title: H3K9ac, untreated, replicate 1

description: Sample name: AC2

tag: cell type

value: triple negative breast adenocarcinoma

tag: chip antibody


title: Input, untreated, replicate 1

status: Public on Nov 05 2015

type: SRA

city: Chicago

first: Douglas

middle: David

last: Thomas

state: IL

address: 900 S Ashland Ave Room 3306

department: Medicinal Chemistry & Pharmacognosy

country: USA

institute: University of Illinois at Chicago

description: Sample name: Input_C2

library_source: genomic

data_processing:
[raw data QC and genome alignment] All raw sequencing data was quality trimmed to a minimum phred score of 20 using trimmomatic 0.32. Alignment to reference genome hg19 was done with BWA 0.7.5. PCR duplicates were removed using Picard MarkDuplicates and alignments with an edit distance greater than 2 to the reference, or that were mapped multiple times to the reference, were removed.
[ChIP-seq peak calling (H3K9ac)] Peak calls for H3K9ac data were created with Macs2 against paired input samples at an FDR threshold of 0.5 to allow for sufficient false peaks for IDR analysis; high-confidence peaks from individual replicates were selected using an FDR threshold of 1e-5 from the called peaks. Highly reproducible peaks were identified using Irreproducible Discovery Rate (IDR) using the IDR R package.
[ChIP-seq peak calling (H3K9me2)] Peak calls for H3K9me2 data were created with SICER against paired input samples using redundancy threshold = 10, window size = 500, fragment size = 400, effective genome fraction = 0.8, gap size = 1500, and an FDR threshold of 1e-5
Genome_build: hg19
Supplementary_files_format_and_content: bed file fields are: chromosome, start, end, peak ID, -log10 p-value or IDR value
Supplementary_files_format_and_content: bigWig files for H3K9ac (from Macs2) are raw read counts, bigWig files for H3K9me2 are normalized by library depth and background-subtracted

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: MDA-MB-231 human triple negative breast cancer cells were obtained from American Type Culture Collection (ATCC) and cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin in a controlled environment (37°C and 5% CO2).

extract_protocol:
MDA-MB-231 cells in culture were crosslinked using 1% formaldehyde for 10 minutes at room temperature, following which excess reagent was quenched by the addition of 125 mM glycine for 5 minutes. Cells were washed with ice cold PBS and the pellet was resuspended in ChIP lysis buffer (1% SDS, 10 mM EDTA pH 8.0, 50 mM Tris-HCl pH 8.1, protease inhibitor cocktail and PMSF). DNA was sheared to 200-500bp using a Branson probe sonicator while keeping the sample on ice. A small aliquot of sheared chromatin was saved as “input”. Chromatin from 2 million cells was used for each ChIP reaction and diluted 10-fold using ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.1, 167 mM NaCl, protease inhibitor cocktail and PMSF). Immunoprecipitation was performed by incubating diluted chromatin with Dynabeads G (Invitrogen, pre-washed with BSA/PBS) and the following antibodies overnight at 4°C: H3K9me2 (Abcam, ab1220; 2 mg per ChIP) or H3K9ac (Millipore #07-352; 3.5 ml per ChIP). Beads were subsequently washed using the following buffers: low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 150 mM NaCl), high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 500 mM NaCl), LiCl buffer (0.25M LiCl, 1% IGEPAL-CA630, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.1) and twice with TE (1 mM EDTA, 10 mM Tris-HCl, pH 8.1). Dissociation of chromatin-antibody complexes from the beads was facilitated by eluting twice using an appropriate buffer (1% SDS, 0.1M NaHCO3) for 15 minutes each at RT. Crosslinks in all ChIP and input samples were reversed by incubating with NaCl overnight at 65°C. Samples were treated with RNAse A for one hour at 37°C followed by addition of Proteinase K for one hour at 45°C for cleanup. In the final step, DNA was purified using the MinElute PCR Purification Kit (Qiagen).
Libraries were made using the Diagenode MicroPlex Library PreparationTM kit as per manufacturer's protocols.

treatment_protocol: For conducting experiments, cells were grown to 80% confluency and serum starved overnight prior to treatment with 500uM DETA/NO for 24 hours.

tag: cell line

value: none (input)


title: H3K9me2, treated, replicate 1

description: Sample name: MD1


title: IC50

status: Public on Nov 04 2015

city: Luebeck

first: Martin

last: Kircher

state: SH

address: Ratzeburger Allee 160

department: Humangenetics

country: Germany

institute: University of Luebeck

description: processed data file(s): CA01.bb

data_processing:
All libraries were sequenced on HiSeq 2000 or NextSeq 500 instruments (Illumina). Barcoded paired end (PE) Illumina sequencing data was split allowing up to one substitution in the barcode sequence. Reads shorter or equal to read length were consensus called and adapter trimmed.
Remaining consensus single end reads (SR) and the individual PE reads were aligned to the human reference genome sequence (GRCh37, 1000 Genomes phase 2 technical reference downloaded from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/) using the ALN algorithm implemented in BWA v0.7.1041. PE reads were further processed with BWA SAMPE to resolve ambiguous placement of read pairs or to rescue missing alignments by a more sensitive alignment step around the location of one placed read end. Aligned SR and PE data was directly converted to sorted BAM format using the samtools API. BAM files of the sample were merged across lanes and sequencing runs.
PE provides information about the two physical ends of DNA molecules used in sequencing library preparation. We extract this information using the SAMtools application programming interface (API) from BAM files. As read starts, we use both outer alignment coordinates of PE data for which both reads aligned to the same chromosome and where reads have opposite orientations. In cases where PE data was converted to single read data by adapter trimming, we consider both end coordinates of the SR alignment as read starts. For coverage, we consider all positions between the two (inferred) molecule ends, including these end positions. We define window protection scores (WPS) of a window size k as the number of molecules spanning a window minus those starting at any bases encompassed by the window. We assign the determined WPS to the center of the window. For molecules in the 35-80 bp range (short fraction), we use a window size of 16 and, for molecules in the 120-180 bp (long fraction), we use a window size of 120.
Local maxima of nucleosome protection are called from the long fraction WPS, which we locally adjust to a running median of zero (1 kb window) and smooth using a Savitzky-Golay filter (window size 21, 2nd order polynomial). The WPS track is then segmented into above zero regions (allowing up to 5 consecutive positions below zero). If the resulting region is between 50-150 bp long, we identify the median value of that region and search for the maximum-sum contiguous window above the median. We report the start, end and center coordinates of this window. Peak-to-peak distances, etc., are calculated from the center coordinates. The score of the call is determined as the distance between maximum value in the window and the average of the two adjacent WPS minima neighboring the region. If the identified region is 150-450 bp long, we apply the same above median contiguous window approach, but only report those windows that are between 50-150bp in size. For score calculation of multiple windows derived from the 150-450bp regions, we assume the neighboring minima within the region to be zero. We discard regions shorter than 50 bp and longer than 450 bp.
Genome_build: GRCh37, 1000 Genomes phase 2 technical reference downloaded from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/
Supplementary_files_format_and_content: Local maxima of nucleosome protection in bigBED (UCSC http://genome.ucsc.edu/FAQ/FAQformat.html#format1.5)

source_name: cell-free DNA

extract_protocol:
Bulk human peripheral blood plasma, containing contributions from an unknown number of healthy individuals, was obtained from STEMCELL Technologies (Vancouver, British Columbia, Canada) and stored in 2 ml aliquots at -80ºC until use. Individual human peripheral blood plasma from anonymous, healthy donors was obtained from Conversant Bio (Huntsville, Alabama, USA) and stored in 0.5 ml aliquots at -80ºC until use. Human peripheral blood plasma for 52 individuals with clinical diagnosis of Stage IV cancer was obtained from Conversant Bio or PlasmaLab International (Everett, Washington, USA) and stored in 0.5 ml or 1 ml aliquots at -80ºC until use. Human peripheral blood plasma for four individuals with clinical diagnosis of systemic lupus erythematosus was obtained from Conversant Bio and stored in 0.5 ml aliquots at -80ºC until use.
Barcoded double-strand preparation sequencing libraries were constructed with the ThruPLEX-FD or ThruPLEX DNA-seq 48D kits (Rubicon Genomics), comprising a proprietary series of end-repair, ligation, and amplification reactions. Between 0.5 ng and 30.0 ng of cfDNA were used as input for all clinical sample libraries. Library amplification for all samples was monitored by real-time PCR to avoid over-amplification, and was typically terminated after 4-6 cycles. Single-strand ligation libraries were prepared from dephosphorylated cell-free DNA. For dephosphorylation, 2X CircLigase II buffer (Epicentre), 5 mM MnCl2, and 1U FastAP alkaline phosphatase (Thermo Fisher) and 0.5-10 ng fragments were incubated in a 20 ul reaction volume at 37ºC for 30 minutes. Fragments were then denatured by heating to 95ºC for 3 minutes, and were immediately transferred to an ice bath. The reaction was supplemented with the biotin-conjugated adapter oligo (5 pmol), 20% PEG-6000 (w/v), and 200U CircLigase II (Epicentre) for a total volume of 40 ul, and was incubated overnight with rotation at 60ºC, heated to 95ºC for 3 minutes, and placed in an ice bath. For each sample, 20 ul MyOne C1 beads (Life Technologies) were twice washed in bead binding buffer (BBB) (10 mM Tris-HCl [pH 8], 1M NaCl, 1 mM EDTA [pH 8], 0.05% Tween-20, and 0.5% SDS), and resuspended in 250 ul BBB. Adapter-ligated fragments were bound to the beads by rotating for 60 minutes at room temperature. Beads were collected on a magnetic rack and the supernatant was discarded. Beads were washed once with 500 ul wash buffer A (WBA) (10 mM Tris-HCl [pH 8], 1 mM EDTA [pH 8], 0.05% Tween-20, 100 mM NaCl, 0.5% SDS) and once with 500 ul wash buffer B (WBB) (10 mM Tris-HCl [pH 8], 1 mM EDTA [pH 8], 0.05% Tween-20, 100 mM NaCl). Beads were combined with 1X Isothermal Amplification Buffer (NEB), 2.5 uM oligo CL9, 250 uM (each) dNTPs, and 24U Bst 2.0 DNA Polymerase (NEB) in a reaction volume of 50 ul, incubated with gentle shaking by ramping temperature from 15ºC to 37ºC at 1ºC/minute, and held at 37ºC for 10 minutes. After collection on a magnetic rack, beads were washed once with 200 ul WBA, resuspended in 200 ul of stringency wash buffer (SWB) (0.1X SSC, 0.1% SDS), and incubated at 45ºC for 3 minutes. Beads were again collected and washed once with 200 ul WBB. Beads were then combined with 1X CutSmart Buffer (NEB), 0.025% Tween-20, 100 uM (each) dNTPs, and 5U T4 DNA Polymerase (NEB) and incubated with gentle shaking for 30 minutes at room temperature. Beads were washed once with each of WBA, SWB, and WBB as described above. Beads were then mixed with 1X CutSmart Buffer (NEB), 5% PEG-6000, 0.025% Tween-20, 2 uM double-stranded adapter 2, and 10U T4 DNA Ligase (NEB), and incubated with gentle shaking for 2 hours at room temperature. Beads were washed once with each of WBA, SWB, and WBB as described above, and resuspended in 25 ul TET buffer (10 mM Tris-HCl [pH 8], 1 mM EDTA [pH 8], 0.05% Tween-20). Second strands were eluted from beads by heating to 95ºC, collecting beads on a magnetic rack, and transferring the supernatant to a new tube. Library amplification for all samples was monitored by real-time PCR to avoid over-amplification, and required an average of 4 to 6 cycles per library.

