title: 1182-4H V147/BS22 (Celniker/RNA:37) rep2 extraction2_seq1 aliquote 1

status: Public on Aug 06 2012

data_processing: sequence analysis protocol. 1. 3' adapter sequences starting with 'CTGTAGG' were mapped and trimmed, allowing 2 mismatches when starting from base 20 in a read. Only reads with recognized 3' adapter and longer than 18 bases were considered in further analysis.2. The trimmed sequences were mapped to genome by BLAT. only sequences can perfectly match to genome were acceptable.  Processed data are obtained using following parameters: genome version is 5

source_name: 1182-4H cell small ncRNA RNA-Seq

extract_protocol:
Protocol for isolation of total RNA from cell cultures, which retains short RNAs.
mRNAs were purified from total RNA extracts, using standard Illumina protocol.  Briefly, 10ug total RNA was bound to oligo(dT) beads, washed twice, and eluted with 10mM Tris-HCl, using Ambion kit.
[A] Gel purification of RNA sample.  1. Spike 50 ug of total RNA with 32P-labeled 19bp and 24bp oligos (~10,000 counts per second) and load the sample in a 15% polyacrylamide/urea gel (Sequagel, National Diagnostics). Run the gel in 1x TBE at constant 10W for 1-2 hours. Expose the gel for 10 minutes in Phosphoimager.  2. Excise the band corresponding to the desired size of small RNA (~19-24 nt) into Eppendorf tubes, including the radio-labeled oligos. Add 400uL of 0.4M NaCl. Freeze rapidly in dry ice. Incubate (thaw) for 16 hours at room temperature with agitation to maximize RNA elution.  3. Spin down gel slice homogenate through micropore filter (Ultrafree-MC, 0.22um, Millipore) for 1 minute at room temperature. Add 20ug of glycogen and 2 volumes of 100% Ethanol (RNase-free). Incubate at -20oC for 4 hours.  4. Spin the sample at 4oC for 30 minutes. Wash the pellet with 70% EtOH, air dry for 2 min and resuspend in DEPC MQ water and proceed to section B. [B] 3'-linker ligation and gel purification of the ligated RNA product.  5. Ligate 50 pmol of Modban oligo (IDT:miRNA cloning linker 1) to the 3' terminus of the purified RNA sample in 1X ATP-free T4 RNA ligase buffer (50mM Tris-HCl (pH 7.5-7.6), 10mM MgCl2, 10mM DTT, 60ug/mL BSA) and 10% DMSO, with 5-10 pmol of T4 RNA ligase 2 Rnl2(1-249) (Ho et al, 2004). Incubate at room temperature for 1 hour 30 min.  6. Load the sample on a 15% polyacrylamide/urea gel as described above and expose the gel for 30 minutes.  7. Excise the band corresponding to the desired size of small RNA (~36-41 nt) into Eppendorf tubes, including the ligated radio-labeled oligos.  8. Proceed again with overnight elution and precipitation as in steps 2-4. [C] 5'-linker ligation and gel purification of the ligated RNA product.  9. Ligate 50 pmol of Solexa linker to the 5' terminus of the RNA sample in 1XT4 RNA ligase buffer (Ambion) and 10% DMSO with 5-10 Units of T4 RNA ligase (Ambion). Incubate at 37oC for 1 hour 30 min.  10. Load the sample on a 15% polyacrylamide/urea gel as described above and expose the gel for 1 hour.  11. Excise the band corresponding to the desired size of small RNA (~68-73 nt) into Eppendorf tubes, including the ligated radio-labeled oligos.  12. Proceed again with overnight elution and precipitation as in steps 2-4.  [D] Reverse transcription and cDNA amplification.  13. Reverse-transcribe the ligated RNA product by using 21 pmol of BanOne primer and 1 ul Superscript III Reverse Transcriptase (Invitrogen), for 1 hour at 50oC in 20 ul of reaction. Then, amplify 5 ul of the cDNA product with 100 pmol of primers Sol_5_SBS3 and Sol_3_Modban, and 5 Units of Taq Polymerase (New England Biolabs): [94oC 15 sec; 54oC 30 sec; 72oC 30 sec] x 5 cycles and [94oC 15 sec; 60oC 30 sec; 72oC 30 sec] x 17 cycles.  14. Clean up the PCR product with phenol:chloroform and chloroform. Precipitate the amplified cDNA with Ethanol 100%.  [E] Digestion of the spikes and gel-purification of the amplified cDNA.  15. Perform PmeI (New England Biolabs) digestion of radiolabeled oligos (spikes) for 3-4 hours at 37oC and purify the amplified cDNA in a 2% low-melt agarose gel (SeaKem).  16. Excise the ~ 120 bp DNA band and proceed to hot-phenol-based gel purification. Transfer aqueous phase to a new eppendorf tube and clean up with phenol:chloroform and chloroform. Precipitate the DNA with Ethanol 100% and resuspend it in 20uL water.  17. Perform Agilent test and dilute the sample to 10nM for Solexa sequencing.
1. cluster generation  2. the length of short reads, i.e., the number of sequencing cycles, should list here. in this protocol, it is 35 cycles of sequencing.  3. after each cycle, a CCD camera will scan the cells to make a image.

value: embryo-derived cell-line

value: late embryonic stage

value: mh

tag: Sex

value: Unknown


title: Pol2-S5P_Day2+8h_ChIP-Seq

status: Public on Aug 07 2012

type: SRA

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

country: USA

institute: Penn State University

description: Chromatin IP against Pol2-S5P

library_source: genomic

data_processing:
Alignment: Sequence reads were aligned to the mouse genome (version mm8) using Bowtie (Langmead et al Genome Biology 2009) version 0.9.9.2 with options -k 2 --best. Only uniquely mapping reads were analyzed further. Multiple hits aligning to the same nucleotide position are discarded above the level expected at a 10^-7 probability from a per-base Poisson model of the uniquely mappable portion of the mouse genome. In practice, this caps the number of hits that start at the same nucleotide to 3 in the RAR ChIP-seq experiments.
Peaks: Binding event detection is carried out using a customized methodology named SEEDS (Sequencing Experiment Event Detection Statistics) that uses statistical significance testing to find regions producing an over-abundance of sequenced reads in the signal experiments compared with the control. The algorithm is run twice across the data. The first pass estimates a scaling factor for control sequencing read depth and a model of the distribution of sequencing read alignment hits around binding events. The second pass applies these parameters to predict a final set of significant events. Before the first pass, the scaling factor is initialized to be the ratio of total hit counts between the signal and control channels. The binding distribution model is initialized to be an empirical distribution estimated around predicted binding events in Oct4 ChIP-seq data (Marson, et al. Cell 2008). All alignment hits are extended in both 3’ and 5’ directions, mirroring the observed distribution of hits around binding events. The extension magnitudes are set equal to the positions where the binding model distribution intersects a uniform distribution over the same area. Control channel hit counts are scaled using the signal-control scaling factor. A sliding window of bin width 50bp and offset 25bp is run over the genome. Overlapping extended hit counts are calculated for both the signal and (scaled) control channels. The background distribution of ChIP-seq hits is modeled as a non-homogenous Poisson process with parameters estimated from the scaled control hit counts. Specifically, the Poisson parameter is chosen as the maximum mean overlapping hit count in 50bp windows of those observed from i) the entire genome, ii) a 5Kbp window centered on the current location, and iii) a 10Kbp window centered on the current location. The use of this dynamic background model is motivated by the desire to correct local ChIP-seq enrichment biases that appear in the signal and control channels, and is similar to the model employed by MACS (Zhang, et al. Genome Biol 2008). A given bin is denoted as potentially enriched if the overlapping hit count exceeds that expected from the background model at a p-value of 10^-9. P-values for each potentially enriched bin’s over-representation in the signal channel over the control are calculated using the binomial distribution CDF (see Rozowsky, et al. Nature Biotech 2009). Neighboring regions in the set of potentially enriched regions are merged, and the maximal p-value observed for the constituent bins is attached to the resulting merged region. The p-values are corrected for multiple hypothesis testing using Benjamini & Hochberg’s method, and all regions with corrected p-values above 0.001 are discarded. False-discovery rates are estimated by repeating the event discovery procedures after swapping the scaled control channel and the signal channel. After the first pass, the scaling factor is estimated by carrying out linear regression on the hit counts observed in 10,000 bp windows that are devoid of potentially significant events in both the signal and control channels. The binding model is estimated from enriched regions with p-values < 10^-7 and signal/control hit count enrichment greater than 10. These regions are aligned around the 'peak' location, defined as the position of maximum probability when scanning the current binding model over the region's hit landscape.

molecule: genomic DNA

organism: Mus musculus

source_name: Day2+8hrs post-RA exposure

growth_protocol: ES cells were differentiated as previously described (Wichterle, et al. Cell 2002).  Briefly, ES cells were trypsinized and seeded at 5x10e5 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Medium was exchanged on Day 1, Day 2 and Day 5 of differentiation.  Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). For ChIP experiments, the same conditions were used but scaled to seed 1x10e7 cells on Day 0.

extract_protocol: ChIP protocols were adapted from http://jura.wi.mit.edu/young_public/hESregulation/ChIP.html.  Descriptions of these protocol modifications have been previously published (Guenther, et al., Genes Dev 2008). Briefly, approximately 6x10e7 cells taken from each developmental time point were cross-linked using formaldehyde and snap-frozen in liquid nitrogen.  Cells were thawed on ice, resuspended in 5ml lysis buffer 1 (50 mM Hepes-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) and mixed on a rotating platform at 4°C for 5 minutes.  Samples were spun down for 3 minutes at 3000rpm, resuspended in 5ml lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), and mixed on a rotating platform for 5 minutes at room temperature.  Samples were spun down once more, resuspended in lysis buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using a Misonix 3000 model sonicator to sheer cross-linked DNA to an average fragment size of approximately 500bp.  Triton X-100 was added to the lysate after sonication to final concentrations of 1% and the lysate spun down to pellet cell debris.  The resulting whole-cell extract supernatant was incubated on a rotating mixer overnight at 4°C with 100 µL of Dynal Protein G magnetic beads that had been preincubated for 24 hours with 10 µg of the appropriate antibody in a PBS/BSA solution. Pol2-S5P (Abcam, ab5131) antibody was used for the ChIP experiment. After approximately 16 hours of bead-lysate incubation, beads were collected with a Dynal magnet.  ChIP samples probing for transcription factor binding were washed with the following regimen, mixing on a rotating mixer at 4°C for 5 minutes per buffer: low-salt buffer (20 mM Tris at pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), high-salt buffer (20 mM Tris at pH 8.1, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), LiCl buffer (10 mM Tris at pH 8.1, 250 mM LiCl, 1 mM EDTA, 1% deoxycholate, 1% NP-40), and TE containing 50 mM NaCl.  ChIP samples probing for histone and chromatin marks were washed 4 times with RIPA buffer (50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and then once with TE containing 50 mM NaCl, again mixing on a rotating mixer at 4°C for 5 minutes per buffer.  After the final bead wash, samples were spun down to collect and discard excess wash solution, and bound antibody-protein-DNA fragment complexes were eluted from the beads by incubation in elution buffer at 65°C with occasional vortexing.  Cross-links were reversed by overnight incubation at 65°C.  Samples were digested with RNase A and Proteinase K to remove proteins and contaminating nucleic acids, and the DNA fragments precipitated with cold EtOH. Purified DNA fragments were processed according to a modified version of the Illumina/Solexa sequencing protocol (Illumina, http://www.illumina.com/pages.ilmn?ID=252).

treatment_protocol: Ectopic exposure to retinoic acid and hedgehog agonist at day 2 during the differentiation protocol.

tag: cell line

tag: cell stage

tag: chip-antibody

value: Pol2-S5P (Abcam, ab5131)


title: ML-DmD9 V125/BS101 (Celniker/RNA:71) rep1 extraction1_seq1 aliquote 1

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

library_source: transcriptomic

molecule: total RNA

organism: Drosophila melanogaster

source_name: ML-DmD9 cell small ncRNA RNA-Seq

tag: tissue

value: dorsal mesothoracic disc

tag: developmental stage

value: third instar larval stage

tag: genotype

value: y v f mal


title: S2-DRSC V145/BS10 (Celniker/RNA:13) rep1 extraction1_seq1 aliquote 1

source_name: S2-DRSC cell small ncRNA RNA-Seq

value: Male


title: WT_8C_DNAseq_rep1

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

description: Sample 1

data_processing:
DNA-Seq reads were were first trimmed to 36mers and mapped with Bowtie (Langmead, et al. 2009 Genome Biol.) to TAIR8 chr1..5, allowing up to 2 mismatches and retaining only uniquely-mapping reads. Reads mapping to identical coordinates were collapsed into one read.
Genome_build: TAIR8
Supplementary_files_format_and_content: DNA-seq data: Column 1 is chromosome. Column 2 is strand read mapped to (+/-). Column 3 is the genomic coordinate.

mRNA-Seq reads were first trimmed to 50mers and mapped with Bowtie (Langmead, et al. 2009 Genome Biol.) to TAIR8 chr1..5, allowing up to 2 mismatches and retaining only uniquely-mapping reads.
Genome_build: TAIR8
Supplementary_files_format_and_content: Each RNA-seq  processed file gives 20- or 25-basepair resolution signal normalized as mapped reads per genomic kilobasepair per million mapped reads. Column 1 is chromosome. Column 2 is the genomic coordinate. Column 3 is the normalized counts.

