title: BMed1_CAChrebp_Mock_D7_Med12

city: Bethesda

first: Kai

last: Ge

address: 50 South Dr Rm 4154

institute: NIH

data_processing:
Basecalls performed using Bcl2fastq.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2.
Peaks were called using SICER with following configuration: For ChIP-seq of histone modifications: Windows (200), Gaps (200), FDR (1e-3); For ChIP-Seq of factors: Windows (50), Gaps (50), FDR (1e-3)
Single or paired-end reads of RNA-seq are aligned to the mm9 genome assembly using STAR.
SICER v1.1 was used to calculate the reads per kilo base per million (RPKM) on exonic regions as expression measurements for each gene.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using in-house script and the scores represent RPKM; tab-delimited text files include FPKM values for each gene.

extract_protocol:
ChIP-seq: Cells were cross-linked with 1.5% formaldehyde for 10 min and quenched by 125 mM glycine for 10 min. 10 million fixed cells were resuspended in ice cold buffer containing 5mM PIPES, pH 7.5, 85mM KCl, 1% NP-40 and protease inhibitors, incubated on ice for 15 min, and centrifuged at 500 g for 5 min at 4°C. Nuclei were resuspended with 1mL buffer containing 50mM Tris-HCl, pH8.0, 10mM EDTA, 0.1% SDS and protease inhibitors, and subjected to sonication. Sheared chromatin was clarified by centrifugation at 13,000 g for 10 min at 4°C. The supernatant was transferred to a new tube and further supplemented with 1% Triton-X100, 0.1% sodium deoxycholate and protease inhibitors. 2% of the mixture was set aside as input and 20ng of spike-in chromatin (Active Motif, #53083) was added to the rest. For each ChIP, 4 - 10 µg of target antibodies and 2μg of spike-in antibody (anti-H2Av, Active Motif, #61686) were added and incubated on a rotator at 4°C overnight. ChIP samples were added with 50μL prewashed protein A Dynabeads (ThermoFisher) and incubated for 3h at 4°C. Beads were then collected on a magnetic rack and washed twice with 1mL cold RIPA buffer, twice with 1mL cold RIPA buffer containing 300mM NaCl, twice with 1mL cold LiCl buffer and once with PBS. Beads were then eluted with 100 μL buffer containing 0.1M NaHCO3, 1% SDS, and 20μg Proteinase K at 65°C overnight. Input sample volumes were adjusted to 100μL with the elution buffer. Samples were then purified using QIAquick PCR purification kit (Qiagen) and eluted in 30 μL 10mM Tris-HCl.
ChIP-seq: Libraries were prepared according to NEB (Illumina kit) instructions. DNA were used to construct libraries using NEBNext® Ultra™ II DNA Library Prep kit with AMPure XP magnetic beads (Beckman Coulter).
ATAC-Seq: 5 × 10^4 freshly collected cells were aliquoted into a new tube and spun down at 500 × g for 5 min at 4 °C. The cell pellet was incubated in 50 µl of ATAC-RSB buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin (Promega) on ice for 3 min and was washed out with 1 ml of ATAC-RSB buffer containing 0.1% Tween-20. Nuclei were collected by centrifugation at 500 × g for 10 min at 4 °C, then resuspended in 50 µl of transposition reaction buffer (25 µl 2x Tagment DNA buffer, 2.5 µl transposase (100 nM final; Illumina), 16.5 µl PBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20, 5 µl H2O). The reaction was incubated at 37 °C for 30 min with mixing (1000 r.p.m.) and directly subjected to DNA purification using the MinElute Reaction Cleanup Kit (Qiagen) according to the manufacturer’s instructions.
ATAC-Seq: DNA was amplified with PCR using Nextera i7- and i5-index primers for Illumina protocols
RNA-Seq: Total RNA was subjected to mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490).
RNA-Seq: Isolated mRNAs were reverse-transcribed into double stranded cDNA and subjected to sequencing library construction using the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (NEB, E7770) according to the manufacturer’s instructions.
nascent RNA-Seq: 10^6 cells were labeled with 0.5 mM ethylene uridine for 30 min at 37 °C. After RNA extraction, 1 μg total RNA was depleted of rRNA using the NEBNext rRNA Depletion kit (NEB). To capture nascent RNA, the sample was biotinylated by the Click-iT Nascent RNA Capture Kit (ThermoFisher, C10365) according to the manufacturer’s instructions.
nascent RNA-Seq: Double-stranded cDNAs were synthesized using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen). Library construction was done using NEBNext Ultra™ II DNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

tag: strain background

value: 129S4/SvJae - C57BL/6 mixed

value: Brown adipocytes (differentiated)

tag: stage of adipogenesis

value: Mature adipocytes (D7)

tag: chip antibody

value: anti-MED12 (A300-774A, Bethyl)


title: C22-PD5-C9-1

status: Public on Mar 17 2021

type: SRA

city: Seoul

first: Ho-Geun

last: Yoon

address: 50-1 Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University College of Medicine

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

molecule: total RNA

organism: Mus musculus

growth_protocol: Mouse clara C22 cell line derived  from transgenic H-2Kb-tsA58 mice capable of being passaged as an immortalised cloned cell line in culture. Cells grow at 33 ºC in the presence of gamma-interferon, at 39ºC in the absence of gamma-interferon cells terminally differentiate.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Differentiated cells were starved serum for 2 hours, 20ng/ml TGF-beta1 was added and incubated for 24 hours.

tag: cell line

tag: cell type

value: Mouse lung clara cell line

tag: genotype/variation

tag: treatment

value: control


title: ADC-3

type: RNA

city: Houston

first: Jiexin

last: Zhang

state: TX

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

country: USA

institute: UT MD Anderson Cancer Center

description:
Run01-RAW.xlsx
J5C

hyb_protocol: The Gene expression assay was performed on the NanoString nCounter platform using the PanCancer Immune Profiling Panel (cat # 115000132). 12 FFPE samples (input of 200 ng to 300 ng based on DV200 value) were run per cartridge following the manufacturer’s protocol. Briefly, Excess probes are hybridized (overnight) at 65C to target RNA molecules to ensure that each target finds a probe pair. After hybridization, excess probes were washed away using the automated nCounter instrument.

scan_protocol: After hybridization washes, the cartridge was read using ncounter digital analyzer (an epifluorescene microscope with CCD capture technology that generates target molecule counts).

data_processing:
nSolver 4.0 software (NanoString Technologies) was applied for quality control with default setting, and all samples passed QC check. Background correction was performed with negative controls, followed by two-steps normalization using geometric mean of 6 positive controls and 40 housekeeping genes. Then global adjustment was achieved by quantile-normalization to remove any unwanted technical variations, which was followed by log2 transformation to obtain variance stabilization.
nSolver processed data are further quantile normalized and log2 transformed for all analysis

molecule: polyA RNA

organism: Homo sapiens

source_name: PreCancer of Lung

growth_protocol: The surgical specimens were subjected to FFPE blocks directly

extract_protocol: RNA was extracted from FFPE using the AllPrep DNA/RNA FFPE kit (QIAGEN, Netherlands) per the manufacturer’s instructions. FFPE samples with tumor area demarcated by a pathologist was manually macro-dissected to enrich for the demarcated tumor area before RNA extraction.  On average, three 10-micron thick sections were used for RNA extraction per patient. Each sample was run on the Agilent TapeStation 4200 to determine the DV200 value (degree of fragmentation of the sample based on the percentage of the sample with greater than 200 intact nucleotides) for the FFPE samples. All the FFPE samples had 11.4% to 91.6% of the RNA having greater than 200 intact nucleotides.

treatment_protocol: no treatment for these surgical specimens

tag: tissue

value: Lung

tag: histology

value: ADC


title: C22-C9-TGF-3

source_name: C22_TGF-beta1 24h

value: negative control

value: TGF-beta1 24h


title: Histone A rep 2

city: Fort Collins

first: Thomas

last: Santangelo

address: 1062 Campus Delivery

institute: Colorado State University

data_processing:
TS6001 and TS622: RNA-Seq reads were first analyzed for quality control using FastQC. To remove adapter sequences and other artifacts, fastx-trimmer was used to trim the first 11 positions in each read. After filtering, the reads were aligned to the Thermococcus kodakarensis (KOD1) reference genome using bowtie with the following parameter: -m 1, this ensured suppressing all multiple-aligned reads. Finally, the bowtie output was converted to BAM format, sorted, and indexed using samtools.
TS6002 and TS620: RNA-Seq reads were first analyzed for quality control using FastQC. To remove adapter sequences and other artifacts, fastx-trimmer was used to trim the first 19 positions in each read. After filtering, the reads were aligned to the Thermococcus kodakarensis (KOD1) reference genome using bowtie2. Next, in each library, reads that aligned to multiple locations were filtered out. Finally, the filtered output was converted to BAM format, sorted, and indexed using samtools.
To quantify differential gene expression while comparing two samples, EdgeR was used. Note that EdgeR relies on read counts across individual biological replicates for both samples under comparison. To generate those read counts for every gene (in Ensembl based annotations), we used a custom python script that used SpliceGrapher and pysam. The EdgeR p-values were adjusted for multiple comparisons using the Benjamini-Hochberg method. Finally, we used a cutoff of 1.00 on the transcript abundance (log CPM) and fold change (log FC).
Genome_build: ASM996v1
Supplementary_files_format_and_content: archive of comma separated differential gene expression results (from EdgeR)

organism: Thermococcus kodakarensis

source_name: Thermococcus kodakarensis

growth_protocol: TS600, TS620 and TS622 were grown in triplicate to an O.D.600 of ~0.5 in liquid ASW-YT-S and used to inoculate (1:100) 300 ml of ASW-YT-Pyr per strain and allowed to grow to an O.D.600 of ~0.05 to encourage chromatin reprogramming

extract_protocol:
Cultures were rapidly chilled and pelleted at 10,000 rpm for 5 min and then resuspended in 1.0 mL of Trizol (Invitrogen) with a 10-minute incubation at room temperature. 200 µl of chloroform was added followed by centrifugation at 15,000 rpm at 4 °C for 15 minutes yielding an RNA-containing aqueous layer which was added to 500 µl of isopropanol and incubated at room temperature for 10 minutes. Centrifugation at 15,000 rpm for 15 minutes at 4° C yielded an RNA pellet that was washed with 1 ml of 75% EtOH and subsequently resuspended in 88 µl of RNase-free H2O, 10 µl of DNaseI buffer and 1 µl of DNaseI (New England Biolabs) to digest residual DNA (37° C for 30 minutes). A second triplicate of TS600 and a triplicate of TS620 were prepared identically.
TS600 and TS620: 1.5 µg of RNA was processed at Novogene for Prokaryotic RNA-seq, specifically for rRNA depletion (Ribo-ZeroTM Magnetic Kit), library construction (NEBNext® Ultra™ RNA Library Prep kit) and 150 bp paired-end sequencing on a HiSeq Illumina® platform.
TS600 and TS622: Using ~120ng of RNA that was ribosomally depleted following the NEBNext® rRNA Depletion Kit (E6310), cDNA libraries were constructed with New England Biolabs NEBNext® Ultra™ Directional RNA Library Prep kit for Illumina® (E7420s) and NEBNext® Multiplex Oligos for Illumina® (Index primer set 1, E7335) according to the manufacture’s procedure. The multiplexed libraries were sequenced at Cofactor Genomics using one high output NextSeq Illumina® run for single-end reads with a minimum read length of 75 bp and with a requested > 40 million reads per sample.

