title: 60 Minutes CNTF Rep 3

description: Sample 18

data_processing:
MiRBase alignment: Data parse, adapter trimming, statistics generation, alignment (miRExpress2)
Whole-genome alignment: Adapter trimming (cutadapt 1.15) “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A GATCGTCGGACTGTAGAACTCTGAAC -m 4 --too-short-output –too-short-paired-output --nextseq-trim 10 -o -p”
Whole-genome alignment: BWA 0.7.17-r1188 alignment (“aln”); sam format output (“sampe”); samtools 1.7 sam file write (“view -bS”)
Whole-genome alignment: bowtie2 2.2.6 alignment (“bowtie2 -k 100 -p 8 –very-sensitive-local”); samtools 1.7 sam file write (“view -bS”)
Count readout for all alignments: R/Rsubread 1.28.1
Genome_build: miRBase v21/GRCh38
Supplementary_files_format_and_content: Comma-delimited files contain raw count values. Rownames in BWA and bowtie2 files give Entrez ID, in miRExpress file mature miR name.

extract_protocol:
Total RNA was extracted by TRIzol lysis with 1 ml of TRIzol per well. RNA was precipitated with pure Ethanol and washed with 85% Ethanol, according to the manufacturers instructions.
An even amount of 150 ng RNA per sample was used for small-RNA library construction using the New England BioLabs NEB-next multiplex small-RNA library construction kit. The library was size selected based on DNA 1000 LabChip kits by 2100 Bioanalyzer (Agilent Technologies) results to 146 bp long transcripts which include the barcodes, adaptors and ca. 20 bp long miRs. This ensures that sequenced transcripts are in the maximum length of 30 bp only. Libraries were quantified using the highly sensitive fluorescent dye-based Qubit® ds DNA HS Assay Kit (Invitrogen). Sequencing was run in the The NextSeq Series desktop sequencing system of the Illumina platform. The number of Pass Filter reads per sample was at the range of (13-14*10^6 reads). Read counts and quality for each sample were evaluated with the BaseSpace Sequencing QC report tool.

treatment_protocol: Cells were treated once with 100 ng/ml (end concentration in well) of CNTF in deionized water, 24h after seeding. CNTF (or pure water for control) was added to existing medium. Medium was not changed for the duration of the experiment (max. 5 days).

value: female

value: Immortalized human nervous cell

tag: time

value: 60 Minutes


title: Serum, C4

status: Public on Oct 15 2019

type: RNA

city: Lublin

first: Marta

last: Rusek

address: Radziwillowska 11

department: Dept. of Dermatology

country: Poland

institute: Medical University of Lublin

description: Gene expression data from serum of healthy control

hyb_protocol: Samples were hybridized overnight to the Affymetrix GeneChip miRNA array (P/N 901326).

scan_protocol: The arrays were washed and stained using standard Affymetrix protocols and scanned using the Affymetrix GCS 3000 7G Scanner. Feature intensities were extracted using the miRNA_4.0 library files.

data_processing: For microarray data analysis, Affymetrix Transcriptome Analysis Console (TAC) Software v4.0 was used.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Control group

label_protocol: RNA samples were obtained from starting material (200 µL of serum), then a total of 16 samples from patients and healthy controls were labeled using the FlashTag™ Biotin HSR RNA Labeling Kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Whole blood (5–10 mL) was collected in BD Monovette plastic tubes (Sarstedt, Germany). The samples were stored on ice and processed within 1 hour of the draw. Serum was isolated by centrifugation at 3 000 x g for 10 min at 4 ºC and stored at -80 ºC, in the absence of freeze-thaw cycles, until analysis.

extract_protocol: RNA was extracted from 100 µL serum using the miRNeasy Serum/Plasma Kit (Qiagen, Germany) following the manufacturer’s protocol. Briefly, after Qiazol solution (1 mL) was added and mixed by vortexing, samples were incubated at room temperature for 5 min, the addition of chloroform was useful to achieve aqueous and organic phase separation. In the next step, the aqueous phase was applied to an RNeasy spin column. The purified RNA was eluted in 14 µL RNase-free water, split into single-use aliquots and stored at -80 ºC.

tag: disease state

value: healthy control

tag: age

tag: sample type

value: serum


title: MYCN Amplifed neuroblastoma, patient MSK4230 RNA-seq

type: SRA

city: New York

first: Emily

last: Bernstein

state: NY

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

country: USA

institute: Mount Sinai School of Medicine

description:
Processed data file: MSKCC_NB_patient_gene_exp.txt
MSK4230

library_source: transcriptomic

data_processing:
[ChIP-seq] Sequence reads were aligned to the GRCh37 (hg19) assembly using Bowtie v1.0.0 with the following parameters: For 100nt reads: -M 10 -k 1 -n 2 --trim5 5 -l 80 --best. Redundant reads were eliminated using the macs2 (v2.1.0) filterdup option with default parameters. The optimal normalization factor between ChIP and Input samples was calculated with the R NCIS package v1.0.1 using a shift size of 75bp.
[ChIP-seq] Peak calling was performed with macs2 callpeak using the following options: --ratio X --broad --bdg -q 1x10-5 OR 1x10-15 OR 0.05 OR 0.005 or 0.0005 --broad-cutoff 1x10-5 OR 1x10-15, where X is the normalization factor estimated by NCIS. ChIP/Input fold enrichment pileups were created with the macs2 bdgcmp tool using the -m FE option and converted to bigWig files using the bedGraphToBigWig program (v4) from the UCSC binaries.
[RNA-seq] Reads were aligned using STAR (Dobin et al., 2013)
[RNA-seq] Transcriptome assemblies in FPKM, and differential expression ratios were computed using the featureCounts program from the Rsubread package (v1.20.6) in R. The FPKM was calculated using the fpkm function from the edgeR package (v 3.12.1). Genes with a count per million < 1 were marked as not transcribed.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: fastq - raw illumina reads. Bam - aligned reads. bigwig - aligned reads pileup. txt - gene expression in FPKM

source_name: Tumor Tissue

extract_protocol:
Tissue was homogenized at 17000 rpm for 30 seconds with a tissue homogenizer (Polytron, PT10-35GT). RNA was prepared using TRIzol (Life Technologies) and cleaned using RNeasy Plus Mini kit (Qiagen #74134)
Total RNA was processed into sequencing libraries using the Illumina TruSeq Stranded Total RNA Library Prep Kit following manufacturer’s protocol.

tag: tissue

value: MYCN Amplifed neuroblastoma (patient MSK4230)

tag: treatment

value: none (untreated)


title: MYCN Amplifed neuroblastoma, patient MSK3820 RNA-seq

description:
Processed data file: MSKCC_NB_patient_gene_exp.txt
MSK3820

value: MYCN Amplifed neuroblastoma (patient MSK3820)


title: 60 Minutes CNTF Rep 2

city: Frankfurt

first: Sebastian

last: Lobentanzer

address: Max-von-Laue-Str. 9

department: Pharmacology

country: Germany

institute: Johann-Wolfgang-von-Goethe University

description: Sample 17

source_name: LA-N-2 neuroblastoma

growth_protocol: Cells were grown in 50/50 mixture of DMEM and RPMI media, with 20% FCS added, under 8% CO2 atmosphere. Cell splitting was performed weekly at 80% confluency.

tag: gender

tag: cell line

tag: cell type

tag: passages

value: CNTF


title: 60 Minutes CNTF Rep 1

description: Sample 16


title: MYCN Amplifed neuroblastoma, patient MSK3261 RNA-seq

description:
Processed data file: MSKCC_NB_patient_gene_exp.txt
MSK3261

value: MYCN Amplifed neuroblastoma (patient MSK3261)


title: GTR0020PRXB

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

description: Sample name: 3998720067_C

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were not normalized. Illumina's raw AVG_Signal is provided in the sample tables and in the supplementary file on the series record (with detection pvalues).

label: biotin-SA Cy3

source_name: Gastric Cancer | PDX

label_protocol: Synthesis of cDNA and biotinylated cRNA were performed using the Illumina Total-Prep RNA Amplification Kit (Ambion, Austin, TX, USA, cat. no. IL1791), according to the manufacturer’s protocol, for which hybridization was carried out on Illumina HumanHT-12 V3 arrays

growth_protocol: Tumor were collected upon surgical resection and stored in liquid nitrogen

extract_protocol: RNA was extracted using the Trizol Plus purification Kit (Invitrogen, Frederick, MD, USA, cat. no.12183555), according to the manufacturer’s protocol. Quantification and quality analysis of RNA was performed on a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).

treatment_protocol: Cryostatic section of the frozen specimens were cut for RNA extraction

value: gastric cancer

value: PDX

tag: patient id


title: GTR0023PRH

description: Sample name: 3998720067_E

source_name: Gastric Cancer | PR

value: primary tumor


title: GTR0020PRH

description: Sample name: 3998720067_B


title: Serum, C2


title: Serum, C3


title: MYCN Amplifed neuroblastoma, patient MSK3071 RNA-seq

description:
Processed data file: MSKCC_NB_patient_gene_exp.txt
MSK3071

value: MYCN Amplifed neuroblastoma (patient MSK3071)


title: GRT0379PDX

description: Sample name: 3998720042_I


title: 30 Minutes CNTF Rep 2

description: Sample 14

value: 30 Minutes


title: GRT0380PDX

description: Sample name: 3998720042_J


title: Serum, S10

description: Gene expression data from serum of systemic sclerosis patient

source_name: SSc group

value: systemic sclerosis


title: 30 Minutes CNTF Rep 1

description: Sample 13


title: MYCN Amplifed neuroblastoma, patient MSK2536 RNA-seq

description:
Processed data file: MSKCC_NB_patient_gene_exp.txt
MSK2536

value: MYCN Amplifed neuroblastoma (patient MSK2536)


title: GTR0060A PRX [200764720064_A]

data_processing: Data were normalized with loess normalization with lumi package (beadscan and HiScanSQ independently, amnd then scaled on the basis of common samples)

source_name: Gastric Cancer | PRX

label_protocol: Synthesis of cDNA and biotinylated cRNA were performed using the Illumina Total-Prep RNA Amplification Kit (Ambion, Austin, TX, USA, cat. no. IL1791), according to the manufacturer’s protocol, for which hybridization was carried out on Illumina HumanHT-12 V4 arrays

value: Gastric Cancer

value: PRX


title: GRT0377PDX

description: Sample name: 3998720042_H


title: Serum, S9


title: Day 4 CNTF Rep 3

description: Sample 12

value: female

value: Immortalized human nervous cell

value: Day 4


title: Day 4 CNTF Rep 2

description: Sample 11


title: 30 Minutes CNTF Rep 3

description: Sample 15


title: ATRX wild-type neuroblastoma, patient MSK3597 RNA-seq

description:
Processed data file: MSKCC_NB_patient_gene_exp.txt
MSK3597

value: ATRX wild-type neuroblastoma (patient MSK3597)


title: ATRX wild-type neuroblastoma, patient MSK4438 RNA-seq

description:
Processed data file: MSKCC_NB_patient_gene_exp.txt
MSK4438

value: ATRX wild-type neuroblastoma (patient MSK4438)

value: none (untreated)


title: ATRX wild-type neuroblastoma, patient MSK3263 RNA-seq

description:
Processed data file: MSKCC_NB_patient_gene_exp.txt
MSK3263

value: ATRX wild-type neuroblastoma (patient MSK3263)


title: Serum, C1

value: healthy control

value: serum


title: ATRX wild-type neuroblastoma, patient MSK1894 RNA-seq

description:
Processed data file: MSKCC_NB_patient_gene_exp.txt
MSK1894

value: ATRX wild-type neuroblastoma (patient MSK1894)


title: Serum, S8


title: GRT0371PDX

description: Sample name: 3998720042_F

value: gastric cancer

value: PDX


title: Serum, S7


title: Day 4 CNTF Rep 1

description: Sample 10

value: CNTF


title: Day 4 Control Rep 3

description: Sample 9

value: Control


title: Serum, S6

value: systemic sclerosis


title: GRT0363PDX

description: Sample name: 3998720042_D


title: GRT0369PDX

description: Sample name: 3998720042_E


title: Serum, S5


title: GRT0373PDX

description: Sample name: 3998720042_G


title: Day 4 Control Rep 2

description: Sample 8


title: Day 4 Control Rep 1

description: Sample 7


title: Serum, S4


title: Day 2 CNTF Rep 3

description: Sample 6

value: Day 2


title: CHLA90 ATRX in-frame fusion metastatic neuroblastoma Input XL

library_source: genomic

molecule: genomic DNA

source_name: Cell Culture

growth_protocol: grown in RPMI supplemented with 10% FBS, penicillin and streptomycin

extract_protocol:
XL ChIP as previously described (Fontanals-Cirera et al., 2017).
Library prepared as previously described (Fontanals-Cirera et al., 2017).

tag: chip antibody


title: ATRX wild-type neuroblastoma, patient MSK1129 RNA-seq

description:
Processed data file: MSKCC_NB_patient_gene_exp.txt
MSK1129

value: ATRX wild-type neuroblastoma (patient MSK1129)


title: Serum, S3


title: ATRX in-frame fusion neuroblastoma. Patient SJNBL047443 ChIP-seq H3K27me3

extract_protocol:
Tissue was homogenized at 17000 rpm for 30 seconds with a tissue homogenizer (Polytron, PT10-35GT). XL-ChIP.
Libaries were prepared at Active Motif.

value: ATRX in-frame fusion neuroblastoma (patient SJNBL047443)

value: H3K27me3 (Millipore, 07-449)


title: Day 2 CNTF Rep 2

description: Sample 5

value: female

value: Immortalized human nervous cell


title: MIIIshSMAD2_3

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from MCF10A-derived cell line MIII treated with shSMAD2.

