title: DHEC_42

city: Toulouse

first: Jean-Philippe

last: Girard

address: 205 Route de Narbonne

country: France

institute: Institut de Pharmacologie et de Biologie Structurale

data_processing:
FASTQ file generated by Illumina CASAVA 1.8
Sequenced reads were trimmed for adaptors and low quality reads then mapped to the mm10 mouse genome using RSEM v1.2.18
FPKM measurements were compiled from RSEM output
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for all samples

source_name: Lymph Node

extract_protocol:
Lymph nodes were removed from mice, dissociated into single cell suspension and High Endothelial Cells or Blood Endothelial Cells were FACS sorted. Purified cells were sorted, RNA was extracted and cDNA constructed using the Fluidigm C1 System.
Libraries were constructed using the Nextera XT kit as per the manufacturer’s instructions
Single Cell RNA-Seq

tag: cell type

value: High Endothelial Cell

tag: condition

value: Dedifferentiated

tag: treament

value: Single I.P. Injection of LTBR-Ig, harvest Day 7


title: DHEC_43

status: Public on Mar 12 2019

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain


title: DHEC_44


title: MCF10AsiSIER_4OHT2h_BLISS_rep3

city: Milano

first: Pier Giuseppe

last: Pelicci

address: Via Adamello, 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

description: processed data file: Dellino_BLISS_Processed_Data_Tier1_DSBs.txt

library_source: genomic

data_processing:
library strategy: Breaks Labeling In Situ and Sequencing (BLISS)
Basecalls performed using CASAVA version 1.9
Data were filtered using the Illumina quality control flag
ChIP-seq: reads were aligned to the hg18 genome assembly using bwa version 0.6.2 with the default parameters
ChIP-seq: low-quality and multiple-mapping reads were removed using Samtools with option ‘‘-q 1’
ChIP-seq: duplicates (reads with the same start and end position mapping) that are potential PCR artifacts are removed with samtools rmdup -s
ChIP-seq: peaks were called using MACS 1.4.1 with default setting
BLISS: reads were aligned to the hg18 genome assembly using bwa version 0.6.2 with the default parameters
BLISS: low-quality and multiple-mapping reads were removed using Samtools with option ‘‘-q 1’
BLISS: duplicates (reads with same start-end position) deriving from the same DSB-end independently generated in different cells, were distinguished from potential PCR artifacts due to the presence, within the BLISS adapters, of random 8-nt long sequences serving as Unique Molecular Identifiers (UMIs; details at https://doi.org/10.1101/091629): using a custom filtering script, duplicated reads with different UMIs were maintained, while the others were discarded.
BLISS: raw BLISS signal was analyzed using the findPeaks algorithm from the HOMER analysis suite enclosed inside a customizable Python-based pipeline.
BLISS: calling of BLISS enrichments was independently performed on each strand, to evaluate the correct orientation of BLISS tags (i.e., reverse tag enrichment upstream and forward tag enrichment downstream the true damaged site).
BLISS: calling of raw tag enrichments was performed using both genome-wide settings (fold-enrichment ≥ 1.5, p-value ≤ 1e-5), and local settings using a 10 kb window (fold-enrichment ≥ 2, p-value ≤ 1e-4), to account for local signal variability.
BLISS: significant BLISS enrichments of 4-OHT-treated samples were called using BLISS signals from untreated samples, while for endogenous DSBs, fold-enrichments of BLISS signals were calculated over random background.
BLISS: from an initial pool of 190,160 raw endogenous DSB clusters, 8,132 (Tier1) showed paired (Pj) p-value ≤ 1e-4, w ≥ 75 and ≥2 fold-enrichment of ChIPseq signals of at least one of three repair factors (NBS1, XRCC4, RAD51) within ±1 kb from the center of the BLISS signal, as compared to the input DNA.
Genome_build: hg18
Supplementary_files_format_and_content: ChIP-seq: bigwig files were obtained with a combination of bedtools (v2.16.1) sub-commands: aligned reads (bam) were converted in bed with bamToBed and extended to approximately 200 bp with slopbed; then genomeCoverageBed were used to generate the wig file, which in turn is transformed to bigwig with the UCSC Genome Browser utility wigToBigWig.
Supplementary_files_format_and_content: BLISS: list of Tier1 DSB clusters identified by BLISS in bed format.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol:
ChIP-seq: MCF10A-AsiSIER cells were routinely grown by re-plating adherent cultures (typically 8 × 10^5 cells into a tissue-culture dish 100mm) in a medium composed of DMEM (Lonza) and HAM's F12 (GibcoLife Technologies) 1:1, supplemented with horse serum 1%, hydrocortisone 0,5mg/ml, hEGF10ug/ml, insulin 5mg/ml, glutamine 0,5% and 100 ng/ml of cholera toxin.
BLISS: MCF10A-AsiSIER cells were grown directly on 22 x 22 mm coverglasses in the same culture conditons used for ChIP-seq preparations.

extract_protocol:
ChIP-seq: Cells were cross-linked by adding formaldehyde to the culture medium to a final concentration of 1% (8 min at RT). Cross-linking was stopped by addition of glycine to a final concentration of 125 mM. Cells were washed twice with PBS and lysed in SDS buffer: 100 mM NaCl, 50 mM Tris HCl (pH 8.1), 5 mM EDTA (pH 8), 0.5% SDS, and protease inhibitors. Chromatin lysate was then pelleted and resuspended in IP buffer (100 mM NaCl, 100 mM Tris HCl at pH 8.1, 5 mM EDTA at pH 8, 0.3% SDS, 1.7% Triton X-100), where it was directly sonicated prior to overnight incubation with antibodies .
ChIP-seq: Libraries were prepared according to HT-ChIP-Seq Library Preparation Protocol. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3´→ 5´ exo minus) and dATP to yield a protruding 3- 'A' base for ligation of indexed oligo adaptors which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with amplification primers for 14 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
BLISS: Cells were fixed for 10 min in 4% formaldehyde at room temperature (RT). After permeabilization, cells were incubated in a blunting reaction mix (NEB, cat. no. E1201L) for 1 h at RT, followed by in situ DSB ligation in a T4 DNA ligase reaction mix (NEB, cat. no. M0202M) for 16–18 h at 16 °C. The next day, genomic DNA (gDNA) was in situ fragmented by incubating the samples with HaeIII (NEB, cat. no. R0108L) for 3 h at 37 °C. Afterwards, the cells were scraped off the coverglass, and gDNA purified using proteinase K (NEB, cat. no. P8107S). Purified gDNA was linearly amplified using the T7 RNA polymerase (Thermo, cat. no. AM1334).
BLISS: Libraries were prepared using a modified Illumina TruSeq Small RNA Library Prep Kit (RS-200-0012). A detailed, step-by-step BLISS protocol can be found at https://doi.org/10.1101/091629.

treatment_protocol:
ChIP-seq: MCF10A-AsiSIER cells were treated for 2 hours with 4-Hydroxytamoxifen 300nM (final conc), adding the drug directly into the medium.
BLISS: MCF10A-AsiSIER cells were treated for 2 hours with 4-Hydroxytamoxifen 300nM (final conc), adding the drug directly into the medium.

tag: cell line

tag: tissue source

value: normal mammary gland

tag: genotype/variation

tag: treated with

value: 4-Hydroxytamoxifen (4OHT) (300 nM for 2h)


title: DHEC_41


title: MCF10AsiSIER_NT_rna_rep2

description: Poly(A)-containing mRNA

data_processing:
Basecalls performed using CASAVA version 1.9
Data were filtered using the Illumina quality control flag
Reads were aligned to the Homo sapiens genome build hg18 using tophat (v2.0.8), which uses Bowtie (2.1.0) and Samtools (v0.1.18) using default parameters and transcriptome Homo sapiens index, UCSC hg18 gtf.
Raw read counts were summarised using HTSeq (v0.5.3p9), then gene expression counts for the i-th gene (n_i) were converted into “transcripts per million” (TPM) of mapped reads, with TPM(i) = 10^6∙(n_i/L_i )/∑_i(n_i/L_i ) , where L_i is the length of the i-th coding sequence. Every variable was converted to base 2 logarithm.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include genomic coordinates, names, strand and expression level means (log2TPM) for each gene.

growth_protocol: MCF10A parental cells and MCF10A AsiSI cells were routinely grown by re-plating adherent cultures (typically 8 × 10^5 cells into a tissue-culture dish 100mm) in a medium composed of DMEM (Lonza) and HAM's F12 (GibcoLife Technologies) 1:1, supplemented with horse serum 1%, hydrocortisone 0,5mg/ml, hEGF10ug/ml, insulin 5mg/ml, glutamine 0,5% and 100 ng/ml of cholera toxin.

extract_protocol:
Total RNA was extracted using Quick-RNA Miniprep kit (Zymo Research, Cat#R1055)
RNA libraries were prepared for sequencing using Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2002), with 600ng of input RNA.


title: DHEC_40


title: DHEC_39


title: DHEC_37


title: DHEC_35


title: DHEC_34


title: DHEC_33


title: Naïve WT CD8+ T cells #2

status: Public on Mar 14 2019

city: Los Angeles

first: Ameya

last: Champhekar

state: California

address: 700 Tiverton Ave, 11-272 Factor Bldg

department: Medicine, HemOnc Division

country: USA

institute: University of California, Los Angeles

data_processing:
Adapter sequences were removed and the resulting 50 bp reads were aligned to the mouse genome release mm10/GRCm38
The splice read aligner TopHat (v2.0.12) was used for alignment with the following command: tophat --library-type fr-firststrand --no-coverage-search
Read counts for each gene were obtained with the HTSeq package (v0.6.1) using the command:  htseq-count -s no -a 10 Mus_musculus.GRCm38.76.gtf
RPKM values were calculated by dividing the number of uniquely mapped reads for each gene by the product of transcript length (kb) and the total reads for that sample (in millions)
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: Tab-delimited file containing the RPKM values for all samples. Only genes expressed at 1 RPKM or more in at least 1 sample are included. The cutoff was applied after averaging RPKM values for replicates of each sample.

source_name: CD8+ T cells from WT spleen

growth_protocol: Naïve CD8+ T cells were enriched from 6 week old WT or Ikaros-Zn4-/- spenocytes by negative selection using the mouse naïve CD8+ T cell isolation kit (StemCell Technologies). Naïve CD8+ T cells, defined as CD8+ CD62Lhi CD44 lo/-,  were then sorted from the enriched samples.

extract_protocol:
Naïve or stimulated CD8+ T cells were harvested and lysed using the TRI reagent (MRC, Inc.). Total RNA was extracted using manufacturer's suggested protocol and directly used for library preparation.
TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc.) was used to construct single-end libraries and sequenced on the Illumina Hiseq 2000 sequencer.

treatment_protocol: Sorted naïve CD8+ T cells were either used directly or stimulated with plate-bound anti-CD3 and anti-CD28 antibodies for up to 24 hours.

tag: background strain

tag: genotype

value: WT

tag: age

value: 6 weeks

tag: Sex

value: Female

tag: tissue

value: Spleen


title: DHEC_31


title: DHEC_32


title: DHEC_30


title: DHEC_28


title: DHEC_29


title: DHEC_23


title: DHEC_24


title: DHEC_26


title: DHEC_27


title: DHEC_25


title: DHEC_19


title: DHEC_15


title: DHEC_17


title: DHEC_18


title: DHEC_16


title: DHEC_21


title: DHEC_20


title: DHEC_13


title: DHEC_12


title: DHEC_14


title: DHEC_38


title: DHEC_10


title: DHEC_09


title: DHEC_08


title: DHEC_07


title: DHEC_11


title: DHEC_06


title: DHEC_05


title: DHEC_22


title: DHEC_03


title: DHEC_02


title: DHEC_01


title: DHEC_04


title: Mouse Adult Cartilage 3

first: Denis

last: Evseenko

state: CA

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

description: Mouse matrix.xlsx

data_processing:
Reads were mapped to the mouse genome (GRCm38) using Ensembl annotation
Transcript estimation was performed using RNA-Seq by Expectation Maximization method (Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC bioinformatics. 2011;12(323)
Differenential expression was performed using the EBSeq method (Leng N, Dawson JA, Thomson JA, et al. EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics. 2013;29(8):1035-1043.)
Genome_build: GRCm38

source_name: Knee

extract_protocol:
Qiagen Micro kit
Library preparation with Kapa mRNA-Seq kit

value: Adult Cartilage

tag: developmental stage

value: 2 months


title: Mouse Embryonic Cartilage 1

description: Mouse matrix.xlsx

value: Embryonic Cartilage


title: Mouse Embryonic Cartilage 2

description: Mouse matrix.xlsx


title: Mouse Adult Cartilage 2

description: Mouse matrix.xlsx


title: Mouse Embryonic Cartilage 3

description: Mouse matrix.xlsx


title: FB-HS

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

country: China

institute: ablife

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (GATCGGAAGAGC) trimmed with cutadapt
mapped using tophat2 --microexon-search --no-coverage-search --b2-N 1
detecting different expression gene using edgeR
We compared the cotton genome with Arabidopsis thaliana, and annotated with the Arabidopsis Symbols
Genome_build: GCA_001856525.1_GbV1.0
Supplementary_files_format_and_content: tab-delimited text files reporting gene reads counts, RPKMs

organism: Gossypium barbadense

source_name: High-susceptible cotton

extract_protocol:
Total RNA was treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at A260/A280 and A260/A230 using smartspec plus (BioRad)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: fusarium wilt resistance

value: Highly-susceptible

tag: infection

value: infected

value: hypocotyls


title: CK-HS

value: control


title: FB-S

source_name: Susceptible cotton

value: Susceptible


title: CK-SHR

source_name: Super resistance cotton

value: Super resistant


title: CK-S


title: FB-SHR


title: FB-HR

source_name: High-resistance cotton

value: Highly-resistant


title: CK-female parent

source_name: female parent


title: CK-male parent

source_name: male parent

value: Resistant


title: CK-HR


title: FB-female parent


title: FB-male parent


title: Ring1b_ChIPSeq

city: London

first: Paul

middle: T.