BS-Seq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics) to TAIR8 chr1..5/C/M, allowing up to 2 mismatches and retaining only uniquely-mapping reads.  Only reference genome cytosines covered with at least 4 reads were considered for analysis.
Genome_build: TAIR8
Supplementary_files_format_and_content: BS-seq data: Column 1 is chromosome (1..5).  Column 2 is the coordinate of the genomic cytosine. Column 2 is genomic strand (+/-) of the cytosine. Column 3 is context (CG, CHG, or CHH) of the genomic cytosine. Column 4 is the empirical observed fraction of 5'-methylation, calculated as (# read C) / (# read C + # read T).

organism: Arabidopsis thaliana

extract_protocol:
DNA-seq libraries: One gram of mature rosette leaves were collected from 3-4-week-old plants, chopped in 0.5 ml of filtered Galbraith buffer, and stained with propidium iodide. A BD FACS Aria II in the UCLA Jonsson Comprehensive Cancer Center (JCCC) Flow Cytometry Core Facility was used to sort the nuclei.  For sequencing, 7,000-9,000 8C nuclei of each sample were collected, and purified DNA with Picopure purification kit (Arcturus) following manufacturer instructions.  Libraries were generated and sequenced following manufacturer instructions (Illumina).

RNA-seq libraries: RNA-seq experiments were performed in two biological replicates for each genotype. 0.1g of tissue was ground in Trizol (Invitrogen).  Total RNA were treated with DNaseI (Roche), and cleaned up with phenol-chlorophorm and precipitated with ethanol. Libraries were generated and sequenced following manufacturer instructions (Illumina).

Bisufite-Seq libraries: 0.5-1g of mature rosette leaves were collected, and genomic DNA was extracted using Plant DNeasey mini purification kit (Qiagen). Libraries were generated and sequenced as previously described (Feng et al., Methods Mol Biol. 2011;733:223-38.).

tag: ecotype

tag: genotype/variation

value: wild type

value: 3 wk leaves


title: CSHL_RnaSeq_CD20+_cell_longPolyA (superseded by GSE90268)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
****************************
GSM981256 record metadata submitted on Aug 06 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90268
****************************

molecule: polyA RNA

organism: Homo sapiens

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: rnaextract

value: longPolyA

tag: rnaextract description

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

tag: biorep

tag: labexpid

tag: labversion

value: iIDR

tag: readtype

tag: readtype description

value: Paired 76 nt directed reads

tag: replicate

tag: spikeinpool

tag: localization description

value: Whole cell


title: ML-DmBG1-c1 V129/BS177 (Celniker/RNA:117) rep2 extraction2_seq1 aliquote 1

source_name: ML-DmBG1-c1 cell small ncRNA RNA-Seq

tag: cell line

tag: tissue

value: CNS-derived cell-line

tag: Sex


title: ML-DmBG3-c2 V130/BS180 (Celniker/RNA:123) rep2 extraction2_seq1 aliquote 1

source_name: ML-DmBG3-c2 cell small ncRNA RNA-Seq

tag: developmental stage

tag: genotype


title: HEK293T_Sample 3_MeRIP-NEB

city: New York

first: Christopher

middle: E

last: Mason

address: 1305 York Ave

department: Physiology and Biophysics

institute: Weill Cornell Medical College

data_processing:
Reads aligned to genome using BWA with default settings, converted to BAM files using SamTools, converted to sorted BAM files using SamTools, converted to bedgraphs using genomeCoverageBed and converted to bigwigs using bedGraphToBigWig
Peaks were found using MeRIPPeR software, inputting BWA-aligned reads, processed across 3 replicates for each organism.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: bigwigs show number of reads mapping to the genome

extract_protocol:
Total RNA was isolated from adult mouse brain and HEK293T cells and subjected to RiboMinus treatment to remove rRNAs.  RNA was then subjected to 2 rounds of m6A RNA immunoprecipitation (MeRIP) using an antibody that recognizes m6A
library strategy: MeRIP-Seq

tag: cell type

value: embryonic kidney cells

tag: tissue source

value: kidney

tag: sample type

value: RNA IP against m6A

tag: merip antibody

tag: merip antibody vendor

value: Synaptic Systems (SYSY)

tag: merip antibody cat. #

tag: merip antibody lot  #

tag: rna subtype

value: RiboMinus RNA


title: HEK293T_Sample 2_Non-IP Control

value: no IP (input RNA)


title: HEK293 4SU nuclear RNA-seq

city: Basel

first: Cem

last: Sievers

address: Mattenstrasse

country: Switzerland

institute: ETH Zurich

data_processing:
quality filtering according to the Illumina quality filter
Bowtie alignment using the following parameter setting:--best --chunkmbs 512 -S -M 100 -p 8 -k 1
Aligned reads were used to compute the relative substitution frequency at positions with coverage of at least 20
Genome_build: hg19
Supplementary_files_format_and_content: The final file contains information about read substitutions with respect to the reference genome at specific genomic positions. Each row specificies one substitution. The columns contain information regarding chromosome, genomic position (zero offset), strand, substitution, coverage at position and number of specified substitions at the position

source_name: HEK293 4SU nuclear RNA-seq

growth_protocol: HEK293 cells were cultured in DMEM medium with 10% FBS at 37°C

extract_protocol: Nuclei were extracted from cells treated with 4SU overnight. Nuclear RNA was extracted using TRIzol (Invitrogen) and reverse transcribed using random hexamer, and sequenced using Illumina Hi-Seq

treatment_protocol: HEK293 cells were incubated with 4-thiouridine over night


title: C57BL/6 Brain_Sample 2_MeRIP - SYSY

description: RNA IP against m6A

source_name: whole brain

extract_protocol: Total RNA was isolated from adult mouse brain and subjected to RiboMinus treatment to remove rRNAs.  RNA was then subjected to 2 rounds of m6A RNA immunoprecipitation (MeRIP) using an antibody that recognizes m6A

tag: strain

tag: age

value: Adult

tag: library strategy

value: MeRIP-Seq


title: HEK293T_Sample 2_MeRIP-SYSY


title: C57BL/6 Brain_Sample 1 MeRIP - SYSY

description: RNA IP against m6A

extract_protocol: Total RNA was isolated from adult mouse brain and subjected to RiboMinus treatment to remove rRNAs. RNA was then subjected to 2 rounds of m6A RNA immunoprecipitation (MeRIP) using an antibody that recognizes m6A

tag: merip antibody lot #


title: C57BL/6 Brain_Sample 1 Non-IP Control

description: no IP (input RNA)


title: HEK293T_Sample 1_Non-IP Control

tag: cell line


title: C57BL/6 Brain_Sample 2_MeRIP - NEB

description: RNA IP against m6A


title: HEK293T_Sample 3_Non-IP Control


title: HEK293T_Sample 1_MeRIP-SYSY


title: Col BSseq

status: Public on Aug 05 2012

city: Seattle

middle: Joel

last: Hale

state: WA

address: 1959 NE Pacific St., HSC H-458

department: Pathology

institute: University of Washington

description: genomic DNA isolated by phenol/chloroform and bisulfite treated; quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane

data_processing:
BS-seq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics), allowing up to 2 mismatches and retaining only uniquely mapping reads. Only cytosines covered with at least 5 reads in both libraries (Col and nrpe1) were considered.
genome build: TAIR8
Variable step UCSC Genome Browser wiggle format files for each chromosome for each cytosine context (CG, CHG, or CHH where H=A,T,C) with following tab-separated information: Chromosome, start coordinate, stop coordinate, and methylation level (#methylated cytosines sequenced/#total cytosines sequenced).

source_name: seedling tissue (10-day)

extract_protocol: Samples 1..7 / 8..11 / 12..13 / are by NEBNext DNA sample preparation protocol using Illumina PE adapters / Illumina TruSeq small RNA / converted and fragmented genomic DNA library as described in Cokus et al., Nature 2008 /

value: Wild type (eco. Columbia)

tag: genetic background

value: Columbia

tag: tissue

value: seedling

value: wild type

value: Bisulfite-treated genomic DNA


title: nrpe1 BSseq

value: nrpe1-12 mutant (eco. Columbia)


title: NRPE1 ChIP rdm1 mutant

description: immunoprecipitated formaldehyde-crosslinked leaf tissue; quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane

data_processing:
ChIPseq reads were filtered for full-length (50bp) reads.  Reads containing adapter were discarded.  Reads were mapped with Bowtie (Langmead et al. 2009 Genome Biol) to the nuclear genome, allowing for 2 mismatches and retaining only uniquely mapping reads.
genome build: TAIR8
Fixed step (50bp) UCSC Genome Browser wiggle format files for each chromosome with the the relative read counts given (reads in 50bp bins / total unique mapping reads)

source_name: floral tissue

value: rdm1-1 (eco. C24) with NRPE1-FLAG transgene

value: floral

tag: transgene

value: NRPE-FLAG

tag: chip antibody

value: anti-FLAG

value: Genomic DNA isolated from immunoprecipitated chromatin using FLAG antibody

tag: chip antibody manufacturer

value: Sigma

tag: chip antibody catalog #

tag: chip antibody lot #


title: ML-DmD32 V022/V132/BS25 (Celniker/RNA:163) rep1 extraction1_seq1 aliquote 1

source_name: ML-DmD32 cell small ncRNA RNA-Seq

value: dorsal mesothoracic disc

tag: developmental stage

value: third instar larval stage

tag: genotype

value: y v f mal

tag: Sex

value: Unknown


title: Col small RNAs - technical replicate 1

description: 15-30nt isolated small RNAs from total RNA Trizol preparation; quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/9 lane

