title: single sperm_229

description: single sperm DNA sequence


title: Ifitm-/- CD4 T cells Rep2

status: Public on Mar 18 2019

type: RNA

city: London

first: Tessa

last: Crompton

address: 30 Guilford Street

department: Immunobiology

country: United Kingdom

institute: UCL

description: KO CD4 T cells R2

hyb_protocol: Hybridisation to Affymetrix Mouse Gene 1.0 ST arrays was performed for 16 hours at 45C with constant rotation. Samples were hybridised according to the Affymetrix specifications: hybridisation cocktails were heated at 99C for 5 minutes and then at 45C for another 5 minutes. Samples were centrifuged at max speed for 1 minute and 200ul was transferred to each array. Hybridisation was carried out for 16 hours at 45C and 60 rpm. Fluidics washing was FS450_0001.

scan_protocol: Arrays were scanned with an Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data was normalised using rma function from the affy package in R

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Ifitm-/-_Murine Adult CD4 T cells

label_protocol: Up to 5.5g of total RNA was fragmented and labelled using the Affymetrix GeneChip Whole Transcript Sense Target Labelling Assay as outlined in the manufacturer's instructions.

extract_protocol: RNA was extracted using the PicoPure RNA Isolation Kit (ThermoFisher, Cat. KIT0202) performed according to the manufacturer's instructions.

treatment_protocol: Fresh single splenocyte suspensions were re-suspended in Ammonium Chloride solution (Stem Cell Technologies Inc, US) and CD4+ T cells were separated using negative selection EasySep system (Stem Cell Technologies Inc, US) according to the manufacturer’s protocol. Microarrays were performed on the purified naïve (resting) CD4 T cells from Ifitm-/- and WT controls. These arrays were done twice with independent biological replicates.

tag: age

value: 6-8 week-old Adults

tag: genotype/variation

value: Ifitm-/-

tag: cell type

value: CD4 T cells


title: Tln1 Pod-rtTA TetO 3

city: New Haven

first: Shuta

last: Ishibe

state: CT

address: 300 Cedar street

country: USA

institute: Yale University

description: Gene expression data from Tln1 Pod-rtTA TetO-Cre mouse glomerulus.

hyb_protocol: standard Affymetrix protocol

scan_protocol: The scanner is a 16-bit sophisticated opto-mechanical confocal scanner which measures fluorescence intensity emitted by the labeled cRNA/cDNA bound to the probe arrays. The scanner uses a high-quality, solid state 532nm Diode-Pumped, Frequency Doubled Nd:YAG (Neodymium-doped Yttrium Aluminum Garnet) Green Laser. The scanner optics are designed to condition the laser beam to deliver an excitation spot size of 3.5.

data_processing: Background correction was done individually for each data using RMA algorithm in limma package. Probes were mapped to gene symbols using the annotation file downloaded from Affymetrix website where probes with no annotation were discarded. The expression values with biological replicates were averaged. Z score for each gene was calculated following the method published by Cheadle et al. (2003). When comparing two samples, Z ratio of each gene was calculated.

source_name: kidney glomerulus

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

growth_protocol: Doxycycline induction for 3 weeks in mice from 8 weeks old age

extract_protocol: RNA isolation of mouse glomerulus using Rneasy kit (Quiagen)

treatment_protocol: vehicle or valproic acid treatment for 2 weeks after completion of doxycyclin induction

value: 13 weeks old age

value: Tln1 Pod-rtTA TetO-Cre

tag: treatment

value: doxyclcline induction for 3 weeks + vehicle


title: Tln1 Pod-rtTA TetO 2


title: WT CD4 T cells Rep2

description: WT CD4 T cells R2

source_name: WT_Murine Adult CD4 T cells

value: Wildtype


title: 9985178087_R01C01 genomic DNA

type: genomic

city: Amsterdam

first: Peter

last: Henneman

state: Noord Holland

address: Meibergdreef 9

department: Clinical Genetics

country: Netherlands

institute: Academic Medical Center Amsterdam

description: peripheral blood sample

hyb_protocol: Bisulfite converted DNA was hybridized to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Minfi (v1.16.0) for reading the data; MethylAid (v1.14.0) for quality control

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina protocol

extract_protocol: Peripheral blood was drawn and stored in EDTA to prevent coagulation. Erythrocytes were lysed before proteins were aggregated out of the sample. Genomic DNA was extracted through ethanol precipitation, after which the DNA was dissolved in tris-ethylenediaminetetraacetic buffer (Tris-EDTA) and stored at 4°C.

tag: gender

value: Male

tag: disease state

value: control

tag: growth

tag: facial

tag: cns


title: Ifitm-/- CD4 T cells Rep1

description: KO CD4 T cells R1


title: Tln1 Pod-rtTA TetO 1


title: 9986360122_R06C02 genomic DNA

description: peripheral blood sample


title: single sperm_2287

type: SRA

city: Oxford

first: Anjali

middle: Gupta

last: Hinch

address: Roosevelt Drive

department: WCHG

institute: Oxford University

description: single sperm DNA sequence

library_source: genomic

data_processing:
Alignment with bwa-0.7.15
Use of platypus-0.5.2 to call variants de novo in bulk sperm samples, filtered as described in Hinch et al
Use of platypus-0.5.2 to call variants in each sperm at sites of de novo variants called in bulk sperm above
Calling crossover breakpoints using in-house algorithm (described in Hinch et al)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with column descriptions in commented header; each line corresponds to one crossover

source_name: single sperm

growth_protocol: Data were generated from sperm from a 10 week old male mouse - no culturing was performed.

extract_protocol:
Sperm samples were isolated mechanically and our novel single-cell DNA amplification protocol was performed on each sample followed by sequencing. Full experimental procedures are reported in accompanying manuscript (Hinch et al).
Libraries were prepared as per NEBNext library  preparation protocol with some modifications. Please see details in Hinch et al.

tag: strain

tag: tissue

value: sperm

tag: prdm9 genotype

value: HUM/CAST


title: single sperm_232

description: single sperm DNA sequence


title: 9985178096_R01C01 genomic DNA

description: peripheral blood sample

value: Female


title: single sperm_2286

description: single sperm DNA sequence


title: 9985178127_R03C02 genomic DNA

description: peripheral blood sample


title: control2

description: Gene expression data from control mouse glomerulus.

value: doxyclcline induction for 3 weeks


title: bulk sperm_012

description: bulk sperm DNA sequence

source_name: bulk sperm


title: bulk sperm_006

description: bulk sperm DNA sequence


title: control1


title: Peyer's Patches F KO  H09

city: Edinburgh

first: Clare

last: Pridans

address: 47 Little France Crescent

department: University of Edinburgh

institute: Centre for Inflammation Research

description: Gene expression data from Peyer's Patches/Ileum

hyb_protocol: GeneTitan

scan_protocol: GeneChip Command Console

data_processing: CEL files were normalised (RMA) in R/Bioconductor.

label: Biotin

source_name: Peyer's Patch/Ileum

label_protocol: GeneChip Whole Transcript Labeling Kit (Applied Biosystems)

extract_protocol: Trizol extraction of total RNA followed by purification with Rneasy Mini kit

value: 6 weeks

tag: genotype

value: FIRE -/-

tag: Sex

value: Peyer's Patches/Ileum


title: Hippocampus F KO  H07

description: Gene expression data from hippocampus

source_name: Hippocampus

value: hippocampus


title: 9986360109_R02C02 genomic DNA

description: peripheral blood sample


title: WT CD4 T cells Rep1

description: WT CD4 T cells R1

value: 6-8 week-old Adults


title: single sperm_2285

description: single sperm DNA sequence


title: single sperm_2283

description: single sperm DNA sequence


title: Hippocampus M WT F07

description: Gene expression data from hippocampus

value: FIRE +/+


title: Peyer's Patches F KO F09


title: single sperm_2282

description: single sperm DNA sequence


title: Hippocampus F WT G07

description: Gene expression data from hippocampus


title: Peyer's Patches M KO G09


title: single sperm_2281

description: single sperm DNA sequence


title: 011_sample_ID_11

city: La jolla

first: Mattias

last: Svensson

state: Ca

address: 9420 athena cir

institute: La jolla Institue for Allergey

data_processing:
Single-end reads from ATAC-seq experiments were aligned to mm10 reference genome using Bowtie2 (version 2.3.3.1) with parameters “-k 4 --mm –threads 8 –X 2000”
Reads corresponding to mitochondrial genome and chrY were filtered out.
Uniquely mappable reads with mapping quality >= 30 were extracted using SAMtools (version 1.6)
Duplicate reads were removed by Picard tools MarkDuplicates (https://broadinstitute.github.io/picard). All reads aligning to the positive (+) strand were shifted by +4 bp, while all reads aligning to the negative (–) strand were shifted by -5 bp, to account for the 9 bp distance between two adapters inserted by Tn5 transposase
Coverage tracks were normalized using “BamCoverage” from deepTools with the arguments “-bs 10 --effectiveGenomeSize 2652783500 --normalizeUsing RPKM -e 200”. We used MACS2 (version 2.1.0) for peak calling, with parameters: “-g mm –q 0.05 --nomodel --nolambda --keep-dup all --call-summits --shift -100 --extsize 200”
The summits of all peak were extended to regions with a uniform size of 500 bp. All of these uniform sized peaks were then merged to a global set of peaks, using bedtools merge routine
The number of transposase insertions for each of these uniform regions were computed with respect to individual samples, and normalized by their respective read counts
Differential ATAC-seq analysis was performed using DESeq2, and differentially accessible regions were filtered by FDR adjusted p-value of less than 0.05 and an estimated fold-change of at least 2
Genome_build: mm10
Supplementary_files_format_and_content: ATAC-counts per peak and normalized ATAC-Seq coverage at selected locus

source_name: Ptpn2+/-_Treg 72h

growth_protocol: Stimulation of Tregs in vitro with IL-6. Tregs were isolated from spleen and lymph nodes of FoxP3eGFP SKG mice by flow cytometry based cell sorting. Sorted Tregs were cultured in complete RPMI 1640 Medium (10% FBS, 1% L-Glutamin, 1% Penicillin-Streptomycin, 1% Non-Essential Amino acids, 0.1% Beta-Mercaptoethanol) in the presence of IL-6 (50 ng/mL) and anti-CD3/CD28 coated DynaBeads (Life Technologies) for 24, 48 and 72h.

extract_protocol:
Live cells were lysed to extract nuclei in Omni-ATAC lysis buffer (10mM Tric-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween20 and 0.01% Digitonin). Nuclei were re-suspended in 50 microL Transposition mix (25 microL 2xTD buffer, 2.5 microL transposase [Nextera, Illumina], 16.5 microL PBS, 0.5 microL, 1% Digitonin, 0.5 microL, 10% Tween20 and 5 microL H2O) and the transposase reaction was conducted for 30 min at 37 °C. Right after tagmentation, fragments were purified by DNA precipitation and capture on columns (Zymo Research), elured and stored for further processing
Library amplification and barcoding were performed using Nextera DNA sample preparation kit and index kit (Illumina). Tagmented fragments were pre-amplified for 5 cycles followed by a second round of amplification based on the cell number (10 cycles for 0.5x105 cells, 9 cycles for 1.0x105 cells and 8 cycles for 1.5x105 cells).  Amplified libraries were purified using 1:1.8 ratio of Ampure XP Beads. Library fragments ranging in size, between 100 to 600bp, were size selected, using Ampure XP beads (ratios 1:0.5 and 1:1.8; Beckman Coulter). Libraries were quantified by Picogreen assay (Invitrogen) and size distribution was assessed using fragment analyzer (Advance Analytics). Single-end sequencing was performed on a HiSeq 2500 (Illumina) generating in total more than 250 millions 50 bp short sequencing reads (HiSeq SBS and SR Cluster v4 kits, Illumina catalog# FC-401-4002 and GD-401-4001, respectively).  Raw data from the sequencer was demultiplexed and FASTQ files were generated using bcl2fastq conversion software (Illumina).

treatment_protocol: Th17 cells (Live CD8-CD19-CD4+FoxP3eGFP-CCR6hi) and Tregs (Live CD8-CD19-CD4+FoxP3eGFP+) were isolated from spleen and lymph nodes of FoxP3eGFP SKG mice by flow cytometry based cell sorting. 1x105 Th17 and Tregs were directly prepared for ATAC-sequencing (as descirbed in extraction protocol). Remaining Tregs were subjected to in vitro stimulation with IL-6 (50 ng/mL) and anti-CD3/CD28 coated beads as in growth protocol. Live FoxP3eGFP+ (Tregs) cells isolated after 24, 48 and 72h of culture by flow cytometry based cell sorting. After 72h live FoxP3eGFP- (exTregs) cells were isolated by flow cytometry based cell sorting.

