title: Subject L63, no dysplasia

tag: tissue

tag: age

tag: unique alignments

tag: read 1 alignment

tag: properly paired alignments

tag: genebody 80/20 ratio

tag: mean gc content


title: Lysate Input 4000 cells rep 3

status: Public on May 25 2017

type: SRA

city: Carlsbad

first: Joanne

last: Yeakley

state: CA

address: 1945 Camino Vida Roble Ste i

country: USA

institute: BioSpyder Technologies, Inc.

description: processed data file: Lysate Input Titration Read Counts.xlsx

library_source: transcriptomic

data_processing:
base calling on instrument with RTA
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
then bcl2fastq v2.17.1.14 or v2.18.0.12 for demultiplexing and generating fastqs
fastqs were aligned to a pseudo transcriptome using Bowtie, allowing up to 2 mis-matches.
Genome_build: Multiple pseudo transcriptomes and hg38 (for GSM2422725 to GSM2422736). Processed data files include the sequences used for alignment in column "Probe_Sequence".
Supplementary_files_format_and_content: Probe_ID (genes) in column 1, Probe_Sequence used for alignment in column 2, Accession Number in column 3. Sample Names in row 1.

molecule: total RNA

organism: Homo sapiens

source_name: MDA MB 231 cell line

growth_protocol: Cell lines were grown in DME with 10% FBS under 5% CO2 in 96-well plates.

extract_protocol:
Cells were washed with 1X PBS, then lysed in 1X Lysis Buffer (BioSpyder Technologies, Inc.) at ~2,000 cells/uL, and stored at -80C.
TempO-Seq targeted expression assay. Addition of adapters by amplification.

tag: cell line

value: MDA MB 231

tag: sample preparation

value: homogeneous cell lysate

tag: input

value: 4000 cells

tag: source material manufacturer

value: BioSpyder


title: Subject L62, dysplasia

city: Boston

first: Jennifer

last: Beane

state: MA

address: 72 East Concord Street, E6

department: School of Medicine

institute: Boston University

data_processing:
Demultiplexing and creation of FASTQ files was performed using Illumina CASAVA v1.8.2 software.
The FASTQ files were aligned to hg19 using TopHat v2.0.4 software and default parameters in addition to the mean insert size and standard deviation determined using MISO based on an initial TopHat alignment.
Alignment and quality metrics, including genebody ratio, were calculated using RSeQC v2.3.3.
Gene count estimates were derived using HTSeq-count v0.5.4 with Python v2.7.3 and the Ensembl v64 GTF annotation file.
Gene filtering was conducted on normalized counts per million (cpm) calculated using R v3.0.0 and edgeR v3.4.2 using a modified version of the mixture model in the SCAN.UPC Bioconductor package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited matrices includes raw count values for each Sample and each filtered Gene, CPM values for each Sample and each filtered Gene, RPKM values for each Sample and each filtered Gene, raw count values for each Sample and each filtered Gene, and RPKM values for each Sample and each filtered Gene

molecule: polyA RNA

source_name: Bronchial brushing

extract_protocol:
Bronchial airway brushings were obtained during autofluorescence bronchoscopy. Autofluorescence bronchoscopy and endobronchial biopsy were used to identify and sample PMLs (if present). The pathological grade of the lesions with the worst histology present was recorded. Total RNA was extracted from bronchial brushings using miRNeasy Mini kit (Qiagen) according to manufacturer's protocol.
Sequencing libraries were prepared from total RNA samples using Illumina® TruSeq® RNA Sample Preparation Kit v2. The libraries from individual samples were pooled in groups of four for cluster generation on the Illumina® cBot® using Illumina® TruSeq® Paired-End Cluster Kit. Each sample was sequenced on the Illumina® HiSeq® 2500 to generate paired-end 100 nucleotide reads

value: Bronchial brushing

tag: Sex

value: Male

tag: smoking status

value: Former smoker

tag: pack years

tag: copd status

value: No COPD

tag: max histology

value: Mild dysplasia

tag: dysplasia status

value: Dysplasia

tag: total alignments

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: non-splice alignments

tag: splice alignments


title: Subject L61, dysplasia

tag: tissue

tag: age

value: Female

value: Current smoker

tag: unique alignments

tag: read 1 alignment

tag: properly paired alignments

tag: genebody 80/20 ratio

tag: mean gc content


title: RNA Input Universal Ref RNA 0_0001 ng rep 3

description: processed data file: RNA Input Titration Read Counts.xlsx

source_name: pooled cell lines

tag: cell line

value: mixture

tag: sample preparation

value: purified total RNA

tag: input

tag: source material manufacturer

value: Agilent


title: Lysate Input 4000 cells rep 1


title: Subject L6, dysplasia

tag: Sex

tag: smoking status

tag: pack years

tag: copd status

value: COPD

tag: max histology

tag: dysplasia status

tag: total alignments


title: RNA Input Universal Ref RNA 0_0001 ng rep 1


title: Subject L60, dysplasia

tag: tissue

tag: age

value: Moderate dysplasia

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: non-splice alignments

tag: splice alignments


title: Subject L68, dysplasia

tag: unique alignments

tag: read 1 alignment

tag: properly paired alignments

tag: genebody 80/20 ratio

tag: mean gc content


title: RNA Input Universal Ref RNA 0_001 ng rep 2

tag: cell line

tag: sample preparation

tag: input

tag: source material manufacturer


title: RNA Input Universal Ref RNA 0_001 ng rep 3


title: Subject L58, no dysplasia

tag: Sex

tag: smoking status

tag: pack years

tag: copd status

tag: max histology

value: Hyperplasia

tag: dysplasia status

value: Normal

tag: total alignments


title: RNA Input Universal Ref RNA 0_01 ng rep 3


title: Subject L57, dysplasia

tag: tissue

tag: age

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: non-splice alignments

tag: splice alignments


title: Subject L55, dysplasia

tag: unique alignments

tag: read 1 alignment

tag: properly paired alignments

tag: genebody 80/20 ratio

tag: mean gc content


title: RNA Input Universal Ref RNA 0_001 ng rep 1

tag: cell line

tag: sample preparation

tag: input

tag: source material manufacturer


title: RNA Input Universal Ref RNA 0_01 ng rep 2


title: Subject L64, dysplasia

tag: Sex

tag: smoking status

tag: pack years

tag: copd status

tag: max histology

tag: dysplasia status

tag: total alignments


title: Subject L54, no dysplasia

tag: tissue

tag: age

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: non-splice alignments

tag: splice alignments


title: RNA Input Universal Ref RNA 0_01 ng rep 1

tag: cell line

tag: sample preparation


title: RNA Input Universal Ref RNA 0_1 ng rep 3

tag: input

tag: source material manufacturer


title: Subject L53, dysplasia

tag: Sex

tag: smoking status

tag: unique alignments

tag: read 1 alignment

tag: properly paired alignments

tag: genebody 80/20 ratio

tag: mean gc content


title: Subject L52, no dysplasia

tag: tissue

tag: age

tag: pack years

tag: copd status

tag: max histology

tag: dysplasia status

tag: total alignments


title: RNA Input Universal Ref RNA 0_1 ng rep 1

tag: cell line

tag: sample preparation


title: Subject L51, no dysplasia

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: non-splice alignments

tag: splice alignments


title: Subject L59, no dysplasia

tag: Sex

tag: smoking status

tag: unique alignments

tag: read 1 alignment

tag: properly paired alignments


title: Subject L50, dysplasia

tag: tissue

tag: age

tag: pack years

tag: genebody 80/20 ratio

tag: mean gc content


title: Subject L65, dysplasia

tag: copd status

tag: max histology

tag: dysplasia status

tag: total alignments


title: RNA Input Universal Ref RNA 1 ng rep 3

tag: cell line

tag: sample preparation

tag: input

value: 1 ng

tag: source material manufacturer


title: RNA Input Universal Ref RNA 1 ng rep 2


title: Subject L49, no dysplasia

tag: Sex

tag: smoking status

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: non-splice alignments

tag: splice alignments


title: Subject L5, dysplasia

tag: tissue

tag: age

tag: pack years

tag: unique alignments

tag: read 1 alignment

tag: properly paired alignments

tag: genebody 80/20 ratio


title: RNA Input Universal Ref RNA 1 ng rep 1

tag: cell line

tag: sample preparation


title: Subject L48, no dysplasia

tag: copd status

tag: max histology

tag: dysplasia status

tag: total alignments

tag: mean gc content


title: Subject L47, dysplasia

tag: Sex

tag: smoking status

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments


title: Subject L56, dysplasia

tag: tissue

tag: age

tag: pack years

tag: non-splice alignments

tag: splice alignments


title: RNA Input Universal Ref RNA 10 ng rep 1

tag: cell line

tag: input

value: 10 ng

tag: source material manufacturer


title: Subject L45, dysplasia

value: Bronchial brushing

tag: copd status

tag: max histology

tag: unique alignments

tag: read 1 alignment

tag: properly paired alignments

tag: genebody 80/20 ratio


title: RNA Input Universal Ref RNA 10 ng rep 2

tag: sample preparation


title: Subject L44, dysplasia

tag: Sex

value: Male

tag: smoking status

tag: dysplasia status

tag: total alignments

tag: read 2 alignment

tag: positive strand alignments

tag: mean gc content


title: RNA Input Universal Ref RNA 10 ng rep 3

tag: cell line


title: RNA Input Universal Ref RNA 100 ng rep 2

tag: input


title: Subject L46, dysplasia

tag: tissue

tag: age

value: Former smoker

tag: pack years

tag: negative strand alignments

tag: non-splice alignments

tag: splice alignments


title: Subject L42, no dysplasia

tag: copd status

tag: max histology

tag: unique alignments

tag: read 1 alignment

tag: properly paired alignments

tag: genebody 80/20 ratio


title: RNA Input Universal Ref RNA 0_1 ng rep 2

tag: sample preparation

tag: source material manufacturer


title: RNA Input Universal Ref RNA 100 ng rep 3


title: Subject L43, dysplasia

tag: Sex

tag: smoking status

value: No COPD

tag: dysplasia status

tag: total alignments

tag: read 2 alignment

tag: positive strand alignments

tag: mean gc content


title: Subject L40, no dysplasia

tag: tissue

tag: age

tag: pack years

tag: negative strand alignments

tag: non-splice alignments


title: RNA Input Universal Ref RNA 0_0001 ng rep 2

tag: cell line

tag: input


title: Repeatability Universal Ref RNA 100 ng rep 2

description: processed data file: Repeatability Read Counts.xlsx


title: Subject L41, no dysplasia

tag: copd status

tag: max histology

tag: unique alignments

tag: read 1 alignment

tag: splice alignments

tag: properly paired alignments

tag: genebody 80/20 ratio


title: Repeatability Universal Ref RNA 100 ng rep 1

tag: sample preparation

tag: source material manufacturer


title: Subject L4, dysplasia

tag: Sex

tag: smoking status

tag: dysplasia status

tag: total alignments

tag: read 2 alignment

tag: positive strand alignments

tag: mean gc content


title: Repeatability Ref Brain 100 ng rep 3

tag: cell line

tag: input


title: Repeatability Ref Brain 100 ng rep 2


title: Subject L38, no dysplasia

tag: tissue

tag: age

tag: pack years

tag: copd status

tag: max histology

tag: negative strand alignments

tag: non-splice alignments


title: Subject L37, dysplasia

value: Severe dysplasia

tag: unique alignments

tag: read 1 alignment

tag: splice alignments

tag: properly paired alignments

tag: genebody 80/20 ratio


title: Subject L35, dysplasia

tag: Sex

tag: smoking status

value: Mild dysplasia

tag: dysplasia status

value: Dysplasia

tag: total alignments

tag: read 2 alignment


title: TSN1

city: Rochester

first: Lynne

last: Maquat

state: NY

address: 601 Elmwood Ave

department: Biochemistry and Biophysics

institute: University of Rochester

data_processing:
For each read, the insert sequence 5' to the Illumina adaptor TGGAATTCT was extracted with an in-house perl script. Only inserts in the range of 15-24 bp were used.
BOWTIE2 was used to map them to mature miRNAs
only miRNAs with raw counts >=10 in all six samples are retained,
Raw reads where normalized by dividing the number of reads by the total number of mapped reads in millions, i.e., RPM
Genome_build: miRBase Release 21
Supplementary_files_format_and_content: EXCEL spreadsheet format. Raw and normalized number of reads mapped to each mature microRNA

growth_protocol: HEK293T cells were propagated in Dulbecco’s Modified Eagle’s Medium (Gibco) supplemented with 10% fetal bovine serum.

