title: Nasal swab specimen from child with Acute asthma/wheeze [MAV115]


title: Nasal swab specimen from child with Control [MAV119]

status: Public on Feb 17 2019

type: RNA

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

hyb_protocol: The samples were hybridized to Human Gene 2.1 ST microarrays according to standard Affymetrix protocols. This was performed by at the Ramaciotti Centre for Genomics, The University of New South Wales.

scan_protocol: The samples were scanned on an Affymetrix scanner at the Ramaciotti Centre for Genomics, The University of New South Wales.

data_processing: The raw microarray data was processed in R employing the RMA algorithm. A custom chip description file was used (hugene21sthsentrezg, version 20).

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Nasal swab specimen

label_protocol: Standardized kits from Affymetrix were used to label the samples at the Ramaciotti Centre for Genomics, The University of New South Wales.

growth_protocol: Samples were collected from children during a naturally occuring asthma or wheezing exacerbation.

extract_protocol: Total RNA was extracted with TRIzol followed by RNeasy.

treatment_protocol: Nasal swab specimens were collected using flocked swabs.

tag: phenotype

value: Control

tag: rv status

value: Rhinovirus negative


title: Nasal swab specimen from child with Control [MAV117]


title: Nasal swab specimen from child with Control [MAV114]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV113]

value: Acute asthma/wheeze

value: Rhinovirus positive


title: HFD EWAT 1

status: Public on Feb 16 2019

type: SRA

city: Oxford

first: Haifei

last: Shi

state: OH

address: 501 E. High Street

department: Biology

country: USA

institute: Miami University

library_source: transcriptomic

data_processing:
Remove Truseq3-SE adapter sequence using Trimmomatic (version 0.36)
Single-end sequencing reads were aligned to the mouse genome (ENSEMBL 84 release, GRCm38.p4) using RSEM (version 1.3.0)
Differential gene expression analysis was performed by DESeq2 (version 1.10.1) using the estimated gene-level counts from RSEM
Genome_build: RNA-Seq clean reads  were mapped to mouse genome (ENSEMBL 84 release, GRCm38.p4)

organism: Mus musculus

source_name: epididymal white adipose tissue

growth_protocol: High-fat diet

extract_protocol:
RNA extraction using E.Z.N.A® Total RNA kit II (Omega Bio-tek)
Libraries were sequenced as single-end 75 bp on Illumina NextSeq500 sequencing system at Cofactor Genomics Inc (St. Louis, MO). Approximately 30 millions of reads were retrieved from each sample
Ribosomal RNA was removed by using TruSeq Standard Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina)

treatment_protocol: Surgical denervation

tag: tissue type

value: white adipose tissue

tag: strain

tag: genotype

value: wild type

tag: Sex

value: male

tag: procedure

value: denervation

tag: diet

value: high-fat rodent diet


title: Nasal swab specimen from child with Convalescent [MAV106]

value: Convalescent


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV097]


title: Nasal swab specimen from child with Convalescent [MAV098]


title: Prolonged normoxia (passage 2), rep 3

city: Seoul

first: Jin-Hong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
FASTQ files were generated by base-calling using Illumina RTA (v1.18) and conversion using bcl2fastq (v1.8.4).
The TruSeq 3′ adapter sequence was removed using cutadapt. Reads shorter than 18 nt, low-quality reads (phred quality <20 or <30 in >95% or >50% of nucleotides, respectively), and artifact reads were discarded using the FASTX-Toolkit.
Reads were mapped to mouse human genome (mm10) with an option of -n 3. For multi-mapped reads, we selected the alignment results which have the best alignment score, allowing mismatches only at the 3′ end of reads using custom scripts.
Reads were classified into annotations from miRBase release 21 (from www.mirbase.org), RefSeq, RepeatMasker (from UCSC genome browser), GtRNAdb (from gtrnadb.ucsc.edu), and Rfam (from rfam.sanger.ac.uk) by intersectBed in BEDTools.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated values (tsv) files containing miRNA names and corresponding read counts.

source_name: chondrocyte

growth_protocol: Primary cultured chondrocytes were maintained in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal bovine serum (Gibco) and antibiotics (penicillin and streptomycin). Cultured cells were maintained in a humidified 37°C, 5% CO2, and 20% O2 atmosphere to induce oxidative stress.

extract_protocol:
Total RNA was isolated using the TRI reagent (Molecular Research enter, Inc.).
Libraries were constructed using the TruSeq small RNA library preparation kit (Illumina).

treatment_protocol: For the chondrocyte passage model, chondrocytes were grown under normoxia. After two serial passages (P2), the cells were harvested.

tag: cell type

value: articular chondrocytes

value: ICR

tag: condition

value: normoxia

tag: treatment

value: Passage 2


title: Control (passage 0), rep 3

value: Passage 0


title: Prolonged normoxia (passage 2), rep 2


title: HFD EWAT 3


title: Prolonged normoxia (passage 2), rep 1


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV105]


title: HFD BAT 2

source_name: interscapular brown adipose tissue

value: brown adipose tissue


title: HFD BAT 1


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV107]


title: HFD BAT 3


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV099]


title: Control (passage 0), rep 2


title: HFD EWAT 2


title: Control (passage 0), rep 1


title: LFD RWAT 3

source_name: retroperitoneal white adipose tissue

growth_protocol: Low-fat diet

value: starndard rodent diet


title: LFD RWAT 2


title: LFD RWAT 1


title: LFD IWAT 3

source_name: inguinal white adipose tissue


title: LFD IWAT 2


title: LFD IWAT 1


title: LFD EWAT 3


title: LFD EWAT 1


title: LFD BAT 3


title: LFD BAT 2


title: trained_baseline_Ex_7

city: Moscow

first: Pavel

last: Makhnovsky

address: 76A Khoroshevskoye shosse

country: Russia

institute: Institute of Biomedical Problems of the Russian Academy of Sciences

data_processing:
Quality control and trimming were performed using Trimmomatic v0.36
High-quality reads were mapped to the reference human genome GRCh38 and exon–exon junctions were identified using HISAT v2.1.0
Reads were counted for known exons of each gene using HTseq v0.6.1
Normalization of read counts provided by DESeq method
Genome_build: GRCh38
Supplementary_files_format_and_content: Two tab-delimited text files include normalized read counts and FPKM for each sample

molecule: polyA RNA

source_name: muscle vastus lateralis

extract_protocol:
Samples from the vastus lateralis muscle were taken using a microbiopsy technique and were frozen in liquid nitrogen; RNA was extracted from the samples using an RNeasy mini kit (Qiagen) with DNase treatment (Fermentas, Lithuania)
Libraries were constructed from 300 ng of RNA using a NEB Next Ultra II RNA kit. Poly-A mRNA was isolated using magnetic particles associated with 24-dT oligonucleotides by means of NEB Next Poly(A) mRNA Magnetic Isolation Module.

treatment_protocol: An exercise session (60 min, one-legged knee extension, ~65% of maximal power in the one-legged ramp test) started 2 h 35 min after a standardized breakfast.  The participants ate a standardized lunch 1 h 20 min after the exercise session. This test session was repeated after an aerobic training programme (2 month, 1 h/day, 5 sessions/week) comprised training sessions on cycle ergometer (60 min) that alternated between continuous and intermittent exercise.

tag: tissue

value: skeletal muscle

tag: individual

tag: age

tag: training status

value: trained

tag: time point

value: baseline

tag: exercised/non-exercised muscle

value: exercised (Ex)


title: LFD EWAT 2

value: white adipose tissue


title: trained_baseline_NE_7

value: non-exercised (NE)


title: trained_+4h_NE_7

value: +4 h after exercise

value: male


title: trained_+4h_Ex_7


title: trained_+1h_NE_7

value: +1 h after exercise


title: trained_+1h_Ex_7


title: untrained_+4h_NE_7

value: untrained


title: untrained_+4h_Ex_7


title: untrained_baseline_Ex_7


title: trained_+1h_Ex_6


title: untrained_+1h_NE_7


title: trained_+4h_Ex_6


title: trained_+4h_NE_6


title: trained_+1h_NE_6


title: untrained_+4h_Ex_6


title: trained_baseline_NE_6


title: trained_baseline_Ex_6


title: LFD BAT 1

value: wild type

value: denervation


title: untrained_+4h_NE_6


title: hsa-miR-182-5p mimic 2

city: Kaohsiung

first: Sung-Chou

last: Li

state: Kaohsiung

address: No.386, Dazhong 1st Rd

department: Department of Medical Education and Research

country: Taiwan

institute: Kaohsiung Veterans General Hospital

description: RNA expression value derived from Expression Console software; gene-level analysis

hyb_protocol: Samples were hybridized with GeneChip Human Transcriptome Array 2.0 (Affymetrix) and scanned with the GeneChip Scanner 3000 7G in Genomics and Proteomics Core lab., Kaohsiung Chang Gung memorial Hospital, Taiwan.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
The raw data of HTA 2.0 chips were first subject to quality control examination as suggested by Affymetrix manuals. And, the chips passing the quality control criteria were then analyzed with Partek. By default, Partek used RMA algorithm to create the expression matrix from Affymetrix data.  The raw intensity values are background corrected, log2 transformed and then quantile normalized.
The file Normalized_data_all_probesets.txt contains data for all analyzed probe sets and is available on the series record. This file includes many control probe sets not included on GPL17586 and 11 probe sets with no gene annotation information that were thus excluded from the sample data tables. These probes sets are:
TC01001343.hg.1
TC09000974.hg.1
TC0X000181.hg.1
TC11001890.hg.1
TC15000184.hg.1
TC15000193.hg.1
TC15001102.hg.1
TC16000429.hg.1
TC16000764.hg.1
TC17001285.hg.1
TC22000803.hg.1

label: biotin

source_name: RNA sample from neutrophil cells transfected with hsa-miR-182-5p mimic

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT PLUS Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: HL-60 cells (BCRC No. 60027) were maintained in Iscove’s modified Dulbecco’s medium supplemented with 20% fetal bovine serum, 4 mM L-glutamine, and 1.5 g/L sodium bicarbonate and incubated at 37°C in 5% CO2. Then, HL-60 cells were differentiated into neutrophil-like cells with the stimulus of 1.3 % DMSO (Sigma-Aldrich, MO, USA).

extract_protocol: We used mirVanaTM miRNA Isolation Kit (Ambion, CA, USA) to extract RNA following the manufacturer’s protocols. The concentration of RNA was measured with NanoDrop 2000 spectrophotometer (Thermo scientific, MA, USA). All RNA samples passed the criterion of RIN≥ 7 assessed with Agilent 2100 Bioanalyzer (Agilent, CA, USA).

treatment_protocol: miRNA mimic Syn-hsa-miR182-5p (MSY0000259) was obtained from QIAGENT. For miRNA mimic transfection, 2*106 neutrophil cells were seeded in 6-well plate and each well contained 200 l complete medium. After 24 hours, 6 l miRNA mimic (20 M) and 12 l HiPerFect transfection reagent (QIAGENT) were mix in 200 l culture medium without serum added. After 6 hours, 800 l culture medium was added into 6-well plate and cells were cultured. Finally, 24 hours after transfection, the cells were harvested for further analysis.

