title: LNCaP_H3K36me3_T00_ChIPSeq


title: Wild-type cells_rep2

status: Public on Jun 03 2012

type: SRA

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

library_source: transcriptomic

data_processing:
HCS v1.5.15.1
Reads were mapped to the Dictyostelium discoideum reference transcriptome downloaded from dictyBase (http://dictybase.org/; version: 2012-Jan-10) using the ELANDv2e (CASAVA v1.8)
RPKM values were calculated based on ELAND mapping output
Genome_build: http://dictybase.org/; version: 2012-Jan-10
Supplementary_files_format_and_content: txt format, RPKMs of all samples

molecule: polyA RNA

organism: Dictyostelium discoideum

source_name: Wild-type cells

growth_protocol: Cells grown in liquid medium (HL-5)

extract_protocol: Samples were processed using Illumina’s TruSeq™ RNA Sample Prep Kit v2 following the manufacturer’s instructions (RS-122-2001/2002)

treatment_protocol: Cells stored as dry pellets frozen at -80°C until RNA preparation

tag: strain

tag: genotype/variation

value: wild type


title: SMC1_ChIPSeq

status: Public on Jun 02 2012

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

country: USA

institute: The Wistar Institute

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: BCBL1 pleural effusion lymphoma, SMC1 ChIP

growth_protocol: BCBL1 cells were grown to 1x10^6 cells/ml in RPMI with 10% FBS supplemented with Glutamax and Penn/Strep.

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

treatment_protocol: According to the publication "Chromatin immunoprecipitation and microarray-based analysis of protein location" from the Natural Protocol (PMID 17406303).

tag: cell line

tag: cell type

value: KSHV-infected pleural effusion lymphoma cells

tag: chip antibody

value: rabbit anti-SMC1

tag: antibody vendor

value: Bethyl

tag: antibody catalog #

tag: antibody lot#


title: LNCaP_Input_ChIPSeq

city: Lebanon

first: xiaoyang

last: zhang

address: 1 Medical Center Driver

institute: Dartmouth Medical School

data_processing: Alignment: Sequence reads were obtained and mapped to the human (Feburary, 2009) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.

source_name: Prostate Cancer Cell Line

growth_protocol: LNCaP cells were maintained in RPMI (Invitrogen) supplemented with 10% FBS

extract_protocol: Library preparation for next-generation sequencing was performed according to manufacturer’s instruction starting with 5 ng of material (Illumina Inc.).

tag: antibody

value: LNCap

tag: treatment


title: Ezh2 RIP-deeper-seq biological replicate

city: Boston

first: Mark

middle: L

last: Borowsky

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: MGH

description: 2 lanes of sequence data from the biological replicate GSM489991

data_processing:
Image processing and base calling were performed using the Illumina RTA pipeline.
Preprocessing: 3' adapter sequences were identified using cross_match and trimmed if a match of at least 5 bp was found.  Reads matching mtDNA or rRNA sequences, reads < 12 bp long, reads containing N's, and homopolymer reads were removed.  Alignment: reads were aligned to the mouse genome (mm9) using shortQueryLookup with a maximum of 1 error and no indels.   Frequencies of unique reads were then tabulated.
the 's.WT.BR.uniq.noribo.nohomop.tsv.gz' processed data file is derived from two Ezh2 RIP-deeper sequencing samples, and available on a Series records
Genome_build: mm9
Supplementary_files_format_and_content: Frequencies of unique reads

molecule: total RNA

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: mouse embryonic stem cells were routinely grown and maintained in T25 or T75 flasks with LIF supplemented in the culture medium.

extract_protocol: Cell nuclei were isolated, nuclear lysate was prepared and incubated with an anti-Ezh2 antibody. Afterwards, the RNA-protein complexes were immunoprecipitated with protein A agarose beads and the RNA fraction was extracted using Trizol reagent. Template switching method was used for the library construction per manufacturer's recommendation (Clontech's SMART cDNA Library Construction Manual).

value: 129X (M.castaneusX129)

value: embryonic stem cells

tag: rip antibody

value: anti-Ezh2 antibody


title: CTCF_ChIPSeq

description: CTCF

source_name: BCBL1 pleural effusion lymphoma, CTCF ChIP

value: rabbit anti-CTCF

value: Millipore


title: Ezh2 RIP-deeper-seq

description: 2 lanes of deeper sequencing from the original sample GSM426848


title: Hematopoietic Stem Cell supernatant

status: Public on Jun 01 2012

city: Bethesda

first: Jens

last: Lichtenberg

state: MD

address: 49 Convent Dr 3A19

department: National Human Genome Research Institute

institute: National Institutes of Health

description: MBD2 Pulldown

data_processing:
Sequenced reads were mapped to the mouse genome using the Eland short-read alignment program
Peaks for each cell-type were called using MACS, version 1.4, with a p-value threshold of p<10-5
Genome_build: UCSC assembly mm9, NCBI build 37
Supplementary_files_format_and_content: BED files were automatically generated by MACS, version 1.4

source_name: Hematopoietic Stem Cell

growth_protocol: Hematopoietic stem cells and common myeloid progenitor cells were harvested from adult female C57BL/6 bone marrow.

extract_protocol: Between 225 ng-540 ng of MBD2-enriched DNA and 1 ug of supernatant for each cell type were used to construct DNA libraries according to the Illumina protocol. The libraries were sequenced on the Illumina Genome Analyzer platform and 36 bp single-end reads were used to uniquely identify the MBD2-bound fraction of the mouse genome.

treatment_protocol: After lysis of red cells in ACK lysing buffer (BioWhittaker®), approximately 109 cells were subjected to lineage depletion using the following rat anti-mouse antibodies: CD8a, CD4, CD11b, Ly-6G/Ly-6C, CD45R, and Ter119 (BD biosciences). Lineage negative cells (lin-) were stained with PE anti-mouse Sca1(clone D7) and APC anti-mouse CD117 (clone 2B8; BD biosciences). Lin- Sca-1+ c-kit+ (HSC; 1-2% of lineage depleted cells) and in- Sca-1- c-kit+ (CMP ;10% of lineage depleted cells) were sorted on a BD FACS Aria instrument.

value: Hematopoietic Stem Cell

tag: genetic background

tag: gender

value: female

value: supernatant


title: Erythroblast MBD2-enriched

description: MBD2 Pulldown

source_name: Erythroblast

value: Erythroblast


title: Common Myeloid Progenitor supernatant

description: MBD2 Pulldown

source_name: Common Myeloid Progenitor

value: Common Myeloid Progenitor


title: Erythroblast supernatant

description: MBD2 Pulldown


title: CbfA mutant expressing DdCbfA-CTD_rep3

source_name: CbfA mutant expressing DdCbfA-CTD

value: CbfA mutant expressing D. discoideum CbfA-CTD


title: E10.5 Atria Tag-Seq

city: Vancouver

first: Pamela

last: Hoodless

state: BC

address: 675 W 10th Ave

department: Terry Fox Laboratory

country: Canada

institute: BC Cancer Agency - Research Centre

description: Tag-Seq

data_processing:
After excision & purification, DNA was run on the Illumina cluster station & analyzer following the manufacturer's instructions.
Sequences were extracted using Bustard 1.8.28 & processed with ELAND.
Quality control was done using the Chastity filter of 0.6 from Illumina.
Tags were truncated to the first 17bp of each read
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include tag and tag count

source_name: E10.5 Atria

growth_protocol: E10.5 embryos were collected and the hearts were manually dissected with 30½G needles to isolate the various regions of the heart. At least 3 litters were pooled in Trizol to obtain at least 400ng of total RNA for Tag-seq library construction. After isolation, RNA quality was assessed using an Agilent Bioanalyzer and the RNA was stored at −80 °C until Tag-seq library construction

extract_protocol: At least 400ng of Dnase I-treated total RNA was used for library construction. As per published protocols, cDNA that was synthesized using oligo(dT) beads was digested with NlaIII and then ligated to an Illumina specific adapter containing the MmeI recognition sequence. Following digestion, a second Illumina adapter was added that contained a 2bp degenerate 3' overhang. The adapters were used to amplify by PCR and the products were run on a 12% PAGE gel.

tag: tissue

value: Atria

tag: developmental stage

value: Embryonic day 10.5; Theiler Stage 17

tag: genotype


title: Common Myeloid Progenitor MBD2-enriched

description: MBD2 Pulldown


title: E10.5 AVC Twist1 KO Tag-Seq

description: Tag-Seq

source_name: E10.5 AVC Twist1 KO

value: ICR

value: Atrioventricular Canal

value: Twist1 Knockout


title: Wild-type cells_rep3

value: wild type


title: E10.5 AVC Tag-Seq

description: Tag-Seq

source_name: E10.5 AVC


title: E10.5 Vent Tag-Seq

description: Tag-Seq

source_name: E10.5 Vent

value: Ventricles


title: Stem Cell Progeny

city: Portland

first: Bret

last: Pearson

state: OR

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

institute: Oregon Health and Science University

data_processing:
Base calls were made using the Illumina pipeline v. 1.6 for Illumina GAIIx and v. OLB 1.9 for HiSeq2000
All RNAseq was pooled and a de novo transcriptome was made using the program Trinity with default settings.
BPKG_transcriptome was deposited into NCBI TSA database as reference number:  SUB086338; BioProject ID: PRJNA163163
Genome_build: BPKG_transcriptome.nt
Supplementary_files_format_and_content: RPKM quantification for all 3 cellular compartments used in this study, as well as top-hit BLAST annotation to mouse homologs.

organism: Schmidtea mediterranea

source_name: FACS purified X2s

growth_protocol: The clonal strain of Schmidtea mediterranea, CIW4, was grown in a milli-Q-based salt solution on beef liver.  Organisms were starved for 1 week, then processed for FACS purification.

extract_protocol: All 3 tissue samples were RNA extracted in Trizol reagent, and RNA quality was analyzed on a bioanalyzer.  RNA samples were library prepped using Illumina's Truseq Library preps, which included polyA selection.

treatment_protocol: To FACS purify stem cells, animals were dounced in eppendorf tubes in cold Calcium, Magnesium-Free (CMF) media, and passed through a 20um filter.  Cells were incubated with 25ug/ml Hoechst 33342 for 30min, pelleted at 400g, resuspended in CMF, and sent through a BD FACSaria.  Cells were sorted by side scatter, forward scatter, then Hoechst red vs. Hoechst Blue.  High DNA-containing cells that were absent in the irradiated controls, were collected as the stem cell fraction.  The side population of low-DNA cells, which are stem cell progeny, were simultaneously collected in a separate tube.  Whole, 7-day lethally irradiated planarians were used as stem cell lineage negative, differentiated tissue samples.  Approximately 1.3 million cells, collected over 7 separate sorts, were pooled for each sample, and RNA extracted.

