title: Mdr2-/- fed SC-435 C

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Biopsy of the caudate lobe of the liver from a Mdr2-/- female mouse treated with high-fat chow + 0.006% SC-435 for 14 days

data_processing:
RNA-Seq analysis was primarily based on the TopHat/Cufflinks pipeline. Sequences were aligned to the mm10 reference genome with TopHat, which efficiently aligns reads spanning known or novel splice junctions.  The aligned reads were then processed with Cufflinks, which quantifies each transcript in each sample.  The reference annotations were produced by UCSC.
Reads per kilobase per megabase (RPKM) was calculated, and normalized using the 75th percentile shift normalization procedure, thresholding the number of reads per entity to 1.
Normalized expression values were baselined to the median of wildtype control diet samples.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing gene symbols and RPKM values (*RPKM.txt), and gene symbols and normalized expression values, for each sample.

source_name: caudate lobe of the liver

growth_protocol: Mdr2-/- and WT mice (all BALB/cJ background) were kept in conventional conditions.

extract_protocol:
At sacrifice, liver tissue from the caudate lobe was snap frozen in liquid nitrogen.  Total RNA was isolated using the Qiagen Rneasy kit.
Illumina TruSeq RNA preparation kit
RNA sequencing (RNA-seq) libraries were prepared using the Illumina TruSeq RNA preparation kit and sequenced on the Illumina Hi-Seq 2000 with single-end 50-bp reads (Illumina, San Diego, CA)

treatment_protocol: 30 day-old female mice were fed high fat chow with and without SC-435 (potent ASBT inhibitor) for 14 days.

tag: genetic background

value: BALB/cJ

tag: trt

value: High-fat breeder chow + 0.006% SC-435

tag: age at study start

value: 30 days

tag: treatment duration

value: 14 days


title: STR-depletion_2weeks rep2

status: Public on Feb 17 2016

type: SRA

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

library_source: transcriptomic

data_processing:
Illumina reads were trimmed for adapters with flexbar v.2.4 (Dodt et al. 2012)
Reads were aligned against the 18b genome sequence (CP007299.1) with Bowtie2 using default parameters.
Counting over features was done with featureCounts from the Subread package v1.4.6 (Liao, Smyth, and Shi 2013).
DESeq2 (Love, Huber, and Anders 2014) was used to infer differentially expressed genes.
Genome_build: CP007299.1

molecule: total RNA

organism: Mycobacterium tuberculosis

source_name: cell culture

growth_protocol: Mycobacterium tuberculosis 18b was grown at 37°C with shaking in 7H9 broth (Difco) supplemented with 10% albumin-dextrose-catalase (ADC) enrichment, 0.2% glycerol, 0.05% Tween 80, 50 μg/ml STR or on solid Middlebrook 7H10 medium (Difco) supplemented with 0.5% glycerol, 10% oleic acid-albumin-dextrose-catalase (OADC), 50 μg/ml STR.

extract_protocol:
Forty milliliters of replicating (i.e. with STR) or STR-starved M. tuberculosis 18b cultures were pelleted and cells were flash frozen in liquid nitrogen and stored at -80°C until use. Bacteria were re-suspended in 1 ml Trizol (Invitrogen) and added to a 2-ml screw-cap tube containing 0.5 ml zirconia beads (BioSpec Products). Cells were disrupted by bead-beating twice for 1 minute with a 2-minute interval on ice. The cell suspension was then transferred to a new tube, where chloroform-isoamylalcohol (24:1) extraction was performed. RNA was precipitated by adding 1/10 volume of sodium acetate (2 M, pH 5.2) and 0.7 volume of isopropanol, washed with 70% ethanol, air-dried and resuspended in DEPC-treated water. DNase treatment was carried out twice using RQ1 RNase-free DNase (Promega), following the manufacturer’s recommendations, and the reactions were subsequently cleaned up by phenol-chloroform extraction and ethanol precipitation. RNA was stored at -80°C in DEPC-treated water. Amount and purity of RNA were determined spectrophotometrically and by Qubit analysis (Life Technologies), integrity of RNA was assessed on 1% agarose gel and by Fragment Analyzer (Advanced Analytical).
100 ng of total RNA were used for library preparation according to the instructions provided in the TruSeq Stranded mRNA LT kit (Illumina). An aliquot of the library was analyzed on Qubit (Life Technologies) and Agilent Fragment Analyzer (Advanced Analytical) prior to sequencing on Illumina HiSeq 2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3.

treatment_protocol: Non-replicating, STR-starved 18b (SS18b) was generated as follows: 18b was grown to mid-logarithmic phase in STR-containing medium and washed three times in phosphate-buffered saline containing 0.05% Tween 80 (PBST). The final bacterial pellets were resuspended in medium without STR and maintained at an optical density at 600 nm (OD600) between 0.2 and 0.5 for 2 weeks (with the addition of fresh medium if necessary), by which time they had stopped replicating.

tag: strain

tag: condition

value: derived after 2 weeks of streptomycin depletion,


title: ARID1B-sh3

city: Singapore

first: Phillip

middle: H

last: Koeffler

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

data_processing:
Paired-end fastq files were aligned to hg19 reference genome using STAR aligner with ensemble75 gtf file as a known junction file and with default parametsrs except –outSAMstrandField set to intronMotif
Expression abundance was measured against ensemble 75 gtf using cufflinks with parameters '-G ens75.gtf -p 12 -b -u –max-bundle-frags 1000000'
Counts were measured against ensemble version 75 gtf using featurecounts with parameters '-O -T 12 -C -Q 10 -p -a ens75.gtf -o count_matrix.txt'
Genome_build: hg19
Supplementary_files_format_and_content: output file generated by cufflinks (genes.fpkm_tracking) representing FPKM values for each gene in ensemble version 75 gtf.

molecule: polyA RNA

organism: Homo sapiens

source_name: NB4 cell line

growth_protocol: Cells were grown in RPMI 1640 medium containig 10% FBS

extract_protocol:
total RNA was extracted using Qiagen Rneasy mini kit
PolyA selected RNA libraries were prepared for sequencing using standard Illumina protocols using TruSeq library prep kit.

tag: cell-line

tag: shRNA

value: shRNA targeting human ARID1B gene


title: Mdr2-/- fed SC-435 B

country: USA

organism: Mus musculus

tag: genotype


title: Mdr2-/- fed SC-435 A


title: Exp rep2

description: EB

value: exponential growth phase, in presence of streptomycin.


title: STR-depletion_2weeks rep1


title: ARID1B-sh2


title: Exp rep1

description: EA


title: con-sh

value: control/non-target shRNA


title: Mdr2-/- control C

description: Biopsy of the caudate lobe of the liver from an Mdr2-/- female mouse treated with high-fat chow for 14 days

value: High-fat breeder chow


title: B6_C

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

institute: ETH/University of Zurich

data_processing:
Raw reads: adapters and low quality ends trimmed
Alignment to the reference  (STAR)
Transcript counts calculated (Genomic Ranges) and differential expression analysis performed (edgeR)
Alternative exone usage computed (DExSeq)
Discordant alleles called (GATK RNA best practices) and annotated (snpEff)
Discordant alleles  divided into putative polymorphisms and RNA editing sites
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: Files with the results of the  two groups comparisons at the gene (obtained with edgeR); they also contain the full matrix of normalized transcripts counts for each sample. They are all tab separated files
Supplementary_files_format_and_content: Files with the results of the  two groups comparison at the exon (with DExSeq) level  They are all tab separated files
Supplementary_files_format_and_content: Files  with the results of the locus-level, RNA editing level from two groups comparisons. They are all tab separated files

source_name: Hippocampus

extract_protocol:
Mice under deep anaesthesia were transcardially perfused with ice-cold PBS heparin treated with diethylpyrocarbonate. Hippocampi were immediately dissected with the help of an adult mouse brain slicer matrix (Zivic Instruments), snap frozen and kept -80°C until homogenization. Total RNA was isolated using the RNeasy Plus universal mini kit (Qiagen), snap frozen, and kept at -80°C until further analysis.
Illumina TruSeq RNA standard

value: PrnpWT/WT

tag: age

value: 3 months

tag: gender

value: male

tag: tissue

value: hippocampus


title: Mdr2-/- control B


title: CS3

city: Toyoake

first: Rei

last: Yoshimoto

state: Aichi

address: 1-98 Dengakugakubo, Kutsukake

department: Institute for Comprehensive Medical Science

country: Japan

institute: Fujita Health University

description:
Cytoplasmic RNA
replicate3

data_processing:
Filter out artificial sequences using tagdust with default parameter. tagdust version is 1.13.
Remove sequences that match to rRNA references up to [error] errors. rRNAdust version is 1.00.
aligning with BWA
convert to bigwig track files
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: HeLa S3

growth_protocol: HeLa S3 cells were grown on DMEM media

extract_protocol:
nuclear and cytoplasmic fractions were isolated using PARIS kit (Life technologies)
HeLa cells were collected, and then nuclear and cytoplasmic RNAs were purified using PARIS kit (Life technologies) according to the manufacturer’s instruction. After rRNA elimination, RNA samples were fragmented by heating at 70°C for 3.5 min with 1 μl fragmentation buffer (Life technologies) and immediately put on ice, and then 1 μl of Stop solution was added to the samples. Fragmented RNA was purified with the RNeasy MinElute kit (Qiagen) following the instructions of the manufacturer except for the volume of 100% ethanol (675 μl) of was used in step two. Purified RNA was mixed with 2 μl of 10× phosphatase buffer, 5 U of Antarctic phosphatase (NEB) and 40 U of RNaseOut (Life technologies) and then incubated at 37°C for 30 min followed by 5 min at 65°C. After incubation, the samples were put on ice and following reagents were added to the sample; 5 µl of 10× PNK buffer, 20 U of T4 polynucleotide kinase (NEB), 5 µl of 10 mM ATP (Epicentre), 40 U of RNaseOut, 17 µl of water. After incubation at 37°C for 60 min, phosphorylated RNA was purified with the RNeasy MinElute kit (Qiagen) as described before. Purified RNA was concentrated to 6 μl by miVac DNA concentrator (Genevac). The concentrated RNA was mixed with 1 µl of 2 uM pre-adenylated 3’ DNA adaptor and then incubated at 70°C for 2 min followed by incubation on ice for 2 min. The samples were mixed with 1 µl of 10× T4 RNA ligase 2 truncated buffer, 0.8 µl of 100 mM MgCl2, 20 U of RNaseOUT and 200 U of RNA ligase 2 truncated (NEB), and then incubated at 20°C for 60 min. One microliter of heat-denatured 5 µM 5’ RNA adapter was ligated to the 3’ adapter ligated products with 20 U of T4 RNA ligase 1 (NEB) and 1 µl of 10 mM ATP (NEB) at 20°C for 60 min. Four microliter of adaptor-ligated RNA with 1 μl of 20 µM RT Primer was added to the reaction, followed by incubation at 70°C for 2 min, and immediately cooled down on ice. Two microliter of 5×Prime Script buffer, 1 µl of 10 mM dNTP, 20 U of RNaseOUT and 200 U of PrimeScript Reverse Transcriptase (Takara) were added the samples, and then the mixture was incubated at 44°C for 30 min. The whole cDNA product was amplified by PCR with 10 µl of 5× HF buffer, 1.25 µl of 10 mM each dNTP mix, 2 µl of 10 µM FWD primer, 2 µl of REV primer and 1 U of Phusion High-Fidelity DNA Polymerase (NEB). The final volume for PCR reaction was 50 µl. PCR reaction was performed with the following condition: 98°C for 30 sec, XX cycles of 98°C for 10 sec, 60°C for 30 sec, 72°C for 15 sec and then 72°C for 5 min. PCR primers were removed using 1.2 volumes of AMPure XP beads (Beckman) two times. Library size and concentration were checked by High-Sensitivity DNA Kit (Agilent). Library was sequenced by HiSeq2000 (Illumina) using custom sequencing primer.

