title: HEK293_control_ChIPSeq

status: Public on Jul 31 2012

city: Cincinnati

first: Iouri

last: Chepelev

state: OH

address: 3200 Vine St

institute: US Department of Veterans Affairs Medical Center

description: DNA from MNase-digested chromatin.

data_processing:
The raw sequence reads were aligned to the hg18 human genome using the Bowtie short read aligner.
Genome_build: hg18
Supplementary_files_format_and_content: The BED files are in UCSC Browser Extensible Data format. These files contain the coordinate and genomic strand information of the Bowtie-aligned reads.
Supplementary_files_format_and_content: The bedGraph files were generated as follows: To avoid possible PCR artifacts, we kept at most one uniquely aligned read at each genomic location per strand. To determine the number of ChIP-Seq sequencing reads in a genomic interval, we shifted the locations of forward and reverse strand tags by 75-bp, half the size of the nucleosomal DNA. The 75-bp shifted non-redundant reads were counted in 200-bp tiling windows along the genome and the read counts were normalized to a library size of 5 million non-redundant uniquely mapped reads in each library.

source_name: HEK293, control

extract_protocol: Mononucleosomes were purified, after (micrococcal nuclease) Mnase digestion, with FLAG-Brd or FLAG-HP1 proteins as described in PMID 18406326 [LeRoy G et al. The double bromodomain proteins Brd2 and Brd3 couple histone acetylation to transcription. Mol Cell 2008, 30(1):51-60] from HEK293 cells. FLAG-HP1 vectors were described in PMID 19567367 [LeRoy G, et al. Heterochromatin protein 1 is extensively decorated with histone code-like posttranslational modifications. Mol Cell Proteomics 2009, 8(11):2432-2442]. All proteins were generated by transient expression as previously described. Nucleosomal DNAs were treated with alkaline phosphatase to remove the 3' phosphates left after MNase digestion and purified by phenol extraction. The DNA fragments (~1 ug) were further prepared using the Solexa® Illumina library kit directly following the manufacturer's protocol. The purified DNA was used directly for cluster generation and sequencing using the Illumina Genome Analyzer II.


title: HepG2_DGE

status: Public on Aug 01 2012

type: SRA

city: Chongqing

first: Ni

last: Bing

address: PLA, Third Military Medical University

department: Institute of Immunology

country: China

institute: PLA, Third Military Medical University

library_source: transcriptomic

data_processing:
Counts: All distinct tags were mapped to the University of California, Santa Cruz (UCSC) human genome (hg18) by SOAP2, which allowed a uniquely aligned tag to have up to one mismatching base. Tags that matched to more than one gene were not used in analyzing differential expression among the libraries. The number of normalized sequence tags of a gene locus=(the number of tags in the gene locus/ the total number of sequence tags of the whole genome)×1,000,000.
Genome Build:
HepG2_TagSeq.txt: UCSC hg18

molecule: total RNA

organism: Homo sapiens

source_name: HepG2 cells

growth_protocol: HepG2.2.15 cells and HepG2 cells were maintained in Dulbecco's Modified Eagle’s Medium (DMEM) supplemented with 10% (v/v) foetal bovine serum (all from Gibco, USA) at 37 ℃, in an atmosphere of 5% CO2; 380µg/mL G418 was added to the HepG2.2.15 cell culture.

extract_protocol: Total RNA was extracted from HepG2 and HepG2.2.15 cells using TRIzol® Reagent (Invitrogen, USA), treated with DNase I (Roche, Germany) and converted to double-stranded cDNA using Oligo dT beads. Subsequently, the cDNA samples were digested using the restriction enzyme NlaIII, which recognizes and cuts the most 3' "CATG". Once digested into fragments, cDNA samples were ligated to Illumina specific adapter A, which contains a recognition site for enzyme MmeI. The Illumina specific adapter B was ligated after MmeI digestion (Illumina, USA). Using this technique, two DGE libraries from the two cells were constructed such that each molecule in the library is a 21 bp tag derived from a single transcript with Illumina specific adapters attached to both ends. Next, the 21 bp tags were enriched using PCR primers that anneal to the adaptors, and clusters were created on a flow cell using a Solexa Cluster Station following the manufacturer's instructions (Illumina, USA). Finally, massively parallel sequencing by synthesis was performed on the Illumina HiSeq™ 2000. Image analysis, base calling, extraction of 21 bp tags, and tag counting were performed using the Illumina pipeline. The number of times that a unique tag sequence is detected represents the quantitative expression level of the corresponding transcript in the cell type.

tag: cell line

tag: cell type

value: human hepatocellular liver carcinoma cells


title: HEK293_HP1b_ChIPSeq

country: USA

description: ChIP using antibodies to FLAG tag.

library_source: genomic

molecule: genomic DNA

source_name: HEK293, HP1b ChIP

tag: chip antibody

value: anti-FLAG M2 affinity gel

tag: antibody vendor

value: Sigma-Aldrich

tag: antibody catalog number


title: HepG2.2.15_DGE

data_processing:
Counts: All distinct tags were mapped to the University of California, Santa Cruz (UCSC) human genome (hg18) by SOAP2, which allowed a uniquely aligned tag to have up to one mismatching base. Tags that matched to more than one gene were not used in analyzing differential expression among the libraries. The number of normalized sequence tags of a gene locus=(the number of tags in the gene locus/ the total number of sequence tags of the whole genome)×1,000,000.
Genome Build:
HepG2.2.15_TagSeq.txt: UCSC hg18

source_name: HepG2.2.15 cells


title: HEK293_Brd3_ChIPSeq

description: ChIP using antibodies to FLAG tag.

source_name: HEK293, Brd3 ChIP


title: HEK293_HP1a_ChIPSeq

description: ChIP using antibodies to FLAG tag.

source_name: HEK293, HP1a ChIP


title: HEK293_Brd4_ChIPSeq

description: ChIP using antibodies to FLAG tag.

source_name: HEK293, Brd4 ChIP


title: HEK293_Brd2_ChIPSeq

description: ChIP using antibodies to FLAG tag.

source_name: HEK293, Brd2 ChIP


title: YY1_ChIPSeq

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

country: Switzerland

institute: CHUV

description: Chromatin IP against YY1

data_processing:
Alignment : The sequenced tags were mapped onto the unmasked genome build hg18 using the fetchGWI software. Only the tags with a unique and perfect match were kept for the analysis
Peak detection : peaks were determined with the sissrs software (www.rajajothi.com/sissrs/). Peaks common to the control input material and the ChIP material, as well as peaks mapping in satellite and micro-satellite repeats and peaks mapping in 18 and 28S rRNA sequences, were eliminated from the analysis.

source_name: Suspension HeLa cells

growth_protocol: HeLa-S cells were grown in suspension in Joklik's modified Eaglesâs medium (JMEM) with 5% of fetal calf serum.

extract_protocol: 5-10ng of ChIP-DNA were transformed into libraries using ChIP-Seq DNA Sample Prep Kit (Illumina) and sequenced on Illumina Genome Analyzer 2 DNA sequencing instrument. Total input DNA was also sequenced.

treatment_protocol: HeLa-S cells were crosslinked for 8â using 1% of formaldehyde, DNA was isolated and sonicated to 100-300 bps using a bioruptor (Bioruptor UCD-200, Diagenode) and 30ââ pulses on and off at maximum power.  Sonicated DNA was immunoprecipitated, washed and eluted as described (Shweta 2007). 2-8 x 107 cells were used per antibody.

value: HeLa, cycling

value: YY1; polyclonal anti-YY1 (sc-1703)


title: PolII_ChIPSeq

description: Chromatin IP against RPB2

value: RPB2; polyclonal anti-Pol II (POLR2B, sc-67318)


title: HapMap MNase-seq GM18522 (Single-end)

city: La Jolla

first: Graham

last: McVicker

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute

description: Single-end (SE) sequencing

data_processing:
Illumina CASAVA version 1.6 or 1.7 was used for base calling
Reads were mapped to the human genome with BWA version 0.5.8 or version 0.6.1-r104, using the commands 'bwa aln' and 'bwa sampe' or 'bwa samse' with default arguments.
SAM files were converted to BAM format, filtered for quality scores >= 10, sorted, and indexed using samtools version 0.1.13.
A python script was used to discarded reads if their fragment size fell outside the central 95% of the fragment size distribution (126-184 bp).
Midpoints of fragments were recorded using a python script. For single-end reads, the midpoint was assumed to be 75 bp from the 5’ end of the mapped read.
Genome_build: hg18
Supplementary_files_format_and_content: Wiggle files containing mapped MNase fragment midpoint counts for each base in the genome. Wiggle files are provided for each individual and for the combined data set. Wiggle files that only contain counts from only single-end (SE) reads or from paired-end reads from a defined fragment size range are also provided.

source_name: lymphoblastoid cell line

growth_protocol: Cell lines were cultured in RPMI 1640 media (supplemented with 2mM L-glutamine and 15% fetal bovine serum) and maintained at a density of between 2-5x10^5 viable cells/ml as per Coriell recommendations.

extract_protocol: 1 ml aliquot of nuclei was digested with 7 μl of 50 U/μl MNase at 37°C for 12 minutes. Reaction was stopped by addition of EDTA, SDS and NaCl to an end concentration of 0.01M, 2% and 0.2M respectively. Reactions were digested with RNaseA (0.1mg) for 1hr at 42°C and further treated with ProteinaseK at 37°C for one hour. DNA was extracted using phenol-chloroform extraction and concentrated by ethanol precipitation. DNA was then run on a 3.3% Nusieve agarose gel at 75 V for 5 hours. 147bp fragments representing the mononucleosomes were excised from the gel and DNA was extracted from the gel by crushing the gel and soaking in soak buffer (300 mM Sodium Acetate, 1 mM EDTA, 0.1% SDS). The resulting DNA fragments in solution were then purified using Qiagen PCR purification kit. DNA fragments were prepared for paired-end sequencing using the standard Illumina protocol.

treatment_protocol: Cells were pelleted at 1000 rpm at 4C and washed in ice-cold PBS buffer. The cell pellet was resuspended in ice-cold NP-40 lysis buffer (10 mM Tris [pH 7.4], 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40, 0.15 mM spermine, 0.5 mM spermidine) and incubated on ice for 5 minutes. The solution was centrifuged at 1000 rpm for 3 minutes at 4C, and then washed in a wash buffer (10 mM Tris [pH 7.4], 15 mM NaCl, 60 mM KCl, 0.15 mM spermine, 0.5 mM spermidine), and centrifuged again at 1000 rpm for 3 minutes at 4C. 1x10^8 cells were then resuspended in 10 ml of ice-cold MNase digestion buffer (10 mM Tris [pH 7.4], 15 mM NaCl, 60 mM KCl, 0.15 mM spermine, 0.5 mM spermidine, 1mM CaCl2).

value: lymphoblastoid cell line

tag: population

value: YRI

tag: ethnicity

value: Yoruba

tag: country of origin

value: Nigeria


title: GABP_ChIPSeq

description: Chromatin IP against GABP

value: GABP; polyclonal anti-GABPa (sc-22810)


title: H3K36Me3_ChIPSeq

description: Chromatin IP against H3K36Me3

value: H3K36Me3; polyclonal H3K36Me3 (Abcam ab-9050)


title: RIKEN_Cage_MCF-7_cytosol_longPolyA

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

molecule: polyA RNA

tag: datatype

value: Cage

tag: datatype description

value: CAGE 5' RNA Tags

tag: rnaextract

value: longPolyA

tag: rnaextract description

value: Poly(A)+ RNA longer than 200 nt

tag: biorep

tag: labexpid

tag: readtype

tag: readtype description

value: Single 50 nt reads

tag: replicate

tag: cell sex

value: F

tag: localization

value: cytosol

tag: localization description

value: The fluid between the cells outer membrane and the nucleus


title: Input_DNA_seq1

description: High-throughput sequencing of control input DNA (collected after the crosslinking and sonication steps)

tag: cell line

value: HeLa, cycling

tag: chip antibody


title: THAP11_ChIPSeq

description: Chromatin IP against THAP11

value: THAP11; polyclonal anti-THAP11 (G4275, {Dejosez, 2008 #99})


title: H3K4Me3_ChIPSeq

description: Chromatin IP against H3K4Me3

value: H3K4Me3; polyclonal H3K4Me3 (Abcam ab-8580)


title: Input_DNA_seq3


title: Input_DNA_seq2


title: ZNF143_ChIPSeq

description: Chromatin IP against ZNF143

value: ZNF143; Polyclonal anti-ZNF143 (ZNF143, {Cold Spring Harbor, 19164 #4})


title: HCFC1_N_ChIPSeq_seq6

description: Chromatin IP against HCFC1 Nterm

value: HCFC1, Nterm;  polyclonal anti-HCF-1N (961-1011, {Machida, 2009 #109})


title: HCFC1_ChIPSeq_seqs1-6

description: Chromatin IP against HCFC1

value: HCFC1; polyclonal anti-HCF-1C (H12,{Wilson, 1993 #21})


title: LNsip53-AR ChIPSeq

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

description: Chromatin IP against AR

data_processing: Reads were aligned using Eland 1.3 with standard parameters to hg18, PartekGS version 6.4  was used for peak prediction using default paramters with fragments predicted at 150bp. A custom python script was used to convert output to bed file format.

