title: ChIP-Seq for Smc1 in MEF

status: Public on Aug 12 2010

description: Chromatin IP against Smc1

data_processing:
Images acquired from the Illumina/Solexa sequencer were processed through the bundled Solexa image extraction pipeline which identified polony positions, performed base-calling and generated QC statistics.
Sequences were aligned using ELAND software to NCBI Build 36 (UCSC mm8) of the mouse genome. Only sequences that mapped uniquely to the genome with zero or one mismatch were used for further analysis. The .ylf files are in [Y]oung [L]ab [F]ormat. It is a compact flat file representation of aligned read locations. The file contains the locations of the ELAND aligned reads with the following format:    #U0 (read category U0)  >1 (chromomsome 1)  -12345 (minus strand read)  -9876 (minus strand read)  54321 (plus strand read)  >2 (chromomsome 2)  -67890 (minus strand read)  98765 (plus strand read)  132323 (plus strand read)  #U1 (read category U1)  (etc.)
Each read was extended 200bp, towards the interior of the sequenced fragment, based on the strand of the alignment. Across the genome, in 25 bp bins, the number of ChIP-Seq reads within each bin was tabulated (replicates combined). Bins with at least 0.5 reads per million were visualized in the WIG files. The 25bp genomic bins that contained statistically significant ChIP-Seq enrichment were identified by comparison to a Poissonian background model, using an 1e-09 cutoff. Enriched bins within 200bp of one another were combined into regions. The Poissonian background model assumes a random distribution of background reads, however we have observed significant deviations from this expectation. Some of these non-random events can be detected as sites of apparent enrichment in negative control DNA samples and can create many false positives in ChIP-Seq experiments. To remove these regions, we compared genomic bins and regions that meet the statistical threshold for enrichment to a set of reads obtained from Solexa sequencing of DNA from whole cell extract(s) (WCE) in matched cell samples [GSM307154 and WCE sample uploaded here for mES, GSM555166 for MEFs]. We required that enriched bins and enriched regions have five-fold greater ChIP-Seq density in the specific IP sample, compared with the control sample, normalized to the total number of reads in each dataset. This served to filter out genomic regions that are biased to having a greater than expected background density of ChIP-Seq reads. For further details see associated publication.

source_name: Mouse embryonic fibroblasts

growth_protocol:
V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates, with the exception of replicate 1 of Med12, which was grown for one passage off of MEFs.
Mouse embryonic fibroblasts were grown in DMEM with 10% FBS.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 350bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: antibody catalog number

value: Bethyl A300-055A

tag: antibody lot number

value: MEF


title: ChIP-Seq for Med1 in MEF

type: SRA

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

country: USA

institute: Whitehead Institute for Biomedical Research

description: Chromatin IP against Med1

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: chip antibody

value: Bethyl A300-793A

tag: strain

tag: cell type


title: ChIP-Seq for Med12 in MEF

description: Chromatin IP against Med12

value: Bethyl A300-774A


title: BiSulfite "S"

status: Public on Aug 15 2010

first: Joshua

middle: Z

last: Levin

address: 320 Charles Street

institute: Broad Institute of MIT & Harvard

library_source: transcriptomic

data_processing: We used Arachne to map the reads to the genome. Reads in single end libraries were mapped uniquely, allowing up to 4 mismatches.  Reads in paired-end libraries were first mapped non-uniquely allowing up to 4 mismatches, and then we searched for unique pairing of the non unique read mappings.  A unique pairing is defined as a single pair of mappings on the same chromosome, up to 500 bp apart, with reads on opposite strands.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Yeast grown in liquid culture

growth_protocol: Cells were grown at 30 C in a shaking water bath (New Brunswick Scientific) in the following medium:  1.5% yeast extract,  1% peptone, 2% dextrose, 0.2% SC amino acid mix  (Sunrise Science).  Cells were then harvested by freezing in liquid nitrogen, spun 5 minutes ,  3700 x g  in a Sorvall Legend RT to pellet the cells, and resuspended in 2 ml RNAlater (Ambion).

extract_protocol:
Library construction: BiSulfite (see Schaefer et al. 2009 Nucleic Acids Res.)
RNA was extracted with the RNeasy kit (Qiagen) and treated with Turbo DNase (Ambion).  Polyadenylated RNA was selected with the MicroPoly(A)Purist kit (Ambion).

tag: growth stage

value: Mid-log


title: NNSR no actD

extract_protocol:
Library construction: “Not-Not-So-Random” primer protocol (‘NNSR’), where we modified the original Not-So-Random (NSR) method (Armour et al. 2009 Nature Methods) by replacing the “not so random” primers for cDNA synthesis with random (or “not not so random”) primers; no actinomycin D
RNA was extracted with the RNeasy kit (Qiagen) and treated with Turbo DNase (Ambion).  Polyadenylated RNA was selected with the MicroPoly(A)Purist kit (Ambion).


title: ChipSeq for CTCF

description: Chromatin IP against CTCF

value: CTCF

value: Upstate 07-729


title: p63_2_ChIPSeq

city: Nijmegen

first: Jo

middle: Huiqing

last: Zhou

address: Geert Grooteplein 26-28

department: Human Genetics

country: Netherlands

institute: NCMLS

description: Chromatin IP against p63

data_processing: Reads were aligned to the human genome (hg18) using ELAND. Peaks were called using MACS with default settings and p-value threshold of 1e-9.

organism: Homo sapiens

source_name: primary keratinocyte

growth_protocol: The human primary keratinocytes were maintained in KGM medium.

extract_protocol: Cells were crosslinked with 1% formaldehyde for 10 min at room temperature, quenched with 0.125 M glycine and washed at 4C with three buffers: (i) PBS, (ii) buffer of composition 0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES pH 7.6 and (iii) 0.15 M NaCl in HEG buffer (1 mM EDTA, 0.5 mM EGTA, 50 mM HEPES pH 7.6). Cells were then suspended in ChIP incubation buffer (0.15% SDS, 1% Triton X-100, 150 mM NaCl, HEG) and sonicated using a Bioruptor Sonicator.

treatment_protocol: undifferentiation condition

tag: tissue

value: epidermis

tag: antibody

value: 4A4 against p63

tag: cell line

value: primary cells

value: keratinocytes


title: WCE in mES cells

description: WCE in mES cells

source_name: Embyonic stem cells

value: V6.5 embryonic stem cells


title: ChIP-Seq for Nipbl in mES cells

description: Chromatin IP against Nipbl

value: Nipbl

value: Bethyl A301-779A


title: ChIP-Seq for Med1 in mES cells (rep 2)

description: Chromatin IP against Med1


title: ChIP-Seq for CTCF in MEF (rep 2)

description: Chromatin IP against CTCF


title: p63_3_ChIPSeq

description: Chromatin IP against p63

growth_protocol: The human primary keratinocytes were maintained in KGM medium

value: H129 against p63


title: ChIP-Seq for Med1 in mES cells

description: Chromatin IP against med1


title: ChIP-Seq for Nipbl in mES cells (rep 2)

description: Chromatin IP against Nipbl


title: mES_Med12_051809_ChipSeq

description: Chromatin IP against mES_Med12_051809


title: ChIP-Seq for Med12 in mES cells (rep 2)

description: Chromatin IP against Med12


title: ChIP-Seq for Smc3 in mES cells (rep 2)

description: Chromatin IP against Smc3

value: Abcam AB9263


title: ChIP-Seq for Smc3 in mES cells

description: Chromatin IP against Smc3


title: E8-16h_disco_ChIPSeq_1 and 2

status: Public on Aug 11 2010

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

data_processing: Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.

organism: Drosophila melanogaster

growth_protocol: 1. the iso1 (y; bw cn sp) flies or the transgenic flies are cultivated in cages with apple juice agar plates covered with yeast powder. and the egg laying is performed for the desired amount of time to correspond to the proper stage. The biological material is collected using a filter mesh and a brush and rinsed extensively with Embryonic Wash Buffer (EWB). The material is then used freshly for cross-linking.

extract_protocol: Drosophila material is crushed in a glass homogenizer in presence of 1.8% of formaldehyde for 15 minutes at room temperature. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the Input reference sample. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IPed material is extracted and purified. The DNA is directly used for Solexa library preparation. If used for hybridization on microarrays, the sample will undergo an LM-PCR amplification before labelling.

treatment_protocol: No Treatment

tag: developmental stage

tag: fraction

value: ChIP


title: E8-16h_disco_INPUT_1

value: input

tag: antibody name

tag: manufacturer

value: White Lab/Aviva

tag: lot/batch#

tag: catalog#


title: ChIP-Seq for Smc1 in MEF (rep 2)

description: Chromatin IP against Smc1

value: Bethyl A300-055A

value: MEF


title: K4me3_INPUT_2

source_name: Kc

value: Kc


title: ChIP-Seq for Smc1 in mES cells

description: Chromatin IP against Smc1


title: Trl-D2_ChIPSeq_1


title: ChIP-Seq for Smc1 in mES cells (rep 2)

description: Chromatin IP against Smc1


title: K4me3 and Trl-D2_INPUT_1


title: K4me3_ChIPSeq_1 and 2

value: Lake PlacidBIO


title: CBP_INPUT_1


title: Trl_INPUT_1


title: CBP_ChIPSeq_1

value: rbCBP

value: Mattias Mannervik


title: kni_INPUT_3


title: kni_INPUT_2


title: kni_INPUT_1


title: Trl_ChIPSeq_1 and 2


title: kni_ChIPSeq_1, 2 and 3


title: 3dFemale_INPUT_1

growth_protocol: 1. y w, VK33 flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a 0-4 hours egg laying for example, new plates are added after a 2hours pre-egglaying and flies are allowed to lay eggs for 4 hours. 3. Embryos are collected using a filter mesh and a brush. They are rinsed with EWB and cross-linked in 1.8% formaldehyde at room temperature for 15 min.

value: 3dFemale from 7T


title: 3dFemale_INPUT_2


title: disco_KW3-D-D2_INPUT_1


title: GFP_INPUT_2

growth_protocol: 1. y w, VK37 flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a 0-4 hours egg laying for example, new plates are added after a 2hours pre-egglaying and flies are allowed to lay eggs for 4 hours. 3. Embryos are collected using a filter mesh and a brush. They are rinsed with EWB and cross-linked in 1.8% formaldehyde at room temperature for 15 min.


