title: TKO_H3K4me3

description: Chromatin

extract_protocol:
For each sample 9x106 cells were harvested by trypsinisation and rinsed well in 1xPBS before being resuspended in 1.5ml of PBS. Each sample was fixed with the addition of 40.5 µl of 37% formaldehyde (Sigma) and incubated for 10minutes at room temperature on rotation. 225 µl of 1M glycine was added to quench the formaldehyde and rotated at room temperature for 5minutes. Samples were then centrifuged at 2000rpm for 4 minutes at 4 oC, supernatant discarded and pellets resuspended in 2ml LB1 (50mM Hepes KOH pH7.9, 140mM NaCl,1mM EDTA, 10% glycerol, 0.5% IPEGAL, 0.25% triton X100, 1xComplete EDTA-free protease inhibitor tablet (Roche)) solution and rotated at 4 oC for 4 minutes. This process was repeated resuspending in 2 ml LB2 (10mM TrisHcl pH8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 1xComplete EDTA-free protease inhibitor tablet (Roche)) solution and then repeated resuspending in 200 µl LB3 (10mM TrisHCl Ph8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na Deoxycholate, 0.5% LaurylSulphate, 1xComplete EDTA-free protease inhibitor tablet (Roche)). Chromatin was then sheared at 4 oC using a Diagenode bioruptor set on high for 45 cycles at 30seconds on/30seconds off. 20 µl of 10% triton X in LB3 was then added to each sample and mixed by inversion. Samples were then centrifuged at 13000rpm at 4 oC for 10 minutes to remove nuclear debris and supernatant transferred to a fresh tube. In order to check the efficiency of the sonication process, 8 µl of sheared chromatin was taken, mixed with 1 µl 5M NaCl and 16 µl dH2O, incubated at 98 oC for 15minutes and treated with RNase cocktail before being purified with Qiagen PCR Clean up kit as per manufacturer’s instructions . Sheared chromatin was then resolved on 1.5% agarose gel post-stained with EtBr. The DNA smear should be between 100-500bp with peak at 250-300bp.
For immunoprecipitation 25 µl of Protein G Dynabeads (Novex Lifetech) was washed 3 times in block solution and then resuspended in 500 µl of block solution. Beads were then incubated with 5 µl of antibody (H3K27me3(Millipore 07449), IgG (Santa Cruz Biotech sc-2027)) and incubated at 4 oC for 4 hours on a rotator. Beads were then washed 3 times in 500 µl block solution and supernatant removed
For ChIP, crosslinked chromatin was prepared using standard conditions or the SimpleChIP® Plus Enzymatic Chromatin IP Kit.  For ChIP libraries, the NEBNext ChIPSeq library kit or the SimpleChIP® Plus Enzymatic Chromatin IP Kit was used as per instructions.
75bp PE sequencing

value: TKO


title: cyclic uterus miRNA rep 2

status: Public on Feb 24 2020

type: SRA

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

country: Belgium

institute: Ghent University

description:
C2BmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv

library_source: transcriptomic

data_processing:
Adapter trimming and removal of reads shorter than 17 bp, having a quality score lower than 20 or containing any ambiguities, was done using cutadapt (v1.11).
Feature counting, identification of known miRNAs and prediction of putative novel miRNA were done using the miRPro pipeline.
MicroRNA data from miRBase (release 22) and the corresponding annotated horse genome (EquCab2.0) were used as a reference. All mammalian data in miRBase was used for the prediction of novel miRNA.
Genome_build: EquCab2.0
Supplementary_files_format_and_content: Comma separated count files. Fasta files of the predicted miRNAs.

molecule: total RNA

organism: Equus caballus

source_name: uterus

growth_protocol: Samples were collected from cycling or pregnant mares 13 days after ovulation

extract_protocol:
Total RNA was extracted from the UF and the YS fluid samples for miRNA analysis, using the miRNeasy Serum/Plasma kit (Qiagen), according to the manufacturers' instructions. For RNA extraction from the B and the E tissue samples, the RNeasy Mini Kit (Qiagen) was combined with the RNeasy MinElute Cleanup Kit (Qiagen) in order to extract both small RNAs and larger RNAs (>200 nt) separately from the same tissue sample for mRNA- and miRNA-Sequencing respectively.
MicroRNA sequencing libraries were constructed and size-selected with the TailorMix miRNA Sample Preparation Kit V2 (SeqMatic, Fremont, CA, USA) using 100 ng total RNA and amplified by 18 PCR cycles.

treatment_protocol: cyclic mares: no treatment, pregnant mares: inseminated and confirmed to be pregnant

tag: tissue

value: uterus

tag: Stage

value: cyclic


title: J1_H3K4me3

status: Public on Feb 23 2020

city: Edinburgh

first: Donncha

middle: S

last: Dunican

address: Western General Hospital

country: United Kingdom

institute: IGMM / MRC HGU

description: Chromatin

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequences assessed for quality using fastQC (v0.11.4)
Sequences trimmed using trimGalore (v0.4.1).
ChIPSeq mapped with bowtie2 (v2.2.6) to mm10.
WGBS mapped with bismark (v0.16.3) (bowtie2) to mm10.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig (bw) file output from bowtie2 (ChIPSeq) or bismark (WGBS). Methylation calls were made with bismark (v0.16.3) , sub-selected for depth n=5 coverage with custom R (v3.6.0) scripts and converted to bigwig format using BEDTools (v2.25.0). ChIPSeq bigwigs were generated using deepTools (v3.2.0).

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse ES cells

growth_protocol:
mESC were cultured on gelatin-coated cell culture flasks using standard mESC culture conditions.
Undifferentiated ES cells were grown in DMEM containing LIF (500U/mL) in pre-gelatinised culture flasks without feeder cells as widely described. Neural progenitors were cultured in neurodifferentiation media (1:1 mix of Neurobasal (Gibco) and DMEM/F-12 media (Gibco) with 0.5% Neuro-2 Supplement (Millipore), 0.5% B27 Supplement (Gibco), 0.2mM L-glutamine and 0.1mM β-mercaptoethanol) and plated onto 0.1% gelatin-coated flasks at a density of 3x105 cells per 75cm2 flask area. Media was changed on day 2 of differentiation and then daily thereafter. Neural progenitor cells (10 days) cultures were enriched using two passes of Magnetic Activated Cell Sorting (MACS) with anti-PSA-NCAM antibody Microbead kit (Miltenyi Biotec).

treatment_protocol: For doxycyline treatment, Dnmt1tet-tet ES cells were incubated with 2ug/mL doxycylcine for 7 days. For reversion/recovery, doxycycline was removed for 7 days.

tag: cell line name

tag: background strain

tag: cell type

value: Mouse ES cells


title: hos15-4 mutant Rep1

city: Ithaca

first: Leiyun

last: Yang

state: NY

address: 360 Tower road

department: Plant Biology

country: USA

institute: Cornell University

data_processing:
The files have been generated by the Illumina pipeline software v2.18; The raw reads obtained from the sequencing facility were analyzed
raw reads were aligned to TAIR 10 transcriptome using STAR
Differentially expressed genes were identified in R with edgeR pakage
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file include raw read values for each sample was generated

organism: Arabidopsis thaliana

source_name: two-week-old shoot

growth_protocol: two-week-old plants growing under 22C, 100 µmol m-2 s-1 constant light and 50% humidity.

extract_protocol: Total RNA was extracted by TRIzol reagent (Invitrogen, 15596026) and purified by RNA clean and concentrator-5 (ZYMO RESEARCH, R1014). Then RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: genotype

value: hos15-4 mutant

tag: age

value: two-week-old

value: whole shoot


title: J1_Kdm2b

description:
Chromatin
non-commercial antibody

extract_protocol:
For each sample 9x10^6 cells were harvested by trypsinisation and rinsed well in 1xPBS before being resuspended in 1.5ml of PBS. Each sample was fixed with the addition of 40.5 µl of 37% formaldehyde (Sigma) and incubated for 10minutes at room temperature on rotation. 225 µl of 1M glycine was added to quench the formaldehyde and rotated at room temperature for 5minutes. Samples were then centrifuged at 2000rpm for 4 minutes at 4 oC, supernatant discarded and pellets resuspended in 2ml LB1 (50mM Hepes KOH pH7.9, 140mM NaCl,1mM EDTA, 10% glycerol, 0.5% IPEGAL, 0.25% triton X100, 1xComplete EDTA-free protease inhibitor tablet (Roche)) solution and rotated at 4 oC for 4 minutes. This process was repeated resuspending in 2 ml LB2 (10mM TrisHcl pH8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 1xComplete EDTA-free protease inhibitor tablet (Roche)) solution and then repeated resuspending in 200 µl LB3 (10mM TrisHCl Ph8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na Deoxycholate, 0.5% LaurylSulphate, 1xComplete EDTA-free protease inhibitor tablet (Roche)). Chromatin was then sheared at 4 oC using a Diagenode bioruptor set on high for 45 cycles at 30seconds on/30seconds off. 20 µl of 10% triton X in LB3 was then added to each sample and mixed by inversion. Samples were then centrifuged at 13000rpm at 4 oC for 10 minutes to remove nuclear debris and supernatant transferred to a fresh tube. In order to check the efficiency of the sonication process, 8 µl of sheared chromatin was taken, mixed with 1 µl 5M NaCl and 16 µl dH2O, incubated at 98 oC for 15minutes and treated with RNase cocktail before being purified with Qiagen PCR Clean up kit as per manufacturer’s instructions . Sheared chromatin was then resolved on 1.5% agarose gel post-stained with EtBr. The DNA smear should be between 100-500bp with peak at 250-300bp.
For immunoprecipitation 25 µl of Protein G Dynabeads (Novex Lifetech) was washed 3 times in block solution and then resuspended in 500 µl of block solution. Beads were then incubated with 5 µl of antibody (H3K27me3(Millipore 07449), IgG (Santa Cruz Biotech sc-2027)) and incubated at 4 oC for 4 hours on a rotator. Beads were then washed 3 times in 500 µl block solution and supernatant removed
For ChIP, crosslinked chromatin was prepared using standard conditions or the SimpleChIP® Plus Enzymatic Chromatin IP Kit.  For ChIP libraries, the NEBNext ChIPSeq library kit or the SimpleChIP® Plus Enzymatic Chromatin IP Kit was used as per instructions.
50bp PE sequencing


title: WT Col-0 Rep 2

value: wild type Col-0


title: hos15-4 mutant Rep3


title: WT Col-0 Rep 1


title: WT Col-0 Rep 3


title: Sarm1-/- mock sample 8

city: New York

first: Melissa

middle: B

last: Uccellini

address: 1468 Madison Ave

institute: Mt Sinai School of Medicine

data_processing:
Adapter removal with cutadapt (https://doi.org/10.14806/ej.17.1.200)
base quality trimming to remove 3' read sequences if more that 20 bases with Q>=20 were present
paired end reads mapped to mm10 reference genome using STAR (v2.5.3a) and reference gene annotations from ENSEMBL
Gene and isoform-level quantifications for all genes, including Xaf1, were calculated using RSEM (v1.2.22) and expressed as normalized transcripts per million counts
Genome_build: mm10
Supplementary_files_format_and_content: bam alignment files show that the Xaf1 gene (and other genes) in the Sarm1-/- strain have sequence differences from the WT C57BL6/J strain and are from the 129 background, isoform files show quantification of transcript isoform levels

source_name: brain

growth_protocol: 8-week old male mice were infected intranasally with 10^7 pfu of VSV-Indiana strain. At 5 days post-infection mice were perfused and whole brain was harvested for RNA extraction.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA quality and quantity was assessed using Agilent Bioanalyzer and Qubit RNA Broad Rand Assay Kit. Barcoded directional RNA-sequencing libraries were prepared using the TruSeq Stranded Total RNA Sample preparation kit (Illumina). Libraries were pooled and sequenced on the HiSeq platform with 100 bp reads.

treatment_protocol: Brains from 1 mouse per condition were sequenced

value: brain

tag: strain

value: C57BL6/J-Sarm1-/- (Ding strain)


title: WT mock sample 26


title: Sarm1-/- VSV sample 17


title: hos15-4 mutant Rep2


title: WT VSV sample 35


title: SC from 2-2-B1_3-2-A6 clone Methyl_SC_2-2-B1_3-2-A6_7C

city: La Jolla

first: Christopher

middle: Jen-Yue

last: Wei

state: CA

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

description: SC from 2-2-B1_3-2-A6 clone

data_processing:
base-callingwith bcl2fastq with barcode-mismatch=0
methylpy on paired-end reads with min-qual-score=30
Genome_build: hg19
Supplementary_files_format_and_content: methylpy tsv file output (column 1=chromosome; column 2=position; column 3=strand; column 4=sequence context; column 5=number methylated reads; column 6=read coverage)

