title: Native_library_input

city: Seattle

first: Georg

last: Seelig

address: 185 Stevens Way, Paul Allen Center - Room AE100R, Box 352500

department: Department of Electrical Engineering

institute: University of Washington

data_processing:
Basecalling by bcl2fastq
starcode to collapse sequences
made synthetic genome
aligned with star and then generated counts for each unique sequence
First, a pseudocount of 1 was added to each sequence count. Sequence counts in each condition (e.g. input, random library) were then normalized to the total counts in that condition. The enrichment was calculated by log2(selection/input)
Supplementary_files_format_and_content: .csv files. Files include columns with the UTR sequence, the raw counts for the input and following selection (t0 and t1, respectively) and the enrichment score.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown in -tryptophan media following transformation to select for the library plasmids.

extract_protocol:
Plasmid DNA was purified using the Zymoprep yeast plasmid prep II (Zymo Research)
PCR for 12 to 20 cycles was used to add sequencing adaptors and to amplify the sample. Deep sequencing of the resulting product was performed on an Illumina Nextseq.

treatment_protocol: After collecting cells for use as the input, the cells were grown in -tryptophan, -histidine media to select for growth.

tag: selection

value: (-)tryptophan

tag: assayed molecule

value: plasmid DNA


title: Evolved_library_input

status: Public on Sep 27 2017

type: SRA

state: Washington

country: USA

library_source: genomic

molecule: genomic DNA

tag: strain


title: Random_library_selected

value: (-)tryptophan,(-)histidine


title: Evolved_library_selected


title: Native_library_selected


title: TETS_ChIP-seq_input_stage9_replicate1

status: Public on Sep 28 2017

city: Nijmegen

first: Simon

last: van Heeringen

address: Geert Grooteplein 28

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud University

description: ChIP-seq input in stage 9 Xenopus tropicalis embryos

data_processing:
ChIP-seq and genomic DNA reads were aligned to the genome using bwa version 0.7.10-r789 with default parameters
Duplicates in genomic DNA were marked using Picard MarkDuplicates version 2.7.1
ChIP-seq peaks were called using macs2 version 2.0.10 with qvalue cutoff=1e-03 relative to respective ChIP input track.
RNA-seq reads were mapped to genome Xla.v91 + transcriptome v1.8 (http://www.xenbase.org) using STAR version 2.4.2a with --quantMode TranscriptomeSAM. Quantification was performed on the reads mapped to the transcriptome by STAR using eXpress v1.5.1.
Genome_build: Xenopus tropicalis: xt9.0; Xenopus laevis: Xla.v91; Xenopus tropicalis x Xenopus laevis: xt9.0 + Xla.v91 (merged)
Supplementary_files_format_and_content: Results from eXpress (.xprs); peak files in BED format.

organism: Xenopus tropicalis

source_name: whole embryo

growth_protocol: Embryos were generated using IVF (in vitro fertilization) with outbred animals.

extract_protocol:
Protein-DNA complexes were isolated with antibody from whole embryo lysates that were fixed, sonicated and yolk depleted.
Libraries were prepared with the Kapa Hyper Prep kit (Kapa Biosystems)

tag: developmental stage

value: NF stage 9

tag: cell type

value: whole embryo

tag: chip antibody

value: None (Input)


title: chid+deci-IP

city: Shanghai

first: Meng-Meng

last: Ji

address: Ruijin No.2 Road

country: China

institute: Shanghai Ruijin Hospital

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were adaptor-trimmed and mapped to human genome (hg19) by bowtie2 software with default parameters.
Peak calling was performed with MACS software (v1.4.3).
Differentially enriched regions were identified by diffReps software (v1.55.4).
The  enriched peaks were then annotated with the latest UCSC RefSeq database to connect the peak information with the gene annotation.
Genome_build: hg19
Supplementary_files_format_and_content: bed format: enriched peaks

organism: Homo sapiens

source_name: Jurkat cell

growth_protocol: Cells were grown in RPMI-1640 medium, supplemented with 10% heat-inactivated fetal bovine serum in a humidified atmosphere containing 95% air-5% CO2 at 37°C.

extract_protocol:
DNA extraction protocol
Chromatin Immunoprecipitation was performed according to Wamstad et al. (2012). The yield of ChIPed DNA was determined via Quant IT fluorescence assay (Life Technologies) and enrichment efficiencies of ChIP reactions were evaluated by qPCR. Illumina sequencing libraries were generated with NEBNext® Ultra™ DNA Library Prep Kit (New England Biolabs) by following the manufacturer’s manual.
The library quality was determined by using Agilent 2100 Bioanalyzer (Agilent), and then, subjected to high-throughput 150 base paired-end sequencing on Illumina Hiseq sequencer according to the manufacturer’s recommended protocol.

treatment_protocol: Jurkat (KMT2D V5486M) cells were treated with Chidamide (5nm)，Decitabine (5μm)，Chidamide (5nm)+Decitabine (5μm)，respectively.

value: Jurkat cell (KMT2D V5486M)

tag: treatment

value: Chidamide (5nm)+Decitabine (5μm)

tag: antibody


title: deci-IP

value: Decitabine (5μm)


title: untreated-IP


title: chid-IP

value: Chidamide (5nm)


title: HSTSCirc

city: Yantai

first: yeying

last: sun

address: No.346 Guanhai road

institute: Binzhou Medical Univeristy

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Cynoglossus semilaevis whole genome using Tophat v2.0.12 with default parameters
Genome_build: Cynoglossus semilaevis (https://www.ncbi.nlm.nih.gov/assembly/GCF_000523025.1/)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for  Sample

molecule: total RNA

organism: Cynoglossus semilaevis

source_name: tissue pool

extract_protocol:
Gonad, liver, spleen, heart, kidney, gill, muscle, and brain tissues were collected individually. Total RNA was isolated from the different tissues with TRIzol to form tissue pool.
RNA sample was prepared following the removal of ribosomal RNA to obtain rRNA-depleted RNAs. rRNA-depleted RNAs were further treated with RNase R and subjected to TRIzol extraction.RNA libraries were prepared for sequencing using NEB Next Ultra Directional RNA Library Prep Kit for Illumina

tag: age

value: adult fish

tag: tissue


title: HSTSLnc

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Cynoglossus semilaevis whole genome using Tophat v2.0.12 with default parameters
Genome_build: Cynoglossus semilaevis
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for  Sample

extract_protocol:
Gonad, liver, spleen, heart, kidney, gill, muscle, and brain tissues were collected individually. Total RNA was isolated from the different tissues with TRIzol to form tissue pool.
RNA libraries were prepared for sequencing using NEB Next Ultra Directional RNA Library Prep Kit for Illumina


title: EtOH 3

city: Rochester

first: Anna

middle: Katarzyna

last: Majewska

state: NY

address: 601 Elmwood avenue box 603

department: Neuroscience

institute: University of Rochester

data_processing:
DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
MAPPING - STAR_2.4.2a "--runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - htseq-count v0.6.1 "-q -f bam -s no -r pos -i gene_name"
Genome_build: GRCm38.p4 + Gencode-M6 Annotation
Supplementary_files_format_and_content: text file include raw expression counts

organism: Mus musculus

source_name: freshly isolated microglia (CD11b+ CD45low cells) from bilateral visual cortex (brain region)

growth_protocol: All procedures were in accordance with the University of Rochester Committee on Animal Resources and abided by National Institutes of Health guidelines.  C57BL/6 mice (originally from Jackson Labs) were generated through in-house continuous breeding in a 2-way vivarium facility. Pups were housed with dam and other littermates from day of birth (P0) through P21 (weaning).  Whenever possible, weanlings were group housed, and always with littermates of the same sex (male).   A 6am light 6pm dark cycle with ad libitum access to chow and water was maintained throughout life. Animals were toe clipped for identification and assigned treatment groups (saline or EtOH) on postnatal day 4, the first day of dosing.  As adolescent animals, all were euthanized between 8:30am-9:30am (see extraction protocol).  Animals were generated from a total of 3 separate litters (mating involving three different dams).

extract_protocol:
Adolescent mice (age specified in column H) with early life exposure to either saline (control) or ethanol (EtOH) were euthanized by intraperitoneal injection of euthasol and transcardially perfused with ice cold 0.15M phosphate buffer. Each brain was removed and bilateral visual cortex was immediately dissected in ice cold, degassed FACS buffer = 0.5% bovine serum albumin (Sigma A2153) in 1X PBS (Invitrogen 20012-027). Tissue was kept on ice throughout. After dounce homogenization, the tissue with passed through a 70µm filter and centrifuged (1200 RPM, 7 min. 4°C).  Supernatant was aspirated from pellets, which were prepared for magnetic labeling with Myelin Removal Beads II (Miltenyi 130-0960733) according to the manufacturer’s instructions.  Magnetic columns (Miltenyi 130-096-733) were primed with FACS buffer and samples applied to the columns through a clean 70µm filter. After centrifugation of column flow-through and gentle supernatant removal, myelin depleted samples were incubated in Fc block (BioLegend 101320) for 15 minutes at 4°C.   Cells were incubated with CD11b-AlexaFluor 488 (BD Pharmingen 557672) and CD45-APC (BD Pharmingen 561018) for 30 minutes in the dark at 4°C.  The following compensation controls were also freshly prepared in conjunction with experimental samples: 488 bead control, APC bead control (eBiosciences 01-111-42), unstained cells, and triton-X treated cells (propidium iodide (PI) dead cell control). An extra non-experimental fully stained cell sample was included to check voltage settings prior to running experimental samples on an 18 color FACS Aria II flow cytometer. Prior to sorting, all samples and controls were re-suspended in a final FACS buffer volume of 300µL.  PI was added to the samples and appropriate controls 1 hour prior to cell sorting.  For immediate cell lysis and preservation of RNA, microglia (PI negative, CD11b positive, CD45 low) were sorted directly into 1.5mL microcentrifuge tubes (Axygen 311-08-051) containing 600µL Buffer RLT PLUS (Qiagen, 1053393) and 6µL β-mercaptoethanol at 4°C, prepared just prior to sorting.  Experimental samples were not pooled: individual samples represent microglia from bilateral visual cortex from one animal.  The number of CD11b positive CD45 low cells collected (considered the number of microglia collected) is listed in column K above.
Total RNA was isolated using the RNeasy Micro Kit (Qiagen). RNA Integrity Number (RIN) was 9.53 ± 0.13 and RNA concentration was 220 ± 17 pg/µL (mean ± SEM) across the 9 samples.  1ng of total RNA was preamplified with the SMARTer Ultra Low Input kit v2 (Clontech). cDNA quality was determined using a Qubit Flourometer (Life Technologies) and Agilent 220 TapeStation. Illumina compatible sequencing libraries were generated from 5ng cDNA with the NexteraXT library prep kit (Illumina).

tag: Sex

value: male

value: 1.8g/kg EtOH (using 20% v/v 200 proof EtOH (Koptec) in saline) was administered by dorsal subcutaneous injection twice each day from postnatal day 4 through postnatal day 9 (P4-P9), for a total daily dose of 3.6g/kg.  The two doses each day were separated by a 2 hour interval. After P9, mice were no longer exposed to any EtOH until time of sacrifice and cell sorting for microglial sample collection that occured in adolescent animals. Animal age for each sample (individual animal) is listed in the next column.

tag: age (postnatal day p)

tag: body weight (grams)

tag: collected tissue weight (mg)

tag: # of microglia cells (pi neg, cd11b pos, cd45 low) collected

tag: rna concentration  (pg/ul)

tag: rna integrity number (rin)


title: Xenopus_tropicalis_genomic

description: Genomic DNA of Xenopus tropicalis embryos

extract_protocol:
Genomic DNA was isolated.
DNA was sonicated to 200-700bp fragments, 300bp fragments were size-selected.

value: NF stage 18


title: EtOH 2


title: Saline 5

value: Instead of 20% EtOH, an equivalent volume of saline (0.9% NaCl) was administered twice each day from postnatal day 4 through postnatal day 9 (P4-P9) by dorsal subcutaneous injection. After P9, mice were no longer injected with saline and were sacrificed as adolescent animals for same day fluorescence assisted cell sorting to collect microglia. Specific ages at sacrifice for each sample (individual mouse) are listed in the next column.


title: Cooling_Control_ctrl

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mouse whole genome using TopHat v2.0.12 and bowtie v1.0.1 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using HTSeq v0.6.0
Genome_build: reference sequences were download from http://www.ensembl.org/index.html
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: GFP positive neural stem cell were isolated from electroporated E15 mice by using FACS and RNA was extract by using trace rna sample extraction kit.

