title: P493-6_T0_MAX

description:
Chromatin IP against Max in P493-6 T=0 hours
barcode (already removed): CGATGT


title: P493-6_T1_RNA_POL2

status: Public on Apr 05 2012

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 Pol2 N20 in P493-6 T=1 hour
barcode (already removed): GGCTAC

library_source: genomic

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 with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: 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.
Supplementary_files_format_and_content: Alignment (ylf) files: The .ylf files are in [Y]oung [L]ab [F]ormat. It is a compact flat file representation of aligned read locations determined by bowtie. The file contains the locations of the bowtie aligned reads with the following format:
#BWT1 (read category BWT1)
>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)
#BWT2 (read category BWT2)
etc..

molecule: genomic DNA

organism: Homo sapiens

source_name: B-cell lymphoma

growth_protocol: RPMI 1640 + FBS.  Tetracycline repressed cMyc transgene expression.  cMyc expression released for 1 hour.

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.

tag: chip antibody

value: RNA Pol II (Rpb1 N-terminus)

tag: antibody details (vendor, catalog number)

value: Santa Cruz SC-899

tag: cell type


title: P493-6_T1_MAX

description:
Chromatin IP against Max in P493-6 T=1 hour
barcode (already removed): TAGCTT

treatment_protocol: Tetracycline repressed cMyc transgene expression.  cMyc expression released for 1 hour.

value: Max

value: Santa Cruz SC-197


title: MM1S_WCE_DMSO_2

description:
Whole cell extract from MM.1S cells (DMSO) for 12022011_B0A1WABXX*
barcode (already removed): ATCACG

source_name: Multiple myeloma

growth_protocol: RPMI 1640 supplemented with 10% FCS and 1% GlutaMAX

treatment_protocol: DMSO treatment for 24 hours

value: None WCE

value: Plasma cell

tag: duration

tag: drug

value: DMSO


title: H128_H3K4ME3

description:
Chromatin IP against H3K4me3 in H128 SCLC rep1
barcode (already removed): GGCTAC

source_name: Small Cell Lung Carcinoma

value: Millipore 07-473


title: P493-6_T24_H3K4ME3

description:
Chromatin IP against H3K4me3 in P493-6 T=24 hours
barcode (already removed): GATCAG

growth_protocol: RPMI 1640 + FBS.  Tetracycline repressed cMyc transgene expression.  cMyc expression released for 24 hours.


title: MM1S_MAX_DMSO

description:
Chromatin IP against Max in MM.1S (DMSO) for 12022011_B0A1WABXX*
barcode (already removed): ACTTGA


title: P493-6_T0_H3K4ME3

description:
Chromatin IP against H3K4me3 in P493-6 T=0 hours
barcode (already removed): ACAGTG

growth_protocol: RPMI 1640 + FBS.  Tetracycline repressed cMyc transgene expression.  cMyc expression released for 0 hours.


title: H2171_H3K27AC

description:
Chromatin IP against H3K27Ac in H2171 SCLC rep1
barcode (already removed): TAGCTT

value: Abcam AB4729


title: P493-6_T1_H3K4ME3

description:
Chromatin IP against H3K4me3 in P493-6 T=1 hour
barcode (already removed): ATCACG


title: H128_H3K27AC

description:
Chromatin IP against H3K27Ac in H128 SCLC rep1
barcode (already removed): CTTGTA


title: U87_MYC

description:
Chromatin IP against cMyc in U87 Rep1
barcode (already removed): ATCACG

source_name: Glioblastoma

growth_protocol: RPMI 1640 + FBS

value: c-Myc

value: Santa Cruz SC-764


title: P493-6_T1_H3K27AC

description:
Chromatin IP against H3K27Ac in P493-6 T=1 hour
barcode (already removed): CTTGTA


title: P493-6_T0_H3K27AC

description:
Chromatin IP against H3K27Ac in P493-6 T=0
barcode (already removed): TGACCA

treatment_protocol: Tetracycline repressed cMyc transgene expression.  cMyc expression released for 0 hours.


title: P493-6_T1_MYC

description:
Chromatin IP against cMyc in P493-6 T=1 hour
barcode (already removed): GATCAG


title: P493-6_T0_MYC

description:
Chromatin IP against cMyc in P493-6 T=0 hours
barcode (already removed): ATCACG


title: P493-6_T24_MYC

description:
Chromatin IP against cMyc in P493-6 T=24 hour
barcode (already removed): ACAGTG

treatment_protocol: Tetracycline repressed cMyc transgene expression.  cMyc expression released for 24 hours.


title: P493-6_T24_H3K27AC

description:
Chromatin IP against H3K27Ac in P493-6 T=24 hours
barcode (already removed): ACTTGA


title: U87_H3K4ME3

description:
Chromatin IP against H3K4me3 in U87 Rep1
barcode (already removed): CAGATC


title: e1a H3K4me1 ChIP-seq

city: Los Angeles

first: Siavash

middle: K

last: Kurdistani

state: CA

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

description: Chromatin IP against H3K4me1

data_processing:
Libraries were sequenced using Illumina Genome Analyser II to obtain 76 bp-long reads (H3K9ac and corresponding input libraries) or Illumina HIseq-2000 to obtain 50 bp-long reads (H3K18ac and correspondent input libraries). ChIP for RB1 was performed as described in Chicas et al. 2010 Cancer Cell
Reads were mapped to the Human (hg19) genome using Bowtie software. Only reads that aligned to a unique position in the genome with no more than two sequence mismatches were retained for further analysis. Duplicate reads that mapped to the same exact location in the genome were counted only once to reduce clonal amplification effects. The genome was tiled with 100 bp windows. Each read was extended by 150 bases (so we refer to tags as the extend read counts within a bin) and was counted as one read to each window to which it partially or fully matched. The total counts of the input and ChIP samples were normalized to each other. The input sample was used to estimate the expected counts in a window; the average value for all windows was assigned to windows with zero counts. Finally, we used the Poisson distribution to estimate the probability of observing the ChIP counts within a window given the expected counts in the input sample window. We considered all windows with P-values less than 1.0E-3 to have significant peaks. P-value < 1.0 E-3 was chosen to give False Discovery Rate (FDR) less than 5%. FDR was calculated by applying the same statistic, described above, to the two halves of the same input library. We considered the total number of significant peaks obtained this way as an estimate of number of false-positive peaks. To compare two ChIP samples to identify regions that are significantly different between the two samples (for instance e1a versus mock), we replaced the input sample with the sample used for comparison; all downstream analyses were identical. Our algorithm produces several files that were subsequently used for analysis: BED files containing the coordinates of the significant windows of enrichment; Wiggle (wig) files (chromosome tiling, fixed step) with normalized reads count for the significant windows (If a window was not significant, we placed zero tags); GR files of normalized raw counts for input and ChIP samples were also created for genome browser visualization.). Tiling profiles of promoter regions for the hg19 annotated human promoters were also generated. These represent the 100-bp tiling of a 10 Kb region spanning the transcription start site (TSS). We reported the number of reads falling into significant windows and zero for the non-significant ones.

source_name: lung fibroblasts

growth_protocol: IMR90 human primary lung embryo fibroblasts (ATCC) were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 100 U/ml penicillin, 100 μg/ml streptomycin, and 10% fetal bovine serum (FBS) at 37°C in 5% CO2. Propagation of dl1500 virus was done as described in1. Briefly, 293 spinner cells were grown in Joklik's modified Eagle minimal essential medium (SMEM) plus 5% FBS with 100 U/ml penicillin, 100 μg/ml streptomycin, and 2mM L-glutamine. Propagation of viruses was in 293 spinner cells with 2% FBS. Ad dl1500 stock titers were determined by plaque assay in duplicate on 293 cells.

extract_protocol: Total RNA was extracted from mock- and dl1500 infected cells using Qiagen easy RNA  kit. Maximum amount of RNA was used to start the library preparation according to the  manufacturer’s instructions (Illumina). Libraries were sequenced using Illumina Genome  Analyser II to obtain 76 bp-long reads. Alignment of mRNA-seq reads was performed using  default parameters of Tophat. Aligned reads were converted to sam format and SAMMate  software6 was used to determine the transcript RPKM (reads per kilobase of exon per million of  reads).

treatment_protocol: Infection with dl1500 adenovirus

tag: cell line

value: contact-inhibited IMR90

tag: passages

tag: infection

value: anti-histone H3

tag: chip antibody catalog number

tag: chip antibody manufacturer

value: Abcam


title: RNA pol II ChIP-Seq TTF2+Xrn2 shRNA

city: Aurora

first: David

middle: L.

last: Bentley

state: CO

department: Biochemistry and Mol. Genetics

institute: U. Colorado School of Medicine

description:
Chromatin IP against RNA pol II.
Rabbit anti-pan C-terminal heptad repeat domain (CTD) (detects phosphorylated and non-phosphorylated Pol II CTD; Schroeder et al. Genes Dev. 14:2435, 2000).

data_processing:
Single-end 34 base reads (after removing barcodes) were mapped to the hg18 UCSC human genome (Mar. 2006) with Bowtie version 0.12.5.
Genome Build:
hg18_xrn2_ttf2_dkd__FC629BP_5_TAT.wig.gz: hg18

source_name: HEK293, TTF2+Xrn2 shRNA, RNA pol II ChIP

extract_protocol: IPs from 2 ug of cross-linked extract were immunoprecipitated and prepared for Illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, gel purification of ~200bp fragments, and amplification (18 cycles) with Illumina PE primers using Phusion DNA polymerase.

treatment_protocol: HEK293 cells were stably infected with lentiviruses expressing the respective shRNAs or uninfected parent control.

tag: shRNA

value: rabbit anti-pan CTD

tag: growth protocol

value: Cells were grown in DMEM 10% FCS + puromycin + G418.


title: RNA pol II ChIP-Seq Dcp1a shRNA

data_processing:
Single-end 34 base reads (after removing barcodes) were mapped to the hg18 UCSC human genome (Mar. 2006) with Bowtie version 0.12.5.
Genome Build:
hg18_dcp1a_kd__FC70FB6b_2_ATT.wig.gz: hg18

source_name: HEK293, Dcp1a shRNA, RNA pol II ChIP

value: Cells were grown in DMEM 10% FCS + puromycin.


title: TTF2 ChIP-Seq (antibody 1)

description:
Chromatin IP against TTF2.
Sheep anti-TTF2 (affinity pure; Jian et al. Mol Cell 14, 375-385, 2004).

data_processing:
Single-end 34 base reads (after removing barcodes) were mapped to the hg18 UCSC human genome (Mar. 2006) with Bowtie version 0.12.5.
Genome Build:
hg18_ttf2_hela1__ACO5E6ACXX_6_TAT.wig.gz: hg18

source_name: HeLa, TTF2 ChIP

value: HeLa

value: sheep anti-TTF2

value: Cells were grown in DMEM 10% FCS.


