title: WT_D4_1

status: Public on May 16 2018

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

data_processing:
BCL files were converted to fastq using bcl2fastq (v2.16-2.19)
RNA-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36) and aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Supplementary_files_format_and_content: Text files are raw counts (1 count per pair of reads) calculated using the summarizeOverlaps function from the GenomicAlignments R package (v10.10.1)

source_name: splenic NK cells

extract_protocol:
Cells were sorted, resuspended in Trizol, and total RNA underwent amplification using SMART-seq V4 (Clontech) Ultra Low Input RNA kit.
Subsequently, 10 ng of amplified cDNA was used to prepare Illumina hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR. Samples were barcoded and run on Hiseq 2500 1T, in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).  An average of 47 million paired reads were generated per sample and the percent of mRNA bases was over to 72% on average.

value: spleen

value: Natural killer (NK)

tag: genotype

value: WT

tag: replicate

value: HPOS

tag: condition


title: WT_D4_3

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type


title: IRF8cKO_D0_2


title: IRF8cKO_D4_2


title: IRF8cKO_D4_1


title: WT_D0_2


title: WT_D0_1


title: IRF8cKO_D4_3


title: WT_D4_2


title: HC1_0E

status: Public on May 17 2018

type: RNA

city: Rozzano, Milan

first: Emilia Maria Cristina

last: Mazza

address: Via Alessandro Manzoni, 56

country: Italy

institute: Humanitas Clinical and Research Center

description: unconventional CD56dim CD16neg (uCD56dim) NK cell subset from healthy donor 1

hyb_protocol: Samples were hybridized to GeneChip Human Transcriptome Arrays 2.0 (Thermo Scientific) following the Encore Biotin Module user guide (NuGen Technlogies) and Affymetrix's Hybridization procedures

scan_protocol: Arrays were scanned following the GCS 3000 7G User guide (Thermo Scientific)

data_processing: RMA of .CEL files using affy Bioconductor library and Brainarray: hta20hsentrezgcdf v21.0.0 custom CDF. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization

label: biotin

organism: Homo sapiens

source_name: sorted NK cell subset from human PBMCs of healthy donor

label_protocol: Samples were amplified an labeled according to Ovation Pico WTA System V2 and Encore Biotin Module user guides (NuGen Technlogies)

extract_protocol: Toral RNAs were isolated following the microRNeasy kit guidelines (Qiagen)

value: PBMC

value: Natural Killer (NK) cells

tag: population


title: IN-wholefishtranscriptome_RNAseq rep4

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Mouse GRCm38 reference using the TopHat splice-aware aligner
Reads Per Kilobase of gene per Million mapped reads (RPKM) were calculated for each sample.
Differential expression of genes were computed between infected and uninfected samples
Genome_build: Danio_rerio(GRCz10)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Danio rerio

growth_protocol: embryos were grown at 28 degrees C in E3 media until 5dpf

extract_protocol:
RNA was isolated from the immunoprecipitated and input samples using the Qiagen RNeasy Plus Micro kit (Cat#74034).HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody (see manuscript for full protocol)
Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit (Illumina) per manufacturer’s instructions, with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Untreated

tag: developmental stage

value: whole fish

tag: antibody


title: HC2_0C

description: conventional CD56dim CD16pos (cCD56dim) NK cell subset from healthy donor 2

value: conventional CD56dim CD16pos (cCD56dim)


title: IRF8cKO_D0_1


title: HC3_0C

description: conventional CD56dim CD16pos (cCD56dim) NK cell subset from healthy donor 3


title: HC1_0C

description: conventional CD56dim CD16pos (cCD56dim) NK cell subset from healthy donor 1


title: 6_G1_HeLa

city: Norwich

first: Conrad

middle: A

last: Nieduszynski

address: Norwich Research Park

country: United Kingdom

institute: Earlham Institute

library_source: genomic

data_processing:
Mapped with STAR (--alignIntronMax 1, --outFilterMismatchNmax 2)
Indexed with SAMTOOLS
Counted unique reads in 50 kb genomic bins (Bedtools and custom script)
Produced ratio of reads in bins between S and G1 samples (custom R script)
Script available at: https://github.com/DNAReplicationLab/batrakou2018
Genome_build: hg38
Supplementary_files_format_and_content: Bed files were generated with custom scripts. Score column contains adjusted S/G1 ratio values (relative copy number).

molecule: genomic DNA

source_name: HeLa S3 cells, sorted G1 phase cell population

growth_protocol: Cells were passaged in DMEM containing 9% v/v FBS and 10 U/mL each Penecillin and Streptomycin.

extract_protocol:
Cells were resuspended in 10 mM Tris-HCl pH 8.0, 0.5% w/v SDS, 100 mM EDTA supplemented with 20 µg/ml RNase A and 0.2 mg/ml proteinase K and incubated at 50˚C for 1 h. The lysate was allowed to cool to room temperature and sample volumes were adjusted to 0.5 mL by addition of TE buffer. The samples were mixed with an equal volume of phenol:chloroform:isoamyl alcohol pH 8.0 (25:24:1) followed by single or double extraction using an equal volume of chloroform. DNA was then precipitated using isopropanol in the presence of potassium acetate.
500 ng of fragmented genomic DNA was used for library construction for Illumina sequencing. Indexed genomic DNA libraries were prepared using a NEBNext Ultra II library prep kit for Illumina without size selection, and NEBNext Multiplex Oligos for Illumina using four cycles of amplification, followed by two rounds of clean-up using Agencourt AMPure XP beads. Library samples were quantified by qPCR using a NEBNext Library Quant Kit for Illumina and a Rotor-Gene real time PCR cycler.

treatment_protocol: Untreated, ethanol fixed, stained with propidium iodide (50 µg/mL) and sorted into G1 and S fractions.

tag: cell line

value: HeLa

value: epithelial (cervix)

tag: cell cycle stage


title: 12_S_HeLa

source_name: HeLa S3 cells, sorted S phase cell population

value: S


title: Tet1KO_Suz12_ChIPSeq

city: seattle

first: xueqiu

last: lin

state: wa

address: 1100 Fairview Ave N

institute: FRED HUTCHINSON CANCER CENTER

data_processing:
Raw reads treated by bisulfite were quality trimmed (Trimgalore), and uniquely mapped to the mm9 reference genome using BWA .
Chromatin marks were compared with Danpos2. Briefly, the experiments were input background-subtracted and normalized to the same read  depth.
Genome_build: mm9
Supplementary_files_format_and_content: The bigWig files were reads density, created from Danpos2 wiggle files. More information may be found in the Danpos2 documentation.

source_name: embryonic stem cells

growth_protocol: ES cells were cultured on 0.1% gelatin-coated dishes in DMEM (Gibco, 11965-092) supplemented with 15% Fetal Bovine Serum (Foundation, 900-108), 1×Non-Essential Amino Acids (Gibco, 11140-050), 1×GlutaMAX (Gibco, 35050-061), 1 μM 2-Mercaptoethanol (Sigma, M7522), 1×Sodium pyruvate (Sigma, S8636), 1×Penicillin/Streptomycin (Gibco, 15140-122) and 1000 U/ml LIF (Millipore, ESG1106).

extract_protocol:
2×10^6 cells were fixed for 10 minutes with 1% formaldehyde, followed by chromatin extraction and sonication to generate 200-500bp fragments. The sheared chromatin was incubated overnight at 4°C with H3K4me3 or H3K27me3 antibody. After incubation, 10 µl of Dynabeads Protein A magnetic beads previously washed in RIPA buffer was added, and samples were incubated for an additional 2 hours at 4°C. Bead-protein complexes were washed three times with RIPA buffer and twice with TE buffer. Genomic DNA was eluted for 2 hours at 68°C in 100 µl of Complete Elution Buffer (20 mM Tris, pH7.5, 5 mM EDTA, 50 mM NaCl, 1% SDS, 50 µg/ml proteinase K) and purified with MinElute PCR purification kit (Qiagen, 28004).
For ChIP-Seq, sequencing libraries were prepared using ThruPLEX DNA-seq 48D kit (Rubicon Genomics, R400406) following standard protocols.

tag: strain background

tag: genotype/variation

value: embryonic stem cells

tag: chip antibody

value: anti-SUZ12(Abcam, ab12073)


title: WT_Suz12_ChIPSeq

value: wild type


title: DKO_Suz12_ChIPSeq

value: Dnmt3a-/- and Tet1-/-


title: 3aKO_Suz12_ChIPSeq


title: HC2_0A

description: conventional CD56bright CD16neg (cCD56bright) NK cell subset from healthy donor 2


title: DKO H3K27me3_SpikeIn_ChIPSeq

description: DKO H3K27me3

value: anti-H3K27me3 (Millipore, 07-449)


title: DKO H3K4me3_SpikeIn_ChIPSeq

description: DKO H3K4me3

value: anti-H3K4me3 (Millipore, 07-473)


title: HC1_0A

description: conventional CD56bright CD16neg (cCD56bright) NK cell subset from healthy donor 1


title: HC3_0A

description: conventional CD56bright CD16neg (cCD56bright) NK cell subset from healthy donor 3


title: 3aKO H3K27me3_SpikeIn_ChIPSeq

description: 3aKO H3K27me3


title: Tet1KO H3K4me3_SpikeIn_ChIPSeq

description: Tet1KO H3K4me3


title: Tet1KO H3K27me3_SpikeIn_ChIPSeq

description: Tet1KO H3K27me3


title: WT H3K4me3_SpikeIn_ChIPSeq

description: WT H3K4me3


title: I_C_OSKM_3d_2w_Input

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

country: Japan

institute: University of Tokyo

description: C-OSKM Pancreas Dox3days2W M Input

data_processing:
The low-quality bases at the 3' read ends and the adaptors were trimmed using cutadapt-1.9.1. Untrimmed and trimmed reads of 20 bp or longer were mapped to mouse genome (mm10) with BWA 0.7.12 with default setting.
Duplicate reads and low mapping quality reads (MAPQ < 20) were removed using Picard and SAMtools.
To handle male and females samples equally, the data on chromosome X and Y were excluded for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bw (bigwig) *The data were normalized as RPM (reads per million)

source_name: Pancreas

extract_protocol:
Purified ChIP DNA (5 ng per sample) was used for generation of sequencing libraries with TruSeq ChIP Sample Prep Kit (Illumina).
The resultant DNA libraries were assessed on an Agilent Bioanalyzer and quantified with KAPA Library Quantification Kits (KAPA BIOSYSTEMS). The libraries were sequenced to generate single-end 86 bp reads using NextSeq 500 (illumina).

value: Pancreas

tag: strains

value: C-OSKM

tag: treatment


title: I_Caerulein_1_Input

description: WT Pancreas Caerulein M Input

value: WT

value: Caerulein


title: WT H3K27me3_SpikeIn_ChIPSeq

description: WT H3K27me3


title: C_WT_H3K27ac

description: WT Pancreas NoCaerulein M H3K27Ac

value: NoCaerulein


title: C_C_OSKM_3d_2w_H3K27ac

description: C-OSKM Pancreas Dox3days2W M H3K27Ac


title: C_Caerulein_1_H3K27ac

description: WT Pancreas Caerulein M H3K27Ac


title: 3aKO H3K4me3_SpikeIn_ChIPSeq

description: 3aKO H3K4me3


title: Group 4 (Biopsy #51)

city: Salt Lake City

first: Aik Choon

last: Tan

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

description: Gene expression data from lung biopsy

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

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

data_processing: The data were analyzed with Affymetrix Power Tools (APT) using RMA normalization.