extract_protocol:
RNA was extract by using trace rna sample extraction kit. Total 100ng RNA for the construction of sequencing libraries
mRNA were enriched by Oligo(dT) bread and then fragmented by fragmentation buffer. cDNA was synthesized by reverse transcription using 6bp random primers and purified by QIAQuick PCR kit. After adapter ligation, DNA was PCR amplified sequences and band isolated from an agarose gel.

treatment_protocol: Neural stem cell at E13 were electroporated withControl or RBM3 knockdown plasmid, the maternal hypothermia was induced at E14, and then theGFP+ cells were isolated by using FACS.

tag: strain background

tag: genotype/variation

value: Control

value: hypothermia induced mouse embryonic brain

value: GFP+ neural stem cells


title: EtOH 4

tag: strain


title: EtOH 1


title: Saline 3


title: Saline 2


title: F88

city: Dallas

first: Marek

last: Napierala

state: TX

address: Marek Napierala

institute: University of Texas Southwestern Medical Center

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to human genome (hg19) by TopHat (version 2.0.7) and Bowtie2 (version 2.1.0).
The number of fragments in each known gene from RefSeq database (downloaded from UCSC Genome Browser on March 6, 2013) was enumerated using htseq-count from HTSeq package (version 0.5.3p9).
Genes with less than 10 fragments in all the samples were removed, and then the normalized fragment count for each gene was calculated by R/Bioconductor package DESeq (version 1.10.1).
Genome_build: hg19
Supplementary_files_format_and_content: The first column is gene symbol. The other columns are normalized expression values (estimated by DESeq) for all the samples.

source_name: fibroblasts

growth_protocol: Primary fibroblast cultures were maintained in DMEM high glucose (Life Technologies) containing 15% fetal bovine serum (Hyclone) and 1% non-essential amino acids (Life Technologies).  Cells were passaged by incubating in 0.25% trypsin-EDTA (Life Technologies) for 5 min, and harvested for RNA isolation when they reached ~80-85% confluence.

extract_protocol:
Fibroblasts were harvested by trypsinization, centrifuged, and rinsed once with ice-cold cold phosphate-buffered saline (PBS).  Total RNA was isolated using a RNeasy Mini Kit (Qiagen) followed by an independent DNase I treatment using the TURBO DNA-free system (Ambion) according to the manufacturer’s recommended rigorous protocol.
RNAs isolated from all 35 fibroblast lines (1 ug/sample) were reverse transcribed to generate sequencing libraries using a Truseq Stranded Total RNA Library Prep kit (Illumina).  This protocol included ribosomal RNA depletion instead of polyA selection.  The cDNA synthesis was conducted using SuperScript II reverse transcriptase followed by second strand synthesis, adenylation of 3’ ends and ligation of adapters. The libraries were sequenced using a 2x76 bases paired end protocol on an Illumina HiSeq 2000 instrument. Totally 35 libraries (18 from FRDA patients and 17 from unaffected controls) were sequenced in 6 lanes, generating 27-39 million pairs of reads per sample. Each pair of reads represents a cDNA fragment from the library.

tag: genotype

value: Friedreich's ataxia

value: primary skin fibroblast cells

tag: sampling age


title: F68


title: Saline 1


title: F66


title: Cooling_RBM3 knockdown_case

tag: developmental stage

value: RBM3 knockdown

tag: cell type


title: F4497


title: F4654


title: F4259


title: F4509


title: F4675


title: F4192


title: Random_library_input

tag: selection

value: (-)tryptophan

tag: assayed molecule

value: plasmid DNA


title: F4230

tag: tissue


title: F4627


title: Saline 4

tag: Sex

tag: treatment


title: F3665


title: GS0259_TEM_secondary

city: La Jolla

first: Mariana

last: Babor

address: 9420 Athena Cir

institute: La Jolla Institute for Allergy and Immunology

description: Microscaled (SmartSeq2) cDNA amplification - RNA seq

data_processing:
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The reads were then aligned to UCSC hg19 reference genome using TopHat (v 1.4.1) (Trapnell et al., 2009). DUST scores were calculated with PRINSEQ Lite (v 0.20.3) (Schmieder et al., 2011) and low-complexity reads (DUST > 4) were removed from the BAM files.  The alignment results were parsed via the SAMtools (Li et al., 2009) to generate SAM files. Read counts to each genomic feature were obtained with the htseq-count program (v 0.6.0) (Anders et al., 2014) using the “union” option.
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements as a matrix table

molecule: polyA RNA

source_name: Cryopreserved PBMC

growth_protocol: Cells were directly isolated post thawing of cryopreserved PBMC samples and lysed, no culture were involved.

extract_protocol:
Cryopreserved PBMC were thawed, stained with antibodies, and 100,000 memory CD4 T cells sorted using BD Aria 3 or BD Aria Fusion cell sorter direclty in Trizol. Naive, TCM, TEM and TEMRA cells were defined as the combination of  CCR7+CD45RA+, CCR7+CD45RA-, CCR7-CD45RA- and CCR7-CD45RA+ populations. Total RNA was purified using a miRNAeasy micro kit (Qiagen, USA) and quantified by qPCR as described previously (Seumois et al., 2012).
Purified total RNA (1 to 5 ng) was amplified following the smart-seq2 protocol (16 cycles of cDNA amplification) (Picelli et al., 2014). cDNA was purified using AMPure XP beads (Beckman Coulter). From this step, 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina).

treatment_protocol: No specific treatment involved

value: PBMC

tag: disease group

value: Sri Lanka Secondary

tag: cell subset

value: TEM CD3+CD4+CCR7-CD45RA- T cells


title: F4078


title: GS0259_TEMRA_secondary

value: TEMRA CD3+CD4+CCR7-CD45RA+ T cells


title: F281


title: D3013

city: Jinan

first: Guangxiang

last: Cao

address: 18877 jingshi Road

institute: Shandong Academy of Medical Sciences

data_processing:
Basecalling were performed by Illumina GA Pipeline v1.5
raw reads were filtered to generate clean data
clean reads were aligned against genome by  S O A P a l i g n e r / S O A P 2（Li， 2009）
Reads per kilobase transcriptome per million mapped reads(RPKM) was used to analyze the expression of genes
Supplementary_files_format_and_content: text files include RPKM values for each Sample .

organism: Streptomyces coelicolor

source_name: mycelium

growth_protocol: the total RNA of S. coelicolor M145 and ΔmtrA was extracted from cultures incubated at 30ºC for 72 h on solid YBP medium covered with cellophane and were then treated with RNase-free DNase I (Invitrogen) twice according to the recommended protocols.

extract_protocol:
the mycelia were collected at various times, ground in liquid nitrogen, and then dispensed into Rezol reagent (SBSBIO). Crude RNA samples were treated twice with ‘Turbo DNA-free’ DNase reagents (Ambion) to remove chromosomal DNA
The integrity of total RNA was determined using a Thermo NanoDrop, and the RNA Integrity Number value of each sample met the standard required for preparing a cDNA library. The cDNA libraries were prepared according to the manufacturer’s instructions (Illumina).

value: SCO3013 mutant strain


title: GS0259_TCM_secondary

value: TCM CD3+CD4+CCR7+CD45RA- T cells


title: GS0259_naive_secondary

value: NAIVE CD3+CD4+CCR7+CD45RA+ T cells


title: F203


title: F188


title: F156


title: GS0117_TEM_secondary


title: C_UM


title: F130


title: GS0117_naive_secondary


title: C_UF


title: GS0117_TCM_secondary


title: Treatment Shunt rep5

city: Goettingen

first: Sara

last: Khadjeh

address: Robert-Koch-Str. 42a

department: Clinic for Cardiology and Pneumology

country: Germany

institute: University Medical Center Göttingen

description: Sample IV5

data_processing:
[base-calling] Sequence images were transformed to bcl files with the software BaseCaller (Illumina), and then demultiplexed to fastq files with CASAVA v1.8.2. Quality checking was done via fastqc.
[alignment] Sequences were aligned to the genome reference sequence of Mus musculus (GRCm38/mm10). The Alignment was performed using the STAR alignment software (version 2.3.0e) 1 allowing for two mismatches within 50 bases.
[filtering] Subsequently, conversion of resulting SAM files to sorted BAM files, filtering of unique hits and counting were conducted with SAMtools (version 0.1.19) 2 and HTSeq (version 0.6.1p1) 3.
Data were preprocessed and analyzed in the R/Bioconductor environment (www.bioconductor.org) using the DESeq2 package (version 1.8) 4.
Specifically, the data were normalized and tested for differentially expressed genes based on a generalized linear model likelihood ratio test assuming negative binomial data distribution. Candidate genes were filtered to a minimum of log2FC>1/-1 and a false discovery rate–corrected P-value < 0.05.
Genome_build: Gene annotation was performed using Mus musculus entries from Ensembl (www.ensembl.org) via the biomaRt package (version 2.18.0) 5.
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

source_name: TreatmentShunt

extract_protocol:
total RNA was isolated from left ventricular tissue using the RNeasy Fibrous Tissue Mini Kit (Qiagen) according to the manufacturer`s protocol.
Library preparation was conducted according to the instructions of the TruSeq RNA Sample Preparation v2 Kit from Illumina (Cat. N°RS-122-2002) using 1µg total RNA as starting material.

treatment_protocol:
TAC Surgery: Surgery was done using a minimally invasive approach as described previously,(42) with the exception that the degree of aortic constriction was reduced to yield comparable survival in wild-type mice with TAC vs. Shunt. Briefly, 8 week old mice were anesthetized using intraperitoneal injections of ketamine and xylazine (100 mg/kg and 5 mg/kg, respectively). A horizontal incision at the jugulum was used to display the transverse aorta. A needle was tied against the aorta using a 5-0 non-absorbable suture. After removal of the needle, skin was closed and the mice were kept on a heating plate until recovered from anesthesia.  Sham animals underwent the same procedure except banding of the aorta. DBA/2J x C3HeB/FeJ) F1 mice exhibit a pronounced gender-based difference in body weight at 8 weeks of age (29.6 +/- 0.8 vs. 23.3 +/- 0.4, males vs. females, n = 10 mice per gender).  Because aortic dimension correlates with body weight,(43, 44) and because aortic dimensions influences the gradient, 25G needles were used to induced TAC in males and 26g needles were used in females. The resulting pressure gradients were measured by echocardiography, and comparable gradients were observed in male and female mice (Supplemental Figures 8 and 9).
Aortocaval Shunt: Surgery was done as described previously.(45) Briefly, 8 week old mice were anesthetized using isofluorane insufflation. A longitudinal abdominal incision was made and the vessels prepared. The aorta was clamped and punctured with a needle (23G) through the vena cava inferior. After removing the needle the external hole in the aorta was closed by a cyanoacrylate glue (Pattex, Düsseldorf, Germany). Successful shunt operation is immediately seen by inflow of oxygenated blood from the abdominal aorta into the vena cava. The abdomen was then closed and the mice were kept on a heating plate until full recovery from anesthesia. Sham animals underwent the same procedure except for the puncture of the vessels. In a previous analysis we showed that a decline of LVEDD after an initial increase is associated with a decrease in right ventricular oxygen saturation as an indicator of shunt closure. In the present study all animals after shunt surgery showed a persistent increase in LVEDD.

tag: genetic backround

value: (DBA/2J x C3HeB/FeJ)F1

value: MHC-cycD2 transgenic

value: Shunt

value: myocardium, left ventricle


title: M145

value: wildtype


title: GS0108_TEMRA_secondary


title: C7525

value: Control


title: C8399

value: primary skin fibroblast cells


title: GS0108_TEM_secondary


title: C7522


title: GS0108_naive_secondary


title: C7492


title: Treatment Shunt rep4

description: Sample IV4


title: Treatment Shunt rep3

description: Sample IV3


title: GS0098_TEMRA_secondary


title: C5879


title: Treatment Shunt rep2

description: Sample IV2


title: Treatment Shunt rep1

description: Sample IV1


title: Treatment TAC rep4

description: Sample III4

source_name: TreatmentTAC

value: TAC


title: GS0098_TEM_secondary


title: C3956


title: Treatment TAC rep2

description: Sample III2


title: GS0117_TEMRA_secondary


title: C3652


title: GS0098_naive_secondary


title: C3348


title: control sham rep5

description: Sample II5

source_name: control sham

value: sham


title: GS0089_TEMRA_secondary


title: GS0098_TCM_secondary


title: C288


title: C2671


title: GS0089_TEM_secondary


title: Treatment TAC rep1

description: Sample III1


title: GS0108_TCM_secondary


title: control sham rep3

description: Sample II3


title: GS0089_TCM_secondary


title: C2169


title: GS0089_naive_secondary


title: control sham rep2

description: Sample II2


title: control sham rep1

description: Sample II1


title: C2153


title: TU0085_TEMRA_negative

value: San Diego Negative


title: TU0085_TEM_negative

value: PBMC


title: control WT rep5

description: Sample I5

source_name: control WT

value: wild type


title: control WT rep4

description: Sample I4


title: C2036


title: C1650


title: control WT rep2

description: Sample I2


title: control WT rep3

description: Sample I3


title: T-ALL1 GSI treated Notch3 ChIP-seq

city: Boston

first: Eric

middle: A

last: Severson

state: MA

address: 75 Francis Street

department: Pathology

institute: Brigham and Women's Hospital

data_processing:
Alignment to hg38 with bowtie2, v2.2.3
Peak calling and bigwig generation by macs2 v2.1.0.20140616
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files with ChIP-seq signal normalized by number of reads and bed files with peak calls

growth_protocol: TALL1 cells were cultured in RPMI1640 medium supplemented with 10% FBS and 1x penicillin and streptomycin.  293T cells were maintained in DMEM medium supplemented with 10% FBS.