treatment_protocol: SSA was treated at a concentration of 100ng ml-1

tag: treatment

value: SSA

tag: cell line

value: HeLa


title: Mdr2-/- control A


title: isw1_chd1_Rpb3_IP_B

city: Bethesda

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

description: Biological replicate 2

library_source: genomic

data_processing:
Sequencing data was aligned to the yeast genome (SacCer3) using Bowtie2 with default settings.
Occupancy profiles in bedGraph format were generated using bedtools.
For further analyses the aligned reads were size-selected as described in the article.
Genome_build: SacCer3
Supplementary_files_format_and_content: Nucleosomal or Rpb3 coverage in each strain/sample

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: GAL-Rsc8 containing strains were grown in synthetic complete (SC) medium containing 2% galactose and then switched to glucose. Rsc8-depleted cells were harvested when their growth reached a plateau after 7.5 hours. Wild-type cells and null mutants were grown to mid-log phase in SC medium containing 2% glucose.

extract_protocol:
In MNase-seq experiments, nuclei were prepared from unfixed yeast cells and then digested with Mnase. Mono-nucleosomal DNA was gel-purified (~150 bp) as described previously (Cole et al. 2012, PMID: 25348398; Ganguli et al. 2014, PMID: 25015381). In ChIP-seq experiments, cells were formaldehyde cross-linked before harvasting. The IP was performed with anti-Rpb3 antibody from Neoclone (cat: WP012, lot: A5081456)
The DNA was repaired using the DNA repair kit from New England Biolabs. The repaired DNA was processed for paired-end sequencing according to the Illumina protocol.

value: YJO484 (isw1D chid1D)

tag: genotype/variation

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ isw1-delta::ADE2 chd1-delta::HIS5

tag: chip antibody

value: anti-Rpb3 antibody

tag: chip antibody vendor

value: Neoclone

tag: chip antibody cat. #

tag: chip antibody lot #


title: CM3

description:
Cytoplasmic RNA
replicate3

value: MeOH


title: NS3

description:
Nuclear RNA
replicate3


title: Wildtype fed SC-435 B

description: Biopsy of the caudate lobe of the liver from a WT female mouse treated with high-fat chow + 0.006% SC-435 for 14 days

tag: genetic background

value: BALB/cJ

tag: trt

value: High-fat breeder chow + 0.006% SC-435

tag: age at study start

value: 30 days

value: 14 days


title: isw1_chd1_Rpb3_Input_B

description: Biological replicate 2

tag: strain


title: RNAseq_IMR-32_Y3mut-infected_2

first: Claudia

last: Scheckel

state: NY

address: Schmelzbergstrasse 12

department: Institute of Neuropathology

institute: University Hospital Zurich

description: overexpression of Y3 mut RNA

data_processing:
alignment with Tophat (unambigous mapping; mean inner distance: 20; st.dev.: 20)
inference of exon junctions (Bayesian method)
Genome_build: hg18
Supplementary_files_format_and_content: txt file containing geneID (Entrez) and symbol, raw reads and rpkm values

source_name: IMR-32 neuroblastoma cells

growth_protocol: IMR-32 neuroblastoma cells were grown under standard conditions.

extract_protocol:
Trizol extraction
Illumina High-throughput TruSeq RNA Sample preparation: ribominus selection (Invitrogen)

treatment_protocol:
For UV treatment, cells were washed in PBS exposed to 0.5 mJ/cm2 UVC and allowed to recover for 24h before being harvested
RNAi protocol: Cells were treated with mock or nELAVL RNAi for 96 hours before being harvested
Lentiviral infection protocol: Cells were infected with lentivirus 72 hours before being harvested

tag: cell type

value: neuroblastoma cells

tag: lentiviral infection

value: infected with Y3 mut RNA


title: isw1_chd1_Rpb3_Input_A

description: Biological replicate 1


title: NM3

description:
Nuclear RNA
replicate3


title: RNAseq_IMR-32_Y3mut-infected_1

description: overexpression of Y3 mut RNA


title: RNAseq_IMR-32_Y3mut-infected_3

description: overexpression of Y3 mut RNA


title: Wildtype control B

description: Biopsy of the caudate lobe of the liver from a WT female mouse treated with high-fat chow for 14 days

tag: genotype

value: High-fat breeder chow

tag: treatment duration


title: chd1_Rpb3_IP_B

description: Biological replicate 2

value: YJO482 (chd1D)

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ chd1-delta::HIS5


title: CS2

description:
Cytoplasmic RNA
replicate2


title: Wildtype control A


title: CM2

description:
Cytoplasmic RNA
replicate2


title: RNAseq_IMR-32_Y3wt-infected_3

description: overexpression of Y3 wt RNA

value: infected with Y3 wt RNA


title: chd1_Rpb3_IP_A

description: Biological replicate 1


title: RNAseq_IMR-32_Y3wt-infected_2

description: overexpression of Y3 wt RNA


title: RNAseq_IMR-32_Y3wt-infected_1

description: overexpression of Y3 wt RNA


title: isw1_chd1_Rpb3_IP_A

description: Biological replicate 1


title: Sptbn1-/-

city: Houston

first: Jian

last: Chen

state: TX

address: 1515 Holcombe Blvd

department: Gastroenterology

institute: UT MD Anderson Cancer Center

data_processing:
Whole-transcriptome RNA sequencing of wild-type and β2SP knockout (β2SP-/-) mouse embryonic fibroblasts was carried out on an Illumina HiSeq 2000 sequencer.
The raw data quality was assessed using a FastQC software.
Adaptor presence was tested using Trimmomatic.
The readings were then aligned to the NCBI mouse reference genome build 37.2 using the splice-aware aligner Tophat2 v2.0.10.
Transcript quantification, normalization and assembly were carried out with Cufflinks.
A gene model gtf file corresponding to the NCBI mouse reference genome build 37.2 was used in the quantification.
Cuffdiff2, part of the Cufflinks suite of tools, was used to identify significant differences in gene expression profiles between the wild-type and β2SP-/- MEF cells.
Genome_build: NCBI mouse reference genome build 37.2
Supplementary_files_format_and_content: FPKM tab-delimited text file format with fold change comparison and p-value calculation

source_name: Mouse embryonic fibroblast

growth_protocol: Sptbn1+/− mice were mated, and the females were euthanized by cervical dislocation when the embryos reached E13.5. Primary MEFs were generated and plated.  After the MEFs’ genotype was confirmed and the cells reached confluence, the MEFs were trypsinized and replated. MEFs were cultured in DMEM/F12 medium (D5671; Sigma Aldrich, St Louis, MO) supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted using TRIZOL reagent (Invitrogen) according to the manufacturer’s instructions.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

value: Sptbn1 knockout

value: embryonic fibroblast

tag: developmental stage


title: chd1_Rpb3_Input_B

description: Biological replicate 2


title: WT

value: Wild type


title: chd1_Rpb3_Input_A

description: Biological replicate 1


title: Wildtype fed SC-435 A


title: isw1_Rpb3_IP_B

description: Biological replicate 2

value: YTT186 (isw1D)

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ isw1-delta::ADE2


title: RNAseq_IMR-32_non-infected_3

description: non-infected

value: non-infected


title: isw1_Rpb3_IP_A

description: Biological replicate 1

value: anti-Rpb3 antibody

value: Neoclone


title: WTKO3_D2

city: New York

first: Jane

last: Skok

address: 550 First Ave, Smillow 307

institute: NYU

description: Single end 50 cycles

data_processing:
library strategy: 4C-Seq
Reads were mapped with Bowtie to a reduced genome consisting of unique fragments adjacent to DpnII sites (bowtie -N 0 -5 26)
Self ligated and undigested fragments were removed after mapping
Genome_build: mm10
Supplementary_files_format_and_content: TXT; chr, start, end, counts at each fragment

source_name: Splenic B cells

growth_protocol: Mature splenic CD43 negative cells were activated and cultured  (or not) with LPS and IL4 for 2 days.

extract_protocol:
4C template was prepared by digestion with DpnII and subsequent ligation and then a second digest with Csp6I and another ligation.
Adaptors were introduced in the gene-specific inverse PCR step

treatment_protocol: Cells were fized in 2% formaldehyde

value: WT

tag: day

tag: Stage

value: Activated

value: Splenic B cells


title: WTKO3_D0

description: Single end 50 cycles

value: Resting


title: CS1

description:
Cytoplasmic RNA
replicate1

tag: treatment

value: SSA

tag: cell line

value: HeLa


title: CM1

description:
Cytoplasmic RNA
replicate1

value: MeOH


title: NS1

description:
Nuclear RNA
replicate1


title: WTKO2_D2

description: Single end 50 cycles

data_processing:
library strategy: 4C-Seq
Reads were mapped with Bowtie to a reduced genome consisting of unique fragments adjacent to DpnII sites (bowtie -N 0 -5 26)
Self ligated and undigested fragments were removed after mapping
Genome_build: mm10
Supplementary_files_format_and_content: bed

growth_protocol: Mature splenic CD43 negative cells were activated and cultured  (or not) with aCD40 and Il4 for 2 days.

