
The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against human mature miRNA databases (downloaded from mirbase.org, release 18).
The frequency of reads matching each miRNAs was calculated by summing the frequency of all the isoforms matching the miRNA
Genome_build: mirbase release 18
Supplementary_files_format_and_content: .txt file with rpm values for each miRNA

source_name: placenta

extract_protocol: Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturer’s instructions. Briefly, 3` adapter was ligated to total RNA using RNL2, followed by 5’ adapter ligation, using T4 ligase. Reverse transcription with SuperScript II generated cDNA which was then PCR-amplified and size-selected on a gel and then purified. Sequencing was performed on two lanes of HiSeq 2000 using v2 clustering and sequencing reagents; seven libraries were multiplexed on each lane.

treatment_protocol: Oligos representing mature, modified and precursor miRNA were artificially introduced to native RNA

tag: spike-in hsa-mir-147

tag: spike-in hsa-mir-211

tag: spike-in hsa-mir-219-5p

tag: spike-in hsa-mir-338-3p

tag: spike-in hsa-mir-383

tag: spike-in hsa-mir-429

tag: precursor spike-in hsa-mir-147

tag: o-methyl spike-in hsa-mir-211

tag: o-methyl spike-in hsa-mir-219-5p

tag: precursor spike-in hsa-mir-338-3p

tag: precursor spike-in hsa-mir-383

tag: o-methyl spike-in hsa-mir-429


title: mix6-rep2


title: TAF3_Full_Mut


title: RNAPII_ChIPSeq

data_processing:
Basecalls performed using Illumina RTA 1.8.70.0
ChIP-seq reads were aligned to the hg19 genome assembly using Illumina Casava 1.8.2
Data were filtered using the following specifications: only unique alignments were used.
peaks were called using MACS version 1.4.2 with the default setting.
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph files were generated using MACS version 1.4.2 and then converted to bigWig format using the bedGraphToBigWig program. Peaks are filtered by fold_enrichment > 5 and FDR < 0.05.

source_name: HCT116 cells

growth_protocol: HCT116 cells were cultured on uncoated tissue-culture plates in Dulbecco’s modified Eagle medium (DMEM, Gibco).

extract_protocol:
Lysates were clarified from sonicated and precleared chromatin was immunoprecipitated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~200 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 36 bp on the Genome Analyzer IIx following the manufacturer's protocols.

treatment_protocol: For TAF3, RNAPII, and H3K4me3 ChIP-seq, cells in monolayer were fixed with 1% Formaldehyde for 10 min at room temperature and quenched by adding glycine to a final concentration of 125 mM (Sigma). 10-50 million cells were used per IP.

value: colorectal carcinoma

tag: passages

tag: cell line

value: HCT116 cells

tag: chip antibody

value: RNAPII (Santa Cruz, N-20:sc-899, Lot E1711)


title: H3K4me3_ChIPSeq


title: TAF3_ChIPSeq

value: Polyclonal antisera raised against amino acid residues 290-389 of the human TAF3 protein (Strategic Diagnostics,SDIX)


title: TAF3_Full_WT

tag: genotype/variation

tag: strain

tag: taf3 status


title: Gli3_SHF_ChIPseq_E9.5

city: Chicago

first: Xinan

middle: "Holly"

state: IL

institute: universty of Chicago

data_processing:
The reads of Gli3 IP is 44bp while the reads of the Input is 36bp. We trimed the left 8bp of the Gli3 IP due to their unexpected low quality scores.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.8 allowing 2 mismatches and assuming genome_size to be 2e9.
Peaks were called using MACS version 2.0.7 with the following setting: ChIP threshold (p<1e-5), m Fold (2,100), band width (200).
The peaks of GLI3 IP was compared with the peaks of Input.
Genome_build: mm9
Supplementary_files_format_and_content: Gli3 binding sites were annotated to the mouse mm9 reference genome by HOMER software, by the nearst  transcription start sites (TSSs).

growth_protocol: Mef2c-AHF-Cre transgenic mice and homozygous Rosa26Gli3TFlag mice (http://jaxmice.jax.org/strain/013124.html) were crossed and dissected at E10.5. SHF tissue was isolated from these animals individually, and litters were pooled in groups of approximately 50 embryos.

extract_protocol:
Chromatin was fixed in 1.8% formaldehyde solution for 10 minutes and sonicated to 300-500 bp fragments using a Misonex 4000 sonicator.  Chromatin was immunoprecipitated overnight using a pre-cleared anti-FlagM2 anitbody (Sigma) and magnetic beads (invitrogen).  Chromatin was eluted, de-crosslinked and column-purified using a PCR cleanup kit (Qiagen) before submission for sequencing.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: strain background

value: C56B/6 and CD-1 mixed

tag: cell type

value: Second Heart Field (SHF) cells disected from Mouse Embryos

tag: tissue

value: E9.5 embryos

value: Monoclonal ANTI-FLAG® M2 antibody

tag: chip antibody vendor

value: Sigma

tag: chip antibody cat. #

tag: chip antibody lot #


title: MP

source_name: mature pollens

tag: inbred line

value: mature pollens


title: Input DNA


title: mix4-rep1

tag: spike-in hsa-mir-147

tag: spike-in hsa-mir-211

tag: spike-in hsa-mir-219-5p

tag: spike-in hsa-mir-338-3p

tag: spike-in hsa-mir-383

tag: spike-in hsa-mir-429

tag: precursor spike-in hsa-mir-147

tag: o-methyl spike-in hsa-mir-211

tag: o-methyl spike-in hsa-mir-219-5p


title: mix4-rep2

tag: precursor spike-in hsa-mir-338-3p

tag: precursor spike-in hsa-mir-383

tag: o-methyl spike-in hsa-mir-429


title: INPUT_pSHF_ChIPseq_E9.5

tag: strain background

tag: cell type

tag: tissue


title: mix5-rep2


title: mix7-rep1


title: mix2-rep1


title: mix6-rep1


title: mix2-rep2


title: mix3-rep2


title: mix5-rep1


title: mix3-rep1


title: mix1-rep1


title: CDK8-ChIP enriched DNA, hypoxia, replicate1

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

description: ChIP-enriched DNA from HCT116 cells under hypoxia.

