title: S9_2

data_processing:
Library strategy: TAC-seq
Reads were trimmed to 88 bp, demultiplexed by sample using FASTX-Toolkit version 0.0.14
Reads were converted to FASTA format, trimmed to 62 bp, shorter than 62 bp reads were removed using FASTX-Toolkit
UMI subsequences were joined using AWK
Reads were demultiplexed by target sequence using FASTX-Toolkit with 6 mismatches
Target sequence (54 bp) were trimmed, reads with N nucleotide were removed using FASTX-Toolkit
Merge sequences by UMI using FASTX-Toolkit
Read and molecule counts were calculated per sample and target (UMI threshold = 2)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file containing targeted read and molecule counts of each sample at fixed UMI threshold

molecule: polyA RNA

source_name: Endometrium

extract_protocol:
Total RNA was extracted from up to 30 mg of endometrial tissue. The biopsy was homogenized in the presence of QIAzol reagent (Qiagen, Venlo, Netherlands) and processed using miRNeasy Mini kit following the manufacturer’s protocol (Qiagen).
Non-skirted low profile PCR Strip Tube Plate (Thermo Fisher) was used with domed cap strips (Thermo Fisher). 1 µl of total-RNA sample was used. The RIN values 7.7 – 9.6 were quantified by Qubit (Invitrogen) and diluted to concentration 90 ng/µl. RT master mix contained 1 µl of 1:50,000 of ERCC RNA Spike-In Mix 1 (Life Technologies) dilution for technical normalization. TAC-seq detector set contained 57 biomarker genes and seven ERCC spike-ins (ERCC-00085; 00170; 00019; 00131; 00092; 00108 and 00004). Altogether 64 TAC-seq detector pairs targeting biomarkers and ERCC spike-in molecules were previously mixed together from 100 µM stock solutions, creating a “100 µM” oligo pool. The mixture was diluted to 5 µM by water and stored at -20°C. 1 µl of total-RNA template for each individual library was added to 2 µl denaturation buffer, containing 5 mM Tris-HCl (pH 7.0) (Sigma-Aldrich), 1 mM dNTP mixture (Thermo Fisher), 400 nM Oligo-T30 primer and 0.05% Triton X-100 (Sigma-Aldrich). Reaction was mixed by pipetting and centrifuged briefly. RNA was denatured by 1 min at 80°C and placed on ice. After that, reverse transcriptase (RT) master mix containing 100 mM Tris-HCl (pH 8.5) (Sigma-Aldrich), 2.5 M betaine (Sigma-Aldrich), 150 mM KCl (Sigma-Aldrich), 10 mM DTT (Sigma-Aldrich), 15 mM MgCl (Sigma-Aldrich), 4 U RiboLock RNase inhibitor (Thermo Fisher) and 20 U Maxima H Minus Reverse Transcriptase (Thermo Fisher) was prepared. The content was mixed on vortex and centrifuged briefly. 2 µl of RT master mix was added to previously denatured RNA (3 µl). All RT pipetting steps were performed on ice. cDNA synthesis was performed by 30 min at 42°C, following 5 min at 85°C for RT inactivation.   Once cDNA synthesis was completed, 1 µl of 5 µM TAC-seq detector mixture was added to RT mixture. The content was mixed on vortex and centrifuged briefly. Strip tubes were placed on thermocycler, denatured 1 min at 98°C and following 1 h at 60°C to enable specific cDNA and TAC-seq probe hybridization. After hybridization, thermostable ligase reaction mixture was added on thermocycler, keeping a constant (60°C) hybridization temperature. The cycler lid was opened and strip caps were removed. 5 µl of Taq DNA ligase master mix, containing 2× Taq DNA ligation buffer (New England Biolabs, NEB) and 1 U Taq DNA ligase (NEB, cat no M0208) were added to each individual reaction tube and mixed by pipetting. The strip tubes were not removed from 60°C thermocycler to avoid self- and mispairing of TAC-seq probes. Ligation reaction was stopped after 20 min incubation by placing reaction plate on ice.   15 µl of previously combined Dynabeads MyOne Carboxylic Acid beads (2 µl) (Thermo Fisher) and 13 µl of capture buffer (30% PEG-6000 (Sigma-Aldrich), 2 M NaCl (Sigma-Aldrich), 5 mM Tris-HCl (pH 7.5) (Sigma-Aldrich), 10 mM EDTA (Sigma-Aldrich) and 0.02% Tween-20 (Sigma-Aldrich)) was added to ice-cooled ligated sample. The content was mixed by vortex. The capture was carried out for 10 min at RT, and after that the samples were placed on DynaMag-96 Side Magnet (Thermo Fisher) holding 8-well strip tubes on VersiPlate Frame (Thermo Fisher). The clean supernatant was removed. The beads on magnet were washed once with 50 µl fresh 80% ethanol. Ethanol was removed by pipetting, and the clean pellet, without ethanol drops, was dried for 2 min. Once beads were dry, strip tubes were removed from the magnet and 18 µl of PCR master mix was added directly to beads. The master mix contained 1× proofreading HOT FIREPol Blend Master Mix (SolisBiodyne, Tartu, Estonia) and 250 nM TAC-seq Left primer. In addition to universal TAC-seq Left, different TAC-seq barcode oligonucleotides were used to introduce a six-nucleotide barcode to each studied sample. For that, 2 µl of 5 µM TAC-seq Barcoded primers were added individually to each PCR reaction. Strip tubes were closed with clean domed caps, mixed on vortex until all beads were suspended. The ERCC spike-in reaction was incubated at 95°C for 12 min, followed by two cycles of 95°C for 20 s, 57°C for 60 s and 72°C for 20 s. In addition, 10 cycles of 95°C for 20 s, 65°C for 20 s and 72°C for 20 s with a final extension at 72°C for 1 min using the default ramp speed of the T100 cycler (Bio-Rad) were performed. PCR products were pooled together into 1.5 ml tube. The pooled tube was placed on magnet to remove carboxylated beads before the following column purification. Clear supernatant was purified with DNA Clean & Concentrator-5 column (Zymo Research) and eluted with 50 µl EB. The library was size-selected using AMPure XP beads (Beckman Coulter) in a single-step selection to reduce 81 bp linear PCR double-stranded by-product. 50 µl beads were added to 50 µl of the purified PCR product, incubated for 5 min at room temperature and captured by a magnet for 3 min. After incubation on magnet, the supernatant was discarded and the remaining beads were centrifuged at 500×g for 10 s. After centrifugation, the beads were placed again on the magnet and all remaining supernatant was removed. The beads were eluted directly without ethanol washing in 25 µl of EB and incubated for 1 min at RT. Finally, the eluted library was transferred to a clean tube after 1 min incubation on the magnet. The library (single 180 bp product) was visualized on a TapeStation High Sensitivity D1000 ScreenTape (Agilent Technologies) and quantified using KAPA Library Quantification Kit (Roche).  Sample1 TGAACT  Sample2 GATCTG  Sample3 ACATCG  Sample4 GCCTAA  Sample5 CGTGAT  Sample6 TGGTCA  Sample7 ACATGT  Sample8 ATTGGC  Sample9 CTGATC  Sample10 CTAGCC  Sample11 CACTGT  Sample12 TCAAGT  Sample13 GTAGCC  Sample14 TACAAG  Sample15 ATCAGT  Sample16 GCTCAT  Sample17 AGGAAT  Sample18 TAGTTG  Sample19 ATCGTG  Sample20 TGAGTG  Sample21 CGCCTG  Sample22 GCCATG  Sample23 TGTTGG  Sample24 AGCATC
Illumina NextSeq 500 high output 75 kit using 2 pM library concentration. Single-read 90 bp and primed by HP10 primer

tag: day

tag: origin

value: Estonia

value: endometrium


title: S7_2

status: Public on Mar 01 2018

type: SRA

city: Tartu

first: Hindrek

last: Teder

address: Tiigi 61b

country: Estonia

institute: The Competence Centre on Health Technologies

library_source: transcriptomic

organism: Homo sapiens

tag: tissue


title: Bel-7402_DMSO_rep1

type: RNA

city: Xi'an

first: Zongfang

last: Li

state: Shaanxi

address: 157 W 5th RD

department: the second affiliated hospital

country: China

institute: Xi’ an Jiaotong University

hyb_protocol: Labeled cDNA was hybridized to the array for 16 hours at 48 ℃ and 60 rpm in Hybridization Oven 645 and were then washed and stained using the GeneChip ® Hybridization Wash and Stain Kit in the 450 Fluidics Station according to the manufacturer's instructions.

scan_protocol: GeneChips were scaned by using Affymetrix GeneChip Command Console (AGCC) which installed in GeneChip Scanner 3000 7G.

data_processing: The raw data (CEL files) were extracted from the scanned images using the Affymetrix GeneChip Command Console. Expression data were generated by Affymetrix.

label: Biotin

molecule: total RNA

source_name: Bel-7402 cell line treated with 0.1%  DMSO for 24h

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using Ambion WT Expression Kit and GeneChip WT Terminal Labeling and Controls Kit.

growth_protocol: Human  hepatocellular carcinoma cell lines Bel-7402 was cultured in Dulbecco’s modified Eagle’s medium (Hyclone, USA) supplemented with 10% fetal bovine serum (Gibco, USA), 1% penicillin-streptomycin (100 U/ml penicillin and 100 μg/ml streptomycin; Hyclone, USA) at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol: After a 24h incubation, the cell were harvested and the total RNA was extracted using TRIzol reagent (Invitrogen, USA) according to the manufacturers’ instructions.

treatment_protocol: The cell lines Bel-7402 was seeded in 6-well plate at a concentration of 2×105 per well and incubated overnight. Then the cells was treated with various concentration (0,40 and 80μM) of baicalein dissolved in DMSO (final DMSO concentration in growth media, 0.1%) for 24h.

tag: cell line

value: Hepatocellular carcinoma


title: S5_2


title: S4_2


title: T21-10-2

description:
acoustically sheared
counts_umi2.tsv

library_source: genomic

data_processing:
Library strategy: TAC-seq
BCLs were converted to FASTQs using Illumina's bcl2fastq2 (version 2.20) with --barcode-mismatches 1
Reads were converted to FASTA format, trimmed to 62 bp, shorter than 62 bp reads were removed using FASTX-Toolkit (version 0.0.14)
UMI subsequences were joined using AWK
Reads were demultiplexed by target sequence using FASTX-Toolkit with 6 mismatches
Target sequence (54 bp) were trimmed, reads with N nucleotide were removed using FASTX-Toolkit
Merge sequences by UMI using FASTX-Toolkit
Read and molecule counts were calculated per sample and target (UMI thresholds 1 and 2 were used)
Supplementary_files_format_and_content: tab-delimited text file containing targeted read and molecule counts of each sample at fixed UMI thresholds

