title: Control6, snRNAseq

description: ovary tissue from Medullablastoma

data_processing:
The BCL files generated by Illumina sequencing were demultiplexed using the Cell Ranger mkfastq default pipeline to obtain fastq files for each sample.
Alignment of reads (genome hg38), filtering and UMI counting was performed to obtain gene barcode matrix file (gene counts per nucleus) using Cell Ranger software from 10x Genomics.
Assembly: h38
Supplementary files format and content: feature_bc_matrix.h5 file. The "matrix.h5 file contains information about the features (genes) and cell-barcodes associated with the matrix rows and columns

source_name: Ovary

extract_protocol:
Nuclei were isolated from flash-frozen ovarian tissues from five CG and four control patients using a modified method from 10X genomics chromium nuclei isolation kit (dx.doi.org/10.17504/protocols.io.6qpvr4jb2gmk/v1).  The nuclei were purified with washing in nuclei suspension buffer and sucrose density gradient centrifugation. Freshly prepared 8,000 nuclei were loaded onto Chromium microfluidic chip used to generate single-cell gel bead emulsions using the 10x Genomics Chromium controller. Later cDNA amplification was performed, and libraries were prepared as per the 10x Genomics manufacturer’s protocol. Libraries were pooled and sequenced on S2 flow cell (paired-end 100 bp) using an Illumina NovaSeq 6000 platform.
snRNAseq libraries from nuclei isolated from ovarian tissue were constructed using 10x Genomics Chromium Next GEM Single Cell 3ʹ Kit v3.1

value: Ovarian cells


title: CG4, ST

status: Public on Feb 19 2025

type: SRA

city: Bethesda

first: Raghuveer

last: Kavarthapu

state: MD

address: 10 Center Dr, Bldg 10, Room 1E3340

department: NICHD

country: USA

institute: National Institutes of Health (NIH)

library_source: transcriptomic

data_processing:
Raw sequencing files generated by Illumina sequencing were demultiplexed & processed using the Space Ranger default pipeline to obtain fastq files for each sample.
Alignment of reads (genome hg38), filtering and UMI counting was performed to obtain gene barcode matrix file (gene counts per nucleus) using Space Ranger software from 10x Genomics.
Assembly: hg38
Supplementary files format and content: filtered_feature_bc_matrix.h5 file : The "matrix.h5 file contains information about the features (genes) and cell-barcodes associated with the matrix rows and columns
Supplementary files format and content: scalefactors_json.json : scale factors in json format
Supplementary files format and content: tissue_positions.csv :  list of barcodes and coordinate specifying visium spots
Supplementary files format and content: tissue_hires_image.png : high-resolution images of the ovarian sections
Library strategy: Visium Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: ovary tissue from CG patient

extract_protocol:
FFPE ovary sections (5 microns) were mounted onto a positively charged slide followed by staining with hematoxylin and eosin. Slides were mounted in 70% glycerol and brightfield images were taken using microscope.  The tissue sections were transferred immediately onto 6.5 × 6.5mm or 11mm x 11mm capture areas on a Visium gene expression slide using Visium CysAssist (10x Genomics). The tissue sections were then subjected to permeabilization followed by reverse transcription for cDNA synthesis. Subsequently, the cDNA amplification was performed, and spatial libraries were constructed. The libraries were pooled and paired-end sequencing was performed on S2 flow cell using an Illumina NovaSeq 6000 platform.
Spatial transcriptome sequencing libraries from ovarian tissue were constructed using 10x Genomics Visium spatial gene expression slide & reagent kit

tag: tissue

value: Ovary

tag: group

value: CG


title: Skin, biopy sampling, bulk, DLB-1655

city: Burnaby

first: Antoine

middle: Etienne

last: Simond

state: BC

address: 8888 university drive

department: Biological Sciences

country: Canada

institute: Simon Fraser University

description: Total RNA were extracted from TRIzol then reverse-transcripted into cDNA, the library used was rRNA-depleted stranded (HMR) and the adapter used was NEBNext_dual