organism: Homo sapiens

source_name: HCT116 colorectal carcinoma cell line

growth_protocol: McCoy's 5A media with 1% Penn-Strep, 15% FBS

extract_protocol:
SDS cell lysis
RETrace methylation post-processing

tag: clone


title: SC from 2-2-B1_3-2-A6 clone Methyl_SC_2-2-B1_3-2-A6_8D

description: SC from 2-2-B1_3-2-A6 clone


title: SC from 2-2-B1_3-2-A6 clone Methyl_SC_2-2-B1_3-2-A6_8F

description: SC from 2-2-B1_3-2-A6 clone


title: SC from 2-2-B1_3-2-A6 clone Methyl_SC_2-2-B1_3-2-A6_7F

description: SC from 2-2-B1_3-2-A6 clone


title: SC from 2-2-B1_3-2-A6 clone Methyl_SC_2-2-B1_3-2-A6_8G

description: SC from 2-2-B1_3-2-A6 clone


title: SC from 2-2-B1_3-2-A6 clone Methyl_SC_2-2-B1_3-2-A6_7B

description: SC from 2-2-B1_3-2-A6 clone


title: SC from 2-2-B1_3-2-A6 clone Methyl_SC_2-2-B1_3-2-A6_8C

description: SC from 2-2-B1_3-2-A6 clone


title: SC from 2-2-B1_3-2-A6 clone Methyl_SC_2-2-B1_3-2-A6_7G

description: SC from 2-2-B1_3-2-A6 clone


title: SC from 2-2-B1_3-2-A6 clone Methyl_SC_2-2-B1_3-2-A6_7E

description: SC from 2-2-B1_3-2-A6 clone


title: SC from 2-2-B1_3-2-A6 clone Methyl_SC_2-2-B1_3-2-A6_9C

description: SC from 2-2-B1_3-2-A6 clone


title: SC from 2-2-B1_3-2-A6 clone Methyl_SC_2-2-B1_3-2-A6_9F

description: SC from 2-2-B1_3-2-A6 clone


title: SC from 2-2-B1_3-2-A6 clone Methyl_SC_2-2-B1_3-2-A6_9B

description: SC from 2-2-B1_3-2-A6 clone


title: SC from 2-2-B1_3-2-A6 clone Methyl_SC_2-2-B1_3-2-A6_8B

description: SC from 2-2-B1_3-2-A6 clone


title: SC from 2-2-B1_3-2-A6 clone Methyl_SC_2-2-B1_3-2-A6_8E

description: SC from 2-2-B1_3-2-A6 clone


title: SC from 2-2-B1_3-2-A6 clone Methyl_SC_2-2-B1_3-2-A6_9G

description: SC from 2-2-B1_3-2-A6 clone


title: SC from 2-2-B1_3-2-A6 clone Methyl_SC_2-2-B1_3-2-A6_9E

description: SC from 2-2-B1_3-2-A6 clone


title: SC from 2-1-H7_3-6-G7 clone Methyl_SC_2-1-H7_3-6-G7_12F

description: SC from 2-1-H7_3-6-G7 clone


title: SC from 2-2-B1_3-2-A6 clone Methyl_SC_2-2-B1_3-2-A6_7D

description: SC from 2-2-B1_3-2-A6 clone


title: SC from 2-2-B1_3-2-A6 clone Methyl_SC_2-2-B1_3-2-A6_9D

description: SC from 2-2-B1_3-2-A6 clone


title: SC from 2-1-H7_3-6-G7 clone Methyl_SC_2-1-H7_3-6-G7_12G

description: SC from 2-1-H7_3-6-G7 clone


title: SC from 2-1-H7_3-6-G7 clone Methyl_SC_2-1-H7_3-6-G7_12E

description: SC from 2-1-H7_3-6-G7 clone


title: ES_R1b_WT_WGBS

description: PE sequencing

extract_protocol:
Genomic DNA was performed using established proecures by alkali lysis.
For ChIP libraries, the NEBNext ChIPSeq library kit or the SimpleChIP® Plus Enzymatic Chromatin IP Kit was used as per instructions. For WGBS libraries, DNA was bisulfite treated using the Zymo EZ DNA Methylation Lightning Kit followed by library preparation using the TruSeq DNA Methylation Kit (Illumina).


title: ES_Cl36_WT_WGBS

description: PE sequencing


title: ES_DKO_WT_WGBS

description: PE sequencing


title: ES_Eed-/-_WT_WGBS

description: PE sequencing


title: SC from 2-1-H7_3-6-G7 clone Methyl_SC_2-1-H7_3-6-G7_12D

description: SC from 2-1-H7_3-6-G7 clone


title: genes expression of SAN2 compared with that of MW2 rep3

type: RNA

city: Kagoshima

first: Miki

last: Kawada-Matsuo

address: 8-35-1, Sakuragaoka

department: Graduate school of medical and dental sciences

country: Japan

institute: Kagoshima University

description: Biological replicate 3 of 3. genes expression of SAN2 compared with control MW2.

hyb_protocol: GE hybribuffer HIRPM and GE Bloking solution (Roche) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 9.5.1.1).
Agilent Feature Extraction Software (v 9.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Staphylococcus aureus

label_protocol: 10 µg of total RNA were primed with 1 µl of 500 µM random primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of AffinityScript HC RTase (Stratagene), and dNTP mix with amino allyl dUTP. 5 µl of the cDNA was mixed with 5 µl of Cy3 or Cy5 for 30 min. The labeled cDNA was purified using nicleotide purification kit (Qiagen).

growth_protocol: S. aureus MW2 and SAN2 strains were grown in TSB at 37֠°C with shaking. When bacterial OD660 reached 0.4, bacterial cells were collected by centrifugation at 5000xg for 5 min at 4֠°C.

extract_protocol: Total RNA extracted using acid phenol following manufacturer's instructions

tag: treatment

value: control (unexposed)

value: nisin high resistant strain derived from MW2


title: SC from 2-1-H7_3-6-G7 clone Methyl_SC_2-1-H7_3-6-G7_12C

description: SC from 2-1-H7_3-6-G7 clone


title: genes expression of SAN2 compared with that of MW2 rep2

description: Biological replicate 2 of 3. genes expression of SAN2 compared with control MW2.


title: genes expression of SAN2 compared with that of MW2 rep1

description: Biological replicate 1 of 3. genes expression of SAN2 compared with control MW2.


title: SC from 2-1-H7_3-6-G7 clone Methyl_SC_2-1-H7_3-6-G7_11D

description: SC from 2-1-H7_3-6-G7 clone


title: SC from 2-1-H7_3-6-G7 clone Methyl_SC_2-1-H7_3-6-G7_11G

description: SC from 2-1-H7_3-6-G7 clone


title: SC from 2-1-H7_3-6-G7 clone Methyl_SC_2-1-H7_3-6-G7_12B

description: SC from 2-1-H7_3-6-G7 clone


title: SC from 2-1-H7_3-6-G7 clone Methyl_SC_2-1-H7_3-6-G7_11C

description: SC from 2-1-H7_3-6-G7 clone


title: SC from 2-1-H7_3-6-G7 clone Methyl_SC_2-1-H7_3-6-G7_11E

description: SC from 2-1-H7_3-6-G7 clone


title: SC from 2-1-H7_3-6-G7 clone Methyl_SC_2-1-H7_3-6-G7_11F

description: SC from 2-1-H7_3-6-G7 clone


title: SC from 2-1-H7_3-6-G7 clone Methyl_SC_2-1-H7_3-6-G7_10C

description: SC from 2-1-H7_3-6-G7 clone


title: SC from 2-1-H7_3-6-C6 clone Methyl_SC_2-1-H7_3-6-C6_12G

description: SC from 2-1-H7_3-6-C6 clone


title: SC from 2-1-H7_3-6-G7 clone Methyl_SC_2-1-H7_3-6-G7_10G

description: SC from 2-1-H7_3-6-G7 clone


title: SC from 2-1-H7_3-6-G7 clone Methyl_SC_2-1-H7_3-6-G7_10E

description: SC from 2-1-H7_3-6-G7 clone


title: SC from 2-1-H7_3-6-G7 clone Methyl_SC_2-1-H7_3-6-G7_10D

description: SC from 2-1-H7_3-6-G7 clone


title: SC from 2-1-H7_3-6-G7 clone Methyl_SC_2-1-H7_3-6-G7_11B

description: SC from 2-1-H7_3-6-G7 clone


title: SC from 2-1-H7_3-6-C6 clone Methyl_SC_2-1-H7_3-6-C6_12D

description: SC from 2-1-H7_3-6-C6 clone


title: SC from 2-1-H7_3-6-G7 clone Methyl_SC_2-1-H7_3-6-G7_10F

description: SC from 2-1-H7_3-6-G7 clone


title: SC from 2-1-H7_3-6-G7 clone Methyl_SC_2-1-H7_3-6-G7_10B

description: SC from 2-1-H7_3-6-G7 clone


title: SC from 2-1-H7_3-6-C6 clone Methyl_SC_2-1-H7_3-6-C6_11G

description: SC from 2-1-H7_3-6-C6 clone


title: SC from 2-1-H7_3-6-C6 clone Methyl_SC_2-1-H7_3-6-C6_11C

description: SC from 2-1-H7_3-6-C6 clone


title: SC from 2-1-H7_3-6-C6 clone Methyl_SC_2-1-H7_3-6-C6_11F

description: SC from 2-1-H7_3-6-C6 clone


title: SC from 2-1-H7_3-6-C6 clone Methyl_SC_2-1-H7_3-6-C6_11E

description: SC from 2-1-H7_3-6-C6 clone


title: SC from 2-1-H7_3-6-C6 clone Methyl_SC_2-1-H7_3-6-C6_12B

description: SC from 2-1-H7_3-6-C6 clone


title: SC from 2-1-H7_3-6-C6 clone Methyl_SC_2-1-H7_3-6-C6_12C

description: SC from 2-1-H7_3-6-C6 clone


title: SC from 2-1-H7_3-6-C6 clone Methyl_SC_2-1-H7_3-6-C6_11B

description: SC from 2-1-H7_3-6-C6 clone


title: SC from 2-1-H7_3-6-C6 clone Methyl_SC_2-1-H7_3-6-C6_10F

description: SC from 2-1-H7_3-6-C6 clone


title: SC from 2-1-H7_3-6-C6 clone Methyl_SC_2-1-H7_3-6-C6_10G

description: SC from 2-1-H7_3-6-C6 clone


title: Sarm-em3AGS, WNV infected, pool of 3 mice, biological replicate 3 [MBU12_S7_L004]

data_processing:
Adapter removal with cutadapt (https://doi.org/10.14806/ej.17.1.200)
base quality trimming to remove 3' read sequences if more that 20 bases with Q>=20 were present
Genome_build: mm10
Supplementary_files_format_and_content: aligned read numbers

growth_protocol: 11 week old female mice maintained in specific pathogen free housing

extract_protocol:
Brainstem was removed and placed in RNAlater overnight, total RNA was extracted with EZNA total RNA kit (Omega) and Rnase-Free Dnase (Omega)
RNA quality and quantity was assessed using Agilent Bioanalyzer and Qubit RNA Broad Rand Assay Kit. Barcoded non-directional RNA-sequencing libraries were prepared using the TruSeq Stranded Total RNA Sample preparation kit (Illumina). Libraries were pooled and sequenced on the NextSeq platform with 150 bp reads.

treatment_protocol: Mice were mock infected with 30 ul PBS or infected intracranially with 100 FFU of West Nile Virus-Kunjin strain in 30 ul PBS. At day 5 post-infection mice were perfused with PBS and the brainstem was removed.

tag: strain background

tag: genotype/variation

value: WNV infected

value: brainstem


title: SC from 2-1-H7_3-6-C6 clone Methyl_SC_2-1-H7_3-6-C6_12F

description: SC from 2-1-H7_3-6-C6 clone


title: Sarm-em3AGS, WNV infected, pool of 3 mice, biological replicate 3 [MBU12_S7_L003]


title: Sarm-em3AGS, WNV infected, pool of 3 mice, biological replicate 2 [MBU11_S13_L004]


title: SC from 2-1-H7_3-6-C6 clone Methyl_SC_2-1-H7_3-6-C6_10B

description: SC from 2-1-H7_3-6-C6 clone


title: Sarm-em3AGS, WNV infected, pool of 3 mice, biological replicate 3 [MBU12_S7_L001]


title: SC from 2-1-H7_3-6-C6 clone Methyl_SC_2-1-H7_3-6-C6_12E

description: SC from 2-1-H7_3-6-C6 clone


title: SC from 2-1-G10_3-1-B1 clone Methyl_SC_2-1-G10_3-1-B1_9F

description: SC from 2-1-G10_3-1-B1 clone


title: SC from 2-1-G10_3-1-B1 clone Methyl_SC_2-1-G10_3-1-B1_9D

description: SC from 2-1-G10_3-1-B1 clone


title: SC from 2-1-G10_3-1-B1 clone Methyl_SC_2-1-G10_3-1-B1_9G

description: SC from 2-1-G10_3-1-B1 clone


title: SC from 2-1-H7_3-6-C6 clone Methyl_SC_2-1-H7_3-6-C6_10C

description: SC from 2-1-H7_3-6-C6 clone


title: Sarm-em3AGS, WNV infected, pool of 3 mice, biological replicate 3 [MBU12_S7_L002]


title: Sarm-em3AGS, WNV infected, pool of 2 mice, biological replicate 1 [MBU10_S14_L004]


title: Sarm-em3AGS, WNV infected, pool of 3 mice, biological replicate 2 [MBU11_S13_L002]


title: SC from 2-1-G10_3-1-B1 clone Methyl_SC_2-1-G10_3-1-B1_9E

description: SC from 2-1-G10_3-1-B1 clone


title: SC from 2-1-G10_3-1-B1 clone Methyl_SC_2-1-G10_3-1-B1_9C

description: SC from 2-1-G10_3-1-B1 clone


title: SC from 2-1-G10_3-1-B1 clone Methyl_SC_2-1-G10_3-1-B1_9B

description: SC from 2-1-G10_3-1-B1 clone


title: SC from 2-1-H7_3-6-C6 clone Methyl_SC_2-1-H7_3-6-C6_10D

description: SC from 2-1-H7_3-6-C6 clone


title: SC from 2-1-H7_3-6-C6 clone Methyl_SC_2-1-H7_3-6-C6_11D

description: SC from 2-1-H7_3-6-C6 clone


title: Sarm-em3AGS, WNV infected, pool of 2 mice, biological replicate 1 [MBU10_S14_L003]


title: Sarm-em3AGS, WNV infected, pool of 2 mice, biological replicate 1 [MBU10_S14_L002]


title: Sarm-em3AGS, mock infected, biological replicate 3 [MBU9_S15_L003]

source_name: Sarm-em3AGS, mock infected

value: mock infected


title: SC from 2-1-G10_3-1-B1 clone Methyl_SC_2-1-G10_3-1-B1_8E

description: SC from 2-1-G10_3-1-B1 clone


title: SC from 2-1-G10_3-1-B1 clone Methyl_SC_2-1-G10_3-1-B1_8F

description: SC from 2-1-G10_3-1-B1 clone


title: SC from 2-1-H7_3-6-C6 clone Methyl_SC_2-1-H7_3-6-C6_10E

description: SC from 2-1-H7_3-6-C6 clone


title: Sarm-em3AGS, mock infected, biological replicate 3 [MBU9_S15_L001]