last: Sharpe

state: Please select one below:

address: Guy's hospitial

department: Centre for Craniofacial and Regenerative Biology

country: United Kingdom

institute: King's College London

data_processing:
The 75-nt sequence reads generated by Illumina sequencing (NextSeq500) are mapped to the genome using BWA algorithm with default settings. Alignment informaiton for each read is stored in the BAM format.
To identify the density of fragment along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined. This information is stored in a bigWig file.
Peak calling used MACS (Zhang et al., Genome Biology 2008, 9:R137) and SICER (Zhang et al., Bioinformatics 25, 1952-1958, 2009)
After defining the peaks, their genomic locations along with their proximities to gene annotations and other genomic features are determined and presented in Excel spreadsheets.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig contains URL and shows peak shapes in the form of a signal histogram. It can be visualized in genome browsers. BED file contains the locations and names of all peaks and can be used for UCSC browser. Excel file lists all genes that have at least one peak within the chosen GeneMargin.

source_name: mouse dental pulp

extract_protocol:
Mouse incisor pulp tissue were freshly dissected and dissociated as single cell suspension. Cells were then fixed and stained by Click-iT EdU kit (Invitrogen C10424). EdU+ cells were flow sorted and collected for ChIP.
ChIP DNA and input genomic DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mice were intraperitoneal injected with one dose EdU (3.3 µg per g body weight) and scarified after 24 hours.

value: mouse incisor pulp

value: postnatal 5 days


title: Input DNA


title: H3K27me3_ChIPSeq

data_processing:
The 75-nt sequence reads generated by Illumina sequencing (NextSeq500) are mapped to the genome using BWA algorithm with default settings. Alignment informaiton for each read is stored in the BAM format.
To identify the density of fragment along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined. This information is stored in a bigWig file.
Peak calling used SICER (Zhang et al., Bioinformatics 25, 1952-1958, 2009)
After defining the peaks, their genomic locations along with their proximities to gene annotations and other genomic features are determined and presented in Excel spreadsheets.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig contains URL and shows peak shapes in the form of a signal histogram. It can be visualized in genome browsers. BED file contains the locations and names of all peaks and can be used for UCSC browser. Excel file lists all genes that have at least one peak within the chosen GeneMargin.


title: Mouse Adult Cartilage 1

description: Mouse matrix.xlsx


title: Y128 YPGal +O2 Rep A

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

description:
Growth of Y128 in galactose +O2.
rRNA depleted RNA.
Processed data file: Y223Y127Y128_ProcessedDataMatrix.txt

data_processing:
Sequencing reads were processed with Trimmomatic version 0.3.0.
Trimmed sequencing reads were aligned to the Y22-3 genome using Bowtie2 version 2.2.2.
Read counts per gene were calculated using HTSeq version 0.6.0.
Read counts per gene were normalized using the reads per kilobase per million mapped reads (RPKM) method.
RPKM values were transformed to log2 values.
Genome_build: Assembly GLBRCY22-3 (BioProject PRJNA279877)
Supplementary_files_format_and_content: Y223Y127Y128_ProcessedDataMatrix.txt: Tab-delimited text file containing RPKM log2 values for each gene for each sample.

organism: Saccharomyces cerevisiae

source_name: Y128 cell culture, aerobic, galactose

growth_protocol: Cultures were grown for ~3 generations until mid-log phase (OD600 ~0.5). Aerobic samples were shaken in flasks at 30°C. Anaerobic samples were grown in a Coy anaerobic chamber at 30°C using a stir bar at 300 rpm to prevent flocculation.

extract_protocol:
RNA was extracted with hot phenol protocol. DNA was digested with treatment of TurboDNase for 30 min at 37°C. rRNA was removed prior to library construction using Ribo-Zero Gold (yeast) kit (Epicentre).
Library was constructed using Illumina TruSeq Stranded Total RNA sample preparation guide RevC using standard protocols. Illumina's PE genomics DNA primer set were used for indexing and multiplexing.

treatment_protocol: Cultures were halted by addition of ice-cold 5% phenol (pH < 5)/95% ethanol mix. Samples were spun at 3000 rpm for 3 min, the supernatant was removed, and the pellets were flash frozen in liquid nitrogen and stored at -80°C until needed.

tag: strain/background

tag: oxygen

value: aerobic

tag: carbon source

value: 2% galactose

tag: growth stage

value: exponential


title: DHEC_36

tag: strain

tag: cell type

value: High Endothelial Cell

tag: condition

value: Dedifferentiated

tag: treament

value: Single I.P. Injection of LTBR-Ig, harvest Day 7


title: Y22-3 YPSor +O2 Rep A

description:
Y22-3 does not grow in sorbitol. Culture incubated from saturated overnight in media at OD ~0.5 for the same time as Y22-3 galactose +O2.
rRNA depleted RNA.
Processed data file: Y223Y127Y128_ProcessedDataMatrix.txt

source_name: Y22-3 cell culture, aerobic, sorbitol

value: 2% sorbitol


title: Y128 YPSor -O2 Rep A

description:
Y128 does not grow in sorbitol. Culture incubated from saturated overnight in media at OD ~0.5 for the same time as Y128 galactose -O2.
rRNA depleted RNA.
Processed data file: Y223Y127Y128_ProcessedDataMatrix.txt

source_name: Y128 cell culture, anaerobic, sorbitol

value: anaerobic


title: Y128 YPSor +O2 Rep A

description:
Y128 does not grow in sorbitol. Culture incubated from saturated overnight in media at OD ~0.5 for the same time as Y128 galactose +O2.
rRNA depleted RNA.
Processed data file: Y223Y127Y128_ProcessedDataMatrix.txt

source_name: Y128 cell culture, aerobic, sorbitol


title: Y22-3 YPSor -O2 Rep A

description:
Y22-3 does not grow in sorbitol. Culture incubated from saturated overnight in media at OD ~0.5 for the same time as Y22-3 galactose -O2.
rRNA depleted RNA.
Processed data file: Y223Y127Y128_ProcessedDataMatrix.txt

source_name: Y22-3 cell culture, anaerobic, sorbitol


title: Y22-3 YPGal -O2 Rep A

description:
Growth of Y22-3 in galactose -O2.
rRNA depleted RNA.
Processed data file: Y223Y127Y128_ProcessedDataMatrix.txt

source_name: Y22-3 cell culture, anaerobic, galactose


title: Y127 YPX -O2 Rep B

description:
Y127 does not grow in xylose -O2. Culture incubated from saturated overnight in anaerobic media at OD ~0.5 for the same time as Y128 xylose -O2 growth.
rRNA depleted RNA.
Processed data file: Y223Y127Y128_ProcessedDataMatrix.txt

source_name: Y127 cell culture, anaerobic, xylose

value: 2% xylose


title: Y127 YPX -O2 Rep A


title: Y128 YPX -O2 Rep A

description:
Growth of Y128 in xylose -O2.
rRNA depleted RNA.
Processed data file: Y223Y127Y128_ProcessedDataMatrix.txt

source_name: Y128 cell culture, anaerobic, xylose


title: Y22-3 YPGal +O2 Rep A

description:
Growth of Y22-3 in galactose +O2.
rRNA depleted RNA.
Processed data file: Y223Y127Y128_ProcessedDataMatrix.txt

source_name: Y22-3 cell culture, aerobic, galactose


title: Y128 YPX -O2 Rep B


title: Y22-3 YPX -O2 Rep B

description:
Y22-3 does not grow in xylose -O2. Culture incubated from saturated overnight in anaerobic media at OD ~0.5 for the same time as Y128 xylose -O2 growth.
rRNA depleted RNA.
Processed data file: Y223Y127Y128_ProcessedDataMatrix.txt

source_name: Y22-3 cell culture, anaerobic, xylose


title: Macrophages_Cisplaitn/anti-CSF-1R [Sample_1400]

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Illumina Casava v1.8 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with TopHat2 (v2.0.11) against the mm10 reference genome
Gene and transcript information was extracted with Partek Genomics Suite (v6.6). Annotated data was normalized using statistical software R (v3.3.1) including DESeq2 package. Normalized read counts lower than 1 were set to the floor value 1.Genes were defined as expressed with normalized RNA-seq values ≥ 10.
Genome_build: mm10
Supplementary_files_format_and_content: Processed DeSeq2 normalized RNA-seq tag counts annotated to the mm10 reference genome

source_name: Intratumoral Macrophages

extract_protocol:
macrophages and neutrophils were FACS-sorted in medium+FCS and stored in TRIZOL (Invitrogen). RNA was isolated by Rneasy Mini and Microkits (Quiagen) following the manufacturers’ protocol and quality was assessed.
10ng of total RNA was converted into cDNA libraries, according to the Ovation RNA-seq system V2 and Encore Rapid library systems protocols (NuGen). cDNA was subsequently sequenced in the HiSeq 1500 system and demultiplexed using CASAVA v1.8 (Illumina)

treatment_protocol: Mice were treated either with control antibody or anti-CSF-1R or cisplatin/control antibody or cisplatin/anti-CSF-1R and were sacrificed one day after second cisplatin injection or when the tumor was 100mm2 (for cisplatin-naive mice)

value: K14cre;Cdh1F/F;Trp53F/F mouse model for the novo mammary tumorigenesis

value: mammary tumor


title: Macrophages_anti-CSF-1R [Sample_1397]


title: Macrophages_anti-CSF-1R [Sample_1398]


title: Y128 YPD -O2 Rep A

description:
Growth of Y128 in glucose -O2.
rRNA depleted RNA.
Processed data file: Y223Y127Y128_ProcessedDataMatrix.txt

source_name: Y128 cell culture, anaerobic, glucose

value: 2% glucose


title: Y128 YPD -O2 Rep B


title: Y22-3 YPX -O2 Rep A


title: Macrophages_Control ab [Sample_1396]


title: Y127 YPD -O2 Rep B

description:
Growth of Y127 in glucose -O2.
rRNA depleted RNA.
Processed data file: Y223Y127Y128_ProcessedDataMatrix.txt

source_name: Y127 cell culture, anaerobic, glucose


title: Y128 YPGal -O2 Rep A

description:
Growth of Y128 in galactose -O2.
rRNA depleted RNA.
Processed data file: Y223Y127Y128_ProcessedDataMatrix.txt

source_name: Y128 cell culture, anaerobic, galactose


title: H3K4me3_ChIPSeq


title: Y127 YPD -O2 Rep A


title: Y22-3 YPD -O2 Rep A

description:
Growth of Y22-3 in glucose -O2.
rRNA depleted RNA.
Processed data file: Y223Y127Y128_ProcessedDataMatrix.txt

source_name: Y22-3 cell culture, anaerobic, glucose


title: Y22-3 YPD -O2 Rep B


title: Macrophages_Cisplatin/Control ab [Sample_1390]


title: Macrophages_Cisplatin/Control ab [Sample_1392]


title: Macrophages_Cisplaitn/anti-CSF-1R [Sample_1399]


title: Macrophages_Cisplatin/Control ab [Sample_1391]


title: Macrophages_Control ab [Sample_1395]


title: Y128 AZF1 MoBY Rep A

description:
Growth of Y128 + MoBY AZF1 plasmid in YPX + G418 -O2.
rRNA depleted RNA.
Processed data file: AZF1_RNAseq_ProcessedDataMatrix.txt

data_processing:
Two FASTQ files were generated for each sample due to using the RapidRun. The FASTQ files were combined using the "cat" command.
Sequencing reads were processed with Trimmomatic version 0.3.0.
Trimmed sequencing reads were aligned to the Y22-3 genome using Bowtie2 version 2.2.2.
Read counts per gene were calculated using HTSeq version 0.6.0.
Read counts per gene were normalized using the reads per kilobase per million mapped reads (RPKM) method.
RPKM values were transformed to log2 values.
Genome_build: Assembly GLBRCY22-3 (BioProject PRJNA279877)
Supplementary_files_format_and_content: AZF1_RNAseq_ProcessedDataMatrix.txt: Tab-delimited text file containing RPKM log2 values for each gene for each sample.

