title: PCGA-01-0021-010-19826-00723BX-1007417R


title: PCGA-01-0017-052-20261-00732BX-1007422R

status: Public on Mar 05 2019

type: SRA

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

country: USA

institute: Boston University School of Medicine

description: Gene Expression from endobronchial biopsy with metaplasia.

library_source: transcriptomic

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

molecule: polyA RNA

organism: Homo sapiens

source_name: endobronchial biopsy

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

tag: cohort

value: discovery cohort

tag: patient id

tag: grade

value: metaplasia

tag: molecular subtype

value: Inflammatory

tag: flow cell id

tag: median tin

tag: passed qc

value: TRUE


title: PCGA-01-0015-043-16954-00863BR-1007521R

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

value: Secretory


title: PCGA-01-0021-089-19826-00722BX-1007416R

description: Gene Expression from endobronchial biopsy with normal histology.

value: normal

value: Proliferative


title: PCGA-01-0014-089-20660-00744BX-1007426R

value: Normal


title: PCGA-01-0021-070-19826-00720BX-1007414R

description: Gene Expression from endobronchial biopsy with hyperplasia.

value: hyperplasia


title: PCGA-01-0010-089-19900-00700BX-1007410R


title: PCGA-01-0031-050-24061-00666BX-1007407R

description: Gene Expression from endobronchial biopsy with mild dysplasia.

value: mild dysplasia


title: PCGA-01-0031-053-24061-00665BX-1007405R

description: Gene Expression from endobronchial biopsy with moderate dysplasia.

value: moderate dysplasia


title: PCGA-01-0018-050-21990-00651BX-1007403R


title: PCGA-01-0003-089-24282-00693BX-1007408R


title: PCGA-01-0003-061-24282-00694BX-1007409R


title: PCGA-01-0031-021-24061-00664BX-1007404R


title: PCGA-01-0010-094-19900-00701BX-1007411R


title: PCGA-01-0018-074-21990-00650BX-1007402R


title: PCGA-01-0029-093-22412-00624BX-1007391R


title: PCGA-01-0029-045-22412-00625BX-1007392R


title: PCGA-01-0016-050-23045-00647BX-1007401R


title: PCGA-01-0029-061-22412-00623BX-1007390R


title: PCGA-01-0004-050-27317-00606BX-1007387R

value: FALSE


title: PCGA-01-0004-093-27317-00605BX-1007386R


title: PCGA-01-0029-089-22412-00622BX-1007389R


title: PCGA-01-0004-089-27317-00604BX-1007589R


title: PCGA-01-0025-050-20884-00601BX-1007588R


title: PCGA-01-0025-074-20884-00599BX-1007586R


title: PCGA-01-0001-089-19300-00588BX-1007584R


title: PCGA-01-0001-037-19300-00589BX-1007585R


title: PCGA-01-0001-070-19300-00587BX-1007583R


title: PCGA-01-0001-074-19300-00586BX-1007582R


title: PCGA-01-0021-089-19623-00582BX-1007580R

description: Gene Expression from endobronchial biopsy with severe dysplasia.

value: severe dysplasia


title: PCGA-01-0021-070-19623-00581BX-1007579R


title: PCGA-01-0015-011-16541-00571BX-1007578R


title: PCGA-01-0015-025-16541-00570BX-1007577R


title: PCGA-01-0011-050-26740-00567BX-1007576R


title: PCGA-01-0009-053-23126-00557BX-1007573R


title: PCGA-01-0007-093-18131-00527BX-1007607R


title: PCGA-01-0025-050-20772-00541BX-1007571R


title: PCGA-01-0025-074-20772-00540BX-1007570R


title: PCGA-01-0009-061-23126-00558BX-1007574R


title: PCGA-01-0031-021-23830-00536BX-1007568R


title: PCGA-01-0007-089-18131-00526BX-1007606R


title: PCGA-01-0010-094-19599-00504BX-1007562R


title: PCGA-01-0007-050-18131-00528BX-1007608R


title: PCGA-01-0016-050-22821-00509BX-1007565R


title: PCGA-01-0001-037-19118-00482BX-1007555R


title: PCGA-01-0025-048-20884-00600BX-1007587R


title: PCGA-01-0001-089-19118-00481BX-1007554R


title: PCGA-01-0028-050-23163-00491BX-1007557R


title: PCGA-01-0001-082-19118-00480BX-1007553R

description: Gene Expression from endobronchial biopsy with unknown histology.

value: unknown


title: PCGA-01-0018-074-21752-00494BX-1007558R


title: PCGA-01-0017-089-19883-00472BX-1007551R


title: PCGA-01-0022-089-20918-00469BX-1007599R


title: PCGA-01-0022-070-20918-00468BX-1007597R


title: PCGA-01-0021-050-19434-00465BX-1007550R


title: PCGA-01-0021-010-19434-00464BX-1007549R


title: PCGA-01-0007-050-18033-00456BX-1007603R


title: PCGA-01-0031-050-23830-00537BX-1007569R


title: PCGA-01-0007-048-18033-00455BX-1007605R


title: PCGA-01-0007-093-18033-00454BX-1007604R


title: PCGA-01-0007-089-18033-00453BX-1007602R


title: PCGA-01-0002-021-24062-00441BX-1007600R


title: PCGA-01-0002-050-24062-00443BX-1007598R


title: PCGA-01-0024-050-23686-00520BX-1007566R


title: PCGA-01-0002-077-24062-00442BX-1007601R


title: PCGA-01-0011-050-26558-00433BX-1007596R


title: PCGA-01-0018-050-21752-00496BX-1007560R


title: PCGA-01-0010-089-19599-00503BX-1007561R


title: PCGA-01-0011-089-26558-00432BX-1007595R


title: PCGA-01-0017-052-19883-00473BX-1007552R


title: PCGA-01-0015-011-16303-00402BX-1007544R


title: PCGA-01-0003-089-23883-00412BX-1007547R


title: PCGA-01-0029-050-22090-00380BX-1007537R


title: PCGA-01-0008-089-21115-00418BX-1007548R


title: PCGA-01-0014-053-20177-00393BX-1007541R


title: PCGA-01-0025-074-20576-00383BX-1007538R


title: PCGA-01-0029-048-22090-00379BX-1007536R


title: PCGA-01-0025-050-20576-00384BX-1007539R


title: PCGA-01-0029-089-22090-00377BX-1007534R


title: PCGA-01-0029-070-22090-00376BX-1007533R


title: PCGA-01-0020-048-23497-00370BX-1007532R


title: PCGA-01-0011-050-26439-00341BX-1007594R


title: PCGA-01-0020-094-23497-00367BX-1007529R


title: PCGA-01-0011-089-26439-00340BX-1007593R


title: PCGA-01-0026-089-21752-00337BX-1007526R


title: PCGA-01-0021-088-19826-00721BX-1007415R


title: PCGA-01-0005-019-16929-00325BX-1007525R


title: PCGA-01-0002-050-23843-00279BX-1007591R


title: PCGA-01-0021-070-19182-00266BX-1007382R


title: PCGA-01-0014-011-20177-00394BX-1007542R


title: NF-H_P_1

city: London

first: Denise

last: Sheer

address: Blizard Institute, 4 Newark Street

department: Neuroscience & Trauma

country: United Kingdom

institute: Barts & The London School of Medicine & Dentistry

description:
processed data file:
Transcripts_IP_NF-H_vs_IgG
J3_S3

data_processing:
Reads were trimmed with Cutadapt/1.13 using the following arguments: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT --minimum-length 10 -p
Trimmed reads were aligned to unmasked gh19 using Star, version 2.5.0 with default settings.
Peaks were called using MACS, version 2.1.0.20140616 using default settings and the IgG samples as control.
Peaks were annotated using Homer, version v4.7.2, with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: Annotated Peak files, generated by MACS2 and annotated by Homer, in Microsoft Excel (xls). These peaks corresponds to enriched regions of RNA which are associated with the immunoprecipitated proteins in lysate from human neurons.

molecule: total RNA

source_name: Neurons, differentiated from NPCs

growth_protocol: Neurons were differentiated from human neural stem cells (hNP1 cells) by withdrawal of basic FGF for 6 days. The majority (>95%) of the cells differentiate into Map2- and  III-tubulin -positive cells within 6 days.

extract_protocol:
Differentiated neural stem cells were detached by trypsin (0.5%, Life Technologies) and collected in RPMI medium with 10% FCS (Life Technologies). Cells were pelleted by centrifugation and washed twice in ice-cold PBS (14190-094) before being lysed in four cell-pellet volumes of either Lysis Buffer 1 [20 mM Tris-HCl pH 7.5, 150 mM NaCl, 3 mM EDTA, 1% Triton X-100, 0.5% Na-Deoxychoalte, 1X protease inhibitors cocktail (Roche), 1 mM DTT Lysed cells were sonicated (Bioruptor, Diagenode) at maximum setting for 5 seconds on ice and centrifuged at 21.000 x g for 30 min at 4oC. The supernatant was filtered through a 0.1 µm syringe filter (Santa Cruz, sc-358809) into new tubes and the protein concentration determined with the BCA kit (Thermo Fisher) according to the manufacturer’s instructions. Lysates were diluted in Lysis Buffer-1 to 2-4 µg/µl and used for IP. Immunoprecipitated RNA from human neuronal lysate were purified on silica columns, and include a DNAse I treatment step to remove DNA contaminants. RNA were eluted from the columns and EtOH precipitated before being used for library preparation.
Library preparation were prepared from RNA using the NEBNext Ultra II Directional RNA Library Prep Kit and Indexing primers (E7760, and E7335, respectively, both NEB) according to the manufacturer’s instructions. Libraries were pooled and pair-end sequenced (2x75 bp) on the NextSeq 500 platform (Illumina).

tag: cell type

value: EnStem-A

tag: capturing technique

value: Antibody

tag: antibody (source)

value: Neurofilament Heavy (N4142, Sigma)


title: Tau_IP_1

description:
processed data file:
Transcripts_IP_tau_vs_IgG
J5_S5

value: Tua (T9450, Sigma


title: PCGA-01-0029-061-22090-00378BX-1007535R

value: discovery cohort


title: NF-H_P_2

description:
processed data file:
Transcripts_IP_NF-H_vs_IgG
J4_S4


title: 4G8_IP_1

description:
processed data file:
Transcripts_IP_4G8_vs_IgG
J2_S2

value: Abeta (4G8, SIG-39220, Covance)


title: Tau_RIP_2

description: Renatured proteins from differentiated human neuronal stem cells (PMID 21811597)

data_processing:
Read from genomic DNA were trimmed and quality checked with Trim galore, version 0.3.7 using the following arguments: -a AGATCGGAAGAGC --paired --length 10 --three_prime_clip_R1 99 --three_prime_clip_R2 99 --retain_unpaired --trim1 --fastqc --fastqc_args
Trimmed DNA reads were aligned to unmasked gh19 usign bowtie2, version 2.2.5 with the following commands: --local
Peaks were called using MACS, version 2.1.0.20140616 using the following commands: callpeak  --format BAMPE --call-summits --bw 188
Enriched sequence motifs were search for using MEME-Chip, version 4.10.2, with the following commands:-meme-mod anr -meme-minw 5 -meme-maxw 50 -meme-nmotifs 6 -dreme-e 0.05 -centrimo-local -centrimo-score 5.0 -centrimo-ethresh 10.0
Genome_build: hg19
Supplementary_files_format_and_content: Peak files, generated by MACS2. These peaks corresponds to enriched regions of genomic DNA or RNA which are associated with soluble proteins after renaturation.

source_name: T-cell

growth_protocol: Jurkat T-cells were maintained in RPMI/10% FSC at 37C, 5% CO2. Human neurons were differentiated for 6 days by removal of growth factors. Cells were plated on Matrigen (1:400, BD) in Nerobasal Media supplemented with B27 and glutamine.