data_processing:
Base-calling: Illumina CASAVA 1.8.2.
Filtering: adapter sequences (~13%) were filtered out using the FASTX toolkit 0.0.13.1.
Alignment to GRCh37/hg19: Bowtie 0.12.7 with zero-mismatches and discarding non-unique alignments.
Peak-calling: enriched CDK8 ChIP peak regions were determined using MACS 2.0.9 with both ChIP and control (input) samples, p<0.05, keeping at most two duplicate reads, with an estimated shift-size of 225bp.
ChIP-seq data analysis and visualization: Raw 50-nucleotide ChIP-seq reads were subjected to quality assessment (97% bases ≥ Q30) using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and adapter sequences (~13%) were filtered out using the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Reads were then aligned to the reference human genome (GRCh37/hg19) using Bowtie 0.12.7 with zero-mismatches and discarding non-unique alignments (~80% uniquely aligned). Enriched CDK8 ChIP peak regions were determined using MACS 2.0.9 (Zhang et al., 2008) with both ChIP and control (input) samples, p<0.05, keeping at most two duplicate reads, with an estimated shift-size of 225bp.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: BED files (listing peaks) and bedgraph files were generated by MACS 2.0.9.

source_name: colorectal cancer cells, hypoxia, CDK8 ChIP

growth_protocol: HCT116 cells were plated in McCoy's 5A Medium supplemented with 10% fetal calf serum 24hrs prior to treatment as indicated.

extract_protocol:
Chromatin immunoprecipitation: Media was removed and the cells were cross-linked by the addition of 1% formaldehyde in PBS for 15 min, followed by the addition of glycine to 0.125 M to quench the formaldehyde. Plates were then washed twice with cold PBS to remove all traces of formaldehyde. Cross-linked cells were harvested by scraping directly into RIPA buffer (150 mM NaCl, 50 mM Tris pH 8, 5 mM EDTA, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, protease/phosphatase/HDAC inhibitors) and snap-frozen. Thawed whole-cell lysates were then fragmented by sonication to give DNA fragments of ~200 bp and centrifuged at 12,000 x g to remove insoluble material. The supernatant was quantified using a BCA protein assay kit (Pierce) and diluted to 1 mg/ml with RIPA buffer. For immunoprecipitation, 1 mg of ChIP extract was first pre-cleared by incubation with RIPA-washed Protein-G sepharose beads (GE Healthcare) at 4°C for 2 hr. Pre-cleared supernatants were then mixed with Protein-G sepharose beads that had been blocked for 2 hr with 1 mg/ml bovine serum albumin (Sigma) and immunoprecipitated by incubating overnight at 4°C with the desired antibody. Each ChIP was then washed (5 min each wash) twice with RIPA buffer, four times with IP wash buffer (100 mM Tris pH 8.5, 0.5 M LiCl, 1% NP-40, 1% sodium deoxycholate), twice more with RIPA buffer, twice with TE (10 mM Tris pH 8, 1 mM EDTA), and finally resuspended in 100 μl TE. Immunocomplexes were then eluted by the addition of two volumes of elution buffer (70 mM Tris pH 8, 1 mM EDTA, 1.5% SDS) and incubated at 65°C for 10 min. To reverse cross-linking, NaCl was added to a final concentration of 200 mM, followed by incubation at 65°C for 5 hr. To digest remaining protein, 20 μg proteinase K was added and incubated at 45°C for 30 min. Immunoprecipitated DNA was then purified by phenol/chloroform extraction, ethanol precipitated, and finally dissolved in 0.1x TE. Input DNA was prepared essentially in the same manner, omitting the immunoprecipitation steps.
ChIP-seq library preparation and Illumina sequencing: Twenty nanograms of ChIP-enriched DNA or input DNA (prepared as above) were used for generation of Illumina sequencing libraries using a modified version of the Illumina ChIP-seq protocol. Briefly, DNA fragments were end-repaired using the End-It DNA End-Repair Kit (Epicentre) and then a single "A" base was added using Klenow fragment (New England Biolabs). The fragments were ligated to Illumina Indexed adaptors (TruSeq DNA Sample Prep Kit) using T4 DNA ligase (New England Biolabs). The ligated products were size-selected for 350-450 bp fragments on a 2% agarose gel to remove the unligated adaptors, and were subjected to 18 PCR cycles (Illumina TruSeq primers). PCR product was purified on a 2% agarose gel to retain fragments between 350-450bp. Libraries were quantified using a Qubit fluorometer (Invitrogen) and by quantitative PCR (Kapa Biosystems).

treatment_protocol: HCT116 cells were subjected to normoxia or hypoxia for 24 h.

tag: cell line

tag: treatment

value: 24hrs hypoxia (1%O2)

tag: chip antibody

tag: antibody vendor

value: Santa Cruz

tag: antibody catalog #

tag: antibody lot#


title: CDK8-ChIP enriched DNA, normoxia

description: ChIP-enriched DNA from HCT116 cells under normoxia.

source_name: colorectal cancer cells, normoxia, CDK8 ChIP

value: normoxia


title: ChIP input DNA

description: ChIP input DNA from HCT116 cells.

