title: GAL_E

first: Iestyn

last: Whitehouse

department: Molecular Biology

institute: Sloan-Kettering Institute

description:
Sld2, Sld3, Dbf4, Dpb11, Cdc45 and Sld7 (SSDDCS) overexpression via galactose induction.
Okazaki fragments.
Columns in sgr files are as follows:
column 1: chromosome
column 2: base pair
column 3: sum of counts of Okazaki fragments overlapping this position
Columns in the average.tab file are as follows:
column 1: chromosome
column 2: base pair
column 3: base pair
column 4: Weighted Average Time
column 5: Sum of Probabilities in Weighted Average
Columns in replicationProfile.tab files:
column 1: chromosome
column 2: line segment's first base pair
column 3: line segment's first time
column 4: line segment's last base pair
column 5: line segment's last time in minutes
column 6: line segment's probability (0-1)
column 7: direction of replication fork progression
column 8: red value (red for forward blue for reverse)
column 9: green value (red for forward blue for reverse)
column 10: blue value (red for forward blue for reverse)
Columns in replicationProfile250bp.tab represent 250 bp interpolated sampling of replicationProfile.tab line segment values:
column 1: chromosome
column 2: base pair sampled by interpolation
column 3: time in minutes
column 4: probability (0-1)
column 5: direction of replication fork progression
column 6: red value (red for forward blue for reverse)
column 7: green value (red for forward blue for reverse)
column 8: blue value (red for forward blue for reverse)
The scripts in the SCRIPTS folder can be run inside of R when they are placed in the same folder as the replication profile files in order to plot the replication profiles per chromosome. Instructions for using the scripts are written in comments inside the scripts.

data_processing:
Data for WT_A and WT_B were aligned to the May 2008 build of the S. cerevisiae genome using in-house software: paired-end reads each beginning with a 20bp perfect match to a unique genomic locus and within 1kb of one another were considered. The count of Okazaki fragments overlapping each base per DNA strand is reported.
Data for GAL_E, GAL_G, and GLU_F were aligned to the May 2008 build of the S. cerevisiae genome using tmap software using the command "tmap mapall -r $(cat fastqName.tab) -f $(cat yeastName.tab).fasta -a 0 -Q 0 -S 0 -n 10 stage1 -v map1 map2 map3 > TMAP/out.sam": single-end reads with a score greater than or equal to 20 matching a unique genomic locus were considered. The count of Okazaki fragments overlapping each base per DNA strand is reported.
For all data sets, Okazaki fragment counts per base per strand were processed using in-house software as described in the coinciding literature in order to produce replication profiles. Scripts are provided for viewing the data in R.
Genome_build: May 2008, supplemented by strain-appropriate recombinant DNA.
Supplementary_files_format_and_content: Strand-specific sgr file scores represent counts of Okazaki fragments that overlap each base. Tables (tab files) contain timing data calculated for forks moving in a specified direction at a specified probability or proportion of cell population most likely represented at such time. Table files named average.tab contain the average time of replication per base. Table files named replicationProfile.tab contain line segments representing fork motion in a specified direction from an origin to the most likely point of merger from a folded probability method described in the coinciding literature at the specified probability or proportion of cell population most likely represented at such times. Tables files named replicationProfile250bp.tab contain the same values as those in replicationProfile.tab but at intervals matching previously reported data. R script files are included with commented instructions for how to plot these values in R.

source_name: WT [yIW160-SSDDCS], galactose

growth_protocol: Cells were grown at 30 degrees in YEP + 2% glucose to O.D. 0.1, and transferred to fresh medium containing either 2% glucose or 2% galactose for 4 hours. Doxycycline was subsequently added to 40ug/ml for 2.5 hours.

extract_protocol: DNA extraction was per the medium resolution double-strand break protocol in Murakami et al., 2009 (PMID 19799180). Adaptor ligation followed the protocol described in Smith and Whitehouse, 2012 (PMID 22419157). Genomic DNA was purified and heat-denatured: DNA was bound to Source 15Q resin in batch at 300mM NaCl, pH12, and eluted in 50mM steps. Fractions from 800-900 mM were collected, neutralized and concentrated by precipitation. Double-stranded sequencing adaptors with N6 random overhangs ligated to each end; after second-strand synthesis using Taq, material from 200-1000bp was gel-purified and amplified by PCR. Products from 200-500 bp were gel-purified from two successive 2.5% agarose gels.

value: WT [yIW160-SSDDCS]

tag: media

value: galactose

tag: cell cycle stage

value: asynchronous culture


title: Dnmt1-/- MEF

status: Public on Mar 01 2013

type: SRA

city: Heidelberg

first: James

middle: P

last: Reddington

address: Meyerhofstrasse 1

country: Germany

institute: EMBL

description: the raw sequence data contains 18 files

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: Dnmt1-/- mouse embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts were cultured under standard conditions

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

tag: cell type

value: Mouse embryonic fibroblasts

tag: strain

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

tag: genotype/variation


title: GLU_F

status: Public on Feb 28 2013

city: New York

state: New York

address: 1275 York Avenue

country: USA

description:
Sld2, Sld3, Dbf4, Dpb11, Cdc45 and Sld7 (SSDDCS) normal expression via glucose media.
Okazaki fragments.
Columns in sgr files are as follows:
column 1: chromosome
column 2: base pair
column 3: sum of counts of Okazaki fragments overlapping this position
Columns in the average.tab file are as follows:
column 1: chromosome
column 2: base pair
column 3: base pair
column 4: Weighted Average Time
column 5: Sum of Probabilities in Weighted Average
Columns in replicationProfile.tab files:
column 1: chromosome
column 2: line segment's first base pair
column 3: line segment's first time
column 4: line segment's last base pair
column 5: line segment's last time in minutes
column 6: line segment's probability (0-1)
column 7: direction of replication fork progression
column 8: red value (red for forward blue for reverse)
column 9: green value (red for forward blue for reverse)
column 10: blue value (red for forward blue for reverse)
Columns in replicationProfile250bp.tab represent 250 bp interpolated sampling of replicationProfile.tab line segment values:
column 1: chromosome
column 2: base pair sampled by interpolation
column 3: time in minutes
column 4: probability (0-1)
column 5: direction of replication fork progression
column 6: red value (red for forward blue for reverse)
column 7: green value (red for forward blue for reverse)
column 8: blue value (red for forward blue for reverse)
The scripts in the SCRIPTS folder can be run inside of R when they are placed in the same folder as the replication profile files in order to plot the replication profiles per chromosome. Instructions for using the scripts are written in comments inside the scripts.

library_source: genomic

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: WT [yIW160-SSDDCS], glucose

value: glucose


title: Non-irradiated Control B

city: Urbana

last: Collins

address: 601 S. Goodwin

institute: University of Illinois at Urbana Champaign

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads Per Kilobase of transcript per Million mapped reads were determined using the RNAseq module in CLC Genomics Workbench (version 4) using default settings.
Samples were mapped to the annotated Schistosoma mansoni genome version 5.  The GFF file used for annotation was downloaded from the Wellcome Trust Sanger Institute Schistosoma mansoni ftp site: ftp://ftp.sanger.ac.uk/pub/pathogens/Schistosoma/mansoni/genome/GFF/
Genome_build: Schistosoma mansoni Version 5
Supplementary_files_format_and_content: A table that includes RPKM values and other important metrics (e.g. Total gene reads) for each sample. Table also includes mean RPKM values for both control and irradiated samples.

organism: Schistosoma mansoni

source_name: Male posterior somatic tissue

growth_protocol: Parasites perfused from mice 43 days post-infection were either irradiated or mock irradiated and cultured in vitro in Basch Media 169 for 48 hours at 37C at 5% CO2.

extract_protocol:
Total RNA was prepared from pools of 14-18 parasites using Trizol (Invitrogen, Carlsbad, CA) and DNase treatment (DNA-free RNA Kit, Zymo Research, Irvine, CA)
Libraries were constucted using the TruSeq RNAseq Sample Prep kit.  The libraries were quantitated by qPCR, pooled and sequenced on one lane for 100 cycles on an Illumina HiSeq2000 using a TruSeq SBS sequencing kit version 3.

treatment_protocol: Parasites (D43 post-infection) were harvested from mice, suspended in Basch media 169, and exposed to 200 Gy of γ-irradiation using a Gammacell-220 Excel with a Co60 source (Nordion, Ottawa, ON, Canada).  Control parasites were mock irradiated.  Parasites were cultured in Basch Media 169 and 48 hours post-irradiation males were separated from female parasites using ethyl 3-aminobenzoate methanesulfonate.  Following separation, the head and testes of males were removed and total RNA was extracted for RNAseq.

value: NMRI

tag: culture conditions

value: in vitro 48 hours

tag: tissue

value: posterior somatic tissue

tag: age

value: Perfused from mice 43 days post-infection

tag: irradiation?

value: No

tag: gender

value: male


title: Irradiated Experimental A


title: Non-irradiated Control C


title: Irradiated Experimental C


title: GAL_G

description:
Replicate Sld2, Sld3, Dbf4, Dpb11, Cdc45 and Sld7 (SSDDCS) overexpression via galactose induction.
Okazaki fragments.
Columns in sgr files are as follows:
column 1: chromosome
column 2: base pair
column 3: sum of counts of Okazaki fragments overlapping this position
Columns in the average.tab file are as follows:
column 1: chromosome
column 2: base pair
column 3: base pair
column 4: Weighted Average Time
column 5: Sum of Probabilities in Weighted Average
Columns in replicationProfile.tab files:
column 1: chromosome
column 2: line segment's first base pair
column 3: line segment's first time
column 4: line segment's last base pair
column 5: line segment's last time in minutes
column 6: line segment's probability (0-1)
column 7: direction of replication fork progression
column 8: red value (red for forward blue for reverse)
column 9: green value (red for forward blue for reverse)
column 10: blue value (red for forward blue for reverse)
Columns in replicationProfile250bp.tab represent 250 bp interpolated sampling of replicationProfile.tab line segment values:
column 1: chromosome
column 2: base pair sampled by interpolation
column 3: time in minutes
column 4: probability (0-1)
column 5: direction of replication fork progression
column 6: red value (red for forward blue for reverse)
column 7: green value (red for forward blue for reverse)
column 8: blue value (red for forward blue for reverse)
The scripts in the SCRIPTS folder can be run inside of R when they are placed in the same folder as the replication profile files in order to plot the replication profiles per chromosome. Instructions for using the scripts are written in comments inside the scripts.


title: Flag-Evi1Δ324 input DNA

city: Singapore

first: Ahmed

last: Sayadi

state: Singapore

address: 61 biopolis

country: Singapore

institute: Genome Institute of Singapore

description: DNA from chromatin before ChIP

data_processing:
The raw images have been processed using the Solexa Pipeline and mapped to the reference genome (NCBI Build 36, hg18) using Eland software with maximal 2 mis-matches.  The sequencing data were mapped to the human reference genome (NCBI v36, hg18), peaks were called and fold change of ChIP DNA versus input DNA was calculated for each peak as described previously (Chen et al., 2008)
Genome_build: NCBI Build 36, hg18
Supplementary_files_format_and_content: bed format
Genome_build: NCBI Build 36, hg18

organism: Homo sapiens

source_name: SKOV-3 cells

growth_protocol: SKOV-3 cells (ATCC, HTB-77) were grown at 37degres in 10%FBS RPMI.