extract_protocol:
RNA fractions enriched in < 200-nt RNAs were purified from cell pellets using miRNeasy and RNeasy MinElute Cleanup Kits (Qiagen).
cDNA libraries were generated using the TruSeq Small RNA library preparation protocol (Illumina). After addition of the TruSeq 3′ adapter (5′ adenylated) using truncated T4 RNA ligase II (New England Biolabs) and, subsequently, the 5′ adapter using T4 RNA ligase I (New England Biolabs), RNA was reverse-transcribed using a 3′ adapter-specific primer. The resulting cDNA was then amplified using 12 cycles of PCR, a universal forward primer and a reverse primer, the latter of which harbors a bar code. cDNA libraries were purified from 8% polyacrylamide and quantified first using an Agilent Bioanalyzer and subsequently using qPCR. Barcoded libraries were mixed at equimolar concentrations and sequenced using a NextSeq 500 machine (Illumina).

tag: cell line

tag: transfected with

value: Tudor-SN siRNA

tag: molecule subtype

value: RNA fractions enriched in < 200-nt RNAs


title: control3_S6

value: Control (Ctl) siRNA


title: TSN2


title: TSN3


title: RNA Input Universal Ref RNA 100 ng rep 1

value: mixture

tag: sample preparation

value: purified total RNA

tag: input

tag: source material manufacturer

value: Agilent


title: Repeatability Universal Ref RNA 100 ng rep 3


title: control2_S5


title: Subject L32, no dysplasia

tag: tissue

tag: age

value: Female

tag: pack years

tag: copd status

tag: max histology

tag: positive strand alignments

tag: negative strand alignments

tag: non-splice alignments

tag: mean gc content


title: Subject L31, no dysplasia

tag: Sex

tag: smoking status

value: Hyperplasia

tag: dysplasia status

value: Normal

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: splice alignments

tag: properly paired alignments

tag: genebody 80/20 ratio


title: Subject L30, no dysplasia

tag: tissue

tag: age

value: Current smoker

tag: read 2 alignment


title: Subject L29, dysplasia

value: Bronchial brushing

tag: pack years

tag: copd status

value: COPD

tag: max histology


title: control1_S4

tag: cell line

tag: transfected with

tag: molecule subtype


title: Subject L3, dysplasia

tag: Sex

value: Male

tag: smoking status

tag: positive strand alignments

tag: negative strand alignments

tag: non-splice alignments

tag: mean gc content


title: Subject L39, dysplasia

value: Former smoker

value: No COPD

value: Moderate dysplasia

tag: dysplasia status

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: splice alignments

tag: properly paired alignments


title: 5C_CTCF-AID-TetO-CTCF_untreated_rep1

city: San Francisco

first: Elphege

last: Nora

address: 555 Mission Bay Boulevard South

department: Cardiovascular Research Institute

institute: University of California San Francisco

library_source: genomic

data_processing:
ChIP-seq and ChIP-exo. Fastq files were trimmed using the fastq-mcf program, aligned to the mm9 reference genome with bowtie2 (Langmead and Salzberg, 2012). Reads with a mapq score of 30 or greater were retained, using Samtools. PCR duplicates were filtered out. for CTCF peaks were called using the geome wide Event finding and Motif Discovery (GEM) algorithm. For H3K27me3 peaks that are broader we used a threshold-based method.
RNA-seq. Alignment was produced using STAR version 2.5.0a , aligned to mm9. Cufflinks version 2.2.1  with Bedtools version 2.17.0 were used as to produce input for differential expression analysis with Cuffdiff . Genes with an FPKM below 1.1 in all conditions were not considered in the differential expression analysis
Hi-C. We mapped the sequence of Hi-C molecules to reference mouse genome assembly mm9 using Bowtie 2.2.8 and the iterative mapping strategy, as described in  (Imakaev et al., 2012; Lajoie et al., 2015). Upon filtering PCR duplicates and reads mapped to multiple or zero locations, we aggregated the reads pairs into 20kb and 100kb genomic bins to produce Hi-C contact matrices. To remove the short-range Hi-C artifacts - unligated and self-ligated Hi-C molecules - we ignored the contacts mapping to the same or adjacent genomic bins in all downstream analyses.
5C. Adapters were trimmed and aligment was performed using Bowtie2 against a pseudo-genome composed of all possible Forward-Reverse pairs of 5C oligonucleotides and matrices were analyzed using my5C (Lajoie et al. 2009 Nature Methods).
Genome_build: mm9
Supplementary_files_format_and_content: 5C - for all forward-reverse possible ligation pair we provide one file with raw 5C counts (not read normalized, including anchors ultimately removed from analysis), and one file with anchor filtered symmetrical read-normalized balanced (Iterative Correction method - ICE) matrices.
Supplementary_files_format_and_content: ChIP-seq and ChIP-exo. _Peaks.bed: position of the peaks. _Footprints.bed: position of ChIP-exo footprint. _tagDensity.bw: ChIP signal.
Supplementary_files_format_and_content: RNA-seq. .bw: tagDensity of signal.

molecule: genomic DNA

organism: Mus musculus

source_name: mouse ES cells E14Tg2a

growth_protocol: E14Tg2a (karyotype 19, XY; 129/Ola isogenic background) and subclones were cultured in DMEM+Glutamax (ThermoFisher cat 10566-016) supplemented with 15% Fetal Bovine Serum (ThermoFisher SH30071.03), 550µM b-mercaptoethanol (ThermoFisher 21985-023), 1mM Sodium Pyruvate (ThermoFisher 11360-070), 1X non-essential amino-acids (ThermoFisher 11140-50) and 104U of Leukemia inhibitory factor (Millipore ESG1107). Cells were maintained at a density of 0.2-1.5x105 cells / cm² by passaging using TrypLE (12563011) every 24-48h on 0.1% gelatin-coated dishes (Millipore cat ES-006-B) at 37°C and 7% CO2. Medium was changed daily when cells were not passaged. Cells were checked for mycoplasma infection every 3-4 months and tested negative. mouse ES cells were targeted to insert an Auxin-Inducible Degron (AID) tag together with an eGFP cassette, and the auxin receptor OsTir1 was expressed from a transgene. ChIP-seq, Hi-C, 5C and RNA-seq were performed at different timepoints after adding auxin to the culture medium.

extract_protocol:
For ChIP-seq cells were  trypsinized and fixed in suspension; For Chromosome Conformation Capture cells were fixed in tissue culture plates and scrapped off; For RNA-seq cells werre washed once with PBS and lysed in Trizol in the tissue culture plate.
ChIP libraries were prepared using standard Illumina protocols; RNA-seq libraries were assembled using the non-stranded kit E7530L from NEB; 5C (in-situ ligation) and Hi-C (dilution ligation) were assembled based on Illumina-compatible protocols. Detailed experimental procedures can be found in the supplementary information of Nora et al. 2017 Cell
ChIP-seq, ChIP-exo, RNA-seq, Hi-C, 5C

treatment_protocol: For induction of the auxin-inducible degron indole-3-acetic acid (IAA, chemical analog of auxin) was added in the medium at 500µM from a 1000X stock diluted in sterile water and kept at 4°C up to 4 weeks or -20°C for long term storage.

tag: strain

value: 129/Ola, XY

tag: genotype

value: WT-untagged

tag: chip epitope


title: 5C_CTCF-AIDline5_untreated_rep1


title: Repeatability Ref Brain 100 ng rep 1

tag: cell line

tag: sample preparation

tag: input

tag: source material manufacturer


title: Subject L28, no dysplasia

tag: tissue

tag: age

tag: Sex

tag: smoking status

tag: pack years

tag: copd status

tag: max histology

tag: read 2 alignment

tag: positive strand alignments

tag: genebody 80/20 ratio


title: 5C_CTCF-AIDline4_auxin1day_rep1

tag: strain


title: Subject L36, dysplasia

tag: dysplasia status

value: Dysplasia

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: negative strand alignments

tag: non-splice alignments

tag: splice alignments

tag: properly paired alignments

tag: mean gc content


title: 5C_CTCF-AIDline4_untreated_rep1

tag: genotype

tag: chip epitope


title: Subject L27, no dysplasia

tag: tissue

tag: age

tag: Sex

tag: smoking status

tag: pack years

tag: copd status


title: Subject L26, no dysplasia

tag: max histology

tag: dysplasia status

tag: read 2 alignment

tag: positive strand alignments

tag: genebody 80/20 ratio


title: 5C_CTCF-AIDline3_auxin1day_rep1

tag: strain


title: Subject L33, no dysplasia

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: negative strand alignments

tag: non-splice alignments

tag: splice alignments


title: Subject L34, dysplasia

tag: tissue

tag: age

tag: properly paired alignments

tag: mean gc content


title: Subject L24, dysplasia

tag: Sex

tag: smoking status

tag: pack years

tag: copd status

value: Mild dysplasia


title: 5C_CTCF-AIDline3_untreated_rep1

tag: genotype

tag: chip epitope


title: Subject L23, no dysplasia

tag: max histology

tag: dysplasia status

tag: read 2 alignment

tag: positive strand alignments

tag: genebody 80/20 ratio


title: 5C_CTCF-AIDline2_auxin1day_rep1

tag: strain


title: 5C_CTCF-AIDline2_untreated_rep1


title: Subject L22, dysplasia

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: negative strand alignments

tag: non-splice alignments

tag: splice alignments


title: 5C_CTCF-AID-TetO-CTCF_auxin1day_rep1


title: Subject L25, no dysplasia

tag: tissue

tag: age

tag: Sex

tag: smoking status

tag: properly paired alignments

tag: mean gc content


title: 5C_CTCF-AIDline5_auxin1day_rep1

tag: genotype

tag: chip epitope


title: Subject L21, dysplasia

tag: pack years

tag: copd status

tag: max histology

tag: dysplasia status

tag: read 2 alignment

tag: positive strand alignments


title: 5C_CTCF-AID-noTir1_auxin1day_rep1

tag: strain


title: 5C_CTCF-AID-noTir1_untreated_rep1


title: Subject L2, no dysplasia

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: negative strand alignments

tag: non-splice alignments

tag: genebody 80/20 ratio


title: Subject L19, dysplasia

tag: tissue

tag: age

tag: Sex

tag: smoking status

tag: splice alignments

tag: properly paired alignments


title: 5C_WT-untagged_auxin1day_rep1

tag: genotype

tag: chip epitope


title: 5C_WT-untagged_untreated_rep2


title: Subject L18, dysplasia

tag: pack years

tag: copd status

tag: max histology

tag: dysplasia status

tag: read 2 alignment

tag: mean gc content


title: 5C_CTCF-AID_auxin2days25µM_rep2

tag: strain


title: Subject L17, dysplasia

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: non-splice alignments


title: 5C_CTCF-AID_auxin2days25µM_rep1


title: 5C_CTCF-AID_auxin2days10µM_rep2


title: Subject L16, dysplasia

tag: tissue

tag: age

tag: Sex

tag: smoking status

tag: splice alignments

tag: genebody 80/20 ratio


title: 5C_CTCF-AID_auxin2days10µM_rep1

tag: genotype

tag: chip epitope


title: Subject P18, time point 1, mild dysplasia

data_processing:
Demultiplexing and creation of FASTQ files was performed using Illumina CASAVA v1.8.2 software.
The FASTQ files were aligned to hg19 using TopHat v2.0.4 software and default parameters in addition to the mean insert size and standard deviation determined using MISO based on an initial TopHat alignment.
Alignment and quality metrics, including genebody ratio, were calculated using RSeQC v2.3.3.
Gene count estimates were derived using RSEM v1.2.1, Bowtie v1.0.0, and the Ensembl v74 GTF annotation file.
Gene filtering was conducted on normalized counts per million (cpm) calculated using R v3.0.0 and edgeR v3.4.2 using a modified version of the mixture model in the SCAN.UPC Bioconductor package.
Genome_build: hg19
Supplementary_files_format_and_content: matrix of raw count values for each Sample and each filtered Gene

extract_protocol:
Bronchial airway brushings were obtained during autofluorescence bronchoscopy. Autofluorescence bronchoscopy and endobronchial biopsy were used to identify and sample PMLs (if present). The pathological grade of the lesions with the worst histology present was recorded. Total RNA was extracted from samples using miRNeasy Mini kit (Qiagen) according to manufacturer's protocol.
Sequencing libraries were prepared from total RNA samples using Illumina® TruSeq® RNA Sample Preparation Kit v2. The libraries from individual samples were pooled in groups of 10 for cluster generation on the Illumina® cBot® using Illumina® TruSeq® Paired-End Cluster Kit. Each sample was sequenced on the Illumina® HiSeq® 2500 to generate 100 nucleotide single-end reads.