title: RNA pol II ChIP-Seq Xrn2 shRNA

data_processing:
Single-end 34 base reads (after removing barcodes) were mapped to the hg18 UCSC human genome (Mar. 2006) with Bowtie version 0.12.5.
Genome Build:
hg18_xrn2_kd__FC6298A_7_GAT.wig.gz: hg18

source_name: HEK293, Xrn2 shRNA, RNA pol II ChIP


title: RNA pol II ChIP-Seq Edc3 shRNA

data_processing:
Single-end 34 base reads (after removing barcodes) were mapped to the hg18 UCSC human genome (Mar. 2006) with Bowtie version 0.12.5.
Genome Build:
hg18_edc3_kd__FC62NV5_8_CTT.wig.gz: hg18

source_name: HEK293, Edc3 shRNA, RNA pol II ChIP


title: RNA pol II ChIP-Seq scr shRNA control

data_processing:
Single-end 34 base reads (after removing barcodes) were mapped to the hg18 UCSC human genome (Mar. 2006) with Bowtie version 0.12.5.
Genome Build:
hg18_scramble__FC62TY3_6_ATT.wig.gz: hg18

source_name: HEK293, scrambled shRNA, RNA pol II ChIP

value: scrambled


title: mock-infected input Hiseq_ChIP-seq

description:
input control
mock-infected input Hiseq

data_processing:
DNA: Libraries were sequenced using Illumina Genome Analyser II to obtain 76 bp-long reads (H3K9ac and corresponding input libraries) or Illumina HIseq-2000 to obtain 50 bp-long reads (H3K18ac and correspondent input libraries). ChIP for RB1 was performed as described in Chicas et al. 2010 Cancer Cell
DNA: Reads were mapped to the Human (hg19) genome using Bowtie software. Only reads that aligned to a unique position in the genome with no more than two sequence mismatches were retained for further analysis. Duplicate reads that mapped to the same exact location in the genome were counted only once to reduce clonal amplification effects. The genome was tiled with 100 bp windows. Each read was extended by 150 bases (so we refer to tags as the extend read counts within a bin) and was counted as one read to each window to which it partially or fully matched. The total counts of the input and ChIP samples were normalized to each other. The input sample was used to estimate the expected counts in a window; the average value for all windows was assigned to windows with zero counts. Finally, we used the Poisson distribution to estimate the probability of observing the ChIP counts within a window given the expected counts in the input sample window. We considered all windows with P-values less than 1.0E-3 to have significant peaks. P-value < 1.0 E-3 was chosen to give False Discovery Rate (FDR) less than 5%. FDR was calculated by applying the same statistic, described above, to the two halves of the same input library. We considered the total number of significant peaks obtained this way as an estimate of number of false-positive peaks. To compare two ChIP samples to identify regions that are significantly different between the two samples (for instance e1a versus mock), we replaced the input sample with the sample used for comparison; all downstream analyses were identical. Our algorithm produces several files that were subsequently used for analysis: BED files containing the coordinates of the significant windows of enrichment; Wiggle (wig) files (chromosome tiling, fixed step) with normalized reads count for the significant windows (If a window was not significant, we placed zero tags); GR files of normalized raw counts for input and ChIP samples were also created for genome browser visualization.). Tiling profiles of promoter regions for the hg19 annotated human promoters were also generated. These represent the 100-bp tiling of a 10 Kb region spanning the transcription start site (TSS). We reported the number of reads falling into significant windows and zero for the non-significant ones.

RNA: Libraries were sequenced using Illumina Genome Analyser IIx to obtain 76 bp-long reads. Alignment of mRNA-seq reads was performed using default parameters of Tophat. Aligned reads were converted to sam format and SAMMate software6 was used to determine the transcript RPKM (reads per kilobase of exon per million of reads).

growth_protocol: IMR90 human primary lung embryo fibroblasts (ATCC) were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 100 U/ml penicillin, 100 u/ml streptomycin, and 10% fetal bovine serum (FBS) at 37°C in 5% CO2. Propagation of dl1500 virus was done as described in1. Briefly, 293 spinner cells were grown in Joklik's modified Eagle minimal essential medium (SMEM) plus 5% FBS with 100 U/ml penicillin, 100 u/ml streptomycin, and 2mM L-glutamine. Propagation of viruses was in 293 spinner cells with 2% FBS. Ad dl1500 stock titers were determined by plaque assay in duplicate on 293 cells.

extract_protocol:
DNA: Chromatin immunoprecipitation for ChIP-seq was performed essentially as described,  with few modifications. Briefly, 1x108 IMR90 lung fibroblasts were grown to confluence in 15  cm dishes. After 24 h, the cells were incubated with mock- or the dl1500 adenovirus for 1 h in  media with 2% serum. After 24 h post infection (p.i.), formaldehyde was added for 10 min at  37°C. After PBS washing, cross-linked cells were scraped from the plates and washed with 1 ml  of PBS containing protease inhibitors (Roche). 2x107 Cells were resuspended in 450 ul of lysis  buffer and incubated for 10 min on ice and immediately sonicated using Misonix cup-horn  sonicator. 100 ul of the lysate (corresponding to 5x106 cells) were used for each  immunoprecipitation with a given antibody (listed below); 10 ul of the lysate was used as input.  After overnight reversal of crosslinking at 65°C, samples were treated with RNase A for 30 min  at 37°C, proteinase K for 2 h at 56°C. DNA was subsequently purified using phenol/chloroform  extraction and precipitation. DNA concentration was measured using Qubit (Invitrogen). At least  10 ng of dsDNA for both input and IP was used for library preparation according to the  manufacturer's instructions (Illumina). Libraries were sequenced using Illumina Genome  Analyser II to obtain 76 bp-long reads (H3K9ac and corresponding input libraries) or Illumina  HIseq-2000 to obtain 50 bp-long reads (H3K18ac and correspondent input libraries).

RNA: Total RNA was extracted from mock- and dl1500 infected cells using Qiagen easy RNA kit. Maximum amount of RNA was used to start the library preparation according to the manufacturer's instructions (Illumina).

treatment_protocol: Infection with dl1500 adenovirus or mock-infection

value: mock-infected

tag: chip target


title: RNA pol II ChIP-Seq TTF2 shRNA

data_processing:
Single-end 34 base reads (after removing barcodes) were mapped to the hg18 UCSC human genome (Mar. 2006) with Bowtie version 0.12.5.
Genome Build:
hg18_ttf2_kd__FC6298A_7_CTT.wig.gz: hg18

source_name: HEK293, TTF2 shRNA, RNA pol II ChIP


title: U87_H3K27AC

description:
Chromatin IP against H3K27Ac in U87 Rep1
barcode (already removed): TGACCA


title: e1a-infected input control Hiseq_ChIP-seq

description:
input control
e1a-infected input control Hiseq

value: IMR90 human primary lung embryo fibroblasts


title: RNA pol II ChIP-Seq Dcp2 shRNA

data_processing:
Single-end 34 base reads (after removing barcodes) were mapped to the hg18 UCSC human genome (Mar. 2006) with Bowtie version 0.12.5.
Genome Build:
hg18_dcp2_kd__FC62TFM_1_ATT.wig.gz: hg18

source_name: HEK293, Dcp2 shRNA, RNA pol II ChIP


title: RNA pol II ChIP-Seq parent control

data_processing:
Single-end 34 base reads (after removing barcodes) were mapped to the hg18 UCSC human genome (Mar. 2006) with Bowtie version 0.12.5.
Genome Build:
hg18_parent_293pa__FC6298G_8_ATT.wig.gz: hg18

source_name: HEK293, RNA pol II ChIP


title: e1a-infected mRNA sequencing

description:
mRNA sequencing
e1a-infected mRNA seq GAIIx
RPKM file linked as supplementary file on Series record.

library_source: transcriptomic

data_processing:
mRNA sequencing
e1a-infected mRNA seq GAIIx
DNA: Libraries were sequenced using Illumina Genome Analyser II to obtain 76 bp-long reads (H3K9ac and corresponding input libraries) or Illumina HIseq-2000 to obtain 50 bp-long reads (H3K18ac and correspondent input libraries). ChIP for RB1 was performed as described in Chicas et al. 2010 Cancer Cell
DNA: Reads were mapped to the Human (hg19) genome using Bowtie software. Only reads that aligned to a unique position in the genome with no more than two sequence mismatches were retained for further analysis. Duplicate reads that mapped to the same exact location in the genome were counted only once to reduce clonal amplification effects. The genome was tiled with 100 bp windows. Each read was extended by 150 bases (so we refer to tags as the extend read counts within a bin) and was counted as one read to each window to which it partially or fully matched. The total counts of the input and ChIP samples were normalized to each other. The input sample was used to estimate the expected counts in a window; the average value for all windows was assigned to windows with zero counts. Finally, we used the Poisson distribution to estimate the probability of observing the ChIP counts within a window given the expected counts in the input sample window. We considered all windows with P-values less than 1.0E-3 to have significant peaks. P-value < 1.0 E-3 was chosen to give False Discovery Rate (FDR) less than 5%. FDR was calculated by applying the same statistic, described above, to the two halves of the same input library. We considered the total number of significant peaks obtained this way as an estimate of number of false-positive peaks. To compare two ChIP samples to identify regions that are significantly different between the two samples (for instance e1a versus mock), we replaced the input sample with the sample used for comparison; all downstream analyses were identical. Our algorithm produces several files that were subsequently used for analysis: BED files containing the coordinates of the significant windows of enrichment; Wiggle (wig) files (chromosome tiling, fixed step) with normalized reads count for the significant windows (If a window was not significant, we placed zero tags); GR files of normalized raw counts for input and ChIP samples were also created for genome browser visualization.). Tiling profiles of promoter regions for the hg19 annotated human promoters were also generated. These represent the 100-bp tiling of a 10 Kb region spanning the transcription start site (TSS). We reported the number of reads falling into significant windows and zero for the non-significant ones.