tag: tissue

value: blood plasma

tag: disease

value: Pancreatic cancer (Ductal carcinoma)

tag: Sex

value: F


title: IC52

description: processed data file(s): CA01.bb

value: Pancreatic cancer (undefined)

value: M


title: IC49

description: processed data file(s): CA01.bb


title: IC51

description: processed data file(s): CA01.bb


title: IC48

description: processed data file(s): CA01.bb

value: Breast cancer (Invasive/infiltrating lobular)


title: IC36

description: processed data file(s): CA01.bb

value: Liver cancer (undefined)


title: IC47

description: processed data file(s): CA01.bb

value: Pancreatic cancer (Ductal adenocarcinoma)


title: IC46

description: processed data file(s): CA01.bb

value: Breast cancer (Ductal carcinoma in situ)


title: IC37

description: processed data file(s): CA01.bb

value: Colorectal cancer (Adenocarcinoma)


title: IC38

description: processed data file(s): CA01.bb

value: Bladder cancer (undefined)


title: IC34

description: processed data file(s): CA01.bb


title: IC33

description: processed data file(s): CA01.bb


title: IC40

description: processed data file(s): CA01.bb

value: Prostate cancer (Adenocarcinoma)


title: H3K9me2, untreated, replicate 1

description: Sample name: MC2


title: IC42

description: processed data file(s): CA01.bb

value: Lung cancer (Adenocarcinoma)


title: IC32

description: processed data file(s): CA01.bb

value: Lung cancer (Small cell)


title: IC30

description: processed data file(s): CA01.bb

value: Esophageal cancer (undefined)


title: IC35

description: processed data file(s): CA01.bb


title: IC25

description: processed data file(s): CA01.bb


title: IC27

description: processed data file(s): CA01.bb

value: Uterine cancer (undefined)


title: IC29

description: processed data file(s): CA01.bb

value: Head and neck cancer (undefined)


title: IC44

description: processed data file(s): CA01.bb

value: blood plasma


title: IC22

description: processed data file(s): CA01.bb


title: IC23

description: processed data file(s): CA01.bb

value: Liver cancer (Hepatocellular carcinoma)


title: IC39

description: processed data file(s): CA01.bb

value: Kidney cancer (undefined)


title: IC17

description: processed data file(s): CA01.bb


title: IC18

description: processed data file(s): CA01.bb

value: Kidney cancer (Clear cell)

value: F


title: IC15

description: processed data file(s): CA01.bb

value: M


title: IC19

description: processed data file(s): CA01.bb

value: Testicular cancer (Seminomatous)


title: IC26

description: processed data file(s): CA01.bb


title: IC14

description: processed data file(s): CA01.bb


title: IC16

description: processed data file(s): CA01.bb


title: IC43

description: processed data file(s): CA01.bb

value: Skin cancer (Melanoma)


title: IC10

description: processed data file(s): CA01.bb

value: Lung cancer (adenocarcinoma)


title: IC12

description: processed data file(s): CA01.bb

value: Breast cancer (Invasive/infiltrating lobular)


title: IC09

description: processed data file(s): CA01.bb

value: Ovarian cancer (serous tumors)


title: IC08

description: processed data file(s): CA01.bb


title: IC05

description: processed data file(s): CA01.bb


title: IC41

description: processed data file(s): CA01.bb


title: IC24

description: processed data file(s): CA01.bb

value: Pancreatic cancer (Ductal adenocarcinoma)


title: IC06

description: processed data file(s): CA01.bb

value: Lung cancer (Mesothelioma)


title: IA07

description: processed data file(s): CA01.bb

value: Systemic Lupus Erythmatosus


title: IA08

description: processed data file(s): CA01.bb


title: IC03

description: processed data file(s): CA01.bb


title: IC28

description: processed data file(s): CA01.bb

value: Lung cancer (Squamous cell carcinoma)


title: IA06

description: processed data file(s): CA01.bb


title: IC20

description: processed data file(s): CA01.bb


title: IA05

description: processed data file(s): CA01.bb


title: IC13

description: processed data file(s): CA01.bb

value: Prostate cancer (undefined)


title: IC11

description: processed data file(s): CA01.bb

value: Colorectal cancer (undefined)


title: IA04

description: processed data file(s): CA01.bb

value: blood plasma

value: Ulcerative Colitis


title: IA02

description: processed data file(s): CA01.bb

value: Crohn's disease


title: IA01

description: processed data file(s): CA01.bb


title: IC04

description: processed data file(s): CA01.bb

value: Breast cancer (Invasive/infiltrating ductal)


title: BH01

description: processed data file(s): CA01.bb, CH01.bb

value: Healthy

value: mixed


title: Myc.gro.rep2

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

description: GRO-seq

library_source: transcriptomic

data_processing:
Sequenced reads were aligned to the human genome (hg19) using bowtie2, and number of reads mapping to annotated genes (Ensembl v69) were counted by HTseq. Quantile normalization was then applied to allow comparisons between different samples. Only genes covered by at least 20 reads in at least one sample were included in the analysis
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts values for each sample.

molecule: total RNA

source_name: U2OS, Myc activation (5 hr)

growth_protocol: Myc-inducible U2OS cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% heat-inactivated fetal calf serum in 5% CO2 at 37°C.

extract_protocol:
Cells were treated with Doxycyline for 5h and 5 x 106 nuclei per condition were isolated and incubated 5 min at 30°C with equal volume of reaction buffer for the nuclear-run on (10 mM Tris-Cl pH 8.0, 5 mM MgCl2, 1mM DTT, 300 mM KCL, 20 units of SUPERase In, 1% sarkosyl, 500 µM ATP, GTP, and Br-UTP, 0.2 µM CTP+32P CTP). The reaction was stopped and RNA extracted with Trizol LS (Invitrogen) according to the manufacturer’s instructions. Base hydrolysis was performed using RNA fragmentation Reagents (Ambion) and the reaction was purified through p-30 RNAse-free spin column (BioRad). BrUTP labeled nascent transcripts were immunoprecipiated with anti-BrUTP agarose beads (Santa Cruz Biotech), washed once in binding buffer, once in low salt buffer (0.2X SSPE, 1 mM EDTA, 0.05% Tween-20), once in high salt buffer (0.25X SSPE, 1 mM EDTA, 0.05% Tween-20, 137.5 mM NaCl) and twice in TET buffer (TE with 0.05% Tween-20). Then, BrUTP-incorporated RNA was eluted with elution buffer (20 mM DTT, 300 mM NaCl, 5 mM Tris-Cl pH 7.5, 1 mM EDTA and 0.1% SDS) and RNA isolated with Trizol LS. End-repair of the enriched BrUTP-incorporated RNAs were achieved by the treatment with tobacco acid pyrophosphatase (TAP; Epicenter) to remove 5’-methyl guanosine caps, and followed by T4 polynucleotide kinase treatment (PNK; NEB) to remove 3’-phosphate group at low pH. Then, the BrU-incorporated RNAs were treated with T4 PNK at high pH in the presence of ATP to add 5’-phosphate group. The reaction was stopped and RNA was extracted with Trizol LS.
Sequencing libraries were generated from two biological replicates using TruSeq Small RNA kit from Illumina. Final libraries were two times cleaned-up and size-selected by Agencourt AMPure XP (Beckman Coulter)

treatment_protocol: U2OS cells containing inducible Myc expression vector were induced or mock-treated in duplicates for 5 hours

tag: treatment

value: Myc activation (5 hr)


title: C.gro.rep2

description: GRO-seq

source_name: U2OS, control

value: control


title: C.gro.rep1

description: GRO-seq


title: Myc.Torin.rp.lane1

description: Ribo-seq

data_processing:
Sequenced reads were aligned to a reference set of human curated protein-coding transcripts (plus the five human rRNA transcripts) using Bowtie. This reference set of transcripts was based on Ensembl's gene annotations (release 65). Only uniquely mapped reads were used in subsequent analyses. Ribosome occupancy levels were estimated by calculating reads per kilobase of mRNA CDS length per million reads (RPKM) per transcript.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

source_name: U2OS, Myc activation + Torin-1

extract_protocol:
Cells were treated with cycloheximide (100 μg/ml) for 5 minutes, washed with ice-cold phosphate-buffered saline (cycloheximide, 100 μg/ml), pelleted, and lysed in buffer A (20 mM Tris-HCl, pH 7.8, 100 mM KCl, 10 mM MgCl2, 1% Triton X-100, 2 mM DTT, 100 μg/ml cycloheximide, 1X complete protease inhibitor). Lysates were centrifuged at 5,000 rpm and the supernatant was treated with 2 U/μl of RNase I (Ambion) for 40 min at room temperature. Lysates were fractionated on a linear sucrose gradient (7% to 47%) using the SW-41Ti rotor at 36,000 rpm for 2 h. Fractions enriched in monosomes were pooled and treated with proteinase K (Roche) in a 1% SDS solution. Released RNA fragments were purified using TRIsure reagent and precipitated in the presence of glycogen. For libraries preparation, RNA was gel-purified on a denaturing 10% polyacrylamide urea (7 M) gel. A section corresponding to 30 to 33 nucleotides, the region where most of the ribosome-protected fragments are comprised, was excised, eluted and ethanol precipitated. The resulting fragments were 3′-dephosphorylated using T4 polynucleotide kinase (New England BioLabs, Inc.) for 6 h at 37°C in 2-(N-morpholino)ethanesulfonic acid (MES) buffer (100 mM MES-NaOH, pH 5.5, 10 mM MgCl2, 10 mM β-mercaptoethanol, 300 mM NaCl). 3′ adaptor was added with T4 RNA ligase 1 (New England BioLabs, Inc.) for 2.5 h at 37°C. Ligation products were 5′-phosphorylated with T4 polynucleotide kinase for 30 min at 37°C. 5′ adaptor was added with T4 RNA ligase 1 for 18 h at 22°C.
3′ adaptor was added with T4 RNA ligase 1 (New England BioLabs, Inc.) for 2.5 h at 37°C. Ligation products were 5′-phosphorylated with T4 polynucleotide kinase for 30 min at 37°C. 5′ adaptor was added with T4 RNA ligase 1 for 18 h at 22°C.

treatment_protocol: U2OS cells containing inducible Myc expression vector were induced or mock-treated in duplicates for 36 hours

value: Myc activation + Torin-1


title: Myc.Torin.rp.lane2

description: Ribo-seq


title: Myc.rp.rep2.lane2

description: Ribo-seq

source_name: U2OS, Myc activation (36 hr)

value: Myc activation (36 hr)


title: Torin.rp.lane2

description: Ribo-seq

source_name: U2OS, Torin-1


title: Torin.rp.lane1

description: Ribo-seq


title: C.rp.rep2.lane1

description: Ribo-seq


title: Myc.rp.rep1

description: Ribo-seq


title: IA03

description: processed data file(s): CA01.bb

value: M


title: Myc.rna.rep1

data_processing:
Sequenced reads were aligned to a reference set of human curated protein-coding transcripts (plus the five human rRNA transcripts) using Bowtie. This reference set of transcripts was based on Ensembl's gene annotations (release 65). Only uniquely mapped reads were used in subsequent analyses. RNA expression levels were estimated by calculating reads per kilobase of mRNA per million reads (RPKM) per transcript.
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each sample.

molecule: polyA RNA

extract_protocol:
RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Torin.rna


title: Myc.Torin.rna


title: C.rna.rep2


title: Myc.gro.rep1

description: GRO-seq


title: IC02

description: processed data file(s): CA01.bb

value: Ovarian cancer (undefined)

value: F


title: U2AF2 RIP-Seq R107 A 2

city: La Jolla

first: Thomas

middle: C

last: Whisenant

state: CA

address: 10550 North Torrey Pines Rd

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

description: U2AF2 RIP from activated CD4 T cells

data_processing:
Basecalls performed using CASAVA version 1.7-1.8.1
Raw reads were quality filtered (q > 25) and 3' adapters were removed using trimgalore version 0.2.7 - trim_galore -q 25 --phred33 --paired --trim1 -a GATCGGAAGAGCACACGTCTGAACTCCAGTC --retain_unpaired forward.fastq reverse.fastq
Reads were aligned to hg19 using Tophat version 2.0.9 - tophat --b2-very-sensitive --prefilter-multihits -G genes.gtf --coverage-search
Aligned reads were quality filtered using picard (markDuplicates) version 1.9
Aligned reads were filtered for quality (q < 20) using samtools
Filtered aligned reads were assigned to genes and analyzed for differential expresson/binding (Resting vs. Activated) according to the vignette for the R Bioconductor package edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet with 3 worksheets: 1) All U2AF2 bound genes; 2) Differentially expressed "bound" genes with adjusted p-value < 0.05 (edgeR)

source_name: primary CD4 T cell culture

growth_protocol: Primary CD4 T cells cultured for two weeks in RPMI supplemented with 10% FBS, 30U/ml IL2, 100U/ml penicillin and 100mg/ml streptomycin at 37C and 5% CO2

extract_protocol:
Eluate from U2AF2 RIP was combined with TRIZOL reagent (Thermo) and the RNA was extracted according to manufacturer's protocol. RNA resuspended in nanopure water was purified over an Rneasy column (QIAGEN).
Script- Seq v2 (Epicentre) with an input of 50ng U2AF2 RIP RNA

treatment_protocol: Primary CD4 T cells cultured were treated with anti-CD3/CD26 activator beads (Thermo) for 0 or 48 hours. Lysates from the cell pellets for both conditions were used as input into U2AF2 RIP.

value: primary CD4 T cell culture

tag: activation

value: anti-CD3/CD28 beads, 48 hours

tag: passages

tag: rip antibody

value: U2AF2 antibody

tag: rip antibody vendor

value: Sigma

tag: rip antibody cat. #

tag: rip antibody lot #

tag: molecule subtype

value: U2AF2 RIP RNA

tag: barcode

value: CGTACG

tag: run


title: CD4_Resting_1

description: RNAseq from resting CD4 T cells

data_processing:
Basecalls performed using CASAVA version 1.5-1.8.1
Raw reads were quality filtered (q > 25) and 3' adapters were removed using trimgalore version 0.2.7 - trim_galore -q 25 --phred33 --paired --trim1 -a GATCGGAAGAGCACACGTCTGAACTCCAGTC --retain_unpaired forward.fastq reverse.fastq
Reads were aligned to hg19 using Tophat version 2.0.0 - tophat --b2-very-sensitive --prefilter-multihits -G genes.gtf -g 2
Aligned reads were quality filtered using picard (markDuplicates) version 1.9
Aligned reads were filtered for quality (q < 20) using samtools
Filtered aligned reads were assigned to genes and analyzed for differential expresson according to the vignette for the R Bioconductor package edgeR. The two resting samples were compared to the two activated samples.
.bam files were used as input into Alt-Analyze (Emig, et al.) for differential splicing analysis. The two resting samples were compared to the two activated samples.
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet with 3 worksheets: 1) Differentially expressed genes with adjusted p-value < 0.05 (edgeR); 2) Alternatively spliced genes; 3) Alternatively spliced exons with ASPIRE score > 0.2 or < -0.2

extract_protocol:
Cell pellets were resuspended in TRIZOL reagent (Thermo) and the RNA was extracted according to manufacturer's protocol. RNA resuspended in nanopure water was purified over an Rneasy column (QIAGEN) and the polyA RNA was selected using oligo dT beads.
Illumina TruSeq RNAseq kit with an input of 1ug of polyA purifed RNA

treatment_protocol: Primary CD4 T cells cultured were treated with anti-CD3/CD26 activator beads (Thermo) for 0 or 48 hours.

