title: Liver_DDE_rep2

description:
J2
Gene expression after 60 days of 450mg/kg feed DDE supplemented diet.
Replicate 2


title: CIN3_2 cervical intraepithelial neoplasia grade 3

status: Public on Jan 30 2020

type: genomic

city: Montreal

first: David

last: Cheishvili

state: Quebec

address: 3655 Sir William Osler

country: Canada

institute: McGill

hyb_protocol: The Illumina hybridization oven was used for incubating amplified DNA (37°C) and for BeadChips hybridization (48°C). A Hybex incubator was used for fragmentation (37°C) and denaturation (95°C) steps.

scan_protocol: Arrays were scanned in Illumina HiScan Reader

data_processing: Raw data were analyzed using the ChAMP package (for HumanMethylationEPIC array) in R.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Exfoliated cervical cell specimen

label_protocol: Illumina Infinium protocol

growth_protocol: Exfoliated cervical cell specimens were suspended in a preservative solution (PreservCyt, Hologic Inc., Mississauga) and stored at 4C.

extract_protocol: Exfoliated cervical cell specimens were suspended in a preservative solution (PreservCyt, Hologic Inc., Mississauga) and stored at 4oC. For specimens in the discovery set, total genomic DNA was extracted using QIAamp DNA Mini Kit (QIAGEN GmbH, Germany).32 Genomic DNA was quantified using Picogreen protocol (Quant-iTTM PicoGreen_ dsDNA Products, Invitrogen, P-7589) and read on a Spectra-MAX GeminiXS Spectrophotometer.

tag: gender

value: Female

tag: grade

value: Grade 3


title: CIN3_17 cervical intraepithelial neoplasia grade 3


title: CIN2_37 cervical intraepithelial neoplasia grade 2

value: Grade 2


title: CIN2_33 cervical intraepithelial neoplasia grade 2


title: CIN2_34 cervical intraepithelial neoplasia grade 2


title: CIN2_38 cervical intraepithelial neoplasia grade 2


title: CIN2_40 cervical intraepithelial neoplasia grade 2


title: CIN2_32 cervical intraepithelial neoplasia grade 2


title: CIN2_36 cervical intraepithelial neoplasia grade 2


title: CIN2_29 cervical intraepithelial neoplasia grade 2


title: CIN2_27 cervical intraepithelial neoplasia grade 2


title: CIN2_35 cervical intraepithelial neoplasia grade 2


title: CIN2_26 cervical intraepithelial neoplasia grade 2


title: CIN2_31 cervical intraepithelial neoplasia grade 2


title: CIN2_30 cervical intraepithelial neoplasia grade 2


title: CIN2_25 cervical intraepithelial neoplasia grade 2


title: CIN3_1 cervical intraepithelial neoplasia grade 3


title: CIN2_22 cervical intraepithelial neoplasia grade 2


title: CIN2_39 cervical intraepithelial neoplasia grade 2


title: CIN2_21 cervical intraepithelial neoplasia grade 2


title: CIN2_23 cervical intraepithelial neoplasia grade 2


title: CIN2_28 cervical intraepithelial neoplasia grade 2


title: CIN2_19 cervical intraepithelial neoplasia grade 2


title: CIN2_20 cervical intraepithelial neoplasia grade 2


title: CIN2_16 cervical intraepithelial neoplasia grade 2


title: CIN2_18 cervical intraepithelial neoplasia grade 2


title: CIN2_14 cervical intraepithelial neoplasia grade 2


title: CIN2_13 cervical intraepithelial neoplasia grade 2


title: CIN2_15 cervical intraepithelial neoplasia grade 2


title: CIN2_11 cervical intraepithelial neoplasia grade 2


title: CIN2_1 cervical intraepithelial neoplasia grade 2


title: CIN2_2 cervical intraepithelial neoplasia grade 2


title: CIN2_5 cervical intraepithelial neoplasia grade 2


title: CIN2_6 cervical intraepithelial neoplasia grade 2


title: CIN2_7 cervical intraepithelial neoplasia grade 2


title: CIN2_9 cervical intraepithelial neoplasia grade 2


title: CIN2_17 cervical intraepithelial neoplasia grade 2


title: CIN2_3 cervical intraepithelial neoplasia grade 2


title: CIN1_50 cervical intraepithelial neoplasia grade 1

value: Grade 1


title: CIN1_49 cervical intraepithelial neoplasia grade 1


title: S714C

status: Public on Jan 31 2020

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.1

source_name: Human eosinophilic leukaemia

label_protocol: Standard Illumina labelling protocol

growth_protocol: The human eosinophilic leukaemia cells, EOL-1 were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, and 1× antibiotic-antimycotic (Gibco by Life Technologies) in a humidified chamber with 5% CO2 atmosphere at 37°C

extract_protocol: Total DNA was isolated by standard procedures

treatment_protocol: Cultured EOL-1 cells were infected with lentivirus in the presence of 8 µg/ml polybrene (Sigma) and cultured for 72 hours. The infected cells were selected with 2 µg/mL puromycin for 2-weeks to obtain stable clones. DNMT3A WT/mutants expression was checked by immunoblot analysis and stable cells used for DNA extraction for methylation microarray analysis.

tag: tissue

value: Blood

tag: cell type

tag: genotype/variation

value: EOL-1 cells transduced with pCDH-MSCV-puro-DNMT3A-S714C lentivirus vector

tag: diagnosis

value: Human eosinophilic leukaemia


title: CIN1_48 cervical intraepithelial neoplasia grade 1


title: R882C

value: EOL-1 cells transduced with pCDH-MSCV-puro-DNMT3A-R882C lentivirus vector


title: EV

value: EOL-1 cells transduced with pCDH-MSCV-puro lentivirus vector


title: CIN2_10 cervical intraepithelial neoplasia grade 2


title: CIN2_8 cervical intraepithelial neoplasia grade 2


title: CIN1_45 cervical intraepithelial neoplasia grade 1


title: CIN1_47 cervical intraepithelial neoplasia grade 1


title: CIN1_43 cervical intraepithelial neoplasia grade 1


title: CIN1_46 cervical intraepithelial neoplasia grade 1


title: CIN2_4 cervical intraepithelial neoplasia grade 2


title: CIN1_42 cervical intraepithelial neoplasia grade 1


title: CIN1_44 cervical intraepithelial neoplasia grade 1


title: CIN1_41 cervical intraepithelial neoplasia grade 1


title: CIN1_40 cervical intraepithelial neoplasia grade 1


title: CIN1_39 cervical intraepithelial neoplasia grade 1


title: CIN1_38 cervical intraepithelial neoplasia grade 1


title: CIN1_36 cervical intraepithelial neoplasia grade 1


title: CIN1_34 cervical intraepithelial neoplasia grade 1


title: CIN1_31 cervical intraepithelial neoplasia grade 1


title: CIN1_37 cervical intraepithelial neoplasia grade 1


title: CIN1_32 cervical intraepithelial neoplasia grade 1


title: DNMT3A-WT

value: EOL-1 cells transduced with pCDH-MSCV-puro-DNMT3A-WT lentivirus vector


title: CIN1_29 cervical intraepithelial neoplasia grade 1


title: CIN1_28 cervical intraepithelial neoplasia grade 1


title: CIN1_27 cervical intraepithelial neoplasia grade 1


title: CIN1_23 cervical intraepithelial neoplasia grade 1


title: CIN1_26 cervical intraepithelial neoplasia grade 1


title: CIN1_25 cervical intraepithelial neoplasia grade 1


title: CIN1_33 cervical intraepithelial neoplasia grade 1


title: CIN1_22 cervical intraepithelial neoplasia grade 1


title: CIN1_24 cervical intraepithelial neoplasia grade 1


title: CIN1_21 cervical intraepithelial neoplasia grade 1


title: CIN1_17 cervical intraepithelial neoplasia grade 1


title: CIN1_18 cervical intraepithelial neoplasia grade 1


title: CIN1_20 cervical intraepithelial neoplasia grade 1


title: CIN1_15 cervical intraepithelial neoplasia grade 1


title: CIN1_16 cervical intraepithelial neoplasia grade 1


title: CIN1_30 cervical intraepithelial neoplasia grade 1


title: CIN1_13 cervical intraepithelial neoplasia grade 1


title: CIN1_19 cervical intraepithelial neoplasia grade 1


title: CIN1_14 cervical intraepithelial neoplasia grade 1


title: CIN1_11 cervical intraepithelial neoplasia grade 1


title: CIN1_12 cervical intraepithelial neoplasia grade 1


title: CIN1_9 cervical intraepithelial neoplasia grade 1


title: CIN1_8 cervical intraepithelial neoplasia grade 1


title: CIN1_5 cervical intraepithelial neoplasia grade 1


title: CIN1_7 cervical intraepithelial neoplasia grade 1


title: CIN1_10 cervical intraepithelial neoplasia grade 1


title: CIN1_2 cervical intraepithelial neoplasia grade 1


title: CIN1_3 cervical intraepithelial neoplasia grade 1


title: CIN1_6 cervical intraepithelial neoplasia grade 1


title: CIN1_4 cervical intraepithelial neoplasia grade 1


title: CIN1_1 cervical intraepithelial neoplasia grade 1


title: Healthy_52

value: Healthy


title: Healthy_50


title: Healthy_49


title: Healthy_51


title: Healthy_54


title: Healthy_48


title: Healthy_47


title: Healthy_44


title: Healthy_45


title: Healthy_46


title: Healthy_43


title: Healthy_40


title: Healthy_38


title: Healthy_41


title: Healthy_37


title: Healthy_39


title: Healthy_34


title: Healthy_36


title: Healthy_53


title: Healthy_33


title: Healthy_29


title: Healthy_31


title: Healthy_32


title: Healthy_28


title: Healthy_42


title: Healthy_30


title: Healthy_25


title: Healthy_24


title: Healthy_35


title: Healthy_26


title: Healthy_23


title: Healthy_22


title: Healthy_21


title: Healthy_27


title: Healthy_20


title: Healthy_17


title: Healthy_16


title: Healthy_15


title: Healthy_12


title: Healthy_6


title: Healthy_13


title: Healthy_4


title: Healthy_11


title: Healthy_8


title: Healthy_19


title: Healthy_9


title: Healthy_10


title: Healthy_2


title: Healthy_5


title: Healthy_14


title: Healthy_7


title: Healthy_1


title: Healthy_18


title: CIN2_24 cervical intraepithelial neoplasia grade 2


title: Healthy_3


title: B79: Grade 3, Stage II, ER+ve

type: RNA

city: Hyderabad

first: Lekha

middle: Dinesh

last: Kumar

state: Andhra Pradesh

address: Uppal road, habshiguda

department: Cancer biology

country: India

institute: Centre for cellular and molecular biology

data_processing:
The microRNA mean cycle threshold values (Ct) were first normalized to their respective endogenous controls (RNA46 and RNU 48) to obtain their - ΔCt values. The mean Δ Ct values (ΔCt) of cancer samples were deducted from the mean ΔCt values of their respective adjacent normals samples to obtain the ΔΔCt values. The fold changes were calculated and analyzed using RealTime StatMiner® Software.
Matrix non-normalized worksheet reports raw Ct values.
Matrix normalized worksheet reports normalized Ct value i.e. ΔCt  (against housekeeping genes).
Fold Change worksheet reports  ΔΔCt values for test/control (i.e., tumour/normal) ratios.

label: FAM

molecule: total RNA

source_name: Grade 3, Stage II, ER+ve

label_protocol: The isolated RNAs were used for reverse transcription (RT) reactions with the help of TaqMan MicroRNA Reverse Transcription Kit followed by Real Time PCR Reactions (ABI 7900 HT) as per illustration provided in kit. A pre -amplification step of cDNA with pre-amp megaplex pool primers was done to significantly enhance the ability to detect highly down regulated miRNAs.

extract_protocol: A portion of the samples stored in RNA later was used for RNA isolation. Total RNAs were isolated by miRvana kit from homogenized samples using automated tissue homogenizer. The quantity of these RNAs were checked using nanodrop, whereas quality were assessed by agarose gel electrophoresis.RNA integrity number (RIN) was determined in Agilent Bioanalyzer (2100) to provide more robust measurement of RNA. The RIN values are algorithm which ranges between 1-10 where 10 indicates total intactness of RNA quality.Those samples >7 was taken for further analysis.