tag: patient id

tag: time point

value: Ever smoker

tag: pack years

tag: copd status

tag: max histology

tag: dysplasia status

tag: read 2 alignment

tag: properly paired alignments


title: 5C_CTCF-AID_auxin2days5µM_rep2

tag: strain


title: Subject L14, dysplasia

tag: tissue

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: non-splice alignments

tag: mean gc content


title: 5C_CTCF-AID_auxin2days5µM_rep1

tag: genotype

tag: chip epitope


title: Subject L13, dysplasia

tag: age

tag: Sex

tag: smoking status

tag: pack years

tag: splice alignments

tag: genebody 80/20 ratio


title: Subject L12, dysplasia

tag: copd status

tag: max histology

tag: dysplasia status

tag: read 2 alignment

tag: properly paired alignments


title: 5C_CTCF-AID_washoff2days_rep2

tag: strain


title: 5C_CTCF-AID_auxin4days_rep2


title: Subject L11, dysplasia

tag: tissue

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: positive strand alignments

tag: negative strand alignments


title: 5C_CTCF-AID_auxin2days_rep2

tag: genotype

tag: chip epitope


title: Subject L20, no dysplasia

tag: age

tag: Sex

tag: smoking status

tag: pack years

tag: non-splice alignments

tag: mean gc content


title: Subject L1, dysplasia

tag: copd status

tag: max histology

tag: dysplasia status

tag: read 2 alignment

tag: splice alignments

tag: genebody 80/20 ratio


title: 5C_CTCF-AID_auxin1day_rep2

tag: strain


title: Subject L10, dysplasia

tag: tissue

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: positive strand alignments

tag: properly paired alignments


title: 5C_CTCF-AID_untreated_rep2

tag: genotype

tag: chip epitope


title: 5C_CTCF-AID_washoff2days_rep1


title: 5C_CTCF-AID_auxin4days_rep1


title: 5C_CTCF-AID_auxin2days_rep1


title: 5C_CTCF-AID_washoff2days_rep3


title: 5C_CTCF-AID_auxin2days_rep3


title: 5C_CTCF-AID_auxin1day_rep1


title: 5C_CTCF-AID_untreated_rep1


title: 5C_CTCF-AID_untreated_rep3


title: 5C_WT-untagged_auxin2days_rep1


title: Subject L15, dysplasia

tag: age

tag: Sex

tag: smoking status

tag: pack years

tag: negative strand alignments

tag: non-splice alignments


title: 5C_WT-untagged_untreated_rep1


title: 5C_CTCF-AID-NPC-sublcone_treatment-scheme-11_rep1


title: 5C_CTCF-AID-NPC-sublcone_treatment-scheme-10_rep1


title: 5C_CTCF-AID-NPC-sublcone_treatment-scheme-13_rep1


title: 5C_CTCF-AID-NPC-sublcone_treatment-scheme-9_rep1


title: 5C_CTCF-AID-NPC-sublcone_treatment-scheme-7_rep1


title: 5C_CTCF-AID-NPC-sublcone_treatment-scheme-8_rep1


title: 5C_CTCF-AID-NPC-sublcone_treatment-scheme-3_rep1


title: 5C_CTCF-AID-NPC-sublcone_treatment-scheme-2_rep1


title: 5C_CTCF-AID-NPC-sublcone_treatment-scheme-5_rep1


title: 5C_CTCF-AID-NPC-sublcone_treatment-scheme-1_rep1


title: RNA-seq_WT-untagged_untreated_rep3

description: RNA-seq


title: 5C_CTCF-AID-NPC-sublcone_treatment-scheme-6_rep1


title: 5C_CTCF-AID-NPC-sublcone_treatment-scheme-4_rep1


title: RNA-seq_WT-untagged_auxin4days_rep3

description: RNA-seq


title: RNA-seq_WT-untagged_auxin2days_rep3

description: RNA-seq


title: RNA-seq_WT-untagged_auxin4days_rep2

description: RNA-seq


title: RNA-seq_WT-untagged_auxin4days_rep1

description: RNA-seq


title: RNA-seq_WT-untagged_untreated_rep2

description: RNA-seq


title: 5C_CTCF-AID-NPC-sublcone_treatment-scheme-12_rep1


title: RF-elf18 Rep1

city: Durham

first: Xinnian

last: Dong

state: NC

address: 124 Science Drive

department: Biology

institute: Duke University

description:
ribosomal associated mRNA
processed data file: RS_RF_countbyCDS.txt
Sample ID: MZ1

data_processing:
Library strategy: Ribo-seq
Basecalls performed using CASAVA version 1.8.2
Illumina adapter removal and size filter by FastX
removal of reads aligned to tRNA and rRNA sequences by Bowtie 2.0, default parameters
align reads to genome by Bowtie 2.0, default parameters
assign reads to genes,(exon,CDS), by HT-seq, default parameters
Genome_build: TAIR10
Supplementary_files_format_and_content: countbyexon.txt: tab delimated file of read counts assigned to genes by exons
Supplementary_files_format_and_content: countbyCDS.txt: tab delimated file of read counts assigned to genes by CDS

organism: Arabidopsis thaliana

source_name: leaf tissue

growth_protocol: Plants were grown on soil (Metro Mix 360) at 22 °C under a 12/12-h light/dark cycle

extract_protocol:
Leaves from ~24 three-week-old plants (2 leaves/plant; ~1.0 g) were collected. Tissue was fast frozen and ground in liquid nitrogen. 5 ml cold polysome extraction buffer [PEB; 200 mM Tris pH 9.0, 200 mM KCl, 35 mM MgCl2, 25 mM EGTA, 5 mM DTT, 1 mM phenylmethanesulfonylfluoride (PMSF), 50 μg/ml cycloheximide, 50 μg/ml chloramphenicol, 1% (vol/vol) Brij-35, 1% (vol/vol) Igepal CA630, 1% (vol/vol) Tween 20, 1% (vol/vol) Triton X-100, 1% Sodium deoxycholate (DOC), 1% (vol/vol) polyoxyethylene 10 tridecyl ether (PTE)] was added. After thawing on ice for 10 min, lysate was centrifuged at 4 °C/16,000 g for 2 min. Supernatant was transferred to 40 μm filter falcon tube and centrifuged at 4 °C/7,000 g for 1 min. Supernatant was then transferred into a 2 ml tube and centrifuged at 4 °C/16,000 g for 15 min and this step was repeated once. 0.25 ml lysate was saved for total RNA extraction for making the RNA-seq library. Another 1 ml lysate was layered on top of 0.9 ml sucrose cushion [400 mM Tris•HCl (pH 9.0), 200 mM KCl, 35 mM MgCl2, 1.75 M sucrose, 5 mM DTT, 50 μg/ml chloramphenicol, 50 μg/ml cycloheximide] in an ultracentrifuge tube (#349623, Beckman). The samples were then centrifuged at 4 °C/70 k rpm for 4 h in a TLA100.1 rotor. The pellet was washed twice with cold water, resuspended in 300 μl RNase I digestion buffer [RNID; 20 mM Tris•HCl (pH 7.4), 140 mM KCl, 35 mM MgCl2, 50 μg/mL cycloheximide, 50 μg/ml chloramphenicol]11 and then transferred to a new tube for brief centrifugation. The supernatant was then transferred to another new tube where 10 μl RNase I (100 U/μl) was added for 60 min incubation at 25 °C/300 rpm. 15 μl SUPERase-In (20 U/μl) was then added to stop reaction.
For RF library, ribosome recovery, footprint fragment purification, PNK treatment and linker ligation were performed according to the public protocol (Ingolia et al.,, 2012, Nature protocol). 2.5 μl 5’ deadenylase (NEB) was then added to the ligation system and incubated at 30 °C for 1 h. 2.5 μl RecJf exonuclease (NEB) was subsequently added for 1 h incubation at 37 °C. The enzymes were inactivated at 70 °C for 20 min and 10 μl of the samples were taken as template for reverse transcription. The rest of steps for the library construction were performedaccording to the public protocol (Ingolia et al., 2012, Nature protocol) except biotinylated oligos, rRNA1 and rRNA2, for Arabidopsis according to another reported method Juntawong et al., 2014, PNAS). For RNA-seq library, 0.75 ml TRIzol® LS (Ambion) was added to the 0.25 ml lysate saved from the Ribo-seq library construction. Total RNA was extracted, quantified and qualified using Nanodrop (Thermo Fisher Scientific Inc). 50-75 μg total RNA was used for mRNA purification with Dynabeads® Oligo (dT)25 (Invitrogen). 20 μl of the purified poly (A) mRNA was mixed with 20 μl 2× fragmentation buffer (2 mM EDTA, 10 mM Na2CO3, 90 mM NaHCO3) and incubated for 40 min at 95 °C before cooling on ice. 500 μl of cold water, 1.5 μl of GlycoBlue and 60 μl of cold 3 M sodium acetate were then added to the samples and mixed. Subsequently, 600 μl isopropanol was added before precipitation at -80 °C for at least 30 min. Samples were then centrifuged at 4°C/12,000 rpm for 30 min to remove all liquid and air dried for 10 min before resuspension in 5 μl of 10 mM Tris (pH 8). The rest of the steps were the same as Ribo-seq library preparation from footprint fragment purification.

treatment_protocol: 3-week-old Arabidopsis plants were infiltrated with either 10 μM elf18 or 10 mM MgCl2 as Mock

tag: ecotype

tag: transgene

value: leaf

value: 3 weeks


title: RF-Mock Rep2

description:
ribosomal associated mRNA
processed data file: RS_RF_countbyCDS.txt
Sample ID: MM3


title: RNA-seq_WT-untagged_untreated_rep1

description: RNA-seq

tag: strain


title: RNA-seq_CTCF-AID_washoff2days_rep2

description: RNA-seq

value: CTCF-AID, Tir1


title: RF-elf18 Rep2

description:
ribosomal associated mRNA
processed data file: RS_RF_countbyCDS.txt
Sample ID: MZ3

tag: tissue


title: RNA-seq_WT-untagged_auxin2days_rep1

description: RNA-seq


title: RNA-seq_CTCF-AID_washoff2days_rep3

description: RNA-seq


title: RS-elf18 Rep2

description:
total mRNA
processed data file: RS_countbyexon.txt, RS_RF_countbyCDS.txt
Sample ID: RME3

data_processing:
Basecalls performed using CASAVA version 1.8.2
Illumina adapter removal and size filter by FastX
removal of reads aligned to tRNA and rRNA sequences by Bowtie 2.0, default parameters
align reads to genome by Bowtie 2.0, default parameters
assign reads to genes,(exon,CDS), by HT-seq, default parameters
Genome_build: TAIR10
Supplementary_files_format_and_content: countbyexon.txt: tab delimated file of read counts assigned to genes by exons
Supplementary_files_format_and_content: countbyCDS.txt: tab delimated file of read counts assigned to genes by CDS


title: RF-Mock Rep1

description:
ribosomal associated mRNA
processed data file: RS_RF_countbyCDS.txt
Sample ID: MM2


title: RS-Mock Rep1

description:
total mRNA
processed data file: RS_countbyexon.txt, RS_RF_countbyCDS.txt
Sample ID: RMM2


title: ERCC Mix2 E-6 rep 3

description: processed data file: ERCC Input Titration Read Counts.xlsx

organism: synthetic construct

source_name: in vitro transcription

tag: sample preparation

value: synthetic RNA

tag: input

value: various

tag: source material manufacturer

value: Thermo Fisher


title: ERCC Mix2 E-6 rep 2


title: RS-Mock Rep2

description:
total mRNA
processed data file: RS_countbyexon.txt, RS_RF_countbyCDS.txt
Sample ID: RMM3


title: RNA-seq_CTCF-AID_washoff2days_rep1

description: RNA-seq


title: ERCC Mix2 E-6 rep 1


title: ERCC Mix2 E-5 rep 3


title: RNA-seq_CTCF-AID_auxin1day_rep1

description: RNA-seq


title: ERCC Mix2 E-5 rep 2


title: ERCC Mix2 E-5 rep 4


title: RNA-seq_WT-untagged_auxin2days_rep2

description: RNA-seq


title: Input_for_H3K27me3_ChIP-seq_CTCF-AID_auxin2days_rep2

description: ChIP-seq

value: Input for H3K27me3 ChIP-seq


title: ERCC Mix2 E-5 rep 1


title: RNA-seq_CTCF-AID_untreated_rep1

description: RNA-seq


title: ERCC Mix2 E-4 rep 4


title: RNA-seq_CTCF-AID_auxin2days_rep1

description: RNA-seq


title: RS-elf18 Rep1

description:
total mRNA
processed data file: RS_countbyexon.txt, RS_RF_countbyCDS.txt
Sample ID: RME1


title: ERCC Mix2 E-4 rep 3


title: ERCC Mix2 E-4 rep 2


title: Cell Mix MCF DOs 0.00001% MCF in MDA rep 1

description: processed data file: Cell Titration Read Counts.xlsx

source_name: MCF-7 and MDA MB 231 cell lines

tag: cell line

value: homogeneous cell lysate

value: 4000 cells

value: BioSpyder


title: ERCC Mix2 E-3 rep 4


title: ERCC Mix2 E-6 rep 4


title: Input_for_H3K27me3_ChIP-seq_CTCF-AID_auxin2days_rep1

description: ChIP-seq


title: H3K27me3_ChIP-seq_CTCF-AID_auxin2days_rep2

description: ChIP-seq

value: H3K27me3 (CST 9733) + Spike in antibody (Active Motif 61686)


title: H3K27me3_ChIP-seq_CTCF-AID_untreated_rep2

description: ChIP-seq


title: ERCC Mix2 E-3 rep 3


title: RNA-seq-p18

city: Bethesda

first: Michaela

last: Willi

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

data_processing:
Total RNA-seq signals were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) to filter low-quality reads and the reads were aligned to the mm10 genome assembly using the Bowtie aligner (Langmead et al., Genome Biology, 2009).  The bam file was used to  to illustrate reads (eRNA) for the manuscript.
Genome_build: mm10
Supplementary_files_format_and_content: BowtieAligned_sorted.bam

growth_protocol: Total RNAs were extracted from mammary tissue at day 18 of pregnancy and purified twice with Trizol and RNeasy® Plus Mini Kit (Qiagen, 74134). Ribosomal RNA was removed from 1 μg of total RNAs and cDNA was synthesized using SuperScript II (Invitrogen). Libraries for sequencing were prepared according to the manufacturer’s instructions with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina, RS-122-2201) and paired-end sequencing was done with a HiSeq 2000 instrument (Illumina).