tag: genotype/variation


title: isw1_Rpb3_Input_B

description: Biological replicate 2


title: RNAseq_IMR-32_non-infected_2

description: non-infected

value: neuroblastoma cells


title: RNAseq_IMR-32_non-infected_1

description: non-infected


title: NM1

description:
Nuclear RNA
replicate1


title: NS2

description:
Nuclear RNA
replicate2


title: SRSF10-rep2P

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

country: China

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

description:
RNA from Flag IP
SRSF10

data_processing:
Library strategy: PAR-CLIP
Reads were aligned to the hg19 genome assembly using bowtie1
Clusters were got by PARalyzer (http://www.genome.duke.edu/labs/ohler/research/PARalyzer/).
Genome_build: hg19
Supplementary_files_format_and_content: csv file containing cluster results.

source_name: Human HeLa cells

extract_protocol:
label the cells overexpressed Flag tagged YTHDC1, SRSF1, SRSF3, SRSF7, SRSF9 and SRSF10  with 4-SU, the RNA bound by YTHDC1 and SRSF proteins can be got by Flag IP followed by RNA isolation by using the TRIzol (Invitrogen) reagent by following the company manual.the RNA was then used for library preparation and sequencing.
the RNA got from IP was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 101 bp.

value: SRSF10 overexpressed HeLa cells


title: isw1_Rpb3_Input_A

description: Biological replicate 1


title: WTKO2_D0

description: Single end 50 cycles


title: HITS-CLIP_AD_16

description:
A16
advanced Alzheimer's Disease subject

data_processing:
filtering (min:0-3:20,mean:4-19:20,min:20-24,mean:25-60)
collapsing of exact sequences
stripping of degenerate linker (25nt; begins with index; ends with a G)
removal of 3'adaptor (GTGTCAGTCACTTCCAGCGG)
alignment with novoalign (unambigous mapping)
collapsing of PCR duplicates
Genome_build: hg18
Supplementary_files_format_and_content: bed file containing genomic coordinates of unique unambigously mapped reads

source_name: advanced Alzheimer's Disease_brain

growth_protocol: Frozen brain tissue from control and advanced AD subjects was obtained from the Mount Sinai Brain Bank.

extract_protocol:
Brain tissue was UV irradiated and subjected to nELAVL HITS-CLIP (detailed description in accompanying paper)
partial RNAse digestion, RNA linker ligation and PCR amplificiation
nELAVL bound fragments were ligated to a degenerate 5'linker and a 3'linker

tag: disease status

value: advanced Alzheimer's Disease

tag: tissue

value: brain

tag: tissue subtype

value: dorsolateral prefrontal cortex


title: isw2_Rpb3_IP_B

description: Biological replicate 2

value: YPE470 (isw2D)

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ isw2-delta::LEU2

tag: chip antibody

tag: chip antibody vendor

tag: chip antibody cat. #

tag: chip antibody lot #


title: NM2

description:
Nuclear RNA
replicate2


title: WTKO1_D0

description: Single end 50 cycles

tag: cell type


title: isw2_Rpb3_IP_A

description: Biological replicate 1

tag: strain


title: YTHDC1-rep2P

description:
RNA from Flag IP
YTHDC1

value: YTHDC1 overexpressed HeLa cells


title: Med1KO3_D2

description: Single end 50 cycles

value: Med1 Mutant


title: HITS-CLIP_AD_15

description:
A15
advanced Alzheimer's Disease subject


title: SRSF3-rep2P

description:
RNA from Flag IP
SRSF3

value: SRSF3 overexpressed HeLa cells


title: SRSF10-rep1P

description:
RNA from Flag IP
SRSF10


title: HITS-CLIP_AD_14

description:
A14
advanced Alzheimer's Disease subject


title: Med1KO3_D0

description: Single end 50 cycles


title: isw2_Rpb3_Input_B

description: Biological replicate 2


title: HITS-CLIP_AD_13

description:
A13
advanced Alzheimer's Disease subject


title: HITS-CLIP_AD_12

description:
A12
advanced Alzheimer's Disease subject


title: Med1KO2_D2

description: Single end 50 cycles


title: SRSF7-rep1P

description:
RNA from Flag IP
SRSF7

value: SRSF7 overexpressed HeLa cells


title: HITS-CLIP_Ctrl_8

description:
C8
control subject

value: control


title: WT_Rpb3_IP_B

description: Biological replicate 2

value: YPE458 (wild type)

value: anti-Rpb3 antibody

value: Neoclone


title: WT_Rpb3_IP_A

description: Biological replicate 1


title: SRSF9-rep1P

description:
RNA from Flag IP
SRSF9

value: HeLa

value: SRSF9 overexpressed HeLa cells


title: isw2_Rpb3_Input_A

description: Biological replicate 1


title: HITS-CLIP_AD_17

description:
A17
advanced Alzheimer's Disease subject


title: SRSF3-rep1P

description:
RNA from Flag IP
SRSF3


title: WTKO1_D2

description: Single end 50 cycles

value: WT

value: Activated

value: Splenic B cells


title: Med1KO1_D2

description: Single end 50 cycles


title: HITS-CLIP_Ctrl_7

description:
C7
control subject

value: brain


title: HITS-CLIP_Ctrl_6

description:
C6
control subject

value: dorsolateral prefrontal cortex


title: SRSF1-rep1P

description:
RNA from Flag IP
SRSF1

value: SRSF1 overexpressed HeLa cells


title: Med1KO1_D0

description: Single end 50 cycles

data_processing:
library strategy: 4C-Seq
Reads were mapped with Bowtie to a reduced genome consisting of unique fragments adjacent to DpnII sites (bowtie -N 0 -5 26)
Self ligated and undigested fragments were removed after mapping
Genome_build: mm10
Supplementary_files_format_and_content: TXT; chr, start,end, count at each fragment

value: Resting


title: WT_Rpb3_Input_A

description: Biological replicate 1


title: YTHDC1-rep1P

description:
RNA from Flag IP
YTHDC1

value: YTHDC1 overexpressed HeLa cells


title: HITS-CLIP_Ctrl_5

description:
C5
control subject


title: SRSF10 deficient HeLa cells rep2

description:
cell type: SRSF10 deficient HeLa cells
siSRSF10-rep10

data_processing:
Reads were aligned to the hg19 genome assembly using TopHat v2.0.9
For each sample, reads counts of all genes were computed using HTSeq v0.5.3p9
Genome_build: hg19
Supplementary_files_format_and_content: Reads count for each gene

extract_protocol:
RNA was isolated from control, YTHDC1, SRSF1, SRSF3, SRSF7, SRSF9 or SRSF10 deficient Human HeLa cells cells using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100
Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in single-read or paired-read mode, creating reads with a length of 101 bp.


title: SRSF3 deficient HeLa cells rep2

description:
cell type: SRSF3 deficient HeLa cells
siSRSF3-rep2


title: RNAseq_IMR-32_nELAVL_UV_3

description:
nElavl UV_3
UV stressed: 0.5mJ/cm2 nELAVL RNAi

value: neuroblastoma cells

tag: treated with

value: nELAVL RNAi for 96hrs

tag: sample group

value: UV stressed:0.5mJ/cm2

tag: RNAi

value: nELAVL


title: RNAseq_IMR-32_nELAVL_UV_2

description:
nElavl UV_2
UV stressed: 0.5mJ/cm2 nELAVL RNAi


title: Med1KO2_D0

description: Single end 50 cycles

value: Med1 Mutant

tag: day


title: isw1_isw2_chd1_A

description: Biological replicate 1

source_name: isw1_isw2_chd1_nucleosome core particles (MNase)

value: YJO488 (isw1D isw2D chd1D)

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ isw1-delta::ADE2, isw2-delta::LEU2 chd1-delta::HIS5


title: isw2_chd1_B

description: Biological replicate 2

source_name: isw2_chd1_nucleosome core particles (MNase)

value: YJO486 (isw2D chd1D)

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ isw2-delta::LEU2 chd1-delta::HIS5


title: YTHDC1 deficient HeLa cells rep2

description:
cell type: YTHDC1 deficient HeLa cells
siYTHDC1-rep2

value: HeLa


title: normal HeLa cells rep3

description:
cell type: normal HeLa cells
siCTRL-rep3


title: RNAseq_IMR-32_mock_UV_3

description:
mock UV_3
UV stressed: 0.5mJ/cm2 mock RNAi

value: mock RNAi for 96hrs

value: mock


title: RNAseq_IMR-32_nELAVL_UV_1

description:
nElavl UV_1
UV stressed: 0.5mJ/cm2 nELAVL RNAi


title: SRSF10 deficient HeLa cells rep1

description:
cell type: SRSF10 deficient HeLa cells
siSRSF10-rep1


title: WT_Rpb3_Input_B

description: Biological replicate 2

value: YPE458 (wild type)


title: RNAseq_IMR-32_mock_UV_1

description:
mock UV_1
UV stressed: 0.5mJ/cm2 mock RNAi


title: SRSF9 deficient HeLa cells rep1

description:
cell type: SRSF9 deficient HeLa cells
siSRSF9-rep1


title: isw2_chd1_A

description: Biological replicate 1


title: chd1_B

description: Biological replicate 2

source_name: chd1_nucleosome core particles (MNase)

value: YJO482 (chd1D)

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ chd1-delta::HIS5


title: RNAseq_IMR-32_mock_UV_2

description:
mock UV_2
UV stressed: 0.5mJ/cm2 mock RNAi


title: isw1_chd1_B

description: Biological replicate 2

source_name: isw1_chd1_nucleosome core particles (MNase)

value: YJO484 (isw1D chid1D)

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ isw1-delta::ADE2 chd1-delta::HIS5


title: SRSF7 deficient HeLa cells rep1

description:
cell type: SRSF7 deficient HeLa cells
siSRSF7-rep1


title: SRSF3 deficient HeLa cells rep1

description:
cell type: SRSF3 deficient HeLa cells
siSRSF3-rep1


title: isw1_B

description: Biological replicate 2

source_name: isw1_nucleosome core particles (MNase)

value: YTT186 (isw1D)