extract_protocol: SKOV3 cells were crosslinked with 1% formaldehyde for 10min at room temperature. Cells were resuspended in lysis buffer (50 mM Hepes KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate) supplemented with 0.1% SDS. After 15min incubation, the nuclei pellet was obtained by centrifugation and washed once with the same 0.1% SDS lysis buffer. The nuclei pellet was then incubated for 15min in lysis buffer supplemented with 1% SDS to break the nuclear membranes. The chromatin was pulled-down by centrifugation at 47,000g for 30min. The supernatant (nucleoplasm) was removed and the chromatin pellet was resuspended in lysis buffer with 0.5% SDS. Sonication was used to generate fragments of 200-500 bp. The chromatin was diluted with 3 volumes of Dilution buffer (50 mM Hepes pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% NP40) and precleared 3hrs to overnight with Dynabeads Protein G (Invitrogen). The chromatin after preclear was used as input DNA and for the ChIP.  10ng of ChIP material, respectively, 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: SKOV-3 cells were transfected with pCMV-Flag-Evi1Δ324 plasmid 3 days before harvest. Then the cells were fixed in 1 % formaldehyde for 10 minutes at room temperature. The formaldehyde was quenched using 125mM glycine before chromatin extract preparation

value: ovarian carcinoma cell line

tag: cell line

value: SKOV-3 cells

tag: chip sample

value: Flag-Evi1Δ324 input

tag: chip antibody

value: Flag M2, Sigma


title: Irradiated Experimental B


title: WT_B

description:
Replicate wild type.
Okazaki fragments.
Columns in sgr files are as follows:
column 1: chromosome
column 2: base pair
column 3: sum of counts of Okazaki fragments overlapping this position
Columns in the average.tab file are as follows:
column 1: chromosome
column 2: base pair
column 3: base pair
column 4: Weighted Average Time
column 5: Sum of Probabilities in Weighted Average
Columns in replicationProfile.tab files:
column 1: chromosome
column 2: line segment's first base pair
column 3: line segment's first time
column 4: line segment's last base pair
column 5: line segment's last time in minutes
column 6: line segment's probability (0-1)
column 7: direction of replication fork progression
column 8: red value (red for forward blue for reverse)
column 9: green value (red for forward blue for reverse)
column 10: blue value (red for forward blue for reverse)
Columns in replicationProfile250bp.tab represent 250 bp interpolated sampling of replicationProfile.tab line segment values:
column 1: chromosome
column 2: base pair sampled by interpolation
column 3: time in minutes
column 4: probability (0-1)
column 5: direction of replication fork progression
column 6: red value (red for forward blue for reverse)
column 7: green value (red for forward blue for reverse)
column 8: blue value (red for forward blue for reverse)
The scripts in the SCRIPTS folder can be run inside of R when they are placed in the same folder as the replication profile files in order to plot the replication profiles per chromosome. Instructions for using the scripts are written in comments inside the scripts.

source_name: WT [yIW160]

value: WT [yIW160]


title: WT_A

description:
Wild type.
Okazaki fragments.
Columns in sgr files are as follows:
column 1: chromosome
column 2: base pair
column 3: sum of counts of Okazaki fragments overlapping this position
Columns in the average.tab file are as follows:
column 1: chromosome
column 2: base pair
column 3: base pair
column 4: Weighted Average Time
column 5: Sum of Probabilities in Weighted Average
Columns in replicationProfile.tab files:
column 1: chromosome
column 2: line segment's first base pair
column 3: line segment's first time
column 4: line segment's last base pair
column 5: line segment's last time in minutes
column 6: line segment's probability (0-1)
column 7: direction of replication fork progression
column 8: red value (red for forward blue for reverse)
column 9: green value (red for forward blue for reverse)
column 10: blue value (red for forward blue for reverse)
Columns in replicationProfile250bp.tab represent 250 bp interpolated sampling of replicationProfile.tab line segment values:
column 1: chromosome
column 2: base pair sampled by interpolation
column 3: time in minutes
column 4: probability (0-1)
column 5: direction of replication fork progression
column 6: red value (red for forward blue for reverse)
column 7: green value (red for forward blue for reverse)
column 8: blue value (red for forward blue for reverse)
The scripts in the SCRIPTS folder can be run inside of R when they are placed in the same folder as the replication profile files in order to plot the replication profiles per chromosome. Instructions for using the scripts are written in comments inside the scripts.


title: SMK5

city: Baltimore

first: Jean Lud

last: Cadet

state: MD

address: 251 Bayview Blvd, Suite 200

department: Molecular Neuropsychiatry Research Branch

institute: NIDA, IRP

data_processing:
Basecalls performed using SCS 2.50 and GAPipeline 1.5.1
First 41 bases of the ChIP-seq reads were aligned to the rn4 genome assembly using ELAND
Peaks were called using CisGenome v1.2 with the following setting: 2 sample anaylsis, input as negative control, FDR <0.01, Cut-Off of 6 tags (with 3 tags per strand), window size of 1000 and boundary refinement.
Genome_build: rn4
Supplementary_files_format_and_content: wig and bed

organism: Rattus norvegicus

source_name: Striatal Brain Tissue

growth_protocol: Animals. Male Sprague-Dawley rats (Charles Rivers Laboratories, Raleigh, NC), weighing 330–370g at the beginning of the experiments were used in the present study. Animals were housed in a humidity- and temperature-controlled room and were given free access to food and water. All animal procedures were performed according to the National Institutes of Health Guide for the Care and Use of Laboratory Animals and were approved by the local Animal Care Committee.

extract_protocol:
The animals were euthanized by decapitation 2 hrs later. Their brains were quickly removed, striatal tissues were dissected on ice, snap frozen on dry ice, and stored at −80°C until used in quantitative PCR experiments as described below.  RNA Extraction:  Total RNA was isolated using Qiagen RNeasy Mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) and showed no degradation. These experiments were not high-throughput in nature.
Briefly, the ends of the fragments were repaired using T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase), and T4 polynucleotide kinase (PNK) and A’s were added to the 3’ end. Adapters were ligated to the DNA fragments and a 18-cycle PCR amplification was performed before size selection (250-300 bases) on a 2% agarose gel, followed by cluster generation and sequencing with Solexa/Illumina Genome Analyzer (GA-II).

treatment_protocol: Following habituation, rats were injected intraperitoneally with either (±) METH-hydrochloride (NIDA, Baltimore, MD) or an equivalent volume of 0.9% saline over a period of two weeks as described in Table 1. The saline- or METH-pretreated animals received a single injection of saline or METH (5 mg/kg×1) at 16-18 hrs after the last saline or METH pretreatment injection. This dose of METH does not cause any neurotoxic effects as much larger doses are required for pathological changes to develop in the rodent brain (Krasnova et al., 2009). The four groups of animals were: saline/saline (SS), saline/METH (SM), METH/saline (MS), and METH/METH (MM).

value: Striatal Brain Tissue

tag: group

value: Saline Meth

value: Sprague Dawley

tag: treatment

value: Saline pretreatment then METH treatment

value: Anti-acetyl-Histone H4 (Lys 5)- polyclonal antibody

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog #

tag: chip antibody lot #


title: INPUT

value: INPUT

value: untreated

value: input


title: MMK5

value: Meth Meth

value: METH pretreatment then METH treatment


title: MSK5

value: Meth Saline

value: METH pretreatment then saline treatment


title: Isw2 WT N ChIP-seq 10' MNase (Isw2FLAG 20120223 5)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Isw2 wildtype native chromatin immunoprecipitation after 10' micrococcal nuclease followed by sequencing

data_processing:
1. We used Novoalign (2.07.00MT - Aug  5 2010) to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file .sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file .wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.
Genome_build: sacCer3
Supplementary_files_format_and_content: wig

source_name: Isw1 wildtype ChIP

tag: sample type

value: nuclei

value: FLAG (Sigma anti-FLAG M2 magnetic beads, catalog #8823, lot #041M6135)

value: W1588-4C (congenic to W303-1A except RAD5+)

tag: genotype

value: Isw2 WT


title: Isw1 WT input 10' MNase (Isw1IN 20120223 2)

description: Isw1 wildtype input after 10' micrococcal nuclease followed by sequencing

source_name: Isw1 WT input

tag: strain

value: Isw1 WT


title: Isw2 WT input 10' MNase (Isw2IN 20120223 4)

description: Isw2 wildtype input after 10' micrococcal nuclease followed by sequencing

source_name: Isw1 wildtype input


title: Isw2 WT input 2.5' MNase (WT inp 20111207 5)

description: Isw2 wildtype input after 2.5' micrococcal nuclease followed by sequencing

source_name: Isw2 K215R input


title: Isw1 K227R input 2.5' MNase (Isw1 K227R input 20120410 3)

description: Isw1 K227R input after 2.5' MNase followed by sequencing

source_name: Isw1 K227R input

value: Isw1 K227R


title: Chd1 WT input 10' MNase (Chd1IN 20120223 6)

description: Chd1 wildtype input after 10' micrococcal nuclease followed by sequencing

source_name: Chd1 wildtype input

value: Chd1 WT


title: Isw1 WT N-ChIP-seq 10' MNase (Isw1FLAG 20120223 3)

description: Isw1 wildtype native chromatin immunoprecipitation after 10' micrococcal nuclease followed by sequencing


title: Isw1 WT input 2.5' MNase (1.25 input 20120410 7)

description: Isw1 wildtype input after 2.5' micrococcal nuclease followed by sequencing

source_name: Chd1 WT input


title: Chd1 WT N-ChIP-seq 10' MNase (Chd1FLAG 20120223 7)

description: Chd1 wildtype native chromatin immunoprecipation after 10' micrococcal nuclease followed by sequencing

source_name: Chd1 WT ChIP


title: Isw1 WT N-ChIP-seq 2.5' MNase (1.25 IP 20120410 6)

description: Isw1 wildtype after 2.5' native micrococcal nuclease followed by sequencing

source_name: Chd1 WT N-ChIP-seq


title: Flag-Evi1Δ324 ChIP DNA

description: ChIP was performed using Flag M2 antibody (Sigma)

tag: cell type

value: ovarian carcinoma cell line

value: SKOV-3 cells

value: Flag-Evi1Δ324 ChIP

value: Flag M2, Sigma


title: Isw2 WT N-ChIP-seq 2.5' MNase (WT Flag 20111207 3)

description: Isw2 wildtype native chromatin immunoprecipitation after 2.5' micrococcal nuclease followed by sequencing

source_name: Isw2 WT ChIP


title: Chd1 WT input 2.5' MNase (WT Chd1 input 20120606 1)

description: Chd1 wildtype input after 2.5' micrococcal nuclease followed by sequencing


title: Non-irradiated Control A

value: NMRI

tag: culture conditions

value: in vitro 48 hours

value: posterior somatic tissue

value: Perfused from mice 43 days post-infection

value: No

value: male


title: Chd1 K407R N-ChIP-seq 2.5' MNase (K407R Chd1 FLAG 20120606 2)

description: Chd1 K407R native chromatin immunoprecipitation after 2.5' micrococcal nuclease followed by sequencing

source_name: Chd1 K407R ChIP

value: nuclei

value: Chd1 K407R


title: Chd1 K407R input 2.5' MNase (K407R Chd1 input 20120606 1)

description: Chd1 K407R input after 2.5' micrococcal nuclease followed by sequencing

source_name: Chd1 K407R input

value: input

value: W1588-4C (congenic to W303-1A except RAD5+)


title: mES 3P-Seq

city: Stanford

first: Noah

last: Spies

state: CA

address: 300 Pasteur Dr

department: Pathology

institute: Stanford University

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

source_name: mouse embryonic stem cells

extract_protocol:
3P-Seq
trizol, poly(A)-selected RNA
a biotinylated oligo was ligated to RNA sequences using a dT10 bridge oligo; mRNA was partially digested with RNase T1, and captured on streptavidin beads; reverse transcription with dTTP and RNase H treatment was used to release 3' end fragments from beads; following adapter ligations, fragments were sequenced from the mRNA 3' end; reads typically include 4-7 nt of the poly(A) tail

