title: human_wbc.paired

source_name: white blood cells


title: human_thyroid.paired

status: Public on Jan 05 2012

type: SRA

city: Cambridge

first: Robert

middle: K

last: Bradley

state: MA

address: 77 Massachusetts Avenue, 68-223A

department: Biology

country: USA

institute: MIT

library_source: transcriptomic

data_processing:
Alignment: The files human.nagnag.junctions.gff and mouse.nagnag.junctions.gff (see Series supplementary files) give the intron-proximal and intron-distal splice junctions of all NAGNAG splicing events analyzed in this study. The 'start' field specifies the last base of the upstream exon and the 'end' field specifies the first base of the downstream exon (upstream and downstream defined with respect to the gene). For each NAGNAG, we extracted the transcript sequence flanking the proximal and distal 3' splice sites and used Bowtie version 0.12.7 to map reads to these two sequences. We required that short reads have at least 6 nt on either side of the splice junction (an "overhang" of 6 nt), and furthermore that there be no mismatches within the overhang region.
Human genome build: hg19
Mouse genome build: mm9

molecule: polyA RNA

organism: Homo sapiens

source_name: thyroid

extract_protocol:
Human: RNA-Seq libraries are from the Body Map 2.0 dataset distributed by Illumina, available at the ENA archive with accession number ERP000546.
Mouse: Tissues from a 10-week-old male were extracted immediately after death and stored in RNAlater per the manufacturerâs instructions (Ambion). Tissue was lysed in Trizol and RNA was extracted with Qiagen miRNeasy mini columns. Using 5ug of total RNA, we performed polyA selection and prepared strand-specific libraries for Illumina sequencing following the dUTP protocol and the SPRIworks Fragment library system (Beckman Coulter). We obtained final insert sizes of approximately 160 bp. We sequenced these libraries using the Illumina HiSeq 2000 and the GAIIx machines.

tag: library type

value: paired-end

tag: read length

tag: insert size

tag: insert standard deviation


title: asbestos exposed SCC 37

status: Public on Jan 30 2012

type: RNA

city: Concord

first: Casey

middle: M

last: Wright

state: NSW

address: Gate 3, Hospital Road

country: Australia

institute: ADRI

description: Lung tumour from asbestos exposed individual (>20AB/gww)

hyb_protocol: Standard Illumina hybridisation protocols were used.

scan_protocol: Standard Illumina scanning protocols were used.

data_processing: Data was normalised using the 75th percentile algorithm in GeneSpring version 9.0 and missing values filled using the K-Nearest Neighbour algorithm.

molecule: total RNA

source_name: Lung Tumour Tissue

label_protocol: Biotinylated cRNA was generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion.

extract_protocol: Total RNA was extracted from fresh-frozen tissue using TRIZOL (Invitrogen) and miRNEASY (QIAGEN) clean-up and quality assessed using the Agilent Bioanalyzer.

tag: age

tag: sex

value: M

tag: smoking pack per year

tag: smoking status

value: Smoker

tag: tnm stage

value: IIIA

tag: self-reported asbestos exposure

value: No

tag: asbestos count

tag: exposure

value: asbestos exposed individual (>20AB/gww)

tag: tissue

value: lung tumor


title: human_skeletal_muscle.paired

source_name: skeletal muscle


title: human_ovary.paired

source_name: ovary


title: mouse_liver.A

organism: Mus musculus

source_name: liver

tag: strain


title: human_lung.paired

source_name: lung


title: mouse_brain.B

source_name: brain


title: Endogenous small RNAs from Brassica napus XZ366 (high seed oil cultivar) siliques planted at Lhasa

status: Public on Dec 28 2011

city: Old Westbury

first: Ying-Tao

last: Zhao

state: NY

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

institute: New York Institute of Technology

data_processing: sequence and count informations for high quality small RNAs

organism: Brassica napus

source_name: Siliques

growth_protocol: Plants were grown in the experimental fields.

extract_protocol: Total RNAs were isolated using Trizol reagent (Invitrogen). Fifteen- to 30-nt small RNAs from total RNA were gel extracted from a 15% denaturing acrylimide gel. The adapter ligation and sequencing were following the Illumina's Solexa sequencing protocol.

tag: cultivar

value: silique

tag: location

value: Lhasa

tag: development stage

value: 3, 7, 14, 21 days after flowering, pooled together


title: human_testes.paired

source_name: testes

tag: library type


title: human_heart.paired

source_name: heart

tag: read length


title: human_brain.paired

tag: insert size


title: human_adrenal.paired

source_name: adrenal

tag: insert standard deviation


title: human_kidney.paired

source_name: kidney


title: human_prostate.paired

source_name: prostate


title: Col0-CMV∆2b_rep2_At_matches

status: Public on Mar 01 2012

city: Riverside

first: JUAN

last: JOVEL

state: CA

address: 3401 Watkins Drive

department: Plant Pathology

institute: University of California Riverside

data_processing:
Reads were extracted using the Illumina pipeline.  Trimming of adapters and down-stream analyses were carried out with in-house Perl scripts, except alignments of short reads to Arabidopsis or CMV sequences, which were performed with bowtie (no mistmatches were allowed).
All sequences containing perfect match 5' barcode (ATC/CGT/TAC) and at least 6 sucessive perfect-matched nucleotides of the 3' linker were kept for later analysis. The barcode and linker sequences were computationally removed by in-house perl scripts. All trimmed sequences in length of 18-30nt were aligned with CMV genome and the perfect matched reads were used for all further analysis.

organism: Arabidopsis thaliana

source_name: Systemically-infected leaves

growth_protocol: Arabidopsis plants were grown in our glass houses under stardard conditions.

extract_protocol:
Low molecular weight RNAs extracted by Trizol (Invitrogen) from the systemically infected leaves 14 days after inoculation with CMV-Δ2b were purified from 15% denatured polyacrylamide gel. Purified small RNAs were directly ligated to the 3′-linkers for miRNA cloning (Integrated DNA Technology) by T4 RNA ligase 2Tr (New England Biolabs). The ligation products were purified and ligated to a suitable 5′ Solexa linker by T4 RNA ligase I (New England Biolabs). The final ligation products were reverse transcribed using a primer targeting the 3′-linker and the cDNA pool was amplified by PCR and sequenced by the Solexa technology (Illumina) in our campus facility. Duplicate libraries were constructed from two independent RNA samples.
immunoprecipitation: Three g systemic leaves from FLAG-AGO1 or HA-AGO2 plants infected with CMV-Δ2b were ground to powder in liquid nitrogen and supplied with 10 ml of extraction buffer [20 mM Tris•HCl, pH 7.5/300 mM NaCl/5 mM MgCl2/5 mM DTT/1% plant protease inhibitor mixture (Sigma)].  The suspension was clarified by centrifugation (10 min, 4ºC, 14,000 rpm) and the supernatant filtered through cheesecloth. The filtered supernatant was incubated with anti-FLAG M2 agarose (Sigma-Aldrich) or anti-HA affinity matrix (Roche), according to manufacturers’ protocols, for 4h at 4ºC.  The beads were then washed twice with extraction buffer supplemented with 0.5% Nonidet P-40 and the AGO-bound RNA extracted with TRIzol.

tag: genotype

tag: source

value: Total RNA


title: human_breast.paired

source_name: breast


title: Endogenous small RNAs from Brassica napus XZ088 (low seed oil cultivar) siliques planted at Nanjing 1

value: Nanjing


title: Endogenous small RNAs from Brassica napus XZ366 (high seed oil cultivar) siliques planted at Nanjing


title: Endogenous small RNAs from Brassica napus XZ088 (low seed oil cultivar) siliques planted at Lhasa


title: pat1.114 5 hours following the temperature shift from 25ºC to 32ºC (second machine run)

status: Public on Dec 20 2011

city: London

first: Danny

middle: Asher

last: Bitton

address: Darwin Building, Gower Street

department: Department of Genetics, Evolution & Environment

country: United Kingdom

institute: University College London

description: Sequencing was performed using two slides (designated with the suffix S1 and S2, respectievly); SOLiD 3.0+

data_processing: Reads of length 50 bases originating from each sample were aligned using Bowtie (Langmead et al, 2009) to the Schizosaccharomyces pombe genome sequence (Ensembl Schizosaccharomyces pombe, Build EF1, version 58.1a) as well as to its corresponding exon-exon junctions database.  Alignments were performed with no mismatches and reads that matched multiple loci were removed from further analysis and the resultant alignment files pre-processed to generate "pile-ups" against each chromosome. Transcription stretches (TBlocks) were detected independently of known annotation using sequence data from samples obtained following the first machine run. Briefly, the algorithm was designed to assemble neighbouring expressed genomic segments into a single transcriptional unit (TBlock) only if those segments were continuously covered by sequence reads across the different samples (with no region larger than 50bp that is not covered).Tblocks were than aligned to the Schizosaccharomyces pombe genome, to define maximum Transcription Start and Termination Sites (TSS and TTS, respectively). The sequencing data was then queried using coordinates from the augmented Schizosaccharomyces pombe annotation including known exons, introns as well as of newly defined untranslated regions (UTRs), anti-sense loci and intergenic TBlocks (UTRs). Using the read counts obtained for a given region, a corresponding expression level was calculated, normalized (by the number of reads in each sample, as well as by the region's length) and log2 transformed. Finally, summarized gene level, antisense, intronic and intergenic TBlocks expression values were reported.