value: Stem cell progeny, X2s


title: Men1-KO PILECs, H3K4me3 ChIP

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

data_processing:
Sequenced 36-bp reads were aligned to the reference genome (mouse mm9 assembly) using Eland algorithm in Illumina Processing Pipeline. Those reads that mapped to unique genomic locations with at most two mismatches were retained for further analysis
Genome_build: mm9
Genome Build:
mm9-EB-MEN1-KO-H3K4me3.bed: mm9

source_name: 3.2N Menin-null Embryonic Stem Cells

growth_protocol: Wild-type mESCs (TC-1) and Men1-ko (menin-null) mESCs (3.2N) [14] were cultured on a feeder layer of IRR-STO irradiated primary MEFs (ATCC) in ESC maintenance medium containing Leukemia Inhibitory Factor (LIF). The mESCs were rendered feeder-free by several rounds of culturing for short periods of time (30 mins) on tissue culture treated dishes to get rid of the attached feeder layer cells, and the unattached mESCs were ultimately cultured on gelatin-coated dishes.

extract_protocol: Input and ChIP DNA were size-selected (~150-400nt) Libraries were prepared from size-selected Input and ChIP DNA (~150-400nt) according to the standard Illimina library preparation protocol

treatment_protocol: Wild-type mESCs and menin-null mESCs were differentiated into pancreatic islet-like endocrine cells (PILECs). Cells in culture dishes were cross-linked with 1% formaldehyde, and processed for chromatin lysate preparation, and chromatin immunoprecipitation (ChIP) using the ChIP assay kit (Millipore). Chromatin lysate was sonicated with a Bioruptor system (Diagenode) to yield a DNA smear averaging 250 bp. Sonicated chromatin lysate from 2 x 106 mESCs undifferentiated or differentiated was used for each ChIP with 5 µg antibody

tag: chip antibody manufacturer

value: Upstate

tag: chip antibody catalog #

tag: chip antibody lot #

value: ES cells were differentiated into pancreatic islet-like endocrine cells (PILECs)


title: Men1-KO PILECs, Control Input

data_processing:
Sequenced 36-bp reads were aligned to the reference genome (mouse mm9 assembly) using Eland algorithm in Illumina Processing Pipeline. Those reads that mapped to unique genomic locations with at most two mismatches were retained for further analysis
Genome_build: mm9
Genome Build:
mm9-EB-MEN1-KO-input.bed: mm9

value: input


title: WT ES cells, Control Input

data_processing:
Sequenced 36-bp reads were aligned to the reference genome (mouse mm9 assembly) using Eland algorithm in Illumina Processing Pipeline. Those reads that mapped to unique genomic locations with at most two mismatches were retained for further analysis
Genome_build: mm9
Genome Build:
mm9-ESC-WT-input.bed: mm9

source_name: TC1 Embryonic Stem Cells

value: Wild-type

value: ES cell


title: WT PILECs, H3K4me3 ChIP

data_processing:
Sequenced 36-bp reads were aligned to the reference genome (mouse mm9 assembly) using Eland algorithm in Illumina Processing Pipeline. Those reads that mapped to unique genomic locations with at most two mismatches were retained for further analysis
Genome_build: mm9
Genome Build:
mm9-EB-WT-H3K4me3.bed: mm9


title: Men1-KO ES cells, Control Input

data_processing:
Sequenced 36-bp reads were aligned to the reference genome (mouse mm9 assembly) using Eland algorithm in Illumina Processing Pipeline. Those reads that mapped to unique genomic locations with at most two mismatches were retained for further analysis
Genome_build: mm9
Genome Build:
mm9-ESC-MEN1-KO-input.bed: mm9


title: Men1-KO ES cells, H3K4me3 ChIP

data_processing:
Sequenced 36-bp reads were aligned to the reference genome (mouse mm9 assembly) using Eland algorithm in Illumina Processing Pipeline. Those reads that mapped to unique genomic locations with at most two mismatches were retained for further analysis
Genome_build: mm9
Genome Build:
mm9-ESC-MEN1-KO-H3K4me3.bed: mm9


title: WT PILECs, Control Input

data_processing:
Sequenced 36-bp reads were aligned to the reference genome (mouse mm9 assembly) using Eland algorithm in Illumina Processing Pipeline. Those reads that mapped to unique genomic locations with at most two mismatches were retained for further analysis
Genome_build: mm9
Genome Build:
mm9-EB-WT-input.bed: mm9


title: ChIP-Seq for Nipbl in hLCL

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: ChIP-Seq for Nipbl

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: Lymphoblastoid cells

growth_protocol: LCLs were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/ml, 100 µg streptomycin/ml sulfate, and 1% L-glutamine.

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

value: Nipbl

tag: antibody catalog number

value: Bethyl A301-779A


title: WT ES cells, H3K4me3 ChIP

data_processing:
Sequenced 36-bp reads were aligned to the reference genome (mouse mm9 assembly) using Eland algorithm in Illumina Processing Pipeline. Those reads that mapped to unique genomic locations with at most two mismatches were retained for further analysis
Genome_build: mm9
Genome Build:
mm9-ESC-WT-H3K4me3.bed: mm9

tag: cell type


title: ChIP-Seq for Smc1 in hLCL

description: ChIP-Seq for Smc1

tag: chip antibody

value: Bethyl A300-055A


title: RNAseq_4SU+6SG_UV

city: Berlin

first: Markus

last: Landthaler

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

institute: Max-Delbrück-Center for Molecular Medicine

data_processing:
We computed transcript abundance estimates (FPKM values) using cufflinks (version 1.03; (Trapnell et al., 2010)) with options --frag-bias-correct and --multi-read-correct.
Genome_build: hg18
Supplementary_files_format_and_content: .csv files contains FPKM values

source_name: HEK293 cell culture

growth_protocol: HEK293 cells were grown in DMEM

extract_protocol: Illumina RNAseq protocol

treatment_protocol: HEK293 cells were metabolically labeled with 4-thiourdine (4SU) anat a final concentration of 200 μM and 6-thioguanosine (6SG) at a final concentration of 200 μM and UV-crosslinked at 365 nm or untreated. mRNA was purified by oligo(dT) precipitation. . To monitor the incorporation of photoreactive nucleotides into mRNA, we isolated 4SU- and 6SG-labeled RNA from the oligo(dT) precipitate of non-crosslinked cells by biotinylation and streptavidin purification (Dolken et al., 2008).

value: 4SU+6SG labeling and UV

tag: purification

value: oligo(dT)


title: Hematopoietic Stem Cell MBD2-enriched

description: MBD2 Pulldown

value: Hematopoietic Stem Cell

value: female


title: F1DPI

city: Canberra

first: Stuart

last: Stephen

state: ACT

address: Black Mountain

department: Plant Industry

country: Australia

institute: CSIRO

description: rRNA depleted total RNA

data_processing:
F1DPI_TAIR10.bed; genome build: TAIR10
F1DPI_TAIR10_ROI.csv; genome build: TAIR10
RNA-seq reads were aligned to the TAIR10 Arabidopsis/Fusarium pseudo genome using the aligner Kanga. Alignment parameters were set to allow up to 5 aligner induced substitutions, microIndels up to 5 bp, splice junctions up to 10000 bp, and only accepting uniquely aligned reads which are at least one Hamming from any other putative alignment. Aligned reads were filtered and only those reads exclusively aligning to the TAIR10 Arabidopsis assembly were retained for subsequent processing. Retained Arabidopsis aligned reads were then mapped on to TAIR10 annotation loci for each individual class of annotation (protein-coding, psuedogene, transposon, miRNA, snoRNA, tRNA, ncRNA and geneid). The digital expression levels (RPKM, reads per kilobase of exon model per million mapped reads) of each annotated protein-coding gene were then calculated and used to identify differentially expressed genes in Fusarium oxysporum infected samples.)

organism: Arabidopsis thaliana

source_name: Fusarium oxysporum infected whole plants

growth_protocol: Plants were grown under 16h light.

extract_protocol: The libraries were constructed according to the procedures detailed in the SOLiDTM Whole Transcriptome Analysis Kit using 1 μg of RQ1 DNase-treated and rRNA-depleted (two rounds of depletion using the RiboMinusTM Plant Kit, Invitrogen) total RNA

treatment_protocol: Fusarium oxysporum inoculation was perfomed using root dipping with 2 week old seedlings

value: 2 week old seedling

tag: ecotype

value: whole plants

value: Fusarium oxysporum infected


title: F6DPI

description: rRNA depleted total RNA

data_processing:
F6DPI_TAIR10.bed; genome build: TAIR10
F6DPI_TAIR10_ROI.csv; genome build: TAIR10
RNA-seq reads were aligned to the TAIR10 Arabidopsis/Fusarium pseudo genome using the aligner Kanga. Alignment parameters were set to allow up to 5 aligner induced substitutions, microIndels up to 5 bp, splice junctions up to 10000 bp, and only accepting uniquely aligned reads which are at least one Hamming from any other putative alignment. Aligned reads were filtered and only those reads exclusively aligning to the TAIR10 Arabidopsis assembly were retained for subsequent processing. Retained Arabidopsis aligned reads were then mapped on to TAIR10 annotation loci for each individual class of annotation (protein-coding, psuedogene, transposon, miRNA, snoRNA, tRNA, ncRNA and geneid). The digital expression levels (RPKM, reads per kilobase of exon model per million mapped reads) of each annotated protein-coding gene were then calculated and used to identify differentially expressed genes in Fusarium oxysporum infected samples.)

value: 3 week old seedling


title: M6DPI

description: rRNA depleted total RNA

data_processing:
M6DPI_TAIR10.bed; genome build: TAIR10
M6DPI_TAIR10_ROI.csv; genome build: TAIR10
RNA-seq reads were aligned to the TAIR10 Arabidopsis/Fusarium pseudo genome using the aligner Kanga. Alignment parameters were set to allow up to 5 aligner induced substitutions, microIndels up to 5 bp, splice junctions up to 10000 bp, and only accepting uniquely aligned reads which are at least one Hamming from any other putative alignment. Aligned reads were filtered and only those reads exclusively aligning to the TAIR10 Arabidopsis assembly were retained for subsequent processing. Retained Arabidopsis aligned reads were then mapped on to TAIR10 annotation loci for each individual class of annotation (protein-coding, psuedogene, transposon, miRNA, snoRNA, tRNA, ncRNA and geneid). The digital expression levels (RPKM, reads per kilobase of exon model per million mapped reads) of each annotated protein-coding gene were then calculated and used to identify differentially expressed genes in Fusarium oxysporum infected samples.)

source_name: Mock treated whole plants

value: mock


title: RNAseq_4SU+6SG_purifiedRNA

value: 4SU+6SG labeling and biotin-purified


title: Seq WCE for hLCL

description: WCE for hLCL

value: None WCE


title: E10.5 OFT Tag-Seq

description: Tag-Seq

source_name: E10.5 OFT

tag: strain

value: Outflow tract

value: Embryonic day 10.5; Theiler Stage 17

value: wild type


title: RNAseq_4SU+6SG_noUV

value: 4SU+6SG labeling and no UV


title: Centenarian 2

city: Bronx

first: Saurabh

last: Gombar

state: NY

address: 1301 Morris Park Avenue

department: Systems and Computational Biology

institute: Albert Einstein College of Medicine

description: Small RNA sequencing

data_processing: Reads were trimmed of adapters using a C++ program and then aligned to mirBase using  bowtie.