title: Sarm-em3AGS, WNV infected, pool of 2 mice, biological replicate 1 [MBU10_S14_L001]


title: SC from 2-1-G10_3-1-B1 clone Methyl_SC_2-1-G10_3-1-B1_8G

description: SC from 2-1-G10_3-1-B1 clone


title: Sarm-em3AGS, mock infected, biological replicate 3 [MBU9_S15_L002]


title: Sarm-em3AGS, mock infected, biological replicate 3 [MBU9_S15_L004]


title: SC from 2-1-G10_3-1-B1 clone Methyl_SC_2-1-G10_3-1-B1_8D

description: SC from 2-1-G10_3-1-B1 clone


title: SC from 2-1-G10_3-1-B1 clone Methyl_SC_2-1-G10_3-1-B1_8C

description: SC from 2-1-G10_3-1-B1 clone


title: Sarm-em3AGS, WNV infected, pool of 3 mice, biological replicate 2 [MBU11_S13_L003]


title: Sarm-em3AGS, WNV infected, pool of 3 mice, biological replicate 2 [MBU11_S13_L001]


title: Sarm-em3AGS, mock infected, biological replicate 2 [MBU8_S9_L004]


title: SC from 2-1-G10_3-1-B1 clone Methyl_SC_2-1-G10_3-1-B1_8B

description: SC from 2-1-G10_3-1-B1 clone


title: SC from 2-1-G10_3-1-B1 clone Methyl_SC_2-1-G10_3-1-B1_7G

description: SC from 2-1-G10_3-1-B1 clone


title: SC from 2-1-G10_3-1-B1 clone Methyl_SC_2-1-G10_3-1-B1_7E

description: SC from 2-1-G10_3-1-B1 clone


title: SC from 2-1-G10_3-1-B1 clone Methyl_SC_2-1-G10_3-1-B1_7F

description: SC from 2-1-G10_3-1-B1 clone


title: SC from 2-1-G10_3-1-B1 clone Methyl_SC_2-1-G10_3-1-B1_7C

description: SC from 2-1-G10_3-1-B1 clone


title: Sarm-em3AGS, mock infected, biological replicate 2 [MBU8_S9_L003]


title: Sarm-em3AGS, mock infected, biological replicate 1 [MBU7_S16_L002]


title: SC from 2-1-G10_3-1-B1 clone Methyl_SC_2-1-G10_3-1-B1_7D

description: SC from 2-1-G10_3-1-B1 clone


title: Sarm-em3AGS, mock infected, biological replicate 2 [MBU8_S9_L001]


title: Sarm-em3AGS, mock infected, biological replicate 1 [MBU7_S16_L001]


title: Sarm-em3AGS, mock infected, biological replicate 1 [MBU7_S16_L004]


title: SC from 2-1-G10_3-1-A2 clone Methyl_SC_2-1-G10_3-1-A2_6G

description: SC from 2-1-G10_3-1-A2 clone


title: WT, WNV infected, pool of 2 mice, biological replicate 3 [MBU6_S10_L004]

source_name: WT, WNV infected, pool of 2 mice

value: WT


title: SC from 2-1-G10_3-1-A2 clone Methyl_SC_2-1-G10_3-1-A2_6F

description: SC from 2-1-G10_3-1-A2 clone


title: Sarm-em3AGS, mock infected, biological replicate 1 [MBU7_S16_L003]


title: WT, WNV infected, pool of 2 mice, biological replicate 3 [MBU6_S10_L003]


title: WT, WNV infected, pool of 2 mice, biological replicate 3 [MBU6_S10_L002]


title: SC from 2-1-G10_3-1-A2 clone Methyl_SC_2-1-G10_3-1-A2_6E

description: SC from 2-1-G10_3-1-A2 clone


title: SC from 2-1-G10_3-1-A2 clone Methyl_SC_2-1-G10_3-1-A2_6C

description: SC from 2-1-G10_3-1-A2 clone


title: SC from 2-1-G10_3-1-A2 clone Methyl_SC_2-1-G10_3-1-A2_6D

description: SC from 2-1-G10_3-1-A2 clone


title: WT, WNV infected, pool of 2 mice, biological replicate 3 [MBU6_S10_L001]


title: SC from 2-1-G10_3-1-A2 clone Methyl_SC_2-1-G10_3-1-A2_6B

description: SC from 2-1-G10_3-1-A2 clone


title: WT, WNV infected, pool of 3 mice, biological replicate 2 [MBU5_S17_L004]

source_name: WT, WNV infected, pool of 3 mice


title: WT, WNV infected, pool of 3 mice, biological replicate 2 [MBU5_S17_L002]


title: SC from 2-1-G10_3-1-A2 clone Methyl_SC_2-1-G10_3-1-A2_5F

description: SC from 2-1-G10_3-1-A2 clone


title: WT, WNV infected, pool of 3 mice, biological replicate 2 [MBU5_S17_L003]


title: Sarm-em3AGS, mock infected, biological replicate 2 [MBU8_S9_L002]


title: WT, WNV infected, pool of 3 mice, biological replicate 2 [MBU5_S17_L001]


title: SC from 2-1-G10_3-1-A2 clone Methyl_SC_2-1-G10_3-1-A2_5D

description: SC from 2-1-G10_3-1-A2 clone


title: WT, WNV infected, pool of 3 mice, biological replicate 1 [MBU4_S11_L003]


title: SC from 2-1-G10_3-1-B1 clone Methyl_SC_2-1-G10_3-1-B1_7B

description: SC from 2-1-G10_3-1-B1 clone


title: WT, WNV infected, pool of 3 mice, biological replicate 1 [MBU4_S11_L002]


title: SC from 2-1-G10_3-1-A2 clone Methyl_SC_2-1-G10_3-1-A2_5C

description: SC from 2-1-G10_3-1-A2 clone


title: SC from 2-1-G10_3-1-A2 clone Methyl_SC_2-1-G10_3-1-A2_5B

description: SC from 2-1-G10_3-1-A2 clone


title: SC from 2-1-A6_3-5-B3 clone Methyl_SC_2-1-A6_3-5-B3_3G

description: SC from 2-1-A6_3-5-B3 clone


title: WT, WNV infected, pool of 3 mice, biological replicate 1 [MBU4_S11_L001]


title: SC from 2-1-A6_3-5-B3 clone Methyl_SC_2-1-A6_3-5-B3_3F

description: SC from 2-1-A6_3-5-B3 clone


title: SC from 2-1-A6_3-5-B3 clone Methyl_SC_2-1-A6_3-5-B3_3E

description: SC from 2-1-A6_3-5-B3 clone


title: WT, mock infected, biological replicate 3 [MBU3_S3_L004]

source_name: WT, mock infected


title: WT, mock infected, biological replicate 3 [MBU3_S3_L003]


title: WT, mock infected, biological replicate 3 [MBU3_S3_L002]


title: WT, mock infected, biological replicate 3 [MBU3_S3_L001]


title: SC from 2-1-A6_3-5-B3 clone Methyl_SC_2-1-A6_3-5-B3_3D

description: SC from 2-1-A6_3-5-B3 clone


title: WT, mock infected, biological replicate 2 [MBU2_S8_L004]


title: SC from 2-1-A6_3-5-B3 clone Methyl_SC_2-1-A6_3-5-B3_3C

description: SC from 2-1-A6_3-5-B3 clone


title: SC from 2-1-A6_3-5-B3 clone Methyl_SC_2-1-A6_3-5-B3_3B

description: SC from 2-1-A6_3-5-B3 clone


title: SC from 2-1-A6_3-5-B3 clone Methyl_SC_2-1-A6_3-5-B3_2G

description: SC from 2-1-A6_3-5-B3 clone


title: WT, mock infected, biological replicate 2 [MBU2_S8_L002]


title: WT, mock infected, biological replicate 2 [MBU2_S8_L003]


title: SC from 2-1-A6_3-5-B3 clone Methyl_SC_2-1-A6_3-5-B3_2F

description: SC from 2-1-A6_3-5-B3 clone


title: WT, mock infected, biological replicate 2 [MBU2_S8_L001]


title: SC from 2-1-A6_3-5-B3 clone Methyl_SC_2-1-A6_3-5-B3_2E

description: SC from 2-1-A6_3-5-B3 clone


title: SC from 2-1-G10_3-1-A2 clone Methyl_SC_2-1-G10_3-1-A2_5E

description: SC from 2-1-G10_3-1-A2 clone


title: SC from 2-1-G10_3-1-A2 clone Methyl_SC_2-1-G10_3-1-A2_5G

description: SC from 2-1-G10_3-1-A2 clone


title: WT, mock infected, biological replicate 1 [MBU1_S18_L003]


title: WT, WNV infected, pool of 3 mice, biological replicate 1 [MBU4_S11_L004]


title: SC from 2-1-A6_3-5-B3 clone Methyl_SC_2-1-A6_3-5-B3_2D

description: SC from 2-1-A6_3-5-B3 clone


title: WT, mock infected, biological replicate 1 [MBU1_S18_L004]


title: SC from 2-1-A6_3-5-B3 clone Methyl_SC_2-1-A6_3-5-B3_2C

description: SC from 2-1-A6_3-5-B3 clone


title: SC from 2-1-A6_3-5-B3 clone Methyl_SC_2-1-A6_3-5-B3_2B

description: SC from 2-1-A6_3-5-B3 clone


title: WT, mock infected, biological replicate 1 [MBU1_S18_L001]


title: SC from 2-1-A6_3-5-B3 clone Methyl_SC_2-1-A6_3-5-B3_1G

description: SC from 2-1-A6_3-5-B3 clone


title: ES_Rev_H3K4me3_ChIPSeq

description:
Chromatin
75bp SE sequencing

growth_protocol:
For Dnmt1tet/tet mESC experiments, (clone termed ‘Ch9’) cells were cultured on gelatin-coated cell culture flasks using standard mESC culture conditions except ESGRO LIF (Millipore) was used at 500U/mL. For Dnmt1 depletion, doxycycline was added to media daily for 7 days at a concentration of 2ug/mL. For recovery, doxycycline was withdrawn for 7 days
Undifferentiated ES cells were grown in DMEM containing LIF (500U/mL) in pre-gelatinised culture flasks without feeder cells as widely described. Neural progenitors were cultured in neurodifferentiation media (1:1 mix of Neurobasal (Gibco) and DMEM/F-12 media (Gibco) with 0.5% Neuro-2 Supplement (Millipore), 0.5% B27 Supplement (Gibco), 0.2mM L-glutamine and 0.1mM β-mercaptoethanol) and plated onto 0.1% gelatin-coated flasks at a density of 3x105 cells per 75cm2 flask area. Media was changed on day 2 of differentiation and then daily thereafter. Neural progenitor cells (10 days) cultures were enriched using two passes of Magnetic Activated Cell Sorting (MACS) with anti-PSA-NCAM antibody Microbead kit (Miltenyi Biotec).

extract_protocol:
For ChIP, crosslinked chromatin was prepared using standard conditions or the SimpleChIP® Plus Enzymatic Chromatin IP Kit. For WGBS, genomic DNA was isolated by alkali lysis using classical methods.
For ChIP libraries, the NEBNext ChIPSeq library kit or the SimpleChIP® Plus Enzymatic Chromatin IP Kit was used as per instructions. For WGBS libraries, DNA was bisulfite treated using the Zymo EZ DNA Methylation Lightning Kit followed by library preparation using the TruSeq DNA Methylation Kit (Illumina).

value: R1 clone Ch9


title: SC from 2-1-A6_3-5-B3 clone Methyl_SC_2-1-A6_3-5-B3_1F

description: SC from 2-1-A6_3-5-B3 clone


title: SC from 2-1-A6_3-5-B3 clone Methyl_SC_2-1-A6_3-5-B3_1D

description: SC from 2-1-A6_3-5-B3 clone


title: SC from 2-1-A6_3-5-B3 clone Methyl_SC_2-1-A6_3-5-B3_1C

description: SC from 2-1-A6_3-5-B3 clone


title: SC from 2-1-A6_3-5-B3 clone Methyl_SC_2-1-A6_3-5-B3_1B

description: SC from 2-1-A6_3-5-B3 clone


title: ES_Rev_H3K27me3_ChIPSeq

description:
Chromatin
75bp SE sequencing


title: ES_serum_H3K4me3_ChIPSeq

description:
Chromatin
75bp SE sequencing


title: ES_Dox_H3K27me3_ChIPSeq

description:
Chromatin
75bp SE sequencing


title: SC from 2-1-A6_3-5-B2 clone Methyl_SC_2-1-A6_3-5-B2_3G

description: SC from 2-1-A6_3-5-B2 clone


title: WT, mock infected, biological replicate 1 [MBU1_S18_L002]


title: ES_Rev_WGBS

description: 150bp PE sequencing


title: SC from 2-1-A6_3-5-B2 clone Methyl_SC_2-1-A6_3-5-B2_3D

description: SC from 2-1-A6_3-5-B2 clone


title: ES_Dox_WGBS

description: 150bp PE sequencing


title: SC from 2-1-A6_3-5-B2 clone Methyl_SC_2-1-A6_3-5-B2_3F

description: SC from 2-1-A6_3-5-B2 clone


title: SC from 2-1-A6_3-5-B2 clone Methyl_SC_2-1-A6_3-5-B2_3E

description: SC from 2-1-A6_3-5-B2 clone


title: SC from 2-1-A6_3-5-B2 clone Methyl_SC_2-1-A6_3-5-B2_3C

description: SC from 2-1-A6_3-5-B2 clone


title: ES_serum_WGBS

description: 150bp PE sequencing


title: SC from 2-1-A6_3-5-B2 clone Methyl_SC_2-1-A6_3-5-B2_2G

description: SC from 2-1-A6_3-5-B2 clone


title: SC from 2-1-A6_3-5-B2 clone Methyl_SC_2-1-A6_3-5-B2_2F

description: SC from 2-1-A6_3-5-B2 clone


title: WT NPC_H3K27me3_ChIPSeq

description:
Chromatin
50bp PE sequencing

source_name: Neural progenitor cells

growth_protocol:
NPCs were derived from E14 mESC as follows. E14 were split at high density 24 hours prior to differentiation, followed by dissociation and PBS washes to remove any traces of differentiation-inhibitory serum. Cells were then cultured in neurodifferentiation media (1:1 mix of Neurobasal (Gibco) and DMEM/F-12 media (Gibco) with 0.5% Neuro-2 Supplement (Millipore), 0.5% B27 Supplement (Gibco), 0.2mM L-glutamine and 0.1mM β-mercaptoethanol) and plated onto 0.1% gelatin-coated flasks at a density of 3x105 cells per 75cm2 flask area. Media was changed on day 2 of differentiation and then daily thereafter. Neural progenitor cells (10 days) cultures were enriched using two passes of Magnetic Activated Cell Sorting (MACS) with anti-PSA-NCAM antibody Microbead kit (Miltenyi Biotec). Fluorescence-activated cell sorting (FACS) using anti-PSA-NCAM antibody was employed to assess NPC purity post MACS.
Undifferentiated ES cells were grown in DMEM containing LIF (500U/mL) in pre-gelatinised culture flasks without feeder cells as widely described. Neural progenitors were cultured in neurodifferentiation media (1:1 mix of Neurobasal (Gibco) and DMEM/F-12 media (Gibco) with 0.5% Neuro-2 Supplement (Millipore), 0.5% B27 Supplement (Gibco), 0.2mM L-glutamine and 0.1mM β-mercaptoethanol) and plated onto 0.1% gelatin-coated flasks at a density of 3x105 cells per 75cm2 flask area. Media was changed on day 2 of differentiation and then daily thereafter. Neural progenitor cells (10 days) cultures were enriched using two passes of Magnetic Activated Cell Sorting (MACS) with anti-PSA-NCAM antibody Microbead kit (Miltenyi Biotec).