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

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

data_processing: Raw Affymetrix CEL files were normalized to produce gene-level expression values using the Robust Multiarray Average (RMA) in Affymetrix Expression Console.

source_name: MCF10A-derived cell line MIII

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

growth_protocol: MIII cells were maintained in DMEM/F12 medium supplemented with 5% Horse Serum (HS), 1% antibiotics, 10 mg/ml Insulin, 20ng/ml epidermal growth factor, 100ng/ml cholera toxin, and 500ng/ml hydrocortisone in a humidified incubator at 37°C with 5% CO2.

extract_protocol: Total RNA was isolated from cells using Trizol (Life Technologies) and the miRNeasy Mini kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: Cells were washed with PBS prior to lysis with Trizol.

tag: shRNA

value: MCF10A-derived cell line MIII


title: MIIIshSMAD2_4


title: GRT0349PDX

description: Sample name: 3998720042_A


title: Day 2 CNTF Rep 1

description: Sample 4


title: SKNFI ATRX wild-type metastatic neuroblastoma Input XL

value: none (untreated)


title: SKNMM ATRX in-frame fusion metastatic neuroblastoma Input XL


title: Serum, S2


title: Serum, S1


title: GRT0359PDX

description: Sample name: 3998720042_B


title: Day 2 Control Rep 3

description: Sample 3


title: GRT0361PDX

description: Sample name: 3998720042_C


title: ATRX in-frame fusion neuroblastoma. Patient SJNBL047443 Input XL


title: GRT0391PRH

description: Sample name: 3998720035_H

value: primary tumor


title: GRT0391PRX

description: Sample name: 3998720035_I


title: GTR0069PRX

description: Sample name: 3998720035_F


title: m6A INPUT Rep1 20H

city: leeds

first: Agne

last: Antanaviciute

address: University of Leeds, St. James’s University Hospital

country: United Kingdom

institute: University of Leeds

description:
processed data file: m6A peak calls.xlsx
processed data column header: 22h rep1

data_processing:
Raw Reads were trimmed using Cutadapt software for Illumina adapter sequences and poor quality bases
Reads were aligned against hg38 analysis set reference genome and KSHV genome sequences using STAR aligner
Duplicates were marked using Picard Tools
Peaks were called using m6aViewer software
Raw read counts were obtained using Rsubread featureCounts software
Size-factor normalisation was performed using DESeq2 r package
Genome_build: hg38
Supplementary_files_format_and_content: [m6A peak calls.xlsx] Excel spreadsheet with m6A peak calls
[SND1_RIP_RAW_COUNTS.txt] tab delimited raw read counts
[RAW_READ_COUNTS_SND1_KO_TREX.txt] tab delimited raw read counts
[RAW_READ_COUNTS_SND1_KO_BCBL.xlsx] Excel spreadsheed with raw read counts

source_name: m6A INPUT 20H, KSHV-infected B-lymphocytes

growth_protocol: BCBL1 cells were grown in RPMI1640 growth medium with glutamine (Gibco) supplemented with 10% (v/v) FCS (Gibco) and 1% (v/v) P/S (Gibco). TREx BCBL1-Rta cells were grown in RPMI1640 growth medium with glutamine (Gibco) supplemented with 10% (v/v) FCS, (Gibco), 1% P/S (v/v) (Gibco) and 100 μg/mL hygromycin B (Thermo Scientific). sodium butyrate (Sigma-Aldrich).

extract_protocol:
Total RNA was used for m6A-seq and RNA-seq. For SND1-seq, input libraries were made from total RNA isolated with TRIzol (Thermo Fisher) and RIP libraries were made from sonicated SND1 enriched RNA which had been purified with TRIzol LS (Thermo Scientific).
m6A-seq libraries were made using NEBNext Ultra kit (NEB) according to the manufacturer’s protocol. RIP-seq and RNA-seq libraries were made using TruSeq Stranded Total RNA library production kit (Illumina)

treatment_protocol: For virus reactivation, TREx BCBL1-Rta cells were induced using 2 μg/mL doxycycline hyclate (Sigma-Aldrich) and BCBL1 cells were induced using 2 nM

value: TREx BCBL1-Rta cells

tag: infection

value: KSHV

tag: ip antibody


title: Day 2 Control Rep 2

description: Sample 2


title: Day 2 Control Rep 1

description: Sample 1


title: m6A INPUT Rep1 8H

description:
processed data file: m6A peak calls.xlsx
processed data column header: 8h rep1

source_name: m6A INPUT 8H, KSHV-infected B-lymphocytes


title: MIIIshGFP_3

description: Gene expression data from MCF10A-derived cell line MIII treated with shGFP.

value: shGFP


title: GTR0069PRH

description: Sample name: 3998720035_E

value: gastric cancer


title: GTR0068PRX

description: Sample name: 3998720035_C

value: PDX


title: m6A INPUT Rep1 0H

description:
processed data file: m6A peak calls.xlsx
processed data column header: 0h rep1

source_name: m6A INPUT 0H, KSHV-infected B-lymphocytes


title: SND1 Scramble Rep2 Lytic TREX

description:
processed data file: RAW_READ_COUNTS_SND1_KO_TREX.txt
processed data column header: Lytic_Scr_0H_2

source_name: SND1 Scramble Lytic TREX, KSHV-infected B-lymphocytes

value: Scramble shRNA (Addgene plasmid # 1864)


title: CHLA90 ATRX in-frame fusion metastatic neuroblastoma ChIP-seq REST

growth_protocol: grown in DMEM supplemented with 20% FBS, penicillin and streptomycin

value: REST (Millipore, 07-579)


title: MIIIshGFP_1


title: MIIIshSMAD2_2


title: m6A IP Rep1 20H

source_name: m6A IP 20H, KSHV-infected B-lymphocytes

value: m6A (Millipore, ABE572)


title: MIIIshGFP_4


title: GTR0068PRH

description: Sample name: 3998720035_B


title: CHLA90 ATRX in-frame fusion metastatic neuroblastoma ChIP-seq ATRX

value: ATRX (Abcam, ab97508)


title: m6A IP Rep1 8H

source_name: m6A IP 8H, KSHV-infected B-lymphocytes


title: GRT0402PDX

description: Sample name: 3998532095_L


title: SND1 KO Rep2 Lytic TREX

description:
processed data file: RAW_READ_COUNTS_SND1_KO_TREX.txt
processed data column header: Lytic_56_0H_2

source_name: SND1 KO Lytic TREX, KSHV-infected B-lymphocytes

value: SND1 shRNA TRCN0000049656, Sigma


title: SKNMM ATRX in-frame fusion metastatic neuroblastoma ChIP-seq REST


title: m6A IP Rep1 0H

source_name: m6A IP 0H, KSHV-infected B-lymphocytes


title: SND1 KO Rep2 Latent TREX

description:
processed data file: RAW_READ_COUNTS_SND1_KO_TREX.txt
processed data column header: Latent_56_0H_2

source_name: SND1 KO Latent TREX, KSHV-infected B-lymphocytes


title: ATRX in-frame fusion neuroblastoma_SJNBL030014_RNA-seq_r1

data_processing:
ChIP-seq: Sequence reads were aligned to the GRCh37 (hg19) assembly using Bowtie v1.0.0 with the following parameters: For 100nt reads: -M 10 -k 1 -n 2 --trim5 5 -l 80 --best. Redundant reads were eliminated using the macs2 (v2.1.0) filterdup option with default parameters. The optimal normalization factor between ChIP and Input samples was calculated with the R NCIS package v1.0.1 using a shift size of 75bp.
ChIP-seq: Peak calling was performed with macs2 callpeak using the following options: --ratio X --broad --bdg -q 1x10-5 OR 1x10-15 --broad-cutoff 1x10-5 OR 1x10-15, where X is the normalization factor estimated by NCIS. ChIP/Input fold enrichment pileups were created with the macs2 bdgcmp tool using the -m FE option and converted to bigWig files using the bedGraphToBigWig program (v4) from the UCSC binaries. A second peak calling was performed using SICER v1.1 using a window of 200bp, allowing gaps of 400pb and filtering for q-values < 1x10-5 OR 1x10-15. All peaks overlapping with the Encode blacklisted regions were eliminated.  The final peak list was generated overlaping the macs2 and SICER peaks with the intersectBed program from bedtools v2.17.0. All SICER peaks overlapping at least one macs2 peak were kept.
RNA-seq: Reads were aligned using TopHat (version 2.1.0).
RNA-seq: Transcriptome assemblies in FPKM, and differential expression ratios were computed with Cufflinks (version 2.1.1) for NB cell lines. For SJNBL030014 sample, aligned reads were assigned to the genes from Ensemble's GRCh37.p13 annotation using the featureCounts program from the Rsubread package (v1.20.6) in R. The FPKM was calculated using the fpkm function from the edgeR package (v 3.12.1). Genes with a count per million < 1 were marked as not transcribed.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bigwig - aligned reads pileup / txt - gene expression in FPKM

source_name: Tumor Tissue

tag: cell line or tissue

tag: cell or tissue type

value: ATRX in-frame fusion neuroblastoma

tag: treated with


title: SND1 Scramble Rep1 Lytic TREX

description:
processed data file: RAW_READ_COUNTS_SND1_KO_TREX.txt
processed data column header: Lytic_Scr_0H_1


title: SKNFI ATRX wild-type metastatic neuroblastoma ChIP-seq ATRX

growth_protocol: grown in DMEM supplemented with 10% FBS, penicillin and streptomycin


title: SKNMM ATRX in-frame fusion metastatic neuroblastoma ChIP-seq ATRX


title: ATRX in-frame fusion neuroblastoma_SJNBL030014_H3K27me3

value: H3K27me3 (Millipore, 07-449)


title: SND1 Scramble Rep1 Latent TREX

description:
processed data file: RAW_READ_COUNTS_SND1_KO_TREX.txt
processed data column header: Latent_Scr_0H_1

source_name: SND1 Scramble Latent TREX, KSHV-infected B-lymphocytes


title: SND1 Scramble Rep2 Latent TREX

description:
processed data file: RAW_READ_COUNTS_SND1_KO_TREX.txt
processed data column header: Latent_Scr_0H_2


title: MuPOX03016_rep3

city: zhengzhou

first: Li

last: Xudong

state: Henan

address: No. 1, Jianshe East Road, Erqi District

country: China

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
Remove reads with adapters;Remove reads in which unknown bases are more than 10%;Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more  than 10).
The clean reads mapped onto the genome of P. oxalicum wild type strain HP7-1 to functional annotation, susing the software BWA v0.7.10-r789 and Bowtie2 v2.1.0.
FPKM, representing gene expression levels, was calculated with the software RSEM v1.2.12
DEGs were screened with NOISeq or DESeq2 tools
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Penicillium oxalicum

source_name: Mycelium

growth_protocol: strains were cultivated under SSF media and static at 28°C for 5 days. SSF media contained 20 mL of mineral salt solution and 10 g of carbon sources, which  were milled to 40-mesh particle size after dried at 50°C

extract_protocol:
Total RNA were extracted using TRIzol RNA Kit
A cDNA library with 100 bp of length was constructed using the extracted total RNA, and assessed with the ABI StepOnePlus Real-Time PCR System and the Agilent 2100 Bioanalyzer. The eligible cDNA library was sequenced via the Illumina HiSeq 4000 system

tag: growth

value: grown on WR as the sole carbon source under solid-state fermentation

tag: strain


title: GTR0199PDX

description: Sample name: 3998532095_K

source_name: Gastric Cancer | PDX

tag: sample type


title: MuPOX03016_rep2


title: SND1 KO Rep1 Lytic TREX

description:
processed data file: RAW_READ_COUNTS_SND1_KO_TREX.txt
processed data column header: Lytic_56_0H_1


title: GTR0181PDX

description: Sample name: 3998532095_I

tag: tissue


title: ATRX in-frame fusion metastatic neuroblastoma_CHLA90_EPZ_D4_R1

description:
processed data file:
NB_EPZ_RNA-gene_exp.txt

extract_protocol:
RNA was prepared as previously described (Chung et al., 2016).
Total RNA was processed into sequencing libraries using the Illumina ScriptSeq Complete Gold kit following manufacturer’s protocol.

