title: 2i-GFPplus-combined-A

city: London

first: Gabriella

last: Ficz

state: Rest of the World

address: Centre for Haemato-Oncology

institute: Barts Cancer Institute, Queen Mary University of London

description: targeted DNA-seq to amplify shRNA sequence

data_processing:
Library strategy: shRNA screen
Alignment of sequencing data was performed using Bowtie2 under standard alignment parameters.
The count table was then imported into R and differential representation analysis was performed using the package EdgeR and using the exactTest function
Supplementary_files_format_and_content: Excel file containing the count table containing the representation, as counts, for each sequenced shRNA species in each sample and replicate. Primer sequences included in the file SupplementaryTable1.docx available on the series record.

source_name: mouse embryonic stem cells

growth_protocol: E14 ESCs in the Serum/LIF state were cultured without feeders in serum containing media (DMEM 4500 mg/l glucose, 4 mM L-glutamine, 110 mg/l sodium pyruvate, 15% fetal bovine serum, 1 U/ml penicillin, 1 μg/ml streptomycin, 0.1 mM nonessential amino acids, 50 μM β-mercaptoethanol and 103 U/ml ESGRO LIF). E14 ESCs in the 2i state were cultured in the 2i media containing serum-free N2B27 – [DMEM/F12, Neurobasal, N2,B27], 103 U/ml ESGRO LIF, PD0325901 [1 μm] and CHIR99021 [3 μM].

extract_protocol:
DNA was extracted using the DNeasy blood and tissue kit (Qiagen) using the standard procedure described in the handbook
For PCR amplification of the library 2 μg of DNA for each sample was used, with the DNA split into four 500 ng reactions. A one-step PCR approach was used with P5 and P7 primers. The P5 and P7 primer were comprised of the P5/P7 flow-cell attachment sequence, the Illumina sequencing primer and the vector binding sequence (primer sequence in shown in Supplementary Table 1.). In addition, to avoid the issue of reduced sequence diversity faced by amplicon libraries, PCR was performed with a mix of P5 primers containing a stagger region of different length.

treatment_protocol: Serum/LIF mESCs were transduced with the TRC lentiviral mouse kinase shRNA library

tag: culture method

value: 2i/LIF cultured

value: E14 UHRF1-GFP

tag: fluorescence sorting

value: GFP positive population


title: synovial tisssue, Inflamed1 (lncRNA)

status: Public on Nov 18 2022

type: SRA

city: Wuhan

first: Xiling

last: Xiao

state: Hubei

address: No.1277, Jiefang Avenue

department: Department of Rehabilitation

country: China

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

library_source: transcriptomic

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) [1] by (1) Removing reads containing sequencing adapter;
Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%;
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4) [2]. After that, Ericscript (v0.5.5) [3]and rMATS (V3.2.5)[4] were used to detect fusion genes and differential splicing genes (DSGs), respectively.
Bowtie2 (v2.2.5) [5]was applied to align the clean reads to the gene set, a database built by BGI (Beijing Genomic Institute in ShenZhen), in which known and novel, coding and noncoding transcripts were included,then expression level of gene was calculated by RSEM (v1.2.12) [6].
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text files include RPKM, FPKM, TPM, read_count values for miRNAs, lncRNAs, and mRNAs

molecule: total RNA

organism: Homo sapiens

source_name: Synovial tissue

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manual instructions.. 1 ug of total RNA was used for the construction of sequencing libraries.
1.According to the manufacturer’s instructions,using target-specific oligos and RNase H maded ncRNA-Seq Library。
2.Total RNA was purified by electrophoretic separation on a 15% urea denaturing polyacrylamide gel electrophoresis (PAGE) gel and small RNA regions corresponding to the 18–30 nt bands in the marker lane (14-30 ssRNA Ladder Marker, TAKARA) were excised and recovered. Then the 18–30 nt small RNAs were ligated to a 5′-adaptor and a 3′-adaptor. The adapter-ligated small RNAs were subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen, USA) and then several rounds of PCR amplification with PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments. The PCR products were selected by agarose gel electrophoresis with target fragments 100~120 bp, and then purified by QIAquick Gel Extraction Kit (QIAGEN, Valencia, CA). The library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe).

tag: tissue

value: Synovial tissue

tag: phenotype

value: Inflamed


title: 2i-GFPplus-combined-C

country: United Kingdom

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: strain


title: 2i-GFPplus-combined-B


title: F14_M_RNA

city: Grand Rapids

first: Ronald

middle: L

last: Chandler

state: Michigan

address: 400 Monroe Ave NW

country: USA

institute: Michigan State University

data_processing:
Raw reads were trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned mm10 genome assembly, indexed to GENCODE (vM16) GFF3 annotation with flag ‘--sjdbOverhang 49’ equivalent to (read length – 1), via STAR aligner with flag ‘--quantMode GeneCounts’ for feature counting.
STAR sample gene counts were concatenated for unstranded (libtype), corresponding to column 2 of STAR output ReadsPerGene.out.tab file.
Low count genes were filtered prior to DESeq2 count normalization (at least 1 count per sample on average). Calculated differential-expression probabilities were corrected for multiple testing by independent hypothesis weighting (IHW) for downstream analysis.
Assembly: mm10 indexed to GENCODE (vM16) GFF3 annotation
Supplementary files format and content: Tabular text files including gene counts (STAR output) for each sample.

source_name: Uterus

growth_protocol: 8 week old mice were placed on high-fat diet or control diet for 18 weeks. Uteri were collected after 18 weeks on diet (26 weeks of age).

extract_protocol:
Uteri were digested using Multi Tissue Dissociation Kit II (Miltenyi Biotec) and filtered using 40 micron mesh filters.Macrophages were magnetically sorted using anti-F4/80 microbeads. Endometrial epithelial cells were magnetically sorted using EpCAM-PE and anti-PE microbeads. Stroma cells were collected following removal of macrophages and epithelia. RNA was collected using the Arcturus PicoPure RNA Isolation Kit (ThermoFisher).
Total RNA material was converted to dsDNA using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, v. 091817 (Takara Bio USA). The Nextera DNA flex library prep kit (Illumina) was used to generate Illumina compatible sequencing libraries.

value: Uterus

tag: cell type

value: Macrophage

tag: genotype

value: wild-type

tag: treatment

value: High-fat diet


title: 2i-GFPminus-combined-C

value: GFP negative population


title: 2i-GFPminus-combined-B


title: synovial tisssue, Control3 (lncRNA)

value: Control


title: synovial tisssue, Control2 (lncRNA)


title: F13_M_RNA


title: 2i-GFPminus-combined-A


title: ApoYap ctrl 1

city: Leuven

first: Georg

last: Halder

address: Herestraat 49

department: VIB-KU Leuven Center for Cancer Biology

country: Belgium

institute: VIB-KU Leuven

data_processing:
Quality control and trimming of the sequencing reads was performed using FastQC and Cutadapt (-q 15 --minmum-length 60, -a AGATCGGAAGAG)
Trimmed sequence reads were mapped to mm10 using STAR v2.6.1d (with default mapping parameters).
Reads were counted with STAR --quantMode GeneCounts
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: Liver

extract_protocol:
Mice were anesthetized by intraperitoneal injection of sodium pentobarbital (Nembutal, 50mg/kg). Livers were perfused for 5min with 40ml of perfusion medium SC-1 to remove the blood and for rapid destruction of intercellular junctions, followed by perfusion with 40ml of SC-2 medium containing 10mg collagenase for 5min to break up the supporting extracellular matrix. Each lobe was dissected off, and the tissue was disrupted inside of a beaker containing 50ml of SC-2 with 20mg collagenase (Roche) and 1ml DNase I (Sigma) followed by rotating incubation for 20min at 37°C. Cells were then filtered through a 100μm strainer and centrifuged at 50g for 2min at room temperature. Hepatocytes were washed once with 1X PBS and centrifuged again at 50g for 2min. Pellet was resuspend with 2ml of 1X PBS containing 0.04% BSA, filtered through a 70µm strainer and FACS sorted. 500,000 sorted cells were collected and lysed for RNA extraction.
RNA was extracted immediately using the RNAeasy mini spin kit (Qiagen) and stored at -80°C.
Library preparation was performed according to the QuantSeq 3’ mRNA-Seq Library Prep kit FWD (Lexogen).

value: Liver

value: Hepatocyte

value: ApoE-rtTA, TRE-hYAP

tag: effective genotype

value: WT

tag: group

value: ApoYap ctrl


title: SerumLIFDay7combined-C

value: Serum/LIF cultured

value: unsorted population


title: WT1

city: DALLAS

last: Yan

state: TEXAS

address: 6000 Harry Hines Blvd

institute: UT Southwestern Medical Center

data_processing:
Raw sequencing data was processed with Astrocyte RNASeq Analysis Workflows at UT Southwestern Bioinformatics Core Facility (https://astrocyte.biohpc.swmed.edu/workflow/12/version/324/docs) to generate Fragments Per Kilobase Million (FPKM) for each transcript.
Genome_build: mouse GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM and TPM values for each Sample

source_name: epidermis

extract_protocol:
RNeasy Mini Kit (QIAGEN, 74104)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: epidermis

value: Skiv2l ctl

tag: developmental stage


title: SerumLIFDay7combined-B

value: E14 UHRF1-GFP


title: SerumLIFDay7combined-A


title: synovial tisssue, Control1 (lncRNA)

value: Synovial tissue


title: F12_M_RNA

value: Uterus


title: SerumLIFDay0combined-C


title: C14_M_RNA

value: Macrophage

value: Control diet


title: SerumLIFDay0combined-B


title: synovial tisssue, Inflamed3 (miRNA)

value: Inflamed


title: synovial tisssue, Inflamed2 (miRNA)


title: F15_M_RNA

value: wild-type

value: High-fat diet


title: KPC_ChIPseq_FoxA1_Exp3

city: San Diego

first: Diana

middle: C.

last: Hargreaves

state: CA

address: 10010 North Torrey Pines Road

institute: The Salk Institute for Biological Studies

description: ChIP-seq for FoxA1 in KPf/fC cells

data_processing:
Basecalls performed using RTA (Illumina)
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5) for RNA-seq and ChIP-seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
HOMER (v4.8) (http://homer.salk.edu/homer/) was used to process alignment files to generate ChIP-seq bed files. ChIP-seq peaks for Smarca4 and Arid1a were found by using the findPeaks program in HOMER with the parameter "-style factor" versus the appropriate ChIP input experiments as background. ChIP-seq peaks for H3K4me, H3K4me3, and H3K27ac were called using the parameter "-style histone." For RNA-Seq, Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq). Differentially expressed genes in shSmarcd3 versus shControl were called using the command getDiffExpression.pl, with DESeq2.
Assembly: mm10
Supplementary files format and content: Bedgraph file Columns: (1) chrom (2) chromStart (3) chromEnd (4) data value. DiffExpOutput tab delimited text file Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-12) FPKM for each experiment (13) Log2 fold change (14) p value (15) adjusted p value

source_name: KPf/fC cells

extract_protocol:
For RNA-seq, total RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research). For SWI/SNF subunit ChIP-seq, 6-7e6 cells were collected per condition and cross-linked first in 3mM disuccinimidyl glutarate (DSG) then in 1% formaldehyde. For histone modification ChIP-seq, 2e6 cells were collected per condition and cross-linked with 1% formaldehyde. After quenching the excess formaldehyde with 125 mM glycine, the fixed cells were washed, pelleted and flash-frozen. Upon thawing, the cells were resuspended in lysis solution (50 mM HEPES-KOH pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100 and incubated on ice for ten minutes. The isolated nuclei were washed with wash solution (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl) and shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris-HCl pH 8) then sheared in a Covaris E229 sonicator for 10 minutes to generate DNA fragments between ~ 200-1000 bp. After clarification of insoluble material by centrifugation, the chromatin was immunoprecipitated overnight at 4C with antibodies against Smarca4, Arid1a, H3K4me, H4K4me3 and H3K27ac then bound to Protein A+G Dynabeads (Invitrogen) in ChIP buffer (50 mM HEPES-KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% DOC, 0.1% SDS). Antibody bound DNA were washed and treated with Proteinase K and RNase A and the purified ChIP DNA was used for library generation for subsequent sequencing.
ChIP-Seq libraries were generated using the NuGen Ovation Ultralow Library System V2 following the manufacturer's instructions. RNA-Seq libraries were prepared using Illumina TruSeq RNA Library Prep Kit v2 following the manufacturer's instructions.