tag: disease state

value: Breast cancer

value: Breast tumor tissue

tag: age

value: 48 years

tag: Stage

value: Stage II


title: B74: Grade 3, Stage II, ER-ve

source_name: Grade 3, Stage II, ER-ve

value: 61 years


title: B35: Grade 3, Stage II, ER+ve

value: 53 years


title: B117: Grade 3, Stage III, ER+ve

source_name: Grade 3, Stage III, ER+ve

value: Female

value: 46 years

value: Stage III


title: B63: Grade 3, Stage III, ER-ve

source_name: Grade 3, Stage III, ER-ve

value: 59 years

value: Grade 3


title: B78: Grade 3, Stage II, ER+ve

value: 57 years


title: B43: Grade 3, Stage II, ER-ve

value: 33 years


title: B23: Grade 3, Stage III, ER-ve

value: 55 years


title: B10: Grade 3, Stage III, ER+ve


title: B146N: Grade 3 Adjacent Normal

source_name: Grade 3 Adjacent Normal

value: Breast Normal tissue

value: 49 years


title: B80N: Grade 3 Adjacent Normal


title: B29N: Grade 3 Adjacent Normal

value: 41 years


title: B72N: Grade 3 Adjacent Normal

value: Breast cancer

value: 64 years


title: CIN2_12 cervical intraepithelial neoplasia grade 2

value: Grade 2


title: B38: Grade 3, Stage I, ER-ve

source_name: Grade 3, Stage I, ER-ve

value: Breast tumor tissue

value: 40 years

value: Stage I


title: B80: Grade 3, Stage III, ER-ve

value: Female

value: 48 years


title: B69N: Grade 3 Adjacent Normal

value: 39 years


title: B66: Grade 3, Stage III, ER+ve

value: 53 years

value: Stage III


title: B69: Grade 3, Stage II, ER-ve

value: Stage II

value: Grade 3


title: B123: Grade 3, Stage II, ER+ve

value: 35 years


title: CIN1_35 cervical intraepithelial neoplasia grade 1

value: Grade 1


title: B33: Grade 3, Stage I, ER-ve

value: 65 years


title: B29: Grade 3, Stage I, ER-ve

value: 41 years


title: B15: Grade 3, Stage I, ER-ve

value: Breast cancer

value: 51 years


title: B53: Grade 3, Stage I, ER+ve

source_name: Grade 3, Stage I, ER+ve

value: 70 years


title: B14: Grade 3, Stage I, ER-ve

value: Breast tumor tissue

value: 47 years


title: B8: Grade 3, Stage I, ER-ve

value: 40 years

value: Stage I


title: B83N: Grade 2 Adjacent Normal

source_name: Grade 2 Adjacent Normal

value: Breast Normal tissue

value: Female

value: 36 years


title: B91N: Grade 2 Adjacent Normal

value: 50 years


title: B116N: Grade 2 Adjacent Normal

value: 60 years


title: B30: Grade 3, Stage I, ER+ve

value: Grade 3


title: B144: Grade 2, Stage III, ER-ve

source_name: Grade 2, Stage III, ER-ve

value: Stage III

value: Grade 2


title: B24: Grade 2, Stage III, ER+ve

source_name: Grade 2, Stage III, ER+ve

value: 55 years


title: B106: Grade 2, Stage II

source_name: Grade 2, Stage II

value: 67 years

value: Stage II


title: B55: Grade 2, Stage II, ER-ve

source_name: Grade 2, Stage II, ER-ve

value: Breast cancer

value: 45 years


title: B56: Grade 2, Stage III, ER+ve

value: Breast tumor tissue

value: 66 years


title: B91: Grade 2, Stage II, ER+ve

source_name: Grade 2, Stage II, ER+ve


title: B83: Grade 2, Stage II, ER+ve


title: B142: Grade 2, Stage III, ER+ve


title: B67: Grade 2, Stage III, ER+ve

value: 56 years


title: B13: Grade 3, Stage III, ER+ve

value: 42 years


title: B71: Grade 2, Stage II, ER+ve


title: B76: Grade 2, Stage I, ER+ve

source_name: Grade 2, Stage I, ER+ve

value: 52 years

value: Stage I


title: B90: Grade 2, Stage I, ER+ve

value: Female

value: 39 years


title: B59: Grade 2, Stage I, ER+ve

value: 65 years


title: B12: Grade 2, Stage II, ER+ve

value: 60 years


title: B96: Grade 2, Stage I, ER+ve


title: B75: Grade 2, Stage II, ER+ve

value: 57 years


title: H4 S47D mutant no stress rep3

type: SRA

city: Barcelona

first: Francesc

last: Posas

address: Carrar Baldiri Reixac 10

country: Spain

institute: Cell Signaling Group, IRB Barcelona

library_source: transcriptomic

data_processing:
Raw sequencing reads were mapped to the sacCer3 genome using TopHat2 v2.1.0
Quantification was performed with featureCounts v1.5.1 using the Ensembl R64-1-1 annotation.
Differential expression testing was performed using DESeq2 v1.14.1
Genome_build: sacCer3
Supplementary_files_format_and_content: DESeq2_raw_counts.tsv contains raw read counts obtained via featureCounts after alignment. Each column represents one sample in lexicographical order.

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: Wild-type and H4-T30(A/D) mutant strains were grown to log-phase on YPD medium at 30ºC (no stress) and then subjected to heat stress (10 min 39°C). Wild-type and H4-S47D mutant strains were grown to log-phase on YPD medium at 30ºC (no stress) and then subjected to osmotic stress (15 min 0,4M NaCl).

extract_protocol:
Total RNA was extracted with standard hot-phenol protocol.
Libraries were prepared using the TruSeq stranded mRNA sample preparation kit v2 (Illumina) according to the manufacturer's protocol, starting with 1 μg of total RNA for poly(A)-mRNA selection. Libraries were first analyzed on an Agilent Bioanalyzer using a DNA 1000 chip to estimate the quantity and check the size distribution. Libraries were then quantified by qPCR using the KAPA library quantification kit (KapaBiosystems) prior to sequencing with 50 bp single-end reads on Illumina's HiSeq 2500 with v4 sequencing chemistry.

treatment_protocol: Untreated (no stress) / osmotic stress (15 min 0.4M NaCl) / heat stress (10 min 39°C)

tag: genotype

value: BY4741 (MATa his3{delta}200 leu2{delta}0 lys2{delta}0 trp1{delta}63 ura3{delta}0 met15{delta}0 can1::MFA1pr-HIS3 hht1-hhf1::NatMX4 hht2-hhf2::[HHTS-HHFS(S47D)]-URA3)

tag: stress

value: no stress

tag: replicate


title: H4 S47D mutant 15min 0.4M NaCl 30ºC rep3

value: 15min 0.4M NaCl 30ºC


title: B116: Grade 2, Stage I, ER+ve

value: Grade 2


title: H4 S47D mutant no stress rep1


title: B58: Grade 2, Stage II, ER+ve

value: Breast cancer

value: 54 years

value: Stage II


title: H4 T30D mutant 10min 39ºC rep2

value: BY4741 (MATa his3{delta}200 leu2{delta}0 lys2{delta}0 trp1{delta}63 ura3{delta}0 met15{delta}0 can1::MFA1pr-HIS3 hht1-hhf1::NatMX4 hht2-hhf2::[HHTS-HHFS(T30D)]-URA3)

value: 10min 39ºC


title: H4 S47D mutant no stress rep2


title: H4 T30D mutant 10min 39ºC rep3


title: B41N: Grade 2 Adjacent Normal

value: Breast Normal tissue

value: 34 years


title: H4 S47D mutant 15min 0.4M NaCl 30ºC rep2


title: H4 T30D mutant no stress rep3


title: H4 T30D mutant no stress rep2


title: H4 T30D mutant no stress rep1


title: H4 T30A mutant 10min 39ºC rep2

value: BY4741 (MATa his3{delta}200 leu2{delta}0 lys2{delta}0 trp1{delta}63 ura3{delta}0 met15{delta}0 can1::MFA1pr-HIS3 hht1-hhf1::NatMX4 hht2-hhf2::[HHTS-HHFS(T30A)]-URA3)


title: H4 T30A mutant no stress rep3


title: H4 T30A mutant 10min 39ºC rep1


title: H4 T30A mutant no stress rep2


title: H4 WT 15min 0.4M NaCl 30ºC rep3

value: BY4741 (MATa his3{delta}200 leu2{delta}0 lys2{delta}0 trp1{delta}63 ura3{delta}0 met15{delta}0 can1::MFA1pr-HIS3 hht1-hhf1::NatMX4 hht2-hhf2::[HHTS-HHFS(WT)]-URA3)


title: H4 WT 15min 0.4M NaCl 30ºC rep2


title: H4 WT 10min 39ºC rep3


title: H4 T30A mutant 10min 39ºC rep3


title: H4 WT 10min 39ºC rep2


title: H4 WT 10min 39ºC rep1


title: H4 T30A mutant no stress rep1


title: Zhr-male4

city: Umea

first: Jan

last: Larsson

address: Umea University

department: Molecular Biology

country: Sweden

institute: Umea University

description:
featureCounts.pB.GENES
featureCounts.1688blocks
featureCounts.pB.REPEATS

data_processing:
Each library had an exclusive barcode sequence as ligated adaptor and the libraries were pooled to make multiplex libraries. The samples were sequenced on HiSeq 2500 High Output mode (2x125bp Illumina). Sequencing was performed by the SNP&SEQ Technology Platform in Uppsala.
Adapter removal and quality trimming of raw fastq reads for all samples was done using Trimmomatic, version 0.36, with the following settings “ILLUMINACLIP: TruSeq3-PE.fa:2:30:!0 LEADING:3 TRAILING:3 SLIDINGWINDO:4:15 MINLEN:36”.
Ribosomal RNA was filtered using SortMeRNA, version 2.1b, using default settings and provided rRNA databases.
Trimmed and filtered reads were aligned to Drosophila melanogaster (D. mel.) reference genome version 6.13 using the STAR, version 2.5.4b, aligner with default settings.
Read counts was obtained by FeatureCounts, version 1.6.3. Gene read counts were quantified using D. mel. 6.13 gene annotation file.
All differential expression calculations were made with DESeq2 and using mutant vs. wild type comparisons.
Genome_build: Dmel 6.13
Supplementary_files_format_and_content: tab-delimited text files include read values for featured transcripts per each sample

organism: Drosophila melanogaster

source_name: Whole organism (10 individual adult flies)

growth_protocol: Flies were cultivated and crossed at 25˚C in vials containing potato mash-yeast-agar. Oregon R was used as wild type strain.

extract_protocol:
The adult flies isolated at each time point were placed in 1.5 ml RNAse free Eppendorf tube and flash frozen in liquid nitrogen. Immediately, 0.1 ml Tri Reagent (Ambion) was added per each individual fly in each tube. The samples were stored at -80° C. Total RNA was purified with Direct-zol RNA MicroPrep kit. The extracted RNAs were quality controlled and quantified using a Fragment Analyzer instrument (Advanced Analytical) and reagents (DNF-471-22 - SS Total RNA 15nt). The RNA samples with a RIN value > 9 were chosen to make cDNA libraries.
cDNA libraries were generated using the NuGene system (Ovation RNA-Seq System 1-16 for Drosophila- PART NOS. 0350). The generated libraries were quality controlled and quantified using a Fragment Analyzer instrument and reagents (DNF-920-22 - DNA 75-15000bp).

value: Male


title: p53_KO-2_TNF_8H: p53-/- MEFs TNF 8hr, replicate 2

city: Los Angeles

first: Kim

last: Ngo

state: CA

address: 611 Charles E Young Dr. East

department: MIMG

country: USA

institute: University of California, Los Angeles

data_processing:
Illumina HiSeq 2000 reads were demultiplexed and trimmed to filter out low-complexity reads, polyA tails, N runs
High-quality reads were then imported into STAR and mapped to Gencode mouse mm9 genome (genome version 37) and featureCounts for alignment into aligned raw count files.
Raw count files were imported into R program using DESeq and annotated to genes based on RefSeq annotation. Induced genes were defined by their normalized counts with FDR >0.001 and top 30 percentile of expression over basal with any stimulation.
Genome_build: mm9
Supplementary_files_format_and_content: TXT, raw non-normalized counts

molecule: polyA RNA

organism: Mus musculus

source_name: Primary mouse embryonic fibroblasts (MEFs)

growth_protocol: MEF cells were grown in DMEM medium containing 10% BCS, supplemented with penicillin (100 units/ml), streptomycin (100 ug/ml). All cells were incubated at 37C in 5% CO2 and grown to 80-90% confluence for passaging

extract_protocol:
Total RNA was isolated with the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions. RNA concentrations were quantified using Epoch Spectrophotometer System (Biotek).
1 ug of total RNA was subjected to library synthesis using Illumina TruSeq Stranded mRNA Sample Preparation Kit. 1 ug of total RNA enriched for polyA+ mRNA and reversed transcribed to double-stranded cDNA. The cDNA was end repaired, adenylate, and ligated with Illumina indexes prior to 15 cycles of PCR amplification. Sequencing was performed by the Broad Stem Cell Research Center core facility at the University of California, Los Angeles with paired-end 50 bp sequencing