extract_protocol: Libraries for sequencing were prepared using standard Illumina protocols.

value: Mammary gland

tag: state

value: pregnancy day 18

value: wild type


title: H3K27me3_ChIP-seq_CTCF-AID_auxin4days_rep2

description: ChIP-seq

value: 129/Ola, XY

tag: genotype


title: ERCC Mix2 E-3 rep 2


title: H3K27me3_ChIP-seq_CTCF-AID_washoff2days_rep1

description: ChIP-seq

tag: chip epitope


title: ERCC Mix1 E-6 rep 4


title: H3K27me3_ChIP-seq_CTCF-AID_auxin2days_rep1

description: ChIP-seq


title: Spike-in-antibody-only_ChIP-seq_CTCF-AID_untreated_rep2

description: ChIP-seq

value: Input for CTCF ChIP-seq


title: ERCC Mix1 E-6 rep 3


title: H3K27me3_ChIP-seq_CTCF-AID_untreated_rep1

description: ChIP-seq


title: ERCC Mix1 E-6 rep 2


title: ERCC Mix1 E-6 rep 1


title: H3K27me3_ChIP-seq_CTCF-AID_washoff2days_rep2

description: ChIP-seq


title: Spike-in-antibody-only_ChIP-seq_CTCF-AID_untreated_rep1

description: ChIP-seq


title: Input_for_CTCF_ChIP-seq_CTCF-AID_auxin2days_rep2

description: ChIP-seq

value: Spike in antibody only (Active Motif 61686)


title: HeLa fccp rep 1

city: Lausanne

first: Johan

last: Auwerx

address: Station 15

department: SV IBI NCEM

country: Switzerland

institute: École Polytechnique Fédérale de Lausanne

data_processing:
The reads obtained were first trimmed out to remove adaptor sequences and then mapped using a combined pipeline of TopHat2 (Kim et al., 2013a) and bowtie2 (Langmead and Salzberg, 2012) against the Human genome (GRCh37). HTSeq-count (Anders et al., 2015) was then used to obtain the counts of each gene. Differential expressed genes in each condition were identified using R/Bioconductor package edgeR (Robinson et al., 2010).
Genome_build: hg19
Supplementary_files_format_and_content: Normalized counts for all treatments

source_name: HeLa

growth_protocol: DMEM plus L-glutamine and pyruvate with 10% inactivated FBS and penicillin and streptomycin

extract_protocol:
Total RNA extracted from HeLa cells was extracted using RNA was extracted using TRIzol (Life Technologies) and purified by column using RNeasy Mini Kit (QIAGEN).
500ng of total RNA was enriched for Poly (A) RNA and then barcoded libraries for sequencing were prepared using the Lexogen mRNA Sense kit for Ion Torrent according to manufacturer’s standard protocol. Libraries were amplified 13 cycles and the quality of each library was checked on an Agilent Bioanalyzer DNA High Sensitivity chip. The libraries were pooled based on the concentration of each sample between 200-350bp, purified on a Pippin Prep gel, quantified by the Agilent Bioanalyzer and sequenced on an Ion Torrent Proton sequencer at 30x coverage depth .

value: HeLa

tag: treatment

value: FCCP (10 uM)


title: HeLa mb rep 2

value: MitoBloCK-6 (50 uM)


title: HeLa acti rep 1

value: Actinonin (50 uM)


title: HeLa fccp rep 2


title: HeLa mb rep 1


title: ERCC Mix2 E-4 rep 1

value: synthetic RNA

value: various


title: ERCC Mix1 E-5 rep 4

value: Thermo Fisher


title: HeLa dox rep2

value: Doxycycline (30 ug/mL)


title: Input_for_CTCF_ChIP-seq_CTCF-AID_auxin2days_rep1

description: ChIP-seq

value: CTCF-AID, Tir1


title: ERCC Mix1 E-5 rep 3


title: HeLa dox rep1


title: CTCF_ChIP-seq_CTCF-AID_auxin2days_rep2

description: ChIP-seq

value: CTCF (Active Motif 61311) + Spike in antibody (Active Motif 61686)


title: HeLa control rep2

value: DMSO


title: ERCC Mix1 E-5 rep 2


title: H3K27me3_ChIP-seq_CTCF-AID_auxin4days_rep1

description: ChIP-seq

value: H3K27me3 (CST 9733) + Spike in antibody (Active Motif 61686)


title: ERCC Mix1 E-5 rep 1


title: HeLa control rep1


title: CTCF_ChIP-seq_CTCF-AID_untreated_rep2

description: ChIP-seq


title: HeLa acti rep 2


title: ERCC Mix1 E-4 rep 3


title: Specificity IOIIII

description: processed data file: Specificity Read Counts.xlsx

value: mixture

value: purified total RNA

value: Agilent


title: CTCF_ChIP-seq_CTCF-AID_washoff2days_rep1

description: ChIP-seq

value: 129/Ola, XY


title: Specificity IIOIII


title: Specificity OIIIII


title: CTCF_ChIP-seq_CTCF-AID_auxin2days_rep1

description: ChIP-seq


title: CTCF_ChIP-seq_CTCF-AID_untreated_rep1

description: ChIP-seq


title: ERCC Mix1 E-4 rep 1


title: Specificity IIIIOI


title: Specificity IIIIIO


title: ERCC Mix1 E-4 rep 2


title: CTCF_ChIP-seq_CTCF-AID_washoff2days_rep2

description: ChIP-seq


title: multidrug-resistant Candida parapsilosis isolate (run 2)

city: Memphis

first: Katherine

middle: S

last: Barker

state: TN

address: 881 Madison Avenue, Room 305

department: Clinical Pharmacy

institute: University of Tennessee Health Science Center

description:
35176B
Each run represents an independent biological sample for which an independent library was prepared.

data_processing:
Individual sample fragments were concatenated to form the whole sample fastq file.
Files were run through FASTQC to check data quality.  Any reads with a phread score<20 were trimmed.
Read counts for each sample were normalized using transcripts per kilobase million (TPM) method.
Genome_build: Reads were aligned to the C. parapsilosis CDC317 reference transcriptome using RNA-Star long method. Read counts for each sample were normalized using transcripts per kilobase million (TPM) method.
Supplementary_files_format_and_content: Processed data is in the form of an Excel matrix. Reads were aligned to the C. parapsilosis CDC317 reference genome for biological Samples A and B for isolates 1 and 2. Read counts aligned to each genomic feature and normalized counts are listed for each sample.  The .csv files contain the raw read counts for each sample.

organism: Candida parapsilosis

source_name: C. parapsilosis clinical isolate

growth_protocol: Cultures were maintained on YPD agar plates.  To initiate cultures, a single colony was used to inoculate a 2-ml culture of YPD liquid medium, and this culture was grown to saturation overnight at 30 degrees Celsius.  An aliquot of the overnight cultures were then used to inoculate 20 ml YPD liquid culture to achieve a final OD(600)= 0.2.  These cultures were then grown at 30 degrees Celsius for 3 hours at which time cells were collected by centrifugation, supernatants removed, and cell pellets frozen at -80 degrees Celsius until RNA isolation.

extract_protocol:
RNA was isolated using the hot phenol method of RNA isolation.  RNA concentrations were determined using a Nanodrop spectrophotometer, and RNA integrity was verified using a Bioanalyzer 2100.
Barcoded libraries were prepared using the Lexogen mRNA Sense kit for Ion Torrent according to the manufacturer's standard protocol.

tag: fluconazole mic (mg/ml)

tag: voriconazole mic (mg/ml)

tag: itraconazole mic (mg/ml)

tag: caspofungin mic (mg/ml)

tag: micafungin mic (mg/ml)

tag: anidulafungin mic (mg/ml)

tag: amphotericin b mic (mg/ml)


title: multidrug-resistant Candida parapsilosis isolate (run 1)

description:
35176A
Each run represents an independent biological sample for which an independent library was prepared.


title: Specificity IIIIII


title: antifungal-susceptible Candida parapsilosis isolate (run 1)

description:
35177A
Each run represents an independent biological sample for which an independent library was prepared.


title: antifungal-susceptible Candida parapsilosis isolate (run 2)

description:
35177B
Each run represents an independent biological sample for which an independent library was prepared.


title: Specificity IIIOII


title: 164_P0_S_Oo

status: Public on May 24 2017

city: Haifa

first: Hiba

last: Zaidan

state: Israel

address: 199 Aba Khoushy Ave

department: Psychology

country: Israel

institute: University of Haifa

data_processing:
Library strategy: mmPCR-seq
Paired-end sequencing reads were combined and mapped as single-end reads onto a combination of the genome (rn4) and exonic sequences surrounding known splicing junctions using BWA samse.
We used samtools mpileup to count the number of 'A' and 'G' reads at each editing site to calculate the editing levels.
Genome_build: rat genome (rn4, Nov. 2004, Baylor HGSC v. 3.4)
Supplementary_files_format_and_content: The processed data files contain editing level measurements. The columns are formatted: editing site chromosome, editing site position, editing site gene, editing site strand, editing site annotation1, editing site annotation2, sequencing coverage, number of edited reads, editing level.

organism: Rattus norvegicus

source_name: Oocytes

growth_protocol: Adolescent female Sprague-Dawley rats from the PRS group underwent a 7-day unpredictable stress procedure, as previously described (Zaidan et al. 2013). Animals from Control and PRS groups were sacrificed two weeks after the end of the stress procedure.

extract_protocol:
Brains and Oocytes were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. cDNA and primer pools were loaded into the 48.48 Access Array IFC (Fluidigm) and performed target amplification as previously described (Zhang et al. 2014) and was sequenced using NextSeq 500 (Illumina, USA) with 76bp paired-end reads.
RNA libraries were prepared for sequencing using by pooling all of the PCR products for a particular sample and barcoding them uniquely using a 15 cycle PCR reaction.