tag: short hairpin rna

tag: antibody

value: FoxA1, Abcam ab170933


title: KPC_ChIPseq_Klf5_Exp3

description: ChIP-seq for Klf5 in KPf/fC cells

value: Klf5, Abcam ab24331


title: C13_M_RNA


title: C12_M_RNA


title: synovial tisssue, Inflamed1 (miRNA)


title: synovial tisssue, Control3 (miRNA)

value: Control


title: KPC_ChIPseq_Input_Exp3

description: Input for ChIP-seq for Klf5 or FoxA1 in KPf/fC cells


title: F11_M_RNA


title: synovial tisssue, Control2 (miRNA)


title: C11_M_RNA


title: F17_S_RNA

value: Stroma


title: Mettl3 d/d, replicate 2, gestational day 3

city: Guangzhou

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

data_processing:
Clean reads were mapped to mouse genome (UCSC mm9) by using HISAT v2.2.1
Mapped reads were assembled by using Cufflinks v2.2.1
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample

source_name: whole oviduct

extract_protocol:
TRIzol reagent (Invitrogen) was used to extract total RNAs according to manufacturers’ instructions.
RNA-seq libraries were created by using the TruSeq RNA sample preparation kit (Illumina).

treatment_protocol: Female mice aged 6-8 weeks were mated with fertile males to induce pregnancy. The appearance of the vaginal plug was designated as gestation day (GD) 1. Pregnant females were sacrificed on GD3.

value: whole oviduct

value: d/d

tag: time

value: gestational day 3


title: Mettl3 d/d, replicate 1, gestational day 3


title: Mettl3 d/d, replicate 3, gestational day 3


title: synovial tisssue, Control1 (miRNA)


title: Mettl3 f/f, replicate 1, gestational day 3

value: f/f


title: FuOXP NP

city: Pittsburgh

first: Song

last: Li

state: Pennsylvania

address: 335 Sutherland Drive, Salk Pavilion

institute: University of Pittsburgh

data_processing:
Reads were mapped to the mouse genome (GRCm38) using STAR Aligner 2.6.1a
Gene expression quantification and differential expression analysis between control and FuOXP NPs treatment were performed using Cuffdiff of Cufflinks 2.2.1

source_name: CT26 Tumor

extract_protocol:
RNA-seq was performed by the Health Sciences Sequencing Core at Children’s Hospital of Pittsburgh.
RNA-seq libraries were sequenced as 75-base paired-end reads at a depth of ~73 to 77 million reads per sample.

value: CT26 Tumor

value: WT

value: FuOXP NP


title: F16_S_RNA

value: Uterus


title: SerumLIFDay0combined-A

value: Serum/LIF cultured

value: E14 UHRF1-GFP

value: unsorted population


title: Mettl3 f/f, replicate 3, gestational day 3


title: Empty NP

value: Empty NP


title: WT HPC P0.3

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 South Euclid Ave

institute: Washington University In St Louis

description:
WT HPC P0.3
2663_gene_level_read_counts.txt

data_processing:
The resulting sequencing reads were demultiplexed by index with a custom Python demultiplexing script and further demultiplexed by barcode with a custom Perl demultiplexing script.
The RNA-Seq reads were then aligned to the Mus musculus Ensembl release 76 top-level assembly with STAR version 3.0.4.b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
Sailfish version 0.6.3. was used to produce isoform estimated counts.
Assembly: Ensemble R76
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: hematopoietic progenitor/MPP

extract_protocol:
Qiagen RNAeasy micro plus
Clontech SMRTr

tag: age

value: P0 (birth)

value: wild type


title: lung, mouse with allergic asthma, challenged by OVA for 30 days, biol rep4

city: Weifang

first: Xiao

last: Niu

state: Shandong

address: Baotong str. 7166

institute: Weifang Medicine University

description:
transcript_fpkm_matrix.txt
gene_fpkm_matrix.txt

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Trimmed sequence reads were mapped to mm10 using STAR
After counts are collected, Deseq2 package was used to identify differentially expressed genes
tab-delimited text files which include normalized counts for each sample
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: lung

extract_protocol:
Total RNA was extracted using RNeasy Kits (Qiagen, Duesseldorf, Germany) and treated with DNase I (Life Technologies, Gaithersburg, USA) according to standard protocols.
Sequencing libraries were constructed using the TruSeq Stranded Total RNA kits (Genesky, Shanghai, China)

treatment_protocol: intraperitoneal sensitization of 49-day-old BALB/c mice, intraperitoneal booster injection of 63-day-old  BALB/c mice

value: lung

value: BABL/c mouse

value: ovalbumin aerosol challenge of 70-day-old sensitized mice three times a week for four consecutive weeks


title: Mettl3 f/f, replicate 2, gestational day 3

value: whole oviduct


title: lung, mouse with allergic asthma, challenged by OVA for 30 days, biol rep2


title: WT HPC P0.4

description:
WT HPC P0.4
2663_gene_level_read_counts.txt


title: lung, mouse with allergic asthma, challenged by OVA for 30 days, biol rep3


title: lung, mouse with allergic asthma, challenged by OVA for 30 days, biol rep1


title: F13_S_RNA

value: Stroma

value: wild-type

value: High-fat diet


title: lung, mouse with allergic asthma, challenged by OVA for 3 days, biol rep4

value: ovalbumin aerosol challenge of 70-day-old sensitized mice for 3 consecutive days


title: lung, mouse with allergic asthma, challenged by OVA for 3 days, biol rep3


title: WT HPC P0.1

description:
WT HPC P0.1
2663_gene_level_read_counts.txt


title: F12_S_RNA


title: lung, mouse with allergic asthma, challenged by OVA for 3 days, biol rep2


title: lung, mouse with allergic asthma, challenged by OVA for 3 days, biol rep1


title: NHD13 HPC P0.4

description:
NHD13 HPC P0.4
2663_gene_level_read_counts.txt


title: lung, normal mouse, challenged by Methacholine for 30 days, biol rep4

value: Methacholine aerosol challenge of 70-day-old sensitized mice three times a week for four consecutive weeks


title: NHD13 HPC P0.3

description:
NHD13 HPC P0.3
2663_gene_level_read_counts.txt


title: lung, normal mouse, challenged by Methacholine for 30 days, biol rep2


title: F15_S_RNA


title: F11_S_RNA


title: NHD13 HPC P0.1

description:
NHD13 HPC P0.1
2663_gene_level_read_counts.txt


title: C13_S_RNA

value: Control diet


title: WT HPC P0.2

description:
WT HPC P0.2
2663_gene_level_read_counts.txt


title: lung, normal mouse, challenged by Methacholine for 30 days, biol rep3


title: lung, normal mouse, challenged by Methacholine for 30 days, biol rep1


title: NHD13 HPC P0.2

description:
NHD13 HPC P0.2
2663_gene_level_read_counts.txt


title: F14_S_RNA

value: Uterus


title: lung, normal mouse, challenged by Methacholine for 4 days, biol rep4

value: Methacholine aerosol challenge of 70-day-old sensitized mice for 3 consecutive days


title: lung, normal mouse, challenged by Methacholine for 4 days, biol rep3


title: lung, normal mouse, challenged by PBS for 30 days, biol rep2

value: PBS aerosol challenge of 70-day-old sensitized mice three times a week for four consecutive weeks


title: C11_S_RNA


title: lung, normal mouse, challenged by Methacholine for 4 days, biol rep1


title: F17_E_RNA

value: Epithelia


title: C12_S_RNA


title: lung, normal mouse, challenged by Methacholine for 4 days, biol rep2


title: ITD/NHD13 HPC P0.4

description:
ITD/NHD13 HPC P0.4
2663_gene_level_read_counts.txt


title: lung, normal mouse, challenged by PBS for 30 days, biol rep3


title: ITD/NHD13 HPC P0.3

description:
ITD/NHD13 HPC P0.3
2663_gene_level_read_counts.txt


title: lung, normal mouse, challenged by PBS for 3 days, biol rep3

value: PBS aerosol challenge of 70-day-old sensitized mice for 3 consecutive days


title: ITD/NHD13 HPC P0.2

description:
ITD/NHD13 HPC P0.2
2663_gene_level_read_counts.txt

value: P0 (birth)


title: F16_E_RNA


title: ITD/NHD13 HPC P0.1

description:
ITD/NHD13 HPC P0.1
2663_gene_level_read_counts.txt


title: C14_S_RNA


title: lung, normal mouse, challenged by PBS for 3 days, biol rep2


title: F15_E_RNA


title: lung, normal mouse, challenged by PBS for 3 days, biol rep1


title: ITD HPC P0.4

description:
ITD HPC P0.4
2663_gene_level_read_counts.txt


title: Mettl3 d/d, replicate 3

source_name: whole uterus

treatment_protocol: Female mice aged 6-8 weeks were mated with fertile males to induce pregnancy. The appearance of the vaginal plug was designated as gestation day (GD) 1. Pregnant females were sacrificed on GD4.

value: whole uterus

value: d/d

value: gestational day 4


title: Mettl3 d/d, replicate 2


title: F14_E_RNA


title: ITD HPC P0.3

description:
ITD HPC P0.3
2663_gene_level_read_counts.txt


title: Mettl3 f/f, replicate 3

value: f/f


title: Mettl3 d/d, replicate 1


title: F13_E_RNA


title: Mettl3 f/f, replicate 2


title: ITD HPC P0.2

description:
ITD HPC P0.2
2663_gene_level_read_counts.txt


title: lung, normal mouse, challenged by PBS for 30 days, biol rep1

value: lung

value: BABL/c mouse


title: F12_E_RNA

value: wild-type


title: Mettl3 f/f, replicate 1


title: 2Z

description:
ITD_Runxf_Vav_H3K27ac
itd_runxf_vav_h3k27ac.narrowPeak.gz
itd_runxf_vav_h3k27ac.pooled.fc.signal.bigwig

data_processing:
Sequencing reads were demultiplexed and aligned to mouse genome (mm10) by BWA with the ENCODE DCC TF/Histone ChIP-Seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2, v1.1.6)
Signal strength relative to the control samples were generated using MACS2.
Optimal set of peaks were generated using the ENCODE DCC TF/Histone ChIP-Seq pipeline v1.1.6
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig, narrowPeak

extract_protocol:
HSCs and HPCs were soted and then fixed for chromatin isolation per Schmidl et l., Nature Methods 10:963.
Chipmentation - Chromatin isolation with the indicated antibody followed by tagmentation with Tn5 as per Schmidl et l., Nature Methods 10:963.