source_name: Y128 cell culture, AZF1 MoBY, anaerobic, xylose

extract_protocol:
RNA was extracted with hot phenol protocol. DNA was digested with treatment of TurboDNase for 30 min at 37°C. rRNA was removed prior to library construction using Ribo-Zero Gold (yeast) kit (Epicentre).
Library was constructed using EpiCentre Strand Specific ScriptSeq Kit using standard protocols. Epicentre ScriptSeq Index PCR Primers were used for indexing and multiplexing.

tag: genotype/variation

value: AZF1 MoBY

tag: antibiotic


title: Neutrophils_Cisplaitn/anti-CSF-1R [Sample_1388]

source_name: Intratumoral Neutrophils


title: Y128 MoBY Control Rep B

description:
Growth of Y128 + MoBY empty vector plasmid in YPX + G418 -O2.
rRNA depleted RNA.
Processed data file: AZF1_RNAseq_ProcessedDataMatrix.txt

source_name: Y128 cell culture, MoBY control, anaerobic, xylose

value: MoBY control


title: Y127 YPX +O2 Rep A

description:
Growth of Y127 in xylose +O2.
rRNA depleted RNA.
Processed data file: Y223Y127Y128_ProcessedDataMatrix.txt

source_name: Y127 cell culture, aerobic, xylose


title: Y127 YPX +O2 Rep B


title: Y128 YPX +O2 Rep A

description:
Growth of Y128 in xylose +O2.
rRNA depleted RNA.
Processed data file: Y223Y127Y128_ProcessedDataMatrix.txt

source_name: Y128 cell culture, aerobic, xylose


title: Neutrophils_Cisplaitn/anti-CSF-1R [Sample_1386]


title: Y128 azf1∆ Rep A

description:
Growth of Y128 azf1∆ at mid-log phase in YPX -O2.
rRNA depleted RNA.
Processed data file: AZF1_RNAseq_ProcessedDataMatrix.txt

source_name: Y128 cell culture, azf1∆, anaerobic, xylose


title: Neutrophils_Cisplaitn/anti-CSF-1R [Sample_1387]


title: Y128 YPD +O2 Rep B

description:
Growth of Y128 in glucose +O2.
rRNA depleted RNA.
Processed data file: Y223Y127Y128_ProcessedDataMatrix.txt

source_name: Y128 cell culture, aerobic, glucose


title: Y128 azf1∆ Rep B


title: Y22-3 YPX +O2 Rep B

description:
Growth of Y22-3 in xylose +O2.
rRNA depleted RNA.
Processed data file: Y223Y127Y128_ProcessedDataMatrix.txt

source_name: Y22-3 cell culture, aerobic, xylose


title: Macrophages_Control ab [Sample_1394]


title: Neutrophils_Cisplaitn/anti-CSF-1R [Sample_1385]


title: Y128 WT Rep B

description:
Growth of Y128 WT at mid-log phase in YPX -O2.
rRNA depleted RNA.
Processed data file: AZF1_RNAseq_ProcessedDataMatrix.txt

source_name: Y128 cell culture, WT, anaerobic, xylose

value: WT


title: Macrophages_Control ab [Sample_1393]


title: Y128 AZF1 MoBY Rep B


title: Y128 YPD +O2 Rep A


title: Neutrophils_anti-CSF-1R [Sample_1383]


title: Y128 WT Rep A


title: Neutrophils_anti-CSF-1R [Sample_1384]


title: Y127 YPD +O2 Rep B

description:
Growth of Y127 in glucose +O2.
rRNA depleted RNA.
Processed data file: Y223Y127Y128_ProcessedDataMatrix.txt

source_name: Y127 cell culture, aerobic, glucose


title: Y128 MoBY Control Rep A


title: Macrophages_Cisplatin/Control ab [Sample_1389]


title: Neutrophils_anti-CSF-1R [Sample_1381]


title: Neutrophils_anti-CSF-1R [Sample_1382]


title: Y22-3 YPD +O2 Rep B

description:
Growth of Y22-3 in glucose +O2.
rRNA depleted RNA.
Processed data file: Y223Y127Y128_ProcessedDataMatrix.txt

source_name: Y22-3 cell culture, aerobic, glucose


title: Y22-3 YPD +O2 Rep A


title: Neutrophils_Control ab [Sample_1380]


title: Neutrophils_Control ab [Sample_1378]


title: Neutrophils_Control ab [Sample_1379]


title: Neutrophils_Cisplatin/control ab [Sample_1375]


title: Neutrophils_Cisplatin/control ab [Sample_1376]


title: Y127 YPD +O2 Rep A


title: Neutrophils_Control ab [Sample_1377]


title: Y22-3 YPX +O2 Rep A


title: WT_rep3

city: Heidelberg

first: Carmen

last: Ruiz de Almodovar

address: Im Neuenheimer Feld 328

institute: Heidelberg University Biochemistry Center (BZH)

description:
mRNA Wild Type cells, rep3
F10P1

data_processing:
The reads were aligned to the mm10 genome assembly using Tophat2 v2.0.14
Fold change and significance was calculatyed with DESeq2 R-package.
Abundance values are regularized log (rlog) transformed.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated value DESeq2 output-file with fold-change between WT and ecKO groups, xlsx file with rolg transformed abundance values.

source_name: brain endothelial cells

extract_protocol:
Freshly dissected postnatal brains were disassociated, followed by myelin depletion, CD45+ cells depletion, and CD31+ cells selection. Total RNA was isolated by using mini RNA isolation kit (Qaigen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Generation of YAP floxed and TAZ floxed mice has been described preciously (Xin et al., 2013). YAPflox/flox TAZflox/flox mice were crossed with Cdh5-Cre/ERT2 mice (Wang et al., 2010) to specifically delete endothelial derived YAP/TAZ expression. Cre recombination was induced by intragastric injection of 50µl tamoxifen (1mg/ml).

value: brain

value: post natal day 5

tag: genotype

value: wild type


title: yaptazecko_rep2

description:
mRNA YAP/TAZ ecKO cells, rep2
F2P6

tag: age

value: YAP/TAZ ecKO


title: WT_rep1

description:
mRNA Wild Type cells, rep1
F2P1


title: yaptazecko_rep3

description:
mRNA YAP/TAZ ecKO cells, rep3
F10P3


title: WT_rep2

description:
mRNA Wild Type cells, rep2
F2P7


title: Neutrophils_Cisplatin/control ab [Sample_1374]


title: yaptazecko_rep1

description:
mRNA YAP/TAZ ecKO cells, rep1
F2P4


title: STAT1-K525A-Re-IFNa

city: shanghai

first: kun

address: No.800 Xiangyin Road, Yangpu District

institute: Zhejiang University

data_processing:
BGISEQ-500 basecalling software
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped clean reads to whole hg38 gene using  Bowtie2 and  to hg38 genome using HISAT.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated as described in Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: HepG2 cell lines

extract_protocol:
HepG2 cells, SETD2-KO, STAT1-KO, and K525A-Re cells (with or without IFNa treatment) were removed, flash frozen on dry ice, and RNAs were harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cells were with/without 1000 U/ml IFNα for 6 hrs

tag: cell line

value: hepatocellular carcinoma

value: STAT1-K525A mutant

tag: treatment

value: treated with IFNa for 6 hrs


title: STAT1-KO_IFNa

value: STAT1 knockout


title: STAT1-K525A-Re-UN

value: untreated


title: STAT1-KO_UN


title: SETD2-KO_UN

value: SETD2 knockout


title: SETD2-KO_IFNa


title: HepG2_IFNa


title: RNAPII HiChIP

status: Public on Mar 11 2019

city: Omaha

first: M

middle: Jordan

last: Rowley

state: NE

address: 601 S Saddle Creek Rd

department: GCBA

institute: Univ of Nebraska Medical Center

data_processing:
ChIP-seq reads were aligned to the dm6 reference genome using bowtie2 and PCR duplicates were removed. Hi-C and HiChIP reads were processed using the Juicer pipeline.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig containing coverage of ChIP-seq and .hic containing Hi-C contact matrices.

organism: Drosophila melanogaster

source_name: HiChIP for RNAPII

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature and quenched with glycine. For ChIP-seq, nuclear lysates were sonicated to generate 200-500 bp fragments . Chromatin was precleared with Protein A or G Dynabeads at 4°C for 2 hours and incubated with antibody overnight at 4°C. Isolated chromatin was washed, eluted, reverse crosslinked and purified by standard methods. For HiChIP nuclei were isolated and chromatin digested by DpnII, filled in with biotin-dCTP, and ligated. After ligation, chromatin was sonicated and precleared with Protein A and G Dynabeads at 4°C for 2 hours, then precipitated using anti-RNAPII or anti-Rad21 antibody overnight. Isolated chromatin was washed, eluted, reverse crosslinked and purified by standard methods, after which ligation events were enriched by streptavidin precipitation.
Libraries were constructed using the standard protocol for ChIP-seq and Hi-C or using a Tn5 library prepartion protocol for HiChIP. Genomic fragments were end repaired, A-tailed by adding  adenosine to  the 3’ ends of fragment using Klenow fragment (3’ to 5’ exo minus, New England Biolabs), and adaptors were ligatedat room temperature for 1 hr with T4 DNA ligase (New England Biolabs). For Tn5 protocol samples were incubated with Tn5 transposase in the presence of adaptors. Libraries were amplified with Illumina primers using the KAPA SYBR FAST qPCR Master Mix.

value: Embryonic Cell Line

tag: chip-antibody

value: RNAPII (biolegend 664906)


title: Slimb KD Hi-C rep2

source_name: Hi-C after knockdown of Slimb

value: Slimb knockdown


title: HepG2_UN


title: Slimb KD Hi-C rep1


title: WT_rep4

description:
mRNA Wild Type cells, rep4
F10P2

tag: tissue


title: Input of control overexpressing Pmel-1 CD8+ T cells 5 days after transduction

city: Bethesda

first: Luca

last: Gattinoni

state: MD

address: 10 Center Drive

department: Center for Cancer Research

institute: National Cancer Institute

data_processing:
Basecall was conducted by the Illumina Casava (version 1.7) software.
reads were mapped to the mouse reference genome mm9 using bowtie2 (version 2.2.6).
Alignments with low mapping quality (<30) were further filtered by samtools (version 1.2), and then were sorted and marked duplication using Picard (version 1.139)
peaks were called using the program sicer (version 1.1) with the command-line setting "mm9 1 200 150 0.74 600 .05"
Genome_build: mm9
Supplementary_files_format_and_content: wig

source_name: CD8+ T cells

growth_protocol: Cells were collected 5 days after transducing Pmel CD8+ T cells with miR-155 or controls

extract_protocol:
T cells were crosslinked with 2% paraformaldehyde at room temperature for 10 min and sonicated to generate fragmented genomic DNA.
Chromatin immunoprecipitation was performed using the following antibodies: anti-H3K27me3 (Millipore). For sequencing of immunoprecipitated DNA, DNA fragments were blunt-end ligated to Illumina adaptors, amplified, and sequenced by using the HiSeq 2000 platform (Illumina).
For sequencing of immunoprecipitated DNA, DNA fragments were blunt-end ligated to Illumina adaptors, amplified, and sequenced by using the HiSeq 2000 platform (Illumina).

treatment_protocol: CD8+ T cells were separated from non-CD8+ T cells with a MACS negative selection kit (Miltenyi Biotech) and were activated on plates coated with anti-CD3ε (2 μg/ml; BD Biosciences) and soluble anti-CD28 (1 μg/ml; BD Biosciences) in culture medium containing rhIL-2 (120 IU/ml; Chiron). Virus was 'spin-inoculated' at 2,000 g for 2 h at 32 °C onto plates coated with retronectin (Takara). CD8+ T cells activated for 24 h were transduced following standard protocol. Cells (3 × 105 to 2 x 106 cells) were adoptively transferred into hosts followed by infection with recombinant vaccinia virus expressing human gp100 (Virapur).