RNA: Libraries were sequenced using Illumina Genome Analyser IIx to obtain 76 bp-long reads. Alignment of mRNA-seq reads was performed using default parameters of Tophat. Aligned reads were converted to sam format and SAMMate software6 was used to determine the transcript RPKM (reads per kilobase of exon per million of reads). RPKM file linked as supplementary file on Series record.

molecule: total RNA


title: Xrn2 ChIP-Seq

description:
Chromatin IP against Xrn2.
Rabbit anti-Xrn2 (aa402-537, affinity pure; Brannan et al. Mol Cell 2012).

data_processing:
Single-end 34 base reads (after removing barcodes) were mapped to the hg18 UCSC human genome (Mar. 2006) with Bowtie version 0.12.5.
Genome Build:
hg18_xrn2_hela__FC61ALC_8_CTT.wig.gz: hg18

source_name: HeLa, Xrn2 ChIP

value: rabbit anti-Xrn2


title: mock-infected p107_ChIP-seq

description:
Chromatin IP against p107
mock-infected p107


title: TTF2 ChIP-Seq (antibody 2)

description:
Chromatin IP against TTF2.
Rabbit anti-TTF2 (Proteintech cat.# 13722-1-AP).

data_processing:
Single-end 34 base reads (after removing barcodes) were mapped to the hg18 UCSC human genome (Mar. 2006) with Bowtie version 0.12.5.
Genome Build:
hg18_ttf2_hela2__FC61THR_3_CTT.wig.gz: hg18

value: rabbit anti-TTF2

tag: antibody vendor

value: Proteintech

tag: antibody catalog #


title: Hela input chromatin

description: Sheared input chromatin.

data_processing:
Single-end 34 base reads (after removing barcodes) were mapped to the hg18 UCSC human genome (Mar. 2006) with Bowtie version 0.12.5.
Genome Build:
hg18_input_hela__FC61ALD_6.wig.gz: hg18

source_name: HeLa, input


title: e1a H3K9ac_ChIP-seq

description:
Chromatin IP against H3K9ac
dl1500-infected H3K9ac 24 h p.i.

value: Upstate H3K9ac (07-352)


title: Dcp1a ChIP-Seq

description:
Chromatin IP against Dcp1a.
Rabbit anti-Dcp1a (Lykke-Andersen, J., and Wagner, E. Genes Dev 19, 351-361, 2005).

data_processing:
Single-end 34 base reads (after removing barcodes) were mapped to the hg18 UCSC human genome (Mar. 2006) with Bowtie version 0.12.5.
Genome Build:
hg18_dcp1_hela.wig.gz: hg18

source_name: HeLa, Dcp1a ChIP

value: rabbit anti-Dcp1a


title: Mock H3K18ac_ChIP-seq

description:
Chromatin IP against H3K18ac
mock-infected H3K18ac 24 h p.i.

value: contact-inhibited IMR90

value: Custom 814 H3K18ac


title: e1a H3K18ac_ChIP-seq

description:
Chromatin IP against H3K18ac
dl1500-infected H3K18ac 24 h p.i.


title: e1a_infected input GAIIx _ChIP-seq

description:
input control
e1a_infected input GAIIx


title: mock-infected input GAIIx DSG_ChIP-seq

description:
input control
mock-infected input GAIIx DSG


title: Mock mRNA control sequencing

description:
mRNA sequencing
mock-infected mRNA seq GAIIx
RPKM file linked as supplementary file on Series record.

data_processing:
mRNA sequencing
mock-infected mRNA seq GAIIx
DNA: Libraries were sequenced using Illumina Genome Analyser II to obtain 76 bp-long reads (H3K9ac and corresponding input libraries) or Illumina HIseq-2000 to obtain 50 bp-long reads (H3K18ac and correspondent input libraries). ChIP for RB1 was performed as described in Chicas et al. 2010 Cancer Cell
DNA: Reads were mapped to the Human (hg19) genome using Bowtie software. Only reads that aligned to a unique position in the genome with no more than two sequence mismatches were retained for further analysis. Duplicate reads that mapped to the same exact location in the genome were counted only once to reduce clonal amplification effects. The genome was tiled with 100 bp windows. Each read was extended by 150 bases (so we refer to tags as the extend read counts within a bin) and was counted as one read to each window to which it partially or fully matched. The total counts of the input and ChIP samples were normalized to each other. The input sample was used to estimate the expected counts in a window; the average value for all windows was assigned to windows with zero counts. Finally, we used the Poisson distribution to estimate the probability of observing the ChIP counts within a window given the expected counts in the input sample window. We considered all windows with P-values less than 1.0E-3 to have significant peaks. P-value < 1.0 E-3 was chosen to give False Discovery Rate (FDR) less than 5%. FDR was calculated by applying the same statistic, described above, to the two halves of the same input library. We considered the total number of significant peaks obtained this way as an estimate of number of false-positive peaks. To compare two ChIP samples to identify regions that are significantly different between the two samples (for instance e1a versus mock), we replaced the input sample with the sample used for comparison; all downstream analyses were identical. Our algorithm produces several files that were subsequently used for analysis: BED files containing the coordinates of the significant windows of enrichment; Wiggle (wig) files (chromosome tiling, fixed step) with normalized reads count for the significant windows (If a window was not significant, we placed zero tags); GR files of normalized raw counts for input and ChIP samples were also created for genome browser visualization.). Tiling profiles of promoter regions for the hg19 annotated human promoters were also generated. These represent the 100-bp tiling of a 10 Kb region spanning the transcription start site (TSS). We reported the number of reads falling into significant windows and zero for the non-significant ones.

RNA: Libraries were sequenced using Illumina Genome Analyser IIx to obtain 76 bp-long reads. Alignment of mRNA-seq reads was performed using default parameters of Tophat. Aligned reads were converted to sam format and SAMMate software6 was used to determine the transcript RPKM (reads per kilobase of exon per million of reads). RPKM file linked as supplementary file on Series record.


title: mock-infected input GAIIx_ChIP-seq

description:
input control
mock-infected input GAIIx


title: mock-infected RB1_ChIP-seq

description:
Chromatin IP against RB1
mock-infected RB1 DSG

value: Cell signalling 4H1


title: mock-infected p130_ChIP-seq

description:
Chromatin IP against p130
mock-infected p130


title: LNCaP_abl_Control_KD_rep2

status: Public on Apr 04 2012

city: La Jolla

first: Hai-Ri

last: Li

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

description: Control siRNA

data_processing:
The tags were mapped to the reference human genome( hg19) with Bowtie by allowing maximum 2 mismatches in the first 28 nt.
Genome Build:
LNCaP_abl_Control_KD_rep2.bed: hg19

source_name: prostate cancer

growth_protocol: LNCaP-abl cells  were cultured in Phenol red-free RPMI 1640 containing 10% charcoal/dextran treated FBS, plus 2 mM GlutaMax, 10 mM HEPES, 1 mM Sodium Pyruvate, 2.5 mg/ml D-(+)-Glucose.

extract_protocol: RNAs were extracted from LNCaP-abl cells using TRIzol Reagent (Life Technologies, cat# 15596-026) . The cDNAs were synthesized with biotinylated P7-dT(20) oligos by reverse transcription and captured to solid phase. The second strand cDNAs were made with Adpator-hexamer by extension using DNA polymerase. The second strand cDNAs were PCR amplified with P7 and P5-index-Adaptor primers. The PCR products were size-selected, pooled and subjected to Illumina sequencers, reading target sequences followed by reading index (Genomics. 2011:98;266)

value: hormone resistant LNCaP-abl

tag: genotype/variation

value: Control knockdown (Control siRNA)


title: LNCaP_abl_Control_KD_rep3

description: Control siRNA

data_processing:
The tags were mapped to the reference human genome( hg19) with Bowtie by allowing maximum 2 mismatches in the first 28 nt.
Genome Build:
LNCaP_abl_Control_KD_rep3.bed: hg19


title: LNCaP_abl_AR_KD_rep2

description: AR siRNA

data_processing:
The tags were mapped to the reference human genome( hg19) with Bowtie by allowing maximum 2 mismatches in the first 28 nt.
Genome Build:
LNCaP_abl_AR_KD_rep2.bed: hg19

value: AR knockdown (AR siRNA)


title: LNCaP_abl_AR_KD_rep3

description: AR siRNA

data_processing:
The tags were mapped to the reference human genome( hg19) with Bowtie by allowing maximum 2 mismatches in the first 28 nt.
Genome Build:
LNCaP_abl_AR_KD_rep3.bed: hg19


title: LNCaP_abl_AR_KD_rep1

description: AR siRNA

data_processing:
The tags were mapped to the reference human genome( hg19) with Bowtie by allowing maximum 2 mismatches in the first 28 nt.
Genome Build:
LNCaP_abl_AR_KD_rep1.bed: hg19


title: AdpA_ChIP_seq

city: Bunkyo-ku, Tokyo

first: Yasuo

last: Ohnishi

department: Department of Biotechnology

country: Japan

institute: Graduate School of Agriculture and Life Science, The University of Tokyo

data_processing:
OHN02_2G_sorted.txt; genome build: NC_01572.1 (Streptomyces griseus NBRC 13350)
Sequence reads were mapped to the S. griseus genomes using ELAND. All reads mapping with two or fewer mismatches were retained. Reads were clustered and analyzed by CisGenome algorithm (http://www.biostat.jhsph.edu/~hji/cisgenome/).

organism: Streptomyces griseus

source_name: DadpA strain expressing His-AdpA

growth_protocol: Streptomyces griseus DadpA strain expressing His-AdpA was grown on YMPD liquid culture for 18 h.

extract_protocol: Lysates were clarified from sonicated nuclei and His-AdpA-DNA complexes were isolated with dynabeads TALON or antibody.  DNA samples were submitted to Takara Bio for sequencing with Illumina Genome Analyzer II. Libraries were prepared according to Illumina's instructions accompanying the ChIP-seq smple preparation kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel, the purified DNA was PCR amplified with Illumina primers for 18 cycles. Amplified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: strain

value: DadpA strain

tag: antibody

value: His-AdpA (Penta-His mouse monoclonal Antibody, BSA-free)

value: Qiagen

tag: antibody catalog

tag: method

value: ChIP


title: AdpA_ChAP_seq

data_processing:
OHN02_1G_sorted.txt; genome build: NC_01572.1 (Streptomyces griseus NBRC 13350)
Sequence reads were mapped to the S. griseus genomes using ELAND. All reads mapping with two or fewer mismatches were retained. Reads were clustered and analyzed by CisGenome algorithm (http://www.biostat.jhsph.edu/~hji/cisgenome/).

extract_protocol:
Lysates were clarified from sonicated nuclei and His-AdpA-DNA complexes were isolated with dynabeads TALON or antibody.  DNA samples were submitted to Takara Bio for sequencing with Illumina Genome Analyzer II. Libraries were prepared according to Illumina's instructions accompanying the ChIP-seq smple preparation kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel, the purified DNA was PCR amplified with Illumina primers for 18 cycles. Amplified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
library_strategy: ChAP-Seq

value: ChAP


title: LNCaP_abl_Strophanthidin_rep3

description: 5 uM Strophanthidin treatment for 24 hours

data_processing:
The tags were mapped to the reference human genome( hg19) with Bowtie by allowing maximum 2 mismatches in the first 28 nt.
Genome Build:
LNCaP_abl_Strophanthidin_rep3.bed: hg19

tag: cardioglycoside treatment

value: Strophanthidin


title: LNCaP_abl_Strophanthidin_rep1

data_processing:
The tags were mapped to the reference human genome( hg19) with Bowtie by allowing maximum 2 mismatches in the first 28 nt.
Genome Build:
LNCaP_abl_Strophanthidin_rep1.bed: hg19


title: solid_1_day_AdpA_ChIP_seq

data_processing:
OHN03_1G_uniq.sam; genome build: NC_01572.1 (Streptomyces griseus NBRC 13350)
OHN03_1G_multi.sam; genome build: NC_01572.1 (Streptomyces griseus NBRC 13350)
Sequence reads were mapped to the S. griseus genomes using Bowtie. All reads mapping with two or fewer mismatches were retained. Reads were clustered and analyzed by CisGenome algorithm (http://www.biostat.jhsph.edu/~hji/cisgenome/).