growth_protocol: LNCaP or LNsip53 cells were incubated in hormone free media for 3 days (RPMI supplimented with 10% CSS)

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

treatment_protocol: Cells were treated with 10 nM of DHT for 1 hour

tag: cell line background

value: LNCaP

tag: genotype/variation

value: p53 knockdown

tag: cell type

value: prostate adenocarcinoma cells

value: Anti-Androgen Receptor (AR)

tag: chip antibody vendor

value: BD Biosciences

tag: chip antibody cat.#


title: LNCaP-AR_ChIPSeq

description: Chromatin IP against AR

source_name: LNCaP

value: wild type


title: wt

status: Public on Jul 30 2012

city: Worcester

first: Craig

last: Mello

state: MA

address: 368 Plantatoin Street, Suite AS5-2047

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description: WT sample

data_processing:
remove 5' barcode, ATCA (or its variants containing a single mutation) for WT and GCTG (or its variants containing a single mutation) for tsn, and then remove the 3' linker CTGTAG or the incomplete linker CTGTA/CTGT/CTG/CT at the very 3' end if failing to find the complete 3' linker. For reads at least 20nt long ending with CCA, such CCA is trimmed off, thus allowing the 3' end of mature tRNA to be matched perfectly
get perfect match using a custom PERL script which guarantees to find all the perfect matches regardless of the match number for each RNA
The sample is normalized to 3 million of total matched reads
A custom pipeline is used to summarize reads matched to tRNA or pre-tRNA
Genome_build: N. crassa assembly 7
Supplementary_files_format_and_content: Fasta format for sequence with id containing the RNA number matched to the genome and a unit of rDNA sequence which is not in the genome

organism: Neurospora crassa

source_name: wild type

growth_protocol: constant light, 1x Vogel's 2% sucrose

extract_protocol: Purified small RNAs of 10-60nt were further resolved on a 15% polyacrylamide 7M Urea Gel, along with 20 picomoles of RNA standard (18- and 40-nt) in separate lanes. Ethidium Bromide staining was used to visualize the RNA standards. A gel fragment was excised from the sample lanes in the migration range between the two standards. RNA was eluted from the gel fragment in (0.3M NaCl-TE pH7.5) solution overnight and ethanol-precipitated with 20mg of glycogen as the carrier. The gel purified RNA and 1µM of each standard were incubated with 10µM of 3’-end linker, 1 Unit/µl of SuperRNaseIN, 10% DMSO and 3 Units/µl T4 RNA ligase (Takara) in 10µl ligation buffer (50mM Tris-Cl pH7.5, 10mM MgCl2,10mg/mL BSA, 10mM DTT).  The 3’ ligated products were gel purified, eluted, precipitated and then incubated with 10µM of 5’ adapter oligonucleotide with 4nt barcode at the 5' end, 1 Unit/µl SuperRNaseIN (Ambion) and 3 Units/µl of T4 RNA ligase in ligation buffer (50mM Tris-HCI pH7.5), 10mM MgCI2, 10mM DTT, 1mM ATP) and 10% DMSO. The ligated products were gel purified and reverse transcribed in a standard 20µl reaction (SuperScript III, Invitrogen). The cDNA was amplified by PCR and purified in a 8% acrylamide gel. PCR products generated for all the samples were sequenced on a Solexa sequencing platform (Illumina, Inc.) and single-end 36 nt reads were obtained.

treatment_protocol: WT and translin mutant

tag: 5' barcode

value: ATCA


title: tsn

description: translin mutant

source_name: tsn mutant

value: TSN mutant

value: GCTG


title: Input DNA

first: Timothy

middle: Michael

last: Chlon

address: 3333 Burnet Ave

department: Oncology

institute: Cincinnati Children's

data_processing:
Mappable reads were aligned to mouse genome mm9 using the Illumina pipeline
Peaks were identified with MACS v1.3.7.1 (Zhang Y, 2008) using the full set of unique IP tags as the ‘treatment’ and an equally-sized, randomly sampled subset of unique input tags as the ‘control,’ with the default p-value (10-5), and an ‘mfold’ value of 15. MACS was run three times for each IP tag set, using a different random subset of input, and the base-wise intersection of the three runs was obtained using intersectBed from BEDTools (Quinlan and Hall, 2010).
Genome Build:
TMC-INPUT-G1ME.bed: mm9

organism: Mus musculus

source_name: G1ME cells

growth_protocol: G1ME cells were cultured in 1% TPO supernatant (v/v)

extract_protocol: Isolated chromatin was sonicated and pre-cleared with isotype-matched mouse non-specific IgG.  Chromatin immunprecipitation was carried out with a HA-tag antibody (Santa Crruz Biotechnology, sc-7392).  The formaldehyde crosslinks were reversed by heating to 65-degrees overnight.  RNA and protein were removed by treatment with RNAse A and Proteinase K, respectively, and the DNA was isolated using the Qiagen PCR Purification Kit.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part#  IP-102-1001).

treatment_protocol: Retroviral supernatant was added to the cells at 1e6 cells per ml, and the culture was centrifuged at 3200rpm for 90min. The cells were incuabted in the virus for an additional 4h, and then the virus was removed.  The cells were crosslinked 48h later.

tag: strain

value: GATA1-deficient cell line with megakaryocyte and erythrocyte differentiation potential

tag: protocol

value: Cells grown in TPO supernatant (10% v/v)

tag: retrovirus

tag: fraction

value: input


title: GATA-1 ChIP-Seq

data_processing:
Mappable reads were aligned to mouse genome mm9 using the Illumina pipeline
Peaks were identified with MACS v1.3.7.1 (Zhang Y, 2008) using the full set of unique IP tags as the ‘treatment’ and an equally-sized, randomly sampled subset of unique input tags as the ‘control,’ with the default p-value (10-5), and an ‘mfold’ value of 15. MACS was run three times for each IP tag set, using a different random subset of input, and the base-wise intersection of the three runs was obtained using intersectBed from BEDTools (Quinlan and Hall, 2010).
Genome Build:
TMC-GATA1-G1ME.bed: mm9
GATA1.wig: mm9
GATA1_ABC_peaks.bed: mm9

tag: antibody

value: HA-tag antibody (Santa Crruz Biotechnology, sc-7392)

value: ChIP


title: V205G ChIP-Seq

data_processing:
Mappable reads were aligned to mouse genome mm9 using the Illumina pipeline
Peaks were identified with MACS v1.3.7.1 (Zhang Y, 2008) using the full set of unique IP tags as the ‘treatment’ and an equally-sized, randomly sampled subset of unique input tags as the ‘control,’ with the default p-value (10-5), and an ‘mfold’ value of 15. MACS was run three times for each IP tag set, using a different random subset of input, and the base-wise intersection of the three runs was obtained using intersectBed from BEDTools (Quinlan and Hall, 2010).
Genome Build:
TMC-V205G-G1ME.bed: mm9
V205G.wig: mm9
V205G_ABC_peaks.bed: mm9


title: m667a_pollen

city: Oxford

first: Dmitry

middle: A

last: Filatov

address: South Parks Road

department: Plant Sciences

country: United Kingdom

institute: University of Oxford

description: paired end, 150-450bp inserts

organism: Silene latifolia

source_name: pollen

growth_protocol: glasshouse

extract_protocol: RNA extracted with Qiagen RNAeasy columns with on-column DNAse digestion. RNA was prepared for Illumina sequencing with standard Illumina kits at the WTCHG genomic centre (Oxford, UK)

tag: gender

value: male

tag: generation

value: not used in the crosses


title: mBen

description: single, not paired end

source_name: shoot with flower buds

value: parent


title: Svulgaris

description: paired end, 150-450bp inserts

organism: Silene vulgaris

value: hermaphrodite


title: f102

description: paired end, 150-450bp inserts

value: female


title: f101

description: single, not paired end


title: m762a_pollen

description: paired end, 150-450bp inserts


title: f833d

description: paired end, 150-450bp inserts


title: m102

description: paired end, 150-450bp inserts


title: Young skin 4

first: Kun

last: Qu

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

description:
Y4
3' RNA-seq

data_processing:
Basecalls were performed using CASAVA version 1.4.
3' seq reads were aligned to the hg18 genome assembly using "Bowtie" (version 0.12.6).
Reads Per Kilobase of exon per Million mappable reads (RPKM, a direct measure of transcript abundance), as well as the number of raw reads falling on to each gene, were calculated using a self-developed script by K. Qu. Only the reads mapping to the 3' UTR and last exon of the RefSeq transcripts were counted.
Genome_build: hg18
Supplementary_files_format_and_content: bedGraph files were generated using the SeqGene sam2wig module.
Supplementary_files_format_and_content: BBL_3seq_GeneExp.txt, which is linked to the Series record as a supplementary file, includes RPKMs.

source_name: skin, young

growth_protocol: Human subjects.

extract_protocol: Total RNA was extracted using the RNeasy Fibrous Tissue Mini Kit (Qiagen). 3'-seq was performed as described in Beck AH et al., 2010 (PMID 20098735). In brief, oligo-dT-directed reverse transcription generated cDNAs corresponding to the 3' ends of poly-adenylated transcripts; the cDNAs were then cloned and subjected to deep sequencing on the Illumina GAIIx platform with raw read length of 36bp.

treatment_protocol: 3 broadband light treatments over 3 months using a 515 nm or 560 nm cut-off filter at a single long pulse of 10-20 ms duration, fluences of 8-14 J/cm2. At each treatment session, two or more passes were performed.

tag: tissue

value: skin

tag: age group

value: <=30 years


title: fBen

description: single, not paired end


title: Young skin 3

description:
Y3
3' RNA-seq


title: Patient 5 without BBL treatment

description:
P5U
3' RNA-seq

source_name: skin, aged, untreated

value: >=50 years

tag: treatment

tag: patient id


title: Patient 4 without BBL treatment

description:
P4U
3' RNA-seq


title: Patient 2 without BBL treatment

description:
P2U
3' RNA-seq


title: Young skin 2

description:
Y2
3' RNA-seq


title: Young skin 5

description:
Y5
3' RNA-seq


title: Young skin 1

description:
Y1
3' RNA-seq


title: Patient 1 without BBL treatment

description:
P1U
3' RNA-seq


title: Patient 5 with BBL treatment

description:
P5T
3' RNA-seq

source_name: skin, aged, BBL treated

value: BBL


title: m222a

description: paired end, 150-450bp inserts


title: Patient 3 without BBL treatment

description:
P3U
3' RNA-seq


title: m101

description: single, not paired end


title: Patient 3 with BBL treatment

description:
P3T
3' RNA-seq


title: Patient 1 with BBL treatment

description:
P1T
3' RNA-seq


title: Patient 2 with BBL treatment

description:
P2T
3' RNA-seq


title: IgG-ChIP-Seq-Control

city: Boston

first: Falak

last: Sher

address: 3 Blackfan Circle, CLs 12220 Center for Life Science Building

department: F.M. Kirby Neurobiology Center

institute: CHB

description: Chromatin IP against IgG control

data_processing: Alignment: Sequence reads were obtained and mapped to the mm9 genomes using Bowtie for Illumina software. Maximum number of mismatches permitted 2

source_name: NSCs & pOLs

growth_protocol: NSCs were cultured in T25 (Nunc, Roskilde) tissue culture flasks containing proliferation medium, consisting of Neurobasal medium supplemented with 2% B27, human recombinant epidermal growth factor (EGF; 20ng/ml), and basic fibroblast growth factor (bFGF; 20ng/ml). Pre-myelinating oligodendrocytes were cultured in standard SATO medium.