extract_protocol:
For each sample 9x10^6 cells were harvested by trypsinisation and rinsed well in 1xPBS before being resuspended in 1.5ml of PBS. Each sample was fixed with the addition of 40.5 µl of 37% formaldehyde (Sigma) and incubated for 10minutes at room temperature on rotation. 225 µl of 1M glycine was added to quench the formaldehyde and rotated at room temperature for 5minutes. Samples were then centrifuged at 2000rpm for 4 minutes at 4 oC, supernatant discarded and pellets resuspended in 2ml LB1 (50mM Hepes KOH pH7.9, 140mM NaCl,1mM EDTA, 10% glycerol, 0.5% IPEGAL, 0.25% triton X100, 1xComplete EDTA-free protease inhibitor tablet (Roche)) solution and rotated at 4 oC for 4 minutes. This process was repeated resuspending in 2 ml LB2 (10mM TrisHcl pH8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 1xComplete EDTA-free protease inhibitor tablet (Roche)) solution and then repeated resuspending in 200 µl LB3 (10mM TrisHCl Ph8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na Deoxycholate, 0.5% LaurylSulphate, 1xComplete EDTA-free protease inhibitor tablet (Roche)). Chromatin was then sheared at 4 oC using a Diagenode bioruptor set on high for 45 cycles at 30seconds on/30seconds off. 20 µl of 10% triton X in LB3 was then added to each sample and mixed by inversion. Samples were then centrifuged at 13000rpm at 4 oC for 10 minutes to remove nuclear debris and supernatant transferred to a fresh tube. In order to check the efficiency of the sonication process, 8 µl of sheared chromatin was taken, mixed with 1 µl 5M NaCl and 16 µl dH2O, incubated at 98 oC for 15minutes and treated with RNase cocktail before being purified with Qiagen PCR Clean up kit as per manufacturer’s instructions . Sheared chromatin was then resolved on 1.5% agarose gel post-stained with EtBr. The DNA smear should be between 100-500bp with peak at 250-300bp.
For immunoprecipitation 25 µl of Protein G Dynabeads (Novex Lifetech) was washed 3 times in block solution and then resuspended in 500 µl of block solution. Beads were then incubated with 5 µl of antibody (H3K27me3(Millipore 07449), IgG (Santa Cruz Biotech sc-2027)) and incubated at 4 oC for 4 hours on a rotator. Beads were then washed 3 times in 500 µl block solution and supernatant removed.
For ChIP libraries, the NEBNext ChIPSeq library kit or the SimpleChIP® Plus Enzymatic Chromatin IP Kit was used as per instructions. For WGBS libraries, DNA was bisulfite treated using the Zymo EZ DNA Methylation Lightning Kit followed by library preparation using the TruSeq DNA Methylation Kit (Illumina).

value: Neural progenitor cells


title: Lsh-/- NPC_H3K27me3_ChIPSeq

description:
Chromatin
50bp PE sequencing


title: SC from 2-1-A6_3-5-B2 clone Methyl_SC_2-1-A6_3-5-B2_3B

description: SC from 2-1-A6_3-5-B2 clone


title: SC from 2-1-A6_3-5-B2 clone Methyl_SC_2-1-A6_3-5-B2_2D

description: SC from 2-1-A6_3-5-B2 clone


title: SC from 2-1-A6_3-5-B2 clone Methyl_SC_2-1-A6_3-5-B2_2E

description: SC from 2-1-A6_3-5-B2 clone


title: ES_Dox_H3K4me3_ChIPSeq

description:
Chromatin
75bp SE sequencing


title: SC from 2-1-A6_3-5-B2 clone Methyl_SC_2-1-A6_3-5-B2_2C

description: SC from 2-1-A6_3-5-B2 clone


title: SC from 2-1-A6_3-5-B2 clone Methyl_SC_2-1-A6_3-5-B2_1G

description: SC from 2-1-A6_3-5-B2 clone


title: SC from 2-1-A6_3-5-B2 clone Methyl_SC_2-1-A6_3-5-B2_2B

description: SC from 2-1-A6_3-5-B2 clone


title: ES_serum_H3K27me3_ChIPSeq

description:
Chromatin
75bp SE sequencing


title: SC from 2-1-A6_3-5-B2 clone Methyl_SC_2-1-A6_3-5-B2_1F

description: SC from 2-1-A6_3-5-B2 clone


title: SC from 2-1-A6_3-5-B3 clone Methyl_SC_2-1-A6_3-5-B3_1E

description: SC from 2-1-A6_3-5-B3 clone


title: SC from 2-1-A6_3-5-B2 clone Methyl_SC_2-1-A6_3-5-B2_1D

description: SC from 2-1-A6_3-5-B2 clone


title: SC from 2-1-A6_3-5-B2 clone Methyl_SC_2-1-A6_3-5-B2_1C

description: SC from 2-1-A6_3-5-B2 clone


title: SC from 1-1-F3_2-2-B1 clone Methyl_SC_1-1-F3_2-2-B1_6G

description: SC from 1-1-F3_2-2-B1 clone


title: SC from 1-1-F3_2-2-B1 clone Methyl_SC_1-1-F3_2-2-B1_6F

description: SC from 1-1-F3_2-2-B1 clone


title: SC from 1-1-F3_2-2-B1 clone Methyl_SC_1-1-F3_2-2-B1_6E

description: SC from 1-1-F3_2-2-B1 clone


title: SC from 1-1-F3_2-2-B1 clone Methyl_SC_1-1-F3_2-2-B1_6D

description: SC from 1-1-F3_2-2-B1 clone


title: hgf_7.5ng_replicate_4

city: Philadelphia

first: Lewis

last: Chodosh

state: Pennsylvania

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

hyb_protocol: Affymetrix Generic Hybridization

scan_protocol: Arrays were scanned using the Affymetrix GeneArray Scanner

data_processing: RMA

label: Biotin

source_name: MCF-10A cells

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

growth_protocol: MCF10A is maintained in DMEM+10%FBS+5ug/ml insulin+10ug/ml EGF+1ug/ml hydrocortisone. Cells are passaged 1:3 every 2-3 days.

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

treatment_protocol: Cells were seeded on 100mm plate with 10% FBS for 24 h and then starved in serum-free media overnight. Increasing concentrations of HGF were then added to cells cultured with serum-free media and RNAs were harvested 4h after HGF addition.

tag: cell line

value: 7.5ng HGF


title: SC from 2-1-A6_3-5-B2 clone Methyl_SC_2-1-A6_3-5-B2_1E

description: SC from 2-1-A6_3-5-B2 clone


title: SC from 1-1-F3_2-2-B1 clone Methyl_SC_1-1-F3_2-2-B1_6B

description: SC from 1-1-F3_2-2-B1 clone


title: hgf_30ng_replicate_4

value: 30ng HGF


title: hgf_3ng_replicate_3

value: 3ng HGF


title: hgf_1ng_replicate_3

value: 1ng HGF


title: hgf_30ng_replicate_3


title: hgf_30ng_replicate_2


title: hgf_15ng_replicate_3

value: 15ng HGF


title: hgf_30ng_replicate_1


title: hgf_0ng_replicate_3

value: 0ng HGF


title: hgf_15ng_replicate_2


title: hgf_3ng_replicate_4


title: hgf_1ng_replicate_4


title: hgf_7.5ng_replicate_3


title: hgf_15ng_replicate_4


title: hgf_7.5ng_replicate_1


title: hgf_7.5ng_replicate_2


title: SC from 1-1-F3_2-2-B1 clone Methyl_SC_1-1-F3_2-2-B1_5F

description: SC from 1-1-F3_2-2-B1 clone


title: SC from 1-1-F3_2-2-B1 clone Methyl_SC_1-1-F3_2-2-B1_6C

description: SC from 1-1-F3_2-2-B1 clone


title: SC from 1-1-F3_2-2-B1 clone Methyl_SC_1-1-F3_2-2-B1_5E

description: SC from 1-1-F3_2-2-B1 clone


title: hgf_0ng_replicate_4


title: SC from 1-1-F3_2-2-B1 clone Methyl_SC_1-1-F3_2-2-B1_5D

description: SC from 1-1-F3_2-2-B1 clone


title: SC from 1-1-F3_2-2-B1 clone Methyl_SC_1-1-F3_2-2-B1_5G

description: SC from 1-1-F3_2-2-B1 clone


title: hgf_3ng_replicate_2


title: hgf_3ng_replicate_1


title: hgf_1ng_replicate_2


title: hgf_15ng_replicate_1


title: hgf_1ng_replicate_1


title: SC from 1-1-F3_2-2-B1 clone Methyl_SC_1-1-F3_2-2-B1_4E

description: SC from 1-1-F3_2-2-B1 clone


title: hgf_0ng_replicate_2


title: SC from 1-1-F3_2-2-B1 clone Methyl_SC_1-1-F3_2-2-B1_4B

description: SC from 1-1-F3_2-2-B1 clone


title: SC from 1-1-F3_2-2-B1 clone Methyl_SC_1-1-F3_2-2-B1_5B

description: SC from 1-1-F3_2-2-B1 clone


title: SC from 2-1-A6_3-5-B2 clone Methyl_SC_2-1-A6_3-5-B2_1B

description: SC from 2-1-A6_3-5-B2 clone


title: 5cell from 2-1-G10_3-1-A2 clone Methyl_5cell_2-1-G10_3-1-A2_6A

description: 5cell from 2-1-G10_3-1-A2 clone


title: SC from 1-1-F3_2-2-B1 clone Methyl_SC_1-1-F3_2-2-B1_4F

description: SC from 1-1-F3_2-2-B1 clone


title: 10cell from 2-2-B1_3-2-A6 clone Methyl_10cell_2-2-B1_3-2-A6_9A

description: 10cell from 2-2-B1_3-2-A6 clone


title: SC from 1-1-F3_2-2-B1 clone Methyl_SC_1-1-F3_2-2-B1_5C

description: SC from 1-1-F3_2-2-B1 clone


title: SC from 1-1-F3_2-2-B1 clone Methyl_SC_1-1-F3_2-2-B1_4D

description: SC from 1-1-F3_2-2-B1 clone


title: TIC10 10uM

city: Toronto

first: Micheal

middle: D

last: Tyers

state: Ontario

address: 555 University Avenue

country: Canada

institute: The Hospital for Sick Children

description: sgRNAs PCR-amplified from genomic DNA

data_processing:
Reads were aligned using Bowtie2.2.5 in the forward direction only (--norc option) with otherwise default parameters and total read counts per sgRNA were tabulated.
Genome_build: EKO sgRNA library (Bertomeu et al. 2017, PMID:29038160), using only the core gene-targting sgRNA set of of the library.
Supplementary_files_format_and_content: tab seperated sgRNA read counts for each sample

source_name: pooled sgRNA library

extract_protocol:
Samples were PBS-washed and cell pellets frozen. Genomic DNA was extracted using the QIAamp DNA blood maxi kit (Qiagen).
sgRNA sequences were recovered and fitted with Illumina adaptors by PCR as previously described (Bertomeu et al., 2017).

value: pre-B lymphoid cell line

value: TIC10 10uM


title: Day 2 control replicate 3

description: sgRNAs PCR-amplified from genomic DNA

value: Day 2 control


title: SC from 1-1-F3_2-2-B1 clone Methyl_SC_1-1-F3_2-2-B1_4C

description: SC from 1-1-F3_2-2-B1 clone


title: SC from 1-1-F3_2-2-B1 clone Methyl_SC_1-1-F3_2-2-B1_4G

description: SC from 1-1-F3_2-2-B1 clone


title: Day 2 control replicate 1

description: sgRNAs PCR-amplified from genomic DNA


title: 5cell from 2-1-G10_3-1-A2 clone Methyl_5cell_2-1-G10_3-1-A2_5A

description: 5cell from 2-1-G10_3-1-A2 clone


title: Day 2 control replicate 2

description: sgRNAs PCR-amplified from genomic DNA


title: ONC212 0.15uM

description: sgRNAs PCR-amplified from genomic DNA


title: 10cell from 2-1-H7_3-6-G7 clone Methyl_10cell_2-1-H7_3-6-G7_12A

description: 10cell from 2-1-H7_3-6-G7 clone


title: tumor w 100mg/kg AMG2100517 12 hr replicate 4

source_name: MTB-TAN recurrent tumor

growth_protocol: MTB-TAN recurrent cells were injected into the number four mammary glands of nude mice. Tumors with sizes of 5mm in diameters were formed around two weeks after injection, at which point the mice received one dose of vehicle or 100mg/kg MET inhibitor (AMG2100517).

