title: 1168V062811_IFN


title: 1168V062811_FLU

status: Public on Oct 04 2018

type: SRA

city: Cambridge

first: Jenny

last: Chen

address: 16 Divinity Ave

country: USA

institute: Harvard

library_source: transcriptomic

data_processing:
Tophat v1.4.1 (--mate-inner-dist 300 --mate-std-dev 500) was used to align reads to hg19.
StringTie v1.2.2 was used with default parameters for de novo reconstruction of transcriptomes.
kallisto v0.42.5 was used to quantify abundances of reconstructed transcripts.
Genome_build: hg19, de novo reconstructed transcriptome
Supplementary_files_format_and_content: *abundance.txt: Tab-delimited text files of transcript ID, length, effective length, estimated counts, and TPM.
Supplementary_files_format_and_content: dcRNASeq.denovo_transcriptome.bed

molecule: total RNA

organism: Homo sapiens

source_name: monocyte-derived dendritic cells, influenza stimulated

extract_protocol:
35-50 mL of peripheral blood from fasting subjects was collected and peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll-Paque (GE Healthcare Life Sciences) centrifugation. Monocytes were isolated from PBMCs by negative selection using the Dynabeads Untouched Human Monocytes kit (Life Technologies) modified to increase throughput and optimize recovery and purity of CD14+ CD16lo monocytes. The remaining monocytes were cultured for seven days in RPMI (Life Technologies) supplemented with 10% FBS, 100 ng/mL GM-CSF (R&D Systems) and 40 ng/mL IL-4 (R&D Systems) to differentiate into monocyte-derived dendritic cells (MoDCs).
Total RNA was isolated from MoDCs using the RNeasy Mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: donor id

tag: disease state

value: healthy

tag: cell type

value: monocyte-derived dendritic cells

tag: condition

value: influenza stimulated


title: 1532V112911_FLU


title: 1314V110911_FLU


title: HS2100_control_S18_R1_001

city: New York

first: Loukia

last: Lili

state: NY

address: 770 Lexington Ave, 14-07 14th floor

department: Icahn School of Medicine at Mount Sinai

institute: The Institute for Next Generation Healthcare

data_processing:
Raw FASTQ files passed the per-base quality control of Fred score > 20 FASTQC (Babraham Bioinformatics: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Alignment to the human genome (hg38) was done with STAR aligner v2.3.1z using the default parameters and guided annotation GTF file from Ensembl (ENSEMBL92 annotation)
Following alignment, the raw counts were further processed with HTSeq, and normalized with the vst normalization method implemented with the DESEq2 R package.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts and vst normalized values for each sample

source_name: full thickness punch skin biopsies

extract_protocol:
Total RNA from whole human skin, and HaCaT keratinocyte cell cultures were isolated with RiboPure kit (Ambion, Life Technologies, Grand Island, NY, USA). The RNA samples were treated with TURBOTM DNase (Ambion), checked for quality and integrity with the Agilent 2100 bioanalyzer and used for RNASeq. Due to the conical shape of punch skin biopsies, the RNA was mostly extracted from keratinocytes with minimal contribution of dermal cells
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Glucocorticoid CBP 0.05% cream was purchased from the pharmacy. CBP was applied once to the internal surface skin of the upper right arm (area relatively protected from the sun light) of healthy volunteers.  Four-millimeter-full-thickness punch skin biopsies were taken 24 h after the CBP application. The biopsies from the untreated left arm skin were used as controls

tag: individual

value: control


title: HS2100_GC_S19_R1_001

value: gc


title: HS2191_control_S7_R1_001


title: HS1659_control_S14_R1_001


title: HS1625_Gc_S4_R1_001


title: HS1660_GC_S17_R1_001


title: 1416V021612_IFN

source_name: monocyte-derived dendritic cells, IFN-beta stimulated

value: IFN-beta stimulated


title: HS1659_GC_S15_R1_001


title: 1607V120811_FLU


title: HS1625_control_S3_R1_001


title: 1437V110911_FLU


title: 1314V110911_IFN


title: 0230V011712_FLU


title: HS2191_GC_S8_R1_001


title: HS1660_control_S16_R1_001


title: 1570V112211_FLU


title: HS1609_control_S12_R1_001


title: 1601V112211_IFN


title: HS1583_control_S1_R1_001


title: HS1609_GC_S13_R1_001


title: 0865V080311_FLU


title: 1416V021612_FLU


title: HS1233_Gc_S11_R1_001


title: 0865V080311_IFN


title: 1452V063011_FLU


title: 1437V110911_baseline

source_name: monocyte-derived dendritic cells, baseline

value: baseline


title: 1437V110911_IFN


title: HS18


title: HS19


title: HS1583_Gc_S2_R1_001


title: HS20


title: HS1233_control_S10_R1_001


title: HS17


title: HS16


title: 1314V110911_baseline


title: aaM3_GC


title: 1272V110111_IFN


title: 1452V063011_baseline


title: 0793V060911_FLU


title: aaM1_GC


title: aaM3


title: 1272V110111_FLU


title: 1266V111511_baseline


title: aaM2


title: 1452V063011_IFN


title: HS15


title: aaM2_GC


title: 1268V102711_FLU


title: 1686V022212_IFN


title: 1686V022212_baseline


title: aaF3


title: 1683V020712_IFN


title: aaF3_GC


title: 1268V102711_IFN


title: aaF2


title: aaF1_GC


title: 1683V020712_FLU


title: aaF2_GC


title: aaF1


title: 1686V022212_FLU


title: aaM1


title: 0398V050311_IFN


title: 1266V111511_FLU


title: 1472V110311_IFN


title: 1472V110311_FLU


title: mRRBS_MCF_WT_Rep2

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description:
Cells with wild type TET2.
Fragmented genomic DNA

library_source: genomic

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl2fastq v2.17.1.14.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp.
Bisulfite-seq reads were trimmed of 10 base pairs from the 5’ end with TrimGalore! v0.4.3 to remove primer and adapter sequences.
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.1.0. Only uniquely mapping reads with at most two mismatches were retained.
Bisulfite-seq reads were aligned to UCSC hg19 and methylation extraction ignoring 1 base at the 3’ end (after reviewing the M-bias plots) were performed with Bismark v0.16.3.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of RNA or ChIP fragments at a given genomic coordinate.
Supplementary_files_format_and_content: Bismark tab-delimited "coverage" files for cytosines in CpG context with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

molecule: genomic DNA

source_name: MCF7 cells

growth_protocol: Cell medium was composed as follows: DMEM 1X (Thermo Fisher), 10% serum (Corning), 1X glutamine (Life Technologies), 1X penicillin/streptomycin (Life Technologies). Cells were grown in a CO2 incubator (5% CO2) at 37˚C.

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit. For Bisulfite-seq, genomic DNA was quantified with a Qubit 3.0 instrument. ~250 ng of genomic DNA was then digested with the restriction endonuclease MspI (New England BioLabs). Resulting fragments underwent size selection for fragments ~100-250-bp in length using SPRI beads (MagBio Genomics) and subsequent bisulfite conversion using the EZ DNA Methylation-Lightning Kit (Zymo Research) per the manufacturer’s protocol. Bisulfite conversion efficiency averaged > 99% as estimated by the measured percent of unmethylated CpGs in λ-bacteriophage DNA (New England BioLabs N3013S) added at a 1:200 ratio to each sample. Libraries for Illumina-based sequencing were prepared with the Pico Methyl-Seq Library Prep Kit (Zymo Research) using Illumina TruSeq DNA methylation barcodes. Libraries were run on a High Sensitivity chip using an Agilent TapeStation 4200 to assess size distribution and overall quality of the amplified library. Fluorometric quantitation and TapeStation size distribution estimates permitted equimolar pooling, and 6 pooled libraries per run were sequenced on an Illumina NextSeq 500 instrument using the NextSeq 500/550 V2 High Output reagent kit (1 x 75 cycles).

treatment_protocol: Cells were grown in phenored free DMEM and 5% of stripped FBS for 96 hours. Then the cells were treated with E2 for either 45 minutes (ChIP-seq) or 4 hours (RNA-seq).

tag: cell line

value: Breast cancer cell

tag: genotype/variation

value: Wild type TET2

tag: passages

value: Low passages (6-10)


title: mRRBS_TET2_KO1_Rep1

description:
Cells with TET2 knockout.
Fragmented genomic DNA

value: TET2 knockout


title: mRRBS_MCF_WT_Rep1


title: mRRBS_TET2_KO2_Rep1


title: MCF7_MLL3_KO_Rep2

description: Cells with MLL3 knockout.

value: MLL3 knockout


title: 1472V110311_baseline


title: mRRBS_TET2_KO2_Rep2


title: MCF7_MLL3_KO_Rep1

description: Cells with MLL3 knockout.


title: 0195V011212_IFN


title: 1683V020712_baseline


title: MCF7_MLL3_WT_Rep1

description: Cells with wild type MLL3.

value: Wild type MLL3


title: 0448V012512_FLU


title: MCF7_MLL3_WT_Rep2

description: Cells with wild type MLL3.


title: 1266V111511_IFN


title: 0398V050311_FLU


title: CAL51_TET2_KO_Rep2

description: Cells with TET2 knockout.

source_name: CAL51 cells


title: mRRBS_TET2_KO1_Rep2


title: 1474V020912_FLU


title: 0064V080311_IFN


title: 0481V110811_FLU


title: CAL51_TET2_KO_Rep1

description: Cells with TET2 knockout.


title: 1684V021612_FLU


title: CAL51_TET2_WT_Rep2

description: Cells with wild type TET2.


title: 1684V021612_IFN


title: MCF7_TET2_KO_Rep2

description: Cells with TET2 knockout.


title: 0481V110811_baseline


title: 0481V110811_IFN


title: 1057V100411_FLU


title: MCF7_TET2_WT_Rep1

description: Cells with wild type TET2.


title: 1057V100411_baseline


title: 1057V100411_IFN


title: shMLL3_E2_Rep2

description: Cells treated with MLL3 shRNA treated with E2.

tag: shRNA

tag: treatment


title: 1136V081011_baseline


title: 1384V072111_IFN


title: MCF7_TET2_WT_Rep2

description: Cells with wild type TET2.


title: 1112V110911_IFN


title: 1556V112311_IFN


title: shMLL3_DMSO_Rep1

description: Cells treated with MLL3 shRNA treated with DMSO.

value: DMSO


title: MCF7_TET2_KO_Rep1

description: Cells with TET2 knockout.


title: shMLL3_DMSO_Rep2


title: 1359V020712_baseline


title: CAL51_TET2_WT_Rep1

description: Cells with wild type TET2.


title: shNONT_E2_Rep1

description: Cells treated with non-targeting shRNA treated with E2.

value: Non-targeting


title: shNONT_E2_Rep2


title: shNONT_DMSO_Rep2

description: Cells treated with non-targeting shRNA treated with DMSO.


title: shNONT_DMSO_Rep1


title: 1384V072111_FLU


title: 1359V020712_IFN


title: 1654V022112_baseline


title: 1589V020812_IFN


title: 1359V020712_FLU


title: DMSO_Rep2

description: Cells treated with DMSO.


title: DMSO_Rep1

description: Cells treated with DMSO.


title: Tamoxifen_Rep2

description: Cells treated with Tamoxifen.

value: Tamoxifen


title: Tamoxifen_Rep1

description: Cells treated with Tamoxifen.


title: shMLL3_E2_Rep1


title: 1474V020912_IFN


title: TET2_KO_E2_Rep1

description: Cells with TET2 knockout treated with E2.


title: TET2_KO_E2_Rep2


title: 1237V021512_baseline


title: 0880V110811_baseline


title: TET2_KO_DMSO_Rep2

description: Cells TET2 knockout treated with DMSO.


title: TET2_WT_E2_Rep2

description: Cells with wild type TET2 treated with E2.


title: 1654V022112_FLU


title: 0880V110811_IFN


title: TET2_KO_DMSO_Rep1

description: Cells TET2 knockout treated with DMSO.


title: 1589V020812_FLU


title: 1237V021512_FLU


title: 0312V011012_IFN


title: TET2_WT_DMSO_Rep2

description: Cells with wild type TET2 treated with DMSO.