tag: experiment

value: Invivo

tag: strain background

value: BALB/c

tag: background

value: FoxP3eGFP SKG

tag: cell-type

value: Treg 72h


title: Spleen Frozen K27me3

city: ROCHESTER

first: JEONG-HEON

last: LEE

state: Minnesota

address: 200 1ST STREET S.W.

department: Epigenomics program/CIM

institute: MAYO CLINIC

data_processing:
Basecalls performed using CASAVA version 1.4
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (mm10) using BWA (v0.5.9) with defautl parameters
Peak calling was performed using MASC2 (v2.0.10)
Genome_build: mm10
Supplementary_files_format_and_content: tdf files were generated from bedGraph files that generated from Mayo HiChIP pipeline

source_name: Spleen

extract_protocol:
Lysates were clarified from Mnase/sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to ThruPLEX® DNA-seq Kit V2 (Rubicon Genomics, Ann Arbor, MI) according to the manufacturer’s instructions. . Briefly,In the first step, the DNA is repaired and yields molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5’ ends are ligated with high efficiency to the 5’ end of the genomic DNA, leaving a nick at the 3’ end. The adaptors cannot ligate to each other and do not have single-strand tails, both of which contribute to non-specific background found with many other NGS preparations. In the final step, the 3’ ends of the genomic DNA are extended to complete library synthesis and Illumina-compatible indexes are added through a high-fidelity amplification. After adapter ligation DNA was PCR amplified with Illumina primers for 12 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were purified by AMpure reagents. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 4000 following the manufacturer's protocols.

value: Spleen

value: No

tag: chip antibody


title: single sperm_2280

description: single sperm DNA sequence


title: Spleen FFPE1 K4me3

value: H3K4me3  (in-house EDL Lot 1)


title: 012_sample_ID_12

source_name: Ptpn2+/-_exTreg 72h

value: exTreg 72h


title: Peyer's Patches F WT E09

tag: age


title: Peyer's Patches M WT D09

value: Male


title: Hippocampus M WT E07

description: Gene expression data from hippocampus


title: 010_sample_ID_10

source_name: Ptpn2+/+_exTreg 72h


title: Hippocampus F KO B09

description: Gene expression data from hippocampus

value: Female


title: Peyer's Patches M WT  C09


title: Spleen FFPE1 K27Ac

tag: treatment

value: H3K27ac (cat.#8173BC,CST)


title: Spleen Frozen K4me3


title: 009_sample_ID_9

source_name: Ptpn2+/+_Treg 72h


title: Hippocampus M KO A09

description: Gene expression data from hippocampus

value: 6 weeks


title: single sperm_228

description: single sperm DNA sequence

value: sperm

value: HUM/CAST


title: single sperm_2276

description: single sperm DNA sequence


title: Spleen Frozen K27Ac


title: Spleen  FFPE input


title: 008_sample_ID_8

source_name: Ptpn2+/-_Treg 48h

value: Treg 48h


title: Spleen Frozen input


title: Liver FFPE2 Pol II

source_name: Liver

value: Liver

value: RNA pol II (Cat.#A300-653A, Bethyl)


title: single sperm_2275

description: single sperm DNA sequence


title: Liver FFPE1 Pol II


title: 007_sample_ID_7

source_name: Ptpn2+/+_Treg 48h

value: Invivo


title: single sperm_2274

description: single sperm DNA sequence


title: Spleen FFPE1 K27me3


title: 006_sample_ID_6

source_name: Ptpn2+/-_Treg 24h

value: BALB/c

value: Treg 24h


title: Liver Frozen2 Pol II


title: 005_sample_ID_5

source_name: Ptpn2+/+_Treg 24h

value: FoxP3eGFP SKG


title: single sperm_2273

description: single sperm DNA sequence


title: Liver Frozen1 Pol II


title: Liver FFPE2 K27me3


title: Liver FFPE1 K27me3


title: Liver Frozen K27me3


title: single sperm_2272

description: single sperm DNA sequence


title: single sperm_2268

description: single sperm DNA sequence


title: single sperm_2267

description: single sperm DNA sequence


title: 002_sample_ID_2

value: Treg


title: Liver FFPE1 K27Ac

value: No


title: Liver Frozen K4me3

value: H3K4me3  (in-house EDL Lot 1)


title: 004_sample_ID_4


title: 001_sample_ID_1


title: Liver FFPE1 input


title: single sperm_224

description: single sperm DNA sequence


title: 37_23935_YFPPos_IL17ANeg

description:
061_MaSv03_31_N726S513
37_23935_YFPPos_IL17ANeg_S61

library_source: transcriptomic

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the mouse mm10  reference using Tophat v1.4.1 (--library-type unstarnded)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: mm10
Supplementary_files_format_and_content: count matrix with rows as genes and columns as samples

growth_protocol: For isolation of in vitro generated IL-17+ exTregs. Tregs were isolated from spleen and lymph nodes of FoxP3eGFP SKG mice by flow cytometry based cell sorting. Sorted Tregs (1x10^5) were cultured in complete RPMI 1640 Medium (10% FBS, 1% L-Glutamin, 1% Penicillin-Streptomycin, 1% Non-Essential Amino acids, 0.1% Beta-Mercaptoethanol) in the presence of IL-6 (50 ng/mL) and anti-CD3/CD28 coated DynaBeads (Life Technologies) for 72h.

extract_protocol:
RNA was extracted from using the miRNeasy micro kit (Qiagen) and quantified as previously descirbed (Seumois G et al. Am J Clin Exp Immunol. 2012; Seumois G et al, Nat Immunol. 2014)
5 ng of purified total RNA was used for poly(A) mRNA selection (Picelli S et al, Nat Protoc. 2014). Purified total RNA (5 ng) was amplified following the Smart-seq2 protocol and amplified cDNA purified with AMPure XP beads (1:1 ratio; Beckman Coulter). 1 ng of cDNA was used for library preparation using Nextera XT DNA sample preparation kit and index kit (Illumina, catalog# FC-131-1096). Samples were sequenced using a HiSeq2500 (Illumina) to obtain 50-bp single end reads. To reduce assay-to-assay variability, both whole transcriptome amplification and sequencing library preparations were performed in a 96-well format. Quality control steps were included to determine total RNA quality and quantity, the optimal number of PCR pre-amplification cycles, and fragment size selection (Bioanalyzer, Agilent), samples that failed quality control were eliminated from further downstream steps. Barcoded Illumina sequencing libraries were generated utilizing an ancillary automated platform (Biomek Fxp, Beckman Coulter). Libraries were sequenced on the HiSeq2500 Illumina platform to obtain 50-bp single-end reads (HiSeq SBS and SR Cluster v4 kits, Illumine catalog# FC-401-4002 and GD-401-4001, respectively), generating an average of 11.4 million mapped reads / sample.

treatment_protocol: Isolation of both in vivo and in vitro generated IL-17+ exTregs and IL-17- Tregs was achieved by utilizing a mouse IL-17 Secretion assay kit (Miltenyl Biotec Inc. cat 130-094-207) according to manufactures protocol. For in vivo samples, single cell suspensions were prepared from pooled spleen and lymph nodes. In vitro samples were prepard as descibed in growth protocol. For detection of IL-17 production, cells were stimulated (10x10^6 cells/mL) with PMA (10 ng/mL) and ionomycin (1 ug/mL) in TexMACS media (Milteny Biotec) containing 5% mouse serum for 3h at 37°C, after which cells were washed and stained with a streptavidin labeled IL-17 capture reagent and incubated for 45 minutes at 37°C in the above media (without PMA and Ionomycin) under slow continuous rotation at a concentration of 1x106 cells/mL. After 45 minutes cells were washed and counterstained with anti-Biotin-APC, CD4, Tcr-beta, CD8, CD19 and fixable viability dye. IL-17+ exTregs and IL-17- Tregs were sorted by flow cytometry directly into Trizol LS and stored at -80 until further processing.

value: Het

tag: genotype/variation

value: Ptpnfl/+

value: Tregs

tag: batch

tag: sub-group


title: Liver FFPE2 input


title: single sperm_2231

description: single sperm DNA sequence


title: PTEN-241

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

data_processing:
Initial QC performed using FastQC v 0.11.2
mapping with STAR mapper
cufflinks v 2.0.1.3 was used to generate FPKM estimates
Genome_build: mm10
Supplementary_files_format_and_content: matrix of fpkm values per sample

source_name: Brain Tumor

extract_protocol:
total RNA was extracted using Thermo Fisher TotalRNA kit
TruSeq RNA v2

tag: model

value: Nestin Cre Sleeping Beauty

value: Brain tumor

tag: site

value: primary


title: 36_23934_YFPNeg_IL17APos

description:
060_MaSv03_30_N724S522
36_23934_YFPNeg_IL17APos_S60

tag: strain

value: WT

value: Ptpn+/+

value: ExTregs


title: PTEN-468

tag: tissue


title: single sperm_223

description: single sperm DNA sequence

value: sperm

tag: prdm9 genotype

value: HUM/CAST


title: Liver FFPE2 K4me3

value: Liver


title: 003_sample_ID_3

value: Invivo

value: BALB/c

tag: genotype


title: 35_23934_YFPPos_IL17ANeg

description:
059_MaSv03_29_N724S521
35_23934_YFPPos_IL17ANeg_S59


title: single sperm_2228

description: single sperm DNA sequence


title: Liver FFPE1 K4me3


title: Liver FFPE2 K27Ac

value: H3K27ac (cat.#8173BC,CST)


title: P53-691


title: single sperm_2226

description: single sperm DNA sequence


title: 34_23745_YFPNeg_IL17APos

description:
058_MaSv03_28_N724S520
34_23745_YFPNeg_IL17APos_S58


title: P53-690


title: Liver Frozen K27Ac

value: No


title: P53-593


title: P53-634


title: Liver Frozen input


title: 33_23745_YFPPos_IL17ANeg

description:
057_MaSv03_27_N724S518
33_23745_YFPPos_IL17ANeg_S57


title: single sperm_226

description: single sperm DNA sequence


title: single sperm_2225

description: single sperm DNA sequence


title: P53-579


title: single sperm_2223

description: single sperm DNA sequence


title: P53-566


title: PREN-1641


title: 32_23743_YFPNeg_IL17APos

description:
056_MaSv03_26_N724S517
32_23743_YFPNeg_IL17APos_S56


title: P53-701


title: P53-546


title: P53-531


title: P53-724


title: 31_23743_YFPPos_IL17ANeg

description:
055_MaSv03_25_N724S516
31_23743_YFPPos_IL17ANeg_S55


title: single sperm_2220

description: single sperm DNA sequence


title: 30_7617exTrPos_Neg

description:
092_MaSv02_24_N729S522
30_7617exTrPos_Neg_S92

value: Invitro

value: FoxP3eGFP BALB/c


title: P53-459


title: single sperm_2219

description: single sperm DNA sequence


title: P53-184


title: 29_7617TrPos_Neg

description:
091_MaSv02_23_N729S521
29_7617TrPos_Neg_S91

value: Het


title: 28_7617exTrPos_Pos

description:
090_MaSv02_22_N729S520
28_7617exTrPos_Pos_S90


title: p53-301


title: Triple363


title: single sperm_2214

description: single sperm DNA sequence


title: 27_7617TrPos_Pos

description:
089_MaSv02_21_N729S518
27_7617TrPos_Pos_S89


title: p53-272


title: p53-308


title: single sperm_2213

description: single sperm DNA sequence


title: GFAP-PTEN-49


title: P53-523


title: single sperm_2210

description: single sperm DNA sequence


title: single sperm_221

description: single sperm DNA sequence


title: 23_81017TrPos_Neg

description:
085_MaSv02_17_N729S513
23_81017TrPos_Neg_S85


title: single sperm_2207

description: single sperm DNA sequence


title: P53-176


title: single sperm_2215

description: single sperm DNA sequence


title: Adult_ht_ChIP_K4_++_2

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Reads were trimmed using Trim Galore v0.4.3 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.
Mapping of ChIP-Seq data was performed using Bowtie 2 v2.3.2 against the mouse GRCm38 genome assembly. The resulting hits were filtered to remove mappings with a MAPQ scores of < 20. Mapping of RNA-Seq data was performed using HISAT2 v2.0.5 against the mouse GRCm38 genome guided by known splice sites taken from Ensembl v68. Hits were again filtered to remove mappings with MAPQ scores of <20.
For PBAT data, reads were trimmed with Trim Galore using --clip_r1 9. Trimmed reads were aligned to the mouse genome using Bismark v0.19.0 (Krueger and Andrews, 2011) with the following parameters: --pbat. Reads were then deduplicated with deduplicate_bismark selecting a random alignment for position that were covered more than once. CpG methylation calls were extracted from the deduplicated mapping output and converted into a Bismark coverage report.
Genome_build: GRCm38
Supplementary_files_format_and_content: ChIP-seq: ChIP-Seq report is tab-delimited and shows histone tail modification enrichments over 2000bp windows, with a 1000bp step over the whole genome as follows: <probe>, <Chromosome>, <Start>, <End> and then listed samples <columns 14-38>.
Supplementary_files_format_and_content: RNA-seq: RNA-Seq report is tab-delimited and shows annotated gene coordinates and their log2(RPKM) values as follows: <gene name>, <Chromosome>, <Start>, <End>, <Probe strand> and then listed samples <columns 14-22>.
Supplementary_files_format_and_content: BiSulfite-seq: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