treatment_protocol: Vehicle ( 2% HPMC 1% Tween ) or 100mg/kg AMG was gavaged into the animals, and tumors were harvested 12 hours after the gavage.

value: FVB

tag: gender

value: F

value: xenograft mammary tumor

value: MTB-TAN


title: tumor w 100mg/kg AMG2100517 12 hr replicate 5


title: tumor w 100mg/kg AMG2100517 12 hr replicate 2


title: tumor w 100mg/kg AMG2100517 12 hr replicate 3


title: tumor w 100mg/kg AMG2100517 12 hr replicate 6


title: hgf_0ng_replicate_1


title: 10cell from 2-1-H7_3-6-C6 clone Methyl_10cell_2-1-H7_3-6-C6_12A

description: 10cell from 2-1-H7_3-6-C6 clone


title: 10cell from 2-1-G10_3-1-B1 clone Methyl_10cell_2-1-G10_3-1-B1_9A

description: 10cell from 2-1-G10_3-1-B1 clone


title: tumor w 100mg/kg AMG2100517 12 hr replicate 1


title: 10cell from 2-1-A6_3-5-B3 clone Methyl_10cell_2-1-A6_3-5-B3_3A

description: 10cell from 2-1-A6_3-5-B3 clone


title: 100cell from 2-2-B1_3-2-A6 clone Methyl_100cell_2-2-B1_3-2-A6_8A

description: 100cell from 2-2-B1_3-2-A6 clone


title: 100cell from 2-1-H7_3-6-G7 clone Methyl_100cell_2-1-H7_3-6-G7_11A

description: 100cell from 2-1-H7_3-6-G7 clone


title: 100cell from 2-1-G10_3-1-B1 clone Methyl_100cell_2-1-G10_3-1-B1_8A

description: 100cell from 2-1-G10_3-1-B1 clone


title: 10cell from 2-1-A6_3-5-B2 clone Methyl_10cell_2-1-A6_3-5-B2_3A

description: 10cell from 2-1-A6_3-5-B2 clone


title: 10cell from 1-1-F3_2-2-B1 clone Methyl_10cell_1-1-F3_2-2-B1_6A

description: 10cell from 1-1-F3_2-2-B1 clone


title: 100cell from 2-1-A6_3-5-B2 clone Methyl_100cell_2-1-A6_3-5-B2_2A

description: 100cell from 2-1-A6_3-5-B2 clone


title: Control 3

city: CHANGCHUN

first: mingyou

last: zhang

state: JILIN

address: 519 dongminzhu

country: China

institute: employer

data_processing:
Illumina Casava1.7 software used for basecalling.
After reads filtering, we map clean reads to reference genome using HISAT.
After genome mapping, we use StringTie  to reconstruct transcripts, and with genome annotation information we identify novel transcripts by using Cuffcompare(a tool of Cufflinks) and predict the coding ability of those new transcripts using CPC.
After genome mapping, we use GATK to call SNP and INDEL variant for each sample.
map clean reads to it using Bowtie2,then calculate gene expression level for each sample with RSEM.
Genome_build: use StringTie to reconstruct transcripts, and use Cuffcompare（Cufflinks tools） to compare reconstructed transcripts to reference annotation, after that, we select 'u','i','o','j' class code types as novel transcripts. And then, we use CPC  to predict coding potential of novel transcripts, then we merge coding novel transcripts with reference transcripts to get a complete reference, and downstream analysis will base on this reference.
Supplementary_files_format_and_content: xls files include FPKM values (calculated by RSEM software) for each Sample …

source_name: Peripheral blood

extract_protocol:
Innate lymphoid cells 1 were sorted,  RNA was harvested using Trizol reagent. Illumina HiSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PBMC

tag: cell subtype

value: Innate lymphoid cells 1

tag: patient diagnosis

value: healthy control


title: 100cell from 2-1-A6_3-5-B3 clone Methyl_100cell_2-1-A6_3-5-B3_2A

description: 100cell from 2-1-A6_3-5-B3 clone


title: Control 2


title: 100cell from 2-1-H7_3-6-C6 clone Methyl_100cell_2-1-H7_3-6-C6_11A

description: 100cell from 2-1-H7_3-6-C6 clone


title: 100cell from 1-1-F3_2-2-B1 clone Methyl_100cell_1-1-F3_2-2-B1_5A

description: 100cell from 1-1-F3_2-2-B1 clone


title: 1000cell from 2-2-B1_3-2-A6 clone Methyl_1000cell_2-2-B1_3-2-A6_7A

description: 1000cell from 2-2-B1_3-2-A6 clone


title: 1000cell from 2-1-H7_3-6-G7 clone Methyl_1000cell_2-1-H7_3-6-G7_10A

description: 1000cell from 2-1-H7_3-6-G7 clone


title: STEMI patient 3

value: ST-segment elevated myocardial infarction (STEMI)


title: 1000cell from 2-1-H7_3-6-C6 clone Methyl_1000cell_2-1-H7_3-6-C6_10A

description: 1000cell from 2-1-H7_3-6-C6 clone


title: Control 1


title: 1000cell from 2-1-G10_3-1-B1 clone Methyl_1000cell_2-1-G10_3-1-B1_7A

description: 1000cell from 2-1-G10_3-1-B1 clone


title: U2OS miR-571 inhibitor Replicate 1 (U2OS_miR571-inhibitor_707)

city: WASHINGTON

first: Wenge

last: Zhu

state: DC

address: 800 22ND ST NW, Room 8480, Science & Engineering Hall

department: Biochemistry and Molecular Medicine

institute: George Washington University

description:
U2OS miR-571 inhibitor transfected Osteosarcoma cell line
U2OS_RNASeq_Con vs miR-571 inhibitor_GEO_RNASeq_Submission_20180822.xlsx

data_processing:
Alignment of paired end reads was performed using the STAR Aligner v. 2.5.1a, default parameters.
Read Counting of bam alignment files was performed using HTSeq (htseq-count) to generate raw per-gene read counts.
DESeq, R package, was used to generate normalized reads, Log2FoldChange, and differential expression statistics
Genome_build: Ensembl Human: GRCh38.p7, and corresponding GTF file.
Supplementary_files_format_and_content: Two matrix files are provided, one containing raw read counts and the other containing normalized read counts.

molecule: polyA RNA

growth_protocol: U2OS cells were cultured at 37 °C with 5% CO2 in DMEM medium (10%FBS serum).

extract_protocol:
RNA isolation was completed using the Qiagen miRNeasy Mini Kit according to the manufacturer’s protocol
RNA samples are converted into cDNA libraries using the Illumina TruSeq Stranded mRNA sample preparation kit (Illumina # RS-122-2103).  Briefly, Total RNA samples are concentration normalized, and poly-adenylated RNA is purified using oligo-dT attached to magnetic beads.  Purified mRNA is fragmented using heat in the presence of divalent cations. Fragmented RNA is converted into double-stranded cDNA, with dUTP utilized in place of dTTP in the second strand master mix.  A single 'A' base is added to the cDNA and forked adaptors that include index, or barcode, sequences are attached via ligation. The resulting molecules are amplified via polymerase chain reaction (PCR). During PCR the polymerase stalls when a dUTP base is encountered in the template. Since only the second strand includes the dUTP base, this renders the first strand the only viable template, thereby preserving the strand information. Final libraries are quantified, normalized and pooled.  Pooled libraries are bound to the surface of a flow cell, and each bound template molecule is clonally amplified up to 1000-fold to create individual clusters.  Four fluorescently labeled nucleotides are then flowed over the surface of the flow cell and incorporated into each nucleic acid chain.  Each nucleotide label acts as a terminator for polymerization, thereby ensuring that a single base is added to each nascent chain during each cycle.  Fluorescence is measured for each cluster during each cycle to identify the base that was added to each cluster. The dye is then enzymatically removed to allow incorporation of the next nucleotide during the next cycle.

treatment_protocol: U2OS cells were transfected with miR-control, miR-571 mimic and miR-571 inhibitor for 48 hours, then harvested cells for RNA isolation and sequencing.

value: Osteosarcoma cell line

tag: cancer type

value: Osteosarcoma

tag: transfection


title: U2OS miR-571 mimic Replicate 2 (U2OS_miR571-mimic_703)

description:
U2OS miR-571 mimic transfected Osteosarcoma cell line
U2OS_RNASeq_Con vs miR-571 mimic_GEO_RNASeq_Submission_20180822.xlsx


title: U2OS miR-571 inhibitor Replicate 2 (U2OS_miR571-inhibitor_708)

description:
U2OS miR-571 inhibitor transfected Osteosarcoma cell line
U2OS_RNASeq_Con vs miR-571 mimic_GEO_RNASeq_Submission_20180822.xlsx


title: U2OS miR-571 mimic Replicate 1 (U2OS_miR571-mimic_706)


title: U2OS miR-Control Replicate 2 (U2OS_Con_705)

description:
U2OS miR-Control transfected Osteosarcoma cell line
U2OS_RNASeq_Con vs miR-571 inhibitor_GEO_RNASeq_Submission_20180822.xlsx

value: control


title: tumor w vehicle 12 hr replicate 4

tag: tissue

value: vehicle


title: tumor w vehicle 12 hr replicate 3


title: tumor w vehicle 12 hr replicate 1


title: tumor w vehicle 12 hr replicate 6


title: tumor w vehicle 12 hr replicate 5


title: tumor w vehicle 12 hr replicate 2


title: 1000cell from 2-1-A6_3-5-B3 clone Methyl_1000cell_2-1-A6_3-5-B3_1A

description: 1000cell from 2-1-A6_3-5-B3 clone


title: STEMI patient 1


title: 1000cell from 2-1-A6_3-5-B2 clone Methyl_1000cell_2-1-A6_3-5-B2_1A

description: 1000cell from 2-1-A6_3-5-B2 clone


title: 1000cell from 1-1-F3_2-2-B1 clone Methyl_1000cell_1-1-F3_2-2-B1_4A

description: 1000cell from 1-1-F3_2-2-B1 clone


title: CKC39_Normal

status: Public on Feb 22 2020

city: Suzhou

first: Sheng

last: Guo

state: Jiangsu

address: Xinghu Street 218 BioBay A6

institute: Crown Bioscience Inc.

data_processing:
Basecalls performed using CASAVA
RNA-Seq reads were aligned to the hg19 genome assembly using STAR version 2.5
Gene expression was estimated by the MMSEQ software and raw gene counts were normalized by the RSEM software
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RSEM normalized FPKM values for all 66 samples, predicted driver mutations for 55 tumor samples and gene fusions for 55 tumor samples.

source_name: non-cancerous matched kidney tissue

extract_protocol:
Total RNAs were extracted from tumor and matched normal tissues. The purity and integrity of the RNA samples (RIN > 7 and 28S/18S > 1) were ensured by Agilent Bioanalyzer.
cDNA library was constructed for RNA sequencing.

tag: subtype

value: normal

value: M

tag: Stage

tag: grade


title: CKC45_Normal


title: CKC42_Normal


title: CKC41_Normal


title: CKC38_Normal


title: CKC37_Normal


title: STEMI patient 2

tag: cell type


title: CKC30_Normal

tag: age


title: CKC74_Tumor

source_name: kidney tumor tissue

value: clear cell renal cell carcinoma


title: CKC82_Tumor


title: CKC78_Tumor


title: CKC80_Tumor


title: CKC81_Tumor


title: CKC29_Normal


title: CKC34_Normal


title: CKC73_Tumor


title: CKC69_Tumor


title: CKC71_Tumor


title: CKC66_Tumor


title: CKC68_Tumor


title: CKC53_Normal


title: U2OS miR-Control Replicate 1 (U2OS_Con_704)


title: CKC35_Normal


title: CKC64_Tumor


title: CKC62_Tumor


title: CKC63_Tumor


title: CKC60_Tumor


title: CKC58_Tumor


title: CKC77_Tumor


title: CKC75_Tumor


title: CKC56_Tumor


title: CKC54_Tumor


title: CKC57_Tumor


title: CKC53_Tumor


title: CKC49_Tumor


title: CKC50_Tumor


title: CKC45_Tumor


title: CKC42_Tumor


title: CKC37_Tumor


title: CKC38_Tumor


title: CKC65_Tumor


title: CKC41_Tumor


title: CKC47_Tumor


title: CKC34_Tumor


title: CKC35_Tumor


title: CKC31_Tumor


title: CKC59_Tumor


title: CKC30_Tumor


title: CKC26_Tumor


title: CKC29_Tumor


title: CKC22_Tumor


title: CKC18_Tumor


title: CKC17_Tumor


title: CKC21_Tumor


title: CKC46_Tumor


title: CKC14_Tumor


title: CKC39_Tumor


title: CKC16_Tumor


title: CKC13_Tumor


title: CKC36_Tumor


title: CKC12_Tumor


title: CKC4_Tumor


title: CKC10_Tumor


title: CKC5_Tumor


title: CKC2_Tumor


title: CKC1_Tumor


title: kethoxal (10 min)

city: Wuhan

first: Xiaocheng

last: Weng

address: Bayi Road

department: School of Pharmaceutical Sciences

institute: Wuhan University

description: kethoxal (10 min)

data_processing:
collapsed duplicated reads as in icSHAPE pipeline (https://github.com/qczhang/icSHAPE)
trimmed 3' adaptor from reads using cutadapt
trimmed low quality bases using trimmomatic
mapping reads to transcriptome (mm10, hg38) by bowtie2 as in icSHAPE pipeline
calculate RPKM as icshape pipeline
calulate reactivity score for each base as in icshape pipeline
Genome_build: mm10,hg38
Supplementary_files_format_and_content: tab-delimited text files for shape reactivity files. Column 1-3 are: Refseq ID, transcript length, RPKM, followed by shape reactivity score of each nucleotide. NULL means no confident score. Tab-delimited text files for read counts and rpkm files. Column 1-5: Refseq ID,  transcript length, unique mapped reads count, mulitple mapped reads count, RPKM.