source_name: colorectal cancer cells, input

extract_protocol:
Chromatin immunoprecipitation: Media was removed and the cells were cross-linked by the addition of 1% formaldehyde in PBS for 15 min, followed by the addition of glycine to 0.125 M to quench the formaldehyde. Plates were then washed twice with cold PBS to remove all traces of formaldehyde. Cross-linked cells were harvested by scraping directly into RIPA buffer (150 mM NaCl, 50 mM Tris pH 8, 5 mM EDTA, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, protease/phosphatase/HDAC inhibitors) and snap-frozen. Thawed whole-cell lysates were then fragmented by sonication to give DNA fragments of ~200 bp and centrifuged at 12,000 x g to remove insoluble material. The supernatant was quantified using a BCA protein assay kit (Pierce) and diluted to 1 mg/ml with RIPA buffer. For immunoprecipitation, 1 mg of ChIP extract was first pre-cleared by incubation with RIPA-washed Protein-G sepharose beads (GE Healthcare) at 4°C for 2 hr. Pre-cleared supernatants were then mixed with Protein-G sepharose beads that had been blocked for 2 hr with 1 mg/ml bovine serum albumin (Sigma) and immunoprecipitated by incubating overnight at 4°C with the desired antibody. Each ChIP was then washed (5 min each wash) twice with RIPA buffer, four times with IP wash buffer (100 mM Tris pH 8.5, 0.5 M LiCl, 1% NP-40, 1% sodium deoxycholate), twice more with RIPA buffer, twice with TE (10 mM Tris pH 8, 1 mM EDTA), and finally resuspended in 100 μl TE. Immunocomplexes were then eluted by the addition of two volumes of elution buffer (70 mM Tris pH 8, 1 mM EDTA, 1.5% SDS) and incubated at 65°C for 10 min. To reverse cross-linking, NaCl was added to a final concentration of 200 mM, followed by incubation at 65°C for 5 hr. To digest remaining protein, 20 μg proteinase K was added and incubated at 45°C for 30 min. Immunoprecipitated DNA was then purified by phenol/chloroform extraction, ethanol precipitated, and finally dissolved in 0.1x TE. Input DNA was prepared essentially in the same manner, omitting the immunoprecipitation steps.

ChIP-seq library preparation and Illumina sequencing: Twenty nanograms of ChIP-enriched DNA or input DNA (prepared as above) were used for generation of Illumina sequencing libraries using a modified version of the Illumina ChIP-seq protocol. Briefly, DNA fragments were end-repaired using the End-It DNA End-Repair Kit (Epicentre) and then a single "A" base was added using Klenow fragment (New England Biolabs). The fragments were ligated to Illumina Indexed adaptors (TruSeq DNA Sample Prep Kit) using T4 DNA ligase (New England Biolabs). The ligated products were size-selected for 350-450 bp fragments on a 2% agarose gel to remove the unligated adaptors, and were subjected to 18 PCR cycles (Illumina TruSeq primers). PCR product was purified on a 2% agarose gel to retain fragments between 350-450bp. Libraries were quantified using a Qubit fluorometer (Invitrogen) and by quantitative PCR (Kapa Biosystems).


title: CDK8-ChIP enriched DNA, hypoxia, replicate2


title: Dnmt1-/- MEF (Bisulfite-seq)

city: Heidelberg

first: James

middle: P

last: Reddington

address: Meyerhofstrasse 1

country: Germany

institute: EMBL

description: fastq files are split into two sets of paired end files

data_processing:
Base calling was performed by BaseClear according to their 'Epiquest Genome-wide' service
Reads were mapped to the bisulfite converted genome using Bismark by BaseClear according to their 'Epiquest Genome-wide' service
For each CpG covered by sequencing reads the proportion of unmethylated C and methylated C were determined by the frequency of conversion of C to T. Only CpGs with a sequencing depth greater than 10 were used.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text. A matrix with the following columns: chr (chromosome); start (start coordinate of CpG); stop (stop coordinate of CpG); wt_depth (number of reads that cover this CpG in Dnmt1+/+); wt_meth_percent (proportion of methyl-cytosine as a percentage of total cytosine in Dnmt1+/+); ko_depth (number of reads that cover this CpG in Dnmt1-/-); ko_meth_percent (proportion of methyl-cytosine as a percentage of total cytosine in Dnmt1-/-)

source_name: Dnmt1-/- mouse embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts were cultured under standard conditions

extract_protocol:
Genomic DNA was isolated by cell lysis and Proteinase K digestion followed by phenol-chloroform extraction. RNA was removed by Rnase treatment.
Bisulfite-converted DNA libraries were prepared by BaseClear (Leiden, Netherlands) according to their 'EpiQuest Genome-wide' service

treatment_protocol: Not applicable

value: Mouse embryonic fibroblasts

tag: strain

value: see Lande-Diner 2007 (PMID:17311920)

tag: genotype/variation


title: Dnmt1+/+ MEF (Bisulfite-seq)

source_name: Dnmt1+/+ mouse embryonic fibroblasts


title: wt_macroH2A2

first: Emily

last: Bernstein

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

data_processing:
100bp Sequence reads were aligned to the mouse genome NCBI build 37 (UCSC, mm9) using Bowtie short read aligner56 (v 0.12.7), with the following parameters: seed of 50bp, maximum 2 mismatches, suppression (m) = 20, and reported alignments (k) = 20. Wiggle files (HAFEZ, unpublished pipeline D.H.), were generated using a 500bp window sliding 250bp, counting the number of aligned reads (5' end of each aligned read), for both ChIP and Input samples. The number of alignments from each window was normalized to the total number of alignments and scaled by factor of 10^7, to allow comparison between different samples. MACS software57 (v 1.4.1) was used to identify peaks and generate Wiggle files (p value cutoff = 1.00e-04 (5e-5 for K27me3 and Ac, 5e-3 for mH2A1 and 5e-4 for mH2A2), (bw) = 300).
Genome Build:
DF_mH2A2_wt_f.bed: mm9 (NCBI Build37)
DF_mH2A2_wt_f.wig: mm9 (NCBI Build37)
DF_mH2A2_wt_f_peaks.bed: mm9 (NCBI Build37)

source_name: Dermal Fibroblasts (wt)

growth_protocol: Cells were grown in 15cm^2 cell culture dishes on DMEM media with 10%FBS and antibiotics.