title: 1112V110911_FLU


title: TET2_WT_DMSO_Rep1


title: 16_5_rep3

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

data_processing:
Runing STAR aligner in "Gene_counts" mode
Merging STAR output ("ReadPerGene.out" files) with R into a single table
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw gene counts for each sample

source_name: Liver

extract_protocol:
For solid tissue biosamples, RNA extraction was performed immediately before preparation of sequencing libraries using QIAGEN RNeasy Kit (Qiagen) for tissues in RNAlater and using the RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Invitrogen) following the manufacturer ’s protocol. Then RNA Integrity Number (RIN) was measured using Agilent 2100 bio-Analyzer. Agilent RNA 6000 Nano or Qubit RNA Assay Kits were used to measure RNA concentration. The Kit for further depletion of ribosomal RNA was selected based on total amount of RNA in every sample: (i) when total amounts of RNA were less than 25 ng, Clontech Smarter stranded total RNA kit-pico (Mammalian only) was used; (ii) when total amount of RNA exceeded 25ng, KAPA RNA Hyper with RiboErase (KAPA Biosystem) kits were used.
For library preparations, we used Ovation® Universal RNA-Seq System 1-96 and KAPA HyperPrep Kit according to the manufacturer’s recommendations. Different adaptors were used for multiplexing samples in one sequencing run. Library concentrations and quality were measured using Qubit ds DNA HS Assay kit (Life Technologies) and Agilent Tapestation (Agilent). RNA sequencing was performed using Illumina HiSeq 3000 equipment for single-end sequencing, 50 bp read length, for approx. 30 million raw reads per each sample. Data quality check was done on Illumina SAV. De-multiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.

tag: tissue

value: Liver

tag: disease


title: 1237V021512_IFN

value: healthy


title: 1282V110811_baseline

value: monocyte-derived dendritic cells


title: H3K4me1_MCF7

description:
Parental cells.
Fragmented genomic DNA

value: Parental cells

tag: chip antibody

value: anti-H3K4me1 (homemade)


title: H3K27Ac_MCF7

description:
Parental cells.
Fragmented genomic DNA

value: anti-H3k27Ac (Cell Signaling Technology)


title: 0880V110811_FLU

value: influenza stimulated


title: Input_KO


title: 16_5_rep2


title: E3_rep3

source_name: Esophagus

value: Esophagus


title: TET2_WT_E2_Rep1

value: Breast cancer cell


title: UTX_MCF7

description:
Parental cells.
Fragmented genomic DNA

value: anti-UTX (homemade)


title: 0559V072011_IFN

value: IFN-beta stimulated


title: 16_5_rep1


title: 1282V110811_FLU


title: 1282V110811_IFN


title: D8

source_name: CD138+ enriched bone marrow cells

value: CD138+ enriched bone marrow cells


title: TET2CST_WT

value: Wild type TET2

value: Low passages (6-10)

value: anti-TET2 (Cell Signaling Technology)


title: Input_shTET2

description:
Cells treated with TET2 shRNA.
Fragmented genomic DNA


title: 0559V072011_FLU


title: TET2CST_KO

value: TET2 knockout


title: 0559V072011_baseline

value: baseline


title: D10


title: D11


title: E3_rep2


title: 1605V021412_IFN


title: E3_rep1


title: D9


title: D6


title: D5


title: D7


title: 1574V112911_FLU


title: TET2_shTET2

value: anti-TET2_NTD (homemade)


title: D3

value: healthy


title: D4


title: 1605V021412_FLU

value: monocyte-derived dendritic cells


title: Input_shNONT (b)

description:
Cells treated with non-targeting shRNA.
Fragmented genomic DNA

value: Non-targeting


title: H3K27me3

description:
Parental cells.
Fragmented genomic DNA

value: Parental cells

value: anti-H3K27me3 (homemade)


title: D2


title: 1538V110211_FLU

value: influenza stimulated


title: Input_WT


title: H3K4me3

description:
Parental cells.
Fragmented genomic DNA

value: anti-H3K4me3 (homemade)


title: WB8

source_name: Whole blood nuclear cells

value: Whole blood nuclear cells


title: WB7


title: 1538V110211_IFN


title: 1538V110211_baseline


title: WB6


title: Input_shMLL3

description:
Cells treated with MLL3 shRNA.
Fragmented genomic DNA

value: Breast cancer cell


title: 1586V112211_IFN

value: IFN-beta stimulated


title: WB5


title: 0980V111611_IFN


title: 0980V111611_FLU


title: 13_19

source_name: Small intestine

value: Small intestine


title: 13_14

source_name: Tonsil

value: Tonsil


title: 13_22

source_name: Prostate

value: Prostate


title: 13_18

source_name: Skin

value: Skin


title: 13_20

source_name: Adrenal gland

value: Adrenal gland


title: 1605V021412_baseline

value: baseline


title: D1

value: CD138+ enriched bone marrow cells


title: 13_4

source_name: Brain (mixed white and gray matter)

value: Brain (mixed white and gray matter)

value: healthy


title: 13_13

source_name: Pancreas

value: Pancreas


title: WB2


title: 13_11

source_name: Stomach

value: Stomach


title: 13_ 2

source_name: Colon

value: Colon


title: WB1


title: Input_DMSO

description:
Cells treated with DMSO.
Fragmented genomic DNA

value: Low passages (6-10)

value: DMSO


title: Input_shNONT

value: Non-targeting


title: MLL3_shMLL3

value: Breast cancer cell

value: anti-MLL3 (homemade)


title: H3K27Ac_E2

description:
Cells treated with E2.
Fragmented genomic DNA

value: anti-H3k27Ac (Cell Signaling Technology)


title: 0719V110211_FLU

source_name: monocyte-derived dendritic cells, influenza stimulated

value: monocyte-derived dendritic cells

value: influenza stimulated


title: MLL3_shNONT


title: Input_E2


title: 15_2

value: Small intestine


title: 15_1

value: Skin


title: 14_4

value: Prostate


title: 1436V110311_baseline

source_name: monocyte-derived dendritic cells, baseline

value: baseline


title: H3K27Ac_DMSO

source_name: MCF7 cells


title: H3K4me1_E2

value: anti-H3K4me1 (homemade)


title: 1131V102711_IFN

source_name: monocyte-derived dendritic cells, IFN-beta stimulated

value: healthy

value: IFN-beta stimulated


title: 1131V102711_baseline


title: 14_1


title: 1436V110311_FLU


title: 14_2

source_name: Small inestine

value: Small inestine


title: 14_3

value: Stomach


title: 16_7

source_name: Ovary

value: Ovary


title: 1131V102711_FLU


title: MLL3_DMSO

value: Low passages (6-10)

value: DMSO


title: 16_10


title: MLL3_E2

value: Breast cancer cell


title: 16_9


title: 16_6

source_name: Mammary gland

value: Mammary gland


title: 1436V110311_IFN


title: TET2_NTD_Tamoxifen

description:
Cells with wild type TET2 treated with Tamoxifen.
Fragmented genomic DNA

value: Wild type TET2

value: Tamoxifen

value: anti-TET2_NTD (homemade)


title: 16_12

value: Tonsil


title: 1458V092711_IFN

value: monocyte-derived dendritic cells


title: 16_11


title: H3K4me1_DMSO


title: 1478V020812_IFN


title: 16_13

source_name: Uterus (myometrium)

value: Uterus (myometrium)


title: 16_3

source_name: Cervix

value: Cervix


title: 1458V092711_FLU

value: influenza stimulated


title: H3K4me3_E2

description:
Cells with wild type TET2 treated with E2.
Fragmented genomic DNA

value: anti-H3K4me3 (homemade)


title: TET2_NTD_DMSO

description:
Cells with wild type TET2 treated with DMSO.
Fragmented genomic DNA


title: 16_4

source_name: Kidney

value: Kidney

value: healthy


title: 0719V110211_IFN

value: IFN-beta stimulated


title: H3K4me3_DMSO


title: 16_1

value: Pancreas


title: 12_16

source_name: Bladder

value: Bladder


title: ERa_DMSO

value: Low passages (6-10)

value: DMSO

value: anti-ERa (Santa Cruz Biotechnology, sc-543)


title: 12_11

value: Stomach


title: 12_14

source_name: Tonsil


title: 1411V110311_baseline

value: baseline


title: TET2_MCF7_TET2_KO

value: Breast cancer cell

value: TET2 knockout

value: TET2_NTD (homemade)


title: 12_17

source_name: Skin

value: Skin


title: 12_13


title: 12_19

value: Small inestine


title: 1170V042011_baseline

value: monocyte-derived dendritic cells


title: 1170V042011_IFN


title: 12_18

source_name: Skeletal muscle

value: Skeletal muscle


title: a-TET2-NTD

description:
Cells with wild type TET2.
Fragmented genomic DNA

value: Wild type TET2


title: TET2_MCF7_TET2_WT


title: 16_5

source_name: Liver

value: Liver

value: healthy


title: 1411V110311_IFN

value: IFN-beta stimulated


title: ERa_E2


title: 12_20

source_name: Adrenal gland

value: Adrenal gland


title: Input for MCF7_TET2_KO_E2

description:
Cells with TET2 knockout treated with E2.
Fragmented genomic DNA

value: Low passages (6-10)


title: 12_6

source_name: Lung

value: Lung


title: 12_15

value: Mammary gland


title: 1331V012412_baseline


title: 1411V110311_FLU

source_name: monocyte-derived dendritic cells, influenza stimulated

value: influenza stimulated


title: 1478V020812_FLU


title: 12_9

value: Cervix


title: 12_4_5

source_name: Brain (mixed white and gray matter)

value: Brain (mixed white and gray matter)


title: 12_10

source_name: Esophagus

value: Esophagus


title: 12_7

value: Uterus (myometrium)


title: 12_8

value: Ovary


title: Input for MCF7_TET2_KO_DMSO

description:
Cells with TET2 knockout treated with DMSO.
Fragmented genomic DNA

source_name: MCF7 cells

value: Breast cancer cell

value: TET2 knockout

value: DMSO


title: 1331V012412_IFN

source_name: monocyte-derived dendritic cells, IFN-beta stimulated

value: monocyte-derived dendritic cells


title: ER-a_MCF7_TET2_KO_DMSO

value: anti-ERa (Santa Cruz Biotechnology, sc-543)


title: 12_2

source_name: Colon

value: Colon

value: healthy


title: 12_12

source_name: Thyroid gland

value: Thyroid gland


title: 8_13

source_name: Pancreas

value: Pancreas


title: 8_6

value: Lung


title: 8_10


title: 1272V110111_baseline

source_name: monocyte-derived dendritic cells, baseline

value: baseline


title: ER-a_MCF7_TET2_KO_E2

value: Low passages (6-10)


title: Input for MCF7_TET2_WT_E2

value: Wild type TET2


title: ER-a_MCF7_TET2_WT_E2


title: 8_20

value: Adrenal gland


title: 8_12


title: 1660V012412_FLU

value: influenza stimulated


title: Input for MCF7_TET2_WT_DMSO


title: 1419V110111_baseline


title: 1660V012412_IFN

value: IFN-beta stimulated


title: RNA-Seq in CH12 cells – ZMYND8 KO2 clone, activated rep3

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

data_processing:
For RNA-Seq data analysis, reads were pseudo-aligned to an index created from the Ensembl mouse GRCm38.p5 assembly and custom annotations of Igh locus features. Transcript-level abundances were quantified using kallisto v0.43.0 and subsequently summarized to the gene-level using the R package tximport. Differential gene expression analysis was performed using DESeq2.
Genome_build: GRCm38.p5 and custom annotations of Igh locus features.  The FASTA of the IgH_germline_regions is available on the series record.
Supplementary_files_format_and_content: TSV files containg transcript abundancies in TPM

organism: Mus musculus

source_name: CH12 cells

growth_protocol: Samples used in RNA-Seq were cultured in activated and unactivated conditions for 48 h.

extract_protocol:
Cultured cells were collected by centrifugation and RNA was extracted with AllPrep DNA/RNA Mini Kit (Qiagen). Ribosomal RNA was depleted using Ribo-Zero Gold rRNA Removal Kit (Illumina).
Libraries were prepared with TruSeq Stranded Total RNA Library Prep Kit (Illumina). Three biological repeats were performed and run in two lanes on the same flow cells on NextSeq High Output 75 SR (Illumina).

