title: RWPE-ILYW

tag: cell line

tag: cell type

value: vector control


title: 1st and 2nd trimester male and female gonads and mesonephros A

status: Public on Jan 02 2024

type: SRA

city: Leiden

first: Susana

last: Chuva de Sousa Lopes

address: Einthovenweg 20

department: Anatomy and Embryology

country: Netherlands

institute: Leiden University Medical Center

description: pool of ten donors

library_source: transcriptomic

data_processing:
For all samples Cell Ranger Single Cell Software Suite 6.1.1 was used to perform sample demultiplexing, barcode processing, read aligning and single cell 3’ gene counting using the Illumina BCL files as input.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

organism: Homo sapiens

source_name: Fetal tests, ovary and mesonephros tissue

extract_protocol:
Tissue was cut in small pieces and treated overnight in 1mg/ml colII in 0.25% Trypsin/EDTA at 4C. Next day, it was incubated 1h at 37C in DMEM/F12 with DNAseI (27 IU/ml), filtered through a 100um strainer and single cells were cryopreserved. Before library preparation, cells were thawed, ressuspended in 1% BSA/DPBS and FACS-sorted for live cells (7AAD-negative cells).
Sequencing libraries were prepared according to the user guide of the 10x Genomics Chromium Single Cell 3' Library and Gel Bead Kit v2, Product Code 120237.

tag: Sex

value: Female and male

tag: trimester

tag: number of donors

tag: age of donors (week of gestation)

tag: sequencing run


title: SCC1 I-BET and INF-r treatment

city: Richmond

first: Jiong

last: Li

state: Virginia

address: 800 E Leigh Street, suite 212

country: USA

institute: VCU

data_processing:
RNAs were single-end sequenced on Illumina machines
Reads was aligned using Tophat with the hg18 build of the human genome.
Transcript assembly and differential expression were determined using Cufflinks with Refseq mRNAs.
RNA-seq data was analyzed using the cummeRbund package in R.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

source_name: HNSCC cells

growth_protocol: 10% FBS in DMEM

extract_protocol:
Total RNA was isolated from cells using NucleoSpin® RNA II RNA purification kit (Machery-Nagel; #740955.20).
Sequencing libraries were generated using a KAPA RNA-Seq Library Preparation Kits (KAPA Biosystems, cat#07960140001)

treatment_protocol: cells were treated with 500nM of JQ1, I-BET, 10ng/ml of INF-r or control overnight

tag: treatment

value: 500nM of I-BET and 10ng/ml of INF-r


title: mouse mammary tumor [mid311]

type: RNA

city: Berkeley

first: Jian-Hua

last: Mao

state: CA

address: One Cyclotron Road

institute: Lawrence Berkeley National Laboratory

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
The data were analyzed with by Robust Multi-array Analysis (RMA).
probe group file: MoEx-2_0-st-v1.r2.pgf
meta-probeset file: MoEx-2_0-st-v1.r2.dt1.mm8.mps

label: biotin

organism: Mus musculus

source_name: biospy of mammary tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2016, Affymetrix).

growth_protocol: spontaneous mammary tumors from genetically diverse MMTV-ErbB2 mice

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

treatment_protocol: Biopsy before docetaxel treatment

tag: genotype

value: F1Bx((C57BL/6J x FVB/NJ) x FVB/NJ MMTV-Erbb2)

value: female

tag: tissue

value: biospy of mammary tumor


title: mouse mammary tumor [mid163]


title: mouse mammary tumor [mid1467]


title: SCC1 INF-r treatment

value: 10ng/ml of INF-r


title: YS-E11-LB-Delta-aroa1

city: PARIS

first: Eric

last: FRAPY

address: 156 rue de vaugirard

department: Immunologie, Infectiologie et Hématologie (I2H)

country: France

institute: INSERM U1151 INEM

data_processing:
CLC Genomics Workbench 23.0.5
Sequence reads were trimmed using CLC genomic benchwork (parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to E11 annotate with CDS using CLC genomic benchwork (parameters- mismath cost:2 insertion cost:3 deletion cost:3 lenght fraction 0.8 similarity fraction 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: E11 annotate with CDS (genome)
Supplementary files format and content: tab-delimited text files and clc files

organism: Escherichia coli K1

growth_protocol: E. coli K1 E11 strains WT and ∆aroA were grown in LB and DMEM broth at 37°C overnight. The following day, bacterial cultures of the 2 strains were grown from OD=0.08 to exponential phage.

extract_protocol:
At OD=0.600, the bacteria were harvested and washed by centrifugation, then recovered in lysis buffer from the RNA extraction kit, Bioanalysis (Valencienner, Germany) reference 740955.50. Total RNA from both strains was extracted using this kit according to the manufacturer's instructions. RNA concentration was quantified using a spectrophotometer (Nanodrop Technologies).
RNA-Seq analysis was carried out by the Genotyping/Sequencing Platform of the Brain Institute - ICM, France. mRNA library preparation was realized following manufacturer’s recommendations (Stranded Total RNA Prep with Ribo-Zero Plus Kit from ILLUMINA). Final samples pooled library prep were sequenced on Nextseq 2000 ILLUMINA P2-200 cartridge (2x400Millions of 100 bases reads) corresponding to 2x14Millions of reads per sample after demultiplexing

tag: strain

tag: cell culture

value: LB medium

value: delta aorA


title: YS-E11-LB-Delta-aroA2


title: 2nd trimester female gonads B

description: pool of two donors

source_name: Fetal ovary tissue

value: Female


title: RAW264.7 cells, high glucose [HG2]

city: Guangzhou

first: Jiaqiong

last: Lin

address: Guangzhou dadaobei 1838

country: China

institute: South medical university

data_processing:
Base Calling by CASAVA
Filtering low-quality sequence
Clean Reads mapped to GRCm39 using Hisat2
Read count extraction by StringTie
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: RAW 264.7 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), which were maintained under controlled conditions of 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated from the study samples using Trizol reagent. 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS® mRNA Isolation Master Kit

treatment_protocol: high glucose group (40 mM), and high glucose group with pre-treatment of emetine (5 nM)

value: macrophages

value: high glucose


title: YS-E11-LB-WT2

value: WT


title: RWPE-CRAF

city: Los Angeles

first: Owen

last: Witte

state: California

address: 675 Charles E Young Dr S, 5720 MRL Bldg; MC 729022

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California, Los Angeles

description: RWPE-CRAF-B1_merged_rsem_genes_expected_counts.txt

data_processing:
TOIL pipeline v 3.12.0 (https://github.com/BD2KGenomics/toil-rnaseq)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CutAdapt and FastQC TOIL pipeline
Trimmed sequence reads were mapped to hg38 using STAR from TOIL pipeline
Transcript read counts were quantified using RSEM from TOIL pipeline
Assembly: hg38 human genome
Supplementary files format and content: tab-delimited text files include raw count values for each sample

growth_protocol: BPH-1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1 mM glutamine and in humidified atmosphere with 5% CO2 at 37C, RWPE were cultured in keratinocyte serum-free medium (K-SFM) (Gibco) supplemented with 0.05 mg/mL bovine pituitary extract (Gibco), 5 ng/mL EGF (Gibco), penicillin (100 U/mL), and streptomycin (100 μg/mL)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using ILMN mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: prostate epithelial

value: C-Raf overexpression


title: RAW264.7 cells, high glucose [HG1]


title: 2nd trimester female gonads A

description: pool of two donors


title: mouse mammary tumor [mid307]


title: YS-E11-LB-WT1


title: SCC1 I-BET treatment

value: 500nM of I-BET


title: 2nd trimester female mesonephros

description: pool of two donors

source_name: Fetal mesonephros tissue


title: mouse mammary tumor [mid279]


title: YS-E11-DM-Delta-aroA

value: DMEM medium


title: SCC1 JQ1 treatment

value: 500nM of JQ1


title: mouse mammary tumor [mid272]


title: mouse mammary tumor [mid249]


title: 1st and 2nd trimester male mesonephros

description: pool of three donors

data_processing:
For all samples Cell Ranger Single Cell Software Suite 2.1.1 was used to perform sample demultiplexing, barcode processing, read aligning and single cell 3’ gene counting using the Illumina BCL files as input.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

value: Male

value: Fetal mesonephros tissue


title: SCC1 JQ1 and INF-r treatment

value: 500nM of JQ1 and 10ng/ml of INF-r


title: YS-E11-DM-WT


title: SCC1 no treatment


title: CUT&RUN MYC shCTR9 Dox rep2

status: Public on Jan 01 2024

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

library_source: genomic

data_processing:
ChIP-sequenced libraries were mapped separately to mouse mm10 genome and human hg19 (spike-in) using Bowtie 2 v2.3.4.1 with default parameters. ChIP-Rx spike-in normalization was performed by calculating spike-in normalization factor, by dividing the number of mapped reads from the spike-in of the smallest sample by the number of mapped reads from the spike-in of each sample. For each sample, this factor was multiplied by the number of reads that mapped to the mouse genome. All bam files for subsequent analysis were adjusted to this read count using. Samtools was used to manipulate the bam files (indexing and subsampling). To visualize read alignments on the Integrated Genome Browser v9.1.10, BAM files were converted to bigwig files using Deeptools with no further normalization and a bin size of 10 bases.
CUT&RUN libraries were mapped to the mouse mm10 genome using default parameters using Bowtie 2 v2.3.4.1. Samples were read-normalized with the number of reads in the smallest sample. BAM files were converted to bigwig files using Deeptools with no further normalization and a bin size of 10 bases.
Assembly: mm10
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: Pancreas

growth_protocol: Cells were grown in DMEM supplemented with 10% FCS and 1% penicillin/streptomycin

extract_protocol:
ChIP-seqCells were treated with 1% formaldehyde for 5 min at 37°C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented using sonication (20 minutes, 25% amplitude, 10 seconds on, 30 seconds off) to a size <300 bp. Chromatin was immunoprecipitated with 15 µg of corresponding antibody for 6 hours. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used. CUT&RUN: cells were harvested using Accutase (Sigma) for cell detachement. Cells were counted and washed in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine). After washing, cells were coupled to ConA-coated magnetic beads (Polysciences Europe) and subsequently permeabilized and followed by addition of primary antibody in antibody binding buffer (wash buffer, 0.05% digitonin, 2 mM EDTA) over night at 4 °C. Cells were wased in Dig-Wash buffer (Wash buffer, 0.05% digitonin) and MNase (700ng/ml) was added to each sample for 1 hr at 4 °C. After washing with Dig-wash buffer and Low-salt Rinse buffer (20 mM HEPES pH 7.5, 0.5 mM Spermidinge, 0.05% digitonin) incubation buffer (3.5 mM HEPES pH 7.5, 10 mM CaCl2, 0.05% digitoin) was added for 30 min at 4°C. STOP buffer (170 mM NaCL, 20 mM EGTA, 0.05% digitonin, 20 ug/ml RMAse A, 25 ug/ml Glycogen was added to stop the MNase digestion. DNA fragments were released at 37 °C for 30 min and proteins digested for 1 h at 50 °C after adding 0.01 % SDS and 10 mg/ml Proteinase K followed by Phenol Chloroform extraction. Precipitated DNA was resuspended in 30 ul 0.1x TE buffer.
ChIP-seq Libraries were prepared according to instructions accompanying the NEBNext Ultra™ II DNA Library Prep Kit for Illumina. Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (150 bp) and eluted. DNA fragments were amplified by 11 to 16 cycles of PCR and library size was tested with the Fragment Analyzer (Advanced Analytical). The amount of library DNA was quantified using a picogreen assay. CUT&RUN: NEBnext Ultra II DNA Library Prep Kit (New England Biolabs) was used. Pre-PCR samples were purified using AmpureXP beads with a ratio of 1.75x. Then half of the eluted material was used with 12-16 PCR cycles. The libraries were cleaned using Agentcourt AMPure XP Beads (ratio 1.1x, Beckman Coulter), quality, quantity and fragment size assessed on the Fragment Analyzer (Agilent) using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent)

treatment_protocol: Treatment as indicated

value: Pancreas

value: PDAC cell line

value: Dox-inducible shRNA targeting Ctr9

value: Dox, 1microg/ml, 48 h


title: ChIP-seq CTR9 shCTR9 EtOH rep2

data_processing:
ChIP-sequenced libraries were mapped separately to mouse mm10 genome and human hg19 (spike-in) using Bowtie 2 v2.3.4.1 with default parameters. ChIP-Rx spike-in normalization was performed by calculating spike-in normalization factor, by dividing the number of mapped reads from the spike-in of the smallest sample by the number of mapped reads from the spike-in of each sample. For each sample, this factor was multiplied by the number of reads that mapped to the mouse genome. All bam files for subsequent analysis were adjusted to this read count using. Samtools was used to manipulate the bam files (indexing and subsampling). To visualize read alignments on the Integrated Genome Browser v9.1.10, BAM files were converted to bigwig files using Deeptools with no further normalization and a bin size of 10 bases.
CUT&RUN libraries were mapped to the mouse mm10 genome using default parameters using Bowtie 2 v2.3.4.1. Samples were read-normalized with the number of reads in the smallest sample. BAM files were converted to bigwig files using Deeptools with no further normalization and a bin size of 10 bases.
Assembly: mm10

