title: i3CBEs_3CBEdel_sti_iCBE_2_3

source_name: CH12F3 murine lymphoma cells

value: CH12F3 murine lymphoma cells

value: AID-/-; non-coding alele deletion; Ia deletion; three CBE insertion with the convergent orientation as 3'CBE downstream of Cg2a


title: Woodchuck_12

status: Public on Sep 25 2019

type: SRA

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

library_source: transcriptomic

data_processing:
Basecalling and sample de-multiplexing was performed with CASAVA-1.8.4 and default parameters
Reads were quality check with fastqc v0.11.5 default parameters
Reads for each sample/replicate were mapped against the woodchuck genome assembly using the gem-tools rna-mapper v1.6.1 with default options
Transcripts were quantified with gemtools version 1.7.1 using the Monax4B annotation.
Genome_build: Monax4B
http://denovo.cnag.cat/woodchuck
Supplementary_files_format_and_content: Read counts per transcript

molecule: polyA RNA

organism: Marmota monax

source_name: Liver

extract_protocol:
Sequencing libraries were prepared from either 100 ng or one µg of total RNA using the Illumina TruSeq RNA Sample preparation Kit v2 according to manufacturer’s instructions. Sequencing libraries were quantified using the Kapa Library Quantification kit (Kapa Biosystems) and quality controlled by capillary electrophoresis on a Bioanalyzer using DNA 1000 chips (Agilent Technologies).
Libraries were sequenced on a HiSeq2500 sequencer (Illumina) for 2 x 125 cycles using version 3 cluster generation kits and version 3 sequencing reagents (Illumina). The PhiX control library (Illumina) was spiked into each sample (at 1%) as a sequencing control.

tag: common name

value: Eastern woodchuck

tag: tissue

value: Liver

tag: individual


title: PD Patient # 12

type: RNA

city: Lille

first: Marie-Christine

last: Chartier-Harlin

address: 1 place de Verdun

country: France

institute: INSERM

description: Trasncriptomic profiling of peripheral blood mononuclear cells from patients with Parkinson's disease and control subjects

hyb_protocol: Scanned on an Agilent G2505B scanner and Agilent-014850 whole Human genome microarrays 4x44K (Probe Name Version).

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.9.5.3.1).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (Grid: 014850_D_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Homo sapiens

source_name: PD Patient # 12

label_protocol: Cyanine-3 (Cya3) labeled cRNA was prepared from 1650 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN), Valencia, CA). Dye incorporation and cRNA yield were with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Blood from control and PD subjects was collected in Vacutainer® CPT Cell Preparation Tubes (Becton Dickinson, Le Pont-de-Claix, France) and PBMC from human samples were isolated on a ficoll gradient. Total RNA from 5 x 106 cells was isolated using Rneasy mini-columns (Qiagen, Courtaboeuf, France). RNA concentration was measured by absorbance at 260nm using a Nanodrop ND-1000 spectrophotometer. RNA quality and integrity were checked using the RNA 6000 NanoChip kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Massy, France). All samples included in the study had a RIN>9.

tag: disease state

value: Parkinson's disease

tag: cell type

value: peripheral blood mononuclear cells


title: Control sample N°20

source_name: Control sample N°20

value: control


title: Control sample N°17

source_name: Control sample N°17


title: Woodchuck_11


title: Woodchuck_10

source_name: Thymus

value: Thymus


title: Control sample N°18

source_name: Control sample N°18


title: Iadel_sti_iEm_2_1

city: Boston

first: Frederick

middle: W

last: Alt

state: MA

address: 1 Blackfan Circle

department: PCMM

country: USA

institute: Boston Children's Hospital

library_source: genomic

data_processing:
Library strategy: 3C-HTGTS
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files were generated for displaying (Jane et al., 2018)

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
About 10 million cells were crosslinked with 2% formaldehyde for 10 minutes at room temperature and quenched with glycine at a final concentration of 125 mM. Then, the crosslinked cells were lysed in the 3C lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, protease inhibitors) and nuclei were digested with NlaIII enzyme (NEB, R0125) at 37 ℃ overnight.  They were then brought to 16℃, 100U of T4 ligase added  (Promega, M1801) and they incubated again overnight at 16℃.  The ligated products were de-crosslinked with Proteinase K (Roche, #03115852001) at 56 ℃ overnight and the 3C templates were purified by phenol/chloroform.
Libraries were prepared using 3C samples by HTGTS (Jane et al., 2018).

treatment_protocol: Purified B cells were stimulated with either aCD40/IL4 for 48 hrs; CH12F3 cell lines were cultured in lymphocyte medium R15 and stimulated with anti-CD40+IL4+TGF-β for 24 hrs.

tag: genotype

value: IaD-AID-/-

tag: activation

tag: treatment

value: cytokine stimulation

tag: target locus


title: Woodchuck_9

source_name: Pancreas

value: Pancreas


title: PD Patient # 6

source_name: PD Patient # 6


title: Control sample N°19

source_name: Control sample N°19


title: Woodchuck_14

source_name: Spleen

value: Spleen


title: Woodchuck_5

source_name: Heart

value: Heart


title: Woodchuck_13

source_name: Kidney

value: Kidney


title: Woodchuck_7


title: Woodchuck_6


title: Control sample N°14

source_name: Control sample N°14


title: Control sample N°15

source_name: Control sample N°15


title: Woodchuck_4

source_name: Lung

value: Lung


title: Iadel_sti_iEm_1_1


title: Control sample N°12

source_name: Control sample N°12


title: Control sample N°13

source_name: Control sample N°13


title: Iadel_nonsti_iEm_1_1

source_name: CH12F3 murine lymphoma cells


title: Control sample N°10

source_name: Control sample N°10


title: Woodchuck_2


title: i3CBEs_sti_iCBE_2_3


title: Woodchuck_1

source_name: Liver


title: Woodchuck_3


title: Control sample N°16

source_name: Control sample N°16


title: soft palate muscle of patients with OSAHS 4

city: Xi'an

first: Jin

last: Hou

state: Shaanxi

address: 157 Xiwu Road

department: Otolaryngology- Head and Neck Department

country: China

institute: The Second Affiliated Hospital of Xi'an Jiaotong University

description: zhanhongxing

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Four replicated spots of each miRNA probe were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs were identified through Fold Change filtering (>=2).

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

growth_protocol: All patients with OSAHS and chronic tonsilitis were inpatients who had surgery in ENT depatment of the Second Affillited Hospital of Xi'an Jiaotong Univesity. 4 patients with OSAHS were received UPPP, and 4 patients with chronic tonsillitis received tonsillectomy.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: Muscles were obtained from the excision soft palate in operation within 10min seperated from patients, immediately putted into liquid nitrogen.

tag: subject status

value: patients with OSAHS

tag: gender

value: male

tag: age

value: adult

value: soft palate muscle

tag: molecule subtype

value: miRNA


title: Iadel_sti_3RR_3

value: CH12F3 murine lymphoma cells

value: AID-/-; non-coding allele deletion; single CBE insertion with the convergent orientation as 3'CBE downstream of Cg2a


title: soft palate muscle of patients with OSAHS 3

description: wangshuai


title: Woodchuck_8

value: Eastern woodchuck


title: soft palate muscle of patients with OSAHS 2

description: wanglian


title: Control sample N°11

source_name: Control sample N°11

value: control

value: peripheral blood mononuclear cells


title: Iadel_nonsti_iEm_2_1

value: IaD-AID-/-

value: AID-/-; non-coding alele deletion; Ia deletion; three CBE insertion with the convergent orientation as 3'CBE downstream of Cg2a


title: Control sample N°9

source_name: Control sample N°9


title: CH12NCdel_sti_3RR_3

value: cytokine stimulation

value: AID-/-; non-coding allele deletion; single CBE insertion with the same orientation as 3'CBE downstream of Cg2a


title: soft palate muscle of patients with OSAHS 1

description: zhaixiumei

value: female


title: soft palate muscle of patients with chronic tonsillitis 4

description: liyuan

value: patients with chronic tonsillitis


title: soft palate muscle of patients with chronic tonsillitis 3

description: wangdan


title: Iadel_sti_iEm_3

value: AID-/-; non-coding alele deletion; Ia deletion


title: soft palate muscle of patients with chronic tonsillitis 2

description: fangyuanyuan


title: CH12NCdel_nonsti_3RR_3

value: AID-/-; non-coding allele deletion


title: Over-2

city: Tainan

first: Yi-Ching

last: Wang

address: No.1, University Road, Tainan 70101, Taiwan, R. O. C.

department: Department of Pharmacology, College of Medicine

country: Taiwan

institute: National Cheng Kung University

data_processing:
High-throughput sequencing was performed by SOLiD 5500xl sequencer (Applied Biosystems) and abound 9~13 million raw reads were obtained from samples.
The raw reads were further analyzed using LifeScopeTM Genomic Analysis Software (version 2.5), and mapped to human genome (hg19) released from UCSC database.
To find the significant peak, the mapped profiles were analyzed using the ChIP-seq tool in CLC Genomics Workbench (version 4.9). The peak-finding algorithm included the following four steps: 1) Calculate the null distribution of the background sequencing signal; 2) Scan the mappings to identify candidate peaks with a higher read count than expected from the null distribution; 3) Merge overlapping candidate peaks; 4) Refine the set of candidate peaks based on the count and the spatial distribution of forward and backward reads within the peaks. The estimate for the null distribution of coverage and the calculation of the false discovery rate (FDR) were based on the window size and maximum FDR (%) parameters. In this study, the window size and FDR were set to 200 bp and 5%, respectively.
To determine the high confidence ZNF322A binding loci, the ChIP-region was identified by scanning the peaks with significantly higher read count in ZNF322A overexpressing cells compared to those in the vector control cells.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph

source_name: H460 lung cancer cell

growth_protocol: Human lung cells H460 were purchased from American Type Culture Collection. H460 cells were cultured in RPMI1640 (Gibco, Grand Island, NY, USA). All media were supplemented with 10% Fetal Bovine Serum (FBS) (Gibco) and 1% penicillin/streptomycin (Gibco). Cells were incubated at 37oC in a humidified incubator containing 5% CO2.

extract_protocol:
Empty vector control and HA-tagged ZNF322A expressing H460 cells (1 × 10^7 cells) were cross-linked with 1% formaldehyde, followed by preparation of nuclear lysates using Magna ChIP protein G Kit (Millipore, Billerica, MA, USA) according to the protocols provided by the manufacturer. Nuclear lysates were sonicated for shearing crosslinked DNA to around 200~300 bps using Covaris-S2 machine (Covaris Inc., Woburn, MA, USA). Chromatin was immunoprecipitated with anti-HA antibody (GeneTex, GTX29110).
Purified chromatin-immunoprecipitated DNA was subjected to preparation of fragment libraries using 5500 SOLiD Fragment Library Core Kit (Applied Biosystems, Foster City, CA, USA) according to the protocols provided by the manufacturer.