extract_protocol:
ChIP was performed using EZ-Magna ChIP (Millipore) according to the manufacturers protocol. In brief, cells were fixed, sheared by sonication and immunoprecipitated with anti-NOTCH3 antibody (Cell Signaling, #2889), or anti-H3K27Ac antibody (Abcam, ab4729).
Libraries were constructed using an NEB NEXT kit.

treatment_protocol: Cells were treated with vehicle (DMSO) for 1 day, GSI (compound E 1μM) for 1 day

value: T-Acute Lymphoblastic Leukemia patient derived cell line (T-ALL1)

tag: treated with

value: GSI (compound E 1μM) for 1 day

tag: chip antibody

value: Notch3 ChIP-seq


title: control sham rep4

description: Sample II4


title: TU0085_TCM_negative

value: TCM CD3+CD4+CCR7+CD45RA- T cells


title: T-ALL1 DMSO treated Notch3 ChIP-seq

value: vehicle (DMSO) for 1 day

value: anti-NOTCH3 antibody (Cell Signaling, #2889)


title: T-ALL1 GSI treated H3K27Ac ChIP-seq

value: H3K27Ac ChIP-seq

value: anti-H3K27Ac antibody (Abcam, ab4729)


title: C21808

value: 1 d


title: T-ALL1 DMSO treated H3K27Ac ChIP-seq


title: TU0084_naive_negative

value: NAIVE CD3+CD4+CCR7+CD45RA+ T cells


title: TU0079_TEMRA_negative

value: TEMRA CD3+CD4+CCR7-CD45RA+ T cells


title: TU0079_TEM_negative

value: TEM CD3+CD4+CCR7-CD45RA- T cells


title: TU0084_TCM_negative


title: TU0084_TEMRA_negative


title: 25N

city: Kolkata

first: BIDYUT

last: ROY

state: West bengal

address: 203 bt road

department: human genetics unit

country: India

institute: indian statistical institute

data_processing:
alignment in STAR in paired-end mode; hg19 and gencode v19 references used
read count to gene features by HTSeq
Differential expression calculated by EdgeR
Genome_build: hg19
Supplementary_files_format_and_content: raw count matrix generated by HTSeq in txt

source_name: Gingivo-buccal

extract_protocol:
All prep DNA/RNA extraction kit
Total RNA sequenced
Paired-end library generated and 100+100bp reads were sequenced

tag: adjacent normal tissue


title: TU0079_TCM_negative


title: 26N


title: 27N


title: TU0079_naive_negative


title: 21N


title: 19N


title: TU0057_TEM_negative


title: TU0085_naive_negative


title: 17N


title: 23N


title: 7N


title: control WT rep1

description: Sample I1

value: (DBA/2J x C3HeB/FeJ)F1

value: myocardium, left ventricle


title: TU0084_TEM_negative

value: San Diego Negative


title: 15N


title: TU0054_TEMRA_negative

value: PBMC


title: TU0057_naive_negative


title: 6N


title: TU0054_TEM_negative


title: TU0054_TCM_negative


title: 2625464_TimePoint4_WholeBlood

city: Atlanta

first: Mary

last: Galinski

state: GA

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

institute: Emory University

data_processing:
Bases were called with Illumina RTA (Real-Time Analysis, v2.7.7) with default parameters. Illumina bcl2fastq v2.17.1.14 was used for demultiplexing. FASTQC (v0.10.1) was used to assess data quality, but the data were not filtered at this stage.
Reads were mapped to a composite reference assembly consisting of host, parasite, and ERCC control references with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Genome_build: RNA-Seq reads were mapped to both a host and parasite genome.  Host: An early version of a new  assembly (as of 5/2014) of the rhesus macaque (MacaM assembly, v4.0, created by Aleksey Zimin at the University of Maryland, Rob Norgren at the University of Nebraska Medical Center and their colleagues.  The MacaM assembly has been deposited in GenBank under BioProject accession  PRJNA214746. Parasite: Plasmodium cynomolgi B strain genome assembly was used. The assembly has been deposited in GenBank under the BioProject accession PRJNA187987.
Supplementary_files_format_and_content: Excel files contain raw counts at the gene level, for each individual. Raw counts are further classified by experimental Time Point (1-7), and Specimen Type (Whole Blood).
Supplementary_files_format_and_content: Host and Parasite Raw Read Counts Column headers are defined as follows:    'Gene ID':  Identifiers of all Genes in the annotation.     'Gene Symbol': Symbols of all Genes in the annotation.    'Raw File List / Sample Identifier / Abundances': Samples were sequenced across multiple lanes, some samples were sequenced at extra depth, all fastq files are listed for each sample. Raw read counts of all genes, from the raw files listed in the column header. The raw file names and sample identifer both contain information regarding Specimen Type, NHP ID, and Time Point.      Notes:  There are 48 columns representing specific Time Points for each of the 6 animals.    There is an read count entry per sample for every gene that appears in the annotation. For genes where there was no detection of expression by reads that mapped to their loci, the raw count is 0."

organism:
Macaca mulatta
Plasmodium cynomolgi strain B

source_name: Whole Blood

growth_protocol: Animals approved for use were moved into experimental housing 10 days prior to the start of the experiment.

extract_protocol:
Whole blood (3 ml) was collected in Tempus tubes (Applied Biosystems) that also preserve mRNA; these samples include erythrocytes, platelets and granulocytes in addition to mononuclear lymphocytes.  RNA was extracted using Tempus-Spin RNA isolation kits. The quality of all RNA samples was confirmed using a Bioanalyzer, with an RNA Integrity Number (RIN) greater than 8 recorded for all samples.
Approximately 1 μg of total RNA per sample was converted to double-stranded cDNA using poly-A beads to enrich for mRNA, and Illumina TruSeq Stranded mRNA Sample Prep kits to generate strand-specific libraries.   As a quality control, 92 spike-in RNAs of known concentration and GC proportions (ERCC Spike-In Control, Life Technologies) were added to constitute approximately 1% of the total RNA for each library.  Adapters were ligated to facilitate multiplexed sequencing on an Illumina HiSeq3000 at the Yerkes Genomics Core, aiming for 50 million paired-end 100 base pair (bp) reads per library.

treatment_protocol: During the 100-day period subjects experienced periods of patent and sub-patent infection. The anti-malarial drug artemether was subcuratively administered to subjects after the initial peak of infection, if subjects were not able to self-resolve.  Blood-stage curative artemether was administered to all subjects following peak infection, and following a period of relapse infection.  All peaks were clinically determined for each subject.  The anti-malarial drugs primaquine and chloroquine were administered to all subjects at the end of the study for curative treatment of the liver and blood-stage infections, respectively.

tag: time point

tag: gender

value: Male

tag: non human primate individual id

tag: infected with

value: Plasmodium cynomolgi strain B


title: 2625084_TimePoint5_WholeBlood


title: 2621406_TimePoint7_WholeBlood


title: 27D

tag: primary tumor tissue


title: TU0054_naive_negative


title: TU0053_TEMRA_negative


title: 26D


title: TU0057_TEMRA_negative


title: 2621405_TimePoint7_WholeBlood


title: TU0057_TCM_negative


title: TU0053_TCM_negative


title: 2621404_TimePoint5_WholeBlood


title: 23D


title: 2621402_TimePoint5_WholeBlood


title: TU0053_naive_negative


title: 2621403_TimePoint7_WholeBlood


title: 21D


title: GS0213_TEMRA _Negative

value: Sri Lanka Negative


title: 19D


title: 2621401_TimePoint4_WholeBlood


title: 5N


title: GS0106_TEMRA _Negative


title: 15D


title: 17D


title: 2N


title: 2621399_TimePoint5_WholeBlood


title: GS0151_TEMRA _Secondary

value: Sri Lanka Secondary


title: 6D


title: GS0121_TEMRA _Secondary


title: 2621398_TimePoint4_WholeBlood


title: GS0072_TEMRA _Secondary


title: 25D


title: 2621397_TimePoint3A_WholeBlood


title: TU0053_TEM_negative


title: 5D


title: 2D


title: 2621396_TimePoint7_WholeBlood


title: 7D


title: GS00144_TEMRA _Secondary


title: GS00144_TEM _Secondary


title: 2621384_TimePoint2_WholeBlood


title: 2621385_TimePoint3_WholeBlood


title: GS00144_NAIVE _Secondary


title: 2621400_TimePoint3A_WholeBlood


title: GS00144_TCM _Secondary

value: TCM CD3+CD4+CCR7+CD45RA- T cells


title: 2621382_TimePoint1_WholeBlood


title: GS0065_TEMRA _Secondary


title: 2621381_TimePoint1A_WholeBlood


title: HCT-116 GL2

city: Stanford

first: Mark

middle: M.

last: Davis

state: CA

address: 279 Campus Drive

department: Department of Microbiology and Immunology

institute: Stanford University

data_processing:
RNA-seq reads were aligned to the hg19 genome using TopHat version v1.4.1 with parameters  -M -n 2  --library-type fr-secondstrand --solexa-quals -r 180  --mate-std-dev 130  -G genes.gtf --transcriptome-index ts_ucsc
FPMK values were calculated using the CuffDiff program version 1.3.0
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files were created from TopHat output files, we separate signals from sense (forward) strand and anti-sense (reverse) strand.

source_name: HCT-116 cell line

growth_protocol: HeLa nd HCT-116 cells were grown in DMEM media containing 10% FCS and antibiotics.

extract_protocol:
total RNA was extarcted using TRIZOL according to manufacturer's protocl
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After transfection of LNA GL2, CAGMM, or CAGPM using Lipofectamine 2000 for 24 hrs, each RNA were extracted

tag: cell line

tag: transfection

value: LNA GL2


title: Hela CAGPM

source_name: HeLa cell line

value: HeLa

value: LNA CGPM


title: Hela CAGMM

value: LNA CAGMM


title: 2621380_TimePoint4_WholeBlood


title: Hela GL2


title: HCT-116 CAGPM


title: GS0065_TEM _Secondary


title: GS0065_Naive _Secondary


title: GS0087_TEMRA _Secondary


title: GS0087_TEM _Secondary


title: 2621379_TimePoint3A_WholeBlood


title: 2621377_TimePoint2_WholeBlood


title: 2621378_TimePoint3_WholeBlood


title: GS0087_TCM _Secondary


title: 2621376_TimePoint1B_WholeBlood


title: GS0065_TCM _Secondary


title: GS0087_Naive _Secondary


title: 2736880_TimePoint7_Whole Blood

data_processing:
Bases were called with Illumina RTA (Real-Time Analysis, v2.7.7) with default parameters. Illumina bcl2fastq v2.17.1.14 was used for demultiplexing. FASTQC (v0.10.1) was used to assess data quality, but the data were not filtered at this stage.
Reads were mapped to a composite reference assembly consisting of host, parasite, and ERCC control references with STAR (v2.5.2b) with default alignment parameters. Note all values for ERCC abundances will be zero as no spike ins were included in sequenced samples. See readme for details.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Genome_build: RNA-Seq reads were mapped to both a host and parasite genome.  Host: An early version of a new  assembly (as of 5/2014) of the rhesus macaque (MacaM assembly, v4.0, created by Aleksey Zimin at the University of Maryland, Rob Norgren at the University of Nebraska Medical Center and their colleagues.  The MacaM assembly has been deposited in GenBank under BioProject accession  PRJNA214746. Parasite: Plasmodium cynomolgi B strain genome assembly was used. The assembly has been deposited in GenBank under the BioProject accession PRJNA187987. The P. cynomolgi B strain genome assembly and annotation was used because a P. cynomolgi strain ceylonensis genome assembly and annotation of equal quality was not available. See reame for details.
Supplementary_files_format_and_content: Excel files contain raw counts at the gene level, for each individual. Raw counts are further classified by experimental Time Point (1-7), and Specimen Type (Whole Blood).
Supplementary_files_format_and_content: Host and Parasite Raw Read Counts Column headers are defined as follows:    'Gene ID':  Identifiers of all Genes in the annotation.     'Gene Symbol': Symbols of all Genes in the annotation.    'Raw File List / Sample Identifier / Abundances': Samples were sequenced across multiple lanes, some samples were sequenced at extra depth, all fastq files are listed for each sample. Raw read counts of all genes, from the raw files listed in the column header. The raw file names and sample identifer both contain information regarding Specimen Type, NHP ID, and Time Point.      Notes:  There are 25 columns representing 5 animals for Time Points T01, T01B, and, T02, T03 and T07.    There is an read count entry per sample for every gene that appears in the annotation. For genes where there was no detection of expression by reads that mapped to their loci, the raw count is 0."