source_name: Lung biopsy

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

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

value: Lung biopsy

tag: bl ffpe dx

tag: f/u bx dx

tag: bl frozen dx

tag: age

tag: smoking pack/yr


title: Group 4 (Biopsy #47)

description: Gene expression data from lung biopsy

tag: tissue


title: Group 4 (Biopsy #50)

description: Gene expression data from lung biopsy


title: Group 4 (Biopsy #60)

description: Gene expression data from lung biopsy


title: Group 4 (Biopsy #48)

description: Gene expression data from lung biopsy


title: Group 4 (Biopsy #62)

description: Gene expression data from lung biopsy


title: Group 4 (Biopsy #59)

description: Gene expression data from lung biopsy


title: Group 4 (Biopsy #57)

description: Gene expression data from lung biopsy


title: Group 4 (Biopsy #56)

description: Gene expression data from lung biopsy


title: Group 4 (Biopsy #58)

description: Gene expression data from lung biopsy


title: Group 4 (Biopsy # 54)

description: Gene expression data from lung biopsy


title: Group 4 (Biopsy #53)

description: Gene expression data from lung biopsy


title: Group 3 (Biopsy #29)

description: Gene expression data from lung biopsy


title: Group 4 (Biopsy #63)

description: Gene expression data from lung biopsy


title: Group 4 (Biopsy #55)

description: Gene expression data from lung biopsy


title: Group 4 (Biopsy #61)

description: Gene expression data from lung biopsy


title: Group 3 (Biopsy #26)

description: Gene expression data from lung biopsy


title: Group 3 (Biopsy #27)

description: Gene expression data from lung biopsy


title: Group 3 (Biopsy #30)

description: Gene expression data from lung biopsy


title: Group 3 (Biopsy #25)

description: Gene expression data from lung biopsy


title: Group 3 (Biopsy #32)

description: Gene expression data from lung biopsy


title: Group 2 (Biopsy #33)

description: Gene expression data from lung biopsy


title: Group 3 (Biopsy #28)

description: Gene expression data from lung biopsy


title: Group 2 (Biopsy #40)

description: Gene expression data from lung biopsy


title: Group 3 (Biopsy #24)

description: Gene expression data from lung biopsy


title: Group 2 (Biopsy #39)

description: Gene expression data from lung biopsy


title: NoDox_4M_H3K27ac

data_processing:
The low-quality bases at the 3' read ends and the adaptors were trimmed using cutadapt-1.9.1. Untrimmed and trimmed reads of 20 bp or longer were mapped to mouse genome (mm10) with BWA 0.7.12 with default setting.
Duplicate reads and low mapping quality reads (MAPQ < 20) were removed using Picard and SAMtools.
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bw (bigwig) *The data were normalized as RPM (reads per million)

source_name: C-OSKM Pancreas NoDox M H3K27Ac

value: pancreas

tag: Sex

value: male

tag: strain

value: Anti-acetyl Histone H3 (Lys27)

tag: chip antibody vendor

value: MBL

tag: chip antibody catalog number


title: NoDox_1F_Input

source_name: C-OSKM Pancreas NoDox F Input

value: female

value: none (input)


title: Group 2 (Biopsy #37)

description: Gene expression data from lung biopsy


title: NoDox_4M_Input

source_name: C-OSKM Pancreas NoDox M Input


title: Group 2 (Biopsy #38)

description: Gene expression data from lung biopsy


title: Group 2 (Biopsy #41)

description: Gene expression data from lung biopsy


title: Group 3 (Biopsy #31)

description: Gene expression data from lung biopsy


title: 3days_2M_Input

source_name: C-OSKM Pancreas 3days M Input


title: Group 2 (Biopsy #42)

description: Gene expression data from lung biopsy


title: Group 2 (Biopsy #46)

description: Gene expression data from lung biopsy


title: Group 2 (Biopsy #45)

description: Gene expression data from lung biopsy


title: Group 2 (Biopsy #43)

description: Gene expression data from lung biopsy


title: NoDox_1F_H3K27ac

source_name: C-OSKM Pancreas NoDox F H3K27Ac


title: Group 1 (Biopsy #6)

description: Gene expression data from lung biopsy


title: Group 1 (Biopsy #1)

description: Gene expression data from lung biopsy


title: Group 2 (Biopsy #52)

description: Gene expression data from lung biopsy


title: Group 2 (Biopsy #36)

description: Gene expression data from lung biopsy


title: Group 1 (Biopsy #2)

description: Gene expression data from lung biopsy

value: ND


title: Group 2 (Biopsy #34)

description: Gene expression data from lung biopsy


title: Group 2 (Biopsy #44)

description: Gene expression data from lung biopsy


title: Group 2 (Biopsy #35)

description: Gene expression data from lung biopsy


title: Group 1 (Biopsy #4)

description: Gene expression data from lung biopsy


title: 3days_2M_H3K27ac

source_name: C-OSKM Pancreas 3days M H3K27Ac


title: Group 1 (Biopsy #19)

description: Gene expression data from lung biopsy


title: Group 1 (Biopsy #5)

description: Gene expression data from lung biopsy


title: Group 1 (Biopsy #16)

description: Gene expression data from lung biopsy


title: Group 1 (Biopsy #3)

description: Gene expression data from lung biopsy


title: Group 1 (Biopsy #11)

description: Gene expression data from lung biopsy


title: 3days_1F_Input

source_name: C-OSKM Pancreas 3days F Input


title: 3days_1F_H3K27ac

source_name: C-OSKM Pancreas 3days F H3K27Ac


title: JIB-04_6h_2

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Raw sequencing reads were aligned to the human hg19 genome with STAR
Read counts per gene were calculated using FeatureCounts
DESeq2 was used to generate FPKM values
Genome_build: hg19
Supplementary_files_format_and_content: comma-separated values containing gene-level quantification (FPKM normalization)

molecule: polyA RNA

source_name: 2D10 Jurkat T cells

growth_protocol: RPMI-1640 medium (Corning, 10-040-CM) plus 10% FBS (Omega Scientific Inc, FB-01) and 1% antibiotic-antimycotic solution (Corning, 30-004-CI) inside 37 ℃ incubator supplied with 5% CO2

extract_protocol:
Total RNA was extracted by Qiagen RNeasy plus kit, purified by the Zymo RNA purification kit and the quality was analyzed by EB Agarose gel.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DMSO or 3-microM JIB-04 was added to cells for over night (16 h). Next morning, TNFa (10 ng/ml) was added to 2D10 cells for 0 h or 6 h.

tag: cell line

value: 2D10 Jurkat T cells

tag: tnfa induction duration

tag: proviral integration

value: HIV-dNef into exon 2 of MSRB1


title: Infected - L2_R1_TGACCA RNA-Seq

city: St. Paul

first: Cheryl

last: Dvorak

state: MN

address: 1971 Commonwealth Avenue

department: Veterinary and Biomedical Sciences

institute: University of Minnesota

data_processing:
fastq data files were analyzed using CLC genomics workbench version 6.0.5 using the reference database Ensembl Sscrofa 10.2 (Ensembl release 89).
Genome_build: Ensembl Sscrofa 10.2, Ensembl release 89
Supplementary_files_format_and_content: Tab delimited table containing CLC software outputs including RPKMs, statistics, and other information for all samples.

organism: Sus scrofa

source_name: VR1BL cells

growth_protocol: VR1BL cells were grown according to published protocols in MEM media supplemented with 1X NEAA, 10 mM HEPES, 0.05 mg/ml gentamycin, 50 ug/ml hygromycin B, and 10% FBS

extract_protocol:
Total RNA was extracted from PCV2b infected and control VR1BL cells using the Qiagen Rneasy mini kit followed by 2 treatments of the Thermo-Fischer TURBO DNA-free Kit to remove any contaminating genomic DNA.
Libraries were prepared using the Illumina mRNA-Seq sample preparation kit following manufacturer's protocols.

treatment_protocol: Infected samples consisted of VR1BL cells which were infected for 4 days at an MOI of 1 with PCV2b (GenBank ID JF290418) when cells were 60-80% confluent. Control samples were mock infected for 4 days.

value: porcine fetal retina

tag: infection status

value: Infected


title: Infected - L2_R1_ACAGTG RNA-Seq


title: Infected - L2_R1_CGATGT RNA-Seq


title: JIB-04_0h_1


title: Group 1 (Biopsy #13)

description: Gene expression data from lung biopsy


title: Group 1 (Biopsy #18)

description: Gene expression data from lung biopsy


title: DMSO_TNFa_6h_2

value: DMSO


title: Group 1 (Biopsy #17)

description: Gene expression data from lung biopsy


title: Group 1 (Biopsy #14)

description: Gene expression data from lung biopsy


title: DMSO_TNFa_6h_1


title: Group 1 (Biopsy #23)

description: Gene expression data from lung biopsy


title: JIB-04_0h_2


title: Group 1 (Biopsy #22)

description: Gene expression data from lung biopsy


title: Group 1 (Biopsy #10)

description: Gene expression data from lung biopsy


title: JIB-04_6h_1


title: Group 1 (Biopsy #12)

description: Gene expression data from lung biopsy


title: Group 1 (Biopsy #21)

description: Gene expression data from lung biopsy


title: Group 1 (Biopsy #9)

description: Gene expression data from lung biopsy


title: Group 1 (Biopsy #8)

description: Gene expression data from lung biopsy


title: Control - L2_R1_GCCAAT RNA-Seq

value: Control


title: Control - L2_R1_CTTGTA RNA-Seq


title: Group 1 (Biopsy #7)

description: Gene expression data from lung biopsy


title: Group 1 (Biopsy # 15)

description: Gene expression data from lung biopsy


title: Group 1 (Biopsy #20)

description: Gene expression data from lung biopsy


title: miR-155_OE_GFP_neg_rep3 [3M30N]

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

data_processing:
Sequenced libraries were mapped to mm0 reference genome using RNA-seq unified mapper(RUM)
Read counts were quantified using RefSeq transcripts
Downstream processing and differential analysis was done using Deseq2
Genome_build: mm9
Supplementary_files_format_and_content: RNA counts file before normalization

source_name: RNA-seq of CD8T cells sorted GFP - from miR-155 overexpressing

extract_protocol:
RNA from sorted cells was isolated using RNA Plus Micro kit(Qiagen)
Libraries were prepared using the SMARTer Ultra low RNA kit(Clontech Laboratories)

tag: strain background

tag: genotype/variation

value: overexpressing miR-155

value: Spleen

tag: cell type

value: CD8T cells

tag: cell subtype

value: GFP negative


title: miR-155_OE_GFP_pos_rep3 [3M30G]

source_name: RNA-seq of CD8T cells sorted GFP + from miR-155 overexpressing

value: GFP positive


title: DMSO_TNFa_0h_2

tag: treatment


title: ctrl_GFP_pos_rep3 [4C30G]

source_name: RNA-seq of CD8T cells sorted GFP + from control

value: control


title: miR-155_OE_GFP_pos_rep2 [2M30G]


title: ctrl_GFP_neg_rep3 [4C30N]

source_name: RNA-seq of CD8T cells sorted GFP - from control


title: miR-155_OE_GFP_neg_rep2 [2M30N]


title: ctrl_GFP_pos_rep2 [3C30G]


title: miR-155_OE_GFP_neg_rep1 [1M30N]


title: Tet1-Flag_WGBS

description: Tet1-Flag WGBS

data_processing:
Bisulfite-treated sequencing reads were be aligned to  the mm9 reference genome using BSMAP. Cytosine methylation ratios were calculated with MOABS.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig file for CpG methylation ratio

source_name: embryonic stem cells

extract_protocol:
1 μg of genomic DNA was isolated from mESCs and fragmented using a Covaris sonication system (Covaris S2).
Following DNA fragmentation, libraries were constructed using the Illumina TruSeq DNA sample preparation kit. After ligation, libraries were treated with bisulfite using the EpiTect Bisulfite kit (Qiagen, 59104). Ligation efficiency was tested by PCR using TruSeq primers and Pfu Turbo Cx Hot-Start DNA polymerase (Stratagene, 600632). After determining the optimal number of PCR cycles for each sample, a large-scale PCR reaction (100 μl) was performed. PCR products were sequenced with Illumina HiSeq sequencing systems.