value: P21 (21 days old)


title: 2X


title: 2Y


title: ITD HPC P0.1

description:
ITD HPC P0.1
2663_gene_level_read_counts.txt


title: F11_E_RNA

value: High-fat diet


title: wt P14 HPC.4

description:
wt P14 HPC.4
2552_gene_level_read_counts.txt

value: P14 (14 days old)

value: wild type


title: 2U

description:
ITD_Nup98_H3K27ac
itd_nup98_h3k27ac.narrowPeak.gz
itd_nup98_h3k27ac.pooled.fc.signal.bigwig


title: C14_E_RNA

value: Uterus

value: Control diet


title: 2W


title: wt P14 HPC.3

description:
wt P14 HPC.3
2552_gene_level_read_counts.txt


title: 2S


title: C13_E_RNA


title: wt P14 HPC.2

description:
wt P14 HPC.2
2552_gene_level_read_counts.txt


title: 2P

description:
Runxf_Vav_H3K27ac
runxf_vav_h3k27ac.narrowPeak.gz
runxf_vav_h3k27ac.pooled.fc.signal.bigwig


title: C12_E_RNA


title: 2N


title: Runx het P14 HPC.4

description:
Runx het P14 HPC.4
2552_gene_level_read_counts.txt


title: 2M

description:
Nup98_H3K27ac
nup98_h3k27ac.narrowPeak.gz
nup98_h3k27ac.pooled.fc.signal.bigwig


title: 2J


title: 2R


title: F05_E_RNA


title: F04_E_RNA


title: 2F

description:
ITD_H3K27ac
itd_h3k27ac.narrowPeak.gz
itd_h3k27ac.pooled.fc.signal.bigwig


title: 2K


title: F03_E_RNA


title: 2T


title: 2D


title: Runx het P14 HPC.3

description:
Runx het P14 HPC.3
2552_gene_level_read_counts.txt


title: RNA-seq: Caprin1 KO clone 4 8h, rep 1

city: Jerusalem

first: Michal

last: Rabani

address: Hebrew University, Edmond J. Safra Campus, Silberman building

country: Israel

institute: Hebrew University of Jerusalem

description: Caprin1 KO clone 4 8h, rep 1

data_processing:
Degradation assay: Raw data quality control was done using FASTQC (Version 0.11.9).
Degradation assay: Reads were aligned to reference genome (GRCm38/mm10, Dec. 2011) with STAR (Version 2.4.0.1). RIP-Seq: Raw RNA/RIP-seq reads for each condition were mapped to the reference mouse genome using TopHat program.
Degradation assay: Read normalization and differential gene expression analysis with multiple testing corrections were conducted using the R Bioconductor DESeq2 package in R Studio. RIP-Seq: TopHat results were used to run Cufflinks that generates a transcriptome assembly file for each input condition, and combined using Cuffmerge. This merged assembly was the final file used to calculate gene and transcript expression in each sample. The reads and the merged assembly provided to Cuffdiff that calculates differential expression levels as well as tests the statistical significance.
Degradation assay: TPM values were fitted to an exponential decay model (X(t) = X0*exp(-bt); b = degradation rate (1/hr)), and transcripts with minimal degradation rate (b<0.05, corresponding to a half-life of >13.86 hours) in WT cells were selected as a control set for normalization, resulting in a control set of 356 genes (Figure S4). All samples were subsequently normalized based on this control set, to a temporally constant average expression level of this control set. These normalized TPM values were fitted again to an exponential decay model, and the resulting degradation rates for each transcript were used for subsequent analysis.
Genome_build: GRCm38/mm10

source_name: ESCs

growth_protocol: Caprin1 KO and R1 cells were cultured for 4 days in ESC medium without LIF and with 1 µM RA in the medium.

extract_protocol:
Degradation assay: RNA was extracted and purified using RNA isolation kit (Qiagen). RIP-Seq: The beads were mixed with RLT buffer and samples were processed according to RNA-isolation kit (Qiagen) following manufacturer’s instruction.
Degradation assay: Indexed RNA-Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems, Inc.) according to the manufacturer’s protocol. Libraries were size-selected with SPRI beads and quantified by QuBIT (Life Technologies). Average size of 300 bp was determined by TapeStation (Agilent Technologies, USA). Libraries are then sequenced using an Illumina Nextseq500 sequencer. RIP-Seq: cDNA libraries for each sample were generated from total RNA using the Quantseq 3′ mRNA-Seq Library Prep kit for Illumina (Lexogen) following the manufacturer’s instructions. Libraries were size-selected with SPRI beads and quantified by QuBIT (Life Technologies). Average size of ∼250 bp was determined by TapeStation (Agilent Technologies, USA). Libraries are then sequenced using an Illumina Nextseq500 sequencer.

treatment_protocol: Degradation assay: On the fourth day the cells were exposed to 2 µg/ml of α-amanitin (Sigma Aldrich) and samples were harvested at different time points (0, 2, 4, 8 hrs). RIP-seq: Whole procedure of IP was performed in an ice bath. Cells were washed (X2) by re-suspending the cell pellet with 0.5 ml of ice-cold PBS buffer, centrifuged for 5 min at 2000 rpm, and the supernatant was discarded. 1 ml of pre-cooled cell lysis buffer was added to the cell pellet. Cells were incubated for 30 min on ice, vortexed for 30 sec every 5 min for 30 min. Cell lysates were centrifuged for 30 min at 20,000 g at 4oC. Supernatant was collected and used for IP (2 mg lysate was used for each IP reaction). Background was pre-cleared by incubating the supernatant with 5 µl protein A beads (Magna ChIP™ Protein A Magnetic Beads, 16-661) for 30 min. The reaction mix was placed on the magnet till supernatant became clear. Supernatants were collected. CAPRIN1 antibody (2 µg) was added along with 20 µl protein A beads to supernatants and incubated for 4 hrs. Eppendorfs were placed on the magnet till supernatants became clear. Supernatants were removed and discarded. The bead was washed 3 times with cell lysate buffer.

value: Embryonic stem cells (ESCs)

value: alpha amanitin

value: Caprin 1 KO


title: C11_E_RNA

value: Epithelia


title: 2E


title: 2C

description:
WT_H3K27ac
wt_h3k27ac.narrowPeak.gz
wt_h3k27ac.pooled.fc.signal.bigwig

value: wildtype


title: Runx het P14 HPC.1

description:
Runx het P14 HPC.1
2552_gene_level_read_counts.txt


title: 2H


title: F02_E_RNA


title: 1Z

description: input

source_name: input chromatin


title: NHD13 P14 HPC.4

description:
NHD13 P14 HPC.4
2552_gene_level_read_counts.txt


title: F01_E_RNA


title: wt P14 HPC.1

description:
wt P14 HPC.1
2552_gene_level_read_counts.txt


title: NHD13 P14 HPC.3

description:
NHD13 P14 HPC.3
2552_gene_level_read_counts.txt


title: 1Y

description:
ITD_Runxf_Vav_H3K4me1
itd_runxf_vav_h3k4me1.narrowPeak.gz
itd_runxf_vav_h3k4me1.pooled.fc.signal.bigwig


title: 1X


title: 1W


title: C04_E_RNA


title: NHD13 P14 HPC.2

description:
NHD13 P14 HPC.2
2552_gene_level_read_counts.txt


title: 1U

description:
ITD_Nup98_H3K4me1
itd_nup98_h3k4me1.narrowPeak.gz
itd_nup98_h3k4me1.pooled.fc.signal.bigwig


title: C03_E_RNA


title: C02_E_RNA


title: 1S


title: 1P

description:
Runxf_Vav_H3K4me1
runxf_vav_h3k4me1.narrowPeak.gz
runxf_vav_h3k4me1.pooled.fc.signal.bigwig


title: ITD/Runx P14 HPC.4

description:
ITD/Runx P14 HPC.4
2552_gene_level_read_counts.txt


title: 1R


title: ITD/Runx P14 HPC.3

description:
ITD/Runx P14 HPC.3
2552_gene_level_read_counts.txt


title: 2B


title: 1M


title: ITD/Runx P14 HPC.2

description:
ITD/Runx P14 HPC.2
2552_gene_level_read_counts.txt


title: 1K

description:
Nup98_H3K4me1
nup98_h3k4me1.narrowPeak.gz
nup98_h3k4me1.pooled.fc.signal.bigwig


title: 2A


title: C01_E_RNA


title: 1J


title: RM-1-Bhlhe22 rep3

first: yin

last: chi

state: Guangdong Province

address: 58# Zhongshan 2rd Road

institute: 1st affliated hospital of Sun yat-sen university

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTP
mRNA-seq reads were aligned to the GRCm38 genome assembly using Hisat2 version 2.1.0 with default parameters
Gene abundance measurements were generationed and normalized  using stringtie version 1.3.4b Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using edgeR function package in R program version 3.4.3
Assembly: mm38
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: RM-1 Cell Line

growth_protocol: All cells were incubated at 37°C in 5% CO2

extract_protocol:
Total RNA from prostate cancer cells (RM-1 cells) were isolated by TRIzol (No.:15596026, Thermo Fisher Scientific, USA) and extracted by chloroform. RNA degradation and contamination were monitored on 1% agarose gels and purity was checked by the NanoPhotometer spectrophotometer (IMPLEN, CA USA). RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer(Life Technologies, CA, USA) and integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzeer 2100 system (Agilent Technologies, CA, USA ).
Sequencing libraries were generated using NEBNest UltraTM RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: RM-1 cells were transfected with Bhlhe22-overexpression lentivirus or blank ventor lentivirus as control group

tag: cell line

value: Bhlhe22 overexpression

tag: cancertype

value: Prostate cancer


title: RM-1-Bhlhe22 rep2


title: C05_E_RNA


title: 1H


title: 1F

description:
ITD_H3K4me1
itd_h3k4me1.narrowPeak.gz
itd_h3k4me1.pooled.fc.signal.bigwig


title: 1E


title: NHD13 P14 HPC.1

description:
NHD13 P14 HPC.1
2552_gene_level_read_counts.txt


title: ITD/NHD13 P14 HPC.3

description:
ITD/NHD13 P14 HPC.3
2552_gene_level_read_counts.txt


title: 1N


title: 1D


title: 1C

description:
WT_H3K4me1
wt_h3k4me1.narrowPeak.gz
wt_h3k4me1.pooled.fc.signal.bigwig


title: 1T


title: RM-1-Vector rep3

value: control (RM-1-Vector)


title: ITD/NHD13 P14 HPC.1

description:
ITD/NHD13 P14 HPC.1
2552_gene_level_read_counts.txt


title: 1B


title: Nup98_ITD_HPC2

description:
N.pooled.fc.signal.bigwig
N.narrowPeak.gz

data_processing:
Sequencing reads were demultiplexed and aligned to mouse genome (mm10) by bowtie2 (versoin 2.2.6)
Signal strength relative to the control samples were generated using MACS2.
Optimal set of peaks were generated using the Kundaje lab ATAC-seq and DNase-seq processing pipeline (https://github.com/kundajelab/atac_dnase_pipelines, version 0.33)
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig, narrowPeak

extract_protocol:
per Corces et al., Nature Methods 14:959
tagmentation with Tn5 transposase followed by

tag: genotype/variation


title: RM-1-Vector rep2


title: ITD/NHD13 P14 HPC.2

description:
ITD/NHD13 P14 HPC.2
2552_gene_level_read_counts.txt


title: ITD/Runx P14 HPC.1

description:
ITD/Runx P14 HPC.1
2552_gene_level_read_counts.txt


title: Nup98_ITD_HPC1


title: RM-1-Vector rep1


title: ITD P14 HPC.4

description:
ITD P14 HPC.4
2552_gene_level_read_counts.txt


title: Flt3_ITD_HPC1

description:
M.pooled.fc.signal.bigwig
M.narrowPeak.gz


title: Nup98_HPC2

description:
L.pooled.fc.signal.bigwig
L.narrowPeak.gz


title: wildtype

library_source: transcriptomic single cell

data_processing:
Generation of fastq files via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Alignment to mm10 genome build via cellranger v6.0.1 https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Assembly: mm10
Supplementary files format and content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: Lin-Kit+ cells

extract_protocol:
10x Genomics Chromium single cell preparation 3' ver3.1
10x Genomics Chromium single cell preparation 3' ver3.1