source_name: mES

growth_protocol: mES cells (E14) were grown on gelatinized dishes in serum and LIF

extract_protocol:
Total RNA was isolated by Qiagen RNeasy plus mini kit, then use Dynabeads® mRNA Purification Kit to isolate mRNA from total RNA samples.
The library was prepared following icSHAPE protocol with slight changes (Nature2015, 519, 486)

treatment_protocol: N3-kethoxal was added into the medium of mES cells directly

value: mES

tag: agent

value: kethoxal (10 min)


title: mES_no-treat-invivo_rep2

data_processing:
Library strategy: N3-Kethoxal-seq
trimmed 3' adaptor from reads using cutadapt
trimmed low quality bases using trimmomatic
collapsed duplicated reads as in icSHAPE pipeline (https://github.com/qczhang/icSHAPE)
mapping reads to transcriptome (mm10, hg38) by bowtie2 as in icSHAPE pipeline
calculate RPKM as icshape pipeline
calulate reactivity score for each base as in icshape pipeline
Genome_build: mm10,hg38
Supplementary_files_format_and_content: tab-delimited text files for shape reactivity files. Column 1-3 are: Refseq ID, transcript length, RPKM, followed by shape reactivity score of each nucleotide. NULL means no confident score. Tab-delimited text files for read counts and rpkm files. Column 1-5: Refseq ID,  transcript length, unique mapped reads count, mulitple mapped reads count, RPKM.

value: no treat ( in vivo)


title: kethoxal (2.5 min)

description: kethoxal (2.5 min)

value: kethoxal (2.5 min)


title: mES_no-treat-invivo_rep1


title: mES_no-treat-invitro_rep2

value: no treat ( in vitro)


title: mES_no-treat-invitro_rep1


title: mES_kethoxal-invivo_rep2

value: kethxoal ( in vivo)


title: mES_kethoxal-invivo_rep1


title: mES_kethoxal-invitro_rep2

value: kethoxal ( in vitro)


title: mES_kethoxal-invitro_rep1


title: mES_kethoxal-5min

value: kethoxal (5 min)


title: mES_kethoxal-1min

value: kethoxal (1 min)


title: mES_kethoxal-remove_rep2

value: kethoxal remove


title: PT57_MDS

city: Prague 2

first: Michaela

last: Dostalova Merkerova

address: U nemocnice 1

department: Department of Genomics

country: Czech Republic

institute: Institute of Hematology and Blood Transfusion

hyb_protocol: The labeled cRNA was hybridized to the Agilent Custom 8x60K format lncRNA expression microarray (AMADID 047718) according to the manufacturer's protocol.

scan_protocol: The hybridized images were scanned using Agilent DNA microarray scanner and quantified with Agilent Feature Extraction Software.

data_processing: Raw data were extracted using the Agilent Feature Extraction Software. Quality control, quantile normalization, and filtering were performed with the Bioconductor project in the R statistical environment using limma package.

source_name: PT57_MDS_CD34+ bone marrow cells

label_protocol: Agilent Low Input Quick Amp Labeling Kit, One Color was used for sample preparation (RNA input was set up to 200 ng) according to the manufacturer’s recommendation.

growth_protocol: Czech patients with primary MDS, acute myeloid leukemia with myelodysplasia-related changes, and healthy donors were tested.

extract_protocol: Mononuclear cells were purified from bone marrow aspirates using Ficoll-Histopaque (GE Healthcare) density centrifugation. CD34+ cells were subsequently isolated using magnetic cell separation according to the manufacturer’s instructions (Miltenyi Biotec). Total RNA was extracted by the acid-guanidine-phenol-chloroform method and the samples were incubated with DNase I to prevent genomic DNA contamination. Quantity of DNA/RNA was quantified using Invitrogen Qubit 3 Fluorometer (Thermo Fisher Scientific) and the RNA integrity was assessed using the Agilent 4200 TapeStation (Agilent Technologies).

treatment_protocol: The patients with no known history of previous malignancy, chemotherapy or radiation therapy. They have not been subjected to the myelodysplasia therapy  or hematopoietic stem cell transplantation before the blood collection.

tag: subject number

value: CD34+ bone marrow cells

value: female

tag: diagnosis

tag: iPSs-r category

value: high

tag: mutations

value: SF3B1, RUNX1, EZH2, STAG2


title: mES_kethoxal-remove_rep1

tag: treatment


title: PT59_MDS

source_name: PT59_MDS_CD34+ bone marrow cells

tag: gender

value: male

value: MDS-RS-SLD

value: very low

value: wild type


title: PT61_MDS

source_name: PT61_MDS_CD34+ bone marrow cells

value: MLL


title: PT58_AML

source_name: PT58_AML_CD34+ bone marrow cells

value: AML-MRC

value: not assessed


title: mES_no-treat_rep2

value: mES

value: no treat


title: PT65_MDS

source_name: PT65_MDS_CD34+ bone marrow cells


title: PT62_AML

source_name: PT62_AML_CD34+ bone marrow cells

value: TET2, BCOR


title: PT50_MDS

source_name: PT50_MDS_CD34+ bone marrow cells

value: low


title: PT68_AML

source_name: PT68_AML_CD34+ bone marrow cells


title: PT64_AML

source_name: PT64_AML_CD34+ bone marrow cells

value: RUNX1, ASXL1, EZH2, RAD21


title: PT56_AML

source_name: PT56_AML_CD34+ bone marrow cells

value: SF3B1, RUNX1, BCOR


title: PT66_MDS

source_name: PT66_MDS_CD34+ bone marrow cells

value: CD34+ bone marrow cells

value: intermediate


title: mES_no-treat_rep1


title: PT54_AML

source_name: PT54_AML_CD34+ bone marrow cells

value: CBL, NRAS


title: PT53_MDS

source_name: PT53_MDS_CD34+ bone marrow cells

value: female

value: high


title: PT60_MDS

source_name: PT60_MDS_CD34+ bone marrow cells

value: male

value: MDS-MLD


title: PT67_MDS

source_name: PT67_MDS_CD34+ bone marrow cells

value: SF3B1, TET2, DNMT3A, JAK2


title: PT55_MDS

source_name: PT55_MDS_CD34+ bone marrow cells

value: PHF6, CBL


title: PT51_MDS

source_name: PT51_MDS_CD34+ bone marrow cells

value: SF3B1, MLL


title: PT63_MDS

source_name: PT63_MDS_CD34+ bone marrow cells

value: SRSF2, SETBP1


title: PT52_AML

source_name: PT52_AML_CD34+ bone marrow cells

value: AML-MRC

value: not assessed


title: mES_kethoxal_rep2

value: mES

value: kethoxal


title: PT48_AML

source_name: PT48_AML_CD34+ bone marrow cells


title: PT49_MDS

source_name: PT49_MDS_CD34+ bone marrow cells

value: very low

value: wild type


title: PT46_MDS

source_name: PT46_MDS_CD34+ bone marrow cells

value: CD34+ bone marrow cells

value: MDS-RS-MLD

value: low

value: SF3B1, TET2, TP53, ASXL1


title: CKC72_Tumor

source_name: kidney tumor tissue

value: clear cell renal cell carcinoma

value: M


title: mES_kethoxal_rep1


title: CKC61_Tumor

value: F


title: LysPPM31

city: RIVERSIDE

first: ZHAOJIE

last: MENG

address: 900 UNIVERSITY AVENUE

institute: UNIVERSITY OF CALIFORNIA, RIVERSIDE

description:
PXRΔMyeLDLR-/-
LysPPM31

data_processing:
The Sailfish tool was used to quantify the expression of each transcript.
Genome_build: mm10
Supplementary_files_format_and_content: Transcripts Per Kilobase Million

source_name: Peritoneal macrophages

growth_protocol: Six-week old PXRF/FLDLR-/- and PXRΔMyeLDLR-/- were intraperitoneally injected with 1 mL of 3% thioglycollate solution 3 days prior to the peritoneal macrophage collection.  The peritoneal macrophages were then collected from abdominal cavity and seeded to six-well plate.

extract_protocol:
Total RNA was isolated from cells using TRIzol Reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Peritoneal macrophages were allowed to attach to cell culture plates for 4 hours and then treated with PXR ligand PCN (20 µM) or DMSO (control) for 12 hr.

tag: strain

value: Peritoneal macrophages (In vitro cultured)

tag: genotype

value: PXRdeltaMyeLDLR-/-

value: Dimethyl sulfoxide (Control)

tag: treatment duration

value: 12 hr


title: LysPPM34

description:
PXRΔMyeLDLR-/-
LysPPM34


title: LysPPM33

description:
PXRΔMyeLDLR-/-
LysPPM33


title: LysPPM38

description:
PXRΔMyeLDLR-/-
LysPPM38

value: Pregnenolone 16alpha-carbonitrile (PCN)


title: LysPPM37

description:
PXRΔMyeLDLR-/-
LysPPM37


title: LysPPM35

description:
PXRΔMyeLDLR-/-
LysPPM35


title: LysPPM30

description:
PXRΔMyeLDLR-/-
LysPPM30


title: LysPPM36

description:
PXRΔMyeLDLR-/-
LysPPM36


title: LysPPM32

description:
PXRΔMyeLDLR-/-
LysPPM32


title: LysPPM28

value: PXRF/FLDLR-/-


title: PT47_MDS

source_name: PT47_MDS_CD34+ bone marrow cells

value: female


title: LysPPM29

description:
PXRΔMyeLDLR-/-
LysPPM29


title: PT42_AML

source_name: PT42_AML_CD34+ bone marrow cells

value: male

value: AML-MRC

value: not assessed


title: PT45_MDS

source_name: PT45_MDS_CD34+ bone marrow cells

value: CD34+ bone marrow cells

value: TET2, DNMT3A, ASXL1, BCOR


title: PT44_MDS

source_name: PT44_MDS_CD34+ bone marrow cells

value: MDS-MLD

value: low

value: ASXL1, SRSF2, STAG2, IDH2


title: PT41_MDS

source_name: PT41_MDS_CD34+ bone marrow cells

value: very high

value: TP53, DNMT3A, U2AF1, CSF3R


title: PT40_MDS

source_name: PT40_MDS_CD34+ bone marrow cells


title: PT35_MDS

source_name: PT35_MDS_CD34+ bone marrow cells

value: MDS-RS-SLD

value: SF3B1, DNMT3A


title: PT37_MDS

source_name: PT37_MDS_CD34+ bone marrow cells

value: high


title: PT39_MDS

source_name: PT39_MDS_CD34+ bone marrow cells

value: MDS-SLD


title: PT32_MDS

source_name: PT32_MDS_CD34+ bone marrow cells

value: intermediate

value: DNMT3A, EZH2


title: PT33_MDS

source_name: PT33_MDS_CD34+ bone marrow cells

value: female


title: PT36_MDS

source_name: PT36_MDS_CD34+ bone marrow cells

value: male

value: wild type


title: PT31_AML

source_name: PT31_AML_CD34+ bone marrow cells

value: AML-MRC

value: not assessed


title: PT38_MDS

source_name: PT38_MDS_CD34+ bone marrow cells

value: CD34+ bone marrow cells

value: TP53, ASXL1, STAG2, NOTCH1, U2AF1, GATA1


title: LysPPM40

description:
PXRΔMyeLDLR-/-
LysPPM40

value: Peritoneal macrophages (In vitro cultured)

value: PXRdeltaMyeLDLR-/-

value: Pregnenolone 16alpha-carbonitrile (PCN)

value: 12 hr


title: LysPPM25

value: PXRF/FLDLR-/-


title: LysPPM26


title: LysPPM22

value: Dimethyl sulfoxide (Control)


title: LysPPM21


title: PT34_MDS

source_name: PT34_MDS_CD34+ bone marrow cells

value: very high


title: LysPPM23


title: PT2_GATA2_Veh_ChIP

city: Chicago

first: Serdar

last: Bulun

state: IL

address: 303 E. Superior Street

department: Obstetrics and Gynecology

institute: Northwestern University

description: GATA2 ChIP DNA

data_processing:
Libraries were sequenced under 75bp single-end sequencing format. Adapters were trimmed using cutadapt. Sequences were aligned to the hg38 reference genome using Bowtie2. Factor style peak calling, differential binding analysis (getDifferentialPeaksReplicates.pl), overlapping region identifications (mergePeaks -d 100) and motif analysis were performed using Homer under default settings.
Genome_build: hg38
Supplementary_files_format_and_content: The processed files are peak files from each individual GATA2 ChIP-Seq

source_name: Primary endometrial stromal cells

growth_protocol: DMEM/F12 w/ 10% FBS and 1x antibiotic/antimycotic

extract_protocol:
7.5e8 cells (patient number = 2) were used for ChIP-Seq using the SimpleChIP Kit (Cell Signaling Technology, #9005). GATA2 antibody was purchased from Santa Cruz (#sc-9008).
Next-generation sequencing libraries were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems, KK8502) and KAPA Single-Indexed Adapter Kit (KAPA Biosystems, KK8710).

