title: Rpb3 ChIP-seq from DmGtsf1-KD (reps 1 and 2)

status: Public on Sep 06 2013

city: Vienna

first: Grzegorz

last: Sienski

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

description:
ChIPseq_Rpb3r1_siDmGtsf1
ChIPseq_Rpb3r2_siDmGtsf1

data_processing:
small RNA-seq libraries
basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0)
fastq files were adapter 'AGATCGGAAGAGCACACGTCT' clipped using cutadapt, version 1.0, default settings
after adapter removal, the first and last 4 bases were trimmed (both linkers contain 4 random nucleotides at their respective termini) from sequence as well using HomerTools, version 3.9
reads were mapped with bowtie v0.12.7 to D. mel. genome (dm3) and BigWig files were created with Samtools v 0.1.16 and BedTools v2.16.1
Genome_build: Release 5
Supplementary_files_format_and_content: [small RNA-seq] file contains collapsed, dm3 genome-aligned reads
RNA-seq
basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0)
fastq files containing 2nd mate were reverse complemented and used together with fastq files containing 1st mate as single-end library; N-containing reads were discarded
reads were trimmed to high-quality bases 6-56 using HomerTools, version 3.9 and mapped to genome and transcriptome using in-house developed pipeline
Genome_build: Release 5
Supplementary_files_format_and_content: [RNA-seq] file contains strand-specific density coverage of uniquely mapped reads to dm3
ChIP-seq
basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0)
reads were trimmed to bases 2-50 using HomerTools, version 3.9;  N-containing reads were discarded; smaller than 50nt-long reads were discarded
reads were mapped with bowtie v0.12.7 to D. mel. genome (dm3) and BigWig files were created with Samtools v 0.1.16 and BedTools v2.16.1
Genome_build: Release 5
Supplementary_files_format_and_content: [ChIP-seq] file contains density coverage of uniquely mapped reads to dm3

source_name: Ovarian Somatic Cells (OSC), ChIPseq_Rpb3r_siDmGtsf1

growth_protocol: flies were grown at 25 degrees; OSC were grown at 27 degrees on M3 medium

extract_protocol:
RNA-seq as in Zhong et al. 2011
ChIP-seq as described in Lee et al. 2006
small-RNAs were cloned as described in Brennecke et al. 2007

treatment_protocol: OSC were transfected twice with siRNAs and analyzed after 4 days

value: Ovarian Somatic Cells (OSC)

value: RNAi DmGtsf1

value: 96h after transfection

tag: molecule subtype

value: Rpb3-bound DNA

tag: chip-seq antibody

value: anti-Rpb3 (gift of Karen Adelman, Adelman et al. Mol Cell 2005)


title: DNA input from DmGtsf1-KD (reps 1 and 2)

type: SRA

description:
ChIPseq_inputr1_siDmGtsf1
ChIPseq_inputr2_siDmGtsf1

library_source: genomic

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Ovarian Somatic Cells (OSC), ChIPseq_inputr_siDmGtsf1

tag: cell type

tag: genotype/variation

tag: Stage

value: total DNA


title: asi1-1_mRNA-Seq

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

country: USA

institute: Purdue University

library_source: transcriptomic

data_processing:
Basecalling, trimming for low quality reads and adaptor sequence were done by BGI (Shenzhen, China)
For mRNA-Seq: Clean reads were mapped to TAIR10 by TopHat2 with preset option --b2-very-sensitive.
For MethylC-Seq: Clean reads were mapped to TAIR10 using BRAT-BW with parameters -m 2 -i 0 -a 1000
Copy-duplicates were remove using remove-dupl command of BRAT-BW
acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
Genome_build: TAIR10
Supplementary_files_format_and_content: The bedGraph files were generated using genomeCoverageBed from bedtools with parameter  -bga -split -trackline -trackopts name="\"TopHat2 - read coverage\"".
Supplementary_files_format_and_content: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (converted_C / ( converted_C+ unconverted_C ) ).

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Seedlings

extract_protocol: Total RNAs of were isolated from 14-d-old seedlings by Trizol reagent (Invitrogen), and were treated with DNase I (Ambion) to remove DNA. mRNAs were enriched with Oligo (dT)-conjugated magnetic beads and were then sent to BGI (Shenzhen, China) for library preparation and Illumina sequencing.

tag: ecotype

tag: genotype

value: asi1-1 mutant


title: ribosomal RNA-depleted total RNA from siGFP

source_name: Ovarian Somatic Cells (OSC), RNAseq_siGFP

value: RNAi GFP

value: 48h after transfection

value: total RNA


title: small RNAs (18-29nt) from CG3893[GS12962] homozygous

source_name: fly ovaries, smallRNAs_DmGtsf1_hom

value: Ovaries

value: CG3893[GS12962] homozygous

value: from 5-6 days old flies

value: small RNA


title: LUCZKO_rep3

status: Public on Sep 07 2013

city: Cincinnati

first: nupur

last: dasgupta

state: OH

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hopital Medical Center

description:
imig treated Lung of 9V/null mice
run0109_lane1_index4=T479_T501_528LU~mouse_align

data_processing:
mRNA-Seq reads were aligned to the mm9 version of the mouse genome reference using the TopHat/Cufflinks pipeline. First, sequences were aligned to the genome with TopHat , which efficiently aligned reads spanning known or novel splice junctions. Each sample was then independently processed with Cufflinks  in order to generate an initial transcriptome.   Finally, the Cuffmerge tool was used to merge the known and any novel isoforms into a single BAM file, and simultaneously extended partial transcripts.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
DESeq and Mixed Model Anova were used to  evaluate the DEGs from the mRNA-Seq data and microrray data.
For DESeq normalization, the sequencing depth is estimated by the read count of the gene with the median read count ratio across all genes.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include DESeq normalised values for each Sample

organism: Mus musculus

extract_protocol:
9V/null mice were sacrificed one wk after the last injection along with WT mice,  lung, liver and spleen were collected for RNA analysis.
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.

treatment_protocol: 9V/null mice were injected weeklyvia tail vein with 60U/kg/wk of imig or vela for 8 wks. Control 9V/null mice weere injected with same volume of saline.

tag: age

value: 28 wks at the time of RNA isolation

tag: background strain

tag: treatment

value: CZ (imiglucerase)

tag: tissue

value: lung


title: LVGCBKO_rep2

description:
vela treated Liver of 9V/null mice
run0109_lane5_index4=T249_T497_T498LV~mouse_align

value: GCB (velaglucerase)

value: liver


title: ribosomal RNA-depleted total RNA from DmGtsf1-KD

source_name: Ovarian Somatic Cells (OSC), RNAseq_siDmGtsf1

value: Ovarian Somatic Cells (OSC)

value: RNAi DmGtsf1

value: 96h after transfection


title: small RNAs (18-29nt) from CG3893[GS12962] heterozygous

source_name: fly ovaries, smallRNAs_DmGtsf1_het

value: CG3893[GS12962] heterozygous


title: Input DNA

city: Newark

first: Danish

last: Sayed

state: NJ

address: 185 south orange avenue

department: CBMM

institute: Rutgers-NJMS

data_processing:
ChIP-Seq analysis done by Active Motif.
The 36-nt sequence reads ("tags") identified by the sequencing service (using Illumina's genome Analyzer 2) are mapped to the genome using ELAND algorithm. Alignment information for each tag is stored in the output file *_ export.txt. Only tags that map uniquely, have no more than 2 mismatches, and that pass quality control filtering are used in the subsequent analysis.
Since the 5'-ends of the tags represent the end of a ChIP/IP-fragments, the tags are extended in silico (using Active motif software)at their 3' -ends to a length of 110-200 bp, depending on the average fragemtn length in the size selected library. To identify the density of fragemnts (extendend tags) along the genome, the genome is divided into 32 nt bins and the number of fragments in each bin is determined. This information is stored in a BAR (binary Analysis results) file that can be reviewed in a browser such as Affymetrix' Integrated Genome Browser (IGB).
An interval is a discrete genomic region, defined by the chromosome number and a start and end coordinate. Intervals represent the locations of the fragment density peaks. For each BAR file, Intervals are calculated and complied into BED files (Browser Extensible Data). A typical threshold setiing is in the range of 10-20, but may be adjusted depending on the number of tags sequenced or based on information on positive and negative test sites, independent estimates for the false discovery rate (FDR), and/or the intent to generate a stringent or relaxed analysis. The applied threshold can be found in the Assay Results report. For an interval to be called, it must contain 3 consecutive bins with fragment densities greater than the threshold.
To compare peak metrics between two samples, overlapping intervals are grouped into"Active regions', which are defined by the start coordinate of the most upstream interval and the end coordinate of the most downstream interval (=union of overlapping Intervals). In locations where only one sample has an interval, this interval defines the Active Region. Active regions are useful to consider because the location and the lenghts of the intervals are rarely exactly the same when comparing different samples.
Supplementary_files_format_and_content: BAR

source_name: Whole heart

growth_protocol: Hearts from 1-2day old C57Bl/6 mice undergoing physiological postnatal growth were extracted.

extract_protocol: ChIP, Library construction and Illumina sequencing performed by Active Motif

treatment_protocol: C57Bl/6 mice (12wks, ~26gms, male) were subjecetd to transaortic coartation (standard protocol described in detail in related publication Sayed et al, 2013) for 4days before hearts were extracted for analysis.

tag: strain

tag: antibody


title: H3K9ac_ChIP-seq neonate

source_name: whole heart

tag: pathology/age

value: Postnatal heart / 1-2day old pups

value: anti-H3K9ac (active motif 39918)


title: H3K9m3 ChIP-seq from DmGtsf1-KD (reps 1 and 2)

description:
ChIPseq_H3K9m3r1_siDmGtsf1
ChIPseq_H3K9m3r2_siDmGtsf1

source_name: Ovarian Somatic Cells (OSC), ChIPseq_H3K9m3r_siDmGtsf1

value: H3K9m3-bound DNA

value: anti-H3K9me3 (abcam, catalog #ab8898, lot/batch #943260)


title: H3K9ac_ChIP-seq TAC-hypertrophied

value: Hypertrophied heart /12wk old mice subjected to Transaortic coarctation (TAC) for 4days


title: ibm1-4_MethylC-Seq

description: treated with bisulfite

data_processing:
Basecalling, trimming for low quality reads and adaptor sequence were done by BGI (Shenzhen, China)
Clean reads were mapped to TAIR10 using BRAT-BW with parameters -m 2 -i 0 -a 1000
Copy-duplicates were remove using remove-dupl command of BRAT-BW
acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
Genome_build: TAIR10
Supplementary_files_format_and_content: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (unconverted_C / ( converted_C+ unconverted_C ) ).

extract_protocol: Genomic DNA was extracted from 14-d-old seedlings and sent to BGI (Shenzhen, China) for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols

value: ibm1-4 mutant

value: Seedlings


title: polII_ChIP-seq neonate

value: anti-pol II CTD  (abcam ab5095)


title: LVCZKO_rep 3

description:
imig treated Liver of 9V/null mice
run0109_lane5_index1=T253_T502_T529LV~mouse_align

value: 28 wks at the time of RNA isolation


title: asi1-1_MethylC-Seq

description: treated with bisulfite

data_processing:
Basecalling, trimming for low quality reads and adaptor sequence were done by BGI (Shenzhen, China)
For mRNA-Seq: Clean reads were mapped to TAIR10 by TopHat2 with preset option --b2-very-sensitive.
For MethylC-Seq: Clean reads were mapped to TAIR10 using BRAT-BW with parameters -m 2 -i 0 -a 1000
Copy-duplicates were remove using remove-dupl command of BRAT-BW
acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
Genome_build: TAIR10
Supplementary_files_format_and_content: The bedGraph files were generated using genomeCoverageBed from bedtools with parameter  -bga -split -trackline -trackopts name="\"TopHat2 - read coverage\"".
Supplementary_files_format_and_content: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (unconverted_C / ( converted_C+ unconverted_C ) ).