data_processing:
Small RNA reads were demultiplexed (perfect matches to each index were required) and then filtered for average QC score > 30.  Adapter sequences (identified by at least a 13 nt perfect match) were trimmed and reads >15 nt in length after trimming were retained.  Reads with no identifiable adapter were discarded.  Reads were mapped with Bowtie (Langmead et al. 2009 Genome Biol) to the nuclear genome, allowing for 2 mismatches and retaining only uniquely mapping reads. As Samples 10 and 11 are technical replicates (resequencing of same libraries in a different flow cell) of samples 8 and 9 respectively, alignments for each genotype were combined for downstream analysis
genome build: TAIR8
Fixed step (50bp) UCSC Genome Browser wiggle format files for each chromosome for both 24nt and 21nt length small RNAs with the the relative read counts given for the combined alignments of samples 8 and 10 (Col) or samples 9 and 11 (nrpe1) (reads in 50bp bins / total unique mapping small RNA reads of all size classes)

tag: sample type

value: Purified small RNAs


title: C57BL/6 Brain_Sample 2_Non-IP Control

description: no IP (input RNA)

value: Adult

value: no IP (input RNA)

tag: rna subtype

value: RiboMinus RNA

value: MeRIP-Seq


title: NRPE1 ChIP dms3 mutant

value: dms3-4 mutant (eco. Columbia) with NRPE1-FLAG transgene

value: Columbia


title: NRPE1 ChIP replicate 2

value: Wild type (eco. Columbia) with NRPE1-FLAG transgene

value: wild type


title: Col ChIP replicate 2

value: Wild type (eco. Columbia)

value: floral


title: Sg4 V133/BS34 (Celniker/RNA:199) rep1 extraction1_seq1 aliquote 1

source_name: Sg4 cell small ncRNA RNA-Seq

value: embryo-derived cell-line

value: late embryonic stage

value: Male


title: NRPE1 ChIP

value: NRPE-FLAG

value: anti-FLAG

value: Genomic DNA isolated from immunoprecipitated chromatin using FLAG antibody

value: Sigma


title: Col ChIP


title: nrpe1 small RNAs - technical replicate 1

value: nrpe1-12 mutant (eco. Columbia)

value: Purified small RNAs


title: HudsonAlpha_MethylRrbs_GM06990

status: Public on Aug 03 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=wgEncodeHaibMethylRrbs

tag: lab

value: HudsonAlpha

tag: lab description

value: Myers - Hudson Alpha Institute for Biotechnology

tag: datatype

value: MethylRrbs

tag: datatype description

value: DNA Methyl Reduced Rep Bisulfite Seq

tag: cell

tag: cell organism

value: human

tag: cell description

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment:Epstein-Barr Virus transformed

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: labexpid

tag: obtainedby

value: UW

tag: obtainedby description

value: Stamatoyannopoulous - University of Washington

tag: replicate


title: mRNASeq_WT_Col_0

city: Beijing

first: Di

last: Fan

state: Beijing

address: 7# Science Park Road Zhongguancun Life Science Park

country: China

institute: National Institute of Biological Sciences

description: polyA RNA isolated

data_processing: mRNA seq reads were mapped to the reference genome of Arabidopsis thaliana (TAIR10). Bowtie was used to map the sequence reads with no more than three mismatches. The 3' adapter sequences for smRNA seq were removed by a custom Perl script. The trimmed smRNA reads were mapped to the Arabidopsis genome using Bowtie with perfect matches.

source_name: seedling

growth_protocol: The seeds are sterilized with 2.25% bleach, washed with sterilized water, kept for three days at 4C, and then dispersed on Murashige and Skoog (MS) medium (Sigma-Aldrich) containing 1% sucrose and 0.3% phytagel (Sigma-Aldrich). Before be harvested,seedlings were growth 10 days under 160 umolm-2s-1 cool white fluorescent light and LD (16 h of light, 22C/8 h of dark, 18C) condition in a growth chamber (Percival CU36L5).

extract_protocol: Total RNA was isolated from 10 days seedlings grown on MS plates using RNAiso plus (Takara) according to the manufacturer's instructions, and was treated with RNase-free DNase (Promega) to remove any possible contaminating genomic DNA.mRNA was extracted from total RNA using Dynabeads Oligo(dT) (Invitrogen Dynal) following the manufacturer's directions. First-and second strand cDNA was generated using SuperscriptII reverse transcriptase (Invitrogen) and random hexamers primers. Double-stranded cDNA was fragmented by nebulization and used for mRNA library construction following the standard Illumina protocol. Small RNAs were gel isolated from total RNA, and were used to create libraries for Illumina sequencing essentially as described previously (Mi et al., 2008).

tag: developmental stage

value: two-leaf stage

tag: strain

value: wild type Col-0

value: polyA RNA isolated


title: smRNAseq_ibm1_3

description: small RNA gel isolated

value: ibm1-3 mutant

tag: rna subtype

value: small RNA gel isolated


title: mRNASeq_ibm1_3

description: polyA RNA isolated


title: BEAF ChIP in Drosophila simulans

city: Nanjing

first: Jingping

last: Yang

state: Jiangsu

address: 22 Hankou Road

department: Medical School

institute: Nanjing University

description: Chromatin IP against BEAF in D. sim

data_processing:
Alignment: Sequence reads were obtained and mapped to the each genome build using Bowtie 0.12.7 software using the default setting.
Genome Build:
dsim1_3-BEAF.bed: dsim1.3 flybase

organism: Drosophila simulans

source_name: embryo

growth_protocol: flies are kept at room temperature

extract_protocol: Two grams of embryos were used for two chromatin preparations, sonicated 20 cycles (10s on / 30s off) on a BRANSON SONIFIER 250 with output control set at 1.5. Libraries were prepared with the Illumina TruSeq DNA Sample Preparation Kit

treatment_protocol: no treatment

value: embryo 0-8h

tag: fraction

value: ChIP

tag: custom antibody

value: BEAF [Bushey AM, Ramos E, Corces VG. Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions. Genes Dev 2009 Jun 1;23(11):1338-50. PMID:19443682]


title: BEAF ChIP in Drosophila virilis

description: Chromatin IP against BEAF in D. vir

data_processing:
Alignment: Sequence reads were obtained and mapped to the each genome build using Bowtie 0.12.7 software using the default setting.
Genome Build:
dvir1_2-BEAF.bed: dvir1.2 flybase

organism: Drosophila virilis

value: embryo 0-12h


title: input in Drosophila virilis

description: input in D. vir

data_processing:
Alignment: Sequence reads were obtained and mapped to the each genome build using Bowtie 0.12.7 software using the default setting.
Genome Build:
dvir1_2-input.bed: dvir1.2 flybase

value: input


title: smRNAseq_WT_Col_0

description: small RNA gel isolated


title: VISA project Vancomycin Sensitive Clinical Isolate A1

city: Atlanta

first: Tim

last: Read

address: 615 Michael Street, Suite 301

institute: Emory University

description:
A1_VSSA
3 biological replicates

data_processing:
Data was imported into CLC Workbench 4.8
Reads under 50 nucleotides in length were discarded.
Reads were paired, using min_distance=180 and max_distance=250
Reads were trimmed, using default settings
A 'Gene Expression' experiment was conducted, using default settings and Staphylococcus aureus TCH1516 (NC_010079) as a reference.
Genome_build: NC_010079.1
Supplementary_files_format_and_content: A1_A2_stringent_USE.txt contains all mapping information.  Expression values are given in RPKM.  The data has been normalized using Quantile normalization, and has also been square root transformed. Statistical analyses were on Proportion, using Baggerley's test – all pairs on the normalized expression values - FDR corrected. The 'Fold Change' column is comparing fold change of A2 against A1.

organism: Staphylococcus aureus

source_name: Mid-log cells

growth_protocol: Cultures grown to OD600 0.7 in 20 mL of Brain Heart Infusion Broth

extract_protocol: Ambion RiboPure Bacteria Kit, was used to isolate total RNA, which was enriched using the Ambion MicrobExpress kit. cDNA was made from the RNA, then paired end libraries were created using standard Illumina protocols.

tag: isolate

tag: vancomycin and daptomycin susceptibility

value: VSSA [sensitive]


title: HudsonAlpha_MethylRrbs_Caco-2

tag: lab

value: HudsonAlpha

tag: lab description

value: Myers - Hudson Alpha Institute for Biotechnology

tag: datatype

value: MethylRrbs

tag: datatype description

value: DNA Methyl Reduced Rep Bisulfite Seq

tag: cell

tag: cell organism

value: human

tag: cell karyotype

value: cancer

value: endoderm

value: M


title: H1 TRA-1-60+ RNA Seq Rep3

city: Los Angeles

first: Sofia

last: Gkountela

state: California

address: 621 Charles E Young Dr S

department: MCDB

institute: UCLA

data_processing:
Illumina Casava1.7 software used for basecalling.
After filtering reads with low quality and reads containing sequencing adapters, we mapped raw reads to the human reference genome (assembly hg19) with the gapped aligner Tophat
Expression levels of gene and transcript were quantified by Cufflinks in the FPKM unit together with confidence intervals.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: A tab-delimited text file include raw read counts for all samples.

source_name: H1 hESCs

growth_protocol: Human embryos were obtained following elected termination and pathological evaluation at the UCLA Tissue Procurement Laboratory, UCLA Gene and Cellular Core Laboratory and the Laboratory of Developmental Biology at the University of Washington, Seattle. All consented material was anonymous and carried no personal identifiers. The BDRL estimates developmental age by prenatal intakes, foot length, Streeter’s stage and crown-rump length. Any conceptus with a documented birth defect or chromosomal abnormality was excluded from our study. At UCLA Translational Pathology Core Laboratory and the UCLA Gene and Cellular Core Laboratory, developmental age is calculated by recall of last menstrual period minus 2 weeks. Human ESC line H1 (WA01, 0043, 46XY) were maintained by culture under self –renewal conditions on mouse embryonic fibroblast (MEF) layer in DMEM:F12 (Gibco BRL), 20% KnockOut Serum (Gibco BRL), 1% nonessential amino acids (NEAA, Gibco BRL), 1 mM L-glutamine (Gibco BRL), 0.1 mM β-mercaptoethanol (Gibco BRL), and 10ng/ml of basic fibroblast growth factor (FGF) from R&D.

extract_protocol: Cells were sorted directly in 75ul RLT buffer (Qiagen) and RNA was extracted using the RNeasy Micro Kit (Qiagen) according to manufacturer’s instructions. RNA was amplified and converted to ssDNA using the WT-Ovation RNA Amplification System (Nugen). dsDNA was generated from ssDNA using the WT-Ovation Exon Module (Nugen) according to the manufactures instructions. dsDNA was sonicated to DNA fragments within a 200-500bp range. Subsequently the libraries were generated starting from 30ng DNA using the TruSeq DNA Sample Preparation Kit (Illumina) according to manufacturers instructions.

treatment_protocol: Human fetal gonads and H1 hESCs were dissociated with 0.25% Trypsin-EDTA for 5 min at 37oC. Dissociated cells were incubated in 1% BSA in PBS containing primary antibodies on ice for 20 min. Primary antibodies used were cKIT-APC conjugated (BD Biosciences) and TRA-1-60 (eBioscience).