treatment_protocol: TS600 and TS622 were grown in triplicate to an O.D.600 of ~0.5 in liquid ASW-YT-S and used to inoculate (1:100) 300 ml of ASW-YT-Pyr per strain and allowed to grow to an O.D.600 of ~0.05 to encourage chromatin reprogramming

tag: strain

tag: genotype

value: dHTKB

tag: growth medium

value: pyruvate


title: BMed1_CAChrebp_4OHT_D7_T7

state: MD

department: NIDDK

library_source: genomic

molecule: genomic DNA

growth_protocol: ChIP-seq: Primary brown preadipocytes were isolated from interscapular BAT of newborn Med1f/f;CreER mice) and immortalized with SV40T-expressing retroviruses generated from the pBabeneo-large T plasmid

treatment_protocol: ChIP-seq: For adipogenesis assay, cells were plated in growth medium (DMEM plus 10% FBS) at a density of 1.8x106 cells per 15-cm dish 4 days before induction of adipogenesis. At D0, confluent cells were induced with 0.02 μM insulin, 1 nM T3, 0.5 mM 3-isobutyl-1-methyl-xanthine (IBMX), 2 μg/ml dexamethasone, and 0.125mM indomethacin. At D2, D4, and D6, the cells were replenished with medium containing 10% FBS, 0.02 μM insulin, and 1 nM T3.

value: anti-T7 (#132469, Cell Signaling)


title: Histone A rep 1


title: Subset_DN2

city: La Jolla

first: Stanislav

last: Dikiy

state: CA

address: 10550 North Torrey Pines Road

department: Immunology

institute: Scripps Research

data_processing:
Trim adapter sequences, removed unpaired reads; Trimmomatic v0.36; options: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Align reads to genome; STAR v2.5.4b; options: --runThreadN 6 --runMode alignReads --genomeLoad NoSharedMemory --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outBAMcompression 6 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.06 --outFilterMatchNminOverLread 0.55 --outFilterMatchNmin 30 --alignIntronMax 1 --alignEndsType Local
Sort by name; samtools v1.10; options: sort -@ 4 -n
Fix mate information; samtools v1.10; options: fixmate -rm
Sort by coordinate; samtools v1.10; options: sort -@ 4
Remove duplicate reads; samtools v1.10; options: markdup -l 1500 -r -d 100
Sort by name; samtools v1.10; options: sort -@ 4 -n
Convert bam to bedgraph and scale for library size; bedtools v2.26.0; options bedtools genomecov -bg -scale -g mm10.genome
Convert bedgraph to bigWig; wigToBigWig; options: wigToBigWig -clip mm10.genome
Genome_build: mm10
Supplementary_files_format_and_content: bigWig format: continuous graph of aligned read density across genome (indexed)

source_name: thymus

extract_protocol:
Combined protocol for extraction and library preparation, see below
cells were pelleted in a fixed rotor benchtop centrifuge at 500g for 5 minutes at 4°C. Cells were then washed in 1ml cold 1x PBS and pelleted again. Supernatant was aspirated and cells were resuspended in 50µl ice-cold cell lysis buffer (10mM Tris-Cl pH 7.4; 10mM NaCl; 3mM MgCl2; 0.1% NP-40) to disrupt plasma membranes. Nuclei were pelleted at 1000g for 10 minutes. Supernatant was aspirated and nuclei were resuspended in 50µl transposition reaction mixture (25µl TD buffer; 2.5µl TDE1; 22.5µl ddH2O; llumina, 20034197). Samples were incubated in a ThermoMixer at 1100rpm for 45 minutes at 42°C. DNA was then purified using a MinElute PCR Purification Kit (QIAGEN, 28004), per manufacturer instructions. DNA was eluted in 10µl buffer EB. Libraries were then barcoded and amplified with NEBNext High-Fidelity Master Mix and primers from (Buenrostro et al., 2013) (50µl reaction with 10µl DNA and 2.5µl of 25µM primers – 1 cycle of 5min at 72°C, 30sec at 98°C; 5 cycles of 10sec at 98°C, 20sec at 63°C, 1min at 72°C). A qPCR on the product determined that an additional 7 cycles (10sec at 98°C, 20sec at 63°C, 1min at 72°C) were required. Library was purified and size selected with AMPure beads (Beckman Coulter, A63881): 45µl of PCR product was incubated with 18µl beads and supernatant was collected (beads bound larger >2000bp fragments). Supernatant (63µl) was then incubated with an additional 63µl of beads for 5 minutes, supernatant was removed, beads were washed 2x with 75% ethanol, and DNA was eluted into 50µl H2O by incubating for 2 minutes.

value: Double negative #2 thymocyte

value: thymus


title: C22-C9-TGF-1


title: Mutant Histone A rep 1

description: TS622 1


title: BMed1_CAChrebp_Mock_D7_T7


title: Mutant Histone A rep 2

description: TS622 2


title: Subset_rTreg

source_name: lymph node and spleen

value: resting regulatory T cell

value: lymph node and spleen


title: C22-C9-TGF-2


title: 5798808007_E

city: Bari

first: Elena

last: Piccinin

state: Ba

address: Piazza Giulio Cesare, 11, Palazzo Morgagni - Lab. Clinica Medica Frugoni - II piano

country: Italy

institute: University of Bari "Aldo Moro"

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: WT Ileum Fraction C1

label_protocol: Not provided

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

treatment_protocol: After sacrifice, the ileum was removed from each mouse, flushed with cold saline solution, and longitudinally cut. The epithelium from the crypt-villus axis was isolated following a modified Weiser method. Briefly, ileum was cut longitudinally and transferred into Hank’s balanced salt solution with 0.5mM-DTT to remove the luminal content (mucus and faeces). Then, ileum was transferred into 30 ml of Chelating Buffer (Na2PO4 5mM, NaCl 96mm, Na Citrate 27mM, KH2PO4 8mM, KCl 1.5 mm, D-Sorbitol 55mM, Sucrose 44mM, DTT 0.5 mM), and incubated at 4°C with constant stirring for 20 minutes. Supernatant was collected and called “V0 fraction”. Intestinal fragment was transferred into a falcon (50 ml) with 15 ml of Chelating buffer and gently shaken by hand (30 inversions). Supernatant was collected twice for each fraction (V1, V2, V3 and C1). All collected fractions were centrifuged at 1000g and the resultant pellets were immediately processed for RNA extraction.

tag: gender

value: Male

tag: age

value: 4 months

value: Ileum epithelial cells


title: 5798808011_L


title: BMed1_CAChrebp_Mock_D7_input

value: 129S4/SvJae - C57BL/6 mixed

value: Brown adipocytes (differentiated)

value: Mature adipocytes (D7)


title: C22-C9-3

value: Mouse lung clara cell line

value: control


title: BMed1_4OHT-D7_S2P-PolII

value: anti-S2P Pol II (ab5095, Abcam)


title: C22-C9-2

value: negative control


title: BMed1_CAChrebp_4OHT_D7_input


title: 5798808014_G


title: BMed1_Mock-D7_S2P-PolII


title: RNA-Seq-siKDM5C-CTL-MCF-7-rep1

city: Xiamen

first: Guosheng

last: Hu

state: Fujian

address: Xiang'an South Road, Xiang'an District

department: School of Pharmaceutical Sciences

country: China

institute: xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Tophat version 2.1.1.
Genome_build: hg19

growth_protocol: MCF-7 cells were cultured in DMEM medium supplemented with 10% FBS and 1%penicillin and streptomycin

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina HiSeq platform at RiboBio Co., Ltd. or Amogene Biotech Co., Ltd.

treatment_protocol: Before experiment, MCF-7 cells were knockdown by siRNA(CTL) or siRNA specifically targeting KDM5C or ZMYND8 and medium was changed to phenol red free DMEM plus 5% charcoal-stripped FBS and 1% penncilin and streptomycin. On the second day, cells were treated with the same way as described above and maintained for another two days, followed by treatemnt of either 100nM 17-β-estrodial or ethanol for 6hrs.

value: Michigan Cancer Foundation-7 (MCF-7) cells

tag: genotype/varaition


title: 5798808007_I

source_name: WT Ileum Fraction V3


title: 5798808007_D


title: BMed1_Mock-D7_S5P-PolII

value: anti-S5P Pol II (ab5131, Abcam)


title: BMed1_CAChrebp_4OHT_D7_Med12

value: anti-MED12 (A300-774A, Bethyl)


title: 5798808014_C


title: 5798808014_H


title: 4HUVEC-IR72hr

first: Yoon-Jin

last: Lee

address: Nowon GU

institute: Korea Institute of Radiological & Medical Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
Read count
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Read Count values for each Sample

source_name: HUVEC

growth_protocol: HUVECs were cultured in Endothelial Cell Growth Medium 2 (Promocell).

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

treatment_protocol: HUVECs were irradiated with gamma rays from a [137Cs] source at 3.81 Gy/min.

value: Human umbilical vein endothelial cells

tag: irradiation


title: BMed1_4OHT-D7_S5P-PolII


title: BMed1_4OHT-D7_input


title: BMed1_Mock-D7_input


title: 3HUVECNoIR

value: No IR


title: RNA-Seq-siCTL-E2-MCF-7-rep1

value: siCTL


title: RNase H1 (LS78D)

city: Davis

first: Frederic

last: Chedin

address: 1 Shields Avenue

department: MCB

institute: UC Davis

data_processing:
Library strategy: sDRIP-seq
Raw fastq reads were trimmed with fastq-mcf v2.4.4 and mappved with bowtie2 v2.2.6 (sDRIP-seq).
sDRIP-seq peaks were called using Macs v2.2.5 with default parameters except for --nomodel. We then merged peaks from all samples. HTseq-count v0.11.2 was then used to count the total number of reads in each merged peak.
Gencode v19 APPRIS gene annotation was used for our analysis, prioritizing highest principal isoform. DESeq2 was used to call differentially expressed regions.
Genome_build: hg19
Supplementary_files_format_and_content: sDRIP-seq bedGraph files were generated using bedtools genomecov and converted into bigWig using wigToBigWig; scores indicate tag per million (x30).

source_name: NTREA-2 D1

growth_protocol: NTERA-2 D1 cells were obtained from ATCC and grown in high-glucose Dulbecco’s Modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin / streptomycin. Cells were seeded 1-2 days prior to experiments and were grown to 40-60% confluency

extract_protocol:
sDRIP-seq: Genomic DNA was gently extracted using salt/ethanol percipitation, sonicated, and immunoprecipitated with S9.6 antibody.
sDRIP-seq: Enriched R-loop fragments were subjected to second strand synthesis using dUTP instead of dTTP for strand-specific library construction. Illumina TruSeq Single adapter was ligated and the cDNA and amplified as per standard Illumina TruSeq Single end protocol.

treatment_protocol: Extracted DNA was subjected to mock or enzymatic treatments (RNase H1, RNase III, RNase T1, or RNase T1+RNase III) prior to immunoprecipitation with the S9.6 antibody.

value: testicular embryonal carcinoma cell line

value: NTREA-2 D1

value: RNase H1


title: 3HUVEC-IR72hr


title: RNA-Seq-siKDM5C-E2-MCF-7-rep1


title: RNase T1+III (DG3L)

value: RNase T1+III


title: 4HUVEC-IR5hr

value: 10 Gy, 5 hr


title: 3HUVEC-IR5hr


title: Mock (LS78A)

value: Mock


title: 5991915010_K

source_name: WT Ileum Fraction V2

value: Male

value: 4 months

value: Ileum epithelial cells


title: 5798808007_H


title: Med1_CreER_4OHT_D7_ATAC

value: 129S4/SvJae - C57BL/6 mixed

value: Brown adipocytes (differentiated)

value: Mature adipocytes (D7)


title: RNA-Seq-siCTL-CTL-MCF-7-rep1

value: Michigan Cancer Foundation-7 (MCF-7) cells

value: control


title: RNase III (DG3K)

value: RNase III


title: Mock (LS78B)


title: 5798808007_G

source_name: WT Ileum Fraction V1


title: RNase T1 (DG3J)

value: RNase T1


title: 5798808007_C


title: NaRNA_Med1_CreER_Mock_D7

data_processing:
Library strategy: Nascent RNA-Seq
Basecalls performed using Bcl2fastq.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2.
Peaks were called using SICER with following configuration: For ChIP-seq of histone modifications: Windows (200), Gaps (200), FDR (1e-3); For ChIP-Seq of factors: Windows (50), Gaps (50), FDR (1e-3)
Single or paired-end reads of RNA-seq are aligned to the mm9 genome assembly using STAR.
SICER v1.1 was used to calculate the reads per kilo base per million (RPKM) on exonic regions as expression measurements for each gene.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using in-house script and the scores represent RPKM; tab-delimited text files include FPKM values for each gene.