extract_protocol: Genomic DNA was extracted from 14-d-old seedlings and sent to BGI (Shenzhen, China) for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols.

value: asi1-1 mutant


title: WT_mRNA-Seq

value: WT


title: polII_ChIP-seq adult

value: Normal heart / 12wk old mice

value: anti-pol II CTD (abcam ab5095)


title: H3K9ac_ChIP-seq adult


title: pol II_ChIP-seq TAC-hypertrophied


title: glucose

city: Campinas

first: Renato

last: Vicentini

state: SP

address: Cidade Universitaria "Zeferino Vaz"

department: Centro de Biologia Molecular e Engenharia Genetica - CBMEG

country: Brazil

institute: Universidade Estadual de Campinas - UNICAMP

data_processing:
Illumina sRNAs reads were analyzed using CLC Genomics Workbench software (CLC bio) with default parameters.
The reads count value indicate the amount of reads with same sequence.
Genome_build: n/a
Supplementary_files_format_and_content: count

source_name: seedling

growth_protocol: Arabidopsis thaliana Col-0 grown for 5 days in liquid MS/2 adjusted to 0.3% at 22°C, under constant light (20 µmol m-2 s-1) and agitation (70 RPM). The media was then replaced for glucose-free MS/2, and seedlings were further grown for 24h, followed by the treatments.

extract_protocol:
Guanidine-HCl
Preparation and deep-sequencing of small RNA libraries was conducted according to the manufacturer’s instructions by Ambry Genetics (Aliso Viejo, CA) using Illumina’s Genome Analyzer IIx.

treatment_protocol: untreated control, and samples treated for 4 h with 2% glucose or 2% mannitol

value: whole seedling

value: glucose


title: mannitol

value: mannitol


title: untreated control

value: untreated


title: AwNB2

status: Public on Sep 05 2013

city: Lake Alfred

first: Neha

last: Jalan

state: Florida

address: CREC, 700 Experiment station road

department: Deptarment of Microbiology and Cell Science

institute: University of Florida

description: Sample 8

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-complexity or low-quality sequence, then mapped to the XccA and Aw whole genomes using CLC Genomics workbench 5.1
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CLC Genomics workbench 5.1 using the annotations on the genome.
The RPKM values were quantile normalized for the triplicates, transformed and t-test was performed for identifying differential gene expression between the strains in different medium as well as among same strain in different media.
Genome_build: Xanthomonas axonopodis pv. citri str. 306 (AE008923.1, AE008924.1, AE008925.1) and Xanthomonas citri subsp. citri str. Aw12879 (CP003778, CP003779, CP003780)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Xanthomonas citri pv. citri

source_name: Aw 12879_Nutrient Broth

growth_protocol: Both strain A and Aw were inoculated in 50ml media NB and XVM2 at initial O.D. of 0.03. Cultures were grown in 250ml flasks at 28C with shaking at 200rpm. Total RNA was extracted from 10ml of the media at O.D. 0.4 (exponential phase) for both cultures in each medium.

extract_protocol: 1ug of the enriched mRNA was used for construction of Illumina libraries according to manufacturers (Illumina) protocols.

treatment_protocol: mRNA was enriched from total RNA using the MICROBexpress Kit (Pseudomonas module) according to the manufacturers instructions.

tag: medium

value: Nutrient Broth

tag: growth stage

value: OD = 0.4 (exponential phase)

value: enriched mRNA


title: AwXVM1

description: Sample 10


title: AwNB1

description: Sample 7


title: AXVM2

description: Sample 5


title: AXVM1

description: Sample 4


title: ANB3

description: Sample 3

source_name: A (306)_Nutrient Broth


title: IMB-1 ChIP-seq in N2 mixed-stage embryos (KI026)

first: Kohta

last: Ikegami

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description:
seq-SDQ4154_IMB1_EE9_N2_MXEMB
Barcode: na

data_processing:
Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using bowtie, allowing up to two mismatches
ChIP-seq reads were extended to the original DNA fragment size estimated computationally as the distance between positive- and negative-strand reads with the highest cross-correlation.
The number of overlapping reads per base was computed using 'basealigncount' function in Zinba (Rashid et al., Genome Biology 2011)
Processed data files are in wig format representing overlappaing read counts at each base in the genome.
Genome_build: ce6, WS190

organism: Caenorhabditis elegans

source_name: Mixed-stage embryos

growth_protocol: The C. elegans N2 strain animals in the liquid S-medium were fed with bacteria HB101 until becoming gravid adults. Mixed-stage embryos were harvested from the adults by hypochlorite treatment.

extract_protocol:
The C. elegans N2 strain mixed-stage embryos were cross-linked in 2% formaldehyde for 30 min at 25ºC. Chromatin extract was prepared by sonication in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl). Five to ten micrograms of antibodies were immobilized on sepharose beads and incubated with the chromatin extract for >12 hours at 4ºC. After washing the immunoprecipitants followed by RNase treatment and reverse-crosslinking, DNA were extracted and purified.
DNA was blunt-ended and A-overhanged with Exo(-) Klenow fragment in the presence of dATP. DNA fragments were ligated with adaptors. DNA was amplified by PCR with single-end primers. Amplicon was loaded on an agarose gel, and DNA at 200-500 bp was recovered from the gel.

treatment_protocol: For RNAi, the N2 strain worms were first arrested at the L1 larva stage in the liquid S medium for synchronization. Synchronized L1 worms were fed with a bacteria strain HB101, which do not contain induction vectors, at 20ºC for 36 hours (L4 stage) in the liquid S medium. L4 worms were harvested, washed and transferred to a new S medium supplemented with a bacteria strain HT115 expressing interfering double-strand RNA from L4440 vector under IPTG (RNAi bacteria). Worms were grown with the RNAi bacteria at 20ºC until the gravid stage. Embryos were harvested from the gravid adults by hypochlorite treatment and used in experiments. In parallel, worms were fed with HT115 bacteria bearing L4440 vector without target DNA insertion (empty vector RNAi).

value: no treatment

tag: chip antibody

value: SDQ4154_IMB1 [not commercial]


title: AwXVM3

description: Sample 12

tag: molecule subtype


title: ANB2

description: Sample 2


title: AwNB3

description: Sample 9


title: AwXVM2

description: Sample 11


title: AXVM3

description: Sample 6


title: RNA-seq in N2 mixed-stage embryos treated with IMB-1 RNAi (BC185)

description:
seq-RNA_RiIMB1_KI2126_MXEMB
Barcode: na

data_processing:
Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using tophat
Coverage of reads in bedgraph format was obtained using Bedtools
Processed data files are in bedGraph format representing overlappaing read counts in the genome.
Genome_build: ce6, WS190

extract_protocol:
First, total RNA were treated with DNase I, and then ribosomal RNA were depleted from the sample using Invitrogen?s RiboMinus Eukaryote Kit for RNA-seq (cat# A10837-08). rRNA-depleted RNA were recovered by ethanol precipitation. RNA were then fragmented by incubating in buffer containing Zn2+ at 70 oC for 5 min (Ambion, Fragmentation Reagent cat# AM8740), followed by ethanol precipitation. Fragmented RNA were used to synthesize double-strand cDNA using the SuperScript II kit (Invitrogen, cat #18064-014) and DNA polymerase I (Enzymatics P705L). cDNA were recovered from the reaction using Qiagen?s Mini elute columns.
DNA was blunt-ended with End Repair Enzyme mix (Epicentre, Madison) and A-overhanged with Exo(-) Klenow fragment in the presence of dATP. DNA fragments were ligated with adaptors. DNA was amplified by PCR with single-end or pair-end primers. Amplicon was loaded on an agarose gel, and DNA at an indicated size range was recovered from the gel.

value: IMB-1 RNAi

tag: isolation

value: RiboMinus RNA (rRNA-depleted total RNA)


title: RNA-seq in N2 mixed-stage embryos treated with empty vector (BC183)

description:
seq-RNA_RiEV_KI2126_N2_MXEMB
Barcode: na

value: Empty vector RNAi


title: TBP-1 ChIP-seq in N2 mixed-stage embryos (FW002)

description:
seq-SDQ0839_TBP1_EE6_N2_MXEMB
Barcode: na

value: SDQ0839_TBP1 [Novus Biologicals, catalog# 29610002, lot# G3048-022, Animal SDQ0839]


title: RNA-seq in N2 mixed-stage embryos treated with NPP-13 RNAi (BC184)

description:
seq-RNA_RiNPP13_KI2126_N2_MXEMB
Barcode: na

value: NPP-13 RNAi


title: Pol III RPC-1 ChIP-seq in N2 mixed-stage embryos treated with empty vector (BC177)

description:
seq-SDQ4663_RPC1_RiEV_KI1967_N2_MXEMB
Barcode: GTTAATC

value: SDQ4663_RPC1 [Novus Biologicals, catalog# 53330002, lot# G3048-240A02, Animal SDQ4663]


title: TBP-1 ChIP-seq in N2 mixed-stage embryos treated with empty vector (BC257)

description:
seq-SDQ0839_TBP1_RiEV_KI2183_N2_MXEMB
Barcode: CACGTCG


title: Pol III RPC-1 ChIP-seq in N2 mixed-stage embryos treated with empty vector (BC179)

description:
seq-SDQ4663_RPC1_RiEV_KI2009_N2_MXEMB
Barcode: CACGTCG


title: Pol III RPC-1 ChIP-seq in N2 mixed-stage embryos treated with NPP-13 RNAi (BC178)

description:
seq-SDQ4663_RPC1_RiNPP13_KI1967_N2_MXEMB
Barcode: ACAGTTG


title: TBP-1 ChIP-seq in N2 mixed-stage embryos (BC057)

description:
seq-SDQ0839_TBP1_EE13_N2_MXEMB
Barcode: ACAGTTG


title: NPP-3 ChIP-seq in N2 mixed-stage embryos (BC076)

description:
seq-SY1540_NPP3_EE14_N2_MXEMB
Barcode: GTTAATC

value: SY1540_NPP3 [not commercial]


title: NPP-3 ChIP-seq in N2 mixed-stage embryos (BC075)

description:
seq-SY1539_NPP3_EE14_N2_MXEMB
Barcode: GATCTTG

value: SY1539_NPP3 [not commercial]


title: Input-seq in N2 mixed-stage embryos (BC089)

description:
seq-input_EE15_N2_MXEMB
Barcode: CGCCCAC

value: na (input)


title: NPP-13 ChIP-seq in N2 mixed-stage embryos (KI024)

description:
seq-SDQ3897_NPP13_EE9_N2_MXEMB
Barcode: na

value: SDQ3897_NPP13 [Novus Biologicals, catalog# 48580002, lot# G3048-202, Animal SDQ3897]


title: Pol III RPC-1 ChIP-seq in N2 mixed-stage embryos treated with NPP-13 RNAi (BC180)

description:
seq-SDQ4663_RPC1_RiNPP13_KI2009_N2_MXEMB
Barcode: GATCTTG


title: ANB1

description: Sample 1


title: TBP-1 ChIP-seq in N2 mixed-stage embryos treated with NPP-13 RNAi (BC258)

description:
seq-SDQ0839_TBP1_RiNPP13_KI2183_N2_MXEMB
Barcode: CGAGAAG


title: Input-seq in N2 mixed-stage embryos (BC071)

description:
seq-input_EE14_N2_MXEMB
Barcode: CGCCCAC


title: IMB-1 ChIP-seq in N2 mixed-stage embryos (BC166)

description:
seq-SDQ4154_IMB1_EE15_N2_MXEMB
Barcode: GATCTTG


title: AMA-1 ChIP-seq in N2 mixed-stage embryos (BC002)

description:
seq-SDQ2357_AMA1_EE9_N2_MXEMB
Barcode: CGAGAAG

value: SDQ2357_AMA1 [Novus Biologicals, catalog# 38520002, lot# G3048-029, Animal SDQ2357]


title: AMA-1 ChIP-seq in N2 mixed-stage embryos (BC085)

description:
seq-SDQ2357_AMA1_EE14_N2_MXEMB
Barcode: AGATGGT


title: NPP-3 ChIP-seq in N2 mixed-stage embryos (BC164)

description:
seq-SY1539_NPP3_EE15_N2_MXEMB
Barcode: CACGTCG


title: Input DNA

city: New Orleans

first: Yuwen

last: Li

address: 1430 Tulane Ave SL37 RM5534

department: Pediatrics

institute: Tulane University

description: Input

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Alignment: Reads were aligned to human genome mm9 using Eland software (Illumina pipeline).
Peaks: MACS peak calling algorithm was used with a cut-off of pvalue = 1.00e-06 (http://liulab.dfci.harvard.edu/MACS/).
Genome_build: mm9
Supplementary_files_format_and_content: bed reports MACS peaks

source_name: E15.5 WT kidney

extract_protocol:
Chromatin was extracted from formaldehyde-crosslinked cells and ChIP-ed using anti-p53 antibody sc-6243 (Santa Cruz Biotech; lot# C1609).
ChIP DNA was processed into library by following the Illumina ChIP-Seq library construction protocol.