value: CH12 cells

tag: genotype

value: ZMYND8 KO


title: ER-a_MCF7_TET2_WT_DMSO

value: Breast cancer cell


title: 8_1

source_name: Kidney

value: Kidney


title: 8_11

source_name: Stomach

value: Stomach


title: 8_14

source_name: Tonsil

value: Tonsil


title: 1660V012412_baseline

value: monocyte-derived dendritic cells


title: 8_18

source_name: Skin

value: Skin

value: healthy


title: 8_17

source_name: Skeletal muscle

value: Skeletal muscle


title: 8_4_5

value: Brain (mixed white and gray matter)


title: 1419V110111_FLU


title: 1105V111511_IFN


title: RNA-Seq in CH12 cells – ZMYND8 KO2 clone, activated rep2


title: 8_3

source_name: Liver

value: Liver


title: RNA-Seq in CH12 cells – ZMYND8 KO2 clone, activated rep1


title: 8_19

source_name: Small inestine

value: Small inestine


title: 1170V042011_FLU

source_name: monocyte-derived dendritic cells, influenza stimulated


title: 1419V110111_IFN


title: 6_16

source_name: Bladder

value: Bladder


title: RNA-Seq in CH12 cells – ZMYND8 KO2 clone, unactivated rep3


title: 4_13

value: Pancreas


title: 5_16


title: 4_12

value: Thyroid gland


title: 4_14


title: 4_17


title: RNA-Seq in CH12 cells – ZMYND8 KO2 clone, unactivated rep1


title: 0839V112211_IFN

value: IFN-beta stimulated


title: 1559V111511_IFN


title: 4_16


title: RNA-Seq in CH12 cells – ZMYND8 KO1 clone, activated rep3

value: CH12 cells


title: 1559V111511_FLU

value: influenza stimulated


title: 3_19


title: 8_2

value: Colon


title: 3_17


title: Subcutaneous innate lymphoid cells

city: Bethesda

first: Tetsuro

last: Kobayashi

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm12N256

institute: NIAMS/NIH

data_processing:
CellRanger (v 2.2.0, 10X Genomics) pipelines were used for demultiplexing base calls into Fastq, filtering, barcode counting and filtering, UMI counting and aligment with reference mouse genome mm10.
The quality control, normalization, linear regression of number of UMIs and scaling were performed using Seurat (v2.3.4).
The merging of the 3 datasets (Epidermis_ILC, dermis_ILC and Subcutis_ILC), cell clustering (8 PC, resolution 0.5) and gene expression quantification analysis were performed using Seurat (v2.3.4).
Genome_build: mm10
Supplementary_files_format_and_content: filtered gene expression matrices with cells identified as cell barcodes and the values representing gene UMI counts

source_name: Subcutaneous innate lymphoid cells

extract_protocol: samples were prepared using 10X Genomics Chromium 3' kit (v2)

tag: strain

tag: tissue compartment

value: subcutaneous

value: innate lymphoid cells

tag: age

value: 8 weeks

value: Wild-type


title: 3_20

source_name: Adrenal gland

value: Adrenal gland


title: 1331V012412_FLU

tag: donor id

value: healthy

value: monocyte-derived dendritic cells


title: 3_16


title: RNA-Seq in CH12 cells – ZMYND8 KO1 clone, unactivated rep3

value: ZMYND8 KO


title: RNA-Seq in CH12 cells – ZMYND8 KO2 clone, unactivated rep2


title: 0760V110211_IFN

source_name: monocyte-derived dendritic cells, IFN-beta stimulated

tag: disease state


title: RNA-Seq in CH12 cells – ZMYND8 KO1 clone, unactivated rep2

tag: cell type


title: Dermal innate lymphoid cells

source_name: Dermal innate lymphoid cells

value: Skin

value: dermis


title: 3_14

value: Tonsil


title: Epidermal innate lymphoid cells

source_name: Epidermal innate lymphoid cells

value: epidermis


title: 0760V110211_baseline

tag: condition

value: baseline


title: 1679V020912_FLU


title: 3_12

source_name: Thyroid gland

value: Thyroid gland


title: 3_11

value: Stomach


title: RNA-Seq in CH12 cells – ZMYND8 KO1 clone, unactivated rep1

value: CH12 cells


title: RNA-Seq in CH12 cells – ZMYND8 KO1 clone, activated rep2


title: IGTB1553_unstim_Exp1

source_name: monocyte-derived dendritic cells, baseline


title: RNA-Seq in CH12 cells – WT clone, activated rep 3

source_name: CH12 cells

value: WT


title: 1679V020912_IFN

value: IFN-beta stimulated


title: 0760V110211_FLU

value: influenza stimulated


title: RNA-Seq in CH12 cells – WT clone, activated rep 2


title: RNA-Seq in CH12 cells – ZMYND8 KO1 clone, activated rep1


title: 0575V081111_IFN


title: RNA-Seq in CH12 cells – WT clone, activated rep 1


title: 1679V020912_baseline


title: RNA-Seq in CH12 cells – WT clone, unactivated rep3


title: 2_17

value: Skeletal muscle


title: 1135V072711_IFN


title: 2_19

value: Small inestine


title: RNA-Seq in CH12 cells – WT clone, unactivated rep2


title: 2_20

value: Adrenal gland


title: RNA-Seq in CH12 cells – WT clone, unactivated rep1


title: 0809V082411_IFN

value: healthy


title: 1433V080211_IFN

value: monocyte-derived dendritic cells


title: 2_12


title: 1654V022112_IFN


title: RNA-Seq in CH12 cells – WT, activated rep3


title: 2_11


title: 2_2

source_name: Colon

value: Colon


title: 0916V111011_baseline


title: 0916V111011_FLU


title: RNA-Seq in CH12 cells – WT, activated rep2


title: 3_2


title: 0916V111011_IFN


title: 2_6

source_name: Lung

value: Lung


title: RNA-Seq in CH12 cells – WT, unactivated rep 3


title: 0109V022912_FLU


title: RNA-Seq in CH12 cells – WT, activated rep1


title: RNA-Seq in CH12 cells – WT, unactivated rep 1


title: RNA-Seq in CH12 cells – WT, unactivated rep 2


title: 1_20


title: 1_19


title: 1_14

source_name: Tonsil


title: ZMYND8 ChIP-Seq in primary B cells – Cd19-Cre/+ rep3

data_processing:
ChIP-Seq for ZMYND8 and RNA Pol II analysis were performed as  it follows.  FASTQ files were aligned against mouse genome (mm10) using BWA mem. Processing and peak-calling of ChIP-Seq data were accomplished with HOMER ChIP-Seq program.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig containing ChIP-Seq profiles

source_name: Primary B cells

extract_protocol:
ChIP-Seq for ZMYND8 and RNA Pol II were performed as it follows. Splenocytes (72 h post-activation) or CH12 cells (48 h post-activation) were fixed with 1% (16% Formaldehyde Methanol-free, Thermo Scientific) at 37°C for 10 min followed by addition of 1/20 volume of 2.5 M glycine (dissolved in PBS pH 7.4) and swirling. Fixed cells were washed with cold PBS,centrifuged and aliquoted. 20 million cells were resuspended in 100 ul of 1% SDS of RIPA buffer supplemented with Complete EDTA free proteinase inhibitor (Roche) and sonication was performed with a Covaris S220 Focused Ultrasonicator at peak value 105, duty factor 5, cycle/burst 200 for 10 minutes. After sonication, samples were adjusted to 0.1% SDS final concentration by diluting with non-SDS containing RIPA buffer. Chromatin fragments were then pre-cleaned by incubation with Dynabeads Protein A (Invitrogen) with rotation at 4°C for 1 h, and immunoprecipitated with antibody-bound Dynabeads. 10 ug antibodies specific for ZMYND8 (Sigma-Aldrich) or RNA Pol II polymerase (4H8, Abcam) were used for each sample.
DNA libraries were prepared by using Illumina compatible adaptors (Bio Scientific) and sequenced on an Illumina NextSeq 500 Sequencer.

value: Splenocytes

tag: antibody

value: ZMYND8 (HPA020949, Sigma-Aldrich)


title: 1_17

source_name: Skeletal muscle


title: ZMYND8 ChIP-Seq in primary B cells – Cd19-Cre/+ rep2


title: 1_12


title: Pol II ChIP-Seq in primary B cells – ZMYND8-F/F Cd19-Cre/+ rep 3

value: Cd19-Cre/+ ZMYND8-F/F

value: anti-RNA Pol II polymerase (4H8, Abcam)


title: ZMYND8 ChIP-Seq in primary B cells – Cd19-Cre/+ rep1


title: 1_2


title: Pol II ChIP-Seq in primary B cells – ZMYND8-F/F Cd19-Cre/+ rep 2


title: Thy_853

city: London

first: Rodney

middle: Peter

last: DeKoter

state: Ontario

address: 1151 Richmond St

department: Microbiology and Immunology

country: Canada

institute: Western University

data_processing:
Data analysis was performed according to Trapnell, et al; 2012 using the tools available on Galaxy suite.
Standard Illumina sequencing adaptors (AGATCGGAAGAGC) and short reads were removed using Trim Galore! V0.2.8.1 in mate-paired mode, Trim low quality: 20, Maximum allowed error rate: 0.1, discard reads that became shorter than length: 20, RRBS specific settings: default.
Trimmed FASTQ files were aligned to the mouse genome (MM10) using the TopHat2 v2.0.9 in mate-paired mode, Mean inner distance between mate pairs: 140, std. dev for distance between mate pairs: 30.
Assembled transcript abundance  was determined using Cufflinks/CuffDiff v2.1.1. .Gff files for mouse transcripts were aquired from mouse UCSC mm10
Genome_build: mm10
Supplementary_files_format_and_content: .csv contains transcript abundance

source_name: Thymus

extract_protocol:
RNA was isolated from mouse thymic leukemias using RNeasy kit from Qiagen. Shortly, thymuses were removed from diseased mice and homogenized. Red blood cells were removed using ACK buffer. Lymphocytes were pellet and RNA was extracted.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Leukemic


title: Pol II ChIP-Seq in primary B cells – Cd19-Cre/+ rep2


title: Pol II ChIP-Seq in primary B cells – Cd19-Cre/+ rep1


title: MN_2

source_name: Mammary gland

value: Mammary gland


title: MN_3


title: Pol II ChIP-Seq in primary B cells – Cd19-Cre/+ rep3


title: ZMYND8 ChIP-Seq in CH12 cells – WT rep1

value: CH12 cells


title: 0109V022912_IFN


title: ZMYND8 ChIP-Seq in CH12 cells – WT rep2

value: WT


title: S_6

source_name: Stomach

value: Stomach


title: S_2


title: S_5


title: Thy_857


title: S_4


title: E_6

source_name: Esophagus

value: Esophagus


title: S_3


title: S_1


title: Thy_854


title: Pol II ChIP-Seq in CH12 - ZMYND8 KO, unactivated

value: ZMYND8 KO


title: ZMYND8 ChIP-Seq in CH12 cells – ZMYND8 KO1


title: 1_11


title: Pol II ChIP-Seq in CH12 - ZMYND8 KO, activated


title: Pol II ChIP-Seq in CH12 - Rif1–KO, activated

value: Rif1 KO


title: MN_1


title: E_3


title: Pol II ChIP-Seq in CH12 - WT, activated rep1


title: E_4


title: Pol II ChIP-Seq in primary B cells – ZMYND8-F/F Cd19-Cre/+ rep 1


title: E_2


title: E_1


title: ZMYND8 ChIP-Seq in CH12 cells – ZMYND8 KO2


title: P_4

source_name: Prostate

value: Prostate


title: E_5

value: healthy


title: P_3


title: O_1

source_name: Ovary

value: Ovary


title: Cer_5

source_name: Cervix, endometrium

value: Cervix, endometrium


title: paired ccRCC normal tissue, P18

type: RNA

city: Houston

first: Yuanqing

last: Ye

state: TX

address: 1155 Pressler st

department: Epidemiology

institute: UT MD Anderson Cancer Center

description: SAMPLE 36

hyb_protocol: Standard NanoString nCounter hybridization protocol.

scan_protocol: Standard NanoString nCounter scan protocol using digital analyzer.

data_processing: The data were normalized to the average expression level of the 100 most-expressed miRNAs across all samples.

source_name: paired ccRCC normal tissue

label_protocol: Standard NanoString nCounter label protocol.

extract_protocol:
Total RNAs were isolated from the 18 pairs of ccRCC tumor and adjacent normal tissues using miRNeasy Mini Kits (Qiagen) according to manufacturer’s protocol.
ligation protocol: 80 to 100 ng of total RNA was used for sample preparation. Preparation of samples involves ligation of a specific DNA tag onto the 3’end of each mature miRNA according to manufacturer's instructions.

