title: Late Treatment Sample 1

city: Cambridge

first: Anna

last: Salzberg

address: 399 Binney St UNIT 300

institute: Rubius Therapeutics

data_processing:
Illumina CASAVA pipeline Version 1.8 was used to extract de-multiplexed sequencing reads.
FastQC (version 0.11.2) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to validate the quality of the raw sequence data. Additional quality filtering used FASTX- Toolkit (http://hannonlab.cshl.edu/fastx_toolkit) using a quality score cutoff of 20.
Next, alignment of the filtered reads to the mouse reference genome (mm10) was done using Tophat (version 2.0.9) allowing 2 mismatches.
Picard (version1.102) (https://github.com/broadinstitute/picard) was used to assess proportion of mapped bases to coding, UTR, intronic, and intergenic regions, respectively. Picard was used to find coverage across gene body to determine 5'- or 3'- bias.
FPKM (Fragments Per Kilobase of Exon Per Million Fragments Mapped) values were calculated using Cufflinks Version 2.0.2 as provided with the Ensembl gene annotation (release 78).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Transcriptome Cufflinks results in tab-delimited text format.

source_name: kidney, diabetic, late treatment

growth_protocol: The animal studies were approved by the Penn State University College of Medicine Institutional Animal Care and Use Committee, and performed in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. All experiments were conducted using male D2.B6-Ins2Akita/MatbJ diabetic animals and their wild type (WT) littermate mice (DBA/2J background), recommended by the Animal Models of Diabetes Complications Consortium (AMDCC) as a model of DN. Mice were provided ad lib access to food and water and were euthanized at the end of the experimental period. Kidney samples for RNA extraction were immediately harvested and frozen in liquid nitrogen at the termination of the experiment.

extract_protocol:
For RNA-seq, we used 13 kidney tissue samples from wild-type mice, 7 from the diabetic Ins2Akita mice, 8 from early P78 treatment of diabetic Ins2Akita mice, and 7 from late P78 treatment the diabetic Ins2Akita 7 mice. Total RNA was extracted using mirVana kit (Life Technologies) with some modifications. Briefly, a bead mill homogenizer (Bullet Blender, Next Advance) was used to homogenize the tissue using a safe-lock microcentrifuge tube (Eppendorf) and a mass of stainless steel beads (Next Advance, cat# SSB14B) equal to the mass of the tissue. Immediately after two volumes of lysis buffer were added to the tube, samples were mixed in the Bullet Blender for 1 min at a speed of six. Samples were visually inspected to confirm desired homogenization and then incubated at 37 °C for 5 min. The lysis buffer was added up to 0.6 ml, and samples were mixed in the Bullet Blender for 1 min. Optical density values of extracted RNA were measured using NanoDrop to confirm an A260:A280 ratio above 1.9. RNA integration number (RIN) was measured using BioAnalyzer (Agilent) RNA 6000 Nano Kit to confirm RIN above 7.
cDNA libraries were prepared using SureSelect Strand Specific RNA Library Preparation Kit (Agilent) as per the manufacturer's instructions. Briefly, polyA RNA was purified from 1000 ng of total RNA using oligo (dT) beads. Extracted RNA was subjected to fragmentation, reverse transcription, end repair, 3'-end adenylation, adaptor ligation and subsequent PCR amplification and SPRI bead purification (Beckman Coulter). The unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent) and Kapa Library Quantification Kit (Kapa Biosystems). 12 libraries were pooled and diluted to 2 nM in EB buffer (Qiagen) and then denatured using the Illumina protocol. The denatured libraries were diluted to 10 pM by pre-chilled hybridization buffer and loaded onto TruSeq SR v3 flow cells on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe (TruSeq SBS Kit v3) according to the manufacturer's instructions (Illumina).

treatment_protocol: Diabetic D2.B6-Ins2Akita mice develop hyperglycemia at 3 wks of age and all treatment carried out when the mice were either 6 wks (3 wks hyperglycemic exposure; early stage treatment) or 12 wks (9 wks hyperglycemic exposure; late stage treatment) of age. Only mice with blood glucose levels > 350 mg/dl. The drug tested was P78, a small pigment epithelium derived factor (PEDF) active peptide. Briefly, P78 peptide at a dose of 0.3 μg/g/day or vehicle (phosphate-buffered saline; PBS) was administered by continuous subcutaneous infusion for 6 weeks via the osmotic minipump (no. 2006; Alzet, Durect, Palo Alto, CA), implanted dorsally between the shoulders of the animals. Transcriptome analysis of wild-type and diabetic kidney samples were performed at two stages of diabetes where treatment was initiated at an early stage (6 wks of age; 3 wks hyperglycemic) and late stage (12 wks of age; 9 wks hyperglycemic). Age-, gender-, and weight-matched diabetic Ins2Akita and wild-type (N) non-diabetic controls (D) were used in the study. All animals, including wild-type, were implanted with an osmotic minipump infused with either vehicle (wt and diabetic controls) or the P78 peptide (diabetic mice). Duration of treatment was 6 wks with either peptide or vehicle. One group received treatment at the early stage of diabetes (ET, early treatment) at 6 wks of age and the experiment terminated at 12 wks of age. Treatment in the second group was initiated at late stage diabetes (LT, late treatment) at 12 wks of age and terminated at 18 wks of age. The study was carried out on four groups: 1. Normal (N, wild-type control); 2. Diabetic (control), 3. P78 early treatment (ET), 4. P78 Late treatment (LT). (n=7-13/group).

tag: strain/background

tag: gender

value: male

tag: disease status

value: diabetes

value: kidney

tag: treatment

value: P78-PEDF at 12 wks for 6 wks


title: BC04_90

status: Public on Dec 09 2016

type: SRA

city: Seoul

first: Woosung

last: Chung

state: State...

address: Samsung Medical Center

country: South Korea

institute: Samsung Genome Institute

description: Single-cell RNA-seq

library_source: transcriptomic

data_processing:
A modified reference was generated by merging the three array control RNA spike-ins (ThermoFisher) and the human genome reference (hg19) with the GENCODE 19 annotations.
Paired-end 100bp reads were aligned to the modified reference by 2-pass mode of STAR_2.4.0b with default parameters.
Transcripts Per Million (TPM) values were estimated using RSEM v1.2.17 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: A processed file is tab-delimited and contains the raw TPM values for 549 single cells and 14 bulk tumors.

molecule: total RNA

organism: Homo sapiens

source_name: BC04_Single-cell RNA-seq

growth_protocol: On the day of surgery, all single cells were dissociated with mechanical and enzymatical method then immediately used for assay without any in vitro culture.

extract_protocol:
Dead cells in single cell suspensions were removed by Ficoll-Paque TM PLUS (GE healthcare) separation before loading to integrated fluidic circuit (IFC) chip. Each suspension was loaded to 10-17um IFC for mRNA sequencing chip then cDNA synthesis and amplification were performed with SMARTer Ultra Low RNA Kit (Clontech) in the C1TM Single-Cell Auto Prep System (Fluidigm). RNA spike-ins 1, 4 and 7 from ArrayControl TM RNA Spikes (ThermoFisher) were added to the lysis mix for validation of array and batch effect. Bulk RNAs were extracted from ~1x10^5 cells of suspensions or tumor tissues using RNeasy Plus Micro kit (Qiagen) and 10ng of total RNAs were amplified with SMARTer kit (Clonetech) under the same conditions as single cells. All of amplified cDNAs were quantified and qualified by the Qubit® 2.0 Fluorometer (Life Technologies) and 2100 Bioanalyzer (Agilent Technologies). Total 549 single cell cDNAs and 14 bulk samples were subjected to the RNA sequencing.
Starting with 0.375 ng of amplified cDNAs, sequencing libraries were constructed with the Nextera XT DNA Sample Prep Kit (Illumina). All of constructed libraries were quantified and qualified by the Qubit® 2.0 Fluorometer (Life Technologies) and 2100 Bioanalyzer (Agilent Technologies) then pooled without index overlapping. Finally pooled libraries were sequenced using the HiSeq2500 (Illumina) as 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit.

tag: patient id

tag: molecular subtype

value: human epidermal growth factor receptor 2 positive (HER2+)

tag: cell type

value: primary breast cancer


title: Late Treatment Sample 2

state: MA

country: USA

organism: Mus musculus

tag: tissue


title: Late Treatment Sample 3


title: Early Treatment Sample 3

source_name: kidney, diabetic, early treatment

value: P78-PEDF at 6 wks for 6 wks


title: BC04_89

description: Single-cell RNA-seq


title: BC04_88

description: Single-cell RNA-seq


title: BC04_86

description: Single-cell RNA-seq


title: BC04_85

description: Single-cell RNA-seq


title: Early Treatment Sample 2


title: Diabetes Sample 2

source_name: kidney, diabetic, vehicle

value: vehicle at 6 wks for 6 wks


title: Early Treatment Sample 1


title: BC04_82

description: Single-cell RNA-seq


title: Diabetes Sample 3


title: Normal Sample 2

source_name: kidney, normal, vehicle

tag: genotype/variation

value: wild-type

value: normal


title: PL-Seq-3

city: New York

first: Hongyan

last: Zou

state: NY

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

library_source: genomic

data_processing:
Library strategy: 5-hmC Hydroxymethyl Collecter-Seq
Raw sequencing reads were aligned to the mouse mm9 genome using default settings of Bowtie (v2.2.0). Only uniquely mapped reads were retained.
Alignments were subsequently filtered using the SAMtools package (v0.1.19) to remove duplicate reads.
Peak-calling was performed using MACS (v2.1.1) with “--broad -q 0.01” setting.
Differential region analysis between conditions was performed using diffReps (v1.55.4) with settings of 200 bp window size, 20 bp moving step size, and a nominal p-value of 0.0001.
Annotation of called peaks and differential regions to their genomic features (promoters, gene bodies, intergenic, etc.) was performed using the RegionAnalysis program of diffReps (v1.55.4)
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel files containing lists of DhMRs identified from PL-vs-ctrl, CL-vs-ctrl, PL-vs-CL comparisons

molecule: genomic DNA

source_name: dorsal root ganglia

extract_protocol:
Tissue was digested overnight at 65°C in TNES with 0.5 mg/ml Proteinase K. RNA was removed by digestion with RNase A (Thermo Scientific) for 1 hour at 37°C. After RNase treatment, DNA was precipitated using high salt and ethanol.
DNA was sheared into fragments of an average size of 250 bp using the Biorupter Twin (Diagenode) device, using the “low” setting and 30 cycles of 30 seconds “on”, followed by 30 seconds “off”. Fragment size was confirmed by gel electrophoresis, and DNA concentrations were confirmed before enrichment. Enrichment for 5-hmC was performed with the Hydroxymethyl Collecter-Seq Kit (Active Motif) according to manufacturer’s instruction. Briefly, 4.3 μg of sheared genomic DNA was used for each sample. The DNA was treated with a β-glucosyltransferase enzyme to chemically modify 5hmC nucleotides with a sugar moiety, which was then conjugated to biotin. The biotinylated 5hmC containing DNA fragments were captured with streptavidin conjugated to magnetic beads, washed, and eluted as 5-hmC-enriched DNA. The 5-hmC enriched DNA samples, plus one un-enriched sample from each experimental condition, designated “input,” were prepared for Illumina sequencing using the NEBNext ChIP-seq kit (New England Biolabs). Briefly, 10ng DNA of each 5-hmC enriched or input sample were subjected to end repair, A-tailing, adapter ligation, size selection, and PCR enrichment according to manufacturer’s directions. DNA concentrations and library fragment sizes were assessed by Qubit and Bioanalyzer. Libraries were submitted to the New York Genome Center for Illumina 50bp paired-end sequencing on an Illumina HiSeq 2500 device, with 6 barcoded samples in each lane.  Enrichment for 5-hmC was performed with the Hydroxymethyl Collecter-Seq Kit (Active Motif) according to manufacturer’s instruction

treatment_protocol: L4, L5, and L6 DRGs were dissected from animals subjected to dorsal column lesion or peripheral lesion 24 hours prior. Contralateral DRGs from animals subjected to the peripheral lesion were collected as uninjured controls. DRGs from three separate animals were pooled for each biological replicate.

