title: Avicel rep3

city: Madison

first: Dan

last: Cullen

state: WI

address: One Gifford Pinchot Dr

institute: UW/FPL

description: processed data column name: run242.Avi3_ATCACG_L001_R1

data_processing:
Cluster generation was performed using a TruSeq Single Read Cluster Kit (v3) and the Illumina cBot.
Images were analyzed using CASAVA version 1.8.2 and FASTQ files generated.
RPKM generated. DNAStar Inc (Madison, WI) modules SeqNGen and Qseq were used for mapping reads and statistical analysis.
Final fastq files processed using DNASTAR modules SeqNGen and Qseq
Genome_build: DoE Joint Genome Institute version 1 at http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=Wolco1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample. Values for 12746 transcript models (Seq_ID column) predicted by the DoE JGI automated pipeline. Ratios and probabilites computed for pairwise comparison of all substrates. Corresponding protein models and InterPro domains also listed.

organism: Wolfiporia cocos

source_name: Avicel medium

growth_protocol: Cultures of 250 ml basal salts contained 0.5% (w/v) wiley-milled (1mm mesh) Populus grandidentata (aspen) or Pinus contorta (lodgepole pine) as sole carbon source. Avicel (Fluka Chemika), a microcrystalline cellulose (MCC), or glucose (Glc) served as carbon source in defined media. Triplicate cultures for each medium were inoculated with mycelia scraped from agar plates. Cultures were harvested by filtration after 5 days incubation on a rotary shaker as described.

extract_protocol:
Extraction buffer was prepared by combining 10 ml 690 mM para-aminosalicylic acid (sodium salt) (Sigma-Aldrich, St. Louis, MO) with 10 ml 56 mM triisopropylnapthalene sulfonic acid (sodium salt) (Sigma-Aldrich), and placed on ice. To this was added 5 ml 5X RNB (1.0 M Tris, 1.25 M NaCl, 0.25 M EGTA). The pH of the 5X RNB was adjusted to 8.5 with NaOH. The mixture was kept on ice and shaken just before use. Frozen fungal pellets were ground to a fine powder with liquid nitrogen in an acid washed, pre-chilled mortar and pestle. The ground mycelia were transferred to Falcon 2059 tubes (VWR International, West Chester, PA), and extraction buffer was added to make a thick slurry. The samples were vortexed vigorously and placed on ice until all samples were processed.  One half volume TE-saturated phenol (Sigma-Aldrich) and ¼ volume chloroform (Sigma-Aldrich) were added to each sample and vortexed vigorously.  Samples were spun at 2940 x g in a fixed-angle rotor for 5 minutes.  The aqueous layer was removed to a new tube, and phenol:chloroform extractions were repeated until the interface between the aqueous and organic layers was clear. The final aqueous extractions were placed in clean 2059 tubes, to which was added 0.1 volume 3M sodium acetate, pH 5.2, (DEPC-treated) and 2 volumes absolute ethanol. The tubes were shaken vigorously and stored overnight at -20˚C.  The tubes were spun 1 hour at 2940 x g, the supernatants were decanted, and the pellets were resuspended in 4 ml RNase-free H2O. Total RNA was purified using the RNeasy Maxi kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol for RNA cleanup. RNAs were eluted from the RNeasy spin columns using two spins, for a final volume of 2 ml. The eluted RNAs were ethanol precipitated and stored overnight at -20˚C.
Messenger RNA was purified from 1μg total RNA using poly-T oligo-attached magnetic beads. Double-stranded cDNAs were synthesized using SuperScript II (Invitrogen, Carlsbad, California, USA) and random primers for first strand cDNA synthesis followed by second strand synthesis using DNA polymerase I and RNAse H for removal of mRNA. Double-stranded cDNA was purified using Agencourt AMPure XP beads (Qiagen, Valencia, California, USA) as recommended in the TruSeq RNA Sample Prep Guide. cDNAs were end-repaired by T4 DNA polymerase and Klenow DNA polymerase and phosphorylated with T4 polynucleotide kinase. The blunt ended cDNA was purified using Agencourt AMPure XP beads. The cDNA products were incubated with Klenow DNA polymerase to add an ‘A’ base (Adenine) to the 3’ end of the blunt phosphorylated DNA fragments and then purified using Agencourt AMPure XP beads. DNA fragments were ligated to Illumina adapters having a single ‘T’ base (Thymine) overhang at their 3’end. The adapter-ligated products were purified using Agencourt AMPure XP beads. Adapter ligated DNA was amplified in a Linker Mediated PCR reaction (LM-PCR) for 15 cycles using PhusionTM DNA polymerase and Illumina's PE genomic DNA primer set and then purified using Agencourt AMPure XP beads. Quality and quantity of the finished libraries were assessed using an Agilent DNA1000 series chip assay (Agilent Technologies, Santa Clara, CA) and Invitrogen Qubit HS Kit (Invitrogen, Carlsbad, California, USA), respectively, and libraries standardized to 2 μM.

tag: carbon source

value: Avicel


title: Aspen rep3

status: Public on Apr 13 2016

type: SRA

country: USA

description: processed data column name: run242.Asp3_TTAGGC_L002_R1

library_source: transcriptomic

molecule: total RNA

source_name: Aspen medium

tag: strain

value: Aspen


title: Lodgepole rep2

description: processed data column name: run242.Lop2_TGACCA_L002_R1

source_name: Lodgepole pine medium

value: Lodgepole


title: 27207 (RR 2 Gy 14 d) rep1

city: Bellaterra

first: Mireia

last: Borràs-Fresneda

address: s/n

country: Spain

institute: Universitat Autònoma de Barcelona

description: irradiated 14 d

data_processing:
Illumina Casava 1.8 software used for basecalling
Sequenced reads were trimmed in order to improve the percentage of mapped reads. Then, reads were aligned to the hg19 using TopHat2 splice-junction mapper (version 2.1.0)
Mapped reads were categorised with htseq-count (HTseq version 0.6.1). Deffault settings were applied with the exception of the overlap resolution mode, where the intersection-noempty mode was used
Normalisation was performed using the default method for edgeR (version 3.10.2), then a matrix was designed and the dispersion values were estimated using Cox-Reid profile-adjusted likelihood method
The generalised linear model likelihood ratio test was used to determine differential expression also with edgeR package. Fold-changes were reported as the log (base 2) of normalized count abundance of the irradiated samples divided by count abundance for the sham-irradiated samples. P values for each gene were then corrected for multiple comparisons using Benjamini & Hochberg false discovery rate
Genome_build: hg19
Supplementary_files_format_and_content: csv files that include reads counts for each sample and different expression results for irradiated versus sham-irradiated samples

organism: Homo sapiens

source_name: lymphocytes

extract_protocol:
Total RNA was extracted using the SPLIT RNA Extraction kit. RNA concentration and purity for each sample were verified as well as RNA integrity
Libraries were prepared according the Lexogen Quantseq 3’ mRNA-Seq Library Prep kit for Illumina following the manufacturer's instructions

tag: cell type

value: lymphoblastoid cell line

tag: cell line

value: radioresistant (RR)

tag: treatment

value: irradiated

tag: time point


title: SN6

city: Beibei

first: Zhi-Liang

last: Zheng

state: Chongqing

address: 15 Ganjuchun

department: Citrus Research Institute

country: China

institute: Southwest University

description: Rep. 3

data_processing:
Basecalls performed by BGI company.
Raw data were preprocessed by removing adaptor sequences and/or low quality reads, resulting in clean reads data.
These clean reads data were then mapped to the sweet orange reference sequences (version 2.0) published in 2013
Genome_build: Sweet orange version 2.0. http://citrus.hzau.edu.cn/orange/  Publication of reference genome: http://www.ncbi.nlm.nih.gov/pubmed/23179022
Supplementary_files_format_and_content: excel files were generated with geneID and raw count.

organism: Citrus sinensis

source_name: Fruit tissue

growth_protocol: Field grown trees

extract_protocol:
Fruits were harvested, and total RNA was extracted using the ethanol- and LiCl-based protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: fruit

tag: fruit stage

value: 142 DPA

tag: cultivar

value: Newhall

tag: fruit acidity

value: Acidic


title: 27206 (RS 2 Gy 14 d) rep1

description: irradiated 14 d

value: radiosensitive (RS)


title: H3.F/F_NGS-6288

city: South Mimms

first: Theo

last: Kantidakis

address: Blanche Lane

department: Clare Hall Laboratories

country: United Kingdom

institute: Francis Crick Institute

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to the mm10 version of the mouse genome assembly using BWA v0.7.10 with default settings.
Mapped reads were extended 3' to a size of 200bp in a strand-specific manner.
Reads Per Kilobase Million (RPKM) scores were calculated for each sample across all Refseq transcripts +/- 500bp.
Peaks were called against a control using MACS v1.4.2 with the following settings: --gsize (mm), --mfold (8,30), --pvalue (0.00001). gH2AX peaks were called against an H3 control, while RNAPII peaks were called against an IgG control.
Genome_build: mm10
Supplementary_files_format_and_content: RPKM scores calculated for each sample across all Refseq transcripts +/- 500bp (tab-delimited text file).  ChIP-seq peaks called by MACS (bed file).

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
Cells were cross-linked with  1% formaldehyde. Nuclei were extracted in low salt conditions and burst in high salt before shearing the DNA to reduce the size to ~400 bp and performing ChIP with the appropriate antibodies.
DNA libraries were prepared according to Illumina's standard instructions.

value: Immortalized Mouse Embryonic Fibroblast (MEF) cells in which both Mll2 alleles had been targeted by loxP (F/F cells)

tag: resulting cell type

value: MLL2 F/F cells

tag: chip antibody

value: anti-H3 (Abcam, catalog# ab1791)


title: 27199 (RR 0 Gy 4 h) rep1

description:
sham-irradiated 4 h
Differential_expression_RR_4h.csv

value: sham-irradiated

value: 4 h


title: SN4

description: Rep. 2


title: H3.FC/FC_NGS-3397

value: 24 hours exposure to tamoxifen

value: MLL2 FC/FC MEF cells


title: 27198 (RS 0 Gy 4 h) rep1

description:
sham-irradiated 4 h
Differential_expression_RS_4h.csv


title: Avicel rep2

description: processed data column name: run242.Avi2_GTGGCC_L001_R1

value: Avicel


title: gH2AX.F/F_NGS-6268

value: anti-gH2AX (Abcam, catalog# ab2893)


title: SN2

description: Rep. 1


title: Aspen rep2

description: processed data column name: run242.Asp2_CGATGT_L002_R1

value: Aspen


title: Glucose rep3

description: processed data column name: run242.Gluc3_GTGAAA_L001_R1

source_name: Glucose medium

value: Glucose medium


title: SB6

description: Rep. 3

value: Bingtang

value: Low acid


title: SZ-1 miR-9 OE1

city: New York

first: Kristen

last: Brennand

state: NY

address: 1425 Madison Ave, 9-20B

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

description: 1835#1 NPC#3 MDH-miR-9 OE a

data_processing:
The Illumina TruSeq RNA kit was used for 100nt/paired end reads, 8 samples were run per lane using the standard Truseq indices.  Raw cDNA reads are aligned to the hg19 reference with the spliced gap aligner STAR, with count-based quantitation carried out via the Subread package featureCounts at geneic level for UCSC annotation build.
Genome_build: hg19
Supplementary_files_format_and_content: txt format; the read count for each gene

source_name: SZ_hiPSC forebrain NPCs

growth_protocol: hiPSC forebrain NPCs were derived as described previously (Brennand et al., 2011). Forebrain NPCs were maintained at high density, grown on Matrigel-coated plates in NPC media (DMEM/F12, 1x N2, 1x B27-RA (Invitrogen), and 20 ng/ml FGF2 (Invitrogen)) and split approximately 1:3-1:4 every week with Accutase (Millipore).