tag: transduction

value: control vector

tag: origin

value: in vitro

tag: antibody


title: Input of miR-155 overexpressing Pmel-1 CD8+ T cells 5 days after transduction


title: H3K27me3 binding profiles of control overexpressing Pmel-1 CD8+ T cells 5 days after transduction


title: Floating-iluc rep2

city: Tianjin

first: Zhenyi

last: Ma

address: 22 Qixiangtai Road

department: Biochemistry and Molecular Biology

institute: Tianjin Medical University

description:
test sample
F_iluc2

data_processing:
Illumina Casava1.9 software used for basecalling.
Low quality reads and adaptor contamination are removed by NGSQC software, then mapped to hg19 genome by HISAT software
FPKM and expression difference analysis are performed and calculated by Cuffquant and the Cuffnorm software
Genome_build: hg19
Supplementary_files_format_and_content: Sample expression file containing normalized FPKM for each gene, by Microsoft Excel format

source_name: non-small cell lung cancer cells

growth_protocol: All cells were cultured as protocol on ATCC

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Thermo RevertAid First Strand cDNA Synthesis Kit (Cat#K1622) was used with 1 ug of total mRNA for the construction of sequencing libraries.
mRNA libraries were prepared for sequencing using standard Thermo protocols

treatment_protocol: The H1703 floating 12h

value: lung

value: squamous cell carcinoma cells

tag: attachment status

value: floating

value: control (Luciferase knockdown)


title: Floating-iSPIB rep1

description:
test sample
F_iSPIB1

value: SPIB knockdown


title: Rad21 HiChIP

source_name: HiChIP for Rad21


title: H3K27me3 binding profiles of miR-155 overexpressing Pmel-1 CD8+ T cells 5 days after transduction


title: Floating-iluc rep1

description:
test sample
F_iluc1


title: Attached-iSPIB rep1

description:
test sample
A_iSPIB1

value: attached


title: Attached-iluc rep1

description:
control sample
A_iluc1


title: Attached-iSPIB rep2

description:
test sample
A_iSPIB2


title: Attached-iluc rep2

description:
control sample
A_iluc2


title: ESAT6_4h

status: Public on Mar 10 2019

city: Chongqing

first: Fake

last: Li

state: Chongqing

address: Changjiangzhilu 10 Yuzhong District

department: Clinical Laboratory Medicine

institute: Daping Hospital

data_processing:
Quality control analysis of the raw sequence files was conducted with FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The quality-checked reads for each condition were first mapped to the latest UCSC transcript set using Bowtie2 (version 2.1.0)
Then the gene expression level was estimated using RSEM (RNA-Seq by Expectation Maximization, v1.2.15) and normalized with TMM (trimmed mean of M-values) to identify differentially expressed genes (DEGs) using the edgeR package.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files include TMM values for each Sample ...

source_name: THP-1 macrophages

growth_protocol: Human monocyte cell line THP-1 was cultured in RPMI 1640 basic medium (Gibco, life technologies, USA) supplemented with 2 mM L-glutamine, Penicillin (100 U/ml)-Streptomycin (100 µg/ml) Solution and 10% fetal bovine serum (FBS) (Catalog No. 04-121-1A, Biological Industries, Israel) at cultural density of 5 × 105 - 1 × 106/ml.

extract_protocol:
The total RNA were isolated with RNeasy mini kit (Qiagen, Germany) according to the manufacturer's instructions
The libraries were prepared with KAPA Stranded mRNA-Seq Kit for Illumina (Kapa biosystems, USA) following the manufacturer's procedure. In Brief, high quality intact total RNA (0.2 ESAT6 in 50 µl RNase-free water) were input for Poly(A) RNA capture with magnetic oligo-dT beads. The RNA was fragmented to the desired size (about 300 bp) by heating in the presence of Mg++. The 1st strand cDNA was synthesized with random primers. The 2nd strand cDNA synthesis converted cDNA:RNA hybrid to double strand cDNA (dscDNA), while marking the 2nd strand with dUTP. Then dAMP was added to 3’-end of dscDNA fragments. Following by ligation of 3’-dTMP adapters (10 nM) to 3’-dAMP library fragments, and PCR amplification (14 cycles) of the adapter-ligated library DNA. The dUTP-marked strand was not amplified. Library fragment size distribution was confirmed by electrophoresis and library concentration was determined with Qubit 2.0 Fluorometric Quantitation (Thermo Fisher Scientific, USA). These libraries were sequenced using the Illumina Hiseq 3000 Sequencer (50 cycles, single read lane).

treatment_protocol: THP-1 macrophages were stimulated in triplicates with 0.8 µg/ml ESAT6 protein (Catlog No. ab124574, Abcam, USA) for 4 h or 24 h. Cells were placed in a humidified, 37℃ 5% CO2 incubator.

value: THP-1 macrophages

value: ESAT6 for 4 hr


title: THP-1 macrophages unstimulated

value: control


title: ESAT6_24h

value: ESAT6 for 24h


title: Y128 YPX +O2 Rep B

tag: strain/background

tag: oxygen

value: aerobic

tag: carbon source

value: 2% xylose

tag: growth stage

value: exponential


title: Phf19_KO3

status: Public on Mar 08 2019

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using R package
log2-transformed RPKM
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include log2-transformed RPKM values for all samples

source_name: Pmel-1 CD8+ T cells in the absence of Phf19 5 days after transfer into C57BL/6 in conjunction with gp100-VV

growth_protocol: Cells were collected 5 days fter transducing miR-155 or control retrovirus or adoptively transferred into hosts followed by gp100-VV infection and sorted (CD8+GFP+: miR-155 and control vector; CD8+Ly5.1+CD62L-KLRG1-: Phf19 WT and Phf19KO) 5 days after transfer

extract_protocol:
RNA was isolated with a miRNeasy Mini kit (Qiagen)
RNA concentration was determined with the Qubit RNA broad range assay in the Qubit Fluorometer (Invitrogen) and RNA integrity was determined with Eukaryote Total RNA Nano Series II ChIP on a 2100 Bioanalyzer (Agilent). RNA-seq libraries were prepared from 4 μg of total RNA via the TruSeq RNA sample prep kit according to manufacturer’s protocol (Illumina). In brief, oligo-dT purified mRNA was fragmented and subjected to first and second strand cDNA synthesis. cDNA fragments were blunt-ended, ligated to Illumina adaptors, and PCR amplified to enrich for the fragments ligated to adaptors.
The resulting cDNA libraries were verified and quantified on Agilent Bioanalyzer and single-end 96 cycle RNA-seq was conducted with the GAIIx Genome Analyzer (Illumina).

tag: cell type

value: Pmel-1 CD8+ T cells

tag: strain

value: Spleen

value: ex vivo

value: Phf19 KO


title: FLV Hi-C

source_name: Hi-C after 3 hours Flv treatment

value: Embryonic Cell Line

value: 3 hours Flv treatment


title: Daughter (compound heterozygote for two HBB mutations)

status: Public on Mar 09 2019

city: Northridge

first: Aida

last: Metzenberg

address: 18111 Nordhoff Street

department: Biology

institute: California State University, Northridge

description: Sample D

data_processing:
The STAR ultrafast universal RNA-seq aligner was used to generate the genome index and perform paired-end alignments. Reads were aligned to a genome index that includes both the genome sequence (GRCh37.71 primary assembly) and the exon/intron structure of known RefSeq transcripts. On average, 80% of the reads (using a similarity score of 66%) were aligned successfully with the genomic sequence.
The Cufflinks suite of tools (version 2.2.1) was used for differential gene expression analysis, which provides and compares gene expression levels in units of FPKMs (Fragments Per Kilobase of transcript per Million mapped reads). The mapped reads were counted for RefSeq transcripts using cuffquant. The cuffquant outputs were passed to cuffdiff to test for significant differences in transcript abundance for each pair-wise comparison between the three samples (N (Normal control), M (Mother), and D (Daughter). Genes were flagged as differentially expressed when the log2|fold change| was >1 and the adjusted p-value was <0.05.
Genome_build: GRCh37.71
Supplementary_files_format_and_content: Per sample expression estimates in units of FPKMs

source_name: blood

extract_protocol:
Total RNA was isolated from blood using EDTA as an anticoagulant and Trizol reagent (Sigma-Aldrich, Germany)
Libraries for RNA-sequencing were prepared with a KAPA Stranded RNA-sequencing Kit (Illumina), following the manufacture’s instructions.

tag: individual

value: Daughter

tag: Sex

value: female

tag: genotype/variation

value: blood


title: Phf19_KO2


title: Normal (an individual with wildtype HBB alleles and normal hematological indices)

description: Sample N

value: Normal

value: male

value: wildtype HBB alleles


title: Phf19_WT3

source_name: Pmel-1 CD8+ T cells in the presence of Phf19 5 days after transfer into C57BL/6 in conjunction with gp100-VV

value: Phf19 WT


title: Phf19_WT1


title: Phf19_KO1


title: mir155_invitro

source_name: Pmel-1 CD8+ T cells overexpressing with miR-155 5 days after transfer into C57BL/6 in conjunction with gp100-VV

value: in vitro

value: miR-155 overexpression


title: mir155_exvivo

source_name: Pmel-1 CD8+ T cells overexpressing with miR-155 5 days after transduction


title: SCR_exvivo

source_name: Pmel-1 CD8+ T cells overexpressing with control 5 days after transduction

value: control vector


title: Mother (Heterozygote for a novel HBB mutation)

description: Sample M

value: Mother

value: Heterozygote for a novel HBB mutation


title: Floating-iSPIB rep2

description:
test sample
F_iSPIB2

value: lung

value: squamous cell carcinoma cells

tag: cell line

value: floating

value: SPIB knockdown


title: SCR_invitro

source_name: Pmel-1 CD8+ T cells overexpressing with control 5 days after transfer into C57BL/6 in conjunction with gp100-VV

value: Pmel-1 CD8+ T cells

value: Spleen


title: Ctrl-siRNA PolyA - BS

city: Salt Lake City

first: Jingtao

last: Guo

state: UT

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

institute: University of Utah School of Medicine

description:
Poly-A selected RNA
Table S6-PseudoU candidate sites

data_processing:
Reference genome: Novoindex (2.8) (http://www.novocraft.com) was used to create a standard and bisulfite reference index on a combination of hg19 chromosome, scaffold and splice junction sequences.  Splice junction sequences were generated with USeq (v8.8.8) 1 MakeTranscriptome using Ensembl transcript annotations (build 74).
Alignment parameters: BS and NBS samples were aligned to the transcriptome indexes described above using Novoalign (v2.08.01) (http://www.novocraft.com) allowing up to 50 alignments and trimming adaptor sequences (TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC GATCGTCGGACTGTAGAACTCTGAAC).
Alignment processing : The alignment files were processed with USeq SamTranscriptomeParser, which reports the best alignment location for each read in bam format and converts the coordinates of splice junction alignments to genomic space. One alignment location is selected at random if a read aligned to multiple locations in the genome with equal confidence.
Alignments were reordered using Picard (v1.87) (http://picard.sourceforge.net) ReorderBam  and all alignments were set as primary using the set_sam_primary.py (https://github.com/HuntsmanCancerInstitute/RBSSeqTools). The alignments were then processed with GATK (v3.4-0) 2 SplitNCigarReads, which splits spliced alignments into multiple alignment segments without N cigar elements.  Reads containing deletions four base pairs or longer were removed using remove_deletions.py (https://github.com/HuntsmanCancerInstitute/RBSSeqTools).
m5C analysis pipeline: BS and NBS sample reads were aligned and processed as outlined above. Alignments were further processed using CreateMethTable (https://github.com/HuntsmanCancerInstitute/RBSSeqTools), which iterates over the alignment file and reports forward alignment base counts at all reference ÒCÓ positions and in reverse alignment base counts at all reference ÒGÓ positions. A Fisher's exact test p-value was calculated for each position by comparing the observed count of unconverted and converted bases to the expected count, which was calculated assuming an error rate of 0.001. The table was filtered to create a final list of candidates by selecting only those sites which had a read depth ³10 in both BS and NBS datasets, a non-conversion rate of ³20% in the BS dataset and a Fisher exact p-value ²0.05. These sites were further screened manually for evidence of mis-mapping due to loss of complexity, or nonconversion arising from nondenatured secondary structure.
m1A analysis pipeline: BS and NBS sample reads were aligned and processed as listed above. CreateMethTable was used to report forward alignment base counts at all reference ÒAÓ positions with at least 100x coverage and in reverse alignment base counts at all reference ÒTÓ positions with at least 100x coverage.  A one-tailed Fisher's exact test, corrected for multiple comparisons using the Benjamini-Hochberg (BH) procedure, was used to test if the mismatch rate in the NBS sample was greater than the BS sample.  One-tailed binomial tests, corrected using BH, were used to test if the number of C, G or T bases were greater than expected given error rate (0.001).  Positions where 1) the mismatch rate of the NBS sample was significantly higher than the BS sample, 2) two of C, G or T were significantly higher than the error rate and 3) the FDR or C was not lower than both G and T were reported as m1A sites.
Pseudouridine analysis pipeline:  BS and NBS samples were aligned to the transcriptome indexes described above. Pseudouridine positions were called using ScorePsuedouridinePositions (https://github.com/HuntsmanCancerInstitute/RBSSeqTools).  This application iterates over a bam file, tracking the number of deletions and overall coverage at each genomic position.  Positions are skipped if 1) BS sample < 5 deletions, 2) BS sample fraction deletion < 0.01, 3) BS sample coverage < 10 reads, 4) NBS sample fraction deletion > 0.01 or NBS sample coverage < 10 reads. Adjacent positions are merged into a single deletion group on the initial analysis pass.  Deletion groups are pruned by removing positions with fraction deletions less than half the maximum observed faction deletion in the group. If pruning results in non-continuous regions, both are used in the remaining analysis.  Deletion groups are then scanned for potential pseudouridine locations using the following steps: 1) T at the position with highest fraction deletion (FirstDelBase) 2) T in the deletion group (AltPositionBase) 3) T in a homopolymer region (considering bisulfite treatment) with deletion at the leftmost position of the homopolymer (LeftAlignBase) or 4) nearest T within 25 bp of deletion (Neighborhood).  If multiple deletion groups share the same predicted pseudouridine position, only the group with the highest fraction deletion is used. A p-value is calculated for each group using the binomial test comparing observed deletion rate to the expected deletion rate.  The expected deletion rate is calculated using an error rate of 0.001. Deletion groups are flagged as false positives if: 1) NBS deletion p-value < 0.01, 2) deletion occurs within 4bp of an exon boundary 3) within 6bp or longer homopolymer or 4) within 5bp of a natural deletion observed in the NBS sample.  Deletion groups that pass these criteria are annotated if they are within a gene or repetitive element.  Finally, FDR values are calculated using the Benjamini Hochberg procedure. Positions were further filtered manually by removing sites that were classified as ÒNeighborhoodÓ when predicting the true pseudouridine position or had a high fraction of insertions at deletion site.
Reads were aligned and processed using the pipeline outlined above, except the Novoalign bisuflite alignment mode was set to 2 and different adapters were used (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT). Validation calls were intersected with the RBS-Seq calls using the predicted pseudouridine position.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files contaning m1A, m5C and pseudouridine candidtate sites.  Column descriptions can be found on the first tab of the spreadsheet

source_name: HeLa cells

growth_protocol: Typical Cell culutre

extract_protocol:
Tryzol extraction of total RNA. For Ribominus RNA samples: Ribosomal RNA depletion. For Small RNA samples: purification of small RNAs <200nt using MirVana kit. For PolyA selected RNA: Isolation of mRNAs using polyA Spin™ mRNA Isolation Kit. For Ribominus and PolyA fractions additioanl RNA fragmentation has been done. The BS samples are treated with sodium bisulfite mix for 16 hours at 50C while the corresponding NBS samples were remained untreated.
Directional (strand-specific) sequencing-library preparation protocol (Illumina) for RNA samples for RNASeq. For the the DNA (pooled PCR amplicons) sample the DNA library preparation protocol for MiSeq (Illumina).
RNASeq for RNA samples, MiSeq for the single DNA sample.