value: HA-tagged ZNF322A overexpressing

tag: chip antibody

value: HA (GeneTex, GTX29110)

tag: cell line


title: Iadel_sti_iEm_2


title: soft palate muscle of patients with chronic tonsillitis 1

description: pengxiaoxiao

value: male

value: adult

value: soft palate muscle


title: Control sample N°8

source_name: Control sample N°8


title: EV-2

value: vector control


title: Control sample N°6

source_name: Control sample N°6


title: Control sample N°5

source_name: Control sample N°5


title: Control sample N°7

source_name: Control sample N°7


title: Iadel_sti_iEm_1

value: CH12F3 murine lymphoma cells


title: Over-1


title: CH12NCdel_sti_iEm_3


title: 0831-siZNF

data_processing:
The libraries were then sequenced using the Applied BioSystems 5500xl SOLiD Sequence
Mapping of sequencing reads and quantification of known RefSeq transcripts were performed using LifeScopeTM Genomic Analysis Software (version 2.5).
Gene expression levels for each transcript were normalized using Reads Per Kilobase of exon model per Million mapped reads (RPKM). RPKM is a method of quantifying gene expression from RNA-seq data by normalizing for total read length and the number of sequencing reads obtained within each sample (Mortazavi et al., 2008).
To determine the differentially expressed genes, we computed the P-values by one-way ANOVA. We used P-values < 0.05 and fold change > 2 as thresholds for determining differentially expressed genes between ZNF322A knockdown and knockdown control samples.
Genome_build: hg19
Supplementary_files_format_and_content: rpkm ANOVAResults.txt and FC2.txt

source_name: A549 lung cancer cell

growth_protocol: Human lung cells A549 were purchased from American Type Culture Collection. A549 cells were maintained in DMEM (Gibco, Grand Island, NY, USA) All media were supplemented with 10% Fetal Bovine Serum (FBS) (Gibco) and 1% penicillin/streptomycin (Gibco). Cells were incubated at 37oC in a humidified incubator containing 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent.
Transcriptome libraries were prepared following Applied BioSystems Library BuilderTM system.

treatment_protocol: siGENOME SMARTpool siRNAs against human ZNF322A were purchased from Dharmacon (Lafayette, CO, USA). RNAi transfections were carried out with Lipofetamine 2000 (Invitrogen) for 12 hours.

tag: transfection

value: ZNF322A si-oligos


title: CH12NCdel_sti_iEm_2


title: OCI-Ly1-OTUD5-sg2-02

city: Cambridge

first: Candace

last: Patterson

address: 75 Ames St

institute: The Broad Institute

description:
DFCI-5308-C-02
rsem.OTUD5_vs_CONTROL.csv

data_processing:
Pooled libraries were normalized to 2 nM and denatured using 0.1 N NaOH prior to sequencing. Flowcell cluster amplification and sequencing were performed according to the manufacturer’s protocols using either the HiSeq 2000 or HiSeq 2500 instrument. Each run generated a 101bp paired-end with an eight-base index barcode read. Data was analyzed using the Broad Picard Pipeline, which includes de-multiplexing and data aggregation.
RNA-seq data were aligned to GRCh38.p5 with STAR-2.5.1b (Dobin et al., 2013).
Gene expression was quantified with RSEM-1.2.31 (Li and Dewey, 2011).
DESeq2 (Love et al., 2014) was applied to call differentially expressed genes between each cell line and control group.
Genome_build: GRCh38.p5
Supplementary_files_format_and_content: tab-delimited text files include gene counts and TPM values for each sample; csv files include expression changes between i) resistant and parental cell lines and ii) engineered vs control cell lines.

growth_protocol: cultured in Iscove's Modified Dulbecco's Media (Gibco) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin/glutamine. Cells were splited twice a week and seeded at 2 × 106 cells into a T75 flask.

extract_protocol:
RNA extraction according the manufacterer's protocol using the RNAeasy mini Kit (Qiagen)
Total RNA was quantified using the Quant-iT™ RiboGreen® RNA Assay Kit and normalized to 5 ng/μl. Following plating, 2 μL of ERCC controls (using a 1:1000 dilution) were spiked into each sample. An aliquot of 200ng for each sample was transferred into library preparation which uses an automated variant of the Illumina TruSeq™ Stranded mRNA Sample Preparation Kit. This method preserves strand orientation of the RNA transcript. It uses oligo dT beads to select mRNA from the total RNA sample, followed by heat fragmentation and cDNA synthesis from the RNA template. The resultant 400bp cDNA then goes through dual-indexed library preparation: ‘A’ base addition, adapter ligation using P7 adapters, and PCR enrichment using P5 adapters. After enrichment, the libraries were quantified using Quant-iT PicoGreen (1:200 dilution). After normalizing samples to 5 ng/μL, the set was pooled and quantified using the KAPA Library Quantification Kit for Illumina Sequencing Platforms.  The entire process was in a 96-well format and all pipetting is done by either Agilent Bravo or Hamilton Starlet.

treatment_protocol: Cell lines resistant to venetoclax were generated over 10 weeks by exposing the cells to increasing doses of venetoclax starting at 10 nM, and then doubling this dose when the cells were able to grow at a rate equivalent to the parental lines until the cells were able to tolerate 1 µM of venetoclax. Stable Cas9-expressing OCI-Ly1 cells were generated by transducing parental cells with lentivirus prepared with lentiCas9-Blast pXR101 (Addgene plasmid # 52962) encoding Cas9 and blasticidin resistance. Selection with blasticidin (10 µg/mL) was initiated 48 h after transduction and sustained throughout culture of Cas9-expressing cell lines. Cas9 expressing cells were transduced (spin infection) with lentiviral constructs encoding the indicated sgRNA.

value: OTUD5 knocked-out


title: 0831-siCon

value: control si-oligos


title: 0829-siZNF


title: 0829-siCon


title: input -12 day

city: Houston

first: Todd

middle: Ryan

last: Heallen

state: Texas

address: One Baylor Plaza

department: Molecular Physiology and Biophysics

institute: Baylor College of Medicine

data_processing:
Basecalling performed on Torrent Suit 3.6.2
ChIP-Seq reads were aligned to mm9 genome assembly using ion-alignment 3.6.3-1
The ChIP-seq signal was normalized to a 10 million read total. Bedgraph file was generated using Homer version 4.2, makeUCSCfile (-o auto) function.
Enriched peaks were called using Homer v4.2 findPeaks function with following parameters: findPeaks -style factor -o auto -fdr 0.001. Poisson p-value threshold 1.00e-04.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files were generated using Homer-v4.2; Y-axis scale represents normalized read number. Bed files include genomic intervals of enriched peaks.

source_name: total heart

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Ion Torrent sequencing libraries were generated according to the manufacturer’s instruction (Life Technologies, 4471252). DNA fragments of the completed library ranged from approximately 170–220 bp in length. Sequencing was performed on an Ion Torrent proton system.

tag: Stage

value: postnatal day 12

tag: strain/background

tag: tissue type

value: whole ventricle


title: OCI-Ly1-OTUD5-sg2-01

description:
DFCI-5308-C-01
rsem.OTUD5_vs_CONTROL.csv


title: CH12NCdel_nonsti_iEm_3


title: Salv CKO -12 day

value: YAP1 Antibody (Novus #NB110-58358)


title: Control sample N°4

source_name: Control sample N°4

value: control

value: peripheral blood mononuclear cells


title: CH12NCdel_nonsti_iEm_2


title: Control sample N°1

source_name: Control sample N°1


title: Control sample N°3

source_name: Control sample N°3


title: Control sample N°2

source_name: Control sample N°2


title: Bp 982

city: Kajang

first: Hirzahida

last: Mohd Padil

state: Selangor

address: Bangi

country: Malaysia

institute: Universiti Kebangsaan Malaysia

data_processing:
Genome sequencing and assembly: The PacBio sequencing reads were filtered and assembled using RS_HGAP_Assembly protocol in SMRT Portal v2.1.1. This involved one round of quiver correction to improve assembly and errors corrections. Three rounds of quiver corrections were then carried out using the RS_Resequencing.1 protocol to obtain very high consensus accuracy (99.998%). After the preliminary assemblies were obtained, the start sites of the assembled genomes were determined based on the reference start site while both 5' and 3' ends were connected by inserting 100 Ns between the cut sequences. This was followed by 4 rounds of quiver corrections to improve the assembly accuracy to 99.999% and close the final 100 Ns gap region.
Gene prediction and genome annotation: Gene predictions for the B. pseudomallei genomes were performed using NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) (Tatusova et al., 2016). PGAP pipeline uses tBLASTn together with ProSplign to detect frameshifted genes and pseudogenes, and subsequently uses GeneMarkS+ program to identify protein coding regions. The annotation of proteins’ functions were performed by BLASTp searches against NCBI Protein Clusters Database (ProtClustDB) (Klimke et al., 2009), UniProt-SwissProt Protein Knowledgebase (Uniprot Consortium, 2015) and curated bacteriophage proteins in RefSeq database.
Base modification Analysis and Motif Detection: Methylation analysis was carried out by RS_Modification_and_Motif_Analysis.1 protocol in SMRT Portal. Raw reads were filtered using SFilter in order to remove short reads and adapter before the high quality reads were aligned using the BLASTR mapper (Bussotti et al., 2011). The base modifications were detected via analysis of the base addition kinetics data where significant changes in the interpulse duration (IPD) indicate the presence of either m6A, m4C or m5C modified sites (Flusberg et al., 2010). The motifs associated with the modified bases were identified using MotifFinder and based on the modification quality value (QV) score, they were then determined to be either methylated or unmethylated
Submitter states that efforts to obtain raw data files were unsuccessful
Supplementary_files_format_and_content: Comma separated value format and base modifications in gff format

organism: Burkholderia pseudomallei

source_name: Clinical isolate

growth_protocol: The isolates were grown overnight at 37°C in Brain Heart Infusion broth (BHIB) and plated on Ashdown selective agar plates.

extract_protocol: The genomic DNA for each isolate was extracted using modifications to the standard protocol described by (Sambrook and Russell, 2001). Briefly, the isolates were grown overnight at 37°C in Brain Heart Infusion broth (BHIB) and plated on Ashdown selective agar plates. A single colony was inoculated into BHIB and grown overnight at 37°C. Pellets from the overnight cultures were resuspended in the remaining 50 μL of supernatant with additional 100ug/ml proteinase K and incubated at 42°C for 10 minutes and 56°C for 30 minutes. Samples were cooled to room temperature and 5 µg RNase A were added to the samples, mixed and incubated for 30 minutes at 37°C. DNA was purified using phenol-chloroform-isoamyl alcohol (25:24:1 ratio), precipitated with ethanol, spooled into deionized water and stored at -20°C.

tag: strain


title: Salv CKO YAP ChIP-Seq

data_processing:
Basecalling performed on Torrent Suit 2.2
ChIP-Seq reads were aligned to mm9 genome assembly using ion-alignment 2.2.4-1
The ChIP-seq signal was normalized to a 10 million read total. BedGraph file was generated using Homer version 4.1, makeUCSCfile (-o auto) function.
Enriched peaks were called using Homer v4.1 findPeaks function with following parameters: findPeaks -style factor -o auto -fdr 0.01. Posson p-value threshold 1.00e-04.
Genome_build: MGSCv37
Supplementary_files_format_and_content: bedGraph files were generated using Homer-v4.1; Y-axis scale represents normalized read number. Bed files include genomic intervals of enriched peaks.

source_name: total heart, YAP ChIP

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA.
Ion Torrent sequencing libraries were generated according to the manufacturer's instruction (Life Technologies, 4471252). DNA fragments of the completed library ranged from approximately 170–220 bp in length. Sequencing was performed on an Ion Torrent PGM system.

