title: toll10b 2-4h replicate 2

data_processing:
toll10b_02to04h_2.bam; genome build: dm3
Reads were aligned to the UCSC dm3 genome using Tophat with a FlyBase release 5.28 GFF annotation file

extract_protocol: mRNA-seq: polyA mRNA was purified from total RNA in two consecutive rounds of oligo(dT) selection. After RNA fragmentation and reverse transcription sequencing libraries were prepared following Illumina's instructions (see ChIP-seq)

value: embryos were collected from Toll10b/+ females obtained from a balanced stock (Toll10b/TM3, Sb, Ser and Toll10b/OR60)

tag: tissue

value: whole-embryo


title: muscle 14-17h replicate 2

status: Public on Dec 20 2012

type: SRA

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

country: USA

institute: Stowers Institute for Medical Research

library_source: transcriptomic

data_processing:
mef2_14to17h_2.bam; genome build: dm3
Reads were aligned to the UCSC dm3 genome using Tophat with a FlyBase release 5.28 GFF annotation file

molecule: total RNA

organism: Drosophila melanogaster

source_name: muscle FAC sorted from dissociated embryos

growth_protocol: D. melanogaster embryos were  collected and aged on yeasted apple juice plates at 25 °C and 60 % humidity.

tag: genetic background

value: muscle

tag: time point

value: 14 to 17h AEL


title: muscle 14-17h replicate 1

data_processing:
mef2_14to17h_1.bam; genome build: dm3
Reads were aligned to the UCSC dm3 genome using Tophat with a FlyBase release 5.28 GFF annotation file


title: muscle 10-12h repliace 2

data_processing:
mef2_10to12h_2.bam; genome build: dm3
Reads were aligned to the UCSC dm3 genome using Tophat with a FlyBase release 5.28 GFF annotation file

value: 10 to 12h AEL


title: muscle 8-10h replicate 2

data_processing:
mef2_08to10h_2.bam; genome build: dm3
Reads were aligned to the UCSC dm3 genome using Tophat with a FlyBase release 5.28 GFF annotation file

value: 08 to 10h AEL


title: muscle 10-12h replicate 1

data_processing:
mef2_10to12h_1.bam; genome build: dm3
Reads were aligned to the UCSC dm3 genome using Tophat with a FlyBase release 5.28 GFF annotation file


title: muscle 8-10h replicate 1

data_processing:
mef2_08to10h_1.bam; genome build: dm3
Reads were aligned to the UCSC dm3 genome using Tophat with a FlyBase release 5.28 GFF annotation file


title: muscle 6-8h replicate 2

data_processing:
mef2_06to08h_2.bam; genome build: dm3
Reads were aligned to the UCSC dm3 genome using Tophat with a FlyBase release 5.28 GFF annotation file

value: 06 to 08h AEL


title: muscle 6-8h replicate 1

data_processing:
mef2_06to08h_1.bam; genome build: dm3
Reads were aligned to the UCSC dm3 genome using Tophat with a FlyBase release 5.28 GFF annotation file


title: neuron 14-17h replicate 1

data_processing:
elav_14to17h_1.bam; genome build: dm3
Reads were aligned to the UCSC dm3 genome using Tophat with a FlyBase release 5.28 GFF annotation file

source_name: neurons FAC sorted from dissociated embryos

value: neuron

tag: cell type


title: neuron 14-17h replicate 2

data_processing:
elav_14to17h_2.bam; genome build: dm3
Reads were aligned to the UCSC dm3 genome using Tophat with a FlyBase release 5.28 GFF annotation file


title: neuron 10-12h replicate 1

data_processing:
elav_10to12h_1.bam; genome build: dm3
Reads were aligned to the UCSC dm3 genome using Tophat with a FlyBase release 5.28 GFF annotation file


title: Pol II ChIP-seq from 6-8 h Drosophila muscle cells, 8WG16 antibody, replicate 2

library_source: genomic

data_processing:
mef2_06to08h_pol_8wg16_2.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.

molecule: genomic DNA

extract_protocol: ChIP-seq: DNA-protein-complexes were isolated with specific antibodies. Sequencing libraries were prepared following Illumina's instructions: DNA was end repaired using T4 DNA polymerase, DNA polymerase I large fragment (Klenow polymerase) and T4 polynucleotide kinase. A single 3'-A overhang was added to the blunted ends using Klenow 3'-5' exo- polymerase. Adapters with single 3'-T overhangs were ligated to the adenylated fragments, and after a size-selection step on a 2 % agarose gel (150-250 bp) the adapter modified DNA was PCR-amplified. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.

tag: chip antibody

value: Pol II (8WG16, Covance)

tag: chip antibody manufacturer

value: Covance

tag: chip antibody catalog #


title: mutant

city: Stanford

first: Rui

last: Zhang

state: California

address: 300 Pasteur Drive

institute: Stanford

description: Sample 2

data_processing:
Illumina Casava1.7 software used for basecalling.
We used BWA to align RNA-seq reads to a combination of the reference genome and exonic sequences surrounding known splicing junctions from available gene models. We chose the length of the splicing junction regions to be slightly shorter than the RNA-seq reads to prevent redundant hits. We obtained gene models from UCSC genome browser: D. melanogaster, FlyBase Genes.  We further used samtools to extract uniquely mapped reads.
We took variant positions with the mismatch supported by two or more reads with a base quality score of >=20 and a mapping quality score >=20. We examined all identified A-to-G sites that are edited in the wild type strain.
Genome_build: UCSC dm3
Supplementary_files_format_and_content: The .txt file reports variant call.

molecule: polyA RNA

source_name: Head

extract_protocol:
We collected heads of 5 day old male dAdar-/- mutant (y, Adar5G1, w)26 and wild type (w1118) flies. Poly(A)+ RNA was used to prepare RNA-seq libraries
RNA libraries were prepared for sequencing using standard Illumina protocols and were subsequently sequenced single-end by an Illumina GAII

tag: strain

value: y, Adar5G1, w

value: Head

tag: age

value: 5 day

tag: genotype

value: mutant


title: Staphylococcus sp.OJ82 11% NaCl

status: Public on Dec 19 2012

city: Seoul

first: Sungjong

last: Choi

address: Anam-dong Seongbuk-Gu

country: South Korea

institute: Korea university

data_processing:
Base-calling: CASAVA v1.6
Alignment: CLC Genomics Workbench 4.5
Generation of normalized abundance measurement: CLC Genomics Workbench 4.5
Genome_build: Staphylococcus sp.OJ82, GenBank : ALPU00000000.1
Supplementary_files_format_and_content: RPKM

organism: Staphylococcus sp. OJ82

source_name: Staphylococcus sp.OJ82 11% NaCl

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

tag: treatment

value: 11% NaCl


title: WT

description: Sample 1

value: wild type


title: Myotis davidii

status: Public on Dec 18 2012

city: shenzhen

first: zhiyong

last: huang

state: Guangdong

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

country: China

institute: BGI-Shenzhen, Shenzhen 518083, China

description: Sequenced reads were generated from Myotis davidii

data_processing:
use Pteropus alecto genome and  Myotis davidii genome as reference, sequenced reads were aligned onto the corresponding reference using TopHat v1.3.1 with default parameters except  -I 50000  --solexa1.3-quals
Genome_build: Pteropus_alecto_v1 and Myotis_davidii_v1
Supplementary_files_format_and_content: bedGraph file, and the format is: scaffold or contig ID, start, end, transcrptome depth

organism: Myotis davidii

source_name: Myotis davidii

extract_protocol: Total RNA was extracted using Trizol. For RNA-seq, poly-A+ RNA was isolated with  30  oligo-dT-coupled beads from 20 μg total RNA of each sample. First strand cDNA synthesis was  performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second  strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with  Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp  fragments. After end repair and addition of a 3’ dA overhang the cDNA was ligated to Illumina PE  adapter oligo mix, and size selected to 200±20 bp fragments by gel purification. After 15 cycles of PCR  amplification the libraries were sequenced using Illumina HiSeq 2000 and the paired-end  sequencing module.

treatment_protocol: total RNA is extracted by TRIzol Reagent

tag: species

value: Myotis davidii


title: BP12-2 seedling treated with rapamycin_rep1

city: Saskatoon

first: Raju

last: Datla

state: SK

address: 110 Gymnasium Place

department: Plant Biotechnology Institute

country: Canada

institute: National Research Council

data_processing:
Paired-end alignments were obtained through aligning short reads onto the reference Arabidopsis Genome (TAIR9) using Bowtie. More than 80% of the reads mapped onto the genome.
Htseq-count was used to count the reads from the Bowtie derived output files.
Differential expressed genes were identified using edgeR. The FDR-corrected P value for differential expression was set to be ≤0.05.
Genome_build: Arabidopsis Genome (TAIR9)

organism: Arabidopsis thaliana

source_name: Seedling

extract_protocol:
The total RNA were isolated from the samples by using RNeasy plant mini kit (QIAGEN, cat. no. 74904) following the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT and BP12-2 seedlings at 15 DAG were treated with rapamycin for 3 days by transferring them from 0.5MS medium to 0.5 MS+10 µg/ml rapamycin along with control (0.5 MS +1µl/ml DMSO)

tag: ecotype

value: Columbia

tag: genotype/variation

value: 10 µg/ml rapamycin


title: Col WT seedling treated with rapamycin_rep3


title: Col WT seedling treated with rapamycin_rep2


title: BP12-2 seedling treated with rapamycin_rep3


title: BP12-2 seedling treated with rapamycin_rep2


title: Col WT seedling treated with rapamycin_rep1


title: toll10b 2-4h replicate 1

data_processing:
toll10b_02to04h_1.bam; genome build: dm3
Reads were aligned to the UCSC dm3 genome using Tophat with a FlyBase release 5.28 GFF annotation file

source_name: Toll10b mutant

value: embryos were collected from Toll10b/+ females obtained from a balanced stock (Toll10b/TM3, Sb, Ser and Toll10b/OR60)

value: whole-embryo

value: 02 to 04h AEL


title: RF

city: cankiri

first: mine

last: turktas

address: ballica campus

country: Turkey

institute: cankiri karatekin university

description: miRNA-Seq

data_processing:
The data processing steps were performed using SOAP2 program (Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J: SOAP2: an improved ultrafast tool for short read alignment. *Bioinformatics* 2009, 25(15): 1966-1967).
Getting rid of low quality reads
Getting rid of reads with 5' primer contaminants
Getting rid of reads without 3' primer
Getting rid of reads without the insert tag
Getting rid of reads with poly A
Getting rid of reads shorter than 18nt
miRNA reads were aligned to Populus trichocarpa genome as reference genome (www.plantgdb.org/PtGDB/)
Genome_build: Populus trichocarpa Genome Assembly Version: Ptr v2.0
Supplementary_files_format_and_content: .txt files: First column (Seq Length) includes length of the reads, second column (read count) includes how many reads were counted, the third column (Seq) includes the sequences of the reads)

organism: Olea europaea

source_name: olive

extract_protocol:
Leaves and fruits were collected, and transferred directly into liquid nitrogen. The total RNA extractions were performed using the RNeasy Plant Mini Kit (Qiagen, Germany) for the construction of each sequencing libraries.
Standard Illumina protocol was performed for the sequencing reactions

tag: cultivar

value: Ayvalik

value: fruits

tag: tissue status

value: ripe


title: JON

description: miRNA-Seq

value: leaves

value: juvenile

tag: year

value: on-year


title: NOFF

description: miRNA-Seq

tag: tissue

value: mature

value: off-year


title: JOFF

description: miRNA-Seq


title: UF

description: miRNA-Seq

value: unripe


title: Pteropus alecto

description: Sequenced reads were generated from Pteropus alecto

organism: Pteropus alecto

source_name: Pteropus alecto

value: Pteropus alecto


title: Ago2 IP (d5)

status: Public on Dec 17 2012

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
Base calling on instrument (SOLiD 4)
Convert CSFASTA/QUAL to FASTQ using solid2fastq.pl from BWA distribution
Alignment to custom genome (see below) using BWA (Version: 0.5.9-r16); default options
Counting of miRNA species with custom python script; source available at: http://cbio.mskcc.org/public/SocciN/Thompson/Olejniczak/GEO_121022_miRNA/
Genome_build: CUSTOM: miRBASE Release 16 Mouse (mmu) miRNA's with ABI adapter (cgccttggccgtacagcag) concated to end. Genome file is available at: http://cbio.mskcc.org/public/SocciN/Thompson/Olejniczak/GEO_121022_miRNA/mouse_Counting_miRNA+ABIAdapter.fasta.gz
Supplementary_files_format_and_content: TAB delimited table of unnormalized counts.