value: wild type


title: BM-MSC

city: Taipei

first: Jui-Yu

last: Hsieh

address: No. 155, Sec 2, Li-Nong Street

country: Taiwan

institute: National Yang-Ming University

description:
Small RNA-Seq
Pooled sample of 4 independent donors.

data_processing:
3' adaptors of the FASTQ raw data were trimmed, and trimmed data were collapsed by the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit).
For all datasets, reads shorter than 17 nt or longer than 30 nt were filtered out.
Trimmed data were aligned to genome (UCSC hg19) using the bowtie aligner.
Sequences that were able to be aligned with the transcribed genomic region of known miRNAs (according to miRBase R19, http://www.mirbase.org/) were quantified as an absolute expression value for each known miRNA.
Genome_build: GRCh37
Supplementary_files_format_and_content: RPM values of mature miRNAs (miRBase R19) in each of the 4 samples.

organism: Homo sapiens

source_name: Bone marrow mesenchymal stem cells

growth_protocol: All MSCs were cultured in MesenCult® (Stem Cells Technology) or MesenPRO RS (Invitrogen) medium at 37°C in a 5% CO2 humidified incubator.

extract_protocol:
Total RNA was extracted by Trizol according to the manufacturer's instructions.
TruSeq Small RNA Sample Prep Kit (Cat# RS-200-0012) was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: As to differentiation, BM-MSCs were incubated in differentiation medium for 2 weeks.

value: bone marrow

tag: cell type

value: mesenchymal stem cells

tag: passage


title: DMSO

status: Public on Sep 04 2013

city: Rochester

first: Jennifer

last: Westendorf

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
Illumina CASAVA 1.7.0 was used for basecalling.
Sequence reads were aligned to the mm9 reference genome using BWA v0.5.9 with default parameters.
Aligned reads with a mapping quality of less than 20 were filtered out using samtools.
Peaks were called using MACS 1.4.0rc2 with default parameters using SAHA as the ChIP file and DMSO as the the background sample.
Genome_build: mm9
Supplementary_files_format_and_content: The peaks text file is a tab delimited output from the MACS peak caller which includes the peak positions, supporting reads, p-value, fold enrichment, and FDR.

source_name: calvaria

growth_protocol: MC3T3 sc4 murine calvarial osteoblasts were maintained in α-Minimal Essential Medium without ascorbic acid containing 10% FBS, 100 U/ml penicillin, and 100 µg/ml streptomycin (maintenance medium)

extract_protocol:
Collagenase digests were performed with 1 mg/ml type II collagenase and 1 mg/ml BSA (Sigma) in Hank’s balanced salt solution for 40 min (cells were exposed to SAHA or vehicle during this incubation).  Cells were then harvested and cross-linked with 1% formaldehyde for 15 min.  Cells were lysed (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.0) and sonicated to generate 200 to 500 bp DNA fragments.
Libraries were prepared and sequenced on an Illumina HiSeq 2000 using standard Illumina protocols

treatment_protocol: MC3T3 sc4 cells were plated in 10cm plates in maintenance medium.  At confluence, maintenance medium was replaced with osteogenic medium (α-Minimal Essential Medium supplemented with 10% FBS, 100 U/ml penicillin, and 100 µg/ml streptomycin, 50 µg/ml ascorbic acid and 4 mM beta glycerol phosphate). Fresh differentiation medium was added three days later. On day four, fresh differeniation medium containing 20µM SAHA and/or its solvent (DMSO) were added for 2 hours. ChIP-Seq analysis was performed.

value: DMSO

value: Histone H4

tag: cell line


title: WJ-MSC

description:
Small RNA-Seq
Pooled sample of 3 independent donors.

source_name: Wharton's jelly of umbilical cord mesenchymal stem cells

value: Wharton's jelly of umbilical cord


title: BM-MSC-adipocyte

description:
Small RNA-Seq
Differentiated BM-MSC after 2 weeks induction.

source_name: Bone marrow mesenchymal stem cells, differentiated adipocytes


title: BM-MSC-osteocyte

source_name: Bone marrow mesenchymal stem cells, differentiated osteocytes


title: Case 15

city: Leuven

first: Julio

last: Finalet

address: Herestraat 49

country: Belgium

institute: KULeuven

data_processing:
RNA-seq reads were obtained using Bustard (Illumina Pipeline version 1.3).
Reads were quality-filtered using standard Illumina process, and a 0 (no) or 1 (yes) was used to define whether a read passed filtering or not.
The fastq files were mapped to the reference human genome (Human.B37.3) using the gene model Ensembl (release 67, May 2012). The mapping was performed with the software ArrayStudio, version 6.0 (Hu et al.) using the default parameters, allowing detection of insersions/deletions (indels).
The mapped reads were used to calculate the expression values per gene, transcript, exon and exon junction. The expression values were initially obtained in FPKM (fragment per kilobase of exon model per million of mapped read).
The Linux applications "Tophat" and 'Cufflinks' (Trapnell et al.) were used as an alternative to the ArrayStudio analysis for confirmation and comparison.
Genome_build: Human NCBI genome build 37.3
Supplementary_files_format_and_content: 8_samples_read counts.Naive.txt: Tab-delimited text file includes naive read counts for all samples.
Supplementary_files_format_and_content: 8_samples_FPKM.txt: Tab-delimited text file includes FPKM for all samples.

source_name: Lymph node, FOXP1 neg by IHC

extract_protocol:
TRIzol LS Reagent (Invitrogen, Carlsbad, CA, USA) was used for a total RNA extraction. cDNA was synthesized from 1 μg of total RNA using reverse transcriptase Superscript II ( Invitrogen, 30 5 Carlsbad, CA, USA) and random primer (Invitrogen, Carlsbad, CA, USA).
The Illumina standard kit (Illumina ® TruSeq™ RNA Sample Preparation Kit, San Diego, CA, USA) was used for the mRNA-sequencing sample preparation according to the manufacturer's protocol. The quality of the libraries was checked by Agilent Technologies 2100 Bioanalyzer, using the Chip (Agilent 7 DNA 1000 Kit).

value: lymphoma

tag: foxp1 expression by ihc

value: negative

tag: karyotype

tag: foxp rearrangement

value: FOXP1 neg by IHC

tag: diagnosis

value: GC-DLBCL


title: input DNA_replicate2

city: New York

first: Alicia

last: Rodriguez-Folgueras

address: 1230 York Ave.

institute: Rockefeller University

description: input DNA

data_processing:
bam files created using bowtie 0.12.7 allowing for only unique reads with 2 mismatches over 36bp
wig files created using igvtools with 100bp extension from bam files using mm9

source_name: Mouse back skins

growth_protocol: HFSCs were purifed by FACS from the backskins of mice

extract_protocol:
Sorted cells were crosslinked by addition of 1/10th volume of fresh 11% formaldehyde solution. Before ChIP, cells were resuspended, lysed, and sonicated to solubilize and shear crosslinked DNAs. The resulting whole-cell extract was incubated LHX2 antibody. After ChIP, samples were washed with low salt, high salt, LiCl, and Tris-EDTA buffer. Bound complexes were eluted and crosslinking was reversed.
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 25 cycles and library fragments of 150-300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: No treatment

tag: gender

value: Female

tag: age

tag: sorting markers

value: integrin α6 and CD34


title: Case 16

tag: tissue

value: ABC-DLBCL


title: Case 12

source_name: Lymph node, non-FOXP1 rearrangement

value: positive

value: non-FOXP1 rearrangement


title: Cmo_2H_0502

city: Golden

first: Shihui

last: YANG

state: CO

address: 1617 Cole Blvd

department: National Bioenergy Center

institute: National Renewable Energy Lab

description: Experiment 2

data_processing:
Basecalls performed using CASAVA version 1.5
FastQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) used for quality assessment.
The raw fastq dataset trimmed, duplicate removal, de novo assembly and RNA-Seq were carried out using CLC Genomics Workbench (version 5.1, CLCBio, Denmark)
Blast2GO used for assembled contig annotation
JMP Genomics 6.0 used for RNA-Seq statistical analyses
Genome_build: Assembled contigs using reads after data trimming and duplicate removal
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Chlamydomonas moewusii

source_name: cell pellet

growth_protocol: C. moewusii SAG 24.91 was grown in 1-L Roux bottles using TAP media at 25oC, and illuminated continuously with white fluorescent light (200 μE m-2s-1).  Cultures were supplemented with 2% CO2 in air and continuously mixed with a stir bar.

extract_protocol:
RNA samples were extracted approximately 5 min following H2 measurement using a gas-tight syringe.  Samples were immediately centrifuged and RNA was extracted with Plant RNA Reagent, following the manufacturer’s instructions (Life Technologies, NY).  RNA was further purified using a Turbo DNA-free kit (Life Technologies) and a Qiagen RNeasy Plant Mini Kit (Qiagen, CA), followed by checking sample quality and quantity with gel electrophoresis and NanoDrop spectrophotometer (Thermo Scientific, DE).
Samples of total RNA were sent to the National Center for Genomic Resources (NCGR) for RNA-Seq using Illumina GA IIx platform according to the manufacturer’s instructions.

treatment_protocol: Liquid cultures grown in Roux bottles were centrifuged at 3000 x g for 1 min and resuspended in 0.1 volume of AIB buffer (50 mM potassium phosphate, pH 7.2, 3 mM MgCl2).  Resuspended cells were transferred to 13-mL glass serum vials and sealed with butyl rubber septa.  Vials were wrapped in aluminum foil and purged with argon to establish dark anaerobiosis.  Cells were sampled at various time points prior to and following initiation of anaerobic conditions

tag: strain

tag: phase

value: Phase II


title: H2O-treated zebrafish liver

city: Singapore

first: Zhiyuan

last: Gong

address: Kent Ridge

country: Singapore

institute: National University of Singapore

description: Wildtype sibling

data_processing:
The SOLiD-generated RNA-Seq reads were 27 bp length and an initial filtering process was taken to remove any non-desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maximum mismatches.
The expression levels of mapped transcripts were normalized into transcript per million (TPM) to faciliate comparison among different samples.
Genome_build: RefSeq Release 58
Supplementary_files_format_and_content: Tab-delimited text file. The mapped transcripts are listed with GI, RefSeq accession, and expression levels in TPM.

organism: Danio rerio

source_name: liver, control

extract_protocol: Library construction was conducted by Mission Biotech (Taiwan) following the standard ABI SOLiD protocol.

treatment_protocol: 3-month-old wildtype zebrafish were treated for 96 hrs. Sodium arsenate treatment was conducted in 3-L tanks with around 15 adults and water was changed every day.