value: wild type

value: embryonic stem cells

tag: molecule subtype

value: bisulfite converted genomic DNA


title: ctrl_GFP_neg_rep2 [3C30N]


title: DMSO_TNFa_0h_1


title: I_WT_Input

description: WT Pancreas NoCaerulein M Input

source_name: Pancreas

value: Pancreas

tag: strains

tag: antibody

value: WT

value: NoCaerulein


title: Tet1KO_WGBS

description: Tet1KO WGBS


title: WT replicate 3

city: Sydney

first: Nicola

middle: J

last: Lee

state: NSW

address: 384 Victoria Street

department: Neuroscience

country: Australia

institute: Garvan Institute of Medical Research

description: osteoblastic cells from WT mouse

hyb_protocol: 5.5 ug of fragmented, labeled ss DNA was prepared for hybridisation. Samples were hybridised to arrays for 16 hours at 45^C in the Affymetrix GeneChip Oven. Arrays were washed on the Affymetrix Fluidics 450 instrument as per manufacturers protocol using the Affymetrix GeneChip Hybridisation Wash and Stain kit for cartridge arrays.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip 3000 7G Scanner instrument as per manufacturers protocol.

data_processing: Normalisation and probe set summarisation was performed using the robust multichip average implemented in the Affy library from R/Bioconductor. Differential gene expression was assessed for each probe set using Limma. All analyses were performed using Gene Pattern software.

source_name: Osteoblastic cells from WT mouse replicate 3

label_protocol: Affymetrix WT Ambion and WT terminal labelling kit was used according to the manufacturers instructions.

growth_protocol: Bone marrow stromal cells isolated from the femora and tibias of male mice expressing GFP under control of a 3.6kb fragment of the rat alpha1(I)-collagen promotor were cultured in control media for 7 days.

extract_protocol: Total RNA was extracted using a Qiagen Micro Rneasy kit according to the manufacturers instructions.

treatment_protocol: GFP-positive osteoblasts were collected by cell sorting using a FACS Vantage SE with FACSDiva SE software from trypsinised bone marrow stromal cell cultures after 7 days in culture.

tag: gender

value: Male

value: Osteoblastic cells

value: WT mouse


title: WT replicate 2

description: osteoblastic cells from WT mouse

source_name: Osteoblastic cells from WT mouse replicate 2


title: Group 4 (Biopsy #49)

description: Gene expression data from lung biopsy

source_name: Lung biopsy

tag: tissue

value: Lung biopsy

tag: bl ffpe dx

tag: f/u bx dx

tag: bl frozen dx

tag: age

tag: smoking pack/yr


title: WT replicate 1

description: osteoblastic cells from WT mouse

source_name: Osteoblastic cells from WT mouse replicate 1


title: KC-OSKM NoDox Stomach-1

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99℃ for 5 minutes, then 45℃ for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 80μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 17 hours at 45° at 60rpm• Fluidics washing is FS450_0007

scan_protocol: Affymetrix Gene ChIP Scanner 3000 TG

data_processing: Data analyses were processed using Genespring software (version13.0). For the analysis, C-OSKM NoDox pancreas-1_(MoGene-1_0-st-v1).CEL(raw), C-OSKM Dox3d pancreas-1_(MoGene-1_0-st-v1).CEL(raw), KC-OSKM NoDox Stomach-1_(MoGene-1_0-st-v1).CEL(raw), KC-OSKM NoDox Stomach-2_(MoGene-1_0-st-v1).CEL(raw), KC-OSKM NoDox Stomach-3_(MoGene-1_0-st-v1).CEL(raw), KC-OSKM 1w3w Stomach-1_(MoGene-1_0-st-v1).CEL(raw), KC-OSKM 2w2w Stomach-1_(MoGene-1_0-st-v1).CEL(raw), KC-OSKM 2w2w Stomach-2_(MoGene-1_0-st-v1).CEL(raw),were loaded using Genespring. Summarization algorithm is RMA-16.

label: Biotin

source_name: Stomach

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: RNeasy Plus Mini kit

value: Stomach

tag: strain

tag: Sex

value: chimeric mice with male ES cells


title: Dnmt3aKO_WGBS

description: Dnmt3aKO WGBS

tag: strain background


title: miR-155_OE_GFP_pos_rep1 [1M30G]

tag: genotype/variation

value: overexpressing miR-155

value: Spleen


title: Y1KO replicate 1

description: osteoblastic cells from Y1 deficient mouse

source_name: Osteoblastic cells from Y1KO mouse replicate 1

tag: cell type

value: Y1 deficient mouse


title: Y1KO replicate 2

source_name: Osteoblastic cells from Y1KO mouse replicate 2


title: KC-OSKM 2w2w stomach-1


title: KC-OSKM NoDox Stomach-2


title: WT replicate 4

description: osteoblastic cells from WT mouse

source_name: Osteoblastic cells from WT mouse replicate 4


title: KC-OSKM 1w3w stomach-1


title: C-OSKM NoDox pancreas-1

value: male


title: KC-OSKM NoDox Stomach-3


title: KC-OSKM 2w2w stomach-2


title: C-OSKM Dox3d pancreas-1


title: ctrl_GFP_neg_rep1 [1C30N]

value: control

value: CD8T cells

tag: cell subtype

value: GFP negative


title: ctrl_GFP_pos_rep1 [1C30G]

value: GFP positive


title: DKO_WGBS

description: DKO WGBS

value: Dnmt3a-/- Tet1-/-

value: embryonic stem cells

value: bisulfite converted genomic DNA


title: Control - L2_R1_CAGATC RNA-Seq

tag: cell line

value: porcine fetal retina

tag: infection status

value: Control


title: rat_right side of TMJ represented treating induced excessive mastication_8week_rep3

city: Hangzhou

first: YU

last: ZHAO

address: Yuhangtang Road 388#

country: China

institute: College of Pharmeceutical Sciences

description: miRNA expression of excessive mastication_8w_rat

hyb_protocol: After purification the labeled miRNAs were hybridized onto the microarray.

scan_protocol: After washing, the arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies). Feature Extraction software (Agilent Technologies) and Genespring software were utilized to analyze array images and the raw data.

organism: Rattus norvegicus

source_name: TMJ_treating induced excessive mastication_8w

label_protocol: Total miRNA was dephosphorylated, denaturated and then labeled with Cyanine-3-CTP.

extract_protocol: Total miRNA was extracted from 20 samples using mirVanaTM RNA Isolation Kit according to the instruction of manufacturer and the integrity was evaluated using agarose gel electrophoresis stained with ethidium bromide. Total miRNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the miRNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

value: temporomandibular joint

tag: time

value: female


title: rat_right side of TMJ represented treating induced excessive mastication_8week_rep4

data_processing: Feature Extraction software (Agilent Technologies) and Genespring software were utilized to analyze array images and the raw data.


title: rat_right side of TMJ represented treating induced excessive mastication_8week_rep1


title: rat_left side of TMJ represented chewing inability_8week_rep4

description: miRNA expression of chewing inability_8w_rat

source_name: TMJ_chewing inability_8w


title: rat_left side of TMJ represented chewing inability_8week_rep3


title: rat_left side of TMJ represented chewing inability_8week_rep1


title: rat_right side of TMJ represented treating induced excessive mastication_4week_rep2

description: miRNA expression of excessive mastication_4w_rat

source_name: TMJ_treating induced excessive mastication_4w


title: rat_left side of TMJ represented chewing inability_8week_rep2


title: rat_right side of TMJ represented treating induced excessive mastication_4week_rep4


title: rat_right side of TMJ represented treating induced excessive mastication_4week_rep1


title: rat_right side of TMJ represented treating induced excessive mastication_4week_rep3


title: MUI_3

city: Guangzhou

first: Lulu

last: Yan

state: Guangdong

address: No. 231 Xingang West Road

institute: South China Sea Fisheries Research Institute, CAFS

data_processing:
NGS QC Toolkit software used for quality control.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Then lean reads were used to undertake de novo transcriptome assembly with Trinity (version: trinityrnaseq_r2013 1110) software and get transcripts. TGICL software was employed to get unigenes based on the assembled transcript.
Fragments Per kb per Million reads (FPKM) were calculated using a protocol from Trapnell et al., Nature Biotechnology, 2010.
Genome_build: NR, SWISSPROT, KOG
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample.

organism: Sthenoteuthis oualaniensis

source_name: intestine

extract_protocol:
Intestines and stomachs were removed, flash frozen on dry ice, and RNA was harvested using mirVanaTM miRNA ISOlation kit, Ambion-1561. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2101) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: intestine

tag: developmental stage

value: immature

tag: form

value: medium form


title: MDS_3

source_name: stomach

tag: tissue

value: stomach

value: mature


title: MUI_2


title: MDS_2


title: MUI_1


title: rat_left side of TMJ represented chewing inability_4week_rep4

description: miRNA expression of chewing inability_4w_rat

source_name: TMJ_chewing inability_4w

tag: gender


title: MUS_1


title: MUS_3


title: MDS_1


title: MDI_3


title: MUS_2


title: WTX Overexpression group

first: Jian

last: Li

address: 1023-1063，Shatai South Road, Baiyun District

institute: Southern Medical University

description:
Gene expression data from AGS overexpressing WTX
OV

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and RMA as normalization method.

source_name: Overexpression cells_WTX

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

extract_protocol: Total RNA of parietal cortex of the patient was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

value: AGS

value: gastric cancer


title: Negative control group

description:
Gene expression data from AGS  negative control
NC

source_name: Negative control cells


title: rat_left side of TMJ represented chewing inability_4week_rep3


title: UM2, biological rep2

city: Chicago

first: Xiaofeng

last: Zhou

state: Illinois

address: 801 S Paulina Street

institute: University of Illinois at Chicago

description:
Gene expression data from oral tongue cancer cell line
UM2B

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: The scanned array images were processed with GeneChip Operating software (GCOS). The microarray data were pre-processed using Robust Multi-array Analysis (RMA).

source_name: UM2 cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: standard protocol and conditions

extract_protocol: Qiagen RNAeasy kit

value: oral tongue cancer cell line UM2


title: UM1, biological rep2

description:
Gene expression data from oral tongue cancer cell line
UM1b

source_name: UM1 cell line

value: oral tongue cancer cell line UM1


title: UM1, biological rep1

description:
Gene expression data from oral tongue cancer cell line
UM1a


title: rat_right side of TMJ represented treating induced excessive mastication_8week_rep2


title: MDI_2


title: MDI_1


title: UM2, biological rep1

description:
Gene expression data from oral tongue cancer cell line
UM2A


title: DUS_3

value: dwarf form


title: rat_left side of TMJ represented chewing inability_4week_rep2


title: DUS_2


title: rat_left side of TMJ represented chewing inability_4week_rep1


title: rat_left side of TMJ represented chewing inability_0week_rep4

description: miRNA expression of chewing inability_0w_rat

source_name: TMJ_chewing inability_0w


title: rat_left side of TMJ represented chewing inability_0week_rep3


title: DUI_3


title: rat_left side of TMJ represented chewing inability_0week_rep1


title: DDS_3


title: DUI_1


title: fbfemale_r1

city: Stanford

first: Peter

middle: Acuña

last: Combs

address: Gilbert Rm 309, 371 Serra Mall

department: Biology

institute: Stanford University

data_processing:
Base calling:
Transcript Quantification: kallisto v0.44.0
Mapping: STAR 2.5.1b
Filtering: Hornet
ASE calling: ASEr commit 7827e53857
Genome_build: FlyBase D. simulans r2.01_FB2016_01
Supplementary_files_format_and_content: Transcript abundances: tab separated values
Supplementary_files_format_and_content: Reference/alternate read counts by gene: tab separated values
Supplementary_files_format_and_content: summary_kallisto.tsv: transcript level abundances
Supplementary_files_format_and_content: summary_kallisto_genes.tsv: gene level abundances
Supplementary_files_format_and_content: summary_ase_refalt.tsv: reference/alternate allele counts by gene

organism: Drosophila sechellia x Drosophila simulans

source_name: Female fat body

growth_protocol: Hybrid flies were reared in a 12hr light:12 hr dark cycle and tissues dissected at equal time intervals across a 24hr period.