organism: Mus musculus

source_name: Mouse embryonic fibroblasts

growth_protocol: MEFs were maintained in DMEM supplemented with 10% FCS.

extract_protocol:
Total RNA was extracted with Trizol and then enriched for small RNA using the PureLink™ miRNA Isolation Kit (Invitrogen, Cat# K1570-01).  Ago2 IP was performed using a microRNA Isolation Kit, Mouse Ago2 from Wako per the manufacturer's instructions.
Libraries were constructed according to the protocol described by the manufacturer (SOLiD Total RNA-seq kit from Life Technologies, Cat# 4452437).  All samples were barcoded.  The final library size varied from 119 to 124 nucleotides.  After equimolar amounts of libraries were combined, sequencing beads were prepared using one E80 with the EZbead system (life Technology).  Six pooled samples were sequenced in 3 octets of a SOLiD 4 slide, generating an average of 21 million 35bp reads per sample.

treatment_protocol: At d0 complete medium was removed, cells washed 2x PBS and then maintained in DMEM lacking glucose supplemented with 10% dialyzed FCS for the next five days.  At d5 glucose-free medium was removed and replaced with complete DMEM containing 25mM glucose and supplemented with 10% FCS.

value: embryonic fibroblasts

tag: immortalization

tag: ip antibody

value: Mouse Ago2 beads (Wako, cat# 299-67311)

value: Glucose starved, 5 days


title: Ago2 IP (d7)

tag: cell type

value: Glucose starved, 5 days then glucose fed for 2 days


title: Ago2 IP (d0)

value: Unstarved


title: Total RNA (d7)


title: CLIP-seq Cstf64 replicate 1 (CLIP-seq)

city: Chicago

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

data_processing:
For forward sequencing, the reads were aligned to the reference genome (mm9) and exon-exon junction database by Bowtie using the first 25 nt as seed, allowing up to 2 mismatches. The exon-exon junction database contained all possible exon-exon junction sequences in the genome. Aligned reads were scored from 5’ to 3’ using the scheme: +1 for match and -2 for mismatch. The position in a read with the maximum score was considered as the last aligned position (LAP). The best hit for each read was chosen, and was considered uniquely mapped if its score was greater than the second best hit by at least 5. If a read contained ≥ 2 non-genomic As immediately after the LAP, we considered the read as a polyA site supporting (PASS) read and the cleavage site is immediately downstream of the LAP. For data from reverse sequencing, we first trimmed the 5’ region of read, including the first 4 random nucleotides and subsequent continuous Ts. We then aligned the reads to the reference genome and exon-exon junction database by Bowtie using the first 36 nt, allowing up to 2 mismatches. For uniquely aligned reads, we compared the trimmed Ts with reference genome and exon-exon junction sequences. The reads with at least 2 non-genomic Ts are PASS reads.
CLIP-seq reads were aligned to the mouse genome (mm9) using the program novoalign (http://www.novocraft.com/). Identical reads in a sample were counted only once.
Genome_build: mm9
Supplementary_files_format_and_content: PASS reads in bed format

source_name: C2C12 proliferation cell

extract_protocol:
Three 15-cm dishes of C2C12 cells were UV-irradiated using Stratalinker (Stratagene) at 254 nm with 2000 x100 μJ/cm2 and then lysed on ice. The lysate was treated with 20 U/ml RNase T1 (Fermentas) at 25oC for 10 min, followed by centrifugation at 14,000 x g for 5 min at 4oC. The supernatant was incubated for 2 hours at 4°C with mouse anti-CstF64 monoclonal antibody (gift from Dr. Clint McDonald, Texas Tech University) conjugated to magnetic Protein G Dynabeads (Invitrogen). Co-immunoprecipitated RNA fragments were dephosphorylated by calf intestinal alkaline phosphatase (NEB) and end-labeled with [γ-32P]-ATP by T4 polynucleotide kinase (NEB). The RNA-protein complex was then resolved with Bis-Tris buffered SDS-PAGE, and transferred to nitrocellulose membrane, which was then exposed to X-ray film. The 85-150 kDa region was cut out, and the RNA from the cut-out membrane was isolated.
cDNA library preparation was based on the protocol for Illumina’s Small RNA v1.5 kit

tag: cell line

tag: sequencing method

value: CLIP-seq


title: CLIP-seq Cstf64 replicate 2 (CLIP-seq)


title: RegularOligo(dT) Cell line mix 1 (3'READS)

source_name: 11 cell line mix from Agilent

extract_protocol:
Total RNA from cells/tissues was isolated using Trizol (Invitrogen) or the Qiagen RNeasy kit. RNA samples were checked for integrity by Agilent Bioanalyzer using the RNA pico6000 kit (Agilent Technologies). RNA samples with the RNA integrity number (RIN) above 8.0 were used for subsequent processing.
Total RNA was subjected to 1 round of poly(A) selection using the Poly(A)PuristTM MAG kit (Ambion) according to manufacturer’s protocol, followed by fragmentation using Ambion’s RNA fragmentation kit at 70oC for 5 min. Poly(A)-containing RNA fragments were isolated using the CU5T45 oligo (Sigma) which were bound to the MyOne streptavidin C1 beads (Invitrogen) through biotin at its 5’ end. The oligo(dT)10-25-coated beads were from the Poly(A)Purist MAG kit. Binding of RNA with CU5T45 oligo-coated beads was carried out at room temperature for 1 hr in the binding buffer (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA), followed by washing with the low salt buffer (10 mM Tris-HCl pH 7.5, 1 mM NaCl, 1 mM EDTA, 10% Formamide). RNA bound to the CU5T45 oligo was digested with RNase H (5 U in 50 μl reaction volume) at 37oC for 1 hr, which also eluted RNA from the beads. Eluted RNA fragments were purified by Phenol:Chloroform extraction and Ethanol precipitation, followed by phosphorylation of the 5' end with T4 kinase (NEB). Phosphorylated RNA was then purified by the RNeasy kit (Qiagen) and was sequentially ligated to a 5’-adenylated 3’ adapter with the truncated T4 RNA ligase II (Bioo Scientific) and to a 5’ adapter with T4 RNA ligase I (NEB). The resultant RNA was reverse-transcribed to cDNA with Superscript III (Invitrogen), and the cDNA was amplified by 12 cycles of PCR with Phusion high fidelity polymerase (NEB). We designed adapter sequences so that the RNA fragments can be sequenced from the 5’ end (forward sequencing) or from the 3’ end (reverse sequencing). cDNA libraries were sequenced on an Illumina Genome Analyzer GAIIx (1x72 nt). RNA-seq was carried out using essentially the same protocol except that 1) the 3’ end region extraction step using the CU5T45 oligo was omitted and 2) fragmented RNA was dephosphorylated at the 3’ end with shrimp alkaline phosphatase (Roche) before ligation with adapters.

tag: sample type

value: 11 cell line mix

value: oligo(dT)10-25 Forward sequencing


title: CU5T45 Cell line mix 1 (3'READS)

value: CU5T45 oligo Forward sequencing


title: NON

description: miRNA-Seq

value: Ayvalik


title: Input_MB_replicate2

status: Public on Dec 15 2012

first: Brian

last: Dynlacht

address: 550 1st avenue

institute: NYU Langone Medical Center

data_processing:
Sequence reads within each individual replicate were filtered to remove identical sequence tags since those were likely generated by the LM-PCR amplification process while identical sequences present after the merging of replicates were retained. The sequence reads were aligned against the mouse mm9 genome build using the Illumina Pipeline and only tags locating to a single unique position were retained.
Peaks were identified using Qeseq, an algorithm developed in collaboration with Dr Klugers bioinformatics group. For sonicated libraries the settings used were: sigma=100 and cut-off=12.
Genome_build: mm9
Supplementary_files_format_and_content: Peak files: bed file format for enriched peaks; Processed files: cisg format for enriched tags, tab-delimited text files include chromosome, strand, starting position

source_name: Growing C1C12 myoblasts

growth_protocol: C2C12 myoblasts were grown in DMEM containing 10% FBS and harvested at ~40% confluency for MB chromatin. For myotube differentiation, cells were allowed to grow to complete confluence at which point differentiation was induced by changing the media to DMEM containing 2% horse serum. Induced cells were incubated for 4 days with one change of media (DMEM/2% horse serum) after two days and myotubes were harvested after 4 days of differentiation.

extract_protocol: Libraries were generated from input chromatin or ChIP enriched chromatin according to Illumina's standard protocol but using reagents from other companies: DNA end-repair was performed using the End-It DNA repair kit, Epicentre (cat:ER81050). A-overhang generation was performed uising Klenow from NED (cat: M0212). Adapter ligation was performede using the LigaFast kit from Promega (cat:M8225). LM-PCR was performed using Phusion DNA pol master mix from NEB (cat:F-531S). Very stringent quality controls were applied to the libraries: 1. Enrichment of a given site had to be preserved in the libraries in a manner comparable to the original ChIP. 10-12 positive and negative sites were tested for library preparation. 2. The total yield of the LM-PCR had to be ~500 ng. 3. The size distribution had to be centred around 250 bp for libraries generated from MNAse chromatin and around 350 bp for sonicated with a variation no larger than +/- 75 bp. Libraries that did not pass these criteria were considered substandard and were not used for sequencing.

treatment_protocol: Isolated chromatin was either sonicated to an average size of 250 bp or digested with MNAse to yield ~85% mono nucleososomal fragments.

tag: chromatin preparation method

value: Sonication


title: c-Jun_MB_replicate2

tag: chip antibody

value: c-Jun, SantaCruz:sc-1694x


title: IgG control

city: Kuopio

first: Sami

last: Heikkinen

address: Yliopistonranta 1E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description: Chromatin IP against IgG

data_processing: NA: processed data was not provided

organism: Homo sapiens

source_name: MCF-7 cells

growth_protocol: Cells were grown in Dulbecco’s Modified Eagle medium supplemented with 5% fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin, and kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol: Standard protocol for SOLiD as utilized at the Finnish Microarray and Sequencing Centre in Turku, Finland

treatment_protocol: Prior to chromatin immunoprecipitation with indicated antibody, cells were grown overnight in phenol red-free medium supplemented with charcoal-stripped fetal bovine serum. Then, cells were treated for 60 min with 10 nM estradiol or vehicle (ethanol)

value: EtOH

tag: antibody

value: IgG


title: c-Jun_MB_replicate1


title: Input_MB_replicate1


title: ER ChIP-seq

description: Chromatin IP against ERa

tag: treatment

value: estradiol

value: ERa


title: 0h_H3K27ac

city: Los Angeles

first: Kevin

last: Peterson

state: CA

address: 1425 San Pablo St.

department: Department of Stem Cell Biology and Regenerative Medicine

institute: Eli and Edythe Broad-CIRM Center for Regenerative Medicine, University of Southern California Keck School of Medicine

description: Embryoid bodies were formed by two days of suspension culture (see Growth Protocol section) and harvested for ChIP

data_processing:
Base calling was performed using Illumina pipeline
The firsty 25 bp of  sequence reads were mapped to unmasked mouse genome using either seqmap or eland allowing up to two mismatches
Peak calling was performed using a modified version of CisGenome peak caller (FDR0.01)
Independent ChIP sampes for YFP (mock FLAP-IP) and Foxa2 were combined prior to peak calling
Histone tag counts were generated using Homer makeTagDirectory function
Genome_build: mm9
Supplementary_files_format_and_content: Processed files include bed files for peak predictions and sequence tag counts for histone data generated by Homer makeTagDirectory function

source_name: Neuralized embryoid bodies

growth_protocol: mouse ESCs were cultured on MEFs in the presence of in LIF/15% FBS prior to differentiation. Cells were in vitro differentiated by suspension culture in DFNB or DNFK (DMEM:F12:Neurobasal=1:1:2 supplemented with 1x B27 or Knockout Serum Replacement) for two days. "t=0" samples were collected at this time (two days of suspension culture). Cells were induced with all-trans retinoic acid (RA, 500nM) with or without a small molecule agonist for Smo (SAG, 50-800nM). Samples were collected 3 days after RA or RA/SAG induction (t=72h RA and t=72h RA/SAG).

