title: one209_4_B10


title: Nine08_5_C1

status: Public on Oct 21 2016

type: SRA

city: Lausanne

first: Fabienne

last: Maurer

address: Bugnon 27

department: Service of genetic medicine

country: Switzerland

institute: CHUV

library_source: transcriptomic

data_processing:
The basecalling software name, version and parameters are OLB-1.9.4/bin/setupBclToQseq.py; --input-dir Data/Intensities/BaseCalls; --output-dir; --use-bases-mask Y*,Y*,Y*
Data filtering steps: remove reads with adaptors; remove reads with unknown nucleotides larger than 5%; remove reads with low quality (more than half of the bases' qualities are less than 5); obtain clean reads
Clean reads were mapped to reference genome and genes sequences respectively using SOAP2 (Li, Bioinformatics. 2009 Aug 1;25(15):1966-7. doi: 10.1093/bioinformatics/btp336. PMID: 19497933); mismatches no more than m (m default is 5) bases were allowed in the alignment.
Gene expression levels are measured as RPKM (Mortazavi, Nat Methods. 2008 Jul;5(7):621-8. doi: 10.1038/nmeth.1226. PMID: 18516045)
Gene coverage is the percentage of a gene covered by reads; the value equals to the ratio of the number of bases in a gene covered by unique mapping reads to the number of total bases in that gene.
Differential expression was computed using edgeR (Robinson, Bioinformatics. 2010 Jan 1;26(1):139–40. doi: 10.1093/bioinformatics/btp616. PMID: 19910308)
Genome_build: NCBI genome build 37, mm9
processed data files format and content: The tab-delimited 178_Mouse.Gene.rpkm.xls file includes Ensembl gene IDs, gene names, gene length, read counts (mapped reads), % coverage and RPKM values of 19176 genes in 178 samples
processed data files format and content: The tab-delimited DE_ATE-CTR.tab file summarizes differential expression data as determined between 54 atenolol-treated (ATE) and 53 untreated (CTR) mice; the data consist in log2-transformed fold-change and FDR values computed over 16155 genes.
processed data files format and content: The tab-delimited DE_ISO-CTR.tab file summarizes differential expression data as determined between 53 isoproterenol-treated (ISO) and 53 untreated (CTR) mice; the data consist in log2-transformed fold-change and FDR values computed over 16208 genes

molecule: total RNA

organism: Mus musculus

source_name: heart

extract_protocol:
Total RNA was purified from the cardiac ventricles following the recommendations of Ambion for the semi-automated MagMax procedure, then stored at -80°C. RNA quality and integrity (RIN >8.1) were verified on a Bioanalyzer (Agilent).
Library preparation and RNA sequencing were performed by the Beijing Genomics Institute (BGI, Hong Kong, China), following Illumina's protocols for poly(A) selection, library preparation and HiSeq2000 paired-end sequencing (2x 91 bp).

tag: mouse id number

tag: mouse strain

value: NOD/ShiLtJ

tag: treatment

value: atenolol 10 mg/kg per day

tag: gender

value: male

tag: tissue

value: cardiac ventricles


title: Nine26_5_D10

value: isoproterenol 10 mg/kg per day


title: Huh7_Flag-YTHDF1_PAR-CLIP

city: Zurich

first: A

last: McIntyre

address: Winterthurerstrasse 190

department: Molecular Life Sciences

institute: University of Zurich

description: processed data file: M6AHCV_Y1-l15-3

data_processing:
library strategy: PAR-CLIP
Basecalls performed using CASAVA version 1.8.2
PAR-CLIP: Bowtie v1 alignment to human genome hg19
PAR-CLIP: Unaligned reads from step 1 aligned to CA JFH HCV with 2 mismatches
PAR-CLIP: PARalyzer v1.1 was applied to step 2 with cluster minimum read depth of 3 reads
PAR-CLIP: Background reads (GFP-FL PAR-CLIP) were subtracted from the YTHDF sets topologically
MeRIP-seq: STAR version 2.5.0 alignment to combined hg19 and viral genomes
MeRIP-seq: Reads aligning to viral genomes were extracted for peak calling
MeRIP-seq: the MeRIPPeR peak caller was applied with a minimum peak width of 100
MeRIP-seq: peaks called in two separate replicates for each viral strain were intersected for final calls
Genome_build: hg19
Supplementary_files_format_and_content: PAR-CLIP: csv files include PARalyzer output showing YTHDF protein binding clusters on the HCV RNA genome, MeRIP: bed files include peaks called by MeRIPPeR

organism: Homo sapiens

growth_protocol: Total of 2x10^7 cells per cell line were seeded in 30 15 cm plates

extract_protocol:
48 hours post-infection, cells were crosslinked, and pellets were harvested by scraping
Illumina Tru-seq Small RNA

treatment_protocol: Cells were infected with HCV, 3 hrs post-infection, they were treated with 4-thiouridine

tag: cell line

tag: cell type

value: liver cell line

tag: viral strain

value: HCV JFH-1 (culture adapted)


title: Nine14_5_C4


title: Nine05_5_D1

value: control


title: Nine24_5_D7


title: Nine01_5_C10


title: Huh7_Flag-YTHDF2_PAR-CLIP

description: processed data file: M6AHCV_Y2-l15-3


title: Nine06_5_D4


title: eight38_1_A7


title: eight22_1_A4


title: Huh7_Flag-GFP_PAR-CLIP


title: one014_3_E4


title: seven41_1_D1

value: A/J


title: eight18_1_A2


title: seven34_1_C4


title: seven40_1_C10


title: GAS+HCQ 24h Patient 2

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
The Illumina bcl2fastq 1.8.4 pipeline was used to generate the sequence data
Reads were aligned to the human genome by Rsubread version 1.18.0
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation
Genome_build: hg19 (NCBI build 37)
Supplementary_files_format_and_content: tab-delimited text files were written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

source_name: GAS+HCQ 24h_PBMCs

growth_protocol: Human PBMC were cultured in IMDM with 5% human male AB serum

extract_protocol:
RNA was extracted using the QIAGEN RNeasy kit following the manufacturer's protocol
DNA libraries were prepared using the Illumina TruSeq v2 protocol and sequenced on an Illumina HiSeq 2000 at the Australian Genome Research Facility (AGRF) Melbourne, following the manufacturer's protocols.

treatment_protocol: Heat killed group A streptococcus was added at MOI = 10, with and without hydroxychloroquine. After 24 hours, RNA was extracted from PBMC.

tag: subject id#

tag: subject status

value: healthy participant

tag: treated with

value: group A streptococcus and hydroxychloroquine

tag: length of culture

value: 24 hours

value: Peripheral blood mononuclear cells (PBMCs)


title: seven35_1_B6


title: Untreated 0h Patient 3

source_name: Untreated 0h_PBMCs

value: none (untreated)

value: 0 hours


title: GAS 24h Patient 1

source_name: GAS 24h_PBMCs

value: group A streptococcus


title: seven25_1_C1


title: seven24_1_B10


title: seven16_1_C7


title: GAS+HCQ 24h Patient 3


title: GAS 24h Patient 2


title: GAS+HCQ 24h Patient 1


title: JINDING rep9

city: Yangzhou

first: Li

middle: hui

last: fang

state: Jiangsu

address: No.58 Cangjie Rd

country: China

institute: Jiangsu Institute of Poultry Science

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count at the same time
Genome_build: ftp://ftp.ensembl.org/pub/release-80/fasta/anas_platyrhynchos/dna/
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Anas platyrhynchos

source_name: breast muscle or Pectoral muscle

extract_protocol:
eighteen polyA mRNA-seq libraries, including nine from Gaoyou duck PM and nine from Jingding duck PM,RNA was harvested using Trizol reagent.Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the Construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Jingding

value: pectoral muscle

tag: age

value: 5 days post-hatching


title: Six25_3_F7

value: CBA/J

value: atenolol 10 mg/kg per day

value: male


title: Six24_3_F4

value: cardiac ventricles


title: GAS 24h Patient 3


title: Six18_3_G4


title: Six37_3_H1

value: isoproterenol 10 mg/kg per day


title: JINDING rep8


title: seven02_1_B1


title: Untreated 24h Patient 2

source_name: Untreated 24h_PBMCs


title: JINDING rep6


title: Six15_3_G10


title: seven00_1_A10


title: JINDING rep7


title: Six05_3_F1


title: JINDING rep5


title: Untreated 24h Patient 3


title: Six02_3_F10

value: control


title: HCQ 24h Patient 3

source_name: HCQ 24h_PBMCs

value: 20 µM hydroxychloroquine (HCQ)


title: Five33_4_B5


title: Five38_4_A7


title: Untreated 0h Patient 1

value: healthy participant


title: JINDING rep3


title: Five31_4_B1


title: HCQ 24h Patient 1


title: JINDING rep2


title: Five22_3_H7


title: Untreated 24h Patient 1


title: Five14_3_H4


title: Five05_4_A4


title: Six14_3_G7


title: GAOYOU rep9

value: Gaoyou


title: JINDING rep1


title: HCQ 24h Patient 2

value: 24 hours


title: Five01_4_A1


title: Five20_4_A10


title: Six04_3_G1


title: GAOYOU rep8


title: Four55_6_B4

value: SJL/J


title: Four57_6_B7


title: Four50_6_C4


title: Four47_6_D1


title: Four48_6_C1


title: GAOYOU rep7


title: JINDING rep4


title: Four34_6_B3


title: Four44_6_C7


title: Four46_6_C10


title: GAOYOU rep5


title: GAOYOU rep6


title: GAOYOU rep3


title: Four31_6_B10


title: GAOYOU rep4


title: two43_1_E7

value: BALB/cByJ


title: GAOYOU rep2


title: two38_1_G7


title: two32_1_E4


title: two61_1_F10


title: Five25_3_H10


title: two27_1_G1


title: Two10_1_F7


title: Untreated 0h Patient 2

value: none (untreated)

value: 0 hours

value: Peripheral blood mononuclear cells (PBMCs)


title: one91_2_G10


title: GAOYOU rep1

value: pectoral muscle


title: two06_1_F1


title: One90_2_G7


title: m23: T2 - at the end of the racing season

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

country: Poland

institute: National Research Institute of Animal Production

data_processing:
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove Illumina adapters and poly-A sequences.
The raw reads were aligned to the Equus caballus genome (EquCab2.0) as a reference, while the whole procedure was followed by alignment parameters from ENCODE3's STAR-RSEM pipeline
The quality control metrics across aligned reads per sample were obtained using RNA-SeQC software
The differential expression estimation was proceed with utilization of DeSeq2 Bioconductor R-project package.
Genome_build: EquCab2.0
Supplementary_files_format_and_content: raw.genes.csv.gz: compressed gzip file containing raw genes counts
Supplementary_files_format_and_content: raw.isoforms.csv.gz: compressed gzip file containing raw isoforms counts
Supplementary_files_format_and_content: res_genes_AB.csv.gz: compressed gzip file containing DeSeq2 results for differential expression analysis (T1 vs T2) for genes
Supplementary_files_format_and_content: res_genes_CA.csv.gz: compressed gzip file containing DeSeq2 results for differential expression analysis (T0 vs T1) for genes
Supplementary_files_format_and_content: res_genes_CB.csv.gz: compressed gzip file containing DeSeq2 results for differential expression analysis (T0 vs T2) for genes
Supplementary_files_format_and_content: res_isoforms_AB.csv.gz: compressed gzip file containing DeSeq2 results for differential expression analysis (T1 vs T2) for isoforms
Supplementary_files_format_and_content: res_isoforms_CA.csv.gz: compressed gzip file containing DeSeq2 results for differential expression analysis (T0 vs T1) for isoforms
Supplementary_files_format_and_content: res_isoforms_CB.csv.gz: compressed gzip file containing DeSeq2 results for differential expression analysis (T0 vs T2) for isoforms

organism: Equus caballus

source_name: muscle tissue

extract_protocol:
The total RNA was isolated using by TriReagent (Ambion, Life Technologies). The biopsy of gluteus medius muscle was performed by using minimally invasive ProMag™ Ultra Automatic Biopsy Instrument with a 2 mm diameter biopsy needle and according procedure detailed described by Stefaniuk et al. (2015).The muscle samples were homogenized with the use of zirconium oxide beads (diameter 0.5 mm) in BulletBlender homogenizer (Next Advance Inc., USA).The concentration and quality of RNA were estimated on TapeStation 2200 (Agilent Technologies, Warsaw, Poland) using RNA Screen Tape (Agilent Technologies). The RNA samples with RIN (RNA integrity number) above 8.5 were used to further analyses.
The cDNA libraries were prepared from 300ng of total RNA by using TruSeq RNA Kit v2 kit (Cat#FC-122-1001) according to protocol.