treatment_protocol: For siRNA samples: treatment of the cells with corresponding siRNAs. For the other samples no treatment on the cells.

tag: treatment

value: Sodium Bisulfite

tag: rna fragmentation

value: RNA fragmentation

tag: sirna

value: Control siRNA


title: Candidate Y site validation - HeLa

description:
DNA (Pooled PCR amplicons)
Table S9-PseudoU candidate site validation

value: No siRNA


title: PolyA RNA - NBS

description:
Poly-A selected RNA
Table S6-PseudoU candidate sites
Table S1-m5C candidate sites
Table S4-m1A candidate sites
Table S9-PseudoU candidate site validation

value: No Sodium Bisulfite


title: Ctrl-siRNA Total Ribominus RNA - NBS

description:
Total ribominus RNA
Table S6-PseudoU candidate sites


title: DKC1-siRNA Total Ribominus RNA - NBS

value: DKC1 siRNA


title: Candidate Y site validation - HEK293


title: DKC1-siRNA PolyA - BS


title: Ctrl-siRNA Total Ribominus RNA - BS


title: Small RNA - BS

description:
Small RNA
Table S6-PseudoU candidate sites
Table S1-m5C candidate sites
Table S4-m1A candidate sites
Table S9-PseudoU candidate site validation

value: No RNA fragmentation


title: DKC1-siRNA Total Ribominus RNA - BS


title: Small RNA - NBS


title: Total Ribominus RNA - BS

description:
Total ribominus RNA
Table S6-PseudoU candidate sites
Table S1-m5C candidate sites
Table S4-m1A candidate sites
Table S9-PseudoU candidate site validation


title: Sox2 ChIP_Singles

status: Public on Mar 07 2019

first: Federico

last: Zambelli

address: Via Giovanni Celoria 26

department: Department of Biosciences

institute: University of Milan

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.5
We used MACS (Zhang et al. 2008) version 2.0.9 to define Sox2 bound regions (peaks). As this tool is very sensitive to the unbalanced number of reads in the real and the input set, we decided to reduce the larger dataset to match the number of mapped reads in the smaller dataset by randomly sampling reads, as described previously (Mateo et al 2015).
Genome_build: mm9
Supplementary_files_format_and_content: *bed.txt: enriched ChIP-Seq peaks

source_name: Neural progenitor cells (Singles)

extract_protocol:
Lysates were clarified from sonicated nuclei and Sox2-DNA complexes were isolated by immunoprecipitation
Libraries were prepared from 10ng of immunoprecipitated or inut DNA according to Illumina's instructions accompanying the ChIp-seq Sample Kit.. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols to generate 50bp single read data.

tag: strain background

value: mixed C57BL/6 x DBA

value: Hippocamus-derived neural progenitor cells

tag: chip antibody

value: Sox2 (Santa cruz sc-17320)


title: Total Ribominus RNA - NBS


title: Sox2-deleted undifferentiated NSC_RNA-seq 3

description: Three biological replicates from three independent brains

data_processing:
Sequences were processed using the RSEM software with default parameters. Expression was measured on the RefSeq mm9 gene annotation as Transcripts per Million (TPM)
Genome_build: mm9
Supplementary_files_format_and_content: tpm_rnaseq.txt: TPM values of the six processed sequence sets

molecule: polyA RNA

source_name: Sox2-deleted undifferentiated NSC

growth_protocol: P0 brain-derived NSC cultures were obtained from dissected telencephalon of three wild type, and three Sox2-deleted mice, and grown, as described in (Favaro et al., 2009) and (Zhang et al., 2013). Cells were grown in parallel for two passages in 10 ng/ml Epidermal Growth Factor (EGF) and 10 ng/ml basic Fibroblast Growth Factor (bFGF), followed by cell dissociation and expansion in the presence of EGF, but not bFGF, for 3-4 more passages, as described in Zhang et al. (2013), for optimal maintenance of mutant NSC (Favaro et al., 2009).

extract_protocol:
RNA extraction was performed on three independent NSC populations for both wild type and mutant cells, using Trizol and RNeasy Kit (Qiagen). 1/5 volume of chloroform was added to one volume of Trizol. Aqueuos phase was transferred into a new tube. 1.5x volume of ethanol was added and mixed well. Mixture was was filtered through Rneasy (Qiagen) column. Column was washed with Buffer RW1. On-column DNase treatment was performed as described by the RNase-Free DNase Kit (Qiagen). Post treatment column was clean up with Buffer RW1 and two washes of RPE buffer. Column was then dried and total RNA was eluted with RNase-free water.
PolyA Stranded Truseq Libraries were generated using the Truseq Stranded mRNA Sample Preparation Kit (Illumina). First, mRNA was purified from 1µg of total RNA using magnetic beads containing poly-T oligos. mRNA was then fragmented and reversed transcribed using Superscript II (Invitrogen), followed by second strand synthesis. Double stranded cDNA was treated with end-pair, A-tailing, adapter ligation and 8 cycles of PCR amplification.

value: forebrain-derived NSC

tag: passages

value: passage 5 to 6


title: Sox2-deleted undifferentiated NSC_RNA-seq 2


title: Input DNA_Spheres

source_name: Neural progenitor cells (Spheres)


title: Sox2 ChIP_Spheres


title: wild type undifferentiated NSC_RNA-seq 1

source_name: wild type undifferentiated NSC

value: wild type


title: wild type undifferentiated NSC_RNA-seq 3


title: Sox2-deleted NSCs_H3K27ac_ChIPSeq

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.5 with at most one substitution. Reads mapping at multiple positions were discarded
MACS2 was used for peak calling (p-value threshold = 10-5, extsize = 400, local lambda = 100,000) and narrowpeaks were extended to a minimum of 2000 basepairs (bps) to match peak resolution.  Overlapping enriched regions were merged.
Genome_build: mm9
Supplementary_files_format_and_content: NR_H3K27ac_EnrichedRegions_Sort.bed and NR_H3K4me1_EnrichedRegions_Sort.bed. Enriched regions for each histone modification in wild type NSC cells

source_name: Sox2-deleted NSC

growth_protocol: P0 brain-derived NSC cultures were obtained from dissected telencephalon of six wild type and six Sox2-deleted mice, and grown, as described in (Favaro et al., 2009) and (Zhang et al., 2013). Cells were grown in parallel for two passages in 10 ng/ml Epidermal Growth Factor (EGF) and 10 ng/ml basic Fibroblast Growth Factor (bFGF), followed by cell dissociation and expansion in the presence of EGF, but not bFGF, for 3-4 more passages, as described in Zhang et al. (2013), for optimal maintenance of mutant NSC (Favaro et al., 2009).

extract_protocol:
For each line, neurospheres were dissociated and 4 million single cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Reaction was quenched with 0.125 M Glycine, cells were washed with cold PBS and lysed according to Vermunt et al., 2016. Nuclei pellets were resuspended in 160μl sonication buffer and divided over two microtubes for shearing in the Covaris S series with the following settings for 12 cycles of 60 seconds: intensity 3, duty cycle 20%, 200 cycles/bursts.  Chromatin immunoprecipitation steps after sonication were performed as described previously (Vermunt et al., 2016) using 50 μl DynaI protein G beads that were preincubated with 5 μg Ab4729 (Abcam) for H3K27ac or 5 μg Ab8894 (Abcam) for H3K4me1. Whole cell extract of 4 million cells was split onto both antibodies, resulting in the use of 2 million cells per ChIP.
Libraries were made using the Illumina Truseq DNA library protocol and sequencing was done at the MIT BioMicro Center (http://openwetware.org/wiki/BioMicroCenter).

value: forebrain-derived neural stem cells (NSCs)

value: passage 3 to 7

tag: chip antibodies

value: Ab4729 (Abcam) for H3K27ac


title: Sox2-deleted NSCs_H3K4me1_ChIPSeq

value: Ab8894 (Abcam) for H3K4me1.


title: Sox2-deleted undifferentiated NSC_RNA-seq 1


title: WT_NSCs_H3K27ac_ChIPSeq

source_name: wild type NSC


title: PolyA RNA - BS

value: Sodium Bisulfite


title: WT_NSCs_H3K4me1_ChIPSeq


title: wild type undifferentiated NSC_RNA-seq 2


title: CyD_plus_LPS

city: Morahalom

first: Balazs

last: Horvath

address: Vallalkozok u. 7.

department: NGSP

country: Hungary

institute: SeqOmics Biotechnology Ltd.

data_processing:
Basecalls performed using 5500xl
Data were filtered using the following specifications: minimum number of nucleotides in reads = 50
RNA reads were aligned to the mm_ref_GRCm38_chr13, mm_ref_GRCm38_chrY, mm_ref_GRCm38_chr15, mm_ref_GRCm38_chr2, mm_ref_GRCm38_chr19, mm_ref_GRCm38_chr18, mm_ref_GRCm38_chr9, mm_ref_GRCm38_chr3, mm_ref_GRCm38_chr4, NC_005089, mm_ref_GRCm38_chr8, mm_ref_GRCm38_chr6, mm_ref_GRCm38_chrX, mm_ref_GRCm38_chr10, mm_ref_GRCm38_chr1, mm_ref_GRCm38_chr14, mm_ref_GRCm38_chr11, mm_ref_GRCm38_chrUn, mm_ref_GRCm38_chr12, mm_ref_GRCm38_chr5, mm_ref_GRCm38_chr17, mm_ref_GRCm38_chr7 genome assembly using CLC Genomics Workbench version 6.0.1 with the following configurations…*
Calculate expression levels and discover novel exons using CLC Genomics Workbench version 6.0.1
Annotation using CLC Genomics Workbench version 6.0.1 (Data from www.geneontology.org)
Genome_build: mm_ref_GRCm38_chr13, mm_ref_GRCm38_chrY, mm_ref_GRCm38_chr15, mm_ref_GRCm38_chr2, mm_ref_GRCm38_chr19, mm_ref_GRCm38_chr18, mm_ref_GRCm38_chr9, mm_ref_GRCm38_chr3, mm_ref_GRCm38_chr4, NC_005089, mm_ref_GRCm38_chr8, mm_ref_GRCm38_chr6, mm_ref_GRCm38_chrX, mm_ref_GRCm38_chr10, mm_ref_GRCm38_chr1, mm_ref_GRCm38_chr14, mm_ref_GRCm38_chr11, mm_ref_GRCm38_chrUn, mm_ref_GRCm38_chr12, mm_ref_GRCm38_chr5, mm_ref_GRCm38_chr17, mm_ref_GRCm38_chr7

source_name: liver

extract_protocol: Total mRNA was isolated from tissue samples (20 mg) using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. To reach higher RNA yields QIAshredder homogenizer was used. RNA quality and quantity measurements were performed on Bioanalyzer (Agilent Technologies) and Qubit (Life Technologies). High quality (RIN >8.5) total RNA samples from three biological replicates were pooled in equimolar concentrations and processed using the SOLiD total RNA-Seq Kit (Life Technologies), according to the manufacturer’s instructions.