tag: genotype/variation

value: wildtype

value: liver

value: 3 months

tag: treatment

value: water (control)


title: Arsenic-treated zebrafish liver

description: Wildtype sibling

source_name: liver, arsenic

value: arsenate sodium


title: Case 11


title: p53 ChIP

description: ChIP against p53

value: wild type

tag: chip antibody

value: anti-p53 antibody (Santa Cruz Biotech; catalog# sc-6243; lot# C1609)


title: LHX2_ChIPSeq_replicate2

description: Chromatin IP against LHX2


title: SAHA

value: suberoylanilidehydroxamic acid

value: Histone H4


title: Cmo_15M_0502

description: Experiment 2

value: Phase I


title: Cmo_5H_427

description: Experiment 1

value: Phase III


title: LHX2_ChIPSeq_replicate3

description: Chromatin IP against LHX2

value: Female


title: input DNA_replicate3

description: input DNA

value: integrin α6 and CD34


title: input DNA_replicate1

description: input DNA


title: Cmo_2H_427

description: Experiment 1


title: LHX2_ChIPSeq_replicate1

description: Chromatin IP against LHX2


title: Case 7

value: lymphoma

value: ABC-DLBCL


title: Cmo_15M_427

description: Experiment 1


title: Case 5

source_name: Lymph node, IGH-FOXP1 rearrangement

value: positive


title: Cmo_10H_0502

description: Experiment 2


title: Case 3

source_name: Lymph node, non-IGH-FOXP1

value: negative

value: MZL


title: PAR-CLIP2

status: Public on Sep 03 2013

city: Gießen

first: Andreas

last: Gogol-Döring

address: Wiesenstraße 14

department: MNI

country: Germany

institute: Technische Hochschule MIttelhessen

data_processing:
Library strategy: PAR-CLIP
PAR-CLIP reads were aligned to the human genome allowing at most one mismatch, or indel of one nucleotide. Uniquely mapped reads were overlapped to define binding clusters. For each cluster, the rbm10 binding site was defined as the site with the highest number of T to C conversions.
processed data files format and content: The .bed files contain RBM10 binding sites. Scores given in column 5 are the numbers of reads per binding cluster.
Base calling was done on the Illumina HiSeq 2000 machine using RTA 1.12. We kept only reads passing the filtering.
Genome_build: hg19

growth_protocol: The HEK293 T-REx Flp-In cells were cultured in a 37 °C incubator with 5 % CO2 and maintainence medium containing: High glucose DMEM (Gibco) supplemented with 10% final concentration FBS (heat inactivated, Gibco), 100 U/ml of penicillin and 100 μg/ml streptomycin (Gibco), 15 μg/ml blasticidin (InvivoGen) and 100 μg/ml zeocin (InvivoGen). The stable cell lines were maintained in selective medium containing: DMEM with 10% final concentration of FBS, 100 U/ml of penicillin and 100 μg/ml streptomycin, 100 μg/ml hygromycin and 15 μg/ml blasticidin.

extract_protocol:
For PAR-CLIP, RBM10-RNA complexes were revovered from the gel followed by protein digestion and phenol choloroform extaction.
PAR-CLIP seqeuncing libraries were constructed using original small RNA library preparation protocols. Briefly, the 3' and 5' adaptors were ligated to RNA separately. The ligated product was reverse transcribed and amplified to generate the sequencing library.

treatment_protocol: siRNA transfections were performed in antibiotics free medium, i.e. DMEM with 10% final concentration FBS, using RNAiMAX (Invitrogen). RBM10 overexpression was induced with 10 ng/mL doxycycline for 16 hours

value: human embryonic kidney (HEK) 293 T-REx Flp-In cell lines

tag: antibody

value: monoclonal anti-FLAG (Sigma, F1804)

tag: rna subset

value: RBM10 bound RNA


title: PAR-CLIP1

tag: cell type


title: Normal.1_RNA-Seq

data_processing:
RNA-seq reads were mapped with at most two mismatches to the human genome reference and a set of sequences consisting of all possible junctions between the exons of each Refseq gene. For each exon E of a RefSeq gene, we computed the number of reads which could only be mapped to E or exon junctions containing E with an overlap of at least 6bp ("spliced-in" event), and the number of reads which could be mapped only to exon junctions skipping E and overlap with both exons by at least 6bp ("spliced-out" event).
processed data files format and content: The .tab.txt files contain the number of reads supporting splicing-in and splicing-out events of exons. Each row of the table represents a single exon of a RefSeq gene. The columns of the list contains the chromosome ("chrom"), the starting position of the exon ("begin", 0-based), the ending position of the exon ("end", 0 based position of the first base after the exon), the name of the gene ("name"), a number which uniquely labels the exon within the gene ("exon"), the definition of the strand ("strand", either "+" or "-"), the number of reads supporting a splicing-in event ("in"), and the number of reads supporting a splicing-out event ("out"). Note that the first 3 columns conform to the bed file format.
Base calling was done on the Illumina HiSeq 2000 machine using RTA 1.12. We kept only reads passing the filtering.
Genome_build: hg19

extract_protocol:
For RNA-Seq, total RNA was extracted using Trizol reagent and poly A RNA was isolated from 1 ug of total RNA for sequencing libraries construction.
RNA-Seq libraries were prepared following Illumina TruSeq RNA Sample Prep Kit protocol.

value: lymphoblastoid cell lines (LCLs) derived from healthy control

value: poly A RNA


title: CD34_LMO2_ChIP-seq

city: Sydney

first: Jason

last: Wong

state: NSW

address: Level 2, Lowy Cancer Research Centre, University of New South Wales

country: Australia

institute: UNIVERSITY OF NEW SOUTH WALES

data_processing:
Base-calling: Illumina Real Time Analysis, scoring metric v1.5
Raw reads were prefiltered to remove all reads that have 3 or more bases with a quality score of less than Q13
All provided cleaned data have had adaptors clipped except the small RNA-seq data which still contains 5' adaptor:  5'-TGGAATTCTCGTATGCCGTCTTCTGCTTG
Alignments were all made against hg19. The following aligners were used. ChIP-seq: bwa (version 0.6.1-r104) default parameters , mRNA-seq: tophat (version 1.3.1) -g 25 -r 20 --segment-length 45 -G "hg19_refseq.gtf" --solexa1.3-quals, smallRNA: bowtie (version 0.12.5) -v 2 -m 25 --solexa1.3-quals --best --strata.
Bed files generated from BAM files using bedtools bamtobed (version 2.15.0). For ChIP-seq files, each bed entry is extended to 200bp in length. For RNA-seq the split option was used.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files contain coordinates for all aligned reads

source_name: CD34+ cells

extract_protocol:
Bone marrow (BM) samples were harvested from normal volunteers with informed consent in accordance with local ethical guidelines.  The CD34+ fraction was obtained by magnetic bead separation using an automated CliniMACS cell separation system (Miltenyi Biotec, Cologne).  Cell purity was assessed by flow cytometry and was â‰¥ 98%. ChIP assays were performed with 15 x 10^6 per condition. Total RNA extraction and purification was performed using miRNeasy mini kits (QIAGEN). The small RNA fraction (<200nt) was collected in a separate fraction from total RNA, as per manufacturerâ€™s standard instructions. Total RNA was amplified using the Ovation RNA-seq system V2 (NuGEN) prior to sequencing.
For ChIP, cells were harvested and washed with phosphate-buffered saline (PBS), followed by incubation of 1% (w/v) formaldehyde for 10 minutes at room temperature. To terminate the cross-link, cells were incubated with 0.125M glycine for 5 minutes. Cells were washed with PBS and lysed on ice in Cell lysis buffer (10mM Tris [pH 8.0], 10mM NaCl, 0.2% NP-40) for 10 minutes to recover nuclei. After centrifugation at 1500xg for 5 minutes, nuclei were lysed in Nucleus lysis buffer (50 mM Tris, 10mM EDTA, 1% SDS [pH 8.0]) on ice for 10 minutes. The lysate was diluted in IP dilution buffer (20mM Tris [pH 8.0], 2mM EDTA, 150mM NaCl, 1% Triton-X100, 0.01% SDS) and sonicated (Settings: High, 30sec pulses) using BioRuptor® sonicator (Diagenode, Liège, Belgium) to yield an average fragmentation size of approximately 200bp. The chromatin was pre-cleared with 100?g rabbit IgG for 1 hour followed by incubation with 100?l protein-G-agarose (Roche Applied Science, Penzberg, Germany) for 2 hours. For each sample, 300?l pre-cleared chromatin was removed (input for the subsequent qRT-PCR analysis) and the remaining chromatin was aliquoted, and incubated with the indicated antibody for 18 hours at 4°C. To collect immune complexes, 50?l protein G-agarose was added to the chromatin and incubated for additional 2 hours at 4°C. Protein-G-agarose pellets were washed at 5000xg; twice with 500?l IP wash buffer 1 (20mM Tris [pH 8.0], 2mM EDTAm 50mM NaCl, 1% Triton-X100, 0.1% SDS), once with IP wash buffer 2 (10mM Tris [pH 8.0], 1mM EDTA, 0.25M LiCl, 1% NP-40, 1% Sodium deoxycholate) and twice with TE (10mM Tris, 1mM EDTA [pH8.0]). Immuno-precipitated chromatin was eluted in 300?l Elution Buffer (100mM NaHCO3, 1% SDS) and reverse-cross link was obtained by incubation with RNase A and NaCl (0.3M final concentration) at 67°C for 18 hours followed by treatment with Proteinase K at 45°C for 2 hours. Input DNA (pre-cleared chromatin) was treated with RNase A and Proteinase K simultaneously.
Library construction was performed as per Illumina protocol Rev A 11257047

value: CD34+ cells


title: CD34_IgG_ChIP-seq

value: IgG


title: CD34_RUNX1_ChIP-seq


title: CD34_GATA2_ChIP-seq

value: GATA2 (Santa Cruz, sc-9008x) I0109


title: CD34_mRNA-seq

tag: rna subtype

value: messenger RNA


title: RBM10.OE.1_RNA-Seq

tag: stable cell line

value: stable cell lines inducibly expressing FLAG/HA-tagged  RBM10


title: RBM10.OE.2_RNA-Seq


title: CD34_smallRNA-seq

value: small RNA


title: RBM10.KD.72h_RNA-Seq


title: RBM10.KD.48h.2_RNA-Seq


title: RBM10.KD.48h.1_RNA-Seq


title: CD34_FLI1_ChIP-seq


title: CD34_SCL_ChIP-seq

value: SCL (Santa Cruz, sc-12984X), B2312


title: RBM10.KD.24h_RNA-Seq


title: Ctrl_RBM10.OE.1_RNA-Seq


title: Cmo_0M_508

description: Experiment 3, data used for de novo assembly to get the refrence sequences for RNA-Seq analysis only.