tag: cell line

value: H1 hESCs

tag: passages

tag: cell type

value: TRA-1-60+ FACS sort


title: H1 TRA-1-60+ RNA Seq Rep2


title: HudsonAlpha_MethylRrbs_UCH-1

tag: cell description

value: chordoma cell line

tag: cell lineage

value: ectoderm

tag: cell sex

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: labexpid

tag: obtainedby

value: Duke

tag: obtainedby description

value: Crawford - Duke University

tag: replicate


title: WT_BS-seq

description: Sample 41

tag: ecotype

tag: genotype/variation

value: wild type

tag: tissue

value: 3 wk leaves


title: NRPE1 ChIP drd1 mutant

tag: genotype

value: drd1-6 mutant (eco. Columbia) with NRPE1-FLAG transgene

tag: genetic background

value: Columbia

value: floral

tag: transgene

value: NRPE-FLAG

tag: chip antibody

value: anti-FLAG

tag: sample type

value: Genomic DNA isolated from immunoprecipitated chromatin using FLAG antibody

tag: chip antibody manufacturer

value: Sigma

tag: chip antibody catalog #

tag: chip antibody lot #


title: UW98, cKIT+ RNA Seq Ovary

source_name: Fetal Ovary

value: ovary

tag: age

value: 16.5 weeks

tag: cell type

value: cKIT+ FACS sort


title: UW92, cKIT+ RNA Seq Ovary

value: 16 weeks


title: input in Drosophila pseudoobscura

description: input in D. pse

data_processing:
Alignment: Sequence reads were obtained and mapped to the each genome build using Bowtie 0.12.7 software using the default setting.
Genome Build:
dpse2_22-input.bed: dpse2.22 flybase

organism: Drosophila pseudoobscura

tag: developmental stage

value: embryo 0-10h

tag: fraction

value: input

tag: custom antibody


title: HudsonAlpha_MethylRrbs_A549_DMSO_0.02pct_7d

tag: lab

value: HudsonAlpha

tag: lab description

value: Myers - Hudson Alpha Institute for Biotechnology

tag: datatype

value: MethylRrbs

tag: datatype description

value: DNA Methyl Reduced Rep Bisulfite Seq

tag: cell

tag: cell organism

value: human

tag: cell description

value: epithelial cell line derived from a lung carcinoma tissue. (PMID:175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2:not in 2011 analysis

tag: cell karyotype

value: cancer

tag: cell lineage

value: endoderm

tag: cell sex

value: M

tag: treatment

tag: treatment description

value: 7 d with 0.02% Dimethyl sufloxide (DMSO) (Myers)

tag: labexpid

tag: obtainedby

tag: obtainedby description

tag: replicate


title: HudsonAlpha_MethylRrbs_HSMMtube_FSHD

value: myotube from Facioscapulohumeral Muscular Dystrophy (FSHD) patient, muscle needle biopsies

value: U

value: No special treatment or protocol applies

value: Duke

value: Crawford - Duke University


title: BEAF ChIP in Drosophila pseudoobscura

description: Chromatin IP against BEAF in D. pse

data_processing:
Alignment: Sequence reads were obtained and mapped to the each genome build using Bowtie 0.12.7 software using the default setting.
Genome Build:
dpse2_22-BEAF.bed: dpse2.22 flybase

tag: developmental stage

value: embryo 0-10h

tag: fraction

value: ChIP

tag: custom antibody

value: BEAF [Bushey AM, Ramos E, Corces VG. Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions. Genes Dev 2009 Jun 1;23(11):1338-50. PMID:19443682]


title: HudsonAlpha_MethylRrbs_ovcar-3

tag: lab

value: HudsonAlpha

tag: lab description

value: Myers - Hudson Alpha Institute for Biotechnology

tag: datatype

value: ovarian adenocarcinoma, "the NIH:OVCAR-3 line was established in 1982 by T.C. Hamilton, et al. from the malignant ascites of a patient with progressive adenocarcinoma of the ovary." - ATCC. (PMID:6604576)

value: mesoderm

value: F

value: UW

value: Stamatoyannopoulous - University of Washington


title: UW30, cKIT+ RNA Seq Testis

source_name: Fetal Testis

tag: tissue

value: testis

tag: age

value: 16 weeks

tag: cell type

value: cKIT+ FACS sort


title: Lai Kc167 cells Sample Kc (Replicate 2) extraction2_seq1 aliquote 1

description: small RNAs

data_processing: raw sequences were clipped by 3' linker sequences recognition, and select clipped sequences longer than 18 nt

source_name: Drosophila melanogaster KC cell

extract_protocol: total RNA from KC cell, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: cell line

value: Kc


title: H1 TRA-1-60+ RNA Seq Rep1

value: H1 hESCs

tag: passages

value: TRA-1-60+ FACS sort


title: HudsonAlpha_MethylRrbs_MCF-7_CTCF_shRNA_knockdown

value: MethylRrbs

tag: datatype description

value: DNA Methyl Reduced Rep Bisulfite Seq

tag: cell

tag: cell organism

value: human

tag: cell description

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

tag: cell karyotype

value: cancer

tag: cell lineage

value: ectoderm

tag: cell sex

tag: treatment

value: CTCF (CCCTC-binding factor) transcript levels were knocked down in cells using lentiviral transduction to express an shRNA targeting the CTCF gene. The lentiviral construct also contained a puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. By western blot, CTCF protein levels in the knockdown cells were <10% of cell lines transduced with a randomized shRNA lentiviral construct.

value: Duke

value: Crawford - Duke University


title: input in Drosophila melanogaster

description: input in D. mel

data_processing:
Alignment: Sequence reads were obtained and mapped to the each genome build using Bowtie 0.12.7 software using the default setting.
Genome Build:
dmel5_39_input.bed: dmel5.39 flybase

tag: developmental stage

value: embryo 0-8h

tag: fraction

value: input

tag: custom antibody


title: HudsonAlpha_MethylRrbs_MCF-7_Randomized_shRNA_control

tag: lab

value: HudsonAlpha

tag: lab description

value: Myers - Hudson Alpha Institute for Biotechnology

tag: datatype

value: F

tag: treatment description

value: Cells were transduced with a lentivirus expressing an shRNA containing a randomized DNA sequence generated by the siRNA Wizard v3.1 (http://www.sirnawizard.com/scrambled2.php) program. Lentiviral constructs also contained the puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct.

tag: labexpid

tag: obtainedby

tag: obtainedby description

tag: replicate


title: HudsonAlpha_MethylRrbs_HL-60

tag: datatype description

tag: cell

tag: cell organism

value: promyelocytic leukemia cells, (PMID:276884)

value: mesoderm

value: No special treatment or protocol applies

value: UW

value: Stamatoyannopoulous - University of Washington


title: untreated

city: Munich

first: Klaus

last: Förstemann

address: Feodor-Lynen 25

department: Gene Center

country: Germany

institute: Ludwig-Maximilians University

data_processing:
Reads were first sorted according to their sample index, then the 3'-adapter sequence and everything else 3'-of it was removed.
Reads were size-selected for 21-23 nt length.
Reads were sorted into unique sequences and sequence counts => e.g. S1.counts
Genome_build: n/a

source_name: S2 cell culture line

growth_protocol: Cells were cultured in standard Schneider's Drosophila medium supplemented with 10% FBS at 25°C.

extract_protocol: Total RNA was isolated using Trizol and size-selected on polyacrylamide/urea gels [~18-30 nt). In a first ligation step, pre-adenylated 3'-linkers were ligated to the 3'-end of the small RNAs (AMP-5'p=5'pCTGTAGGCACCATCAATdideoxyC-3') in the absence of ATP. After gel-purification of the ligation products, a 5'-Adapter was ligated in the presence of ATP  5('-rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrC rUrCrUrUrCrCrGrArUrCrU-3'). Following reverse transcription with 5'-ATTGATGGTGCCTACAG-3', PCR was performed to append Adapter sequences for Illumina sequencing as well as indexes for multiplexing. A constant 5'-primer  (5'-AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACG-3') was combined with one of four 3'-index primers (5'-CAAGCAGAAGACGGCATACGAGGATCCGATTGATGGTGCCTACAG-3', 5'-CAAGCAGAAGACGGCATACGACAGCTGGATTGATGGTGCCTACAG-3', 5'-CAAGCAGAAGACGGCATACGATCTAGAGATTGATGGTGCCTACAG-3', 5'-CAAGCAGAAGACGGCATACgaATCGATGATTGATGGTGCCTACAG-3'). Sequencing was single-end (either 50, 75 or 78 nt length), 3'-adapters and indexes were sequenced together with the small RNAs.

treatment_protocol: Transfection was performed with Fugene HD (24 ul per 3 ml final culture volume) and 300 ng  of each DNA type (see tags above) per 3 ml final volume in 6-well plates. Three days after transfection, the cells were harvested and total RNA was extracted with Trizol.

tag: transfection

tag: tag

tag: cell line


title: pKF63 EcoRI

tag: treatment

value: pKF63 EcoRI cut

value: pRS425 circular

value: Firefly luciferase PCR product


title: pKF63 SacI

value: pKF63 SacI cut


title: pKF63 AlwI

value: pKF63 AlwI cut


title: pKF63 circular

value: pKF63 circular

value: pRS425 BamHI


title: pKF63 BamHI

value: pKF63 BamHI cut


title: pKF63 NotI

value: pKF63 NotI cut


title: Wild type flower Rep2

status: Public on Aug 02 2012

city: Lincoln

first: Bin

last: Yu

state: NE

address: 1901 Vine Street

department: Biological Sciences

institute: University of Nebraska - Lincoln

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to TAIR9 whole genome using bowtie bowtie -v 0 -S -a --best --strata
Reads counts for each miRNA with trimmed mean of M values (TMM) normalization method. Robinson and Oshlack Genome Biology 2010.
Genome_build: TAIR9
Supplementary_files_format_and_content: Tab-delimited plain text files: the first column is MicroRNA gene IDs and the second column is normalized reads counts

source_name: flowers and flower buds

growth_protocol: 16 hour light; 8 hour dark;  at 22 oC

extract_protocol: Illumina small RNA library protocol

tag: tissue

value: flowers and flower buds

tag: genotype

value: wild type

tag: genetic background


title: UW99, cKIT+ RNA Seq Testis

value: testis

tag: age

value: 16.5 weeks

tag: cell type

value: cKIT+ FACS sort


title: BEAF ChIP in Drosophila melanogaster

description: Chromatin IP against BEAF in D. mel

data_processing:
Alignment: Sequence reads were obtained and mapped to the each genome build using Bowtie 0.12.7 software using the default setting.
Genome Build:
dmel5_39_BEAF.bed: dmel5.39 flybase

tag: developmental stage

value: embryo 0-8h

tag: fraction

value: ChIP

tag: custom antibody

value: BEAF [Bushey AM, Ramos E, Corces VG. Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions. Genes Dev 2009 Jun 1;23(11):1338-50. PMID:19443682]


title: Wild type flower Rep1


title: 60hpf-DMSO-3

city: Woods Hole

first: Neelakanteswar

last: Aluru

state: MA

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

data_processing:
CLC Bio Genomics Work bench version 4.7 was used
Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16.
Remaining reads were mapped to other non-coding RNAs downloaded from ncRNA.org
Statistical analysis was done using edgeR, a bioconductor package (R project)
Genome_build: miRBase version 16
Supplementary_files_format_and_content: tab-delimited text files

organism: Danio rerio

source_name: Embryos

extract_protocol: Small RNA libraries were prepared using the small RNA expression kit (SREK) protocol (Applied Biosystems, Foster City, CA). Sequencing was done on a SOLiD V3 system (Applied Biosystems).

tag: strain

value: TL wild type

value: embryos

tag: time

value: 60 hpf

value: DMSO


title: 60hpf-DMSO-1


title: 60hpf-TCDD-2

value: TCDD


title: 60hpf-DMSO-2


title: 60hpf-TCDD-3


title: 36hpf-TCDD-2

value: 36 hpf


title: 36hpf-TCDD-3


title: tgh-1 flower Rep2


title: Mm 173-02

city: Tucson

first: Darren

middle: A.

last: Cusanovich

state: AZ

address: 1230 N Cherry Avenue, BSRL 421

department: Cellular and Molecular Medicine

institute: University of Arizona

data_processing:
Reads were aligned to the genome using Maq v0.6.8.
Reads not mapping to the genome, mapping ambiguously, or mapping with a quality score less than 10 were filtered out (custom perl script).
The number of reads aligning to a previously defined set of exons were counted (custom perl script).
The number of reads mapping to all exons for each gene were summed to generate a gene-level expression estimate (custom perl script).
Genome_build: panTro2 and rheMac2
Supplementary_files_format_and_content: exoncounts.txt files: Each line represents an exon. Column 1 contains information about the exon (gene ID, location). Column 2 lists the number of reads mapping to that exon for that sample.