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe cells

growth_protocol: Cells were grown in EMM2 media at  25ºC. For pat1.114 induced meioses the appropriate pat1.114 diploid strains were transferred to 32ºC and samples taken before (0) and 3, 5 and 10 hours after the shift.

extract_protocol: RNA extraction: Total RNA was extracted from Schizosaccharomyces pombe cells as described previously (Lyne et al, 2003). Cells were treated with hot acidic phenol-chloroform, followed by phenol-chloroform extraction, RNA precipitation and column purification. RNA quality was determined using an Agilent 2100 Bioanalyser. Ribosomal reduction: Total RNA (9 ug) was "ribosomally reduced" using the Ribominus Eukaryote Kit for RNA Seq (Invitrogen A10837-08) and the Ribominus Concentration Module (Invitrogen K155005). Samples had one or several rounds of ribosomal reduction until they showed a ribosomal reduction of 90% or above on the Agilent Bioanalyser. Libraries were prepared with 500 ng of ribosomally reduced total RNA using the SOLiD Whole Transcriptome Analysis Kit for the first sequencing run; vegetative, IH5974 and IH2912 (before (timepoint 0) and 3, 5, and 10 hours after temperature shift from 25°C to 32°C) (Applied Biosystems 4425680) and the SOLiD Total RNA-Seq Kit for the second sequencing run that included additional 14 samples; vegetative, asynchronous IH5974 (wild type), and a vegetative, asynchronous IH3365 (wild type diploid) alongside temperature shifted: IH2912 (pat1.114 diploid), IH8832 (atf21.delta diploid) and IH8814 (atf31.delta diploid) before, and 3, 5, and 10 hours after a shift from 25ºC to 32ºC to induce meiosis (Applied Biosystems 4445374) with the following changes: RNase III digestion time was increased to 25 minutes, size selection was carried using E-GEL Size Select 2% Agarose Gels (Invitrogen G661002) on the E-GEL iBase power system (Invitrogen G6400UK). Sample barcoding was carried out using the SOLiD Transcriptome Multiplexing Kit (Applied Biosystems 4427046). The libraries were measured on the Qubit Fluorometer (Invitrogen Q3287) using the Quant-IT DSDNA HS Assay Kit (Invitrogen Q32851) and the molarities assessed by a DNA1000 assay (Agilent Technologies) on the Agilent Bioanalyzer (G2938C) before pooling the libraries in equimolar quantities. Sequencing was performed on an AB SOLiD machine (first run 3.0; second run 3.0+).

tag: cell type

value: Diploid

tag: cell state

value: Meiotic


title: pat1.114 3 hours following the temperature shift from 25ºC to 32ºC (second machine run)


title: atf21.delta pat1.114  diploid before the temperature shift from 25ºC to 32ºC (t 0; second machine run)

value: Vegetative growth


title: pat1.114 before the temperature shift from 25ºC to 32ºC (t 0; second machine run)


title: Asynchronous diploid (second machine run)

value: Asynchronous; vegetative growth


title: atf21.delta pat1.114 3 hours following the temperature shift from 25ºC to 32ºC (second machine run)


title: atf31.delta pat1.114 5 hours following the temperature shift from 25ºC to 32ºC (second machine run)


title: atf31.delta pat1.114 before the temperature shift from 25ºC to 32ºC (t 0; second machine run)


title: atf31.delta pat1.114 3 hours following the temperature shift from 25ºC to 32ºC  (second machine run)


title: atf21.delta pat1.114 10 hours following the temperature shift from 25ºC to 32ºC (second machine run)


title: atf21.delta pat1.114 5 hours following the temperature shift from 25ºC to 32ºC (second machine run)


title: pat1.114 10 hours following the temperature shift from 25ºC to 32ºC (second machine run)


title: pat1.114 10 hours following the temperature shift from 25ºC to 32ºC (first machine run)

description: Sequencing was performed using a single slide; SOLiD 3.0; file 1 of 1


title: Asynchronous haploid (second machine run)


title: atf31.delta pat1.114 10 hours following the temperature shift from 25ºC to 32ºC (second machine run)


title: pat1.114 5 hours following the temperature shift from 25ºC to 32ºC (first machine run)


title: SuperSAGE data from skunk cabbage spadices (male stage_1)

status: Public on Dec 22 2011

city: Miyazaki

first: Takehito

last: Inaba

state: Miyazaki

address: 1-1 Gakuenkibanadai-nishi

department: Interdisciplinary Research Organization

country: Japan

institute: University of Miyazaki

description: The sequence data was obtained using 454 GS-20.

data_processing: The software 454 pipe was applied to analyze the sequence data.

organism: Symplocarpus renifolius

source_name: Skunk cabbage spadices

extract_protocol: Total RNA of spadices in different developmental stage (immature, female, bisexual, and male) were isolated using RNAiso reagent.

value: Spadices

tag: developmental stage

value: Male stage


title: asbestos exposed SCC 32

tag: age

tag: sex

value: M

tag: smoking pack per year

tag: smoking status

tag: tnm stage

value: IB

tag: self-reported asbestos exposure

value: unknown


title: non-exposed SCC 26

description: Lung tumour from non-exposed individual (0AB/gww)

value: Smoker

value: No

tag: asbestos count

tag: exposure

value: non-exposed individual (0AB/gww)

tag: tissue


title: 0-2 hr embryo

status: Public on Dec 16 2011

city: Blacksburg

first: Zhijian

last: Tu

state: VA

address: 309 Engel Hall

department: Biochemistry

institute: Virginia Tech

data_processing:
sam01_fa_bowtie.bed; genome build: AaegL1
a. NGS transcriptome raw data were alinged to the Ae. aegypti        supercontigs genome (AaegL1 by http://www.vectorbase.org)        using Bowtie (Ver. 0.12.7 - http://bowtie-bio.sourceforge.net)        alignment program.               Options: default quality policy (-n 2 -l 28 -e 70) with       --best option. See the Bowtie manual at        http://bowtie-bio.sourceforge.net/manual.shtml      b. Bowtie outputs (.map) were converted to the SAM format by        SAMtools (http://samtools.sourceforge.net/).      c. SAM files were converted to the BAM binary format by       SAMtools.      d. BAM binary format were converted to the BED format by       bedtools (http://code.google.com/p/bedtools/).

organism: Aedes aegypti

source_name: embryo, Liverpool strain

growth_protocol: Mosquitoes were reared in a 28 degree C incubator.

extract_protocol: RNA-Seq

treatment_protocol: Female mosquitoes were both blood fed or nonbloodfed depending on the sample

tag: strain

value: Liverpool

value: embryo

value: 0-2 hr embryo


title: 4-8 hr embryo

data_processing:
sam03_fa_bowtie.bed; genome build: AaegL1
a. NGS transcriptome raw data were alinged to the Ae. aegypti        supercontigs genome (AaegL1 by http://www.vectorbase.org)        using Bowtie (Ver. 0.12.7 - http://bowtie-bio.sourceforge.net)        alignment program.               Options: default quality policy (-n 2 -l 28 -e 70) with       --best option. See the Bowtie manual at        http://bowtie-bio.sourceforge.net/manual.shtml      b. Bowtie outputs (.map) were converted to the SAM format by        SAMtools (http://samtools.sourceforge.net/).      c. SAM files were converted to the BAM binary format by       SAMtools.      d. BAM binary format were converted to the BED format by       bedtools (http://code.google.com/p/bedtools/).

value: 4-8 hr embryo


title: 8-12 hr embryo

data_processing:
sam04_fa_bowtie.bed; genome build: AaegL1
a. NGS transcriptome raw data were alinged to the Ae. aegypti        supercontigs genome (AaegL1 by http://www.vectorbase.org)        using Bowtie (Ver. 0.12.7 - http://bowtie-bio.sourceforge.net)        alignment program.               Options: default quality policy (-n 2 -l 28 -e 70) with       --best option. See the Bowtie manual at        http://bowtie-bio.sourceforge.net/manual.shtml      b. Bowtie outputs (.map) were converted to the SAM format by        SAMtools (http://samtools.sourceforge.net/).      c. SAM files were converted to the BAM binary format by       SAMtools.      d. BAM binary format were converted to the BED format by       bedtools (http://code.google.com/p/bedtools/).

value: 8-12 hr embryo


title: SuperSAGE data from skunk cabbage spadices (female stage_2)

value: Female stage


title: 2-4 hr embryo

data_processing:
sam02_fa_bowtie.bed; genome build: AaegL1
a. NGS transcriptome raw data were alinged to the Ae. aegypti        supercontigs genome (AaegL1 by http://www.vectorbase.org)        using Bowtie (Ver. 0.12.7 - http://bowtie-bio.sourceforge.net)        alignment program.               Options: default quality policy (-n 2 -l 28 -e 70) with       --best option. See the Bowtie manual at        http://bowtie-bio.sourceforge.net/manual.shtml      b. Bowtie outputs (.map) were converted to the SAM format by        SAMtools (http://samtools.sourceforge.net/).      c. SAM files were converted to the BAM binary format by       SAMtools.      d. BAM binary format were converted to the BED format by       bedtools (http://code.google.com/p/bedtools/).

value: 2-4 hr embryo


title: Asynchronous haploid (first machine run)


title: SuperSAGE data from skunk cabbage spadices (male stage_2)


title: pat1.114 3 hours following the temperature shift from 25ºC to 32ºC (first machine run)

value: Diploid

value: Meiotic


title: SuperSAGE data from skunk cabbage spadices (immature stage)

description: The sequence data were obtained using 454 GS-20.

value: Spadices

value: immature stage


title: pat1.114 before the temperature shift from 25ºC to 32ºC (t 0; first machine run)

value: Vegetative growth


title: SuperSAGE data from skunk cabbage spadices (female stage_1)


title: SuperSAGE data from skunk cabbage spadices (bisexual stage_2)

source_name: Skunk cabbage spadies

value: Bisexual stage


title: SuperSAGE data from skunk cabbage spadices (bisexual stage_1)

value: bisexual stage


title: SuperSAGE data from skunk cabbage spadices (male stage_3)

value: Male stage


title: stalk

status: Public on Dec 12 2011

city: Tainan

first: Feng-Ming

last: An

address: No. 59, Silaya Blvd., Sinshi Dist.

department: Biotechnology Center in Southern Taiwan

country: Taiwan

institute: Academia Sinica

description: analysis of miRNA against miRBase 15

data_processing:
Raw data were processed by removing the adaptor/acceptor sequences, contaminants and low quality reads. To identify degradation tags of rRNA, tRNA, snRNA and snoRNA, sequences were aligned using Rfam 10.0 (http://rfam.sanger.ac.uk/) and the Genbank database (http://www.ncbi.nlm.nih.gov/). The final dataset containing reads of orchid smRNA sequences were used for this study.
Known miRNAs were downloaded from the miRBase15.0 database (http://www. mirbase.org/ftp.shtml). Alignment of fully complementary sequences, those with one mismatch or two mismatches, was performed using the BLAST algorithm to identify conserved miRNA orthologs. The number of aligned sequences was restricted by limiting the mismatch plus gap to fewer than 5 residues.

organism: Phalaenopsis aphrodite subsp. formosana

source_name: stalk

growth_protocol: Seedlings of Phalaenopsis aphrodite subsp. formosana (M1624) were purchased from Chain Port Orchid Co., Ltd (Chengde Village, Taiwan) and grown in 2.5 in. diameter plastic pots filled with sphagnum moss in an environment-controlled greenhouse, at a constant temperature of 28ºC for 7-8 months.

extract_protocol: Total RNA extraction was performed using Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. Small RNAs were size fractionized on a 15% denaturing polyacrylamide gel. Subsequently, gel bands corresponding to fragments in the size range of 20–25 nt were excised and eluted into 0.3 M NaCl. The eluted smRNAs were sequentially ligated to 5’- and 3’-adaptors and converted to DNA using RT-PCR.