source_name: Hypothalamus

extract_protocol:
ChIP-seq: Hypothalamus, liver, pituitary or epiblast was collected and flash frozen in liquid nitrogen.
RNA-seq: Hypothalamus was collected and flash frozen in liquid nitrogen, when need RNA was extracted using TRIzol (Invitrogen) and cleaned using RNA Clean & Concentrator (Zymo research) and Ribo-Zero rRNA removal kit (Illumina).
BiSulfite-seq: Hypothalamus or epiblats was collected and flash frozen in liquid nitrogen. Hypothalamus DNA was extracted using DNeasy Blood & Tissue kit (Qiagen), epiblast was first permeabilised and digested using micrococcal nuclease (New England Biolans) and then purified using SPRI beads.
ChIP-seq: 2.5% of a whole hypothalamus was permeabilised and digested using micrococcal nuclease (New England Biolabs), and precleared using Dynabeads Protein A/G beads (ThermoFisher Scientific). Antibodies for H3K4me3 (Diagenode C15410003), H3K27me3 (Millipore 07-449), or H3K36me3 (Diagenode C15410192) were pre-bound to Protein A/G beads and incubated with chromatin for immunoprecipitation. Bound DNA was purified by SPRI purification using Sera-Mag carboxylate-modified Magnetic SpeedBeads (Fisher Scientific). MicroPlex Library Preparation kit v2 (Diagenode) was used as per manufacturer’s instructions to generate libraries of immunoprecipitated samples.
RNA-seq: Libraries were generated using NEBNext Ultra RNA library preparation kits (New England Biolabs) as per manufacturer's instructions.
BiSulfite-seq: Imprint DNA modification kit (Sigma) one-step procedure was used to bisulphite convert the DNA. First strand synthesis was done using Klenow exo- (New England Biolabs) and biotin-tagged Illumina 9bp random sequence adaptor, followed by Exo-I treatment (New England Biolabs) and SPRI purification. Biotinylated DNA was captured using Dynabeads Strepatavidin M-280 beads (ThermoFisher Scientific) and second strand synthesis was carried out using reverse Illumina 9bp random sequence adaptor, followed by library amplification using Phusion HF (Thermo Scientific) or KAPA HiFi (Kapa Biosystems) for 10-16 cycles.

value: Hypothalamus

value: ~14 weeks

tag: antibody

value: H3K4me3 (Diagenode C15410003)


title: Adult_ht_ChIP_K4_del-mut_3


title: 21_81017TrPos_Pos

description:
083_MaSv02_15_N728S521
21_81017TrPos_Pos_S83

tag: experiment


title: Adult_ht_ChIP_K4_del-mut_1


title: single sperm_2205

description: single sperm DNA sequence


title: Adult_ht_ChIP_K4_++_1


title: Adult_ht_ChIP_K36_del-mut_3

value: H3K36me3 (Diagenode C15410192)


title: 16_8317exTrPos_Pos

description:
078_MaSv02_10_N728S515
16_8317exTrPos_Pos_S78

tag: strain background

value: WT


title: Adult_ht_ChIP_K4_del-mut_2


title: Adult_ht_ChIP_K36_del-mut_2


title: single sperm_2206

description: single sperm DNA sequence


title: single sperm_220

description: single sperm DNA sequence


title: Adult_ht_ChIP_K36_del-mut_1


title: 18_8317exTrPos_Neg

description:
080_MaSv02_12_N728S517
18_8317exTrPos_Neg_S80


title: Adult_ht_ChIP_K36_++_2


title: single sperm_2204

description: single sperm DNA sequence


title: 17_8317TrPos_Neg

description:
079_MaSv02_11_N728S516
17_8317TrPos_Neg_S79


title: Adult_ht_ChIP_K36_++_1


title: 15_8317TrPos_Pos

description:
077_MaSv02_9_N728S513
15_8317TrPos_Pos_S77


title: Adult_ht_ChIP_K36_++_3


title: Adult_ht_ChIP_K27_del-mut_3

value: H3K27me3 (Millipore 07-449)


title: Adult_ht_ChIP_K27_del-mut_2


title: 22_81017exTrPos_Pos

description:
084_MaSv02_16_N728S522
22_81017exTrPos_Pos_S84

value: ExTregs


title: Adult_ht_ChIP_K27_++_3


title: single sperm_218

description: single sperm DNA sequence

value: sperm


title: 11_20086_FoxP3Pos_IL17Neg

description:
073_MaSv01_11_N727S518
11_20086_FoxP3Pos_IL17Neg_S73

value: Ptpnfl/+

value: Tregs


title: Adult_ht_ChIP_K27_del-mut_1


title: 12_20086_FoxP3Neg_IL17Pos

description:
074_MaSv01_12_N727S520
12_20086_FoxP3Neg_IL17Pos_S74

value: Invivo


title: single sperm_217

description: single sperm DNA sequence

value: HUM/CAST


title: Adult_ht_ChIP_K27_++_2


title: 10_20085_FoxP3Neg_IL17Pos

description:
072_MaSv01_10_N727S517
10_20085_FoxP3Neg_IL17Pos_S72

value: Ptpn+/+


title: single sperm_215

description: single sperm DNA sequence


title: Adult_ht_ChIP_K27_++_1


title: Adult_ht_ChIP_input_del-mut_3


title: Adult_ht_ChIP_input_del-mut_2


title: Adult_ht_ChIP_input_++_3


title: Adult_ht_ChIP_input_++_1


title: 09_20085_FoxP3Pos_IL17Neg

description:
071_MaSv01_9_N727S516
09_20085_FoxP3Pos_IL17Neg_S71


title: single sperm_214

description: single sperm DNA sequence


title: single sperm_213

description: single sperm DNA sequence


title: 08_20193_YfpNeg_IL17Pos

description:
070_MaSv01_8_N727S515
08_20193_YfpNeg_IL17Pos_S70


title: Adult_ht_RNA_del-mut_4_RNAseq


title: single sperm_219

description: single sperm DNA sequence


title: single sperm_212

description: single sperm DNA sequence


title: Adult_ht_RNA_del-mut_3_RNAseq


title: Adult_ht_RNA_del-mut_2_RNAseq


title: Adult_ht_RNA_del-mut_1_RNAseq


title: 06_20192_YfpNeg_IL17Pos

description:
068_MaSv01_6_N726S522
06_20192_YfpNeg_IL17Pos_S68


title: Adult_ht_RNA_++_5_RNAseq


title: Adult_ht_ChIP_input_del-mut_1


title: 38_23935_YFPNeg_IL17APos

description:
062_MaSv03_32_N726S515
38_23935_YFPNeg_IL17APos_S62


title: Adult_ht_RNA_++_3_RNAseq


title: Adult_ht_RNA_++_4_RNAseq


title: Adult_ht_ChIP_input_++_2


title: single sperm_208

description: single sperm DNA sequence


title: Adult_ht_RNA_++_2_RNAseq


title: single sperm_206

description: single sperm DNA sequence


title: 03_20191_YfpPos_IL17Neg

description:
065_MaSv01_3_N726S518
03_20191_YfpPos_IL17Neg_S65


title: 04_20191_YfpNeg_IL17Pos

description:
066_MaSv01_4_N726S520
04_20191_YfpNeg_IL17Pos_S66


title: 07_20193_YfpPos_IL17Neg

description:
069_MaSv01_7_N727S513
07_20193_YfpPos_IL17Neg_S69


title: 02_20190_YfpNeg_IL17Pos

description:
064_MaSv01_2_N726S517
02_20190_YfpNeg_IL17Pos_S64


title: P25_ht_PBAT_del-mut_1


title: P25_ht_PBAT_del-mut_2


title: P25_ht_PBAT_++_1


title: P1_ht_PBAT_del-mut_2


title: 01_20190_YfpPos_IL17Neg

description:
063_MaSv01_1_N726S516
01_20190_YfpPos_IL17Neg_S63


title: P25_ht_PBAT_++_2


title: Adult_ht_RNA_++_1_RNAseq


title: single sperm_204

description: single sperm DNA sequence


title: single sperm_210

description: single sperm DNA sequence


title: single sperm_205

description: single sperm DNA sequence


title: P1_ht_PBAT_del-mut_1


title: inflamed_IC_4

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

institute: University of Cambridge

data_processing:
Illumina Casava was used for base calling
Fastq files were alligned to the mm10 genome using Hisat2
Gene counts were produced using featureCounts within Rsubread
Normalization and differential gene expression was carried out using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: [CountTable.csv] csv file containing count matrix
[DE_IC_from_DSS.csv] Results of differential expression analysis comparing the effect of IC stimulation in the group which received DSS only

growth_protocol: C57bl/6 mice were maintainted under SPF coditions at the University of Cambridge

extract_protocol:
A single cell suspension was produced from the murine colons. Cells were stained for FACS and live CX3CR1+ CD11b+ MHCII high F4/80+ cells were sorted. 7x10^4 cells were plated per well in 96 well round bottom plate and stimulated for 4 hours with either 400ng OVA alone or 400ng of OVA pre opsonized with 12ug anti OVA antibody to produce immune complexes(OIC).  After 4 hours RNA was extracted using RNeasy plus micro kit (Qiagen) and RNA quantified and RNA intregraty assessed using pico bioanalyzer chips.
For the preparation of libraries, SMARTer stranded total RNA-Seq mammalian pico input kit (Takara) was used as per the manufacturer’s instructions.  To produce the libraries, 1.5-3.55 ng of total RNA was used and libraries were amplified for 14 cycles of PCR.

treatment_protocol: Mice from the inflamed group were treated for 7 days with 2% DSS in their drinking water. The resting group remained on normal drinking water. After 7 days the mice were culled and their colons removed.