extract_protocol: mH2A1 ChIP (ab37264, ABCAM), mH2A2 (Berrnstein lab) H3K27me3 (Millipore, 07-449) and H3K27ac (Abcam 4729) was preformed with 100ug of MNase digested chromatin as previously described (Hori et al. 2008). Total of 25ng MNase-ChIPed DNA was processed for library preparation from each sample. All enzymes used are from NEB unless stated otherwise. 1. DNA was End Repaired in 50ul reaction containing 40ul of DNA, 5ul T4 DNA ligase buffer with 10mM ATP, 2ul 10mM dNTP, 1ul Klenow DNA pol (1u/ul), 1ul T4 DNA pol and 1ul T4 PNK. The reaction was incubated for 30min at 20C. Products were purified in Qiagen PCR purification column in 35ul. 2. Adding over-hang A to the 3’ end in 50ul reaction containing 34ul DNA, 5ul 10X NEB buffer 2, 10ul 1mM dATP and 1ul Klenow exo-. The reaction was incubated for 30min at 37C. Products were purified in Qiagen PCR Mini elute purification column in 14ul. 3. Adapter ligation in 30ul reaction containing 13ul DNA, 15ul 2X T4 DNA ligase buffer, 1ul of 1:200 dilution of Illumina true seq DNA sample prep kit and 1ul quick T4 DNA ligase. The reaction was incubated for 15min at 25C. Products were purified in Qiagen Mini elute PCR purification column in 15ul. 4. Size selection. Ligated products were loaded onto 2% Agarose gel (1XTAE), and run for 1 hour at 120V. DNA was viewed on low-wave trans illuminator and size selected at the 300-400bp range using the Kb+ invitrogen DNA ladder. Products were purified in Qiagen PCR purification column in 25ul. 5. PCR amplification was done in 50ul reaction containing 25ul 2X master mix (2X Phusion HF, FINZYMES), 2ul PCR primers (illumina) and 23ul DNA. PCR program according to the illumina protocol. Products were purified in Qiagen Mini elute PCR purification column in 15ul. PCR products were then run on an Agilent DNA 1000 chip for quantification and submitted for sequencing on the Hi-Seq 2000 illumina platform.

treatment_protocol: no treatment

tag: genotype

value: mH2A1 ChIP (ab37264, ABCAM)

tag: antibody

value: wild type


title: naïve B cells

city: Research Triangle Park

first: Paul

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

data_processing:
Basecalls performed using CASAVA version 1.7
Raw data was filtered by the following steps:  reads trimmed to 60 bases to remove poor quality ends, removed read pairs for which one or both mates have average base quality score <20, and removed read pairs with sequence matching to adapter/primer.
Multiple lanes per sample were concatenated to a single FASTQ file (one file per end, per sample).
Read pairs were mapped against hg19 reference genome (excluding haplotype chromosomes) with Bismark v0.7.7 using the folowing parameters:  -n 2 -l 40 -e 70 -I -X 10000.
Duplicate mapped read pairs were removed with deduplicate_bismark_alignment_output.pl from the Bismark package.
Mapped data was separated into two files (per sample) according to the source strand of the read.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph file per sample per strand showing mapped read coverage; generated by BEDtools (v2.17.0) genomeCoverageBed.

source_name: tonsil

extract_protocol:
Naïve (CD20+CD38-IgD+) and germinal-center B cells (Cd20+CD38+IgD-) were purified by FACS from a human tonsil for direct analysis ex vivo.  Genomic DNA was extract from each sample using Qiagen All prep columns.  Genomic DNA was fragmented to 200-500 bps in length by sonication.  Methylated DNA was enriched using MBD2/MBD3L protein complex (MethylCollector Ultra kit from Active Motif).
End repair, A-tailing, and adapter ligation steps were performed following Illumina’s protocol.  Adapter ligated DNA was size selected for 250-600 bps on a 3% NuSieve 3:1 agarose gel.  Gel purified DNA (Qiagen) was then treated with sodium bisulfite for 5 hours (EZ DNA Methylation-Gold Kit, Zymo Research), followed by 18 cycles of PCR amplification using Pfu Turbo Cx (Strategene).

value: naive (CD20+CD38-IgD+) B cells

value: tonsil


title: Dnmt1+/+ MEF

description: the raw sequence data contains 18 files

data_processing:
Base calling was performed as standard by Ambry Genetics (Aliso Viejo, CA, USA)
Reads were mapped to the mm9 build of the mouse genome using Tophat
Transcript abundance in the form of RPKM was calculated using Cufflinks/Cuffdiff
Genome_build: mm9
Supplementary_files_format_and_content: Output file from Cuffdiff giving the RPKM for each measured transcript in each sample

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen) according to manufacturer's instructions and was treated with Dnase
Illumina's strand-specific mRNA library preparation was performed according to Illumina's instructions by Ambry Genetics (Aliso Viejo, CA, USA)

value: unknown [see Lande-Diner 2007 (PMID:17311920)]


title: Rad51_ChIPSeq_Cd19_panel4C&D

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie requiring unique alignment (-m 1)
Uniquely aligned reads were analyzed by SICER using an expectation value E of 0.05 in a random background model
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using SICER

source_name: Primary B cells

growth_protocol: CD43- resting B cells were isolated from mouse spleens by negative selection with magnetic beads (Miltenyi Biotech). Following isolation, resting B cells were stimulated with LPS (50 mcg/ml), IL-4 (2.5 ng/ml) and anti-Cd180 (RP105) (250 ng/ml) for 72 hrs.