molecule: genomic DNA

extract_protocol:
Genomic DNAs from GM01359 and GM04616 cell lines (NIGMS Human Genetic Cell Repository at the Coriell Institute of Medical Research (USA)) were extracted using DNeasy Blood and Tissue kit (Qiagen). To mimic cfDNA, the genomic DNAs were fragmented to 150-200 bp using Covaris M220 Focused-ultrasonicator (Thermo Fisher) with following settings: 50 μl volume, 10% duty cycle, 75 W peak incident power, 200 cycles per burst and 360 s. Concentrations were quantified by Qubit dsDNA HS (Thermo Fisher).
10 ng of acoustically sheared (Covaris) cell-free like DNAs were combined to create excess rates of chromosome 21 above diploidy level, that mimic 5 to 30% fetal fraction. 100% fraction is the GM04616 cell line DNA with trisomy 21. Samples were pipetted into strip tubes, adding 1 μl of 5 µM TAC-seq probe mixture and 1 µl 10× hybridization buffer, containing 100 mM Tris-HCl (pH 7.5) (Sigma-Aldrich), 500 mM KCl (Sigma-Aldrich), 0.2% Tween-20 (Sigma-Aldrich) and 0.1 mM EDTA (Sigma-Aldrich). The final hybridization volume was 12 µl. The content was mixed on vortex and centrifuged briefly. Strip tubes were placed on thermocycler, denatured 2 min at 98°C and following 2 h at 60°C for hybridization. After hybridization, thermostable ligase reaction master mix was added on thermocycler, keeping constant (60°C) hybridization temperature. Following, 2.5 µl Taq DNA ligase mixture, containing 1.5 µl 10× Taq DNA ligation buffer (NEB) and 1 U Taq DNA ligase (NEB) was added to each individual reaction tube and mixed by pipetting. Ligation reaction was stopped after 20 min incubation by placing reaction tubes on ice. 25 μl of previously combined Dynabeads MyOne Carboxylic Acid beads (3 µl) (Thermo Fisher) and 22 µl of capture buffer was added to ice-cooled ligated sample. The content was mixed by vortex. The capture was carried out for 10 min at RT, and after that the samples were placed on DynaMag-96 Side Magnet (Thermo Fisher) holding 8-well strip tubes on VersiPlate Frame (Thermo Fisher). The clean supernatant was removed. The beads on magnet were washed once with 50 µl fresh 80% ethanol. Ethanol was removed by pipetting, and the clean pellet, without ethanol drops, was dried for 2 min. Once beads were dry, strip tubes were removed from the magnet and 18 µl of PCR master mix was added directly to beads. The master mix contained 1× proofreading HOT FIREPol Blend Master Mix (SolisBiodyne, Tartu, Estonia) and 250 nM TAC-seq Left primer. In addition to universal TAC-seq Left, 16 different TAC-seq barcode oligonucleotides were used to introduce a six-nucleotide barcode to each studied sample. For that, 2 µl of 5 µM TAC-seq Barcoded primers were added individually to each PCR reaction. Strip tubes were closed with clean domed caps, mixed on vortex until all beads were suspended. The ERCC spike-in reaction was incubated at 95°C for 12 min, followed by two cycles of 95°C for 20 s, 57°C for 60 s and 72°C for 20 s. In addition, 19 cycles of 95°C for 20 s, 65°C for 20 s and 72°C for 20 s with a final extension at 72°C for 1 min using the default ramp speed of the T100 cycler (Bio-Rad) were performed. PCR products were pooled together into 1.5 ml tube. The pooled tube was placed on magnet to remove carboxylated beads before the following column purification. Clear supernatant was purified with DNA Clean & Concentrator-5 column (Zymo Research) and eluted with 50 µl EB. The library was size-selected using AMPure XP beads (Beckman Coulter) in a single-step selection to reduce 81 bp linear PCR double-stranded by-product. 50 µl beads were added to 50 µl of the purified PCR product, incubated for 5 min at room temperature and captured by a magnet for 3 min. After incubation on magnet, the supernatant was discarded and the remaining beads were centrifuged at 500×g for 10 s. After centrifugation, the beads were placed again on the magnet and all remaining supernatant was removed. The beads were eluted directly without ethanol washing in 25 µl of EB and incubated for 1 min at RT. Finally, the eluted library was transferred to a clean tube after 1 min incubation on the magnet. The library (single 180 bp product) was visualized on a TapeStation High Sensitivity D1000 ScreenTape (Agilent Technologies) and quantified using KAPA Library Quantification Kit (Roche).
Library was analyzed by Illumina NextSeq500 instrument using custom LNA barcode primer, 1.8 pM loading concentration, 63 bp for read-1 and 6 bp for barcode read-2

tag: t21 cell line

tag: t21 cell line proportion

tag: t13 cell line

tag: t13 cell line proportion


title: S8_2


title: T21-25-1

description:
acoustically sheared
counts_umi2.tsv


title: S10_2


title: S3_2


title: S1_2


title: S10_1


title: S2_2


title: S3_1


title: S5_1


title: S2_1


title: Blood_AA3

city: Shanghai

first: Youyu

last: Sheng

address: 12 Middle Wulumuqi Road, Shanghai 200040, China.

institute: Huashan hospital

description: miRNA expression in blood of patient with alopecia areata

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 22.5 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human miRNA Microarray (8*60K) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies)

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, Genespring software (version 12.5; Agilent Technologies) was employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 75.0 percent of samples in any 1 condition out of 2 conditions have flags in Detected were chosen for further data analysis. Differentially expressed miRNAs were then identified through fold change as well as P value calculated using t-test.

source_name: Peripheral Blood, Alopecia areata, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556) following the manufacturer’s instructions. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

value: whole blood

tag: gender

value: female


title: NV25_LH2_S15

first: Kaarel

last: Krjutskov

state: Tartumaa

address: Teaduspargi tänav 13

description: processed data file:

data_processing:
Library strategy: TAC-seq (targeted allele counting by sequencing)
Illumina bcl2fastq2 used for per-cycle base call (BCL) files conversion to FASTQ files and demultiplexing. Parameters: barcode-mismatches 1 and no-lane-splitting.
Trim 1 nucleotide using fastx_trimmer (fastx_toolkit-0.0.14).
Demultiplex by MiRNA using fastx_barcode_splitter.pl (fastx_toolkit-0.0.14).
Calculated total read count and total molecule count with different threshold of UMI effect.
Supplementary_files_format_and_content: comma delimited text files (for each UMI separate file) containing molecule counts for each sample.

extract_protocol:
RNA was extracted with miRNeasy Mini kit (Qiagen)
Non-skirted low profile PCR Strip Tube Plate (Thermo Fisher) was used with domed cap strips (Thermo Fisher). miRNA profiles were analyzed from endometrial total-RNA. 3' ligation was carried out overnight in 5 ul volume. The reaction contained 100 ng of total-RNA, 1 RNA T4 RNA Ligase Reaction Buffer (NEB), 20 U RNase inhibitor (Thermo Fisher), 10% PEG-8000 (NEB), 100 nM adenylated 3' linker (rApp-AGATCGGAAGAGCACACGTCT-NH2) and 40 U T4 RNA ligase 2 (truncated, NEB). After ligation, the free ligation adapter was removed by adding 0.5 ul 5'-Deadenylase (25 U/ul, NEB) and 0.5 ul Lambda exonuclease (5 U/ul, NEB) and incubated 10 min at 37°C and following 10 min 75°C. Complementary DNA was synthesized after adding 0.4 ul 100 mM DTT (Invitrogen), 0.4 ul 2 M KCl (Sigma-Aldrich), 0.4 ul 10 mM dNTPs (Thermo Fisher), 0.4 ul RNase inhibitor (40 U/ul, Thermo Fisher), 0.2 ul 10 uM micro RT biotin primer (biotin-GCTCCAGAGACGTGTGCTCTTCCGATCT) and 0.2 ul Maxima H Minus Reverse Transcriptase (200 U/ul, Thermo Fisher) which were all together mixed into one 2 ul master mix. Complementary DNA incubation was carried out for 15 min at 50°C and following 5 min at 80°C. Excess of free primers were removed by adding 1 ul Exonuclease I (20 U/ul, Thermo Fisher) and incubated 10 min at 37°C and 5 min at 95°C. 1 ul of 5 uM TAC-seq detector mixture, containing miRNA-specific left detectors and miRNA universal 5' phosphorylated detector oligonucleotide, was added to previous 9 ul product and incubated first 2 min at 98°C to denature the template and probes and then for 1 h at 60°C. After the hybridization, thermostable ligase reaction mixture was added on thermocycler, keeping a constant (60°C) hybridization temperature. The cycler lid was opened and strip caps were removed. 5 ul of Taq DNA ligase mixture, containing 2 Taq DNA ligation buffer (NEB) and 1 U Taq DNA ligase (NEB) were added to each individual reaction tube and mixed by pipetting. Ligation was stopped after 20 min incubation by placing reaction tubes on ice. 3 ul of Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were washed according to protocol and suspended in 15 ul recommended B&W buffer. The beads were added to ligated product on ice, mixed well by pipetting and incubated 10 min at RT. After capturing the beads on magnet for 1 min, the supernatant was removed and the beads were washed once with B&W buffer. Beads were resuspended in 18 ul of PCR master mix was added directly to beads. The master mix contained 1 proofreading HOT FIREPol Blend Master Mix (SolisBiodyne, Tartu, Estonia) and 250 nM TAC-seq Left primer. In addition to universal TAC-seq Left, different TAC-seq barcode oligonucleotides were used to introduce a six-nucleotide barcode to each studied sample. For that, 2 ul of 5 uM TAC-seq Barcoded primers were added individually to each PCR reaction. Strip tubes were closed with clean domed caps, mixed on vortex until all beads were suspended. The ERCC spike-in reaction was incubated at 95°C for 12 min, followed by two cycles of 95°C for 20 s, 57°C for 60 s and 72°C for 20 s. In addition, 18 cycles of 95°C for 20 s, 65°C for 20 s and 72°C for 20 s with a final extension at 72°C for 1 min using the default ramp speed of the T100 cycler (Bio-Rad) were performed. PCR products were pooled together into 1.5 ml tube. The pooled tube was placed on magnet to remove carboxylated beads before the following column purification. Clear supernatant was purified with DNA Clean & Concentrator-5 column (Zymo Research) and eluted with 50 ul EB. The library was size-selected using AMPure XP beads (Beckman Coulter) in a single-step selection to reduce 81 bp linear PCR double-stranded by-product. 50 ul beads were added to 50 ul of the purified PCR product, incubated for 5 min at room temperature and captured by a magnet for 3 min. After incubation on magnet, the supernatant was discarded and the remaining beads were centrifuged at 500g for 10 s. After centrifugation, the beads were placed again on the magnet and all remaining supernatant was removed. The beads were eluted directly without ethanol washing in 25 ul of EB and incubated for 1 min at RT. Finally, the eluted library was transferred to a clean tube after 1 min incubation on the magnet. The library (single 170 bp product) was visualized on a TapeStation High Sensitivity D1000 ScreenTape (Agilent Technologies) and quantified using KAPA Library Quantification Kit (Roche).
Illumina NextSeq500 high output 75 cycles kit and 2 pM library concentration using LNA custom barcode primer. The read-1 length was 32 bp plus 6 bp barcode.

tag: cycle day


title: NV13_LH8_S12

description: processed data file:


title: NV13_LH2_S11

description: processed data file:


title: T21-20-1

description:
acoustically sheared
counts_umi2.tsv


title: S7_1


title: NV12_LH8_S10

description: processed data file:


title: NV06_LH8_S7

description: processed data file:


title: NV12_LH2_S9

description: processed data file:


title: S8_1


title: 12013_LH8_S3

description: processed data file:


title: NV06_LH2_S6

description: processed data file:


title: NV25_LH8_S16

description: processed data file:


title: NV16_LH8_S14

description: processed data file:


title: S4_1


title: NV16_LH2_S13

description: processed data file:


title: H3K27ac_DOX

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

description: H3K27ac was profiled in RMG-1 clone in ARID1A-KD condition  (doxyclicline inducible KD [72h])

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control FastQC
Adapter Trimming TRIM-GALORE
alignment (ChIPseq) BWA
aignment (RNA-seq) STAR 2-pass
tag density files deepTools package was used to generate BigWiggle files
Genome_build: hg 19
Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

growth_protocol: RMG-1 cells were maintained in DMEM/F12 50/50 medium (Corning) supplemented with 10% (v/v) of TET-free fetal bovine serum (Clontech) or super calf serum (GEMcell) and 2 mM of L-glutamine (Corning).

extract_protocol: NEBNext ChIP-Seq ULTRAII DNA Sample Prep Kit (New England Biolabs, inc.)

treatment_protocol: Doxycicline (2ug/ml, 72 hours) was used to induced the knock-down of ARID1A with a TET-inducible shRNA.