value: Salv CKO

value: postnatal day 8

value: anti-YAP1 (Novus #NB110-58358)


title: Salv CKO input

source_name: total heart, input


title: OCI-Ly1-UBR5-sg2-02

description:
DFCI-5306-C-02
rsem.UBR5_vs_CONTROL.csv

value: UBR5 knocked-out


title: iadel-i3CBEc_sti_3

description: Run-on RNA

data_processing:
Library strategy: GRO-Seq
Reads were aligned using bowtie 2.2.8 with --non-deterministic flag
reads were quantified for specific loci using samtools version 1.8
wig files were produced using RseqQ package
Genome_build: mm9
Supplementary_files_format_and_content: wig files contain peak information for samples

source_name: CH12F3 murine lymphoma cells

extract_protocol:
Briefly, 10 million cells were collected and permeabilized with the buffer (10 mM Tris-HCl pH 7.4, 300 mM sucrose, 10 mM KCl, 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.1% NP40 substitute, 0.5 mM DTT, protease inhibitors and Rnase inhibitor). The permeabilized cells were resuspended in 100 ml of storage buffer (10 mM Tris-HCl pH 8.0, 25% (V/V) glycerol, 5 mM MgCl2, 0.1 mM EDTA and 5 mM DTT) for nuclear run-on with 2X run-on mix (5 mM Tris-HCl PH 8.0, 2.5 mM MgCl2, 0.5 mM DTT, 150 mM KCl, 0.5 mM ATP, 0.5 mM CTP, 0.5 mM GTP, 0.5 mM BrUTP, RNase inhibitor, 1% sarkosyl) at 37o for 5 min. RNA was extracted by Trizol and followed by hybrolyzation with NaOH at a final concentration of 0.2 N on ice for 18 min. After quenching with ice-cold Tris-HCl PH6.8 at a final concentration of 0.55 M and exchanging buffer via Bio-Rad P30 columns, the RNA was incubated with Br-dU antibody-conjugated beads (Santa Cruz biotechnology, sc-32323-ac) for 1 hr. The enriched run-on samples were incubated with RppH (NEB, M0356S) and hydroxyl repair with T4 PNK (NEB, M0201S), followed by ligating the 5’ and 3’ RNA adaptor. RT-PCR was performed from the adaptor-ligated RNA to obtain cDNA
Half of the cDNA was subjected to making Groseq libraries by two rounds of PCR with barcode primers.  200-500 bp products from the first round of PCR were subjected to the second round of PCR with the number of PCR cycles determined by test PCR amplification. The second round of PCR products were size-selected by SPRIselect beads (Beckman Coulter, B23318).

value: AID-deficient CH12F3 murine lymphoma cells

value: with aCD40/IL4/TGFb stimulation


title: OCI-Ly1-OTUD5-sg1-01

description:
DFCI-5307-C-01
rsem.OTUD5_vs_CONTROL.csv


title: Bp R15

description: Submitter states that efforts to obtain raw data files were unsuccessful


title: Bp PMC2000


title: Bp H10


title: Bp D286


title: CH12NCdel_nonsti_iEm_1

value: AID-/-; non-coding allele deletion


title: OCI-Ly1-UBR5-sg2-01

description:
DFCI-5306-C-01
rsem.UBR5_vs_CONTROL.csv


title: AO-3

city: Zhengzhou

first: Dongyun

last: Ma

address: No.15 Longzihu College Park,Zhengzhou New District,Zhengzhou

institute: Henan Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw sequencing reads were referred to the Illumina pipeline filter (Solexa 0.3), and then an in-house program (Fastp, https://github.com/OpenGene/fastp) was used to process the dataset for removing adapter dimers, ploy-N, low quality reads.
The clean reads were mapped onto the wheat “Chinese Spring” reference genome (IWGSC1_popseq.31) by using HISAT2
Supplementary_files_format_and_content: text files include RPKM values for each Sample ...

organism: Triticum aestivum

source_name: WHEAT

growth_protocol: Field experiment

extract_protocol:
endosperm RNA was harvested using Trizol reagent. Illumina’s TruSequ  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Endosperm were divided into two part.

tag: tissue

value: ENDOSPERM

tag: developmental stage

value: 25day after anthsis

tag: part

value: outer


title: AO-2


title: OCI-Ly1-OTUD5-sg1-02

description:
DFCI-5307-C-02
rsem.OTUD5_vs_CONTROL.csv

tag: genotype

value: OTUD5 knocked-out


title: OCI-Ly1-UBR5-sg1-02

description:
DFCI-5305-C-02
rsem.UBR5_vs_CONTROL.csv


title: OCI-Ly1-UBR5-sg1-01

description:
DFCI-5305-C-01
rsem.UBR5_vs_CONTROL.csv


title: iadel-i3CBEc_sti_2

description: Run-on RNA

tag: cell type

tag: treatment


title: AI-2

value: inner


title: AO-1


title: AI-3


title: AI-1


title: Iadel_sti_2

description: Run-on RNA

value: I-alpha-delta-AID-/-


title: Iadel_sti_1

description: Run-on RNA


title: OCI-Ly1-CONTROL-sg2-02

value: CONTROL (non targeting sgRNAs)


title: iadel-i3CBEc_sti_1

description: Run-on RNA


title: CH12F3NCdel_sti_3

description: Run-on RNA


title: CH12F3NCdel_sti_2

description: Run-on RNA


title: OCI-Ly1-CONTROL-sg1-01


title: CH12F3NCdel_sti_1

description: Run-on RNA


title: CH12F3NCdel_nonsti_3

description: Run-on RNA

value: without stimulation


title: OCI-Ly1-ID3-sg2-01

description:
DFCI-5302-C-01
rsem.ID3_vs_CONTROL.csv

value: ID3 knocked-out


title: OCI-Ly1-ID3-sg1-02

description:
DFCI-5301-C-02
rsem.ID3_vs_CONTROL.csv


title: OCI-Ly1-CONTROL-sg2-01


title: MCF7 TRIB3-shRNA1 cells-rept3

city: Beijing

first: Jinmei

last: Yu

address: 1 Xian Nong Tan Street

institute: The Institute of Materia Medica

description: Gene expression data from MCF7 cells stably expressing TRIB3-shRNA1

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: Slides were scanned using the Axon GenePix 4000B microarray scanner.

data_processing:
Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 12.1) for further analysis
First, high quality expression values will be selected for analysis. Then differentially expressed genes were identified through Fold change filtering between two samples or t-test filtering between two groups. Hierarchical clustering was performed using R scripts. GO analysis and Pathway analysis were performed using the standard enrichment computation methods.

source_name: breast cancer cell line

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from 5 μg of total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., USA). For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA).

growth_protocol: MCF7 cells were cultured in DMEM media at 37°C.

extract_protocol: Total RNA was extracted by Trizol according to the manufacturer's instructions.

treatment_protocol: TRIB3-shRNA or Con-shRNA were added into MCF7 cells . After 48 hr of infection, cells were lysed with Tizol.


title: CH12F3NCdel_nonsti_1

description: Run-on RNA


title: L0_4

city: chengdu

first: peng

last: wang

state: Sichuan province

address: No. 211, Huimin Road, Wenjiang District

department: Institute of Animal Nutrition

institute: Sichuan agricultural university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts,clean data (clean reads) were obtained.
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 v2.0.9
The mapped reads of each sample were assembled by both Scripture (beta2) (Guttman et al. 2010) and Cufflinks (v2.1.1) (Trapnell et al. 2010) in a reference-based approach
Transcripts predicted with coding potential by either/all of the four tools (CNCI (Coding-Non-Coding-Index) (v2), CPC (Coding Potential Calculator) (0.9-r2), Pfam Scan (v1.3) and PhyloCSF (phylogenetic codon substitution frequency) (v20121028)) were filtered out, and those without coding potential were our candidate set of lncRNAs.
We used phyloFit to compute phylogenetic models for conserved and non-conserved regions among species and then gave the model and HMM transition parameters to phastCons to compute a set of conservation scores of lncRNA and coding genes.
Cis role is lncRNA acting on neighboring target genes,trans role is lncRNA to identify each other by the expression level.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Cuffdiff also provides statistical routines for determining differential expression in digital transcript or gene expression data using a model based on the negative binomial distribution (Trapnell, C. et al. 2010).
Gene Ontology (GO) enrichment analysis of differentially expressed genes or lncRNA target genes were implemented by the GOseq R package, in which gene length bias was corrected.
Genome_build: ftp://ftp.ensembl.org/pub/release-82/fasta/sus_scrofa/dna/
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Sus scrofa

source_name: placenta

extract_protocol:
Total RNA was isolated from each individual sample using TRIzol reagent (Invitrogen, USA)
RNA libraries were prepared for sequencing using standard illumina protocols

value: placenta

value: Farrowing day


title: MCF7 TRIB3-shRNA1 cells-rept2

value: MCF7 cells stably expressing TRIB3-shRNA1


title: CH12F3NCdel_nonsti_2

description: Run-on RNA


title: MCF7 Con-shRNA cells-rept3

description: Gene expression data from MCF7 cells stably expressing Con-shRNA

value: MCF7 cells stably expressing Con-shRNA


title: MCF7 TRIB3-shRNA1 cells-rept1


title: EA1690_29: brain metastases

city: Okayama

first: TAKAYUKI

last: IWAMOTO

address: 2-5-1 Shikata-cho, Kitaku

country: Japan

institute: Okayama university hospital

hyb_protocol: Genome-wide expression levels of transcripts were analyzed using the Affymetrix U133A gene chips (Affymetrix) according to the manufacture’s instructions.

data_processing: All gene expression data were normalized with the MAS5 algorithm (http://www.bioconductor.org) with the mean expression centered to 600 and log 2 transformed.

label: biotin

source_name: brain metastases

label_protocol: Not provided.

growth_protocol: Sixteen paired matched samples from primary breast cancers and brain metastases diagnosed between April 1, 2001 and December 31, 2012 were collected from 8 institutions.

extract_protocol: Matching primary breast cancers and brain metastases Formalin-Fixed Paraffin-Embedded (FFPE) specimens for gene expression analysis were collected into RNA. RNA from specimens was isolated, and quantity and quality of the each RNA was using an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Two of 16 patients were found to have brain metastases when first diagnosed with breast cancer; the remaining patients were diagnosed with brain metastases subsequent to treatment for early or advanced breast cancer.

tag: diagnosis

value: breast cancer

value: brain metastases

tag: origin

value: brain

tag: er-by-gene

value: ERnegative

tag: paired sample


title: EA1690_32: brain metastases

scan_protocol: Genome-wide expression levels of transcripts were analyzed using the Affymetrix U133A gene chips (Affymetrix) according to the manufacture’s instructions.


