title: MEF_IR-senescent_shRela-1_2

treatment_protocol: RNA-sequencing analyses on senescent cells induced by gamma-irradiation. After 10 days (D10) post-irradiation, cells were infected with shRNA-containing lentivirus to produce D10 irradiated cells with Rela knockdown (with 2 independent shRNAs, termed -1 and -2) or scrambled control knockdown (shScr).


title: siControl_TEAD1_Rep1

status: Public on Oct 29 2021

type: SRA

city: Stanford

first: Zohar

last: Shipony

state: CA

address: Beckman Center B-279A  279 Campus Drive West

country: USA

institute: Stanford University

description: CnR FaDu Control TEAD1

library_source: genomic

data_processing:
Library strategy: Cut&Run
sequencing was performed on the NextSeq 500 sequencing system (Illumina) with 75-cycle, paired-end sequencing setup. Reads were first trimmed from Illumina adapters using SeqPurge. Demultiplexed fastq files were mapped to the hg19 assembly of the human genome as 2×36 mers using Bowtie2 , and generated BAM files were then filtered for low-quality reads and duplicated reads. Coverage bigwigs were generated using bamCoverage with CPM normalization. Peaks were called using macs2 with the nomodel option
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

organism: Homo sapiens

source_name: pharynx, cell line

growth_protocol: FaDu, a pharyngeal squamous cell carcinoma cell line, was cultured in ATCC-formulated Eagle's Minimum Essential Medium supplemented with 10% fetal bovine serum (FBS; Omega Scientific) and antibiotics (100 units/mL Penicillin and 100 µg/mL Streptomycin; Gibco).  Adult (HEKa) were purchased from Gibco (C0055C) and cultured on Geltrex (Gibco) coated plates with EpiLife basal medium with 60 µM calcium (Gibco) plus 100 µg/mL insulin, 15 µg/mL transferrin, 10ng/mL epidermal growth factor, 15 µM forskolin, 500nM VX-745, 250nM RO4929097, 100nM dexamethasone and antibiotics.  Cells were maintained in a humidified incubator at 37 °C in the presence of 5% CO2 and passaged every 2–3 days. Cell lines were routinely tested for mycoplasma and immediately tested upon suspicion. None of the cell lines used in the reported experiments tested positive.

extract_protocol:
See Skene PJ et al 2018 (PMID: 29651053)
250,000 cells were bound to 10 µl concanavalin-A beads and collected into a 0.2 ml PCR tube. Antibody binding was conducted in the volume of 50 µl on thermomixer for 96-well PCR plates (Eppendorf) in 4 °C cold room for 2 hours, and Protein A-MNase binding for 1 hour. Wash buffer volume was adjusted to 150 µl. The digestion was performed under high Ca2+/low salt condition on ice for 15 minutes, followed by incubation at 37 °C for 30 min to release CUT&RUN fragments. Antibodies were diluted 1/100 . For histone marks profiling, CUT&RUN fragments were purified by spin column-based methods (Zymo DNA clean & concentrator-5 kit). For transcription factors and BAF complex profiling, CUT&RUN fragments were extracted by phenol-chloroform to recover small fragments. The libraries were generated by using the NEBNext ultraII DNA library prep kit for Illumina coupled with NEBNext multiplex oligos for Illumina (New England Biolabs) with few modifications optimized for small fragments (detailed in dx.doi.org/10.17504/protocols.io.wvgfe3w.)

treatment_protocol: siRNA transfections were performed with DharmaFECT 1 transfection reagents (Horizon Discovery) in the antibiotics-free medium according to the manufacturer’s instructions. Lentiviral transduction was used for overexpression experiments.

tag: tissue

value: pharynx

tag: treatment

value: siRNA Control

tag: antibody

value: TEAD1 (cell signaling, 12292S)

tag: cell line

value: FaDu


title: MEF_IR-senescent_shRela-1_3

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

library_source: transcriptomic

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with Tophat 2.0.14  to the reference genome UCSC mm10 using Bowtie2 2.2.6 with default parameters.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts in tab-delimited text file

molecule: total RNA

organism: Mus musculus

source_name: Mouse embryonic fibroblasts

extract_protocol:
RNA was column-extracted using Rneasy Micro kit (qiagen)
RNA-seq libraries were prepared from 100-200 ng high-quality RNA using TruSeq RNA Library Prep Kit v2 (Illumina)

value: embryo

tag: strain


title: MEF_IR-senescent_shRela-2_1


title: MEF_IR-senescent_shScr_2 (dataset 11)


title: siControl_YAP_Rep1

description: CnR FaDu Control YAP

value: YAP (cell signaling, 14074T)


title: SCC_siPartial_ATAC_seq_Rep2

description: ATAC-seq partial BAF53A knockdown

data_processing:
Demultiplexed and trimmed fastq files were mapped to the hg19 assembly of the human genome as 2×36 mers using Bowtie2. Duplicate reads were removed using picard-tools (v.1.99). Low-quality reads and chrM reads were removed using samtools. Fixed width peaks were called using macs2
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

extract_protocol: As described at Omni-ATAC method in Corces MR et al

value: siBAF53 partial

value: SCC


title: SCC_siFull_ATAC_seq_Rep2

description: ATAC-seq full BAF53A knockdown

value: siBAF53 full


title: MEF_IR-senescent_shRela-2_3


title: MEF_IR-senescent_shScr_3 (dataset 11)


title: SCC_siControl_ATAC_seq_Rep2

description: ATAC-seq siControl

value: Vector


title: MEF_IR-senescent_shScr_1 (dataset 11)


title: SCC_siControl_ATAC_seq_Rep1

description: ATAC-seq siControl


title: MEF_IR-senescent_shRela-1_1


title: MEF_IR-senescent_shRela-2_2


title: SCC_siFull_ATAC_seq_Rep1

description: ATAC-seq full BAF53A knockdown


title: AR3085_01

type: RNA

city: Sinjuku-ku

first: Hidekazu

last: Sugiura

state: Tokyo

address: Kawada-cho 8-1

country: Japan

institute: Tokyo Women’s Medical University

description: Agilent Human 1 cDNA Microarray (G4100A) [layout A]

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: HEK293T, vehicle, 24 hours.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Cell lines of human embryonic kidney cells 293T (HEK293T) were grown to confluence in DMEM/F-12,Hepes (Thermo Fisher Scientific), respectively, on plastic dishes (Falcon). The medium was supplemented with 10% fetal bovine serum (Invitrogen), 100 units/mL penicillin, and 100 μg/mL streptomycin (Thermo Fisher Scientific).

extract_protocol: Total RNA was isolated from cells using RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: 80% confluence 293T (HEK293T) were incubated in DMEM/F-12,Hepes without 10% fetal bovine serum (Invitrogen), 100 units/mL penicillin, and 100 μg/mL streptomycin for 24 hr. Then HEK293T  were challenged with 1064 µg/cm2 calcium oxalate monohydrate (COM)  or sodium oxalate (NaOx) 4mM or vehicle for 24 hours.

value: vehicle, 24 hours.


title: VCAP-MYC-4hr

city: TORONTO

first: Haiyang

last: Guo

state: Ontario

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

country: Canada

institute: UNIV HEALTH NETWORK

description: MYC ChIP-Seq in VCaP cells

data_processing:
ChIP-Seq reads were aligned to hg19 human genome by Bowtie2 (version 2.2.1). The bam files were then subjected to MACS2 for peak calling with the parameter “--SPMR” on and --keep-dup=1. Significant peaks were identified by q-value < 0.05. UCSC bedGraphToBigWig tool was used to convert Resultant bedgraph files to bigWig files, which were then used for peak shape visualization in IGV (version 2.8.2) and heatmap analysis by deeptools (version 3.3.1).
Genome_build: hg19
Supplementary_files_format_and_content: Tab separated txt files containing ChIP-Seq peak regions.

source_name: VCaP cells

growth_protocol: VCaP cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) medium containing 10% FBS.

extract_protocol:
ChIP experiment was performed as previously described. Briefly, cell crosslinking was conducted in 1% formaldehyde for 10 minutes and quenched by glycine. Cell nuclear fraction was extracted by LB1 buffer (50 mM Hepes–KOH, pH 7.5; 1 mM EDTA; 140 mM NaCl; 10% Glycerol; Igepal CA-630; 0.25% Triton X-100) followed by washing in LB2 (10 mM Tris–HCL,pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA) and LB3 buffer (10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine). Chromatin was sheared to 300-500 bp by Diagenode’s bioruptor sonicator and then incubated with antibody-conjugated protein A and G beads for overnight at 4°C with rotation. After washing in RIPA buffer (50 mM Tris, pH 7.6, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 1% Igepal CA630, 0.5% sodium deoxycholate, Protease inhibitor and RNase inhibitor), the beads were eluted in elution buffer (0.1M NaHCO3, 1% SDS and Proteinase K) for 8~16 hours at 65°C. ChIPed DNA was purified by phenol–chloroform extraction and then used for ChIP-qPCR or ChIP-Seq library preparation.
ThruPLEX DNA-Seq kit

treatment_protocol: For androgen-starving conditions, cells were grown in medium containing CDS (charcoaldextran stripped serum, from Hyclone). Plasmids and siRNA transfections were carried out using the Lipofectamine 2000 (Invitrogen), following the manufacturer’s directions.

value: VCaP cells

tag: cell type

value: prostate cancer


title: siControl_YAP_Rep2

description: CnR FaDu Control YAP


title: VCAP-MYC-0hr

description: MYC ChIP-Seq in VCaP cells


title: SCC_siPartial_ATAC_seq_Rep1

description: ATAC-seq partial BAF53A knockdown


title: HEKa_CnR_H3K27me3_hBAF53a_2

description: CnR HEKa hBAF53a

data_processing:
Library strategy: Cut&Run
sequencing was performed on the NextSeq 500 sequencing system (Illumina) with 75-cycle, paired-end sequencing setup. Reads were first trimmed from Illumina adapters using SeqPurge. Demultiplexed fastq files were mapped to the hg19 assembly of the human genome as 2×36 mers using Bowtie2 , and generated BAM files were then filtered for low-quality reads and duplicated reads. Coverage bigwigs were generated using bamCoverage with CPM normalization. Peaks were called using macs2 with the nomodel option
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: Human Epidermal Keratinocytes, adult (HEKa)

value: normal epidermal keratinocytes

value: skin

value: BAF53a OE

value: H3K27me3 (cell signaling, 9733)


title: HEKa_CnR_H3K27me3_hBAF53a_1

description: CnR HEKa hBAF53a


title: CUR_RNASeq

city: Ste-Anne-de-Bellevue

first: Martina

last: Stromvik

state: Quebec

address: 21,111 Lakeshore Rd

department: Department of Plant Science

institute: McGill University

data_processing:
Raw reads were trimmed and cleaned using trimmomatic with the following parameters: TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:50
RNA-Seq reads were aligned to the potato DM v4.04 genome using STAR aligner.
Regions with read depth less than 10 were removed. Bases with quality less than 20 were removed.
Variant calling was performed with Freebayes.
The RNA-Seq data were de novo assembles using Trans-ABySS software.
Genome_build: DM v4.04
Supplementary_files_format_and_content: gene-level expression, Cufflinks output
Supplementary_files_format_and_content: transcript-level expression, Cufflinks output

organism: Solanum x curtilobum

source_name: Young Leaf

growth_protocol: In vitro plants.

extract_protocol:
Leaves from young plants were collected, put on dry ice, and RNA was harvested using TIANGEN RNAprep Pure Plant Kit(Polysaccharides& Polyphenolies-rich). The RNA extraction was performed by Novogene.
RNA libraries were prepared by Novogene for sequencing standard Illumina protocols.

treatment_protocol: No special treatment. The leaves of young plant material were used for the extraction of RNA.

tag: potato landraces

value: CUR


title: HEKa_CnR_H3K27me3_Vector_2

description: CnR HEKa Control


title: MEF_EV_D10_control_3 (dataset 11)

treatment_protocol: RNA-sequencing analyses on cells overexpressing p27 via lentivirus. Cells were harvested and RNA was isolated 10 days after p27 overexpression, at this timepoint cells have entered cellular senescence.