title: 10T-E16-24h_GFP_INPUT_1


title: E16-24h_10T(Dfd-GFP)_ChIPSeq_1 and 2

value: NWG-GFP

value: White Lab/Chemicon


title: 3dFemale_7T(cad-GFP)_ChIPSeq_1 and 2


title: GFP_INPUT_1


title: Pcl_INPUT_1


title: Pcl_ChIPSeq_1, 2 and 3


title: hkb_INPUT_1


title: Sin3A_INPUT_1


title: w3L_10T(Dfd-GFP)_ChIPSeq_1 and 2


title: Sin3A_ChIPSeq_1 and 2

value: Ross Cagan/Proteintech


title: hkb_ChIPSeq_1 and 2


title: H3K27me3 hiPS PDB2lox_21

status: Public on Aug 09 2010

first: Garrett

middle: M

last: Frampton

department: Biology

institute: Whitehead Instute - MIT

description: Chromatin IP against H3K27me3

data_processing:
ChIP-Seq reads were aligned using the software Bowtie (Langmead et al., 2009) to NCBI build 36.1 (hg18) of the human genome with default settings. Sequences uniquely mapping to the genome with zero or one mismatch were used in further analysis.
The analysis methods used were derived from previously published methods (Barski et al., 2007; Johnson et al., 2007; Mikkelsen et al., 2007; Robertson et al., 2007).  The genome was divided into bins 100 base pairs in width, beginning at the first base of each chromosome.  For identification of genomic regions with statistically significant differential ChIP-Seq occupancy 250 bp bins were used due to computer memory constraints.  Each ChIP-Seq read was shifted 100 bp from its mapped genomic position and strand to the approximate middle of the sequenced DNA fragment.  The ChIP-Seq density within each genomic bin was then calculated as the number of ChIP-Seq reads mapping within a 1kb window (+/- 500bp) surrounding the middle of that genomic bin.
In order to facilitate comparison of ChIP-Seq samples a quantile normalization method was used.  In each ChIP-Seq sample the genomic bin with the greatest ChIP-Seq density was identified.  The mean of these values was calculated and the bin with the greatest signal in each sample was assigned this mean value.  This was repeated for all genomic bins from the greatest signal to the least, assigning each the average ChIP-Seq signal for all bins of that rank across all samples.  H3K4me3 and H3K27me3 samples were subjected to quantile normalization as separate groups.

source_name: hiPS line PDB2lox_21

growth_protocol:
All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ).  Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20,  iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml).  hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.

extract_protocol:
Protocols describing chromatin immunoprecipitation (ChIP) materials and methods can be downloaded from http://web.wi.mit.edu/young/hES_PRC and have previously been described in detail (Lee et al. 2006).
Human ES, iPS or fibroblast cells were grown to a final count of ~50 million cells to obtain starting material for six chromatin immunoprecipitations.  Cells were chemically cross-linked by the addition of one-tenth volume of fresh 11% formaldehyde solution for 15 minutes at room temperature.  Cells were rinsed twice with 1X PBS, harvested by centrifugation, and flash frozen in liquid nitrogen.  Cross-linked cells were stored at –80 degrees C prior to use.
Cells were re-suspended, lysed and sonicated to solubilize and shear cross-linked DNA.  Sonication was performed using a Misonix Sonicator 3000 at a power of 27W for ten 30 second pulses with a 90 second pause between each pulse.  Samples were kept on ice at all times.
The resulting whole cell extract was incubated overnight at 4 degrees C with 10µl of Dynal Protein G magnetic beads that had been pre-incubated with approximately 3 µg of the appropriate antibody.  Each individual immunoprecipitation used 1/6 of the 3ml total, or ~8 million cells per IP.  The immunoprecipitation was allowed to proceed overnight.  Beads were washed three times (3 x 1.5ml) with RIPA buffer and one time (1x 1.5ml) with TE containing 50 mM NaCl.  Bound complexes were eluted from the beads by heating at 65 degrees C with occasional vortexing and cross-linking was reversed by overnight incubation at 65 degrees C.  Whole cell extract DNA (reserved from the sonication step) was also treated for cross-link reversal.  Immunoprecipitated DNA and whole cell extract DNA were then purified by treatment with RNAse A, proteinase K and 2x phenol:chloroform:isoamyl alcohol extractions.
The ChIP antibodies used were ab8580 (Abcam, Cambridge, MA) for H3K4me3 and ab6002 (Abcam) for H3K27me3.
All protocols for Solexa sample preparation and sequencing are provided by Illumina (http://www.illumina.com/).  A brief summary of the technique, minor protocol modifications, and data analysis methods are described below.
Purified ChIP DNA was prepared for sequencing according to a modified version of the Illumina/Solexa Genomic DNA protocol. Approximately 50-200ng of IP DNA was prepared for ligation of Solexa linkers by repairing the ends and adding a single adenine nucleotide overhang to allow for directional ligation.  A 1:100 dilution of the Adaptor Oligo Mix (Illumina) was used in the ligation step.  A subsequent PCR step with 18 amplification cycles added additional linker sequence to the fragments to prepare them for annealing to the Genome Analyzer flow-cell.  Amplified material was purified by Qiaquick MinElute (Qaigen) and a narrow range of fragment sizes was selected by separation on a 2% agarose gel and excision of a band between 150-300 bp, representing IP fragments between 50 and 200nt in length and ~100bp of primer sequence.  The DNA was purified from the agarose and diluted to 10 nM for loading on the flow cell.
The DNA library (2-4 pM) was applied to one lane of the flow-cell (eight samples per flow-cell) using a Cluster Station device (Illumina).  The concentration of library applied to the flow-cell was calibrated so that polonies generated in the bridge amplification step originate from single strands of DNA.  Multiple rounds of amplification reagents were flowed across the cell in the bridge amplification step to generate polonies of approximately 1,000 strands in 1µm diameter spots.  Double stranded polonies were visually checked for density and morphology by staining with a 1:5000 dilution of SYBR Green I (Invitrogen) and visualizing with a microscope under fluorescent illumination. Validated flow-cells were stored at 4 degrees C until sequencing.
Flow-cells were removed from storage and subjected to linearization and annealing of sequencing primer on the Cluster Station.  Primed flow-cells were loaded into the Genome Analyzer 1G (Illumina).  After the first base was incorporated in the sequencing-by-synthesis reaction the process was paused for a key quality control checkpoint.  A small section of each lane was imaged and the average intensity value for all four bases was compared to minimum thresholds.  Flow-cells with low first base intensities were re-primed and if signal was not recovered the flow-cell was aborted.  Flow-cells with signal intensities meeting the minimum thresholds were resumed and sequenced.
Images acquired from the Genome Analyzer were processed through the bundled image extraction pipeline (Illumina), which identified polony positions, performed base-calling and generated QC statistics.

value: hiPS line PDB2lox_21


title: H3K27me3 hiPS PDB1lox_21puro_26

description: Chromatin IP against H3K27me3

source_name: hiPS line PDB1lox_21puro_26

value: hiPS line PDB1lox_21puro_26


title: disco_ChIPSeq_1 and 2


title: H3K27me3 hiPS PDB2lox_17

description: Chromatin IP against H3K27me3

source_name: hiPS line PDB2lox_17

value: hiPS line PDB2lox_17


title: H3K27me3 hiPS PDB1lox_17puro_5

description: Chromatin IP against H3K27me3

source_name: hiPS line PDB1lox_17puro_5

value: hiPS line PDB1lox_17puro_5


title: H3K27me3 hiPS A1

description: Chromatin IP against H3K27me3

source_name: hiPS line A1

value: hiPS line A1


title: H3K27me3 hiPS 4

description: Chromatin IP against H3K27me3

source_name: hiPS line 4

value: hiPS line 4


title: H3K27me3 hiPS A6

description: Chromatin IP against H3K27me3

source_name: hiPS line A6

value: hiPS line A6


title: H3K27me3 hES WIBR7

description: Chromatin IP against H3K27me3

source_name: hES line WIBR7

value: hES line WIBR7


title: H3K27me3 hES WIBR1

description: Chromatin IP against H3K27me3

source_name: hES line WIBR1

value: hES line WIBR1


title: H3K27me3 hES WIBR2

description: Chromatin IP against H3K27me3

source_name: hES line WIBR2

value: hES line WIBR2


title: H3K27me3 hiPS C1

description: Chromatin IP against H3K27me3

source_name: hiPS line C1

value: hiPS line C1


title: H3K27me3 hES BG01

description: Chromatin IP against H3K27me3

source_name: hES line BG01

value: hES line BG01


title: H3K27me3 hES WIBR3

description: Chromatin IP against H3K27me3

source_name: hES line WIBR3

value: hES line WIBR3


title: H3K27me3 hES BG03

description: Chromatin IP against H3K27me3

source_name: hES line BG03

value: hES line BG03


title: H3K4me3 hiPS PDB2lox_21

description: Chromatin IP against H3K4me3


title: H3K4me3 hiPS PDB1lox_17puro_5

description: Chromatin IP against H3K4me3


title: H3K4me3 hiPS C1

description: Chromatin IP against H3K4me3


title: H3K4me3 hiPS 4

description: Chromatin IP against H3K4me3


title: H3K27me3 human fibroblast GM

description: Chromatin IP against H3K4me3

source_name: human fibroblast line GM

value: human fibroblast line GM


title: H3K4me3 hiPS PDB1lox_21puro_26

description: Chromatin IP against H3K4me3


title: H3K4me3 hES WIBR7

description: Chromatin IP against H3K4me3


title: H3K4me3 hiPS PDB2lox_17

description: Chromatin IP against H3K4me3


title: H3K4me3 hES WIBR2

description: Chromatin IP against H3K4me3


title: H3K4me3 hiPS A1

description: Chromatin IP against H3K4me3


title: H3K4me3 hiPS A6

description: Chromatin IP against H3K4me3


title: H3K4me3 hES WIBR3

description: Chromatin IP against H3K4me3


title: H3K4me3 hES WIBR1

description: Chromatin IP against H3K4me3


title: H3K4me3 hES BG03

description: Chromatin IP against H3K4me3


title: H3K4me3 human fibroblast GM

description: Chromatin IP against H3K4me3


title: H3K4me3 hES BG01

description: Chromatin IP against H3K4me3


title: Footprint_wild-type_runs1-2

status: Public on Aug 03 2010

city: Singapore

first: Huili

last: Guo

address: 28 Medical Drive

country: Singapore

institute: National University of Singapore

description:
Footprint_wild-type_run1
Footprint_wild-type_run2
polyA RNA

data_processing: Reads were mapped to the indicated genome build (mm9) using the Bowtie short-read mapping program. For each sample, uniquely-mapping reads from multiple runs were combined to generate the processed data file.

molecule: total RNA

source_name: Neutrophils cultured from wild-type mouse bone marrow

growth_protocol: Haematopoietic progenitors were isolated from wild-type and mir-223 knockout male mice and cultured in media containing granulocyte colony-stimulating factor (G-CSF) and stem cell factor (SCF) for six days before harvesting.

extract_protocol:
mRNA-Seq: poly(A)-selected RNA was randomly fragmented by partial alkaline hydrolysis. Size-selected RNA fragments (25-45 nt) were used for library preparation.
Ribosome profiling: Cell extracts were digested with RNase I for 30 min at room temperature, and monosomes were purified by sucrose gradient centrifugation. Size-selected RNA fragments (~27-33 nt) were used for library preparation.
Library preparation: Libraries were prepared as in Grimson et al, 2008 (GSE12578) but with the following modifications. Because RNase I-digestion and alkaline-fragmentation products terminate with a 5'-hydroxyl and a 3'-phosphate, they were 3'-dephosphorylated before ligation to the 3' adaptor.  Gel-purified 3'-ligation products were then 5'-phosphorylated before the 5'-ligation step.

treatment_protocol: All samples were treated with cycloheximide (100 ug/ml) for 8 min just before harvesting.

tag: genotype

value: wild-type


title: mRNASeq_mir-223-knockout_runs1-3

description:
mRNASeq_mir-223-knockout_run1
mRNASeq_mir-223-knockout_run2
mRNASeq_mir-223-knockout_run3
polyA RNA

source_name: Neutrophils cultured from  mir-223 knockout mouse bone marrow

value: mir-223 knockout


title: mRNASeq_wild-type_runs1-3

description:
mRNASeq_wild-type_run1
mRNASeq_wild-type_run2
mRNASeq_wild-type_run3
polyA RNA


title: mRNASeq_miR-1_12hr_runs1-2

description:
mRNASeq_miR-1_12hr_run1
mRNASeq_miR-1_12hr_run2
polyA RNA

data_processing: Reads were mapped to the indicated genome build (hg18) using the Bowtie short-read mapping program. For each sample, uniquely-mapping reads from multiple runs were combined to generate the processed data file.