tag: cell line

value: neutrophil cell


title: untrained_+1h_Ex_7


title: untrained_+1h_Ex_6


title: Scrambled control 1

source_name: RNA sample from neutrophil cells transfected with scrambled control


title: hsa-miR-182-5p mimic 1


title: untrained_baseline_Ex_6


title: untrained_+1h_NE_6


title: untrained_baseline_NE_7


title: untrained_baseline_NE_6


title: Scrambled control 2


title: trained_baseline_NE_5


title: untrained_+4h_Ex_5


title: trained_+1h_NE_5


title: trained_baseline_Ex_5


title: trained_+4h_NE_5


title: trained_+4h_Ex_5


title: untrained_baseline_NE_5


title: PSRNA_SACC_rep3

city: Illkirch-Graffenstaden

first: Jules

last: Deforges

address: Boulevard Gonthier d'Andernach

country: France

institute: Transgene SA

data_processing:
Mapping with Hisat2
De novoannotation with Cufflinks using TAIR10.31 transcriptome as guide
Readcount with Htseq-count
Normalization and differential expression analysis with DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: Raw read count: contains raw readcount from HTSeq-counts for each locus
Supplementary_files_format_and_content: Table of raw read count: table compiling the raw readcount per locus determined for each experimental condition and biological replicate
Supplementary_files_format_and_content: Table of normalize read count: Table of raw read count normalized with DESeq2

organism: Arabidopsis thaliana

source_name: seedlings

extract_protocol:
Trizol extraction
TrueSeq stranded kit (Illumina)

value: shoot

value: ACC

tag: days after germination


title: untrained_+1h_NE_5


title: untrained_+1h_Ex_5


title: PSRNA_SACC_rep2


title: PSRNA_SACC_rep1


title: PSRNA_SmeJA_rep3

value: Methyl Jasmonate


title: trained_+1h_Ex_5


title: PSRNA_SmeJA_rep2


title: PSRNA_SmeJA_rep1


title: PSRNA_SABA_rep3

value: ABA


title: untrained_+4h_NE_5

value: skeletal muscle


title: untrained_baseline_Ex_5


title: PSRNA_SABA_rep2


title: PSRNA_SIAA_rep3

value: Auxin


title: PSRNA_SIAA_rep2


title: PSRNA_RACC_rep3

value: root


title: PSRNA_Sctrl_rep3

value: control


title: PSRNA_SABA_rep1


title: PSRNA_Sctrl_rep1


title: PSRNA_SIAA_rep1


title: PSRNA_Sctrl_rep2


title: PSRNA_RmeJA_rep1


title: PSRNA_RABA_rep2


title: PSRNA_RACC_rep2


title: PSRNA_RABA_rep3


title: PSRNA_RACC_rep1


title: PSRNA_RIAA_rep2


title: PSRNA_RIAA_rep3


title: PSRNA_RABA_rep1


title: PSRNA_RIAA_rep1


title: Tibia Hematoma Resting-2

city: Montréal

first: Haider

last: Al-Waeli

state: QC

address: #500 2001 McGill College Avenue

department: Dentistry

country: Canada

institute: McGill University

description: Gene expression from RNA of hematoma of fracture tibia bone in mouse

hyb_protocol: Following fragmentation, 3.5 ug of DNA were hybridized for 17 hrs at 60 rpm at 450C GeneChip ® Hybridization oven 640 (Affymetrix, Waltham, MA) and washed in GneChips® Fluidics Station 450 (Affymetrix)

scan_protocol: The microarrays were scanned on a GeneChip® scanner 3000 (Affymetrix)

data_processing: The data was normalized and only the entities that were flagged as being present in the samples inlucded in the analysis

source_name: Tibia bone

label_protocol: ssDNA were prepared according to the Affymetrix GeneChip®WT Terminal Labeling Kit (Thermofisher, Waltham, MA) from 100 ng total RNA

extract_protocol: The total RNA was isolated fromt eh bone tissue using Qalzol (Qigen, Toronto, Ontario) and then purified using Rneasy Lipid TissueMini kit Columns following manufactur's instructions

treatment_protocol: Hematoma of fractured tibia bone of the mouse right leg was harvested on day three and stored in Alloprotect (Qiagen, Toronto, Ontario) solution

value: female

value: 2 months

value: tibia bone fracture site

value: NSAID for three days after bone fracture during resting time of the day


title: Tibia Hematoma Active-2

value: NSAID for three days after bone fracture during active time of the day


title: Tibia Hematoma Resting-3


title: Tibia Hematoma Resting-1


title: Tibia Hematoma Active-1


title: Tibia Hematoma Control-2

description: Gene expression from RNA of tibia bone in mouse

value: tibia bone no fracture


title: Tibia Hematoma Control-3


title: Tibia Hematoma Active-3


title: Tibia Hematoma Control-1


title: PSRNA_Rctrl_rep1


title: PSRNA_Rctrl_rep2


title: PSRNA_lowPi_rep3

value: whole seedlings

value: Phosphate starvation


title: PSRNA_Rctrl_rep3


title: PSRNA_lowPi_rep1


title: PSRNA_HighPi_rep2


title: PSRNA_HighPi_rep3


title: PSRNA_RmeJA_rep3


title: PSRNA_HighPi_rep1


title: PSRNA_RmeJA_rep2


title: PSRNA_lowPi_rep2


title: totRNA_SACC_rep3


title: totRNA_SACC_rep2


title: totRNA_SmeJA_rep3


title: totRNA_SACC_rep1


title: totRNA_SmeJA_rep2


title: J1 (for Myc KO) rep3

city: Melbourne

first: Partha

last: Das

state: Victoria

address: 211 Wellington Road

department: Anatomy & Developmental Biology

institute: Monash University

description:
DS_J1wt3_S3
processed data file:
Taf5l_Taf6l_Myc_KovsWT_RawCounts.tsv
Taf5l_Taf6l_Myc_KovsWT_NormalizedCounts.tsv
Taf5l_Taf6l_Myc_KovsWT_FPKM.tsv
Taf5l_Taf6l_Myc_KovsWT_TPM.tsv

data_processing:
Gene expression quantification, both raw counts and TPM (Transcripts Per Million) values, was done using Salmon (v0.8.2) with default parameters. The mm9-based GENCODE version M1 mouse transcriptome was used.
Normalized counts and FPKM (Fragments Per Kilobase per Million mapped reads) expression values were calculated using the DESeq2 R Bioconductor package (v1.14.1).
Genome_build: mm9
Supplementary_files_format_and_content: Comma-separated text files containing raw counts, normalized counts, FPKM expression values and TPM expression values.

source_name: J1 (for Myc KO)_ESCs

growth_protocol: Mouse ESCs (mESCs) were cultured in mouse ESC media that contains DMEM, supplemented with 15% fetal calf serum, 0.1mM b-mercaptoethanol, 2mM L-glutamine, 0.1mM NEAA, 1% of nucleoside mix , 1000 U/ml LIF/ESGRO, and 50U/ml Penicillin/Streptomycin. mESCs were cultured at 37ºC, 5% CO2.

extract_protocol:
Total RNA was isolated, and ribosomal RNAs were depleted using ribosomal RNA depletion kit (rRNA Depletion Kit, NEB).
Ribosomal depleted RNA was used to make the RNAseq libraries using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: mESCs were harvested, washed with 1X PBS- twice at 4C, followed by RNA isolation

value: Embryonic Stem Cell

tag: genotype/variation

value: wild type control


title: J1 (for Myc KO) rep2

description:
DS_J1wt2_S2
processed data file:
Taf5l_Taf6l_Myc_KovsWT_RawCounts.tsv
Taf5l_Taf6l_Myc_KovsWT_NormalizedCounts.tsv
Taf5l_Taf6l_Myc_KovsWT_FPKM.tsv
Taf5l_Taf6l_Myc_KovsWT_TPM.tsv


title: totRNA_SABA_rep2

value: shoot


title: cMyc-KO rep3

description:
DS_J1_MycC5_3_S6
processed data file:
Taf5l_Taf6l_Myc_KovsWT_RawCounts.tsv
Taf5l_Taf6l_Myc_KovsWT_NormalizedCounts.tsv
Taf5l_Taf6l_Myc_KovsWT_FPKM.tsv
Taf5l_Taf6l_Myc_KovsWT_TPM.tsv

value: cMyc-KO


title: totRNA_SABA_rep3

value: ABA


title: totRNA_SmeJA_rep1

value: Methyl Jasmonate


title: totRNA_SABA_rep1


title: totRNA_SIAA_rep1

value: Auxin


title: totRNA_SIAA_rep3


title: cMyc-KO rep1

description:
DS_J1_MycC5_1_S4
processed data file:
Taf5l_Taf6l_Myc_KovsWT_RawCounts.tsv
Taf5l_Taf6l_Myc_KovsWT_NormalizedCounts.tsv
Taf5l_Taf6l_Myc_KovsWT_FPKM.tsv
Taf5l_Taf6l_Myc_KovsWT_TPM.tsv


title: totRNA_SIAA_rep2


title: totRNA_Sctrl_rep3


title: J1 (for Myc KO) rep1

description:
DS_J1wt1_S1
processed data file:
Taf5l_Taf6l_Myc_KovsWT_RawCounts.tsv
Taf5l_Taf6l_Myc_KovsWT_NormalizedCounts.tsv
Taf5l_Taf6l_Myc_KovsWT_FPKM.tsv
Taf5l_Taf6l_Myc_KovsWT_TPM.tsv


title: totRNA_Sctrl_rep2


title: cMyc-KO rep2

description:
DS_J1_MycC5_2_S5
processed data file:
Taf5l_Taf6l_Myc_KovsWT_RawCounts.tsv
Taf5l_Taf6l_Myc_KovsWT_NormalizedCounts.tsv
Taf5l_Taf6l_Myc_KovsWT_FPKM.tsv
Taf5l_Taf6l_Myc_KovsWT_TPM.tsv


title: totRNA_RACC_rep3

value: root

value: ACC


title: totRNA_RACC_rep1


title: totRNA_RmeJA_rep3


title: totRNA_RACC_rep2


title: totRNA_RmeJA_rep2


title: totRNA_RABA_rep3


title: totRNA_RABA_rep2


title: totRNA_RmeJA_rep1


title: Breast Cancer BC1976

city: Kamakura

first: Ichikawa

last: Makiko

state: Kanagawa

country: Japan

institute: Toray Industries, Inc.