extract_protocol:
Total RNA was purified using the miRNeasy Mini Kit (Qiagen), treated on the column with RNAse-free DNAse Kit (Qiagen) and eluted in water.
RNA libraries were prepared for sequencing using standard Illumina protocols (rRNA depleted (ribozero)).
Hi-Seq, 100nt, Paired-End Read, 8 samples per lane

tag: patient id

tag: diagnosis

value: Schizophrenia (SZ)

tag: gender

value: female

tag: repository source fibroblast id

value: forebrain neural progenitor cells (NPCs)

tag: transduced with


title: gH2AX.F/F_NGS-3388


title: SZ-1 miR-9 OE2

description: 1835#1 NPC#3 MDH-miR-9 OE b


title: gH2AX.F/F_NGS-3400


title: Lodgepole rep3

description: processed data column name: run242.Lop3_GAGTGG_L002_R1

tag: carbon source

value: Lodgepole


title: SZ-1 WT3 (MDH)

description: 1835#1 NPC#3 MDH-GFP b

value: RV GFP


title: SZ-1 WT2 (MDH)

description: 1835#1 NPC#3MDH-GFP a


title: SB2

description: Rep. 1

value: fruit

value: 142 DPA


title: gH2AX.FC/FC_NGS-6273

value: Immortalized Mouse Embryonic Fibroblast (MEF) cells in which both Mll2 alleles had been targeted by loxP (F/F cells)


title: Lodgepole rep1

description: processed data column name: run242.Lop1_CGTACG_L002_R1

tag: strain


title: SA6_A6R1

description: Rep. 3

value: Succari

value: Acidless


title: gH2AX.FC/FC_NGS-3406

tag: cell type

value: 24 hours exposure to tamoxifen

value: MLL2 FC/FC MEF cells


title: gH2AX.FC/FC_NGS-3394

value: anti-gH2AX (Abcam, catalog# ab2893)


title: Avicel rep1

description: processed data column name: run242.Avi1_ATTCCT_L001_R1

value: Avicel


title: SA2_A2R1

description: Rep. 2


title: Glucose rep2

description: processed data column name: run242.Gluc2_ACTGAT_L001_R1

value: Glucose medium


title: SZ-1 miR-9 KD

description: 1835#1 NPC#3 miR-9 KD

tag: transfected with

value: miR-9 LNA probes (miR-9 KD)


title: SZ-1 WT1 (scr)

description: 1835#1 NPC#3 SCRAMBLED

value: scrambled control


title: Aspen rep1

description: processed data column name: run242.Asp1_GTTTCG_L002_R1

value: Aspen


title: Glucose rep1

description: processed data column name: run242.Gluc1_GTCCGC_L001_R1


title: SB4

description: Rep. 2

value: Bingtang

value: Low acid


title: JX4

description: Rep. 3

value: 45 DPA

value: Xinhui

value: Acidic


title: SZ-2 WT (scr)

description: 2038#1 NPC#A SCRAMBLED

value: Schizophrenia (SZ)

value: male

value: forebrain neural progenitor cells (NPCs)


title: JX2

description: Rep. 1

value: fruit


title: CC-1 miR-9 OE1

description: 9319#2 NPC#A MDH-miR-9 OE a

source_name: control_hiPSC forebrain NPCs

value: Control

value: female


title: CC-1 miR-9 OE2

description: 9319#2 NPC#A MDH-miR-9 OE b


title: MSCV-expressing STAT3 knockout astrocytes

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description:
MSCV-expressing STAT3 knock-out astrocytes
sample 12

data_processing:
Reads processed with CASAVA.
Reads mapped with tophat (v1.2.0)
Transcripts assembled with cufflinks (v0.9.3)
Genome build:  mm9
Supplementary files format and content: Tab-delimited .txt file containing gene symbols, gene locations and FPKM expression values

source_name: Astrocyte cell line

growth_protocol: Glial cells were grown in DMEM media supplied with 10% FBS. Brain tumor Stem cells were grown in BTSC media according to manufacturer instructions.

extract_protocol:
Total RNA was isolated using the RNeasy kit (Qiagen).
The quality of RNA was assessed by bioanalyzer prior to sequencing. Libraries were prepared according to Illumina protocols.

treatment_protocol: No specific tratment was carried out on any of the cells prior to harvesting them for ChIP-Seq or RNA-Seq studies.

tag: cell line

value: Astrocyte

tag: derivation

value: MSCV-expressing astrocytes were established as previously described (de La Iglesia et al 2008, Genes and Dev, 22(4):449-62.).

tag: genotype/variation

value: MSCV-expressing STAT3 knockout


title: JX3

description: Rep. 2

tag: tissue

tag: fruit stage


title: control-ChIP-Rabbit-IgG_EGFRvIII expressing astrocytes

description:
EGFRvIII expressing astrocytes were subject to ChIP-Seq using an IgG antibody
sample 14

data_processing:
Reads processed with CASAVA
Reads mapped with bowtie
Peaks called with BayesPeak (R package)
Genome build:  mm9
Supplementary files format and content: BED files for peak locations
Supplementary files format and content: The .txt file reports the following: 16,078 negative peaks were called by BayesPeak with flipped STAT3 ChIP-Seq dataset and IgG ChIP-Seq dataset and represent genomic regions enriched by IgG compared to the STAT3 antibody. Of these, 7,672 negative peaks with identical length distribution as STAT3 peaks were randomly selected from the total negative peak pool and included in this study as negative control.

extract_protocol:
Chromatin was immunoprecipitated using rabbit IgG (Millipore, Cat # 12-370). Antibody–protein–DNA complexes were collected, washed and eluted and the crosslinks were reversed
The quality of RNA was assessed by bioanalyzer prior to sequencing. Libraries were prepared according to Illumina protocols.

value: EGFRvIII-expressing astrocytes were established as previously described (de La Iglesia et al 2008, Genes and Dev, 22(4):449-62.).

value: EGFRvIII expressing

value: IgG (Millipore, Cat # 12-370)


title: STAT3-ChIP_EGFRvIII expressing astrocytes

description:
EGFRvIII expressing astrocytes were subject to ChIP-Seq using a Stat3 antibody.
sample 13

data_processing:
Reads processed with CASAVA
Reads mapped with bowtie
Peaks called with BayesPeak (R package)
Genome build:  mm9
Supplementary files format and content: BED files for peak locations

extract_protocol:
Chromatin was immunoprecipitated using a ChIP-grade STAT3 antibody (Cell Signaling Technology, Cat# 9132) Antibody–protein–DNA complexes were collected, washed and eluted and the crosslinks were reversed
The quality of RNA was assessed by bioanalyzer prior to sequencing. Libraries were prepared according to Illumina protocols.


title: MSCV-expressing STAT3 floxed astrocytes

description:
MSCV-expressing STAT3 floxed astrocytes
sample 11

value: MSCV-expressing STAT3 floxed


title: JN4

description: Rep. 3

tag: cultivar

value: Newhall

tag: fruit acidity


title: EGFRvIII-expressing STAT3 knockout astrocytes

description:
EGFRvIII-expressing STAT3 knock-out astrocytes
sample 10

value: EGFRvIII-expressing STAT3 knockout


title: CC-1 WT3 (MDH)

description: 9319#2 NPC#A MDH-GFP b

value: RV GFP


title: CC-1 WT2 (MDH)

description: 9319#2 NPC#A MDH-GFP a


description:
EGFRvIII-expressing STAT3 floxed astrocytes
sample 9

value: EGFRvIII-expressing STAT3 floxed


title: BTSC90_EGFRvIII positive BTSC

description: sample 7

data_processing:
Reads processed with CASAVA v1.8.2 to generate fastq
Reads mapped with tophat (v2.0.0)
Transcripts assembled with cufflinks (v2.0.0)
Genome build:  hg19
Supplementary files format and content: Tab-delimited .txt file containing gene symbols, gene locations and FPKM expression values

source_name: Glioblastoma

value: Glioblastoma

value: Cell line generated by culture of surgically excised tumor in defined culture media

value: EGFRvIII positive


title: CC-1 miR-9 KD

description: 9319#2 NPC#A miR-9 KD

value: forebrain neural progenitor cells (NPCs)

value: miR-9 LNA probes (miR-9 KD)


title: CC-1 WT1 (scr)

description: 9319#2 NPC#A SCRAMBLED

value: Control

value: female

value: scrambled control


title: BTSC73_EGFRvIII positive BTSC

description: sample 6


title: SZ-2 miR-9 KD

description: 2038#1 NPC#A miR-9 KD

value: Schizophrenia (SZ)

value: male


title: nLC-HFSCs_IgG_ctrl

city: Houston

first: Jayhun

last: Lee

state: TX

address: 6431 Fannin St. MSE R222

department: Microbiology and Molecular Genetics

institute: The University of Texas Health Science Center at Houston

data_processing:
FASTX barcode splitter to split multiplexed samples
Trimmomatic tool (v0.22) to clip out adapter sequences
FASTQ quality filter to filter out low quality reads
Bowtie2 to align reads to mm9 genome assembly
BamTools to filter aligned reads
MACS and HOMER used for peak calling
Combining and merging of all MACS peaks from all samples into a customized non-overlapping genomic annotation
Quantification of reads using HOMER or Cuffdiff on pre-annotated genomic location as well as on a customized non-overlapping annotation
Genome_build: mm9
Supplementary_files_format_and_content: Reads aligned with Bowtie2 were filtered with BamTools to generate bam files

source_name: Mouse skin

extract_protocol:
15-20 mice of CD1 x FVB wild-type strain between PD22-25 (early anagen, anagen I-IIIa) and PD38-44 (late catagen, catagen VII-VIII) were used. ~3-4 million bulge and non-bulge cell nuclei were isolated and treated with microccoccal nuclease (MNase) (50U, Affymetrix) (~12min, room temperature) to generate mono-nucleosomal fragments. Isolated chromatin was processed further for immunoprecipitation. Eluted ChIP DNA were used for sequencing library generation.
ChIP DNA was quantified using Quant-iT dsDNA HS reagent (Invitrogen). Nanograms of ChIP DNA for each sample were processed using following steps: 1) end-repair using End-It DNA End-Repair Kit (Epicentre Biotechnologies), 2) addition of single A-base using Klenow Fragment (3’->5’ exo-) (New England Biolabs) and dATP (Invitrogen), 3) ligation of barcoded adapters to A-overhang (Enzymatics), 4) gel purification using SYBR gold (Invitrogen) and low Tm agarose gel, 5) PCR enrichment (13-14 cycles) using Phusion Polymerase (New England Biolabs), 6) PCR purify using AMPure kit (Agencourt), 7) native acrylamide gel purification, 8) PCIAA (Phenol-Chloroform-Isoamylalchol) extraction, and 9) ethanol precipitation. Purified DNA samples were measured in their quality and quantity using bioanalyzer before sequencing at the Cornell University Institute for Biotechnology.