source_name: HeLa

tag: transfection

value: miR-1 duplex

tag: time


title: Footprint_miR-155_12hr_run1

description:
Footprint_miR-155_12hr_run1
polyA RNA

value: miR-155 duplex


title: mRNASeq_miR-155_12hr_runs1-2

description:
mRNASeq_miR-155_12hr_run1
mRNASeq_miR-155_12hr_run2
polyA RNA


title: Footprint_miR-1_12hr_run1

description:
Footprint_miR-1_12hr_run1
polyA RNA


title: Footprint_mock_12hr_run1

description:
Footprint_mock_12hr_run1
polyA RNA

value: mock


title: Footprint_mir-223-knockout_runs1-2

description:
Footprint_mir-223-knockout_run1
Footprint_mir-223-knockout_run2
polyA RNA


title: Footprint_miR-1_32hr_runs1-2

description:
Footprint_miR-1_32hr_run1
Footprint_miR-1_32hr_run2
polyA RNA


title: mRNASeq_miR-155_32hr_runs1-3

description:
mRNASeq_miR-155_32hr_run1
mRNASeq_miR-155_32hr_run2
mRNASeq_miR-155_32hr_run3
polyA RNA


title: mRNASeq_mock_32hr_runs1-3

description:
mRNASeq_mock_32hr_run1
mRNASeq_mock_32hr_run2
mRNASeq_mock_32hr_run3
polyA RNA


title: Footprint_mock_32hr_runs1-2

description:
Footprint_mock_32hr_run1
Footprint_mock_32hr_run2
polyA RNA


title: trifoliate orange

status: Public on Aug 18 2010

city: Nanjing

first: Changnian

last: Song

address: Weigang No.1

department: College of Horticulture

country: China

institute: Nanjing Agricultural University

description: Non-coding RNA profiling by high throughput deep sequencing

data_processing:
The sequenced small RNA were compared to known plant miRNAs from miRBase using a BLASTn search.  No mismatches were allowed between identified C. trifoliata miRNAs and currently known miRNAs in other plant species.
All 560, 271 citrus ESTs were downloaded from the National Center for Biotechnology Information (NCBI) GenBank EST database (March 2009), including data from Citrus sinensis (207,500), C. clementina (118,365), C. trifoliata (58,483), C. reticulata (55,319) and all other taxa (120,604).  The ESTs were aligned to all the small RNA sequences from C. trifoliata, then miRNA candidates were generated by miRCat (http://srna-tools.cmp.uea.ac.uk/plant/cgi-bin/srna-tools.cgi?rm=input_form&tool=mircat) using default parameters.

organism: Citrus trifoliata

source_name: flowers and fruits

extract_protocol: Small RNA samples were sequenced by Beijing Genomics Institute (BGI) (Shenzhen, Guangdong, China) using the high throughput pyrosequencing technology developed by Illumina.  Small RNAs with 16-30 nt in length were first separated from the total RNA by size fractionation with 15% TBE urea polyacrylamide gel (TBU).  The small RNA (16-30 nt in length) were excised from the gel and submerged in 600 μL of 0.3 M sodium chloride overnight at 4 °C.  The gel slurry was then passed through a Spinfilter column (Corning, Beijing, China), and RNA precipitated by addition of 3 μL of 5 mg/mL mussel glycogen (Invitrogen, Carlsbad, CA, USA) and 800 μL of ethanol.  The RNA pellets were then washed with 75% ethanol and air dried at 25 °C.  The small RNA was resuspended in 5.0 μL of diethylpyrocarbonate (DEPC) treated water (Ambion, Austin, TX, USA).  The isolated small RNAs were then ligated to 5’ adaptor (5’UCAGAGUUCUACAGUCCGACGAUC) using T4 RNA ligase (Promega, Madison, WI) in the presence of RNase Out (Invitrogen) overnight at 4 °C according to the manufacturer’s instructions.  After selecting the ligated products by size fractionation, a 3’adaptor (5’UCGUAUGCCGUCUUCUGCUUGUidT) was ligated to the small RNAs following the same procedure as the ligation of the 5’adaptor.  Finally, the ligated RNAs were size fractionated on a 10% TBE urea polyacrylamide gel and the 70 nt RNAs were excised.  The 3’adaptorgated small RNAs were then purified from the gel and precipitated as described above followed by resuspension in 5.0 μL DEPCeated water (Ambion).  The small RNA with 5’ and 3’adaptors were selected and reversely transcribed to cDNA with the RT primer (CAAGCAGAAGACGGCATACGA) using Superscript II reverse transcriptase (Invitrogen).  The cDNA was further purified by 15% TBU followed by dissolving in 100 μL1× NEB.  The cDNA was quantified by Agilent 2100 and dilutioned to 10 nM at final concentration, 18 ng cDNA was loaded into the Illumina 1 G Genome Analyzer for sequencing.

value: flower bud, half-open-flower, open flower, development fruit tissues in different sizes (0.3, 0.5, 0.8, 1, and 1.5 cm in diameter)


title: Transgenic5

status: Public on Jul 31 2010

city: Baltimore

first: Jonathan

last: Ling

state: MD

address: 720 Rutland Ave.

department: Neuropathology

institute: Johns Hopkins University

data_processing: ELAND mapping, genome build: mm9

source_name: spinal cord

growth_protocol: Transgenic founder was bred with C57BL/6 mice for two genenrations

extract_protocol: Polyadenylated mRNA were harvested using oligo-dT dynabeads.  The construction of the cDNA libraries were created according to the protocol described by Illumina.

treatment_protocol: Transgenic mice and their nontransgenic littermates were housed under the same condition

tag: genotype/variation

value: transgenic

tag: age

value: 21 days of age


title: Embryo_Morpholino.Injected_Infected

status: Public on Aug 01 2010

city: Amsterdam

first: Oliver

last: Stockhammer

state: NH

address: Meibergdreef 15

department: Medical Microbiology

institute: AMC

description: The total RNA of three biological samples was pooled using equal amounts of RNA

data_processing:
RNA-seq reads were mapped to the Ensembl 56 Zv8 'all cDNA' zebrafish transcript set using the CLC Genomics Workbench version 3.6.5 (www.clcbio.com).
Settings: maximum number of mismatches 2, no more than 5 matches for a read.
Reported values for a read are:
UGR (unique gene reads): number of reads mapping uniquely to the transcript.
TGR (total gene reads): if a read matches multiple (but no more than 5) transcripts, its count is allocated based on the UGR values of those transcripts. For example, if transcript A has an UGR of 20, and transcript B an UGR of 80, a single read mapping non-uniquely to both A and B contributes 0.2 to the TGR of transcript A, and 0.8 to the TGR of transcript B.
RPKM (reads per kilobase exon model per million mapped reads): the TGR value normalized for both reference length and total number of mapped reads (Mortazavi et al., 2008). In case of a cDNA reference, the 'kilobase exon model' simplifies to 'kilobase transcript'.

organism: Danio rerio

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5-30°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol: RNAseq libraries were made from 4 µg of each sample, using the Illumina mRNA-Seq Sample Preparation Kit according to the manufacturer’s instructions

treatment_protocol: Embryos were injected with a translation blocking morpholino directed against traf6 (traf6 mo) at the 1 cell stage. Subsequently these embryos were injected with Salmonella typhimurium strain SL1027 at 27 hours post fertilization and samples were collected at 8 hours post injection and immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. For the duration of bacteria injections embryos were kept under anaesthesia in egg water containing 0.02% buffered 3-aminobenzoic acid ethyl ester (tricaine, Sigma).

tag: agent/injection

value: Traf6 morpholino and Salmonella typhimurium

tag: development stage

value: embryos

tag: strain

value: ABxTL


title: Transgenic8


title: Nontransgenic7

value: nontransgenic


title: Nontransgenic2


title: Nontransgenic6


title: mRNASeq_mock_12hr_runs1-2

description:
mRNASeq_mock_12hr_run1
mRNASeq_mock_12hr_run2
polyA RNA


title: Embryo_Morpholino.Injected_Not.Infected

treatment_protocol: Embryos were injected with a translation blocking morpholino directed against traf6 (traf6 mo) at the 1 cell stage. Subsequently these embryos were injected with PBS at 27 hours post fertilization and samples were collected at 8 hours post injection and immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. For the duration of bacteria injections embryos were kept under anaesthesia in egg water containing 0.02% buffered 3-aminobenzoic acid ethyl ester (tricaine, Sigma).

value: Traf6 morpholino and PBS


title: time point 4

status: Public on Jul 30 2010

first: Huiyi

last: Chen

address: 12 Oxford St

department: Chemistry

institute: Harvard University

description: cDNA from time point 4

data_processing:
Sequence reads were obtained and mapped to the W3110 genome (NCBI) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained. Repeated sequences were ignored (rRNA). The counts in each sample was normalized by ssrA RNA and then converted to logarithmic values. A value of 1 was added to every count before the logarithmic conversion to avoid an undefined logarithm of 0. The lifetime was determined from the inverse of the slope of a linear fit to the logarithmic values.
The measured lifetime of mRNA is available as a supplementary file (real_rna_life.txt) on the Series record.

organism: Escherichia coli

source_name: Escherichia coli

growth_protocol: E.coli strain, DY330, was grown at 30C in M9 media supplemented with 0.4% glucose, vitamins and amino acids.

extract_protocol:
RNA was purified from lysates by phenol/chloroform method. rRNA was first removed using MICROBExpress following manufacturer’s protocol, except RNA was collected using Zymo’s RNA columns. A second rRNA removal step was performed following the protocol described in Affymetrix Expression Handbook, substituting enzymes MMLV (Ambion), RNase H (NEB), and DnaseI (Amplification grade, Invitrogen).
The RNA was fragmented using Ambion’s Fragmentation Reagent at 70°C for 5 min, and collected by Zymo’s RNA columns. RNA seq libraries were prepared according to Illumna’s protocol, using NEB enzymes and barcoded adapters (Integrated DNA Technologies). The libraries were pooled and sequenced with an Illumina GA II machine (Center for Systems Biology, Harvard University).

treatment_protocol: At time point 0, rifampicin was added to a final concentration of 500ug/ml. Samples were collected at 0, 2, 4, 6, and 8 minutes.

tag: treatment group

value: rifampicin time point 4


title: Footprint_miR-155_32hr_runs1-2

description:
Footprint_miR-155_32hr_run1
Footprint_miR-155_32hr_run2
polyA RNA


title: time point 8

description: cDNA from time point 8

value: rifampicin time point 8


title: Embryo_Control morpholino.Injected_Not.Infected

treatment_protocol: Embryos were injected with a 5bp mismatch morpholino (mm) directed against traf6 at the 1 cell stage. Subsequently these embryos were injected with PBS at 27 hours post fertilization and samples were collected at 8 hours post injection and immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. For the duration of bacteria injections embryos were kept under anaesthesia in egg water containing 0.02% buffered 3-aminobenzoic acid ethyl ester (tricaine, Sigma).