tag: subject status

value: clear cell renal cell carcinoma (ccRCC)

tag: subject id

tag: subject ethnicity

value: non-Hispanic white patient

value: kidney

tag: tissue type

value: normal tissue

tag: sample type

value: fresh frozen tissue


title: paired ccRCC normal tissue, P16

description: SAMPLE 34

tag: tissue


title: paired ccRCC normal tissue, P17

description: SAMPLE 35


title: O_5

tag: disease


title: Cer_1


title: paired ccRCC normal tissue, P14

description: SAMPLE 32


title: paired ccRCC normal tissue, P15

description: SAMPLE 33


title: P_2


title: paired ccRCC normal tissue, P12

description: SAMPLE 30


title: paired ccRCC normal tissue, P11

description: SAMPLE 29


title: paired ccRCC normal tissue, P13

description: SAMPLE 31


title: Lu_5

value: Lung


title: Lu_7


title: paired ccRCC normal tissue, P10

description: SAMPLE 28


title: Lu_8


title: paired ccRCC normal tissue, P8

description: SAMPLE 26


title: paired ccRCC normal tissue, P9

description: SAMPLE 27


title: paired ccRCC normal tissue, P7

description: SAMPLE 25


title: Lu_4


title: Lu_3


title: paired ccRCC normal tissue, P5

description: SAMPLE 23


title: B_6

source_name: Brain (mixed white and gray matter)

value: Brain (mixed white and gray matter)


title: paired ccRCC normal tissue, P4

description: SAMPLE 22


title: paired ccRCC normal tissue, P6

description: SAMPLE 24


title: B_5


title: B_4


title: Dnmt3L_mKO_3

first: Yue

last: Lu

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Basecalling was done by Illumina HiSeq Control Software (version 3.3.76).
The adapters were removed from the 3’ends of the reads by Trim Galore! (version 0.4.1) and cutadapt (version 1.9.1).
Then the reads were mapped to mouse genome mm10 by the bisulfite converted read mapper Bismark (version v0.16.1) and Bowtie (version 1.1.2).
The methylation percentages for the CpG sites were calculated by the bismark_methylation_extractor script from Bismark and an in-house Perl script.
Genome_build: mm10
Supplementary_files_format_and_content: Methylation calling for each CpG site with at least 1x coverage. The file is in methylkit input format: chrBase, chr, base, strand, coverage, freqC, freqT.

source_name: Dnmt3Lz+/m- (maternal KO), ESC, male (XY)

growth_protocol: mESCs were cultured in regular ES medium containing serum and LIF.

extract_protocol:
Genomic DNA was extracted with phenol-chloroform treatment and precipitated with ethanol.
Genomic DNA was digested with MspI, end-repaired and A-tailed, and Illumina-compatible cytosine-methylated adaptor was ligated to the enzyme-digested DNA. Size-selected fragments were bisulfite-converted, and library preparation was done by PCR amplification.

value: Embryonic stem cell (derived from blastocyst)

value: Dnmt3Lz+/m- (maternal KO)

tag: gender

value: male


title: paired ccRCC normal tissue, P2

description: SAMPLE 20


title: B_3


title: Dnmt3L_mKO_1

tag: genotype


title: B_1


title: B_2


title: Li_6

source_name: Liver

value: Liver


title: Dnmt3L_mKO_2

tag: strain


title: paired ccRCC tumor tissue, P16

description: SAMPLE 16

source_name: paired ccRCC tumor tissue

value: tumor tissue


title: Dnmt3L_KO_1

source_name: Dnmt3L-/- (zygotic KO), ESC, male (XY)

value: Dnmt3L-/- (zygotic KO)


title: Li_4


title: Li_5


title: Dnmt3L_KO_2


title: Li_3


title: WT_3

source_name: Wild-type, male (XY)

value: Wild-type


title: WT_1


title: Li_2

value: healthy


title: paired ccRCC tumor tissue, P12

description: SAMPLE 12


title: WT_2


title: paired ccRCC tumor tissue, P15

description: SAMPLE 15


title: paired ccRCC tumor tissue, P14

description: SAMPLE 14


title: paired ccRCC normal tissue, P3

description: SAMPLE 21


title: paired ccRCC tumor tissue, P13

description: SAMPLE 13


title: Li_1


title: paired ccRCC normal tissue, P1

description: SAMPLE 19


title: Dnmt3L_mzKO_3

source_name: Dnmt3L-/- (maternal & zygotic KO), ESC, male (XY)

value: Dnmt3L-/- (maternal & zygotic KO)


title: paired ccRCC tumor tissue, P11

description: SAMPLE 11


title: paired ccRCC tumor tissue, P10

description: SAMPLE 10


title: paired ccRCC tumor tissue, P17

description: SAMPLE 17


title: paired ccRCC tumor tissue, P18

description: SAMPLE 18


title: Dnmt3L_mzKO_2


title: С_6

source_name: Colon, epithelium

value: Colon, epithelium


title: С_5


title: Dnmt3L_mzKO_1


title: С_4


title: С_3


title: paired ccRCC tumor tissue, P9

description: SAMPLE 9

value: clear cell renal cell carcinoma (ccRCC)


title: paired ccRCC tumor tissue, P8

description: SAMPLE 8

value: non-Hispanic white patient


title: C_2


title: paired ccRCC tumor tissue, P7

description: SAMPLE 7

value: kidney


title: paired ccRCC tumor tissue, P6

description: SAMPLE 6


title: paired ccRCC tumor tissue, P5

description: SAMPLE 5


title: K_5

source_name: Kidney

value: Kidney


title: K_6


title: С_1


title: paired ccRCC tumor tissue, P4

description: SAMPLE 4

value: fresh frozen tissue


title: K_4


title: paired ccRCC tumor tissue, P1

description: SAMPLE 1


title: K_3


title: paired ccRCC tumor tissue, P2

description: SAMPLE 2


title: K_2


title: K_1


title: Epicardial fat, Case, Biological Rep 8

city: Worcester

first: Timothy

middle: P

last: Fitzgibbons

address: 55 Lake Avenue North

department: Molecular Medicine

institute: University of Massachusetts Medical School

description: epicardial fat biopsied adjacent to the right coronary artery

hyb_protocol: The labeled mix was hybridized to Human Gene 1.0 ST arrays (Affmetrix) in the GeneChip hybridization oven 640 (Affymetrix) overnight at the UMASS Medical School Genomics Core facility

scan_protocol: The arrays were scanned with a GeneChip scanner 7G (Affymetrix)

data_processing: The probe cell intensity data was processed with Transcriptome Analysis Console 4.0 to generate CHP files using the Robust Multichip Analysis (RMA)-sketch algorithm workflow

label: biotin

source_name: Epicardial fat, Case, Biological Rep 8

label_protocol: Single stranded cDNA was synthesized using 500 ng total RNA and labeled using the GeneChip WT Plus Reagent kit

extract_protocol: Samples were flash frozen in liquid nitrogen and then total RNA was extracted with QIAGEN mini lipid kits.  Samples were analyzed on an Agilent Bioanalyzer.  Only samples with a RIN>8 were used.

value: epicardial fat

value: M

value: coronary disease


title: Epicardial fat, Case, Biological Rep 7

source_name: Epicardial fat, Case, Biological Rep 7


title: Epicardial fat, Case, Biological Rep 3

source_name: Epicardial fat, Case, Biological Rep 3


title: Epicardial fat, Case, Biological Rep 9

source_name: Epicardial fat, Case, Biological Rep 9

value: F


title: Epicardial fat, Control, Biological Rep 10


title: Epicardial fat, Case, Biological Rep 4

source_name: Epicardial fat, Case, Biological Rep 4


title: Epicardial fat, Case, Biological Rep 1

source_name: Epicardial fat, Case, Biological Rep 1


title: Epicardial fat, Case, Biological Rep 6

source_name: Epicardial fat, Case, Biological Rep 6


title: Epicardial fat, Case, Biological Rep 2

source_name: Epicardial fat, Case, Biological Rep 2


title: paired ccRCC tumor tissue, P3

description: SAMPLE 3


title: Epicardial fat, Case, Biological Rep 5

source_name: Epicardial fat, Case, Biological Rep 5


title: hek_trex4039_mo113

city: Boston

first: Andrew

middle: Ryan

last: Field

state: MA

address: 45 Shattuck St

department: BCMP

institute: Harvard Medical School

description: CRISPR activation with 5 sgRNAs targeting transiently expressed lncRNA 4039

data_processing:
Paired-end Illumina reads were trimmed from the 3’ end of read1 and read2 to 90x90bp. Bowtie2 v2.2.1 was used with the “--very-sensitive” parameter to filter reads against the repeatMasker library for each respective species which were removed from further analysis.
STAR v2.5.1b was used to map RNA-seq reads to hg19 (human, Genome Reference Consortium GRCh37, 2009). STAR was run with the default parameters with the following exceptions: --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, and --alignMatesGapMax 1000000. STAR alignments were converted to genomic position coverage with the bedtools command genomeCoverageBed -split.
DESeq2 v1.14.1 was used to provide basemean expression values and differential expression analysis between each CRISPR activated lncRNA and the non-targeting controls using custom Cufflinks generated transcript annotations (provided in GSE106245).
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited files include basemean values calculated by DESeq

molecule: polyA RNA

growth_protocol: HEK293FT cells were cultured with DMEM+GlutaMAX (ThermoFIsher) supplemented with 10% FBS. Each well of a 6-well plate was seeded with 500k cells the day prior to transfection.

extract_protocol:
RNA was extracted using TRIzol Reagent (ThermoFisher) and purified over Direct-zol columns (ZYMO).
RNA-seq libraries were prepared in biological triplicates with the NEXTflex Rapid Directional qRNA-Seq Library Prep Kit (PerkinElmer).

treatment_protocol: HEK293FT cells were co-transfected with plasmids containing dCas9-VP64 (addgene #61425), MS2 + p65 + HSF1 (addgene #61426), and 5 custom guide RNAs (details in manuscript) either targeting 50-450bp upstream of a lncRNA transcription start site or containing non-targeting sequence. Cells were treated with 2ug/mL puromycin at 24 hours and harvested for RNA at 48 hours post transfection.

tag: sgrna target

tag: cell line


title: hek_trex4039_mo114


title: hek_trex4039_mo115


title: hek_trex5008_mo112

description: CRISPR activation with 5 sgRNAs targeting transiently expressed lncRNA 8168


title: Epicardial fat, Control, Biological Rep 7


title: hek_trex0108_mo108

description: CRISPR activation with 5 sgRNAs targeting transiently expressed lncRNA 108


title: hek_trex5008_mo111


title: hek_trex0108_mo107


title: Epicardial fat, Control, Biological Rep 8


title: hek_trex0108_mo109


title: hek_scramxxx_mo103

description: Negative control transfection using 5 non-targeting sgRNAs for CRISPR activation

value: non-targeting negative control


title: hek_trex8168_mo104

description: CRISPR activation with 5 sgRNAs targeting transiently expressed lncRNA 5008


title: hek_trex5008_mo110


title: hek_trex8168_mo106


title: hek_scramxxx_mo101


title: Epicardial fat, Control, Biological Rep 9


title: hek_trex8168_mo105


title: hek_scramxxx_mo102


title: Epicardial fat, Control, Biological Rep 6


title: Subcutaneous fat, Case, Biological Rep 8

description: subcutaneous fat from sternum

value: subcutaneous fat


title: Epicardial fat, Control, Biological Rep 4


title: Epicardial fat, Control, Biological Rep 3


title: Epicardial fat, Control, Biological Rep 2


title: WT-2

city: Philadelphia

first: Wayne

middle: W

last: Hancock

state: PA

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

hyb_protocol: 10 microgram of labeled aRNA was fragmented, and 6.5 microgram of the fragmented aRNA was hybridized to the Affymetrix Mouse 430A_2 chips.  Hybridization conditions were 16hrs at 45C.

scan_protocol: The chips were washed using Fluidics protocol midiEuk2v3_450 on an Affymetrix GeneChip Fluidics Station 450 and scanned on an Affymetrix Genechip Scanner.

data_processing: Array data were analyzed using MAYDAY software (http://it.inf.uni-tuebingen.de/?page_id=248) version 2.12. Array data were subjected to robust multiarray average normalization. To assess differential gene expression, fold changes of up- and downregulated genes were calculated, and significance assessed via Significance Analysis of Microarrays (SAM) using 100 permutations and false discovery rate <0.1, and data with >1.5-fold differential expression were included in the analysis.