value: CD1 x FVB

value: Male

tag: age

tag: sorting markers

value: CD34- / α6-integrin+

tag: chip antibody

value: IgG (Cell Signaling)


title: JN2

description: Rep. 1

value: fruit

value: 45 DPA

value: Newhall

value: Acidic


title: JB3

description: Rep. 3

value: Bingtang

value: Low acid


title: SA1_A1R1

description: Rep. 1

value: 142 DPA

value: Succari

value: Acidless


title: CC-2 miR-9 KD

description: 3440#5 NPC#A miR-9 KD

tag: patient id

tag: diagnosis

value: Control

tag: gender

value: forebrain neural progenitor cells (NPCs)

value: miR-9 LNA probes (miR-9 KD)


title: BTSC68_EGFRvIII positive BTSC

description: sample 5

value: Glioblastoma

value: Cell line generated by culture of surgically excised tumor in defined culture media

value: EGFRvIII positive


title: JB2

description: Rep. 2


title: nLC-HFSCs_H3K27me3

value: CD1 x FVB

value: Male

value: CD34- / α6-integrin+

value: H3K27me3 (Millipore)


title: JN3

description: Rep. 2

value: fruit

value: 45 DPA

value: Newhall


title: CC-2 WT (scr)

description: 3440#5 NPC#A SCRAMBLED

value: male

tag: repository source fibroblast id

value: scrambled control


title: BTSC41_EGFRvIII negative BTSC

description: sample 8

value: EGFRvIII negative


title: nLC-HFSCs_H3K4me3

tag: strain

value: H3K4me3 (ActiveMotif)


title: JA4

description: Rep. 3

value: Succari

value: Acidless


title: JA3

description: Rep. 2


title: 5 RNA mix control 12h : replicate 1

first: Gad

last: Shaulsky

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
After demultiplexing, the data was mapped to the D. discoideum genome with bowtie version 0.12.7. Read qualities were used. Other parameters: seed length = 28, allowed mismatches = 2, allowed up to 1 alignment per read, with bowtie options -a, --strata, --best. Unmapped reads were trimmed from 3' by 2 nucleotides, which was repeated 5 times.
Raw expression values were computed as the number of reads that were uniquely mapped to gene exons.
Normalized expression were scaled with mappable exon lengths. This normalization is similar to the RPKM normalization (Reads Per Kilobase of exon per Megabase of library size), but instead of dividing by exon lengths we used the uniquely mappable parts of the exon. To obtain uniquely mappable parts, all possible subsequences of the reference genome (of the same length as reads in raw data) are mapped back to the reference genome, obtaining the number of uniquely mapped sequences to the exons (Exon_mappable). As a library size we used the total number of all uniquely mapped reads from the experiment, excluding the non-polyadenylated genes (N_unique). Normalized expressions were computed as follows: Exp = 10^9*raw/(N_unique * Exon_mappable).
Genome_build: D. discoideum Chromosomal DNA: 1,2,3,4,5,6,M, and floating contigs (created: 05-13-2009 13:53) from the DictyBase (chromosomes 1,2,3,4,5,6 and mitochondrial DNA are the same as on NCBI assembly "dicty_2.7"). Regions [3016085, 3768655] from chr2, [64985, 72996] from chrBF and [42801, 78150] from chrR were masked.
Supplementary_files_format_and_content: Processed data files are tab-separated files with two columns: the first containing gene names and the second its expression. Files ending with "_expr_raw.tab" contain raw expression values while files ending with "_expr_norm.tab" contain normalized expression values.

organism: Dictyostelium discoideum

source_name: 5 RNA mix control 12h : replicate 1

growth_protocol: Wild-type and gene replaceent strain cell lines were cultured axenically in HL5 supplemented with 20µg/mL uracil

extract_protocol:
At each time point, we harvested the cells directly into 1 mL of Trizol® (life technologies, CA, USA) and extracted total RNA according to the manufacturer’s recommended protocol. We performed two rounds of poly-A selection and fragmented 100 ng of the resulting mRNA into approximately 200 bases fragments. We prepared cDNA and the second strand.
We prepared Illumina multiplexed libraries. We prepared 15 (or 20) individual libraries separately (one from each sample) and added a unique barcode to each library at the final step of PCR amplification. We pooled equal amounts of DNA from each library and sequenced one pool per lane of a flow cell on Illumina Genome Analyzer II using the manufacturer's recommended pipeline (versions 1.2 and 1.3, read length = 50 bases)

treatment_protocol: cells were washed with PDF and plated on nitrocellulse filter on filter paper saturated in PDF at 1.8x106 cells/cm2.

value: AX4, tgrBC(QS4), tgrBC(QS31), tgrBC(QS38), tgrBC(QS45)

tag: genotype

value: tgrB1/tgrC1 allele replacement strains and their parental strain

tag: replicate

tag: developmental time

value: 12 hr


title: JA2

description: Rep. 1


title: 5-strain co-development 12h : replicate 2

value: 8 hr


title: nLC-HFSCs_H3K9me3

value: CD1 x FVB

value: H3K9me3 (Millipore and Abcam)


title: Vector-control-EGFRvIII expressing astrocytes

description:
Empty vector (PLKO.1) control was introduced into astrocytes by lentiviral mediated delivery and selection with blasticidin.
sample 4

data_processing:
Reads processed with CASAVA v1.8.2 to generate fastq
Reads mapped with tophat (v.1.4.1) guided by transcripts from Ensembl release 67
Transcripts annotated with cufflinks (v.1.3.0)
Genome build:  mm9
Supplementary files format and content: Tab-delimited .txt file containing gene symbols, gene locations and FPKM expression values

tag: cell line

value: Astrocyte

tag: derivation

value: EGFRvIII-expressing astrocytes were established as previously described (de La Iglesia et al 2008, Genes and Dev, 22(4):449-62.).

value: Vector-control-EGFRvIII expressing


title: 5 RNA mix control 12h : replicate 2

source_name: 5 RNA mix control 12h : replicate 2


title: 5 RNA mix control 8h : replicate 2

source_name: 5 RNA mix control 8h : replicate 2

value: 4 hr


title: JB1

description: Rep. 1

tag: tissue

value: fruit

value: 45 DPA

value: Bingtang

value: Low acid


title: Scramble control-EGFRvIII expressing astrocytes

description:
Scramble control was introduced into astrocytes by lentiviral mediated delivery and selection with blasticidin
sample 3

tag: genotype/variation

value: Scramble control-EGFRvIII expressing


title: 5-strain co-development 12h : replicate 1


title: 5-strain co-development 8h : replicate 2


title: OSMR-KD1_EGFRvIII expressing astrocytes

description:
shOSMR1  was introduced into astrocytes by lentiviral mediated delivery and selection with blasticidin
Sample 1

value: OSMR-KD1_EGFRvIII expressing


title: 5 RNA mix control 4h : replicate 2

source_name: 5 RNA mix control 4h : replicate 2


title: 5-strain co-development 8h : replicate 1


title: 5 RNA mix control 8h : replicate 1

source_name: 5 RNA mix control 8h : replicate 1


title: NIP_UT

city: Beijing

first: jingyu

last: zhang

address: Xiangshan Nanxincun 20 #

department: Plant Biology

institute: Institute of Botany, CAS

data_processing:
Illumina GA Pipeline  (in-house perl scripts) used for basecalling.
For the obtained  Illumina sequencing reads, low quality reads were removed. Reference genome and gene model annotation files were downloaded from MSU Rice Genome Annotation Project Release 7 (http://rice.plantbiology.msu.edu/). Index of the reference genome was built using Bowtie v2.0.6 and single-end clean reads were aligned to the reference genome using TopHat v2.0.9.
HTSeq v0.5.4p3 was used to count the reads numbers mapped to each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene (Mortazavi et al, 2008, Nature Methods. 5: 621-8).
Genome_build: MSU Rice Genome Annotation Project Release 7
Supplementary_files_format_and_content: text file showing  RPKM value for all the samples

organism: Oryza sativa

source_name: Oryza sativa_untreated

growth_protocol: Oryza sativa ssp. japonica cv. Nipponbare and ssp. indica cv. 93-11 were grown in plastic pots filled with nutrient soil and kept under flooded lowland conditions. The 15-day seedlings were subjected to chilling treatment by transferring from greenhouse (28°C day /25°C night) to 4 °C ± 1 °C for  33 h.

extract_protocol:
Total RNA was extracted with the mirVana miRNA Isolation Kit (Life Technologies) from Nipponbare and 93-11 seedlings with and without chilling treatment.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB) following manufacturer’s recommendations. Briefly, The mRNAs were enriched using oligo(dT) magnetic beads and broken into short fragments. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I. NEBNext Adaptor was ligated. The fragments were purified with Agencourt AMPure XP Kit (Beckman Coulter) to select cDNA fragments of preferentially 150~200 bp. PCR amplification was performed with size-selected and adaptor-ligated cDNA with Phusion High-Fidelity DNA Polymerase. PCR products were purified and sequenced on an Illumina Hiseq 2000 platform.

treatment_protocol: The aerial part of rice seedlings treated or untreated with chilling   (4 °C for 33 h) were pooled and used for  library construction.

tag: developmental stage

value: Seedling

tag: variety

value: Nipponbare

value: 15 day old

tag: treatment

value: no treatment


title: 93-11_CT

source_name: Oryza sativa_cold-treated

tag: cultivar

tag: age

value: with chilling teatment (4℃, 33h)


title: 93-11_UT


title: NIP_CT


title: 5 RNA mix control 4h : replicate 1

source_name: 5 RNA mix control 4h : replicate 1

value: AX4, tgrBC(QS4), tgrBC(QS31), tgrBC(QS38), tgrBC(QS45)

value: tgrB1/tgrC1 allele replacement strains and their parental strain

value: 8 hr


title: 5-strain co-development 4h : replicate 2


title: 5-strain co-development 4h : replicate 1


title: OSMR-KD2 EGFRvIII expressing astrocytes

description:
shOSMR2  was introduced into astrocytes by lentiviral mediated delivery and selection with blasticidin
Sample 2

value: Astrocyte

value: EGFRvIII-expressing astrocytes were established as previously described (de La Iglesia et al 2008, Genes and Dev, 22(4):449-62.).

value: OSMR-KD2 EGFRvIII expressing


title: HCT116kiTop1_input_ChIPSeq

status: Public on Apr 12 2016

city: Bethesda

first: Damian

last: Wojtowicz

state: MD

address: 8600 Rockville Pike; Rm 8N811N

institute: NCBI/NLM/NIH

data_processing:
Illumina Analysis Pipeline
PolII ChIP-Seq, BRD4 ChIP-Seq, Top1 ChIP-Seq and Top1-Seq sequencing reads were aligned to the hg19 genome assembly using Bowtie 2 version 2.2.2. To minimize potential PCR bias, duplicate reads were removed from ChIP-Seq data using SAMtools. Peaks were called in RNAPII and Top1 ChIP-Seq data using QuEST software (version 2.4) with a random background model; signal enrichment in Top1 ChIP-Seq data was sought in wide regions, as Top1 did not have a narrow binding sites. All reads of Top1-Seq sample are presented in 50bp bins for each replicate separately.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq peaks, RNA-seq abundance measurements

source_name: HCT116 with homozygous Top1 knock-in

growth_protocol: Human colon cancer cells HCT116 and the derived HCT116-siTOP1 and HCT116KI were grown in DMEM supplemented with 10% heat-inactivated FCS.  CRISPR-Cas9 System for HCT116kiTop1: MIT CRISPR Design Tool selected small guide RNAs targeting TOP1 exon 4 that were cloned in pX330-PGK-puro-SV40PA (gift of R. Casellas; NIAID, NIH). The recombination donor was made by cloning a gBlock Gene Fragment in a ColE1 origin vector. The gBlock contained 3 HA tag sequences replacing most of exon 4, flanked by two homology arms. Following puromycin selection, clones were screened by genomic PCR, and verified by sequencing and immunoblot. Positive clones were grown from single cells prior to experiments.