value: 5 uM EPZ-6438 for 4 days


title: MuPOX03016_rep1


title: GTR0165PDX

description: Sample name: 3998532095_H


title: SND1 Scramble Rep2 Lytic

description:
processed data file: RAW_READ_COUNTS_SND1_KO_BCBL.xlsx
processed data column header: LyticScr_0H

source_name: SND1 Scramble Lytic, KSHV-infected B-lymphocytes

value: BCBL1 cells


title: ATRX in-frame fusion metastatic neuroblastoma_CHLA90_EPZ_D7_R1

value: 5 uM EPZ-6438 for 7 days


title: SND1 KO Rep1 Latent TREX

description:
processed data file: RAW_READ_COUNTS_SND1_KO_TREX.txt
processed data column header: Latent_56_0H_1


title: GTR0187PDX

description: Sample name: 3998532095_J


title: Ku70_rep3


title: SND1 Scramble Rep2 Latent

description:
processed data file: RAW_READ_COUNTS_SND1_KO_BCBL.xlsx
processed data column header: LatentScr_0H

source_name: SND1 Scramble Latent, KSHV-infected B-lymphocytes


title: ATRX in-frame fusion metastatic neuroblastoma_CHLA90_EPZ_DMSO_R1

source_name: Cell Culture

value: DMSO for 4 days


title: GTR0157PDX

description: Sample name: 3998532095_G


title: GTR0133PRX0B

description: Sample name: 3998532095_E


title: Ku70_rep2


title: Ku70_rep1


title: GTR0128PRX0A

description: Sample name: 3998532095_D


title: ATRX in-frame fusion neuroblastoma_SJNBL030014_XL_Input

description:
processed data file:
NB_RNA-gene_exp.txt

value: none (untreated)


title: SND1 KO Rep2 Lytic

description:
processed data file: RAW_READ_COUNTS_SND1_KO_BCBL.xlsx
processed data column header: Lytic56_0H

source_name: SND1 KO Lytic, KSHV-infected B-lymphocytes

value: KSHV


title: ATRX in-frame fusion metastatic neuroblastoma_SKNMM_EPZ_D7_R1

value: SKNMM


title: GTR0126PRX0B

description: Sample name: 3998532095_C

value: gastric cancer


title: SND1 KO Rep2 Latent

description:
processed data file: RAW_READ_COUNTS_SND1_KO_BCBL.xlsx
processed data column header: Latent56_0H

source_name: SND1 KO Latent, KSHV-infected B-lymphocytes


title: EU2101_WB_RS_rep3


title: ATRX in-frame fusion metastatic neuroblastoma_SKNMM_EPZ_D4_R1


title: GTR0119PRX0B

description: Sample name: 3998532095_B

value: PDX


title: EU2101_WB_RS_rep2


title: ATRX in-frame fusion metastatic neuroblastoma_SKNMM_EPZ_DMSO_R1


title: GTR0109PDX

description: Sample name: 3998532095_F


title: EU2101_WB_RS_rep1


title: ATRX wild-type metastatic neuroblastoma_SKNFI_EPZ_D4_R1

value: SKNFI

value: ATRX wild-type metastatic neuroblastoma


title: SND1 KO Rep1 Lytic

description:
processed data file: RAW_READ_COUNTS_SND1_KO_BCBL.xlsx
processed data column header: S0HLyticscr


title: EU2101_WB_rep3

value: grown on WB as the sole carbon source under solid-state fermentation


title: ATRX wild-type metastatic neuroblastoma_SKNFI_EPZ_DMSO_R1


title: SND1 KO Rep1 Latent

description:
processed data file: RAW_READ_COUNTS_SND1_KO_BCBL.xlsx
processed data column header: S0HLatentSND1


title: ATRX in-frame fusion metastatic neuroblastoma_CHLA90_RNA-seq_r1

extract_protocol:
RNA was prepared using TRIzol (Life Technologies) and cleaned using RNeasy Plus Mini kit (Qiagen #74134).
Total RNA was processed into sequencing libraries using the Illumina TruSeq Stranded Total RNA Library Prep Kit following manufacturer’s protocol.


title: SND1 INPUT Rep2 20H

description:
processed data file: SND1_RIP_RAW_COUNTS.txt
processed data column header: run3_20HInput

source_name: SND1 INPUT 20H, KSHV-infected B-lymphocytes

value: TREx BCBL1-Rta cells

tag: time


title: EU2101_WB_rep1


title: GTR0221PRH

description: Sample name: 200143170012_I

source_name: Gastric Cancer | PR

value: primary tumor


title: GTR0221PRX0B01001

description: Sample name: 200143170012_J


title: GTR0219PRX0B01001

description: Sample name: 200143170012_F


title: GTR0219PRH

description: Sample name: 200143170012_E


title: ATRX wild-type metastatic neuroblastoma_SKNFI_EPZ_D7_R1


title: SND1 Scramble Rep1 Latent

description:
processed data file: RAW_READ_COUNTS_SND1_KO_BCBL.xlsx
processed data column header: S0HLatentscr

value: Scramble shRNA (Addgene plasmid # 1864)


title: SND1 Scramble Rep1 Lytic

description:
processed data file: RAW_READ_COUNTS_SND1_KO_BCBL.xlsx
processed data column header: S0HLyticSND1


title: GTR0110PRX0B

description: Sample name: 3998532095_A


title: EU2101_WB_AV_rep3

value: grown on WB plus WA as the sole carbon source under solid-state fermentation


title: EU2101_WB_AV_rep2


title: SND1 INPUT Rep2 8H

description:
processed data file: SND1_RIP_RAW_COUNTS.txt
processed data column header: run3_8HInput

source_name: SND1 INPUT 8H, KSHV-infected B-lymphocytes


title: ATRX in-frame fusion metastatic neuroblastoma_CHLA90_H3K27me3

extract_protocol:
Native ChIP as previously described (Valle-Garcia et al., 2016).
Library prepared as previously described (Valle-Garcia et al., 2016).

value: H3K27me3 (Millipore, 07-449)


title: SND1 INPUT Rep1 8H

description:
processed data file: SND1_RIP_RAW_COUNTS.txt
processed data column header: run2_8HInput


title: GTR0044PRX0B01001

description: Sample name: 200143170012_B


title: EU2101_WB_rep2


title: ATRX in-frame fusion metastatic neuroblastoma_CHLA90_nChIP_Input


title: EU2101_WB_AV_rep1


title: GTR0181PRH

description: Sample name: 200143170010_J


title: SND1 INPUT Rep2 0H

description:
processed data file: SND1_RIP_RAW_COUNTS.txt
processed data column header: run3_0HInput

source_name: SND1 INPUT 0H, KSHV-infected B-lymphocytes


title: SND1 INPUT Rep1 20H

description:
processed data file: SND1_RIP_RAW_COUNTS.txt
processed data column header: run2_20HInput


title: ZT44_rep3

city: Ames

first: Wei

last: Wang

state: IA

address: 415 Bessey Hall

department: Department of Plant Pathology and Microbiology

institute: Iowa State University

data_processing:
The data processing is mainly according to Li L, et al. (2015) QQS orphan gene regulates carbon and nitrogen partitioning across species via NF-YC interactions. Proceedings of the National Academy of Sciences 112(47):14734-14739. Briefly, for each sample, RNA-seq data was collected in three lanes, and the raw reads were trimmed and cleaned separately. The cleaned reads are combined together and aligned to soybean genome Glycine_max_v1.0 using the spliced alignment identification tool TopHat (V2.1.0). The aligned reads were counted using HTseq-count (Version: 0.6.0). Only genes with non-zero FPKM values in all 36 samples were included for further analysis.
Genome_build: soybean genome Glycine_max_v1.0
Supplementary_files_format_and_content: Excel file include FPKM for all samples in one file

organism: Glycine max

source_name: Unifoliolate leaf

growth_protocol: Seedlings of Williams82 were grown in soil (Sun Gro Horticulture, Vancouver, BC, Canada) under long-day conditions (16 h light/8 h dark) for 9 days in growth chamber at the temperature of 28°C, 50% relative humidity, and a light intensity of 100 μmol/m2/s.

extract_protocol:
Total RNA was extracted using RNeasy Plant Mini Kits (Qiagen). RNA quality was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols by BGI Americas (bgi-international.com/us)

treatment_protocol: On the 10th day, the light was switched to constant conditions. Seedlings were sampled every 4 hours for 44 hours starting at ZT0 on the 11th day, totally 12 time points. For each time point, there was 3 biological repeats, and each sample was pooled from the unifoliolate leaves of three individual seedlings.

tag: cultivar

value: Williams 82

tag: zeitgeber time (h)

tag: biological replicate

tag: age

value: 11-day old


title: ATRX in-frame fusion metastatic neuroblastoma_CHLA90_H3K9ac

value: H3K9ac (Abcam, ab10812)


title: ZT40_rep3


title: SND1 INPUT Rep1 0H

description:
processed data file: SND1_RIP_RAW_COUNTS.txt
processed data column header: run2_0HInput

tag: cell type


title: GTR0165PRH

description: Sample name: 200143170010_G

tag: patient id


title: GTR0044PRH

description: Sample name: 200143170012_A


title: SND1 IP Rep3 20H

description:
processed data file: SND1_RIP_RAW_COUNTS.txt
processed data column header: run3_20HSND1IP

source_name: SND1 IP 20H, KSHV-infected B-lymphocytes

value: SND1 (Protein tech, 10760-1-AP)


title: ATRX in-frame fusion metastatic neuroblastoma_SKNMM_H3K9ac

value: none (untreated)

tag: chip antibody


title: ZT36_rep3


title: ZT32_rep3


title: SND1 IP Rep2 20H

description:
processed data file: SND1_RIP_RAW_COUNTS.txt
processed data column header: run2_20HIP

tag: infection

value: KSHV


title: GTR0213PRX0B01001

description: Sample name: 200058720031_L


title: ZT28_rep3


title: ATRX in-frame fusion metastatic neuroblastoma_SKNMM_nChIP_Input

value: SKNMM


title: ATRX in-frame fusion metastatic neuroblastoma_SKNMM_H3K27me3


title: SND1 IP Rep3 8H

description:
processed data file: SND1_RIP_RAW_COUNTS.txt
processed data column header: run3_8HSND1IP

source_name: SND1 IP 8H, KSHV-infected B-lymphocytes

tag: ip antibody


title: ZT24_rep3


title: ATRX in-frame fusion metastatic neuroblastoma_SKNMM_RNA-seq_r1

tag: cell line or tissue


title: ATRX wild-type metastatic neuroblastoma_SKNFI_RNA-seq_r1

tag: cell or tissue type


title: SND1 IP Rep1 8H

description:
processed data file: SND1_RIP_RAW_COUNTS.txt
processed data column header: 8h_SND1_IP


title: ATRX wild-type metastatic neuroblastoma_SKNFI_H3K9ac

tag: treated with


title: SND1 IP Rep3 0H

description:
processed data file: SND1_RIP_RAW_COUNTS.txt
processed data column header: run3_0HSND1IP

source_name: SND1 IP 0H, KSHV-infected B-lymphocytes


title: ATRX in-frame fusion metastatic neuroblastoma_SKNMM_H3K9me3

value: H3K9me3 (Abcam, ab8898)


title: ATRX wild-type metastatic neuroblastoma_SKNFI_H3K9me3


title: SND1 IP Rep1 20H

description:
processed data file: SND1_RIP_RAW_COUNTS.txt
processed data column header: 20h_SND1_IP


title: ZT20_rep3


title: ATRX wild-type metastatic neuroblastoma_SKNFI_H3K27me3


title: ZT8_rep3


title: GTR0032PRH

description: Sample name: 200143170010_A

value: gastric cancer


title: GTR0202PRXB01001

description: Sample name: 200058720031_I

value: PDX


title: GTR0207PRXA01001

description: Sample name: 200058720031_J


title: SND1 IP Rep1 0H

description:
processed data file: SND1_RIP_RAW_COUNTS.txt
processed data column header: 0h_SND1_IP