source_name: Wild type C57BL6 (regular chow, 25% kcal from fat)

label_protocol: 100ng of totalRNA was labeled using Ambion's MessageAmp Premier RNA Amplification Kit (PN:4383452)

extract_protocol: Whole livers from 8 to 12-week-old female HDAC6–/–, HDAC9–/– and wild type mice C57BL/6 with or without high fat diet were harvested, and RNA was extracted using RNeasy kits (Qiagen, Hilden, Germany). RNA integrity and quantity were analyzed by photometry (Nanodrop 2000, Thermo Fischer).

value: Whole liver

value: female

tag: age

value: 8-12 weeks

value: Wild type


title: WT-1

description: Ambion's MessageAmp Premier RNA Amplification Kit (PN:4383452)


title: Tumor_OV170

type: genomic

city: Gothenburg

first: Hanna

last: Engqvist

address: Medicinaregatan 1G

country: Sweden

institute: University of Gothenburg

description: Genomic DNA was extracted from primary ovarian carcinomas was genotyped using Infinum Omni 2.5-8 v1.3 Genotyping BeadChips (Illumina)

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina iScan N240 scanning protocol.

data_processing: GenomeStudio software version 2011.1.

label: cy3 and cy5

source_name: Primary invasive ovarian carcinomas

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was isolated from fresh frozen tissue specimens using the Wizard Genomic DNA extraction kit, including proteinase K treatment followed by phenol chloroform purification.

value: Primary invasive ovarian carcinoma

tag: figo stage

value: I


title: Tumor_OV387


title: Epicardial fat, Control, Biological Rep 1


title: OB-3

source_name: Wild type C57BL6 (high fat diet, 60% kcal from fat)


title: Subcutaneous fat, Case, Biological Rep 5

description: subcutaneous fat from sternum


title: Tumor_OV364


title: Subcutaneous fat, Case, Biological Rep 1

description: subcutaneous fat from sternum


title: Subcutaneous fat, Case, Biological Rep 7

description: subcutaneous fat from sternum


title: Epicardial fat, Control, Biological Rep 5


title: Tumor_OV346


title: Tumor_OV155

value: II


title: Tumor_OV340


title: WT-3


title: Subcutaneous fat, Control, Biological Rep 9

description: subcutaneous fat from sternum


title: Subcutaneous fat, Case, Biological Rep 6

description: subcutaneous fat from sternum


title: Subcutaneous fat, Case, Biological Rep 2

description: subcutaneous fat from sternum


title: Subcutaneous fat, Control, Biological Rep 8

description: subcutaneous fat from sternum


title: Tumor_OV336


title: Tumor_OV326


title: OB-2


title: OB-1


title: Subcutaneous fat, Control, Biological Rep 6

description: subcutaneous fat from sternum


title: H6-3

source_name: HDAC6 knock out

value: HDAC6 knock-out


title: Hela_cell_RNC_seq

city: Guangzhou

first: Li

last: Dehua

state: Guangdong

address: Huangpu avenue west NO.601

country: China

institute: Jinan University

data_processing:
library strategy: translatome sequencing (RNC-seq)
Illumina Casava1.7 software used for basecalling.
Hela_RNC reads were aligned to the Human_refseq_mrna.fasta and 97H_RNC reads and LM3_RNC reads were aligned to the Human_refseq_mrna.fasta using FANSe3 with  configurations: 1.-L50 --all --rename -E3 --indel(Hela_RNC reads). 2.-L150 --all --rename -E7(97H_RNC reads and LM3_RNC reads)
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.
The 97HRNC and LM3RNC mutation sites had been cover more than 10 reads and had pass the chi square test.
Supplementary_files_format_and_content: The *-rpkm-SVmerge.txt files contain  RPKM data. The *mutation.txt are the sites lists of single amion acid polymorphisms. For this example:ENST00000411463 185:R::K 347:V::M 403:L::R , there is two column were separated with tab, so the first column is ENST00000411463 which is a transcript's name.  And then the second column is 185:R::K 347:V::M 403:L::R , it indicates that ENST00000411463 has three sites of single amion acid polymorphisms. The three sites are 185,347 and 403, and the three amino acid substitution events are R is replaced with K, V is replaced with M, L is replaced with R. The different single amion acid polymorphisms sites are separated by blank.

source_name: Hela cell lines

growth_protocol: Hela and MHCCLM3 and MHCC97H cells were cultured in 75 cm2 culture flasks in the complete medium DMEM (Life Technologies, Carlsbad, CA, USA) supplemented with 10% FBS (Life Technologies, Carlsbad, CA, USA), 100U/mL penicillin/ 0.1mg/mL streptomycin (GBCBIO Technologies Inc, Guangzhou, China), and 10 μg/mL ciprofloxacin. All cells were cultured in a 5% CO2 incubator at 37 ℃ and were negative for mycoplasma detection by PCR analysis.

extract_protocol:
Hela and MHCCLM3 and MHCC97H cells were washed by pre-chilled phosphate buffered saline twice and addition of 2 ml cell lysis buffer [1% Triton X-100 in ribosome buffer (RB buffer) [20 mM HEPES-KOH (pH 7.4), 15 mM MgCl2, 200mM KCl, 100 mg/ml cycloheximide and 2mM dithiothreitol]. After 30-min ice-bath, cell lysates were scraped and transferred to pre-chilled 1.5 ml tubes. Cell debris was removed by centrifuging at 16 200 g for 10 min at 4C. Supernatants were transferred on the surface of 20 ml of sucrose buffer (30% sucrose in RB buffer). RNCs were pelleted after ultra-centrifugation at 185000 g for 5h at 4C. Then RNC-RNA were isolated by using TRIzol RNA extraction reagent (Ambion, Austin, TX), following the manufacturer’s instructions.
The Hela RNC-mRNA libraries were prepared according to BGI-MGIEasy's instructions accompanying the MGIEasy mRNA Library Prep Kit V2 (Part# 85-05536-01). The polyA+ mRNA was selected using NEB Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). The mRNA libraries were constructed using the MGIEasy mRNA Library Prep Kit V2 for MGI (BGISEQ, Shen Zhen, China) following the manufacturer’s protocol. The MHCC97H RNC-mRNA  libraries were prepared according to VAHTS mRNA-seq V3 Library Prep Kit (Part# NR611-01/02). The polyA+ mRNA was selected using NEB Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). The mRNA libraries were constructed using the VAHTS mRNA-seq V3 Library Prep Kit for Illumina® (Vazyme, Nanjing, China) following the manufacturer’s protocol.
RNA-Seq (Hela cell RNC-mRNA sequencing were performed on a BGISEQ-500 sequencer for single-end 50, and the MHCC97H RNC-mRNA sequencing were performed on an Illumina HiSeq X Ten sequencer for paired-end 150.

treatment_protocol: Hela and MHCCLM3 and MHCC97H cells were cultured in culture flasks after growth to 80-90% confluence, then were pre-treated with 100 mg/ml cycloheximide for 15 min.

value: Hela

tag: cell type

value: Cervical cancer cell

tag: state

value: steady


title: PMN1

status: Public on Oct 03 2018

city: Omaha

first: Sean

last: West

state: NE

institute: University of Nebraska

data_processing:
Illumina reads were checked for quality and subsequently trimmed using Illumina software.
The resulting paired fastq files were sorted and mapped against the Ensembl GRCm38.p5 primary assembly cDNA library using Salmon v0.8.2 with Quasi indexing and default parameters.
Differential expression was conducted using DESeq2 on counts directly from Salmon output. DESeq2 was used for normalization and statistical modeling.
Genome_build: Ensembl GRCm38.p5 primary assembly cDNA
Supplementary_files_format_and_content: differential expression CSV files include exact DESeq2 output using R write.table(); [sample]_salmon_quant.ensembl.txt contain the same information as Salmon 'quant.sf' files; salmon_gene_counts.ensembl.txt contains the count data for each sample derived from the Salmon 'quant.sf' files

source_name: Neutrophils

growth_protocol: Equal numbers of male and female C57BL/6 mice (8 weeks-old).

extract_protocol:
Mice received a single i.p. injection of 2.5µg EdU (Invitrogen) at day 7 post-infection. Mice were sacrificed 3 h following EdU injection and the amount of EdU incorporation was measured using a PacificBlue™ Click-iT™ Plus Edu Flow Cytometry Assay Kit (Invitrogen).
RNA sequencing libraries were prepared beginning with 250 ng of total RNA using a ScriptSeq Complete Kit – Low Input protocol (Illuminia, San Diego, CA). The RNAseq libraries were denatured with 0.2N NaOH and 1.2 pM of each library was sequenced on a NextSeq500 instrument (Illumina, San Diego, CA).  The libraries were subjected to 75 base pair paired-end sequencing at a depth of 20 million paired reads per sample.

treatment_protocol: An orthopedic-grade K-wire (0.6mm diameter) was inserted into the intramedullary canal of the femur, and a total of 1,000 CFU of S. aureus USA300 LAC 13C was inoculated at the implant tip.

value: Ly6G+Ly6C+CD11b low PMNs

tag: days post infection

tag: agent

value: S. aureus USA300


title: PMN2


title: MONO3

source_name: Monocytes

value: Ly6G-Ly6C+ monocytes


title: Subcutaneous fat, Control, Biological Rep 7

description: subcutaneous fat from sternum

value: M


title: H9-3

source_name: HDAC9 knockout

value: HDAC9 knock-out


title: H9-1


title: Subcutaneous fat, Control, Biological Rep 3

description: subcutaneous fat from sternum

value: subcutaneous fat


title: Subcutaneous fat, Control, Biological Rep 4

description: subcutaneous fat from sternum


title: H6-2

value: Whole liver


title: Subcutaneous fat, Control, Biological Rep 1

description: subcutaneous fat from sternum


title: Tumor_OV315


title: H6-1

value: female


title: Subcutaneous fat, Control, Biological Rep 5

description: subcutaneous fat from sternum

value: F


title: MONO2


title: MDSC4

source_name: Myeloid-Derived Suppressor Cells

value: Ly6G+Ly6C+CD11bhigh MDSCs


title: Subcutaneous fat, Case, Biological Rep 3

description: subcutaneous fat from sternum

value: coronary disease


title: PMN3


title: Subcutaneous fat, Control, Biological Rep 2

description: subcutaneous fat from sternum


title: MDSC2


title: MDSC1


title: MSC_Input1

city: Chengdu

first: Quan

last: Yuan

state: Sichuan

address: 14 Third section, Renmin Nan Road

institute: West China Hospital of Stomatology, Sichuan University

description:
Input RNA
m6A_genes

data_processing:
For RNA-Seq, Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 version 2.0.4 with default parameter.
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.
For m6A-Seq, Reads were aligned to mm9 using tophat
Peak calling was done with MACS2
Genome_build: mm10 for RNAseq, mm9 for m6A-Seq
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: MSCs

growth_protocol: α-MEM (Hyclone) supplemented with 10% fetal bovine serum (Gibco),100 units/ml penicillin (Gibco) and 100 μg/ml streptomycin (Gibco)

extract_protocol:
Total RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® was used with 3 ug of total RNA for the construction of sequencing libraries. mRNA was purified from total RNA. 2ug mRNA was used for the m6A-Seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MSCs were seeded in six-well plates and treated with osteogenic medium containing 50 μg/ml ascorbic acid, 5 mM β-glycerophosphate, and 100nM dexamethasone (all from Sigma) for 2 days

value: bone marrow MSCs

value: wild type


title: MSC_Input2

description:
Input RNA
m6A_genes


title: MSC_m6A_IP1

description:
m6A IP RNA
m6A_genes


title: MSC_m6A_IP2

description:
m6A IP RNA
m6A_genes


title: H9-2

value: 8-12 weeks


title: 1099_met_d10_replicate_2

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

state: Basel

address: Mattenstrasse 28

department: Departement Biomedizin

country: Switzerland

institute: University of Basel

description:
MET
1099_MET_CPM_data.txt
met.d10_2

data_processing:
Base calling was done using Illumina software
Sequenced reads were mapped to MM10 version of mouse genome using RNA-STAR using parameters (outFilterMultimapNmax=10 and outFilterType="BySJout")
Counts are obtained using qcount in qusaR and CPM (counts per million) was computed for each sample
Genome_build: mm10
Supplementary_files_format_and_content: txt file and contains counts as CPM values for each sample

source_name: Breast cancer cells

growth_protocol: PyMT-1099 were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich, D5671) supplemented with 10% Fetal Bovine Serum (FBS, 10%; Sigma-Aldrich), 2 mM glutamine (Sigma-Aldrich, G7513), 100 U penicillin (Sigma-Aldrich) and 0.1 mg/ml streptomycin (Sigma-Aldrich). All cell lines were grown at 37°C, 5% CO2, 95% humidity.