tag: molecule subtype

value: Nascent RNA


title: 5798808007_B


title: 1HUVEC-IR72hr

value: Human umbilical vein endothelial cells


title: 5991915010_L


title: 1HUVECNoIR

value: No IR


title: RNase III (DG3H)

value: testicular embryonal carcinoma cell line

value: NTREA-2 D1


title: 4HUVECNoIR


title: ADC-1 corresponding

description:
Run01-RAW.xlsx
J2N

value: Lung

value: N


title: RNA_Med1_CreER_Mock_D7

tag: strain background


title: 5991915010_H

value: Male


title: CDK9-siZMYND8-E2-MCF-7

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Bowtie version 2.2.6 with the default options.
The bigwig files were generated by using HOMER 4.9, in which the total tags are normalized to 1.00e+07.
Peaks are called by using Homer findPeaks script
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

growth_protocol: MCF-7 cells were cultured in DMEM medium supplemented with 10% FBS and 100 units/mL penicillin/100 ug/mL streptomycin

extract_protocol:
For ChIP assays, cells were fixed with disuccinimidyl glutarate (DSG) (2 mM) (Proteochem) for 45 mins at RT, washed twice with PBS and then double-fixed with 1% formaldehyde for another 10 mins at RT (for KDM5C (Bethyl Laboratory, A301-034A), ZMYND8 (Bethyl Laboratory, A302-090A)) or fixed with 1% glutaraldehyde for 10mins at RT(for CDK9 (CST, 2316S) ChIP). Fixation was stopped by adding glycine (0.125 M) and incubating for 5 mins at RT, followed by washing with PBS twice. Chromatin DNA was sheared to 200-500 bp average in size through sonication. Resultant was immunoprecipitated with control IgG or specific antibodies overnight at 4 ℃, followed by incubation with protein G magnetic beads (Biorad) for an additional 3 hrs. After washing and elution, formaldehyde or DSG and formaldehyde fixed chromatin was treated at 65 ℃ overnight whereas glutaraldehyde fixed chromatin was treated with 0.2mg/mL proteinase K at 55℃ for two hours then 65℃ overnight with interval shaking. Immunoprecipitated DNA was purified by using QIAquick spin columns (Qiagen) and subjected to either qPCR analysis or high throughput sequencing.
The libraries were constructed following Illumina ChIP-seq Sample prep kit. Briefly, ChIP DNA was end-blunted and added with an ‘A’ base so the adaptors from Illumina with a ‘T’ can ligate on the ends. Then 200-400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

treatment_protocol: Before experiment, medium was changed to phenol red free DMEM plus 5% charcoal-stripped FBS and 1% penncilin and streptomycin to culture for 3 days, followed by treatemnt of either 100nM 17-β-estrodial or ethanol for 1hr.


title: Med1_CreER_Mock_D7_ATAC

tag: stage of adipogenesis


title: RNA_Med1_CreER_4OHT_D7


title: RNase T1 (DG3G)


title: RNA_TRAP_AdipoQ_P2.5_ingWAT_rep2

description:
TRAP_AdipoQ_P2.5_ingWAT_rep2
processed data file: TRAP_Adipoq-Cre_BAT_iWAT_RPKM_exon.txt

data_processing:
Library strategy: TRAP-seq
Basecalls performed using Bcl2fastq.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2.
Peaks were called using SICER with following configuration: For ChIP-seq of histone modifications: Windows (200), Gaps (200), FDR (1e-3); For ChIP-Seq of factors: Windows (50), Gaps (50), FDR (1e-3)
Single or paired-end reads of RNA-seq are aligned to the mm9 genome assembly using STAR.
SICER v1.1 was used to calculate the reads per kilo base per million (RPKM) on exonic regions as expression measurements for each gene.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using in-house script and the scores represent RPKM; tab-delimited text files include FPKM values for each gene.

value: TRAP;Adipoq-Cre

value: White adipocytes (purified)

value: Mature adipocytes

tag: chip antibody

value: anti-GFP (ab290, Abcam)


title: 5991915010_G

value: 4 months

value: Ileum epithelial cells


title: RNA_TRAP_AdipoQ_P2.5_ingWAT_rep1

description:
TRAP_AdipoQ_P2.5_ingWAT_rep1
processed data file: TRAP_Adipoq-Cre_BAT_iWAT_RPKM_exon.txt

value: 129S4/SvJae - C57BL/6 mixed


title: NaRNA_Med1_CreER_4OHT_D7

value: Brown adipocytes (differentiated)

value: Mature adipocytes (D7)


title: RNase T1+III (DG3I)

tag: cell line

value: RNase T1+III


title: 5798808007_F

source_name: WT Ileum Fraction V0


title: 5798808007_A


title: CDK9-siKDM5C-E2-MCF-7

value: Michigan Cancer Foundation-7 (MCF-7) cells


title: CDK9-siKDM5C-CTL-MCF-7

value: control


title: HuD-KO-2

city: Albuquerque

first: Nora

last: Perrone-Bizzozero

state: NM

address: 1 University of New Mexico MSC08 4740

department: Neurosciences

institute: University of New Mexico

data_processing:
MATLAB code for PCA analyses: One of the HuD KO sequencing pairs (HuD-KO-2) was considered an outlier and this replicate was excluded from the analysis
FastQC software (version 0.11.5) : To evaluate quality
Cutadapt and Trimmomatic: To remove adapters
STAR (version 2.7.3a): To align files
rMATS (version 4.0.2) : To identify alternative splicing
DaPars software (version 0.9.1): To determine alternative polyadenylation
Ingenuity Pathway Analysis (IPA) : To identify biological pathways, networks, functions and diseases
Genome_build: mm10

source_name: neocortex

growth_protocol: adult mouse

extract_protocol:
TRIzol RNA extraction from flash-frozen neocortices
NovaSeq 6000 S4 Reagent Kits
Library preps for paired-end RNA-sequencing
1) Fragmentation of the RNA molecules;
2) Reverse transcription to synthesis first strand cDNA;
3) Second strand cDNA synthesis incorporating dUTP;
4) End-repair and A-tailing of the double stranded cDNA;
5) Illumina compatible adapter ligation;
6) PCR amplification and purification for the final RNA-seq library.

treatment_protocol: wild tye and knock-out mice

value: neocortex


title: 1HUVEC-IR5hr

tag: cell type

value: Human umbilical vein endothelial cells

value: 10 Gy, 5 hr


title: HuD-KO-3


title: CDK9-siCTL-E2-MCF-7

value: siCTL


title: HuD-KO-1


title: L1866-Triptolide_time_course_96h_washout_high_dose_Hi-C

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

data_processing:
read alignment: juicer_tools.1.8.9
Genome_build: custom
Supplementary_files_format_and_content: bedGraph of read coverage, normalized to RPM (Read Per Million) except for dSMF samples, where the bedGraph shows the methylation percentage

organism: Breviolum minutum

extract_protocol:
Symbiodinium minutum SSBO1 cells were first crosslinked using 37% formaldehyde (Sigma) at a final concentration of 1% for 15 minutes at room temperature. Formaldehyde was then quenched using 2.5 M Glycine at a final concentration of 0.25 M. Cells were subsequently centrifuged at 2,000 g for 5 minutes, washed once in 1X PBS, and stored at -80C.
Symbiodinium minutum SSBO1 cells were first crosslinked using 37% formaldehyde (Sigma) at a final concentration of 1% for 15 minutes at room temperature. Formaldehyde was then quenched using 2.5 M Glycine at a final concentration of 0.25 M. Cells were subsequently centrifuged at 2,000 g for 5 minutes, washed once in 1X PBS, and stored at -80C.

value: a-amanitin treatment, 4ug/mL, 96h washout


title: 5991915010_D

value: Male


title: L1865-Amanitin_time_course_96h_washout_high_dose_Hi-C

value: triptolide treatment, 40uM, 96h washout


title: L1864-NT_time_course_96h_washout_Hi-C

value: a-amanitin treatment, 0ug/mL, 96h


title: CDK9-siCTL-CTL-MCF-7


title: Kdm6b stimulated_rep2

city: Clayton

first: Monash

middle: Bioinformatics

last: Platform

state: VIC

address: Wellington Road

country: Australia

institute: Monash Bioinformatics Platform

data_processing:
The RNAsik pipeline (v1.5.4) was run to process the data
In brief, RNAsik uses STAR to align raw data to a reference genome (GRCm38)
RNAsik performs a variety of quality control checks using fastQC, samtools, picard, qualimap to assess the quality of the data
Finally, RNAsik uses featureCounts to count reads to annotated genes
The counts file is uploaded to Degust for differential gene expression analysis. Degust utilises the R packages voom & limma
Genome_build: GRCm38
Supplementary_files_format_and_content: csv count file

source_name: Naïve (CD44int/lo CD62Lhi) CD8+ T cells

growth_protocol: Naïve (CD44hi, CD62Lhi) CD8+ T cells were sorted purified from male mice (6-12 weeks old).

extract_protocol:
Total RNA was extracted using the Qiagen Rneasy kit with on-column DNAse treatment
Poly-A mRNA selection, MGIEasy stranded mRNA V2 chemsity

treatment_protocol: They were either left non-stimulated or stimulated in vitro with plate-bound anti-CD3 (1ug/mL) and anti-CD28 (5ug/mL) for 5hr in the presence of IL-2 (10U/mL)

value: Vav-Tta Kdm6b

value: CD8 T cells

value: In vitro stimulation with plate-bound CD3 and anti-CD28


title: HuD-ctr-2

value: wild type


title: 5991915010_C

value: 4 months

value: Ileum epithelial cells


title: CDK9-siZMYND8-CTL-MCF-7


title: Kdm6b non-stimulated_rep2

value: non-stimulated


title: Kdm6b stimulated_rep1


title: L1862-Amanitin_time_course_48h_high_dose_Hi-C

value: a-amanitin treatment, 4ug/mL, 48h


title: L1863-Triptolide_time_course_48h_high_dose_Hi-C

value: triptolide treatment, 40uM, 48h


title: RNA_Med1_male_4wk_AKO_WAT

value: 129S4/SvJae - C57BL/6 mixed

tag: genotype/variation

value: Inguinal white adipose tissue


title: Bif3_ear_primordia_rep3

city: Piscataway

first: Andrea

last: Gallavotti

state: NJ

address: 190 Frelinghysen Rd.