title: Ctrl_RBM10.OE.2_RNA-Seq


title: Patient_RNA-Seq

value: lymphoblastoid cell lines (LCLs) derived from patient


title: CD34_LYL1_ChIP-seq


title: Ctrl_RBM10.KD.24h_RNA-Seq


title: Ctrl_RBM10.KD.48h.1_RNA-Seq


title: HBC 5mC

city: San Francisco

first: Michael

last: Brainard

state: CA

address: 675 Nelson Rising Ln

institute: University of California, San Francisco

description: gDNA immunoprecipitated with anti-5mC antibody (Active Motif)

data_processing:
Alignment: Samples were aligned using either Bowtie (DIP) or Tophat (mRNA) keeping only reads that matched uniquely to the mouse genome (mm9). Wig:
Wig: Values are the average number of reads within a given 200 bp window normalized by the library size in millions of reads.
FPKM tracking: Aligned mRNA samples were assembled to the UCSC refGene GTF using Cufflinks with bias correction against the mouse genome (mm9) and multi-read correction.
Genome_build: mm9
Supplementary_files_format_and_content: WIG

source_name: anti-CD54-PE positive cells

extract_protocol:
DNA was extracted using DNeasy (Qiagen) according to manufacturers instructions.
Libraries were constructed from gDNA samples by sonication to 200-1000 bp, end repair (NEB End Repair Kit), terminal A addition (Klenow), and Illumina adaptor ligation (NEB Quick Ligase). Samples were then immunoprecipitated with the indicated antibodies and amplified for 12-15 cycles

value: 4 weeks

value: main olfactory epithelium

value: anti-CD54-PE positive cells

tag: ip antibody

value: anti-5mC antibody (Active Motif)


title: Normal.2_RNA-Seq


title: GBC 5mC

source_name: Neurog1-EGFP positive cells

value: Neurog1-EGFP positive cells


title: mOSN 5mC

source_name: OMP-ires-EGFP positive cells

value: OMP-ires-EGFP positive cells


title: DHFR-TS-GFP_glmS integrant GlcN treated rep. #2

city: Pathumthani

first: Philip

middle: James

last: Shaw

state: Pathumthani

address: 113 Phahonyothin Road

department: National Center for Genetic Engineering and Biotechnology

country: Thailand

institute: National Science and Technology Development Agency

description:
Saponin-liberated parasites
processed data file: edgeR_results_integrant.txt
processed data file: Integrant_rep2_AS.txt
SRX212152

data_processing:
Poor quality reads were removed from the data (reads with adaptors, >10% of bases with no call, and >50% base calls with Phred score <5). Filtered data were mapped to to the P. falciparum 3D7 version 3 genome with the SOAP2 program
Differentially expressed genes were identified by edgeR analysis. Genes with fewer than 5 mapped reads were excluded, leaving a total of 2316 (DHFR-TS-GFP_glmS transgenic line) and 2285 (3D7 wild-type) annotated genes for analysis. The trimmed mean of M values (TMM) was determined separately in each sample group and used to calculate normalization factors.
Alternative splicing events comparing treated vs untreated samples were investigated using the MATS algorithm
Genome_build: P. falciparum 3D7 version 3 (http://www.ncbi.nlm.nih.gov/assembly/GCF_000002765.3/)
Supplementary_files_format_and_content: tab-delimited text files include results from alternative splicing and differential gene expression

organism: Plasmodium falciparum

source_name: DHFR-TS-GFP_glmS integrant GlcN treated

growth_protocol: P. falciparum strain 3D7 was cultured in human RBC (5% haematocrit) in RPMI-1640 medium (Invitrogen™) supplemented with 0.3 g/l L-glutamine, 5 g/l hypoxanthine and 10% human serum under an atmosphere of 1% O2 and 5% CO2.

extract_protocol:
Total RNA was extracted from the parasites using TRizol reagent following the manufacturer’s recommendations (Invitrogen). Genomic DNA was removed using a Turbo DNA-free™kit (Applied Biosystems). mRNA was obtained from 10-20 micrograms of Total RNA per sample by oligo dT capture.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: DHFR-TS-GFP_glmS integrant

value: 10 mM Glucosamine for 24 h


title: DHFR-TS-GFP_glmS integrant GlcN treated rep. #1

description:
Saponin-liberated parasites
processed data file: edgeR_results_integrant.txt
processed data file: Integrant_rep1_AS.txt
SRX212151


title: 3D7 GlcN treated rep. #2

description:
Saponin-liberated parasites
processed data file: edgeR_results_3D7wildtype.txt
processed data file: 3D7_rep2_AS.txt
SRX212148

source_name: 3D7 GlcN treated

value: wild-type


title: GBC mRNA

description: Poly-A selected RNA

extract_protocol:
RNA was extracted using Trizol (Invitrogen) according to manufacturers instructions.
Total RNA was isolated from sorted cells. Poly-A RNA was isolated using the FastTrack Micro MAG (Invitrogen) kit, and samples were prepared using the Illumina mRNA library preparation kit. Libraries were amplified for 16 cycles.


title: CD34_ERG_ChIP-seq

value: ERG (Santa Cruz, sc-354X), A2510 & H1612

value: CD34+ cells


title: mOSN mRNA

description: Poly-A selected RNA


title: 3D7 GlcN treated rep. #1

description:
Saponin-liberated parasites
processed data file: edgeR_results_3D7wildtype.txt
processed data file: 3D7_rep1_AS.txt
SRX212147


title: DHFR-TS-GFP_glmS integrant untreated rep. #2

description:
Saponin-liberated parasites
processed data file: edgeR_results_integrant.txt
processed data file: Integrant_rep2_AS.txt
SRX212150

source_name: DHFR-TS-GFP_glmS integrant untreated

value: untreated


title: Ctrl_RBM10.KD.48h.2_RNA-Seq

value: human embryonic kidney (HEK) 293 T-REx Flp-In cell lines

value: poly A RNA


title: 3D7 untreated rep. #2

description:
Saponin-liberated parasites
processed data file: edgeR_results_3D7wildtype.txt
processed data file: 3D7_rep2_AS.txt
SRX212146

source_name: 3D7 untreated


title: HBC 5hmC

description: gDNA immunoprecipitated with anti-5hmC antibody (Active Motif)

value: anti-5hmC antibody (Active Motif)


title: Ctrl_RBM10.KD.72h_RNA-Seq


title: 3D7 untreated rep. #1

description:
Saponin-liberated parasites
processed data file: edgeR_results_3D7wildtype.txt
processed data file: 3D7_rep1_AS.txt
SRX212145


title: GBC 5hmC


title: HBC mRNA

description: Poly-A selected RNA

extract_protocol:
RNA was extracted using Trizol (Invitrogen) according to manufacturers instructions.
Total RNA was isolated from sorted cells. Poly-A RNA was isolated using the FastTrack Micro MAG (Invitrogen) kit, and samples were prepared using ScriptSeq (Epicentre). Libraries were amplified for 16 cycles.


title: mOSN ribominus RNA

description: rRNA-depleted total RNA

data_processing:
DIP reads were aligned to mm9 using bowtie (-m 1) or bowtie2 (--end-to-end)
RNA reads were aligned to the iGenomes Ensembl gene GTF (-max-multihits 1, --no-coverage-search)
Low quality reads were removed by filtering for MAPQ >= 30
FPKMs for rmRNA samples were generated using cuffdiff aligned to the iGenomes Ensemble gene GTF
Genome_build: mm9
Supplementary_files_format_and_content: WIG files were generated by first counting the number of paired-end midpoints (DIP) or ends (RNA) that aligned to contiguous 25 bp windows. These values were then normalized by the total number of paired-end fragments multiplied by 1000.
Supplementary_files_format_and_content: rmRNA text file values are log2(FPKM + 1) from cuffdiff analysis. 'ott3.omp' is the difference between 'ott3' and 'omp' values.

extract_protocol:
Total RNA was isolated from sorted cells.
rRNA-depleted RNA was isolated using two rounds of the RiboMinus Eukaryote Kit for RNA-seq (Invitrogen), and samples were prepared using the ScriptSeq kit (Epicentr). Libraries were amplified for 16 cycles.

tag: feature

value: rRNA-depleted total RNA


title: Tet3-tg 5hmC

source_name: OMP-tTA / tetO-Tet3-GFP

extract_protocol:
Libraries were constructed from gDNA samples by sonication to 200-1000 bp, end repair (NEB End Repair Kit), terminal A addition (Klenow), and Illumina adaptor ligation (NEB Quick Ligase).
Samples were then immunoprecipitated with the indicated antibodies and amplified for 12-15 cycles

value: Fvb

value: anti-5hmC antibody (Active Motif, cat - 39769, lot - 16210001)


title: Coculture Rep 1

city: HangZhou

first: Bin

state: Zhejiang

address: 866-Yuhangtang Road

department: Biotechnology

country: China

institute: Zhejiang University

description: Sample 5

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 tophat 2.0.8 with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks 2.1.1
Genome_build: CP002521
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Paracidovorax avenae RS-1

source_name: Aaa strain RS-1_coculture

growth_protocol: The samples of Aaa strain RS-1 for in vitro and in vivo analysis were prepared as described before (Ibrahim et al., 2012)

extract_protocol:
RNA extraction and puriﬁcation were performed with RNeasy Mini Kit (Qiagen).
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: The co-culture analysis of Aaa strain RS-1 with B. seminalis strain R456 were conducted according to Ruiz et al. (2009) and Di Cagno et al. (2009).

tag: culture type

value: Coculture with  B. seminalis strain R456

tag: growth phase

value: exponential phase


title: Coculture Rep 2

description: Sample 6


title: mOSN 5hmC

tag: age

value: 4 weeks

value: main olfactory epithelium


title: In vivo Rep 2

description: Sample 4

source_name: Aaa strain RS-1_in vitro

value: In vivo


title: O/Tet3 ribominus RNA

description: rRNA-depleted total RNA


title: In vitro Rep 1

description: Sample 1

source_name: Aaa strain RS-1_in vivo

value: in vitro (control)


title: DHFR-TS-GFP_glmS integrant untreated rep. #1

description:
Saponin-liberated parasites
processed data file: edgeR_results_integrant.txt
processed data file: Integrant_rep1_AS.txt
SRX212149

value: DHFR-TS-GFP_glmS integrant


title: In vitro Rep 2

description: Sample 2


title: Foc4 27h

status: Public on Sep 01 2013

city: Houston

first: Jiaofang

last: Shao

state: Texas

address: 6431 Fannin St

department: Department of Biochemistry and Molecular Biology

institute: McGovern Medical School, University of Texas Health Science Center

data_processing:
Illumina GApipeline 1.6 software used for basecalling.
For RNA-seq data, the raw reads were cleaned by removing adaptor sequences and low quality reads with ambiguous ‘N’. TopHat, a splice junction mapper for RNA-Seq reads, was used to align RNA-seq reads to the Musa genome sequence (http://banana-genome.cirad.fr) with default parameters (minimal intron length 50 and maximum intron length 500000). For DGE data, the adapter sequences “(N10)TCGTATGCCGTCTTCTGCTTG” were cut from the raw reads using FASTX-Toolkit (Version 0.0.13). The processed unique sequence tags were mapped by BLAST (version 2.26) with the word length 17.
Genome_build: Musa genome sequence (http://banana-genome.cirad.fr)
Supplementary_files_format_and_content: Tab-delimited text file (linked as supplementary file on Series record) includes TPM values for each Sample

organism: Musa acuminata

source_name: roots, pseudostems, leaves, floral organs, and developing fruits of banana

growth_protocol: Banana plantlets were propagated under a sterile tissue culture condition. Suckers were used for multiplication and rooting by placing in plastic bags containing a growth medium. The medium for subculturing contains 1x Murashige & Skoog (MS) basal salt mixture, 3% sucrose, 7% agar, 4.0 mg L-1 6-benzylaminopurine, 0.5 mgL-1 α-naphthlcetic acid, pH5.8. The rooting medium is the same as above expect with 2.0 mg L-1 6-benzylaminopurine and 2.0 mgL-1α-naphthlcetic acid. The plantlets were grown in a 28ºC growth room with a 16h/8h light/dark period and light intensity of 5000 lux. Plantlets in the sealed bags were transferred to a greenhouse for 3-5 days and then removed from the bags and grown hydroponically for 50 days in the medium containing ¼ MS salts.

extract_protocol:
Total RNA was extracted from roots, pseudostems, leaves, floral organs, and developing fruits separately using a modified CTAB method briefly described below. Two to five grams of tissues were grounded in liquid nitrogen, and the powder was mixed with 20 mL CTAB buffer (3% CTAB, 2% PVP, 2.0 M NaCl, 20 mM EDTA, 100 mM Tris pH 8.0, 2% β- mercaptoethanol) and incubated at 65ºC for 20 min. The extract was mixed with 0.6 volume of chloroform by vortexing and span at 12000g for 15 min at room temperature. The supernatant was transferred to a new tube and extracted with an equal volume of chloroform, and the supernatant was then mixed with 0.5 volume of 12 M LiCl and incubated at -20ºC for 2 hours. RNA was precipitated by centrifugation at 12000g for 15 min at 4ºC and the pellet was re-suspended in 1 mL 0.2 M NaCl. The RNA solution was extracted sequentially with an equal volume of water-saturated phenol (pH 4.2) and chloroform. RNA was precipitated by mixing the solution with three volumes of ethanol and leaving on ice for 30 min before centrifugation at 14000g for 20 min at 4ºC. After washing the pellet with 75% ethanol, the RNA pellet was dissolved in 50 μL RNase-free water.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Roots of banana plants grown hydroponically for 50 days (as described above) were cut at approximately 0.5-1cm from the root tips, dipped into the Foc spore solution, and inoculated for 2.5 hours. For the control plants, their roots were dipped into PDB 9mock-inoculation). The plants were then placed back to the normal hydroponic condition for the indicated time. The inoculated banana plants were examined daily following inoculation.

