title: 2065483_TimePoint1_WholeBlood

city: Atlanta

first: Mary

last: Galinski

state: GA

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

institute: Emory University

description:
E04RM99FGMmCyDaWB_Mulatta-Genes-DESeq2NormalizedCountsReSequence-Results_MULTIPL_GEO.xlsx
E04RM99FGMmCyDaWB_Cynomolgi-Genes-RawCountsReSequence-Results_MULTIPL_GEO.xlsx

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.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
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 either normalized transcript abundances or raw counts at the gene level, for each individual.  Abundances and raw counts are further classified by experimental Time Point (1-7), and Specimen Type (Whole Blood).
Supplementary_files_format_and_content: "Host DESeq2Normalized 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. DESeq2 normalized 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 33 columns representing 5 animals for Time Points T01-T03 and 4 animals for Time Points T04-T07 with two additional samples.    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."
Supplementary_files_format_and_content: Host 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 33 columns representing 5 animals for Time Points T01-T03 and 4 animals for Time Points T04-T07 with two additional samples.    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 3-plex sequencing on an Illumina HiSeq2000 at the Yerkes Genomics Core, aiming for 80 million paired-end 100 base pair (bp) reads per library.

treatment_protocol: During the 100-day experiment, artemether was delivered for blood-stage treatment.  Chloroquine were administered at the end of the study to treat liver- and blood-stages.

tag: time point

tag: gender

value: Male

tag: non human primate individual id

tag: infected with

value: Plasmodium cynomolgi strain B


title: B2_12

status: Public on Sep 07 2017

type: SRA

city: BETHESDA

first: Jianfei

last: Hu

state: MD

address: 40 CONVENT DR

department: Vaccine Research Center

country: USA

institute: NIH

library_source: transcriptomic

data_processing:
Illumina bcl2fastq-2.17 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 repeat-masked  genome using tophat v2.0.13 with parameters  -p 4 --coverage-search --library-type fr-unstranded
Gene transcript isoform expression level was calculated by cufflinks v2.1.1
Genome_build: hg19
Supplementary_files_format_and_content: Gene transcript isoform expression file
gene.Ensembl.gtf.txt: Ensemble gene set file (based on Homo_sapiens.GRCh37.74.gtf)
gene.Merged.gtf.txt: Merged gene set file (predicted by cuffmerge with the reference annotation of Homo_sapiens.GRCh37.74.gtf)
geneExpr.Ensembl.txt: Gene Transcript isoform expression file based on Ensembl gene set
geneExpr.Merged.txt: Gene Transcript isoform expression file based on merged gene set

molecule: total RNA

organism: Homo sapiens

source_name: central memory (CM)_Activated

extract_protocol:
Sorted cells were lysed and total RNA was extracted using RNAzol RT (Molecular Research Center Inc., Cincinnati, OH). Poly-adenylated RNA was purified using Dynabeads oligo (dT)25 (Invitrogen, Carlsbad, CA) and fragmented
cDNA was synthesized and Illumina-ready libraries were generated using a modified Illumina TruSeq mRNA Library preparation protocol (paired end HiSeq 2x100 reads)

tag: donor id

value: Donator 1

tag: t cell type

value: central memory (CM)

tag: status

value: Activated

tag: sorting phenotype

value: CM (CD45RO+CD27+CCR7+)


title: Spleen_control_rep1

city: Burlington

first: Diana

middle: Lea

last: Gerrard

state: VT

address: 89 Beaumont Ave C141C Given

department: Cellular molecular and biomedical sciences

institute: University of Vermont

data_processing:
FastX toolkit to filter adaptors, non-coding RNA, low quality reads, and raw reads with average lengths less than 20 bases
The Trinity program was employed for De novo transcriptome assembly. Parameters used were as follows: minimum contig length= 300 and minimum kmer coverage=2. The remaining contigs were further processed with Bowtie and RSEM
Genome_build: denovo
Supplementary_files_format_and_content: The De novo transcriptome assembly for bat (Trinity.fasta) was generated from pooled RNA-seq data from the different organ tissue

organism: Artibeus jamaicensis

source_name: Spleen

extract_protocol:
Organ samples were homogenized using zirconia/silica beads and a mini-bead-beater and RNA was extracted using QiaShredder columns and RNeasy minikits.
RNA libraries were prepared for sequencing using the Kapa Biosystems stranded-RNA sample prep kit

treatment_protocol: Two Jamaican fruit bats were inoculated with 100 μl of sterile DPBS to act as negative controls, and two bats were inoculated with 100 μl containing 106 TCID50 Tacaribe virus.  Negative control bats were euthanized at the end of the experimental period (45 days p.i,), while TCRV inoculated bats were euthanized as they became moribund.  Kidney, liver, and spleen samples were collected in RNAlater and used for RNA extraction.

tag: tissue

value: Spleen

tag: treatment

value: 100 ul of sterile DPBS to act as negative controls


title: 2065481_TimePoint5_WholeBlood


title: 2065482_TimePoint4_WholeBlood


title: A3_6

source_name: Effector Memory (EM)_resting

value: Effector Memory (EM)

value: resting

value: EM (CD45RO+CD27-)


title: 2065479_TimePoint3_WholeBlood


title: A1_5

source_name: Transitional Memory (TM)_resting

value: Transitional Memory (TM)

value: TM (CD45RO+CD27+CCR7-)


title: 2065480_TimePoint3_WholeBlood


title: 2065478_TimePoint2_WholeBlood


title: A5_7

value: Donator 2


title: 2065477_TimePoint1_WholeBlood


title: A8_4

source_name: central memory (CM)_resting


title: Kidney_control_rep1

source_name: Kidney

value: Kidney


title: 2065474_TimePoint5_WholeBlood


title: 3T3C5 Bio_2 RNASeq

city: Pasadena

first: Yaron

middle: E

last: Antebi

state: CA

address: 1200 E California Blvd, MC114-96

department: Biology and Bioengineering

institute: Caltech

data_processing:
Base calls were performed with RTA 1.13.48.0 followed by conversion to FASTQ with bcl2fastq 1.8.4.
Alignment was performed in Galaxy using the TopHat algorithm.
Transcript assembly and FPKM estimates in Galaxy were performed using the Cufflinks algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx files for all samples include tracking ID for each gene and a corresponding FPKM.

organism: Mus musculus

growth_protocol: All cells were cultured in a humidity controlled chamber at 37°C with 5% CO2. NMuMG cells were cultured in DMEM supplemented with 10% FBS (Clonetech #631367), 1mM sodium pyruvate, 1unit/ml penicillin, 1ug/ml streptomycin, 2mM L-glutamine and 1X MEM non-essential amino acids. NIH-3T3 cells were cultured in DMEM supplemented with 10% CCS (Hyclone #SH30087), 1mM sodium pyruvate, 1unit/ml penicillin, 1ug/ml streptomycin and 2mM L-glutamine. ES cells were plated on tissue culture plates pre-coated with 0.1% gelatin and cultured in a standard pluripotency maintaining conditions using DMEM supplemented with 15% FBS (ES qualified, Gibco #16141), 1mM sodium pyruvate, 1unit/ml penicillin, 1ug/ml streptomycin, 2mM Lglutamine 1X MEM non-essential amino acids 55mM beta-mercaptoethanol and 1000 Units/ml leukemia inhibitory factor (LIF).

extract_protocol:
Total RNA was collected from cells using the RNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
NEBNext Ultra RNA-seq (NEB #E7530) following manufactures's instructions

tag: strain

value: NIH/Swiss

tag: transgene

value: BRE reporter


title: 2065473_TimePoint3_WholeBlood

value: Male


title: 2065475_TimePoint4_WholeBlood

value: Plasmodium cynomolgi strain B


title: 2064625_TimePoint2_WholeBlood


title: B8_2

value: Donator 1

value: Naive

value: Naive (CD45RO-CD27+)


title: 2064624_TimePoint4_WholeBlood


title: 2065476_TimePoint2_WholeBlood


title: 3T3C5 Bio_1_RNASeq


title: 2064622_TimePoint1_WholeBlood


title: 2064623_TimePoint5_WholeBlood


title: E14SDY7_Bio_2_RNASeq

source_name: E14 mouse ES cells


title: 3T3 Bio_1_RNASeq


title: E14_Bio_1_RNASeq


title: E14SDY7_Bio_1_Tech_1_RNASeq


title: NMuMGC5_Bio_2_RNASeq

source_name: NMuMG

value: NAMRU


title: E14SDY7_Bio_1_Tech_2_RNASeq


title: 2064614_TimePoint4_WholeBlood


title: 2064613_TimePoint5_WholeBlood


title: 2064612_TimePoint3_WholeBlood


title: 2064611_TimePoint1_WholeBlood


title: 2064615_TimePoint2_WholeBlood


title: NMuMGC5_Bio_1_RNASeq


title: 2064610_TimePoint3_WholeBlood


title: 2064609_TimePoint2_WholeBlood


title: NMuMG_Bio_1_RNASeq


title: 2064229_TimePoint1_WholeBlood


title: 2064227_TimePoint7_WholeBlood


title: 2064226_TimePoint7_WholeBlood


title: 2064224_N/A_WholeBlood

description:
Time Point characteristic is not applicable because animal REe6 was an uninfected control animal.
E04RM99FGMmCyDaWB_Mulatta-Genes-DESeq2NormalizedCountsReSequence-Results_MULTIPL_GEO.xlsx
E04RM99FGMmCyDaWB_Cynomolgi-Genes-RawCountsReSequence-Results_MULTIPL_GEO.xlsx


title: 2063488_TimePoint6_WholeBlood


title: 2064219_N/A_WholeBlood

description:
Time Point characteristic is not applicable because animal CF97 was a transfusion donor for experimental animal RFv13
E04RM99FGMmCyDaWB_Mulatta-Genes-DESeq2NormalizedCountsReSequence-Results_MULTIPL_GEO.xlsx
E04RM99FGMmCyDaWB_Cynomolgi-Genes-RawCountsReSequence-Results_MULTIPL_GEO.xlsx


title: Sham-H3K27me3-1

city: Sendai

first: Yoshihiro

last: Sato

state: Miyagi

address: 2-1 Seiryo-machi, Aobaku

department: Biochemistry

country: Japan

institute: Tohoku University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 genome assembly using bwa version 0.7.10
peaks were called using MACS2 version 2.1.0 with the default setting
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using bam2bigwig.sh from BAM files

molecule: genomic DNA

source_name: Liver

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared from ~10 ng each of ChIP and input DNA with the use of an Ovation Ultralow DR Multiplex System (NuGEN, Cat No. 0330-32, 0331-32). Two rapid mode flow cells of an Illumina HiSeq 2500 were used for this analysis. Libraries were clonally amplified in the flow cells and sequenced with the use of Hiseq Control Software ver. 2.2.38 (Illumina) and a 51- nucleotide paired-end sequence. Image analysis and base calling were performed using real-time analysis software (RTA ver. 1.18.61, Illumina).

treatment_protocol: We performed portal vein branch ligation in mouse, and hypertrophic right lobe was collected as a regenerationg liver (RL). Sham operated liver was used as control.