value: Oocytes

tag: age

tag: Sex

value: Female

tag: generation

value: PRS

tag: strain

value: Sprague-Dawley


title: ERCC Mix1 E-3 rep 3

tag: sample preparation

tag: input

tag: source material manufacturer


title: 1-0b_P0_S_Oo

tag: tissue


title: 167_P0_S_Oo


title: ERCC Mix1 E-4 rep 4


title: 165_P0_S_Oo


title: 4-2s_P0_S_Oo


title: 166_P0_C_Oo

value: Control


title: ERCC Mix1 E-3 rep 4

value: synthetic RNA


title: 170_P0_S_Oo


title: 1-7b_P0_S_Oo


title: 163_P0_C_Oo


title: 1-8b_P0_C_Oo


title: 129_P0_S_PFC

source_name: Brain region

value: PFC


title: 168_P0_C_Oo


title: 169_P0_C_Oo


title: 1-3c_P0_C_Oo


title: ERCC Mix2 E-3 rep 1

value: various

value: Thermo Fisher


title: ERCC Mix1 E-3 rep 1


title: 126_P0_S_PFC


title: 133_P0_S_PFC


title: 159_P0_S_PFC

value: Male


title: ERCC Mix1 E-3 rep 2


title: 158_P0_S_PFC


title: 124_P0_S_PFC


title: 118_P0_S_AMY

value: AMY


title: 116_P0_S_AMY


title: 146_P0_S_AMY


title: 117_P0_S_AMY


title: 115_P0_S_AMY


title: 120_P0_S_AMY


title: 70_P0_S_PFC


title: 67_P0_S_PFC


title: 64_P0_S_PFC


title: 37_P0_S_PFC


title: 39_P0_S_PFC


title: 36_P0_S_PFC


title: 132_P0_S_PFC


title: 55_P0_S_AMY


title: 60_P0_S_AMY


title: 53_P0_S_AMY


title: 52_P0_S_AMY


title: 30_P60_S_PFC


title: 49_P0_S_AMY


title: 24_P60_S_PFC


title: 50_P0_S_AMY


title: 21_P60_S_PFC


title: 10_P60_S_AMY


title: 18_P60_S_PFC


title: 162_P60_S_AMY


title: 33_P60_S_PFC


title: 27_P60_S_PFC


title: 14_P60_S_AMY


title: 6_P60_S_AMY


title: 5_P60_S_AMY


title: 141_P0_C_AMY


title: 16_P60_S_AMY


title: 138_P0_C_AMY


title: 9_P60_S_AMY


title: 142_P0_C_AMY


title: 121_P0_C_AMY


title: 140_P0_C_AMY


title: 136_P0_C_AMY


title: 145_P0_C_AMY


title: 157_P0_C_PFC


title: 160_P0_C_PFC


title: 131_P0_C_PFC


title: 150_P0_C_PFC


title: 155_P0_C_PFC


title: 130_P0_C_PFC


title: 154_P0_C_PFC


title: 11_P60_C_AMY


title: 56_P0_C_AMY


title: 4_P60_C_AMY


title: 61_P0_C_AMY


title: 46_P0_C_AMY


title: 40_P0_C_AMY


title: 17_P60_C_PFC


title: 29_P60_C_PFC


title: MCF7.NicE-seq

city: Ipswish

first: V K Chaithanya

last: Ponnaluri

state: Massachusetts

address: 240 County Road, 3W031

department: Genome Biology

institute: New England Biolabs

data_processing:
Library strategy: NicE-seq
For NicE-seq, adaptor and low quality sequences (Phred score < 20) were trimmed from NicE-seq reads using the trim_galore package (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with the parameter of --paired. Reads were mapped to the human reference genome hg19 using Bowtie2. MACS2 was used to call the peaks with the following parameters: -f BAMPE, -g hs, --broad, --broad-cutoff 0.1, --bedgraph, --keep-dup 1, -m 5 50, --slocal 1000, --llocal 10000
genome build: hg19
processed data files format and content: broadPeak and bedgraph format

source_name: Human mammary gland adenocarcinoma

growth_protocol: HCT116 cells were cultured in McCoy's 5A media supplemented with 10% Fetal Bovine Serum. MCF7 cells were cultured in DMEM media supplemented with 10% of Fetal Bovine Serum.

extract_protocol:
For NicE-seq and ATAC-seq, genomic DNA was extracted using phenol chloroform method.
For NicE-seq, varying number of crosslinked and native cells were used. Nuclei were isolated by incubating the cross-linked cells in cytosolic buffer (15 mM Tris-HCl pH 7.5, 5 mM MgCl2, 60 mM KCl, 0.5 mM DTT, 15 mM NaCl, 300 mM sucrose and 1% NP40) for 10 min on ice with occasional agitation. Nuclei were precipitated by spinning at 1000 × g, 4 °C for 5 min and the supernatant was discarded. Open chromatin DNA was labeled with biotin by incubating the nuclei in presence of 2.5 U of Nt.CviPII (NEB R0626S), 50 U of DNA polymerase I (M0209S) and 30 μM of each dNTP including 6 μM of biotin-14-dATP (Invitrogen, 19524-016) and 6 μM of biotin-16-dCTP (ChemCyte, CC-6003-1) in 200 μL of 1 × NEB buffer 2. Labeling reaction was carried out at 37°C in a thermo-mixer at 800 RPM for 2 h. 20 μL of 0.5 M EDTA and 2 μg of RNase A was added to the labeling reaction and incubated at 37°C for 0.5 h to stop the labeling reaction and digest RNA. Finally DNA-protein cross-linking was reversed by adding 20 μL of proteinase K (NEB, P8107S) and 20 μL of 20% SDS to the reaction and incubating at 65°C for 1 h. Biotin labeled genomic DNA was extracted using phenol chloroform. Open chromatin labeling in native cells was performed without formaldehyde crosslinking step. Biotin-labeled genomic DNA from fixed (HCT116, MCF7 and decitabine treated HCT116 cells) and native (HCT116) reactions were sonicated into 150 bp fragments (Covaris) and 1 μg of DNA was end-repaired, dA-tailed and ligated with NEB Illumina adaptor (NEB, E7370S). Without further purification, the ligation product was mixed with 50 μL of Streptavidin magnetic beads (Invitrogen 65001, blocked using 0.1% cold fish gelatin in 1 × PBS overnight at 4°C) in 1 mL of B&W buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 2 M NaCl). Biotin-labeled open chromatin DNA was captured by streptavidin at 4°C for 2 h with end-over-end rotation. The beads were washed four times with B&W buffer plus 0.005% of Triton X-100 followed by one wash with TE plus Triton X-100. The beads were resuspended in 40 μL of nuclease free water and 4 μL was used for library amplification using PCR (NEB, #E7370S). 10 PCR cycles were usually sufficient to generate the amount of library DNA needed for sequencing.  For library construction using 250 cells, all procedures remained same except addition of 10 μg of glycogen during genomic DNA extraction. In the case of 25 cells, 0.25 U of Nt.CviPII and 5 U of DNA polymerase I were used. The entire DNA was sonicated, 10 μL of streptavidin beads were used to capture the biotinylated DNA and were used as template for library amplification. For input library preparation 1 µg of purified genomic DNA was used instead of the labeled chromatin.

treatment_protocol: Decitabine (5 µM) treatment was given for 6 days. After two days, media was replaced and fresh decitabine was added and incubated for another 4 days.

tag: cell line


title: Oct1 ChIPseq

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

institute: University of Utah

data_processing:
ChIP-seq reads were aligned to the mouse reference genome (mm10) with the Burrows-Wheeler Aligner (BWA, version: 0.5.9).
Genome_build: mm10
Supplementary_files_format_and_content: MACSv2 peak caller (version: 2.1) was used to call ChIP-seq regions of enrichment with the following parameters (-p 1e-5 --nomodel - shiftsize <fragment_length/2> for Oct1, Oct4 and -p 1e-2 --broad for H3K4me3). To estimate the --shiftsize parameter we performed strand cross-correlation analysis using SPP R package (version: 1.10.1) with default parameters.

source_name: Embryonic stem cells

growth_protocol: Embryonic stem cells were grown the media containing LIF and routinely passaged and plated on plates with a layer of feeder MEFs.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIPseq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ESCs were trypsinized and MEFs were allowed to settle on the dish for 2 hours. Feeder depleted ESCs were collected and fixed using 1% formaldehyde for 15 minutes. Formaldehyde was quenced using 0.125M Glycine for 5 minutes. Cells were washed in PBS containing protease inhibitors and sonicated.

value: Embryonic stem cells


title: Oct4 ChIPseq


title: H3K4me3 ChIPseq


title: 20_P60_C_PFC

tag: treatment


title: HCT116.Control.WGBS_run2

data_processing:
For WGBS, adaptor and low quality sequences (Phred score < 20) were trimmed from WGBS reads using the trim_galore package (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with the parameter of --paired. Reads were mapped to the human reference genome hg19 using Bismark with Bowtie2. CpG methylation was extracted from uniquely mapped reads using Bismark methylation extractor with the parameter of -p --no_overlap --merge_non_CpG. Differential methylation analysis was carried out using the bsseq package. Regions with 3 CpG sites and a mean methylation difference of 0.1 across both replicates were considered significantly differentially methylated.
genome build: hg19
processed data files format and content: Bismark output

source_name: Human colorectal carcinoma

extract_protocol:
Genomic DNA for WGBS was extracted using QIAamp gDNA Purification Kit (Qiagen).
For WGBS, 1 μg of genomic DNA from control and 5 µM decitabine treated cells was fragmented by sonication, end-repaired and dA-tailed according to manufacturer’s conditions (New England Biolabs). Methylated NEB Illumina loop adaptor was ligated to DNA (E7370S, New England Biolabs). Ligated library was digested with USER and bisulfite converted using the EZ DNA Methylation Kit (Zymo Research). Libraries were enriched by PCR using EpiMark Hot Start Taq DNA Polymerase (New England Biolabs).


title: 32_P60_C_PFC


title: HCT116.ATAC-seq

data_processing:
For ATAC-seq, adaptor and low quality sequences (Phred score < 20) were trimmed from ATAC-seq reads using the trim_galore package (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with the parameter of --paired. Reads were mapped to the human reference genome hg19 using Bowtie2. MACS2 was used to call the peaks with the following parameters: -f BAMPE, -g hs, --broad, --broad-cutoff 0.1, --bedgraph, --keep-dup 1, -m 5 50, --slocal 1000, --llocal 10000
genome build: hg19
processed data files format and content: broadPeak and bedgraph format

extract_protocol:
For NicE-seq and ATAC-seq, genomic DNA was extracted using phenol chloroform method.
For ATAC-seq, 25000 HCT116 cells were processed according to previously published protocol (Buenrostro et. al, doi:10.1038/nmeth.2688) with the following modifications. After addition of lysis buffer the cell suspension was passed through a 27 G ½ needle six times to facilitate cell lysis. ATAC-seq library was size-selected for 250-500 bp and 75 bp paired-end sequenced on NextSeq 500 Illumina platform.


title: Input


title: 19_P60_C_PFC


title: HCT116.Control.WGBS_run1


title: 68_P0_C_PFC


title: 71_P0_C_PFC


title: 59_P0_C_AMY


title: 66_P0_C_PFC


title: HCT116.Decitabine.WGBS_run1

value: Decitabine treated


title: HCT116.Decitabine.WGBS_run2


title: 3_P60_C_AMY


title: 2_P60_C_AMY


title: 8_P60_C_AMY


title: 69_P0_C_PFC


title: HCT116.25-2.NicE-seq


title: 43_P0_C_PFC


title: HCT116.250.NicE-seq


title: HCT116.2500.NicE-seq


title: HCT116.25-1.NicE-seq


title: EPF_AR_ChIPSeq

city: Montréal

first: Claire

middle: Elizabeth

last: Nash

state: QC

address: 1001 Decarie Blvd

department: Urology

country: Canada

institute: Research Institute of McGill University Health Centre

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 with default parameters
Duplicate reads were removed using MarkDuplicates and uniquely mapped reads were determined using MAPQ score>=25 with Samtools
Peaks were called using MACS 2.0.10 cutoff of p-value = 1e-7
Peaks were called using HOMER with default settings
Shared peaks (called by both algorithms) were determined using HOMER mergePeaks
For WPMY1-AR, peaks called using both EPF and CAF input controls and both peak calling algorithms were combined to make shared peaks file using HOMER mergePeaks
RNAseq reads were aligned to the hg19 genome assembly using Tophat 2.1.0
Uniquely mapped reads were determined using MAPQ score>=25 with Samtools
Read counts were quantified with featureCounts and TPM calculated
bigwig files were generated by converting bedgraph to bigwig files using the Galaxy Bedgraph-bigWig converter. Scores represent treatment pileup
Genome_build: hg19

source_name: Primary Fibroblast

growth_protocol: All cells were maintained in DMEM supplemented with 10% FBS and used at passages between 5 and 7 for all assays

extract_protocol:
Lysates were clarified from sonicated nuclei and AR-DNA complexes were isolated with antibody.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end)

tag: cell type

value: Human fetal prostate fibroblasts

tag: passages

tag: chip antibody

value: AR (Santa Cruz, H280, sc-13062, Lot D0414)


title: EPF_Input_DNA


title: HCT116.Decitabine.NicE-seq


title: HCT116.250000.NicE-seq


title: WPMY-AR_AR_ChIPSeq

source_name: Myofibroblast cell line

value: Myofibroblast cell line that overexpresses AR


title: HCT116.25000.NicE-seq


title: Plate R2; Treatment Milrinone

city: Basel

first: Jitao David

last: Zhang

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

institute: F. Hoffmann-La Roche

data_processing:
Base-calling, filtering, QC, and alignment was handled automatically by IonTorrent Server Suite (version 4.0.2)
Amplicon coverage is reported by IonTorrent Server Suite (version 4.0.2) as a tab-delimited file, which was converted into GCT format by in-house scripts.
Genome_build: hg19
Supplementary_files_format_and_content: GCT format, with amplicon counts for pathway reporter genes in each sample

source_name: iPS-derived cardiomyocytes_Milrinone

growth_protocol: Human iPSC lines were derived from anonymized human skin biopsies following full informed consent and approval by the Partners Healthcare Human Research Committee (Protocol number 2010-P-000122/1). iPSC were generated by retroviral reprogramming using OCT4, SOX2, KLF4 and C-MYC and checked for pluripotency and normality of karyotype. iPSC lines were transferred to CDI (Madison, Wisconsin) for differentiation into cardiomyocytes. Following cardiomyocyte production, culture protocols were identical to those used for the standard cardiomyocytes.