value: mouse embryonic stem cells

value: 3P protocol


title: Isw1 K227R N-ChIP-seq 2.5' MNase (Isw1 K227R FLAG IP 20120410 2)

description: Isw1 K227R native chromatin immunoprecipitation after 2.5' of micrococcal nuclease followed by sequencing

source_name: Isw1 K227R N-ChIP-Seq

value: FLAG (Sigma anti-FLAG M2 magnetic beads, catalog #8823, lot #041M6135)

value: Isw1 K227R


title: 3T3 3P-Seq

source_name: 3T3 cells

value: 3T3 cells


title: Chd1 WT N-ChIP-seq 2.5' MNase (WT Chd1 FLAG 20120606 2)

description: Chd1 WT native chromatin immunoprecipitation after 2.5' micrococcal nuclease followed by sequencing

value: Chd1 WT


title: P500_1

city: Davis

first: Vadim

last: Mozhayskiy

address: One Shields Avenue

department: Genome Center

institute: UC Davis

description:
Two technical reps: P500_1_1, P500_1_2
evolved for 500 generations in pH 5.5 + M9 with 0.4% (w/v) glucose as carbon source minimal medium

data_processing:
Illumina GAII reads were filtered by SGA version 0.9.9 with the following options: sga preprocess -q 10 -f 10 -m 25 (quality trim 10, quality filter 10, minimal length 25)
preprocessed RNA-Seq reads were mapped to the reference Escherichia coli strain K12 sub-strain MG1655 genome (GenBank accession no. U00096.2) by BWA toolkit version 0.5.9-r16 with the following options: bwa aln -q 20
Differentially expressed genes were identified by processing raw counts of mapped reads with edgeR R library version 2.6.9. Normalized counts for each biological replicate were averaged between two technical replicates.
Differentially expressed (DE) genes in all stress evolved strains were found relative to the expression levels in the reference G500 strain using the edgeR R package.
Genes with BH (Benjamini and Hochberg) adjusted p-values below 0.05 threshold were selected as DE genes.
Genes from the amplified regions in O500 (12-fold) and P500 (two-fold) strains are significantly over-expressed relative to the reference: average log Fold Change for concentrations is +3.6 and +0.8 (both with p-values<10-20), respectively.
Genome_build: Escherichia coli strain K12 sub-strain MG1655 genome (GenBank accession no. U00096.2)
Supplementary_files_format_and_content: Tab delimited text file; includes: gene differential expression levels relative to the G500 strain with corresponding p-values and processed counts for each biological replicate (each normolized and averaged between 2 technical replicates).  Linked as supplementary file on Series record.

organism: Escherichia coli

source_name: Bacterial cell

growth_protocol: Clones were grown in M9 with 0.4% (w/v) glucose as carbon source minimal medium with 0.3M NaCl (osmotic stress medium) to mid-log phase (OD600 approx. 0.8).

extract_protocol: RNA was extracted using an RNeasy kit (Qiagen) and after 1st and 2nd strand cDNA synthesis, linker ligation and size selection subjected to shotgun sequencing using single read 40bp read length runs on an Illumina Genome Analyzer GAII.

treatment_protocol: 1mL aliquots were harvested and mixed with 0.5mL Phenol/ethanol (5% (v/v) Phenol in EtOHabs). Cells were collected by centrifugation and stored at -80°C until use.

tag: stress

value: acidic

tag: biological replicate

tag: technical replicates


title: O500_2

description:
Two technical reps: O500_2_1, O500_2_2
evolved for 500 generations in 0.3M NaCl + M9 with 0.4% (w/v) glucose as carbon source minimal medium

value: osmotic


title: H500_1

description:
Two technical reps: H500_1_1, H500_1_2
evolved for 500 generations in 100μM H2O2 M9 with 0.4% (w/v) glucose as carbon source minimal medium

value: oxidative


title: B500_1

description:
Two technical reps: B500_1_1, B500_1_2
evolved for 500 generations in 0.6% n-butanol + M9 with 0.4% (w/v) glucose as carbon source minimal medium

value: n-butanol


title: O500_1

description:
Two technical reps: O500_1_1, O500_1_2
evolved for 500 generations in 0.3M NaCl + M9 with 0.4% (w/v) glucose as carbon source minimal medium


title: G500_1

description:
Two technical reps: G500_1_1, G500_1_2
evolved for 500 generations in M9 with 0.4% (w/v) glucose as carbon source minimal medium

value: Minimal medium


title: rdm16-2 RNA-seq

status: Public on Feb 26 2013

city: Shanghai

first: Lan

last: Yang

address: 300 Fenglin Road

country: China

institute: Institute of Plant Physiol & Ecology, Chinese Academy of Sciences

description: Sample 2

data_processing:
Sequenced reads were aligned to tair10 whole genome using TopHat v2.0.4 with parameters -p 10 -I 10000 --solexa1.3-quals --library-type fr-unstranded -r 20 -G tair10_genes.gtf
Unique mapped reads were choosed to calculate the RPKM value of each intron in each sample and the fold change between mutant and wild type samples with a local perl script
Differential expression genes obtained by cuffdiff module of cufflinks v2.0.1 with parameters  -u  -p 10  --FDR 0.05  -b tair10_genome.fa
Genome_build: TAIR10 http://www.ncbi.nlm.nih.gov/assembly/237408/
Supplementary_files_format_and_content: bedGraph files were generated using wiggles v1.3.2,then normalized by covrage*10^6/library_size

organism: Arabidopsis thaliana

growth_protocol: Plants were grown on soils under long day condition at 22 ℃

extract_protocol:
Leaves of 4-week-old plants were havested for RNA isolation by  the RNeasy Mini Kit (Qiagen)
The extracted RNA was sent to BGI (Shenzhen, China) for RNA-seq library preparation and whole transcriptome sequencing. Briefly, The total RNA was treated with DNaseI and then subjected for mRNA enrichment. The derived mRNA was used as the template for first strand cDNA synthesis by using oligo dT primer. The adaptor was added to the 5’ end of the first strand cDNA and then the second strand cDNA was synthesized by using the primer pairing to the adaptor. The double strand cDNA was sonicated into 300-500 bp fragments for pair-ended sequencing with HiSeq 2000.

tag: genotype/variation

value: rdm16-2 mutant

tag: age

value: 4 weeks

tag: tissue

value: leaves


title: sta1 RNA-seq

description: Sample 3

value: sta1 mutant


title: LIN28B_rep2 PAR-CLIP

first: Miguel

last: Brown

address: 1230 York Ave Box 186

institute: The Rockefeller University

description:
LIN28B ribonucleoprotein complexes
LIN28B.xlsx

data_processing:
Mapping Reads: The reads from the LIN28A and B PAR-CLIP deep sequencing library were stripped of the 3’ adapter sequence using the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).  Reads that were less than 20 nt in length or contained an ambiguous nucleotide were discarded.  The remaining reads were aligned to the human genome (hg19), with up to 1 mismatch allowed, by the Bowtie algorithm (Langmead et al., 2009).  Mapped locations were only reported for those with the minimum number of observed mismatches for each read.  All T to C mismatches between the RNA fragment and the genome were subtracted from the mismatch count for each mapped location.  After subtraction only reads that mapped to a single genomic location at the minimum number of mismatches were used for further analysis.  The location that a read mapped, relative to a known transcript, was determined based on the ENSEMBL v57 database 1(Hubbard et al., 2007).  If a read mapped to a location representing multiple categories, it was reported to belong to the category based on the following order of preference: 3’UTR, coding sequence, 5’UTR, intron, non-coding RNA, intergenic. Defining HuR binding sites by PARalyzer: Overlapping reads were grouped together for further analysis. A group must have contained ≥5 reads with T-to-C conversions at two or more locations and at least 25% of mapped sequence reads. PARalyzer is available at http://www.genome.duke.edu/labs/ohler/research/PARalyzer
Genome_build: hg19

source_name: HEK 293

growth_protocol: HEK293 T-REx Flp-In cells (Invitrogen) were grown in D-MEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, 1% (v/v) 10,000 U/ml penicillin/10,000 µg/ml streptomycin, 100 µg/ml zeocin and 15 µg/ml blasticidin. Cell lines stably expressing FLAG/HA-tagged LIN28A or B were generated by co-transfection of pFRT/TO/FLAG/HA/LIN28A or pFRT/TO/FLAG/HA/LIN28B construct with pOG44 (Invitrogen). Cells were selected by exchanging zeocin with 100 µg/ml hygromycin. Expression of FLAG/HA-LIN28A or FLAG/HA-LIN28B was induced by addition of 250 ng/ml doxycycline 15 to 20 h before crosslinking.

extract_protocol: The pellets of cells crosslinked with UV 365 nm were resuspended in NP40 lysis buffer and incubated on ice for 10 min. The cell lysate was cleared by centrifugation at 13,000g. RNase T1 (Fermentas) was added to the cleared cell lysates and the reaction mixture was incubated at 22ºC for 15 min and subsequently cooled for 5 min on ice before addition of antibody-conjugated magnetic beads. The recovered RNA was carried through a cDNA library preparation protocol originally described for cloning of small regulatory RNAs (Hafner et al., 2008). The first step, 3' adapter ligation, was carried out as described on a 20 ul scale using 10.5 ul of the recovered RNA. UV 365 nm crosslinked sample RNAs were processed using Solexa sequencing adapter sets. Depending on the amount of RNA recovered, 5'-adapter-3'-adapter products without inserts may be detected after amplification of the cDNA as additional PCR bands. In such case, the longer PCR product of expected size was excised from a 3% NuSieve low-melting point agarose gel, eluted from the gel pieces with the Illustra GFX-PCR purification kit (GE Healthcare) and Solexa sequenced.

treatment_protocol: For UV crosslinking, cells were washed once with ice-cold PBS while still attached to the plates. PBS was removed completely and cells were irradiated on ice with 365 nm UV light in a Stratalinker 2400 (Stratagene). Cells were scraped off with a rubber policeman in 1 ml PBS per plate and collected by centrifugation at 500×g for 5 min.

tag: crosslinker and crosslinking wavelength

tag: antibody

value: Flag M2

tag: immunoprecipitated protein


title: Col RNA-seq

description: Sample 1

value: wild type


title: LIN28A PAR-CLIP

description:
LIN28A ribonucleoprotein complexes
LIN28A.xlsx


title: LIN28B_rep1 PAR-CLIP


title: LIN28B_knockdown_rep1

description: Gene expression data from HEK293 cells inducibly expressing FLAG/HA tagged LIN28B after knockdown with siRNA

data_processing:
Reads are assigned to their respective samples using custom perl scripts.  Requirements are that the barcode in its entirety must be found, and the first 5 nt of the 3' adapter sequence allowing for one error (mismatch, indel).  Reads ranging from 19-15 nt are analyzed
Mapping against the human genome release hg19 and custom non-coding (ncRNA) RNA database is performed using BWA version 0.5.9, with paramters "-n 2 -t 12" against the ncRNA database, "-n 1 -t 12" against the human genome
Cutsom scripts are used to assign reads first by assigning reads by lowest error maping error, then by hierarchy accounting for relative biological abundance of ncRNA species as well as enrichment of 5'-p 3'-OH small RNA cDNA cloned according to protocol outlined above.
Genome_build: hg19, custom annotation database containing genbank defined ncRNAs and in-house miRNA definitions
Supplementary_files_format_and_content: first column contains the read with barcode and adapter removed, the second the read count, the third the annotated miRNA name or non-coding RNA type if applicable

source_name: HEK 293 cells inducibly expressing FLAG/HA tagged LIN28B; transgene not induced; siRNA transfected; replicate 1

growth_protocol: HEK293 T-REx Flp-In cells (Invitrogen) were grown in D-MEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, 1% (v/v) 10,000 U/ml penicillin/10,000 µg/ml streptomycin, 100 µg/ml zeocin and 15 µg/ml blasticidin. Cell lines stably expressing FLAG/HA-tagged LIN28B were generated by co-transfection of pFRT/TO/FLAG/HA/LIN28B construct with pOG44 (Invitrogen). Cells were selected by exchanging zeocin with 100 µg/ml hygromycin. Expression of FLAG/HA-LIN28B was induced by addition of 250 ng/ml doxycycline 15 to 20 h before crosslinking.