extract_protocol:
Total RNA and genomic DNA isolated from Jurkat T cells using Trizol according to the manufacturer’s instructions (Thermo Fisher Scientific)
Library preparation were prepared from RNA using the NEBNext Directional Ultra RNA kit and Indexing primers (E7530, and E7335, respectively, both NEB) according to the manufacturer’s instructions, except that no initial RNA fragmentation were performed. Libraries were pooled and pair-end sequenced (2x75 bp) on the MiSeq platform (Illumina). Sequencing libraries for DNA were prepared using the NEBNext DNA ultra kit (E7370, NEB), using NEBNext Indexing primers (E7335, NEB), and the libraries pooled and sequenced on the MiSeq system (Illumina) using pair-end reads of 300 bp.

tag: cell type (source of nucleic acids)

value: Jurkat

value: Tua (T9450, Sigma)


title: GFP_RIP_1

value: GFP (11122, Thermo Fisher Scientific)


title: IgG_ChIP_2

library_source: genomic

molecule: genomic DNA

value: mouse IgG (I5381, Sigma)


title: NF-H_RIP_1


title: NF-H_RIP_2


title: Tau_RIP_1


title: IgG_ChIP_1


title: PCGA-01-0030-089-27868-00358BX-1007527R

value: Normal

value: TRUE


title: 4G8_ChIP_1


title: Membrane_Negative

data_processing:
Library strategy: membrane capture
Read from genomic DNA were trimmed and quality checked with Trim galore, version 0.3.7 using the following arguments: -a AGATCGGAAGAGC --paired --length 10 --three_prime_clip_R1 99 --three_prime_clip_R2 99 --retain_unpaired --trim1 --fastqc --fastqc_args
Trimmed DNA reads were aligned to unmasked gh19 usign bowtie2, version 2.2.5 with the following commands: --local
Peaks were called using MACS, version 2.1.0.20140616 using the following commands: callpeak  --format BAMPE --call-summits --bw 188
Enriched sequence motifs were search for using MEME-Chip, version 4.10.2, with the following commands:-meme-mod anr -meme-minw 5 -meme-maxw 50 -meme-nmotifs 6 -dreme-e 0.05 -centrimo-local -centrimo-score 5.0 -centrimo-ethresh 10.0
Genome_build: hg19
Supplementary_files_format_and_content: Peak files, generated by MACS2. These peaks corresponds to enriched regions of genomic DNA or RNA which are associated with soluble proteins after renaturation.

value: Nitrocellulose membrane


title: 4G8_ChIP_2


title: Membrane_Total_2


title: Membrane_Total_1


title: Tau_IP_2

description:
processed data file:
Transcripts_IP_tau_vs_IgG
J6_S6


title: IgG_IP_2


title: 4G8_RIP_2


title: 4G8_RIP_1


title: Patient 261796 Polysome-associated RNA (>3 ribosomes)

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

description: Polysome-associated RNA (>3 ribosomes)

data_processing:
Primary analysis and de-multiplexing were performed using Illumina CASAVA software 1.8.2.
The resulting RNA sequencing reads were mapped and aligned to hg19 using HISAT (default parameters).
Reads mapped to multiple locations in the genome were discarded.
Gene expression was quantified as described using default settings (PMID: 20011106) and refSeq gene annotation.
Genes with 0 counts in >4 samples were removed from the analysis prior to transformation. Raw counts were rlog transformed.
Genome_build: hg19
Supplementary_files_format_and_content: Each processed file contains the counts for all quantified genes. These were then further filtered and normalized as described.

source_name: Non-cancerous lung tissue

extract_protocol:
Frozen lung tissue samples ranging in weight from 25-60 mg were individually ground to a fine powder using a liquid nitrogen cooled ceramic mortar and pestle. For RNA quality control (QC), approximately 20% of each sample was processed with Tri Reagent (Sigma-Aldrich, St. Louis, MO). Once the initial RNA QC was completed, polyribosome preparations were performed.  For this purpose, the remainder of each frozen powdered sample was solubilized in 100 µl of lysis buffer (10 mM Tris-HCl at pH 8.0, 150 mM NaCl, 5 mM MgCl2, 1% Nonidet-P40, 1% sodium deoxycholate, 40 mM dithiothreitol, 500 U/mL RNAsin RNAsin [Promega, Madison, WI], 40 mM VRC [vanadyl ribonucleoside complex], and 150 μg/ml cycloheximide [Sigma-Aldrich, St. Louis, MO]) and mixed by pipetting.  Nuclei and insoluble material were removed by centrifugation (12,000 x g, 10 minutes, at 4°C). Extraction buffer (50 μL; 0.2 M Tris-HCl at pH 7.5, 0.3 M NaCl, 10 mM PMSF) was added to the supernatant and the sample was mixed by pipetting.  The sample was centrifuged (12,000 x g, 5 minutes, at 4°C) and 25% of the supernatant was processed with Tri Reagent to generate a total mRNA sample.  The remaining supernatant was layered onto a 5 mL, linear sucrose gradient (10-50%), 10 mM Tris-HCl pH 7.5, 140 mM NaCl, 3 mM MgCl2, 10 mM DTT (Sigma-Aldrich, St. Louis, MO). Gradients were centrifuged (200,000 x g in a Beckman SW55Ti rotor, Beckman Coulter, Chaska, MN) for 80 min at 4˚C and the gradients were fractionated into ten, 0.5 mL fractions utilizing an ISCO density gradient fractionator with absorbance monitored at 254 nm. Each fraction was collected into a tube containing 50 μL 1% SDS and 20 μL 0.5M EDTA.  The polysome-associated mRNA from fractions 7, 8, 9 and 10 were individually processed with 1 mL of Tri Reagent and 200 μL chloroform and the resultant RNA pellets from these four fractions were combined to create the polysome-associated mRNA sample corresponding to each tissue sample.
Smart-Seq2

tag: cancer status

tag: tissue

value: non-cancerous lung stroma tissue


title: Patient 276427 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 70403 Total RNA


title: Patient 15473 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 15837 Total RNA


title: Patient 51242 Total RNA


title: Patient 70403 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 276427 Total RNA


title: Patient 15473 Total RNA


title: Patient 51242 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 133110 Total RNA


title: Patient 133110 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 261796 Total RNA


title: Patient 4427 Total RNA


title: Patient 4427 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: IgG_IP_1


title: Patient 54921 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 41742 Total RNA


title: Patient 54921 Total RNA


title: Patient 15837 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 227628 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 227628 Total RNA


title: Patient 158231 Total RNA


title: Patient 30586 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 30586 Total RNA


title: GFP_RIP_2


title: Patient 15511 Total RNA


title: Patient 177023 Total RNA


title: Patient 15511 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 41742 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 284144 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 35961 Total RNA


title: Patient 24201 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 177023 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 42988 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 284144 Total RNA


title: Patient 35961 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 24201 Total RNA


title: Patient 267445 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 140099 Total RNA


title: Patient 267445 Total RNA


title: Patient 257649 Total RNA


title: Patient 257649 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 196768 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 42988 Total RNA


title: Patient 7206 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 140099 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 158231 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 196768 Total RNA


title: Patient 57164 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 116903 Total RNA


title: Patient 57164 Total RNA


title: Patient 7206 Total RNA


title: Patient 4226 Total RNA


title: Patient 4226 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 70021 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 70021 Total RNA


title: Patient 81498 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 81498 Total RNA


title: Patient 260111 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 260111 Total RNA


title: chr III tDNA-D Monoclonal 9E10 ChIP-Seq Biological replicate 2

city: Bethesda

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

description: ChIP biological replicate 2

data_processing:
Sequencing data were mapped to the S. cerevisiae reference genome sacCer3, using bowtie2 (Langmead and Salzberg, Nature Methods, 2012) with the default settings.
The typical DNA fragment length was estimated based on strand cross-correlation maxima using the SPP package (Kharchenko et al., Nat Biotechnol., 2008) (available at https://github.com/hms-dbmi/spp/).
The reads were extended to the estimated typical fragment size of 170 bp and genome-wide coverage profiles were computed in MATLAB. The coverage profiles were normalized such that the average coverage for every chromosome is 1.
IGV tracks (tdf files) were generated using igvtools.
Genome_build: sacCer3
Supplementary_files_format_and_content: tdf files containing the normalized occupancy profiles, for the IGV browser

organism: Saccharomyces cerevisiae

source_name: Monoclonal 9E10 ChIP-Seq_chr III tDNA-D

growth_protocol: Cells were grown to early log phase in 300ml YPD

extract_protocol:
Cells were fixed with 1% formaldehyde, quenched, lysed and sonicated to generate small DNA fragments. ChIPs were performed with 5ug of 9E10 from Covance (now Biolegend).
Libraries were prepared at the Functional Genomics Laboratory, UC Berkeley and sequenced at the Vincent J Coates Sequencing Laboratory at UC Berkeley.

tag: strain

tag: genotype

value: MATa SCC2-13xMyc::KanMX ade2-1  trp1-1 ura3-1 chrIII (t0D, t1D, t3D, t4D, t5D, t6D, t7D, t8D+t9D::LEU2), T1+T7::HIS3

tag: chip antibody

value: anti-Myc (monoclonal 9E10)


title: Patient 4685 Total RNA


title: Patient 4685 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: JKY690 chrIII tDNAD biological replicate 1

description:
Total RNA from chIII tDNA D cells biological replicate 1
690a

data_processing:
Pseudo-alignment was performed using Kallisto (Bray et al., Nat. Biotechnol., 2016)
Differentially expressed genes were obtained using Sleuth (Pimentel et al., Nature Methods, 2017).
Genome_build: sacCer3
Supplementary_files_format_and_content: abundance.tsv - text file containing the Kallisto estimates of transcript abundances.

source_name: JKY690 chrIII tDNAD

growth_protocol: Cells were grown to early log phase in YPD, spun, washed in PBS and aliquots were flash frozen in liquid nitrogen.

extract_protocol:
Total RNA was isolated by ACGT Inc., Wheeling IL using the Qiagen Rneasy kit.
Libraries were constructed and sequenced by ACGT Inc., Wheeling IL using the NEXTflex Rapid Directional RNA-Seq kit

treatment_protocol: No treatment

value: MATa ade2-1  trp1-1 ura3-1 chrIII (t0D, t1D, t3D, t4D, t5D, t6D, t7D, t8D+t9D::LEU2), T1+T7::HIS3


title: Wild-type Monoclonal 9E10 ChIP-Seq Biological replicate 2

description: ChIP biological replicate 2

source_name: Monoclonal 9E10 ChIP-Seq_wildtype

value: MATa SCC2-13xMyc::KanMX ADE2 his3-11,15 leu2-3, 112 lys2D trp1-1 ura3-1


title: Wild-type Total Input DNA Seq

description: Total Input DNA

value: none (input)


title: Patient 116903 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: Patient 19062 Total RNA


title: chr III tDNA-D Total Input DNA Seq

description: Total Input DNA

source_name: chr III tDNA-D Total Input_chr III tDNA-D


title: JRY2334 wild type biological replicate 1

description:
Total RNA from wild-type cells biological replicate 1
2334a

source_name: JRY2334 wild type


title: JKY690 chrIII tDNAD biological replicate 2

description:
Total RNA from chIII tDNA D cells biological replicate 2
690b


title: MLE001

status: Public on Mar 03 2019

city: Barcelona

first: Luca

last: Cozzuto

state: Barcelona

address: Carrer Dr. Aiguader 88

department: CRG core facilities

country: Spain

institute: Centre for genomic regulation (CRG)

description:
Reporter for Wnt pathway activation
mESCs cultured in conventional Seru/LIF
ESCs were purified from the ICM of the mouse blasotcyst and adapted in culture

data_processing:
Base calling and adaptor trimming were performed by using RTA (Illumina) and CASAVA (v1.8.2).
Mapping was done with Tophat (v2.0.4) on mm9 genome allowing 4 mismatches and maximum 10 multiple hits.
HTSeq-count (v0.5.4p5) was used to count the mapped tags within the exons without considering the strand orientation
Raw counts were then analyzed with DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: htseq-count output, tabular format with read counts per gene.