extract_protocol:
Chromatin precipitation protocol was previously described (Odom et al. 2006; Vokes et al. 2007).  A previously characterized Gli1FLAG cell line that constitutively expresses Gli1FLAG cDNA under Rosa26 transcriptional regulation was used for Gli1FLAG ChIP (Vokes et al. 2007). EBs were dissociated in trypsin then crosslinked in 1% formaldehyde at room-temperature for 30 minutes. Cells were lysed in lysis buffer (140mM NaCl, 0.5% NP40, 0.25% Triton-X 100, 10% glycerol, 1mM EDTA, 50mM HEPES-KOH, pH7.5) or (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) at 4˚C with agitation for 10 minutes then washed with Buffer 2 (200mM NaCl, 1mM EDTA, 0.5mM EGTA, 10mM Tris-Cl pH8.0) for 10 minutes at room-temperature. Chromatin was fragmented by sonication (Branson digital sonifier with microtip) in Buffer 3 (1mM EDTA, 0.5mM EGTA, 10mM Tris-Cl pH8.0). Lysate was cleared by centrifugation and supplemented with NaCl, NaDeoxycholate, and TritonX 100 to the final concentrations of 100mM, 0.1%, and 1%, respectively. Magnetic beads (Dynal/Invitrogen, sheep anti-mouse IgG, anti-rabbit IgG, and Protein G for mouse, rabbit, and goat antibodies, respectively) were blocked with a blocking buffer (5mg/ml BSA in PBS) then incubated with an antibody in the blocking buffer overnight.  Unbound antibody was washed away by extensive wash with the blocking buffer. Beads/antibody complex was incubated with the lysate overnight at 4°C.  Beads were washed 5 times with RIPA buffer (1% NP40, 0.7% NaDeoxycholate, 0.5M LiCl, 1mM EDTA, 50mM HEPES-KOH, pH7.5). DNA was eluted with elution buffer (1% SDS, 1mM EDTA, 50mM Tris-Cl, pH8.0) at 65˚C for 15 min, and the eluate was incubated further overnight at 65˚C to reverse crosslinking.  DNA was purified by phenol/chloroform extraction and ethanol precipitation or by PCR purification kit (Qiagen).  All buffers except RIPA buffer was supplemented with protease inhibitor cocktail mix (Roche).
Libraries were prepared according to Illumina protocols


title: Sox2-72h-SAG

description: Embryoid bodies were treated with all trans retinoic acid (RA) and SAG for 3 days before harvested for ChIP analysis (see Growth Protocol section)


title: 72h_SAG_H3K27ac

value: all trans retinoic acid (RA) and SAG for 3 days before harvested


title: Foxa2-ChIP

description:
This sample contains two biological replicates
Embryoid bodies were treated with all trans retinoic acid (RA) and SAG for 3 days before harvested for ChIP analysis (see Growth Protocol section)


title: 72h_RA_H3K27ac

description: Embryoid bodies were treated with all trans retinoic acid (RA) for 3 days before harvested for ChIP analysis (see Growth Protocol section)


title: 72h_RA_H3K4me2

value: all trans retinoic acid (RA) for 3 days before harvested


title: 0h_H3K4me2

value: Embryoid bodies were formed by two days of suspension culture


title: p300_MT_replicate3

data_processing:
Sequence reads within each individual replicate were filtered to remove identical sequence tags since those were likely generated by the LM-PCR amplification process while identical sequences present after the merging of replicates were retained. The sequence reads were aligned against the mouse mm9 genome build using the Illumina Pipeline and only tags locating to a single unique position were retained.
Peaks were identified using Qeseq, an algorithm developed in collaboration with Dr Klugers bioinformatics group. Setting for all MNAse libraries: sigma=50 and cut-off=15. For sonicated libraries the settings used were: sigma=100 and cut-off=12.
Genome_build: mm9
Supplementary_files_format_and_content: Peak files: bed file format for enriched peaks; Processed files: cisg format for enriched tags, tab-delimited text files include chromosome, strand, starting position

source_name: C1C12 myotubes differentiated for 96h

value: p300, SantaCruz:sc-585x


title: 72h_SAG_H3K4me2


title: p300_MT_replicate1


title: Total RNA (d5)

value: embryonic fibroblasts

tag: genotype

value: Glucose starved, 5 days


title: p300_MB_replicate2


title: p300_MB_replicate3


title: p300_MT_replicate2


title: Iron_depleted_rep2

city: SEATTLE

first: Gowthaman

last: Ramasamy

state: WASHINGTON

address: 307 WESTLAKE AVE N

department: GHBC

institute: SEATTLE BIOMEDICAL RESEARCH INSTITUTE

description:
AH066
Replicate 2 of parsite culture grown in the absense of iron

data_processing:
Filtering; In-house PERL script; Only reads that are starting with SL signatures(NTG) are retained. Others are discarded
Alignment; bowtie; v.0.12.7; Filtered reads are alilgned using bowtie (0.12.7) after trimming 3 bases from the 5' end
Count data generation; In-house PERL script; Number of reads hiting each gene and its 5' UTR/intergenic region was counted using in-house perl scripts
Differntial expression analysis; edgeR; v.2.6.10; DE analysis was performed using bioconductor package Deseq (version 2.6.10)
Genome_build: Leishmania mexicana V4.0 From TriTrypDB
Supplementary_files_format_and_content: bed files in bed12 fromat containing read pileup data

organism: Leishmania amazonensis

source_name: Lab culture_Iron_depleted

growth_protocol: L. amazonensis IFLA/BR/67/PH8 wild type promastigotes were maintained in vitro at 26C in M199 growth media containing 40 mM HEPES (pH 7.4) and supplemented with 10% heat inactivated FBS, 0.1% hemin (Frontier scientific; 25 mg/ ml in 50% triethanolamine), 0.1 mM adenine (pH 7.5), 10 mM adenine, biotin (0.0001% v/v), 5 mM L-glutamine and 100 U/ml penicillin/0.1 mg/ml streptomycin. Differentiation into axenic amastigotes was initiated by mixing log-phase promastigote cultures (~2x106 /ml) with equal volumes of acidic amastigote media (M199 supplemented with 0.25% glucose, 0.5% trypticase and 40 mM sodium succinate pH 4.5) and elevating the temperature to 32C. Differentiated amastigotes were maintained in amastigote media at 32C.

extract_protocol:
L. amazonensis cells were harvested, washed with PBS (930g / 5 min / RT), and used to isolate total RNA using Qiagen RNeasy kit (Qiagen) as per manufacturer’s protocol. An on-column DNAse digestion step was performed using RNAse-Free DNase Set (Qiagen) to ensure removal of any contaminating DNA.
Superscript III (Invitrogen) and primer 1 (5’- TCCGATCTCTNNNNNNN-3’). The reaction was carried out by incubating for 90 min at 40°C followed by 15 min at 70°C. The samples were then treated with 2U RNAse H (Invitrogen) (37°C for 20 min) to remove the RNA component of the RNA:DNA heteroduplex and the resulting first strand DNA was purified on a QIAquick PCR purification column (Qiagen). Second strand synthesis reaction was performed using the first strand DNA as template in a reaction mix containing a primer (5’-TCAGTTTCTGTA-3’) that matches the Leishmania SL sequence and 3’-5’ exo- Klenow Fragment (New England Biolabs) following the manufacturer’s protocol (incubation at 37°C for 30 min). The resulting double stranded DNA was purified using QIAquick PCR purification kit. Enrichment of DNA fragments with adapters was performed by PCR amplification of the purified double stranded DNA samples using ExpandPlus High Fidelity PCR System (Roche) and primers (5’- CAAGCAGAAGACGGCATACGAGCTCTTCCGATCTCT-3’, 5’- AATGATACGGCGACCACCGACACTCTTTCCCTACATCAGTTTCTGTACTTTA-3’). 2 min denaturation step at 94°C followed by 2 cycles (94°C for 10 s, 40°C for 2 min, 72°C for 1 min) and an additional 13-16 cycles (94°C for 10 s, 60°C for 30 s and 72°C for 1 min) with a final 5 min, 72°C elongation step. The resulting enriched fragments were purified on a QIAquick PCR purification column and represented the SL RNA library.

treatment_protocol: L. amazonensis promastigotes grown to mid-log phase (1-2x10^6/ml) in regular growth media were harvested by centrifugation (930g for 5 min RT) and resuspended in iron- depleted media at final concentrations of 1x10^6 or 4x10^6 /ml. Live and dead parasites were distinguished by incubating culture samples for 5 min at RT with 100 mM fluorescein diacetate (FDA) to detect living parasites, and 150 μM propidium iodide (PI) to detect dead parasites. Parasites were transferred to a brightline hemocytometer and viewed on a Nikon Eclipse E200 microscope with a 40X NA 0.75 objective (Nikon). Green fluorescent parasites following FDA treatment were scored as “live” while red fluorescent parasites following propidium iodide were scored as “dead”. Parasite growth was determined by counting the FDA-stained cells in culture samples at 24 h intervals.

tag: strain

tag: developmental stage

value: Procyclic Promastigotes


title: p300_MB_replicate1


title: H3K27ac_MT_replicate2

value: MNAse digestion

value: H3K27Ac, Abcam:Ab4729


title: H3K27ac_MT_replicate1


title: Iron_depleted_rep1

description:
AH064
Replicate 1 of parsite culture grown in the absense of iron


title: H3K27ac_MB_replicate2


title: YFP- (mock)

description:
This sample contains two biological replicates
Embryoid bodies were treated with all trans retinoic acid (RA) and SAG for 3 days before harvested for ChIP analysis (see Growth Protocol section). YFP3.1 is the parental line to R26-Gli1-FLAG and serves as a non-FLAG negative control.


title: H3K27ac_MB_replicate1


title: Sham-injected

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

data_processing:
Sequencing reads were mapped to the reference genome (bosTau7) using the software package Tophat.
Cufflinks (v2.0.2) was used to assemble transcript models from alignments and to estimate their abundance in the transcriptome.
Abundances of transcripts were upper-quartile normalized and also corrected for sequence bias in order to improve expression estimates.
Genome_build: Btau_4.6.1
Supplementary_files_format_and_content: tab-delimited text files include gene name, location and FPKM values

organism: Bos taurus

source_name: IVF embryos, Control

extract_protocol:
Total RNA from sham-injected and CDKN1C-siRNA-injected embryo pools underwent amplification using the MessageAmp II aRNA Amplification Kit (Ambion).
Libraries of amplified RNA for each pool were prepared following the Illumina mRNA-Seq protocol. Sequencing libraries were created from 50 ng samples and sequenced with Illumina’s HiSeq 2000 at the University of Wisconsin-Madison Biotechnology Center.

value: IVF embryos

tag: genotype/variation

value: Sham-injected


title: CDKN1C-siRNA-injected

source_name: IVF embryos, CDKN1C knockdown


title: Gli1FLAG


title: PC

city: Qingdao

first: Xuelin

last: Zhao

address: Yushan Road 5

department: Fisheries College

institute: Ocean University of China

data_processing:
Basecalls performed using Off-line Base Caller version 1.8
Raw data were preprocessed to remove nonsense sequences and was assembled as contigs by Velvet (version 1.0.15) and Oases (version 0.1.18) software.
Sequenced reads were masked for low-complexity or low-quality sequence, then mapped to contigs assembled using Bowtie version 0.12.5
Reads Per Kilo bases per Million reads (RPKM) were calculated using a protocol from Mortazavi et al., Nat Methods, 2008. In short, The number of reads falling in the contigs assembled were counted and normalized by the size of the two libraries, respectively.
Genome_build: contigs by assembling two libraries
Supplementary_files_format_and_content: List files were generated using Newbler version 2.7, including sequences that were aligned the same ones and the occurrence of each sequence.