tag: treatment of mouse

value: DSS

value: colon

tag: cell type

value: macrophage

tag: in vitro stimulation

value: OIC


title: 05_20192_YfpPos_IL17Neg

description:
067_MaSv01_5_N726S521
05_20192_YfpPos_IL17Neg_S67

tag: cell-type


title: P1_ht_PBAT_++_2

value: Hypothalamus

tag: age


title: single sperm_207

description: single sperm DNA sequence


title: single sperm_203

description: single sperm DNA sequence


title: single sperm_202

description: single sperm DNA sequence


title: inflamed_IC_3


title: inflamed_IC_2


title: E7.5_epi_PBAT_+mut_4

source_name: Epiblast

value: Epiblast


title: single sperm_201

description: single sperm DNA sequence

source_name: single sperm


title: E7.5_epi_PBAT_+mut_2


title: E7.5_epi_PBAT_+mut_3


title: single sperm_1296

description: single sperm DNA sequence


title: inflamed_IC_1


title: p53-581

value: Nestin Cre Sleeping Beauty

value: Brain tumor

value: primary


title: E7.5_epi_PBAT_+mut_1


title: single sperm_1294

description: single sperm DNA sequence


title: inflamed_OVA_4

value: OVA


title: E7.5_epi_PBAT_del-mut_3


title: E7.5_epi_PBAT_del-mut_1


title: E7.5_epi_PBAT_del+_4


title: E7.5_epi_PBAT_del-mut_2


title: E7.5_epi_PBAT_del+_3


title: inflamed_OVA_2


title: E7.5_epi_PBAT_del-mut_4


title: inflamed_OVA_3


title: E7.5_epi_PBAT_del+_2


title: single sperm_1293

description: single sperm DNA sequence


title: single sperm_1288

description: single sperm DNA sequence


title: E7.5_epi_PBAT_del+_1


title: inflamed_OVA_1


title: single sperm_1287

description: single sperm DNA sequence


title: resting_IC_2


title: E7.5_epi_PBAT_++_3


title: E7.5_epi_PBAT_++_4


title: E7.5_epi_PBAT_++_2


title: resting_OVA_2


title: E7.5_epi_PBAT_++_1


title: Adult_pit_PBAT_del-mut_2

source_name: Pituitary

value: Pituitary

value: ~14 weeks


title: single sperm_1285

description: single sperm DNA sequence

value: sperm


title: Adult_pit_PBAT_del-mut_3


title: single sperm_1284

description: single sperm DNA sequence


title: Adult_pit_PBAT_++_3


title: Adult_pit_PBAT_del-mut_1


title: resting_OVA_1


title: Adult_pit_PBAT_++_2


title: Adult_pit_PBAT_++_1


title: single sperm_1281

description: single sperm DNA sequence


title: Adult_liv_PBAT_del-mut_1

value: Liver


title: Adult_liv_PBAT_++_3


title: single sperm_1280

description: single sperm DNA sequence


title: Adult_liv_PBAT_++_2


title: single sperm_1279

description: single sperm DNA sequence


title: Adult_liv_PBAT_++_1


title: Adult_ht_PBAT_+mut_2


title: single sperm_1286

description: single sperm DNA sequence


title: Adult_ht_PBAT_del-mut_3


title: Adult_ht_PBAT_+mut_1


title: resting_IC_1


title: Adult_ht_PBAT_del-mut_2


title: single sperm_1273

description: single sperm DNA sequence


title: Adult_ht_PBAT_del-mut_1


title: Adult_ht_PBAT_del+_3


title: single sperm_1271

description: single sperm DNA sequence


title: Adult_ht_PBAT_del+_2


title: single sperm_1269

description: single sperm DNA sequence


title: Adult_ht_PBAT_del+_1


title: Adult_ht_PBAT_++_3


title: Adult_ht_PBAT_++_2


title: single sperm_1283

description: single sperm DNA sequence


title: single sperm_1267

description: single sperm DNA sequence


title: Adult_liv_PBAT_del-mut_2


title: single sperm_1265

description: single sperm DNA sequence


title: Adult_ht_PBAT_++_1


title: single sperm_1256

description: single sperm DNA sequence


title: single sperm_1278

description: single sperm DNA sequence


title: single sperm_1255

description: single sperm DNA sequence


title: single sperm_1254

description: single sperm DNA sequence


title: single sperm_1251

description: single sperm DNA sequence


title: single sperm_1249

description: single sperm DNA sequence


title: C2C12_Cells_JQ1_Replicate_3_12h

first: Panagis

last: Filippakopoulos

state: Oxfordshire

address: ORCRB - Roosevelt Drive

department: Nuffield Department of Medicine

description: Gene expression data from C2C12 mouse myoblast cells treated with JQ1 (replicate 3) for 12h

hyb_protocol: Labelled ss-cDNA were hybridised to the Affymetrix Clariom™ S Assay HT, mouse -24 Array Plate

scan_protocol: Processing was carried out on the Affymetrix GeneTitan platform and analysed using the Affymetrix Expression console software

data_processing:
Raw CEL data were processed in R (v.3.5.1) using Bioconductor (v.3.7) and the oligo package (v.1.44). Quality controls were carried out using the arrayQualityMetrics package (v.3.36.0) taking into account array intensity distributions, distance between arrays and variance mean-dependence. Principal component analysis was used to decide which arrays to process together. On this basis one of the three arrays treated with BSP was considered to be an outlier and was discarded (sample 'BSP_rep3', file 'BSP_rep3.CEL'), with the rest of the analysis performed without taking it into account. Background correction and normalization were carried out employing the Robust Multichip Array (RMA) method implemented in the oligo package. Data were filtered using the genefilter package (v.1.62.0) employing the nsFilter function and an interquartile range (IQR) cut-off of 0.28 (or >log(1.2), determined by the midpoint of the shortest interval containing half of the data. Probe sets that did not have an Entrez gene identifier were also removed. From the 29129 features available on the Clariom S Mouse HT chip, 14538 remained after filtering. A linear model was applied employing the limma package (v.3.36.2) followed by empirical Bayesian analysis to determine differential expression between not-treated and treated samples.  Genes were considered differentially expressed if the adjusted P-value, calculated using the Benjamini–Hochberg method  in order to minimize false discovery rate, was less than 0.05 and the mean level of expression was greater than 1.5-fold. Data were annotated using the clariomsmousehttranscriptcluster.db annotation data (https://www.bioconductor.org/packages/release/data/annotation/html/clariomsmousehttranscriptcluster.db.html).
Clariom_S_Mouse_HT.r1.pgf (from http://www.affymetrix.com/Auth/analysis/downloads/lf/xta/Clariom_S_Mouse_HT/Clariom_S_Mouse_HT_TAC_Analysis.r1.zip)
Clariom_S_Mouse_HT.na36.mm10.transcript.csv (from http://www.affymetrix.com/Auth/analysis/downloads/na36/xta/Clariom_S_Mouse_HT.na36.mm10.transcript.csv.zip)

source_name: C2C12 cells, 0.5 μΜ JQ1, 12h treatment

label_protocol: Mouse RNA samples were processed using the Affymetrix GeneChip WT PLUS Reagent kit, the manual target preparation for GeneChip whole transcript expression arrays

growth_protocol: C2C12 mouse myoblast cells were grown in DMEM containing 20% FBS. 0.3x106 cells were seeded and allowed to grow for 36 hrs before switching to differentiation media (DMEM containing 2% horse serum, 10 µg/ml insulin and 10 µg/ml Transferrin)

extract_protocol: Total RNA was extracted using PureLinkTM RNA kit as per the manufacturer’s protocol.

treatment_protocol: C2C12 cells were incubated with the indicated drugs at concentrations of 500 nM (JQ1 & LP99) or 2 µM (GSK2801, BAZ2ICR & BSP) for 12 h before they were harvested for extraction of total RNA

tag: cell line

tag: agent

tag: replicate


title: P1_ht_PBAT_++_1


title: single sperm_1247

description: single sperm DNA sequence


title: Adult_ht_ChIP_K4_++_3

value: H3K4me3 (Diagenode C15410003)


title: C2C12_Cells_LP99_Replicate_3_12h

description: Gene expression data from C2C12 mouse myoblast cells treated with LP99 (replicate 3) for 12h

source_name: C2C12 cells, 0.5 μΜ LP99, 12h treatment


title: C2C12_Cells_JQ1_Replicate_2_12h

description: Gene expression data from C2C12 mouse myoblast cells treated with JQ1 (replicate 2) for 12h


title: single sperm_1244

description: single sperm DNA sequence

value: HUM/CAST


title: single sperm_1246

description: single sperm DNA sequence


title: 24_81017exTrPos_Neg

description:
086_MaSv02_18_N729S515
24_81017exTrPos_Neg_S86

value: Invitro

value: FoxP3eGFP BALB/c

value: Het

tag: genotype/variation

value: ExTregs

tag: batch

tag: sub-group


title: C2C12_Cells_JQ1_Replicate_1_12h

description: Gene expression data from C2C12 mouse myoblast cells treated with JQ1 (replicate 1) for 12h


title: Cj [degradome]

city: Wuhan

first: Juxun

last: Wu

state: Hubei

address: No.1 of Shizishan street, Hongshan District

country: China

institute: Huazhong Agricultral University

description:
Organism: Citrus junos Sieb. ex Tanaka
Degradome

data_processing:
Library strategy: Degradome-seq
The raw reads of small RNA libraries were pre-processed to remove low-quality reads, adaptors and contaminants to obtain clean reads. The clean reads were used to search Silva database, GtRNAdb database, Rfam database (Rfam 13.0) and Repbase database by Bowtie (Langmead et al., 2009) to filter ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA) and other ncRNA and repeats. Then, reads matching the reference genome C. sinensis (Xu et al., 2013) were annotated. These reads were used to detect known miRNA (comparing with miRBase 22 database) and novel miRNA predicted by miRDEEP2 (Zhang et al., 2015). The novel miRNAs were confirmed based on the criteria of a previous publication (Meyers et al., 2008) and secondary structure of the hairpins visualized by VisSR (version 1.0). Raw miRNA counts were normalized to TPM (reads per million) using the equation TPM = (Read count/Total mapped reads) × 1 000 000. The differential expression analysis was performed using the R-package DESeq (1.10.1) (Anders and Huber, 2010). miRNAs with an adjusted P-value < 0.05 found by DESeq were assigned as differentially expressed miRNAs.
Genome_build: Citrus sinensis Annotation Project (CAP) (http://citrus.hzau.edu.cn/).
Supplementary_files_format_and_content: All_miRNA.xlsx: File was generated by Microsoft Excel, TPM represents the expression of genes.

organism: Citrus junos

source_name: seedling

growth_protocol: The seeds of Cj and Pt were surface-sterilized and their germination accelerated. The seedlings were grown in a growth chamber until they had four leaves. Then, the seedlings were selected by uniform size and transferred into hydroponics with 4 L solution in a green house.

extract_protocol:
Approximately 2 to 3 g of powdered material was subjected to each RNA extraction, including 10 mL buffer extraction, 5 mL chloroform-isoamylalcohol extraction (twice), 5 mL isopropanol precipitation, 5 mL 75% ethanol cleaning and RNA purification as described by Camacho-Villasana YM et al.
A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra small RNA Sample Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, first of all, ligated the 3′ SR Adaptor. Mixed 3′ SR Adaptor for Illumina, RNA and Nuclease-Free Water, mixture system after incubation for 2 minutes at 70 degrees in a preheated thermal cycler. Tube was transfer to ice. Then, add 3′ Ligation Reaction Buffer (2X) and 3′ Ligation Enzyme Mix ligate the 3′ SR Adaptor. Incubated for 1 hour at 25°C in a thermal cycler. To prevent adaptor-dimer formation, the SR RT Primer hybridizes to the excess of 3′ SR Adaptor (that remains free after the 3′ ligation reaction) and transforms the single stranded DNA adaptor into a double-stranded DNA molecule. dsDNAs are not substrates for ligation mediated. The second, ligated the 5′ SR Adaptor. Then, reverse transcription synthetic first chain. Last, PCR amplification and Size Selection. PAGE gel was used to electrophoresis fragment screening purposes, rubber cutting recycling as the pieces get small RNA libraries. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Three different pH gradients (6.5, 8.0 and 9.5) were set up. Because most natural soils have a weak acidity, we set pH 6.5 as the normal condition. After 8 weeks of culture, three biological replicates (three seedling plants per replicate) were harvested randomly for each treatment.

tag: tissue

value: root

tag: ph treatment


title: single sperm_1243

description: single sperm DNA sequence

tag: strain

tag: prdm9 genotype


title: C2C12_Cells_BAZ2ICR_Replicate_3_12h

description: Gene expression data from C2C12 mouse myoblast cells treated with BAZ2ICR (replicate 3) for 12h

source_name: C2C12 cells, 2 μΜ BAZ2ICR, 12h treatment


title: Cj3R3 [miRNA-seq]

description:
Organism: Citrus junos Sieb. ex Tanaka
small RNA
processed data file: All_miRNA.xlsx

data_processing:
The raw reads of small RNA libraries were pre-processed to remove low-quality reads, adaptors and contaminants to obtain clean reads. The clean reads were used to search Silva database, GtRNAdb database, Rfam database (Rfam 13.0) and Repbase database by Bowtie (Langmead et al., 2009) to filter ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA) and other ncRNA and repeats. Then, reads matching the reference genome C. sinensis (Xu et al., 2013) were annotated. These reads were used to detect known miRNA (comparing with miRBase 22 database) and novel miRNA predicted by miRDEEP2 (Zhang et al., 2015). The novel miRNAs were confirmed based on the criteria of a previous publication (Meyers et al., 2008) and secondary structure of the hairpins visualized by VisSR (version 1.0). Raw miRNA counts were normalized to TPM (reads per million) using the equation TPM = (Read count/Total mapped reads) × 1 000 000. The differential expression analysis was performed using the R-package DESeq (1.10.1) (Anders and Huber, 2010). miRNAs with an adjusted P-value < 0.05 found by DESeq were assigned as differentially expressed miRNAs.
Genome_build: Citrus sinensis Annotation Project (CAP) (http://citrus.hzau.edu.cn/).
Supplementary_files_format_and_content: All_miRNA.xlsx: File was generated by Microsoft Excel, TPM represents the expression of genes.