title: Splenic_aCD40_IL4_3

description: Run-on RNA

source_name: Splenic mature B cells

value: AID-deficient splenic mature B cells

value: AID-deficient primary splenic B cells

value: with aCD40/IL4 stimulation


title: EA1690_31: brain metastases

value: ERpositive


title: MCF7 Con-shRNA cells-rept2


title: OCI-Ly1-ID3-sg1-01

description:
DFCI-5301-C-01
rsem.ID3_vs_CONTROL.csv


title: EV-1

source_name: H460 lung cancer cell

value: vector control

tag: chip antibody

value: HA (GeneTex, GTX29110)


title: EA1690_30: brain metastases


title: L0_3

tag: age


title: MCF7 Con-shRNA cells-rept1


title: L0_2


title: EA1690_28: brain metastases


title: Splenic_aCD40_IL4_2

description: Run-on RNA


title: OCI-Ly1-NFKBIA-sg2-02

description:
DFCI-5300-C-02
rsem.NFKBIA_vs_CONTROL.csv

tag: cell line

value: NFKBIA knocked-out


title: EA1690_27: brain metastases


title: EA1690_26: brain metastases


title: OCI-Ly1-ID3-sg2-02

description:
DFCI-5302-C-02
rsem.ID3_vs_CONTROL.csv


title: OCI-Ly1-NFKBIA-sg2-01

description:
DFCI-5300-C-01
rsem.NFKBIA_vs_CONTROL.csv


title: L0_1


title: Splenic_aCD40_IL4_1

description: Run-on RNA


title: OCI-Ly1-CONTROL-sg1-02

value: CONTROL (non targeting sgRNAs)


title: G90_3

value: day 90 of gestation


title: OCI-Ly1-NFKBIA-sg1-02

description:
DFCI-5299-C-02
rsem.NFKBIA_vs_CONTROL.csv


title: EA1690_24: brain metastases


title: OCI-Ly1-NFKBIA-sg1-01

description:
DFCI-5299-C-01
rsem.NFKBIA_vs_CONTROL.csv


title: Splenic_nonsti_2

description: Run-on RNA

value: without stimulation


title: Splenic_nonsti_1

description: Run-on RNA


title: OCI-Ly1-IKZF5-sg2-02

description:
DFCI-5298-C-02
rsem.IKZF5_vs_CONTROL.csv

value: IKZF5 knocked-out


title: G90_1

value: placenta


title: Splenic_nonsti_NIPBL_3

data_processing:
Reads were aligned using bowtie2 with --non-deterministic flag
peaks were called with MACS2 with the following flags: --nomodel --keep-dup all --extsize 51 --nolambda -B --SPMR
wig files were generated using USCS utilities bedGraphToBigWig
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated for displaying

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (IP-202-1012).

value: AID-deficient Splenic mature B cells

tag: passages

value: 0 (primary mature splenic B cells)

value: NIPBL (Bethyl, A301-779A)


title: G60_3

value: day 60 of gestation


title: OCI-Ly1-IKZF5-sg1-02

description:
DFCI-5297-C-02
rsem.IKZF5_vs_CONTROL.csv


title: G60_2


title: OCI-Ly1-IKZF5-sg1-01

description:
DFCI-5297-C-01
rsem.IKZF5_vs_CONTROL.csv


title: EA1690_25: brain metastases

value: breast cancer

value: brain metastases

value: brain

value: ERnegative


title: Splenic_nonsti_NIPBL_2


title: EA1690_21: brain metastases


title: G60_1


title: G90_2


title: Splenic_aCD40_IL4_NIPBL_1

value: with aCD40/IL4 stimulation


title: Rnh1_Hybrid_S_37_INPUT

type: genomic

city: Milano

first: Mohamood Adhil

last: Mohammed Iqbal

state: Lombardia

address: Via Adamello 16

country: Italy

institute: IFOM - The FIRC Institute of Molecular Oncology

description: RNA-DNA hybrid mapping of across the genome

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R array for 16 hours at 42 C in a hybridization oven at 60 rpm

scan_protocol: Arrays were scanned on Affymetrix geneChip Scanner 3000 7G

data_processing:
The CEL files are processed using rMAT R package for normalization, MAT score calculation and calling enriched regions or peaks. The following commands and parameters are used; i) (Normalization) SetNorm = NormalizeProbes(Set, method="MAT", robust=T, all=T, standard=TRUE, verbose=FALSE), where 'Set' is the probe map object created using CEL file and probe annotation file (Sc03b_MR_v04.bpmap) ii) (MAT score calculation) RD = computeMATScore(SetNorm, dMax=300, verbose=FALSE, cName = InputColumnName), iii) (Calling Enriched Region) peak = callEnrichedRegions(RD, dMax=300, dMerge=300, nProbesMin=8, method=method, threshold=1.5, verbose=FALSE)
Bed file containing the enriched regions with respective MAT score and BedGraph file containing the score for short interval bases. Both bed and bedGraph files are generated using rMAT R package and these files are UCSC genome compatible with sacCer3 reference.

organism: Saccharomyces cerevisiae

source_name: Input fraction of RNA-DNA Hybrid in rnh1 deletion at 37 degree S Phase

label_protocol: Both IP and Input samples are amplified by using Whole genome amplificatio ki protocol ( Sigma-Aldrich WGA1-50RXN) pripor to labelling with Biotin-N11-ddATP (1nMole/ul).

growth_protocol: 1X10e7 cells were synchronized at G1 phase using Alpha-factor and cells were harvested for "G1" samples. For "S" phase samples cells were released into fresh medium after washing cells with 2X YP-medium. After 15 mins of the realese from alpha factor arrest cells were harvested for Chip protocols

extract_protocol: Cells were crosslinked with 1% formaldehyde in culture medium for 30 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (50mM Hepes KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate) using Zirconia beads. The crosslinked chromatin was sheared to an average size of 500 bp by 6X 15-second pulses using a Biorupter sonicator. The lysate was then centrifuged to remove cell debris. The chromatin fraction was incuabted with magnetic beads coated with anti-DNA:RNA hybrid monoclonal mouse antibody S9.6 overnight at 4C. The immune complexes were washed with the following buffers 2X; Chip-lysis buffer, high-salt lysis buffer (Chip-lysis buffer + 360mM NaCl), Chip-wash buffer (250 mM LiCl, 10 mM Tris pH8.0, 0.5% Na deoxycholate, 0.5% NP40, 1mM EDTA) and 1x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 250 µl elution buffer (1% SDS, 50 mM Tris pH8.0, 10mM EDTA) at 65C for 20 min followed by the addition of proteinaseK to 500 µg/ml and overnight incubation at 65C. Input DNA was isolated from sheared chromatin input (1/100 of the material used for ChIP).

tag: category

value: RNA-DNA Hybrid

tag: cellcycle

value: S Phase

tag: antibody

value: Glucose

tag: temperature


title: EA1690_23: brain metastases

tag: tissue


title: EA1690_22: brain metastases


title: EA1690_18: brain metastases

value: ERpositive


title: EA1690_19: brain metastases


title: Rnh1_Hybrid_S_37_IP

source_name: IP fraction of RNA-DNA Hybrid in rnh1 deletion at 37 degree S Phase

value: S9.6 Monoclonal Antibody

tag: strain


title: OCI-Ly1-EP300-sg2-01

description:
DFCI-5296-C-01
rsem.EP300_vs_CONTROL.csv

tag: genotype

value: EP300 knocked-out


title: Sen1_Hybrid_S_37_INPUT

source_name: Input fraction of RNA-DNA Hybrid in sen1 deletion at 28 degree S Phase


title: Splenic_aCD40_IL4_NIPBL_3

tag: cell type


title: CH12NCdel_sti_iEm_1

value: CH12F3 murine lymphoma cells

tag: activation

tag: treatment

value: cytokine stimulation

tag: target locus

value: AID-/-; non-coding allele deletion


title: Splenic_aCD40_IL4_NIPBL_2

value: AID-deficient Splenic mature B cells

value: 0 (primary mature splenic B cells)


title: Sen1_Hybrid_S_37_IP

source_name: IP fraction of RNA-DNA Hybrid in sen1 deletion at 28 degree S Phase


title: CH12F3NCdel_nonsti_NIPBL

value: AID-deficient CH12F3 murine lymphoma cells

value: NIPBL (Bethyl, A301-779A)

value: without stimulation


title: OCI-Ly1-EP300-sg1-01

description:
DFCI-5295-C-01
rsem.EP300_vs_CONTROL.csv


title: OCI-Ly1-EP300-sg2-02

description:
DFCI-5296-C-02
rsem.EP300_vs_CONTROL.csv


title: OCI-Ly1-vene-resistant-02

description:
DFCI-5294-C-02
rsem.vene.resistant_vs_parental.csv

value: OCI-Ly1 resistant to venetoclax


title: EA1690_14: primary breast cancer

source_name: primary breast cancer

tag: diagnosis

value: breast cancer

value: primary breast cancer

tag: origin

value: primary

tag: er-by-gene


title: RRM3_Hybrid_S_28_INPUT

source_name: Input fraction of RNA-DNA Hybrid in rrm3 deletion at 28 degree S Phase

value: RNA-DNA Hybrid

value: S Phase


title: OCI-Ly1-EP300-sg1-02

description:
DFCI-5295-C-02
rsem.EP300_vs_CONTROL.csv


title: Splenic_nonsti_input

tag: chip antibody


title: RRM3_Hybrid_S_28_IP

source_name: IP fraction of RNA-DNA Hybrid in rrm3 deletion at 28 degree S Phase

value: Glucose


title: EA1690_20: brain metastases

value: brain metastases

value: brain

value: ERpositive

tag: paired sample


title: Splenic_aCD40_IL4_input

tag: passages

value: with aCD40/IL4 stimulation


title: EA1690_17: brain metastases

value: ERnegative


title: CH12F3NCdel_aCD40_IL4_TGFb_NIPBL

value: with aCD40/IL4/TGFb stimulation


title: EA1690_15: primary breast cancer


title: CH12F3NCdel_aCD40_IL4_TGFb_input


title: CD2mR2

first: Stephen

last: Gisselbrecht

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics, Department of Medicine

institute: Brigham and Women's Hospital

data_processing:
Reads were aligned to dm3 using bwa.
Read pairs were created and deduplicated using pairsamtools.
Chromosomal Interaction Maps were built and corrected and differential interactions between samples called using the chromoR package.
Output (sigChanges) from chromoR was formatted with each interaction duplicated and reversed to facilitate analysis with bedtools.
Genome_build: dm3
Supplementary_files_format_and_content: Text files of significant differential contacts from chromoR contain the following fields: chr1,start1,end1,chr2,start2,end2,scores[concatenated Bayes Factor and values from chromoR output],reverse[0 for original contact entry, 1 for reversed duplicate]

organism: Drosophila melanogaster

source_name: sorted embryonic non-mesoderm

growth_protocol: Embryos were collected for 2.25 hours from pre-layed cages of twi:CD2 flies and aged 11 hours at 18°.

extract_protocol:
Chromatin from lysed cells was digested with DpnII, 5' overhangs were filled with biotin-14-dATP, and proximal ends were ligated in situ. After thermal reversion of crosslinking, DNA was purified, biotin was removed from unligated ends, and the population of molecules was sonicated to 200-300 bp. Biotin-containing ligation junctions were selected by streptavidin affinity pulldown.
DNA fragments were A-tailed and ligated to Illumina PE adapters, followed by PCR enrichment.

treatment_protocol: Single-cell suspensions were prepared from dechorionated embryos and stained with Alexa647-anti-rat CD2 (Biorad MCA154A647), fixed 10 minutes in 1% formaldehyde, then sorted into CD2-positive and -negative populations.