organism:
Macaca mulatta
Plasmodium cynomolgi ceylonensis

extract_protocol:
Whole blood (3 ml) was collected in Tempus tubes (Applied Biosystems) that also preserve mRNA; these samples include erythrocytes, platelets and granulocytes in addition to mononuclear lymphocytes.  RNA was extracted using Tempus-Spin RNA isolation kits. The quality of all RNA samples was confirmed using a Bioanalyzer, with an RNA Integrity Number (RIN) greater than 8 recorded for all samples.
Approximately 1 μg of globin depleted total RNA per sample was converted to double-stranded cDNA following poly-A beads selection to enrich for mRNA, and Illumina TruSeq Stranded mRNA Sample Prep kits to generate strand-specific libraries.  Adapters were ligated to facilitate multiplexed sequencing on an Illumina HiSeq3000 at the Yerkes Genomics Core, aiming for 50 million paired-end 100 base pair (bp) reads per library.

treatment_protocol: The experiment included, 8 pre-inoculation days, 49 experiment days, and 4 post-experiment days.  Pre- and post-experiment days were used to prepare subjects and administer post-experiment curative treatments respectively.  The anti-malarial drug artemether was subcuratively administered to subjects at the initial peak of infection, if subjects were not able to self-resolve their parasitemias.  Peak infection was determined clinically for each subject.  The anti-malarial drugs primaquine and chloroquine were administered to all subjects at the end of the study for curative treatment of the liver and blood-stage infections, respectively.

value: Plasmodium cynomolgi ceylonensis


title: 2736899_TimePoint7_Whole Blood


title: 2621375_TimePoint1_WholeBlood


title: 2621383_TimePoint1B_WholeBlood


title: 2621374_TimePoint1A_WholeBlood


title: GS0231_TEMRA _Secondary


title: GS0231_TEM _Secondary


title: 2736861_TimePoint7_Whole Blood


title: 2736842_TimePoint7_Whole Blood


title: 2736823_TimePoint7_Whole Blood


title: HCT-116 CAGMM


title: 2621371_TimePoint3_WholeBlood


title: 2621370_TimePoint2_WholeBlood


title: GS0231_Naive _Secondary

value: NAIVE CD3+CD4+CCR7+CD45RA+ T cells


title: 2706926_TimePoint3_Whole Blood


title: GS0105_TEMRA _Secondary

value: TEMRA CD3+CD4+CCR7-CD45RA+ T cells


title: 2621369_TimePoint1B_WholeBlood


title: 2706888_TimePoint3_Whole Blood


title: 2621368_TimePoint1_WholeBlood


title: GS0166_TEMRA _Negative


title: GS0105_TCM _Secondary


title: 2706869_TimePoint3_Whole Blood


title: GS0105_NAIVE _Secondary


title: 2621367_TimePoint1A_WholeBlood


title: 2621366_TimePoint3_WholeBlood


title: 2621365_TimePoint2_WholeBlood


title: GS0272_TEMRA _Secondary


title: 2621373_TimePoint3A_WholeBlood


title: 2691651_TimePoint2_Whole Blood


title: GS0272_TEM _Secondary

value: TEM CD3+CD4+CCR7-CD45RA- T cells


title: 2691670_TimePoint2_Whole Blood


title: 2621372_TimePoint5_WholeBlood


title: GS0105_TEM _Secondary


title: GS0231_TCM _Secondary


title: 2621364_TimePoint1B_WholeBlood


title: GS0272_TCM _Secondary


title: 2691632_TimePoint2_Whole Blood


title: 2621363_TimePoint1_WholeBlood


title: 2706907_TimePoint3_Whole Blood


title: GS0272_NAIVE _Secondary


title: 2621361_TimePoint3_WholeBlood


title: 2621362_TimePoint1A_WholeBlood


title: 2621360_TimePoint2_WholeBlood


title: 2691594_TimePoint2_Whole Blood


title: 2691613_TimePoint2_Whole Blood


title: 2679318_TimePoint1B_Whole Blood


title: 2679299_TimePoint1B_Whole Blood


title: 2706850_TimePoint3_Whole Blood


title: 2679280_TimePoint1B_Whole Blood


title: 2621358_TimePoint1_WholeBlood


title: 2621359_TimePoint1B_WholeBlood


title: 2621356_TimePoint3A_WholeBlood


title: 2621357_TimePoint1A_WholeBlood


title: 2650372_TimePoint1_Whole Blood


title: 2679242_TimePoint1B_Whole Blood


title: 2650353_TimePoint1_Whole Blood


title: 2621353_TimePoint1B_WholeBlood


title: 2621354_TimePoint2_WholeBlood


title: 2650315_TimePoint1_Whole Blood


title: 2650296_TimePoint1_Whole Blood


title: 2621352_TimePoint1_WholeBlood


title: 2621351_TimePoint1A_WholeBlood


title: 2650334_TimePoint1_Whole Blood


title: Output RNA, replicate #5

status: Public on Sep 26 2017

city: Cambridge

first: Xinchen

last: Wang

address: 32 Vassar St, D514

institute: MIT

description:
RNA output sequencing only 3' UTR of reporter gene
processed data file:
HiDRA_RNAsignal.bw
HiDRA_RNAtoDNARatio_0.1Pseudocount.bw
HiDRA_counts_per_fragmentgroup.txt

data_processing:
Reads were split by sample barcode and aligned to hg19 using bowtie2 (v2.2.9) with flags -p 6, -q and --phred33.
Alignments were filtered using grep to remove unaligned fragments, and remove mitochondrial reads
We filtered reads mapping to multiple genomic locations in samtools v1.3.1 (-q 30 flag) and removed reads mapping to ENCODE blacklist regions (bedtools v2.26.0)
Finally, only fragments with size between 100-600nt were kept for further analysis
illumina MiSeq reads were first processed with cutadapt as read length was longer than minimum fragment size
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for signal tracks were generated using genomeCoverageBed (bedtools), unionBedGraphs (bedtools), and bedGraphToBigWig (UCSC utilities). Matrix of count information for all samples and text file listing assignment of fragments to SNPs for illumina MiSeq_Fragment_to_SNP_group_by_90percent_overlap was generated using custom shell and perl scripts. Please see first lines of text files for more detailed description of processed files.

source_name: GM12878_output RNA

growth_protocol: Cells were grown in suspension in RPMI 1640 Medium with GlutaMAX Supplement with 15% fetal bovine serum and 1% pen/strep added in. Cells were split every 2-3 days to maintain a density between 2x10^5 and 1x10^6 cells/mL.

extract_protocol:
RNA was collected using the Qiagen RNEasy Maxi kit following manufacturer's instructions and performing the optional on-column Dnase treatment. PolyA+ RNA was extracted using the Oligotex mRNA Midi kit.
We used a custom library construction protocol, see Methods section in paper for detailed protocol. Briefly, for RNA, following PolyA+ selection we performed reverse transcription using a sgGFP reporter gene-specific primer and performed PCR to add barcoded Illumina sequencing adapters. For plasmid reporter library, we directly performed PCR to add sequencing adapters off of the plasmid.

treatment_protocol: RNA was extracted 24 hours post-transfection from GM12878 cells. Transfection was performed with 100uL tips using the Neon electroporation system.

tag: cell type

value: lymphoblastoid cell line

tag: molecule subtype

value: RNA


title: Output RNA, replicate #4


title: Output RNA, replicate #2


title: Output RNA, replicate #1


title: Input plasmid library, replicate #5

description:
Input plasmid library for transfection
processed data file:
HiDRA_Plasmidsignal.bw
HiDRA_RNAtoDNARatio_0.1Pseudocount.bw
HiDRA_counts_per_fragmentgroup.txt

source_name: GM12878_input plasmid library

extract_protocol:
Plasmid DNA was extracted from MegaX DH10B electrocompetent bacteria transformed with cloned library using Qiagen's Plasmid Plus MegaPrep Kit following manufacturer's instructions
We used a custom library construction protocol, see Methods section in paper for detailed protocol. Briefly, for RNA, following PolyA+ selection we performed reverse transcription using a sgGFP reporter gene-specific primer and performed PCR to add barcoded Illumina sequencing adapters. For plasmid reporter library, we directly performed PCR to add sequencing adapters off of the plasmid.

value: Plasmid Reporter Library


title: Input plasmid library, replicate #4


title: 2679261_TimePoint1B_Whole Blood


title: Input plasmid library, replicate #2


title: Input plasmid library, replicate #1


title: Mll2KO_RNA_1

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: total RNA

data_processing:
Basecalls were performed using  bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC mm9 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC mm9 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

source_name: embryonic stem cell

growth_protocol: ESCs were grown in N2B27 media supplemented with MEK inhibitor, GSK3 inhibitor, and LIF (2i/LIF). EBs were generated via the hanging drop method in serum-containing media without 2i/LIF.

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen) following manufacturer's instructions.
For ChIP, ESCs were fixed in 1% formaldehyde, followed by quenching and cell lysis before chromatin sonication using a E220 focused-ultrasonicator (Covaris). Sheared chromatin was then subjected to immunoprecipitation, and immunoprecipitated DNA was then washed, eluted, reverse cross-linked, and purified prior to submission for library preparation. For EB ChIP experiments, EBs were dounce homogenized prior to sonication.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and IP samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit.

value: embryonic stem cell

tag: genotype/variation

value: Mll2 Knockout/KO


title: Mll2KO_RNA_2

description: total RNA


title: Mll2KO_EBD6_RNA_2

description: total RNA


title: 2621355_TimePoint3_WholeBlood

value: Male

value: Plasmodium cynomolgi strain B


title: WT_EBD6_RNA_4

description: total RNA

value: Wildtype/WT


title: Mll2KO_EBD6_RNA_1

description: total RNA


title: WT_EBD6_RNA_3

description: total RNA


title: Mll2KO_ChIP_H3K4me3

description: fragmented genomic DNA

value: H3K4me3 (Homemade, #28)


title: Mll2KO_EBD6_ChIP_H3K4me3

description: fragmented genomic DNA

value: H3K4me3 (Homemade, #519)


title: WT_EBD6_ChIP_H3K4me3_3

description: fragmented genomic DNA


title: WT_RNA_5

description: total RNA


title: Set1AdSET_ChIP_Set1A_2

description: fragmented genomic DNA

value: Set1A SET deletion

value: SET1A (Homemade, #919)


title: Set1AdSET_ChIP_Set1A_1

description: fragmented genomic DNA


title: WT_ChIP_H3K4me3_3

description: fragmented genomic DNA


title: Output RNA, replicate #3


title: WT_RNA_4

description: total RNA


title: WT_ChIP_input_1

description: fragmented genomic DNA


title: Input plasmid library, replicate #3


title: WT_EBD6_RNA_2

description: total RNA


title: WT_RNA_3

description: total RNA


title: WT_EBD6_ChIP_input_1

description: fragmented genomic DNA


title: WT_EBD6_ChIP_input_2

description: fragmented genomic DNA


title: WT_RNA_2

description: total RNA


title: WT_EBD6_RNA_1

description: total RNA


title: WT_EBD6_ChIP_H3K4me3_1

description: fragmented genomic DNA


title: WT_ChIP_input_4

description: fragmented genomic DNA


title: WT_ChIP_input_2

description: fragmented genomic DNA


title: WT_ChIP_input_3

description: fragmented genomic DNA


title: WT_ChIP_Set1A_1

description: fragmented genomic DNA


title: WT_ChIP_H3K4me3_2

description: fragmented genomic DNA


title: WT_ChIP_H3K4me3_2_less

description: fragmented genomic DNA


title: WT_ChIP_Pol2_1

description: fragmented genomic DNA

value: Rpb1 (CST, D8L4Y)


title: WT_RNA_1

description: total RNA


title: WT_ChIP_H3K4me3_1

description: fragmented genomic DNA


title: WT_ChIP_H3K4me2_1

description: fragmented genomic DNA

value: H3K4me2 (Homemade, #27)