title: MEF_EV_D10_control_2 (dataset 11)


title: HEKa_CnR_H3K27me3_Vector_1

description: CnR HEKa Control


title: MEF_p27OE_senescent_D10_1


title: MEF_p27OE_senescent_D10_3


title: PHU_RNASeq

organism: Solanum phureja

value: PHU


title: FaDu_CnR_TEAD1_siBAF53a_1

description: CnR FaDu siBAF53a

value: pharyngeal squamous cell carcinoma

value: pharynx

value: siRNA BAF53A

value: TEAD1 (cell signaling, 12292S)


title: SW_Con_TSA

city: Newcastle upon Tyne

first: Matt

last: Barter

address: International Centre For Life

country: United Kingdom

institute: Newcastle University

description: Replicate 1

hyb_protocol: Standard

scan_protocol: Standard

data_processing: Raw expression data were processed using R/Bioconductor package lumi with a variance stabilising transformation and robust spline normalization as standard

label: biotin

source_name: SW1353 chondrocyte

label_protocol: Standard

growth_protocol: SW1353 cells cultured in DMEM

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: SW1353 cells treated with TSA (250ng/ml) or DMSO control for 1 hour prior to stimulation with IL-1alpha for 6 hours

value: chondrocyte


title: SW_IL1_TSA

description: Replicate 1


title: MEF_p27OE_senescent_D10_2

value: embryo


title: SW_IL1

description: Replicate 1


title: AJH_RNASeq

organism: Solanum ahanhuiri

value: AJH


title: SW_Con

description: Replicate 1


title: FaDu_CnR_TEAD1_siControl_2

description: CnR FaDu Control

value: FaDu

value: siRNA Control


title: MEF_EV_D10_control_1 (dataset 11)


title: FaDu_CnR_TEAD1_siBAF53a_2

description: CnR FaDu siBAF53a


title: MEF_p27OE_non-senescent_D4_3

treatment_protocol: RNA-sequencing analyses on cells overexpressing p27 via lentivirus. Cells were harvested and RNA was isolated 4 days after p27 overexpression, at this timepoint cells have not entered cellular senescence yet.


title: MEF_p27OE_non-senescent_D4_2


title: MEF_p27OE_non-senescent_D4_1


title: HDAC6_IL-1_2

description: Replicate 2

treatment_protocol: SW1353 cells transfected with QIAGEN HDAC6 siRNA or non-targetting Allstars control siRNA 24 hours prior to stimulation with IL-1alpha for 6 hours


title: FaDu_CnR_TEAD1_siControl_1

description: CnR FaDu Control


title: FaDu_CnR_rbYAP_siBAF53a_2

description: CnR FaDu siBAF53a

value: YAP (cell signaling, 14074T)


title: MEF_EV_D4_control_3 (dataset 10)


title: MEF_EV_D4_control_2 (dataset 10)


title: MEF_EV_D4_control_1 (dataset 10)


title: HDAC6_Control_1

description: Replicate 1


title: FaDu_CnR_rbYAP_siControl_2

description: CnR FaDu Control


title: FaDu_CnR_rbYAP_siBAF53a_1

description: CnR FaDu siBAF53a


title: HDAC6_IL-1_1

description: Replicate 1


title: HDAC6_Control_2

description: Replicate 2


title: S9.4: RNA-seq co-culture Trogo 4

city: Seoul

first: Jaechul

last: Lim

state: CT

address: 1 Gwanak-ro, 1 Gwanak-gu

country: South Korea

institute: Seoul National University

description: RNA-seq

data_processing:
The sequences were basecalled by Illumina RTA.
The sequencing reads were aligned onto Mus musculus GRCm38/mm10 reference genome using the HISAT2. The mapped reads were transformed into the count matrix with default parameters using the StringTie v1.3.3 software, then normalized using the DESeq v2 software. Differentially expressed genes (DEGs) were identified using the same software based on a negative binomial generalized linear model.
Genome_build: mm10(GRCm38)
Supplementary_files_format_and_content: a tab-delimited file including Gene ID, Gene Name, Reference, Strand, Start, End, Coverage, FPKM, TPM

molecule: polyA RNA

source_name: B6 mouse splenocytes co-cultured with the sorted trogocytic colon cancer cells

growth_protocol: Liver metastasized colon cancer cells were generated by splenic injection of colon cancer organoids carrying a tdTomato reporter gene. Trogocytic and non-trogocytic metastasized cancer cells were sorted based on the protein levels of tdTomato (tumor cell reporter) and CD4 (CD4 T cell marker). Isolated cancer cells were co-cultured with syngeneic splenocytes from Actin-GFP reporter mice as 1:50 ratio for 5 days.

extract_protocol:
RNA was purified from the co-cultured splenocytes and colon cancer cells using QIAGEN miRNeasy kit (217004) with on-column DNase digestion according to the manufacturer’s instructions.
RNA-seq libraries were constructed using NEBNext Low Input RNA kit by YCGA (Yale Center for Genome Analysis). The RNA-seq libraries were sequenced on the Illumina NovaSeq6000 instrument platform (100 bp paired-end sequencing).

value: Spleen and Liver metastasized colon cancer

value: splenocytes and metastasized colon cancer cells


title: FaDu_CnR_rbYAP_siControl_1

description: CnR FaDu Control


title: Allstars_Control_2

description: Replicate 2


title: S9.3: RNA-seq co-culture Trogo 3

description: RNA-seq


title: MEF_p21OE_senescent_D10_2

description: processed data file: counts.txt

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with Tophat 2.0.14 to the reference genome UCSC mm10 using Bowtie2 2.2.6 with default parameters.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages.
Genome_build: mm10
Supplementary_files_format_and_content: counts.txt: Raw counts in tab-delimited text file.

extract_protocol:
RNA was column-extracted using RNeasy Micro kit (Qiagen).
RNA-seq libraries were prepared from 100-200 ng high-quality RNA using TruSeq RNA Library Prep Kit v2 (Illumina).

treatment_protocol: RNA-sequencing analyses on cells overexpressing p21 via lentivirus. Cells were harvested and RNA was isolated 10 days after p21 overexpression, at this timepoint cells have entered cellular senescence.

value: mouse embryonic fibroblasts (MEF)

tag: cell status

value: senescent

tag: lentivirus

value: p21 overexpression


title: FaDu_CnR_H3K4me3_siBAF53a_2

description: CnR FaDu siBAF53a

value: H3K4me3 (Active motif, 39159)


title: MEF_p21OE_senescent_D10_3

description: processed data file: counts.txt


title: Allstars_Control_1

description: Replicate 1


title: MEF_H3K27Ac_OI_input_1

data_processing:
Fastq files of pair-end reads were mapped with Bowtie 1.1.2 50 using parameters -k 1 -m 1 -e 70 -l 51 --best to the mouse reference genome mm10.
MACS 1.4.2 was used to identify peaks for each sample against the background using a p-value cutoff of 10e-5. All the other parameters were left as default.
Super enhancers were identified using ROSE by stitch neighboring peaks within 12.5kb from each other were stitched together while excluding regions ± 2000 bps from any transcription start site.
BigWig files of H3K27Ac occupancy profiles were generated using deepTools 3.1.0 by first normalizing each ChIP sample and its matching input to CPM and then subtracting the input signal from each ChIP sample.
Genome_build: mm10
Supplementary_files_format_and_content: H3K27ac occupancy profile bw files; bed files for super enhancers called by ROSE

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared from 1-5 ng precipitated chromatin or input DNA using the Ovation ultralow DR Multiplex kit (NuGEN) or the ThruPLEX DNA-seq Kit V2 (Rubicon Genomics).

treatment_protocol: For IR-experiments, we established the following three cultures from each independent MEF line: proliferating MEFs (to derive Control1 MEFs); MEFs exposed to 10 Gy gamma-radiation (137Caesium source) and cultured for two days (to derive Control2 MEFs); and MEFs exposed to 10 Gy gamma-radiation and cultured for 10 days (to derive IR-senescent MEFs). ). For REP-experiments, we prepared two  cultures from each independent MEF line: proliferating P3 MEFs (to derive Control1 MEFs); and P10 MEFs cultured at 20% oxygen between P4 and P10 (to derive REP-senescent MEFs). For OI-experiments, cells were infected with a KRASG12V-containing lentivirus (prepared using the pLenti-PGK-ER-KRASG12V from Addgene #35635), selected with hygromycin B and then harvested (to derive Ccontrol1 MEFs) or treated with 200 nM 4-hydroxytamoxifen (4’-OHT) to induce KRASG12V for 2 days (to derive Control2 MEFs) or 10 days (to derive OI-induced senescent MEFs). IR-, REP- and OI-induced senescent MEFs were enriched by sterile FACS. Samples with ~70% or more senescent cells were used for H3K27ac-ChIP-Seq experiments). Control1 and Ccontrol2 MEFs cultures were also subjected to FACS but here fractions devoid of senescent cells were collected.

value: proliferating

tag: induced by

value: KRASG12V-oncogene induciton (OI)


title: S9.2: RNA-seq co-culture Trogo 2

description: RNA-seq


title: S9.1: RNA-seq co-culture Trogo 1

description: RNA-seq


title: MEF_p21OE_senescent_D10_1

description: processed data file: counts.txt


title: MEF_H3K27Ac_IR_senescent_input_3

value: irradiation (IR)


title: MEF_H3K27Ac_OI_input_2


title: Allstars_IL-1_1

description: Replicate 1


title: FaDu_CnR_H3K4me3_siBAF53a_1

description: CnR FaDu siBAF53a

value: pharyngeal squamous cell carcinoma

value: pharynx

value: siRNA BAF53A


title: Allstars_IL-1_2

description: Replicate 2

value: chondrocyte


title: S6.4: RNA-seq co-culture control 4

description: RNA-seq

source_name: B6 mouse splenocytes co-cultured with the sorted non-trogocytic colon cancer cells


title: FaDu_CnR_H3K4me3_siControl_1

description: CnR FaDu Control


title: S6.3: RNA-seq co-culture control 3

description: RNA-seq


title: MEF_H3K27Ac_IR_senescent_input_2


title: MEF_H3K27Ac_IR_control2_input_1

value: induced


title: FaDu_CnR_H3K4me3_siControl_2

description: CnR FaDu Control

value: FaDu


title: MEF_EV_D10_control_3

description: processed data file: counts.txt

value: control


title: S6.2: RNA-seq co-culture control 2

description: RNA-seq


title: MEF_H3K27Ac_IR_senescent_input_1


title: MEF_H3K27Ac_IR_control1_input_3


title: MEF_EV_D10_control_1

description: processed data file: counts.txt


title: FaDu_CnR_H3K4me1_siBAF53a_2

description: CnR FaDu siBAF53a

value: H3K4me1 (Abcam, ab8895)


title: MEF_EV_D10_control_2

description: processed data file: counts.txt


title: MEF_H3K27Ac_IR_control1_input_2


title: FaDu_CnR_H3K4me1_siBAF53a_1

description: CnR FaDu siBAF53a


title: HKO [ATAC-seq]

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

country: China

institute: Harbin Institute of Technology

data_processing:
Nextera adaptor sequences were firstly trimmed from the reads using skewer (0.2.2). These reads were aligned to a reference genome using BWA, with standard parameters. These reads were then filtered for high quality (MAPQ≥13), non mitochondrial chromosome, and properly paired reads (longer than 18 nt).
All peak calling was performed with macs2 using ‘macs2 callpeak --nomodel --keepdup all --call-summits’. For simulations of peaks called per input read, aligned and de-duplicated BAM files were used without any additional filtering.
Genome_build: Ensemble_GRCm38.90
Supplementary_files_format_and_content: HKO_vs_FF_peak_compare_table.tsv

source_name: Mettl3 HKO (Mettl3 flox/flox Alb-Cre+/-)

extract_protocol:
Nuclei was extracted from liver samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min.
Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina NovaSeq 6000 platform and 150 bp paired-end reads were generated.

treatment_protocol: Mettl3flox/flox and HKO mice were fed with normal chow diet for 8 weeks old

tag: strain background

tag: genotype/variation

tag: age

value: 8 weeks

value: Liver


title: FaDu_CnR_H3K4me1_siControl_1

description: CnR FaDu Control

value: siRNA Control


title: FaDu_CnR_H3K4me1_siControl_2

description: CnR FaDu Control


title: MEF_p21OE_non-senescent_D4_2

description: processed data file: counts.txt

treatment_protocol: RNA-sequencing analyses on cells overexpressing p21 via lentivirus. Cells were harvested and RNA was isolated 4 days after p21 overexpression.