extract_protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. DNA was precipitated using Phenol/chloroform/IAA method. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (IP-102-1001) Following the instructions on the kit "A" bases were added to the 3' End of the DNA fragments and fragments were ligated to Adapters. Subsequently, the Adapter-Modified DNA fragments were run on a 2% agarose gel to generate the DNA libraries based on fragments length (200 +/-25bp). Finally the Adapter-Modified DNA fragment libraries were enriched by PCR. After validating (quality control) libraries by Bioanalyzer, the sequencing reactions were performed with system components and reagents on the Genome Analyzer following the manufacturer's protocols.

value: eNSCs & p2-pOLs

tag: passage

value: eNSCs:2-3 & p2-pOLs:0

tag: chip antibody

value: IgG (isotypic control antibody) [Abcam; Cat. no.:ab46540]


title: Ezh2-ChIP-Seq-NSCs

description: Chromatin IP against Ezh2

source_name: Neural stem cells (NSCs)

tag: cell type

value: Embyonic (E14) neural stem cells (eNSCs)

value: 2-3 (cultured as neurospheres)

value: Anti Ezh2 [Diagenode (http://www.diagenode.com/en/index.php); Cat. no.:CS-039-100; Lot no.:001]


title: small RNA-Seq of HRDE-1 co-IP small RNAs, FLAG::HRDE-1 protein was immuno-precipitated with anti-FLAG M2 Ab

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: NJ

address: Nelson Labs A125, 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

data_processing:
For each 36-nt sequence tag, remove the 4-nt barcode from the 5' end and removing sequences that correspond the linker sequence (CTG TAG GCA CCA TCA AT) from the 3' end. The remaining sequence was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.
for chip-seq: After removing the 3-nt barcode, the first 25-nt sequence for each tag was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.
for small RNA seq: For each 36-nt sequence tag, remove the 4-nt barcode from the 5' end and removing sequences that correspond the linker sequence (CTG TAG GCA CCA TCA AT) from the 3' end. The remaining sequence was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.
Genome_build: WS190
Supplementary_files_format_and_content: bed

organism: Caenorhabditis elegans

source_name: adult C. elegans

extract_protocol: Libraries of small RNAs were prepared using a protocol similar to one previously described for miRNA cloning (LAU, N. C., L. P. LIM, E. G. WEINSTEIN and D. P. BARTEL, 2001 An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294: 858–862.), in which small RNA species were flanked by adapter sequences to allow for PCR and sequencing. We modified the original protocol at several key steps to allow for capture of triphosphorylated species and for sequencing with the Illumina genome analyzer system. To remove the bias for 5′ monophosphorylated species but preserve the bias toward 3′ hydroxylated species, we removed both monophosphates and polyphosphates from the 5′-end of the small RNA with Antarctic Phosphatase (New England Biolabs) following the addition of the 3′ adapter with T4 RNA ligase 1 (New England Biolabs). The resulting hydroxylated 5′-ends were phosphorylated by treatment with T4 polynucleotide kinase (New England Biolabs) and ATP to form a subtrate for T4 RNA ligase 1-mediated addition of the 5′ adapter. T4 polynucleotide kinase treatment after addition of the 3′ adapter is important because of its 3′ phosphatase and 2′,3′ cyclic phosphodiesterase activity, which can convert unwanted RNA degradation products into a substrate for the 3′ adapter ligation reaction. After ligation of both the 3′ and 5′ adapters, the adapters were extended during the reverse transcription and PCR steps to include complete primer binding sites for subsequent amplification and sequencing reactions. To protect against cross-contamination and to allow for pooling of samples, we modified the 5′ adapter sequence to include the Illumina genomic sequencing primer immediately followed by a 4-nt barcode. The samples were PAGE purified at three stages: after initial RNA extraction and after each ligation step (except with the isolated spermatogenic cell sample, where the first PAGE purification was skipped to conserve material).  The following oligos were used:    3′ adapter (IDT linker-1 with 5′ adenylation and 3′ dideoxyC): rAppCTGTAGGCACCATCAATC;    5′ adapter (i.e., AF-PP-341 DNA/RNA hybrid oligo with a 5′ amino modifier and 4-nt barcode at the 3′-end): ACGCTCTTCCGATCTrGrUrUrA;    Dual reverse transcription primer and PCR primer (AF-JIG-37, complementary to IDT linker-1): CAAGCAGAAGACGGCATACGAattgatggtgcctacag;    PCR primer (AF-JIG-40, containing 5′ adapter sequence): AATGATACGGCGACCACCGACACTCTTTCCCTACACGACGCTCTTCCGATCT.

tag: developmental stage

value: adult

tag: barcode (first 3 nt for fastq files of chip-seq libraries, first 4 nt for fastq files of small rna libraries)

value: TCGC

value: anti-FLAG M2 antibody for FLAG::NRDE-2 protein

tag: antibody manufacturer

value: Sigma

tag: antibody catalog #


title: 454_stage2

status: Public on Jul 27 2012

city: Beijing

first: Wei

last: Chen

address: No.5 Yiheyuan Road

institute: Peking University

data_processing:
The validated reads were mapped to rice genome MSU 6.1
discarding the tRNA- and rRNA-related loci
The consensus sequences of these multiple reads loci met each of the following criteria before being considered as a putative ncRNA:a) at least one perfectly matched read with the annotated rice genome was observed; b) the novel non-coding transcript had at least one trim and defined terminus; c) at least two non-redundant reads or reads from different sequencing libraries were found.
Genome_build: MSU 6.1
Supplementary_files_format_and_content: bed files were generated against ref genome MSU6.1; Scores represent mapped reads;

organism: Oryza sativa

source_name: anther, pistil and grouting embryo

extract_protocol: The total RNAs were extracted and fractionated according to the user manual of Qiagen RNA/DNA kit. The RNA fractions between 50-500 nt in length were collected and checked by the polyacylamide gel before the cDNA library was constructed. 5’ end structure specific adaptors and 3’ end adaptors were sequentially ligated to the isolated ncRNAs according to previously established methods (Deng et al., 2006). cDNAs were obtained by reverse transcription without amplification. The cDNAs with both end adaptors served as the single stranded DNA (ssDNA) library for the deep 454 sequencing.

value: anther, pistil and grouting embryo


title: H3K9me3 chip-IP from nrde-3(gg066) mutant C. elegans that underwent smg-1 RNAi

data_processing:
After removing the 3-nt barcode, the first 25-nt sequence for each tag was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.
for chip-seq: After removing the 3-nt barcode, the first 25-nt sequence for each tag was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.
for small RNA seq: For each 36-nt sequence tag, remove the 4-nt barcode from the 5' end and removing sequences that correspond the linker sequence (CTG TAG GCA CCA TCA AT) from the 3' end. The remaining sequence was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.
Genome_build: WS190
Supplementary_files_format_and_content: bed

extract_protocol: DNA was treated with 0.5 U/μl T4 polynucleotide kinase (NEB) in 1x T4 DNA ligase buffer (NEB, containing 1 mM ATP) at 37°C for 1 hour to phosphorylate 5’ ends and dephosphorylate 3’ ends.  Ends were then blunted in a reaction containing 0.75 U/μl of T4 DNA polymerase (NEB), dNTP (100 μM each, Roche), and 1x NEB buffer 1 at 12°C for 15 min.  Nucleosome core DNA was then ligated to previously annealed DNA oligos 5’ Pi-/barcode/-AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG-OH 3’ and 5’ OH-CCCTACACGACGCTCTTCCGATCT-/barcode/-OH 3’) (NEB Quick Ligation Kit).  Nucleosome core DNA captured by linker oligos was purified using 6 % polyacrylamide (acrylamide:bis-acrylamide = 19:1) gels containing 8 M urea, followed by PCR amplification with primers AF-SG-135 (5’ OH-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-OH 3’) and AF-SG-137 (5’ OH-CAAGCAGAAGACGGCATACGAGCT-OH 3’).  A series of PCR reactions with increasing cycle numbers were then carried out; we carefully choose cycle numbers for which product levels have not saturated (i.e. product levels still able to increase substantially with additional cycles); this ensures that the majority of amplified segments are still annealed to a true complement and avoids reannealing-distortion in the resulting sequence libraries. After separating PCR products on 2 % agarose gels, DNA bands of the expected size (~210-240 bp) were extracted (QIAchange® Gel Extraction Kit (Invitrogen); omitting the 50°C heating step) and used for Illumina GAIIx.

treatment_protocol: 50-100 μl frozen embryo pellets or 100 - 200 μl frozen adult worm pellets were used for each nucleosome immunoprecipitation experiment.  Crushed pellets (pulverized by grinding in liquid nitrogen with a mortar and pestle) were resuspended in 1 ml buffer A (15 mM Hepes-Na, pH 7.5, 60 mM KCl, 15 mM NaCl, 0.15 mM beta-mecaptoethonal, 0.15 mM spermine, 0.15 mM spermidine, 0.34 M sucrose, 1x HALT protease and phosphatase inhibitor cocktail (Thermo Scientific)). To crosslink, formaldehyde was added to the resulting crude extract to a final concentration of 2%, followed by incubation at room temperature for 15 min. 0.1 ml 1 M Tris.Cl (pH 7.5) was then added to quench formaldehyde. Lysate was spun (15,000xg for 1 min). Pellets were washed with ice-cold buffer A and then resuspended in 0.3 ml buffer A with 2 mM CaCl2. Micrococcal nuclease (Roche) was added to the lysate to a final concentration of 0.3 U/μl, followed by 5 minutes incubation at 37°C (inverting the tube several times per minute). Micrococcal Nuclease (MNase) digestion was optimized so that approximately 70% of DNA entered the mono-nucleosome band, with the remainder predominantly in di- and trinucleosome bands.  Digestion reactions were stopped by adding EGTA to a final concentration of 20 mM. After centrifugation (15,000xg, 1 min) pellets were washed with ice-cold RIPA buffer (1xPBS, 1% NP40, 0.5% Sodium Deoxycholate, 0.1% SDS, 1x HALT protease and phophatase inhibitor and 2 mM EGTA), resuspended in 0.8 ml ice-cold RIPA buffer, and solubilized by sonication (Microson TM XL 2000 sonicating machine with a micro tip, output level: 5, three times of 30-second sonication). Sonication was used here to efficiently solubilize crosslinked chromatin without further fragmenting the chromatin (data not shown). Crude lysate was cleared by centrifugation at 15,000xg for 2 min. 80 μl of the supernatant was used to make "IP input" nucleosome libraries.  The remaining supernatant was used for IP, adding 2 μg of anti-H3K9me3 antibody (Abcam, ab8898) and agitating gently at 4°C overnight before 50 μl of protein A Dynabeads (10% slurry in 1x PBS buffer) was added and the resulting mixture shaken for 2hr at 4°C . The beads were then washed four times (four minutes each) with ice-cold 600 μl LiCl washing buffer (100mM Tris.Cl, pH 7.5, 500mM LiCl, 1%NP-40, 1% Sodium deoxycholate), transferring to a new tube after the first wash. To elute the immunoprecipitated nucleosome and reverse crosslinks, beads were incubated with 450 μl worm lysis buffer (0.1M Tris.Cl, pH 8.5, 100 mM NaCl, 1% SDS) containing 200 μg/ml protease K at 65°C for four hours with agitation every 30 minutes (total nucleosome aliquots were treated similarly to reverse crosslink), followed by organic extraction and DNA precipitation.