department: Waksman Institute of Microbiology

institute: Rutgers University

data_processing:
Illumina software used for base calling
Sequenced reads were trimmed for adaptor sequence using trimmomatic, then mapped to ZmB73v3 whole genome using Tophat v2.1.1
Differentially expressed genes were identified using cuffdiff
Genome_build: ZmB73v3.19
Supplementary_files_format_and_content: Bif3v3.19_7samples_genecounts_GEO_Submit.csv
Bif3v3.19-edgeR-7samples_qlf_results-with-normalized_GEO_Submit.xlsx

organism: Zea mays

source_name: 3-4 mm maize B73 field-grown Bif3 ear primordia

extract_protocol:
samples were snap frozen in liquid nitrogen and total RNA was extracted using RNeasy kit (Qiagen) with DNAse treatment
Stranded Illumina mRNA sequencing libraries were generated using TruSeq (Illumina)

treatment_protocol: 3-4 mm maize B73 field-grown ear primordia were harvested. Bif3 samples included ear primordia with Bif3 mutant appearance

tag: background

value: Bif3 mutant

value: ear primordia


title: Bif3_ear_primordia_rep4

growth_protocol: 3-4 mm maize B73 field-grown ear primordia

tag: tissue


title: L1861-NT_time_course_48h_Hi-C

tag: treatment

value: a-amanitin treatment, 0ug/mL, 48h


title: Bif3_ear_primordia_rep2


title: L1859-Triptolide_time_course_8h_NT_intactHi-C

tag: strain

value: no SDS Hi-C


title: RNA_Med1_male_4wk_AKO_BAT

value: Brown adipose tissue


title: Kdm6B non-stimulated_rep1


title: 5798808014_D

value: Male


title: RNA_Med1_male_4wk_flox_WAT


title: L1860-NT_time_course_0h_Hi-C

value: a-amanitin treatment, 0ug/mL, 0h


title: L1334-SSB01-a_amanitin_high-48h-Hi-C 2


title: wildtype_ear_primordia_rep2

source_name: 3-4 mm maize B73 field-grown ear primordia

tag: genotype

value: wildtype


title: Lc1309 non-stimulated_rep1

value: Vav-Tta Lc1309

value: CD8 T cells


title: L1332-SSB01-a_amanitin-0h-Hi-C 2

value: a-amanitin treatment, 1ug/mL, 0h


title: second_set_Histone A rep 2

value: dHTKB

tag: growth medium

value: pyruvate


title: Bif3_ear_primordia_rep1


title: RNA_Med1_male_4wk_flox_BAT


title: Lc1309 stimulated_rep1

value: In vitro stimulation with plate-bound CD3 and anti-CD28


title: second_set_Histone A rep 1


title: wildtype_ear_primordia_rep3


title: HuD-ctr-3

value: neocortex

value: wild type


title: 24 hr ST 3

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

description: Tx 24 hr 3

data_processing:
Fastqs generated, trimmed, aligned with STAR followed by DeSeq2, EdgeR and Cuffdiff for DEG
Genome_build: hg19

source_name: Metastatic colonic carcinoma

extract_protocol:
Library construction was performed according to Illumina TruSeq Starnded Total RNA sample preparation protocol
Coding and non-coding RNA-seq

value: Intestinal epithelial cells

value: Treated with 100 ng ST for 24 hr


title: Senescent IMR90 cells rep1

first: Jaejin

last: Kim

address: Gwanak-ro 1

institute: Seoul National University

data_processing:
The sequence reads were trimmed with Trimmomatic version 0.36 and mapped against the human reference genome (hg38) using Hisat2 version 2.1.0.
Read counts per gene were calculated by using featureCounts version 1.6.3.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: IMR90 cells

growth_protocol: IMR90 cells were maintained in 3% O2 and cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 15% fetal bovine serum (FBS), penicillin/streptomycin, and 0.1 mM nonessential amino acids.

extract_protocol:
Total RNAs were isolated using the acidic phenol extraction method.
One microgram of high-quality RNA samples (RIN > 7.0) was used to construct RNA-seq libraries using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina). Total RNA integrity was checked using an Agilent 2200 TapeStation. RNA-seq was performed on an Illumina NovaSeq 6000 sequencer at Macrogen.

treatment_protocol: IMR90 cells were treated with bleomycin (10 ug/ml for 24 h) to induce senescence.

value: Lung fibroblast

value: 10 days after exposure to bleomycin (10 ug/ml for 24 h)


title: normal-lung-RNA

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

description:
PolyA RNA
processed data file: counts.raw.csv
processed data file: counts.normalized.csv
processed data file: counts.fpkm.csv

data_processing:
Base calling and demultiplexing were performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the mouse genome (build mm10/GRCm38) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.csv: CSV files contain raw and normalized counts for all genes and samples.
Supplementary_files_format_and_content: counts.raw.csv: Raw counts
Supplementary_files_format_and_content: counts.normalized.csv: Normalized counts
Supplementary_files_format_and_content: counts.fpkm.csv: FPKMs (Fragments Per Kilobase of transcript per Million mapped reads)

source_name: Normal lung tissue

growth_protocol: The genetically engineered mouse model (GEMM) harboring a conditional activating mutation of endogenous Kras (KrasLSL-G12D/+) crossed with Lkb1 or p53 conditional knockout (Lkb1fl/fl or Trp53fl/fl) has been previously described. Briefly, this KrasLSL-G12D strain carries a Lox-Stop-Lox (LSL) sequence followed by the KrasG12D point mutation allele commonly associated with human cancer. Trp53 exons 2-10 are flanked by loxP sites in this conditional targeted mutation. For Lkb1fl/fl mice, the transcript from the Lkb1 null allele eliminates exons 2–6, resulting in a translational frameshift. All the mice are crossed and confirmed with higher than 90% C57BL/6 genetic background by SNP analysis. CRE recombinase was induced through intranasal inhalation of 1x10e7 p.f.u. adeno-Cre (University of Iowa adenoviral core). The induced mice were evaluated by MRI imaging to quantify the lung tumor burden, and KP (KrasG12DTrp53fl/fl) and KL (KrasG12DLkb1fl/fl) lung tumor nodules were obtained and tumor cell lines were generated from these nodules ex vivo similar as previously reported.

extract_protocol:
Total cell RNA were extracted using RNeasy Plus mini kit (Qiagen). RNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep (for 96 Samples, catalog number 20020595), starting from 500 ng of total RNA, with 10 cycles of PCR amplification.
All libraries were uniquely barcoded with IDT 8 bp indices, pooled and sequenced on a NovaSeq 6000, on an S4 300 flow cell, as paired-end 150bp reads.

tag: strain/background

value: Lung


title: HuD-ctr-1


title: KLE-RNA

description:
Lung tumor from conditional activating mutation of endogenous Kras (KrasLSL-G12D/+) crossed with Lkb1 induced by Ad-Cre.
PolyA RNA
processed data file: counts.raw.csv
processed data file: counts.normalized.csv
processed data file: counts.fpkm.csv

source_name: Lung tumor

value: Cell line generated from lung nodules


title: wildtype_ear_primordia_rep1

value: ear primordia


title: Lc1309 non-stimulated_rep2

value: non-stimulated


title: KLD-RNA


title: Senescent IMR90 cells rep2


title: second_set_Histone A rep 3

source_name: Thermococcus kodakarensis


title: D6-D10_Pool_HN

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

institute: Indiana University School of Medicine

data_processing:
CellRanger 3.0.2 was utilized to process the raw sequence data generated. The filtered gene-cell barcode matrices generated by CellRanger were used for further analysis.
Seurat 3.1.0 was used for hashtag demultiplexing, data normalization, data scaling, graph-based clustering, cluster marker genes idenfification, and integrative analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: HDF5 file of filtered gene-barcode matrices

source_name: Breast

growth_protocol: These are normal human breast tissues

extract_protocol:
The cells from the tissue were extracted using Tumor Dissociation kit human, cat# 130-095-929 from Miltenyl Biotec. Cells were extracted from either freshly collected tissues or cryopreserved using a procedure described in PMID: 26311223
10x Genomics protocol for chromium single cell 3' reagent kits V3

treatment_protocol: No treatment

tag: disease

value: healthy

value: Breast


title: D6-D10_Pool_CMG


title: KL155mix-control-2-RNA


title: 24 hr ST 2

description: Tx 24 hr 2


title: KL47-1-untreated-1-RNA


title: Mutant Histone A and B deletion rep 3

description: TS620 3

data_processing:
TS6001 and TS622: RNA-Seq reads were first analyzed for quality control using FastQC. To remove adapter sequences and other artifacts, fastx-trimmer was used to trim the first 11 positions in each read. After filtering, the reads were aligned to the Thermococcus kodakarensis (KOD1) reference genome using bowtie with the following parameter: -m 1, this ensured suppressing all multiple-aligned reads. Finally, the bowtie output was converted to BAM format, sorted, and indexed using samtools.
TS6002 and TS620: RNA-Seq reads were first analyzed for quality control using FastQC. To remove adapter sequences and other artifacts, fastx-trimmer was used to trim the first 19 positions in each read. After filtering, the reads were aligned to the Thermococcus kodakarensis (KOD1) reference genome using bowtie2. Next, in each library, reads that aligned to multiple locations were filtered out. Finally, the filtered output was converted to BAM format, sorted, and indexed using samtools.
To quantify differential gene expression while comparing two samples, EdgeR was used. Note that EdgeR relies on read counts across individual biological replicates for both samples under comparison. To generate those read counts for every gene (in Ensembl based annotations), we used a custom python script that used SpliceGrapher and pysam. The EdgeR p-values were adjusted for multiple comparisons using the Benjamini-Hochberg method. Finally, we used a cutoff of 1.00 on the transcript abundance (log CPM) and fold change (log FC).
Genome_build: ASM996v1
Supplementary_files_format_and_content: archive of comma separated differential gene expression results (from EdgeR)

value: HTkAG17D, dHTKB


title: CK2 (control group)

city: Da lian

first: zelong

last: li

address: Ling shui

department: Environmental Science and Engineering

institute: Dalian University of Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample ...

organism: uncultured marine bacterium

source_name: Marine Sediment

extract_protocol:
consortium were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample type type

value: Marine bacteria

value: untreated


title: 24 hr ST 1

description: Tx 24 hr 1


title: Normal IMR90 cells rep2


title: CK3 (control group)


title: D5


title: D4


title: Lc1309 stimulated_rep2

value: Vav-Tta Lc1309

value: CD8 T cells


title: Normal IMR90 cells rep1


title: KLC-RNA


title: 6 hr ST 3

description: Tx 6 hr 3

value: Treated with 100 ng ST for 6 hr


title: D11


title: 6 hr ST 2

description: Tx 6 hr 2


title: 6 hr ST 1

description: Tx 6 hr 1


title: DA3（experiment group）

value: domoic acid 1mg/L for 7 days


title: 3 hr ST 3

description: Tx 3 hr 3

value: Intestinal epithelial cells

value: Treated with 100 ng ST for 3 hr


title: Untx 3

description: Untx 3 hr 3

value: Untreated


title: 3 hr ST 2

description: Tx 3 hr 2


title: CK1 (control group)


title: B6AL10-5-RNA

description:
Lung tumor from activating mutation of endogenous Kras (KrasLSL-G12D/+) crossed with p53 conditional knockout induced by Ad-Cre.
PolyA RNA
processed data file: counts.raw.csv
processed data file: counts.normalized.csv
processed data file: counts.fpkm.csv


title: D2


title: 3 hr ST 1

description: Tx 3 hr 1


title: DA1（experiment group）


title: Mutant Histone A and B deletion rep 2

description: TS620 2

value: pyruvate


title: B6AL10-4-RNA


title: D1


title: Mutant Histone A and B deletion rep 1

description: TS620 1


title: HEK293_siBAHD1_W667G_mutant_cell_H3K27me3_ChIP

status: Public on Mar 16 2021

city: Durham

first: Greg

last: Wang

state: NC

address: 3 Genome Court

department: Duke Department of Pharmacology and Cancer Biology  and Duke Cancer Institute

institute: Duke University School of Medicine, and Department of Biochemistry and Biophysics, UNC at Chapel Hill (adjunct)

data_processing:
ChIP-seq reads were aligned to human genome build GRCh37/hg19 using STAR version 2.7.1a  (mismatches are extended and low quality sequences are trimmed at this step). Non-primary alignment and PCR duplicates were then removed by samtools.  Alignment files in the bam format were transformed into read coverage files (bigwig format) using DeepTools. Genomic binding profiles were generated using the deepTools “bamCompare” functions with options [--operation ratio ---pseudocount 1 -binSize 10 --extendReads 250] and normalized to the matched input.
Profiles of ChIP-seq read densities were displayed with the Integrative Genomics Viewer (IGV, Broad Institute).
Genome_build: hg19

source_name: HEK293 cells

growth_protocol: HEK293 cells with stable expression of exogenous BAHD1 were grown in the DMEM base medium plus 10% of FBS and 1% of antibiotics. The BAHD1-targeting RNAi was transfected into cells and cells collected 48 hours later.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes isolated with specific antibodies against H3K9me3 (Abcam cat# ab8898), H3K27me3 (Abcam cat# ab6002), Anti-acetyl-Histone H3 (Lys9) Antibody (Millipore cat# 06-942) and H3K27ac (Abcam cat# ab4729).
Libraries were prepared using the NEB Ultra II DNA Library Prep Kit per manufacturer's instructions (NEB #E7103).