tag: tissue

value: liver


title: CyD_plus_CTRL


title: RNApolII ChIA-PET, Sox2-deleted cultured NSC

data_processing:
library strategy: ChIA-PET
base-calling: Software Name="Illumina RTA" Version="1.6.32.0"
alignment: BATMIS - Basic Alignment Tool for Mismatches http://code.google.com/p/batmis/
Interaction cluster calling: ChIA-PET data was processed with ChIA-PET Tool software: Li, G., Fullwood, M.J., Xu, H., Mulawadi, F.H., Velkov, S., Vega, V., Ariyaratne, P.N., Mohamed, Y.B., Ooi, H.S., Tennakoon, C., Wei, C.L., Ruan, Y. and Sung, W.K. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol, 11 (2). R22
Genome_build: mm9
Supplementary_files_format_and_content: left_anchors.bed.txt and right_anchors.bed.txt contain the interacting regions. Regions with the same number in both files form a left/right anchor pair

source_name: Sox2-deleted cultured NSC

growth_protocol: P0 brain-derived NSC cultures were obtained from dissected telencephalon of six Sox2-deleted mice, and grown, as described in (Favaro et al., 2009) and (Zhang et al., 2013). Cells were grown in parallel for two passages in 10 ng/ml Epidermal Growth Factor (EGF) and 10 ng/ml basic Fibroblast Growth Factor (bFGF), followed by cell dissociation and expansion in the presence of EGF, but not bFGF, for 3-4 more passages, as described in Zhang et al. (2013), for optimal maintenance of mutant NSC (Favaro et al., 2009).  The culture of Sox2-deleted NSC was performed in parallel with that of wild type NSC (Zhang Y et al., Nature 2013, 504:306-10).

extract_protocol: ChIA-PET: ChIPed Chromatin DNA was added in linkers with MmeI site contained at both ends and cyclized. MmeI was used to release pair end di-tags to discover the enhancer-promoter interactions. With the adding on the sequencing adaptors and 15 PCR cycles amplification, the ChIA-PET libraries were sequenced by 2x36 bp with Illumina GAIIx.

treatment_protocol: All subsequent procedures were exactly as in Zhang Y et al., 2013, Nature 504:306-10; see GEO submission GSE44067

value: RNAPII monoclonal antibody (8WG16, Covance)


title: shLOXL2_RNA-seq R2

status: Public on Mar 06 2019

city: Barcelona

first: Sandra

last: Peiró

address: Aiguader 88

department: Programa de Recerca en Càncer

country: Spain

institute: IMIM-Hospital del Mar

description:
Second replicate of two (experimental condition)
genes.fpkm_table

data_processing:
a) H3K4ox ChIP-seq in MDA-MB-231 cells
Alignment of DNA reads to reference genome (bowtie)
Peak calling (MACS)
The bam file of sample H3 ChIP-seq (1a_H3_9552_GGCTAC.bam) was employed as the control in calling the peaks of H3K4ox ChIP-seq R1 and H3K4ox ChIP-seq R1 using the MACS algorithm, and subsequently, no processed file was produced for it
b) ATACseq in MDA-MB-231 infected with shRNA against LOXL2
Alignment of DNA reads to reference genome (bowtie)
Peak calling (MACS)
c) RNA seq in MDA-MB-231 infected with shRNA against LOXL2
Alignment of DNA reads to reference genome (bowtie)
Detection of differentially expressed genes (Cufflinks)
Genome_build: GRCh37
Supplementary_files_format_and_content: JP01_9549_peaks.bed (Bed file with H3K4ox peaks (R1))
JP01_9550_peaks.bed (Bed file with H3K4ox peaks (R2))
J*.bed files column headers : chr, start, end, length, summit, tags, -10*log10(pvalue), fold_enrichment, FDR(%)
shLOXL2_ATAC_peaks.bed
genes.fpkm_table (Cufflinks differential expression file)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
RNA was extracted with an RNA extraction kit (GenElute Mammalian Total RNA) (Sigma)
Libraries were prepared according to Illumina's instructions

value: LOXL2 depletion


title: CyD_neg_CTRL

value: CypD-/-


title: shControl_RNA-seq R2

description:
Second replicate of two (control condition)
genes.fpkm_table

value: control


title: shControl_RNA-seq R1

description:
First replicate of two (control condition)
genes.fpkm_table


title: 559J_1_200U

first: Josefina

last: Ocampo

address: 6 Center Drive

department: NICHD

institute: NIH

description: Biological replicate 1

data_processing:
Nucleosome sequences were aligned to the yeast genome (SacCer3) using Bowtie2 with default settings.
Occupancy profiles in bigWig format were generated in R using Rsamtools and rtracklayer packages.
For further analyses the aligned reads were size-selected for fragments from 120-180bp as described in the article.
Genome_build: SacCer3
Supplementary_files_format_and_content: bigWig

source_name: nucleosome core particles (MNase)_8 tRNA genes on chromosome III deleted

growth_protocol: Wild-type cells and null mutant were grown to mid-log phase in Synthetic Complete (SC) medium containing 2% glucose.

extract_protocol:
For MNase experiments, nuclei were prepared from unfixed yeast cells and then digested with MNase. Mono-nucleosomal DNA was gel-purified (~150 bp)in experiment 1. See paper for details.
The DNA was repaired using the DNA repair kit from New England Biolabs. The repaired DNA was processed for paired-end sequencing according to the Illumina protocol.

tag: strain name

value: JKY690 (8 tRNA genes on chromosome III deleted)

tag: genotype

value: W303 MATa C0-9D T1/T7::HIS3 LEU2 ade2-1 LYS+


title: 558J_2_200U

description: Biological replicate 2

source_name: nucleosome core particles (MNase)_wildtype

value: JRY2334 (wild type)


title: Input DNA_Singles

value: mixed C57BL/6 x DBA

value: Hippocamus-derived neural progenitor cells


title: 558J_1_200U

description: Biological replicate 1


title: shControl_ATAC-seq

description:
control condition
shLOXL2_ATAC_peaks.bed


title: H3 ChIP-seq

description:
unique sample (control)
Barcode: GGCTAC

source_name: H3 ChIP-seq

value: anti-H3 (ab1791, Abcam)


title: CyD_neg_LPS


title: H3K4ox ChIP-seq R1

description:
First replicate of two
JP01_9549_peaks.bed
Barcode: ATCACG

source_name: H3K4ox ChIP-seq

value: anti-H3K4ox (developed in house using modified peptides coupled to Keyhole limpet hemocyanin (KLH))


title: 559J_2_200U

description: Biological replicate 2


title: shLOXL2_RNA-seq R1

description:
First replicate of two (experimental condition)
genes.fpkm_table


title: EE2_10nM_8

city: Bergen

first: Fekadu

last: Yadetie

address: Thormøhlensgt. 53A/B

country: Norway

institute: University of Bergen

data_processing:
The quality of the sequenced RNA samples was verified using FastQC v0.11.5
Paired reads were aligned to the published CDS of Atlantic cod using HISAT v2.1.0
Counts were generated from the alignments using idxstats from SAMtools v1.4.1
Genome_build: ftp://ftp.ensembl.org/pub/release-90/fasta/gadus_morhua/cds/Gadus_morhua.gad
Supplementary_files_format_and_content: TAB-delimited text files with each line consisting of reference sequence name, sequence length, # mapped reads and # unmapped reads

organism: Gadus morhua

source_name: Precision cut liver slices

extract_protocol:
Total RNA was isolated from frozen slices using mirVana™ miRNA Isolation Kit (Cat# AM1560, Ambion, Austin, TX, USA). The RNA was treated using TURBO DNase (TURBO DNA-free kit, Ambion) and further purified using RNA Clean & Concentrator-5 (Zymo Research Corp, Irvine, CA, USA) and eluted with RNase-free water. The concentration of total RNA was measured using NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).  RNA quality was assessed using the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).
RNA samples (0.4 μg total RNA per sample) were sequenced according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide on Illumina HiSeq 4000 (Illumina, Inc., San Diego, CA, USA).

tag: agent

value: Liver

value: Female

tag: body weight (g)

tag: liver weight (g)


title: shLOXL2_ATAC-seq

description:
experimental condition
shLOXL2_ATAC_peaks.bed


title: BaP_10nM_8


title: Mix_10nM_8


title: Mix_1μM_6


title: DMSO_8

value: DMSO


title: DMSO_7

value: Male


title: BaP_1μM_7


title: Mix_10nM_6


title: EE2_1μM_8


title: DMSO_6


title: Mix_1μM_8


title: Mix_10nM_7


title: Mix_10nM_5


title: Mix_1μM_5


title: BaP_10nM_6


title: EE2_1μM_6


title: EE2_10nM_6


title: H3K4ox ChIP-seq R2

description:
Second replicate of two
JP01_9550_peaks.bed
Barcode: ACTTGA


title: BaP_1μM_5


title: BaP_10nM_5


title: EE2_1μM_5


title: DMSO_5


title: EE2_10nM_7


title: Mix_1μM_4


title: Mix_10nM_4


title: BaP_1μM_6


title: EE2_1μM_4


title: BaP_1μM_4


title: BaP_10nM_4


title: DMSO_4


title: EE2_10nM_2


title: EE2_10nM_3


title: BaP_1μM_3


title: Mix_10nM_2


title: DMSO_3


title: BaP_1μM_2


title: SSL27H2

city: yantai

first: cheng-gang

last: ren

state: shandong

address: 17 Chunhui Road, Laishan District

institute: Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, China

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
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. All the downstream analyses were based on clean  data with high quality.
The left files (read1 files) from all libraries/samples were pooled into one big left.fq file, and right  files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the  left.fq and right.fq using Trinity (Grabherr et al, 2011) with min_kmer_cov set to 2 by default and all  other parameters set default.
Gene expression levels were estimated by RSEM (Li et al, 2011) for each sample:  1. Clean data were mapped back onto the assembled transcriptome  2. Readcount for each gene was obtained from the mapping results
Genome_build: De novo transcriptome assembly
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Sesbania cannabina

source_name: leaf

extract_protocol:
Total RNA from the samples was isolated in two biological replicates using TRIzol (Invitrogen, USA) following the manufacture’s instructions.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit  for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added  to attribute sequences to each sample.

tag: mycorrhizal or non-mycorrhizal

value: non-mycorrhizal

value: 150mM NaCl

tag: time

value: 27 hours

value: leaf

tag: developmental stage

value: 30 days old seedling

value: wild type


title: SSL27H1


title: Mix_1μM_2

tag: Sex


title: EE2_1μM_3


title: SSR3H2

source_name: root

tag: treatment

value: 3 hours

value: root


title: BaP_10nM_3


title: SSR27H1


title: Mix_1μM_3


title: EE2_10nM_1


title: EE2_1μM_1


title: BaP_10nM_2


title: BaP_1μM_1


title: SSR3H1


title: SSR27H2


title: EE2_10nM_4


title: BaP_10nM_1


title: SSL3H2


title: ScR2

value: no treatment

value: control


title: SSL3H1


title: DMSO_1


title: ScR1


title: DMSO_2


title: ScL2


title: ScL1


title: ScASSR27H2

value: mycorrhizal


title: ScASSR27H1


title: ScASSR3H2


title: ScASSL27H2


title: ScASSL3H1


title: ScASSL3H2


title: ScASSL27H1


title: ScAL2


title: ScAL1


title: ScAR1


title: ScAR2


title: PCGA-01-0048-086-25102-00880BR-1034027R

status: Public on Mar 05 2019

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description: Gene Expression from normal fluorescing large airway bronchial epithelial cells in subject where the worst histological grade sampled by biopsy was moderate dysplasia.

data_processing:
Demultiplexing and creation of FASTQ files were performed either using Illumina CASAVA (v1.8.2), trimming off the last base of each read, or using BaseSpace, without trimming off the last base of each read.
Samples were aligned using hg19 and 2-pass STAR alignment (v2.5.2b). Gene and transcript level counts were calculated using RSEM (v1.3.0) using Ensembl v74 annotation.
Quality metrics were calculated by STAR and RSeQC. Sample relatedness within a patient was confirmed using Peddy software. Samples in which sex annotation did not correlate with gene expression (CYorf15A, DDX3Y, KDM5D, RPS4Y1, USP9Y, UTY), or with a high-rate of heterozygosity (more than 3 standard deviations above the median) or samples with low relatedness to samples from the same patient (more than 3 standard deviations below the median) were removed from further analyses. Samples were subsequently divided into discovery (DC) and validation (VC) cohorts. Subsequent sample and gene filtering was conducted separately on each set (DC biopsies, DC brushes, VC biopsies, and VC brushes) as follows: edgeR was used to compute normalized data (library sizes normalized using trimmed mean of M-values, and log2 counts per million computed) and genes were excluded that either had an interquartile range equal to zero or a sum across samples equal or less than 1.  Samples were excluded based on values greater than 2 standard deviations from the mean for 1) mean Pearson correlation with all other samples calculated across all filtered genes 2) the 1st or 2nd principal components calculated using the filtered gene expression matrix 3) transcript integrity number (TIN, computed by RSeQC).  After sample filtering, gene filtering was recomputed as described above on the final set of high-quality samples.
For each set (DC biopsies, DC brushes, VC biopsies, and VC brushes), residual gene expression values adjusting for RNA quality (median TIN) and batch (Illumina flow cell) were calculated using the limma package and voom-transformed data.
Genome_build: hg19
Supplementary_files_format_and_content: exp_count.txt: a tab-delimited file containing the expression counts for this dataset
residuals.txt: a tab-delimited file containing residuals computed for this dataset