value: mouse embryonic fibroblasts (MEF)

value: non-senescent


title: FaDu_CnR_H3K27me3_siBAF53a_2

description: CnR FaDu siBAF53a

value: H3K27me3 (cell signaling, 9733)


title: MEF_EV_D4_control_3

description: processed data file: counts.txt


title: MEF_H3K27Ac_IR_control1_input_1

value: proliferating


title: KO ABA rep3

city: shanghai

first: li

last: peng

institute: PSC

data_processing:
The paired-end reads were cleaned by Trimimomatic (version 0.36).
After trimming the adapter sequence, removing low quality bases, and filtering short reads, clear read pairs were retained for further analysis.
Number of reads that were mapped to each gene was calculated with the htseq-count script in HTSeq
EdgeRwas used to identify genes that were differentially expressed.
Genome_build: tair10
Supplementary_files_format_and_content: DEG_expression_table.xlsx

organism: Arabidopsis

growth_protocol: 1/2 MS, 1/2 MS nutrients, pH 5.7, 1% Surose

extract_protocol:
RNeasy Plant Mini Kit (Qiagen)
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

tag: genotype

value: aph-1 mutant

tag: developmental stage

value: 14 day

value: Whole seedling

value: Abscisic acid, 50 micromole, 6h


title: S6.1: RNA-seq co-culture control 1

description: RNA-seq

value: Spleen and Liver metastasized colon cancer

value: splenocytes and metastasized colon cancer cells


title: MEF_H3K27Ac_OI_senescent_2

value: senescent

value: KRASG12V-oncogene induciton (OI)

tag: chip-antibody


title: FF [ATAC-seq]

source_name: Mettl3 flox/flox

value: Mettl3 flox/flox


title: MEF_EV_D4_control_2

description: processed data file: counts.txt

value: control


title: KO ABA rep2


title: MEF_p21OE_non-senescent_D4_3

description: processed data file: counts.txt

value: p21 overexpression


title: FaDu_CnR_H3K27me3_siBAF53a_1

description: CnR FaDu siBAF53a

value: FaDu

value: pharyngeal squamous cell carcinoma

value: pharynx

value: siRNA BAF53A


title: MEF_H3K27Ac_OI_control2_2

value: mouse embryonic fibroblasts (MEF)

value: induced


title: MEF_EV_D4_control_1

description: processed data file: counts.txt

value: non-senescent


title: FaDu_CnR_H3K27me3_siControl_2

description: CnR FaDu Control

value: siRNA Control

value: H3K27me3 (cell signaling, 9733)


title: MEF_H3K27Ac_OI_control1_2

value: proliferating


title: Pooled Blood-1

type: genomic

city: Kashiwa

first: Ken

last: Watanabe

state: Chiba

address: 6-3-1, Kashiwanoha

institute: National Research Institute of Police Science

description: pooled samples from three individuals

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

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: BeadStudio software v2011.1

label: Cy3, Cy5

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using QIAamp DNA mini Kit

value: blood


title: KO ABA rep1

value: aph-1 mutant

value: 14 day

value: Whole seedling

value: Abscisic acid, 50 micromole, 6h


title: Pooled Semen-1

description: pooled samples from three individuals

value: semen


title: FaDu_CnR_H3K27me3_siControl_1

description: CnR FaDu Control


title: MEF_IR-non-senescent_D4_shRb_3

description: processed data file: counts.txt

extract_protocol: RNA-seq libraries were prepared from 100-200 ng high-quality RNA using TruSeq RNA Library Prep Kit v2 (Illumina).

treatment_protocol: RNA-sequencing analyses on cells induced by gamma-irradiation after 2 days (D2) or 4 days (D4) as well as proliferating cells (D0). D2 irradiated cells were infected with shRNA-containing lentivirus to produce D4 irradiated cells with p21 knockdown, Rb knockdown or scrambled control knockdown (shScr).

value: irradiation (IR)

value: shRNAs against Rb


title: MEF_H3K27Ac_OI_control2_1


title: KO control rep3

value: NO


title: MEF_H3K27Ac_OI_senescent_1

value: senescent

value: KRASG12V-oncogene induciton (OI)


title: MEF_IR-non-senescent_D4_shRb_2

description: processed data file: counts.txt

value: mouse embryonic fibroblasts (MEF)


title: FaDu_CnR_H3K27ac_siBAF53a_2

description: CnR FaDu siBAF53a

value: FaDu

value: pharyngeal squamous cell carcinoma

value: pharynx

value: siRNA BAF53A

value: H3K27Ac (Abcam, ab4729)


title: Pooled Blood-2

description: pooled samples from three individuals

value: blood


title: KO control rep1

value: aph-1 mutant


title: MEF_IR-non-senescent_D4_shRb_1

description: processed data file: counts.txt

value: induced


title: MEF_H3K27Ac_OI_control1_1

value: proliferating


title: FaDu_CnR_H3K27ac_siBAF53a_1

description: CnR FaDu siBAF53a


title: FaDu_CnR_H3K27ac_siControl_2

description: CnR FaDu Control

value: siRNA Control


title: WT ABA rep3

value: WT

value: 14 day

value: Whole seedling

value: Abscisic acid, 50 micromole, 6h


title: MEF_IR-non-senescent_D4_shp21_3

description: processed data file: counts.txt

value: irradiation (IR)

value: shRNAs against p21


title: Pooled Saliva-2

description: pooled samples from three individuals

value: saliva


title: MEF_H3K27Ac_IR_senescent_2

value: mouse embryonic fibroblasts (MEF)

value: senescent


title: MEF_p21OE_non-senescent_D4_1

description: processed data file: counts.txt

value: non-senescent

value: p21 overexpression


title: KO control rep2

value: NO


title: WT ABA rep2


title: MEF_IR-non-senescent_D4_shp21_2

description: processed data file: counts.txt


title: Pooled Semen-2

description: pooled samples from three individuals

value: semen


title: MEF_H3K27Ac_IR_senescent_3


title: MEF_H3K27Ac_IR_senescent_1


title: WT ABA rep1


title: MEF_IR-non-senescent_D4_shp21_1

description: processed data file: counts.txt


title: FaDu_CnR_BAF155_siBAF53a_2

description: CnR FaDu siBAF53a

value: FaDu

value: pharyngeal squamous cell carcinoma

value: pharynx

value: siRNA BAF53A

value: BAF155 (Crabtree laboratory),


title: Pooled Saliva-1

description: pooled samples from three individuals


title: FaDu_CnR_BAF155_siBAF53a_1

description: CnR FaDu siBAF53a


title: Pooled Vaginal Fluid-2

description: pooled samples from three individuals

source_name: Vaginal Fluid4-6

value: vaginal fluid


title: MEF_H3K27Ac_IR_control2_3

value: induced


title: Pooled Vaginal Fluid-1

description: pooled samples from three individuals

source_name: Vaginal Fluid1-3


title: WT control rep3

value: WT

value: 14 day

value: Whole seedling


title: MEF_IR-non-senescent_D4_shScr_3

description: processed data file: counts.txt

value: irradiation (IR)

value: scrambled control shRNA


title: MEF_IR-non-senescent_D4_shScr_2

description: processed data file: counts.txt

value: mouse embryonic fibroblasts (MEF)


title: FaDu_CnR_BAF155_siControl_2

description: CnR FaDu Control

value: siRNA Control


title: MEF_H3K27Ac_IR_control2_2


title: FaDu_CnR_H3K27ac_siControl_1

description: CnR FaDu Control

value: H3K27Ac (Abcam, ab4729)


title: MEF_H3K27Ac_IR_control1_3

value: proliferating


title: HEKa_hBAF53a_2_ATACseq

description: ATAC-seq HEKa BAF53A

data_processing:
Demultiplexed and trimmed fastq files were mapped to the hg19 assembly of the human genome as 2×36 mers using Bowtie2. Duplicate reads were removed using picard-tools (v.1.99). Low-quality reads and chrM reads were removed using samtools. Fixed width peaks were called using macs2
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

value: normal epidermal keratinocytes

value: skin

value: BAF53a OE


title: MEF_IR-non-senescent_D4_shScr_1

description: processed data file: counts.txt


title: MEF_H3K27Ac_IR_control2_1


title: MEF_IR_D2_3

description: processed data file: counts.txt


title: FaDu_CnR_BAF155_siControl_1

description: CnR FaDu Control

value: FaDu

value: pharyngeal squamous cell carcinoma

value: pharynx


title: WT control rep1

value: NO


title: Spt3_rep_3

city: Kansas City

first: Hua

state: MO

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

description: ChIP-seq

data_processing:
bcl2fastq2-v2.20.0.422 was used to generate fastq files.
Reads were aligned to dm6 genome using bowtie2-2.3.4.1 with the default parameters.
Genome_build: dm6

organism: Drosophila melanogaster

source_name: Ovary

growth_protocol: Kc167 cells were maintained at 1-2 e6 cells/mL in SFX medium (HyQ SFX-Insect;HyClone Laboratories, Inc) at 27 dC. Drosophila melanogaster were grown on standardsyrup  medium at 25 °C.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit

tag: chip antibody

value: wild type


title: Spt3_rep_2

description: ChIP-seq


title: MEF_H3K27Ac_IR_control1_1


title: HEKa_Vector_2_ATACseq

description: ATAC-seq HEKa Vector

tag: tissue

value: Vector


title: MEF_H3K27Ac_IR_control1_2


title: Spt3_rep_1

description: ChIP-seq


title: HEKa_hBAF53a_1_ATACseq

description: ATAC-seq HEKa BAF53A

tag: treatment


title: MEF_IR_D2_1

description: processed data file: counts.txt

value: induced


title: SAF6_rep_3

description: ChIP-seq


title: MEF_IR_D2_2

description: processed data file: counts.txt


title: FaDu_siBAF53A_2_ATACseq

description: ATAC-seq FaDu siBAF53A

value: siRNA BAF53A


title: MEF_non-IR_D0_control_3

description: processed data file: counts.txt


title: SAF6_rep_2

description: ChIP-seq


title: WT control rep2

value: WT

value: 14 day

value: Whole seedling


title: HEKa_Vector_1_ATACseq

description: ATAC-seq HEKa Vector


title: SAF6_rep_1

description: ChIP-seq


title: FaDu_siBAF53A_1_ATACseq

description: ATAC-seq FaDu siBAF53A


title: BE2C-GSKJ4-2_H3K27me3

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
Library strategy: CUT&Tag
Raw reads were first trimmed low-quality ends using trim-galore (0.4.4; default parameter) and then aligned to the human reference genomes (hg19) using BWA (version 0.7.12; default parameter) and duplicated reads were then marked with Picard (version 1.65), with only nonduplicated reads kept by samtools (version 1.3.1, parameter ‘‘-q 1 -F 1024’’). Only reads with fragment size between 150- 2000bp were used for downstream analysis ( bigwig file generation, peak calling etc.).
To utilize E.Coli reads as a spike-in control, unmapped reads were further aligned to E.Coli genome and  calculated ChIP-Rx scaling factor as described by Meers et. al. (eLife 2019).
MACS2 (version 2.1.1 20160309) was used to call narrow peaks  using 'macs2 callpeak  -t cut_tag_file -f BEDPE -q 0.05 --keep-dup all' .  For calling broad peaks, we used SICER (version 1.1) with parameters of redundancy threshold 1, window size 200bp, effective genome fraction 0.86, gap size 600bp and E 0.00001.
We utilized genomeCoverageBed (bedtools 2.25.0) to obtain genome-wide coverage in BEDGRAPH file format and then converted it to bigwig file format by bedGraphToBigWig. The bigwig signals were adjusted by E.Coli spike-in scaling factor and scaled to 15 million reads to allow comparison across samples.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig, narrowPeak,bed

source_name: cell line

growth_protocol: BE2C cells were cultured with RPMI 1640 media supplemented with 100 U/mlpenicillin/streptomycin and 10% fetal bovine serum. Cells were maintained at 37 °C in an atmosphere of 5% CO2.