value: EtOH


title: CUT&RUN MYC shCTR9 EtOH rep2


title: ChIP-seq SPT6 shCTR9 Dox rep2


title: ChIP-seq Input merged rep2

value: merged


title: ChIP-seq SPT5 shCTR9 Dox rep2


title: ChIP-seq RNAPII shCTR9 Dox rep2


title: ChIP-seq RNAPII shCTR9 EtOH rep2


title: ChIP-seq SPT5 shCTR9 EtOH rep2


title: mouse mammary tumor [mid222]

value: F1Bx((C57BL/6J x FVB/NJ) x FVB/NJ MMTV-Erbb2)

value: female

value: biospy of mammary tumor


title: 4sU shCTR9 Dox rep3

description: Nascent RNA

data_processing:
Base calling performed using Illumina's fastq.gz Generation software v1.0.0.
Reads were mapped to the mouse reference genome (mm10) with Bowtie 2 v2.3.4.1. Reads mapping to exons and regions in the ENCODE Blacklist were removed from BAM files using bedtools v2.26.0.
Samples were then normalized by the bamCoverage function in deepTools using counts per million mapped reads, and then bigwig files were generated.
Assembly: mm10
Library strategy: 4sU-seq

extract_protocol:
Subconfluent cells were treated as described. During the last 15 min of treatment, cells were incubated with 2mM 4-thiouridine (4sU; Sigma-Aldrich) before lysis with QIAzol reagent (QIAGEN). Total RNA extraction was performed using the miRNeasy kit (QIAGEN) with on-column DNase digestion, and RNA quantity and quality were assessed using a Nanodrop spectrophotometer and a Fragment Analyzer (Thermo Fisher Scientific), respectively. 20-40 µg of RNA with RQN values greater than 9 was then biotinylated by adding EZ-Link Biotin-HPDP (Pierce) in 0.2 mg/ml dimethylformamide and biotin labeling buffer (10 mM Tris pH 7.4, 1 mM EDTA) and incubating for 2h at RT with rotation. Biotinylated RNA was then purified by chloroform isoamyl alcohol extraction in MaXtract high-density tubes (QIAGEN). The upper aqueous phase was collected and 1/10 volume of 5 M NaCl and an equal volume of isopropanol were added. All samples were centrifuged at 20,000g for 20 min at 4°C, the RNA pellets were washed with 75% ethanol and centrifuged at 20,000g for 10 min at 4°C. After drying, the pellets were resuspended in nuclease-free water. Biotinylated RNA samples were then eluted using Dynabeads MyOne Streptavidin T1 beads (Invitrogen) in Dynabeads Wash Buffer (2 M NaCl, 10 mM Tris pH 7.5, 1 mM EDTA, 0.1% v/v Tween 20) for 15 min at RT with rotation. After stringent washing, 4sU-labeled RNA was eluted from the beads with 100 ml of freshly prepared 100 mM DTT in nuclease-free water and purified using the RNeasy MinElute Kit (QIAGEN).
Samples were quantified using the RiboGreen Assay (Invitrogen), and 5-20 ng RNA was used for cDNA library preparation by first depleting rRNA using the NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (New England Biolabs) and then the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs). cDNA libraries were amplified using appropriate multiplexed index primers in 11-14 cycle PCR, depending on the amount of RNA input.

value: Dox-inducible control shRNA targeting Ctr9

value: Dox, 1µg/ml, 48 h


title: 4sU shCTR9 Dox rep2

description: Nascent RNA


title: 4sU shCTR9 Dox rep1

description: Nascent RNA


title: 4sU-seq shLuciferase Dox rep2

description: Nascent RNA

value: Dox-inducible control shRNA targeting luciferase


title: 4sU-seq shLuciferase Dox rep3

description: Nascent RNA


title: 4sU-seq shLuciferase Dox rep1

description: Nascent RNA


title: NP-specific Germinal Center B cell, Day12 Immunized AAN,rep4

city: Wexford

first: PARTHA

middle: SARATHI

last: BISWAS

state: PA

address: 103 Blue Heron Dr

department: Medicine

institute: University of Pittsburgh

data_processing:
The read quality before and after trimming was checked using FastQC v-0.11.9
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v- 0.38
Trimmed sequence reads were aligned to mm10 and quantified using Kallisto version 0.46.1
Assembly: mm10
Supplementary files format and content: comma-separated values file that include TPM values for each sample
Supplementary files format and content: tpm_names.csv

source_name: Spleen

extract_protocol: Cells were sorted into 12.5 ul of lysis buffer and cDNA was generated using the Takara Smart-Seq HT kit (Takara: 634438) following manufactures instructions, with 15 cycles of cDNA amplification. Smart-Seq cDNA was assessed for quality on an Agilent Fragment Analyzer 5300 using the High sensitivity NGS kit (Agilent: DNF-474-1000). Samples that passed QC with full length cDNA proceeded to library preparation using Illumina Nextera DNA prep (Illumina: 20018705) with UDI indexes (Illumina: 20042666) added using 8 PCR cycles. Libraries were pooled and sequenced on an Illumina NextSeq 2000 using a P3 100 cycle flow cell (Illumina: 20046812), 2x59 bp, for an average of ~35 million reads per sample. Libraries were demultiplexed using the NextSeq 2000 Dragen server and BCL Convert (v 3.8.4).

value: Spleen

value: Germinal Center B cells

value: Immunized AAN

value: Aristolochic acid I


title: serum_miRNA_miRNeasy_serum/plasma_advanced_kit

city: Hirosaki

first: Mitsuru

last: Chiba

state: Aomori

address: 66-1 Hon-cho

department: Graduate School of Health Sciences

country: Japan

institute: Hirosaki University

description: gene expression using miRNeasy serum/plasma advanced kit

hyb_protocol: SurePrint G3 Mouse miRNA microarray slides (8x60K rel 21.0) (G4872A) (Agilent Technologies) were hybridized with the 1.8 ng of Cy3-labeled miRNA in a hybridization solution, which was prepared using a Gene Expression Hybridization lit (Agilent Technologies) for 20 hours at 55°C in a rotating hybridization oven (Agilent Technologies), according to the manufacturer’s instructions. After hybridization, microarray slides were washed for 5 min at room temperature with GE Wash Buffer 1 (Agilent Technologies) and for 5 min at 37°C with GE Wash buffer 2 (Agilent Technologies), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G4900DA) (Agilent Technologies) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 2 μm high sensitivity, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5 (Agilent Technologies) using default parameters (Protocol name: miRNA_1105_Oct12 and Grid name: 070155_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Serum

label_protocol: Cy3-labeled miRNA was synthesized from 1.8 ng of serum RNA using a miRNA Complete Labeling and Hyb kit (Agilent Technologies), according to the manufacturer’s instructions.

growth_protocol: Eight-week-old C57BL/6NJcl male mice were purchased from Clea Japan and acclimatized for a week before starting the experiment.

extract_protocol: RNAs were extracted using 200 μL of serum from 8-week-old C57BL/6NJcl male mice and 2 reagents: miRNeasy serum/plasma advanced kit (QIAGEN), and mirVana™ PARIS™ RNA and Native Protein Purification Kit (Thermo Fisher Scientific)  according to each manufacturer’s protocol. In addition, RNAs were extracted using exoRNeasy midi kit (QIAGEN) to extract RNA from the aqueous layer of 200 μL of serum to which 700 μL of QIAzol Lysis Reagent (QIAGEN) was added and separated in two layers to determine the amount of total RNA in the serum.

treatment_protocol: Eight-week-old C57BL/6NJcl male mice were collected blood under anesthesia.Blood samples were serum-separated immediately after collection. Blood was placed in a Microtainer (Becton Dickinson) for serum separation. The collected blood was centrifuged at 6000 G for 3 min to separate the serum.

tag: gender

value: male

tag: age

value: 8 weeks


title: NP-specific Germinal Center B cell, Day12 Immunized AAN,rep5


title: serum_miRNA_exoRNeasy_midi_kit

description: gene expression using exoRNeasy midi kit


title: NP-specific Germinal Center B cell, Day12 Immunized control,rep5

value: Immunized control

value: PBS


title: serum_miRNA_mirVana™_PARIS™_RNA_and_Native_Protein_Purification_Kit

description: gene expression using mirVana™ PARIS™ RNA and Native Protein Purification Kit


title: NP-specific Germinal Center B cell, Day12 Immunized AAN,rep1


title: NP-specific Germinal Center B cell, Day12 Immunized AAN,rep2


title: NP-specific Germinal Center B cell, Day12 Immunized AAN,rep3


title: NP-specific Germinal Center B cell, Day12 Immunized control,rep4


title: NP-specific Germinal Center B cell, Day12 Immunized control,rep3


title: ChIP-seq SPT6 shCTR9 EtOH rep2

value: Pancreas

value: PDAC cell line

value: Dox-inducible shRNA targeting Ctr9


title: NP-specific Germinal Center B cell, Day12 Immunized control,rep2


title: NP-specific Germinal Center B cell, Day12 Immunized control,rep1


title: C3_input

city: Rochester

first: Huihuang

last: Yan

state: Minnesota

address: 200 First Street SW

institute: Mayo Clinic

data_processing:
Data were analyzed by the HiChIP pipeline (PMID: 25128017)
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 20, using cutadapt v0.4.4, discarding reads with length < 25 bp after trimming.
Reads were mapped to the mm10 reference genome using BWA v0.7.17. Only pairs of reads with one or both ends being uniquely mapped with mapping quality ≥30 were retained
Duplicates were removed using Picard v1.67 (https://broadinstitute.github.io/picard/).
Peaks were identified using MACS v2.0.10, with the significance cut-off of q-value <=0.01
Normalized signals in reads-per-million were generated using BEDTools v 2.27.1 and then converted to bigwig format using wigToBigWig command (http://hgdownload.cse.ucsc.edu/admin/exe/)
Assembly: mm10
Supplementary files format and content: bigWig, encodePeak (except for Input sample)

source_name: Liver sinusoidal endothelial cell

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes, followed by quenching with 125 mM glycine for 5 min at room temperature. Chromatin was sonicated in the Diagenode bioruptor (Diagenode Inc.).
The cleared supernatant was incubated with anti-H3K27ac antibody. After adding 15 𝜇l of prewashed protein G-magnetic beads, the reactions were incubated for 3 hours. The beads were extensively washed with ChIP buffer, high salt buffer, LiCl2 buffer, and TE buffer. Bound chromatins were eluted and reverse-crosslinked at 65°C overnight. DNAs were purified using Min-Elute PCR purification kit (Qiagen) after treatment with RNase A and proteinase K. ChIP-seq libraries were prepared from 10 ng of ChIP and input DNAs with the ThruPLEX® DNA-seq Kit (Takara Bio, Cat# R400675).

value: Liver sinusoidal endothelial cell

tag: chip antibody


title: C2_input


title: C3_H3K27ac

value: H3K27ac (CST cat # 8173, lot 1))


title: C2_H3K27ac

value: H3K27ac (CST cat # 8173, lot 1)


title: BLISS shMYC Dox AZD6738 rep2

data_processing:
Base calling performed using Illumina's FASTQ Generation software v1.0.0. Reads were demultiplexed according to sample-barcode with UMI-tools v1.0.1. barcodes used as following: A1: CATCACGC, A2: GTCGTTCC, A3: TGATGATC, A4: ACGACATC
Reads were mapped to the mouse reference genome (mm10) using Bowtie2 v2.3.4.1
Assembly: mm10

extract_protocol:
blunting of DSB, adapter ligation, DNA purification and fragmentation, in vitro transcription, fragmentation
libraries were prepared for sequencing using a modified NEBNext Small RNA library preperation protocol

value: Dox-inducible shRNA targeting Myc


title: BLISS shMYC Dox AZD6738 rep1


title: BLISS shMYC EtOH AZD6738 rep2


title: BLISS shMYC EtOH AZD6738 rep3


title: BLISS shMYC EtOH AZD6738 rep1


title: BLISS shMYC Dox rep3

value: Dox, 1µg/ml, 48 h


title: BLISS shMYC Dox rep2


title: ALS_7

city: Catania

first: Sebastiano

last: Cavallaro

address: Via Paolo Gaifami, 18

country: Italy

institute: IRIB-CNR

description: Gene expression of skin fibroblast from SALS patient

hyb_protocol: Aliquots (750 ng) of Cy3 labeled cRNA targets were co-hybridized on 4x44K Whole Human Genome Oligo Microarrays (Agilent Technologies, Italy). Microarray hybridi-zation and washing were performed using reagents and instruments (hybridization chambers and rotating oven) as indicated by the manufacturer (Agilent Technologies, Palo Alto, CA, USA).