tag: strain

value: CAT

tag: RNAi target

value: Abcam


title: Ezh2-ChIP-Seq-pOLs

description: Chromatin IP against Ezh2

source_name: Pre-myelinating oligodendrocytes (pOLs)

value: pOLs from postnatal (P2) brain (p2-pOLs)

value: 0 (single time monolayer cultures)


title: E. coli TSS 1

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

data_processing: The amplified cDNA libraries from two biological replicates for each E. coli and K. pneumoniae were sequenced on an Illumina Genome Analyzer. Sequence reads for cDNA libraries were aligned onto E. coli K12 MG1655 genome and K. pneumoniae MGH78578 genome with 5 plasmids, respectively, using Mosaik with following arguments: hash size=10, mismatch=0. Only reads that aligned to the unique genomic location were retained. Two biological replicates were processed seperatedly, and only sequence reads presented in both biological replciates were considered for further process. The genomic coordinates of the 5'-end of these uniquely aligned reads were defined as potential TSSs. Among potential TSSs, only TSSs with the strongest signal within 10 bp window were kept to remove possible noise signals, and TSSs with greater than or equal to 50% of the strongest signal upstream of an annotated gene were considered as multiple TSSs.

organism: Escherichia coli K-12

source_name: Cells at mid-log phase (OD600nm 0.5)

growth_protocol: E. coli K12 MG1655 and K. pneumoniae MGH78678 was grown to mid-log phase (O.D.600nm 0.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose.

extract_protocol: Total mRNA isolated from each cell culture was treated with Terminator 5' Phosphate Dependent Exonuclease (Epicentre) to enrich 5' tri-phosphorylated mRNAs. Intact tri-phosphorylated RNAs were then treated with RNA 5'-Polyphosphatase (Epicentre) to generate 5'-end monophosphorylated RNA for ligation to RNA adaptors. cDNAs were synthesized using the adaptor-ligated mRNAs as template using a modified small RNA RT primer from Illumina and Superscript II Reverse Transcriptase (Invitrogen). The cDNA samples were amplified, and size fractionated from 100 to 300 bp.

treatment_protocol: The cell culture was treated with the RNAprotect reagent (Qiagen).

tag: strategy

value: TSS-Seq

tag: genome build

value: E. coli K12 MG1655 reference genome (NC_000913)


title: K. pneumoniae TSS 1

organism: Klebsiella pneumoniae


title: E. coli TSS 2


title: H3K9me3 chip-IP from nrde-4(gg129) mutant C. elegans that underwent smg-1 RNAi

value: GTC

tag: antibody


title: K. pneumoniae TSS 2


title: 454_stage1

source_name: coleoptiles, radicals, shoot, and tillering leaves


title: CSHL_RnaSeq_HSaVEC_cell_TAP-Only_shortTotal

status: Public on Jul 26 2012

source_name: HSaVEC

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: rnaextract

value: shortTotal

tag: rnaextract description

value: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation

tag: biorep

tag: labexpid

tag: labversion

value: iIDR

tag: readtype

tag: readtype description

value: Single 101 nt reads

tag: replicate

tag: localization

value: cell

tag: localization description

value: Whole cell

tag: protocol

value: TAP-Only

tag: protocol description

value: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.


title: Patient 4 with BBL treatment

description:
P4T
3' RNA-seq

tag: tissue

value: skin

tag: age group

value: >=50 years

tag: treatment

value: BBL

tag: gender

value: female

tag: patient id


title: CSHL_RnaSeq_HMEpC_cell_TAP-Only_shortTotal

source_name: HMEpC

value: primary cell

value: mammary epithelial cell

tag: datatype

tag: datatype description

tag: rnaextract


title: CSHL_RnaSeq_NHEM_M2_cell_TAP-Only_shortTotal

tag: rnaextract description

tag: biorep

tag: labexpid


title: CSHL_RnaSeq_GM12878_chromatin_TAP-Only_shortTotal

molecule: nuclear RNA

tag: labversion

tag: readtype

tag: readtype description

value: chromatin

value: Nuclear DNA and associated proteins


title: CSHL_RnaSeq_HPIEpC_cell_TAP-Only_shortTotal

source_name: HPIEpC

value: RnaSeq

value: Sequencing analysis of RNA expression

tag: replicate

tag: localization

tag: localization description


title: CSHL_RnaSeq_hMSC-UC_cell_TAP-Only_shortTotal

source_name: hMSC-UC

value: shortTotal

value: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation

tag: protocol

tag: protocol description


title: CSHL_RnaSeq_NHEM.f_M2_cell_TAP-Only_shortTotal

value: iIDR

value: Single 101 nt reads


title: CSHL_RnaSeq_HWP_cell_TAP-Only_shortTotal

source_name: HWP

value: cell

value: Whole cell


title: CSHL_RnaSeq_hMSC-AT_cell_TAP-Only_shortTotal

source_name: hMSC-AT

value: TAP-Only

value: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.


title: H3K9me3 chip-IP from glp-4(bn2) mutant C. elegans that underwent smg-1 RNAi

tag: strain

tag: developmental stage

value: adult

tag: barcode (first 3 nt for fastq files of chip-seq libraries, first 4 nt for fastq files of small rna libraries)

value: ACG

tag: RNAi target

tag: antibody

tag: antibody manufacturer

value: Abcam

tag: antibody catalog #


title: CSHL_RnaSeq_Monocytes-CD14+_cell_TAP-Only_shortTotal

value: primary cell

value: CD14-positive monocyte

tag: datatype

tag: datatype description

tag: rnaextract

tag: rnaextract description

tag: biorep

value: Single 36 nt reads


title: CSHL_RnaSeq_HAoEC_cell_TAP-Only_shortTotal

source_name: HAoEC

tag: labexpid

tag: labversion

tag: readtype

tag: readtype description

tag: replicate


title: CSHL_RnaSeq_CD20+_cell_TAP-Only_shortTotal

tag: localization

tag: localization description

tag: protocol

tag: protocol description


title: CSHL_RnaSeq_HOB_cell_TAP-Only_shortTotal

source_name: HOB

value: osteoblast


title: CSHL_RnaSeq_NHDF_cell_TAP-Only_shortTotal

source_name: NHDF

value: fibroblast of dermis

value: RnaSeq


title: CSHL_RnaSeq_SkMC_cell_TAP-Only_shortTotal

source_name: SkMC

value: Sequencing analysis of RNA expression

value: shortTotal


title: CSHL_RnaSeq_H1-neurons_cell_CIP-TAP_shortTotal

value: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation

value: iIDR

value: CIP-TAP

value: This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs.


title: FUS-CLIP cerebrum

city: Nagoya

first: Akio

last: Masuda

state: Aichi

address: 65 tsurumai-cho, Showa-ku

country: Japan

institute: Nagoya University Graduate School of Medicine

data_processing:
SOLiD reads were mapped to the mouse genome (NCBI Build 37.1/mm9) with default parameters using the BioScope 1.3 (Life Technologies).
We next removed multiply aligned reads, unreliable reads, and PCR duplicates with Avadis NGS software 1.3 (Strand).
Genome_build: mm9

source_name: cerebrum

extract_protocol: HITS-CLIP was performed in biological replicates using anti-FUS mouse monoclonal antibody (4H11, Santacruz), following the method developed by Darnell and coworkers (Chi, S. W. et al. 2009) with some modifications, as preveously described (Masuda A. et al. 2012). High-throughput 50-bp single-end sequencing was performed with the SOLiD 3 sequencer (Life Technologies) using one quad of a SOLiD sequencing slide for each sample.

tag: antibody

value: ant-FUS mouse monoclonal

value: Santa Cruz

tag: strain

tag: tissue

value: cerebrum

tag: age

tag: genotype

value: wild type


title: CSHL_RnaSeq_HPC-PL_cell_TAP-Only_shortTotal

source_name: HPC-PL

tag: datatype

tag: datatype description

tag: rnaextract

value: Single 101 nt reads

value: cell

value: Whole cell

value: TAP-Only

value: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.


title: CSHL_RnaSeq_HVMF_cell_TAP-Only_shortTotal

source_name: HVMF

tag: rnaextract description

tag: biorep

tag: labexpid


title: CSHL_RnaSeq_H1-neurons_cell_TAP-Only_shortTotal

tag: labversion

tag: readtype

tag: readtype description


title: CSHL_RnaSeq_HAoAF_cell_TAP-Only_shortTotal

source_name: HAoAF

tag: replicate

tag: localization

tag: localization description


title: CSHL_RnaSeq_IMR90_cell_CIP-TAP_shortTotal

tag: protocol

tag: protocol description


title: CSHL_RnaSeq_IMR90_cell_shortTotal

value: No special treatment or protocol applies


title: CSHL_RnaSeq_GM12878_nucleolus_TAP-Only_shortTotal

value: RnaSeq

value: nucleolus

value: The part of the nucleus where ribosomal RNA is actively transcribed


title: CSHL_RnaSeq_MCF-7_cell_shortTotal

value: immortalized cell line

tag: line

value: Sequencing analysis of RNA expression

value: shortTotal

value: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation


title: CSHL_RnaSeq_SK-N-SH_cytosol_CIP-TAP_shortTotal

molecule: cytoplasmic RNA

source_name: SK-N-SH

value: iIDR

value: cytosol

value: The fluid between the cells outer membrane and the nucleus

value: CIP-TAP

value: This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs.


title: CSHL_RnaSeq_SK-N-SH_cytosol_TAP-Only_shortTotal

value: Single 101 nt reads


title: CSHL_RnaSeq_hMSC-BM_cell_TAP-Only_shortTotal

source_name: hMSC-BM

tag: cell sex

value: B

value: cell

value: Whole cell


title: CSHL_RnaSeq_A549_nucleus_shortTotal

value: nucleus

value: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA

value: No special treatment or protocol applies


title: CSHL_RnaSeq_MCF-7_nucleus_shortTotal

value: RnaSeq


title: CSHL_RnaSeq_HFDPC_cell_TAP-Only_shortTotal

source_name: HFDPC

value: TAP-Only

value: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.


title: CSHL_RnaSeq_MCF-7_nucleus_TAP-Only_shortTotal

value: Sequencing analysis of RNA expression

value: shortTotal


title: CSHL_RnaSeq_HCH_cell_TAP-Only_shortTotal

source_name: HCH

value: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation

value: iIDR


title: CSHL_RnaSeq_A549_nucleus_TAP-Only_shortTotal


title: CSHL_RnaSeq_H1-neurons_cell_shortTotal


title: CSHL_RnaSeq_IMR90_cell_TAP-Only_shortTotal


title: CSHL_RnaSeq_MCF-7_cytosol_TAP-Only_shortTotal

value: cytosol

value: The fluid between the cells outer membrane and the nucleus


title: CSHL_RnaSeq_IMR90_nucleus_shortTotal


title: CSHL_RnaSeq_IMR90_nucleus_TAP-Only_shortTotal


title: CSHL_RnaSeq_SK-N-SH_cell_shortTotal

value: immortalized cell line

value: SK-N-SH


title: CSHL_RnaSeq_MCF-7_cytosol_shortTotal

value: Single 101 nt reads


title: CSHL_RnaSeq_A549_cell_CIP-TAP_shortTotal

value: cell

value: CIP-TAP

value: This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs.


title: CSHL_RnaSeq_SK-N-SH_cell_CIP-TAP_shortTotal

value: Whole cell


title: CSHL_RnaSeq_MCF-7_cell_CIP-TAP_shortTotal


title: CSHL_RnaSeq_IMR90_cytosol_TAP-Only_shortTotal


title: CSHL_RnaSeq_IMR90_cytosol_CIP-TAP_shortTotal


title: CSHL_RnaSeq_A549_cytosol_TAP-Only_shortTotal


title: CSHL_RnaSeq_IMR90_nucleus_CIP-TAP_shortTotal

value: nucleus

value: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA


title: CSHL_RnaSeq_SK-N-SH_nucleus_TAP-Only_shortTotal

value: RnaSeq

value: TAP-Only


title: CSHL_RnaSeq_A549_cytosol_CIP-TAP_shortTotal

value: Sequencing analysis of RNA expression


title: CSHL_RnaSeq_SK-N-SH_nucleus_shortTotal

value: shortTotal

value: No special treatment or protocol applies


title: CSHL_RnaSeq_A549_cytosol_shortTotal

value: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation

value: iIDR


title: CSHL_RnaSeq_IMR90_cytosol_shortTotal

value: cytosol

value: The fluid between the cells outer membrane and the nucleus


title: CSHL_RnaSeq_SK-N-SH_cell_TAP-Only_shortTotal

value: immortalized cell line

value: SK-N-SH

value: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.