source_name: Immortalized B-Cell

extract_protocol: Total RNA was extracted from lympocyte samples via trizol agent.  All samples were prepared according to Illumina Small RNA prep kit (FC-930-1004)

value: EBV transformed B-cell

tag: age

value: average is 104 y (centenarian)

tag: ethnicity

value: Ashkenazi Jew

tag: subject


title: Centenarian 3

description: Small RNA sequencing


title: Centenarian 1

description: Small RNA sequencing


title: Control 3

description: Small RNA sequencing

value: average is 63 y (young control)


title: Control 2

description: Small RNA sequencing


title: M1DPI

description: rRNA depleted total RNA

data_processing:
M1DPI_TAIR10.bed; genome build: TAIR10
M1DPI_TAIR10_ROI.csv; genome build: TAIR10
RNA-seq reads were aligned to the TAIR10 Arabidopsis/Fusarium pseudo genome using the aligner Kanga. Alignment parameters were set to allow up to 5 aligner induced substitutions, microIndels up to 5 bp, splice junctions up to 10000 bp, and only accepting uniquely aligned reads which are at least one Hamming from any other putative alignment. Aligned reads were filtered and only those reads exclusively aligning to the TAIR10 Arabidopsis assembly were retained for subsequent processing. Retained Arabidopsis aligned reads were then mapped on to TAIR10 annotation loci for each individual class of annotation (protein-coding, psuedogene, transposon, miRNA, snoRNA, tRNA, ncRNA and geneid). The digital expression levels (RPKM, reads per kilobase of exon model per million mapped reads) of each annotated protein-coding gene were then calculated and used to identify differentially expressed genes in Fusarium oxysporum infected samples.)

tag: treatment


title: MLLr_#1_Rep#1

city: New York

first: Altuna

last: Akalin

address: 1305 york

institute: Weill Cornell Medical College

description:
Flowcell: FC70904AAXX
Lanes: 2, 3, 5, 6

data_processing:
Reads were created by CASAVA 1.7 from the GA Iix and HiSeq2000, and these are all reads which pass filter
Reads were filtered from the adapter sequences using FAR software (Dodt, M,  Ahmed R, Dieterich C. FAR – flexible adapter remover. FAR project website (2011)( http://sourceforge.net/projects/theflexibleadap/). Reads were aligned to whole genome using the bismark(http://www.bioinformatics.babraham.ac.uk/projects/bismark/) alignment tool with a maximum of 2 mismatches in a directional manner and only uniquely aligning reads were retained. In order to call methylation score for a base position, we required that read bases aligning to that position have at least 20 phred quality score and the base position should have at least 10X coverage. Only CpG dinucleotides that satisfy these coverage and quality criteria were retained for subsequent analysis. *myCpG.txt files are constructed for each CpG position in the genome. The file contains location of the CpG, total read coverage on the C base, percentage of bisulfite converted Cs (representing unmethylated Cs) and non-converted Cs (representing methylated Cs). The pipeline that aligns and calls for methylation percentage per base is available at http://code.google.com/p/amp-errbs
Genome_build: hg18

source_name: MLL rearranged Acute Myeloid Leukemia patient sample

extract_protocol: DNA was extracted using Qiagen Puregene kit protocol; Library construction protocol: Genomic DNA was purified from cell lines and primary human samples, digested with MspI restriction enzyme (200U MspI per reaction), subjected to end repair and adenylation followed by ligation to cytosine methylated paired-end Illumina adaptors (2000U T4 DNA ligase per reaction). Fragments of 150-250 bp (reduced representation bisulfite sequencing) and 150-400 bp (for enhanced reduced representation bisulfite sequencing) were isolated after agarose gel electrophoresis and subjected to bisulfite conversion (single conversion round using Zymo Research EZ DNA Methylation Kit) and PCR amplification using paired-end Illumina primers (18 cycles).  Libraries were sequenced using an Illumina Genome Analyzer II or HiSeq2000 per manufacturer’s recommended protocol for 50bp single end read runs.

treatment_protocol: not applicable

tag: tissue type

value: bone marrow

value: MLL rearranged Acute Myeloid Leukemia


title: Control 1

description: Small RNA sequencing


title: AML_Rep#1

description:
Flowcell: FC61MRUAAXX and FC70904AAXX
Lanes: 6, 7, 8 and 1

source_name: Acute Myeloid Leukemia patient sample

value: Acute Myeloid Leukemia


title: MLLr_#1

description:
Flowcell: 70904AAXX
Lanes: 2, 3


title: NBM_#2_Rep#1

description:
Flowcell: FC70904AAXX and FC61MRUAAXX
Lanes: 7 and 2, 3, 5

source_name: CD34+ normal bone marrow control

value: CD34+ normal


title: HCT116 1µg

description:
Flowcell: FC61CM8AAXX and FC60003AAXX
Lanes: 1, 2, 3 and  1

source_name: Colon cancer derived cell line

value: HCT116 cell line

value: colon cancer


title: NBM_#2

description:
Flowcell: FC438V4AAXX and FC61MPJAAXX
Lanes: 1, 2, 3 and 8


title: HCT116 5ng_Rep#1

description:
Flowcell: FC61K96AAXX
Lanes: 1, 2, 3, 5


title: HCT116 5ng_Rep#2

description:
Flowcell: FC63577AAXX
Lanes: 5, 6, 7, 8


title: HCT116 50ng

description:
Flowcell: FC628YFAAXX
Lanes: 1, 2, 3, 5, 6, 7


title: ZN776

city: Notre Dame

first: Yunjuan

last: Bao

state: Indiana

address: 1234 Notre Dame Avenue

institute: University of Notre Dame

data_processing: Sequencing reads were mapped to human genome assembly (NCBI Build GRCh37.1) using CLC GenomicsWorkbench. Only sequencing reads with at most 2 mismatches and a maximum of 10 mappable locations were retained for calculation of gene expression. The gene expression level is measured by RPKM (number of exon reads mapped per kilobase per million mapped reads).

source_name: non-tumor

growth_protocol: Esophageal squamous cell carcinoma and adjacent non-tumorous tissues were obtained from patients immediately following resection, snapped-frozen in liquid nitrogen and stored in -80C freezer prior to RNA extraction.

extract_protocol: The total RNA samples were treated with DNA-free Kit (Ambion, Inc. TX, USA) to digest the DNA. Large 18S and 28S rRNAs were removed from 1Î¼g total RNA with the RiboMinusTM Transcriptome Isolation kit (Human/Mouse) (Invitrogen, Carlsbad, CA, USA). The rRNA-depleted RNA was precipitated with Pellet Paint (Novagen Inc., Madison, Wis.), quality checked on the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, Calif.). The rRNA-depleted RNA from 1 Âµg of total RNA was fragmented by incubation for 5 min at 94Â°C in 5 Ã Array Fragmentation Buffer (Ambion, Inc. TX, USA). The reaction was stop by chilling the tube on ice and precipitated with Pellet Paint. Double strand cDNA was synthesized with the SuperScript Double Stranded cDNA synthesis kit (Invitrogen, Carlsbad, CA, USA) using random hexamers according to the manufacturer's instructions. The reaction was cleaned up on a QiaQuick PCR column (Qiagen, Valencia, CA, USA). Ds cDNA fragments were repaired with DNA Terminator End Repair Kit End (Lucigen, Middleton, WI, USA) by incubation for 30 min at 30Â°C and then were cleaned up on a QiaQuick PCR column. The Klenow 3â to 5â exo- (NEB, Ipswich, MA) was used to add a single âAâ base to the 3âend of blunt phosphorylated DNA fragments by incubation for 30 min at 30Â°C. After clean-up on a QiaQuick PCR column, Illumina PE Adapter was ligated to the end of DNA fragments with the Quick Ligationâ¢ Kit (NEB, Ipswich, MA) by incubation for 15 min at room temperature. The reaction was cleaned up on a QiaQuick PCR column. 180-200 bp fragments were excised from a 2% low range agarose gel. Fragments were enriched by 10 cycles using AccuPrimeâ¢ Pfx DNA Polymerase (Invitrogen, Carlsbad, CA, USA). PCR product was run on Novex 8% TBE polyacrylamide gel (Invitrogen, Carlsbad, CA, USA) and stained with SYBR Gold (Invitrogen, Carlsbad, CA, USA). The gel slice was cut off and cleaned up by QiaQuick Gel Extraction Kit (Qiagen, Valencia, CA, USA). The concentration of gel purified DNA fragments was measured by using a ND-1000 UV/Vis spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA)

tag: sample id

value: esophageal

value: non-tumor


title: RNAseq_mRNA

value: no treatment (mRNA)

value: oligo(dT)


title: ZN779

source_name: tumor

value: tumor


title: ZN777


title: ZN778


title: ZN775


title: ZN633


title: rev

city: Frederiksberg C

first: Stephan

last: Wenkel

address: Thorvaldsensvej 40

country: Denmark

institute: University of Copenhagen

data_processing: Standard Illumina base calling software was used to base call the 40-42 nucleotide sequence reads. We used SHORE (http://shore.sourceforge.net) as a platform for further analysis. The obtained reads were quality filtered and low quality bases at the 3’ end were pruned as described. GenomeMapper (http://1001genomes.org/software/) was used for mapping to the TAIR9 genome, allowing for up to four mismatching nucleotides and no gaps. To proceed, the mapped data were subjected to a heuristic for removal of duplicate sequence reads which were assumed to be uninformative for the detection of enriched loci. A threshold was applied limiting the number of 5’ ends mapping to the same position on the same strand. To retain the power to discriminate between multiple strongly enriched regions, the threshold for any particular position was varied depending on the coverage in close vicinity, such that the variance of the number of reads per position would roughly equal its mean in a 30 bp sliding window. We further applied a two-step procedure to identify regions significantly enriched in the positive sample when compared to the control. First, potentially enriched regions were identified based on the positive samples only. These sites were then directly compared to the corresponding control sample regions to assess statistical significance. For estimation of the depth of coverage for each position in the genome, all positive sample reads mapping to unique positions were extended in 3’ direction to 130 bp, corresponding to half the experimentally observed approximate DNA fragment size, while discarding all other reads. To detect possible peak sites, a 2 kb wide sliding window was applied to the coverage graph in single base steps. In each step a p-value was assigned to the coverage value at the central base using a one-sided Poisson test, with the distribution parameter set to the average coverage within the sliding window. Only positions with coverage greater than zero were included in the calculation of the average, assuming all other positions to be inaccessible to the experiment. Finally, any consecutive stretch of positions with p-value <0.05 and length >130 bp was retained as a potentially enriched site. To further reduce the number of regions to be considered, each was checked for unwarranted high average coverage in the control sample. A potential peak in the positive sample was discarded if the coverage mean in the control sample in the corresponding region was larger than the median average control coverage plus a tolerance of three standard deviations in all peak regions. For assignment of final p-values to each candidate region, in each replicate a one-sided binomial test was applied to the number of reads mapping to the region in the positive sample, with the distribution parameter N set to the joint read count for the site for the positive and the corresponding control sample. To estimate the probability parameter for the test, from now on called r, we computed a scaling factor s for the control sample and the chromosome containing the considered region. The complete chromosome sequence was subdivided into 400 base pair bins, and for each bin the positive sample as well as the control sample read counts were recorded. Then s was chosen such that the median ChIP sample read count for all bins equaled the median control sample read count multiplied by s. From this the binomial test parameter r was calculated as r=s/(s+1). Finally, false discovery rates were obtained through the Benjamini-Hochberg correction method. To establish a ranking of peak regions across replicates, the rank product over the per-replicate fdr ranks was used. To define the bound DNA set, we used all peaks with fdr > 0.1 in both ChIP experiments, resulting in a set of 1564 peaks.