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetEsophageal Cancerted) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

source_name: Serum from breast cancer patient during eribulin treatment

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: disease state

value: metastatic breast cancer

tag: new distant metastasis

value: Yes

value: Serum


title: totRNA_RABA_rep1


title: Breast Cancer BC1977


title: Breast Cancer BC1978


title: totRNA_Sctrl_rep1

value: control


title: Breast Cancer BC1971

value: No


title: totRNA_RIAA_rep1


title: totRNA_Rctrl_rep3


title: totRNA_RIAA_rep3


title: totRNA_Rctrl_rep2


title: Breast Cancer BC1970


title: totRNA_Rctrl_rep1


title: totRNA_lowPi_rep3


title: Breast Cancer BC1968


title: totRNA_lowPi_rep2


title: totRNA_lowPi_rep1


title: Breast Cancer BC1966


title: Breast Cancer BC1975


title: Breast Cancer BC1964


title: Breast Cancer BC1963


title: Breast Cancer BC1961


title: Breast Cancer BC1962


title: Breast Cancer BC1972


title: totRNA_HighPi_rep3


title: Breast Cancer BC1960


title: totRNA_RIAA_rep2


title: Breast Cancer BC1965


title: totRNA_HighPi_rep1


title: trained_+4h_Ex_4

value: skeletal muscle

value: trained

value: +4 h after exercise

value: exercised (Ex)

tag: Sex

value: male


title: totRNA_HighPi_rep2

value: whole seedlings


title: trained_+4h_NE_4

value: non-exercised (NE)


title: Breast Cancer BC1959


title: trained_+1h_NE_4

value: +1 h after exercise


title: Breast Cancer BC1956


title: Breast Cancer BC1958


title: Breast Cancer BC1954


title: Breast Cancer BC1955


title: untrained_+4h_Ex_4

value: untrained


title: Breast Cancer BC1953


title: Breast Cancer BC1952


title: trained_baseline_NE_4

value: baseline


title: untrained_+1h_Ex_4


title: untrained_baseline_Ex_4


title: Breast Cancer BC1951


title: Breast Cancer BC1949


title: untrained_+1h_NE_4


title: Breast Cancer BC1950


title: untrained_+4h_NE_4


title: Breast Cancer BC1948


title: trained_+1h_Ex_4


title: Breast Cancer BC1957


title: trained_baseline_Ex_4


title: untrained_baseline_NE_4


title: Breast Cancer BC1946


title: Breast Cancer BC1947


title: Breast Cancer BC1945


title: Breast Cancer BC1944


title: trained_+4h_Ex_3


title: trained_+1h_Ex_3


title: trained_baseline_Ex_3


title: trained_+1h_NE_3


title: Breast Cancer BC1942


title: untrained_+4h_Ex_3


title: Breast Cancer BC1940


title: Breast Cancer BC1941


title: trained_baseline_NE_3


title: untrained_+1h_Ex_3


title: Breast Cancer BC1939


title: untrained_+4h_NE_3


title: untrained_+1h_NE_3


title: untrained_baseline_NE_3


title: untrained_baseline_Ex_3


title: Breast Cancer BC1943


title: trained_+4h_Ex_2


title: Breast Cancer BC1936


title: Breast Cancer BC1937


title: Breast Cancer BC1935


title: trained_+4h_NE_3


title: trained_+1h_Ex_2


title: trained_baseline_Ex_2


title: Breast Cancer BC1934


title: Breast Cancer BC1933


title: Breast Cancer BC1932


title: Breast Cancer BC1931


title: Breast Cancer BC1930


title: trained_+1h_NE_2


title: Breast Cancer BC1929


title: trained_baseline_NE_2


title: Breast Cancer BC1926


title: Breast Cancer BC1938


title: untrained_+4h_Ex_2


title: untrained_+1h_Ex_2


title: untrained_baseline_Ex_2


title: Breast Cancer BC1925


title: untrained_+4h_NE_2


title: untrained_+1h_NE_2


title: untrained_baseline_NE_2


title: trained_+4h_Ex_1


title: trained_+1h_Ex_1


title: trained_+4h_NE_2


title: trained_+4h_NE_1


title: Breast Cancer BC1924


title: Breast Cancer BC1928


title: Breast Cancer BC1922


title: trained_baseline_Ex_1


title: Breast Cancer BC1920


title: Breast Cancer BC1917


title: trained_+1h_NE_1


title: Breast Cancer BC1916


title: Breast Cancer BC1915


title: Breast Cancer BC1919


title: trained_baseline_NE_1


title: Breast Cancer BC1921


title: Breast Cancer BC1914


title: untrained_+1h_Ex_1


title: Breast Cancer BC1923


title: untrained_baseline_Ex_1


title: Breast Cancer BC1912


title: Breast Cancer BC1910


title: Breast Cancer BC1911


title: untrained_+4h_NE_1


title: Breast Cancer BC1918


title: untrained_+1h_NE_1


title: PM rep3

city: Raleigh

first: Jigar

last: Desai

state: NC

address: 128 Polk Hall

department: Biochemistry

institute: NCSU

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality sequence (Trimmomatic version 0.33)
Mapped to MSU (Japonica subspecies) using STAR
The resulting bam files were then piped to HTseq count version 0.6.1. Using the options -f bam, -s reverse, and -m intersection-nonempty, counts per gene were generated for the annotated genes in MSU.
Genome_build: MSU 7.0
Supplementary_files_format_and_content: tab-delimited text file of gene names and associated counts

organism: Oryza sativa

source_name: Seedling

growth_protocol: Rice plants were grown on Chu's media in climate controlled chambers. 12hrs Light and 12hrs Dark at 28C.

extract_protocol:
Whole seedlings were pulled and flash frozen on liquid nitrogen. Total RNA was extracted with Qiagen Plant RNA extraction kit. NEB ultra directional Sample Prep Kit was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: AM samples were harvest 30min prior to light coming on. PM samples were harvest 30min prior to lights going off

tag: organ

value: panicle

tag: genotype

value: Nipponbare


title: Breast Cancer BC1907

value: metastatic breast cancer


title: Breast Cancer BC1908

value: Yes


title: untrained_baseline_NE_1


title: Breast Cancer BC1909

value: Serum


title: Breast Cancer BC1906


title: untrained_+4h_Ex_1


title: PM rep2


title: Breast Cancer BC1913


title: AM rep3


title: AM rep1


title: Breast Cancer BC1905


title: Breast Cancer BC1903


title: AM rep2


title: Breast Cancer BC1904


title: Tumor5GFP

city: Baltimore

first: Daniele

middle: Marie

last: Gilkes

state: MD

address: 1650 N Orleans St, CRB1 128, None

department: Oncology

institute: Johns Hopkins

data_processing:
Preliminary analysis was performed by Quick Biology. The reads were then mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0.
Gene expression level was estimated using RSEM v1.2.15.
TMM (Trimmed Mean of M-values) was used to normalize gene expression.
Differentially expressed genes were identified using the edgeR program.
Genome_build: human genome assembly GRCh38
Supplementary_files_format_and_content: Comma delimited text file containing gene-level counts

source_name: orthotopic mouse tumor generated from MDA-MB-231 cells

growth_protocol: Our dual-vector approach to fate-map hypoxia was delivered to MDA-MB-231 cells obtained directly from the ATCC.

extract_protocol:
Total RNA was extracted from cells using TRIzol (Invitrogen) and purified using Direct-zol RNA mini kit (Zymo Research) with DNase I treatment.
Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit. The workflow consisted of mRNA enrichment, cDNA generation, end repair to generate blunt ends, A-tailing, adaptor ligation and 12 cycles of PCR amplification. Unique adaptors were used for each sample in order to multiplex samples into several lanes. Sequencing was performed on Illumina Hiseq 4000 with a 150bp pair-end run. A data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.

treatment_protocol: Orthotopic tumors implanted in the mammary fat pad of NSG mice were resected 2 weeks post-implantation, mechanically disrupted and digested with collagenase to obtain a cell suspension. The cell suspension was enriched using magnetic-activated cell sorting (MACS) and DsRed+ cells were isolated from GFP+ cells by fluorescence-activated cell sorting (FACS) directly into Tris Reagent (Zymo Research).

tag: tumor #

tag: system reporter

value: GFP


title: Tumor1DsRed

value: DsRed


title: Tumor5DsRed


title: Rgt1_exponential_input_3

city: Stanford

first: Seungsoo

state: CA

address: 265 Campus Dr

department: Chemical and Systems Biology

institute: Stanford University

description:
Rgt1_exponential_merged_FE.bdg.gz
Rgt1_exponential_merged_peaks.narrowPeak.gz

library_source: genomic

data_processing:
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were quality-trimmed (cutadapt -q 20), trimmed of adapter sequences, excluding read pairs in which either read was shorter than 28 bp after trimming.
Reads were mapped using bowtie2 2.2.3 using the parameter set --very-sensitive -X 2000
PCR duplicates (with identical fragment start and end positions) were removed.
Coverage across the genome was calculated using bedtools genomecov, using only read pairs with a minimum MAPQ score of 30.
Fold enrichment and significant peaks were calculated for merged replicates using MACS2
genome build: sacCer3
Supplementary_files_format_and_content: for each sample, a bedgraph file of fragment coverage across the genome; for set of replicates, a bedgraph of merged fold enrichment across the genome and a set of called significant peaks (merged files are available in tar archives on the series record).

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: TAP-tagged Rgt1

growth_protocol: Cells were grown overnight, shaking at 30C in YPD media (1% yeast extract, 2% peptone, 2% dextrose), and then diluted to OD600=0.125 and grown to OD600=0.7-0.8.

extract_protocol:
Crosslinked cell pellets were resuspended in 500 µl FA lysis buffer with 1x Pierce EDTA-free protease inhibitor cocktail, and then 700 µl of 500 µm acid-washed glass beads were added. The cells were vortexed for 12 minutes total, in cycles of 2 minutes shaking and 2 minutes resting on ice. The lysate was pelleted and resuspended in fresh lysis buffer, and then sonicated for 3x10 min runs on a Diagenode Bioruptor, on high power with cycles of 30 seconds on and 30 seconds off, to an average of ~300 bp. The sonicate was cleared by centrifugation, and the resulting supernatant was split into an input aliquot (1/20 of IP volume) and an IP aliquot. For each sample, 10 ul of Pan-Mouse IgG beads (Thermo Fisher Scientific catalog #11041) were washed in fresh lysis buffer for 2 hours and then added to the lysate and then incubated overnight. After washing the beads twice in FA lysis buffer, once in lysis buffer with 500 mM NaCl, twice in RIPA buffer, and once in TE, and the DNA was eluted in 100 ul TE+1% SDS and a second time in 150 ul TE+0.67% SDS. The eluate and inputs were treated with RNase A and Proteinase K and then reverse crosslinked overnight at 65C. DNA was purified using Zymo ChIP DNA Clean & Concentrator and eluted in 15 µl 10 mM Tris-HCl pH 8.
ChIP-seq libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift) with dual indexing, from either 1 ng total from input samples or 10 ul of IP samples. Input and IP libraries were amplified for 9 and 12-15 cycles, respectively.

treatment_protocol: Cells were crosslinked by addition of 37% formaldehyde to 1% v/v and incubation at room temperature for 15 minutes, then quenched by addition of glycine to 150 mM and washed with Tris-buffered saline.

tag: growth conditions

value: exponential in YPD


title: Rgt1_exponential_input_2


title: Breast Cancer BC1897

tag: tissue


title: Breast Cancer BC1902


title: PM rep1


title: Breast Cancer BC1900


title: Rgt1_exponential_input_1


title: Breast Cancer BC1895


title: Breast Cancer BC1896

value: No


title: Breast Cancer BC1894


title: Breast Cancer BC1893


title: KDM1A KO rep4: MVBG418KO

city: Ste Anne-de-Bellevue

first: Romain

last: Lambrot

address: 21111 Lakeshore road

department: Animal Science

data_processing:
Basecalling was performed with RTA 1.13.48.
The filtered reads were mapped to the mouse genome (mm10) by using a combination of TopHat and Bowtie software. Cufflinks was used to assemble aligned RNA-seq reads into transcripts and to estimate their abundance in fragments per kilobase of exon per million fragments mapped (FPKM). Transcripts were then annotated with the known reference set of transcripts obtained from the Ensembl database. The differentially expressed genes were identified using the transcript quantification engine Cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values of all transcripts for each sample.