value: Traf6 mismatch morpholino and PBS


title: mRNASeq_miR-1_32hr_runs1-3

description:
mRNASeq_miR-1_32hr_run1
mRNASeq_miR-1_32hr_run2
mRNASeq_miR-1_32hr_run3
polyA RNA


title: time point 6

description: cDNA from time point 6

value: rifampicin time point 6


title: Control rice seedlings

city: Beijing

first: Tian

last: Li

address: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

description: control small RNA library

data_processing: The adaptor sequences in Illumina sequencing reads were removed by using vectorstrip in the EMBOSS package. The small RNA reads with high sequencing accuracy and with length of more than 18 nt were were retained for further analysis.

organism: Oryza sativa

source_name: rice seedlings

growth_protocol: Rice seedlings were grown in a growth chamber with 28/21ºC (16 h day/8 h night) and relative humidity of 70%. To provide whole nutrition to rice seedlings, Hogland solution was supplied every 2 days.

extract_protocol: Total RNA was isolated from the frozen seedlings by using the Trizol Reagent (Invitrogen) according to the manufacturer's instructions. For small RNA library construction and deep sequencing, RNA samples were prepared as follows: equal quantities (10 μg) of total RNA isolated from rice seedlings treated with three H2O2 concentrations were mixed together to construct the H2O2-treated small RNA library, and total RNA prepared from the control sample was used to construct the control small RNA library. In brief, total RNA was separated by 15% polyacrylamide gel electrophoresis (PAGE), and RNA molecules in the range of 18–30 nt were enriched and ligated with proprietary adapters to the 5' and 3' termini. The samples were used as templates for cDNA synthesis and the resulting cDNA was amplified to produce sequencing libraries. The Illumina sequencing was performed by Beijing Genomics Institute (BGI).

treatment_protocol: 12-day-old seedlings were treated with three H2O2 concentrations (0.6, 3.0, and 15.0 mM) for 6 h in plastic containers, respectively. Seedlings immersed in dd H2O were used as a control.

value: indica 93-11

tag: stress

value: Control


title: Embryo_Control morpholino.Injected_Infected

treatment_protocol: Embryos were injected with a 5bp mismatch morpholino (mm) directed against traf6 at the 1 cell stage. Subsequently these embryos were injected with Salmonella typhimurium strain SL1027 at 27 hours post fertilization and samples were collected at 8 hours post injection and immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. For the duration of bacteria injections embryos were kept under anaesthesia in egg water containing 0.02% buffered 3-aminobenzoic acid ethyl ester (tricaine, Sigma).

value: Traf6 mismatch morpholino and Salmonella typhimurium


title: time point 2

description: cDNA from time point 2

value: rifampicin time point 2


title: time point 0

description: cDNA from time point 0

value: rifampicin time point 0


title: Myers_H1-hESC_cell_2x75_400_1

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

data_processing: For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeCaltechRnaSeq

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/human/H1_ES_protocol.pdf

extract_protocol: For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeCaltechRnaSeq

tag: cell line

tag: cell organism

value: Human

tag: cell description

value: Human Embryonic Stem Cells

tag: cell karyotype

value: normal

tag: cell lineage

value: embryonic stem cells

tag: cell sex

value: M

tag: localization

value: cell

tag: readtype

tag: insertlength

tag: replicate


title: H2O2-treated rice seedlings

description: H2O2-treated small RNA library


title: Transgenic1

tag: genotype/variation

value: transgenic

value: 21 days of age


title: Myers_H1-hESC_cell_1x75D_ilNA_1

value: ilNA


title: IgG_control

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

description: Chromatin IP against non-specific IgG

data_processing: .wig files were generated using Findpeaks (v4.0.12) briefly, the reads were first aligned (bowtie v0.9.9) then converted to a bed file format (ConvertToBed.jar from Findpeaks) and sorted. Then Findpeaks was used to identify significant accumulations of reads (FindPeaks.jar  with - aligner = bed and -dist_type = 1 all other settings default) these accumulations are identified in the .wig file

source_name: breast carcinoma cell line

growth_protocol: MCF-7 cells, obtained from ATCC were maintained in MEM supplemented with 10% FBS, 10units/ml penicellin G, 10ug/ml streptomycin and 6ng/ml bovine insulin at 37C 5% C02

extract_protocol: Chromatin was sonicated using conditions determined empirically for MCF-7 cells to achieve an optimal fragment length between 400 to 100 bp.  After sonication, samples were centrifuged at 20,000 x g for 10 min at 4°C.  The supernatant containing cross-linked DNA/histones was diluted with IP dilution buffer to 2 mg/ml.  Half the sample was immunoprecipitated with 10 μg of TFAP2C monoclonal antibody SC-12762X (Santa Cruz Biotechnology), which was previously shown to be specific for TFAP2C without cross reactivity to TFAP2A, and half with control nonspecific IgG (Upstate)

tag: cell type

value: breast carcinoma cell line

tag: antibody

value: non-specific IgG (Upstate)


title: TFAP2C

description: Chromatin IP against TFAP2C

value: TFAP2C monoclonal antibody SC-12762X (Santa Cruz Biotechnology)


title: WCE in MDER 10T cells

status: Public on Jul 24 2010

description: WCE in MDER 10T cells

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie.
For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 reads per million are shown.

source_name: MDER cells

growth_protocol: MDER cells were cultured in DMEM/F12 (without phenol red) with 10% FCS.

tag: chip antibody

value: fibroblast


title: ChIP-Seq for H3K27me3 in MDER 10T cells

description: Chromatin IP against H3K27me3

tag: antibody catalog number

tag: antibody manufacturer

value: Abcam


title: ChIP-Seq for H3K9me3 in MDER 10T cells

description: Chromatin IP against H3K9me3


title: Jurkat_H3K79me2_ChipSeq

description: Chromatin IP against H3K79me2 in Jurkat

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie.
For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: T-ALL cell line

growth_protocol: Human Jurkat cells were purchased from the American Type Culture Collection (ATCC), Manassas, VA. Cells were maintained under typical conditions in RPMI media with 10% Bovine Calf Serum. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linked with formaldehyde for 20 min.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 1000 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: Jurkat E6-1

tag: cell number

value: 50 million


title: RNAP2 Jurkat_ChipSeq Rpb1 N-terminus

description: Chromatin IP against RNAP2 in Jurkat

value: RNA Pol II (Rpb1 N-terminus)

tag: cell line

value: Santa Cruz


title: WCE_Jurkat

description: Jurkat Chromatin Input Control


title: mock_14hpi_rep1

status: Public on Jul 23 2010

city: St. Louis

first: Weixiong

last: Zhang

state: MO

address: Campus Box 1045

department: Computer Science and Engineering

institute: Washington University in St. Louis

description: plants inoculated with buffer for 14h

data_processing: Raw sequence reads were parsed to remove the 3'-adaptor, and those reads that do not have the 3'-adaptor and contain N were removed.  The processed files are named as "condition"_"time".uniq, where "condition" corresponds to mock or one of the 3 bacterial treatment (i.e., R2, hrcc, and ev), "time" indicates either 6 or 14hpi, and uniq means the files contain unique sequence reads with copy numbers.  The first column in a processed file is the number of copies of the sequence listed in the second column.

organism: Arabidopsis thaliana

source_name: 4-week-old Col-0 WT Arabidopsis

growth_protocol: 4-week-old plants grown at 23°C with 12h light

extract_protocol: Total RNA was isolated from infiltrated leaves and fractionated on 15% denaturing polyacrylamide gel. RNA molecules ranging from 18 to 26 nt was excised and ligated to 5’- and 3’-RNA adaptors using T4 RNA ligase followed by RT-PCR and gel purification as described in the Instruction from Illumina Inc. The small RNA libraries were sequenced by Illumina Inc and UCR core facility

treatment_protocol: Leaves of 4-weekold Arabidopsis plants were infiltrated with Mock (10mM MgCl2), non-pathogenic strain Pst DC3000 hrc C, Pst DC3000 (EV) and Pst DC3000 (avrRpt2) at a concentration of 2 X 107 cfu/ml. The samples were collected at 6 and 14 hpi.

tag: tissue type

value: leaves

tag: infection

value: mock (10mM MgCl2)

tag: time point


title: ev_14hpi

description: plants inoculated with (Pst) DC3000 EV for 14h

value: Pst DC3000 carrying an empty vector (EV)


title: hrcc_14hpi_rep2

description: plants inoculated with (Pst) DC3000 hrcC- for 14h

value: Pseudomonas syringae pv tomato (Pst) DC3000 hrcC-


title: R2_14hpi_techrep3

description: plants inoculated with (Pst) DC3000 avrRpt2 for 14h

value: Pst DC3000 carrying an effector gene avrRpt2


title: R2_14hpi_rep1


title: R2_14hpi_rep2


title: H3K4m3 ChipSeq Jurkat

description: Chromatin IP against H3K4m3 in Jurkat

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: 10 million


title: R2_6hpi

description: plants inoculated with (Pst) DC3000 avrRpt2 for 6h


title: hrcc_14hpi_rep1


title: mock_14hpi_rep2

description: plants inoculated with buffer for 14h


title: hrcc_6hpi

description: plants inoculated with (Pst) DC3000 hrcC- for 6h


title: mock_6hpi_rep2

description: plants inoculated with buffer for 6h


title: ev_6hpi

description: plants inoculated with (Pst) DC3000 EV for 6h


title: ChIP-Seq for H3K4me3 in MDER 10T

description: Chromatin IP against H3K4me3

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 350bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.


title: mock_6hpi_rep1

description: plants inoculated with buffer for 6h


title: RNAP2 Jurkat_ChipSeq 8WG16

description: Chromatin IP against RNAP2 Jurkat

value: RNA Pol II (8WG16)

value: 30 million

value: Covance


title: H3 ChIP atxr5 atxr6

status: Public on Jul 21 2010

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

data_processing: Alignment: Sequence reads were mapped to the Arabidopsis genome using SeqMap (Jiang and Wong, 2008). Uniquely mapping reads with two or fewer mismatches were retained.

source_name: leaves

extract_protocol: Genomic DNA was extracted from the sorted nuclei using the PicoPure DNA Extraction Kit (Molecular Devices, Sunnyvale, CA) according to the manufacturer’s recommendations. ChIP was performed as previously described (Zhang et al, 2009)  Illumina libraries for genomic DNA extracted from sorted nuclei and ChIP samples were  made following manufacturer instructions (Illumina).

tag: strain

value: Columbia

tag: genotype

value: atxr5 atxr6

tag: tissue

value: leaf

tag: chip antibody manufacturer

tag: chip antibody catalog #


title: Human naive B cell [09-001]

city: bethesda

first: Seolkyoung

last: Jung

address: 10 Center Dr

department: NIAMS

institute: NIH

description: Cell surface markers used for cell sorting: CD19+IgM+CD27-CD38-/low

data_processing: Image analysis, base calling, quality filtering: Standard settings of GAPipeline 1.0-1.4 using PhiX control; Fastq files contain 30 nt length reads that passed the chastity filter. Qualities are in phred64 format for all files.  Alignments were done with a custom software that used bowtie 0.9.9.3 to find the longest, mismatch-free alignable prefix of each read, trimmed any remaining adapter sequence, and then stored the unique sequence reads and their frequency.  This data is given in the data table, which therefore gives frequencies only for alignable reads.  For further analysis, the alignments were matched up with annotation to determine where the small RNA reads originated from and to profile miRNA expression in different tissues.