data_processing:
Total RNA extraction using TRIzol
RNA cleaning
Library preparation using the library preparation kit NEBNext® rRNA Depletion (Human/Mouse/Rat)
Analyses were carried out by Genome Quebec (Montreal, QC, Canada) using an Illumina NovaSeq 6000 S4 system, with an average of 37 million reads per sample
Sequencing reads were processed using the genPipes framework. Briefly, adaptor sequences and low-quality score containing bases (Phred score < 30) were trimmed from reads using Trimmomatic.
Assembly: The resulting Reads were aligned to the beluga ASM228892v3 genome, using 2 passes of STAR.
Supplementary files format and content: The file "raw_counts.csv" contains the raw counts obtained using HTSeq.
Supplementary files format and content: The file "traits.csv" contains traits data of each samples, i.e., contaminant data (ng/g lw), population, sampling date, RNA quality (RIN number)
Supplementary files format and content: The file "gene_IDs.tsv" contains the IDs of the genes that were measured. Identified genes are originally given in ENSEMBL IDs. This file allows the conversion of ENSEMBL IDs into others such as Symbol IDs (abbreviations and full names) and Entrez IDs.

organism: Delphinapterus leucas

source_name: skin

extract_protocol:
TRIzol
Library preparation kit NEBNext® rRNA Depletion (Human/Mouse/Rat)

value: skin

tag: population

value: SLE

tag: Sex

value: M


title: CG3, ST


title: Control2, ST

source_name: ovary tissue from Dock9 deficiency patient

value: control


title: ATACseq-RFTS-KD-IAA_replicate-3

city: La Tronche

first: Christopher

last: Swale

address: Batiment Jean Roger

department: U1209 - Institute of Advanced Biosciences

country: France

institute: INSERM

description: ATACseq-RFTS-IAA-merged.bw

library_source: genomic

data_processing:
Following the demultiplexing of raw reads by bcl2fastq V3, trimming, quality control, alignment to the ME49 reference genome (using bwa2).
Aligned reads were used for peak calling of the ChIP enriched peaks using Generich with a cutoff p-value of 0.1. Reads were counted on annotated peaks by featureCounts and counts were processed by DeSeq2 to generate global statistical analysis of peak intensities in between conditions using biological triplicates.
Assembly: Assembly: Toxoplasma gondii genome (ME49 strain) file "ToxoDB-13.0_TgondiiME49_Genome.fasta" dowloaded from the ToxoDB website : http://toxodb.org/common/downloads/release-13.0/TgondiiME49/fasta/data/
Supplementary files format and content: Supplementary files format and content: Data visualization:  Merged bam files were converted to bigWig file format using a bin size of 5 by bamCoverage (Deeptools).

molecule: genomic DNA

organism: Toxoplasma gondii

source_name: RH

growth_protocol: Toxoplasma gondii type I strains were maintained by serial passage Human foreskin fibroblast (HFF) monolayer under tachyzoite conditions in DMEM (Life) supplemented with 10% (vol/vol) FBS (Life) and 25 mM Hepes buffer, pH 7.2.

extract_protocol:
Diagenode ATAC-SEQ kit protocol (C01080002)
Diagenode ATAC-SEQ kit protocol (C01080002) in 100 000 tachyzoites

treatment_protocol: HFF cells were grown to confluence and infected with HK80 SNF2h KD, RHK80 RFTS KD, RHK80 SNF2L KD or RHK80  MORC KD strains. Genome-wide Tn5 transposase accessiblity profiles in each strain left untreated (UT) and treated with IAA (indole-3-acetic acid) for 24 hours.

tag: cell line

value: RH

tag: cell type

value: Intracellular tachyzoites

tag: genotype

tag: treatment

value: IAA treated for 24h


title: Cre-MAG4/Pt (biol rep 2)