value: gluteus medius

value: 3 year old

value: Arabian horses


title: m22: T2 - at the end of the racing season

value: male


title: m20: T2 - at the end of the racing season


title: One23point1_3_A4

value: cardiac ventricles


title: One19point1_3_A1

value: isoproterenol 10 mg/kg per day


title: m21: T2 - at the end of the racing season

value: female


title: One72_2_G4

value: atenolol 10 mg/kg per day


title: two79_1_E10


title: two77_1_G10


title: One13point1_2_H10


title: one08point1_2_H7

value: control


title: One03point1_2_H1


title: m19: T2 - at the end of the racing season


title: m18: T2 - at the end of the racing season


title: m17: T2 - at the end of the racing season


title: Jun d1BC WT

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

library_source: genomic

data_processing:
Base-calling (CASAVA)
Demultiplexing (bcl2fastq)
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie 1.00 to sorted BAM via stdoutput using --all --best --strata --v 2 -m 1 -S | samtools view -S - -b | samtools sort -
Tag shift (macs14)
Wig coverage track generation (macs14)
Peak detection (macs14)
Genome_build: mm10
Supplementary_files_format_and_content: Variable step 10bp wig files depicting ChIP-Seq coverage

molecule: genomic DNA

source_name: Jun d1BC WT

growth_protocol: A Flag-tagged dominant negative FOS (dnFOS) construct was PCR-amplified from CMV plasmid (CMV500-8584hep-fosLZ(MO), A-FOS, kindly provided by Charles Vinson (Olive et al, 1997)) and HindIII as well as Not1 sites were introduced. The GFP of the p2lox plasmid (kindly provided by Michael Kyba (Kyba et al, 2002)) was exchanged for Flag-tagged dnFOS. A2lox ESCs (a gift from Michael Kyba (Kyba et al, 2002)) or Bry-GFP ESCs were cultured as described before (Gilmour et al, 2014; Regha et al, 2015). Briefly, cells were grown on mitomycin C-inactivated mouse embryonic feeder cells (MEFs) in DMEM medium supplemented with 15% FCS (Stem Cell Technologies), 1 mM sodium pyruvate, 1 mM glutamine, 100 units per ml penicillin and 100 μg ml−1 streptomycin, 25 mM HEPES buffer, 1 × non-essential amino acids, 0.15 mM MTG and 103 units per ml LIF (ESGRO mLIF, Millipore ESG1107). Medium was changed every day and cells were passaged every 2nd day using TrypLE Express (Thermo Fisher). For transfection with p2lox-dnFOS plasmid, 2.5x106 A2lox ESCs were resuspended in 100 µl PBS (Sigma D8537), 20 µg of each p2lox-dnFOS plasmid and Cre-expressing plasmid were added and cells were electroporated at 240 V, 7 ms settings on a EPI 2500 electroporator (Fischer). Cells were plated quickly on NEO-resistant feeder cells in ESC medium and 1 day later selection was started by adding 300µg/ml G418. Clones were picked after 6 days of selection, assessed for their differentiation ability and transgene expression upon doxycycline addition. ESCs were cultured for one day on gelatinized plates in DMEM ESC medium and for another day on gelatinized plates in IMDM ESC medium in the presence of LIF. Subsequently, cells were differentiated as embryoid bodies (EBs) in 15cm bacterial-grade dishes at 1.25x106 cells per 50 ml for 3.75 days in IMDM differentiation medium without LIF. EBs were then dispersed to single cells by TrypLE Express treatment and Flk1pos cells were purified using MACS technology. Purified Flk1pos cells were cultured in gelatinized T150 tissue culture-grade flask at 1.2x106 cells per flask in blast culture medium (IMDM supplemented with 10% FCS, 100 units per ml penicillin and 100 μg ml−1 streptomycin, 1 mM glutamine, 0.45 mM MTG, 0.18 mg ml−1 Human transferrin (Roche 10652202001) 25 μg ml−1 ascorbic acid, 20% D4T conditioned media, 5 μg l−1 recombinant mouse Vascular Endothelial Growth Factor (Peprotech: 450-32), 10 μg l−1 mIL-6 (Peprotech: 216–16)).

extract_protocol: Chromatin was prepared and immunoprecipitation was carried out as previously described (Lichtinger et al). Cells were resuspended in PBS at 3.3x106 cells/ml and cross-linked with 0.83mg/ml disuccinimidyl glutarate (DSG) for 45 minutes at room temperature with rotation. Cells were washed four times with PBS and further crosslinked in PBS at 2x106 cells/ml with 1% formaldehyde for 10 minutes at room temperature. Crosslinking was quenched with 0.125M glycine, cells were washed twice in PBS and incubated with Buffer A at 4oC for 10 minutes followed by buffer B at 4oC for 10 minutes. Double cross-linked chromatin was then used for immunoprecipitation as previously described (Lichtinger et al). Antibodies used were for the antibodies, Fos (sc-253-X), Jun (sc-1694-X) and TEAD4 (ab58310).

treatment_protocol: cells were treated with 1µg/ml doxycycline for the duration indicated in each experiment.

value: d1 blast culture Flk1+ IVD cells

tag: dox treatment

tag: chip antibody

value: c-Jun (Santa Cruz Biotechnology, catalog# sc-1694-X)


title: m16: T2 - at the end of the racing season


title: m15: T2 - at the end of the racing season


title: Input_Arid1aflfl_Tam

city: Houston

first: H. Courtney

last: Hodges

state: TX

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

country: USA

institute: Baylor College of Medicine

description: Input sample for Arid1aflfl mES cells following tamoxifen treatment

data_processing:
Basecalls performed using Illumina CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 1.1.1, allowing no more than a single mismatch. Duplicate reads were discarded.
Peaks were called by comparing ChIP and input samples using MACS 1.4.2 with with default settings.
Peaks with less than 30 reads per million were discarded to ensure high-quality peak calls.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated by extending all read fragments to 200 bp, then calculating the basepair coverage for each replicate using Bedtools, normalizing by the total number of reads within called peaks. For samples with multiple replicates, values in the bigWig files represent coverage calculated in this way averaged across both replicates using bwtool.

source_name: Mouse embryonic stem cells

growth_protocol: Cells are grown in DMEM media supplemented with 15% FBS and LIF.

extract_protocol:
Lysates were obtained from sonicated nuclei crosslinked with formaldehyde, and protein-DNA complexes were isolated by immunoprecipitation.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.

treatment_protocol: For conditional knockout cell lines (Arid1aflfl and Smarca4flfl), cells were incubated with either ethanol or 0.8 uM 4-hydroxytamoxifen for 48 h. Cells were then harvested 72 h after the start of the treatment. Heterozygous Smarca4 mutant cells received no treatment.

tag: strain

value: Mouse embryonic stem cells

tag: passage

tag: genotype/variation

value: 0.8 uM 4-hydroxytamoxifen (Tam)


title: Input_Smarca4V5_Y860H

description: Input sample for mES cells expressing Y860H Smarca4V5

value: expressing Y860H Smarca4V5

value: none (untreated)


title: Input_Smarca4V5_WT

description: Input sample for mES cells expressing WT Smarca4V5

value: expressing WT Smarca4V5


title: Input_Smarca4flfl_EtOH

description: Input sample for Smarca4flfl mES cells following ethanol treatment

value: ethanol (EtOH)


title: Input_Smarca4V5_R885H

description: Input sample for mES cells expressing R885H Smarca4V5

value: expressing R885H Smarca4V5


title: Input_Arid1aflfl_EtOH

description: Input sample for Arid1aflfl mES cells following ethanol treatment


title: m14: T2 - at the end of the racing season

value: gluteus medius

value: 3 year old


title: Input_Smarca4flfl_Tam

description: Input sample for Smarca4flfl mES cells following tamoxifen treatment


title: m13: T0 - untrained horses

value: 2,5 year old

value: Arabian horses


title: Input_Smarca4V5_E882K

description: Input sample for mES cells expressing E882K Smarca4V5

value: expressing E882K Smarca4V5


title: Input_Smarca4V5_G784E

description: Input sample for mES cells expressing G784E Smarca4V5

value: expressing G784E Smarca4V5


title: Input_Smarca4V5_K785R

description: Input sample for mES cells expressing K785R Smarca4V5

value: expressing K785R Smarca4V5


title: Input_Smarca4V5_E861K

description: Input sample for mES cells expressing E861K Smarca4V5

value: expressing E861K Smarca4V5


title: m12: T0 - untrained horses

value: male


title: One05point1_2_H4

tag: mouse id number

tag: mouse strain

tag: treatment

value: control

value: cardiac ventricles


title: Suz12_Smarca4flfl_Tam

description: anti-Suz12 ChIP in Smarca4flfl mES cells following tamoxifen treatment

value: Mouse embryonic stem cells

value: 0.8 uM 4-hydroxytamoxifen (Tam)

value: Rabbit anti-Suz12

tag: chip antibody vendor

value: Active Motif

tag: chip antibody cat. #

tag: chip antibody lot/batch #


title: m11: T1 - horses after intense gallop phase (before flat racing season)

tag: tissue

tag: gender

value: female


title: Suz12_Arid1aflfl_Tam

description: anti-Suz12 ChIP in Arid1aflfl mES cells following tamoxifen treatment

tag: cell type

tag: treated with


title: Suz12_Smarca4flfl_EtOH

description: anti-Suz12 ChIP in Smarca4flfl mES cells following ethanol treatment

value: ethanol (EtOH)


title: Suz12_Arid1aflfl_EtOH

description: anti-Suz12 ChIP in Arid1aflfl mES cells following ethanol treatment


title: HP DHS

data_processing:
Base-calling (CASAVA)
Demultiplexing (bcl2fastq)
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie 1.00 to sorted BAM via stdoutput using --all --best --strata --v 2 -m 1 -S | samtools view -S - -b | samtools sort -
Tag shift (macs14)
Wig coverage track generation (macs14)
Peak detection (macs14)
Optional footprinting (wellingtion_footprints)
Genome_build: mm10
Supplementary_files_format_and_content: Variable step 10bp wig files depicting DNaseI hypersensitivity coverage

source_name: HP

extract_protocol:
NP-40 permeabilized cells were digested with DNase I for 3 minutes at 22oC as previously described (Bert et al). A range of DNase I concentrations was used to get the optimal digestion, the initial amounts varied depending on the cell type. Following DNA purification, samples were analyzed by qPCR comparing the amount of PCR product generated between regions expected to be DNase I hypersensitive (e.g. TBP promoter) and regions which should not be cleaved (e.g. a gene desert region of chromosome 1). Optimally digested samples gave a ratio of ~0.7. DNA fragments (80-300bp) were isolated from favorable samples by agarose gel extraction and further validated by qPCR analysis before library preparation.
Libraries were prepared from approximately 10ng DNA from DNaseI samples, according to manufacturer's instructions (Illumina).  Samples were sequenced using 50bp single end reads

value: WT hematopoietic progenitor IVD cells

tag: dnasei origin

value: Worthington


title: Ring1b_Smarca4flfl_Tam

description: anti-Ring1b ChIP in Smarca4flfl mES cells following tamoxifen treatment

value: Rabbit anti-Ring1b

value: Cell Signaling


title: HE1 DHS

value: WT hemogenic endothelium 1 IVD cells


title: Ring1b_Smarca4flfl_EtOH

description: anti-Ring1b ChIP in Smarca4flfl mES cells following ethanol treatment


title: m9: T0 - untrained horses

value: gluteus medius

tag: age

value: 2,5 year old

tag: breed

value: Arabian horses


title: Ring1b_Smarca4V5_Y860H

description: anti-Ring1b ChIP in mES cells expressing Y860H Smarca4V5

value: expressing Y860H Smarca4V5

value: none (untreated)

tag: chip antibody


title: Ring1b_Smarca4V5_WT

description: anti-Ring1b ChIP in mES cells expressing WT Smarca4V5

tag: strain

value: expressing WT Smarca4V5


title: m8: T0 - untrained horses

value: male


title: m6: T1 - horses after intense gallop phase (before flat racing season)

value: 3 year old


title: m7: T1 - horses after intense gallop phase (before flat racing season)


title: Ring1b_Smarca4V5_G784E

description: anti-Ring1b ChIP in mES cells expressing G784E Smarca4V5

value: Mouse embryonic stem cells

tag: passage

value: expressing G784E Smarca4V5


title: Ring1b_Smarca4V5_R885H

description: anti-Ring1b ChIP in mES cells expressing R885H Smarca4V5

tag: genotype/variation

value: expressing R885H Smarca4V5


title: Ring1b_Smarca4V5_E882K

description: anti-Ring1b ChIP in mES cells expressing E882K Smarca4V5

value: expressing E882K Smarca4V5


title: m5: T1 - horses after intense gallop phase (before flat racing season)


title: Ring1b_Smarca4V5_E861K

description: anti-Ring1b ChIP in mES cells expressing E861K Smarca4V5

value: expressing E861K Smarca4V5


title: m10: T0 - untrained horses

value: female


title: cyr1∆/∆::CYR1 pH 4 replicate 1

city: Hanover

first: Deborah

middle: A

last: Hogan

state: NH

department: Microbiology and Immunology

institute: Dartmouth College

description: Mutant derivatives of wild-type strain SC5314

data_processing:
Reads were trimmed for adaptor sequences and mapped to the Candia albicans SC5314 whole genome with CLC Genomics Workbench platform (v8.5.1) using default parameters.
Mapped reads were quantile normalized to all reads using CLC Genomics Workbench.
Genome_build: C_albicans_SC5314_version_A21-s02-m09-r04
Supplementary_files_format_and_content: Processed data file is a data matrix that contains raw unique gene reads and quantile normalized reads.