source_name: Testis of GOF/deltaPE-Oct4/GFP mice

extract_protocol:
Testes were removed and decapsulated. They were then digested with collagenase B (2mg/mL) for 10 minutes at 37°C. After rinsing in PBS, another digestion with 0.25% trypsin-EDTA for 5 minutes at 37°C was performed. The resulting cell suspension was washed twice, resuspended in sterile phosphate buffer solution (PBS) with DNase (50μg/mL) and filtered (40μm). Spermatogonia were isolated by fluorescence-activated cell sorting of Oct4-GFP positive germ cells with a FACSAria III laser sorter.
Total RNAs from control and Kdm1a-cKO isolated PND 6 spermatogonia (n = 4 for each group) were extracted using the PicoPure RNA isolation kit (Arcturus, Burlington, ON, Canada). A total of 250 ng of each sample was used to prepare libraries using the TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer’s instructions.

value: KDM1A KO

tag: strain

value: 6 dpp


title: KDM1A KO rep2: MVBG305KO

tag: age


title: Rgt1_exponential_IP_3


title: KDM1A KO rep1: MVBG11KO


title: Breast Cancer BC1899


title: Breast Cancer BC1892


title: Rgt1_exponential_IP_2


title: Tumor1GFP


title: Control rep4: MVBG428C

value: Control


title: Control rep3: MVBG412C


title: Breast Cancer BC1891


title: Rgt1_exponential_IP_1


title: Control rep2: MVBG233C


title: Breast Cancer BC1890


title: Rgt1_saturated_input_3

description:
Rgt1_saturated_merged_FE.bdg.gz
Rgt1_saturated_merged_peaks.narrowPeak.gz

growth_protocol: Cells were grown overnight, shaking at 30C in YPD media (1% yeast extract, 2% peptone, 2% dextrose).

value: saturated in YPD


title: Breast Cancer BC1888


title: Control rep1: MVBG16C


title: Breast Cancer BC1887


title: Rgt1_saturated_input_1


title: KDM1A KO rep3: MVBG413KO


title: Rgt1_saturated_IP_3


title: Breast Cancer BC1884


title: Breast Cancer BC1885


title: Rgt1_saturated_IP_2


title: Rgt1_saturated_IP_1


title: Sdd4_exponential_input_3

description:
Sdd4_exponential_merged_FE.bdg.gz
Sdd4_exponential_merged_peaks.narrowPeak.gz

source_name: TAP-tagged Sdd4


title: Breast Cancer BC1883


title: Rgt1_saturated_input_2


title: Sdd4_exponential_input_1


title: Sdd4_exponential_IP_3


title: Sdd4_exponential_IP_2


title: Breast Cancer BC1877


title: Breast Cancer BC1876


title: Breast Cancer BC1880


title: Breast Cancer BC1878


title: Breast Cancer BC1879


title: Breast Cancer BC1881


title: Sdd4_exponential_input_2


title: Sdd4_exponential_IP_1


title: Breast Cancer BC1874


title: Breast Cancer BC1882


title: Left carotid-Gel-1day-Replicate3

first: Olga

last: Plekhanova

address: Lomonosovsky prospect, 27-1

institute: Lomonosov Moscow State University

description: 3-month-old male Wistar-Kyoto rats.

hyb_protocol: Microarray analysis was performed at the University of Rochester Microarray Core Facility in accordance to Affymetrix recommendations using Affymetrix rat genome U34A oligonucleotide microarrays with 8799 known genes and expressed sequence tags (ESTs) (Santa Clara, CA). Streptavidin phycoerythrin stain (SAPE, Molecular Probes) was used.

scan_protocol: Target hybridization was detected and quantified with a Gene Array Scanner (Hewlett Packard/Affymetrix). “Array performance” was assessed. Hybridization efficiency and sensitivity were controlled using control transcripts spiked into the hybridization cocktail.

data_processing: Inter-array variability was assessed by Microarray Analysis Suite 5.0. For data normalization global scaling with target intensity of 500 across all probe sets was used.

organism: Rattus norvegicus

source_name: Wistar Kyoto rats common carotid arteries

label_protocol: Labeled with biotin.

extract_protocol:
For microarrays, 1 and 4 days after the operation carotids were rapidly removed and frozen in liquid nitrogen. Total RNA was extracted from carotid arteries of injured, sham-operated and intact rats.
Total RNA was isolated with the use of Qiagen RNeasy Micro kit, the quality of RNA was confirmed. For each probe vessels from 3 rats were pooled.

treatment_protocol: Ketamine anesthesia was used (100 mg/kg body wt) and the balloon catheter (Fogarty 2F) injury of rats left common carotid arteries was performed. Following balloon catheter injury, 20 nmol/kg of recombinant tissue-type plasminogen activator dissolved in pluronic gel or 500 μl of plain Pluronic gel, F-127 (BASF) was applied to the adventitial side of the left common carotid arteries.

tag: strain/background

value: Wistar-Kyoto

tag: gender

value: Male

value: 3 months

value: Left carotid

tag: surgery

value: Balloon catheter injury of left carotid

tag: treatment

value: Gel applied to left carotid

value: 1 day


title: Left carotid-Gel-1day-Replicate2

description: 3-month-old male Wistar-Kyoto rats.

tag: time point


title: Sdd4_saturated_input_3

description:
Sdd4_saturated_merged_FE.bdg.gz
Sdd4_saturated_merged_peaks.narrowPeak.gz


title: Breast Cancer BC1873

value: metastatic breast cancer

value: Yes


title: Right carotid-tPA-1day-Replicate1

description: 3-month-old male Wistar-Kyoto rats.

value: Right carotid

value: tPA applied to left carotid


title: Left carotid-tPA-1day-Replicate3

description: 3-month-old male Wistar-Kyoto rats.


title: Sdd4_saturated_input_2


title: Sdd4_saturated_input_1


title: Breast Cancer BC1872

value: Serum


title: Left carotid-tPA-1day-Replicate1

description: 3-month-old male Wistar-Kyoto rats.


title: Right carotid-tPA-1day-Replicate2

description: 3-month-old male Wistar-Kyoto rats.


title: Right carotid-tPA-1day-Replicate3

description: 3-month-old male Wistar-Kyoto rats.


title: Right carotid-Gel-1day-Replicate3

description: 3-month-old male Wistar-Kyoto rats.


title: Left carotid-Gel-1day-Replicate1

description: 3-month-old male Wistar-Kyoto rats.


title: Breast Cancer BC1871

value: No


title: Breast Cancer BC1870


title: Right carotid-Gel-1day-Replicate2

description: 3-month-old male Wistar-Kyoto rats.


title: Left carotid-tPA-1day-Replicate2

description: 3-month-old male Wistar-Kyoto rats.


title: Carotid-Intact-Replicate5

description: 3-month-old male Wistar-Kyoto rats.

value: Intact


title: Carotid-Intact-Replicate4

description: 3-month-old male Wistar-Kyoto rats.


title: Carotid-Intact-Replicate6

description: 3-month-old male Wistar-Kyoto rats.


title: Breast Cancer BC1868


title: Right carotid-Gel-1day-Replicate1

description: 3-month-old male Wistar-Kyoto rats.


title: Breast Cancer BC1869


title: Breast Cancer BC1866


title: Sdd4_saturated_IP_3


title: Leu3_exponential_input_3

description:
Leu3_exponential_merged_FE.bdg.gz
Leu3_exponential_merged_peaks.narrowPeak.gz

source_name: TAP-tagged Leu3

value: exponential in YPD


title: Sdd4_saturated_IP_2


title: Leu3_exponential_input_2


title: Sdd4_saturated_IP_1


title: Breast Cancer BC1867


title: Leu3_exponential_input_1


title: Breast Cancer BC1864


title: Breast Cancer BC1863


title: Carotid-Sham-4days-Replicate6

description: 3-month-old male Wistar-Kyoto rats.

value: Sham operated

value: 4 days


title: Leu3_exponential_IP_3


title: Leu3_exponential_IP_2


title: Carotid-Intact-Replicate2

description: 3-month-old male Wistar-Kyoto rats.

value: Wistar-Kyoto


title: Carotid-Sham-4days-Replicate5

description: 3-month-old male Wistar-Kyoto rats.

value: Male


title: Carotid-Intact-Replicate3

description: 3-month-old male Wistar-Kyoto rats.

value: 3 months


title: Breast Cancer BC1862


title: Carotid-Sham-4days-Replicate4

description: 3-month-old male Wistar-Kyoto rats.

value: Left carotid


title: Carotid-Intact-Replicate1

description: 3-month-old male Wistar-Kyoto rats.


title: Carotid-Sham-4days-Replicate3

description: 3-month-old male Wistar-Kyoto rats.


title: Breast Cancer BC1861


title: Leu3_exponential_IP_1


title: Leu3_saturated_input_3

description:
Leu3_saturated_merged_FE.bdg.gz
Leu3_saturated_merged_peaks.narrowPeak.gz

value: saturated in YPD


title: Breast Cancer BC1860


title: Breast Cancer BC1859


title: Carotid-Sham-4days-Replicate2

description: 3-month-old male Wistar-Kyoto rats.


title: Carotid-Sham-4days-Replicate1

description: 3-month-old male Wistar-Kyoto rats.


title: Leu3_saturated_input_2


title: Breast Cancer BC1858


title: Leu3_saturated_input_1


title: Carotid-Sham-1day-Replicate4

description: 3-month-old male Wistar-Kyoto rats.


title: Carotid-Sham-1day-Replicate3

description: 3-month-old male Wistar-Kyoto rats.


title: Leu3_saturated_IP_3


title: Carotid-Sham-1day-Replicate2

description: 3-month-old male Wistar-Kyoto rats.


title: Breast Cancer BC1857


title: Breast Cancer BC1855


title: Leu3_saturated_IP_1


title: Leu3_saturated_IP_2


title: Breast Cancer BC1856


title: rgt1D_3

data_processing:
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were quality-trimmed (cutadapt -q 20), trimmed of adapter sequences, excluding read pairs in which either read was shorter than 28 bp after trimming.
Reads were mapped using bowtie2 2.2.3 using the parameter set --very-sensitive -X 500
The number of read pairs with a minimum MAPQ score of 30 that overlap each gene uniquely were counted using HTSeq-count.
genome build: sacCer3 or ScSu.fa
Supplementary_files_format_and_content: sacCer3_genes.gff are the gene annotations used for S. cerevisiae; ScSu_genes.gff are the annotations for S. cerevisiae x S. uvarum; tab-delimited text files ending in "counts.txt" include the number of read pairs mapping to each gene.

source_name: Cells

extract_protocol:
RNA was purified using acid phenol extraction, and then treated with Turbo DNase and purified with a Qiagen RNeasy kit.
Illumina libraries were prepared from 800-900 ng of total RNA, using the Truseq Stranded mRNA Library Prep (Illumina).


title: Left carotid-tPA-4days-Replicate3

description: 3-month-old male Wistar-Kyoto rats.

value: Balloon catheter injury of left carotid


title: Carotid-Sham-1day-Replicate1

description: 3-month-old male Wistar-Kyoto rats.

value: 1 day


title: Breast Cancer BC1854

value: metastatic breast cancer


title: Left carotid-tPA-4days-Replicate2

description: 3-month-old male Wistar-Kyoto rats.


title: Left carotid-tPA-4days-Replicate1

description: 3-month-old male Wistar-Kyoto rats.


title: rgt1D_2


title: Breast Cancer BC1853


title: rgt1D_1


title: semen-BTHO-44

type: genomic

city: Beltsville

first: George

middle: E

last: Liu

address: 10300 Baltimore Avenue

institute: USDA

description: Processed data files are pair file coordinates for probe locations. The initial data analysis (normalization and segmentation) was performed on NimbleScan v2.6 software with segMNT algorithm. log2-transformed (test/control) ratios.