source_name: complete seedlings

growth_protocol: liquid culture

extract_protocol: Chromatin‐immunoprecipitation experiments were carried out as described by Kwon et al. (Kwon et al, 2005), except that anti‐FLAG M2 magnetic beads (Sigma) were used and immunoprecipitations were only performed for two hours. The ChIP‐seq libraries and the Illumina was performed as described by Yant et al. (Yant et al, 2010).

value: Col-0 transgene

tag: tissue

value: seedling

value: F3165 Sigma Monoclonal ANTI-FLAG M2


title: rev-ctrl


title: PARCLIP_ZC3H7B

description:
binding sites
barcode for 1_qseq.txt: TCTCACGTCGTATGCCGTCTTCTGCTTG
barcode for 2_qseq.txt: TCTCTGCTCGTATGCCGTCTTCTGCTTG

data_processing:
Adapters were removed with FAR 1.81 (the felxible adapter remover: http://sourceforge.net/projects/theflexibleadap/) aligned to hg18 and a set of RefSeq pre-mRNA sequences with BWA 0.5.8c.
Unique alignments were converted to a pileup and read clusters scored for characteristic conversions and read variability with a custom script.
After stringent-false positive filtering (using antisense clusters as a decoy database) remaining clusters were output as bed files. See Lebedeva et al. 2011 Mol Cell 43, 340–352 for details
Genome_build: hg18
Supplementary_files_format_and_content: bed file reporting binding sites

growth_protocol: HEK293 cells 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

extract_protocol: PAR-CLIP and small RNA cloning (Hafner et al. 2010 Cell 141, 129–141)

treatment_protocol: HEK293 cells stably expressing His/FLAG/HA-tagged proteins of interest were grown in medium supplemented with 4-thiouridine at a final concentration of 200 microM for 16 hour. Cells were UV-crosslinked at 365 nm.

tag: cell line

tag: cell line stably expressing

value: HIS/FLAG/HA-tagged ZC3H7B

tag: par-clip antibody

value: FLAG

tag: culture medium

value: DMEM


title: profiling library 1

description:
ProtOccProf library 1
Binding Profile
barcode for Library1_1_qseq.txt: TCTCACGTCGTATGCCGTCTTCTGCTTG
barcode for Library1_2_qseq.txt: TCTCACGTCGTATGCCGTCTTCTGCTTG
barcode for Library1_3_qseq.txt: TCTCACGTCGTATGCCGTCTTCTGCTTG

data_processing:
We used tophat (version 1.32) (Trapnell et al., 2009) for spliced alignment of single-end reads to the human reference genome sequence (hg18). Prior knowledge on candidate splice junctions was obtained from EnsEMBL (release 54, www.ensembl.org) to increase the sensitivity of the mapping process.
We separated all reads by strand and generated two strand-specific mpileup file with samtools 0.1.18 (Li et al., 2009). These file were subsequently input into custom PERL scripts to produce a separate bedgraph file for each strand (Watson / Crick). Bedgraph files were loaded into our local UCSC hg18 genome browser instance for visualization purposes. Additionally, a single bedgraph file for strand-specific T to C conversions was produced in a similar manner. T to C conversion sites are only included in the final file if at least two conversion events were observed.
Genome_build: hg18
Supplementary_files_format_and_content: bed file reporting consensus profiles

extract_protocol: Hafner et al. Methods. 2008 Jan;44(1):3-12

treatment_protocol: HEK293 cells stably were grown in medium supplemented with 4-thiouridine at a final concentration of 200 microM for 16 hour. Cells were UV-crosslinked at 365 nm.

value: 4SU labeling and UV

value: oligo(dT) beads


title: AML

description:
Flowcell: FC61MRUAAXX
Lanes: 6, 7

value: bone marrow

value: Acute Myeloid Leukemia


title: PARCLIP_CAPRIN1

description:
binding sites
barcode for 1_qseq.txt: TCTCCCATCGTATGCCGTCTTCTGCTTG
barcode for 2_qseq.txt: TCTCCCATCGTATGCCGTCTTCTGCTTG

value: HIS/FLAG/HA-tagged CAPRIN1


title: profiling library 2

description:
ProtOccProf library 2
Binding Profile
barcode for Library2_1_qseq.txt: TCTCTGCTCGTATGCCGTCTTCTGCTTG
barcode for Library2_2_qseq.txt: TCTCTGCTCGTATGCCGTCTTCTGCTTG
barcode for Library2_3_qseq.txt: TCTCTGCTCGTATGCCGTCTTCTGCTTG


title: sRNA_s_6

city: Shenzhen

first: Hong

middle: zhi

last: Cao

state: Guangdong

address: F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District

country: China

institute: BGI-SHENZHEN

data_processing: De novo assembly using SOAPdenovo program (http://soap.genomics.org.cn/soapdenovo.html)

organism:
Acer pseudoplatanus
Corylus avellana
Fagus sylvatica
Tilia platyphyllos
Ulmus glabra

source_name: pooled leaves from various tree species

growth_protocol: Natural condition at Wytham Woods, Oxfordshire, UK

extract_protocol: Total RNAs were extracted from each of 30 tree leaf sample harvested in May 2008 (1 g fresh weight) using Tri-Reagent (Sigma-Aldrich), and small RNAs were isolated by polyacrylamide gel electrophoresis as previously described 1. Each small RNA sample was qualitatively and quantitatively measured by using NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific). The individual samples were mixed in equal quantities in two pools: Pool-1 contains 9 Acer pseudoplatanus, 1 Fagus sylvatica, 1 Tilia platyphyllos, 1 Betula pendula, 4 Fraxinus excelsior, 2 Quercus robur, and 1 Aesculus hippocastanum; Pool-2 contains 1 Ulmus glabra, 2 Tilia platyphyllos, 1 Acer pseudoplatanus, 1 Corylus avellana, and 6 Fagus sylvatica. Adaptor ligation and RT-PCR amplification were performed for each pool by using the Small RNA Sample Prep Kit (Illumina).  Sequencing run was performed using the Genome Analyzer II for 34 cycles by commercial service (Source BioScience, Nottingham, UK). Two lanes of the flowcell were used for each of the two pools For each pooled sample, a lane with 3pM (lanes 3&5) and a lane with 6pM (lanes 4&6) of sample were used. The resulting small RNA reads were filtered by the Illumina GA pipeline software (version 1.0, Illumina software) and excised for the adaptor sequences.

treatment_protocol: Sampled in May 2008

tag: sample type

value: leaf extract


title: sRNA_s_5


title: sRNA_s_3

organism:
Betula pendula
Acer pseudoplatanus
Fagus sylvatica
Fraxinus excelsior
Quercus robur
Aesculus hippocastanum
Tilia platyphyllos


title: DKO

description:
Flowcell: FC61CM8AAXX
Lanes: 5, 6, 7, 8

value: DKO cell line

tag: cell type

value: colon cancer


title: sRNA_s_4


title: PARCLIP_C22orf28

description:
binding sites
barcode for 1_qseq.txt: TCTCTGCTCGTATGCCGTCTTCTGCTTG
barcode for 2_qseq.txt: TCTCCATTCGTATGCCGTCTTCTGCTTG

value: HIS/FLAG/HA-tagged C22orf28


title: AML_Rep#2

description:
Flowcell: FC80J8TABXX
Lanes: 5


title: IDH-mut_#2

description:
Flowcell: FC81NGBABXX
Lanes: 5

source_name: IDH mutated Acute Myeloid Leukemia patient sample

value: IDH mutated Acute Myeloid Leukemia


title: IDH-mut_#1

description:
Flowcell: FC81NGBABXX
Lanes: 7


title: PARCLIP_C17orf85

description:
binding sites
barcode for 1_qseq.txt: TCTTTTATCGTATGCCGTCTTCTGCTTG
barcode for 2_qseq.txt: TCTCCCATCGTATGCCGTCTTCTGCTTG

value: HIS/FLAG/HA-tagged C17orf85


title: PARCLIP_ALKBH5

description:
binding sites
barcode for 1_qseq.txt: TCTCTGCTCGTATGCCGTCTTCTGCTTG
barcode for 2_qseq.txt: TCTTTTATCGTATGCCGTCTTCTGCTTG

value: HIS/FLAG/HA-tagged ALKBH5


title: MLLr_#1_Rep#2

description:
Flowcell: FC80J8TABXX
Lanes: 6

value: MLL rearranged Acute Myeloid Leukemia


title: NBM_#1

description:
Flowcell: FCA806LBABXX
Lanes: 3

value: CD34+ normal


title: HCT116 50ng_ERRBS

description:
Flowcell: FC80J8TABXX
Lanes: 1

value: HCT116 cell line


title: Differentiated tissues

data_processing:
Base calls were made using the Illumina pipeline v. 1.6 for Illumina GAIIx and v. OLB 1.9 for HiSeq2000
All RNAseq was pooled and a de novo transcriptome was made using the program Trinity with default settings.
BPKG_transcriptome was deposited into NCBI TSA database as reference number:  SUB086338; BioProject ID: PRJNA163163
Genome_build: BPKG_transcriptome.nt
Supplementary_files_format_and_content: RPKM quantification for all 3 cellular compartments used in this study, as well as top-hit BLAST annotation to mouse homologs.

source_name: D7 gamma irradiated planarians

value: All tissues minus stem cells and progeny


title: Stem Cells

source_name: FACS purified X1s

value: Stem cells, neoblasts, X1s


title: pAseq_Fly_ZT12_SE

status: Public on May 31 2012

city: Waltham

first: Joseph

last: Rodriguez

address: 415 South Street

department: Biology

institute: Brandeis University

description: PolyA RNA.