tag: treatment

value: DOX

tag: chip antibody

value: Abcam ab4279


title: NV06_LH2_S5

description: processed data file:


title: 12013_LH8_S4

description: processed data file:


title: 12013_LH2_S2

description: processed data file:


title: NV06_LH8_S8

description: processed data file:


title: S9_1


title: 12013_LH2_S1

description: processed data file:


title: IWP2_d15

city: Houston

first: Edwin

middle: Justin

last: Ostrin

state: Texas

address: 1515 Holcombe Blvd, Unit 1465

department: Pulmonary Medicine

country: USA

institute: MD Anderson Cancer Center

data_processing:
The libraries were bar-coded (New England BioLabs, E7335S) and sequenced on a NextSeq 500 at the UT MD Anderson Sequencing and Microarray Facility to obtain 20−30 million 76 nucleotide pair-end reads for each sample.
Alignment to the mm10 genome using a tophat2 v2.0.14 /bowtie2 v2.2.3 pipeline followed by normalization with cufflinks  v2.2.1 pipeline
Pairwise comparisons made using cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated FPKM files
Supplementary_files_format_and_content: tab-separated cuffdiff gene differential expression analysis
Supplementary_files_format_and_content: tab-separated cuffdiff isoform differential expression analysis
Supplementary_files_format_and_content: tab-separated cuffdiff transcription start site differential expression analysis

source_name: Lung progenitor cells (Nkx2.1+ RUES2)

growth_protocol: Human lung progenitors were derived from Rockefeller University Embryonic Stem Cell Line 2 (RUES2, NIH Registration number 0013, a gift from Dr. Ali Brivanlou) as previously described with small modifications (Huang et al., 2014; Huang et al., 2015). Briefly, RUES2 were maintained on irradiated mouse embryonic fibroblasts (Global Stem, GSC-6001G) before starting a differentiation experiment. Definitive endoderm (DE) induction starts on day 1 and takes 3 days. DE induction medium contains 10 μM Y-27632 dihydrochloride, 0.5 ng/ml human BMP4, 2.5 ng/ml human bFGF and 100 ng/ml human Activin A. DE induction was performed in 6-well Ultra-Low Attachment plates to form embryoid bodies (EBs). On day 4, EBs are dissociated with trypsin into single cells and plated onto 24-well fibronectin-coated tissue culture plates for anterior foregut endoderm (AFE) induction and subsequent lung progenitor induction. For days 4 – 6 AFE induction, cells were cultured in the presence of 2 μM Dorsomorphin dihydrochloride (BMP signaling antagonist; abbreviated as DSM) and 10 μM SB431542 (TGF-β signaling antagonist; abbreviated as SB) for 24 h, and then switched to 24 h of 10 μM SB431542 and 1 μM IWP2 (Wnt production inhibitor) treatment. Day 6 to 15 lung progenitor induction and expansion medium contains 3 μM CHIR99021 (WNT signaling agonist), 10 ng/ml human FGF10, 10 ng/ml human FGF7 (or KGF), 10 ng/ml human BMP4 and 50nM all-trans retinoic acid (ATRA). All the cytokines are from R&D Systems, all the small molecules are from Tocris (R&D Systems).

extract_protocol:
QIAgen RNeasy Mini
100~200 ng total RNA was used to prepare an RNAseq library using an mRNA isolation kit (New England BioLabs, E7490) and a NEBNext Ultra RNA library prep kit (New England BioLabs, E7530S) with a final double (0.65 x -1 x bead volume) size selection step using a SPRIselect reagent kit (Beckman Coulter, B23318).

treatment_protocol: To examine the role of CTNNB1-mediated Wnt signaling pathway in regulating NKX2.1-expressing lung progenitors, at day 12 of the differentiation, some cultures were switched to a medium lacking WNT signaling agonist (no CHIR) or additionally containing 1 μM IWP2 (no CHIR and with IWP2), but in the presence of the other lung induction morphogens FGF7, FGF10, BMP4 and ATRA, and carried in such medium for 3 days before immunofluorescence analysis of NKX2.1 expression at day 15. As we reported previously, 19  around day 15 of the differentiation, the cultured cells would become confluent and require replating (Huang et al., 2014; Huang et al., 2015). In the current study, differentiated RUES2 cells analyzed on day 15 were replated on day 10.

tag: cell type

value: ES-derived lung progenitor cells

tag: time point

value: day 15


title: control_d15

value: control


title: S1_1


title: chrom-RNAseq_DOX

description: RNA-seq was performed in RMG-1 clone on chromatin fraction in ARID1A-KD condition  (doxyclicline inducible KD [72h])

extract_protocol: NEBNext Ultra Directional Strand specific RNA-Seq  Sample Prep Kit (New England Biolabs, inc.)


title: chrom-RNAseq_CTRL

description: RNA-seq was performed in RMG-1 clone on chromatin fraction in WT condition

value: CTRL


title: control_d12

value: day 12


title: CHIR_d15


title: T21-5-2

description:
acoustically sheared
counts_umi2.tsv


title: GROSEQ_DOX_REP2

description:
nascent RNA
GRO-seq was performed in RMG-1 clone in ARID1A-KD condition  (doxyclicline inducible KD [72h])

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control:  FastQC
Adapter Trimming:  TRIM-GALORE
alignment (ChIPseq, ATAC-seq):  BWA
alignment (RNAseq):  STAR
tag density files:  deepTools package was used to generate BigWiggle files
Genome_build: hg 19
Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

extract_protocol: Original GRO-seq protocol (Core et al 2008)


title: RNASEQ_DOX_REP2

description:
ribodepleted RNA
RNA-seq was performed in RMG-1 clone in ARID1A-KD condition  (doxyclicline inducible KD [72h])

extract_protocol: NEBNext Ultra Directional Strand specific RNA-Seq Sample Prep Kit (New England Biolabs, inc.)


title: RNASEQ_CTRL_REP2

description:
ribodepleted RNA
RNA-seq was performed in RMG-1 clone in WT condition


title: Glioma patient 08-1556

city: Oslo

first: Jeanmougin

last: Jeanmougin

address: Ullernchausséen 70

department: Molecular Oncology

country: Norway

institute: Norwegian Radium Hospital

description: Expression profiling from glioma patient.

hyb_protocol: Samples were hybridized with Affymetrix Human Exon 1.0. ST Array (Thermo Fisher Scientific)

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

data_processing: Pre-processing and statistical analyses were performed using R version 3.2.2. For each sample, a CEL file storing intensity measures was generated by the Affymetrix GeneChip Command Console software (V.1.0). These files were further processed by background correction, quantile normalization, and summarization at the gene level by the robust multi-array average (RMA) approach using package oligo (version 1.34.2). The features were filtered using ‘expFilter’ function implemented in EMA (version 1.4.5), with default parameters.

label: biotin

source_name: Glioma patient

label_protocol: Total RNA (250 ng) was used as input and processed according to the manufacturer's instructions, using the Ambion WT Expression Kit protocol (Ambion) and Affymetrix GeneChip WT terminal labeling.

growth_protocol: Tumor tissue samples were collected on RNAlater (Qiagen) and total RNA was extracted using a standard TRIzol protocol. Quantity and quality of RNA was assessed by NanoDrop ND-1000 Spectrophotometer (Thermo Fisher Scientific) and Agilent BioAnalyzer 2100 (Agilent Technologies), respectively.

extract_protocol: Total RNA was extracted using a standard TRIzol protocol

value: Male

tag: age

tag: diagnosis

value: pGBM


title: Control 2

description: Expression profiling from control.

source_name: Male control donor


title: Control 1

description: Expression profiling from control.

source_name: Pool of 5 male donors


title: Control 3

description: Expression profiling from control.

source_name: Pool of 23 donors


title: Glioma patient 08-1516


title: Glioma patient 0992-0111

value: Female


title: Glioma patient 09-0201


title: Glioma patient 07-0196

value: sGBM


title: Glioma patient 09-0133


title: Glioma patient 08-0194


title: Glioma patient 08-0243


title: Glioma patient 06-1223


title: Glioma patient 08-0417


title: Glioma patient 09-0194


title: GROSEQ_CTRL_REP2

description:
nascent RNA
GRO-seq was performed in RMG-1 clone in WT condition


title: Glioma patient 08-1253


title: Glioma patient 08-0193


title: Glioma patient 08-0315


title: Glioma patient 08-0316


title: Glioma patient 09-0380


title: Glioma patient 0992-0314


title: RNASEQ_DOX_REP1

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control FastQC
Adapter Trimming TRIM-GALORE
alignment (ChIPseq, ATAC-seq) BWA
alignment (RNAseq) STAR
tag density files deepTools package was used to generate BigWiggle files
Genome_build: hg19
Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

source_name: RNA-seq was performed in RMG-1 clone in ARID1A-KD condition  (doxyclicline inducible KD [72h])


title: Glioma patient 08-0123


title: Glioma patient 08-0308


title: Glioma patient 08-0723


title: Glioma patient 08-0269


title: Glioma patient 07-1568


title: RMG1_INPUT

source_name: Input, prepared using 5% of original sample, no treatment


title: POL2_DOX_REP2

source_name: RNAPII was profiled in RMG-1 clone in ARID1A-KD condition  (doxyclicline inducible KD [72h])

value: Custom, rabbit polyclonal, raised against N terminus of RNAPII


title: POL2_DOX_FLAVOPIRIDOL

source_name: RNAPII was profiled in RMG-1 clone in ARID1A-KD condition after a treatment with Flavopiridol for 2 hours


title: POL2_CTRL_REP2

source_name: RNAPII was profiled in RMG-1 clone in WT condition


title: POL2_CTRL_REP1

value: RNAPII Custom, rabbit polyclonal, raised against N terminus


title: RNASEQ_CTRL_REP1

source_name: RNA-seq was performed in RMG-1 clone in WT condition


title: H3K36me3_DOX

source_name: H3K36me3 was profiled in RMG-1 clone in ARID1A-KD condition  (doxyclicline inducible KD [72h])

value: Abcam ab9050


title: Glioma patient 07-1562


title: Glioma patient 07-0968


title: GROSEQ_CTRL_REP1

data_processing:
Library strategy: GRO-seq
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control FastQC
Adapter Trimming TRIM-GALORE
alignment (ChIPseq, ATAC-seq) BWA
alignment (RNAseq) STAR
tag density files deepTools package was used to generate BigWiggle files
Genome_build: hg19
Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

source_name: GRO-seq was performed in RMG-1 clone in WT condition


title: ATACSEQ_DOX_REP2

source_name: ATAC-seq was performed in RMG-1 clone in ARID1A-KD condition  (doxyclicline inducible KD [72h])

extract_protocol: NextERA DNA Library prep Kit


title: POL2_DOX_REP1


title: Glioma patient 06-1591


title: Glioma patient 07-1380


title: POL2_DOX_NO_FLAVOPIRIDOL


title: Glioma patient 06-1163


title: ATACSEQ_DOX_REP1

source_name: ATAC-seq was performed in RMG-1 clone in WT condition


title: Glioma patient 07-1024


title: H3K27ac_CTRL

source_name: H3K27ac was profiled in parental RMG-1


title: H3K36me3_CTRL

source_name: H3K36me3 was profiled in RMG-1 clone in WT condition


title: Glioma patient 07-0173


title: Glioma patient 07-0666


title: ATACSEQ_CTRL_REP1


title: Glioma patient 06-1603


title: GROSEQ_DOX_REP1

source_name: GRO-seq was performed in RMG-1 clone in ARID1A-KD condition  (doxyclicline inducible KD [72h])


title: ARID1A_REP2

source_name: ARID1A was profiled in parental RMG-1

value: Abcam ab182560


title: Glioma patient 06-1051

source_name: Glioma patient


title: ATACSEQ_CTRL_REP2

source_name: ATAC-seq was performed in RMG-1 clone in ARID1A-KD condition (doxyclicline inducible KD [72h])


title: Glioma patient 06-1471


title: Glioma patient 06-1277


title: Glioma patient 06-0849


title: Glioma patient 06-1126


title: Glioma patient 06-0823


title: ARID1A_REP1

value: Abcam ab97995


title: Glioma patient 06-0984


title: Glioma patient 07-0860


title: Glioma patient 09-0349

value: OII


title: Glioma patient 06-0811


title: Glioma patient 07-1656

value: AII


title: Primary ABC, WT, replicate 1 (ATAC-Seq)

city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

data_processing:
Pair-end sequencing was performed at the Weill Cornell Epigenomics Core using HiSeq2500.  Read quality was evaluated using FASTQC.
RNAseq: 50-bp paired reads were mapped to annotated mouse genome (mm10, build 38.75, 41,128 genes and 87,108 transcripts) with CLC Bio Genomic Workbench 7.5 software (Qiagen). Duplicated reads with more than 5 copies were discarded
RNAseq: Read count tables were created using using unique exon read counts and the differential expression was analyzed using EDGER (Bioconductor). Genes with the expression levels less than 1 cpm in at least three conditions were considered non-expressing and removed from further analysis. A negative binomial generalized log-linear model was fit to read counts for each gene. A likelihood ratio tests with the null hypothesis that the pairwise contrasts of the coefficients are equal to zero was used to evaluate the significance of differences in expression between analyzed groups. Benjamini-Hochberg false discovery rate (FDR) procedure was used to correct for multiple testing. Genes with a FDR)-corrected p-value > 0.01 and less than 2 fold change were filtered out. Genes that passed the filtering were considered to be differentially expressed.
Additional data for the WT ABC and matching DKO ABC cells (ABC_WT_ad and ABC_DKO_ad, Fig5) were generated and analyzed using the same protocol.
ATAC-seq: We used the makeTagDirectory  followed by findPeaks command from HOMER version 4.7.2 (http://homer. salk.edu/homer/) to   identify peaks of ATAC-seq. A false discovery rate (FDR) threshold of 0.001 was used for all data  sets. The following HOMER command was used: cmd = findPeaks <sample tag directory> -style  factor or histone -o <output file> -i <input tag directory>. The total number of mapped reads in each  sample was normalized to ten million mapped reads
Genome_build: mm10, build 38.75
Supplementary_files_format_and_content: comma-separated values, containing the expression values (log-transformed cpm), nominal and FDR-corrected pavalues and fold changes for all processed samples

organism: Mus musculus

source_name: Splenocytes

growth_protocol: C57BL/6 mice and DKO mice were maintained in the Hospital for Special Surgery Animal Facility in full compliance with institutional guidelines approved by the HSS Animal Care and Use Committee.