tag: chip antibody

value: H3K27me3 (07-449, Millipore)

value: sham operated


title: RL-H3K27me3-2

value: portal vein branch ligation in mouse


title: Sham-input


title: Sham-H3K27me3-2


title: RL-input


title: RL-H3K27me3-1


title: NMuMG_Bio_2_RNASeq


title: 2063486_TimePoint6_WholeBlood


title: Sham-H3K4me3-1

value: H3K4me3 (ab8580, abcam)


title: 2063487_TimePoint6_WholeBlood


title: Sham-H3K4me3-2


title: fruit mesocarp_30 DAF-1

status: Public on Sep 06 2017

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

description: small RNA

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:TGGAATTCTCGGGTGCCAAGG;end2:GATCGTCGGACTGTAGAACTCTGAAC) trimmed with fastx_clipper
mapped using bowtie -v 1
Genome_build: Cucumis melo L. CM_v3.5 (Hami melon is a variant of Cucumis melo L.）
Supplementary_files_format_and_content: tab-delimited text file includes miRNA TPM values for each Sample

organism: Cucumis melo

source_name: fruit mesocarp separated from Hami melon 30 days after flowering

extract_protocol:
Total RNA was extracted by using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions, and RQ1 DNase (Promega, Madison, WI, USA) was used to remove contaminating genomic DNA. The quality and quantity of the purified RNA was monitored at the ratios of A260/A280 and A260/230 on SmartSpec Plus Spectrophotometer (BioRad, Philadelphia, PA, USA). RNA integrity was further verified by 1.5% agarose gel electrophoresis.
Three μg of total RNA was used for small RNA cDNA library preparation with Balancer NGS Library Preparation Kit for small/microRNA (GnomeGen, San Diego, CA, USA) based on manufacturer’s instruction. Briefly, RNAs were ligated to 3’ and 5’ adaptor sequentially, reverse transcribed to cDNA and PCR amplified. Whole library was applied to 10% native PAGE gel electrophoresis and bands corresponding to miRNA insertion were cut and eluted. After ethanol precipitation and washing, the purified small RNA libraries were quantified with Qubit Fluorometer (Invitrogen, Carlsbad, CA, USA), used for cluster generation and applied to Illumina GAIIx (Illumina, San Diego, CA, USA) 73 nt single-end sequencing or Illumina NextSeq 500 76 nt pair-end sequencing according to the manufacturer’s instructions. The small RNA libraries sequencing was perfomed in ABLife, Inc. (Wuhan, China).The smallRNA libraries sequencing was perfomed in ABLife, Inc. (Wuhan, China).

tag: age

value: 30 days after flowering

tag: developmental stage

value: fruit

value: fruit mesocarp


title: 2063485_TimePoint7_WholeBlood


title: fruit mesocarp_20 DAF-1

description: small RNA

source_name: fruit mesocarp separated from Hami melon 20 days after flowering

value: 20 days after flowering


title: RL-H3K4me3-1


title: fruit mesocarp_40 DAF-1

description: small RNA

source_name: fruit mesocarp separated from Hami melon 40 days after flowering

value: 40 days after flowering


title: 2063483_TimePoint7_WholeBlood


title: 2063484_TimePoint6_WholeBlood


title: fruit mesocarp_10 DAF-1

description: small RNA

source_name: fruit mesocarp separated from Hami melon 10 days after flowering

value: 10 days after flowering


title: L-goat_spleen3

city: Chengdu

first: Mingzhou

last: Li

state: Sichuan

address: No.211 Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

description: Ya'an,Sichuan,China,500m altitude

data_processing:
Illumina Casava1.82 software was used for basecalling.
High-quality reads were obtained by discarding reads containing over 10% Ns, or overlapping at least 10 bp with adaptor sequences at mismatch rate equal to or less than 10%, or including over 50% bases with base quality score less than five, and then mapped to respective genome of the species using Tophat 2.0.11.
Cufflinks version 2.2.1 were applied to quantify gene expression and obtain FPKM expression values (denoted as the fragments per Kb of transcript per Mb mapped reads).
Genome_build: Galgal4, UMD3.1, Suscrofa 10.2, Oar_v3.1 and CHIR_1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Capra hircus

source_name: spleen

extract_protocol:
The total RNA was extracted using the TrIzol reagent (Life Technologies, Beijing, China) according to the manufacturer’s protocols. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
The dUTP based strand-specific RNA libraries were prepared for sequencing using standard Illumina protocols; Strand-specific mRNA-Seq

tag: altitude

value: low

value: spleen

value: adult(>3 years old)


title: L-goat_spleen1

description: Ya'an,Sichuan,China,500m altitude


title: H-goat_liver1

description: Songpan,Sichuan,China,3000m altitude

source_name: liver

value: high

value: liver


title: H-goat_spleen2

description: Songpan,Sichuan,China,3000m altitude


title: H-goat_spleen3

description: Songpan,Sichuan,China,3000m altitude


title: H-goat_kidney3

description: Songpan,Sichuan,China,3000m altitude

source_name: kidney

value: kidney


title: H-goat_kidney2

description: Songpan,Sichuan,China,3000m altitude


title: H-goat_liver3

description: Songpan,Sichuan,China,3000m altitude


title: H-goat_kidney1

description: Songpan,Sichuan,China,3000m altitude


title: goat_kidney_2

description:
TSY_shen2
processed data file: goat_PCA_new.txt

data_processing:
Illumina Casava1.82 software was used for basecalling.
High-quality reads were obtained by discarding reads containing over 10% Ns, or overlapping at least 10 bp with adaptor sequences at mismatch rate equal to or less than 10%, or including over 50% bases with base quality score less than five.
Cufflinks version 2.2.1 were applied to quantify gene expression and obtain FPKM expression values (denoted as the fragments per Kb of transcript per Mb mapped reads).
Genome_build: cattle: bosTau6 or UMD3.1, sheep: oviAri3, goat: chinese assembly v2 (http://www.goatgenome.org/projects.html)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.  The goat protein sequences are available in the file goat.v4.gff.filter.pep.txt on the series record.

value: indigenous

tag: location

value: Ya'an, Sichuan province, China

value: ~3 years old


title: goat_liver_2

description:
TSY_gan2
processed data file: goat_PCA_new.txt


title: goat_kidney_1

description:
TSY_shen1
processed data file: goat_PCA_new.txt


title: L-goat_spleen2

description: Ya'an,Sichuan,China,500m altitude


title: goat_kidney_3

description:
TSY_shen3
processed data file: goat_PCA_new.txt


title: goat_liver_3

description:
TSY_gan3
processed data file: goat_PCA_new.txt


title: goat_heart_2

description:
TSY_xin2
processed data file: goat_PCA_new.txt

source_name: heart

value: heart


title: B1_6

value: Donator 7

value: Effector Memory (EM)

value: resting

value: EM (CD45RO+CD27-)


title: goat_liver_1

description:
TSY_gan1
processed data file: goat_PCA_new.txt


title: 3000m_2_heart

description: A'ba Tibetan autonomous area, Sichuan province, China, 3,000m altitude

data_processing:
Illumina Casava1.82 software was used for basecalling.
High-quality reads were obtained by discarding reads containing over 10% Ns, or overlapping at least 10 bp with adaptor sequences at mismatch rate equal to or less than 10%, or including over 50% bases with base quality score less than five, and then mapped to goat genome using Tophat 2.0.11.
Cufflinks version 2.2.1 were applied to quantify gene expression and obtain FPKM expression values (denoted as the fragments per Kb of transcript per Mb mapped reads). The list of Gene IDs can be obtained from the website http://www.goatgenome.org/projects.html.
Genome_build: goat genome "chinese assembly v2".  http://www.goatgenome.org/projects.html
Supplementary_files_format_and_content: tab-delimited text file includes normalized abundance measurements of genes in FPKM values

extract_protocol:
The total RNA was extracted using the TrIzol reagent (Life Technologies, Beijing, China) according to the manufacturer’s protocols. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
The dUTP based strand-specific RNA libraries were prepared for sequencing using standard Illumina protocols

tag: location/altitude


title: goat_heart_1

description:
TSY_xin1
processed data file: goat_PCA_new.txt


title: 3000m_3_heart

value: A'ba Tibetan autonomous area, Sichuan province, China, 3,000m altitude


title: RL-H3K4me3-2

tag: gender

value: Male

value: H3K4me3 (ab8580, abcam)

value: portal vein branch ligation in mouse


title: 3000m_1_heart


title: ein2_ENAP1_C2H4_ChIPseq_rep2

city: Austin

first: Hong

last: Qiao

state: TEXAS

address: 2506 speedway, NMS5.324

department: Department of Molecular Biosciences

institute: The University of Texas at Austin

description:
macs2.optimal.C16_C12vsC11_C15.narrowPeak
C16_C12vsC11_C15_control_lambda.bdg
C16_C12vsC11_C15_treat_pileup.bdg

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using bwa with default parameters
For each ENAP1 binding in each condition,mapped reads were pooled across ChIP-seq replicates as described (Gjoneska, Pfenning et al.Nature, 2015)
Peaks significantly enriched in ChIP-seq tags were identified by Model-based Analysis for ChIP-Seq (MACS2, version 2.1.0.20150603) following IDR pipeline (https://sites.google.com/site/anshulkundaje/projects/idr)
Genome_build: tair10
Supplementary_files_format_and_content: the  bdg and narrowPeak (after cutoff according IDR pipeline) files are generated using MACS2 (version 2.1.0.20150603) software.

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Arabidopsis seeds were  dark-grown at 24 ºC for 3 days

extract_protocol:
ENAP1 proteins were extracted from seedlings and ENAP1-DNA complexes were isolated with antibody.
Libraries were prepared according to NEB instructions of the ChIP-seq Library Kit (NEB #E6240S/L)

treatment_protocol: Treated with air (hydrocarbon-free air (Zero grade air, AirGas)) or ethylene (hydrocarbon-free air with 10 parts per million  (ppm) ethylene) for 4 hours

value: whole seedling after ethylene treatment

tag: ecotype

value: anti-green fluorescent protein (life technologies:A11122)

value: ethylene treated for 4 hours


title: 3000m_3_muscle

source_name: muscle

value: muscle


title: goat_heart_3

description:
TSY_xin3
processed data file: goat_PCA_new.txt


title: 3000m_2_lung

source_name: lung

value: lung


title: H-goat_liver2

description: Songpan,Sichuan,China,3000m altitude

value: high

value: liver

value: adult(>3 years old)


title: H-goat_spleen1

description: Songpan,Sichuan,China,3000m altitude

value: spleen


title: 3000m_1_lung

value: ~3 years old


title: 3000m_2_muscle


title: 3000m_1_muscle


title: 2000m_3_heart

description: Zhaotong, Yunnan province, China, 2,000m altitude

value: heart


title: 2000m_2_lung

value: Zhaotong, Yunnan province, China, 2,000m altitude


title: 2000m_3_lung


title: 2000m_2_heart


title: 3000m_3_lung


title: 2000m_1_muscle


title: 600m_3_lung

description: Ya'an, Sichuan province, China, 600m altitude


title: 2000m_2_muscle


title: 600m_2_lung

value: Ya'an, Sichuan province, China, 600m altitude


title: 600m_3_muscle


title: 600m_1_lung


title: 600m_1_heart


title: 2000m_3_muscle


title: 600m_1_muscle


title: 600m_3_heart


title: dgk suppressor 2-1 Sample 56

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
base calls with quality metrics were generated using the HiSeq 2500 Control software
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3)
transcript abundance was quantified using rockhopper
Genome_build: E. coli strain BW25113

organism: Escherichia coli

source_name: Escherichia coli cell lysate

growth_protocol: cells were grown in M9 glucose (0.4% w/v)

extract_protocol:
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit.
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit


title: dgk suppressor 3-1 Sample 57


title: 600m_2_muscle


title: ∆dgk parent Sample 54


title: dgk suppressor 1-1 Sample 55


title: entC suppressor 1-1 Sample 51


title: ∆entC parent Sample 50


title: dapF suppressor 3-1 Sample 49


title: entC suppressor 2-1 Sample 52


title: entC suppressor 3-1 Sample 53


title: 2000m_1_heart


title: ∆dapF parent Sample 47


title: 2000m_1_lung


title: dapF suppressor 1-1 Sample 48


title: ppk suppressor 2-1 Sample 45


title: ppk suppressor 1-1 Sample 44


title: 600m_2_heart


title: zwf suppressor 1-2 Sample 42


title: dgk suppressor 3-1 Sample 38


title: ∆zwf parent Sample 40


title: zwf suppressor 1-1 Sample 41


title: entC suppressor 3-1 Sample 34


title: dapF suppressor 3-1 Sample 30


title: ppk suppressor 3-1 Sample 27


title: dapF suppressor 1-1 Sample 29


title: ∆dgk parent Sample 35


title: dgk suppressor 1-1 Sample 36


title: WT- Keio Sample 39


title: ∆dapF parent Sample 28


title: entC suppressor 2-1 Sample 33


title: entC suppressor 1-1 Sample 32


title: ppk suppressor 2-1 Sample 26


title: zwf suppressor 1-2 Sample 23


title: ppk suppressor 1-1 Sample 25


title: ∆ppk parent Sample 24


title: zwf suppressor 1-1 Sample 22


title: ppk suppressor 3-1 Sample 46


title: ∆zwf parent Sample 21


title: WT- Keio Sample 20


title: ∆dgk parent Sample 16


title: dgk suppressor 1-1 Sample 17


title: entC suppressor 3-1 Sample 15


title: dgk suppressor 3-1 Sample 19


title: dgk suppressor 2-1 Sample 18


title: ∆ppk parent Sample 43


title: dgk suppressor 2-1 Sample 37


title: entC suppressor 2-1 Sample 14


title: dapF suppressor 3-1 Sample 11


title: entC suppressor 1-1 Sample 13


title: dapF suppressor 1-1 Sample 10


title: ∆dapF parent Sample 9


title: ∆entC parent Sample 12


title: ppk suppressor 2-1 Sample 7


title: ∆zwf parent Sample 2


title: ppk suppressor 3-1 Sample 8


title: ∆ppk parent Sample 5


title: WT- Keio Sample 1


title: ppk suppressor 1-1 Sample 6


title: H-pig_lung3

description: Songpan,Sichuan,China,3000m altitude

organism: Sus scrofa

value: adult(>1 year old)