treatment_protocol: Plants comprising the untreated group were subsequently grown at 32°C/27°C (light/dark) to inhibit phase transition. Low ambient temperature treatment was carried out at 24°C/18°C (light/dark) for two months to complete phase transition. Leaves with or without low temperature treatment were collected at 0.5 month intervals from zero to two months. Stalks and flower buds were only present in the low temperature treatment group. Stalks were collected at 1.5 and 2 months, while flower buds were collected at 3.5 months.

value: stalk

tag: treatment

value: low temprature


title: flower_bud

description: analysis of miRNA against miRBase 15

source_name: flower bud

value: flower bud


title: low_temp_leaf

description: analysis of miRNA against miRBase 15

source_name: leaf

value: leaf


title: mouse_colon.A

source_name: colon

tag: library type

value: paired-end

tag: read length

tag: insert size

tag: insert standard deviation


title: untreated_leaf

description: analysis of miRNA against miRBase 15


title: S461_wt90

status: Public on Dec 15 2011

city: Erlangen

first: Roland

last: Lang

address: Wasserturmstr. 3-5

country: Germany

institute: University Hospital Erlangen

description: Gene expression data from bone marrow derived macrophages

hyb_protocol: 5 µg of biotinylated DNA were hybridized to Mouse Gene ST 1.0 GeneChips overnight, followed by washing and staining procedures, and scanning, following Affymetrix protocols.

scan_protocol: Scanning following Affymetrix protocols

data_processing: For generation of probe set expression values, CEL files containing probe level data were normalized using RMA (Affymetrix Expression Console).

label: biotin

source_name: bone marrow derived macrophages

label_protocol: RNA samples were processed and hybridised to Affymetrix Mouse Gene ST 1.0 GeneChips according to the manufacturer’s protocols. In brief, 200 ng total RNA and 100 ng nascent RNA were reverse transcribed introducing by random priming a T7-binding site into the cDNA that allows in vitro transcription. The resulting cRNA was subjected to a second round of random primed cDNA synthesis in the presence of dUTP, that allows fragmentation of the cDNA with uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1. Biotinylation of the fragmented cDNA was accomplished by incubation with Terminal Deoxynucleotidyltransferase (TdT).

growth_protocol: Bone marrow cells from C57Bl/6 mice were differentiated to macrophages (BMDM) with M-CSF-containing medium

extract_protocol: Total RNA was extracted with Trizol (Invitrogen Life Technologies, Carlsbad, CA) according to the manufacturer’s instruction. Concentration and integrity of total RNA were determined by spectrophotometry (Nanodrop) and Experion automated electrophoresis system (Biorad, Munich, Germany).

treatment_protocol: BMDMs from Wt and TTP-/- mice were treated with LPS for 3 h. Medium was then replaced by fresh medium containing actinomycin D and SB203580 for 0, 45 and 90 min before RNA preparation.

tag: cell type

value: bone marrow cells

tag: genotype

value: WT

tag: time after actd

value: 90 min

tag: rep


title: S464_KO90

value: TTP-/-


title: S460_wt45

value: 45 min


title: S468_KO_2

value: 0 min


title: S463_KO45


title: S459_wt


title: S467_WT90_2


title: S462_KO


title: S335_KO90_3


title: S332_wt90_3


title: S469_KO45_2


title: S333_KO_3


title: S334_KO45_3


title: S466_WT45_2


title: S331_wt_45_3


title: S465_WT_2


title: S330_wt_3

tag: time fter actd


title: S470_KO90_2


title: panicle, heat + salt rep1

city: NEWARK

first: Dong-Hoon

last: Jeong

state: DE

address: 15 Innovation Way

institute: University of Delaware

data_processing: The adaptor sequences were identified and removed by using a Perl script. Small RNAs shorter than 15 nt were removed. Data matrix contains distinct small RNAs with their raw abundance after removing the adapter sequences.

organism: Oryza sativa

source_name: panicle, heat + salt

growth_protocol: Rice seeds (Oryza sativa L, ssp. japonica cv. Nipponbare) were husked, surface-sterilized with 3% sodium hydrochlorite, washed with sterile water three times, and germinated on half-strength Murashige and Skoog (MS) medium containing 0.2% (w/v) Phytagel in a sterile plastic box. Plants were grown in a growth chamber under conditions of 12 h light at 28°C and 12 h dark at 25°C.

extract_protocol: Small RNA libraries were constructed as previously described (Lu et al. 2007) and sequenced on llumina 1G or IIGX analyzer. Sequencing was performed at Illumina, National Center for Genome Research, Cold Spring Harbor Laboratory, or the Delaware Biotechnology Institute.

treatment_protocol: Nine-day-old seedlings were acclimated for five days by opening the plastic cap and adding tap water onto the MS agar medium. Five days later, 2-week-old seedlings were moved to tap water in a glass tube and used for stress treatments and controls. For drought treatment, seedlings were air-dried for 8 h. For salt stress treatment, seedlings were transferred to 300 mM NaCl solution for 8 h. For cold stress treatment, seedlings were transferred to 4° C in a cold room under continuous light for 8 h. For heat stress treatment, seedlings were moved to 42°C for 8 h. Dual stresses were also treated under the same conditions. Control plants were sampled at the same time. All the collected tissues were immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction. For nutrient starvation treatments, the endosperm was first removed from 9-day-old seedlings to avoid nutrient transport. Seedlings were then transferred to MS nutrient-deficient media or MS media (for control). For MS nutrient-deficient media, specific components of MS were omitted or substituted with others as follows: For nitrogen-deficient medium, NH4NO3 was omitted and KCl was substituted for KNO3. For phosphate-deficient medium, KH2PO4 was omitted. For potassium-deficient medium, KNO3 was omitted. For sulfate-deficient medium, all SO4 was substituted with Cl2. After five days of treatment, shoots and roots were separated for independent analysis. Mature plants at the booting stage were treated with various environmental stresses under the same conditions as described above, but for three days with the exception of the drought treatment. For drought treatment, pots were removed from the water, and holes were punched in the pots to help draining, and dehydrated for seven days. After stress treatment, mature panicles were sampled, which were about 15 cm and wrapped with panicle sheath.

tag: cultivar

value: panicle


title: panicle, OsDCL1 RNAi rep2-1

source_name: panicle, OsDCL1 RNAi

value: Oryza sativa L, ssp. japonica cv. Nipponbare


title: panicle, OsDCL1 RNAi rep1-1


title: panicle, cold + salt rep1

source_name: panicle, cold + salt


title: panicle, heat + drought rep1

source_name: panicle, heat + drought


title: panicle, cold rep1

source_name: panicle, cold


title: shoot, -K rep1

source_name: shoot, potassium-deficient medium

value: shoot


title: panicle, salt rep1-1

source_name: panicle, salt


title: panicle, drought rep1-1

source_name: panicle, drought


title: shoot, -K +salt rep1

source_name: shoot, potassium-deficient medium +salt


title: shoot, -N rep1

source_name: shoot, nitrogen-deficient medium


title: panicle, heat rep1

source_name: panicle, heat


title: panicle, control rep1-1

source_name: panicle, control


title: shoot, -S rep1

source_name: shoot, sulfate-deficient medium


title: seedling, drought rep1

source_name: seedling, drought

value: seedling


title: shoot, -P rep1

source_name: shoot, phosphate-deficient medium


title: root, -K +salt rep1

source_name: root, potassium-deficient medium +salt

value: root


title: seedling, salt rep1

source_name: seedling, salt


title: root, drought rep1

source_name: root, drought


title: root, -K rep1

source_name: root, potassium-deficient medium


title: panicle, OsDCL1 RNAi rep2-2

source_name: panicle, OsDCL1 RNAi


title: root, -N rep1

source_name: root, nitrogen-deficient medium


title: shoot, -K +salt rep2

source_name: shoot, potassium-deficient medium+salt


title: panicle, cold rep2

source_name: panicle, cold


title: panicle, drought rep2


title: root, -P rep1

source_name: root, phosphate-deficient medium


title: panicle, salt rep2

source_name: panicle, salt


title: root, -S rep1

source_name: root, sulfate-deficient medium


title: panicle, salt rep1-2


title: shoot, control rep1

source_name: shoot, control


title: panicle, drought rep1-2

source_name: panicle, drought


title: shoot, -N rep2

source_name: shoot, nitrogen-deficient medium


title: shoot, -S rep2

source_name: shoot, sulfate-deficient medium


title: seedling, control rep1

source_name: seedling, control


title: panicle, OsDCL1 RNAi rep1-2


title: seedling, cold rep1

source_name: seedling, cold


title: root, drought rep2


title: root, control rep1

source_name: root, control


title: panicle, control rep1-2

source_name: panicle, control


title: Homo_sapiens_genome_rep1_F

status: Public on Dec 08 2011

type: genomic

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

description: replicate-1 chip-F

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Supplementary files contain results from Model Based analysis of tiling arrays (MAT) was used to process the data as described previously: Johnson, et al, 2006, PMID: 16895995

molecule: genomic DNA

source_name: FoxA1 ChIP DNA (abl)

label_protocol: The amplified ChIP'ed DNA was labelled with biotin.

growth_protocol: LNCaP and abl were cultured in RPMI 1640/10% FBS and RPMI 1640/10% charcoal-stripped FBS, respectively.

extract_protocol: FoxA1 ChIP was performed followed by amplification using ligation-mediated PCR.