scan_protocol: Arrays were then scanned at 3 µm resolution using an Agilent G4900DA SureScan Mi-croarray Scanner System (Agilent Technologies, Palo Alto, CA, USA).

data_processing: Raw microarray data were acquired and analyzed using Agilent’s Feature Extraction v.12.1 software to assess the array spot quality, as well as to check signal and background intensity statistics in the default setting.

source_name: Primary fibroblast lines from punch skin biopsy of SALS patient 7

label_protocol: 1 ug of total RNA from each sample was amplified and transcribed into fluorescent complementary DNA (cDNA) using the Low RNA Input Fluorescent Linear Amplifica-tion Kit (Agilent Technologies, Inc., CA, USA), after which labelled RNA was cleaned using by RNeasy column purification (Qiagen, Venlo, the Netherlands). The Cyanine-3 (Cy3) labelled cRNA samples were hybridized onto the Whole Human Genome Oligo Microarray (4×44K; Agilent Technologies, Inc., Santa Clara, CA, USA).

growth_protocol: Primary fibroblast lines were established from punch skin biopsy samples, in accordance with guidelines set by the local ethics committee. Once established, primary fibroblast cultures were maintained in Dulbecco's Modified Eagle Medium (DMEM) high glucose (Life Technologies, Carlsbad, CA) medium sup-plemented with 10% calf serum, 2 mM L-glutamine, 5 mM pyruvate, 100 U/mL penicillin and 100 μg/mL streptomycin. The medium was changed every 3–4 days until the fi-broblasts were grown to confluence. Fibroblasts were maintained in culture through passages on flask. All experiments were performed in confluent cells at the 3rd/4th passage on flask

extract_protocol: Total RNA was extracted from fibroblasts by standardized protocols using TRIzol Reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s guidelines. Total RNA was quantified on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and samples with an RNA integrity score (RIN) higher than 9 were qualified for further processing.

tag: age at biopsy

value: F

value: Skin Fibroblast

tag: disease state

value: Sporadic Amyotrophic Lateral Sclerosis (SALS)


title: ALS_5

source_name: Primary fibroblast lines from punch skin biopsy of SALS patient 5


title: ALS_3

source_name: Primary fibroblast lines from punch skin biopsy of SALS patient 3


title: ALS_8

source_name: Primary fibroblast lines from punch skin biopsy of SALS patient 8


title: ALS_4

source_name: Primary fibroblast lines from punch skin biopsy of SALS patient 4

value: M


title: BLISS shMYC Dox AZD6738 rep3

tag: cell line


title: BLISS shMYC Dox rep1

tag: cell type


title: mouse mammary tumor [mid214]

value: F1Bx((C57BL/6J x FVB/NJ) x FVB/NJ MMTV-Erbb2)

tag: Sex

value: female

value: biospy of mammary tumor


title: ALS_1

source_name: Primary fibroblast lines from punch skin biopsy of SALS patient 1


title: ALS_6

source_name: Primary fibroblast lines from punch skin biopsy of SALS patient 6


title: ALS_9

source_name: Primary fibroblast lines from punch skin biopsy of SALS patient 9


title: Ctrl_1

description: Gene expression of skin fibroblast from control subject

source_name: Primary fibroblast lines from punch skin biopsy of control 1

value: healthy control


title: Ctrl_3

source_name: Primary fibroblast lines from punch skin biopsy of control 3


title: BLISS shMYC EtOH rep2

value: EtOH, 48h


title: Ctrl_2

source_name: Primary fibroblast lines from punch skin biopsy of control 2


title: RNA-seq shCDC73 Dox rep3

data_processing:
Base calling performed using Illumina's FASTQ Generation software v1.0.0.
Reads were mapped to mm10 using Bowtie 2 v2.3.4.1 then samples were normalized to the number of mapped reads in the smallest sample.
Reads per gene were counted using the featureCounts function from the R package Rsubread. Non- and low-expressed genes were removed with less than 5 reads per gene. Differentially expressed genes relative to shLuciferase were retrieved using edgeR and P values were adjusted for multiple testing using the Benjamini-Höchberg procedure.
Assembly: mm10

extract_protocol:
RNA was isolated using peqGOLD TriFast (PeqLab). Total RNA was extracted using the miRNeasy kit (QIAGEN) including on-column DNase I digestion.
mRNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the instructions. Libraries were size selected using Agentcourt AMPure XP Beads (Beckman Coulter), followed by amplification with 11 cycles of PCR.

value: Pancreas

value: Dox-inducible control shRNA targeting Cdc73


title: RWPE-CRAF-Bone5

description: RWPE-CRAF_merged_rsem_genes_expected_counts.txt

value: prostate epithelial

value: C-Raf overexpression bone met


title: The dam was cared for in >90% oxygen chamber (HOX) from postnatal day 1 to day 10 (P1-P10), rat6

city: Milwaukee

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Gene expression interrogating 31099 transcripts

hyb_protocol: The Affymetrix GeneChip rat genome RG230 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Array images were quantified with Affymetrix Expression Console Software and normalized with Robust Multichip Analysis (Bioconductor - www.bioconductor.org) to determine signal log ratios [26].  Gene expression differences were also evaluated by principle component analyses, and the statistical significance of differential gene expression and false discovery rates (FDR) were derived through Partek GS ANOVA statistic and ToppCluster.

organism: Rattus norvegicus

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Time-dated-pregnant Sprague-Dawley rats were obtained from Envigo (Madison, WI) and were acclimated to our animal facility for 7 days. The use of animals was approved by the Medical College of Wisconsin Institutional Animal Care and Use Committee and conformed to the National Institute of Health Guide for the Care and Use of Laboratory Animals.

extract_protocol: Total RNA was extracted Trizol (Invitrogen, Carlsbad, CA, USA).  RNA was amplified/labeled using Affymetrix 3' IVT Express Kit (Affymetrix, Santa Clara, CA).

treatment_protocol: Nursing dams were cared for in a 12-h dark-light cycle and had free access to chow and water. According to the study design, two or four pregnant rats were used for each experiment. The dam and pups were cared for in either >90% oxygen chamber (HOX) or room air (NOX) from postnatal day 1 to day 10 (P1-P10), and then all of them were caged in room air between P11 and P21.  Oxygen concentrations were continuously monitored with an oxygen sensor (Reming Bioinstruments Co., Redfield, NY). Pups were caged with nursing dams while the dams were alternated between oxygen environments to diminish oxygen toxicity.

value: Lung

value: 21 days old

value: Sprague-Dawley rats


title: RNA-seq shCDC73 Dox rep2

value: PDAC cell line

value: Dox, 1µg/ml, 48 h


title: RNA-seq shCDC73 Dox rep1


title: BLISS shMYC EtOH rep3

value: Dox-inducible shRNA targeting Myc


title: ALS_2

source_name: Primary fibroblast lines from punch skin biopsy of SALS patient 2

value: F

value: Skin Fibroblast

value: Sporadic Amyotrophic Lateral Sclerosis (SALS)


title: Primary hepatocytes, Control

city: Nanjing

first: Yuhui

last: Zang

address: 163 Xianlin Road

institute: Nanjing University

description: mmhcRNA-control

data_processing:
Basecalls performed using CASAVA version 1.4
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data
RNA-seq reads were aligned to the mm10 genome assembly using TopHat2
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: Tab-delimited txt files include RPKM values for each Sample

source_name: Liver

growth_protocol: The mice were maintained under pathogen-limited conditions and had free access to rodent chow and water.

extract_protocol:
Total RNA was extracted from the isolated hepatocytes with TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The mice were intraperitoneally injected with of 20% CCl4 solution in sterile mineral oil at a dose of 2.5 ml CCl4 per kilogram body weight twice per week for eight weeks. Afterwards, the primary hepatocytes were isolated.

value: Liver

value: Hepatocyte

value: WT

value: Intraperitoneal injection of oil


title: Primary hepatocytes, Model

description: mmhcRNA-model

value: Intraperitoneal injection of CCl4


title: The dam was cared for in >90% oxygen chamber (HOX) from postnatal day 1 to day 10 (P1-P10), rat5

source_name: Time-dated-pregnant Sprague-Dawley rats were obtained from Envigo


title: The dam was cared for in >90% oxygen chamber (HOX) from postnatal day 1 to day 10 (P1-P10), rat3


title: The dam was cared for in >90% oxygen chamber (HOX) from postnatal day 1 to day 10 (P1-P10), rat2


title: The dam was cared for in >90% oxygen chamber (HOX) from postnatal day 1 to day 10 (P1-P10), rat1


title: RNA-seq shCTR9 Dox rep2

source_name: Pancreas

value: Pancreas

value: Dox-inducible control shRNA targeting Ctr9


title: Mtmr2 null niacin [4508]

city: Madison

first: John

last: Svaren

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

description: DEseq2_results_Mtmr2 null niacin vs. Mtmr2 null.csv

data_processing:
Illumina Pipeline  Casava 1.9
Reads were aligned to GRCm38/mm10 genome using the STAR aligner
Data were analyzed using DEseq2
Assembly: mm10
Supplementary files format and content: DEseq2 output

source_name: sciatic nerve

growth_protocol: Mice were housed with a normal light/dark cycles and ad libitum access to chow and water. Mtmr2 null mice were used.

extract_protocol:
Total RNA was purified using Zymo RNA purification kit
Illumina, RNA with PolyA selection,
Illumina HiSeq 2x150bp, performed by Genewiz (South Plainfield, NJ)

treatment_protocol: Niacin was administered from P10 to P30, P10 by i.p. injection of niacin at 120 mg/Kg until P21. Then gavage using Niacin-SR (slow release) from P21-P30.

value: sciatic nerve

value: 1 month

value: niacin

value: Mtmr2 -/-


title: Mtmr2 null niacin [4506]


title: RNA-seq shCTR9 Dox rep3

value: PDAC cell line


title: BLISS shMYC EtOH rep1

value: EtOH, 48h


title: The pup cared for in room air (NOX) from postnatal day 1 to day 10 (P1-P10), rat6

value: Lung

value: 21 days old

value: Sprague-Dawley rats


title: The dam was cared for in >90% oxygen chamber (HOX) from postnatal day 1 to day 10 (P1-P10), rat4


title: Mtmr2 null niacin [4505]


title: The pup cared for in room air (NOX) from postnatal day 1 to day 10 (P1-P10), rat5


title: The pup cared for in room air (NOX) from postnatal day 1 to day 10 (P1-P10), rat4


title: The pup cared for in room air (NOX) from postnatal day 1 to day 10 (P1-P10), rat2


title: Mtmr2 null [4504]

description: DEseq2_Mtmr2 null v control.csv


title: RNA-seq shMYC Dox rep3

description: shMYC.xlsx

value: Dox-inducible control shRNA targeting Myc

value: Dox, 1µg/ml, 48 h


title: RNA-seq shCTR9 Dox rep1


title: RNA-seq shLuciferase Dox rep3

value: Dox-inducible control shRNA targeting luciferase


title: RNA-seq shLuciferase Dox rep2


title: RNA-seq shMYC Dox rep2

description: shMYC.xlsx


title: RNA-seq shLuciferase Dox rep1


title: Mtmr2 null [4502]

description: DEseq2_Mtmr2 null v control.csv


title: Mtmr2 null [4501]

description: DEseq2_Mtmr2 null v control.csv


title: Control [4500]