title: H-pig_muscle3

description: Songpan,Sichuan,China,3000m altitude


title: H-pig_heart2

description: Songpan,Sichuan,China,3000m altitude


title: H-pig_heart3

description: Songpan,Sichuan,China,3000m altitude


title: zwf suppressor 1-1 Sample 3


title: zwf suppressor 1-2 Sample 4


title: H-pig_lung2

description: Songpan,Sichuan,China,3000m altitude


title: H-pig_heart1

description: Songpan,Sichuan,China,3000m altitude


title: H-pig_muscle1

description: Songpan,Sichuan,China,3000m altitude


title: H-pig_muscle2

description: Songpan,Sichuan,China,3000m altitude


title: L-pig_lung2

description: Rongchang,Sichuan,China,400m altitude

value: low


title: L-pig_heart3

description: Rongchang,Sichuan,China,400m altitude


title: L-pig_muscle2

description: Rongchang,Sichuan,China,400m altitude


title: L-pig_lung3

description: Rongchang,Sichuan,China,400m altitude


title: L-pig_lung1

description: Rongchang,Sichuan,China,400m altitude


title: L-pig_heart2

description: Rongchang,Sichuan,China,400m altitude


title: L-pig_heart1

description: Rongchang,Sichuan,China,400m altitude


title: L-pig_muscle3

description: Rongchang,Sichuan,China,400m altitude


title: fruit mesocarp_40 DAF-2

description: small RNA

value: 40 days after flowering

value: fruit

value: fruit mesocarp


title: fruit mesocarp_30 DAF-2

description: small RNA

value: 30 days after flowering


title: fruit mesocarp_20 DAF-2

description: small RNA

value: 20 days after flowering


title: fruit mesocarp_10 DAF-2

description: small RNA

value: 10 days after flowering


title: EL38_Exp_3

city: Verona

first: Massimo

last: Delledonne

address: Strada le Grazie 15

country: Italy

institute: Universita' degli Studi di Verona

data_processing:
CASAVA 1.8.2
Reads with more than 10% of undetermined bases or more than 50 bases with a quality score < 7 were discarded
Reads were then clipped from adapter sequences using Scythe software (https://github.com/vsbuffalo/scythe), and low quality ends (Q score < 20 on a 10 nt window) were trimmed with Sickle (https://github.com/vsbuffalo/sickle).
Alignment of reads to reference Vitis vinifera PN40024 (12x) was performed using TopHat 2 (http://tophat.cbcb.umd.edu/)
Expression values (FPKM) and  transcripts isoforms were reconstructed with cufflinks program (from Cufflinks 2 package (http://cufflinks.cbcb.umd.edu/))
Genome_build: Vitis vinifera PN40024 (12x)
Supplementary_files_format_and_content: expression data table contains expression values (FPKM) as calculated by Cufflinks 2

organism: Vitis vinifera

source_name: Grape berry

growth_protocol: Field-grown grapevines according to published protocol

extract_protocol:
Total RNA was extracted according to protocol (Reid et al., 2006).
Indexed cDNA libraries were prepared using TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA) according to manufacturer's instructions. Adapter-ligated cDNA libraries with an insert size of 350-550 bp were size selected on 1.5% agarose gel cassettes using Pippin Prep instrument (Sage Science, Beverly, MA, USA).

treatment_protocol: Removal of leaves and lateral shoots in the berry bunch zone

tag: cultivar

value: Sauvignon blanc

tag: developmental stage (el)

value: Exposed

value: Whole-berry (no seeds)


title: L-pig_muscle1

description: Rongchang,Sichuan,China,400m altitude

value: muscle


title: EL38_Cntrl_2

value: Control


title: EL34_Cnrtrl_3


title: EL38_Exp_2


title: EL34_Exp_3


title: EL34_Exp_1


title: EL38_Exp_1


title: EL34_Cnrtrl_2


title: EL34_Cnrtrl_1


title: EL33_Cntrl_2


title: EL33_Cntrl_1


title: EL33_Exp_1


title: EL31_Cntrl_3


title: EL33_Cntrl_3


title: ∆entC parent Sample 31


title: EL33_Exp_2


title: EL31_Cntrl_2


title: EL31_Exp_3


title: EL31_Cntrl_1


title: EL31_Exp_2


title: EL38_Cntrl_1


title: EL31_Exp_1


title: H-pig_kidney2

description: Songpan,Sichuan,China,3000m altitude

value: high

value: kidney


title: H-pig_kidney3

description: Songpan,Sichuan,China,3000m altitude


title: H-pig_spleen1

description: Songpan,Sichuan,China,3000m altitude

value: spleen


title: EL34_Exp_2


title: H-pig_liver1

description: Songpan,Sichuan,China,3000m altitude

value: liver


title: L-pig_spleen3

description: Rongchang,Sichuan,China,400m altitude

value: adult(>1 year old)


title: L-pig_liver3

description: Rongchang,Sichuan,China,400m altitude

value: low


title: H-pig_liver2

description: Songpan,Sichuan,China,3000m altitude


title: L-pig_liver2

description: Rongchang,Sichuan,China,400m altitude


title: L-pig_spleen1

description: Rongchang,Sichuan,China,400m altitude


title: H-pig_spleen2

description: Songpan,Sichuan,China,3000m altitude


title: EL33_Exp_3


title: L-pig_kidney2

description: Rongchang,Sichuan,China,400m altitude


title: L-pig_kidney1

description: Rongchang,Sichuan,China,400m altitude


title: L-pig_kidney3

description: Rongchang,Sichuan,China,400m altitude


title: L-sheep_spleen1

description: Jining,Shandong,China,50m altitude

organism: Ovis aries

value: adult(>3 years old)


title: L-sheep_spleen2

description: Jining,Shandong,China,50m altitude


title: H-sheep_liver3

description: Songpan,Sichuan,China,3000m altitude


title: H-sheep_spleen2

description: Songpan,Sichuan,China,3000m altitude


title: H-sheep_liver1

description: Songpan,Sichuan,China,3000m altitude


title: H-pig_spleen3

description: Songpan,Sichuan,China,3000m altitude


title: H-pig_liver3

description: Songpan,Sichuan,China,3000m altitude


title: H-sheep_kidney2

description: Songpan,Sichuan,China,3000m altitude


title: H-sheep_spleen1

description: Songpan,Sichuan,China,3000m altitude


title: H-pig_lung1

description: Songpan,Sichuan,China,3000m altitude

value: lung


title: H-pig_kidney1

description: Songpan,Sichuan,China,3000m altitude


title: H-sheep_kidney3

description: Songpan,Sichuan,China,3000m altitude


title: H-sheep_kidney1

description: Songpan,Sichuan,China,3000m altitude


title: sheep_kidney_1

description:
XW_shen1
processed data file: sheep_PCA_new.txt

value: small tail han sheep

value: Jining, Shandong province, China

value: ~3 years old


title: sheep_kidney_2

description:
XW_shen2
processed data file: sheep_PCA_new.txt


title: sheep_liver_2

description:
XW_gan2
processed data file: sheep_PCA_new.txt


title: sheep_kidney_3

description:
XW_shen3
processed data file: sheep_PCA_new.txt


title: L-pig_spleen2

description: Rongchang,Sichuan,China,400m altitude


title: sheep_liver_3

description:
XW_gan3
processed data file: sheep_PCA_new.txt


title: H-sheep_liver2

description: Songpan,Sichuan,China,3000m altitude


title: ChIP-Seq-H3K27me3 RescueK339A Repl3

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

country: Germany

institute: Philipps University of Marburg

data_processing:
ChIP-Seq data were aligned to mouse genome mm9 using bowtie 1.0 with n = 1 and m = 3 as parameter
Bigwig files were created using Galaxy/deepTools, duplicated tags were ignored
RNA-Seq data were aligned by Tophat v2.1.0 to mm10, using the Galaxy Platform. Normalized Values were derived using Cuffdiff v2.2.1.3 using a gffread filtered gencode.vM13.basic.annotation.gtf file as template
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: E14 ES cells

growth_protocol: E14 mouse ES cells (ES-E14TG2a) were cultured in DMEM, 15% FCS, 1 x L-Glutamine (Invitrogen), 1 x Non-essential amino acids (Invitrogen), 1 x Penicillin/Streptomycin(Invitrogen) and LIF (Millipore) on gelatin-coated plates

extract_protocol:
Genomic DNA were extracted using antibodies for MTF2, SUZ12, H3K27me3. RNA-Seq samples were prepared by isolating total RNA using Trizol, mRNA Isolation using Oligo-dT-coupled beads, heat fractionation, reverse transcription and second strand synthesis.
Libraries were constructed of 10-50 ng of DNA following Illumina’s® protocol

treatment_protocol: For ChIP cells were crosslinked with 1% formaldehyd for 10 min and sonicated to 200 bps.

tag: cell type

value: E14 ES cells

value: H3K27me3, Millipore, 07-449

tag: genotype

value: Rescue K339A


title: Input


title: L-sheep_spleen3

description: Jining,Shandong,China,50m altitude


title: ChIP-Seq-H3K27me3 RescueWT Repl3

value: Rescue Wildtye


title: ChIP-Seq-H3K27me3 MTF2KO Repl3

value: MTF2 KO


title: ChIP-Seq-SUZ12 RescueK339A Repl3

value: SUZ12, Cell Signaling, D39F6


title: H-sheep_spleen3

description: Songpan,Sichuan,China,3000m altitude

value: high


title: sheep_liver_1

description:
XW_gan1
processed data file: sheep_PCA_new.txt


title: ChIP-Seq-SUZ12 RescueWT Repl3


title: ChIP-Seq-SUZ12 Control Repl3

value: Control


title: ChIP-Seq-H3K27me3 Control Repl3


title: ChIP-Seq-MTF2 RescueK339A Repl3

value: MTF2, Proteintech, 16208-1-AP


title: ChIP-Seq-MTF2 RescueWT Repl3


title: ChIP-Seq-MTF2 MTF2KO Repl3


title: ChIP-Seq-MTF2 Control Repl3


title: ChIP-Seq-H3K27me3 RescueWT Repl2

data_processing:
ChIP-Seq data were aligned to mouse genome mm9 using bowtie 1.0 with n = 1 and m = 3 as parameter
Bigwig files were created using Galaxy/deepTools, duplicated tags were ignored
RNA-Seq data were aligned by Tophat v2.1.0 to mm10, using the Galaxy Platform. Normalized Values were derived using Cuffdiff v2.2.1.3 using a gffread filtered gencode.vM13.basic.annotation.gtf file as template
Genome_build: mm9

extract_protocol:
Genomic DNA were extracted using antibodies for MTF2, SUZ12, H3K27me3
Libraries were constructed of 10-50 ng of DNA following Illumina’s® protocol


title: RNA-Seq Control Repl3

extract_protocol: RNA-Seq samples were prepared by isolating total RNA using Trizol, mRNA Isolation using Oligo-dT-coupled beads, heat fractionation, reverse transcription and second strand synthesis.