treatment_protocol: For ChIP-seq experiments, cells were grown in regular medium and collected, followed by cell fixation with 1% of formaldehyde, sonication, antibody enrichment, ChIP DNA recovery, library preparation, and subsequent deep sequencing.

tag: antibody used

tag: treatment condition

value: Stable expression of W667G mutant BAHD1, followed by knockdown (KD) of endogenous BAHD1


title: D3


title: HEK293_siBAHD1_W667G_mutant_cell_H3K9ac_ChIP

value: H3K9ac (Millipore 06-942)


title: B6AL10-2-RNA

value: Cell line generated from lung nodules


title: Untx 1

description: Untx 3 hr 1


title: HEK293_siBAHD1_W667G_mutant_cell_H3K9me3_ChIP


title: Untx 2

description: Untx 3 hr 2


title: HEK293_siBAHD1_WT_cell_H3K27me3_ChIP

value: Stable expression of wildtype BAHD1, followed by knockdown (KD) of endogenous BAHD1


title: B6AL10-1-RNA


title: HEK293_siBAHD1_WT_cell_H3K27ac_ChIP


title: HEK293_siBAHD1_W667G_mutant_cell_H3K27ac_ChIP


title: HEK293_siBAHD1_WT_cell_H3K9ac_ChIP


title: HEK293_UNC1999_1

data_processing:
RNA-seq reads were mapped using MapSplice and quantified using RSEM. Read counts were upper-quantile normalized and log2 transformed. Raw read counts were used for differential gene expression analysis by DESeq.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited matrix of gene level count estimates

growth_protocol: HEK293 cells were grown in DMEM base medium plus 10% of FBS and 1% of antibiotics.

extract_protocol:
RNA was extracted by using Qiagen RNeasy Mini Kit.
RNA libraries were made with standard Illumina protocols.

treatment_protocol: For the BAHD1 rescue experiments, HEK293 cells were stably transduced with a vector encoding either Flag-tagged wildtype (WT) BAHD1 or its BAH-mutated (W667G) version (this BAHD1 cDNA engineered to be resistant to the BAHD1-targeting siRNA used in the next step), followed by transfection of BAHD1-targeting siRNA to induce knockdown (KD) of endogenous BAHD1; cells were collected to verify the KD of endogenous BAHD1, as well as expression of exogenous BAHD1, either WT or its BAH-mutated version. For compound treatment experiments, HEK293 cells were treated with 5 µM of DMSO or UNC1999 for three days and collected. For all RNA-seq experiments, replicated cell samples were collected.


title: HEK293_DMSO_2

value: DMSO


title: HEK293_siBAHD1_W667G_mutant_cell_Input


title: HEK293_UNC1999_3


title: HEK293_UNC1999_2


title: HEK293_BAHD1_KD_rescue_W667G_3

value: BAHD1 KD


title: C22-C9-1

first: Ho-Geun

last: Yoon

address: 50-1 Yonsei-ro, Seodaemun-gu

institute: Yonsei University College of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: Mouse lung clara cell line

value: negative control

value: control


title: HEK293_BAHD1_KD_rescue_WT_2


title: HEK293_DMSO_1


title: HEK293_BAHD1_KD_rescue_W667G_2


title: HEK293_BAHD1_KD_rescue_WT_3


title: HEK293_BAHD1_KD_rescue_W667G_1


title: HEK293_BAHD1_KD_rescue_WT_1


title: NCI-H209 experiment-rep2 conditioned by HBMEC

city: shengyang

first: Bo

last: Li

state: Liaoning

address: shengyang puhe road 77

department: Department of Developmental Cell Biology

institute: China medical university

data_processing:
illumina Casava 1.8 software was used for base-calling
clean data (clean reads) were obtained by removing reads of low quality and that containing adapters from the raw data
the clean data was mapped to GRCh38 whole genome using STAR v2.6.1b
the expression amounts of genes were generated using STAR v2.6.1b with parameters -quantMode GeneCounts
differentially expressed genes between the experiment group and the control were determined using R language with package DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files including the counts number of genes for each sample
Supplementary_files_format_and_content: comma-seperated-value file including the expression amount of genes in the experiment group and the control

source_name: human small-cell lung cancer cell line conditioned by human brain microvascular endothelial cell

growth_protocol: NCI-H209 tumor cells were cultured in RPMI-1640 medium with 10% fetal bovine serum

extract_protocol:
the RNA of tumor cells was harvested with Trizol reagent and a total amount of 3 RNA per sample were used as input material for the RNA sample preparations. The sequencing libraries were generated using rRNA-depleted RNA by NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA).
The library used for sequencing was constructed by the standard Illumina protocol

treatment_protocol: NCI-H209 tumor cells were conditioned by HBMEC via trans-well chamber for 24 hours

value: lung cancer cel line

value: conditioned by HBMEC


title: HEK293_siBAHD1_WT_cell_H3K9me3_ChIP


title: NCI-H209 control-rep2

source_name: human small-cell lung cancer cell line

value: untreated


title: RNA-seq_D6_MDMs_TLR4_1h

city: Dallas

first: Edward

last: Wakeland

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

data_processing:
Illumina bcl2fastq2.17.04 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, and mapped to hg19 whole genome using CLC-Bio Genomics Workbench
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CLC-Bio Genomics Workbench.
Genome_build: hg19

source_name: Human monocyte-derived macrophages

growth_protocol: Human monocytes were cultured in RPMI-1640 medium with 10% FBS, 2mM L-glutamine, 10mM HEPES, 1mM sodium pyruvate, 100U/ml penicillin, and 100 µg/mL streptomycin. To differentiate monocytes into macrophages or dendritic cells, recombinant human M-CSF (50ng/mL) or recombinant human GM-CSF (100ng/mL) and recombinant human IL-4 (50ng/mL) were used, respectively. The culture medium which contained fresh recombinant human M-CSF or recombinant human GM-CSF and recombinant human IL-4 was replaced every 2 days.

extract_protocol:
RNA was extracted using TRIzol reagent and RNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol.
RNA-seq libraries were prepared with the Illumina TruSeq RNA Sample Preparation kit (Illumina) according to the manufacturer’s protocol.

treatment_protocol: Monocytes, MDMs or MDDCs were stimulated with Pam3CSK4 (1 μg/ml), LPS (10 ng/ml), R837 (10 μg/ml), TL8-506 (0.5 ug/ml) or R848 (10 μg/ml) for the indicated times.

value: Human monocyte-derived macrophages

tag: donor number

value: Donor 6


title: RNA-seq_D6_MDMs_unstimulated

value: NT


title: RNA-seq_D6_MDMs_TLR4_18hr


title: NCI-H209 experiment-rep1 conditioned by HBMEC


title: HEK293_siBAHD1_WT_cell_Input


title: NCI-H209 control-rep3


title: RNA-seq_D6_mono_TLR8_18hr

source_name: Human monocytes

value: Human monocytes


title: RNA-seq_D6_mono_TLR7_18hr


title: RNA-seq_D6_mono_TLR7_1hr


title: NCI-H209 control-rep1


title: RNA-seq_D6_mono_TLR4_6hr


title: HEK293_DMSO_3


title: RNA-seq_D6_mono_TLR7-8_18hr


title: RNA-seq_D6_mono_TLR7-8_6hr


title: RNA-seq_D6_mono_TLR4_1hr


title: RNA-seq_D6_mono_unstimulated


title: RNA-seq_MDDCs_7day

source_name: Human monocyte-derived dendritic cells

value: Human monocyte-derived dendritic cells


title: RNA-seq_D6_mono_TLR7-8_1hr


title: RNA-seq_D6_mono_TLR8_6hr


title: RNA-seq_D6_MDMs_TLR4_6hr


title: RNA-seq_D6_mono_TLR8_1hr


title: RNA-seq_D6_mono_TLR7_6hr


title: RNA-seq_MDDCs_4day


title: RNA-seq_MDMs_6day


title: RNA-seq_MDMs_5day


title: RNA-seq_MDDCs_5day


title: RNA-seq_MDDCs_1day


title: RNA-seq_D6_mono_TLR4_18hr


title: RNA-seq_MDMs_4day


title: RNA-seq_MDDCs_6day


title: RNA-seq_MDDCs_2day


title: RNA-seq_MDDCs_4hours


title: RNA-seq_mono


title: RNA-seq_MDMs_2day


title: upf1-5_upf3-1_27C

city: Seoul

first: Zeeshan

last: Nasim

address: Anam-ro 145, Seongbuk-Gu

department: School of Life Sciences and Biotechnology

institute: Korea University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to TAIR 10 reference genome using tophat
Cufflinks package used for gene expression level
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: Seedling

extract_protocol:
For RNA extraction, plants were grown on MS plates under long days conditions (16h light and 8h dark), at specified temperatures. All samples were collected at ZT16 and RNA was extracted using Plant RNA Purification Reagent (Invitrogen) following manufacturer's protocol. Library construction was carried out for RNA sequencing using Illumina TruSeq Stranded Total RNA Sample Prep kit according to manufacturer's manual.   After library construction and normalization, sequencing was conducted as paired-end reads on an Illumina HiSeq2000 sequencer.
We sequenced mRNA of WT, upf1-5, upf3-1 and their double mutant seedlings grown at 16C and 27°C, day 8 after germination, ZT 16

tag: develpmental stage

value: ZT 16

tag: temperature


title: upf3-1_27C


title: RNA-seq_MDMs_7day


title: RNA-seq_MDMs_1day


title: upf1-5_upf3-1_16C


title: WT_27C

value: WT


title: upf3-1_16C


title: RNA-seq_MDDCs_3day


title: upf1-5_16C


title: WT_16C


title: ColtotalRNA3_IP

city: Beijing

first: Jing

last: Sun

address: No. 1 West Beichen Road

department: IGDB

institute: Chinese Academy of Sciences

description: m6A-IP sample of Col in MeRIP-seq

data_processing:
Library strategy: MeRIP-seq
Tags less than 20 nt after removal of the 3’ linker and 4 nt random sequences were discarded. All tags were reverse-complemented because the tags were sequenced from 3'-end of transcripts (Fu et al., 2011). Trimmed tags were then mapped to the Arabidopsis genome (TAIR10) using Bowtie (0.12.7) (Langmead et al., 2009), allowing 2 mismatches. Only uniquely mapped tags were kept for downstream analyses. Uniquely located tags with six or more continuous adenines downstream from the poly(A) junction in a 10-nt window were identified as internal priming tags and discarded (Shepard et al., 2011).
For MeRIP-seq data, low-quality reads were discarded and the adaptor sequences were trimmed using Trimmomatic(0.36). Clean Reads were further treated with in-house scripts to eliminate duplication bias. The de-duplicated consensus sequences were further aligned the Arabidopsis thaliana genome (TAIR10) using STAR (2.5.3a).
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig files were generated using bedtools and bedGraphToBigWig program

source_name: seedlings

growth_protocol: All of the Arabidopsis thaliana lines used in this study were in the Col background.The seedlings were grown in 1/2 MS medium (aseptic hydroponics) for 12 d.