extract_protocol:
Immediately following dissection tissues were placed into cell lysis buffer to aid in preserving the integrity of the RNA. Total RNA was isolated using the RNeasy Micro kit (Qiagen).
NextFLEX RNA-seq library preparation kit (BioO Scientific, Austin, TX)

treatment_protocol: The oenocytes and fat body of 10-day-old D. simulans/D. sechellia hybrid flies were isolated separately from the dorsal abdominal segments of both adult male and female abdomens.

value: fat body

tag: genetic background

value: D. sechellia x D. simulans F1 hybrid


title: fbmale_r1

source_name: Male fat body

value: male


title: fbmale_r2


title: fbfemale_r2


title: deltaNP63-2

first: Wen

last: Luo

address: Wushan

institute: South China Agricultural University

description: chicken deltaNp63α overexpressing myoblast

data_processing:
BGI SOAPnuke software used for trimming and filtering.
Sequenced reads were mapped to gga5 whole genome using HISAT2 v2.0.4 with parameters --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
Gene expression analysis step 1: sequenced reads were then mapped to gga5 whole genome using Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression analysis step 2: Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using RSEM v1.2.12.
Genome_build: gga5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Gallus gallus

source_name: chicken embryo myoblast

growth_protocol: chicken primary myoblasts were growed in growth medium containing RPMI-1640, 15% FBS and 2% pen/srep

extract_protocol:
Total RNA of the proliferating myoblasts were harvested using Trizol reagent according to the manufacturer’s direction.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: chicken primary myoblasts were transfected with TAp63α, deltaNp63α, or GFP overexpression vectors using lip3000 reagent

value: chicken embryo skeletal muscle derived myoblasts

value: proliferating myoblast

tag: passages

tag: transfection


title: GFP-1

description: chicken GFP overexpressing myoblast

value: GFP vector


title: DDS_1


title: deltaNP63-1


title: GFP-2

description: chicken GFP overexpressing myoblast


title: GFP-3

description: chicken GFP overexpressing myoblast


title: deltaNP63-3


title: TAp63-3

description: chicken TAp63α overexpressing myoblast


title: oemale_r2

source_name: Male oenocyte

value: oenocyte


title: oemale_r1


title: TAp63-2

description: chicken TAp63α overexpressing myoblast


title: DDI_2

value: intestine


title: DUS_1

value: immature


title: TAp63-1

description: chicken TAp63α overexpressing myoblast


title: oefemale_r2

source_name: Female oenocyte

value: female


title: DDI_1


title: DUI_2


title: rat_left side of TMJ represented chewing inability_0week_rep2

value: temporomandibular joint


title: DDS_2

value: stomach

value: mature


title: oefemale_r1


title: DDI_3


title: MV4-11_APTO-253 Rep2

status: Public on May 15 2018

city: San Diego

first: Hongying

last: Zhang

address: 3550 General Atomics Court, MS G02/420

institute: Aptose Biosciences

data_processing:
The FASTQ files were downloaded from UCSD and the overall quality of the data was assessed first by quality score distribution, read base distribution and sequence overrepresentation using FastQC v0.11.4  was assessed first by quality score distribution, read base distribution and sequence overrepresentation using  FastQC v0.11.4
The reads were aligned to the human genome build 37 using SubRead v1.5.0-p1 keeping only uniquely mapped reads.  were aligned to the human genome build 37 using SubRead v1.5.0-p1
The featureCounts v1.5.0-p1 program was used to counts reads relative to  Ensembl 75 gene models with respect to strandedness  to Ensembl 75 gene models with respect to strandedness.
A multi dimensional scaling (MDS) plot using the edgeR package was generated.  package was generated.
Trimmed mean of M saling normalization factors were computed and used with the voom approach. Empirical Bayes approach implemented by limma was used to fit a linear model contrasting vehicle and APTO-253 treated samples. The p-values were adjusted using the false discovery rate method of Benjamin and Hochberg. Genes were considered to be differentially expressed if their adjusted p-value was less than 0.05 level and their fold change was greater than 2 in either direction.
Genome_build: Human GRCh37/hg19
Supplementary_files_format_and_content: bigWig files and an excel spreadsheet of expression summary values, fold change expression and p-values were generated.

growth_protocol: MV4-11 cells were seeded in RPMI media supplemented with 10% FBS at 0.4 x 106 cells per ml. Cells were treated with either 0.1% DMSO or 500 nM APTO-253 fro 6 hours before harvesting.

extract_protocol:
Total cellular RNA was isolated using the RNeasy mini kit (QIAGEN cat# 74134) from 2 independent samples for each treatment condition. Total RNA was polyA selected and libraries were contructed using the Iluumina Tru-seq kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: AML cell line

tag: treatment

tag: treatment time

value: 6 hours


title: MV4-11_APTO-253 Rep1


title: MV4-11_Vehicle Rep2

value: DMSO


title: MV4-11_Vehicle Rep1


title: Sheep 27:rep 2

city: Camden

first: Auriol

middle: Cecilia

last: Purdie

address: 402 Werombi Rd

department: Faculty of Science, Sydney School of Veterinary Sciences

institute: University of Sydney

description: This sample failed quality control. No processed data available.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Bovine Affymetrix® GeneChip® 3’IVT array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

data_processing: Affymetrix genechip operating software (command console) derived raw expression values were obtained as .CEL files and transferred to Partek Genomic Suite 7 software (Partek Inc.) for analysis.

organism: Ovis aries

source_name: White Blood Cells, MAP exposed

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated from WBC samples using the RNAspin Mini RNA isolation kit (Illustra, GE Healthcare)

value: White Blood Cells

tag: animal #

value: MpTb

tag: disease status

value: resilient

tag: weeks post map


title: Sheep 26:rep5

tag: cell type


title: Sheep 30:rep 1


title: Sheep 30:rep 6


title: Sheep 26:rep4


title: Sheep 30:rep 4


title: P3GBM_HighPDGFA_rep1

city: Beijing

first: Hua-Jun

last: Wu

state: Beijing

address: 8 science park road, zhongguancun life science park

department: School of Basic Medical Sciences

institute: Peking University Health Science Center

description:
hPDGF-A;hPDGFRα;p53lox,DOX 600mg/kg
PDGFRA_600_1

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix mouse GeneChip 2.0 ST microarrays. The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Affymetrix MoGene-2_0-st microarray data were processed using R packages and BioConductor. The raw hybridization signals were normalized using the robust multichip average method and transformed to log 2 values. The SVA method was then used to remove undersigned variations.

label_protocol: Labeling was performed according to manufacturer’s guidelines for use with the Affymetrix Mouse HuGene-2_0-st-v1 GeneChips (Affymetrix, Inc).

extract_protocol: Total RNA was isolated from flash frozen tumors freshly excised from mice using Qiagen RNeasy RNA Isolation Kit.

value: tumor from mouse model of GBM

tag: genotype

value: 600mg/kg DOX


title: Sheep 30:rep 5


title: 3D13-16_100mJ+ANS_d3_2

city: Aachen

first: Sebastian

last: Huth

address: Pauwelsstr. 30

country: Germany

institute: Uniklinik RWTH Aachen

hyb_protocol: Hybridization cocktails containing 5.5 Ig of fragmented, end-labelled cDNA were prepared and applied to GeneChip Human Gene 2.0 ST arrays. Hybridization was performed in 45°C hybridization oven at 60 rpm for 16 hours. Using the GeneChip® Fluidics Station 450 the hybridized GeneChip® Human Gene 2.0 ST Arrays were washed and stained (Fluidics Protocol FS450_0001).

scan_protocol: Arrays were scanned using Affymetrix GeneChip® Scanner 3000 7G controlled by GeneChip®Operating Software (GCOS) version 1.4 to produce CEL intensity files.

data_processing:
Data analysis from the arrays were processed using GeneSpring GX 14.9 software (Agilent Technologies).
[probe group file] HuGene-2_0-st
[meta-probeset file] Affymetrix.ExonExprChip.HuGene-2_0-st_na35_hg19_2015-04-15
Expression values of each probe set were determined using the GeneSpring GX 14.9 software (Agilent Technologies). Normalization method: Quantile.

source_name: fibroblasts and keratinocytes

label_protocol: 300µg total RNA from each model were processed using the WT Expression Kit (Ambion)  to generate amplified sense-strand cDNA. Fragmentation and labeling was done using the Affymetrix® GeneChip® WT Terminal Labeling Kit Assay (Affymetrix, Inc., Santa Clara, CA, USA).

growth_protocol: Normal primary human keratinocytes and fibroblasts were isolated from biopsies of adult non-keratinized oral mucosa. Single cell suspension of NHOK was grown in serum free KGM (Lonza). Isolated fibroblasts were grown in DMEM Medium high glucose and L-Glutamin (Invitrogen), containing 10% FCS (Biochrom, Berlin, Germany). To construct the lamina propria equivalent, collagen gels were prepared by mixing 8 volumes of ice-cold bovine collagen I solution (Vitrogen; Cohesion Technologies, Palo Alto, CA, USA) with 1 volume of 10x Hank’s balanced salt solution (Gibco/Invitrogen). After neutralization with 1 M NaOH, 1 volume of NHOF suspended in FCS was added. The final concentration of NHOF in this gel solution was 5 x 105 cells/ml. Three milliliters of this gel solution were poured into each polycarbonate membrane insert (3,0 µm pore size; Thermo Fisher Scientific, Langenselbold, Germany) on 1 ml acellular collagen gel and placed in 6-well plates. Following complete polymerization, gels were covered with DMEM containing 10% FCS, 50µg/ml ascorbic acid, 100 U/ml penicillin and 100 mg/ml streptomycin and incubated in a humidified atmosphere at 37 ° C and 5% CO2. After 2 days, 2 x 106 NHOK were seeded on each lamina propria equivalent. The originated models were cultured in equal volumes of DMEM and keratinocyte growth medium containing 5% FCS, 100 U/ml penicillin, 100 mg/ml streptomycin, 50 µg/ml ascorbic acid and 10ng/ml KGF.  After 2 days of submerged culture, the mucous membrane equivalents were lifted to the air-liquid interface. Cultivation of the models was continued and medium change was done every other day.

extract_protocol: Total RNA was isolated using the Nucleo Spin II RNA Mini Kit, (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions, including on-column digestion of DNA with RNase-free DNase I.

treatment_protocol: Irradiation induced lesions were performed on complete stratified and organized 3D mucous membrane models. Models were irradiated with the non‐sequential ultrapulsed fractional carbon dioxid (CO2) laser (Encore®, Lumenis, Dreieich, Germany; CPG handpiece, energy 100 mJ, 100 Hz, density 1, 1 pass). During laser irradiation, culture medium was removed and models were placed on a cooling plate to compensate and reduce thermal effects of laser Radiation intensity was kept under equal conditions by fixing the laser head on a tripod.  After treatment, models were cultivated with fresh culture medium and harvested on day 0, 3 and 5 in OCT compound for cryosectioning. An untreated model was maintained as a negative control at given times.  Lesional 3D skin equivalents were subsequently treated topically with 5% dexpanthenol-containing verum (eye and nose ointment®;Bayer, Leverkusen, Germany), or without 5% dexpanthenol-containing placebo (Bayer) on a daily basis.