tag: cell line

value: abl

tag: antibody

tag: phenotype

value: androgen-independent

tag: antibody manufacturer

value: Abcam

tag: antibody catalog #

source_name: FoxA1 ChIP DNA (LNCaP)

value: androgen-dependent

value: LNCaP


title: Homo_sapiens_genome_rep3_E

description: replicate-3 chip-E


title: Homo_sapiens_genome_rep2_F

description: replicate-2 chip-F


title: seedling, heat + drought rep1

source_name: seedling, heat + drought

tag: tissue


title: Homo_sapiens_genome_rep3_G

description: replicate-3 chip-G


title: seedling, heat + salt rep1

source_name: seedling, heat + salt


title: shoot, -K rep2

source_name: shoot, potassium-deficient medium


title: Homo_sapiens_genome_rep2_E

description: replicate-2 chip-E


title: Homo_sapiens_genome_rep1_E

description: replicate-1 chip-E


title: seedling, OsDCL1 RNAi rep1-1

source_name: seedling, OsDCL1 RNAi


title: Homo_sapiens_genome_rep3_B

description: replicate-3 chip-B


title: Homo_sapiens_genome_rep1_G

description: replicate-1 chip-G


title: seedling, heat rep1

source_name: seedling, heat


title: Homo_sapiens_genome_rep3_A

description: replicate-3 chip-A


title: Homo_sapiens_genome_rep3_F

description: replicate-3 chip-F


title: Homo_sapiens_genome_rep2_A

description: replicate-2 chip-A


title: Homo_sapiens_genome_rep2_G

description: replicate-2 chip-G


title: Homo_sapiens_genome_rep2_B

description: replicate-2 chip-B


title: seedling, control rep2


title: Homo_sapiens_genome_rep1_B

description: replicate-1 chip-B


title: root, -K +salt rep2

source_name: root, potassium-deficient medium +salt


title: Homo_sapiens_genome_rep1_A

description: replicate-1 chip-A


title: Homo_sapiens_genome_rep3_D

description: replicate-3 chip-D


title: seedling, cold + salt rep1

source_name: seedling, cold + salt


title: Homo_sapiens_genome_rep1_D

description: replicate-1 chip-D


title: root, -K rep2

source_name: root, potassium-deficient medium


title: Pellet_15min_(Pellet_20110428_5)

status: Public on Dec 07 2011

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Insoluble MNase-protected DNA fragments, 15 minute digestion

library_source: genomic

data_processing: 1. We used Novoalign to map paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. 50bp reads were trimmed to 25bp. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file Pellet_20110428_5..sam) Because the DNA sample was pooled with DNA from Drosophila melanogaster, we removed all paired reads that mapped to both organisms. 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file Pellet_20110428_5..wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

organism: Saccharomyces cerevisiae

source_name: input DNA

extract_protocol: Yeast nuclei were prepared as described [Furuyama, S., and Biggins, S. (2007), Centromere identity is specified by a single centromeric nucleosome in budding yeast, Proc Natl Acad Sci USA 104, 14706-14711], flash-frozen in liquid nitrogen and stored at -80oC. Nuclei were thawed at room temperature and digested with MNase followed by chromatin preparation as described [Furuyama and Biggins, (2007)], except that after MNase digestion, the slurry was passed four times through a 20 guage needle, then four times through a 26 guage needle [Jin, C., and Felsenfeld, G. (2007), Nucleosome stability mediated by histone variants H3.3 and H2A.Z, Genes Dev 21, 1519-1529].DNA from insoluble pellet was extracted using a standard protocol [Mito, Y., Henikoff, J., and Henikoff, S. (2005), Genome-scale profiling of histone H3.3 replacement patterns, Nat Genet 37, 1090-1097]. A modified Illumina Solexa library protocol was used as described in supplementary file Solexa_library_protocol_GEO.pdf.

tag: strain

tag: medium

value: YEPD grown:OD=0.8

tag: sample type


title: Homo_sapiens_genome_rep2_C

description: replicate-2 chip-C


title: Cse4_20min_(B20_20110622_3)

description: MNase-protected DNA fragments from Cse4-FLAG immunoprecipitation of native chromatin, 20 minute digestion

data_processing: 1. We used Novoalign to map 25bp paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file B20_20110622_3.bam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file B20_20110622_3.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

source_name: DNA from Cse4-FLAG chromatin immunoprecipitation

extract_protocol:
Yeast nuclei were prepared as described [Furuyama, S., and Biggins, S. (2007), Centromere identity is specified by a single centromeric nucleosome in budding yeast, Proc Natl Acad Sci USA 104, 14706-14711], flash-frozen in liquid nitrogen and stored at -80oC. Nuclei were thawed at room temperature and digested with MNase followed by chromatin preparation as described [Furuyama and Biggins, (2007)], except that after MNase digestion, the slurry was passed four times through a 20 guage needle, then four times through a 26 guage needle [Jin, C., and Felsenfeld, G. (2007), Nucleosome stability mediated by histone variants H3.3 and H2A.Z, Genes Dev 21, 1519-1529], and the combined S1+S2 supernatants were clarified by centrifugation in a fixed-angle Sorvall SS34 rotor at 12,000 rpm at 4oC for 10 min at least twice or until no visible pellet remained. ChIP was performed as previously described [Furuyama and Biggins, (2007)], and DNA was extracted using a standard protocol [Mito, Y., Henikoff, J., and Henikoff, S. (2005), Genome-scale profiling of histone H3.3 replacement patterns, Nat Genet 37, 1090-1097]. A modified Illumina Solexa library protocol was used as described in supplementary file Solexa_libarary_protocol_GEO.pdf.
For Flag IP, we used Sigma A2220 Anti Flag M2 Affinity gel; lot 020M6014.

value: Sigma A2220 Anti Flag M2 Affinity gel


title: shoot, -P rep2

source_name: shoot, phosphate-deficient medium


title: panicle, control rep2


title: H2A_15min_(H2A_20110428_8)

description: MNase-protected DNA fragments from H2A-FLAG immunoprecipitation of native chromatin, 15 minute digestion

data_processing: 1. We used Novoalign to map paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. 50bp reads were trimmed to 25bp. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file H2A_20110428_8.sam) Because the DNA sample was pooled with DNA from Drosophila melanogaster, we removed all paired reads that mapped to both organisms. 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file H2A_20110428_8.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

extract_protocol: Yeast nuclei were prepared as described [Furuyama, S., and Biggins, S. (2007), Centromere identity is specified by a single centromeric nucleosome in budding yeast, Proc Natl Acad Sci USA 104, 14706-14711], flash-frozen in liquid nitrogen and stored at -80oC. Nuclei were thawed at room temperature and digested with MNase followed by chromatin preparation as described [Furuyama and Biggins, (2007)], except that after MNase digestion, the slurry was passed four times through a 20 guage needle, then four times through a 26 guage needle [Jin, C., and Felsenfeld, G. (2007), Nucleosome stability mediated by histone variants H3.3 and H2A.Z, Genes Dev 21, 1519-1529], and the combined S1+S2 supernatants were clarified by centrifugation in a fixed-angle Sorvall SS34 rotor at 12,000 rpm at 4oC for 10 min at least twice or until no visible pellet remained. ChIP was performed as previously described [Furuyama and Biggins, (2007)], and DNA was extracted using a standard protocol [Mito, Y., Henikoff, J., and Henikoff, S. (2005), Genome-scale profiling of histone H3.3 replacement patterns, Nat Genet 37, 1090-1097]. A modified Illumina Solexa library protocol was used as described in supplementary file Solexa_library_protocol_GEO.pdf.

value: Sigma A2220 Anti Flag M2 Affinity gel; lot 020M6014


title: root, -S rep2

source_name: root, sulfate-deficient medium


title: Pellet_20min_(P20P_20110706_8)

description: Insoluble MNase-protected DNA fragments, 20 minute digestion

data_processing: 1. We used Novoalign to map 25bp paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file P20P_20110706_8.bam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file P20P_20110706_8.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

source_name: insoluble chromatin


title: Nuclei_15min_(Nuc_20110428_4)

description: All MNase-protected DNA fragments, 15 minute digestion

data_processing: 1. We used Novoalign to map paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. 50bp reads were trimmed to 25bp. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file Nuc_20110428_4..sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file Nuc_20110428_4..wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

extract_protocol: Yeast nuclei were prepared as described [Furuyama, S., and Biggins, S. (2007), Centromere identity is specified by a single centromeric nucleosome in budding yeast, Proc Natl Acad Sci USA 104, 14706-14711], flash-frozen in liquid nitrogen and stored at -80oC. Nuclei were thawed at room temperature and digested with MNase as described [Furuyama and Biggins, (2007)]. DNA was extracted using a standard protocol [Mito, Y., Henikoff, J., and Henikoff, S. (2005), Genome-scale profiling of histone H3.3 replacement patterns, Nat Genet 37, 1090-1097]. A modified Illumina Solexa library protocol was used as described in supplementary file Solexa_library_protocol_GEO.pdf.


title: Pellet_20min_(P20_20110726_8)

data_processing: 1. We used Novoalign to map 25bp paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file P20_20110726_8.bam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file P20_20110726_8.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

value: Insoluble MNase-protected DNA fragments, 20 minute digestion


title: root, -P rep2

source_name: root, phosphate-deficient medium


title: OverproducingInput_15min_(20101103_B7_KK_input)

description:
All MNase-protected DNA fragments, 15 minute digestion
Illumina HiSeq 2000

data_processing: 1. We used Novoalign to map paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. 50bp reads were trimmed to 25bp. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file KK_input.Novoalign.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file KK_input.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

extract_protocol: Yeast nuclei were prepared as described [Furuyama, S., and Biggins, S. (2007), Centromere identity is specified by a single centromeric nucleosome in budding yeast, Proc Natl Acad Sci USA 104, 14706-14711], flash-frozen in liquid nitrogen and stored at -80oC. Nuclei were thawed at room temperature and digested with MNase followed by chromatin preparation as described [Furuyama and Biggins, (2007)], except that after MNase digestion, the slurry was passed four times through a 20 guage needle, then four times through a 26 guage needle [Jin, C., and Felsenfeld, G. (2007), Nucleosome stability mediated by histone variants H3.3 and input.Z, Genes Dev 21, 1519-1529], and the combined S1+S2 supernatants were clarified by centrifugation in a fixed-angle Sorvall SS34 rotor at 12,000 rpm at 4oC for 10 min at least twice or until no visible pellet remained. ChIP was performed as previously described [Furuyama and Biggins, (2007)], and DNA was extracted using a standard protocol [Mito, Y., Henikoff, J., and Henikoff, S. (2005), Genome-scale profiling of histone H3.3 replacement patterns, Nat Genet 37, 1090-1097]. Standard Illumina protocol wa used Catalog #PE-930-1001, except size selected 100bp to 300bp.