title: Flt3_ITD_HPC2


title: RM-1-Bhlhe22 rep1


title: ITD P14 HPC.3

description:
ITD P14 HPC.3
2552_gene_level_read_counts.txt


title: ITD/NHD13 P14 HPC.4

description:
ITD/NHD13 P14 HPC.4
2552_gene_level_read_counts.txt


title: Nup98_HPC1


title: wt_HPC2

description:
K.pooled.fc.signal.bigwig
K.narrowPeak.gz


title: P21_ITD-Runx_1

description:
D.pooled.fc.signal.bigwig
D.narrowPeak.gz


title: Flt3-ITD; Runx1-het

value: Flt3-ITD; Runx1-het


title: ITD P14 HPC.1

description:
ITD P14 HPC.1
2552_gene_level_read_counts.txt


title: Runx1-et


title: 1A


title: Flt3-ITD


title: P21_Runx_2

description:
C.pooled.fc.signal.bigwig
C.narrowPeak.gz


title: P21_Runx_1


title: Flt3-ITD; NUP98-HOXD13; Ifnar -/-

value: Flt3-ITD; NUP98-HOXD13; Ifnar -/-


title: P21_ITD_1

description:
B.pooled.fc.signal.bigwig
B.narrowPeak.gz


title: P21_wt_2

description:
A.pooled.fc.signal.bigwig
A.narrowPeak.gz


title: Flt3-ITD; NUP98-HOXD13; Ifnar +/-

value: Flt3-ITD; NUP98-HOXD13; Ifnar +/-


title: P21_wt_1

value: P21 (21 days old)


title: NUP98-HOXD13; Ifnar -/-

value: NUP98-HOXD13; Ifnar -/-


title: ITD P14 HPC.2

description:
ITD P14 HPC.2
2552_gene_level_read_counts.txt

value: P14 (14 days old)


title: wt_HPC1


title: NUP98-HOXD13; Ifnar +/-

value: NUP98-HOXD13; Ifnar +/-


title: P21_ITD-Runx_2


title: Flt3-ITD; Ifnar -/-

value: Flt3-ITD; Ifnar -/-


title: Flt3-ITD; Ifnar +/-

value: Flt3-ITD; Ifnar +/-


title: P21_ITD_2


title: Ifnar -/-

value: Ifnar -/-


title: Ifnar +/-

value: Ifnar +/-


title: Yap/Taz KO + CCl4 3

data_processing:
Quality control and trimming of the sequencing reads was performed using FastQC and Cutadapt (-q 15 --minmum-length 30)
Trimmed sequence reads were mapped to mm10 using STAR v2.6.1d (with default mapping parameters).
Reads were counted with STAR --quantMode GeneCounts
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file with raw gene counts for every gene and every sample

treatment_protocol: Induction of hepatocyte-specific recombination of floxed alleles in Yapflox/flox; Tazflox/flox mice was achieved by injection of Adeno-associated virus serotype 8 (AAV8) expressing Cre recombinase under the hepatocyte specific TBG promoter which was purchased from UPenn (AAV8.TBG.PI.Cre.rBG, catalog AV-8-PV1091). Mice received 5x1011 GC (genome complements) of AAV8.TBG.PI.Cre.rBG diluted in 200μl of 1x phosphate-buffered saline (PBS) by tail vein injection. Acute liver injury was induced by intraperitoneal injection of carbon tetrachloride (CCl4) at a concentration of 1ml/kg in corn oil. AAV8-Cre was administered 3 weeks before CCl4 injection. Animals were sacrificed 48 hours after CCl4 administration.

value: Liver

value: Hepatocyte

value: Yapflox/flox; Tazflox/flox

value: AAV8-Cre injection + CCl4 injection

value: Yap/Taz KO

value: Yap/Taz KO + CCl4


title: KPC_ChIPseq_Input_histone_shSmarcd3_Exp2

description: Input for ChIP-seq for histone in KPf/fC cells transduced with shSmarcd3

data_processing:
Basecalls performed using RTA (Illumina)
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5) for RNA-seq and ChIP-seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
HOMER (v4.8) (http://homer.salk.edu/homer/) was used to process alignment files to generate ChIP-seq bed files. ChIP-seq peaks for Smarca4 and Arid1a were found by using the findPeaks program in HOMER with the parameter "-style factor" versus the appropriate ChIP input experiments as background. ChIP-seq peaks for H3K4me, H3K4me3, and H3K27ac were called using the parameter "-style histone." For RNA-Seq, Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq). Differentially expressed genes in shSmarcd3 versus shControl were called using the command getDiffExpression.pl, with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Bedgraph file Columns: (1) chrom (2) chromStart (3) chromEnd (4) data value. DiffExpOutput tab delimited text file Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-12) FPKM for each experiment (13) Log2 fold change (14) p value (15) adjusted p value

growth_protocol: Cell lines were maintained in 2D cultue in 10% DMEM, 1%pen/strep, 1%NEAA for all studies

treatment_protocol: A CD133High primary mouse pancreatic cancer cell line derived from an end-stage KPf/fC tumor was infected with an RFP-tagged shRNA against Smarcd3 or a control; vector+ cells were sorted 72hrs after transduction and grown for another 5 days and then collected for parallel analysis by RNA-seq and ChIP-seq. RNA-seq was conducted in technical triplicate, H3k27ac ChiP-seq was conduted in biological duplicate using the same cell line at the same passage.

value: KPf/fC tumor

tag: antibody source


title: KPC_ChIPseq_H3K27ac_Rep1_shSmarcd3_Exp2

description: ChIP-seq for H3K27ac in KPf/fC cells transduced with shSmarcd3

value: H3K27ac (Abcam ab4729)


title: KPC_ChIPseq_Input_histone_shControl_Exp2

description: Input for ChIP-seq for histone in KPf/fC cells transduced with shControl

value: shControl


title: KPC_ChIPseq_H3K27ac_Rep2_shSmarcd3_Exp2


title: b1

description: Flt3-ITD/NHD13 Ifnar1-/- AML

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq2 software.  R software.
NA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8
Assembly: Ensemble R101
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: AML

value: Ifnar1 -/-


title: Yap/Taz KO + CCl4 2

tag: tissue


title: Yap/Taz KO + CCl4 1


title: KPC_ChIPseq_Input_histone_shSmarcd3_Exp1


title: b2

description: Flt3-ITD/NHD13 Ifnar1-/- AML


title: KPC_ChIPseq_H3K27ac_Rep1_shControl_Exp2

description: ChIP-seq for H3K27ac in KPf/fC cells transduced with shControl


title: KPC_ChIPseq_H3K27ac_Rep2_shControl_Exp2


title: HeLa_Total-RNA_SuperScript-IV_50uM-dNTP_1mM-dATP

city: Chicago

first: Li-Sheng

last: Zhang

state: IL

address: 929 E 57th St Rm E313

department: Department of Chemistry

institute: The University of Chicago

data_processing:
The sequencing data was all trimmed with cutadapt tool to remove adapters and low-quality reads. PCR duplicates were removed with BBMap tool (https://sourceforge.net/projects/bbmap/), 5-mer random barcodes at reads ends were trimmed, and low-quality or short reads (less than 20 nt) were removed using cutadapt tool. Remaining reads were aligned to hg38 genome using Tophat2 (version 2.1.1) and bowtie2 (version 2.3.5.1) allowing at most three mismatches. The generated .bam files were split into positive and negative strands and sorted using Samtools (http://samtools.sourceforge.net/). Sequence variants were identified by measuring the base composition at each position using fine-tuned bam-readcount (https://github.com/genome/bam-readcount). The generated bam-readcount results were parsed and analyzed by in-house scripts. G to T or C or A mutation ratios as well as deletion ratios at each internal m7G site were calculated by data output from bam-readcount pipeline and confirmed by direct visualization through IGV software (https://software.broadinstitute.org/software/igv/).
genome build: hg38

source_name: cell

growth_protocol: HeLa cell line used for internal m7G analysis in this study was purchased from the American Type Culture Collection (ATCC). Cells were maintained in DMEM medium (4.5g/L glucose) supplemented with 10% v/v FBS and 1% penicillin/streptomycin (GIBCO). Cells were cultured at 37 °C with 5.0% CO2 in a Heracell™ VIOS 160i incubator (Thermo Scientific).

extract_protocol:
Cellular total RNA was isolated with TRIzol reagent (Invitrogen) following manufacturer’s protocol by isopropanol precipitation.
The starting amount of total RNA could be 200 ng before fragmentation. Then Zinc RNA Fragmentation Rea-gents (Invitrogen, AM8740) was used as 15X (add 1.0 µL buffer into 14 µL of RNA), which is originally 10X. The heating condition is always 70 °C for 14 min, followed by Oligo Clean and Concentrator kit (OCC). Elute RNA to 22 µL (twice, 11 µL each time). Prepare a stock containing 22 µL RNA + 3 µL 10X PNK buffer + 3 µLT4 PNK + 1.5 µL SUPERase•In™ with a final volume of 30 µL. Mix the stock well and incubate at 37 °C for 1 hour. Recover RNA with Oligo Clean and Concen-trator kit (OCC) and elute to 10 µL with RNase-free water. Mix 1.0 µL 20 µM 3’ linker (5’rApp + random-barcode + adaptor sequence + C3-spacer) with repaired 10 µL RNA fragments and incubate the mixture at 70 °C for 2 min for denaturation. Immediately move onto ice. Then add 2.5 µL 10X T4 RNA Ligase Rxn Buffer, 7.5 µL 50% PEG8000, 1 µL SUPERnaseIn, and 1 µL H2O. Mix everything well before adding T4 RNA ligase 2 truncated KQ. Then add 2.0 µL T4 RNA lig-ase 2 truncated KQ and mix well again. Incubate the reaction at 25 °C for 2 hours, followed by 16 °C for 12 hours.   Then add 23 µL RNase-free water to dilute the reaction mixture. Add 2.0 µL 5-deadenylase, mix well/incubate at 30 °C for 30 min; then add 1.0 µL RecJf, mix well/incubate at 37 °C for another 30 min. Recover RNA with RNA Clean and Concentrator kit (RCC) and elute to 12 µL with RNase-free water. Save 2 µL as 'input'; use the rest for the following steps. Put the eluted RNA in 10 µL RNase-free water. Prepare a fresh 1.0M KBH4 buffer in RNase-free water. Add 40 µL KBH4 buffer into RNA and mix well. Incubate at room temperature for 2 hours (avoid the light). Recover RNA with RNA Clean and Concentrator kit (RCC) and elute to 45 µL with RNase-free water. Add 5.0 µL 1.0M NaOAc/AcOH buffer pH 2.9 into the purified RNA and mix well. Incubate with heating for 4 hours (avoid the light). Recover RNA with Oligo Clean and Concentrator kit (OCC) and elute to 10 µL with RNase-free water. Mix 1.0 µL 2 uM RT-primer with 10 µL depurinated RNA fragments and incubate the mixture at 65 °C for 2 min for denaturation. Immediately move onto ice. Then screen different dNTP/dATP ratios under different RTs. After RT, add 1.0 µL RNaseH (NEB) into the reaction mixture. Mix well/incubate at 37 °C for 20 min. Then 70 °C for 5 min to denature. Recover RNA with Oligo Clean and Concentrator kit (OCC) and elute to 10 µL with RNase-free water. Mix 1.0 µL 50 uM cDNA 3'-adapter with 10 µL cRNA and incubate the mixture at 75 °C for 2 min for denaturation. Immediately move onto ice. Then add 3 µL 10X T4 RNA Ligase Rxn Buffer, 15 µL 50% PEG8000, and 3 µL 10mM ATP. Mix everything well before adding T4 RNA Ligase 1. Then add 1.0 µL T4 RNA Ligase 1 and mix well again. Add ligase enzyme to one sample followed by mixing this sample immediately. Mix each sample one by one. Do not add ligase enzyme to all samples and then start mixing everything.  Incubate the reaction at 25 °C for 12 hours. After the 12-hour cDNA ligation, heat at 65 °C for 5 min for denature. Purify the cDNA by DNA Clean & Concentrator-5. Elute cDNA with 20 µL DNase-free water the reaction mixture. Mix again and then use 4 µL per sample for each PCR amplification.
RNA-Seq. All libraries were sequenced on Illumina NovaSeq 6000 with single-end 100 bp read length.