organism: Macaca mulatta

source_name: lymphoblastoid cell line_rhesus macaque

growth_protocol: Cells were cultured in RPMI-1640 media supplemented with 15% FBS, 2mM L-glutamine, 100 IU/mL penicillin and 100ug/mL streptomycin. Cells were incubated at 37°C with 5% CO2 . Cells were split every 2-3 days.

extract_protocol: RNA was extracted using the Qiagen RNeasy Mini kit. For library costruction, T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK were used to end-repair cDNA from each sample. A 3' adenosine overhang was added to the end-repaired DNA using Klenow fragment (3’ to 5’ exouclease minus) and dATP as a substrate. DNA ligase was used to ligate Illumina adapters to the samples and fragments were size selected (~200bp) by gel extraction. Finally, gel extracted samples were amplified by PCR (15 cycles). Libraries were subsequently sequenced on a GAII by standard protocol.

tag: gender

value: Female


title: Mm 150-99


title: 36hpf-DMSO-3


title: tgh-1 flower Rep1


title: 36hpf-TCDD-1


title: Mm 303-97

value: Male


title: Mm 265-95


title: Mm 153-99


title: Mm 256-95


title: input in Drosophila simulans

description: input in D. sim

data_processing:
Alignment: Sequence reads were obtained and mapped to the each genome build using Bowtie 0.12.7 software using the default setting.
Genome Build:
dsim1_3-input.bed: dsim1.3 flybase

value: input


title: AG18359

organism: Pan troglodytes

source_name: lymphoblastoid cell line_chimpanzee


title: S003641


title: S003659


title: S004973


title: MeOH DNA enriched genomic DNA_SL55

city: Cambridge

first: Krys

last: Kelly

address: Downing Street

department: Plant Sciences

country: United Kingdom

institute: University of Cambridge

data_processing: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline.  The 3 prime adaptor sequence was removed from the small RNA reads and the reads were aligned to the Chlamydomonas genome, assembly 4.  Only reads with 100% match to the genome were retained.

organism: Chlamydomonas reinhardtii

source_name: vegetative cells, Methylated-DNA enriched genomic DNA

growth_protocol: Chlamydomonas cells were grown in liquid culture.

extract_protocol:
DNA fragments were prepared for sequencing by digestion with micrococcal nuclease.
The genomic library contained DNA from Chlamydomonas strain cw15_325arg and the methylated-DNA library used the same strain but enriched the DNA for methylated sequences by immuno-precipitating with Methyl-cytosine antibody.

treatment_protocol: Small RNAs were isolated from different strains of Chlamydomonas and from cells at different phases of the Chlamydomonas sexual cycle.  Genomic DNA was isolated from vegetative cells.

tag: 3prime adaptor

tag: antibody

value: Methyl-cytosine


title: small RNAs from zygotes_SL256

source_name: zygotes 6h

extract_protocol: RNA was extracted using Trizol (Invitrogen) and small RNA isolated from the total RNA fraction using mirVana (Ambion),  adapter sequences appropriate Illumina sequencing were ligated.

value: TCGTATGCCGTCTTCTGCTTGT


title: small RNAs from vegetative cells_SL305

source_name: vegetative cells


title: small RNAs from zygotes_SL255

source_name: zygotes 2h


title: small RNAs from the nuclei of vegetative cells_SL166

source_name: nuclei from vegetative cells


title: S003610


title: small RNAs from zygotes_SL254

source_name: zygotes 30 min


title: small RNAs from gametes induced by nitrogen starvation_SL144

source_name: gametes

value: NO-


title: 36hpf-DMSO-2


title: 36hpf-DMSO-1


title: AG18358


title: Genomic DNA_SL54

source_name: vegetative cells, genomic DNA


title: small RNAs from gametes induced by nitrogen starvation_SL143


title: small RNAs from nitrogen starved vegetative cells_SL141

source_name: starved vegetative cells


title: T2 Tryptamin treated rep2

first: Bernward

last: Klocke

address: Bayerstr. 85a

institute: Genomatix Software GmbH

data_processing:
Base conversion was done using Illumina's OLB v1.9.
Mapping to mouse genome on Genomatix Mining Station with Genomatix Mapper version 3.5
Differential expression analysis on Genomatix GGA with RegionMiner program version 4.4 for transcript identification (Genomatix ElDorado database 08-2011) and DESeq (Anders & Huber, 2010) for assessment of differential expression.
Expression was summarized for genes where an annotated transcript was detected as differentially expressed with an adj. P-value < 0.05 (DESeq) and a log2fold - change >1 (uregulation) or < -1 (downregulation)
For assessment of Ahr induced gene expression only the profiles of upregulated genes were further used.
genome build: Mus musculus NCBI build 37
Supplementary_files_format_and_content: FB_result_transcript_summary.tsv: Mapping and contrast of FICZ treatment samples / Background samples to all transcripts in Genomatix' ElDorado annotation, raw counts, normalized expression, and evaluation of differential expression by DESeq Format description (1)
Supplementary_files_format_and_content: TB_result_transcript_summary.tsv: Mapping and contrast of Tryptamine treatment samples / Background samples to all transcripts in Genomatix' ElDorado annotation, raw counts, normalized expression, and evaluation of differential expression by DESeq Format description (1)
Supplementary_files_format_and_content: FT_result_transcript_summary.tsv: Contrast of FICZ treatment samples / Tryptamine samples to all transcripts in Genomatix' ElDorado annotation, raw counts, normalized expression, and evaluation of differential expression by DESeq Format description (1)
Supplementary_files_format_and_content: F_vs_B_up.txt: Differentially upregulated genes FICZ vs Background, summarized from the transcript data, adj. P - value < 0.05 (DESeq) and log2fold - change >1,  Format description (2)
Supplementary_files_format_and_content: T_vs_B_up.txt: Differentially upregulated genes Tryptamine vs Background, summarized from the transcript data, adj. P - value < 0.05 (DESeq) and log2fold - change >1,  Format description (2)
Supplementary_files_format_and_content: File Format(1) tab sparated text; Columns:
Supplementary_files_format_and_content: 1: accession number of the transcript (e.g. RefSeq, Genbank, Ensembl)
Supplementary_files_format_and_content: 2: symbol of the gene
Supplementary_files_format_and_content: 3: gene ID (NCBI Entrez Gene, 0 if not available, -2 if ambiguous)
Supplementary_files_format_and_content: 4: length of the transcript (sum of exons)
Supplementary_files_format_and_content: 5: number of exons
Supplementary_files_format_and_content: 6: p-value (DESeq)
Supplementary_files_format_and_content: 7: adjusted p-value (Benjamini - Hochberg)
Supplementary_files_format_and_content: 8: log2(fold change), i.e. log2(expression value of control data set / expression value of treatment data set), note, that this value can be -Inf/+Inf if one of the conditions shows no expression
Supplementary_files_format_and_content: 9: Regulation of treatment (set1) compared to control (set2), (values can be "up", "down", "no")
Supplementary_files_format_and_content: 10, 11, 12: number of reads for each replicate from the treatment set
Supplementary_files_format_and_content: 13, 14, 15: number of reads for each replicate from the control set
Supplementary_files_format_and_content: 16, 17, 18: normalized expression value for each replicate from the treatment set
Supplementary_files_format_and_content: 19, 20, 21: normalized expression value for each replicate from the control set
Supplementary_files_format_and_content: 22: the mean normalized expression value across the treatment replicates
Supplementary_files_format_and_content: 23: the standard deviation of the normalized expression values across the treatment replicates
Supplementary_files_format_and_content: 24: the mean normalized expression value across the control replicates
Supplementary_files_format_and_content: 25: the standard deviation of the normalized expression values across the control replicates
Supplementary_files_format_and_content: File Format(2) tab sparated text; Columns:
Supplementary_files_format_and_content: 1: gene ID (NCBI Entrez Gene)
Supplementary_files_format_and_content: 2: symbol of the gene
Supplementary_files_format_and_content: 3: number of alternative transcripts for this gene that are up-/down-regulated regulated
Supplementary_files_format_and_content: 4: total number of alternative transcripts for this gene
Supplementary_files_format_and_content: 5: mean log2 fold change of up-/down-regulated transcripts
Supplementary_files_format_and_content: 6: min log2 fold change of up-/down-regulated transcripts
Supplementary_files_format_and_content: 7: max log2 fold change of up-/down-regulated transcripts
Supplementary_files_format_and_content: 8: standard deviation across the log2 fold change values of the alternative transcripts
Supplementary_files_format_and_content: 9: minimum p_value for the alternative transcripts
Supplementary_files_format_and_content: 10: mean NE(treat):   mean normalized expression value for the alternative transcripts in the treatment data
Supplementary_files_format_and_content: 11: stddev NE(treat): standard deviation across the NE values for the alternative transcripts in the treatment data
Supplementary_files_format_and_content: 12: mean NE(ctrl):    mean normalized expression value for the alternative transcripts in the control data
Supplementary_files_format_and_content: 13: stddev NE(ctrl):  standard deviation across the NE values for the alternative transcripts in the control data
Supplementary_files_format_and_content: Normalized expression/enrichment value (NE-value)  The NE-value is calculated based on the following formula:        NE = c * #readsregion / (#readsmapped * lengthregion)    where NE is the normalized expression or enrichment value,  #readsregion: the reads (sum of base pairs) of falling into either the transcript or the cluster region,  #readsmapped: all mapped reads (in base pairs),  lengthregion: the transcript or cluster length in base pairs  and c a normalization constant set to 10E7. Except for the constant this is equivalent to RPKM

source_name: Hepa 1 WT cells

extract_protocol: Total RNA was isolated using RNAeasy kit (QIAGEN, Valencia, CA). Samples were treated with de- oxyribonuclease (Invitrogen) before RNA quality control.

treatment_protocol: Mouse Hepa cells were treated with vehicle control, FICZ (10 nM), or TA (50 uM) for 6 h.

value: Mouse Hepatoma

value: TA (50 uM) for 6 h


title: small RNAs from nitrogen starved vegetative cells_SL142


title: T3 Tryptamin treated rep3


title: T1 Tryptamin treated rep1


title: small RNAs from vegetative cells_SL140


title: small RNAs from vegetative cells_SL139


title: F3 FICZ treated rep3

value: FICZ (10 nM) for 6 h


title: F1 FICZ treated rep1


title: Tdc2-Input

city: Ashburn

first: Fred

middle: P

last: Davis

state: VA

address: 19700 Helix Dr

institute: HHMI Janelia Farm Research Campus

description: Tdc2-GAL4 (Cole et al., 2005) driving unc84-GFP, primarily in octopaminergic neurons

data_processing:
Base calling performed by Illumina CASAVA 1.8
Reads were aligned to dm3 using BOWTIE v0.12.7 (bowtie -S -t -p 8 -m 1)
Coverage over all genomic positions counted with BEDTOOLS v2.15 (genomeCoverageBed -split -bg)
Coverage scaled to 10M total alignments. (custom Perl script)
Scaled coverage was converted to bigWig (wigToBigWig from ucsc)
Coverage over annotated genebodies, promoters (1kb centered around TSS), and all 10kb windows (scanned in 5kb increment across whole genome) was counted using BEDTOOLS v2.15 (coverageBed -counts -split -abam $BAM_FN -b $FEATUREBED)
Genome_build: dm3
Supplementary_files_format_and_content: bigWig tracks for visualization. supplemental file #1 (chipseq_perisoform_summary.txt) is a tab-delimited text file describing the modification levels across the genebody and promoter (1kb around TSS) in each sample. Supplemental file #2 (chipseq_perwindow_summary.txt) is a tab-delimited file containing H3K27ac, H3K27me3, and input signal in 10kb genomic windows for the OK107 and Tdc2 samples.