title: Nuclei_2.5min_(N2_5A_20110519_1)

description: All MNase-protected DNA fragments, 2.5 minute digestion

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file N2_5A_20110519_1.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file N2_5A_20110519_1.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

source_name: total nuclei

extract_protocol: Yeast nuclei were prepared as described [Furuyama, S., and Biggins, S. (2007), Centromere identity is specified by a single centromeric nucleosome in budding yeast, Proc Natl Acad Sci USA 104, 14706-14711], flash-frozen in liquid nitrogen and stored at -80oC. Nuclei were thawed at room temperature and digested with MNase followed by chromatin preparation as described [Furuyama and Biggins, (2007)], except that after MNase digestion, the slurry was passed four times through a 20 guage needle, then four times through a 26 guage needle [Jin, C., and Felsenfeld, G. (2007), Nucleosome stability mediated by histone variants H3.3 and H2A.Z, Genes Dev 21, 1519-1529], and the combined S1+S2 supernatants were clarified by centrifugation in a fixed-angle Sorvall SS34 rotor at 12,000 rpm at 4oC for 10 min at least twice or until no visible pellet remained. ChIP was performed as previously described [Furuyama and Biggins, (2007)], and DNA was extracted using a standard protocol [Mito, Y., Henikoff, J., and Henikoff, S. (2005), Genome-scale profiling of histone H3.3 replacement patterns, Nat Genet 37, 1090-1097]. A modified Illumina Solexa library protocol was used as described in supplementary file Solexa_libarary_protocol_GEO.pdf. >>>>Accuprime, not Phusion<<<<<<


title: root, -N rep2

source_name: root, nitrogen-deficient medium


title: Homo_sapiens_genome_rep3_C

description: replicate-3 chip-C

source_name: FoxA1 ChIP DNA (abl)

source_name: FoxA1 ChIP DNA (LNCaP)


title: OverproducingH2A_15min_(20101103_B5_KK_H2A)

description:
MNase-protected DNA fragments from H2A-FLAG immunoprecipitation of native chromatin, 15 minute digestion
Illumina HiSeq 2000

data_processing: 1. We used Novoalign to map paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. 50bp reads were trimmed to 25bp. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file KK_H2A.Novoalign.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file KK_H2A.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

source_name: DNA from H2A-FLAG chromatin immunoprecipitation

extract_protocol:
Yeast nuclei were prepared as described [Furuyama, S., and Biggins, S. (2007), Centromere identity is specified by a single centromeric nucleosome in budding yeast, Proc Natl Acad Sci USA 104, 14706-14711], flash-frozen in liquid nitrogen and stored at -80oC. Nuclei were thawed at room temperature and digested with MNase followed by chromatin preparation as described [Furuyama and Biggins, (2007)], except that after MNase digestion, the slurry was passed four times through a 20 guage needle, then four times through a 26 guage needle [Jin, C., and Felsenfeld, G. (2007), Nucleosome stability mediated by histone variants H3.3 and H2A.Z, Genes Dev 21, 1519-1529], and the combined S1+S2 supernatants were clarified by centrifugation in a fixed-angle Sorvall SS34 rotor at 12,000 rpm at 4oC for 10 min at least twice or until no visible pellet remained. ChIP was performed as previously described [Furuyama and Biggins, (2007)], and DNA was extracted using a standard protocol [Mito, Y., Henikoff, J., and Henikoff, S. (2005), Genome-scale profiling of histone H3.3 replacement patterns, Nat Genet 37, 1090-1097]. Standard Illumina protocol wa used Catalog #PE-930-1001, except size selected 100bp to 300bp.
For Flag IP, we used Sigma A2220 Anti Flag M2 Affinity gel; lot 020M6014.


title: Cse4_5min_(20110115_6_Cse45)

description:
MNase-protected DNA fragments from Cse4-FLAG immunoprecipitation of native chromatin, 5 minute digestion
Illumina HiSeq 2000

data_processing: 1. We used Novoalign to map paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. 50bp reads were trimmed to 20bp. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file Cse45.Novoalign.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file Cse45.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.


title: Cse4_20min_(20110115_4_Cse420)

description:
MNase-protected DNA fragments from Cse4-FLAG immunoprecipitation of native chromatin, 20 minute digestion
Illumina HiSeq 2000

data_processing: 1. We used Novoalign to map paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. 50bp reads were trimmed to 20bp. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file Cse420.Novoalign.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file Cse420.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.


title: Homo_sapiens_genome_rep2_D

description: replicate-2 chip-D


title: shoot, control rep2

source_name: shoot, control


title: Input_15min_(20101103_B3_FLAG_input)

data_processing: 1. We used Novoalign to map paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. 50bp reads were trimmed to 25bp. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file FLAG_input.Novoalign.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file FLAG_input.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

extract_protocol: Yeast nuclei were prepared as described [Furuyama, S., and Biggins, S. (2007), Centromere identity is specified by a single centromeric nucleosome in budding yeast, Proc Natl Acad Sci USA 104, 14706-14711], flash-frozen in liquid nitrogen and stored at -80oC. Nuclei were thawed at room temperature and digested with MNase followed by chromatin preparation as described [Furuyama and Biggins, (2007)], except that after MNase digestion, the slurry was passed four times through a 20 guage needle, then four times through a 26 guage needle [Jin, C., and Felsenfeld, G. (2007), Nucleosome stability mediated by histone variants H3.3 and H2A.Z, Genes Dev 21, 1519-1529], and the combined S1+S2 supernatants were clarified by centrifugation in a fixed-angle Sorvall SS34 rotor at 12,000 rpm at 4oC for 10 min at least twice or until no visible pellet remained. ChIP was performed as previously described [Furuyama and Biggins, (2007)], and DNA was extracted using a standard protocol [Mito, Y., Henikoff, J., and Henikoff, S. (2005), Genome-scale profiling of histone H3.3 replacement patterns, Nat Genet 37, 1090-1097]. Standard Illumina protocol wa used Catalog #PE-930-1001, except size selected 100bp to 300bp.

value: All MNase-protected DNA fragments, 15 minute digestion


title: Soluble_10min_(20110115_8_Input102)

description:
All MNase-protected DNA fragments, 10 minute digestion
Illumina HiSeq 2000

data_processing: 1. We used Novoalign to map paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. 50bp reads were trimmed to 20bp. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file Input102.Novoalign.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file Input102.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

source_name: soluble chromatin (input)

extract_protocol: Yeast nuclei were prepared as described [Furuyama, S., and Biggins, S. (2007), Centromere identity is specified by a single centromeric nucleosome in budding yeast, Proc Natl Acad Sci USA 104, 14706-14711], flash-frozen in liquid nitrogen and stored at -80oC. Nuclei were thawed at room temperature and digested with MNase followed by chromatin preparation as described [Furuyama and Biggins, (2007)], except that after MNase digestion, the slurry was passed four times through a 20 guage needle, then four times through a 26 guage needle [Jin, C., and Felsenfeld, G. (2007), Nucleosome stability mediated by histone variants H3.3 and H2A.Z, Genes Dev 21, 1519-1529], and the combined S1+S2 supernatants were clarified by centrifugation in a fixed-angle Sorvall SS34 rotor at 12,000 rpm at 4oC for 10 min at least twice or until no visible pellet remained. ChIP was performed as previously described [Furuyama and Biggins, (2007)], and DNA was extracted using a standard protocol [Mito, Y., Henikoff, J., and Henikoff, S. (2005), Genome-scale profiling of histone H3.3 replacement patterns, Nat Genet 37, 1090-1097]. A modified Illumina Solexa library protocol was used as described in supplementary file Solexa_libarary_protocol_GEO.pdf.


title: Soluble_5min_(20110115_2_Input52)

description:
All MNase-protected DNA fragments, 5 minute digestion
Illumina HiSeq 2000

data_processing: 1. We used Novoalign to map paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. 50bp reads were trimmed to 20bp. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file Input52.Novoalign.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file Input52.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.


title: Soluble_2.5min_(20110115_3_Input252)

description:
All MNase-protected DNA fragments, 2.5 minute digestion
Illumina HiSeq 2000

data_processing: 1. We used Novoalign to map paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. 50bp reads were trimmed to 20bp. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file Input252.Novoalign.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file Input252.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.


title: OverproducingCse4_15min_(20101103_B6_KK_Cse4)

description:
MNase-protected DNA fragments from Cse4-FLAG immunoprecipitation of native chromatin, 15 minute digestion
Illumina HiSeq 2000

data_processing: 1. We used Novoalign to map paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. 50bp reads were trimmed to 25bp. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file KK_Cse4.Novoalign.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file KK_Cse4.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

source_name: DNA from Cse4-Myc chromatin immunoprecipitation

extract_protocol: Yeast nuclei were prepared as described [Furuyama, S., and Biggins, S. (2007), Centromere identity is specified by a single centromeric nucleosome in budding yeast, Proc Natl Acad Sci USA 104, 14706-14711], flash-frozen in liquid nitrogen and stored at -80oC. Nuclei were thawed at room temperature and digested with MNase followed by chromatin preparation as described [Furuyama and Biggins, (2007)], except that after MNase digestion, the slurry was passed four times through a 20 guage needle, then four times through a 26 guage needle [Jin, C., and Felsenfeld, G. (2007), Nucleosome stability mediated by histone variants H3.3 and Cse4.Z, Genes Dev 21, 1519-1529], and the combined S1+S2 supernatants were clarified by centrifugation in a fixed-angle Sorvall SS34 rotor at 12,000 rpm at 4oC for 10 min at least twice or until no visible pellet remained. ChIP was performed as previously described [Furuyama and Biggins, (2007)], and DNA was extracted using a standard protocol [Mito, Y., Henikoff, J., and Henikoff, S. (2005), Genome-scale profiling of histone H3.3 replacement patterns, Nat Genet 37, 1090-1097]. Standard Illumina protocol wa used Catalog #PE-930-1001, except size selected 100bp to 300bp.

value: Sigma A7470 Anti-c-Myc-Agarose affinity gel; lot 058K4813


title: seedling, drought rep2

data_processing: The adaptor sequences were identified and removed by using a Perl script. Small RNAs shorter than 15 nt were removed. Data matrix contains distinct small RNAs with their raw abundance after removing the adapter sequences.

source_name: seedling, drought


title: Cse4_10min_(20110115_5_Cse410)

description:
MNase-protected DNA fragments from Cse4-FLAG immunoprecipitation of native chromatin, 10 minute digestion
Illumina HiSeq 2000

data_processing: 1. We used Novoalign to map paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. 50bp reads were trimmed to 20bp. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file Cse410.Novoalign.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file Cse410.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.


title: Cse4_15min_(20101103_B4_FLAG_IP)

data_processing: 1. We used Novoalign to map paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. 50bp reads were trimmed to 25bp. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file FLAG_IP.Novoalign.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file FLAG_IP.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

value: MNase-protected DNA fragments from Cse4-FLAG immunoprecipitation of native chromatin, 15 minute digestion


title: Soluble_15min_(Input_20110428_6)

description: Solubilized MNase-protected DNA fragments, 15 minute digestion

data_processing: 1. We used Novoalign to map paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. 50bp reads were trimmed to 25bp. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file Input_20110428_6..sam) Because the DNA sample was pooled with DNA from Drosophila melanogaster, we removed all paired reads that mapped to both organisms. 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file Input_20110428_6..wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

source_name: soluble chromatin


title: Cse4_2.5min_(20110115_7_Cse425)

description:
MNase-protected DNA fragments from Cse4-FLAG immunoprecipitation of native chromatin, 2.5 minute digestion
Illumina HiSeq 2000

data_processing: 1. We used Novoalign to map paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. 50bp reads were trimmed to 20bp. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file Cse425.Novoalign.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file Cse425.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.