treatment_protocol: Wild-type cells were used for library construction.

value: cell culture

value: HeLa

tag: tag


title: HeLa_SmallRNA_HIV-RT_Input_rep1

growth_protocol: HeLa and HEK293T were used for internal m7G analysis in this study were purchased from the American Type Culture Collection (ATCC). Cells were maintained in DMEM medium (4.5g/L glucose) supplemented with 10% v/v FBS and 1% penicillin/streptomycin (GIBCO). Cells were cultured at 37 °C with 5.0% CO2 in a Heracell™ VIOS 160i incubator (Thermo Scientific).

extract_protocol:
Cellular total RNA was isolated with TRIzol reagent (Invitrogen) following manufacturer’s protocol by isopropanol precipitation. Then, cellular small RNAs (<200 nt) were extracted by mirVana™ miRNA Isolation Kit following manufacturer's protocol.
The starting amount of cellular small RNA (< 200 nt) could be 200 ng before fragmentation. Then Zinc RNA Fragmentation Rea-gents (Invitrogen, AM8740) was used as 15X (add 1.0 µL buffer into 14 µL of RNA), which is originally 10X. The heating condition is always 70 °C for 14 min, followed by Oligo Clean and Concentrator kit (OCC). Elute RNA to 22 µL (twice, 11 µL each time). Prepare a stock containing 22 µL RNA + 3 µL 10X PNK buffer + 3 µLT4 PNK + 1.5 µL SUPERase•In™ with a final volume of 30 µL. Mix the stock well and incubate at 37 °C for 1 hour. Recover RNA with Oligo Clean and Concen-trator kit (OCC) and elute to 10 µL with RNase-free water. Mix 1.0 µL 20 µM 3’ linker (5’rApp + random-barcode + adaptor sequence + C3-spacer) with repaired 10 µL RNA fragments and incubate the mixture at 70 °C for 2 min for denaturation. Immediately move onto ice. Then add 2.5 µL 10X T4 RNA Ligase Rxn Buffer, 7.5 µL 50% PEG8000, 1 µL SUPERnaseIn, and 1 µL H2O. Mix everything well before adding T4 RNA ligase 2 truncated KQ. Then add 2.0 µL T4 RNA lig-ase 2 truncated KQ and mix well again. Incubate the reaction at 25 °C for 2 hours, followed by 16 °C for 12 hours. Then add 23 µL RNase-free water to dilute the reaction mixture. Add 2.0 µL 5-deadenylase, mix well/incubate at 30 °C for 30 min; then add 1.0 µL RecJf, mix well/incubate at 37 °C for another 30 min. Recover RNA with RNA Clean and Concentrator kit (RCC) and elute to 12 µL with RNase-free water. Save 2 µL as 'input'; use the rest for the following steps. Put the eluted RNA in 10 µL RNase-free water. Prepare a fresh 1.0M KBH4 buffer in RNase-free water. Add 40 µL KBH4 buffer into RNA and mix well. Incubate at room temperature for 2 hours (avoid the light). Recover RNA with RNA Clean and Concentrator kit (RCC) and elute to 45 µL with RNase-free water. Add 5.0 µL 1.0M NaOAc/AcOH buffer pH 2.9 into the purified RNA and mix well. Incubate with heating for 4 hours (avoid the light). Recover RNA with Oligo Clean and Concentrator kit (OCC) and elute to 10 µL with RNase-free water. Mix 1.0 µL 2 uM RT-primer with 10 µL depurinated RNA fragments and incubate the mixture at 65 °C for 2 min for denaturation. Immediately move onto ice. Then add 2 µL 10X AMV RT Rxn Buffer, 2 µL 10mM dNTP, 0.5 µL RNaseOut, and 2.5 µL H2O. Mix everything well before adding HIV RT. Then add 2.0 µL HIV RT and mix well again. Incubate the reaction at 37 °C for 1.5 hours. After RT, add 1.0 µL RNaseH (NEB) into the reaction mixture. Mix well/incubate at 37 °C for 20 min. Then 70 °C for 5 min to denature. Recover RNA with Oligo Clean and Concentrator kit (OCC) and elute to 10 µL with RNase-free water. Mix 1.0 µL 50 uM cDNA 3'-adapter with 10 µL cRNA and incubate the mixture at 75 °C for 2 min for denaturation. Immediately move onto ice. Then add 3 µL 10X T4 RNA Ligase Rxn Buffer, 15 µL 50% PEG8000, and 3 µL 10mM ATP. Mix everything well before adding T4 RNA Ligase 1. Then add 1.0 µL T4 RNA Ligase 1 and mix well again. Add ligase enzyme to one sample followed by mixing this sample immediately. Mix each sample one by one. Do not add ligase enzyme to all samples and then start mixing everything.  Incubate the reaction at 25 °C for 12 hours. After the 12-hour cDNA ligation, heat at 65 °C for 5 min for denature. Purify the cDNA by DNA Clean & Concentrator-5. Elute cDNA with 20 µL DNase-free water the reaction mixture. Mix again and then use 4 µL per sample for each PCR amplification.
RNA-Seq. All libraries were sequenced on Illumina NovaSeq 6000 with single-end 100 bp read length.


title: HEK293T_SmallRNA_HIV-RT_Treated_rep1


title: HeLa_SmallRNA_HIV-RT_Treated_rep2


title: HEK293T_SmallRNA_HIV-RT_Treated_rep2


title: HEK293T_SmallRNA_HIV-RT_Input_rep2


title: HEK293T_SmallRNA_HIV-RT_Input_rep1


title: HeLa_SmallRNA_HIV-RT_Input_rep2


title: HeLa_Total-RNA_SuperScript-IV_25uM-dNTP_1mM-dATP


title: HeLa_SmallRNA_HIV-RT_Treated_rep1


title: HeLa_Total-RNA_SuperScript-IV_100uM-dNTP_1mM-dATP


title: KPC_ChIPseq_H3K4me3_shSmarcd3_Exp1

description: ChIP-seq for H3K4me3 in KPf/fC cells transduced with shSmarcd3

value: H3K4me3 (Millipore 05-745)


title: b3

description: Flt3-ITD/NHD13 Ifnar1-/- AML


title: b4

description: Flt3-ITD/NHD13 Ifnar1-/- AML


title: KPC_ChIPseq_H3K4me_shSmarcd3_Exp1

description: ChIP-seq for H3K4me in KPf/fC cells transduced with shSmarcd3

value: H3K4me (Abcam ab8895)


title: Yap/Taz KO 2

treatment_protocol: Induction of hepatocyte-specific recombination of floxed alleles in Yapflox/flox; Tazflox/flox mice was achieved by injection of Adeno-associated virus serotype 8 (AAV8) expressing Cre recombinase under the hepatocyte specific TBG promoter which was purchased from UPenn (AAV8.TBG.PI.Cre.rBG, catalog AV-8-PV1091). Mice received 5x1011 GC (genome complements) of AAV8.TBG.PI.Cre.rBG diluted in 200μl of 1x phosphate-buffered saline (PBS) by tail vein injection. Animals were sacrificed 3 weeks after AVV-Cre injection.

tag: strain

value: AAV8-Cre injection


title: Yap/Taz KO 3

tag: cell type


title: KPC_ChIPseq_Input_histone_shControl_Exp1


title: HeLa_Total-RNA_SuperScript-IV_1mM-dNTP


title: Yap/Taz KO 1


title: HeLa_Total-RNA_SuperScript-II_25uM-dNTP_1mM-dATP


title: b5

description: Flt3-ITD/NHD13 Ifnar1-/- AML

tag: genotype


title: ctrl + CCl4 3

treatment_protocol: Acute liver injury was induced by intraperitoneal injection of carbon tetrachloride (CCl4) at a concentration of 1ml/kg in corn oil. Animals were sacrificed 48 hours after CCl4 administration.

tag: treatment

value: CCl4 injection

value: WT

value: ctrl + CCl4


title: KPC_ChIPseq_H3K4me3_shControl_Exp1

description: ChIP-seq for H3K4me3 in KPf/fC cells transduced with shControl


title: ctrl + CCl4 2

value: Liver

value: Hepatocyte

tag: effective genotype


title: ctrl + CCl4 1

value: Yapflox/flox; Tazflox/flox

tag: group


title: KPC_ChIPseq_H3K4me_shControl_Exp1

description: ChIP-seq for H3K4me in KPf/fC cells transduced with shControl


title: a1

description: Flt3-ITD/NHD13 Ifnar1+/- AML

value: Ifnar1 +/-


title: a3

description: Flt3-ITD/NHD13 Ifnar1+/- AML


title: a2

description: Flt3-ITD/NHD13 Ifnar1+/- AML


title: KPC_ChIPseq_Input_shControl

description: Input for ChIP-seq for Arid1a in KPf/fC cells transduced with shControl


title: HeLa_Total-RNA_SuperScript-II_100uM-dNTP_1mM-dATP


title: KPC_ChIPseq_Arid1a_shSmarcd3

description: ChIP-seq for Arid1a in KPf/fC cells transduced with shSmarcd3

value: Arid1a CST 12354


title: HeLa_Total-RNA_SuperScript-II_50uM-dNTP_1mM-dATP


title: Runx het P14 HPC.2

description:
Runx het P14 HPC.2
2552_gene_level_read_counts.txt

value: P14 (14 days old)


title: ctrl 2

value: ctrl


title: ctrl 3


title: a4

description: Flt3-ITD/NHD13 Ifnar1+/- AML


title: control cells_1a

type: RNA

city: LOS ANGELES

first: MARINA

last: KOUTSIOUMPA

address: 650 Charles E. Young Dr South, CHS 33-315

department: MEDICINE

institute: UCLA

description: Gene expression data from MIA PaCa_2 cells transduced with GFP lentiviral expressing construct.

hyb_protocol: Hybridize at 45C for 16 hours with rotation at 60rpm (GeneChip Hybridization Oven 645)

scan_protocol: Affymetrix GeneChip Scanner 7G with default settings

data_processing: Affymetrix Expression Console MAS5.0

label: Biotin

source_name: MIA PaCa-2

label_protocol: Ambion MessageAmp Premier protocol

growth_protocol: To make the complete growth medium, the following components were added to the Gibco™ DMEM, High Glucose base medium: fetal bovine serum to a final concentration of 10%; horse serum to a final concentration of 2.5%. 1:5 split was 70-80% confluent and ready for experiment in 3 days.

extract_protocol: RNA was isolated using  TRIzol (Invitrogen product name) and subsequently the Qiagen  RNeasy mini Kit (cat 74104).  Column based.

treatment_protocol: MIA PaCa-2 cells were transduced with FLAG-ING3 or GFP as control (73582, Addgene) lentiviral expressing constructs. Full length ING3 sequence embedded in the pENTR223.1 vector (clone: HsCD00080478, DNASU) was amplified by PCR and cloned into the pLenti CMV/TO Puro DEST vector (17293, Addgene), using the pENTR/D-TOPO Cloning Kit (K2435) and Gateway LR Clonase II Enzyme mix (11791, Life Technologies). Upon selection of the stably-transfected clones, cells were plated and when 80% confluence in serum and antibiotic-containing media was reached, RNA isolation was performed.

value: MIA PaCa-2

value: Established epithelial pancreatic carcinoma cell line

value: control


title: ctrl 1


title: KPC_ChIPseq_Arid1a_shControl

description: ChIP-seq for Arid1a in KPf/fC cells transduced with shControl

value: KPf/fC tumor

value: shControl


title: ING3-overexpressing cells_2a

description: Gene expression data from MIA PaCa_2 cells transduced with FLAG-ING3 expressing construct.