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10 (v3.0.0)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: lung

growth_protocol: Female mice aged 5 months were used for experiments. All mice were kept under specific pathogen-free conditions and cared for according to regulations reviewed and approved by Baylor College of Medicine Committee on the Use and Care of Animals

extract_protocol:
Lungs were digested using Miltenyi mouse lung digestion kit and gentleMACs Tissue Dissociator, and sorted for live cells on Sony SH800 using 70μm sorting chip. 1-3 lungs were pooled together. The viability of cells was greater than 90% as confirmed with 0.2% Trypan blue staining.The samples were performed on the 10X Genomics Chromium pltaform following the user guide manualXXXX and Single CEll 3' Reagent Kit.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: multiple

value: lung

tag: strain

tag: age

value: 5 months


title: Skin, biopy sampling, bulk, DLB-1662


title: ATACseq-RFTS-KD-UT_replicate-2

description: ATACseq-RFTS-UT-merged.bw

value: untreated sample


title: Control4, snRNAseq

description: ovary tissue from Rhabdosarcoma


title: Skin, biopy sampling, bulk, DLB-1664


title: ATACseq-RFTS-KD-UT_replicate-1

description: ATACseq-RFTS-UT-merged.bw


title: Control5, snRNAseq

description: ovary tissue from Medullablastoma


title: MAG4/Pt

description: 10x Genomics


title: ATACseq-RFTS-KD-IAA_replicate-1

description: ATACseq-RFTS-IAA-merged.bw


title: ATACseq-RFTS-KD-UT_replicate-3

description: ATACseq-RFTS-UT-merged.bw


title: Skin, biopy sampling, bulk, DLB-1666


title: ATACseq-SNF2h-KD-IAA_replicate-3


title: Control3, snRNAseq

description: ovary tissue from Ewing sarcoma


title: Skin, biopy sampling, bulk, DLB-1668


title: Wnt2-CreERT2 driven EYFP lineage, E10.5, sequencing lane 1

city: Philadelphia

first: Sylvia

middle: N

last: Michki

state: PA

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

data_processing:
Reads from L1 and L2 from each experimental condition were simultaneously aligned to the GRCm39 genome using STAR-solo to generate gene by cell counts matrices, using the parameters soloUMIdedup=”1MM_CR”, soloUMIfiltering=”MultiGeneUMI_CR”, and soloCellFilter=”EmptyDrops_CR”.
Counts matrices processed using anndata and scanpy
Assembly: GRCm39
Supplementary files format and content: h5ad anndata-readable annotated scRNA-seq dataset processed with scanpy

molecule: polyA RNA

source_name: lung/heart

extract_protocol:
Single cell suspensions were made from tissue dissected from the thoracoabdominal area of two litters of whole embryos at E10.5, combined heart and lung dissected out from four embryos at E12.5, and four separated hearts that included the pulmonary vein and artery up to the hilum of the lung at E17.5, and four separated lungs containing only intrapulmonary tissue at E17.5. EYFP+ cells were isolated via FACS .
10Xv3 GEX

value: lung/heart


title: CG5, snRNAseq

description: ovary tissue from CG patient


title: ATACseq-SNF2h-KD-IAA_replicate-2


title: Skin, biopy sampling, bulk, DLB-1657


title: MAG4

description: 10x Genomics


title: Skin, biopy sampling, bulk, DLB-1670


title: Cre-MAG4/Pt (biol rep 1)

description: 10x Genomics


title: CG4, snRNAseq

description: ovary tissue from CG patient


title: Skin, biopy sampling, bulk, DLB-1672


title: Pt

description: 10x Genomics


title: ATACseq-SNF2h-KD-IAA_replicate-1


title: HA_4

city: Jinan

first: Shourui

last: Hu

address: wenhuaxi road 44

country: China

institute: Shandong University

data_processing:
We used Bowtie2 to align Clean reads to the reference gene sequence and then used RSEM to calculate gene expression levels for individual samples.
The DEseq2 method is based on the principle of negative binomial distribution and this project is based on the method described in Michael I, et al for differential gene DEG.
Assembly: Ensembl_release110
Supplementary files format and content: Text file with raw gene counts for every gene and every sample

source_name: islet

extract_protocol:
1 μg of total RNA was subjected to library synthesis using RNeasy Mini Kit (Qiagen, Hiden, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: islet