extract_protocol:
CUT&Tag DNAs of BE2C cell with siRNAs and compounds treatment were prepared by following the protocol as described previously (Kaya-Okur et al. 2019 and https://www.protocols.io/view/bench-top-cut-amp-tag-bcuhiwt6?step=1 ) with minor modifications. BE2C with siRNAs (siCtrl or siKDM6B) or compounds (DMSO 0.1% or GSKJ4 2.5µM) treated for 72 hours approximately 500,000 cells were washed with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail). Nuclei were isolated with cold NE1 buffer (20 mM HEPES–KOH, pH 7.9; 10 mM KCl 0.1%; Triton X-100; 20% Glycerol, 0.5 mM Spermidine; 1x Protease Inhibitor) for 10 min on ice. Nuclei were collected by 600 x g centrifuge and resuspended in 1ml washing buffer containing with 10 µL of activated concanavalin A-coated beads (Bangs laboratories, BP531) at RT for 10 min.  Bead-bound nuclei were collected with placing tube on magnet stand and removing clear liquid. The nuclei bound with bead were resuspended in 50 µL Dig-150 buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail; 0.05% Digitonin; 2 mM EDTA) and incubated with a 1:50 dilution of H3K4me1 (Abcam, ab8895) and H3K27me3 (CST, 9733S) antibodies overnight at 4 °C. The unbound primary antibody was removed by placing the tube on the magnet stand and withdrawing the liquid. The primary antibody bound nuclei bead was mixed with Dig-150 buffer 100uL containing guinea pig anti-Rabbit IgG antibody (Antibodies, ABIN101961) 1:100 dilution for 1 hour at RT. Beads bound nuclei were washed using the magnet stand 3× for 5 min in 1 mL Dig-150 buffer to remove unbound antibodies.  A 1:100 dilution of pA-Tn5 adapter complex was prepared in Dig-300 buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 0.05% Digitonin, 1× Protease inhibitor cocktail).  After removing the liquid on the magnet stand, 100 µL mixture of pA-Tn5 and Dig- 300 buffer was added to the nuclei bound beads with gentle vortex and incubated at RT for 1 h. After 3× 5 min in 1 mL Dig-300 buffer to remove unbound pA-Tn5 protein, nuclei were resuspended in 250 µL Tagmentation buffer (10 mM MgCl2 in Dig-300 buffer) and incubated at 37 °C for 1 h. EDTA 10 µL of 0.5 M, 3 µL of 10% SDS and 2.5 µL of 20 mg/mL Proteinase K were added to stop tagmentation and incubated at 55 °C for 1 hour. DNA was then precipitated by phenol/chloroform/isoamylalcohol followed by ethanol precipitation with glycogen and then dissolved in water.
Sequencing libraries were prepared using NEBNext HiFi 2× PCR Master Mix (NEB, M0541L) according to the manufacturer's instructions. The PCR products were cleaned up with SPRIselect beads and quantified using Qubit dsDNA HS assay kit (Agilent Technologies). The libraries were sequenced on a HiSeq2500 with paired-end 50-bp reads (Illumina).

treatment_protocol: For siRNA knockdown, BE2C cells were treated with siCtrl or siKDM6B for 72h. For GSK-J4 treatment,  BE2C cells were cultured with DMSO or GSKJ4 for 72h.


title: WDA_rep_3

description: ChIP-seq

value: WDA


title: FaDu_siControl_2_ATACseq

description: ATAC-seq FaDu siControl

value: siRNA Control


title: MEF_non-IR_D0_control_2

description: processed data file: counts.txt

value: mouse embryonic fibroblasts (MEF)

value: proliferating


title: MEF_IR-senescent_shScr_2

treatment_protocol: For IR-senescent MEFs were generated by exposing proliferating MEFs to 10 Gy gamma-radiation (137Caesium source) and cultured for 10 days. Cells were replated and infected with lentivirus containing shRNAs against p21 or Rb, or scrambled control shRNA (shScr). 72 hrs after the first infection cells were harvest and RNA was extracted.

value: embryo

tag: cell state

value: senescent

value: scrambled control shRNA


title: BE2C-GSKJ4-1_H3K27me3

tag: cell line


title: BE2C-GSKJ4-2_H3K4me1


title: FaDu_siControl_1_ATACseq

description: ATAC-seq FaDu siControl

value: FaDu

value: pharyngeal squamous cell carcinoma


title: MEF_IR-senescent_shScr_3

tag: strain


title: TT_siBAF53A_2_RNAseq

description:
RNA-seq siRNA BAF53A_TT
FaDu_KYSE70_TT_TPM_table_express.tsv

data_processing:
Deep sequencing was performed on the NextSeq 500 sequencing system (Illumina) with a 75-cycle, paired-end sequencing. Alignment of RNA-sequencing reads was performed with STAR with ENCODE standard options to GENCODE v19, read counts were generated with using express
Genome_build: hg19
Supplementary_files_format_and_content: TPM counts

source_name: esophageal squamous cell carcinoma

growth_protocol: FaDu, a pharyngeal squamous cell carcinoma cell line, was cultured in ATCC-formulated Eagle's Minimum Essential Medium supplemented with 10% fetal bovine serum (FBS; Omega Scientific) and antibiotics (100 units/mL Penicillin and 100 µg/mL Streptomycin; Gibco). T.T esophageal squamous cell carcinoma cells were purchase from JCRB Cell Bank (JCRB0262) and cultured in medium Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12 (DMEM/F-12; Gibco, catalog no. 10565) supplemented with 10% FBS, and antibiotics. KYSE70 esophageal squamous cell carcinoma cells were purchase from Sigma (94072012) and cultured in medium RPMI-1640 (Gibco, catalog no. 21870092) supplemented with 10% FBS, 10 mM HEPES (Gibco), 1 mM sodium pyruvate (Gibco), 2mM GlutaMax (Gibco) and antibiotics.  Adult (HEKa) were purchased from Gibco (C0055C) and cultured on Geltrex (Gibco) coated plates with EpiLife basal medium with 60 µM calcium (Gibco) plus 100 µg/mL insulin, 15 µg/mL transferrin, 10ng/mL epidermal growth factor, 15 µM forskolin, 500nM VX-745, 250nM RO4929097, 100nM dexamethasone and antibiotics.  Cells were maintained in a humidified incubator at 37 °C in the presence of 5% CO2 and passaged every 2–3 days. Cell lines were routinely tested for mycoplasma and immediately tested upon suspicion. None of the cell lines used in the reported experiments tested positive.

extract_protocol:
72 hours after siRNA transfection, cells were lysed directly on culture plates with TRIsure reagents (Bioline), and RNA was extracted using Direct-zol RNA MiniPrep kits (Zymo Research) with in-column DNase I digestion to remove residual genomic DNA.
RNA-seq libraries were generated by using NEBNext ultra II directional RNA library prep kit coupled with NEBNext multiplex oligos for Illumina (New England Biolabs) and following the manufacturer’s directions.

value: TT

tag: cell type

value: esophageal squamous cell carcinoma

value: esophageal


title: MEF_IR-senescent_shScr_1

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with Tophat 2.0.14  to the reference genome UCSC mm10 using Bowtie2 2.2.6 with default parameters.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts in tab-delimited text file


title: BE2C-GSKJ4-1_H3K4me1


title: Ada2b_rep_3

description: ChIP-seq

value: wild type


title: TT_siControl_2_RNAseq

description:
RNA-seq siRNA Control_TT
FaDu_KYSE70_TT_TPM_table_express.tsv


title: TT_siBAF53A_1_RNAseq

value: siRNA BAF53A


title: BE2C-DMSO-2_H3K27me3

value: DMSO


title: TT_siControl_1_RNAseq


title: MEF_IR-senescent_shRb_3

value: shRNAs against Rb


title: MEF_IR-senescent_shp21_3

value: shRNAs against p21


title: MEF_IR-senescent_shRb_1


title: Ada2b_rep_2

description: ChIP-seq


title: Ada2b_rep_1

description: ChIP-seq


title: BE2C-DMSO-1_H3K27me3


title: MEF_IR-senescent_shRb_2


title: KYSE70_siBAF53A_2_RNAseq

description:
RNA-seq siRNA BAF53A_KYSE70
FaDu_KYSE70_TT_TPM_table_express.tsv


title: BE2C-DMSO-1_H3K4me1


title: BE2C-siKDM6B33-2_H3K27me3

value: siKDM6B #33 knockdown


title: BE2C-DMSO-2_H3K4me1


title: WDA_rep_1

description: ChIP-seq

value: WDA


title: KYSE70_siBAF53A_1_RNAseq


title: MEF_IR-senescent_shp21_2


title: Input_rep_3

description: ChIP-seq


title: MEF_IR-senescent_shp21_1


title: BE2C-siKDM6B33-1_H3K27me3


title: HEKa_hBAF53A_2

description:
RNA-seq BAF53a OE_HEKa
RNA_HEKa_TPM_table_express.tsv

value: normal epidermal keratinocytes

value: skin

value: BAF53a OE


title: MEF_REP_control1_1

treatment_protocol: For IR-experiments, we established the following cultures from each independent MEF line: proliferating MEFs (to derive Control1 MEFs) and MEFs exposed to 10 Gy gamma-radiation (137Caesium source) and cultured for 10 days to derive IR-senescent MEFs). For REP-experiments, we prepared proliferating P3 MEFs (to derive Control1 MEFs); and P10 MEFs cultured at 20% oxygen between P4 and P10 (to derive REP-senescent MEFs). For OI-experiments, cells were infected with a KRASG12V-containing lentivirus (prepared using the pLenti-PGK-ER-KRASG12V from Addgene #35635), selected with hygromycin B and then harvested (to derive Ccontrol1 MEFs) or treated with 200 nM 4-hydroxytamoxifen (4’-OHT) to induce KRASG12V for 10 days (to derive OI-induced senescent MEFs). IR-, REP- and OI-induced senescent MEFs were enriched by sterile FACS. Samples with ~70% or more senescent cells were used for H3K27ac-ChIP-Seq experiments). Control1 MEFs cultures were also subjected to FACS but here fractions devoid of senescent cells were collected.

value: embryo


title: Input_rep_1

description: ChIP-seq


title: WDA_rep_2

description: ChIP-seq


title: Colony_72h_OxicCellsCollected_rep4

city: Marburg

first: Francisco

last: Diaz-Pascual

address: Karl-von-Frisch-Straße 10

country: Germany

institute: Max Planck Institute for Terrestrial Microbiology

data_processing:
Sequencing of the cDNA libraries was performed by MPGC
cDNA reads were imported into CLC Genomics Workbench v11.0 and analysed using mostly standard parameters.
The reads were checked for quality and mapped to the E. coli reference genome: NCBI Acc.number: AP009048 using the default settings in CLC Genomics Workbench v11.0.
Reads mapping in CDS were counted, and read counts were normalized (TPM), and transformed (log2). Differential expression was tested using the built in tool with CLC Genomics Workbench v11.0. Genes with a FDR adjusted p-value < 0.05 were considered to be differentially expressed.
Genome_build: AP009048; Escherichia coli str. K-12 substr. W3110 DNA, complete genome
Supplementary_files_format_and_content: Read count table by TPM normalization

organism: Escherichia coli

source_name: Fluorescent cells from colony

growth_protocol: Colonies were grown on solid M9 medium supplemented with glucose at 37 degrees.

extract_protocol:
RNA was isolated by the hot phenol method (Jahn et al, J Microbiol Methods,2008) with some modifications. Prepared RNA was DNase-digested and cleaned up using RNACleanXP. Depletion of ribosomal RNA was performed using Ribo-Zero kits (Epicentre) for Gram-negative bacteria. Integrity of the prepared RNA was tested using a Bioanalyzer.
Directional cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Libary Prep Kit for Illumina (NEB E7760) according to the manufacturers instructions. Quality of the prepared libraries was tested using a Bioanalyzer.

treatment_protocol: Cells from cononies were suspended in PBS. After removal of PBS, cells were snap frozen in liquid nitrogen until further processing. If FACS was required, cells were fixed with formaldehyde after disrupting them in PBS.

tag: condition

value: 72 h colony, formaldehyde fixation, oxic cells collected after FACS

tag: replicate

value: Replicate 4


title: MEF_REP_control1_3

extract_protocol:
RNA was column-extracted using Rneasy Micro kit (qiagen)
RNA-seq libraries were prepared from 100-200 ng high-quality RNA using TruSeq RNA Library Prep Kit v2 (Illumina)


title: Colony_72h_OxicCellsCollected_rep3

value: Replicate 3


title: BE2C-siKDM6B33-1_H3K4me1


title: BE2C-siCtrl-2_H3K27me3

value: siCtrl knockdown


title: Colony_72h_OxiCellsCollected_rep2

value: Replicate 2


title: Input_rep_2

description: ChIP-seq


title: HEKa_hBAF53A_1

treatment_protocol: siRNA transfections were performed with DharmaFECT 1 transfection reagents (Horizon Discovery) in the antibiotics-free medium according to the manufacturer’s instructions. Lentiviral transduction was used for overexpression experiments.