treatment_protocol: ~80% confluent MEF cells were serum-starved by overnight incubation in Dulbecco’s Modified Eagle’s Medium supplemented with 0.5% bovine calf serum (BCS), 1% penicillin-streptomycin and 1% L-Glutamine prior to stimulation. IL-1b (10 ng/ml), TNF (10 ng/ml), and LPS (100 ng/ml) were prepared and added to cell culture medium for stimulation

tag: developmental stage

value: embryo

tag: strain

tag: agent

value: TNF


title: T24 SP cells without M.SssI treatment

first: Gangning

last: Liang

address: 1441 Biggy street

department: Urology

institute: USC Keck school of medicine

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Illumina iScan technology using standard recommended scanner setting

data_processing: R package minfi for data processing and background normalization

source_name: T24 SP cells without M.SssI treatment

label_protocol: Standard Illumina Protocol

growth_protocol: RPMI 1640 medium with 10% FBS 37 degree

extract_protocol: Nuclei were purified and incubated with/without M.SssI enzyme with SAM supplied for 15 min at 37 degree. DNA were extacted with phenol/chloroform

tag: cell line

value: bladder cancer

tag: cell subpopulation

value: Side population (SP)

tag: treatment

value: No treatment


title: T24 NSP cells with M.SssI treatment

source_name: T24 NSP cells with M.SssI treatment

value: Non-side population (NSP)


title: J82 SP cells without M.SssI treatment

description: J82 SP-NE

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

source_name: J82 SP cells without M.SssI treatment

growth_protocol: DMEM medium with 10% FBS 37 degree

extract_protocol: Nuclei were purified and incubated with/without M.SssI enzyme with SAM supplied for 15 min at 37 degree. DNA were extracted with phenol/chloroform

value: Human bladder cancer cell line J82


title: Zhr-male2

tag: gender


title: J82 NSP cells without M.SssI treatment

description: J82 NSP-NE

source_name: J82 NSP cells without M.SssI treatment


title: Zhr-male1


title: p53_KO-2_TNF_0.5H: p53-/- MEFs TNF 0.5hr, replicate 2

tag: tissue

value: Primary mouse embryonic fibroblasts (MEFs)


title: Zhr-female4

value: Female


title: H4 T30D mutant 10min 39ºC rep1


title: p53_KO-2_TNF_3H: p53-/- MEFs TNF 3hr, replicate 2


title: p53_KO-2_TNF_1H: p53-/- MEFs TNF 1hr, replicate 2


title: Zhr-male3


title: p53_KO-2_TNF_0H: p53-/- MEFs TNF 0hr, replicate 2


title: H4 S47D mutant 15min 0.4M NaCl 30ºC rep1

value: BY4741 (MATa his3{delta}200 leu2{delta}0 lys2{delta}0 trp1{delta}63 ura3{delta}0 met15{delta}0 can1::MFA1pr-HIS3 hht1-hhf1::NatMX4 hht2-hhf2::[HHTS-HHFS(S47D)]-URA3)

value: 15min 0.4M NaCl 30ºC


title: H4 WT no stress rep2

value: no stress


title: p53_KO-2_LPS_8H: p53-/- MEFs LPS 8hr, replicate 2

value: LPS


title: p53_KO-2_LPS_3H: p53-/- MEFs LPS 3hr, replicate 2


title: Zhr-female2


title: p53_KO-2_LPS_1H: p53-/- MEFs LPS 1hr, replicate 2


title: Zhr-female1


title: T24 SP cells with M.SssI treatment

source_name: T24 SP cells with M.SssI treatment

tag: cell type


title: p53_KO-2_LPS_0.5H: p53-/- MEFs LPS 0.5hr, replicate 2


title: p53_KO-2_LPS_0H: p53-/- MEFs LPS 0hr, replicate 2


title: J82 SP cells with M.SssI treatment

description: J82 SP-SssI

source_name: J82 SP cells with M.SssI treatment


title: PoX-male3


title: J82 NSP cells with M.SssI treatment

description: J82 NSP-SssI

source_name: J82 NSP cells with M.SssI treatment


title: T24 NSP cells without M.SssI treatment

source_name: T24 NSP cells without M.SssI treatment


title: p53_KO-2_IL1b_8H: p53-/- MEFs IL-1b 8hr, replicate 21


title: p53_KO-2_IL1b_3H: p53-/- MEFs IL-1b 3hr, replicate 2


title: PoX-male1


title: PoX-male2


title: PoX-female2


title: PoX-female4


title: p53_KO-2_IL1b_0H: p53-/- MEFs IL-1b 0hr, replicate 2


title: PoX-female3


title: p53_KO-2_IL1b_0.5H: p53-/- MEFs IL-1b 0.5hr, replicate 2


title: POF-male4


title: p53_KO-1_TNF_8H: p53-/- MEFs TNF 8hr, replicate 1


title: PoX-female1


title: PoX-male4


title: H4 WT 15min 0.4M NaCl 30ºC rep1


title: POF-male3


title: p53_KO-1_TNF_0.5H: p53-/- MEFs TNF 0.5hr, replicate 1


title: p53_KO-1_TNF_1H: p53-/- MEFs TNF 1hr, replicate 1


title: p53_KO-1_TNF_3H: p53-/- MEFs TNF 3hr, replicate 1


title: p53_KO-1_TNF_0H: p53-/- MEFs TNF 0hr, replicate 1


title: POF-male1


title: p53_KO-1_LPS_3H: p53-/- MEFs LPS 3hr, replicate 1


title: POF-female3


title: POF-female4


title: p53_KO-1_LPS_8H: p53-/- MEFs LPS 8hr, replicate 1


title: p53_KO-1_LPS_1H: p53-/- MEFs LPS 1hr, replicate 1


title: B106N: Grade 2 Adjacent Normal

source_name: Grade 2 Adjacent Normal

value: Breast cancer

value: Breast Normal tissue

value: 67 years

tag: grade


title: p53_KO-2_IL1b_1H: p53-/- MEFs IL-1b 1hr, replicate 2


title: POF-female1


title: OR-male4

value: Oregon-R

value: Male


title: p53_KO-1_LPS_0.5H: p53-/- MEFs LPS 0.5hr, replicate 1

value: embryo


title: p53_KO-1_LPS_0H: p53-/- MEFs LPS 0hr, replicate 1


title: p53_KO-1_IL1b_1H: p53-/- MEFs IL-1b 1hr, replicate 1


title: Zhr-female3


title: p53_KO-1_IL1b_3H: p53-/- MEFs IL-1b 3hr, replicate 1


title: OR-male1


title: POF-male2


title: p53_KO-1_IL1b_0.5H: p53-/- MEFs IL-1b 0.5hr, replicate 1


title: p53_KO-1_IL1b_8H: p53-/- MEFs IL-1b 8hr, replicate 1


title: OR-male2


title: OR-female3


title: OR-female2


title: WT_TNF_8H: WT MEFs TNF 8hr

value: WT

value: TNF


title: OR-female4


title: p53_KO-1_IL1b_0H: p53-/- MEFs IL-1b 0hr, replicate 1


title: WT_TNF_3H: WT MEFs TNF 3hr


title: WT_TNF_1H: WT MEFs TNF 1hr


title: OR-female1


title: POF-female2


title: WT_TNF_0.5H: WT MEFs TNF 0.5hr


title: WT_TNF_0H: WT MEFs TNF 0hr


title: stt-3_PA14_1st

city: Daejeon

first: Seung-Jae

middle: V

address: 291 Daehak-ro

department: Biological Sciences

country: South Korea

institute: KAIST

data_processing:
Sequencing reads were aligned to the C. elegans trascriptome and genome WBcel235 (ce11) by using HISAT2 (v.2.0.5). Aligned transcripts were assembled and quantified by using StringTie (v.1.3.3b) and Ballgown (v.2.0.0).
The batch effects of samples were removed by upper-quartile normalization followed by RUVSeq with control genes (v1.16.1).
Genome_build: WBcel235 (ce11)
Supplementary_files_format_and_content: txt files with read counts were generated by using StringTie (v.1.3.3b) and Ballgown (v.2.0.0), then RUVseq (v1.61.1).

organism: Caenorhabditis elegans

source_name: Whole body

growth_protocol: Worms were grown on NGM plates as previously described in 'Maintenance of C. elegans (Stiernagle T, WormBook, 2006)'.

extract_protocol:
Total RNA in the animals was isolated by using RNAiso plus (Takara, Seta, Kyoto, Japan).
Libraries were constructed with TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001 or RS-122-2002) by Macrogen Inc. (Seoul, South Korea) following the manufacture’s instruction.

treatment_protocol: Wild-type N2 worms fed with control RNAi, pmk-1 RNAi or OST component RNAi bacteria were grown to L4 stage and then transferred to corresponding RNAi bacteria- or PA14-seeded plates after washing with M9 buffer 3-4 times. After 12 hours, worms were harvested by washing with M9 buffer 3-4 times to remove residual bacteria.

value: wild type

tag: devlopment stage

value: adult

tag: RNAi

value: stt-3 RNAi

tag: infection


title: stt-3_PA14_3rd


title: WT_LPS_8H: WT MEFs LPS 8hr

value: Primary mouse embryonic fibroblasts (MEFs)


title: stt-3_PA14_2nd


title: OR-male3

tag: age


title: WT_LPS_3H: WT MEFs LPS 3hr

tag: genotype


title: WT_LPS_1H: WT MEFs LPS 1hr


title: stt-3_ctrl_2nd


title: WT_LPS_0.5H: WT MEFs LPS 0.5hr


title: H4 WT no stress rep3

value: BY4741 (MATa his3{delta}200 leu2{delta}0 lys2{delta}0 trp1{delta}63 ura3{delta}0 met15{delta}0 can1::MFA1pr-HIS3 hht1-hhf1::NatMX4 hht2-hhf2::[HHTS-HHFS(WT)]-URA3)

tag: stress


title: stt-3_ctrl_1st


title: WT_LPS_0H: WT MEFs LPS 0hr


title: ctrl_PA14_2nd

value: control RNAi


title: ctrl_PA14_3rd


title: WT_IL1b_8H: WT MEFs IL-1b 8hr


title: ctrl_PA14_1st


title: WT_IL1b_1H: WT MEFs IL-1b 1hr


title: WT_IL1b_3H: WT MEFs IL-1b 3hr


title: ctrl_ctrl_3rd


title: ctrl_ctrl_1st


title: WT_IL1b_0.5H: WT MEFs IL-1b 0.5hr


title: WT_IL1b_0H: WT MEFs IL-1b 0hr


title: RelA-TA2_CI_S467A-dTA1  MEFs TNF 8hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-CI-S467A-dTA1_TNF-8H

data_processing:
Illumina HiSeq 2000 reads were demultiplexed and trimmed (cutadapt 1.9.1) to filter out low-complexity reads, polyA tails, N runs
High-quality reads were then imported into STAR aligner to Gencode mouse mm10 genome
Read quality was checked for each sample using Qualimap
Filtered bam files were used to generate counts file using featureCounts v1.5.0
counts were converted to RPKM and annotated to genes based on RefSeq annotation using DESeq2. RPKM values were log-transformed with an offset value of 1.0. Induced genes were defined with >= 2-fold expression over basal with any stimulation and FDR >0.01.
Genome_build: mm10
Supplementary_files_format_and_content: TXT

growth_protocol: p53-/-crel-/-rela-/- MEF cells were grown in DMEM medium containing 10% BCS, supplemented with penicillin (100 units/ml), streptomycin (100 ug/ml). All cells were incubated at 37C in 5% CO2 and grown to 80-90% confluence for passaging.