extract_protocol:
Total RNA was isolated from the samples above using the miRNeasy Mini Kit (Qiagen, 217004) with on-column DNAse digestion according to the manufacturer’s instructions. 5g of RNA was then subjected to rRNA depletion using the Ribozero magnetic gold kit (Epicentre, MRZG12324) followed by concentrating it using the  RNeasy MinElute Cleanup Kit (Qiagen, 74204).
Total RNA was isolated from the samples above using the miRNeasy Mini Kit (Qiagen, 217004) with on-column DNAse digestion according to the manufacturer’s instructions. RNA quality control was performed with an RNA ScreenTape on the Agilent 4200 TapeStation and the concentration measured by using the Quanti-iT RiboGreen RNA assay Kit (Life Technologies). 200 ng of RNA were subjected to rRNA depletion and utilized for library preparation with the Truseq Stranded Total RNA Library Prep kit with Ribo-Zero Gold (Illumina). Library QC was performed with a Fragment Analyzer (AATI) using the Standard Sensitivity NGS Fragment Analysis Kit (DNF-473). RNA-seq libraries were sequenced SR81 with NextSeq 500 High Output v2 kit (Illumina) on an Illumina NextSeq 500 using protocols defined by the manufacturer; primary data analysis was done using Illumina RTA Version: 2.4.11.

treatment_protocol: For the EMT time-course, PyMT-1099 or NMuMG (E9) cells were treated with 2ng/ml TGF for 2h, 6h, 12h, 24h, 36h, 48h, 72h, 96h, 7d or 10d. Untreated cells served as control. For the MET timecourse, TGF was withdrawn from PyMT-1099 or NMuMG (E9) cells after 10d treatment. Cells were then seeded without TGFfor 1, 2, 3, 4, 7 or 10d. 10d TGF treated cells (MET d0) served as the control for MET experiment

value: MMTV-PyMT (FVB/N)

value: Tumor developed in mammary gland 2/3

tag: transgene

value: PyMT

tag: time point

tag: treatment

value: Tgfbeta


title: 1099_met_d7_replicate_2

description:
MET
1099_MET_CPM_data.txt
met.d7_2


title: MONO1

value: S. aureus USA300


title: 1099_met_d0_replicate_2

description:
MET
1099_MET_CPM_data.txt
met.d0_2


title: MDSC3


title: 1099_met_d7_replicate_1

description:
MET
1099_MET_CPM_data.txt
met.d7_1


title: 1099_met_d1_replicate_2

description:
MET
1099_MET_CPM_data.txt
met.d1_2


title: 1099_met_d4_replicate_2

description:
MET
1099_MET_CPM_data.txt
met.d4_2


title: 1099_met_d10_replicate_1

description:
MET
1099_MET_CPM_data.txt
met.d10_1


title: 1099_met_d3_replicate_2

description:
MET
1099_MET_CPM_data.txt
met.d3_2


title: 1099_met_d1_replicate_1

description:
MET
1099_MET_CPM_data.txt
met.d1_1


title: 1099_met_d3_replicate_1

description:
MET
1099_MET_CPM_data.txt
met.d3_1


title: 1099_met_d2_replicate_2

description:
MET
1099_MET_CPM_data.txt
met.d2_2


title: 1099_emt_7d_replicate_2

description:
EMT
1099_EMT_CPM_data.txt
emt.7d_2


title: 1099_emt_96h_replicate_2

description:
EMT
1099_EMT_CPM_data.txt
emt.96h_2


title: 1099_met_d2_replicate_1

description:
MET
1099_MET_CPM_data.txt
met.d2_1


title: 1099_emt_10d_replicate_2

description:
EMT
1099_EMT_CPM_data.txt
emt.10d_2


title: 1099_emt_60h_replicate_2

description:
EMT
1099_EMT_CPM_data.txt
emt.60h_2


title: 1099_emt_72h_replicate_2

description:
EMT
1099_EMT_CPM_data.txt
emt.72h_2


title: 1099_met_d0_replicate_1

description:
MET
1099_MET_CPM_data.txt
met.d0_1


title: 1099_emt_48h_replicate_2

description:
EMT
1099_EMT_CPM_data.txt
emt.48h_2


title: 1099_emt_24h_replicate_2

description:
EMT
1099_EMT_CPM_data.txt
emt.24h_2


title: 1099_emt_36h_replicate_2

description:
EMT
1099_EMT_CPM_data.txt
emt.36h_2


title: 1099_met_d4_replicate_1

description:
MET
1099_MET_CPM_data.txt
met.d4_1


title: 1099_emt_6h_replicate_2

description:
EMT
1099_EMT_CPM_data.txt
emt.6h_2


title: 1099_emt_12h_replicate_2

description:
EMT
1099_EMT_CPM_data.txt
emt.12h_2


title: 1099_emt_2h_replicate_2

description:
EMT
1099_EMT_CPM_data.txt
emt.2h_2


title: 1099_emt_72h_replicate_1

description:
EMT
1099_EMT_CPM_data.txt
emt.72h_1


title: 1099_emt_10d_replicate_1

description:
EMT
1099_EMT_CPM_data.txt
emt.10d_1


title: 1099_emt_60h_replicate_1

description:
EMT
1099_EMT_CPM_data.txt
emt.60h_1


title: 1099_emt_48h_replicate_1

description:
EMT
1099_EMT_CPM_data.txt
emt.48h_1


title: 1099_emt_6h_replicate_1

description:
EMT
1099_EMT_CPM_data.txt
emt.6h_1


title: 1099_emt_ut_replicate_1

description:
EMT
1099_EMT_CPM_data.txt
emt.ut_1


title: 1099_emt_24h_replicate_1

description:
EMT
1099_EMT_CPM_data.txt
emt.24h_1


title: 1099_emt_36h_replicate_1

description:
EMT
1099_EMT_CPM_data.txt
emt.36h_1


title: 1099_emt_2h_replicate_1

description:
EMT
1099_EMT_CPM_data.txt
emt.2h_1


title: 1099_emt_96h_replicate_1

description:
EMT
1099_EMT_CPM_data.txt
emt.96h_1


title: SUM159_TRPS1_1 [ChIP-seq]

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
RNA-Seq: Illumina Casava1.7 software used for basecalling.
RNA-seq: Quality check was performed using the Broad Firehose pipeline (screen data) and VIPER [https://bitbucket.org/cfce/viper/src/master/] (validation data).
RNA-Seq: The datasets were aligned to the human reference GRCh37/hg19 genome using the STAR RNA-Seq aligner in Firehose and VIPER using the default parameters.
RNA-Seq: The read counts for individual genes were generated using the 'RNASeqMetricsSetSummary' module of Firehose and VIPER using the default parameters and the hg19 Ensembl and RefSeq annotation files.
Genome_build: hg19
ChIP-Seq: Illumina Casava1.7 software used for basecalling
ChIP-Seq: Read quality check was performed using the chilin pipeline (https://github.com/cfce/chilin).
ChIP-Seq: Reads were aligned to GRCh37/hg19 using BWA in chilin.
ChIP-Seq: Peak calling was performed using MACS2 in chilin.
Supplementary_files_format_and_content: RNA-Seq: Tab-separated file of the raw read counts of the screened samples or each validation samples for each gene.
Supplementary_files_format_and_content: ChIP-Seq: Bigwig (bw) files generated using MACS2 in the chilin pipeline.

growth_protocol: HCC3153 cells were cultured in RPMI1640 supplemented with 10% FBS and 1% penicillin/streptomycin. MDA-IBC3 and SUM159 cells were cultured in a 1:1 mixture of DMEM/F12 supplemented with 10% FBS and 1% penicillin/streptomycin and Human Mammary Epithelial Cell Medium. For genomic profiling, 59 cell lines were grown in corresponding media described in Table S1.

extract_protocol:
For RNA-seq total RNA was extracted using the RNeasy Kit (Qiagen). For ChIP-seq 5-8 × 10^6 cells were fixed by adding 1:20 volume of fixing buffer (11% paraformaldehyde (Electron Microscopy Sciences, cat# 15714), 0.1M NaCl, 1mM EDTA pH 8.0, 50mM HEPES pH 8.0) directly to the tissue culture medium for 10 min at room temperature for histone modification ChIPs or at 37°C for transcription factor ChIPs and subsequently quenched by glycine. Cells were lysed in lysis buffer (50mM HEPES pH 8.0, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) for 10 min at 4°C. Nuclei were pelleted and washed in wash buffer (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) for 10 min at 4°C and then pelleted and resuspended shearing buffer (10mM Tris-HCl pH 7.4, 1mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate, 0.25% sarkosyl, 1mM DTT) and sonicated in a Covaris sonicator. Debris was removed by centrifugation (5 min at 10,000g) and 970µl of the lysate was mixed with 30µl of 5M NaCl. Chromatin was pre-cleared for 1 hr at 4°C with 40µl of Dynabeads Protein G (LifeTechnologies, cat# 10003D) washed in 0.5% BSA in PBS. Lysates were then incubated with corresponding primary antibody overnight at 4°C. Complexes were precipitated by incubation with 40µl of washed Dynabeads Protein G for 2 hrs at 4°C, washed with low salt wash buffer (20mM Tris-HCl pH 8.0, 150mM NaCl, 2mM EDTA pH 8.0, 1% Triton X-100, 0.1% SDS), high salt wash buffer (20mM Tris-HCl pH 8.0, 500mM NaCl, 2mM EDTA pH 8.0, 1% Triton X-100, 0.1% SDS), LiCl wash buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1mM EDTA pH 8.0, 1% NP40, 1% sodium deoxycholate), and twice with TE pH 8.0. DNA was eluted in elution buffer (100mM NaHCO3, 1% SDS) by incubating overnight at 65°C, followed by 30 min treatment with RNase A at 37°C and 2 hrs treatment with proteinase K at 55°C. DNA was purified with phenol-chloroform extraction and precipitated with isopropanol. For methylation analysis, DNA was isolated using QIAamp DNA Mini kit (QIAGEN, cat# 51304). DNA methylation profiling was carried out on Infinium HumanMethylation450K BeadChip arrays (Illumina, discontinued) at the Harvard Medical School-Partners HealthCare Center for Genetics and Genomics.
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols. ChIP-seq libraries were prepared using the Rubicon ThruPLEX DNA-seq Kit from purified ChIP DNA or input DNA according to the manufacturer’s protocol.

treatment_protocol: Were indicated as "dox+", cells were treated with 100 ng/ml of doxycycline.

tag: chip antibody

tag: chip antibody info

value: Bethyl, cat# A303-563A


title: IBC3_TRPS1_1 [ChIP-seq]


title: HCC3153_sh2_dox-_TRPS1_2 [ChIP-seq]

tag: hairpin

value: No Dox


title: SUM159_TRPS1_2 [ChIP-seq]


title: HCC3153_sh1_dox+_TRPS1_2 [ChIP-seq]

value: Dox


title: input for SUM159_TRPS1 samples [ChIP-seq]

source_name: input for SUM159_TRPS1 samples


title: HCC3153_sh1_dox-_TRPS1_1 [ChIP-seq]


title: HCC3153_sh2_dox+_H3K27ac_2 [ChIP-seq]


title: HCC3153_sh2_dox-_TRPS1_1 [ChIP-seq]


title: IBC3_TRPS1_2 [ChIP-seq]


title: HCC3153_sh1_dox-_TRPS1_2 [ChIP-seq]


title: HCC3153_sh1_dox+_TRPS1_1 [ChIP-seq]


title: 1099_emt_7d_replicate_1

description:
EMT
1099_EMT_CPM_data.txt
emt.7d_1

tag: tissue


title: HCC3153_sh2_dox+_TRPS1_2 [ChIP-seq]


title: 1099_emt_12h_replicate_1

description:
EMT
1099_EMT_CPM_data.txt
emt.12h_1


title: HCC3153_sh2_dox+_TRPS1_1 [ChIP-seq]


title: HCC3153_sh2_dox-_H3K27ac_2 [ChIP-seq]


title: HCC3153_sh2_dox+_H3K27ac_1 [ChIP-seq]


title: HCC3153_sh1_dox+_H3K27ac_2 [ChIP-seq]


title: HCC3153_sh1_dox+_H3K27ac_1 [ChIP-seq]


title: HCC3153_sh1_dox-_H3K27ac_2 [ChIP-seq]


title: HCC3153_sh1_dox-_H3K27ac_1 [ChIP-seq]


title: HCC3153_sh2_dox-_H3K27ac_1 [ChIP-seq]