title: BE2C-siCtrl-1_H3K27me3


title: MEF_REP_control1_2


title: HEKa_Vector_2

description:
RNA-seq Vector_HEKa
RNA_HEKa_TPM_table_express.tsv

value: Vector


title: MEF_REP_senescent_3


title: MEF_non-IR_D0_control_1

description: processed data file: counts.txt

value: mouse embryonic fibroblasts (MEF)

tag: cell status

value: proliferating


title: HEKa_Vector_1


title: BE2C-siCtrl-2_H3K4me1


title: KYSE70_siControl_1_RNAseq

description:
RNA-seq siRNA Control_KYSE70
FaDu_KYSE70_TT_TPM_table_express.tsv

value: esophageal squamous cell carcinoma

value: esophageal

value: siRNA Control


title: MEF_REP_senescent_1


title: Colony_72h_AnoxicCellsCollected_rep4

source_name: Non-fluorescent cells from colony

value: 72 h colony, formaldehyde fixation, anoxic cells collected after FACS


title: BE2C-siCtrl-1_H3K4me1


title: MEF_REP_senescent_2

source_name: Mouse embryonic fibroblasts


title: Colony_72h_OxicCellsCollected_rep1

value: Replicate 1


title: BE2C-siKDM6B33-2_H3K4me1

value: siKDM6B #33 knockdown


title: FaDu_siBAF53A_2_RNAseq

description:
RNA-seq siRNA BAF53A_FaDu
FaDu_KYSE70_TT_TPM_table_express.tsv

source_name: pharynx, cell line

value: FaDu

value: pharyngeal squamous cell carcinoma

value: pharynx

value: siRNA BAF53A


title: Colony_72h_AnoxicCellsCollected_rep3


title: FaDu_siBAF53A_1_RNAseq


title: RNASeq_VCaP_FBS_siMYC_26_rep1

description:
RNASeq_VCaP_FBS_siMYC_26_rep1
RNASeq_expression_2.txt

data_processing:
Sequencing reads were aligned to hg19 human genome using STAR (version 2.4.2a). Reads per kilobase per million mapped reads (RPKM) was then calculated based on gene read count and GENCODE v24 GRCh37 annotation.
Genome_build: hg19
Supplementary_files_format_and_content: txt files contain the gene expression matrices

source_name: VCaP cells

growth_protocol: LNCaP were grown in RPMI-1640 containing 10% FBS (GIBCO, 10437-028); LNCaP cell line overexpression of Flag-tagged AR (LNCaP-AR, or LA) was based on LNCaP cells infection with lenti-viral AR expression vector and selected on hygromycin B (200ug/ml); VCaP cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) medium containing 10% FBS.

extract_protocol:
Total RNA was extracted using RNeasy MiniKit (74106, Qiagen) following manufacturer’s procedure.
Whole transcriptome sequencing libraries were prepared using TruSeq® Stranded mRNA Library Prep Kit (RS-122-2101, Illumina, San Diego, CA, USA) by following the manufacturer’s instructions.

value: VCaP

value: prostate cancer

value: MYC knockdown, siMYC #26

value: FBS medium


title: MEF_OIS_senescent_3

value: embryo


title: RNASeq_VCaP_FBS_siMYC_26_rep2

description:
RNASeq_VCaP_FBS_siMYC_26_rep2
RNASeq_expression_2.txt


title: Colony_72h_AnoxiCellsCollected_rep2

value: Replicate 2


title: FaDu_siControl_2_RNAseq

description:
RNA-seq siRNA Control_FaDu
FaDu_KYSE70_TT_TPM_table_express.tsv


title: Colony_72h_AnoxicCellsCollected_rep1


title: MEF_OIS_senescent_2


title: FaDu_siControl_1_RNAseq


title: RNASeq_VCaP_FBS_siMYC_1094_rep2

description:
RNASeq_VCaP_FBS_siMYC_1094_rep2
RNASeq_expression_2.txt

value: MYC knockdown, siMYC #1094


title: MEF_OIS_senescent_1


title: Colony_72h_AllCellsCollected_rep4

source_name: Whole colony

value: 72 h colony, formaldehyde fixation, all cells collected after FACS

value: Replicate 4


title: RNASeq_VCaP_FBS_siMYC_1094_rep1

description:
RNASeq_VCaP_FBS_siMYC_1094_rep1
RNASeq_expression_2.txt


title: MEF_OIS_control1_3


title: Colony_72h_AllCellsCollected_rep3

value: Replicate 3


title: RNASeq_VCaP_FBS_siCtrl_rep2

description:
RNASeq_VCaP_FBS_siCtrl_rep2
RNASeq_expression_2.txt

value: Control siRNA-#2


title: KO scRNAseq rep 1

city: Bethesda

first: Apratim

last: Mitra

state: MD

address: 6 Center Dr Building 6B Room 2B206

department: Division of Developmental Biology

institute: NICHD

data_processing:
Basecalling was performed using RTA 3.9.2.
Barcode was demultiplexed allowing 1 mismatch with Bcl2fastq 2.20.
Alignment, tagging and gene counting were done with Cellranger 5.0.0.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: .h5 file of gene-by-barcode matrix.

source_name: Thymus

extract_protocol: Two 10x Genomics Single Cell Chromium 5' mRNA libraries were made within one replicate and sequenced on one NextSeq run. Read length: R1: 26bps, R2: 8bps, R3: 91bps (NextSeq).

value: 2:1:1 mixture of sorted DN, DP, and CD8 ISP thymocytes


title: Colony_72h_AllCellsCollected_rep2


title: MEF_OIS_control1_1


title: RNASeq_VCaP_FBS_siCtrl_rep1

description:
RNASeq_VCaP_FBS_siCtrl_rep1
RNASeq_expression_2.txt

value: Control siRNA-#1


title: WT scRNAseq rep 2


title: MEF_OIS_control1_2


title: KO scRNAseq rep 2


title: RNASeq_LNCaP_AR_REP2

description:
RNASeq_LNCaP_AR_REP2
RNASeq_expression_2.txt

source_name: LNCaP cells

value: LNCaP

value: AR overexpression


title: WT scRNAseq rep 1


title: RNASeq_LNCaP_AR_REP1

description:
RNASeq_LNCaP_AR_REP1
RNASeq_expression_2.txt


title: Colony_72h_AllCellsCollected_rep1

value: Replicate 1


title: Colony_72h_2hFixation_rep3

value: 72 h colony, formaldehyde fixation for 2 h


title: MEF_IR_senescent_3


title: RNASeq_LNCaP_AR_MYC_REP2

description:
RNASeq_LNCaP_AR_MYC_REP2
RNASeq_expression_2.txt

value: AR and MYC overexpression


title: Colony_72h_2hFixation_rep2


title: SCAF505_11-28_KO_PBS

first: Mark

middle: R

last: Cookson

address: NIHBC 35 - PNRC I BG RM 1A-116

institute: National Institutue on Aging, NIH

data_processing:
10X Genomics cellranger (version 3.0.0)
10X Genomics cellranger (version 2.2.0)
Seurat V4
Genome_build: mm10
Supplementary_files_format_and_content: The processed data file includes raw counts for genes output from Seurat, and the processed file is in .RDS format.

source_name: adult mouse brain

extract_protocol:
The mouse brain was dissociated using the Adult Brain Dissociation kit (Miltenyi Biotech, Cat#130–107- 677), following by demyelination with Debris Removal Solution according to manufacturer's recommendation. For microglia isolation, the cell suspensions were labelled with CD11b microbeads (Miltenyi Biotech, Cat#130–093-634) and loaded onto MACS columns (cat#130–042-201).
Single cell suspension generated from the half-brain sample were subjected to scRNA-Seq using a 10× genomics Chromium analyzer with Chromium Next GEM Single Cell 3' regent kit v3.1 at the NCI single cell analysis facility, Bethesda MD.
Sequencing was performed with NCI single cell facility, using 50,000 reads per cell.

value: brain isolated microglia

value: 1 year old mouse brain

value: Lrrk2-/- Cx3cr1GFP+/-

value: PBS


title: SCAF504_11-28_KO_LPS

value: LPS


title: MEF_IR_senescent_1

value: embryo


title: MEF_IR_senescent_2


title: RNASeq_LNCaP_AR_MYC_REP1

description:
RNASeq_LNCaP_AR_MYC_REP1
RNASeq_expression_2.txt

value: prostate cancer

value: FBS medium


title: SCAF503_11-28_WT_LPS


title: Colony_72h_2hFixation_rep1


title: Colony_72h_0hFixation_rep3

value: 72 h colony, formaldehyde fixation for 0 h

value: Replicate 3


title: SCAF502_11-28_WT_PBS


title: RNA-siKDM6B_N33_2

data_processing:
Basecalls performed using CASAVA
Data were analyzed using Warden workflow at https://platform.stjude.cloud/workflows
To brief, raw paired-end reads were mapped by STAR_2.5.3a(parameters "--outFilterMultimapNmax 20   --outFilterMismatchNmax 10   --alignIntronMax 500000   --chimSegmentMin 20   --chimJunctionOverhangMin 20") and counted by Htseq.
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: gene-based raw counts txt file

source_name: Cell Line

growth_protocol: BE2C cells were cultured in RPMI medium, supplemented with 100 U/mL penicillin/streptomycin, and 10% FBS. CHLA15, CHLA20, NB1643 and NB1691 were culture with DMEM medium, supplemented with 2 mM L-glutamine and 10% FBS.

extract_protocol:
Total RNA was extracted from xenograft tissues by RNeasy Mini Kit (cat. # 74104) from QIAGEN.
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.

treatment_protocol: BE2C cells were treated with GSK-J4 2.5 uM for 0h, 24h or 48h. For siRNA knockdown treatment, BE2C cell were treated with siRNA control and siKDM6B N1, N2 and N33 for  72h. CHLA15 and CHLA20 cell were treated with palbociclib 300nM for 72 h and NB1643 and NB1691 cells were treated with palbociclib 3 uM for 72 h.

value: BE2C siKDM6B N33 treatment


title: MEF_IR_control1_3


title: Colony_72h_0hFixation_rep2

value: Replicate 2


title: MEF_IR_control1_2


title: MEF_IR_control1_1


title: Colony_72h_0hFixation_rep1


title: RNA-siKDM6B_N2_2

value: BE2C siKDM6B N2 treatment


title: RNA-siKDM6B_N33_1


title: SCAF469_11-08_KO_LPS


title: Colony_72h_NoFixation_rep3

value: no formaldehyde


title: SCAF468_11-08_WT_PBS


title: RNA-siKDM6B_N2_1


title: MEF_H3K27Ac_REP_input_1

value: mouse embryonic fibroblasts (MEF)

value: proliferating

tag: induced by

value: serial passaging (REP)


title: SCAF470_11-08_KO_PBS

value: brain isolated microglia


title: SCAF467_11-08_WT_LPS

value: 1 year old mouse brain


title: Colony_72h_NoFixation_rep2


title: RNA-siKDM6B_N1_2

value: BE2C siKDM6B N1 treatment


title: RNA-siKDM6B_N1_1


title: MEF_H3K27Ac_REP_control1_1

value: senescent


title: MEF_H3K27Ac_REP_input_2


title: Liquid_rep2

source_name: Liquid culture

value: Exponential growing


title: F124-RNA

city: Bar Harbor

first: Christopher

last: Baker

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
Bulk RNA reads were aligned to transcriptome (mm10 or modified to include known D2 SNPs, R78-REL1505) using bowtie v.1.0.0. ChIP and ATAC reads were aligned to genome using hisat2 v.2.0.5.
Allele specific gene counts were performed using EMASE. For ChIP and ATAC, peaks were called using MACS v.1.4.2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt files representing ensembl gene id along with normalized read counts for each sample. tab-delimited txt files representing the position of identified ChIP peaks in mm10 coordinates along with normalized read counts. Expression libraries for single cell RNAseq gene-cell: matrices are provided in the format produced by CellRanger. MULTI-seq Libraries for single cell RNAseq: barcode-cell matrices are provided in CSV format. The columns in the matrix Byers_EB_lipidhash_deMULTIplex_matrix.csv.gz represent individual embryoid body samples identified by unique lipid-modified oligos.