title: HeLa_Total-RNA_ProtoScript-II_50uM-dNTP_1mM-dATP

value: cell culture

value: HeLa


title: HeLa_Total-RNA_ProtoScript-II_25uM-dNTP_1mM-dATP


title: a6

description: Flt3-ITD/NHD13 Ifnar1+/- AML


title: HeLa_Total-RNA_ProtoScript-II_100uM-dNTP_1mM-dATP


title: HeLa_Total-RNA_SuperScript-II_1mM-dNTP


title: a5

description: Flt3-ITD/NHD13 Ifnar1+/- AML


title: ING3-overexpressing cells_2b


title: KPC_ChIPseq_Input_shSmarcd3_Exp1

description: Input for ChIP-seq for Smarca4 in KPf/fC cells transduced with shSmarcd3


title: 6-month Terc KO brain

city: Shanghai

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
Brain: 1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 40%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Bonemarrow: 1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: 6-month brain

extract_protocol:
Bone marrow was flushed and kept in MACS Tissue Storage Solution (Miltenyi Biotec). Samples were sieved through 40µm cell strainers, and centrifuged at 300 g for 5 min. Pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) for lysing red blood cells.Brain tissues were surgically removed and minced into small pieces (approximately 1mm3) on ice and digested by 200 U/mL Papine (Diamond) and Cysteine-HCL (Sigma). Then samples were sieved through 70 µm cell strainers, centrifuged at 300 g for 10 min, and further cleaned for red blood cells using red blood cell lysis buffer (Miltenyi Biotec).
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

value: Terc KO


title: HeLa_Total-RNA_ProtoScript-II_1mM-dNTP


title: KPC_ChIPseq_Input_shControl_Exp1

description: Input for ChIP-seq for Smarca4 in KPf/fC cells transduced with shControl


title: control cells_1b


title: 6-month Terc KO bone marrow

source_name: 6-month bone marrow


title: KPC_ChIPseq_Input_shSmarcd3

description: Input for ChIP-seq for Arid1a in KPf/fC cells transduced with shSmarcd3


title: KPC_ChIPseq_Smarca4_shSmarcd3_Exp1

description: ChIP-seq for Smarca4 in KPf/fC cells transduced with shSmarcd3

value: BRG1/Smarca4 Abcam 110641


title: HeLa_Total-RNA_RT1306_25uM-dNTP_1mM-dATP


title: WT_v_4

city: Ulm

first: Giorgio

last: Caratti

address: Helmholzstraße 8/1

country: Germany

institute: University of Ulm

data_processing:
Index of reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12
HTSeq v0.6.1 was used to count the read numbers mapped to each gene. FKPM of each gene was then calculated on the length of the gene and the reads count mapped to this gene
Differential expression analysis of two conditions/groups (2-3 biological replicates per condition) was performed using the DESeq2 R package.
Genome_build: GRCM38 (mm10)
Supplementary_files_format_and_content: tab delim text files contain FKPM values per sample

source_name: Bone marrow derived macrophages

growth_protocol: To culture bone marrow derived macrophages, total bone marrow was isolated from mice by flushing the femur and tibiae bone  marrow with culture medium. Extracted bone marrow was cultured in DMEM high glucose high  pyruvate containing 20% of FBS, 1% of penicillin/streptomycin, 1% of  fungizone and 30% of L929 conditioned medium for 5 to 7 days.

extract_protocol:
RNA was extracted using TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene

treatment_protocol: Differentiated BMDMs exposed to vehicle (DMSO), dexamethasone (100nM) 24 hours before RNA isolation

value: FVB/N

value: bone marrow

tag: agent

value: DMSO

value: wildtype


title: WT_v_3


title: HeLa_Total-RNA_RT1306_50uM-dNTP_1mM-dATP


title: WT_v_2


title: HeLa_Total-RNA_RT1306_100uM-dNTP_1mM-dATP


title: KPC_ChIPseq_Smarca4_shControl_Exp1

description: ChIP-seq for Smarca4 in KPf/fC cells transduced with shControl

tag: short hairpin rna


title: HeLa_Total-RNA_HIV-RT_25uM-dNTP_1mM-dATP


title: HeLa_Total-RNA_RT1306_1mM-dNTP


title: KPC_RNAseq_shSmarcd3_Rep2

description: RNA-seq in KPf/fC cells transduced with shSmarcd3


title: KPC_RNAseq_shSmarcd3_Rep3


title: WT_v_1


title: KPC_RNAseq_shSmarcd3_Rep1


title: HeLa_Total-RNA_HIV-RT_50uM-dNTP_1mM-dATP


title: WT_d_4

value: dexamethasone (100nM)


title: KPC_RNAseq_shControl_Rep3

description: RNA-seq in KPf/fC cells transduced with shControl


title: WT_d_3


title: KPC_RNAseq_shControl_Rep2


title: WT_d_2


title: HeLa_Total-RNA_HIV-RT_1mM-dNTP


title: KO_v_4


title: Strand-specific RNA-seq in cells deleted for the siRNA target site and treated with VINK-1 siRNA -Replicate #2

city: Toulouse

first: Estelle

last: Nicolas

address: 118 route de Narbonne

country: France

institute: INSERM

description: 20211126_DESEQ2_Del_siVINKEX2_vs_siCtle3_normDESeq.csv

data_processing:
The quality of each raw sequencing file (fastq) was verified with FastQC. Files were aligned to the reference human genome (hg38) in paired-end mode with STAR Version 2.5.2b and processed (sorting and indexing) with samtools. rDNA contamination was removed in the alignment process.
Uniquely aligned reads were counted, per gene_id, using HT-seq Version 0.6.1 in a strand specific mode with the union count method parameter [43]. The features annotation used for counts was constructed from NCBI refseq annotation gtf file from UCSC, taking the entire locus of reference for each gene.
After removing lowly expressed counts (> 4 reads over the 4 samples), differential analysis was performed with DESeq2 Bioconductor R package, Version 1.22.1. Counts were normalized using DESeq2 normalization method. Both treatment (siRNA VINK/siRNA Ctrl) and batch (replicates) effects were taken into account to estimate parameters and fit the model, in order to apply Wald test.
Genome_build: hg38
Supplementary_files_format_and_content: Tables with the differential analysis from Deseq2.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample from HTSeq.

source_name: total RNA (ribosomal RNA depleted) from VINK-1 siRNA-treated senescent WI38 hTERT RAF1-ER cells

growth_protocol: WI38 hTERT RAF1-ER wild type or deleted for the siVINK1 target sequence were induced in senescence by 3 days-treatment of 20nM 4-hydroxytamoxifen.

extract_protocol:
Total RNAs were prepared using the MasterPure RNA Purification Kit (Epicentre Biotechnologies) supplemented with Baseline-ZERO DNAse (Epicentre). EMBL-GeneCore performed the ribosomal RNA depletions.
Library construction (NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®) and sequencing were performed by EMBL GeneCore (Heidelberg, Germany) (stranded rRNA-minus RNA-seq). Samples were barcoded, sequenced paired-end  in one run of Illumina NextSeq 75PE high for 8 samples, and demultiplexed.

treatment_protocol: Senescent cells were transfected with 100 nM of siRNA and harvested 3 days later.

value: WI38 hTERT RAF1-ER deleted for siRNA VINK1 target site

value: induced in senescence for 3 days and then transfected with VINK-1 siRNA for 3 days


title: PC-3-Bhlhe22 rep3

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTP
mRNA-seq reads were aligned to the GRCh38 genome assembly using Hisat2 version 2.1.0 with default parameters
Gene abundance measurements were generationed and normalized  using stringtie version 1.3.4b Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using edgeR function package in R program version 3.4.3
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: PC-3 Cell Line

extract_protocol:
Total RNA from prostate cancer cells (PC-3 cells) were isolated by TRIzol (No.:15596026, Thermo Fisher Scientific, USA) and extracted by chloroform. RNA degradation and contamination were monitored on 1% agarose gels and purity was checked by the NanoPhotometer spectrophotometer (IMPLEN, CA USA). RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer(Life Technologies, CA, USA) and integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzeer 2100 system (Agilent Technologies, CA, USA ).
Sequencing libraries were generated using NEBNest UltraTM RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: PC-3 cells were transfected with Bhlhe22-overexpression lentivirus or blank ventor lentivirus as control group

tag: bhlhe22 status

value: Overexpression

tag: cancer type

value: Prostate cancer


title: PC-3-Bhlhe22 rep1


title: hiPSCs cultured under 5iLAF conditions

city: Pamplona

first: Asier

last: Ullate-Agote

state: Navarra

address: Av. de Pío XII, 55

department: Hemato-Oncology

country: Spain

institute: CIMA

data_processing:
Demultiplexing, alignment to the Homo sapiens (hg38) genome and quantification using the annotation from Ensembl v98 was performed using 10X Genomics Cell Ranger (v5.0.1)
Downstream analysis steps (quality control filtering, normalization,  clustering and differential expression) were performed using the R package Seurat (v4.0.5)
Genome_build: hg38
Supplementary_files_format_and_content: HDF5 Feature Barcode Matrix containing a Gene x Cells UMI count matrix

source_name: hiPSCs

growth_protocol: Cells were maintained on irradiated mouse embryonic fibroblast (iMEF) feeders in primed conditions: DMEM Knock-Out (Gibco #10829-018), 20% Knock-Out Serum Replacement (KSR, Gibco #10828-028), 1% GlutaMAX (Gibco #35050-038), 1% non-essential amino acids (Gibco #11140-035), 1% Antibiotic-Antimycotic (Gibco #15240-062), 0.1 mM β-mercaptoethanol (Gibco #31350-010) and 20 ng/mL human FGF-basic (Peprotech #100-18B). After reaching 70% confluence (5-7 days), cells were passaged by detaching them with 200 U/mL collagenase type IV (Gibco #17104-019) for 10 minutes, followed by mechanical disruption of the colonies with cell scrapper and gentle pipetting. Cells were cultured in a humidified atmosphere at 37ºC, 20% O2, 5% CO2 in air.

extract_protocol:
Twenty-four hours before single-cell dissociation, 5iLAF human cells were treated with rock inhibitor Y27632 (5 µM - Axon Medchem #1683). Next day, human cells were dissociated using 1:1 TrypLE (Gibco #12605-028) 1X PBS and 0.25 mM EDTA (Invitrogen #AM9260G) for 5 min at 37 °C and resuspended in FACS buffer (1X PBS, 1 mM EDTA, 25 mM HEPES pH=7 and 1% BSA). Then, tdTomato+ human cells were FACS sorted with FACS AreaI and AreaII through a nozzle of 100 µm in 1X PBS 0.05% BSA, and the number of cells was quantified in a Neubauer chamber.  Cell suspensions were loaded onto a well of a 10X Chromium Single Cell instrument. Barcoding and cDNA synthesis were performed according to the manufacturer´s instructions. The cDNA libraries were constructed using the 10X Chromium Single cell 3' Library Kit v3 according to the manufacturer's original protocol and sequenced either with a NextSeq 500 (R1:28, R2:49, i7:8) instrument.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were converted into naïve-like cells using 5iLAF media: 1:1 Neurobasal (Gibco #21103-049), DMEM-F12 (Sigma-Aldrich #D6421), 1X B27 Supplement (Gibco #17504-044), 1X N2 Supplement (Gibco #17502-048), 1% GlutaMAX (Gibco #35050-038), 1% Non-Essential Amino Acids (Gibco #11140-035), 1% Antibiotic-Antimycotic (Gibco #15240-062) 0.5% Knock-Out Serum Replacement (KSR Gibco #10828-028), 20 ng/mL recombinant human LIF (Peprotech #300-05-100UG), 20 ng/mL recombinant human Activin A (Peprotech #120-14-10UG), 8 ng/mL human FGF-basic (Peprotech #100-18b-50UG), and the following small molecule inhibitors: 10 µM Y27632 (Axon Medchem #1683); 1 µM WH-4-23 (Biovision #2827-10), 1 µM PD0325901 (Axon Medchem #1408), 1 µM IM-12 (Sigma-Aldrich #SML0084-5MG); 0.5 µM SB590885 (TOCRIS #2650). Briefly, hiPSCs were passaged every 7–9 days by single-cell disaggregation with 1:1 TrypLE (Gibco #12605-028) 1X PBS/0.25 mM EDTA (Invitrogen #AM9260G) and plated on an iMEF feeder layer. Culture medium was supplemented with additional Y27632 inhibitor for the first 24 h at 5 µM. Cells were cultured in a humidified atmosphere at 37ºC, 5% O2, 5% CO2 in air