title: RNA-Seq Control Repl2


title: RNA-Seq MTF2KO Repl1


title: ChIP-Seq-H3K27me3 RescueK339A Repl2


title: ChIP-Seq-H3K27me3 MTF2KO Repl2


title: ChIP-Seq-H3K27me3 Control Repl2


title: ChIP-Seq-H3K27me3 MTF2KO Repl1


title: ChIP-Seq-H3K27me3 Control Repl1


title: ChIP-Seq-SUZ12 RescueK339A Repl2


title: ChIP-Seq-H3K27me3 RescueK339A Repl1


title: ChIP-Seq-SUZ12 RescueWT Repl2


title: ChIP-Seq-SUZ12 MTF2KO Repl2


title: ChIP-Seq-SUZ12 MTF2KO Repl3


title: ChIP-Seq-SUZ12 RescueWT Repl1


title: ChIP-Seq-SUZ12 RescueK339A Repl1


title: ChIP-Seq-SUZ12 Control Repl1


title: RNA-Seq MTF2KO Repl2


title: ChIP-Seq-SUZ12 MTF2KO Repl1


title: ChIP-Seq-MTF2 RescueWT Repl2


title: ChIP-Seq-MTF2 RescueK339A Repl2


title: ChIP-Seq-MTF2 MTF2KO Repl2


title: RNA-Seq MTF2KO Repl3


title: RNA-Seq Control Repl1


title: ChIP-Seq-SUZ12 Control Repl2


title: ChIP-Seq-MTF2 RescueK339A Repl1


title: ChIP-Seq-MTF2 RescueWT Repl1


title: ChIP-Seq-MTF2 Control Repl1


title: ChIP-Seq-MTF2 MTF2KO Repl1


title: ChIP-Seq-H3K27me3 RescueWT Repl1


title: L-pig_liver1

description: Rongchang,Sichuan,China,400m altitude

value: liver


title: Endothelial_GFP-_rep3

city: Philadelphia

first: Long

last: Gao

state: PA

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

institute: The Children’s Hospital of Philadelphia

description: Processed data file: Gene_FPKM.txt

data_processing:
Paired-end reads were mapped to the reference mouse genome.
Uniquely mapped reads with fewer than 2 mismatches were used.
Cufflinks was used to assemble transcripts and estimate expression level.
Gene level read count was estimated using FeatureCounts.
Differential gene expression analysis was conducted using edgeR and DESeq.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Gene_FPKM.txt: Gene-level FPKM values across all samples (tab-delimited text file).

source_name: major arteries in E11.5 mouse embryos, endothelial cells, Ly6a-GFP-

growth_protocol: Tg(Ly6a-GFP) conceptuses were generated by crossing C57BL/6 x 129S1/SVImJ F1 females with Tg(Ly6a-GFP) males.

extract_protocol:
Cells were sorted into TRIzol-LS (Invitrogen) and pooled into three independent biological samples. The cells were lysed in TRIzol-LS and the aqueous phase was collected after adding chloroform. The aqueous phase was homogenized by 70% ethanol and RNA isolated using Qiagen RNeasy micro kit. Isolated RNA was treated with TURBO DNA-free DNA Removal Kit to remove contaminating DNA.
mRNA was isolated from total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, NEB), fragmented to average size of 300 nt, reverse transcribed to generate double-stranded cDNA, and followed by NEBNext Ultra RNA Library Prep Kit for Illumina (E7530, NEB) according to manufacturer's instructions including the optional double size selection procedure using Agencourt AMPure XP beads. Prepared libraries were quantified with dsDNA HS Kit (Q32851) for Qubit and the size distribution assessed using High Sensitivity DNA Kit (5067-462) Bioanalyzer.

treatment_protocol: Major arteries in dorsal aorta, umbilical, vitelline (A+U+V) from 122 embryonic day 11.5 Ly6a-GFP+ embryos were dissected and disaggregated with collagenase, and 53,000 Ly6a-GFP+ hematopoietic cluster cells (CD31+ CD144+ ESAM+ c-Kit+), 413,000 Ly6a-GFP- hematopoietic cluster cells, 377,000 Ly6a-GFP+ endothelial cells (CD31+ CD144+ ESAM+ c-Kit-), and 791,000 Ly6a-GFP- endothelial cells collected.

tag: strain/background

value: embryonic day 11.5

value: endothelial cells


title: Endothelial_GFP-_rep1

description: Processed data file: Gene_FPKM.txt


title: ChIP-Seq-MTF2 Control Repl2


title: Endothelial_GFP+_rep2

description: Processed data file: Gene_FPKM.txt

source_name: major arteries in E11.5 mouse embryos, endothelial cells, Ly6a-GFP+


title: Endothelial_GFP+_rep1

description: Processed data file: Gene_FPKM.txt


title: KO2

city: Dallas

first: Andres

last: Ramirez-Martinez

state: TX

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: UTSW Medical Center

data_processing:
Quality assessment of the RNA-Seq data was done using NGS-QC-Toolkit (Patel and Jain, 2012) with default setting
Quality filtered reads generated by the tool were then aligned to the mouse reference genome GRCm38 (mm10) using the Tophat2 (v 2.0.0 ) aligner (Kim et al., 2013) using default setting.
Differential gene expression analysis was done using the R package DESeq2 (v 1.6.3) (Anders and Huber, 2010).
Read counts were normalized by taking the median of each gene count across samples and dividing each sample gene count by the relative ratio of library sizes between the calculated median and sample size. The averaged normalized expressions values of the samples were used to calculate fold change and p-values.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: CPM value for all genes calculated using edgeR
Supplementary_files_format_and_content: edgeR output in .txt format containing log2foldchange, log2CPM and LR values and p values. Data present reflect change in averaged KO samples (KO1, KO2, KO3) with respect to WT (WT1,WT2,WT3) samples. Fdr = 0.01, p-value = 0.05 were used as cut-offs.

source_name: hindlimb muscle

extract_protocol:
P0 mice were sacrificed, deskinned, and hindlimb muscle was removed from the leg and flash frozen. Total RNA was extracted using QIAGEN Rneasy mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: skeletal muscle


title: Hematopoietic_GFP+_rep3

description: Processed data file: Gene_FPKM.txt

source_name: major arteries in E11.5 mouse embryos, hematopoietic cells, Ly6a-GFP+

value: hematopoietic cells


title: Hematopoietic_GFP+_rep1

description: Processed data file: Gene_FPKM.txt


title: Hematopoietic_GFP+_rep2

description: Processed data file: Gene_FPKM.txt


title: KO3


title: Hematopoietic_GFP-_rep1

description: Processed data file: Gene_FPKM.txt

source_name: major arteries in E11.5 mouse embryos, hematopoietic cells, Ly6a-GFP-


title: WT2

value: WT


title: Hematopoietic_GFP-_rep2

description: Processed data file: Gene_FPKM.txt


title: WT3


title: H-chicken_lung3

description: Daocheng,Sichuan,China,3000m altitude

organism: Gallus gallus

value: lung

value: adult(>200 days old)


title: H-chicken_heart3

description: Daocheng,Sichuan,China,3000m altitude

value: heart


title: H-chicken_lung2

description: Daocheng,Sichuan,China,3000m altitude


title: Endothelial_GFP-_rep2

description: Processed data file: Gene_FPKM.txt


title: H-chicken_muscle3

description: Daocheng,Sichuan,China,3000m altitude

value: muscle


title: WT1


title: H-chicken_heart2

description: Daocheng,Sichuan,China,3000m altitude


title: H-chicken_muscle2

description: Daocheng,Sichuan,China,3000m altitude


title: H-chicken_heart1

description: Daocheng,Sichuan,China,3000m altitude


title: L-chicken_lung3

description: Ya'an,Sichuan,China,500m altitude

value: low


title: H-chicken_lung1

description: Daocheng,Sichuan,China,3000m altitude


title: Endothelial_GFP+_rep3

description: Processed data file: Gene_FPKM.txt


title: Hematopoietic_GFP-_rep3

description: Processed data file: Gene_FPKM.txt


title: H-chicken_muscle1

description: Daocheng,Sichuan,China,3000m altitude


title: L-chicken_lung2

description: Ya'an,Sichuan,China,500m altitude


title: L-chicken_lung1

description: Ya'an,Sichuan,China,500m altitude


title: L-chicken_muscle3

description: Ya'an,Sichuan,China,500m altitude


title: L-chicken_muscle2

description: Ya'an,Sichuan,China,500m altitude


title: L-chicken_heart2

description: Ya'an,Sichuan,China,500m altitude


title: KO1


title: L-chicken_muscle1

description: Ya'an,Sichuan,China,500m altitude


title: L-chicken_heart1

description: Ya'an,Sichuan,China,500m altitude


title: Sample34_SNI_PAG

city: New York

first: Venetia

last: Zachariou

state: New York

address: 1425 Madison Ave Icahn School of Medicine

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description:
2.5 months after injury or sham surgery.
Processed data file: rpkm.txt

data_processing:
RNA-seq reads were aligned to mouse genome mm10 using Tophat2.
Uniquely aligned short reads were counted against the Gencode vM2 annotation using HTSeq-counts.
RPKM values were calculated with a custom R script using total uniquely aligned read values and gene lengths from the Gencode vM4 annotation.
Genome_build: mm10 (MGSCv37)
Supplementary_files_format_and_content: rpkm.txt: Tab-delimited text file with tabulated RPKM values for all RNA-seq samples and genes.

source_name: periaqueductal grey, SNI

extract_protocol:
Brain regions were dissected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Poly-A-containing mRNA was purified by using poly-T oligo-attached magnetic beads, and the mRNA-seq library was prepared from each pooled RNA sample by using the Illumina TruSeq RNA Sample Preparation Kit v2, according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Sham or spared nerve injury to the sciatic nerve.

value: Brain (periaqueductal grey)

tag: Sex

value: Male

value: Adult

tag: treatment

value: Spared nerve injury model (SNI)

tag: time after treatment

value: 2.5 months


title: Sample36_SNI_PAG


title: Sample35_SNI_PAG


title: Sample33_SNI_PAG


title: DGM-10284_LA-BC (HIV)

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description:
DGM-10284
basal cells cultured from airway epithelium samples

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Expression analysis was performed using Bowtie (v0.12.8.0, http://bowtie-bio.sourceforge.net), Tophat (v2.0.4, http://tophat.cbcb.umd.edu) and Cufflinks (v2.0.2, http://cufflinks.cbcb.umd.edu)
To correct for transcript length and depth of coverage, raw paired-end sequenced reads were converted into fragments per kilobase of exon per million fragments sequenced (FPKM) resulting in the fpkm_tracking files.
Resultant fragments were aligned (mapped) to the reference genome build UCSC hg19 using Bowtie
Non-aligned reads were segmented using Tophat and re-aligned to the genome, aligning reads that span introns and determining junction splice sites. Cufflinks assembled reads into transcripts and assembled reads merged using Cuffmerge; the reads generated from a transcript are directly proportional to the transcripts relative abundance. For the analysis, Tophat (which automatically runs Bowtie) was run for each read pair in a given lane
For each read pair, Tophat produced one file which contained all reads mapped to the human_g1k_v37 genome and RefSeq (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz) transcriptome.
This process was carried out independently for each sample lane. Before running Cufflinks, Samtools (v0.1.18.0, http://samtools.sourceforge.net) was used to merge each sample's independent Tophat results into one file. This file contains all of the aligned reads for each read pair. Finally, Cufflinks was run on the merged Tophat output to produce a file with FPKM values for each sample.
Data was analyzed using Tuxedo pipeline software.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: fpkm_tracking files are text files that include the RefSeq gene ID and location, the FPKM value, high and low confidence and status.

source_name: airway basal cells, nonsmoker

growth_protocol: Airway epithelial cells collected by brushing were cultured supplemented with growth factors according to the manufacturer’s instructions. Media was changed every 2 days until time of harvest at day 7, when the cells had reached 70 to 80% confluence.

extract_protocol:
Total RNA from harvested nonsmoker basal cells was extracted with TRIzol with subsequent RNA clean-up using the RNeasy MinElute RNA purification kit to remove residual DNA
The TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) was utilized as per protocol to generate cDNA that was then purified with QIAquick PCR purification kit (Qiagen, Valencia, CA).
Samples were loaded onto an Illumina flowcell for paired-end 101 x 2 sequencing reactions using the Illumina HiSeq 2000, using a single flow cell with 4 samples multiplexed per lane of flow cell.