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ isw1-delta::ADE2


title: HITS-CLIP_Ctrl_4

description:
C4
control subject

value: control

value: brain

value: dorsolateral prefrontal cortex


title: chd1_A

description: Biological replicate 1


title: RNAseq_IMR-32_nELAVL_noUV_3

description:
nElavl noUV_3
non-stressed nELAVL RNAi

value: neuroblastoma cells

value: nELAVL RNAi for 96hrs

value: non-stressed

value: nELAVL


title: RNAseq_IMR-32_nELAVL_noUV_2

description:
nElavl noUV_2
non-stressed nELAVL RNAi


title: isw1_isw2_chd1_B

description: Biological replicate 2

value: YJO488 (isw1D isw2D chd1D)

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ isw1-delta::ADE2, isw2-delta::LEU2 chd1-delta::HIS5


title: SRSF1 deficient HeLa cells rep1

description:
cell type: SRSF1 deficient HeLa cells
siSRSF1-rep1

value: HeLa


title: HITS-CLIP_IMR-32_UV5_3

data_processing:
library strategy: HITS-CLIP
filtering: 25nt degenerate linker: min:0-24:20,mean:25-70:20; 7nt degenerate linker: 0-6:20,mean:7-40:20
collapsing of exact sequences
stripping of degenerate linker (7 or 25nt; ends with a G)
removal of 3'adaptor (GTGTCAGTCACTTCCAGCGG)
alignment with novoalign (unambigous mapping)
collapsing of PCR duplicates
Genome_build: hg18
Supplementary_files_format_and_content: bed file containing genomic coordinates of unique unambigously mapped reads

growth_protocol: Nonstressed and UV-stressed IMR-32 neuroblastoma cells were grown under standard conditions.

extract_protocol:
Nonstressed and stressed cells were UV irradiated and subjected to nELAVL HITS-CLIP (detailed description in accompanying paper)
partial RNAse digestion, RNA linker ligation and PCR amplificiation
nELAVL bound fragments were ligated to a degenerate 5'linker and a 3'linker

treatment_protocol: Cells were washed in PBS and for UV treatment exposed to either 0.2 or 0.5 mJ/cm2 UVC; cells were allowed to recover for 24h before being harvested

value: UV stressed:0.5mJ/cm2

tag: degenerate linker

value: 25nt:begins with AGTG, ends with G


title: RNAseq_IMR-32_nELAVL_noUV_1

description:
nElavl noUV_1
non-stressed nELAVL RNAi


title: isw1_A

description: Biological replicate 1


title: HITS-CLIP_IMR-32_UV5_2

tag: treatment

value: 25nt:begins with CATG, ends with G


title: normal HeLa cells rep2

description:
cell type: normal HeLa cells
siCTRL-rep2

tag: cell line


title: isw2_B

description: Biological replicate 2

source_name: isw2_nucleosome core particles (MNase)

value: YPE470 (isw2D)

tag: genotype/variation

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ isw2-delta::LEU2


title: RNAseq_IMR-32_mock_noUV_3

description:
mock noUV_3
non-stressed mock RNAi

value: mock RNAi for 96hrs

value: mock


title: isw1_chd1_A

description: Biological replicate 1

value: YJO484 (isw1D chid1D)

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ isw1-delta::ADE2 chd1-delta::HIS5


title: HITS-CLIP_IMR-32_UV5_1

value: 25nt:begins with GTGC, ends with G


title: RNAseq_IMR-32_mock_noUV_2

description:
mock noUV_2
non-stressed mock RNAi

value: neuroblastoma cells


title: normal HeLa cells rep1

description:
cell type: normal HeLa cells
siCTRL-rep1


title: HITS-CLIP_IMR-32_UV2_3

value: UV stressed:0.2mJ/cm2

value: 25nt:begins with TCAC, ends with G


title: RNAseq_IMR-32_mock_noUV_1

description:
mock noUV_1
non-stressed mock RNAi

value: non-stressed


title: RNAseq_AD_17

description:
A17
advanced Alzheimer's Disease subject

tag: disease status

value: advanced Alzheimer's Disease

value: brain

value: dorsolateral prefrontal cortex


title: isw1_isw2_A

description: Biological replicate 1

source_name: isw1_isw2_nucleosome core particles (MNase)

value: YPE460 (isw1D isw2D)

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1ura3-1 RAD5+ isw1-delta::ADE2, isw2-delta::LEU2


title: HITS-CLIP_IMR-32_UV2_1

value: 25nt:begins with CGTA, ends with G


title: RNAseq_AD_15

description:
A15
advanced Alzheimer's Disease subject

tag: tissue


title: isw2_A

description: Biological replicate 1

value: YPE470 (isw2D)


title: HITS-CLIP_IMR-32_noUV_3

value: 7nt:begins with AC, ends with G


title: WT_A

description: Biological replicate 1

source_name: WT_nucleosome core particles (MNase)

value: YPE458 (wild type)


title: RNAseq_AD_16

description:
A16
advanced Alzheimer's Disease subject

tag: tissue subtype


title: isw1_isw2_B

description: Biological replicate 2


title: WT_B

description: Biological replicate 2


title: HITS-CLIP_IMR-32_noUV_2

value: 7nt:begins with GA, ends with G


title: RNAseq_AD_14

description:
A14
advanced Alzheimer's Disease subject


title: STR-depletion_2weeks rep4

source_name: cell culture

tag: condition

value: derived after 2 weeks of streptomycin depletion,


title: STR-depletion_2weeks rep3


title: YTHDC1 deficient HeLa cells rep1

description:
cell type: YTHDC1 deficient HeLa cells
siYTHDC1-rep1

value: HeLa


title: RNAseq_AD_13

description:
A13
advanced Alzheimer's Disease subject


title: HITS-CLIP_IMR-32_noUV_1

value: 25nt:begins with GATC, ends with G


title: E. coli I-E replicate 2 - PostSort

city: Raleigh

first: Chase

last: Beisel

state: NC

address: 840 Main Campus Drive, Partners II Rm 2109

department: Chemical and Biolmolecular Engineering

institute: North Carolina State University

description: Sample 4

data_processing:
for samples 1-4, and 7-14, underlined regions change per sample: grep 'TTCATTAAAAATTGAATTGACATTAACCTATAAAAATAGGCGTCGAGGCCCTTTCGTCTTC[TCAG][TCAG][TCAG][TCAG]GTCGAGTGCA' Sample1.fastq | cut -c 62-65 | sort | uniq -c | sort -nr | less > Sample1List.txt
for samples 5 and 6, underlined regions change per sample: grep 'TTCATTAAAAATTGAATTGACATTAACCTATAAAAATAGGCGTCGAGGCCCTTTCGTG[TCAG][TCAG][TCAG][TCAG][TCAG]GGGTCGAGTGCA' file.fastq | cut -c 59-63 | sort | uniq -c | sort -nr | less > File1List.txt
Supplementary_files_format_and_content: Tab delimited Excel sheets containing sequence counts

molecule: other

organism: Escherichia coli

source_name: Native E. coli CRISPR-Cas system

extract_protocol:
Plasmid DNA from sorted cells was isolated using a mini-prep kit (Zymo).
Libraries were constructed by amplifying the DNA region with Illumina adapters with a 24 cycle Q5 polymerase (NEB). Following amplification, samples were cleaned up with AMPure XP beads. These dsDNAs were then indexed using Nextera barcodes 501, 502, and 707-709.

tag: extracted molecule

value: Plasmid DNA


title: RNAseq_AD_12

description:
A12
advanced Alzheimer's Disease subject


title: Exp rep4

description: CSEB

value: exponential growth phase, in presence of streptomycin.


title: RNAseq_AD_11

description:
A11
advanced Alzheimer's Disease subject


title: Control_706

city: Portici

first: Elena

last: Alexandrova

state: Napoli

address: Viale Stazione, 22

department: Faculty of Medicine and Surgery

country: Italy

institute: University of Salerno

data_processing:
Basecalls was performed using CASAVA version 1.8
Adaptor sequences and low-quality terminal nucleotide positions within the reads were removed using Trimmomatic software
The pre-processed reads were mapped to the human genome, version HG 19, using the software Bowtie2
The mapped reads were attributed to known human genes using the published Ensembl human genome annotation Vers. 75
Differential gene expression data normalized on the overall number of mapped sequenced reads were obtained using DESeq software
Genome_build: hg 19
Supplementary_files_format_and_content: .txt file include DESeq normalized gene expression values for each Sample …

source_name: lung

growth_protocol: BSM cells were established and grown in RPMI 1640 (Lonza, Basel, Switzerland) supplemented with 5% fetal calf serum (FCS), 8 mM L-glutamine, 20 mM hydroxyethyl piperazine ethane sulfonic acid and 1% modified Eagle’s medium vitamin mix (Gibco, Paisley, UK). Neither antibiotics nor antimycotics were added at any time.

extract_protocol:
RNA isolation was performed with mirVana miRNA isolation kit (Ambion, Life Science, Zug, Switzerland). RNA concentration of each sample was evaluated with a ND-1000 spectrophotometer (NanoDrop) and its quality was analysed with the Agilent 2100 Bioanalyzer using Agilent RNA 6000 nano kit (Agilent Technologies, Milano, Italy).
5 µg of total RNA was reverse transcribed with RT random N15 primer using PrimeScript Reverse Transcriptase in the presence of 0.132 M trehalose and 0.66 M sorbitol. The 5’ RNA caps were than oxidated with NaIO4, biotinilated and treated with RNAseI ribonuclease in order to cleave single-stranded RNA regions that were not protected by cDNA. Next, 5’-completed cDNA-RNA hybrids were cap-trapped, cDNA molecules were released and a specific linker (5'-linker), containing a 3-bp barcode sequence and the type III restriction-modification enzyme EcoP15I was ligated to the single-strand cDNA. The priming of the second strand was made with specific biotinilated primer. After second strand synthesis and cleavage with EcoP15I, another linker (3'-linker) was ligated. Purified cDNA was amplified with 1 μM each, forward and reverse primers with 15 PCR cycles. PCR products were purified and concentration was adjusted to 10 nM.