data_processing:
Base calls were performed using GA Pipeline 1.5.1 for the 6 time point single-end sequences.
Cs single-end samples were aligned to the Drosophila melanogaster dm3 genome assembly with Tophat using the parameters: "-m 1 -F 0 -g 1 --microexon-search --no-closure-search -G exon20110421.gtf --solexa1.3-quals -I 50000". The gtf file corresponds to UCSC genome table gene annotation from the RefSeq table.
Base frequencies were calculated within exons and introns of UCSC annotation. Genes with multiple isoforms were flattened, where overlapping exons generate one exon. Base positions with one or more Gs in the nascent datasets and zero Gs in the sequenced genomic DNA were identified. We required that editing sites occur in at least 5 of 6 samples within each set of replicate time points, for a total of 10 of 12 independent occurrences for each site. To avoid potential mismapping of reads at splice junctions by Tophat, we required that edited sites occur in at least one of the two middle quadrants of at least one read. Intronic sites that occurred within 10 bases of an annotated splice site were also discarded. We applied a similar approach to the yw pA-seq data, with the exception that we required that the editing site occur in both samples (2 of 2). Editing levels were then calculated for the sites found in the nascent analysis. For reproducibility of the nascent level, we pooled the editing counts for each replicate set of 6 time points together and calculated the percent editing level. The final percent editing level was determined by pooling the editing counts for all 12 samples and dividing by the total pooled counts of the 12 samples. Editing was similarly calculated for the yw pA-seq data and the small-scale Nascent-seq data by pooling both replicate samples. The editing level for the Cs pA-seq data was calculated by pooling all 12 samples. The exon and intron editing sites identified in the 12 Nascent-seq replicates were scanned in the small-scale ADAR0, FM7a, yw Nascent-seq data. We required editing to occur in both replicates of the FM7a and yw data, and sites with zero sequence coverage in any sample were not considered.
Cs single-end files were trimmed to 72 basepairs with the FASTX tool kit before tophat alignment.
Processed data (available as a supplementary file on the Series record): Editing frequencies.
Genome_build: dm3

organism: Drosophila melanogaster

source_name: head, ZT12, mRNA

extract_protocol: Fly heads were isolated with brass sieves. Total RNA was extracted from fly heads with TRIzol Reagent (Invitrogen) using the manufacturer’s protocol. pA+ RNA was extracted from yw and Cs total RNA with Ambion Oligo dT Cellulose or Invitrogen Dynabeads oligo dT using the manufacturer’s protocol. Sequencing library construction was performed by using the standard Illumina protocol for mRNA samples using lab reagents starting with 100 nanograms of mRNA.

treatment_protocol: Drosophila flies were entrained to 3-4 days of 12hr light : 12hr dark cycles.

value: Canton s (Cs)

value: head

value: 3-4 days

tag: time point


title: pAseq_Fly_ZT20_SE

description: PolyA RNA.

source_name: head, ZT20, mRNA


title: As_mRNASeq

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

description: Illumina mRNA-seq

data_processing: Alignment: mRNA-seq reads each were mapped to TAIR9 genome and cDNA sequence using BFAST software (http://bfast.sourceforge.net)

organism: Arabidopsis suecica

source_name: Rosette leaves

growth_protocol: All plants were grown under a 16/8-hour light/dark cycle with temperatures of 22C (light) and 20C (dark).

extract_protocol: Total RNA was isolated from mature leaves (3-4 weeks old A. thaliana; 6-7 weeks old A. arenosa or allotetraploids plants) prior to bolting using plant RNA purification reagent (Invitrogen, Carlsbad, CA). The integrity of extracted RNA was verified by resolving 1ug RNA in an 1% formaldehyde denaturing agarose gel. An aliquot of 10ug total RNA was used to prepare mRNA-seq libraries using Illumina mRNA-seq sample preparation kit (Illumina Inc., San Diego, CA). Libraries with a range of 200-25 bp were excised and amplified for subsequent cluster generation and massively parallel sequencing using the Illumina Genome Analyzer with read lengths ranged from 60 to 83 bp.

tag: Stage

value: before bolting

tag: ploidy

value: allotetraploids

tag: sample

value: Rosette leaves

value: 6-7 weeks old


title: AlloF8_mRNASeq

description: Illumina mRNA-seq

organism: Arabidopsis arenosa x Arabidopsis thaliana

tag: generation

value: F8 allotetraploids

tag: age


title: Aa_mRNASeq

description: Illumina mRNA-seq

organism: Arabidopsis arenosa

tag: ecotype

value: autotetraploids


title: AlloF1_mRNASeq

description: Illumina mRNA-seq

value: F1 resynthesized allotetraploids


title: pAseq_Fly_ZT0_SE

description: PolyA RNA.

source_name: head, ZT0, mRNA

tag: strain


title: pAseq_Fly_ZT4_SE

description: PolyA RNA.

source_name: head, ZT4, mRNA


title: pAseq_Fly_ZT8_SE

description: PolyA RNA.

source_name: head, ZT8, mRNA


title: pAseq_Fly_ZT20_PE

description: PolyA RNA.

data_processing:
Base calls were performed using GA Pipeline 1.0 for the paired-end sequences.
Cs paired-end samples were aligned to the Drosophila melanogaster dm3 genome with Tophat using the parameters: "-r 50 -m 1 -F 0 -I 50000 -g 1 -G exon20110421.gtf", and reads with overlapping ends were removed and remapped. The gtf file corresponds to UCSC genome table gene annotation from the RefSeq table.
Base frequencies were calculated within exons and introns of UCSC annotation. Genes with multiple isoforms were flattened, where overlapping exons generate one exon. Base positions with one or more Gs in the nascent datasets and zero Gs in the sequenced genomic DNA were identified. We required that editing sites occur in at least 5 of 6 samples within each set of replicate time points, for a total of 10 of 12 independent occurrences for each site. To avoid potential mismapping of reads at splice junctions by Tophat, we required that edited sites occur in at least one of the two middle quadrants of at least one read. Intronic sites that occurred within 10 bases of an annotated splice site were also discarded. We applied a similar approach to the yw pA-seq data, with the exception that we required that the editing site occur in both samples (2 of 2). Editing levels were then calculated for the sites found in the nascent analysis. For reproducibility of the nascent level, we pooled the editing counts for each replicate set of 6 time points together and calculated the percent editing level. The final percent editing level was determined by pooling the editing counts for all 12 samples and dividing by the total pooled counts of the 12 samples. Editing was similarly calculated for the yw pA-seq data and the small-scale Nascent-seq data by pooling both replicate samples. The editing level for the Cs pA-seq data was calculated by pooling all 12 samples. The exon and intron editing sites identified in the 12 Nascent-seq replicates were scanned in the small-scale ADAR0, FM7a, yw Nascent-seq data. We required editing to occur in both replicates of the FM7a and yw data, and sites with zero sequence coverage in any sample were not considered.
Cs paired-end reads were mapped and reads hitting multiple chromosomes or overlapping ends were removed, and remapped with tophat.
Processed data (available as a supplementary file on the Series record): Editing frequencies.
Genome_build: dm3


title: At_mRNASeq

description: Illumina mRNA-seq

value: Landsberg erecta

value: 3-4 weeks old


title: pAseq_Fly_ZT8_PE

description: PolyA RNA.


title: pAseq_Fly_ZT16_PE

description: PolyA RNA.

source_name: head, ZT16, mRNA


title: pAseq_Fly_ZT12_PE

description: PolyA RNA.


title: pAseq_Fly_ZT0_PE

description: PolyA RNA.


title: pAseq_Fly_ZT2_yw

description: PolyA RNA.

data_processing:
Base calls were performed using CASAVA 1.6 for the 2 time point yw sequences.
yw mRNA samples were aligned to the Drosophila melanogaster dm3 genome with Tophat using the parameters: "-m 1 -F 0 --microexon-search --no-closure-search -G exon20110421.gtf --solexa1.3-quals -I 50000". The gtf file corresponds to UCSC genome table gene annotation from the RefSeq table.
Base frequencies were calculated within exons and introns of UCSC annotation. Genes with multiple isoforms were flattened, where overlapping exons generate one exon. Base positions with one or more Gs in the nascent datasets and zero Gs in the sequenced genomic DNA were identified. We required that editing sites occur in at least 5 of 6 samples within each set of replicate time points, for a total of 10 of 12 independent occurrences for each site. To avoid potential mismapping of reads at splice junctions by Tophat, we required that edited sites occur in at least one of the two middle quadrants of at least one read. Intronic sites that occurred within 10 bases of an annotated splice site were also discarded. We applied a similar approach to the yw pA-seq data, with the exception that we required that the editing site occur in both samples (2 of 2). Editing levels were then calculated for the sites found in the nascent analysis. For reproducibility of the nascent level, we pooled the editing counts for each replicate set of 6 time points together and calculated the percent editing level. The final percent editing level was determined by pooling the editing counts for all 12 samples and dividing by the total pooled counts of the 12 samples. Editing was similarly calculated for the yw pA-seq data and the small-scale Nascent-seq data by pooling both replicate samples. The editing level for the Cs pA-seq data was calculated by pooling all 12 samples. The exon and intron editing sites identified in the 12 Nascent-seq replicates were scanned in the small-scale ADAR0, FM7a, yw Nascent-seq data. We required editing to occur in both replicates of the FM7a and yw data, and sites with zero sequence coverage in any sample were not considered.
Cs single-end files were trimmed to 72 basepairs with the FASTX tool kit before tophat alignment.
Processed data (available as a supplementary file on the Series record): Editing frequencies.
Genome_build: dm3

source_name: head, ZT2, mRNA

value: yellow white (yw)


title: Nascentseq_Fly_ZT22_R2

description: Nascent RNA.

data_processing:
Base calls performed using CASAVA v1.6.
Nascent-seq reads were aligned to the dm3 genome assembly using tophat with the following parameters: "-m 1 -F 0 --microexon-search --no-closure-search -G exon20110421.gtf --solexa1.3-quals -I 50000". yw, FM7a, ADAR0 male sequences were aligned with the following parameters: "-m 1 -F 0 --microexon-search --no-closure-search -G exon20110421.gtf --solexa-quals -I 50000". The gtf file corresponds to UCSC genome table gene annotation from the RefSeq table.
Base frequencies were calculated within exons and introns of UCSC annotation. Genes with multiple isoforms were flattened, where overlapping exons generate one exon. Base positions with one or more Gs in the nascent datasets and zero Gs in the sequenced genomic DNA were identified. We required that editing sites occur in at least 5 of 6 samples within each set of replicate time points, for a total of 10 of 12 independent occurrences for each site. To avoid potential mismapping of reads at splice junctions by Tophat, we required that edited sites occur in at least one of the two middle quadrants of at least one read. Intronic sites that occurred within 10 bases of an annotated splice site were also discarded. We applied a similar approach to the yw pA-seq data, with the exception that we required that the editing site occur in both samples (2 of 2). Editing levels were then calculated for the sites found in the nascent analysis. For reproducibility of the nascent level, we pooled the editing counts for each replicate set of 6 time points together and calculated the percent editing level. The final percent editing level was determined by pooling the editing counts for all 12 samples and dividing by the total pooled counts of the 12 samples. Editing was similarly calculated for the yw pA-seq data and the small-scale Nascent-seq data by pooling both replicate samples. The editing level for the Cs pA-seq data was calculated by pooling all 12 samples. The exon and intron editing sites identified in the 12 Nascent-seq replicates were scanned in the small-scale ADAR0, FM7a, yw Nascent-seq data. We required editing to occur in both replicates of the FM7a and yw data, and sites with zero sequence coverage in any sample were not considered.
Processed data (available as a supplementary file on the Series record): Editing frequencies.
Genome_build: dm3

source_name: head, ZT22, nascent RNA

extract_protocol: Fly heads were isolated with brass sieves. Fly head nuclei were purified and Nascent RNA was extracted as described in Wuarin and Schibler, 1994 (PMID 7523861). Nascent RNA was extracted from the NUN pellet with Invitrogen TRIzol Reagent using the manufacturer’s protocol. Nascent RNA replicate set 1 was ribosomal RNA depleted as described in Khodor and Rosbash, 2011. All Nascent RNA samples were depleted of mRNA by two rounds of pA depletion using Invitrogen Dynabeads Oligo dT using the manufacturer’s protocol. Sequencing library construction was performed by using the standard Illumina protocol for RNA starting with 100 nanograms of Nascent RNA.