value: oral mucosa

value: fibroblasts and keratinocytes


title: Sheep 30:rep 2


title: P3GBM_LowPDGFA_rep2

description:
hPDGF-A;hPDGFRα;p53lox,DOX 25mg/kg
PDGFRA_25_3

value: 25mg/kg DOX


title: Sheep 27:rep 4


title: P3GBM_HighPDGFA_rep3

description:
hPDGF-A;hPDGFRα;p53lox,DOX 600mg/kg
PDGFRA_600_3


title: OPC_rep1

description:
hPDGFRα;p53,DOX 600mg/kg
CK_600_1

source_name: OPC

value: oligodendrocyte precursor cells from mouse model of GBM


title: Sheep 27:rep 5


title: Sheep 27:rep 1


title: Sheep 30:rep 3


title: P3GBM_LowPDGFA_rep1

description:
hPDGF-A;hPDGFRα;p53lox,DOX 25mg/kg
PDGFRA_25_1


title: P3GBM_HighPDGFA_rep2

description:
hPDGF-A;hPDGFRα;p53lox,DOX 600mg/kg
PDGFRA_600_2


title: 3D13-16_100mJ Placebo_d3_1

value: 100mJ Placebo


title: P3GBM_LowPDGFA_rep3

description:
hPDGF-A;hPDGFRα;p53lox,DOX 25mg/kg
PDGFRA_25_4


title: Sheep 26:rep3


title: OPC_rep2

description:
hPDGFRα;p53,DOX 600mg/kg
CK_600_2


title: Sheep 23:rep 4


title: Sheep 26:rep2


title: Sheep 23:rep 5


title: Sheep 26:rep1


title: Sheep 23:rep 3


title: OPC_rep3

description:
hPDGFRα;p53,DOX 600mg/kg
CK_600_3


title: Sheep 20:rep 4


title: Sheep 20:rep 3


title: Sheep 18:rep 5


title: Sheep 20:rep 2


title: Sheep 19:rep 2


title: Sheep 20:rep 1


title: Sheep 27:rep 3


title: Sheep 19:rep 1


title: Sheep 17:rep 3


title: Sheep 23:rep 2


title: Sheep 23:rep 1


title: Sheep 17:rep 4


title: Sheep 18:rep 3


title: Sheep 17:rep 2


title: Sheep 19:rep 3


title: Sheep 20:rep 5


title: Sheep 18:rep 4


title: Sheep 18:rep 1


title: Sheep 17:rep 1


title: Sheep 12:rep 5


title: Sheep 14:rep 4


title: Sheep 18:rep 2


title: Sheep 19:rep 5


title: Sheep 14:rep 1


title: Sheep 17:rep 5


title: Sheep 12:rep 2


title: Sheep 19:rep 4


title: Sheep 14:rep 3


title: Sheep 14:rep 2


title: Sheep 12:rep 4


title: Sheep 21:rep 5

value: paucibacillary


title: Sheep 21:rep 4


title: Sheep 11:rep 2


title: Sheep 16:rep 4


title: Sheep 16:rep 5


title: Sheep 21:rep 2


title: Sheep 16:rep 3


title: Sheep 21:rep 1


title: Sheep 21:rep 3


title: Sheep 11:rep 3


title: Sheep 16:rep 6


title: Sheep 15:rep 3


title: Sheep 11:rep 4


title: Sheep 15:rep 2


title: Sheep 16:rep 1


title: Sheep 16:rep 2


title: Sheep 12:rep 3


title: Sheep 15:rep 1


title: Sheep 15:rep 4


title: Sheep 11:rep 1


title: Sheep 28:rep 5

value: multibacillary


title: Sheep 28:rep 4


title: Sheep 15:rep 5


title: Sheep 28:rep 3


title: Sheep 29:rep 2


title: Sheep 29:rep 3


title: Sheep 29:rep 1


title: Sheep 25:rep 2


title: Sheep 28:rep 1


title: Sheep 22:rep 3


title: Sheep 24:rep 4


title: Sheep 25:rep 1


title: Sheep 24:rep 1


title: Sheep 25:rep 3


title: Sheep 22:rep 5


title: Sheep 22:rep 4


title: Sheep 22:rep 2


title: Sheep 24:rep 3


title: Sheep 22:rep 1


title: Sheep 13:rep 1


title: Sheep 25:rep 4


title: Sheep 5:rep 6

source_name: White Blood Cells, unexposed

value: Unexposed

value: Control


title: Sheep 5:rep 5


title: Sheep 29:rep 4


title: Sheep 13:rep 5


title: Sheep 5:rep 4


title: Sheep 13:rep 2


title: Sheep 4:rep 4


title: Sheep 25:rep 5


title: Sheep 5:rep 3


title: Sheep 13:rep 3


title: Sheep 5:rep 1


title: Sheep 2:rep 2


title: Sheep 4:rep 3


title: Sheep 4:rep 5


title: Sheep 4:rep 1


title: Sheep 4:rep 2


title: Sheep 24:rep 2


title: Sheep 3:rep 5


title: Sheep 3:rep 1


title: Sheep 3:rep 2


title: Sheep 13:rep 4


title: Sheep 3:rep 3


title: Sheep 5:rep 2


title: Sheep 2:rep 3


title: Sheep 2:rep 1


title: Sheep 2:rep 4


title: Sheep 3:rep 4


title: Sheep 1:rep 1


title: Sheep 1:rep 3


title: Sheep 1:rep 4


title: Sheep 1:rep 5


title: Sheep 1:rep 2


title: Sheep 28:rep 2


title: 80WtD

city: Vestec by Prague

first: Gabriela

last: Pavlínková

address: Průmyslová 595

department: Laboratory of Molecular Pathogenetics

country: Czech Republic

institute: Institute of Biotechnology, CAS, v.v.i

data_processing:
Ribosomal RNA sequences were removed using sortmerna (version 2) and the SILVA rRNA database (version 119). Low quality reads and adaptor sequences were removed using Trimmomatic PE. Reads were aligned against the reference Mus musculus genome v GRCm38 using STAR (version 2.5.2b).
Annotated reads were counted using htseq-count with the reference model gencode.vM8.annotation.gtf
Normalized number of reads was generated by DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include non-normalized and DESeq2 normalized number of reads for each Sample

source_name: cardiac left ventricle

extract_protocol:
Total RNA was isolated using TRIzol, libraries were prepared following manufacturer’s instructions at the Genomics Core Facility (EMBL Heidelberg, Germany) (KIT?)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cardiac left ventricle

tag: age

value: 12 weeks

value: female

tag: biological replicate

value: wild type

tag: experiment

value: diabetic pregnancy


title: 66Hif1D


title: 72Hif1D


title: 89WtC

value: non-diabetic pregnancy


title: 44Hif1C


title: 42WtC


title: 25WtC


title: 32Hif1C


title: 77Hif1D


title: 14Hif1C


title: 7WtD


title: 50WtD


title: Sheep 2:rep 5

value: White Blood Cells


title: WT_E10.0_CHD4_ChIP_Rep3

city: Chapel Hill

first: Austin

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
RNA fastq files were first filtered for reads containing adapter sequences using TagDust (v1.12) with and FDR of 0.001. Reads were then mapped to the mm10 genome using Bowtie (v1.2.0) and options: -m 1, --best, --seed=123, and --nomaqround. Post-alignment, samtools (v1.6) and BedTools (v2.25.0) were used to interconvert and manipulate files. HTSeq (v0.6.2), using the refFlat gtf from UCSC Genome Browser, was run to get read counts over genes and these counts were used in DESeq2 (v1.6.3) to determine differential transcripts.
ChIP fastq files were first filtered for reads containing adapter sequences using TagDust (v1.12) with and FDR of 0.001. In-house scripts were used to ensure TagDust filtered reads were maintained in the proper order for alignment. Reads were then mapped to the mm10 genome using Bowtie (v1.2.0) using options: -m 1, --best, --seed=123, --nomaqround. Aligned fragments were then filtered for any duplicate reads based on alignment position using in-house scripts. Samtools (v1.6) and BedTools (v2.25.0) were used to interconvert and manipulate files. Peaks were called with MACS2, and only high confidence peaks (found in at least two of the three replicates) were used in downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files contain genomic signal tracks, normalized by total read depth per million. Duplicate and unproperly paired (for paired-end) reads have been filtered out. Bed files contain peaks called by MACS2 between the control sample as its relative input sample. The combined bed contains the merged collection of peaks that were found in at least 2 of 3 replicates. DESeq2 files contain the differentially expressed genes between Chd4(flox/flox) and Chd4(Δflox/Δflox) cardiac tissues for each timepoint (E9.5 and E10.5). RPKM files contain a tab-delimited matrix of all calculated RPKMs for each gene in each RNA timepoint.

source_name: E10.0 cardiac tissue

extract_protocol:
Embryonic hearts were collected in PBS, fixed and DNA was isolated for ChIP-seq according to methods in [Wilczewski et. Al, 2017].
Libraries were prepared using the Nextera XT DNA Library Kit.

tag: strain

value: WT

tag: development stage

value: Embryonic day 10.0

value: cardiac

tag: chip antibody

value: Anti-CHD4 antibody [3F2/4] - ChIP Grade, Abcam, catalog# ab70469, mouse monoclonal


title: WT_E10.0_ChIP_Input_for_Rep2and3

tag: tissue


title: WT_E10.0_ChIP_Input_for_Rep1


title: Localized tumor H3K27me3_FigS4C_T4

city: Boston

first: Matthew

last: Freedman

state: Massachusetts

address: 450 Brookline Avenue

institute: Dana Faber Cancer Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using Bowtie.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline

source_name: Localized tumor H3K27me3

extract_protocol:
One (histone ChIP) or three (transcription factor ChIP) 2 mm2 frozen cores were pulverized using the Covaris CryoPrep system. Tissue was fixed using 1% formaldehyde and chromatin sheared to 300-500 bp in size using the Covaris E220 ultrasonicator. Resulting chromatin was incubated overnight with indicated antibodies. Purified immunoprecipitates were isolated and quantified by Qubit fluorometer.
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep kit (Rubicon Genomics). Libraries were sequenced using 75-bp reads on the Illumina platform at the Dana-Farber Cancer Institute.

value: localized prostate tumor tissue

tag: chip antibody vendor

value: Cell Signaling Technology

tag: chip antibody cat.#

tag: chip antibody lot/batch#

tag: chromosome

value: Control location


title: WT_E10.0_CHD4_ChIP_Rep1


title: WT_E10.0_CHD4_ChIP_Rep2


title: monocytes_3d_R848_rep2

city: Heidelberg

first: Mariel

last: Eberle

address: Im Neuenheimer Feld 324

department: Department of Hygiene and Microbiology

institute: University Hospital Heidelberg

description: 114_4 R848

hyb_protocol: 200 ng of labeled miRNA was hybridized for 20 hrs at 55°C on Agilent human miRNA Microarray Release 16.0, 8x60k.

scan_protocol: For scanning process of the microarrays, Agilent Scanner G2505C was used (DKFZ core facility, TP3, Heidelberg, Germany).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default settings.

source_name: human blood monocytes_R484

label_protocol: Fluorescently labeled (Cyanine-3) mi-c-RNA was prepared according to the respective protocol from Agilent (miRNA Complete labeling and Hyb kit, Agilent Technologies, Berlin, Germany).

growth_protocol: Cells were isolated via AutoMACS (possel) and seeded in 24-well plate format. To obtain immature DCs, cells were supplemented with 10 ng/ml rhGM-CSF and 20 ng/ml rhIL-4. After 3 days of culture, cells were harvested, lysed and RNA was isolated.

extract_protocol: After 72h in culture, 4x10^6 cells were harvested, lysed and total RNA was extracted using the High Pure RNA Isolation kit (Roche, Mannheim, Germany). At least 500 ng of purified RNA was applied to miRNA analysis. Purity and concentration of total RNA was determined via Gel analysis using the Nanodrop 2100 bioanalyzer, version 2.6 (DE54700489, Agilent Technologies, Berlin, Germany).

treatment_protocol: In Order to obtain R848-treated APCS, 1 µg/ml R848 was  added to the cell culture samples

value: CD14+ monocytes

tag: treated with

tag: age of cells in culture

value: 3 days

tag: monocytic phenotype

value: CD1a- CD14+

tag: molecule subtype

value: microRNA


title: Localized tumor H3K27me3_FigS4C_T3


title: Localized tumor H3K4me2_FigS4C_T4

source_name: Localized tumor H3K4me2

value: Millipore


title: Localized tumor H3K27me3_FigS4C_T1


title: monocytes_3d_R848_rep3

description: 114_5 R848

tag: cell type


title: monocytes_3d_rep2

description: 114_4 G4

source_name: human blood monocytes


title: Localized tumor H3K27me3_FigS4C_T2


title: monocytes_3d_R848_rep1

description: 114_1 R848


title: monocytes_3d_rep1

description: 114_1 G4


title: Localized tumor H3K4me2_FigS4C_T2


title: Localized tumor H3K4me2_FigS4C_T1


title: A375 24h 3 µM vem treatment 2

first: Jochen

last: Utikal

address: Im Neuenheimer Feld 280

department: Clinical Cooperation Unit Dermato-Oncology

institute: German Cancer Research Center

description: A375 + 24h vem (3µM) 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: melanoma metastasis