extract_protocol:
TRizol extraction according to the manufacturer's protocol
small RNA cDNA library according to Hafner et al, Methods, 2012, and Hafner et al., RNA, 2011

treatment_protocol: Expressoin of LIN28B was induced with 0.25 µg/ml of doxycyclin

tag: cell line


title: SSK5

source_name: Striatal Brain Tissue

value: Striatal Brain Tissue

tag: group

value: Saline Saline

value: Sprague Dawley

tag: treatment

value: Saline pretreatment then saline treatment

tag: chip antibody

value: Anti-acetyl-Histone H4 (Lys 5)- polyclonal antibody

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog #


title: Isw2 K215R N-ChIP-seq 2.5' MNase (K215R Flag 20111207 4)

description: Isw2 K215R native chromatin immunoprecipitation after 2.5' micrococcal nuclease followed by sequencing

source_name: Isw2 K215R ChIP

tag: sample type

value: nuclei

value: FLAG (Sigma anti-FLAG M2 magnetic beads, catalog #8823, lot #041M6135)

tag: strain

value: W1588-4C (congenic to W303-1A except RAD5+)

tag: genotype

value: Isw2 K215R


title: Isw2 K215R input 2.5' MNase (K215Rinp 20111207 6)

description: Isw2 K215R input after 2.5' micrococcal nuclease followed by sequencing

source_name: Isw2 K215R input

value: input


title: LIN28B_induced_rep2

description: Gene expression data from HEK293 cells inducibly expressing FLAG/HA tagged LIN28B; FH/LIN28B  induced

source_name: HEK 293 cells expressing FLAG/HA tagged LIN28B; transgene expression induced; mock transfected; replicate 2


title: LIN28B_induced_rep1

source_name: HEK 293 cells expressing FLAG/HA tagged LIN28B; transgene expression induced; mock transfected; replicate 1


title: LIN28B_knockdown_rep2

source_name: HEK 293 cells inducibly expressing FLAG/HA tagged LIN28B; transgene not induced; siRNA transfected; replicate 2


title: LIN28B_not_induced_rep2

description: Gene expression data from HEK293 cells inducibly expressing FLAG/HA tagged LIN28B; FH/LIN28B not induced

source_name: HEK 293 cells inducibly expressing FLAG/HA tagged LIN28B; transgene expression not induced; mock transfected; replicate 2


title: Gld-2 knock-down

status: Public on Feb 23 2013

city: Worcester

first: Craig

last: Mello

state: MA

address: 368 Plantatoin Street, Suite AS5-2047

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

data_processing:
Human genome GRC37.65 and miRBase release 18 were used as genomic and miRNA annotation databases, respectively.  Custom PERL scripts were used to “de-barcode” the sample and remove the 5’ and 3’ linkers.  Bowtie (Langmead et al., 2009) 0.12.7 with parameters -v 3 -a --best --strata -m 200 was used to map deep-sequence reads to the genome. Total count linear scaling was used as a normalization method for differential miRNA analysis. Matches were assigned to miRNA loci plus 4 nucleotides upstream and downstream to allow for non-templated nucleotide addition analysis; only loci with at least 500 matched reads were considered. The mutation rates for each miRNA nucleotide position plus and minus 4 nucleotides was computed.  Divergent nucleotides at position +1 over the wild-type were calculated with custom PERL scripts available upon request
Supplementary_files_format_and_content: fasta format with id containing read number after '_x' (such as >001ps_x100).

source_name: Gld-2 knock-down_miRNA-seq

growth_protocol: DMEM, 10% FBS, 1x Gibco Antibiotic-Antimicotic, split every 3 days

extract_protocol: Small RNA libraries were prepared as described in Gu et al. (2009); small RNA cloning, 5' and 3' ligation dependent (no enzymatic treatments required for the 5' and 3' ends)

treatment_protocol: Primary human foreskin fibroblasts obtained from the Cell Culture Core Facility of the Yale University Skin Disease Research Center were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 10% fetal bovine serum and Antibiotic-Antimycotic 1X  (Life Technologies).  All experiments were performed with cells that underwent fewer than 10 passages.  Gld2 depletion was performed by electroporating (Amaxa, LONZA) siGENOME SMARTpool Human PAPD4 (Dharmacon) or siGENOME Non-Targeting siRNA pool#1 as a control, according to the manufacturers’ protocols.

tag: cell type

value: primary neonatal human foreskin fibroblasts

value: Gld-2 knock-down

tag: molecule subtype

value: miRNA

tag: 5' barcode

value: 5' barcode ATCA

tag: 3' linker

value: Starting with CTGTAGGCA


title: LIN28B_not_induced_rep1

source_name: HEK 293 cells inducibly expressing FLAG/HA tagged LIN28B; transgene expression not induced; mock transfected; replicate 1


title: WT

description: wt

tag: genotype/variation

value: WT

value: 5' barcode GCTG


title: LIN28B_rep3 PAR-CLIP

tag: crosslinker and crosslinking wavelength

value: Flag M2


title: Dbip_Male_replicate1

status: Public on Feb 22 2013

city: Bethesda

first: Brian

last: Oliver

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

data_processing:
Base calls and quality scores were generated by the Illumina analysis pipeline (Casava 1.4 for GAIIx, and Casava 1.6 for Hiseq 2000).  All reads were trimmed to the same length (75bp) for downstream analysis.
Reads were mapped to their respective genomes using Tophat 2 (v2.0.3), accepting only uniquely-mapped reads.  Parameters supplied to Tophat were:  ‘-g 1 -r 150 --solexa1.3-quals.’  Genome references used for each species were: D.biarmipes (Dbia_1.0), D.bipectinata (Dbip_1.0), D.elegans (Dele_1.0), D.eugracillis (Deug_1.0), D.ficusphila (Dfic_1.0), D.kikkawai (Dkik_1.0), D.rhopaloa (Drho_1.0) and D.takahashi (Dtak_1.0), and were downloaded from NCBI.
We used the UCSC genome browser liftover software (Kent, 2002) to project D. melanogaster annotation coordinates (FlyBase r5.45 and ModENCODE Transcriptome V2) to the reference genome of the fourteen sister species.  After defining orthologous regions for features, we estimated expression of these features in the non-melanogaster species by quantifying reads mapping to them.  This was performed by coordinate intersections with base-level genomic coverage data using BedTools (Quinlan, 2010) on each alignment BAM file.  Splice junctions were quantified from BAM files using the Splicing Analysis Toolkit (Spanki, http://www.cbcb.umd.edu/software/spanki/)
Genome_build: dm3, Dbia_1.0, Dbip_1.0, Dele_1.0, Deug_1.0, Dfic_1.0, Dkik_1.0, Drho_1.0, Dtak_1.0
Supplementary_files_format_and_content: Text files (*.rpkm) provide RPKM values for five-prime orthologous coding exons.  Additional text files (*.juncs.txt) provide splice junction coverages.

molecule: polyA RNA

organism: Drosophila bipectinata

source_name: Whole body

growth_protocol: Flies were inbred by single pair, full-sib crosses for 10-18 generations (with the exception of D. rhopaloa, which did not tolerate inbreeding).  For RNA-seq experiments, animals were reared on cornmeal media with a 12:12 light cycle at 25C in a humidified incubator.  Adults were aged 1-4 days, and total RNA was extracted using Trizol from pools of 30 adult males, pools of 30 adult females, and from 200-300 ml of 0-24 hour embryos

extract_protocol:
mRNA was purified from total RNA using Dynabeads® mRNA Purification Kit (Life tech, catalog number: 610-06). Briefly, 2.5 ug total RNA in 50ul DEPC-treated H2O was denatured at 65°C for 5 minutes to disrupt the secondary structure, and immediately cooled on ice for 1 minute. 100 ul of oligo (dT)25 Dynabeads were washed and resuspended in 50 ul of binding buffer before use. The denatured total RNA was added into prewashed Dynabeads and incubated at room temperature for 5 minutes on a rotary shaker.  mRNA-Bead complex was captured on magnet rack and washed twice with 200 ul wash buffer.  The mRNA was eluted by adding 11 ul of H2O to mRNA-Bead complex followed by heated to 75°C for 2 minutes. Tube was placed on magnet rack immediately for 30 seconds. Supernatant containing the purified mRNA was transferred to a fresh RNAse-free PCR tube while the tube was on magnet rack.
The first strand cDNA was reverse transcribed from poly-A mRNA using random hexamer and SuperScript® First-Strand Synthesis kit (Life Tech, catalog number: 11904-018).  Random hexamer was annealed to mRNA by heating mRNA/random hexamer mixture to at 65°C for 5 minutes then cooled on ice.  8.5 ul of The first strand synthesis reaction mix containing 500 uM dNTP, 20 units RNaseOut, 10 mM DTT, 200 unit Superscript II as added to mRNA/random hexamer.  The first strand cDNA was synthesized by incubation reaction at 25C 10 minutes, 42°C 60 minutes, 70°C 15 minutes and hold at 4°C.  The second strand cDNA was synthesized using DNA polymerase I (life Tech, catalog number: 18010-025).  The second strand cDNA synthesis was incubated at 16°C for 2 hrs in a thermocycler. The double strand cDNA was purified with 1.8X Agencourt AMPure XR beads (Beckman coulter, catalog number: A63882 ).
Double stranded cDNA was constructed into Illumina paired-end libraries according to the manufacturer’s protocol (Illumina Inc.). Double strand cDNA was sheared to fragments of approximately 400 bp with the Covaris S2 or E210 system (Covaris, Inc. Woburn, MA). The setting was 10% Duty cycle, Intensity of 4,200 Cycles per Burst, for 55 seconds. Fragments were processed through DNA End-Repair in 100ul containing sheared DNA, 10ul 10X buffer, 5ul EndRepair Enzyme Mix and H2O (NEBNext End-Repair Module; Cat. No. E6050L) at 20°C for 30 minutes; A-tailing was performed in 50ul containing End-Repaired DNA, 5ul 10X buffer, 3ul Klenow Fragment (NEBNext dA-Tailing Module; Cat. No. E6053L) at 37°C for 30 minutes, each step followed by purification using a QIAquick PCR purification kit (Cat. No. 28106).  Resulting fragments were ligated with Illumina PE adapters and the NEBNext Quick Ligation Module (Cat. No. E6056L).  After ligation, size selection was carried out by using 2% low-melt agarose gel running in 1X TBE. Gel slices were excised from 290bp to 340bp and the size-selected DNA was purified using a Qiagen MinElute gel extraction kit and eluted in 30ul EB buffer.  PCR with Illumina PE 1.0 and 2.0 primers was performed in 25-μl reactions containing 12.5 ul of 2x Phusion High-Fidelity PCR master mix, 2.5ul size-selected fragment DNA, 0.3ul each primer and H2O. The standard thermocycling for PCR was 30 s at 98°C for the initial denaturation followed by 12 cycles of 10 s at 98°C, 30 s at 65°C and 30 s at 72°C and a final extension of 5 min. at 72°C.  1.8X Agencourt® XP® Beads (Beckman Coulter Genomics, Inc.; Cat. No. A63882) were used to purify the PCR products. After Bead purification, PCR products were quantified using PicoGreen (Cat. No. P7589) and their size distribution analyzed using the Agilent Bioanalyzer 2100 DNA Chip 7500 (Cat. No. 5067-1506).
From the 10nM final library, 15ul was sequenced on Illumina’s Genome Analyzer IIx or HiSeq 2000 instrument according to the manufacturer’s specifications (specified for each sample in SRA entries). Briefly, cluster generations were performed on an Illumina cluster station. Paired-end sequencing was performed, for 90-125 cycles of sequencing for each mate.  Each library was sequenced in a separate, single flow cell lane.