title: OCI-Ly1-parental-01

description:
DFCI-5293-C-01
rsem.vene.resistant_vs_parental.csv

tag: cell line


title: CD2mR1


title: OCI-Ly1-parental-02

description:
DFCI-5293-C-02
rsem.vene.resistant_vs_parental.csv


title: CH12F3NCdel_nonsti_input


title: EA1690_13: primary breast cancer


title: CD2pR2

source_name: sorted embryonic mesoderm


title: SSB_No-RNAse-rep2

city: New York

first: Doowon

last: Huh

state: New York

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
The CTK package (Shah et al., 2017) was used to analyze the SSB HITS-CLIP data
The reads were distributed to individual samples based on the integrated 4nt barcodes.
The reads were then collapsed, trimmed, and aligned to the human genome (hg19) using bwa (0.7.17-r1188; -n 0.06 -q 20).
The CTK toolkit was then used parse the alignments, remove PCR duplicates, and call mutations in reads
The results from biological replicates were then combined and the CIMS tool (CTK) was used to call peaks (FDR<0.1).
Genome_build: hg19
Supplementary_files_format_and_content: A normalized count table was generated

source_name: MDA-231 cells

growth_protocol: MDA-231 cells were grown in D10F media

extract_protocol:
Cells were UV crosslinked and lysates were treated with low RNAse or no RNAse before IP by anti-SSB antibody
HITS-CLIP for endogenous SSB was done as described by (Licatalosi et al., 2008) with the modifications previously used for YBX1 small RNA CLIP (Goodarzi et al., 2015). MDA-MB-231 cells were UV-crosslinked at 400 mJ/cm2 before cell lysis. Samples with and without RNase treatment were immunoprecipitated with an anti-SSB antibody (MBL, RN074PW) for protein-RNA complexes. Polyphosphatase (Epicentre) was incubated with smRNA samples before ligation and PCR amplification with primers described by (Goodarzi et al., 2015).

tag: clip antibody

value: anti-SSB antibody (MBL, RN074PW)


title: EA1690_16: primary breast cancer


title: EA1690_12: primary breast cancer


title: Iadel-i3CBEc_3RR_2-3

data_processing:
Library strategy: 3C-HTGTS
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files were generated for displaying (Jane et al., 2018)

source_name: CH12F3 murine lymphoma cells

extract_protocol:
About 10 million cells were crosslinked with 2% formaldehyde for 10 minutes at room temperature and quenched with glycine at a final concentration of 125 mM. Then, the crosslinked cells were lysed in the 3C lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, protease inhibitors) and nuclei were digested with NlaIII enzyme (NEB, R0125) at 37 ℃ overnight.  They were then brought to 16℃, 100U of T4 ligase added  (Promega, M1801) and they incubated again overnight at 16℃.  The ligated products were de-crosslinked with Proteinase K (Roche, #03115852001) at 56 ℃ overnight and the 3C templates were purified by phenol/chloroform.
Libraries were prepared using 3C samples by HTGTS (Jane et al., 2018).

value: CH12F3 murine lymphoma cells

value: cytokine stimulation

value: AID-/-; non-coding alele deletion; Ia deletion; three CBE insertion with the convergent orientation as 3'CBE downstream of Cg2a


title: SSB_No-RNAse-rep1


title: EA1690_10: primary breast cancer


title: CD2pR1


title: OCI-Ly1-vene-resistant-01

description:
DFCI-5294-C-01
rsem.vene.resistant_vs_parental.csv

value: OCI-Ly1 resistant to venetoclax


title: Iadel-i3CBEc_3RR_2-2


title: EA1690_11: primary breast cancer

value: breast cancer


title: SSB_Low-RNAse-LMW-rep2


title: SSB_Low-RNAse-LMW-rep1


title: Top2-ChIA-PET

description: Log cells at 28 degree

data_processing:
FASTX Toolkit (fatsq_quality_filter) is used to filter raw reads based on the quality value -q 20 and -p 30
Reads were scanned for bridge linker (ACGCGATATCTTATCTGACT, AGTCAGATAAGATATCGCGT  ) with maximum two mismatches using cutadapt. The data were analysed based on this protocol (Li et al., 2017 Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions).
The filtered reads were aligned to the reference genome (Saccer2011) using bwa mem module
PCR duplicates were removed using Picard Markduplicates module
BAM file after alignment is converted to bedpe using bedtools bamtobed module for cluster generation
The interactions were classified into self ligation and inter ligation cluster using the distance (<1kb - self ligation and >1kb - inter ligation)  for PET clustering. The self ligation PETs were removed and PET interactions were extended by 500 bp. PETs overlapping at both ends are clustered together as single PET cluster
Genome_build: Saccer2011
Supplementary_files_format_and_content: Tab delimeted text file containing the PET clusters

source_name: Saccharomyces cerevisiae

growth_protocol: Strains were grown at 280C YPD medium. G1 synchronization was carried out using 3-5 µg/ml of alpha-factor.  Cells were washed twice in YP medium and allowed to grow for 15 mins in fresh medium.

extract_protocol:
Cells were  lysed in 1 ml of lysis buffer (50mM Hepes KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate) using Zirconia beads. Crosslinked chromatin was sheared to an average size of 500 bp by 6X 15-second pulses using a Biorupter sonicator. The lysate was then centrifuged to remove cell debris. The chromatin fraction was incubated with Dynabeads protein G beads (Invitrogen, cat no 10003D) coated with anti-Flag antibody (M2-antiflag, Sigma) overnight at 40C. The immune complexes were washed with the following buffers 2X; Chip-lysis buffer, high-salt lysis buffer (Chip-lysis buffer + 360mM NaCl), Chip-wash buffer (250 mM LiCl, 10 mM Tris pH8.0, 0.5% Na deoxycholate, 0.5% NP40, 1mM EDTA) and 1x TE (20 mM Tris pH8.0, 2 mM EDTA).
Beads were pooled and End-repair was carried out using T4 DNA polymerase (NEB, cat no. M0203L) by rotating on a Intelli-Mixer at 370C for 40 mins. Beads were washed 3X with ice cold ChIA-PET wash buffer (10mM Tris pH 7.4, 1mM EDTA, 500mM NaCl). A-tailing was carried out using Klenow fragment (3’-5’ exo-) (NEB, cat no. M0212M) in the presence of 100uM dATP by by rotating on a Intelli-Mixer at 370C for 50 mins. Beads were washed 3X with ice cold ChIA-PET wash buffer (10mM Tris pH 7.4, 1mM EDTA, 500mM NaCl).  Proximity ligation was carried out by T4 DNA ligase (NEB cat no. M0202M), in the presence of bridge linker at a concentration of 0.57ng/ul by rotating at 160C overnight. Beads were washed once in ChIA-PET wash buffer and eluted in elution buffer (10mM Tris pH8.0, 1mMEDTA, 1%SDS) at 650C for 15 mins. Reverse –cross linking was carried out at 650C in the presence of Proteinase K. DNA was purified using Phenol-Chloroform-Isoamyl alcohol (pH 7.9) and MaXtract High Density-2ml (QIAGEN, cat no 129056) and precipitated with Isopropanol. Tagmentation of proximity ligated DNA was carried by Tn5 transposome by using Nextera® DNA Sample Preparation Kit (24) (Illumina FC-121-1030). Tagmentated DNA was purified using Zymo Genomic DNA Clean & Concentrator™ kit (Zymo Research, cat. no. D4014) and fragments containing linker DNA was enriched with Dynabeads M-280 Streptavidin (Invitrogen, cat. no.11205D). Beads were washed with 2×SSC/0.5% (wt/vol) SDS five times and twice in 1X B&W buffer (10mM Tris pH 8.0, 1mM EDTA, 1M NaCl). Sequencing library was amplified by using beads and purified library was used for pair-end sequencing using MiSeq® Reagent Kit v3 (600 cycle) on Illumina MiSeq instrument.
Long Read ChIA-PET (Chromatin interaction analysis by paired-end tag sequencing)

treatment_protocol: Cells were crosslinked with 1% formaldehyde in culture medium for 30 min at room temperature followed by quenching with 0.125 M glycine for 5 min. Cells were washed twice with ice-cold PBS.

value: Wildtype

tag: cell cycle

value: Log Cells


title: Iadel-i3CBEc_3RR_2-1


title: Iadel_sti_3RR_2-3

value: I-alpha-delta-AID-/-

value: AID-/-; non-coding alele deletion; Ia deletion


title: EA1690_08: primary breast cancer

value: primary breast cancer

value: primary


title: SSB_Low-RNAse-HMW-rep1


title: Iadel-i3CBEc_iEm_2-2


title: MCF10a_oxid_rep1

data_processing:
Raw data from fastq files were aligned to hg19 tRNA  sequences using bowtie2
Reads were sorted, indexed, and counts were generated by samtools
Raw counts were imported into Rstudio and differential analysis was calculated using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: A normalized count table was generated

source_name: MCF10A cells

growth_protocol: MCF10A cells were grown in MCF10A media

extract_protocol:
RNA was extracted using the Norgen Biotek microRNA purification kit
Libraries were prepared according to Biooscientific's instructions for the NEXTflex small RNA sequencing kit v3.

treatment_protocol: Experimental cells were treated with 200uM H2O2 while control cells were untreated.


title: MCF10a_oxid_rep2


title: EA1690_09: primary breast cancer


title: Iadel-i3CBEc_iEm_2-1


title: SSB_Low-RNAse-HMW-rep2


title: MCF10a_normox_rep1


title: Iadel_sti_3RR_2-2


title: Iadel_sti_iEm_2-2


title: Iadel_sti_iEm_2-1


title: Iadel_sti_3RR_2-1


title: MCF10A_H2O2_24hr_rep3

data_processing:
Raw data from fastq files were aligned to tRNA probe sequences using bowtie2
Reads were sorted, indexed, and counts were generated by samtools
Raw counts were imported into R and normalized with EdgeR
Genome_build: tRNA probe sequences
Supplementary_files_format_and_content: A normalized count table was generated

extract_protocol:
RNA was extracted using the mirVana miRNA isolation kit
Transfer RNA profiling was done as described by (Goodarzi et al., 2016). Briefly, biotinylated probe-pairs against nuclear encoded tRNAs were designed to hybridize to each half of the tRNA. A nick at the anticodon end of the DNA-RNA hybrid was filled using T4 DNA ligase and SplintR ligase (NEB). MyOne-C1 Streptavidin Dynabeads (Invitrogen) were used to purify the DNA-RNA hybrids and ligated probes were eluted following RNase H and RNase A incubation. Eluted probes were PCR amplified and high-throughput sequenced.


title: G-TPP+LXR623 1

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from NCH644 cells treated with G-TPP+LXR623 in 0.1% DMSO.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene20sthsentrezg R package (version 17.0.0).