extract_protocol:
RNA-seq:Total RNA was isolated using QIAGEN RNAeasy plus mini kit from FACS sorted FoB or ABC cells
ATAC-seq:  The nuclei of sorted DKO ABC or DKO Follicular B cells  were prepared by incubation of cells with nuclear preparation buffer (0.30 M sucrose, 10 mM Tris, pH  7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.1% NP40, 0.15 mM spermine, 0.5 mM  spermidine and 2 mM 6AA)
RNA-seq: Sequence-compatible libraries were prepared using Seq v3 Ultra Low Input RNA Kit (Clontech) followed by Nextera library preparation at the Weil Cornell Epigenomics core. Quality of all RNA and library preparations were evaluated with BioAnalyser 2100 (Agilent)
ATAC-seq: Sequencing libraries were constructed as discribed in PMID: 26083756 :Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang  HY, Greenleaf WJ. Single-cell chromatin accessibility reveals principles of  regulatory variation. Nature. 2015 Jul 23;523(7561):486-90. doi:  10.1038/nature14590. Epub 2015 Jun 17. PubMed PMID: 26083756; PubMed Central  PMCID: PMC4685948.

treatment_protocol: not applicable

tag: breed

value: > 20 weeks

tag: Sex

value: female

value: spleen

tag: sorting strategy


title: Primary ABC, DKO, additional, replicate 1

tag: tissue


title: Glioma patient 1002-0413


title: Primary ABC, WT, additional, replicate 1


title: Glioma patient 06-1206


title: Glioma patient 07-0704


title: Glioma patient 06-1467


title: T21-15-1

description:
acoustically sheared
counts_umi2.tsv


title: Glioma patient 06-0813


title: Primary ABC, DKO, additional, replicate 2


title: Primary ABC, WT, additional, replicate 2


title: Glioma patient 07-0450


title: Glioma patient 08-1510


title: Glioma patient 08-1592


title: Glioma patient 08-1321


title: 15wt-fb-2

city: Brisbane

first: Stefan

last: Thor

state: QLD

address: Skerman Bldg (65) room 506  Faculty of Medicine

department: School of Biomedical Sciences

country: Australia

institute: The University of Queensland

data_processing:
LaserGene suite v14-v15, DNASTAR SeqMan Ngen Qseq alignment (unpacked FASTQ)
Reference mm9 genome, focus on CDS/mRNA/ncRNA
RPKM normalization
Genome_build: mm9 (GRCm38)
Supplementary_files_format_and_content: .csv (genesymbol annotation with linear RPKM per sample, column 1: genesymbol, column 2-9 samples, row 1: headers, each subsequent row is a gene, RPKM values rounded to one decimal place); .xlsx is supplied for quick access, formatted as table, with integer rounding.

source_name: Mouse E15.5 forebrain wt

growth_protocol: Pregnant females under standard mouse housing conditions.

extract_protocol:
CNS dissected, forebrain and spinal cord kept at -80°C until RNA extraction with Qiagen Rneasy kit
NEBNext Ultra RNA Library Prep Kit
RNA-seq Illumina HiSeq2500 ~50M reads SE 50bp unstranded

treatment_protocol: Embryos dissected at Embryonic day (E) 13.5 or 15.5.

value: forebrain

tag: genotype

value: wt


title: 15ko-fb-1

source_name: Mouse E15.5 forebrain EED-cKO

value: EED-cKO


title: 15ko-fb-2


title: 15wt-fb-1


title: 13wt-sc-2

source_name: Mouse E13.5 spinal cord

value: spinal cord


title: Glioma patient 07-0139

value: Male


title: Glioma patient 08-1498

value: Female


title: Glioma patient 07-0350


title: Glioma patient 07-0697


title: 13wt-fb-2

source_name: Mouse E13.5 forebrain


title: 13wt-fb-1


title: Glioma patient 07-1341


title: Glioma patient 07-0372


title: Day 8 KLRG1- Reporter+ OT-I cells (exp1)

city: Vienna

first: Dietmar

last: Herndler-Brandstetter

address: Borschkegasse 8a

department: Institute of Cancer Research

country: Austria

institute: Medical University of Vienna

data_processing:
Raw sequencing reads were first processed with cutadapt-1.8.3 (Martin, 2011) to trim adapters.
Bowtie-2 (Langmead and Salzberg, 2012) was used then to align the trimmed reads to the mouse genome mm10 with default parameters. Duplicated reads were marked and removed from the analysis with Picard MarkDuplicate tool (http://broadinstitute.github.io/picard).
BEDTools (Quinlan and Hall, 2010) was used to turn the alignment file to a bed file, which was the input of MACS2 (Zhang et al., 2008) to call peaks and produce BedGraph files.
Visualizations of coverage on regions of interest were produced with IGV (Robinson et al., 2011).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_treat_pileup.bedgraph: bedGraph files include peak calls.

source_name: OT-I cell subset purified from spleen

extract_protocol:
OT-I cell subsets were isolated from spleen, purified by FACS and DNA was extracted from 50,000 OT-I cell subsets using cold lysis buffer (as described by Buenrostro et al. 2015).
Nuclei pellets were resuspended in the transposition reaction mix (Nextera Kit) and incubated at 37°C for 30 min. Qiagen MinElute PCR Purification Kit was used to purify DNA. To amplify transposed DNA fragments, PCR with barcoded PCR primers (Buenrostro et al., 2013) and NEBNext High-Fidelity 2x PCR Master Mix was performed. To reduce GC and size bias in PCR, the appropriate number of PCR cycles was determined using qPCR. The amplified library was purified using a Qiagen MinElute PCR Purification Kit.

tag: strain/background

tag: genotype/variation

value: wild type

value: Spleen

value: KLRG1- Reporter+ OT-I cells

value: Infection with ovalbumin-expressing Listeria monocytogenes

tag: days post-infection


title: 13wt-sc-1


title: Day 8 KLRG1- Reporter+ OT-I cells (exp2)


title: Naive OT-I cells (exp1)

value: OT-I cells

value: Naive


title: Day 8 KLRG1+ Reporter+ OT-I cells (exp1)

value: KLRG1+ Reporter+ OT-I cells


title: Day 8 KLRG1+ Reporter+ OT-I cells (exp2)


title: Day 8 KLRG1- Reporter- OT-I cells (exp1)

value: KLRG1- Reporter- OT-I cells


title: Day 8 KLRG1- Reporter- OT-I cells (exp2)


title: Naive OT-I cells (exp2)


title: KLRG1- Reporter- OT-I cells (exp3)

description:
Sample 3
processed data file: Matrix_table.txt

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38/mm10 whole genome using TopHat2 version 2.0.8.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks version 2.1.1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Matrix_table.txt: Tab-delimited text file includes FPKM values of all three samples.

extract_protocol:
OT-I cell subsets were isolated from spleen, purified by FACS and RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using a low input Library Prep Kit v2.

value: Infection with ovalbumin-expressing vesicular stomatitis virus (VSV-OVA)

tag: day post-infection


title: KLRG1- Reporter+ OT-I cells (exKLRG1) (exp3)

description:
Sample 2
processed data file: Matrix_table.txt


title: Glioma patient 07-0025

tag: gender

value: AII


title: Glioma patient 07-0841


title: Glioma patient 08-1168


title: Glioma patient 1002-0669


title: Glioma patient 06-1563


title: Glioma patient 08-1169


title: KLRG1+ Reporter+ OT-I cells (exp3)

description:
Sample 1
processed data file: Matrix_table.txt


title: Glioma patient 07-0658


title: Glioma patient 07-1082


title: Glioma patient 08-0706


title: F3 41.3mGy/h

city: Saint Paul lez Durance

first: olivier

last: ARMANT

address: Cadarache BP3

department: SERIS

country: France

institute: IRSN

data_processing:
Quality (selection of Q>30) and adapter trimming with Trimgalor v0.4.2
Deduplication and Mapping with Bismark v0.16.3
Genome_build: Daphnia magna v2.4 (Eugenes 20100422)
Supplementary_files_format_and_content: CpG Methylation report from Bismark

organism: Daphnia magna

source_name: Generation 4

extract_protocol:
genomic DNA extracted from Daphnia magna whole organisms with the Qiagen DNeasy Blood & Tissue Kit
Libraries were produced following the MethylC-Seq protocol (Urich MA, et al. Nat Protoc 2015). Briefly, genomic DNA was fragmented by sonication, end repaired and 3' Adenylated, ligated with methylated adpaters, size selected, bisufite converted with  ZYMO EZ DNA Methylation-Gold kit and PCR amplified with a last round of library size selection.
Whole genome bisuflite sequencing  using the MethylC-seq protocol

treatment_protocol: 25-day irradiation phase of a first generation (F0 exposed form  eggs stage to adulthood)   followed with a recovery phase (no exposure) in subsequent generations F1, F2 and F3

value: Wild type Clone A

value: Progeny of F1 grown in recovery condition  (F1, F2 and F3 were not exposed to ionising radiation anymore, only F0)

value: Whole organism


title: F3 Control


title: F3 0.0065mGy/h


title: F2 0.0065mGy/h

source_name: Generation 3


title: F2 41.3mGy/h


title: liver_zonation_21_KO_infusion_150

city: Tarrytown

first: Yurong

last: Xin

state: NY

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals, Inc.

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Reads were decoded based on their barcodes. Read quality was evaluated using FastQC.
Reads were mapped to the reference genome (mouse: GRCm38) using using ArrayStudio® software (OmicSoft®, Cary, NC) allowing two mismatches.
RPKM calculated by ArrayStudio
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Liver

extract_protocol:
Liver were removed, flash frozen liquid nitrogen, and RNA was harvested using Trizol reagent. Total RNA was purified from all samples using MagMAX™-96 for Microarrays Total RNA Isolation Kit (Ambion by Life Technologies) according to manufacturer’s specifications. Genomic DNA was removed using MagMAX™Turbo™DNase Buffer and TURBO DNase from the MagMAX kit listed above (Ambion by Life Technologies). mRNA was purified from total RNA using Dynabeads mRNA Purification Kit (Invitrogen).
Strand-specific RNA-seq libraries were prepared using KAPA mRNA-Seq Library Preparation Kit (Kapa Biosystems).

value: Liver

value: Gcg KO

value: 150 ug/d Gcg


title: liver_zonation_20_KO_infusion_150


title: liver_zonation_19_KO_infusion_150


title: F0 41.3mGy/h

source_name: Generation 1 exposed to gamma radiation

value: Life long exposure to ionising radiation of the F0 generation


title: F0 0.0065mGy/h


title: F0 Control


title: liver_zonation_18_WT_infusion_150

value: WT


title: Apple fruit peel, line GS, 14 day 1-MCP treatment, biol. rep. 2

city: Davis

first: Abhaya

middle: M

last: Dandekar

state: CA

address: One Shields Ave

department: Plant Sciences

institute: University of California, Davis

hyb_protocol: Each array slide was prehybridized in 5x sodium chloride sodium citrate (SSC), 0.1% (w/v) sodium dodecyl sulfate (SDS), and 1% (w/v) bovine serum albumin (BSA) for 45 at 42°C. After prehybridization, the slides were rinsed briefly twice in water and then once in isopropanol, prior to being dried by centrifugation at 500 g for 5 . The lyophilized labeled probe was re-suspended in hybridization buffer containing 5x SSC, 5x Denhardt's solution, 50% (v/v) formamide, 0.5% (w/v) SDS, 200 ng poly A+ RNA, and 200 ng of calf thymus DNA. After denaturation at 95°C for 3 , the probe was applied directly to the prehybridized array slide, covered with a HybriSlip (Schleicher & Schuell) cover slip, and placed in a hybridization cassette (Corning). Arrays were incubated for 16 hours at 42°C and then processed through three consecutive washes of decreasing ionic strength and dried by centrifugation for 5 minutes at 500 g.

scan_protocol: Microarray images were obtained by scanning each slide in a GenePix 4000B (Axon Instruments, Union City, CA) scanner. Settings were 33% and 100% laser power for cDNA and oligonucleotide arrays, respectively. Image quantization was performed using the associated software. GenePix 4.0 and median intensity values (non-background subtracted) for each spot were used in subsequent data analysis.