title: SND1 IP Rep2 8H

description:
processed data file: SND1_RIP_RAW_COUNTS.txt
processed data column header: run2_8HIP


title: GTR0193PRX0A01001

description: Sample name: 200058720031_G


title: ZT4_rep3


title: GTR0060PRH

description: Sample name: 200143170010_D


title: ATRX wild-type metastatic neuroblastoma_LAN6_RNA-seq_r1

description:
processed data file:
NB_RNA-gene_exp.txt

value: ATRX wild-type metastatic neuroblastoma


title: ATRX wild-type metastatic neuroblastoma_SKNFI_nChIP_Input

value: SKNFI


title: ZT16_rep3


title: GTR0164PRXA01001

description: Sample name: 200058720031_F


title: ZT0_rep3


title: ZT12_rep3


title: ATRX wild-type metastatic neuroblastoma_LAN6_H3K9ac


title: m6A INPUT Rep2 8H

description:
processed data file: m6A peak calls.xlsx
processed data column header: 8h rep2

source_name: m6A INPUT 8H, KSHV-infected B-lymphocytes

value: TREx BCBL1-Rta cells


title: GTR0124PRX0A1001

description: Sample name: 200058720031_D


title: GTR0208PRX0A01001

description: Sample name: 200058720031_K


title: GTR0105PRX0B1001

description: Sample name: 200058720031_C


title: ZT44_rep2


title: GTR0103PRX0B1001

description: Sample name: 200058720031_B


title: m6A INPUT Rep2 0H

description:
processed data file: m6A peak calls.xlsx
processed data column header: 0h rep2

source_name: m6A INPUT 0H, KSHV-infected B-lymphocytes


title: ATRX wild-type metastatic neuroblastoma_LAN6_H3K9me3


title: ATRX wild-type metastatic neuroblastoma_LAN6_H3K27me3


title: ATRX wild-type metastatic neuroblastoma_LAN6_nChIP_Input


title: m6A IP Rep2 8H

source_name: m6A IP 8H, KSHV-infected B-lymphocytes

value: m6A (Millipore, ABE572)


title: C-16_rep3

city: Shanghai

first: Faming

last: Chen

address: 320 Yue Yang Road

department: CAS-MPG Partner Institute for Computational Biology

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Read quality was checked using FastQC.
Adaptor and low quality reads of raw sequencing reads were trimmed using trim_galore. Adaptor of read1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC; Adaptor of read2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
Cleaned reads were mapped to the rice reference genome (Os-Nipponbare-Reference-IRGSP-1.0) using STAR 2.5.3a with "--quantMode GeneCounts" option to report the read counts per gene.
Differentially expressed genes were determined using DESeq2 with read counts per gene as input.
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary_files_format_and_content: tab-delimited text files include read counts per gene for each sample

organism: Oryza sativa

source_name: top second leaf of the C-16 line

growth_protocol: The rice grew at Songjiang breeding stating (30°56' N, 121°8' E) of the Shanghai Institutes of Plant Physiology and Ecology, Shanghai, China. Seedlings were transplanted into field and plant spacing was 0.2 m for both row and column.

extract_protocol:
For gene expression profiling, we took the leaf samples at the early heading stage. 3 replications of the top second leaves for WT, the OE lines (OE-2, OE-3, OE-4) and the CRISPR lines (C-13, C-14, C-16) were harvested in the field at about 9:00 a.m. Leaf samples were frozen in liquid nitrogen immediately and then stored in -80℃ fridge before RNA extraction. For RNA extraction, we used the PureLink RNA Mini Kit (Life Technologies Corporation). We firstly grinded the leaf sample with liquid nitrogen, then followed the protocol of PureLink RNA Mini Kit.
RNA libraries were prepared for sequencing based on standard Illumina protocols.

tag: genotype/variation

value: knockout NRP using CRISPR/Cas9 technology

tag: growth stage

value: Heading stage

value: top second leaf


title: ZT36_rep2

value: Williams 82


title: ZT28_rep2

value: 11-day old


title: m6A IP Rep2 0H

source_name: m6A IP 0H, KSHV-infected B-lymphocytes


title: C-16_rep2


title: GTR0194PRX0B01001

description: Sample name: 200058720031_H

source_name: Gastric Cancer | PDX

tag: sample type


title: ZT24_rep2


title: ZT40_rep2


title: GTR0102PRX0A1001

description: Sample name: 200058720031_A

tag: tissue


title: GTR0263PRX0B01001

description: Sample name: 200058720014_K


title: PG-lAna-2: Late_Anagen Sample 2

city: Gandarbal

first: Basharat

middle: Ahmad

last: Bhat

state: Kashmir

address: Shuhama

department: Animal Biotechnology

country: India

institute: Sher-e-Kashmir University of Agricultural Sciences and Technology

description: 2x100 paired-end sequence reads

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Capra hircus  whole genome using bowtie v2 with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Capra hircus

source_name: SKIN

extract_protocol:
The skin sample was collected from the flanking region of each goat at same time point. Prior to sampling, the site was sheared, shaved and locally anesthetized with 2% lignocaine. Approximately 7mm diameter skin samples were harvested aseptically with a single-use biopsy punch.
The quality of purified total RNA provided will be checked on the Agilent Tapestation using the RNA cartridge. Total RNA with RNA Integrity Number (RIN) value greater than or equal to 8 is considered good quality. ~4ug of total RNA will be used to prepare the RNA seq library using the TruSeq RNA Sample Prep Kits (Illumina). The libraries will be prepared as per the kit protocol. In short, poly-A containing mRNA molecules will be purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA will be fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments will be used to synthesize first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments will then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products will be purified and enriched with PCR to create the final cDNA library. Bioanalyzer plots will be used at every step to assess mRNA quality, enrichment success, fragmentation sizes, and final library sizes. Both Qubit and qPCRwill be used for measuring the quantity of the library before sequencing.

tag: breed

value: Chanthangi Pashmina Goat

value: skin

value: 26 months

tag: pashmina fiber cycling

value: Late Anagen

tag: Sex

value: Male


title: GTR0220PRX0_01001

description: Sample name: 200058720014_L


title: GTR0145PRXA01001

description: Sample name: 200058720031_E


title: m6A IP Rep2 20H

description:
processed data file: m6A peak calls.xlsx
processed data column header: 22h rep2

source_name: m6A IP 20H, KSHV-infected B-lymphocytes

value: KSHV

tag: time


title: C-14_rep3

source_name: top second leaf of the C-14 line


title: PG-lAna-1: Late_Anagen Sample 1

description: 2x100 paired-end sequence reads

tag: age


title: ZT16_rep2

tag: cultivar

tag: zeitgeber time (h)

tag: biological replicate


title: C-14_rep2


title: m6A INPUT Rep2 20H

source_name: m6A INPUT 20H, KSHV-infected B-lymphocytes

tag: cell type

tag: infection


title: ZT12_rep2


title: C-16_rep1


title: GTR0255PRX0A01001

description: Sample name: 200058720014_I

value: gastric cancer

tag: patient id


title: PG-lAna-3: Late_Anagen Sample 3

description: 2x100 paired-end sequence reads


title: C-14_rep1


title: PG-eAna-3: Early_Anagen Sample 3

description: 2x100 paired-end sequence reads

value: Early Anagen


title: GTR0249PRX0B01001

description: Sample name: 200058720014_H

value: PDX


title: ZT20_rep2


title: GTR0245PRX0B01001

description: Sample name: 200058720014_F


title: ZT8_rep2


title: PG-eAna-2: Early_Anagen Sample 2

description: 2x100 paired-end sequence reads


title: GTR0259PRX0C01001

description: Sample name: 200058720014_J


title: GTR0247PRX0A01001

description: Sample name: 200058720014_G


title: GTR0244PRX0A01001

description: Sample name: 200058720014_E


title: C-13_rep3

source_name: top second leaf of the C-13 line


title: PG-eAna-1: Early_Anagen Sample 1

description: 2x100 paired-end sequence reads


title: ZT4_rep2


title: C-13_rep2


title: PG-Cat-2: Catagen Sample 2

description: 2x100 paired-end sequence reads

value: Catagen


title: ZT0_rep2


title: PG-Cat-1: Catagen Sample 1

description: 2x100 paired-end sequence reads


title: C-13_rep1


title: OE-4_rep3

source_name: top second leaf of the OE-4 line

value: over-expression of NRP


title: PG-Tel-3: Telogen Sample 3

description: 2x100 paired-end sequence reads

value: Telogen


title: GTR0233PRX0C01001

description: Sample name: 200058720014_D


title: OE-4_rep2


title: ZT40_rep1


title: ZT44_rep1


title: GTR0227PRX0A01001

description: Sample name: 200058720014_B


title: OE-4_rep1


title: PG-Tel-1: Telogen Sample 1

description: 2x100 paired-end sequence reads


title: ZT36_rep1


title: ZT32_rep1


title: GTR0222PRX0A01001

description: Sample name: 200058720014_A


title: ZT28_rep1


title: MO-depleted embr. 3

city: Rochester

first: Alin

last: Vonica

address: 4245 East Avenue

department: Biology

institute: The Nazareth College

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Xenopus laevis

source_name: MO-depleted embryos

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 0.1X MMR until stage 10.5, at 16 deg. C

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

treatment_protocol: 2 dorsal injection of 10 ng Apcdd1 morpholino oligonucleotides at 4 cell stage

value: gastrula dorsal half

tag: genotype

value: anti apcdd1 MO


title: MO-depleted embr. 1


title: MO-depleted embr. 2


title: GTR0230PRX0B01001

description: Sample name: 200058720014_C


title: ZT24_rep1

source_name: Unifoliolate leaf


title: NT_2cell_2

city: Yangling

first: rui

last: cheng

address: No. 3, Taicheng Road

institute: Northwest A&F University

data_processing:
bcl2fastq2 Conversion software (v2.16) was used for basecalling with the parameters bcl2fastq2-v2.16/bin/bcl2fastq --input-dir <runfolder-dir>/Data/Intensities/BaseCalls/ --output-dir <output-dir> --use-bases-mask Y*,Y*,Y*,Y*
Noise reads were removed in raw reads followed as: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases(N) are more than 10%; 3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 20 is greater than 50% in a read).
The filtered reads were stored in FASTQ format and mapped with HISAT (v0.1.6-beta) to the bovine UMD3.1.1 reference genome with the parameters: --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000.
We used StringTie (v1.0.4) to reconstruct transcripts, and used CuffCompare (v2.2.1) to compare reconstructed transcripts to reference annotation. We then selected  'u','i','o','j' class code types as novel transcripts, and used CPC (v0.9-r2) to predict coding potential of novel transcripts. Complete reference consisted of coding novel   transcripts and reference transcripts.
Clean reads were mapped to the complete reference using Bowtie2 (v2.2.5). Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments) using RSEM (v1.2.12).
Genome_build: UMD3.1.1
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each transcript in different samples.

organism: Bos taurus

extract_protocol:
Pools of  embryos were washed three times in RNase-free PBS solution, collected in a drop of PBS within 1 μL, and transferred into the lysis buffer immediately on ice. Samples were then centrifuged at 10000 rpm for 30 s at 4°C, and stored at -80°C.
Samples were thawed for cDNA synthesis using SuperScript® III (Thermo Fisher Scientific). After free primer removal and 3’ poly(A) tailing steps, cDNA was amplified by Ex Taq® HS (TaKaRa) and fragmented by Covaris S220 System. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. The suitable fragments are selected for the PCR amplification. During the Quality Control steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. Sequencing libraries were made with the fragmented DNA using NEBNext Ultra DNA Library Prep Kit (New England Biolabs) for Illumina according to manufacturer’s instruction.