extract_protocol:
Total RNA was isolated with the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions. RNA concentrations were quantified using Epoch Spectrophotometer System (Biotek).
1 ug of total RNA was subjected to library synthesis using KAPA Stranded mRNA-Seq Kit. 1 ug of total RNA enriched for polyA+ mRNA and reversed transcribed to double-stranded cDNA. The cDNA was end repaired, adenylate, and ligated with Illumina indexes prior to 12 cycles of PCR amplification. Sequencing was performed by the Broad Stem Cell Research Center core facility at the University of California, Los Angeles with single-end 50 bp sequencing

treatment_protocol: ~80% confluent p53-/-crel-/-rela-/-MEF cells were serum-starved by overnight incubation in Dulbecco’s Modified Eagle’s Medium supplemented with 0.5% bovine calf serum (BCS), 1% penicillin-streptomycin and 1% L-Glutamine prior to stimulation. TNF (10 ng/ml) were prepared and added to cell culture medium for stimulation

tag: plasmid vector

value: pBABE-puro

tag: time


title: RelA-TA2_CI_S467A-dTA1  MEFs TNF 1hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-CI-S467A-dTA1_TNF-1H

tag: developmental stage

tag: strain


title: RelA-TA2_CI_S467A-dTA1  MEFs TNF 3hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-CI-S467A-dTA1_TNF-3H

tag: agent


title: RelA-TA2_CI_S467A-dTA1  MEFs TNF 0.5hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-CI-S467A-dTA1_TNF-0.5H


title: stt-3_ctrl_3rd


title: RelA-TA2_CI_S467A-dTA1  MEFs TNF 0hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-CI-S467A-dTA1_TNF-0H


title: Ste12_K150I_variant rep 2

city: seattle

first: wei

last: zhou

state: wa

address: 4747 30th ave NE

department: genome sciences

institute: University of Washington

description:
Calling Card experiment
peak_count.txt

library_source: genomic

data_processing:
Library strategy: Calling card-seq
For RNA-seq processing, base calls were converted to fastq format and demultiplexed using Illumina’s bcl2fastq/ 2.16.0.10 tolerating one mismatched base in barcodes (edit distance (ED) < 2). RT barcode (10bp) and UMI (8bp) sequence in Read1 is attached to the read name of Read2. Reads not matching to the expected RT barcodes were discarded. Read2 were then adaptor clipped using trim_galore/0.4.1 with default settings.  Trimmed reads were mapped to the yeast reference genome (R64), using STAR/v 2.5.2b (38) with default settings and gene annotations (R64-1-1.87). Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, and read 2 end-coordinate. Mapped reads were split into constituent cellular indices by further demultiplexing reads using the RT index (ED < 2, including insertions and deletions). To generate digital expression matrices, we calculated the number of strand-specific UMIs mapping to the exonic and intronic regions of each gene, for each cell; generally, fewer than 3% of total UMIs strand-specifically mapped to multiple genes. For multi-mapped reads, reads were assigned to the closest gene, except in cases where another intersected gene fell within 100 bp to the end of the closest gene, in which case the read was discarded.
For calling-card processing, base calls were converted to fastq format and demultiplexed using Illumina’s bcl2fastq/ 2.16.0.10 tolerating one mismatched base in barcodes (edit distance (ED) < 2). In read1, the first segment is the universal primer sequence: CGTCAATTTTACGCAGACTATCTTTCTAGGG followed by the flanking genome sequence of 39 bp. The first 8 bp of read2 is the UMI sequence used to identify unique insertion events. UMI (8bp) sequence in Read2 is attached to the read name of Read1. Reads not matching to the expected universal primer sequence were discarded. Read2 were then adaptor clipped using trim_galore/0.4.1 with default settings.  Trimmed reads were mapped to the yeast reference genome (R64), using STAR/v 2.5.2b (38) with default settings . Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), and read end-coordinate. Then we quantified independent PiggyBac insertions based on the UMIs detected in each sample. Finally, we called significant PiggyBac insertion peaks by MACS2, a peak-calling algorithm (Zhang et al. 2008).
Genome_build: R64
Supplementary_files_format_and_content: Processed data files are in txt format including a variant annotation file, gene (for RNA-seq) or peak (for Calling card-seq) annotation file, and a gene count sparse matrix (for RNA-seq) or peak count sparse matrix (for Calling card-seq).

source_name: Saccharomyces cerevisiae

growth_protocol: Paired donor plasmid and helper plasmid were transformed into yeast (BY4705 MATα) by high-efficiency lithium acetate transformation (Gietz et al. 2002). After transformation, cells were collected and put on the induction plates with galactose. Cells were induced for 5 days to express the Ste12-PBase. Cells were then 7 collected, diluted back to OD600=0.45, and cultured in rich medium for 6 hours recovery (to OD600=~1.6). Cells were put onto selection plates with 5-FOA and G418 at varying dilutions and it takes around 2-3 days.

extract_protocol:
Cells were collected from selection plates and genomic DNA was extracted from each sample using the Smash and Grab method as described (Hoffman and Winston 1987).
Each DNA sample was divided into two 20-μg aliquots and digested by TaqI and RsaI (NEB) individually. Digested products were purified by DNA purification column (Zymo Research) and ligated overnight at 15°C in dilute solution to encourage self-ligation. Self-ligated DNA was purified by DNA purification column (Zymo Research) and used as template in an inverse PCR. Primers that anneal to the PiggyBac donor sequences (primer 316: GATGTCCTAAATGCACAGCGAC and primer 317: GAGGCGTGCTTGTCAATGC) were used to amplify the genomic regions flanking the transposon, and then adaptor sequences that allow the PCR products to be sequenced on Illumina sequencing platforms were added by primer 367 (AATGATACGGCGACCACCGAGATCTACACCTCCATCGAGACACTCTTTCCCTACACGACG CTCTTCCGATCTCGTCAATTTTACGCAGACTATC) and 377 (CAAGCAGAAGACGGCATACGAGATTGCTTGTCAATGCGGTAAG). The PCR products were purified using a DNA purification column (Zymo Research). For each sample, the same amount of PCR product from digestion with each restriction endonuclease was pooled and submitted for Illumina sequencing.

treatment_protocol: helper plasmids with six different Ste12 variant were transformed into yeast strain seperatedly

tag: yeast strain

value: BY4705 strain

tag: expression method

value: plasmid overexpression

tag: group setting

tag: replicate

value: replicate 2


title: Ste12_K152L_variant rep 1

description:
Calling Card experiment
peak_count.txt

value: replicate 1


title: Ste12_K150I_variant rep 1

description:
Calling Card experiment
peak_count.txt


title: Ste12_A160P_variant rep 2

description:
Calling Card experiment
peak_count.txt


title: Ste12_A160P_variant rep 1

description:
Calling Card experiment
peak_count.txt


title: RelA-TA2_CI_S467A  MEFs TNF 8hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-CI-S467A_TNF-8H

tag: cell type

tag: treatment


title: ctrl_ctrl_2nd

tag: devlopment stage


title: Ste12_S158H_variant rep 1

description:
Calling Card experiment
peak_count.txt


title: Ste12_S158H_variant rep 2

description:
Calling Card experiment
peak_count.txt


title: RelA-TA2_CI_S467A  MEFs TNF 1hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-CI-S467A_TNF-1H


title: Ste12_K150A_variant rep 2

description:
Calling Card experiment
peak_count.txt


title: RelA-TA2_CI_S467A  MEFs TNF 0hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-CI-S467A_TNF-0H


title: Ste12_K152L_variant rep 2

description:
Calling Card experiment
peak_count.txt


title: RelA-TA2_S467A  MEFs TNF 8hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-S467A_TNF-8H


title: RelA-TA2_S467A  MEFs TNF 3hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-S467A_TNF-3H


title: RelA-TA2_CI_S467A  MEFs TNF 0.5hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-CI-S467A_TNF-0.5H


title: Ste12_K146D_variant rep 1

description:
Calling Card experiment
peak_count.txt


title: Ste12_K146D_variant rep 2

description:
Calling Card experiment
peak_count.txt


title: Ste12_K150A_variant rep 1

description:
Calling Card experiment
peak_count.txt


title: Ste12_WT rep 2

description:
Calling Card experiment
peak_count.txt


title: RelA-TA2_S467A  MEFs TNF 1hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-S467A_TNF-1H


title: Ste12_WT rep 1

description:
Calling Card experiment
peak_count.txt


title: RelA-TA2_S467A  MEFs TNF 0hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-S467A_TNF-0H


title: RelA-TA2_S467A  MEFs TNF 0.5hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-S467A_TNF-0.5H


title: RelA-dTA1  MEFs TNF 8hr, replicate 2

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-dTA1_2-TNF-8H


title: control_transposase_only rep 2

description:
Calling Card experiment
peak_count.txt


title: RelA-dTA1  MEFs TNF 3hr, replicate 2

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-dTA1_2-TNF-3H


title: RelA-dTA1  MEFs TNF 1hr, replicate 2

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-dTA1_2-TNF-1H


title: RelA-dTA1  MEFs TNF 0.5hr, replicate 2

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-dTA1_2-TNF-0.5H


title: control_transposase_only rep 1

description:
Calling Card experiment
peak_count.txt


title: RelA-TA2_CI_S467A  MEFs TNF 3hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-CI-S467A_TNF-3H


title: RelA-dTA1  MEFs TNF 0hr, replicate 2

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-dTA1_2-TNF-0H


title: RelA-dTAD  MEFs TNF 8hr, replicate 2

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-dTAD_2-TNF-8H

value: RelA-dTAD


title: H4 WT no stress rep1

value: no stress


title: RelA-dTAD  MEFs TNF 3hr, replicate 2

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-dTAD_2-TNF-3H


title: RelA-dTAD  MEFs TNF 1hr, replicate 2

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-dTAD_2-TNF-1H


title: RelA-dTAD  MEFs TNF 0hr, replicate 2

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-dTAD_2-TNF-0H


title: RelA-TA2_CI-dTA1  MEFs TNF 8hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-CI-dTA1_TNF-8H


title: RelA-dTAD  MEFs TNF 0.5hr, replicate 2

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-dTAD_2-TNF-0.5H


title: RelA-TA2_CI  MEFs TNF 3hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-CI_TNF-3H


title: RelA-TA2_CI  MEFs TNF 1hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-CI_TNF-1H


title: RelA-TA2_CI-dTA1  MEFs TNF 0.5hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-CI-dTA1_TNF-0.5H


title: RelA-TA2_CI-dTA1  MEFs TNF 1hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-CI-dTA1_TNF-1H


title: RelA-TA2_CI-dTA1  MEFs TNF 0hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-CI-dTA1_TNF-0H


title: RelA-WT  MEFs TNF 1hr, replicate 2

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-WT_2-TNF-1H

value: RelA-WT


title: RelA-WT  MEFs TNF 8hr, replicate 2

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-WT_2-TNF-8H

value: embryo


title: RelA-WT  MEFs TNF 0.5hr, replicate 2

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-WT_2-TNF-0.5H


title: Empty Vector (EV)  MEFs TNF 8hr, replicate 2

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
EV_2-TNF-8H

value: Empty Vector (EV)


title: RelA-TA2_CI  MEFs TNF 8hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-CI_TNF-8H

value: TNF


title: Empty Vector (EV)  MEFs TNF 3hr, replicate 2

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
EV_2-TNF-3H


title: RelA-dTA1  MEFs TNF 8hr, replicate 1

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-dTA1_1-TNF-8H


title: RelA-dTA1  MEFs TNF 3hr, replicate 1

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-dTA1_1-TNF-3H


title: Empty Vector (EV)  MEFs TNF 1hr, replicate 2

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
EV_2-TNF-1H


title: RelA-dTA1  MEFs TNF 1hr, replicate 1

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-dTA1_1-TNF-1H


title: Empty Vector (EV)  MEFs TNF 0hr, replicate 2

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
EV_2-TNF-0H


title: RelA-TA2_CI  MEFs TNF 0hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-CI_TNF-0H


title: RelA-TA2_CI  MEFs TNF 0.5hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-CI_TNF-0.5H


title: Empty Vector (EV)  MEFs TNF 0.5hr, replicate 2

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
EV_2-TNF-0.5H


title: RelA-dTAD  MEFs TNF 8hr, replicate 1

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-dTAD_1-TNF-8H


title: RelA-dTAD  MEFs TNF 1hr, replicate 1

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-dTAD_1-TNF-1H


title: RelA-dTA1  MEFs TNF 0hr, replicate 1

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-dTA1_1-TNF-0H


title: RelA-dTA1  MEFs TNF 0.5hr, replicate 1

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-dTA1_1-TNF-0.5H


title: RelA-dTAD  MEFs TNF 0hr, replicate 1

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-dTAD_1-TNF-0H


title: RelA-dTAD  MEFs TNF 0.5hr, replicate 1

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-dTAD_1-TNF-0.5H


title: RelA-dCterm  MEFs TNF 8hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-dCterm_TNF-8H

value: RelA-dCterm


title: RelA-dCterm  MEFs TNF 3hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-dCterm_TNF-3H


title: RelA-dCterm  MEFs TNF 1hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-dCterm_TNF-1H


title: RelA-dCterm  MEFs TNF 0.5hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-dCterm_TNF-0.5H


title: RelA-WT  MEFs TNF 0hr, replicate 2

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-WT_2-TNF-0H


title: RelA-dCterm  MEFs TNF 0hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-dCterm_TNF-0H


title: RelA-WT  MEFs TNF 3hr, replicate 2

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-WT_2-TNF-3H


title: RelA-DB  MEFs TNF 8hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-DB_TNF-8H

value: RelA-DB


title: RelA-DB  MEFs TNF 3hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-DB_TNF-3H


title: RelA-DB  MEFs TNF 0.5hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-DB_TNF-0.5H


title: RelA-DB  MEFs TNF 1hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-DB_TNF-1H


title: RelA-DB  MEFs TNF 0hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-DB_TNF-0H


title: RelA-TA2_CI-dTA1  MEFs TNF 3hr

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set2.txt
RelA-TA2-CI-dTA1_TNF-3H


title: RelA-WT  MEFs TNF 3hr, replicate 1

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-WT_1-TNF-3H


title: RelA-WT  MEFs TNF 1hr, replicate 1

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-WT_1-TNF-1H


title: RelA-dTAD  MEFs TNF 3hr, replicate 1

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-dTAD_1-TNF-3H


title: RelA-WT  MEFs TNF 0.5hr, replicate 1

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-WT_1-TNF-0.5H


title: RelA-WT  MEFs TNF 0hr, replicate 1

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-WT_1-TNF-0H


title: HD72: 30 Cerebellar Grey Matter

city: Moscow

first: Pavel

last: Mazin

address: Skolkovo Innovation Center, Building 3

department: Biomed

country: Russia

institute: Skolkovo Institute of Science and Technology

data_processing:
Read trimming: trimmomatic-0.36 PE -phred33 ILLUMINACLIP:all.fa:2:30:10:2:true SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:20
Read alignment: hisat2 --no-softclip --max-intronlen 1000000 -k 20 –no-unal -q
abundance (TPM) estimation: stringtie -e -A -G -b; TPM outputed by -A option was used as expression estimates and provided in processed data files
Genome_build: Ensemble genomes and annotation were used for all species: GRCh38.91, Pan_tro_3.0.91, panpan1.1.91, Mmul_8.0.1
Supplementary_files_format_and_content: csv files with TPM for all samples

source_name: 30 Cerebellar Grey Matter

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, California).
Sequencing libraries were prepared with TruSeq RNA Sample Preparation Kit (Illumina) according to manufacturer’s instruction. Briefly, poly-T oligo-attached magnetic beads were used to isolate long polyadenylated RNA from 1 μg of total RNA. After fragmentation, first-strand cDNA was reverse transcribed with random hexamer-primers, followed by second-strand cDNA synthesis, end repair, adenylation of 3′ ends, and ligation of the adapters. Fragments were then enriched by PCR.