growth_protocol: Streptomyces griseus DadpA strain expressing His-AdpA was grown on YMPD-cellophane plate for 1, 2, and 3 days.

extract_protocol: Lysates were clarified from sonicated nuclei and His-AdpA-DNA complexes were isolated with dynabeads TALON.  DNA samples were submitted to Takara Bio for sequencing with illumina Genome Analyzer II. Libraries were prepared according to Illumina's instructions accompanying the ChIP-seq smple preparation kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel, the purified DNA was PCR amplified with Illumina primers for 18 cycles. Amplified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.


title: LNCaP_abl_Peruvoside_rep3

description: 5 uM Peruvoside treatment for 24 hours

data_processing:
The tags were mapped to the reference human genome( hg19) with Bowtie by allowing maximum 2 mismatches in the first 28 nt.
Genome Build:
LNCaP_abl_Peruvoside_rep3.bed: hg19

value: Peruvoside


title: LNCaP_abl_Digoxin_rep3

description: 5 uM Digoxin treatment for 24 hours

data_processing:
The tags were mapped to the reference human genome( hg19) with Bowtie by allowing maximum 2 mismatches in the first 28 nt.
Genome Build:
LNCaP_abl_Digoxin_rep3.bed: hg19

value: Digoxin


title: LNCaP_abl_Peruvoside_rep1

description: 5 uM Peruvoside treatment for 24 hours

data_processing:
The tags were mapped to the reference human genome( hg19) with Bowtie by allowing maximum 2 mismatches in the first 28 nt.
Genome Build:
LNCaP_abl_Peruvoside_rep1.bed: hg19


title: LNCaP_abl_Peruvoside_rep2

description: 5 uM Peruvoside treatment for 24 hours

data_processing:
The tags were mapped to the reference human genome( hg19) with Bowtie by allowing maximum 2 mismatches in the first 28 nt.
Genome Build:
LNCaP_abl_Peruvoside_rep2.bed: hg19


title: solid_3_days_AdpA_ChIP_seq

data_processing:
OHN03_3G_uniq.sam; genome build: NC_01572.1 (Streptomyces griseus NBRC 13350)
OHN03_3G_multi.sam; genome build: NC_01572.1 (Streptomyces griseus NBRC 13350)
Sequence reads were mapped to the S. griseus genomes using Bowtie. All reads mapping with two or fewer mismatches were retained. Reads were clustered and analyzed by CisGenome algorithm (http://www.biostat.jhsph.edu/~hji/cisgenome/).


title: solid_2_days_AdpA_ChIP_seq

data_processing:
OHN03_2G_uniq.sam; genome build: NC_01572.1 (Streptomyces griseus NBRC 13350)
OHN03_2G_multi.sam; genome build: NC_01572.1 (Streptomyces griseus NBRC 13350)
Sequence reads were mapped to the S. griseus genomes using Bowtie. All reads mapping with two or fewer mismatches were retained. Reads were clustered and analyzed by CisGenome algorithm (http://www.biostat.jhsph.edu/~hji/cisgenome/).


title: Mock H3K9ac_ChIP-seq

description:
Chromatin IP against H3K9ac
mock-infected H3K9ac 24 h p.i.

data_processing:
DNA: Libraries were sequenced using Illumina Genome Analyser II to obtain 76 bp-long reads (H3K9ac and corresponding input libraries) or Illumina HIseq-2000 to obtain 50 bp-long reads (H3K18ac and correspondent input libraries). ChIP for RB1 was performed as described in Chicas et al. 2010 Cancer Cell
DNA: Reads were mapped to the Human (hg19) genome using Bowtie software. Only reads that aligned to a unique position in the genome with no more than two sequence mismatches were retained for further analysis. Duplicate reads that mapped to the same exact location in the genome were counted only once to reduce clonal amplification effects. The genome was tiled with 100 bp windows. Each read was extended by 150 bases (so we refer to tags as the extend read counts within a bin) and was counted as one read to each window to which it partially or fully matched. The total counts of the input and ChIP samples were normalized to each other. The input sample was used to estimate the expected counts in a window; the average value for all windows was assigned to windows with zero counts. Finally, we used the Poisson distribution to estimate the probability of observing the ChIP counts within a window given the expected counts in the input sample window. We considered all windows with P-values less than 1.0E-3 to have significant peaks. P-value < 1.0 E-3 was chosen to give False Discovery Rate (FDR) less than 5%. FDR was calculated by applying the same statistic, described above, to the two halves of the same input library. We considered the total number of significant peaks obtained this way as an estimate of number of false-positive peaks. To compare two ChIP samples to identify regions that are significantly different between the two samples (for instance e1a versus mock), we replaced the input sample with the sample used for comparison; all downstream analyses were identical. Our algorithm produces several files that were subsequently used for analysis: BED files containing the coordinates of the significant windows of enrichment; Wiggle (wig) files (chromosome tiling, fixed step) with normalized reads count for the significant windows (If a window was not significant, we placed zero tags); GR files of normalized raw counts for input and ChIP samples were also created for genome browser visualization.). Tiling profiles of promoter regions for the hg19 annotated human promoters were also generated. These represent the 100-bp tiling of a 10 Kb region spanning the transcription start site (TSS). We reported the number of reads falling into significant windows and zero for the non-significant ones.

RNA: Libraries were sequenced using Illumina Genome Analyser IIx to obtain 76 bp-long reads. Alignment of mRNA-seq reads was performed using default parameters of Tophat. Aligned reads were converted to sam format and SAMMate software6 was used to determine the transcript RPKM (reads per kilobase of exon per million of reads).

value: IMR90 human primary lung embryo fibroblasts

tag: cell type

value: mock-infected

tag: chip antibody

value: Upstate H3K9ac


title: LNCaP_abl_Digoxin_rep2

description: 5 uM Digoxin treatment for 24 hours

data_processing:
The tags were mapped to the reference human genome( hg19) with Bowtie by allowing maximum 2 mismatches in the first 28 nt.
Genome Build:
LNCaP_abl_Digoxin_rep2.bed: hg19

tag: cell line


title: LNCaP_abl_Digoxin_rep1

description: 5 uM Digoxin treatment for 24 hours

data_processing:
The tags were mapped to the reference human genome( hg19) with Bowtie by allowing maximum 2 mismatches in the first 28 nt.
Genome Build:
LNCaP_abl_Digoxin_rep1.bed: hg19


title: N depleted

city: East Lansing

first: Guangxi

last: Wu

state: MI

address: S308 Plant Bio Bld

institute: Michigan State University

data_processing:
After the genome assembly was generated, transcriptomic reads from N-replete and N-depleted conditions were mapped to the genome using Tophat [170] (parameters: -I 10 –I 3000 –library-type fr-unstranded –g 1) separately. Then, Cufflinks [171] (-I 3000 --library-type fr-secondstrand) was used to assemble the read into transcripts and a set of transcripts was generated for each condition.
Genome_build: de novo assembly
Supplementary_files_format_and_content: gff

molecule: polyA RNA

organism: Nannochloropsis oceanica

source_name: whole cells

growth_protocol: To generate material for RNA-sequencing, cells were grown in 200 ml f/2+N to 1x107 cells ml-1. The cultures were split in half and cells were collected by centrifugation (4,500 x g, 5 min), with one pellet being resuspended in 200 mL f/2+N, and the other in 200 mL f/2-N.

extract_protocol: After 30 hours, the total RNA was isolated using TRIzol Reagent (Invitrogen) according to manufacturer’s instructions. The RNA samples were cleaned up using RNeasy columns (Qiagen, http://www.qiagen.com) following the manufacturer’s instruction.

tag: treatment

value: Nitrogen depleted


title: N replete

value: Nitrogen replete


title: LNCaP_abl_Control_KD_rep1

description: Control siRNA

data_processing:
The tags were mapped to the reference human genome( hg19) with Bowtie by allowing maximum 2 mismatches in the first 28 nt.
Genome Build:
LNCaP_abl_Control_KD_rep1.bed: hg19


title: LNCaP_abl_Strophanthidin_rep2

data_processing:
The tags were mapped to the reference human genome( hg19) with Bowtie by allowing maximum 2 mismatches in the first 28 nt.
Genome Build:
LNCaP_abl_Strophanthidin_rep2.bed: hg19


title: CD4 H2A

city: Singapore

first: Jung Kyoon

last: Choi

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description: Chromatin IP against H2A

data_processing: Sequence reads were obtained and mapped to the hg18 human (March, 2006) genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and extended to the library fragment size (200bp) to create the BED files.

source_name: blood cells

growth_protocol: Jurkat and HL-60 cells were obtained from the American Type Culture Collection (ATCC). Cells were grown as a suspension culture in RPMI-1640 medium supplemented with 10% inactivated fetal bovine serum (Gibco/BRL, USA). Cells were routinely cultured in 100mm culture dishes under 5% CO2 in air in a humidified atmosphere at 37°C.