tag: stock number

tag: developmental stage

value: Adult

tag: Sex

value: Male


title: Dele_Male_replicate1

organism: Drosophila elegans

value: HK


title: Dele_Female_replicate1

value: Female


title: Dbip_Female_replicate1


title: Dbip_Embryo_replicate1

source_name: Embryos

value: Embryo

value: Pooled male and female


title: Dbia_Male_replicate1

organism: Drosophila biarmipes


title: Dbia_Embryo_replicate1


title: Drho_Embryo_replicate1

organism: Drosophila rhopaloa


title: Dtak_Male_replicate1

organism: Drosophila takahashii


title: Dtak_Female_replicate1


title: Dtak_Embryo_replicate1


title: Drho_Male_replicate1


title: Dbia_Female_replicate1


title: GCK_control_GLUCOSE

city: Ansan

first: Abimbola

middle: Comfort

last: Badejo

address: 1271 Sa3dong

country: South Korea

institute: Hanyang University

data_processing:
Illumina Pipeline (CASAVA) v1.8.2 used for basecalling
Data was treated with low-quality filtering using Prinseq 0.19.3.
Filtered reads were mapped with reference genome  using Bowtie2 version 2.0.0, default option
Differential expression analysis using Cuffdiff in Cufflinks 2.0.2 package.
Genome_build:   ASM1636v1; GenBank CP000656
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample and statistical analysis of gene expression between control and induced samples

organism: Mycolicibacterium gilvum PYR-GCK

source_name: Prokaryotic cell contents

growth_protocol: Cultivation in 200ml defined minimal media

extract_protocol:
Total RNA extracted using RNAiso reagent and 45 seconds bead-beating. mRNA enrichment with Ribo-Zero rRNA removal kit.  Illumina TruSeq RNA Sample Prep Kit used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: separate supplements of 25mM pyrene substrate and 0.38g/L D-glucose substrate (supplements identified as induced and control in analyzed data, respectively)

value: PYR-GCK

tag: protocol


title: Drho_Female_replicate1


title: MM1S_CDK9_500nM_JQ1

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
Chromatin IP against CDK9 in MM1.S multiple myeloma
barcode (already removed): CGTACG
sample name: 08282012_C1260ACXX_6.CGTACG

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.

source_name: Multiple myeloma

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

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.

treatment_protocol: 500nM JQ1 treatment for 6hr

tag: treated with

value: 500nM JQ1 treatment for 6hr

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #


title: MM1S_MED1_500nM_JQ1

description:
Chromatin IP against MED1 in MM1.S multiple myeloma
barcode (already removed): CCGTCC
sample name: 08282012_C1260ACXX_5.CCGTCC

tag: chip antibody

value: Bethyl


title: Deug_Embryo_replicate1

organism: Drosophila eugracilis


title: GCK_induced_PYRENE


title: Dele_Embryo_replicate1


title: MM1.S_CDK9_DMSO

description:
Chromatin IP against CDK9 in MM1.S multiple myeloma
barcode (already removed): GTGAAA
sample name: 08282012_C1260ACXX_5.GTGAAA

treatment_protocol: 0.05% DMSO for 6h

value: 0.05% DMSO for 6h


title: Dkik_Male_replicate1

organism: Drosophila kikkawai


title: Dfic_Male_replicate2

organism: Drosophila ficusphila


title: Dfic_Male_replicate1


title: Dfic_Female_replicate2


title: Dfic_Female_replicate1


title: H9_stranded

first: Li

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

description: stranded RNAseq

data_processing:
Basecalling using Illumina Casava1.8.2 software.
Map to human genome hg19 using Bowtie( v 0.12.8) with parameters “-5 5 -3 5 -m 1 -k 1 -v 3 -y -p 40 -B 1 --best”.
Separate reads from sense or anti-sense strand, respectively.
Pileup the mapping results and call A-to-I RNA editing after filtering
Validate selected  A-to-I RNA editing sites from non-stranded H9 sequencing dataset (GEO:GSE24399).
Genome_build: hg19
Supplementary_files_format_and_content: txt file. Genomic locations of predicted A-to-I RNA editing sites and stranded information.

source_name: hES h9 cells

growth_protocol: hES H9 cells were maintained on plates coated with Matrigel (BD Biosciences) in either defined mTeSR medium (StemCell Technologies Inc.) or conditioned medium (CM) with irradiated mouse embryo fibroblasts supplemented with 4 ng/mL human Basic Fibroblast Growth Factor (bFGF)

extract_protocol:
Total RNAs were prepared using Trizol Reagent and treatment with DNase I
RNA-Seq libraries preparation with prereleased Directional mRNA-seq Libraty Kit with minor modifications.

tag: cell line

value: human embryonic stem cells

tag: chromosome

value: diploid

tag: passages


title: Dfic_Embryo_replicate1

tag: strain


title: Dkik_Female_replicate1


title: Deug_Male_replicate1


title: DR1(pAST2)-TC

status: Public on Feb 21 2013

city: Seoul

first: Hyerim

last: Hong

address: Korea Univ. Anam Campus, Anam-dong 5-ga, Seongbuk-gu

department: Environmental Science and Ecological Engineering

institute: Korea University

data_processing:
Base-calling: CASAVA v1.6
Alignment: CLC Genomics Workbench 4.5
Generation of normalized abundance measurement: CLC Genomics Workbench 4.5
Genome_build: Acinetobacter oleivorans DR1 chromosome, complete genome RefSeq (NC_014259.1)
Supplementary_files_format_and_content: txt

organism: Acinetobacter oleivorans DR1

source_name: stationary cells

extract_protocol: Total RNA was isolated from 5 ml of stationary cells, using the RNeasy Mini kit (QIAGEN, USA), according to the manufacturer’s instructions. The RNA was subjected to a subtractive Hyb-based rRNA removal process using the MICROBExpress Bacterial mRNA Enrichment Kit (Ambion). RNA sequencing was performed using the Illumina Genome Analyzer IIx to generate single-ended 36-bp reads.

value: Acinetobacter oleivorans DR1

value: Wild type harboring pAST2

tag: growth phase

value: exponential

tag: treatment

value: treated with tetracycline (1ug/ml) over a period of 15 min


title: DR1-TC

value: Wild type


title: ko_H3K27me3

status: Public on Feb 20 2013

description: Sample 2

data_processing:
Base calling was performed as standard by Ambry Genetics (Aliso Viejo, CA, USA)
Reads were mapped to the mm9 build of the mouse genome using the bowtie short read aligner. Where a read mapped to a number of potential locations, only the best hit was retained (in terms of the number of mismatches and their qualities; as specified by the bowtie '–best' parameter
BEDTools was used to count the number of mapped reads that overlap genomic windows. This was outputted as a BedGraph
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph files containing count data. Columns: chromosome; start coordinate of genomic window; stop coordinate of genomic window; number of mapped reads that overlap this window (windows with less than 5 overlapping windows are not shown)

organism: Mus musculus

extract_protocol:
Native ChIP was performed as described previously (Eskeland et al, 2010, Mol Cell, 38: 452-464) with the following adaptations. Protein-A coated Dynabeads (Invitrogen) were used throughout. Chromatin was digested with 25U of Mnase (micrococcal nuclease)(Worthington) for exactly 10min at room temperature. Following immunoprecipitation beads were washed three times for 10 min at 4°C in N-ChIP wash buffer (150mM NaCl; 10mM Tris pH8; 2mM EDTA; 1% NP40; 1% sodium deoxycholate w/v). Controls for N-ChIP experiments included a species matched IgG to control for background, negative and positive genomic regions to show specificity, and the use of input DNA to control for technical variations between cell lines or treatments. Antibodies were tested by western blot for recognition of histone-sized proteins only and by specific enrichment at positive control regions by N-ChIP. Enrichments were measured by qPCR.
Libraries were prepared according to Illumina's instructions by Ambry Genetics (Aliso Viejo, CA, USA)

tag: strain/cell line background

tag: cell type

value: Mouse embryonic fibroblasts (MEFs)

value: DNA methylation deficient; Dnmt1-/-

value: Millipore


title: Deug_Female_replicate1

value: Adult

value: Female


title: wt_H3K27me3

description: Sample 1

tag: genotype/variation

value: wild type; Dnmt1+/+


title: Healthy leaves

city: Beijing

first: WEIMIN

last: LI

address: No.12 Zhongguancun St.

institute: Biotechnology Research Institute, CAAS

data_processing:
Illumina GA Pipeline v1.6 software used for basecalling.
The raw reads were filtered to remove low quality reads as well as reads with adaptor sequences or containing unknown nucleotides larger than 5%, then mapped to the foliar transcriptome of Chenopodium amaranticolor whole genome using SOAPaligner/soap2 with a maximum of no more than 2 nucleotides mismatches.
For gene expression analysis, the number of expressed reads was counted and normalized using RPKM (reads per kb per million reads) as described by Mortazavi et al. at Nature Methods, 2008.
Genome_build: The foliar transcriptome of Chenopodium amaranticolor constructed in the current work
Supplementary_files_format_and_content: text file includes RPKM values for each sample

organism: Chenopodium amaranticolor

source_name: Healthy leaves

extract_protocol: The poly(A) mRNA was first isolated from 6 μg of total RNA using oligo (dT) magnetic beads (Invitrogen). The mRNA was then fragmented into smaller pieces at 70℃ for 5min in the fragmentation buffer (Ambion). Taking these short mRNA fragments as templates, reverse transcriptase and random hexamer-primer were used to synthesize the first-strand cDNA. This was followed by second strand cDNA synthesis using DNA polymerase I (Invitrogen) and RNaseH (Invitrogen). The resulted short cDNA fragments were purified with QiaQuick PCR extraction kit (Qiagen) followed by end repair, adding poly(A), and ligation of sequencing adaptors with Illumina’s adaptor oligo mix. The fragments were purified for the section of approximate 200 bp long using Qiaquick Gel Extraction Kit (Qiagen) and were further enriched with PCR to create the final sequencing cDNA library.

treatment_protocol: Leaves of 6~7 week-old C. amaranticolor grown in the greenhouse were inoculated with CMV SD strain and TMV U1, respectively. Briefly, infectious sap was prepared with one gram of fresh TMV- or CMV-infected Nicotiana tabacum leaves that were macerated in 10 mL of inoculation buffer (50 mM KH2P04, pH 7.0, 1% Celite), and was mechanically inoculated onto C. amaranticolor leaves dusted with carborundum powder (600 mesh). The leaves inoculated with TMV and CMV were first sampled at 6 hpi, then were collected at 20 hpi for CMV-inoculated leaves and at 28 hpi for TMV-inoculated leaves, at which time point local lesions became just visible. Leaves of the healthy plants were also harvested as control. All samples were immediately frozen in liquid nitrogen and were stored at -80℃ until use.