extract_protocol:
Cells were fixed with 1% paraformaldehyde at 37°C for 10 minutes followed by quenching with glycine and sonication. Chromatin fragments were then immunoprecipitated with the antibodies shown in the sample characteristics following standard protocols. Immunoprecipitates were processed following Illumina’s protocol and sequenced on a HiSeq 2000.
The ChIP-DNA was blunt-ended with End-It DNA end repair kit (Epicentre) and A-tailed with Taq DNA polymerase (Invitrogen) in the presence of 200mM of dATP for 40 minutes at 70°C. The sample was purified by phenol-chloroform extraction after each reaction. Illumina compatible adaptors (Illumina or Bioo Scientific) were then ligated with T4 DNA ligase (Enzymatics) and the reaction was purified once with AMpure XP magnetic beads (Beckman Coulter). Samples were PCR amplified for 18-cycles with KAPA HiFi DNA polymerase mix (KAPA biosystems). The amplicon was run on a 2% agarose gel and size-selected at 200-300 bp.

value: Splenocyte (B lymphocytes)

value: anti-RAD51(H-92) Santa Cruz sc-8349, lot#H1810


title: Rad51_ChIPSeq_Rif1_panel4C&D


title: RPA_ChIPSeq_Rif1_panel4B

value: anti-RPA32 Calbiochem NA19L, lot#D00127062


title: RPA_ChIPSeq_Cd19_panel4A


title: RPA_ChIPSeq_Rif1_panel4A


title: dKO_macroH2A1

data_processing:
100bp Sequence reads were aligned to the mouse genome NCBI build 37 (UCSC, mm9) using Bowtie short read aligner56 (v 0.12.7), with the following parameters: seed of 50bp, maximum 2 mismatches, suppression (m) = 20, and reported alignments (k) = 20. Wiggle files (HAFEZ, unpublished pipeline D.H.), were generated using a 500bp window sliding 250bp, counting the number of aligned reads (5' end of each aligned read), for both ChIP and Input samples. The number of alignments from each window was normalized to the total number of alignments and scaled by factor of 10^7, to allow comparison between different samples. MACS software57 (v 1.4.1) was used to identify peaks (p value cutoff = 1.00e-04 (5e-5 for K27me3 and Ac and 5e-3 for mH2A), (bw) = 300).
Genome_build: mm9 (NCBI Build37)

source_name: Dermal Fibroblasts (macroH2A double KO)

extract_protocol: mH2A1 ChIP (ab37264, ABCAM), H3K27me3 (Millipore, 07-449) and H3K27ac (Abcam 4729) was preformed with 100ug of MNase digested chromatin as previously described (Hori et al. 2008). Total of 25ng MNase-ChIPed DNA was processed for library preparation from each sample. All enzymes used are from NEB unless stated otherwise. 1. DNA was End Repaired in 50ul reaction containing 40ul of DNA, 5ul T4 DNA ligase buffer with 10mM ATP, 2ul 10mM dNTP, 1ul Klenow DNA pol (1u/ul), 1ul T4 DNA pol and 1ul T4 PNK. The reaction was incubated for 30min at 20C. Products were purified in Qiagen PCR purification column in 35ul. 2. Adding over-hang A to the 3’ end in 50ul reaction containing 34ul DNA, 5ul 10X NEB buffer 2, 10ul 1mM dATP and 1ul Klenow exo-. The reaction was incubated for 30min at 37C. Products were purified in Qiagen PCR Mini elute purification column in 14ul. 3. Adapter ligation in 30ul reaction containing 13ul DNA, 15ul 2X T4 DNA ligase buffer, 1ul of 1:200 dilution of Illumina true seq DNA sample prep kit and 1ul quick T4 DNA ligase. The reaction was incubated for 15min at 25C. Products were purified in Qiagen Mini elute PCR purification column in 15ul. 4. Size selection. Ligated products were loaded onto 2% Agarose gel (1XTAE), and run for 1 hour at 120V. DNA was viewed on low-wave trans illuminator and size selected at the 300-400bp range using the Kb+ invitrogen DNA ladder. Products were purified in Qiagen PCR purification column in 25ul. 5. PCR amplification was done in 50ul reaction containing 25ul 2X master mix (2X Phusion HF, FINZYMES), 2ul PCR primers (illumina) and 23ul DNA. PCR program according to the illumina protocol. Products were purified in Qiagen Mini elute PCR purification column in 15ul. PCR products were then run on an Agilent DNA 1000 chip for quantification and submitted for sequencing on the Hi-Seq 2000 illumina platform.

value: macroH2A double KO


title: RPA_ChIPSeq_53BP1_panel4A


title: dKO_H3K27ac

value: H3K27ac (Abcam 4729)


title: input DNA

first: Ilaria

last: Rebay

address: 929 E. 57th St. GCIS W340M

department: Ben May Department

institute: University of Chicago

data_processing:
The quality-filtered 36bp sequence reads were aligned to the April 2006 Drosophila melanogaster genome reference sequence using ELAND (Efficient Local Alignment of Nucleotide Data) software to yield sorted.txt files.
A smoothed kernel density of combined reads by spp (Kharchenko et al, 2008) with bandwidth=200, step=100 was used for visualization (wig file).
Peak calling from the combined IP lanes versus input was performed using Model-based Analysis of ChIP-seq (MACS, Zhang et al, 2008) using default parameters, genome size of 1.2x 10-8 and p-values 1x10-5 (bed and xls files).