value: peripheral lesion of sciatic nerve

value: dorsal root ganglia

tag: enrichment method

value: hmC-pulldown according to Hydroxymethyl Collector kit


title: BC04_69

description: Single-cell RNA-seq


title: Normal Sample 1


title: BC04_71

description: Single-cell RNA-seq


title: PL-Seq-2


title: BC04_64

description: Single-cell RNA-seq


title: BC04_91

description: Single-cell RNA-seq


title: BC04_66

description: Single-cell RNA-seq


title: BC04_61

description: Single-cell RNA-seq


title: BC04_60

description: Single-cell RNA-seq


title: Diabetes Sample 1


title: Input-PL


title: Normal Sample 3


title: Input-Ctl

value: uninjured control


title: BC04_58

description: Single-cell RNA-seq


title: BC04_59

description: Single-cell RNA-seq


title: BC04_78

description: Single-cell RNA-seq


title: BC04_56

description: Single-cell RNA-seq


title: BC04_63

description: Single-cell RNA-seq


title: DCL-Seq-3

value: central dorsal column lesion


title: BC04_77

description: Single-cell RNA-seq


title: DCL-Seq-2


title: BC04_53

description: Single-cell RNA-seq


title: BC04_54

description: Single-cell RNA-seq


title: Ctl-Seq-2


title: Ctl-Seq-1


title: BC04_49

description: Single-cell RNA-seq


title: BC04_41

description: Single-cell RNA-seq


title: PL-Seq-1


title: BC04_40

description: Single-cell RNA-seq


title: 8W-KOTAC5

city: Philadelphia

first: Long

last: Gao

state: PA

address: 4002 Colket Translational Research Building (CTRB) 3501 Civic Center Boulevard

institute: The Children’s Hospital of Philadelphia

data_processing:
Read quality assessed via FastQC
Sequenced reads mapped to the reference mouse genome (release mm9) through Tophat
Gene level read counts estimated by GenomicRanges for Ensembl genes(release 66)
Gene level FPKM estimated by Cufflinks for Ensembl genes(release 66)
Genome_build: mm9
Supplementary_files_format_and_content: excel file, FPKM matrix

growth_protocol: All animal procedures were performed with the approval of the Institutional Animal Care and Use Committee of the University of Washington. Mice were fed on rodent diet and water available ad libitum with a 12-hour light/dark cycle in a vivarium. Cardiac restricted Ndufs4-deletion was generated by crossing mice harbouring the modified ndufs4 gene containing loxP sites 8 with transgenic C57BL6 mice expressing CRE recombinase under the αMHC promoter.

extract_protocol:
Cardiac tissues were harvested and snap frozen in liquid nitrogen at 1, 2, 4, and 8 weeks after surgery. Total RNA was isolated from frozen cardiac tissue using the RNeasy Kit for fibrotic tissues (Qiagen) and treated with Dnase to remove genomic DNA contamination. Purity and integrity of RNA was checked using Agilent Bioanalyzer 2100. All samples used for RNA sequencing had a Bioanalyzer RIN number of at least 8.
Illumina TruSeq RNA sample preparation kit was used to generate sequencing libraries.  Illumina Multiplexing barcode adapters were added during library preparation.

treatment_protocol: Adult male mice (3-4 months old) received transverse aortic constriction (TAC) to induce chronic pressure overload or sham surgeries. Surgeries were performed as previously described. Briefly, mice were anesthetized with sodium pentobarbital (75 mg/kg), the aortas were exposed with left thoracotomy, and constrictions on each animal were created using a 7-0 ligature around the vessels that were tied against a 27-gauge blunt needle.  Sham surgeries were performed as above without the constriction of the aorta. Cardiac geometry and function were recorded at 1, 2, 4, and 8 weeks using echocardiography with the VEVO 770 system equipped with a 707B scan head. All measurements were averaged from six cardiac cycles.

value: Cardiac tissue

tag: time after surgery

value: 8 week

tag: environmental stress

value: trans-aortic constriction

tag: strain

value: Ndufs4 knockout


title: 8W-KOTAC4

value: male


title: BC04_39

description: Single-cell RNA-seq


title: 8W-KOTAC3


title: DCL-Seq-1


title: 8W-KOTAC2


title: Ctl-Seq-3


title: BC04_36

description: Single-cell RNA-seq


title: BC04_33

description: Single-cell RNA-seq


title: 8W-KOSh3

value: Sham control


title: BC04_37

description: Single-cell RNA-seq

value: human epidermal growth factor receptor 2 positive (HER2+)


title: 8W-KOSh4


title: BC04_45

description: Single-cell RNA-seq

value: primary breast cancer


title: BC04_31

description: Single-cell RNA-seq


title: 3C-Dorso_48h_rep3

city: Münster

first: Sara

middle: A

last: Wickström

address: Röntgenstraße 20

department: Cell & Tissue Dynamics

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description:
Diff gene exp of cultured HFSCs treated 48h with Dorso or Cyclo 3C-Dorso vs 3C-Cyclo
Tophat2 alignment

data_processing:
Fastqc (0.11.2) was used for basecalling.
Adapters were removed using Cutadapt (1.5)
Fastq files were mapped to M. musculus genome (GRCm38_79) using Tophat2 (2.0.13).
Reads were counted from the bam files using the featureCount algorithm from the SubRead software package (1.4.2).
Differential gene expression was analyzed using the DESeq2 (1.8.1). Adjusted p-values ≤ 0.05 have been computed.
Genome_build: GRCm38_79
Supplementary_files_format_and_content: fpkm

molecule: polyA RNA

source_name: epidermis

growth_protocol: Total epidermal cells were grown in HFSC cultures (also known as 3C cultures) for 10-14 days

extract_protocol:
Total RNA was isolated with the RNeasy Plus Micro Kit (Qiagen). RNA quality was determined using an Agilent 2200 TapeStation.
Libraries were prepared with NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs)

treatment_protocol: Inhibitor treatment was carried out for 48 h by adding the inhibitors to the culture medium

value: keratinocyte

value: cell cultured


title: 8W-KOSh2


title: 3C-Dorso_48h_rep2


title: 3C-Dorso_48h_rep1


title: BC04_32

description: Single-cell RNA-seq


title: 3C-Cylo_48h_rep3


title: 8W-WTTAC7

value: WT


title: 3C-Cylo_48h_rep2


title: BC04_29

description: Single-cell RNA-seq


title: 8W-WTTAC6


title: 3C-Cylo_48h_rep1


title: 3C-CD34neg a6+_rep3

description:
Diff gene exp of cultured HFSCs 3C-CD34+ a6+ vs 3C-CD34neg a6+
Tophat2 alignment


title: BC04_28

description: Single-cell RNA-seq


title: 8W-WTTAC5


title: BC04_27

description: Single-cell RNA-seq


title: 3C-CD34neg a6+_rep2


title: 3C-CD34neg a6+_rep1


title: 8W-WTTAC2


title: 8W-KOSh1


title: 3C-CD34+ a6+_rep3


title: 3C-CD34+ a6+_rep2


title: 3C-CD34+ a6+_rep1


title: 8W-WTSh4


title: BC04_24

description: Single-cell RNA-seq


title: 3C-HFSCs-rep2

description: TopHat2 alignment

data_processing:
fastqc 0.11.3 - quality check
flexbar 2.5 - quality trimming
hisat 0.1.6-beta - aligner
stringtie 1.1.0 - transcripts assembly
cuffmerge (cufflinks 2.2.1) - merging of assemblies (ensembl GTF-guided de-novo assembly)
cuffquant (cufflinks 2.2.1)- transcript expression profiles / quantification
cuffdiff (cufflinks 2.2.1) - differential expression analysis
cummeRbund 2.6.1- QC
Genome_build: GRCm38_80

extract_protocol:
RNA was isolated with RNAeasy Micro Plus Kit (Qiagen) according to manufacturer's instructions.
Libraries were prepared with NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs)

value: Cultured hair follicle stem cells (HFSCs)

tag: genotype

value: wild type


title: BC04_25

description: Single-cell RNA-seq


title: 3C-HFSCs-rep3

description: TopHat2 alignment


title: 8W-WTSh3


title: 8W-WTSh2


title: BC04_21

description: Single-cell RNA-seq


title: Epi-rep3

description: TopHat2 alignment

value: total epidermal cells


title: BC04_23

description: Single-cell RNA-seq


title: Epi-rep1

description: TopHat2 alignment


title: 3C-HFSCs-rep1

description: TopHat2 alignment


title: 8W-WTSh1


title: Epi-rep2

description: TopHat2 alignment


title: 4W-KOTAC5

value: 4 week


title: BC04_15

description: Single-cell RNA-seq


title: BC04_20

description: Single-cell RNA-seq


title: HFSCs-rep1

description: TopHat2 alignment

value: FACS purified hair follicle stem cells (HFSCs)


title: 4W-KOTAC3


title: BC04_13

description: Single-cell RNA-seq


title: 4W-KOTAC2


title: HFSCs-rep2

description: TopHat2 alignment


title: 4W-KOTAC1


title: HFSCs-rep3

description: TopHat2 alignment


title: BC04_09

description: Single-cell RNA-seq


title: 4W-KOSh4


title: BC04_11

description: Single-cell RNA-seq


title: BC04_07

description: Single-cell RNA-seq


title: BC04_05

description: Single-cell RNA-seq


title: 4W-KOSh2


title: 4W-KOSh3


title: 4W-KOSh1


title: BC04_08

description: Single-cell RNA-seq


title: Input-DCL

value: central dorsal column lesion

value: dorsal root ganglia


title: 4W-WTTAC4

value: Cardiac tissue


title: BC04_02

description: Single-cell RNA-seq


title: BC01_95

description: Single-cell RNA-seq

source_name: BC01_Single-cell RNA-seq

value: estrogen receptor positive (ER+)