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

treatment_protocol: after exposure to 10Gy of γ-ray, incubated at 37°C for 30 minutes

value: CD4+ T cells

tag: chip antibody vendor

value: abcam

tag: chip antibody lot#

tag: chip antibody catalog#


title: Input DNA

description: input DNA

value: Jurkat cells


title: HL60 H2AX

description: Chromatin IP against H2AX

value: HL-60 cells

value: millipore


title: LNCaP_abl_Control_rep3

description: vehicle (DMSO) treatment

data_processing:
The tags were mapped to the reference human genome( hg19) with Bowtie by allowing maximum 2 mismatches in the first 28 nt.
Genome Build:
LNCaP_abl_Control_rep3.bed: hg19

value: hormone resistant LNCaP-abl

value: Control


title: Jurkat γ-H2AX

description: Chromatin IP against γ-H2AX


title: LNCaP_abl_Control_rep2

description: vehicle (DMSO) treatment

data_processing:
The tags were mapped to the reference human genome( hg19) with Bowtie by allowing maximum 2 mismatches in the first 28 nt.
Genome Build:
LNCaP_abl_Control_rep2.bed: hg19


title: CD4 γ-H2AX after irradiation

description: Chromatin IP against γ-H2AX


title: LNCaP_abl_Control_rep1

description: vehicle (DMSO) treatment

data_processing:
The tags were mapped to the reference human genome (hg19) with Bowtie by allowing maximum 2 mismatches in the first 28 nt.
Genome Build:
LNCaP_abl_Control_rep1.bed: hg19


title: Wholeflies_ED776_Male_DNASeq_R1

status: Public on Apr 03 2012

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

data_processing: Libraries were sequenced on an Illumina GA II or multiplexed on an Illumina HiSeq 2000 to generate 36 bp single end reads and those reads passing the Illumina quality filter were mapped with Bowtie 0.12.7 using -v 2 -m 1 to assembly 5 of the Drosophila melanogaster genome excluding chromosome Uextra (dm3 from UCSC Genome Broswer). We used the unique mapping reads to generate coverage plots using the genomeCoverageBed in BEDTools. Normalized coverage, along with the start and stop positions of Df/+ regions were visualized on the UCSC Genome Browser. Deficient regions were characterized by a loss of read coverage in the region and most were unambiguously definable.  Results for 20 Df(2L)EDs were as expected (e.g. nucleotide level breakpoint accuracy and approximate 2-fold differences in DNA-Seq read density, but we did observe an additional deficiency region in the Df(2L)ED478 line, which we named Df(2L)Hsp60c.

organism: Drosophila melanogaster

source_name: Wholeflies, 5 day mated adults

growth_protocol: Flies were grown under constant light, temperature, and humidity (25°C; 60% relative humidity) on San Diego Stock Center cornmeal media (DSSC, 2008)

extract_protocol: Flies were homogenized in 200 μl Buffer A (100mM Tris-HCl, pH 7.5, 100 mM EDTA, 100 mM NaCl, 0.5% SDS), then an additional 200 μl of Buffer A was added followed by homogenization. Samples were incubated at 65°C for 30 minutes, then 800 μl LiCl/KAc solution (1 part 5 M KAc: 2.5 parts 6 M LiCl) was added. Samples were spun for 15 minutes at room temperature at 14000 rpm in a microcentrifuge. One ml of clear supernatant was removed from samples and placed in a new 1.5 ml Eppendorf tube, then 600 μl of isopropanol was added, and the samples were spun for 15 minutes at room temperature at 14000 rpms. Supernatant was removed and the DNA pellet was washed with equal volume 70% EtOH. Pellets were dried for 5-10 minutes, then re-suspended in 150 μl TE Buffer. Five μg genomic DNA in 200 μl TE buffer was sonicated on high for 30 sec on and 30 sec off for a total of 30 min using a Bioruptor UCD-200 (Diagenode, Sparta New Jersey). The fragmented DNA was then purified using a QIAGEN QIAquick PCR purification kit. We prepared 1-1.5 μg of fragmented DNA and followed the Illumina protocols for paired-end sequencing library preparation or following standard protocols from Illumina TruSeq kits.  For the samples we sequenced with TruSeq, we performed multiplexing of samples for sequencing on a Illumina HiSeq 2000 instrument with four samples per lane in six lanes and six samples per lane in two lanes of a flowcell.

treatment_protocol: We outcrossed the balancer chromosome using females of w1118 and collected 30 -100 adult, 5 day old sexed flies containing Df/+ for DNA collection.

tag: gender

value: Male

tag: tissue

value: whole flies

tag: development stage

value: 5 day old mated adults


title: CD4 H2AX

description: Chromatin IP against H2AX


title: Wholeflies_ED776_Female_DNASeq_R1

value: Female


title: Wholeflies_ED489_Female_R3_Illumina

description: Same poly A mRNA prep used for microarray hybridization

data_processing: Reads that passed the default parameters of the Illumina quality filter were mapped with Bowtie. We combined the sequences of the spike-in controls and the dm3 from the UCSC Genome Browser which corresponds to the April 2006 Drosophila melanogaster draft assembly from the Berkeley Drosophila Genome Project (Release 5) to create a reference index for mapping. The reference index was created using the bowtie-build function with default parameters. Reads were mapped using -v 2 - m 1 in Bowtie v. 0.12.7 and then unique mapping sequences that mapped to spike-in controls and Flybase gene models were counted using the union mode in HTSeq.  We used the unique mapping reads to calculated the Reads Per Million Mapped Reads (RPKM) as the normalized metric of gene expression and for comparison to intensities from microarrays.

extract_protocol: We obtained 8 clones and the preparation protocol found in Mortazavi et al. 2008. Nat. Methods 5:621-628 (kindly provided by the Wold lab) and prepared transcripts by in vitro transcription using the Ambion MEGAScript kit (Ambion, Austin, Texas). We checked for full length transcripts using MOP gels and measured RNA concentration using the Nanodrop ND-1000 UV spectrophotometer. We made cocktails of these 8 spike-in controls by performing dilutions to obtain a range of concentrations from 5 x 108 to 1 x 102 transcripts (Gene: Number of Transcripts: OBF-1:5x108; VATG:5x107; Lambda1-1:5x106; Apetala- 2:1x106; AGP-2:5x105; EPR-1:1x105; Lambda2-3:5x104; PDF:1x102).  We fragmented mRNA using alkaline hydrolysis. First, 9 μl of 100 ng of mRNA along with 1 ng of eight spike-in controls from the Wold lab (Mortazvi et al. 2008) and 1 μl of 10X fragmentation buffer (Ambion, Austin, Texas) was incubated at 70°C for 5 minutes to fragment mRNA. One microliter of Stop Buffer (Ambion, Austin, Texas) was added and samples were placed on ice. Fragments were precipitated with 1 μl 3 M NaOAC (pH 5.2), 2 μl glycogen (5 μg/μl, Ambion, Austin, Texas), and 30 μl 100% EtOH and then incubated for 30 minutes at -80°C. Fragmented RNA was pelleted at 14000 rpm with a microcentrifuge at 4°C. The pellet was washed with 70% EtOH, air dried and resuspended with 10.5 μl RNase free H2O. Fragmented mRNA was reverse transcribed to create cDNA. One microliter of random hexamer primers (3μg/μl, Invitrogen, Carlsbad, California) was placed with 10.5 μl of fragmented mRNA, then samples were incubated at 65°C for 5 minutes and placed on ice. Four microliters 5X first strand buffer, 2 μl 100 mM DTT, 1 μl dNTP, and 0.5 μl RNaseOUT were added to the mRNA and samples were incubated at 25°C for 2 minutes. One microliter of SuperScript II (200 U/μl, Invitrogen, Carlsbad, California) was added and samples were incubated under the following conditions: 25°C-10 minutes, 42°C-50 minutes, 70°C-15 minutes. Samples were then placed on ice. Second strand cDNA was synthesized by adding 61 μl H2O to the first strand mix, 10 μl 10X second strand buffer (500 mM Tris-HCl pH 7.8, 50 mM MgCl2, 10 mM DTT), and 3 μl dNTP (10 mM), mixed, incubated on ice for 5 minutes, then 1 μl RNaseH (2U/μl, Invitrogen, Carlsbad, California) and 5 μl DNA Pol I (10 U/μl, Invitrogen, Carlsbad, California) were added. Samples were incubated at 16°C for 2.5 hours and DNA products purified using a QIAquick spin column and following manufacture directions and eluted with 30 μl. The ends of cDNA fragments were repaired using 30 μl of DNA, 45 μl H2O, 10 μl T4 DNA ligase buffer with 10 mM ATP, 4 μl dNTP mix (10 mM), 5 μl T4 DNA polymerase (3 U/μl), 1 μl Klenow DNA polymerase (5U/μl), and 5 μl T4 PNK(10 U/μl). Samples were incubated for 30 minutes at 20°C, purified with QIAquick PCR spin columns, and eluted with 32 μl of Buffer EB. A single 'A' base was added to the ends of cDNA by using 5 μl Klenow buffer, 10 μl dATP (1 mM) and 3 μl Klenow 3' to 5' exonuclease (5 U/μl). Samples were incubated at 37°C for 30 minutes, purified with a QIAquick MiniElute column, and eluted with 19μl of EB solution. Adaptor oligonucleotdies were ligated fragments as follows. Overhang fragments were combined with 25 μl DNA ligase buffer, 1 μl adaptor olio mix, and 5 μl DNA ligase (1U/μl). Samples were incubated at room temperature for 15 minutes, purified with a QIAquick MiniElute column, and eluted with 10 μl of buffer EB. cDNA templates were sized selected by gel purification then amplified by PCR using oligo- specific primers. Samples were loaded into a 2% agarose gel with 1X TAE buffer and run for 50 minutes with a 100 bp ladder. The gel was stained with ethidium bromide and bands were visualized under UV fluorescence. For each sample, a gel slice was cut at the 200 - 300 bp region, purified with a QIAquick gel extraction kit, and eluted with 30 μl buffer EB. Purified cDNA was amplified in a 50 μl reaction using 25 μl Phusion Mix (Phusion polymerase, dNTPs, and buffer), 1 μl primer 1.1, 1 μl primer 2.1, and 23 μl template along with the following cycling conditions: initial denaturation 98°C-30 sec, cycle denaturation 98°C-10 sec, anneal 65°C-30 sec, and extend 72°C -30 sec with 15X cycles and a final extension of 72°C for 5 minutes followed by a hold at 4°C. The amplified product was purified using a QIAquick column and eluted with 30 μl buffer EB. Libraries were prepared for 36 bp single end Illumina sequencing following standard protocols for clustering and imaging.

treatment_protocol: We collected replicates for experiments by outcrossing the balancer chromosome with the original wild-type stock (w1118) as follows; 18-24 vials were setup with 15 less than 8 day old virgin w1118 females paired with 5 less than 8 day old males of a particular deficiency line per vial. Df/+ female and males were placed together in vials at less than 60 per vial and then aged for five days. On day five, flies were anesthetized with CO2, sorted into males and females, then placed into 1.5 ml Eppendorf tubes and flash frozen on dry ice. All flies aged together for 5 days constituted a replicate. Flash frozen flies were stored in -80°C before RNA extraction.

tag: developmental stage


title: Wholeflies_EDHsp60cED478_Male_DNASeq_R1


title: Wholeflies_EDHsp60cED478_Female_DNASeq_R1


title: Wholeflies_w1118_Female_DNASeq_R1

data_processing: Libraries were sequenced on an Illumina GA II or multiplexed on an Illumina HiSeq 2000 to generate 36 bp single end reads and those reads passing the Illumina quality filter were mapped with Bowtie 0.12.7 using -v 2 -m 1 to assembly 5 of the Drosophila melanogaster genome excluding chromosome Uextra (dm3 from UCSC Genome Broswer). We used the unique mapping reads to generate coverage plots using the genomeCoverageBed in BEDTools. Normalized coverage, along with the start and stop positions of Df/+ regions were visualized on the UCSC Genome Browser.


title: Wholeflies_ED489_Male_R1_Illumina


title: Wholeflies_w1118_Male_R2_Illumina (ln8)


title: Wholeflies_ED499_Male_R1_Illumina


title: Wholeflies_ED7007_Female_R2_Illumina


title: Jurkat H2AX

description: Chromatin IP against H2AX


title: Wholeflies_w1118_Female_R3_Illumina


title: Chlamydomonas reinhardtii sor1 mutant

city: Dübendorf

first: Beat

middle: B

last: Fischer

address: Ueberlandstr. 133

department: Department of Environmental Toxicology

country: Switzerland

institute: Eawag

description:
Illumina's RNA-Seq whole transcriptome analysis
poly-A purification, random fragmentation

library_source: non-genomic

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 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 or half of the read length) 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. For differential expression analysis, per-base unique hits from both strands were pooled and summed across the genome to obtain gene counts. Additional normalization was performed to estimate gene expression levels.