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell line

tag: agent

value: vemurafenib


title: monocytes_3d_rep3

description: 114_5 G4


title: Localized tumor H3K27Ac_FigS4C_T4

source_name: Localized tumor H3K27Ac

value: Diagenode


title: Localized tumor H3K4me2_Fig5A_T1

value: AR enhancer location


title: Localized tumor FOXA1_Fig5A_T4

source_name: Localized tumor FOXA1

value: Abcam


title: Localized tumor H3K27me3_Fig5A_T1


title: A375 24h 3 µM vem treatment

description: A375 + 24h vem (3µM)


title: Localized tumor FOXA1_Fig5A_T1


title: A375 24h DMSO treatment 2

description: A375 + 24h DMSO 2

value: DMSO


title: Sheep 12:rep 1

value: White Blood Cells

tag: animal #

tag: treatment

value: MpTb

tag: disease status

value: resilient

tag: weeks post map


title: A375 24h 3 µM vem treatment 1

description: A375 + 24h vem (3µM) 1


title: SULF2_MUT2

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

country: South Korea

institute: Ajou University School of Medicine

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: SULF2_MUT, Hep3B

growth_protocol: Hep3B cells were grown in DMEM medium supplemented with 10% FBS.

extract_protocol: Total RNA was isolated using the mirVana total RNA extraction Kit.

treatment_protocol: SULF2_MUT refers to cells with N491K mutation in SULF2 gene.

value: liver cancer cell line Hep3B

tag: genotype/variation

value: SULF2_MUT (N491K mutation)


title: A375 24h DMSO treatment

description: A375 + 24h DMSO


title: Localized tumor H3K27Ac_FigS4C_T3

tag: tissue

value: localized prostate tumor tissue

tag: chip antibody


title: Localized tumor H3K27Ac_FigS4C_T2

tag: chip antibody vendor

tag: chip antibody cat.#

value: Control location


title: Vector2

source_name: Vector, Hep3B

value: control


title: SULF2_MUT1


title: Localized tumor H3K4me2_FigS4C_T3

tag: chip antibody lot/batch#

tag: chromosome


title: Localized tumor H3K27Ac_FigS4C_T1


title: Localized tumor FOXA1_Fig5A_T3


title: A375 24h DMSO treatment 1

description: A375+ 24h DMSO 1


title: Localized tumor HOXB13_Fig5A_T2

source_name: Localized tumor HOXB13

value: Santa Cruz Biotechnology


title: SULF2_WT1

source_name: SULF2_WT, Hep3B


title: Localized tumor HOXB13_Fig5A_T1


title: Metastatic tumor H3K27Ac_Fig1_M4

source_name: Metastatic tumor H3K27Ac

value: metastatic prostate tumor tissue


title: Anti ELL2 plasma cell line ChIPseq

city: Pittsburgh

first: Christine

last: Milcarek

address: 200 Lothrop Street

department: Immunology

institute: University of Pittsburgh

data_processing:
Sequences (50 nt reads, single end) were aligned to the mouse genome (mm10) using the BWA algorithm.
Alignments were extended in silico at their 3’-ends to a length of 150 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome.
ZNF384 peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of pvalue = 1e-7. RNA Pol II enriched regions were identified using the SICER algorithm (v1.1) with a cutoff of FDR = 1E-10 and a gap size of 3x fragment size (200 bp). Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Genome_build: UCSC genome broswer, mm10

source_name: AxJ plasma cell line

growth_protocol: AxJ cells (IgG2a) were grown in IMDM (Invitrogen) with 10% FCS, 10mM glutamax, 100u Pen strep.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. An aliquot of chromatin (30 ug) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 ug antibody against ELL2, or 3 ul of antibody against H3K4me3 (Active Motif, 39159). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
ChIP and Input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the 3’-ends. Illumina genomic adapters were ligated and the sample was size-fractionated (200-300 bp) on an agarose gel. After a final PCR amplification step (18 cycles), the resulting DNA libraries were quantified and sequenced on HiSeq 2000.

treatment_protocol: Cell were verified as plasma cells by RT-PCR and western blots for increased blimp-1, J chain, ELL2 and PC4 expression. The V-region was sequenced as previously described Shell et al (2007) JI 179:7663-7673. Extract protocol as described below.

value: AxJ


title: Anti ELL2 plasma cell line ChIPseq CONTROL


title: Localized tumor HOXB13_Fig5A_T4


title: Vector1


title: Localized tumor H3K27Ac_Fig1_T2


title: Localized tumor FOXA1_Fig5A_T2


title: Localized tumor H3K27Ac_Fig5A_T1


title: Metastatic tumor H3K27Ac_Fig1_M3


title: Metastatic tumor H3K27Ac_Fig1_M2


title: Localized tumor H3K27Ac_Fig1_T5


title: Metastatic tumor H3K27Ac_Fig1_M1


title: SULF2_WT2


title: Localized tumor HOXB13_Fig5A_T3


title: HeLa_G2M_ChIP-Seq_rep2

city: NEW HAVEN

first: MANOJ

last: PILLAI

state: CT

address: 300 GEORGE STREET #786

institute: YALE UNIVERSITY

description:
Two replicates (G2M1 and G2M2)
G2M.bw
G2M_Peaks_annotated.txt

data_processing:
Illumina Casava software used for basecalling.
ChIP-Seq files were trimmed with trimmomatic and aligned with Bowtie2 to hg19 build
ChIP-Seq peak calls performed with HOMER V4.9
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files generated for ChIP-Seq data using deepTools, tab limited peak files for ChIP-Seq data, tab limited Cufflinks output files for gene expression and tab limited files.

source_name: HeLa Cell line, G2/M synchronized

growth_protocol: HeLa cells were cultured in DMEM (Gibco Life Technologies) supplemented with 10% fetal bovine serum (FBS) (Gemini Bioproducts) and 1X penicillin/streptomycin (Pen/Strep) (Gibco Life Technologies).

extract_protocol:
For ChIP-Seq, Cells were lysed using nucleosome lysis buffer (60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 15 mM Tris-HCl pH 7.5, 0.2% NP-40) supplemented with 0.1 mM DTT and PPI. Lysates were then passed through a sucrose cushion (50 mM Tris-HCl pH 7.5, 5 mM MgCl2, 25 mM KCl, 1.2M Sucrose) by centrifugation at 3.5g for 15 minutes at 4 ˚C. The pellet (containing the nuclei) was resuspended in the digestion buffer (50 mM Tris-HCl pH 7.5, 4mM MgCl2, 1mM CaCl2, 0.32 M Sucrose) with 200U micrococcal nuclease (Mnase) (Worthington Biochemical) and incubated for 10 minutes at 37 ˚C. Digestion was stopped by the addition of 1 mM each of EDTA and EGTA. Nuclei were pelleted by centrifugation at 3.5g for 10 minutes at 4 ˚C. Pellet was resuspended in 500 µl solubilization buffer ( 50mM HEPES pH 7.6, 500mM LiCl, 1mM EDTA, 0.7% sodium deoxycholate, 0.1% SDS and 1% NP-40) and rotated at 4 ˚C for 1 hour followed by centrifugation at 12,000g for 10 minutes at 4 ˚C. The pellet was discarded and the supernatant, the nucleosome enriched fraction, was used for immunoprecipitations and immunoblot assays. DNA was extracted from a small aliquot of the nucleosome-enriched fraction using phenol: chloroform: isoamyl alcohol (Thermo Fisher Scientific 15593031) and run on a 2% agarose gel to confirm the expected size of the digested DNA (147 bp and multiples thereof).  For immunoprecipitations, nucleosome enriched fractions were diluted to 1 ml in dilution buffer (0.005% SDS, 0.1% Triton X-100, 1.2 mM EDTA, 1.67 mM Tris HCl pH8.0, 167 mM NaCl ) and incubated with antibodies (2 µg/sample) conjugated to Sepharose A or G beads with rotation at 4 ˚C overnight. Beads were washed with dilution buffer 3x and immunoblots were performed as described above. RNAse-A treatment was performed as described in [REF Ast Paper].
ChIP-Seq Libraries for sequencing were prepared using NEBNext Ultra DNA Library Preparation Kit (NEB E7370).

treatment_protocol: HeLa cells were synchronized in G2/M by culturing in their respective growth media with 40 ng/mL Nocodazole (Sigma-Aldrich, M1404) for 20 hours. For G1/S synchronization, HeLa cells were cultured in growth media with 40 ng/mL Nocodazole for 16 hours.

tag: cell cycle

value: G2/M synchronized

value: MBL D221-3 (Abcam)

value: HeLa


title: Localized tumor H3K27Ac_Fig1_T1

value: Diagenode

value: AR enhancer location


title: CHD4_null_E10.5_RNA_Rep2

description: polyA/Stranded

source_name: E10.5 Chd4(Δflox/Δflox) cardiac tissue

extract_protocol:
Embryonic hearts were collected in PBS, then RNA was collected in Trizol reagent. 300ng RNA was used for library preparation.
Illumina Tru-seq stranded mRNA sample prep kit was used for library preparation.

tag: strain

tag: genotype

tag: development stage

value: Embryonic day 10.5

value: cardiac


title: HeLa_G2M_RNA-Seq

description:
Two replicates (G2M1 and G2M2)
gene_exp.diff

data_processing:
Illumina Casava software used for basecalling.
ChIP-Seq files were trimmed with trimmomatic and aligned with Bowtie2 to hg19 build
RNA-Seq files were trimmed with trimmomatic and aligned with STAR aligner to hg19
ChIP-Seq peak calls performed with HOMER V4.9
RNA-Seq differential expression analysis performed with Cufflinks package version 2.2.0
RNA-Seq differential expression analysis performed with Cufflinks package version 2.2.0
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files generated for ChIP-Seq data using deepTools, tab limited peak files for ChIP-Seq data, tab limited Cufflinks output files for gene expression and tab limited files  rMATS files for differential expression

extract_protocol:
For ChIP-Seq, Cells were lysed using nucleosome lysis buffer (60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 15 mM Tris-HCl pH 7.5, 0.2% NP-40) supplemented with 0.1 mM DTT and PPI. Lysates were then passed through a sucrose cushion (50 mM Tris-HCl pH 7.5, 5 mM MgCl2, 25 mM KCl, 1.2M Sucrose) by centrifugation at 3.5g for 15 minutes at 4 ˚C. The pellet (containing the nuclei) was resuspended in the digestion buffer (50 mM Tris-HCl pH 7.5, 4mM MgCl2, 1mM CaCl2, 0.32 M Sucrose) with 200U micrococcal nuclease (Mnase) (Worthington Biochemical) and incubated for 10 minutes at 37 ˚C. Digestion was stopped by the addition of 1 mM each of EDTA and EGTA. Nuclei were pelleted by centrifugation at 3.5g for 10 minutes at 4 ˚C. Pellet was resuspended in 500 µl solubilization buffer ( 50mM HEPES pH 7.6, 500mM LiCl, 1mM EDTA, 0.7% sodium deoxycholate, 0.1% SDS and 1% NP-40) and rotated at 4 ˚C for 1 hour followed by centrifugation at 12,000g for 10 minutes at 4 ˚C. The pellet was discarded and the supernatant, the nucleosome enriched fraction, was used for immunoprecipitations and immunoblot assays. DNA was extracted from a small aliquot of the nucleosome-enriched fraction using phenol: chloroform: isoamyl alcohol (Thermo Fisher Scientific 15593031) and run on a 2% agarose gel to confirm the expected size of the digested DNA (147 bp and multiples thereof).  For immunoprecipitations, nucleosome enriched fractions were diluted to 1 ml in dilution buffer (0.005% SDS, 0.1% Triton X-100, 1.2 mM EDTA, 1.67 mM Tris HCl pH8.0, 167 mM NaCl ) and incubated with antibodies (2 µg/sample) conjugated to Sepharose A or G beads with rotation at 4 ˚C overnight. Beads were washed with dilution buffer 3x and immunoblots were performed as described above. RNAse-A treatment was performed as described in [REF Ast Paper].
For RNA-Seq, Synchronized HeLa cells were resuspended in TRIzol (Thermo Fisher Scientific 15596026). Total RNA was extracted from TRIzol using the manufacturer’s protocol and quantified using a Qubit fluorometer (Thermo Fisher Scientific). Poly-A mRNA was enriched using NEBNext Poly-A mRNA isolation kit (NEB E7490).
ChIP-Seq Libraries for sequencing were prepared using NEBNext Ultra DNA Library Preparation Kit (NEB E7370). RNA-Seq libraries were prepared using NEBNext RNA Library Preparation Kit (NEB E7530), both following detailed manufacturer's instructions