organism: Mus musculus

source_name: Mouse ES cells

growth_protocol: ES were coltured in Serum/LIF or 2i/LIF( containing the GSK3 inhibitor [3uM] and ERK inhibitor PD [1uM] on gelatin coated plates. Cells were generally splitted every 48hours.

extract_protocol:
Total RNA was extract from ES cells cultured in Serum/LIF and 2i/LIF using the RNeasy kit (Qiagen). High quality RNA was used for RnaSeq
RNA libraries were prepared for sequencing using standard Quiagen protocol

tag: culture media

value: Serum/LIF

value: ESCs carrying a reporter fot Wnt/beta Catenin pathway activation


title: Patient 19062 Polysome-associated RNA (>3 ribosomes)

description: Polysome-associated RNA (>3 ribosomes)


title: JRY2334 wild type biological replicate 2

description:
Total RNA from wild-type cells biological replicate 2
2334b


title: MLE003

description:
Reporter for Wnt pathway activation
mESCs cultured in 2i/LIF
ESCs were purified from the ICM of the mouse blasotcyst and adapted in culture

value: 2i/LIF Media >13 passages


title: MLE002

value: 2i/LIF Media 5-6 passages


title: LEM004

description:
Reporter for Wnt pathway activation
mESCs cultured before in 2i/LIF and then in Serum/LIF
ESCs were purified from the ICM of the mouse blasotcyst and adapted in culture

value: 2i/LIF >13pass; Serum/LIF 6 pass


title: MLE005

description:
Reporter for Wnt pathway activation
mESCs cultured before in 2i/LIF and then in Serum/LIF media and finally switched again in 2i/LIF
ESCs were purified from the ICM of the mouse blasotcyst and adapted in culture

value: 2i/LIF 13pass; Serum/LIF 6 pass; 2i/LIF 4-5 pass


title: LEM005


title: LEM002


title: MLE004


title: LEM003


title: chr III tDNA-D Monoclonal 9E10 ChIP-Seq Biological replicate 1

description: ChIP biological replicate 1


title: Wild-type Monoclonal 9E10 ChIP-Seq Biological replicate 1

description: ChIP biological replicate 1


title: LEM001


title: b-catenin mutant cranial mesecnhyme + ectoderm

status: Public on Mar 01 2019

city: Cleveland

first: Radhika

middle: Paresh

last: Atit

state: Ohio

address: 2074 Adelbert Road, Millis 316

department: Biology

institute: Case Western Reserve University

data_processing:
ChIP-seq reads were aligned to mm9 genome using Bowtie2
Peaks were called using Macs1.4 default settings
Drosophila DNA was “spiked in” during immunoprecipitation. The ratio of aligned Drosophila reads in the mutant versus control samples (calculated to be 1.3) was used to normalize the number of reads in the mouse samples by downsampling the larger sample (mutant, in this case).
Genome_build: mm9
Supplementary_files_format_and_content: called peaks. BigWig

source_name: Manually dissected cranial mesenchyme plus ectoderm

extract_protocol:
At E13.5, En1Cre;b-cateninfl/fl mutant and En1Cre;b-cateninfl/+ control cranial mesenchyme was isolated by manual dissection. An incision was made around the circumference of the neurocranium, and the tissue covering the brain was manually disassociated. The supraorbital cranial mesenchyme isolated consists of the neural crest and mesoderm derived cranial mesenchyme plus the ectoderm. 14 µg chromatin was immunoprecipitated with 4 µg rabbit anti-H3K27me3 (Millipore #07-449).
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500. The libraries were made using the standard Illumina PE adaptor: ACACTCTTTCCCTACACGACGCTCTTCCGATC*T; p-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG

tag: antibody

value: H3K27me3 (Millipore #07-449)

tag: developmental stage

tag: genotype/variation

value: EnlCre/+;RRbgal;Bcatflox/null

value: whole tissue


title: INPUT

value: Pooled samples from control and mutant


title: b-catenin control cranial mesecnhyme + ectoderm

value: EnlCre/+;RRbgal;Bcatflox/+


title: WW45cKO

city: Seoul

first: Jiyeon

last: Park

address: 222, Banpo-daero

department: Catholic Center for Precision Medicine Research

country: South Korea

institute: The Catholic University of Korea

data_processing:
Basecalls performed using Illumina CASAVA
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 genome using HiSAT2 (Nat Methods. 2015;12(4):357-60)
mRNA expression was normalized and mRNA regulation between samples was calculated using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM

source_name: heart; baseline conditions; cardiac specific WW45 knockout

extract_protocol:
Total RNA was extracted from mouse hearts using the RNeasy Plus Universal Kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: 3 months old

value: heart

value: WW45 flox/flox-alpha-MHC-CRE


title: CT

source_name: heart; baseline conditions;

value: WW45 flox/flox


title: WW45cKO TAC

source_name: heart; transverse aortic constriction; cardiac specific WW45 knockout

treatment_protocol: 4-week TAC


title: MIG replicate 1

city: Bangalore

first: Calvin

last: Rodrigues

address: GKVK, Off Bellary Road

country: India

institute: National Centre for Biological Sciences

description: Migrated fraction derived mRNA, replicate 1

data_processing:
Base calling was performed using CASAVA_v1.8.2, Data quality was assessed using FASTX-toolkit (v0.0.13.2)
Reads were aligned using Tophat2 (vTophat2.0.12)  with parameters -i 50 -I 250000. Next, transcript assembly was performed using Cufflinks2(v2.2.1) using parameters -u -N --total-hits-norm. GTF files were merged using Cuffmerge (from cufflinks 2.2.1).
Read counts (FPKM) were calculated and differential expression analysis was performed using Cuffdiff2 (from cufflinks v2.2.1), using parameters -u -N --total-hits-norm
R package cummeRbund was used to extract significantly differentially expressed genes (FDR/q value < 0.05) from cuffdiff output
For deriving lists of low and high expression genes, .bam files were imported into SeqMonk (v1.37). Reads were counted across genes using the feature probe option, normalising to the largest dataset. Genes were then filtered using the Filter>Filter on values>Position in distribution function, into low expression (0-25 percentile expression across all samples) and high expression (75-100 percentile expression across all samples).
Genome_build: hg19
Supplementary_files_format_and_content: 1. .xls file listing FPKM(averaged across replicates) and significance values 2. File listing FPKM across individual replicates 3,4. lists of low and high expression genes (0-25 percentile expression and 75-100 percentile expression)
Supplementary_files_format_and_content: RNA_Seq_mig_non_migdiffgenes.xls: abundance measurement (FPKM) and significance values
Supplementary_files_format_and_content: RNA_Seq_mig_non_mig_genes.read_group_tracking: abundance measurement (FPKM) of genes across individual replicates
Supplementary_files_format_and_content: RNA Seq low expression genes list.txt: list of low expression genes (0-25 percentile across all samples)
Supplementary_files_format_and_content: RNA Seq high expression genes list.txt: list of high expression genes (75-100 percentile across all samples)

source_name: SiHa cell line

growth_protocol: SiHa cells were grown in DMEM with 10% FCS, in T75 flasks

extract_protocol:
RNA was extracted using the Trizol method. RNA was treated using DNAse, and column cleanup was performed
Tru Seq RNA sample preparation kit v2 (Catalog No.: RS-122-2001) from Illumina

treatment_protocol: 0.75 x 106 cells were seeded per well of a 6 well migration transwell set up. 10h post seeding, cells were then scraped in PBS, pooled and used for further processing.

tag: tissue type

value: Squamous cell carcinoma of the cervix (primary site)

tag: passages

tag: cell line

value: SiHa


title: NON MIG replicate 1

description: Non Migrated fraction derived mRNA, replicate 1


title: NON MIG replicate 2

description: Non Migrated fraction derived mRNA, replicate 2


title: MIG replicate 3

description: Migrated fraction derived mRNA, replicate 3


title: NON MIG replicate 3

description: Non Migrated fraction derived mRNA, replicate 3


title: MIG replicate 2

description: Migrated fraction derived mRNA, replicate 2


title: WT ES cell_in situ HiC

first: Hongjae

last: Sunwoo

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital, Harvard Medical School, HHMI

data_processing:
CHART-seq and ChIP-seq: Reads were aligned separately to the mus/129 and cas genomes using novoalign with default parameters for paired-end alignment, the coordinates of these alignments were then converted to mm9 coordinates with custom scripts. Following alignment, coverage files were generated for the composite set of reads (comp), as well as allelic reads that aligned better to mus (mus) or cas (cas) using custom perl scripts, SAMtools and bedtools to extract and sort allelic reads, remove duplicates and generate coverage files. After input normalization using SPP, the coverage tracks presented in the paper were further normalizated between experiments to have equal coverage within a 1-MB region flanking the Xist locus (chrX:100150712-100650712 and 100683572-101183572).
ChIP-seq: Reads were aligned separately to the mus/129 and cas genomes using novoalign with default parameters for paired-end alignment, the coordinates of these alignments were then converted to mm9 coordinates with custom scripts. Following alignment, coverage files were generated for the composite set of reads (comp), as well as allelic reads that aligned better to mus (mus) or cas (cas) using custom perl scripts, SAMtools and bedtools to extract and sort allelic reads, remove duplicates and generate coverage files. The coverage files presented in the paper are input normalized using SPP.
RNA-seq: PCR duplicates were removed and reads separately aligned to custom mus/129 and cas genomes using Tophat. Final allele-specific mapping to reference mm9 genome was generated based on SNPs. Only uniquely aligned concordantly mapped sequences were used in downstream analysis. Counts per gene were calculated using featureCounts. Using MatLab, library sizes were normalized and genes with insufficient allelic information (<13 allele-specific reads) were removed. We also removed potentially miscalled genes from our alignment pipeline, defined as genes incorrectly assigned to mus from a pure cas RNA-seq library. Allele-specific RPKM was calculated using allelic ratio (allele-specific counts) applied to comp RPKM (total counts).
In situ Hi-C:  Reads were trimmed using cutadapt with the options --adapter=GATCGATC (MboI ligation junction) and --minimum-length=20. Reads of each pair were individually mapped to the mus (Xi) and cas (Xa) reference genomes using novoalign and default parameters, then merged into Hi-C summary files and filtered using HOMER with custom scripts (parameters for HOMER filtering (makeTagDirectory): -removePEbg -restrictionSite GATC -both -removeSelfLigation). Hi-C contact maps were generated from reads in the filtered HOMER mus and cas tag directories using the ‘pre’ command of Juicer tools with the genomeID mm9 .
Genome_build: mm9
Supplementary_files_format_and_content: CHARTP-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bigWig files are input normalized. Log2 ration bw files are ratio after further normalization to have equal coverage within a 1-MB region flanking the Xist locus (chrX:100150712-100650712 and 100683572-101183572).
Supplementary_files_format_and_content: ChIP-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bigWig files are input normalized.
Supplementary_files_format_and_content: RNA-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bw files are rpkm values.  Raw exonic reads in each RNA-seq library were quantified and summarized in RNAseq_experiment_count_rep1 or 2.txt.
Supplementary_files_format_and_content: In situ Hi-C:  Compressed Hi-C matrix (.hic) files for cas-specific and mus-specific filtered Hi-C reads. File can be loaded onto Juicebox to view either raw or normalized Hi-C interaction matrices at 5kb to 2.5Mb resolutions.

source_name: WT ES cell

growth_protocol: ES cells were grown on γ-irradiated MEF feeders for 3 days prior to differentiationin in ES medium (1% Pen/Strep, high-glucose DMEM+GlutaMAX, LIF) with 15% FBS. For differentiation, ES colonies were trypsinized and feeders removed. ES cells were allowed to differentiate in suspension, forming embryoid bodies (EBs), for 4 days in differentiation medium (1% Pen/Strep, high-glucose DMEM+GlutaMAX) with 15% FBS. EBs were settled down on gelatin-coated plates at day 4 and allowed to further differentiate for 10 days until harvesting.