title: CSHL_RnaSeq_SK-N-SH_cytosol_shortTotal

value: Single 101 nt reads


title: CSHL_RnaSeq_CD34+_Mobilized_cell_TAP-Only_shortTotal


title: CSHL_RnaSeq_A549_nucleus_CIP-TAP_shortTotal

value: CIP-TAP

value: This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs.


title: HEK293 medium

city: Berkeley

first: Nicholas

middle: T

last: Ingolia

email: ingolia@berkeley.edu, nick@ingolia.org

address: 1 Barker Hall # 3202

department: Molecular and Cell Biology

institute: University of California, Berkeley

data_processing:
Basecalling by Casava 1.8.1
Read preprocessing by fastx toolkit 0.0.13
rRNA read alignment by bowtie 0.12.7
Footprint alignment by TopHat 1.2.0
Footprint fragment quantitation using custom scripts
Genome_build: hg19
Supplementary_files_format_and_content: qexpr.txt files contain three columns: 1. A UCSC knownGene identifier; 2. The length of the coding sequence in the gene model, less the 15 codons excluded at the 5' end and the 5 codons excluded at the 3' end; 3. The raw count of footprint reads whose A site maps to the coding sequence in the gene model
Supplementary_files_format_and_content: frame_len.txt files contain one row per footprint length (footprint lengths here are given after 1 nt trimming from the 5' end, this nucleotide is restored in the length and reading frame reported in the manuscript). For each row there are eight columns: 1. The trimmed length; 2. Fraction of all reads at that length; 3. - 5. Number of reads at that length that start on the 1st, 2nd, and 3rd nucleotide of a codon, respectively; 6. - 8. Fraction of reads at that length that start on the 1st, 2nd, and 3rd nucleotide of a codon, respectively

source_name: HEK293 medium

extract_protocol:
Cell extract preparation by detergent lysis, RNase I footprinting of ribosomes, ribosome purification by ultracentrifugation through a sucrose cushion, RNA extraction, polyacrylamide gel size selection for footprint fragments, preadenylylated linker ligation, reverse transcription, first-strand cDNA circularization
library_strategy: Ribosome profiling

tag: cell line

tag: cell type

value: human embryonic kidney


title: HEK293 low

source_name: HEK293 low


title: HEK293 high

source_name: HEK293 high


title: ES_CTCF

status: Public on Jul 25 2012

city: Rotterdam

first: frank

last: sleutels

address: Dr Molewaterplein 50

department: cell biology and genetics

country: Netherlands

institute: ErasmusMC

data_processing:
Sequence reads were obtained and mapped to the mouse MM9 genomes using the Illumina Genome Analyzer Pipeline.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

growth_protocol: CTCFL_V5_GFP transgenic ES cell were grown in ES+LIF medium on gelatin coated plastic

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

treatment_protocol: Cells were induced with doxycyclin during 3 days for CTCFL_V5_GFP expression and sorted for GFP expression or not-induced with doxycyclin and not sorted.

tag: cell

value: embryonic stem

tag: protein

value: CTCF

tag: antibody


title: ES_CTCFL_V5_DOX

value: CTCFL


title: Stanford_RnaSeq_CH12 (superseded by GSE78620)

description:
****************************
GSM973234 record metadata submitted on Jul 24 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78620
****************************

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: cell organism

value: mouse

tag: cell description

value: B-cell lymphoma (GM12878 analog)

value: F

tag: treatment

tag: treatment description

tag: age

value: immortalized

tag: age description

value: Immortal cells

value: Paired 101 nt directed reads

tag: strain

tag: strain description

value: Derived by inbreeding from selected F2 progeny of B10.A X B10.129


title: CSHL_RnaSeq_A549_cell_shortTotal

tag: rnaextract

value: shortTotal

tag: rnaextract description

value: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation

tag: biorep

tag: labexpid

tag: labversion

value: iIDR

tag: readtype

tag: readtype description

value: Single 101 nt reads

tag: replicate

tag: localization

value: cell

tag: localization description

value: Whole cell

tag: protocol

tag: protocol description

value: No special treatment or protocol applies


title: Stanford_RnaSeq_ES-E14 (superseded by GSE90277)

description:
****************************
GSM973235 record metadata submitted on Jul 24 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90277
****************************

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

value: mouse embryonic stem cell line E14

tag: cell sex

value: M

tag: treatment

tag: treatment description

value: Embryonic day 0 (stem cell)

value: The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice.


title: Stanford_RnaSeq_MEL_DMSO_2.0pct (superseded by GSE90279)

description:
****************************
GSM973233 record metadata submitted on Jul 24 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90279
****************************

source_name: MEL

value: RnaSeq

value: Sequencing analysis of RNA expression

value: MEL

value: mouse

value: Leukemia (K562 analog)

value: 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman)

tag: age

value: immortalized

tag: age description

tag: readtype

tag: strain

value: Unknown

tag: strain description

value: Unknown strain origin


title: N9-HD-r1

status: Public on Jul 23 2012

first: Helio

last: Pais

address: Jonh Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

description: Random oligo, 9 nucleotides, HD protocol, replicate 1

data_processing: 3' adapter was trimmed, reads summarized after adapter trimming

organism: synthetic construct

source_name: Random oligo, 9 nucleotides

extract_protocol: For N9 RNA and N21 RNA cloning for NGS approximately 3 and 100 pmoles of oligonucleotide were used respectively. Library preparation was based on the Illumina small RNA v1.5 sample preparation guide. RNA was ligated to the pre-adenylated 3' adapter (custom synthesised by Bioo Scientific) with T4 Rnl2 truncated ligase (NEB). The ligated fragment was then ligated to the 5' adapter (Dharmacon) using T4 Rnl1.  For Illumina protocol recommended adapter sequences were used. For HD protocol four degenerate nucleotides (with uniform probability distribution) were added both to the 5' end of the 3' adapter and to the 3 end of the 5' adapter.  The ligated fragment was then reverse transcribed using the SRA RT primer followed by 8-14 cycles of PCR. The PCR products were size fractionated by polyacrylamide gel electrophoresis (8% PAGE). A band corresponding to approximately 100bp was gel purified and sent for NGS sequencing on a Illumina Genome Analyzer IIx with 50 nt read length (Baseclear).

tag: adapters

value: HD

tag: length

tag: molecule

value: Random oligo, 9 nucleotides


title: N21-HD-r3

description: Random oligo, 21 nucleotides, HD protocol, replicate 3

source_name: Random oligo, 21 nucleotides

value: Random oligo, 21 nucleotides


title: N21-HD-r2

description: Random oligo, 21 nucleotides, HD protocol, replicate 2


title: Mm TN K36me3 b

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

institute: Friedrich Miescher Institute for Biomedical Research

data_processing: 2007 M. musculus genome assembly (mm9) was used as a basis for all analyses. Low-complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). Alignments to the M. musculus genome were performed by the software bowtie (Langmead et al. 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches. The wiggle files are showing the read counts in log2 scale.

source_name: Terminally differentiated Neurons (TN) derived from mouse embryonic stem cells

growth_protocol: Wild-type embryonic stem cells (129Sv-C57Bl/6) were cultured and differentiated as previously described (M. Bibel, J. Richter, E. Lacroix, Y. A. Barde, Nat Protoc 2, 1034 (2007)) and differentiated to Neuronal Progenitors and further to Terminally differentiated Neurons (TN). Mouse embryonic fibroblasts were isolated from wild-type embryos (C57Bl/6).

extract_protocol: ChIP experiments were performed, starting with 50 Âµg of chromatin and 2 Âµg of the following antibody: anti-trimethyl-H3K36 (Abcam, ab9050). The ChIP libraries were prepared with the Illumina ChIP-Seq DNA Sample Prep Kit (Cat# IP-102-1001) according to Illumina's instructions and sequenced on the Genome Analyzer 2 following the manufacturer's protocols.

tag: cell type

tag: chip antibody

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #


title: CENPA_ChIPSeq

city: Durham

first: Karen

middle: Elizabeth

last: Hayden

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences and policy

institute: Duke University

description: Chromatin IP against CENP-A

data_processing:
peak calling:  QuEST (v2.4)
Genome_build: canFam2
Supplementary_files_format_and_content: QuEST results are presented as an unfiltered bed file

organism: Canis lupus familiaris

source_name: Madin-Darby canine cell line (MDCK; ATCC CCL-34)

growth_protocol: Kidney cell–derived canine cells (MDCK, normal adult female cocker spaniel) were routinely generated by re-plating of typically 2–3 × 106 cells into a T75 flask in Eagle’s minimum essential medium with 2mM L-glutamine and Earle’s BSS adjusted to contain 1.5 g/L sodium bicarbonate, 0.1mM non-essential amino acids, and 1.0mM sodium pyruvate, 90%; fetal bovine serum, 10%.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody (monoclonal antibody designed for human CENP-A.  Stressgen; KAM-CC006).  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: breed

value: cocker spaniel

tag: cell line

value: MDCK (Madin-Darby Canine Kidney) cell line

tag: passages

tag: chip antibody details

value: Stressgen, cat# KAM-CC006, lot# 03020605


title: Stanford_RnaSeq_MEL (superseded by GSE90278)

description:
****************************
GSM973232 record metadata submitted on Jul 24 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90278
****************************

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

tag: cell sex

value: M

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

value: Immortal cells

tag: readtype description

value: Paired 101 nt directed reads

tag: replicate


title: CSHL_RnaSeq_SK-N-SH_nucleus_CIP-TAP_shortTotal

value: RnaSeq

value: Sequencing analysis of RNA expression

tag: rnaextract

value: shortTotal

tag: rnaextract description

value: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation

tag: biorep

tag: labexpid

tag: labversion

value: iIDR

tag: readtype

value: Single 101 nt reads

tag: localization

value: nucleus

tag: localization description

value: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA

tag: protocol

value: CIP-TAP

tag: protocol description

value: This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs.


title: Mm ES K36me3 a

source_name: Embryonic Stem (ES) Cells

tag: cell type

value: Embryonic Stem (ES) cells

tag: strain

tag: chip antibody

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #


title: Mm TN K36me3 a

source_name: Terminally differentiated Neurons (TN)  derived from mouse embryonic stem cells


title: Mm NP K36me3 a

source_name: Neuronal progenitor (NP) cells derived from mouse embryonic stem cells


title: Mm NP K36me3 b

value: Neuronal progenitor (NP) cells derived from mouse embryonic stem cells


title: N21-HD-r4

description: Random oligo, 21 nucleotides, HD protocol, replicate 4

tag: adapters

value: HD

tag: length

tag: molecule

value: Random oligo, 21 nucleotides


title: ES_CTCFL_V5_NODOX

tag: cell

value: embryonic stem

tag: protein

value: CTCFL

tag: antibody


title: N21-HD-r1

description: Random oligo, 21 nucleotides, HD protocol, replicate 1


title: N9-Illumina-r1

description: Random oligo, 9 nucleotides, Illumina protocol, replicate 1

value: Illumina

value: Random oligo, 9 nucleotides


title: N21-Illumina-r4

description: Random oligo, 21 nucleotides, Illumina protocol, replicate 4


title: N21-Illumina-r3

description: Random oligo, 21 nucleotides, Illumina protocol, replicate 3


title: N21-Illumina-r2

description: Random oligo, 21 nucleotides, Illumina protocol, replicate 2


title: TN RNA a

extract_protocol: RNA was isolated using Trizol (Invitrogen) following the manufacturer's instructions. Ribosomal RNA was removed using the Ribo-Zero  kit (Epicentre).  Libraries for sequencing were prepared with the Illumina small RNA-Seq Prep Kit (Cat#FC-102-1009) according to Illumina's Directional mRNA-Seq Library Prep. (Pre-Release Protocol Rev.A). The DNA was PCR amplified with Illumina primers for 12 cycles, purified and loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

value: Terminally differentiated Neurons (TN) derived from mouse embryonic stem cells


title: TN RNA b


title: Mouse brain s_7_HCT20919_MoBr-0.1ng

status: Public on Jul 22 2012

city: Stockholm

first: Daniel

last: Ramsköld

address: Nobels väg 3

country: Sweden

institute: Karolinska Institutet

description:
PolyA+ RNA
Mouse brain: Clontech catalog #ST0356.
Mouse brain RNA diluted to 100 pg total RNA.