s_1_sorted.txt; genome build: dmel_April2006
Yan_s23_1e-5_negative_peaks.txt; genome build: dmel_April2006

organism: Drosophila melanogaster

source_name: Stage 11 Drosophila embryos

extract_protocol: Embryos were dechorionated in 50% bleach, incubated for 15 minutes at room temperature in 10ml of Cross-linking Solution (50mM HEPES, pH 7.6, 1mM EDTA, 0.5mM EGTA, 100mM NaCl, 1.8% formaldehyde) and 30ml of n-Heptane, washed twice in Stop Solution (PBS, 0.1% Triton X-100, 125mM Glycine), twice in PBS/T (PBS, 0.1% Triton X-100), and twice in Wash Solution (10mM HEPES, 10mM EDTA, 0.5mM EGTA, 0.25% Triton X-100). After homogenization in ChIP Lysis Buffer (50mM HEPES, 140mM NaCl, 1mM EDTA, 1mM EGTA, 1% Triton X-100, 0.1 Sodium Deoxycholate, protease inhibitor tablet [Roche]), the lysates were subjected to 9 cycles of sonication at 15% amplitude for 15 seconds/cycle (Sonic Dismembrator Model 500, Fisher Scientific). Clarified lysates were halved and were either incubated with guinea pig anti-Yan or mock-treated. After overnight incubation at 4°C, 30μl of 50% GammaBind Sepharose (GE Healthcare) slurry was added and incubated for 4 hours at 4° C. The beads were washed 3 times in ChIP Lysis Buffer, once in High Salt ChIP Lysis Buffer (500mM NaCl in ChIP Lysis Buffer), and once in TE (10mM Tris, pH=8.0, 1mM EDTA) for 5 minutes each, resuspended in 150μl of TE/SDS (TE, 1% SDS), incubated at 65°C for 15 minutes with vortexing at 3 minute intervals to elute the DNA, and the supernatants incubated at 65°C overnight to reverse the cross-linking. For input, 5μl of lysates before immunoprecipitation were added to 145μl of TE/SDS and reverse-cross-linked. ChIP DNA was purified using the QIAquick PCR Purification Kit (Qiagen). Native ChIP DNA was amplified using the linker-mediated PCR (LM-PCR) method (Lee et al., 2006). Briefly, ChIP DNA was treated with Klenow DNA Polymerase (NEB) and then ligated with a linker produced by annealing the two oligos: 5’-/5Phos/AGAAGCTTGAATTCGAGCAGTCAG-3’ and 5’-CTGCTCGAATTCAAGCTTCT-3’. After adding the linker, DNA was amplified using the 20-mer primer as shown above and purified using the QIAquick PCR Purification Kit (Qiagen). An adenine residue was added with Klenow [3’-5’ exo-] enzyme.  Adaptors from Illumina for LM-PCR were then ligated to the end of DNA molecules and the product of the reaction was run on a 2% Agarose gel.  A band corresponding to 200bp was extracted and purified. 18 cycles of PCR was performed using phusion polymerase (Finnzyme F-530S) and the Illumina oligos. The PCR product was purified by gel electrophoresis and high throughput sequencing performed on an Illumina Genome Analyzer with standard Illumina 36 cycles.

value: embryo

tag: developmental stage

value: Stage 11


title: Input control

value: wildtype

value: Input control


title: mix1-rep2

tag: spike-in hsa-mir-147

tag: spike-in hsa-mir-211

tag: spike-in hsa-mir-219-5p

tag: spike-in hsa-mir-338-3p

tag: spike-in hsa-mir-383

tag: spike-in hsa-mir-429

tag: precursor spike-in hsa-mir-147

tag: o-methyl spike-in hsa-mir-211

tag: o-methyl spike-in hsa-mir-219-5p

tag: precursor spike-in hsa-mir-338-3p


title: wt_H3K27me3

value: H3K27me3 (Millipore, 07-449)


title: wt_macroH2A1


title: Yan_ChIPSeq

data_processing:
The quality-filtered 36bp sequence reads were aligned to the April 2006 Drosophila melanogaster genome reference sequence using ELAND (Efficient Local Alignment of Nucleotide Data) software to yield sorted.txt files.
A smoothed kernel density of combined reads by spp (Kharchenko et al, 2008) with bandwidth=200, step=100 was used for visualization (wig file).
Peak calling from the combined IP lanes versus input was performed using Model-based Analysis of ChIP-seq (MACS, Zhang et al, 2008) using default parameters, genome size of 1.2x 10-8 and p-values 1x10-5 (bed and xls files).

s_2_sorted.txt; genome build: dmel_April2006
s_3_sorted.txt; genome build: dmel_April2006
Yan_s23.wig; genome build: dmel_April2006
Yan_s23_1e-5_peaks.bed; genome build: dmel_April2006
Yan_s23_1e-5_peaks.txt; genome build: dmel_April2006

tag: tissue

tag: chip antibody

value: gp anti-Yan


title: germinal-center B cells

tag: cell type

value: germinal-center (Cd20+CD38+IgD-) B cells


title: noGSK_input

city: Cambridge

first: Xiaoxiao

last: Zhang

address: 7 Divinity Ave.

department: Molecular and Cellular Biology

institute: Harvard University

data_processing:
Base calling was performed using Illumina pipeline
The firsty 25 bp of  sequence reads were mapped to unmasked mouse genome using either seqmap or eland allowing up to two mismatches
Peak calling was performed using MACS1.3 with p-value cutoff 1e-5.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files include bed files for peak predictions.