title: BC01_87

description: Single-cell RNA-seq


title: 4W-WTTAC2

value: trans-aortic constriction


title: 4W-WTSh4

value: male


title: 4W-WTTAC1


title: 4W-WTTAC3


title: BC04_01

description: Single-cell RNA-seq


title: 4W-WTSh3

value: Sham control


title: BC01_74

description: Single-cell RNA-seq


title: BC01_72

description: Single-cell RNA-seq


title: 4W-WTSh1


title: BC01_70

description: Single-cell RNA-seq


title: BC01_66

description: Single-cell RNA-seq


title: BC01_69

description: Single-cell RNA-seq


title: 2W-KOTAC4

value: 2 week

value: Ndufs4 knockout


title: BC01_57

description: Single-cell RNA-seq

value: primary breast cancer


title: 2W-KOTAC2


title: BC01_55

description: Single-cell RNA-seq


title: BC01_77

description: Single-cell RNA-seq


title: 2W-KOSh2


title: BC01_34

description: Single-cell RNA-seq


title: 2W-KOSh3


title: 2W-KOSh4


title: BC01_53

description: Single-cell RNA-seq


title: BC01_12

description: Single-cell RNA-seq


title: BC01_33

description: Single-cell RNA-seq


title: 2W-WTTAC2


title: 2W-WTTAC3


title: BC01_10

description: Single-cell RNA-seq


title: BC01_05

description: Single-cell RNA-seq


title: 4W-WTSh2


title: BC01_06

description: Single-cell RNA-seq


title: 2W-KOSh1


title: 2W-WTTAC1


title: BC01_04

description: Single-cell RNA-seq


title: BC01_03

description: Single-cell RNA-seq


title: 2W-WTSh3


title: 2W-WTSh4


title: 2W-KOTAC3


title: 2W-WTSh2


title: BC01_02

description: Single-cell RNA-seq


title: BC07LN_Pooled

description: Pooled RNA-seq

source_name: BC07LN_Pooled RNA-seq

value: triple-negative breast cancer (TNBC)

value: metastatic breast cancer


title: 2W-KOTAC1


title: 2W-WTSh1

value: WT


title: 2W-WTTAC4


title: BC01_08

description: Single-cell RNA-seq


title: BC07_Tumor

description: Bulk RNA-seq

source_name: BC07_Tumor RNA-seq


title: BC03LN_Pooled

description: Pooled RNA-seq

source_name: BC03LN_Pooled RNA-seq

value: double positive (ER+ and HER2+)


title: BC04_Pooled

description: Pooled RNA-seq

source_name: BC04_Pooled RNA-seq

value: human epidermal growth factor receptor 2 positive (HER2+)


title: BC03_Pooled

description: Pooled RNA-seq

source_name: BC03_Pooled RNA-seq


title: 1W-KOTAC1

value: 1 week


title: 1W-KOSh3


title: BC01_Tumor

description: Bulk RNA-seq

source_name: BC01_Tumor RNA-seq


title: Brain RNA N 2

city: Innsbruck

first: Alexandra

last: Lusser

state: Tyrol

address: Innrain 80

department: Molecular Biology

country: Austria

institute: Biocenter Medical University Innsbruck

data_processing:
raw fastq files filtered (fastq_quality_filter -p 85 -q 30) and quality trimmed (fastq_quality_trimmer -t 30 -l 35) using fastx_tookit (version 0.0.14), adapter sequences were removed using flexbar (version 2.5)
clean reads were aligned to the GRCm38/mm10 genome using meRanGs available with meRanTK (version 1.0) using default settings
m5C candidate sites were called using meRanCall available with meRanTK (version 1.0) (Rieder et al. 2016) with FDR < 0.01. Based on the m-bias plots obtained from meRanGs, 10 bases on the 5’ end of forward- and 7 bases on the 5’ end of reverse reads were excluded from methylation calling. Furthermore, only bases with a base-call quality score of Q >= 35 for single end- and Q >= 30 for paired-end reads were considered for methylation calling. Candidate cytosine positions were covered by at least 10 reads and had a conversion rate less than 0.8.
An m5C candidate had to be present in all three replicates of a given sample. Subsequently, the full length transcripts containing an m5C candidate were extracted from the RefSeq database (GRCm38.p3) and subjected to secondary structure analysis using the RNAfold of the Vienna RNA package (version 2.2.8) (Lorenz R et al. 2011). We calculated the maximum expected accuracy (MEA) structure at 70°C using a gamma of 0.1. The maximum allowed distance between two bases in a pair was set to 150 nt. For introns and non-annotated sequences only 300 nt around the m5C candidate position were subjected to folding analysis. Only candidate m5C sites that were predicted not to be base-paired in the resulting structure were retained
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content:
Excel (.xlsx) files containing methylation sites found in minimum 3 replicates - additionally, excel files with information about m5C sites in individual replicates
Files containing m5C sites in minimum 3 replicates (Brain_total; Brain_nuclear; ESC_total; ESC_nuclear) - files containing m5C sites in the individual replicates (Brain nuclear_indReplicates; Brain total_indReplicates; ESC nuclear_indReplicates; ESC total_indReplicates)

source_name: nuclear poly(A)RNA

extract_protocol:
RNA was isolated in biological triplicates from pulverized whole brain tissue and mouse embryonic stem cells (CN) as well as from nuclei (N) of both sources using TRIzol (Sigma Aldrich) following the manufacturer’s recommendations. RNA was treated with 2U of DNase I (NEB) for 15 min at 37°C and purified using RNA Clean & Concentrator 25 Kit (Zymo Research). Isolated RNA was then subjected to two rounds of poly(A)RNA enrichment  using fresh Dynabeads (Ambion) for each round.
Sequencing libraries were prepared using the ScriptSeq V2 RNA-Seq Library Preparation Kit (Epicentre), purified with AMPure XP beads (Beckman Coulter) and quantified using KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems). RNA fragmenting was omitted as bisulfite treatment results in fragmentation to 100-250 nt. Libraries were multiplexed at 11 pM and sequenced on an Illuma HiSeq 1500 plattform using 100 bp single end reads

tag: Sex

value: female

tag: age

value: 7 weeks

value: brain


title: 1W-KOSh4

value: Cardiac tissue


title: Brain RNA N 3


title: 1W-KOTAC3


title: 1W-KOSh1


title: Brain RNA N 1


title: miR17-92 knockout 3

first: Seung-Nam

last: Kim

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Whole RNA sequencing was performed at the Weill Cornell Genomics Core Facility using an IlluminaHiseq 1000.
Homopolymers, adapters, and distribution of base quality of raw sequences from each sample were investigated using FastQC (version 0.10.1).
Reads were aligned to the mm9 mouse transcripts using STAR (Dobin et al., 2013) (version 2.3.0e) using default parameters, and resulting bam files were sorted and the index was analyzed using the samtools (Li et al., 2009).
Gene counts were obtained by applying HTSeq (Anders et al., 2014) to the sorted bam files, and only unique-mapping reads were used.
The DESeq2 (Love and Anders) (version 1.4.5) R package was employed to normalize gene count data, and to detect differentially expressed genes (DEGs) between wild type (WT) and miR-17-92 KO with false discovery rate (FDR) q<0.1.
Genome_build: mm9
Supplementary_files_format_and_content: counts files include values for each Sample

source_name: hippocampus

extract_protocol:
The adult hippocampi of the 13 weeks old mice were dissected from three wild-type and three miR-17-92 KO mice, each of them from a different litter. Total RNA was extracted and purified using the RNeasy mini kit with optional on-column DNAse digestion (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hippocampus

value: miR17-92 knockout


title: BC01_Pooled

description: Pooled RNA-seq

source_name: BC01_Pooled RNA-seq

value: estrogen receptor positive (ER+)


title: miR17-92 knockout 2


title: Brain RNA CN 3

source_name: poly(A)RNA


title: wildtype 3

value: wildtype


title: miR17-92 knockout 1


title: 1W-WTTAC4

value: trans-aortic constriction

value: male


title: 1W-WTTAC5


title: wildtype 2


title: Brain RNA CN 1


title: 1W-KOTAC2

value: Ndufs4 knockout


title: 1W-KOTAC6


title: 1W-WTTAC2


title: 1W-WTTAC1


title: wildtype 1


title: ESC RNA N 2

value: embryonic stem cells


title: ESC RNA N 3


title: 1W-WTSh4

value: Sham control


title: ESC RNA N 1


title: ESC RNA CN 3


title: 1W-WTSh2

value: WT


title: 1W-WTSh1


title: ESC RNA CN 2


title: Brain RNA CN 2


title: ESC RNA CN 1


title: TSPO KO rep3

status: Public on Dec 08 2016

city: Beijing

first: Jianmin

last: Zhang

state: Beijing

address: 5# Dong Dan San Tiao

department: Immunology

country: China

institute: Peking Union Medical College

data_processing:
Raw data was filtered and got Clean data
Reads  mapping using tophat
Gfold was employed for transcription  expression counts
TMM method for count adjust
Negative binomial distribution test was used for Significant difference test
FDR for p value adjust
Genome_build: mm10
Supplementary_files_format_and_content: all six sample COUNTS were presented in worksheet"Processed data files"

source_name: TSPO KO_lung

growth_protocol: mice were breeding in SPF condition

extract_protocol:
TSPO WT and KO mice were anesthetized by 2% sodium pentobarbital, after abdominal aorta bleeding, lung tissues were removed and immerse them into RNAlater® (Thermofisher), flash frozen in liquid nitrogen then -80℃, RNA extraction and sequencing were performed using standard illumina protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: stain background

value: 6-8 weeks

value: TSPO knockout (KO)

value: lung


title: TSPO WT rep1

source_name: TSPO WT_lung

value: wild type (WT)


title: TSPO KO rep1


title: H9-1-C48_S88.IPF003

city: Los Angeles

first: Jie

last: Tang

address: 8700 Beverly Blvd

institute: Cedars Sinai Medical Center

data_processing:
Briefly, the analytic pipeline consisted of four components that included: gene pre-filtering and normalization, reiterative cell type mapping (hierarchical clustering followed by PCA), cell specific signature genes identification, and driving forces prediction for each cell type.  Detailed methods and code for this analytic pipeline are found in “SINCERA: A pipeline for single-cell RNA-Seq profiling analysis.” (3) and are available on line at https://research.cchmc.org/pbge/sincera.html as an open access program.
Genome_build: gencode 23
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: lung

extract_protocol:
Cells were isolated from two normal controls and six IPF tissue samples prepared as described for FACS except that cells were sorted initially with CD326 prior to single cell isolation.  For single cell analysis cell capture, lysis, reverse transcription and cDNA amplification were performed on the C1 IFC for mRNA-seq on Fluidigm C1 Single-Cell Auto Prep System following the manufacturer’s protocol.
Medium sized C1 mRNA-Seq chips were used to capture each cell-cycle fraction.  The C1 Auto-prep system captures the dissociated single cells across 96 wells and performs cell lysis, cDNA synthesis with reverse transcription and PCR reaction using the SMARTer Ultra Low Input RNA Kit v3 (ClonTech, Mountain View, CA).  Cells captured across the 96 wells are manually inspected as a quality control measure to remove empty well, doublets or debris containing wells.  cDNA from several representative cells are checked by High Sensitivity DNA chips using Fragment Analyzer (Advanced Analytical) and all cDNA libraries are quantitated via Qubit (Thermo Fisher Scientific, Carlsbad, CA).  Libraries for each of the 96 captured cells are prepared using the Illumina Nextera XT DNA sample preparation kit with 96 dual barcoded indices