extract_protocol:
ChIP samples were prepared from HCT116, HCT116-siTOP1 and HCT116KI cells following Barski et al. protocol (Barski et al., 2007) with minor changes. Briefly, 5x107 cells were cross-linked with 1% formaldehyde for 10 min. Cross-linking was stopped by the addition of glycine to 125 mM final concentration and cells were washed twice with PBS. After harvesting cells by scraping, the pellet was washed once with PBS plus 0.5% BSA and resuspended in TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0) supplemented with complete protease inhibitor tablet (Roche) to a final concentration of 1x106 cells/ml. Samples were sonicated 20 times with 20-sec pulses, 30 sec resting, using the Ultrasonic Processor XL (HEAT System) to produce chromatin fragments of 300 bp on average. After clarification by centrifugation, sonicated extracts were adjusted to the conditions of RIPA buffer by adding 1% Triton X100, 0.1% Na-Deoxycholate, 0.1% SDS and 200 mM NaCl.  4 μg of anti-RNAPII (ab817) or anti- TOP1 (ab109374) or anti-BRD4 (A301-985A) were mixed with 40 μl of Dynabeads Protein A (Invitrogen) and incubated at 4°C for 6 hr with rotation. Chromatin from 5×106 cells was added to the Protein A-antibody complexes and incubated overnight at 4°C with rotation. Immunoprecipitates were washed twice with RIPA buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 1% Triton X100, 0.1% Na-Deoxycholate, 0.1% SDS, 200 mM NaCl); twice with RIPA buffer plus 300 mM NaCl; twice with LiCl buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-Deoxycholate); and twice with TE.  The beads were then resuspended in TE plus 0.25% SDS supplemented with proteinase K (500 μg/ml, Roche) and incubated overnight at 65ºC. After pooling, the DNA was recovered from the eluate by phenol chloroform extraction followed by ethanol precipitation in the presence of 20 μg of glycogen (Roche) and dissolved in TE.
The Epicentre DNA END-Repair kit (Epicentre Biotechnologies) was used to generate blunt-ended DNA. DNA was incubated for 45 min at room temperature with a mixture of End repair buffer (33 mM Tris-acetate pH 7, 66 mM potassium acetate, 10 mM magnesium acetate, 0.5 mM DTT), 0.25 mM of each dNTPs, 1 mM ATP, and 1 μl End-Repair Enzyme mix (T4 DNA polymerase + T4 PNK). After purification, the blunt-ended DNA was treated with 15 units of Klenow(exo-) for 30 min at 37°C in the presence of 0.2 mM dATP to generate a protruding 3′ A base used for adaptor ligation. Illumina adapter was ligated to the end of DNA fragments by incubating with 0.1 μl Adaptor oligo mix and 1,000 units of T4 DNA ligase at room temperature for 30 min. After one step of DNA purification using QIAquick PCR Purification Kit the DNA was eluted. A size selection of the adapter ligated DNA was performed through 2% E-Gel (Invitrogen) electrophoresis. The gel slice, around the 200-400 bp region was excised, then DNA was extracted using the MinElute gel extraction kit (QIAGEN) in a final volume of 12 μl elution buffer. The DNA was then amplified for 18 cycles using Illumina primers (Fw: 5'-aca ctc ttt ccc tac acg acg c-3'/ Rv: 5'-caa gca gaa gac ggc ata cga gc-3') according to the following protocol: 98°C for 30 sec; 98°C for 10 sec; 65°C for 30 sec; 72°Cfor 30 sec. The PCR product was obtained by excising 220bps-500bps DNA from a 2.5% agarose gel and purifying it through a Qiagen gel extraction kit (QIAGEN).The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer following manufacturer protocols.

treatment_protocol: CPT (Sigma) treatments were performed for 10 mins on exponentially growing cells at 37ºC with a final concentration of 10 μM. JQ1 treatments were performed for 2 h with a final concentration of 250 nM.

tag: tissue source

value: Epithelial Tumor Colon

tag: cell type

value: human colon cancer cells

tag: chip antibody


title: HCT116kiTop1_Top1_ChIPSeq


title: HCT116kiTop1_BRD4_+JQ1_ChIPSeq

source_name: HCT116 with homozygous Top1 knock-in + JQ1

tag: treated with

value: 250 nM (final con .) JQ1 for 2hrs


title: HCT116kiTop1_Top1_Seq_mod

data_processing:
library strategy: Top1-seq
Illumina Analysis Pipeline
PolII ChIP-Seq, BRD4 ChIP-Seq, Top1 ChIP-Seq and Top1-Seq sequencing reads were aligned to the hg19 genome assembly using Bowtie 2 version 2.2.2. To minimize potential PCR bias, duplicate reads were removed from ChIP-Seq data using SAMtools. Peaks were called in RNAPII and Top1 ChIP-Seq data using QuEST software (version 2.4) with a random background model; signal enrichment in Top1 ChIP-Seq data was sought in wide regions, as Top1 did not have a narrow binding sites. All reads of Top1-Seq sample are presented in 50bp bins for each replicate separately.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq peaks, RNA-seq abundance measurements

extract_protocol:
Cell were treated with CPT for 4 minutes and quickly incubated in TE-SDS 0.1%. Samples were sonicated to produce chromatin fragments of 300 bp on average. After clarification by centrifugation, sonicated extracts were adjusted to the conditions of FA_lysis buffer (50 mM HEPES, 150 mM NaCl, 2 mM EDTA pH 8.0 with 0.1% SDS). Standard ChIP was performed as previously described (Venters and Pugh, 2009).
Samples were immunoprecipitated as described for ChIP, treated with tyrosyl-DNA phosphodiesterase 1 (TDP1), poly-nucleotide kinase (PNK) and Illumina sequenced.


title: HCT116kiTop1_BRD4_ChIPSeq


title: HCT116kiTop1_PolII_+JQ1_ChIPSeq

value: anti-RNAPII (ab817)


title: HCT116kiTop1_Top1_+JQ1_Seq_mod


title: HCT116kiTop1_PolII_ChIPSeq


title: HCT116_wt_Top1_+JQ1_ChIPSeq

source_name: HCT116 + JQ1


title: HCT116_wt_input_ChIPSeq


title: HCT116_wt_Top1_+JQ1_Seq_mod


title: HCT116_wt_Top1_Seq_mod


title: HCT116kiTop1_input_noXL_Seq


title: HCT116_wt_Top1_ChIPSeq_rep


title: HCT116_wt_PolII_ChIPSeq_rep


title: HCT116_wt_PolII_+JQ1_ChIPSeq


title: nm_ux_tn_E1_141204

status: Public on Apr 15 2016

city: La Jolla

first: Fred

middle: H

last: Gage

state: CA

address: 10010 N Torrey Pines Rd

institute: The Salk Institute for Biological Studies

description:
sn_ne_counts.txt
sn_ne_tpm.txt

data_processing:
sequencing reads were trimmed for low base-quality and aligned to mm10 using rsem-calculate-expression running bowtie version 1.0.0
expected counts (counts) and normalized transcripts per million (TPM) were calculated using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: sn_hc_counts.txt: tab-delimited file of counts (abundance measurements) from nuclei dissociated from a homecage mouse
Supplementary_files_format_and_content: sn_hc_tpm.txt: tab-delimited file of TPM values (normalized abundance) from nuclei dissociated from a homecage mouse
Supplementary_files_format_and_content: sn_ne_counts.txt: tab-delimited file of counts (abundance measurements) from FOS positive and FOS negative nuclei dissociated from a mouse exposed to a novel environment
Supplementary_files_format_and_content: sn_ne_tpm.txt:  tab-delimited file of TPM values (normalized abundance) from FOS positive and FOS negative nuclei dissociated from a mouse exposed to a novel environment
Supplementary_files_format_and_content: wc_counts.txt: tab-delimited file of counts (abundance measurements) from PTZ- and saline-treated whole cells
Supplementary_files_format_and_content: wc_tpm.txt: tab-delimited file of TPM values (normalized abundance) from PTZ- and saline-treated whole cells

source_name: DGC_novel environment_single-nuclei

growth_protocol: All animal procedures were performed in accordance with the animal guidelines at the Salk Institute for Biological Studies.

extract_protocol:
dissociation protocol: Dounce
Smart-seq2
TSO concentration: 10uM
ERCC dilution: 1:2000

tag: sequencing method

value: single-nuclei RNA-seq

tag: strain

value: novel environment

tag: facs sort

value: dentate granule cell


title: HCT116_siTop1_Top1_ChIPSeq

data_processing:
Illumina/ABSOLiD Analysis Pipeline
PolII ChIP-Seq, BRD4 ChIP-Seq, Top1 ChIP-Seq and Top1-Seq sequencing reads were aligned to the hg19 genome assembly using Bowtie 2 version 2.2.2. To minimize potential PCR bias, duplicate reads were removed from ChIP-Seq data using SAMtools. Peaks were called in RNAPII and Top1 ChIP-Seq data using QuEST software (version 2.4) with a random background model; signal enrichment in Top1 ChIP-Seq data was sought in wide regions, as Top1 did not have a narrow binding sites. All reads of Top1-Seq sample are presented in 50bp bins for each replicate separately.
RNA-Seq short reads were aligned against the human (hg19) genome using Tophat (version 1.4.1) with default settings. Resulting alignments were analyzed using Cufflinks software (version 1.3.0) provided with the annotation of Ensembl 60 genes after removing germline antigen fragments, mitochondrial rRNA genes, miRNAs and small nuclear RNAs. Expression values were determined in terms of Fragments Per Kilobase of exon per Million fragments mapped (FPKM).
Genome_build: hg19
Supplementary_files_format_and_content: Files report ChIP-Seq peaks, RNA-seq abundance measurements

source_name: human colon cancer cells HCT116 + siTop1

growth_protocol: Human colon cancer cells HCT116 and the derived HCT116-siTOP1 and HCT116KI were grown in DMEM supplemented with 10% heat-inactivated FCS.  CRISPR-Cas9 System for HCT116kiTop1: MIT CRISPR Design Tool selected small guide RNAs targeting TOP1 exon 4 that were cloned in pX330-PGK-puro-SV40PA (gift of R. Casellas; NIAID, NIH). The recombination donor was made by cloning a gBlock Gene Fragment in a ColE1 origin vector. The gBlock contained 3 HA tag sequences replacing most of exon 4, flanked by two homology arms. Following puromycin selection, clones were screened by genomic PCR, and verified by sequencing and immunoblot. Positive clones were grown from single cells prior to experiments.^SAMPLE = GSM1385718

extract_protocol:
As described in Barski, A., et al., High-resolution profiling of histone methylations in the human genome. Cell, 2007. 129(4): p. 823-37.
The Epicentre DNA END-Repair kit (Epicentre Biotechnologies) was used to generate blunt-ended DNA. DNA was incubated for 45 min at room temperature with a mixture of End repair buffer (33 mM Tris-acetate pH 7, 66 mM potassium acetate, 10 mM magnesium acetate, 0.5 mM DTT), 0.25 mM of each dNTPs, 1 mM ATP, and 1 μl End-Repair Enzyme mix (T4 DNA polymerase + T4 PNK). After purification, the blunt-ended DNA was treated with 15 units of Klenow(exo-) for 30 min at 37°C in the presence of 0.2 mM dATP to generate a protruding 3′ A base used for adaptor ligation. Illumina adapter was ligated to the end of DNA fragments by incubating with 0.1 μl Adaptor oligo mix and 1,000 units of T4 DNA ligase at room temperature for 30 min. After one step of DNA purification using QIAquick PCR Purification Kit the DNA was eluted. A size selection of the adapter ligated DNA was performed through 2% E-Gel (Invitrogen) electrophoresis. The gel slice, around the 200-400 bp region was excised, then DNA was extracted using the MinElute gel extraction kit (QIAGEN) in a final volume of 12 μl elution buffer. The DNA was then amplified for 18 cycles using Illumina primers according to the following protocol: 98°C for 30 sec; 98°C for 10 sec; 65°C for 30 sec; 72°Cfor 30 sec. The PCR product was obtained by excising 220bps-500bps DNA from a 2.5% agarose gel and purifying it through a Qiagen gel extraction kit (QIAGEN).The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer following manufacturer protocols.