extract_protocol:
CHART-seq: Sheared chromatin from 2.5x10^7 cells was prepared as described earlier as in Simon et al., Nature 504, 465-469 (2013).  160 μL chromatin was mixed with 320 μL 2X hybridization buffer (50 mM Tris-HCl pH 7.0, 750 mM NaCl, 1% SDS, 1 mM EDTA, 15% formamide, 1 mM DTT, 200 mM PMSF, 1 cOmplete EDTA-free protease inhibitor cocktail tablet [Roche], and 100 U/mL RNase Inhibitor [Roche]) and pre-cleared with 60 μl MyOne Streptavidin C1 beads blocked with yeast total RNA and bovine serum albumin at room temperature for 1 hr. The pre-cleared chromatin was mixed with 36 pmol of either antisense (Xist-targeting) or sense (control) capture probes. We used a pool of 9 capture probes (biotinylated oligos). Hybridization was carried out at 37°C for 4 hr followed by incubation with 240 μL blocked MyOne Streptavidin C1 beads at 37°C for 1 hr. The beads were washed once with 1X hybridization buffer (1:2 mixture of sonication buffer and 2X hybridization buffer) at 37°C for 10 min, five times with wash buffer (10 mM HEPES pH 7.6, 150 mM NaCl, 2% SDS, 2 mM EDTA, 2 mM EGTA, and 1 mM DTT) at 37°C for 5 min, and twice with elution buffer (10 mM HEPES pH 7.6, 150 mM NaCl, 0.5% NP-40, 3 mM MgCl2, and 10 mM DTT) at 37°C for 5 min. CHART-enriched DNA was eluted by 20 μL RNase H (5 U/μL, New England BioLabs) in 200 μL elution buffer two times at 37°C for 30 min. Eluent was treated with 10 μL RNase A (20 mg/mL) at 37°C for 1 hr and then treated with SDS (final 1%), EDTA (final 10 mM), and 10 μL proteinase K (20 mg/mL) at 55°C for 1 hr. Reversal of crosslinks was performed by supplementing the eluent with NaCl (final 0.3 M) and incubation at 65°C overnight. DNA was extracted by phenol-chloroform and further sheared to below 500-bp fragments.
ChIP-seq: Cells were crosslinked with 1% formaldeyde for 10 min, then nuclei were isolated and lysed. Chromatin was sheared by sonication to a size of ~200-400 bp. Cleared lysates were precleared for 1 hour, then 10% saved as input, and lysates were incubated with Dynabeads Protein G pre-bound with the antibody of choice. After stringent washes, ChIP DNA was eluted from beads, and together with input chromtain was reverse-crosslinked with proteinase K. DNA was purified by phenol/chloroform extraction and ethanol precipitation.
RNA-seq: Total cell RNA was extracted using TRIzol (Thermo Fisher), from which mRNA was isolated using oligo(dT) beads and RNA-seq libraries prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) as per manufacturer’s instructions.
in situ Hi-C: As described in Rao et al. (2014), 3-5 million cells were crosslinked with 1% formaldehyde for 10min. Crosslinked cell pellets were lysed with 300uL ice-cold HiC lysis buffer (10mM Tris HCl pH 8, 10mM NaCl, 0.2% Igepal CA630) with protease inhibitors (Roche). Cell suspension was incubated for 30min at 4C with rotation, then pelleted at 2500xg for 5min. Pelleted nuclei were then washed with 500ul ice-cold HiC lysis buffer and resuspended in 50uL 0.5% SDS solution and incubated at 62C for 10min. 145ul H2O and 25ul 10% Triton X-100 were added to quench SDS and nuclei incubated at 37C for 15min. 26.1ul of 10X NEB Buffer 2 and 100U of MboI restriction enzyme were added and nuclei digested overnight at 37C with rotation. MboI was then heat activated at 62C for 20min, then nuclei cooled to room temperature. To fill in MboI fragment overhangs and mark DNA ends with biotin, 50ul of fill-in master mix was added (37.5ul 0.4mM biotin-14-dATP, 1.5ul 10mM dCTP, 1.5ul 10mM dGTP, 1.5ul 10mM dTTP, 8ul 5U/ul DNA Polymerase I, Large (Klenow) Fragment) and mixed by pipetting. Nuclei were then incubated at 37C for 1h with rotation. To ligate biotinylated DNA ends together, 900ul ligation master mix was added (649ul H2O, 120ul 10X NEB T4 ligase buffer, 100ul 10% Triton X-100, 6ul of 20mg/ml BSA, 25ul of 400U/ul T4 DNA ligase). Reaction was mixed by inverting and incubated at room temperature for 4h with rotation. Reaction was then centrifuged at 1700xg for 5min at room temperature. Pelleted nuclei were resuspended in 750ul TES buffer (1mM EDTA, 10mM Tris-HCl pH 8, 0.5% SDS), 50ul Proteinase K (20mg/ml) added and incubated at 55C for 1h with rotation. To reverse crosslinks, 88.9ul 3M NaCl was added and crosslinks reversed by incubated overnight at 65C with shaking (Eppendorf thermomixer, 950rpm). Samples were cooled to room temperature and DNA extracted with phase-lock gel tubes (5Prime). RNA was digested from purifying DNA by adding 2ul RNAse A (20mg/ml) and incubating at 37C for 1h. DNA was then extracted with phase-lock gel tubes (5Prime) and resuspended in 130ul 1X Tris buffer (10mM Tris-HCl, pH 8). To ensure complete resuspension, DNA was then incubated at 37C for 15min. DNA was then sonicated to a size of 300-500bp using a Covaris with the following parameters: 140W, 10% duty cycle, 200 bursts/cycle, 100s. Samples were then size selected to 300-500bp using AMPure XP beads and eluted in 300ul 1X Tris buffer. To pulldown biotinylated ligation products, 30ul (per sample) of MyOne Streptavidin C1 beads were washed with 400ul of 1X Tween washing buffer (5mM Tris-HCl pH 7.5, 0.5mM EDTA, 1M NaCl, 0.05% Tween 20) and resuspended in 300ul 2X binding buffer (10mM Tris-HCl pH 7.5, 1mM EDTA, 2M NaCl). Beads were then added to purified DNA and sample incubated at room temperature for 15min with rotation. Beads were washed twice with 600ul 1X Tween Washing buffer. Subsequent library preparation steps were then done directly on beads.
Libraries were constructed using the NEBNext ChIP-seq Library Preparation Kit with no modifications to the protocol. We used 9-14 cycles of PCR amplification, depending on library concentration measured by qPCR.

tag: strain background

value: CAST/Ei x 129/Sv/Jae

tag: cell type

value: ES cell

value: WT


title: Repeat B MEF_H2AK119ub, input DNA, rep1

data_processing:
CHART-seq and ChIP-seq: Reads were aligned separately to the mus/129 and cas genomes using novoalign with default parameters for paired-end alignment, the coordinates of these alignments were then converted to mm9 coordinates with custom scripts. Following alignment, coverage files were generated for the composite set of reads (comp), as well as allelic reads that aligned better to mus (mus) or cas (cas) using custom perl scripts, SAMtools and bedtools to extract and sort allelic reads, remove duplicates and generate coverage files. After input normalization using SPP, the coverage tracks presented in the paper were further normalizated between experiments to have equal coverage within a 1-MB region flanking the Xist locus (chrX:100150712-100650712 and 100683572-101183572).
ChIP-seq: Reads were aligned separately to the mus/129 and cas genomes using novoalign with default parameters for paired-end alignment, the coordinates of these alignments were then converted to mm9 coordinates with custom scripts. Following alignment, coverage files were generated for the composite set of reads (comp), as well as allelic reads that aligned better to mus (mus) or cas (cas) using custom perl scripts, SAMtools and bedtools to extract and sort allelic reads, remove duplicates and generate coverage files. The coverage files presented in the paper are input normalized using SPP.
RNA-seq: PCR duplicates were removed and reads separately aligned to custom mus/129 and cas genomes using Tophat. Final allele-specific mapping to reference mm9 genome was generated based on SNPs. Only uniquely aligned concordantly mapped sequences were used in downstream analysis. Counts per gene were calculated using featureCounts. Using MatLab, library sizes were normalized and genes with insufficient allelic information (<13 allele-specific reads) were removed. We also removed potentially miscalled genes from our alignment pipeline, defined as genes incorrectly assigned to mus from a pure cas RNA-seq library. Allele-specific RPKM was calculated using allelic ratio (allele-specific counts) applied to comp RPKM (total counts).
In situ Hi-C:  Reads were trimmed using cutadapt with the options --adapter=GATCGATC (MboI ligation junction) and --minimum-length=20. Reads of each pair were individually mapped to the mus (Xi) and cas (Xa) reference genomes using novoalign and default parameters, then merged into Hi-C summary files and filtered using HOMER with custom scripts (parameters for HOMER filtering (makeTagDirectory): -removePEbg -restrictionSite GATC -both -removeSelfLigation). Hi-C contact maps were generated from reads in the filtered HOMER mus and cas tag directories using the ?pre? command of Juicer tools with the genomeID mm9 .
Genome_build: mm9
Supplementary_files_format_and_content: CHARTP-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bigWig files are input normalized. Log2 ration bw files are ratio after further normalization to have equal coverage within a 1-MB region flanking the Xist locus (chrX:100150712-100650712 and 100683572-101183572).
Supplementary_files_format_and_content: ChIP-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bigWig files are input normalized.
Supplementary_files_format_and_content: In situ Hi-C:  Compressed Hi-C matrix (.hic) files for cas-specific and mus-specific filtered Hi-C reads. File can be loaded onto Juicebox to view either raw or normalized Hi-C interaction matrices at 5kb to 2.5Mb resolutions.

source_name: Repeat B MEF_H2AK119ub_input DNA

growth_protocol: MEF cells were cultured in regular fibroblast medium (1% Pen/Strep, high-glucose DMEM+GlutaMAX) with 10% FBS