treatment_protocol: 10 day treatment. IVD treatment: 1 µM MPA, 35nM ß-estradiol, 0.05 mM 8-bromo cAMP; Vehicle treatment: equal volume ethanol

value: Isolated stromal cells post-hysterectomy

tag: patient id

value: Patient 2

tag: antibody

value: GATA2 ChIP DNA


title: PT2_GATA2_IVD_ChIP

description: GATA2 ChIP DNA


title: PT29_MDS

source_name: PT29_MDS_CD34+ bone marrow cells

value: low

value: TET2, NOTCH1, CUX1, ZRSR2


title: PT26_MDS

source_name: PT26_MDS_CD34+ bone marrow cells

value: female

value: MDS-MLD

value: intermediate

value: CEBPA


title: PT24_MDS

source_name: PT24_MDS_CD34+ bone marrow cells

value: CD34+ bone marrow cells


title: PT43_MDS

source_name: PT43_MDS_CD34+ bone marrow cells


title: PT2_GATA2_Veh_ChIP_Input

description: Chromatin input from PT2_GATA2_Veh_ChIP sample


title: PT25_MDS

source_name: PT25_MDS_CD34+ bone marrow cells

value: male

value: high

value: RUNX1, EZH2, IKZF1


title: PT27_MDS

source_name: PT27_MDS_CD34+ bone marrow cells

value: MDS-RS-SLD

value: SF3B1, TET2


title: PT30_AML

source_name: PT30_AML_CD34+ bone marrow cells

value: AML-MRC

value: not assessed

value: JAK2, KDM6A


title: PT1_GATA2_Veh_ChIP

description: GATA2 ChIP DNA

value: Isolated stromal cells post-hysterectomy

value: Patient 1


title: PT1_GATA2_IVD_ChIP

description: GATA2 ChIP DNA

value: GATA2 ChIP DNA


title: PT22_MDS

source_name: PT22_MDS_CD34+ bone marrow cells

value: MDS-SLD

value: very low

value: wild type


title: PT28_MDS

source_name: PT28_MDS_CD34+ bone marrow cells

value: female

value: intermediate

value: TP53, BCORL1, CDKN2A


title: PT19_MDS

source_name: PT19_MDS_CD34+ bone marrow cells

value: CD34+ bone marrow cells

value: MDS-MLD

value: low


title: PT20_MDS

source_name: PT20_MDS_CD34+ bone marrow cells

value: high

value: TET2, RUNX1, ASXL1, EZH2, PHF6


title: PT14_AML

source_name: PT14_AML_CD34+ bone marrow cells

value: male

value: AML-MRC

value: DNMT3A, BCOR, IDH2, PHF6


title: PT21_AML

source_name: PT21_AML_CD34+ bone marrow cells

value: not assessed

value: SF3B1, IDH2


title: PT16_MDS

source_name: PT16_MDS_CD34+ bone marrow cells

value: very high

value: CUX1, ZRSR2


title: PT1_GATA2_IVD_Input

description: Chromatin input from PT1_GATA2_IVD_ChIP sample

value: Isolated stromal cells post-hysterectomy

value: Patient 1


title: PT12_MDS

source_name: PT12_MDS_CD34+ bone marrow cells

value: female

value: SF3B1, TET2, CUX1


title: PT18_MDS

source_name: PT18_MDS_CD34+ bone marrow cells

value: wild type


title: PT1_GATA2_Veh_ChIP_Input

description: Chromatin input from PT1_GATA2_Veh_ChIP sample

source_name: Primary endometrial stromal cells


title: PT10_MDS

source_name: PT10_MDS_CD34+ bone marrow cells

value: CD34+ bone marrow cells

value: MDS-SLD


title: PT17_MDS

source_name: PT17_MDS_CD34+ bone marrow cells


title: PT8_MDS

source_name: PT8_MDS_CD34+ bone marrow cells

value: MDS-MLD

value: very low

value: RUNX1, SRSF2, IKZF1, SETBB1


title: PT3_IVD

data_processing:
Libraries were sequenced under 75bp single-end sequencing format. Adapters were trimmed using cutadapt. Trimmed reads were aligned to the hg38 reference genome using Tophat default parameters. Raw count files were generated using HTSeq based on Ensembl Release 75 annotation. Differentially expressed genes were detected using edgeR following the cutoff FDR-adjusted P<0.05.
Genome_build: hg38
Supplementary_files_format_and_content: The processed files are HTSeq raw count files from each RNA-Seq sample.

extract_protocol:
Confluent cells from 1-10cm plate were collected in RLT Buffer + beta-mercaptoethanol. Total RNA was extracted from using Qiagen RNeasy RNA micro kit (Qiagen, 74004).
Next-generation sequencing libraries were prepared using KAPA Stranded RNA-Seq Kit with RiboErase (Roche, #7962282001).

tag: cell t ype

value: IVD

tag: tag

value: Patient 3


title: PT2_Veh

value: Patient 2


title: PT13_MDS

source_name: PT13_MDS_CD34+ bone marrow cells

value: male

value: low

value: IKZF1, U2AF1


title: PT2_IVD


title: PT11_MDS

source_name: PT11_MDS_CD34+ bone marrow cells

value: intermediate

value: RUNX1, ASXL1, IKZF1, ETV6, PTPN11


title: PT23_MDS

source_name: PT23_MDS_CD34+ bone marrow cells

value: very high


title: PT15_MDS

source_name: PT15_MDS_CD34+ bone marrow cells

value: female


title: PT1_IVD

value: Isolated stromal cells post-hysterectomy

value: Patient 1


title: PT1_Veh


title: PT9_AML

source_name: PT9_AML_CD34+ bone marrow cells

value: CD34+ bone marrow cells

value: AML-MRC

value: not assessed

value: wild type


title: PMP.A2.S3

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

description:
Primitive macrophage precursor cells
pmp_norm.txt

data_processing:
Illumina bcl2fastq2-v2.17.1.14 software used for basecalling.
Fastq files were stripped of primer sequences with fastp v.0.12.2 and aligned with hg38 reference genome using HISAT2 v.2.1.0 with default parameters, outputting to a sam file.
Genome_build: hg38
Supplementary_files_format_and_content: Counts were extracted from sam alignments with featureCount and loaded into a DESeq2 model with default normalization and scaling.  Normalized counts were output using the assay command and saved as a tab-delimited text file.

source_name: A2 iPSC-derived PMP cultures

growth_protocol: Primitive macrophage precursor (PMP) cells were prepared from human iPSC via yolk sac embryoid bodies, which were plated and stimulated with IL-3 and M-CSF to promote myeloid differentiation.  PMP emerged into the medium.

extract_protocol:
Cells were harvested by centrifugation and RNA was extracted with a Qiagen RNAEasy kit.
Illumina TruSeq RNA Sample Preparation Kit v2.

tag: tissue

value: primitive macrophage progenitors


title: PT6_MDS

source_name: PT6_MDS_CD34+ bone marrow cells

tag: cell type


title: PT7_MDS

source_name: PT7_MDS_CD34+ bone marrow cells

tag: age

value: MDS-SLD


title: PT3_Veh

tag: agent

value: Patient 3


title: PMP.C5.S2

source_name: C5 iPSC-derived PMP cultures


title: Clone 4_6

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
Reads were aligned to the human genome using STAR aligner.
Raw 50bp paired-end reads were aligned via the Spliced Transcripts to Alignment Reference (STAR 2.3.0e) [40] to the human genome build hg19 and annotation file gencode v19. The non-default and non-directory parameters for building the reference genome in STAR were: STAR --runMode genomeGenerate --sjdbOverhang 49 --runThreadN 8, and the parameters for alignment were STAR --readFilesCommand bzcat --outFilterMismatchNmax 6 --outFilterIntronMotifs RemoveNoncanonicalUnannotated. Raw counts from the alignment files were extracted using HT-seq (v0.5.4) with the following parameters: htseq-count -i gene_id -q -m union -s reverse.
Genome_build: hg19
Supplementary_files_format_and_content: CSV file contains read counts.

source_name: Preadipocyte

extract_protocol: Total RNA was harvested from a 100% confluent 10-cm plate with 1 mL Trizol and stored at −80 °C. Samples were thawed, homogenized with a 25-gauge needle, and 200 μL chloroform was added. The samples were vortexed (20 s), centrifuged (15,000 g, 30 min), and the aqueous phase was isolated for purification. The aqueous phase was combined with 1 volume of isopropanol, centrifuged (15,000 g, 60 min), and washed with 70% ethanol. The resulting RNA pellet was air dried for 1 h and resuspended in 30 μL RNase-free water. RNA quality was assessed on an Agilent 2100 Bioanalyzer to ensure RIN values were greater than 8.0. For library prep, we used the NEBNext Ultra Directional Library Prep Kit (New England Biolabs). Briefly, 500 ng of RNA in 50 μL water was combined with 15 μL NEBNext Oligo d(T)25 magnetic beads (pre-washed twice with RNA binding buffer) and incubated at 65 °C for 5 min. The beads were washed twice with 200 μL wash buffer and eluted with 200 μL elution buffer. The binding-washing was repeated once more. The final elution was in 15 μL first strand synthesis buffer and incubated at 94 °C for 15 min. Then 10 μL of the supernatant was used for cDNA synthesis reaction, which was purified using Agencourt AMPure XP beads. End-repair was performed with NEBNext end repair reaction buffer and purified with AMPure XP beads. Library enrichment and multiplexing was performed using the NEBNext High-Fidelty PCR Master Mix (14 cycles of PCR) and NEBNext Multiplex Oligos. The cDNA libraries were multiplexed on the Illumina HiSeq 2000.

value: Neck

tag: subject

tag: pparg

tag: differentiation

value: High

tag: cell line

value: clonally-expanded white preadipocyte cell line


title: Clone 4_4

tag: ocr


title: PMP.C5.S1


title: LysPPM39

description:
PXRΔMyeLDLR-/-
LysPPM39

source_name: Peritoneal macrophages

value: Peritoneal macrophages (In vitro cultured)

value: PXRdeltaMyeLDLR-/-

value: Pregnenolone 16alpha-carbonitrile (PCN)

value: 12 hr


title: Clone 4_36

value: Low


title: Clone 4_3


title: Clone 4_31


title: Clone 4_35


title: PT2_MDS

source_name: PT2_MDS_CD34+ bone marrow cells

tag: subject number

tag: gender

value: male

tag: diagnosis

tag: iPSs-r category

value: very low

tag: mutations


title: Clone 4_2


title: Third instar larval ovary cleaned of fat body with papain rep 8.

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description: Pool of 25 ovaries with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.

data_processing:
We called bases using RTA v1.13 (Illumina, San Diego, CA), and demultiplexed and converted BCL to FASTQ using bcl2fastq v1.8 (Illumina, San Diego, CA).
We created a custom reference by concatenating the ERCC (SRM2374) as described in (Jiang et al. 2011. PMID: 21816910 and Lee et al. 2016 PMID: 27512518) to the standard Drosophila melanogaster genome assembly release 6 plus ISO1 MT (GCA_000001215.4).
We aligned reads with Hisat2 v2.1.0 (Kim et al. 2015. PMID: 25751142) using default settings except --max-introlen 300000. We also provided a set of know splice sites generated from FlyBase r6.16 to the --known-splicesite-infile option.
Prior to calculating coverage, we removed multi-mapping reads and low quality alignments with Samtools v1.7 (Li et al. 2009. PMID: 19505943) -q 20. We created two GTF files to estimating coverage, which are included in (GSE115478). The first GTF contains gene models from FlyBase r6.16 GTF and ERCC gene models that we generated. The second GTF contains intergenic regions that we created based on FlyBase r6.16.
We generated gene level, ERCC level, and intergenic level counts using featureCounts v1.6.1 (Liao et al., 2014. PMID: 24227677) with default options except: (-s 2) to create strand specific read counts for genic and ERCC, and (-s 0) to create non-stranded counts for intergenic regions.
Genome_build: Drosophila melanogaster Release 6 plus ISO1 MT (GCA_000001215.4).
Supplementary_files_format_and_content: *.pos.bigwig: Is a first strand bigWig file generated using DeepTools v3.0.2 using options ( --minMappingQuality 20, --ignoreDuplicates, --smoothLength 10, --normalizeUsing RPKM, and --filterRNAstrand forward)
Supplementary_files_format_and_content: *.neg.bigwig: Is a second strand bigWig file generated using DeepTools v3.0.2 using options ( --minMappingQuality 20, --ignoreDuplicates, --smoothLength 10, --normalizeUsing RPKM, and --filterRNAstrand reverse)
Supplementary_files_format_and_content: *.featurecounts.s2.txt: Contains gene level + ERCC level raw counts generated using featureCounts v1.6.1 with options (-s 2)
Supplementary_files_format_and_content: *.featurecounts.intergenic.s0.txt: Contains intergenic level raw counts generated using featureCounts v1.6.1 with options (-s 0)

organism: Drosophila melanogaster

source_name: tissue

growth_protocol:
Flies were grown on fly food A (LabExpress Ann Arbor, MI) at 25°C under constant light and 60% relative humidity.
We grew w1118 flies (FBst0005905; Bloomington stock center, Bloomington, IN) on Fly food A (LabExpress Ann Arbor, MI) in constant light at 25°C and 60% relative humidity. We collected eggs every 8-16 hr from six mated females, and allowed larvae to develop until the late third instar larval stage. For larval staging, we fed second and third instar larvae with water/yeast paste containing 0.5 mg/ml Sulforhodamine B sodium salt (Sigma-Aldrich, Cat. No. S1402-25G. St. Louis, MO).

extract_protocol:
We selected late third instar larvae that were immobilized, but that had not extended their anterior spiracles. We dissected larvae in PBS at 22°C (Gibco Life Technologies, Carlsbad, CA), and collected ovaries from individuals with Sulforhodamine B dye located only in the mid and hindgut. Ovaries were collected in 350 μl RLT buffer (Qiagen, Cat. No. 79216. Valencia, CA), vortexed two times for 30 sec with a 30 sec interval in between, quick frozen in a dry ice ethanol bath, and stored at -80°C until RNA extraction. We had four different treatment conditions: We collected 15 ovaries with fatbody still attached around the gonads. We collected 30 ovaries without fatbody by enzymatically removing the fatbody by treating with 0.075 mg/ml Papain (Sigma-Aldrich, St. Louis, MO) and 0.075 mg/ml Collagenase enzymes (Sigma-Aldrich, St. Louis, MO) in PBS in 1.5 ml eppendorf tube for 3 min with gentle vortexing by flicking the tube with a forefinger. We collected fatbody only from 10 ovaries by dissecting the fatbody and disposing of the ovaries. We dissociated 30 ovaries after removing the fatbody by treating with 2 mg/ml Papain and 2 mg/ml Collagenase enzymes. We pelleted cells from all treatments using a table top centrifuge at 0.9 g for 5 min and resuspended in 350 μl RLT buffer. Using the RNeasy 96 kit, we extracted total RNA (Qiagen, Cat. No. 1019545. Valencia, CA) by following the manufacturer’s protocol. We used Quant-iT RiboGreen quantification kit (Life Technologies, Cat. No. R11490. Carlsbad, CA) to quantify the RNA. RNA was stored in -80°C until the library preparation.
We used 200 ng of total RNA and performed RNA-seq library preparation according to Lee et al (doi:10.1101/032920 and Gene Expression Omnibus GSE73920). Briefly, PolyA+ selection was done using Dynabeads Oligo(dT)25 (Life technologies, Grand Island, NY). Selected mRNA was fragmented, and RT was performed with the second strand synthesis by incorporating dUTPs. We used External RNA control consortium spike-ins pools 78A and 78B (SRM2374, Zook et al., 2012. PMID: 22859977) transcribed from standard reference. We used barcoded adaptors for indexing the libraries (Qiagen, 98 TruSeq v2 kit barcoded adaptors, Valencia, CA), and sequenced stranded 42 multiplexed libraries using a single-ended 50 bp strategy on one lane using a HiSeq Illumina 2500 (Illumina, San Diego, CA).