organism: Candida albicans

source_name: cyr1∆/∆::CYR1 pH 4

growth_protocol: Cells were grown overnight in YPD and back-diluted into treatment medium at 1.5*10^7 cells per ml in 10 mls per tube

extract_protocol:
Cells were pelleted by centrifugation at 5k RPM for 5 minutes and RNA was extracted from cells using the Epicentre Yeast RNA extraction kit and subjected to RNA seq
mRNA was enriched by hybridization to oligo dT beads. Directional RNAseq libraries were prepared with TruSeq Stranded mRNA Library Prep chemistry with unique TruSeq indexes, using an automated liquid-handling system. Libraries were pooled and sequenced on a NextSeq500 instrument, 2X75bp PE sequencing (high-output flow cell).

treatment_protocol: Growth in 10 ml YNB medium/0.2% glucose/5mM GlcNAc/50mM citrate at pH 4 or pH 7 for 4 hours with shaking at 37C. 5ml used for RNA isolation

tag: parental strain

tag: genotype

value: cyr1 delta/delta::CYR1

tag: medium ph


title: Ring1b_Arid1aflfl_Tam

description: anti-Ring1b ChIP in Arid1aflfl mES cells following tamoxifen treatment

value: 0.8 uM 4-hydroxytamoxifen (Tam)

value: Rabbit anti-Ring1b

tag: chip antibody vendor

value: Cell Signaling


title: Ring1b_Arid1aflfl_EtOH

description: anti-Ring1b ChIP in Arid1aflfl mES cells following ethanol treatment

value: ethanol (EtOH)

tag: chip antibody cat. #


title: cyr1∆/∆::CYR1 pH 4 replicate 2


title: cyr1∆/∆::CYR1 pH 7 replicate 1

source_name: cyr1∆/∆::CYR1 pH 7


title: cyr1∆/∆::CYR1 pH 7 replicate 2


title: m4: T1 - horses after intense gallop phase (before flat racing season)

value: gluteus medius

value: Arabian horses


title: H3K27me3_Smarca4V5_R885H

description: anti-H3K27me3 ChIP in mES cells expressing R885H Smarca4V5

value: none (untreated)

value: Rabbit anti-H3K27me3

value: EMD Millipore

tag: chip antibody lot/batch #


title: H3K27me3_Smarca4V5_Y860H

description: anti-H3K27me3 ChIP in mES cells expressing Y860H Smarca4V5

value: expressing Y860H Smarca4V5


title: H3K27me3_Smarca4V5_WT

description: anti-H3K27me3 ChIP in mES cells expressing WT Smarca4V5

value: Mouse embryonic stem cells

value: expressing WT Smarca4V5


title: H3K27me3_Smarca4V5_K785R

description: anti-H3K27me3 ChIP in mES cells expressing K785R Smarca4V5

value: expressing K785R Smarca4V5


title: H3K27me3_Smarca4V5_G784E

description: anti-H3K27me3 ChIP in mES cells expressing G784E Smarca4V5

value: expressing G784E Smarca4V5


title: m3: T1 - horses after intense gallop phase (before flat racing season)

tag: tissue

value: 3 year old

value: male


title: m2: T1 - horses after intense gallop phase (before flat racing season)

tag: gender

value: female


title: H3K27me3_Smarca4V5_E882K

description: anti-H3K27me3 ChIP in mES cells expressing E882K Smarca4V5

tag: cell type

value: expressing E882K Smarca4V5


title: cyr1∆/∆ pH 4 replicate 2

source_name: cyr1∆/∆ pH 4

value: cyr1 delta/delta


title: cyr1∆/∆ pH 7 replicate 1

source_name: cyr1∆/∆ pH 7


title: H3K27me3_Smarca4V5_E861K

description: anti-H3K27me3 ChIP in mES cells expressing E861K Smarca4V5

value: expressing E861K Smarca4V5

tag: treated with


title: Ring1b_Smarca4V5_K785R

description: anti-Ring1b ChIP in mES cells expressing K785R Smarca4V5

value: Rabbit anti-Ring1b

value: Cell Signaling


title: m1: T1 - horses after intense gallop phase (before flat racing season)

value: gluteus medius

value: Arabian horses


title: cyr1∆/∆ pH 7 replicate 2


title: cyr1∆/∆ pH 4 replicate 1


title: DBP-FITC, TN, Replicate 2

status: Public on Oct 20 2016

city: Wellington

first: Franca

last: Ronchese

address: Kelburn Parade

department: Immune Cell Biology

country: New Zealand

institute: Malaghan Instititute of Medical Research

description:
Exp_TN.DBP.FITC.2_1500.5
DBP+FITC-treated Triple Negative cells

data_processing:
Paired-end raw read FASTq files ere pre-processed using Trimmomatic (v0.32) and quality checked using qrqc R package (v1.20.0)
Reads were mapped to mouse and ERCC reference transcripts using TopHat2 (v2.0.10)
Read hits to annotated genes were counted using HtSeq-count (HT-Seq, v0.6.0)
Technical replicates (across multiple flow cell lanes) were combined,see processed data file ('JEMsampleFiltered_collapsed_counts_JEM_2016-May-05.csv')
Data were split into the two experiments (Nb, DBP+FITC), then analysed separately with DESeq2 (v1.6.3) with sex as an additional model covariate for the Nb experiment
A variance-stabilised transformation was generated from the count data using DESeq2 (v1.6.3), and normalised based on the sum of gene exon lengths
Genome_build: C57BL/6 mouse reference genome (GRCm38.p3)
Supplementary_files_format_and_content: JEMsampleFiltered_collapsed_counts_JEM_2016-May-05.csv -- Gene Count Data as determined by HTSeq-count

source_name: Dendritic cells (DC)

extract_protocol:
Total RNA was prepared from frozen purified cell pellets using QIAzol Lysis Reagent and RNeasy Micro Kit.
Ribosomal RNA was removed using RiboZero before RNA libraries were prepared for sequencing using the Illumina TruSeq kits.

tag: Sex

value: Pooled skin-draining lymph nodes

value: Dendritic cells (DC)

tag: number of mice/sample

tag: ercc mix

tag: cell population

value: CD11c int, MHCII hi, CD24 neg, CD326 neg, CD11b lo (TN)

tag: treatment

value: DBP+FITC


title: Untreated, TN, Replicate 3

description:
Exp_TN.UT.3_1500.3
Untreated Triple Negative cells

tag: strain

value: Untreated (UT)


title: DBP-FITC, CD11b, Replicate 2

description:
Exp_CD11b.DBP.FITC.2_1500.14
DBP+FITC-treated CD11b cells

value: CD11c int, MHCII hi, CD11b+


title: DBP-FITC, CD11b, Replicate 1

description:
Exp_CD11b.DBP.FITC.1_1500.13
DBP+FITC-treated CD11b cells


title: DBP-FITC, TN, Replicate 3

description:
Exp_TN.DBP.FITC.3_1500.6
DBP+FITC-treated Triple Negative cells


title: Untreated, TN, Replicate 1

description:
Exp_TN.UT.1_1500.1
Untreated Triple Negative cells


title: Untreated, TN, Replicate 2

description:
Exp_TN.UT.2_1500.2
Untreated Triple Negative cells


title: Nb, CD103, Replicate 2

description:
Exp_CD103.Nb.2_1500.23
Nb-treated CD103 cells

value: Auricular lymph nodes

value: CD11c int, MHCII hi, CD103+

value: Nb


title: DBP-FITC, TN, Replicate 1

description:
Exp_TN.DBP.FITC.1_1500.4
DBP+FITC-treated Triple Negative cells

value: male


title: Untreated, CD11b, Replicate 3

description:
Exp_CD11b.UT.r2_1890.17
Untreated CD11b cells


title: Nb, CD103, Replicate 3

description:
Exp_CD103.Nb.3_1500.24
Nb-treated CD103 cells

value: female


title: Nb, TN, Replicate 2

description:
Exp_TN.Nb.2_1257.2
Nb-treated Triple Negative cells

value: CD11c int, MHCII hi, CD103 neg, CD326 neg, CD11b lo (TN)


title: Nb, TN, Replicate 1

description:
Exp_TN.Nb.1_1257.1
Nb-treated Triple Negative cells


title: Nb, CD11b, Replicate 3

description:
Exp_CD11b.Nb.3_1500.21
Nb-treated CD11b cells


title: Nb, CD103, Replicate 1

description:
Exp_CD103.Nb.1_1500.22
Nb-treated CD103 cells


title: Nb, TN, Replicate 3

description:
Exp_TN.Nb.3_1257.3
Nb-treated Triple Negative cells


title: Fos d1BC minus dox

source_name: Fos d1BC minus dox

value: d1 blast culture Flk1+ IVD cells

tag: dox treatment

tag: chip antibody

value: c-Fos (Santa Cruz Biotechnology, catalog# sc-253-X)


title: Nb, CD11b, Replicate 2

description:
Exp_CD11b.Nb.2_1500.20
Nb-treated CD11b cells


title: Nb, CD11b, Replicate 1

description:
Exp_CD11b.Nb.1_1500.19
Nb-treated CD11b cells


title: PBS, CD103, Replicate 2

description:
Exp_CD103.PBS.2_1500.26
PBS-treated CD103 cells

value: PBS


title: PBS, CD103, Replicate 3

description:
Exp_CD103.PBS.3_1500.27
PBS-treated CD103 cells


title: PBS, TN, Replicate 3

description:
Exp_TN.PBS.3_1257.6
PBS-treated Triple Negative cells


title: PBS, TN, Replicate 2

description:
Exp_TN.PBS.2_1257.5
PBS-treated Triple Negative cells


title: PBS, TN, Replicate 1

description:
Exp_TN.PBS.1_1257.4
PBS-treated Triple Negative cells


title: DBP-FITC, CD11b, Replicate 3

description:
Exp_CD11b.DBP.FITC.3_1500.15
DBP+FITC-treated CD11b cells


title: PBS, CD11b, Replicate 2

description:
Exp_CD11b.PBS.2_958.05.2.1
PBS-treated CD11b cells


title: Untreated, CD11b, Replicate 2

description:
Exp_CD11b.UT.3_1500.12
Untreated CD11b cells


title: Untreated, CD11b, Replicate 1

description:
Exp_CD11b.UT.4_1500.11.LY
Untreated CD11b cells


title: PBS, CD11b, Replicate 3

description:
Exp_CD11b.PBS.3_958.06.2.1
PBS-treated CD11b cells


title: PBS, CD11b, Replicate 1

description:
Exp_CD11b.PBS.1_958.04.2.1
PBS-treated CD11b cells


title: SK14

city: Jacksonville

first: Yan

middle: W.

last: Asmann

state: FL

address: 4500 San Pablo Road South

institute: Mayo Clinic

data_processing:
Samples were sequenced using Illumina HiSeq 2000
Raw exon and gene read counts, along with sequencing QC, were generated using Mayo Clinic-developed RNAseq analytic pipeline: MAP-RSeq Version 2.0
Conditional Quantile Normalization (CQN) was applied to raw gene counts to correct for GC bias and technical variations
Based on the bi-modal distribution of the CQN normalized and log2 transformed RPKM (reads per kb per million) gene expression values, genes with average log2 RPKM < -2 across all experimental groups were considered to be too lowly expressed and were excluded from further analysis
Genome_build: mm10
Supplementary_files_format_and_content: One tab-delimited text file include CQN normalized, log2 transformed RPKM values for all samples

source_name: hemi-brain, Lcn2-/-, LPS

extract_protocol:
Total RNA was isolated from sonicated tissues using a Direct-zol total RNA isolation kit according to manufacturer’s instructions with in-column DNase I treatment
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hemi-brain

tag: age

value: 3-4 months

tag: genotype/variation

tag: agent (injection)

value: LPS


title: SK10

source_name: hemi-brain, wild type, LPS

value: wild type


title: SK12


title: SK7

source_name: hemi-brain, Lcn2-/-, saline

value: saline


title: SK16


title: SK11


title: SK9


title: SK5


title: SK8b


title: SK3

source_name: hemi-brain, wild type, saline


title: PBS, CD103, Replicate 1

description:
Exp_CD103.PBS.1_1500.25
PBS-treated CD103 cells

value: Dendritic cells (DC)


title: SK1


title: SK2


title: whole chromatin WT thymocytes

city: Boston

first: Kenzie

last: MacIsaac

state: MA

address: 33 Avenue Louis Pasteur

department: Genetics and Pharmacogenomics

institute: Merck Research Labs

data_processing:
Reads were aligned to the mouse genome using bwa algorithm.
Peaks were called using the macs2 algorithm using the IP from RORc-/- thymocytes as the control.
Genome_build: mm10
Supplementary_files_format_and_content: bed files contain Macs2 peak call coordinates and associated p-values, fold enrichment values, and q-values for each condition

source_name: thymocytes

growth_protocol: 10X106 Total thymocytes from C57BL/6 mice and DP thymocytes from Rorc-/- mice were used for RORγT ChIP assay. Anti-RORγ Ab (B2D and AFKJS-9 from eBioscience) were used in ChIP assay. Pulled-down DNA was sequenced on Illumina Seq. .