description: DEseq2_results_Mtmr2 null niacin vs control.csv

value: Mtmr2 wt/wt


title: CUT&RUN MYC shMYC Dox

extract_protocol:
ChIP-seqCells were treated with 1% formaldehyde for 5 min at 37°C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <300 bp using sonification. Chromatin was immunoprecipitated with 15 µg of corresponding antibody for 6 hours. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used. CUT&RUN: cells were harvested using Accutase (Sigma) for cell detachement. Cells were counted and washed in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine). After washing, cells were coupled to ConA-coated magnetic beads (Polysciences Europe) and subsequently permeabilized and followed by addition of primary antibody in antibody binding buffer (wash buffer, 0.05% digitonin, 2 mM EDTA) over night at 4 °C. Cells were wased in Dig-Wash buffer (Wash buffer, 0.05% digitonin) and MNase (700ng/ml) was added to each sample for 1 hr at 4 °C. After washing with Dig-wash buffer and Low-salt Rinse buffer (20 mM HEPES pH 7.5, 0.5 mM Spermidinge, 0.05% digitonin) incubation buffer (3.5 mM HEPES pH 7.5, 10 mM CaCl2, 0.05% digitoin) was added for 30 min at 4°C. STOP buffer (170 mM NaCL, 20 mM EGTA, 0.05% digitonin, 20 ug/ml RMAse A, 25 ug/ml Glycogen was added to stop the MNase digestion. DNA fragments were released at 37 °C for 30 min and proteins digested for 1 h at 50 °C after adding 0.01 % SDS and 10 mg/ml Proteinase K followed by Phenol Chloroform extraction. Precipitated DNA was resuspended in 30 ul 0.1x TE buffer
ChIP-seq Libraries were prepared according to instructions accompanying the NEBNext Ultra™ II DNA Library Prep Kit for Illumina. Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (150 bp) and eluted. DNA fragments were amplified by 11 to 16 cycles of PCR and library size was tested with the Fragment Analyzer (Advanced Analytical). The amount of library DNA was quantified using a picogreen assay. CUT&RUN: NEBnext Ultra II DNA Library Prep Kit (New England Biolabs) was used. Pre-PCR samples were purified using AmpureXP beads with a ratio of 1.75x. Then half of the eluted material was used with 12-16 PCR cycles. The libraries were cleaned using Agentcourt AMPure XP Beads (ratio 1.1x, Beckman Coulter), quality, quantity and fragment size assessed on the Fragment Analyzer (Agilent) using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent)

value: Dox-inducible shRNA targeting Myc

tag: antibody

value: MYC upon MYC depletion


title: CUT&RUN IgG shCTR9 EtOH

value: Pancreas

value: Dox-inducible shRNA targeting Ctr9

value: IgG

value: EtOH


title: Mtmr2 null niacin [4507]

value: sciatic nerve

value: 1 month

value: niacin


title: RNA-seq shMYC Dox rep1

description: shMYC.xlsx

value: PDAC cell line


title: Control [4499]


title: Control [4498]


title: CUT&RUN MYC shCTR9 Dox

value: MYC upon CTR9 depletion


title: CUT&RUN MYC shMYC EtOH


title: The pup cared for in room air (NOX) from postnatal day 1 to day 10 (P1-P10), rat1

value: Lung

value: 21 days old


title: Control [4497]


title: CUT&RUN MYC shCTR9 EtOH


title: organoids, APK, shUsp10-2, rep3

city: Berlin

first: Michaela

last: Reissland

address: Ihnestr. 63

department: Genome Regulation

institute: Max Planck Institut for molecular genetics

data_processing:
Illumina’s FASTQ Generation software v1.0.0
Sequenced reads were mapped to mm10 using bowtie2 v2.4.1
reads were count using featureCounts package in R
counts were normalised using edgeR package in R
Assembly: mm10
Supplementary files format and content: .txt file with normalised counts for shNTC and shUsp10-1
Supplementary files format and content: .txt file with normalised counts for shNTC and shUsp10-2

source_name: small intestine

growth_protocol: isolated small intestinal organoids from a constitutive Cas9 expressing mouse were targeted using CRISPR/Cas9 in Apc (exon9), Trp53 and Kras (incorporation of G12D mutant) and subsequently infected with shNTC and shUsp10-1 and -2

extract_protocol:
ReliaPrepTM RNA Cell miniprep System Promega Kit
NEBNext Poly(A) mRNA Magnetic Isolation Module; NEBNext Ultra II Directional RNA Library Prep Kit for Illumina; SPRI select reagent; NEBNext Multiplex Oligos for Illumina (Dual Index Set 1)

value: small intestine

value: Cas9 mouse, genetically modified to Apc:Trp53:KRasG12D


title: organoids, APK, shUsp10-2, rep2


title: ChIP-seq SPT6 shCTR9 Dox

value: Dox, 1µg/ml, 48 h


title: organoids, APK, shUsp10-1, rep2


title: ChIP-seq SPT5 shCTR9 Dox


title: organoids, APK, shUsp10-1, rep3


title: ChIP-seq SPT6 shCTR9 EtOH


title: organoids, APK, shUsp10-1, rep1


title: Mtmr2 null [4503]

description: DEseq2_Mtmr2 null v control.csv

value: Mtmr2 -/-


title: ChIP-seq CTR9 shCTR9 Dox


title: ChIP-seq CTR9 shCTR9 EtOH


title: organoids, APK, shNTC, rep3

description:
APK9_ntc_vs_sh1_norm_counts.txt
APK9_ntc_vs_sh2_norm_counts.txt

value: shNTC


title: ChIP-seq SPT5 shCTR9 EtOH


title: ChIP-seq RNAPII shCTR9 EtOH

value: RNAPII


title: organoids, APK, shNTC, rep2


title: ChIP-seq RNAPII shCTR9 Dox

value: Pancreas


title: control-3

city: Zhanjiang

first: Ji

middle: Xin

last: Tang

state: Guangdong

address: No.57 South Renmin Avenue, Xiashan District

department: Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China.

institute: Mouse kidney

data_processing:
Transcriptome sequencing procedures include RNA extraction, RNA sample quality detection, library construction, library purification, library detection, library quantification, generation of sequencing clusters, and computer sequencing. In order to ensure the accuracy and reliability of source data, we carried out strict quality control for each step of the experimental process.
Different libraries were mixed according to the requirements of effective concen-tration and target data volume and then sequencing by Illumina.
Bcl2fastq (v2.17.1.14) was used for image Base Calling for preliminary quality analysis to obtain the original sequencing Data (Pass Filter Data), and the results were stored in FASTQ file format. It contains sequencing sequence information and its corresponding sequencing quality information. The sequencing data quality was evaluated by FastQC (v0.10.1) software.
Raw data was preprocessed using Cutadapt (version 1.9.1) software and low quality data was filtered to remove contamination and joint sequences. The filtered sequenc-ing Clean Data was compared with the reference genome for analysis.
Hisat2(v2.0.1) software was used to compare short reads with the default parameters. Gene expres-sion was calculated using Cuffdiff software (v2.2.1), which calculated gene expression using FPKM (Fragments Per Kilo bases per Million reads)[38]. Genetic difference anal-ysis was performed using cuffdiff(v2.2.1), which was based on a negative binomial distribution model. The detection results were screened according to the differential significance criteria (differential gene expression changes of more than 2 times and qvalue(fdr, padj<=0.05), and the down-regulation of significant differential gene ex-pression was counted.
Assembly: Mus_musculus(GRCm38.89)
Supplementary files format and content: The “processed data.xls”contains the count value and fpkm value of each sample, and the corresponding gene ID.

source_name: kidney

extract_protocol:
Total RNA from mouse kidney was extracted from cultured cells using RNAiso Plus (Takara, 9108, Japan) according to the manufacturer’s protocol.
The RNA concentration and purity were quantified using NanoDrop 2000 ultrafine spectrophotometer (Thermo Scientific, Massachusetts, America). And then the genome DNA was elimi-nated with the RNase-free DNase H. The RNA was then reverse-transcribed with 5× FastKing-RT SuperMix kit (TIANGEN, KR118–01, Beijing, China) according to the manufacturer’s protocols. The reverse-transcribed cDNA was used as template for qPCR using Genious 2X SYBR Green Fast qPCR Mix (ABclonal, RK21204) according to the manufacturer’s protocol. LightCycler 480 II real-time fluorescence quantitative PCR instrument was used for PCR reaction. The primer sequences used for amplifying the target fragments and GAPDH as internal control were listed in Table1. Gene’s rela-tive expression levels were calculated by the 2-ΔΔCt (threshold cycle) method.

value: kidney


title: control-1


title: control-2


title: WT differentiated macrophages, Control, replicate 2, Day 8

city: Houston

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

data_processing:
Fastq quality control and filtering was performed using fastp (0.12.4) set to default parameters.
Filtered fastqs were aligned to the mouse genome (mm10, m22 Gencode annotation file) using STAR (2.7.9a). Sorting and indexing were performed using samtools (1.9).
Mapped reads were counted using featureCounts (v1.6.2) with parameters "-t exon -g gene_name" to the m22 Gencode annotation file.
Assembly: mm10
Supplementary files format and content: counts_table.txt: Tab-delimited text file of featureCounts output (read counts) including all samples as columns, genes as rows.

source_name: Macrophage

growth_protocol: Bone marrow was collected from 3 male mice per genotype at 13 weeks of age (Day 0). Whole bone marrow was plated at 4 x10^5 cells per 10 cm dish in macrophage differentiation medium (DMEM, 10% FBS, 1x GlutaMAX, 1x non-essential amino acids, 1x sodium pyruvate, 1x penicillin/streptomycin, 1 uM beta-mercaptoethanol, and 50 ng/mL M-CSF) until Day 6.

extract_protocol:
On Day 8, macrophages were collected for RNA isolation using the RNeasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA library prep kit according to the manufacturer's instructions.

treatment_protocol: On Day 6, half of Het or WT samples were treated with IL-6 at a concentration of 10 ng/mL for 2 days.

value: Macrophage

value: WT

value: Male

value: Control


title: WT differentiated macrophages, IL6 treated, replicate 1, Day 8

value: IL-6 treated


title: cko-3


title: WT differentiated macrophages, Control, replicate 1, Day 8


title: DNMT3A-HET differentiated macrophages, Control, replicate 2, Day 8


title: cko-2


title: cko-1


title: DNMT3A-HET differentiated macrophages, IL6 treated, replicate 2, Day 8


title: DNMT3A-HET differentiated macrophages, Control, replicate 1, Day 8


title: OL9

city: New Brunswick

first: Daniel

last: Herranz

state: New Jersey

address: 195 Little Albany Street

institute: Rutgers Cancer Institute of New Jersey

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Gene abundance estimates were obtained for each sample using kallisto 0.44.0, with the UCSC mm10 transcriptome as the reference
The abundance levels were normalized using the DESeq between-sample normalization approach
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated values file includes the DESeq normalized counts for all samples

source_name: Spleen

growth_protocol: Sirt1 conditional knockout T-ALLs were injected intravenously in sub-lethally Irradiated mice.

extract_protocol:
Leukemic spleens were removed, single-cell suspensions were obtained by pressing them through a 40mm filter, and subsequently subjected to red blood cell lysis. RNA was extracted using QIAGEN QIAshredder (#79656) and Rneasy Mini (#74106) kits. 1mg of Total RNA was used for the construction of sequencing libraries by Genewiz.
Strand-specific RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were trated with vehicle only (control: corn oil, C8267, Sigma-Aldrich) or tamoxifen (T5648, Sigma-Aldrich; 3 mg per mouse in corn oil) administered by intraperitoneal injection.

value: Leukemic spleen

value: Sirt1 deleted


title: DNMT3A-HET differentiated macrophages, IL6 treated, replicate 1, Day 8


title: organoids, APK, shNTC, rep1


title: OL7


title: OL8


title: WT-HUR80-ChIP-rep2

city: Charlestown

first: Richard

last: Joh

state: MA

department: Center for Cancer Research

institute: Mass General Hospital

data_processing:
Mapping by BWA
BW generated by DeepTools
Assembly: S pombe
Supplementary files format and content: BW

organism: Schizosaccharomyces pombe

source_name: cells

extract_protocol:
H3K9me2 ChIP
NEB Ultra II Library Prep Kit for Illumina

value: cells


title: OL6


title: WT-HUR50-ChIP-rep2


title: WT-HUR60-ChIP-rep2


title: WT differentiated macrophages, IL6 treated, replicate 2, Day 8


title: WT-HUR20-ChIP-rep2


title: OL3


title: WT-HU Sync-ChIP-rep2

value: HU Sync


title: WT-HUR40-ChIP-rep2


title: WT-Unsync-ChIP-rep2

value: Unsync


title: OL1


title: OL4


title: WT-HUR120-Input-rep2


title: IgAKO...46.1170.IgAKO.P8

city: New York

first: Lewis

middle: E

last: Tomain

state: NY

address: 225 East 95th Street, Apt16E

department: Population Health Science and Policy

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The fastq files generated from Illumina RNA-Seq were preprocessed and quality controlled using the CLC Genomics Workbench Version 9.0.1.
The raw reads were trimmed and filtered to remove possible adapter sequences and low-quality nucleotides at the ends.
After trimming, sequence reads shorter than 50 nucleotides were discarded according to the following parameters: phred score > Q30, base error probability score > 0.05, and base ambiguities < 2, read-length < 50 bp.
Trimmed reads were aligned to the Mus musculus genome, and count data was generated using CLC Genomics Workbench Version 9.0.1.
Genome_build: Mus musculus genome
Supplementary_files_format_and_content: Voom normalized counts

source_name: Marginal Zone B cells (MZB)

extract_protocol:
Single cell suspensions were created from mouse spleen through tissue homogenization between frosted glass slides, straining through 40μm filters, treatment with Ack to lyse red blood cells, followed by a PBS wash. B cells were purified using a Miltenyi Pan B cell isolation Kit II (Cat nr: 130-104-443), followed by FACS staining for sorting. Cells were resuspended in PBS with CD16/32 Fc Block and Live/Dead staining (Invitrogen) before staining with antibodies to surface markers. Live CD11c-Ly6G-CD3- B220+AA4.1- CD21highCD23lo Marginal Zone (MZ) B cells (P8) and CD21+CD23+ follicular (FO) B cells (P9) were FACS-sorted (Influx BD). RNA was extracted from sorted MZ and FO B cells using QIAshredder and RNeasy Plus Micro Kit (Qiagen).
Library preparation and sequencing were performed by GENEWIZ using standard Illumina protocols.