title: Homo_sapiens_genome_rep1_C

description: replicate-1 chip-C

data_processing: Supplementary files contain results from Model Based analysis of tiling arrays (MAT) was used to process the data as described previously: Johnson, et al, 2006, PMID: 16895995


title: seedling, OsDCL1 RNAi rep2-1

source_name: seedling, OsDCL1 RNAi


title: Soluble_20min_(20110115_1_Input202)

description:
All MNase-protected DNA fragments, 20 minute digestion
Illumina HiSeq 2000

data_processing: 1. We used Novoalign to map paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. 50bp reads were trimmed to 20bp. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file Input202.Novoalign.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file Input202.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.


title: Ribominus total RNA from fetal head 10

status: Public on Dec 06 2011

city: Klosterneuburg

first: Florian

last: Pauler

address: Am Campus 1

country: Austria

institute: IST Austria

description: Ribominus total RNA, Trizol isolated

data_processing: Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and mapped to the mouse genome (mm9, July 2007) using Bowtie. All reads mapping with two or fewer mismatches were retained.

source_name: 14.5dpc fetal head

growth_protocol: CCE feeder-independent ES cells were grown under standard conditions, and differentiation was induced by withdrawal of LIF and addition of 0.266µM retinoic acid (RA). Mouse fetal heads were dissected at 14.5 days postcoitum.

extract_protocol: DNase I treated 10µg of high quality total RNA from cells or tissues was subjected to ribosomal RNA depletion by using the RiboMinus Transcriptome Isolation Kit (Human/Mouse) according to the manufacturer’s  protocol. The quality of the purified RNA was checked on Agilent 2100 Bioanalyzer with Agilent RNA 6000 Pico Kit according to the manufacturer’s protocol. The purified Ribominus RNA fraction (100ng) was subsequently fragmented by addition of 5× fragmentation buffer (200mM Tris pH8.2, 500mM KAc and 150mM MgAc2) and heating at 94°C for 3.5min in a total volume of 100µl. The reaction was stopped by putting the sample on ice. The fragmented RNA was purified by RNeasy Mini Kit according to the manufacturer protocol, and subsequently ethanol precipitated and dissolved in 10µl nuclease-free ddH2O.The fragmented RNA was used as template for cDNA synthesis using 5µg random hexamers in a total volume of 20µl according to the Superscript II Reverse Transcriptase standard protocol. Second-strand synthesis was performed by adding 91.8µl water, 30µl 5× Second strand buffer, 3µl 10mM dNTP, 4µl DNA polymerase I, 1µl E. coli DNA ligase and 0.2µl RNase H, followed by incubation at 16°C for 2hour. T4 DNA Polymerase (1µl) was added followed by an additional 10 min at 16 °C. The ds-cDNA was purified by using the MinElute Reaction Cleanup Kit according to the manufacturer’s  protocol.

value: FVB/N

tag: tissue type

value: fetal head dissected from 14.5dpc mouse embryo

tag: fragmentation method

value: DNA shearing/RNA hydrolysis

tag: rrna depletion

value: 1 round/2rounds

tag: sequencing facility

value: IMP Solexa Sequencing facility, Vienna & NCMLS Solexa Sequencing facility, Nijmegen


title: Total nuclei DNA 2 (PD5_rep2_20110622_3)

status: Public on Dec 05 2011

description:
MNase-protected DNA fragments in total nuclei
Illumina HiSeq 2000, Flow cell:v3.0, Software:HCS1.4.5/RTA 1.12.4

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release W220 of the C. elegans genomic sequence obtained from WormBase. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file Total_nuclei_2_20110622_3.bam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file Total_nuclei_2_20110622_3.bedgraph) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

organism: Caenorhabditis elegans

extract_protocol: INTACT (supplementary file INTACT_ChIP_protocol.rtf) but with MNase digestion for 5 minutes.

tag: age

value: adult

tag: cell type

value: whole organism

value: total nuclei


title: Ribominus total RNA from ES 12

description: Ribominus total RNA, Trizol isolated

source_name: Day5 differentiated CCE

value: differentiated ES cells induced by retinoic acid for 5 days

value: 1 round


title: Muscle nuclei DNA 2 (nuc5_20110622_7)

description:
MNase-protected DNA fragments in muscle nuclei
Illumina HiSeq 2000, Flow cell:v3.0, Software:HCS1.4.5/RTA 1.12.4

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release W220 of the C. elegans genomic sequence obtained from WormBase. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file Muscle_nuclei_2_20110622_7.bam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file Muscle_nuclei_2_20110622_7.bedgraph) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

source_name: INTACT-purified muscle nuclei

extract_protocol: INTACT (supplementary file INTACT_ChIP_protocol.txt) but with MNase digestion for 5 minutes.

value: muscle cell

value: INTACT affinity-purified muscle nuclei


title: sir4delta

status: Public on Dec 02 2011

city: Nashville

first: William

last: Tansey

address: 425 @1st Avenue South

institute: Vanderbilt University

data_processing: Bowtie software (25) was used to align reads to the S. cerevisiae genome (sacCer2 assembly, June 2008), and ribosomal RNA-aligning reads and multi-aligning reads filtered out prior to analysis.

source_name: whole cell extraction

growth_protocol: Strains were grown in YPAD and collected in OD ~0.8

extract_protocol: Total RNA was extracted using the Rneasy Mini Kit (Qiagen), Messenger RNA was isolated using the OligoTex mRNA Isolation Kit (Qiagen) and converted to double-stranded, adapter-ligated, cDNA using the Illumina mRNA Sample Prep Kit.

value: FGY8.10 (MATa htb1delta htb2delta leu2-3,-112 his3-11,-15 trp1-1 ura3-1 ade2-1 can1-100 sir4delta::NatMX [p413-HTB1-HA]


title: seedling, OsDCL1 RNAi rep1-2

value: Oryza sativa L, ssp. japonica cv. Nipponbare

value: seedling


title: wildtype

value: FGY8.2(MATa htb1delta htb2delta leu2-3,-112 his3-11,-15 trp1-1 ura3-1 ade2-1 can1-100 [p413-HTB1-HA]


title: seedling, cold rep2

source_name: seedling, cold


title: root, control rep2

source_name: root, control

value: root


title: htbK123R

value: FGY8.3(MATa htb1delta htb2delta leu2-3,-112 his3-11,-15 trp1-1 ura3-1 ade2-1 can1-100 [ [p413-htb1K123R-HA] )


title: seedling, salt rep2

source_name: seedling, salt


title: HeLa_ZZZ3-chip-seq

status: Public on Nov 05 2011

city: Strasbourg

first: Krishanpal

last: Karmodiya

email: krish@igbmc.fr, laszlo@igbmc.fr

address: 1 rue Laurent Fries / BP 10142

country: France

institute: Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)

description: Chromatin IP against ZZZ3

data_processing: ChIP-seq data were mapped using the ELAND software (Illumina) allowing one mismatch.

source_name: HeLa

growth_protocol: GM cells were grown according to the instructions of Coriell Cell Repositories

extract_protocol: ChIP DNA and input DNA were first band-isolated on a 2% agarose to obtain fragments between 150 and 350 base pairs and DNA was extracted using the QIAquick gel extraction kit (Qiagen) and eluted in 34 uL. For input DNA, because DNA amounts are higher than DNA recovered by ChIP, input DNA after gel extraction was diluted 1:5. After end-repair and addition of a single adenosine ("A") nucleotide, adapters were ligated to samples for 15 min at room temperature in the following fashion: the samples eluted from the MinElute column in 10 uL were ligated to 1 uL of adapters using 1.3 uL of LigaFast T4 DNA Ligase (3 Units/uL; Promega) and 12.3 uL Rapid Ligation Buffer (Promega). For DNA libraries, the Illumina genomic DNA adapters were diluted 1:10. After 15 min, samples were purified with the MinElute PCR purification kit (Qiagen).

value: HeLa cells

value: Rabbit polyclonal

tag: chip antibody

tag: vendor

value: Laszlo Tora


title: GM_SPT20-chip-seq r2

description: Chromatin IP against SPT20

value: B lymphoblasts


title: GM_ZZZ3-chip-seq r2

description: Chromatin IP against ZZZ3


title: GM_ZZZ3-chip-seq r1

description: Chromatin IP against ZZZ3


title: seedling, control rep3

source_name: seedling, control

extract_protocol: Small RNA libraries were constructed as previously described (Lu et al. 2007) and sequenced on llumina 1G or IIGX analyzer. Sequencing was performed at Illumina, National Center for Genome Research, Cold Spring Harbor Laboratory, or the Delaware Biotechnology Institute.

tag: cultivar


title: h3k27me3_rates

status: Public on Nov 16 2011

city: Oxford

first: Magnus

middle: David

last: Lynch

address: John Radcliffe Hospital

department: Molecular Haematology Unit

institute: Weatherall Institute of Molecular Medicine

description: chromatin IP against H3K27me3

data_processing:
Reads were aligned with Bowtie to the mm9 or rn4 reference genomes
For the transgenic mouse data set, we assayed binding of Ezh2 within a transgenically modified chromosomal region containing both endogenous mouse sequence and human sequence. Therefore, SAM files for the reads mapped to both the human genome and the mouse genome are provided.

organism: Rattus norvegicus

source_name: Rat ES cells

extract_protocol:
Chromatin immunoprecipitation was performed with the Millipore ChIP Assay Kit (Millipore, 17-295). Briefly, ES cells were crosslinked with 1% formaldehyde in PBS for 10 mins at 37°c. Chromatin was prepared according to the Millipore protocol and sonicated to an average size of 500-1000bp using a Diagenode Bioruptor. Chromatin fragments were immunoprecipitated with antibodies to H3K27me3 (Millipore 07-449) or Ezh2 (Abnova pAB0649). DNA was extracted with phenol:choloform.
Libraries were prepared for ChIP-seq according to the standard Illumina protocol.

value: Fischer F344 inbred strain


title: ezh2_transgenic

description: chromatin IP against Ezh2

source_name: Transgenic mouse ES cells

value: E14 ES cells


title: seedling, OsDCL1 RNAi rep2-2


title: Medium TSC2 KO + Rapa (30min)

status: Public on Nov 12 2011

city: Ithaca

first: Shu-Bing

last: Qian

address: 301 Biotech Bldg.

department: Division of Nutritional Sciences

institute: Cornell University

description:
Tuberous Sclerosis 2(TSC2) Knock Out
Ribosome Protected RNA Fragments

data_processing: Each run file contains 3 barcoded samples. The fastq files were first splited into different groups so that each barcoded sample ends up with a dedicated run file based on the barcode sequences (raw files). Then,  reads were cleaned by filtering out reads with less than 10 nt polyA (allowing one nt mismatch of polyA). After removing poly-A tails, only reads which are longer than 20bp were retained for further process. The first 3 nucleotides (2 nt barcodes + 1st nt) were removed because the first nucleotide showed the highest rate of mismatch. Finally, the sequences of ribosome protected fragments were obtained(processed files).