tag: bardcode

value: GATCAG


title: U2AF2 RIP-Seq R107 R 2

description: U2AF2 RIP from resting CD4 T cells

tag: cell type

value: GAGTGG


title: CD4_Resting_2

description: RNAseq from resting CD4 T cells

value: GTTTCG


title: U2AF2 RIP-Seq R107 A 1

description: U2AF2 RIP from activated CD4 T cells


title: CD4_Activated_1

description: RNAseq from activated CD4 T cells

value: TAGCTT


title: C.rp.rep1

description: Ribo-seq


title: U2AF2 RIP-Seq R107 R 1

description: U2AF2 RIP from resting CD4 T cells

value: ATTCTT


title: U2AF2 RIP-Seq R91 A 1

description: U2AF2 RIP from activated CD4 T cells

value: TGACCA


title: C.rna.rep1

value: control


title: Myc.rp.rep2.lane1

description: Ribo-seq

value: Myc activation (36 hr)


title: U2AF2 RIP-Seq R91 A 2

description: U2AF2 RIP from activated CD4 T cells

value: ACTTGA


title: U937.Con.Total

city: shanghai

first: Huanwei

last: Wang

state: shanghai

address: 197 Ruijin Rd II

department: Shanghai Institute of Hematology

country: China

institute: Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine (RJH-SJTU-SM)

data_processing:
Sequencing reads were aligned to the unmasked reference genome sequence (hg19) by BWA (version 0.7.7). The uniquely mapped and non-redundant reads were left to do peak calling.
ChIP-seq peak regions were called using MACS (version 1.4.2) at a p-vaue cut off of 10e-8 (Ka.Con.AML1-C19, Ka.Con.ETO, U937.Con.AML1) or 10e-5 (Ka.Con.AML1-N20)
Genome_build: hg19
Supplementary_files_format_and_content: peak.bed files were generated by MACS software; bigWig files were converted from wig files, which were the output of MACS.

source_name: U937 Cells

extract_protocol:
ChIP and amplification were performed according to the Affymetrix protocol as described (Carroll et al., 2005).Total input DNA was extracted from sonicated nuclei. Protein-DNA complexes were isolated with specific antibodies and protein A/G beads. The following antibodies were used for protein-DNA complexes isolation: anti-ETO antibody (sc9737 X) that recognizes AML1/ETO, anti-AML1 (C19) antibody (ab23980) that recognizes AML1, anti-AML1 (N20) antibody (sc8563 X) that recognizes both AML1/ETO and AML1.
Libraries were prepared according to the Illumina genomic prep kit (Illumina, San Diego, CA, USA)

tag: chip antibody

value: none (input control)

value: U937 macrophage cell line


title: CD4_Activated_2

description: RNAseq from activated CD4 T cells


title: IC21

description: processed data file(s): CA01.bb

value: blood plasma

value: Pancreatic cancer (Ductal adenocarcinoma)

value: M


title: U2AF2 RIP-Seq R91 R 2

description: U2AF2 RIP from resting CD4 T cells

value: primary CD4 T cell culture

value: U2AF2 antibody

value: Sigma

value: TTAGGC


title: U937.Con.AML1

value: anti-AML1 (C19) (ab23980; Abcam)

tag: cell line


title: U2AF2 RIP-Seq R67 R

description: U2AF2 RIP from resting CD4 T cells

value: U2AF2 RIP RNA

value: TTCAGC


title: U2AF2 RIP-Seq R91 R 1

description: U2AF2 RIP from resting CD4 T cells


title: U2AF2 RIP-Seq R80 A

description: U2AF2 RIP from activated CD4 T cells

value: anti-CD3/CD28 beads, 48 hours


title: Ka.Con.Total

source_name: Kasumi-1 Cells

value: AML1-ETO bearing AML patient cell lines Kasumi-1


title: Ka.Con.ETO

value: anti-ETO (C20) (sc-9737 X; Santa Cruz Biotechnology


title: Ka.Con.AML1-N20

value: anti-AML1 (N20) (sc-8563 X; Santa Cruz Biotechnology)


title: lnc-OPC knockdown repeat1

city: houston

first: Xiaomin

last: Dong

state: Texas

address: 1825 Pressler Street

department: Department of neurosurgery

institute: UT health

data_processing:
Reads were mapped to reference genome (version mm9) using Tophat (version 1.3.3) which uses the Bowtie (version 0.12.7)read mapper, Tophat was fed with the option of“–no-novel-juncs”and  option "–G" which supplies Tophat with known transcript mm9 GTF file (download from cufflinks website).
Mapped reads were converted to sam files with SAMTOOLS (version 0.1.18) and raw counts were calculated by HTSeq (version 0.6.1)
DESeq was used for differential gene expression analysis caused by lnc-OPC knockdown. The output from Deseq was filtered using the following more stringent criteria: (1) padj<0.02; (2) foldChange<0.5 (3) foldChange>2.
GO functional term enrichment analysis of differentially expressed protein coding genes was performed by using DAVID functional annotation.
Genome_build: mm9
differentially expressed protein coding genes identified by DESeq and DAVID GO term enrichment analysis
Supplementary_files_format_and_content: raw counts

organism: Mus musculus

source_name: cerebral cortex

growth_protocol: Neural stem cells were cultured and passaged every 2 days as monolayers in MEM/F12 medium containing Glutamax, non-essential amino acids, B27, N2 supplement, 20 ng/ml EGF, and 20 ng/ml FGF. Cells were dissociated using Accutase (Invitrogen) and seeded onto poly-d-lysine-coated plates or dishes.

extract_protocol:
Total RNA was extracted using the miRNeasy kit (Qiagen) under manufactor’s protocols. The quality was accessed by Bioanalyzer. Samples with high RNA integrity number (RIN) (>8) were used for library construction. 100ng total RNAs were used for each sequencing library.
RNA-Seq was performed on the polyadenylated fraction of RNA isolated from differentiated cell samples. Two biological replicates were used. 100 ng total RNAs were used for each sequencing library. RNA samples were polyA selected and paired-end sequencing libraries were constructed using TruSeq RNA Sample Prep Kit as described in the TruSeq RNA Sample Preparation V2 Guide (Illumina).The samples were then sequenced using the Illumina HiSeq 2000 sequencer.

treatment_protocol: Neural stem cells were transduced with recombinant lentivirus after 24 h of culture on poly-d-lysine pre-coated plates. Non-infected cells were eliminated using fresh culture medium containing 0.5 mg/ml of puromycin 1 day after infection. Infected cells were proliferated for 3-4 days and then were differentiated into OPCs for 3 days in DMEM/F12 medium containing Glutamax, non-essential amino acids, BSA, B27, N2 supplement, 20 ng/ml CNTF, and 40 ng/ml T3.

tag: tissue

value: cerebral cortex

value: Differentiated NSC


title: lnc-OPC knockdown repeat2


title: knockdown control (shRNA against luciferase) repeat2


title: knockdown control (shRNA against luciferase) repeat1


title: Mouse neural stem cell_2

data_processing:
We mapped the paired-end reads to the mouse reference genome (UCSC version mm10) using TopHat (version 2.0.11) and Bowtie2 (version 2.2.2). Cufflinks (version 1.3.0) was used to assemble transcripts from genomic read alignments. TopHat was run using default settings, except using the option “-G mm10_genes.gtf” (mm10_genes.gtf is an annotation file within the Illumina iGenome package. Cufflinks was run using default settings without any annotation file to identify novel transcripts. All transcripts were then merged using Cuffmerge and then compared to a reference annotation file (mm10_genes.gtf) using Cuffcompare. Transcripts not matching any reference transcripts were given a class code ‘u’ (to designate them as unknown intergenic transcripts) by Cuffcompare and the considered as ‘novel’ transcripts not present in the reference file. The resulting .gtf was then filtered and only multi-exonic transcripts were retained.
In order to generate a comprehensive lncRNA annotation for downstream analysis, we surveyed available lncRNA annotations in the public domain, including lncRNAdb, GENCODE, Ensembl, and UCSC RefSeq genes. For lncRNAdb, the transcript structures were obtained using the BLAT program when only sequence information was available. We also added several recently published RNA-Seq datasets related to brain or CNS development to our analyses, including RNA-Seq data from subventricular zone (SVZ) tissue and olfactory bulb (OB), among others. To combine lncRNA annotations generated using RNA-Seq, we merged lncRNA transcripts identified from the same loci that were not annotated by GENCODE, or any other canonical lncRNA database, into single transcripts because distinguishing full-length isoforms from partially reconstructed fragments is not always possible without further experimental evidence, especially when sequencing depths vary among different RNA-Seq datasets. Subsequently, we combined lncRNA annotations from all sources into one non-redundant annotation file. Because there are overlaps between various annotation resources, a procedure was implemented to eliminate redundancy. Among these annotation resources, lncRNAdb contains the most detailed information for ~100 lncRNAs collected from the literature. When transcripts from different sources overlapped, we retained the gene information (gene_id, gene_name etc.) for the loci in the following order of priority: 1) lncRNAdb, 2) GENCODE, 3) RefSeq, 4) Ensembl, or 5) annotated by RNA-Seq experiments. We further combined the resulting lncRNA annotation .gtf with iGenome mm10 gtf annotation and removed any redundancy.
To quantify transcript expression, we re-ran Cufflink with option –G and supplied the comprehensive .gtf. The multi-read correction and bias correction algorithms in the Cufflinks package were enabled (option: -u -b). Expression level estimation was reported as Fragments per Kilobase of transcript sequence per Million mapped fragment (FPKM) values together with confidence intervals. Transcripts with an FPKM > 0, FPKM_conf_lo (lower bound of confidence interval) > 0, and status = OK were considered as detected with confidence.
To facilitate downstream analysis (such as fold change, enrichment analysis, and other procedures), a previously calculated threshold of FPKM = 0.1 was adopted. Any FPKM < 0.1 were set to 0.1 for fold enrichment calculations in order to avoid ratio inflation.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file include FPKM values for each Sample

growth_protocol: Mouse neural stem cells were cultured and passaged every 2 days as monolayers in MEM/F12 medium containing Glutamax, non-essential amino acids, B27, N2 supplement, 20 ng/ml EGF, and 20 ng/ml FGF. Cells were dissociated using Accutase (Invitrogen) and seeded onto poly-d-lysine-coated plates or dishes.

extract_protocol:
Total RNA was extracted using the miRNeasy kit (Qiagen) under manufactor’s protocols. The quality was accessed by Bioanalyzer. Samples with high RNA integrity number (RIN) (>8) were used for library construction. 100ng total RNAs were used for each sequencing library.
RNA samples were polyA selected and paired-end sequencing libraries were constructed using TruSeq RNA Sample Prep Kit as described in the TruSeq RNA Sample Preparation V2 Guide (Illumina).

value: Mouse neural stem cell


title: Mouse neural stem cell_1


title: U2AF2 RIP-Seq R67 A

description: U2AF2 RIP from activated CD4 T cells


title: U2AF2 RIP-Seq R80 R

description: U2AF2 RIP from resting CD4 T cells

value: AGGACG


title: Input for ChIP-Seq in mouse neural stem cells

data_processing:
The generated reads were mapped to the mouse genome mm10 using Bowtie version 0.12.7 and MACS version 1.4.2 were used to call peaks for ChIP-Seq data
The output from MACS was filtered using the following more stringent criteria: (1) p value cutoff <10−9; (2) fold_enrichment > 5-fold (3) tag number >20.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file include peaks(OLIG2 binding site) call by MACS

extract_protocol:
ChIP was performed using 107 mouse neural stem cells per reaction. Cells were dissociated by treatment with Accutase and cross-linked in 1% (vol/vol) formaldehyde for 10 min at RT with rotation. Then, 0.125 M glycine was used to quench the cross-linking reaction. Cells were pelleted and washed with ice-cold PBS. Next, nuclei were isolated and a Bioruptor sonicator (Diagenode) was used to shear chromatin DNA. Either 5 ml of OLIG2 antibody (AB9610, Chemicon) or 5 ml of normal rabbit IgG (#2729, Cell Signaling) was added to Dynabeads Protein A (Invitrogen) beads and incubated for 3 h at 4 °C with rotation. Then, the Dynabeads-antibody complexes were incubated with sheared chromatin DNA overnight at 4 °C. After immunoprecipitation, the precipitated complex was treated with RNase A and Proteinase K, and incubated at 65 °C overnight to reverse crosslinks.
The ChIP-Seq library was constructed by using DNA SMART ChIP-Seq Kit according to the manufacturer's instructions (Clontech) and was sequenced on the Illumina HiSeq 2000 Sequencer.