tag: mousenumber


title: OL10


title: IgAKO...26.1166.IgAKO.P8


title: WT-HUR140-Input-rep2


title: IgAKO...36.1168.IgAKO.P8


title: WT-HUR80-Input-rep2


title: WT-HUR60-Input-rep2


title: WT-HUR100-Input-rep2


title: IgAKO...16.1164.IgAKO.P8


title: IgAKO...6.1162.IgAKO.P8


title: OL5


title: Wt...11.1163.Wt.P8


title: Wt...31.1167.Wt.P8


title: OL2


title: WT-HUR50-Input-rep2


title: WT-Unsync-Input-rep2


title: WT-HUR20-Input-rep2


title: WT-HUR40-Input-rep2


title: Sir2-FLAG-HUR140-ChIP-rep1


title: Wt...41.1169.Wt.P8


title: IgAKO...27.1166.IgAKO.P9

source_name: Follicular B Cells (FOB)


title: Sir2-FLAG-HUR120-ChIP-rep1


title: Sir2-FLAG-HUR100-ChIP-rep1


title: IgAKO...7.1162.IgAKO.P9


title: IgAKO...47.1170.IgAKO.P9


title: Wt...22.1165.Wt.P9


title: Sir2-FLAG-HUR80-ChIP-rep1


title: Sir2-FLAG-HUR50-ChIP-rep1


title: IgAKO...17.1164.IgAKO.P9


title: Sir2-FLAG-HUR60-ChIP-rep1


title: IgAKO...37.1168.IgAKO.P9


title: Sir2-FLAG-HUR20-ChIP-rep1


title: Wt...2.1161.Wt.P9


title: Sir2-FLAG-HU Sync-ChIP-rep1


title: Sir2-FLAG-Unsync-ChIP-rep1


title: Wt...21.1165.Wt.P8


title: WT-HU Sync-Input-rep2


title: Wt...32.1167.Wt.P9


title: Sir2-FLAG-HUR140-Input-rep1


title: CD140

city: nanjing

first: yifan

last: lv

state: jiangsu

address: 300 Guangzhou Road

department: Department of Geriatrics

institute: the First Affiliated Hospital to Nanjing Medical University

data_processing:
Here is DMR identification with the DSS(DSS_2.12.0) software, it is based on strict Wald beta binomial model test
Genome_build: mm10
Supplementary_files_format_and_content: bw and bed

source_name: PDGFRa+ adipocyte progenitor subgroup with DEX treatment

growth_protocol: CD137+ and PDGFRα+ cells were isolated from SAT or VAT by MACS. Cells were cultured in cultured under growth condition and then exposed toadipogenesis cocktail.

extract_protocol:
After extracting the sample DNA, DNA concentration and integrity were detected by electrophoresis. After passing the detection, the database was built.
The DNA was randomly interrupted to about 350BP by ultrasound. After terminal repair, base A was added, and sequencing joint was added, the unmethylated C in the disulfite DNA fragment was converted into U, and then fragment screening and PCR amplification were performed to complete the preparation of DNA methylated library. After the library quality control, the library can be sequenced.

treatment_protocol: Differentiated CD137+ and PDGFRα+ cells were cultured in adipogenic medium.

value: adipose tissue

value: adipose progenitors

value: DEX treatment


title: Sir2-FLAG-HUR120-Input-rep1


title: Sir2-FLAG-HUR100-Input-rep1


title: CD137

source_name: CD137+ adipocyte progenitor subgroup with DEX treatment


title: Sir2-FLAG-HUR80-Input-rep1


title: Sir2-FLAG-HUR60-Input-rep1


title: Sir2-FLAG-HUR50-Input-rep1


title: Wt...12.1163.Wt.P9


title: Sir2-FLAG-HUR20-Input-rep1


title: Sir2-FLAG-HU Sync-Input-rep1


title: Wt...42.1169.Wt.P9


title: Sir2-FLAG-Unsync-Input-rep1


title: immunoprecipitation of co-10, rep2

city: Sevilla

first: Pedro

last: de los Reyes

address: c/Americo Vespucio 49

department: Institute for Plant Biochemistry and Photosynthesis

country: Spain

institute: CSIC

data_processing:
QC of reads: FastQC
Alignment: bowtie
Peak calling: MACS2
Bigwig files: bamCoverage
Assembly: TAIR10 Arabidopsis thaliana genome
Supplementary files format and content: bw and narrowPeak files

organism: Arabidopsis thaliana

source_name: seedlings

extract_protocol:
Tissue was fixed with 1% formaldeyde for 20 min and with 1 mM of DSG for 10 min.
kit ThruPLEX DNA-Seq from Takara Bio Europe

value: seedlings

tag: antibodies

value: anti-CO

value: Long Day


title: WT-HUR140-ChIP-rep1


title: immunoprecipitation of co-10, rep1


title: immunoprecipitation of 35SCO, rep1


title: WT-HUR120-ChIP-rep1


title: WT-HUR80-ChIP-rep1


title: immunoprecipitation of 35SCO, rep2


title: Input of co-10, rep2


title: WT-HUR100-ChIP-rep1


title: WT-HUR50-ChIP-rep1


title: Input of 35SCO, rep2


title: WT-HUR60-ChIP-rep1


title: Input of co-10, rep1


title: WT-HUR20-ChIP-rep1


title: Input of 35SCO, rep1


title: WT-HU Sync-ChIP-rep1


title: shPEA15_1

first: Ju-Seog

last: Lee

state: Texas

address: 6565 MD Anderson Blvd

institute: UT MD Anderson Cancer Ctr.

description: replicate 1

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V4.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

source_name: liver cancer cells

label_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

tag: cell name

value: FOCUS

tag: shRNA


title: WT-Unsync-ChIP-rep1

tag: genotype

tag: treatment


title: WT-HUR140-Input-rep1


title: shPEA15_2

description: replicate 2

data_processing: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)


title: WT-HUR120-Input-rep1


title: shGFP_1

description: replicate 1

value: shGFP


title: shGFP_3

description: replicate 3


title: WT-HUR100-Input-rep1

value: WT


title: shPEA15_3

description: replicate 3


title: WT-HUR60-Input-rep1


title: shGFP_2

description: replicate 2


title: WT-HUR50-Input-rep1


title: WT-HUR20-Input-rep1


title: WT-HU Sync-Input-rep1


title: clr3Dsir2Dalp13D-Input-rep3

data_processing:
Mapping by BWA
Wig generated by Bedtools
Assembly: S pombe
Supplementary files format and content: Wig

tag: tissue


title: clr3Dsir2D-Input-rep3


title: clr4D-Input-rep3


title: WT-Unsync-Input-rep1


title: ARPE-19, non-transduced control, rep.2

city: Sochi

first: Alima

last: Galieva

state: Krasnodar region

address: Olympic Ave, 1

department: Gene therapy department

country: Russia

institute: Sirius University of Science and Technology

data_processing:
Base-calling was performed with HiSeq Analysis Software, default parameters
Reads were mapped with STAR, 2.7.10b, default parameters
Summarizing reads per gene were conducted by HTSeq-count, 0.11.1, “exon union” mode
Assembly: GRCh38 primary assembly
Supplementary files format and content: tab files for each sample represent raw read counts per gene
Supplementary files format and content: counts.txt file for all samples contains summarised raw read counts per gene

growth_protocol: ARPE-19 cells were cultured at 37°C in a 5% CO2 humid air atmosphere. Tissue culture dishes with a diameter of 35 mm and 6-well plates were used for culturing the cells

extract_protocol:
Cells were lysed with Lyra+ reagent (Biolabmix, Russia), freshly frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted with PureLink RNA Micro Kit
RNA libraries were prepared with New England Biolabs NEBNext® Ultra™ RNA II Library Prep Kit for lllumina® with Poly(A) mRNA Magnetic Isolation protocol module

treatment_protocol: To induce trans-differentiation, confluent ARPE-19 cell cultures were treated for 120 hours with a concentration of 3 µM N-(4-hydroxyphenyl)retinamide

value: no treatment


title: alp13D-Input-rep3


title: ARPE-19, non-transduced control, rep.3


title: ARPE-19, AAV9-AIPL1co, rep.1


title: WT-HUR80-Input-rep1


title: WT-Input-rep3


title: clr3D-Input-rep3


title: ARPE-19, AAV9-GFP, rep.1


title: sir2D-Input-rep3


title: ARPE-19, AAV9-AIPL1wt, rep.2


title: clr3Dsir2Dalp13D-ChIP-rep3

value: H3K9me2 antibody (ab1220)


title: ARPE-19, AAV9-GFP, rep.3


title: ARPE-19, non-transduced control, rep.1


title: ARPE-19, AAV9-GFP, rep.2


title: ARPE-19, AAV9-AIPL1co, rep.3


title: clr4D-ChIP-rep3


title: ARPE-19, AAV9-AIPL1co, rep.2


title: alp13D-ChIP-rep3


title: ARPE-19, AAV9-AIPL1wt, rep.3


title: clr3D-ChIP-rep3


title: ARPE-19, AAV9-AIPL1wt, rep.1


title: sir2D-ChIP-rep3


title: WT-ChIP-rep3


title: clr3Dsir2Dalp13D-Input-rep2


title: clr3Dsir2D-Input-rep2


title: clr3Dsir2D-ChIP-rep3


title: clr4D-Input-rep2


title: alp13D-Input-rep2


title: clr3D-Input-rep2


title: sir2D-Input-rep2


title: ShRINT1_MIAPaCa-2_Dox 96h_replicate 2

city: Ulm

first: Hans

middle: A

last: Kestler

address: Albert-Einstein-Allee 11

department: Research Group Bioinformatics and Systems Biology

institute: University of Ulm

description: Biological replicate 2 of 2. shRINT1 MIAPaca-2, 96h doxycycline treated

scan_protocol: Microarray slides were scanned on a G2565CA microarray scanner (Agilent Technologies, Santa Clara, CA, USA).

data_processing: Raw data files were extracted using the Feature Extraction software (v.10.7.3.1, Agilent Technologies, Santa Clara, CA, USA). Pre-processing of expression data was performed according to Agilent’s standard workflow. Using 5 quality flags (gIsPosAndSignif, gIsFeatNonUnifOL, gIsWellAboveBG, gIsSaturated, and gIsFeatPopnOL) from the Feature Extraction software output (Agilent Technologies, Santa Clara, CA, USA), probes were labeled as detected, not detected, or compromised. Gene expression levels were background corrected, and signals for duplicated probes were summarized by geometric mean of non-compromised probes. After log2 transformation, a percentile shift normalization at the 75% level and a baseline shift to the median baseline of all probes was performed.