source_name: Embryonic Fibroblast

growth_protocol: TSC2-/- MEFs were maintained in Dulbeccoâs Modified Eagleâs Medium (DMEM) with 10% fetal bovine serum (FBS).

extract_protocol: The library construction protocol is described in the accompanying manucript (under review). Briefly, ribosome profiling was performed to separate the lysates into three fractions, including small (1 ribosome), medium(2-4 ribosomes) and large(â¥5 ribosomes). RNAs were digested by RNAse I and extracted from each fraction. Then, ribosome protected mRNA fragments were selected and purifed. Next, Poly-(A) tails were added to the framents and then the framents were converted to cDNA with barcodes by reverse transcription reaction. Furthermore, the cDNA was circulated and re-linealized. Finally, cDNA was PCR amplified and library fragments were isolated. Libraries were sequenced on the Illumina Genome Analyzer following the manufacturer's protocols.

treatment_protocol: TSC2-/- MEFs were treated with 20 nM Rapamycin(Sigma) at 37â for 30 minutes

value: mouse embryonic fibroblast

tag: genotype

value: TSC2 KO

tag: treatment

value: 20nM Rapamycin

tag: genetic background

value: 129S4/SvJae, C57BL/6, CBA

tag: time

value: 30 min

value: Medium (2-4 ribosomes)


title: Small TSC2 KO + Rapa (30min)

value: Small (1 ribosome)


title: Large TSC2 KO + Rapa (30min)

value: Large (≥5 ribosomes)


title: Female_UNR_IP_rep2

status: Public on Oct 25 2011

city: Milan

first: Giulio

last: Pavesi

address: Via Celoria 26

department: Biosciences

country: Italy

institute: Università di Milano

description: RIP IP against UNR

data_processing: Reads were mapped on the genome using the seqmap tool allowing at most one substitution per read. Reads were assigned to genes according to genomic coordinates using the FlyBase 5.12 annotation. Sequences from replicate experiments were pooled together. Enrichment of the IP samples with respect to the IgG control was computed using a 2x2 Chi-Square table.

organism: Drosophila melanogaster

source_name: whole body RNA

extract_protocol:
RNA from UNR immunoprecipitates was extracted with Trizol (Invitrogen). Immunoprecipitation from total extracts was performed using protein A-magnetic beads (Invitrogen). After extensive washing with 1xNET (50 mM TRISxHCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% NP40), beads were resuspended in elution buffer (50 mM Tris-HCl, pH 7.4, 5 mM EDTA, 10 mM DTT, 1% SDS) and treated with 40 µg proteinase K. RNA was then extracted from the supernatant using Trizol, precipitated and treated with DNase (TURBODNA free kit, Ambion). The amount of RNA was assessed by Nanodrop measurement. The quality of the RNA was assessed in  Bioanalyzer (Agilent Technologies). The efficiency of immunoprecipitation and the integrity of UNR were monitored by Western blot.
The UNR antibody was generated as described in Abaza et al. 2006. Genes Dev 20: 380-389 (Pubmed PMID 16452509). Is a rabbit polyclonal antibody. Purified anti-UNR IgG was used. The non-specific rabbit IgG was from Sigma, catalog num: I5006.
Sequencing of the Drosophila transcriptome was performed from total RNA of adult male and female flies following the RNA-Seq protocols. RIP-Seq samples were produced with the Solexa NlaIII protocol.

treatment_protocol: Adult male and female flies of mixed ages were manually separated, snap-frozen and grinded in liquid nitrogen.

tag: tissue

value: female whole body

tag: library strategy

value: RIP-Seq

tag: ip antibody

value: UNR


title: htbK123R sir4delta

tag: strain

value: FGY8.11(MATa htb1delta htb2delta leu2-3,-112 his3-11,-15 trp1-1 ura3-1 ade2-1 can1-100 sir4delta::NatMX [ [p413-htb1K123R-HA] )


title: Female_IgG_IP

description: RIP IP against IgG

value: IgG


title: Female_UNR_IP_rep1

description: RIP IP against UNR


title: Male_IgG_IP

description: RIP IP against IgG

value: male whole body


title: Male_UNR_IP_rep2

description: RIP IP against UNR


title: Male_UNR_IP_rep1

description: RIP IP against UNR


title: TNC knockout biological rep2

status: Public on Oct 20 2011

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

hyb_protocol: 45°C 16hrs 60rpm according to Affymetrix protocol, Fluidics Station Program FS45_00007

scan_protocol: Array Scanner 30007G, AGCC

data_processing: The image data were analyzed with Affymetrix® GeneChip® Command Console® Software (AGCC) (Affymetrix, USA), Normalization was performed using the RMA algorithm.

source_name: E15.5 lumbar spinal cord tissue

label_protocol: As per manufacturers (WT expression kit Ambion, WT terminsal labelling kit Affymetrix)

growth_protocol: mouse lumbar dissected from day E15.5 mouse embryos

extract_protocol: RNeasy Qiagen

treatment_protocol: not applicable

value: lumbar spinal cord

value: TNC -/-


title: TNC knockout biological rep1


title: TNC wildtype biological rep2

value: wild-type


title: TNC wildtype biological rep1


title: TNC wildtype biological rep3


title: Rhesus cerebellar cortex rep1 (microRNA-Seq)

status: Public on Oct 18 2011

city: shanghai

first: Song

last: Guo

address: 320 Yue Yang Road

country: China

institute: PICB

description: miRNA sequencing raw reads from post-mortem cerebellar cortex of 5 pooled rhesus macaque individuals from 4 years to 20 years

data_processing: supplementary files contain small RNA sequences from purified low molecular weight RNA

organism: Macaca mulatta

source_name: Dissected 5 pooled rhesus macaque post-mortem cerebellar cortex

extract_protocol: Total RNA was isolated from the frozen prefrontal cortex tissue using the Trizol (Invitrogen, USA) protocol with no modifications. Low molecular weight RNA was isolated, ligated to the adapters, amplified, and sequenced following the Small RNA preparation protocol (Illumina, USA) with no modifications.

treatment_protocol: All human postmortem brain tissue samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders (NICHDBB)(Baltimore, MD, USA). All subjects were defined as normal controls by forensic pathologists at the NICHDBB. No subjects with prolonged agonal state were used.

value: cerebellar cortex of brain

tag: batch

value: rhesus batch 1


title: Chimpanzee superior frontal gyrus rep1 (microRNA-Seq)

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of 3 pooled chimpanzee individuals age from 12 years to 35 years

organism: Pan troglodytes

source_name: Dissected 3 pooled  chimpanzee post-mortem superior frontal gyrus

value: superior frontal gyrus of the brain

value: chimpanzee batch 1


title: TNC knockout biological rep3


title: Rhesus superior frontal gyrus rep1 (microRNA-Seq)

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of 10 pooled rhesus individuals age from 6 years to 15 years

source_name: Dissected 10 pooled rhesus macaque post-mortem superior frontal gyrus


title: WT(T+S)_sRNA

status: Public on Dec 01 2011

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description:
sRNA library constructed from mixed stage inflorescence of Arabidopsis ago6-4/21.4y.The sRNA library was created using the protocol published by Cheng Lu in Methods
Processed data file: Text containing distinct smallRNAs with their raw abundance after removing the adapter sequences.
Processed data file name: SS_691_chopped.txt (represented in data table below).

data_processing:
Library selection: PCR
Adapter sequences were removed using a Perl script, generating small RNA sequences plus abundances. The data were matched to the Arabidopsis genome (TAIR v9) as well as the transgenes described in Kanno et al. (2008). Of the 4,510,985 total reads from transgenic wild type and 2,327,100 from the ago6-4 mutant, 2,846,684 (wt) and 1,261,189 (ago6-4) reads matched the genome, excluding 362,400 (wt) and 207,909 (ago6-4) that matched tRNA, rRNA, snRNA or snoRNAs.

source_name: Mixed stage inflorescence tissue

growth_protocol: Seeds were germinated on soil and grown for approximately 5 weeks at 22-23°C under a light cycle of 8 hours dark, 16 hours light. Mixed stage floral inflorescences (inflorescence meristem and floral buds to stage 12) were harvested between 9 and 12 AM and stored in 50 ml Falcon tubes at -80°C.

extract_protocol: Total RNA was isolated from mixed stage inflorescence tissues of the transgenic wild type and the ago6-4 mutant using TRIzol reagent (Invitrogen). Total RNA (200 ug) for each sample was used to construct the small RNA libraries as described previously (Lu et al., 2007) but with different adapters. The RNA oligos (Dharmacon) used for small RNA ligations were as follows: 5' RNA Adapter (5'OH-GUUCAGAGUUCUACAGUCCGACGAUC-OH 3') and 3' RNA Adapter: (5'pUCGUAUGCCGUCUUCUGCUUGUidt 3'; p, phosphate; idT, inverted deoxythymidine). Libraries were sequenced on an Illumina GAII following the manufacturer's protocols at the Delaware Biotechnology Institute.

tag: genotype/variation

value: transgenic wild type plant (contains trigger and silencer transgenes)

tag: ecotype


title: Chimpanzee cerebellar cortex rep1 (microRNA-Seq)

description: miRNA sequencing raw reads from post-mortem cerebellar cortex of 4 pooled chimpanzee individuals age from 6 years to 35 years

source_name: Dissected 4 pooled  chimpanzee post-mortem cerebellar cortex


title: Human superior frontal gyrus rep2 (microRNA-Seq)

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of 22 pooled human individuals age from 15 years to 58 years

source_name: Dissected 22 pooled human post-mortem superior frontal gyrus

value: human batch 2


title: Human superior frontal gyrus rep1 (microRNA-Seq)

value: human batch 1


title: Rhesus superior frontal gyrus rep2 (microRNA-Seq)

value: rhesue batch 2


title: Human cerebellar cortex rep1 (microRNA-Seq)

description: miRNA sequencing raw reads from post-mortem cerebellar cortex of 5 pooled human individuals age from 8 years to 53 years

source_name: Dissected 5 pooled human post-mortem cerebellar cortex


title: Human cerebellar cortex rep2 (microRNA-Seq)

description: miRNA sequencing raw reads from post-mortem cerebellar cortex of 5 pooled human individuals age from 12 years to 53 years

source_name: Dissected 5 pooled human post-mortem cerebellar cortex biological replicate

value: human batch 2, biological replicate


title: RARg_metaprofile_ChIP-seq

status: Public on Oct 11 2011

city: Illkirch; Strasbourg

first: Marco Antonio

last: Mendoza-Parra

address: 1, rue Laurent Fries

institute: IGBMC

description:
Metaprofile insilico generated.
RARg_metaprofile_ChIP-seq has been generated by combining the sequenced reads associated to ChIP-seq profiles: RARg_48h_EtOH; RARg_2h_ATRA, RARg_6h_ATRA, RARg_24_ATRA and RARg_48h_ATRA (insilico combination).
Metaprofiles have been generated in such way for enhancing the peak calling procedure.