title: C2C12_Cells_BAZ2ICR_Replicate_2_12h

description: Gene expression data from C2C12 mouse myoblast cells treated with BAZ2ICR (replicate 2) for 12h


title: Cj3R2 [miRNA-seq]


title: Cj3R1 [miRNA-seq]


title: C2C12_Cells_BAZ2ICR_Replicate_1_12h

description: Gene expression data from C2C12 mouse myoblast cells treated with BAZ2ICR (replicate 1) for 12h


title: C2C12_Cells_LP99_Replicate_1_12h

description: Gene expression data from C2C12 mouse myoblast cells treated with LP99 (replicate 1) for 12h


title: C2C12_Cells_BSP_Replicate_1_12h

description: Gene expression data from C2C12 mouse myoblast cells treated with BSP (replicate 1) for 12h

source_name: C2C12 cells, 2 μΜ BSP, 12h treatment

value: BSP


title: C2C12_Cells_BSP_Replicate_2_12h

description: Gene expression data from C2C12 mouse myoblast cells treated with BSP (replicate 2) for 12h


title: single sperm_1242

description: single sperm DNA sequence


title: C2C12_Cells_GSK2801_Replicate_3_12h

description: Gene expression data from C2C12 mouse myoblast cells treated with GSK2801 (replicate 3) for 12h

source_name: C2C12 cells, 2 μΜ GSK2801, 12h treatment


title: C2C12_Cells_LP99_Replicate_2_12h

description: Gene expression data from C2C12 mouse myoblast cells treated with LP99 (replicate 2) for 12h


title: C2C12_Cells_DMSO_Replicate_3_12h

description: Gene expression data from C2C12 mouse myoblast cells treated with DMSO (replicate 3) for 12h

source_name: C2C12 cells, DMSO, 12h treatment

value: DMSO


title: C2C12_Cells_GSK2801_Replicate_2_12h

description: Gene expression data from C2C12 mouse myoblast cells treated with GSK2801 (replicate 2) for 12h


title: C2C12_Cells_DMSO_Replicate_2_12h

description: Gene expression data from C2C12 mouse myoblast cells treated with DMSO (replicate 2) for 12h


title: C2C12_Cells_DMSO_Replicate_1_12h

description: Gene expression data from C2C12 mouse myoblast cells treated with DMSO (replicate 1) for 12h


title: C2C12_Cells_GSK2801_Replicate_1_12h

description: Gene expression data from C2C12 mouse myoblast cells treated with GSK2801 (replicate 1) for 12h


title: single sperm_1241

description: single sperm DNA sequence


title: Cj2R1 [miRNA-seq]


title: single sperm_1231

description: single sperm DNA sequence


title: Cj2R3 [miRNA-seq]


title: Cj2R2 [miRNA-seq]


title: Cj1R2 [miRNA-seq]


title: Cj1R1 [miRNA-seq]


title: single sperm_1227

description: single sperm DNA sequence


title: Cj1R3 [miRNA-seq]


title: single sperm_1224

description: single sperm DNA sequence


title: single sperm_1225

description: single sperm DNA sequence


title: single sperm_1213

description: single sperm DNA sequence


title: single sperm_1212

description: single sperm DNA sequence


title: single sperm_1206

description: single sperm DNA sequence


title: single sperm_1203

description: single sperm DNA sequence


title: single sperm_1202

description: single sperm DNA sequence


title: single sperm_1201

description: single sperm DNA sequence


title: BENaC_Smoke_Male_5day_Rep5

city: Chapel Hill

first: Claire

middle: M

last: Doerschuk

state: NC

address: 125 Mason Farm Rd. CB#7248

institute: UNC Chapel Hill

hyb_protocol: Fragmented and labeled cDNA was used to prepare a hybridization cocktail with the Affymetrix GeneTitan Hybridization Wash and Stain Kit for WT Arrays. Hybridization, washing, staining and scanning of the Affymtrix peg plate arrays was carried out using the Affymetrin GeneTitan MC Instrument. GeneChip Command Console Software (AGCC) was used for GeneTitan Instrument control.

scan_protocol: Scanning of the Affymetrix peg plate arrays was carried out using the Affymetrix GeneTitan MC Instrument. GeneChip Command Console Software (AGCC) was used for GeneTitan Instrument control.

data_processing: Data were evaluated using Affymetrix Expression Console v1.4 software for quality control based on summary statistics, and Partek Genomics Suite v6.6 for normalization. Expression signals from CEL files were preprocessed and normalized by RMA (Robust Multiarray Average) background correction, GC content and probe sequence correction, quantile normalization, and median polish summarization of probe signals mapped to specific genes. Custom probeset-to-gene mappings were generated from Affymetrix Probeset and Transcript Annotation release 35 by consolidating all probesets mapped, in order of preference, to Ensembl 81 gene ID, Refseq mRNA, and Genbank accession numbers. The RMA-normalized log2 intensity values were used as input for the General Linear Model (glm) function in R.

source_name: RNA isolated from whole lung tissue from male BENaC mice given 5 days of smoke exposure

label_protocol: Total RNA (250 ng) was used to synthesize fragmented and labeled sense-strand cDNA and hybridize onto Affymetrx arrays. All 80 samples were run on the same 96 well array plate.  The Affymetrix HT WT User Manual was followed to prepare the samples. Briefly, the WT Expression HT Kit for Robotics (Ambion) was used to generate sense-strand cDNA from total RNA.  Following synthesis of sense-strand cDNA, the cDNA was fragmented and labeled with the Affymetrix GeneChip HT Terminal Labeling Kit.  The Beckman Coulter Biomek FXP Laboratory Automation Workstation with the Target Express set up was used to prepare the samples with these two kits.

extract_protocol: Total RNA was isolated using miRNeasy kits from Qiagen (Valencia, CA, USA) according to the manufacturer's instructions. RNA was isolated from lung tissue homogenates using the miRNeasy kit (Qiagen). Spectrophotometric ratios of A260/A280 and A260/A230 were 1.7-2.1 and greater than 1.6, respectively. RIN values were greater than 7.4; the average RIN for all samples was 9.1.

treatment_protocol: Sex-matched 5-7-week old WT and βENaC littermates were exposed to cigarette smoke or sham (room air) exposure.  Each exposure and genotype group included both males and females (n=5 animals of each sex per group for most groups. In the 5-day female group, there were n=6 WT sham animals and n=4 βENaC sham animals). Exposure occurred in a plexiglass chamber attached to a smoke delivery device using an exposure chamber and smoking machine (inExpose Exposure System, SCIREQ, Chandler, AZ). The chamber contained pie-slice separators and positions for 16 mice. Mice were exposed to mainstream + side-stream smoke from 6 reference cigarettes with filters removed per day (College of Agriculture Reference Cigarette Program, University of Kentucky, 3R4F research cigarettes) [18].  Each cigarette was puffed for 2 sec every 25 sec, using the standard Federal Trade Commission smoking machine protocol [18]. The sham-exposed control mice were exposed to room air in the exposure chamber for a time equivalent to that needed for active smoke exposure. Mice were exposed to cigarette or sham smoke for 1 day or 5 consecutive days. Samples were harvested 4 hours after the completion of the final smoke exposure. The right lung was used for gene expression analysis.

value: Homogenized whole lung tissue

tag: genotype

value: Scnn1b-overexpressing (BENaC)

tag: exposure

value: Smoke

tag: Sex

value: Male

tag: exposure duration

value: 5 day


title: WT_Smoke_Male_5day_Rep5

value: Wildtype (WT)


title: WT_Sham_Male_1day_Rep5

source_name: RNA isolated from whole lung tissue from male WT mice given 1 day of sham exposure

value: Sham

value: 1 day


title: BENaC_Sham_Male_5day_Rep4

source_name: RNA isolated from whole lung tissue from male BENaC mice given 5 days of sham exposure


title: WT_Sham_Female_1day_Rep5

source_name: RNA isolated from whole lung tissue from female WT mice given 1 day of sham exposure

value: Female


title: WT_Sham_Male_5day_Rep4

source_name: RNA isolated from whole lung tissue from male WT mice given 5 days of sham exposure


title: WT_Smoke_Male_5day_Rep4


title: BENaC_Sham_Male_1day_Rep5

source_name: RNA isolated from whole lung tissue from male BENaC mice given 1 day of sham exposure


title: WT_Sham_Male_5day_Rep5


title: BENaC_Smoke_Male_1day_Rep5

source_name: RNA isolated from whole lung tissue from male BENaC mice given 1 day of smoke exposure


title: BENaC_Sham_Male_5day_Rep5


title: BENaC_Sham_Male_5day_Rep3


title: WT_Smoke_Male_5day_Rep2


title: WT_Sham_Female_5day_Rep5

source_name: RNA isolated from whole lung tissue from female WT mice given 5 days of sham exposure


title: WT_Smoke_Male_5day_Rep3


title: WT_Sham_Male_5day_Rep2


title: BENaC_Smoke_Male_5day_Rep3


title: WT_Sham_Male_5day_Rep3


title: BENaC_Smoke_Male_5day_Rep4


title: WT_Sham_Male_5day_Rep1


title: WT_Sham_Female_5day_Rep6


title: WT_Sham_Female_5day_Rep4


title: BENaC_Sham_Male_5day_Rep2


title: BENaC_Sham_Female_5day_Rep4

source_name: RNA isolated from whole lung tissue from female BENaC mice given 5 days of sham exposure


title: BENaC_Smoke_Male_5day_Rep1


title: WT_Sham_Female_5day_Rep3


title: WT_Smoke_Female_5day_Rep5

source_name: RNA isolated from whole lung tissue from female BENaC mice given 5 days of smoke exposure


title: BENaC_Smoke_Male_5day_Rep2


title: BENaC_Sham_Female_5day_Rep3


title: BENaC_Smoke_Female_5day_Rep3


title: BENaC_Sham_Female_5day_Rep1


title: WT_Smoke_Female_5day_Rep3


title: single sperm_1215

description: single sperm DNA sequence

source_name: single sperm

value: sperm

value: HUM/CAST


title: WT_Sham_Female_5day_Rep2


title: BENaC_Sham_Female_5day_Rep2


title: WT_Smoke_Female_5day_Rep4


title: BENaC_Smoke_Female_5day_Rep2


title: BENaC_Sham_Male_5day_Rep1


title: WT_Sham_Female_5day_Rep1


title: MSC 5 with miR-7977

city: Sapporo

first: Masayoshi

last: Kobune

state: Hokkaido

address: Chuo-Ku, South-1, West-16

department: Hematology

country: Japan

institute: Sapporo Medical University

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Samples were hybridized with GeneChip Human Exon 2.0 ST Arrays (Affymetrix) and scanned at the Genetic laboratory Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with customized R codes (version 2.3.1, http://www.r-project.org/). We defined a probeset as present when it had a P value <0.001 and an Intensity value >200. These criteria were suggested by the results of preliminary experiments. The SECT includes all probesets present in at least 16 of the 18 arrays. In addition, we refined the SECT to remove GC-rich (i.e., >=80%) probesets. The concordance between the SECT and the normal salivary core transcriptome (NSCT) was evaluated assuming hypergeometric distributions.
affymetrix-algorithm-name = rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: The MSCs were cultured in MSCGM™ hMSC basal medium with addition of supplements from the MSCGM hMSC SingleQuot Kit (Lonza Japan Ltd, Tokyo, Japan).

extract_protocol: Total RNA was isolated from mesenchymal stem cells with the Trizol reagent (Invitrogen), according to the manufacturer’s instructions.All samples were treated with TURBO DNA-free (Ambion) to remove trace amounts of genomic DNA. A 2-round amplification was performed with the ExpressArt TRinucleotide mRNA Amplification Kit (AmpTec) according to the manufacturer’s instructions.

treatment_protocol: Transfection of miRNA mimic (5 to 20 nM) was conducted using HiPerFect Transfection Reagent (QIAGEN). The mRNA expression was analyzed by qRT-PCR 48-72 hrs after miRNA transfer.