source_name: Human Naive B cells, Tonsil, FACS

extract_protocol: RNA isolation method: Trizol. Small RNA library preparation: Illumina protocol "Preparing Samples for Analysis of Small RNA" (Part # 11251913 Rev. A)

value: naive B cell

tag: source tissue

value: tonsil

tag: gender

value: female

tag: age

value: 5 years

tag: isolation

value: fluorescence activated cell sorting


title: input wild-type

value: wildtype

tag: chip antibody


title: input atxr5 atxr6


title: 16C atxr5 atxr6

tag: ploidy


title: 8C atxr5 atxr6


title: 4C atxr5 atxr6


title: 2C atxr5 atxr6


title: 16C wild-type


title: 8C wild-type


title: 2C wild-type


title: 160x9_testes_total

status: Public on Jul 19 2010

city: Cold Spring Harbor

first: Nikolay

middle: V

last: Rozhkov

email: nik.rozhkov@gmail.com, rozhkov@cshl.edu

state: NY

address: 1 Bungtown Rd.

institute: CSHL

description:
19-30nt RNA isolated from testes of hybrids from crosses between strain 160 females and strain 9 males
processed_file_build: droVir3

data_processing: Sequenced reads were clipped to remove 3' adapter, collapsed to obtain multiplicity, then mapped to relevant genome with no mismatches. Annotations were made based on genomic co-ordinates after mapping. Mapping count refers to number of times a sequence is mapped to the genome.

organism: Drosophila virilis

source_name: testes

extract_protocol: RNA was size selected (19-30nt) or small RNA-protein complexes were immunoprecipitated from extracts using specific polyclonal antibodies. These were then ligated to linkers at the 3' and 5' end using T4 RNA ligase, then PCR amplified and gel purified.

value: testes


title: 160_ovaries_total

description:
19-30nt RNA isolated from ovaries of strain 160
processed_file_build: droVir3

source_name: ovaries

value: ovaries


title: Wholefly_female_rep1

status: Public on Jul 20 2010

city: Farmington

first: Brenton

middle: R

last: Graveley

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

description: Oligo-dT selected, double stranded cDNA, Paired-end sequencin

data_processing: For comparison to other data, reads were trimmed to include only the first 37 nts.  Sequence reads were aligned to the dm3 and droSec1 assemblies of the D. melanogaster and D. sechellia databases (available at UCSC genome browser downloads). Allele-specific read assignment was performed by comparing the alignment results for each genome. For the Hybrid and Mixed_Control samples, reads were aligned to both genomes, and alignments were compared to identify reads that map to only one species (species-specific). Alignment positions were subsequently converted to dm3 coordinates using the UCSC liftover tool.  Pairs of reads in which each read mapped to the same (cis) or opposite (trans) species were identified and GFF files were prepared (processed data files). GFF files are provided for pairs of reads mapping to any chromosome (*all_chr.GFF.gz) and for pairs mapping to the same chromosome within 100,000 bp of each other (*same_chr.GFF.gz).  **Note that the *all_chr.GFF files will not be browser viewable as many pairs contain reads which map to different chromosomes.

organism: Drosophila melanogaster x Drosophila sechellia

source_name: Whole fly

growth_protocol: Cornmeal / molasses

extract_protocol: Total RNA was prepared using Trizol (Invitrogen). Oligo-dT beads (Dynal, Invitrogen) were used to enrich for polyadenylated RNAs. Ambion fragmentation reagent was used to fragment poly-A+ RNA, which was subsequently reverse transcribed using random primers and SuperScript II RT (Invitrogen). Library preparation was performed using the Illumina paired-end genomic DNA library preparation kit as described by the manufacturer.  Insert size for these libraries is ~350 bp +/- 20 bp.

value: D.melanogaster strain 14021-0231.36 crossed to D. sechellia strain 14021-0248.25

value: whole fly

tag: sex

value: Female

tag: stage

value: Adult (0-2d post eclosion)


title: 9_0-2h_embryos_total

description:
19-30nt RNA isolated from 0-2h embryos of strain 9
processed_file_build: droVir3

source_name: embryos

value: embryos


title: Wholefly_femalemix_rep1

organism:
Drosophila melanogaster
Drosophila sechellia

value: D.melanogaster strain 14021-0231.36 and D. sechellia strain 14021-0248.25


title: Argx9_0-2h_embryos_total

description:
19-30nt RNA isolated from 0-2h embryos of hybrids from crosses between strain Argentina females and strain 9 males
processed_file_build: droVir3


title: 4C wild-type

value: Columbia


title: H3K27me1 ChIP wild-type

value: Upstate


title: Human plasma cell [09-001]

description: Cell surface markers used for cell sorting: CD19-/lowIgD-CD27hiCD38hi

source_name: Human Plasma cells, Tonsil, FACS

tag: cell type

value: plasma cell

value: 3 years


title: Human pre-germinal center B cell [09-001]

description: Cell surface markers used for cell sorting: CD19+IgD+CD38+/intCD77-

source_name: Human Pre-Germinal Center B cells, Tonsil, FACS

value: pre-germinal center B cell

value: tonsil


title: Human memory B cell [09-001]

description: Cell surface markers used for cell sorting: CD19+CD27+D38-/low

source_name: Human Memory B cells, Tonsil, FACS

value: memory B cell

value: female

value: 5 years


title: 9xArg_0-2h_embryos_total

description:
19-30nt RNA isolated from 0-2h embryos of hybrids from crosses between strain 9 females and strain Argentina males
processed_file_build: droVir3


title: Human centrocyte [09-001]

description: Cell surface markers used for cell sorting: CD19+IgD-CD38+/intCD77-

source_name: Human Centrocytes (Germinal Center B cells), Tonsil, FACS

value: centrocyte

value: fluorescence activated cell sorting


title: Trypanosoma brucei gambiense strain STIB 386 cultured procyclic forms library A

status: Public on Jul 22 2010

city: Glasgow

first: Annette

last: MacLeod

address: GBRC, 120 University Place

department: Wellcome Centre for Molecular Parasitology

country: United Kingdom

institute: University of Glasgow

description:
tag length: 17
tag count: 2466628 (user supplied)
Trypanosoma brucei gambiense type 2 strain STIB 386 originally isolated from a human in the Ivory Coast in 1978.

data_processing: Normalization was carried out by dividing by the total number of tags per library.

organism: Trypanosoma brucei gambiense

growth_protocol: Procyclic form T. b. gambiense STIB 386 were grown in SDM-70 media with 10% fetal bovine serum and harvested during mid-log phase (approximately 4,500,000 cells per library).

extract_protocol: The cells were pelleted at 1100g for 10 mins at 4ºC and immediately re-suspended in RLT buffer (Qiagen RNeasy kit). The cells were disrupted by serial passage through a 26 gauge needle and stored at -80ºC before use. RNA was isolated from the cells using RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase treatment step, to ensure that there was no DNA contamination. The RNA was measured for quantity and quality by Nanodrop ND-1000 spectrophotometer and Agilent 2100 Bioanalyzer according to the manufacturer’s instructions. Sequence tag preparation was performed with Digital Gene Expression Tag Profile Kit (Illumina) using NlaIII, according to the manufacturer’s instructions.

value: STIB 386

tag: type

tag: life cycle

value: procyclic stage

tag: library

value: A


title: 9x140_0-2h_embryos_total

description:
19-30nt RNA isolated from 0-2h embryos of hybrids from crosses between strain 9 females and strain 140 males
processed_file_build: droVir3

tag: strain


title: 140x9_0-2h_embryos_total

description:
19-30nt RNA isolated from 0-2h embryos of hybrids from crosses between strain 140 females and strain 9 males
processed_file_build: droVir3


title: 160_testes_total

description:
19-30nt RNA isolated from testes of strain 160
processed_file_build: droVir3

value: testes


title: Argx9_testes_total

description:
19-30nt RNA isolated from testes of hybrids from crosses between strain Argentina females and strain 9 males
processed_file_build: droVir3


title: 140x9_testes_total

description:
19-30nt RNA isolated from testes of hybrids from crosses between strain 140 females and strain 9 males
processed_file_build: droVir3


title: 140x9_ovaries_total

description:
19-30nt RNA isolated from ovaries of hybrids from crosses between strain 140 females and strain 9 males
processed_file_build: droVir3

value: ovaries


title: 9x140_testes_total

description:
19-30nt RNA isolated from testes of hybrids from crosses between strain 9 females and strain 140 males
processed_file_build: droVir3


title: 9xArg_ovaries_total

description:
19-30nt RNA isolated from ovaries of hybrids from crosses between strain 9 females and strain Argentina males
processed_file_build: droVir3


title: 9xArg_testes_total

description:
19-30nt RNA isolated from testes of hybrids from crosses between strain 9 females and strain Argentina males
processed_file_build: droVir3


title: 9x140_ovaries_total

description:
19-30nt RNA isolated from ovaries of hybrids from crosses between strain 9 females and strain 140 males
processed_file_build: droVir3


title: 9_ovaries_total

description:
19-30nt RNA isolated from ovaries of strain 9
processed_file_build: droVir3


title: Trypanosoma brucei gambiense strain STIB 386 cultured procyclic forms library B

description:
tag length: 17
tag count: 2180993 (user supplied)
Trypanosoma brucei gambiense type 2 strain STIB 386 originally isolated from a human in the Ivory Coast in 1978.

treatment_protocol: Procyclic form T. b. gambiense STIB 386 were grown in SDM-70 media with 10% fetal bovine serum and harvested during mid-log phase (approximately 4,500,000 cells per library).

value: B


title: 9x160_females_carcasses_total

description:
19-30nt RNA isolated from female carcassess of hybrids from crosses between strain 9 females and strain 160 males
processed_file_build: droVir3

source_name: carcasses

value: carcasses


title: Argx9_ovaries_total

description:
19-30nt RNA isolated from ovaries of hybrids from crosses between strain Argentina females and strain 9 males
processed_file_build: droVir3


title: Human centroblast [09-001]

description: Cell surface markers used for cell sorting: CD19+IgD-CD38+/intCD77+

source_name: Human Centroblasts (Germinal Center B cells), Tonsil, FACS

value: centroblast


title: 160x9_females_carcasses_total

description:
19-30nt RNA isolated from female carcasses of hybrids from crosses between strain 160 females and strain 9 males
processed_file_build: droVir3


title: 160x9_males_carcasses_total

description:
19-30nt RNA isolated from male carcasses of hybrids from crosses between strain 160 females and strain 9 males
processed_file_build: droVir3


title: 9_testes_total

description:
19-30nt RNA isolated from testes of strain 9
processed_file_build: droVir3


title: 160_males_carcasses_total

description:
19-30nt RNA isolated from female carcasses of strain 160
processed_file_build: droVir3


title: Trypanosoma brucei gambiense strain STIB 386 cultured bloodstream forms library C

description:
tag length: 17
tag count: 1218797 (user supplied)
Trypanosoma brucei gambiense type 2 strain STIB 386 originally isolated from a human in the Ivory Coast in 1978.

growth_protocol: Bloodstream form T. b. gambiense STIB 386 were grown in HMI9 media with 20% fetal bovine serum at 37ºC with 5% CO2 and harvested during mid-log phase (approximately 4,500,000 cells per library).