data_processing:
Alignment by Bowtie (version 0.12.7, option –best) to genome and exon-exon junctions.
Filtering for uniquely mapping reads (removal of reads aligning with same number of mismatches to several coordinates).
Conversion by samtools to bam format.
Conversion by bedtools to bed format.
Generation of RPKM (reads per kilobase and million mapped reads) values by rpkmforgenes.py available at http://sandberg.cmb.ki.se/rnaseq/.
Genome_build: mm9 for mouse; hg19 for human.
Supplementary_files_format_and_content: Bed12 format with uniquely aligned reads.
Supplementary_files_format_and_content: Tab-delimited plain text format with gene expression values in RPKM.

source_name: Brain

extract_protocol: cDNA was generated as described in the manual for "SMARTer Ultra Low RNA Kit for Illumina sequencing" marketed by Clontech. Then, a sequencing library was generated using the Epicentre Nextera sample preparation kit, with 5 min tagmentation at 55C with 0.25 ul transposase and 4 ul 5x HMW Nextera reaction buffer, then 35 ul of PB, then 88 ul SPRI XP beads.

tag: tissue

value: brain


title: Mouse brain mbrNoAmp-s_2

description:
PolyA+ RNA
Mouse brain: Clontech catalog #ST0356.
Mouse brain RNA, no dilution.

extract_protocol: A sequencing library was generated using Illumina's TruSeq RNA sample preparation kit.


title: Mouse brain s_6_HCT20918_MoBr-1ng

description:
PolyA+ RNA
Mouse brain: Clontech catalog #ST0356.
Mouse brain RNA diluted to 1 ng total RNA.


title: N21-Illumina-r1

description: Random oligo, 21 nucleotides, Illumina protocol, replicate 1


title: Mouse brain mbrain_500pg_3

description:
PolyA+ RNA
Mouse brain: Clontech catalog #ST0356.
Mouse brain RNA diluted to 500 pg total RNA.

extract_protocol: cDNA was generated as described in the manual for "SMARTer Ultra Low RNA Kit for Illumina sequencing" marketed by Clontech. Then, a sequencing library was generated as described in Illumina's "Ultra Low Input mRNA-Seq Guide".


title: Mm ES K36me3 b


title: Mouse brain mbrain_500pg_2


title: Mouse brain mbrain_500pg_1


title: Mouse brain mbrain_100pg_3


title: Whitebloodcell_1

description:
PolyA+ RNA
Single leukocyte (note: poor read quality).

source_name: Cell from blood of healthy individual

value: leukocyte from blood of healthy individual


title: Mouse brain mbrain_100pg_1


title: Mouse brain mbrain_100pg_2


title: Mouse brain mbrain_1ng_1


title: Mouse brain 62J01-10pg-18-s_8

description:
PolyA+ RNA
Mouse brain: Clontech catalog #ST0356.
Mouse brain RNA diluted to 10 pg total RNA.


title: Mouse brain 62J01-50pg-16-s_6

description:
PolyA+ RNA
Mouse brain: Clontech catalog #ST0356.
Mouse brain RNA diluted to 50 pg total RNA.


title: Whitebloodcell_3


title: Mouse brain 62J01-10pg-18-s_7


title: Mouse brain 62J01-1ng-12-s_1


title: Mouse brain 62J01-50pg-16-s_5


title: Mouse brain 62HYJ-1ng-18-s_3


title: Mouse brain 62J01-1ng-12-s_2


title: Sjaponicus-wt-sRNA

city: Huddinge

first: Agata

last: Smialowska

address: Halsovagen 7

department: Biosciences and Nutrition

institute: Karolinska Institute

data_processing: Data was analyzed using in-house developed Perl scripts. Read sequences which contained both adapters were retained, the adapter sequences trimmed and the read frequency calculated.

organism: Schizosaccharomyces japonicus

source_name: asynchronous culture

growth_protocol: S. japonicus wt cells were grown on YEA medium

extract_protocol: sRNA libraries were cloned from total, size-selected RNA. RNAs of the size range 40-10 nt were enriched from 40ug of total RNA using flashPAGE (Ambion). The adapters (Small RNA Oligo Only, Illumina) were ligated sequentially using T4 RNA Ligase (Promega). The ligation of the 5' adapter was dependent on the 5'-monophosphate on sRNA and the ligation of the 3' adapter was dependent on the 3'-OH on sRNA. Following ligation of each adapter, reaction products were purified by denaturing 7M urea-PAGE (15% 19:1 acrylamide:bisacrylamide), eluted from the gel slice and precipitated. RNA was reverse-transcribed using Superscript II (Invitrogen) and the library was amplified by PCR using Pfusion Hot Start High Fidelity DNA Polymerase (Finnzymes). PCR products were precipitated and purified by native PAGE.


title: MII_oocyte_CASTEi_2

description:
PolyA+ RNA
Single MII oocyte, from mouse strain CAST/Ei.

source_name: Oocyte

value: CAST/Ei

value: MII oocyte


title: MII_oocyte_CASTEi_3


title: Mouse brain 62HYJ-1ng-12-s_2


title: Mouse brain 62HYJ-1ng-12-s_1


title: Mouse brain 62HYJ-1ng-18-s_4


title: Mouse brain 62HYJ-0.1x1ng-18-s_6

description:
PolyA+ RNA
Mouse brain: Clontech catalog #ST0356.
Mouse brain RNA diluted to 1 ng total RNA, then only 10% of pre-amplification cDNA used.


title: MII_oocyte_CASTEi_1


title: Mouse brain mbrNoAmp-s_1


title: Mouse brain 62HYJ-0.1x1ng-15-s_8


title: Mouse brain 62HYJ-0.1x1ng-18-s_5


title: UR6_wildtype

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

data_processing:
Reads were created by CASAVA 1.7 from the GA Iix and HiSeq2000, and these are all reads which pass filter
Reads were filtered from the adapter sequences using FAR software (Dodt, M, Ahmed R, Dieterich C. FAR – flexible adapter remover. FAR project website (2011)( http://sourceforge.net/projects/theflexibleadap/).
Reads were aligned to whole genome using the bismark(http://www.bioinformatics.babraham.ac.uk/projects/bismark/) alignment tool with a maximum of 2 mismatches in a directional manner and only uniquely aligning reads were retained.
In order to call methylation score for a base position, we required that read bases aligning to that position have at least 20 phred quality score and the base position should have at least 10X coverage. Only CpG dinucleotides that satisfy these coverage and quality criteria were retained for subsequent analysis. *myCpG.txt files are constructed for each CpG position in the genome. The file contains location of the CpG, total read coverage on the C base, percentage of bisulfite converted Cs (representing unmethylated Cs) and non-converted Cs (representing methylated Cs). The pipeline that aligns and calls for methylation percentage per base is available at http://code.google.com/p/amp-errbs
Genome_build: mm9
Supplementary_files_format_and_content: myCpG.txt = tab delimited file with the following column heades: chrBase chr base strand coverage freqC freqT

source_name: LSK_wild type

extract_protocol:
ERRBS (Extended Reduced Representation Bisulfite Sequencing) libraries were constructed as following:
i) 5ng of genomic DNA were digested with 200 U of MspI (New England Biolabs, NEB) in a 100µl reaction for up to 16 hours at 37C. DNA was isolated using standard phenol chloroform extraction and ethanol precipitation and resuspended into 30µl of 10mM TrIs pH 8.0. ii) End repair of digested DNA was performed in a 100µl reaction using 15U of T4 DNA polymerase (NEB M0203L), 5U of Klenow DNA polymerase (NEB M0210L), 50U of T4 Polynucleotide Kinase (NEB M0201L), 4µl of premixed nucleotide triphosphates each at 10mM (NEB N0447L) using T4 DNA ligase buffer with 10mM dATP (NEB B0202S). The reaction was incubated at 20C for 30 minutes and products were isolated using QIAquick PCR purification columns per manufacturer’s recommended protocol (Qiagen) into 32µl of EB buffer.  iii) Adenylation was performed in a 50µl reaction using 15U Klenow fragment (3’ to 5’ exo minus, NEB M0212L), 10µl of dATP at 1mM concentration using Klenow buffer (NEB).  The reaction was incubated at 37 oC for 30 minutes and products were isolated using MinElute PCR purification columns per manufacturer’s recommended protocol (Qiagen) into 10µl EB buffer.  iv) Adenylated DNA fragments were ligated with pre-annealed 5-methylcytosine-containing Illumina adapters in a 20 µl reaction using 2000U T4 DNA ligase (NEB M0202T) and 1.2µM final concentration of methylated adapters at 16oC for a minimum of 16 hours. Products were isolated using MinElute columns per manufacturer’s recommended protocol (Qiagen) into 10µl EB buffer.  v) Library fragments 150-250bp and 250-400bp were gel isolated from a 1.5% agarose gel using the Qiaquick Gel Extraction kit per manufacturer’s recommended protocol (Qiagen) into 40µl EB buffer.  vi) bisulfite treatment was performed using the EZ DNA Methylation Kit (Zymo Research) per manufacturer’s recommended protocol with the following modifications: 1) incubation after the addition of CT conversion reagent was conducted in a thermocycler (Mastercycler  ep gradient, Eppendorf) with the following conditions: 30 seconds at 95C followed by 15 minutes at 50C for 55 cycles and, 2) products were eluted into 40µl nuclease free water.  vii) PCR amplification for each library was performed in a 200µl reaction containing 2µl FastStart Hifidelity DNA Polymerase (Roche), 0.5µM each of Illumina PCR primers PE1.0 and 2.0, 0.25mM each nucleotide triphosphate using buffer 2 per manufacturer’s recommendation and divided into four 50µl reactions.  The thermocycler conditions were: 5 minutes at 94C, 18 cycles of 20 seconds at 94C, 30 seconds at 65C, 1 minutes at 72C, followed by 3 minutes at 72C.  PCR products were isolated using AMPure XP beads per manufacturer’s recommended protocol (Agencort) into 50µl of EB buffer. viii) All amplified libraries underwent quality control steps including using Qubit 1.0 fluorometer and a Quant-iT dsDNA HS Assay Kit for quantitation (Invitrogen) and bioanalyzer visualization (Agilent 2100 Bioanalyzer).

tag: strain background

value: 129Ola x C57Bl/6J

tag: genotype/variation

value: Wild-type

tag: tissue source

value: Bone marrow

value: Hematopoietic cells Lin- Sca1+ Kit+


title: UR16_Idh1-R132H

source_name: LSK_Idh1-R132H Knock-in

value: Idh1-R132H Knock-in


title: UR18_wildtype


title: Mouse brain 62J01-0.1ng-15-s_4


title: Mouse brain 62J01-0.1ng-15-s_3


title: Mouse brain 62HYJ-0.1x1ng-15-s_7


title: Mouse brain 62HWT-10ng-12-s_2

description:
PolyA+ RNA
Mouse brain: Clontech catalog #ST0356.
Mouse brain RNA diluted to 10 ng total RNA.


title: Mouse brain 62HWT-10ng-12-s_1


title: Universal human reference RNA s_8_HCT21016-UHR-10pg

description:
PolyA+ RNA
Universal Human Reference RNA: Stratagene catalog #740000.
Universal human reference RNA diluted to 10 pg total RNA.