data_processing: The Illumina Pipeline v1.4.0 was used for primary data analysis (image processing: Firecrest; base calling: Bustard; alignment: Gerald) from which uniquely aligned reads with up to two mismatches relative to the mouse mm9 reference genome were kept.

source_name: embryonal carcinoma cells

growth_protocol: Embryonal carcinoma cells were cultured in Dubelccoâs modified Eagleâs medium supplemented with 10% foetal calf serum and 40ug/ml Gentamicin. Cells were seeded in gelatine-coated tissue culture plates (0.1%) and all-trans retinoic acid (ATRA) was added to the plates in a final concentration of 1x10-6 M at different time points.

extract_protocol: Immunoprecipitated chromatin was quantified using Qubit (Quant-It dsDNA HS Assay Kit; Invitrogen). 10ng of the ChIPed material was used for preparing the sequencing library (ChIP-seq DNA sample preparation kit, Illumina). 5 pmol of the library was used per flowcell in the Solexa 2G Genome analyzer (Illumina).

treatment_protocol: F9 cells induced into differentiation (ATRA treatment) at different time-points were fixed with 1% para-formaldehyde (Electron Microscopy Sciences) for 30 minutes at room temperature. ChIP assays for RARg, RXRa and RNA Polymerase II were performed following standard conditions.

tag: cell line

value: F9 embryonal carcinoma cells


title: RNA-PolII_induced_metaprofile_ChIP-seq

description:
Metaprofile insilico generated.
RNA-PolII_induced_metaprofile has been generated by combining the sequenced reads associated to PolII ChIP-seq profiles treated with ATRA (EtOH treated ChIP-seq dataset not included): RNA-PolII_2h_ATRA, RNA-PolII_6h_ATRA, RNA-PolII_24h_ATRA and RNA-PolII_48h_ATRA.
Metaprofiles have been generated in such way for enhancing the peak calling procedure.


title: RXRa_metaprofile_ChIP-seq

description:
Metaprofile insilico generated.
RXRa_metaprofile_ChIP-seq has been generated by combining the sequenced reads associated to ChIP-seq profiles: RXRa_48h_EtOH; RXRa_2h_ATRA, RXRa_6h_ATRA, RXRa_24_ATRA and RXRa_48h_ATRA (insilico combination).
Metaprofiles have been generated in such way for enhancing the peak calling procedure.


title: Chimpanzee superior frontal gyrus rep2 (microRNA-Seq)

source_name: Dissected 3 pooled chimpanzed post-mortem superior frontal gyrus

value: chimpanzee batch 2


title: H3-T7 (new) generation 3

status: Public on Oct 06 2011

city: Jerusalem

first: Assaf

last: Weiner

address: Givat Ram

department: Computer Science

country: Israel

institute: The Hebrew University of Jerusalem

data_processing: Mapped Reads: Unique reads were mapped to the yeast genome (S288C_reference_genome_R61-1-1_20080605; 05-Jun-2008) with minimal errors (as described in Yassour et al. PNAS, 2009 (PMID 19208812)).

source_name: H3-T7, wt, generation 3

growth_protocol: For tag switch experiments, yeast cells were grown overnight in YPD in the presence of Hygromycin B (200 μg/mL, Invitrogen). The cells were then diluted 1:10 into fresh YPD and incubated for 30–36 h. Recombination was induced by the addition of 1 μM β-estradiol (E-8875, Sigma-Aldrich). Subsequently, cells were diluted 1:25 in fresh YPD media to release the cells back into the cell cycle and kept in log phase by 1:2 dilutions into fresh media after each population doubling. Samples were taken after 1, 3, and 6 cell divisions or after 5 hours of G2/M arrest. The number of population doublings was determined by microscopy and OD. G2/M arrest was induced by addition of 15 μg/ml Nocodazole (Sigma-Aldrich) and confirmed by FACS analysis.

extract_protocol: The majority of obtained fragments was around 150bp, as determined on a 2% TAE agarose gel stained with ethidium bromide. The isolated chromatin of the equivalent of 3x10^8 cells was immunoprecipitated overnight at 4°C using magnetic Dynabeads (Invitrogen), which were previously incubated with antibody O/N at 4°C.

treatment_protocol: ChIP was performed as described previously (PMID 20018668) with the following modifications. All steps were done at 4°C unless otherwise indicated. Following cell lysis by bead beating, the insoluble chromatin of 1x10^9 cells was washed, resuspended in 400 μl FA lysis buffer (50 mM HEPESKOH [pH 7.6], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), and sheared using a Bioruptor (Diagenode) for 6 minutes with 30 seconds intervals at high. The 16 soluble fraction was diluted three fold in buffer 15mM Tris-HCl pH 7.4, 50mM NaCl, 1.5mM CaCl2, 5mM β-meracptoethanol, 5mM MgCl2,  after which 25 units of micrococcal nuclease (MNase; Worthington) were added. The digestion reaction was incubated 20 minutes at 37°C and stopped by the addition of 10mM EDTA and 10mM EGTA, and tubes were placed on ice.

value: wt

tag: epitope tag

tag: histone h3

value: new

tag: sampling time

value: at 3 cell divisions


title: Dnmt3b-deficient Lymphoma, biological replicate 4

status: Public on Nov 21 2011

city: Omaha

first: Ryan

last: Hlady

state: Nebraska

department: Eppley

institute: UNMC

description: Methyl-sensitive cut counting high-throughput sequencing data from Dnmt3b-deficient tumors

data_processing: The resulting 18 bp sequence tags were aligned with the mouse genome (mm9) using the short read sequence aligner Bowtie (40). The library was matched to all possible unique tags (courtesy of Madeleine Ball, Harvard University) and the appropriate gene using perl scripts developed by the UNO/UNMC Genetic Sequence Analysis Facility and Microsoft Access and Excel. Counts of each sequence tag that represented a unique unmethylated HpaII site were determined.

source_name: Dnmt3b-deficient tumor cells harvested from thymic lymphoma of Dnmt3b-deficient tumor mice

growth_protocol: Th-1, Th-2, Th-3, 3b24-1, 3b24-2, 3b24-3 were harvested at 24 days and sorted based on EGFP expression. All Final tumor mice were harvested when lymphoma tumor burden became apparent.

extract_protocol:
2 μg of genomic DNA was digested with 20 units of the restriction enzyme HpaII (NEB) and an adapter containing a recognition site for the restriction enzyme MmeI was ligated to digested DNA fragments using T4 DNA ligase (NEB). DNA was ethanol precipitated and nick repaired with eight units of Bst DNA polymerase (NEB). The DNA was digested with 2 units of MmeI to capture the 18 bases adjacent to HpaII sites and the fragments were subsequently ligated to a second adapter to allow PCR amplification and final high throughput sequencing.
After appropriate tag size purification using a 10% PAGE gel, DNA was PCR amplified using BioRad iProof high fidelity polymerase and quantitative PCR procedures to avoid over amplification and skewing the production of final tags. Final tags were checked for proper size and concentration using an Agilent, Bioanalyzer High Sensitivity DNA chip and Invitrogen, Qubit Fluorometer. High throughput sequencing of library tags was performed by Tufts University Core Facility and University of Nebraska Medical Center using an Illumina Genome Analyzer II.

value: Thymus

tag: tumor stage

value: Final Tumor


title: Dnmt3b-deficient Lymphoma, biological replicate 5


title: ago6-4_sRNA

description:
sRNA library constructed from mixed stage inflorescence of Arabidopsis EDT. The sRNA library was created using the protocol published by Cheng Lu in Methods
Processed data file: Text containing distinct smallRNAs with their raw abundance after removing the adapter sequences.
Processed data file name: SS_690_chopped.txt (represented in data table below).

value: ago6-4 mutant contains a premature stop codon

value: Mixed stage floral inflorescences (inflorescence meristem and floral buds to stage 12)


title: Wild-Type Lymphoma, biological replicate 1

description: Methyl-sensitive cut counting high-throughput sequencing data from Wild-Type Tumors

source_name: Tumor cells harvested from thymic lymphoma of Wild-Type Tumor mice


title: brain_vpfc_methylmaps_s6

status: Public on Oct 05 2011

city: New York

first: Fatemeh

last: Haghighi

address: 1051 Riverside Drive, Box 42

institute: Columbia University

description: Methyl-MAPS sequencing data

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (hg18, March, 2006) or mouse (mm9) genomes using the SOLiD mapping software. All reads mapping with two or fewer mismatches were retained.
Methyl-Analyzer: Mapped mate-pair reads were parsed to retore fragment information (i.e., start and end cooridinates), fragments were filtered based on enzyme recognition sites, and methylation probabilites were estimated using both methylated and unmethylated fragment information.

source_name: Brain ventral prefrontal cortex

extract_protocol:
Genomic DNA was isolated using phenol-chloroform extraction and RNase A treatment followed by ethanol precipitation. Methylation-sensitive enzymes are HpaII, HhaI, AciI, BstUI and HpyCH4IV, and methylation-dependent enzyme is McrBC.
Follow Methyl-MAPS protocol: genomic DNA was digested by methylation-sensitive and -dependent enzymes, separately. Digested fragments were contructed into mate-pair libraries and sequenced on SOLiD platform.
Sequencing libraries were prepared by following an adaptation of Applied Biosystems  SOLiD System Mate-paired Library Preparation Protocol (http://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_059675.pdf), and the corresponding adaptation for the library preparation can be found in: Xin Y, O'Donnell AH, Ge Y, et al. (2011). Role of CpG context and content in evolutionary signatures of brain DNA methylation. Epigenetics

value: Brain

tag: phenotype

value: Control


title: 24 day pre-tumor Dnmt3b-deficient thymocytes, biological replicate 1

description: Methyl-sensitive cut counting high-throughput sequencing data from Dnmt3b-deficient pre-tumor thymocytes

source_name: Dnmt3b-deficient pre-tumor cells harvested from thymus of 24 day old Dnmt3b-deficient mice

tag: genotype

value: 24 day pre-tumor


title: forebrain_methylmaps

description: Methyl-MAPS sequencing data

source_name: Forebrain


title: brain_vpfc_methylmaps_s4

description: Methyl-MAPS sequencing data


title: Wild-Type Lymphoma, biological replicate 5


title: brain_vpfc_methylmaps_s5

description: Methyl-MAPS sequencing data