tag: strain

tag: Sex

value: female

tag: developmental stage

value: Late third instar larval stage:immobilized, partial gut clearance as dyed yeast paste exist partly in midgut and hindgut, prior to anterior spiracle eversion.

tag: spike-in

value: ERCC (SRM2374) 78B

value: A


title: Clone 4_14

tag: tissue


title: PT4_MDS

source_name: PT4_MDS_CD34+ bone marrow cells

tag: cell type

value: CD34+ bone marrow cells

tag: age

value: high

value: TET2, RUNX1, BCOR, SRSF2, STAG2, NOTCH1, RAD21


title: PT1_MDS

source_name: PT1_MDS_CD34+ bone marrow cells

value: MDS-RS-MLD

value: very high

value: not assessed


title: Clone 4_13

value: Neck

tag: subject

value: High

value: clonally-expanded white preadipocyte cell line


title: PT5_MDS

source_name: PT5_MDS_CD34+ bone marrow cells


title: CTR8

source_name: healthy donor no. 8, CD34+ bone marrow cells

value: healthy

value: wild type


title: CTR7

source_name: healthy donor no. 7, CD34+ bone marrow cells


title: Clone 3_9

tag: pparg

value: Low


title: Third instar larval ovary cleaned of fat body with papain rep 6.


title: CTR1

source_name: healthy donor no. 1, CD34+ bone marrow cells

value: male


title: Third instar larval ovary cleaned of fat body with papain rep 7.

value: female

value: ERCC (SRM2374) 78A


title: Third instar larval ovary cleaned of fat body with papain rep 5.

value: Late third instar larval stage:immobilized, partial gut clearance as dyed yeast paste exist partly in midgut and hindgut, prior to anterior spiracle eversion.


title: CTR9

source_name: healthy donor no. 9, CD34+ bone marrow cells


title: CTR6

source_name: healthy donor no. 6, CD34+ bone marrow cells


title: CTR5

source_name: healthy donor no. 5, CD34+ bone marrow cells


title: Clone 3_7


title: Clone 3_8

tag: differentiation


title: CTR3

source_name: healthy donor no. 3, CD34+ bone marrow cells


title: Clone 3_4

tag: cell line


title: CTR4

source_name: healthy donor no. 4, CD34+ bone marrow cells


title: CTR2

source_name: healthy donor no. 2, CD34+ bone marrow cells


title: Clone 3_6


title: Clone 3_16


title: Clone 3_10


title: Clone 3_1

tag: ocr


title: Clone 2_8


title: Clone 2_15


title: Clone 2_14


title: Clone 3_2


title: Clone 2_1


title: Clone 2_10


title: Clone 2_12


title: sSKOV3-3_RNA-seq

city: Beijing

first: Xiao

last: Huo

address: No.1 ShuaiFuYuan,Dongcheng District

department: Department of Obstetrics and Gynecology

country: France

institute: Peking Union Medical College Hospital

data_processing:
RNA-Seq：Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences, reads with >5% ambiguous bases (noted as N) and low-quality reads containing more than 20 percent ofbases with qualities of <20. The clean reads were then aligned to hg38_UCSC_2013 genome using the star program.
Htseq-count was used to calculate gene expression
The RNA-seq differential gene expression analysis was performed using DESeq2 algorithm
ChIP-seq raw reads were aligned to hg38 using bwa program (version 0.7.2).
The resulted sam files are converted to bam with samtools (version 0.1.18). MACS2 (version 2.0.10.20131216) was used to call peak with cutoff p value < 0.00001.
The HOMER's (version 4.10) findMotifsGenome.pl tool was used for Motif analysis.
ChIP-seq reads distributions (from bigwig) across gene body are presented as an average plot (average of reads signals across all genes) and the analysis of plotFingerprint were both used the deeptools (version 2.0).
Genome_build: hg38
Supplementary_files_format_and_content: Htseq-count; bigwig

source_name: SKOV3_wild type_RNA-seq

growth_protocol: The SKOV3 cells were cultured in McCOY’5A medium supplemented with 10% fetal bovine serum (FBS, USA), 100μg/ml streptomycin and 100 U/ml penicillin. All cells were incubated in a 75 humidified atmosphere of 5% CO2 at 37 °C.

extract_protocol:
For RNA-Seq，SKOV3 and SKOV3/sgEZH2 cells were harvested for RNA extraction using RNeasy mini kits (Qiagen).  For ChIP-seq, SKOV3 and SKOV3/sgEZH2 cells were fixed and then lysed, and the chromatin  was sheared to 200-500 bp in size using the Bioruptor sonicator (Diagenode). The chromatin was incubated with H3K27me3 antibody (Millipore 07-622) bound to protein G beads (Thermo Fisher) for overnight. After immunoprecipitation, samples were reversely crosslinked in 65°C water bath, and DNA was extracted with QIAquick PCR purification kit (Qiagen).
RNA-Seq library preparation with KAPA Stranded mRNA-Seq Kit (Illumina® platform) and then sequenced using Illumina HiSeq 4000. The ChIP-Seq libraries were prepared using NEBNext® UltraTMII DNA (NEB E7645S) and then sequenced using Illumina HiSeq 2500.

treatment_protocol: CRISPR/Cas9 system was used to establish the knock-out EZH2 SKOV3 cells

value: Human epithelial ovarian cancer cell

tag: genotype/variation


title: sSKOV3-1_RNA-seq


title: s1B11H-1_RNA-seq


title: sSKOV3-2_RNA-seq


title: s1B11H-3_RNA-seq


title: PT3_MDS

source_name: PT3_MDS_CD34+ bone marrow cells

tag: subject number

value: CD34+ bone marrow cells

tag: gender


title: Clone 1_9

source_name: Preadipocyte


title: Clone 1_6


title: Clone 1_3


title: Patient5-poor response

city: GuangZhou

first: Bing

last: Zeng

address: Yuan Cun second road

department: Department of Gastroenterology, Hernia and Abdominal Wall Surgery

institute: Sun Yat-sen University

description: lncRNA and Gene expression

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Tumor Tissue

label_protocol: cDNA labeled with a fluorescent dye (C5-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Tissue biopsies were obtained from patients before CRT and Total RNA containing small RNA was extracted.

tag: subject status

value: locally advanced rectal cancer (LARC) patient

tag: response to crt

value: poor

value: rectal tumor tissue


title: Patient2-goodresponse

description: lncRNA and Gene expression

value: good


title: Muscle-F-O

first: Shuai

last: Ma

address: No.15, Da Tun road

institute: Chinese Academy of Sciences

description: Single-Nucleus RNA

data_processing:
Sequences from the microfluidic droplet platform were de-multiplexed and aligned using CellRanger version 2.2.1, available from 10x Genomics with default parameters.
Genome_build: rat6.0
Supplementary_files_format_and_content: tab-delimited text files include barcodes, gene and count matrix for each Sample

organism: Rattus norvegicus

source_name: Muscle

extract_protocol:
The organs and tissues were isolated from young, old, and calorie-restricted (CR) SD rats. Pooled samples of 2 to 3 rats were quickly minced into ∼1 mm3 pieces on ice with scissors in cold 1× PBS (Sigma-Aldrich) and transferred into 15-ml centrifuge tubes, rinsed twice with cold 1× PBS and then incubate with the same volume of dissociation buffer with the addition of trypsin-EDTA (0.125%) at 37°C for 1 hr (Han et al., 2018a, b).
sc/snRNA-seq libraries were constructed as per the 10x Genomics protocol using GemCode Single-Cell 3′ Gel Bead and Library V2 Kit.

tag: Stage

value: O-AL

value: Skeletal muscle


title: Patient6-poor response

description: lncRNA and Gene expression


title: Patient3-goodresponse

description: lncRNA and Gene expression


title: Muscle-F-CR

description: Single-Nucleus RNA

value: O-CR


title: Clone 1_2

value: Neck

value: High

value: clonally-expanded white preadipocyte cell line


title: s1B11H-2_RNA-seq


title: Clone 2_3


title: Muscle-F-Y

description: Single-Nucleus RNA

value: Y-AL


title: Patient4-poor response

description: lncRNA and Gene expression

value: male


title: Patient1-goodresponse

description: lncRNA and Gene expression


title: Muscle-M-CR

description: Single-Nucleus RNA


title: Clone 2_13


title: Clone 1_10

value: Low


title: Muscle-M-O

description: Single-Nucleus RNA


title: Clone 1_13


title: Muscle-M-Y

description: Single-Nucleus RNA


title: Clone 1_14


title: FSK_FA_1

city: Research Triangle Park

first: Cristina

last: Nadalutti

state: NC

address: 111 T W Alexander Dr., A030 Rall Bldg.

department: Genome Integrity and Structural Biology Laboratory

institute: National Institute of Environmental Health Sciences

description: Gene expression after 24hr in FA

hyb_protocol: For each sample, 1.65 μg of Cy3-labeled cRNA was fragmented and hybridized for 17 h in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner. Data were obtained with Agilent Feature Extraction software (v.9.5), using the one-color defaults for all parameters, performed error modeling, adjusting for additive and multiplicative noise.

data_processing: The resulting data were processed using OmicSoft Array Studio software (v.7.0). Significant probes were determined by filtering data to include only probes with fold changes >1.5 or <1.5 compared with the control and adjusted p-values <0.01, which was determined by an error-weighted one-way analysis of variance (ANOVA) and Bonferroni multiple test correction using the OmicSoft software.

source_name: Human primary foreskin cells after 24h exposed to FA

label_protocol: Gene expression analysis was performed using Agilent Whole Human Genome 4x44 multiplex format oligo arrays (Agilent Technologies, CA, USA) following the Agilent one-color microarray-based gene expression analysis protocol. Starting with 500 ng of total RNA, Cy3-labeled cRNA was produced according to the manufacturer’s protocol.

growth_protocol: Primary cultures of human fibroblasts (FSK) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco, Carlsbad, California), supplemented with 10% FBS (Hyclone, Fisher Scientific, Canada, USA), 100 nM non-essential amino acids (Gibco) and 50 mg/ml of penicillin/streptomycin in a humidified incubator at 37 °C in an atmosphere of 5% CO2.

extract_protocol: FSK cells were seeded in 145-mm dishes at 1x10^6 cells/dish and cultured to 80% confluence. Cells were then treated with 250 μM FA for 24 h and washed twice in PBS. Total cellular RNA was isolated using an RNeasy Midi Kit (Qiagen, TX, USA) according to the manufacturer’s instructions. Genomic DNA was removed by on-column digestion with RNase-free DNase I (Qiagen) and denaturing formaldehyde/agarose gel electrophoresis was performed to validate the quality and integrity of the RNA samples. The samples were quantified using a Nanodrop ND-1000 spectrophotometer (Thermo Scientific, DE, USA), and the purity was assessed by 260/280 absorbance. Three biological replicates were collected and isolated from control and 250 mM FA-treated cells.

treatment_protocol: FSK cells were exposed to 250 μM FA for 24 hours.

value: primary foreskin cells


title: FSK_FA_2

description: Gene expression after 24hr in FA


title: FSK_control_1

description: Gene expression after 24hr without FA

source_name: Human primary foreskin cells without FA


title: FSK_FA_3

description: Gene expression after 24hr in FA


title: FSK_control_2

description: Gene expression after 24hr without FA


title: FSK_control_3

description: Gene expression after 24hr without FA


title: Clone 1_11


title: Clone 1_1


title: Brain-F-O

description: Single-Nucleus RNA

source_name: Brain

value: Brain


title: PRF_MPRA_RNA

city: Haifa

first: Martin

last: Mikl

address: Abba Khoushy 199

department: Department of Human Biology

country: Israel

institute: University of Haifa

description: frameshifting library integrated in the AAVS1 locus (single copy per cell)

data_processing:
base-calling (Illumina)
mapping to the designed sequence libraries with custom Python scripts (will be provided as part of the published manuscript)
identifying reads coming from synthesis errors vs those that perfectly match the library sequence ("wt")
For each variant, obtain the distribution across expression bins (by identifying the bin specific barcode incorporated during PCR amplification from genomic DNA)
In the case of RNA, determine the number and fraction of reads that might constitute cryptic splicing events
Supplementary_files_format_and_content: csv, contains the sequences of the library and the computed splicing ratios/splicing values

source_name: K562 cells with integrated reporter construct

growth_protocol: 37deg Celsius, 5% CO2

extract_protocol:
NucleoSpin RNA II kit (MACHEREY-NAGEL), SuperScript® III First-Strand Synthesis System (Thermo Fisher Scientific) for RNA samples, DNeasy Blood & Tissue Kit (Qiagen) for genomic DNA samples
PCR to amplify the reporter library, library preparation following Illumina protocols for Truseq. End repair, poly A addition, adaptor ligation, enrichment.
Sequencing of PCR amplicons (from cDNA or genomic DNA)

tag: condition

value: 1 AAVS1 site mutated