source_name: MIAPaCa-2, shRINT1, 96h doxycycline treatment

label_protocol: 200 ng RNA was labeled with the Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's guidelines

growth_protocol: MIA PaCa-2 cells were kept in growth medium (DMEM, 10%FBS, 1%P/S)

extract_protocol: Total RNA extracted using RNAeasy plus kit following manufacturer's instructions

treatment_protocol: one day after seeding cells were treated with doxycycline (1 µg/ml) in normal growth modum for indicated time points

value: MIA PaCa-2 (CRL-1420)

value: pancreatic ductal adenocarcinoma (PDAC) cell line

tag: genotype/variation

value: 96h doxycycline


title: ShRINT1_MIAPaCa-2_Dox 48h_replicate 2

description: Biological replicate 2 of 2. shRINT1 MIAPaca-2, 48h doxycycline treated

hyb_protocol: according to the manufacturer's guidelines

source_name: MIAPaCa-2, shRINT1, 48h doxycycline treatment

value: 48h doxycycline


title: clr3Dsir2Dalp13D-ChIP-rep2

value: cells


title: ShRINT1_MIAPaCa-2_Dox 96h_replicate 1

description: Biological replicate 1 of 2. shRINT1 MIAPaca-2, 96h doxycycline treated


title: ShRINT1_MIAPaCa-2_Dox 48h_replicate 1

description: Biological replicate 1 of 2. shRINT1 MIAPaca-2, 48h doxycycline treated


title: ShRINT1_MIAPaCa-2_Dox 24h_replicate 2

description: Biological replicate 2 of 2. shRINT1 MIAPaca-2, 24h doxycycline treated

source_name: MIAPaCa-2, shRINT1, 24h doxycycline treatment

value: 24h doxycycline


title: alp13D-ChIP-rep2


title: ShRINT1_MIAPaCa-2_Dox 24h_replicate 1

description: Biological replicate 1 of 2. shRINT1 MIAPaca-2, 24h doxycycline treated


title: ShRINT1_MIAPaCa-2_Dox 0h_replicate 2

description: Biological replicate 2 of 2. shRINT1 MIAPaca-2, untreated

source_name: MIAPaCa-2, shRINT1, 0h doxycycline treatment

value: 0h doxycycline


title: Scramble MIAPaCa-2_Dox 96h_replicate 2

description: Biological replicate 2 of 2. scramble MIAPaca-2, 96h doxycycline treated

source_name: MIAPaCa-2, scramble, 96h doxycycline treatment

value: scramble


title: clr3D-ChIP-rep2


title: ShRINT1_MIAPaCa-2_Dox 0h_replicate 1

description: Biological replicate 1 of 2. shRINT1 MIAPaca-2, untreated


title: WT-Input-rep2


title: clr4D-ChIP-rep2


title: Scramble MIAPaCa-2_Dox 96h_replicate 1

description: Biological replicate 1 of 2. scramble MIAPaca-2, 96h doxycycline treated


title: clr3Dsir2D-ChIP-rep2


title: Scramble MIAPaCa-2_Dox 48h_replicate 1

description: Biological replicate 1 of 2. scramble MIAPaca-2, 48h doxycycline treated

source_name: MIAPaCa-2, scramble, 48h doxycycline treatment


title: clr3Dsir2D-Input-rep1


title: Scramble MIAPaCa-2_Dox 24h_replicate 1

description: Biological replicate 1 of 2. scramble MIAPaca-2, 24h doxycycline treated

source_name: MIAPaCa-2, scramble, 24h doxycycline treatment


title: p53-cas9_dsRNA-3

city: Qingdao

first: tong

last: lu

address: 72, binghai rd

institute: ShanDong University

description: 50% epi stage

data_processing:
Each library was amplified by a 11-cycle PCR, and 150 bp paired-end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data.
The quality was examined by Cutadapt and FastQC.
Sequencing results from three biological repeat samples were assembled and aligned using StringTi.
Differential expression was calculated with DESeq2 and edgeR.
Assembly: GRCz10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C

extract_protocol:
Total RNAs were extracted from 6 hpf embryos using TRIzol reagent (Invitrogen), and were precipitated by cold isopropanol (50%, v/v) in the presence of carrier glycogen (20 µg/each sample). Polyadenylated mRNAs were purified by the poly(A) mRNA Magnetic Isolation Module (NEB).
The mRNA libraries were then generated using NEBNext Ultra RNA Library Prep Kit for lllumina following manufacturer’s instruction. Briefly, mRNA fragmentation and priming were carried out via NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. ProtoScript II Reverse Transcriptase and Second Strand Synthesis Enzyme Mix were used to synthesize first and second strand cDNAs. AxyPrep Mag PCR Clean-up (Axygen) kit were then used to purify the cDNAs. After that, cDNAs were treated with End Prep Enzyme Mix to repair 3’ and 5’ ends, followed by dA-tailing and adaptor ligation. Following size selection by AxyPrep Mag PCR Clean-up (Axygen) kit, fragments haboring around 300 bp inserts were recovered.

treatment_protocol: Zebrafish embryos injected with cas9 mRNA, tol2 mRNA or dsRNA were maintained in 1/3x Ringer's at 28.5C

value: whole embryo

tag: time

value: 6 hpf

value: dsRNA


title: Scramble MIAPaCa-2_Dox 48h_replicate 2

description: Biological replicate 2 of 2. scramble MIAPaca-2, 48h doxycycline treated


title: clr3D-Input-rep1


title: sir2D-Input-rep1


title: Scramble MIAPaCa-2_Dox 24h_replicate 2

description: Biological replicate 2 of 2. scramble MIAPaca-2, 24h doxycycline treated


title: sir2D-ChIP-rep2


title: clr3Dsir2Dalp13D-ChIP-rep1


title: clr3Dsir2Dalp13D-Input-rep1


title: p53-cas9_dsRNA-2

description: 50% epi stage


title: WT-ChIP-rep2


title: clr3Dsir2D-ChIP-rep1


title: p53-cas9_dsRNA-1

description: 50% epi stage


title: p53-uninj-3

description: 50% epi stage

value: uninjected


title: wt-uninj-3

description: 50% epi stage

value: wide type


title: clr4D-Input-rep1


title: alp13D-Input-rep1


title: Scramble MIAPaCa-2_Dox 0h_replicate 2

description: Biological replicate 2 of 2. scramble MIAPaca-2, untreated

source_name: MIAPaCa-2, scramble, 0h doxycycline treatment


title: clr3D-ChIP-rep1


title: p53-uninj-2

description: 50% epi stage


title: K-562 cell line, RCB1897

type: genomic

city: Tsukuba

first: Fumio

last: Kasai

address: Koyadai 3-1-1

institute: RIKEN

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The data analyses can be carried out using the Chromosome Analysis Suite software, ChAS 4.2 (Thermo Fisher Scientific).

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen 80204).

value: CML


title: WT-Input-rep1

value: WT


title: sir2D-ChIP-rep1


title: wt-cas9_dsRNA-3

description: 50% epi stage


title: TP450-3

description: 50% epi stage

value: tol2 mRNA


title: TP450-2

description: 50% epi stage


title: wt-cas9_dsRNA-1

description: 50% epi stage


title: wt-cas9_dsRNA-2

description: 50% epi stage


title: shNS A375 cells, biological rep3

first: Nihal

last: Ahmad

state: Wisconsin

address: WIMR II, 1111 Highland Ave

department: Dermatology

hyb_protocol: All samples hybridized to HTA 2.0 ST arrays at 45°C for 16 hrs O/N following all procedures outlined in the GeneChip WT Terminal Labeling and Hybridization User Manual ( P/N 702808 Rev.7)

scan_protocol: GeneChips were scanned on the GC3000 G7 Scanner (Serial #50208130)

data_processing: Data extracted and processed using Affymetrix Command Console version 4.0.0.1567G. RMA data.

source_name: A375 melanoma cells

label_protocol: All samples end-terminus labeled using Affymetrix WT terminal Labeling Kit following the guidelines in the GeneChip WT Terminal Labeling.

extract_protocol: RNeasy Plus Mini Kit (QIAGEN, CA) was used for total RNA isolation as per manufacturer's instructions.

treatment_protocol:
shRNA plasmid DNA (TRIPZ Inducible Lentiviral shNS Control (GE Dharmacon #RHS4743) or TRIPZ Lentiviral Human shPLK1 (GE Dharmacon #RHS4696- 99638417, 99707812, 101347498, 101349871, 101352079 or 101353597) were used as per manufacturer's instruction. Cells . Cells were tested for PLK1 knockdown by western blotting and RT-qPCR.
Cell lines A375 shNS and shPLK1 were plated in 6 well plates and treated with doxycycline for 48 h to induce PLK1 knockdown.

value: melanoma cell line

value: control cells (shNS)


title: K-562 cell line, RCB0027


title: Scramble MIAPaCa-2_Dox 0h_replicate 1

description: Biological replicate 1 of 2. scramble MIAPaca-2, untreated

value: MIA PaCa-2 (CRL-1420)

value: pancreatic ductal adenocarcinoma (PDAC) cell line


title: wt-uninj-2

description: 50% epi stage


title: alp13D-ChIP-rep1

source_name: cells

value: H3K9me2 antibody (ab1220)


title: wt-uninj-1

description: 50% epi stage


title: ago1-RI-C11-Clr4_ChIP-rep2-reintro

extract_protocol:
Clr4 ChIP
NEB Ultra II Library Prep Kit for Illumina

value: cells

tag: replicates

value: Clr4 reintroduction


title: ago1-RI-C3-Clr4_ChIP-rep2-reintro


title: ago1-RI-C4-Clr4_ChIP-rep2-reintro


title: ago1clr4-Clr4_ChIP-rep2-Clr4


title: TP450-1

description: 50% epi stage


title: ago1-Clr4_ChIP-rep2-Clr4


title: Uninj-3

description: 50% epi stage


title: Uninj-2

description: 50% epi stage


title: shNS A375 cells, biological rep4


title: shNS A375 cells, biological rep1


title: cas9-5hpf-1

description: 50% epi stage

value: cas9 mRNA


title: shPLK1 A375 cells, biological rep2

value: PLK1 k/d (shPLK1)


title: shPLK1 A375 cells, biological rep3


title: cas9-5hpf-3

description: 50% epi stage

value: whole embryo


title: shNS A375 cells, biological rep2


title: wt-Clr4_ChIP-rep2-Clr4

value: wt


title: cas9-5hpf-2

description: 50% epi stage

value: 6 hpf


title: ago1-RI-C4-input-rep2-reintro

description: input


title: K-562 cell line, RCB1635


title: uninj-5hpf-3

description: 50% epi stage

value: uninjected


title: ago1-RI-C3-input-rep2-reintro

description: input


title: uninj-5hpf-2

description: 50% epi stage

value: wide type


title: ago1-RI-C11-input-rep2-reintro

description: input


title: shPLK1 A375 cells, biological rep4


title: dc-hiOL_09

city: Münster

first: Christian

last: Thomas

address: Pottkamp 2

institute: Institute of Neuropathology Münster, Germany

hyb_protocol: bisulphite converted DNA was hybridised to the MethylationEPIC BeadChip array.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Illumina processing

source_name: dciOL iO3H

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from formalin-fixed paraffin-embedded tumor samples using the Maxwell 16 FFPE Tissue LEV DNA Purification Kit (Promega).

tag: gender

value: Male

tag: sample type

value: dc-hiOL (cell line)


title: dc-hiOL_08

source_name: dciOL 82A

value: Female


title: wt-input-rep2-Clr4

description: input


title: ago1-input-rep2-Clr4

description: input


title: uninj-5hpf-1

description: 50% epi stage


title: ago1-RI-C11-input-rep3-reintro

description: input


title: dc-hiOL_06

source_name: dciOL 4L6


title: dc-hiOL_05

source_name: dciOL FW


title: dc-hiOL_04

source_name: dciOL ME


title: ago1-input-rep3-Clr4

description: input


title: dc-hiOL_03

source_name: dciOL GM41


title: wt-input-rep3-Clr4

description: input


title: ago1clr4-input-rep3-Clr4

description: input


title: dc-hiOL_02

source_name: dciOL GM80


title: ago1-RI-C11-Clr4_ChIP-rep3-reintro


title: WM_15

description: CNS white matter

label: Cy3, Cy5

tag: age

value: old

value: non-neoplastic brain tissue


title: dc-hiOL_01

source_name: dciOL 010


title: ago1clr4-input-rep2-Clr4

description: input


title: ago1-RI-C3-Clr4_ChIP-rep3-reintro


title: dc-hiOL_07

source_name: dciOL G3G


title: WM_13

description: CNS white matter

value: adult


title: ago1-Clr4_ChIP-rep3-Clr4


title: ago1-RI-C4-input-rep3-reintro

description: input


title: WM_14

description: CNS white matter


title: Uninj-1

description: 50% epi stage


title: ago1clr4-Clr4_ChIP-rep3-Clr4


title: WM_12

description: CNS white matter


title: WM_11

description: CNS white matter

value: young


title: wt-Clr4_ChIP-rep3-Clr4


title: ago1-RI-C4-Clr4_ChIP-rep1-reintro


title: ago1-RI-C3-input-rep3-reintro

description: input


title: shPLK1 A375 cells, biological rep1

value: melanoma cell line

tag: cell line


title: clr4D-ChIP-rep1

value: cells

value: H3K9me2 antibody (ab1220)


title: WM_10

description: CNS white matter


title: WM_09

description: CNS white matter


title: ago1-RI-C3-Clr4_ChIP-rep1-reintro

value: Clr4 reintroduction


title: ago1-RI-C4-Clr4_ChIP-rep3-reintro


title: WM_07

description: CNS white matter


title: wt-Clr4_ChIP-rep1-Clr4


title: WM_06

description: CNS white matter


title: WM_05

description: CNS white matter


title: WM_04

description: CNS white matter


title: ago1-C1-input-rep5-Ec230

description: input

value: Ectopic lnc230 insertion


title: ago1-C2-input-rep5-Ec230

description: input


title: wt-input-rep5-Ec230

description: input


title: WM_01

description: CNS white matter


title: clr4-input-rep5-Ec230

description: input


title: WM_02

description: CNS white matter


title: ago1-C1-input-rep3-Ec230

description: input


title: PA_50

city: Hamburg

first: Helena

last: Bode

address: Martinistrasse 52

institute: Research Institute Children‘s Cancer Center Hamburg

description:
206238130099_R08C01
Sample 70

hyb_protocol: 100-500 ng DNA were used for bisulfite conversion with the EZ DNA Methylation Kit (Zymo Research). Afterwards, the DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were used to clean and restore the converted DNA.