extract_protocol:
Cell were harvested 12 after compound addition by removing the culture medium. Cell lysates in 50 µl RLT buffer (QIAGEN, Hombrechtikon, Switzerland) were immediately frozen and stored at -80°C.
10 ng of total RNA from each sample were reverse transcribed to cDNA by poly-A-priming followed by PCR pre-amplification (15 cycles) according to the protocol supplied with the Ion AmpliSeq™ RNA Library Kit (Life Technologies, Carlsbad, USA, Catalog number 4482335). After primer digestion, adapters and molecular barcodes were ligated to the amplicons followed by magnetic bead purification. This library was amplified, purified and stored at -20°C. Amplicon size and DNA concentration were measured using an Agilent High Sensitivity DNA Kit (Agilent Technologies, Waldbronn, Germany) according to the manufacturer’s recommendation.

treatment_protocol: To screen for drugs that prevent development of the diabetic phenotype, an 80-compound subset of the Screen-well ICCB Known Bioactives library (Enzo life sciences) was used. For each 96-well plate: vehicle control (DMSO); GEC negative control (glucose 1 mM, ET-1 5 nM, cortisol 1 µM) and BM positive control (mDM + bosentan 100 µM, mifepristone 10 µM) and GEC+BM conditions were performed. The remaining wells were treated with mDM plus the test compound at 1 µM. 1 well was used per drug. Following 12 hours of treatment, medium was removed and cells were prepared for molecular phenotyping.

value: iPS-derived cardiomyocytes

tag: plate

tag: compound name

value: Milrinone

tag: time point

value: after 12h of compound treatment

tag: barcode id


title: CAF_AR_RNASeq

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human prostate cancer-associated fibroblasts


title: EPF_AR_RNASeq


title: Plate R1; Treatment Propafenone

source_name: iPS-derived cardiomyocytes_Propafenone

value: Propafenone


title: CAF_AR_ChIPSeq


title: CAF_Input_DNA


title: Plate R1; Treatment 5(S)-HETE

source_name: iPS-derived cardiomyocytes_5(S)-HETE


title: Plate R2; Treatment AG-1296

source_name: iPS-derived cardiomyocytes_AG-1296


title: Plate R2; Treatment GEC_Ctrl

source_name: iPS-derived cardiomyocytes_GEC_Ctrl


title: HCT116.Native.NicE-seq


title: Plate R2; Treatment GEC_MB

source_name: iPS-derived cardiomyocytes_GEC_MB


title: Plate R2; Treatment Tolbutamide

source_name: iPS-derived cardiomyocytes_Tolbutamide

value: Tolbutamide


title: Plate R2; Treatment SDZ-201106

source_name: iPS-derived cardiomyocytes_SDZ-201106


title: Plate B1; Treatment Phenamil

source_name: iPS-derived cardiomyocytes_Phenamil

value: Phenamil


title: Plate B1; Treatment Quinine-HCl-2H2O


title: Plate B1; Treatment Propafenone


title: Plate B1; Treatment Phentolamine

source_name: iPS-derived cardiomyocytes_Phentolamine

value: Phentolamine


title: Plate B1; Treatment Paxilline

source_name: iPS-derived cardiomyocytes_Paxilline

value: Paxilline


title: Plate B1; Treatment media_Ctrl

source_name: iPS-derived cardiomyocytes_media_Ctrl


title: Plate B1; Treatment MB

source_name: iPS-derived cardiomyocytes_MB

value: MB


title: Plate B1; Treatment Niguldipine

source_name: iPS-derived cardiomyocytes_Niguldipine

value: Niguldipine


title: RNA pol II ChIP-seq Rpb1  H1108Y

city: Aurora

first: David

middle: L.

last: Bentley

state: CO

department: Biochemistry and Mol. Genetics

institute: U. Colorado School of Medicine

description: Chromatin IP against RNA total pol II

data_processing:
Single-end 50 base reads (after removing barcodes) or 125 base reads (after removing barcodes and trimming adaptor sequences) were mapped to the hg19 UCSC human genome  or sacCer3 yeast genome with Bowtie version 0.12.5 for ChIP-seq and with Hisat2 version 2.0.4 for t-NET-seq
Genome_build: GRCh37/hg19 assembly or SacCer_Apr2011/sacCer3
Supplementary_files_format_and_content: bigwig or TDF format

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr H1108Y

growth_protocol: Rpb1 WT and mutant cells were grown in DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin, and pen/strep

extract_protocol:
cross-linked Chromatin was sonicated with a Bioruptor
1-2 mg of cross-linked extract was immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, gel purification of ~200bp fragments, and amplification (18cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.

treatment_protocol: Amr Rpb1 was induced with doxycycline (2.0 mg/ml)  for 12-16 hr then treated with a-amanitin (2.5 mg/ml) for a further 42 hr before cross-linking and harvesting for ChIP-seq.

tag: growth conditions

tag: antibody

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)


title: Plate B1; Treatment FPL-64176

source_name: iPS-derived cardiomyocytes_FPL-64176


title: Plate B1; Treatment Flecainide acetate

value: Flecainide acetate


title: Plate B1; Treatment AM 92016-HCl

source_name: iPS-derived cardiomyocytes_AM 92016-HCl


title: Plate A1; Treatment Misoprostol, free acid

source_name: iPS-derived cardiomyocytes_Misoprostol, free acid

value: Misoprostol, free acid


title: Plate A1; Treatment GEC_MB


title: Plate A1; Treatment Lyso-PAF C16

source_name: iPS-derived cardiomyocytes_Lyso-PAF C16

value: Lyso-PAF C16


title: Plate B1; Treatment TTNPB

source_name: iPS-derived cardiomyocytes_TTNPB

value: TTNPB


title: Plate R2; Treatment SKF-96365

source_name: iPS-derived cardiomyocytes_SKF-96365


title: Plate A1; Treatment Farnesylthioacetic acid

value: Farnesylthioacetic acid


title: Plate A1; Treatment Prostaglandin B1

value: iPS-derived cardiomyocytes

value: Prostaglandin B1


title: Plate A1; Treatment Eicosadienoic acid (20:2 n-6)

source_name: iPS-derived cardiomyocytes_Eicosadienoic acid (20:2 n-6)

value: Eicosadienoic acid (20:2 n-6)

value: after 12h of compound treatment


title: Plate A1; Treatment Carbacyclin

source_name: iPS-derived cardiomyocytes_Carbacyclin

value: Carbacyclin


title: Plate A1; Treatment C8 Dihydroceramide

value: C8 Dihydroceramide


title: Plate A1; Treatment MB


title: Plate C1; Treatment MBCQ

source_name: iPS-derived cardiomyocytes_MBCQ

value: MBCQ


title: Plate A1; Treatment 9(S)-HPODE

source_name: iPS-derived cardiomyocytes_9(S)-HPODE


title: Plate B1; Treatment Loperamide-HCl

value: Loperamide-HCl


title: Plate C1; Treatment GEC_Ctrl

source_name: iPS-derived cardiomyocytes_GEC_Ctrl


title: Plate A1; Treatment Prostaglandin J2

value: Prostaglandin J2


title: Plate C1; Treatment 17-Allylamino-geldanamycin


title: Plate A1; Treatment GEC_Ctrl


title: Plate C1; Treatment Tyrphostin AG490

value: Tyrphostin AG490


title: Plate A1; Treatment PAF C18

source_name: iPS-derived cardiomyocytes_PAF C18

value: PAF C18


title: Plate C1; Treatment Aphidicolin

source_name: iPS-derived cardiomyocytes_Aphidicolin

value: Aphidicolin


title: Plate C1; Treatment Rolipram

source_name: iPS-derived cardiomyocytes_Rolipram

value: Rolipram


title: Plate C1; Treatment MB

source_name: iPS-derived cardiomyocytes_MB

value: MB


title: Plate C1; Treatment U-74389G

source_name: iPS-derived cardiomyocytes_U-74389G


title: RNA pol II Ser2-P tNET-seq Rpb1  WT

description:
nascent nuclear RNA
Anti-pol IISer2-P tNET-seq
processed data file: WT_Ser2p_negative.bedgraph.tdf, WT_Ser2p_positive.bedgraph.tdf

data_processing:
Library strategy: tNET-Seq
Single-end 50 base reads (after removing barcodes) or 125 base reads (after removing barcodes and trimming adaptor sequences) were mapped to the hg19 UCSC human genome  or sacCer3 yeast genome with Bowtie version 0.12.5 for ChIP-seq and with Hisat2 version 2.0.4 for t-NET-seq
Genome_build: GRCh37/hg19 assembly or SacCer_Apr2011/sacCer3
Supplementary_files_format_and_content: bigwig or TDF format

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr WT

extract_protocol:
cross-linked Chromatin was sonicated with a Bioruptor
IP's were prepared from DNAseI solublilized nuclear extracts (~1.5X 10E7 cells). RNA was purified by Trizol extraction and processed  using the KAPA RNA-seq kit (#07962169001) to create stand-specific random-primed libraries

value: rabbit anti Ser2-P CTD (Glover-Cutter eta l NSMB. 15:71, 2008)


title: RNA pol II Ser2-P tNET-seq Rpb1  R749H

description:
nascent nuclear RNA
Anti-pol IISer2-P tNET-seq
processed data file: R749H_Ser2p_tNetSeq_negative_bedgraph.tdf, R749H_Ser2p_tNetSeq_postive_bedgraph.tdf

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr R749H


title: Plate C1; Treatment 10-hydroxycamptothecin


title: Plate A1; Treatment media_Ctrl

source_name: iPS-derived cardiomyocytes_media_Ctrl


title: Plate C1; Treatment Nigericin

source_name: iPS-derived cardiomyocytes_Nigericin

value: Nigericin


title: Plate B1; Treatment Nicardipine-HCl

value: Nicardipine-HCl


title: Plate B1; Treatment Glipizide

source_name: iPS-derived cardiomyocytes_Glipizide

value: iPS-derived cardiomyocytes

value: Glipizide


title: Plate A1; Treatment 9b,11a-Prostaglandin F2

value: 9b,11a-Prostaglandin F2


title: Plate C1; Treatment Betulinic acid

value: Betulinic acid

value: after 12h of compound treatment


title: RNA pol II tNET-seq Rpb1  H1108Y Rep2

description:
nascent nuclear RNA
Anti-pol II tNET-seq
processed data file: H1108Y_tNetSeq_merge_negative_bedgraph.tdf, H1108Y_tNetSeq_merge_positive_bedgraph.tdf

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr H1108Y

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)


title: Plate C1; Treatment A-3

source_name: iPS-derived cardiomyocytes_A-3


title: RNA pol II tNET-seq Rpb1  H1108Y Rep1


title: Plate C1; Treatment Tosyl-Phe-CMK (TPCK)

value: Tosyl-Phe-CMK (TPCK)


title: Plate C1; Treatment Tyrphostin AG1478

value: Tyrphostin AG1478


title: Plate E1; Treatment Bosentan

source_name: iPS-derived cardiomyocytes_Bosentan

value: Bosentan


title: Plate E1; Treatment GEC_MB

source_name: iPS-derived cardiomyocytes_GEC_MB


title: Plate E1; Treatment GEC_Ctrl


title: Plate E1; Treatment Mycophenolic acid

value: Mycophenolic acid


title: Plate E1; Treatment Tunicamycin

source_name: iPS-derived cardiomyocytes_Tunicamycin

value: Tunicamycin


title: Plate E1; Treatment Z-Leu3-VS

source_name: iPS-derived cardiomyocytes_Z-Leu3-VS


title: Plate E1; Treatment Tyrphostin AG-825

value: Tyrphostin AG-825


title: Plate C1; Treatment Lycorine

source_name: iPS-derived cardiomyocytes_Lycorine

value: Lycorine


title: Plate C1; Treatment media_Ctrl


title: RNA pol II ChIP-seq Rpb1 Tyr1--P WT

description: Chromatin IP against RNA pol II Tyr1-P

value: rat monoclonal anti-Ty1-P 3D12 (Chromotek)


title: Plate E1; Treatment Resveratrol

source_name: iPS-derived cardiomyocytes_Resveratrol

value: Resveratrol


title: RNA pol II ChIP-seq Rpb1 Ser5-P R749H Rep2

description: Chromatin IP against RNA pol II Ser5-P

value: rat monoclonal anti-Ser5-P 3E8 (Chromotek)


title: RNA pol II ChIP-seq Rpb1 Ser5-P WT

description: Chromatin IP against RNA pol II Ser5-P


title: RNA pol II ChIP-seq Rpb1 Tyr1-P R749H Rep1

description: Chromatin IP against RNA pol II Tyr1-P


title: RNA pol II ChIP-seq Rpb1 Ser7-P R749H Rep2

description: Chromatin IP against RNA pol II Ser7-P

value: rat monoclonal anti-Ser7-P 4E12 (Chromotek)