organism: Magallana gigas

source_name: Gill

extract_protocol: Gills were removed and kept in RNA store. The total RNA was harvested using TRIzol reagent. Poly-A RNA was extracted from each total RNA sample using MicroPoly(A)PuristTM Kit (Part# AM1919M) according to manufacturer’s instructions and pooled for cDNA synthesis. cDNA samples were prepared following the protocol from Ng et al., Nat Methods, 2009. Briefly, first-strand cDNA was synthesized using SuperScript II reverse transcriptase (Cat#18064-014) with Gsul-oligo-dT primer. The second-strand cDNA was synthesized using Ex Taq polymerase (Cat# RR001A). The synthetic cDNA was mode to 300-500 bp by a UTR200 sonication device, The fragments were amplified with TruSeq PE cluster kit v3-cBot-HS (Cat# PE-401-3001) and used to construct libraries with TruSeqTM DNA sample prep kit-set A (Cat#FC-121-1001) according to the manufacturer’s instructions.

treatment_protocol: Twenty four oysters were devided evenly into two groups, one was exposed in optimal salinity seawater (25‰) and the other was exposed in low salinity seawater (8‰) for 8 hours.

value: Gill

tag: handling time

value: 8 hours

tag: condition

value: in optimal salinity seawater

tag: development stage

value: adult


title: PT

tag: tissue

value: in low salinity seawater


title: Iron_containing_rep2

description:
AH065
Replicate 2 of parsite culture grown in the presence of iron

source_name: Lab culture_Iron_containing


title: Iron_containing_rep1

description:
AH063
Replicate 1 of parsite culture grown in the presence of iron


title: 50% Human / 50% Human Replicate 3

status: Public on Dec 14 2012

city: Miami

first: Camilo

last: Valdes

state: FL

address: Locator C-213.  1120 NW 14 Street

department: Center for Computational Science

institute: University of Miami

data_processing:
Basecalls performed using CASAVA version 1.3
RNA-Seq reads were aligned to the Ensembl human (hg19) and mouse (mm9) assemblies using the TopHat 1.4.1 spliced-read aligner.
Alignments were filtered based on their MAPQ values (MAPQ=30).
Read counts were calculated for genes of interest (GTF files) using the MAPQ filtered alignments that mapped to the gene's genomic interval.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: Read Counts.  Tab delimited read counts for the gene in column 1.  Column 2 contains the read counts in the genomic interval. Column 3 is an alternate gene name if one is available, otherwise it is the same as column 1.  Column 4 is the chromosome.  Columns 5 and 6 are the start and end positions (genomic coordinates).
Supplementary_files_format_and_content: GTF.  Standard format GTF files describing the genes for Ensembl (Ensembl GTF) and CCDS (CCDS GTF).

organism:
Homo sapiens
Mus musculus

source_name: human breast & mouse normal lung tissue

growth_protocol: MDA-MB-231 human breast carcinoma cell line was obtained from the American Type Culture Collection, and maintained according to the supplier’s instructions.  RNA was isolated from three independent cultures of sub-confluent MDA-MB-231 cells in the exponential phase of growth.

extract_protocol:
RNA was extracted from cultured MDA-MB-231 cells and normal lung tissue using Trizol Reagent (Invitrogen) according to the manufacturer’s instructions.  Concentration and yield of RNA samples were determined using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies).  RNA integrity was determined by analysis on an Agilent 2100 Bioanalyzer (Agilent Technologies) following the manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols. Briefly, mRNA (200ng) was fragmented at 70 uC for 5 minutes in a fragmentation buffer (Ambion), and converted to first-strand cDNA using Superscript III (Invitrogen); followed by second-strand cDNA synthesis using Escherichia coli DNA pol I (Invitrogen).  The double stranded cDNA library was further processed by illumina Genomic DNA Sample Prep Kit.

value: NOD scid gamma

tag: human portion (%)

tag: mouse portion (%)


title: 25% Human / 75% Mouse Replicate 1

tag: cell line


title: 25% Human / 75% Mouse Replicate 2


title: 50% Human / 50% Human Replicate 2


title: 75% Human / 25% Mouse Replicate 1B


title: 75% Human / 25% Mouse Replicate 2


title: Low Mg2+ 7 days treatment

city: Hangzhou

first: Gulei

last: Jin

state: Zhejiang

address: Yuhangtang Road 388#

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using CLC Genomics Workbench 5.1.5 with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CLC Genomics Workbench 5.1.5
Genome_build: TAIR v10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

growth_protocol: All plants were grown in the controlled-environment growth chambers (Conviron E7/2, Winnipeg, Manitoba, Canada) with a humidity of 80%, a daily cycle of 24 °C, 10-h day and 20 °C, 14-h night. The daytime light intensity was 120 µmol photons m−2 s−1. The wild ecotype line was from the Nottingham Arabidopsis Stock Centre (http://nasc.nott.ac.uk).

extract_protocol:
The roots were ground in liquid nitrogen and total RNA was subsequently extracted with RNAisoPlus reagent from 70 mg of tissue powder according to the manufacturer’s instructions (Takara, Otsu, Shiga, Japan). All RNA samples were checked for DNA contamination.
Purified RNA was analyzed on a ND-8000 spectrophotometer (Nanodrop, Technologies, Wilmington, DE), agarose electrophoresis or a 2100-Bioanalyzer (Agilent Technologies, Santa Clara, CA), to determine the quantity. RNA samples were used if there was no smear on the agarose. RNA samples were also used if the 260/280 ratio was above 2.0 and the RIN (RNA integrity number) was greater than 7.0.

treatment_protocol: Roots were sampled from five-week-cultivated Arabidopsis after 7 d treatment of low Mg (supplied with 0.5 μM Mg2+) and high Mg (supplied with 10 mM Mg2+).

value: Root

tag: cultivar


title: 75% Human / 25% Mouse Replicate 3


title: 25% Human / 75% Mouse Replicate 3


title: 100% Human Replicate 3B

source_name: human breast


title: 100% Mouse Replicate 2

source_name: mouse normal lung tissue


title: Total RNA (d0)

tag: cell type

tag: immortalization

tag: ip antibody

value: Unstarved


title: 100% Human Replicate 3A


title: 100% Human Replicate 2B


title: 100% Human Replicate 1B


title: 100% Human Replicate 2A


title: 100% Human Replicate 1A


title: Nfib-null rep2

status: Public on Dec 13 2012

city: Cheonan

first: Keunsoo

last: Kang

state: Chungnam

address: Dandae-ro 119

department: Microbiology

institute: Dankook University

data_processing:
Basecalls performed using the CASAVA software
Sequenced reads were aligned to the mm9 genome assembly using the TopHat program (Trapnell et al., Bioinformatics, 2009)
In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted. RPKM (reads per kilobase of transcript per million mapped reads) were calculated using a protocol (Mortazavi et al., Nat. Methods, 2008).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: Mammary tissues

extract_protocol:
Mammary tissues without lymph nodes from mice of each genotype were collected, frozen in liquid nitrogen, and stored at -80 °C. Total RNA was extracted using TRIzol reagent, followed by a cleanup step using the RNeasy Plus Mini Kit (QIAGEN). Poly(A) RNA was purified twice from 1 mg total RNA and cDNA was synthesized using SuperScript II (Invitrogen) and TruSeq RNA Sample Preparation Kit (Illumina Inc., San Diego, CA), and sequenced using HiSeq 2000 (Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mammary gland

value: Day of parturition within less than 12 hours after delivery

value: Outbred

value: Nfib-null (KO)


title: Nfib-null rep1


title: Nfib-WT rep2

value: wild type


title: Nfib-null rep3


title: Nfib-WT rep1


title: H2AZ_WT_3_RNA

city: Berkeley

first: Toshiro

last: Nishimura

address: 211 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

data_processing:
For Bisulfite Sequencing, we used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted  reference scaffold, allowing up to two mismatches per read. 76 base reads were divided into the first 45 and the last 31 bases. 50 base reads were processed as single reads.  Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first. Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T. 50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
For ChAP-Sequencing, nucleosomal midpoints were estimated based on an average 150-bp nucleosome length by adding 75bp to the start position of each read.   Differences between IP and input over each single-base window were generated to give an overall genome-wide map of H2A.Z-enrichment.  Genes were aligned at either their 5' or 3' ends, and average H2A.Z-enrichment values were calculated over each 50bp window between 3kb up and downstream of the point of alignment. Sequencing was carried out on the HiSeq platform and sequence alignments were performed using Bowtie and the TAIR8 Genome Annotation
Genome_build: TAIR8
Supplementary_files_format_and_content: For Bisulfite Sequencing gff files, they contain  fractional methylation data either for individual cytosines (single-c) or in 50 bp windows. For ChAP-Sequencing gff files, they contain data either for individual basepairs (w1) or in 50 bp windows (w50) for the H2A.Z enrichment data (mutant - WT normalized read counts). For all three Sequence dataset types, including RNA-Sequencing, the raw reads are presented in FASTQ format.

source_name: H2AZ-WT Rosettes 4 weeks

growth_protocol: Arabidopsis plants were grown according to one of the following methods: 1) For bisulfite sequencing of seedling tissues, seeds were planted on 1x Murashige and Skoog Media with micronutrients and 1.5% Sucrose (Caisson Laboratories) and grown under 16h light/ 8h dark for 14 days in a growth chamber.  2) For bisulfite sequencing of rosette and cauline leaf tissue, seeds were planted on soil and grown in greenhouse conditions with LD 16h light / 8h dark.  3) For phenotype analysis of the h2a.z mutant, seeds were planted on soil and grown in greenhouse conditions with either 16h light / 8h dark (LD) or 8h light/ 16h dark (SD).

extract_protocol: For Bisulfite-Sequencing, approximately 100-500 ng genomic DNA was isolated from either seedling, rosette or cauline leaf tissues. Seedling tissue was obtained from 14 days post germination seedlings grown on Murishige and Skoog media in LD (16h light/ 8h dark). Mature rosette leaves and mature cauline leaves were obtained from 4 week post germination mature plants grown on soil in LD (16h light/ 8h dark).  In general, multiple biological replicates were generated for each mutant and WT line; a complete list of all generated libraries is available in Table S4.  WT datasets for each mutant were generated from plants derived from recent relatives of the relevant mutant.  Bisulfite conversion and Illumina library construction and sequencing were performed as described previously. We used single ends (SE) Illumina sequencing for bisulfite sequencing on the GAII and HiSeq platforms and  sequence alignments were performed using Bowtie and the TAIR8 Genome Annotation (http://www.arabidopsis.org/) as described previously. The average percent methylation plots were generated as described previously. For RNA -Sequencing, approximately 30 ug total RNA was isolated from 4 week post germination mature rosette leaves  using the RNEasy Plant Extraction Kit (Qiagen) with the optional on-column DNAse treatment.  mRNA was purified from total RNA by two treatments of poly-A enrichment using the Oligotex kit (Qiagen #72022), followed by a rRNA removal step using the RiboMinus Plant Kit for RNA-sequencing (Invitrogen #A1083702). Illumina library construction and RNA-sequencing were performed as described in [34]. We used single ends (SE) Illumina sequencing for RNA-sequencing on the GAII platform and sequence alignments were performed using Bowtie  and the TAIR8 Genome Annotation and cDNA Annotation. For ChAP-Sequencing, H2A.Z-containing nucleosomes were chromatin affinity purified (ChAP) from 4 week post germination  Arabidopsis roots of our H2A.Z-BLRP transgenic lines grown in LD conditions as in [16]. Illumina libraries were constructed for IP and input DNA samples and sequenced generating SE 50 bp reads.

value: h2a.z-related wild type (F2 sibling)

value: rosettes

tag: age

value: 4 weeks


title: High Mg2+ 7 days treatment

tag: treatment


title: H2AZ_WT_1_RNA


title: H2AZ_HO_3_RNA

source_name: H2A.Z Rosettes 4 weeks

value: h2a.z mutant


title: H2AZ_WT_2_RNA


title: H2AZ_HO_2_RNA


title: H2AZ_HO_1_RNA


title: PIE1_WT_1

source_name: PIE1_WT seedlings 3 weeks

value: pie1-5-related wild type (F2 sibling)

value: seedlings

value: 3 weeks


title: IBM_HO_1

source_name: IBM_HO seedlings 2 weeks

value: ibm1-6 mutant

value: 2 weeks


title: PIEIBM_HO_1

source_name: PIEIBM_HO seedlings 2 weeks

value: pie1-5;ibm1-6 double mutant


title: METH2AZ_HO_1

source_name: METH2AZ_HO seedlings 2 weeks

value: h2a.z;met1-6 double mutant


title: H2AZ_HO_1

source_name: H2AZ_HO cauline 6 weeks

value: cauline

value: 6 weeks


title: Pol II ChIP-seq from 10-12 h Drosophila muscle cells, 4H8 antibody, replicate 2

city: Kansas City

first: Julia

last: Zeitlinger

institute: Stowers Institute for Medical Research

data_processing:
mef2_10to12h_pol_4h8_2.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.