data_processing: Data were analyzed using the R/maanova package. The complete array set was normalized using the global median approach to bring the median signal intensity of each array to the same value. A background value, the average signal intensity of the weakest 5% of control probe signals in each array, was calculated and subtracted from each data point of the array. All negative values were then converted into a common value of twice the standard background deviation for the whole array set.

organism: Malus domestica

source_name: Peel, line GS, 14-day 1-MCP treatment

label_protocol: cDNA was synthesized from 30 to 50 μg of each total RNA sample using the SuperScript Indirect cDNA Labeling System (Invitrogen Corporation, Carlsbad, CA). Fifty μg of total RNA was reverse-transcribed using Super Script Indirect cDNA Labeling System (Invitrogen Corporation, Carlsbad, CA) following the manufacturer’s protocol. Random hexamer and anchored oligo(dT)20 primers were added to the samples to be hybridized to cDNA arrays in the first-strand cDNA synthesis reaction. Only oligo(dT)20 was used with samples hybridized to oligonucleotide microarrays. In each case, the resulting amino-modified cDNA was labeled according to the manufacturer’s protocols using Cy5 fluorescent dyes (Amersham Biosciences, Piscataway, NJ). Independent cDNA syntheses were performed to generate labeled products for each biological replicate. The fluorescently-labeled cRNA was purified using vacuum manifold by RNeasy mini-column (RNeasy kit; Qiagen, Valencia, CA) as described by the manufacturer.

extract_protocol: Total RNA was isolated from the cortical and peel samples using the hot borate method of Wan and Wilkins (1994) with the modifications described by Hunter et al (2002) and Chairat (2003). Three biological replicates of five fruit each were used. Protocol for Purification of Total RNA from Plant Cells and Tissues from Qiagen RNeasy mini kit (www.Qiagen.com) was followed with the optional on-column DNase digestion. The purified RNA was suspended in 30μl of DEPC water and quantified using the spectrophotometer. RNA integrity and quality was assessed using a 2100 Bioanalyzer instrument and an RNA 6000 Nano LabChip assay (Agilent Technologies, Palo Alto, CA) per manufacturer’s recommendation.

treatment_protocol: 1-MCP treatment: half of the harvested fruits were kept at 20ºC, and the other half were treated with 1 μL/L 1-MCP in a 20 L sealed glass jar. Ethylene inhibited transgenic apples (68G and 103Y) were treated with 80 μL/L ethylene for the enhancement of ethylene production for 14 days. Half of the harvested fruits were kept at 20ºC in an ethylene-free atmosphere and the other half was treated in a 20 L sealed glass jar and treated with 80 μL/L ethylene at 20ºC for 14 days.

value: apple fruit peel

tag: cultivar

value: Greensleeves

value: non-transgenic


title: Apple fruit peel, line 68 ACO antisense, 14 day no ethylene treatment, biol. rep. 2

source_name: Peel, line 68G, 14-day no ethylene treatment

tag: treatment

value: binary vector expressing ACO gene in antisense orientation


title: Apple fruit peel, line GS, 14 day 1-MCP treatment, biol. rep. 1


title: Apple fruit peel, line 68 ACO antisense, 14 day no ethylene treatment, biol. rep. 3


title: Apple fruit peel, line 68 ACO antisense, 14 day ethylene treatment, biol. rep. 1

source_name: Peel, line 68G, 14-day ethylene treatment


title: Apple fruit peel, line 103 ACS sense, 14 day no ethylene treatment, biol. rep. 3

source_name: Peel, line 103Y, 14-day no ethylene treatment

value: binary vector expressing ACS gene in sense orientation


title: Apple fruit peel, line 68 ACO antisense, 14 day ethylene treatment, biol. rep. 2


title: Apple fruit peel, line 68 ACO antisense, 14 day ethylene treatment, biol. rep. 3


title: liver_zonation_22_KO_infusion_150


title: Apple fruit peel, line 68 ACO antisense, 14 day no ethylene treatment, biol. rep. 1


title: F2 Control

value: Progeny of F1 grown in recovery condition  (F1, F2 and F3 were not exposed to ionising radiation)


title: liver_zonation_17_WT_infusion_150


title: Apple fruit peel, line 103 ACS sense, 14 day no ethylene treatment, biol. rep. 1


title: Apple fruit peel, line 103 ACS sense, 14 day no ethylene treatment, biol. rep. 2


title: liver_zonation_16_WT_infusion_150


title: liver_zonation_15_WT_infusion_150


title: liver_zonation_13_KO_infusion_30

value: 30 ug/d Gcg


title: liver_zonation_14_KO_infusion_30


title: liver_zonation_12_KO_infusion_30


title: Apple fruit peel, line 103 ACS sense, 14 day ethylene treatment, biol. rep. 3

source_name: Peel, line 103Y, 14-day ethylene treatment


title: liver_zonation_11_KO_infusion_30


title: Apple fruit peel, line 103 ACS sense, 14 day ethylene treatment, biol. rep. 1


title: sj2

city: Philadelphia

first: T.S. Karin

last: Eisinger

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

description: gene expression data from SAHA/JQ1 (48 hrs) treated cells derived from a KP tumor

hyb_protocol: 5.5 micrograms of biotinylated cDNA were hybridized for 16 hours at 45 degrees Celsius to mouse transcriptome 2.0 ST GeneChips from Affymetrix Inc. GeenChops were washed and stained with streptavidin-phycoerythin.

scan_protocol: GeneChips were scanned with a GeneChip 3000 7G scanner.Affymetrix command conseole and expression console were used to quantify expresison levels for targeted genes.

data_processing: RMA SST gene-level chp files were produced using Affymetrix Expression Console software with default settings

source_name: KP cells

label_protocol: 250 nanograms of total RNA were converted to first strand cDNA then second strand cDNA and then cRNA using T7 polymerase. cRNA was converted to cDNA, fragmented and biotinylated by terminal transferase end labeling

growth_protocol: Cells were grown in DMEM with sodum pyruvate, 10% FBS, 5mM L-glutamine at 37 degrees Celcius, 5% CO2

extract_protocol: RNA was extracted with Trizol according to manufacturer's protocol

treatment_protocol: Growth media was supplemented with DMS0 or 500 nanomolar JQ1 and 2 micromolar SAHA for 48 hrs


title: Apple fruit peel, line GS (wild type), untreated, biol. rep. 2

source_name: Peel, line GS, untreated


title: Apple fruit peel, line 103 ACS sense, 14 day ethylene treatment, biol. rep. 2


title: dmso5

description: gene expression data from vehicle (DMSO)(48 hrs) treated cells derived from a KP tumor

value: dmso


title: dmso3


title: sj3


title: Apple fruit peel, line GS (wild type), untreated, biol. rep. 1


title: liver_zonation_10_WT_infusion_30


title: Apple fruit peel, line GS (wild type), untreated, biol. rep. 3


title: sj1


title: dmso2


title: Apple fruit cortex, line GS, 14 day 1-MCP treatment, biol. rep. 3

source_name: Cortex, line GS, 14-day 1-MCP treatment

value: apple fruit cortex


title: KPY_1195

description: gene expression data from 1miligram of UPS tumor from the murine KPY model

hyb_protocol: 5.5 micrograms of biotinylated cDNA were hybridized for 16 hours at 45 degrees Celsius to mouse transcriptome 2.0 ST GeneChips from Affymetrix Inc. GeneChips were washed and stained with streptavidin-phycoerythin.

source_name: sarcoma (UPS)KP  GEMM

growth_protocol: Tumors develop ~45 days post Adeno-Cre injection and are harvested when KP control tumors reach maximum size (2 cm3)

treatment_protocol: Tumors were collected and store at -80 degrees celcius prior to homogenization and RNA extraction

value: KPY


title: liver_zonation_9_WT_infusion_30


title: KP_1411

description: gene expression data from 1miligram of UPS tumor from the murine KP model

value: KP


title: KP_1


title: KPY_1501


title: KP_1591


title: KPY_1539


title: Apple fruit cortex, line GS, 14 day 1-MCP treatment, biol. rep. 2


title: KPY_1543


title: KP_1592


title: KP_1410


title: liver_zonation_7_WT_infusion_30


title: liver_zonation_6_KO_no_infusion

value: No infusion


title: Apple fruit cortex, line GS, 14 day 1-MCP treatment, biol. rep. 1


title: Apple fruit cortex, line 68 ACO antisense, 14 day no ethylene treatment, biol. rep. 2

source_name: Cortex, line 68G, 14-day no ethylene treatment


title: liver_zonation_5_KO_no_infusion

value: Liver


title: liver_zonation_4_KO_no_infusion

value: Gcg KO


title: Apple fruit cortex, line 68 ACO antisense, 14 day no ethylene treatment, biol. rep. 3


title: Apple fruit cortex, line 68 ACO antisense, 14 day ethylene treatment, biol. rep. 3

source_name: Cortex, line 68G, 14-day ethylene treatment


title: liver_zonation_3_WT_no_infusion


title: Anti-H3K4me2 in HeLa cells Replicate1

type: genomic

city: bologna

first: Samuele

last: Gherardi

state: Bologna

address: via selmi 3

country: Italy

institute: UNIBO

hyb_protocol: Hybridisation was performed following the protocols provided by Agilent (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol v5.0).

scan_protocol: The array was analysed with the Agilent scanner and the Feature Extraction software (v9.1)

data_processing: A graphical overview and analysis of the data were obtained using the Agilent Genomic Workbench software (v7.0.4). Row data were statistically analysed by using Blank Subtraction and Variance stabilization algorythm (Agilent Technologies) for data normalization, Whitehead Per-Array Neighbourhood Model and Whitehead Error Model method algorythms for peak detection and statistical significance (Agilent Technogies).

source_name: adenocarcinoma

label_protocol: . Labelling was performed following the protocols provided by Agilent (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol v5.0).

growth_protocol: Human rhabdomyosarcoma SJCHR30 cells were cultured in Dulbecco's modified Eagle's medium containing 10% fetal bovine serum (FBS) and 50 mg/ml gentamycin and grown at 37 ºC and 7% CO2. Human HeLa cells were cultured in Dulbecco's modified Eagle's medium containing 10% heat-inactivated FBS and 50 mg/ml gentamycin and grown at 37 ºC and 5% CO2.

extract_protocol: 107 cells were used for each immunoprecipitation.  Cells were resuspended in 10ml of PBS 1X and formaldehyde was added to final concentration of 1%.  After a 10 min incubation in a rotating wheel, Glycine was added to stop crosslinking reaction. After three washes with 10 ml ice-cold PBS1X/ 1 mM PMSF, nuclei were obtained and lysed in 600 µl ice-cold RIPA buffer for 20 minutes. Chromatin was shared with a Diogene Bioruptor. After sonication 50µl of shared DNA was taken as INPUT control. 5 µg of specific antibody (Anti-RNA polymerase II Abcam (ab76123), Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) Abcam (ab5095), Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) Abcam (ab5131), Anti-Acethyl Histone H3 Upstate (06-599), Anti-Dimethyl Histone H3 (Lys4) Upstate (07030), Anti-Trimethyl Histone H3 (Lys 36) Abcam (ab9050)) was added and  samples were incubated. O/N  in a rotating wheel at 4°C. Immunocomplexes were rescued by incubation with 50 µl of rec-Protein A- sepharose (Invitrogen cod: 101141) for 30 min at room temperature. Beads were resuspended in 70µl of TE buffer and  RNA was removed adding 10 µg RNAse A and incubating at 37°C for 30 minutes. Immunoprecipitated DNA was de-crosslinked by adding 120 µg of proteinase K and incubating at 65°C in a shaker at 950 rpm for 6 hrs. DNA was extracted with phenol/chlorophorm/isoamylalcohol and resuspended in  50-100 µl 10 mM TrisHCl pH 8. Immunoprecipitated DNA from ChIP was amplified with GenomePlex® Whole Genome Amplification (WGA) Kit according to manufacturer's instructions

tag: cell line

value: HeLa cells

tag: antibody

tag: sample type

value: Immunoprecipitated DNA

tag: input dna

value: Input DNA

value: Not-immunoprecipitated DNA


title: Anti-H3ac in HeLa cells Replicate1


title: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) in HeLa cells Replicate2


title: Glioma patient 07-0041

source_name: Glioma patient

value: Female

tag: age

tag: diagnosis

value: AII


title: Apple fruit cortex, line 68 ACO antisense, 14 day no ethylene treatment, biol. rep. 1

value: Greensleeves

value: binary vector expressing ACO gene in antisense orientation


title: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) in HeLa cells Replicate1


title: Apple fruit cortex, line 68 ACO antisense, 14 day ethylene treatment, biol. rep. 2


title: Anti-H3K4me2 in SJCRH30 Replicate2

source_name: Rabdomiosarcoma

value: SJCRH30 cells


title: Anti-RNA Poyimerase II in HeLa cells Replicate2

value: Anti-RNA Poyimerase II


title: Anti-RNA Poyimerase II in HeLa cells Replicate1


title: Anti-H3K4me2 in SJCRH30 Replicate1


title: Anti-H3ac in SJCRH30 Replicate2


title: Anti-H3ac in SJCRH30 Replicate1


title: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) in HeLa cells Replicate1


title: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) in SJCRH30 Replicate1


title: liver_zonation_1_WT_no_infusion

value: WT


title: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) in SJCRH30 Replicate2


title: Apple fruit cortex, line 68 ACO antisense, 14 day ethylene treatment, biol. rep. 1

value: apple fruit cortex


title: liver_zonation_2_WT_no_infusion


title: Apple fruit peel, line GS, 14 day 1-MCP treatment, biol. rep. 3

value: apple fruit peel

value: non-transgenic


title: liver_zonation_11_KO

extract_protocol:
Liver were removed, flash frozen liquid nitrogen, and RNA was harvested using Trizol reagent. Total RNA was purified from all samples using MagMAX™-96 for Microarrays Total RNA Isolation Kit (Ambion by Life Technologies) according to manufacturer’s specifications. Genomic DNA was removed using MagMAX™Turbo™DNase Buffer and TURBO DNase from the MagMAX kit listed above (Ambion by Life Technologies). mRNA was purified from total RNA using Dynabeads mRNA Purification Kit (Invitrogen).
Strand-specific RNA-seq libraries were prepared using KAPA mRNA-Seq Library Preparation Kit (Kapa Biosystems).