source_name: mouse embryonic stem cells

growth_protocol: All ESCs were maintained in complete ES media (15% fetal bovine serum, 0.1 mM non-essential amino acids, 0.1 mM b-mercaptoethanol, 2 mM L-glutamine, 10^3 units/ml LIF, and 1X nucleotide mix in DMEM high glucose) with feeder cells isolated from DR4 mice

extract_protocol:
After treated with CHIR99021 (3 mM ) for 16 hours, Ctnnb1-BioFLneo;BirA and BirA ESC were collected with feeder cells using 0.25% trypsin-EDTA.  After leaving cells on gelatinized plates for an hour, we collected floating cells as an ESC-enriched fraction. 10,000,000 cells were used per ChIP. Chromatin was sonicated by 6 sessions of 30 pulses (1 sec on and 1 sec off) at 50% amplitude using the Branson sonifier 250D. Isolation of chromatin and FLAG-ChIP were performed as described (Development. 2007;134:1977-1989). For Biotin-ChIP, sonicated chromatins were first incubated with protein A dynabeads (Invitrogen, 100-01D) at 4 °C for an hour. Dynabeads MyOne Streptavidin T1 (Invitrogen, 656.01) was incubated with 2% Gelatin from cold water fish skin (Sigma, G7041) in PBS at 4 °C for an hour prior to use. Precleared chromatins were incubated with 60 mL of Dynabeads MyOne Streptavidin T1 overnight with rotation at 4 °C. Beads were washed with 2% SDS, 10 mM Tris, and 0.5 M EDTA five times, and with TE once. ChIP DNA was eluted by the overnight incubation of beads in 10 mM Tris, 1 mM EDTA, 1% SDS, and 0.5 M NaCl at 65 °C. DNA was purified as described (Development. 2007;134:1977-1989).
ChIP-seq libraries were constructed using ChIP-seq DNA Sample Prep Kit (Illumina, IP-102-1001) according to manufacturer’s instruction.

treatment_protocol: Cells were treated for 16 hours with CHIR99021 (3 μM)

tag: cell line

value: Ctnnb1-Biotin-3xFLAG knock-in V6.5 ESC line

tag: chip-antibody

tag: treatment

value: DMSO (3uM)


title: GSK_input


title: bCatenin-Biotin

value: Streptavidin


title: bCatenin-BIOTINnoGSK


title: bCatenin-FLAG

value: anti-FLAG


title: dKO_H3K27me3

tag: genotype

tag: antibody


title: 2P-Seq fraction 5

status: Public on Feb 28 2013

city: Stanford

first: Noah

last: Spies

address: 300 Pasteur Dr

institute: Stanford University

data_processing:
Reads were aligned the mouse mm9 genome using Bowtie. 3P-Seq reads were used to annotate poly(A) sites. Reads within +/- 20 nt of these annotated poly(A) sites were combined when calculating read totals for 2P-Seq datasets.
Genome_build: mm9
Supplementary_files_format_and_content: tab separated file: poly(A) site annotations, reads, half-lives, translation rates per poly(A) site

source_name: 3T3 cells

extract_protocol:
2P-Seq, barcoded
sucrose gradient fractionation, poly(A)-selected RNA
2P-Seq: partial digested with RNase T1, poly(A)-primed reverse transcription, circularization, PCR and sequencing from putative poly(A) tail

value: 3T3 cells

value: 2P protocol and sucrose gradient fractionation


title: RPA_ChIPSeq_Cd19_panel4B

value: Splenocyte (B lymphocytes)


title: 2P-Seq fraction 3


title: 2P-Seq fraction 4


title: 2P-Seq fraction 2


title: 2P-Seq fraction 1


title: 2P-Seq actD 4h

extract_protocol:
2P-Seq, barcoded
trizol, poly(A)-selected RNA
2P-Seq: partial digested with RNase T1, poly(A)-primed reverse transcription, circularization, PCR and sequencing from putative poly(A) tail

treatment_protocol: Actinomycin D was added at a final concentration of 10 ug/ml and treated for the indicated number of hours

value: 2P protocol and actD for 4h


title: 2P-Seq actD 1h

value: 2P protocol and actD for 1hr


title: wt_H3K27ac

value: H3K27ac (Abcam 4729)


title: 2P-Seq actD 8h

value: 2P protocol and actD for 8h


title: 2P-Seq control 1

value: 2P protocol and control


title: 2P-Seq control 2


title: 2P-Seq actD 2h

value: 2P protocol and actD for 2hr


title: Dnmt1+/+ MEF

data_processing:
Base calling was performed as described in Suzuki et al 2010 (PMID: 20359321)
Reads were processed and tags were mapped to the reference genome as described in Suzuki et al 2010 (PMID: 20359321)
The number of tags in this HpaII library, together with an existing mouse reference MspI library, was used to determine a level of CpG methylation at each CCGG site covered as described in Suzuki et al 2010 (PMID: 20359321)
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph format. Columns: chromosome; start coordinate; stop coordinate; methylation score (value from -5 to 100; 100 being highest levels of methyl CpG; values of 0 were set to -5 in order for visualisation on this plot)

extract_protocol:
Genomic DNA was isolated by cell lysis and Proteinase K digestion followed by phenol-chloroform extraction. RNA was removed by Rnase treatment. HELP-seq was performed as described in Suzuki et al 2010 (PMID: 20359321)
Library preparation was performed as described in Suzuki et al 2010 (PMID: 20359321)

value: Mouse embryonic fibroblasts

tag: strain

value: see Lande-Diner 2007 (PMID:17311920)


title: AGO1_4su_ML_MM_8

city: Berlin

first: Marvin

last: Jens

address: Robert Rössle Str. 10 (H. 87)

department: Systems Biology of Gene Regulatory Elements

institute: Max Delbrueck Center for Molecular Medicine

description: library strategy: PAR-CLIP

data_processing:
Adapters were removed with FAR 1.86 (the felxible adapter remover: http://sourceforge.net/projects/theflexibleadap/) and aligned to hg19 reference sequence with BWA 0.5.8c.
Unique alignments were grouped into read clusters and scored for characteristic conversions and read variability with a custom script.
The mappings of all libraries were analyzed with two published (Hafner et al. 2010 Cell 141, 129–141) AGO1, AGO3 libraries (see also our Suppl. Methods).
After stringent false-positive filtering, using clusters that aligned antisense to a catalog of transcripts as decoys (see Lebedeva et al. 2011 Mol Cell 43, 340–352 for details), remaining clusters were output as bed files.
Genome_build: hg19
Supplementary_files_format_and_content: bed file; binding sites

source_name: HEK293 cell culture

growth_protocol: HEK293 cells were grown in D-MEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, 1% (v/v) 10,000 U/ml penicillin/10,000 µg/ml streptomycin,

extract_protocol: PAR-CLIP and small RNA cloning (Hafner et al. 2010 Cell 141, 129–141)

treatment_protocol: HEK293 cells stably expressing His/FLAG/HA-tagged proteins of interest were grown in medium supplemented with 4-thiouridine at a final concentration of 200 microM for 16 hour. Cells were UV-crosslinked at 365 nm.