tag: diagnosis

value: IPF

tag: patientid


title: TSPO WT rep2


title: H9-1-C48_S41.IPF002


title: H9-1-C48_S40.IPF012


title: H9-1-C48_S35.IL006


title: 1W-WTSh3

value: 1 week

tag: gender


title: H8-1-C47_S61.IPF002


title: H7-1-C46_S8.CC006

value: Control


title: H7-1-C46_S69.IPF002


title: H8-1-C47_S40.IPF003


title: H7-1-C46_S38.IPF012


title: H7-1-C46_S16.IPF003


title: H6-1-C91_S57.IL006


title: H5-1-C92_S77.IPF002


title: H4-1-C93_S74.IPF003


title: H4-1-C93_S92.IL006


title: TSPO KO rep2


title: TSPO WT rep3


title: H4-1-C93_S56.IPF012


title: H3-1-C45_S10.IPF012


title: 1W-KOSh2

value: Cardiac tissue


title: H3-1-C45_S5.CC006


title: H3-1-C45_S26.IPF003


title: H3-1-C45_S67.IPF002


title: H3-1-C45_S20.IL006


title: H1-1-C43_S73.IPF003


title: H2-1-C44_S66.IPF002


title: H2-1-C44_S61.IPF012


title: H1-1-C43_S65.IPF002


title: H11-1-C95_S60.IL006


title: H10-1-C96_S41.IPF003


title: G9-1-C42_S79.CC006


title: H10-1-C96_S12.IL006


title: G9-1-C42_S76.IPF003


title: G9-1-C42_S37.IPF012


title: G9-1-C42_S30.IPF002


title: G8-1-C41_S78.CC006


title: G8-1-C41_S58.IL006


title: G8-1-C41_S28.IPF003


title: G8-1-C41_S51.IPF002


title: H2-1-C44_S65.CC006


title: H2-1-C44_S43.IL006


title: H1-1-C43_S64.CC006


title: G7-1-C40_S60.IPF002


title: G7-1-C40_S77.CC006


title: G7-1-C40_S10.IL006


title: G7-1-C40_S4.IPF003


title: G6-1-C85_S7.CC006


title: G3-1-C39_S8.IL006


title: G5-1-C86_S39.IPF003


title: G3-1-C39_S57.IPF002


title: G2-1-C38_S56.IPF002


title: G3-1-C39_S47.IPF012


title: G6-1-C85_S68.IPF002


title: G2-1-C38_S55.CC006


title: G5-1-C86_S37.CC006


title: G3-1-C39_S24.CC006


title: G3-1-C39_S14.IPF003


title: H9-1-C48_S10.CC006


title: G10-1-C90_S20.IPF002


title: G1-1-C37_S14.IPF012


title: G1-1-C37_S54.CC006


title: F9-1-C36_S70.CC006


title: F9-1-C36_S23.IL006


title: F5-1-C80_S45.IL006


title: F8-1-C35_S40.IPF002


title: F5-1-C80_S73.IPF002


title: F7-1-C34_S50.IPF002


title: F7-1-C34_S68.CC006


title: F5-1-C80_S27.IPF003


title: F4-1-C81_S62.IPF003


title: F3-1-C33_S14.CC006


title: F3-1-C33_S91.IL006


title: F2-1-C32_S45.CC006


title: F12-1-C82_S89.IPF003


title: F12-1-C82_S32.IPF002


title: F2-1-C32_S31.IL006


title: F12-1-C82_S53.CC006


title: F10-1-C84_S9.IPF002


title: F1-1-C31_S1.IPF012


title: F1-1-C31_S55.IPF002


title: F11-1-C83_S53.IPF002


title: H8-1-C47_S9.CC006


title: F1-1-C31_S44.CC006


title: E9-1-C30_S11.IL006


title: E8-1-C29_S59.CC006


title: F6-1-C79_S59.IPF002


title: E9-1-C30_S24.IPF012


title: E8-1-C29_S46.IL006


title: E8-1-C29_S28.IPF012


title: E8-1-C29_S29.IPF002


title: E7-1-C28_S58.CC006


title: E6-1-C73_S67.CC006


title: E7-1-C28_S39.IPF002


title: F4-1-C81_S37.IPF002


title: F3-1-C33_S47.IPF002


title: E5-1-C74_S58.IPF002


title: F2-1-C32_S46.IPF002


title: E6-1-C73_S49.IPF002


title: E3-1-C27_S4.CC006


title: E4-1-C75_S80.IL006


title: E3-1-C27_S79.IL006


title: E3-1-C27_S36.IPF002


title: E7-1-C28_S30.IPF012


title: E3-1-C27_S29.IPF012


title: E9-1-C30_S60.CC006


title: E2-1-C26_S34.CC006


title: E2-1-C26_S35.IPF002


title: E2-1-C26_S19.IL006


title: E1-1-C25_S45.IPF002


title: E11-1-C77_S52.CC006


title: E11-1-C77_S48.IL006


title: E10-1-C78_S81.IPF002


title: E12-1-C76_S21.IPF002


title: E10-1-C78_S61.CC006


title: D9-1-C22_S94.IL006


title: E10-1-C78_S22.IPF012


title: D9-1-C22_S54.IPF012


title: D9-1-C22_S64.IPF003


title: D9-1-C22_S19.IPF002


title: D8-1-C23_S18.IPF002


title: D7-1-C24_S93.IL006


title: D8-1-C23_S49.CC006


title: D7-1-C24_S44.IPF012


title: D7-1-C24_S48.CC006


title: D7-1-C24_S28.IPF002


title: D6-1-C69_S75.IPF003


title: D5-1-C68_S33.IL006


title: D6-1-C69_S38.IPF002


title: D5-1-C68_S15.IPF003


title: D4-1-C67_S46.CC006


title: D4-1-C67_S15.IPF002


title: D4-1-C67_S68.IL006


title: D3-1-C19_S67.IL006


title: E10-1-C78_S83.IL006


title: D2-1-C20_S7.IL006


title: D2-1-C20_S22.CC006


title: D2-1-C20_S60.IPF012


title: D12-1-C72_S10.IPF002


title: D3-1-C19_S25.IPF002


title: D12-1-C72_S43.CC006


title: D1-1-C21_S61.IPF003


title: D1-1-C21_S34.IPF002


title: D1-1-C21_S33.CC006


title: D1-1-C21_S30.IL006


title: D11-1-C71_S65.IPF003


title: D11-1-C71_S42.CC006


title: D11-1-C71_S20.IPF012


title: D1-1-C21_S12.IPF012


title: D10-1-C70_S71.IPF002


title: D5-1-C68_S48.IPF002


title: D4-1-C67_S50.IPF003


title: D10-1-C70_S51.CC006


title: D5-1-C68_S16.CC006


title: D10-1-C70_S71.IL006


title: D3-1-C19_S35.CC006


title: C9-1-C16_S8.IPF002


title: C9-1-C16_S82.IL006


title: C9-1-C16_S40.CC006


title: C8-1-C17_S39.CC006


title: C7-1-C18_S81.IL006


title: C8-1-C17_S45.IPF012


title: C6-1-C63_S63.IPF012


title: C6-1-C63_S27.IPF002


title: C9-1-C16_S32.IPF012


title: C6-1-C63_S63.IPF003


title: C5-1-C62_S6.CC006


title: C5-1-C62_S3.IPF003


title: C5-1-C62_S21.IL006


title: C4-1-C61_S56.R1.IL006


title: D11-1-C71_S36.IL006


title: C5-1-C62_S39.IPF012


title: C4-1-C61_S4.IPF002


title: C3-1-C13_S14.IPF002


title: C3-1-C13_S23.CC006


title: C2-1-C14_S90.IL006


title: C4-1-C61_S33.IPF012


title: C2-1-C14_S13.IPF002


title: C2-1-C14_S12.CC006


title: C12-1-C66_S77.IPF003


title: C8-1-C17_S34.IL006


title: C12-1-C66_S82.IPF002


title: C1-1-C15_S5.IPF012


title: C1-1-C15_S49.IPF003


title: C12-1-C66_S13.IPF012


title: C11-1-C65_S42.IPF002


title: C1-1-C15_S21.CC006


title: C11-1-C65_S31.CC006


title: C10-1-C64_S62.IPF002


title: C10-1-C64_S41.CC006


title: C1-1-C15_S23.IPF002


title: C1-1-C15_S18.IL006


title: B9-1-C10_S70.IL006


title: C10-1-C64_S29.IPF003


title: B9-1-C10_S29.CC006


title: B8-1-C11_S53.IPF012


title: B8-1-C11_S7.IPF002


title: B8-1-C11_S28.CC006


title: B9-1-C10_S80.IPF002


title: C4-1-C61_S36.CC006


title: B7-1-C12_S69.IL006


title: B6-1-C57_S57.CC006


title: B6-1-C57_S6.IPF012


title: B5-1-C56_S41.IPF012


title: B6-1-C57_S51.IPF003


title: B6-1-C57_S16.IPF002


title: B4-1-C55_S76.IPF002


title: B4-1-C55_S62.IPF012


title: B4-1-C55_S38.IPF003


title: B4-1-C55_S44.IL006


title: B3-1-C07_S46.IPF012


title: B3-1-C07_S3.IPF002


title: B2-1-C08_S85.IPF003


title: B3-1-C07_S2.IPF003


title: B2-1-C08_S78.IL006


title: B2-1-C08_S2.IPF002


title: B1-1-C09_S37.IPF003


title: B11-1-C59_S31.IPF012


title: B11-1-C59_S31.IPF002


title: B10-1-C58_S57.IPF012


title: B10-1-C58_S59.IL006


title: B12-1-C60_S72.IPF002


title: B1-1-C09_S12.IPF002


title: B10-1-C58_S52.IPF002


title: B10-1-C58_S17.IPF003


title: A9-1-C04_S70.IPF002


title: A9-1-C04_S52.IPF003


title: B7-1-C12_S17.IPF002


title: A8-1-C05_S79.IPF002


title: A8-1-C05_S3.IPF012


title: A8-1-C05_S22.IL006


title: A7-1-C06_S87.IPF003


title: A5-1-C50_S9.IL006


title: A7-1-C06_S21.IPF012


title: A6-1-C51_S55.IPF012


title: A6-1-C51_S5.IPF002


title: A7-1-C06_S6.IPF002


title: A5-1-C50_S11.IPF012


title: B1-1-C09_S23.IPF012


title: A5-1-C50_S86.IPF003


title: A4-1-C49_S32.IL006


title: A3-1-C01_S49.IPF012


title: A12-1-C54_S63.IPF002


title: A4-1-C49_S15.IPF012


title: A3-1-C01_S55.IL006


title: A1-1-C03_S6.IL006


title: A11-1-C53_S24.IL006


title: A11-1-C53_S4.IPF012


title: A1-1-C03_S64.IPF012


title: 94-N710-S508-F3.IPF009


title: 94-F3.CC019


title: A1-1-C03_S25.IPF003


title: A10-1-C52_S5.IPF003


title: 93-N709-S508-H10.CC002


title: 93-D4.CC019


title: 93-N709-S508-G1.IPF009


title: 92-N708-S508-H9.CC002


title: 92-N708-S508-H1.IPF009


title: 91-N707-S508-D5.IPF009


title: 92-D2.CC019


title: 91-H9.CC019


title: A12-1-C54_S72.IL006


title: 90-E8.CC019


title: 90-N706-S508-F2.IPF009


title: A12-1-C54_S48.IPF012


title: 89-N705-S508-E6.CC002


title: 89-N705-S508-B8.IPF009


title: 94-N710-S508-H11.CC002


title: 89-N705-S508-A8.IPF010


title: 88-N704-S508-F7.IPF009


title: A10-1-C52_S47.IL006


title: 88-N704-S508-A1.IPF010


title: 88-A2.CC019


title: 87-N703-S508-C1.IPF010


title: 89-A12.CC019


title: 87-N703-S508-D8.IPF009


title: 87-N703-S508-B4.CC002


title: 87-H6.CC019


title: 86-N702-S508-H2.CC002


title: 90-N706-S508-G9.IPF010


title: 91-N707-S508-G8.CC002


title: 86-N702-S508-D2.IPF009


title: 86-N702-S508-A11.IPF010


title: 86-C1.CC019


title: 82-N710-S507-G8.IPF009


title: 85-N701-S508-B8.IPF010


title: 82-N710-S507-G11.CC002


title: 85-N701-S508-H1.CC002


title: 82-D1.CC019


title: 81-N709-S507-E9.IPF009


title: 81-N709-S507-G10.CC002


title: 80-F7.CC019


title: 88-N704-S508-D5.CC002


title: 81-E4.CC019


title: 80-N708-S507-G9.CC002


title: 79-N707-S507-D6.IPF009


title: 79-A3.CC019


title: 78-N706-S507-E7.CC002


title: 79-N707-S507-F8.CC002


title: 80-N708-S507-A6.IPF009


title: 78-N706-S507-A3.IPF009


title: 78-B7.CC019


title: 78-N706-S507-E8.IPF010


title: 77-N705-S507-C6.CC002


title: 85-E10.CC019


title: 77-E3.CC019


title: 76-N704-S507-G5.IPF009


title: 76-N704-S507-D9.IPF010


title: 76-N704-S507-C5.CC002


title: 75-N703-S507-F7.IPF010


title: 75-N703-S507-D11.IPF009


title: 75-N703-S507-A4.CC002


title: 74-N702-S507-F4.IPF010


title: 74-B4.CC019


title: 73-N701-S507-A5.IPF010


title: 71-N711-S506-F12.CC002


title: 70-N710-S506-H3.IPF009