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Human stem cell like glioma cells (NCH644) were cultured in GBM-MG medium (CLS, Heidelberg, Germany) at 37°C in 5% CO2.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (QIAGEN, Hiden, Germany) according to the manufacturer's protocol.

treatment_protocol: After one day of cell seeding, NCH644 cells were treated with 1 µM of G-TPP, 5 µM of LXR623, both, or neither (in 0.1% DMSO) for 24 hours.

value: stem cell like glioma cells


title: EA1690_04: primary breast cancer


title: EA1690_07: primary breast cancer


title: G-TPP+LXR623 2

source_name: NCH644 cells treated with G-TPP+LXR623 in 0.1% DMSO


title: MCF10a_normox_rep2


title: Iadel-i3CBEc_iCBE_2-3


title: MCF10A_H2O2_24hr_rep2


title: OCI-Ly1-IKZF5-sg2-01

description:
DFCI-5298-C-01
rsem.IKZF5_vs_CONTROL.csv

data_processing:
Pooled libraries were normalized to 2 nM and denatured using 0.1 N NaOH prior to sequencing. Flowcell cluster amplification and sequencing were performed according to the manufacturer’s protocols using either the HiSeq 2000 or HiSeq 2500 instrument. Each run generated a 101bp paired-end with an eight-base index barcode read. Data was analyzed using the Broad Picard Pipeline, which includes de-multiplexing and data aggregation.
RNA-seq data were aligned to GRCh38.p5 with STAR-2.5.1b (Dobin et al., 2013).
Gene expression was quantified with RSEM-1.2.31 (Li and Dewey, 2011).
DESeq2 (Love et al., 2014) was applied to call differentially expressed genes between each cell line and control group.
Genome_build: GRCh38.p5
Supplementary_files_format_and_content: tab-delimited text files include gene counts and TPM values for each sample; csv files include expression changes between i) resistant and parental cell lines and ii) engineered vs control cell lines.

extract_protocol:
RNA extraction according the manufacterer's protocol using the RNAeasy mini Kit (Qiagen)
Total RNA was quantified using the Quant-iT™ RiboGreen® RNA Assay Kit and normalized to 5 ng/μl. Following plating, 2 μL of ERCC controls (using a 1:1000 dilution) were spiked into each sample. An aliquot of 200ng for each sample was transferred into library preparation which uses an automated variant of the Illumina TruSeq™ Stranded mRNA Sample Preparation Kit. This method preserves strand orientation of the RNA transcript. It uses oligo dT beads to select mRNA from the total RNA sample, followed by heat fragmentation and cDNA synthesis from the RNA template. The resultant 400bp cDNA then goes through dual-indexed library preparation: ‘A’ base addition, adapter ligation using P7 adapters, and PCR enrichment using P5 adapters. After enrichment, the libraries were quantified using Quant-iT PicoGreen (1:200 dilution). After normalizing samples to 5 ng/μL, the set was pooled and quantified using the KAPA Library Quantification Kit for Illumina Sequencing Platforms.  The entire process was in a 96-well format and all pipetting is done by either Agilent Bravo or Hamilton Starlet.

value: IKZF5 knocked-out


title: LXR623 1

description: Gene expression data from NCH644 cells treated with LXR623 in 0.1% DMSO.


title: 09.7.28 N

city: Chang Sha

first: Hao

last: Pan

address: Xiangya NO.72

department: Department of Periodontics

institute: Xiangya Stomatological Hospital & School of Stomatology, Central South University

description: RNA from tumor tissues of patients with OSCC

hyb_protocol: The labled RNA were hybridized for 16 hr at 48C on Affymetrix miRNA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed with miRNA QCTool using Affymetrix default analysis settings and quantile as normalization method.

source_name: tongue

label_protocol: About 1ug total RNA were polyA tailed and labled with FlashTag™ Biotin HSR Labeling Kit. This kit can be used to label any RNA sample, including total RNA, severely degraded RNA, plant RNA, and low molecular weight RNA.

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

treatment_protocol: Paired primary tumor tissues were obtained from patients with OSCC. The tumor tissues were obtained from surgical excision. All tissues were snap-frozen in liquid  nitrogenat at -80C until use.

tag: gender

value: female

value: tongue

value: squamous cell carcinoma (OSCC)

tag: molecule subtype

value: miRNA


title: EA1690_03: primary breast cancer

tag: tissue

value: ERpositive


title: EA1690_02: primary breast cancer


title: 09.7.20 N

source_name: oral buccal

value: male

value: oral buccal


title: G-TPP 2

description: Gene expression data from NCH644 cells treated with G-TPP in 0.1% DMSO.

value: G-TPP


title: EA1690_01: primary breast cancer

value: breast cancer

value: ERnegative


title: EA1690_05: primary breast cancer


title: G-TPP 1

source_name: NCH644 cells treated with G-TPP in 0.1% DMSO


title: Liver428

city: Miami

first: Augusto

middle: F

last: Schmidt

state: FL

address: 1611 NW 12th ave

institute: University of Miami Miller School of Medicine

description:
processed data file:
countsliver.csv
run0196_lane91_read*_indexD711-D508=RhLiver428-18

data_processing:
Alignment to the MMUL8.01 done with STAR
Read counts was done using FeatureCounts
Differential expression analysis was performed with DESEq2
Genome_build: MMUL8.01
Supplementary_files_format_and_content: counts

organism: Macaca mulatta

source_name: PO Betamethasone-phosphate_Liver

extract_protocol:
total RNA was extracted with Trizol per manufacturer's guidelines.
Afer polyA selection, paired-end RNA-sequencing with 75bp was done with a depth of 30M reads.

tag: gestational age

value: 131 days

tag: treatment route and drug

value: PO Betamethasone-phosphate

tag: dose

value: 0.15mg/kg x3 12h apart

tag: treatment to delivery interval

value: 5 days

value: Liver


title: Control 2

description: Gene expression data from NCH644 cells treated with 0.1% DMSO.

source_name: NCH644 cells treated with 0.1% DMSO

tag: cell type

value: stem cell like glioma cells

tag: treatment

value: Control


title: MCF10A_H2O2_24hr_rep1


title: Iadel-i3CBEc_iCBE_2-1

value: CH12F3 murine lymphoma cells

tag: genotype

tag: activation

value: cytokine stimulation

tag: target locus

value: AID-/-; non-coding alele deletion; Ia deletion; three CBE insertion with the convergent orientation as 3'CBE downstream of Cg2a


title: Control 1


title: Liver422

description:
processed data file:
countsliver.csv
run0201_lane91_read*_indexD707-D508=RhLiver422-18

value: 127 days


title: 09.6.22 N

value: tongue

value: squamous cell carcinoma (OSCC)

value: miRNA


title: Iadel_sti_iCBE_2-3

value: I-alpha-delta-AID-/-

value: AID-/-; non-coding alele deletion; Ia deletion


title: 09.7.27 N

value: male


title: LXR623 2

source_name: NCH644 cells treated with LXR623 in 0.1% DMSO


title: Liver420

description:
processed data file:
countsliver.csv
run0196_lane91_read*_indexD710-D503=RhLiver420-18

value: 129 days


title: Iadel_sti_iCBE_2-1


title: MCF10A_H2O2_8hr_rep2


title: MCF10A_H2O2_8hr_rep1


title: i3CBEc_sti_iEm_3

value: AID-/-; non-coding allele deletion; three CBE insertion with the convergent orientation as 3'CBE downstream of Cg2a


title: Liver412

description:
processed data file:
countsliver.csv
run0196_lane91_read*_indexD708-D505=RhLiver412-18

value: 133 days

value: 0.25mg/kg x2 24h apart


title: CH12F3NCdel_sti_iEm_3

value: AID-/-; non-coding allele deletion


title: 09.5.19 N


title: Splenic_nonsti_NIPBL_1

source_name: Splenic mature B cells

value: AID-deficient Splenic mature B cells

value: 0 (primary mature splenic B cells)

tag: strain

tag: chip antibody

value: NIPBL (Bethyl, A301-779A)

value: without stimulation


title: 09.7.28 P

value: female


title: MCF10A_NT_rep3


title: 09.6.1 N


title: Liver410

description:
processed data file:
countsliver.csv
run0196_lane91_read*_indexD706-D507=RhLiver410-18

value: 5 days

value: Liver


title: MCF10A_NT_rep2


title: CH12F3NCdel_sti_iEm_2

value: CH12F3 murine lymphoma cells

value: cytokine stimulation


title: Liver411

description:
processed data file:
countsliver.csv
run0196_lane91_read*_indexD707-D506=RhLiver411-18


title: MCF10A_NT_rep1


title: EA1690_06: primary breast cancer

source_name: primary breast cancer

tag: diagnosis

value: breast cancer

value: primary breast cancer

tag: origin

value: primary

tag: er-by-gene

value: ERnegative

tag: paired sample


title: 09.7.20 P

tag: gender

value: male

value: oral buccal

value: squamous cell carcinoma (OSCC)

tag: molecule subtype

value: miRNA


title: i3CBEc_sti_iCBE_1-3

value: AID-/-; non-coding allele deletion; three CBEs insertion with the convergent orientation as 3'CBE downstream of Cg2a


title: Liver409

description:
processed data file:
countsliver.csv
run0196_lane91_read*_indexD712-D508=RhLiver409-18

tag: gestational age

value: 132 days

value: 0.25mg/kg x2 24h apart

tag: tissue


title: MCF10A_H2O2_8hr_rep3


title: sample 4; Hypoxia

city: Incheon

first: Hara

last: Kang

address: 119 Academy-ro

country: South Korea

institute: Incheon National University

data_processing:
bcl2fastq v1.8.4 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Homo sapiens using Hisat2-2.0.5, which is capable of reporting split-read alignments across splice junctions and determined using Stringtie-1.3.3b software in default options.
The reference genome sequence of Homo sapiens (hg38) and annotation data were downloaded from UCSC. The transcript counts in isoform level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks.
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Genome_build: hg38
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

source_name: Human pulmonary artery smooth muscle cell

extract_protocol:
RNAs were extracted from the cell of Homo Sapiens. Poly(A) mRNA using the Illumina  TruSeq RNA Sample Prep Kit v2, according to the manufacturer’s instructions.
Libraries were prepared for multiplex sequencing using Illumina TruSeq RNA Sample Prep Kit , according to the manufacturer’s protocol.

value: Cultured smooth muscle cell

tag: condition

value: hypoxia


title: Hippocampus428

description:
processed data file:
countshippocampus.csv
run0198_lane91_read*_indexD709-D504=RhHippo428-18

source_name: PO Betamethasone-phosphate_Hippocampus

value: 131 days

tag: treatment route and drug

value: PO Betamethasone-phosphate

tag: dose

value: 0.15mg/kg x3 12h apart

tag: treatment to delivery interval

value: 5 days

value: Hippocampus


title: 09.6.22 P

value: tongue

tag: cell type


title: CH12F3NCdel_sti_iCBE_1-3

first: Frederick

last: Alt

address: 1 Blackfan Circle

institute: Boston Children's Hospital

value: CH12F3 murine lymphoma cells

tag: genotype

tag: activation

tag: treatment

value: cytokine stimulation

value: AID-/-; non-coding allele deletion


title: sample 3; Normoxia

value: normoxia


title: Hippocampus422

description:
processed data file:
countshippocampus.csv
run0198_lane91_read*_indexD707-D506=RhHippo422-18

value: 127 days


title: i3CBEc_sti_iEm_2

tag: target locus

value: AID-/-; non-coding allele deletion; three CBE insertion with the convergent orientation as 3'CBE downstream of Cg2a


title: Hippocampus420

description:
processed data file:
countshippocampus.csv
run0198_lane91_read*_indexD706-D507=RhHippo420-18

value: 129 days


title: Iadel_sti_3RR_2

value: I-alpha-delta-AID-/-

value: AID-/-; non-coding allele deletion; single CBE insertion with the convergent orientation as 3'CBE downstream of Cg2a


title: 09.5.19 P

value: male

value: squamous cell carcinoma (OSCC)

value: miRNA


title: sample 2; Hypoxia

data_processing:
bcl2fastq v1.8.4 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To identify miRNA sequences, the unique sequences found after clustering were searched on the miRBase database by blast.
For non-miRNA sequences of unmatched trimmed read excluded from miRBase, they are blasted to non-miRNA of Rfam database.
Genome_build: hg38
Supplementary_files_format_and_content: Excel files include Read counts for each Sample

value: Cultured smooth muscle cell

value: hypoxia


title: CH12NCdel_sti_3RR_2

value: AID-/-; non-coding allele deletion; single CBE insertion with the same orientation as 3'CBE downstream of Cg2a


title: sample 1; Normoxia


title: Hippocampus416

description:
processed data file:
countshippocampus.csv
run0198_lane91_read*_indexD712-D508=RhHippo416-18

value: 132 days

value: PO Betamethasone-phosphate

value: 0.15mg/kg x3 12h apart

value: 5 days

value: Hippocampus


title: 09.6.1 P

value: tongue


title: Iadel_sti_3RR_1

value: CH12F3 murine lymphoma cells

value: cytokine stimulation


title: Hippocampus412

description:
processed data file:
countshippocampus.csv
run0198_lane91_read*_indexD710-D501=RhHippo412-18

value: 133 days

value: 0.25mg/kg x2 24h apart


title: BRD3_ChIP-seq_MCF-7_E2_rep2

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
FastQC
Alignment using BOWTIE (version 0.12.7) with the default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

growth_protocol: MCF-7 cells, kindly provided by Dr. Benita Katzenellenbogen (University of Illinois, Urbana-Champaign, IL), were maintained in Minimum Essential Medium (MEM) Eagle with Hank’s salts (Sigma, M1018) supplemented with 5% HyClone calf serum (GE Healthcare, SH30072) and 20mM HEPES (ThermoFisher Scientific, BP310).  Prior to gene expression and ChIP experiments, the cells were grown for three days in phenol red-free MEM Eagle medium supplemented with 5% charcoal-dextran-treated calf serum.