tag: feeding

value: Fed


title: liver_zonation_9_KO

value: Liver


title: Anti-RNA Poyimerase II in SJCRH30 Replicate2


title: Apple fruit cortex, line 103 ACS sense, 14 day ethylene treatment, biol. rep. 2

source_name: Cortex, line 103Y, 14-day ethylene treatment

value: binary vector expressing ACS gene in sense orientation


title: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) in SJCRH30 Replicate2


title: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) in SJCRH30 Replicate1


title: Apple fruit cortex, line 103 ACS sense, 14 day no ethylene treatment, biol. rep. 2

source_name: Cortex, line 103Y, 14-day no ethylene treatment


title: Apple fruit cortex, line 103 ACS sense, 14 day no ethylene treatment, biol. rep. 1


title: Apple fruit cortex, line 103 ACS sense, 14 day no ethylene treatment, biol. rep. 3


title: liver_zonation_8_KO

source_name: Liver

value: Gcg KO


title: liver_zonation_12_KO


title: liver_zonation_7_KO


title: liver_zonation_10_KO


title: liver_zonation_6_WT


title: Apple fruit cortex, line 103 ACS sense, 14 day ethylene treatment, biol. rep. 3


title: Anti-RNA Poyimerase II in SJCRH30 Replicate1

value: Immunoprecipitated DNA


title: KPY_1541

value: KPY


title: Apple fruit cortex, line 103 ACS sense, 14 day ethylene treatment, biol. rep. 1


title: liver_zonation_5_WT


title: Apple fruit cortex, line GS (wild type), untreated, biol. rep. 3

source_name: Cortex, line GS, untreated


title: sham-VSG (obese), biological rep3

city: Jackson

first: Michael

middle: R

last: Garrett

state: MS

address: 2500 North State Street

department: Pharmacology

institute: University of Mississippi Medical Center

description: 1/4 of the placenta was processed for RNA extraction using qiagen kit

hyb_protocol: Following fragmentation, cRNA were hybridized to Rat GeneChip 2.0ST Arrays. GeneChips were automatically washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G

data_processing: Analysis of microarray data was performed using software provided by Affymetrix (Affymetrix® Expression Console™ Software) and commercially available GeneSifter™ software platform using RMA

organism: Rattus norvegicus

source_name: freshly isolated placenta following euthanisia

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol for Rat GeneChip 2.0ST Arrays

growth_protocol: Females were harem mated at approximate age 21 weeks and removed from breeding when sperm were identified. Rats were singly housed for pregnancy and parturition.

extract_protocol:
Placenta in the number 3 and 4 positions counting from the right and left ovary as position 1 were preferentially collected for RNA and protein processing to control for uterine position
RNA was isolated using TRIzol® and Rneasy Mini Kit  and evaluated for quality and integrity (Bio-Rad Experion™ System)

treatment_protocol: Whole genome transcript analysis was performed using Affymetrix platform on  placental tissue isolated from three groups of animals: lean sham-VSG (n=6), obese shame-VSG (n=6), and VSG (n=6)

tag: group

value: obese shame-VSG

tag: breed

value: Long Evans

value: 24 weeks old


title: Apple fruit cortex, line GS (wild type), untreated, biol. rep. 2

tag: tissue

value: Greensleeves


title: sham-VSG (obese), biological rep4


title: sham-VSG (obese), biological rep1


title: sham-VSG (obese), biological rep6


title: sham-VSG (obese), biological rep2


title: Apple fruit cortex, line GS (wild type), untreated, biol. rep. 1


title: VSG, biological rep6

value: VSG


title: liver_zonation_4_WT

tag: genotype


title: sham-VSG (obese), biological rep5


title: liver_zonation_3_WT


title: VSG, biological rep3


title: liver_zonation_2_WT


title: liver_zonation_1_WT


title: VSG, biological rep4


title: VSG, biological rep2


title: sham-VSG (lean), biological rep5

value: lean sham-VSG


title: sham-VSG (lean), biological rep6


title: VSG, biological rep5


title: VSG, biological rep1


title: sham-VSG (lean), biological rep3


title: Ependymom Sample 52

city: Copenhagen

first: Wiktor

last: Majewski

address: Blegdamsvej 9

department: Center for Genomic Medicine

country: Denmark

institute: Copenhagen University Hospital

hyb_protocol: affymetrix manufactures procedure

scan_protocol: affymetrix manufactures procedure

data_processing: CEL file data were processed using quantile normalization, background correction and summarized using RMA algorithm implemented in Bioconductor package 'affy'

source_name: tumor biopsy

label_protocol: affymetrix manufactures procedure

extract_protocol: Qiagen manufactures procedure automatized on QiaCube; specifically Rneasy MIniPrep. RNA quality and quantity was controled by BioAnalyzer and Nanodrop.

tag: condition

value: Ependymom


title: sham-VSG (lean), biological rep2


title: Anaplastic ependymoma Sample 50

value: Anaplastic ependymoma


title: Rhabdomyosarcoma Sample 51

value: Rhabdomyosarcoma


title: Ulcerative Colitis Adipose-derived Stroma Cell Replicate 6

city: Los Angeles

first: Iordanis

last: Karagiannidis

address: 675 Charles E. Young Dr. South

institute: UCLA, David Geffen School of Medicine

hyb_protocol: Hybridization was performed in Agilent’s SureHyb Hybridization Chambers

scan_protocol: After washing, slides were scanned with the Agilent DNA Microarray Scanner. Data was extracted using Agilent Feature Extraction software. Results were provided in the Raw Data Folder

data_processing: Raw signal intensities were normalized in quantile method by GeneSpring GX v12.1, and low intensity mRNAs were filtered (mRNAs that at least 3 out of 30 samples have flags in Present or Marginal were chosen for further analysis, these mRNAs can be found from the mRNA Expression Profiling Data.xls file)

source_name: Mesenteric Adipose-derived Stroma Cells

label_protocol: Agilent Quick Amp Labeling Kit was used for sample labeling

growth_protocol:
Undifferentiated cells grown on maintenance medium
Cells were grown in DMEM+10% FBS for 4 passages

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: disease

value: Ulcerative Colitis

tag: passage

tag: cell type

value: Fibroblast-like precursors isolated from whole mesenteric adipose tissue


title: Bone3

city: Saskatoon

first: Brian

last: Eames

state: Saskatchewan

address: 107 Wiggins Road

department: Anatomy and Cell Biology

country: Canada

institute: University of Saskatchewan

data_processing:
The paired-end Illumina reads were trimmed using Trimmomatic v0.30 (Bolger et al. 2014).
Mapped to the mm10 mouse genome fom Ensembl using TopHat2 and Bowtie2 (Langmead and Salzberg 2012; Kim et al. 2013)
Counts were obtained using HTSeq-count (Anders et al. 2015)
TMM normalization (Robinson and Oshlack 2010) was performed using edgeR. Cutoff of genes considered expressed was determined by calculationg the minimum value of the bimodal distribution of counts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes TMM normalized counts for each sample

source_name: osteoblasts

extract_protocol:
RNA was isolated using the ARCTURUS PicoPure RNA Isolation Kit (ThermoFisher Scientific; Cat# KIT0204) according to the manufacturer’s instructions and DNase treatment was done using RNase-Free DNase (Qiagen; Cat#79254). RNA was amplified one round using MessageAmp II aRNA Kit (ThermoFisher Scientific; Cat# AM1751). The RNA integrity was evaluated on the observation of a signature eletropherogram pattern (Bioanalyzer). A minimum of 50 ng of amplified RNA was used per sample for the construction of each library.
RNA-seq libraries were prepared by the National Research Council (NRC, Saskatoon) using the Illumina TruSeq RNA Sample Prep Kit v2 with the following modification: the protocol was started at the Elute, Prime, Fragment step using 5 µl amplified mRNA (minimum amount was 50 ng mRNA as determined using Quant-iT RiboGreen RNA Assay Kit (Invitrogen)).  The quality of each cDNA library was checked on a DNA 1000 chip using the 2100 Bioanalyzer (Agilent Technologies Inc.).

tag: strain

value: Bone

value: osteoblasts


title: Bone2


title: Bone1


title: MatC3

source_name: mature chondrocytes

value: Mature cartilage

value: mature chondrocytes


title: MatC2


title: liver_zonation_8_WT_infusion_30

value: Liver

value: WT

tag: treatment

value: 30 ug/d Gcg


title: sham-VSG (lean), biological rep1

value: Long Evans


title: Ulcerative Colitis Adipose-derived Stroma Cell Replicate 3


title: Adrenocortical carcinoma Sample 48

value: Adrenocortical carcinoma


title: MatC1


title: Ulcerative Colitis Adipose-derived Stroma Cell Replicate 2


title: Malignant peripheral nerve sheeth tumor Sample 46

value: Malignant peripheral nerve sheeth tumor


title: sham-VSG (lean), biological rep4

value: 24 weeks old


title: Ulcerative Colitis Adipose-derived Stroma Cell Replicate 4


title: Ulcerative Colitis Adipose-derived Stroma Cell Replicate 1


title: Obese Adipose-derived Stroma Cell Replicate 4

value: Obese


title: Osteochondroma Sample 43

value: Osteochondroma


title: Obese Adipose-derived Stroma Cell Replicate 5


title: Obese Adipose-derived Stroma Cell Replicate 6


title: Obese Adipose-derived Stroma Cell Replicate 3


title: Crohn's Disease Adipose-derived Stroma Cell Replicate 5

value: Crohn's Disease


title: Enchodroms Sample 40

value: Enchodroms


title: Obese Adipose-derived Stroma Cell Replicate 1


title: Crohn's Disease Adipose-derived Stroma Cell Replicate 6


title: Anaplastic ependymoma Sample 38

value: Anaplastic ependymoma


title: Neuroblastoma Sample 37

value: Neuroblastoma


title: ImC3

source_name: immature chondrocytes

value: Immature cartilage

value: immature chondrocytes


title: Pineoblastoma Sample 41

value: Pineoblastoma


title: Crohn's Disease Adipose-derived Stroma Cell Replicate 4

value: Fibroblast-like precursors isolated from whole mesenteric adipose tissue


title: ImC2


title: Obese Adipose-derived Stroma Cell Replicate 2


title: Crohn's Disease Adipose-derived Stroma Cell Replicate 3


title: ImC1


title: BATcells_BLEB_r3

city: Berkeley

first: Greg

last: Timblin

department: MCB

institute: UC Berkeley

data_processing:
Unmanipulated reads were aligned to the mouse geneome (mm9) using STAR, producing SAM files.
SAM files were converted to tag directories using HOMER.
For reporting, HOMER was used to calculate nomalized reads per gene (reads per kilobase per million mapped reads, or RPKM).
For differential expression analysis, HOMER was used to count raw reads per gene. Thes raw read counts were using as input to EdgeR to call differential expression.
Genome_build: mm9
Supplementary_files_format_and_content: xlsx files containing either RPKM values for each gene, or EdgeR differential expression analysis output.