value: Anti-Topoisomerase I antibody [EPR5375] (Abcam, catalog# ab109374, lot# YH0901152)


title: HCT116_wt_Top1_ChIPSeq

source_name: human colon cancer cells HCT116

value: untreated


title: HCT116_wt_RNASeq

growth_protocol:
Human colon cancer cells HCT116 and the derived HCT116-siTOP1 and HCT116KI were grown in DMEM supplemented with 10% heat-inactivated FCS.  CRISPR-Cas9 System for HCT116kiTop1: MIT CRISPR Design Tool selected small guide RNAs targeting TOP1 exon 4 that were cloned in pX330-PGK-puro-SV40PA (gift of R. Casellas; NIAID, NIH). The recombination donor was made by cloning a gBlock Gene Fragment in a ColE1 origin vector. The gBlock contained 3 HA tag sequences replacing most of exon 4, flanked by two homology arms. Following puromycin selection, clones were screened by genomic PCR, and verified by sequencing and immunoblot. Positive clones were grown from single cells prior to experiments.^SAMPLE = GSM1385718
Human colon cancer cells HCT116 and the derived HCT116-siTOP1 and HCT116KI were grown in DMEM supplemented with 10% heat-inactivated FCS.  CRISPR-Cas9 System for HCT116kiTop1: MIT CRISPR Design Tool selected small guide RNAs targeting TOP1 exon 4 that were cloned in pX330-PGK-puro-SV40PA (gift of R. Casellas; NIAID, NIH). The recombination donor was made by cloning a gBlock Gene Fragment in a ColE1 origin vector. The gBlock contained 3 HA tag sequences replacing most of exon 4, flanked by two homology arms. Following puromycin selection, clones were screened by genomic PCR, and verified by sequencing and immunoblot. Positive clones were grown from single cells prior to experiments.^SAMPLE = GSM1385719

extract_protocol:
Total RNAs were purified and quality check was performed on Agilent Bioanalyzer. RNA-Seq library preparation and sequencing for HCT116 cells followed the procedure described in Chepelev, I., et al., Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq. Nucleic Acids Res, 2009. 37(16): p. e106.
As described in Chepelev, I., et al., Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq. Nucleic Acids Res, 2009. 37(16): p. e106.


title: HCT116_wt_+CPT_PolII_ChIPSeq

source_name: human colon cancer cells HCT116 + CPT

value: CPT (Camptothecin, a topoisomerase I inhibitor)

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S) [4H8] antibody (Abcam, catalog# ab5408, lot# GR106949-6)


title: HCT116_wt_PolII_ChIPSeq


title: HCT116_siTop1_PolII_ChIPSeq


title: HCT116kiTop1_Top1_+JQ1_ChIPSeq


title: Ribo-Seq (HEK393T, Methionine Starvation)

city: Ithaca

first: Ji

last: Wan

address: 303 Biotech 526 Campus Road

institute: Cornell University

data_processing:
Library strategy: Ribo-Seq
Sequencing reads were mapped to genome and NCBI refseq genes by Tophat ((--bowtie1 --no-novel-juncs -G)
P-site of RPF (13th nt) was extracted
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: wiggle file of all unique-mapping reads; ribosome occupancy file of NCBI Refseq mRNAs (according to psite of RPF)

source_name: Human Embryonic Kidney Cells

extract_protocol:
Rnase I Digestion, RNA dephosphorylation, Size Selection
Poly-A Tailing, cDNA synthesis, Size selection, circularization, DNA precipitation, Linearization, PCR amplification

treatment_protocol: cycloheximide for 3 mins (100 ug/ml)

value: Embryonic Kidney


title: HCT116_wt_BRD4_+JQ1_ChIPSeq


title: Ribo-Seq (HEK293 cells)


title: H3K27ac juvenile endocrine (EA69)

city: Stanford

first: Seung

last: Kim

address: 279 Campus Dr B303

department: Developmental Biology

institute: Stanford University

data_processing:
Reads were aligned to hg19 using Bowtie.
A custom script was used to calculate ChIP-Seq read counts 2 kb upstream and downstream of transcription start site of age-dependent genes. The TSS coordinates were downloaded from the UCSC genome browser using RefSeq reference transcriptome list.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Tab-delimited text files include tag counts normalized to the sequencing depth. 'adult_*.txt' and 'juv_*.txt' files include different gene loci that were categorized as adult or juvenile genes, respectively.

source_name: pancreas, juvenile, H3K27ac ChIP

extract_protocol:
Nextera Tagmentation (Buenrostro et al. 2013 [PMID:24097267]).
Illumina HiSeq/TruSeq

value: endocrine

value: juvenile

value: rabbit H3K27ac (Abcam, ab4729)

value: pancreas


title: HCT116_wt_BRD4_ChIPSeq


title: WT pro-B VDJ-seq Rep1

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Library strategy: VDJ-seq
Libraries were sequenced on the Illumina GAIIx or HiSeq1000 platforms using the default RTA analysis software.
ChIP-Seq reads were trimmed using Trim Galore v0.4.0 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.  They were mapped to the mouse NCBIM37/mm9 genome assembly using Bowtie using default parameters. BAM files were imported to Seqmonk for quantitation
Nuclear RNA-Seq reads were trimmed using Trim Galore v0.4.0 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.  They were mapped to the mouse NCBIM37/mm9 genome assembly using Bowtie using default parameters. BAM files were imported to Seqmonk for quantitation
VDJ-seq sequences were first demultiplexed based on Truseq barcodes and then adaptor- and low quality trimmed (Phred <20) using Trim Galore (Babraham Bioinformatics). Next, JH sequences were identified in read 2 (JH end). By analysing the sequence immediately downstream of each JH primer sequence in each JH read we determined that JH2 PCR primers significantly cross-amplified JH4 sequences, leading to chimaeric JH2-JH4 J reads. We concluded this mis-priming was unavoidable due to sequence similiarity between JH2 and JH4 and the requirement to use reverse JH primers at a set position 10bp distal to the start of the JH gene to ensure equal capture of all sequences including those that had undergone substantial exonuclease nibbling during DH-to-JH joining. To correct this we used the 4bp of bona fide JH2 sequence downstream of the JH2 primer sequence to reassign the chimaeric sequences to JH4 and replaced the incorrect JH2 sequence with the correct JH4 sequence before further processing. No significant mispriming was seen for the other JH genes (<5%). Following this, the low number of JH reads that extended less than 60bp beyond the JH primer sequence were discarded and for the remainder the 60bp of downstream sequence was scanned for duplicates. These could be either technical (PCR) or biological. In order to differentiate between these, the opposite end reads (read 1, VH or DH end) were mapped to the NCBIM37/mm9 mouse genome assembly using Bowtie allowing no mismatches (-n 0 -l 100) and discarding multimapping hits (-m 1 --strata --best) and then scanned for start position in the VH region. Read pairs that had identical read 2/JH end sequences (produced by combinatorial joining of VH, DH and JH) and the same start position at the read 1/VH or DH end (a product of the random sonication of the DNA) were considered duplicates and only one retained. The previously mapped read 1 (VH/DH) reads for these were then output as bowtie mapped BAM files.
Genome_build: NCBIM37/mm9
Supplementary_files_format_and_content: ChIP-seq: Quantitated ChIP-seq datafile is tab delimited and shows log2 RPM values for MACS peaks across the genome (p=1e-5). Replicate 2 was used for MACs peak determination, relative to input: (1) Chromosome; (2) Start; (3) End; (4-6) log2 RPM value
Supplementary_files_format_and_content: RNA-seq: Quantitated Nuclear RNA-seq datafile is tab delimited and shows log2 RPM values for 1kb windows spanning the genome: (1) Chromosome; (2) Start; (3) End; (4-5) log2 RPM value
Supplementary_files_format_and_content: VDJ-seq: Quantitated VDJ-seq datafile is tab delimited and contains the following columns: (1) Igh V gene name (from Johnson et al. 2006); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6-7) Count of unique sense-oriented (relative to V gene) reads over the 1.1kb proximal to the V RSS encompassing the V exon, intron, leader exon and ~600bp of proximal sequence.

source_name: Progenitor B cells

growth_protocol: All cells were flow sorted directly from bone marrow single cell suspensions

extract_protocol:
ChIP-seq: ChIP was performed as described (Schoenfelder et al., 2010), using an antibody against histone H3K4me3 (Ab8580, Abcam). Cross links were reversed with 200 mM NaCl, 12.5 mM EDTA, 50 mM NaHCO3, 0.5% SDS, 100 _g/ml proteinase K overnight at 65°C, and ChIP DNA was purified by PCI extraction and isopropanol precipitation.
RNA-seq: Nuclei were obtained from 2-5 x 10(6) flow-sorted Rag1-/- pro-B cells (B220+CD19+CD43+) by incubation in 5 ml 50 mM Tris-HCl pH 7.5, 140 mM NaCl, 1.5 mM MgCl2, 1 mM DTT, 0.4% NP40, 5 min on ice. RNA was isolated with a RNeasy mini kit (Qiagen) and treated with Turbo DNAse (Ambion).
VDJ-seq:  Genomic DNA was isolated using a Qiagen Dneasy blood and tissue kit
ChIP-seq: Paired end ChIP-seq libraries were prepared according to standard Illumina ChIP-seq library protocols.
RNA-seq: Paired-end strand-specific RNA-seq libraries for Illumina sequencing were generated as described (Parkhomchuk et al., 2009) except polyA+ RNA selection was omitted, first strand cDNA synthesis was performed with solely random hexamer primers, and double-stranded cDNA was fragmented with a Diagenode Bioruptor.
VDJ-seq: For each sample 10mg of DNA were sonicated to 500bp using a Covaris E220 sonicator using recommended settings then end-repaired and A-tailed using standard protocols and a short asymmetric adaptor ligated to both fragment ends. DNA was cleaned with a PCR cleanup kit (Qiagen) after end-repair, following A-tailing and following adaptor ligation. Biotinylated primers located in JH intergenic regions were then used in primer extension reactions (8 x 50_l) using Vent Exo- polymerase (2 units per tube; NEB) followed by purification with a PCR cleanup kit. Due to the placement of these primers and the fragment size of the sonicated DNA, primer extension of unrecombined JH segments would be favoured over that of DJH or VDJH recombined segments. Primer-extended sequences (enriched for unrecombined JH intergenic sequences) were then removed using streptavidin beads (My-one C1; Invitrogen) following the manufacturers protocol with incubation for 4 hours at room temperature (20 _l beads per sample). Following a further cleanup, a second primer extension (6 x 50 _l reactions, 2 units per tube) was performed using biotinylated reverse primers located immediately downstream of each JH gene. Streptavidin beads (20_l) were again used to isolate primer extended JH-specific products by incubation overnight with rotation. Illumina PE1 primers corresponding to the long strand of the asymmetric adaptor and JH-specific PE2 primers were then used to amplify the library off the beads in 15 cycle PCR reactions (4 x 25_l) using Pwo master mix (Roche). Following 1x size selection (to remove small products) and cleanup using AMPure XP beads (Beckman Coulter), a second round 5 cycle PCR was performed to add the remainder of the Illumina PE1 and PE2 adaptors, incorporating Truseq bar codes at the PE2 end, followed by a second 1x size selection/cleanup with AMpure XP beads. If necessary, a 'double-sided' Ampure XP size selection (0.5x followed by 1x) was used to remove a low quantity of library products >1kb as these are too large for efficient cluster generation in Illumina sequencing.