tag: age

value: 6~7 week-old

tag: tissue

value: Leaves

tag: inoculated with

value: none (healthy)


title: ko_H3K4me3

address: Meyerhofstrasse 1

description: Sample 4


title: Luminal OVX K27me3 ChIPSeq

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

data_processing:
Basecalls performed using CASAVA version 1.7
Reads were mapped to the mouse reference genome mm9 using the Subread aligner (http://subread.sourceforge.net). Six subreads were selected from each read and at least two consensus subreads were required for reporting a hit. No mismatches were allowed when mapping extracted subreads to the reference genome. A fragment was judged to be successfully mapped if the paired ends mapped to locations between 50 and 500 bp apart.
Mapped fragments were assigned to each gene by comparing the location of fragments to the chromosomal coordinates of regions defined for each gene. For H3K27me3 marks, each gene was assigned two values in each sample, which gave the H3K37me3 marking levels for the TSS region and the broad region. For H3K4me3 marks, only marking levels in the TSS region were used. The ‘TSS’ region is defined as the region 3 kb upstream and 2 kb downstream sequence of the transcriptional start site of the gene, and the ‘broad’ region defined as the genomic span of the gene including 3kb of sequence upstream of the transcriptional start site.
Statistical analysis of the count data was performed using edgeR package of the Bioconductor software project. Genes were called as significantly enriched for each histone mark using the normalizeChIPtoInput function, which normalizes the ChIP counts to input and evaluates enrichment using a negative binomial statistical model. Log2-fold-changes in histone mark coverage between cell populations or between conditions were computed using the predFC function. This function adjusted the ChIP counts for input by fitting a negative binomial log-linear generalized linear model, using a prior count of 0.5 per sample to avoid unreliably large log-fold-changes that might otherwise arise from zero or small counts. The negative binomial dispersion was set to 0.01 for all calculations, allowing for a degree of biological variation typical of mouse experiments.
Genome_build: mm9
Supplementary_files_format_and_content: Bed fies were generated using in-house C code. They include the chromosomal coordinates of each mapped fragment.

source_name: mammary gland

growth_protocol: Freshly sorted cells

extract_protocol:
The standard ChIP protocol was used to isolate genomic DNA marked with the above histone modifications.
Libraries for paired-end sequencing were prepared by Geneworks using 10 ng ChIP DNA according to the Illumina ChIP-seq Sample Preparation protocol, revision A, with the following modifications. Paired-end adapters were substituted for standard genomic adapters, and library amplification (18 cycles) performed using primers PE 1.0 and 2.0. Size selection for 300 bp DNA was performed prior to amplification. Final libraries were analyzed using the Agilent Bioanalyzer High Sensitivity DNA Kit and sequenced on the Illumina Genome Analyzer IIx running SCS 2.8, generating 35 base paired-end reads using the CASAVA 1.7 analysis pipeline.

treatment_protocol: Cells obtained by Flow cytometry were fixed with paraformaldehyde  and snap frozen

value: Luminal cells

tag: state

value: ovariectomized

value: Histone H3 trimethyl Lys27

value: FVB/N

tag: chip antibody manufacturer

tag: chip antibody catalog #


title: CMV-20h

value: CMV at 20 hpi


title: TMV-28h

value: TMV at 28 hpi


title: Luminal OVX Input DNA ChIPSeq


title: wt_H3K4me3

institute: EMBL

description: Sample 3

tag: chip antibody vendor

tag: chip antibody cat. #


title: Luminal pregnancy K27me3 ChIPSeq

value: 12.5 days pregnant

tag: chip antibody


title: CMV-6h

value: CMV at 6 hpi


title: Luminal OVX K4me3 ChIPSeq

value: Histone H3 trimethyl Lys4


title: Luminal pregnancy K4me3 ChIPSeq


title: Luminal pregnancy Input DNA ChIPSeq


title: Mixture

description: Mixture of healthy leaves, leaves inoculated with TMV at 6 hpi and 28 hpi, and leaves inoculated with CMV at 6 hpi and 20 hpi

source_name: Mixed leaves

value: TMV at 6 hpi and 28 hpi, CMV at 6 hpi and 20 hpi


title: Luminal K27me3 ChIPSeq

value: virgin

value: Millipore


title: MS OVX Input DNA ChIPSeq

value: Mammary stem cells


title: MS OVX K27me3 ChIPSeq


title: Luminal K4me3 ChIPSeq


title: Dkik_Embryo_replicate1

tag: stock number

tag: developmental stage

value: Embryo

tag: Sex

value: Pooled male and female


title: MS OVX K4me3 ChIPSeq

tag: strain


title: MS pregnancy Input DNA ChIPSeq


title: MS pregnancy K27me3 ChIPSeq


title: MS pregnancy K4me3 ChIPSeq


title: MS K27me3 ChIPSeq rep2


title: MS K4me3 ChIPSeq rep2


title: Luminal Input DNA ChIPSeq


title: MS Input DNA ChIPSeq rep2


title: TMV-6h

value: 6~7 week-old

value: Leaves

value: TMV at 6 hpi


title: ML K4me3 ChIPSeq

value: Mature luminal cells


title: LP Input DNA ChIPSeq

value: Luminal progenitor cells


title: LP K9me2 ChIPSeq

value: Histone H3 dimethyl Lys9

value: FVB/N

value: Abcam


title: MS K4me3 ChIPSeq rep1


title: MS K27me3 ChIPSeq rep1

value: Histone H3 trimethyl Lys27


title: LP K4me3 ChIPSeq


title: ML K27me3 ChIPSeq


title: MS K9me2 ChIPSeq


title: EOS-labile-thymus_RRBS

city: Augusta

first: Huidong

state: GA

department: Georgia Cancer Center

institute: Augusta University

description: DNA methylation analysis using bisulfite sequencing

data_processing:
Base-calling: CASAVA version 1.8
Alignment: Bowtie
Sequence reads were trimmed for adaptor sequence and low-quality sequence in the both end.
- C->T converted sequence reads were mapped to C->T converted strands of mm9 genome using bowtie V0.12.7 with -n 2 -e 150 -k 10 --chunkmbs 250 --maxbts 800 --best -t -S
- For each read, the best alignment was chosen based on the number of mismatches
- Filtered out reads that were mapped to multiple locations
- Filtered out reads with percent identity of alignment < 95%
- For each CpG, methylation fraction (Beta value) was calculated by the number
Genome_build: mm9
Supplementary_files_format_and_content: bed files
The 7 columns in the bed file are:
1. Chromosome
2. Start
3. End
4. Number of reads
5. Methylation fraction
6. Strand direction
7. Number of methylated reads

source_name: EOS labile FoxP3+ T-cells

growth_protocol: Mouse spleen and thymus tissues were harvested and minced into small pieces. Treg cells were fragile during staining, and we found that it was important to disaggregate LNs rapidly (by passing once through a 40 um mesh) and stain quickly using short incubation times (10 min on ice). The stained cells were sorted immediately and proceeded for DNA isolation. At least 250,000 cells were sorted for the methylation analysis.

extract_protocol:
RRBS was performed according to a previously published protocol (Gu et al. 2010; Meissner et al. 2008) with minor modifications.
For each sample, 1 ug genomic DNA was first digested overnight using 20 units of MspI (New England Biolabs, NEB). The digested DNA was end-repaired and adenylated in a 20 ul reaction consisting of 10U of Klenow fragments (exo-, Enzymatics, MA, USA), and 2 ul premixed nucleotide triphosphates (1 mM dGTP, 10 mM dATP, 1 mM methylated dCTP). The reaction was incubated at 30 C for 30 min followed by 37 C for an additional 30 min. The methylated Illumina adapters were ligated with adenylated DNA fragments in a 20 ul reaction containing 1 ul concentrated T4 ligase (Enzymatics) at room temperature for 15 minutes. The ligation products were gel-selected for fragments with insertion sizes of 40 to 120 bp and 120 to 220 base pairs as previously suggested (Gu et al. 2010; Meissner et al. 2008).  Bisulfite treatment of the sequencing library was conducted using the EZ DNA methylation kit (Zymo Research, Irvine, CA) according to manufacturer's protocol. The final libraries were generated by PCR amplification of 5 um of bisulfite-converted template using PfuTurbo Cx Hotstart polymerase and Illumina pair-end PCR primers (PE1.0 and PE2.0).

treatment_protocol: No treatment involved.

value: Thymus

value: BAC-tg Foxp3/GFP-Cre (Bluestone)


title: EOS-stable-spleen_RRBS

source_name: EOS stable FoxP3+ T-cells

value: Spleen

value: Foxp3-GFP knock-in (Rudensky)


title: Non-Tregs_RRBS

source_name: Non-Treg T-cells


title: LP K27me3 ChIPSeq

value: virgin

value: Millipore


title: H3 ChIP-Seq Day2 rtta, rep1

first: Michael

last: Lodato

institute: Whitehead Institute

data_processing:
Images acquired from the Illumina/Solexa sequencer were processed using the bundled Solexa image extraction pipeline.
36 bp or 40 bp sequences were aligned using Bowtie software (PMID:19261174) using murine genome NCBI Build 36 (UCSC mm8) as the reference genome with default settings for mismatch tolerance, non-unique mapping events, etc.
Sequences were extended +200 bp for transcription factors and allocated in 25 bp bins (1.05x10^8 bins total). Statistically significant enriched bins were identified using a Poissonian background model, generally with a p-value threshold of 10-8 to minimize false positives. We used an empirical background model (whole cell extracts (WCE)) that require genomic bins to be enriched at least 5-fold above background to correct for non-random enrichment observed previously.
Genome_build: MGSCv36 (mm8)
Supplementary_files_format_and_content: Wig files. One track for each dataset reflects ChIP-Seq density across the genome in 25bp bins with a minimum cutoff of 0.1 reads per million. Another track depicts enriched regions for each dataset at a p-value threshold of 10-8.
Background for other samples.

source_name: Day2 differentiating rtta ESCs, H3 ChIP

growth_protocol: ESCs were grown under standard conditions in DMEM supplemented with 10% fetal bovine serum, LIF, glutamine, pen-strep, and beta-mercaptoethanol. NPCs were derived from these ESCs using an established protocol (PMID:8892235), then grown in N3 medium (see manuscript methods section). Day 2 differentiated cells were obtained from TetO-Brn2 and rtta ESCs plated in ESM with 2 ug/ml doxycycline, then 24 hours later the medium was switched to N2B27 plus doxycycline (see manuscript methods), and 48 hours after that cells were harvested for ChIP.

extract_protocol: For ESCs and Day 2 differentiating cells: Approximately 5x10^7 formaldehyde-crosslinked cells were lysed and as above on an IP-Star (Diagenode). Chromatin was sonicated on the Bioruptor (Diagenode) to an average size of 0.2-1 kb. ChIP was performed on chromatin from approximately 5 million cells with 3 μg of antibody (above) using the IP-Star Automated System (Diagenode), and 2.5% of chromatin was used for each whole cell extract (WCE). Following reversal of crosslinks, sample and WCE DNA was purified. ChIP DNA was dissolved in water and placed on the SPRI-TE (Beckman Coulter) for Illumina sample preparation. NPCs: ChIP-enriched and input DNA were purified and genomic libraries were prepared using the ChIP-Seq Sample Prep Kit (Illumina 1003473) according to the manufacturer's protocol (Illumina 11257047) for selecting library fragments between 200 and 350 bp.