source_name: embryonic stem cell

growth_protocol: Mouse embryonic stem cells were derived and maintained in naive conditions following protocol from Czechanski et al. 2014 (Nature Protocols). Culture conditions to transition ESCs to EpiLCs followed Buecker et al. 2014 (Cell Stem Cell). Spontaneous differentiation of ESCs to EBs was achieved by first transitioning through EpiLC state for 48 hours followed by seeding cells on AggreWell400 Plates (STEMCELL Technologies) in EB medium ensuring 750 cells/EB. Aggregates were allowed to form for 48 hours and then filtered to remove unincorporated cells. Collected EBs were then plated on 100mm Corning Ultra-low attachment culture dishes and continued growth with rotation on BellyButton rotator for another 48 hours.

extract_protocol:
A single cell suspension of ESCs and EpiLCs were harvested at a concentration of 1 million cells/mL; 1 million cells were lysed and RNA extracted using RNeasy (Qiagen) RNA extraction kit; 100,000 cells were used for transposition reaction. For ChIP, 10 million cells were harvested and nuclei isolated using hypotonic lysis. Chromatin was fragmented using Covaris followed by dialysis and immunoprecipitation against protein targets was performed. For single cell RNAseq, single cell suspension was achieved for EB cultures and 500,000 cells for each individual sample was labeled with unique Multiseq LMO barcode. Labelled samples were pooled at 3,000 cells per sample and 40,000 cells were loaded onto a single lane of a 10X Chromium microfluidic chip. Cells were lysed in droplets using 10X Chromium instrument and reverse transcription was performed in droplet and library construction performed according to 10X Chromium v3 chemistry.
Libraries were constructed using the KAPA mRNA HyperPrep Kit for ESC and EpiLC bulk RNA samples. Modified Illumina Nextera adapters were used to construct ATAC libraries. ChIP-seq librariers were constructed using KAPA HyperPrep Kit. Single cell RNA-seq library preparation was performed using 10X Chromium v3.

value: naive esc

tag: mouse strain


title: RNA-siCtrl_2_2

value: BE2C siRNA control treatment


title: Liquid_rep3


title: Liquid_rep1

value: Replicate 1


title: F116-RNA


title: F117-RNA


title: MEF_H3K27Ac_REP_senescent_1


title: MEF_H3K27Ac_REP_input_3


title: RNA-siCtrl_1_2


title: F117-ATAC


title: MEF_H3K27Ac_REP_control1_3


title: Colony_60h_rep3

value: 60 h of growth


title: Colony_72h_rep3

value: 72 h of growth

value: Replicate 3


title: MEF_H3K27Ac_REP_control1_2


title: Colony_72h_NoFixation_rep1


title: RNA-siCtrl_1_1


title: RNA-NB1691-Ctrl_2

value: NB1691 no  treatment


title: MEF_H3K27Ac_REP_senescent_3


title: Colony_48h_rep3

value: 48 h of growth


title: RNA-NB1691-Ctrl_1


title: RNA-siCtrl_2_1


title: BS31-wt-NI

city: Montreal

first: Silvia

middle: M

last: Vidal

address: 3649 Promenade Sir-William-Osler

department: Human Genetics

data_processing:
Low-quality bases (Phred < 33) and adaptor sequences were removed with Trimmomatic v.0.36 using arguments ILLUMINACLIP:TruSeq3-PE.fa:2:30:10, HEADCROP:4, LEADING:5, TRAILING:3, SLIDINGWINDOW:4:20, MINLEN:36
Trimmed reads were aligned to the mm10 reference genome using TopHat2 v2.1.1 with Bowtie2 v2.3.1 with default arguments.
Raw counts for host genes were calculated per gene by counting the number of strand-specific reads aligning to gene exon features using featureCounts (Subread package v1.5.2) with default arguments.
Trimmed reads were also aligned to an indexed HSV-1 strain 17 reference genome (GenBank: JN555585.1) using HISAT2 v2.1.0 with default arguments.
Raw counts for viral features were calculated per viral feature by counting the number of strand-specific reads aligning to gene and/or exon features using featureCounts (Subread package v1.5.2) using the “M” and “primary” arguments in addition to default arguments.
Library sizes were normalized using TMM normalization, residual rRNA reads were discarded, and CPM were calculated per gene using the Bioconductor package EdgeR.
Genome_build: mm10; HSV-1 strain 17 reference genome (GenBank: JN555585.1)
Supplementary_files_format_and_content: For each individual sample, a tab-delimited text files with raw counts for all host genes.
Supplementary_files_format_and_content: For all samples, a matrix table with raw host gene counts genes.
Supplementary_files_format_and_content: For all samples, matrix tables with CPM values for all host genes expressed at or greater than 3 CPM in at least 3 samples
Supplementary_files_format_and_content: For all samples, a matrix table with raw gene counts for all viral genes.
Supplementary_files_format_and_content: For all samples, matrix tables with CPM values for all viral genes.

source_name: Brainstem

extract_protocol:
Following transcardiac perfusion with 10 mL cold 1X PBS, brainstems were excised, flash frozen in liquid nitrogen, and transferred to 1 ml TRIzol reagent (Invitrogen) and homogenized at speed 6000 for 30 seconds with a MagNA Lyser Instrument (Roche). Total RNA was extracted as per the Invitrogen’s standard protocol for TRIzol RNA extraction. RNA samples were further cleaned-up using the RNeasy Mini Kit (Qiagen #74104) and treated with DNase I, as per the manufacturer’s standard protocol. RNA integrity was assessed using a Bioanalyzer RNA Pico kit (Agilent).
rRNA depletion and library preparation was performed using the KAPA Stranded RNA-Seq kit (Roche).

treatment_protocol: 6 RelC307X mice and 5 Rel+/+ mice were infected in vivo with 50000 PFU/20 g HSV-1 strain 17 delivered intranasally. An additional 4 RelC307X mice and 4 Rel+/+ mice were used as non-infected controls.

value: Rel+/+ (wild-type)

tag: Sex

value: female

value: 8 weeks

tag: infection

value: non-infected

tag: timepoint

tag: response type to infection

value: Brainstem


title: Colony_42h_rep3

value: 42 h of growth


title: F124-ATAC


title: Colony_32h_rep3

value: 32 h of growth


title: E. coli 042 wt (aggR3UTRFRT control)

city: Barcelona

first: Mario

last: Huttener Queiroz

address: Av. Diagonal 643

country: Spain

institute: Universitat de Barcelona

data_processing:
We used an Illumina NextSeq 500 system and a MID 150 Kit with 1x75 bp read length. Base-calling was perform online during the sequencing procedure with the Real-Time Analysis (RTA) software version 2.4.11 and System Suite Version 2.1.2.1.
Illumina sequencing instruments generate per-cycle BCL base call files as primary sequencing output in bcl2 format. Conversion of the bcl2 file to gzipped fastq files was performed using the bcl2fastq script v. 2.18.0.12 provided by Illumina.
Quality and adapter trimming was performed with the CLC Genomics Workbench 9.0 software package using the 'Trim Sequences' tool with standard parameters.
Mapping of the trimmed reads to the reference sequences was also performed with the CLC Genomics Workbench 9.0 using the 'Map Reads to Reference' tool with standard parameters.
For quantification of gene expression (read counting), the alignments generated with the Genomics Workbench were exported in BAM format. Read counting was then performed with the FeatureCounts v. 1.5.0-p1 program using the following parameters; Level : meta-feature leve. Paired-end : no. Strand specific : yes. Multimapping reads : counted (as fractions). Multi-overlapping reads : not counted. Overlapping bases : 30. Read orientations : fr
Genome_build: NCBI reference sequence (NC_017626 for the E. coli 042 chromosome) and (NC_017627 for the pAA plasmid).
Supplementary_files_format_and_content: The expression_1_FN554766_7_GEO.xlsx archive contains expression values in RPKM (Reads Per Kb exon (contig) per Million mapped  reads ( see Mortazavi et al. 2008, Nat Methods. 5(7):621-8 ) and can be directly compared to each other)  tab-delimited text files include RPKM values for each Sample.

organism: Escherichia coli 042

source_name: E. coli 042 wt

growth_protocol: LB medium at 37ºC with 200rpm agitation.

extract_protocol:
Total RNA was isolated from the cell pellets using the RNAsnap protocol developed by Stead et al. 2012. The total RNA preparations were examined by capillary electrophoresis. From the total RNA samples, ribosomal RNA molecules were depleted using the in-house developed depletion probes.
The ribodepleted RNAs were first fragmented using ultrasound (2 pulses of 30 s each at 4°C). Then, an oligonucleotide adapter was ligated to the 3' ends of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. For Illumina NextSeq sequencing, the cDNAs were pooled in approximately equimolar amounts. The cDNA pool was fractionated in the size range of 200 – 500 bp using a differential clean-up with the Agencourt AMPure kit. An aliquot of the size fractionated cDNA pool was analyzed by capillary electrophoresis. The cDNAs have a size range of 200 - 500 bp. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina. The cDNA pool was paired-end sequenced on an Illumina NextSeq 500 system using 75 bp read length.

tag: genotype

value: wild type


title: BS29-wt-NI

tag: age


title: KYSE70_siControl_2_RNAseq

city: Stanford

first: Zohar

last: Shipony

address: Beckman Center B-279A  279 Campus Drive West

institute: Stanford University

value: esophageal squamous cell carcinoma

tag: tissue

value: esophageal

value: siRNA Control


title: E. coli 042 aggR3UTRFRT

source_name: E. coli 042 aggR3UTRFRT

value: insertion of FRT sequence in the 3' UTR of aggR gene


title: Colony_24h_rep3

value: 24 h of growth


title: RNA-NB1691-Palbociclib-1

tag: treatment

value: NB1691 Palbociclib treatment


title: F116-ATAC

value: naive esc


title: MEF_H3K27Ac_REP_senescent_2

city: Rochester

first: Hu

last: Li

address: 200 First Street, Gonda Building G19-408

institute: Mayo Clinic

data_processing:
Fastq files of pair-end reads were mapped with Bowtie 1.1.2 50 using parameters -k 1 -m 1 -e 70 -l 51 --best to the mouse reference genome mm10.
MACS 1.4.2 was used to identify peaks for each sample against the background using a p-value cutoff of 10e-5. All the other parameters were left as default.
Super enhancers were identified using ROSE by stitch neighboring peaks within 12.5kb from each other were stitched together while excluding regions ± 2000 bps from any transcription start site.
BigWig files of H3K27Ac occupancy profiles were generated using deepTools 3.1.0 by first normalizing each ChIP sample and its matching input to CPM and then subtracting the input signal from each ChIP sample.
Genome_build: mm10
Supplementary_files_format_and_content: H3K27ac occupancy profile bw files; bed files for super enhancers called by ROSE

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared from 1-5 ng precipitated chromatin or input DNA using the Ovation ultralow DR Multiplex kit (NuGEN) or the ThruPLEX DNA-seq Kit V2 (Rubicon Genomics).

value: mouse embryonic fibroblasts (MEF)

value: proliferating

value: serial passaging (REP)

tag: chip-antibody


title: BS28-mut-NI

value: RelC307X (mutant)

value: female

value: 9 weeks


title: Colony_18h_rep3

value: 18 h of growth

value: Replicate 3


title: Colony_12h_rep3

value: 12 h of growth


title: BS27-mut-NI

value: non-infected

value: Brainstem


title: RNA-NB1643-Ctrl_1

tag: cell line

value: NB1643 no  treatment


title: RNA-NB1643-Palbociclib-2

value: NB1643 Palbociclib treatment


title: BS25-wt-NI

tag: strain

value: Rel+/+ (wild-type)

value: 12 weeks


title: Colony_72h_rep2

value: 72 h of growth

value: Replicate 2


title: RNA-NB1691-Palbociclib-2

value: NB1691 Palbociclib treatment


title: Colony_60h_rep2

value: 60 h of growth


title: RNA-NB1643-Palbociclib-1


title: BS30-wt-NI

value: 8 weeks


title: HstAWCE_2

city: Durham

first: Amy

last: Schmid

state: NC

address: 3242 French Family Science Center

institute: Duke University

description: Input control for HstA ChIP-Seq, replicate 2

data_processing:
Gzipped FASTQ files were assessed for quality using FastQC and adapter sequences trimmed using Cutadapt/Trim Galore, with --paired flag used to indicate paired-end samples.
Trimmed and pair-validated fastq files were aligned to the Haloferax volcanii DS2 genome (GCF_000025685.1) using Bowtie2. Samtools was used to generate and sort BAM files. Sorted BAM files were used for further analysis.
Peak-calling was done using Mosaics R package (papameters: analysis type = 2-sample IO, background estimation bgEst using robust method of moment rMOM) on individual samples.
WIG files were generated using the samtools mpileup command. Per-base count files were generated using bedtools genomecov.
Genome_build: GCF_000025685.1
Supplementary_files_format_and_content: WIG files

organism: Haloferax volcanii DS2

source_name: Archaeal cells

growth_protocol: Colonies of AKS217 (Empty vector negative control) and AKS233 (HstA-HA; 3 biological replicates) were pre-cultured in rich media for ~96-120 hrs and diluted to OD~0.05. These were then grown in rich media (YPC-18) supplemented with Novobiocin 0.1ug/mL for plasmid maintenance. At exponential phase (OD600 ~0.2-0.3;13-20 hrs of growth), 45 mL cell pellets were harvested, crosslinked with formaledhyde, and frozen for immunoprecipitation.