value: Holstein

tag: developmental stage

tag: cell/tissue type

value: SCNT embryos


title: OE-3_rep2

source_name: top second leaf of the OE-3 line

tag: genotype/variation

tag: growth stage

value: Heading stage

value: top second leaf


title: PG-Tel-2: Telogen Sample 2

description: 2x100 paired-end sequence reads

value: Chanthangi Pashmina Goat

tag: tissue

value: skin


title: OE-3_rep1


title: control embryos 3

source_name: control embryos

value: control MO


title: NT_2cell_1

tag: breed


title: ZT20_rep1

value: Williams 82

value: 11-day old


title: OE-2_rep3

source_name: top second leaf of the OE-2 line


title: MII_3

source_name: MII

value: oocyte

value: wild embryos


title: ZT16_rep1


title: control embryos 2


title: NT_2cell_3


title: R5

city: Stanford

last: Jiang

state: CA

address: 269 Campus Dr. CCSR1200

department: Pediatrics

institute: Stanford University

description:
TCRalpha/beta mRNA transcripts and 25 selected phenotypic mRNA transcripts in up to 96 single cells were sequenced.
mRNA
processed data file: S2_All wells containing single cells_NC.xlsx

data_processing:
Data were processed and de-multiplexed using a customized VDJFasta algorithm as described (PubMed PMID: 24952902).
All paired ends are assembled by finding a consensus of at least 100 bases in the middle of the read. The resulting paired-end reads are then assigned to wells according to barcode. Primer dimers are filtered out by establishing minimum length of 100 bases for each amplicon.
A consensus sequence is obtained for each TCR gene. Because multiple TCR genes might be present in a given well, our software establishes a cutoff of >95% sequence identity within a given well. All sequences exceeding 95% sequence identity are assumed to derive from the same TCR gene and a consensus sequence is determined. For phenotyping transcripts, the number of reads containing a 95% match to the customized database of transcription factor and cytokine genes are scored.
For TCR analysis, establishing thresholds for clone dominance within the well further excludes the majority of negative-control wells and wells potentially containing more than one cell. For beta chains, a domain dominance cutoff is set at >85%. Domain dominance is determined based on 100% identity in sequence. Thus, this threshold of 85% is considerably lower than 100% because it accounts for the presence of PCR mutation or sequencing error. Because multiple TCRα chains can exist within a given cell, the threshold for domain dominance is more permissive and set to 10%. For phenotypic parameters, unlike for TCR genes, not all cells express a given parameter. Therefore, background is expected to depend upon number of cells expressing a given parameter as well as read depth.
Supplementary_files_format_and_content: S2_All wells containing single cells_NC.xlsx: De-multiplexed data were pooled into one excel sheet containing wells that returned both TCRalpha and TCRbeta gene information. "Well ID" indicates which well a sequenced cell is from. "WellReads" indicates how many raw sequence reads per well. T cell receptor alpha and beta information include V, D, J genes, CDR sequences, the confidence of called sequences in the well, and the number of reads assigned to the specific well. "Index FI" indicates the background corrected fluorescence intensity of tetramer staining signal (a parameter acquired during FACS). "Phenotyping Markers" include the 25 phenotypic transcripts that were sequenced for each single T cells (numbers indicates reads). "Nucleotide Sequences" are the called TCR (VDJ region) sequences with the indicated well dominance (e.g., BetaConfi or AlphaConfi). Each T cell may express multiple alpha chain, therefore information for "TCR alpha (secondary)" or alternative alpha was also reported.
Supplementary_files_format_and_content: *csv: Using a customized pipeline, all original fastq files were processed and a csv file was returned as a readout file.

source_name: Peripheral blood

extract_protocol:
CD4+ T cells were isolated from PBMCs using CD4+ cell isolation kit (Miltenyi Biotc) and then stained with DQ6/hypocretin tetramers, followed by FACS-sorting. Sorted single cells on a 96-well plate were directly used as template for reverse-transcription PCR (QIagen one step RT-PCR kit) with customized TCR and phenotyping primer sets to generate cDNAs.
cDNAs in each well were amplified using another two steps of PCR and barcoded before gel extraction and pooling for paired-end Illumina Miseq sequencing. Illumina Miseq sequencing was performed at Stanford Human Immune Monitoring Center using standard protocols.

tag: diagnosis

value: mixed sample (non-demultiplexed)

value: CD4+ T cells

tag: hla type

tag: dq6 tetramer specificity


title: OE-2_rep2

value: over-expression of NRP


title: ZT12_rep1

tag: age


title: OE-2_rep1


title: control embryos 1


title: ATRX in-frame fusion metastatic neuroblastoma_CHLA90_H3K9me3

source_name: Cell Culture

tag: cell line or tissue

tag: cell or tissue type

tag: treated with

value: none (untreated)

tag: chip antibody

value: H3K9me3 (Abcam, ab8898)


title: WT-rep3

source_name: top second leaf of the WT

value: wild type


title: IVF_2cell_3

value: Holstein

value: IVF embryos


title: WT-rep2

value: Heading stage


title: ZT4_rep1

tag: cultivar

tag: zeitgeber time (h)

tag: biological replicate


title: R2

tag: cell type


title: ZT8_rep1


title: R3


title: IVF_2cell_2

tag: developmental stage

tag: cell/tissue type


title: R1


title: WT-rep1

tag: genotype/variation

tag: growth stage

value: top second leaf


title: IVF_2cell_1

tag: breed


title: ZT0_rep1


title: RNA-seq_Brx68_lung_mets_x1_1

status: Public on Oct 14 2019

city: Los Angeles

first: Min

last: Yu

address: 1450 Biggy Street, NRT 3507

department: USC Norris Comprehensive Cancer Center, Keck School of Medicine

institute: University of Southern California

data_processing:
Sequenced reads were trimmed for adaptor sequence and were mapped to hg19 (GRCh37) reference using STAR v2.5.2b.
Genes annotated in the ENSEMBL GRCh37.p13 GTF (release 75) were quantified using HTSeq-count.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with raw counts

source_name: lung

growth_protocol: CTC lines were cultured in ultra-low attachment plates with RPMI 1640 medium, supplemented with EGF (20ng/ml), bFGF (20ng/ml), 1X B27 and 1X antibiotic/antimycotic, in 4% O2 and 5% CO2. Metastatic tumors were established by inoculation of 100,000 GFP-LUC labeled CTCs in 100 µl of PBS into the left cardiac ventricles of 6-8 weeks old female NSG mice supplemented with subcutaneous slow release estrogen pills. Metastatic lesions were further dissociated into single-cell suspension by automated dissociation. CTC-derived metastatic cells (GFP+ cells) were sorted for RNA sequencing.

extract_protocol: Sorted cells were collected into a pre-chilled tube maintained at 4°C containing PBS with 1% BSA. RNA was collected from 50,000 sorted cells, according to the manufacturer’s instructions (Quick RNA, Zymo). RNA integrity was measured using Bioanalyzer (Agilent).

tag: cell line

tag: parental or metastasis?

value: metastatic sample

tag: metastatic site

value: lung

value: yes

tag: generation


title: RNA-seq_Brx68_parental_CTC_Rep2

source_name: culture

value: parental CTC


title: MII_2


title: R4

tag: diagnosis

tag: hla type

tag: dq6 tetramer specificity


title: RNA-seq_Brx68_parental_CTC_disso_Rep5

value: parental CTC undergone dissociation protocol


title: RNA-seq_Brx68_parental_CTC_Rep1


title: RNA-seq_Brx68_bone_leg_mets_2_1

source_name: bone

value: bone


title: RNA-seq_Brx68_brain_mets_2_1

source_name: brain

value: brain


title: RNA-seq_Brx68_bone_jaw_mets_2_1


title: RNA-seq_Brx68_bone_mets_84_2

value: no


title: RNA-seq_Brx68_parental_CTC_disso_Rep4


title: RNA-seq_Brx68_parental_CTC_Rep3


title: RNA-seq_Brx68_bone_mets_23_1


title: RNA-seq_Brx68_bone_mets_22_1


title: MII_1

value: oocyte

value: wild embryos


title: RNA-seq_Brx68_bone_mets_21_1


title: RNA-seq_Brx50_parental_CTC_disso_Rep4


title: RNA-seq_Brx50_brain_mets_84_2


title: RNA-seq_Brx50_parental_CTC_Rep1


title: RNA-seq_Brx50_parental_CTC_Rep2


title: RNA-seq_Brx50_brain_mets_83_2


title: RNA-seq_Brx50_brain_mets_59_3


title: RNA-seq_Brx50_brain_mets_58_3


title: RNA-seq_Brx50_bone_mets_83_2


title: RNA-seq_Brx50_brain_mets_56_3


title: RNA-seq_Brx42_parental_CTC_disso_Rep4


title: RNA-seq_Brx42_parental_CTC_Rep2


title: RNA-seq_Brx42_parental_CTC_disso_Rep5


title: RNA-seq_Brx42_parental_CTC_Rep1


title: RNA-seq_Brx50_parental_CTC_disso_Rep3


title: RNA-seq_Brx07_ovary_mets_28_2

source_name: ovary

value: ovary


title: RNA-seq_Brx42_brain_mets_66_1


title: RNA-seq_Brx42_brain_mets_74_1


title: RNA-seq_Brx07_ovary_mets_30_2


title: RNA-seq_Brx07_ovary_mets_12_1


title: RNA-seq_Brx07_lung_mets_30_2


title: RNA-seq_Brx07_ovary_mets_27_2


title: RNA-seq_Brx07_lung_mets_71_1


title: RNA-seq_Brx07_parental_CTC_Rep2


title: RNA-seq_Brx07_parental_CTC_Rep3


title: RNA-seq_Brx07_parental_CTC_disso_Rep5


title: RNA-seq_Brx07_lung_mets_28_2


title: RNA-seq_Brx07_Kidney_mets_80_1

source_name: Kidney

value: Kidney


title: RNA-seq_Brx07_lung_mets_77_1


title: RNA-seq_Brx07_parental_CTC_Rep1


title: RNA-seq_Brx42_ovary_mets_73_1


title: RNA-seq_Brx07_parental_CTC_disso_Rep4


title: RNA-seq_Brx42_parental_CTC_Rep3


title: ATAC-seq_Brx68_boneleg_mets_2_2

description:
metastatic sample
X68brai.2.1

data_processing:
Sequencing reads were trimmed for Nextera adapter sequences with trimgalore and mapped to hg19 reference using Bowtie2 v2.2.8 with parameters -X 2000 –fr –no-discordant –no-mixed –minins 38. Only non-mitochondrial reads with a minimum mapping quality score (>= 30) were kept for the downstream analysis.
Duplicate reads were removed using Picard. All mapped reads were offset by +4 bp for the positive strand and -5 bp for the negative strand.
Accessible sites were identified for each sample using MACS2 with parameters -q 0.01 –shift -100 –extsize 200 –nomodel –nolambda. Peaks intersecting with the ENCODE blacklisted regions were removed.
Peaks across conditions were merged using BEDtools to obtain a union set, and reads aligning to this set were counted using featurecounts
Genome_build: hg19
Supplementary_files_format_and_content: bed files of MACS2 peaks, bigwig files,raw counts table

growth_protocol: CTC lines were cultured in ultra-low attachment plates with RPMI 1640 medium, supplemented with EGF (20ng/ml), bFGF (20ng/ml), 1X B27 and 1X antibiotic/antimycotic, in 4% O2 and 5% CO2. Metastatic tumors were established by inoculation of 100,000 GFP-LUC labeled CTCs in 100 µl of PBS into the left cardiac ventricles of 6-8 weeks old female NSG mice supplemented with subcutaneous slow release estrogen pills. Metastatic lesions were further dissociated into single-cell suspension by automated dissociation. CTC-derived metastatic cells (GFP+ cells) were sorted for ATAC sequencing.