source_name: Universal human reference RNA

tag: sample type

value: universal human reference RNA


title: Universal human reference RNA s_8_HCT21024-UHR-10pg


title: Universal human reference RNA s_7_HCT21023-UHR-10pg


title: UR9_Idh1-R132H


title: Universal human reference RNA s_6_HCT21022-UHR-10pg


title: Universal human reference RNA s_4_HCT21012-UHR-100pg

description:
PolyA+ RNA
Universal Human Reference RNA: Stratagene catalog #740000.
Universal human reference RNA diluted to 100 pg total RNA.


title: Universal human reference RNA s_7_HCT21015-UHR-10pg


title: Universal human reference RNA s_5_HCT21021-UHR-10pg


title: Universal human reference RNA s_7_HCT21007-UHR-1ng

description:
PolyA+ RNA
Universal Human Reference RNA: Stratagene catalog #740000.
Universal human reference RNA diluted to 1 ng total RNA.


title: Universal human reference RNA s_4_HCT21004-UHR-10ng

description:
PolyA+ RNA
Universal Human Reference RNA: Stratagene catalog #740000.
Universal human reference RNA diluted to 10 ng total RNA.


title: Universal human reference RNA s_3_HCT21011-UHR-100pg


title: Universal human reference RNA HCT20412-UHR0.01ng


title: Universal human reference RNA s_3_HCT21003-UHR-10ng


title: Universal human reference RNA HCT20410-UHR1ng


title: Mouse brain mbrain_1ng_2


title: Universal human reference RNA HCT20321-UHR0.01ng


title: Universal human reference RNA HCT20323-UHR0.01ng


title: Universal human reference RNA HCT20320-UHR0.01ng


title: UACC257_cell2

description:
PolyA+ RNA
Single cell from the melanoma cell line UACC257.

source_name: UACC257 cell

tag: cell line


title: T24 s5_HCT20631-T24-14

description:
PolyA+ RNA
Single cell from the bladder cancer cell line T24.

source_name: T24 cell


title: UR12_Idh1-R132H

tag: cell type


title: UACC257_cell1


title: Universal human reference RNA HCT20322-UHR0.01ng


title: T24 s6_HCT20632-T24-14


title: UACC257_cell3


title: Universal human reference RNA s_8_HCT21008-UHR-1ng


title: T24 s3-HCT20637-T24-15


title: T24 s4-HCT20638-t24-15


title: Melanocyte HCT21026_pm

description:
PolyA+ RNA
Single melanocyte.

source_name: Primary melanocyte

value: primary melanocyte


title: Universal human reference RNA HCT20411-UHR0.1ng


title: SKMEL5_cell1

description:
PolyA+ RNA
Single cell from the melanoma cell line SKMEL5.

source_name: SKMEL5 cell


title: Melanocyte HCT21025_pm

description:
PolyA+ RNA
Single melanocyte.


title: Universal human reference RNA HCT20325-UHR0.01ng


title: PC3 s2-HCT20636-PC3-15

description:
PolyA+ RNA
Single cell from the prostate cancer cell line PC3.

source_name: PC3 cell


title: PC3 s3_HCT20629-pc3-14


title: SKMEL5_cell4


title: SKMEL5_cell2


title: SKMEL5_cell3


title: PC3 s4_HCT20630-PC3-14


title: Circulating melanoma cell HCT21032_CTC

description:
PolyA+ RNA
Single circulating tumour cell from blood of a melanoma patient.

source_name: NG2-sorted cell from blood

value: NG2-sorted cell from blood of melanoma patient


title: Circulating melanoma cell HCT21029_CTC


title: Circulating melanoma cell HCT21030_CTC


title: Circulating melanoma cell HCT21028_CTC


title: LNCaP s_8_25c

description:
PolyA+ RNA
25 cells from the prostate cancer cell line LNCaP, spiked into blood and picked by EPCAM marker.

source_name: LNCaP cells

value: LNCaP


title: LNCaP s_7_HCT20883_25c

description:
PolyA+ RNA
25 cells from the prostate cancer cell line LNCaP.


title: Circulating melanoma cell HCT21027_CTC


title: LNCaP s_5_HCT20881_10c

description:
PolyA+ RNA
10 cells from the prostate cancer cell line LNCaP.


title: LNCaP s_4_HCT20880_10c


title: LNCaP s_6_HCT20882_25c


title: LNCaP s_7_25c


title: LNCaP s_6_10c

description:
PolyA+ RNA
10 cells from the prostate cancer cell line LNCaP, spiked into blood and picked by EPCAM marker.


title: LNCaP s_5_10c


title: LNCaP s_3_HCT20878_5c

description:
PolyA+ RNA
5 cells from the prostate cancer cell line LNCaP.


title: LNCaP s_4_5c

description:
PolyA+ RNA
5 cells from the prostate cancer cell line LNCaP, spiked into blood and picked by EPCAM marker.


title: LNCaP s1_HCT20627-Lncap-14

description:
PolyA+ RNA
Single cell from the prostate cancer cell line LNCaP.

source_name: LNCaP cell


title: LNCaP s_2_1c

description:
PolyA+ RNA
Single cell from the prostate cancer cell line LNCaP, spiked into blood and picked by EPCAM marker.


title: cell8_hESC

description:
PolyA+ RNA
Single human embryonic stem cell.

source_name: Embryonic stem cell

value: embryonic stem cell


title: LNCaP s8_HCT20634-Lncap-15


title: LNCaP s_1_1c


title: PC3 s1-HCT20635-PC3-15


title: cell5_hESC


title: LNCaP s_3_5c


title: Circulating melanoma cell HCT21031_CTC


title: LNCaP s_2_HCT20877_3c

description:
PolyA+ RNA
3 cells from the prostate cancer cell line LNCaP.


title: LNCaP s2_HCT20628-Lncap-14


title: LNCaP s_1_HCT20876_3c


title: cell7_hESC


title: Human brain s_4_HCT21020-BR-10pg

description:
PolyA+ RNA
Human Brain Reference RNA: Ambion catalog #AM6051.
Human reference brain RNA diluted to 10 pg total RNA.

value: human reference brain RNA


title: Human brain s_2_HCT21002-BR-10ng

description:
PolyA+ RNA
Human Brain Reference RNA: Ambion catalog #AM6051.
Human reference brain RNA diluted to 10 ng total RNA.


title: Human brain s_2_HCT21010-BR-100pg

description:
PolyA+ RNA
Human Brain Reference RNA: Ambion catalog #AM6051.
Human reference brain RNA diluted to 100 pg total RNA.


title: cell6_hESC


title: Human brain s_5_HCT21005-BR-1ng

description:
PolyA+ RNA
Human Brain Reference RNA: Ambion catalog #AM6051.
Human reference brain RNA diluted to 1 ng total RNA.


title: cell3_hESC


title: Human brain s_5_HCT21013-BR-10pg


title: Human brain s_3_HCT21019-BR-10pg


title: cell2_hESC


title: Human brain s_6_HCT21006-BR-1ng


title: Human brain s_1_HCT21009-BR-100pg


title: Human brain HCT20424-BR0.1ng


title: Human brain s_1_HCT21017-BR-10pg


title: Human brain HCT20413-BR1ng


title: Human brain HCT20422-BR0.1ng


title: Human brain HCT20423-BR0.01ng


title: LNCaP s7_HCT20633-Lncap-15


title: cell1_hESC


title: cell4_hESC


title: Human brain HCT20421-BR1ng


title: HL1 Day4 Rep2

status: Public on Jul 21 2012

city: Acton

first: Hardip

middle: Rameshbhai

last: Patel

state: Australian Capital Territory

address: Bld 131, ANU Campus,

department: Genome Biology Department

country: Australia

institute: The Australian National University

data_processing:
The SOLiD™ Small RNA Pipeline was used to map tags to miRBase version 16 and the mouse genome (mm37 assembly).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw tag count for each sequence observed

source_name: HL1 Cardiomyocyte cells

extract_protocol: Total RNA was prepared from HL-1 cultures using the TRIzol® reagent. Small RNA <70 nt was enriched by flashPAGE™ electrophoresis. Libraries were created with the SOLiD™ Small RNA Expression Kit and sequenced using SOLiD™ version 2 reagents.

tag: time

value: 4 days in culture


title: HL1 Day1 Rep1

value: 1 day in culture


title: HL1 Day4 Rep1


title: HL1 Day1 Rep2


title: HL1 Day3 Rep1

value: 3 days in culture


title: HL1 Day3 Rep2


title: Human brain s_1_HCT21001-BR-10ng

source_name: Brain

value: brain


title: UW_RnaSeq_Liver_E14.5_C57BL/6

status: Public on Jul 20 2012

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

source_name: Liver

tag: lab

value: UW-m

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

value: Liver

tag: cell organism

value: mouse

tag: cell description

tag: cell sex

value: M

tag: age

tag: age description

value: Embryonic day 14.5

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse

tag: labversion

value: coverage

tag: readtype

tag: readtype description

value: Single 50 nt reads

tag: replicate


title: UW_RnaSeq_Lung_adult-8wks_C57BL/6

source_name: Lung

tag: cell

value: Lung

value: Adult 8 weeks


title: UW_RnaSeq_GenitalFatPad_adult-8wks_C57BL/6

source_name: GenitalFatPad

value: GenitalFatPad

value: Genital Adipose tissue


title: UW_RnaSeq_MEL_adult-8wks_Unknown

source_name: MEL

value: MEL

value: Leukemia (K562 analog)

value: Unknown

value: Unknown strain origin


title: UW_RnaSeq_B-cell_(CD43-)_adult-8wks_C57BL/6

value: UW-m

value: Stamatoyannopoulous - University of Washington

value: RnaSeq

value: mouse spleen B cells, CD43-,CD11b-


title: UW_RnaSeq_Patski_immortalized_Spretus.BL6-Xist

source_name: Patski

value: Sequencing analysis of RNA expression

value: Patski

value: mouse

value: Mouse Embryonic Kidney Fibroblast. As described in Lingenfelter et al., 1998 (Nat Genet. 1998 18:212-3) and Yang et al., 2010 (Genome Res.  2010 20:614-22), PATSKI is a female interspecific mouse fibroblast that was derived from the embryonic  kidney of an M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is  always the inactive X. This is an adherent cell line.

value: F

value: immortalized

value: Immortal cells


title: UW_RnaSeq_LgIntestine_adult-8wks_C57BL/6

source_name: LgIntestine

value: LgIntestine

value: Large Intestine

value: M

value: Adult 8 weeks

value: C57 black 6, the most common inbred strain of laboratory mouse

value: coverage

value: Single 50 nt reads


title: Human brain s_6_HCT21014-BR-10pg

tag: tissue

value: brain

tag: sample type

value: human reference brain RNA


title: UW_RnaSeq_WholeBrain_E14.5_C57BL/6

source_name: WholeBrain

tag: lab

value: UW-m

tag: lab description

value: Stamatoyannopoulous - University of Washington

value: RnaSeq

value: WholeBrain

value: Whole Brain

value: Embryonic day 14.5


title: UW_RnaSeq_Spleen_adult-8wks_C57BL/6

source_name: Spleen

tag: datatype

tag: datatype description

value: Sequencing analysis of RNA expression

value: Spleen

value: mouse


title: UW_RnaSeq_Liver_adult-8wks_C57BL/6

value: Liver

tag: cell organism

tag: cell description


title: UW_RnaSeq_Heart_adult-8wks_C57BL/6

source_name: Heart

value: Heart

tag: cell sex

value: M

tag: age


title: UW_RnaSeq_Cerebrum_adult-8wks_C57BL/6

source_name: Cerebrum

value: Cerebrum

tag: age description

value: Adult 8 weeks

tag: strain

value: C57 black 6, the most common inbred strain of laboratory mouse


title: UW_RnaSeq_Cerebellum_adult-8wks_C57BL/6

source_name: Cerebellum

value: Cerebellum

tag: strain description

tag: labversion

value: coverage

value: Single 50 nt reads


title: UW_RnaSeq_B-cell_(CD19+)_adult-8wks_C57BL/6

value: UW-m

value: Stamatoyannopoulous - University of Washington

value: B Cell , CD19+

tag: readtype

tag: readtype description


title: UW_RnaSeq_HeadlessEmbryo_E11.5_CD-1

source_name: HeadlessEmbryo

value: RnaSeq

tag: cell

value: HeadlessEmbryo

value: Whole embryos with heads removed

value: Embryonic day 11.5

value: Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy.