extract_protocol:
CHART-seq: Sheared chromatin from 2.5x10^7 cells was prepared as described earlier as in Simon et al., Nature 504, 465-469 (2013).  160 μL chromatin was mixed with 320 μL 2X hybridization buffer (50 mM Tris-HCl pH 7.0, 750 mM NaCl, 1% SDS, 1 mM EDTA, 15% formamide, 1 mM DTT, 200 mM PMSF, 1 cOmplete EDTA-free protease inhibitor cocktail tablet [Roche], and 100 U/mL RNase Inhibitor [Roche]) and pre-cleared with 60 μl MyOne Streptavidin C1 beads blocked with yeast total RNA and bovine serum albumin at room temperature for 1 hr. The pre-cleared chromatin was mixed with 36 pmol of either antisense (Xist-targeting) or sense (control) capture probes. We used a pool of 9 capture probes (biotinylated oligos). Hybridization was carried out at 37°C for 4 hr followed by incubation with 240 μL blocked MyOne Streptavidin C1 beads at 37°C for 1 hr. The beads were washed once with 1X hybridization buffer (1:2 mixture of sonication buffer and 2X hybridization buffer) at 37°C for 10 min, five times with wash buffer (10 mM HEPES pH 7.6, 150 mM NaCl, 2% SDS, 2 mM EDTA, 2 mM EGTA, and 1 mM DTT) at 37°C for 5 min, and twice with elution buffer (10 mM HEPES pH 7.6, 150 mM NaCl, 0.5% NP-40, 3 mM MgCl2, and 10 mM DTT) at 37°C for 5 min. CHART-enriched DNA was eluted by 20 μL RNase H (5 U/μL, New England BioLabs) in 200 μL elution buffer two times at 37°C for 30 min. Eluent was treated with 10 μL RNase A (20 mg/mL) at 37°C for 1 hr and then treated with SDS (final 1%), EDTA (final 10 mM), and 10 μL proteinase K (20 mg/mL) at 55°C for 1 hr. Reversal of crosslinks was performed by supplementing the eluent with NaCl (final 0.3 M) and incubation at 65°C overnight. DNA was extracted by phenol-chloroform and further sheared to below 500-bp fragments.
ChIP-seq: Cells were crosslinked with 1% formaldeyde for 10 min, then nuclei were isolated and lysed. Chromatin was sheared by sonication to a size of ~200-400 bp. Cleared lysates were precleared for 1 hour, then 10% saved as input, and lysates were incubated with Dynabeads Protein G pre-bound with the antibody of choice. After stringent washes, ChIP DNA was eluted from beads, and together with input chromtain was reverse-crosslinked with proteinase K. DNA was purified by phenol/chloroform extraction and ethanol precipitation.
RNA-seq: Total cell RNA was extracted using TRIzol (Thermo Fisher), from which mRNA was isolated using oligo(dT) beads and RNA-seq libraries prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) as per manufacturer’s instructions.
insitu HiC: As described in Rao et al. (2014), 3-5 million cells were crosslinked with 1% formaldehyde for 10min. Crosslinked cell pellets were lysed with 300uL ice-cold HiC lysis buffer (10mM Tris HCl pH 8, 10mM NaCl, 0.2% Igepal CA630) with protease inhibitors (Roche). Cell suspension was incubated for 30min at 4C with rotation, then pelleted at 2500xg for 5min. Pelleted nuclei were then washed with 500ul ice-cold HiC lysis buffer and resuspended in 50uL 0.5% SDS solution and incubated at 62C for 10min. 145ul H2O and 25ul 10% Triton X-100 were added to quench SDS and nuclei incubated at 37C for 15min. 26.1ul of 10X NEB Buffer 2 and 100U of MboI restriction enzyme were added and nuclei digested overnight at 37C with rotation. MboI was then heat activated at 62C for 20min, then nuclei cooled to room temperature. To fill in MboI fragment overhangs and mark DNA ends with biotin, 50ul of fill-in master mix was added (37.5ul 0.4mM biotin-14-dATP, 1.5ul 10mM dCTP, 1.5ul 10mM dGTP, 1.5ul 10mM dTTP, 8ul 5U/ul DNA Polymerase I, Large (Klenow) Fragment) and mixed by pipetting. Nuclei were then incubated at 37C for 1h with rotation. To ligate biotinylated DNA ends together, 900ul ligation master mix was added (649ul H2O, 120ul 10X NEB T4 ligase buffer, 100ul 10% Triton X-100, 6ul of 20mg/ml BSA, 25ul of 400U/ul T4 DNA ligase). Reaction was mixed by inverting and incubated at room temperature for 4h with rotation. Reaction was then centrifuged at 1700xg for 5min at room temperature. Pelleted nuclei were resuspended in 750ul TES buffer (1mM EDTA, 10mM Tris-HCl pH 8, 0.5% SDS), 50ul Proteinase K (20mg/ml) added and incubated at 55C for 1h with rotation. To reverse crosslinks, 88.9ul 3M NaCl was added and crosslinks reversed by incubated overnight at 65C with shaking (Eppendorf thermomixer, 950rpm). Samples were cooled to room temperature and DNA extracted with phase-lock gel tubes (5Prime). RNA was digested from purifying DNA by adding 2ul RNAse A (20mg/ml) and incubating at 37C for 1h. DNA was then extracted with phase-lock gel tubes (5Prime) and resuspended in 130ul 1X Tris buffer (10mM Tris-HCl, pH 8). To ensure complete resuspension, DNA was then incubated at 37C for 15min. DNA was then sonicated to a size of 300-500bp using a Covaris with the following parameters: 140W, 10% duty cycle, 200 bursts/cycle, 100s. Samples were then size selected to 300-500bp using AMPure XP beads and eluted in 300ul 1X Tris buffer. To pulldown biotinylated ligation products, 30ul (per sample) of MyOne Streptavidin C1 beads were washed with 400ul of 1X Tween washing buffer (5mM Tris-HCl pH 7.5, 0.5mM EDTA, 1M NaCl, 0.05% Tween 20) and resuspended in 300ul 2X binding buffer (10mM Tris-HCl pH 7.5, 1mM EDTA, 2M NaCl). Beads were then added to purified DNA and sample incubated at room temperature for 15min with rotation. Beads were washed twice with 600ul 1X Tween Washing buffer. Subsequent library preparation steps were then done directly on beads.
Libraries were constructed using the NEBNext ChIP-seq Library Preparation Kit with no modifications to the protocol. We used 9-14 cycles of PCR amplification, depending on library concentration measured by qPCR.

treatment_protocol: ES cells were grown on γ-irradiated MEF feeders for 3 days prior to differentiationin in ES medium (1% Pen/Strep, high-glucose DMEM+GlutaMAX, LIF) with 15% FBS. For differentiation, ES colonies were trypsinized and feeders removed. ES cells were allowed to differentiate in suspension, forming embryoid bodies (EBs), for 4 days in differentiation medium (1% Pen/Strep, high-glucose DMEM+GlutaMAX) with 15% FBS. EBs were settled down on gelatin-coated plates at day 4 and allowed to further differentiate for 10 days until harvesting.

value: Mouse embryonic fibroblasts (MEF)

value: Loss of Repeat B

tag: pull down oligo/chip antibody


title: WT, MEF_in situ HiC

source_name: WT, MEF


title: Repeat B MEF_RNAseq, rep1

description: processed data: RNA_MEF_count_rep1.txt

source_name: Repeat B MEF_RNAseq


title: WT MEF_RNAseq, rep1

description: processed data: RNA_MEF_count_rep1.txt

source_name: WT MEF_RNAseq

value: wild type


title: Repeat B -/- ES cell_RNAseq, rep1

description: processed data: RNA_ES_count_rep1.txt

source_name: Repeat B -/- ES cell_RNAseq

value: Repeat B -/-


title: Repeat B +/- ES cell_RNAseq, rep2

description: processed data: RNA_ES_count_rep2.txt

source_name: Repeat B +/- ES cell_RNAseq

value: Repeat B +/-


title: WT MEF_H2AK119ub, ChIP DNA, rep1

source_name: WT MEF_H2AK119ub_ChIP DNA

value: H2AK119ub (Cell Signaling Technology, 8240, lot 2)


title: Repeat B MEF_H2AK119ub, ChIP DNA, rep1

source_name: Repeat B MEF_H2AK119ub_ChIP DNA


title: Repeat B +/- ES cell_RNAseq, rep1

description: processed data: RNA_ES_count_rep1.txt


title: Repeat B MEF_H3K27me3, ChIP DNA, rep2

source_name: Repeat B MEF_H3K27me3_ChIP DNA


title: WT MEF_H2AK119ub, input DNA, rep1

source_name: WT MEF_H2AK119ub_input DNA


title: CT TAC

source_name: heart; transverse aortic constriction;


title: Repeat B MEF_in situ HiC

source_name: Repeat B MEF


title: WT MEF_H3K27me3, input DNA, rep2

source_name: WT MEF_H3K27me3_input DNA


title: Repeat B MEF_H3K27me3, input DNA, rep2

source_name: Repeat B MEF_H3K27me3_input DNA


title: Repeat B -/- ES cell_RNAseq, rep2

description: processed data: RNA_ES_count_rep2.txt


title: WT MEF_H3K27me3, ChIP DNA, rep2

source_name: WT MEF_H3K27me3_ChIP DNA


title: Repeat B MEF_H3K27me3, ChIP DNA, rep1


title: Repeat B MEF_H3K27me3, input DNA, rep1


title: Repeat B -/- ES cell_in situ HiC

source_name: Repeat B -/- ES cell


title: WT MEF_H3K27me3, ChIP DNA, rep1


title: WT ES cell_RNAseq, rep2

description: processed data: RNA_ES_count_rep2.txt

source_name: WT ES cell_RNAseq


title: WT ES cell_RNAseq, rep1

description: processed data: RNA_ES_count_rep1.txt


title: WT MEF_H3K27me3, input DNA, rep1


title: Repeat B MEF_Xist CHART, rep2

description: processed data: CHART_log2ratio_Rep2.bw

data_processing:
library strategy: CHART-seq
CHART-seq and ChIP-seq: Reads were aligned separately to the mus/129 and cas genomes using novoalign with default parameters for paired-end alignment, the coordinates of these alignments were then converted to mm9 coordinates with custom scripts. Following alignment, coverage files were generated for the composite set of reads (comp), as well as allelic reads that aligned better to mus (mus) or cas (cas) using custom perl scripts, SAMtools and bedtools to extract and sort allelic reads, remove duplicates and generate coverage files. After input normalization using SPP, the coverage tracks presented in the paper were further normalizated between experiments to have equal coverage within a 1-MB region flanking the Xist locus (chrX:100150712-100650712 and 100683572-101183572).
ChIP-seq: Reads were aligned separately to the mus/129 and cas genomes using novoalign with default parameters for paired-end alignment, the coordinates of these alignments were then converted to mm9 coordinates with custom scripts. Following alignment, coverage files were generated for the composite set of reads (comp), as well as allelic reads that aligned better to mus (mus) or cas (cas) using custom perl scripts, SAMtools and bedtools to extract and sort allelic reads, remove duplicates and generate coverage files. The coverage files presented in the paper are input normalized using SPP.
RNA-seq: PCR duplicates were removed and reads separately aligned to custom mus/129 and cas genomes using Tophat. Final allele-specific mapping to reference mm9 genome was generated based on SNPs. Only uniquely aligned concordantly mapped sequences were used in downstream analysis. Counts per gene were calculated using featureCounts. Using MatLab, library sizes were normalized and genes with insufficient allelic information (<13 allele-specific reads) were removed. We also removed potentially miscalled genes from our alignment pipeline, defined as genes incorrectly assigned to mus from a pure cas RNA-seq library. Allele-specific RPKM was calculated using allelic ratio (allele-specific counts) applied to comp RPKM (total counts).
In situ Hi-C:  Reads were trimmed using cutadapt with the options --adapter=GATCGATC (MboI ligation junction) and --minimum-length=20. Reads of each pair were individually mapped to the mus (Xi) and cas (Xa) reference genomes using novoalign and default parameters, then merged into Hi-C summary files and filtered using HOMER with custom scripts (parameters for HOMER filtering (makeTagDirectory): -removePEbg -restrictionSite GATC -both -removeSelfLigation). Hi-C contact maps were generated from reads in the filtered HOMER mus and cas tag directories using the ?pre? command of Juicer tools with the genomeID mm9 .
Genome_build: mm9
Supplementary_files_format_and_content: CHARTP-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bigWig files are input normalized. Log2 ration bw files are ratio after further normalization to have equal coverage within a 1-MB region flanking the Xist locus (chrX:100150712-100650712 and 100683572-101183572).
Supplementary_files_format_and_content: ChIP-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bigWig files are input normalized.
Supplementary_files_format_and_content: In situ Hi-C:  Compressed Hi-C matrix (.hic) files for cas-specific and mus-specific filtered Hi-C reads. File can be loaded onto Juicebox to view either raw or normalized Hi-C interaction matrices at 5kb to 2.5Mb resolutions.