title: RNA pol II ChIP-seq Rpb1 Ser7-P R749H Rep1

description: Chromatin IP against RNA pol II Ser7-P


title: Plate C1; Treatment Ac-Leu-Leu-Nle-CHO

value: iPS-derived cardiomyocytes

value: Ac-Leu-Leu-Nle-CHO


title: Plate E1; Treatment media_Ctrl


title: Plate E1; Treatment MB

value: MB


title: RNA pol II ChIP-seq Rpb1 Ser7-P WT

description: Chromatin IP against RNA pol II Ser7-P


title: Plate E1; Treatment Rottlerin

source_name: iPS-derived cardiomyocytes_Rottlerin

value: Rottlerin


title: Plate E1; Treatment Tamoxifen

source_name: iPS-derived cardiomyocytes_Tamoxifen

value: Tamoxifen

value: after 12h of compound treatment


title: RNA pol II ChIP-seq Rpb1 Se5-P R749H Rep1

description: Chromatin IP against RNA pol II Ser5-P


title: RNA pol II ChIP-seq Rpb1 Ser2-P H1108Y

description: Chromatin IP against RNA pol II Ser2-P

value: rat monoclonal anti-Ser2-P 3E10 (Chromotek)


title: RNA pol II ChIP-seq Rpb1 Ser2-P E1126G

description: Chromatin IP against RNA pol II Ser2-P

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr E1126G


title: RNA pol II ChIP-seq Rpb1 Ser2-P R749H Rep3

description: Chromatin IP against RNA pol II Ser2-P


title: Plate E1; Treatment (+/-)-Epibatidine

value: (+/-)-Epibatidine


title: Plate E1; Treatment SP-600125

source_name: iPS-derived cardiomyocytes_SP-600125


title: Plate E1; Treatment Manoalide

source_name: iPS-derived cardiomyocytes_Manoalide

value: Manoalide


title: Plate E1; Treatment K252A

source_name: iPS-derived cardiomyocytes_K252A


title: Plate E1; Treatment ICRF-193

source_name: iPS-derived cardiomyocytes_ICRF-193


title: RNA pol II ChIP-seq Rpb1 Ser2-P R749H Rep1

description: Chromatin IP against RNA pol II Ser2-P

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr R749H


title: RNA pol II ChIP-seq Rpb1 Ser2-P WT Rep2

description: Chromatin IP against RNA pol II Ser2-P

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr WT


title: RNA pol II ChIP-seq Rpb1 Ser2-P R749H Rep2

description: Chromatin IP against RNA pol II Ser2-P


title: Plate D1; Treatment GEC_Ctrl

source_name: iPS-derived cardiomyocytes_GEC_Ctrl


title: ChIP-seq H3 Cter R749H pol II

description: Chromatin IP against histone H3 Cter

value: rabbit anti  H3 Cter (Zhang et al EMBO J, 24:2379, 2005 )


title: Plate D1; Treatment GEC_MB


title: ChIP-seq H3 Cter WT pol II

description: Chromatin IP against histone H3 Cter


title: Plate D1; Treatment Genistein

source_name: iPS-derived cardiomyocytes_Genistein

value: Genistein


title: Plate D1; Treatment H-89

source_name: iPS-derived cardiomyocytes_H-89


title: RNA pol II ChIP-seq Rpb1 Ser2-P WT Rep1

description: Chromatin IP against RNA pol II Ser2-P


title: Plate D1; Treatment Etoposide

source_name: iPS-derived cardiomyocytes_Etoposide

value: Etoposide


title: ChIP-seq H3K4me3 R749H pol II

description: Chromatin IP against histone H3K4me3

value: rabbit anti  H3K4me3 (Zhang et al EMBO J, 24:2379, 2005 )


title: Plate D1; Treatment E-64-d

source_name: iPS-derived cardiomyocytes_E-64-d


title: ChIP-seq H3K4me3 WT pol II

description: Chromatin IP against histone H3K4me3


title: Plate E1; Treatment CITCO

source_name: iPS-derived cardiomyocytes_CITCO

value: CITCO


title: Plate D1; Treatment YC-1

source_name: iPS-derived cardiomyocytes_YC-1


title: ChIP-seq H3K4me2 R749H pol II Rep1

description: Chromatin IP against histone H3K4me2

value: rabbit ant H3K4me2 (this study)


title: ChIP-seq H3K4Me2 WT pol II Rep1

description: Chromatin IP against histone H3K4me2


title: ChIP-seq H3K36me3 R749H pol II Rep2

description: Chromatin IP against histone H3K36me3

value: rabbit anti  H3K36me3 (Kim et al PNAS 108:13564, 2011 )


title: Plate D1; Treatment E6 berbamine

source_name: iPS-derived cardiomyocytes_E6 berbamine

value: E6 berbamine


title: ChIP-seq H3K36me3 R749H pol II Rep1

description: Chromatin IP against histone H3K36me3


title: Plate D1; Treatment Cycloheximide

value: iPS-derived cardiomyocytes

value: Cycloheximide


title: Plate D1; Treatment Cytochalasin D

value: Cytochalasin D


title: ChIP-seq H3K36me3 WT pol II Rep2

description: Chromatin IP against histone H3K36me3


title: Plate D1; Treatment MB

source_name: iPS-derived cardiomyocytes_MB

value: MB


title: ChIP-seq H3K36me3 WT pol II Rep1

description: Chromatin IP against histone H3K36me3

value: rabbit anti H3K36me3 (Kim et al PNAS 108:13564, 2011 )


title: Plate D1; Treatment Curcumin

source_name: iPS-derived cardiomyocytes_Curcumin

value: Curcumin

value: after 12h of compound treatment


title: Plate D1; Treatment CinnGEL 2Me

source_name: iPS-derived cardiomyocytes_CinnGEL 2Me

value: CinnGEL 2Me


title: Plate D1; Treatment Castanospermine

value: Castanospermine


title: Truseq TF

city: los angeles

first: Qin

last: An

state: CALIFORNIA

address: Room 6554 Gonda Building, UCLA

department: Department of Human Genetics

institute: ucla

description:
TF
transcriptomic mRNA

data_processing:
Basecalls performed using CASAVA version 1.4
Fastq files are mapped back to human reference genome hg19 using Tophat 2.0.4 (relay on bowtie2), and FPKM calling is done by using Cufflinks 2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: iPS-derived cells

extract_protocol:
RNA were extracted from cell samples during all 6 stages of in-vitro differentiation of two pluripotent stem cell lines (H9 and HDF-hiPSCs) and 2 fetal livers samples originated from 17 weeks and 18 weeks gestational fetus using the RNeasy Micro Kit (Qiagen). RNA concentration was detected by Nanodrop 2000c Spectrophotometer (Thermo Scientific).
RNA libraries were prepared for sequencing using standard Illumina Truseq protocols

value: HDF-iPSCs

tag: protocol

value: directed in-vitro differentiation

value: IPS-derived mature hepatocytes


title: Truseq Fetal Liver 18

description:
18W
transcriptomic mRNA

source_name: fetal liver

value: liver from week 18 gestational fetus


title: Truseq Fetal Liver 17

description:
17W
transcriptomic mRNA

value: liver from week 17 gestational fetus


title: Truseq TE

description:
TE
transcriptomic mRNA

value: IPS-derived immature hepatocytes


title: Plate D1; Treatment Camptothecin

source_name: iPS-derived cardiomyocytes_Camptothecin

value: Camptothecin


title: Plate D1; Treatment SB-415286

source_name: iPS-derived cardiomyocytes_SB-415286


title: Plate D1; Treatment BADGE

source_name: iPS-derived cardiomyocytes_BADGE

value: BADGE


title: Plate D1; Treatment IB-MECA

source_name: iPS-derived cardiomyocytes_IB-MECA

value: iPS-derived cardiomyocytes

value: IB-MECA


title: Truseq TD

description:
TD
transcriptomic mRNA

value: IPS-derived hepatic endoderm cells


title: Truseq TA

description:
TA
transcriptomic mRNA

source_name: iPS

value: control

value: IPS cells


title: Truseq TB

description:
TB
transcriptomic mRNA

value: IPS-derived definitive endoderm cells


title: Truseq TC

description:
TC
transcriptomic mRNA

value: IPS-derived foregut endoderm cells


title: Plate F1; Treatment media_Ctrl

source_name: iPS-derived cardiomyocytes_media_Ctrl

value: after 12h of compound treatment


title: Truseq T5

description:
T5
transcriptomic mRNA

source_name: ES-derived cells

value: ES-derived immature hepatocytes


title: Plate F1; Treatment GEC_Ctrl

source_name: iPS-derived cardiomyocytes_GEC_Ctrl


title: Truseq T4

description:
T4
transcriptomic mRNA

value: ES-derived hepatic endoderm cells


title: Truseq T3

description:
T3
transcriptomic mRNA

value: directed in-vitro differentiation

value: ES-derived foregut endoderm cells


title: Plate D1; Treatment media_Ctrl


title: Truseq T2

description:
T2
transcriptomic mRNA

value: ES-derived definitive endoderm cells


title: Truseq T1

description:
T1
transcriptomic mRNA

source_name: ES

value: ES cells


title: Plate F1; Treatment MB

value: MB


title: 13-2-14-3

data_processing:
Bases called with Illumina CASAVA version 1.8.2
Fastq quality evaluated with FastQC version 1.10.1
Reads aligned to genome and splice junctions using novoalign version 2.08.03
Splice junction alignments translated to genomic coordinates using Useq SamTranscriptomeParser version 8.8.8
Gene counts calculated with Useq RNAseq application, version 8.8.8.
Differential expression testing performed using DESeq2
Genome_build: Mm10
Supplementary_files_format_and_content: tab-delimited text file with count value for each sample and each detected gene

source_name: Mouse embryonic stem cell culture

extract_protocol:
QIAGEN RNeasy Mini Kit
Illumina TruSeq Stranded mRNA Library Preparation Kit with poly(A) selection

treatment_protocol: ESCs were differentiated using retinoic acid for 14 days.

tag: genotype

value: Oct1 inducible deletion

tag: time

value: day 14

tag: replicate


title: Plate F1; Treatment GEC_MB

source_name: iPS-derived cardiomyocytes_GEC_MB

value: iPS-derived cardiomyocytes


title: 13-2-14-2


title: 13-2-14-1


title: Plate F1; Treatment RO0483007-000-001


title: 13-2-0-3

value: day 0


title: Plate F1; Treatment RO0062687-000-005


title: 13-2-0-2


title: Plate F1; Treatment RO0460254-000-001


title: C2-14-3

value: wild type


title: 13-2-0-1


title: C2-14-2


title: Truseq T6

description:
T6
transcriptomic mRNA

value: ES-derived mature hepatocytes


title: Plate D1; Treatment Bafilomycin A1

value: Bafilomycin A1


title: Plate F1; Treatment RO0475819-001-001


title: RNA pol II ChIP-seq yRpb1  Ser2-P rpb1-N488D Rep3

description: Chromatin IP against RNA pol II Ser2-P

organism: Saccharomyces cerevisiae

tag: strain

value: YEPD

value: rat monoclonal anti-Ser2-P 3E10 (Chromotek)


title: C2-0-2


title: Plate F1; Treatment RO0470203-000-017

value: after 12h of compound treatment


title: C2-0-1


title: Plate F1; Treatment RO0611790-000-012


title: RNA pol II ChIP-seq yRpb1  Ser2-P rpb1-N488D Rep2

description: Chromatin IP against RNA pol II Ser2-P


title: RNA pol II ChIP-seq yRpb1  Ser2-P WT Rep3_GRY3031

description: Chromatin IP against RNA pol II Ser2-P

source_name: GRY3031 RPB1

value: GRY3031 RPB1


title: RNA pol II ChIP-seq yRpb1  Ser2-P WT Rep2_GRY3031

description: Chromatin IP against RNA pol II Ser2-P


title: ChIP-seq H3K4me2 R749H pol II Rep2

description: Chromatin IP against histone H3K4me2

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr R749H

value: rabbit ant H3K4me2 (this study)


title: RNA pol II ChIP-seq yRpb1  Ser2-P rpb1-N488D Rep1

description: Chromatin IP against RNA pol II Ser2-P


title: RNA pol II ChIP-seq yRpb1  Ser2-P WT Rep1_GRY3031

description: Chromatin IP against RNA pol II Ser2-P


title: overfed

city: Wuhan

first: fang

last: chen

state: Hubei

address: No1, Nanhu Road

country: China

institute: Hubei Academy of Agricultural Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
After removing the adaptors, low quality tags and contaminants reads, the clean reads were aligned with the goose genome
we filtered the known non-miRNA reads, such as rRNA, tRNA, snRNA, and snoRNA by screening against ncRNA deposited in the GenBank and Rfam databases.
The expressions of miRNAs were normalized by Fragments per Kilobase of Transcript per Million Fragments Mapped (FPKM)
Genome_build: AnsCyg_PRJNA183603_v1.0 (AOGC00000000.1)
Supplementary_files_format_and_content: [.txt] reports abundance measurements; column headers:
1. small RNA sequence Id
2. length of small RNA sequence
3. count of small RNA sequence
4. small RNA sequnce
5. homolog (best one)
6. homolog length
7. homolog sequence
8. family
9. match number
10. mismatch number
11. gap number
12. score

organism: Anser anser

source_name: liver

growth_protocol: The experiment was carried out using 90 days-old male Landes Geese. 60 animals were divided into two groups and bred under natural conditions of light and  temperature.