title: WT_ChIP_H3K4me2_2

description: fragmented genomic DNA


title: WT_ChIP_H3K4me1_1

description: fragmented genomic DNA

value: H3K4me1 (Homemade, #24)


title: WT_EBD6_ChIP_H3K4me3_2

description: fragmented genomic DNA


title: Set1AdSET_RNA1_1

description: total RNA


title: Set1AdSET_EBD6_RNA2_2

description: total RNA


title: Set1AdSET_EBD6_RNA2_1

description: total RNA


title: Set1AdSET_RNA1_2

description: total RNA


title: Set1AdSET_RNA2_1

description: total RNA


title: Set1AdSET_RNA2_2

description: total RNA


title: Set1AdSET_EBD6_RNA1_2

description: total RNA


title: WT_ChIP_Set1A_2

description: fragmented genomic DNA


title: Set1AdSET_EBD6_ChIP_input_2

description: fragmented genomic DNA


title: Set1AdSET_EBD6_ChIP_H3K4me3_2

description: fragmented genomic DNA


title: Set1AdSET_ChIP_input_2

description: fragmented genomic DNA


title: WT_ChIP_H3K4me3_1_less

description: fragmented genomic DNA


title: Set1AdSET_EBD6_RNA1_1

description: total RNA


title: Set1AdSET_EBD6_ChIP_input_1

description: fragmented genomic DNA


title: Set1AdSET_EBD6_ChIP_H3K4me3_1

description: fragmented genomic DNA


title: Set1AdSET_ChIP_input_1

description: fragmented genomic DNA


title: Set1AdSET_ChIP_Pol2_2

description: fragmented genomic DNA


title: Set1AdSET_ChIP_Pol2_1

description: fragmented genomic DNA


title: Set1AdSET_ChIP_H3K4me2_2

description: fragmented genomic DNA


title: Set1AdSET_ChIP_H3K4me3_1

description: fragmented genomic DNA


title: Set1AdSET_ChIP_H3K4me2_1

description: fragmented genomic DNA


title: Set1AdSET_ChIP_H3K4me1_2

description: fragmented genomic DNA


title: WT_ChIP_H3K4me1_2

description: fragmented genomic DNA


title: Set1AdSET_ChIP_H3K4me1_1

description: fragmented genomic DNA


title: moDCs of PBS4

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

description: Sample name: Sample_PBS4

data_processing:
Trimming reads with Trimmomatic 0-32
Alignment with STAR (STAR_2.3.0_r291)
Count reads with HT-Seq 0.5.3 with Ensembl72 gtf annotation
Differential Expression analysis with limma/voom
Genome_build: UCSC mm10 (downloaded June, 2012)
Supplementary_files_format_and_content: xlsx file with log2 Normalized Values generated with voomWithQualityWeights function in limma package for expressed genes

source_name: mouse CNS with MOG35-55 EAE

extract_protocol:
RNeasy Plus Micro kit (Qiagen) was used according manufaturer's protocol to extract RNA from sorted moDCs. Quantity and quality of total RNA was assessed by Bionanalyzer (Agilent). All samples had a RIN≥8.
Amplification of cDNA from total RNA was performed using the Ovation RNA-Seq system V2 (Nugen). Then, cDNA was fragmented and ligated into a sequencing library using Ovation(R) Ultralow Library System V2 | NuGEN. Libraries were PCR amplified for 12 cycles and sequenced on an Illumina NextSeq 500 System with TruSeq reagent kits and software, generating single-end 150 base-pair reads.

treatment_protocol: CNS leukocytes were isolated (7 days post-treatment) from hindbrain and spinal cord of PBS- of NPC- intrathcally transplanted EAE mice (4 days after onset). Extracted CNS tissue was cut into small pieces, and incubated for 30 minutes with 0.2 mg/ml collagenase type IV (Sigma-Aldrich) and afterwards passed through a 19G syringe to obtain a homogeneous cell suspension. CNS cell suspensions were further enriched by a Percoll gradient. Monocyted derived- dendritic cells (moDCs) were FACS sorted as CD45hiCD11b+Ly6G-Ly6C+CD11cintMHCII+.

tag: strain

tag: disease state

value: experimental autoimmune encephalomyelitis (EAE)

tag: cell population

tag: tissue source

value: hindbrain and spinal cord

tag: condition

value: ic treated with PBS 10μL


title: moDCs of NPCB

description: Sample name: Sample_NPCB

value: ic treated with 10^6 NPCs in PBS 10μL


title: moDCs of PBS3

description: Sample name: Sample_PBS3


title: HBCx-22 PDX treated with RAD140 #6

city: Waltham

first: ZiYang

last: Yu

address: 950 Winter Street

institute: Radius Health

description:
RAD140 tumor #6
12_L7.D710

data_processing:
De-multiplexed FASTQ files were aligned to HG19 human genome using the STAR aligner version 2.4 and genetic features were quantified using RSEM version 1.2.14.
Genome_build: HG19

source_name: HBCx-22 PDX treated with RAD140

growth_protocol: HBCx-22 PDX model were established by implanting tumor fragments subcutaneously in the flank female athymic nude mice (Foxn1nu).

extract_protocol:
Total RNA from xenograft samples and cells was extracted using the RNeasy Mini Kit (Qiagen), with a DNase incubation step included to ensure complete removal of genomic DNA.
Purified RNA samples were converted into cDNA libraries using the TrueSeq Stranded mRNA sample preparation kit (Illumina, San Diego, CA). Libraries were quantified, normalized, and pooled before being subjected to HiSeq 2×50bp paired end sequencing on an Illumina sequencing platform.

treatment_protocol: Mice were randomized based on tumor size and allocated to treatment groups and then treated with vehicle (0.5% carboxylmethylcellulose, CMC, p.o.) or RAD140 100 mg/kg. Treatment lasted 51 days before mice were euthanized and tumor specimen were snapfrozen.

tag: xenograft host

value: female athymic nude mice (Foxn1nu)

tag: tissue

value: breast cancer patient-derived xenografts (PDX)

tag: tissue type

value: snapfrozen xenograft specimen

tag: tag

value: Hormone receptor positive


title: HBCx-22 PDX treated with RAD140 #4

description:
RAD140 tumor #4
10_L7.D708


title: HBCx-22 PDX treated with RAD140 #5

description:
RAD140 tumor #5
11_L7.D709


title: moDCs of NPCD

description: Sample name: Sample_NPCD


title: moDCs of PBS2

description: Sample name: Sample_PBS2


title: moDCs of NPCC

description: Sample name: Sample_NPCC


title: moDCs of PBS1

description: Sample name: Sample_PBS1


title: HBCx-22 PDX treated with vehicle #2

description:
veh tumor #2
8_L6.D706

source_name: HBCx-22 PDX treated with vehicle


title: moDCs of NPCA

description: Sample name: Sample_NPCA


title: HBCx-22 PDX treated with vehicle #3

description:
veh tumor #3
9_L7.D707


title: Set1AdSET_ChIP_H3K4me3_2

description: fragmented genomic DNA

value: embryonic stem cell

tag: chip antibody


title: HFD.DIEC.5

city: Pittsburgh

first: Zheng

last: Kuang

state: PA

address: 4400 Fifth Avenue

department: Biological Sciences

institute: Carnegie Mellon University

description:
C57BL/6 Nfiil3 ΔIEC
Processed data file: otus.fa.OTU.txt

data_processing:
Library strategy: 16S DNA-seq
Sequences were joined, depleted of barcodes then sequences <150bp removed, sequences with ambiguous base calls removed. Sequences were denoised, OTUs generated and chimeras removed. Operational taxonomic units (OTUs) were defined by clustering at 3% divergence (97% similarity). Final OTUs were taxonomically classified using BLASTn against a curated database derived from RDPII and NCBI (www.ncbi.nlm.nih.gov, http://rdp.cme.msu.edu).
Genome_build: RDPII and NCBI
Supplementary_files_format_and_content: otus.fa.OTU.txt: Tab-delimited text file with OTU counts for each sample.

organism: mouse gut metagenome

source_name: Feces, Nfiil3 ΔIEC, high-fat diet, ZT4

extract_protocol:
Fecal DNA was extracted and purified from freshly collected feces using the FastDNA Spin Kit (MP Biomedicals 116560-200).
Sequencing libraries were prepared using the HotStarTaq Plus Master Mix Kit (Qiagen).

treatment_protocol: High-fat diet.

tag: strain/background

value: Nfiil3 <delta>IEC

value: Feces

tag: diet

value: High fat

tag: circadian time


title: HFD.DIEC.4


title: HFD.FLOX.1

description:
C57BL/6 Nfiil3 fl/fl
Processed data file: otus.fa.OTU.txt

source_name: Feces, Nfiil3 fl/fl, high-fat diet, ZT4

value: Nfiil3 fl/fl


title: HFD.FLOX.4


title: HFD.FLOX.3


title: HBCx-22 PDX treated with vehicle #1

description:
veh tumor #1
7_L6.D705


title: HFD.FLOX.5


title: Chow.FLOX.5

source_name: Feces, Nfiil3 fl/fl, chow diet, ZT4

treatment_protocol: Chow diet.

value: Chow


title: HFD.FLOX.2


title: HFD.DIEC.3


title: Chow.FLOX.3


title: Chow.FLOX.4


title: Chow.FLOX.2


title: HFD.DIEC.1


title: HFD.DIEC.2


title: Chow.FLOX.1


title: Chow.DIEC.2

source_name: Feces, Nfiil3 ΔIEC, chow diet, ZT4


title: Chow.DIEC.5


title: Chow.DIEC.1


title: Chow.DIEC.4


title: Chow.DIEC.3


title: cic_wts_d9_S3_mRNA

city: Vienna

first: Jelle

last: Jacobs

address: Campus-Vienna-Biocenter 1

department: VBC

country: Austria

institute: Institute of molecular Pathology

description:
mRNA
Processed data file: RNA_seq_rawcounts_18samples.tsv

data_processing:
Cleaning (fastq-mcf).
Mapping to the dm6 genome using bowtie2 tophat2.
Obtaining raw counts per gene using htseq-count.
Library size normalisation and differential expression using R DESeq2.
Genome_build: Drosophila melanogaster FlyBase version 6.03
Supplementary_files_format_and_content: RNA_seq_rawcounts_18samples.tsv: Tab-separated text file includes raw counts matrix dmel 6.03.

organism: Drosophila melanogaster

source_name: wing discs

growth_protocol: Normal fly food, 25 degrees.

extract_protocol:
Wing discs were collected from 12-35 larvae under sterile conditions and immediately lysed. RNA extraction was done using Ambion RNAqueous Micro kit.
Illumina TruSeq mRNA Library Prep reagents used according to the protocol recommended by the manufacturer.

tag: treatment

value: hand dissections

value: wing discs

value: y w ubxflp/ y w; FRT82B M(3) ubiGFP/ FRT82B cicQ474X wts149

tag: age

value: 3rd instar-day9


title: cic_wts_d9_S2_mRNA


title: wts149_d9_S1_mRNA

value: y w ubxflp/ y w; FRT82B M(3) ubiGFP/ FRT82B wts149


title: wts149_d5_S1_mRNA

value: 3rd instar-day5


title: wts149_d9_S3_mRNA


title: wts149_d9_S2_mRNA


title: wts149_d5_S2_mRNA


title: wts149_d5_S3_mRNA


title: cic_wts_d5_S3_mRNA


title: cic_wts_d9_S1_mRNA


title: cic_d5_S2_mRNA

value: y w ubxflp/ y w; FRT82B M(3) ubiGFP/ FRT82B cicQ474X


title: cic_d5_S1_mRNA


title: FRT82B_d5_S3_mRNA

value: y w ubxflp/ y w; FRT82B M(3) ubiGFP/ FRT82B


title: FRT82B_d5_S2_mRNA


title: cic_wts_d5_S2_mRNA


title: cic_d5_S3_mRNA


title: FRT82B_d5_S1_mRNA


title: cic_wts_d5_S1_mRNA


title: Inj-6

city: Portland

first: Sean

middle: David

last: Speese

state: Oregon

address: 3181 SW Sam Jackson Road

department: Neurology

institute: OHSU-Jungers Center for Neurosciences Research

description: Injured - All legs, wings and head severed 5 hours prior to VNC dissection

data_processing:
RNA-seq alignement was performed with PerkinElmer GeneSifter Analysis Edition (GSAE) software.  Briefly, HiSeq 2500 reads were uploaded to Geospiza's server for alignment to the Drosophila melanogaster genome (Release 5.57) via the Burrow-Wheeler Alignment tool.  Raw read counts were transformed to Transcripts Per Kilobase Million (TPM) via first dividing by the length of the longest annotated transcript for a given gene and then dividing by the number of mapped reads for that particular biological replicate, thereby normalizing for differences in transcript length and read depth.  Before statistical analysis, the gene list was filtered to ensure at least one group (Injured or UnInjured) had an average TPM value >2. This produced a list of 9,364 expressed genes that were analyzed for differential expression via the Shiny Transcriptome Analysis Resource Tool (START) application.
Briefly, START performs TMM normalization, then transforms with mean-variance modelling at the observational level (voom) and then tests for group effects via a linear regression model. Lastly, false discovery rate is corrected via the Benjamini-Hochberg procedure.  In our studies, we utilized a conservative adjusted p-value of <0.03 and a fold change (FC) of >1.2 or >log2FC=.263 for considering differential gene expression significant.
Genome_build: Drosophila melanogaster (Release 5.57)

source_name: Dissected Ventral Nerve Cord (VNC)

growth_protocol: Adult w1118 animals (3-10 days old) were reared on standard culture food at 25 degrees C. until the time of the experiment.