title: pAseq_Fly_ZT4_PE

description: PolyA RNA.


title: Nascentseq_Fly_ZT6_R2

description: Nascent RNA.

source_name: head, ZT6, nascent RNA


title: Nascentseq_Fly_ZT18_R2

description: Nascent RNA.

source_name: head, ZT18, nascent RNA


title: Nascentseq_Fly_ZT10_R2

description: Nascent RNA.

source_name: head, ZT10, nascent RNA


title: pAseq_Fly_ZT14_yw

description: PolyA RNA.

source_name: head, ZT14, mRNA


title: Nascentseq_Fly_ZT2_R2

description: Nascent RNA.

source_name: head, ZT2, nascent RNA


title: pAseq_Fly_ZT16_SE

description: PolyA RNA.


title: Nascentseq_Fly_ZT14_R2

description: Nascent RNA.

source_name: head, ZT14, nascent RNA


title: NBM_#2_Rep#2

description:
Flowcell: FC80J8TABXX
Lanes: 3

source_name: CD34+ normal bone marrow control

tag: tissue type

value: bone marrow

value: CD34+ normal


title: Nascentseq_Fly_ZT22_R1

description: Nascent RNA.


title: Nascentseq_Fly_ZT18_R1

description: Nascent RNA.


title: Nascentseq_Fly_ADAR0_R2

description:
Nascent RNA.
Small-scale prep from 40-45 heads.

data_processing:
Small-scale prep base calls performed using CASAVA v1.8.
Nascent-seq reads were aligned to the dm3 genome assembly using tophat with the following parameters: "-m 1 -F 0 --microexon-search --no-closure-search -G exon20110421.gtf --solexa1.3-quals -I 50000". yw, FM7a, ADAR0 male sequences were aligned with the following parameters: "-m 1 -F 0 --microexon-search --no-closure-search -G exon20110421.gtf --solexa-quals -I 50000". The gtf file corresponds to UCSC genome table gene annotation from the RefSeq table.
Base frequencies were calculated within exons and introns of UCSC annotation. Genes with multiple isoforms were flattened, where overlapping exons generate one exon. Base positions with one or more Gs in the nascent datasets and zero Gs in the sequenced genomic DNA were identified. We required that editing sites occur in at least 5 of 6 samples within each set of replicate time points, for a total of 10 of 12 independent occurrences for each site. To avoid potential mismapping of reads at splice junctions by Tophat, we required that edited sites occur in at least one of the two middle quadrants of at least one read. Intronic sites that occurred within 10 bases of an annotated splice site were also discarded. We applied a similar approach to the yw pA-seq data, with the exception that we required that the editing site occur in both samples (2 of 2). Editing levels were then calculated for the sites found in the nascent analysis. For reproducibility of the nascent level, we pooled the editing counts for each replicate set of 6 time points together and calculated the percent editing level. The final percent editing level was determined by pooling the editing counts for all 12 samples and dividing by the total pooled counts of the 12 samples. Editing was similarly calculated for the yw pA-seq data and the small-scale Nascent-seq data by pooling both replicate samples. The editing level for the Cs pA-seq data was calculated by pooling all 12 samples. The exon and intron editing sites identified in the 12 Nascent-seq replicates were scanned in the small-scale ADAR0, FM7a, yw Nascent-seq data. We required editing to occur in both replicates of the FM7a and yw data, and sites with zero sequence coverage in any sample were not considered.
Processed data (available as a supplementary file on the Series record): Editing frequencies.
Genome_build: dm3

source_name: head, ADAR0, nascent RNA

tag: gender

value: male


title: Nascentseq_Fly_ADAR0_R1

tag: tissue


title: Nascentseq_Fly_ZT14_R1

description: Nascent RNA.


title: Nascentseq_Fly_ZT10_R1

description: Nascent RNA.


title: Nascentseq_Fly_ZT6_R1

description: Nascent RNA.


title: Nascentseq_Fly_FM7a_R1

source_name: head, FM7a, nascent RNA


title: Nascentseq_Fly_yw_R2

source_name: head, yw, nascent RNA


title: Nascentseq_Fly_FM7a_R2


title: Nascentseq_Fly_ZT2_R1

description: Nascent RNA.


title: Nascentseq_Fly_yw_R1


title: MGG4 = H3K79 SEM_ChipSeq

description: Chromatin IP against H3K79me2 in SEM Cells

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie 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: SEM

growth_protocol: Human B cell precursor leukemia SEM cells reported to carry the t(4;11) MLL-AF4 were purchased from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ). Cells were maintained under typical conditions in RPMI media with 10% Fetal Bovine Serum at the National Cell Culture Center (NCCC). For location analysis, cells were grown to a density of 0.5 million cells per ml and 99% viability prior to crosslinking with formaldehyde for 20 min.

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

tag: chip antibody

tag: antibody catalog number

value: Abcam AB3594

value: SEM


title: gDNA_Fly_yw

description: Genomic-Seq.

data_processing:
Base calls performed using CASAVA v1.6.
gDNA-seq reads were aligned to the Drosophila melanogaster dm3 genome assembly using tophat with the following parameters: "-m 1 -F 0 --microexon-search --no-closure-search -G exon20110421.gtf --solexa1.3-quals -I 50000". The gtf file corresponds to UCSC genome table gene annotation from the RefSeq table.
Base frequencies were calculated within exons and introns of UCSC annotation. Genes with multiple isoforms were flattened, where overlapping exons generate one exon. Base positions with one or more Gs in the nascent datasets and zero Gs in the sequenced genomic DNA were identified. We required that editing sites occur in at least 5 of 6 samples within each set of replicate time points, for a total of 10 of 12 independent occurrences for each site. To avoid potential mismapping of reads at splice junctions by Tophat, we required that edited sites occur in at least one of the two middle quadrants of at least one read. Intronic sites that occurred within 10 bases of an annotated splice site were also discarded. We applied a similar approach to the yw pA-seq data, with the exception that we required that the editing site occur in both samples (2 of 2). Editing levels were then calculated for the sites found in the nascent analysis. For reproducibility of the nascent level, we pooled the editing counts for each replicate set of 6 time points together and calculated the percent editing level. The final percent editing level was determined by pooling the editing counts for all 12 samples and dividing by the total pooled counts of the 12 samples. Editing was similarly calculated for the yw pA-seq data and the small-scale Nascent-seq data by pooling both replicate samples. The editing level for the Cs pA-seq data was calculated by pooling all 12 samples. The exon and intron editing sites identified in the 12 Nascent-seq replicates were scanned in the small-scale ADAR0, FM7a, yw Nascent-seq data. We required editing to occur in both replicates of the FM7a and yw data, and sites with zero sequence coverage in any sample were not considered.
Processed data (available as a supplementary file on the Series record): Editing frequencies.
Genome_build: dm3

source_name: head gDNA

extract_protocol: Genomic DNA was extracted using standard protocols.  Briefly, whole yw flies were ground in 65ml mortars on dry ice. 150ul of crushed flies were incubated with 500ul of Solution A [Tris HCI (pH 8), 100mM EDTA, 100mM NaCl, 1% SDS] and incubated with 15ul of Ambion RNAse Cocktail (A/T1) at 65C for 1hr. Sample was spun down to remove debris, and supernatant was transferred to new eppendorf tubes. Sample was incubated at 37C for 2hr. 2.5ul of Invitrogen Proteinase K Solution was added to the sample and incubated overnight at 55C. Sequencing library construction was performed by using the standard Illumina protocol for genomic DNA samples using lab reagents.  The genomic library was made with 5ug of gDNA and subjected to 3 rounds of 15 second sonication using a Fisher Scientific 550 Sonic Dismembrator with a probe tip at the power 2 setting.

value: head


title: MGG16=WCESEM_ChipSeq

description: Sonicated WCE from SEM Cells

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

value: None WCE


title: MGG8= H3K4SEM110907.M3_ChipSeq

description: Chromatin IP against H3K4me3 in SEM Cells

value: Abcam AB8580


title: 30day_old_testes

city: Cold Spring Harbor

first: Benjamin

last: Czech

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

description: small RNA sequencing

data_processing:
The 36nt Illumina reads were stripped of the 3’ linker, collapsed, and the resulting small RNA sequences were matched without mismatches to the Drosophila release 5 genome using nexalign. Only reads that met these conditions were subjected to further analyses.
For annotations we used a combination of UCSC [dm3], miRBase [release 14], and Flybase [r5.26] tracks for protein coding genes, repeats/transposons, non-coding RNAs and microRNAs, as well as custom tracks (for synthetic markers, endo-siRNAs from structured loci, miR and miR* strands) with different priorities (annotation priority list available upon request).
Genome_build: dm3
Supplementary_files_format_and_content: txt files contain genome-matching small RNA sequences, read lengths, annotation names and read counts. Formate: SEQ = the sequence of the small RNA. LENGTH = the length of the small RNA. NAME = annotation name of the small RNA. READS = read count in respective library. All small RNAs were converted into DNA for sequencing, therefore U's are represented as T's.

source_name: D. melanogaster testes_30 day

growth_protocol: Flies were raised at 25°C on standard cornmeal-molasses agar medium.

extract_protocol: Total RNA from testes of 1005 (1-day) and 1018 (30-day) old wild-type (OreR) males was isolated using TRIzol (Invitrogen). 19- to 28-nt small RNAs were cloned as described (Brennecke et al., 2007).

treatment_protocol: Aging paradigm was used as described previously (Boyle et al., 2007).

value: Wild-type flies (Oregon R)

value: testes


title: MGG7= H3K4REH110907.M1_ChipSeq

description: Chromatin IP against H3K4me3 in REH Cells

source_name: REH

growth_protocol: Human SEM cells with the t(4;11) translocation and REH control cells were purchased from the American Type Culture Collection (ATCC). All cell lines were maintained in RPMI medium 1640 supplemented with 10% FBS. Cells were cross-linked with 1% formaldehyde for 20 min.