treatment_protocol: No treatments

value: bone marrow

value: Wild-type ex vivo flow sorted pro-B cells

tag: markers


title: H3K27ac adult endocrine (EA25)

source_name: pancreas, adult, H3K27ac ChIP

value: adult


title: WT pro-B VDJ-seq Rep2


title: H3K4me3 adult endocrine (EA15)

source_name: pancreas, adult, H3K4me3 ChIP

value: rabbit H3K4me3 (Abcam, ab8580)


title: H3K4me3 adult endocrine (EA27)


title: Rag-/- pro-B nuclear RNA-seq Rep2

data_processing:
Libraries were sequenced on the Illumina GAIIx or HiSeq1000 platforms using the default RTA analysis software.
ChIP-Seq reads were trimmed using Trim Galore v0.4.0 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.  They were mapped to the mouse NCBIM37/mm9 genome assembly using Bowtie using default parameters. BAM files were imported to Seqmonk for quantitation
Nuclear RNA-Seq reads were trimmed using Trim Galore v0.4.0 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.  They were mapped to the mouse NCBIM37/mm9 genome assembly using Bowtie using default parameters. BAM files were imported to Seqmonk for quantitation
VDJ-seq sequences were first demultiplexed based on Truseq barcodes and then adaptor- and low quality trimmed (Phred <20) using Trim Galore (Babraham Bioinformatics). Next, JH sequences were identified in read 2 (JH end). By analysing the sequence immediately downstream of each JH primer sequence in each JH read we determined that JH2 PCR primers significantly cross-amplified JH4 sequences, leading to chimaeric JH2-JH4 J reads. We concluded this mis-priming was unavoidable due to sequence similiarity between JH2 and JH4 and the requirement to use reverse JH primers at a set position 10bp distal to the start of the JH gene to ensure equal capture of all sequences including those that had undergone substantial exonuclease nibbling during DH-to-JH joining. To correct this we used the 4bp of bona fide JH2 sequence downstream of the JH2 primer sequence to reassign the chimaeric sequences to JH4 and replaced the incorrect JH2 sequence with the correct JH4 sequence before further processing. No significant mispriming was seen for the other JH genes (<5%). Following this, the low number of JH reads that extended less than 60bp beyond the JH primer sequence were discarded and for the remainder the 60bp of downstream sequence was scanned for duplicates. These could be either technical (PCR) or biological. In order to differentiate between these, the opposite end reads (read 1, VH or DH end) were mapped to the NCBIM37/mm9 mouse genome assembly using Bowtie allowing no mismatches (-n 0 -l 100) and discarding multimapping hits (-m 1 --strata --best) and then scanned for start position in the VH region. Read pairs that had identical read 2/JH end sequences (produced by combinatorial joining of VH, DH and JH) and the same start position at the read 1/VH or DH end (a product of the random sonication of the DNA) were considered duplicates and only one retained. The previously mapped read 1 (VH/DH) reads for these were then output as bowtie mapped BAM files.
Genome_build: NCBIM37/mm9
Supplementary_files_format_and_content: ChIP-seq: Quantitated ChIP-seq datafile is tab delimited and shows log2 RPM values for MACS peaks across the genome (p=1e-5). Replicate 2 was used for MACs peak determination, relative to input: (1) Chromosome; (2) Start; (3) End; (4-6) log2 RPM value
Supplementary_files_format_and_content: RNA-seq: Quantitated Nuclear RNA-seq datafile is tab delimited and shows log2 RPM values for 1kb windows spanning the genome: (1) Chromosome; (2) Start; (3) End; (4-5) log2 RPM value
Supplementary_files_format_and_content: VDJ-seq: Quantitated VDJ-seq datafile is tab delimited and contains the following columns: (1) Igh V gene name (from Johnson et al. 2006); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6-7) Count of unique sense-oriented (relative to V gene) reads over the 1.1kb proximal to the V RSS encompassing the V exon, intron, leader exon and ~600bp of proximal sequence.

molecule: nuclear RNA

value: Rag1-/- ex vivo flow sorted pro-B cells


title: Rag-/- pro-B H4K4me3 ChIP-seq Rep2

data_processing:
Libraries were sequenced on the Illumina GAIIx or HiSeq1000 platforms using the default RTA analysis software.
ChIP-Seq reads were trimmed using Trim Galore v0.4.0 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.  They were mapped to the mouse NCBIM37/mm9 genome assembly using Bowtie using default parameters. BAM files were imported to Seqmonk for quantitation
Nuclear RNA-Seq reads were trimmed using Trim Galore v0.4.0 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.  They were mapped to the mouse NCBIM37/mm9 genome assembly using Bowtie using default parameters. BAM files were imported to Seqmonk for quantitation
VDJ-seq sequences were first demultiplexed based on Truseq barcodes and then adaptor- and low quality trimmed (Phred <20) using Trim Galore (Babraham Bioinformatics). Next, JH sequences were identified in read 2 (JH end). By analysing the sequence immediately downstream of each JH primer sequence in each JH read we determined that JH2 PCR primers significantly cross-amplified JH4 sequences, leading to chimaeric JH2-JH4 J reads. We concluded this mis-priming was unavoidable due to sequence similiarity between JH2 and JH4 and the requirement to use reverse JH primers at a set position 10bp distal to the start of the JH gene to ensure equal capture of all sequences including those that had undergone substantial exonuclease nibbling during DH-to-JH joining. To correct this we used the 4bp of bona fide JH2 sequence downstream of the JH2 primer sequence to reassign the chimaeric sequences to JH4 and replaced the incorrect JH2 sequence with the correct JH4 sequence before further processing. No significant mispriming was seen for the other JH genes (<5%). Following this, the low number of JH reads that extended less than 60bp beyond the JH primer sequence were discarded and for the remainder the 60bp of downstream sequence was scanned for duplicates. These could be either technical (PCR) or biological. In order to differentiate between these, the opposite end reads (read 1, VH or DH end) were mapped to the NCBIM37/mm9 mouse genome assembly using Bowtie allowing no mismatches (-n 0 -l 100) and discarding multimapping hits (-m 1 --strata --best) and then scanned for start position in the VH region. Read pairs that had identical read 2/JH end sequences (produced by combinatorial joining of VH, DH and JH) and the same start position at the read 1/VH or DH end (a product of the random sonication of the DNA) were considered duplicates and only one retained. The previously mapped read 1 (VH/DH) reads for these were then output as bowtie mapped BAM files.
Genome_build: NCBIM37/mm9
Supplementary_files_format_and_content: ChIP-seq: Quantitated ChIP-seq datafile is tab delimited and shows log2 RPM values for MACS peaks across the genome (p=1e-5). Replicate 2 was used for MACs peak determination, relative to input: (1) Chromosome; (2) Start; (3) End; (4-6) log2 RPM value
Supplementary_files_format_and_content: RNA-seq: Quantitated Nuclear RNA-seq datafile is tab delimited and shows log2 RPM values for 1kb windows spanning the genome: (1) Chromosome; (2) Start; (3) End; (4-5) log2 RPM value
Supplementary_files_format_and_content: VDJ-seq: Quantitated VDJ-seq datafile is tab delimited and contains the following columns: (1) Igh V gene name (from Johnson et al. 2006); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6-7) Count of unique sense-oriented (relative to V gene) reads over the 1.1kb proximal to the V RSS encompassing the V exon, intron, leader exon and ~600bp of proximal sequence.
Important notice:
The sample Rag-/- pro-B H4K4me3 ChIP-seq Rep2 contains a small proportion of contaminating DNA from BAC RP24-179E20, which maps to chr6:69158968-69326718 in NCBIM37/mm9.


title: Rag-/- pro-B input


title: H3K4me3 juvenile endocrine (EA45)

source_name: pancreas, juvenile, H3K4me3 ChIP


title: Ribo-Seq (HEK393T, control sample for Methionine Starvation)

tag: cell line


title: r10_603

first: Peter

middle: W

last: Reddien

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Expressed muscle markers by qPCR

data_processing:
Basecalls performed using CASAVA version 1.7.0
Reads were trimmed using cutadapt to remove Nextera transposon sequences and low quality 3′ base pairs
Reads were mapped to dd_Smed_v4 planarian transcriptome assembly [https://idisk.mpi-cbg.de/~brandl/planaria/dd_Smed_v4.nuc.fasta.zip] using bowtie 1 with --best. Reads for isotigs of contigs (all contig ids that vary only by the final number) were summed. Reads for significant mitochondrial and ribosomal RNA (dd_smedV4_0_0_1, dd_Smed_v4_7_0_1, and dd_Smed_v4_4_1_1) were discarded to generate readcount file.
Contigs with 2 or fewer reads total within all cells were discarded. Read counts were normalized to cpm and log transformed for visualizations.
True muscle cells were identified by principle component analysis on highly-expressed highly-varient genes. Troponin-expressing cells which fell within the clear muscle-like population of cells by PCA were used for further differential expression analyses.
SCDE analyses between cells from anterior regions and cells from posterior regions were performed to identify potential regionally expressed genes: anterior (regions 1, 2, 3; n=23 cells) versus posterior (regions 8, 9, 10; n=38 cells); head (region 1; 11 cells) versus post-pharyngeal (regions 7, 8, 9; n=35 cells); pre-pharyngeal (regions 2, 3, 4; n=22 cells) versus tail (region 10; n=12 cells)
Genome_build: dd_Smed_v4
Supplementary_files_format_and_content: [Read counts] Tab-delineated text file includes unnormalized read counts of contigs (summed isotigs) used for further analysis for all 177 cells. SCDE analyses: tab-delineated text file generated per Kharchenko et al, 2014 for each anterior-versus-posterior comparison between 115 muscle cells (anterior-enriched as positive values and posterior-enriched as negative values). Each file indicates the fold change as the maximum likelihood estimate (mle) with a lower (lb) and upper bound (ub) and a conservative estimate (ce, equal to lb (positive), ub (negative) or 0 (lb and ub have different signs)) and statistical significance as signed Z-score (Z) and conservative Z-score (cZ, Z score corrected for multiple hypothesis using Holm procedure).
Supplementary_files_format_and_content: [SCDE analyses] tab-delineated text file generated per Kharchenko et al, 2014 for each anterior-versus-posterior comparison between 115 muscle cells (anterior-enriched as positive values and posterior-enriched as negative values). Each file indicates the fold change as the maximum likelihood estimate (mle) with a lower (lb) and upper bound (ub) and a conservative estimate (ce, equal to lb (positive), ub (negative) or 0 (lb and ub have different signs)) and statistical significance as signed Z-score (Z) and conservative Z-score (cZ, Z score corrected for multiple hypothesis using Holm procedure).

molecule: polyA RNA

organism: Schmidtea mediterranea

source_name: Isolated planarian cell

growth_protocol: Asexual Schmidtea mediterranea strain (CIW4) animals starved 7-14 days before dissectioninto regions

extract_protocol:
Cells were lysed in total cell lysis buffer supplemented with 1% β-mercaptoethanol
cDNA libraries were constructed using SmartSeq2. Sequencing libraries were made using Nextera XT kit for cells expressing muscle markers.

treatment_protocol: Single cell suspensions for each region were stained with Hoechst, and non-dividing single cells were sorted by flow cytometry into 96 well plates

value: asexual CIW4

tag: ploidy

value: 2N (non-dividing)

tag: ap-region

value: non-muscle


title: r10_592

description: Expressed muscle markers by qPCR

value: muscle


title: H3K4me3 juvenile endocrine (EA51)

tag: tissue


title: RSq46_6_alpha

data_processing:
Raw reads were mapped to hg19 transcriptome using STAR version 2.3.0.1.
Genome_build: hg19 transcriptome, aggregated from UCSC, RefSeq and GENCODE v12 databases.
Supplementary_files_format_and_content: STAR_sorted_rpkm.txt: The processed data file contains 30 columns: the first column is transcript ID, second column is gene symbol and columns that come after are the RPKM counts of the respective samples.

extract_protocol:
ABI picopure RNA extraction kit.
Illumina HiSeq/TruSeq.