extract_protocol:
The seedlings were ground into fine power in liquid nitrogen and RNA was extracted by TRNzol reagent (Tiangen).
MeRIP-seq libraries generated from Col were constructed following the published method in skeletal muscle (Zhang et al., 2020).

tag: developmental stage

value: 12-day-old seedlings

value: Col (wild type)


title: RNA-seq_MDMs_4hours

tag: cell type


title: ColtotalRNA1_IP

description: m6A-IP sample of Col in MeRIP-seq


title: ColtotalRNA1_Input

description: input sample of Col in MeRIP-seq


title: RNA-seq_MDMs_3day


title: ColtotalRNA3_Input

description: input sample of Col in MeRIP-seq


title: upf1-5_27C

tag: genotype/variation


title: Mock (empty vectorplasmid DNA) transfected cells

city: Delhi

first: NITIKA

last: GAURAV

state: Delhi

address: INDIAN INSTITUTE OF TECHNOLOGY DELHI -110016, INDIA

department: Kusuma School of Biological Sciences

country: India

institute: INDIAN INSTITUTE OF TECHNOLOGY DELHI

data_processing:
Quality control and adapter trimming was performed using Trimmomatic tool
Bowtie2  (version 2.2.4) was used for contamination removal
Preprocessed data were aligned to human reference genome (hg19) using HiSAT2
Uniquely mapped reads were counted using featurecounts and were normalized using DESeq
Genome_build: human reference genome (hg19)
Supplementary_files_format_and_content: tA single tab-delimited text files include FPKM values for each Sample C3, V3 and N2

source_name: Hepatocyte derived human carcinoma cell line

growth_protocol: Huh7 cell were grown in DMEM (Dulbecco's Modified Eagle Medium) supplemented with 10% FBS (Fetal Bovine Serum) and 1% Penicillin-Streptomycin antibiotic solution. Cells were incubated at 37 °C in humidified 5% CO₂ atmosphere and routinely passaged.

extract_protocol:
Capsid gene, mock-transfeced (empty vector plasmid DNA), and Chikungunya virus infected Huh7 cells were washed with 1X PBS and cells were lysed using TRIzol reagent (Sigma) according to manufacturer’s protocol.
RNA libraries were prepared for sequencing using NEB Next RNA Ultra protocol

tag: cell line


title: Chikungunya virus infected cells

value: Chikungunya virus infected cells


title: ColtotalRNA2_IP

description: m6A-IP sample of Col in MeRIP-seq


title: P20_C2

city: Greater Noida

first: Anindita

last: Chakrabarty

state: UP

address: NH91 Tehsil Dadri

department: Life Sciences

institute: Shiv Nadar University

hyb_protocol: Cy3-labelled cRNA was hybridized with Agilent MA_GXP_4X44K_human array accoding to standard protcol.

scan_protocol: Slides were scanned with  Microarray Scanner (G2600D by Aglent) using one color scan setting.

data_processing: Standard protocol.

source_name: Cell line MCF10A with HER2 and WT PIK3CA

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared according to standard protocol.

growth_protocol: MCF10A/HER2/WT [C] and MCF10A/HER2/HR [T] PIK3CA cell lines from two different passages (p18 and p20) were grown in media containing DMEM/F12, 5% horse serum, 20ng/ml EGF, 100ng/ml cjolera toxin, 10mg/ml insulin, 0.5mg/ml hydrocortisone.  Cells were grown at 37 degree C and 5% CO2.

extract_protocol: RNA (total) was prepared using the TRIzom method (Thermo-Fisher Scientific). RNA QC was done by using the Agilent Bioanalyzer.

value: HER2 overexpression and WT PIK3CA

tag: gender

value: Female

tag: passages


title: P18_T1

source_name: Cell line MCF10A with HER2 and HR PIK3CA

value: HER2 overexpression and H1047R PIK3CA


title: P18_C1


title: parental PTX-sensitive cells (OVCAR-3) _rep1

city: Shanghai

first: GUOXIONG

last: XU

state: Shanghai

address: 1508 Longhang Road

department: Research Center for Clinical Medicine

institute: Jinshan Hospital of Fudan University

description: Biological replicate 1 of 3:PTX-sensitive cells line (OVCAR-3)

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: parental PTX-sensitive cells (OVCAR-3)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by Nucleospin® Extract II kit (MN,,Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: cells of each group were cultured in RPMI 1640 medium supplemented with 10%  fetal bovine serum and incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using TRIzol™ Reagent (Invitrogen) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: PTX-resistant cells (OV3R-PTX) were established from patental OVCAR-3 cells by  treatment with a gradually increasing dose of PTX for 6 months

value: ovarian cancer cell line OVCAR-3 obtain from ATCC (HTB-161™)

value: female

tag: age


title: Sample 264

city: Columbus

first: Christopher

middle: J

last: Walker

state: Ohio

address: 1276 Eastwood Ave

institute: Ohio State

data_processing:
STAR alignment
FeatureCounts gene-leve quantification
DeSeq2 Normailzation
Genome_build: hg38
Supplementary_files_format_and_content: norm and raw counts

source_name: CN-AML blasts

growth_protocol: Patient samples were thawed and directly used for RNA extraction. No cytokines or cell culture techniques were used to expand leukemic blasts.

extract_protocol: On average, 20 million leukemic blasts isolated from cryopreserved samples were thawed and subjected to total RNA extraction using the Trizol reagent and previously published protocols

tag: tissue

value: CN-AML blasts

tag: group

value: relapse


title: parental PTX-sensitive cells (OVCAR-3) _rep3

description: Biological replicate 3 of 3:PTX-sensitive cells line (OVCAR-3)


title: P20_T2


title: Sample 267

value: maintaincr


title: PTX-resistant cells (OV3R-PTX)_rep2

description: Biological replicate 2 of 3:PTX-resistant cells line (OV3R-PTX)

source_name: PTX-resistant cells (OV3R-PTX)

value: paclitaxel-resistant ovarian cancer cell lines established by treating  parental OVCAR-3 cell line  for 6 months


title: Capsid transfected cells

tag: treatment

value: Capsid transfected cells


title: Sample 268


title: Sample 261


title: PTX-resistant cells (OV3R-PTX)_rep1

description: Biological replicate 1 of 3:PTX-resistant cells line (OV3R-PTX)


title: LMNA-V6 exU1-U3

city: Toskushima

first: Yuki

last: Kuwano

address: Kuramoto-cho

department: Pathophysiology

country: Japan

institute: The University of Tokushima Graduate School

description: Gene expression in pcDNA3 LMNA-V6 exU1-U3-overexpressing cells

hyb_protocol: Hybridizations were performed using GE Hybridization Kit (P/N 5188-5242) and GE Wash Buffer 1 and 2 (P/N 5188-5325, -5326) as following Agilent's protocol. The fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (SurePrint G3 Human GE v3 8x60K) for 17 hours at 65C in a rotating Agilent hybridization oven.

scan_protocol: Microarrays were scanned using Agilent’s DNA Microarray Scanner (P/N G2600D).

data_processing: Data extracted using Agilent's Feature Extraction software. Raw data output was imported into Genespring GX14.9 (Agilent) and normalized each chip to the 75th percentile of all measurements (per chip normalization).

source_name: colon cancer cell line

label_protocol: Sample labeling, array processing and scanning, and data extraction were performed as described in One-Color Microarray-Based Gene Expression Analysis’ Protocol. These protocols are available for download from Agilent's DNA Microarray Manuals website. For microarray analysis, total RNA (400 ng) was used for amplification and labeling of complementary RNA (cRNA) using a Low RNA Input Liner Amplification Kit PLUS (Agilent Technology) and a succinimide-containing fluorescent dye (Cy3)-CTP according to the manufacturer’s protocol.

extract_protocol: The total RNA was extracted using RNAiso Plus reagent (Thermo Fisher Scientific).

treatment_protocol: HCT116 cells were transfected with pcDNA3.1 encoding LMNA-V6 exU1-U3 or empty vector (Thermo Fisher Scientific) using Lipofectamine 2000 (Thermo Fisher Scientific) for 48 hours according to the manufacturer’s protocol. HCT116 cells were treated with 10 nM of control or LMNA-V6 siRNA using Lipofectamine RNAiMax (Thermo Fisher Scientific) for 48 hours.

value: HCT116  cells

tag: sirna

value: LMNA-V6 exU1-U3


title: parental PTX-sensitive cells (OVCAR-3) _rep2

description: Biological replicate 2 of 3:PTX-sensitive cells line (OVCAR-3)


title: PTX-resistant cells (OV3R-PTX)_rep3

description: Biological replicate 3 of 3:PTX-resistant cells line (OV3R-PTX)


title: mock

description: Gene expression in pcDNA3 empty vector-overexpressing cells

value: mock


title: Sample 266


title: Sample 265


title: Sample 260


title: Sample 263


title: Sample 250


title: Sample 251


title: Sample 253


title: Sample 262


title: DA2（experiment group）

tag: sample type type

value: Marine bacteria

value: domoic acid 1mg/L for 7 days


title: B6AL10-3-RNA

source_name: Lung tumor

tag: strain/background

value: Cell line generated from lung nodules


title: Sample 252


title: Sample 256


title: Sample 249


title: Sample 254


title: Sample 255


title: THP-1_co-culture

first: Yiming

last: Lu

address: Taiping Road

institute: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine

description: THP-1 cells treated with PMA for 24 hours and then co-cultured with HCC cells for 48 hours

data_processing: The Bulk RNA-seq data were processed using the STAR-rsem pipeline. Read counts per gene were normalized to gene length and to the total read counts.

extract_protocol:
Total RNAs were extracted from the co-cultured THP-1 cells, or FACS-sorted cells from the tumor and non-tumor liver tissues using the RNeasy Mini Kit (QIAGEN, Germany) according to the manufacturer’s instructions. The qualities of total RNAs were measured by spectrophotometer (NanoDrop, Thermo Fisher, USA).
Libraries were constructed using the NEBNext Poly(A) mRNA Magnetic Isolation Module kit (NEB, USA) and NEBNext Ultra RNA Library Prep Kit for Illumina Paired-end Multiplexed Sequencing Library (NEB, USA). Samples were sequenced on the Illumina Hiseq 4000 sequencer with 150 bp paired-end reads.

value: THP-1 cell line


title: THP-1_control

description: THP-1 cells treated with PMA for 24 hours


title: Sample 258


title: Sample 248


title: Sample 245


title: control siRNA

description: Gene expression in control siRNA-transfected cells

value: control siRNA


title: Sample 259


title: Sample 247


title: Sample 244


title: Sample 246


title: LMNA-V6 siRNA

description: Gene expression in LMNA-V6 siRNA-transfected cells

value: LMNA-V6 siRNA


title: Sample 243


title: Sample 241


title: Sample 239


title: Sample 240


title: Sample 238


title: Sample 232


title: Sample 237


title: Sample 230


title: Sample 226


title: Sample 228


title: Sample 229


title: Sample 225


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title: Sample 165


title: Sample 164


title: Sample 163


title: Sample 183


title: Sample 179


title: ColtotalRNA2_Input

description: input sample of Col in MeRIP-seq

value: 12-day-old seedlings

tag: genotype

value: Col (wild type)


title: Sample 161


title: Sample 157


title: Sample 155


title: Sample 162


title: Sample 151


title: Sample 159


title: Sample 160


title: Sample 154


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title: Sample 116


title: KW14 cDNA

city: Tachikawa-shi,

first: Shu-Kuan

last: Wong

state: Tokyo

address: 10-3, Midori-cho,

institute: National Polar Research Institute

hyb_protocol: Each dried and labelled DNA sample was resuspended in 42 µL of hybridization solution. This solution consisted of 1 x HI-RPM hybridization buffer, 1 x comparative genome hybridization blocking agent, 0.05 µg・µL-1 Cot-1 DNA, 10 pM universal standard, and 10% formamide (final concentrations). The solution was later denatured by remaining at 95 ℃ for 3 min. To remove the bubbles created during the denaturation process, the conditions were maintained at 37 ℃ for 30 min. The hybridizations were carried out at 67 ℃ for 24 h

scan_protocol: The scanned images of the GeoChip hybridizations were obtained and converted by means of the Agilent Feature Extraction 11.5 software (Agilent Technologies, California, USA)

data_processing: The signal intensities, used as a proxy of abundances, were quantified and processed based on previous pipelines48 as follows: (i) removing probes with a signal-to-noise ratio of less than 2.0; (ii) normalizing the signal intensity of each probe by dividing the total signal intensity of a sample and multiplying by a constant

organism: soil metagenome

source_name: Environmental soil

label_protocol: The DNA from each sample (500 ng) was labelled with the fluorescent dye Cy-3 by random priming.