title: Subcutaneous fat, Case, Biological Rep 4

description: subcutaneous fat from sternum

value: subcutaneous fat

tag: gender

tag: disease


title: HCC3153_sh2_dox+_GATAD2B_2 [ChIP-seq]

value: Bethyl, cat# A301-283A


title: HCC3153_sh2_dox-_GATAD2B_1 [ChIP-seq]


title: HCC3153_sh1_dox+_GATAD2B_1 [ChIP-seq]


title: HCC3153_sh2_dox-_GATAD2B_2 [ChIP-seq]


title: HCC3153_sh1_dox-_GATAD2B_2 [ChIP-seq]


title: HCC3153_sh1_dox+_GATAD2B_2 [ChIP-seq]


title: HCC3153_sh2_dox+_GATAD2A_2 [ChIP-seq]


title: HCC3153_sh2_dox-_GATAD2A_2 [ChIP-seq]


title: HCC3153_sh1_dox-_GATAD2A_1 [ChIP-seq]


title: HCC3153_sh1_dox-_GATAD2B_1 [ChIP-seq]


title: HCC3153_sh2_dox+_H3K27me3_2 [ChIP-seq]

value: abcam, cat# ab6002, lot GR275911-2


title: HCC3153_sh1_dox+_GATAD2A_1 [ChIP-seq]


title: HCC3153_sh2_dox+_H3K27me3_1 [ChIP-seq]


title: HCC3153_sh1_dox+_GATAD2A_2 [ChIP-seq]


title: HCC3153_sh1_dox+_H3K27me3_2 [ChIP-seq]


title: HCC3153_sh2_dox-_GATAD2A_1 [ChIP-seq]


title: HCC3153_sh1_dox+_H3K27me3_1 [ChIP-seq]


title: HCC3153_sh2_dox-_H3K27me3_2 [ChIP-seq]


title: HCC3153_sh2_dox-_H3K27me3_1 [ChIP-seq]


title: HCC3153_sh2_dox+_GATAD2A_1 [ChIP-seq]


title: HCC3153_sh2_dox+_GATAD2B_1 [ChIP-seq]


title: HCC3153_sh1_dox-_H3K27me3_2 [ChIP-seq]


title: HCC3153_sh1_dox-_GATAD2A_2 [ChIP-seq]


title: 21MT2 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
21MT2_bam


title: input for HCC3153_sh*_dox* samples [ChIP-seq]

source_name: input for HCC3153_sh*_dox* samples


title: HCC3153_sh1_dox-_H3K27me3_1 [ChIP-seq]


title: 21PT [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
21PT_bam


title: 21NT [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
21NT_bam


title: Kelly [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
Kelly_bam

source_name: Kelly

value: Kelly


title: BE(2)-C [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
BE_2_-C_bam


title: SW1222 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
SW1222_bam


title: LIM2551 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
LIM2551_bam


title: LIM2405 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
LIM2405_bam


title: GI-ME-N [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
GI-ME-N_bam

source_name: GI-ME-N

value: GI-ME-N


title: HCA-7 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
HCA-7_bam


title: LIM1899 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
LIM1899_bam


title: C32 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
C32_bam


title: SUM149R w/o JQ1 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
SUM149PT_JQ1R_wo_JQ1_bam

source_name: SUM149R w/o JQ1


title: SUM159R w/o JQ1 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
SUM159PT_JQ1R_wo_JQ1_bam

source_name: SUM159R w/o JQ1


title: TTC 709 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
TTC_709_bam

source_name: TTC 709

value: TTC 709


title: LNCaP-abl [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
LNCaP-abl_bam

source_name: LNCaP-abl

value: LNCaP-abl


title: input for IBC3_TRPS1 samples [ChIP-seq]

source_name: input for IBC3_TRPS1 samples


title: TTC 642 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
TTC_642_bam

source_name: TTC 642

value: TTC 642


title: MDA-IBC-3 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
MDA-IBC-3_bam


title: VCaP [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
VCaP_bam

source_name: VCaP

value: VCaP


title: C80 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
C80_bam


title: TTC 549 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
TTC_549_bam

source_name: TTC 549

value: TTC 549


title: 21MT1 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
21MT1_bam


title: 2004 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
2004_bam


title: BT12 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
BT12_bam


title: LAPC-4 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
LAPC-4_bam


title: C4-2B [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
C4-2B_bam


title: CWR22Rv1 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
CWR22Rv1_bam


title: SMS-SAN [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
SMS-SAN_bam

source_name: SMS-SAN

value: SMS-SAN


title: C99 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
C99_bam


title: NB69 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
NB69_bam


title: CHP-134 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
CHP-134_bam


title: CHP-126 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
CHP-126_bam


title: HCA2 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
HCA2_bam


title: NGP [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
NGP_bam

source_name: NGP

value: NGP


title: UOCB1 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
UOCB1_bam


title: HCT116 ARID1A WT [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
HCT116WT_bam

source_name: HCT116 ARID1A WT


title: HCC3153 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
HCC3153_bam


title: KOPT-K1 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
KOPT-K1_bam


title: HCT116 ARID1A HET [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
HCT116HET_bam

source_name: HCT116 ARID1A HET


title: MHH-NB-11 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
MHH-NB-11_bam


title: Blin1 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
Blin1_bam


title: MOLM14 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
MOLM14_bam


title: PMC42 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
PMC42_bam


title: SMS-KCN [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
SMS-KCN_bam

source_name: SMS-KCN

value: SMS-KCN


title: COG-N-367 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
COG-N-367_bam


title: COG-N-278 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
COG-N-278_bam


title: NLF [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
NLF_bam

source_name: NLF

value: NLF


title: LS [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
LS_bam

source_name: LS

value: LS


title: SUM159_sh2_dox+_d5 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_SUM159PT_Day_3-4-5_combined-gene-level-counts.csv
SUM159PT_sh43_plus_day_5

tag: days


title: FC-IBC02 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
FC-IBC02_bam

tag: cell line


title: HCA24 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
HCA24_bam


title: COG-N-305 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
COG-N-305_bam


title: SUM159_sh2_dox-_d5 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_SUM159PT_Day_3-4-5_combined-gene-level-counts.csv
SUM159PT_sh43_minus_day_5

value: No Dox


title: HCT116 ARID1A KO [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
HCT116KO_bam

source_name: HCT116 ARID1A KO


title: SUM159_sh2_dox+_d4 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_SUM159PT_Day_3-4-5_combined-gene-level-counts.csv
SUM159PT_sh43_plus_day_4

value: Dox


title: 1099_emt_ut_replicate_2

description:
EMT
1099_EMT_CPM_data.txt
emt.ut_2

source_name: Breast cancer cells

tag: strain

value: MMTV-PyMT (FVB/N)

value: Tumor developed in mammary gland 2/3

value: PyMT

value: Tgfbeta


title: Nalm14 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
Nalm14_bam


title: TM87 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
TM87_bam


title: SUM159_sh2_dox-_d4 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_SUM159PT_Day_3-4-5_combined-gene-level-counts.csv
SUM159PT_sh43_minus_day_4


title: SUM159_sh2_dox-_d3 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_SUM159PT_Day_3-4-5_combined-gene-level-counts.csv
SUM159PT_sh43_minus_day_3


title: SUM159_sh1_dox-_d5 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_SUM159PT_Day_3-4-5_combined-gene-level-counts.csv
SUM159PT_sh41_minus_day_5


title: SUM159_sh1_dox+_d4 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_SUM159PT_Day_3-4-5_combined-gene-level-counts.csv
SUM159PT_sh41_plus_day_4


title: SUM159_sh1_dox-_d4 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_SUM159PT_Day_3-4-5_combined-gene-level-counts.csv
SUM159PT_sh41_minus_day_4


title: Co-infection

first: Zhanbiao

last: Li

address: NO.382 Wushan Road, Tianhe District

institute: South China Agricultural University

data_processing:
Bowtie were used for filtering the data(allowed 1 mismatch) ,18~ 30 nt sRNA obtained  and then matched to the virus genome.
Genome_build: GenBank accession numbers:NC_014708~NC_014717
Genome_build: GenBank accession numbers: NC_003749.1~NC_003752.1,NC_003757.1~NC_003759.1,NC_003769.1~NC_003771.1

organism: Oryza sativa

source_name: virus-infected leaves

growth_protocol: greenhouse

extract_protocol:
Leaf samples from rice plants infected with SRBSDV, RRSV, and SRBSDV+RRSV were harvested at 15 dpi. Samples from at least ten rice plants of the same infection status were collected together to form a pool of samples for RNA extraction using RNA isolater Total RNA Extraction Reagent (Vazyme Biotech Co., China)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaves

tag: development stage

value: virus-infected 15 dpi

tag: infection


title: SUM159_sh1_dox+_d3 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_SUM159PT_Day_3-4-5_combined-gene-level-counts.csv
SUM159PT_sh41_plus_day_3


title: SUM159_sh1_dox-_d3 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_SUM159PT_Day_3-4-5_combined-gene-level-counts.csv
SUM159PT_sh41_minus_day_3


title: SUM159_sh1_dox+_d5 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_SUM159PT_Day_3-4-5_combined-gene-level-counts.csv
SUM159PT_sh41_plus_day_5


title: SRBSDV

value: SRBSDV


title: HCC3153_sh2_dox+_d5 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_HCC3153_Day_3-4-5_combined-gene-level-counts.csv
HCC3135_sh43_plus_day_5


title: RRSV

value: RRSV


title: HCC3153_sh2_dox+_d4 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_HCC3153_Day_3-4-5_combined-gene-level-counts.csv
HCC3135_sh43_plus_day_4


title: HCC3153_sh2_dox-_d5 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_HCC3153_Day_3-4-5_combined-gene-level-counts.csv
HCC3135_sh43_minus_day_5


title: HCC3153_sh2_dox+_d3 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_HCC3153_Day_3-4-5_combined-gene-level-counts.csv
HCC3135_sh43_plus_day_3


title: HCC3153_sh2_dox-_d4 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_HCC3153_Day_3-4-5_combined-gene-level-counts.csv
HCC3135_sh43_minus_day_4


title: HCC3153_sh2_dox-_d3 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_HCC3153_Day_3-4-5_combined-gene-level-counts.csv
HCC3135_sh43_minus_day_3


title: MMTV-ErbB2

city: Indianapolis

first: Xiongbin

state: Indiana

address: 980 W. Walnut Street, R3-C218D	MMGE

institute: Indiana University School of Medicine

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina HiSeq 4000.
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the mouse genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to Gencode M15 genes using featureCounts (from subread v1.5.3) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 2 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.20.8).
Genome_build: GENCODE M15 GRCm38
Supplementary_files_format_and_content: Raw counts

source_name: Mammary epithelial cells

extract_protocol:
Total mRNA was extracted using Direct-zol RNA extraction kit (duplicates, Zymo Research)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: WT


title: HCC3153_sh1_dox+_d5 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_HCC3153_Day_3-4-5_combined-gene-level-counts.csv
HCC3135_sh41_plus_day_5


title: HCC3153_sh1_dox+_d4 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_HCC3153_Day_3-4-5_combined-gene-level-counts.csv
HCC3135_sh41_plus_day_4


title: MMTV-ErbB2;miR21-/-

value: Knockout


title: HCC3153_sh1_dox-_d5 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_HCC3153_Day_3-4-5_combined-gene-level-counts.csv
HCC3135_sh41_minus_day_5


title: SUM159_sh2_dox+_d3 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_SUM159PT_Day_3-4-5_combined-gene-level-counts.csv
SUM159PT_sh43_plus_day_3


title: HCC3153_sh1_dox+_d3 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_HCC3153_Day_3-4-5_combined-gene-level-counts.csv
HCC3135_sh41_plus_day_3


title: HCC3153_sh1_dox-_d4 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_HCC3153_Day_3-4-5_combined-gene-level-counts.csv
HCC3135_sh41_minus_day_4


title: P541T

city: Nijmegen

first: Suzan

last: Stelloo

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

data_processing:
Strand-specific libraries were generated with the TruSeq Stranded mRNA sample preparation kit (Illumina, Part # 15031047 Rev. E) and sequenced on a HiSeq2500
Sequencing data was aligned to hg38 using TopHat and number of reads per gene were measured with HTSeq count.
EdgeR-Limma workflow was used for gene expression analysis. The ComBat normalization method within the R package SVA was used to correct the batch effects observed by day of RNA isolation. Genes with >1 count per million in at least 10 samples were included. Normalized data is provided in the table Porto_ge_table
Genome_build: hg38
Supplementary_files_format_and_content: Expression table of samples (columns) by transcript (rows) reporting normalized counts.