extract_protocol:
ChIP was performed as previously described with a few modifications.  MCF-7 cells were plated at a density of 2.5 x 106 cells in a 15 cm diameter dish, grown for three days in estrogen-free medium, and treated as described above (± 45 minutes with 100 nM E2; ± 3 hour pretreatment with 500 nM JQ1). The cells were cross-linked with 1% formaldehyde for 10 min at 37oC and quenched in 125 mM glycine for 5 min at 4oC.  The cells were then collected and lysed in Farnham lysis buffer [5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, 1 mM DTT, and 1x complete protease inhibitor cocktail (Roche, 11697498001)].  For acetyl-histone H4 ChIP assays, 10 mM sodium butyrate was added to all buffers to prevent deacetylation of the histones.  The crude nuclear pellet was collected by centrifugation, resuspended in lysis buffer [Tris-HCl pH 7.9, 1% SDS, 10 mM EDTA, 50 mM, 1 mM DTT, and 1x complete protease inhibitor cocktail], and incubated on ice for 10 minutes.  The chromatin was sheared by sonication at 4¡C using a Bioruptor UC200 at the highest setting for five 5-minute cycles of 30 seconds on and 60 seconds off to generate chromatin fragments of ~200-400 bp in length.  The soluble chromatin was diluted 1:10 with dilution buffer [20 mM Tris-HCl pH 7.9, 0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 1 mM DTT and 1x complete protease inhibitor cocktail] and pre-cleared with protein A agarose beads.  Five percent of the material was removed and saved as input, and the rest of the pre-cleared supernatant was incubated overnight at 4oC with the specified antibodies of interest or without antibody as a control (each 15 cm diameter dish yielded two immunoprecipitations) with continuous mixing. After the incubation, the immune complexes were collected by adding protein A agarose beads and incubating for 2 hours at 4°C.  The immunoprecipitated material was washed once with low salt wash buffer [20 mM Tris-HCl pH 7.9, 2 mM EDTA, 125 mM NaCl, 0.05% SDS, 1% Triton X-100, and 1x complete protease inhibitor cocktail], once with high-salt wash buffer [20 mM Tris-HCl pH 7.9, 2 mM EDTA, 500 mM NaCl, 0.05% SDS, 1% Triton X-100, and 1x complete protease inhibitor cocktail], once with LiCl wash buffer [10 mM Tris-HCl pH 7.9, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, and 1x complete protease inhibitor cocktail], and twice with Tris-EDTA (TE) containing 1x complete protease inhibitor cocktail.  The immunoprecipitated material was eluted at room temperature in elution buffer [100 mM NaHCO3, 1% SDS], and reverse crosslinked by adding 100 mM NaCl and incubating at 65oC overnight.  The eluted material was then digested with proteinase K and RNase A to remove protein and RNA, respectively, and the enriched genomic DNA was extracted with phenol:chloroform:isoamyl alcohol, followed by isopropanol precipitation.  The ChIPed DNA was dissolved in water and purified again using AMPure Beads XP.
ChIP-seq libraries were generated using two biological replicates the ChIPed DNA described above for each condition.  The DNA was purified using a MiniElute PCR Purification Kit (Qiagen, 28004).  After purification, 50 ng of ChIPed DNA for each condition was used to generate libraries for deep sequencing, as previously described {Quail, 2008 #8;Quail, 2008 #8;Franco, 2015 #9}, with some modifications.  Briefly, the DNA was end-repaired and a single ÒAÓ-base overhang was added using the Klenow fragment of E. coli DNA polymerase.  The A-modified DNA was ligated to Illumina sequencing adaptors using the Illumina TruSeq DNA Sample Prep Kit.  The ligated DNA (300-500 bp) was size-selected by agarose gel electrophoresis and purified using a QIAquick Gel Extraction kit (Qiagen, 28704).  The size-selected fragments were PCR amplified using Illumina TruSeq P5 and P7 PCR primers, and purified using AMPure beads (Beckman Coulter, A63881).  After quality control analyses, the libraries were sequenced on an Illumina HiSeq 2000 (single-end sequencing, 50 nt).

treatment_protocol: Cells were treated with vehicle (EtOH) or 100 nM E2 for 45 min.

tag: cell line

tag: chip antibody

tag: chip antibody vendor

value: Bethyl Laboratories

tag: chip antibody cat. #

tag: chip antibody  lot #


title: 09.7.28 Ca

tag: gender

value: female

tag: molecule subtype


title: Hippocampus411

description:
processed data file:
countshippocampus.csv
run0064_lane91_read*_indexD709-D502=RhHippo411-18

tag: gestational age

tag: tissue


title: 09.7.20 Ca

value: male

value: oral buccal

value: squamous cell carcinoma (OSCC)


title: CH12NCdel_sti_3RR_1


title: CH12NCdel_nonsti_3RR_2

value: AID-/-; non-coding allele deletion


title: 09.6.22 Ca

value: miRNA


title: 09.7.27 Ca


title: BRD3_ChIP-seq_MCF-7_Veh_rep2

value: EtOH, 45 min


title: BRD3_ChIP-seq_MCF-7_E2_rep1


title: Hippocampus410

description:
processed data file:
countshippocampus.csv
run0064_lane91_read*_indexD708-D503=RhHippo410-18

tag: treatment route and drug


title: CH12NCdel_nonsti_3RR_1


title: 09.5.19 Ca

description: RNA from tumor tissues of patients with OSCC


title: Hippocampus409

description:
processed data file:
countshippocampus.csv
run0064_lane91_read*_indexD707-D504=RhHippo409-18

value: 132 days

tag: dose


title: Splenic_aCD40_IL4_iEm_3

value: Splenic mature B cells

value: AID-deficient primary splenic B cells


title: BRD3_ChIP-seq_MCF-7_Veh_rep1


title: Lung428

description:
processed data file:
countslung.csv
run0064_lane91_read*_indexD712-D506=RhLung428-18

source_name: PO Betamethasone-phosphate_Lung

value: 131 days

value: PO Betamethasone-phosphate

value: 0.15mg/kg x3 12h apart

tag: treatment to delivery interval

value: 5 days

value: Lung


title: 09.7.27 P

value: tongue

tag: cell type


title: Splenic_aCD40_IL4_iEm_1

tag: genotype

value: cytokine stimulation


title: Input_ChIP-seq_MCF-7_E2_rep2


title: Lung422

description:
processed data file:
countslung.csv
run0064_lane91_read*_indexD710-D508=RhLung422-18

value: 127 days


title: Lung420

description:
processed data file:
countslung.csv
run0064_lane91_read*_indexD711-D501=RhLung420-18

value: 129 days


title: Splenic_nonsti_iEm_3

tag: activation


title: MI+CIH3

city: beijing

first: hui

middle: yun

last: du

state: beijing

address: 2 Anzhen Rd, Chaoyang District, Beijing

department: the Beijing Institute of Heart, Lung, and Blood Vessel Diseases

institute: Beijing Anzhen Hospital, Capital Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data(raw reads) of fastq format were firstly processed through in-houseperl scripts.In this step,clean data(clean reads) were obtained by removing reads containing adapter,reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly.Index of the reference genome was built using Hisat 2v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat 2v2.0.5.
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.And then FPKM of each gene was calculated based on the length of the gene and readscount mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
Genome_build: mm10

source_name: Heart

extract_protocol:
Hearts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext Multiplex Small RNA Library Prep Set for Illumina was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Heart

tag: group

value: MI+CIH

tag: strain


title: Lung416

description:
processed data file:
countslung.csv
run0064_lane91_read*_indexD710-D502=RhLung416-18


title: MI+CIH2


title: RNA-seq_MCF7_JQ1_E2_rep2

data_processing:
FastQC
Alignment to the human reference genome (hg19) and one complete copy of an rDNA repeat (GenBank ID: U13369.1) using the BWA aligner
Genome_build: hg19

extract_protocol:
MCF-7 cells were grown in 10 cm diameter dish to the density of 8.8 x 106 cells and treated as described above (± 3 hours with 100 nM E2; ± 3 hour pretreatment with 500 nM JQ1).  The cells were collected and total RNA was isolated using the RNeasy Plus kit (Qiagen, 74134).
PolyA+ RNA was purified from the total RNA using Dynabeads Oligo(dT)25 (Life Technologies, 61002).  Strand-specific libraries were prepared according to the “deoxyuridine triphosphate (dUTP)” method as described previously {Zhong, 2011 #6}.  After quality control analyses, the libraries were sequenced on an Illumina HiSeq 2000 (single-end sequencing, 50 nt).

treatment_protocol: Cells were treated with vehicle (EtOH) or 100 nM E2 for 3 hr with or without 3 hr pre-treatment with 500 nM JQ1.

tag: cell line

value: Breast Cancer Cells

tag: treatment


title: 09.6.1 Ca

value: male

value: squamous cell carcinoma (OSCC)

value: miRNA


title: Lung411

description:
processed data file:
countslung.csv
run0064_lane91_read*_indexD708-D504=RhLung411-18

value: 133 days

value: 0.25mg/kg x2 24h apart


title: MI+CIH1


title: RNA-seq_MCF7_JQ1_E2_rep1


title: Lung412

description:
processed data file:
countslung.csv
run0064_lane91_read*_indexD709-D503=RhLung412-18


title: CIH3

value: CIH


title: Throphoblast_control_20uM Pioglitatsoni_72h, Rep 6

city: Kuopio

first: Jaana

last: Rysae

address: Yliopistonranta 1C

department: School of Pharmacy

country: Finland

institute: University of Eastern Finland

description: Replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was log2-transformed, normalized with shift to 75 percentile and baseline transformed to median of all samples in GeneSpring 12.6 Software

label: Biotin

source_name: primary throphoblasts

label_protocol: Biotinylated cRNA were prepared with the Illumina® Total PrepT RNA Ampification kit (Life Technologies) for Illumina arrays

growth_protocol: primary throphoblasts were growth as described in Petroff MG, Phillips TA, Ka H, Pace JL, Hunt JS.Isolation and culture of term human trophoblast cells. Methods Mol Med. 2006;121:203-17.