growth_protocol: Samples collected directly from the environment

extract_protocol: Total DNA and RNA were extracted from each soil sample using ZymoBIOMICS DNA & RNA kit. The total RNA extracted were subjected to DNAse I treatment and cDNA was generated from the RNA template using SuperScript IV First-Strand Synthesis System for RT-PCR according to the manufacturer’s instruction.

treatment_protocol: Soil samples were collected using a sterile scoop and placed into a 5 mL sampling tube containing RNAlater Stabilization Solution

tag: geographic location


title: KW13 cDNA


title: KW7 cDNA


title: KW6 cDNA


title: oocyte c1

city: Nanjing

first: Li

last: Yu

address: No. 1 Weigang, Nanjing City, Jiangsu Province

institute: College of Animal Science and Technology, Nanjing Agricultural University

data_processing:
All RNA-seq reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads then were aligned to the mm10 reference genome using tophat2 (v2.0.13)
Reads aligned to genes are counted by cufflinks (v2.2.1). The FPKMs are normalized using cuffnorm. Differentially expressed genes are calculated using cuffdiff.
Genome_build: susScr11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Sus scrofa

source_name: porcine oocyte

extract_protocol:
The cell was lysised and the RNA was amplificated according to Smart-seq2 procedures.
The mRNA library was constructed using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) according to the instruction manual, which includes sequential RNA fragmentation, reverse transcription using random primers, second strand cDNA synthesis, end repair, dA-tailing, adapter ligation, U excision, and PCR enrichment.

value: oocyte

tag: development stage

value: Metaphase II

value: control


title: Sample 112

value: CN-AML blasts

value: relapse


title: Sample 110


title: Sample 111


title: oocyte sirt6-1

value: sirt6 inhibited


title: Sample 105


title: Sample 108


title: oocyte c2


title: Sample 104


title: Sample 103

value: maintaincr


title: Sample 106


title: oocyte sirt6-2


title: Sample 109


title: NF1;TP53-cKO rep2

city: ShanTou

first: juan

middle: juan

last: Luo

address: Xinling street 22

institute: ShanTou University

data_processing:
Basecalls was performed using CASAVA version 1.8
During data pre-processing, Seqtk was applied to remove adaptor sequences, bases with quality value lower than 20 at 3'-end, reads shorter than 25bp, and ribosome RNA reads.
Reads were mapped to GRCz10.81 genome assembly with the spliced mapping algorithm of Hisat2 (version 2.0.4).
Gene expression was quantified and then normalized as FPKM(Fragments Per Kilobase of exon model per Million mapped reads). In this step, fragments of each gene were counted with Stringtie (version 1.3.0) and normalized into trimmed mean of M values (TMM), after which FPKM values of every gene were calculated by Perl scripts.
Genome_build: GRCz10.81

organism: Danio rerio

source_name: Brain

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Cat# 74004, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain


title: NF1;TP53-cKO rep3


title: RB1;TP53-cKO rep2


title: NF1;TP53-cKO rep1


title: RB1;TP53-cKO rep3


title: KW14 DNA

type: genomic


title: Sample 107


title: KW6 DNA


title: KW7 DNA


title: KW4 DNA


title: KW13 DNA


title: Sample 114


title: Sample 113


title: NF1-KO rep2


title: WT rep1

description: AB

value: wild type


title: NF1-KO rep1


title: Sample 96


title: Sample 102


title: RB1;TP53-cKO rep1


title: Sample 101


title: THP1_PMA_IRF1 KO2_LPS_6hr

state: TX

department: Immunology

source_name: THP-1 cells +PMA

growth_protocol: THP-1 cells were cultured in T-75 flasks between 2-8 x 10^5 cells/mL in growth medium containing RPMI-1640, 10% FBS, 2mM L-glutamine, 10mM HEPES, 1mM sodium pyruvate, 100U/ml penicillin, and 100 µg/mL streptomycin. THP-1 monocytes were differentiated into macrophages by 48 hr incubation with 50 ng/ml PMA followed by 48 hr without PMA.

treatment_protocol: PMA-differentiated control clonal THP-1 cell line and PMA-differentiated IRF1 deficient clonal THP-1 cell lines were stimulated with LPS (10 ng/ml) for the indicated times.

value: Human macrophages


title: NF1-KO rep3


title: Sample 99


title: Sample 97


title: Sample 100


title: THP1_PMA_IRF1 KO2_LPS_1hr


title: Sample 95


title: Sample 93


title: Sample 94


title: THP1_PMA_IRF1 KO2_unstimulated

value: NT


title: Sample 92


title: THP1_PMA_IRF1 KO1_unstimulated


title: Sample 98


title: THP1_PMA_IRF1 KO1_LPS_1hr


title: THP1_PMA_ctrl_LPS_1hr


title: THP1_PMA_ctrl_LPS_6hr


title: THP1_PMA_ctrl_unstimulated


title: Sample 89


title: Sample 91


title: Sample 88


title: Sample 90


title: THP1_PMA_R848

treatment_protocol: THP-1 or PMA-differentiated THP-1 cells were stimulated with LPS (10 ng/ml) or R848 (10 μg/ml) for 18 hours.


title: THP1_PMA_unstimulated


title: Sample 86


title: Sample 84


title: Sample 85


title: Sample 87


title: THP1_PMA_IRF1 KO1_LPS_6hr


title: KW4 cDNA


title: THP1_R848

source_name: THP-1 cells

value: Human monocytes


title: Sample 83


title: Sample 80


title: THP1_LPS


title: ATAC-seq_THP1_PMA_IRF1 KO_LPS_6hr

data_processing:
We used trimgalore version 0.4.1 (Martin, 2011) on the raw reads to remove reads shorter than 35bp or with phred quality scores less than 20 and then aligned trimmed reads to the human reference genome (GRCh37) using default parameters in BWA version 0.7.12 (Li and Durbin, 2009).
The aligned reads were subsequently filtered for quality and uniquely mappable reads were retained for further analysis using Samtools version 1.3 (Li et al., 2009) and Sambamba version 0.6.6 (Tarasov et al., 2015).
Library complexity was measured using BEDTools version 2.26.0 (Quinlan and Hall, 2010) and meets ENCODE data quality standards (Landt et al., 2012).
Relaxed peaks were called using MACS version 2.1.0 (Feng et al., 2012) with a p-value of 1x10-2.
Peak calls that are either observed in both pseudoreplicates were used for subsequent analysis.
Genome_build: hg19
Supplementary_files_format_and_content: ATAC-seq BigWig files were generated using MACS version 2.1.0; Scores represent the ATAC-seq fold change over background

extract_protocol:
50,000 cells were used for each tranposition reaction. Nuclei were pelted by centrifugation for 10 min at 500 g, 4°C
ATAC-seq was performed using Nextera DNA library prep kit as previously described (Buenrostro et al., 2013)

treatment_protocol: PMA-differentiated control clonal THP-1 cell line and PMA-differentiated IRF1 deficient clonal THP-1 cell line were stimulated with LPS (10 ng/ml) for the indicated times.


title: Sample 81


title: ATAC-seq_THP1_PMA_IRF1 KO_LPS_1hr


title: ATAC-seq_THP1_PMA_IRF1 KO_LPS_3hr


title: Sample 78


title: ATAC-seq_THP1_PMA_IRF1 KO_unstimulated


title: ATAC-seq_THP1_PMA_ctrl_LPS_6hr


title: Sample 79


title: Sample 76


title: Sample 77


title: THP1_PMA_LPS


title: Sample 75


title: ATAC-seq_THP1_PMA_ctrl_LPS_3hr


title: ATAC-seq_THP1_PMA_ctrl_LPS_1hr


title: ATAC-seq_THP1_PMA_ctrl_unstimulated


title: ATAC-seq_D6_MDMs_LPS_6h

source_name: Human monocyte-derived macrophages

value: Human monocyte-derived macrophages

tag: donor number


title: Sample 73


title: Sample 71


title: ATAC-seq_D6_MDMs_unstimulated


title: Sample 72


title: ATAC-seq_D6_MDMs_LPS_1h


title: Sample 70


title: Sample 82


title: THP1_unstimulated


title: ATAC-seq_D6_mono_LPS_18h

source_name: Human monocytes


title: ATAC-seq_D6_mono_LPS_1h


title: ATAC-seq_D6_mono_LPS_6h


title: ATAC-seq_D6_mono_unstimulated


title: Sample 67


title: Sample 65


title: Sample 66


title: ATAC-seq_MDDCs_7day

source_name: Human monocyte-derived dendritic cells

value: Human monocyte-derived dendritic cells


title: ATAC-seq_MDDCs_6day


title: ATAC-seq_MDDCs_4day


title: Sample 62


title: Sample 63


title: ATAC-seq_MDDCs_3day


title: Sample 64


title: ATAC-seq_D6_MDMs_LPS_18h


title: ATAC-seq_MDDCs_5day


title: ATAC-seq_MDDCs_2day


title: Sample 61


title: Sample 60


title: ATAC-seq_MDMs_7day


title: ATAC-seq_MDDCs_1day


title: ATAC-seq_MDMs_6day


title: Sample 69


title: Sample 58


title: Sample 57


title: Sample 56


title: ATAC-seq_MDMs_5day


title: Sample 74


title: ATAC-seq_MDDCs_4hours


title: Sample 68


title: Sample 55


title: ATAC-seq_MDMs_3day


title: Sample 53


title: Sample 54


title: ATAC-seq_MDMs_2day


title: Sample 52


title: Sample 50


title: ATAC-seq_MDMs_1day


title: ATAC-seq_MDMs_4hours


title: Sample 49


title: Sample 59


title: Sample 51


title: Sample 47


title: Sample 44


title: VNC JmjC*_rep3

city: Bronx

first: Julie

last: Secombe

state: NY

address: 1300 Morris park ave

institute: Albert Einstein College of Medicine

data_processing:
Reads were filter using SOAPnuke (v1.5.2) to remove low quality reads, reads with adaptors and reads with unknown bases.
Clean reads were mapped to dm6 Drosophila genome with Bowtie2 (v2.2.5) and gene expression levels were calculated with RSEM (v1.2.12).
To compare transcriptome changes between genotypes, differential gene expression analysis was performed using DEseq2. Adjusted Pvalue <= 0.05. No cutoff for Log2FoldChange
Genome_build: dm6
Supplementary_files_format_and_content: Differential gene expression and counts data and expected counts

organism: Drosophila melanogaster

source_name: larval ventral nerve cord

growth_protocol: Flies were grown on standard media at 25C

extract_protocol:
Trizol extraction of total RNA from VNC was performed according to manufacturer's instructions.
The TruSeq Stranded mRNA LT Sample Prep Kit was used for library construction.
Libraries were evaluaded for quantification and quality using Agilent 2100 Analyzer and ABI StepOnePlus Real-Time PCR System and were sequenced on an Illumina NovaSeq 6000 sequencing platform (2 x 150bp). cycles.