value: REH


title: 1day_old_testes

description: small RNA sequencing

source_name: D. melanogaster testes_1 day


title: MGG15=WCEREH_ChipSeq

description: Sonicated WCE from REH Cells


title: yxy-8

city: Wuhan

first: Xiyan

last: Yang

state: Hubei

address: Shizishan 1, Hongshan

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing output raw data were first filtered to remove adaptor tags, low quality sequences (tags with unknown sequences 'N') and tags with a copy number of 1 (probably sequencing error).
all tags were mapped to the reference sequences (cotton unigenes from NCBI) and allowed no more than one nucleotide mismatch. All the tags mapped to reference sequences from multiple genes were filtered and the remaining tags were designed as unambiguous tags.
For gene expression analysis, the number of expressed tags was calculated and then normalized to TPM (number of transcripts per million clean tags). To minimize false positives and negatives, we estimated that statistical analysis was reliable when applied to genes showing a TPM ≥ 20 in at least one of these stages
To obtain statistical confirmation of the differences in gene expression among the developmental stages, we then compared  the TPM-derived read count all the timepoints/stages to ck (0h) using a threshold value of P ≤ 0.001 and the absolute value of log2Ratio ≥1 based on the FDR < 0.05.
Genome_build: geneme unavailable, use cotton unigenes from NCBI for reads alignment
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample, and a matrix nomalized tablelist for differentially expressed gene from all timepoints/stages

organism: Gossypium hirsutum

source_name: somatic torpedo embryos

growth_protocol: Sterilized seeds of YZ1 (Gossypium hirsutum L.) were germinated on 1/2 MS (1/2 macro salts plus 15 g of glucose, pH 6.0) and cultured at 28°C in the dark for 6 d. Hypocotyls were excised from germfree seedlings and cut into 5-7 mm segments. The explants were then cultured on MSB (MS medium plus B5 vitamins) medium supplemented with the combination of 1.0 mg/L IBA plus 0.1 mg/L kinetin. After 40 d of culture, all explants were transferred to fresh MSB medium for induction of embryogenic calli (ECs). The ECs were subcultured monthly on MSB medium, with KNO3 doubled but NH4NO3 removed, and supplemented with 3% (w/v) glucose, 0.25% (w/v) Phytagel, 0.5 mg/L IBA, 0.15 mg/L kinetin, 1.0g/L glutamine and 0.5 g/L asparagines, for embryo maturation. All media were autoclaved at 121°C for 15 min. Cultures were maintained in a room at 28 ± 2 °C under a 14-h photoperiod (irradiance of 135 μmol/m∙s). Different stages of explants during initial cellular dedifferentiation (0 h, 6 h, 24 h, 48 h), NECs (40 d), ECs and somatic embryos [globular embryos (GEs), torpedo embryos (TEs) and cotyledon embryos (CEs)] were sampled

extract_protocol: Total RNA was isolated from each sample by using a modified guanidine thiocyanate method, Twenty micrograms of total RNA was sent to Beijing Genomics Institute (Shenzhen) where the libraries were constructed and sequenced using Illumina’s Genome Analyzer.

tag: varieties/line

value: somatic torpedo embryos

tag: developmental stages


title: yxy-9

source_name: somatic cotyledon embryos

value: somatic cotyledon embryos


title: MGG2 = (H3K79 REH)_ChipSeq

description: Chromatin IP against H3K79me2 in REH Cells


title: yxy-6

source_name: embryogenic calli

value: embryogenic calli


title: yxy-4

source_name: 48 h-hypocotyl after induction

value: hypocotyl

value: 48 h-hypocotyl after induction (initial cellular dedifferentiation)


title: yxy-5

source_name: nonembryogenic calli

value: nonembryogenic calli


title: yxy-7

source_name: somatic globular embryos

value: somatic globular embryos


title: yxy-3

source_name: 24 h-hypocotyl after induction

value: 24 h-hypocotyl after induction (initial cellular dedifferentiation)


title: HOXA9 ChIP-Seq in SEM Rep 2

description: Chromatin IP against HOXA9 in SEM

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

value: Abcam AB33382

tag: cell number

value: 50 million

tag: library prep protocol

tag: replicate


title: MEIS1 ChIP-seq in SEM Rep 2

description: Chromatin IP against MEIS1 in SEM

value: Abcam AB19867

tag: cell type

value: SEM


title: yxy-2

source_name: 6 h-hypocotyl after induction

value: 6 h-hypocotyl after induction (initial cellular dedifferentiation)


title: HOXA9 ChIP-Seq in SEM Rep 1

description: Chromatin IP against HOXA9 in SEM


title: Input

status: Public on May 30 2012

city: Barcelona

first: Conchi

last: EI

address: Baldiri Reixac 15

country: Spain

institute: IBMB

data_processing:
Basecalls performed with CASAVA
ChIP-seq reads were mapped to mm9 whole genome using bowtie v0.12.7 with default parameters and –best --chunkmbs 512 --sam
Peaks were called with MACS 1.4 with default parameters and -f BAM -g mm --pvalue=1e-4 --keep-dup 1 -w -S –call-subpeaks
Genome_build: mm9
Supplementary_files_format_and_content: BED files were generated with MACS 1.4 (see data processing step)

source_name: neural stem cells

growth_protocol: Mouse NSCs, provided by Dr. K. Helin, were dissected out from cerebral cortex of mouse embryos (E12.5) and cultured in a poly-D-lysine (5mg/ml, 2h 37°C) and laminine (5 mg/ml 37°C, 4 h 37ºC) precoated dishes growing with a media composed by equal parts of DMEM F12 (without Phenol Red, Gibco) and Neural Basal Media (Gibco) containing Penicillin/Streptomycin and Glutamax (1%), N2 and B27 supplements (Gibco), non essential aminoacids (0.1mM), sodium pyruvat (1mM), Hepes (5 mM), Heparin (2 mg/l), bovine serum albumin (25 mg/l) and βmercaptoethanol (0.01 mM). We add fresh recombinant human EGF (R&D systems) and FGF (Invitrogen) to 20 ng/ml and 10 ng/ml final concentrations respectively. Under our growing conditions NSCs preserve the ability to self-renew and to generate a wide range of differentiated neural cell types upon the activation of appropriate signals (Calloni et al, 2009; Gossrau et al, 2007; Sasaki et al, 2006).

extract_protocol: Before sequencing, ChIP DNA was prepared by simultaneously blunting, repairing and phosphorylating ends using a mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase according to manufacturer’s instruction (Illumina). The DNA was adenylated at 3´end and recovered by Qiaquick PCR purification kit (Qiagen) according to the manufacturer’s recommendations. Adaptors were added by ligation and the ligated fragments were amplified by PCR, resolved in a gel and purified by Qiagen columns. The purified DNA was quantified by picogreen (Invitrogen) and diluted to a working concentration of 10 nM. Samples were loaded into individual lanes of flow cell.

treatment_protocol: TGFb (Millipore) was used at a final concentration of 5 ng/ml for the times specified.

tag: tissue source

value: cerebral cortex

tag: age of source

tag: genotype

value: wild type

value: neural stem cells

tag: treatment

value: TGFb


title: ChIP-seq JMJD3


title: ChIP-seq Smad3


title: MEF_KO_iPS1_H3K27me3

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: Utx KO cells that underwent improper reprogramming. Clone #1

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files. We aligned reads to mm9 reference genome using bowtie version 0.12.5. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.  We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (WCE) as control in order to define a background model.
Genome Build:
MEF_KO_iPS1_H3K27me3_peaks.bed: mm9

source_name: Mouse V19-OSKM Aberrant iPS cells, Utx-/Y, Clone #1

growth_protocol: Utx+/Y and Utx-/Y V6.5 Mouse ESCs were expaned in N2B27 2i/LIF conditions. MEFs were expanded in 2i/LIF condition with or without Doxycycline as indicated.

extract_protocol: 120ul SPRI AMPure XP beads (Agencourt) were added to the reverse-crosslinked samples, pipette-mixed 15 times and incubated for 2 minutes. Supernatant were separated from the beads using a magnet for 4 minutes. Beads were washed on the magnet with 70% ethanol and then air dried for 4 minutes. The DNA was eluted in 40 ul EB buffer (10 mM Tris-HCl pH 8.0) by pipette mixing 25 times. For the remainder of the library construction process (DNA end-repair, A-base addition, adaptor ligation and enrichment) a general SPRI cleanup involves addition of buffer containing 20% PEG and 2.5 M NaCl to the DNA reaction products (without moving them from their original well position). After thorough mixing and a 2-minute incubation at room temperature, plates are transferred to a magnet plate, incubated for 4 minutes and supernatant removed. Beads are then washed on the magnet with 150ul 70% ethanol and then air dried for 4 minutes. The DNA is eluted with 40ul of EB buffer by pipette mixing 25 times. Reagent kits are prepared in advance for all enzymatic steps (New England Biolabs). The DNA end-repair was performed by adding 27 µl of a master mix (17 µl master mix (5 ul T4 buffer, 5ul BSA-1mg/ml, 5ul ATP-10mM -2ul dNTPs 10 mM), 5 ul T4 PNK enzyme, 5 µl T4 polymerase (3 units) to each well. Samples were incubated in a thermal cycler at 12C for 15 min, 25C for 15 min, and finally cooled to 4C. The SPRI bead clean up method was used to purify the product (147 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). The A-base addition was performed by adding 20 µl master mix (17 µl A-base add mix, 3 µl Klenow (3’->5’ exonuclease) to each well and incubated at 37C for 30 min. in a thermal cycler. SPRI bead clean up method was used to purify the product (132 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 19 µl EB). Adaptor ligation was performed by adding 34 µl of a master mix (29 µl 2x DNA ligase buffer, 5 µl DNA ligase) to each well. Finally 5 µl PE Indexed oligo adaptors (0.75 uM ) was added to each well and samples were incubated 25C for 15 min in a thermal cycler. SPRI bead clean up with size selection was used to purify the ligated products (15.5 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). Finally, enrichment PCR was performed by adding 10 µl of a master mix (2 µl Forward/Reverse Index Primer, 0.5 µl dNTP mix, 5 µl 10x Pfu Ultra Buffer, 1 µl Pfu Ultra-II Fusion, 1.5 µl Nuclease free water) to each well. Plate was transferred to a thermal cycler and ran a Pfu amplification program at 95C for 2 min, 16 cycles of: 95C for 30 sec, 55C for 30 sec, 72C for 60 sec, and finally 72C for 10 min. The final SPRI clean up coupled to size selection was performed (35 µl SPRI beads was added to each sample and eluted in 40 µl). Approximately 5 picomoles of DNA library was then applied to each lane of the flow cell. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hiseq2000 Analyzer following the manufacturer's protocols.

treatment_protocol: Approximately 60*10^6 cells were cross-linked in formaldehyde (1% final concentration, 10 min at room temperature (RT)), and then quenched with glycine (5 min at RT). Fixed cells were lysed in 50mM HEPES KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40 alternative, 0.25% Triton supplemented with protease inhibitor at 4°C (Roche, 04693159001), centrifuged at 950 x g for 10 min and re-suspended in 0.2% SDS, 10mM EDTA, 140mM NaCl and 10mM Tris-HCL. Cells were then fragmented with a Branson Sonifier (model S-450D) at -4°C to a size range between 200 and 800 bp, and precipitated by centrifugation. 10 ug of antibody were pre-bound by incubating with Protein-G Dynabeads (Invitrogen100-07D) in blocking buffer (PBS supplemented with 0.5% TWEEN and 0.5% BSA) for 2 hours at room temperature. Washed beads were added to the chromatin lysate, and then incubated overnight. Samples were washed 5 times with RIPA buffer, twice with RIPA buffer supplemented with 500 mM NaCl, twice with LiCl buffer (10 mM TE, 250mM LiCl, 0.5% NP-40, 0.5% DOC), once with TE (10Mm Tris-HCl pH 8.0, 1mM EDTA), and then eluted in 0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris Hcl pH 8.0 at 65°C. Eluate was incubated in 65°C for 4 hours, and then treated sequentially with RNaseA (Roche, 11119915001) for 30 min and Proteinase K (NEB, P8102S) for two hours. DNA was purified with The Agencourt AMPure XP system (Beckman Coulter Genomics, A63881).