title: 73-B8.CC019


title: 70-N710-S506-F11.CC002


title: 73-N701-S507-G1.CC002


title: 74-N702-S507-G2.CC002


title: 73-N701-S507-A2.IPF009


title: 75-C10.CC019


title: 69-N709-S506-C8.IPF009


title: 68-E9.CC019


title: 69-A11.CC019


title: 74-N702-S507-F11.IPF009


title: 70-D10.CC019


title: 68-N708-S506-G7.IPF009


title: 77-N705-S507-C7.IPF010


title: 68-N708-S506-F9.CC002


title: 67-N707-S506-E8.CC002


title: 77-N705-S507-A9.IPF009


title: 67-N707-S506-E2.IPF009


title: 66-N706-S506-D7.CC002


title: 66-N706-S506-B4.IPF009


title: 67-B12.CC019


title: 66-H10.CC019


title: 66-N706-S506-A4.IPF010


title: 65-N705-S506-C8.IPF010


title: 65-N705-S506-B6.CC002


title: 90-N706-S508-F7.CC002


title: 65-N705-S506-B2.IPF009


title: 69-N709-S506-F10.CC002


title: 65-C2.CC019


title: 64-N704-S506-B10.IPF010


title: 64-N704-S506-B5.CC002


title: 64-N704-S506-A8.IPF009


title: 64-G4.CC019


title: 63-N703-S506-G3.CC002


title: 63-N703-S506-B3.IPF010


title: 63-N703-S506-A11.IPF009


title: 62-N702-S506-C5.IPF009


title: 62-N702-S506-C3.IPF010


title: 62-N702-S506-F2.CC002


title: 62-E1.CC019


title: 61-N701-S506-F1.CC002


title: 61-C9.CC019


title: 57-N709-S505-D3.IPF009


title: 58-A7.CC019


title: 57-N709-S505-E10.CC002


title: 58-N710-S505-E11.CC002


title: 57-F10.CC019


title: 61-N701-S506-D2.IPF010


title: 56-N708-S505-C3.IPF009


title: 56-A5.CC019


title: 59-N711-S505-E12.CC002


title: 56-N708-S505-E9.CC002


title: 55-N707-S505-B12.IPF009


title: 55-N707-S505-D8.CC002


title: 55-B5.CC019


title: 54-N706-S505-F8.IPF010


title: 53-N705-S505-E12.IPF009


title: 54-N706-S505-D7.IPF009


title: 54-N706-S505-C7.CC002


title: 54-F2.CC019


title: 53-N705-S505-B4.IPF010


title: 53-N705-S505-A6.CC002


title: 63-H8.CC019


title: 58-N710-S505-B11.IPF009


title: 52-N704-S505-B9.IPF009


title: 61-N701-S506-E7.IPF009


title: 53-D3.CC019


title: 52-E5.CC019


title: 52-N704-S505-A5.CC002


title: 51-N703-S505-F3.CC002


title: 50-N702-S505-D1.IPF010


title: 50-N702-S505-F6.IPF009


title: 51-N703-S505-D7.IPF010


title: 51-C8.CC019


title: 50-H3.CC019


title: 50-N702-S505-E2.CC002


title: 49-N701-S505-A5.IPF009


title: 49-N701-S505-H8.IPF010


title: 49-F5.CC019


title: 47-N711-S504-D12.CC002


title: 46-D5.CC019


title: 46-N710-S504-D11.CC002


title: 45-N709-S504-D10.CC002


title: 46-N710-S504-H7.IPF009


title: 44-N708-S504-E5.IPF009


title: 44-N708-S504-D9.CC002


title: 52-N704-S505-B12.IPF010


title: 45-N709-S504-A1.IPF009


title: 45-F9.CC019


title: 43-N707-S504-C8.CC002


title: 42-N706-S504-B7.CC002


title: 42-N706-S504-C9.IPF009


title: 43-N707-S504-D9.IPF009


title: 42-N706-S504-B1.IPF010


title: 51-N703-S505-H10.IPF009


title: 42-C5.CC019


title: 49-N701-S505-E1.CC002


title: 41-N705-S504-H5.CC002


title: 41-N705-S504-G2.IPF010


title: 40-N704-S504-H2.IPF009


title: 41-C11.CC019


title: 41-N705-S504-B6.IPF009


title: 40-N704-S504-G4.CC002


title: 40-N704-S504-A2.IPF010


title: 40-G9.CC019


title: 39-N703-S504-E3.CC002


title: 39-N703-S504-A6.IPF010


title: 39-N703-S504-E1.IPF009


title: 44-F8.CC019


title: 38-N702-S504-D2.CC002


title: 38-N702-S504-C10.IPF009


title: 38-N702-S504-B2.IPF010


title: 39-A6.CC019


title: 37-N701-S504-D1.CC002


title: 37-N701-S504-D12.IPF009


title: 37-N701-S504-B5.IPF010


title: 38-C7.CC019


title: 37-F6.CC019


title: 43-A4.CC019


title: 34-N710-S503-F1.IPF009


title: 35-N711-S503-C12.CC002


title: 34-D9.CC019


title: 33-N709-S503-C10.CC002


title: 33-N709-S503-B3.IPF009


title: 34-N710-S503-C11.CC002


title: 33-C12.CC019


title: 32-N708-S503-B9.CC002


title: 31-N707-S503-D4.IPF010


title: 31-N707-S503-C6.IPF009


title: 31-N707-S503-A8.CC002


title: 31-D11.CC019


title: 30-N706-S503-C12.IPF009


title: 32-C3.CC019


title: 29-N705-S503-G9.IPF009


title: 29-N705-S503-G5.CC002


title: 29-N705-S503-D10.IPF010


title: 28-N704-S503-F4.CC002


title: 28-N704-S503-C6.IPF010


title: 28-N704-S503-B1.IPF009


title: 30-B6.CC019


title: 30-N706-S503-D8.IPF010


title: 27-N703-S503-B7.IPF010


title: 28-E7.CC019


title: 26-N702-S503-C2.CC002


title: 29-B9.CC019


title: 26-N702-S503-A10.IPF010


title: 26-A8.CC019


title: 25-N701-S503-C4.IPF010


title: 25-N701-S503-C1.CC002


title: 23-N711-S502-B12.CC002


title: 32-N708-S503-B10.IPF009


title: 25-G12.CC019


title: 22-N710-S502-B11.CC002


title: 22-C4.CC019


title: 21-N709-S502-B10.CC002


title: 21-N709-S502-C4.IPF009


title: 30-N706-S503-A7.CC002


title: 21-F11.CC019


title: 20-N708-S502-A9.CC002


title: 20-N708-S502-A4.IPF009


title: 19-N707-S502-H7.CC002


title: 27-N703-S503-D3.CC002


title: 19-N707-S502-E6.IPF009


title: 27-D8.CC019


title: 18-N706-S502-G6.CC002


title: 18-N706-S502-A12.IPF009


title: 18-N706-S502-F1.IPF010


title: 18-G3.CC019


title: 17-G5.CC019


title: 16-N704-S502-G1.IPF010


title: 19-G2.CC019


title: 16-N704-S502-E4.CC002


title: 22-N710-S502-F8.IPF009


title: 16-N704-S502-C1.IPF009


title: 17-N705-S502-C2.IPF009


title: 16-G10.CC019


title: 17-N705-S502-B6.IPF010


title: 15-N703-S502-H8.IPF009


title: 15-N703-S502-E3.IPF010


title: Md_ED17.0

city: Lyon

first: Marie

last: Semon

address: 46, allée d’Italie

department: Biologie

country: France

institute: ENS de Lyon

description: Each sample contained 2 tooth germs, the left and right first molars (M1) of the same male individual, and for a given stage, the upper and lower samples came from the same individual.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  masked for low-quality sequence (threshold = 20) and for ribosomal RNAs, then mapped to mm10  whole genome using bowtie  (version 2.0.2) and Tophat2 (version 2.0.6) with standard settings.
The number of reads per gene was then counted using HTSeq (version 0.5.3p9; option : “intersection-nonempty”; 21938 genes with an UCSC annotation)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts  values per gene for each Sample.

source_name: Germ of lower first molar

growth_protocol: The heads of harvested embryo were kept for a minimal amount of time in cooled PBS (small scale) or advanced DMEM medium (large scale). The M1 lower and upper germs were dissected under a stereomicroscope and stored in 200ul of RNA later (SIGMA).

extract_protocol:
Total RNA was prepared using the RNeasy micro kit from QIAGEN following lysis with a Precellys homogenizer. RNA integrity was controlled on a Bioanalyzer (Agilent Technologies, a RIN of 10 was reached for all samples used in this study).
PolyA+ libraries of the large-scale dataset were prepared with the Truseq V2 kit (Illumina), starting with 150ng total mRNA and reducing the amplification step to only 12 cycles.  Sequencing was done on an Illumina Hi-seq2000sequencer (100 bp paired-end sequences)

tag: developmental stage

value: lower tooth germ (the left and right first molars (M1))

tag: individual


title: 15-N703-S502-C3.CC002


title: 20-D7.CC019


title: Md_ED17.5


title: Md_ED18.0


title: 15-H2.CC019


title: Md_ED16.5


title: 14-N702-S502-E2.IPF010


title: 19-N707-S502-B11.IPF010


title: Md_ED15.5


title: 14-N702-S502-B2.CC002


title: 14-E12.CC019


title: 14-N702-S502-C11.IPF009


title: 17-N705-S502-F5.CC002


title: 13-N701-S502-A3.IPF010


title: 13-N701-S502-B1.CC002


title: Md_ED15.0


title: 13-B10.CC019


title: Md_ED14.5


title: 11-N711-S517-A12.CC002


title: Mx_ED18.0

source_name: Germ of upper first molar

value: upper tooth germ (the left and right first molars (M1))


title: 10-N710-S517-A11.CC002


title: Sperm_BGT_MspI

city: Kunming

first: Tao

last: Tan

address: No. 1 Boda Road, Yuhua Area, Chenggong District, Kunming, Yunnan,

institute: Primate Translational Medicine Research Center, Kunming University of Science and Technology

description: processed data file: Sperm.modified.sites.txt.gz

data_processing:
Library strategy: HMST-Seq
Illumina BclConverter-1.9.0 software used for basecalling.
Adaptor sequences were removed, and low-quality sequence reads were trimmed. The clean HMST-seq reads were mapped to hg19 virtual library with no more than one mismatch using open-source programming language Perl.
The data for three libraries were normalized according to a previous method (Global Rank-invariant Set Normalization, GRSN) (Pelz et al. 2008) based on the normalized tag counts, and the modification abundance of a specific CCGG site was determined as the ratio between the tag counts of two libraries. For instance, the hydroxymethylation level can be defined as the ratio between “C+mC+hmC” and “C+mC” tags. Furthermore, CCGG sites with significantly different tag counts (sequencing depth >10X, FDR <0.001) based on Poisson distribution with a ratio of tags between two libraries larger than 1 were determined to be significantly modified sites.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include cytosine chromosome, cytosine position, "C" tags abundance, "C+mC" tags abundance, p-value of Poisson test for mC,  FDR of p-value, "C+mC" tags abundance, "C+mC+hmC" tags abundance, p-value of Poisson test for hmC,  FDR of p-value.