value: FLAG


title: AGO1_4su_ML_MM_7

description: library strategy: PAR-CLIP


title: Genome-wide nucleosome positioning in nup170∆ cells

city: Nanjing

first: Yakun

last: Wan

address: Sipailou #2

institute: Southeast University

description: Typical digested Mnase-seq genomic DNA

data_processing:
Reads of 35 bps were initially processed and mapped to the genomic sequences of S. cerevisiae by CASAVA software allowing up to two mismatches, and the raw profiles were further analyzed by our newly developed program to determine nucleosome profiles as follows. 1) all reads were first mapped to the genomic sequences of S. cerevisiae, 2) each read was extended toward the 3'-end to 150 nt, 3) the center of the extended reads (75th nucleotide) of all extended reads was then taken as each read's signal, and 4) in order to detect all fine-grained or coarse-grained peak calls, we design a flexible and customizable Gaussian filter that can define a series of Gaussian templates with different windows and standard deviations to infer possible nucleosome calls.
genome build: yeast S288C strain (NC_001138 - NC_001148)

organism: Saccharomyces cerevisiae

source_name: Mnase-seq genomic DNA

growth_protocol: Wild type (YWY003) and nup170∆ (YWY973) cells were grown in YPD medium to an OD600 of 1.0

extract_protocol: Cell permeablization, micrococcal nuclease digestion, protein degradation and DNA purification steps were performed as described in (Yuan et al., 2005). DNA samples were treated with RNase A and analyzed in a 2% agarose gel to quantify nucleosomal content.  The bands corresponding to mononucleosomal DNA were extracted using a Qiagen gel extraction kit (Qiagen) and analyzed by Illumina sequencing (Illumina Inc.) as previously described (Shivaswamy et al., 2008 and Weiner et al., 2010).

treatment_protocol: Cells were treated with 1% formaldehyde for 20 min, followed by a 5 min incubation with 125 mM glycine prior to cell harvesting.

tag: genotype/variation

value: nup170-del: YWY973 (MATa  his3∆1 leu2∆0 ura3∆0 lys2∆0 nup170∆::natR)


title: Genome-wide nucleosome positioning in sth1p_depletion_2h cells

description: Typical digested Mnase-seq genomic DNA

data_processing:
Reads were initially processed and mapped to the genomic sequences of S. cerevisiae by CASAVA software allowing up to two mismatches, and the raw profiles were further analyzed by our newly developed program to determine nucleosome profiles as follows. 1) all reads were first mapped to the genomic sequences of S. cerevisiae, 2) each read was extended toward the 3'-end to 150 nt, 3) the center of the extended reads (75th nucleotide) of all extended reads was then taken as each read's signal, and 4) in order to detect all fine-grained or coarse-grained peak calls, we design a flexible and customizable Gaussian filter that can define a series of Gaussian templates with different windows and standard deviations to infer possible nucleosome calls.
Genome_build: yeast S288C strain (NC_001138 - NC_001148)

growth_protocol: sth1p depletion cells were grown in YPD medium to an OD600 of 1.0


title: Genome-wide nucleosome positioning in wild type cells

description: Typical digested Mnase-seq genomic DNA

value: wild type: YWY003 (MATa  his3∆1 leu2∆0 ura3∆0 lys2∆0)


title: Genome-wide nucleosome positioning in sth1p_depletion_0h cells

description: Typical digested Mnase-seq genomic DNA


title: AGO2_4su_3_ML_LG

description: library strategy: PAR-CLIP

growth_protocol: HEK293 cells were grown in DMEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, 1% (v/v)

treatment_protocol: HEK293 cells were grown in medium supplemented with 4-thiouridine at a final concentration of 100 microM for 16 hour. Cells were UV-crosslinked at 365 nm.

value: AGO2 11A9 (Ruedel et al., 2008 RNA)


title: 2P-Seq fraction 6


title: RIBOMINUS_HEK293

description: expressed RNA, rRNA depleted

data_processing:
Raw data were aligned to hg19 with bowtie2, keeping only unaligned reads for detection of head-to-tail spanning spliced reads. Data were pooled with already published human leukocyte ribominus data from other sources (See Suppl. Table 1).
Initially unaligned reads were split and 20nt anchors from both ends aligned independently against hg19
Anchor alignments were processed and extended to find circRNA head-to-tail splice sites (See Methods, Suppl. Methods)
Genome_build: hg19
Supplementary_files_format_and_content: bed file; circRNA head-to-tail splice sites, i.e genomic bounds, spanning internal introns

source_name: HEK293T-Rex cell culture

extract_protocol:
Total HEK293 RNA was isolated using Trizol as recommended by manufacturer. Ribosomal RNA was depleted from total RNA using the Ribominus Kit (Invitrogen)
A cDNA library was generated from rRNA-depleted RNA according to the Illumina RNAseq protocol. The cDNA library was sequenced on an Illumina GAIIx by a 2X76 bp run.


title: AGO1_4su_ML_MM_6

description: library strategy: PAR-CLIP