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas cultured cells

growth_protocol: The strains were grown mixotrophically in a Tris-acetate phosphate (TAP) medium at 25°C and 100 μmol photons m-2 s-1 photosynthetically active radiation (PAR) in a 12 h day night cycle.

extract_protocol: Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced at Illumina by whole transcriptome analysis.

treatment_protocol: Cells of cultures grown in 12 h light dark cycles for several days were adjusted to 2×106 cells ml-1 at the beginning of the dark cycle and the cells were collected 6 h after the lights came on from three independent biological replicates.

tag: genotype

value: sor1 mutant

tag: medium

value: TAP

tag: sequencing cycles / read length

tag: library type

value: single-end


title: Wholeflies_ED1305_Male_DNASeq_R1

tag: strain


title: Wholeflies_w1118_Male_DNASeq_R1


title: Wholeflies_w1118_Male_R2_Illumina (ln7)


title: Wholeflies_ED499_Female_R2_Illumina


title: PAPD5_PAR-CLIP_rep2

city: Palo Alto

first: Biter

last: Bilen

address: 3801 Miranda Ave.

institute: Stanford University

data_processing:
Basecalls performed using IPAR_1.01 (Firecrest1.9.5/Bustard 1.9.5)
PAR-CLIP reads were aligned to the hg18 genome assembly with oligomap after adapter removal as described in Hafner et al., Cell, 2010.
Reads per 100-nucleotide-long-windows were calculated in PAPD5 and IGF2BP1 libraries with custom scripts and normalized as described in Balwierz et al., 2010, Genome Research.
Differential expression of normalized read counts in PAPD5 and IGF2BP1 is estimated as described in Balwierz et al 2009.
Genome_build: hg18
Supplementary_files_format_and_content: tab delimited text including coordinates of top enriched/depleted 100-nucleotide windows and their annotations with UCSC gene/repeat tracks.

source_name: human embryonic kidney 293

growth_protocol: cells expressing His8-Flag-PAPD5 were grown in DMEM containing 10%FCS

extract_protocol: PAR-CLIP (Hafner M et al. 2010. Cell 141: 129–141). Briefly, RNA–protein complexes were crosslinked by exposure of the cells to UV light (366 nm, 150 mJ/cm2), and lysed in buffer containing 50 mM HEPES (pH 7.4), 150 mM KCl, 2 mM EDTA, 1 mM NaF, 0.5% NP-40, 0.5 mM DTT, 1 mM PMSF, 1 mg/L Pepstatin, and 1 mg/L Leupeptin. After removal of cell debris by centrifugation, the cleared lysate was incubated with RNase T1 to allow bound RNAs to be partially digested to an average size of 40 to 60 nt. RNA–protein complexes were isolated with M2 anti-Flag antibody (Sigma-Aldrich) coupled to protein G Dynabeads (Invitrogen). The RNA–protein complexes were gel-purified, the RNA was isolated, and linkers were ligated to the 5' and 3' ends of the RNA (Hafner et al. 2008). After reverse transcription and amplification, the resulting DNA library was sequenced by Solexa sequencing.

treatment_protocol: medium containing 100 mM 4-thiouridine (16h)

tag: recombinant protein


title: PAPD5_PAR-CLIP_rep1


title: Wholelfies_ED800_Male_DNASeq_R1


title: Wholeflies_ED1305_Female_DNASeq_R1


title: Wholeflies_ED800_Female_DNASeq_R1


title: Wholeflies_ED1231_Female_DNASeq_R1


title: Wholeflies_ED1231_Male_DNASeq_R1


title: Wholeflies_ED777_Male_DNASeq_R1


title: Wholeflies_ED793_Female_DNASeq_R1


title: Wholeflies_ED777_Female_DNASeq_R1


title: Wholeflies_ED775_Female_DNASeq_R1


title: Wholeflies_ED7007_Male_R3_Illumina


title: Wholeflies_ED695_Male_DNASeq_R1


title: Wholeflies_ED623_Male_DNASeq_R1


title: Wholeflies_ED695_Female_DNASeq_R1


title: Wholeflies_ED499_Female_DNASeq_R1


title: Wholeflies_ED475_Male_DNASeq_R1


title: Wholeflies_ED475_Female_DNASeq_R1


title: Wholeflies_ED489_Male_DNASeq_R1


title: Wholeflies_ED489_Female_DNASeq_R1


title: Wholeflies_ED499_Male_DNASeq_R1


title: Wholeflies_ED7007_Female_DNASeq_R1


title: Wholeflies_ED623_Female_DNASeq_R1


title: Wholeflies_ED385_Female_DNASeq_R1


title: Wholeflies_ED292_Male_DNASeq_R1


title: Wholeflies_ED793_Male_DNASeq_R1


title: Wholeflies_ED7007_Male_DNASeq_R1


title: Wholeflies_ED280_Male_DNASeq_R1


title: Wholeflies_ED775_Male_DNASeq_R1


title: Wholeflies_ED87_Male_DNASeq_R1


title: Wholeflies_ED80_Male_DNASeq_R1


title: Patient30_smRNA-seq

city: Houston

first: Han

last: Liang

state: TX

address: 1400 Pressler Street

department: Bioinformatics and Computational Biology

institute: University of Texas MD Anderson Cancer Center

description: smRNA-seq

data_processing:
WT-seq short reads were mapped to the human reference genome (hg19) and exon junctions (defined as RefSeq gene annotation) using the ABI BioscopeTM (version 1.21) WT-seq analysis pipeline with default parameters.
The reads mapped to the sequences that were not of biological interest, such as rRNAs, tRNAs, and repetitive elements, were first filtered. Then mapped reads with mapping SOLiD_native_quality ≥10 were defined as uniquely mapped reads and used in the downstream analysis.
The “reads per kilobase of exon per million mapped sequence reads” (RPKM) values of the human RefSeq genes were calculated using the RNA-seq flow in the Partek® Genomics Suite™ (version 6.5 beta, Partek Inc., St. Louis, MO, USA).
For the small RNA-seq dataset, the SOLiD System Small RNA Analysis Pipeline Tool (corona RNA2MAP version 0.50) was used: first, the reads mapped to the sequences of no biological interest were filtered, and then the remaining reads were mapped to annotated mature miRNAs (miRBase 13.0) and the human reference genome (key parameters: seed length = 18, seed error = 2, and maximum number of errors = 4).
MiRNA expression was quantified as reads per million (RPM) of reads mapped to known miRNAs.
Genome_build: hg19
Supplementary_files_format_and_content: GeneExpressionRPKM_30Sample_WT.xls; excel file; gene expression (in terms of RPKM) in 30 samples;
Supplementary_files_format_and_content: miRNAExpressionRPM_25Sample_smRNA.xls; excel file; miRNA expression (in terms of RPM) in 25 samples;

source_name: tissue specimen

extract_protocol:
The Miravana Kit (Ambion/Applied Biosystems, Foster City, CA, USA) was used to isolate total RNA according to the vendor’s protocol. The whole-transcriptome-sequencing (WT-seq) and small RNA-seq libraries were prepared using the small RNA expression kit (SREK, PN 4397682) of Applied Biosystems Inc. (ABI), based on SOLiD WT and small RNA standard protocols provided by ABI. The individual prepared “barcode” libraries were quantified and pooled equally together for multiplexing. The sequencing runs were performed on SOLiD v 3.0 for both WT-seq and small RNA-seq
WT-seq samples were sequenced in 1/4 slide per sample using 50-nucleotide (nt) single tags; and small RNA-seq samples were sequenced in 1/10 slide per sample using 35-nt single tags.

value: M

tag: age

value: unknown

tag: Stage

value: II

tag: histologics


title: Patient28_smRNA-seq

description: smRNA-seq

value: III

value: Diffuse


title: Patient29_smRNA-seq

description: smRNA-seq

value: IV


title: Wholeflies_ED87_Female_DNASeq_R1


title: Wholeflies_ED80_Female_DNASeq_R1


title: Wholeflies_ED62_Male_DNASeq_R1


title: Wholeflies_ED62_Female_DNASeq_R1


title: Wholeflies_ED2809_Male_DNASeq_R1


title: Patient27_smRNA-seq

description: smRNA-seq


title: Wholeflies_ED385_Male_DNASeq_R1


title: Patient26_smRNA-seq

description: smRNA-seq

value: I


title: Wholeflies_ED2809_Female_DNASeq_R1


title: Patient25_smRNA-seq

description: smRNA-seq

value: Intestine


title: Patient20_smRNA-seq

description: smRNA-seq


title: Wholeflies_ED280_Female_DNASeq_R1


title: Patient17_smRNA-seq

description: smRNA-seq

value: F

value: Normal


title: Patient16_smRNA-seq

description: smRNA-seq


title: H3K4me3_ChIP

city: Chicago

first: Sebastian

last: Pott

state: Il

address: 920 58th Street

department: Human Genetics

institute: University of Chicago

data_processing:
The raw images have been processed using the Solexa Pipeline. Read have been mapped to the reference genome (NCBI Build 36, mm8) using Bowtie (Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.) with default settings
For visualization purposes bedgraphs were generated based on the aligned sequencing reads using Homer (Heinz S, Benner C, Spann N, Bertolino E et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 2010 May 28;38(4):576-589.)
Genome Build:
CMS010_H3K4me3_aligned.bed: mm8
H3K4me3_CMS010.ucsc.bedGraph.gz: mm8

organism: Mus musculus

source_name: splenic B cells

growth_protocol: mature B cells were purified from spleens of adult mice. In brief, spleens were harvested and cell suspensions were then immuno-stained with magnetic anti-B220 from Miltenyi and sorted for B220 positive cells by magnetic cell separation (MACS), subsequently using fluorochrome labelled antibodies against CD19-V450 (Biolegend), CD21-Fitc (BD) and CD23-PE-Cy7 (eBioscience) the B220 positive cells were sorted by fluorescence activated cell sorting (FACS) for CD19 positive, CD21 intermediate and CD23 psoitive cells to gain pure mature splenic follicular B cells. For ChIP 37.5*10^6 sorted cells were resuspended in 18ml of  room temperature PBS, crosslinked in 1% formaldehyde for 10min (see Gyoery et al. for details)