hyb_protocol: Hybridization was performed by the third party provider, Nimblegen. Dye swap experiments with the Dominette reference sample were performed to test probe quality

scan_protocol: Scanning was performed by the third party provider, Nimblegen

organism: Bos taurus

label_protocol: Labeling was performed by the third party provider, Nimblegen

extract_protocol: DNA was extracted from semen or blood using a Qiagen DNEasy tissue and blood kit (QIAGEN, Valencia, CA, USA).

value: semen

value: male

source_name: Reference (L1 Dominette whole blood DNA extract)

value: Blood

value: female


title: semen-BTHO-45

data_processing: Processed data files are pair file coordinates for probe locations. The initial data analysis (normalization and segmentation) was performed on NimbleScan v2.6 software with segMNT algorithm.


title: semen-BTHO-46


title: Breast Cancer BC1852

value: No

value: Serum


title: semen-BTHO-38


title: sdd4D_3


title: Breast Cancer BC1851


title: Right carotid-tPA-4days-Replicate3

description: 3-month-old male Wistar-Kyoto rats.

value: Right carotid

value: tPA applied to left carotid


title: semen-BTHO-40


title: semen-BTHO-37


title: semen-BTHO-41


title: semen-BTHO-43


title: semen-BTHO-39


title: semen-BTHO-36


title: semen-BTHO-34


title: semen-BTHO-42


title: Right carotid-tPA-4days-Replicate2

description: 3-month-old male Wistar-Kyoto rats.

value: 4 days


title: Right carotid-tPA-4days-Replicate1

description: 3-month-old male Wistar-Kyoto rats.

value: Wistar-Kyoto


title: sdd4D_1


title: Breast Cancer BC1849

value: Yes


title: Breast Cancer BC1848


title: Left carotid-Gel-4days-Replicate2

description: 3-month-old male Wistar-Kyoto rats.

value: Male

value: 3 months

value: Gel applied to left carotid


title: semen-BTHO-47


title: sdd4D_2

value: saturated in YPD


title: leu3D_2


title: Breast Cancer BC1847


title: Left carotid-Gel-4days-Replicate3

description: 3-month-old male Wistar-Kyoto rats.

value: Left carotid

value: Balloon catheter injury of left carotid


title: leu3D_3


title: Left carotid-Gel-4days-Replicate1

description: 3-month-old male Wistar-Kyoto rats.


title: semen-BTHO-27

value: semen


title: semen-BTHO-33

value: male


title: Breast Cancer BC1846

value: metastatic breast cancer


title: leu3D_1


title: semen-BTHO-31

value: Blood

value: female


title: Breast Cancer BC1850

value: Serum


title: semen-BTHO-30


title: Breast Cancer BC1845


title: WT_3


title: Right carotid-Gel-4days-Replicate3

description: 3-month-old male Wistar-Kyoto rats.

value: Right carotid


title: semen-BTHO-24


title: semen-BTHO-26


title: WT_2


title: Right carotid-Gel-4days-Replicate1

description: 3-month-old male Wistar-Kyoto rats.


title: WT_1


title: Breast Cancer BC1843

value: No


title: Rgt1_muts_genomic_3

description:
fixed-locus_ko_barcodes.fa.gz
Rgt1_muts_associations.txt.gz

data_processing:
Library strategy: Rgt1 deletion trans MAP-C
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were trimmed to a fixed length of 25 bp and mapped to the set of possible barcodes using bowtie2 2.2.3. Barcodes were associated with Rgt1 mutants based on programmed barcode associations.
genome build: Barcode file fixed-locus_ko_barcodes.fa
Supplementary_files_format_and_content: tab-delimited text files ending in "counts.txt" include the Rgt1 mutation or gene deletion names and the number of reads containing each barcode. FASTA files ending in ".fa" contain the possible barcodes used for mapping. tab-delimited text files ending in "associations.txt" include the Rgt1 mutations or gene deletions associated with each barcode.

extract_protocol:
Cells were lysed using glass beads and chromatin was extracted, digested using restriction enzyme, and ligated. Crosslinks were reversed and DNA was purified by phenol/chloroform extraction.
DNA was amplified with primers containing sequencing and flowcell adapter sequences.

treatment_protocol: Cells were crosslinked by addition of 37% formaldehyde to a 1% final concentration, for 20 minutes at room temperature, and then quenched by addition of 2.5M glycine, incubation for 5 minutes, and a TBS (Tris-buffered saline) wash.

tag: restriction enzyme

value: EcoRI-HF


title: semen-BTHO-23


title: Rgt1_muts_genomic_2


title: Breast Cancer BC1841

tag: disease state


title: Breast Cancer BC1842

tag: new distant metastasis


title: HK1EBV-treated with DMSO

city: Nanning

first: Yushan

last: Liang

address: 6# Shuangyong Road

department: Department of Otolaryngology Head & Neck Surgery

country: China

institute: First Affiliated Hospital of Guangxi Medical University

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 1.0 in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

source_name: HK1EBV cells treated with DMSO for 24 hours

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using GeneChip® WT PLUS Reagent Kit

growth_protocol: All cells were incubated at 37℃ in a humidified atmosphere containing 5% CO2 and cultured in Modified Eagles Medium/High glucose (DMEM) medium supplemented with 10% fetal bovine serum (FBS) in the presence of streptomycin and penicillin.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit and RNase-Free Dnase Set.

treatment_protocol: Cell lines HK1 and HK1EBV were originally established as derived from human nasopharyngeal carcinoma (NPC) cells. HK1-DMSO,HK1EBV-DMSO was pretreated with DMSO (0.1%) for 24h as control group. HK1-drug,HK1EBV-drug was pretreated with CAPE (110 µM) for 24h as experimental group

tag: cell line

tag: cell type

value: nasopharyngeal carcinoma (NPC) cell line

value: 0.1% DMSO for 24hrs


title: Rgt1_muts_genomic_1


title: semen-BTHO-35


title: Rgt1_muts_3C_3


title: semen-BTHO-28


title: Breast Cancer BC1839

value: Yes


title: HK1-treated with DMSO

source_name: HK1 cells treated with DMSO for 24 hours


title: Breast Cancer BC1840


title: Right carotid-Gel-4days-Replicate2

description: 3-month-old male Wistar-Kyoto rats.

value: Wistar-Kyoto

value: Male

value: 3 months

value: 4 days


title: semen-BTHO-29


title: Rgt1_muts_3C_2

value: saturated in YPD


title: semen-BTHO-32

value: semen


title: Breast Cancer BC1838


title: Rgt1_muts_3C_1


title: 48Hr RAAAG mutant-Rep3

city: Berkeley

first: Britt

last: Glaunsinger

address: 565 Li Ka Shing Center

institute: UC Berkeley

data_processing:
Reads were analyzed using FastQC and trimmed using TrimGalore using default parameters.
The trimmed reads were aligned to both the viral (NC_009333.1) and host genomes (hg19) using STAR aligner (ver2.5.3a).
The aligned reads were counted using htseq-counts.
Genome_build: hg19 (GRCh37), NC_009333.1
Supplementary_files_format_and_content: *.txt: Text files with read counts for human and viral genes generated by htSeq-counts.

organism:
Homo sapiens
Human gammaherpesvirus 8

source_name: Cell culture

extract_protocol:
Cells were lysed using Trizol and RNA extracted using Zymo RNA extraction kit as per protocol mentioned by manufacturer.
Libraries were prepared by the qb3 facility at UC Berkeley.

value: iSLK

tag: latent infection

value: ORF24-RAAAG mutant

value: 48 hr


title: RPE18_TNT_S9

city: New York

first: Timothy

middle: Adam

last: Blenkinsop

state: NY

address: 1425 Madison Ave, Icahn Building, Floor 13, Room 13-70A

department: Cell, Development and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Mapped with the STAR aligner to UCSC.hg19.sparse genome and gencode v19 annotation.
Following parameters used: --twopassMode Basic --quantMode GeneCounts  --outSAMtype BAM SortedByCoordinate --alignSJDBoverhangMin 10 --alignSJoverhangMin 20
Gene count files were read into R and differential gene expression was determined using the DESeq2 and EdgeR packages.
Genome_build: human GRch37/hg19
Supplementary_files_format_and_content: data table of the raw counts

source_name: Retinal

growth_protocol: Healthy retinal pigment epithelial cells were dissected from human donors and maintained in culture for a  minimum of one month.

extract_protocol:
After 5 days, RNA from healthy and disease-modeled retinal pigment epithelial cells were extracted using Qiagen RNeasy Plus Mini Kit (Cat#:74136). Diseased Proliferative Vitreoreinopathy membranes were surgically dissected and RNA was extracted using Qiagen RNeasy Plus Mini Kit (Cat#:74136).
Libraries were prepared using standard Illumina protocols.

treatment_protocol: A subset of the healthy dissected cells were treated with a Proliferative Vitreoretinopathy disease-modeling protocol for a minimum of 5 days (DMEM/F12 base media + 3% fetal bovine serum supplemented with 10 ng/ml of both TGFβ1 and TNFα).

value: Disease-modeled retinal pigment epithelial cells

tag: source

value: Primary donor


title: RPE15_TNT_S10


title: semen-BTHO-20

value: male

value: Blood

value: female


title: Breast Cancer BC1837

value: metastatic breast cancer

value: No

value: Serum


title: 48Hr RAAAG mutant-Rep2


title: Breast Cancer BC1836

value: Yes


title: RPE37_TNT_S11


title: ScHAS1pr-TDA1pr_rgt1x2_3

description:
ScSu_genes.gff
ScSu.fa

organism: Saccharomyces cerevisiae x Saccharomyces uvarum

extract_protocol:
RNA was purified using acid phenol extraction, and then treated with Turbo DNase and purified with a Qiagen RNeasy kit.
Illumina libraries were prepared from 800-900 ng of total RNA, using the Truseq RNA Library Prep kit v2 (Illumina).


title: semen-BTHO-25


title: RPE_37_S8

value: Retinal pigment epithelial cells


title: Breast Cancer BC1834


title: 48Hr RAAAG mutant-Rep1


title: 48Hr mutant rescue-Rep3

description: Wild type

value: Mutant rescue


title: 48Hr mutant rescue-Rep2

description: Wild type


title: Breast Cancer BC1844


title: semen-BTHO-21


title: semen-BTHO-22


title: Breast Cancer BC1833


title: Breast Cancer BC1835


title: HK1-treated with CAPE

source_name: HK1 cells treated with CAPE for 24 hours

value: nasopharyngeal carcinoma (NPC) cell line

value: 110 µM caffeic acid phenethyl ester (CAPE) for 24hrs


title: ScHAS1pr-TDA1pr_leu3_3

description:
ScSu_genes.gff
ScSu.fa

value: saturated in YPD


title: ScHAS1pr-TDA1pr_rgt1x2_1

description:
ScSu_genes.gff
ScSu.fa


title: 48Hr mutant rescue-Rep1

description: Wild type

value: iSLK


title: ScHAS1pr-TDA1pr_leu3_2

description:
ScSu_genes.gff
ScSu.fa


title: RPE_18_S12


title: 24Hr mutant rescue-Rep3

description: Wild type

value: 24 hr


title: ScHAS1pr-TDA1pr_rgt1x2_2

description:
ScSu_genes.gff
ScSu.fa


title: PVR6_Sub

value: Diseased Proliferative Vitreoretinopathy membranes

value: Patient-dissected


title: semen-BTHO-15

value: semen


title: ScHAS1pr-TDA1pr_WT_3

description:
ScSu_genes.gff
ScSu.fa


title: HK1EBV-treated with CAPE

source_name: HK1EBV cells treated with CAPE for 24 hours


title: semen-BTHO-14

value: male


title: Breast Cancer BC1830


title: 24Hr mutant rescue-Rep1

description: Wild type


title: Breast Cancer BC1831


title: PVR7


title: HA-Input-Rep2

description:
iSLK-HA-ORF34
Genomic and viral DNA

data_processing:
Reads were analyzed using FastQC and adapters were trimmed with TrimGalore.
Trimmed reads were aligned using Bowtie2 alignment program.
The aligned reads were converted to BAM files, filtered with a q cutoff of 10 and sorted using SAMTools.
The sorted files were converted to tdf using IGV.
Genome_build: hg19 (GRCh37), GQ994935.1
Supplementary_files_format_and_content: *tdf: tdf files for each sample.