title: OLIG2 ChIP-Seq in mouse neural stem cells


title: SOX2 ChIP-Seq

city: Toulouse

first: Nicolas

last: Chassaing

address: Place du Dr Baylac

department: Service de Génétique Médicale

country: France

institute: CHU Toulouse

data_processing:
Instrument: Hi-seq 2000, Number of sequencing cycles: 1 x 50 + 7 (index); Sequencing kit: TruSeq(TM) SBS v5; Tiles: 32; Data Analysis Pipeline: HiSeq Control Soft. v. 1.3.8, RTA 1.10.36, CASAVA 1.7.0; OLB-1.9.0
Reference mapping: Mapping (BWA) of GDZ-9-13 reads on the NCBI37/mm9 genome and output conversion into BAM format (SAMTOOLS)
Peak detection,count of coverage:Detection of genomic peaks, count of coverage and annotation with closest gene (SEQMONK), normalisation. Paramters allows the detection of a peak when more than 15 reads spaced by less than 150bp are observed in the same region of the genome.
Genome_build: NCBI37/mm9 genome
Supplementary_files_format_and_content: the number of peak detected using either the IgG or SOX2 antibodies. A comparison of the peaks counts between the two samples is provided. Genes located close to these peaks and their distance from these peaks is also indicated.

source_name: CCE-Rx cells

growth_protocol: 2x10^6 undifferentiated adherent CCE-RX cells were plated in plated in 10 cm tissue-culture-treated Petri dishes in LIF-free DMEM supplemented with 10% of BSA, 100 µM 2-mercaptoethanol, 2mM glutamin and 100 µM non-essential amino acids. 48 hours later, CCE-Rx embryoid bodies were treated with formaldehyde for 10 minutes, crosslinking was then stopped by Glycin 1M (125µl/ml). Cromatin was prepared in low-bind DNA tubes: cell were washed in PBS with proteases inhibitor; cell pelet was lysate in 500 µl of lysis SDS buffer. After 20 minutes at room temperature, we performed 6 sonication runs of 30 sec each (with one minute between each sonication) at 4°C, then after a new centrifugation (12000 rpm 10 minutes 4°C), we performed 6 sonication runs of 30 sec each (with one minute between each sonication) at 4°C on the retrieved supernatant. Then, after a new centrifugation  (12000 rpm 10 minutes 4°C) the suprenatant is retrieved and dilute with 500 µl of ChIP dilution buffer (Upstate) and ChIP was performed according to the Upstate (Millipore) protocol, using 10 μg of anti-Sox2 antibody (Santa Cruz Biotechnology, sc-17320) or mouse IgG (Millipore, PP54) as a control.

extract_protocol:
Lysates were clarified from sonicated transcription factor-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.

value: Stem cells overexpressing the RAX gene (PMID:15121868)

value: Mouse SOX2

tag: chip antibody vendor

value: Santa Cruz Biotechnology

tag: chip antibody cat. #


title: IgG ChIP-Seq

value: Mouse IgG

value: Millipore


title: PN28_rep2

city: LA

first: Jaegyoon

last: Ahn

address: 611 Charles E. Young Drive

department: IBP

institute: UCLA

description: postnatal day (P)28, replicate 2

data_processing:
RNA-Seq reads were mapped to mm9 using the mapping pipeline described in (Bahn JH et al., Accurate Identification of A-to-I RNA editing in human by transcriptome sequencing. Genome Research, 2012).
We counted reads mapped to RefSeq genes and calculated RPKMs for those genes.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited files contain read counts and RPKMs of RefSeq genes.

extract_protocol:
Mouse liver RNA was isolated with Trizol (Invitrogen).
Standard Hi-Seq libraries were prepared.

tag: strain

value: FVB

value: liver

tag: developmental stage

value: postnatal day (P)28


title: E18_rep2

description: embryonic day (E)18, replicate 2

value: embryonic day (E)18


title: PN14_rep1

description: postnatal day (P)14, replicate 1

value: postnatal day (P)14


title: A3M_rep1

description: adult, replicate 1

value: adult


title: CH6: p8 + dox 4h (13.03.13)

city: Tübingen

first: Günter

last: Jäger

address: Calwerstr. 7

institute: Institute of Medical Genetics Tübingen

data_processing:
Basecalls performed using CASAVA version 1.4
Read alignment was performed with STAR v. 2.3.0e
Read count data was produced with htseq-count v.0.6.0
Read count normalization (counts per million mapped counts) was performed in R using the edgeR package
Features with less than 10 reads in any sample were removed from the data set
Genome_build: hg19
Supplementary_files_format_and_content: htseq-count raw data for each sample in tsv text-based format
Supplementary_files_format_and_content: edgeR normalized data for each sample in tsv text-based format

source_name: CIN612-9E/pInd IFN-kappa

growth_protocol: Cells were maintained in monolayer culture with mitomycin-C treated NIH3T3 J2 cells

extract_protocol:
RNeasy mini kit (Qiagen)
Illumina TruSeq Stranded RNA Sample Prep Kit was used with 500 ng of total RNA

treatment_protocol: addition of 1µg/ml doxycyline or medium as a negative control

value: HPV31-positive, CIN612-9E cells

tag: treatment

value: dox to induce IFN-kappa expression


title: CH4: p8 + dox 4h (05.02.13)


title: CH2: p7 + dox 4h (21.2.13)


title: Ka.Con.AML1-C19

value: anti-AML1 (C19) (ab23980; Abcam)

value: AML1-ETO bearing AML patient cell lines Kasumi-1


title: Mesp1Cre mut rep3

city: San Francisco

first: Siang-Yun

last: Ang

address: 1650 Owens St

institute: Gladstone Institute of Cardiovascular Disease

description:
Name of sample in FPKM_and_Counts_computed_by_USEQ_8.6.4.txt: F_mut_439_reps replicate 3
SYA_439_mut_07_748_9_mut_BC15_GTGGCC

data_processing:
Aligned to mouse genome build "mm9" using the program Tophat 2.0.8b. Gene annotation (GTF file) used was ENSEMBL version 65. Specific settings: --min-anchor=5 --segment-length=25 --no-coverage-search --segment-mismatches=2 --splice-mismatches=2 --microexon-search  --mate-inner-dist=150 --no-discordant --no-mixed
Per-gene counts and FPKM values provided by "DefinedRegionDifferentialSeq" version 8.6.4, part of the USeq software package (http://useq.sourceforge.net/). Gene annotation used was ENSEMBL version 65.
No additional filtering was performed.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM and raw count data

source_name: E9.0 whole embryonic heart

growth_protocol: Male mice with a heterozygous Kmt2d floxed allele and expressing the Cre recombinase (Cre; Kmt2d fl/+) were crossed to female mice homozygous for Kmt2d floxed alleles and the Rosa26-Cre reporter mTmG (Kmt2d fl/fl; mTmG/mTmG). The females will carry litters with the WT control genotype (Cre; Kmt2d fl/+; mTmG/+) and the mutant genotype (Cre; Kmt2d fl/fl; mTmG/+).

extract_protocol:
Total RNA was isolated from samples using RNAqueous-Micro Total RNA Isolation Kit (Ambion, AM1931) and followed with DNase I digestion. Total RNA was quantified on Nanodrop and quality was checked using Bioanalyzer.
RNA-seq libraries were prepared with ovation RNA-seq system v2 kit (NuGEN). The double-stranded DNA was then amplified using single primer isothermal amplification (SPIA). Random hexamers were used to amplify the second-strand cDNA linearly.  Finally, libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit (NuGEN).
The RNA-seq libraries were analyzed by Bioanalyzer and quantified by qPCR (KAPA). For each group of mutant and WT control samples (either 6 or 8 indexed samples total), they were sequenced in two lanes on an Illumina HiSeq 2500 or Illumina HiSeq 4000 for a total of at least 360 million reads.

treatment_protocol: Both WT and mutant embryos were harvested at embryonic day E11.5 and embryonic hearts were dissected in cold PBS. Hearts were mechanically dissociated in Lysis Buffer from RNAqueous-Micro Total RNA Isolation Kit (Ambion, AM1931).

value: GTGGCC

tag: age

value: whole embryonic heart

tag: genotype/variation

value: Mesp1Cre mut

tag: replicate number

value: Replicate 3


title: Mesp1Cre mut rep2

description:
Name of sample in FPKM_and_Counts_computed_by_USEQ_8.6.4.txt: F_mut_439_reps replicate 2
SYA_439_mut_06_747_6_mut_BC14_CACCTC

value: CACCTC

value: Replicate 2


title: PN28_rep1

description: postnatal day (P)28, replicate 1


title: Mesp1Cre mut rep4

description:
Name of sample in FPKM_and_Counts_computed_by_USEQ_8.6.4.txt: F_mut_439_reps replicate 4
SYA_439_mut_08_751_6_mut_BC16_TGTTGC

value: TGTTGC

value: Replicate 4


title: Mesp1Cre mut rep1

description:
Name of sample in FPKM_and_Counts_computed_by_USEQ_8.6.4.txt: F_mut_439_reps replicate 1
SYA_439_mut_05_747_1_mut_BC13_ACAAAC

value: ACAAAC

value: Replicate 1


title: CH5: p8 - dox 4h (13.03.13)

value: control


title: Mesp1Cre WT rep4

description:
Name of sample in FPKM_and_Counts_computed_by_USEQ_8.6.4.txt: E_WT_439_reps replicate 4
SYA_439_WT_04_751_7_WT_BC12_TGTGAA

value: TGTGAA

value: Mesp1Cre WT


title: CH3: p8 - dox 4h (05.02.13)

value: HPV31-positive, CIN612-9E cells


title: A3M_rep2

description: adult, replicate 2

value: FVB

value: liver

value: adult


title: Mesp1Cre WT rep3

description:
Name of sample in FPKM_and_Counts_computed_by_USEQ_8.6.4.txt: E_WT_439_reps replicate 3
SYA_439_WT_03_748_4_WT_BC11_GTGTTA

value: GTGTTA


title: PN14_rep2

description: postnatal day (P)14, replicate 2

value: postnatal day (P)14


title: Tnnt2::Cre mutant rep2

description:
Name of sample in FPKM_and_Counts_computed_by_USEQ_8.6.4.txt: A_MUTcTnT_246_reps replicate 2
SYA_246_A_02_477_2_BC02_mutant_cTnT_rep2_CCTTCA

source_name: E11.5 whole embryonic heart

value: CCTTCA

value: whole embryonic heart

value: Tnnt2::Cre mutant


title: E18_rep1

description: embryonic day (E)18, replicate 1

value: embryonic day (E)18


title: Tnnt2::Cre mutant rep1

description:
Name of sample in FPKM_and_Counts_computed_by_USEQ_8.6.4.txt: A_MUTcTnT_246_reps replicate 1
SYA_246_A_01_477_1_BC01_mutant_cTnT_rep1_AAGGGA

value: AAGGGA


title: Mesp1Cre WT rep2

description:
Name of sample in FPKM_and_Counts_computed_by_USEQ_8.6.4.txt: E_WT_439_reps replicate 2
SYA_439_WT_02_747_5_WT_BC10_CACACA

value: CACACA

value: Replicate 2


title: Tnnt2::Cre mutant rep3

description:
Name of sample in FPKM_and_Counts_computed_by_USEQ_8.6.4.txt: A_MUTcTnT_246_reps replicate 3
SYA_246_A_03_477_4_BC03_mutant_cTnT_rep3_GGACCC

value: GGACCC

value: Replicate 3


title: Tnnt2::Cre WT rep1

description:
Name of sample in FPKM_and_Counts_computed_by_USEQ_8.6.4.txt: B_WTcTnT_246_reps replicate 1
SYA_246_B_04_477_5_BC04_WT_cTnT_rep1_TTCAGC

value: TTCAGC

value: Tnnt2::Cre WT

value: Replicate 1


title: Tnnt2::Cre WT rep3

description:
Name of sample in FPKM_and_Counts_computed_by_USEQ_8.6.4.txt: B_WTcTnT_246_reps replicate 3
SYA_246_B_06_477_7_BC06_WT_cTnT_rep3_CCTCGG

value: CCTCGG


title: Tnnt2::Cre WT rep2

description:
Name of sample in FPKM_and_Counts_computed_by_USEQ_8.6.4.txt: B_WTcTnT_246_reps replicate 2
SYA_246_B_05_477_6_BC05_WT_cTnT_rep2_AAGACG

value: AAGACG


title: Mesp1Cre WT rep1

description:
Name of sample in FPKM_and_Counts_computed_by_USEQ_8.6.4.txt: E_WT_439_reps replicate 1
SYA_439_WT_01_747_2_WT_BC09_ACACGA

value: ACACGA

value: Mesp1Cre WT


title: BMS-Akt1 CC-Alone 2

city: New York

first: Olivier

last: Elemento

state: NY

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

description: PolyA RNA

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq: Sequence reads were aligned to mm9 using TopHat with default parameters.
RNA-seq: FPKM values were obtained using CuffLinks with upper-quartile and GC normalization.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: RNA-seq: Tab-delimited text files include FPKM values for each RefSeq gene.