source_name: Repeat B MEF_Xist CHART

value: Oligos to pull down Xist RNA


title: Repeat B MEF_CHART, input DNA, rep2

source_name: Repeat B MEF_CHART_input DNA


title: Repeat B MEF_Tsix CHART, rep2

source_name: Repeat B MEF_Tsix CHART

value: Control antisense oligos


title: WT MEF_Tsix CHART, rep2

source_name: WT MEF_Tsix CHART


title: WT MEF_CHART, input DNA, rep2

source_name: WT MEF_CHART_input DNA


title: Repeat B MEF_Tsix CHART, rep1


title: Repeat B MEF_Xist CHART, rep1

description: processed data: CHART_log2ratio_Rep1.bw


title: Repeat B MEF_CHART, input DNA, rep1


title: Mig H3K9me3 Rep2

description:
Migrated fraction H3K9me3 ChIP sample, Replicate 2
H3K9me3 ChIP Seq promoter counts replicate set 2.txt

data_processing:
Read quality was assessed using FASTQC(version 0.11.5), Reads were mapped using bowtie2 (v bowtie 2.2.9) using hg19 as a reference
Sam files were converted to bam format, using samtools View (samtools v1.3, using htslib 1.3), and bam files were coordinate sorted using the samtools Sort tool
Bam files were imported into Seqmonk(v 1.37.1), using a threshold min. mapping quality of 20
Using the Seqmonk define probe tab, the feature probe option was used, feature was defined as -2000bp +100 bp upstream of genes (gene promoters). Reads within these features were counted, normalised to the largest dataset, and log2 transformed. Since replicate set 1 showed a high degree of sequence duplication, the option to count duplicate reads only once was used during feature read counting for this entire replicate set.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited files with log2 transformed read counts (normalised to largest dataset)

source_name: SiHa cell line

extract_protocol:
Sonicated chromatin was centrifuged to clarify debris, and DNA-antibody complexes were immunoprecipitated using antibody to H3K9me3 (abcam 8898, lot number GR232099-3)
Libraries for replicate1 were constructed using Illumina TruSeq ChIP Sample Prep kit (cat no 15027084) with gel extraction. As a high degree of duplication was noted in this replicate, likely due to DNA losses during gel extraction, library preparation for a second biological replicate (replicate2), was performed with the help of Ampure XP beads, using NEB Ultra DNA library kit (Ref E7370L). This resulted in much lower duplication rates. Analysis was performed on replicate2, and major findings were confirmed in replicate1 after deduplication.

treatment_protocol: 0.75 x 106 cells were seeded per well of a 6 well migration transwell set up. 10h post seeding, migrated and non migrated fractions of cells were then scraped in PBS and used for further processing.


title: WT MEF_CHART, input DNA, rep1


title: WT MEF_Xist CHART, rep1

description: processed data: CHART_log2ratio_Rep1.bw

source_name: WT MEF_Xist CHART


title: WT MEF_Tsix CHART, rep1


title: Mig Input Rep2

description:
Migrated fraction Input sample, Replicate 2
H3K9me3 ChIP Seq promoter counts replicate set 2.txt


title: (HN)-SCC25_SOX2_ChIP

city: New York

first: Markus

last: Schober

state: NY

address: 550 First Ave, Smilow 407

department: Dermatology

institute: New York University School of Medicine

description: epithelial

data_processing:
Human assembly version hg19/NCBI GRCh37 build were used for sequence alignments with bowtie 45 version 2.1.0.
Sequences with MAPQ scores <30 were removed with samtools50 and duplicates were removed with picard-tools version 1.88
IGV viewer files were generated with igvtools count -z 5 -w 25 -e 250.
ChIP-seq peaks were called with MACS51 version 2.1.0 in comparison to input controls with the parameters -q 0.001 --nomodel --extsize 400.
Motif discovery was performed with MEME-ChIP52,53 using 200bp sequence surrounding peak summits.
Motif containing ChIP-seq peaks were analyzed with the GREAT: Genomic Regions Enrichment of Annotations Tool54, using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bed

source_name: Head and neck squamous cell carcinoma

growth_protocol: Cells were grown DMEM-F12 media 10% FBS

extract_protocol:
Chromatin was prepared from 2x10^7 SCC cells or 1x10^6 sorted cells using the ChIP-IT High Sensitivity kit (53040, Active Motif) according to manufacturers instructions.
Library prep was performed with ThruPLEX DNA-seq kit (Rubicon Genomics, R400427) using 200pg of ChIP DNA or KAPA Hyper Prep kit (KAPA, KK8505) using 1ng of ChIP DNA

value: tongue

value: anti-Sox2 (R&D, AF2018), 4ug.

tag: condition

value: Cells were grown DMEM-F12 media 10% FBS


title: (HN)-SCC25_PITX1_ChIP

description: epithelial

value: anti-Pitx1 (Santa Cruz, 18922), 4ug.


title: (HN)-SCC25_input

description: epithelial


title: (HN)-SCC25_TP63_ChIP

description: epithelial

value: anti-TP63 (Cell Signaling, 13109), 4ug.


title: Non mig Input Rep2

description:
Non migrated fraction Input sample, Replicate 2
H3K9me3 ChIP Seq promoter counts replicate set 2.txt

value: Squamous cell carcinoma of the cervix (primary site)

value: SiHa


title: Mig Input Rep1

description:
Migrated fraction Input sample, Replicate 1
H3K9me3 ChIP seq promoter counts replicate set 1.txt


title: Non mig H3K9me3 Rep1

description:
Non migrated fraction H3K9me3 ChIP sample, Replicate 1
H3K9me3 ChIP seq promoter counts replicate set 1.txt


title: Non mig Input Rep1

description:
Non migrated fraction Input sample, Replicate 1
H3K9me3 ChIP seq promoter counts replicate set 1.txt


title: Mig H3K9me3 Rep1

description:
Migrated fraction H3K9me3 ChIP sample, Replicate 2
H3K9me3 ChIP seq promoter counts replicate set 1.txt


title: Non mig H3K9me3 Rep2

description:
Non migrated fraction H3K9me3 ChIP sample, Replicate 2
H3K9me3 ChIP Seq promoter counts replicate set 2.txt


title: WT MEF_Xist CHART, rep2

description: processed data: CHART_log2ratio_Rep2.bw

value: CAST/Ei x 129/Sv/Jae


title: negative, sample3

city: Oulu

first: Antti

last: Haapalainen

address: Aapistie 5A

department: CRC

country: Finland

institute: University of Oulu

description:
siRNA universal negative control
neg_3

data_processing:
The base calling was done using bcl2fastq (v1.8.4)
Read alignment was done using star (2.5.2b) to hg38 human genome reference
Genewise read counts were calculated using subread (v1.5.1)
Genome_build: hg38
Supplementary_files_format_and_content: countdata.txt is a tab delimited text file and contains the raw read count numbers for each sample.

source_name: placenta

growth_protocol: The HTR-8/Svneo cells were cultured in RPMI 1640 medium supplemented with 10 % fetal bovine serum, 100 U/ml penicillin, 100 mg/ml streptomycin, 2 mM glutamine and 1 mM sodium pyruvate.

extract_protocol:
RNA was isolated by using Trizol reagent and RNeasy Micro Kit
Library preparation was done according to Illumina TruSeq® RNA Sample Preparation v2 Guide

treatment_protocol: The transfection with siRNA was done either with 30 nM siRNA pair or 30 nM siRNA universal negative control and using approximately 100 000 cells and duoble transfection. The first transfection was done in suspension and the second transfection in adherent cells.

tag: passage

tag: host strain


title: negative, sample2

description:
siRNA universal negative control
neg_2


title: negative, sample1

description:
siRNA universal negative control
neg_1


title: Donor2 - 3 - Macrophage + TNF

first: David

last: Kuo

address: 1300 York Avenue

institute: Weill Cornell Medical College

description:
mt_r2
processed data file:
coculture_htseq_counts.txt

data_processing:
Alignment: STAR Aligner v2.4.2a against hg19
Read Counting: HTSeq 0.6.0 was run on the UCSC annotation for hg19
Genome_build: hg19
Supplementary_files_format_and_content: htseq count table

source_name: primary macrophages

growth_protocol: Human CD14+ cells isolated from PBMCs were differentiated into macrophages for 1 day with MCSF (10ng/mL) in RPMI/10% FBS. Transwell chambers with or without synovial fibroblasts were then placed above the macrophages. (Human synovial fibroblast cell lines were generated from synovial tissue extracted during knee arthroplasty, minced and collagenase digested. Adherent cells at passage 4 or beyond were used for macrophage-fibroblast co-cultures.)

extract_protocol:
Macrophage RNA was isolated with RNAeasy mini kit (Qiagen) and polyA mRNA purified with the Truseq kit (Illumina).
Libraries were generated with the Truseq kit (Illumina).

treatment_protocol: Mono- or co-cultures were then treated with or without TNFa (20ng/mL) for 2 days.

value: primary macrophages

tag: cultured with

value: tumor necrosis factor (TNF)

tag: barcode

value: CTTGTA


title: Donor2 - 2 - Macrophage + Fibroblast

description:
mf_r2
processed data file:
coculture_htseq_counts.txt

value: fibroblasts

value: GCCAAT


title: CPPED1, sample2

description:
CPPED1 silenced cell
CPPED1_5


title: Donor2 - 1 - Macrophage

description:
m_r2
processed data file:
coculture_htseq_counts.txt

value: none (alone)

value: TGACCA


title: Donor2 - 4 - Macrophage + Fibroblast + TNF

description:
mtf_r2
processed data file:
coculture_htseq_counts.txt

value: tumor necrosis factor (TNF) +fibroblasts

value: AGTTCC


title: CPPED1, sample3

description:
CPPED1 silenced cell
CPPED1_6


title: Control Cells

city: Sherbrooke

first: Bisaillon

last: Martin

state: Québec

address: 3201, rue Jean-Mignault

department: Biochimie

country: Canada

institute: Université de Sherbrooke

description: RNA immunoprecipitated using anti-HA beads

data_processing:
header were then remove using samtools and the custom following awk command, because they are unsuitable for the analysis with RIPSeeker:  samtools view -h file.bam | awk '((NR<=197 && length($2)<10) || (NR>=198 && length($3)<5 && $3 !~ /[*]/)){print $0}' > file.out.sam  The output file was then converted to the bam format using samtools and analyzed using the R package RIPSeeker. RIPSeeker, a specifically designed tool to detect enriched peaks in RIP data, was used on both HEK293T and HEK293T-EBNA1 using HEK293T as a control.  Upon sequencing, 22,887,816 and 21,858,499 reads were obtained for control and EBNA1 RIP libraries, with respective average quality score of 39 and 38. Reads corresponding to both conditions were first trimmed and adaptors were removed using Trimmomatic (Galaxy Tool Version 0.32.2). STAR (version 2.5.1b) was used to align reads to hg38 human genome with annotation release 89 from the ENSEMBL database. Reads were sorted by names via samtools (version 1.3.2) and the rmdup function was used to remove PCR and sequencing duplicates. Reads unmapped or mapped to the scaffolds and their respective ID in the header were then remove using samtools (version 1.3.2) and the custom following awk command, because they are unsuitable for the analysis with RIPSeeker:  samtools view -h file.bam | awk '((NR<=197 && length($2)<10) || (NR>=198 && length($3)<5 && $3 !~ /[*]/)){print $0}' > file.out.sam  The output file was then converted to the bam format using samtools and analyzed using the R package RIPSeeker (version 1.10.0) . RIPSeeker, a specifically designed tool to detect enriched peaks in RIP data, was used on both HEK293T and HEK293T-EBNA1 using HEK293T as a control.
Genome_build: hg38
Supplementary_files_format_and_content: excel file from RIPSeeker containing detected peaks in EBNA1 sample using HEK293T cells as control

source_name: HEK293T cell line

growth_protocol: grown in DMEM (Wisent) containing 10% fetal bovine serum, cells passaged as recommended by ATCC