extract_protocol:
Cells were crosslinked and immunoprecipitated with HA antibody (ab9110) as described in Wilbanks et al 2012 (doi: 10.1093/nar/gks063) with the following changes to the protocol: the cross-linking reaction was allowed to proceed for 20 minutes rather than 10, and cell pellets were resupended in 800 μL lysis buffer instead of 1.6mL.
Libraries were constructed using the KAPA Hyper Prep kit and Illumina TruSeq adapters according to manufactuer's instructions. DNA library quality was assessed by Bioanalyzer using a High Sensitivity DNA chip (Agilent) . Samples were pooled and run on an Illumina NovaSeq 6000 (Duke Sequencing and Genomics Technologies core) for paired-end sequencing.

value: delta-pyrE-delta-hstA/hstA-HA

tag: epitope tag

value: HA

tag: antibody


title: HstAIP_3

description: ChIP-Seq of HstA, replicate 3

value: anti-HA (ab9110)


title: HAWCE

description: Input control for HA tag-alone ChIP-Seq

value: delta-pyrE-delta-hstA/HA


title: HAIP

description: Negative control for ChIP-Seq with HA tag-alone, no HstA


title: RNA-NB1643-Ctrl_2


title: BS20-mut-NI

value: RelC307X (mutant)

value: female

value: 9 weeks


title: BS19-wt-HSV-LO

value: 10 weeks

value: HSV-1 (intranasal)

value: day 5 post-infection

value: low-responder

value: Brainstem


title: BS18-wt-HSV-HI

value: Rel+/+ (wild-type)

value: high-responder


title: HstAWCE_3

description: Input control for HstA ChIP-Seq, replicate 3


title: RNA-GSKJ4_48h_1_2

value: BE2C GSK-J4 treamtent 48h


title: RNA-GSKJ4_48h_2_1


title: RNA-GSKJ4_48h_2_2


title: HstAWCE_1

description: Input control for HstA ChIP-Seq, replicate 1


title: HstAIP_1

description: ChIP-Seq of HstA, replicate 1


title: HstAIP_2

description: ChIP-Seq of HstA, replicate 2


title: BS21-mut-NI

value: non-infected


title: RNA-GSKJ4_48h_1_1


title: Colony_32h_rep2

tag: condition

value: 32 h of growth

tag: replicate

value: Replicate 2


title: BS16-wt-HSV-HI


title: RNA-GSKJ4_24h_2_2

value: BE2C GSK-J4 treamtent 24h


title: BS17-wt-HSV-HI


title: Colony_48h_rep2

value: 48 h of growth


title: Colony_12h_rep2

value: 12 h of growth


title: Colony_18h_rep2

value: 18 h of growth


title: RNA-GSKJ4_24h_2_1


title: BS15-wt-HSV-LO

value: female


title: RNA-GSKJ4_24h_1_2


title: Colony_42h_rep2

value: 42 h of growth


title: RNA-GSKJ4_0h_2_2

value: BE2C GSK-J4 treamtent 0h


title: RNA-GSKJ4_24h_1_1


title: BS6-mut-HSV-LO

value: RelC307X (mutant)

value: 9 weeks

value: HSV-1 (intranasal)


title: Colony_60h_rep1

value: 60 h of growth

value: Replicate 1


title: Colony_24h_rep2

value: 24 h of growth


title: BS7-mut-HSV-HI

value: day 5 post-infection

value: high-responder

value: Brainstem


title: BS4-mut-HSV-HI


title: BS5-mut-HSV-LO

value: low-responder


title: RNA-GSKJ4_0h_2_1


title: Colony_48h_rep1


title: Colony_42h_rep1


title: RNA-GSKJ4_0h_1_2


title: Colony_32h_rep1

value: 32 h of growth


title: BS3-mut-HSV-HI


title: Colony_72h_rep1

value: 72 h of growth


title: RNA-GSKJ4_0h_1_1


title: RNA-CHLA20-Ctrl_2

value: CHLA20 no treatment


title: BS2-mut-HSV-LO


title: JUZ_RNASeq

first: Martina

data_processing:
Raw reads were trimmed and cleaned using trimmomatic with the following parameters: TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:50
RNA-Seq reads were aligned to the potato DM v4.04 genome using STAR aligner.
Regions with read depth less than 10 were removed. Bases with quality less than 20 were removed.
Variant calling was performed with Freebayes.
The RNA-Seq data were de novo assembles using Trans-ABySS software.
Genome_build: DM v4.04
Supplementary_files_format_and_content: gene-level expression, Cufflinks output
Supplementary_files_format_and_content: transcript-level expression, Cufflinks output

organism: Solanum x juzepczukii

source_name: Young Leaf

extract_protocol:
Leaves from young plants were collected, put on dry ice, and RNA was harvested using TIANGEN RNAprep Pure Plant Kit(Polysaccharides& Polyphenolies-rich). The RNA extraction was performed by Novogene.
RNA libraries were prepared by Novogene for sequencing standard Illumina protocols.

treatment_protocol: No special treatment. The leaves of young plant material were used for the extraction of RNA.

tag: potato landraces

value: JUZ


title: Colony_18h_rep1

value: 18 h of growth


title: RNA-CHLA20-Ctrl_1


title: RNA-CHLA20- Palbociclib-1

value: CHLA20 Palbociclib treatment


title: Colony_12h_rep1

value: 12 h of growth


title: RNA-TM.18R002_KD1

description: RNA-seq in MDA-MB-231 with siRNA knockdown hTrmt13, Replicate1

data_processing:
Paired-end 150-cycle sequencing was performed on HiSeq X or HiSeq 2500, per the manufacturer’s directions (Illumina).
After adapter trimming by cutadapt RNA-Seq was mapped to human genome hg19(GRCh37) by STAR(version 2.5.2b, parameters “--outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --twopassMode Basic”) and HTSeq(version 0.6.1 p1) were used to count the gene-based reads using gene annotation from GENCODE(v24lift37).
For differential expression analysis, we performed trimmed mean normalization then Voom was used to identify differential expressed genes. Gene ontology analysis were performed on PANTHER that level 1 terms from Biological Process were used for presentation.
For GSEA analysis, gene sets downloaded from MSigDB database(v6.0) were analyzed against the log2 fold change from differential analysis using GSEA prerank mode (version 3.0).
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: txt file with abuabundance measurements

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

tag: cell type

value: hTrmt13 siKnockdown


title: HKO_In

data_processing:
library strategy: MeRIP-seq
The quality control of RAW data was used by fastqc (Version: v0.11.5).
Sequenced reads were trimmed for adaptor sequence by using skewer (Version: 0.1.126), and then mapped to Ensemble_GRCm38.90 whole genome using BWA (Version: 0.7.12-r1039) with parameters -T 25; -k 18.
Peaks were called using MACS2 (Version 2.1.0).
Motif search was detected by using homer findMotifGenome.pl (Version: v4.9.1) with parameters –gc; -len 8,10,12,14.
Genome_build: Ensemble_GRCm38.90

extract_protocol:
Total RNAs were extracted using TriPure Isolation Reagent (Roche, Mannheim, Germany) from liver of Mettl3flox/flox and HKO mice .
Poly(A)+ RNA was purified using Dynabeads™ mRNA Purification Kit (Invitrogen) following the manufacturer’s instructions. Chemically fragmented poly(A)+ RNA was incubated with m6A antibody (Synaptic System, 202003) for immunoprecipitation following the standard protocol of Magna MeRIPTM m6A Kit (MERK, 17-10499). Enrichment of m6A mRNA was then analyzed by high-throughput sequencing using Illumina Hiseq X platform.

tag: strain background

tag: genotype/variation

value: HKO (Mettl3 flox/flox Alb-Cre)

value: Liver

tag: rip antibody


title: RNA-TM.18R001_KCtrl1

description: RNA-seq in MDA-MB-231 control, Replicate1

value: hTrmt13 siControl


title: muscle_CON_pre_21

city: Hamilton

first: Athan

middle: G

last: Dial

state: ON

address: 1280 Main Street West

department: Medical Sciences

institute: McMaster University

hyb_protocol: RNA samples were normalized to recommended input and processed according to protocol using the Clariom™ S Pico Assay which includes poly-A reverse transcription, cRNA amplification and conversion to biotinylated cDNA and hybridization to the Clariom™ S human GeneChip and detection using the GeneChip Scanner 3000 system (Thermo Fisher Scientific, Waltham, MA, USA).

scan_protocol: standard Affymetrix protocol

data_processing:
From microarray results, we examined the expression set for significantly enriched pathways/gene sets (reference gene sets available from http://baderlab.org/GeneSets using gene set enrichment analysis (GSEA). The EnrichmentMap plug-in of Cytoscape was used to create network visualization of the GSEA results, depicting the overlap among pathways, with similar biological processes grouped together as subnetworks(19–21). Gene sets and pathways with q < 0.1 were used as input, and a conservative overlap coefficient (0.5) was used to build the enrichment map. The AutoAnnotate plug-in identified clusters with ≥ 3 connected gene sets in an automated manner, visually annotating them with summary labels. GSEA was performed on a pre-ranked gene list from the differential expression results between participants with and without type 1 diabetes at each timepoint. The group by timepoint interaction term was used to examine if there were differential effects of the eccentric exercise protocol on the muscle transcriptome in each respective group, as provided by Transcriptome Analysis Control software (Thermo Fisher Scientific, Waltham, MA, USA).
Clariom_S_Human.r1.pgf
Clariom_S_Human.r1.mps

source_name: vastus lateralis muscle, CON, pre-exercise

label_protocol: standard Affymetrix protocol

extract_protocol: RNA was extracted from ~10-25 mg frozen human muscle tissue using the Qiagen AllPrep DNA/RNA/miRNA Universal Kit including homogenization with the TissueRuptor II according to manufacturer’s protocol (Qiagen GmbH, Hilden, Germany).

treatment_protocol: Percutaneous needle biopsies were collected by a trained physician from the midportion of the vastus lateralis using a 5 mm Bergstrom needle. Muscle biopsies were obtained at rest and repeated 48-hours following eccentric exercise. Each repeated biopsy was spaced 3 cm apart to minimize any effect of the previous biopsies. Upon excision, muscles were flash-frozen in liquid nitrogen and subsequently stored at -80°C.

value: muscle

tag: group

value: CON

tag: exercise status

tag: Sex

value: female


title: muscle_CON_pre_15

tag: tissue


title: RNA-CHLA15-Ctrl_2

tag: treatment

value: CHLA15 no treatment


title: INPUT-18C035

description: CHIPSEQ INPUT in MDA-MB-231 cells

data_processing:
150bp paired-end reads were obtained, trimmed for adapters by cutadapt and aligned to human genome hg19(GRCh37) by BWA (version 0.7.12-r1039, default parameter).
Then duplicated reads were marked by biobambam2 (version 2.0.57) and uniquely mapped reads were retained by samtools (parameter “-q 1 -F 1024” version 1.4). We followed ENCODE criterion for quality control and confirmed high quality (>30 million reads each replicates).
Center 80bp of each fragment were used for generating bigwig tracks and normalized to 15 million reads. Tracks were inspected on IGV for clear peak shape and confirmed for good reproducibility.
Peaks for each replicate were called by MACS2 (version 2.1.1.20160309, paired-end mode) twice independently using cutoff q-value 0.05 as high confidence peaks also cutoff q-value 0.5 as low confidence peaks. We then finalized reproducible peaks as called in high confidence peaks in one replicate also overlap the low confidence peak called from the other replicate. Reproducible peaks were then used for motif analysis by homer (v4.9.1)
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: bigwig

extract_protocol:
Discard the cytoplasmic components. Lysates were clarified from sonicated nuclei and hTrmt13-DNA or FLAG-hTrmt13-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.