source_name: Octopaminergic neurons

extract_protocol: Adult flies were anesthetized by CO2 and flash frozen in liquid N2. Heads were separated from abdominal-thoracic segments, wings and legs by vigorous vortexing followed by separation over dry ice cooled sieves. 600 - 10,000 frozen heads were added to 50mls of 10mM b-glycerophosphate pH7, 2mM MgCl2, 5mM sodium butyrate, 1X complete protease inhibitor cocktail (Roche: 11873580001) and the suspension was passed over a Yamato continuous flow homogenizer, set at 90-100 rpm, five to seven times. The homogenate was filtered over Miracloth (EMD Biosciences: 475855) and bought to 0.7mM b-mercaptoethanol and 0.5% NP-40. After six tractions in a 40ml Dounce homogenizer (pestle B), 600uls of antibody-adsorbed beads were added to 50mls of lysate. The binding reaction was run under continuous agitation at 4oC for 30 minutes. Beads were then collected on a magnet and washed three to four times in 50mls 10mM β-glycerophosphate pH7, 250mM sucrose, 2mM MgCl2, 25mM KCl, 5mM sodium butyrate. Bead bound nuclei in 20mls wash buffer were then passed over a 20um nylon mesh, returned to the magnet stand and resuspended in 1ml of 10mM β-glycerophosphate pH7, 250mM sucrose, 2mM MgCl2, 25mM KCl, 5mM sodium butyrate. Bead bound nuclei were collected on a magnet stand and resuspended in 2X500μls of 15mM Hepes pH7, 1mM KCl, 5mM MgCl2, 2mM CaCl2, 340mM sucrose, 0.5mM spermidine, 0.15mM spermine, 5mM sodium butyrate. Nuclei were then digested at 37oC after the addition of Micrococcal nuclease (Worthington: LS004798) to 0.025units/ul. The reaction was terminated by the addition of EGTA at 2mM. Nucleosomes were then extracted on ice for 30 minutes in 200-400μls of 15mM Hepes pH7, 200mM NaCl, 1mM KCl, 5mM MgCl2, 2mM EGTA, 340mM sucrose, 0.5mM spermidine, 0.15mM spermine, 5mM sodium butyrate. The extraction was repeated with the same buffer adjusted to 400mM NaCl. The supernatant from the second extraction was combined with the first and dialyzed for two hours at 4oC against 15mM Hepes ph7, 25mM KCl, 1mM β-mercaptoethanol, 1mM PMSF, 5mM sodium butyrate. Purified nucleosomes were then subjected to native-ChIP, and enriched DNA was end-repaired, linker-adapted and sequenced on an Illumina HiSeq 2000 to 50bp read length (Barski et al., 2007). The following antibodies were used to detect modified histones: H3K4me3 (Abcam: 8580), H3K27Ac (Abcam: 4729) and H3K27me3 (Millipore: 07-449).

value: Head

tag: chip antibody

value: Adult


title: B3 Control rep3

value: untreated control


title: Tdc2-H3K27ac


title: Tdc2-H3K4me3


title: Tdc2-H3K27me3-rep1

value: H3K27me3 (Millipore:07-449)


title: OK107-H3K27ac

description: OK107-GAL4 (Adachi et al., 2003) driving unc84-GFP, primarily in Kenyon cells

source_name: Kenyon cells


title: OK107-input


title: OK107-H3K27me3


title: R57C10-Input

description: R57C10-GAL4 (Pfeiffer et al., 2008) driving unc84-GFP in all mature neurons

source_name: Head neurons


title: B1 Control rep1


title: Tdc2-H3K27me3-rep2


title: F2 FICZ treated rep2


title: R57C10-H3K27ac-rep2


title: R57C10-H3K27ac-rep1


title: R57C10-H3K27me3-rep2


title: R57C10-H3K27me3-rep1


title: OK107-H3K4me3


title: R57C10-H3K4me3-rep1


title: Tdc2 rep1

data_processing:
Base calling performed by Illumina CASAVA 1.8
Five base pairs were trimmed from 5'-end of all reads to remove possible adaptor contamination, using FASTX toolkit v0.0.13 (fastx_trimmer -f 6 -z -Q33)
Reads were aligned to dm3/ERCC92 combined index using TOPHAT v1.4.0 (--num-threads 8 --GTF flybase_r5.41_ERCC92.gtf --no-novel-juncs --min-intron-length 30 --max-intron-length 200000)
Expression levels (FPKM) and differential expression were estimated using CUFFDIFF v 1.3.0 (cuffdiff --num-threads 8 --multi-read-correct --frag-bias-correct dm3_ercc92.fa -M $MASK_GTF)
Coverage over genomic positions counted with BEDTOOLS v2.15 (genomeCoverageBed -split -bg)
Coverage scaled to 10M total alignments. (custom Perl script)
Scaled coverage was converted to bigWig (wigToBigWig from ucsc)
Genome_build: dm3
Supplementary_files_format_and_content: bigWig tracks for visualization; supplemental files are tab-delimited files containining CUFFDIFF estimated expression levels and differential expression from pairwise comparisons for (1) annotated isoforms and (2) genes.

molecule: nuclear RNA

source_name: Octopaminergic cells

extract_protocol: Adult flies were anesthetized by CO2 and flash frozen in liquid N2. Heads were separated from abdominal-thoracic segments, wings and legs by vigorous vortexing followed by separation over dry ice cooled sieves. 600 - 10,000 frozen heads were added to 50mls of 10mM b-glycerophosphate pH7, 2mM MgCl2, 5mM sodium butyrate, 1X complete protease inhibitor cocktail (Roche: 11873580001) and the suspension was passed over a Yamato continuous flow homogenizer, set at 90-100 rpm, five to seven times. The homogenate was filtered over Miracloth (EMD Biosciences: 475855) and bought to 0.7mM b-mercaptoethanol and 0.5% NP-40. After six tractions in a 40ml Dounce homogenizer (pestle B), 600uls of antibody-adsorbed beads were added to 50mls of lysate. The binding reaction was run under continuous agitation at 4oC for 30 minutes. Beads were then collected on a magnet and washed three to four times in 50mls 10mM β-glycerophosphate pH7, 250mM sucrose, 2mM MgCl2, 25mM KCl, 5mM sodium butyrate. Bead bound nuclei in 20mls wash buffer were then passed over a 20um nylon mesh, returned to the magnet stand and resuspended in 1ml of 10mM β-glycerophosphate pH7, 250mM sucrose, 2mM MgCl2, 25mM KCl, 5mM sodium butyrate. Bead bound nuclei were collected on a magnet stand, then resuspended in 400μls of 100mM Tris pH7, 4M guanidinium thiocyanate. After 30 minutes of agitation at 4oC the supernatant containing nuclear RNA was removed from the beads and extracted with an equal volume of phenol:CHCl3. After the addition of 0.1 volume 3M sodium acetate pH5, the sample was extracted with acid phenol. The Agencourt RNA-Advantage kit (Beckman Coulter: 47942) was then used to purify RNA directly from the aqueous layer of the last extraction. Nuclear RNA was then converted to cDNA using a Nugen Ovation RNA-seq v2 kit (Nugen: 7102). Amplified cDNA was then sheared in a Corvaris s2 instrument, end-repaired, linker-adapted and sequenced on an Illumina HiSeq 2000 to 50bp read length. RNA was isolated from whole dissected brains in 100mM Tris pH7, 4M guanidinium thiocyanate.

value: Tdc2-GAL4 cells


title: Tdc2 rep2


title: OK107 rep2

value: OK107-GAL4 cells


title: R57C10 rep1

value: R57C10-GAL4 cells


title: OK107 rep1


title: R57C10 rep2


title: B2 Control rep2


title: Whole brain

description: whole dissected brain

source_name: Brain

value: Brain

value: all cells in brain


title: Ago4 mRNAAgo4 KO Day8

status: Public on Aug 01 2012

city: Ithaca

first: Stephanie

middle: Renee

last: Hilz

address: Biotech 445, Cornell University

institute: Cornell University

data_processing:
mRNA
Data were filtered using Illumina's automated quality filter.  Low quality bases were also trimmed using custom software.
Reads were aligned to the transcriptome using TopHat (v1.3.0).
Differential expression between paired wild-type and knock-out samples was determined using Cuffdiff, a sub-package of Cufflinks (v1.1.0).
small RNA
Data was filtered to remove reads shorter than 14 nucleotides, lacking the proper cloning adapters sequence, and containing low quality bases (bases called as 'N').
Sequences were aligned to genome using Bowtie (v0.12.7).
Genome matching reads were aligned to hairpins from miRBase (release 18).
Genome_build: Mus Musculus NCBI Build 37
Supplementary_files_format_and_content: Cuffdiff (a sub-package of Cufflinks) differential expression spreadsheet, containing, for each gene, RPKM values for wild-type (sample_2) and AGO4 knock-out (sample_1) samples.
Supplementary_files_format_and_content: All sequenced reads in the format of a non-redudnant list of unique sequences, followed by the number of times each sequence appeared in  wild-type (columns 1 and 2) and AGO4 knock-out (columns 3 and 4) mouse small RNA libraries.

source_name: Day 8 Whole Testis

extract_protocol: Tissues were removed or isolated and homogenized. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001, FC-122-1002) was used with 2 ug of total RNA for the construction of sequencing libraries.

value: 8 days

value: testis


title: Ago4 mRNAAgo4 WT Day8


title: Ago4 mRNAAgo4 KO Day3

source_name: Day 3 Whole Testis

value: 3 days


title: Ago4 mRNAAgo4 WT L/Z

source_name: Leptotene/Zygotene Cells

value: 70 days

value: Leptotene/Zygotene Cells


title: Ago4 small RNA KO

description: 18-30nt RNA from total RNA

source_name: Total Small RNA from Pachytene Cells

extract_protocol: Technique as described previously (Grimson et al., 2008). Briefly, isolated pachytene spermatocytes from Ago4+/+ and Ago4-/- littermate adult (70-80 dpp) mice were placed in TRIZOL (Invitrogen) and total RNA was extracted according to manufacturer‟s directions. The library was constructed as described (Grimson et al., 2008) and sequenced on the Illumina platform (Illumina, San Diego CA, USA).

value: Pachytene Cells


title: Ago4 small RNA WT

description: 18-30nt RNA from total RNA


title: R57C10-H3K4me3-rep2


title: Ago4 mRNAAgo4 WT PACH

source_name: Pachytene Cells


title: Ago4 mRNAAgo4 WT Day3


title: Ago4 mRNAAgo4 KO PACH


title: UtxFlx WCE

first: Albert

middle: W

last: Cheng

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

data_processing:
ChIP-Seq reads were aligned using the software Bowtie (Langmead et al., 2009) to NCBI build 36 (mm8) of the mouse genome with default settings. Sequences uniquely mapping to the genome with zero or one mismatch were used in further analysis. When multiple reads mapped to the same genomic position, a maximum of two reads mapping to the same position were used. Multi-mapping reads were then re-aligned to a Bowtie sequence index comprised of regions from the mouse repeat masker table using the parameters: -n2, -e70, -M1, -k1, --best.
The Young error model was used to generate wiggle files and enriched region information
Genome_build: mm8
Supplementary_files_format_and_content: gzipped WIG file

source_name: ESCs

growth_protocol: ES cells were grown on gelatin in an undifferentiated state (ES medium (+LIF)).