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Library construction and sequencing were performed using the standard Active Motif ChIP-seq protocol.


title: untreated WT thymocytes

value: B2D and AFKJS-9 from eBioscience


title: untreated RORC-/- KO thymocytes

source_name: RORC-/- thymocytes


title: MRL-871 treated thymocytes


title: SK13


title: saline control 3

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Sequencing reads from RNA-seq libraries were first trimmed of polyA tails, adapters, and low quality ends using cutadapt with parameters --match-read-wildcards --times 2 -e 0 -O 5 --quality-cutoff' 6 -m 18 -b TCGTATGCCGTCTTCTGCTTG -b ATCTCGTATGCCGTCTTCTGCTTG -b CGACAGGTTCAGAGTTCTACAGTCCGACGATC -b TGGAATTCTCGGGTGCCAAGG -b AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -b TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT.
Reads were then mapped against a database of repetitive elements derived from RepBase18.05. Bowtie version 1.0.0 with parameters -S -q -p 16 -e 100 -l 20 was used to align reads against an index generated from Repbase sequences (Langmead et al., 2009).
Reads not mapped to Repbase sequences were aligned to the mm9 human genome (UCSC assembly) using STAR (Dobin et al., 2013) version 2.3.0e with parameters --outSAMunmapped Within –outFilterMultimapNmax 1 –outFilterMultimapScoreRange 1.
Alternative polyadenylation sites were identified from RNA-seq data using the bioinformatics algorithm DaPars (Xia et al., 2014), which uses a regression model to locate endpoints of alternative polyadenylation sites, was used to identify differences in APA events between hnRNP A2/B1 depleted samples and controls. To identify significant APA events, we used the following cutoffs: FDR < 0.05, |ΔPDUI| ≥ 0.2, and |dPDUI| ≥ 0.2. APA scatter plots were generated using the R-Studio program with the ggplot2 library.
counts of reads for each gene annotated in gencode vM1 were calculated from featureCounts
Genome_build: mm9
Supplementary_files_format_and_content: rpkm file, containts rpkm for each sample

source_name: spinal cord

growth_protocol: eight-week old female C57Bl/6j mice were grown under normal coniditons

extract_protocol:
RNA was extracted by standard Trizol extraction.
TruSeq Stranded Total RNA Sample Preparation Kit

treatment_protocol: Sterotactic injections of ASO complementary to Hnrnpa2b1 were performed in eight-week old female C57Bl/b mice to deplete hnRNP A2/B1. ASOs were delivered specifically to the lateral ventricle (12.5 mg)  injection (300 mg). Mice were regularly monitored for 28 days until sacrificed.

tag: tissue type

value: spinal cord


title: hnRNP A2/B1 ASO 2

value: ASO Hnrnpa2/b1


title: SK15


title: saline control 1


title: hnRNP A2/B1 ASO 3


title: hnRNP A2/B1 ASO 4


title: saline control 2


title: SK6


title: hnRNPA2/B1_iCLIP_001

description: iCLIP RNA

data_processing:
Raw CLIP-seq reads were trimmed of polyA tails, adapters and low quality ends using Cutadapt with parameters --match-read-wildcards --times 2 -e 0 -O 5 --quality-cutoff' 6 -m 18 -b TCGTATGCCGTCTTCTGCTTG -b ATCTCGTATGCCGTCTTCTGCTTG -b CGACAGGTTCAGAGTTCTACAGTCCGACGATC -b TGGAATTCTCGGGTGCCAAGG -b AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -b TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT. Trimmed reads were mapped against a database of repetitive elements derived from RepBase (version 18.05) using Bowtie (version 1.0.0) with parameters -S -q -p 16 -e 100 -l 20 (Langmead et al. 2009). Reads not mapped to repetitive elements were mapped to the mm9 mouse genome (UCSC assembly) using STAR (version 2.3.03) with parameters --outSAMunmapped Within –outFilterMultimapNmax 1 –outFilterMultimapScoreRange 1 (Dobin et al. 2013). Reads having the same 5’ mapping position were collapsed to a single read to eliminate PCR duplication. CLIP-seq peaks were identified as previously described (Zisoulis et al, NSMB 2010).
Genome_build: mm9
Supplementary_files_format_and_content: peaks.bed and bigwig

growth_protocol: eight-week old female c57bl/6j mice were ordered from Jackson Labs and kept under standard conditions

extract_protocol:
Spinal cords were rapidly extracted by hydro-extrusion and snap frozen in liquid nitrogen. Frozen samples were finely ground and UV crosslinked before lysis and immunoprecipitation.
8 week old, female, C57/BL6J mice were obtained from Jackson Labs (Bar Harbor, ME). Mice were sacrificed and the spinal cords were removed, flash frozen in liquid nitrogen, and ground finely with a mortar and pestle. The frozen cords were UV crosslinked at λ=258nm with 4000 mJ/cm2 of energy. iCLIP libraries were prepared as previously described (Huppertz et al. 2014) using rabbit polyclonal antibody GTX127928 (Genetex) (10 mg per sample). Libraries were sequenced on the HISEQ 2500 platform in single end mode with a read length of 50 base pairs.

tag: antibody

value: hnRNP A2/B1

tag: vendor

value: Genetex

tag: catalog number

tag: lot number


title: hnRNP A2/B1 ASO 1


title: RNAseq_Zeb2_Ctrl_D4_rep3

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

institute: DFCI

data_processing:
Illumina software was used for basecalling.
alignment: Sequence reads were mapped to the mus musculus reference genome (mm10) via TopHat2 v2.0.13
counts: featureCounts v1.4.6 was used to count the number of genes for GRCm38 annotated genes with parameters -t exon and -g gene_name.
counts were converted to transcripts per million (TPM) and genes were filtered based on expression (> 5 TPM in minimum 3 samples) and variability (removed 20% lowest variable genes)
differential expression: raw counts from filtered genes were used to detect differential expression in timeseries and pairwise comparisons using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix with TPM values for all genes after filtering steps.
Supplementary_files_format_and_content: Excel files contain the top contributing genes for the Principal Components 1 and 2 of the PCA (III), timeseries (IV) and pair-wise (V) comparisons.

growth_protocol: ESCs were maintained feeder-cell free in 2i+LIF. N2B27 was prepared as described (Ivanova et al., 2009). For 2i+LIF medium, 0.4 μM PD0325901 and 1 μM CHIR99021 were added (Ying et al., 2008). LIF (Millipore, ESG1107) was added to a final concentration of 1,000 U/ml. On d0, 3x106 ESCs were plated in a 10-cm bacterial petri dish in EB medium [KO DMEM (Invitrogen, 10829018), 15% FBS (Life Technologies, 10270106), 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 0.1mM 2-mercaptoethanol, 50 U/ml of penicilline/streptomycine]. On d2 the EB medium was refreshed. On d4 the medium was changed to N2B27 medium and retinoic acid (Sigma, R2625) was added to 500 nM. On d6 the medium was refreshed. Between d8 and d15 the EBs were cultured in N2B27, and this medium was refreshed every other day.

extract_protocol:
Total RNA was isolated using Qiagen RNeasy mini kit (Qiagen, 74104)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Zeb2 fl/fl


title: RNAseq_Zeb2_Ctrl_D6_rep1


title: RNAseq_Zeb2_Ctrl_D4_rep1


title: RNAseq_Zeb2_KO_D4_rep3


title: RNAseq_Zeb2_KO_D4_rep2


title: RNAseq_Zeb2_Ctrl_D6_rep2


title: MRL-248 treated thymocytes


title: SK4

tag: tissue


title: RNAseq_Zeb2_KO_D6_rep1


title: RNAseq_Zeb2_Ctrl_D4_rep2


title: RNAseq_Zeb2_KO_D6_rep2


title: RNAseq_Zeb2_Ctrl_D0_rep3


title: RNAseq_Zeb2_KO_D0_rep2


title: RNAseq_Zeb2_Ctrl_D0_rep2


title: RNAseq_Zeb2_KO_D0_rep1


title: risk (CC) (sample 57)

city: Farmington

first: Annabelle

last: Rodriguez

state: CT

address: 263 Famington Ave, MC-3501

department: Center for Vascular Biology

institute: UCONN Health

data_processing:
Perkin Elmer's Genesifter Analysis Edition Software
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Human Build 37.2 using BWA.
Raw read count was normalized by total mapped million reads (RPM).
Benjamini-Hochberg correction
Genome_build: 37.2
Supplementary_files_format_and_content: Excel files include raw and RPM values for combined triplicate samples.

source_name: PBMCs

growth_protocol: Cells were maintained in RPMI and the media was changed every third day.

extract_protocol:
Total RNA from EBV (Epstein Barr Virus)-transformed B lymphocyte cells, from 3 carriers of the risk (CC) allele and 3 non-carriers of the (GG) reference allele, was isolated using the Qiagen RNeasy-Midi kit (Cat#75142). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: (CC)


title: RNAseq_Zeb2_KO_D6_rep3


title: RNAseq_Zeb2_Ctrl_D6_rep3


title: reference (GG) (sample 36)

value: EBV (Epstein Barr Virus)-transformed B lymphocyte cells

value: (GG)


title: risk (CC) (sample 8)


title: risk (CC) (sample 98)


title: CNGD_sequence

city: Nanjing

first: Wei

last: Wu

address: Nanjing Normal University, #1 Wenyuan Road, Qixia District, Nanjing, China

institute: Nanjing Normal University

data_processing:
A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis (Li et al. 2010; Wei et al. 2011). A Public software package, CleaveLand3.0 was used for analyzing Degradome sequencing data.
Genome_build: Tcas_3.0 (http://www.ncbi.nlm.nih.gov/assembly/2778/)
Supplementary_files_format_and_content: Table S2; Conservered miRNAs identified in T.castanuem (The sequences that mapped to selected mirs in miRBase and that further mapped to the genome of T. castaneum).
Supplementary_files_format_and_content: Table S3; Known candidate microRNAs identified in Tribolium castanuem; The condidate microRNAs not mapped to T.castanuem genome but mapped mirs in miRBase.
Supplementary_files_format_and_content: Table S4; Novel miRNAs identified in T.castanuem and the genome location

organism: Tribolium castaneum

source_name: T. castaneum_small RNA

extract_protocol: Total RNA was isolated with the Total RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada) according to the manufacturer’s instructions. Small RNA libraries were generated from the two samples using the Illumina Truseq Small RNA Preparation kit according to Illumina’s TruSeq Small RNA Sample Preparation Guide. The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina GAIIx following vendor’s instruction for running the instrument. Raw sequencing reads were obtained using Illumina’s Sequencing Control Studio software version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70). A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis. Degradome library was constructed following with methods previously described by German et al.(2008).CleaveLand3.0 and LC Science’s ACGT301-DGEv1.0 program were used to detect potentially sliced targets of known and novel miRNA.

treatment_protocol: The beetles were harvested at 1-day-old early embryo, 3-day-old late embryo, 1-day-old early larva, 20-day-old late larva, 1-day-old early pupa, 6-day-old late pupa, 1-day-old early adult, 7-day-old late adult without physical injuries or infections.