value: human induced pluripotent stem cells (hiPSCs)

tag: culture protocol

value: naïve 5iLAF culture conditions for three passages


title: KO_v_3


title: Strand-specific RNA-seq in cells deleted for the siRNA target site and treated with Ctle-1 siRNA -Replicate #2

source_name: total RNA (ribosomal RNA depleted) from Ctle-1 siRNA-treated senescent WI38 hTERT RAF1-ER cells

value: induced in senescence for 3 days and then transfected with Ctle-1 siRNA for 3 days


title: KO_v_2


title: PC-3-Vector rep2

tag: cell line

value: Normal


title: Strand-specific RNA-seq in cells deleted for the siRNA target site and treated with Ctle-1 siRNA -Replicate #1


title: KO_v_1


title: HeLa_Total-RNA_HIV-RT_100uM-dNTP_1mM-dATP

value: cell culture


title: MGC803 cells, Input

city: Beijing

first: Xiaohong

last: Wang

address: Haidian district

institute: Peking university cancer hospital

data_processing:
ChIRP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIRP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Assembly: GRCh38
Supplementary files format and content: txt file representing the annotated peaks of the ChIRP pull down products
Library strategy: ChIRP-seq

growth_protocol: Cells were cultured in Dulbecco’ s modified Eagle’ s medium (Gibco BRL, supplemented with 10% fetal bovine serum

extract_protocol:
ChIRP assays were performed using Magna ChIRPTM RNA Interactome Kits
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were stably transfected with DUSP5P1 plasmid  respectively.

value: cancer cells

value: DUSP5P1 ectopic expression

value: 10% FBS DMEM

tag: time

value: 2 weeks

tag: fraction

value: full DNA of cells


title: PC-3-Vector rep1


title: KO_d_4

value: FVB/N

value: bone marrow


title: lncFAM siRNA 48h-3

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: lncFAM siRNA replicate-3 48h

data_processing:
BCL files were de-multiplexed and converted to standard FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed for adapter sequences using Cutadapt version v1.18 and aligned to human genome hg19 Ensembl v82 using STAR software v2.4.0j.
featureCounts (v1.6.4) were used to create gene counts from the samples.
Assembly: hg19
Supplementary files format and content: geneCOUNT.txt: Tab-delimited text files containing counts.

source_name: human myoblast

growth_protocol: Human myoblasts were cultured in growth medium (equal volume mixture of Hamm's F10 media with 20% FBS and Promocell Skeletal Muscle Cell Growth Medium). Human myoblasts were induced to differentiate by growth to high density and replacement of the growth medium with differentiation medium (DMEM with 2% horse serum).

extract_protocol:
Total RNA from cultured cells was isolated using the Direct-zol™ RNA MiniPrep kit (Zymo Research), which includes a digestion step using DNase I.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Final concentration of 50 nM siRNA and Lipofectamine RNAiMAX (Thermo Fisher Scientific) of control small interfering RNA (Ctrl siRNA) or LncFAM siRNA was transfected 24 h before induction of differentiation.

value: Myoblast

tag: sirna

value: lncFAM siRNA 48h


title: KPC_RNAseq_shControl_Rep1

source_name: KPf/fC cells

extract_protocol:
For RNA-seq, total RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research). For SWI/SNF subunit ChIP-seq, 6-7e6 cells were collected per condition and cross-linked first in 3mM disuccinimidyl glutarate (DSG) then in 1% formaldehyde. For histone modification ChIP-seq, 2e6 cells were collected per condition and cross-linked with 1% formaldehyde. After quenching the excess formaldehyde with 125 mM glycine, the fixed cells were washed, pelleted and flash-frozen. Upon thawing, the cells were resuspended in lysis solution (50 mM HEPES-KOH pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100 and incubated on ice for ten minutes. The isolated nuclei were washed with wash solution (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl) and shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris-HCl pH 8) then sheared in a Covaris E229 sonicator for 10 minutes to generate DNA fragments between ~ 200-1000 bp. After clarification of insoluble material by centrifugation, the chromatin was immunoprecipitated overnight at 4C with antibodies against Smarca4, Arid1a, H3K4me, H4K4me3 and H3K27ac then bound to Protein A+G Dynabeads (Invitrogen) in ChIP buffer (50 mM HEPES-KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% DOC, 0.1% SDS). Antibody bound DNA were washed and treated with Proteinase K and RNase A and the purified ChIP DNA was used for library generation for subsequent sequencing.
ChIP-Seq libraries were generated using the NuGen Ovation Ultralow Library System V2 following the manufacturer's instructions. RNA-Seq libraries were prepared using Illumina TruSeq RNA Library Prep Kit v2 following the manufacturer's instructions.

value: KPf/fC tumor

value: shControl

tag: antibody source


title: MGC803 cells, DNA-2

value: ChIRP pull down product


title: Strand-specific RNA-seq in VINK-2 siRNA treated cells- Replicate #2

description: 2021216_DESEQ2_siVINKvssiCtle_NormDESeq.csv

source_name: total RNA (ribosomal RNA depleted) from VINK-2 siRNA-treated senescent WI38 hTERT RAF1-ER cells

value: WI38 hTERT RAF1-ER

value: induced in senescence for 3 days and then transfected with VINK-2 siRNA for 3 days


title: PC-3-Bhlhe22 rep2

value: Overexpression

value: Prostate cancer


title: KO_d_3

tag: tissue

value: dexamethasone (100nM)


title: WT_d_1

tag: strain

value: wildtype


title: PC-3-Vector rep3

value: Normal


title: Strand-specific RNA-seq in VINK-2 siRNA treated cells- Replicate #1

tag: cell type


title: lncFAM siRNA 48h-2

description: lncFAM siRNA replicate-2 48h


title: Gene expression in MM.1S cells cultured with lenalidomide

city: Shimotsuke

first: Yusuke

last: Furukawa

state: Tochigi

address: 3311-1 Yakushiji

department: Center for Molecular Medicine

country: Japan

institute: Jichi Medical University

hyb_protocol: Labeled cRNAs were hybridized with SurePrint G3 Human Gene Expression 8x60K version 3.0 Microarray (Agilent-072363) in Agilent In Situ Hybridization buffer Kit Plus enclosed in Agilent SureHyb-enabled hybridization chambers.

scan_protocol: Arrays were scanned on an Agilent G2505C scanner. Images were quantified using the Agilent Feature Extraction Software (version 12.0.3.1).

data_processing: Agilent Feature Extraction Software (version 12.0.3.1) was used for background subtraction and LOWESS normalization.

source_name: MM.1S cells

label_protocol: RNA samples (50 ng) were primed with T7 primer at 65°C for 10 min and reversed transcribed at 40°C for 2 h in the presence of AffinityScript, followed by T7 transcription in the presence of Cy3- or Cy5-CTP at 40°C for 2 h.

growth_protocol: We cultured KMS12 and MM.1S cells in RPMI1640 medium supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted after 24 hours using Trizol according to manufacturer's instructions.

treatment_protocol: KMS12 and MM.1S cells were cultured with 10 μM lenalidomide or 0.1% dimethylsulfoxide (DMSO) for 24 hours.

tag: condition

value: Cultured with lenalidomide

value: 24 hours in culture


title: Gene expression in KMS12 cells cultured with lenalidomide

source_name: KMS12 cells


title: MGC803 cells, DUSP5P1

data_processing:
The quality control of raw data were completed by removing low-quality reads, adaptor sequences, empty reads, reads with N sequences over 10% and rRNA reads.
aligned to the GRCh38 genome assembly using Hisat2（version:2.0.4）
Uniquely mapped reads with mapping quality >=20 were retrieved for downstream analysis.
The expression levels of the transcripts were expressed as FPKM (fragments per kilobase of transcript per million mapped reads) values of mRNA and lncRNA using the Stringtie v1.3.0
Differentially expressed mRNAs and lncRNAs were calculated by edgeR
Assembly: GRCh38
Supplementary files format and content: Excel files include FPKM values for each Sample

extract_protocol:
Total RNA was harvested using Qiagen Kit.1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were stably transfected with negative control and DUSP5P1 plasmid  respectively.

value: cancer cells

tag: genotype

value: DUSP5P1 ectopic expression

tag: treatment

value: 10% FBS DMEM

value: 2 weeks


title: Strand-specific RNA-seq in Ctle-2 siRNA treated cells- Replicate #2

description: 2021216_DESEQ2_siCtle4vssiCtle3_NormDESeq.csv; 2021216_DESEQ2_siVINKvssiCtle_NormDESeq.csv

source_name: total RNA (ribosomal RNA depleted) from Ctle-2 siRNA-treated senescent WI38 hTERT RAF1-ER cells

value: induced in senescence for 3 days and then transfected with Ctle-2 siRNA for 3 days


title: KO_d_2

value: FVB/N

value: bone marrow


title: MGC803 cells, DNA-1

value: ChIRP pull down product


title: Gene expression in MM.1S cells cultured with vehicle (DMSO) alone

value: Cultured with DMSO


title: KO_d_1


title: Gene expression in KMS12 cells cultured with vehicle (DMSO) alone


title: Strand-specific RNA-seq in cells deleted for the siRNA target site and treated with VINK-1 siRNA -Replicate #1

value: WI38 hTERT RAF1-ER deleted for siRNA VINK1 target site

value: induced in senescence for 3 days and then transfected with VINK-1 siRNA for 3 days


title: Control siRNA 48h-3

description: Control siRNA replicate-3 48h

value: Myoblast

value: Control siRNA 48h


title: Strand-specific RNA-seq in Ctle-2 siRNA treated cells- Replicate #1

value: WI38 hTERT RAF1-ER


title: Strand-specific RNA-seq in VINK-1 siRNA treated cells- Replicate #2

description: 2021216_DESEQ2_siVINKEX2vssiCtle3_NormDESeq.csv; 2021216_DESEQ2_siVINKvssiCtle_NormDESeq.csv


title: 20-month bone marrow

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: bone marrow

extract_protocol:
Bone marrow was flushed and kept in MACS Tissue Storage Solution (Miltenyi Biotec). Samples were sieved through 40µm cell strainers, and centrifuged at 300 g for 5 min. Pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) for lysing red blood cells.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

tag: age


title: 6-month bone marrow


title: MGC803 cells, ctrl

value: WT


title: Control siRNA 48h-2

description: Control siRNA replicate-2 48h


title: CalibrationCurves_HIV-RT_80%_AP-site

data_processing:
The sequencing data was all trimmed with cutadapt tool to remove adapters and low-quality reads. PCR duplicates were removed with BBMap tool (https://sourceforge.net/projects/bbmap/), 5-mer random barcodes at reads ends were trimmed, and low-quality or short reads (less than 20 nt) were removed using cutadapt tool. Remaining reads were aligned to the RNA oligo sequence using Tophat2 (version 2.1.1) and bowtie2 (version 2.3.5.1) allowing at most three mismatches. The generated .bam files were split into positive and negative strands and sorted using Samtools (http://samtools.sourceforge.net/). Sequence variants were identified by measuring the base composition at each position using fine-tuned bam-readcount (https://github.com/genome/bam-readcount). The generated bam-readcount results were parsed and analyzed by in-house scripts. G to T or C or A mutation ratios as well as deletion ratios at each AP site were calculated by data output from bam-readcount pipeline and confirmed by direct visualization through IGV software (https://software.broadinstitute.org/software/igv/).
genome build: Synthetic oligos

organism: synthetic construct

source_name: synthetic RNA oligo

growth_protocol: The 31-mer RNA probe GAACGNN/irSp/NNUUCCCAGUACGUGAUGCCAAU was used as “100% AP-site” standard. The RNA oligo GAACGNNGNNUUCCCAGUACGUGAUGCCAAU was used as “0% AP-site”. Then the “100% AP-site” and “0% AP-site” standard were mixed and generated 6 oligo mixtures with different modification fractions (100%, 80%, 60%, 40%, 20% and 0%).