extract_protocol: ChIP-DNA gets loaded onto SPRI in which the following is performed: (1) End Repair (Blunt Ends) (2) "A" base addition (3) Adapter Ligation (4) Size Selection (200-400bp). Libraries are taken off SPRI and are enriched. For enrichment, we used HIFI KAPA Enzymes for PCR followed by an in-house primer for barcoding which substitutes the Illumina Primer 2.0. Libraries undergo quality control and submitted to sequencing

treatment_protocol: ES media was replaced with ES media minus LIF plus 1x10-7M retinoic acid (RA).  Cells were cultured for an additional 48 hours with one media exchange.

value: ESCs

value: UtxFlx

value: untreated


title: UtxFlx H3K27me3

value: H3K27 trimethyl (Millipore 07-449)


title: UtxKO WCE

value: UtxKO


title: UtxKO + RA H3K27me3

source_name: RA-treated ESCs

value: RA for 48 hours


title: UtxKO H3K4me3

value: H3K4 trimethyl (Millipore 07-473)


title: UtxKO H3K27me3


title: UtxFlx H3K4me3


title: UtxKO + RA H3K4me3


title: UtxKO + RA WCE


title: UtxFlx + RA H3K4me3


title: UtxFlx + RA H3K27me3


title: H4K20me1 ChIP-seq of set-4 mutant, rep2

first: Przemyslaw

middle: Aleksander

last: Stempor

state: United Kingdom

address: Tennis Court Road

department: The Gurdon Institute

data_processing:
ChIP-seq reads were aligned to the WS190 assembly of the C. elegans genome using BWA (Li and Durbin, 2010 (PMID 20080505)) with default settings.
Data were normalized using BEADS (Cheung et al., 2011 (PMID 21646344)). BEADS scores were converted to log2, and then the datasets were z-scored.
Signals were averaged in 50bp windows and wig files were generated.
Genome_build: WS190
Supplementary_files_format_and_content: Wig files were generated using the BEADS pipeline in R. Scores represent log2-transformed BEADS scores (single experiments). The wig file for the mean of AA015 and AA016 was generated by z-scoring the average of the single log2 scores.

organism: Caenorhabditis elegans

source_name: L3 larvae, set-4 mutant, H4K20me1 ChIP

growth_protocol: About 2-7 million worms are bleached and then hatched in M9 for 24-42 hrs. About 100 embryos are seeded onto the plate to test for contamination and hatching efficiency. Remaining hatched L1 larvae are inoculated in a proper volume of liquid culture. The next day when larvae reach the L3 stage, they are cleaned by M9 washes and sucrose gradient and collected by freezing in liquid nitrogen. Just before collection, DIC pictures are taken and about 50ul of worms are stained for DAPI to assess the stage.

extract_protocol: Libraries were made using the TruSeq DNA Sample Prep kit (Illumina). 1-10ng of ChIP or 10ng of input are blunted (T4 polymerase), an A-overhang is added (Klenow), DNA is ligated to adaptors, amplified by PCR, and the library is size-selected to a 250-400 bp range using Agencourt AMPure XP beads.

treatment_protocol: Worms are frozen, ground and crosslinked for 10 minutes in 1% formaldehyde. Formaldehyde is quenched and cross-linked tissue is washed, resuspended in FA buffer and sonicated to an average size of 200bp using a Bioruptor. Extracts are then spun down and the soluble fraction is used for ChIP.

value: whole body

value: L3 larvae

tag: chip antibody vendor

value: Abcam

tag: antibody catalog#

tag: antibody lot#


title: H4K20me1 ChIP-seq of set-4 mutant, rep1

tag: tissue


title: UtxFlx + RA WCE

tag: genotype

tag: treatment


title: H4K20me1 ChIP-seq of wild-type

source_name: L3 larvae, wild-type, H4K20me1 ChIP

value: wild-type


title: HudsonAlpha_MethylRrbs_HSMM_FSHD

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

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=wgEncodeHaibMethylRrbs

value: in vitro differentiated cells

value: myotube

tag: lab

value: HudsonAlpha

tag: lab description

value: Myers - Hudson Alpha Institute for Biotechnology

tag: datatype

value: MethylRrbs

tag: datatype description

value: DNA Methyl Reduced Rep Bisulfite Seq

tag: cell

tag: cell organism

value: human

tag: cell description

value: primary myoblast from Facioscapulohumeral Muscular Dystrophy (FSHD) patients, muscle needle biopsies

tag: cell sex

value: U

tag: treatment description

value: No special treatment or protocol applies

tag: labexpid

tag: obtainedby

value: Duke

tag: obtainedby description

value: Crawford - Duke University

tag: replicate


title: Barcode_B13_rna_46c_d5_nuc_pa_r3_10

city: San Francisco

first: Courtney

last: Onodera

address: 1450 Third St, HD374

institute: University of California, San Francisco

data_processing:
Reads were mapped in sequential stages to the mouse genome using the Applied Biosystems SOLiD Small RNA Analysis pipeline (Corona), as described previously (Underwood JG et al., Nat Methods. 2010 Dec;7(12):995-1001). In summary, we generated a filter file that included SOLiD adaptor sequence, rRNAs, and small RNAs (including tRNAs, miRNAs, and others). We also generated a target file (exon+introns) based on UCSC Known Genes: this file contains for each gene the complete genomic sequence from transcription start to transcription end; overlapping genes were merged. Finally, we generated a file containing known exon junction sequences; this file contains 50 bases upstream and downstream of all unique splices represented in UCSC Known Genes. To map reads, we first removed any reads mapping to the filter file, then mapped to the exon+introns target file (sense and antisense). Any remaining reads were then mapped to the genome. We then performed a second round of mapping, first filtering the reads as in the first round, and then mapping to the splice junction file. At each mapping stage, up to 15 hits per read were allowed. Any reads mapping more than 15 times were discarded. Mapping to the genome was performed chromosome by chromosome, and thus up to 15 hits per chromosome were allowed.
Sense and antisense mappings from the exon+introns target file were converted to positive and negative strand mappings to the genome. All read mappings for a given barcode were combined to one bed file.
Genome_build: mm9
Supplementary_files_format_and_content: All files in UCSC bed format.

source_name: 46C mESC cell line

growth_protocol: mESCs (cell line 46C) were cultured without feeder layers according the BayGenomics protocol adapted from (Skarnes WC, Methods Enzymol. 2000;328:592-615). mESCs were differentiated to Day 5 neural precursors with the protocol described by Ying et al. (Ying QL et al., Methods Enzymol. 2003;365:327-41; Ying QL et al., Nat Biotechnol. 2003 Feb;21(2):183-6). Briefly, undifferentiated ES cells are plated as a monolayer on gelatin-coated dishes in media lacking leukemia inhibitory factor (LIF), serum, and any growth factors; the absence of LIF prompts mESC differentiation, and in conditions without serum or growth factors the cells largely commit to the neural lineage. The cells acquire a neural precursor morphology by 5 days after plating.

extract_protocol: Extracted RNAs (approximately 100-600 ug) were treated with DNase to remove contaminating DNA, then polyadenylated transcripts were selected with Oligotex resin (Invitrogen). We then chose to remove the polyA tails to allow sequencing up to the very 3' ends of the transcripts; to do this we annealed an oligo dT primer (Invitrogen) to the RNA samples, then treated with RNase H (New England Biolabs). We purified these RNAs using a G50 column (Roche) to remove oligos smaller than 25bp, followed by another DNase treatment, and then used the Ribominus kit (Invitrogen) to deplete our RNAs further of rRNA. Next, RNAs (400 ng) were fragmented using either 1 ug Nuclease P1 (Sigma) for 10 or 60 minutes or 1 U RNase III (Applied Biosystems, now Life Technologies) for 10 minutes, according to the instructions in the SOLiD Whole Transcriptome Analysis Kit (Applied Biosystems). The final libraries were generated from these fragmented RNAs using the Small RNA Expression Kit (SREK, Applied Biosystems), with insert sizes of approximately 90-190 bp. Equimolar concentrations of each library (excepting Barcode B06, for which we used twice the concentration) were used as the starting material for emulsion PCR.

treatment_protocol: Cells were fractionated to their nuclear and cytoplasmic components using a gentle detergent to disrupt the outer cell membrane while preserving intact nuclei before RNA extraction.

tag: cell type

value: ES-derived neural precursors (46C)

tag: cell compartment

value: nucleus

tag: fragmentation

value: RNase III, 10 min


title: Barcode_B12_rna_46c_d5_nuc_pa_p1_60

value: Nuclease P1, 60 min


title: Ago4 mRNAAgo4 KO L/Z

tag: age

value: 70 days

tag: strain

tag: genotype

value: Leptotene/Zygotene Cells


title: Barcode_B11_rna_46c_d5_nuc_pa_p1_10

value: Nuclease P1, 10 min


title: Barcode_B09_rna_46c_d5_cyt_pa_p1_60

value: cytoplasm


title: Barcode_B07_rna_46c_un_nuc_pa_r3_10

value: undifferentiated mESCs (46C)


title: Barcode_B06_rna_46c_un_nuc_pa_p1_60


title: Barcode_B04_rna_46c_un_cyt_pa_r3_10


title: Barcode_B03_rna_46c_un_cyt_pa_p1_60


title: Barcode_B01_rna_46c_un_cyt_pa_p1_10


title: Barcode_B08_rna_46c_d5_cyt_pa_p1_10


title: RIKEN_Cage_HUVEC_nucleus_longNonPolyA

source_name: HUVEC

tag: datatype

value: Cage

value: CAGE 5' RNA Tags

tag: rnaextract

value: longNonPolyA

tag: rnaextract description

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

tag: biorep

tag: readtype

tag: readtype description

value: Single 36 nt reads

tag: cell lineage

value: mesoderm

tag: localization

tag: localization description

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


title: RIKEN_Cage_HeLa-S3_nucleus_longNonPolyA

tag: datatype description

tag: labexpid

value: ectoderm

tag: cell sex

value: F


title: RIKEN_Cage_NHDF_cell_longPolyA

source_name: NHDF

value: longPolyA

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

value: Single 50 nt reads

tag: replicate

value: cell

value: Whole cell


title: RIKEN_Cage_HWP_cell_longPolyA

source_name: HWP

value: B


title: RIKEN_Cage_NHEM.f_M2_cell_longPolyA

value: M


title: RIKEN_Cage_IMR90_cytosol_longPolyA

value: cytosol

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


title: RIKEN_Cage_HVMF_cell_longPolyA

source_name: HVMF

value: Cage

value: CAGE 5' RNA Tags


title: HapMap MNase-seq GM18507

city: La Jolla

first: Graham

last: McVicker

address: 10010 N Torrey Pines Rd

institute: Salk Institute

description: Paired-end 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).

tag: cell type

value: lymphoblastoid cell line

tag: population

value: YRI

tag: ethnicity

value: Yoruba

tag: country of origin

value: Nigeria


title: Barcode_B10_rna_46c_d5_cyt_pa_r3_10

value: ES-derived neural precursors (46C)

tag: cell compartment

value: cytoplasm

tag: fragmentation

value: RNase III, 10 min


title: RIKEN_Cage_Monocytes-CD14+_cell_longPolyA

city: Stanford

tag: datatype

tag: rnaextract

value: longPolyA

tag: rnaextract description

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

value: F


title: RIKEN_Cage_IMR90_nucleus_longPolyA

tag: biorep

tag: readtype

tag: readtype description

value: Single 50 nt reads

value: nucleus

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


title: VISA project Vancomycin intermediate sensitive clinical isolate A2

description:
A2_VISA
3 biological replicates

data_processing:
Data was imported into CLC Workbench 4.8
Reads under 50 nucleotides in length were discarded.
Reads were paired, using min_distance=180 and max_distance=250
Reads were trimmed, using default settings
A 'Gene Expression' experiment was conducted, using default settings and Staphylococcus aureus TCH1516 (NC_010079) as a reference.
Genome_build: NC_010079.1
Supplementary_files_format_and_content: A1_A2_stringent_USE.txt contains all mapping information.  Expression values are given in RPKM.  The data has been normalized using Quantile normalization, and has also been square root transformed. Statistical analyses were on Proportion, using Baggerley's test – all pairs on the normalized expression values - FDR corrected. The 'Fold Change' column is comparing fold change of A2 against A1.