extract_protocol:
Total RNA of each sample was extracted with Trizol (Invitrogen, USA). Using a Novex 15% TBE-Urea gel, 20–30-nt long RNA fragments were isolated and purified from 10 μg of total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Geese in control group were fed basal diet (2873 kCal and 171 g protein/ kg ) and ad libitum. Geese in overfed group were fed carbohydrate-rich diet contains 3353 kcal, 15 g fat, and 76 g protein / kg for 21 days.

tag: breed

value: Landes

tag: tissue

value: fatty liver

value: given carbohydrate-rich diet and overfed for 21d


title: RNA pol II ChIP-seq yRpb1 Ser2-P rpb2-10 Rep2

description: Chromatin IP against RNA pol II Ser2-P


title: ChIP-seq H3K4me2 WT pol II Rep2

description: Chromatin IP against histone H3K4me2

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr WT

tag: cell line


title: RNA pol II ChIP-seq yRpb1  Ser2-P WT Rep2_DY103

description: Chromatin IP against RNA pol II Ser2-P

source_name: DY103 RPB2

value: DY103 RPB2


title: yS2

city: Kunming

first: Qiangming

last: Sun

state: Yunnan

address: 935 Jiaoling Road

institute: Chinese Academy of Medicine Science and Peking Union Medical College

description: microRNA sequencing after 6h in Vero cells with DENV-2 adapted strain of  Vero cells infection

data_processing:
illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rhesus genome using bowtie-0.12.9 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Afterward, the mapped clean reads were mapped to known miRNA precursors, and the mature miRNAs were deposited in miRBase 19.0 (available online: http://www.mirbase.org/).Unmappable sequences were used to predict potentially novel candidate miRNAs with miREvo_v1.1 with parameters -i -r -M -m  -k -p 10 -g 50000 and mirdeep2_0_0_5 with parameters -p -m  -r -y -g 0 -T 10  .
The samples were normalized by calculating tags per million of total RNA reads (TPM) and used to compare the relative abundances of specific miRNAs within each data set.
Supplementary_files_format_and_content: Fasta files generated using bowtie-0.12.9  and xlsx files are comprised of two sheets, one for knonw miRNAs, the other for novel miRNAs, and each a sheet include gene_id,reacount and tpm values for each Sample.

organism: Chlorocebus sabaeus

growth_protocol: Vero cells were maintained in DMEM (BI, USA) supplemented with L-glutamine, penicillin, streptomycinand 10% foetal bovine serum (FBS, Gibco, USA)at 37°C in a 5% CO2-containing incubator.For in vitro virus infection, approximately 1×105 Vero cells per well were plated in 6-well platesand incubated overnight at 37°Cunder 5%CO2.

extract_protocol: 6h after infection, total RNA was extracted from the DENV-infected cells and the corresponding mock-infected cells using TRIzol reagent (Invitrogen China Ltd., Shanghai, China) according to manufacturer's instructions.  Subsequently, the isolated RNA was treated with DNase I (TaKaRa, Dalian, China) to remove DNA contaminants. Total RNA was electrophoresed by 15% denaturing polyacrylamide gel electrophoresis (PAGE) with 8 M urea, and small RNAs, of 15～30 nt, were excised out of the gel and purified. Subsequently, 5' RNA adaptors and 3' RNA adapters were ligated to the sRNA ends. The sRNAs with adapters were amplified by RT-PCR using the Small RNA Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions, and the generated cDNA libraries were sequenced using Illumina HiSeqTM 2500 sequencing technology(Novogene Biological Mdt InfoTech Ltd, Tianjin,China).

treatment_protocol: The Vero cellsgrown to 80% confluenceand infected with DENV-2 adpted strain of  Vero cells (DV01091 stain , GenBank: MF043956) or its source strain derived from C6/36 (D01090 strain, GenBank: KY882458).

value: Vero cells

value: kidney epithelial cells of  African green monkey


title: C2-14-1

value: day 14


title: yNT

description: microRNA sequencing after 6h in Vero cells with DENV-2-none infection


title: yS1

description: microRNA sequencing after 6h in Vero cells with DENV-2  source strain infection


title: RNA pol II ChIP-seq yRpb1  WT

description: Chromatin IP against RNA pol II

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)


title: RNA pol II ChIP-seq yRpb1  rpb1-N488D

description: Chromatin IP against RNA pol II


title: wild-type CBS138 (YC9)

city: Taipei city

first: Shang Jie

last: Yu

state: Taiwan (R.O.C)

address: No. 1, Sec. 4, Roosevelt Rd

department: Plant Pathology and Microbiology

country: Taiwan

institute: National Taiwan University

data_processing:
Illumina Pipeline v1.5+ was used to generate the quality values and they are  ranged from 2 to 41.
Clean reads were mapped to reference sequences and/or reference gene set using SOAPaligner/SOAP2. No more than 2 mismatches were allowed in the alignment.
The gene expression level is calculated by using RPKM method.
Genome_build: C. glabrata CBS 138
Supplementary_files_format_and_content: tab-delimited text files include RPKM, annotation values for each sample

organism: Nakaseomyces glabratus

source_name: C. glabrata cells

growth_protocol: C. glabrata wild-type and ada2 mutant were grown overnight at 24°C, washed twice with sterile ddH2O and diluted to 0.2 OD600/ml in 20 ml YPD broth, then incubated for 3 hr at 24°C with shaking at 250 rpm.

extract_protocol:
The 20 ml cultures were immediately added to 30 ml pre-cooled methanol to make final 60% methanol in order to stop the cellular processes and RNase activity. Cells were centrifuge at -4°C and the total RNAs were extracted using the RiboPureTM-Yeast Kit (Ambion).
Total RNAs were extracted and treated with DNase to remove DNA contamination. The mRNAs were enriched by oligo(dT) magnetic beads and then broken into short fragments (~ 200 bp). The first strand of cDNA was synthesized using random hexamer primer, while second strand was synthesized using DNA polymerase I. The double strand cDNA was further purified with magnetic beads. End reparation and 3’ end single nucleotide A (adenine) addition was performed. Sequencing adaptors were ligated to these fragments and fragments were enriched by PCR. During the QC step, Agilent 2001 bioanalyzer and ABI StepOnePlus Realtime PCR System were used to qualify of the sample library. The library products were sequencing via Illumina HiSeqTM 2000.


title: RNA pol II ChIP-seq yRpb1  Ser2-P WT Rep1_DY103

description: Chromatin IP against RNA pol II Ser2-P


title: RNA pol II ChIP-seq yRpb1 rpb2-10

description: Chromatin IP against RNA pol II


title: ada2 null mutant (YSJ4)

value: ada2 mutant


title: RNA pol II ChIP-seq yRpb1  WT Rep1

description: Chromatin IP against RNA pol II


title: C2-0-3

value: wild type

value: day 0


title: WT_seedlings_rep3

city: Cologne

first: Eva-Maria

last: Willing

address: Carl-von-Linne Weg 10

country: Germany

institute: MPIPZ

data_processing:
tophat (v2.0.10) was used for spliced alignments against A. thaliana reference genome (TAIR10)
cufflinks (version 2.2.1) was used to extract FPKM counts
Genome_build: TAIR10
Supplementary_files_format_and_content: text files, cufflinks output files

source_name: 7 days old seedlings

growth_protocol: 7 days old seedlings growing on 1/2 MS medium with 0,8% phytoagar on continuous light conditions at 22°C.

extract_protocol:
Total RNA  was extracted with Direct-zol™ RNA MiniPrep Kit (Zymo Research) and 4 µg was used to isolate polyadenylated RNAs with NEBNext Oligo d(T)25 Magnetic Beads (E7490, Biolabs).
The libraries were done with ScriptSeq™ Plant Leaf kit (Epicentre) following the manufacturer's instruction. Single end sequencing was performed on an Illumina HiSeq2000.

tag: ecotype/genotype

value: WT Col-0

tag: developmental stage

value: 7 days old seedlings


title: RNA pol II ChIP-seq yRpb1 Ser2-P rpb2-10 Rep1

description: Chromatin IP against RNA pol II Ser2-P

value: YEPD

value: rat monoclonal anti-Ser2-P 3E10 (Chromotek)


title: p45–/– Tfh rep2

city: Washington

first: Weiqun

last: Peng

state: DC

address: 1918 F Street, NW , DC

institute: The George Washington University

data_processing:
The sequencing quality of RNA-Seq libraries was assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
RNA-Seq libraries were mapped to mouse genome using Tophat (v2.1.0, Trapnell et al., Bioinformatics). UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
Mapped reads were then processed by Cuffdiff (v2.2.1, Trapnell et al., Nature biotechnology) to estimate expression levels of all genes and identify differentially expressed genes (FDR = 0.05). The expression level of a gene is expressed as a gene-level Fragments Per Kilobase of transcripts per Million mapped reads (FPKM) value.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file includes FPKM values for each Sample …

source_name: non-GC-Tfh cells

extract_protocol:
non-GC Tfh cells were sort-purified and total RNA was extracted using standard Qiagen RNase columns.
RNA libraries were prepared for sequencing using stardard Illumina protocol

value: spleen

tag: cell phenotype

value: CD45.2+CD4+CXCR5+PD-1 negative


title: luc7_seedlings_rep2

value: triple mutant (luc7 a-2, b-1, rl-1)


title: WT_seedlings_rep1


title: p45–/– Tfh rep1


title: control (WT) Tfh rep1


title: luc7_seedlings_rep1


title: WT_seedlings_rep2


title: RNA pol II ChIP-seq yRpb1  WT Rep2

description: Chromatin IP against RNA pol II


title: ath_circRNA salt stress

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

data_processing:
the NGS QC Toolkit v2.3.3 was used to filiter the reads with adapter sequences, reads with an N (unknown bases in a read＞5%) and low-quality reads (reads with a base quality ≤ 20).
Sequence alignments were performed using tophat2 with BOWTIE2 (v2.0.5) (Langmead and Salzberg, 2012) for mapping to the reference genome (Arabidopsis_thaliana TAIR10.30 ENSEMBL).
The circRNAs were predicted using the find_circ program with the same parameters as described previously
Chimeric mapped reads were selected for circular (“back-spliced”) junctions if the sequence reads mapped to one chromosome on the same strand, while the two sequence segments mapped to the genomic region with reverse order. CircRNA abundance was predicted on the basis of circular junction read counts.
Genome_build: TAIR10
Supplementary_files_format_and_content: Text file includes CircRNA_name, chr,start,end, circRNA_type, gene_id,  strand, Mean_junction, gene_length
Supplementary_files_format_and_content: CircRNA abundance

source_name: ath circRNA salt stress

growth_protocol: Wild-type (WT) A. thaliana Columbia ecotype (Col-0) was cultivated at 23/18℃ under 16/8 light/dark cycle.

extract_protocol: Strand-specific RNA library was prepared according to Illumina's instructions.  Briefly,The rRNA-depleted RNAs was firstly fragmented into short sequences in fragmentation buffer at 94 °C for 15 min. Secondly, these fragments were used as templates for first-strand cDNA synthesis primed with random hexamers. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H, and DNA polymerase I, followed by AMPure XP beads purification. Thirdly, the short fragments were further resolved with NEBNext End Repair Reaction Buffer and NEBNext Pre Enzyme Mix for end repair and poly (A) ligation. After that, the fragments are connected with adapters, then the second strand containing “U” is degraded using USER (uracil-specific excision reagent). Finally, suitable fragments were selected as templates for the PCR amplification after agarose gel electrophoresis. The quantification and qualification of the libraries were further assessed by using Agilent 2100 Bioanaylzer (Agilent Technologies, Palo Alto, CA) and Qubit® 2.0 Fluorometer (Invitrogen).

treatment_protocol: seedlings at stage 3.90 were exposed to the following stress environments: 300 mM/L mannitol (drought), 200 mM NaCl (salinity), and 38℃ (heat).

value: whole plants


title: ath_circRNA drought stress

source_name: ath circRNA drought stress


title: ath_circRNA heat stress

source_name: ath circRNA heat stress


title: control

value: Landes

value: normal liver

tag: treatment

value: given basal diet and ad libitum