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (QIAgen).
Sequencing libraries were prepared using the Illumina TruSeq RNA Kit v2.
The libraries were multiplexed in groups of four using Illumina TruSeq Paired-End Cluster Kit. Each sample was sequenced on the Illumina HiSeq 2500 to generate paired-end 100-nucleotide reads.

tag: cohort

value: validation cohort

tag: patient id

tag: grade

value: moderate dysplasia

tag: molecular subtype

value: Secretory

tag: flow cell id

tag: median tin

tag: passed qc

value: TRUE


title: PCGA-01-0047-086-19447-01214BR-1034054R

description: Gene Expression from normal fluorescing large airway bronchial epithelial cells in subject where the worst histological grade sampled by biopsy was mild dysplasia.

value: mild dysplasia

value: Normal


title: PCGA-01-0044-086-17898-01128BR-1034107R

source_name: normal fluorescing large airway bronchial epithelial cells


title: PCGA-01-0044-086-16659-00291BR-1034025R

description: Gene Expression from normal fluorescing large airway bronchial epithelial cells in subject where the worst histological grade sampled by biopsy was metaplasia.

value: metaplasia


title: PCGA-01-0042-086-23680-00904BR-1033973R

value: Proliferative


title: PCGA-01-0046-086-27138-00950BR-1034029R

value: Inflammatory


title: PCGA-01-0046-086-27551-01289BR-1034049R

description: Gene Expression from normal fluorescing large airway bronchial epithelial cells in subject where the worst histological grade sampled by biopsy was hyperplasia.

value: hyperplasia


title: PCGA-01-0036-086-22885-00909BR-1034028R


title: PCGA-01-0052-086-20842-01011BR-1033959R


title: PCGA-01-0046-043-26739-00763BR-1034026R


title: PCGA-01-0035-086-21168-01032BR-1034024R


title: PCGA-01-0034-086-23331-01164BR-1034044R

description: Gene Expression from normal fluorescing large airway bronchial epithelial cells in subject where the worst histological grade sampled by biopsy was severe dysplasia.

value: severe dysplasia


title: PCGA-01-0039-086-19554-01000BR-1034013R


title: PCGA-01-0033-043-20582-00972BR-1034012R


title: PCGA-01-0048-086-25305-48962BR-1033957R


title: PCGA-01-0045-086-17021-00889BR-1034009R


title: ScASSR3H1

value: 150mM NaCl

tag: tissue

value: 30 days old seedling

value: wild type


title: PCGA-01-0043-043-21235-01040BR-1033961R


title: PCGA-01-0041-086-21703-00920BR-1033965R


title: PCGA-01-0036-086-21975-00295BR-1034007R


title: PCGA-01-0038-086-20756-00767BR-1033999R


title: PCGA-01-0044-086-17646-44963BR-1034002R


title: PCGA-01-0047-086-19263-01019BR-1033996R


title: PCGA-01-0041-086-21430-00793BR-1033972R


title: PCGA-01-0034-086-22969-00915BR-1033992R


title: PCGA-01-0042-086-23911-01023BR-1033969R


title: PCGA-01-0036-086-23647-01402BR-1034126R


title: PCGA-01-0044-086-18295-01393BR-1034115R


title: PCGA-01-0038-086-21699-01387BR-1034121R

value: FALSE


title: PCGA-01-0050-086-23482-00995BR-1033967R


title: PCGA-01-0039-086-19757-01218BR-1034109R


title: PCGA-01-0049-086-23272-01339BR-1034114R


title: PCGA-01-0041-086-22044-01180BR-1034108R


title: PCGA-01-0048-086-25835-01378BR-1034127R


title: PCGA-01-0045-086-17497-01236BR-1034101R


title: PCGA-01-0052-086-21157-01294BR-1034077R


title: PCGA-01-0040-043-19895-01281BR-1034076R


title: PCGA-01-0033-043-20864-01243BR-1034065R


title: PCGA-01-0049-086-23043-01185BR-1034081R


title: PCGA-01-0051-086-22577-01160BR-1034062R


title: PCGA-01-0038-086-21323-01072BR-1034088R


title: PCGA-01-0043-043-21599-01347BR-1034087R


title: PCGA-01-0040-086-19706-01093BR-1034052R


title: PCGA-01-0035-086-21364-01254BR-1034093R


title: PCGA-01-0050-086-23699-01226BR-1034055R


title: PCGA-01-0048-086-25669-01271BR-1034112R


title: PCGA-01-0051-086-22786-01331BR-1034095R


title: PCGA-01-0047-086-19809-01409BR-1034120R


title: PCGA-01-0033-092-21079-01369BX-1034051R

description: Gene Expression from endobronchial biopsy with metaplasia.

source_name: endobronchial biopsy


title: PCGA-01-0033-061-20864-01246BX-1034047R

description: Gene Expression from endobronchial biopsy with normal histology.

value: normal


title: PCGA-01-0033-085-21079-01370BX-1034042R

description: Gene Expression from endobronchial biopsy with moderate dysplasia.


title: PCGA-01-0035-042-21364-01260BX-1034048R

description: Gene Expression from endobronchial biopsy with hyperplasia.


title: PCGA-01-0037-086-28409-00749BR-1033962R


title: PCGA-01-0036-048-22885-00913BX-1034010R


title: PCGA-01-0035-042-21168-01035BX-1034006R


title: PCGA-01-0036-089-22885-00911BX-1034019R


title: PCGA-01-0038-037-21699-01390BX-1034119R

description: Gene Expression from endobronchial biopsy with mild dysplasia.


title: PCGA-01-0047-037-19809-01411BX-1034118R


title: PCGA-01-0039-066-19554-01003BX-1033995R


title: PCGA-01-0044-048-17646-44967BX-1033975R


title: PCGA-01-0046-050-27551-01293BX-1034104R


title: PCGA-01-0048-061-25835-01381BX-1034123R


title: PCGA-01-0050-050-23699-01235BX-1034110R


title: PCGA-01-0035-074-21364-01256BX-1034084R


title: PCGA-01-0048-025-25669-01275BX-1034085R


title: PCGA-01-0049-050-23272-01344BX-1034096R


title: PCGA-01-0043-085-21235-01044BX-1034097R


title: PCGA-01-0045-085-17021-00891BX-1034000R


title: PCGA-01-0044-050-17898-01133BX-1034071R


title: PCGA-01-0052-048-21157-01302BX-1034050R


title: PCGA-01-0039-066-19757-01221BX-1034091R


title: PCGA-01-0052-093-21157-01299BX-1034068R


title: PCGA-01-0045-045-17497-01239BX-1034083R


title: PCGA-01-0049-010-23043-01187BX-1034072R


title: PCGA-01-0040-093-19706-01098BX-1034043R


title: PCGA-01-0051-089-22577-01162BX-1034053R


title: PCGA-01-0042-048-23911-01029BX-1034033R


title: PCGA-01-0047-037-19447-01216BX-1034045R


title: PCGA-01-0052-093-20842-01014BX-1034032R


title: PCGA-01-0050-050-23482-00998BX-1034031R


title: PCGA-01-0052-050-20842-01015BX-1034023R


title: PCGA-01-0042-010-23911-01028BX-1033960R


title: PCGA-01-0050-041-23482-00999BX-1034022R


title: PCGA-01-0050-084-23482-00997BX-1033958R


title: PCGA-01-0048-093-25102-00882BX-1034018R


title: PCGA-01-0046-089-27138-00952BX-1034020R


title: PCGA-01-0044-070-16659-00293BX-1034016R


title: PCGA-01-0046-089-26739-00765BX-1034017R


title: PCGA-01-0035-019-21168-01034BX-1034015R


title: PCGA-01-0046-047-26739-00766BX-1034008R


title: PCGA-01-0039-076-19554-01002BX-1034004R


title: PCGA-01-0044-070-17646-44965BX-1033993R


title: PCGA-01-0033-048-20582-00974BX-1034003R


title: PCGA-01-0036-089-21975-00297BX-1033998R


title: PCGA-01-0045-045-17021-00893BX-1033991R


title: PCGA-01-0042-048-23680-00907BX-1033955R


title: PCGA-01-0035-061-21168-01037BX-1033988R


title: PCGA-01-0041-050-21703-00922BX-1033956R


title: PCGA-01-0047-037-19263-01021BX-1033987R

description: Gene Expression from endobronchial biopsy with severe dysplasia.


title: PCGA-01-0036-048-21975-00298BX-1033989R


title: PCGA-01-0048-025-25305-48965BX-1034021R


title: PCGA-01-0038-037-20756-00770BX-1033990R


title: PCGA-01-0033-085-20582-00976BX-1033985R


title: PCGA-01-0044-089-17646-44966BX-1033984R


title: PCGA-01-0039-089-19554-01004BX-1033986R


title: PCGA-01-0045-048-17021-00894BX-1033982R


title: PCGA-01-0041-050-21430-00796BX-1033954R


title: PCGA-01-0052-048-20842-01017BX-1034014R


title: PCGA-01-0034-050-22969-00918BX-1033983R


title: PCGA-01-0038-050-20756-00771BX-1033981R


title: PCGA-01-0052-036-20842-01018BX-1034005R


title: PCGA-01-0035-093-21168-01038BX-1033979R


title: PCGA-01-0035-074-21168-01036BX-1033997R


title: PCGA-01-0041-093-21703-00919BX-1033974R


title: PCGA-01-0036-050-22885-00914BX-1034001R


title: PCGA-01-0039-093-19554-01005BX-1033977R


title: PCGA-01-0037-089-27849-00344BX-1033971R


title: PCGA-01-0046-050-27138-00953BX-1034011R


title: PCGA-01-0033-050-20582-00977BX-1033976R


title: PCGA-01-0036-050-23647-01405BX-1034122R


title: PCGA-01-0044-089-18295-01396BX-1034130R


title: PCGA-01-0044-050-18295-01397BX-1034128R


title: PCGA-01-0035-050-21168-01039BX-1033970R


title: PCGA-01-0038-048-21699-01391BX-1034117R


title: PCGA-01-0038-050-21699-01392BX-1034116R


title: PCGA-01-0033-048-20864-01248BX-1034111R


title: PCGA-01-0048-093-25835-01380BX-1034125R


title: PCGA-01-0046-047-27551-01292BX-1034113R


title: PCGA-01-0048-061-25669-01273BX-1034103R


title: PCGA-01-0036-089-23647-01404BX-1034124R


title: PCGA-01-0039-076-19757-01220BX-1034100R


title: PCGA-01-0033-048-21079-01371BX-1034129R


title: PCGA-01-0033-050-20864-01249BX-1034102R


title: PCGA-01-0047-050-19263-01022BX-1033978R


title: PCGA-01-0048-093-25669-01274BX-1034094R


title: PCGA-01-0041-093-22044-01182BX-1034099R


title: PCGA-01-0045-085-17497-01238BX-1034092R


title: PCGA-01-0041-050-22044-01183BX-1034090R


title: PCGA-01-0042-010-23680-00906BX-1033964R


title: PCGA-01-0051-089-22786-01334BX-1034086R


title: PCGA-01-0044-089-17898-01131BX-1034089R


title: PCGA-01-0038-037-21323-01075BX-1034079R


title: PCGA-01-0043-085-21599-01349BX-1034078R


title: PCGA-01-0035-061-21364-01257BX-1034075R


title: PCGA-01-0043-037-21235-01043BX-1034106R


title: PCGA-01-0044-050-17646-44968BX-1033966R


title: PCGA-01-0033-043-21079-01367BR-1034060R


title: PCGA-01-0044-070-17898-01130BX-1034098R


title: PCGA-01-0038-050-21323-01077BX-1034061R


title: PCGA-01-0052-036-21157-01301BX-1034059R


title: PCGA-01-0043-037-21599-01350BX-1034069R


title: PCGA-01-0041-093-21430-00795BX-1033963R


title: PCGA-01-0039-093-19757-01224BX-1034073R


title: PCGA-01-0038-048-21323-01076BX-1034070R


title: PCGA-01-0035-093-21364-01258BX-1034066R


title: PCGA-01-0045-048-17497-01241BX-1034074R


title: PCGA-01-0049-050-23043-01188BX-1034063R


title: PCGA-01-0021-086-19077-00134BR-1007322R

value: discovery cohort


title: PCGA-01-0001-086-19300-00584BR-1007492R


title: PCGA-01-0019-043-21625-00866BR-1007522R


title: PCGA-01-0032-086-24226-00634BR-1007496R

description: Gene Expression from normal fluorescing large airway bronchial epithelial cells in subject where the worst histological grade sampled by biopsy was normal.