tag: individual

value: hd

tag: brain region

value: 30 Cerebellar Grey Matter


title: HB72: 30 Cerebellar Grey Matter

value: hb


title: HA71: 28 Cerebellar White Matter

source_name: 28 Cerebellar White Matter

value: ha

value: 28 Cerebellar White Matter


title: HA74: 13 Prefrontal (BA10)

source_name: 13 Prefrontal (BA10)

value: 13 Prefrontal (BA10)


title: HB74: 13 Prefrontal (BA10)


title: HD74: 13 Prefrontal (BA10)


title: HB67: 10 2ary Visual (BA18/19)

source_name: 10 2ary Visual (BA18/19)

value: 10 2ary Visual (BA18/19)


title: HA72: 30 Cerebellar Grey Matter


title: HD71: 28 Cerebellar White Matter


title: HB71: 28 Cerebellar White Matter


title: HD67: 10 2ary Visual (BA18/19)


title: HC74: 13 Prefrontal (BA10)

value: hc


title: Empty Vector (EV)  MEFs TNF 3hr, replicate 1

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
EV_1-TNF-3H

value: Primary mouse embryonic fibroblasts (MEFs)

value: pBABE-puro


title: HC72: 30 Cerebellar Grey Matter


title: Empty Vector (EV)  MEFs TNF 8hr, replicate 1

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
EV_1-TNF-8H


title: HA67: 10 2ary Visual (BA18/19)


title: Empty Vector (EV)  MEFs TNF 1hr, replicate 1

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
EV_1-TNF-1H


title: Empty Vector (EV)  MEFs TNF 0.5hr, replicate 1

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
EV_1-TNF-0.5H


title: RelA-WT  MEFs TNF 8hr, replicate 1

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
RelA-WT_1-TNF-8H


title: HC66: 9 1ary Visual (BA17)

source_name: 9  1ary Visual (BA17)

value: 9  1ary Visual (BA17)


title: HB66: 9 1ary Visual (BA17)


title: HA66: 9 1ary Visual (BA17)


title: HC67: 10 2ary Visual (BA18/19)


title: HC71: 28 Cerebellar White Matter


title: HD62: 3 Precuneus (BA7)

source_name: 3  Precuneus (BA7)

value: 3  Precuneus (BA7)


title: HC62: 3 Precuneus (BA7)


title: RelA-TA-KI  MEFs LPS 3hr

description: WT_RelA-TA-KI.MEFs_LPS_polyIC_non-normalized-counts.txt

data_processing:
Illumina HiSeq 2000 reads were demultiplexed and trimmed (cutadapt 1.9.1) to filter out low-complexity reads, polyA tails, N runs
High-quality reads were then imported into STAR aligner to Gencode mouse mm10 genome
Read quality was checked for each sample using Qualimap
Filtered bam files were used to generate counts file using featureCounts v1.4.6
counts were converted to RPKM and annotated to genes based on RefSeq annotation using DESeq2. RPKM values were log-transformed with an offset value of 1.0. Induced genes were defined with >= 2-fold expression over basal with any stimulation and FDR >0.01 (TNF-stimulated data).
Genome_build: mm10
Supplementary_files_format_and_content: TXT

source_name: Primary mouse embryonic fibroblasts (MEFs)

growth_protocol: MEF cells were grown in DMEM medium containing 10% BCS, supplemented with penicillin (100 units/ml), streptomycin (100 ug/ml). All cells were incubated at 37C in 5% CO2 and grown to 80-90% confluence for passaging.

treatment_protocol: ~80% confluent MEF cells were serum-starved by overnight incubation in Dulbecco’s Modified Eagle’s Medium supplemented with 0.5% bovine calf serum (BCS), 1% penicillin-streptomycin and 1% L-Glutamine prior to stimulation. LPS (100 ng/ml), Poly(I:C) (20ug/mL), and TNF (10 ng/ml) were prepared and added to cell culture medium for stimulation

value: embryo

value: RelA-TA-KI homozygous

value: LPS


title: RelA-TA-KI  MEFs LPS 0hr


title: WT  MEFs Poly(I:C) 8hr

value: WT


title: RelA-TA-KI  MEFs Poly(I:C) 1hr


title: HC58: 1 Supramarginal (BA40)

source_name: 1  Supramarginal (BA40)

value: 1  Supramarginal (BA40)


title: HD66: 9 1ary Visual (BA17)

value: hd


title: HB58: 1 Supramarginal (BA40)


title: RelA-TA-KI  MEFs LPS 8hr


title: HA62: 3 Precuneus (BA7)


title: HD56: 25 Corpus Callosum Posterior

source_name: 25 Corpus Callosum Posterior

value: 25 Corpus Callosum Posterior


title: RelA-TA-KI  MEFs LPS 0.5hr


title: RelA-TA-KI  MEFs Poly(I:C) 0.5hr


title: Empty Vector (EV)  MEFs TNF 0hr, replicate 1

description:
recon.RelA.MEFs_TNF_non-normalized-counts_set1.txt
EV_1-TNF-0H

value: Empty Vector (EV)


title: HB62: 3 Precuneus (BA7)

value: hb


title: HD58: 1 Supramarginal (BA40)


title: HA58: 1 Supramarginal (BA40)

value: ha


title: HC56: 25 Corpus Callosum Posterior


title: WT  MEFs Poly(I:C) 1hr


title: WT  MEFs Poly(I:C) 3hr


title: WT  MEFs Poly(I:C) 0.5hr


title: WT  MEFs LPS 3hr


title: WT  MEFs LPS 8hr


title: RelA-TA-KI  MEFs Poly(I:C) 3hr


title: RelA-TA-KI  MEFs Poly(I:C) 8hr


title: HB56: 25 Corpus Callosum Posterior


title: HA56: 25 Corpus Callosum Posterior


title: HD52: 2 2ary Auditory (BA22)

source_name: 2  2ary Auditory (BA22)

value: 2  2ary Auditory (BA22)


title: WT  MEFs LPS 1hr


title: RelA-TA-KI  MEFs LPS 1hr


title: HA50: 21 Hippocampus

source_name: 21 Hippocampus

value: 21 Hippocampus


title: HC50: 21 Hippocampus

value: hc


title: RelA-TA-KI MEFs TNF 1hr, replicate 2

description: WT_RelA-TA-KI.MEFs_TNF_non-normalized-counts.txt

value: TNF

value: Primary mouse embryonic fibroblasts (MEFs)


title: WT  MEFs LPS 0.5hr


title: RelA-TA-KI MEFs TNF 3hr, replicate 2


title: HC46: 29 Substantia Nigra

source_name: 29 Substantia Nigra

value: 29 Substantia Nigra


title: RelA-TA-KI MEFs TNF 0.5hr, replicate 2


title: HB46: 29 Substantia Nigra


title: HD46: 29 Substantia Nigra


title: RelA-TA-KI MEFs TNF 8hr, replicate 2


title: RelA-TA-KI MEFs TNF 8hr, replicate 1


title: HD44: 23 Thalamus

source_name: 23 Thalamus

value: 23 Thalamus


title: HB50: 21 Hippocampus


title: HC52: 2 2ary Auditory (BA22)


title: HC44: 23 Thalamus


title: RelA-TA-KI MEFs TNF 1hr, replicate 1

value: embryo


title: HA52: 2 2ary Auditory (BA22)


title: RelA-TA-KI MEFs 0hr, replicate 2

value: RelA-TA-KI homozygous


title: RelA-TA-KI MEFs TNF 0.5hr, replicate 1


title: HA44: 23 Thalamus


title: HB52: 2 2ary Auditory (BA22)


title: HD42: 15 Insular Posterior Cortex

source_name: 15 Insular Posterior Cortex

value: 15 Insular Posterior Cortex


title: HC42: 15 Insular Posterior Cortex


title: HB44: 23 Thalamus


title: WT  MEFs LPS 0hr

value: WT


title: HB42: 15 Insular Posterior Cortex


title: HD50: 21 Hippocampus


title: HA42: 15 Insular Posterior Cortex


title: RelA-TA-KI MEFs TNF 3hr, replicate 1


title: HB40: 4 Cingulate Posterior (BA31)

source_name: 4  Cingulate Posterior (BA31)

value: 4  Cingulate Posterior (BA31)


title: HD40: 4 Cingulate Posterior (BA31)

value: hd


title: HA40: 4 Cingulate Posterior (BA31)


title: HA46: 29 Substantia Nigra


title: WT  MEFs TNF 3hr, replicate 2


title: HC40: 4 Cingulate Posterior (BA31)


title: WT  MEFs TNF 8hr, replicate 2


title: WT  MEFs TNF 1hr, replicate 2


title: HA39: 7 1ary Auditory (BA41/42)

source_name: 7  1ary Auditory (BA41/42)

value: 7  1ary Auditory (BA41/42)


title: RelA-TA-KI MEFs 0hr, replicate 1


title: HD39: 7 1ary Auditory (BA41/42)


title: HD37: 14 Inferior Temporal (BA20)

source_name: 14 Inferior Temporal (BA20)

value: 14 Inferior Temporal (BA20)


title: WT  MEFs TNF 0.5hr, replicate 2


title: HC39: 7 1ary Auditory (BA41/42)


title: HB39: 7 1ary Auditory (BA41/42)

value: hb


title: WT  MEFs 0hr, replicate 2


title: HC37: 14 Inferior Temporal (BA20)


title: WT  MEFs TNF 8hr, replicate 1


title: HC34: 20 Entorhinal Cortex

source_name: 20 Entorhinal Cortex

value: 20 Entorhinal Cortex


title: HA34: 20 Entorhinal Cortex

value: ha


title: HA37: 14 Inferior Temporal (BA20)


title: HB34: 20 Entorhinal Cortex


title: WT  MEFs TNF 3hr, replicate 1


title: HB37: 14 Inferior Temporal (BA20)


title: HC33: 19 Amygdala

source_name: 19 Amygdala

value: 19 Amygdala


title: WT  MEFs TNF 1hr, replicate 1


title: WT  MEFs TNF 0.5hr, replicate 1


title: HD33: 19 Amygdala


title: HB33: 19 Amygdala


title: WT  MEFs 0hr, replicate 1


title: HA33: 19 Amygdala


title: HD32: 22 Hypothalamus

source_name: 22 Hypothalamus

value: 22 Hypothalamus


title: HB32: 22 Hypothalamus


title: HC32: 22 Hypothalamus

value: hc


title: HA32: 22 Hypothalamus


title: HD30: 27 Globus Pallidus

source_name: 27 Globus Pallidus

value: 27 Globus Pallidus


title: HB30: 27 Globus Pallidus


title: HC29: 6 1ary Somatosensory (BA3/1/2)

source_name: 6  1ary Somatosensory (BA3/1/2)

value: 6  1ary Somatosensory (BA3/1/2)


title: HD29: 6 1ary Somatosensory (BA3/1/2)


title: HB29: 6 1ary Somatosensory (BA3/1/2)


title: HD28: 8 1ary Motor (BA4)

source_name: 8  1ary Motor (BA4)

value: 8  1ary Motor (BA4)


title: HA28: 8 1ary Motor (BA4)