source_name: Bone marrow stroma, non-co-cultured

extract_protocol:
RNA was harvested using Trizol treatment.
Illumina TruSeq PE 51x2 (RNA-seq).

tag: strain/background

value: bone marrow stroma

tag: co-culture

value: alone

tag: sample type

value: in vitro


title: CH1: p7 - dox 4h (21.2.13)

value: HPV31-positive, CIN612-9E cells

value: control


title: BMS-Akt1 CC-Alone 3

description: PolyA RNA


title: BMS-Akt1 CC+HSPC 3

description: PolyA RNA

source_name: Bone marrow stroma, co-cultured with HSCs

value: hematopoietic stem cells


title: BMS-Akt1 CC+HSPC 1

description: PolyA RNA


title: BMS-In vivo 1

description: PolyA RNA

source_name: Bone marrow stroma, in vivo

value: in vivo


title: BMS-Akt1 CC-Alone 1

description: PolyA RNA


title: BMEC-In vivo 2

description: PolyA RNA

source_name: Bone marrow endothelial cells, in vivo

value: bone marrow endothelial cells


title: BMS-Akt1 CC+HSPC 2

description: PolyA RNA


title: BMEC-In vivo 3

description: PolyA RNA


title: BMEC-Akt1 CC+HSPC 2

description: PolyA RNA

source_name: Bone marrow endothelial cells, co-cultured with HSCs


title: BMS-In vivo 3

description: PolyA RNA


title: BMEC-Akt1 CC+HSPC 1

description: PolyA RNA


title: BMS-In vivo 2

description: PolyA RNA


title: BMEC-Akt1 CC+HSPC 3

description: PolyA RNA


title: BMEC-Akt1 CC-Alone 3

description: PolyA RNA

source_name: Bone marrow endothelial cells, non-co-cultured


title: BMEC-Akt1 CC-Alone 1

description: PolyA RNA


title: BMEC-Akt1 CC-Alone 2

description: PolyA RNA


title: BMS-Akt1 2

description: PolyA RNA

source_name: Bone marrow stroma, in vitro


title: BMS-Akt1 1

description: PolyA RNA


title: BMS-Akt1 3

description: PolyA RNA


title: BMEC-In vivo 1

description: PolyA RNA


title: C.rp.rep2.lane2

description: Ribo-seq

source_name: U2OS, control


title: BMEC-Akt1 3

description: PolyA RNA

source_name: Bone marrow endothelial cells, in vitro


title: ATM_Chip_seq_in_MEF_Hmga2_Ko

city: Nancy Cedex

first: Guillermo

last: Barreto

address: 9, Avenue de la Forêt de Haye ‐ BP 20199

department: Campus Biologie-Santé. Faculté de Médecine

institute: CNRS Director of Research

description:
ATM_Chip_seq_in_MEF_Hmga2_Ko_raw_data
Processed data description: contig file to use for ngs.plot use; to see the enrichment of ATM in wt and ko Hmga2 MEF samples in the promoter region
Processed data file: 01_contigs_ATM_in_Hmga2_MEF_wt_vs_ATM_in_Hmga2_MEF_ko_in_promoter_wt

data_processing:
Visualization of raw reads was done using FASTX-ToolKit, trimmed of the raw reads using Trimmomatic (Bolger et al. 2014), min lemgh of 60 bp and Quality score of minimum 15, remove Illumina Adapters TruSeq3.
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 default settings
samtools were used to convert sam files to bam files, after sorted bam files were merge using bamtools merge (default)
MACS14 was used for the peak calling 4 (p < 0.01) with a shiftsize of 30 bp
homer makeUCSC (normalized to 30 millions) was used to obtain bedgraph files to Visualize in UCSC genome browser
ngsplot was used to obtain the Normalized Taq (log2) to the promoter area of Wt samples of H2AXS139ph and ATM compared to Ko samples
homer annotatepeaks was used to perform the taq density ofHMGA2,  H2AXS139ph,  and ATM to the peaks of HMGA2 in Wt samples
Genome_build: mm10
Supplementary_files_format_and_content: bed files obtained after MACS14, promoter files from H2AXS139ph and ATM obtained after annotation of peaks files by the location on promoter using homer annotatepeak
Supplementary_files_format_and_content: [H2AXS139ph_and_ATM_in_Hmga2_MEF_wt_compared_HMGA2_in_MEF_Hmga2_wt_peaks.txt] this Text file is the output file obtained after using homer annotatePeaks.pl ; it is a quantitative file considered relevant for the context of the project
Supplementary_files_format_and_content: [01_contigs_H2AXS139ph_in_Hmga2_MEF_wt_vs_H2AXS139ph_in_Hmga2_MEF_Ko.txt] it is a text file that is required for ngs.plot (program to visualize Chip-sea data) , needed to reproduce the figure of the manuscript
Supplementary_files_format_and_content: [01_contigs_ATM_in_Hmga2_MEF_wt_vs_ATM_in_Hmga2_MEF_ko_in_promoter_wt.txt] it is a text file that is required for ngs.plot , needed to reproduce the figure of the manuscript

source_name: Mouse Embryonic Fibroblast (MEF)

growth_protocol: MEF cells were kept at 37°c in DMEM medium containing 10 % Fetal Calf Serum, and 1% P/S/G (penicillin/Streptomycin/L-glutamine)

extract_protocol:
Lysates were clarified from sonicated chromatin and Protein-DNA complexes were isolated with the antibody.
Libraries were prepared according to Illumina's instructions accompanying the Ovation Ultra Low Kit

tag: cells

value: Mouse Embryonic Fibroblast (MEF)

tag: embryo stage

tag: passages

value: Hmga2 Ko

value: ATM (Santa Cruz, cat:sc-23922, lot:E3111)


title: HMGA2_Chip_seq_in_MEF_Hmga2_wt

description:
HMGA2_Chip_seq_in_MEF_Hmga2_wt_raw_data
Processed data description: peak file of HMGA2 obtained after calling of binding region by MACS14; with the setting; --no-model, p value of p1e-2 and shiftsize 30 bp.
Processed data file: HMGA2_in_MEF_Hmga2_wt_peaks.bed
Processed data file: H2AXS139ph_and_ATM_in_Hmga2_MEF_wt_compared_HMGA2_in_MEF_Hmga2_wt_peaks.txt

value: Hmga2 wt

tag: chip antibody

value: HMGA2 (Santa cruz, cat. sc-30223, lot:F1407 )


title: BMEC-Akt1 2

description: PolyA RNA

tag: cell type


title: H2AXS139ph_Chip_seq_in_MEF_Hmga2_wt

description:
H2AXS139ph_Chip_seq_in_MEF_Hmga2_wt_raw_data
Processed data description: peak file of H2AXS139ph obtained after calling of binding region by MACS14; with the setting; --no-model, p value of p1e-2 and shiftsize 30 bp
Processed data file: H2AXS139ph_in_Hmga2_MEF_wt_peaks.bed
Processed data file: H2AXS139ph_and_ATM_in_Hmga2_MEF_wt_compared_HMGA2_in_MEF_Hmga2_wt_peaks.txt
Processed data file: H2AXS139ph_promoter_in_Hmga2_MEF_wt.bed
Processed data file: 01_contigs_H2AXS139ph_in_Hmga2_MEF_wt_vs_H2AXS139ph_in_Hmga2_MEF_Ko.txt


title: BMEC-Akt1 1

description: PolyA RNA


title: H2AXS139ph_Chip_seq_in_MEF_Hmga2_Ko

description:
H2AXS139ph_Chip_seq_in_MEF_Hmga2_Ko_raw_data
Processed data description: contig file to use for ngs.plot use; to see the enrichment of H2AXS139ph in wt and ko Hmga2 MEF samples in the promoter region
Processed data file: 01_contigs_H2AXS139ph_in_Hmga2_MEF_wt_vs_H2AXS139ph_in_Hmga2_MEF_Ko.txt


title: Input_Chip_seq_in_MEF_Hmga2_Ko

description:
Input_Chip_seq_in_MEF_Hmga2_Ko_raw_data
Processed data description: contig file to use for ngs.plot use; to see the enrichment of H2AXS139ph in wt and ko Hmga2 MEF samples in the promoter region normalized to Input
Processed data file: 01_contigs_ATM_in_Hmga2_MEF_wt_vs_ATM_in_Hmga2_MEF_ko_in_promoter_wt
Processed data file: 01_contigs_H2AXS139ph_in_Hmga2_MEF_wt_vs_H2AXS139ph_in_Hmga2_MEF_Ko.txt


title: rasV12FRT82Bscrib1ets21cRNAi_4

city: Cologne

first: Mirka

last: Uhlirova

state: NRW

address: Joseph-Stelzmann Str. 26

department: Institute for Genetics

institute: CECAD Research Center  Cologne

data_processing:
Illumina Casava 1.7 and 1.8.2 software used for basecalling
RNA-Seq reads mapped with Tophat, version 2.0.10
FPKM calculated by Cufflinks, version 2.1.1
Genome_build: drosophila melanogaster 75 (Ensembl build 75 uses the BDGP5 assembly)
Supplementary_files_format_and_content: Excel file reports FPKMs for a given sample.

organism: Drosophila melanogaster

source_name: Mosaic eye/antennal imaginal discs

growth_protocol: MARCM fly crosses were carried out at 25°C on standard media

extract_protocol:
Total RNA was isolated from eye/antennal imaginal discs dissected from third-instar larvae with Isol-RNA Lysis Reagent (5 Prime).
Sequencing libraries were generated according to the Illumina protocol for total RNA library preparation and loaded onto Illumina flow cells (Illumina, San Diego, CA)

value: epithelial cells

tag: tissue

value: eye/antennal imaginal discs

value: 3d instar larval stage


title: Myc.rna.rep2

source_name: U2OS, Myc activation (36 hr)

value: Myc activation (36 hr)


title: ATM_Chip_seq_in_MEF_Hmga2_wt

description:
ATM_Chip_seq_in_MEF_Hmga2_wt_raw_data
Processed data description: peak file of ATM obtained after calling of binding region by MACS14; with the setting; --no-model, p value of p1e-2 and shiftsize 30 bp
Processed data file: ATM_in_Hmga2_MEF_wt_peaks.bed
Processed data file: H2AXS139ph_and_ATM_in_Hmga2_MEF_wt_compared_HMGA2_in_MEF_Hmga2_wt_peaks.txt
Processed data file: ATM_promoter_in_Hmga2_MEF_wt.bed
Processed data file: 01_contigs_ATM_in_Hmga2_MEF_wt_vs_ATM_in_Hmga2_MEF_ko_in_promoter_wt


title: rasV12FRT82Bscrib1ftzf1RNAi_2


title: HMGA2_Chip_seq_in_MEF_Hmga2_Ko

description:
HMGA2_Chip_seq_in_MEF_Hmga2_Ko_raw_data
Processed data description: control Hmga2 knock out MEF cells
Processed data file: none (note: this file was internal control of the Chip -seq)


title: rasV12FRT82Bscrib1ets21cRNAi_3


title: rasV12FRT82Bscrib1ftzf1RNAi_4


title: rasV12FRT82Bscrib1ftzf1RNAi_3


title: Input_Chip_seq_in_MEF_Hmga2_wt

description:
Input_Chip_seq_in_MEF_Hmga2_wt_raw_data
Processed data description: contig file to use for ngs.plot use; to see the enrichment of H2AXS139ph in wt and ko Hmga2 MEF samples in the promoter region normalized to Input
Processed data file: 01_contigs_ATM_in_Hmga2_MEF_wt_vs_ATM_in_Hmga2_MEF_ko_in_promoter_wt
Processed data file: 01_contigs_H2AXS139ph_in_Hmga2_MEF_wt_vs_H2AXS139ph_in_Hmga2_MEF_Ko.txt


title: rasV12FRT82Bscrib1_4

data_processing:
Illumina Casava 1.8.2 software used for basecalling
RNAseq reads were aligned drosophila melanogaster
Fragments Per Kilobase of exon per Million mapped fragments (FPKM) were calculated using a Cufflinks
Genome_build: drosophila melanogaster 75
Supplementary_files_format_and_content: Excel file reports FPKMs for a given sample.
Supplementary_files_format_and_content: Table_S1_transcriptome_analysis.xlsx (linked as supplementary file on Series record) reports fold-change between samples.