value: C57BL/6:129 SvJae F1

value: Day2 differentiating rtta ESCs

tag: passage

tag: antibody vendor, catalog#

value: Abcam, ab1791


title: H3K27Ac ChIP-Seq Day2 rtta, rep1

data_processing:
The processed data for this sample is included in GSE35496_H3K27Ac_rtta_Day2_Wig_min0.1.WIG.gz
Images acquired from the Illumina/Solexa sequencer were processed using the bundled Solexa image extraction pipeline.
36 bp or 40 bp sequences were aligned using Bowtie software (PMID:19261174) using murine genome NCBI Build 36 (UCSC mm8) as the reference genome with default settings for mismatch tolerance, non-unique mapping events, etc.
Sequences were extended +200 bp for transcription factors and allocated in 25 bp bins (1.05x10^8 bins total). Statistically significant enriched bins were identified using a Poissonian background model, generally with a p-value threshold of 10-8 to minimize false positives. We used an empirical background model (whole cell extracts (WCE)) that require genomic bins to be enriched at least 5-fold above background to correct for non-random enrichment observed previously.
Genome_build: MGSCv36 (mm8)
Supplementary_files_format_and_content: Wig files. One track for each dataset reflects ChIP-Seq density across the genome in 25bp bins with a minimum cutoff of 0.1 reads per million. Another track depicts enriched regions for each dataset at a p-value threshold of 10-8.

source_name: Day2 differentiating rtta ESCs, H3K27Ac ChIP

tag: cell type

value: Abcam, ab4729


title: H3K27Ac ChIP-Seq Day2 rtta, rep2

data_processing:
Images acquired from the Illumina/Solexa sequencer were processed using the bundled Solexa image extraction pipeline.
36 bp or 40 bp sequences were aligned using Bowtie software (PMID:19261174) using murine genome NCBI Build 36 (UCSC mm8) as the reference genome with default settings for mismatch tolerance, non-unique mapping events, etc.
Sequences were extended +200 bp for transcription factors and allocated in 25 bp bins (1.05x10^8 bins total). Statistically significant enriched bins were identified using a Poissonian background model, generally with a p-value threshold of 10-8 to minimize false positives. We used an empirical background model (whole cell extracts (WCE)) that require genomic bins to be enriched at least 5-fold above background to correct for non-random enrichment observed previously.
Genome_build: MGSCv36 (mm8)
Supplementary_files_format_and_content: Wig files. One track for each dataset reflects ChIP-Seq density across the genome in 25bp bins with a minimum cutoff of 0.1 reads per million. Another track depicts enriched regions for each dataset at a p-value threshold of 10-8.
The processed data for this sample is included in GSE35496_H3K27Ac_rtta_Day2_Wig_min0.1.WIG.gz, which is linked to the Series GSE35496 record as a supplementary file.


title: H3K4me1 ChIP-Seq Day2 rtta

data_processing:
Images acquired from the Illumina/Solexa sequencer were processed using the bundled Solexa image extraction pipeline.
36 bp or 40 bp sequences were aligned using Bowtie software (PMID:19261174) using murine genome NCBI Build 36 (UCSC mm8) as the reference genome with default settings for mismatch tolerance, non-unique mapping events, etc.
Sequences were extended +200 bp for transcription factors and allocated in 25 bp bins (1.05x10^8 bins total). Statistically significant enriched bins were identified using a Poissonian background model, generally with a p-value threshold of 10-8 to minimize false positives. We used an empirical background model (whole cell extracts (WCE)) that require genomic bins to be enriched at least 5-fold above background to correct for non-random enrichment observed previously.
Genome_build: MGSCv36 (mm8)
Supplementary_files_format_and_content: Wig files. One track for each dataset reflects ChIP-Seq density across the genome in 25bp bins with a minimum cutoff of 0.1 reads per million. Another track depicts enriched regions for each dataset at a p-value threshold of 10-8.
The processed data for this sample is included in GSE35496_H3K4me1_rtta_Day2_Wig_min0.1.WIG.gz, which is linked to the Series GSE35496 record as a supplementary file.

source_name: Day2 differentiating rtta ESCs, H3K4me1 ChIP

value: Abcam, ab8895


title: H3 ChIP-Seq Day2 rtta, rep2


title: H3 ChIP-Seq Day2 TetoBrn2, rep1

source_name: Day2 differentiating Teto-Brn2 ESCs, H3 ChIP

value: Day2 differentiating Teto-Brn2 ESCs


title: H3 ChIP-Seq Day2 TetoBrn2, rep2


title: H3K27Ac ChIP-Seq Day2 TetoBrn2, rep2

data_processing:
Images acquired from the Illumina/Solexa sequencer were processed using the bundled Solexa image extraction pipeline.
36 bp or 40 bp sequences were aligned using Bowtie software (PMID:19261174) using murine genome NCBI Build 36 (UCSC mm8) as the reference genome with default settings for mismatch tolerance, non-unique mapping events, etc.
Sequences were extended +200 bp for transcription factors and allocated in 25 bp bins (1.05x10^8 bins total). Statistically significant enriched bins were identified using a Poissonian background model, generally with a p-value threshold of 10-8 to minimize false positives. We used an empirical background model (whole cell extracts (WCE)) that require genomic bins to be enriched at least 5-fold above background to correct for non-random enrichment observed previously.
Genome_build: MGSCv36 (mm8)
Supplementary_files_format_and_content: Wig files. One track for each dataset reflects ChIP-Seq density across the genome in 25bp bins with a minimum cutoff of 0.1 reads per million. Another track depicts enriched regions for each dataset at a p-value threshold of 10-8.
The processed data for this sample is included in GSE35496_H3K27Ac_TetOBrn2_Day2_Wig_min0.1.WIG.gz, which is linked to the Series GSE35496 record as a supplementary file.

source_name: Day2 differentiating Teto-Brn2 ESCs, H3K27Ac ChIP


title: MS Input DNA ChIPSeq rep1

value: Mammary stem cells


title: ML K9me2 ChIPSeq

value: Mature luminal cells

value: Histone H3 dimethyl Lys9


title: H3K4me1 ChIP-Seq Day2 TetoBrn2

data_processing:
Images acquired from the Illumina/Solexa sequencer were processed using the bundled Solexa image extraction pipeline.
36 bp or 40 bp sequences were aligned using Bowtie software (PMID:19261174) using murine genome NCBI Build 36 (UCSC mm8) as the reference genome with default settings for mismatch tolerance, non-unique mapping events, etc.
Sequences were extended +200 bp for transcription factors and allocated in 25 bp bins (1.05x10^8 bins total). Statistically significant enriched bins were identified using a Poissonian background model, generally with a p-value threshold of 10-8 to minimize false positives. We used an empirical background model (whole cell extracts (WCE)) that require genomic bins to be enriched at least 5-fold above background to correct for non-random enrichment observed previously.
Genome_build: MGSCv36 (mm8)
Supplementary_files_format_and_content: Wig files. One track for each dataset reflects ChIP-Seq density across the genome in 25bp bins with a minimum cutoff of 0.1 reads per million. Another track depicts enriched regions for each dataset at a p-value threshold of 10-8.
The processed data for this sample is included in GSE35496_H3K4me1_TetOBrn2_Day2_Wig_min0.1.WIG.gz, which is linked to the Series GSE35496 record as a supplementary file.

source_name: Day2 differentiating Teto-Brn2 ESCs, H3K4me1 ChIP


title: ML Input DNA ChIPSeq

value: FVB/N


title: EOS-labile-spleen_RRBS

tag: genotype/variation


title: Sox2 ChIP-Seq Day2 TetoBrn2, rep2

data_processing:
Images acquired from the Illumina/Solexa sequencer were processed using the bundled Solexa image extraction pipeline.
36 bp or 40 bp sequences were aligned using Bowtie software (PMID:19261174) using murine genome NCBI Build 36 (UCSC mm8) as the reference genome with default settings for mismatch tolerance, non-unique mapping events, etc.
Sequences were extended +200 bp for transcription factors and allocated in 25 bp bins (1.05x10^8 bins total). Statistically significant enriched bins were identified using a Poissonian background model, generally with a p-value threshold of 10-8 to minimize false positives. We used an empirical background model (whole cell extracts (WCE)) that require genomic bins to be enriched at least 5-fold above background to correct for non-random enrichment observed previously.
Genome_build: MGSCv36 (mm8)
Supplementary_files_format_and_content: Wig files. One track for each dataset reflects ChIP-Seq density across the genome in 25bp bins with a minimum cutoff of 0.1 reads per million. Another track depicts enriched regions for each dataset at a p-value threshold of 10-8.
The processed data for this sample is included in GSE35496_Sox2_TetOBrn2_Day2_Wig_min0.1.WIG.gz, which is linked to the Series GSE35496 record as a supplementary file.

source_name: Day2 differentiating Teto-Brn2 ESCs, Sox2 ChIP

value: R & D Systems (R&D), AF2018


title: Day2 TetoBrn2 WCE Seq, rep2

data_processing:
Images acquired from the Illumina/Solexa sequencer were processed using the bundled Solexa image extraction pipeline.
36 bp or 40 bp sequences were aligned using Bowtie software (PMID:19261174) using murine genome NCBI Build 36 (UCSC mm8) as the reference genome with default settings for mismatch tolerance, non-unique mapping events, etc.
Sequences were extended +200 bp for transcription factors and allocated in 25 bp bins (1.05x10^8 bins total). Statistically significant enriched bins were identified using a Poissonian background model, generally with a p-value threshold of 10-8 to minimize false positives. We used an empirical background model (whole cell extracts (WCE)) that require genomic bins to be enriched at least 5-fold above background to correct for non-random enrichment observed previously.
Genome_build: MGSCv36 (mm8)
Supplementary_files_format_and_content: Wig files. One track for each dataset reflects ChIP-Seq density across the genome in 25bp bins with a minimum cutoff of 0.1 reads per million. Another track depicts enriched regions for each dataset at a p-value threshold of 10-8.
Input sample.

source_name: Day2 differentiating Teto-Brn2 ESCs, WCE


title: Brn2 ChIP-Seq Day2 rtta, rep2

data_processing:
Images acquired from the Illumina/Solexa sequencer were processed using the bundled Solexa image extraction pipeline.
36 bp or 40 bp sequences were aligned using Bowtie software (PMID:19261174) using murine genome NCBI Build 36 (UCSC mm8) as the reference genome with default settings for mismatch tolerance, non-unique mapping events, etc.
Sequences were extended +200 bp for transcription factors and allocated in 25 bp bins (1.05x10^8 bins total). Statistically significant enriched bins were identified using a Poissonian background model, generally with a p-value threshold of 10-8 to minimize false positives. We used an empirical background model (whole cell extracts (WCE)) that require genomic bins to be enriched at least 5-fold above background to correct for non-random enrichment observed previously.
Genome_build: MGSCv36 (mm8)
Supplementary_files_format_and_content: Wig files. One track for each dataset reflects ChIP-Seq density across the genome in 25bp bins with a minimum cutoff of 0.1 reads per million. Another track depicts enriched regions for each dataset at a p-value threshold of 10-8.
The processed data for this sample is included in GSE35496_Brn2_rtta_Day2_Wig_min0.1.WIG.gz, which is linked to the Series GSE35496 record as a supplementary file.

source_name: Day2 differentiating rtta ESCs, Brn2 ChIP

value: Santa Cruz, SC-6029


title: Brn2 ChIP-Seq Day2 rtta, rep1


title: Brn2 ChIP-Seq Day2 TetoBrn2, rep1

data_processing:
Images acquired from the Illumina/Solexa sequencer were processed using the bundled Solexa image extraction pipeline.
36 bp or 40 bp sequences were aligned using Bowtie software (PMID:19261174) using murine genome NCBI Build 36 (UCSC mm8) as the reference genome with default settings for mismatch tolerance, non-unique mapping events, etc.
Sequences were extended +200 bp for transcription factors and allocated in 25 bp bins (1.05x10^8 bins total). Statistically significant enriched bins were identified using a Poissonian background model, generally with a p-value threshold of 10-8 to minimize false positives. We used an empirical background model (whole cell extracts (WCE)) that require genomic bins to be enriched at least 5-fold above background to correct for non-random enrichment observed previously.
Genome_build: MGSCv36 (mm8)
Supplementary_files_format_and_content: Wig files. One track for each dataset reflects ChIP-Seq density across the genome in 25bp bins with a minimum cutoff of 0.1 reads per million. Another track depicts enriched regions for each dataset at a p-value threshold of 10-8.
The processed data for this sample is included in GSE35496_Brn2_TetOBrn2_Day2_Wig_min0.1.WIG.gz, which is linked to the Series GSE35496 record as a supplementary file.