value: bloodstream stage

value: C


title: 160_females_carcasses_total

description:
19-30nt RNA isolated from male carcasses of strain 160
processed_file_build: droVir3


title: 9x160_males_carcasses_total

description:
19-30nt RNA isolated from male carcasses of hybrids from crosses between strain 9 females and strain 160 males
processed_file_build: droVir3


title: 9_females_carcasses_total

description:
19-30nt RNA isolated from male carcasses of strain 9
processed_file_build: droVir3


title: 160_0-2h_embryos_total

description:
19-30nt RNA isolated from 0-2h embryos of strain 160
processed_file_build: droVir3

value: embryos


title: 9_males_carcasses_total

description:
19-30nt RNA isolated from female carcasses of strain 9
processed_file_build: droVir3


title: Trypanosoma brucei gambiense strain STIB 386 cultured procyclic forms library C

description:
tag length: 17
tag count: 966319 (user supplied)
Trypanosoma brucei gambiense type 2 strain STIB 386 originally isolated from a human in the Ivory Coast in 1978.


title: Trypanosoma brucei gambiense strain STIB 386 cultured bloodstream forms library D

description:
tag length: 17
tag count: 1860336 (user supplied)
Trypanosoma brucei gambiense type 2 strain STIB 386 originally isolated from a human in the Ivory Coast in 1978.

value: D


title: 9x160_0-2h_embryos_total

description:
19-30nt RNA isolated from 0-2h embryos of hybrids from crosses between strain 9 females and strain 160 males
processed_file_build: droVir3


title: Trypanosoma brucei gambiense strain STIB 386 cultured bloodstream forms library A

description:
tag length: 17
tag count: 883737 (user supplied)
Trypanosoma brucei gambiense type 2 strain STIB 386 originally isolated from a human in the Ivory Coast in 1978.


title: 140_ovaries_total

description:
19-30nt RNA isolated from ovaries of strain 140
processed_file_build: droVir3


title: Argentina_testes_total

description:
19-30nt RNA isolated from testes of strain Argentina
processed_file_build: droVir3

value: Argentina


title: hs-Penelope_ ovaries_total

description:
19-30nt RNA isolated from ovaries of strain hs-Penelope
processed_file_build: dm3

value: hs-Penelope


title: 9x160_ovaries_total

description:
19-30nt RNA isolated from ovaries of hybrids from crosses between strain 9 females and strain 160 males
processed_file_build: droVir3


title: A2_ovaries_Ago3

description:
Ago3-assosiated small RNA isolated from ovaries of strain A2
processed_file_build: dm3


title: 140_testes_total

description:
19-30nt RNA isolated from testes of strain 140
processed_file_build: droVir3


title: A1_testes_total

description:
19-30nt RNA isolated from testes of strain A1
processed_file_build: dm3


title: A2_ovaries_FLAG-Piwi

description:
FLAG-Piwi-assosiated small RNA isolated from ovaries of strain A2
processed_file_build: dm3


title: A2_ovaries_FLAG-Aub

description:
FLAG-Aub-assosiated small RNA isolated from ovaries of strain A2
processed_file_build: dm3


title: hs-Penelope_testes_total

description:
19-30nt RNA isolated from testes of strain hs-Penelope
processed_file_build: dm3


title: Argentina_ovaries_total

description:
19-30nt RNA isolated from ovaries of strain Argentina
processed_file_build: droVir3


title: 160x9_0-2h_embryos_total

description:
19-30nt RNA isolated from 0-2h embryos of hybrids from crosses between strain 160 females and strain 9 males
processed_file_build: droVir3


title: yw67c23(2)_testes_total

description:
19-30nt RNA isolated from testes of strain yw67c23(2)
processed_file_build: dm3


title: 9x160_testes_total

description:
19-30nt RNA isolated from testes of hybrids from crosses between strain 9 females and strain 160 males
processed_file_build: droVir3


title: 160x9_ovaries_total

description:
19-30nt RNA isolated from ovaries of hybrids from crosses between strain 160 females and strain 9 males
processed_file_build: droVir3


title: A2_testes_total

description:
19-30nt RNA isolated from testes of strain A2
processed_file_build: dm3


title: A2_ovaries_total

description:
19-30nt RNA isolated from ovaries of strain A2
processed_file_build: dm3


title: iTDPKO-1

status: Public on Jul 15 2010

description: TDP-43 deleted

data_processing: ELAND mapping

growth_protocol: Grown in N2B27 + Leukemia inhibitory factor, CHIR99021, and PD0325901

treatment_protocol: ES cells were treated with 100ng/ml 4-hydroxytamoxyfen for 72 hours

tag: cell

value: ES cells

tag: passages


title: cTDP-2

description: TDP-43 remained


title: iTDPKO-2

description: TDP-43 deleted


title: Endougenous small RNA from MHV-68 infected mouse S11 cell, treated with TPA

city: Martinsried

first: Gunter

last: Meister

address: Am Klopferspitz 18

department: Center for Integrated Protein Science Munich (CIPSM)

country: Germany

institute: Max Planck Institute of Biochemistry

description: Total endogenous small RNAs from NPC sample of patient1

data_processing: Processed data file contains the reads with 5' and 3' adapters removed. Same reads are sorted together and the numbers of repetitivity are illustrated

source_name: mouse B lymphoma S11 cells, treated with TPA

growth_protocol: S11 cells were cultured in RPMI 1640 (Cell Concepts, Umkirch, Germany) supplemented with 10% FCS, 2 mM L-Glutamine, 100 U/ml Penicillin, 100 μg/ml Streptomycin and 50 µM 2-Mercaptoethanol.

extract_protocol: From all samples, RNA species smaller than 200 bases were enriched with the mirVana  miRNA isolation kit (Ambion, Austin, Texas, USA). The small RNAs from all 4 samples were  separated on a denaturing 12,5% polyacrylamide (PAA) gel and stained with SYBRgreenII.  As molecular mass standard a mixture of oligonucleotides was used that range in size  between 15 and 30 bases. The population of miRNAs with a length of 15 – 30  bases was obtained by passive elution of the RNAs from the gel. The miRNAs were then  precipitated with ethanol and dissolved in water. For cDNA synthesis the RNAs were first poly(A)-tailed using poly(A) polymerase followed by  ligation of a RNA adapter to the 5´-phosphate of the miRNAs. First-strand cDNA synthesis  was then performed using an oligo(dT)-linker primer and M-MLV-RNase H- reverse  transcriptase. The resulting cDNAs were then PCR-amplified to about 20 ng/μl using the high fidelity polymerase Phusion (Finnzymes). The fusion primers used for PCR amplification were designed for amplicon sequencing  according to the instructions of 454 Live Sciences. Barcode sequences for each cDNA  species are attached to the 5'-ends of the cDNAs. cDNAs of 4 samples were mixed in  equal amounts. The correct size range was obtained by separation of the mixed cDNAs on  and electroelution of the 120 – 135 bp fraction from 6% PAA-gels followed by purification of  the eluted cDNAs using Nucleospin Extract II (Macherey and Nagel). The cDNAs were pooled (Volume: 30 μl; Concentration: 13 ng/μl; dissolved in 5 mM Tris pH:8,5) and sent for 454 sequencing.

treatment_protocol: S11 cells were treated with TPA (20 ng/ml) for 48h.

value: mouse B lymphoma

tag: cell line


title: Endougenous small RNA from MHV-68 infected mouse S11 cell, without TPA treatment

source_name: mouse B lymphoma S11 cells, without TPA treatment

treatment_protocol: No further treatment.


title: Endougenous small RNA from mouse NIH3T3 cell, infected with MHV-68

source_name: mouse fibroblast NIH3T3 cells, infected with MHV-68

growth_protocol: NIH3T3 cells (ATCC CRL-1658) were grown in DMEM High Glucose (Cell Concepts, Umkirch, Germany) supplemented with 10% FCS, 2 mM L-Glutamine, 100 U/ml Penicillin and 100 μg/ml Streptomycin.

treatment_protocol: NIH3T3 cells were infected with wildtype MHV-68 at an MOI of 1, and harvested after 24h.

value: mouse embryo fibroblast


title: A2_ovaries_FLAG-Ago2

description:
FLAG-Ago2-assosiated small RNA isolated from ovaries of strain A2
processed_file_build: dm3

tag: tissue


title: yw67c23(2)_ovaries_total

description:
19-30nt RNA isolated from ovaries of strain yw67c23(2)
processed_file_build: dm3


title: Endougenous small RNA from mouse NIH3T3 cells, without MHV-68 infection

source_name: mouse fibroblast NIH3T3 cells, without MHV-68 infection


title: retina 1

status: Public on Jul 13 2010

city: Philadelphia

first: Lifeng

last: Tian

state: PA

address: 422 Curie Bldv

institute: University of Pennsylvania

description: cDNAs were prepared from mRNA.

data_processing: Reads were mapped to hg19 and splice junctions were detected using SplicePL (ver 3.3), TopHat (ver 1.0.13), SpliceMap (ver 1.0), and BLAT (37x7).

extract_protocol:
Total RNA was extracted from human retina tissue samples using the TRIzol reagent protocol (Cat. #: 15596-026; Invitrogen).  Brieflly, ~400 mg of tissue was homogenized in 4 mL of TRIzol (1:10 weight:volume ratio) using a PowerGen 125 mechanical homogenizer (Cat. #: 14-261-02; Fisher Scientific).  A 400 mcL aliquot of BCP (1-Bromo-3-Chloropropane; Cat. #: BP151; Molecular Research Center) was added to the homogenate instead of chloroform to induce phase separation (1:10 volume:volume ratio based on starting TRIzol volume), followed by vortexing for ~15 sec., incubation at room temperature for 2 - 3 min., and centrifugation at 3000 rcf for 15 min. using an Eppendorf 5810R benchtop centrifuge set to ~4°C.  The resultant clear supernatant was transferred to a new tube, followed by the addition of 2 mL isopropal alcohol (1:2 volume:volume ratio based on starting TRIzol volume), inversion of the sample by hand ~10x to mix, incubation at room temperature for ~10 min., and centrif  ugation at 3000 rcf for 15 min. using an Eppendorf 5810R benchtop centrifuge set to ~4°C.  The resulting total RNA pellet was dried by removing the supernatant, drying the inside of the tube with a Kimwipe (CAUTION: do not touch/disturb the pellet) and inverting the sample over a new Kimwipe for ~5 - 10 min.  The pellet was resuspended in ~150 - 200 mcL of DNase/RNase free water, and concentration and quality of the sample was assessed using an RNA 6000 Nano Chip (Cat. #: 5067-1511; Agilent Technologies) on an Agilent Bioanalyzer 2100 (Cat. #: G2943CA; Agilent Technologies).

Messenger RNA samples for Illumina GA-IIx analysis were generated by following the mRNA Sequencing Sample Preparation Guide (Cat. #: RS-930-1001; Part #: 1004898 Rev. D, September 2009; Illumina, Inc.) that came with the mRNA-Seq 8-sample Prep Kit (Cat. #: RS-100-0801; Illumina, Inc.).  The key modifications to this protocol was as follows: mRNA quality and concentration was assessed using an RNA 6000 Nano Chip (Cat. #: 5067-1511; Agilent Technologies) on an Agilent Bioanalyzer 2100 (Cat. #: G2943CA; Agilent Technologies).