extract_protocol:
Cells were lysed, nuclei were isolated and sonicated to fragment chromatin which was used for immunoprecipitation with the indicated antibody.
Libraries were prepared using the Swift Biosciences protocol.

value: 48 hr

tag: chip antibody


title: ScHAS1pr-TDA1pr_WT_1

description:
ScSu_genes.gff
ScSu.fa

tag: growth conditions


title: 4T1-HD-5

city: Madison

first: Patricia

last: Keely

state: Wisconsin

address: 1111 Highland Ave

institute: University of Wisconsin-Madison

description: Gene expression data from 4T1 cells cultured in a HD collagen matrix

hyb_protocol: All samples hybridized to Mouse Transcriptome 1.0 ST arrays at 45°C for 16 hrs O/N following all procedures outlined in Affymetrix GeneChip WT Plus Reagent Kit User Guide (Rev.2)

scan_protocol: GeneChips post processed on the AFX Fluidics 450 Station according to all AFX protocols and procedures defined for the Mouse Transcriptome 1.0 ST Array (FS450_0001) GC scanned on the GC3000 G7 Scanner (Serial #50208130)

data_processing:
Data extracted and processed using Affymetrix Command Console version 4.0.0.1567G.  The data were analyzed with RMA:
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0

source_name: 4T1 mammary carcinoma cells in HD collagen gel

label_protocol: Fragment ss cDNA end-terminus labeled with biotin following procedure outlined Affymetrix GeneChip WT Plus Reagent Kit Manual

growth_protocol: Gels were cultured 5 days in a 5% CO2 37 C incubator in RPMI 1640 media +10% FBS. Media was changed on the evening of day 3.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Density of collagen in the gel was changed between 2 mg/mL (LD) and 3.5 mg/mL HD. For information on collagen gel protocol see Burkel et al. JOVE 2016

value: 4T1 mammary carcinoma cell line

tag: gel density

value: 3.5 mg/mL


title: WT-Input-Rep2

description:
iSLK-WT BAC16
Genomic and viral DNA

value: WT BAC16


title: Breast Cancer BC1827

source_name: Serum from breast cancer patient during eribulin treatment

value: metastatic breast cancer

tag: tissue

value: Serum


title: wild type_rep3

city: Beijing

first: ziyi

last: cheng

address: Tsinghua East Road 35, Haidian District

institute: Beijing Forestry University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based onthe clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: NCBI

source_name: mature stem

growth_protocol: All the plants grew in greenhouse at 20 oC (16h light, 8h dark).

extract_protocol:
Total RNA was isolated from the main stem of different developmental stage of Arabidopsis plant, using EASYspin Plant RNA kit RN09 (Aidlab, China) according to the manufacturer's instructions.
In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: stem

tag: Stage

value: 42 days after flowering

tag: genotype/variation

value: wild type


title: 4T1-HD-4


title: HA-ChIP-Rep2

description:
iSLK-HA-ORF34
Genomic and viral DNA

value: HA-Tag (C29F4) (Cell Signaling)


title: wild type_rep2


title: RPE_15_S7

value: Retinal pigment epithelial cells

value: Primary donor


title: ScHAS1pr-TDA1pr_leu3_1

last: Kim

description:
ScSu_genes.gff
ScSu.fa

value: saturated in YPD


title: semen-BTHO-12

tag: gender

value: Blood

value: female


title: 4T1-HD-2


title: 4T1-HD-3


title: Breast Cancer BC1832

tag: age

value: No


title: Breast Cancer BC1826


title: WT-ChIP-Rep2

description:
iSLK-WT BAC16
Genomic and viral DNA

value: iSLK


title: Breast Cancer BC1828


title: semen-BTHO-10

value: semen

value: male


title: 4T1-LD-5

description: Gene expression data from 4T1 cells cultured in a LD collagen matrix

source_name: 4T1 mammary carcinoma cells in LD collagen gel

value: 4T1 mammary carcinoma cell line

value: 2 mg/mL


title: semen-BTHO-7


title: semen-BTHO-16


title: wild type_rep1


title: semen-BTHO-13


title: HA-Input-Rep1

description:
iSLK-HA-ORF34
Genomic and viral DNA

value: 48 hr


title: WT-Input-Rep1

description:
iSLK-WT BAC16
Genomic and viral DNA

value: WT BAC16


title: Breast Cancer BC1824

value: metastatic breast cancer

value: Serum


title: Breast Cancer BC1825

value: Yes


title: HA-ChIP-Rep1

description:
iSLK-HA-ORF34
Genomic and viral DNA

value: HA-Tag (C29F4) (Cell Signaling)


title: γvpe mutant_rep2

value: stem

value: 42 days after flowering

value: gamma-VPE mutant


title: γvpe mutant_rep1


title: semen-BTHO-18

value: Blood


title: Breast Cancer BC1823


title: semen-BTHO-8

value: female


title: ScHAS1pr-TDA1pr_WT_2

description:
ScSu_genes.gff
ScSu.fa

value: saturated in YPD


title: WT-ChIP-Rep1

description:
iSLK-WT BAC16
Genomic and viral DNA

value: iSLK


title: 4T1-HD-1

value: 3.5 mg/mL


title: 4T1-LD-3


title: semen-BTHO-19

value: semen

value: male


title: 4T1-LD-2

value: 4T1 mammary carcinoma cell line

value: 2 mg/mL


title: semen-BTHO-11


title: AM31_Q35_EV_3

status: Public on Feb 15 2019

city: Jerusalem

first: Ehud

last: Cohen

address: The Hebrew University of Jerusalem, Ein Kerem

department: Biochemistry and Molecular Biology

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Processing was done with a modified CEL-Seq2 pipeline, based on the one described by its developers.
Demultiplexing: CEL-seq2 is uses paired-end sequencing, in which read-end 1 is mapped to the genome, while read-end 2 possess the barcode and UMI-sequence, as well as a polyT-stretch. CEL-seq2 sequencing is performed to multiplexed samples, and the barcodes of read-end 2 are used to extract the sample source that relates to read-end 1. During CEL-Seq sample preparation, each sample is marked with a primer containing a unique barcode. Each initial RNA sample was barcoded using a pool of three different CEL-Seq primers. Using several primers to create technical replicates for each sample reduces the possibility of technical variability caused by differences in barcode efficiency. Barcode splitting was done with the developers pipeline, with parameters: stats_file=stats.tab, min_bc_quality=10, bc_length=6, umi_length=6, cut_length=51. The "RAW FILES" are the demultiplexed reads that correspond to each sample. See the paper that was published by the CEL-seq2 developers for more details.
Adapter and quality trimming were performed using cutadapt, version 1.12, with parameters: -e 0, -q 10, -u 9, -a "A{100}", -a "A{15}N{100}", -a GATCGTCGGACT, -n 3, -m 28. The set parameters mean no errors, trimming quality below 10 in a phred+33 scale, removing the first 9 bases, trimming adapters, polyA and polyN tails, and keeping only reads of length at least 28. Two sequences were set for removal: (1) "Small RNA 5' adapter" – GATCGTCGGACT; (2) Poly A, as during sample preparation a poly T sequence is used to capture the 3' end of the transcripts. After adapter and quality trimming over 90% of the reads remained.
Mapping to the C. elegans genome, Ensembl: WBcel235, release 36 (June, 2017), joint with the ERCC sequences (CEL-Seq2 control Spike-In), was done using Tophat2 version 2.1.1, with parameters: -N 2, --read-edit-dist 2, -G protein_coding_ERCC.gtf. The set parameters mean up to 2 mismatches, and up to an edit distance of 2, using annotations of protein coding genes (from Ensembl WBcel235 release 36), and the ERCC Spike-In. A mapping percentage of over 94% was reached.
Gene counting was done using HTseq-count version 0.6.1, with parameters: gff_file=protein_coding_ERCC.gtf, umi=false. The set parameters mean that the counting was done using the same annotations as in the mapping step (protein coding and ERCC Spike-In), and ignoring UMIs. This was done since UMIs are too short to capture the full repertoire of transcripts in the samples, and using them would cause a flattening of the signal for genes with a higher expression.
Normalization and differential expression analysis done using the R/Bioconductor (Huber et al., 2015; R Core Team, 2018) package DESeq2 version 1.22.2 with default parameters (Love et al., 2014).
Genome_build: Ensembl: WBcel235, release 36 (June, 2017)
Supplementary_files_format_and_content: CSV files include DESeq normalized count values for each sample

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans homogenate

growth_protocol: Hermaphrodite C. elegans were synchronized using hypochlorite and potassium hydroxide, and cultured at 20 °C. For each time-point, 6,000 synchronized eggs were placed on NG-ampicillin plates seeded with HT115 bacteria and supplemented with IPTG. The worms were washed daily with M9 to discard of progeny.

extract_protocol:
Total RNA was isolated using NucleoSpin® RNA kit (MACHEREY-NAGEL, 740955). On each time-point, we washed the worms with M9 to remove bacteria, and resuspended them in 350 µl buffer RA1 (kit reagent), 5.5 µl 1M DTT, and a small amount of 0.5 mm zirconium oxide beads (Next Advance, ZrOB05). The worms were homogenized using a Bullet Blender® (Next Advance) set to speed eight, for three minutes, and then set to speed nine and for an additional two minutes. Homogenates were transferred to fresh tubes and centrifuged at 14,000 x g for 5 minutes. The supernatant was transferred to NucleoSpin® Filter (kit reagent), and the next steps followed the manufacturer’s standard protocol. Following RNA isolation, the RNA integrity and quantity was assessed using the Agilent 2200 TapeStation System. The RNA purity was assessed by loading 1.5 µl of each sample onto a NanoDrop™ 2000c Spectrophotometer and reading the A260 nm emission, as well as the A260/A280 and A260/A230 ratios.
Isolated RNA samples were prepared and sequenced by the Technion Genome Center (Technion, Haifa, Israel) according to the CEL-Seq2 protocol, as described by its developers (Hashimshony et al., 2016).

treatment_protocol: Worms were fed with the E. coli strain HT115 that expresses dsRNA for RNA interference. Bacteria were grown overnight at 37 °C in LB media supplemented with 100 µg/ml ampicillin. NG plates containing 100 µg/ml ampicillin were seeded with bacterial cultures.  To induce RNAi, the seeded plates were treated with 120 µl 100 mM Isopropyl-β-D-Thiogalactopyranoside (IPTG) (Inalco, 1758-1400). The bacteria were obtained from the Vidal RNAi library.