organism: Macaca mulatta

source_name: sperm

extract_protocol:
Genomic DNA was extracted from all cells using the QIAamp DNA Kit (Qiagen).
HMST-Seq library construction was performed following our previously reported protocol (Gao et al. 2013). The libraries were sequenced using single-end 50 bp sequencing strategy with an Illumina HiSeq2000 sequencing system.

value: sperm


title: Sperm_HpaII


title: Mx_ED17.5


title: Md_ED16.0


title: Sperm_MspI


title: 10-N710-S517-C7.IPF009


title: 10-A1.CC019


title: Mx_ED17.0


title: 09-N709-S517-A10.CC002


title: 08-N708-S517-H5.IPF009


title: 08-N708-S517-H8.CC002


title: haESC_MspI

description: processed data file: haESC.modified.sites.txt.gz

source_name: haploid embryonic stem cells

value: haploid embryonic stem cells


title: 09-A9.CC019


title: Mx_ED16.5


title: haESC_BGT_MspI


title: 08-D6.CC019


title: 07-N707-S517-H3.IPF010


title: Mx_ED16.0


title: haESC_HpaII


title: 07-N707-S517-G7.CC002


title: Mx_ED15.5


title: 06-N706-S517-F6.CC002


title: 07-B11.CC019


title: 06-N706-S517-E1.IPF010


title: Mx_ED15.0


title: Mx_ED14.5


title: 09-N709-S517-G2.IPF009


title: 06-N706-S517-B7.IPF009


title: 06-D12.CC019


title: 05-N705-S517-E11.IPF009


title: 05-N705-S517-E5.CC002


title: 05-B2.CC019


title: 04-N704-S517-C4.CC002


title: 04-N704-S517-D12.IPF010


title: 04-N704-S517-A10.IPF009


title: 04-A10.CC019


title: 05-N705-S517-D3.IPF010


title: 03-N703-S517-A12.IPF010


title: 03-E6.CC019


title: 02-N702-S517-G3.IPF009


title: 03-N703-S517-A3.CC002


title: 02-N702-S517-C9.IPF010


title: 03-N703-S517-D10.IPF009


title: 02-N702-S517-A2.CC002


title: 07-N707-S517-E3.IPF009


title: 02-B3.CC019


title: 01-N701-S517-B5.IPF009


title: 01-N701-S517-A1.CC002


title: 01-H12.CC019


title: 01-N701-S517-H1.IPF010


title: U87-LKB1_TGACCA

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

description: RNA subjected to RNAseq

data_processing:
Illumina Casava1.8 software used for basecalling. Raw short sequence fragments were accepted if they passed the quality filtering parameters used in the Illumina GA Pipeline GERALD stage.
Sequenced reads were mapped to hg19 whole genome using tophat-v2.0.8b
Aligned reads was normalized by edgeR bioconductor package and outputed as normalized counts file
Genome_build: Genome Reference Consortium GRCh37
Supplementary_files_format_and_content: normalized counts in txt format for all 15 samples

source_name: Brain

growth_protocol: Cells were routinely cultured in DMEM medium with 10% FBS and  1% PenStrep (100 U/mL )

extract_protocol:
RNA extraction protocol not provided.
Transcriptome libraries were constructed with TruSeq RNA Sample Preparation Kit V2  (Illumia, San Diego, USA) with minor modifications.

treatment_protocol: LipofectaminE RNAiMAX reagent mediated siRNA transfection/RNA interference

tag: cell line

value: Glioblastoma

tag: sirna knockdown

value: LKB1 siRNA

tag: posttransfection

value: Total RNA was extracted at 72h posttransfection


title: U87-LKB1_GTGAAA

description: RNA subjected to RNAseq

tag: cell type


title: U87-control_GTCCGC

description: RNA subjected to RNAseq

value: Control siRNA


title: T98-LKB1_GTTTCG

description: RNA subjected to RNAseq


title: T98-control_GCCAAT

description: RNA subjected to RNAseq


title: U87-control_CGATGT

description: RNA subjected to RNAseq


title: T98-control_GTGGCC

description: RNA subjected to RNAseq


title: Pt12Bx1

first: Rebecca

middle: A.

last: Sosa

state: California

address: 1000 Veteran Ave

department: Pathology & Lab Medicine

institute: UCLA

data_processing:
Demultiplexing was performed with Illumina CASAVA 1.8.2.
Demultiplexed FASTQ files were checked with FASTQC.
Reads were trimmed with Cutadapt to remove adapters and low-quality ends
Alignment to the hg38 human genome assembly was performed using STAR 2.5.1b.
Unmapped reads, multi-mappers and low-quality alignments were removed with Samtools.
Reads mapping gene exons were counted using featureCounts
Counts were imported in R version 3.2.3 for analysis using the edgeR and ggplot2 packages.
A negative binomial generalized log-linear model was fitted to the read counts for each gene.
Genome_build: human NCBI genome build 38
Supplementary_files_format_and_content: tab-delimited text files include counts for each sample

source_name: IRI positive_pre-reperfusion

extract_protocol:
2mm core needle biopsies placed in RNAlater (ThermoFisher) and RNA was enriched for mRNA with NEBNext Poly(A) mRNA Magnetic isolation kit, then put on IntegenX Apollo 324 system for automated library preparation using IntegenX PrepX RNA-Seq Library reagent kit for Illumina.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: transplant stage

value: pre-reperfusion

tag: ischemia reperfusion injury (iri)

value: positive

tag: tissue

value: Liver


title: Pt12Bx2

source_name: IRI positive_post-reperfusion

value: post-reperfusion


title: Pt9Bx2


title: Pt10Bx1


title: Pt8Bx1

source_name: IRI negative_pre-reperfusion

value: negative


title: Pt6Bx1


title: Pt6Bx2

source_name: IRI negative_post-reperfusion


title: OCBx1


title: Pt2Bx1


title: OCBx2


title: HBBX1


title: RJBx2


title: MJBx2


title: RJBx1


title: T98-LKB1_ACTTGA

description: RNA subjected to RNAseq


title: RNA-seq of mES total RNA after ZFP281 shRNA-1-rep1

city: Nanjing

first: Chengqi

last: Lin

state: Jiangsu

address: 2 Sipailou

department: Institute of Life Sciences

institute: Southeast University

data_processing:
ChipSeq samples were aligned using bowtie aligner v1.1.2  allowing uniquely mapping reads only and allowing up to two mismatches for ChIP-seq samples
RNA-seq samples were aligned using TopHat v2.0.13 build on bowtie aligner v2.2.4.0 to mouse reference genome (mm9)
Genome_build: UCSC mm9
Supplementary_files_format_and_content: for chipseq, bigwig files contains RPM normalized signal. For RNA-seq file, bigwig files contain RPKM normalized signal

PLEASE BE AWARE THAT THE SUBMITTER REQUESTED DELETION OF BIGWIG AND PEAK-CALL FILES POST-PUBLICATION. PLEASE CONTACT SUBMITTER FOR FURTHER INFORMATION.

source_name: murine embryonic stem cells

growth_protocol: Mouse embryonic stem cells V6.5 were cultured on irradiated mouse embryonic fibroblast (MEF) feeder layers in 0.1% gelatin-coated tissue culture flask. Cells were grown in DMEM (D6546, Sigma) supplemented with 15% ES-certified fetal bovine serum, 2 mM L-glutamine, 0.1 mM nonessential amino acids, 0.1 mM β-mercaptoethanol, and ecombinant LIF. For ChIP and RNA analysis, cells were grown for one passage off feeders on tissue culture plates for 30 minutes.

extract_protocol:
For ChIP-Seq, 5×107 cells were used per immunoprecipitation according to previously described protocols (Lee et al., 2006). ChIP-Seq libraries were prepared with Illumina's ChIP-Seq sample prep kit (0801-0303).ES cells (V6.5) were infected with lentivirus carrying either Non-targeting shRNA or ZFP281 shRNA in the presence of 8 ug/ml of polybrene. 24 hours later, ES cells were selected with 2 ug/ml of puromycin for additional 48 hours and then were grown one passage off feeders for 30 min before harvesting. Total RNA was isolated with the RNeasy (74106 Qiagen) kit, treated with DNase I (M0303L NEB), and re-purified with RNeasy. For total RNA-seq analyses, 2.5 µg of total RNA was depleted of ribosomal RNA with the Ribo-Zero kit from Epicentre (#RZH1046). Ribosomal RNA-depleted samples were used for library preparation with the TruSeq RNA Sample Prep Kit (Illumina) for next-generation sequencing.
NEBNext® DNA Library Prep Master Mix Set for Illumina; TruSeq RNA Sample Prep Kit (Illumina)

treatment_protocol: The Non-targeting shRNA construct (SHC002) was purchased from Sigma. Lentiviral particle preparation and infection were performed as previously described (Lin et al. 2011). Briefly, around 70% confluent 293T cells in a 150 mm tissue culture plate were co-transfected with 8μg of the shRNA construct or a Non-targeting control shRNA, 6 μg of PsPAX2 packaging plasmids and 2 μg of pMD2.G envelope plasmids using X-tremeGENE HP (Roche). The media was replaced with fresh DMEM supplemented with 10% FBS after 16 hours of transfection. The lentiviral supernatants were collected 48 and 72 hours after the transfection, filtered through 0.45 μm filters and concentrated at 18K rpm for 2 hours. The V6.5 ES cells were infected with concentrated lentiviral particles with polybrene at the concentration of 8 μg/ml. At 24 hours after infection, the ES cells were subjected to selection with 2 ug/ml of puromycin for an additional 48 hours. For Pol II occupancy analysis, the 3-day control and ZFP281-knockdown ES cells were grown one passage off feeders before harvesting for paraformaldehyde cross-linking.