tag: tissue source

value: Bone marrow derived

tag: cell type

value: Mesenchymal stem cells (MSCs)

tag: transduced with

value: miR-7977 mimic


title: BENaC_Smoke_Female_5day_Rep4


title: WT_Sham_Male_1day_Rep4


title: WT_Smoke_Female_5day_Rep2


title: MSC 3 with miR-7977


title: MSC 2 with miR-7977


title: WT_Smoke_Female_5day_Rep1


title: WT_Sham_Female_1day_Rep4


title: BENaC_Sham_Male_1day_Rep3


title: BENaC_Sham_Female_1day_Rep5

source_name: RNA isolated from whole lung tissue from female BENaC mice given 1 day of sham exposure


title: Susceptible soybean stem 96 hours post infection biological replicate 3

city: Madison

first: Mehdi

last: Kabbage

state: Wisconsin

address: Department of Plant Pathology, 583 Russell Labs 1630 Linden Dr

department: Department of Plant Pathology

institute: University of Wisconsin Madison

data_processing:
The raw sequence reads were mapped to the genome using Subjunc aligner from Subread. The alignment bam files were compared against the gene annotation GFF file, and raw counts for each gene were generated using the featureCounts tool from subread.
Next, we performed additional QC at gene level, including number of genes detected, percentage of reads belonging to the top genes, normalization for RNA composition, and grouping and correlation between samples. Click here to view full QC report at gene level.
The raw counts data were normalized using voom method from the R Limma package, then used for differential expression analysis. See section 3 above for further technical details.
Based on expression changes, we further carried out analyses to detect enriched functions
Genome_build: The fungal genome, gene annotations, and mitochondrial genome were provided by the Broad Institute (INSDC: AAGT00000000.1 and KT283062.1).
Supplementary_files_format_and_content: comma-delimited text files include RPKM values for each Sample

organism: Sclerotinia sclerotiorum

growth_protocol: Soybean seedlings and plants were maintained in the greenhouse or growth chamber at 24 ± 2◦C with 16 h light/8 h dark photoperiod cycle. S. sclerotiorum strain 1980 was grown at room temperature on potato dextrose agar (PDA) for inoculations. Culture control (P1-3) was grown at room temperature in glucose minimal media (GMM).

extract_protocol:
Total RNA was extracted from the stem tissues and fungal material using a Trizol protocol. Samples were cleaned using the RNeasy Plant Mini Kit protocol (RNeasy Plant Mini Kit, Qiagen, Hilden, Germany). RNA concentration and purity were determined by Nanodrop and sample quality was assessed using an Agilent Bioanalyzer 2100 and a RNA 6000 Nano Kit.
RNA from each sample was randomly fragmented, and individually indexed libraries were prepared using the TruSeq RNA Sample Preparation v2 kit according to the manufacturer’s instructions  protocol. Library was quantified with Qubit HS DNA kit. The quality of the library was checked with an Agilent Bioanalyzer 2100 and an Agilent DNA 1000 kit.

treatment_protocol: Inoculations were performed using the cut petiole method as described by (Ranjan et al. 2017). Plant tissue was sampled by cutting horizontally above and below (1.5 cm) the node of the first trifoliate with a clean straight-edge razor. Tissue samples were collected at 24, 48, and 96 h post inoculation (hpi) and immediately frozen in liquid nitrogen prior to RNA extraction. As a control, Sclerotinia sclerotiorum strain 1980 cultures were grown on a shaker in glucose minimal media for 48 hours (150 rpm, 25℃).

tag: soybean plant phenotype

value: Susceptible

tag: infection

value: S. sclerotiorum (fungal pathogen)

tag: fungal condition

value: In planta

tag: time

value: 96hr hpi

value: stem tissues and fungal material


title: WT_Smoke_Male_1day_Rep5

source_name: RNA isolated from whole lung tissue from male WT mice given 1 day of smoke exposure

value: Homogenized whole lung tissue

value: Smoke


title: Susceptible soybean stem 96 hours post infection biological replicate 1


title: Susceptible soybean stem 48 hours post infection biological replicate 3

value: 48hr hpi


title: Gli36_Exo_Low_smallRNA_2

city: Nashville

first: Jie

last: Ping

state: TN

address: 2525 West End Ave

institute: Vanderbilt University Medical Center

description: Small RNA

data_processing:
Illumina Casava 1.8.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR v2.5.3a with parameters --twopassMode Basic --outSAMprimaryFlag AllBestScore
Read counts were calculated by using HTSeq-Count v0.11.0 with parameters -f bam -r name -m intersection-nonempty -s no -t gene -i gene_name.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read counts values for all samples
Illumina Casava 1.8.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using ncPRO-seq v1.5.1.
Read counts were calculated by using ncPRO-seq v1.5.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts values of mRNAs and mature miRNAs for all samples

source_name: low

extract_protocol:
Total RNA was extracted from pelleted samples using the miCURY RNA Isolation Kit (Exiqon) according to the manufacturers protocol
Short RNA libraries were prepared using NEBNext Small RNA Library Prep Set for Illumina. For long RNA library preparation a Ribo-zero Magnetic Gold rRNA removal kit was used to remove ribosomal RNA from the total RNA. First strand synthesis was performed using NEBNext RNA first strand synthesis module. Immediately thereafter, directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this, cDNAs were used for standard library preparation protocol using NEBNext DNA Library Prep Master Mix Set.

value: Glioblastoma cells

tag: compartment

value: Extracellular low density fractions


title: Susceptible soybean stem 48 hours post infection biological replicate 2


title: BENaC_Smoke_Female_5day_Rep5

value: Scnn1b-overexpressing (BENaC)

value: 5 day


title: Gli36_Exo_Low_smallRNA_4

description: Small RNA


title: Gli36_Exo_High_smallRNA_4

description: Small RNA

source_name: high

value: Extracellular high density fractions


title: MSC 2 with negative control

source_name: MSCs_negative control

value: negative control


title: Susceptible soybean stem 48 hours post infection biological replicate 1


title: MSC 3 with negative control

value: Bone marrow derived


title: Gli36_Exo_Low_smallRNA_3

description: Small RNA


title: WT_Sham_Male_1day_Rep3

value: Wildtype (WT)

value: Sham

value: Male

value: 1 day


title: BENaC_Smoke_Female_5day_Rep1

value: Female


title: WT_Sham_Female_1day_Rep3


title: WT_Smoke_Female_1day_Rep5

source_name: RNA isolated from whole lung tissue from female BENaC mice given 1 day of smoke exposure


title: Gli36_Exo_Low_smallRNA_1

description: Small RNA


title: BENaC_Smoke_Female_1day_Rep5


title: BENaC_Sham_Female_1day_Rep4


title: BENaC_Sham_Male_1day_Rep4


title: WT_Sham_Male_1day_Rep2


title: BENaC_Sham_Male_1day_Rep1


title: BENaC_Sham_Male_1day_Rep2


title: Susceptible soybean stem 24 hours post infection biological replicate 3

value: Susceptible

value: S. sclerotiorum (fungal pathogen)

value: In planta

value: 24hr hpi


title: Gli36_Exo_Cell_smallRNA_4

description: Small RNA

source_name: cell

value: Cell


title: Susceptible soybean stem 24 hours post infection biological replicate 2

value: stem tissues and fungal material


title: Gli36_Exo_Cell_smallRNA_3

description: Small RNA

value: Glioblastoma cells


title: Susceptible soybean stem 24 hours post infection biological replicate 1


title: resistant soybean stem 96 hours post infection biological replicate 3

value: resistant

value: 96hr hpi


title: BENaC_Sham_Female_1day_Rep3

value: Homogenized whole lung tissue

value: Scnn1b-overexpressing (BENaC)


title: BENaC_Sham_Female_1day_Rep2


title: resistant soybean stem 96 hours post infection biological replicate 2


title: Gli36_Exo_Cell_smallRNA_2

description: Small RNA


title: Gli36_Exo_Cell_smallRNA_1

description: Small RNA


title: resistant soybean stem 96 hours post infection biological replicate 1


title: DKO1_Exo_High_smallRNA_3

description: Small RNA

value: Colorectal cancer cells

value: Extracellular high density fractions


title: resistant soybean stem 48 hours post infection biological replicate 3

value: 48hr hpi


title: DKO1_Exo_High_smallRNA_2

description: Small RNA


title: DKO1_Exo_High_smallRNA_4

description: Small RNA


title: DKO1_Exo_High_smallRNA_1

description: Small RNA


title: resistant soybean stem 48 hours post infection biological replicate 2


title: resistant soybean stem 48 hours post infection biological replicate 1


title: resistant soybean stem 24 hours post infection biological replicate 3


title: DKO1_Exo_Low_smallRNA_4

description: Small RNA

value: Extracellular low density fractions


title: resistant soybean stem 24 hours post infection biological replicate 2


title: resistant soybean stem 24 hours post infection biological replicate 1


title: DKO1_Exo_Low_smallRNA_3

description: Small RNA


title: DKO1_Exo_Low_smallRNA_2

description: Small RNA


title: BENaC_Smoke_Male_1day_Rep4

value: Smoke

value: Male

value: 1 day


title: WT_Sham_Female_1day_Rep2

value: Wildtype (WT)

value: Sham

value: Female


title: WT_Sham_Male_1day_Rep1

source_name: RNA isolated from whole lung tissue from male WT mice given 1 day of sham exposure


title: BENaC_Sham_Female_1day_Rep1


title: BENaC_Smoke_Male_1day_Rep3


title: S. sclerotiorum culture control biological replicate 3

source_name: S. sclerotiorum culture control

value: In vitro

value: fungal material


title: DKO1_Exo_Low_smallRNA_1

description: Small RNA


title: WT_Smoke_Male_1day_Rep2


title: WT_Smoke_Male_1day_Rep3


title: Yeast_CSTARVE (scRNA-seq)

city: New York

first: Christopher

last: Jackson

state: NY

address: 101 Avenue of the Americas

department: Center for the Genomics of Neurodegenerative Disease

institute: New York Genome Center

data_processing:
Cellranger mkfastq v2.1.1 to generate FASTQ
Cellranger count v2.1.1 to generate count matrix
FastqTomat0 BCLinker v0.1.0 to call cell genotype
FastqTomat0 tenXtoMatrix v0.1.0 to assign per-cell metadata and output final count matrix
Genome_build: Saccharomyces_cerevisiae R64
Supplementary_files_format_and_content: [TSV]  tab-separated value file with an index column
Supplementary_files_format_and_content: [Cellranger files]  comprising a MatrixMarket file (matrix.mtx) and two tab separated metadata files (barcodes.tsv, genes.tsv)

organism: Saccharomyces cerevisiae

source_name: Yeast grown in Carbon Starvation

extract_protocol: 10x Genomics Chromium 3’ v2 Single Cell Gene Expression Kit

tag: growth condition

value: CSTARVE

value: mixed sample (non-demultiplexed)


title: Yeast_RAPA (scRNA-seq)

source_name: Yeast grown in YPD and treated with 200 ng/mL Rapamycin

value: RAPA


title: S. sclerotiorum culture control biological replicate 2

tag: tissue


title: DKO1_Exo_MV_smallRNA_4

description: Small RNA

source_name: microvesicle

value: Extracellular microvesicle


title: Yeast_YPD (scRNA-seq)

source_name: Yeast grown in YPD

value: YPD


title: S. sclerotiorum culture control biological replicate 1


title: DKO1_Exo_MV_smallRNA_3

description: Small RNA

value: Colorectal cancer cells


title: WT_Smoke_Female_1day_Rep4

value: Homogenized whole lung tissue


title: Yeast_NLIM-PRO (scRNA-seq)

source_name: Yeast grown in Nitrogen Limiting Media + 0.8 mM Proline

value: NLIM-PRO


title: BENaC_Smoke_Male_1day_Rep2

source_name: RNA isolated from whole lung tissue from male BENaC mice given 1 day of smoke exposure

value: Scnn1b-overexpressing (BENaC)


title: DKO1_Exo_MV_smallRNA_2

description: Small RNA


title: Pt [degradome]

description:
Organism: Poncirus trifoliata (L.) Raf.
Degradome

organism: Citrus trifoliata

source_name: seedling

value: root

tag: ph treatment


title: DKO1_Exo_MV_smallRNA_1

description: Small RNA

tag: strain


title: Yeast_NLIM-GLN (scRNA-seq)

source_name: Yeast grown in Nitrogen Limiting Media + 0.8 mM L-Glutamine

value: NLIM-GLN


title: WT_Sham_Female_1day_Rep1

source_name: RNA isolated from whole lung tissue from female WT mice given 1 day of sham exposure