value: lung

tag: sample type

value: bronchial smooth muscle cells

tag: disease state

value: healthy


title: HITS-CLIP_IMR-32_UV2_2

tag: cell type

value: neuroblastoma cells

value: UV stressed:0.2mJ/cm2

value: 25nt:begins with GCAT, ends with G


title: E. coli I-E replicate 1 - PostSort

description: Sample 3


title: Exp rep3

description: CSEA

tag: strain


title: RNAseq_AD_10

description:
A10
advanced Alzheimer's Disease subject

value: advanced Alzheimer's Disease

value: brain

value: dorsolateral prefrontal cortex


title: Control_705


title: E. coli I-E replicate 2 - PreSort

description: Sample 2


title: E. coli I-E replicate 1 - PreSort

description: Sample 1


title: Control_704


title: RNAseq_Ctrl_7

description:
C7
control subject

value: control


title: RNAseq_AD_9

description:
A9
advanced Alzheimer's Disease subject


title: RNAseq_Ctrl_8

description:
C8
control subject


title: Asthma_738

value: asthma


title: Asthma_739


title: Asthma_695


title: RNAseq_Ctrl_4

description:
C4
control subject


title: Asthma_670


title: Control_747


title: RNAseq_Ctrl_5

description:
C5
control subject


title: RNAseq_Ctrl_3

description:
C3
control subject


title: Asthma_669


title: Asthma_667


title: RNAseq_Ctrl_1

description:
C1
control subject


title: F. novicida replicate 2 - PostSort

description: Sample 10

organism: Francisella tularensis subsp. novicida

source_name: Imported CRISPR-Cas system


title: Asthma_662


title: Asthma_638


title: B. halodurans replicate 1 - PostSort

description: Sample 13

organism: Halalkalibacterium halodurans


title: B. halodurans replicate 2 - PostSort

description: Sample 14


title: Control_685


title: F. novicida replicate 1 - PostSort

description: Sample 9


title: B. halodurans replicate 2 - PreSort

description: Sample 12


title: F. novicida replicate 2 - PreSort

description: Sample 8


title: B. halodurans replicate 1 - PreSort

description: Sample 11


title: Control_653


title: TipR+Nalidixic_ChIPseq

city: Geneva

first: Antonio

last: Frandi

address: rue michel servet 1

department: Microbiology and Molecular Medicine

institute: University of Geneva

data_processing:
Base calling: HiSeq Control Software 2.0.12.0, RTA 1.17.21.3, CASAVA-1.8.2
Alignment: Bowtie-0.12.9, samtools-0.1.18
Peak calling: SeqMonk software (Braham Bionformatics Institute)
Peak refinement and annotation: SeqMonK output were processed by Java and Perl programs (in house written, decribed in the paper) to refine the peaks annotation and eliminate background
ChIPseq comparisons: Peaks list after being proccessed were scanned for common target, then ratio of each peak abundance were computed and reported as the log2 fold variation
Genome_build: Caulobacter crescentus : NC_011916.1;
Supplementary_files_format_and_content: the xls files reporting peaks annotations and abundance were generated by Java and Perl programs (described in the paper) and consist of two sheet the ANNO and the NO-ANNO sheet. The ANNO probes sheets are organized in columns as follows:
Supplementary_files_format_and_content: column 1: gene name to which the peak is associated is reported in the reference genome used for the reads alignment
Supplementary_files_format_and_content: column 2 : probe start
Supplementary_files_format_and_content: column 3 : probe end
Supplementary_files_format_and_content: column 4 : COG categories to which the gene associated to the corresponding peak belongs to
Supplementary_files_format_and_content: column 5 : PubMed Identification number of the protein encoded by the gene associated to the peak
Supplementary_files_format_and_content: column 6 : Length of the protein
Supplementary_files_format_and_content: column 7 : The gene strand of the gene associated to the peak (0 plus strand, 1 reverse strand)
Supplementary_files_format_and_content: column 8 : Gene start
Supplementary_files_format_and_content: column 9 : Gene end
Supplementary_files_format_and_content: column10: Probe distance, the distance of the probe from ORF start
Supplementary_files_format_and_content: column 11 : It is reported here the abundance of reads per probe expressed as the percentage of total reads number
Supplementary_files_format_and_content: column 12: N possible association, it is reported here the number of possible association that the probe associated to the gene reported in the first column can have (i.e.: two genes that are divergent but shares the same peak)
Supplementary_files_format_and_content: column 13 : Name of the gene that can be associated to this probe and the distance of the probe from the gene start)
Supplementary_files_format_and_content: The NO-ANNO probes files contain all those probes that made the cut off, (are recognized as peaks) but they cannot be associated to any genes. File organization is the same as before except that only information about the probe location and reads abundance are reported.

organism: Caulobacter vibrioides NA1000

source_name: Wild-type Caulobacter crescentus NA1000

growth_protocol: Caulobacter crescentus and derivatives were grown at 30°C in PYE (Peptone yeast extract). For sample 4, nalidixic acid at 20 μg/ml was added to the cells for three hours.

extract_protocol:
Mid-log phase cells were cross-linked in 10 mM sodium phosphate (pH 7.6) and 1%  formaldehyde at room temperature for 10 min and on ice for 30 min thereafter, washed  thrice in phosphate buffered saline (PBS) and lysed in a Ready-Lyse lysozyme solution  (Epicentre, Madison, WI) according to the manufacturer`s instructions. Lysates were  sonicated (Sonifier Cell Disruptor B-30; Branson Sonic Power. Co., Danbury, CT) on ice  using 10 bursts of 20 sec at output level 4.5 to shear DNA fragments to an average length  of 0.3-0.5 kbp and cleared by centrifugation at 14,000 rpm for 2 min at 4°C. Lysates were  normalized by protein content, diluted to 1 mL using ChIP buffer (0.01% SDS, 1.1%  Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl [pH 8.1], 167 mM NaCl plus protease  inhibitors (Roche) and pre-cleared with 80 μL of protein-A agarose (Roche, Switzerland)  and 100 uμg BSA. Ten % of the supernatant was removed and used as total chromatin  input DNA as described before (Radhakrishnan et al., 2008).  Two microliters of polyclonal antibodies were added to the remains of the  supernatant, incubated overnight at 4°C with 80 μL of protein-A agarose beads pre  saturated with BSA, washed once with low salt buffer (0.1% SDS, 1% Triton X-100, 2  mM EDTA, 20 mM Tris-HCl (pH 8.1), 150 mM NaCl), high salt buffer (0.1% SDS, 1%  Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 500 mM NaCl) and LiCl buffer  (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl (pH  8.1) and twice with TE buffer (10 mM Tris-HCl (pH 8.1) and 1 mM EDTA). The  protein•DNA complexes were eluted in 500 μL freshly prepared elution buffer (1% SDS,  0.1 M NaHCO3), supplemented with NaCl to a final concentration of 300 mM and  incubated overnight at 65°C to reverse the crosslinks. The samples were treated with 2 μg  of Proteinase K for 2 h at 45°C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA  extracted using phenol:chloroform:453 isoamyl alcohol (25:24:1), ethanol-precipitated  using 20 ug glycogen as carrier and re-suspended in 100uL of water. For deep  sequencing (ChIP-seq) total chromatin input DNA was not saved.
DNA libraries were prepared for sequencing using standard Illumina protocols by FASTERIS SA, Switzerland

tag: genotype

value: wild type


title: S. thermophilus - PreSort

description: Sample 5

organism: Streptococcus thermophilus


title: TipR_ChIPseq


title: HigA_ChiPseq


title: RNAseq_Ctrl_6

description:
C6
control subject


title: LexA_ChIPseq


title: Ribosome profiling exercise rep2

status: Public on Feb 16 2016

city: Tokorozawa

first: Hiroaki

last: Sako

institute: Waseda University

data_processing:
Base-calling and alignment were conducted by using the built-in Ion torrent software (V4.0.1).
Sequenced reads shorter than 24 nt were removed.
Sequenced reads were mapped and aligned to coding DNA sequences extended to 25 nt upstream of translational start site of each gene, retrieved from Ensembl genes.
Read counts were converted to RPM (reads per million).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each sample.

source_name: gastrocnemius

extract_protocol:
After cycloheximide injection into right gastrocnemius, gastrocnemius was immediately harvested and flash-frozen in liquid nitrogen. The skeletal muscle was processed by either ribosome profiling or mRNA-Seq protocols, followed by Ion PGM total RNA-Seq protocols.
Sequence library was constructed using Ion Total RNA-Seq Kit v2 kit.

treatment_protocol: exercise mice underwent a 60min treadmill running at 20 m/min

value: gastrocnemius

tag: age

value: 9-10 weeks

tag: protocol

value: acute endurance exercise

tag: profiling

value: Ribo-Seq


title: Ribosome profiling no exercise rep1


title: RNAseq_Ctrl_2

description:
C2
control subject


title: Ribosome profiling exercise rep1


title: mRNA-Seq exercise rep2

value: mRNA-Seq


title: mRNA-Seq no exercise rep2


title: mRNA-Seq no exercise rep1


title: mRNA-Seq exercise rep1


title: ERalpha ChIP-seq LTED cells

city: London

first: Luca

last: Magnani

address: DuCane road

department: Surgery and Cancer

country: United Kingdom

institute: Imperial College London

data_processing:
Basecalls performed using CASAVA version 1.4
Alignment was performed with Bowtie v1.1.2
Peak calling was perfromed using MACS 2.0
Genome_build: Hg19
Supplementary_files_format_and_content: bed file reports peaks

source_name: LTED breast cancer cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
NEB ultra kit

value: LTED

tag: chip antibody

value: ERα antibody (HC-20) (Santa Cruz, catalog# sc-543)

tag: passage


title: ERalpha ChIP-seq LTED Tamoxifen resistant cells

source_name: LTED breast cancer cells, Tamoxifen resistant

tag: cell line

value: LTEDT


title: ERalpha ChIP-seq MCF7 Tamoxifen resistant cells

source_name: MCF7 breast cancer cells, Tamoxifen resistant


title: Eralpha ChIP-seq MCF7 cells

source_name: MCF7 breast cancer cells


title: H9 ESC RNA-seq

city: Taipei

first: Trees-Juen

last: Chuang

address: 128, Academia Road, Sec. 2, Nankang

department: Genomic Research Center

country: Taiwan

institute: Academic Sinica

description: total RNA with rRNA

data_processing:
Genes expression (FPKM) of H9 ESC RNA-seq was analyzed using TopHat,Cufflinks. genome build : hg19; gene annotation version: ensembl 75
Genome build: hg19
Supplementary_files_format_and_content: FPKM

growth_protocol: To generate feeder cells to support ESCs, mouse embryonic fibroblasts (MEFs) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS, Level), 1× non-essential amino acids (NEAA, Invitrogen), and 2 mM L-glutamine (Invitrogen), and treated with Mitomycin C. All primate ESCs (human: H9 (WiCell Bank); rhesus macaque: ORMES6) were grown onMitomycin C-treated MEF feeders (2 × 104 cells/cm2) in DMEM/F12 media plus 20% Knockout Serum Replacement (Invitrogen) and 4 ng/ml bFGF (Sigma-Aldrich). Primate ESC colonies were manually expanded to new feeder cells every four days (9,45).