data_processing:
R (v4.1.1)
Normalized Beta using "preprocessedNoob" from the minfi package.
File signals.txt (unmethylated and methylated signal intensities) is linked to the Series record.
File Normalized_Beta.txt is linked to the Series record.

label: Cy5 and Cy3

source_name: supratentorial

extract_protocol: DNA was isolated from FFPE tissue using the ReliaPrep™ FFPE gDNA Miniprep System (Promega) according to manufacturer’s instructions.

value: PA (supratentorial)

tag: material

value: FFPE

tag: array type

value: epic

value: female

tag: brain tumor classifier result (v12.5)

tag: mapk-pathway alteration

value: BRAF/KIAA1549 Fusion

tag: initial histological diagnosis

value: Pilocytic Astrocytoma


title: PA_30

description:
206486310150_R03C01
Sample 71

tag: Sex

value: unknown


title: ago1-C2-input-rep3-Ec230

description: input

tag: antibody


title: PA_22

description:
206238130093_R08C01
Sample 69

source_name: infratentorial

value: PA (infratentorial)

value: male


title: wt-input-rep3-Ec230

description: input

tag: genotype

value: wt


title: PA_23

description:
206238130093_R07C01
Sample 68

value: PXA

value: BRAF V600E


title: WM_08

description: CNS white matter

value: Female

value: adult

value: non-neoplastic brain tissue


title: ago1-Clr4_ChIP-rep1-Clr4

value: cells


title: clr4-input-rep3-Ec230

description: input

tag: treatment

value: Ectopic lnc230 insertion


title: PA_40

description:
206238130093_R06C01
Sample 67

tag: tissue

value: PA (supratentorial)

value: no match


title: ago1-C2-input-rep2-Ec230

description: input


title: ago1-C1-input-rep2-Ec230

description: input


title: PA_28

description:
206238130093_R05C01
Sample 66

source_name: not available

value: PA (not available)

value: FFPE

value: epic


title: clr4-input-rep2-Ec230

description: input


title: wt-input-rep2-Ec230

description: input


title: ago1clr4-Clr4_ChIP-rep1-Clr4


title: PA_31

description:
206238130093_R04C01
Sample 65

value: BRAF/KIAA1549 Fusion

value: Pilocytic Astrocytoma


title: PA_42

description:
206238130093_R03C01
Sample 64

value: PA (infratentorial)

value: female


title: ago1-C1-input-rep1-Ec230

description: input


title: wt-input-rep1-Ec230

description: input

value: wt


title: PA_62

description:
206238130093_R02C01
Sample 63

value: None of the above


title: PA_3

description:
206238130093_R01C01
Sample 62

value: male


title: clr4-input-rep1-Ec230

description: input


title: sir2∆ clr3∆ alp13∆FLAG-Clr4 -Input-rep3

value: sir2D clr3D alp13DFLAG-Clr4


title: organoids, APK, shUsp10-2, rep1

data_processing:
Illumina’s FASTQ Generation software v1.0.0
Sequenced reads were mapped to mm10 using bowtie2 v2.4.1
reads were count using featureCounts package in R
counts were normalised using edgeR package in R
Assembly: mm10
Supplementary files format and content: .txt file with normalised counts for shNTC and shUsp10-1
Supplementary files format and content: .txt file with normalised counts for shNTC and shUsp10-2

source_name: small intestine

extract_protocol:
ReliaPrepTM RNA Cell miniprep System Promega Kit
NEBNext Poly(A) mRNA Magnetic Isolation Module; NEBNext Ultra II Directional RNA Library Prep Kit for Illumina; SPRI select reagent; NEBNext Multiplex Oligos for Illumina (Dual Index Set 1)

value: small intestine

tag: cell type

value: Cas9 mouse, genetically modified to Apc:Trp53:KRasG12D


title: PA_26

description:
206238130091_R01C01
Sample 61


title: sir2∆ clr3∆ ago1∆FLAG-Clr4 -Input-rep3

value: cells

value: sir2D clr3D ago1DFLAG-Clr4


title: PA_52

description:
206238130054_R08C01
Sample 60


title: alp13∆FLAG-Clr4 -Input-rep3


title: PA_8

description:
206036790129_R03C01
Sample 59

value: PA (supratentorial)


title: PA_27

description:
206036790129_R02C01
Sample 58

value: RGNT


title: PA_25

description:
206036790129_R01C01
Sample 57

value: no match


title: sir2∆ clr3∆ alp13∆FLAG-Clr4 -Input-rep2


title: PA_15

description:
205762850100_R08C01
Sample 56

value: FFPE


title: sir2∆ clr3∆ ago1∆FLAG-Clr4 -Input-rep2


title: PA_58

description:
205762850100_R07C01
Sample 55

value: epic


title: clr3∆ ago1∆FLAG-Clr4 -Input-rep2

value: clr3D ago1DFLAG-Clr4


title: clr3∆ ago1∆FLAG-Clr4 -Input-rep3


title: alp13∆FLAG-Clr4 -Input-rep2


title: PA_29

description:
205762850100_R06C01
Sample 54

source_name: spinal

value: PA (spinal)

value: BRAF/KIAA1549 Fusion

value: Pilocytic Astrocytoma


title: PA_69

description:
205756380099_R03C01
Sample 53

value: female


title: WT-ChIP-rep1

value: WT

value: H3K9me2 antibody (ab1220)


title: PA_64

description:
205756370079_R01C01
Sample 52

value: HGAP


title: PA_32

description:
205751530097_R08C01
Sample 51

value: PA (infratentorial)


title: WT FLAG-Clr4 ago1∆-C2-Input-rep2

value: WT FLAG-Clr4 ago1D-C2


title: WT FLAG-Clr4-C2-Input-rep2

value: cells

value: WT FLAG-Clr4-C2


title: sir2∆ ago1∆FLAG-Clr4 -Input-rep2

value: sir2D ago1DFLAG-Clr4


title: PA_66

description:
205751530097_R07C01
Sample 50

value: male


title: PA_14

description:
205751530097_R06C01
Sample 49


title: WT FLAG-Clr4 ago1∆-C2-Input-rep3


title: PA_78

description:
205751530097_R05C01
Sample 48

value: no match


title: WT FLAG-Clr4-C2-Input-rep3


title: PA_47

description:
205751530097_R04C01
Sample 47

value: FFPE

value: BRAF V600E


title: untagged-C2-Input-rep3


title: untagged-C2-Input-rep2


title: sir2∆ clr3∆ alp13∆FLAG-Clr4 -Input-rep1

value: sir2D clr3D alp13DFLAG-Clr4


title: sir2∆ ago1∆FLAG-Clr4 -Input-rep3


title: PA_21

description:
205735130176_R05C01
Sample 46

value: epic


title: alp13∆FLAG-Clr4 -Input-rep1


title: PA_71

description:
205735130115_R03C01
Sample 45

value: PA (supratentorial)

value: BRAF/KIAA1549 Fusion


title: PA_67

description:
205689110159_R03C01
Sample 43

value: Pilocytic Astrocytoma


title: PA_34

description:
205735130115_R02C01
Sample 44


title: sir2∆ clr3∆ ago1∆FLAG-Clr4 -Input-rep1

value: sir2D clr3D ago1DFLAG-Clr4


title: clr3∆ ago1∆FLAG-Clr4 -Input-rep1

value: clr3D ago1DFLAG-Clr4


title: sir2∆ ago1∆FLAG-Clr4 -Input-rep1


title: PA_2

description:
205689110158_R03C01
Sample 41

value: female


title: WM_03

description: CNS white matter

value: Male

value: old

value: non-neoplastic brain tissue


title: WT FLAG-Clr4 ago1∆-C2-Input-rep1

value: cells

value: WT FLAG-Clr4 ago1D-C2


title: PA_41

description:
205689110152_R05C01
Sample 40

value: male

value: unknown


title: WT FLAG-Clr4-C2-Input-rep1

value: WT FLAG-Clr4-C2


title: PA_16

description:
205537620146_R07C01
Sample 38

value: PA (infratentorial)

value: FFPE

value: no match


title: PA_60

description:
205624890169_R07C01
Sample 39

value: PA (supratentorial)

value: epic


title: untagged-C2-Input-rep1


title: sir2∆ clr3∆ alp13∆FLAG-Clr4 -ChIP-rep3

value: sir2D clr3D alp13DFLAG-Clr4


title: alp13∆FLAG-Clr4 -ChIP-rep3


title: sir2∆ clr3∆ ago1∆FLAG-Clr4 -ChIP-rep3

value: sir2D clr3D ago1DFLAG-Clr4


title: PA_19

description:
205061430109_R03C01
Sample 35

value: Pilocytic Astrocytoma


title: PA_33

description:
204949780005_R08C01
Sample 34


title: clr3∆ ago1∆FLAG-Clr4 -ChIP-rep3

value: clr3D ago1DFLAG-Clr4


title: PA_49

description:
204894630041_R02C01
Sample 33

value: PA (not available)

value: female


title: WT FLAG-Clr4 ago1∆-C2-ChIP-rep3


title: PA_44

description:
205689110159_R02C01
Sample 42


title: PA_72

description:
204361730158_R07C01
Sample 29

value: BRAF V600E


title: untagged-C2-ChIP-rep3

value: cells


title: PA_59

description:
204361730158_R08C01
Sample 30


title: PA_4

description:
204808700061_R01C01
Sample 31


title: WT FLAG-Clr4-C2-ChIP-rep3


title: sir2∆ clr3∆ alp13∆FLAG-Clr4 -ChIP-rep2


title: alp13∆FLAG-Clr4 -ChIP-rep2


title: clr3∆ ago1∆FLAG-Clr4 -ChIP-rep2


title: PA_7

description:
204361730157_R06C01
Sample 26


title: sir2∆ clr3∆ ago1∆FLAG-Clr4 -ChIP-rep2


title: PA_48

description:
205537620122_R03C01
Sample 37


title: PA_18

description:
204361720098_R08C01
Sample 24


title: sir2∆ ago1∆FLAG-Clr4 -ChIP-rep2

value: sir2D ago1DFLAG-Clr4


title: PA_55

description:
204361730157_R08C01
Sample 28

value: PA (spinal)


title: WT FLAG-Clr4 ago1∆-C2-ChIP-rep2

value: WT FLAG-Clr4 ago1D-C2


title: WT FLAG-Clr4-C2-ChIP-rep2

value: WT FLAG-Clr4-C2


title: PA_53

description:
204361730145_R08C01
Sample 25

value: male


title: untagged-C2-ChIP-rep2


title: PA_17

description:
204316970071_R02C01
Sample 22

value: FFPE

value: unknown


title: PA_35

description:
204894630018_R02C01
Sample 32

value: PA (supratentorial)

value: no match


title: sir2∆ clr3∆ alp13∆FLAG-Clr4 -ChIP-rep1

value: sir2D clr3D alp13DFLAG-Clr4


title: PA_43

description:
204294120068_R07C01
Sample 21

value: PA (infratentorial)

value: epic

value: BRAF/KIAA1549 Fusion


title: PA_76

description:
204294120068_R06C01
Sample 20

value: Pilocytic Astrocytoma


title: alp13∆FLAG-Clr4 -ChIP-rep1


title: sir2∆ clr3∆ ago1∆FLAG-Clr4 -ChIP-rep1

value: sir2D clr3D ago1DFLAG-Clr4


title: PA_68

description:
204361730157_R07C01
Sample 27


title: PA_63

description:
204294120068_R01C01
Sample 18

value: RGNT


title: clr3∆ ago1∆FLAG-Clr4 -ChIP-rep1

value: cells

value: clr3D ago1DFLAG-Clr4


title: PA_38

description:
204294120068_R05C01
Sample 19

value: female


title: sir2∆ ago1∆FLAG-Clr4 -ChIP-rep1

value: sir2D ago1DFLAG-Clr4


title: WT FLAG-Clr4 ago1∆-C2-ChIP-rep1

value: WT FLAG-Clr4 ago1D-C2


title: PA_46

description:
204234160044_R07C01
Sample 16

value: PA (spinal)