Illumina RNA-seq protocol. Average insert size is 250 bp +/- 20 bp standard deviation.

value: retina


title: PHF8_ChIPSeq

status: Public on Jul 14 2010

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

description: Chromatin IP against PHF8

data_processing: Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline (Eland). Uniquely mapped reads were kept, and for positions where multiple reads were mapped, only one read was retained.

source_name: Hela cells

growth_protocol: HeLa cells were cultured in DMEM medium with 10% FBS.

extract_protocol: X-linked HeLa cells were sonicated to about 200-500 bp of the DNA fragment to prepare the chromatin templates. Four or eight microgram of antibodies were used to incubate with chromatin templates.  The resulting ChIP-DNA was used for library construction according to the protocol (Wang et al., 2008 Nature Genetics (PMID 18552846); 2009 Cell (PMID: 19698979)).  Basically, DNA was end-repaired and ligated with adapters  Ligation products wer amplified with 17 cycles and purified from agrose gel.  DNA concentration was measured before the loading to machine.

treatment_protocol: HeLa cells were transfected with pBabe control or PHF8 shRNA and puromycin-selected for more that 6 days. The stable cell lines of control and PHF8 RNAi retransfected with the corresponding shRNA for additional three day, then followed with chromatin preparation.

value: HeLa cells

tag: antibody (antibody name, vendor, batch/lot#, catalog#)

value: Anti-PHF8 antibody, abcam, lot# AP266823, ab36068


title: H3K9me1_PHF8_RNAi_control_ChIPSeq

description: Chromatin IP against H3K9me1

tag: protocol

value: control

value: Anti-H3K9me1 antibody, abcam, lot# 815310, ab8896


title: H3K9me2_PHF8_RNAi_ChIPSeq

description: Chromatin IP against H3K9me2

value: PHF8 depletion

value: Anti-H3K9me2 antibody, abcam, lot# 765092, ab1220


title: H4K20me1_PHF8_RNAi_ChIPSeq

description: Chromatin IP against H4K20me1

value: Anti-H4K20me1 antibody, abcam, lot# 713902, ab9051


title: H4K20me1_PHF8_RNAi_control_ChIPSeq

description: Chromatin IP against H4K20me1


title: RAP1_ko2 RAP1-Chip-seq

status: Public on Jul 10 2010

city: Madrid

first: Paula

last: Martinez

state: Madrid

address: Melchor Fernandez Almagro 3

country: Spain

institute: CNIO

description:
mixed background
Chromatin IP against RAP1

data_processing:
Alignment: Sequence reads were mapped to the mm9 mouse assembly genome (NCBI m37, April 2007) using the Illumina Genome Analyzer Pipeline 1.4.0 [default ELAND_SEED_LENGTH 32, which allows for no more than 2 mismatches within the seed].
Peaks: Peak detection was performed with the CisGenome algorithm (http://www.biostat.jhsph.edu/~hji/cisgenome/), Processed files include peaks for (WT_1+WT_2) vs (RAP1_ko1+RAP1_ko2)

source_name: embryonic fibroblast

growth_protocol: SV40-large T immortalized mouse embryonic fibroblast were grown on DMEM supplemented with fetal calf serum and with puromycin.

extract_protocol: Lysates were clarified from sonicated nuclei and RAP1-DNA complexes were isolated with antibody.  Illumina's "ChIP Sequencing Sample Prep Guide" (part # 11257047 Rev. A) was followed for library preparation. Briefly, DNA was a) end-repaired by T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase; b) treated with Klenow exo (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base; c) ligated to Illumina's adapters by T4 DNA ligase; d) PCR amplified with Illumina primers for 18 cycles. Library was electrophoresed on agarose gel and a fraction of 200+/-25 bp was extracted. The purified DNA was subsequently applied to an Illumina flow cell for cluster generation. Clusters were sequenced on the Genome Analyzer IIx following manufacturer's protocols.

tag: antibody


title: WT_2 RAP1-Chip-seq


title: cTDP-1

description: TDP-43 remained

extract_protocol: Polyadenylated mRNA were harvested using oligo-dT dynabeads.  The construction of the cDNA libraries were created according to the protocol described by Illumina.


title: Input


title: H3K9me2_PHF8_RNAi_control_ChIPSeq

description: Chromatin IP against H3K9me2


title: iTDPKO-3

description: TDP-43 deleted


title: WT_1 RAP1-Chip-seq


title: E15_F1i_RNASeq_techrep4

status: Public on Jul 08 2010

city: Cambridge

first: Catherine

last: Dulac

address: BL4017 16 Divinity Ave

department: Molecular and Cellular Biology

description:
poly A purified RNA from embryonic and adult brain converted to cDNA
mm9 UCSC annotated transcriptome

data_processing:
Sequence data (reads were trimmed to 32 bases for analysis) was aligned using NovoAlign to the UCSC annotated mouse transcriptome (mm9) and mouse genome (mm9) and to the functional RNA database.
A reference table of CAST and C57 SNP sites was generated relative to the annotated reference transcriptome and genome for genes expressed in the E15 brain and adult mPFC and POA using the CastEiJ and C57BL/6J sequence data (E15 brain, POA, and mPFC).  In cases where reads disagreed with the base call at a given SNP position, only SNP sites with a consensus of >80% for the base call at the SNP site were included in the final SNP reference table.  Importantly, the base calls were confirmed by both parental strains.  Transcript UCSC IDs (transcriptome alignment) or genome positions (genomic alignment) were recorded for each SNP containing read alignment, for example: uc007aeu.1_1263 (UCSC transcript ID_SNP base position).  The SNP position was recorded relative to the first base of the transcript, or the base position relative to the start of the chromosome was recorded in the case of genomic alignments.  Base calls at SNP sites for CAST and C57 samples relative to the annotated mouse transcriptome, genome, or fRNAdb were assembled into a CAST/C57 SNP Reference Table (see all tables labeled with "_SNP_calls.txt") and these SNP sites were used to assess allele-specific expression in the F1 hybrids.  RNA Seq data from initial (F1i) and reciprocal (F1r) crosses of F1 hybrid mice was used to measure maternal and paternall allele specific expression at each SNP site.  In the manuscripts, SNP site calls were further refined by requiring a minimum of 10 reads per SNP site for both the F1i and F1r crosses in the F1 hybrid datasets, however all SNP calls are presented in the raw processed files here.

Processed data file: E15_TranscriptomeAligned.csv
Processed data file: E15_GenomicAligned.csv
Processed data file: E15_fRNAdbAligned.csv
Processed data file(s) linked as supplementary files on Series GSE22131.

source_name: embryonic day 15 whole brain

extract_protocol:
Sample isolation protocol: Whole embryonic day 15 brain tissue or adult (5 week old) medial prefrontal cortex or preoptic area was microdissected and RNA was isolated in Trizol, Dnase treated, and purified with Qiagen Rneasy MicroKit.  For E15 brain samples, RNA was pooled from 4-5 different individuals for each sample.  For adult mPFC and POA samples, RNA was pooled from 8-10 individuals per sample.  RNA purity and quality was measured on an Agilant bioanalyzer and only samples with an RNA integrity score >9 were included.  RNA was fragmented and converted to cDNA with random hexamer primers according to the Illumina RNA-Seq protocol. Size selection was done at 200+- 25 bp.
RNA-seq was performed accoring to the Illumina RNA-Seq protocol and cluster station reactions and sequencing was performed accoring to the Illumina sequencing kit protocols for 36 sequencing cycles.  Each RNA sample was subject to 2 or more technical replicates and read data for each replicate was summed to generate the final processed dataset.

value: F1 hybrid initial cross (F1i) Hybrid [Mother:CastEiJ, Father:C57BL6J]

tag: developmental stage

value: embryo

tag: age

value: day 15

value: brain

tag: brain region

value: whole brain

tag: data type

value: transcriptome single nucleotide polymorphisms read counts


title: Chlamydomonas-ars11-Sulfur-Depleted

first: Arthur

last: Grossman

address: 260 Panama Street

department: Plant Biology

institute: Carnegie Institute for Science

description: Illumina's RNA-Seq whole transcriptome analysis

data_processing:
Processed sequence files from the Solexa pipeline output were aligned against the v.3.1 assembly of the Chlamydomonas genome. The SOAP alignment program (Li et al., 2008) was used to map the short reads in two steps. In a first alignment round, the raw 35-mers sequences were aligned to the genomic sequence with a tolerance of up to two mismatches and no indels. For those sequences that did not align to the genome a second round alignment was performed in which we recursively trim one base at a time (up to 21-mers) at either the 5’ or 3’ end of the reads until we found a (perfect) match to the genome.
Alignments from both rounds were tagged as either unique or not unique and combined. The most 5’ position of each alignment is recorded along with the length of the alignment.
Reference sequence: Chlamydomonas V3.1 unmasked assembly (JGI's Chlre3_1.fasta.gz, md5: c14cb6c004b90983e3a82404b1902173)  with a total of 1266 scaffolds. Global genomic coordinates in the accompanying processed files refer to the first base of scaffold_1 when the reference sequence is sorted as in Chlre3_1.fasta.gz.
Processed files: k-hits files. Format (tab delimited). Headers: Global genomic position - length of the alignment - number of unique hits

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas cultured cells

growth_protocol: Cells were cultured under continuous light of ~60 μmol photon m-2s-1 at 23ºC in liquid and on solid Tris-Acetate-Phosphate (TAP) medium.

extract_protocol: Cell aliquots were collected for RNA isolation just prior to and 1, 6 and 24 h after being transferred to TAP and TAP-S medium. Total RNA from cells after 0 and 6 h of being transferred to -S medium were submitted to Illumina for sequencing.

treatment_protocol: To impose S deprivation, cells in mid-logarithmic growth phase were washed twice with liquid TAP medium without S (TAP-S), and equal numbers of cells were resuspended in TAP or TAP-S.

tag: medium

value: TAP -S

tag: sulfur deprivation time

value: 6 hours


title: E15_F1r_RNASeq_techrep4

value: F1 hybrid reciprocal cross (F1i) Hybrid [Mother:C57BL6J, Father:CastEiJ]


title: Chlamydomonas-ars11-Sulfur-Replete

value: TAP


title: E15_F1r_RNASeq_techrep3


title: PFC_F1r_Female_RNASeq_techrep2

data_processing:
Sequence data (reads were trimmed to 32 bases for analysis) was aligned using NovoAlign to the UCSC annotated mouse transcriptome (mm9) and mouse genome (mm9) and to the functional RNA database.
A reference table of CAST and C57 SNP sites was generated relative to the annotated reference transcriptome and genome for genes expressed in the E15 brain and adult mPFC and POA using the CastEiJ and C57BL/6J sequence data (E15 brain, POA, and mPFC).  In cases where reads disagreed with the base call at a given SNP position, only SNP sites with a consensus of >80% for the base call at the SNP site were included in the final SNP reference table.  Importantly, the base calls were confirmed by both parental strains.  Transcript UCSC IDs (transcriptome alignment) or genome positions (genomic alignment) were recorded for each SNP containing read alignment, for example: uc007aeu.1_1263 (UCSC transcript ID_SNP base position).  The SNP position was recorded relative to the first base of the transcript, or the base position relative to the start of the chromosome was recorded in the case of genomic alignments.  Base calls at SNP sites for CAST and C57 samples relative to the annotated mouse transcriptome, genome, or fRNAdb were assembled into a CAST/C57 SNP Reference Table (see all tables labeled with "_SNP_calls.txt") and these SNP sites were used to assess allele-specific expression in the F1 hybrids.  RNA Seq data from initial (F1i) and reciprocal (F1r) crosses of F1 hybrid mice was used to measure maternal and paternall allele specific expression at each SNP site.  In the manuscripts, SNP site calls were further refined by requiring a minimum of 10 reads per SNP site for both the F1i and F1r crosses in the F1 hybrid datasets, however all SNP calls are presented in the raw processed files here.