tag: strain

value: C57BL/6 (female) x 129/S (male)

value: murine embryonic stem cells (mES)


title: RNA-seq of mES total RNA after non-targeting shRNA-rep2


title: RNA-seq of mES total RNA after ZFP281 shRNA-1-rep2


title: MJBx1


title: Pt9Bx1


title: ChIP-seq of AFF3 in mESC after ZFP281 shRNA

tag: antibody


title: ChIP-seq of AFF3 in mESC after non-targeting shRNA


title: TUBO, replicate #2

city: Regensburg

first: Christoph

middle: Andreas

last: Klein

state: Bavaria

address: Franz-Josef-Strauß-Allee 11

department: Experimental Medicine and Therapy Research

institute: University of Regensburg

description: small RNA sequencing data

data_processing:
MiSeq analysis pipeline: MCS 2.4.1, RTA 1.18.54, MSR 2.4.60
Following data analysis was completely done using custom scripts:
3' adapter and not reliable parts of the reads were trimmed
Remaining read-sequences with at least 18 nt were mapped to murine miRNAs listed in miRBase (version 20). In this mapping no mismatches were allowed.
Annotated reads were normalized as RPM-values regarding the total number of annotated miRNA-reads
Calculation of additional statistical values for comparison of triplicate samples (mean RPM values, log2-foldchanges, p-values)
Genome_build: miRBase 20
Supplementary_files_format_and_content: tab-delimited TXT-file; trimmed read sequence followed by a tab and the number of reads
Supplementary_files_format_and_content: MS Excel-file; tab1: annotated normalized reads (mean RPM, CV), tab2: annotated log2-folds, p-values (t-test), FDR-adjusted p-values for MM3MG-Her2 vs. MM3MG comparison

source_name: Murine cell line

growth_protocol: Cells were cultured in DMEM, 10% FCS mediume

extract_protocol:
Total RNA was isolated using TRIzol reagent (Life Technologies) following the manufacturer’s recommendations.
In short, an adenylated adapter was ligated to the 3’ end of the total RNA by a truncated T4 RNA Ligase 2, followed by the ligation of a 5’ RNA-adapter by T4 RNA Ligase 1 (NEB). After reverse-transcription using a specific primer, the cDNA was amplified by PCR. After gel-fractionation bands corresponding to miRNA inserts were cut out. PCR products from these bands were eluted in elution buffer, precipitated and dissolved in water. The quality of the libraries was assessed by qPCR and Bioanalyzer measurements.

tag: source

value: Mouse breast cancer cell line derived from primary tomors of Balb-NeuT


title: ChIP-seq of Pol II in mESC after ZFP281 shRNA-1-rep2

value: Pol II


title: Pt8Bx2


title: TUBO, replicate #3

description: small RNA sequencing data


title: ChIP-seq of Pol II in mESC after non-targeting shRNA-rep2


title: ChIP-seq of Pol II in mESC after ZFP281 shRNA-1-rep1


title: HBBx2


title: ChIP-seq of Pol II in mESC after non-targeting shRNA-rep1


title: Supernatant of TUBO cells, replicate #2

description: small RNA sequencing data

source_name: supernatant from exosome-isolation

value: supernatant from exosome-isolation


title: Pt2Bx2


title: Supernatant of TUBO cells, replicate #3

description: small RNA sequencing data


title: MM3MG-Her2, replicate #2

description: small RNA sequencing data

value: MM3MG is a normal mammary epithelial cell line from BALB/c mouse strain

tag: transduction

value: Transduced wit pLSXN-Neu (Retro viral particles)


title: TUBO, replicate #1

description: small RNA sequencing data


title: MM3MG-Her2, replicate #1

description: small RNA sequencing data


title: ChIP-seq of WCE in mESC after ZFP281 shRNA-1


title: MM3MG-Her2, replicate #3

description: small RNA sequencing data


title: ChIP-seq of ZFP281 in mESC


title: RNA-seq of mES total RNA after non-targeting shRNA-rep1


title: MM3MG, replicate #3

description: small RNA sequencing data


title: MM3MG, replicate #2

description: small RNA sequencing data


title: Exosomes, replicate #3

description: small RNA sequencing data

source_name: TUBO cell

value: Exosomes extracted from supernatant of TUBO cell cultures


title: ChIP-seq of V6 5 SHC Input in mESC


title: Exosomes, replicate #2

description: small RNA sequencing data


title: Supernatant of TUBO cells, replicate #1

description: small RNA sequencing data


title: MM3MG, replicate #1

description: small RNA sequencing data


title: Exosomes, replicate #1

description: small RNA sequencing data


title: ChIP-seq of WCE in mESC after non-targeting shRNA


title: SH-SY5Y cell line undifferentiated replicate 2

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

data_processing:
CASAVA 1.8.2
Reads with more than 10% of undetermined bases or more than 50 bases with a quality score < 7 were discarded
Reads were then clipped from adapter sequences using Scythe software (https://github.com/vsbuffalo/scythe), and low quality ends (Q score < 20 on a 10 nt window) were trimmed with Sickle (https://github.com/vsbuffalo/sickle).
Alignment of reads to reference human genome (hg19) was performed using TopHat 2 (http://tophat.cbcb.umd.edu/)
Normalized expression values expressed as Fragments per Kilobase per Million Mapped Reads (FPKM) for each transcript were calculated using Cufflinks 2 with default parameters (http://cole-trapnell-lab.github.io/cufflinks/) using Ensemble GRCh37 annotation as reference
Genome_build: hg19
Supplementary_files_format_and_content: expression data matrix (expression_matrix.txt) contains expression values expressed as Fragments per Kilobase per Million Mapped Reads (FPKM)

source_name: SH-SY5Y cell line

growth_protocol: Human neuroblastoma SH-SY5Y cells (catalogue number #94030304, purchased by European Collection of Cell Cultures) were cultured in DMEM-High glucose medium (DMEM/HIGH) supplemented with 15% Foetal Bovine Serum (FBS), 2 mM L-glutamine and 1% non-essential aminoacids (all purchased from Euroclone, Pero, Italy) at 37°C and 5% CO2.

extract_protocol:
Cells were collected in three independent experiments and total RNA was isolated using TRI Reagent.
Indexed directional cDNA libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA, USA) according to manufacturer's instructions. Adapter-ligated cDNA libraries with an insert size of 200-250 bp were size selected on 1.5% agarose gel cassettes using Pippin Prep instrument (Sage Science, Beverly, MA, USA).

treatment_protocol: For neuronal differentiation, we set up a 9 days long paradigm (hereafter referred as RA-NBM treatment) including a 6 days pre-differentiation step in DMEM/HIGH supplemented with 5% FBS and 10 μM all trans Retinoic Acid (RA, Sigma-Aldrich, Milan, Italy) followed by a 3 days differentiation step in neurobasal medium (GIBCO, Life Technologies) enriched with 50 ng ml-1 recombinant human BDNF (rhBDNF, Peprotech, Rocky Hill, NJ, USA), 2 mM dibutyryl-cyclic AMP (db-cAMP, Sigma-Aldrich), 20 mM KCl, B27 and 1% GlutaMAX (both purchased form GIBCO, Life Technologies, Monza, Italy). Control (not treated, NT) cells were grown under basal conditions at low FBS concentration (5%) for comparison with RA-NBM treated cells.

tag: treatment

value: 5% FBS


title: SH-SY5Y cell line differentiated (RA-NBM treated) replicate 1

value: RA-NBM


title: SH-SY5Y cell line undifferentiated replicate 3


title: SH-SY5Y cell line differentiated (RA-NBM treated) replicate 2

data_processing:
CASAVA 1.8.2
Reads with more than 10% of undetermined bases or more than 50 bases with a quality score < 7 were discarded
Reads were then clipped from adapter sequences using Scythe software (https://github.com/vsbuffalo/scythe), and low quality ends (Q score < 20 on a 10 nt window) were trimmed with Sickle (https://github.com/vsbuffalo/sickle).
Normalized expression values expressed as Fragments per Kilobase per Million Mapped Reads (FPKM) for each transcript were calculated using Cufflinks 2 with default parameters (http://cole-trapnell-lab.github.io/cufflinks/) using Ensemble GRCh37 annotation as reference
Alignment of reads to reference human genome (hg19) was performed using TopHat 2 (http://tophat.cbcb.umd.edu/)
Genome_build: hg19
Supplementary_files_format_and_content: expression data matrix (expression_matrix.txt) contains expression values expressed as Fragments per Kilobase per Million Mapped Reads (FPKM)


title: SH-SY5Y cell line undifferentiated replicate 1


title: SH-SY5Y cell line differentiated (RA-NBM treated) replicate 3


title: polyA mRNA RNA-seq from subcutaneous adipose tissue (ENCLB555AZW)

status: Public on Dec 07 2016

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR000BZF/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week subcutaneous fat pad tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BZF
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-06-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AZW
size range: >200
spikeins used: /references/ENCSR402QNO/

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Mus musculus strain C57BL/6J subcutaneous adipose tissue mixed sex adult (8 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/d54453c5-93bc-4ec5-9941-5da9718fdb6f/@@download/attachment/LID21181.pdf

value: subcutaneous adipose tissue

value: tissue

tag: description

value: Subcutaneous Adipose tissue

tag: biosample encode accession

tag: dev stage

value: adult

tag: Sex

value: pooled male and female

tag: age

value: 8 week

tag: health state

value: unknown

tag: lab

value: Thomas Gingeras, CSHL

tag: link

value: ENCBS304ENC at ENCODE; https://www.encodeproject.org/ENCBS304ENC/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/

value: ENCODE dbxrefs SubcFatPad; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=SubcFatPad


title: polyA mRNA RNA-seq from G1E (ENCLB967FOW)

description:
https://www.encodeproject.org/experiments/ENCSR000CIG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse G1E (single end)
experiment encode accession: ENCSR000CIG
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB967FOW
size range: >175

source_name: Mus musculus G1E immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/d6ec08a9-8b45-424d-aad9-55cbc02d527f/@@download/attachment/wgEncodePsuRnaSeq.html.pdf

tag: line

value: immortalized cell line

value: Gata1- erythroid progenitor

value: postnatal

value: male

value: 0 day

value: Ross Hardison, PennState

value: ENCBS324ENC at ENCODE; https://www.encodeproject.org/ENCBS324ENC/

value: Derived from ENCODE donor ENCDO089AAA; https://www.encodeproject.org/ENCDO089AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_D046; http://web.expasy.org/cellosaurus/CVCL_D046

value: ENCODE dbxrefs G1E; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=G1E


title: polyA mRNA RNA-seq from G1E (ENCLB330VLB)

description:
https://www.encodeproject.org/experiments/ENCSR000CIG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on mouse G1E (single end)
experiment encode accession: ENCSR000CIG
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB330VLB
size range: >175


title: polyA mRNA RNA-seq from small intestine (ENCLB555AYJ)

description:
https://www.encodeproject.org/experiments/ENCSR000BZD/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week small intestine tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BZD
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-02-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AYJ
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J small intestine tissue mixed sex adult (8 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/09af6d37-20d0-49a7-a63c-3a6b295d1169/@@download/attachment/LID20820.pdf

value: small intestine

value: tissue

value: Small Intestine

value: adult

value: pooled male and female

value: ENCBS298ENC at ENCODE; https://www.encodeproject.org/ENCBS298ENC/

value: ENCODE dbxrefs SmIntestine; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=SmIntestine


title: polyA mRNA RNA-seq from ovary (ENCLB555AZG)

description:
https://www.encodeproject.org/experiments/ENCSR000BZC/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week ovaries tissue from female littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BZC
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-02-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AZG
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J ovary tissue female adult (8 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6e49faba-31f4-464c-beef-444a6f1cd155/@@download/attachment/LID20821.pdf