value: H3K27me3; ChIP grade, 07-449, Millipore

tag: doxycycline induction

tag: genotype/variation

value: KO Utx-/Y


title: IgG control, ChIP-seq

first: Anagha

middle: M

last: Joshi

address: Wellcome trust/MRC building, Hills road

department: Dept. of haematology, CIMR

country: United Kingdom

institute: University of cambridge

description: Chromatin IP against IgG.

data_processing: Processed alignment files include .map.txt files. The .map.txt files were created using the Maq software package using the default alignment settings. All alignments were made to the mm9 mouse genome. The .bw files were created using an in-house script and show the sequence read density across the mm9 mouse genome.

source_name: Runx1(Venus/+) ES cell line, IgG control

growth_protocol: 1 x 10^5 undifferentiated ES cells were cultured on confluent OP9 cell layers in 10-cm dishes to induce differentiation. After 6 days of ES cell differentiation, cultured cells were harvested for FACS analysis and sorting.

extract_protocol:
The genomic DNA extraction and ChIP protocols are described in the supplemental experimental procedure of: Wilson et al. Combinatorial transcriptional control in blood stem/progenitor cells:  genome-wide analysis of ten major transcriptional regulators. Cell Stem Cell. 2010 Oct 8;7(4):532-44. (PMID 20887958).
Chromatin was fixed in 1% formaldehyde, sheared to 200-500bp using a Bioruptor (Diagenode), immunoprecipitated using the indicated antisera, purified and sequenced using the Illumina Genome Analyzer II as recommended by the manufacturer.

treatment_protocol: No treatment beyond the normal growth protocol was used.

tag: cell line

value: Runx1(Venus/+) ES cell line

value: differentiated ES cells

tag: days of differentiation

tag: cell subpopulation

value: unsorted

value: IgG


title: MEF_KO_iPS1_H3K4me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files. We aligned reads to mm9 reference genome using bowtie version 0.12.5. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.  We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (WCE) as control in order to define a background model.
Genome Build:
MEF_KO_iPS1_H3K4me3_peaks.bed: mm9

tag: chip antibody

value: H3K4me3; ChIP grade, ab8580, abcam

tag: strain


title: MEF_KO_iPS1_WCE

data_processing: We used Illumina CASAVA 1.8.2 software to generate fastq files. We aligned reads to mm9 reference genome using bowtie version 0.12.5. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.  We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (WCE) as control in order to define a background model.


title: MEF_KO_iPS2_H3K4me3

description: Utx KO cells that underwent improper reprogramming, Clone #2

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files. We aligned reads to mm9 reference genome using bowtie version 0.12.5. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.  We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (WCE) as control in order to define a background model.
Genome Build:
MEF_KO_iPS2_H3K4me3_peaks.bed: mm9

source_name: Mouse V19-OSKM Aberrant iPS cells, Utx-/Y, Clone #2


title: V65_KO_WCE

source_name: Mouse V6.5 ESCs, Utx-/Y


title: MEF_KO_iPS2_WCE


title: MEF_KO_iPS2_H3K27me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files. We aligned reads to mm9 reference genome using bowtie version 0.12.5. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.  We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (WCE) as control in order to define a background model.
Genome Build:
MEF_KO_iPS2_H3K27me3_peaks.bed: mm9


title: MLLr_#2

description:
Flowcell: FC80J8TABXX
Lanes: 8

data_processing:
Reads were created by CASAVA 1.7 from the GA Iix and HiSeq2000, and these are all reads which pass filter
Reads were filtered from the adapter sequences using FAR software (Dodt, M,  Ahmed R, Dieterich C. FAR – flexible adapter remover. FAR project website (2011)( http://sourceforge.net/projects/theflexibleadap/). Reads were aligned to whole genome using the bismark(http://www.bioinformatics.babraham.ac.uk/projects/bismark/) alignment tool with a maximum of 2 mismatches in a directional manner and only uniquely aligning reads were retained. In order to call methylation score for a base position, we required that read bases aligning to that position have at least 20 phred quality score and the base position should have at least 10X coverage. Only CpG dinucleotides that satisfy these coverage and quality criteria were retained for subsequent analysis. *myCpG.txt files are constructed for each CpG position in the genome. The file contains location of the CpG, total read coverage on the C base, percentage of bisulfite converted Cs (representing unmethylated Cs) and non-converted Cs (representing methylated Cs). The pipeline that aligns and calls for methylation percentage per base is available at http://code.google.com/p/amp-errbs
Genome_build: hg18

source_name: MLL rearranged Acute Myeloid Leukemia patient sample

extract_protocol: DNA was extracted using Qiagen Puregene kit protocol; Library construction protocol: Genomic DNA was purified from cell lines and primary human samples, digested with MspI restriction enzyme (200U MspI per reaction), subjected to end repair and adenylation followed by ligation to cytosine methylated paired-end Illumina adaptors (2000U T4 DNA ligase per reaction). Fragments of 150-250 bp (reduced representation bisulfite sequencing) and 150-400 bp (for enhanced reduced representation bisulfite sequencing) were isolated after agarose gel electrophoresis and subjected to bisulfite conversion (single conversion round using Zymo Research EZ DNA Methylation Kit) and PCR amplification using paired-end Illumina primers (18 cycles).  Libraries were sequenced using an Illumina Genome Analyzer II or HiSeq2000 per manufacturer’s recommended protocol for 50bp single end read runs.

tag: tissue type

value: bone marrow

value: MLL rearranged Acute Myeloid Leukemia


title: MEIS1 ChIP-seq in SEM Rep 1

description: Chromatin IP against MEIS1 in SEM

source_name: SEM

tag: antibody catalog number

value: 50 million


title: V65_KO_H3K4me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files. We aligned reads to mm9 reference genome using bowtie version 0.12.5. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.  We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (WCE) as control in order to define a background model.
Genome Build:
V65_KO_H3K4me3_peaks.bed: mm9


title: yxy-1

source_name: 7-day-hypocotyl section

tag: varieties/line

tag: tissue

value: hypocotyl

tag: developmental stages

value: 7-day-hypocotyl (initial cellular dedifferentiation)


title: V65_WCE

source_name: Mouse V6.5 ESCs

value: WT Utx+/Y


title: V65_KO_H3K27me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files. We aligned reads to mm9 reference genome using bowtie version 0.12.5. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.  We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (WCE) as control in order to define a background model.
Genome Build:
V65_KO_H3K27me3_peaks.bed: mm9


title: Runx1+/VE-cadherin+/CD41+, ChIP-seq

description: Chromatin IP against the Runx1 protein.

source_name: FACS-sorted day 6 differentiated ES cells, Runx1+/VE-cadherin+/CD41+, Runx1 ChIP

tag: cell type

tag: antibody vendor

value: Abcam

tag: antibody lot number


title: V65_H3K4me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files. We aligned reads to mm9 reference genome using bowtie version 0.12.5. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.  We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (WCE) as control in order to define a background model.
Genome Build:
V65_H3K4me3_peaks.bed: mm9


title: MEF_KO_WCE

source_name: Mouse V19-OSKM Fibroblast, Utx-/Y


title: MEF_KO_H3K4me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files. We aligned reads to mm9 reference genome using bowtie version 0.12.5. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.  We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (WCE) as control in order to define a background model.
Genome Build:
MEF_KO_H3K4me3_peaks.bed: mm9


title: MEF_KO_dox_H3K4me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files. We aligned reads to mm9 reference genome using bowtie version 0.12.5. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.  We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (WCE) as control in order to define a background model.
Genome Build:
MEF_KO_dox_H3K4me3_peaks.bed: mm9

value: DOX


title: MEF_KO_H3K27me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files. We aligned reads to mm9 reference genome using bowtie version 0.12.5. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.  We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (WCE) as control in order to define a background model.
Genome Build:
MEF_KO_H3K27me3_peaks.bed: mm9


title: MEF_KO_dox_H3K27me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files. We aligned reads to mm9 reference genome using bowtie version 0.12.5. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.  We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (WCE) as control in order to define a background model.
Genome Build:
MEF_KO_dox_H3K27me3_peaks.bed: mm9


title: Runx1+/VE-cadherin-/CD41+, ChIP-seq

description: Chromatin IP against the Runx1 protein.

source_name: FACS-sorted day 6 differentiated ES cells, Runx1+/VE-cadherin-/CD41+, Runx1 ChIP


title: V65_H3K27me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files. We aligned reads to mm9 reference genome using bowtie version 0.12.5. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.  We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (WCE) as control in order to define a background model.
Genome Build:
V65_H3K27me3_peaks.bed: mm9


title: Runx1+/VE-cadherin+/CD41-, ChIP-seq

description: Chromatin IP against the Runx1 protein.

source_name: FACS-sorted day 6 differentiated ES cells, Runx1+/VE-cadherin+/CD41-, Runx1 ChIP


title: MEF_dox_WCE

source_name: Mouse V19-OSKM Fibroblast


title: MEF_dox_H3K4me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files. We aligned reads to mm9 reference genome using bowtie version 0.12.5. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.  We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (WCE) as control in order to define a background model.
Genome Build:
MEF_dox_H3K4me3_peaks.bed: mm9


title: MEF_dox_Utx

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files. We aligned reads to mm9 reference genome using bowtie version 0.12.5. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.  We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (WCE) as control in order to define a background model.
Genome Build:
MEF_dox_Utx_peaks.bed: mm9


title: MEF_KO_dox_WCE


title: MEF_WCE


title: V65_Utx

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files. We aligned reads to mm9 reference genome using bowtie version 0.12.5. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.  We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (WCE) as control in order to define a background model.
Genome Build:
V65_Utx_peaks.bed: mm9


title: MEF_Utx

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files. We aligned reads to mm9 reference genome using bowtie version 0.12.5. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.  We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (WCE) as control in order to define a background model.
Genome Build:
MEF_Utx_peaks.bed: mm9


title: mule3680_day33_CG_RNAseq

status: Public on May 29 2012

city: Ithaca

first: Andrew

last: Clark

address: 227 Biotech Building

institute: Cornell University

data_processing:
The reads were and aligned to the horse reference genome (UCSC version equCab2) using TopHat with a maximum of three mismatches. Genome-wide allelic expression ratios were quantified for each individual mule or hinny sample at informative SNP positions.
Genome Build:
mule3680CG_SNP_counts.txt: UCSC equCab2

organism: Equus asinus x Equus caballus

source_name: mule_embryonic day33_chorionic girdle

extract_protocol: The mRNA-seq libraries were made with 3 ug of starting total RNA samples using the mRNA-Seq 8-Sample Prep Kit (Illumina Inc., CA), following the Illumina protocol for mRNA sequencing sample preparation.

value: invasive trophoblast tissue of the chorionic girdle

tag: developmental stage

value: embryonic day 33

tag: gender

value: female