extract_protocol:
After collecting 60-80 dissected VNCs on dry ice, the tissue wash crushed in 500ul of Trizol with glass beads and a pestle.  This preparation was then stored at -80 degrees until all the samples were ready for RNA extraction.  RNA extraction was performed by first spinning the crushed material at 11,000G for 10 minutes at 4 degrees C to pellet cuticle and lipids.  Trizol supernatant was pulled off the pellet and 1/5 volume of chloroform was added and mixed in a 5’ Prime- heavy phase lock gel and centrifuged.  The aqueous phase was pulled off and the RNA was cleaned and isolated on a Zymo Research RCC5 column.  An on column DNAse digestion was performed to degrade genomic DNA.   The RNA was quantified using the Qubit fluorometer before sending total RNA samples to the Massively Parallel Sequencing Shared Resource (MPSSR) at Oregon Health and Science University (OHSU) for library preparation.
Briefly, total RNA concentration and sample integrity was assessed via running on an Agilent RNA 6000 Pico chip on an Agilent Technologies 2100 Bioanalyzer instrument.  Following quantification and quality control, 325ng of total RNA was subjected to ribosomal RNA reduction via Epicenter’s Ribo-Zero™ Gold kit (Human/Mouse/Rat).  The output of this was taken into Illumina’s TruSeq® RNA Sample Preparation v2, beginning with the RNA fragmentation step.  It should be noted that a poly(A) selection was not performed due to limited starting total RNA. Barcode indexing adapters were ligated and all 10 samples (5 control and 5 injured) were sequenced (100 bp single reads) on a single flow cell lane on the Illumina HiSeq 2500 Seqeuncer

treatment_protocol: Uninjured controls were starved for 5 hours in 2% agar vials before the VNC was dissected and immediately frozen on dry ice (~ 2-3 minutes for dissection and freezing of a single VNC).  Injured animals had all 6 legs, 2 wings and the head severed with Vanas scissors.  The animals were then placed ventral side up on a 2% agar plate and kept at 98% humidity for 5 hours, after which the VNC was dissected and frozen.

tag: sex composition

value: ~30 males and 30 females

value: 3-10 day old adults

value: Dissected Ventral Nerve Cord


title: Inj-3


title: Inj-5


title: Inj-4


title: No_Inj-G

description: No Injury - Adults starved for 5 hours before VNC dissection


title: No_Inj-D


title: No_Inj-C


title: sp1

city: Guangzhou

first: Ganlin

last: Xu

address: CB

institute: shbiochip

data_processing:
RNA-Seq of E. coli were done using blind and fit-only parameter in DE-Seq pakage
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
first strand cDNA was performed by the use of SuperScriptII and the second strand cDNA synthesis was done before end-pair and dA-tailing
Reads longer than 25 nt and ≤ 2 N (ambiguous nucleotides) were preserved.
Using blind and fit-only parameter in DE-Seq pakage, expressions of genes in all samples were changed to count per gene, using RNA-Seq protocol on Illumina HiSeq2500 platform
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

organism: Escherichia coli

source_name: Broiler Fecal

growth_protocol: Strains were harvested in MH broth at log phase

extract_protocol:
Total RNAs were extracted from the bacterial isolates using TRIzol
Following "TruSeq RNA Sample Preparation Guide".

treatment_protocol: No treatment

value: Poultry E. coli Virulent and multidrug resistant


title: sp2


title: ATCC3

source_name: Human

value: E. coli ATCC 25922


title: No_Inj-B


title: Mafb_HA-Input

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

description:
Mafb-HA overexpressed, none
Mafb-HA-ChIP_peaks.txt

data_processing:
Sequenced reads were aligned to the mouse (mm10) reference genome with TopHat (version 2.0.12)
The aligned reads were used to quantify mRNA expression by using HTSeq-count (version 0.6.1)
DESeq2 (Love et al., 2014) was used to identify DEGs across the samples.
Genome_build: mm10
Supplementary_files_format_and_content: Xlsx file include FPKM values for each sample / (Sample 19/20) tab-delimited text file include peaks called by Bowtie2 followed by HOMER analysis.

source_name: Mile Sven1 mouse endothelial cells

growth_protocol: (Sample 19/20) MS1 mouse pancreas ECs (CRL-2279; ATCC) were cultured in DMEM medium supplemented with 5% fetal calf serum (FCF) at 37°C and 5% CO2.

extract_protocol:
Mouse retinas were isolated, immersed in liquid nitrogen immediately to snap freeze, and stored at -80 °C for later use. We added 400μl of polysome buffer (50 mM Tris, pH 7.5, 100 mM KCl, 12 mM MgCl2, 1% Nonidet P-40, 1mM DTT, 200 U/ml RNasin, 1 mg/ml heparin, 100 μg/ml cyclohexamide, and 1x protease inhibitor mixture) to each sample and disrupted the tissue in 1.5 ml microcentrifuge tubes using pellet pestles (749540-0000; Kimble Chase). Postmitochondrial supernatant was formed by centrifugation for 10 minutes at 12,000 rpm at 4 °C and 10μl of the supernatant were saved for input. For IP against HA, we added 25μl of anti-HA antibody-conjugated magnetic beads (M180-11; MBL) to the retinal supernatant prior to incubation on an orbital shaker at 4°C overnight. IP beads were washed for four times with high-salt buffer (50 mM Tris, pH 7.5, 300 mM KCl, 12 mM MgCl2, 1% Nonidet P-40, 1mM DTT, and 100 μg/ml cyclohexamide) and resuspended in 350μl of RLT plus buffer plus β-mercaptoethanol. Total RNAs were extracted using RNeasy Micro kit (Qiagen) according to manufacturer’s instructions.
RNA library construction was performed with the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero (Illumina) according to the manufacturer’s instructions.
RNA-Seq / (Sample 19/20) ChIP-Seq

treatment_protocol: (Sample 19/20) HA-tagged Mafb construct was amplified by PCR, sub-cloned into pCR8/GW/TOPO (Invitrogen), and cloned with pLEX_307 (Addgene, #41392) by an LR recombination reaction. To produce lentiviruses, HEK293 cells were plated at a density of 8 x 106 per 10 cm dish. On the next day, the cells were transfected with 3μg of psPAX2 (Addgene, #12260), 1.5μg of pMD2.G (Addgene, #12259) and 4.5μg of lentiviral vector pLEX_307-HA-Mafb using 27μl Fugene 6 in 600µl Opti-MEM per dish. Virus-containing supernatants were collected at 24 hour, filtered through a 0.4-µm PVDF filter (Millipore), concentrated at 20,000 rpm for 2 hours using a optima L-100 XP ultracentrifuge (Beckman Coulter), re-suspended in knockout DMEM and then stored at -80°C until use. The lentivirus-infected cells were then subcultured and selected in puromycin (Sigma) or blasticidin (Calbiochem) to generate stable cell lines.

value: pancreas


title: Inj-1


title: No_Inj-A


title: ATCC2


title: P6-MafbcKO_rEC_rep2

description:
PdgfbiCre-Ribotag
MafbcKO_all_FPKMs.xlsx

source_name: retinal endothelial cells

value: retinal endothelial cells

value: postnatal day 6


title: Mafb_HA-ChIP

description:
Mafb-HA overexpressed, anti-HA IP
Mafb-HA-ChIP_peaks.txt


title: P50_rEC_rep2

description:
PdgfbiCre-Ribotag
rEC_all_FPKMs.xlsx

value: postnatal day 50


title: P50_rEC_rep1

description:
PdgfbiCre-Ribotag
rEC_all_FPKMs.xlsx


title: P21_rEC_rep2

description:
PdgfbiCre-Ribotag
rEC_all_FPKMs.xlsx

value: postnatal day 21


title: P10_rEC_rep2

description:
PdgfbiCre-Ribotag
rEC_all_FPKMs.xlsx

value: postnatal day 10


title: P21_rEC_rep1

description:
PdgfbiCre-Ribotag
rEC_all_FPKMs.xlsx


title: P15_rEC_rep3

description:
PdgfbiCre-Ribotag
rEC_all_FPKMs.xlsx

value: postnatal day 15


title: P21_rEC_rep3

description:
PdgfbiCre-Ribotag
rEC_all_FPKMs.xlsx


title: P10_rEC_rep1

description:
PdgfbiCre-Ribotag
rEC_all_FPKMs.xlsx


title: C4KGFACXX.6.28d_05_Left_K4me3

city: Lexington

first: Darrell

middle: Orlyn

last: Ricke

address: 244 Wood Street

department: Group 48 Bioengineering Systems & Technology

institute: MIT Lincoln Laboratory

description: 28 days injured

data_processing:
Filter low read samples with custom getReadCounts.sh script
Call peaks with MACS2
Genome_build: mouse mm9
Supplementary_files_format_and_content: bed & gappedPeak

source_name: tibialis anterior muscle

extract_protocol:
Frozen tissue thawed, homogenized, cells lysed
Chromatin sheared and incubated overnight at 4C with antibodies using constant agitation; co-immunoprecipitated

treatment_protocol: Freeze injury was induced by applying a 6 mm diameter steel probe (cooled to the temperature of dry ice, −70C) to the belly of the TA muscle (directly below incision site) for 10 seconds

value: tibialis anterior muscle

tag: timepoint

value: 28 days

value: freeze injury


title: P10_rEC_rep3

description:
PdgfbiCre-Ribotag
rEC_all_FPKMs.xlsx

tag: strain


title: P6_rEC_rep1

description:
PdgfbiCre-Ribotag
rEC_all_FPKMs.xlsx


title: P6_rEC_rep3

description:
PdgfbiCre-Ribotag
rEC_all_FPKMs.xlsx


title: P6_rEC_rep2

description:
PdgfbiCre-Ribotag
rEC_all_FPKMs.xlsx


title: P6-MafbcKO_rEC_rep1


title: C4KGFACXX.6.28d_05_Left_K27ac

description: 28 days injured

value: H3 K27ac (Active Motif 39133)


title: P50_rEC_rep3

description:
PdgfbiCre-Ribotag
rEC_all_FPKMs.xlsx


title: C4KGFACXX.6.28d_05_Right_K4me1

description: 28 days injured

value: control


title: C4KDJACXX.3.28d_04_Left_K27ac

description: 28 days injured


title: C4KGFACXX.6.28d_05_Left_K4me1

description: 28 days injured


title: C4KGFACXX.6.28d_05_Right_K4me3

description: 28 days injured


title: C4KDJACXX.3.28d_04_Left_K4me1

description: 21 days injured


title: C4KDJACXX.3.28d_03_Left_K4me3

description: 21 days injured


title: P15_rEC_rep2

description:
PdgfbiCre-Ribotag
rEC_all_FPKMs.xlsx


title: 846_GTCCGC

city: Ithaca

first: Praveen

last: Sethupathy

address: Cornell University

institute: Cornell University

data_processing:
Illumina HiSeq
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm9 whole genome using miRquant 2.0 pipeline (bowtie and SHRiMP)
Reads per millions mapped to miRNAs (RPMMM) were calculated
Genome_build: mm9
Supplementary_files_format_and_content: Comma separated values file containing RPMMMs for all miRNAs and all samples

source_name: Liver tissue

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen, and homogenized. RNA was harvested using Norgen Total RNA Purification Kit (Cat# 24300). Small RNA was selected by gel electrophoresis
RNA libraries were prepared using New England Biosciences NEBNext Multiplex Small RNA Library Prep Set for Illumina