value: airway basal cells

tag: smoking status

value: nonsmoker

tag: disease state

value: healthy HIV


title: DGM-10194_LA-BC (HIV)

description:
DGM-10194
basal cells cultured from airway epithelium samples


title: DGM-10565_LA-BC (HIV)

description:
DGM-10565
basal cells cultured from airway epithelium samples


title: Sample31_SNI_PAG

tag: age


title: DGM-11852_LA-BC (HIV)

description:
DGM-11852
basal cells cultured from airway epithelium samples


title: DGM-01774_LA-BC (HIV)

description:
DGM-01774
basal cells cultured from airway epithelium samples


title: L-chicken_heart3

description: Ya'an,Sichuan,China,500m altitude

tag: altitude


title: DGM-10503_LA-BC (HIV)

description:
DGM-10503
basal cells cultured from airway epithelium samples


title: Sample32_SNI_PAG


title: DGM-10568_LA-BC (HIV)

description:
DGM-10568
basal cells cultured from airway epithelium samples


title: DGM-01657_LA-BC (HIV)

description:
DGM-01657
basal cells cultured from airway epithelium samples


title: DGM-11374_LA-BC (HIV)

description:
DGM-11374
basal cells cultured from airway epithelium samples


title: Sample30_SHAM_PAG

source_name: periaqueductal grey, sham

value: Sham surgery


title: Sample29_SHAM_PAG


title: GSC10-control-2

city: San Antonio

first: Yidong

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: GSC10 cells trated with vehicle

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: GSC10 (glioma stem cells)

growth_protocol: GSC10 were cultured in neurobasal medium supplemented with B27 serum-free supplement, EGF (20 ng/mL), bFGF (20 ng/mL), LIF (10 ng/mL) and heparin (5 µg/mL)

extract_protocol: Total RNA samples about 1-2 mg were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 100bp single-end (SE) sequencing protocol.

treatment_protocol: Total RNA was isolated from glioma stem cells (GSC10) that are trated with vehicle or NCD-38 were subjected to RNAseq analysis

value: vehicle


title: DGM-01620_LA-BC (HIV)

description:
DGM-01620
basal cells cultured from airway epithelium samples


title: CR mito small RNA seq rep3

city: Beijing

first: De-Pei

last: Liu

address: Dong Dan San Tiao 5, Dongcheng District

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas (clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw datas were calculated.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2 (Friedlander et al., 2011) andsrna-tools-cli were used to obtain the potential miRNAs.
To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself.
miRNA expression levels were estimated by TPM (transcript per million) through he following criteria (Zhou et al., 2010): normalization formula: Normalized expression = mapped readcount/Total reads*1000000.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample.

source_name: Mouse liver mitochondria

growth_protocol: Eight-week-old male WT C57BL/6J mice were housed individually. The mice were housed in a temperature-controlled environment with a 12-h light:12-h dark cycle and were allowed free access to water.

extract_protocol:
For ATL and CTL, Trizol extraction of total RNA was performed according to the manufacturer's instructions. Three RNA samples in the same group were pooled together in equal amounts. For AM1, AM2, AM3, CM1, CM2 and CM3, mitochondria were isolated through differential centrifugation (mitoplast purified) before Trizol extraction of mitochondrial total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The mice were randomly allocated into 2 groups. AL mice were fed AL food ad libitum for 12 weeks. CR mice were fed a 20% restricted diet for the first week and a 40% restricted diet for the remaining 11 weeks of the CR diet.

value: Liver mitochondria

tag: food regimen

value: Caloric restriction

tag: strain


title: Sample28_SHAM_PAG


title: GSC10-NCD38-2

description: GSC10 cells trated with NCD-38


title: GSC10-control-1

description: GSC10 cells trated with vehicle


title: AL mito small RNA seq rep3

value: Ad libitum


title: CR mito small RNA seq rep2


title: CR mito small RNA seq rep1


title: GSC10-NCD38-1

description: GSC10 cells trated with NCD-38


title: AL mito small RNA seq rep2


title: AL mito small RNA seq rep1


title: Sample25_SHAM_PAG


title: CR total small RNA seq

description: CTL

source_name: Mouse whole liver

value: Liver


title: Sample26_SHAM_PAG


title: Sample23_SNI_PFC

source_name: prefrontal cortex, SNI

value: Brain (prefrontal cortex)


title: Sample24_SNI_PFC


title: Sample22_SNI_PFC


title: Input_DNMT3b 12

city: Seville

first: Villalba

last: Leticia

address: Avda. Manuel Siurot s/n

country: Spain

institute: FISEVI

data_processing:
Basecalls performed automatically by MiSeq Control Software using Real-Time Analysis
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie for Illumina (Galaxy Version 1.1.2) with default parameters
Peaks were called using MACS Model-based Analysis for ChIP-Seq (version 1.0.0) with default parameters
BETA-minus: Targets prediction with binding only (version 1.0.0), PAVIS and PAPST 1.0 tools, were used to assign the ChIP-seq peak data to the neighboring genes (annotation) with default parameters
Genome_build: mm9
Supplementary_files_format_and_content: Bed files were generated using MACS Model-based Analysis for ChIP-Seq (version 1.0.0); Columns: Chr peak; Start peak; End peak; -10*log10(pvalue)

source_name: Enteric precursor cells

growth_protocol: Enteric precursor cells were extracted from ganglionic bowels of 7 days aged CD-1 mice. Bowels were dissected and incubated in a solution of 0.26 mg/ml trypsin collagenase, 5 mg/ ml dispase, 0.28 mg/ml hyaluronidase, 3.3 μg/ml elastase, and 0.6 mg/ml collagenase in phosphate-buffered saline for up to 30 minutes at 37 °C. Digested tissue was triturated and washed, and the cells were cultured in Dulbecco’s modified Eagle medium (1 mg/ml glucose) containing 100 U/ml penicillin, 100 g/ml streptomycin, supplemented with 2 mmol/l l-glutamine (Gibco Life Technologies, Carlsbad, CA), 0.05 mmol/l 2-mercaptoethanol, 1% (volume/volume) N1 (Sigma Aldrich, Poole, Dorset, UK), 10% (volume/volume) human serum, 20 ng/ml basic fibroblast growth factor, 20 ng/ml epidermal growth factor, and 10 ng/ml glial cell–derived neurotrophic factor (Peprotech, London, UK).

extract_protocol:
Cells were fixed with 1%  formaldehyde and was sonicated in a Bioruptor System (Diagenode, USA). ChIP assay was performed with the Magna Chip Hisens Kit (Millipore,USA) according to manufacturer’s instructions and using the Anti-Dnmt3b antibody-ChIP Grade (Abcam, USA). 10% of samples volume/reaction was kept as controls (input) before immunoprecipitation.
ChIP and input samples were processed with the ChIP-Seq DNA sample prep kit (Illumina, USA), following the manufacturer’s instructions. Size-selection was then performed by agarose gel electrophoresis to isolate fragments with size between 200 and 300bp. Afterwards, purified libraries were amplified by PCR and size range was subsequently checked in the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit (Agilent, USA). Quantification was performed in the 7500-Real Time PCR System (Applied Biosystems) with the Library Quantification Kit (Kapa Biosystems). After proper dilutions, 4 nM libraries were processed, to obtain pools at a final concentration of 8 pM following the instructions of the Miseq Reagent kit V2. (50 cycles) (Illumina, USA).

value: ganglionic gut

value: Enteric precursor cells

tag: chip antibody

value: none (input)

tag: pool number


title: AL total small RNA seq

description: ATL


title: Sample21_SNI_PFC

value: Male


title: Input_DNMT3b 11


title: Input_DNMT3b 10


title: Input_DNMT3b 9


title: Sample20_SNI_PFC

value: Adult


title: Sample27_SHAM_PAG

value: Brain (periaqueductal grey)


title: Input_DNMT3b 6


title: Input_DNMT3b 8


title: Input_DNMT3b 5


title: Input_DNMT3b 3


title: Input_DNMT3b 2


title: Sample17_SHAM_PFC

source_name: prefrontal cortex, sham

value: 2.5 months


title: Input_DNMT3b 1


title: ChIP-Seq_DNMT3b 12

value: Anti-Dnmt3b antibody-ChIP Grade  (ab2851, Abcam)


title: ChIP-Seq_DNMT3b 11


title: ChIP-Seq_DNMT3b 10


title: Sample16_SHAM_PFC


title: Input_DNMT3b 7


title: ChIP-Seq_DNMT3b 8


title: ChIP-Seq_DNMT3b 7


title: ChIP-Seq_DNMT3b 6


title: Sample15_SHAM_PFC


title: Sample14_SHAM_PFC


title: ChIP-Seq_DNMT3b 5


title: ChIP-Seq_DNMT3b 4


title: ChIP-Seq_DNMT3b 3


title: Sample13_SHAM_PFC


title: Input_DNMT3b 4


title: ChIP-Seq_DNMT3b 1


title: Sample19_SNI_PFC

value: Spared nerve injury model (SNI)


title: ChIP-Seq_DNMT3b 2


title: L-cow_lung2

description: Chengdu,Sichuan,China,500m altitude

organism: Bos taurus

source_name: lung

value: low

value: lung

value: adult(>4 years old)


title: L-cow_muscle3

description: Chengdu,Sichuan,China,500m altitude

source_name: muscle

value: muscle


title: L-cow_lung3

description: Chengdu,Sichuan,China,500m altitude


title: L-cow_muscle2

description: Chengdu,Sichuan,China,500m altitude


title: Sample18_SHAM_PFC

value: Sham surgery


title: ChIP-Seq_DNMT3b 9


title: Sample12_SNI_Nac

source_name: adult nucleus accumbens, SNI

value: Brain (adult nucleus accumbens)


title: L-cow_muscle1

description: Chengdu,Sichuan,China,500m altitude


title: Sample10_SNI_Nac


title: Sample9_SNI_Nac


title: Sample8_SNI_Nac


title: Sample7_SNI_Nac


title: L-cow_spleen3

description: Chengdu,Sichuan,China,500m altitude

source_name: spleen

value: spleen


title: cattle_heart_2

description:
C_xin2
processed data file: cattle_PCA_new.txt

source_name: heart

value: indigenous

tag: location

value: Chengdu, Sichuan province, China

value: heart

value: ~4 years old


title: cattle_heart_3

description:
C_xin3
processed data file: cattle_PCA_new.txt


title: Sample6_SHAM_Nac

source_name: adult nucleus accumbens, sham

value: Male


title: L-cow_spleen1

description: Chengdu,Sichuan,China,500m altitude


title: Sample5_SHAM_Nac

value: Adult


title: Sample3_SHAM_Nac


title: Sample4_SHAM_Nac


title: cattle_kidney_1

description:
C_shen1
processed data file: cattle_PCA_new.txt

source_name: kidney

value: kidney


title: cattle_kidney_2

description:
C_shen2
processed data file: cattle_PCA_new.txt


title: cattle_kidney_3

description:
C_shen3
processed data file: cattle_PCA_new.txt


title: cattle_liver_2

description:
C_gan2
processed data file: cattle_PCA_new.txt

source_name: liver

value: liver


title: Sample2_SHAM_Nac

description:
2.5 months after injury or sham surgery.
Processed data file: rpkm.txt

value: 2.5 months


title: Sample1_SHAM_Nac


title: cattle_liver_1

description:
C_gan1
processed data file: cattle_PCA_new.txt


title: TNB_ANT_2_RNA-Seq

city: Harbin

first: shipeng

last: shang

address: XueFu Road 194, NanGang District

institute: Department of Breast Surgery, Harbin Medical University Cancer Hospital

data_processing:
Sequenced reads mapped to hg19 whole genome using tophat version 2.0.9 with parameters by default to get bam files
Cullinks-2.1.1  was used to get the file includes FPKM
Genome_build: hg19
Supplementary_files_format_and_content: txt file includes  FPKM about isoforms

source_name: Adjacent noncancerous breast tissue for 325RC2_R1

extract_protocol:
RNA was harvested using Trizol reagent, Ribo-Zero™ Gold Kits(Human). 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: adjacent noncancerous tissue

tag: subtype

value: HER2 and triple negative


title: L-cow_lung1

description: Chengdu,Sichuan,China,500m altitude

value: low

value: lung


title: TNB_ANT_1_RNA-Seq

source_name: Adjacent noncancerous breast tissue for FC100895_R1


title: cattle_heart_1

description:
C_xin1
processed data file: cattle_PCA_new.txt


title: TNB_ANT_0_RNA-Seq

source_name: Adjacent noncancerous breast tissue for RC100884_R1


title: TNB_2_RNA-Seq

source_name: HER2 and triple negative breast cancer

value: cancer


title: gfp 15605

first: Immanuel

last: Purushothaman

address: 1425 Madison Avenue

data_processing:
Name : Version : Parameters
Bowtie2 : 2.1.0 : defaults
TopHat2 : 2.0.9 : --no-novel-juncs --b2-very-sensitive
Genome_build: GRCm38/mm10

source_name: TET1 loxp/loxp mice

extract_protocol:
Trizol standard protocol
RNA integrity was confirmed by Bioanalyzer with RIN >8.0. 0.5µg of total RNA wasere used for mRNA library construction following instructions ofusing Illumina truseq mRNA sample prep kit.
RNAs from each mice were individually barcoded into libraries by following illumina kit protocol.