tag: replicate


title: UW_RnaSeq_FatPad_adult-8wks_C57BL/6

source_name: FatPad

value: Sequencing analysis of RNA expression

value: FatPad

value: mouse

value: Adipose tissue


title: UW_RnaSeq_T-Naive_adult-8wks_C57BL/6

source_name: T-Naive

value: T-Naive

value: Naive T cells:CD4+, CD25-

value: M

value: Adult 8 weeks


title: UW_RnaSeq_416B_immortalized_B6D2F1/J

value: myeloid progenitor cells, CD34+

value: immortalized

value: Immortal cells

value: Derived from cross between C57BL/6J Female x DBA/2J Male (C57BL/6xDBA/2)F1.

value: coverage

value: Single 50 nt reads


title: UW_RnaSeq_A20_immortalized_BALB/cAnN

value: UW-m

value: Stamatoyannopoulous - University of Washington

value: RnaSeq

value: B cell lymphoma line derived from a spontaneous reticulum cell neoplasm

value: BALB/cAnN

value: ccMyeloma high incidence H2d


title: UW_RnaSeq_Kidney_adult-8wks_C57BL/6

source_name: Kidney

value: Sequencing analysis of RNA expression

value: Kidney

value: mouse

value: C57 black 6, the most common inbred strain of laboratory mouse


title: HL1 Day2 Rep2

source_name: HL1 Cardiomyocyte cells

tag: cell line

tag: time

value: 2 days in culture


title: Miwi S8

city: Wilmington

first: Qi

last: Zheng

state: DE

address: 1701 Rockland Road

institute: Nemours Children's Health

description: Miwi CLIP RNA tag from mouse testis

data_processing:
HITS-CLIP raw reads were processed using a balanced pipeline as described in Zheng, Q. et al. 2010, which can retain reads both with recognizable 3ˊ-adapters (trimmed) or not (untrimmed); up to 8% of mismatches were allowed in the 3ˊ-adapter sequences. Both trimmed and untrimmed reads were reduced to non-redundant (NR) sequences first prior to the mapping step to decrease the computation efforts required in this study. We will use the term “reads” and “NR sequences” interchangeably hereafter. All reads were mapped to mouse genome (UCSC mm9 assembly) as described in the pipeline with up to 6% mismatches. We set the mismatch criteria differently for reads (6%) and for 3ˊ-adapters (8%) intentionally, as the sequencing quality is usually worse toward the 3ˊ-end of raw reads. Besides, all the mismatch criteria were carefully set according to the average base-wise quality checking (QC) result of all libraries (data not shown). At last, genome mapping loci as well as clone-abundance information was combined for trimmed and untrimmed reads for each library, and loaded into local MySQL database for further queries.
barcode (3'-adapter sequence): gtgtcagtcacttccagcggtcgtatgccgtcttctgcttg
GSMxxx_NR_mm9_loc_class.txt: alignment coordinates for all mapped Non-Redundant sequence (NR-seq) on mouse genome (UCSC mm9 assembly)
GSMxxx_mapped_NR_info.txt:  mapped NR-seq information
GSMxxx_mapped_NR_seq_fas.txt: mapped NR-seq after trimming of 3'-adapters

source_name: testis from adult mice

extract_protocol: HITS-CLIP was performed in biological replicates using anti-Mili mouse monoclonal antibody (17-8, described in Kirino, Y. et al. 2009, Nat Cell Biol), and anti-Miwi affinity-purified rabbit polyclonal (described in Kirino, Y. et al. 2010 RNA), following the method developed by Darnell and coworkers (Chi, S. W. et al. 2009 Nature) with modifications, as described in supplementary methods.

tag: antibody

value: Our own rabbit polyclonal anti-Miwi antibody described in (Kirino, Y et al. 2010, RNA)

tag: antibody vendor

value: our own antibody

tag: clip tag enrichment

value: large CLIP tags


title: UW_RnaSeq_Liver_E14.5_129

source_name: Liver

tag: lab

tag: lab description

tag: datatype

tag: datatype description

value: Liver

tag: cell organism

value: M

value: Embryonic day 14.5

value: Strain 129, has widely available embryonic stem cells


title: UW_RnaSeq_Thymus_adult-8wks_C57BL/6

source_name: Thymus

value: UW-m

value: Stamatoyannopoulous - University of Washington

value: Thymus

tag: cell description

tag: cell sex

tag: age

tag: age description

value: Adult 8 weeks

tag: strain

value: coverage

value: Single 50 nt reads


title: Miwi S6

description: Miwi CLIP RNA tag from mouse testis


title: Miwi S2

description: Miwi CLIP RNA tag from mouse testis


title: Miwi S1

description: Miwi CLIP RNA tag from mouse testis

value: piRNA


title: Mili S3

description: Mili CLIP RNA tag from mouse testis

extract_protocol: HITS-CLIP was performed in biological replicates using anti-Mili mouse monoclonal antibody (17-8, described in Kirino, Y. et al. 2009, Nat Cell Biol), and anti-Miwi affinity-purified rabbit polyclonal (described in Kirino, Y. et al. 2010, RNA), following the method developed by Darnell and coworkers (Chi, S. W. et al. 2009 Nature) with modifications, as described in supplementary methods.

value: anti-mili 17-8 mouse monoclonal Ab, ascites fluid

value: our own antibody (described in Kirino et al 2009, Nat Cell Biol)


title: Mili S5

description: Mili CLIP RNA tag from mouse testis


title: Mili S6

description: Mili CLIP RNA tag from mouse testis


title: UW_RnaSeq_WholeBrain_E18.5_C57BL/6

value: RnaSeq

value: Sequencing analysis of RNA expression

tag: cell

value: WholeBrain

value: mouse

value: Whole Brain

value: Embryonic day 18.5

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse

tag: labversion

tag: readtype

tag: readtype description


title: UW_RnaSeq_SkMuscle_adult-8wks_C57BL/6

source_name: SkMuscle

value: SkMuscle

value: Skeletal Muscle

value: M

tag: replicate


title: Mili S1

description: Mili CLIP RNA tag from mouse testis

tag: antibody

tag: antibody vendor

tag: clip tag enrichment


title: 14d_testis_S2

description: total RNA from mouse testis

data_processing:
RNA-seq raw reads were processed using a balanced pipeline as described in Zheng, Q. et al. 2010, which can retain reads both with recognizable 3ˊ-adapters (trimmed) or not (untrimmed); up to 8% of mismatches were allowed in the 3'-adapter sequences. Both trimmed and untrimmed reads were reduced to non-redundant (NR) sequences first prior to the mapping step to decrease the computation efforts required in this study. We will use the term “reads” and “NR sequences” interchangeably hereafter. All reads were mapped to mouse genome (UCSC mm9 assembly) as described in the pipeline with up to 6% mismatches. We set the mismatch criteria differently for reads (6%) and for 3'-adapters (8%) intentionally, as the sequencing quality is usually worse toward the 3'-end of raw reads. Besides, all the mismatch criteria were carefully set according to the average base-wise quality checking (QC) result of all libraries (data not shown). At last, genome mapping loci as well as clone-abundance information was combined for trimmed and untrimmed reads for each library, and loaded into local MySQL database for further queries.
barcode (3'-adapter sequence): gtgtcagtcacttccagcggtcgtatgccgtcttctgcttg
GSMxxx_NR_mm9_loc.txt: alignment coordinates for all mapped Non-Redundant sequence (NR-seq) on mouse genome (UCSC mm9 assembly)
GSMxxx_mapped_NR_seq_fas.txt: mapped NR-seq after trimming of 3'-adapters
GSMxxx_mapped_NR_info.txt: mapped NR-seq information

source_name: testis

extract_protocol: Total RNA was isolated from mouse testes using Trizol reagent, and was depleted from ribosomal RNA using the RiboMinus Eukaryote Kit for RNA-Seq (Invitrogen A10837). RiboMinus RNA was fragmented using metal ion hydrolysis (Ambion AM8740) and was ligated with 3´-adapter , which carries a biotin group at the 3´-end. Ligated RNA was selected using Streptavidin beads prior to 5´-adapter ligation, then reverse transcribed and amplified. cDNA was size selected on Metaphore gels, extracted, and subjected to Illumina sequencing.

value: Swiss-Webster

tag: postnatal time-point

value: 14 dpp

tag: enriched spermatogenesis stage

value: pachytene spermatocytes


title: 6d_testis_S1

description: total RNA from mouse testis

value: 6 dpp

value: spermatogonia


title: 30d_testis_S5

description: total RNA from mouse testis

value: 30 dpp

value: elongating spermatids


title: adult_testis_S7

description: total RNA from mouse testis

value: adult

value: mixture of all stages


title: adult_testis_S6

description: total RNA from mouse testis


title: 21d_testis_S3

description: total RNA from mouse testis

value: 21 dpp

value: haploid round spermatids


title: IgG_for_CTCF_SMC1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Mouse IgG_ChIPSeq

data_processing:
Illumina Genome Analyzer II
Alignment: Alignment was performed using Bowtie software on both human HG18 genome downloaded from ucsc browser site and  viral genome HQ404500BAC36 with 35 repeat added to terminal.
Wiggle files were created using moving average of raw reads at each base. Peaks were identified on wiggle profile based on Mathematical maxima in local regions.
Genome_build: HQ404500BAC36 with 35 repeat added to terminal
Supplementary_files_format_and_content: WIG: Single-column UCSC Wiggle file format.
Supplementary_files_format_and_content: BED: Six-column peak bed format.

source_name: BCBL1 pleural effusion lymphoma, IgG ChIP

growth_protocol: BCBL1 cells grown to 1x106 cells/ml in RPMI with 10% FBS supplemented with Glutamax and Penn/Strep

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

treatment_protocol: According to the publication " Chromatin immunoprecipitation and microawway-based analysis of protein location" from the Natural Protocol.

tag: cell line

tag: cell type

value: KSHV-infected pleural effusion lymphoma cells

tag: chip antibody

value: Mouse IgG [Santa Cruz, Cat#2025, Lot#B1710]


title: UMass-Dekker_5C_HeLa-S3

status: Public on Jul 19 2012

extract_protocol:
Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUmassDekker5C
library_strategy: 5C (Chromatin Conformation Capture Carbon Copy)

tag: lab

value: UMass-Dekker

tag: lab description

value: Dekker - University of Massachusettes

tag: datatype

tag: datatype description

value: 5C Chromatin Interactions

tag: cell organism

value: human

tag: cell description

value: cervical carcinoma

tag: cell karyotype

value: cancer

tag: cell lineage

value: ectoderm

tag: cell sex

value: F

tag: region

value: ENM

tag: region description

value: ENCODE pilot manually-selected regions (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/referenceSequences/encodePilotRegions.hg19.bed)


title: UMass-Dekker_5C_H1-hESC

tag: cell

value: embryonic stem cells

value: normal

value: inner cell mass

value: M

tag: replicate


title: IgG_for_KSHV_LANA

description: Rabbit IgG_ChIPSeq

value: Rabbit IgG [Santa Cruz, Cat#sc-2027, Lot#12310]


title: UW_RnaSeq_NIH-3T3_immortalized_NIH/Swiss

value: UW-m

value: Stamatoyannopoulous - University of Washington

value: RnaSeq

value: Sequencing analysis of RNA expression

value: mouse

value: fibroblast

tag: age

value: immortalized

tag: age description

value: Immortal cells

tag: strain

value: NIH/Swiss

tag: strain description

value: An outbred Swiss mouse  used as a general-purpose stock. Used extensively for pertussis HSF testing.

tag: labversion

value: coverage

tag: readtype

tag: readtype description

value: Single 50 nt reads