tag: developmental stage

value: mixed (described in the treatment protocol)

value: whole body


title: reference (GG) (sample 3)


title: RNAseq_Zeb2_KO_D4_rep1


title: RNAseq_Zeb2_Ctrl_D0_rep1


title: L012_3a

city: Köln

first: Felix

middle: Peter

last: Frey

address: Carl-von-Linné-Weg 10

department: Quantitative Genetics

institute: Max-Planck Institute for Plant Breeding Research

data_processing:
Outcoming single-end sequence reads were cleaned for reads containing primer or adaptor sequences.
Sequencing reads with more than 30% of bases with a Phred quality score of ≤20 were excluded from the following analyses
High quality reads were aligned to the B73 reference sequence (AGPv3 release 20) using TopHat (Version 2.0.3)
We used the R package easyRNASeq (Version 1.6.2) to filter the aligned reads for protein-coding genes located on the nuclear chromosomes and counted transcript reads per gene model in the 47 samples.
we excluded poorly expressed genes which did not show at least two counts per million reads in at least two samples
Genome_build: B73 reference sequence (AGPv3 release 20)
Supplementary_files_format_and_content: count_table_new_clean.txt includes the transcript count for each gene model and each sample; generated by easyRNASeq

organism: Zea mays

extract_protocol:
At the end of the previously described growing period, leaf samples of the inbred lines were collected at the three heat levels with n=10 replications at each of the three heat levels. A sample of about 0.5 cm2 was cut from the centre of the latest fully developed leaf of each plant, immediately frozen in liquid nitrogen, and stored at −80°C. The leaf tissue of five replications was pooled to a total of two replications for each genotype - heat level combination to reduce biological variation for the following RNA sequencing. This resulted in a total of 47 samples (the sample for one replication of a genotype - heat level combination was missing). Total RNA was isolated using the RNeasy Plant Kit (Qiagen, Hilden, Germany). RNA quantity was assessed and quality control was performed using a Qubit fluorometer (Life Technologies, Darmstadt, Germany) and the 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). DNA was removed using the TURBO DNA free Kit (Ambion, Kaufungen, Germany) and the solution was purified using the RNeasy Ⓡ MinElute Ⓡ Cleanup spin columns (Qiagen). rRNA was depleted prior to sequencing using the RiboMinus™Plant Kit (Invitrogen, Life Technologies, Darmstadt, Germany).
Library preparation and RNA sequencing were performed at the Max Planck Genome Centre Cologne using an Illumina HiSeq2000 sequencing machine (Illumina, Inc., San Diego, CA USA)

tag: growing temperature

tag: replicate

value: seedling leaf


title: P040_3a


title: S070_3a


title: S070_3b


title: S067_3a


title: RNAseq_Zeb2_KO_D0_rep3

tag: strain


title: P040_3b


title: L017_3a


title: S067_3b


title: L017_3b


title: L012_3b


title: L023_3b


title: L023_3a


title: L043_3b


title: S058_3b


title: S058_3a


title: L043_3a


title: reference (GG) (sample 22)


title: P040_2a


title: P040_2b


title: S070_2b


title: L012_2b


title: S067_2b


title: S070_2a


title: L012_2a


title: L023_2b


title: S067_2a


title: L023_2a


title: L017_2a


title: S058_2b


title: P040_1a


title: S067_1b


title: S070_1a


title: S058_2a


title: S067_1a


title: S070_1b


title: L023_1a


title: L043_2b


title: L017_1b


title: S058_1b


title: L012_1a


title: L043_2a


title: L012_1b


title: L017_1a


title: L043_1a


title: L043_1b


title: saline control 3 [human]

description:
C3
mature_counts_hg19.csv

data_processing:
Sequencing reads from small RNA-seq libraries were first trimmed adapters using cutadapt
Reads were then mapped against a database of repetitive elements derived from RepBase18.05. Bowtie version 1.0.0 with parameters -S -q -p 16 -e 100 -l 20 was used to align reads against an index generated from Repbase sequences (Langmead et al., 2009).
Reads not mapped to Repbase sequences were aligned to the mm9 or hg19 genome (UCSC assembly) using bowtie version 1.1.1 with parameters -p 8 -k 1 -m 10 -l 25 --best --chunkmbs 128
counts of reads for each gene annotated in gencode vM3 were calculated from featureCounts for mouse and v19 for human
Genome_build: mm10/hg19 for mouse and human, respectively
Supplementary_files_format_and_content: count file, csv

source_name: CVBiPS

growth_protocol: craig venter fibroblast-derived induced pluripotent stem cells were cultured under normal conditions

extract_protocol:
RNA was extracted by standard Trizol extraction.
TruSeq small-RNA Sample Preparation Kit

treatment_protocol: ASO complementary to Hnrnpa2b1 was added to media for XXX days to deplete hnRNP A2/B1.

value: craig venter iPS cells

tag: treatment


title: saline control 2 [human]

description:
C2
mature_counts_hg19.csv


title: hnRNP A2/B1 ASO 1 [human]

description:
501-1
mature_counts_hg19.csv


title: hnRNP A2/B1 ASO 2 [human]

description:
501-2
mature_counts_hg19.csv


title: saline control 1 [human]

description:
C1
mature_counts_hg19.csv


title: hnRNP A2/B1 ASO 3 [human]

description:
501-3
mature_counts_hg19.csv


title: Hypoxia_6days (precursor miRNA)_12

city: HOUSTON

first: anil

middle: k

last: sood

state: TEXAS

address: 7777 knight road, unit 173

department: Gyn Oncology and Rep Medicine

institute: UT MD Anderson Cancer Center

description:
Library_12
precursor miRNA

data_processing:
XSQ files containing the read sequences and quality values were loaded onto a compute cluster and the reads mapped in colorspace using the Life Technologies LifeScope 2.5.1 software using default parameters. Reads were mapped to the human genome (hg19) downloaded from the UCSC Genome Bioinformatics Site (http://genome.ucsc.edu). The hg19 genome was slightly modified by deleting the Y chromosome in order to make a female genome. An hg19 exon reference file provided by Life Technologies was required by LifeScope in order to create the exon junction libraries needed to map reads that cross exon boundaries. This file was derived from the refGene database from UCSC. Also, a human filter reference file was required (provided by Life Technologies) that contains the sequences of ribosomal and repetitive regions of the genome in order to filter reads that mapped to those regions. Mapped reads were outputted in the standard BAM (Binary Alignment/Map) format. BAM files were imported into Partek Genomics Suite 6.6 (Partek Incorporated, St. Louis, MO) for gene expression analysis. Mapped reads contained in the BAM files were cross-referenced against the RefSeq database (downloaded from UCSC Genome Browser) and a smallRNA database (UCSC Genome Browser) to generate RPKM (Reads Per Kilobase of exon per Million mapped reads) values for each gene. Low expressing genes were excluded. Differential expression using the derived RPKM values was performed using ANOVA. Genes with a False Discovery Rate (FDR) < 5% were considered significant.
Genome_build: hg19
Supplementary_files_format_and_content: Two tab-delimited text file include RPKM values for mRNAs (Sood_Ovarian_RefSeq_RPKM_Values.txt) and Precursor miRNAs (Sood_Ovarian_Precursor_microRNAs_RPKM_Values.txt) for each Sample

source_name: A2780 cancer cells

growth_protocol: Cells were maintained in 5% CO2 at 37°C in RPMI 1640 supplemented with 10-15% fetal bovine serum (FBS) and 0.1% gentamicin sulfate. For Hypoxia treatments, cells were incubated in an oxygen-controlled hypoxia chamber at 1% O2 for respective treatment intervals.

extract_protocol:
RNA was isolated using miRVANA RNA isolation kit (Lifetechnologies). RNA qulaity was meassured using Agilent Bioanalyzer, with atleast RIN<8.
Starting with 3ug of total RNA for each sample, Ribosomal RNA was depleted using Ribominus (Invitrogen/Life Technologies, Carlsbad, CA) following manufacturer's recommendations.  Sequencing libraries were then prepared and barcoded individually using  the SOLiD™ Total RNA-Seq Kit for Whole Transcriptome Libraries (Life Technologies, Inc., Carlsbad, CA) following manufacturer's recommendations. Prepared samples were then pooled and sequenced using the Life Technology 5500xl sequencer using 75 base forward read only.

treatment_protocol: Cells  incubated in an oxygen-controlled hypoxia chamber at 1% O2 for 6hr, 48hr, 6days.

tag: tissue of origin

value: Ovarian cancer

tag: cell line

value: epithelial ovarian cancer cell line A2780

tag: stress

value: Hypoxia

tag: time


title: Hypoxia_6days (precursor miRNA)_11

description:
Library_11
precursor miRNA


title: Normoxia_6days (precursor miRNA)_10

description:
Library_10
precursor miRNA

value: control


title: P040_1b


title: Hypoxia_48hr (precursor miRNA)_8

description:
Library_8
precursor miRNA


title: L023_1b


title: Normoxia_6days (precursor miRNA)_9

description:
Library_9
precursor miRNA


title: S058_1a


title: Normoxia_48hr (precursor miRNA)_5

description:
Library_5
precursor miRNA


title: Normoxia_48hr (precursor miRNA)_6

description:
Library_6
precursor miRNA


title: Hypoxia_6hr (precursor miRNA)_4

description:
Library_4
precursor miRNA


title: Hypoxia_6hr (precursor miRNA)_3

description:
Library_3
precursor miRNA


title: Normoxia_6hr (precursor miRNA)_2

description:
Library_2
precursor miRNA


title: Normoxia_6hr (precursor miRNA)_1

description:
Library_1
precursor miRNA


title: 59713sacCer3XO_BY4741_i5006_NoTag_rep1

city: University Park

first: Alain

middle: Roger

last: Bataille

state: PA

address: 453 North Frear

department: BMB

institute: Penn State University

description:
Biological replicate 1 of 4, IP with rabbit IgG (sigma i5006), no-tag, negative control used for normalization of bedgraphs
protocol: ChIP-exo

data_processing:
Basecalls performed using bcl2fastq ver 2.16 for NextSeq paired reads
ChIP-exo reads were aligned to sacCer3 genome assembly using bwa mem version 0.7.9a for paired reads. Read1 tags were shift 6 bp in the 3' direction (to better reflect the crosslinking coordinates). After total tag normalization of the datasets each experiment and its control were smoothed using an average sliding window of 50 bp and the value in the no-tag strain subtracted to the value in the tag strain for each window.
Genome_build: sacCer3/R64
Supplementary_files_format_and_content: Bedgraph format. Tags (Read1 only) were shift 6 bp in the 3' direction and files were normalize by total tag number before generating bedgraph (Med subunits datasets and TFIIB datasets were normalized independantly). For combined file, after total tag normalization of the datasets (combine experiment with combined controls) each experiment and its control were smoothed using an average sliding window of 20 bp and the value in the no-tag strain subtracted to the value in the tag strain for each window.

organism: Saccharomyces cerevisiae

growth_protocol: All yeast cells were grown to an OD600 of 0.6-0.8 in YPD following standard procedures and crosslinked at 1% formaldehyde.

extract_protocol:
ChIP-exo experiments were carried out essentially as described (Rhee and Pugh, 2012). Briefly, crosslinked cells were lysed, and chromatin pellets were isolated and then fragmented by sonication. Chromatin was then immunoprecipitated using Dyna PanMouse (samples 1-6) antibody-conjugated magnetic beads or Dyna conjugated with rabbit IgG (samples 7-12), followed by DNA polishing, A-tailing, Illumina adaptor ligation (ExA2), and on beads digestion by lambda and recJ exonuclease. After elution of the single-stranded DNA, a primer was annealed to EXA2 and extended with phi29 DNA polymerase, then A-tailed. A second Illumina sequencing adaptor was ligated to exonuclease treated ends, and the products PCR-amplified and gel-purified.
ChIP-exo libraries were prepared for sequencing using standard Illumina protocols; Reference paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/

treatment_protocol: kin28as strains and their controls were treated with 6μM of 1-Naphthyl PP1 (NAPP1; Tocris Bioscience) for 15 min prior to crosslinking.

value: IgG from rabbit serum

tag: antibody catalogue number

value: Sigma i5006

tag: antibody lot number

value: MAT_alpha his3_delta_1 leu2_delta_0 ura3_delta_0 met15_delta_0


title: Hypoxia_6days (total RNA)_11

description:
Library_11
RNA


title: 59714sacCer3XO_BY4741_i5006_NoTag_rep2

description:
Biological replicate 2 of 4, IP with rabbit IgG (sigma i5006), no-tag, negative control used for normalization of bedgraphs
protocol: ChIP-exo

tag: antibody


title: 59716sacCer3XO_BY4741_i5006_NoTag_rep4

description:
Biological replicate 4 of 4, IP with rabbit IgG (sigma i5006), no-tag, negative control used for normalization of bedgraphs
protocol: ChIP-exo


title: 59715sacCer3XO_BY4741_i5006_NoTag_rep3

description:
Biological replicate 3 of 4, IP with rabbit IgG (sigma i5006), no-tag, negative control used for normalization of bedgraphs
protocol: ChIP-exo


title: Hypoxia_48hr (total RNA)_8

description:
Library_8
RNA


title: 59710sacCer3XO_BY4741-Sua7-TAP_i5006_Sua7-TAP_rep1

description:
Biological replicate 1 of 2, IP with rabbit IgG (sigma i5006)in strain Sua7-TAP
protocol: ChIP-exo

value: MAT_alpha SUA7-TAP his3_delta_1 leu2_delta_0 ura3_delta_0 met15_delta_0

tag: protein tag

value: TAP


title: Normoxia_6days (total RNA)_10

description:
Library_10
RNA


title: Hypoxia_48hr (total RNA)_7

description:
Library_7
RNA


title: 60011sacCer3XO_yFR1902_9E10_Med7-13MYC_Kin28as_15mNAPP1_rep1

description:
Biological replicate 1 of 2, Med7-13MYC IP with 9E10 antibody in kin28as strain
protocol: ChIP-exo

data_processing:
Basecalls performed using bcl2fastq ver 2.16 for NextSeq paired reads
ChIP-exo reads were aligned to sacCer3 genome assembly using bwa mem version 0.7.9a for paired reads. Read1 tags were shift 6 bp in the 3' direction (to better reflect the crosslinking coordinates). After total tag normalization of the datasets each experiment and its control were smoothed using an average sliding window of 50 bp and the value in the no-tag strain subtracted to the value in the tag strain for each window.
genome build: sacCer3/R64
processed data files format and content: Bedgraph format. Tags (Read1 only) were shift 6 bp in the 3' direction and files were normalize by total tag number before generating bedgraph (Med subunits datasets and TFIIB datasets were normalized independantly). For combined file, after total tag normalization of the datasets (combine experiment with combined controls) each experiment and its control were smoothed using an average sliding window of 20 bp and the value in the no-tag strain subtracted to the value in the tag strain for each window.

growth_protocol: All yeast cells were grown to an OD600 of 0.6-0.8 at 30 °C following standard procedures and crosslinked at 1% formaldehyde.