treatment_protocol: TET1 loxp/loxp mice received AAV-Cre injection in nucleus accumbens. RNA was extracted from each of the seven animals and sequenced individually. In parallel, seven TET1 loxp/loxp mice that received AAV-GFP injection were included as control.

tag: protocol

value: AAV-GFP injection

value: brain


title: gfp 16101


title: TNB_1_RNA-Seq


title: gfp 16103


title: L-cow_spleen2

description: Chengdu,Sichuan,China,500m altitude

data_processing:
Illumina Casava1.82 software was used for basecalling.
High-quality reads were obtained by discarding reads containing over 10% Ns, or overlapping at least 10 bp with adaptor sequences at mismatch rate equal to or less than 10%, or including over 50% bases with base quality score less than five, and then mapped to respective genome of the species using Tophat 2.0.11.
Cufflinks version 2.2.1 were applied to quantify gene expression and obtain FPKM expression values (denoted as the fragments per Kb of transcript per Mb mapped reads).
Genome_build: Galgal4, UMD3.1, Suscrofa 10.2, Oar_v3.1 and CHIR_1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

extract_protocol:
The total RNA was extracted using the TrIzol reagent (Life Technologies, Beijing, China) according to the manufacturer’s protocols. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
The dUTP based strand-specific RNA libraries were prepared for sequencing using standard Illumina protocols; Strand-specific mRNA-Seq

value: spleen

value: adult(>4 years old)


title: gfp 15961


title: gfp 15596


title: gfp 15594


title: gfp 15603


title: cre 16105

value: AAV-Cre injection


title: Normal_1_RNA-Seq

source_name: Normal breast tissue

value: normal tissue


title: Sample11_SNI_Nac

value: Brain (adult nucleus accumbens)

value: Spared nerve injury model (SNI)


title: cre 16104


title: cattle_liver_3

description:
C_gan3
processed data file: cattle_PCA_new.txt

data_processing:
Illumina Casava1.82 software was used for basecalling.
High-quality reads were obtained by discarding reads containing over 10% Ns, or overlapping at least 10 bp with adaptor sequences at mismatch rate equal to or less than 10%, or including over 50% bases with base quality score less than five.
Cufflinks version 2.2.1 were applied to quantify gene expression and obtain FPKM expression values (denoted as the fragments per Kb of transcript per Mb mapped reads).
Genome_build: cattle: bosTau6 or UMD3.1, sheep: oviAri3, goat: chinese assembly v2 (http://www.goatgenome.org/projects.html)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.  The goat protein sequences are available in the file goat.v4.gff.filter.pep.txt on the series record.

value: indigenous

value: Chengdu, Sichuan province, China

value: ~4 years old


title: cre 16102


title: LB(HER2+)_ANT_1_RNA-Seq

source_name: Adjacent noncancerous breast tissue for RC100841_R1

value: luminal B HER2 positive


title: LB(HER2+)_ANT_2_RNA-Seq

source_name: Adjacent noncancerous breast tissue for 327FC1_R1

value: adjacent noncancerous tissue


title: cre 15604


title: LB(HER2+)_ANT_0_RNA-Seq

source_name: Adjacent noncancerous breast tissue for RC100031_R1


title: cre 15597


title: cre 15593


title: LB(HER2+)_2_RNA-Seq

source_name: luminal B (HER2 positive)


title: LB(HER2-)_ANT_2_RNA-Seq

source_name: Adjacent noncancerous breast tissue for FC100870_R1

value: luminal B HER2 negative


title: TNB_0_RNA-Seq

value: HER2 and triple negative


title: LB(HER2+)_1_RNA-Seq


title: LB(HER2-)_ANT_1_RNA-Seq

source_name: Adjacent noncancerous breast tissue for RC200883_R1


title: LB(HER2-)_2_RNA-Seq

source_name: luminal B (HER2 negative)


title: LB(HER2+)_0_RNA-Seq


title: LB(HER2-)_1_RNA-Seq


title: LB(HER2-)_ANT_0_RNA-Seq

source_name: Adjacent noncancerous breast tissue for 346RC1_R1


title: Normal_2_RNA-Seq


title: LA_ANT_2_RNA-Seq

source_name: Adjacent noncancerous breast tissue for 323RP1_R1

value: luminal A


title: LA_2_RNA-Seq

source_name: luminal A

value: cancer


title: LB(HER2-)_0_RNA-Seq


title: LA_ANT_0_RNA-Seq

source_name: Adjacent noncancerous breast tissue for RC100896_R1


title: LA_1_RNA-Seq


title: LA_ANT_1_RNA-Seq

source_name: Adjacent noncancerous breast tissue for FC100875_R1


title: Normal_0_RNA-Seq


title: LA_0_RNA-Seq


title: HER2_ANT_2_RNA-Seq

source_name: Adjacent noncancerous breast tissue for RC200876_R1

value: HER2 positive


title: cre 15960

value: brain


title: HER2_ANT_1_RNA-Seq

source_name: Adjacent noncancerous breast tissue for FC100868_R1


title: stranded_RNA-seq_Non-targeting sgRNA Day 7 Rep-2

city: Princeton

first: Trinna

middle: L.

last: Cuellar

state: New Jersey

address: Lewis Thomas Lab, Washington Rd/MOF223C

institute: Princeton University

data_processing:
Illumina Casava 1.8 software was used for basecalling
Consensus sequences for elements for upregulated TEs were downloaded from the Dfam database (Hubley et al., 2016).
Stranded RNA-seq data was then aligned to consensus sequences using BWA-MEM and quantified using HTseq-count(Anders et al., 2015; Li, 2013).
Reads were visualized using the IGV genome browser, using a custom pseudogenome that was generated from the Dfam consensus sequences (Robinson et al., 2011; Thorvaldsdottir et al., 2013).
Genome_build: obtained consensus TE sequences, see file on series record.
Supplementary_files_format_and_content: Excel file including counts for each strand of TEs

source_name: Blood

growth_protocol: THP-1 cells were grown in RPMI+10% FBS and 1X L-glutamine

extract_protocol:
At each time-point, cells were spun down, washed with PBS, flash frozen on dry ice, and RNA was isolated with Qiagen RNeasy micro kits.
100 ng of total RNA, for each sample, was used for library preparation with a TruSeq Stranded Total RNA Library Prep Kit (Illumina). Size of the libraries was confirmed using a 2200 TapeStation and High Sensitivity D1K screen tape (Agilent Technologies) and their concentration was determined via qPCR (Library quantification kit, KAPA

treatment_protocol: Cells were spin-transduced with sgRNAs and 48 hours post transduction, cells were placed under selection with 1ug/ml of puromycin.

tag: cell line

tag: cell type

value: AML Cell Line

tag: disease

value: Acute Myeloid Leukemia (AML)


title: stranded_RNA-seq_Non-targeting sgRNA Day 7 Rep-3


title: HER2_ANT_0_RNA-Seq

source_name: Adjacent noncancerous breast tissue for 301RC1_R1

tag: tissue


title: HER2_2_RNA-Seq

source_name: HER2 positive breast cancer


title: HER2_1_RNA-Seq


title: stranded_RNA-seq_Non-targeting sgRNA Day 7 Rep-1


title: stranded_RNA-seq_SETDB1 sgRNA 9 Day 7 Rep-2


title: HER2_0_RNA-Seq


title: stranded_RNA-seq_SETDB1 sgRNA 9 Day 7 Rep-1


title: stranded_RNA-seq_SETDB1 sgRNA 9 Day 7 Rep-3


title: stranded_RNA-seq_SETDB1 sgRNA 9 Day 4 Rep-3


title: stranded_RNA-seq_Non-targeting sgRNA Day 4 Rep-3


title: stranded_RNA-seq_SETDB1 sgRNA 9 Day 4 Rep-2


title: stranded_RNA-seq_Non-targeting sgRNA Day 4 Rep-2


title: stranded_RNA-seq_Non-targeting sgRNA Day 4 Rep-1


title: stranded_RNA-seq_SETDB1 sgRNA 9 Day 4 Rep-1


title: RNA-seq_Non-targeting sgRNA Day 7 Rep-3

description:
SAM24158156
[processed data files:]
std exp analysis: NGS809_counts.xls
RNAseq_Diff_exp_SETDB1vsNTC.xls
repeat analysis: RepEnrich_Transposable_elements_fraction_counts.xlsx

data_processing:
Illumina Casava 1.8
Sequencing reads were filtered to have at least an average base quality of 23 and were then aligned to GRCh38  using GSNAP
Expression counts per gene were obtained by counting the number of reads aligned uniquely to each gene locus as defined by NCBI and Ensembl gene annotations and RefSeq mRNA sequences
For Transposable element analysis reads for first mapped to hg19 with bowtie command: -p 16 -t -m 1 -S --max, and then RepEnrich was run on the data using python command: python RepEnrich.py /data/hg19_LTR_repeatmasker.bed /data/sample_A sample_A /data/hg19_setup_folder sampleA_multimap.fastq sampleA_unique.bam --is_bed TRUE --cpus 16
Differential expression analysis was performed on the RepEnrich fractional counts using EdgeR.
Genome_build: Standard gene expression GRCh38, For RepEnrich hg19 was used and hg19 repeat masker annotations
Supplementary_files_format_and_content: Excel files including counts for the standard gene expression analysis and differential expression analysis. For the transposable element analysis, a fractional counts excel file is included.

extract_protocol:
At each time-point, cells were spun down, washed with PBS, flash frozen on dry ice, and RNA was isolated with Qiagen RNeasy micro kits.
0.5 ug of total RNA was used as an input material for library preparation using a TruSeq RNA Sample Preparation Kit v2 (Illumina)


title: HCT116_J2_Combo (v2)

city: Grand Rapids

first: Peter

middle: A

last: Jones

state: MI

address: 333 Bostwick Ave

department: Center for Epigenetics

institute: Van Andel Research Institute

description:
double stranded RNA
J2-RNAseq-ERVconts-MarkDuplicates.xlsx

data_processing:
Alignment with Bowtie2
MarkDuplicate in picard
Count reads aligned to annotation from RepeatMasker after removing PCR duplicates by MarkDuplicates in Picard tool.
Genome_build: hg19
Supplementary_files_format_and_content: dsRNA measurement from J2 antibody pull down experiment in HCT116 cell line

growth_protocol: HCT116 were maintained in McCoy’s 5A medium and cultured according to standard mammalian tissue culture protocols and sterile technique.

extract_protocol: The 5-Aza-CdR treated cells were lysed with lysis buffer (30 mM HEPES-KOH at pH 7.4, 20mM MgOAc, 5mM DTT, 150mM KOAc, 0.1% NP-40, protease inhibitors). RNase T1(single-strand-specific RNA endonuclease) was added into the lysis buffer. The cell lysates were used for dsRNA pull-down with 3μg of J2 antibody (Scicons) on Dynabeads Protein G (Invitrogen) for 2 hours at 4°C. The beads were washed with wash buffer (30 mM HEPES-KOH at pH 7.4, 20mM MgOAc, 5mM DTT, 150mM KOAc, 0.1% NP-40, protease inhibitors). Digestions of single-stranded RNA were carried out by RNase T1 (Roche). Digestions of DNA were carried out by TURBO DNase (Thermo Fisher). dsRNA was purified and fragmented into 200 bp by shearing (Covaris). cDNA library preparation. RNA-seq libraries were prepared by using the NEBNext Multiplex Small RNA Library Prep Set for Illumina.

treatment_protocol: HCT116 (3 x 10^5) cells were treated with 0.3 μM of 5-Aza-CdR (Sigma-Aldrich). After 24 hours, medium was replaced and maintained at Day 5.