growth_protocol: Cells were maintained in DMEM with 10% serum and 1% penicillin/streptomycin (p/s) (Gibco), and induced to differentiate with the maintenance media fortified with 5 µg/ml Insulin, 1 nM T3, 2 µg/ml Dexamethasone, and 500 µM IBMX (Sigma), and 100 nM rosiglitazone (beige cells). After 3 days of differentiation media cells were maintained in DMEM with 10% serum, 1% p/s. Cells were considered fully differentiated on day 6 of differentiation as they stably expressed BAT comparable levels of UCP1,  (UCP1-GAPDH ΔCT of ~2-3).

extract_protocol:
Cells were lysed with TRIzol reagent for total mRNA isolation.
Libraries were prepared from 500ng of total mRNA using Stranded mRNA-seq Kit (KAPA) and NEXTFlex barcoded adaptors (Bioo Scientific).

treatment_protocol: Cells induced to differentiate with the maintenance media fortified with 5 µg/ml Insulin, 1 nM T3, 2 µg/ml Dexamethasone, and 500 µM IBMX (Sigma), and 100 nM rosiglitazone (beige cells). After 3 days of differentiation media cells were maintained in DMEM with 10% serum, 1% p/s. 7 days after differentation was induced , cells were treated with 100 µM Blebbistatin (EMD Milipore) or vehicle (DMSO) [1:500 dilution] for 24 h.

tag: cell line

value: BAT

tag: agent

value: Blebbistatin


title: BATcells_BLEB_r2


title: Crohn's Disease Adipose-derived Stroma Cell Replicate 2


title: Cancer Adipose-derived Stroma Cell Replicate 6

value: Cancer


title: Crohn's Disease Adipose-derived Stroma Cell Replicate 1


title: BATcells_control_r3

value: vehicle control


title: Atypical neurocytoma Sample 34

value: Atypical neurocytoma


title: Alveolar rhabdomyosarcoma Sample 33

value: Alveolar rhabdomyosarcoma


title: Cancer Adipose-derived Stroma Cell Replicate 2


title: Gastrointestinal neuroectodermal tumour Sample 32

value: Gastrointestinal neuroectodermal tumour


title: Cancer Adipose-derived Stroma Cell Replicate 4


title: Cancer Adipose-derived Stroma Cell Replicate 5


title: BATcells_control_r1


title: Cancer Adipose-derived Stroma Cell Replicate 3


title: Control Adipose-derived Stroma Cell Replicate 6

value: Control


title: BATcells_BLEB_r1


title: Cancer Adipose-derived Stroma Cell Replicate 1


title: Control Adipose-derived Stroma Cell Replicate 5


title: Control Adipose-derived Stroma Cell Replicate 4


title: Control Adipose-derived Stroma Cell Replicate 2


title: Ganglioneuroblastoma Sample 30

value: Ganglioneuroblastoma


title: Neuroblastoma Sample 29


title: Anaplastic ependymoma Sample 31


title: Control Adipose-derived Stroma Cell Replicate 1


title: BATcells_control_r2


title: tissue_WAT_r4

growth_protocol: C57BL/6N mice were housed at ambient temperature and fed a high-fat diet (60% kcal fat).

extract_protocol:
Tissues were homogenized in TRIzol reagent for total mRNA isolation.
Libraries were prepared from 500ng of total mRNA using Stranded mRNA-seq Kit (KAPA) and NEXTFlex barcoded adaptors (Bioo Scientific).

treatment_protocol: Mice were euthanized and extracted tissues flash-frozen and stored at -80C.

value: 22 week-old


title: tissue_WAT_r3


title: tissue_BAT_r4


title: tissue_WAT_r1


title: tissue_BAT_r3


title: tissue_WAT_r2


title: Control Adipose-derived Stroma Cell Replicate 3


title: Pilocytic astrocytoma Sample 24

value: Pilocytic astrocytoma


title: Malignant peripheral nerve sheeth tumor Sample 23

value: Malignant peripheral nerve sheeth tumor


title: Choroid plexus carcinoma / Malignant peripheral nerve sheeth tumor Sample 28


title: Nephroblastoma Sample 27

value: Nephroblastoma


title: Ganglioglioma / Diffuse astrocytoma Sample 22

value: Ganglioglioma / Diffuse astrocytoma


title: Glioblastoma Sample 21

value: Glioblastoma


title: tissue_BAT_r2


title: tissue_BAT_r1


title: Precursor T-lymphoblastic lymphoma Sample 20

value: Precursor T-lymphoblastic lymphoma


title: Alveolar rhabdomyosarcoma Sample 19


title: mRNA_ded1-ts(hcDBP1)_ replicate 2_37 deg

city: Bethesda

first: Alan

middle: G

last: Hinnebusch

state: MD

address: 6 CENTER DR Room 230, MSC 0609

institute: NICHD

description:
mRNA
Experiment 3
ded1ts_hcDBP1_37deg.csv

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
rRNA alignment with Bowtie2-2.6.0
Transcriptome alignment with TopHat v2.1.0
Read quantitation using custom scripts
Analysis of reads using DESeq2
Genome_build: sacCer2
Supplementary_files_format_and_content: processed  txt (csv) files per experiment show a matrix (with columns: yORF name, gene name, WT ribosome occupancy, mutant ribosome occupancy, WT mRNA occupancy, mutant mRNA occupancy, ribosome occupancy change, mRNA occupancy change, TE change). All numerical columns have log values with base 2

organism: Saccharomyces cerevisiae

source_name: Whole cells

growth_protocol: Cells were generally grown to an OD600 of ~  0.7 in SC medium (maintaining selection for plasmids as needed) and subjected to temperature shifts as indicated

extract_protocol:
Cells were rapidly vacuum filtered and flash frozen. Whole cell extracts were prepared by breaking cells in a freezer mill.
Ribosome profiling (Rnase I footprinting, size selection, RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification) was done as described in Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324(5924):218-223

treatment_protocol: All cultures were treated  with cycloheximide (100 ug / ml) for 2 min prior to harvesting

tag: strain (genetic background)

value: ded1-ts_hcDBP1 (NSY73)


title: Ewing sarcoma Sample 47

value: Ewing sarcoma


title: Ulcerative Colitis Adipose-derived Stroma Cell Replicate 5

value: Ulcerative Colitis

value: Fibroblast-like precursors isolated from whole mesenteric adipose tissue


title: Diffuse midline glioma H3K27M-mutated Sample 18

value: Diffuse midline glioma H3K27M-mutated


title: Ganglioglioma / Diffuse astrocytoma Sample 17


title: mRNA_ded1-ts_ replicate 1_37 deg

description:
mRNA
Experiment 3
ded1ts_37deg.csv

value: ded1-ts  (NSY71)


title: WT_input DNA-2

city: Montreal

first: William

last: Muller

state: Quebec

address: 1160 Avenue des Pins

institute: McGill University

description:
WT-rep2_input
WT sample-2 input

data_processing:
Raw reads were trimmed for length (n>=32), quality (phred score >= 30) and adaptor sequence using fastx v0.0.13.1.
Trimmed reads were (pools of 5 different tumors per genotype) then aligned to the mouse reference genome mm10 using BWA v0.5.9
Broad peaks were called using MACS v1.4.1 software (mfold=10,30; bandwith=300; pvalue cutoff=1E-5) using sequenced libraries of input DNA as control
Peak list intersections were done using BEDTools v2.12.0. Binding peaks were considered overlapping if at least 1 base of the peaks overlapped.
Genome_build: mm10
Supplementary_files_format_and_content: Bedgraph files for visualization for each file

source_name: WT_input DNA

growth_protocol: For tumor tissue, 0.5g of tumor was chopped with a tissue chopper and then homogenized using a tissue homogenizer in 1% final concentration of formaldehyde and let to fix for 10 minutes after which the samples were lysed and sonicated.

extract_protocol:
For each sample, tail DNA was extracted to determine the genotype of the sample. Samples were flash frozen and also examined by immunblot analysis to confirm EZH2 status. DNA Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
DNA library preparation was performed using the TruSeq DNA sample preparation kit according to Illumina recommendations

tag: strain background

value: FVB

tag: genotype/variation

value: wild type

value: mammary gland

tag: tissue type

value: endpoint tumour

tag: chip antibody


title: mRNA_DED1-TS_ replicate 1_37 deg

description:
mRNA
Experiment 3
ded1ts_37deg.csv & ded1ts_hcDBP1_37deg.csv

value: DED1-TS WT (NSY67)


title: Anaplastisc pleomorfic xanthoastrocytoma / Glioblastoma Sample 16


title: ribo_ded1-ts(hcDBP1)_ replicate 2_37 deg

description:
Ribosome-protected RNA
Experiment 3
ded1ts_hcDBP1_37deg.csv

data_processing:
Library strategy: ribosome profiling
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
rRNA alignment with Bowtie2-2.6.0
Transcriptome alignment with TopHat v2.1.0
Read quantitation using custom scripts
Analysis of reads using DESeq2
Genome_build: sacCer2
Supplementary_files_format_and_content: processed  txt (csv) files per experiment show a matrix (with columns: yORF name, gene name, WT ribosome occupancy, mutant ribosome occupancy, WT mRNA occupancy, mutant mRNA occupancy, ribosome occupancy change, mRNA occupancy change, TE change). All numerical columns have log values with base 2


title: mRNA_DED1-TS_ replicate 2_37 deg


title: KO_H3K27me3_ChIPSeq-2

description:
PyVMT-KO-rep2_H3
KO sample-2

value: Ezh2-/-; KO

value: H3K27me3 (Cell Signaling)


title: WT_H3K27me3_ChIPSeq-2

description:
PyVMT-WT-rep2_H3
WT sample-2


title: Anaplastisc ependymoma Sample 15

value: Anaplastisc ependymoma


title: WT_input DNA-1

description:
WT-rep1_input
WT sample-1 input


title: Juvenile xanthogranuloma Sample 14

value: Juvenile xanthogranuloma


title: ribo_ded1-ts(hcDBP1)_ replicate 1_37 deg


title: ribo_ded1-ts_ replicate 1_37 deg

description:
Ribosome-protected RNA
Experiment 3
ded1ts_37deg.csv


title: ribo_DED1-TS_ replicate 2_37 deg

description:
Ribosome-protected RNA
Experiment 3
ded1ts_37deg.csv & ded1ts_hcDBP1_37deg.csv


title: ribo_DED1-TS_ replicate 1_37 deg


title: KO_H3K27me3_ChIPSeq-1

description:
PyVMT-KO-rep1_H3
KO sample-1


title: mRNA_ded1-cs(hcDBP1)_ replicate 2_15 deg

description:
mRNA
Experiment 2
ded1cs_hcDBP1_15deg.csv

value: ded1-cs_hcDBP1 (NSY56)


title: Chondroblastic osteosarcoma Sample 35

value: Chondroblastic osteosarcoma


title: WT_H3K27me3_ChIPSeq-1

description:
PyVMT-WT-rep1_H3
WT sample-1


title: Anaplastisc ependymoma Sample 13


title: HC 3

city: Gainesville

first: Laurence

last: Morel

state: FL

address: 1395 Center Drive, D6-6

department: Pathology and Immunology

institute: University of Florida

description:
High or Low grouping was based on attempts to group samples by expression of the Pbx1 gene
9077_Control low3_(HTA-2_0)

hyb_protocol: Labeled cDNA was hybridized to microarrays according to Affymetrix (currently Thermo Fisher) instructions. Prehybridization mix was applied for 30 minutes to all microarray, after which  5.2 ug of ss-DNA was injected and hybridized for 16 hours at 45C at 60 rpm.

scan_protocol: GeneChip Scanner 3000 7G using AGCC software

data_processing: Data was analyzed using Partek Genomic Suite version 6.6. Raw CEL files were imported and normalized with the RMA procedure with quantile normalization.  and median polish. Statistical testing was performed with Student's unpaired test between SLE and HC groups.

source_name: Control CD4 T cell_low Pbx1 expression

label_protocol: Amplified cDNA was fragmented with UDG and APE1 enzymes according to Affymetrix instructions. Labeling was performed with TdT with biotin reagent followed by streptavidin/phycoerythrin.

growth_protocol: ex vivo T cells were not cultured or grown.

extract_protocol: RNA from CD4 T cells in RLT buffer with 2-mercaptoethanol. Isolation was according to manufacturer instructions (Qiagen Rneasy). RNA was eluted with ddH20 and stored in -80c until further use.