extract_protocol:
The mRNAs were purified using the Oligotex mRNA Min Kit (QIAGEN), according to the manufacturer’s instructions. After DNase treatment, 20 _g of total RNA were heated at 70◦C for 3 min to disrupt RNA secondary structure; the RNA was then incubated withOligotex suspension at 30◦C for 10 min. Oligotex-bound mRNAs were then centrifuged, washed and eluted with buffers provided in the kit.
Total RNA (10 mg) was harvested from ESCs using TRI reagent (Ambion) for cDNA library preparation. Enrichment of mRNA by depletion of ribosomal RNA was performed using a RiboMinus transcriptome isolation kit (Invitrogen). RiboMinus RNA (1 mg) was then fragmented using RNase III for 10 min and cleaned up using a RiboMinus concentration module (Invitrogen).

value: ESC


title: S. thermophilus - PostSort

description: Sample 6

value: Plasmid DNA


title: Sox9CreER_iKO2_Tel

first: Kenneth

last: Lay

address: 1230 York Avenue

institute: The Rockefeller University

description: Processed data file:Cuffdiff_all_HFSCs.txt.gz

data_processing:
Alignment: Tophat with mm9 build of mouse genome
Transcript assembly: Cufflinks
Differential analysis: Cuffdiff
Genome_build: mm9

source_name: mouse dorsal skin

extract_protocol:
FACS-purified HFSCs were lysed in Trizol-LS. Total RNA was extracted using DirectZol kit from Zymo Research.
Illumina TruSeq mRNA sample preparation was used as per manufacturer's instructions.

treatment_protocol: For Sox9CreER samples, mice were treated with tamoxifen by intraperitoneal injection to induce nuclear localization of Cre, FOXC1 ablation, and YFP reporter activity.

value: 2nd Telogen HFSCs purified from a FOXC1-Sox9CreER-iKO male mouse_replicate 2

value: Black Swiss/ C57BL/6 mix

value: Postnatal day 60


title: WT_1st_Tel

value: 1st Telogen HFSCs purified from Shh-Het female mouse

value: Agouti

value: Postnatal day ~23


title: MT4 HIV 2 RNA-Seq

first: Christopher

middle: E

last: Mason

address: 1305 York Ave

department: Physiology and Biophysics

institute: Weill Cornell Medical College

data_processing:
Aligner: STAR 2.3.0e
Peak calling: MeRIPPeR 0.9.1
Coverage: bedtools 2.24.0
Genome_build: hg19 + HIV-1
Supplementary_files_format_and_content: Peak files in bed file format generated with MeRIPPeR 0.9.1, coverage files computed using bedtools 2.24.0

source_name: MT4 T-cells

growth_protocol: HIV-1 LAI virus was produced by transfection of 293T cells with the proviral pLAI2 plasmid (NIH AIDS program) at 3 µg/106 cells using Lipofectamine 2000 (Invitrogen), according to the manufacturer’s instructions. After 4 h incubation, the medium was replaced with DMEM supplemented with 10% foetal bovine serum (FBS). Two days after transfection, the virus-containing supernatant was collected and filtered.

extract_protocol:
Total RNA extracted using TRIzol reagent (Invitrogen), poly(A) RNA purified using oligo dT Dynabeads (Invitrogen), and MeRIP-Seq performed using Cell 2012 protocol.
Illumina TruSeq mRNA Stranded LT

treatment_protocol: Treated cells were infected with HIV-1 LAI virus (106 cpm of RT activity/106 cells) for 12 hours, centrifuged, washed with PBS, and resuspended in RPMI/10% FBS

tag: treatment

value: HIV-1 infected


title: O6 ESC RNA-seq

description: total RNA with rRNA

data_processing:
Genes expression (RPKM) of O6 ESC RNA-seq was analyzed using TopHat,Cufflinks. genome build : rheMac3; gene annotation version: ensembl 75
Genome build: rheMac3
Supplementary_files_format_and_content: FPKM

organism: Macaca mulatta


title: Sox9CreER_iKO1_Tel

value: 2nd Telogen HFSCs purified from a FOXC1-Sox9CreER-iKO male mouse_replicate 1


title: MT4 Control 2 MeRIP-Seq

value: control


title: MT4 Control 1 MeRIP-Seq


title: MT4 Control 2 RNA-Seq


title: F. novicida replicate 1 - PreSort

description: Sample 7


title: MT4 HIV 2 MeRIP-Seq


title: K14Cre_cKO2_Tel

description: Processed data file:Cuffdiff_Telogen_HFSCs.txt.gz

value: 2nd Telogen HFSCs purified from a FOXC1-K14Cre-cKO female mouse_replicate 2

value: Black Swiss

value: Postnatal day 46


title: WT1_Tel

value: 2nd Telogen HFSCs purified from a WT male mouse_replicate 1

value: Postnatal day 42


title: Sox9CreER_iKO2_Ana

description: Processed data file:Cuffdiff_Anagen_HFSCs.txt.gz

value: Anagen HFSCs purified from a FOXC1-Sox9CreER-iKO male mouse_replicate 2

value: Postnatal day 30


title: K14Cre_cKO1_Tel

value: 2nd Telogen HFSCs purified from a FOXC1-K14Cre-cKO male mouse_replicate 1


title: Ribosome profiling no exercise rep2

value: gastrocnemius

value: 9-10 weeks

tag: genotype/variation

value: wild type

value: Ribo-Seq


title: Sox9CreER_iKO1_Ana

value: Anagen HFSCs purified from a FOXC1-Sox9CreER-iKO male mouse_replicate 1

value: Black Swiss/ C57BL/6 mix


title: Sox9CreER_Het2_Ana

value: Anagen HFSCs purified from a FOXC1-Sox9CreER-heterozygous male mouse_replicate 2


title: WT_AnaII

value: Anagen-substage II HFSCs purified from Shh-Het female mouse

value: Agouti

value: Postnatal day ~26


title: WT2_Tel

value: 2nd Telogen HFSCs purified from a WT female mouse_replicate 2

value: Black Swiss


title: NHD13 & Musashi2 overexpression sample rep2

first: Alexendar

middle: Reinaldo

last: Perez

department: Computational Biology

institute: Memorial Sloan Kettering

description:
Sample_274_LC_NHD13_MSI2_dox
NHD13&MS2 replicate 2
Processed data file: Musashi2_4Month_CountTable.txt
Processed data file column: NHD13 w/ Musashi2 OE Rep2

data_processing:
Alignment using STAR genome aligner with the mm9 reference genome
Read count tabulation using HTSeq with mm9 gtf file
Processed genes with RPK >5 filtering from count table
Differential analysis with DESeq
Genome_build: mm9
Supplementary_files_format_and_content: txt file with raw counts from HTSeq

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 4 months

tag: induced overexpression

value: LSK


title: NHD13 & Musashi2 overexpression sample rep3

description:
Sample_274_RC_NHD13_MSI2_dox
NHD13&MS2 replicate 3
Processed data file: Musashi2_4Month_CountTable.txt
Processed data file column: NHD13 w/ Musashi2 OE Rep3


title: Sox9CreER_Het1_Ana

value: Anagen HFSCs purified from a FOXC1-Sox9CreER-heterozygous male mouse_replicate 1


title: NHD13 overexpression sample rep2

description:
Sample_273_RC_wt_het
NHD13 replicate 2
Processed data file: Musashi2_4Month_CountTable.txt
Processed data file column: NHD13 Rep2

source_name: NHD13 overexpression sample rep2


title: NHD13 & Musashi2 overexpression sample rep1

description:
Sample_274_NC_NHD13_MSI2_dox
NHD13&MS2 replicate 1
Processed data file: Musashi2_4Month_CountTable.txt
Processed data file column: NHD13 w/ Musashi2 OE Rep1


title: MT4 HIV 1 MeRIP-Seq

value: HIV-1 infected


title: MT4 HIV 1 RNA-Seq


title: NHD13 overexpression sample rep1

description:
Sample_273_NC_NHD13_wt_het
NHD13 replicate 1
Processed data file: Musashi2_4Month_CountTable.txt
Processed data file column: NHD13 Rep1

source_name: NHD13 overexpression sample rep1


title: 5µM AGE-BSA with BMP2

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

data_processing:
The complementary DNA (cDNA) libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions. The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols. Samples were diluted and mixed, the mixture was processed on a OneTouch 2 instrument (Life Technologies) and enriched on a OneTouch 2 ES station (Life Technologies) for preparing the template-positive Ion PI™ Ion Sphere™ Particles (Life Technologies) according to Ion PI™ Template OT2 200 Kit v2.0 (Life Technologies). After enrichment, the mixed template-positive Ion PI™ Ion Sphere™ Particles of samples was loaded on to 1 P1v2 Proton Chip (Life Technologies) and sequenced on Proton Sequencers according to Ion PI Sequencing 200 Kit v2.0 (Life Technologies).
The clean reads were then aligned to human genome (version: hg19) using the MapSplice program (v2.1.6). In alignment, preliminary experiments were performed to optimize the alignment parameters (-s 22 -p 15 --ins 6 --del 6 --non-canonical) to provide the largest information on the AS events.
We applied HTseq to calculate the mRNA counts based on the mapping result
Genome_build: hg19
Supplementary_files_format_and_content: fastq file and txt file

source_name: ligament cells_stimulated

growth_protocol: Normal posterior longitudinal ligament were dissected during the surgery, all tissues were obtained with written informed consent signed by the donors voluntarily for research. Ligaments were further cut into pieces and cultured in DMEM supplemented with 20% fetal bovine serum, and cells of passage 3 were used for the experiments.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
The complementary DNA (cDNA) libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions. The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols. Samples were diluted and mixed, the mixture was processed on a OneTouch 2 instrument (Life Technologies) and enriched on a OneTouch 2 ES station (Life Technologies) for preparing the template-positive Ion PI™ Ion Sphere™ Particles (Life Technologies) according to Ion PI™ Template OT2 200 Kit v2.0 (Life Technologies). After enrichment, the mixed template-positive Ion PI™ Ion Sphere™ Particles of samples was loaded on to 1 P1v2 Proton Chip (Life Technologies) and sequenced on Proton Sequencers according to Ion PI Sequencing 200 Kit v2.0 (Life Technologies).