value: ovary

value: Ovary

value: female

value: 8 week

value: unknown

value: Thomas Gingeras, CSHL

value: ENCBS295ENC at ENCODE; https://www.encodeproject.org/ENCBS295ENC/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: polyA mRNA RNA-seq from stomach (ENCLB555AYH)

description:
https://www.encodeproject.org/experiments/ENCSR000BZE/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week stomach tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BZE
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-02-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AYH
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J stomach tissue mixed sex adult (8 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/cf2bdd40-d007-4393-a789-7fd63480d8ff/@@download/attachment/LID20732.pdf

value: stomach

value: Stomach

value: ENCBS302ENC at ENCODE; https://www.encodeproject.org/ENCBS302ENC/


title: polyA mRNA RNA-seq from small intestine (ENCLB555AYK)

description:
https://www.encodeproject.org/experiments/ENCSR000BZD/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week small intestine tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BZD
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-02-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AYK
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bb01b792-3e5e-4931-a834-e394ddff956c/@@download/attachment/LID20819.pdf

value: small intestine

value: tissue

value: ENCBS297ENC at ENCODE; https://www.encodeproject.org/ENCBS297ENC/


title: polyA mRNA RNA-seq from stomach (ENCLB555AYG)

description:
https://www.encodeproject.org/experiments/ENCSR000BZE/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week stomach tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BZE
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-02-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AYG
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/629145c4-9f8c-41e5-a35e-bdbdb99bc857/@@download/attachment/LID20733.pdf

value: adult

value: pooled male and female

value: ENCBS303ENC at ENCODE; https://www.encodeproject.org/ENCBS303ENC/


title: polyA mRNA RNA-seq from ovary (ENCLB555AXZ)

description:
https://www.encodeproject.org/experiments/ENCSR000BZC/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week ovaries tissue from female littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BZC
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-02-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AXZ
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/a3bfccd3-8697-47b7-9658-e8a60988eed9/@@download/attachment/LID20822.pdf

value: ovary

value: ENCBS296ENC at ENCODE; https://www.encodeproject.org/ENCBS296ENC/


title: polyA mRNA RNA-seq from mammary gland (ENCLB555AYR)

description:
https://www.encodeproject.org/experiments/ENCSR000BZB/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week mammary gland tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BZB
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-02-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AYR
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J mammary gland tissue mixed sex adult (8 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/a4a44ac1-2378-4577-9ef3-f003c32d76ac/@@download/attachment/LID20925.pdf

value: mammary gland

value: Mammary Gland

value: ENCBS294ENC at ENCODE; https://www.encodeproject.org/ENCBS294ENC/

value: ENCODE dbxrefs MammaryGland; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=MammaryGland


title: polyA mRNA RNA-seq from mammary gland (ENCLB555AXX)

description:
https://www.encodeproject.org/experiments/ENCSR000BZB/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week mammary gland tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BZB
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-02-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AXX
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/8c8e8270-c4f4-46f6-833b-f2d399cf207e/@@download/attachment/LID20924.pdf

value: 8 week

value: unknown

value: Thomas Gingeras, CSHL

value: ENCBS293ENC at ENCODE; https://www.encodeproject.org/ENCBS293ENC/


title: polyA mRNA RNA-seq from large intestine (ENCLB555AZE)

description:
https://www.encodeproject.org/experiments/ENCSR000BZA/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week large intestine tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BZA
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-02-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AZE
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J large intestine tissue mixed sex adult (8 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/278afc7b-1349-4f9e-9a79-b4a8f8294a13/@@download/attachment/LID21183.pdf

value: large intestine

value: Large Intestine

value: ENCBS273ENC at ENCODE; https://www.encodeproject.org/ENCBS273ENC/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/

value: ENCODE dbxrefs LgIntestine; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=LgIntestine


title: polyA mRNA RNA-seq from gonadal fat pad (ENCLB555AZP)

description:
https://www.encodeproject.org/experiments/ENCSR000BYZ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week genital fat pad tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BYZ
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-06-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AZP
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J gonadal fat pad tissue mixed sex adult (8 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/e0677db7-50c7-4878-a5ca-7d136f1040e1/@@download/attachment/LID21179.pdf

value: gonadal fat pad

value: tissue

value: Genital Adipose tissue

value: adult

value: pooled male and female

value: ENCBS264ENC at ENCODE; https://www.encodeproject.org/ENCBS264ENC/

value: ENCODE dbxrefs GenitalFatPad; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=GenitalFatPad


title: polyA mRNA RNA-seq from gonadal fat pad (ENCLB555AZQ)

description:
https://www.encodeproject.org/experiments/ENCSR000BYZ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week genital fat pad tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BYZ
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-06-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AZQ
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6349399f-70c8-4e11-a441-8efb6b6b5957/@@download/attachment/LID21180.pdf

value: ENCBS265ENC at ENCODE; https://www.encodeproject.org/ENCBS265ENC/


title: polyA mRNA RNA-seq from large intestine (ENCLB555AZF)

description:
https://www.encodeproject.org/experiments/ENCSR000BZA/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week large intestine tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BZA
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-02-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AZF
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/71a0fab8-1ea3-4eb6-858b-133e02bcd5b7/@@download/attachment/LID21184.pdf

value: 8 week

value: ENCBS274ENC at ENCODE; https://www.encodeproject.org/ENCBS274ENC/


title: polyA mRNA RNA-seq from duodenum (ENCLB555AZT)

description:
https://www.encodeproject.org/experiments/ENCSR000BYY/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week duodenum tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BYY
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-02-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AZT
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J duodenum tissue mixed sex adult (8 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/d11b7677-68e8-4dfa-9459-39ebb5cb7484/@@download/attachment/LID20730.pdf

value: duodenum

value: Duodenum

value: unknown

value: Thomas Gingeras, CSHL

value: ENCBS260ENC at ENCODE; https://www.encodeproject.org/ENCBS260ENC/


title: polyA mRNA RNA-seq from adrenal gland (ENCLB555AYO)

description:
https://www.encodeproject.org/experiments/ENCSR000BYX/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week adrenal gland tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BYX
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-06-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AYO
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J adrenal gland tissue adult (8 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/628152fa-fbcb-4623-8b70-57e40a3b1fb5/@@download/attachment/LID20729.pdf

value: adrenal gland

value: Adrenal gland

value: not collected

value: ENCBS245ENC at ENCODE; https://www.encodeproject.org/ENCBS245ENC/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: polyA mRNA RNA-seq from testis (ENCLB555AYU)

description:
https://www.encodeproject.org/experiments/ENCSR000BYW/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week testes tissue from male littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BYW
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-02-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AYU
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J testis tissue male adult (8 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/14e60f28-7042-4696-8ea0-c8eab1caeff7/@@download/attachment/LID20869.pdf

value: testis

value: tissue

value: Testis

value: adult

value: male

value: ENCBS307ENC at ENCODE; https://www.encodeproject.org/ENCBS307ENC/


title: polyA mRNA RNA-seq from subcutaneous adipose tissue (ENCLB555AZX)

description:
https://www.encodeproject.org/experiments/ENCSR000BZF/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week subcutaneous fat pad tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BZF
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-06-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AZX
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/fc8d184c-53b8-4d64-97fb-f5ec7ab9668c/@@download/attachment/LID21182.pdf

value: subcutaneous adipose tissue

value: Subcutaneous Adipose tissue

value: pooled male and female

value: 8 week

value: ENCBS305ENC at ENCODE; https://www.encodeproject.org/ENCBS305ENC/

value: ENCODE dbxrefs SubcFatPad; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=SubcFatPad


title: polyA mRNA RNA-seq from duodenum (ENCLB555AYV)

description:
https://www.encodeproject.org/experiments/ENCSR000BYY/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week duodenum tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BYY
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-02-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AYV
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/c308acc6-ad67-4329-be9f-e5d7fba1f627/@@download/attachment/LID20731.pdf

value: duodenum

value: Duodenum

value: unknown

value: Thomas Gingeras, CSHL

value: ENCBS261ENC at ENCODE; https://www.encodeproject.org/ENCBS261ENC/


title: polyA mRNA RNA-seq from thymus (ENCLB555AZA)

description:
https://www.encodeproject.org/experiments/ENCSR000BYV/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week thymus tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BYV
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-02-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AZA
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J thymus tissue mixed sex adult (8 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2380dc9a-8fe1-42bd-80fa-a367556b245d/@@download/attachment/LID20923.pdf

value: thymus

value: Thymus

value: ENCBS309ENC at ENCODE; https://www.encodeproject.org/ENCBS309ENC/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: polyA mRNA RNA-seq from testis (ENCLB555AYT)

description:
https://www.encodeproject.org/experiments/ENCSR000BYW/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week testes tissue from male littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BYW
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-02-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AYT
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/878f6c2b-705d-4980-94af-416c2a4c30bb/@@download/attachment/LID20868.pdf

value: testis

value: tissue

value: Testis

value: adult

value: male

value: ENCBS306ENC at ENCODE; https://www.encodeproject.org/ENCBS306ENC/


title: Pt10Bx2

source_name: IRI positive_post-reperfusion

extract_protocol:
2mm core needle biopsies placed in RNAlater (ThermoFisher) and RNA was enriched for mRNA with NEBNext Poly(A) mRNA Magnetic isolation kit, then put on IntegenX Apollo 324 system for automated library preparation using IntegenX PrepX RNA-Seq Library reagent kit for Illumina.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: transplant stage

value: post-reperfusion

value: positive

value: Liver


title: polyA mRNA RNA-seq from spleen (ENCLB555AZD)

description:
https://www.encodeproject.org/experiments/ENCSR000BYU/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week spleen tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BYU
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-02-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AZD
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J spleen tissue adult (8 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b2e80747-90ef-49b6-ba5f-0908a3bf7246/@@download/attachment/LID21039.pdf

value: spleen

value: Spleen

value: not collected

value: 8 week

value: ENCBS300ENC at ENCODE; https://www.encodeproject.org/ENCBS300ENC/


title: polyA mRNA RNA-seq from spleen (ENCLB555AZC)

description:
https://www.encodeproject.org/experiments/ENCSR000BYU/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week spleen tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BYU
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-02-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AZC
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/18dd5e36-9d47-44a9-8b41-edcff87acdb2/@@download/attachment/LID21038.pdf

value: unknown

value: Thomas Gingeras, CSHL

value: ENCBS299ENC at ENCODE; https://www.encodeproject.org/ENCBS299ENC/


title: polyA mRNA RNA-seq from lung (ENCLB555AYI)

description:
https://www.encodeproject.org/experiments/ENCSR000BYT/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week lung tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BYT
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-02-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AYI
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J lung tissue mixed sex adult (8 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/434ce9d5-8ef2-4fdb-9e7b-acf4eb9669ab/@@download/attachment/LID20920.pdf

value: lung

value: Lung

value: pooled male and female

value: ENCBS291ENC at ENCODE; https://www.encodeproject.org/ENCBS291ENC/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: polyA mRNA RNA-seq from liver (ENCLB555AYY)

description:
https://www.encodeproject.org/experiments/ENCSR000BYS/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week liver tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BYS
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-06-29
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AYY
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J liver tissue mixed sex adult (8 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/d90f3c0e-2213-4cb2-a6e0-d2fbc3375d79/@@download/attachment/LID21042.pdf

value: liver

value: tissue

value: adult

value: ENCBS278ENC at ENCODE; https://www.encodeproject.org/ENCBS278ENC/