title: Colony_24h_rep1

value: 24 h of growth

value: Replicate 1


title: FF_In

value: Mettl3 flox/flox


title: HKO_IP

value: m6A antibody (Synaptic System, 202003)


title: muscle_CON_48-hours_post_15

source_name: vastus lateralis muscle, CON, 48-hours post-exercise


title: muscle_T1D_48-hours_post_12

source_name: vastus lateralis muscle, T1D, 48-hours post-exercise


title: CLIP-seq_19L098

description: CLIP-seq in MDA-MB-231 cells, Replicate 2

data_processing:
CLIP-seq data have been analysis by adapted from  PARalyzer(version 1.5) and PIPE-CLIP.
Briefly, raw reads were trimmed for adapters using Timmomatic (version 0.36) (parameters: “ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25 HEADCROP:9”) and then mapped to human genome hg19 (GRCh37) by bowtie2 (version 2.3.5.1, parameters “--local -k 1 --rdg 0,6 --rfg 13,1 -p 1 -U”).
tRNA annotation were downloaded from GtRNAdb 2.0. Result mapped file were converted to bed format and counted by bedtools (version 2.24.0) at tRNA annotations.
We confirmed the results from this pipeline were good by re-processing data from GSE109183 and compared with the supplementary data from their paper
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: gzipped txt file with abuabundance measurements

extract_protocol:
hTrmt13-RNA  complexes were isolated with antibody.
The RNA is dephosphorylated and then removed modifications by Alkbs, an adaptor is ligated to the 3' end of the RNA and 5' end is radioactively labled. SDS-PAGE and transfer to nitrocellilose membrane anable to proremove free RNA and to stringently purify the crosslinked protein-RNA complexes. The RNA is then reverse trancribed in cDNA. Size selection of cDNA removes free primers, and is followed by cDNA circularization. Restriction enzyme digestion linearizes the cDNA before PCR amplification


title: muscle_CON_48-hours_post_21


title: RNA-CHLA15-Ctrl_1


title: muscle_CON_pre_10


title: muscle_T1D_pre_12

source_name: vastus lateralis muscle, T1D, pre-exercise


title: CLIP-seq_19L097

description: CLIP-seq in MDA-MB-231 cells, Replicate 1


title: muscle_CON_48-hours_post_10


title: muscle_CON_48-hours_post_7


title: muscle_T1D_pre_6


title: muscle_T1D_48-hours_post_6


title: FF_IP


title: RNA-CHLA20-Palbociclib-2


title: muscle_T1D_48-hours_post_5


title: RNA-CHLA15-Palbociclib-1

value: CHLA15 Palbociclib treatment


title: hTrmt13-18C034

description: CHIPSEQ target hTrmt13 in MDA-MB-231 cells

value: hTrmt13 (customized from Abclonal, China)


title: hTrmt13-18C036

description: CHIPSEQ target FLAG-hTrmt13 in MDA-MB-231 cells

value: FLAG (Sigma, M8823, lot SLCD1942)


title: flox

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 Ensemble_GRCm38.90 whole genome using tophat2  with parameters  -p 8 -N 2 --read-edit-dist 2
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then   F  PKM   of each gene was calculated based on the length of the gene and reads count mapped   to this   gene.  F  PKM,   expected  number  of  Fragment  s  Per  Kilobase  of  transcript  sequence  per   Millions  base  pairs  sequenced  ,  considers  the  effect  of  sequencing  depth  and  gene  length   for the reads count at the same time, and is currently the most commonly used method for   estimating gene expression  levels (  Tr  apnell, Cole, et al., 2010  )
Genome_build: Ensemble_GRCm38.90

source_name: Liver

extract_protocol:
Livers were removed, flash frozen on liqid nitrogen, and total RNA was harvested using TriPure reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: 8 weeks

tag: genotype


title: muscle_CON_pre_7


title: KO-Ascl1-9

status: Public on Oct 28 2021

city: Indianapolis

first: Guoli

last: Dai

state: IN

address: 723 W Michigan St. SL306

department: Biology

institute: Indiana University Purdue University Indianapolis

data_processing:
The sequencing data were first assessed using FastQC (ver 0.11.5, Babraham Bioinformatics, Cambridge, UK) for quality control.
Then all sequenced libraries were mapped to the mouse genome (UCSC mm10) using STAR RNA-seq aligner (ver 2.5) with the following parameter: “--outSAMmapqUnique 60”.
The reads distribution across the genome was assessed using bamutils (from ngsutils, ver. 0.5.9).
Uniquely mapped sequencing reads were assigned to mm10 refGene genes using featureCounts (from subread, ver. 1.5.1) with the following parameters: “-s 2 –p –Q 10”.
Quality control of sequencing and mapping results was summarized using MultiQC.
Genes with read count per million (CPM) > 0.5 in more than 4 of the samples were kept.
The data was normalized using TMM (trimmed mean of M values) method.
Differential expression analysis was performed using edgeR (ver. 3.12.1). False discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure.
Genome_build: mm10

source_name: Maternal Liver

growth_protocol: 3-month-old female mice

extract_protocol:
Total RNA was isolated from snap-frozen liver tissue using the RNeasy Plus Mini Kit (Qiagen, 74134). The concentration and quality of total RNA samples was first assessed using Agilent 2100 Bioanalyzer. A RIN (RNA Integrity Number) of five or higher was required to pass the quality control. Then 200 nanograms of RNA per sample were used to prepared dual-indexed strand-specific cDNA library using KAPA mRNA Hyperprep Kit (Rocke).
The resulting libraries were assessed for its quantity and size distribution using Qubit and Agilent 2100 Bioanalyzer. Two hundred pico molar pooled libraries were utilized per flowcell for clustering amplification on cBot using HiSeq 3000/4000 PE Cluster Kit and sequenced with 2×75bp paired-end configuration on HiSeq4000 (Illumina) using HiSeq 3000/4000 PE SBS Kit. A Phred quality score (Q score) was used to measure the quality of sequencing.

tag: strain

value: Maternal Liver

tag: gestation day

value: hepatocyte-specific Ascl1 KO


title: KO-Ascl1-7


title: KO-Ascl1-8


title: WT-Ascl1-3

value: control


title: WT-Ascl1-4


title: KO-Ascl1-5


title: HKO

first: Zheng

value: Liver

value: Mettl3 HKO (Mettl3 flox/flox Alb-Cre+/-)


title: RNA-CHLA15-Palbociclib-2

tag: cell line


title: WT-Ascl1-1


title: muscle_T1D_48-hours_post_3

value: muscle


title: VCaP_AU4h_AR_Milli

city: Ann Arbor

first: Pushpinder

middle: Singh

last: Bawa

state: Michigan

address: 1500 East Medical Center Drive

department: Pathology

institute: University of Michigan

description: Crosslinked DNA from 5M cells was sheared to a 200-500bp size range, which was used for immunoprecipitation using 7-10ug of target antibody per ChIP.

data_processing:
ChIP-Seq reads were aligned to the human reference genome (GRC h38/hg38) with BWA. The SAM file obtained after aliment was converted into BAM format using SAMTools
Using deepTools bamCoverage a coverage file (bigWig format) for each sample was created. The coverage is calculated as the number of reads per bin, where bins are short consecutive counting windows.
ChIP-Seq peak calling was done using MASC2
Genome_build: GRCh38
Supplementary_files_format_and_content: BED

source_name: VCaP

growth_protocol: All cell lines were purchased from ATCC and were grown in ATCC-suggested culture media. They were bimonthly tested for mycoplasma contamination, including within a week of NGS-experiments.

extract_protocol:
Treated cells were crosslinked using 1% PFA for 10 mins and then processed following instructions from the Diagenode HighCell ChIP Kit (Cat No. C01010063).
ChIP experiments were carried out using the HighCell# ChIP-Protein G kit (Diagenode) as per the manufacturer’s protocol. Chromatin from five million cells was used per ChIP reaction with 10 μg of the target protein antibody. In brief, cells were trypsinized and washed twice with 1× PBS, followed by cross-linking for 8 min in 1% formaldehyde solution. Crosslinking was terminated by the addition of 1/10 volume 1.25 M glycine for 5 min at room temperature followed by cell lysis and sonication (Bioruptor, Diagenode), resulting in an average chromatin fragment size of 200 bp. Fragmented chromatin was then used for immunoprecipitation using various antibodies, with overnight incubation at 4 °C. ChIP DNA was de-crosslinked and purified using the iPure Kit V2 (Diagenode) using the standard protocol. Purified DNA was then prepared for sequencing as per the manufacturer’s instructions (Illumina). ChIP samples (1–10 ng) were converted to blunt-ended fragments using T4 DNA polymerase, E. coli DNA polymerase I large fragment (Klenow polymerase), and T4 polynucleotide kinase (New England BioLabs (NEB)). A single A base was added to fragment ends by Klenow fragment (3′ to 5′ exo minus; NEB) followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-ligated DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size-selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (Qiagen). Libraries were quantified and quality checked using the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2500 Sequencer (125-nucleotide read length).

treatment_protocol: Cell were plated at 70-80% confluence in a 150mm culture plate and treated with AU-15330 dissolved in DMSO at indicated concentrations (1uM) and for labeled durations (6-24h).

tag: dosage & duration

value: 1uM for 4h

tag: antibody details

value: prostate cancer


title: VCaP_AU2h_H3K27Ac_abcam


title: KO-Ascl1-6


title: VCaP_AU4h_H3K27Ac_abcam


title: VCaP_AU4h_FOXA1-TFS

value: 1uM for 24h


title: VCaP_AU2h_AR_Milli


title: AU-CBH-15330 @1uM for 1h-R2

description: Intact nuclei were extracted from 50,000 cells and tagmented using 2.5ul of Tn5 enzyme for 30mins.

data_processing:
Paired-end .fq.gz files were trimmed and uniquely aligned to the GRCh38/hg38 human genome assembly using Novoalign (Novocraft) (with the parameters -r None -k -q 13 -k -t 60 -o sam –a CTGTCTCTTATACACATCT), and converted to .bam files using SAMtools (version 1.3.1).
Reads mapped to mitochondrial or duplicated reads were removed by SAMtools and PICARD MarkDuplicates (version 2.9.0), respectively.
Filtered .bam files from replicates were merged for downstream analysis. MACS2 (2.1.1.20160309) was used to call ATAC-seq peaks.
The coverage tracks were generated using the program bam2wig (http://search.cpan.org/dist/Bio-ToolBox/) with the following parameters:–pe–rpm–span–bw.
Genome_build: hg38
Supplementary_files_format_and_content: BED files for called peaks

extract_protocol:
Nuclei extraction and tagmentation of open chromatin was performed as described in the Buenrostro et al. 2013 Nat Methods.
ATAC-seq was performed as previously described in Buenrostro et al. 2013 Nat Methods. In brief, 50,000 cancer cells were washed in cold PBS and resuspended in cytoplasmic lysis buffer (CER-I from the NE-PER kit, Invitrogen, cat. no. 78833). This single-cell suspension was incubated on ice for 5-8 min (depending on the cell line) with gentle mixing by pipetting every 2 min. The lysate was centrifuged at 1,300g for 5 min at 4 °C. Nuclei were resuspended in 50μl of 1× TD buffer, then incubated with 2-2.5 μl Tn5 enzyme for 30 min at 37 °C (Nextera DNA Library Preparation Kit; cat. no. FC-121-1031). Samples were immediately purified by Qiagen minElute column and PCR-amplified with the NEBNext High-Fidelity 2X PCR Master Mix (NEB; cat. no. M0541L) following the original protocol27. qPCR was used to determine the optimal PCR cycles to prevent over-amplification. The amplified library was further purified by Qiagen minElute column and SPRI beads (Beckman Coulter; cat. no. A63881). ATAC-seq libraries were sequenced on the Illumina HiSeq 2500 (125-nucleotide read length).

treatment_protocol: Cell were plated at 70-80% confluence in a 6-well plate and treated with AU-15330 dissolved in DMSO at 1uM concentration for labeled durations (4-24h). For genetic models, LNCaP cells were treated with sgRNAs to stably knockout the SMARCA2 gene followed by dox-inducible shRNA-mediated knockdown of the SMARCA4 gene for 72h.

value: vehicle control