tag: develomental stage

value: wandering third instar

value: JmjC (demethylase inactive) mutant

tag: tag

value: ventral nerve cord (VNC)


title: VNC JmjC*_rep4


title: Sample 45


title: VNC JmjC*_rep1


title: VNC L854F_rep4

value: L854F mutant


title: VNC JmjC*_rep2


title: VNC L854F_rep3


title: VNC L854F_rep2


title: ATAC-seq_MDMs_4day

tag: cell type


title: VNC L854F_rep1


title: Sample 42


title: Sample 41


title: VNC WT_rep4


title: ATAC-seq_mono


title: Sample 40


title: VNC WT_rep3


title: Sample 39


title: Sample 37


title: Sample 38


title: VNC WT_rep1


title: KO_Male_4hr_NIR_3

city: Detroit

first: Ekta

last: Shah

state: Michigan

address: 275 E.  Hancock

institute: Wayne State University

data_processing:
After de-multiplexing with Illumina’s CASAVA 1.8.2 software, the 50 bp reads were aligned to the Drosophila genome (Build dm3) with STAR_2.4 and tabulated for each gene region.
Differential gene expression analysis was used to compare transcriptome changes between conditions using edgeR v.3.22.3 and transcripts were defined  as significantly differentially expressed at absolute Log2 fold change >1, FDR <0.05
Genome_build: Dm3

extract_protocol:
Direct-zol RNA MicroPrep kit
QuantSeq 3' mRNA-Seq Library Prep Kit FWD (low-input protocol and 15 ng RNA input)

tag: strain

value: Tau-KO


title: KO_Male_4hr_NIR_2


title: Sample 36


title: Sample 35


title: Sample 34


title: KO_Male_4hr_NIR_1


title: KO_Male_2hr_NIR_2


title: Sample 33


title: KO_Male_2hr_NIR_1


title: KO_Male_2hr_NIR_3


title: Sample 30


title: Sample 31


title: Sample 32


title: KO_Male_1hr_NIR_3


title: KO_Male_1hr_NIR_2


title: KO_Male_1hr_NIR_1


title: VNC WT_rep2


title: Sample 26


title: KO_Male_Ctrl_NIR_1


title: Sample 27


title: KO_Male_Ctrl_NIR_2


title: KO_Female_4hr_NIR_3


title: KO_Female_4hr_NIR_1


title: KO_Female_4hr_NIR_2


title: Sample 23


title: Sample 24


title: Sample 22


title: KO_Female_2hr_NIR_3


title: Sample 21


title: Sample 20


title: KO_Male_Ctrl_NIR_3


title: Sample 29


title: Sample 18


title: Sample 19


title: KO_Female_1hr_NIR_3


title: Sample 17


title: KO_Female_2hr_NIR_2


title: Sample 16


title: KO_Female_2hr_NIR_1


title: KO_Female_1hr_NIR_1


title: KO_Female_Ctrl_NIR_3


title: Sample 14


title: KO_Female_Ctrl_NIR_2


title: KO_Female_Ctrl_NIR_1


title: Sample 15


title: Sample 25


title: w1118_Male_4hr_NIR_3


title: Sample 12


title: Sample 13


title: w1118_Male_4hr_NIR_1


title: w1118_Male_4hr_NIR_2


title: Sample 11


title: w1118_Male_2hr_NIR_3


title: Sample 10


title: Sample 9


title: w1118_Male_2hr_NIR_2


title: Sample 7


title: Sample 8


title: w1118_Male_1hr_NIR_2


title: Sample 6


title: w1118_Male_1hr_NIR_1


title: KO_Female_1hr_NIR_2


title: Sample 4


title: Sample 3


title: w1118_Male_Ctrl_NIR_3


title: w1118_Male_Ctrl_NIR_1


title: Sample 2


title: Sample 1


title: w1118_Female_4hr_NIR_2


title: P8_20umDCVC_12hrs

city: San Diego

first: Elana

middle: R

last: Elkin

state: CA

address: 5500 Campanile Drive

department: School of Public Health

institute: San Diego State University

data_processing:
Reads were aligned to the human genome using STAR, with the options "outFilterMultimapNmax 10" and "sjdbScore 2".
Aligned reads were assigned to GRCh37 genes using featureCounts.
Genes with mean read counts-per-million less than five across all samples were filtered out and excluded from the analysis.
Data were normalized using the trimmed mean of M values (TMM) method
Differential gene expression testing was performed using the edgeR package (version 3.1) for R statistical computing. Quasi-likelihood general linear modeling was used for differential gene expression testing.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

source_name: placental villous explant tissue

growth_protocol: Tissue sections were plated, one per well, free-floating in clear 24-well cell culture plates and allowed to acclimate in a 5% CO2 humidified incubator for 24 h.

extract_protocol:
Each explant was transferred to a 1.5 mL microcentrifuge tube, lysed in QIAzol reagent and homogenized in a TissueLyser LT (Qiagen) for 5 minutes at 50 Hz, using one 3.2 mm stainless steel bead per tube. mRNA was extracted using the miRNeasy Mini Kit (Qiagen) following the manufacturer’s recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Culture media was removed and explants were treated with fresh DMEM/F12 complete medium alone (control) or complete medium plus DCVC diluted to a final concentration of 20 µM for 12 h. Five independent biological replicate experiments were performed. Villous explants used for non-treated and treated groups, respectively within each experiment, were sourced and matched from the same placenta.

value: placenta

tag: gestational age

value: 9.3 weeks

tag: placental donor

value: Donor 5

value: 20 microM DCVC

tag: treatment duration

value: 12 hours


title: P6_20umDCVC_12hrs

tag: tissue

value: 8.4 weeks

value: Donor 3


title: P7_20umDCVC_12hrs

value: 9.5 weeks

value: Donor 4


title: w1118_Female_4hr_NIR_3


title: w1118_Female_4hr_NIR_1


title: w1118_Female_2hr_NIR_3


title: w1118_Male_2hr_NIR_1


title: w1118_Female_2hr_NIR_2


title: Sample 28

value: CN-AML blasts

tag: group

value: maintaincr


title: P4_20umDCVC_12hrs

value: 11 weeks

value: Donor 1

tag: treatment


title: w1118_Male_1hr_NIR_3


title: Sample 5


title: P8_NT_12hrs

value: No Treatment


title: w1118_Female_2hr_NIR_1


title: w1118_Female_1hr_NIR_3


title: P7_NT_12hrs


title: w1118_Female_1hr_NIR_2


title: P6_NT_12hrs


title: w1118_Female_1hr_NIR_1


title: w1118_Female_Ctrl_NIR_2


title: P4_NT_12hrs


title: w1118_Female_Ctrl_NIR_3


title: P5_NT_12hrs

value: 10.2 weeks

value: Donor 2


title: w1118_Female_Ctrl_NIR_1


title: 24_N4_20uMDCVC_12hrs

data_processing:
Reads were aligned to the human genome using STAR, with the options "outFilterMultimapNmax 10" and "sjdbScore 2".
Aligned reads were assigned to GRCh37 genes using featureCounts.
Genes with mean read counts-per-million less than four across all samples were filtered out and excluded from the analysis.
Data were normalized using the trimmed mean of M values (TMM) method
Differential gene expression testing was performed using the edgeR package (version 3.1) for R statistical computing. Quasi-likelihood general linear modeling was used for differential gene expression testing.
Genome_build: hg19

source_name: placental extravillous trophblast cells

growth_protocol: Cells were cultured between passages 78–84 in RPMI 1640 medium supplemented with 10% FBS and 1% P/S at 37°C in a 5% CO2 humidified incubator. Cells were grown to 70–90% confluence at least 24 h after plating prior to use in any experiments. Cells were seeded at a density of 800,000 cells per well in 6-well cell culture plates. Twenty-four hours later, cells were treated with RPMI 1640 complete medium alone (control) or complete medium plus DCVC diluted to a final concentration of 10 or 20 µM for 6 or 12 h.  Four independent biological replicate experiments were performed.

extract_protocol:
Cells were scraped and lysed with RLT lysis buffer containing beta-mercaptoethanol. Cell lysates were homogenized using QIA shredders (Qiagen), and mRNA was extracted using the RNeasy Plus Mini Kit (Qiagen) following the manufacture’s recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: replicate

value: 20 uM DCVC


title: 23_N4_10uMDCVC_12hrs

treatment_protocol: Cells were seeded at a density of 800,000 cells per well in 6-well cell culture plates. Twenty-four hours later, cells were treated with RPMI 1640 complete medium alone (control) or complete medium plus DCVC diluted to a final concentration of 10 or 20 µM for 6 or 12 h.  Four independent biological replicate experiments were performed.

value: 10 uM DCVC


title: P5_20umDCVC_12hrs

value: placenta


title: 22_N4_NT_12hrs


title: 21_N4_20uMDCVC_6hrs

value: 6 hours


title: 19_N4_NT_6hrs


title: 20_N4_10uMDCVC_6hrs


title: Endodermal cells treated with RA 8 somites rep3 RNA-seq

city: Pamplona

first: Ana

middle: Rosa

last: López-Pérez

address: Calle Irunlarrea, 3

country: Spain

institute: Navarrabiomed - Fundacion Migues Servet

data_processing:
Illumina Casava1.7 software used for basecalling.
Aligment using STAR v2.5.4 : -outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --seedSearchStartLmax 12 --outFilterScoreMinOverLread 0.3 --alignSJoverhangMin 15 -- outFilterMismatchNmax 33 --outFilterMatchNminOverLread 0 --outFilterType BySJout --outSAMunmapped Within --outSAMattributes NH HI AS NM MD -- outSAMstrandField intronMotif --quantMode GeneCounts
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each Sample

source_name: Endodermal cells (sox17:GFP +)

growth_protocol: Embryos were obtained by incrossing Tg(sox17:GFP) zebrafish adults. Embryos were collected and grow at 23 degrees in E3 media

extract_protocol:
Embryos were dechorionated and deyolked prior to cell isolation by pippeting up and down several times. Singles cells were FACS sorted and GFP+ and GPF- cells were collected. Cells were pelleted and lysed.
RNA was retrotranscribed using an Oligo dT primer to enriched in polyA RNA prior to library preparation using Nextera XT kit

treatment_protocol: Embryos were treated either with DMSO, RA or BMS493 from 2 cell stage until the 3 somites stage.

tag: developmental stage

value: 8 somites

value: RA

value: Endodermal cells (sox17:GFP +)


title: Endodermal cells treated with BMS 8 somites rep2 RNA-seq


title: Endodermal cells treated with BMS 8 somites rep1 RNA-seq


title: Endodermal cells treated with BMS 8 somites rep3 RNA-seq


title: Endodermal cells treated with RA 8 somites rep2 RNA-seq


title: 17_N3_10uMDCVC_12hrs

value: 12 hours


title: Endodermal cells treated with RA 8 somites rep1 RNA-seq


title: Endodermal cells treated with DMSO 8 somites rep3 RNA-seq

value: DMSO (control)


title: 16_N3_NT_12hrs


title: 18_N3_20uMDCVC_12hrs


title: Endodermal cells treated with DMSO 8 somites rep2 RNA-seq


title: 14_N3_10uMDCVC_6hrs


title: Endodermal cells treated with DMSO 8 somites rep1 RNA-seq


title: Non endodermal cells 8 somites rep2 RNA-seq

source_name: Non endodermal cells (sox17:GFP -)

value: Non endodermal cells (sox17:GFP -)


title: Non endodermal cells 8 somites rep3 RNA-seq


title: 15_N3_20uMDCVC_6hrs


title: 12_N2_20uMDCVC_12hrs


title: Non endodermal cells 8 somites rep1 RNA-seq


title: Endodermal cells treated with BMS 3 somites rep3 RNA-seq

value: 3 somites


title: 10_N2_NT_12hrs


title: 11_N2_10uMDCVC_12hrs


title: Endodermal cells treated with BMS 3 somites rep2 RNA-seq


title: 9_N2_20uMDCVC_6hrs