extract_protocol:
Nuclei preparation was generated by resuspension of 25,000 or 50,000 sorted cells in nonionic lysis buffer (10 mM Tris pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Igepal CA630).
Transposition reaction was performed by using the Tn5 transposase (Nextera kit) at 37ºC for 30 minutes. Transposed DNA was further amplified by PCR, and the generated libraries were purified using Agencourt AMPure XP (Beckman Coulter). Library quality was controlled by using a Bioanalyzer high-sensitivity DNA analysis kit (Agilent)

value: braindisso


title: ATAC-seq_Brx68_lung_mets_x1_1

description:
metastatic sample
X68lung.x1.1

value: lungdisso


title: ATAC-seq_Brx68_bone_mets_x1_1

description:
metastatic sample
X68bone.x1.1

value: bonedisso


title: ATAC-seq_Brx68_boneleg_mets_2_1

description:
metastatic sample
X68boneleg.2.1


title: ATAC-seq_Brx68_bonejaw_mets_2_1

description:
metastatic sample
X68bonejaw.2.1


title: ATAC-seq_Brx68_bone_mets_84_2

description:
metastatic sample
X68bone.84.2


title: ATAC-seq_Brx68_bone_mets_26_1

description:
metastatic sample
X68bone.26.1


title: ATAC-seq_Brx68_bone_mets_21_1

description:
metastatic sample
X68bone.21.1


title: ATAC-seq_Brx68_parental_CTC_Rep2

description:
parental CTC
X68HR


title: ZT32_rep2

value: Williams 82

tag: age

value: 11-day old


title: ATAC-seq_Brx68_parental_CTC_disso_Rep4

description:
parental CTC undergone dissociation protocol
X68HD.R3


title: ATAC-seq_Brx68_parental_CTC_Rep1

description:
parental CTC
X68H


title: ATAC-seq_Brx68_parental_CTC_Rep3

description:
parental CTC
X68H.R3


title: ATAC-seq_Brx50_brain_mets_84_2

description:
metastatic sample
X50brai.84.2

value: metastatic sample


title: ATAC-seq_Brx50_brain_mets_83_2

description:
metastatic sample
X50brai.83.2


title: ATAC-seq_Brx50_brain_mets_56_3

description:
metastatic sample
X50brai.56.3


title: ATAC-seq_Brx50_parental_CTC_disso_Rep4

description:
parental CTC undergone dissociation protocol
X50HD.R4


title: ATAC-seq_Brx50_parental_CTC_disso_Rep3

description:
parental CTC undergone dissociation protocol
X50HD.R3


title: ATAC-seq_Brx50_parental_CTC_Rep2

description:
parental CTC
X50HR


title: ATAC-seq_Brx50_bone_mets_83_2

description:
metastatic sample
X50bone.83.2


title: ATAC-seq_Brx50_parental_CTC_Rep1

description:
parental CTC
X50H


title: ATAC-seq_Brx42_brain_mets_69_1

description:
metastatic sample
X42brai.69.1


title: ATAC-seq_Brx42_brain_mets_74_1

description:
metastatic sample
X42brai.74.1


title: ATAC-seq_Brx42_brain_mets_66_1

description:
metastatic sample
X42brai.66.1


title: ATAC-seq_Brx68_bone_mets_22_1

description:
metastatic sample
X68bone.22.1


title: ATAC-seq_Brx42_parental_CTC_disso_Rep4

description:
parental CTC undergone dissociation protocol
X42HD.R2


title: ATAC-seq_Brx42_parental_CTC_Rep2

description:
parental CTC
X42HR


title: ATAC-seq_Brx07_ovary_mets_27_2

description:
metastatic sample
X07ovar.27.2


title: ATAC-seq_Brx07_ovary_mets_24_2

description:
metastatic sample
X07ovar.24.2


title: ATAC-seq_Brx07_ovary_mets_12_1

description:
metastatic sample
X07ovar.12.1


title: ATAC-seq_Brx07_lung_mets_71_1

description:
metastatic sample
X07lung.71.1

value: lung


title: ATAC-seq_Brx42_parental_CTC_disso_Rep3

description:
parental CTC undergone dissociation protocol
X42HD.R1

value: yes


title: ATAC-seq_Brx07_ovary_mets_30_2

description:
metastatic sample
X07ovar.30.2


title: ATAC-seq_Brx42_parental_CTC_Rep1

description:
parental CTC
X42H

value: parental CTC


title: ATAC-seq_Brx07_ovary_mets_28_2

description:
metastatic sample
X07ovar.28.2


title: ATAC-seq_Brx68_parental_CTC_disso_Rep5

description:
parental CTC undergone dissociation protocol
X68HD.R4


title: ATAC-seq_Brx07_parental_CTC_disso_Rep7

description:
parental CTC undergone dissociation protocol
X07HD.R3


title: ATAC-seq_Brx07_Kidney_mets_80_1

description:
metastatic sample
X07kidn.80.1


title: ATAC-seq_Brx07_lung_mets_28_2

description:
metastatic sample
X07lung.28.2


title: Stim_Rep3 [ATAC]

city: Charlestown

first: Debattama

middle: R

last: Sen

department: Cancer Center

institute: MGH/Harvard

description: Stim_merged_peaks_0.001_peaks.narrowPeak

data_processing:
Quality trimming of Fastqs was performed using Trimmomatic
Trimmed reads were aligned to the mm9 mouse genome using Bowtie2
Aligned reads were sorted and biological replicates were merged for peak-calling with samtools
Peak-calling was performed on merged bams using MACS2
Union and merging of peaks across all condition was done using BEDtools
BEDtools was used to quantify raw ATAC cut-sites within each peak in universe for each biological replicate to obtain a raw counts matrix
Library size normalization was performed using DESeq2 to obtain a final normalized counts matrix
Genome_build: mm9
Supplementary_files_format_and_content: NarrowPeak files are the output of consensus peak-calling for each biological condition from MACS2

organism: Mus musculus

source_name: CD8+ T-cells

growth_protocol: CD8+ T cells were activated in vitro (Alpha-mem media + 10% FBS and 1% pen strep) for 48 hours with 0.25μg/ml of soluble anti-CD3/CD28 (Stim), 0.25μg/ml anti-CD3/CD28 plus 100ng/ml recombinant IL-6 (IL-6) or activated with 0.25μg/ml anti-CD3/CD28 in the presence of Nos2-/- FRCs (FRCs).

extract_protocol:
Pelleted cells were lysed in 50 μl of reaction mix (25 μl of 2× TD, 2.5 μl of Tn5 enzyme, 0.25 μl of 2% digitonin, 22.25 μl of nuclease-free water) as previously described (Corces et al., Nature Genetics, 2016). Reaction was incubated at 37 °C for 30 min with agitation at 300 RPM. DNA was purified using a QIAgen MinElute Reaction Cleanup kit and Nextera sequencing primers ligated using PCR amplification. Agencourt AMPure XP bead cleanup (Beckman Coulter/Agencourt) was used post-PCR and library quality was verified using a Tapestation machine.
Library construction was performed as per standard ATAC-seq protocol, as outlined in Corces et al., Nature Genetics 2016

treatment_protocol: 50.000 CD8+ T cells per replicate were sorted (as CD8α+, MHCII-) from in vitro cultures into PBS (10% FBS) via FACSAria.

value: CD8+ T cells activated in vitro within whole splenocyte mixtures

tag: organism strain

tag: isolation of cd8+ t cells

value: CD8+ T cells were sorted (as CD8alpha+, MHCII-) from in vitro cultures via FACSAria

tag: agent


title: ATAC-seq_Brx07_parental_CTC_disso_Rep8

description:
parental CTC undergone dissociation protocol
X07HD.R4


title: ATAC-seq_Brx07_parental_CTC_Rep5

description:
parental CTC
X07H


title: ATAC-seq_Brx07_parental_CTC_Rep4

description:
parental CTC
X07H.R3


title: ATAC-seq_Brx07_parental_CTC_Rep1

description:
parental CTC
X07.15K.3


title: ATAC-seq_Brx07_parental_CTC_Rep3

description:
parental CTC
X07.5K.3


title: ATAC-seq_Brx07_lung_mets_77_1

description:
metastatic sample
X07lung.77.1


title: ATAC-seq_Brx07_parental_CTC_Rep2

description:
parental CTC
X07.50K.3


title: Stim_Rep2 [ATAC]

tag: cell type


title: Stim_Rep1 [ATAC]


title: IL6_Rep3 [ATAC]

value: recombinant IL-6


title: FRC_Rep1 [ATAC]

value: Nos2-/- FRCs


title: IL6_Rep2 [ATAC]


title: ATAC-seq_Brx07_lung_mets_30_2

description:
metastatic sample
X07lung.30.2


title: ATAC-seq_Brx07_parental_CTC_Rep6

description:
parental CTC
X07HR


title: FRC_Rep2 [ATAC]


title: IL6_Rep1 [ATAC]


title: FRC_Rep3 [ATAC]


title: FRC_Rep3

data_processing:
NextSeq raw data demultiplexed and converted to fastq files using the Illumina software Bcl2fastq v2.19.1
Fastq files were quality-trimmed and illumina adaptors removed using Trimmomatic v0.33
Fastq files were aligned to the mm10 genome assembly using Bowtie2 v2.2.4
Feature counts were aggregated into a single data matrix using HTSeq v0.6.1p1.
DESeq2 library size normalization by scale factor of normcounts. Differential expression performed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Aggregated raw count matrix (output from HTSeq) in tab-delimited .txt file

growth_protocol: CD8+ T cells were activated in vitro (Alpha-mem media + 10% FBS and 1% pen strep) for 48 hours with soluble 0.25μg/ml anti-CD3/CD28 (Stim), soluble 0.25μg/ml anti-CD3/CD28 plus 100ng/ml recombinant IL-6 (IL-6) or activated with 0.25μg/ml anti-CD3/CD28 in the presence of Nos2-/- FRCs (FRCs).

extract_protocol:
RNA was isolated from cell pellets using the Qiagen RNeasy Mini kit according to the manufacturer’s instructions. First-strand Illumina-barcoded libraries were then generated using the NEB RNA Ultra Directional kit according to manufacturer’s instructions, including 12-cycles of PCR enrichment.
Libraries were constructed using the NEB Ultra-Directional RNA kit using the mRNA magnetic isolation module, according to manufacturer's instructions.
Directional libraries were barcoded using NEB dual index barcodes and sequenced on the NextSeq (high output flowcell) by pair-end sequencing of 37bp.

treatment_protocol: CD8+ T cells were sorted (as CD8α+, MHCII-) from in vitro cultures via FACSAria.

tag: strain


title: Stim_Rep1


title: Stim_Rep3


title: FRC_Rep1


title: SND1 IP Rep2 0H

description:
processed data file: SND1_RIP_RAW_COUNTS.txt
processed data column header: run2_0HIPNorRNADepletion

source_name: SND1 IP 0H, KSHV-infected B-lymphocytes

value: TREx BCBL1-Rta cells

tag: infection

value: KSHV

tag: ip antibody

value: SND1 (Protein tech, 10760-1-AP)

tag: time


title: FRC_Rep2


title: IL6_Rep1


title: lung.menv.control_rep2

description:
lung micro-enviroment control
lung.menv.control_2

data_processing:
Sequenced reads were trimmed for adaptor sequence and were mapped to a custom genome combining hg19 (GRCh37) and mm10 (GENCODE GRCm38.p5) using STAR v2.5.2b.
Only reads mapped to mm10 genome were quantified using HTSeq-Count
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with raw counts

source_name: lung micro-enviroment control

growth_protocol: CTC lines were cultured in ultra-low attachment plates with RPMI 1640 medium, supplemented with EGF (20ng/ml), bFGF (20ng/ml), 1X B27 and 1X antibiotic/antimycotic, in 4% O2 and 5% CO2. Metastatic tumors were established by inoculation of 100,000 GFP-LUC labeled CTCs in 100 µl of PBS into the left cardiac ventricles of 6-8 weeks old female NSG mice supplemented with subcutaneous slow release estrogen pills. Metastatic lesions were further dissociated into single-cell suspension by automated dissociation. Stromal cell (GFP- cells) were sorted for RNA sequencing.

extract_protocol: Sorted cells were collected into a pre-chilled tube maintained at 4ºC containing PBS with 1% BSA. RNA was collected from 50,000 sorted cells, according to the manufacturer’s instructions (Quick RNA, Zymo). RNA integrity was measured using Bioanalyzer (Agilent).