extract_protocol:
HEK293T cells and HEK293T stable cells expressing EBNA1-FLAG-HA were grown upon confluency in P150 dishes, harvested and pelleted. They were then washed twice in cold PBS, and resuspended in the same volume as the pellet of polysome lysis buffer (10 mM Hepes pH 7.0, 100 mM KCl, 5 mM MgCl2, 0.5% NP-40, 1 mM DTT, 100 u/mL RNase inhibitor and complete protease inhibitor (Roche)). After an incubation of 5 minutes on ice, they were frozen at -80°C to complete the lysis. After a rapid thaw, tubes were centrifuged 20 minutes at 4°C, 13 000g. The supernatant was dosed using the Bradford assay (Thermo Scientific Coomassie Protein Assay) in triplicate. For each IP, 50 uL of Anti-Ha matrix (Roche) was centrifuged 1 min at 13,400 rpm and the supernatant was discarded. Beads were washed with 1 mL of NT2 buffer (50 mM Tris-HCl, pH 7.4, 150 mM NaCl, 1 mM MgCl2, 0.05% NP-40) followed by 1 min centrifugation at 13,400 rpm for 5 times. They were then resuspended in 900 uL of NET-2 buffer (NT2 buffer supplemented with 20 mM EDTA, pH 8.0, 1 mM DTT and 100 u/mL RNase inhibitor) and 100 uL (adjusted with NT-2 buffer to a total protein quantity of 2.5 mg) of lysate from either control or EBNA1 expressing cells was added. Tubes were inverted a couple of times, centrifuged 1 min at 13,400 rpm, 4°C and 100 uL was removed as the input to evaluate RNA degradation. All tubes were incubated on a rotating wheel at 4°C overnight. Beads were precipitated at 5000g for 5 min, 4°C and washed five times with ice-cold NT2 buffer. Upon the last washing, beads were resuspended in 90 uL of NT-2 buffer and 10 uL of RQ1 DNase and incubated at 37°C for 30 minutes. Input tubes were directly added 10 uL of RQ1 DNase. Dnase-treated IP were diluted with 1 mL NT-2 buffer, centrifuged and supernatant was discarded. Beads were resuspended in 150 uL of proteinase K buffer (1% SDS, 1.2 mg/mL proteinase K from Boehringer Mannheim), and input tubes were directly added SDS and proteinase K to the same volume. Tubes were incubated at 55°C during 30 minutes with inversion at every 10 minutes. RNA was then extracted with phenol-chloroform, followed by a second chloroform extraction step. Precipitation of RNA using 272 mM ammonium acetate, 122 mM LiCl and 27 ug/mL glycogen in ice-cold ethanol was carried out during 2 hours at -80°C and followed by high-speed centrifugation. Pellets were washed in 75% ethanol, ethanol was thoroughly removed and RNA was resuspended in water.
Quality (input) and quantity (input and IP) assessments were performed on Agilent Nano Chip (Catalog number 5067-1511). Inputs from both control and EBNA1 expressing cells both showed good RNA integrity (RIN = 8.9 and 9.2, respectively), thus underlining RNA was not deteriorated due to experimental procedures. RNA was ribodepleted using Illumina Ribo-Zero rRNA Removal Kit as per manufacturer’s protocol. The RNA-seq library was then built using Illumina SSV21106 kit from 9 l ribo-depleted RNA. Library quality was assessed using Agilent DNA HS Chip (Catatalog number 5067-4626). Library quantification was performed by qPCR following Illumina Kappa library quantification protocol. HEK293T and HEK293T-EBNA1 libraries were multiplexed and sequencing was done using Illumina HiSeq 4000 at 100bp paired-end reads at McGill University and Génome Québec Innovation Centre Sequencing Service.

treatment_protocol: HEK293T-EBNA1-FLAG-HA were selected in puromycin (3ug/mL)

value: Human embryonic kidney cells containing the  SV40 Large T-antigen

tag: growth protocol

value: Growth in DMEM/10% FBS


title: P4_MT

description: Barcode: ACTGAT

data_processing:
Alignment: STAR Aligner v2.4.2a against hg19
Read Counting: HTSeq 0.6.0 was run on the UCSC annotation for hg19
Genome_build: hg19
Supplementary_files_format_and_content: htseq counts

treatment_protocol: Mono- or co-cultures were then treated with or without TNFa (20ng/mL) for 1 day.

tag: treatment

value: TNF


title: P4_MTF_plus_AG

description: Barcode: GCCAAT

value: Fib + TNF + AG


title: P4_MTF_plus_A77

description: Barcode: AGTTCC

value: Fib + TNF + A77


title: P4_MTF_plus_NAP

description: Barcode: CAGATC

value: Fib + TNF + Naprox


title: P4_MTF

description: Barcode: ATTCCT

value: Fib + TNF


title: P4_MT_plus_A77

description: Barcode: CTTGTA

value: TNF + A77


title: P4_MT_plus_AG

description: Barcode: TGACCA

value: primary macrophages

value: TNF + AG


title: P3_MTF_plus_A77

description: Barcode: GTCCGC


title: P4_M

description: Barcode: GAGTGG


title: P3_MTF_plus_NAP

description: Barcode: AGTCAA


title: P3_MT

description: Barcode: ACTTGA


title: P3_MTF

description: Barcode: GATCAG


title: P3_MT_plus_NAP

description: Barcode: CTTGTA

value: TNF + Naprox


title: P3_MTF_plus_AG

description: Barcode: ATGTCA


title: P3_MTF_plus_AUR

description: Barcode: CGTACG

value: Fib + TNF + Aur


title: P3_MT_plus_AUR

description: Barcode: GTTTCG

value: TNF + Aur


title: P3_MT_plus_A77

description: Barcode: CCGTCC


title: CPPED1, sample1

description:
CPPED1 silenced cell
CPPED1_4


title: P3_MT_plus_AG

description: Barcode: AGTTCC


title: P2_MTF_plus_METH

description: Barcode: CCGTCC

value: Fib + TNF + meth


title: P2_MTF_plus_DI

description: Barcode: CGATGT

value: Fib + TNF + Diclo


title: P2_MTF_plus_NAP

description: Barcode: ATTCCT


title: P3_M

description: Barcode: CAGATC


title: P3_MT_plus_3

description: Barcode: GTGAAA

value: TNF + Triple


title: EBNA1-HA-FLAG expressing cells

value: Human embryonic kidney cells containing the  SV40 Large T-antigen stably transfected with MSCV-EBNA1-HA-FLAG

value: Growth in DMEM/10% FBS/3ug/ml puromycin


title: P2_MTF_plus_HY

description: Barcode: CTTGTA

value: Fib + TNF + hydrox


title: P2_MTF_plus_AUR

description: Barcode: TAGCTT


title: P2_MTF_plus_TOF

description: Barcode: ACTTGA

value: Fib + TNF + tofa


title: P2_MTF_plus_A77

description: Barcode: TGACCA


title: P2_MTF_plus_3

description: Barcode: GTGAAA

value: Fib + TNF + Triple


title: P2_MTF_plus_AG

description: Barcode: GAGTGG

value: Fib + TNF + AG


title: P2_MT_plus_SUL

description: Barcode: AGTCAA

value: TNF + Sulf


title: P2_MT_plus_NAP

description: Barcode: ACTGAT


title: P3_MTF_plus_3

description: Barcode: GTGGCC


title: P2_MT_plus_METH

description: Barcode: ATGTCA

value: TNF + Meth


title: P2_MT_plus_HY

description: Barcode: GGCTAC

value: TNF + Hydrox


title: P2_MT_plus_DI

description: Barcode: ATCACG

value: primary macrophages

value: TNF + Diclo


title: P2_MT_plus_DEX

description: Barcode: ACAGTG

value: TNF + Dex


title: P2_MT_A77

description: Barcode: TTAGGC

value: TNF + A77


title: P2-MTF_plus_SUL

description: Barcode: AGTTCC

value: Fib + TNF + Sulf


title: P2_MT_plus_3

description: Barcode: GTCCGC


title: P2_MT

description: Barcode: TTAGGC

value: TNF


title: P4_MT_plus_NAP

description: Barcode: CGATGT

value: TNF + Naprox


title: P2_MT_plus_AUR

description: Barcode: GATCAG

value: TNF + Aur


title: P2_MT_plus_AG

description: Barcode: CGTACG

value: TNF + AG


title: P2_MTF

description: Barcode: TGACCA

value: Fib + TNF


title: P2_M

description: Barcode: CGATGT


title: P2_MT_plus_TOF

description: Barcode: CAGATC

value: TNF + tofa


title: P1_MT_plus_Meth

description: Barcode: TTAGGC


title: P1_MT_plus_Hydrox

description: Barcode: TGACCA


title: P1_MT_plus_Sulf

description: Barcode: CTTGTA


title: P1_MTF_plus_Diclo

description: Barcode: TAGCTT

value: Fib + TNF + Diclo


title: P1_MTF_plus_Naprox

description: Barcode: CCGTCC

value: Fib + TNF + Naprox


title: P1_MT_plus_A77

description: Barcode: GGCTAC


title: P1_MT_plus_Naprox

description: Barcode: ATGTCA


title: P1_MT_plus_Triple

description: Barcode: GATCAG

value: TNF + Triple


title: P1_MTF_plus_Triple

description: Barcode: GTTTCG

value: Fib + TNF + Triple


title: P1_MT

description: Barcode: CAGATC


title: P1_MT_plus_Tofa

description: Barcode: GTGGCC

value: TNF + Tofa


title: P1_MTF_plus_Sulf

description: Barcode: AGTTCC


title: P1_MTF_plus_Meth

description: Barcode: ACTTGA

value: Fib + TNF + Meth


title: P1_MTF_plus_A77

description: Barcode: CGTACG

value: primary macrophages

value: Fib + TNF + A77


title: P1_MT_plus_Aur

description: Barcode: ATTCCT


title: P1_MTF_plus_Hydrox

description: Barcode: GCCAAT

value: Fib + TNF + Hydrox


title: P1_MTFT_plus_Aur

description: Barcode: TGACCA

value: Fib + TNF + Aur


title: P1_MTF_plus_Tofa

description: Barcode: GAGTGG

value: Fib + TNF + Tofa


title: P1_M

description: Barcode: CGATGT


title: P1_MT_plus_Dex

description: Barcode: GTGAAA

value: TNF + Dex


title: P1_MTF_plus_Dex

description: Barcode: ATCACG

value: Fib + TNF + Dex


title: P1_MTF

description: Barcode: AGTCAA


title: SCC_2_Scr_RFP

data_processing:
Analysis was performed using tophat (version 2.0.9) for read alignment (default parameters)
Cufflinks (version 2.2.0) for transcriptome assembly (with parameters  --no-coverage-search and --no-novel-juncs)
Cuffdiff (version 2.2.0) for identifying differentially expressed genes (default parameters)
Mouse assembly mm10 was used and transcriptome annotations were obtained from ENSEMBL release 69.
Genome_build: mm10
Supplementary_files_format_and_content: txt

source_name: squamous cell carcinoma

growth_protocol: 200,000 cells grownth in Elow calcium media

extract_protocol:
Total RNA was extracted from 2x10^5 SCC cells using the Absolutely RNA Nanoprep Kit (400753, Agilent Technologies) according to manufacturers instructions.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded Ribozero Gold kit

treatment_protocol: cells were infected with shRNA shScr or shPitx1 lentivirus and collected 72 hours after infection for RNA extraction

tag: strain

tag: tissue

value: skin

value: control


title: SCC_1_Scr_RFP

tag: genotype/variation


title: SCC_1_Pitx1_RFP

value: Pitx1 deficient


title: ATAC_SCC1_2

description: 15,000 cells were injected intradermally to form tumor allografts. In the end point of the experiment, 100,000 cells were sorted gatting in integrin α6 and integrin b1

data_processing:
Mouse assembly version mm10/NCBI m38 build were used for sequence alignments with bowtie 45 version 2.1.0.
ATAC-seq peaks were called with PeaKDEck55 and the parameter (-sig 0.0001).
Genome_build: mm10
Supplementary_files_format_and_content: File with MACS2 peak calling

extract_protocol: 100,000  TPCs were isolated by FACS and washed once with cold 1x PBS. Cells were pelleted and lysed in 50 μl and spun at 500g for 25min at 4C to collect nuclei. Pelleted nuclei were incubated for 30min at 37 C with 2.5ul of Tn5 transposase (Illumina Cat #FC-121-1030) before transposed DNA fragments were purified with a Qiagen MinElute Kit for ATAC-seq library generation.