tag: antibody manufacturer

value: produced in lab of Francois Robert from the 9E10 hybridoma line (batch 14-02-15)

value: MAT_alpha ade2::hisG his3_delta_200 leu2_delta_0 lys2_delta_0 met15_delta_0 trp1_delta_63 ura3_delta_0 kin28::kin28as (L83G) [pSH579, CEN URA3 kin28as (L83G)] MED7-13xMYC::HPHr


title: Normoxia_6days (total RNA)_9

description:
Library_9
RNA


title: 60012sacCer3XO_yFR1902_9E10_Med7-13MYC_Kin28as_15mNAPP1_rep2

description:
Biological replicate 1 of 2, Med7-13MYC IP with 9E10 antibody in kin28as strain
protocol: ChIP-exo
processed data file: 60011-12sacCer3XO_yFR1902_9E10_Med7-13MYC_kin28as_15mNAPP1_comb_shift6_1.0_normMean20_Roman.bedgraph is avilable on GSM2143303

tag: genotype


title: 60008sacCer3XO_yFR1638_9E10_Med15-9MYC_Kin28as_15mNAPP1_rep2

description:
Biological replicate 2 of 2, Med15-9MYC IP with 9E10 antibody in kin28as strain
protocol: ChIP-exo
processed data file: 60007-08sacCer3XO_yFR1638_9E10_Med15-9MYC_kin28as_15mNAPP1_comb_shift6_1.06_normMean20_Roman.bedgraph is available on GSM2143301

value: MAT_alpha ade2::hisG his3_delta_200 leu2_delta_0 lys2_delta_0 met15_delta_0 trp1_delta_63 ura3_delta_0 kin28::kin28as (L83G) MED15-9xMYC::klTRP1 [pSH579, CEN URA3 kin28as (L83G)]


title: 60004sacCer3XO_yFR763_9E10_NoTag_Kin28as_15mNAPP1_rep2

description:
Biological replicate 2 of 2, IP with 9E10 antibody, no-tag control for kin28as strain,  negative control used for normalization of bedgraphs
protocol: ChIP-exo

value: MAT_alpha ade2::hisG his3_delta_200 leu2_delta_0 lys2_delta_0 met15_delta_0 trp1_delta_63 ura3_delta_0 kin28::kin28as (L83G) [pSH579, CEN URA3 kin28as (L83G)]


title: Hypoxia_48hr (precursor miRNA)_7

description:
Library_7
precursor miRNA


title: Normoxia_48hr (total RNA)_5

description:
Library_5
RNA


title: Normoxia_48hr (total RNA)_6

description:
Library_6
RNA


title: 60007sacCer3XO_yFR1638_9E10_Med15-9MYC_Kin28as_15mNAPP1_rep1

description:
Biological replicate 1 of 2, Med15-9MYC IP with 9E10 antibody in kin28as strain
protocol: ChIP-exo


title: 60003sacCer3XO_yFR763_9E10_NoTag_Kin28as_15mNAPP1_rep1

description:
Biological replicate 1 of 2, IP with 9E10 antibody, no-tag control for kin28as strain, negative control used for normalization of bedgraphs
protocol: ChIP-exo


title: Hypoxia_6hr (total RNA)_4

description:
Library_4
RNA


title: Hypoxia_6days (total RNA)_12

description:
Library_12
RNA


title: Line 202 Sorafenib Replicate 1

city: Stanford

first: Jared

last: Churko

address: 265 Campus Dr G1105 SIM1

department: Radiology

institute: Stanford

description:
72 hour 1uM Sorafenib Treatment
202S

data_processing:
RNA-seq: reads were deduplicated using prinseq, mapped to reference Ensembl GRCh38 genome using Tophat and RPKM values were obtained using AltAnalyze 2.0.8
Genome_build: GRCh38
Supplementary_files_format_and_content: text file with RPKM values.

source_name: hiPSC-CM d30

growth_protocol: CDM3 differentiation protocol, day 30 hiPSC-CMs from TKI healthy control lines

extract_protocol:
Qiagen RNAEasy Micro Kit
Libraries were made with random hexamer priming instead of poly-A

treatment_protocol: 72 hour treatment with/without 1uM Sorafenib (VEGFR2/PDGFR2-inhibiting TKI) (LC Labs)

value: Induced Pluripotent Stem Cell Cardiomyocytes

value: 72 hour 1uM Sorafenib Treatment

value: hiPSC-CM line 202


title: Line 78 Sorafenib Replicate 1

description:
72 hour 1uM Sorafenib Treatment
78S

value: hiPSC-CM line 78


title: Normoxia_6hr (total RNA)_2

description:
Library_2
RNA

value: Ovarian cancer


title: Hypoxia_6hr (total RNA)_3

description:
Library_3
RNA

value: epithelial ovarian cancer cell line A2780


title: Line 113 Sorafenib Replicate 1

description:
72 hour 1uM Sorafenib Treatment
113S

value: hiPSC-CM line 113


title: Line 116 Sorafenib Replicate 1

description:
72 hour 1uM Sorafenib Treatment
116S

value: hiPSC-CM line 116


title: Normoxia_6hr (total RNA)_1

description:
Library_1
RNA

value: control


title: Line 112 Sorafenib Replicate 1

description:
72 hour 1uM Sorafenib Treatment
112S

value: hiPSC-CM line 112


title: tel1 5 h sample 1

city: New York

first: Neeman

last: Mohibullah

state: NY

address: 1275 York Avenue

department: Molecular Biology

institute: MSKCC

description: Spo11-associated DNA oligonucleotides

data_processing:
Base calls perfomed using HiSeq Control Software v.2.0.10.0 for samples sequenced on Illumina HiSeq 2500
Adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were clipped from reads using fastx_clipper, part of the FASTX Toolkit 0.0.13.2, with parameters -l 15 -n -v -Q33 -i
First five bases (diffusion primer added in library prep) in each sequence were trimmed and trimmed sequence was recorded in the FASTQ ID tag for downstream tracking
Clipped reads were mapped using SHRiMP 2.1.1b with parameters -N 15 -U -g -1000 -q -1000 -m 10 -i -20 -h 100 -r 50% -n 1 -s 1111111111,11110111101111,1111011100100001111,1111000011001101111 -o 1001 -Q -E --sam-unaligned --strata
Sequences clipped from a read during mapping should be polyC on the 3' end or polyG on the 5' end. If clipped bases were not polyC or polyG the alignment score was corrected by deducting the mismatch score for each non-C,G base in the clipped sequence.
Maps of 5' ends of sequence reads were compiled and analyzed in R (RStudio version 0.98.1091, R version 3.0.1)
Genome_build: Reads were mapped to the SGD assembly released in June 2008, called "sacCer2" by UCSC: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=340067645
Supplementary_files_format_and_content: wig files include RPM (reads per million mapped) for each sample at each non-zero base position in the genome

source_name: tel1∆ 5 h_meiotic culture

growth_protocol: Synchronized meiotic cultures were prepared in 2% potassium acetate at 30°C by the SPS pre-growth method as described in Murakami et al. (2009) Methods Mol Biol 557: 117-142

extract_protocol:
Based on Thacker et al 2014 Nature, with modifications. Whole cell extracts were prepared by grinding frozen cells in a bead mill and resuspending powder in 10%TCA. Pellets were then extracted with SDS and soluble protein was subjected to affinity purification of Spo11-Protein A fusion with IgG-coated Dynabeads. Protein was digested with proteinase K and Spo11-associated oligonucleotides were recovered by ethanol precipitation.
Based on Pan et al. 2011 Cell, and Thacker et al. 2014 Nature. Oligonucleotides were tailed with ribo-G using rGTP and terminal transferase, then ligated to duplex DNA adaptors with a dC overhang using T4 RNA ligase 2. Complementary strands were synthesized with Klenow, then purified by denaturing polyacrylamide electrophoresis. Purified complementary strands were subjected to 3' tailing with ribo-G using rGTP and terminal transferase, then another duplex adaptor was ligated using T4 RNA ligase 2. Ligated material was amplified with 16 cycles of PCR to add Illumina HiSeq adaptors

tag: epitope tag

tag: artificial hotspot

tag: time in meiosis

value: 5 hr in meiosis


title: tel1 5 h sample 2

description: Spo11-associated DNA oligonucleotides


title: Line 78 Control Replicate 1

description:
Control
78C

tag: cell type

value: Control


title: Taf1Med14AAGCrap_20m_(20160115_SG_Sc_59_pRap_mSM_5)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Taf1 ChEC-seq in Med14 anchor-away strain in GC medium with rapamycin, 20 minutes after calcium addtion

data_processing: 1. We used Novoalign 2.08.03 (http://www.novocraft.com) with options -a -r Random to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. If a read was mapped to multiple locations, one location was picked at random.  2. We extracted properly paired reads (Supplementary file .bed). 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of fragment ends mapped, and then multiplying by the total number of mapped base pairs (Supplementary file .wig).  Generation and normalization of tracks was performed with https://github.com/zentnerlab/chec-seq/blob/master/pairs_single_end_sizes.pl.

source_name: Taf1 ChEC-seq

extract_protocol: See Series supplementary file Zenter_protocol.rtf

tag: growth medium

value: GC-ile-val + 1 _g/mL rapamycin


title: Taf1Med14AAGCrap_10m_(20160115_SG_Sc_59_pRap_mSM_4)

description: Taf1 ChEC-seq in Med14 anchor-away strain in GC medium with rapamycin, 10 minutes after calcium addtion

tag: strain


title: Line 113 Control Replicate 1

description:
Control
113C

tag: treatment


title: Taf1Med14AAGCrap_30s_(20160115_SG_Sc_59_pRap_mSM_1)

description: Taf1 ChEC-seq in Med14 anchor-away strain in GC medium with rapamycin, 30 seconds after calcium addition


title: Taf1Med14AAGCrap_1m_(20160115_SG_Sc_59_pRap_mSM_2)

description: Taf1 ChEC-seq in Med14 anchor-away strain in GC medium with rapamycin, 1 minute after calcium addition


title: Taf1Med14AAGCrap_0s_(20160115_SG_Sc_59_pRap_mSM_0)

description: Taf1 ChEC-seq in Med14 anchor-away strain in GC medium with rapamycin, no calcium


title: Line 112 Control Replicate 1

description:
Control
112C


title: Line 202 Control Replicate 1

description:
Control
202C


title: Taf1Med14AAGCnorap_20m_(20160115_SG_Sc_59_mRap_mSM_5)

description: Taf1 ChEC-seq in Med14 anchor-away strain in GC medium without rapamycin, 20 minutes after calcium addtion

value: GC-ile-val


title: 9941_H460-RNF-2

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

description: RNA subjected to RNAseq

data_processing:
Illumina Casava1.8 software used for basecalling. Raw short sequence fragments were accepted if they passed the quality filtering parameters used in the Illumina GA Pipeline GERALD stage.
Sequenced reads were mapped to hg19 whole genome using tophat-v2.0.8b
Aligned reads was normalized by edgeR bioconductor package and outputed as normalized counts file
Genome_build: Genome Reference Consortium GRCh37
Supplementary_files_format_and_content: normalized counts in txt format for all 14 samples

source_name: Lung cancer cell lines

growth_protocol: In vitro cell culture

extract_protocol:
Total RNA was extracted at 72h posttransfection with RNAeasy Kit (Qiagen)
Transcriptome libraries were constructed with TruSeq RNA Sample Preparation Kit V2 (Illumia, San Diego, USA) with minor modifications.

treatment_protocol: siRNA-mediated knockdown of target gene

tag: tissue

value: Lung cancer cell lines

tag: sirna knockdown

value: RNF20 siRNA 2 tranfected


title: Line 116 Control Replicate 1

description:
Control
116C

tag: cell line


title: cisplatin_model_seq

city: Hangzhou

first: Xushen

last: Xiong

state: Zhejiang

address: Wenyi Road West

department: Medical Center

institute: Zhejiang University

data_processing:
Tirm_galore[version 0.3.7, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/] was used to remove or trim adaptor contained reads and low quality reads, requiring the minimum length of trimmed reads to be 25 bases.
Remaining paired reads were mapped to the human reference genome (Assembly hg19, downloaded from UCSC) using bowtie2 (version 2.1.0),  with parameters "--sensitive --end-to-end --no-discordant -N 1".
Artificial duplicated reads were marked and removed with picard tools (version 1.128) under default parameters
Reads mapped to forward strand and reverse strand of genome were separated for subsequent analysis. Performed with samtools (version 1.3.1).
Peak calling was performed using MACS2 (version 2.1.0.20140616), other analyses were performed with in-house perl scripts.
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] peak files generated with MACS2, including the 10 columns: chromsome id; start position; end position; peak length; peak summit; peak reads pileup; -log10(p-value); fold_enrichment; -log10(q-value); peak-id

molecule: other

organism: synthetic construct

source_name: In vitro synthesized cisplatin-DNA adducts model sequences

growth_protocol: cells maintained in DMEM with 10% FBS and penicillin/streptomycin.