tag: strain

value: day 6 of adulthood

tag: genotype

tag: treatment-rnai

value: empty vector

tag: replicate


title: AM42_Q35_anc-1_4


title: NT21_WT_EV_2

value: wild type


title: AM32_Q35_anc-1_3


title: NT32_WT_anc-1_3


title: NT22_WT_anc-1_2


title: AM12_Q35_anc-1_1


title: AM22_Q35_anc-1_2


title: AM41_Q35_EV_4


title: AM21_Q35_EV_2


title: AM11_Q35_EV_1


title: Breast Cancer BC1829

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: disease state

value: metastatic breast cancer

tag: new distant metastasis

value: No

value: Serum


title: NT31_WT_EV_3


title: NT12_WT_anc-1_1


title: NT11_WT_EV_1


title: WT_SL1h_rep1

city: Pittsburgh

first: Zheng

last: Kuang

state: PA

address: 4400 Fifth Avenue

department: Biological Sciences

institute: Carnegie Mellon University

description: ChIP DNA

data_processing:
Reads were mapped using Bowtie2 against yeast genome SacCer2 (bowtie2 -p 26 -x ./index/saccer2).
Peaks were called using MACS and peak intensities were calculated using CountOverlaps function in R and normalized by the total number of reads.
Genome_build: SacCer2
Supplementary_files_format_and_content: Tab delimited txt file. Each row represents one peak and each column represents normalized read counts from one sample.

source_name: yeast cells

growth_protocol: For YPL samples, cells were collected in log phase when OD600 reached ~1.0; for SL samples, cells were collected 1hour after switching YPL growing cells to SL.

extract_protocol:
yeast cells were grown in  YPL to OD600 = 1 before switching to SL for 1 hour. 50 units of OD600 cells were quenched in 1% formaldehyde for 15 minutes  and then quenched with glycine for 10 minutes. Cell pellets were washed twice with a buffer containing 100 mM NaCl, 10 mM  Tris-HCl pH 8.0, 1 mM PMSF, and 1 mM benzamide-HCl, and snap-frozen in liquid nitrogen. Frozen pellets were lysed in 0.45 mL  ChIP lysis buffer (50 mM HEPES-KOH pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% deoxycholate, 0.1% SDS,  1 mM PMSF, 10 mM leupeptin, 5 mM pepstatin A, and Roche protease inhibitor cocktail) and lysed by bead-beating. Lysates were  split to two tubes containing 280 mL lysate each and sonicated for 16 cycles (30 sec on, 1 min off, high output) using the Bioruptor  (Diagenode). The lysates were then cleared by two consecutive spins at 16,100 g for 10 minutes. 50 mL was saved as input. For ChIP,  50 mL lysate was diluted at 1:10 and incubated overnight with 2 mg antibody of H3, H3K36me3, or HA. 20 mL magnetic beads were  added and incubated for an additional 1.5 hours. Beads were then washed twice with ChIP lysis buffer, once with deoxycholate buffer  (10mMTris-HCl, 0.25MLiCl, 0.5% deoxycholate, 1mMEDTA), and once with TE (50mMTris-HCl pH 8.0, 10mMEDTA). Elution was  performed with 2 consecutive 10 min incubations with 60 mL TES buffer (50mMTris-HCl pH 8.0, 10mMEDTA, and 1% SDS) at 65 C.  Reverse crosslinking was performed by further overnight incubation at 65 C. An equal volume of TE containing 1.25 mg/mL proteinase  K was then added and incubated for 2 hours at 37 C. DNA was then column purified using the Qiagen PCR purification kit.
Please refer to KAPA Hyper Prep Kit manual for the protocol.

value: CEN.PK; MATa; RPH1-HA-HYG

tag: medium

value: SL, 0.17% yeast nitrogen base without amino acids

tag: tag

value: HA


title: WT_YPL_rep2

description: ChIP DNA

value: YPL, 1% yeast extract, 2% peptone and 2% lactate


title: WT_SL1h_rep2

description: ChIP DNA

value: SL, containing 0.5% ammonium sulfate (Difco), 2% lactate


title: ppm1Δ_YPL_rep1

description: ChIP DNA

value: CEN.PK; MATa; RPH1-HA-HYG; ppm1::kanMX


title: S412A_YPL

description: ChIP DNA

value: CEN.PK; MATa; RPH1-S412A-HA-HYG


title: semen-BTHO-9

value: semen

value: Blood

value: female


title: semen-BTHO-17

value: male


title: ppm1Δ_YPL_rep2

description: ChIP DNA


title: V2D12

first: Nicholas

last: Tatonetti

state: New York

address: 622 W 168th Street

department: Department of Biomedical Informatics

institute: Columbia University

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA TTG TCC TTT TTT TTT TTT TTT TTT TTT TTT TT

data_processing:
Base calling was performed by the Illumina HiSeq 4000's built-in control software
Reads were matched to original samples based on primer-linked barcode sequences (indicated on per-sample basis in the "Samples" table) - refer to Bush et al for further details.
Reads were demultiplexed and mapped to the human genome (GRCh38) and spike-ins library (ERCC92, Ambion) using the STAR aligner.
Counts for each gene are computed as the number of uniquely mapped reads associated with that gene.
Genome_build: hg38
Supplementary_files_format_and_content: Each processed data file is a tab-delimited text file where the first column is a gene symbol (or spike-in ID), and the second column is the number of counts of that gene (or spike-in) in the current sample.

source_name: IMR-32 neuroblastoma cells in culture

growth_protocol: IMR-32 cells were grown to confluence in FBS-supplemented EMEM.

extract_protocol: The PLATE-Seq protocol was used, as described by Bush et al (https://doi.org/10.1038/s41467-017-00136-z)

treatment_protocol: Treatments of 25 crude venoms (or water) were applied at the indicated timepoint prior to mRNA isolation in each sample, as described in the "Samples" table.

tag: venom treatment

value: Water

tag: time post-treatment

tag: cell line


title: V2A12

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT GGC TCT ATT TTT TTT TTT TTT TTT TTT TTT TT

tag: venom concentration (ug/ul)


title: V2B11

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC CCA AAC ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2F11

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA TTG TGG CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2C12

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT AGC ATA CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2H12

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA CGA CTG TTT TTT TTT TTT TTT TTT TTT TTT TT

value: Untreated


title: V2G11

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG TCG CAC ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2C11

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT CCA AGT CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2G12

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG TCG ACG ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2B12

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT TGG AAA CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2E12

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT ATC GGT CTT TTT TTT TTT TTT TTT TTT TTT TT


title: γvpe mutant_rep3

tag: tissue

value: stem

value: 42 days after flowering

value: gamma-VPE mutant


title: V2F12

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA TGT AAC CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2H11

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC GGT GAT ATT TTT TTT TTT TTT TTT TTT TTT TT


title: WT_YPL_rep1

description: ChIP DNA


title: V2D11

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC CGG TGA ATT TTT TTT TTT TTT TTT TTT TTT TT


title: 24Hr mutant rescue-Rep2

description: Wild type

value: iSLK

tag: latent infection

value: Mutant rescue

tag: time point

value: 24 hr


title: V2H10

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC ACA TTC CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2F10

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA GAT GCT ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2E10

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG TGG GAC TTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2A11

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG CAT AGT CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2C10

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG AGT TAC TTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2D10

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG TTA GCG TTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2E11

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC TAG CAT CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2G10

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC CAG GCA ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2B10

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT AGA GAT CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2A10

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC GTT TCA TTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2E09

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC TAC TGA CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2F09

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC AGT TCG GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2D09

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC GCA AAA TTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2A09

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC GCG TTA TTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2C09

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG GTT TCG CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2B09

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC GCG AAT CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2F08

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG AAT TGT GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2E08

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC TTT CCC TTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2G08

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT GTT ACG TTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2H08

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT CGT TAA GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2A08

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT GAG GAC TTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2B08

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA AAG CGA GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2G09

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC TGA GAC GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2D08

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC TCC CCT TTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2G07

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG TGT GCT ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2D07

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG TCA AGG TTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2H07

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA AGA GAG GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2H09

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT GTC CCC ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2C08

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG CAA CTA GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2F07

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG TAC CCA CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2B07

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT TCA CAT GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2C07

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT AGC TAG CTT TTT TTT TTT TTT TTT TTT TTT TT


title: 4T1-LD-1

description: Gene expression data from 4T1 cells cultured in a LD collagen matrix

value: 4T1 mammary carcinoma cell line

tag: gel density

value: 2 mg/mL


title: V2E07

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG ACT CCC ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2G06

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA CTT TGC GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2A07

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC CTC AAG CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2F06

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT CAT TGG ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2E06

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT TTC TCC CTT TTT TTT TTT TTT TTT TTT TTT TT


title: 4T1-LD-4


title: Breast Cancer BC1821

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetEsophageal Cancerted) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

value: metastatic breast cancer

tag: age

value: No

value: Serum


title: V2H06

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT CCT GTC ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2F04

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG TGT ACA CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2B04

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA TGC CTC ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2C04

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC ATA ACC CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2D04

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA GGA AGA ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2H04

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT TCA GTC CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2G04

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG GAA ATT GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2A04

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT TCG ACT GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2B06

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC TTC GTC TTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2F05

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT TGC GGA TTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2C05

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT TCC CGC ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2D06

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA CAC GCC ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2A05

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC TTA GTT GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2B05

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT CTC AGA ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2D05

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA CGA CCT CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2H05

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC TTA GGC ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2H03

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG CGC CTT ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2G05

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG CAA GAC GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2C06

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA ACA GTT GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2A06

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC GTG CTG ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2E04

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC CAG ATA CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2E05

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG GTG ATC TTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2G03

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT ACG AGC ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2E03

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT TAC CGT GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2F03

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT GCT TAA CTT TTT TTT TTT TTT TTT TTT TTT TT


title: Breast Cancer BC1789


title: V2C03

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG CTA ACG GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2B03

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC GAC TTG TTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2H02

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG AGA CCG ATT TTT TTT TTT TTT TTT TTT TTT TT


title: MPNST_atrx_mut_A1

city: Boston

first: Kenneth

middle: N

last: Ross

state: MA

address: 450 Brookline Ave., Rm M640

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: MPNST tumors from zebrafish with a heterozygous loss of atrx in context of combined p53/nf1-deficiency

data_processing:
FastQC was used to evaluate read quality on raw RNA-Seq reads and trimmed reads.
Trimming of low quality reads and clipping of sequencing adapters was done using the program Trimmomatic version 0.36 and all reads shorter than 36bp after trimming were dropped (Trimmomatic was run with settings of ILLUMINACLIP:adapters/TruSeq3-PE-2.fa: 2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 AVGQUAL:10).
Reads were aligned to the zebrafish (Danio rerio) reference genome with TopHat version 2.1.0 using UCSC danRer10 and settings of -x 1 -g 1 -r 44 --mate-std-dev 223 (with values for the flags -r and --mate-std-dev coming from the mean fragment size).
Bam sorting and indexing was done with SamTools and duplicate reads were removed using Picard-tools (http://picard.sourceforge.net).
Aligned reads processed to Fragments Per Kilobase of exon per Million fragments mapped (FPKM) using cufflinks version 2.2.1 (http://cufflinks.cbcb.umd.edu/index.html) with the -G flag to use the danRer10 reference annotation to estimate isoform expression and not assemble novel transcripts and the flags --max-bundle-frags 4000000 -N --compatible-hits-norm.
Gene level counts were obtained with htseq-count version 0.9.1.
Differential gene expression was evaluated with the R Bioconductor package DESeq2 and normalized expression values for individual samples were obtained from DESeq2 using the variance stabilizing transform on the raw counts. The variance stabilizing transformed data were used for GSEA.
Genome_build: GRCz10
Supplementary_files_format_and_content: genes.fpkm_tracking files are tab delimited text files output by cufflinks in a generic FPKM tracking format with estimated gene-level expression values in the form of FPKM values and raw_count.txt files are tab delimited text files output by htseq-count with gene level counts

organism: Danio rerio

source_name: Zebrafish malignant peripheral nerve sheath tumors (MPNSTs)

growth_protocol: Zebrafish were raised and maintained according to standard procedures. They were derived from the p53/nf1-deficient background (Shin et al., Disease Models & Mechanisms, 2012). All zebrafish studies and maintenance were done in accord with Dana-Farber Cancer Institute IACUC-approved protocol (#02-107).