title: SCC_2_Pitx1_RFP


title: ATAC_SCC1_1

growth_protocol: 15,000 cells were injected intradermally to form tumor allografts


title: HJ-0006

city: Birmingham

first: Hao

last: Jiang

state: AL

address: 1825 University Blvd

department: Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

data_processing:
Basecalls performed using CASAVA version 1.8.4
RNA-Seq: reads were mapped using TopHat2 and Calculating insert size and standard deviation for paired-end RNA-Seq data were performed using Picard v.1.126
RNA-Seq: read counting performed using HTSeq v0.6.0 (--mode=union --stranded=no --minaqual=30 --idattr=gene_name –type=exon)
RNA-Seq: Normalization and Deferential expression analysis performed using DEseq v3.0
RNA-Seq: BAM to bedgraph performed using bedtools v2.17.0 and were normalized based on Read Per Million (RPM) and then bedgraph to bigwig was performed using bedGraphToBigWig v4
Genome_build: mm10
Supplementary_files_format_and_content: BigWig (coverage for mapped reads), count tables (read counts for genomic features)

source_name: Fetal liver

extract_protocol:
Total RNAs were isolated using Micro (for HSCs) Kit (Qiagen).
Two rounds of polyA+ selection was performed, followed by conversion to cDNAs. We used the mRNA library generation kits per manufacturer’s instructions (Agilent, Santa Clara, CA). The indexed cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for library quantitation (Kapa Biosystems, Woburn, MA) prior to cluster generation.

treatment_protocol: Fetal liver HSCs were isolated from E14.5 embryos of indicated genotypes, and were FACS purified by HSC surface markers.

value: Fetal liver

value: Purified HSCs

tag: litter

value: litter 3

tag: genotype

value: Vav-Cre; Dpy30F/-


title: HJ-0002

value: litter 1


title: HJ-0001

value: Vav-Cre; Dpy30F/+


title: HJ-0003

value: litter 2


title: Six2TGC;miR-17~92fl/fl Mutant 1

city: Pittsburgh

first: Jacqueline

last: Ho

state: PA

address: 4401 Penn Avenue

department: Pediatrics

institute: Children's Hospital of Pittsburgh

data_processing:
The quality of the reads was assessed by FastQC
The Rsubread and limma-voom packages were used for the analysis of the RNA-Seq data in R
Genes with a B-statistics score of >0 were considered statistically significant
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing RPKM values for each sample

source_name: Embryonic kidney

extract_protocol:
Nephron progenitors were FACS sorted directly into QIAzol (Qiagen #79306), and total RNA extraction carried out with the use of miRNeasy Micro Kit (Qiagen #217084) per manufacturer's protocol. The quality and integrity of the RNA was assessed on an Agilent 2100 Bioanalyzer using an Agilent RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA, USA; #5067-1513). RNA samples with an RNA Integrity Number (RIN) score of >9 were used for whole transcriptome RNA sequencing.
Total RNA quantity and quality were first assessed by Fragment Analyzer™ (Advanced Analytical Technologies, Ankeny, IA, USA), followed by cDNA library construction from equivalent amounts of RNA using an Ovation® RNA-Seq System V2 (NuGEN, San Carlos, CA, USA; #7102-08). 2X100bp sequencing was performed using a Dual Flow Cell on a HiSeq 2500 Sequencing System (Illumina, San Diego, CA, USA), with all samples multiplexed across 2 lanes, yielding ~70 million reads per sample. Whole transcriptome RNA sequencing was performed at the TUCF Genomics Core Facility, an Illumina-accredited facility.

tag: age

value: Six2+ nephron progenitors


title: Six2TGC;miR-17~92fl/fl Mutant 3


title: Six2TGC;miR-17~92fl/fl Mutant 2


title: Six2TGC Control 2


title: P2_MTF_plus_DEX

description: Barcode: GCCAAT

value: primary macrophages


title: Six2TGC Control 3


title: HJ-0005


title: Six2TGC Control 1


title: FCNT3_methyl

city: Athens

first: Kristen

middle: Jean

last: Navara

state: GA

address: 203 Poultry Science Building

department: Poultry Science

institute: The University of Georgia

data_processing:
Library strategy: MethylC-Seq
RNA-seq data: Reads were trimmed using Cutadapt v1.9.1, and PRINSEQ v0.20.4, reads were then mapped to the T. guttata genome using Tophat2 v2.1.1. Gene expression was quantified and differentially expressed genes called using Cuffquant, followed by Cuffdiff2 from Cufflinks v2.2.1.
MethylC-seq data: Read trimming, alignment, and methylation calling were performed using the methylpy pipeline from Schultz et al. Human body epigenome maps reveal noncanonical DNA methylation variation Nature 523, 212–216 (2015).
Genome_build: Taeniopygia guttata v3.2.4
Supplementary_files_format_and_content: RNA-seq data: all_genes_fpkm.tsv.gz, gene_exp.diff.gz.
Supplementary_files_format_and_content: MethylC-seq data (marked as “allc_total.tsv”): column 1 = chr = chromosome; column 2 = pos = coordinate for the cytosine position on the chromosome; column 3 = strand = + or - strand; column 4 = mc_class = context of the cytosine and the two following bases from the same strand; column 5 = mc_count = number of reads supporting a methylated cytosine; column 6 = total = total number of reads at that position; column 7 = methylated = cytosine is considered methylated if there is a 1 or unmethylated if there is a 0.

organism: Taeniopygia guttata

source_name: nucleus taenia of the amygdala

extract_protocol:
Brains were flash frozen in liquid nitrogen, embedded in optimal cutting temperature compound, and 50um sections were cut with a cryostat until 1mm biopsy punch was used to make vertical punches to obtain the hypothalamus and nucleus taenia of the amygdala. Tissue was homogenized with a Mini-BeadBeater-16 (BioSpec Products) using 0.2g of 1mm beads for 10s in TRIzol/TRI Reagent to extract total RNA with a Direct-zol RNA MicroPrep kit (Zymo Research) with a DNase treatment step to remove DNA contamination or in Genomic Lysis Buffer to extract genomic DNA with a Quick-gDNA MicroPrep kit (Zymo Research).
Stranded mRNA-Seq libraries were made using KAPA Stranded mRNA-Seq Kit (Kapa Biosystems).
Methyl-Seq libraries were prepared according to Urich et al. (2015) Nature protocols 10:475-483.

treatment_protocol: Testosterone: 500pg of testosterone dissolved in 5ul peanut oil injected into egg the morning it was laid; Control: 5ul of peanut oil injected into egg the morning it was laid.

value: brain

tag: brain region

value: nucleus taenia of the amygdala

tag: developmental stage

value: adult

tag: Sex

value: female


title: FCNT1_methyl


title: FCNT2_methyl


title: En1Cre;b-cat mut4

data_processing:
The resulting 100bp reads were aligned to the mouse genome release mm9 genome using TopHat
mm9_reFlat was used to annotate the data with a max intron length of 20,000 and genomic bias correction.
Cufflinks FPKMs below 0.3 were floored to 0.3.
Differential gene expression was determined with CuffDiff using the default settings plus genomic bias correction.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

source_name: Manually dissected cranial mesenchyme plus ectoderm

extract_protocol:
At E13.5, En1Cre;b-cateninfl/fl mutant and En1Cre;b-cateninfl/+ control cranial mesenchyme was isolated by manual dissection. An incision was made around the circumference of the neurocranium, and the tissue covering the brain was manually disassociated. The supraorbital cranial mesenchyme isolated consists of the neural crest and mesoderm derived cranial mesenchyme plus the ectoderm.
Illumina TruSeq Stranded Total RNA kit-with Ribo Zero Gold

tag: develpmental stage

value: EnlCre/+;RRbgal;Bcatflox/null

value: whole tissue


title: En1Cre;b-cat control1

value: EnlCre/+;RRbgal;Bcatflox/+


title: En1Cre;b-cat mut2


title: En1Cre;b-cat control2


title: En1Cre;b-cat control3


title: En1Cre;b-cat mut1


title: FTNT2_methyl

value: testosterone


title: FTNT1_methyl


title: FTNT3_methyl


title: En1Cre;b-cat mut3


title: MCNT3_methyl

value: male

value: control


title: MCNT2_methyl


title: MCNT1_methyl


title: HJ-0004

value: Fetal liver

tag: cell type

value: Purified HSCs


title: P1_MT_plus_Diclo

description: Barcode: GTCCGC

value: TNF + Diclo


title: FCH3_methyl

source_name: hypothalamus

value: hypothalamus


title: MTNT2_methyl


title: MTNT1_methyl


title: FCH1_methyl


title: FTH1_methyl


title: MCH1_methyl


title: MTH3_methyl


title: MTH2_methyl


title: FTH2_methyl


title: FCH2_methyl


title: MTH1_methyl


title: MCH2_methyl


title: FCNT2_rna

description:
Processed data file: all_genes_fpkm.tsv.gz
Processed data file: gene_exp.diff.gz

data_processing:
RNA-seq data: Reads were trimmed using Cutadapt v1.9.1, and PRINSEQ v0.20.4, reads were then mapped to the T. guttata genome using Tophat2 v2.1.1. Gene expression was quantified and differentially expressed genes called using Cuffquant, followed by Cuffdiff2 from Cufflinks v2.2.1.
MethylC-seq data: Read trimming, alignment, and methylation calling were performed using the methylpy pipeline from Schultz et al. Human body epigenome maps reveal noncanonical DNA methylation variation Nature 523, 212–216 (2015).
Genome_build: Taeniopygia guttata v3.2.4
Supplementary_files_format_and_content: RNA-seq data: all_genes_fpkm.tsv.gz, gene_exp.diff.gz.
Supplementary_files_format_and_content: MethylC-seq data (marked as “allc_total.tsv”): column 1 = chr = chromosome; column 2 = pos = coordinate for the cytosine position on the chromosome; column 3 = strand = + or - strand; column 4 = mc_class = context of the cytosine and the two following bases from the same strand; column 5 = mc_count = number of reads supporting a methylated cytosine; column 6 = total = total number of reads at that position; column 7 = methylated = cytosine is considered methylated if there is a 1 or unmethylated if there is a 0.


title: FTNT2_rna


title: FTNT1_rna


title: FCNT3_rna


title: MCNT3_rna


title: FTNT3_rna


title: MTNT2_rna


title: MCNT1_rna


title: FCH3_rna


title: MCNT2_rna


title: FCH2_rna


title: MTNT1_rna


title: MTNT3_methyl


title: MTNT3_rna


title: FTH3_methyl


title: MCH3_methyl


title: MCH3_rna


title: FTH2_rna


title: FCNT1_rna


title: MCH1_rna


title: MCH2_rna


title: MTH1_rna


title: FCH1_rna


title: F8MV

city: Botucatu

first: Danillo

last: Pinhal

state: SP

address: R. Prof. Dr. Antonio C. W. Zanin s/n

department: Genetics

country: Brazil

institute: Sao Paulo State University

description: microRNA sequencing

data_processing:
Base-calling was performed using Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70).
Adaptor sequences were trimmed. FASTQ files were converted into FASTA with a custom Perl script. Reads were counted, collapsed to unique reads and filtered using the UEA small RNA Workbench. Reads were exactly matched to tilapia genome (Orenil1.1v) with PatMaN
Precursors from miRBase were searched against the tilapia genome using BLAST. Novel tilapia miRNA loci were predicted with both miRCat 79 and miRDeep2
An in-house Python pipeline selected matched reads from each precursor locus and estimated the read counts by weight count (raw read count divided by number of precursor locus aligned).
Reads were normalized by DESeq method for miRNA 5p and 3p using Bioconductor package in R
Genome_build: Orenil 1.1
Supplementary_files_format_and_content: counts

organism: Oreochromis niloticus

source_name: Red Muscle

extract_protocol:
Tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Illumina TruseqTM Small RNA Preparation kit was used for the construction of small RNA sequencing libraries, following manufacture's protocol.

tag: developmental period

value: Adult

tag: Stage

value: Chitralada


title: M26BR

description: microRNA sequencing

source_name: Brain


title: FpHE

description: microRNA sequencing

source_name: Heart


title: Dev4D

description: microRNA sequencing

value: Embryo

value: Pharyngula


title: Dev5D

description: microRNA sequencing

value: Hatching


title: F8MB

description: microRNA sequencing

source_name: White Muscle


title: M1MV

description: microRNA sequencing


title: F25G

description: microRNA sequencing

source_name: Gonad


title: M2MB

description: microRNA sequencing


title: M27GO

description: microRNA sequencing


title: F25BR

description: microRNA sequencing