treatment_protocol: AGE-BSA (1µM or 5µM) or BSA with or without 5µM of BMP2 were added to the medium, and cells were collected for further analysis after 3 days of treatment

value: Primary human posterior longitudinal ligament cells

tag: stimulated with

value: 5µM AGE-BSA with BMP2


title: 1µM AGE-BSA with BMP2

value: 1µM AGE-BSA with BMP2


title: Control sample rep1

description:
Sample_272_Bulk_b6
control replicate 1
Processed data file: Musashi2_4Month_CountTable.txt
Processed data file column: Wild-type Rep1

source_name: Control sample rep1

value: control


title: WT_progenitors

city: Cambridge

first: Omer

last: Yilmaz

state: MA

address: 77 Massachusetts Avenue, 76-353D

department: Biology

institute: Koch Institute for Integrated Cancer Research at MIT

data_processing:
Adapters were trimmed with cutadapt (-a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -e 0.1 -O 6 -m 15).
Low-quality reads were removed with fastq_quality_filter (-q 20 -p 75)
Low-quality bases at the end of reads were trimmed with fastq_quality_trimmer (-t 20 -l 35)
Reads were mapped with tophat 1.4.1 (--segment-length 20)
Genes were quantified with htseq-count (-m intersection-strict --stranded=yes) using Ensembl release 70 gene models.
Genome_build: mouse GRCm38 (mm10)
Supplementary_files_format_and_content: Read count for each Ensembl gene (text format)

source_name: GFP-Low

extract_protocol:
Total RNA was extracted from 200K sorted GFPhi ISCs or GFPlow progenitors by pooling two to five 71-week old male mice per HFD and HFD-control using Tri Reagent (Life Technologies) according to the manufacturer's instructions, except for a overnight isopropanol precipitation at –20°C. From the total RNA, poly(A)+ RNA was selected using Oligo(dT)25-Dynabeads (Life technologies) according to the manufacturer’s protocol.
Strand-specific RNA-seq libraries were prepared using the dUTP-based, Illumina-compatible NEXTflex Directional RNA-Seq Kit (Bioo Scientific) according to the manufacturer’s directions.

value: progenitors

tag: diet

value: normal


title: 5µM AGE-BSA

value: 5µM AGE-BS


title: HFD_progenitors

value: high-fat


title: Control sample rep2

description:
Sample_B6_control_MPP_HSC_208BC
control replicate 2
Processed data file: Musashi2_4Month_CountTable.txt
Processed data file column: Wild-type Rep2

source_name: Control sample rep2


title: MT4 Control 1 RNA-Seq


title: 1µM AGE-BSA

value: 1µM AGE-BSA


title: WT_intestinal stem cells

source_name: GFP-Hi

value: intestinal stem cells


title: NHD13 & Musashi2 overexpression sample rep4

description:
Sample_274_RP_NHD13_MSI2_dox
NHD13&MS2 replicate 4
Processed data file: Musashi2_4Month_CountTable.txt
Processed data file column: NHD13 w/ Musashi2 OE Rep4


title: Wild Type 6 month Female Skin mRNA rep2

status: Public on Feb 15 2016

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

description:
299721_Q20B0005_03_L2.D712
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling
Genome mapped via Omnisoft OSA 2.0
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using fastq-mcf sequence quality filter, clipping and processor with following settings for Omnisoft: Trimming  /Mode=TrimByQuality /ReadTrimQuality=2;  Options  /ParallelJobNumber=4 /PairedEnd=True /FileFormat=FASTQ /AutoPenalty=True /FixedPenalty=2 /Greedy=false /IndelPenalty=2 /DetectIndels=False /MaxMiddleInsertionSize=10 /MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /ExcludeNonUniqueMapping=False /ReportCutoff=10 /WriteReadsInSeparateFiles=True /GenerateSamFiles=False /ThreadNumber=6 /InsertSizeStandardDeviation=40 /ExpectedInsertSize=300 /MatePair=False /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic /CompressionMethod=Gzip /Gzip=True /SearchNovelExonJunction=False /ExcludeUnmappedInBam=False /KeepFullRead=False /Replace=False /Platform=ILLUMINA /CompressBam=False;
Genome_build: Genome version Mouse B.38, gene models version Ensembl R.75
Supplementary_files_format_and_content: Text file containing abundance measurements in FPKM
Supplementary_files_format_and_content: Text file containing abundance measurements in counts

source_name: Skin

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen miRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 1.25 ug of total RNA were used to collect polyA-enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: Skin

value: Wild Type

value: 6 month

tag: Sex

value: Female

tag: housing condition

value: housed with Het (Q20) mice


title: Wild Type 6 month Male Skin mRNA rep2

description:
299722_Q20B0001_07_L2.D701
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Male


title: Wild Type 6 month Female Skin mRNA rep1

description:
299715_Q20B0005_05_L1.D708
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HFD_intestinal stem cells

tag: cell type


title: Wild Type 6 month Male Skin mRNA rep1

description:
299712_Q20B0001_01_L1.D705
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

tag: strain


title: Wild Type 6 month Female Skin mRNA rep3

description:
299725_Q20B0005_07_L3.D704
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

tag: genotype


title: Het (Q175) Knock-In 6 month Male Skin mRNA rep4

description:
299720_Q175B0574_10_L2.D711
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Het (Q175) Knock-In

tag: age

value: housed with Het (Q175) mice


title: Wild Type 6 month Male Skin mRNA rep3

description:
299723_Q20B0001_03_L3.D702
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Skin mRNA rep2

description:
299717_Q175B0574_06_L2.D709
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Skin mRNA rep1

description:
299713_Q175B0574_04_L1.D706
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Skin mRNA rep4

description:
299726_Q175B0575_02_L3.D705
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Control sample rep3

description:
Sample_B6_control_MPP_HSC_B6_DOB050914
control replicate 3
Processed data file: Musashi2_4Month_CountTable.txt
Processed data file column: Wild-type Rep3

source_name: Control sample rep3

value: 4 months

value: LSK


title: Het (Q175) Knock-In 6 month Male Skin mRNA rep3

description:
299718_Q175B0574_02_L2.D710
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Skin mRNA rep2

description:
299714_Q175B0575_04_L1.D707
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Skin mRNA rep3

description:
299724_Q175B0575_10_L3.D703
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male Heart mRNA rep3

description:
299751_Q20B0001_01_L8.D706
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

source_name: Heart

value: Heart


title: Wild Type 6 month Male Heart mRNA rep2

description:
299749_Q20B0001_03_L8.D704
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Heart mRNA rep4

description:
299754_Q20B0005_05_L1.D709
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Heart mRNA rep3

description:
299752_Q20B0005_09_L8.D707
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male Heart mRNA rep1

description:
299745_Q20B0001_07_L7.D712
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Heart mRNA rep2

description:
299748_Q20B0005_03_L8.D703
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Heart mRNA rep1

description:
299747_Q20B0005_07_L7.D702
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Heart mRNA rep3

description:
299755_Q175B0574_10_L1.D710
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Skin mRNA rep1

description:
299711_Q175B0575_08_L1.D704
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Heart mRNA rep1

description:
299743_Q175B0574_04_L7.D710
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male Heart mRNA rep4

description:
299757_Q20B0001_05_L1.D712
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: BSA Control

source_name: ligament cells_control

value: Primary human posterior longitudinal ligament cells

value: BSA (control)


title: Het (Q175) Knock-In 6 month Male Heart mRNA rep2

description:
299744_Q175B0574_02_L7.D711
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Heart mRNA rep4

description:
299756_Q175B0575_02_L1.D711
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Heart mRNA rep3

description:
299753_Q175B0575_08_L1.D708
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Heart mRNA rep2

description:
299750_Q175B0575_10_L8.D705
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male Gastrocnemius mRNA rep2

description:
299737_Q20B0001_07_L5.D704
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

source_name: Gastrocnemius

value: Gastrocnemius


title: Wild Type 6 month Female Gastrocnemius mRNA rep4

description:
299731_Q20B0005_09_L4.D710
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male Gastrocnemius mRNA rep4

description:
299740_Q20B0001_05_L6.D707
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male Gastrocnemius mRNA rep3

description:
299738_Q20B0001_01_L6.D705
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male Gastrocnemius mRNA rep1

description:
299728_Q20B0001_03_L4.D707
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Gastrocnemius mRNA rep2

description:
299729_Q20B0005_03_L4.D708
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Gastrocnemius mRNA rep3

description:
299730_Q20B0005_07_L4.D709
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Gastrocnemius mRNA rep1

description:
299727_Q20B0005_05_L3.D706
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Heart mRNA rep1

description:
299746_Q175B0575_04_L7.D701
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Gastrocnemius mRNA rep4

description:
299742_Q175B0574_02_L6.D709
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Gastrocnemius mRNA rep2

description:
299735_Q175B0574_10_L5.D702
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Gastrocnemius mRNA rep1

description:
299732_Q175B0574_06_L4.D711
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Heart mRNA rep4

description:
299758_Q175B0574_06_L2.D701
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male Corpus callosum mRNA rep3

description:
299898_Q20B0001_01_L8.D706
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

source_name: Corpus callosum

value: Corpus callosum


title: Wild Type 6 month Male Corpus callosum mRNA rep4

description:
299901_Q20B0001_07_L22
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Gastrocnemius mRNA rep3

description:
299736_Q175B0575_10_L5.D703
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Gastrocnemius mRNA rep2

description:
299734_Q175B0575_04_L5.D701
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Corpus callosum mRNA rep2

description:
299895_Q20B0005_03_L44
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Gastrocnemius mRNA rep4

description:
299741_Q175B0575_02_L6.D708
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Gastrocnemius mRNA rep1

description:
299733_Q175B0575_08_L5.D712
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Corpus callosum mRNA rep1

description:
299889_Q20B0005_05_L3
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Corpus callosum mRNA rep4

description:
299902_Q20B0005_09_L38
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Corpus callosum mRNA rep3

description:
299899_Q20B0005_07_L48
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male Corpus callosum mRNA rep1

description:
299893_Q20B0001_03_L18
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Corpus callosum mRNA rep2

description:
299891_Q175B0574_02_L39
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Corpus callosum mRNA rep3