value: 1 day


title: BENaC_Smoke_Female_1day_Rep4

value: Smoke


title: Yeast_NLIM-UREA (scRNA-seq)

source_name: Yeast grown in Nitrogen Limiting Media + 0.8 mM Urea

value: NLIM-UREA


title: DKO1_Exo_Cell_smallRNA_4

description: Small RNA

value: Cell


title: WT_Smoke_Female_1day_Rep3

value: Wildtype (WT)

value: Female


title: WT_Smoke_Male_1day_Rep4

source_name: RNA isolated from whole lung tissue from male WT mice given 1 day of smoke exposure

value: Male


title: Yeast_NLIM-NH4 (scRNA-seq)

source_name: Yeast grown in Nitrogen Limiting Media + 0.8 mM Ammonium Sulfate

value: mixed sample (non-demultiplexed)


title: BENaC_Smoke_Male_1day_Rep1


title: DKO1_Exo_Cell_smallRNA_3

description: Small RNA


title: WT_Smoke_Female_1day_Rep2


title: DKO1_Exo_Cell_smallRNA_2

description: Small RNA


title: WT_Smoke_Male_1day_Rep1


title: Pt3R3 [miRNA-seq]

description:
Organism: Poncirus trifoliata (L.) Raf.
small RNA
processed data file: All_miRNA.xlsx


title: Pt2R3 [miRNA-seq]


title: Pt2R2 [miRNA-seq]


title: Pt2R1 [miRNA-seq]


title: NSC9

city: Houston

first: Stephen

middle: Mack

last: Christopher

state: TX

address: 1102 Bates Avenue C1030.02

department: Pediatrics

institute: Baylor College of Medicine

hyb_protocol: According to Illumina default protocol and recommendations

data_processing:
.idat files were processed using R bioconductor with the Minfi package. Signal from CpG probes were pre-processed with background correction and dye-bias normalization using the 'preprocessNoob' method (Triche et al., 2013). Following pre-processing, probes found to contain SNPs or found withing chromosome X and Y were removed for downstream analysis.
Matrices are provided for all samples as processed Beta values: GBM_GSC_i850K_beta_formatted.txt, Methylated signal: GBM_GSC_i850K_meth_formatted.txt, unmethylated signal: GBM_GSC_i850K_unmeth_formatted.txt, p-values: GBM_GSC_i850K_pvals_formatted.txt

extract_protocol: DNA was extracted using the Invitrogen PureLink Genomic DNA kit, and quantity assesed with Nanodrop and Picogreen quantification. Genomic DNA was submitted to McGill University and Genomic Quebec Innovation center for bisulphite treatment and  subsequent array hybridization according to Illumina recommendations.

value: neural stem cells


title: Pt3R2 [miRNA-seq]


title: Pt3R1 [miRNA-seq]


title: Pt1R3 [miRNA-seq]


title: DKO1_Exo_High_RNA_4

description: RNA

source_name: high

value: Extracellular high density fractions


title: Yeast_DIAUXY (scRNA-seq)

source_name: Yeast grown in YPD 10H (Dauxic Shift)

value: DIAUXY


title: Gli36_Exo_High_smallRNA_2

description: Small RNA

value: Glioblastoma cells


title: Yeast_MMETOH (scRNA-seq)

source_name: Yeast grown in Minimal Media + 2% Ethanol

value: MMETOH


title: NSC8

scan_protocol: According to Illumina default protocol and recommendations


title: DKO1_Exo_High_RNA_3

description: RNA

value: Colorectal cancer cells


title: Pt1R2 [miRNA-seq]


title: MSC 5 with negative control

source_name: MSCs_negative control

value: Bone marrow derived

value: Mesenchymal stem cells (MSCs)

value: negative control


title: Yeast_MMD (scRNA-seq)

source_name: Yeast grown in Minimal Media + 2% (w/v) Glucose

value: MMD


title: BENaC_Smoke_Female_1day_Rep1

source_name: RNA isolated from whole lung tissue from female BENaC mice given 1 day of smoke exposure

value: Homogenized whole lung tissue

value: Scnn1b-overexpressing (BENaC)

value: Smoke

value: 1 day


title: DKO1_Exo_Low_RNA_4

description: RNA

source_name: low

value: Extracellular low density fractions


title: NSC6

label_protocol: According to Illumina default protocol and recommendations


title: BENaC_Smoke_Female_1day_Rep2

value: Female


title: NSC7


title: Pt1R1 [miRNA-seq]

value: root


title: Flagellin-treated 1 hour replicate 2

city: Cleveland

first: Florian

last: Rieder

state: OH

address: 9500 Euclid Ave

department: I & I

institute: Cleveland Clinic

data_processing:
Single-ended 50 bp reads were trimmed with Trim Galore! (v.0.3.7) and checked for quality with FastQC (v0.11.3) [ref: http://www.bioinformatics.babraham.ac.uk/projects] before alignment to the human genome (GRCh38.p10 using Gencode Release 27 annotations).
Reads were aligned using STAR (v.2.5.3a, https://github.com/alexdobin/STAR) in single (24 hour samples) or two-pass mode (1 hour samples) using default parameters and --quantMode GeneCounts.
For two-pass alignment, splice junctions from the first pass for all samples were combined and filtered to remove chrM and non-standard scaffolds as well as non-canonical junctions and those supported by < 10 reads.
Genome_build: GRCh38.p10

source_name: Intestinal Myofibroblasts

growth_protocol: All HIMF were cultured in DMEM supplemented with 10% FBS, 2% L-Glut, 1% PSF, and 2.5% HEPES at 37 degree, 5% CO2 incubator.

extract_protocol:
RNA was isolated from HIMF using the Qiagen Mini RNeasy Kit
RNA-SEQ libraries were generated using Illumina TruSEQ kits following the manufacturer’s protocol

treatment_protocol: HIMF were treated with FLA-ST Ultrapure for 1 hour and 24 hours, respectively

value: normal colon

tag: passages

value: passage 8-10

tag: treatment

value: FLA-ST Ultrapure

tag: timepoint


title: DKO1_Exo_Low_RNA_3

description: RNA


title: Flagellin-treated 1 hour replicate 3


title: Flagellin-treated 1 hour replicate 1


title: NSC4

value: neural stem cells


title: DKO1_Exo_Low_RNA_2

description: RNA


title: DKO1_Exo_Cell_smallRNA_1

description: Small RNA

source_name: cell

value: Cell


title: NSC5


title: Untreated 1 hour replicate 3

value: untreated


title: Untreated 1 hour replicate 2


title: DKO1_Exo_MV_RNA_4

description: RNA

source_name: microvesicle

value: Colorectal cancer cells

value: Extracellular microvesicle


title: DKO1_Exo_MV_RNA_3

description: RNA


title: NSC10


title: Gli36_Exo_High_smallRNA_1

description: Small RNA

value: Glioblastoma cells

value: Extracellular high density fractions


title: NSC1


title: Flagellin-treated 24 hours replicate 3


title: DKO1_Exo_MV_RNA_2

description: RNA


title: Flagellin-treated 24 hours replicate 2


title: Untreated 1 hour replicate 1


title: DKO1_Exo_Low_RNA_1

description: RNA


title: GSC9

value: glioblastoma stem cell model


title: metastatic CRC_8

city: GUANGZHOU

first: Liang

last: Zhao

state: GUANGDONG

address: 1838 Guangzhou Avenue North

department: Department of Pathology

institute: Nanfang Hospital, Southern Medical University

description:
LncRNA and mRNA expression profile
Sample name: 71CA

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3‐labeled cRNA using Gene Expression Hybridization Kit (Cat#5188‐5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188‐5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit.

data_processing:
Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).
Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US)

source_name: metastatic human CRC Tiissue

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One‐Color (Cat#5190‐2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer ’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596‐018,Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase‐Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

value: metastatic human CRC Tiissue

tag: age

tag: gender

value: Male


title: metastatic CRC_5

description:
LncRNA and mRNA expression profile
Sample name: 42CA


title: metastatic CRC_7

description:
LncRNA and mRNA expression profile
Sample name: 65CA


title: NSC2


title: metastatic CRC_6

description:
LncRNA and mRNA expression profile
Sample name: 52CA


title: DKO1_Exo_MV_RNA_1

description: RNA


title: Flagellin-treated 24 hours replicate 1


title: Untreated 24 hours replicate 3


title: GSC7


title: Gli36_Exo_High_smallRNA_3

description: Small RNA


title: GSC8


title: BENaC_Smoke_Female_1day_Rep3

value: Homogenized whole lung tissue

tag: genotype

value: Scnn1b-overexpressing (BENaC)

tag: exposure

value: Smoke

tag: Sex

tag: exposure duration

value: 1 day


title: GSC6

tag: cell type


title: Untreated 24 hours replicate 2

value: normal colon


title: DKO1_Exo_Cell_RNA_4

description: RNA


title: DKO1_Exo_Cell_RNA_2

description: RNA


title: DKO1_Exo_Cell_RNA_3

description: RNA


title: Susceptible soybean stem 96 hours post infection biological replicate 2

tag: soybean plant phenotype

value: Susceptible

tag: infection

value: S. sclerotiorum (fungal pathogen)

tag: fungal condition

value: In planta

value: 96hr hpi

value: stem tissues and fungal material


title: Untreated 24 hours replicate 1

value: passage 8-10

value: untreated


title: metastatic CRC_3

description:
LncRNA and mRNA expression profile
Sample name: 20CA

value: Female


title: DKO1_Exo_Cell_RNA_1

description: RNA

value: Colorectal cancer cells

tag: compartment

value: Cell


title: WT_Smoke_Female_1day_Rep1

source_name: RNA isolated from whole lung tissue from female WT mice given 1 day of smoke exposure

tag: tissue

value: Wildtype (WT)


title: GSC5

value: glioblastoma stem cell model


title: XSUVI-5_Ctl_RNA-seq

city: Memphis

first: Hongjian

last: Jin

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

data_processing:
Basecalls performed using CASAVA
fastq files werer mapped to hg19 with internal pipeline StrongARM hat employs BWA and STAR
contaminant mouse reads were then removed from bam files with  internal pipeline XenoCP
reads were counted using htseq and converted to FPKM using hg19
Genome_build: hg19
Supplementary_files_format_and_content: matrix txt file with FPKM for each gene symbol  for each sample

source_name: SU-DIPGVI (established as neurospheres in vitro, implanted in brain for this experiment)

growth_protocol: human xenografts grown as implants in nude mouse brain

extract_protocol:
RNA extracted with Trizol following manufacturer's protocol
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit (Illumina.)

treatment_protocol: Xenografts dissected from mouse brain, cells dissociated and for each experiment, the same pool of cells was transduced with lentivirus expressing non-silencing control or specific shRNA, then cultured for 12 days under puro selection. Transduced cells were reimplanted into multiple mouse brains for each shRNA construct. The resulting tumors were dissected for ChIP-seq and RNAseq.

tag: cell source

value: in vivo xenograft dissected from mouse brain

tag: experiment id

tag: shRNA id

value: non silencing shRNA

tag: shRNA backbone

value: miRE


title: GSC44


title: non-metastatic CRC_8

description:
LncRNA and mRNA expression profile
Sample name: 67CA

source_name: non-metastatic human CRC Tiissue

value: non-metastatic human CRC Tiissue

value: Male


title: metastatic CRC_1

description:
LncRNA and mRNA expression profile
Sample name: 14CA

value: metastatic human CRC Tiissue


title: metastatic CRC_4

description:
LncRNA and mRNA expression profile
Sample name: 38CA


title: XSUVI-4_Ctl_RNA-seq


title: metastatic CRC_2

description:
LncRNA and mRNA expression profile
Sample name: 18CA


title: resistant_OMM1_PLX51107_1

city: hackensack

first: Benjamin

last: Tycko

state: NJ

address: 40 prospect avenue

department: Epigenetics

institute: HUMC

data_processing:
RTA (Illumina) was used for base calling and bcl2fastq (version 1.8.4) for converting BCL to FASTQ format, coupled with adaptor trimming.
The reads were mapped to the human reference genome using Tophat with 4 mismatches and 10 maximum multiple hits
The relative expression level of genes was estimate by FPKM using Cufflinks with default settings
Genome_build: NCBI/build37.2
Supplementary_files_format_and_content: tab-delimited matix of gene-level FPKM estimates, annotated for the gene ID (gene_id), gene symbol (gene_short_name), TSS ID (tss_id), and gene coodinates (locus).