title: rasV12FRT82Bscrib1bskDN_2


title: rasV12FRT82Bscrib1ets21cRNAi_1


title: rasV12FRT82Bscrib1ets21cRNAi_2


title: rasV12FRT82Bscrib1ftzf1RNAi_1


title: rasV12FRT82B_2


title: rasV12FRT82Bscrib1_1


title: rasV12FRT82B_1


title: rasV12FRT82Bscrib1_3


title: FRT82B_4


title: rasV12FRT82Bscrib1bskDN_1


title: FRT82B_3


title: FRT82B_2


title: FRT82B_1


title: Mo17-root-1

city: East Lansing

first: Erich

last: Grotewold

state: MI

address: 603 Wilson Road

institute: Michigan State University

description: barcode ATGTCA

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to the maize genome assembly using TopHat
Alignment files were used as input for individual quantification of gene expression with the Cufflink program
Genome_build: Zea mays B73 genome assembly (Maize B73 RefGen v3) obtained from GRAMENE was used as the reference genome across all the steps
Supplementary_files_format_and_content: genes.fpkm_tracking and isoforms.fpkm_tracking are tabulated delimited files generated with Cufflinks. genes.fpkm_tracking tracks the summed FPKM of transcripts sharing each gene_id and isoforms.fpkm_tracking tracks the FPKM of the individual transcripts. A consolidated GTF file with the identifiers as generated by Cufflinks is also provided

organism: Zea mays subsp. mays

source_name: seedling

growth_protocol: 25degree, 16h light, 8h dark

extract_protocol: RNA was isolated from shoot and root of 2-week-old Mo17 seedlings by Direct-zol™ RNA MiniPrep.

value: root

tag: genotype

value: wild type


title: Mo17-shoot-2

description: barcode GTGAAA

value: shoot


title: Mo17-root-2

description: barcode CCGTCC


title: prdm12_engR_RNAseq_rep_2

first: Ian

middle: K

last: Quigley

address: 10010 North Torrey Pines Road

department: Molecular Neurobiology Lab

institute: Salk Institute

description: poly-A mRNA

data_processing:
RNAseq reads were mapped to a Xenopus transcriptome (X. tropicalis, courtesy of M. Gilcrist and X. laevis Unigene sequences) with bowtie2 (PMID: 22388286, http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
RNAseq counts normalized and differential expression tested with edgeR (PMID: 19910308)
ChIPseq reads were mapped to the X. laevis genome v7.1 with bowtie2 (PMID: 22388286, http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
ChiPseqd peaks were called with HOMER (PMID: 20513432), using input as a background.
Genome_build: RNAseq: X. tropicalis transcriptome (courtesy M. Gilchrist) and X. laevis Unigene sequences. ChIPseq: X. laevis genome build v7.1 (courtesy of the Xenopus Genome Project Consortium, PMID: 25313157).
Supplementary_files_format_and_content: RNAseq: normalized read counts. ChIPseq: bed files.

organism: Xenopus laevis

source_name: neuralized animal cap (neuroectoderm)

extract_protocol:
mRNAs were isolated with an RNAspin Mini RNA isolation kit. ChIPseq embryos were first fixed in 1% formaldehyde for 30 minutes and lysed in RIPA buffer prior to sonication. See PMID: 24934224 for a more detailed protocol.
RNAseq libraries were constructed with Illumina Truseq v2 non-stranded mRNA kits. Following IP, ChIPseq libraries were constructed with end repair mix (NEB), a-tailed (NEB), Truseq v2 adapters ligated (Illumina, NEB) and amplified with Phusion polymerase (NEB).

treatment_protocol: 2-cell X. laevis embryos were injected with synthetic mRNAs of indicated constructs. Ectoderm (animal caps) was dissected at roughly stage 10 and cultured in 0.5X MMR prior to harvest for RNAseq or ChIPseq.

value: noggin + prdm12_engR_mRNA + RA


title: Mo17-shoot-1

description: barcode GTCCGC


title: prdm12_VP16_RNAseq_rep_2

description: poly-A mRNA

value: noggin + prdm12_VP16_mRNA + RA


title: rasV12FRT82Bscrib1_2


title: prdm12_FLAG_noggin_RA_ChIPseq_input

description: genomic DNA

value: prdm12-FLAG + noggin mRNA, RA


title: prdm12_FLAG_ChIPseq_input

description: genomic DNA

source_name: animal cap (ectoderm)

value: prdm12-FLAG mRNA


title: prdm12_RNAseq_rep_2

description: poly-A mRNA

value: noggin + prdm12 mRNA _ RA


title: wt_RNAseq_rep_2

description: poly-A mRNA


title: noggin_RNAseq_rep_1

description: poly-A mRNA

value: noggin mRNA + RA


title: noggin_RNAseq_rep_2

description: poly-A mRNA


title: prdm12_engR_RNAseq_rep_1

description: poly-A mRNA


title: prdm12_RNAseq_rep_1

description: poly-A mRNA


title: Tamrabta_needles_3

city: Malaga

first: Rafael

middle: A

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

country: Spain

institute: Universidad de Málaga

description: Gene expression in Tamrabta needles

data_processing:
Base conversion was done using Illumina’s OLB version 1.9
Sequenced reads were trimmed for adaptor sequence, for contaminants, for low-complexity and for low-quality sequences with SeqTrimNext software (Falgueras et al., 2010. BMC bioinformatics 11: 38).
Reads were mapped against a reference transcriptome composed by 35,374 contigs from SustainPineDB (http://www.scbi.uma.es/sustainpinedb/home_page). Bowtie2 was employed allowing only for concordant mapped pairs (–no-mixed–no-discordant).
Read count was done with a Phyton script from the Andalusian Platform of Bioinformatics (PAB).
Normalization and differential expression analysis were done using edgeR package for R.
Genome_build: Reference transcriptome composed by 35,374 contigs from SustainPineDB (http://www.scbi.uma.es/sustainpinedb/home_page)
Supplementary_files_format_and_content: Tab-delimited text files include CPM values for each sample (L6, L7, T3 and T6).The column ID_REF is the sequence identifier and CONTIG_ID column is the contig identifier in SustainPineDB.

organism: Pinus pinaster

source_name: Tamrabta needles replicate 1

growth_protocol: Plants were rooted cuttings of 17 months of age, planted in 2-l pots filled with a mixture of Sphagnum peat (PINSTRUD®) and vermiculite (VERLITE®) of grade 3, with a proportion 4:1 in volume. The entire experiment was performed at SERIDA’s greenhouse at Villaviciosa (Asturias, Spain). Potted plants were ferti-irrigated following the protocol by Majada et al. (2009, 5th Congreso Forestal Español. Ávila, 1–10.). Prior to the assessment, all branches were pruned to trigger the formation of new axillary shoots, mostly deriving from the activation of the proventitious meristems in the extant dwarf shoots. This was intended to be a ‘‘resetting’’ of the plants shoots, minimising the differences due to previous pruning done for cutting collection.

extract_protocol:
Total RNA was isolated following the protocol described by Liao et al. (2004, Preparative biochemistry & biotechnology 34: 209–14) and modified by Cañas et al. (2014, Tree Physiology doi:10.1093/treephys/tpt113). The RNA concentration and purity were determined spectrophotometrically, the purity was considered using A260/A280 nm and A260/A230 nm ratios. RNA quality was further confirmed by agarose gel electrophoresis and using the RNA Pico Assay for the 2100 Bioanalyzer (Agilent, USA). The RNA samples with a RIN higher than 7 were used for the RNA-Seq. The amount of the RNA for the RNA-Seq procedure was calculated using the Quant-iT™ RiboGreen® RNA Assay Kit (Invitrogen, Paisley, UK).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: organ

value: Adult needles

tag: provenance

value: Tamrabta

tag: culture

value: Rooted cuttings

tag: culture place


title: Leiria_needles_7

description: Gene expression in Leiria needles

source_name: Leiria needles replicate 2

value: Leiria

value: SERIDA’s greenhouse at Villaviciosa (Asturias, Spain)


title: Leiria_needles_6

description: Gene expression in Leiria needles

source_name: Leiria needles replicate 1


title: Tamrabta_needles_6

description: Gene expression in Tamrabta needles

source_name: Tamrabta neeldes replicate 2


title: prdm12_FLAG_noggin_RA_ChIPseq

description: genomic DNA

tag: treatment

value: Sigma anti-FLAG, cat# F1804


title: wt_RNAseq_rep_1

description: poly-A mRNA


title: prdm12_FLAG_ChIPseq

description: genomic DNA


title: PX5

city: Dublin

first: Peadar

last: O'Gaora

address: Belfield

country: Ireland

institute: UCD

data_processing:
Libraries were sequenced on the HiSeq 2500 platform (50bp PE) and basecalls were made by HiSeq Control Software.
Reads were quality trimmed (error probability 0.001) and 13 bp were removed from the 5’ end of each read with CLC Genomics Server 6.0
Mapped to Ensembl gene UMD 3.1.75 with CLC Genomics Server 6.0
Statistical analysis was completed using the Empirical Analyisis of DGE (EDGE) tool in CLC Genomics Workbench with default settings
Genome_build: Bos_taurus_UMD_3.1
Supplementary_files_format_and_content: RPKM data

organism: Bos taurus

source_name: Oviduct

extract_protocol:
Total RNA was extracted from oviduct epithelial cells using the Trizol method as per manufacturers' instructions (Invitrogen, Carlsbad, CA, USA) and RNA clean up and on-column DNAse digestion was perfored using the Qiagen Rneasy columns as per manufacturers' instructions (Qiagen, Crawley, West Sussex, UK).
Standard Illumina TruSeqstranded mRNA HT library construction. One microgram of total RNAwas used as input material. mRNA was enriched using oligo-dT magnetic beads and fragmented to 100-300 bp with a single shearing and RT primer hybridization before generating cDNA. Following adapter ligation and PCR amplification (14 cycles), library validation was perfomred using the Fragment Analyzer (Advanced Analytical) with the hiSens NGS reagents followed by quantitation using the QuBit HS DNA assay (Life Technologies) and qPCR kit for Illumina (Kapa Biosystems, Inc.).

value: oviduct

value: Pregnant - transfer of 50 in vitro produced presumptive zygotes


title: Set1 ChIP-seq

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

description: Set1 ChIP-seq

data_processing:
Image analysis was performed with Illumina RTA 1.18.61. Basecalling was performed with illumina bcl2fastq 1.8.3.
Primary analysis pipeline was run with CASAVA 1.8.2.
Reads were aligned to sacCer3 from UCSC using bowtie2 version 2.1.0 with -k 1.
Data was read into R 3.1.0 for visualization and analysis.
log2 of smoothed IP/input bigWig files were generated in R by taking the running mean (101-base window) of the log2 ratio of IP/input.
Genome_build: sacCer3
Supplementary_files_format_and_content: BigWig format files of 101-base smoothed log2(ip/input).

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Yeast cells were grown in YPD medium until log phase

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Treated with 1% formaldehyde, quenched with glycine

tag: antibody

value: anti-FLAG (Sigma-Aldrich, F1804-1MG)

tag: flag tagged


title: prdm12_VP16_RNAseq_rep_1

description: poly-A mRNA


title: PX3


title: PX4


title: Pyk1 ChIP-seq rep2

description: Pyk1 ChIP-seq rep2


title: Pyk1 Input rep2

description:
Pyk1 Input rep2
s_2pyk1_ip.log2rat.smoothed.101.bw


title: PX2


title: C4

value: Control - sham transfer


title: C5


title: C1


title: Set1 Input

description:
Set1 Input
s_1set1_ip.log2rat.smoothed.101.bw


title: Pyk1 Input rep1

description:
Pyk1 Input rep1
s_1pyk1_ip.log2rat.smoothed.101.bw


title: Ser33 Input rep2

description:
Ser33 Input rep2
s_2ser33_ip.log2rat.smoothed.101.bw


title: Ser33 ChIP-seq rep2

description: Ser33 ChIP-seq rep2


title: PX1


title: Sam1 ChIP-seq rep2

description: Sam1 ChIP-seq rep2


title: Mef2cAHF::Cre WT rep2

description:
Name of sample in FPKM_and_Counts_computed_by_USEQ_8.6.4.txt: H_mut_511_reps replicate 2
SYA_511_WT_bc2_CCTTCA_R1.fastq.gz

source_name: E11.5 right ventricle and outflow tract

tag: strain

tag: barcode

value: CCTTCA

tag: age

value: right ventricle and outflow tract

tag: genotype/variation

value: Mef2cAHF::Cre WT

tag: replicate number

value: Replicate 2


title: Pyk1 ChIP-seq rep1

description: Pyk1 ChIP-seq rep1


title: Mef2cAHF::Cre WT rep3

description:
Name of sample in FPKM_and_Counts_computed_by_USEQ_8.6.4.txt: H_mut_511_reps replicate 3
SYA_511_WT_bc3_GGACCC_R1.fastq.gz

value: GGACCC

value: Replicate 3


title: Ser33 Input rep1

description:
Ser33 Input rep1
s_1ser33_ip.log2rat.smoothed.101.bw


title: C2


title: Sam1 Input rep2

description:
Sam1 Input rep2
s_2sam1_ip.log2rat.smoothed.101.bw


title: Ser33 ChIP-seq rep1

description: Ser33 ChIP-seq rep1


title: Sam1 Input rep1

description:
Sam1 Input rep1
s_1sam1_ip.log2rat.smoothed.101.bw


title: Sam1 ChIP-seq rep1

description: Sam1 ChIP-seq rep1


title: Mef2cAHF::Cre mutant rep3

description:
Name of sample in FPKM_and_Counts_computed_by_USEQ_8.6.4.txt: G_WT_511_reps replicate 3
SYA_511_MUT_bc6_CCTCGG_R1.fastq.gz

value: CCTCGG

value: Mef2cAHF::Cre mutant


title: MAC_1

city: Iowa City

first: S. Scott

last: Whitmore

state: IA

address: 375 Newton Road

department: The University of Iowa Institute for Vision Research

institute: The University of Iowa

description: NHS 1

data_processing:
Reads mapped to Mmul_1 using Tophat (ver. 2.0.7) (-r 150, no coverage search, library type fr-unstranded, GTF from Illumina iGenomes package for Mmul_1)
Junction mapping and abundance estimated using Cufflinks (ver 2.1.1) (max-bundle-frags 20000000)
Differential expression analysis using Cuffdiff (ver 2.1.1)
Genome_build: Mmul_1
Supplementary_files_format_and_content: rf6a_matrix.txt reports FPKMs

organism: Macaca mulatta

source_name: Cultured RF/6A choroidal endothelial cells

growth_protocol: RF/6A cells (5x10^5) grown in 200µl 5% FBS DMEM with 1% penicillin/streptomycin, plated on Transwell tissue culture insert (0.4µm pores) with lower chamber filled with 800µl medium. Grown to confluency prior to treatment.