extract_protocol: 10ng of  genomic DNA obtained by ChIP, as per manufacturers protocol. Briefly, using the Solexa ChIP Seq DNA sample preparation kit universal linkers were added to the chromatin fragments and DNA was PCR amplified for 15 cycles. DNA was gel-purified and fragments between 200-300bp were selected for sequencing

treatment_protocol: cells were obtained from wildtype animals under normal conditions

value: adult

tag: chip antibody

value: H3K4me3; abcam; lot# GR37544-1; catalog# ab8580


title: Wholeflies_ED292_Female_DNASeq_R1

value: whole flies

value: 5 day old mated adults


title: Patient24_smRNA-seq

description: smRNA-seq


title: Wholeflies_ED499_Male_R1_SOLiD_b

description: Flowcell 2; Same poly A mRNA prep used for microarray hybridization

data_processing: High quality reads were matched to individual samples based on the 10 bp bar code tag and using default parameters in SOLiD Experimental Tracking Software (SETS) v4.0.1. We used only the forward read and trimmed these reads from 50 to 36 bp based on analysis of read quality. Trimmed reads were mapped with Bowtie.  The dm3 from the UCSC Genome Browser which corresponds to the April 2006 Drosophila melanogaster draft assembly from the Berkeley Drosophila Genome Project (Release 5) plus sequences of the 96 synthetic RNAs were used to build a reference index for mapping colorspace data. The reference index was created using the bowtie-build function with default parameters for colorspace. Reads were mapped using -v 2 -m 1 in Bowtie v. 0.12.7 and then unique mapping sequences that mapped to spike-in controls and Flybase gene models were counted using the union mode in HTSeq. Technical replicates for each sample were highly comparable and we pooled reads between the two flow cells for each sample.

source_name: Whole flies, 5 day mated adults

extract_protocol:
The spike-in control mixtures were designed to assess technical performance of a typical gene expression experiment examining enrichment between two conditions. These mixtures consist of the 96 distinct control RNAs from the ERCC (External RNA Control Consortium) project. The RNAs were synthesized, purified, and mixed at NIST. The mixtures (Mix 1 and Mix 2) contain 3 subsets of 32 RNAs: one subset at equal abundance in Mix 1 and Mix 2, representing a “no-change” control; one subset at 1.5 fold enrichment in Mix 1 relative to Mix 2; and another subset at 1.5 fold enrichment in Mix 2 relative to Mix 1. Each subset of 32 control RNAs was designed to span a concentration dynamic range of 220, or 1048576:1. The control IDs and concentrations in Mix 1 and Mix 2 are annotated in the supplementary file linked to the GSE31401 record.
ERCC Spike-in Mix 1 was combined with the diploid control mRNA samples (female and male w1118) and ERCC Spike-in Mix 2 was combined with mRNA from all other DrosDel samples at about 10% concentration the total quantity of mRNA.
Approximately 150-200 ng of polyA selected mRNA was converted to cDNA, using the SOLiDTM Total RNA-Seq Kit PN 4445374 and accompanying kit protocol PN4452437 Rev. A (Life Technologies, Carlsbad, CA). RNA was enzymatically fragmented with RNase III using stated protocol methods and kit supplied components. The fragmented RNA was then cleaned and concentrated using the RiboMinusTM Concentration Module (Invitrogen Corporation, Carlsbad, CA) and eluted in 12 u L of nuclease-free water. The fragmented RNA was then assessed for size distribution and concentration on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) with the RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA) and the Qubit® RNA assay (Invitrogen Corporation, Carlsbad, CA), respectively. Fragment distributions were found to have a mean distribution of approximately 150 nts. In preparation for library construction the RNA needed to be sufficiently concentrated such that less than or equal to  3u L of fragmented RNA contained 50 ng. Concentration was performed in a SpeedVac® Concentrator (Savant Instruments Inc., Holbrook, NY) under vacuum and medium heat for approximately 10 minutes. Each dried fragmented RNA sample was then rehydrated to a final concentration of 17 ng/u L in nuclease-free water. Hybridization and ligation of partial P1 adaptor and internal adaptor, at the 5' or 3' end respectively, was performed using concentrated fragmented RNA and kit supplied adaptors and hybridization mixtures. Reverse transcription was then performed as directed by protocol with kit supplied ArrayScriptTM Reverse Transcriptase (Ambion Inc., Austin, TX) and necessary reaction components. Resulting cDNA was then purified using the MinElute® PCR Purification Kit (Qiagen Inc., Valencia, CA) and eluted in 10 u L of Buffer EB supplied by the purification kit. cDNA libraries were then size selected for 150-250 nts fragments that represent cDNA with target sequence and 5' and 3' SOLiDTM sequencing adaptors. The cDNA was run on a Novex® 6% TBE-Urea Gel 1.0 mM (Invitrogen Corporation, Carlsbad, CA) using the XCell SureLockTM Mini-Cell system (Invitrogen Corporation, Carlsbad, CA) to separate the constituent sizes of cDNA. Samples and ladder were loaded on to gel, separated by a lane to minimize cross contamination, and run at 180 V for approximately 30 minutes. The gels were then stained in 50 u L of 1X SYBR Gold nucleic acid gel stain (Invitrogen Corporation, Carlsbad, CA) solution prepared with 1X TBE Running Buffer. Gel and stain were agitated in the dark at room temperature for 10 minutes then imaged with blue-light transilluminator. Using a clean razor blade for each cut the targeted size range of 150-250 nts was excised and, with vertical orientation maintained, vertically cut into four ~ 1mm x 6mm slices. Two of the four slices were used in amplification while the remaining two slices were stored for future use, if necessary, at -20°C. In-gel Polymerase Chain Reaction (PCR) amplification was then performed using excised gel slices and reaction components and primers supplied by the kit. The primers supplied extend and complete the P1 adaptor at the 5' end while primers containing unique barcodes were used to add a unique barcode and P2 adaptor to the 3' end. All samples were uniquely barcoded using the SOLiDTM RNA Barcoding Kit, Modules 17-32 (Life Technologies, Carlsbad, CA). Samples were amplified with AmpliTaq® DNA Polymerase (Applied Biosystems, Carlsbad, CA) using thermal cycling parameters designated by the kit protocol on a PTC-200 DNA Engine (MJ Research, Watertown, MA) for 15 cycles to avoid overamplification. Amplified samples were purified using the PureLink PCR Micro Kit (Invitrogen, Carlsbad, CA). Samples were eluted in 20 u L of Elution Buffer supplied with the purification kit. Following barcoding and amplification, completed cDNA libraries were assessed for size distribution and yield on the 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent Technologies, Santa Clara, CA). A smear analysis was performed and confirmed <20% of resulting cDNA was smaller than 200 nucleotides and therefore appropriate for templated bead preparation. Individual cDNA libraries were quantified using quantitative PCR (qPCR) on a 7900 HT Real-Time PCR System (Life Technologies, Carlsbad, CA) and pooled with other barcoded samples to create an equimolar pool. Pooled libraries were quantified using qPCR to confirm final molar concentration for use in templated bead preparation. Templated beads were prepared with emulsion polymerase chain reaction (ePCR) using the Applied Biosystems EZ Bead System (Life Technologies, Carlsbad, CA). Two library titration points, 0.4 and 0.8 pM, were initially used for work flow analysis (WFA) to determine input for full ePCR. Upon completion of WFA run on the SOLiDTM v4 instrument it was determined that a 0.6 pM titration point would be used in templated bead preparation to achieve maximum yield of high quality (greather than or equal to  77% On-Axis, less than or equal to 7% Noise to Signal) P2 enriched beads. Samples were run in duplicate in quads on two flow cells of a SOLiDTM v4 platform using ToP chemistry to generate paired-end reads of 50 base pair forward, 35 base pair reverse and a 10 base pair barcode.

value: Male


title: Wholeflies_ED499_Male_R1_SOLiD_a

description: Flowcell 1; Same poly A mRNA prep used for microarray hybridization


title: Wholeflies_ED499_Female_R2_SOLiD_b

value: Female


title: Patient14_smRNA-seq

description: smRNA-seq

value: Mixed


title: Ebf1_ChIP

data_processing:
The raw images have been processed using the Solexa Pipeline and mapped to the reference genome (NCBI Build 36, mm8) using Eland software with maximal 2 mis-matches.
Peak detection was performed using CCAT ( Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK. A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics. 2010 May 1;26(9):1199-204.). The sequence tag density generated from the input library was used as background. Regions enriched in the Ebf1 ChIP sample were identified as peaks. The bed files provides the peak summits within a 150bp interval (columns 1-3), Peak ID (colum 4), and enrichment score (column 5). To reduce the number of false-positives top 25% of the binding sites (by enrichment score) were used for further analysis.
For visualization purposes bedgraphs were generated based on the aligned sequencing reads using Homer (Heinz S, Benner C, Spann N, Bertolino E et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 2010 May 28;38(4):576-589.)
Genome Build:
CMB005_EBF1.bed.gz: mm8
EBF1_CMB005_CCAT_significant.peaks.txt: mm8
EBF1_CMB005.ucsc.bedgraph.gz: mm8

growth_protocol: spleens of adult mice were prepared, the cells were first immuno-stained with biotinylated anti-CD43 (BD), anti-AA4.1 (eBioscience) and anti-CD9 (BD), secondly magnetic anti-CD4, anti-CD8 and Streptavidinbeads from Miltenyi were added and finally the cells were two times depleted of the labeled cells (CD43, AA4.1, CD4, CD8, CD9) by magnetic cell separation (MACS). Subsequently a small proportion of the remaining cells was analyzed by fluorescence activated cell sorting (FACS) after being stained with anti-B220-Fitc (BD) anti CD23-PE (BD) and anti CD21-APC (BD). It could be shown that ~97% of those cells were B220 positive and of those ~92% were CD23 positive and CD21 intermediate and therefore mature follicular splenic B cells

extract_protocol: ChIP-seq libraries were prepared from 10ng of  genomic DNA obtained by ChIP, as per manufacturers protocol. Briefly, using the Solexa ChIP Seq DNA sample preparation kit universal linkers were added to the chromatin fragments and DNA was PCR amplified for 15 cycles. DNA was gel-purified and fragments between 200-300bp were selected for sequencing