extract_protocol:
Synthetic RNA oligo probes were used for library construction.
For 200 ng of each mixed RNA oligo set (100%, 80%, 60%, 40% ,20% and 0% AP-site), proceed with RNA 3'ligation directly. Mix 1.0 µL 20 µM 3’ linker (5’rApp + random-barcode + adaptor sequence + C3-spacer) with repaired 10 µL RNA fragments and incubate the mixture at 70 °C for 2 min for denaturation. Immediately move onto ice. Then add 2.5 µL 10X T4 RNA Ligase Rxn Buffer, 7.5 µL 50% PEG8000, 1 µL SUPERnaseIn, and 1 µL H2O. Mix everything well before adding T4 RNA ligase 2 truncated KQ. Then add 2.0 µL T4 RNA lig-ase 2 truncated KQ and mix well again. Incubate the reaction at 25 °C for 2 hours, followed by 16 °C for 12 hours. Then add 23 µL RNase-free water to dilute the reaction mixture. Add 2.0 µL 5-deadenylase, mix well/incubate at 30 °C for 30 min; then add 1.0 µL RecJf, mix well/incubate at 37 °C for another 30 min. Recover RNA with RNA Clean and Concentrator kit (RCC) and elute to 10 µL with RNase-free water. Mix 1.0 µL 2 uM RT-primer with 2 µL ligated RNA fragments and incubate the mixture at 65 °C for 2 min for denaturation. Immediately move onto ice. Then add 2 µL 10X AMV RT Rxn Buffer, 2 µL 10mM dNTP, 0.5 µL RNaseOut, and 10.5 µL H2O. Mix everything well before adding HIV RT. Then add 2.0 µL HIV RT and mix well again. Incubate the reaction at 37 °C for 1.5 hours. After RT, add 1.0 µL RNaseH (NEB) into the reaction mixture. Mix well/incubate at 37 °C for 20 min. Then 70 °C for 5 min to denature. Recover RNA with Oligo Clean and Concentrator kit (OCC) and elute to 10 µL with RNase-free water. Mix 1.0 µL 50 uM cDNA 3'-adapter with 10 µL cRNA and incubate the mixture at 75 °C for 2 min for denaturation. Immediately move onto ice. Then add 3 µL 10X T4 RNA Ligase Rxn Buffer, 15 µL 50% PEG8000, and 3 µL 10mM ATP. Mix everything well before adding T4 RNA Ligase 1. Then add 1.0 µL T4 RNA Ligase 1 and mix well again. Add ligase enzyme to one sample followed by mixing this sample immediately. Mix each sample one by one. Do not add ligase enzyme to all samples and then start mixing everything.  Incubate the reaction at 25 °C for 12 hours. After the 12-hour cDNA ligation, heat at 65 °C for 5 min for denature. Purify the cDNA by DNA Clean & Concentrator-5. Elute cDNA with 20 µL DNase-free water the reaction mixture. Mix again and then use 4 µL per sample for each PCR amplification.
RNA-Seq. All libraries were sequenced on Illumina NovaSeq 6000 with single-end 100 bp read length.

value: synthetic RNA oligo

tag: tag


title: Control siRNA 48h-1

description: Control siRNA replicate-1 48h


title: 1-month bone marrow


title: Strand-specific RNA-seq in Ctle-1 siRNA treated cells- Replicate #2

description: 2021216_DESEQ2_siCtle4vssiCtle3_NormDESeq.csv; 2021216_DESEQ2_siVINKEX2vssiCtle3_NormDESeq.csv

value: induced in senescence for 3 days and then transfected with Ctle-1 siRNA for 3 days


title: Strand-specific RNA-seq in VINK-1 siRNA treated cells- Replicate #1


title: Strand-specific RNA-seq in Ctle-1 siRNA treated cells- Replicate #1


title: lncFAM siRNA 16h-2

description: lncFAM siRNA replicate-2 16h

value: lncFAM siRNA 16h


title: lncFAM siRNA 16h-3

description: lncFAM siRNA replicate-3 16h


title: 20-month brain

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 40%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: brain

extract_protocol:
Brain tissues were surgically removed and minced into small pieces (approximately 1mm3) on ice and digested by 200 U/mL Papine (Diamond) and Cysteine-HCL (Sigma). Then samples were sieved through 70 µm cell strainers, centrifuged at 300 g for 10 min, and further cleaned for red blood cells using red blood cell lysis buffer (Miltenyi Biotec).
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols


title: CalibrationCurves_HIV-RT_40%_AP-site

treatment_protocol: Synthetic RNA oligo probes were used for library construction.


title: MIA PACa-2 siING3 IP H1.2

description: MIA PaCa-2cells were transiently transfected with siRNA against ING3 followed by chromatin immunoprecitation with antibody against Anti-Histone H1.2

data_processing:
alignment: Sequencing reads in fastq‐format were aligned to the UCSC hg38 reference genome using BWA (version 0.7.9a bwa mem with default options). Duplicate reads were removed with Picard tools (v. 1.115) MarkDuplicates and were filtered to retain only primary alignments with samtools (v0.1.19, view command with ‐F 0x100 flag).
peak calling: ChIP‐seq peaks were called using HOMER (v4.7) findPeaks using matched input samples with default settings (Poisson pvalue of <= 1E‐4 and fold change >=4.0). For histone marks, the histone option was employed. Further, peaks are annotated using HOMER's annotatePeaks utility using the hg19 annotations database provided with the software.
Genome_build: UCSC hg38 reference genome
Supplementary_files_format_and_content: The processed data files are in bedGraph format and tab-delimited text format and represent a detailed description of the peak chromosomal coordinates enriched in each sample, peak scores, focus ratio/region size, distance to TSS and detail annotation. Furthermore, all relevant information for the nearest promoter is provided.

source_name: MIA PACa-2 siING3

extract_protocol:
Chromatin immunoprecipitation and final DNA purification was carried out using the SimpleChIP Plus Enzymatic Chromatin IP Kit (9005, Cell Signaling Technology)
NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® (E6240, New England BioLabs)

treatment_protocol: MIA PaCa-2 cells were trypsinized and transfected with 50nΜ siRNA for ING3 or scramble siRNA. Lipofectamine ® RNAiMAX was used as transfection reagent. RNA-Lipofectamine complexes were made in Opti-MEM (serum free). Cells were plated at a 50% confluence in serum and antibiotic-containing media. 24h later double transfection was performed with the same amounts of siRNAs and cells were incubated for 24h before chromatin isolation.

value: MIA PaCa-2 pancreatic cancer cell line

value: epithelial cells derivef from pancreatic carcinoma

tag: genotype/variation

tag: chip antibody

value: Anti-Histone H1.2 (Abcam, ab4086, GR257 602-2)


title: CalibrationCurves_HIV-RT_0%_AP-site


title: lncFAM siRNA 16h-1

description: lncFAM siRNA replicate-1 16h


title: 1-month brain


title: SARS-CoV-2 pseudovirus infected 18-month BMMs

source_name: Bone marrow derived macrophage (BMM)

growth_protocol: BMMs were grown in Minimum Essential Media (alpha-MEM, Thermo) supplemented with 10% fetal bovine serum (FBS, Thermo) and 1% penicillin-streptomycin (Thermo) and maintained at 37 ℃ in a fully humidified incubator containing 5% CO2, and in the presence of M-CSF (30 ng/ml)

extract_protocol:
BMM Sample washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA. Dissociated single cells were then stained with AO/PI for viability assessment using Countstar Fluorescence Cell Analyzer.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

treatment_protocol: BMMs were seeded on to plates for 24 hrs, and infected with SARS-CoV-2 pseudovirus

tag: infection

value: SARS-CoV-2 pseudovirus infected


title: MIA PaCa-2 siING3 2% input

description: 2% input (sequencing control) for the following sample: MK14C_siING3 IP H1.2

source_name: MIA PaCa-2 siING3


title: 6-month brain


title: MIA PACa-2 sicon IP H1.2

description: MIA PaCa-2cells were transiently transfected with scramble siRNA followed by chromatin immunoprecitation with antibody against Anti-Histone H1.2

source_name: MIA PACa-2 sicon

value: siControl


title: CalibrationCurves_HIV-RT_100%_AP-site


title: Control siRNA 16h-2

description: Control siRNA replicate-2 16h

value: Control siRNA 16h


title: MIA PaCa-2 sicon 2% input

description: 2% input (sequencing control) for the  following sample: MK10C_si control IP H1.2

source_name: MIA PaCa-2 sicon


title: SARS-CoV-2 pseudovirus infected 1-month BMMs


title: Control siRNA 16h-1

description: Control siRNA replicate-1 16h


title: WFB10ZE3_rep3

status: Public on Nov 17 2022

city: 南昌

first: Jianmin

last: Bian

state: 江西 (Jiāngxī)

address: 志敏大道1101

institute: 江西农业大学

data_processing:
Illumina Casava1.7 software used for basecalling.
A cDNA library constructed by technology from the pooled RNA from brain samples of pig was sequenced run with Illumina 4000 sequence platform. Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon paired-end reads of bp length. This yielded gigabases (Gb) of sequence. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed .After that, a total of G bp of cleaned ,paired-end reads were produced. The raw sequence data have been submitted to the NCBI Short Read Archive with accession number .
RNA-seq reads mapping:we aligned reads of sample A and sample B to the UCSC (http://genome.ucsc.edu/) homo sapiens reference genome using HISAT package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT allows multiple alignments pe read (up to 20 by default) and a maximum of two mismatchs when mapping the reads to the reference.HISAT build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
Transcript abundance estimation and differentially expressed testing:The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the ﬁnal transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package.
Genome_build: Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Oryza sativa

source_name: grain

growth_protocol: The plants were cultivated at the experimental feld of Jiang xi Agricultural University, Nanchang province (28°68′ N, 115°86′ E;   long-day conditions) in 2019 Nanchang.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 1000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Following purification, the mRNA is fragmented into smallpieces using divalent cations under elevated temperature. Then the cleaved RNA fragments werereverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNASeq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-endlibraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an IlluminaHiseq4000 at the (LC Sceiences,USA) following the vendor’s recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: grain filling stage

value: 10th day of post-anthesis

value: grain

tag: cultivar

value: Wufeng B


title: WFB10ZE2_rep2

tag: time


title: WFB1ZE1_rep1

value: 1st day post-anthesis


title: WFB10ZE1_rep1


title: CalibrationCurves_HIV-RT_60%_AP-site


title: WFB1ZE2_rep2


title: WFB1ZE3_rep3


title: WFY10ZE2_rep2


title: WFY10ZE1_rep1


title: Control siRNA 16h-3

description: Control siRNA replicate-3 16h

value: Myoblast


title: WFY10ZE3_rep3


title: WFY1ZE1_rep1


title: CH10ZE2_rep2

value: Changhui T025


title: CH1ZE3_rep3


title: CH10ZE1_rep1


title: WFY1ZE2_rep2


title: CH1ZE1_rep1


title: CalibrationCurves_HIV-RT_20%_AP-site


title: WFY1ZE3_rep3


title: CH10ZE3_rep3