source_name: muscle FAC sorted from dissociated embryos

extract_protocol: ChIP-seq: DNA-protein-complexes were isolated with specific antibodies. Sequencing libraries were prepared following Illumina's instructions: DNA was end repaired using T4 DNA polymerase, DNA polymerase I large fragment (Klenow polymerase) and T4 polynucleotide kinase. A single 3'-A overhang was added to the blunted ends using Klenow 3'-5' exo- polymerase. Adapters with single 3'-T overhangs were ligated to the adenylated fragments, and after a size-selection step on a 2 % agarose gel (150-250 bp) the adapter modified DNA was PCR-amplified. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.

tag: genetic background

tag: time point

value: 10 to 12h AEL

tag: chip antibody

value: Pol II (CTD48H, Millipore)

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog #


title: H2AZ_WT_1

source_name: H2AZ_WT cauline 6 weeks

tag: genotype/variation


title: H2AZ_HO_2

source_name: H2AZ_HO rosettes 6 weeks


title: H2AZ_ChAP_in_2

description: ChAP-Seq datasets rely on the interaction of streptavidin covered beads and Biotin tagged proteins (in this case, the biotin tagged version of H2A.Z). In these samples, "IP" refers to the DNA pulled down through this interaction. More information in:  "H2A.Z and DNA methylation are mutually exclusive epigenetic marks" Nature. 456, 125-129 (6 November 2008).

data_processing:
Library strategy: ChAP-Seq
For Bisulfite Sequencing, we used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted  reference scaffold, allowing up to two mismatches per read. 76 base reads were divided into the first 45 and the last 31 bases. 50 base reads were processed as single reads.  Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first. Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T. 50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
For ChAP-Sequencing, nucleosomal midpoints were estimated based on an average 150-bp nucleosome length by adding 75bp to the start position of each read.   Differences between IP and input over each single-base window were generated to give an overall genome-wide map of H2A.Z-enrichment.  Genes were aligned at either their 5' or 3' ends, and average H2A.Z-enrichment values were calculated over each 50bp window between 3kb up and downstream of the point of alignment. Sequencing was carried out on the HiSeq platform and sequence alignments were performed using Bowtie and the TAIR8 Genome Annotation
Genome_build: TAIR8
Supplementary_files_format_and_content: For Bisulfite Sequencing gff files, they contain  fractional methylation data either for individual cytosines (single-c) or in 50 bp windows. For ChAP-Sequencing gff files, they contain data either for individual basepairs (w1) or in 50 bp windows (w50) for the H2A.Z enrichment data (mutant - WT normalized read counts). For all three Sequence dataset types, including RNA-Sequencing, the raw reads are presented in FASTQ format.

source_name: H2AZ_CHAP_IN Roots 3 weeks

value: roots


title: H2AZ_ChAP_IP_1

source_name: H2AZ_CHAP_IP Roots 3 weeks


title: PIEH2AZ_HO_1

source_name: PIEH2AZ_HO seedlings 2 weeks

value: h2a.z;pie1-5 double mutant


title: IBMH2AZ_HO_3

source_name: IBMH2AZ_HO seedlings 2 weeks

value: h2a.z; ibm1-6 double mutant


title: IBMH2AZ_HO_1


title: PIEIBM_HO_3


title: Staphylococcus sp.OJ82 1% NaCl

first: Sungjong

last: Choi

institute: Korea university

data_processing:
Base-calling: CASAVA v1.6
Alignment: CLC Genomics Workbench 4.5
Generation of normalized abundance measurement: CLC Genomics Workbench 4.5
Genome_build: Staphylococcus sp.OJ82, GenBank : ALPU00000000.1
Supplementary_files_format_and_content: RPKM

source_name: Staphylococcus sp.OJ82 1% NaCl

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

value: 1% NaCl

tag: strain


title: mRNASeq_skip_rep1

city: Shenyang

first: Xiaoxue

last: Wang

state: Liaoning

address: 120 Dongling Road, Shenhe District

department: Rice Research Institute

institute: Shenyang Agricultural University

description: polyA RNA isolated

data_processing: After removing reads containing sequencing adapters, we mapped reads to the Arabidopsis TAIR9 genome build with BOWTIE (Langmead et al., 2009) allowing up to two mismatches.

source_name: Seedling

growth_protocol: Seedlings of wild type (Col-0) and skip-2 mutant were grown under 16 hour light/ 8 hour dark photocyles (LD) with cool white fluorescent light (70 Âµmol m-2 s-1) at 22oC for the day and 18oC for the night.

extract_protocol: For mRNA sequencing, total RNA was isolated using TRI Reagent (Ambion, Cat# AM9738) according to the manufacturer's instructions. mRNA was extracted from total RNA using Dynabeads mRNA DIRECT Kit (Invitrogen, Cat# 610.11) following the manufacturer's directions. First and second strand cDNA was synthesized using Superscript II reverse transcriptase (Invitrogen, Cat# 18064.022 ) and random hexamers primers. DNA Sample Prep Master Mix Set 1 (New England Biolabs, Cat# E60404 L) was used to add adapters to the ends of the cDNA following the manufacturer's protocol. Then, the products of the ligation reaction were purified on a gel to select a size range of templates for downstream enrichment by PCR amplification. After enrichment, the library was sequenced thoroughly.

tag: tissue

value: 7-day-old seedling

value: skip-2 mutant


title: mRNASeq_WT_rep1

description: polyA RNA isolated

value: wild type (Col-0)


title: I304N FLAG-HA FMR1 iso7

first: Manuel

last: Ascano

address: 1230 York Avenue Box 186

department: HHMI/Laboratory of RNA Molecular Biology

institute: The Rockefeller University

description:
PAR-CLIP
iso7_I304N_1
I304N FMR1 iso7 crosslinked ribonucleoprotein complexes

data_processing:
Fastq was converted to fasta using FASTX Toolkit 0.0.13: fastq_to_fasta -v
Adapters were removed using FASTX Toolkit: fastx_clipper -v -a TCGTATGCCGTCTTCTGCTTG -l 13
Reads were mapped to hg19 using bowtie version 0.12.7: bowtie bowtie/base/hg19 -v 2 -m 10 --all --best --strata
Sites were determined using PARalyzer v1.1
Genome_build: hg19
Supplementary_files_format_and_content: bed files reporting target sites for RNA-binding proteins

source_name: FlpIn T-Rex Human embryonic kidney 293 stable cell line

growth_protocol: FlpIn T-Rex HEK293 stable cell lines were cultured in DMEM (11995, Invitrogen) supplemented with 10% Fetal bovine serum, 2 mM L-Glutamine, 50 units of Penicillin, 50 µg/ml Streptomycin, 100 µg/ml Hygromycin, and 15 µg/ml Blasticidin

extract_protocol: Cell pellets were lysed in NP40 lysis buffer, centrifuged, and the resulting supernatants used in subsequent steps. The cleared supernatants were incubated with Rnase T1 (Fermentas) at  22ºC, for 15 min, then cooled on ice. FLAG-antibody conjugate paramagnetic beads (Dynabeads, Invitrogen) were added to each supernatant to begin immunoprecipitation. Immunoprecipitates were subjected to dephosphorylation using calf-intestinal alkaline phosphatase (NEB), followed by three buffer washes, then treatment with T4 polynucleotide kinase (NEB) using gamma radiolabelled - 32P ATP. Radiolaballed immunoprecipitates were then fractionated by SDS-PAGE. The immunoprecipitated bands of interest were excised, electroeluted, and treated with Proteinase K to isolate crosslinked RNAs. Crosslinked RNAs were taken through a standard adapter-mediated small RNA cloning protocol and sequenced using Illumina GAII platform (or HiSeq).

treatment_protocol: Expression of stable transgenes were induced by incubation with 1 µg/ml doxycyline concurrent with 100 µM 4-Thiouridine (4SU, Sigma) for 16 h. For harvesting, cells were rinsed with ice-cold PBS, irradiated with 365 nM UV light (0.15 J/sq cm), collected and pelleted, and finally snap-frozen (-80 deg C)

tag: photoactivatable ribonucleoside and crosslinking wavelength

tag: antibody

value: anti-FLAG M2 [Sigma-Aldrich, cat# F1804, lot#101M6216]

tag: immunoprecipitated protein

value: I304N FLAG-HA FMR1 iso7


title: IBM_WT_2

source_name: IBM_WT seedlings 2 weeks

value: ibm1-6-related wild type (F2 sibling)

value: seedlings

value: 2 weeks


title: IBM_WT_1


title: I304N FLAG-HA FMR1 iso1

description:
PAR-CLIP
iso1_I304N_1
I304N FMR1 iso1 crosslinked ribonucleoprotein complexes

tag: cell line

value: FlpIn T-Rex Human embryonic kidney 293 stable cell line

value: I304N FLAG-HA FMR1 iso1


title: mRNASeq_skip_rep2

description: polyA RNA isolated


title: PIEIBM_HO_2

value: pie1-5;ibm1-6 double mutant


title: wt FLAG-HA FMR1 iso7

description:
PAR-CLIP
iso7_WT
wt FMR1 iso7 crosslinked ribonucleoprotein complexes

value: wt FLAG-HA FMR1 iso7


title: 50% Human / 50% Human Replicate 1

source_name: human breast & mouse normal lung tissue

value: NOD scid gamma

tag: human portion (%)

tag: mouse portion (%)


title: MET_HO_2

source_name: MET_HO seedlings 2 weeks

value: met1-6 mutant


title: wt FLAG-HA FXR2

description:
PAR-CLIP
FXR2
wt FXR2 crosslinked ribonucleoprotein complexes

value: wt FLAG-HA FXR2


title: IBM_HO_2

source_name: IBM_HO seedlings 2 weeks

value: ibm1-6 mutant


title: wt FLAG-HA FXR1

description:
PAR-CLIP
FXR1
wt FXR1 crosslinked ribonucleoprotein complexes

value: wt FLAG-HA FXR1


title: MET_HO_1


title: PIE1_WT_3

source_name: PIE1_WT seedlings 2 weeks

value: pie1-5-related wild type (F2 sibling)


title: PIE1_WT_2


title: PIE1_HO_2

source_name: PIE1_HO seedlings 2 weeks

value: pie1-5 mutant


title: mRNASeq_WT_rep2

description: polyA RNA isolated

value: 7-day-old seedling

value: wild type (Col-0)


title: PIE1_HO_1


title: H2AZ_WT_7

value: h2a.z-related wild type (F2 sibling)

value: cauline

value: 6 weeks


title: H2AZ_WT_6

source_name: H2AZ_WT rosettes 6 weeks

value: rosettes


title: H2AZ_HO_7

source_name: H2AZ_HO cauline 6 weeks

value: h2a.z mutant


title: H2AZ_WT_4

source_name: H2AZ_WT seedlings 2 weeks

value: seedlings

value: 2 weeks


title: wt FLAG-HA FMR1 iso1

description:
PAR-CLIP
iso1_WT
wt FMR1 iso1 crosslinked ribonucleoprotein complexes

value: FlpIn T-Rex Human embryonic kidney 293 stable cell line

value: anti-FLAG M2 [Sigma-Aldrich, cat# F1804, lot#101M6216]

value: wt FLAG-HA FMR1 iso1


title: H3K4me2_PN7_ChIPSeq

city: Hershey

first: Samuel

middle: Shao-Min

last: Zhang

state: PA

address: 500 University Drive

department: Neural and Behavioral Sciences

institute: Penn State University College of Medicine

description: Histone modification H3K4me2 at developmental stage PN7

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie (v0.12.4)
The number of unique-mapped reads was counted for each 100bp window along all chromosomes, and then normalized by the number of total unique-mapped reads in the sample.
RefSeq database from NCBI was used to for gene annotation.
LOWESS function was used to calculate a smoothed density curve
NextGENe software (v2.10) was used to detect enriched regions based on Poisson distribution.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files with normalized tag counts of histone modifications by gene for each sample

source_name: retina

extract_protocol: At least 20 mouse retinas were rapidly isolated from each developmental stage at E17.5, PN1, PN7, and PN15 for chromatin isolation by a routine method (Supplemental Methods). Pde6b (rd1/rd1) mutant mice were used as rod photoreceptor subtraction control. Anti-H3K4me2 and anti-H3K27me3 were used and anti-GFP served as control. Validated antibodies (Supplementary Fig. 2) were used for ChIP to prepare libraries with Illumina ChIP-Seq DNA Sample Preparation Kit (IP-102-101). Quality and quantity of DNA of the libraries were validated on Agilent Technologies 2100 Bioanalyzer.