extract_protocol:
Genomic DNA was extracted by DNAzol (Invitrogen), followed by ultrasonic fragmention, and then rotated with HMGB1 domain A coupled beads in pull-down buffer.
Purified DNA was used for End Repair/ dA –Tailing and adaptor ligation (New England Biolabs, NEBNext® Ultra™ DNA Library Prep Kit E7370) following the manufacturer’s guidelines. The adaptor was self-designed (1st 3’block adaptor) to ensure only the 3’ end of DNA can be ligated with adaptor. After the adaptor ligation reaction, DNA was purified using 1 volumes of Ampure XP. Bio-elong primer (10 μM, 0.5 μL) was used for primer extension by NEBNext® High-Fidelity 2X PCR Master Mix. PCR machine program for primer extension is 98℃ 40s, 54℃ 30s, 72℃ 5 min. Then 1 μL exonucleaseⅠwas added to remove free primers in 37 ℃ for 1 h and heat inactivated by 80 ℃ 20 min. Extended DNA was purified by streptavidin C1 beads (Invitrogen) and the non-biotinylated templates were removed by 0.15 M NaOH. Biotinylated DNA was eluted by 95 ℃ 3 min using deionized water. Subsequently, ssligation adaptor (100 μM, 0.6 μL) was ligated by circLigaseⅡ ssDNA Ligase (EpiCenter) in 20 μL reaction with MnCl2 and Betaine according to the instruction for 16 h at 60℃. After ligation, biotinylated DNA fragments were captured on streptavidin C1 beads (Invitrogen) and redundant ssligation adaptor was removed by wash three times. Eluted DNA was subjected to PCR amplification.

treatment_protocol: 50 μM cisplatin was added to the growth medium for different times

tag: sample type

value: synthesized cisplatin-DNA adducts

tag: enrichment


title: Taf1Med14AAGCnorap_10m_(20160115_SG_Sc_59_mRap_mSM_4)

description: Taf1 ChEC-seq in Med14 anchor-away strain in GC medium without rapamycin, 10 minutes after calcium addtion


title: Taf1Med14AAGCrap_5m_(20160115_SG_Sc_59_pRap_mSM_3)

description: Taf1 ChEC-seq in Med14 anchor-away strain in GC medium with rapamycin, 5 minutes after calcium addtion


title: 9940_H460-RNF-1

description: RNA subjected to RNAseq

value: RNF20 siRNA 1 tranfected


title: 9937_H1299-RNF-2

description: RNA subjected to RNAseq


title: Taf1Med14AAGCnorap_1m_(20160115_SG_Sc_59_mRap_mSM_2)

description: Taf1 ChEC-seq in Med14 anchor-away strain in GC medium without rapamycin, 1 minute after calcium addition


title: Taf1Med14AAGCnorap_0s_(20160115_SG_Sc_59_mRap_mSM_0)

description: Taf1 ChEC-seq in Med14 anchor-away strain in GC medium without rapamycin, no calcium


title: Taf1Med14AAGCnorap_30s_(20160115_SG_Sc_59_mRap_mSM_1)

description: Taf1 ChEC-seq in Med14 anchor-away strain in GC medium without rapamycin, 30 seconds after calcium addition


title: 9939_H460-Ctrl-2

description: RNA subjected to RNAseq

value: Control siRNA 2 transfected


title: Taf1Med14AAGCnorap_5m_(20160115_SG_Sc_59_mRap_mSM_3)

description: Taf1 ChEC-seq in Med14 anchor-away strain in GC medium without rapamycin, 5 minutes after calcium addtion


title: 9936_H1299-RNF-1

description: RNA subjected to RNAseq


title: Med8Taf1AAGCrap_10m_(20160115_SG_Sc_61_pRap_mSM_4)

description: Med8 ChEC-seq in Taf1 anchor-away strain in GC medium with rapamycin, 10 minutes after calcium addtion

source_name: Med8 ChEC-seq


title: Med8Taf1AAGCrap_5m_(20160115_SG_Sc_61_pRap_mSM_3)

description: Med8 ChEC-seq in Taf1 anchor-away strain in GC medium with rapamycin, 5 minutes after calcium addtion


title: 9935_H1299-Ctrl-2

description: RNA subjected to RNAseq


title: 9933_A549-RNF-2

description: RNA subjected to RNAseq


title: 9932_A549-RNF-1

description: RNA subjected to RNAseq


title: Med8Taf1AAGCrap_1m_(20160115_SG_Sc_61_pRap_mSM_2)

description: Med8 ChEC-seq in Taf1 anchor-away strain in GC medium with rapamycin, 1 minute after calcium addition


title: 9931_A549-Ctrl-2

description: RNA subjected to RNAseq


title: Med8Taf1AAGCrap_30s_(20160115_SG_Sc_61_pRap_mSM_1)

description: Med8 ChEC-seq in Taf1 anchor-away strain in GC medium with rapamycin, 30 seconds after calcium addition


title: Med8Taf1AAGCrap_0s_(20160115_SG_Sc_61_pRap_mSM_0)

description: Med8 ChEC-seq in Taf1 anchor-away strain in GC medium with rapamycin, no calcium


title: Med8Taf1AAGCnorap_20m_(20160401_SG_Sc_61_mRap_mSM_5)

description: Med8 ChEC-seq in Taf1 anchor-away strain in GC medium without rapamycin, 20 minutes after calcium addtion


title: 9929_BEAS-2B-RNF-2

description: RNA subjected to RNAseq

source_name: Normal lung epithelial cell

value: Normal epithelial cells


title: Med8Taf1AAGCnorap_10m_(20160401_SG_Sc_61_mRap_mSM_4)

description: Med8 ChEC-seq in Taf1 anchor-away strain in GC medium without rapamycin, 10 minutes after calcium addtion


title: 9926_BEAS-2B-Ctrl-1

description: RNA subjected to RNAseq

value: Control siRNA 1 transfected


title: 9927_BEAS-2B-Ctrl-2

description: RNA subjected to RNAseq


title: hnRNPA2/B1_eCLIP_014

description: eCLIP RNA

data_processing:
Reads were demultiplexed using custom scripts and the randomer was appended to the read name. Reads were trimmed, filtered for repetitive elements, and mapped to human genome assembly hg19 as described in iCLIP computational analysis. PCR duplicated reads were removed based on the start positions of read1, read2, and the sequence of the randomer. eCLIP peaks were identified using CLIPPER with parameters  –s hg19 –o –bonferroni –superlocal --threshold-method binomial --save-pickle (Lovci et al. NSMB, 2013). Peak strength was then normalized against a size matched input by calculating fold enrichment of number of reads in IP versus number of reads in size matched input.  Peaks were called significant if the number of reads in IP was greater than the number of reads in input and the the peaks a Bonferroni corrected fisher exact p-value of less than .05.
Genome_build: hg19
Supplementary_files_format_and_content: peaks.bed and bigwig

source_name: iPSC derived motor neurons

growth_protocol: CTRL.JCV iPSCs were differentiated into motor neurons as described. Samples were harvested 28 days post neural induction.

extract_protocol:
10cm dishes of motor neuros were rinsed in PBS and UV crosslinked. Crosslinked cells were peletted and snap frozen in liquid nitrogen
eCLIP libraries were prepared as previously described (Van Nostrand et al. 2016) using rabbit polyclonal antibody GTX127928 (Genetex) (10 mg per sample). Human iPSC-MNs were differentiated in culture for 28 days. Approximately 20 million cells were UV crosslinked at λ=254nm with 4000 mJ/cm2 of energy. Crosslinked cell pellets were lysed and treated with RNAse I (Ambion). Lysate was immunoprecipitated using rabbit polyclonal antibody GTX127928 (Genetex) (10 g per sample) and Dynabeads Protein G (Thermo Fisher Scientific). Immunoprecipitated samples were washed and dephosphorylated with Fast AP (Thermo Fisher Scientific). 3’ phosphates were applied using T4 PNK (NEB) and a 3’ RNA adapter was ligated using T4 RNA Ligase (NEB). Samples were run on PAGE gels and transferred to nitrocellulose membranes. A region of membrane spanning 75kDa above the molecular weight of hnRNP A2/B1 was cut and RNA was recovered using Proteinase K and phenol-chloroform. RNA was reverse transcribed using Affinityscript (Agilent Technologies) and treated with ExoSAP-IT (Affymetrix). A DNA adapter containing a 5nt randomer was then ligated to the 3’ end (T4 RNA Ligase, NEB). Samples were purified using Dynabeads MyOne Silane (Thermo Fisher Scientfic), quantified by qPCR, and then PCR amplified to the appropriate number of cycles. Amplified libraries were size selected with an agarose gel, quantified using the Agilent Tapestation, and sequenced on the Illumina HiSeq 2500 platform using paired end 50bp reads.

tag: age

value: 28 days

tag: tissue type

value: iPSC-MNs

tag: vendor

tag: catalog number

tag: lot number


title: 9928_BEAS-2B-RNF-1

description: RNA subjected to RNAseq


title: Med8Taf1AAGCnorap_5m_(20160401_SG_Sc_61_mRap_mSM_3)

description: Med8 ChEC-seq in Taf1 anchor-away strain in GC medium without rapamycin, 5 minutes after calcium addtion

tag: genotype


title: Med8Taf1AAGCnorap_30s_(20160401_SG_Sc_61_mRap_mSM_1)

description: Med8 ChEC-seq in Taf1 anchor-away strain in GC medium without rapamycin, 30 seconds after calcium addition


title: Med8Taf1AAGCnorap_1m_(20160401_SG_Sc_61_mRap_mSM_2)

description: Med8 ChEC-seq in Taf1 anchor-away strain in GC medium without rapamycin, 1 minute after calcium addition


title: 9938_H460-Ctrl-1

description: RNA subjected to RNAseq


title: Med8Taf1AAGCrap_20m_(20160115_SG_Sc_61_pRap_mSM_5)

description: Med8 ChEC-seq in Taf1 anchor-away strain in GC medium with rapamycin, 20 minutes after calcium addtion


title: Med8Taf1AAGCnorap_0s_(20160401_SG_Sc_61_mRap_mSM_0)

description: Med8 ChEC-seq in Taf1 anchor-away strain in GC medium without rapamycin, no calcium


title: Med8Kin28ASnoNAPP1_10m_(20160212_SG_Sc_69d15_M8mSM_4)

description: Med8 ChEC-seq in Kin28AS strain in GC medium without 1-Napththyl PP-1 (NA-PP1), 10 minutes after calcium addtion


title: Med8Kin28ASnoNAPP1_20m_(20160212_SG_Sc_69d15_M8mSM_5)

description: Med8 ChEC-seq in Kin28AS strain in GC medium without 1-Napththyl PP-1 (NA-PP1), 20 minutes after calcium addtion


title: hnRNPA2/B1_eCLIP_013

description: eCLIP RNA

tag: antibody

value: hnRNP A2/B1

value: Genetex


title: 9934_H1299-Ctrl-1

description: RNA subjected to RNAseq


title: hnRNPA2/B1_eCLIP_011

description: eCLIP RNA


title: hnRNPA2/B1_eCLIP_010

description: eCLIP RNA


title: hnRNPA2/B1_eCLIP_012

description: eCLIP RNA


title: Med8Kin28ASnoNAPP1_5m_(20160212_SG_Sc_69d15_M8mSM_3)

description: Med8 ChEC-seq in Kin28AS strain in GC medium without 1-Napththyl PP-1 (NA-PP1), 5 minutes after calcium addtion


title: hnRNPA2/B1_eCLIP_009

description: eCLIP RNA


title: hnRNPA2/B1_eCLIP_008

description: eCLIP RNA


title: Med8Kin28ASnoNAPP1_1m_(20160212_SG_Sc_69d15_M8mSM_2)

description: Med8 ChEC-seq in Kin28AS strain in GC medium without 1-Napththyl PP-1 (NA-PP1), 1 minute after calcium addition


title: hnRNPA2/B1_eCLIP_007

description: eCLIP RNA


title: Med8Kin28ASNAPP1_20m_(20160315_SG_Sc_69_pNAmSM_5)

description: Med8 ChEC-seq in Kin28AS strain in GC medium with 1-Napththyl PP-1 (NA-PP1), 20 minutes after calcium addtion

value: GC-ile-val + 6 _M NA-PP1


title: hnRNPA2/B1_eCLIP_006

description: eCLIP RNA


title: Med8Kin28ASNAPP1_10m_(20160315_SG_Sc_69_pNAmSM_4)

description: Med8 ChEC-seq in Kin28AS strain in GC medium with 1-Napththyl PP-1 (NA-PP1), 10 minutes after calcium addtion


title: hnRNPA2/B1_eCLIP_004

description: eCLIP RNA


title: hnRNPA2/B1_eCLIP_005

description: eCLIP RNA


title: Med8Kin28ASNAPP1_5m_(20160315_SG_Sc_69_pNAmSM_3)

description: Med8 ChEC-seq in Kin28AS strain in GC medium with 1-Napththyl PP-1 (NA-PP1), 5 minutes after calcium addtion


title: hnRNPA2/B1_eCLIP_003

description: eCLIP RNA


title: Med8GCSM_20m_(20150724_GZ_Sc_SM_20m)