source_name: Day2 differentiating Teto-Brn2 ESCs, Brn2 ChIP


title: Sox2 ChIP-Seq Day2 TetoBrn2, rep1


title: Day2 rtta WCE Seq, rep2

source_name: Day2 differentiating rtta ESCs, WCE


title: Sox2 ESC ChIP-Seq

data_processing:
Images acquired from the Illumina/Solexa sequencer were processed using the bundled Solexa image extraction pipeline.
36 bp or 40 bp sequences were aligned using Bowtie software (PMID:19261174) using murine genome NCBI Build 36 (UCSC mm8) as the reference genome with default settings for mismatch tolerance, non-unique mapping events, etc.
Sequences were extended +200 bp for transcription factors and allocated in 25 bp bins (1.05x10^8 bins total). Statistically significant enriched bins were identified using a Poissonian background model, generally with a p-value threshold of 10-8 to minimize false positives. We used an empirical background model (whole cell extracts (WCE)) that require genomic bins to be enriched at least 5-fold above background to correct for non-random enrichment observed previously.
Genome_build: MGSCv36 (mm8)
Supplementary_files_format_and_content: Wig files. One track for each dataset reflects ChIP-Seq density across the genome in 25bp bins with a minimum cutoff of 0.1 reads per million. Another track depicts enriched regions for each dataset at a p-value threshold of 10-8.
The processed data for this sample is included in GSE35496_Sox2_ESC_Wig_min0.1.WIG.gz, which is linked to the Series GSE35496 record as a supplementary file.

source_name: Embryonic stem cells, Sox2 ChIP

value: embryonic stem cells (ESCs)


title: ESC WCE Seq, rep2

source_name: Embryonic stem cells, WCE


title: ESC WCE Seq, rep1


title: EOS-stable-thymus_RRBS

value: Thymus

value: BAC-tg Foxp3/GFP-Cre (Bluestone)


title: Sox2 NPC ChIP-Seq, rep2

data_processing:
Images acquired from the Illumina/Solexa sequencer were processed using the bundled Solexa image extraction pipeline.
36 bp or 40 bp sequences were aligned using Bowtie software (PMID:19261174) using murine genome NCBI Build 36 (UCSC mm8) as the reference genome with default settings for mismatch tolerance, non-unique mapping events, etc.
Sequences were extended +200 bp for transcription factors and allocated in 25 bp bins (1.05x10^8 bins total). Statistically significant enriched bins were identified using a Poissonian background model, generally with a p-value threshold of 10-8 to minimize false positives. We used an empirical background model (whole cell extracts (WCE)) that require genomic bins to be enriched at least 5-fold above background to correct for non-random enrichment observed previously.
Genome_build: MGSCv36 (mm8)
Supplementary_files_format_and_content: Wig files. One track for each dataset reflects ChIP-Seq density across the genome in 25bp bins with a minimum cutoff of 0.1 reads per million. Another track depicts enriched regions for each dataset at a p-value threshold of 10-8.
The processed data for this sample is included in GSE35496_Sox2_NPC_Wig_min0.1.WIG.gz, which is linked to the Series GSE35496 record as a supplementary file.

source_name: ES-derived neural progenitor cells, Sox2 ChIP

value: ES-derived neural progenitor cells (NPCs)


title: Sox2 NPC ChIP-Seq, rep1


title: Kdm2b_Ctrl

city: Boston

last: Shen

address: 200 Longwood Ave

institute: HHMI/Boston Children's Hospital/Harvard Medical School

description: Kdm2b ChIP-seq was done by Flag antibody because we knocked in a Flag tag upstream of Kdm2b gene.

data_processing:
Basecalls were performed using CASAVA version v.1.8.2
Sequenced reads were de-multiplexed, trimmed and mapped to mm8 whole genome using bowtie v0.12.7
Peak calling were performed using MACS 1.4.1, meanwhile, wiggle files were generated
Genome_build: mm8
Supplementary_files_format_and_content: wiggle files (scores represent tag numbers per 10 million reads)

source_name: Control mouse ES cells

growth_protocol: E14 mESCs are cultured on the 0.1% gelatin coated plates in the DMEM medium (Sigma) supplemented with 100U/ml penicillin/streptomycin, 15% fetal bovine serum (Sigma), 1x nonessential amino acid, 1x sodium pyruvate, 1x GlutaMax, 1x beta-mercaptoethanol (Invitrogen) and 1000 units/ml leukemia inhibitory factor (ESGRO, EMD Millipore).

extract_protocol: Libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (NEB) following manufacture's instructions.

treatment_protocol: Around 1x10^5 ES cells/well in 24-well plates are infected with lentiviral vectors at 10 MOI. 48 hours after transduction, puromycin (2ug/ml) is added to the medium for selecting transduced cells.

value: Flag

tag: antibody manufacturer

value: Sigma

tag: antibody catalog number

tag: antibody lot number

value: inbred 129

tag: cell line

value: embryonbic stem cells

tag: genotype

value: Control


title: IgG_Ctrl

value: IgG


title: IgG_Kdm2bKD

source_name: Kdm2b knockdown mouse ES cells

value: Kdm2b knockdown


title: Ezh2_Kdm2bKD

value: Cell signaling Technology


title: Brn2 ChIP-Seq Day2 TetoBrn2, rep2

value: C57BL/6:129 SvJae F1

value: Day2 differentiating Teto-Brn2 ESCs


title: H3K27Ac ChIP-Seq Day2 TetoBrn2, rep1

value: Abcam, ab4729


title: Brn2 NPC ChIP-Seq, rep1

data_processing:
Images acquired from the Illumina/Solexa sequencer were processed using the bundled Solexa image extraction pipeline.
36 bp or 40 bp sequences were aligned using Bowtie software (PMID:19261174) using murine genome NCBI Build 36 (UCSC mm8) as the reference genome with default settings for mismatch tolerance, non-unique mapping events, etc.
Sequences were extended +200 bp for transcription factors and allocated in 25 bp bins (1.05x10^8 bins total). Statistically significant enriched bins were identified using a Poissonian background model, generally with a p-value threshold of 10-8 to minimize false positives. We used an empirical background model (whole cell extracts (WCE)) that require genomic bins to be enriched at least 5-fold above background to correct for non-random enrichment observed previously.
Genome_build: MGSCv36 (mm8)
Supplementary_files_format_and_content: Wig files. One track for each dataset reflects ChIP-Seq density across the genome in 25bp bins with a minimum cutoff of 0.1 reads per million. Another track depicts enriched regions for each dataset at a p-value threshold of 10-8.
The processed data for this sample is included in GSE35496_Brn2_NPC_Wig_min0.1.WIG.gz, which is linked to the Series GSE35496 record as a supplementary file.

source_name: ES-derived neural progenitor cells, Brn2 ChIP


title: Day2 rtta WCE Seq, rep1

value: Day2 differentiating rtta ESCs


title: Sox2 ChIP-Seq Day2 rtta, rep2

data_processing:
Images acquired from the Illumina/Solexa sequencer were processed using the bundled Solexa image extraction pipeline.
36 bp or 40 bp sequences were aligned using Bowtie software (PMID:19261174) using murine genome NCBI Build 36 (UCSC mm8) as the reference genome with default settings for mismatch tolerance, non-unique mapping events, etc.
Sequences were extended +200 bp for transcription factors and allocated in 25 bp bins (1.05x10^8 bins total). Statistically significant enriched bins were identified using a Poissonian background model, generally with a p-value threshold of 10-8 to minimize false positives. We used an empirical background model (whole cell extracts (WCE)) that require genomic bins to be enriched at least 5-fold above background to correct for non-random enrichment observed previously.
Genome_build: MGSCv36 (mm8)
Supplementary_files_format_and_content: Wig files. One track for each dataset reflects ChIP-Seq density across the genome in 25bp bins with a minimum cutoff of 0.1 reads per million. Another track depicts enriched regions for each dataset at a p-value threshold of 10-8.
The processed data for this sample is included in GSE35496_Sox2_rtta_Day2_Wig_min0.1.WIG.gz, which is linked to the Series GSE35496 record as a supplementary file.

source_name: Day2 differentiating rtta ESCs, Sox2 ChIP

value: R & D Systems (R&D), AF2018


title: Brn2 NPC ChIP-Seq, rep2

value: Santa Cruz, SC-6029


title: Ring1b_Ctrl


title: NPC WCE Seq

source_name: ES-derived neural progenitor cells, WCE


title: Sox2 ChIP-Seq Day2 rtta, rep1


title: C. elegans_degradome_12.03.2007

status: Public on Feb 19 2013

city: SEOUL

first: Chanseok

last: Shin

address: Gwanak-gu Daehak-dong

institute: Seoul National University

data_processing:
7.6 million of 20-nt tags from wild-type adult cleavage libraries were mapped to the C. elegans genome (ce6), requiring a perfect match.
For tags mapped to at most 10 genomic loci, the final tag number was normalized with the loci number.
Of genome-mapping tags, ~70% mapped to exons of annotated genes (RefSeq with new 3′UTR annotations), including rRNAs, ~25% mapped to intergenic regions, ~3% mapped to intronic regions of genes, and 0.5% mapped antisense to annotated genes.
Genome_build: C. elegans genome (ce6)

organism: Caenorhabditis elegans

source_name: Whole organ

extract_protocol:
Worms were harvested at the appropriate stage, washed twice with M9 buffer, and frozen in liquid nitrogen. Total RNA was extracted using Tri-Reagent (Ambion), which was further purified with phenol:chloroform followed by precipitation with ethanol.
Poly(A) RNA was enriched from wild-type adult C. elegans total RNA using the Oligotex mRNA kit (QIAGEN). A custom 5' RNA adapter containing a MmeI recognition site was ligated to the poly(A) RNA possessing a 5'-monophosphate, by T4 RNA ligase, and the ligated products were reverse transcribed. This cDNA was amplified and then digested with restriction enzyme MmeI, which cleaves 20 nts 3’ of the recognition site. This MmeI digested product was ligated to a 3’ double strand adaptor, amplified by PCR, gel-purified and submitted for Illumina sequencing.

value: Wild-type (N2)

value: Adult stage


title: C. elegans_degradome_01.08.2008


title: RN2/shRnf20.3277

city: Cold Spring Harbor

first: Shinpei

last: Kawaoka

address: 1 Bungtown road

institute: Cold Spring Harbor Laboratory

data_processing:
FastaX-trimmer was used for removing adaptor sequences
The trimmed reads were mapped to mouse genome (mm9) using bowtie
Cufflinks software was used to compare gene expression profiles between shRen.713-treated cells and shRNF20 shRNAs-treated cells
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

growth_protocol: The Tet-on-competent leukemia cells (RN2) were cultured in RPMI1640 media supplemented with 10%FBS and 1%P/S

extract_protocol:
Total RNAs were extracted using Trizol reagent.
"Not so random" primer-based RNA-seq libraries were constructed as described previously (Armour et al. 2009 Nature Methods)

treatment_protocol: RN2 cells harboring a Doxyclycline-inducible shRNA (shRen.713/shRNF20.3277/shRNF20.3595) were treated with doxycycline for 4 days and harvested.

value: Acute myeloid leukemia


title: Day2 TetoBrn2 WCE Seq, rep1