value: Pde6b (rd1/rd1) mutant mice

value: H3K4me2 (07-449, Upstate, Charlottesville, VA, lot 26335, cat#07-030)

tag: developmental stage

value: retina


title: PN56_Anti_GFP_ChIPSeq

description: Control

value: GFP (Santa Cruz, lot #F2508, sc8334)


title: H3K4me2_PN15_ChIPSeq

description: Histone modification H3K4me2 at developmental stage PN15


title: H3K27me3_PN15_ChIPSeq

description: Histone modification H3K27me3 at developmental stage PN15

value: H3K27me3 (07-030, Upstate, Charlottesville, VA, lot 24440, cat.#07-449)


title: H3K27me3_E17_ChIPSeq

description: Histone modification H3K27me3 at developmental stage E17


title: H2AZ_HO_4

source_name: H2AZ_HO seedlings 2 weeks

tag: age


title: H3K27me3_PN7_ChIPSeq

description: Histone modification H3K27me3 at developmental stage PN7


title: H3K27me3_PN1_ChIPSeq

description: Histone modification H3K27me3 at developmental stage PN1


title: h4k16ac

status: Public on Dec 11 2012

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

description: service: Norwegian Sequencing Centre, Oslo, Norway

data_processing:
Sequenced reads were mapped to dm3 whole genome using bowtie version 0.12.7 with parameters  -m 1 (single reads) and --trim3 65 -X 1500 (paired end reads)
calculation of genomic coverage vectors for each sample using a 150 bp read extension for single read samples
arcsine transformation of coverages
averaging of replicate samples
subtraction of common background (input)
Genome_build: dm3
Supplementary_files_format_and_content: bedgraph files of the mean genomic coverage

source_name: H4K16ac ChIP-Seq

extract_protocol: As performed by sequencing service

tag: cell type

tag: ip antibody

value: polyclonal rabbit H4K16ac, Active Motif 39167

tag: shearing technologie

value: Bioruptor

tag: chromatin size (bp)


title: H3K4me2_PN30_rd1_ChIPSeq

description: Histone modification H3K4me2 at developmental stage PN30

tag: chip antibody


title: H3K4me2_E17_ChIPSeq

description: Histone modification H3K4me2 at developmental stage E17


title: mle_1

source_name: MLE ChIP-Seq

value: monoclonal rat 6E11


title: H1_H1.5_ChIPseq

first: Jing-Yu

last: Li

address: 615 Charles E. Young Dr. South BSRB 357

institute: University of California, Los Angeles

description: Chromatin IP against human HIST1H1B (H1.5)

data_processing:
Unique sequences (duplicated sequences were removed and mapped only once to the genome) were aligned to human genome reference HG19 by using Bowtie-0.12.7 (command: bowtie -r -t -o 6 -a -m 1 --best --strata -v 2). Each chromosome was divided into windows of 100 bp. Number of reads in each window was calculated. To normalize total reads of ChIP enriched and Input DNA, the ratio of total reads from ChIP and Input DNA was calculated to generate a normalization factor which was applied to each value of the Input sample. To effectively capture local biases in the genome, we calculated the ratio of ChIP versus Input value in each window, and Poisson distribution was used to calculate a p-value for each window [2]. Significant peaks were defined as enrichment of ChIPed DNA over input DNA within a 100-base pair (bp) window at a Poisson p-value ≤ 0.001. Windows with significant p-values but with no neighboring significant peak or with no input reads were filtered out. To visualize large enrichment blocks, moving average was performed with moving window size of 10 kb and moving steps of 100 bp.
Genome_build: hg19
Supplementary_files_format_and_content: BED files containing genomic intervals of significant peaks

source_name: H1 human embryonic stem cells

growth_protocol: H1 hESCs were plated on Matrigel (BD Biosciences)-coated plates, and maintained in mTeSR (StemCell). Before purification, cells were trypsinized to single cells and TRA-1-60 expressing cells were isolated by using MACS cell separation columns (Miltenyi Biotec). Isolated cells were tested by flow cytometry, and samples with >99% purity were used. IMR90 human primary lung embryo fibroblasts (ATCC) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) plus 10% FBS (Hyclone), 100 U/ml penicillin (Gibco), and 100 µg/ml streptomycin (Gibco) at 37°C in 5% CO2. Growing cells with 50~70% confluence were used for further assay.

extract_protocol:
Standard chromatin immunoprecipiation protocol
~20 ng of ChIP and Input double strand DNA were end-repaired, added ‘A’ base to the 3-prime end, and ligated to adaptors by using Illumina ChIP-seq DNA Sample Prep. Kit Box 1. DNA fragments with 150 – 300 bp were selected and purified by agarose gel extraction, and amplified by PCR using Phusion polymerase (Illumina ChIP-seq DNA Sample Prep. Kit Box 1) according to manufacturer’ instrctions. Amplified DNA were purified by gel extraction and quantified by Qubit dsDNA BR assay (Invitrogen). DNA sequencing was performed by Illumina GAIIx sequencer with read length of 75 base pairs as per manufacturer’s protocol. Raw reads data were generated by the software SCS2.6. Further data analysis is available via online supporting information.

tag: passages

tag: antibody manufacturer

value: Abcam

tag: antibody catalog #


title: mof_1

source_name: MOF ChIP-Seq

value: polyclonal rabbit MOF SA 4897, crude serum


title: IMR90_input DNA

description: Chromatin IP input DNA

source_name: IMR90 human lung fibroblasts


title: IMR90_H1.5_ChIPseq


title: msl3_1

source_name: MSL3 ChIP-Seq

value: polyclonal rabbit MSL3, crude serum


title: H2AZ_HO_5

tag: genotype/variation

value: h2a.z mutant

tag: tissue


title: H2AZ_HO_6

source_name: H2AZ_HO rosettes 6 weeks

value: rosettes

value: 6 weeks


title: H2AZ_WT_5

value: h2a.z-related wild type (F2 sibling)

value: seedlings

value: 2 weeks


title: msl1_1

source_name: MSL1 ChIP-Seq

value: polyclonal rabbit MSL1, crude serum


title: msl2_2

description: service: Deep Sequencing Facility, D-BSSE, Basel, Switzerland

source_name: MSL2 ChIP-Seq

value: polyclonal rabbit MSL2, crude serum


title: input_3

description: service: Fasteris, Geneva, Switzerland

source_name: Input

value: none (input)


title: input_4

value: Covaris S220


title: OGT ChIP-seq results

city: Ann arbor

first: qiang

last: chen

state: Michigan

address: 1150 W. medical school road

institute: umich

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2. Parameter settings were listed as follows: -v, 3 (reported alignments with at most 3 mismatches), -5, 3 and -3, 3 (trim3 bases from 5’ and 3’ end to remove low-quality bases).
Peak detection was performed using MACS software from Galaxy browser (www.galaxy.psu.edu).
Genome_build: mm9
Supplementary_files_format_and_content: bed generated by MACS

source_name: Mouse ES cell

growth_protocol: Mouse ES cells were maintained on gelatin-coated dishes in Glasgow Minimum Essential medium (GMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovine serum, 55 mM b-mercaptoethanol (GIBCO), 2mM L-glutamine, 0.1mM MEM non-essential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of ESGRO (Chemicon) under feeder-free conditions

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
DNA fragments isolated from ChIP were repaired to blunt ends by T4 DNA polymerase and phosphorylated with T4 polynucleotide kinase using the END-IT kit (Epicentre). A single “A” base was added to 3’ end with Klenow. Double-stranded adaptors (75 bp with a “T” overhang) were ligated to the fragments with DNA ligase. Ligation products between 200 and 600 bp were gel purified to remove unligated adaptors and subjected to 20 PCR cycles. Completed libraries were quantified with PicoGreen.

value: mouse ES cells

tag: strain

value: OGT antibody

tag: chip antibody manufacturer

value: Novus

tag: chip antibody catalog #


title: H2B S112 GlcNAc ChIP-seq results

value: H2B S112 GlcNAc antibody

value: Ryoji Fujiki (Nature 480:557-560)


title: TET2 ChIP-seq results

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2. Parameter settings were listed as follows: -v, 3 (reported alignments with at most 3 mismatches), -5, 3 and -3, 3 (trim3 bases from 5’ and 3’ end to remove low-quality bases).
Peak detection was performed using MACS software from Galaxy browser (www.galaxy.psu.edu).
Genome_build: mm9
Supplementary_files_format_and_content: bed file

value: in-house made mouse TET2 antibody


title: 75% Human / 25% Mouse Replicate 1A

source_name: human breast & mouse normal lung tissue

tag: cell line

value: NOD scid gamma

tag: human portion (%)


title: LFB_HOXA1KD_hiseq_repC

city: Cambridge

first: Cole

last: Trapnell

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
All reads aligned with TopHat version 1.4.0 using the following options:  "-a 5" against hg19 and annotated UCSC coding transcripts.
Aligments were processed with Cuffdiff version 2.0.0 using default options.
Genome_build: hg19
Supplementary_files_format_and_content: Cuffdiff expression tracking

extract_protocol:
Total RNA from human cell lines or human fat was extracted with Trizol (Invitrogen) and purified via the RNeasy mini kit (Qiagen) according to the manufacturers’ instructions. RNA quality was assessed using an Aglient Bioanalyzer.  RNA-Seq libraries were prepared with the TruSeq mRNA-Seq kit (v1) according to manufacturer's instructions.  Sequenced insert length for all libraries was approximately 180bp with a standard deviation of 50bp.
TruSeq RNA-Seq kit v1

value: lung fibroblasts

tag: transfection

value: HOXA1 knockdown


title: polS5p

description: service: Fasteris, Geneva, Switzerland

source_name: RNA Pol II S5p ChIP-Seq

value: monoclonal rat Pol S5p 3E8

value: Bioruptor


title: 100% Mouse Replicate 3

source_name: mouse normal lung tissue

tag: mouse portion (%)


title: LFB_HOXA1KD_miseq_repC


title: H2AZ_WT_2

source_name: H2AZ_WT rosettes 6 weeks

value: h2a.z-related wild type (F2 sibling)

value: rosettes

tag: age

value: 6 weeks


title: mle_2

tag: cell type

tag: ip antibody

value: monoclonal rat 6E11


title: LFB_HOXA1KD_hiseq_repA


title: LFB_HOXA1KD_miseq_repA


title: LFB_HOXA1KD_miseq_repB


title: mof_2

value: polyclonal rabbit MOF SA 4897, crude serum

tag: shearing technologie

tag: chromatin size (bp)


title: LFB_scramble_hiseq_repC

value: Scramble siRNA


title: LFB_scramble_hiseq_repB


title: 100% Mouse Replicate 1


title: LFB_scramble_miseq_repB


title: LFB_scramble_miseq_repC


title: msl3_2

value: polyclonal rabbit MSL3, crude serum

value: Covaris S220


title: LFB_scramble_hiseq_repA


title: LFB_scramble_miseq_repA


title: msl1_2

value: polyclonal rabbit MSL1, crude serum


title: msl2_3

value: polyclonal rabbit MSL2, crude serum


title: HPRT knockdown SNM (10 day)

status: Public on Dec 10 2012

city: La Jolla

first: Tae Hyuk

address: 9500 Gilman Drive # 0634

department: Pediatrics

institute: University of California, San Diego

data_processing:
Basecalls performed using CASAVA version 1.8.2.
RNA-Seq reads were aligned to the mm9 mouse genome using ELAND alignment algorithm.
Aligned data were imported to Avadis NGS 1.3.1 (Strand Scientific Intelligence), and the reads were filtered by Illumina tile plot filter.
The normalization algorithm was DESeq, and the differential gene expression (≥1.5 or ≥ 2.0 fold) during the neuronal differentiation of HPRT knockdown and control SNMs was selected.
The biological significance of the altered gene expressions were interpreted by GO and signaling pathway analyses using Avadis NGS and Panther Classification System.
Genome_build: mm9

source_name: D3 embryonic stem cell

growth_protocol: The D3 embryonic stem cells were maintained on primary mouse embryo fibroblast feeder cells in ES medium consisting of DMEM/F12 medium, 20% (v/v) KOSR, 1 mM of L-glutamine, 4ng/ml of bFGF, 1,000 U/ml of LIF, 1% (v/v) NEAA, 50 U/ml of penicillin, 50 ug/ml of streptomycin and 0.1 mM of 2-mercaptoethanol. All cell cultrue and neuronal differentiations were carried out in established cell culture conditions (5% CO2, 37 °C). Dopaminergic neuronal differentiation of SNMs derived from D3 embryonic stem cells was carried out according to the protocol published Cho et al. (Nature Protocols 2008, 3, 1888 - 1894.