value: stromal cells

tag: tissue

value: no

tag: ctc cell line


title: brain.menv.control_rep2

description:
brain micro-enviroment control
brain.menv.control_3

source_name: brain micro-enviroment control

value: brai


title: bone.menv.control_rep1

description:
bone micro-enviroment control
bone.menv.control_1

source_name: bone micro-enviroment control

value: bone


title: brain.menv.control_rep1

description:
brain micro-enviroment control
brain.menv.control_2


title: 68lung.menv.99.2

description:
lung micro-environment exposed to Brx68 CTC
X68lung.menv.99.2


title: bone.menv.control_rep3

description:
bone micro-enviroment control
bone.menv.control_3


title: 68bone.menv.99.2

description:
bone micro-environment exposed to Brx68 CTC
X68bone.menv.99.2


title: bone.menv.control_rep2

description:
bone micro-enviroment control
bone.menv.control_2


title: 68bone.menv.22.1

description:
bone micro-environment exposed to Brx68 CTC
X68bone.menv.22.1


title: 68bone.menv.84.2

description:
bone micro-environment exposed to Brx68 CTC
X68bone.menv.84.2


title: 68bone.menv.24.1

description:
bone micro-environment exposed to Brx68 CTC
X68bone.menv.24.1


title: 50lung.menv.83.2

description:
lung micro-environment exposed to Brx50 CTC
X50lung.menv.83.2


title: 68bone.menv.23.1

description:
bone micro-environment exposed to Brx68 CTC
X68bone.menv.23.1


title: 50lung.menv.48.1

description:
lung micro-environment exposed to Brx50 CTC
X50lung.menv.48.1


title: IL6_Rep3


title: 50brai.menv.83.2

description:
brain micro-environment exposed to Brx50 CTC
X50brai.menv.83.2

value: brain


title: 68bone.menv.21.1

description:
bone micro-environment exposed to Brx68 CTC
X68bone.menv.21.1


title: 50brai.menv.58.3

description:
brain micro-environment exposed to Brx50 CTC
X50brai.menv.58.3


title: 68bone.menv.48.2

description:
bone micro-environment exposed to Brx68 CTC
X68bone.menv.48.2


title: 50lung.menv.84.2

description:
lung micro-environment exposed to Brx50 CTC
X50lung.menv.84.2


title: 50bone.menv.9.3

description:
bone micro-environment exposed to Brx50 CTC
X50bone.menv.9.3


title: OE-3_rep3

source_name: top second leaf of the OE-3 line

tag: genotype/variation

value: over-expression of NRP

tag: growth stage

value: Heading stage

value: top second leaf


title: 50bone.menv.84.2

description:
bone micro-environment exposed to Brx50 CTC
X50bone.menv.84.2

value: yes


title: 50bone.menv.83.2

description:
bone micro-environment exposed to Brx50 CTC
X50bone.menv.83.2


title: 50bone.menv.7.3

description:
bone micro-environment exposed to Brx50 CTC
X50bone.menv.7.3


title: 42lung.menv.73.1

description:
lung micro-enviroment exposed to Brx42 CTC
X42lung.menv.73.1

value: lung


title: lung.menv.control_rep1

description:
lung micro-enviroment control
lung.menv.control_1


title: 07lung.menv.28.2

description:
lung micro-environment exposed to Brx07 CTC
X07lung.menv.28.2


title: 07boneskull.menv.2.1

description:
bone micro-environment exposed to Brx07 CTC
X07boneskull.menv.2.1


title: 07boneleg.menv.2.1

description:
bone micro-environment exposed to Brx07 CTC
X07boneleg.menv.2.1


title: 50brai.menv.48.1

description:
brain micro-environment exposed to Brx50 CTC
X50brai.menv.48.1


title: het4D_-CMC

city: Cambridge

first: Thomas

middle: M

last: Carlile

state: Massachusetts

address: 77 Massachusetts Ave

institute: MIT

description: RNA was fragmented, treated with CMC as indicated, and captured by 3' adaptor ligation. RT was perfromed with AMV-RT, and truncated cDNA fragments were size selected on a gel, circularized, PCR amplified, and sequenced.

data_processing:
library strategy: Pseudo-seq
PCR duplicates were collapsed using fastx_collapser
Reads were trimmed of the first 10 nucleotides (corresponding to 10 Ns in RT primer), and adapter sequence
Reads were mapped to the genome using tophat2
Mapped reads were processed using custom bash and python scripts (see text), and Carlile et al. Nature 2014, and Stanley et al. Sci Transl Med (2016)
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab delimited text file of Pseudo-seq peak values for sites of pseudouridylation in the mouse rRNA.

growth_protocol: hPSC derived CNS neurons derived from H9 (WiCell: WAe009-A) cells as described in text, in Yuchen, Q, et al. Nat Biotechnol. 2017, and Stuart, C, et al. Nat Biotechnol. 2009.

extract_protocol:
Total RNA was isolated from hPSC derived CNS neurons using the RNeasy Mini Kit following manufacturer’s protocol (Qiagen)
Pseduo-seq libraries were prepared as described (Carlile et al. Nature 2014) Briefly, total RNA was fragmented, and was subsequently derivatized with CMC followed by reversal of CMC adducts. Fragments were size selected, followed by 3′ adapter ligation, and reverse transcription. Truncated RT fragents were size selected, circularized, and PCR amplified. PCR products were gel purified, and sequenced on an Illumina HiSeq 2000.

tag: cell line

value: H9 (WiCell:WAe009-A)

value: hPSC derived CNS neurons

value: heterozygous disruptions of SNORA31


title: hom33A_-CMC

value: homozygous disruptions of SNORA31


title: hom33B_+CMC

tag: treated with

value: 0.4M CMC


title: het4D_+CMC


title: hom33B_-CMC


title: het4C_+CMC


title: hom33D_-CMC


title: het4B_+CMC


title: het4C_-CMC


title: hom33D_+CMC


title: het4A_+CMC


title: H9D_-CMC

value: wild type control


title: het4B_-CMC


title: H9C_-CMC


title: 07lung.menv.77.1

description:
lung micro-environment exposed to Brx07 CTC
X07lung.menv.77.1


title: het4A_-CMC


title: H9D_+CMC


title: H9B_+CMC


title: hom33A_+CMC


title: H9B_-CMC


title: H9A_-CMC


title: AGS-EBV set 1

city: Seoul

first: Suk Kyeong

last: Lee

address: 222, Banpo-daero

country: South Korea

institute: Catholic University of korea

description:
AGS-EBV independent culture 1
P1

scan_protocol: Microarrays were scanned using an Illumina BeadArray Reader.

data_processing: statistical analyses were performed using Geneplex 2.3 software (ISTECH Inc., Goyang, Korea).

source_name: AGS-EBV cell line

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Total RNA was prepared using RNAzol B reagent (Tel-Test, Friendswood, TX) from five each independent cultures of AGS and AGS-EBV cells. The quantity and quality of total RNA were assessed with a Bioanalyzer (Agilent Technologies, Santa Clara, CA) and Experion (Bio-Rad, Hercules, CA).

value: AGS

value: gastric adenocarcinoma cell line

tag: ebv status

value: EBV-positive


title: AGS set 3

description:
AGS independent culture 3
N3

source_name: AGS cell line

value: EBV-negative


title: Cdk8 KO RasG12V Rep3

city: Montpellier

first: Damien

middle: J

last: Grégoire

address: 1919, route de Mende

country: France

institute: CNRS

description:
Sample9_36.3
rRNA-depleted total RNA

data_processing:
Base calling was performed with Illumina RTA software. FastQC was used to perform quality control of the sequencing.
All the reads that passed the quality control were aligned to the mouse reference genome and the counts per gene were quantified using the tool STAR 2.6.0a.
The Ensembl mouse genome annotations (release 93) were used for establishing the coordinates of each gene and their corresponding transcripts.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: *_ensembl_ReadsPerGene.out.tab: Standard STAR software output files. Tab-delimited text file with the raw read counts for each gene.

source_name: BMEL cells

growth_protocol: BMEL (Bipotential Mouse Embryonic Liver) cell line was isolated from CDK8F/F mouse. Cells were grown on collagen-coated plates in RPMI medium (Gibco/Life Technologies) supplemented with 10% fetal calf serum (Pan-Biotech), insulin 10 ug/mL (Sigma), IGFII 30 ng/mL (Peprotech), EGF 50 ng/mL (Peprotech), 100 units/ml penicillin, and 100 mg/ml streptomycin. Cells were grown under standard conditions at 37°C in a humidiﬁed incubator containing 5% CO2. All cells were routinely tested to confirm absence of mycoplasma contamination.

extract_protocol:
RNA was harvested using Qiagen RNeasy kit following manufacturer instructions. DNaseI treatment (Qiagen) was used to remove residual genomic DNA. RNA integrity was assessed by Agilent BioAnalyser. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: NO

value: BMEL

value: Bipotential mouse embryonic liver cells

tag: transformation

tag: condition

value: Exponentially growing on collagen coated plates


title: Cdk8 KO RasG12V Rep1

description:
Sample7_36.1
rRNA-depleted total RNA


title: H9C_+CMC


title: WT RasG12V rep1

description:
Sample4_33.1
rRNA-depleted total RNA

value: Wild type


title: H9A_+CMC


title: AGS set 5

description:
AGS independent culture 5
N5


title: AGS set 2

description:
AGS independent culture 2
N2


title: AGS set 1

description:
AGS independent culture 1
N1


title: AGS-EBV set 4

description:
AGS-EBV independent culture 4
P4


title: AGS-EBV set 5

description:
AGS-EBV independent culture 5
P5


title: AGS-EBV set 2

description:
AGS-EBV independent culture 2
P2


title: AGS set 4

description:
AGS independent culture 4
N4


title: WT rep3

description:
Sample3_31.3
rRNA-depleted total RNA


title: WT rep2

description:
Sample2_31.2
rRNA-depleted total RNA


title: WT rep1

description:
Sample1_31.1
rRNA-depleted total RNA


title: AGS-EBV set 3

description:
AGS-EBV independent culture 3
P3


title: WT RasG12V rep3

description:
Sample6_33.4
rRNA-depleted total RNA


title: WT RasG12V rep2

description:
Sample5_33.2
rRNA-depleted total RNA


title: Cdk8 KO RasG12V Rep2

description:
Sample8_36.2
rRNA-depleted total RNA


title: Ehmt1/Zic2_KO1_32h_RNAseq

city: Basel

first: Joerg

last: Betschinger

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

data_processing:
RNA-seq reads from cells in 2i and 16h and 32h after 2i withdrawal were aligned to the mouse GRCm38/mm10 genome using qAlign from the Bioconductor package QuasR (Gaidatzis et al., 2015) (package version 1.22.0) with default parameters except for splicedAlignment=TRUE.
Alignments were quantified for known UCSC genes obtained from the TxDb.Mmusculus.UCSC.mm10.knownGene package (package version 3.4.4) using qCount from the Bioconductor package QuasR with default parameters
Only transcripts with at least 3 counts per million in at least two biological samples were considered as expressed genes (total: 13,096 genes).
For identification of significantly deregulated genes, edgeR (Robinson and Oshlack, 2010) (package version 3.24.0) was used and detected genes were fitted to two generalized linear models. Raw P values were corrected for multiple testing by calculating false discovery rates (FDR). Significant genes were identified as genes with an absolute log2 fold-change greater than 1.0 and an FDR of less than 0.01.
For visualization of RNA-seq data log2 fold-change values that were obtained from edgeR were used.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing raw read counts for each Sample (column) and gene (row).

molecule: polyA RNA

source_name: mouse embryonic stem cells RGd2

growth_protocol: ESCs (female RGd2 cells containing a Rex1:GFPd2-IRES-Blasticidin (Wray et al., 2011)) were cultured on plastic coated with gelatin in N2B27 medium (DMEM/F12 (Life Technologies), Neurobasal (Gibco) supplemented with N2 (homemade) and B-27 Serum-Free Supplement (Gibco), 2mM L-glutamine (Gibco), and 0.1mM 2-mercaptoethanol (Sigma)) with 2i (3µM CHIR99021 and 1µM PD0325901 (Steward lab, Dresden)).

extract_protocol:
Cellular RNA from ESCs and cells 16h and 32h after 2i withdrawal was purified using RNAeasy (Qiagen).
For Zfp281 KO and corresponding WT cells, total RNA was subjected to ribosomal RNA depletion using Ribozero removal kit (Illumina) followed by library construction using ScriptSeq V2 library preparation kit (Illumina). For Ehmt1, Zic2, Ehmt1/Zic2 KO and corresponding WT cells RNA-seq libraries were prepared using TruSeq mRNA Library preparation kit (Illumina).

treatment_protocol: For differentiation, ESCs were seeded on gelatin-coated plates at 1.5 x 104 cells/cm2 in 2i and the following day 2i was withdrawn and cells cultured for additional 16h or 32h.