treatment_protocol: ex vivo T cells were not stimulated

tag: subject status

value: healthy control

tag: gender

value: female

tag: age

tag: ethnicity

value: white

tag: sledai

tag: prednisone use

value: unstimulated CD4 T cell

tag: pbx1 gene expression

value: low


title: mRNA_ded1-ts_ replicate 2_37 deg

description:
mRNA
Experiment 3
ded1ts_37deg.csv

value: ded1-ts  (NSY71)


title: ribo_ded1-ts_ replicate 2_37 deg


title: mRNA_ded1-cs_ replicate 1_15 deg

description:
mRNA
Experiment 2
ded1cs_15deg.csv

value: ded1-cs  (NSY54)


title: Diffuse midline glioma H3K27M-mutated Sample 12

tag: condition

value: Diffuse midline glioma H3K27M-mutated


title: HC 8

description:
High or Low grouping was based on attempts to group samples by expression of the Pbx1 gene
9082_Control high4_(HTA-2_0)

source_name: Control CD4 T cell_high Pbx1 expression

tag: cell type

value: high


title: LNn_rep3

city: Lausanne

first: Freddy

last: Radtke

state: VAUD

address: Station 19

department: ISREC

country: Switzerland

institute: Ecole Polytechnique Fédérale de Lausanne

data_processing:
Mapping and RNA-seq analyses were done through HTSstation (David et al, 2014 PLoS ONE and http://htsstation.epfl.ch/).
Reads were mapped to the mm10 with bowtie2 with parameters --end-to-end --sensitive -k 20
Counts preprocessing and differential analysis was done with the R packages limma [ref limma] and voom [ref voom]
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with raw counts and rpkm per transcript.

source_name: Metastatic Lymphnode

extract_protocol:
Primary or metastatic cMyc high (GFP+) or low (GFP-) melanoma cells melanoma cells were FACS sorted from fresh tumors. Total RNA was prepared from GFP+ or GFP- FACS-sorted cells and collected in triplicates using RNAqueous-Micro kit (Ambion).
An RNA amplification step was done using Ovation® RNA Amplification System V2 (Nugen). The Ovation® Ultralow Library System V2 (Nugen) was used for library preparation. Library sequencing was done using an Illumina HiSeq 2500 sequencer.

tag: strain

value: metastatic melanoma

tag: tissue

value: Metastatic Lymph node

tag: cmyc status

value: low (GFP-)


title: LNn_rep2


title: mRNA_DED1-CS_ replicate 2_15 deg

description:
mRNA
Experiment 2
ded1cs_15deg.csv & ded1cs_hcDBP1_15deg.csv

tag: strain (genetic background)

value: DED1-CS WT (NSY52)


title: HC 2

description:
High or Low grouping was based on attempts to group samples by expression of the Pbx1 gene
9076_Control low2_(HTA-2_0)

value: hispanic


title: mRNA_DED1-CS_ replicate 1_15 deg


title: Hepatoblastoma Sample 11

value: Hepatoblastoma


title: ribo_ded1-cs(hcDBP1)_ replicate 2_15 deg

description:
Ribosome-protected RNA
Experiment 2
ded1cs_hcDBP1_15deg.csv

value: ded1-cs_hcDBP1 (NSY56)


title: SLE 6

description:
High or Low grouping was based on attempts to group samples by expression of the Pbx1 gene
9072_SLE high2_(HTA-2_0)

source_name: SLE CD4 T cell_high Pbx1 expression

value: systemic lupus erythematosus (SLE) patient

value: Yes


title: LNn_rep1


title: HC 1

description:
High or Low grouping was based on attempts to group samples by expression of the Pbx1 gene
9075_Control low1_(HTA-2_0)

value: healthy control

value: female

value: black


title: ribo_ded1-cs(hcDBP1)_ replicate 1_15 deg


title: mRNA_ded1-ts(hcDBP1)_ replicate 1_37 deg

value: ded1-ts_hcDBP1 (NSY73)


title: SLE 4

description:
High or Low grouping was based on attempts to group samples by expression of the Pbx1 gene
9070_SLE low4_(HTA-2_0)

source_name: SLE CD4 T cell_low Pbx1 expression

value: white

value: No

value: unstimulated CD4 T cell

value: low


title: ribo_ded1-cs_ replicate 2_15 deg

description:
Ribosome-protected RNA
Experiment 2
ded1cs_15deg.csv

value: ded1-cs  (NSY54)


title: HC 4

description:
High or Low grouping was based on attempts to group samples by expression of the Pbx1 gene
9078_Control low4_(HTA-2_0)


title: SLE 5

description:
High or Low grouping was based on attempts to group samples by expression of the Pbx1 gene
9071_SLE high1_(HTA-2_0)

value: high


title: LNp_rep3

value: metastatic melanoma

value: Metastatic Lymph node

value: high (GPF+)


title: ribo_ded1-cs_ replicate 1_15 deg


title: HC 7

description:
High or Low grouping was based on attempts to group samples by expression of the Pbx1 gene
9081_Control high3_(HTA-2_0)


title: HC 5

description:
High or Low grouping was based on attempts to group samples by expression of the Pbx1 gene
9079_Control high1_(HTA-2_0)


title: mRNA_ded1-cs_ replicate 2_15 deg

description:
mRNA
Experiment 2
ded1cs_15deg.csv


title: SLE 3

description:
High or Low grouping was based on attempts to group samples by expression of the Pbx1 gene
9069_SLE low3_(HTA-2_0)


title: ribo_DED1-CS_ replicate 2_15 deg

description:
Ribosome-protected RNA
Experiment 2
ded1cs_15deg.csv & ded1cs_hcDBP1_15deg.csv

value: DED1-CS WT (NSY52)


title: ribo_DED1-CS_ replicate 1_15 deg


title: Chordoma, dedefferentiated/anaplatic type (INI1-loss) Sample 10


title: mRNA_ded1-tsdbp1Δ replicate 1_37 deg

description:
mRNA
Experiment 1
ded1tsdbp1_37deg.csv

value: ded1-ts dbp1delta (NSY15)


title: LNp_rep2


title: SKn_rep2

source_name: Skin

value: primary melanoma

value: Skin

value: low (GFP-)


title: LNp_rep1


title: mRNA_ded1-tsdbp1Δ replicate 2_37 deg

description:
mRNA
Experiment 1
ded1tsdbp1_37deg.csv


title: mRNA_dbp1Δ replicate 2_37 deg

description:
mRNA
Experiment 1
dbp1_37deg.csv

value: dbp1delta (NSY14)


title: ribo_ded1tsdbp1Δ replicate 2_37 deg

description:
Ribosome-protected RNA
Experiment 1
ded1tsdbp1_37deg.csv


title: mRNA_dbp1Δ replicate 1_37 deg

description:
mRNA
Experiment 1
dbp1_37deg.csv


title: SKn_rep1


title: SKp_rep2


title: Chondrosarkoma Sample 9

value: Chondrosarkoma


title: Mesoblastisc nephroma Sample 6

value: Mesoblastisc nephroma


title: Signetringcell carcinoma Sample 7

value: Signetringcell carcinoma


title: SKp_rep1


title: Pilocytisc/pilomyxoid astrocytoma Sample 3

value: Pilocytisc/pilomyxoid astrocytoma


title: HC 6

description:
High or Low grouping was based on attempts to group samples by expression of the Pbx1 gene
9080_Control high2_(HTA-2_0)

value: healthy control

value: female

value: white

value: unstimulated CD4 T cell


title: Warm whiite adipocyte H3K27ac ChIP rep 1

city: Boston

first: Evan

last: Rosen

state: MA

address: 3 Blackfan Cir

department: Endocrinology

institute: Beth Israel Deconess Medical Center

description: biological replicate

data_processing:
ChIP-seq data were aligned to the mm10 mouse genome using Bowtie2 (Langmead and Salzberg, 2012).
Duplicates and low quality reads were removed by Picard (http://picard.sourceforge.net)
Reads were processed using samtools (Li et al., 2009)
Peaks were called by MACS2 (Zhang et al., 2008), and low peaks (4<fold higher coverage than whole cell extract (WCE)) were removed.
Reads were assigned to peaks, normalized and quantified using featureCounts and EdgeR. Low signal peaks (log2 CPM<2) were removed, and differential peaks were defined at log2 FC≥1 and log2 FDR≤0.05 (except H3K4me1 which used FDR≤0.25).
For ChIP-seq track visualization, reads were processed to the BigWig file format using bedtools (Quinlan and Hall, 2010) and bedGraphToBigWig (Kent et al., 2010).
Processed Bigwig files were viewed in WashU Epigenome Browser (Zhou and Wang, 2012).
ChIP-seq peak heatmaps and distribution plots were generated with the normalized BigWig files within 10kb genomic regions surrounding peaks by using deepTools2 (Ramirez et al., 2016).
Overlaps between H3K27ac and H3K4me1 were determined using bedtools. Peaks were assigned to genomic annotations and genes with HOMER (Heinz et al., 2010), and GO pathway analysis was performed by DAVID Bioinformatics Resources 6.8.
Motif enrichment analysis was conducted using FIMO from the MEME package (Grant et al., 2011) with the JASPAR database (Mathelier et al., 2014)
genome build: mm10
processed data files format and content: bigwig

source_name: inguinal WAT

growth_protocol: Mice were maintained on a standard chow diet (8664 Harlan Teklad, 6.4% w/w fat) under a regular 12h light/12h dark cycle at constant temperature (23°C).

extract_protocol:
Tissues were dounce homogenized, and cross-linked nuclei were isolated and sorted by BD FACS Aria II using mCherry fluorescence. Sorted nuclei were sheared by Covaris E220 and used for ChIP for overnight. Immunoprecipitates were washed and subjected to elution and reverse crosslinking. DNA was then extracted by AMPure XP beads according to the manufacturer’s manual.
Sequencing libraries were constructed using the “on-bead” preparation method as previously described (Roh et al., Cell Rep, 2017). ChIP-isolated DNA was subjected to end repair/phosphorylation using the End-It DNA End-Repair Kit (Epicentre), A-tailing using the Klenow Fragment and index adaptor ligation using Quick Ligase (NEB). AMPure XP beads were left in all the reactions to allow isolation of DNA using PEG (Polyethylene Glycol 8000)/NaCl solution, thus minimizing loss between reactions. After ligation, DNA was eluted and amplified by PCR for 14-16 cycles using the PfuUltra II Hotstart PCR Master Mix. DNA sized between 250 and 600bp was selected by gel electrophoresis and extraction using E-Gel EX Agarose Gels (Invitrogen) and MinElute Gel Extraction kits (Qiagen). Libraries were analyzed using the Qubit and Agilent Bioanalyzer, pooled at a final concentration of 12pM and sequenced on a HiSeq2500 or NextSeq500 system.

treatment_protocol: Mice were exposed to cold (4°C for 1 week (cold brown/beige adipocyte samples), and subsequently incubated at 30°C for 4 weeks (warm brown/beige adipocyte samples). Mice born and maintained at 30°C at all times used for warm white adipocyte samples.

value: adipose

value: H3K27ac (Active Motif, 39133)


title: Warm beige adipocyte H3K27ac ChIP rep 1

description: biological replicate


title: SLE 1

description:
High or Low grouping was based on attempts to group samples by expression of the Pbx1 gene
9067_SLE low1_(HTA-2_0)

value: systemic lupus erythematosus (SLE) patient

value: black

value: Yes

value: low


title: SLE 7

description:
High or Low grouping was based on attempts to group samples by expression of the Pbx1 gene
9073_SLE high3_(HTA-2_0)

value: hispanic

value: high


title: ribo_ded1tsdbp1Δ replicate 1_37 deg

value: ded1-ts dbp1delta (NSY15)


title: SLE 8

description:
High or Low grouping was based on attempts to group samples by expression of the Pbx1 gene
9074_SLE high4_(HTA-2_0)

value: No


title: ribo_dbp1Δ replicate 2_37 deg

description:
Ribosome-protected RNA
Experiment 1
dbp1_37deg.csv

value: dbp1delta (NSY14)


title: Pleomorphic xanthoastrocytoma Sample 5

value: Pleomorphic xanthoastrocytoma


title: Ganglioglioma / Diffuse astrocytoma Sample 8

value: Ganglioglioma / Diffuse astrocytoma


title: SLE 2 (SLE 1 + 6 months)

description:
High or Low grouping was based on attempts to group samples by expression of the Pbx1 gene
9068_SLE low2_(HTA-2_0)


title: ribo_dbp1Δ replicate 1_37 deg