extract_protocol:
Total RNAs from HPRT knockdown and control cells were purified by Rneasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer's instruction. The  total RNA of each SNM sample was obtained from the independently replicated cultures.
Library preparation was performed with TruSeq RNA Sample Preparation Kit v2 of Illumina, and the prepared libraries were validated and quantified with Agilent bionalyzer.

treatment_protocol: HPRT knockdown cells were infected by retrovirus with shRNA against HPRT and control cells were infected by retrovirus with shRNA against luciferase.

value: spherical neural mass derived form D3 embryonic stem cells

tag: development

value: neuronal differentiation

tag: treatment

tag: differentiation day


title: HPRT knockdown SNM (14 day)

value: infected by retrovirus with shRNA against HPRT


title: HPRT knockdown SNM (12 day)


title: 293T40Tet3

city: Shanghai

first: Feizhen

last: Wu

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

institute: Fudan Univ, Shanghai, China

data_processing:
Basecalls were performed using CASAVA version 1.6.
ChIP-Seq reads were aligned to the hg19 genome assembly using Bowtie (v0.12.7).
Bias sequences generated by PCR were filtered.
Each read was extended from the start position to 300bp of downstream.
Genome_build: hg19
Supplementary_files_format_and_content: .bed files.

source_name: Human embryonic kidney cells, pull-down of GST-tagged TET3 CXXC domain protein

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

extract_protocol:
Cells were harvested and the genomic DNA was purified using the DNeasy Blood and Tissue Kit (Qiagen).
DNA was end repaired using the End-It DNA End-repair kit (Epicentre), and purified with the QiaQuick PCR purification kit. DNA was treated with Klenow exo- (NEB) in NEB buffer 2 with 1mM ATP. After incubating at 37 degree for 50min, the "A" base added DNA was purified with the QiaQuick PCR purification kit. Illumina adapters were ligated using quick T4 DNA ligase. The final DNA was purified with the QiaQuick PCR purification kit and amplified using Illumina sequencing primers for 16-18 cycles.

value: embryonic kidney cells

tag: pull-down

value: GST-tagged TET3 CXXC domain protein


title: LFB_HOXA1KD_hiseq_repB

tag: tissue

value: lung fibroblasts

value: HOXA1 knockdown


title: HPRT knockdown SNM (6 day)

tag: strain


title: HPRT knockdown SNM (4 day)


title: HPRT knockdown SNM (8 day)


title: HPRT knockdown SNM (2 day)


title: HPRT knockdown SNM (1 day)


title: HPRT knockdown SNM (0 day)


title: Control SNM (14 day)

value: infected by retrovirus with shRNA against luciferase


title: Control SNM (12 day)


title: Control SNM (10 day)


title: Control SNM (8 day)


title: Control SNM (6 day)


title: Control SNM (3 day)


title: Control SNM (2 day)


title: Control SNM (0 day)


title: Control SNM (1 day)


title: Small RNA from fly ovary of w1118: loqsf00791/CyO

status: Public on Dec 07 2012

city: Worcester

first: Ryuya

last: Fukunaga

state: Ma

address: 364 Plantation st.

department: BMP

institute: Umass Medical School

description:
OVloqsHypCyOUn
Small RNA

data_processing:
The Illumina fastq files generated from the sequencing machine were processed by the following steps:
(1) (Required for libraries with barcodes) Using an in-house C++ script, fastq files were split into 3 or 4 fastq files based on the first 4 nucleotides of each sequence. Sequences whose first 4 nucleotides did not match any barcodes were discarded.
(2) Inserts from each fastq file were retrieved by identifying the first appearance of the first six nucleotides of the 3' adaptor in each sequence. Sequences with 'N' were discarded. Quality strings were ignored.
(3) Same insert sequences were pooled together, and their total number of being sequenced are indicated in the second column of the processed file.
Genome_build: dm3
Supplementary_files_format_and_content: Sequences + number of reads. Barcode and adapter sequences are removed, and the same reads are pooled together.

source_name: fly ovary, w1118: loqsf00791/CyO

extract_protocol: Total RNA was isolated from 0-10 day female fly heads or 3-5 day ovaries using mirVana (Ambion, Austin, TX, USA). For MEFs, total RNA was isolated using Trizol (Ambion, Austin, TX, USA). The RNA was quantified by absorbance at 260 nm. 18-30 nt RNAs was selected from 100 micrograms total RNA by running a 15% denaturing urea-polyacrylamide gel (National Diagnostics, Atlanta, GA, USA). For fly samples, 2S rRNA was depleted by hybridization using a complementary, immobilized DNA oligonucleotide (5'-biotin-TCA ATG TCG ATA CAA CCC TCA ACC ATA TGT AGT CCA AGC A-3'). Briefly, for each library, 400 µl MyOne Streptavidin C1 Dynabeads (Invitrogen) were washed twice in 0.5× SSC (1× SSC: 150 mM sodium chloride, 15 mM sodium citrate, pH 7.0) at 4°C, then re-suspended in 400 µl 0.5× SSC. The beads were then loaded with 200 pmole DNA oligonucleotide at 4°C for 30 min, washed once in 0.5× SSC, re-suspended in 1 ml 0.5× SSC, and then warmed to 65°C for 5 min. Size-selected RNA (50 µg) was incubated at 80°C for 5 min, and then added to the pre-warmed beads and incubated at 50°C for 1 h. The beads were then removed by magnetic capture and the supernatant mixed with 3 volumes of ethanol, 0.3 M (f.c.) sodium acetate, pH 5.2, and 1 µl (20 µg/µl) glycogen (Roche, Indianapolis, IN, USA). 100 pmole of 3' pre-adenylated adapter (5'-rAppTCG TAT GCC GTC TTC TGC TTG T/ddC/-3') was ligated to small RNAs using Rnl2_1-249 (New England Biolabs) at 4 °C for overnight in 20 microliters in 50 mM Tris-HCl, pH 7.5, 10 mM MgCl2, 10 mM DTT, 60 mg/ml BSA, and 10% (v/v) DMSO. 3' ligated product was purified from a 15% denaturing urea-polyacrylamide gel (National Diagnostics), and then ligated to 100 pmole of 5' RNA adapter (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3' for non-barcoded library and 5'-GUU CAG AGU UCU ACA GUC CGA CGA UCNNNN-3' for barcoded library, NNNN=CGTC, TAGC, ATCC, or GCAC) using T4 RNA ligase (Ambion, Austin, TX, USA) at 4 °C for overnight in 20 microliters in 50 mM Tris-HCl, pH 7.8, 10 mM MgCl2, 10 mM DTT, 1 mM ATP, and 10% DMSO. The ligated product was purified from a 10% denaturing urea-polyacrylamide gel (National Diagnostics). Half the ligated product was used to synthesize cDNA using Superscript III (Invitrogen) and the reverse transcription primer (5'-CAA GCA GAA GAC GGC ATA CGA-3'), and half was used as a minus RT control. The small RNA library was amplified using forward (5'-AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GA-3') and reverse (5'-CAA GCA GAA GAC GGC ATA CGA-3') primers, and then purified from a NuSieve GTG agarose gel (Lonza, Basel, Switzerland). Purified libraries were sequenced using an Illumina Genome Analyzer II (Illumina, San Diego, CA, USA).

tag: genotype/variation

tag: gender

value: female

value: ovary


title: Small RNA from fly ovary of w1118: loqsKO/CyO

description:
OVloqsKOCyOUn
Small RNA

source_name: fly ovary, w1118: loqsKO/CyO


title: Small RNA from fly ovary of w1118: loqsKO; loqs-PA, loqs-PB, loqs-PD/TM3

description:
OVloqsKOPABDUn
Small RNA

source_name: fly ovary, w1118: loqsKO; loqs-PA, loqs-PB, loqs-PD/TM3

value: w1118:loqsKO; loqs-PA, loqs-PB, loqs-PD/TM3


title: H1_input DNA

city: Los Angeles

description: Chromatin IP input DNA

source_name: H1 human embryonic stem cells

tag: cell line

tag: passages

tag: antibody


title: Small RNA from fly ovary of w1118: loqsf00791

description:
OVloqsHypUn
Small RNA

source_name: fly ovary, w1118: loqsf00791


title: Small RNA from fly ovary of w1118: loqsKO; loqs-PB, loqs-PD/TM3

description:
OVloqsKOPBDUn
Small RNA

source_name: fly ovary, w1118: loqsKO; loqs-PB, loqs-PD/TM3

value: w1118:loqsKO; loqs-PB, loqs-PD/TM3


title: Small RNA from female fly head of wIR: loqsf00791/CyO

description:
wIRloqsHypCyOUn
Small RNA

source_name: female fly head, wIR: loqsf00791/CyO

value: head


title: Small RNA from female fly head of wIR: loqsf00791

description:
wIRloqsHypUn
Small RNA

source_name: female fly head, wIR: loqsf00791


title: Small RNA from fly ovary of w1118: loqsKO; loqs-PA/TM3

description:
OVloqsKOPAUn
Small RNA

source_name: fly ovary, w1118: loqsKO; loqs-PA/TM3

value: w1118:loqsKO; loqs-PA/TM3


title: Small RNA from fly ovary of w1118: loqsKO; loqs-PB/TM3

description:
OVloqsKOPBUn
Small RNA

source_name: fly ovary, w1118: loqsKO; loqs-PB/TM3

value: w1118:loqsKO; loqs-PB/TM3


title: Small RNA from fly ovary of w1118

description:
OVw1118Un
Small RNA

source_name: fly ovary, w1118


title: HPRT knockdown SNM (3 day)


title: Small RNA from fly ovary of w1118: loqsKO; loqs-PA, loqs-PB/TM3

description:
OVloqsKOPABUn
Small RNA

source_name: fly ovary, w1118: loqsKO; loqs-PA, loqs-PB/TM3

value: w1118:loqsKO; loqs-PA, loqs-PB/TM3


title: Small RNA from fly ovary of w1118: loqsKO; loqs-PA, loqs-PD/TM3

description:
OVloqsKOPADUn
Small RNA

source_name: fly ovary, w1118: loqsKO; loqs-PA, loqs-PD/TM3

value: w1118:loqsKO; loqs-PA, loqs-PD/TM3


title: Small RNA from female fly head of wIR: loqsKO/CyO

description:
wIRloqsKOCyOUn
Small RNA

source_name: female fly head, wIR: loqsKO/CyO


title: Small RNA from female fly head of wIR: loqsKO; loqs-PA, loqs-PB, loqs-PD/TM3

description:
wIRloqsKOPABDUn
Small RNA

source_name: female fly head, wIR: loqsKO; loqs-PA, loqs-PB, loqs-PD/TM3

value: wIR:loqsKO; loqs-PA, loqs-PB, loqs-PD/TM3


title: Small RNA from female fly head of wIR: loqsKO; loqs-PA, loqs-PD/TM3

description:
wIRloqsKOPADUn
Small RNA

source_name: female fly head, wIR: loqsKO; loqs-PA, loqs-PD/TM3

value: wIR:loqsKO; loqs-PA, loqs-PD/TM3


title: Small RNA from female fly head of wIR: loqsKO; loqs-PA, loqs-PB/TM3

description:
wIRloqsKOPABUn
Small RNA

source_name: female fly head, wIR: loqsKO; loqs-PA, loqs-PB/TM3

value: wIR:loqsKO; loqs-PA, loqs-PB/TM3


title: Small RNA from female fly head of wIR: loqsKO; loqs-PB/TM3

description:
wIRloqsKOPBUn
Small RNA

source_name: female fly head, wIR: loqsKO; loqs-PB/TM3

value: wIR:loqsKO; loqs-PB/TM3


title: Small RNA from female fly head of wIR

description:
wIR++Un
Small RNA

source_name: female fly head, wIR

value: wIR


title: Small RNA from TRBP-/- mouse tail fibroblast

description:
MTFTRBP-Un
Small RNA

data_processing:
The Illumina fastq files generated from the sequencing machine were processed by the following steps:
(1) (Required for libraries with barcodes) Using an in-house C++ script, fastq files were split into 3 or 4 fastq files based on the first 4 nucleotides of each sequence. Sequences whose first 4 nucleotides did not match any barcodes were discarded.
(2) Inserts from each fastq file were retrieved by identifying the first appearance of the first six nucleotides of the 3' adaptor in each sequence. Sequences with 'N' were discarded. Quality strings were ignored.
(3) Same insert sequences were pooled together, and their total number of being sequenced are indicated in the second column of the processed file.
Genome_build: mm9
Supplementary_files_format_and_content: Sequences + number of reads. Barcode and adapter sequences are removed, and the same reads are pooled together.