description: Med8 ChEC-seq in GC medium with sulfometuron methyl (SM), 20 minutes after calcium addtion

value: GC-ile-val + 0.5 _g/mL SM


title: Med8GCSM_10m_(20150724_GZ_Sc_SM_10m)

description: Med8 ChEC-seq in GC medium with sulfometuron methyl (SM), 10 minutes after calcium addtion


title: Med8Kin28ASNAPP1_30s_(20160315_SG_Sc_69_pNAmSM_1)

description: Med8 ChEC-seq in Kin28AS strain in GC medium with 1-Napththyl PP-1 (NA-PP1), 30 seconds after calcium addition


title: hnRNPA2/B1_eCLIP_001

description: eCLIP RNA


title: hnRNPA2/B1_eCLIP_002

description: eCLIP RNA


title: Med8GCSM_5m_(20150724_GZ_Sc_SM_5m)

description: Med8 ChEC-seq in GC medium with sulfometuron methyl (SM), 5 minutes after calcium addtion


title: INPUT

city: Beijing

first: xiong

middle: will

last: wei

address: 7 Science Park Road ZGC Life Science Park

institute: NIBS,Beijing

description: no

data_processing:
FASTX-Toolkit  for assessing sequencing quality
Alignment: Bowtie 2 version 2.2.1 for chip-seq
peaks were called using MACS1.4
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files chip-seq

source_name: U2OS cells

growth_protocol: DMEM plus 10% FBS for U2OS cells

extract_protocol:
NEXTflex ChIP-seq Kit, Bioo Scientific for chip-seq
ChIP-seq procedure as previously described (Cell. 2013 May 9;153(4):855-68). For the Bmal1 and IgG ChIP-seq, the RIPA buffer was diluted 1 to 10. For HIF1A CHIP-seq, protocols are used as described (ChIP-IT high sensitive kit (Cat# 53040, Active Motif)). The library was constructed using a commercially available kit (NEXTflex ChIP-seq Kit, Bioo Scientific). Samples were indexed using NEXTflex™ DNA Barcodes (Bioo Scientific). The library was qualified using an Agilent 2100 Bioanalyzer (Agilent) and quantified using KAPA Library Quantification Kits (Kappa Biosystems). Finally, the indexed libraries were sequenced using a HiSeq 2500 (Illumina).

treatment_protocol: serum shock the U2OS cell for 30h (circadian peak) and 42h (circadian trough) and treated with DMOG and DMSO respectively

value: ATCC HTB-96

value: bone

value: circadian peak  wildtype

tag: chip antibody

value: no


title: Med8GCSM_1m_(20150724_GZ_Sc_SM_1m)

description: Med8 ChEC-seq in GC medium with sulfometuron methyl (SM), 1 minute after calcium addition


title: ChIP_hHIF1a-trough-DMSO CHIP-Seq

description: ChIP-IT high sensitive kit (Cat# 53040, Active Motif)

value: active motif (cat # 39668).


title: Med8GCSM_30s_(20150724_GZ_Sc_SM_30s)

description: Med8 ChEC-seq in GC medium with sulfometuron methyl (SM), 30 seconds after calcium addition


title: ChIP_hHIF1a-peak-DMOG CHIP-Seq

value: cry1, cry2 double knockout

value: active motif (cat # 39665).


title: ChIP_hHIF1a-trough-DMOG CHIP-Seq

value: circadian trough wildtype

value: active motif (cat # 39666).


title: ChIP_hBMAL1-trough-DMSO CHIP-Seq

description: using standard  protocol as cited in the paper (Cell. 2013 May 9;153(4):855-71)

value: abcam ab3350


title: Med8GCnoSM_20m_(20150724_GZ_Sc_ctrl_20m)

description: Med8 ChEC-seq in GC medium without sulfometuron methyl (SM), 20 minutes after calcium addtion

value: GC-ile-val


title: Med8Kin28ASnoNAPP1_30s_(20160212_SG_Sc_69d15_M8mSM_1)

description: Med8 ChEC-seq in Kin28AS strain in GC medium without 1-Napththyl PP-1 (NA-PP1), 30 seconds after calcium addition


title: ChIP_hHIF1a-peak-DMSO CHIP-Seq

value: active motif (cat # 39667).


title: ChIP_hBMAL1-trough-DMOG CHIP-Seq

description: using standard  protocol as cited in the paper (Cell. 2013 May 9;153(4):855-69)

value: osteosacoma


title: ChIP_hBMAL1-peak-DMOG CHIP-Seq

description: using standard  protocol as cited in the paper (Cell. 2013 May 9;153(4):855-68)


title: Med8Kin28ASNAPP1_1m_(20160315_SG_Sc_69_pNAmSM_2)

description: Med8 ChEC-seq in Kin28AS strain in GC medium with 1-Napththyl PP-1 (NA-PP1), 1 minute after calcium addition


title: Med8GCnoSM_10m_(20150724_GZ_Sc_ctrl_10m)

description: Med8 ChEC-seq in GC medium without sulfometuron methyl (SM), 10 minutes after calcium addtion


title: Med8GCnoSM_5m_(20150724_GZ_Sc_ctrl_5m)

description: Med8 ChEC-seq in GC medium without sulfometuron methyl (SM), 5 minutes after calcium addtion


title: Hela_IP_24h_rep2

value: Hela cervical cancer cell line

value: Enriched with HMGB1 domain A

value: cisplatin

tag: time


title: Hela_IP_24h_rep1


title: Hela_IP_12h_rep2


title: Med8GCnoSM_1m_(20150724_GZ_Sc_ctrl_1m)

description: Med8 ChEC-seq in GC medium without sulfometuron methyl (SM), 1 minute after calcium addition

tag: growth medium


title: Hela_IP_12h_rep1


title: Med8GCnoSM_30s_(20150724_GZ_Sc_ctrl_30s)

description: Med8 ChEC-seq in GC medium without sulfometuron methyl (SM), 30 seconds after calcium addition

tag: strain


title: Med8GCnoSM_0s_(20150724_GZ_Sc_ctrl_0s)

description: Med8 ChEC-seq in GC medium without sulfometuron methyl (SM), no calcium


title: Hela_IP_3h_rep1

tag: treatment


title: Hela_IP_3h_rep2


title: Med8GCSM_0s_(20150724_GZ_Sc_SM_0s)

description: Med8 ChEC-seq in GC medium with sulfometuron methyl (SM), no calcium

value: GC-ile-val + 0.5 _g/mL SM


title: Hela_IP_ctrl_rep1


title: Med8YPD_10m_(20150513_GZ_Sc_Med8_10m)

description: Med8 ChEC-seq in YPD medium, 10 minutes after calcium addtion

value: YPD


title: Med8YPD_20m_(20150513_GZ_Sc_Med8_20m)

description: Med8 ChEC-seq in YPD medium, 20 minutes after calcium addtion


title: Hela_IP_ctrl_rep2


title: hnRNP A2/B1 ASO 3 [mouse]

description:
D3
mature_counts_mm10.csv

value: spinal cord

value: ASO Hnrnpa2/b1


title: Hela_input


title: Med8YPD_5m_(20150513_GZ_Sc_Med8_5m)

description: Med8 ChEC-seq in YPD medium, 5 minutes after calcium addtion


title: UHR-86

city: Rochester

first: Numrah

middle: Mohammadali

last: Fadra

state: Minnesota

address: 200 2nd Street SW

department: Health Sciences Research

data_processing:
Base calling was performed by the instrument computer using Illumina Real Time Analysis (RTA) software that is integrated with HiSeq Control Software (HCS) and provides a summary of quality statistics as per Illumina's acceptance criteria for sequencing. CASAVA 1.8.2 was used for de-multiplexing and conversion of base calls to paired-end FASTQ files
RNA-Seq data was analyzed using the MAP-RSeq(http://www.ncbi.nlm.nih.gov/pubmed/24972667) pipeline v 1.2 which uses TopHat 2.0.6 to align reads to the human reference GRCh37  without alternative haplotypes. During alignment,TopHat was supplied transcript models from UCSC (March 2012 version) available from Illumina’s iGenomes Project. For the degraded KU812 samples we obtained > 13 million reads per sample and for the degraded UHR and clinical samples we obtained > 80 million reads per sample. Fusion calling was performed using TopHat-Fusion (http://www.ncbi.nlm.nih.gov/pubmed/21835007) with a minimum of 5 fusion supporting reads required
For the UHR samples read coverage was normalized to 50 million reads per sample. The utility DepthOfCoverage from the Genome Analysis Toolkit (GATK) v.1.6.7 was used to query the alignment files to obtain read depth coverage information. Read coverage as a function of the distance to the 3’ end was calculated for genes with expression > 10x at a position 300 bases from the 3’ end.  Linear models and plots were created in R (version 3.1) using ggplot2 v 2.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include fusions found in each sample with annotations on the 5' and 3' gene partners, exons, syupporting read information and genomic breakpoints for each fusion

source_name: cell line

extract_protocol:
RNA quality [RNA Integrity Number (RIN)] was assessed on an Agilent 2100 Bioanalyzer with the RNA 6000 Nano Kit and quantified with a Qubit® 2.0 fluorometer with the Qubit® RNA BR Assay Kit. The TruSeq® RNA Sample Preparation v2 Kit (Illumina, San Diego, CA) was used for isolation of polyadenylated mRNA with oligo-dT beads, second strand cDNA synthesis and NGS library preparation
Paired-end, 101 bp sequencing was performed on a HiSeq 2500 (Illumina) instrument in Rapid Run mode.

tag: histology

value: UHR tumor*

tag: rin score


title: hnRNP A2/B1 ASO 1 [mouse]

description:
D1
mature_counts_mm10.csv


title: hnRNP A2/B1 ASO 2 [mouse]

description:
D2
mature_counts_mm10.csv


title: Med8YPD_1m_(20150513_GZ_Sc_Med8_1m)

description: Med8 ChEC-seq in YPD medium, 1 minute after calcium addition


title: ChIP_hBMAL1-peak-DMSO CHIP-Seq

description: using standard  protocol as cited in the paper (Cell. 2013 May 9;153(4):855-70)

value: ATCC HTB-96

tag: tissue

value: bone


title: RNAseq_Bmal1KO RNA-seq

address: 5 Yiheyuan Rd, Haidian, Beijing, China

institute: peking university

description: oligoT matrix facilitated

data_processing:
FASTX-Toolkit  for assessing sequencing quality
Alignment: Bowtie 2 version 2.2.1 for chip-seq  and TopHat v2.0.11 for RNA-seq
cufflinks v2.2.0 for RNA-seq assembling and differential analysis
peaks were called using MACS1.4
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: bigwig files for RNA-seq and chip-seq

source_name: MEF cells

growth_protocol: DMEM plus 10% for both MEF and U2OS cells

extract_protocol:
total RNA was extracted using a RNeasy MinElute Cleanup Kit
NEBNext DNA Library Prep Master Mix Set for Illumina for RNA-seq and NEXTflex ChIP-seq Kit, Bioo Scientific for chip-seq
RNA-seq: total RNA was extracted using a RNeasy MinElute Cleanup Kit (QIAGEN, Catalog no. 74204). Double-stranded cDNA was synthesized according to the mRNA Sequencing Sample Preparation Guide (part#1004898 Rev.D, Illumina, San Diego, CA) and single-end libraries were prepared using the NEBNext DNA Library Prep Master Mix Set for Illumina (New England BioLabs, Catalog no.74204 E6040L).   For RNA-seq of RNaseH treated MEF cells, the protocols were mainly adopted as previously described (Nat Methods 10: 623-629).  For qRNA-seq of MEF cells, the GeneRead rRNA Depletion Kit (Qiagen) was used to remove ribosome RNA.  Nascent RNA-seq of U2OS cells was performed as previously described (Science 322: 1845-1848), with the exception of not applying a strand specific method.
ChIP-seq procedure as previously described (Cell. 2013 May 9;153(4):855-68). For the Bmal1 and IgG ChIP-seq, the RIPA buffer was diluted 1 to 10. For HIF1A CHIP-seq, protocols are used as described (ChIP-IT high sensitive kit (Cat# 53040, Active Motif)). The library was constructed using a commercially available kit (NEXTflex ChIP-seq Kit, Bioo Scientific). Samples were indexed using NEXTflex™ DNA Barcodes (Bioo Scientific). The library was qualified using an Agilent 2100 Bioanalyzer (Agilent) and quantified using KAPA Library Quantification Kits (Kappa Biosystems). Finally, the indexed libraries were sequenced using a HiSeq 2500 (Illumina).

treatment_protocol: serum shock the MEF cell for 24h (circadian peak) and 36h (circadian trough)

value: embryonic-fibrobalst


title: RNAseq_CryDKO RNA-seq

description: oligoT matrix facilitated

value: cry1, cry2 double knockout


title: RNAseq_WT-T RNA-seq

description: oligoT matrix facilitated

value: circadian peak  wildtype


title: saline control 3 [mouse]

description:
A3
mature_counts_mm10.csv

value: saline


title: RNAseq_WT-P RNA-seq

description: oligoT matrix facilitated

value: circadian trough wildtype


title: UHR76

tag: sample type