tag: sibling pair

value: Liver

tag: DO mouse

value: DO mouse on HP diet


title: 844_CGATGT


title: C4KDJACXX.3.28d_03_Left_K4me1

description: 21 days injured


title: 841_TAGCTT


title: 840_TAGCTT


title: P15_rEC_rep1

description:
PdgfbiCre-Ribotag
rEC_all_FPKMs.xlsx


title: 842_GTGGCC


title: 843_CCGTCC


title: 838_GCCAAT


title: C4KDJACXX.3.28d_03_Left_K27ac

description: 28 days injured


title: 839_CAGATC


title: C4KGFACXX.3.28d_02_Left_K4me3

description: 21 days injured


title: C4KGFACXX.3.28d_02_Left_K4me1

description: 21 days injured


title: P6-MafbcKO_rEC_rep3


title: 834_ATGTCA


title: 837_GGCTAC


title: C4KGFACXX.7.28d_02_Left_K27ac

description: 28 days injured


title: C4KDJACXX.3.28d_04_Left_K4me3

description: 21 days injured


title: 835_ACAGTG


title: C4KGFACXX.3.28d_02_Right_K4me3

description: 28 days injured


title: 823_ACTTGA


title: 826_AGTTCC


title: 825_ATGTCA


title: 831_GGTAGC


title: 830_ATGTCA


title: 827_TGACCA


title: 829_ATGTCA


title: C4KGFACXX.7.28d_01_Left_K4me1

description: 21 days injured


title: C4KGFACXX.3.28d_02_Left_K27ac

description: 28 days injured


title: 828_TAGCTT


title: 821_GTTTCG


title: 822_CTTGTA


title: C4KGFACXX.3.28d_02_Right_K4me1

description: 28 days injured


title: 833_AGTCAA


title: C4KGFACXX.7.28d_01_Left_K27ac

description: 28 days injured


title: 816_ATCACG


title: 817_GAGTGG


title: 836_GATCAG


title: 818_GTGGCC


title: C4KGFACXX.3.28d_02_Right_K27ac

description: 28 days control


title: 815_GCCAAT


title: 824_GGTAGC


title: 814_GTAGAG


title: 812_TTAGGC


title: 813_GTGAAA


title: C4KGFACXX.5.28d_01_Right_K4me1

description: 28 days injured


title: C4KGFACXX.7.28d_01_Left_K4me3

description: 21 days injured


title: C4KGFACXX.5.28d_01_Right_K27ac

description: 28 days control


title: 809_AGTTCC


title: 819_GTGGCC


title: 808_TGACCA


title: C4KDJACXX.7.21d_05_Left_K4me1

description: 21 days injured

value: 21 days


title: 807_CCGTCC


title: C4KDJACXX.5.21d_05_Right_K4me3

description: 21 days control


title: 805_CGATGT


title: 788_ATCACG

value: DO mouse on HFCA diet


title: 803_AGTCAA


title: 810_GTGAAA


title: C4KDJACXX.7.21d_05_Left_K27ac

description: 21 days injured


title: 801_GTCCGC


title: C4KGFACXX.5.28d_01_Right_K4me3

description: 28 days injured


title: 802_AGTCAA


title: C4KDJACXX.5.21d_05_Right_K4me1

description: 21 days control


title: C4KDJACXX.5.21d_05_Right_K27ac

description: 21 days control


title: 744_TGACCA


title: 743_GTGAAA


title: 742_CGTACG


title: C4KDJACXX.6.21d_04_Left_K4me1

description: 21 days injured


title: C4KDJACXX.7.21d_05_Left_K4me3

description: 21 days injured


title: 740_GTGAAA


title: 804_GATCAG


title: 741_GCCAAT


title: C4KDJACXX.5.21d_04_Right_K4me3

description: 21 days control


title: 737_GTTTCG


title: C4KDJACXX.6.21d_04_Left_K4me3

description: 21 days injured


title: 739_TTAGGC


title: 739_CTTGTA


title: C4KDJACXX.6.21d_03_Left_K4me3

description: 21 days injured


title: 735_GAGTGG


title: 727_ATCACG


title: 734_GGCTAC


title: 729_TAGCTT


title: C4KDJACXX.6.21d_04_Left_K27ac

description: 21 days injured


title: 731_GTCCGC


title: 733_ATGTCA


title: 730_GGCTAC


title: C4KDJACXX.5.21d_04_Right_K27ac

description: 21 days control


title: 745_GGCTAC


title: C4KDJACXX.6.21d_03_Left_K27ac

description: 21 days injured


title: 725_TAGCTT


title: 736_GTGGCC


title: 739_GCCAAT


title: C4KDJACXX.6.21d_03_Left_K4me1

description: 21 days injured


title: 723_AGTCAA


title: 721_GTGGCC


title: C4KDJACXX.4.21d_03_Right_K4me3

description: 21 days control


title: 720_GTGAAA


title: 722_TTAGGC


title: C4KDJACXX.5.21d_04_Right_K4me1

description: 21 days control


title: C4KDJACXX.4.21d_03_Right_K4me1

description: 21 days control


title: C4KDJACXX.4.21d_03_Right_K27ac

description: 21 days control


title: 719_CAGATC


title: 717_GTAGAG


title: 715_AGTCAA


title: 718_ATGTCA


title: 713_ATCACG


title: C4KDJACXX.7.21d_01_Left_K27ac

description: 21 days injured


title: 712_GGTAGC


title: 714_TGACCA


title: C4KDJACXX.7.21d_01_Left_K4me1

description: 21 days injured


title: C4KDJACXX.4.21d_01_Right_K4me3

description: 21 days control


title: C4KDJACXX.7.21d_01_Left_K4me3

description: 21 days injured


title: 724_AGTTCC


title: 710_GTTTCG


title: 709_GATCAG


title: C4KDJACXX.4.21d_01_Right_K4me1

description: 21 days control


title: 708_AGTTCC


title: C4KDJACXX.4.21d_01_Right_K27ac

description: 21 days control


title: 726_ACAGTG


title: 706_ATCACG


title: 704_AGTCAA


title: 705_CAGATC


title: C4KGFACXX.8.14d_05_Right_K4me3

description: 14 days control

value: 14 days


title: 703_ACAGTG


title: C4KGFACXX.8.14d_05_Right_K4me1

description: 14 days control


title: 702_CTTGTA


title: 701_CGATGT


title: 716_CTTGTA


title: 599_GTTTCG


title: 598_CGTACG


title: 711_CGTACG


title: C4KGFACXX.8.14d_05_Right_K27ac

description: 14 days control


title: C3A8DACXX140504.6.14d_04_Left_K4me3

description: 14 days injured


title: 593_GTCCGC


title: C3A8DACXX140504.6.14d_04_Left_K27ac

description: 14 days injured


title: 597_CAGATC


title: C3A8DACXX140504.6.14d_04_Left_K4me1

description: 14 days injured


title: 589_CGTACG


title: C4KGFACXX.8.14d_04_Right_K4me3

description: 14 days control


title: 588_ATCACG


title: 592_ACAGTG


title: 596_CGTACG


title: 594_GTCCGC


title: 707_ACTTGA


title: 591_GATCAG


title: 590_GGTAGC


title: C3A8DACXX140504.6.14d_03_Left_WCE

description: 14 days injured

value: WCE - whole cell extract


title: 583_TAGCTT


title: 586_GGTAGC


title: C3A8DACXX140504.6.14d_03_Left_K4me3

description: 14 days injured


title: C4KGFACXX.8.14d_04_Right_K27ac

description: 14 days control


title: 582_GCCAAT


title: 578_GAGTGG


title: 581_ATGTCA


title: 579_GTTTCG


title: C3A8DACXX140504.6.14d_03_Left_K4me1

description: 14 days injured


title: 577_CTTGTA


title: 576_GTAGAG


title: 587_GATCAG


title: C3A8DACXX140504.3.14d_02_Left_WCE

description: 14 days injured


title: C3A8DACXX140504.6.14d_03_Left_K27ac

description: 14 days injured


title: C4KGFACXX.8.14d_04_Right_K4me1

description: 14 days control


title: 575_CGATGT


title: 572_CCGTCC


title: 585_GGTAGC


title: C3A8DACXX140504.3.14d_02_Left_K4me3

description: 14 days injured


title: 573_CCGTCC


title: C3A8DACXX140504.6.14d_04_Left_WCE

description: 14 days injured


title: 584_CGATGT


title: 568_GGTAGC


title: 569_GCCAAT


title: C3A8DACXX140504.3.14d_02_Left_K27ac

description: 14 days injured


title: C3A8DACXX140504.2.14d_02_Right_K4me3

description: 14 days control


title: 566_CTTGTA


title: 562_GTAGAG


title: 571_GAGTGG


title: C3A8DACXX140504.2.14d_02_Right_WCE

description: 14 days control


title: 563_GTGGCC


title: 560_GTCCGC


title: C3A8DACXX140504.2.14d_02_Right_K4me1

description: 14 days control


title: 567_CGTACG


title: C3A8DACXX140504.2.14d_02_Right_K27ac

description: 14 days control


title: 561_CGTACG


title: 556_GTAGAG


title: 559_GTGAAA


title: 555_ATGTCA


title: 558_AGTTCC


title: 553_AGTCAA


title: 580_AGTCAA


title: 550_GTTTCG


title: 549_CGATGT


title: C3A8DACXX140504.3.14d_02_Left_K4me1

description: 14 days injured


title: C3A8DACXX140504.3.14d_01_Left_K4me1

description: 14 days injured


title: C3A8DACXX140504.3.14d_01_Left_WCE

description: 14 days injured


title: 570_TTAGGC


title: 551_TGACCA


title: 547_CTTGTA


title: C3A8DACXX140504.2.14d_01_Right_WCE

description: 14 days control


title: 548_GGCTAC


title: 546_GAGTGG


title: 545_ACTTGA


title: 543_GTCCGC


title: C3A8DACXX140504.3.14d_01_Left_K4me3

description: 14 days injured


title: 541_CTTGTA


title: C3A8DACXX140504.2.14d_01_Right_K4me1

description: 14 days control


title: C3A8DACXX140504.2.14d_01_Right_K27ac

description: 14 days control


title: 542_CCGTCC


title: 536_ACTTGA


title: 540_GGCTAC


title: C3A8DACXX140504.4.7d_05_Left_WCE

description: 7 days injured

value: 7 days


title: 535_ATGTCA


title: C3A8DACXX140504.4.7d_05_Left_K4me3

description: 7 days injured


title: C3A8DACXX140504.3.14d_01_Left_K27ac

description: 14 days injured


title: 539_GTAGAG


title: 532_AGTCAA


title: C3A8DACXX140504.4.7d_05_Left_K27ac

description: 7 days injured


title: 531_AGTTCC


title: 533_GTGAAA


title: 557_GATCAG


title: 530_GTCCGC


title: 528_TTAGGC


title: C3A8DACXX140504.4.7d_05_Left_K4me1

description: 7 days injured


title: 529_CAGATC


title: 544_CCGTCC


title: 528_TAGCTT


title: C3A8DACXX140504.4.7d_05_Right_K4me3

description: 7 days control


title: 527_ACAGTG


title: C3A8DACXX140504.4.7d_05_Right_WCE

description: 7 days control


title: C3A8DACXX140504.2.14d_01_Right_K4me3

description: 14 days control


title: 525_CAGATC


title: 524_GATCAG


title: 523_GCCAAT


title: C3A8DACXX140504.4.7d_05_Right_K4me1

description: 7 days control


title: 537_GTGGCC


title: 534_GGCTAC


title: 522_ACTTGA


title: C3A8DACXX140504.4.7d_05_Right_K27ac

description: 7 days control


title: C3A8DACXX140504.8.7d_04B_Left_WCE

description: 7 days injured


title: 518_ATCACG


title: 517_GGCTAC


title: 521_AGTTCC


title: C3A8DACXX140504.8.7d_04B_Left_K4me1

description: 7 days injured


title: C3A8DACXX140504.8.7d_04B_Left_K4me3

description: 7 days injured


title: 513_TGACCA


title: 514_GTTTCG


title: C3A8DACXX140504.8.7d_04B_Left_K27ac

description: 7 days injured


title: 516_CAGATC


title: C3A8DACXX140504.7.7d_04B_Left_K4me3

description: 7 days injured


title: C3A8DACXX140504.7.7d_04B_Left_WCE

description: 7 days injured


title: 511_ACAGTG


title: 509_AGTTCC


title: 512_GTAGAG


title: 507_CAGATC


title: 508_GAGTGG


title: C3A8DACXX140504.7.7d_04B_Left_K4me1

description: 7 days injured


title: 564_GTGAAA


title: C3A8DACXX140504.7.7d_04B_Left_K27ac

description: 7 days injured


title: 510_GTAGAG


title: 503_GTTTCG


title: C3A8DACXX140504.8.7d_04B_Right_WCE

description: 7 days control


title: 504_TTAGGC


title: 499_GAGTGG


title: 501_TGACCA


title: C3A8DACXX140504.8.7d_04B_Right_K4me3

description: 7 days control


title: 498_TGACCA


title: 497_CCGTCC


title: C3A8DACXX140504.8.7d_04B_Right_K4me1

description: 7 days control


title: 498_CTTGTA