value: male


title: PA_37

description:
204234160044_R08C01
Sample 17

value: FFPE


title: sir2∆ ago1∆FLAG-Clr4 -ChIP-rep3


title: WT FLAG-Clr4-C2-ChIP-rep1

value: WT FLAG-Clr4-C2


title: untagged-C2-ChIP-rep1


title: FLAG-Clr4 in K9R ago1∆-ChIP-rep3

value: FLAG-Clr4 in K9R ago1D


title: PA_20

description:
205537620122_R01C01
Sample 36

value: PA (supratentorial)


title: WT FLAG-Clr4 ago1∆-ChIP-rep3

value: WT FLAG-Clr4 ago1D


title: PA_57

description:
204229190153_R01C01
Sample 14

value: epic

value: no match

value: unknown


title: PA_65

description:
204234160044_R06C01
Sample 15

value: Pilocytic Astrocytoma


title: FLAG-Clr4 in K9R-ChIP-rep3

value: FLAG-Clr4 in K9R


title: PA_77

description:
204229190151_R07C01
Sample 13


title: PA_39

description:
204316970076_R05C01
Sample 23

value: PA (infratentorial)

value: RGNT


title: PA_79

description:
204229190151_R05C01
Sample 11

value: female

value: BRAF/KIAA1549 Fusion


title: PA_61

description:
204229190151_R06C01
Sample 12

value: None of the above


title: PA_54

description:
204229190151_R04C01
Sample 10


title: untagged-ChIP-rep3

value: cells

value: untagged


title: WT FLAG-Clr4-ChIP-rep3

value: WT FLAG-Clr4


title: PA_75

description:
204086170050_R04C01
Sample 9

value: FFPE

value: male


title: FLAG-Clr4 in K9R ago1∆-Input-rep3

value: FLAG-Clr4 in K9R ago1D


title: PA_73

description:
203537580055_R05C01
Sample 8

value: PA (supratentorial)


title: PA_1

description:
203189480075_R04C01
Sample 7

value: epic


title: WT FLAG-Clr4-Input-rep3


title: FLAG-Clr4 in K9R-Input-rep3


title: PA_74

description:
203049640097_R04C01
Sample 6

value: PA (N.Opticus)


title: PA_51

description:
202775690045_R01C01
Sample 5

value: no match

value: unknown


title: untagged-Input-rep3


title: PA_13

description:
202274990137_R06C01
Sample 3

value: Pilocytic Astrocytoma


title: FLAG-Clr4 in K9R ago1∆-ChIP-rep2


title: WT FLAG-Clr4 ago1∆-ChIP-rep2

value: WT FLAG-Clr4 ago1D


title: PA_36

description:
202163550013_R06C01
Sample 1

value: PA (spinal)


title: FLAG-Clr4 in K9R-ChIP-rep2

value: FLAG-Clr4 in K9R


title: WT FLAG-Clr4-ChIP-rep2


title: untagged-ChIP-rep2


title: WT FLAG-Clr4 ago1∆-Input-rep2


title: FLAG-Clr4 in K9R ago1∆-Input-rep2


title: WT FLAG-Clr4-Input-rep2


title: WT FLAG-Clr4 ago1∆-Input-rep3


title: FLAG-Clr4 in K9R-Input-rep2


title: NGT-131

city: Cairo

first: Shahenda

last: El-Naggar

address: 1 Sekket El Emam, El Madbah El Kadeem Yard, Sayeda Zeinab

department: Research Department

country: Egypt

institute: Children’s Cancer Hospital Egypt 57357

hyb_protocol: Sodium bisulfite-converted genomic DNA samples were hybridized to the Illumina Infinium Human Methylation 850K EPIC Bead Chips array.

scan_protocol: EPIC BeadChip array were scanned using the Illumina iScan microarray scanner according to the manufacturer’s recommendations

data_processing:
IDAT files were processed using minfi R package. Samples quality control steps included; sample swap and detection of p-value. Samples with p-value > 0.01 (n=2) were excluded from further analysis. Normalization was performed using Functional normalization (FunNorm). Beta and M values were then extracted.
Average beta values

source_name: Pediatric Choroid plexus Tumors

label_protocol: standard

extract_protocol: Genomic DNA was extracted from the mammalian cell lines using the Gene JET genomic DNA (Thermo Fisher) according to the manufacturer’s instructions.

value: Male

value: Tumor cell line


title: CCHE-45


title: PA_45

description:
202711530016_R05C01
Sample 4

value: female

value: HGAP


title: FLAG-Clr4 in K9R ago1∆-ChIP-rep1

value: cells


title: PA_56

description:
202242420148_R03C01
Sample 2

value: FFPE


title: p53-uninj-1

description: 50% epi stage

source_name: whole embryo

value: whole embryo

tag: time

value: 6 hpf

value: uninjected


title: untagged-ChIP-rep1

source_name: cells

value: untagged


title: WT FLAG-Clr4-ChIP-rep1

value: WT FLAG-Clr4


title: FLAG-Clr4 in K9R ago1∆-Input-rep1

value: FLAG-Clr4 in K9R ago1D


title: WT FLAG-Clr4 ago1∆-Input-rep1


title: untagged-Input-rep2


title: FLAG-Clr4 in K9R-Input-rep1


title: WT FLAG-Clr4-Input-rep1


title: WT FLAG-Clr4 ago1∆-ChIP-rep1


title: Sir2-FLAG-HUR120-ChIP-rep2


title: FLAG-Clr4 in K9R-ChIP-rep1


title: Sir2-FLAG-HUR140-ChIP-rep2


title: Sir2-FLAG-HUR100-ChIP-rep2


title: Sir2-FLAG-HUR80-ChIP-rep2


title: untagged-Input-rep1


title: Sir2-FLAG-HUR40-ChIP-rep2


title: Sir2-FLAG-HUR20-ChIP-rep2


title: right hippocampus, corticosterone, biological replicate 1 KO

city: Melbourne

first: Maria

last: Kuznetsova

state: Victoria

address: 30 Royal parade

department: Florey Institute

country: Australia

institute: University of Melbourne

data_processing:
Primers were trimmed from the reads using Cutadapt v2.3.
mirnaQC was used to check the quality of the reads. Reads between 18 and 40 nucleotides were retained for the subsequent analysis.
All reads were aligned to the GRCm38/mm10 mouse genome using Burrows–Wheeler Alignment (BWA) tool.
https//github.com/mariku01/miRNA_data_analysis_script_2023/tree/5c76f898779855dcb0e229d4d86fe46e30353e34.
The reads were then mapped to the miRNA database to perform feature counting using subread featureCounts[26]. miRNAs were only considered for the subsequent analysis if they had a minimum abundance of 20 CPM and were present in at least half of the samples.
Normalization and differential gene expression analysis on the miRNA count data was performed using limma-voom software package v. 3.54.1. The significance threshold for FDR-adjusted p value was set at < 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimites text file includes raw counts for each sample

source_name: right hippocampus

extract_protocol:
Frozen samples of hippocampus were homogenised in QIAzol lysis buffer (QIAGEN, Clayton, VIC, Australia). Total RNA was isolated according to the manufacturer’s instructions and eluted in RNase-free water (QIAGEN). The concentration and quality of small RNA and total RNA were determined using the small RNA and RNA6000 assay and run on the Agilent Bioanalyser (Agilent Technologies, Santa Clara, CA, USA).
Total RNA of 3 ug per sample was enriched for small RNA and ligated to sequencing adapters to construct small RNA libraries using the Ion Total RNA-Seq Kit V2 (Life Technologies, Australia) according to the manufacturers’ protocol and as previously published (14). Libraries also contained a unique index barcode (Ion Xpress™ RNA-Seq Barcode 1-16 Kit, Life Technologies, Australia). The yield and size distribution of the small RNA libraries were assessed using the Agilent 2100 Bioanalyzer™ instrument with the High sensitivity DNA chip (Agilent Technologies). Equally pooled libraries were prepared for deep sequencing using the Ion Chef system (Life Technologies) and sequenced on the Ion Torrent S5™ using Ion™ 540 chips (Life Technologies) and 200bp chemistry (Life Technologies).

value: right hippocampus

value: 5-HTT KO

tag: strain

value: C57Bl/6 J

value: corticosterone

tag: biological replicate

value: biological replicate 1


title: Sir2-FLAG-HUR50-ChIP-rep2


title: right hippocampus, exercise, biological replicate 4 KO

value: exercise

value: biological replicate 4


title: Sir2-FLAG-HUR60-ChIP-rep2


title: right hippocampus, exercise, biological replicate 5 WT

value: wildtype

value: biological replicate 5


title: Sir2-FLAG-HU Sync-ChIP-rep2

value: cells

value: HU Sync


title: right hippocampus, water, biological replicate 7 WT

value: water

value: biological replicate 7


title: Sir2-FLAG-HUR120-Input-rep2


title: Sir2-FLAG-HUR140-Input-rep2


title: right hippocampus, exercise, biological replicate 5 KO


title: Sir2-FLAG-HUR100-Input-rep2


title: Sir2-FLAG-Unsync-ChIP-rep2

value: Unsync


title: right hippocampus, exercise, biological replicate 4 WT


title: right hippocampus, water, biological replicate 6 KO

value: biological replicate 6


title: Sir2-FLAG-HUR80-Input-rep2


title: right hippocampus, water, biological replicate 5 KO


title: Sir2-FLAG-HUR50-Input-rep2


title: Sir2-FLAG-HUR60-Input-rep2


title: right hippocampus, water, biological replicate 6 WT


title: right hippocampus, corticosterone, biological replicate 6 WT


title: right hippocampus, corticosterone, biological replicate 2 KO

value: biological replicate 2


title: Sir2-FLAG-HU Sync-Input-rep2


title: Sir2-FLAG-Unsync-Input-rep2


title: right hippocampus, exercise, biological replicate 2 WT


title: WT-HUR140-ChIP-rep2

value: WT


title: HumanMethylation 450 Epic Array OVCAR5 NTX301_100nM_2

city: Chicago

first: Daniela

last: Matei

address: 420 E. Superior St.

institute: Northwestern University Feinberg School of Medicine

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

label: Cy3 and Cy5

label_protocol: standard Illumina protocol

growth_protocol: OVCAR5 were maintained in RPMI-1640 with L-glutamine (Corning, Cat# 10-040-CV) plus 10% FBS, 1% GlutaMAX, and 1% penicillin-streptomycin.

extract_protocol: For HumanMethylation 450 Epic Array, genomic DNA were extracted using QIAmp DNA Mini Kit.

treatment_protocol: OVCAR5 cells were treated with DMSO, NTX301 (10nM, 100nM) for 3 days.


title: right hippocampus, corticosterone, biological replicate 2 WT

value: right hippocampus


title: WT-HUR120-ChIP-rep2

data_processing:
Mapping by BWA
BW generated by DeepTools
Assembly: S pombe
Supplementary files format and content: BW

extract_protocol:
H3K9me2 ChIP
NEB Ultra II Library Prep Kit for Illumina


title: right hippocampus, exercise, biological replicate 1 WT


title: WT-HUR100-ChIP-rep2


title: Sir2-FLAG-HUR40-Input-rep2


title: HumanMethylation 450 Epic Array OVCAR5 DMSO_3

value: DMSO


title: right hippocampus, water, biological replicate 1 KO

value: 5-HTT KO

value: C57Bl/6 J


title: HumanMethylation 450 Epic Array OVCAR5 NTX301_100nM_3


title: right hippocampus, corticosterone, biological replicate 1 WT

value: corticosterone

value: biological replicate 1


title: right hippocampus, water, biological replicate 2 KO


title: HumanMethylation 450 Epic Array OVCAR5 DMSO_2


title: HumanMethylation 450 Epic Array OVCAR5 NTX301_100nM_1


title: right hippocampus, water, biological replicate 4 KO

value: biological replicate 4


title: genomic DNA from polyp patient 2

city: Harbin

first: Xishan

last: Wang

address: Xue Fu Road 246

institute: The Second Affiliated Hospital of Harbin Medical University

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

data_processing: BeadStudio

source_name: polyp 2

label_protocol: Standar Illumina protocol

extract_protocol: genomic DNA was extracted and purified from tissue samples using QIAamp DNA Blood and Tissue Kit according to standard instructions

treatment_protocol: Standard Illumina Protocol

tag: gender

value: Male

tag: disease state

value: polyp

value: colorectal polyp sample