extract_protocol:
RNeasy kit (Qiagen, Valencia, CA)
Illumina TruSeq RNA Sample Preparation v2 library preparation kit (Illumina, San Diego, CA)

treatment_protocol: 4 hour treatment with either 50% heat-inactivated human serum or 50% normal human serum

tag: cell line

value: 50% normal human serum


title: MAC_3

description: NHS 3


title: MAC_2

description: NHS 2


title: Untagged Input

description:
Untagged Input
s_wt_ip.log2rat.smoothed.101.bw


title: CONTROL_3

description: HIS 3

value: 50% heat-inactivated human serum


title: CONTROL_2

description: HIS 2


title: C3


title: Mef2cAHF::Cre mutant rep2

description:
Name of sample in FPKM_and_Counts_computed_by_USEQ_8.6.4.txt: G_WT_511_reps replicate 2
SYA_511_MUT_bc5_AAGACG_R1.fastq.gz

value: AAGACG


title: Untagged ChIP-seq

description: Untagged ChIP-seq


title: CONTROL_1

description: HIS 1


title: Mef2cAHF::Cre mutant rep1

description:
Name of sample in FPKM_and_Counts_computed_by_USEQ_8.6.4.txt: G_WT_511_reps replicate 1
SYA_511_MUT_bc4_TTCAGC_R1.fastq.gz

value: TTCAGC

value: Replicate 1


title: SM9913 planktonic

status: Public on Nov 03 2015

city: Guangzhou

first: Xingsheng

last: Cai

state: Guangdong

address: Room 302, Building 2, #164 Xingang West Road, Haizhu District

department: Key laboratory of Tropical Marine Bio-resources and Ecology

institute: South China Sea Institute of Oceanology, Chinese Academy of Sciences

data_processing:
Sequencing was performed on Illumina HiSeq2000 platform
Dirty raw reads were filtered. Clean reads were mapped to reference genome and genes sequences respectively using SOAP2 (Li, 2009).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated as mentioned (Mortazavi, Williams et al. 2008). Then, the calculated gene expression can be directly used for comparing the difference of gene  expression among samples.
Genome_build: genome sequence of Pseudoalteromonas sp. SM9913: http://www.ncbi.nlm.nih.gov/genome/2279?genome_assembly_id=172312
Supplementary_files_format_and_content: xlsx files including RPKM values for each samples. And difference of gene expression between initial pellicle and planktonic, and between mature pellicle and planktonic.

organism: Pseudoalteromonas sp. SM9913

source_name: OD600~1 planktonic cells

growth_protocol: Planktonic cells were collected at shaking growth cultured with OD 600 ~1. Day 1 pellicle (initial stage pellicle) and day 5 pellicle (mature pellicle) were harvested after static cultured with initial OD600 ~0.1 for 1 day and 5 days, respectively

extract_protocol:
Total RNA was isolated using Tiangen RNAprep Pure Cell (Tiangen Biotech, China) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina Hiseq 2000  protocols

value: wild type

tag: growth stage

value: planktonic


title: SM9913 Initial pellicle

source_name: Initial pellicle cells

value: pellicle

value: 1 day after inoculated


title: Mef2cAHF::Cre WT rep1

description:
Name of sample in FPKM_and_Counts_computed_by_USEQ_8.6.4.txt: H_mut_511_reps replicate 1
SYA_511_WT_bc1_AAGGGA_R1.fastq.gz

value: AAGGGA


title: SM9913 mature pellicle

source_name: Mature pellicle cells

value: 5 day after inoculated


title: WT 6 months Male  Hippocampus miRNA rep4

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

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: Excel files include FPKM and Count values for each Sample

source_name: WT 6 months_Male_Hippocampus miRNA

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 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Wild Type