extract_protocol: Total RNA from human primary trophoblasts was isolated as described previously by  Huuskonen P, Amezaga MR, Bellingham M, Jones LH, Storvik M, Häkkinen M, Keski-Nisula L, Heinonen S, O’Shaughnessy PJ, Fowler PA,. The human placental proteome is affected by maternal smoking. Reproductive Toxicology 2016; 63:22-31.

treatment_protocol: The term trophoblast cells were exposed to 20 µM pioglitazone (Sigma-Aldrich) and 25 µM β-naphthoflavone (BNF) (Sigma-Aldrich) for 72 h. The control cells were exposed to 0.25 % DMSO.

tag: agent

value: 20uM Pioglitatsoni

value: Placenta

tag: developmental stage

value: Term

value: Throphoblast


title: Throphoblast_control_20uM Pioglitatsoni_72h, Rep 4

description: Replicate 1


title: RNA-seq_MCF7_JQ1_Veh_rep2

value: 500 nM JQ1, 3 hr; Veh, 3 hr


title: Lung409

description:
processed data file:
countslung.csv
run0196_lane91_read*_indexD706-D506=RhLung409-18

value: 132 days

value: 5 days

value: Lung


title: RNA-seq_MCF7_JQ1_Veh_rep1


title: Input_ChIP-seq_MCF-7_E2_rep1


title: Lung410

description:
processed data file:
countslung.csv
run0196_lane91_read*_indexD707-D505=RhLung410-18


title: CIH2

value: Heart


title: CIH1


title: MI3

value: MI


title: RNA-seq_MCF7_E2_rep1

value: Breast Cancer Cells


title: RNA-seq_MCF7_E2_rep2


title: MI1


title: RNA-seq_MCF7_Veh_rep2

value: Veh, 3 hr


title: RNA-seq_MCF7_Veh_rep1


title: Treatment_input_DNA

city: nanning

first: xuefang

last: mei

address: 100, Daxue Road, Xixiangtang Area, Nanning, China

institute: College of Animal Science and Technology, Guangxi University

data_processing:
library strategy: hMeDIP-seq
Base calling were performed using Off-Line Basecaller software (OLB V1.8)
After passing Solexa CHASTITY quality filter, the clean reads were aligned to Bubalus genome (NCBI UMD_CASPUR_WB2) using HISAT2 software (V2.1.0).
hMeDIP enriched regions (peaks) with statistical significance were identified for each sample, using a q-value threshold of 10-5 by MACS v2.
hMeDIP enriched regions (peaks) were annotated by the nearest gene using the newest NCBI database.
Differentially hydromethylated regions (DhMRs) within promoter between two groups with statistically significant were identified by diffReps (Cut-off: log2FC=1.0, p-value=0.05).
Genome_build: NCBI UMD_CASPUR_WB2
Supplementary_files_format_and_content: The Ded format files contain genomic alignment result for the reads which passed Solexa CHASTITY quality filter (*_Bubalus_bubalis_UMD_CASPUR_WB2_hisat2_alignment.bed.gz, based on NCBI UMD_CASPUR_WB2).The xlsx format files contain all DNA methylation status of gene promoters and the gene body regions in all samples (*_peak_annotation.xlsx files).

organism: Bubalus bubalis

source_name: treatment_dendritic cells

extract_protocol:
The genomic DNA of DCs were used for hMeDIP and library construction; it was isolated from each individual sample using a DNeasy Blood & Tissue Kit (Qiagen, USA). Quantification and quality assurance were evaluated using the NanoDrop 1000 (Agilent, USA).
To generate the library, the products of the hMeDIP, as well as the supernatant input DNA, were purified using Qiagen MinElute columns and eluted in 16 μL of elution buffer (Qiagen, USA). Fourteen cycles of PCR were performed on 5 μL of the immunoprecipitated DNA using the single-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns; then, a final size selection (~300-600 bp) was performed using AMPure XP beads. Quality control of the libraries was performed by the Agilent 2100 Bioanalyzer using the Agilent DNA 1000 chip kitChip Kit (Agilent, USA). An aliquot of each library was diluted in EB to 5 ng/μL, and 1 μL was used in real-time PCR reactions to confirm enrichment of the hydroxymethylated region.

value: water buffalo

tag: source cell type

value: peripheral blood mononuclear cells

value: PBMCs-derived dendritic cells

value: Fasciola gigantica excretory/secretory products (FgESPs)

tag: medip antibody


title: Throphoblast_control_25uM Beta-naphtoflavone_72h, rep 1

description: Replicate 5

value: 25uM Beta-naphtoflavone


title: Throphoblast_control_25uM Beta-naphtoflavone_72h, Rep 2

description: Replicate 6


title: sham2

value: sham


title: Throphoblast_control_20uM Pioglitatsoni_72h, Rep 2

description: Replicate 2

value: 20uM Pioglitatsoni

value: Placenta


title: Treatment 3_hMeDIP-seq

value: a human monoclonal anti-5-hydroxymethylcytosine antibody (Diagenode, USA)


title: Throphoblast_control_20uM Pioglitatsoni_72h, Rep 5

description: Replicate 2

value: Term

value: Throphoblast


title: Throphoblast_control_25uM Beta-naphtoflavone_72h, Rep 3

description: Replicate 7


title: sham1


title: V6.5

city: Hefei

first: junru

last: feng

address: huangshan road #443

institute: USTC

data_processing:
As to RNA-seq data, raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
clean reads were aligned to the reference genome mm9 using TopHat v2.1.0
Transcipts were assembled by StringTie v1.3.4d
Gene expression analysis was performed using Ballgown v2.2.0
Sequenced reads were visualized by samtools v1.7 and IGV v2.5.2
Genome_build: mm10

source_name: mouse embryonic stem cells

growth_protocol: Feeder-independent mouse ES and iPS cells were cultured on gelatinized dishes in DMEM supplemented with 15% KSR (KnockOut Serum Replacement, Thermo), 1% FBS (Gibco), 2 mM L-glutamax, 55 μM β-mercaptoethanol, 0.1 mM nonessential amino acids, 1 mM sodium pyruvate, 100 ug/ml penicillin and streptomycin, and 1000 U/ml mouse leukaemia inhibitory factor (mLIF, Millipore).MEF cells  were cultured in DMEM supplemented with 10% FBS (Gibco), 0.1 mM nonessential amino acids, and 100 ug/ml penicillin and streptomycin.

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Life technologies) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100.Qualified total RNA was further purified by RNeasy micro kit and RNase-Free DNase Set.Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: shRNAs were purchased form Sigma

value: mouse embryonic stem cells


title: IPS

source_name: induced pluripotent stem cells

value: induced pluripotent stem cells


title: V6.5_NTC

tag: transfection

value: non-targeting control shRNA


title: V6.5_shGLDC

value: Gldc shRNA


title: MEF

source_name: mouse embryonic fibroblasts

value: mouse embryonic fibroblasts


title: Zar-KO-MII-Rep2

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

data_processing:
RNA-Seq was performed with biological replicates for all samples. Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) and ERCC spike-in sequences with Tophat v2.1.1. Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1. Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments) and was further normalized with the ERCC spike-in. Samples prepared in different batches were normalized by the 1Cell-stage embryo sample in each batch.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of all RNA-seq samples

source_name: Zar1/2-null Mouse MII Oocyte

growth_protocol: Growing oocytes were collected from 13.5-day old female mice, GV stage oocytes were collected from 21-day old female mice 44 h after PMSG injection and MII stage oocytes were collected 16 h after hCG injection

extract_protocol:
Oocytes were collected from indicated genotypes (10 oocytes per sample). Each sample was directly lysed with 4.2 ul lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers, and 1:1000 ERCC spike-in) and immediately used for cDNA synthesis using the Smart-seq2 method as described previously (Picelli et al, 2014).
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform with 150 bp paired-end reads

treatment_protocol: No treatment

tag: stain

value: C57BL6/ICR hybrid strain


title: A351Yanhong (T02)

first: weitao

last: Mao

state: Beijing

department: Innovation group

institute: BEIJING ACADEMY OF FORESTRY AND POMOLOGY SCIENCES

data_processing:
We use internal software SOAPnuke to filter reads，1) Remove reads with adaptors；2) Remove reads in which unknown bases(N) are more than 55%；3) Remove low quality reads
After filtering, the remaining reads are called "Clean Reads" and stored in FASTQ formatWe use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step. For HISAT which is much faster, sensitive and high accuracy analysis software
then calculate gene expression level with RSEM . RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data
Genome_build: no reference
Supplementary_files_format_and_content: excel files include FPKM values for each Sample

organism: Castanea mollissima

source_name: Normal catkins

extract_protocol:
The extraction of total RNA from the berries was carried out by a Plant RNA extraction kit (Aidlab Biotechnologies, Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Yanshanhong

value: recessive

tag: tissue

value: catkins


title: A351Heiqi (T01)

source_name: Shorter catkins (mutant)


title: MI2

value: Heart

value: MI


title: Treatment 2_hMeDIP-seq

value: water buffalo

value: peripheral blood mononuclear cells

value: PBMCs-derived dendritic cells

value: Fasciola gigantica excretory/secretory products (FgESPs)


title: Throphoblast_control_20uM Pioglitatsoni_72h, Rep 3

description: Replicate 3

value: 20uM Pioglitatsoni

value: Placenta

value: Term


title: Throphoblast_control_20uM Pioglitatsoni_72h, Rep 1

description: Replicate 1

value: Throphoblast


title: yccT mutant_H2O2 treated_rep3

city: Saint Paul

first: Sinisa

last: Vidovic

state: MN

address: 1971 Commonwealth Avenue

institute: University of Minnesota

data_processing:
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via Hisat2 (v2.0.2) using the S. enterica (P125109) as a reference.
Cuffdiff 2.2.1 was used to quantify the expression level of each known gene in units of FPKM (fragment mapped per kilobase of exons per million mapped reads)
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
Genome_build: S. enterica (P125109)
Supplementary_files_format_and_content: raw read counts

organism: Salmonella enterica subsp. enterica serovar Enteritidis

source_name: Bacterial cells

growth_protocol: Each culture of the wild type and its yccT mutant was inoculated into 100 mL of freshly preapared LB broth followed incubation at 37 C with constant shaking 190 rpm.

extract_protocol: RNA was extracted using the RNAeasy Kit from Qiagen. All bacterial samples were re-suspended in RNAprotect bacterial agent (Qiagen, Valencia, CA, USA) and stored at -20°C until RNA extraction

treatment_protocol: The Salmonella cultures reaching their mid log growth phase (i.e., OD 600 nm 0.5) were treated with 3 uM of H2O2 followed by centrifugation and washing.

value: Isogenic yccT mutant

value: H2O2 treatment


title: Zar-KO-MII-Rep1


title: Throphoblast_control_DMSO_72 h, Rep 2

description: Replicate 2

value: DMSO


title: Throphoblast_control_DMSO_72 h, Rep 1

description: Replicate 1


title: Throphoblast_control_DMSO_72 h, Rep 3

description: Replicate 3