tag: cell line


title: HeLa_Unsynchronized_input

description: One replicate

source_name: HeLa Cell line,  Unsynchronized

value: Unsynchronized


title: Localized tumor H3K27Ac_Fig1_T3


title: Localized tumor H3K27Ac_Fig1_T6


title: Localized tumor H3K27Ac_Fig1_T4


title: HeLa_G2M_ChIP-Seq_rep1


title: CHD4_null_E10.5_RNA_Rep3

description: polyA/Stranded


title: CHD4_flox_E10.5_RNA_Rep1

description: polyA/Stranded

source_name: E10.5 Chd4(flox/flox) cardiac tissue


title: CHD4_flox_E10.5_RNA_Rep2

description: polyA/Stranded


title: CHD4_flox_E10.5_RNA_Rep3

description: polyA/Stranded


title: CHD4_null_E9.5_RNA_Rep4

description: polyA/Stranded

source_name: E9.5 Chd4(Δflox/Δflox) cardiac tissue

extract_protocol:
Embryonic hearts were collected in PBS, then RNA was collected in Trizol reagent. 200ng RNA was used for library preparation.
Illumina Tru-seq stranded mRNA sample prep kit was used for library preparation.

value: Embryonic day 9.5


title: SCP2

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

description: Rat Schwann cells

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Rat Schwann cell precursors

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Rat Schwann cell precursors are cultured in modified Sato medium and grown.

extract_protocol: RNA samples were extracted from cells using ISOGEN（NIPPON GENE) and RNeasy mini kit (QIAGEN).

treatment_protocol: Rat oligodendrocyte precursors are cultured in modified Sato medium for around one week.

tag: cell type

value: Rat Schwann cell precursors

tag: culture conditions

value: Normal


title: cqs1△_V8+512nM_Qsp2_2

city: beijing

first: lei

last: chen

address: NO.1 Beichen West  Road, Chaoyang District, Beijing 100101, China

institute: the institute of microbiology chinese academy of sciences

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to XL280α whole genome using HISAT v0.1.6beta with parameters  hisat -p -x  -S (for non-strand-specific RNA-seq)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to XL280α whole genome using HISAT v0.1.6beta with parameters  hisat -p -x  -S --rna-strandness RF (for strand-specific RNA-seq)
Framents Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Stingtie v1.2.1 with parameters stringtie -p -e -G -o -A-C
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using GFOLD v1.1.2 with parameters gfold count -ann -tag -o
Genome_build: XL280α
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Cryptococcus deneoformans

growth_protocol: 50 ODs of cells from overnight YPD cultures were washed twice in water and resuspended in water at a final concentration of 1 DO600, dropped onto V8 (pH7) plates, and incubated for 12 hours at 25℃ in dark. ;about 50 OD of cells from overnight YPD cultures were washed twice in water and resuspended in water at a final concentration of 1 OD, dropped onto YPD or YPG plates, and incubated for 1, 6, 12, 24,72 hour at 25℃ in dark

extract_protocol:
Frozen pellets were ground in liquid nitrogen and total RNA was purified using the Ultrapure RNA Kit (Kangweishiji, CW0581S) according to the manufacturer's instructions, and then reverse-transcribed with the Fastquant RT Kit (Tiangen KR106-02, with gDNase).
Illumina cDNA libraries were generated using VAHTSTM mRNA-seq v2 Library Prep Kit (Vazyme Biotech Co., Ltd, Nanjing, China) as described by the manufacture. Samples were clustered using VAHRS RNA adapters set1/set2 and then sequenced using Illunima Hiseq 4000 platform in a 2x150 pair-ended manner.

treatment_protocol: Total RNA was purified using the Ultrapure RNA Kit. Illumina cDNA libraries were generated using VAHTSTM mRNA-seq v2 Library Prep Kit.

value: serotype D XL280 MATalpha

tag: protocol

value: V8 agar (5% v/v V8 juice, 0.5g/l KH2PO4, 4% agar)  at 25C


title: cqs1△_V8+512nM_Qsp3_2


title: HeLa_G1S_ChIP-Seq_rep1

description:
Two replicates (G1S1 and G1S2)
G1S.bw
G1S_Peaks_annotated.txt

source_name: HeLa Cell line, G1/S synchronized

value: G1/S synchronized


title: HeLa_G1S_ChIP-Seq_rep2


title: HeLa_G1S_RNA-Seq

description:
Two replicates (G1S1 and G1S2)
gene_exp.diff


title: cqs1△_V8+4nM_Qsp1_2


title: cqs1△_V8_2


title: SCP1

description: Rat Schwann cells


title: CHD4_null_E9.5_RNA_Rep5

description: polyA/Stranded


title: opt1△_V8_2


title: SCP3

description: Rat Schwann cells


title: Tim-4+CD4+ small intestine macrophages  - replicate 3 from 3 pooled mice

city: Manchester

first: Tovah

middle: N

last: Shaw

address: 46 Grafton Street

department: Division of Infection, Immunity and Respiratory Medicine

institute: University of Manchester

data_processing:
Bcl2fastq 2.17.1.14
Trimmomatic 0.36
star 2.5.3
Htseq-count 0.6.1p1
DESeq2
Genome_build: GRCm38.p4,gencode.vM11.annotation.gtf
Supplementary_files_format_and_content: raw counts and normalised counts(xls)

source_name: small intestine

extract_protocol:
Cells were isolated by fluorescence-activated cell sorting (FACS) from the small intestine or peripheral blood of 3-4 pooled adult wild type C57/BL6 mice. Cells were sorted directly into RLT buffer (Qiagen) and stored on dry ice before storage at -80oC for subsequent RNA extraction. RNA was extracted from 120,000 – 200,000 cells using an RNeasy micro kit (Qiagen) following manufacturer’s instructions.
Strand-specific RNA-seq libraries were prepared using the Illumina workflow with the TruSeq® Stranded mRNA Sample Preparation Kit.

value: Tim-4+CD4+ small intestine macrophages

value: small intestine

tag: Sex

value: male


title: CHD4_null_E10.5_RNA_Rep1

description: polyA/Stranded


title: CHD4_null_E9.5_RNA_Rep2

description: polyA/Stranded


title: CHD4_null_E9.5_RNA_Rep3

description: polyA/Stranded


title: cqs1△_V8+512nM_Qsp1_2


title: WT_V8_2

source_name: wild type

value: wild type


title: WT_YPD_2

value: YPD solid plate (20g/l glucose, 20g/l peptone, 10g/l yeast extract, 2% agar) at 30C


title: Tim-4+CD4+ small intestine macrophages  - replicate 2 from 3 pooled mice


title: CHD4_null_E9.5_RNA_Rep1

description: polyA/Stranded


title: cqs1△_YPG_72h_2

value: YPG solid plate (20g/l galactose, 20g/l peptone, 10g/l yeast extract, 2% agar) at 30C


title: cqs1△_YPG_24h_2


title: cqs1△_V8+16nM Qsp1_2


title: CHD4_flox_E9.5_RNA_Rep5

description: polyA/Stranded

source_name: E9.5 Chd4(flox/flox) cardiac tissue


title: CHD4_flox_E9.5_RNA_Rep4

description: polyA/Stranded


title: Tim-4–CD4+ small intestine macrophages  - replicate 4 from 3 pooled mice

value: Tim-4-CD4+ small intestine macrophages


title: cqs1△_YPG_1h_2


title: cqs1△_YPG_12h_2


title: CHD4_flox_E9.5_RNA_Rep3

description: polyA/Stranded


title: WT_YPG_72h_2


title: Tim-4+CD4+ small intestine macrophages  - replicate 1 from 3 pooled mice


title: CHD4_flox_E9.5_RNA_Rep2

description: polyA/Stranded


title: Tim-4–CD4+ small intestine macrophages  - replicate 3 from 3 pooled mice


title: WT_YPG_12h_2


title: WT_YPG_1h_2


title: WT_YPG_6h_2


title: cqs1△_YPD_72h_2


title: Tim-4–CD4+ small intestine macrophages  - replicate 1 from 3 pooled mice


title: Tim-4–CD4+ small intestine macrophages  - replicate 2 from 3 pooled mice


title: Tim-4–CD4– small intestine macrophages  - replicate 4 from 3 pooled mice

value: Tim-4-CD4- small intestine macrophages


title: cqs1△_YPD_6h_2


title: cqs1△_YPD_24h_2


title: WT_YPD_72h_2


title: cqs1△_YPD_1h_2


title: Tim-4–CD4– small intestine macrophages  - replicate 2 from 3 pooled mice


title: CHD4_flox_E9.5_RNA_Rep1

description: polyA/Stranded


title: Tim-4–CD4– small intestine macrophages  - replicate 3 from 3 pooled mice


title: Tim-4–CD4– small intestine macrophages  - replicate 1 from 3 pooled mice


title: WT_YPD_24h_2


title: WT_YPD_12h_2


title: cqs1△_YPG_6h_2


title: WT_YPD_6h_2


title: WT_YPD_1h_2


title: cqs1△_YPD_12h_2


title: WT_YPG_24h_2


title: cqs2delta_V8 (Strand-specific RNA-seq)_2

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to XL280α whole genome using HISAT v0.1.6beta with parameters  hisat -p -x  -S (for non-strand-specific RNA-seq)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to XL280α whole genome using HISAT v0.1.6beta with parameters  hisat -p -x  -S --rna-strandness RF (for strand-specific RNA-seq)
Framents Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Stingtie v1.2.1 with parameters stringtie -p -e -G -o -A-C
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using GFOLD v1.1.2 with parameters gfold count -ann -tag -o
Genome_build: XL280α
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.


title: WT_V8 (Strand-specific RNA-seq)_2

value: wild strain


title: cqs2delta_V8+512nM_Qsp1 (Strand-specific RNA-seq)_2


title: Ly6Chi peripheral blood monocytes  - replicate 1 from 3 pooled mice

source_name: peripheral blood

value: Ly6Chi peripheral blood monocytes

value: peripheral blood


title: Ly6Chi peripheral blood monocytes  - replicate 2 from 4 pooled mice


title: Ly6Chi peripheral blood monocytes  - replicate 3 from 3 pooled mice


title: cqs1delta_V8+512nM_Qsp2

description: treatment: 512nM Qsp1

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to JEC21α whole genome using HISAT v0.1.6beta with parameters  hisat -p -x  -S (for non-strand-specific RNA-seq)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to JEC21α whole genome using HISAT v0.1.6beta with parameters  hisat -p -x  -S --rna-strandness RF (for strand-specific RNA-seq)
Framents Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Stingtie v1.2.1 with parameters stringtie -p -e -G -o -A-C
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using GFOLD v1.1.2 with parameters gfold count -ann -tag -o
Genome_build: JEC21α
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol:
V8 agar (5% v/v V8 juice, 0.5g/l KH2PO4, 4% agar)  at 25°C
50 ODs of cells from overnight YPD cultures were washed twice in water and resuspended in water at a final concentration of 1 DO600, dropped onto V8 (pH7) plates, and incubated for 12 hours at 25C in dark.