description:
299892_Q175B0574_04_L31
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Corpus callosum mRNA rep4

description:
299897_Q175B0575_04_L10
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Corpus callosum mRNA rep2

description:
299888_Q175B0575_10_L54
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male Corpus callosum mRNA rep2

description:
299894_Q20B0001_05_L37
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Corpus callosum mRNA rep3

description:
299896_Q175B0575_08_L7.D704
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Corpus callosum mRNA rep1

description:
299890_Q175B0574_06_L5
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Gastrocnemius mRNA rep3

description:
299739_Q175B0574_04_L6.D706
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male Brain - Hypothalamus/Thalamus mRNA rep2

description:
299877_Q20B0001_01_L28
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

source_name: Brain - Hypothalamus/Thalamus

value: Brain - Hypothalamus/Thalamus


title: Wild Type 6 month Male Brain - Hypothalamus/Thalamus mRNA rep4

description:
299885_Q20B0001_03_L6.D704
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Corpus callosum mRNA rep1

description:
299887_Q175B0575_02_L33
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Brain - Hypothalamus/Thalamus mRNA rep4

description:
299884_Q20B0005_05_L5.D703
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male Brain - Hypothalamus/Thalamus mRNA rep1

description:
299872_Q20B0001_07_L69
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Brain - Hypothalamus/Thalamus mRNA rep3

description:
299883_Q20B0005_03_L12
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Brain - Hypothalamus/Thalamus mRNA rep2

description:
299879_Q20B0005_09_L19
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Brain - Hypothalamus/Thalamus mRNA rep1

description:
299874_Q20B0005_07_L4.D705
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Brain - Hypothalamus/Thalamus mRNA rep4

description:
299880_Q175B0574_04_L4
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Brain - Hypothalamus/Thalamus mRNA rep2

description:
299873_Q175B0574_10_L4.D704
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Brain - Hypothalamus/Thalamus mRNA rep1

description:
299871_Q175B0574_06_L50
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Brain - Hypothalamus/Thalamus mRNA rep3

description:
299881_Q175B0575_10_L21
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Brain - Hypothalamus/Thalamus mRNA rep4

description:
299886_Q175B0575_02_L76
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Corpus callosum mRNA rep4

description:
299900_Q175B0574_10_L23
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Brain - Hypothalamus/Thalamus mRNA rep3

description:
299878_Q175B0574_02_L7
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male Brain - Hippocampus mRNA rep3

description:
299842_Q20B0001_05_L45
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

source_name: Brain - Hippocampus

value: Brain - Hippocampus


title: Het (Q175) Knock-In 6 month Female Brain - Hypothalamus/Thalamus mRNA rep2

description:
299876_Q175B0575_04_L4.D707
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Brain - Hypothalamus/Thalamus mRNA rep1

description:
299875_Q175B0575_08_L2
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male Brain - Hippocampus mRNA rep4

description:
299853_Q20B0001_03_L40
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male Brain - Hippocampus mRNA rep2

description:
299841_Q20B0001_01_L14
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male Brain - Hypothalamus/Thalamus mRNA rep3

description:
299882_Q20B0001_05_L1
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Brain - Hippocampus mRNA rep3

description:
299848_Q20B0005_07_L41
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Brain - Hippocampus mRNA rep2

description:
299847_Q20B0005_09_L46
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Brain - Hippocampus mRNA rep3

description:
299846_Q175B0574_06_L9
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male Brain - Hippocampus mRNA rep1

description:
299839_Q20B0001_07_L32
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Brain - Hippocampus mRNA rep3

description:
299851_Q175B0575_04_L8.D706
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Brain - Hippocampus mRNA rep1

description:
299843_Q20B0005_05_L17
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Brain - Hippocampus mRNA rep2

description:
299850_Q175B0575_08_L8.D705
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Brain - Hippocampus mRNA rep4

description:
299849_Q20B0005_03_L15
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Brain - Hippocampus mRNA rep1

description:
299840_Q175B0574_10_L35
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Brain - Hippocampus mRNA rep1

description:
299845_Q175B0575_10_L34
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Brain - Hippocampus mRNA rep2

description:
299844_Q175B0574_04_L27
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male Brain - Cerebellum mRNA rep4

description:
299838_Q20B0001_05_L42
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

source_name: Brain - Cerebellum

value: Brain - Cerebellum


title: Wild Type 6 month Male Brain - Cerebellum mRNA rep3

description:
299837_Q20B0001_01_L6.D704
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Wild Type


title: Wild Type 6 month Male Brain - Cerebellum mRNA rep1

description:
299824_Q20B0001_03_L3.D703
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: 6 month


title: Wild Type 6 month Female Brain - Cerebellum mRNA rep4

description:
299836_Q20B0005_05_L24
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Female


title: Wild Type 6 month Male Brain - Cerebellum mRNA rep2

description:
299827_Q20B0001_07_L4.D706
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: housed with Het (Q20) mice


title: Wild Type 6 month Female Brain - Cerebellum mRNA rep3

description:
299834_Q20B0005_07_L11
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Brain - Cerebellum mRNA rep2

description:
299831_Q20B0005_09_L5.D710
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Brain - Cerebellum mRNA rep3

description:
299828_Q175B0574_04_L36
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Male


title: Wild Type 6 month Female Brain - Cerebellum mRNA rep1

description:
299830_Q20B0005_03_L30
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Brain - Cerebellum mRNA rep1

description:
299823_Q175B0574_06_L3.D702
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Het (Q175) Knock-In


title: Het (Q175) Knock-In 6 month Female Brain - Cerebellum mRNA rep4

description:
299833_Q175B0575_04_L47
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: housed with Het (Q175) mice


title: Het (Q175) Knock-In 6 month Male Brain - Hippocampus mRNA rep4

description:
299854_Q175B0574_02_L52
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male Brain - Brainstem mRNA rep4

description:
299864_Q20B0001_03_L16
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

source_name: Brain - Brainstem

value: Brain - Brainstem


title: Wild Type 6 month Male Brain - Brainstem mRNA rep1

description:
299858_Q20B0001_01_L72
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Brain - Cerebellum mRNA rep1

description:
299826_Q175B0575_10_L4.D705
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Brain - Hippocampus mRNA rep4

description:
299852_Q175B0575_02_L8
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Brain - Brainstem mRNA rep4

description:
299870_Q175B0574_06_L56
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Brain - Brainstem mRNA rep3

description:
299867_Q20B0005_05_L3.D710
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male Brain - Brainstem mRNA rep2

description:
299862_Q20B0001_05_L2.D705
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Brain - Cerebellum mRNA rep3

description:
299832_Q175B0575_02_L5.D711
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Brain - Brainstem mRNA rep3

description:
299868_Q175B0574_04_L65
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male Brain - Brainstem mRNA rep3

description:
299863_Q20B0001_07_L64
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Brain - Brainstem mRNA rep1

description:
299856_Q20B0005_09_L73
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Brain - Cerebellum mRNA rep2

description:
299829_Q175B0575_08_L13
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Brain - Brainstem mRNA rep2

description:
299866_Q175B0574_10_L20
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Brain - Brainstem mRNA rep2

description:
299860_Q20B0005_07_L1.D703
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Brain - Brainstem mRNA rep4

description:
299865_Q175B0575_02_L26
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Brain - Brainstem mRNA rep3

description:
299861_Q175B0575_08_L2.D704
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female Brain - Brainstem mRNA rep4

description:
299869_Q20B0005_03_L62
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Brain - Brainstem mRNA rep2

description:
299857_Q175B0575_10_L25
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female Brain - Brainstem mRNA rep1

description:
299855_Q175B0575_04_L29
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male White Adipose tissue around Intestine mRNA rep4

description:
299787_Q20B0001_01_L4.D702
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

source_name: White Adipose tissue around Intestine

value: White Adipose tissue around Intestine


title: Het (Q175) Knock-In 6 month Male Brain - Cerebellum mRNA rep2

description:
299825_Q175B0574_02_L4.D704
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Brain - Cerebellum mRNA rep4

description:
299835_Q175B0574_10_L43
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male White Adipose tissue around Intestine mRNA rep2

description:
299782_Q20B0001_03_L3.D709
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male White Adipose tissue around Intestine mRNA rep3

description:
299783_Q20B0001_05_L3.D710
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male White Adipose tissue around Intestine mRNA rep1

description:
299779_Q20B0001_07_L3.D706
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female White Adipose tissue around Intestine mRNA rep2

description:
299777_Q20B0005_03_L2.D704
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female White Adipose tissue around Intestine mRNA rep4

description:
299785_Q20B0005_05_L4.D712
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female White Adipose tissue around Intestine mRNA rep3

description:
299784_Q20B0005_07_L4.D711
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male Brain - Brainstem mRNA rep1

description:
299859_Q175B0574_02_L1.D702
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male White Adipose tissue around Intestine mRNA rep2

description:
299780_Q175B0574_06_L3.D707
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female White Adipose tissue around Intestine mRNA rep1

description:
299775_Q20B0005_09_L2.D702
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male White Adipose tissue around Intestine mRNA rep4

description:
299790_Q175B0574_04_L5.D705
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female White Adipose tissue around Intestine mRNA rep3

description:
299786_Q175B0575_10_L4.D701
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male White Adipose tissue around Intestine mRNA rep1

description:
299778_Q175B0574_10_L2.D705
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male White Adipose tissue around Intestine mRNA rep3

description:
299788_Q175B0574_02_L4.D703
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female White Adipose tissue around Intestine mRNA rep1

description:
299776_Q175B0575_02_L2.D703
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male White Adipose tissue around Gonad mRNA rep1

description:
299808_Q20B0001_03_L8.D712
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

source_name: White Adipose tissue around Gonad

value: White Adipose tissue around Gonad


title: Wild Type 6 month Male White Adipose tissue around Gonad mRNA rep3

description:
299815_Q20B0001_01_L2.D707
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Female White Adipose tissue around Gonad mRNA rep3

description:
299813_Q20B0005_03_L1.D705
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Wild Type 6 month Male White Adipose tissue around Gonad mRNA rep4

description:
299822_Q20B0001_07_L3.D701
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Female White Adipose tissue around Intestine mRNA rep2

description:
299781_Q175B0575_04_L3.D708
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Het (Q175) Knock-In 6 month Male White Adipose tissue around Gonad mRNA rep4

description:
299819_Q175B0574_06_L3.D711
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000