title: crel-/-RelA-TA-KI MEFs IL-1b 3hr

data_processing:
Illumina HiSeq 2000 reads were demultiplexed and trimmed (cutadapt 1.12) to filter out low-complexity reads, polyA tails, N runs
High-quality reads were then imported into STAR aligner to Gencode mouse mm10 genome
Read quality was checked for each sample using Qualimap
Filtered bam files were used to generate counts file using featureCounts v1.5.1
counts were converted to RPKM and annotated to genes based on RefSeq annotation using DESeq2. RPKM values were log-transformed with an offset value of 1.0. Induced genes were defined with FDR >0.01 and >= 2-fold expression over basal with any stimulation.
Genome_build: mm10
Supplementary_files_format_and_content: TXT with all 20 samples

source_name: Primary mouse embryonic fibroblasts (MEFs)

value: embryo

value: crel-/-RelA-TA-KI


title: crel-/-RelA-TA-KI MEFs TNF 0.5hr

value: Primary mouse embryonic fibroblasts (MEFs)

value: TNF


title: crel-/-RelA-TA-KI MEFs TNF 1hr


title: crel-/-RelA-TA-KI MEFs LPS 0.5hr

value: LPS


title: crel-/-RelA-TA-KI MEFs TNF 3hr


title: crel-/-RelA-TA-KI MEFs LPS 1hr


title: crel-/-RelA-TA-KI MEFs LPS 3hr


title: crel-/-RelA-TA-KI MEFs IL-1b 1hr


title: HD25: 26 Internal Capsule

source_name: 26 Internal Capsule

value: hd

value: 26 Internal Capsule


title: HD34: 20 Entorhinal Cortex


title: crel-/-RelA-TA-KI MEFs IL-1b 0.5hr


title: HD23: 31 Putamen

source_name: 31 Putamen

value: 31 Putamen


title: HA29: 6 1ary Somatosensory (BA3/1/2)


title: HC23: 31 Putamen


title: HA30: 27 Globus Pallidus


title: crel-/-  MEFs TNF 3hr

value: crel-/-


title: HA23: 31 Putamen


title: crel-/-  MEFs TNF 1hr


title: HC21: 11 Cingulate Anterior (BA24)

source_name: 11 Cingulate Anterior (BA24)

value: 11 Cingulate Anterior (BA24)


title: HD21: 11 Cingulate Anterior (BA24)


title: HB28: 8 1ary Motor (BA4)

value: hb


title: crel-/-  MEFs TNF 0.5hr


title: HD19: 5 Premotor (BA6)

source_name: 5  Premotor (BA6)

value: 5  Premotor (BA6)


title: HA21: 11 Cingulate Anterior (BA24)

value: ha


title: HC25: 26 Internal Capsule

value: hc


title: HB21: 11 Cingulate Anterior (BA24)


title: crel-/-  MEFs LPS 1hr


title: HB19: 5 Premotor (BA6)


title: HD16: 24 Corpus Callosum Anterior

source_name: 24 Corpus Callosum Anterior

value: 24 Corpus Callosum Anterior


title: HA25: 26 Internal Capsule


title: crel-/-RelA-TA-KI MEFs 0hr


title: crel-/-  MEFs IL-1b 3hr


title: HC16: 24 Corpus Callosum Anterior


title: HA19: 5 Premotor (BA6)


title: HA16: 24 Corpus Callosum Anterior


title: HB16: 24 Corpus Callosum Anterior


title: HD15: 33 Nucleus Accumbens

source_name: 33 Nucleus Accumbens

value: 33 Nucleus Accumbens


title: crel-/-  MEFs LPS 0.5hr


title: HB23: 31 Putamen


title: crel-/-  MEFs IL-1b 1hr


title: HC15: 33 Nucleus Accumbens


title: crel-/-  MEFs IL-1b 0.5hr


title: HB15: 33 Nucleus Accumbens


title: HC19: 5 Premotor (BA6)


title: crel-/-  MEFs LPS 3hr


title: HD14: 32 Caudate

source_name: 32 Caudate

value: 32 Caudate


title: HA15: 33 Nucleus Accumbens


title: HC14: 32 Caudate


title: crel-/-  MEFs 0hr

value: embryo


title: HA14: 32 Caudate


title: HB14: 32 Caudate


title: RelA-TA-KI BMDMs TNF 3hr

data_processing:
Illumina HiSeq 2000 reads were demultiplexed and trimmed (cutadapt 1.12) to filter out low-complexity reads, polyA tails, N runs
High-quality reads were then imported into STAR aligner to Gencode mouse mm10 genome
Read quality was checked for each sample using Qualimap
Filtered bam files were used to generate counts file using featureCounts v1.5.0
counts were converted to RPKM and annotated to genes based on RefSeq annotation using DESeq2. RPKM values were log-transformed with an offset value of 1.0.
Genome_build: mm10
Supplementary_files_format_and_content: TXT with all 18 samples

source_name: Primary mouse bone marrow-derived macrophages (BMDMs)

growth_protocol: Bone marrow cells were cultured in suspension in L929-conditioned IMDM (IMDM supplemented with 30% L929 conditioned media, 10% ES-grade FBS with 1% penicillin (100 units/ml) and streptomycin (100 ug/ml), and 55uM beta-mercaptoethanol on 10 6-cm plates for 6 days. All cells were incubated at 37C in 5% CO2 and grown to day 7 before addition of TNF (10 ng/ml) and LPS (100 ng/ml) prepared and added to cell culture medium.

treatment_protocol: BMDMs were cultured for 6 days prior to usefor experiment on day 7. TNF (10 ng/ml) and LPS (100 ng/ml) were prepared and added to cell culture medium for stimulation

tag: age

value: RelA-TA-KI


title: 92-HFD knockout

city: Salt Lake City

first: Chris

last: Stubben

state: Utah

address: 2000 Cir of Hope Dr

department: University of Utah

institute: Huntsman Cancer Institute

data_processing:
The mouse GRCm38 FASTA and GTF files were downloaded from Ensembl release 92.
The reference database was created using STAR version 2.5.4a with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.5.1.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw counts (featureCounts output files combined into a single tab-delimited matrix).

source_name: Liver

extract_protocol:
30-50 mg tissue was homogenized using bullet blender and the lysate was used for the RNA extraction using the RNAeasy kit (Qiagen) as per the manufacturer instructions
Illumina TruSeq Stranded RNA Kit with Ribo-Zero Gold

tag: tissue

value: liver

tag: sample id

tag: diet

value: High fat diet

value: Liver specific Degs1 knockout


title: RelA-TA-KI BMDMs TNF 8hr

value: Primary mouse bone marrow-derived macrophages (BMDMs)

tag: genotype

value: TNF

tag: time


title: RelA-TA-KI BMDMs TNF 1hr

tag: strain


title: RelA-TA-KI BMDMs TNF 0.5hr

tag: agent


title: HB25: 26 Internal Capsule

value: 26 Internal Capsule


title: 89-HFD knockout


title: 90-HFD knockout


title: HB12: 12 Cingulate Anterior (BA32)

source_name: 12 Cingulate Anterior (BA32)

value: 12 Cingulate Anterior (BA32)


title: RelA-TA-KI BMDMs LPS 8hr

value: LPS


title: HA12: 12 Cingulate Anterior (BA32)


title: HD11: 18 Ventrolateral Prefrontal (BA44)

source_name: 18 Ventrolateral Prefrontal (BA44)

value: hd

value: 18 Ventrolateral Prefrontal (BA44)


title: HD12: 12 Cingulate Anterior (BA32)


title: HC11: 18 Ventrolateral Prefrontal (BA44)


title: HB11: 18 Ventrolateral Prefrontal (BA44)

value: hb


title: 82-HFD knockout


title: RelA-TA-KI BMDMs LPS 3hr


title: HD7: 17 Orbitofrontal (BA11)

source_name: 17 Orbitofrontal (BA11)

value: 17 Orbitofrontal (BA11)


title: 76-HFD control

value: Control


title: HC7: 17 Orbitofrontal (BA11)

value: hc


title: RelA-TA-KI BMDMs LPS 1hr


title: HB7: 17 Orbitofrontal (BA11)


title: 71-HFD control


title: RelA-TA-KI BMDMs LPS 0.5hr


title: HC12: 12 Cingulate Anterior (BA32)


title: 70-HFD control


title: HD3: 16 Dorsolateral Prefrontal (BA9)

source_name: 16 Dorsolateral Prefrontal (BA9)

value: 16 Dorsolateral Prefrontal (BA9)


title: HA7: 17 Orbitofrontal (BA11)

value: ha


title: RelA-TA-KI BMDMs 0hr

value: RelA-TA-KI


title: HB3: 16 Dorsolateral Prefrontal (BA9)


title: 61-HFD control

value: liver


title: 187-NCD knockout

value: Normal chow diet


title: WT BMDMs TNF 3hr

value: WT


title: HA11: 18 Ventrolateral Prefrontal (BA44)


title: WT BMDMs TNF 1hr

value: Primary mouse bone marrow-derived macrophages (BMDMs)


title: 186-NCD knockout

value: Liver specific Degs1 knockout


title: HA3: 16 Dorsolateral Prefrontal (BA9)


title: 179-NCD knockout


title: 185-NCD knockout


title: 220-NCD control


title: WT BMDMs LPS 8hr


title: WT BMDMs LPS 3hr


title: WT BMDMs LPS 1hr


title: 198-NCD control


title: 209-NCD control


title: 194-NCD control


title: WT BMDMs LPS 0.5hr


title: WT BMDMs 0hr


title: HC3: 16 Dorsolateral Prefrontal (BA9)


title: WT BMDMs TNF 8hr

value: TNF


title: UT2_GFPn

city: San Francisco

first: Tatsuya

last: Tsukui

address: 555 Mission Bay Blvd South, 282

department: Medicine

institute: UCSF

data_processing:
Sequencing data were demultiplexed, aligned to the mouse genome mm10 or human genome GRCh38, and UMI-collapsed with the Cell Ranger toolkit (version 2.0 or 3.0, 10X Genomics).
Genome_build: mm10 (mouse), GRCh38 (human)
Supplementary_files_format_and_content: barcodes.tsv: barcodes
Supplementary_files_format_and_content: genes.tsv: genes
Supplementary_files_format_and_content: matrix.mtx: gene-barcode matrix

source_name: Lung

extract_protocol:
Lung tissues were minced into 1 x 1 x 1 mm pieces and digested with protease solution (Collagenase A, Dispase II, DNase I in RPMI with 10 mM HEPES) at 37°C for 60 min with trituration every 20 min. Cells were stained with antibodies. For murine samples, Col-GFP+ or Col-GFP- cells were sorted. For human samples, lineage (CD31, CD45, CD235a, EPCAM)- cells, or all cells (CD235a-) were sorted. Approximately 10,000 sorted cells were loaded onto 10x Genomics Chromium controller.
Single cell libraries were generated using Chromium Single Cell 3' v2 Reagent Kit (10x Genomics) according to the manufacturer's protocol. The libraries were sequenced on Illumina HiSeq 4000 for murine samples or NovaSeq 6000 for human samples.

tag: genotype/variation

value: Col1a1-GFP reporter

value: Untreated

tag: sorted cell type

value: GFP-

tag: individual identifier


title: UT2_GFPp

value: GFP+


title: Bleo1_GFPn

value: Bleomycin


title: UT1_GFPn


title: UT1_GFPp


title: Bleo1_GFPp


title: WT BMDMs TNF 0.5hr


title: crel-/-rela-/-  MEFs TNF 45min (caRNAseq)

description:
crel.rela.ko.45min
chromatin-associated RNA

data_processing:
Illumina HiSeq 4000 reads were demultiplexed and trimmed (cutadapt 1.12) to filter out low-complexity reads, polyA tails, N runs
High-quality reads were then imported into STAR aligner to Gencode mouse mm10 genome
Read quality was checked for each sample using Qualimap
Filtered bam files were used to generate counts file using featureCounts v1.5.0
counts were converted to RPKM and annotated to genes based on RefSeq annotation using DESeq2. RPKM values were log-transformed with an offset value of 1.0. Induced genes were defined with FDR >0.01 and >= 2-fold expression over basal with any stimulation.
Genome_build: mm10
Supplementary_files_format_and_content: TXT with RPKMs for all 8 samples

extract_protocol:
Chromatin-associated RNA was isolated using TRIzol (Life Technologies) and purified using Direct-zol RNA Miniprep Kit (Zymo Research) according to the manufacturer’s instructions. RNA concentrations were quantified using Epoch Spectrophotometer System (Biotek).
400ng of chromatin-associated RNA was subjected to library synthesis using KAPA Stranded RNA-Seq Kit with RiboErase. 400ng of total chromatin-associated RNA was subjected for ribosomal RNA depletion, fragmented using heat and magnesium, and reversed transcribed to double-stranded cDNA. The cDNA was end repaired, adenylate, and ligated with Illumina indexes prior to 12 cycles of PCR amplification. Sequencing was performed by the Broad Stem Cell Research Center core facility at the University of California, Los Angeles with single-end 50 bp sequencing

treatment_protocol: ~80% confluent MEF cells were serum-starved by overnight incubation in Dulbecco’s Modified Eagle’s Medium supplemented with 0.5% bovine calf serum (BCS), 1% penicillin-streptomycin and 1% L-Glutamine prior to stimulation. TNF (10 ng/ml) was prepared and added to cell culture medium for stimulation

tag: developmental stage

value: embryo

value: crel-/-rela-/-

value: Primary mouse embryonic fibroblasts (MEFs)


title: Bleo2_GFPp


title: R62 4

city: Cambridge

first: Myriam

last: Heiman

state: Massachusetts

address: The Picower Institute of Learning & Memory

institute: MIT

description:
R6/2 4
R62_3
processed data file: FPKM_table.txt
processed data file: Table_S3_R62_data.xlsx

data_processing:
The raw fastq data of 50-bp single-end sequencing reads were aligned to the mouse GRCm38 reference genome using the STAR 2.4.0 RNA-Seq aligner.
The mapped reads were processed by cuffquant of cufflinks software with gencode.vM9 gene annotation to quantify reads mapped to each gene.
Gene differential expression test between different animal groups was performed using cuffdiff module of cufflinks software.
Genes with adjusted p-value <0.05 were chosen as differentially expressed genes.
Genome_build: GRCm38
Supplementary_files_format_and_content: FPKM_table.txt: Tab-delimited text file includes FPKM gene counts for each sample.
Supplementary_files_format_and_content: Table_S3_R62_data.xlsx: Excel file includes statistics table.