title: cqs1delta_V8+512nM_Qsp1

description: treatment: 512nM Qsp1


title: WT_V8 (Strand-specific RNA-seq)

source_name: WT_V8 (Strand-specific RNA-seq)


title: cqs1delta_V8+512nM_Qsp3

description: treatment: 512nM Qsp1


title: cqs2delta_V8+512nM_Qsp1 (Strand-specific RNA-seq)

description: treatment: 512nM Qsp1


title: cqs1delta_V8+16nM Qsp1

description: treatment: 16nM Qsp1

source_name: cqs1△_V8+16nM Qsp1


title: cqs2delta_V8 (Strand-specific RNA-seq)

source_name: cqs2△_V8 (Strand-specific RNA-seq)


title: cqs1delta_V8+4nM_Qsp1

description: treatment: 4nM Qsp1


title: WT_YPD

growth_protocol:
YPD solid plate (20g/l glucose, 20g/l peptone, 10g/l yeast extract, 2% agar) at 30°C
50 ODs of cells from overnight YPD cultures were washed twice in water and resuspended in water at a final concentration of 1 DO600, dropped onto V8 (pH7) plates, and incubated for 12 hours at 25C in dark.


title: WT_V8


title: ratOLs DIV3-3

description: Rat miRNA comparison

source_name: Rat oligodendrocyte precursors

growth_protocol: Rat oligodendrocyte precursors are cultured in standard Raff medium and grown.

treatment_protocol: Rat oligodendrocyte precursors are cultured in Raff medium and allowed to be differentiated in standard grwoth factor changes.

value: Rat oligodendrocyte precursors

value: Differentiated condition


title: cqs1delta_V8


title: ratOLs DIV0-3

description: Rat miRNA comparison

value: Normal condition


title: rongfengA-rongfengB-2

city: Yangzhou

first: Chen

last: Chen

state: Jiangsu

address: 12 E. Wenhui Rd.

department: Agricultural College

institute: Yangzhou University

data_processing:
Raw reads were processed using the Trimmomatic v0.32 package to remove adaptors and discard low quality reads.
The paired-end reads were aligned to the rice reference genome (MSU) by Bowtie 2  (Version: 2.2.1) with default parameters.
Aligned reads were firstly filtered by mapping quality -q 20 using samtools (Version: 0.1.16). GATK (Version: 3.5) was used to process aligned reads and call SNPs. SNPs coverage>10 were qualified to be candidate for further analysis.
Imprinted genes were identified by calculating the ratio of maternal to paternal reads at each SNP site that deviated from the expected 2:1 ratio using χ2 tests.
Supplementary_files_format_and_content: abundance measurements of imprinted genes of two interspecific crosses of rice

organism: Oryza sativa

source_name: endosperm (5 DAF)

growth_protocol: Wufeng-A and -B, Rongfeng-A and -B, Liuqianxin-A and -B, Yu6-A and -B, and wild rice were grown in Nanchang, Jiangxi Province, China. The RL-LR and WY-YW reciprocal crosses were performed in the summer of 2014. Plants were grown in a paddy field under regular conditions. The ovary donors were emasculated before flowering and moved to a growth chamber on a 14 h/10 h light-dark cycle at 30°C.

extract_protocol:
At 5 DAF, the endosperm was carefully collected with a pipette to avoid maternal tissue contamination per the method used by Luo et al. (2011). Two (WY-YW) or three (LR-RL) replicates were used for mining of imprinted genes. Each replicate was pooled with 20–30 endosperm.  RNA was extracted from endosperm or seedlings using a Plant RNA Kit (OMEGA) and treated with RNA-free DNase set (OMEGA) to remove DNA contamination per the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: hybrid

value: rongfengA-rongfengB

value: endosperm of intraspecific hybrids

tag: developmental stage

value: 5 days after fertilization


title: rongfengA-liuqianxinB-3

value: rongfengA-liuqianxinB

tag: tissue


title: rongfengA-rongfengB-1


title: rongfengA-liuqianxinB-2


title: M+BTU1_Cross1_8h

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics, CNRS

data_processing:
Sequence reads were filtered as described (Schoeberl et al. 2012; Noto et al. 2015). Briefly, following removal of the adapter sequences from the sequence reads, the reads from rRNAs, tRNA, snRNAs, the mitochondrial genome, and mixed phiX174 phage DNA were removed.
Genome_build: Tetrahymena thermophila MIC genome assembly released in 2016 was used for mapping. All information about MIC chromosome, including the Chr5, were obtained from http://ciliate.org/index.php/home/downloads/2016_mic.genome.fasta
Supplementary_files_format_and_content: Sequenced 26 to 32 nt RNAs that map uniquely to the sense and antisense strands of the 30 kb CL1 locus, 30 kb M locus, and the whole MIC chromosome 5 (Chr5) are counted, and normalized numbers (reads per million reads [RPM] for the CL1 and M loci and reads per kb per million reads [RPKM] for the Chr5) are shown in histograms with 100 nt and 50 kb bins, respectively.
Chromosome coordinates used in processed data files:
CL1: 16473376 to 16503399 of the MIC Chr2
M: 15091812 to 15121604 of the MIC Chr4
R3-R4: 15117953 to 15147831 of the MIC Chr4
note: CL1-Cal and CL1 are the same region
Bins are named with bp count (e.g. 50, 100, 150, etc for 50kb bins) indicating that 'bin 50' includes first base in region to +50.  For example:  in file 10508_CL1_Hist.txt, Bin 50 = MIC  Chr2:16473376-16473426.

organism: Tetrahymena thermophila

source_name: M+BTU1 cells small RNAs @8 hpm

growth_protocol: Cells were grown in SPP medium (Gorovsky et al., 1975) containing 2% proteose peptone at 30⁰C overnight.

extract_protocol:
Total RNA was extracted with TRIzol reagent . 1 mL of Trizol reagent was used to lyse1x10e6 cells.
RNA libraries were prepared for sequencing according to Noto et al. (2014) Methods in Molecular Biology 1093,209-24

treatment_protocol: To induce conjugation, exponentially growing cells (~3-5x 10e5/ml) of two different mating types were starved in 10 mM Tris-HCl (pH 7.5) at 30°C for 8-14 h and mixed for conjugation (7x 10e5/ml) at 30°C.

value: M IES @ BTU1 locus in MAC


title: M+BTU1_Cross2_8h


title: ratOLs DIV0-2

description: Rat miRNA comparison


title: ratOLs DIV3-1

description: Rat miRNA comparison


title: rongfengA-liuqianxinB-1


title: M+BTU1_Cross1_3h

source_name: M+BTU1 cells small RNAs @3 hpm


title: liuqianxinA-rongfengB-3

value: liuqianxinA-rongfengB


title: ratOLs DIV0-1

description: Rat miRNA comparison


title: N001_F_Bsseq.R2

city: Pamplona

first: Raul

last: Castanera

address: Campus Arrosadia, DPTO Producción Agraria

country: Spain

institute: Public University of Navarre

data_processing:
Bs-seq:  Raw reads from bisulfite treatment were checked for quality using FastQC and aligned to the reference genome (PC15 v2.0) using the BS-Seeker2 pipeline
Genome_build: https://genome.jgi.doe.gov/pages/search-for-genes.jsf?organism=PleosPC15_2
Supplementary_files_format_and_content: files include read count values for sRNA,  RPKM values for mRNA and methylation levels (0 to 1) for BS-seq

organism: Pleurotus ostreatus

source_name: N001 dikaryotic strain (fruitbody)

extract_protocol:
Total RNA isolation for mRNA (mRNA-seq) and small RNA (sRNA-seq) sequencing was performed using a Fungal RNA E.Z.N.A Kit (Omega Bio-Tek, Norcross, GA, USA) according to the manufacturer’s guidelines. Genomic DNA (gDNA) from the fungal samples was extracted using an E.Z.N.A Fungal DNA Mini Kit (Omega Bio-Tek, Norcross, GA)
Library preparation was performed using the Illumina TruSeq DNA Sample Prep  according to the manufacturer’s instruction

value: Fruitbody


title: N001_F_Bsseq.R3


title: N001_F_Bsseq.R1


title: CL1+BTU1_Cross2_3h

source_name: CL1+BTU1 cells small RNAs @3 hpm

value: CL1 IES @ BTU1 locus in MAC


title: opt1delta_V8

value: serotype D XL280 MATalpha


title: liuqianxinA-rongfengB-2


title: liuqianxinA-liuqianxinB-3

value: liuqianxinA-liuqianxinB


title: ratOLs DIV3-2

description: Rat miRNA comparison


title: CL1+BTU1_Cross1_3h


title: CD4 T cells stimulated with Wt APC

city: HOUSTON

first: Xiaolong

last: Zhang

state: Texas

address: 6670 Bertner Avenue, R7-211

department: Immunobiology & Transplant Research Center

institute: Houston Methodist Research Institute

hyb_protocol: The GeneChip HT MG-430 PM 24 Array Plate consists of 24 single MG-430 PM arrays arranged into standard 96 well plate format. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations on a GeneTitan Instrument.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument.

data_processing: Expression estimates were calculated using RMA in Bioconductor.

source_name: spleen

label_protocol: All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430 PM arrays.

growth_protocol: Naive CD4+ T cells were FACS sorted from 6 weeks old Foxp3-eGFP reporter mice with FACSaria (BD Biosciences).

extract_protocol: Total RNA was prepared from mouse adipose tissue using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Wild type (Wt) B6 and OX40L-Tg APCs (CD3‒ splenocytes) were prepared by depleting T cells from the splenocytes with PE–anti-CD3 (clone 2C11) and anti-PE microbeads (Miltenyi Biotec), followed by a brief treatment with mitomycin C (50μg/ml; Sigma-Aldrich). Naive CD4+ T cells were activated in vitro with soluble anti-CD3 mAb and mitomycin C-treated Wt APCs or OX40L-Tg APCs in 96-well round bottom tissue-culture plates. Forty-eight hours later, living CD4+ T cells were sorted from cultures by flow cytometry.

value: CD4 T cells

tag: treatment

value: stimulated with Wt APC

tag: background strain

tag: age

value: 6 weeks-old


title: N001_F_sRNA_R1

data_processing:
SRNA-seq: Small RNA (sRNA) raw reads were first processed to trim the adapter sequence and filter by size (17 to 30 nt) using BBduk software. Reads mapping to a custom database of ribosomal RNA (rRNA) and transfer RNA (tRNA) were also removed. The remaining sRNA reads were mapped to the reference genome using Butter 0.3.2
Genome_build: https://genome.jgi.doe.gov/pages/search-for-genes.jsf?organism=PleosPC15_2
Supplementary_files_format_and_content: files include read count values for sRNA,  RPKM values for mRNA and methylation levels (0 to 1) for BS-seq


title: N001_F_sRNA_R2


title: liuqianxinA-liuqianxinB-2


title: R3-R4_coDel_Cross2_3h

source_name: R3-R4_coDel @3 hpm

value: Deletion @ R3-R4 locus in MAC


title: CD4 T cells stimulated with OX40L-Tg APC

value: stimulated with OX40L-Tg APC


title: R3-R4_coDel_Cross1_3h


title: N001_F_polyA_R2

data_processing:
mRNAseq: RNA-seq data were filtered for quality using FastQC and trimmed with BBDuk from the BBMap package (https://sourceforge.net/projects/bbmap/) 5 to remove sequences of adapters and low-quality reads. The resulting reads were aligned to the reference genome assembly using STAR v2.3.16 restricted to single hit mapping using the following parameters: --outReadsUnmapped Fastx --outFilterMismatchNoverLmax 0.04 --outFilterMultimapNmax 1
Genome_build: https://genome.jgi.doe.gov/pages/search-for-genes.jsf?organism=PleosPC15_2
Supplementary_files_format_and_content: files include read count values for sRNA,  RPKM values for mRNA and methylation levels (0 to 1) for BS-seq


title: liuqianxinA-rongfengB-1


title: CL1+BTU1_Cross2_8h

source_name: CL1+BTU1 cells small RNAs @8 hpm