title: 496_AGTTCC


title: C3A8DACXX140504.8.7d_04B_Right_K27ac

description: 7 days control


title: 495_GGTAGC


title: C3A8DACXX140504.7.7d_04B_Right_K4me3

description: 7 days control


title: 494_AGTTCC


title: 493_GATCAG


title: C3A8DACXX140504.7.7d_04B_Right_WCE

description: 7 days control


title: 505_ACTTGA


title: 491_CGTACG


title: 489_GAGTGG


title: 492_CCGTCC


title: 490_CGATGT


title: 487_GCCAAT


title: 486_GCCAAT


title: 488_GTGGCC


title: C3A8DACXX140504.8.7d_04_Left_WCE

description: 7 days injured


title: 506_CGTACG


title: 485_GTGAAA


title: C3A8DACXX140504.8.7d_04_Left_K4me3

description: 7 days injured


title: C3A8DACXX140504.7.7d_04B_Right_K4me1

description: 7 days control


title: 483_CCGTCC


title: C3A8DACXX140504.8.7d_04_Left_K4me1

description: 7 days injured


title: 481_GTAGAG


title: 484_GTCCGC


title: 480_GAGTGG


title: 482_ACAGTG


title: 479_GGCTAC


title: 476_TAGCTT


title: 477_GTCCGC


title: C3A8DACXX140504.8.7d_04_Left_K27ac

description: 7 days injured


title: C3A8DACXX140504.7.7d_04_Left_WCE

description: 7 days injured


title: 475_GTTTCG


title: 478_ACTTGA


title: 474_GGTAGC


title: C3A8DACXX140504.7.7d_04_Left_K4me3

description: 7 days injured


title: 473_TGACCA


title: 475_CGTACG


title: C3A8DACXX140504.7.7d_04_Left_K27ac

description: 7 days injured


title: 472_TTAGGC


title: C3A8DACXX140504.7.7d_04B_Right_K27ac

description: 7 days control


title: 471_TAGCTT


title: C3A8DACXX140504.8.7d_04_Right_WCE

description: 7 days control


title: 471_TTAGGC


title: 468_GTAGAG


title: 470_ACTTGA


title: C3A8DACXX140504.8.7d_04_Right_K4me3

description: 7 days control


title: C3A8DACXX140504.7.7d_04_Right_WCE

description: 7 days control


title: C3A8DACXX140504.8.7d_04_Right_K4me1

description: 7 days control


title: 467_ACAGTG


title: C3A8DACXX140504.7.7d_04_Right_K4me1

description: 7 days control


title: 467_TAGCTT


title: 469_ATGTCA


title: C3A8DACXX140504.7.7d_04_Right_K4me3

description: 7 days control


title: 465_CCGTCC


title: C3A8DACXX140504.5.7d_03_Left_WCE

description: 7 days injured


title: 464_TTAGGC


title: 463_CAGATC


title: C3A8DACXX140504.5.7d_03_Left_K4me1

description: 7 days injured


title: C3A8DACXX140504.5.7d_03_Left_K4me3

description: 7 days injured


title: 462_GTTTCG


title: C3A8DACXX140504.7.7d_04_Left_K4me1

description: 7 days injured


title: C3A8DACXX140504.5.7d_03_Left_K27ac

description: 7 days injured


title: 462_CGATGT


title: 461_GTGAAA


title: C3A8DACXX140504.5.7d_03_Right_K4me1

description: 7 days control


title: C3A8DACXX140504.5.7d_03_Right_WCE

description: 7 days control


title: 460_AGTCAA


title: 459_AGTCAA


title: C3A8DACXX140504.5.7d_03_Right_K4me3

description: 7 days control


title: C3A8DACXX140504.5.7d_03_Right_K27ac

description: 7 days control


title: 466_GATCAG


title: 457_GGTAGC


title: 455_GCCAAT


title: 456_GAGTGG


title: C3A8DACXX140504.1.7d_02_Left_K27ac

description: 7 days injured


title: C3A8DACXX140504.1.7d_02_Left_K4me1

description: 7 days injured


title: 454_GGCTAC


title: C3A8DACXX140504.1.7d_02_Right_WCE

description: 7 days control


title: 452_ATGTCA


title: 451_GCCAAT


title: 450_ACTTGA


title: C3A8DACXX140504.1.7d_02_Right_K4me3

description: 7 days control


title: C3CBFACXX.8.72hr_05_Left_K4me3

description: 72 hours injured

value: 72 hours


title: C3CBFACXX.8.72hr_05_Left_WCE

description: 72 hours injured


title: C3A8DACXX140504.1.7d_02_Right_K4me1

description: 7 days control


title: C3A8DACXX140504.1.7d_02_Right_K27ac

description: 7 days control


title: 449_GTGAAA


title: 447_TTAGGC


title: 458_GTTTCG


title: 448_GTGGCC


title: C3A8DACXX140504.1.7d_02_Left_WCE

description: 7 days injured


title: C3CBFACXX.8.72hr_05_Right_K4me3

description: 72 hours control


title: C3CBFACXX.8.72hr_05_Left_K27ac

description: 72 hours injured


title: C3CBFACXX.8.72hr_05_Left_K4me1

description: 72 hours injured


title: 446_GATCAG


title: 445_TGACCA


title: C3CBFACXX.8.72hr_05_Right_WCE

description: 72 hours control


title: C3A8DACXX140504.1.7d_02_Left_K4me3

description: 7 days injured


title: 444_GAGTGG


title: 442_GTAGAG


title: C3CBFACXX.8.72hr_05_Right_K4me1

description: 72 hours control


title: C3CBFACXX.7.72hr_04_Left_WCE

description: 72 hours injured


title: 453_TTAGGC


title: C3CBFACXX.8.72hr_05_Right_K27ac

description: 72 hours control


title: 451_ATCACG


title: C4KDJACXX.1.72h_04_Left_K4me3

description: 72 hours injured


title: 441_GGTAGC


title: C4KDJACXX.1.72h_04_Left_K4me1

description: 72 hours injured


title: 441_CGATGT


title: 441_ACTTGA


title: C4KDJACXX.1.72h_04_Left_K27ac

description: 72 hours injured


title: 439_GTCCGC


title: C3CBFACXX.7.72hr_04_Left_K4me3

description: 72 hours injured


title: 437_CTTGTA


title: 438_ACAGTG


title: C3CBFACXX.7.72hr_04_Right_WCE

description: 72 hours control


title: C3CBFACXX.7.72hr_04_Right_K4me3

description: 72 hours control


title: C3CBFACXX.7.72hr_04_Right_K4me1

description: 72 hours control


title: 443_CAGATC


title: 435_GTGGCC


title: C3CBFACXX.7.72hr_04_Right_K27ac

description: 72 hours control


title: 436_AGTTCC


title: C3CBFACXX.6.72hr_03_Left_K4me3

description: 72 hours injured


title: 433_CGTACG


title: 434_GGCTAC


title: 432_CCGTCC


title: 431_AGTTCC


title: C3CBFACXX.6.72hr_03_Right_WCE

description: 72 hours control


title: 429_CTTGTA


title: C3CBFACXX.6.72hr_03_Left_K4me1

description: 72 hours injured


title: C3CBFACXX.7.72hr_04_Left_K4me1

description: 72 hours injured


title: C3CBFACXX.6.72hr_03_Left_K27ac

description: 72 hours injured


title: 440_TAGCTT


title: 426_GTGGCC


title: C3CBFACXX.7.72hr_04_Left_K27ac

description: 72 hours injured


title: C3CBFACXX.6.72hr_03_Right_K4me1

description: 72 hours control


title: C3CBFACXX.6.72hr_03_Right_K27ac

description: 72 hours control


title: 428_TAGCTT


title: C3CBFACXX.5.72hr_02_Left_WCE

description: 72 hours injured


title: 425_TTAGGC


title: 434_TGACCA


title: 423_ATCACG


title: 422_ACAGTG


title: C3CBFACXX.6.72hr_03_Left_WCE

description: 72 hours injured


title: 424_CTTGTA


title: C3CBFACXX.5.72hr_02_Left_K4me3

description: 72 hours injured


title: C3CBFACXX.5.72hr_02_Left_K27ac

description: 72 hours injured


title: C3CBFACXX.5.72hr_02_Left_K4me1

description: 72 hours injured


title: C3CBFACXX.4.72hr_02_Left_WCE

description: 72 hours injured


title: 421_ATCACG


title: 430_GAGTGG


title: C3CBFACXX.6.72hr_03_Right_K4me3

description: 72 hours control


title: C3CBFACXX.4.72hr_02_Left_K4me1

description: 72 hours injured


title: 419_CGATGT


title: C3CBFACXX.4.72hr_02_Left_K27ac

description: 72 hours injured


title: C3CBFACXX.4.72hr_02_Left_K4me3

description: 72 hours injured


title: 417_TGACCA


title: C3CBFACXX.5.72hr_02_Right_WCE

description: 72 hours control


title: 416_ACTTGA


title: C3CBFACXX.5.72hr_02_Right_K4me3

description: 72 hours control


title: C3CBFACXX.5.72hr_02_Right_K4me1

description: 72 hours control


title: 415_ATGTCA


title: 414_CCGTCC


title: C3CBFACXX.5.72hr_02_Right_K27ac

description: 72 hours control


title: 413_GTAGAG


title: 412_AGTCAA


title: C3CBFACXX.4.72hr_02_Right_K4me3

description: 72 hours control


title: C3CBFACXX.4.72hr_02_Right_WCE

description: 72 hours control


title: C3CBFACXX.4.72hr_02_Right_K4me1

description: 72 hours control


title: 410_GTTTCG


title: C3CBFACXX.4.72hr_02_Right_K27ac

description: 72 hours control


title: 408_GTCCGC


title: 409_GTGAAA


title: 407_ACAGTG


title: C3CBFACXX.3.72hr_01_Left_WCE

description: 72 hours injured


title: C3CBFACXX.3.72hr_01_Left_K4me1

description: 72 hours injured


title: C3CBFACXX.3.72hr_01_Left_K4me3

description: 72 hours injured


title: 406_GATCAG


title: 420_GCCAAT


title: C3CBFACXX.2.72hr_01_Left_WCE

description: 72 hours injured


title: C3CBFACXX.3.72hr_01_Left_K27ac

description: 72 hours injured


title: 404_CGATGT


title: 403_CGATGT


title: C3CBFACXX.2.72hr_01_Left_K4me3

description: 72 hours injured


title: 405_CGTACG


title: C3CBFACXX.2.72hr_01_Left_K4me1

description: 72 hours injured


title: 403_ATCACG


title: 402_ATCACG


title: C3CBFACXX.3.48hr_05_Left_WCE

description: 48 hours injured

value: 48 hours


title: C3CBFACXX.3.48hr_05_Left_K4me3

description: 48 hours injured


title: C3CBFACXX.2.72hr_01_Left_K27ac

description: 72 hours injured


title: 411_CAGATC


title: C3CBFACXX.3.48hr_05_Left_K4me1

description: 48 hours injured


title: 401_GGTAGC


title: C4KDJACXX.8.48h_05_Left_K4me1

description: 48 hours injured


title: immortallized bone marrow derived macrophages treated with Dpo at a concentration of 8ng/ul for 12 hours

city: beijing

first: fuping

last: you

address: xueyuan street

institute: Peking University Health Science Center

data_processing:
Base-calling:   Illumina Real time analysis (RTA) 2.7 software used for base calling.
Raw data filtering:   cutadapt (Martin M. Embnet Journal, 2011) was used to trim the low-quality sequence. The filtered sequence is as follows:  1, the low-quality bases in the both ends of the reads, the threshold value is Q30;  2, adapters;  3, bases N;  4, sequence length < 60 bp.
Reference genome alignment:   clean data was mapped to GRCm38 mouse genome using Tophat2(Kim D etal., Genome Biol, 2013) which the core program is bowtie2.
Normalized abundance measurements:  FPKM (Fragments Per Kilobase of transcript per Million fragments  Mapped) were calculated using a protocol from Trapnell C et al., Nat. Biotechnol, 2010.
Differential Expression Analysis  Using cuffdiff (Trapnell C et al., Nat. Biotechnol, 2013) to analyze. The criterion:  1, the sum of mapping reads between two samples is greater than 10;  2, | log2(fold change) | >1;  3, P value ≤0.05 and Q value ≤0.05
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: mouse immortallized bone marrow derived macrophages

extract_protocol:
immortallized bone marrow derived macrophages were treated with medium or Dpo for 12 hours and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow


title: immortallized bone marrow derived macrophages treated with control medium

description: con