value: human colon carcinoma cell line HCT116

tag: treatment

value: Combination

tag: antibody

value: J2 antibody


title: RNA-seq_Non-targeting sgRNA Day 7 Rep-2

description:
SAM24158155
[processed data files:]
std exp analysis: NGS809_counts.xls
RNAseq_Diff_exp_SETDB1vsNTC.xls
repeat analysis: RepEnrich_Transposable_elements_fraction_counts.xlsx


title: HCT116_J2_Aza (v2)


title: J2E pStat5 ChIPseq Input

city: Melbourne

first: Kevin

middle: Robert

last: Gillinder

state: Victoria

address: 99 Commercial Road

department: Australian Centre for Blood Diseases

country: Australia

institute: Monash University

description:
wildtype immortalised fetal liver erythroid cell line
pStat5_J2E-30mEPO_peaks.xls

data_processing:
Base calling was performed with Torrent Suite v4.0.1
TMAP (v3.0.1) with the following options: mapall, -v, -Y, -u, -o 2, stage1, map4 was used to map reads to the reference genome (mm9; ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/UCSC/mm9/Mus_musculus_UCSC_mm9.tar.gz)
Fragments mapping to the same position on the same strand were taken to be PCR duplicates and were subsequently discarded, retaining only unique alignments with the highest MAPQ score.
Reads were further filtered to remove repetitive RNA, DNA and satellite elements by Repeatmasker software (Wheeler and Eddy 2013) and ENCODE blacklist regions (Maher 2012).
ChIP-seq peaks were called with MACS (v2.1.0) using uniquely mapped ChIP and input sequence alignments.
Genome_build: mm9
Supplementary_files_format_and_content: comma separated values of gene expression
Supplementary_files_format_and_content: MACS2 peak calling results

source_name: J2E erythroid cell line (Klinken et al. 1998)

growth_protocol: Erythroid cell lines were passaged (1:5) every 2-3 days in DMEM supplemented with 10% FBS, 1% Glutamine & 1% Penicillin-Streptomycin in a standard tissue culture incubator at 37 °C with 5% CO2

extract_protocol:
ChIP was performed as described (Gillinder KR et al. Promiscuous DNA-binding of a mutant zinc finger protein corrupts the transcriptome and diminishes cell viability. Nucleic Acids Res 2016). Five replicates J2E cell lines induced with EPO and incubated for 30 mins before fixation with 1% formaldehyde. Chromatin was fragmented to approximately 200-400bp by sonication (Diagenode Bioruptor® Pico for 5 minutes cycling between 30 seconds ‘ON’ and 30 seconds ‘OFF’), pre-cleared and immunoprecipitated with protein A sepharose beads (GE Healthcare).
Sequencing libraries were generated from 5 pooled replicates using the Ion Xpress™ Plus gDNA Fragment Library Preparation Kit following the ChIP-Seq Library Preparation for the Ion Proton™ System.

treatment_protocol: Cells were treated with 10 U/ml erythropoietin (EPO) for 30 mins.

tag: transgene

value: treated with erythropoietin


title: J2E pStat5 ChIPseq ChIP

tag: chip antibody reference

value: Thermofisher Scientific #716900


title: HCT116_J2_Vc

value: Vc


title: J2E 4sU-RNA-seq minus epo rep1

description:
wildtype immortalised fetal liver erythroid cell line
4sU-labelled RNA
counts_J2E_EPO_RNAseq.csv

data_processing:
Base calling was performed with Torrent Suite v4.0.1
Tophat2 (v2.0.10) was used to perform spliced alignment to the reference transcriptome and genome (mm9; ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/UCSC/mm9/Mus_musculus_UCSC_mm9.tar.gz) using default options with the following additional parameters: -N 4, --read-gap-length 4, --read-edit-dist 4, --read-realign-edit-dist 0, -a 5, -i 50, -g 6, --coverage-search, --microexon-search, --library-type fr-firststrand.
Unaligned sequences were subsequently remapped using TMAP (v3.0.1) with the following options: mapall, -v, -Y, -u, -o 2, stage1, map4.
Successful alignments were merged back into the Tophat2 SAM file.
Alignments of less than 30 nt were discarded.
Reads Per Million (RPM) was calculated with htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) using full transcripts (intron and exon mapped reads) and differential expression was determined with DEseq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html) in R
Genome_build: mm9
Supplementary_files_format_and_content: comma separated values of gene expression
Supplementary_files_format_and_content: MACS2 peak calling results

extract_protocol:
Total RNA was extracted using TRIzol® Reagent (Life Technologies, #15596026) according to the manufacturer’s instructions with manually dissociated cells washed in 1 ml DPBS (Gibco™, #14190-136). Extracted RNA was subsequently treated with DNase I (New England Biolabs, #M0303L) to remove residual gDNA contamination. Isolation of 4sU-RNA was performed essentially as previously described (Rabani et al. Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat Biotechnol 2011) with minor modifications. Purified RNA was biotinylated with EZ-Link Biotin-HPDP (Pierce; #21341) and isolated using µMacs Streptavidin Kit (Miltenyi; #130-074-101). 4sU-enriched RNA was then purified with RNeasy MinElute Spin Columns (Qiagen; #74204).
Purified 4sU-labelled RNA was used with the Ion Total RNA-Seq Kit v2 (Life Technologies; #4479789) to prepare libraries for sequencing on the Ion Proton™ System.

treatment_protocol: Cells were treated to label newly transcribed RNA labeled with 500 μM 4sU for 30 minutes prior to harvesting.

value: untreated


title: J2E 4sU-RNA-seq minus epo rep2


title: J2E 4sU-RNA-seq plus epo rep2

treatment_protocol: Cells were treated with 10 U/ml erythropoietin (EPO) for 40 mins and newly transcribed RNA labeled with 500 μM 4sU for  final 30 minutes.


title: J2E 4sU-RNA-seq plus epo rep1


title: RNA-seq_SETDB1 sgRNA 9 Day 7 Rep-3

description:
SAM24158153
[processed data files:]
std exp analysis: NGS809_counts.xls
RNAseq_Diff_exp_SETDB1vsNTC.xls
repeat analysis: RepEnrich_Transposable_elements_fraction_counts.xlsx


title: H-chicken_kidney3

first: Mingzhou

address: No.211 Huimin Road, Wenjiang District

description: Daocheng,Sichuan,China,3000m altitude

source_name: kidney

value: high

value: kidney

tag: age

value: adult(>200 days old)


title: RNA-seq_Non-targeting sgRNA Day 7 Rep-1

description:
SAM24158154
[processed data files:]
std exp analysis: NGS809_counts.xls
RNAseq_Diff_exp_SETDB1vsNTC.xls
repeat analysis: RepEnrich_Transposable_elements_fraction_counts.xlsx


title: HCT116_J2_PBS (v2)

value: PBS


title: H-chicken_kidney2

description: Daocheng,Sichuan,China,3000m altitude

tag: altitude


title: RNA-seq_SETDB1 sgRNA 9 Day 7 Rep-2

description:
SAM24158152  note: sample excluded from final repeat analysis
[processed data files:]
std exp analysis: NGS809_counts.xls
RNAseq_Diff_exp_SETDB1vsNTC.xls


title: RNA-seq_SETDB1 sgRNA 9 Day 7 Rep-1

description:
SAM24158151
[processed data files:]
std exp analysis: NGS809_counts.xls
RNAseq_Diff_exp_SETDB1vsNTC.xls
repeat analysis: RepEnrich_Transposable_elements_fraction_counts.xlsx


title: H-chicken_kidney1

description: Daocheng,Sichuan,China,3000m altitude


title: L-chicken_kidney3

description: Ya'an,Sichuan,China,500m altitude

value: low


title: L-chicken_kidney2

description: Ya'an,Sichuan,China,500m altitude


title: RNA-seq_SETDB1 sgRNA 6 Day 7 Rep-2

description:
SAM24158149
[processed data files:]
std exp analysis: NGS809_counts.xls
RNAseq_Diff_exp_SETDB1vsNTC.xls
repeat analysis: RepEnrich_Transposable_elements_fraction_counts.xlsx


title: RNA-seq_SETDB1 sgRNA 6 Day 7 Rep-1

description:
SAM24158148
[processed data files:]
std exp analysis: NGS809_counts.xls
RNAseq_Diff_exp_SETDB1vsNTC.xls
repeat analysis: RepEnrich_Transposable_elements_fraction_counts.xlsx


title: RNA-seq_SETDB1 sgRNA 6 Day 7 Rep-3

description:
SAM24158150
[processed data files:]
std exp analysis: NGS809_counts.xls
RNAseq_Diff_exp_SETDB1vsNTC.xls
repeat analysis: RepEnrich_Transposable_elements_fraction_counts.xlsx


title: RNA-seq_Non-targeting sgRNA Day 4 Rep-1

description:
SAM24158145
[processed data files:]
std exp analysis: NGS809_counts.xls
RNAseq_Diff_exp_SETDB1vsNTC.xls
repeat analysis: RepEnrich_Transposable_elements_fraction_counts.xlsx


title: L-chicken_kidney1

description: Ya'an,Sichuan,China,500m altitude


title: RNA-seq_Non-targeting sgRNA Day 4 Rep-3

description:
SAM24158147
[processed data files:]
std exp analysis: NGS809_counts.xls
RNAseq_Diff_exp_SETDB1vsNTC.xls
repeat analysis: RepEnrich_Transposable_elements_fraction_counts.xlsx


title: H-chicken_spleen3

description: Daocheng,Sichuan,China,3000m altitude

source_name: spleen

value: spleen


title: H-chicken_liver3

description: Daocheng,Sichuan,China,3000m altitude

source_name: liver

value: liver


title: RNA-seq_SETDB1 sgRNA 9 Day 4 Rep-2

description:
SAM24158143
[processed data files:]
std exp analysis: NGS809_counts.xls
RNAseq_Diff_exp_SETDB1vsNTC.xls
repeat analysis: RepEnrich_Transposable_elements_fraction_counts.xlsx


title: L-chicken_spleen3

description: Ya'an,Sichuan,China,500m altitude


title: H-chicken_liver1

description: Daocheng,Sichuan,China,3000m altitude


title: RNA-seq_SETDB1 sgRNA 9 Day 4 Rep-3

description:
SAM24158144
[processed data files:]
std exp analysis: NGS809_counts.xls
RNAseq_Diff_exp_SETDB1vsNTC.xls
repeat analysis: RepEnrich_Transposable_elements_fraction_counts.xlsx


title: H-chicken_spleen2

description: Daocheng,Sichuan,China,3000m altitude


title: H-chicken_liver2

description: Daocheng,Sichuan,China,3000m altitude


title: RNA-seq_SETDB1 sgRNA 6 Day 4 Rep-2

description:
SAM24158140
[processed data files:]
std exp analysis: NGS809_counts.xls
RNAseq_Diff_exp_SETDB1vsNTC.xls
repeat analysis: RepEnrich_Transposable_elements_fraction_counts.xlsx


title: RNA-seq_SETDB1 sgRNA 6 Day 4 Rep-1

description:
SAM24158139
[processed data files:]
std exp analysis: NGS809_counts.xls
RNAseq_Diff_exp_SETDB1vsNTC.xls
repeat analysis: RepEnrich_Transposable_elements_fraction_counts.xlsx


title: L-chicken_liver3

description: Ya'an,Sichuan,China,500m altitude


title: L-chicken_spleen2

description: Ya'an,Sichuan,China,500m altitude


title: L-chicken_spleen1

description: Ya'an,Sichuan,China,500m altitude


title: H-chicken_spleen1

description: Daocheng,Sichuan,China,3000m altitude


title: RNA-seq_SETDB1 sgRNA 9 Day 4 Rep-1

description:
SAM24158142
[processed data files:]
std exp analysis: NGS809_counts.xls
RNAseq_Diff_exp_SETDB1vsNTC.xls
repeat analysis: RepEnrich_Transposable_elements_fraction_counts.xlsx


title: ChIP-seq_THP-1-gRNA9-H3K9-Input

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie 2.2.3 and processed with MACS2. Peak calling was performed using  bandwidth of 150, tag size of 50 and q-value cut-off of 0.05
For mapping to transposable elements, the repenrich pipeline was employed using repeat masker annotations for hg19 (https://github.com/nskvir/RepEnrich)
For Transposable element analysis reads for first mapped to hg19 with bowtie command: -p 16 -t -m 1 -S --max, and then RepEnrich was run on the data using python command: python RepEnrich.py /data/hg19_LTR_repeatmasker.bed /data/sample_A sample_A /data/hg19_setup_folder sampleA_multimap.fastq sampleA_unique.bam --is_bed TRUE --cpus 16
Genome_build: hg19
Supplementary_files_format_and_content: bdg files were generated with MACS2

extract_protocol:
Lysates were clarified from Mnase treated chromatin and histone-DNA complexes were isolated with antibody.
Standard illumina library construction

treatment_protocol: THP-1 cells were spin-transduced with lentiviral sgRNAs against SETDB1 (sgRNA 6 and 9) or non-targeting control (NTC) in 96-well plates.Two days post-transdiction cells were selected with 1ug/m of puromycin.