molecule: polyA RNA

source_name: uveal melanoma cell line

growth_protocol: The cells were cultured in RPMI medium supplemented with 10% fetal bovine serum, 100 units/ml penicillin and 100µg/ml streptomycin, and maintained at 37°C in 5% CO2. The resistant cell lines were derived from the corresponding parental cell lines after at least 8 weeks of exposure to escalating doses of PLX51107. The surviving cells were then routinely grown in 0.2-0.5 μM PLX51107. PLX51107 and PLX8573 were from Plexxikon, Inc. JQ1 and QNZ (EVP4593) were from Selleck Chemicals.

extract_protocol:
Total RNA was extracted using the RNeasyMini kit (Qiagen) according to the manufacturer's instructions.
Poly-A pull-down was used to enrich for mRNAs, and libraries were prepared using the Illumina TruSeq RNA kit according to Illumina's instructions.

treatment_protocol: Parental and naive cells were treated with DMSO or 0.5 μM PLX51107 for 24 hours.

tag: cell line

value: BETI-resistant OMM1

tag: treatment

value: 0.5 μM PLX51107 for 24 hours

value: uveal melanoma cell line


title: XSUVI-3_Ctl_RNA-seq


title: GSC42


title: GSC40


title: resistant_OMM1_DMSO_1

value: DMSO


title: GSC43


title: XSUVI-1_Ctl_RNA-seq


title: non-metastatic CRC_7

description:
LncRNA and mRNA expression profile
Sample name: 59CA

tag: age

tag: gender


title: XSUVI-2_Ctl_RNA-seq


title: resistant_OMM1_DMSO_2


title: GSC4


title: resistant_MEWO_PLX51107_2

source_name: cutaneous melanoma cell line

value: BETI-resistant MEWO

value: cutaneous melanoma cell line


title: resistant_OMM1_PLX51107_2


title: X37-9_shH3F3A_RNA-seq

source_name: SJ-DIPGx37 (PDX)

value: H3F3A shRNA #2


title: GSC41


title: non-metastatic CRC_6

description:
LncRNA and mRNA expression profile
Sample name: 57CA

value: Female


title: non-metastatic CRC_5

description:
LncRNA and mRNA expression profile
Sample name: 55CA


title: X37-6_shH3F3A_RNA-seq

value: H3F3A shRNA #1


title: GSC39


title: X37-5_Ctl_RNA-seq


title: resistant_MEWO_DMSO_2


title: resistant_MEWO_PLX51107_1


title: non-metastatic CRC_1

description:
LncRNA and mRNA expression profile
Sample name: 21CA


title: non-metastatic CRC_2

description:
LncRNA and mRNA expression profile
Sample name: 28CA


title: non-metastatic CRC_3

description:
LncRNA and mRNA expression profile
Sample name: 34CA


title: non-metastatic CRC_4

description:
LncRNA and mRNA expression profile
Sample name: 35CA


title: resistant_MEWO_DMSO_1


title: GSC38


title: X37-4_Ctl_RNA-seq


title: GSC36


title: X37-3_Ctl_RNA-seq


title: X37-2_Ctl_RNA-seq


title: GSC35


title: parental_MEWO_PLX51107_1

value: parental MEWO


title: parental_MEWO_DMSO_1


title: GSC37

value: glioblastoma stem cell model


title: parental_MEWO_DMSO_2


title: X37-1_Ctl_RNA-seq

value: in vivo xenograft dissected from mouse brain


title: XSUVI-5_Ctl_H3K4me3_ChIP-seq

data_processing:
We used BWA (version 0.7.12, default parameter) to align the reads to the human hg19 + mouse mm9 + drosophila
marked duplicated reads with Picard with only nonduplicated reads kept by samtools
Only mapped human reads were extracted by samtools for quality contol and peak calling
To control the quality of the data and estimate the fragment size, the nonduplicated version of SPP (version 1.11) was used to draw cross-correlation with support of R (version 2.14.0)
peaks were called using MACS2 (for narrow peak histone marks) or Sicer V1.1 (for broad peak marks)
bam was converted to BigWig using bedtools (v2.25.0) and UCSC tools (20150811). Read coverage was scaled according to normalization factor using mouse contaminant reads as internal reference
Genome_build: hg19
Supplementary_files_format_and_content: bed files containing locations of defined peaks
Supplementary_files_format_and_content: bigWig files containing normalized read coverage

extract_protocol:
ChIP and library construction for SJDIPGX7 xenografts using H3K27me3 (Millipore 07-449), H3K27ac (Active Motif 39133) and H3K4me3 (Active Motif 39159) was performed by Active Motif.  All other ChIP was performed at St. Jude using the following method.  Xenograft tumors were snap frozen and ground to a powder before fixation.  Single cell suspensions were generated from cultured cells then fixed. For histone ChIP, samples were fixed for 5 minutes with 1% paraformaldehyde in PBS (from a frozen stock) at room temperature.  For BMI1 and RNF2 ChIP, samples were fixed with 2mM disuccinimidyl glutarate in PBS for 45 minutes at room temperature followed by 1% paraformaldehyde in PBS for 15 minutes at room temperature following the method established in Gargiulo et al. (van Lohuizen lab, 2013 Cancer Cell 23:660-676). Bare nuclei were sheared on a Covaris M220.  For histone mark ChIPs, the reads arising from mouse cells entrapped within the xenograft to normalize the post ChIP samples to the human/mouse read ratio obtained for the pre-ChIP material (input library).  For some experiments, chromatin from drosophila S2 cells was also spiked-in and used to validate the use of mouse reads for normalization.  ChIP reactions were performed using a modified Upstate Biotechnology protocol. Antibodies used were (μl antibody per IP shown): H3K27me3 (Cell Signaling 9733, lot 8; 4 μl), H3K27ac (Cell Signaling 8173, lot 1; 4 μl), H3K4me3 (Cell Signaling 9751, lot 8; 5 μl), BMI1 (Bethyl A301-694A, lot 4; 5 μl) and RNF2 (Bethyl A302-869A, lot 1; 5 μl).
Libraries were prepared from 5-10 ng of DNA using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina with NEBNext Q5 Hot Start HiFi PCR Master Mix according to the manufacturer’s instructions (New England Biolabs) with the following modifications: a second 1:1 Ampure cleanup was added after adaptor ligation. The Ampure size selection step prior to PCR was eliminated. Completed libraries were analyzed for insert size distribution on a 2100 BioAnalyzer High Sensitivity kit (Agilent) or Caliper LabChip GX DNA High Sensitivity Reagent Kit (Perkin Elmer).  Libraries were quantified using the Quant-iT PicoGreen dsDNA assay (Life Technologies), Kapa Library Quantification kit (Kapa Biosystems) or low pass sequencing on a MiSeq Nano v2 run (Illumina).

value: non silencing shRNA

tag: chip antibody

value: H3K4me3(Cell Signaling, #9751, lot 8)


title: GFPneg4

city: Moscow

first: Diana

last: Mitchell

state: Idaho

address: 875 Perimeter Dr, MS 3051

department: Biological Sciences

institute: University of Idaho

description: library prepared with 3' mRNA Quant-Seq kit (Lexogen)

data_processing:
Raw reads were quantified using salmon 0.9.1 against Zebrafish transcriptome build. Salmon was run with –noLengthCorrection and -l A
Transcript abundance files (quant.sf) were imported into R/Bioconductor and summarized to gene-level estimates following instructions from Love et al. 2016 (doi: 10.12688/f1000research.7035.2)
QC/cluster/etc plots were generated using R/Bioconductor scripts and packages (ggplot2, pheatmap, RcolorBrewer, dplyr, pvclust).
Differential expression analysis was done with Deseq2, using a contrast to compare treatment groups with fish as a blocking factor.
Genome_build: Ensemble release-90, Danio_rerio.GRCz10.cdna.all.fa
Supplementary_files_format_and_content: Salmon quantified “quant.sf” files.

organism: Danio rerio

source_name: Retina

extract_protocol:
RNA was extracted from FACS sorted cells using Machery-Nagel NucleoSpin RNA XS kit.
3' mRNA Quant-Seq using Lexogen Kit for Illumina

tag: transgenic line

value: mpeg1:GFP (gl22)

value: adult (10-12 months)

value: sorted from pool of 8 retinas (Sample 4)

value: GFP-


title: resistant_UM004_PLX51107_3

value: BETI-resistant UM004

value: 0.5 μM PLX51107 for 24 hours


title: GSC33


title: GFPneg3

value: sorted from pool of 8 retinas (Sample 3)


title: tumor,Epinephrine,biological rep1

city: Dalian

first: jinxin

last: lu

state: Liaoning

address: lvshunkou district lvshun south goad west sector No.9

institute: Dalian Medical University

scan_protocol: Affymetrix  human primeview

data_processing: RMA data were processed using Expression Console software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.

label_protocol: standard Affymetrix protocol

growth_protocol: Human breast cancer cell line (MDA-MB-231) was maintained in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen Corp) supplemented with 10% fetal bovine serum (Invitrogen Corp) at 37°C in a humidified incubator containing 5% CO2.

extract_protocol: Primary cells were extracted from the xenograft tumors with PBS or Epinephrine treated.All samples were extracted total RNA using Trizol.

treatment_protocol: Four- to six-week-old NOD/SCID mice were used in each experimental group. MDA-MB-231 cells (1 × 10^6 in PBS:Matrigel (1:1)) cells were injected subcutaneously into both flanks of mice. Epinephrine (2 mg kg-1 d-1 (s.c.)) was injected 7 days before tumor cell injection. The control group of mice received an equal volume of PBS.

value: breast cancer tumor cells

tag: treated with

value: Epinephrine (2 mg kg-1 d-1 (s.c.)


title: tumor,Epinephrine,biological rep2

tag: cell type


title: tumor,PBS,biological rep1

value: PBS


title: XSUVI-5_Ctl_H3K27me3_ChIP-seq

value: miRE

value: H3K27me3 (Cell Signaling, #9733, lot 8)


title: resistant_UM004_PLX51107_2

value: uveal melanoma cell line


title: tumor,PBS,biological rep2


title: tumor,PBS,biological rep3


title: tumor,Epinephrine,biological rep3


title: GFPneg2

value: sorted from pool of 8 retinas (Sample 2)


title: GSC32

value: glioblastoma stem cell model


title: GSC31


title: GSC3


title: GFPneg1

value: sorted from pool of 8 retinas (Sample 1)


title: GSC27


title: GFPpos4

value: GFP+


title: resistant_UM004_PLX51107_1


title: resistant_UM004_DMSO_3

value: DMSO


title: resistant_UM004_DMSO_2


title: XSUVI-3_Ctl_H3K4me3_ChIP-seq

value: in vivo xenograft dissected from mouse brain

value: non silencing shRNA

value: H3K4me3(Cell Signaling, #9751, lot 8)


title: XSUVI-3_Ctl_H3K27me3_ChIP-seq


title: GFPpos3

value: mpeg1:GFP (gl22)

value: adult (10-12 months)


title: resistant_UM004_DMSO_1

value: BETI-resistant UM004


title: GSC26


title: XSUVI-2_Ctl_H3K4me3_ChIP-seq


title: Yeast_YPETOH (scRNA-seq)

source_name: Yeast grown in YP + 2% Ethanol

tag: growth condition

value: YPETOH

tag: genotype

value: mixed sample (non-demultiplexed)


title: GSC34


title: GSC25


title: GFPpos2


title: resistant_OMM1_3B_PLX51107_3

value: BETI-resistant OMM1.3B

value: 0.5 μM PLX51107 for 24 hours


title: XSUVI-4_Ctl_H3K27me3_ChIP-seq

value: miRE

value: H3K27me3 (Cell Signaling, #9733, lot 8)


title: XSUVI-4_Ctl_H3K4me3_ChIP-seq


title: GFPpos1


title: GSC24


title: resistant_OMM1_3B_PLX51107_2

value: uveal melanoma cell line


title: XSUVI-2_Ctl_H3K27me3_ChIP-seq


title: resistant_OMM1_3B_PLX51107_1


title: GSC23

value: glioblastoma stem cell model


title: XSUVI-1_Ctl_H3K4me3_ChIP-seq


title: resistant_OMM1_3B_DMSO_3


title: XSUVI-1_Ctl_H3K27me3_ChIP-seq


title: GSC22


title: GSC21