value: Foc4 infection

tag: time


title: Foc4 51h

tag: tissue

value: roots, pseudostems, leaves, floral organs, and developing fruits of banana


title: Foc1 51h

value: Foc1 infection


title: Mock 51h

value: PDB mock-inoculation


title: Foc1 3h


title: Mock 27h


title: Foc1 27h


title: Foc4 3h


title: Mock 3h


title: ST-HSC2

city: Lund

first: Shamit

last: Soneji

address: Sölvegatan 19

department: Biomedicinskt Centrum

country: Sweden

institute: Lund University

data_processing:
Reads aligned using Tophat
Read quantitated using SeqMonk
Genome_build: mm9
Supplementary_files_format_and_content: fastq files and SeqMonk quantities for each gene

source_name: Bone marrow

extract_protocol:
RNA from 2000 sorted cells was processed using the SMARTer cDNA synthesis kit (Clontech)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: immunophenotype


title: LT-HSC2


title: ST-HSC1


title: In vivo Rep 1

description: Sample 3

tag: strain


title: 3 day old heads normal food 2

city: Nijmegen

first: Jamie

middle: M

last: Kramer

address: Geert Grootplein 10

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

data_processing:
Raw data was processed using the default Illumina CASAVA pipeline, with mapping to the dm3 genome using ELAND with 0 or 1 mismatches.
Normalized expression values were generated using the Genomatix Genome Analyser v2. 40901.
Genome_build: BDGP R5 / dm3
Supplementary_files_format_and_content: bed files contain one line for each mapped read; wig files are standard

molecule: polyA RNA

source_name: Drosophila heads

growth_protocol: Flies were cultures according to standard methods at 25 degrees with a 12 hour light dark cycle

extract_protocol: Spd- and Spd+ flies were frozen in liquid nitrogen and heads were collected after vortexing by mechanical separation. Poly A+ RNA was extracted from approximately 50 ul of heads per sample using the RNeasy Lipid tissue Mini kit (Qiagen) and the Oligotex mRNA mini kit (Quiagen). RNA was reverse transcribed into a cDNA using the Superscript III Reverse Transcriptase Kit (Invitrogen) for first strand synthesis. Second strand synthesis was performed with E.coli and T4 DNA polymerases (New England Biolabs). DNA end repair was performed on 9-20 ng of cDNA followed by ligation of adaptors, and size selection for 300 bp fragments using the E-gel Size Select gel (Invitrogen). Fragments were amplified using 14 PCR cycles and linear amplification was validated by qPCR.

treatment_protocol: Flies were cultured either in the presence or absence of 5mM spermidine

tag: food

value: standard Drosophila media

value: 3 days after eclosion

value: heads


title: H3K4me2_Th17_ChIPSeq

city: Almada

first: Ana

middle: Rita

last: Grosso

address: Campus de Caparica

department: Departamento Ciências da Vida

country: Portugal

institute: Unidade de Ciências Biomoleculares Aplicadas (UCIBIO)/Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa

data_processing:
High-throughput sequencing reads were aligned to the reference mouse (mm9) genome using Bowtie. Reads quality was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We filtered out reads with bad-quality scores, reads not uniquely mapped and PCR duplicates (identical coordinates). SAMtools and BEDtools were used for filtering steps and file formats conversion. Three different peak calling tools were used to detect enrichment of histone modifications density: MACS, SICER, and RSEG. The analyses were performed using the recommended settings for histone modifications, and we only considered peaks that were consistently detected by the three methods. For quantitative calculation and profiles of histone modifications levels for all genes, all uniquely mapped reads were extended in the 3’ direction to reach 150nt using the Pyicos tool. Only read counts overlapping with histone enriched regions identified above were considered. For a gene without enriched regions, the modification level was defined as zero. BedGraphs showing enrichment of histone modifications density for each cell type were generated using BEDtools and are provided as processed data files.
Genome_build: mm9

source_name: Th17 cells

extract_protocol: ChIP was carried out on FACS-sorted cells from pooled spleen/ lymph nodes. The following antibodies were used: anti-histone H3K4me2 (07-030, Millipore) and anti-histone H3k27me3 (07-449, Millipore). Between 105 - 106 cells were crosslinked with formaldehyde and nuclei were isolated and sonicated with a Sanyo Soniprep 150 at an amplitude of 10 microns with 17 times 10s bursts, resulting in 200–400bp chromatin fragments. IP was carried out as previously described (PMID: 17682057). The Immunoprecipitated DNA released from crosslinked proteins was extracted with the QiaQuick kit (Qiagen) in accordance with the manufacturer´s instructions. Deep sequencing was performed at the GeneCore facility of EMBL (http://www.genecore.embl.de/). At least 1 ng of immunoprecipitated DNA was used for library preparation according to the Illumina protocol.

value: Differentiated CD4+ T cells from lymph nodes and spleen (Th17 conditions:4 days anti-CD3 (2ug/ml), anti-CD28 (5ug/ml), IL-6 (20ug/ml), IL-1b (10ug/ml), TGF-b (1ug/ml), anti-IFN-g(10ug/ml) after performed a mouse IL-17 secretion assay (Miltenyi, 130-094-212)

tag: protocol

value: In vitro

value: H3K4me2 (Millipore, 07-030)


title: H3K27me3_Th1_ChIPSeq

source_name: Th1 cells

value: Differentiated CD4+ T cells from lymph nodes and spleen (Th1 conditions:7 days anti-CD3 (10ug/ml), anti-CD28 (2ug/ml), IL-12 (5ug/ml), anti-IL-4 (10ug/ml)

value: H3K27me3 (Millipore, 07-449)


title: H3K27me3_gdCCR6p_ChIPSeq

source_name: CD27-CCR6+ gd T cells

value: primary cells (Lymph node and spleen)

value: ex vivo


title: H3K4me2_gdCD27p_ChIPSeq

source_name: CD27+ gd T cells


title: H3K27me3_gdCD27p_ChIPSeq


title: Col-0

city: Harbin

first: Lili

last: Zhang

state: Hei Longjiang

address: Mucai street

institute: Northeast Agricultural University

data_processing:
Illumina Casava version 1.7 software was used for basecalling
Reads Per Kilobase of exon model per Million mapped reads (RPKM) were calculated using a protocol from Mortazavi et al., Nature, 2008
MARS (MA-plot-based method with Random Sampling model) from DEGseq package was used for identifying differentially expressed genes (Wang et al., 2010)
Pathways and Gene Ontology (GO) analysis were performed using Molecule Annotation System (MAS)
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample and Pathway and Gene Ontology analysis of differentially expressed genes

source_name: Aerial part

growth_protocol: Seedlings of 35S:SsCBF1-11 and Col-0 (WT) plants were grown in a chamber at 22 ℃ in a photoperiod of 16 h light and 8 h darkness.

extract_protocol: Materials from 20 plants of each genotype were pooled for RNA isolation.Total RNA was isolated with Trizol reagent ( Invitrogen , USA ) from the aerial part of our material and purified with Micropoly(A) PuristTM mRNA purification kit (Ambion, USA, Cat. No:1919). About 10 μg total RNA of each sample was used for the construction of sequencing libraries. cDNA first- and second-strand synthesis was performed using Superscript II reverse transcriptase (Invitrogen,USA) and Ex Taq polymerase (TaKaRa, Japan), respectively.The newly synthesized double-strand cDNA was fractured into 300-500bp fragments using an ultrasonic instrument (Fisher) and then purified with AMPure beads ( Agencourt , USA ). The sequencing library was prepared and PCR amplified using TruSeqTM DNA Sample Prep Kit-Set A  (illumina, USA) and TruSeq PE Cluster Kit  (illumina,  USA), respectively. Sequencing was performed on the illumina HiSeq 2000 sequencing platform.

tag: developmental stage

value: 4-week-old seedlings

tag: number of plants

value: 20 seedlings

tag: genotype

value: wild-type

tag: cultivar


title: H3K27me3_Th17_ChIPSeq

tag: cell type

tag: antibody


title: H3K4me2_Th1_ChIPSeq


title: H3K4me2_gdCCR6p_ChIPSeq


title: 35S:SsCBF1-11

value: SsCBF1-overexpressing line


title: Mouse digit 10d

first: Jeff

last: Nie

state: MN

address: 200 First St. SW

data_processing: For data analysis, paired-end reads were treated as two separate single-end reads. After the sequencing was complete, the data were processed by Illumina Pipeline software for quality analysis. For transcript quantification and differential analyses, we used an axolotl contig set assembled with MIRA (Chevreux et al., 2004) from a combination of Sanger and 454 EST sequences. Details of the assembly process are provided in Supplemental Experimental Procedures. We used BLAST to align the contigs against human RefSeq (Pruitt et al., 2009) RNA and protein sequences, taking the best BLAST hit with e-value less than 10-5 as the most closely related human homolog for each contig. RSEM (Li and Dewey, 2011) was used to estimate the relative abundances and expected read counts for the contigs. Contigs mapping to rRNA transcripts were removed and abundances were renormalized. The expected read counts for contigs mapping to the same homologous human transcript were summed to give abundances. Read counts for transcripts belonging to the same gene were summed to give human gene-level abundances.

source_name: mouse tissue

growth_protocol:
For Mouse: Mice were housed at the animal facility at the University of Pittsburgh
For Axolotl: The animals were housed in 40% Holtfreter’s salts, kept at 16-18O C with a pH range of 7.0-7.4.

extract_protocol: We linearly amplified axolotl polyA+ RNAs using a modified T7 amplification method (Sengupta et al., 2010) resulting in cDNA. Subsequent steps followed the Illumina Paired End (PE) preparation kit (PE-102-1001, Illumina, San Diego, CA). After the Illumina PE adapters were ligated, 150-250 bp DNA fragments were isolated via gel electrophoresis. Then ten cycles of polymerase chain reaction (PCR) were performed to amplify the selected fragments using the Illumina supplied PCR primers and protocol. The sample was quantitated with the Invitrogen Qubit fluorometer (Q32857).  Samples were loaded on the flowcell cluster station at a concentration of 8pM. The Genome Analyzer II Paired End recipe was used. Some runs were single-read runs, while some runs were paired-end.

treatment_protocol:
For Mouse: Following induction of surgical plane anesthesia with 1-2% inhaled isoflurane (assessed by intact breathing, intact femoral pulses bilaterally, and lack of response to tail and foot stimulus), adult, 6 to 8 week old C57/BL6 mice (Jackson Laboratories, Bar Harbor, ME) were subjected to aseptic, mid-second phalanx amputation of the third digit of each hindfoot. Post surgical buprenorphine and baytril were administered for 3 days post-surgery for analgesia and antibiotic prophylaxis, respectively. Animals were sacrificed and the distal portion of each amputated digit (distal to the proximal joint) was harvested into RNAlater solution (Ambion, Austin, TX) and immediately flash frozen in liquid nitrogen. Time points of harvest included 0 hours, 3 hours, 6 hours, 12 hours, 1 day, 5 days, 10 days, and 14 days. Following transfer of each sample overnight on dry ice to the Morgridge Institute for Research  (Madison, WI), RNA from each sample was isolated using Trizol (Invitrogen, Carlsbad, CA) and treated with Dnase I. Then the RNA was purified by extraction with phenol:chloroform.
For Axolotl: For all surgical procedures, the animals were anesthetized with 0.5-1 g/L Tricaine (MS-222, Sigma, St. Louis, MO) until they were unresponsive to a tail pinch stimulus.We amputated juvenile limbs at the mid-stylopod level. Tissue was harvested as described in Figure 1 at 0 hours, 3 hours, 6 hours, 12 hours, 1 day, 3 days, 5 days, 7 days, 10 days, 14 days, 21 days, and 28 days. Note that for the early time points, some tissue was harvested proximal to the original amputation plane owing to the small amount of regenerative tissue distal to the amputation plane at the time of harvesting. In all cases the harvested tissues were stored in RNAlater (Qiagen, Valencia, CA) at 4OC until the RNA was purified using the RNeasy purification kit from Qiagen.