value: mouse embryonic stem cells

tag: genotype

value: Ehmt1/Zic2 KO.1

tag: time point


title: Ehmt1/Zic2_KO2_32h_RNAseq

value: Ehmt1/Zic2 KO.2


title: Cdk19 KO RasG12V Rep2

description:
Sample11_40.2
rRNA-depleted total RNA


title: Ehmt1/Zic2_KO2_ESC_RNAseq

value: ESC


title: Zic2_KO1_32h_RNAseq

value: Zic2 KO.1


title: Zfp281_KO1_16h_RNAseq

value: Zfp281 KO.1


title: WT_16h_RNAseq

value: WT


title: Zfp281_KO2_16h_RNAseq

value: Zfp281 KO.2


title: Ehmt1/Zic2_KO1_ESC_RNAseq


title: Zfp281_WT_16h_RNAseq


title: Zic2_KO1_ESC_RNAseq


title: Zic2_KO2_ESC_RNAseq

value: Zic2 KO.2


title: Ehmt1_KO2_32h_RNAseq

value: Ehmt1 KO.2


title: Ehmt1_WT_ESC_RNAseq


title: Zfp281_KO2_32h_RNAseq


title: Ehmt1_KO2_ESC_RNAseq


title: Ehmt1_WT_32h_RNAseq


title: Ehmt1_KO1_ESC_RNAseq

value: Ehmt1 KO.1


title: Zic2_WT_ESC_RNAseq


title: Zfp281_KO1_32h_RNAseq


title: Zfp281_KO1_ESC_RNAseq


title: Zfp281_WT_32h_RNAseq


title: Zfp281_WT_ESC_RNAseq


title: WT_32h_RNAseq


title: Zic2_KO2_32h_RNAseq


title: Zfp281_KO2_ESC_RNAseq


title: Ehmt1_KO1_32h_RNAseq


title: Zic2_WT_32h_RNAseq


title: input-for-Bio-Ehmt1_Zfp281-KO-32h_II

data_processing:
ChIP-seq reads were aligned to mouse GRCm38/mm10 genome using qAlign from the Bioconductor package QuasR (Gaidatzis et al., 2015) (package version 1.22.0) with default parameters.
We observed a non-linear relationship in Zfp281 ChIP-seq data when comparing read counts in Zfp281 peaks between ChIP-seq replicates in WT ESCs, and therefore performed loess regression using normalizeBetweenArrays function of the Bioconductor package limma (Ritchie et al., 2015) (package version 3.38.2) with method=cyclingloess.
In Bio-Ehmt1 ChIP-seq data we detected a variable dependency of read counts in genomic tiles on the tile’s GC composition (GC bias) which was most pronounced in input samples. In order to reduce this bias, we used a loess-based normalization method: First, reads were counted in each sample in 10kb windows. The counts were then scaled (divided by the total number of aligned reads (library size), multiplied with minimal library size, and added with a pseudocount of 8) and log2 transformed. A loess curve was fit to the log2-transformed counts as a function of the fraction of G+C bases in the window using the R function loess with span = 0.3. This fit robustly captures the global signal dependency on the underlying GC composition. GC-corrected log2 read counts were then obtained by subtracting the values predicted by the loess fit from the observed log2 read counts (residuals of the fit).
Peaks for Zfp281 or Zic2 were called on all replicates and in all conditions of Zfp281 or Zic2 ChIP-seq reads, respectively, using Macs2 (Zhang et al., 2008) (version 2.1.1.20160309) with default parameters. Peaks that were at least two-fold enriched (IP over respective inputs) in at least one ChIP samples were considered.
Peaks were assigned to genes by calculating the distances of peak midpoint to the nearest transcriptional start site (TSS) using a set of non-redundant TSSs with a single start site randomly selected for each gene.
Due to the broad chromatin distribution of Ehmt1 and H3K9me2, ChIP-seq reads were first quantified in genome-tiling windows of 10kb which were generated using tileGenome function from Bioconductor package GenomicRanges (Lawrence et al., 2013) (package version 1.34.0) with tilewidth=10000 and cut.last.tile.in.chrom=TRUE. To quantify Ehmt1 and H3K9me2 enrichment at Zfp281 binding sites, Zfp281 peak regions were extended to 10kb centered on the peak midpoint using the function resize from the Bioconductor package GenomicRanges. As a control set, DHS-seq peaks (peak annotation downloaded from ENCODE; accession number: ENCSR000CMW) were extended to 10kb centered on the peak midpoint and only regions non-overlapping with 10kb extended Zfp281 peaks were considered. The final set of control regions was obtained by randomly sampling one DHS 10kb peak per Zfp281 10kb peak, such that the distributions of DHS-seq signal (log2 RPM) and GC-content between Zfp281 10kb extended peaks and the selected control regions matched closely.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using the qExportWig function from the Bioconductor package QuasR with default parameters using scaling=TRUE and binsize=100. The scores in the wig file therefore represent the number of alignments per 100bp window and scaled by the total number of aligned reads per sample.

extract_protocol:
Cells were fixed with 1% formaldehyde and neutralized with glycine to a final concentration of 0.125 mM. After nuclei extraction, DNA for ChIPs of endogenous proteins and corresponding inputs was sonicated using Diagenode Bioruptor Plus in 15 ml Diagenode Falcon tubes, cell lysates incubated with corresponding antibody over night at 4°C and Dynabeads were added the next day. In case of Bio-Ehmt1 and corresponding inputs, DNA was digested with Micrococcal Nuclease (Cell Signaling) and incubated with M-280 Streptavidin coupled Dynabeads (Invitrogen) for 1h at 4°C. Beads were washed, eluted and the suspension was de-crosslinked over night at 65 °C. DNA of ChIPs from endogenous proteins and corresponding inputs was purified using MinElute PCR Purification Kit (QIAGEN) and of Bio-Ehmt1 ChIPs and corresponding inputs using AMPure XP beads (Beckman Coulter).
ChIP-seq libraries were prepared using NEBNext Ultra kit (New England BioLabs) following the manufacturer’s recommendations.

treatment_protocol: For differentiation, ESCs were seeded on gelatin-coated plates at 1.5 x 104 cells/cm2 in 2i and the following day 2i was withdrawn.

tag: chip antibody

value: input


title: Bio-Ehmt1-ChIP_Zfp281-KO-ESC_I

tag: cell type

value: M-280 Streptavidin coupled Dynabeads (Invitrogen)


title: Bio-Ehmt1-ChIP_Zfp281-KO-ESC_II


title: input-for-Bio-Ehmt1_Zfp281-KO-ESC_I


title: Bio-Ehmt1-ChIP_WT-32h_II


title: WT_ESC_RNAseq


title: Bio-Ehmt1-ChIP_Zfp281-KO-32h_I


title: input-for-Bio-Ehmt1_Zfp281-KO-ESC_II


title: input-for-Bio-Ehmt1_Zfp281-KO-32h_I


title: Bio-Ehmt1-ChIP_WT-32h_I


title: Bio-Ehmt1-ChIP_WT-ESC_I


title: input-for-Bio-Ehmt1_WT-32h_II


title: Bio-Ehmt1-ChIP_WT-ESC_II


title: input-for-Bio-Ehmt1_WT-32h_I


title: input-for-Bio-Ehmt1_WT-ESC_II


title: Zic2-ChIP_Zfp281-KO-ESC_II

value: Zic2 (Abcam, ab150404)


title: Zic2-ChIP_Zfp281-KO-32h_II


title: Zic2-ChIP_Zfp281-KO-32h_I


title: Bio-Ehmt1-ChIP_Zfp281-KO-32h_II


title: H3K9me2-ChIP_Zfp281-KO-32h_II

value: H3K9me2 (Abcam, ab1220)


title: H3K9me2-ChIP_Zfp281-KO-ESC_II


title: H3K9me2-ChIP_Zfp281-KO-ESC_I


title: H3K9me2-ChIP_Zfp281-KO-32h_I


title: input_Zfp281-KO-32h_II


title: input_Zfp281-KO-ESC_I


title: input_Zfp281-KO-32h_I


title: Zic2-ChIP_WT-32h_II


title: Zic2-ChIP_WT-32h_I


title: Zic2-ChIP_WT-ESC_II


title: Zfp281-ChIP_WT-32h_II

value: Zfp281 (Bethyl Laboratories, A303-118A)


title: NDMA+ESP 3

first: Eunmin

last: Kim

address: 50, Yonsei-ro, Seodaemun-gu

institute: Yonsei University

description:
4-3
Liver
processed data file: Normalized_FPKM.txt

data_processing:
bcl2fastq v1.8.4 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Homo sapiens using Tophat 2.0.13, which is capable of reporting split-read alignments across splice junctions and determined using Cufflinks 2.2.1 software in default options.
The reference genome sequence of Homo sapiens (hg19) and annotation data were downloaded from UCSC. The transcript counts in isoform level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks.
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Normalized_FPKM.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: Bile duct epithelial cell

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

value: Bile duct epithelial cells

tag: treatment

value: NDMA+ESP


title: Zfp281-ChIP_WT-32h_I

value: mouse embryonic stem cells


title: input-for-Bio-Ehmt1_WT-ESC_I


title: NDMA+ESP 2

description:
4-2
Liver
processed data file: Normalized_FPKM.txt


title: Zfp281-ChIP_WT-ESC_II


title: ESP 3

description:
3-3
Liver
processed data file: Normalized_FPKM.txt

value: ESP


title: Zic2-ChIP_WT-ESC_I

value: ESC


title: Zic2-ChIP_Zfp281-KO-ESC_I


title: ESP 2

description:
3-2
Liver
processed data file: Normalized_FPKM.txt


title: H3K27ac-ChIP_WT-32h_II

value: H3K27ac (Active Motif, 39135)


title: NDMA 3

description:
2-3
Liver
processed data file: Normalized_FPKM.txt

value: NDMA


title: NDMA 2

description:
2-2
Liver
processed data file: Normalized_FPKM.txt


title: input_Zfp281-KO-ESC_II

value: Zfp281 KO.1


title: NDMA 1

description:
2-1
Liver
processed data file: Normalized_FPKM.txt


title: H3K27ac-ChIP_WT-32h_I

value: WT


title: H3K27ac-ChIP_WT-ESC_II


title: Control3

description:
1-3
Liver
processed data file: Normalized_FPKM.txt

value: Control


title: sigmoid biopsy, allogenic FMT, subject 015, 8 weeks after intervention

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.48.0).

source_name: sigmoid biopsy, uncleansed colon

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: The study was conducted according to the principles of the Declaration of Helsinki and its revisions, and ethical approval was obtained from the Central Ethical Review Board of Uppsala, Sweden (registration number 2013/180). The study was performed at Örebro University Hospital in Örebro, Sweden, from May 2014 to April 2016. All participants were recruited in the greater area of Örebro and gave their written informed consent before participation. The trial has been registered at ClinicalTrials.gov (NCT02092402) on March 20, 2014. Adult IBS patients that fulfilled the Rome III diagnostic criteria for irritable bowel syndrome (IBS) were included in this study. All IBS subtypes, including postinfectious IBS, were eligible for the study. Reasons for exclusion were any other known organic gastrointestinal disease, previous complicated gastrointestinal surgery, nongastrointestinal malignancy, dementia, severe depression, major psychiatric disorder, severe endometriosis, recent diagnosis of lactose intolerance, celiac disease, pregnancy or breast-feeding, antimicrobial treatment within 4 weeks prior to first screening visit, regular consumption of probiotics within 4 weeks prior to randomization, abuse of alcohol and drugs, or any other clinically significant disease/condition which in the investigator’s opinion could interfere with the results of the trial. The patients were asked to keep their medication and diet stable  over the entire study period.

extract_protocol: RNA was isolated using Qiagen RNeasy Mini Kit (Qiagen), quantified using NanoDrop, and quality was checked with the Agilent 2100 bioanalyzer (Agilent Technologies). Samples were only included for further analyses in case of intact bands corresponding to 18S and 28S ribosomal subunits and absence of chromosomal peaks or RNA degradation products.

treatment_protocol: Two weeks before the FMT (baseline) as well as two and eight weeks after the FMT, the participants underwent a sigmoidoscopy, and biopsies were collected at a standardised location (20-25 cm from the anal verge at the crossing with the arteria iliaca communis) from an uncleansed sigmoid. Biopsies were transfered in RNAlater and immediately frozen at -80°C until further analysis.

value: uncleansed colon

tag: sex (female=1, male=0)

tag: subjectid

tag: age (yrs)

tag: moment of sampling (pre/post intervention)

value: 8 weeks after intervention

tag: time of sampling

value: Morning, after overnight fasting

tag: experimental condition

value: Allogenic FMT


title: sigmoid biopsy, autologous FMT, subject 016, baseline

tag: tissue

value: Baseline (app. 2w before intervention)

value: Autologous FMT


title: sigmoid biopsy, allogenic FMT, subject 015, baseline


title: sigmoid biopsy, autologous FMT, subject 016, 8 weeks after intervention


title: sigmoid biopsy, allogenic FMT, subject 013, 8 weeks after intervention


title: sigmoid biopsy, autologous FMT, subject 014, 8 weeks after intervention


title: sigmoid biopsy, autologous FMT, subject 014, 2 weeks after intervention

value: 2 weeks after intervention


title: sigmoid biopsy, autologous FMT, subject 014, baseline


title: sigmoid biopsy, allogenic FMT, subject 015, 2 weeks after intervention


title: H3K9me2-ChIP_WT-32h_II

tag: cell line

value: H3K9me2 (Abcam, ab1220)


title: sigmoid biopsy, autologous FMT, subject 012, 8 weeks after intervention


title: sigmoid biopsy, autologous FMT, subject 016, 2 weeks after intervention