Processed data file: PFC_TranscriptomeAligned.csv
Processed data file: PFC_GenomicAligned.csv
Processed data file: PFC_fRNAdbAligned.csv
Processed data file(s) linked as supplementary files on Series GSE22131.

source_name: adult (5 week old) medial prefrontal cortex

value: adult

value: 5 weeks old

value: medial prefrontal cortex


title: E15_F1i_RNASeq_techrep3


title: PFC_F1i_Female_RNASeq_techrep2


title: POA_F1r_Female_RNASeq_techrep2

data_processing:
Sequence data (reads were trimmed to 32 bases for analysis) was aligned using NovoAlign to the UCSC annotated mouse transcriptome (mm9) and mouse genome (mm9) and to the functional RNA database.
A reference table of CAST and C57 SNP sites was generated relative to the annotated reference transcriptome and genome for genes expressed in the E15 brain and adult mPFC and POA using the CastEiJ and C57BL/6J sequence data (E15 brain, POA, and mPFC).  In cases where reads disagreed with the base call at a given SNP position, only SNP sites with a consensus of >80% for the base call at the SNP site were included in the final SNP reference table.  Importantly, the base calls were confirmed by both parental strains.  Transcript UCSC IDs (transcriptome alignment) or genome positions (genomic alignment) were recorded for each SNP containing read alignment, for example: uc007aeu.1_1263 (UCSC transcript ID_SNP base position).  The SNP position was recorded relative to the first base of the transcript, or the base position relative to the start of the chromosome was recorded in the case of genomic alignments.  Base calls at SNP sites for CAST and C57 samples relative to the annotated mouse transcriptome, genome, or fRNAdb were assembled into a CAST/C57 SNP Reference Table (see all tables labeled with "_SNP_calls.txt") and these SNP sites were used to assess allele-specific expression in the F1 hybrids.  RNA Seq data from initial (F1i) and reciprocal (F1r) crosses of F1 hybrid mice was used to measure maternal and paternall allele specific expression at each SNP site.  In the manuscripts, SNP site calls were further refined by requiring a minimum of 10 reads per SNP site for both the F1i and F1r crosses in the F1 hybrid datasets, however all SNP calls are presented in the raw processed files here.

Processed data file: POA_TranscriptomeAligned.csv
Processed data file: POA_GenomicAligned.csv
Processed data file: POA_fRNAdbAligned.csv
Processed data file(s) linked as supplementary files on Series GSE22131.

source_name: adult (5 week old) preoptic area

value: preoptic area


title: POA_F1i_Female_RNASeq_techrep2


title: PFC_F1r_Male_RNASeq_techrep2


title: H3K9me1_PHF8_RNAi_ChIPSeq

description: Chromatin IP against H3K9me1

value: HeLa cells

value: PHF8 depletion

value: Anti-H3K9me1 antibody, abcam, lot# 815310, ab8896


title: RAP1_ko1 RAP1-Chip-seq


title: PFC_F1i_Male_RNASeq_techrep2

value: F1 hybrid initial cross (F1i) Hybrid [Mother:CastEiJ, Father:C57BL6J]


title: POA_F1r_Male_RNASeq_techrep2


title: POA_F1i_Male_RNASeq_techrep2


title: E15_F1r_RNASeq_techrep2

value: embryo


title: PFC_F1i_Male_RNASeq_techrep1


title: POA_F1r_Male_RNASeq_techrep1


title: POA_F1i_Male_RNASeq_techrep1


title: POA_F1i_Female_RNASeq_techrep1


title: PFC_F1i_Female_RNASeq_techrep1


title: PFC_F1r_Male_RNASeq_techrep1


title: PFC_F1r_Female_RNASeq_techrep1


title: E15_F1i_RNASeq_techrep1

value: day 15


title: PFC_CastEiJ_RNASeq_techrep1

data_processing:
Sequence data (reads were trimmed to 32 bases for analysis) was aligned using NovoAlign to the UCSC annotated mouse transcriptome (mm9) and mouse genome (mm9) and to the functional RNA database.
A reference table of CAST and C57 SNP sites was generated relative to the annotated reference transcriptome and genome for genes expressed in the E15 brain and adult mPFC and POA using the CastEiJ and C57BL/6J sequence data (E15 brain, POA, and mPFC).  In cases where reads disagreed with the base call at a given SNP position, only SNP sites with a consensus of >80% for the base call at the SNP site were included in the final SNP reference table.  Importantly, the base calls were confirmed by both parental strains.  Transcript UCSC IDs (transcriptome alignment) or genome positions (genomic alignment) were recorded for each SNP containing read alignment, for example: uc007aeu.1_1263 (UCSC transcript ID_SNP base position).  The SNP position was recorded relative to the first base of the transcript, or the base position relative to the start of the chromosome was recorded in the case of genomic alignments.  Base calls at SNP sites for CAST and C57 samples relative to the annotated mouse transcriptome, genome, or fRNAdb were assembled into a CAST/C57 SNP Reference Table (see all tables labeled with "_SNP_calls.txt") and these SNP sites were used to assess allele-specific expression in the F1 hybrids.  RNA Seq data from initial (F1i) and reciprocal (F1r) crosses of F1 hybrid mice was used to measure maternal and paternall allele specific expression at each SNP site.  In the manuscripts, SNP site calls were further refined by requiring a minimum of 10 reads per SNP site for both the F1i and F1r crosses in the F1 hybrid datasets, however all SNP calls are presented in the raw processed files here.

Processed data file: PFC_SNP_calls.txt
Processed data file(s) linked as supplementary files on Series GSE22131.

value: CastEiJ

value: brain


title: E15_F1r_RNASeq_techrep1

value: whole brain

value: transcriptome single nucleotide polymorphisms read counts


title: POA_C57BL/6J_RNASeq_techrep1

data_processing:
Sequence data (reads were trimmed to 32 bases for analysis) was aligned using NovoAlign to the UCSC annotated mouse transcriptome (mm9) and mouse genome (mm9) and to the functional RNA database.
A reference table of CAST and C57 SNP sites was generated relative to the annotated reference transcriptome and genome for genes expressed in the E15 brain and adult mPFC and POA using the CastEiJ and C57BL/6J sequence data (E15 brain, POA, and mPFC).  In cases where reads disagreed with the base call at a given SNP position, only SNP sites with a consensus of >80% for the base call at the SNP site were included in the final SNP reference table.  Importantly, the base calls were confirmed by both parental strains.  Transcript UCSC IDs (transcriptome alignment) or genome positions (genomic alignment) were recorded for each SNP containing read alignment, for example: uc007aeu.1_1263 (UCSC transcript ID_SNP base position).  The SNP position was recorded relative to the first base of the transcript, or the base position relative to the start of the chromosome was recorded in the case of genomic alignments.  Base calls at SNP sites for CAST and C57 samples relative to the annotated mouse transcriptome, genome, or fRNAdb were assembled into a CAST/C57 SNP Reference Table (see all tables labeled with "_SNP_calls.txt") and these SNP sites were used to assess allele-specific expression in the F1 hybrids.  RNA Seq data from initial (F1i) and reciprocal (F1r) crosses of F1 hybrid mice was used to measure maternal and paternall allele specific expression at each SNP site.  In the manuscripts, SNP site calls were further refined by requiring a minimum of 10 reads per SNP site for both the F1i and F1r crosses in the F1 hybrid datasets, however all SNP calls are presented in the raw processed files here.

Processed data file: POA_SNP_calls.txt
Processed data file(s) linked as supplementary files on Series GSE22131.


title: POA_CastEiJ_RNASeq_techrep1


title: POA_F1r_Female_RNASeq_techrep1


title: E15_C57BL/6J_RNASeq_techrep2

data_processing:
Sequence data (reads were trimmed to 32 bases for analysis) was aligned using NovoAlign to the UCSC annotated mouse transcriptome (mm9) and mouse genome (mm9) and to the functional RNA database.
A reference table of CAST and C57 SNP sites was generated relative to the annotated reference transcriptome and genome for genes expressed in the E15 brain and adult mPFC and POA using the CastEiJ and C57BL/6J sequence data (E15 brain, POA, and mPFC).  In cases where reads disagreed with the base call at a given SNP position, only SNP sites with a consensus of >80% for the base call at the SNP site were included in the final SNP reference table.  Importantly, the base calls were confirmed by both parental strains.  Transcript UCSC IDs (transcriptome alignment) or genome positions (genomic alignment) were recorded for each SNP containing read alignment, for example: uc007aeu.1_1263 (UCSC transcript ID_SNP base position).  The SNP position was recorded relative to the first base of the transcript, or the base position relative to the start of the chromosome was recorded in the case of genomic alignments.  Base calls at SNP sites for CAST and C57 samples relative to the annotated mouse transcriptome, genome, or fRNAdb were assembled into a CAST/C57 SNP Reference Table (see all tables labeled with "_SNP_calls.txt") and these SNP sites were used to assess allele-specific expression in the F1 hybrids.  RNA Seq data from initial (F1i) and reciprocal (F1r) crosses of F1 hybrid mice was used to measure maternal and paternall allele specific expression at each SNP site.  In the manuscripts, SNP site calls were further refined by requiring a minimum of 10 reads per SNP site for both the F1i and F1r crosses in the F1 hybrid datasets, however all SNP calls are presented in the raw processed files here.

Processed data file: E15_SNP_calls.txt
Processed data file(s) linked as supplementary files on Series GSE22131.


title: PFC_C57BL/6J_RNASeq_techrep1


title: Chlamydomonas-D66-Sulfur-Depleted

value: TAP -S

value: 6 hours


title: E15_C57BL/6J_RNASeq_techrep1


title: E15_CastEiJ_RNASeq_techrep1


title: E15_CastEiJ_RNASeq_techrep2


title: Kluyveromyces waltii genome-wide nucleosome data

status: Public on Jul 06 2010

city: Boston

first: Alex

last: Tsankov

address: 155 Bay State

institute: MIT

description: Mnase digested DNA and size selected for mononucleosomes (~150bp)

data_processing:
Read Extended Nucleosome Map: Each uniquely mapped read was then extended to a length of 100bp.  To generate a genomic nucleosome occupancy landscape, we cumulatively summed all extended reads covering each base pair.  The *.wig files use the WIGGLE fixed_step format.
Alignment: Sequence reads were mapped to the appropriate reference genome (fasta file attached) using BLAT. All reads mapping to a unique location in the genome with 4 or fewer mismatches were retained.  *.read files are tab delimited text files containing each uniques reads chromosomal coordinates.  The files have 4 columns and the following headers: readChrom, readStart, readStop, onForwardStrand (1=forward strand or +, 0=reverse strand or -).
Genomes: The version of the species' genomic sequences used in this study are attached as fasta files (*.fsa).

organism: Lachancea waltii

source_name: in vivo cells

growth_protocol: Overnight cultures for each species were grown in 450ml of media at 220 RPM in a New Brunswick Scientific air-shaker at 30°C until reaching mid log-phase.

extract_protocol:
Libraries were prepared according to standard Illumina instructions. Briefly, DNA was end-repaired. The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 19 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
Mnase digestion and gel purification of mononucleosomal DNA

treatment_protocol: Formaldehyde crosslink, shearing with MNase, isolation of mononucleosomal DNA using gel purification of DNA band ~150bp.

value: NCYC 2644


title: Candida albicans genome-wide nucleosome data

organism: Candida albicans


title: E15_F1i_RNASeq_techrep2