value: alpha

tag: age group

value: young


title: r10_602

description: Expressed muscle markers by qPCR


title: RSq40_1.4_beta

value: beta


title: RSq42_1.4_alpha


title: RSq39_0.8_beta


title: RSq38_0.8_alpha


title: r10_583

description: Expressed muscle markers by qPCR


title: r10_538

description: Expressed muscle markers by qPCR


title: r10_547

description: Expressed muscle markers by qPCR


title: RSq37_5_beta


title: r10_556

description: Expressed muscle markers by qPCR


title: H3K27ac juvenile endocrine (EA73)


title: r10_523

description: Expressed muscle markers by qPCR


title: RSq35_5_alpha


title: r10_513

description: Expressed muscle markers by qPCR


title: RSq34_42_acinar

value: acinar

value: old


title: RSq33_54_duct

value: duct


title: r10_502

description: Expressed muscle markers by qPCR


title: RSq32_1.5_duct


title: r10_503

description: Expressed muscle markers by qPCR


title: r10_493

description: Expressed muscle markers by qPCR


title: RSq29_48_alpha


title: RSq26_5_beta


title: r10_492

description: Expressed muscle markers by qPCR


title: RSq25_5_alpha


title: r10_483

description: Expressed muscle markers by qPCR


title: r10_472

description: Expressed muscle markers by qPCR


title: RSq24_5_duct


title: r10_482

description: Expressed muscle markers by qPCR


title: r10_462

description: Expressed muscle markers by qPCR


title: r10_452

description: Expressed muscle markers by qPCR


title: RSq18_66_beta


title: RSq14_28_beta


title: RSq15_33_duct


title: r09_601

description: Expressed muscle markers by qPCR


title: r09_591

description: Expressed muscle markers by qPCR


title: RSq16_66_alpha


title: r09_590

description: Expressed muscle markers by qPCR


title: RSq13_28_alpha


title: r09_582

description: Expressed muscle markers by qPCR


title: RSq31_48_beta


title: r09_581

description: Expressed muscle markers by qPCR


title: RSq10_40_beta


title: r09_555

description: Expressed muscle markers by qPCR


title: RSq06_33_acinar


title: RSq12_33_beta


title: RSq09_40_alpha


title: r09_573

description: Expressed muscle markers by qPCR


title: r09_554

description: Expressed muscle markers by qPCR


title: RSq03_33_alpha


title: RSq02_1.5_acinar


title: r09_546

description: Expressed muscle markers by qPCR


title: r09_536

description: Expressed muscle markers by qPCR


title: r09_545

description: Expressed muscle markers by qPCR


title: HCT116_wt_+CPT_Top1_Seq_rep2

description: library strategy: Top1-Seq

growth_protocol: Human colon cancer cells HCT116 and the derived HCT116-siTop1 were grown in DMEM supplemented with 10% heat-inactivated FCS.

extract_protocol:
Cell were treated with CPT for 4 minutes and quickly incubated in TE-SDS 0.1%. After harvesting cells by scraping, the samples were sonicated 60 times with 30-sec pulses, 30 sec resting, using the Bioruptor (Diagenode) to produce chromatin fragments of 300 bp on average. After clarification by centrifugation, sonicated extracts were adjusted to the conditions of FA‐lysis buffer (50 mM HEPES, 150 mM NaCl, 2 mM EDTA pH 8.0 with 0.1% SDS). Standard chromatin immunoprecipitation (ChIP) was performed as previously described in Venters, B.J. and B.F. Pugh, A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome. Genome Res, 2009. 19(3): p. 360-71.
While still on the sepharose resin, the immunoprecipitated DNA was polished, ligated with P2 adaptors and eluted from the resin. Crosslinks were reversed and proteins degraded with proteinase K at 65°C. DNA samples were precipitated with ethanol and denatured at 95°C. DNA samples were primer-extended using a P2 primer. P1 adaptors were ligated and the resulting DNA was PCR-amplified, gel purified, and sequenced using the SOLiD genome sequencer (AppliedBiosystems).

value: Epithelial Tumor Colon

tag: genotype/variation

value: CPT (Camptothecin, a topoisomerase I inhibitor)

value: Anti-Topoisomerase I antibody [EPR5375] (Abcam, catalog# ab109374, lot# YH0901152)


title: HCT116_wt_+CPT_Top1_Seq_rep1

description: library strategy: Top1-Seq

tag: treatment


title: r09_491

description: Expressed muscle markers by qPCR


title: r09_501

description: Expressed muscle markers by qPCR


title: RNA-Seq (MEF cells)

data_processing:
Sequencing reads were mapped to genome and NCBI refseq genes by Tophat ((--bowtie1 --no-novel-juncs -G)
P-site of RPF (13th nt) was extracted
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: wiggle file of all unique-mapping reads; ribosome occupancy file of NCBI Refseq mRNAs (according to psite of RPF)

source_name: Mouse Embryonc Fibroblasts

value: MEF

value: Embryonc Fibroblasts


title: r09_471

description: Expressed muscle markers by qPCR


title: r09_481

description: Expressed muscle markers by qPCR


title: Ribo-Seq (MEF cells, mutant 18S rRNA)


title: r09_511

description: Expressed muscle markers by qPCR


title: Ribo-Seq (MEF cells, WT 18S rRNA)


title: RSq28_5_acinar

value: pancreas


title: Ribo-Seq (MEF cells)


title: r09_451

description: Expressed muscle markers by qPCR


title: A-WT3

city: Zürich

first: Martin

last: Braunschweig

address: Reckenholzstrasse 191

country: Switzerland

institute: Agroscope

data_processing:
The quality of the reads was assessed using fastqc v. 0.10.1.
The reads were mapped against mouse nuclear and mitochondrial rRNA genes using bowtie2 v. 2.1.0 with default parameters (Langmead & Salzberg, 2012) to remove ribosomal RNA.
The resulting data was mapped against the mouse reference genome UCSC mm10 assembly with tophat v. 2.0.9 (Trapnell et al. 2009), and number of reads per gene was counted using htseq-count v. 0.5.4p3 (http://www-huber.embl.de/users/anders/HTSeq/).
Tests for differential gene expression between wild-type and knockout mice samples were performed using DESeq2 v. 1.4.5 (Love et al. 2014) (Bioconductor).
Genome_build: mm10
Supplementary_files_format_and_content: bam

source_name: Skeletal muscle

extract_protocol:
Trizol followed by Qiagen RNeasy cleanup and DNase treatment. RNA was measured with a Qubit® (1.0) Fluorometer (Life Technologies) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). RNA samples were ribo-depleted using Ribo Zero (Epicentre®, USA). The quality and quantity of the libraries was analyzed by using Qubit® (1.0) Fluorometer and the Caliper GX LabChip® GX (Caliper Life Sciences, Inc., USA).
For cluster generation, the TruSeq PE Cluster Kit v3-cBot-HS or TruSeq SR Cluster Kit v3-cBot-HS (Illumina, Inc, California, USA) were used. Paired-end sequencing was performed on an Illumina HiSeq 2000 using the TruSeq SBS Kit v3-HS (Illumina, Inc, California, USA).

treatment_protocol: wild-type and ∆DMR1-U2 female newborn mice

value: skeletal muscle

value: post natal day 2

tag: genotype

value: wild-type

tag: Sex

value: female


title: r08_600

description: Expressed muscle markers by qPCR

value: asexual CIW4

value: 2N (non-dividing)

value: non-muscle


title: A-WT1A

tag: age


title: r08_599

description: Expressed muscle markers by qPCR

value: muscle


title: A-WT2


title: r09_522

description: Expressed muscle markers by qPCR


title: r10_512

description: Expressed muscle markers by qPCR


title: r08_580

description: Expressed muscle markers by qPCR


title: r08_571

description: Expressed muscle markers by qPCR


title: A-KO1B


title: A-KO1A


title: r08_562

description: Expressed muscle markers by qPCR


title: Nucleus-9

city: los angeles

first: Qin

last: An

state: CALIFORNIA

address: Room 6554 Gonda Building, UCLA

department: Department of Human Genetics

institute: ucla

description:
genomic DNA from nucleus
matched_promoter_methylation_expression.txt
matched_genebody_methylation_expression.txt

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, and mapped to mm10, and methylation level was called by using the BS-Seeker2 according to the protocol guo et al, 2013, BMC Genomics
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, and mapped to mm10, using Tophat 2.0.4, with default settings; result bam were introduced to Cufflinks 2.1.1 and converted into FPKM metrics using default settings.
Fundamental statistical analysis are accomplished using R 3.1.1 built-in functions and Matlab 2014a built-in functions.
methylation data was mapped to mm10, methylation value for CpG sites was called by using the BS-Seeker2 according to the protocol guo et al, 2013, BMC Genomics
methylation data was filter by the specification that CpG sites were covered by more than 3 reads
averaged methylation value was calculated by Bedtools for promoter or gene body region with CpG sites more than 5
Genome_build: mm10
Supplementary_files_format_and_content: [RNA-Seq] FPKM_table.txt reports quantile normalized FPKM values
Supplementary_files_format_and_content: [RRBS] matched*txt files report methylation call value of promoter and genebody of each Sample.  Nucleus-* columns show the methylation level on promoter. Cytosol-* columns show the gene expression level in the cytosol. Nucleus sample and Cytosol sample with the same number    are from exactly the same cell.

source_name: Nucleus

growth_protocol: Dorsal Root Ganglion was dissected from B6D2F1 mice and trypsined into single cells

extract_protocol:
cytosol and nucleus were mannually isolated to get RNA and DNA from the same single cell
RNA-seq libraries were constructed by smart2-seq, methylome libraries were constructed by scRRBS

tag: cell #

tag: cell type

value: Dorsal root ganglion neuron

tag: cell structure

value: nucleus


title: Nucleus-7


title: r08_553

description: Expressed muscle markers by qPCR


title: Nucleus-8


title: Nucleus-6


title: Nucleus-3


title: r08_544

description: Expressed muscle markers by qPCR


title: Nucleus-2


title: A-KO3


title: Nucleus-1


title: A-WT1B


title: r08_535

description: Expressed muscle markers by qPCR


title: Nucleus-12


title: Nucleus-13


title: r08_521

description: Expressed muscle markers by qPCR


title: r08_520

description: Expressed muscle markers by qPCR


title: Nucleus-11


title: A-KO2


title: Nucleus-10


title: Cytosol-99

description:
mRNA from cytosol
FPKM_table.txt

source_name: Cytosol

value: cytosol


title: r08_490

description: Expressed muscle markers by qPCR


title: Nucleus-5


title: Cytosol-98

description:
mRNA from cytosol
FPKM_table.txt


title: Nucleus-4


title: r08_480

description: Expressed muscle markers by qPCR


title: Cytosol-97

description:
mRNA from cytosol
FPKM_table.txt


title: r08_450

description: Expressed muscle markers by qPCR


title: r08_534

description: Expressed muscle markers by qPCR


title: Cytosol-95

description:
mRNA from cytosol
FPKM_table.txt


title: Nucleus-15


title: Nucleus-14


title: r08_429

description: Expressed muscle markers by qPCR


title: Cytosol-94

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-93

description:
mRNA from cytosol
FPKM_table.txt


title: r08_419

description: Expressed muscle markers by qPCR


title: Cytosol-92

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-91

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-90

description:
mRNA from cytosol
FPKM_table.txt


title: r08_409

description: Expressed muscle markers by qPCR


title: Cytosol-87

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-88

description:
mRNA from cytosol
FPKM_table.txt


title: r08_399

description: Expressed muscle markers by qPCR


title: Cytosol-89

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-86

description:
mRNA from cytosol
FPKM_table.txt


title: r08_389

description: Expressed muscle markers by qPCR


title: Cytosol-84

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-83

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-96

description:
mRNA from cytosol
FPKM_table.txt


title: r08_379

description: Expressed muscle markers by qPCR


title: Cytosol-82

description:
mRNA from cytosol
FPKM_table.txt


title: r07_598

description: Expressed muscle markers by qPCR


title: Cytosol-81

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-79

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-80

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-78

description:
mRNA from cytosol
FPKM_table.txt


title: r07_588

description: Expressed muscle markers by qPCR


title: RSq45_6_beta

value: beta

value: young


title: r07_579

description: Expressed muscle markers by qPCR


title: Cytosol-77

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-76

description:
mRNA from cytosol
FPKM_table.txt


title: r07_578

description: Expressed muscle markers by qPCR


title: Cytosol-73

description:
mRNA from cytosol
FPKM_table.txt


title: r07_570

description: Expressed muscle markers by qPCR


title: Cytosol-74

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-72

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-71

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-68

description:
mRNA from cytosol
FPKM_table.txt


title: r07_560

description: Expressed muscle markers by qPCR


title: Cytosol-69

description:
mRNA from cytosol
FPKM_table.txt


title: r07_569

description: Expressed muscle markers by qPCR


title: Cytosol-67

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-85

description:
mRNA from cytosol
FPKM_table.txt


title: r07_552

description: Expressed muscle markers by qPCR


title: r07_551

description: Expressed muscle markers by qPCR


title: H3K27ac adult endocrine (EA13)