value: hindfoot digit

tag: time course


title: Mouse digit 14d


title: Mouse digit 1d


title: Mouse digit 5d


title: BC_3

city: Stockholm

first: Rickard

last: Sandberg

address: Berzelius vag 35

department: Department of Cell and Molecular Biology

institute: Karolinska Institutet

description: PolyA+ RNA

data_processing:
All reads were aligned to the human (hg19) or mouse (mm10) genomes using STAR (Dobin et al. 2013).
Non-uniquely mapped reads were removed.
Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE. Gene annotations used were transcripts in RefSeq (Feb 2013).
Genome_build: GRCh37
Supplementary_files_format_and_content: Gene expression values (tab-delimited text file).

source_name: single cell, DG-75, SMART-Seq2

extract_protocol:
Lysis buffer from the kit 'SMARTer Ultra Low Input RNA for Illumina Sequencing' (Clontech).
We prepared sequencing libraries according to the optimized Smart-Seq2 protocol, variants of Smart-Seq2 and using the standard Smart-Seq procedure ('SMARTer Ultra Low Input RNA for Illumina Sequencing' from Clontech).

tag: cell line

tag: library prep protocol


title: Mouse digit 6hr


title: Mouse digit 0hr


title: BC_8

description: PolyA+ RNA


title: BC_12

description: PolyA+ RNA


title: LT-HSC1


title: BC_15

description: PolyA+ RNA


title: Mouse digit 12hr


title: Mouse digit 3hr


title: BC_11

description: PolyA+ RNA


title: HEK10cells_3

description: PolyA+ RNA

source_name: 10 cells, HEK293T, SMART-Seq2


title: HEK10cells_2

description: PolyA+ RNA


title: HEK10cells_1

description: PolyA+ RNA


title: HEK50cells_2

description: PolyA+ RNA

source_name: 50 cells, HEK293T, SMART-Seq2


title: HEK50cells_3

description: PolyA+ RNA


title: MEF_40

description: PolyA+ RNA

data_processing:
All reads were aligned to the human (hg19) or mouse (mm10) genomes using STAR (Dobin et al. 2013).
Non-uniquely mapped reads were removed.
Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE. Gene annotations used were transcripts in RefSeq (Feb 2013).
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene expression values (tab-delimited text file).

source_name: single cell, mouse embryonic fibroblast, SMART-Seq2

value: mouse embryonic fibroblast


title: HEK50cells_1

description: PolyA+ RNA


title: HEK100cells_2

description: PolyA+ RNA

source_name: 100 cells, HEK293T, SMART-Seq2


title: MEF_37

description: PolyA+ RNA


title: HEK100cells_3

description: PolyA+ RNA


title: MEF_38

description: PolyA+ RNA


title: MEF_39

description: PolyA+ RNA


title: ds_HEK_10pg_2

description: PolyA+ RNA

source_name: total RNA, 10pg, HEK293T, SMART-Seq2


title: HEK100cells_1

description: PolyA+ RNA


title: BC_10

description: PolyA+ RNA


title: MEF_33

description: PolyA+ RNA


title: MEF_35

description: PolyA+ RNA


title: ds_HEK_10pg_1

description: PolyA+ RNA


title: MEF_36

description: PolyA+ RNA


title: C2C12_13

description: PolyA+ RNA

source_name: single cell, C2C12, SMART-Seq2


title: BC_1

description: PolyA+ RNA


title: ds_HEK_100pg_4

description: PolyA+ RNA

source_name: total RNA, 100 pg, HEK293T, SMART-Seq2


title: C2C12_16

description: PolyA+ RNA


title: ds_HEK_100pg_3

description: PolyA+ RNA


title: C2C12_14

description: PolyA+ RNA


title: C2C12_10

description: PolyA+ RNA


title: ds_HEK_1ng_1

description: PolyA+ RNA

source_name: total RNA, 1ng, HEK293T, SMART-Seq2


title: ds_HEK_100pg_1

description: PolyA+ RNA


title: C2C12_12

description: PolyA+ RNA


title: ds_HEK_1ng_2

description: PolyA+ RNA


title: C2C12_9

description: PolyA+ RNA


title: HEK_SMRT_6

description: PolyA+ RNA

source_name: single cell, HEK293T, standard SMART-Seq

value: standard SMART-Seq


title: HEK_SMRT_1

description: PolyA+ RNA


title: HEK_SMRT_5

description: PolyA+ RNA


title: mouse stomach

city: Dallas

first: Gary

middle: Chung

last: Hon

state: TX

address: 5323 Harry Hines Blvd.

department: OB/GYN

institute: UT Southwestern

data_processing:
Reads were trimmed for adapter sequences and mapped with bowtie to the computationally bisulfite-converted mm9 genome as in Lister et al, Nature, 2009. After PCR duplicate removal with Picard, basecalls of cytosines in CpG context were tabulated as methylated or unmethylated (Phred score >= 20). The processed tables indicate the number of methylated cytosines, total sequencing depth, and %mCG for each CpG dinucleotide, combined over both Watson and Crick strands.
Genome Build:
stomach.CpG.calls.txt.gz: mm9

source_name: mouse stomach

extract_protocol: Purified genomic DNA was fragmented to an average size of 300bp with a Biorupter 300 (high power, 15s on, 15s off, 40 cycles). Spike in unmethylated lambda DNA control was added prior to sonication at 0.5% of total genomic DNA. DNA was end-repaired, adenylated, and ligated to methylated (5mC) adapters (Illumina) according to standard Illumina protocols for genomic DNA library construction, maintaining the proper molar ratios of adapter to insert. Adapter ligated fragments of size 200-650bp were gel purified by 2% agarose gel electrophoresis and sodium-bisulfite treated using the MethylCode kit (Invitrogen). Bisulfite treated adapter-ligated DNA was amplified by PCR with the following conditions in a 50uL final reaction volume:  2.5U PfuTurbo Cx Hotstart DNA polymerase, 5uL 10X PfuTurbo Cx reaction buffer, 0.75uL 20mM dNTPs, 5uL Illumina PCR Primers. Cycling parameters: 95ºC 5min, 98ºC 30 sec, followed by 8-11 cycles of 98ºC 15 sec, 60ºC 30 sec, 72ºC 4 min, and ending with 72ºC 10 min. The number of PCR cycles used was determined by quantification of bisulfite treated adapter-ligated DNA by qPCR (KAPABiosystems library quant kit for Illumina libraries) such that the final library concentration obtained was approximately 20nM. Final sequencing libraries were purified by 2% agarose gel electrophoresis and quantified by qPCR (KAPABiosystems library quant kit for Illumina libraries).

value: stomach

value: adult


title: HEK_98

description: PolyA+ RNA

source_name: single cell, HEK293T, SMART-Seq2 (variant 2)

value: SMART-Seq2 (variant 2)


title: mouse thymus

data_processing:
Reads were trimmed for adapter sequences and mapped with bowtie to the computationally bisulfite-converted mm9 genome as in Lister et al, Nature, 2009. After PCR duplicate removal with Picard, basecalls of cytosines in CpG context were tabulated as methylated or unmethylated (Phred score >= 20). The processed tables indicate the number of methylated cytosines, total sequencing depth, and %mCG for each CpG dinucleotide, combined over both Watson and Crick strands.
Genome Build:
thymus.CpG.calls.txt.gz: mm9

source_name: mouse thymus

value: thymus


title: mouse spleen

data_processing:
Reads were trimmed for adapter sequences and mapped with bowtie to the computationally bisulfite-converted mm9 genome as in Lister et al, Nature, 2009. After PCR duplicate removal with Picard, basecalls of cytosines in CpG context were tabulated as methylated or unmethylated (Phred score >= 20). The processed tables indicate the number of methylated cytosines, total sequencing depth, and %mCG for each CpG dinucleotide, combined over both Watson and Crick strands.
Genome Build:
spleen.CpG.calls.txt.gz: mm9

source_name: mouse spleen

value: spleen


title: mouse skin

data_processing:
Reads were trimmed for adapter sequences and mapped with bowtie to the computationally bisulfite-converted mm9 genome as in Lister et al, Nature, 2009. After PCR duplicate removal with Picard, basecalls of cytosines in CpG context were tabulated as methylated or unmethylated (Phred score >= 20). The processed tables indicate the number of methylated cytosines, total sequencing depth, and %mCG for each CpG dinucleotide, combined over both Watson and Crick strands.
Genome Build:
skin.CpG.calls.txt.gz: mm9

source_name: mouse skin

value: skin


title: ds_HEK_1ng_3

description: PolyA+ RNA


title: HEK_SMRT_3

description: PolyA+ RNA


title: HEK_99

description: PolyA+ RNA


title: mouse uterus

data_processing:
Reads were trimmed for adapter sequences and mapped with bowtie to the computationally bisulfite-converted mm9 genome as in Lister et al, Nature, 2009. After PCR duplicate removal with Picard, basecalls of cytosines in CpG context were tabulated as methylated or unmethylated (Phred score >= 20). The processed tables indicate the number of methylated cytosines, total sequencing depth, and %mCG for each CpG dinucleotide, combined over both Watson and Crick strands.
Genome Build:
uterus.CpG.calls.txt.gz: mm9

source_name: mouse uterus

value: uterus


title: mouse pancreas

data_processing:
Reads were trimmed for adapter sequences and mapped with bowtie to the computationally bisulfite-converted mm9 genome as in Lister et al, Nature, 2009. After PCR duplicate removal with Picard, basecalls of cytosines in CpG context were tabulated as methylated or unmethylated (Phred score >= 20). The processed tables indicate the number of methylated cytosines, total sequencing depth, and %mCG for each CpG dinucleotide, combined over both Watson and Crick strands.
Genome Build:
pancreas.CpG.calls.txt.gz: mm9

source_name: mouse pancreas

value: pancreas


title: mouse placenta

data_processing:
Reads were trimmed for adapter sequences and mapped with bowtie to the computationally bisulfite-converted mm9 genome as in Lister et al, Nature, 2009. After PCR duplicate removal with Picard, basecalls of cytosines in CpG context were tabulated as methylated or unmethylated (Phred score >= 20). The processed tables indicate the number of methylated cytosines, total sequencing depth, and %mCG for each CpG dinucleotide, combined over both Watson and Crick strands.
Genome Build:
placenta.CpG.calls.txt.gz: mm9

source_name: mouse placenta

value: placenta


title: mouse olfactory bulb

data_processing:
Reads were trimmed for adapter sequences and mapped with bowtie to the computationally bisulfite-converted mm9 genome as in Lister et al, Nature, 2009. After PCR duplicate removal with Picard, basecalls of cytosines in CpG context were tabulated as methylated or unmethylated (Phred score >= 20). The processed tables indicate the number of methylated cytosines, total sequencing depth, and %mCG for each CpG dinucleotide, combined over both Watson and Crick strands.
Genome Build:
olfactory_bulb.CpG.calls.txt.gz: mm9

source_name: mouse olfactory bulb

value: olfactory bulb


title: HEK_84

description: PolyA+ RNA

source_name: single cell, HEK293T, SMART-Seq2


title: mouse lung

data_processing:
Reads were trimmed for adapter sequences and mapped with bowtie to the computationally bisulfite-converted mm9 genome as in Lister et al, Nature, 2009. After PCR duplicate removal with Picard, basecalls of cytosines in CpG context were tabulated as methylated or unmethylated (Phred score >= 20). The processed tables indicate the number of methylated cytosines, total sequencing depth, and %mCG for each CpG dinucleotide, combined over both Watson and Crick strands.
Genome Build:
lung.CpG.calls.txt.gz: mm9