treatment_protocol: 210000000 sorted cells were resuspended in 18ml of  room temperature RPMI Medium, crosslinked in 1% formaldehyde for 10min, quenched with 125mM ice-cold glycine and washed three times with ice-cold PBS; finally they were resuspended in 1200µl of lysisbuffer (1% SDS, 10mM EDTA pH 8.0, 50mM Tris-HCL pH 8.0, Protease inhibitor mix) and sonified with a Bioruptor® Standard for 15min using high power and an intervall of 30s; sonification efficiency was analysed on a 1,5% agarose gel and sonification was continued until genomic DNA was fragmented into 200bp fragments; this chromatin was stored at -80°C and subsequently used for ChIP experiments. Chromatin was 1/10 diluted with dilution buffer (0.5% NP40, 5mM EDTA pH 8.0, 200mM NaCl, 50mM Tris-HCl pH 8.0, protease inhibitor mix) and 4µg of antibody against murine EBF-1 (noncommercial polyclonal rabbit anti EBF1 antibody, protein G purified) was added to each sample;samples were rotated for 16-20 hours at 4 °C and washed Protein-A Sepharose beads were added for another two hours. Subsequently beads were washed five times with wash buffer (0.1% SDS, 1% NP-40, 2mM EDTA, 500mM NaCl, 20mM Tris-HCl pH 8.0) and four times with TE buffer (10mM Tris-HCl pH8, 1mM EDTA pH8.0). Immunoprecipitated chromatin was eluted two times with 50µl elution buffer (2%SDS, 10mM Tris-HCl pH8, 1mM EDTA pH8.0) for 10min at 65°C shaking. Elutions were pooled and decrosslinked for at least six hours at 65°C. DNA was finally purified with MinElute® PCR purification Kit (Qiagen Cat.No. 28994) and eluted in three 10µl steps with water. DNA concentration was meassured by Quant-iT PicoGreen from invitrogen

value: Ebf1 (custom-made against murine Ebf1b)


title: Wholeflies_ED499_Female_R2_SOLiD_a


title: Wholeflies_ED489_Female_R1_SOLiD_a


title: Patient13_smRNA-seq

description: smRNA-seq

value: M


title: Patient10_smRNA-seq

description: smRNA-seq


title: Input

data_processing:
The raw images have been processed using the Solexa Pipeline and mapped to the reference genome (NCBI Build 36, mm8) using Eland software with maximal 2 mis-matches.
Peak detection was performed using CCAT ( Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK. A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics. 2010 May 1;26(9):1199-204.). The sequence tag density generated from the input library was used as background. Regions enriched in the Ebf1 ChIP sample were identified as peaks. The bed files provides the peak summits within a 150bp interval (columns 1-3), Peak ID (colum 4), and enrichment score (column 5). To reduce the number of false-positives top 25% of the binding sites (by enrichment score) were used for further analysis.
For visualization purposes bedgraphs were generated based on the aligned sequencing reads using Homer (Heinz S, Benner C, Spann N, Bertolino E et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 2010 May 28;38(4):576-589.)
Genome Build:
CMB004_input.bed.gz: mm8


title: Wholeflies_ED489_Female_R1_SOLiD_b


title: Wholeflies_ED7007_Male_R1_SOLiD_a


title: Patient12_smRNA-seq

description: smRNA-seq


title: Patient11_smRNA-seq

description: smRNA-seq

value: II


title: Patient22_smRNA-seq

description: smRNA-seq


title: Wholeflies_ED7007_Female_R2_SOLiD_b


title: Patient19_smRNA-seq

description: smRNA-seq


title: Wholeflies_ED7007_Female_R2_SOLiD_a


city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: RNA-Seq analysis of fetal brain tissue from HuFNSC02 (A07825) using Illumina HiSeq 2000
library name: A07825
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 10
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 6.8
RNA_PREPARATION_INITIAL_RNA_QNTY: 10 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 280-440 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM817250_UCSF-UBC.Fetal_Brain.mRNA-Seq.HuFNSC02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A07825-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Brain, Donor HuFNSC02 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11956
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FB mRNA 02 25
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Fetal Brain mRNA-Seq Donor HuFNSC02 Library A07825 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 108,391,857
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
PERCENT_READS_MAPPING_TO_UCSC_GENES: 90.1
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.91

**********************************************************************

extract_protocol: library construction protocol: Refer to document 'Strand Specific 96-well Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

tag: Sex

value: female

tag: body site

value: Brain

tag: histological type

value: Brain tissue

tag: is tumor

value: No

value: primary tissue

value: fetal brain tissue


title: Patient7_smRNA-seq

description: smRNA-seq

tag: gender

value: I

value: Diffuse


title: Wholeflies_ED7007_Male_R1_SOLiD_b

tag: tissue

tag: developmental stage


title: Wholeflies_EDHsp60cED478_Male_R3_SOLiD_b


description:
design description: MeDIP-Seq analysis of fetal brain tissue from H23284 (A02299) using Illumina HiSeq 2000
library name: A02299
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 25 min
MeDIP_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MeDIP_PROTOCOL_DNA_AMOUNT: 2 ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: 1 ug
MeDIP_ANTIBODY: Methylcytidine
MeDIP_ANTIBODY_PROVIDER: Eurogentec
MeDIP_ANTIBODY_CATALOG: BI-MECY-0100
MeDIP_ANTIBODY_LOT: 80808
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM817249_UCSF-UBC.Fetal_Brain.MeDIP-Seq.H-23284.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02299-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Brain MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Fetal Brain, Donor H-23284 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11933
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 68,648,894
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0805
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.249
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.886
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4054
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

ANALYSIS FILE NAME: GSM817249_UCSF-UBC.Fetal_Brain.MeDIP-Seq.H-23284.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02299-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Fetal Brain, Donor H-23284 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11935
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FB MeDIP 84 99
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Fetal Brain MeDIP-Seq Donor H-23284 Library A02299 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 68,648,894
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0805
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.249
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.886
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4054
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

extract_protocol: library construction protocol: Refer to document 'MeDIP-seq library construction protocol v2' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)


title: H3K4me2_ChIP

data_processing:
The raw images have been processed using the Solexa Pipeline. Read have been mapped to the reference genome (NCBI Build 36, mm8) using Bowtie (Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.) with default settings
For visualization purposes bedgraphs were generated based on the aligned sequencing reads using Homer (Heinz S, Benner C, Spann N, Bertolino E et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 2010 May 28;38(4):576-589.)
Genome Build:
CMS007_H3K4me2_aligned.bed.gz: mm8
H3K4me2_CMS007.ucsc.bedGraph.gz: mm8

value: adult

value: H3K4me2; millipore; lot# DAM1724042; catalog# 07-030


description:
design description: MeDIP-Seq analysis of fetal brain tissue from H23266 (A02298) using Illumina HiSeq 2000
library name: A02298
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 25 min
MeDIP_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MeDIP_PROTOCOL_DNA_AMOUNT: 2 ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: 1 ug
MeDIP_ANTIBODY: Methylcytidine
MeDIP_ANTIBODY_PROVIDER: Eurogentec
MeDIP_ANTIBODY_CATALOG: BI-MECY-0100
MeDIP_ANTIBODY_LOT: 80808
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM817248_UCSF-UBC.Fetal_Brain.MeDIP-Seq.H-23266.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02298-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Brain MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Fetal Brain, Donor H-23266 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11932
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,754,248
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.1719
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3269
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9249
IROC_PERCENTILE: 100
POISSON_SCORE: 0.444
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

ANALYSIS FILE NAME: GSM817248_UCSF-UBC.Fetal_Brain.MeDIP-Seq.H-23266.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02298-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Fetal Brain, Donor H-23266 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11934
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FB MeDIP 66 98
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Fetal Brain MeDIP-Seq Donor H-23266 Library A02298 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,754,248
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.1719
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3269
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9249
IROC_PERCENTILE: 100
POISSON_SCORE: 0.444
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************


title: Patient5_smRNA-seq

description: smRNA-seq

value: F


title: Patient2_smRNA-seq

description: smRNA-seq

value: IV


title: Patient3_smRNA-seq

description: smRNA-seq

value: III

value: Intestine


title: Wholeflies_w1118_Male_R2_SOLiD_b

value: Male

value: whole flies

value: 5 day old mated adults


title: Patient8_smRNA-seq

description: smRNA-seq

value: Normal


title: Wholeflies_w1118_Male_R2_SOLiD_a


title: Patient30_RNA-seq

description: WT-RNA-seq

value: M

value: unknown

value: II


title: Patient9_smRNA-seq

description: smRNA-seq


title: Patient1_smRNA-seq

description: smRNA-seq

value: Mixed


title: Patient15_smRNA-seq

description: smRNA-seq


title: Patient29_RNA-seq

description: WT-RNA-seq


title: Endogenous small RNAs from Hevea brasiliensis, PB260, young leaves

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

country: China

institute: shenzhen university

description: barcode CT

data_processing: The raw sequences were filtered to remove low quality reads and the ones that passed the quality filter were trimmed to remove the adaptor sequences. Next, reads shorter than 18 nt and ones that were only present once in a library were removed to generate the raw small RNA sequences.

organism: Hevea brasiliensis

source_name: young leaves, PB260

extract_protocol: 500 µg of RNA was resolved in a 15% polyacrylamide/8M urea/0.5xTBE gel. A gel slice corresponding to small RNAs between 18 nt and 30 nt was excised and the RNA was eluted and dissolved in 20 µl RNase-free water. Small RNAs were then ligated to a 3’ adaptor using T4 RNA ligase and the ligated species were recovered after size fractionation by denaturing polyacrylamide gel electrophoresis. The 5’ adaptor was then ligated and the ligated products were similarly recovered. The ligated small RNAs were reverse transcribed to cDNA and amplified by PCR. The amplified products were purified by gel electrophoresis and sequenced in the Hiseq2000 (Illumina). In this study, libraries from young and mature leaves of PB217 and PB260 were separately constructed with 5’ adaptors containing different bar codes, mixed and sequenced together. The unique barcodes allowed the identification of reads from the different sources.

value: young leaves

tag: clone


title: Endogenous small RNAs from Hevea brasiliensis, PB260, mature leaves

description: barcode AG

source_name: mature leaves, PB260

value: mature leaves


title: Patient28_RNA-seq

description: WT-RNA-seq

value: Diffuse


title: Patient24_RNA-seq

description: WT-RNA-seq


title: Patient17_RNA-seq

description: WT-RNA-seq


title: Patient22_RNA-seq

description: WT-RNA-seq


title: Endogenous small RNAs from Hevea brasiliensis, PB217, mature leaves

description: barcode AG

source_name: mature leaves, PB217


title: Patient19_RNA-seq

description: WT-RNA-seq

value: I


title: Patient18_RNA-seq

description: WT-RNA-seq


title: Endogenous small RNAs from Hevea brasiliensis, PB217, young leaves

description: barcode CT

source_name: young leaves, PB217


title: Patient16_RNA-seq

description: WT-RNA-seq


title: Wholeflies_EDHsp60cED478_Male_R3_SOLiD_a


title: Patient25_RNA-seq

description: WT-RNA-seq


title: Patient26_RNA-seq

description: WT-RNA-seq


title: Patient27_RNA-seq

description: WT-RNA-seq


title: Patient20_RNA-seq

description: WT-RNA-seq


title: Patient23_RNA-seq

description: WT-RNA-seq


title: Patient14_RNA-seq

description: WT-RNA-seq


title: Patient12_RNA-seq

description: WT-RNA-seq


title: Patient11_RNA-seq

description: WT-RNA-seq