value: endocrine

value: adult

tag: chip antibody

value: rabbit H3K27ac (Abcam, ab4729)


title: Cytosol-63

description:
mRNA from cytosol
FPKM_table.txt

tag: strain


title: Cytosol-66

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-75

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-61

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-60

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-62

description:
mRNA from cytosol
FPKM_table.txt


title: r07_542

description: Expressed muscle markers by qPCR


title: Cytosol-59

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-58

description:
mRNA from cytosol
FPKM_table.txt


title: r07_533

description: Expressed muscle markers by qPCR


title: Cytosol-70

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-56

description:
mRNA from cytosol
FPKM_table.txt


title: r07_561

description: Expressed muscle markers by qPCR


title: r07_425

description: Expressed muscle markers by qPCR


title: Cytosol-55

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-57

description:
mRNA from cytosol
FPKM_table.txt


title: r07_446

description: Expressed muscle markers by qPCR


title: r07_415

description: Expressed muscle markers by qPCR


title: Cytosol-54

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-64

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-51

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-50

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-53

description:
mRNA from cytosol
FPKM_table.txt


title: r07_543

description: Expressed muscle markers by qPCR


title: Cytosol-48

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-52

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-65

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-49

description:
mRNA from cytosol
FPKM_table.txt


title: r07_395

description: Expressed muscle markers by qPCR


title: r07_385

description: Expressed muscle markers by qPCR


title: r07_405

description: Expressed muscle markers by qPCR


title: r07_375

description: Expressed muscle markers by qPCR


title: Cytosol-45

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-4-1

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-29

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-46

description:
mRNA from cytosol
FPKM_table.txt


title: r06_597

description: Expressed muscle markers by qPCR


title: Cytosol-4-2

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-28

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-27

description:
mRNA from cytosol
FPKM_table.txt


title: r06_587

description: Expressed muscle markers by qPCR


title: Cytosol-24

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-25

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-23

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-26

description:
mRNA from cytosol
FPKM_table.txt


title: r06_596

description: Expressed muscle markers by qPCR


title: r06_586

description: Expressed muscle markers by qPCR


title: Cytosol-22

description:
mRNA from cytosol
FPKM_table.txt


title: r06_577

description: Expressed muscle markers by qPCR


title: Cytosol-47

description:
mRNA from cytosol
FPKM_table.txt


title: r06_568

description: Expressed muscle markers by qPCR


title: r06_559

description: Expressed muscle markers by qPCR


title: r06_550

description: Expressed muscle markers by qPCR


title: Cytosol-18

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-17

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-20

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-19

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-21

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-14

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-15

description:
mRNA from cytosol
FPKM_table.txt


title: r06_549

description: Expressed muscle markers by qPCR


title: Cytosol-11

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-16

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-13

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-12

description:
mRNA from cytosol
FPKM_table.txt


title: r06_541

description: Expressed muscle markers by qPCR


title: Cytosol-1-2

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-1-1

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-106

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-105

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-103

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-102

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-104

description:
mRNA from cytosol
FPKM_table.txt


title: r06_531

description: Expressed muscle markers by qPCR


title: r06_449

description: Expressed muscle markers by qPCR


title: Cytosol-10-2

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-10-1

description:
mRNA from cytosol
FPKM_table.txt


title: r06_439

description: Expressed muscle markers by qPCR


title: Cytosol-100

description:
mRNA from cytosol
FPKM_table.txt


title: r06_540

description: Expressed muscle markers by qPCR


title: Cytosol-9

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-7

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-5

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-42

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-41

description:
mRNA from cytosol
FPKM_table.txt


title: r06_408

description: Expressed muscle markers by qPCR


title: Cytosol-6

description:
mRNA from cytosol
FPKM_table.txt


title: r06_388

description: Expressed muscle markers by qPCR


title: r06_418

description: Expressed muscle markers by qPCR


title: Cytosol-8

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-44

description:
mRNA from cytosol
FPKM_table.txt


title: r06_398

description: Expressed muscle markers by qPCR


title: r06_532

description: Expressed muscle markers by qPCR


title: r06_378

description: Expressed muscle markers by qPCR


title: Cytosol-40

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-43

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-101

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-37

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-38

description:
mRNA from cytosol
FPKM_table.txt


title: r05_595

description: Expressed muscle markers by qPCR


title: Cytosol-3

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-36

description:
mRNA from cytosol
FPKM_table.txt


title: r05_594

description: Expressed muscle markers by qPCR


title: Cytosol-39

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-34

description:
mRNA from cytosol
FPKM_table.txt


title: r05_584

description: Expressed muscle markers by qPCR


title: Cytosol-33

description:
mRNA from cytosol
FPKM_table.txt


title: r05_576

description: Expressed muscle markers by qPCR


title: Cytosol-32

description:
mRNA from cytosol
FPKM_table.txt


title: Cytosol-30

description:
mRNA from cytosol
FPKM_table.txt


title: r05_575

description: Expressed muscle markers by qPCR


title: r05_567

description: Expressed muscle markers by qPCR


title: Soma-7

description:
mRNA from soma
FPKM_table.txt

source_name: Soma

value: soma


title: Soma-8

description:
mRNA from soma
FPKM_table.txt


title: r05_566

description: Expressed muscle markers by qPCR


title: r05_558

description: Expressed muscle markers by qPCR


title: Soma-50

description:
mRNA from soma
FPKM_table.txt


title: Soma-9

description:
mRNA from soma
FPKM_table.txt


title: Soma-5

description:
mRNA from soma
FPKM_table.txt


title: r05_557

description: Expressed muscle markers by qPCR


title: Soma-49

description:
mRNA from soma
FPKM_table.txt


title: Soma-48

description:
mRNA from soma
FPKM_table.txt


title: Soma-47

description:
mRNA from soma
FPKM_table.txt


title: r05_548

description: Expressed muscle markers by qPCR


title: Cytosol-35

description:
mRNA from cytosol
FPKM_table.txt


title: Soma-46

description:
mRNA from soma
FPKM_table.txt


title: 2C3_S17

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing reads were mapped back usig STAR 2.5
Bam files were introduced to Htseq 0.6, to count raw read count per gene
Genome_build: mm10
Supplementary_files_format_and_content: text file with read counts for genes.

source_name: Dorsal root ganglion neuron

extract_protocol:
cytosol and nucleus were manually isolated to get RNA and DNA from the same single cell
RNA-seq libraries were constructed by smart2-seq


title: 2C4-1_S20


title: Soma-45

description:
mRNA from soma
FPKM_table.txt


title: Soma-44

description:
mRNA from soma
FPKM_table.txt


title: 2C1_S13


title: Cytosol-31

description:
mRNA from cytosol
FPKM_table.txt


title: r05_539

description: Expressed muscle markers by qPCR


title: Cytosol-2

description:
mRNA from cytosol
FPKM_table.txt


title: Soma-43

description:
mRNA from soma
FPKM_table.txt


title: Soma-6

description:
mRNA from soma
FPKM_table.txt


title: r05_530

description: Expressed muscle markers by qPCR


title: Soma-42

description:
mRNA from soma
FPKM_table.txt


title: Soma-41

description:
mRNA from soma
FPKM_table.txt


title: C3_S7


title: r05_469

description: Expressed muscle markers by qPCR


title: Soma-40

description:
mRNA from soma
FPKM_table.txt


title: sc5-1_S2


title: r05_459

description: Expressed muscle markers by qPCR


title: 2C5-1_S12


title: C6_S10


title: r05_444

description: Expressed muscle markers by qPCR


title: r05_434

description: Expressed muscle markers by qPCR


title: r05_433

description: Expressed muscle markers by qPCR


title: Soma-35

description:
mRNA from soma
FPKM_table.txt


title: Soma-33

description:
mRNA from soma
FPKM_table.txt


title: Soma-39

description:
mRNA from soma
FPKM_table.txt


title: C1_S5


title: Soma-4

description:
mRNA from soma
FPKM_table.txt


title: Soma-32

description:
mRNA from soma
FPKM_table.txt


title: 2C2_S15


title: r05_424

description: Expressed muscle markers by qPCR


title: Soma-37

description:
mRNA from soma
FPKM_table.txt


title: Soma-38

description:
mRNA from soma
FPKM_table.txt


title: Soma-34

description:
mRNA from soma
FPKM_table.txt


title: Soma-31

description:
mRNA from soma
FPKM_table.txt


title: C2_S6


title: 2C4_S19


title: r05_423

description: Expressed muscle markers by qPCR


title: Soma-30

description:
mRNA from soma
FPKM_table.txt


title: Soma-3

description:
mRNA from soma
FPKM_table.txt


title: Soma-29

description:
mRNA from soma
FPKM_table.txt


title: C4_S8


title: r05_414

description: Expressed muscle markers by qPCR


title: Soma-28

description:
mRNA from soma
FPKM_table.txt


title: 2C2-1_S16


title: Soma-27

description:
mRNA from soma
FPKM_table.txt


title: r05_413

description: Expressed muscle markers by qPCR


title: Soma-36

description:
mRNA from soma
FPKM_table.txt


title: Soma-25

description:
mRNA from soma
FPKM_table.txt


title: 2C3-1_S18


title: r06_428

description: Expressed muscle markers by qPCR


title: r05_404

description: Expressed muscle markers by qPCR


title: Soma-24

description:
mRNA from soma
FPKM_table.txt


title: C5_S9


title: Soma-22

description:
mRNA from soma
FPKM_table.txt


title: 2C1-1_S14


title: sc5_S1


title: Soma-2

description:
mRNA from soma
FPKM_table.txt


title: Soma-20

description:
mRNA from soma
FPKM_table.txt


title: r05_403

description: Expressed muscle markers by qPCR


title: r05_394

description: Expressed muscle markers by qPCR


title: r05_393

description: Expressed muscle markers by qPCR


title: 2C5_S11


title: Soma-21

description:
mRNA from soma
FPKM_table.txt


title: r05_384

description: Expressed muscle markers by qPCR


title: Soma-18

description:
mRNA from soma
FPKM_table.txt


title: Soma-19

description:
mRNA from soma
FPKM_table.txt


title: Soma-17

description:
mRNA from soma
FPKM_table.txt


title: Soma-15

description:
mRNA from soma
FPKM_table.txt


title: Soma-14

description:
mRNA from soma
FPKM_table.txt


title: Soma-16

description:
mRNA from soma
FPKM_table.txt


title: r05_383

description: Expressed muscle markers by qPCR


title: r05_374

description: Expressed muscle markers by qPCR


title: Soma-26

description:
mRNA from soma
FPKM_table.txt


title: Soma-13

description:
mRNA from soma
FPKM_table.txt


title: r05_373

description: Expressed muscle markers by qPCR


title: Soma-12

description:
mRNA from soma
FPKM_table.txt


title: Soma-10

description:
mRNA from soma
FPKM_table.txt


title: Soma-11

description:
mRNA from soma
FPKM_table.txt


title: Soma-23

description:
mRNA from soma
FPKM_table.txt


title: r04_443

description: Expressed muscle markers by qPCR


title: Soma-1

description:
mRNA from soma
FPKM_table.txt


title: r04_432

description: Expressed muscle markers by qPCR


title: r04_442

description: Expressed muscle markers by qPCR


title: r04_422

description: Expressed muscle markers by qPCR


title: r04_411

description: Expressed muscle markers by qPCR