source_name: Purified striatal RNA

extract_protocol:
Qiagen RNeasy Lipid Tissue Kit.
NuGEN Ovation RNA-Seq v2, Nextera library preparation.
The quality of prepared bar-coded libraries was assessed using an Advanced Analytical-fragment Analyzer before mixing for sequencing on the Illumina HiSeq 2000 platform at the MIT BioMicro Center.

value: R6/2 hemizygous

tag: age at harvest

value: 11 weeks

value: Striatum


title: crel-/-rela-/-  MEFs TNF 0min (caRNAseq)

description:
crel.rela.ko.0min
chromatin-associated RNA

value: control

tag: cell type


title: crel-/-rela-/-  MEFs TNF 15min (caRNAseq)

description:
crel.rela.ko.15min
chromatin-associated RNA


title: R62 3

description:
R6/2 3
R62_2
processed data file: FPKM_table.txt
processed data file: Table_S3_R62_data.xlsx


title: WT  MEFs TNF 15min (caRNAseq)

description:
WT.15min
chromatin-associated RNA


title: WT  MEFs TNF 60min (caRNAseq)

description:
WT.60min
chromatin-associated RNA


title: R62 5

description:
R6/2 5
R62_4
processed data file: FPKM_table.txt
processed data file: Table_S3_R62_data.xlsx


title: WT  MEFs TNF 45min (caRNAseq)

description:
WT.45min
chromatin-associated RNA


title: KM012

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

country: Germany

institute: Klinikum rechts der Isar

data_processing:
RTA (Illumina) was used for base calling
bcl2fastq (version 2.17) was used to convert BCL to fastq format, coupled with adaptor trimming
STAR (version 2.5.2b) was used to map reads to the reference genome
featureCounts(v1.5.0-p3) software was used to count reads per gene
Genome_build: UCSC/mm10
Supplementary_files_format_and_content: tab-delimited text file includes raw read counts for each sample

source_name: KPFSR

extract_protocol:
Qiagen RNeasy micro Kit
Clontech’s SMART-seq v4 Ultra Low Input RNA Kit to create amplified cDNA. Illumina Nextera XT kit to prepare library.

value: tumor epithelia

value: pancreatic ductal adenocarcinoma (PDA)

tag: treatment

value: Tamoxifen


title: R62 1

description:
R6/2 1
R62_0
processed data file: FPKM_table.txt
processed data file: Table_S3_R62_data.xlsx


title: WT  MEFs TNF 0min (caRNAseq)

description:
WT.0min
chromatin-associated RNA

source_name: Primary mouse embryonic fibroblasts (MEFs)

value: WT


title: R62 2

description:
R6/2 2
R62_1
processed data file: FPKM_table.txt
processed data file: Table_S3_R62_data.xlsx


title: Control 5

description:
Control 5
CTRL_4
processed data file: FPKM_table.txt
processed data file: Table_S3_R62_data.xlsx

value: Isogenic wild-type control


title: KM010


title: Bleo2_GFPn

value: Col1a1-GFP reporter


title: Control 4

description:
Control 4
CTRL_3
processed data file: FPKM_table.txt
processed data file: Table_S3_R62_data.xlsx


title: KM008


title: Control 3

description:
Control 3
CTRL_2
processed data file: FPKM_table.txt
processed data file: Table_S3_R62_data.xlsx


title: crel-/-rela-/-  MEFs TNF 60min (caRNAseq)

description:
crel.rela.ko.60min
chromatin-associated RNA

value: TNF


title: Control 2

description:
Control 2
CTRL_1
processed data file: FPKM_table.txt
processed data file: Table_S3_R62_data.xlsx


title: Control 1

description:
Control 1
CTRL_0
processed data file: FPKM_table.txt
processed data file: Table_S3_R62_data.xlsx


title: KM007


title: KM005

value: Corn Oil


title: Input_Rep1_K27me3

city: Dunedin

first: Megan

last: Wilson

address: 270 Great King St

country: New Zealand

institute: University of Otago

description: dissected urogenital ridge from embryos staged at E11.5

data_processing:
Illumina1.9 software used for basecalling.
Bowtie2 (Galaxy Version 2.2.6.2) using default settings
Genome_build: mm9
Supplementary_files_format_and_content: Alignment files (BAM).  Alignment of sequenced reads to the mm9 genome assembly.
Supplementary_files_format_and_content: bigWig files were generated from bedgraph files using Galaxy.
Supplementary_files_format_and_content: bedgraph files,generated using bamCompare. Readcounts normalized to Input

source_name: Mouse gonad

extract_protocol:
Gonad lysates were clarified from MNase digested nuclei and histone-DNA complexes were isolated with specific antibodies
Thruplex-FD

tag: sex/age

value: embryo E11.5

value: gonad

tag: antibody


title: Input_Rep2_K27me3


title: KM004


title: H3K27me3_Rep2


title: KM003


title: H3K27me3_Rep1


title: HC30: 27 Globus Pallidus

source_name: 27 Globus Pallidus

tag: individual

value: hc

tag: brain region

value: 27 Globus Pallidus


title: KM001

tag: tissue


title: Input_Rep2_K4me3


title: Input_Rep1_K4me3


title: A011AAL-CD4-V3 vs. RF-href

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization [details provided in the Series supplementary file 'protocol_details.txt']

scan_protocol: scanning of slides using Agilent G256BA; features were extracted using Imagene software from Biodiscovery. Imagene feature extraction

data_processing: [genes, no bg corr]: Normalization was done using  LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve.

label_protocol: robot amplification and labeling v1.0 [details provided in the Series supplementary file 'protocol_details.txt']

extract_protocol: RNA extraction cellLine [details provided in the Series supplementary file 'protocol_details.txt']

tag: sample group

value: RF-iv-nr-

value: peripheral blood mononuclear cell (PBMC)

tag: cell subpopulation

value: CD4-positive cells

source_name: RF-href

tag: reference

value: Stratagene Universal Human Reference RNA


title: A009AAJ-CD4-V3 vs. RF-href

value: RF-iv-r-


title: A011AAL-CD14-V3 vs. RF-href

value: CD14-positive cells


title: A008AAI-CD4-V3 vs. RF-href


title: A012AAM-CD4-V3 vs. RF-href


title: A012AAM-CD14-V3 vs. RF-href


title: H3K4me3_Rep2

tag: strain

value: anti-H3K4me3 Abcam (ab8580, lot# GR273043-3)


title: HC28: 8 1ary Motor (BA4)

source_name: 8  1ary Motor (BA4)

value: 8  1ary Motor (BA4)


title: A007AAH-CD14-V3 vs. RF-href


title: A007AAH-CD4-V3 vs. RF-href


title: Non-side population (NSP)

hyb_protocol: Following fragmentation, samples were hybridized for at 60 RPM for 16 hrs at 45C on GeneChip Human Exome 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 4G.

data_processing: The data were analyzed with Partek® Genomics Suite® software, version 6.6.  CEL files were imported using the RMA algorithm with background correction and quantile normalization.  Probeset values were log2 transformed and summarized using median polish.

label: biotin

source_name: Non-side population (NSP)

label_protocol: The standard Ambion WT protocol was used to generate cDNA from 250 ng total RNA. First and second strand cDNA synthesis was followed by in vitro transcription and a second round of cDNA synthesis according to the manufacturer’s instructions. Fragmentation of 5.5ug of single-stranded cDNA was performed using the Affymetrix GeneChip WT Terminal Labeling and Hybridization protocol per the manufacturer's instructions.

growth_protocol: J82 cells were grow in DMEM with 10%FBS at 37 degreee, 5% CO2

extract_protocol: Total RNA were extracted using the RNA-Bee reagent (TEL-TEST, Friendswood, TX)

tag: cell line

value: Human bladder cancer cell line J82

value: Non-side population (NSP)


title: KM009

value: tumor epithelia

value: pancreatic ductal adenocarcinoma (PDA)

value: Tamoxifen


title: H3K4me3_Rep1

value: embryo E11.5


title: SCD2_All

tag: disease diagnosis

value: Scleroderma

value: All cells


title: A008AAI-CD14-V3 vs. RF-href


title: Side population (SP)

source_name: Side population (SP)

value: Side population (SP)


title: A006AAG-CD4-V3 vs. RF-href

value: RF-iv-nr-


title: A009AAJ-CD14-V3 vs. RF-href

value: peripheral blood mononuclear cell (PBMC)


title: SCD2_Lin

tag: sorted cell type

value: Lineage-


title: SCD1_All

tag: individual identifier


title: A006AAG-CD14-V3 vs. RF-href

value: Stratagene Universal Human Reference RNA


title: SCD1_Lin


title: BxPC3-KO 1

city: Bunkyo-ku

first: Shu

last: Shimada

state: Tokyo

address: 1-5-45 Yushima

department: Department of Molecular Oncology

country: Japan

institute: Tokyo Medical and Dental University

description: Gene expression profile of BxPC3-KO

hyb_protocol: Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) were performed following the manufacturer's instruction by using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with Affymetrix GeneChip Scanner 3000.

data_processing: The data were normalized by robust multichip analysis (RMA) using affy package in R/Bioconductor.

source_name: KDM6A-knockout human pancreatic ductal adenocarcinoma cell line BxPC3

label_protocol: Amplified RNA was prepared by using 3' IVT Express Kit (Affymetrix).

extract_protocol: Total RNA was extracted from cells by using RNeasy Protect Mini Kit (QIAGEN). Contaminating DNA was removed by digestion with RNase-Free DNase Set (QIAGEN). The RNA Integrity Number (RIN) of all the samples was confirmed to be greated than 7.0 by using 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Human pancreatic adenocarcinoma cell line BxPC3 was purchased from the American Type Culture Collection, and then grown in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were cultured in a humidified incubator at 37°C with 5% CO2. Oligoes targeting KDM6A (5'--ATTCGTGCTGCAAGTGCAG-3') were cloned into the lentiCRISPR v2 vector, and lentivirus was produced from Lenti-X 293T cells (TaKaRa) were transfected with the vector by using polyethyenimine for lentivirus production. Cells were infected with the lentivirus, and then treated with puromycin (Thermo Fisher Scientific). KDM6A-konckout clones were obtained by limiting dilution.