source_name: Mid-log cells

extract_protocol: Ambion RiboPure Bacteria Kit, was used to isolate total RNA, which was enriched using the Ambion MicrobExpress kit. cDNA was made from the RNA, then paired end libraries were created using standard Illumina protocols.

tag: strain

tag: isolate

tag: vancomycin and daptomycin susceptibility

value: VISA [intermediate sensitive]


title: RIKEN_Cage_SkMC_cell_longPolyA

source_name: SkMC

tag: datatype description

tag: labexpid

tag: cell sex

value: B

tag: localization

value: cell

tag: localization description

value: Whole cell


title: RIKEN_Cage_hMSC-BM_cell_longPolyA

source_name: hMSC-BM

value: Cage

value: CAGE 5' RNA Tags

tag: replicate


title: RIKEN_Cage_IMR90_cell_longPolyA


title: RIKEN_Cage_hMSC-AT_cell_longPolyA

source_name: hMSC-AT


title: RIKEN_Cage_NHEM_M2_cell_longPolyA


title: RIKEN_Cage_hMSC-UC_cell_longPolyA

source_name: hMSC-UC


title: RIKEN_Cage_SK-N-SH_cytosol_longPolyA

source_name: SK-N-SH

value: cytosol

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


title: RIKEN_Cage_SK-N-SH_nucleus_longPolyA


title: RIKEN_Cage_SK-N-SH_cell_longPolyA


title: RIKEN_Cage_HPC-PL_cell_longPolyA

source_name: HPC-PL


title: RIKEN_Cage_HMEpC_cell_longPolyA

source_name: HMEpC

tag: cell lineage

value: ectoderm


title: RIKEN_Cage_HOB_cell_longPolyA

source_name: HOB

value: M


title: RIKEN_Cage_HCH_cell_longPolyA

source_name: HCH


title: RIKEN_Cage_HFDPC_cell_longPolyA

source_name: HFDPC


title: RIKEN_Cage_HPIEpC_cell_longPolyA

source_name: HPIEpC


title: RIKEN_Cage_HSaVEC_cell_longPolyA

source_name: HSaVEC


title: RIKEN_Cage_MCF-7_nucleus_longPolyA


title: RIKEN_Cage_CD34+_Mobilized_cell_longPolyA


title: RIKEN_Cage_HAoAF_cell_longPolyA

source_name: HAoAF


title: HapMap MNase-seq GM19239

description: Paired-end sequencing

tag: cell type

value: lymphoblastoid cell line

tag: population

value: YRI

tag: ethnicity

value: Yoruba

tag: country of origin

value: Nigeria


title: RIKEN_Cage_CD20+_cell_longPolyA

tag: datatype

tag: rnaextract

value: longPolyA

tag: rnaextract description

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

tag: biorep

value: Single 50 nt reads

value: F


title: pigmented cluster H9

first: Kevin

last: Huang

address: Gonda BLDG Rm. 6554, P.O.Box 957088

department: Human Genetics

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters  -v1 -a -m 10 --best --strata
Reads Per  Megabase of library size (RPM) were calculated by counting the number of reads falling in the miRNA locus and normalizing by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each sample

source_name: pigmented cluster

growth_protocol: Pluripotent stem cells (hESC and iPSCs) were plated onto gamma-rays irradiation mouse embryonic feeder cells with DMEM/F12 culture medium containing 20% Knock-Out Serum Replacement, 0.1 mM nonessential amino acids, 0.1 mM b-mercaptoethanol and 100 ng/ml zebrafish basic fibroblast growth factor (zfbFGF) on a 6-well plate. Briefly, cells were cultured at 37°C in 5% CO2 for 6-10 days after which zfbFGF was omitted to facilitate spontaneous cell differentiation.Pigmented colonies were observed within 4 weeks and allowed to expand for a few weeks, with media changes every 2–3 days. Pigmented cells were enriched by manual dissection using insulin needle followed by seeded on growth factor reduced Matrigel (BD Biosciences, diluted 1:30) coated plate and transwell membranes. RPE medium were changed to support pigment cluster expansion[containing a-MEM, 1 x N2 supplement(Gibco), 1x Non-essential amino acid solution, 250 mg/ml taurine, 13 ng/ml Triiodo thyronin (Sigma-Aldrich, Gillingham, UK), 20 ng/ml Hydrocortisone (Sigma), 2mM L298 glutamine (Invitrogen, Paisley,UK), 1x Penicillin-streptomycin and 10% Hyclone heat inactivated foetal bovine serum(Thermo Scientific, Northumberland, UK)], which was replaced daily. After 2 to 3 months，under these conditions, hESC-RPE and hiPSC RPE would form monolayer sheets of pigmented cells that can be dissected for gene expression analysis.

extract_protocol: Total RNA (1~10μg) was ligated with a pair of Illumina adaptors to their 5′and 3′ends. After reverse transcription, the small RNA molecules were amplified using multiplex adaptor primers for 12 cycles and the fragments around 93~100 bp (small RNA+adaptors) were then isolated from agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina's HiSeq2000 sequencing according to the manufacturer's instructions.

value: pigmented cluster

tag: parental cell line


title: RIKEN_Cage_A549_nucleus_longPolyA

tag: readtype

tag: readtype description

value: nucleus

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


title: RIKEN_Cage_A549_cytosol_longPolyA

value: Cage

tag: datatype description

tag: labexpid


title: partially differentiated ESC BG01 partial diff

source_name: partially differentiated ESC

value: partially differentiated ESC


title: ES-RPE H9

source_name: ES-RPE

value: ES-RPE


title: fetal RPE

source_name: fetal RPE

value: primary fetal RPE


title: ES-RPE HSF1


title: ESC H9 ESC

source_name: ESC

value: ESC


title: RIKEN_Cage_HAoEC_cell_longPolyA

source_name: HAoEC

value: CAGE 5' RNA Tags

tag: cell sex

value: B

tag: localization

value: cell

value: Whole cell


title: ESC BG01 rep1

tag: cell line


title: ESC BG01 rep2


title: 60hpf-TCDD-1

source_name: Embryos

tag: strain

value: TL wild type

tag: tissue

value: embryos

tag: time

value: 60 hpf

tag: treatment

value: TCDD


title: HapMap MNase-seq GM19238

description: Paired-end sequencing

source_name: lymphoblastoid cell line

tag: cell type

value: lymphoblastoid cell line

tag: population

value: YRI

tag: ethnicity

value: Yoruba

tag: country of origin

value: Nigeria


title: partial differentiated ESC H9

source_name: partial differentiated ESC

value: partial differentiated ESC


title: HapMap MNase-seq GM19193

description: Paired-end sequencing


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

description: Paired-end sequencing


title: HapMap MNase-seq GM18516 (Paired-end)

description: Paired-end sequencing


title: HapMap MNase-seq GM18516 (Single-end)

description: Single-end (SE) sequencing


title: HapMap MNase-seq GM18508

description: Paired-end sequencing


title: ES-RPE hiPS2


title: HepG2.H3K4me3_ChIP-Seq

city: Chongqing

first: Ni

last: Bing

address: PLA, Third Military Medical University

department: Institute of Immunology

institute: PLA, Third Military Medical University

data_processing:
ChIP-seq reads of ~49 bp were mapped to the University of California, Santa Cruz (UCSC) human genome (hg18) by SOAP2, which allowed a uniquely aligned read to have up to two mismatching bases. The output of the SOAP analysis data was converted to browser-extensible data (BED) files in order to view the data in the UCSC Genome Browser. The reads were binned into nonoverlapping windows of 200 bp. The number of normalized sequence reads of a gene locus=(the sequence read counts from 1 kb upstream of the transcription start site to the end of the gene / the total number of sequence reads of each modification)×the bigger total number of sequence reads of each modification between the two cells.
Genome Build:
HepG2_H3K4.bed: UCSC hg18

source_name: HepG2 cells, H3K4me3 ChIP

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: In brief, 1×10^7 HepG2 and HepG2.2.15 cells were crosslinked with formaldehyde and sonicated to obtain chromatin fragments of 200 to 300 bp. Sonicated chromatin was pre-cleared and incubated with 2 µg of anti-H3K4me3 (Abcam, United Kingdom), anti-H3K27me3 (Abcam) or anti-rabbit IgG (Upstate, USA) overnight at 4℃. The crosslinks were reversed, and DNA was treated sequentially with Proteinase K and RNase A, and purified using the Qiaquick PCR-purification kit (Qiagen, Germany). ChIP samples were tested for enrichment by qPCR. For ChIP-Seq, the precipitated DNA was repaired using PNK and Klenow enzyme, and ligated to adapters according to manufacturer’s instructions. Subsequently, PCR-amplified fragments of approximately 220 bp were sequenced using Illumina HiSeq™ 2000 following the manufacturer’s protocols (www.illumina.com).

value: human hepatocellular liver carcinoma cells

tag: chip antibody

tag: antibody vendor

value: Abcam

tag: antibody catalog #

tag: antibody lot #


title: HepG2.H3K27me3_ChIP-Seq

data_processing:
ChIP-seq reads of ~49 bp were mapped to the University of California, Santa Cruz (UCSC) human genome (hg18) by SOAP2, which allowed a uniquely aligned read to have up to two mismatching bases. The output of the SOAP analysis data was converted to browser-extensible data (BED) files in order to view the data in the UCSC Genome Browser. The reads were binned into nonoverlapping windows of 200 bp. The number of normalized sequence reads of a gene locus=(the sequence read counts from 1 kb upstream of the transcription start site to the end of the gene / the total number of sequence reads of each modification)×the bigger total number of sequence reads of each modification between the two cells.
Genome Build:
HepG2_H3K27.bed: UCSC hg18

source_name: HepG2 cells, H3K27me3 ChIP


title: HepG2.2.15.H3K4me3_ChIP-Seq

data_processing:
ChIP-seq reads of ~49 bp were mapped to the University of California, Santa Cruz (UCSC) human genome (hg18) by SOAP2, which allowed a uniquely aligned read to have up to two mismatching bases. The output of the SOAP analysis data was converted to browser-extensible data (BED) files in order to view the data in the UCSC Genome Browser. The reads were binned into nonoverlapping windows of 200 bp. The number of normalized sequence reads of a gene locus=(the sequence read counts from 1 kb upstream of the transcription start site to the end of the gene / the total number of sequence reads of each modification)×the bigger total number of sequence reads of each modification between the two cells.
Genome Build:
HepG2_2_15_H3K4.bed: UCSC hg18

source_name: HepG2.2.15 cells, H3K4me3 ChIP


title: HepG2.2.15.H3K27me3_ChIP-Seq

data_processing:
ChIP-seq reads of ~49 bp were mapped to the University of California, Santa Cruz (UCSC) human genome (hg18) by SOAP2, which allowed a uniquely aligned read to have up to two mismatching bases. The output of the SOAP analysis data was converted to browser-extensible data (BED) files in order to view the data in the UCSC Genome Browser. The reads were binned into nonoverlapping windows of 200 bp. The number of normalized sequence reads of a gene locus=(the sequence read counts from 1 kb upstream of the transcription start site to the end of the gene / the total number of sequence reads of each modification)×the bigger total number of sequence reads of each modification between the two cells.
Genome Build:
HepG2_2_15_H3K27.bed: UCSC hg18

source_name: HepG2.2.15 cells, H3K27me3 ChIP