extract_protocol:
RNA was isolated from one half of p53/nf1/atrx-deficient MPNSTs and p53/nf1-deficient control MPNSTs using the AllPrep DNA/RNA Mini Kit from Qiagen (Hilden, Germany) and the other half was set asside for analysis by histopathology.
Library preparation, quality control, and next-generation sequencing were conducted by the Molecular Biology Core Facility of the Dana-Farber Cancer Institute following standard protocols.

treatment_protocol: The zebrafish atrx mutant lines were generated by the CRISPR-Cas9 genome editing system using the previous described protocol (Hwang et al., Nature Biotechnology, 2013). The plasmid constructs pDR274 (#42250) and pMLM3613 (#42251) were purchased from Addgene. Oligonucleotides 5’-TAG GTC CTG AGT TCC GTA ACA A-3’ and 5’-AAA CTT GTT ACG GAA CTC AGG A-3’ were annealed and cloned into the pDR274 vector to generate single guide RNAs (gRNAs) targeting atrx exon 4. Each embryo was injected with 1 nl of solution containing 25 ng/μl gRNA and 600 ng/μl Cas9 mRNA at the 1 cell stage. Mosaic F0 fish with germline mutation were identified, and stable mutant lines were established by outcrossing.

tag: atrx


title: V2F02

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC AGG CGT ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2G02

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC CTC TTA GTT TTT TTT TTT TTT TTT TTT TTT TT


title: MPNST_atrx_mut_A16


title: MPNST_atrx_WT_A14

description: MPNST tumors from zebrafish with wild type atrx in context of combined p53/nf1-deficiency

value: wt


title: V2F01

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT GCA GCT GTT TTT TTT TTT TTT TTT TTT TTT TT


title: MPNST_atrx_WT_A9


title: V2A02

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC GTT GTC ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2E02

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC GAG TAA ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2H01

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG CCA TTG GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2B02

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC AGT ACC TTT TTT TTT TTT TTT TTT TTT TTT TT


title: MPNST_atrx_WT_A11


title: V2C02

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT TTT ACC GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2G01

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC ATG CCT TTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2D03

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT CTC TAG TTT TTT TTT TTT TTT TTT TTT TTT TT


title: 24h-treated_bio1

city: Wuhan

first: Weiwu

last: Zeng

state: Hubei

address: Bayi Road

department: College of Chemistry and Molecular Sciences

institute: Wuhan University

description:
cell line
24h-gene_exp.txt

data_processing:
For pull-down data, raw fastq reads were trimmed by Trim Galore (v0.4.4_dev) to remove adapters and mapped to the human reference genome GRCh38.p7 using Bowtie2 (v2.2.9), respectively. Reads with MAPQ < 10 were discarded by SAMtools (v1.3.1), and duplicates were discarded by Picard. HOMER (v4.9.1) was employed for further process, including peak calling, annotation, motif analysis and enrichment of Gene Ontology and KEGG Pathway. Tag directories were created and subjected to peak calling in factor mode. Only peaks occuring across replicates were retained for further analysis (fold change cutoff: 4). For motif analysis, random sequences grabbed from human genome were used as backgroud. Results of enrichment of Gene Ontology and KEGG were plotted using R.
After trimming adapters, RNA-seq data were mapped to GRCh38.p7 using Hisat2 (v2.0.5), and only reads with MAPQ > 30 were retained. Differential genes were decided with cufflinks (v2.2.1). The GO and KEGG analysis of RNA-seq was performed using KOBAS 3.0.
Genome_build: GRCh38
Supplementary_files_format_and_content: Peak files contain each peak's coordinate range and correspongding peak score, fold change, etc. FPKM matrix contains each gene's Ensembl ID and corresponding FPKM, etc.

source_name: HEK 293T

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS and 1 × penicillin-streptomycin at 37 °C with 5% CO2

extract_protocol:
Total RNA was extracted using Trizol
PolyA RNA was captured and library was constructed under the instruction of VAHTS Stranded mRNA-seq Library Prep Kit for Illumina®

treatment_protocol: PDP for 24 h

value: HEK 293T

tag: treatment

value: PDP

tag: time


title: V2E01

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA CTG ACT TTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2D01

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA TCT AGG ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V2B01

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC AAG GAA GTT TTT TTT TTT TTT TTT TTT TTT TT


title: 24h-treated_bio2

description:
cell line
24h-gene_exp.txt


title: V2D02

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA TCA TGT GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V2A01

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT GAA CAC GTT TTT TTT TTT TTT TTT TTT TTT TT


title: 72h-treated_bio1

description:
cell line
72h-gene_exp.txt

treatment_protocol: PDP for 72 h


title: 3h-cnt_bio2

description:
cell line
3h-gene_exp.txt

treatment_protocol: DMSO for 3 h

value: DMSO

value: 3 h


title: V2A03

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT GAA TCA GTT TTT TTT TTT TTT TTT TTT TTT TT


title: MPNST_atrx_mut_A15

description: MPNST tumors from zebrafish with a heterozygous loss of atrx in context of combined p53/nf1-deficiency


title: 72h-treated_bio2

description:
cell line
72h-gene_exp.txt


title: V2C01

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA GAC TCG CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V1H12

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA CGA CTG TTT TTT TTT TTT TTT TTT TTT TTT TT

value: Untreated


title: 3h-cnt_bio1

description:
cell line
3h-gene_exp.txt


title: V1F12

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA TGT AAC CTT TTT TTT TTT TTT TTT TTT TTT TT


title: 3h-treated_bio1

description:
cell line
3h-gene_exp.txt

treatment_protocol: PDP for 3 h


title: 3h-treated_bio2

description:
cell line
3h-gene_exp.txt


title: V1G12

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG TCG ACG ATT TTT TTT TTT TTT TTT TTT TTT TT


title: input_bio2

description: cell line

extract_protocol:
See methods section in the associated manuscript
under the instruction of ThruPLEX® DNA-seq Kit

treatment_protocol: not applicable

value: not applicable


title: V1D12

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA TTG TCC TTT TTT TTT TTT TTT TTT TTT TTT TT

value: Water


title: V1C12

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT AGC ATA CTT TTT TTT TTT TTT TTT TTT TTT TT


title: annealed_bio2

description:
cell line
annealed_peak.txt


title: input_bio1

description: cell line


title: V1E12

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT ATC GGT CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V1B12

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT TGG AAA CTT TTT TTT TTT TTT TTT TTT TTT TT


title: annealed_bio1

description:
cell line
annealed_peak.txt


title: V1A12

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT GGC TCT ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V1H11

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC GGT GAT ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V1F11

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA TTG TGG CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V1E11

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC TAG CAT CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V1G11

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG TCG CAC ATT TTT TTT TTT TTT TTT TTT TTT TT


title: i2

city: Kyoto

first: Kenji

last: Sakurai

address: 54 Shogoin Kawara-cho, Sakyo

department: Dermatology

institute: Kyoto University

hyb_protocol: 2 ug of labeled DNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with RMA (quantile) using Affymetrix default analysis settings.

source_name: whole ear skin

label_protocol: Amplified sense-strand DNA products were synthesized by the Ambion WT Expression Kit, and were fragmented and labeled by the WT Terminal Labeling and Controls Kit.

growth_protocol: Seven to 9-week-old female mice were used in this study. All animals used were of C57BL/6 genetic background.

treatment_protocol: Anisomycin (Wako Pure Chemical Industries, Osaka, Japan) solution was applied on inner and outer sides of a murine ear once daily. The concentration was 2 mg/ml in 99.5% ethanol, and the dose was 10 uL per one side of the ear. For IMQ model, 10 mg of IMQ-containing cream, Aldara (Beselna Cream5%, Mochida Pharmaceuticals), was applied onto inner and outer sides of a murine ear once daily for 5 days.

value: Imiquimod treatment 2

tag: strain

value: whole ear skin

tag: gender

value: female


title: v2

value: Vehicle treatment 2


title: Wild-type #6

city: Setagaya-ku

first: Keisuke

last: Sasaki

state: Tokyo

address: 1-1-1, Sakuragaoka

department: Department of BioScience

institute: Tokyo University of Agriculture

description: Gene expression data from the heart of a wild-type mouse at 8-week of age.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 460.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)

data_processing:
The array data were analyzed in GeneSpring v12.4 (Agilent Technology) to filter out probes with raw value less than 200 in all the samples. Differentially expressed genes between DNMTs-Tg and WT samples were determined by moderated t-test (Benjamini-Hochberg FDR, p < 0.05).
algorithm-name-0 = rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
Q_probeset_summarize-Version = V916
affymetrix-algorithm-name = rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0

label_protocol: Biotin-labeled cDNA was prepared using GeneChip IVT labeling Kit (Affymetrix) according to the manufacturer's instructions.

growth_protocol: DNMTs-Tg mice were generated by crossing FVB-Tg(Ddx4-cre)1Dcas/J (006954, The Jackson Laboratory) female mouse with the flox male mouse (Hara et al., 2014 Hum Mol Genet).

extract_protocol: Total RNA was extracted using RNeasy Fibrous Tissue Mini Kit (Qiagen) according to the manufacturer's instructions. The first-strand cDNA was synthesized using the Eukaryotic Poly-A RNA Control Kit (Affymetrix) and One-cycle cDNA synthesis Kit (Affymetrix).Obtained cDNA was purified using Sample Clean Up Module (Affymetrix)

treatment_protocol: Heart tissues were freezed inliquid nitrogen immediately after sampling and homogenized in RLT Buffer containing 2-mercaptoethanol (Qiagen).

tag: genotype/variation

value: wild type

tag: Sex

value: male

value: heart


title: i1

value: Imiquimod treatment 1


title: v1

value: Vehicle treatment 1


title: v3

value: Vehicle treatment 3


title: DNMTs-Tg #1

description: Gene expression data from the heart of a DNMTs-Tg mouse at 8-week of age.

value: DNMTs-Tg


title: i3

value: Imiquimod treatment 3


title: Wild-type #4


title: Wild-type #1


title: a2

value: Anisomycin treatment 2


title: DNMTs-Tg #6


title: V1C11

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT CCA AGT CTT TTT TTT TTT TTT TTT TTT TTT TT


title: a3

value: Anisomycin treatment 3