source_name: mouse tail fibroblast, TRBP-/-

extract_protocol: Total RNA was isolated from 0-10 day female fly heads or 3-5 day ovaries using mirVana (Ambion, Austin, TX, USA). For mouse cells, total RNA was isolated using Trizol (Ambion, Austin, TX, USA). The RNA was quantified by absorbance at 260 nm. 18-30 nt RNAs was selected from 100 micrograms total RNA by running a 15% denaturing urea-polyacrylamide gel (National Diagnostics, Atlanta, GA, USA). For fly samples, 2S rRNA was depleted by hybridization using a complementary, immobilized DNA oligonucleotide (5'-biotin-TCA ATG TCG ATA CAA CCC TCA ACC ATA TGT AGT CCA AGC A-3'). Briefly, for each library, 400 µl MyOne Streptavidin C1 Dynabeads (Invitrogen) were washed twice in 0.5× SSC (1× SSC: 150 mM sodium chloride, 15 mM sodium citrate, pH 7.0) at 4°C, then re-suspended in 400 µl 0.5× SSC. The beads were then loaded with 200 pmole DNA oligonucleotide at 4°C for 30 min, washed once in 0.5× SSC, re-suspended in 1 ml 0.5× SSC, and then warmed to 65°C for 5 min. Size-selected RNA (50 µg) was incubated at 80°C for 5 min, and then added to the pre-warmed beads and incubated at 50°C for 1 h. The beads were then removed by magnetic capture and the supernatant mixed with 3 volumes of ethanol, 0.3 M (f.c.) sodium acetate, pH 5.2, and 1 µl (20 µg/µl) glycogen (Roche, Indianapolis, IN, USA). 100 pmole of 3' pre-adenylated adapter (5'-rAppTCG TAT GCC GTC TTC TGC TTG T/ddC/-3') was ligated to small RNAs using Rnl2_1-249 (New England Biolabs) at 4 °C for overnight in 20 microliters in 50 mM Tris-HCl, pH 7.5, 10 mM MgCl2, 10 mM DTT, 60 mg/ml BSA, and 10% (v/v) DMSO. 3' ligated product was purified from a 15% denaturing urea-polyacrylamide gel (National Diagnostics), and then ligated to 100 pmole of 5' RNA adapter (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3' for non-barcoded library and 5'-GUU CAG AGU UCU ACA GUC CGA CGA UCNNNN-3' for barcoded library, NNNN=CGTC, TAGC, ATCC, or GCAC) using T4 RNA ligase (Ambion, Austin, TX, USA) at 4 °C for overnight in 20 microliters in 50 mM Tris-HCl, pH 7.8, 10 mM MgCl2, 10 mM DTT, 1 mM ATP, and 10% DMSO. The ligated product was purified from a 10% denaturing urea-polyacrylamide gel (National Diagnostics). Half the ligated product was used to synthesize cDNA using Superscript III (Invitrogen) and the reverse transcription primer (5'-CAA GCA GAA GAC GGC ATA CGA-3'), and half was used as a minus RT control. The small RNA library was amplified using forward (5'-AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GA-3') and reverse (5'-CAA GCA GAA GAC GGC ATA CGA-3') primers, and then purified from a NuSieve GTG agarose gel (Lonza, Basel, Switzerland). Purified libraries were sequenced using an Illumina Genome Analyzer II (Illumina, San Diego, CA, USA).

value: TRBP-/-

value: mouse tail fibroblasts


title: Small RNA from PACT-/- mouse embryonic fibroblast

description:
MEFPACT-Un
Small RNA

source_name: mouse embryonic fibroblast, PACT-/-

value: PACT-/-

value: mouse embryonic fibroblasts (MEFs)


title: H3K4me2_PN1_ChIPSeq

description: Histone modification H3K4me2 at developmental stage PN1

source_name: retina

value: Pde6b (rd1/rd1) mutant mice

tag: chip antibody

value: H3K4me2 (07-449, Upstate, Charlottesville, VA, lot 26335, cat#07-030)

tag: developmental stage

value: retina


title: Small RNA from wild-type mouse embryonic fibroblast

description:
MEFPACT+Un
Small RNA

source_name: mouse embryonic fibroblast, wild-type

value: wild-type


title: CMLPh-008T

city: Monza

first: Roberta

last: Spinelli

state: MB

address: Via Cadore 48

department: Department of Health Science

country: Italy

institute: University of Milano Bicocca

data_processing:
Image processing and basecall were performed using the Illumina Real Time Analysis Software RTA v1.9.35. Qseq files were deindexed and converted in the Sanger-FastQ file format using in-house scripts.
FastQ sequences were aligned to the human genome database (NCBI36/hg18) by using TopHat 1 vs 1.2.0 using default parameters and the gene and splice junctions models supplied by the Human Ensembl GTF annotation file vs54 (Homo_Sapiens.NCBI36.54.GTF) downloaded from the Ensembl FTP server (ftp://ftp.ensembl.org/pub/release-54/gtf/homo_sapiens/).
The quantitative gene expression profile was estimated by SAMMate vs.2.6.1 by using the Human Ensembl GTF annotation file vs54 and the default parameters
To focus on the gene expression profile of known coding transcripts, a dataset of 20,907 protein-coding Ensembl Genes was selected from the whole transcriptome matrix of FPKM expression values for 36,655 unique Ensembl Gene obtained by SAMMate
A splice junction map for SETBP1-mutated and non-mutated cases was inferred by TopHat
Genome_build: Human genome database (NCBI36/hg18)
Supplementary_files_format_and_content: Tab-delimited text files include the chromosome, the Gene Name, the Ensembl Gene ID, Biotype, sum exon length of the gene, the gene reads counts and the normalized FPKM measurements of each protein_coding biotype for each sample generated by SAMMate using the Human GTF annotation file (vs54) and default parameters

source_name: Atypical Chronic Myeloid Leukemia cells

extract_protocol:
Total RNA was extracted with TRIzol® (Invitrogen, Life technology, Grand Island, NY, USA) using the standard protocol.
2ug total RNA was processed according to Illumina TruSeqTM RNA Sample Preparation Kit (FC-122-1001) protocol modified for the time of fragmentation: mRNA was shared for 1 minute at 94°C and, after the ligation of the adapters, fragments of 400-500bp were selected on 2% agarose gel

treatment_protocol: Leukemic cells were obtained by separation on a Ficoll-Paque Plus gradient (GE Healthcare, UK). The phenotype was evaluated by FACS analysis and myeloid cells (CD33, CD13, CD117) were >80% of total cells.

tag: genotype

value: wild type


title: CMLPh-009T

value: SETBP1 S869G -/+


title: CMLPh-0012T

value: SETBP1 I871T -/+


title: CMLPh-0013T

value: SETBP1 D868N -/+


title: CMLPh-0010T


title: CMLPh-0011T

value: SETBP1 E858K -/+


title: CMLPh-007T


title: CMLPh-006T


title: Control SNM (4 day)

source_name: D3 embryonic stem cell

tag: cell type

value: spherical neural mass derived form D3 embryonic stem cells

value: neuronal differentiation

value: infected by retrovirus with shRNA against luciferase


title: CMLPh-001T

description: GA pipeline version 1.5


title: CMLPh-005T

value: SETBP1 G870S -/+


title: CMLPh-002T

description: GA pipeline version 1.5


title: 18.5 Ctrl6Epi

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Reads were mapped to mm9 using TopHat 1.3.2/bowtie 0.12.7.0 with default settings
FPKM values and fold changes were calculated using cufflinks/cuffdiff 1.3.0
Genome_build: mm9
Supplementary_files_format_and_content: Series supplementary files include FPKM values and fold changes for 3 comparisons

source_name: E18.5 epidermis

extract_protocol: Skin was removed and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

value: Epidermis

tag: age

value: embryonic day 18.5


title: 18.5 EncKO9Epi


title: 18.5 Ctrl1Der

source_name: E18.5 dermis

value: Dermis


title: 16.5 CypKO2

source_name: E16.5 skin

value: skin

value: embryonic day 16.5


title: CMLPh-004T


title: 18.5 EncKO7Der


title: 16.5 CypKO1


title: 16.5 WT2


title: K80.8-WT

city: Leuven

first: Bram

last: Van de Sande

address: Herestraat 49

department: Center for Human Genetics

country: Belgium

institute: KU Leuven

data_processing:
alignment: Sequence reads were mapped to the mus musculus reference genome (mm9) via TopHat v1.2.0. Only uniquely mapping reads were taken into account.
counts: HTSeq v0.5.3p3 was used to count the number of genes for annotated genes. HTSeq was used in the “union” mode, with gene annotations from Ensembl release 62, grouping exons together based on gene_name (i.e., MGI symbols for protein-coding genes).
differential expression: normalization of gene expression levels and differential gene expression between WT and KO was calculated with DESeq v1.2.2.
Genome Build:
K80.8-WT-CTTGTA.counts.txt: mm9

source_name: Nkx2-1-iCre targeted eGFP+ cells

extract_protocol: Trizol followed by RNeasy micro. RNA seq library is prepared for analysis according to the Illumina TruSeq protocol (www.illumina.com). Briefly, 100 ng of Total RNA is purified using poly-T oligo-attached magnetic beads to end up with poly-A containing mRNA. The Poly-A tailed mRNA is fragmented and cDNA is synthesized using SuperScript II. cDNA fragments is end repaired, purified with AMPure XP beads, A-tailed using Klenow exo-enzyme in the presence of dATP. Illumina provided paired end adapters with index are ligated to the A-tailed cDNA fragments and purified using AMPure XP beads. The resulting adapter-modified cDNA fragments are enriched by PCR using Phusion polymerase as follow: 30 s at 98°C, 15 cycles of (10 s at 98°C, 30 s at 60°C, 30 s at 72°C), 5 min at 72°C. PCR products are purified using AMPure XP beads and eluted in 30 µl of resuspension buffer. One microliter is loaded on an Agilent Technologies 2100 Bioanalyzer using a DNA 1000 assay to determine the library concentration and to check for quality. Cluster generation was performed according to the Illumina TruSeq SR Cluster kit v2 (cBot) Reagents Preparation Guide (www.illumina.com). Briefly, 6 RNA-seq libraries were pooled together to get a stock of 10 nM. One microliter of the 10 nM stock was denaturated with NaOH, diluted to 6.5 pM and hybridized onto the flowcell. The hybridized products are sequentially amplified, linearized and end-blocked according to the Illumina Single Read Multiplex Sequencing user guide. After hybridization of the sequencing primer, sequencing-by-synthesis was performed using the HiSeq 2000 with a 36-cycle protocol. The sequenced fragments were denaturated with NaOH using the HiSeq 2000 and the index-primer was hybridized onto the fragments. The index was sequenced with a 7-cycle protocol.

treatment_protocol: FACsorting

value: Swiss

value: WT

value: telencephalon

tag: method

value: FACsorted cells