title: PCGA-01-0040-093-19895-01283BX-1034067R

value: validation cohort


title: PCGA-01-0032-086-24051-00543BR-1007376R


title: PCGA-01-0044-048-17898-01132BX-1034080R


title: PCGA-01-0014-009-19848-00096BR-1007320R


title: PCGA-01-0006-043-20238-00773BR-1007510R


title: PCGA-01-0006-043-19783-00445BR-1007361R


title: PCGA-01-0001-086-20343-01312BR-1031645R


title: PCGA-01-0012-086-20660-00422BR-1007356R


title: PCGA-01-0015-043-17638-01324BR-1031652R


title: PCGA-01-0021-086-20687-01304BR-1031640R


title: PCGA-01-0040-050-19895-01284BX-1034058R


title: PCGA-01-0035-019-21364-01259BX-1034057R


title: PCGA-01-0028-086-24262-01262BR-1031634R


title: PCGA-01-0012-086-21836-01250BR-1031631R


title: PCGA-01-0021-086-20218-00938BR-1031580R


title: PCGA-01-0009-086-24085-01205BR-1031627R


title: PCGA-01-0018-086-22732-01143BR-1031615R


title: PCGA-01-0008-086-22263-01189BR-1031622R

value: moderate dysplasia


title: PCGA-01-0025-043-21689-01103BR-1031602R


title: PCGA-01-0021-086-20449-01087BR-1031597R


title: PCGA-01-0001-086-20126-01113BR-1031607R


title: PCGA-01-0022-086-21996-01167BR-1031618R


title: PCGA-01-0003-086-24730-00945BR-1031586R


title: PCGA-01-0022-086-21548-00874BR-1031578R


title: PCGA-01-0021-086-19266-00317BR-1007342R


title: PCGA-01-0022-086-20750-00327BR-1007344R

value: Secretory


title: PCGA-01-0006-086-19580-00281BR-1007341R

value: TRUE


title: PCGA-01-0009-086-23882-00989BR-1031589R


title: PCGA-01-0009-043-22704-00228BR-1007333R


title: PCGA-01-0031-086-24726-01058BR-1031592R

value: mild dysplasia


title: PCGA-01-0014-086-19953-00201BR-1007327R


title: PCGA-01-0019-086-20715-00198BR-1007326R


title: PCGA-01-0024-086-23581-00426BR-1007357R


title: PCGA-01-0001-086-19762-00896BR-1007524R


title: PCGA-01-0026-086-22473-00858BR-1007520R


title: PCGA-01-0031-086-24285-00853BR-1007519R


title: PCGA-01-0022-086-21548-00875BR-1007523R


title: PCGA-01-0017-086-20422-00848BR-1007518R

value: Normal


title: PCGA-01-0023-086-21429-00821BR-1007515R


title: PCGA-01-0009-086-23497-00843BR-1007517R

value: metaplasia


title: PCGA-01-0008-086-21682-00836BR-1007516R


title: PCGA-01-0020-043-24050-00782BR-1007512R


title: PCGA-01-0021-043-19623-00577BR-1031577R


title: PCGA-01-0024-086-24050-00778BR-1007511R


title: PCGA-01-0029-086-22678-00809BR-1007514R

value: Proliferative


title: PCGA-01-0028-086-23527-00756BR-1007508R


title: PCGA-01-0014-086-20660-00742BR-1007507R


title: PCGA-01-0014-009-19953-00205BR-1007328R


title: PCGA-01-0010-086-19900-00699BR-1007502R


title: PCGA-01-0017-086-20261-00730BR-1007505R


title: PCGA-01-0021-043-19826-00719BR-1007503R


title: PCGA-01-0005-086-17489-00726BR-1007504R

value: Inflammatory


title: PCGA-01-0031-086-24061-00663BR-1007500R


title: PCGA-01-0018-043-21990-00649BR-1007499R

value: hyperplasia


title: PCGA-01-0016-086-23045-00644BR-1007498R


title: PCGA-01-0029-086-22412-00620BR-1007381R


title: PCGA-01-0009-043-23126-00556BR-1007377R


title: PCGA-01-0006-043-21015-01276BR-1031637R


title: PCGA-01-0004-086-27317-00603BR-1007380R


title: PCGA-01-0015-043-16541-00569BR-1007378R


title: PCGA-01-0025-086-20772-00539BR-1007375R


title: PCGA-01-0016-086-22821-00507BR-1007370R


title: PCGA-01-0024-086-23686-00518BR-1007371R


title: PCGA-01-0031-086-23830-00535BR-1007374R


title: PCGA-01-0010-086-19599-00502BR-1007369R


title: PCGA-01-0007-086-18131-00525BR-1007373R


title: PCGA-01-0018-043-21752-00493BR-1007368R


title: PCGA-01-0003-043-24282-00692BR-1007501R

value: severe dysplasia


title: PCGA-01-0007-086-18033-00452BR-1007362R


title: PCGA-01-0021-043-19434-00460BR-1007363R


title: PCGA-01-0028-086-23163-00489BR-1007367R


title: PCGA-01-0022-043-20918-00467BR-1007364R


title: PCGA-01-0011-086-26558-00429BR-1007358R


title: PCGA-01-0001-086-19118-00479BR-1007366R


title: PCGA-01-0008-086-21115-00417BR-1007355R


title: PCGA-01-0014-086-20177-00391BR-1007351R


title: PCGA-01-0015-043-16303-00401BR-1007352R


title: PCGA-01-0025-086-20884-00598BR-1007379R


title: PCGA-01-0029-043-22090-00375BR-1007349R


title: PCGA-01-0030-086-27868-00357BR-1007347R


title: PCGA-01-0020-043-23497-00366BR-1007348R


title: PCGA-01-0021-086-19182-00263BR-1007337R


title: PCGA-01-0026-086-21752-00336BR-1007345R


title: PCGA-01-0005-086-16929-00324BR-1007343R


title: PCGA-01-0002-043-23843-00276BR-1007339R


title: PCGA-01-0021-050-20218-00944BX-1031585R


title: PCGA-01-0015-011-17638-01327BX-1031654R


title: PCGA-01-0021-025-20218-00942BX-1031583R


title: PCGA-01-0032-088-24226-00635BX-1007494R

description: Gene Expression from endobronchial biopsy with unknown histology.

value: unknown


title: PCGA-01-0003-043-23883-00411BR-1007354R


title: PCGA-01-0001-074-20343-01315BX-1031647R


title: PCGA-01-0002-086-24062-00440BR-1007360R


title: PCGA-01-0001-076-20343-01314BX-1031646R


title: PCGA-01-0025-086-20576-00382BR-1007350R


title: PCGA-01-0021-089-20218-00941BX-1031582R


title: PCGA-01-0021-025-20687-01310BX-1031643R


title: PCGA-01-0021-050-20687-01311BX-1031644R


title: PCGA-01-0021-089-20687-01308BX-1031642R


title: PCGA-01-0011-086-26439-00339BR-1007346R


title: PCGA-01-0021-070-20687-01307BX-1031641R


title: PCGA-01-0012-050-21836-01253BX-1031633R


title: PCGA-01-0028-041-24262-01264BX-1031635R


title: PCGA-01-0009-092-24085-01209BX-1031630R


title: PCGA-01-0009-053-24085-01207BX-1031628R


title: PCGA-01-0021-070-20218-00940BX-1031581R


title: PCGA-01-0008-050-22263-01196BX-1031626R


title: PCGA-01-0021-010-20218-00943BX-1031584R


title: PCGA-01-0022-089-21996-01170BX-1031620R


title: PCGA-01-0022-093-21996-01171BX-1031621R


title: PCGA-01-0008-089-22263-01194BX-1031624R


title: PCGA-01-0008-074-22263-01191BX-1031623R


title: PCGA-01-0018-050-22732-01146BX-1031617R


title: PCGA-01-0022-070-21996-01169BX-1031619R


title: PCGA-01-0015-011-17129-00932BX-1031579R


title: PCGA-01-0018-074-22732-01145BX-1031616R


title: PCGA-01-0001-037-20126-01120BX-1031613R


title: PCGA-01-0028-050-24262-01265BX-1031636R


title: PCGA-01-0006-037-21015-01279BX-1031639R


title: PCGA-01-0001-077-20126-01115BX-1031608R


title: PCGA-01-0025-074-21689-01105BX-1031603R


title: PCGA-01-0001-089-20126-01118BX-1031611R


title: PCGA-01-0025-048-21689-01106BX-1031604R


title: PCGA-01-0001-029-20126-01119BX-1031612R


title: PCGA-01-0021-025-20449-01091BX-1031600R


title: PCGA-01-0031-021-24726-01062BX-1031595R


title: PCGA-01-0031-053-24726-01061BX-1031594R


title: PCGA-01-0001-074-20126-01116BX-1031609R


title: PCGA-01-0031-050-24726-01063BX-1031596R


title: PCGA-01-0025-094-21689-01107BX-1031605R


title: PCGA-01-0021-050-20449-01092BX-1031601R


title: PCGA-01-0025-050-21689-01108BX-1031606R


title: PCGA-01-0021-070-20449-01089BX-1031598R


title: PCGA-01-0001-070-20126-01117BX-1031610R


title: PCGA-01-0031-074-24726-01060BX-1031593R


title: PCGA-01-0009-061-23882-00992BX-1031591R


title: PCGA-01-0009-053-23882-00991BX-1031590R


title: PCGA-01-0003-089-24730-00947BX-1031587R


title: PCGA-01-0001-029-19762-00897BX-1007485R


title: PCGA-01-0009-092-23497-00846BX-1007468R


title: PCGA-01-0008-074-21682-00837BX-1007461R


title: PCGA-01-0025-094-21164-00806BX-1007443R


title: PCGA-01-0008-050-21682-00841BX-1007465R


title: PCGA-01-0006-037-20238-00776BX-1007437R


title: PCGA-01-0012-050-21101-00736BX-1007424R


title: PCGA-01-0028-041-23527-00757BX-1007431R


title: PCGA-01-0032-088-24051-00544BX-1007572R


title: PCGA-01-0001-074-19762-00901BX-1007489R


title: PCGA-01-0001-077-19762-00899BX-1007487R


title: PCGA-01-0001-089-19762-00900BX-1007488R


title: PCGA-01-0022-070-21548-00876BX-1007482R


title: PCGA-01-0001-037-19762-00898BX-1007486R


title: PCGA-01-0031-053-24285-00855BX-1007473R


title: PCGA-01-0014-010-20177-00395BX-1007543R


title: PCGA-01-0001-076-19300-00585BX-1007581R


title: PCGA-01-0031-074-24285-00854BX-1007472R


title: PCGA-01-0026-089-22473-00859BX-1007475R


title: PCGA-01-0001-070-19762-00902BX-1007490R


title: PCGA-01-0021-025-19266-00319BX-1007385R


title: PCGA-01-0022-093-21548-00878BX-1007484R


title: PCGA-01-0017-052-20422-00850BX-1007470R


title: PCGA-01-0017-089-20422-00849BX-1007469R


title: PCGA-01-0015-025-16954-00864BX-1007478R


title: PCGA-01-0009-061-23497-00845BX-1007467R


title: PCGA-01-0009-053-23497-00844BX-1007466R


title: PCGA-01-0008-089-21682-00838BX-1007462R


title: PCGA-01-0008-045-21682-00840BX-1007464R


title: PCGA-01-0023-048-21429-00829BX-1007459R


title: PCGA-01-0023-010-21429-00830BX-1007460R


title: PCGA-01-0023-050-21429-00828BX-1007458R


title: PCGA-01-0008-010-21682-00839BX-1007463R


title: PCGA-01-0001-050-19762-00903BX-1007491R


title: PCGA-01-0023-089-21429-00825BX-1007455R


title: PCGA-01-0023-066-21429-00824BX-1007454R


title: PCGA-01-0023-026-21429-00827BX-1007457R


title: PCGA-01-0029-048-22678-00815BX-1007450R


title: PCGA-01-0029-093-22678-00813BX-1007448R


title: PCGA-01-0029-089-22678-00811BX-1007446R


title: PCGA-01-0029-070-22678-00810BX-1007445R


title: PCGA-01-0029-045-22678-00814BX-1007449R


title: PCGA-01-0029-050-22678-00816BX-1007451R


title: PCGA-01-0017-086-19883-00471BR-1007365R


title: PCGA-01-0031-050-24285-00856BX-1007474R


title: PCGA-01-0024-050-24050-00780BX-1007439R


title: PCGA-01-0020-048-24050-00784BX-1007441R


title: PCGA-01-0025-050-21164-00807BX-1007444R


title: PCGA-01-0028-050-23527-00758BX-1007432R


title: PCGA-01-0020-094-24050-00783BX-1007440R


title: PCGA-01-0014-010-20660-00748BX-1007430R


title: PCGA-01-0014-053-20660-00745BX-1007427R


title: PCGA-01-0014-011-20660-00747BX-1007429R


title: PCGA-01-0029-061-22678-00812BX-1007447R


title: PCGA-01-0025-074-21164-00805BX-1007442R


title: PCGA-01-0017-089-20261-00731BX-1007421R


title: PCGA-01-0005-050-17489-00728BX-1007420R


title: PCGA-01-0005-019-17489-00727BX-1007419R


title: PCGA-01-0021-050-19826-00724BX-1007418R


title: PCGA-01-0023-061-21429-00826BX-1007456R