value: 6 months

tag: Sex

value: Male

tag: housing condition

value: housed with Het (Q20) and WT mice

value: Brain - Hippocampus

tag: molecule subtype

value: miRNA


title: WT 6 months Male  Hippocampus miRNA rep3

tag: tissue


title: WT 2 months Male  Hippocampus miRNA rep4

source_name: WT 2 months_Male_Hippocampus miRNA

value: 2 months


title: WT 2 months Male  Hippocampus miRNA rep1


title: WT 2 months Female  Hippocampus miRNA rep4

source_name: WT 2 months_Female_Hippocampus miRNA

value: Female


title: WT 6 months Female  Hippocampus miRNA rep4

source_name: WT 6 months_Female_Hippocampus miRNA


title: WT 6 months Female  Hippocampus miRNA rep1


title: WT 6 months Female  Hippocampus miRNA rep2


title: WT 2 months Male  Hippocampus miRNA rep3


title: WT 2 months Male  Hippocampus miRNA rep2


title: WT 6 months Male  Hippocampus miRNA rep2


title: WT 6 months Female  Hippocampus miRNA rep3


title: WT 6 months Male  Hippocampus miRNA rep1


title: WT 2 months Female  Hippocampus miRNA rep3


title: WT 2 months Female  Hippocampus miRNA rep1


title: WT 2 months Female  Hippocampus miRNA rep2


title: WT 10 months Female  Hippocampus miRNA rep4

source_name: WT 10 months_Female_Hippocampus miRNA

value: 10 months


title: WT 10 months Male  Hippocampus miRNA rep4

source_name: WT 10 months_Male_Hippocampus miRNA


title: WT 10 months Male  Hippocampus miRNA rep3


title: WT 10 months Male  Hippocampus miRNA rep1


title: WT 10 months Male  Hippocampus miRNA rep2


title: WT 10 months Female  Hippocampus miRNA rep3


title: WT 10 months Female  Hippocampus miRNA rep2


title: WT 10 months Female  Hippocampus miRNA rep1


title: Het (Q92) 6 months Male  Hippocampus miRNA rep3

source_name: Het (Q92) 6 months_Male_Hippocampus miRNA

value: Het (Q92) Knock-In

value: housed with Het (Q92) mice


title: Het (Q92) 6 months Male  Hippocampus miRNA rep4


title: Het (Q92) 6 months Female  Hippocampus miRNA rep4

source_name: Het (Q92) 6 months_Female_Hippocampus miRNA


title: Het (Q92) 6 months Male  Hippocampus miRNA rep2


title: Het (Q92) 6 months Female  Hippocampus miRNA rep3


title: Het (Q92) 10 months Male  Hippocampus miRNA rep4

source_name: Het (Q92) 10 months_Male_Hippocampus miRNA


title: Het (Q92) 2 months Male  Hippocampus miRNA rep4

source_name: Het (Q92) 2 months_Male_Hippocampus miRNA


title: Het (Q92) 2 months Female  Hippocampus miRNA rep4

source_name: Het (Q92) 2 months_Female_Hippocampus miRNA


title: Het (Q92) 10 months Male  Hippocampus miRNA rep2


title: Het (Q92) 2 months Male  Hippocampus miRNA rep3


title: Het (Q92) 10 months Male  Hippocampus miRNA rep3


title: Het (Q92) 2 months Female  Hippocampus miRNA rep2


title: Het (Q92) 10 months Female  Hippocampus miRNA rep3

source_name: Het (Q92) 10 months_Female_Hippocampus miRNA


title: Het (Q92) 10 months Female  Hippocampus miRNA rep1


title: Het (Q92) 6 months Female  Hippocampus miRNA rep2


title: Het (Q92) 10 months Female  Hippocampus miRNA rep2


title: Het (Q92) 10 months Male  Hippocampus miRNA rep1


title: Het (Q92) 2 months Female  Hippocampus miRNA rep3


title: Het (Q80) 6 months Male  Hippocampus miRNA rep4

source_name: Het (Q80) 6 months_Male_Hippocampus miRNA

value: Het (Q80) Knock-In

value: housed with Het (Q80) mice


title: Het (Q80) 6 months Male  Hippocampus miRNA rep3


title: Het (Q92) 2 months Male  Hippocampus miRNA rep1


title: Het (Q80) 6 months Male  Hippocampus miRNA rep1


title: Het (Q92) 10 months Female  Hippocampus miRNA rep4


title: Het (Q80) 6 months Female  Hippocampus miRNA rep4

source_name: Het (Q80) 6 months_Female_Hippocampus miRNA


title: Het (Q92) 6 months Male  Hippocampus miRNA rep1


title: Het (Q80) 6 months Female  Hippocampus miRNA rep2


title: Het (Q80) 6 months Female  Hippocampus miRNA rep3


title: Het (Q80) 6 months Female  Hippocampus miRNA rep1


title: Het (Q80) 2 months Male  Hippocampus miRNA rep5

source_name: Het (Q80) 2 months_Male_Hippocampus miRNA


title: Het (Q80) 2 months Male  Hippocampus miRNA rep3


title: Het (Q80) 2 months Male  Hippocampus miRNA rep4


title: Het (Q92) 2 months Male  Hippocampus miRNA rep2


title: Het (Q92) 2 months Female  Hippocampus miRNA rep1


title: Het (Q92) 6 months Female  Hippocampus miRNA rep1


title: Het (Q80) 2 months Male  Hippocampus miRNA rep1


title: Het (Q80) 2 months Female  Hippocampus miRNA rep2

source_name: Het (Q80) 2 months_Female_Hippocampus miRNA


title: Het (Q80) 2 months Female  Hippocampus miRNA rep1


title: Het (Q80) 2 months Female  Hippocampus miRNA rep3


title: Het (Q80) 10 months Male  Hippocampus miRNA rep3

source_name: Het (Q80) 10 months_Male_Hippocampus miRNA


title: Het (Q80) 10 months Male  Hippocampus miRNA rep4


title: Het (Q80) 6 months Male  Hippocampus miRNA rep2


title: Het (Q80) 10 months Female  Hippocampus miRNA rep4

source_name: Het (Q80) 10 months_Female_Hippocampus miRNA


title: Het (Q80) 10 months Male  Hippocampus miRNA rep2


title: Het (Q80) 10 months Female  Hippocampus miRNA rep2


title: Het (Q80) 10 months Female  Hippocampus miRNA rep1


title: Het (Q80) 10 months Female  Hippocampus miRNA rep3


title: Het (Q20) 6 months Male  Hippocampus miRNA rep1

source_name: Het (Q20) 6 months_Male_Hippocampus miRNA

value: Het (Q20) Knock-In


title: Het (Q20) 6 months Male  Hippocampus miRNA rep3


title: Het (Q20) 6 months Female  Hippocampus miRNA rep4

source_name: Het (Q20) 6 months_Female_Hippocampus miRNA


title: Het (Q80) 10 months Male  Hippocampus miRNA rep1


title: Het (Q20) 6 months Male  Hippocampus miRNA rep2


title: Het (Q20) 6 months Female  Hippocampus miRNA rep3


title: Het (Q20) 2 months Female  Hippocampus miRNA rep4

source_name: Het (Q20) 2 months_Female_Hippocampus miRNA


title: Het (Q20) 2 months Male  Hippocampus miRNA rep3

source_name: Het (Q20) 2 months_Male_Hippocampus miRNA


title: Het (Q20) 6 months Female  Hippocampus miRNA rep2


title: Het (Q20) 2 months Male  Hippocampus miRNA rep2


title: Het (Q20) 2 months Female  Hippocampus miRNA rep3


title: Het (Q80) 2 months Male  Hippocampus miRNA rep2


title: Het (Q20) 2 months Female  Hippocampus miRNA rep2


title: Het (Q20) 2 months Female  Hippocampus miRNA rep1


title: Het (Q20) 10 months Male  Hippocampus miRNA rep2

source_name: Het (Q20) 10 months_Male_Hippocampus miRNA


title: Het (Q20) 10 months Female  Hippocampus miRNA rep4

source_name: Het (Q20) 10 months_Female_Hippocampus miRNA


title: Het (Q20) 10 months Male  Hippocampus miRNA rep1


title: Het (Q20) 10 months Female  Hippocampus miRNA rep5


title: Het (Q20) 10 months Female  Hippocampus miRNA rep3


title: Het (Q20) 6 months Male  Hippocampus miRNA rep4


title: Het (Q20) 10 months Female  Hippocampus miRNA rep2


title: Het (Q175) 6 months Female  Hippocampus miRNA rep3

source_name: Het (Q175) 6 months_Female_Hippocampus miRNA

value: Het (Q175) Knock-In

value: housed with Het (Q175) mice


title: Het (Q175) 6 months Male  Hippocampus miRNA rep3

source_name: Het (Q175) 6 months_Male_Hippocampus miRNA


title: Het (Q175) 6 months Male  Hippocampus miRNA rep2


title: Het (Q175) 6 months Female  Hippocampus miRNA rep4


title: Het (Q175) 6 months Male  Hippocampus miRNA rep4


title: Het (Q175) 6 months Female  Hippocampus miRNA rep2


title: Het (Q175) 6 months Female  Hippocampus miRNA rep1


title: Het (Q20) 2 months Male  Hippocampus miRNA rep4


title: Het (Q20) 6 months Female  Hippocampus miRNA rep1


title: Het (Q20) 2 months Male  Hippocampus miRNA rep1


title: Het (Q175) 2 months Male  Hippocampus miRNA rep3

source_name: Het (Q175) 2 months_Male_Hippocampus miRNA


title: Het (Q175) 2 months Male  Hippocampus miRNA rep2


title: Het (Q175) 2 months Female  Hippocampus miRNA rep4

source_name: Het (Q175) 2 months_Female_Hippocampus miRNA


title: Het (Q175) 2 months Male  Hippocampus miRNA rep1


title: Het (Q175) 2 months Female  Hippocampus miRNA rep3


title: Het (Q175) 2 months Female  Hippocampus miRNA rep2


title: Het (Q175) 2 months Female  Hippocampus miRNA rep1


title: Het (Q20) 10 months Male  Hippocampus miRNA rep3


title: Het (Q175) 10 months Male  Hippocampus miRNA rep4

source_name: Het (Q175) 10 months_Male_Hippocampus miRNA


title: Het (Q175) 10 months Male  Hippocampus miRNA rep2


title: Het (Q175) 10 months Male  Hippocampus miRNA rep3


title: Het (Q175) 10 months Female  Hippocampus miRNA rep4

source_name: Het (Q175) 10 months_Female_Hippocampus miRNA


title: Het (Q175) 10 months Male  Hippocampus miRNA rep1


title: Het (Q175) 6 months Male  Hippocampus miRNA rep1


title: Het (Q20) 10 months Female  Hippocampus miRNA rep1


title: Het (Q175) 10 months Female  Hippocampus miRNA rep1


title: Het (Q140) 6 months Male  Hippocampus miRNA rep4

source_name: Het (Q140) 6 months_Male_Hippocampus miRNA

value: Het (Q140) Knock-In

value: housed with Het (Q140) mice


title: Het (Q140) 6 months Male  Hippocampus miRNA rep3

value: 6 months


title: Het (Q140) 6 months Male  Hippocampus miRNA rep1

value: Male


title: Het (Q140) 6 months Male  Hippocampus miRNA rep2


title: Het (Q140) 6 months Female  Hippocampus miRNA rep2

source_name: Het (Q140) 6 months_Female_Hippocampus miRNA


title: Het (Q140) 6 months Female  Hippocampus miRNA rep3


title: Het (Q140) 2 months Male  Hippocampus miRNA rep4

source_name: Het (Q140) 2 months_Male_Hippocampus miRNA


title: Het (Q175) 2 months Male  Hippocampus miRNA rep4


title: Het (Q140) 6 months Female  Hippocampus miRNA rep1


title: Het (Q140) 6 months Female  Hippocampus miRNA rep4


title: Het (Q140) 2 months Male  Hippocampus miRNA rep3


title: Het (Q140) 2 months Female  Hippocampus miRNA rep4

source_name: Het (Q140) 2 months_Female_Hippocampus miRNA


title: Het (Q140) 2 months Male  Hippocampus miRNA rep2


title: Het (Q140) 2 months Female  Hippocampus miRNA rep1


title: Het (Q140) 2 months Female  Hippocampus miRNA rep3


title: Het (Q140) 2 months Female  Hippocampus miRNA rep2


title: Het (Q140) 10 months Male  Hippocampus miRNA rep4

source_name: Het (Q140) 10 months_Male_Hippocampus miRNA


title: Het (Q175) 10 months Female  Hippocampus miRNA rep3


title: Het (Q140) 10 months Male  Hippocampus miRNA rep2


title: Het (Q140) 10 months Male  Hippocampus miRNA rep3


title: Het (Q140) 10 months Male  Hippocampus miRNA rep1


title: Het (Q175) 10 months Female  Hippocampus miRNA rep2


title: Het (Q140) 10 months Female  Hippocampus miRNA rep4

source_name: Het (Q140) 10 months_Female_Hippocampus miRNA


title: Het (Q140) 10 months Female  Hippocampus miRNA rep3


title: Het (Q111) 6 months Male  Hippocampus miRNA rep4

source_name: Het (Q111) 6 months_Male_Hippocampus miRNA

value: Het (Q111) Knock-In

value: housed with Het (Q111) mice


title: Het (Q140) 10 months Female  Hippocampus miRNA rep2

value: Brain - Hippocampus

value: miRNA


title: Het (Q111) 6 months Male  Hippocampus miRNA rep2


title: Het (Q111) 6 months Male  Hippocampus miRNA rep3


title: Het (Q111) 6 months Female  Hippocampus miRNA rep4

source_name: Het (Q111) 6 months_Female_Hippocampus miRNA

value: Female


title: Het (Q111) 6 months Male  Hippocampus miRNA rep1


title: Het (Q111) 6 months Female  Hippocampus miRNA rep2


title: Het (Q111) 6 months Female  Hippocampus miRNA rep3


title: Het (Q140) 2 months Male  Hippocampus miRNA rep1

value: 2 months


title: Het (Q111) 6 months Female  Hippocampus miRNA rep1


title: Het (Q111) 2 months Male  Hippocampus miRNA rep4

source_name: Het (Q111) 2 months_Male_Hippocampus miRNA


title: Het (Q111) 2 months Male  Hippocampus miRNA rep3


title: Het (Q111) 2 months Male  Hippocampus miRNA rep2


title: Het (Q111) 2 months Female  Hippocampus miRNA rep4

source_name: Het (Q111) 2 months_Female_Hippocampus miRNA


title: Het (Q111) 2 months Female  Hippocampus miRNA rep2


title: Het (Q111) 10 months Male  Hippocampus miRNA rep2

source_name: Het (Q111) 10 months_Male_Hippocampus miRNA

value: 10 months


title: Het (Q111) 10 months Male  Hippocampus miRNA rep3


title: Het (Q111) 2 months Female  Hippocampus miRNA rep1


title: Het (Q111) 2 months Female  Hippocampus miRNA rep3


title: Het (Q111) 10 months Male  Hippocampus miRNA rep4


title: Het (Q111) 10 months Male  Hippocampus miRNA rep1


title: Het (Q111) 10 months Female  Hippocampus miRNA rep4

source_name: Het (Q111) 10 months_Female_Hippocampus miRNA


title: Het (Q111) 10 months Female  Hippocampus miRNA rep3


title: Het (Q111) 10 months Female  Hippocampus miRNA rep2


title: WT 6 months Male  Cerebellum miRNA rep4

source_name: WT 6 months_Male_Cerebellum miRNA

tag: strain background

value: Wild Type

value: Brain - Cerebellum

value: housed with Het (Q20) and WT mice


title: WT 6 months Male  Cerebellum miRNA rep2


title: Het (Q111) 10 months Female  Hippocampus miRNA rep1


title: Het (Q140) 10 months Female  Hippocampus miRNA rep1


title: WT 6 months Male  Cerebellum miRNA rep1


title: WT 6 months Female  Cerebellum miRNA rep3

source_name: WT 6 months_Female_Cerebellum miRNA


title: WT 6 months Female  Cerebellum miRNA rep2


title: WT 6 months Female  Cerebellum miRNA rep1


title: Het (Q111) 2 months Male  Hippocampus miRNA rep1


title: WT 2 months Male  Cerebellum miRNA rep4

source_name: WT 2 months_Male_Cerebellum miRNA


title: WT 2 months Male  Cerebellum miRNA rep1


title: WT 2 months Female  Cerebellum miRNA rep3

source_name: WT 2 months_Female_Cerebellum miRNA


title: WT 2 months Female  Cerebellum miRNA rep2


title: WT 10 months Male  Cerebellum miRNA rep4

source_name: WT 10 months_Male_Cerebellum miRNA


title: WT 2 months Female  Cerebellum miRNA rep1


title: WT 10 months Male  Cerebellum miRNA rep2


title: WT 10 months Female  Cerebellum miRNA rep3

source_name: WT 10 months_Female_Cerebellum miRNA


title: WT 10 months Female  Cerebellum miRNA rep2


title: WT 10 months Male  Cerebellum miRNA rep1


title: WT 10 months Female  Cerebellum miRNA rep4


title: WT 10 months Male  Cerebellum miRNA rep3


title: WT 10 months Female  Cerebellum miRNA rep1


title: Het (Q92) 6 months Male  Cerebellum miRNA rep2

source_name: Het (Q92) 6 months_Male_Cerebellum miRNA

value: Het (Q92) Knock-In

value: housed with Het (Q92) mice


title: Het (Q92) 6 months Male  Cerebellum miRNA rep4


title: Het (Q92) 6 months Male  Cerebellum miRNA rep3


title: WT 6 months Male  Cerebellum miRNA rep3


title: Het (Q92) 6 months Female  Cerebellum miRNA rep3

source_name: Het (Q92) 6 months_Female_Cerebellum miRNA


title: Het (Q92) 6 months Male  Cerebellum miRNA rep1


title: WT 6 months Female  Cerebellum miRNA rep4


title: Het (Q92) 6 months Female  Cerebellum miRNA rep1


title: WT 2 months Male  Cerebellum miRNA rep2


title: Het (Q92) 6 months Female  Cerebellum miRNA rep2


title: Het (Q92) 2 months Male  Cerebellum miRNA rep4

source_name: Het (Q92) 2 months_Male_Cerebellum miRNA


title: Het (Q92) 2 months Male  Cerebellum miRNA rep2


title: Het (Q92) 2 months Male  Cerebellum miRNA rep3


title: WT 2 months Male  Cerebellum miRNA rep3


title: Het (Q92) 2 months Male  Cerebellum miRNA rep1


title: Het (Q92) 6 months Female  Cerebellum miRNA rep4


title: WT 2 months Female  Cerebellum miRNA rep4


title: Het (Q92) 2 months Female  Cerebellum miRNA rep3

source_name: Het (Q92) 2 months_Female_Cerebellum miRNA


title: Het (Q92) 2 months Female  Cerebellum miRNA rep1


title: Het (Q92) 2 months Female  Cerebellum miRNA rep4


title: Het (Q92) 10 months Male  Cerebellum miRNA rep3

source_name: Het (Q92) 10 months_Male_Cerebellum miRNA


title: Het (Q92) 10 months Male  Cerebellum miRNA rep2


title: Het (Q92) 10 months Male  Cerebellum miRNA rep1


title: Het (Q92) 10 months Female  Cerebellum miRNA rep4

source_name: Het (Q92) 10 months_Female_Cerebellum miRNA


title: Het (Q92) 10 months Female  Cerebellum miRNA rep3


title: Het (Q80) 6 months Male  Cerebellum miRNA rep3

source_name: Het (Q80) 6 months_Male_Cerebellum miRNA

value: Het (Q80) Knock-In

value: housed with Het (Q80) mice


title: Het (Q80) 6 months Male  Cerebellum miRNA rep4


title: Het (Q92) 10 months Female  Cerebellum miRNA rep1


title: Het (Q80) 6 months Male  Cerebellum miRNA rep1


title: Het (Q80) 6 months Female  Cerebellum miRNA rep1

source_name: Het (Q80) 6 months_Female_Cerebellum miRNA


title: Het (Q80) 6 months Female  Cerebellum miRNA rep2


title: Het (Q80) 6 months Female  Cerebellum miRNA rep4


title: Het (Q92) 10 months Female  Cerebellum miRNA rep2


title: Het (Q92) 10 months Male  Cerebellum miRNA rep4


title: Het (Q80) 2 months Male  Cerebellum miRNA rep4

source_name: Het (Q80) 2 months_Male_Cerebellum miRNA


title: Het (Q80) 2 months Male  Cerebellum miRNA rep2


title: Het (Q92) 2 months Female  Cerebellum miRNA rep2


title: Het (Q80) 2 months Female  Cerebellum miRNA rep1

source_name: Het (Q80) 2 months_Female_Cerebellum miRNA


title: Het (Q80) 2 months Male  Cerebellum miRNA rep1


title: Het (Q80) 6 months Female  Cerebellum miRNA rep3


title: Het (Q80) 2 months Male  Cerebellum miRNA rep5


title: Het (Q80) 2 months Female  Cerebellum miRNA rep2


title: Het (Q80) 2 months Female  Cerebellum miRNA rep3


title: Het (Q80) 10 months Male  Cerebellum miRNA rep2

source_name: Het (Q80) 10 months_Male_Cerebellum miRNA


title: Het (Q80) 10 months Male  Cerebellum miRNA rep3


title: Het (Q80) 10 months Male  Cerebellum miRNA rep1


title: Het (Q80) 10 months Male  Cerebellum miRNA rep4