source_name: mouse lung

value: lung


title: HEK_79

description: PolyA+ RNA

source_name: single cell, HEK293T, SMART-Seq2 (variant 3)

value: SMART-Seq2 (variant 3)


title: HEK_97

description: PolyA+ RNA


title: mouse intestine

data_processing:
Reads were trimmed for adapter sequences and mapped with bowtie to the computationally bisulfite-converted mm9 genome as in Lister et al, Nature, 2009. After PCR duplicate removal with Picard, basecalls of cytosines in CpG context were tabulated as methylated or unmethylated (Phred score >= 20). The processed tables indicate the number of methylated cytosines, total sequencing depth, and %mCG for each CpG dinucleotide, combined over both Watson and Crick strands.
Genome Build:
intestine.CpG.calls.txt.gz: mm9

source_name: mouse intestine

value: intestine


title: HEK_69

description: PolyA+ RNA


title: mouse kidney

data_processing:
Reads were trimmed for adapter sequences and mapped with bowtie to the computationally bisulfite-converted mm9 genome as in Lister et al, Nature, 2009. After PCR duplicate removal with Picard, basecalls of cytosines in CpG context were tabulated as methylated or unmethylated (Phred score >= 20). The processed tables indicate the number of methylated cytosines, total sequencing depth, and %mCG for each CpG dinucleotide, combined over both Watson and Crick strands.
Genome Build:
kidney.CpG.calls.txt.gz: mm9

source_name: mouse kidney

value: kidney


title: HEK_67

description: PolyA+ RNA


title: mouse heart

data_processing:
Reads were trimmed for adapter sequences and mapped with bowtie to the computationally bisulfite-converted mm9 genome as in Lister et al, Nature, 2009. After PCR duplicate removal with Picard, basecalls of cytosines in CpG context were tabulated as methylated or unmethylated (Phred score >= 20). The processed tables indicate the number of methylated cytosines, total sequencing depth, and %mCG for each CpG dinucleotide, combined over both Watson and Crick strands.
Genome Build:
heart.CpG.calls.txt.gz: mm9

source_name: mouse heart

value: heart


title: HEK_66

description: PolyA+ RNA

source_name: single cell, HEK293T, SMART-Seq2 (variant 4)

value: SMART-Seq2 (variant 4)


title: mouse cortex

data_processing:
Reads were trimmed for adapter sequences and mapped with bowtie to the computationally bisulfite-converted mm9 genome as in Lister et al, Nature, 2009. After PCR duplicate removal with Picard, basecalls of cytosines in CpG context were tabulated as methylated or unmethylated (Phred score >= 20). The processed tables indicate the number of methylated cytosines, total sequencing depth, and %mCG for each CpG dinucleotide, combined over both Watson and Crick strands.
Genome Build:
cortex.CpG.calls.txt.gz: mm9

source_name: mouse cortex

value: cortex


title: mouse colon

data_processing:
Reads were trimmed for adapter sequences and mapped with bowtie to the computationally bisulfite-converted mm9 genome as in Lister et al, Nature, 2009. After PCR duplicate removal with Picard, basecalls of cytosines in CpG context were tabulated as methylated or unmethylated (Phred score >= 20). The processed tables indicate the number of methylated cytosines, total sequencing depth, and %mCG for each CpG dinucleotide, combined over both Watson and Crick strands.
Genome Build:
colon.CpG.calls.txt.gz: mm9

source_name: mouse colon

value: colon


title: HEK_64

description: PolyA+ RNA


title: HEK_82

description: PolyA+ RNA


title: mouse liver

data_processing:
Reads were trimmed for adapter sequences and mapped with bowtie to the computationally bisulfite-converted mm9 genome as in Lister et al, Nature, 2009. After PCR duplicate removal with Picard, basecalls of cytosines in CpG context were tabulated as methylated or unmethylated (Phred score >= 20). The processed tables indicate the number of methylated cytosines, total sequencing depth, and %mCG for each CpG dinucleotide, combined over both Watson and Crick strands.
Genome Build:
liver.CpG.calls.txt.gz: mm9

source_name: mouse liver

value: liver

value: adult


title: HEK_62

description: PolyA+ RNA

data_processing:
All reads were aligned to the human (hg19) or mouse (mm10) genomes using STAR (Dobin et al. 2013).
Non-uniquely mapped reads were removed.
Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE. Gene annotations used were transcripts in RefSeq (Feb 2013).
Genome_build: GRCh37
Supplementary_files_format_and_content: Gene expression values (tab-delimited text file).


title: HEK_63

description: PolyA+ RNA


title: HEK_65

description: PolyA+ RNA


title: HEK_70

description: PolyA+ RNA


title: HEK_56

description: PolyA+ RNA


title: HEK_39

description: PolyA+ RNA


title: HEK_38

description: PolyA+ RNA


title: HEK_58

description: PolyA+ RNA


title: HEK_57

description: PolyA+ RNA


title: HEK_124

description: PolyA+ RNA

source_name: single cell, HEK293T, SMART-Seq2 (variant 2)

value: SMART-Seq2 (variant 2)


title: mouse cerebellum

data_processing:
Reads were trimmed for adapter sequences and mapped with bowtie to the computationally bisulfite-converted mm9 genome as in Lister et al, Nature, 2009. After PCR duplicate removal with Picard, basecalls of cytosines in CpG context were tabulated as methylated or unmethylated (Phred score >= 20). The processed tables indicate the number of methylated cytosines, total sequencing depth, and %mCG for each CpG dinucleotide, combined over both Watson and Crick strands.
Genome Build:
cerebellum.CpG.calls.txt.gz: mm9

source_name: mouse cerebellum

value: cerebellum


title: HEK_55

description: PolyA+ RNA


title: HEK_40

description: PolyA+ RNA


title: HEK_123

description: PolyA+ RNA


title: HEK_35

description: PolyA+ RNA


title: HEK_122

description: PolyA+ RNA


title: HEK_120

description: PolyA+ RNA


title: HEK_108

description: PolyA+ RNA

source_name: single cell, HEK293T, SMART-Seq2 (variant 1)

value: SMART-Seq2 (variant 1)


title: HEK_114

description: PolyA+ RNA


title: HEK_113

description: PolyA+ RNA


title: HEK_106

description: PolyA+ RNA


title: wild-type_ChIPSeq

city: beijing

first: xiaoquan

last: zhu

address: N01 dahua road dongdan beijing

institute: beijing hospital

description: Chromatin IP against tnni2

data_processing: Raw reads were aligned with the mouse reference 8 using Bowtie software and viewed with the IGV browser.

source_name: osteoblast

growth_protocol: The primary osteoblasts of Tnni2del175k/175k mice and wild-type littermates was used for ChiP-Seq

extract_protocol: The part of ChIP assays in ChIP-seq study are performed as the protocol of this paper, Schmidt, D. et al., ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 48 (3), 240-248 (2009).

tag: genotype/variation

value: wild type

tag: vendor

value: Santa Cruz biotechnology

value: primary osteoblast


title: del175k mutant_ChIPSeq

description: Chromatin IP against tnni2

value: del175k mutant


title: mouse bone marrow

data_processing:
Reads were trimmed for adapter sequences and mapped with bowtie to the computationally bisulfite-converted mm9 genome as in Lister et al, Nature, 2009. After PCR duplicate removal with Picard, basecalls of cytosines in CpG context were tabulated as methylated or unmethylated (Phred score >= 20). The processed tables indicate the number of methylated cytosines, total sequencing depth, and %mCG for each CpG dinucleotide, combined over both Watson and Crick strands.
Genome Build:
bone_marrow.CpG.calls.txt.gz: mm9

source_name: mouse bone marrow

value: bone marrow


title: HEK_102

description: PolyA+ RNA


title: HEK_101

description: PolyA+ RNA


title: HEK_100

description: PolyA+ RNA


title: HEK_103

description: PolyA+ RNA


title: 822_MCF-10A

city: Duarte

first: Xiwei

last: Wu

address: 1500 E Duarte Rd

department: Molecular and Cellular Biology

institute: Beckman Research Institute

data_processing:
Sequenced reads from Solexa were first mapped onto human genome version hg18 using novoalign software and the expression level of mature miRNAs in the miRBase human miRNA database v15 was summarized.
Normalization and identification of differentially expressed miRNAs between groups were carried out using Bioconductor package “edgeR”.
genome build: hg18
Log2 transformed Quantile Normlaized counts

source_name: cell

growth_protocol: MDA-MB-231 cells were grown in DMEM plus 10% FBS.  MCF-10A cells were grown in DMEM/F12 (1:1) supplemented with 5% horse serum, 10 ug/ml insulin, 20 ng/ml EGF, 0.1 ug/ml Cholera Toxin and 0.5 ug/ml Hydrocortisone.

extract_protocol:
TRIZOL reagent (Invitrogen) and TRIZOL LS reagent (Invitrogen) were used to extract total RNA from cells and exosomes, respectively, following the manufacturer’s protocols.  RNA pellet was dissolved in RNase-free water, and subjected to library construction and deep sequencing.
Each sample was independently subjected to library preparation and deep sequencing. All small RNAs of 15–52 nts were selected and sequenced using the Solexa system, following the manufacturer’s protocol (Illumina Inc., San Diego, CA). Library preparation, as well as cluster generation and deep sequencing, was performed according to the 5' ligation-dependent (5′ monophosphate-dependent) manufacturer’s protocol (Digital Gene Expression for small RNA; Illumina). Small RNAs were size-selected between 17 and 52 nt according to the single-stranded DNA marker in the small RNA sequencing kit (Illumina). The library was quantified using picoGreen and qPCR. Sequencing was performed on a Genome Analyzer IIx (Illumina), and image processing and base calling were conducted using Illumina’s pipeline.


title: HEK_107

description: PolyA+ RNA


title: 749_MCF-10A

source_name: exosome


title: 841_MDA-MB-231


title: Brain

city: Aarhus

first: Morten

middle: Muhlig

last: Nielsen

address: Palle Juul-Jensens Bouleward 99

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University

description: Normal tissue provided by Biochain

data_processing:
Illumina Casava software used for basecalling, and Tophat and Cufflinks used for transcript FPKM estiamtes.
Genome_build: hg18
Supplementary_files_format_and_content: Total transcript FPKM values in the GTF file format

extract_protocol:
Normal tissue provided by Biochain. Total RNA was isolated by a modified guanidine thiocyanate technique according to BioCahin certificate of analysis F-753-1-6 revA.
Using 500 ng of total-RNA from each of the samples, RNA-Seq libraries were constructed by depletion of rRNA followed by synthesis of directional, paired-end and indexed RNA-Seq libraries. The rRNA depleted RNA was purified using the RNA Clean & Concentrator™-5 columns (Zymo Research). Speed-vac was used to reduce the remaining sample volume to 9.5μL followed by synthesis of directional, paired-end and indexed RNA-Seq libraries using the ScriptSeq kit (Epicentre). Briefly, rRNA depleted RNA was chemically fragmented and cDNA was synthesized from a tagged random hexamer. The cDNA was terminal tagged using a 3’-end blocked and tagged oligo followed by MiniElute (Qiagen) purification. The di-tagged cDNA was then used as template in a 10 cycle PCR reaction. Libraries were purified by agarose gel electrophoresis selecting elements of 200-600 bp in size. The RNA-Seq libraries were denaturated and diluted to 10 pM with pre-chilled Hybridization buffer (Illumina) and loaded into TruSeq PE v3 flowcells (Illumina) on an Illumina cBot followed by indexed paired-end sequencing (101+7+101 bp) on a Illumina HiSeq 2000 using TruSeq SBS Kit v3 chemistry.

value: brain


title: Kidney

description: Normal tissue provided by Biochain


title: Muscle

description: Normal tissue provided by Biochain

value: muscle


title: Prostate

description: Normal tissue provided by Biochain

value: prostate


title: Heart

description: Normal tissue provided by Biochain

value: heart


title: Ovary

description: Normal tissue provided by Biochain

value: ovary