value: H3K9me3 ThermoFisher 49-1008


title: L-chicken_liver2

description: Ya'an,Sichuan,China,500m altitude


title: ChIP-seq_THP-1-gRNA6-H3K9-Input

value: AML Cell Line


title: ChIP-seq_THP-1-NTC-H3K9-Input


title: H-cow_heart3

description: Songpan,Sichuan,China,3000m altitude

organism: Bos grunniens

source_name: heart

value: heart

value: adult(>4 years old)


title: L-chicken_liver1

description: Ya'an,Sichuan,China,500m altitude


title: ChIP-seq_THP-1-gRNA9-H3K9IP-2


title: ChIP-seq_THP-1-gRNA6-H3K9IP-1


title: ChIP-seq_THP-1-NTC-H3K9IP-2


title: H-cow_heart2

description: Songpan,Sichuan,China,3000m altitude


title: H-cow_lung3

description: Songpan,Sichuan,China,3000m altitude

source_name: lung

value: lung


title: H-cow_lung2

description: Songpan,Sichuan,China,3000m altitude


title: RNA-seq_SETDB1 sgRNA 6 Day 4 Rep-3

description:
SAM24158141
[processed data files:]
std exp analysis: NGS809_counts.xls
RNAseq_Diff_exp_SETDB1vsNTC.xls
repeat analysis: RepEnrich_Transposable_elements_fraction_counts.xlsx

value: Acute Myeloid Leukemia (AML)


title: CD34+_erthrocyte_T4 [hs80l2s4]

city: Cambridge

first: Xiaofei

state: MA

institute: Whitehead Institute for Biomedical Research

description:
treated with  1 μM GC-1 for 6 hrs
erythocyte-hg19HS80-Groseqgenes-rpkm.txt
Erythrocyte_hs80l2s4_GC1

data_processing:
Library strategy: GRO-seq
Illumina 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 hg19 whole genome using bowtie2-2.2.6. Samtools were used to keep only aligned reads with MAPQ>10.
Mapped reads were separated based on the strand, bigwig files were generated using HOMER-4.8.2. Threshold of maximal three tag per genomic location were used to get rid of spiky regions.
The analyzeRepeats.pl command from Homer software (http://homer.ucsd.edu/homer/ngs/analyzeRNA.html) was used to get reads counts for each gene.
We followed the commands on “http://homer.ucsd.edu/homer/ngs/diffExpression.html” to obtained differentially expressed genes by using the EdgeR method.
Genome_build: hg19
Supplementary_files_format_and_content: wigfiles and text files containing rpkm and differntial expression analysis.

source_name: erythroblasts

growth_protocol: Primary human CD34+ cells were grown by the erythroid differentiation method by Lee et al. (2015) Nature. doi:10.1038/nature14326

extract_protocol:
Cells were swelled by hyptonic buffer and cellular membrane lysed in 0.5% NP40. The nuclei were subjected to nuclear run-on for 5minutes at 30 degree with BrU labeling. The run-on RNAs were pull down by BrU beads and subjected to library preparation for deep sequencing.
We followed a previous published protocol (Ingolia et al., 2009 Science; Wang et al., 2011 Nature; Li et al., 2013 Nature). Briefly, the run-on RNA were first added with a polyA tracts by RNA polyA polymerase. This polyA tail enables the run-on RNA to be reverse transcribed into single strand cDNA by Reverse Transcriptase. The cDNA was circularized by CircLigase (Epicentre) and re-linearized by Ape1, subsequently subjected to PCR amplification and deep sequencing.

treatment_protocol: At day 14, cells were switched to regular terminal differentiation medium containing fetal bovine serum and supplemented with or without 1 μM GC-1 for 6 hrs and then harvested for GRO-seq.

value: erythroblasts

tag: agent

tag: genotype

value: wild type


title: CD34+_erthrocyte_veh [hs80l2s3]

description:
treated with vehicle
erythocyte-hg19HS80-Groseqgenes-rpkm.txt
Erythrocyte_hs80l2s3_veh

tag: strain

value: vehicle


title: H-cow_muscle1

institute: Sichuan Agricultural University

description: Songpan,Sichuan,China,3000m altitude

source_name: muscle

value: muscle


title: H-cow_lung1

description: Songpan,Sichuan,China,3000m altitude

value: high


title: CD34+_erthrocyte_T4

description:
treated with  1 μM GC-1 for 6 hrs
erythocyte-HS66-Groseqgenes-rpkm.txt
Erythrocyte_GC1


title: L-sheep_lung1

description: Jining,Shandong,China,50m altitude

value: adult(>3 years old)


title: H3K4Me1_GC1_ChIPSeq

data_processing:
Adapters were removed with cutadapt and reads shorter than 20nt were discarded. Sequences where filtered with fastx_artifacts_filter tool from the FASTX-toolkit.
Reads were mapped with bowtie1 uising the following parameters:  -k 1 -n 1 -l 20 --best --sam --solexa1.3-quals.
For the NCOA4_GC1_ChIPSeq sample we caculated the fragment size with the run_spp.R script from the phantompeakqualtools package.
We called peaks on the NCOA4_GC1_ChIPSeq sample with MACS 1.4 using the "input DNA" sample as input and the :mfold: parameter set to 5,30.
We kept peaks with a fold enrichment >= 10.
Genome_build: hg19

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with specific antibodies.
Genomic DNA was purified from BFU-Es sheared by sonication to 50-500 bp and processed with the Illumina ChIP-Seq DNA Sample Prep Kit (http://support.illumina.com/sequencing/sequencing_kits/chip-seq_dna_sample_prep_kit.html). Samples were sequenced using the Illumina HiSeq system

treatment_protocol: At day 14, cells were switched to regular terminal differentiation medium containing fetal bovine serum and supplemented with or without 1 μM GC-1.

tag: chip antibody

value: Abcam, ab8895


title: L-sheep_muscle1

description: Jining,Shandong,China,50m altitude


title: H3K4Me3_GC1_ChIPSeq

value: Millipore, 07-473


title: H-cow_muscle2

description: Songpan,Sichuan,China,3000m altitude


title: input DNA (NCOA4_GC1 control)


title: L-sheep_lung3

description: Jining,Shandong,China,50m altitude

value: low


title: CD34+_erthrocyte_veh

description:
treated with vehicle
erythocyte-HS66-Groseqgenes-rpkm.txt
Erythrocyte_veh


title: NCOA4_untreated_ChIPSeq

value: Santa Cruz, sc-373739


title: H-sheep_heart3

description: Songpan,Sichuan,China,3000m altitude


title: L-sheep_muscle3

description: Jining,Shandong,China,50m altitude


title: NCOA4_GC1_ChIPSeq


title: H-cow_heart1

description: Songpan,Sichuan,China,3000m altitude


title: H-cow_muscle3

description: Songpan,Sichuan,China,3000m altitude


title: LacZ control rep2

data_processing:
Reads were trimmed to remove low quality reads using FASTQ quality trimmer with quality threshold of 20 (-t 20) and minimum length to keep 25 nt (-l 25).
Reads that still had both pairs after the trimming step were mapped with Tophat2 using the options “--no-coverage-search”, “--segment-length 20”, “ --no-novel-juncs” and gene models from ENSEMBL Genes 72, Human genes NCBIM37 (Homo_sapiens.GRCh37.p11).
The number of reads mapped to each gene was obtained with HTseq-count with the setting “--mode=intersection-strict”.
Differential expression was assayed using DE-seq.
Genome_build: hg19
Supplementary_files_format_and_content: excel file containing raw counts, normalized counts, and differential expression analysis (fold change, log2 of the fold change, p-value and adjusted p-value)

extract_protocol:
Total RNA of human erythroblasts was harvested using Trizol reagent. Samples for Paired-End mRNA-seq were prepared using the Solexa kit according to the manufacturer’s instructions.
Samples were prepared for sequencing with the Illumina TruSeq RNA Sample Prep kit according to the standard protocol

treatment_protocol: Primary human CD34+ hematopoietic cells were transduced with lentivirus vectors encoding shRNAs targeting either LacZ (control) or  one day after thawing with the presence of 2 µg/mL polybrene (Sigma). 24 hrs after viral transduction, cells were selected by growing in culture medium containing 1 µg/mL puromycin (Sigma) for 2 days. Cells were harvested at day 14 of erythroid differentiation.

value: normal donor


title: NCOA4 kd rep1


title: LacZ control rep1


title: H-sheep_muscle3

description: Songpan,Sichuan,China,3000m altitude


title: NCOA4 kd rep2


title: H-sheep_lung3

description: Songpan,Sichuan,China,3000m altitude


title: RNA-seq_Non-targeting sgRNA Day 4 Rep-2

description:
SAM24158146
[processed data files:]
std exp analysis: NGS809_counts.xls
RNAseq_Diff_exp_SETDB1vsNTC.xls
repeat analysis: RepEnrich_Transposable_elements_fraction_counts.xlsx


title: ChIP-seq_THP-1-NTC-H3K9IP-1

value: H3K9me3 ThermoFisher 49-1008


title: L-sheep_muscle2

description: Jining,Shandong,China,50m altitude


title: L-sheep_lung2

description: Jining,Shandong,China,50m altitude


title: H3K27Ac_GC1_ChIPSeq

value: Abcam, ab4729


title: PolI_GC1_ChIPSeq

value: Santa Cruz, sc-899


title: H-sheep_muscle2

description: Songpan,Sichuan,China,3000m altitude


title: H-sheep_lung2

description: Songpan,Sichuan,China,3000m altitude


title: H-sheep_heart1

description: Songpan,Sichuan,China,3000m altitude

value: heart


title: H-sheep_lung1

description: Songpan,Sichuan,China,3000m altitude

value: lung


title: H-sheep_muscle1

description: Songpan,Sichuan,China,3000m altitude


title: sheep_heart_3

description:
XW_xin3
processed data file: sheep_PCA_new.txt

value: small tail han sheep

tag: location

value: Jining, Shandong province, China

value: ~3 years old


title: sheep_heart_2

description:
XW_xin2
processed data file: sheep_PCA_new.txt


title: sheep_heart_1

description:
XW_xin1
processed data file: sheep_PCA_new.txt


title: CRISPR_screen_THP-1 Day7- Biorep 2

data_processing:
Library strategy: DNA sgRNA-Amplicon-Seq
Reads exactly matching gRNAs were counted by a custom script
Genome_build: N/A
Supplementary_files_format_and_content: Excel file including ncounts

source_name: THP-1 Cells

growth_protocol: Cells were grown in RPMI + 10%FBS + 1X L-glutamine. Puromycin selection was at 1ug/ml.

extract_protocol:
At each time-point, cells were spun down, washed with PBS, flash frozen on dry ice, and genomic DNA was harvested with Qiagen DNeasy Kits and sgRNAs were amplified by PCR. The ~221 bp sgRNA products were isolated.
NGS libraries were prepared with NuGen Ovation low complexity kits, followed by PCR amplification for 6 cycles. 6pM of samples were sequenced on an Illumina MiSeq with reagent kit v3 for 150 cycles.

treatment_protocol: THP-1 cells were transduced with the sgRNA library and an MOI of 0.3. Cells were selected with 1ug/ml 2 days post-transduction. Cells were kept at a 1000X coverage, at least 6X10^6 cells in every flask.

value: Blood

value: Acute Myelogenous Leukemia


title: H-cow_liver3

description: Songpan,Sichuan,China,3000m altitude

value: high

value: liver

value: adult(>4 years old)


title: CRISPR_screen_THP-1 Day 21- Biorep 1


title: H-cow_spleen2

description: Songpan,Sichuan,China,3000m altitude

value: spleen


title: H-cow_spleen3

description: Songpan,Sichuan,China,3000m altitude