source_name: primary prostate cancer

growth_protocol: fresh frozen material

extract_protocol:
RNA was extracted using the AllPrep DNA/RNA universal kit (Qiagen) according to the manufacturer’s instruction with Qiagen’s QIAcube robot. Samples with a RIN>8 were considered for library preparation.
Strand-specific libraries were generated with the TruSeq Stranded mRNA sample preparation kit (Illumina, Part # 15031047 Rev. E).

treatment_protocol: prostatectomy samples, labeled according to recurrence status (case/control/exclude) and ERG expression (low/high)

tag: patient id

tag: erg expression

value: low

tag: case/control

value: Control

value: primary prostate cancer


title: P262T


title: P552T

value: Case


title: P279T


title: P544T

value: high


title: P266T


title: P263T


title: P272T


title: P527T


title: P462T


title: P511T


title: P513T


title: P416T


title: P274T


title: P254T

value: Exclude


title: HCC3153_sh1_dox-_d3 [RNA-seq]

description:
processed data file:
TRPS1_sh41_sh43_HCC3153_Day_3-4-5_combined-gene-level-counts.csv
HCC3135_sh41_minus_day_3

value: No Dox


title: P230T


title: P560T


title: P265T.2

value: P265T replicate


title: P355T


title: P298T


title: P342T


title: P352T


title: P618T


title: P611T


title: P643T


title: miR-548ac overexpression, 24 h post-transfection, replicate 2

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

country: Germany

institute: University of Rostock

description: Transcriptome data for HeLa cell culture after transfection of mir-548ac plasmid

hyb_protocol: Labeled single-stranded DNA in the sense orientation was hybridized for 16 hours at 45 °C on Affymetrix HTA 2.0 microarrays. The microarrays were washed and stained with a streptavidin-phycoerythrin conjugate in an Affymetrix Fluidics Station 450. Signal amplification with antibodies was applied following the instructions provided by Affymetrix.

scan_protocol: The microarrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data preprocessing of the raw microarray scans was performed using the Affymetrix GeneChip Command Console (AGCC) software version 4.0. The signal intensities of the >6 million oligonucleotide probes were further processed using the Transcriptome Analysis Console (TAC) version 4.0 (Affymetrix) in the default configuration. The signal space transformation robust multi-array average (SST-RMA) algorithm was applied for background adjustment, quantile normalization, gene-level probe set summarization and log2 transformation. The TAC software was also utilized for differential gene expression analysis.

label: Biotin

source_name: HeLa cells + mir-548ac plasmid

label_protocol: According to the Affymetrix Whole Transcript (WT) manual, cRNA was prepared from 210 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.

growth_protocol: The HeLa cells were cultured in DMEM (Thermo Fisher Scientific) supplemented with 10% FBS (Biochrom) and 50 U/ml penicillin-streptomycin (Thermo Fisher Scientific) in T25 flasks (Greiner Bio-One).

extract_protocol: Total RNA was isolated 24 h and 48 h after transfection with the miRNeasy Mini Kit (Qiagen) and an on-column DNase digestion step.

treatment_protocol: The cells were transiently transfected with the mir-548ac expression plasmid (HmiR1085-MR04, GeneCopoeia) or the negative control plasmid (CmiR0001-MR04, GeneCopoeia) using the FuGENE HD transfection reagent (Promega).

value: HeLa

tag: plasmid

value: mir-548ac expression plasmid


title: P603T


title: shTLP_nt2

city: Yokohama

first: Hidefumi

last: Suzuki

address: Fukuura 3-9

country: Japan

institute: Yokohama City University

data_processing:
Mapping of sequenced reads to the human genome reference hg19 and calculation of RPKM was performed using the software CLC Genomic Workbench (Qiagen)
Genome_build: hg19
Supplementary_files_format_and_content: RPKM

growth_protocol: HeLa cells were maintained in Dulbecco’s modified Eagle’s medium containing glucose and 10% fetal calf serum at 37ºC.

extract_protocol:
Total cellular RNAs were prepared from HeLa cells using RNeasy Mini Kit (Qiagen) as described by the manufacturer, and ribosomal RNA was removed from samples using RiboMinus Eukaryote Kit (Thermo Fisher Scientific)
Libraries for mRNA-seq were prepared using Ion Total RNA-seq Kit v2 (Thermo Fisher Scientific). The sizes of fragmented RNA and library cDNA were determined using the MultiNA microchip electrophoresis system (Shimadzu), and the quantity of library cDNA was determined by qPCR using KAPA Library Quantification Kit (KAPA Biosystems)

treatment_protocol: HeLa cells were treated with DMSO or 50 μM etoposide for 24 hours.

tag: cell type

value: cervical adenocarcinoma

tag: genotype/variation

value: TLP knockdown

value: DMSO-treatted


title: shTLP_eto2

tag: treatment

value: etoposide-treated


title: P593T


title: miR-548ac overexpression, 24 h post-transfection, replicate 3

tag: time point


title: shTLP_nt1


title: ctrl_eto2

value: control knockdown


title: miR-548ac overexpression, 48 h post-transfection, replicate 1


title: negative control, 48 h post-transfection, replicate 2

description: Transcriptome data for HeLa cell culture after transfection of control plasmid

source_name: HeLa cells + control plasmid

value: negative control plasmid


title: miR-548ac overexpression, 24 h post-transfection, replicate 1


title: ctrl_nt2


title: ctrl_eto1


title: miR-548ac overexpression, 48 h post-transfection, replicate 2


title: P559T


title: miR-548ac overexpression, 48 h post-transfection, replicate 3


title: negative control, 48 h post-transfection, replicate 1


title: negative control, 24 h post-transfection, replicate 2


title: negative control, 24 h post-transfection, replicate 1


title: P555T


title: shTLP_eto1


title: P301T


title: NMuMG_E9_MET_d10_rep2

description: rRNA depleted total RNA

growth_protocol: NMuMG (E9) cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich, D5671) supplemented with 10% Fetal Bovine Serum (FBS, 10%; Sigma-Aldrich), 2 mM glutamine (Sigma-Aldrich, G7513), 100 U penicillin (Sigma-Aldrich) and 0.1 mg/ml streptomycin (Sigma-Aldrich). All cell lines were grown at 37°C, 5% CO2, 95% humidity.

extract_protocol:
Total RNA was isolated from the samples above using the miRNeasy Mini Kit (Qiagen, 217004) with on-column DNAse digestion according to the manufacturer’s instructions. 5g of RNA was then subjected to rRNA depletion using the Ribozero magnetic gold kit (Epicentre, MRZG12324) followed by concentrating it using the  RNeasy MinElute Cleanup Kit (Qiagen, 74204).
RNA-Seq libraries were sequenced SR50 with Illumina HiSeq 2500 High Output v2 kit (Illumina) on an Illumina Illumina HiSeq 2500 using protocols defined by the manufacturer

treatment_protocol: For the MET timecourse, TGFbeta was withdrawn from NMuMG (E9) cells after 10d treatment. Cells were then seeded without TGFbeta for 1, 2, 3, 4, 7 or 10d. 10d TGFbeta treated cells (MET d0) served as the control for MET experiment.

value: NMuMG

tag: source tissue

value: Normal mammary gland

tag: clone

value: Epithelial 9 (E9) clone

tag: tgfbeta withdrawal for


title: P540T

value: Control

tag: tissue

value: primary prostate cancer


title: P261T

value: low

value: Case


title: NMuMG_E9_MET_d7_rep2

description: rRNA depleted total RNA


title: P730T

value: high


title: NMuMG_E9_MET_d10_rep1

description: rRNA depleted total RNA


title: P717T


title: P536T


title: NMuMG_E9_MET_d7_rep1

description: rRNA depleted total RNA


title: NMuMG_E9_MET_d4_rep2

description: rRNA depleted total RNA


title: P533T


title: NMuMG_E9_MET_d3_rep2

description: rRNA depleted total RNA


title: ctrl_nt1


title: UACC3199 [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
UACC3199_bam


title: P531T


title: P475T


title: LNCaP [RNA-seq]

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
LNCaP_bam

source_name: LNCaP

value: LNCaP


title: NMuMG_E9_MET_d3_rep1

description: rRNA depleted total RNA


title: P466T


title: P464T


title: P444T


title: P324T


title: NMuMG_E9_MET_d2_rep1

description: rRNA depleted total RNA


title: P431T


title: P255T


title: NMuMG_E9_MET_d2_rep2

description: rRNA depleted total RNA


title: NMuMG_E9_MET_d1_rep2

description: rRNA depleted total RNA


title: P313T


title: NMuMG_E9_MET_d1_rep1

description: rRNA depleted total RNA


title: P305T


title: NMuMG_E9_MET_d0_rep1

description: rRNA depleted total RNA


title: P509T


title: P506T


title: P507T


title: NMuMG_E9_MET_d4_rep1

description: rRNA depleted total RNA


title: WT_2

description:
total RNA
all_genes.expression

source_name: MSCs

value: bone marrow MSCs

tag: genotype

value: wild type


title: cKO_1

description:
total RNA
all_genes.expression


title: P500T


title: cKO_2

description:
total RNA
all_genes.expression


title: P457T


title: WT_1

description:
total RNA
all_genes.expression


title: P456T


title: Loxp_T9_LPS Loxp T9 LPS 3 SAM24331102

city: South San Francisco

first: Sarah

middle: K

last: Kummerfeld

state: CA

address: 1 DNA Way

institute: Genentech

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: RNA from BMDMs from mice that are COP1-wt Rosa26-CreERT2 or COP1-floxed Rosa26-CreERT2

extract_protocol: At day 7 of differentiation, BMDMs were treated with 100 ng/ml of LPS or not. BMDMs were directly harvested in lysis buffer (from Qiagen RNeasy mini kit) at different time points following LPS stimulation. Total RNA was isolated using the Qiagen RNeasy mini kit as per manufacturer’s protocol including the on-column DNase digestion

tag: group

value: Loxp

tag: time

value: LPS

tag: individual

value: BMDMs


title: P488T


title: WT_T4_LPS WT T4 LPS 1 SAM24331070

value: WT


title: Loxp_T9_LPS Loxp T9 LPS 1 SAM24331090


title: WT_T9_LPS WT T9 LPS 1 SAM24331072


title: Loxp_T0_Untreated Loxp T0 Untreated 3 SAM24331098

value: Untreated


title: P450T


title: NMuMG_E9_MET_d0_rep2

description: rRNA depleted total RNA

tag: cell line


title: Loxp_T0_Untreated Loxp T0 Untreated 1 SAM24331086


title: P832T

tag: patient id


title: P433T

tag: erg expression


title: P427T

tag: case/control


title: WT_T13_LPS WT T13 LPS 2 SAM24331079


title: P327T


title: WT_T0_Untreated WT T0 Untreated 2 SAM24331074


title: Loxp_T13_LPS Loxp T13 LPS 2 SAM24331097


title: P779T


title: P811T


title: P747T


title: WT_T13_LPS WT T13 LPS 1 SAM24331073


title: WT_T2.5_LPS WT T2.5 LPS 2 SAM24331075


title: P737T


title: WT_T9_LPS WT T9 LPS 3 SAM24331084


title: P349T


title: P449T


title: P452T


title: Loxp_T6_LPS Loxp T6 LPS 1 SAM24331089


title: P426T


title: P343T


title: Loxp_T2.5_LPS Loxp T2.5 LPS 1 SAM24331087


title: P309T


title: Loxp_T6_LPS Loxp T6 LPS 3 SAM24331101


title: WT_T6_LPS WT T6 LPS 3 SAM24331083


title: P710T


title: WT_T0_Untreated WT T0 Untreated 3 SAM24331080


title: P695T


title: WT_T9_LPS WT T9 LPS 2 SAM24331078


title: P660T


title: Loxp_T13_LPS Loxp T13 LPS 1 SAM24331091


title: WT_T2.5_LPS WT T2.5 LPS 3 SAM24331081


title: P534T


title: WT_T6_LPS WT T6 LPS 1 SAM24331071


title: Loxp_T6_LPS Loxp T6 LPS 2 SAM24331095


title: P680T


title: P310T


title: P300T


title: Loxp_T2.5_LPS Loxp T2.5 LPS 2 SAM24331093


title: Loxp_T4_LPS Loxp T4 LPS 3 SAM24331100


title: P823T


title: Loxp_T4_LPS Loxp T4 LPS 2 SAM24331094