value: Pancreatic ductal adenocarcinoma cell line BxPC3

tag: genotype

value: KDM6A KO


title: KM006


title: BxPC3-WT 2

description: Gene expression profile of BxPC3-WT

source_name: KDM6A wild-type human pancreatic ductal adenocarcinoma cell line BxPC3

value: control


title: A004AAE-CD4-V3 vs. RF-href

value: RF-iv-r-

value: CD4-positive cells


title: IPF2_All

value: Idiopathic pulmonary fibrosis (IPF)


title: BxPC3-WT 1

description: Gene expression profile of BxPC3-WT


title: A004AAE-CD14-V3 vs. RF-href

value: CD14-positive cells


title: A003AAD-CD14-V3 vs. RF-href


title: A002AAC-CD4-V3 vs. RF-href


title: Panc1-WT

description: Gene expression profile of Panc1-WT

source_name: KDM6A wild-type human pancreatic ductal adenocarcinoma cell line Panc1

treatment_protocol:
Human pancreatic adenocarcinoma cell line Panc1 was purchased from the American Type Culture Collection, and then grown in DMEM medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were cultured in a humidified incubator at 37°C with 5% CO2. Oligoes targeting KDM6A (5'--ATTCGTGCTGCAAGTGCAG-3') were cloned into the lentiCRISPR v2 vector, and lentivirus was produced from Lenti-X 293T cells (TaKaRa) were transfected with the vector by using polyethyenimine for lentivirus production. Cells were infected with the lentivirus, and then treated with puromycin (Thermo Fisher Scientific). KDM6A-konckout clones were obtained by limiting dilution.
Human pancreatic adenocarcinoma cell line BxPC3 was purchased from the American Type Culture Collection, and then grown in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were cultured in a humidified incubator at 37°C with 5% CO2. Oligoes targeting KDM6A (5'--ATTCGTGCTGCAAGTGCAG-3') were cloned into the lentiCRISPR v2 vector, and lentivirus was produced from Lenti-X 293T cells (TaKaRa) were transfected with the vector by using polyethyenimine for lentivirus production. Cells were infected with the lentivirus, and then treated with puromycin (Thermo Fisher Scientific). KDM6A-konckout clones were obtained by limiting dilution.

value: Pancreatic ductal adenocarcinoma cell line Panc1


title: A001BBB-CD4-V3 vs. RF-href


title: IPF2_Lin


title: A002AAC-CD14-V3 vs. RF-href


title: BxPC3-KO 2

description: Gene expression profile of BxPC3-KO


title: Panc1-KO

description: Gene expression profile of Panc1-KO

source_name: KDM6A-knockout human pancreatic ductal adenocarcinoma cell line Panc1


title: IPF3_All


title: IPF1_All


title: IPF3_Lin


title: IPF1_Lin


title: NML3_All

value: Normal


title: Fetal Border 1 [FB1]

city: Manchester

first: Mitchell

middle: C

last: Lock

address: 46 Grafton Street

department: Division of Cardiovascular Sciences

country: United Kingdom

institute: University of Manchester

hyb_protocol: Fragmentation and hybridization were performed using protocols from Agilent. 600 ng of each labeled cRNA was fragmented and then mixed with hybridization buffer using the Agilent Gene Expression Hybridization Kit.

scan_protocol: The labelled cRNA was hybridized to Agilent 8 × 15k microarray slides (Ovine 019221 Arrays; GPL14112 platform, containing eight arrays with 15,744 oligomers each with a length of 60 bases and hybridized at 65°C for 17 h at 10 rpm), washed, and scanned with an Agilent G2505B 2 dye scanner at the Interdisciplinary Center for Biotechnology Research Core at the University of Florida.

data_processing: Raw microarray data were imported into R (http://www.r-project.org) using the limma package for background correction and normalization using the quantile normalization method. 7,631 probes on the microarray were excluded from further analysis due to low expression (probes were filtered out if they were not at least 10% stronger in signal than the negative controls on at least four arrays).

organism: Ovis aries

source_name: Fetal sheep mycardial infarction three day border sample

label_protocol: 1 μg of DNase-treated RNA was labelled with cyanine 3 (Cy3) CTP using the Agilent Quick Amp kit (Agilent, USA) and purified with the Qiagen RNeasy kit (Qiagen, Germany), as previously described. The labelled cRNA was analyzed with the Nanodrop spectrophotometer, and the specific (Cy3) activities and the yields of the cRNAs were calculated and stored at -80°C until use.

extract_protocol: RNA was extracted from each ventricular tissue area. RNA concentration was determined using a Nanodrop spectrophotometer (ND-1000, ThermoFisher, Wilmington DE) and its integrity using an Agilent Bioanalyzer, 2100 model. RNA Integrity Number (RIN) values were between 7.6 and 9.5 for all samples.

tag: developmental stage

value: Fetal

tag: tissue area

value: Border


title: NML2_All

value: All cells


title: untransduced-HK1s vs. MH870-A1

hyb_protocol: Tecan HS4800 hybridization: * 60 ul labeled sample is combined with 60 ul 2x-hybmix, containing 50% formamide, 10xSSC, 0.2% SDS, 200 ug/ml herring sperm DNA.  * Hybridizations of spotted oligo-arrays (Codelink glass) or Agilent microarrays are performed on a HS4800Pro Hybstation (Tecan).  * Priming: 5xSSC, 0.1%SDS.  * Probe injection: pre-hyb, 5xSSC, 25% formamide, 0.1%SDS, 1%BSA, Volume 110ul.  * Hybridization: 45 min at 42C.  * Wash 2x: milliQ.  * Wash: 5xSSC, 0.1%SDS.  * Probe injection: sample. Volume 110ul (Agilent 4packs: 55ul).  * Hybridization: 16 hours at 42C.  * Wash 2x: 1xSSC, 0.2%SDS at 23C.  * Wash 2x: 0.1xSSC, 0.2%SDS at 23C.  * Wash 2x: 0.1xSSC at 23C.  * Drying: blow with nitrogen for 3min at 30C.

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. ImaGene feature extraction: Features were extracted using ImaGene software from Biodiscovery.

data_processing: Genes, no bg corr, hybset spec. dye corr: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background subtraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009.

label_protocol:
Robot amplification and labeling v1.0: All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrofotometer (Molecular Devices), and a magnetic bead-locator (Beckman).
mRNA amplification protocol description: * all RNAs are diluted to 0.6 ug/ul and 5 ul is put in a 96-wells plate (Abgene). All subsequent steps are performed by the robot script. * mix1 containing 100 ng T7 Mlu VN primer (custom mix) and EC-control RNA per 5 ul is added and mixed in each well. * plate is incubated @ 70C for 10 mins, cooled to 48C. * mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNAse Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and 1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well. * plate is incubated @ 48C for 2 hours and cooled to room temperature. * 10^6 ul water and subsequently mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 1 ul T4 DNA ligase, 4 ul E.coli DNA polymerase I and 1 ul RNAseH (Promega) is added and mixed in each well. * plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturers protocol, to an end volume of 25 ul. * 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn-buffer, 2 ul each ATP, CTP, GTP, 0.6 ul UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems), and 2.1 ul 50 mM 5-(3-aminoallyl)-UTP (Ambion, Applied Biosystems). * Plate is incubated @37C for 4 hours. * cRNA product is purified with RNAClean (Agencourt, Beckman) according to manufacturer's protocol. * Concentration is measured (SpectraMax 190) and adjusted to 600 ng/ul by the robot. * Resulting cRNA plates are sampled for Bioanalyzer QC, snapfrozen and stored at -80C.
Labeling protocol description: * NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): entire tube is resuspended in 100 ul DMSO (Merck 8.02912.10).  All subsequent steps are performed by the robot script: * 8 ul of each cRNA (0.6 ug/ul) is put in a 96-wells plate (Abgene), the accompanying reference sample is put in the next column (final step combines Cy3 and Cy5 labeled material). * 3 ul 0.5 M NaBicarbonate buffer, pH 9 is added and mixed to all wells. * 3 ul cy-dye solution is added and mixed to the appropriate wells, plate is incubated at 18C for 1 hour. * 4.5 ul 5M hydroxylamine is added and mixed, incubated at 18o C for 15 minutes. * Labeled cRNA product is purified with RNA Clean (Agencourt, GC biotech) according to manufacturer's protocol. * RNA concentration and labeling incorporation are measured (SpectraMax 190). * 2.5 ug of each labeled sample and reference cRNA are pooled and subjected to fragmentation according to protocol (Ambion, Applied Biosystems), 15 min 70C. * Samples are stored at -20C until hybridization.

growth_protocol: Growth of cell lines: Cell line HK-1 cells were grown and maintained in Dulbeccos modified Eagle medium (DMEM; Life Technologies), supplemented with 10% FCS (Sigma), 2 mM L-glutamine, 100 U/mL penicillin, and 100 mg/mL streptomycin.

extract_protocol: RNA extraction cell line: 1. Add 1 ml Trizol per 5x 10^6 cells in suspension (1 ml trizol per 10 cm culture disk) and mix by pipetting, transfer to 1.5 ml eppendorf tube; 2. Incubate 5 min at room temperature; 3. Add chloroform (200 µl per ml Trizol), mix for 15 seconds by shaking vigorously. Incubate 2-3 min at room temperature; 4. Centrifuge 20 min at 14000 rpm 4°C. After centrifugation, transfer the water-phase to a new 1.5-ml micro centrifuge tube; 5. add isopropanol to precipitate RNA. Use 0.5 ml per 1 ml trizol. Mix by shaking, leave samples at RT for 10 minutes. Centrifuge at 14000 rpm for 15 min.; 6. wash pellet with 75% ethanol. Centrifuge at 14000 rpm for 15 min. Carefully pipet off all ethanol (respin briefly and use a P20 for the last microliters). Air-dry pellets briefly before dissolving in MilliQ water. Depending on pellet-size, this may take a while. Continue with RNeasy columns (Qiagen) for clean-up of RNA (maximal 100 µg/column); 7. Adjust each sample to a volume of 300 µl with sterile MilliQ water. Add 160 µl buffer RLT to the samples, and mix (= lysis buffer); 8. Add 240 µl ethanol (100% stored at -20 °C) to the lysate, mix well by pipetting and immediately apply the sample to an RNeasy mini spin column sitting in a 2 ml collection tube (use a second P1000 pipet and work as quick as possible). Next lysate, and so on; 9. Centrifuge at 8000 rpm for 15 seconds in an Eppendorf centrifuge. Discard flowthrough, reuse collection tube. All centrifugation steps at roomtemperature! DNAse treatment: D1. Pipet 350 µl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm to wash. Discard the flow-through. Reuse the collection tube in step D3. D2. Prepare DNase I incubation mix (80 µl/reaction): add 10 µl DNase I stock solution to 70 µl Buffer RDD. Mix by gently inverting the tube. Buffer RDD is supplied with the RNase-Free DNase Set. Note: DNase I is especially sensitive to physical denaturation. Mixing should only be carried out by gently inverting the tube. Do not vortex. D3. Pipet the DNase I incubation mix (80 µl) directly onto the RNeasy silica-gel membrane, and place on the benchtop (20-30°C) for 15 min. Note: Make sure to pipet the DNase I incubation mix directly onto the RNeasy silica-gel membrane. DNase digestion will be incomplete if part of the mix sticks to the walls or the O-ring of the RNeasy column. D4. Pipet 350 µl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm. Discard the flow-through and collection tube; 10. Transfer the RNeasy column into a new 2 ml collection tube. Add 500 µl buffer RPE, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse the collection tube in next steps; 11. Pipet 500 µl buffer RPE onto the RNeasy column, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse collection tube; 12. Centrifuge at 10,000 rpm for 2 minutes (to dry the RNeasy membrane); 13. Transfer the RNeasy column into a new 1.5 ml collection tube. Pipet 100 µl milliQ directly onto the RNeasy membrane and incubate for 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. Note: When small yields are expected, the elution volume can be lowered to a minimum of 35 µl milliQ; 14. Pipet the eluate of step 13 again onto the RNeasy membrane and incubate for another 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. After elution, put all RNA-samples on ice. 15. Determine RNA concentration by measuring A260, and RNA intactness by Bioanalyzer. Snap-freeze and store eluate at -80 °C.

treatment_protocol: Treatment of cell lines: HK-1 cells were lentivirally transduced to express either the empty control vector or a vector expressing the BART cluster 1 miRNAs. (The miRNA cluster designated BART cluster 1 consisted of miR-BART1, 3, 4, 5, 6, 15, 16, 17, 18 and 21.) Following FACS sorting of GFP+ cells, RNA was isolated through Trizol RNA extraction (Life Technologies) and purified using the RNeasy Mini kit according to manufacturer's protocol (Qiagen). Following treatment with DNase I (Qiagen), RNA quality was assessed by using the Agilent 2100 Bioanalyzer. Common reference RNA of untransduced HK-1 cells was obtained in the same manner.

tag: transduction

source_name: pLenti-Blast-eGFPintron


title: Fetal Sham 1 [FS1]

source_name: Fetal sheep sham surgery sample

value: Sham


title: A001BBB-CD14-V3 vs. RF-href

tag: cell type


title: Fetal Infact 1 [FI1]

source_name: Fetal sheep mycardial infarction three day infarct sample

value: Infarct


title: Adolescent Infarct 1 [LI1]

source_name: Adolescent sheep mycardial infarction three day infarct sample

value: Adolescent


title: Fetal Remote 1 [FR1]

source_name: Fetal sheep mycardial infarction three day remote sample

value: Remote


title: MH870-clus1-B1 vs. untransduced-HK1s


title: untransduced-HK1s vs. MH870-clus1-A1


title: NML3_Lin

source_name: Lung

value: Lineage-


title: MH870-B1 vs. untransduced-HK1s


title: NML1_All