value: hyperandrogenism


title: CG3, snRNAseq

description: ovary tissue from CG patient

value: Ovarian cells


title: ATACseq-SNF2h-KD-UT_replicate-3


title: Skin, biopy sampling, bulk, DLB-1675


title: CG2, snRNAseq

description: ovary tissue from CG patient

value: Ovary


title: HA_2


title: HA_3


title: ATACseq-SNF2h-KD-UT_replicate-2


title: Skin, biopy sampling, bulk, DLB-1677


title: ATACseq-SNF2h-KD-UT_replicate-1


title: Skin, biopy sampling, bulk, DLB-1679


title: RNAseq_Molm13_sgCOX4I1#3

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

data_processing:
Illumina RTA was used to create .bcl files, and bcl2fastq v2.20.0.422 software was used for base calling (for samples split between flowcells and later merged per run)
RNA-seq reads aligned to the GRCh38 genome assembly using STAR_2.6.0a, Aligned reads was normalized by edgeR bioconductor package and outputed as rpkm.txt file
Assembly: GRCh38
Supplementary files format and content: raw count table in txt format of every sample in RNAseq project

growth_protocol: Cas9-expressing Molm13 cells transduced with sgCtrl or sgCOX4I1 and seleted in 1.0 ug/ml puromycine.

extract_protocol:
Total RNA was extracted using the RNeasy kit (QIAGEN) for RNAseq.
Eukaryotic mRNA directional library prep were used for RNAseq.

treatment_protocol: sgCtrl and sgCOX4I1 were cloned into ipUSEPR vector and transduced via lentiviral infection.

value: MLL-r leukemia

tag: transduction


title: SNF2h-KD-HA_MORC-antibody_IAA24h

data_processing:
Data Analysis: After receiving demultiplexed fastq files from the sequencing service provider (ArrayStar), reads were aligned to Toxoplasma gondii reference genome (TGME49) using BOWTIE2. Aligned reads were used for peak calling of the ChIP regions using MACS2. Statistically significant ChIP-enriched regions (peaks) were identified individually using a p-value threshold of 10-5. BigWig datasets were generated using  bedGraphToBigWig to convert the bedgraph file generated by MACS2
Data visualization: The mapped 100 bp reads represent enriched DNA fragments by ChIP experiment. Any region of interest in the raw ChIP-seq signal profile can be directly visualized in genome browser. We use 10-bp resolution intervals (10-bp bins) to partition the stacked reads region, and count the number of reads in each bin.  All the 10 bp resolution ChIP-seq profiles of each sample are saved as UCSC wig format files, which can be visualized in Toxoplasma gondii Genome Browser (http://protists.ensembl.org/Toxoplasma_gondii/Info/ Index).
Assembly: Toxoplasma gondii genome (ME49 strain) file "ToxoDB-13.0_TgondiiME49_Genome.fasta" to upload at ToxoDB website : http://toxodb.org/common/downloads/release-13.0/TgondiiME49/fasta/data/
Supplementary files format and content: Statistically significant ChIP-enriched regions (peaks) were identified individually, using a p-value threshold of 10-4. Te BigWig format file containing the ChIP-enriched regions and was generated for each sample. We use 10-bp resolution intervals (10-bp bins) to partition the stacked reads region, and count the number of reads in each bin.  All the 10 bp resolution ChIP-seq profiles of each sample are saved as UCSC wig format files, which can be visualized in Toxoplasma gondii Genome Browser (http://protists.ensembl.org/Toxoplasma_gondii/Info/ Index).

extract_protocol:
Crosslinked chromatin was lysed in ice-cold lysis buffer (50mM HEPES KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5%NP-40, 0.125% triton X-100, protease inhibitor cocktail) and sheared in shearing buffer (1mM EDTA pH8.0, 0.5mM EGTA pH8.0, 10mM Tris pH8.0, protease inhibitor cocktail) by sonication using a Diagenode Biorupter. Samples were sonicated, for 16 cycles (30 seconds ON and 30 seconds OFF), to 200-500 base-pair average size. Immunoprecipitation was carried out using sheared chromatin, 5% BSA, protease inhibitor cocktail, 10% triton X-100, 10% deoxycholate, DiaMag Protein A-coated magnetic beads (Diagenode) and antibodies (H4K5acK8acK12acK16ac, H4K31me1, HDAC3, and HA). A rabbit IgG antiserum was used as a control mock. After overnight incubation at 4°C on rotating wheel, chromatin-antibody complexes were washed and eluted from beads by using iDeal ChIP-seq kit for Histones (Diagenode) according to the manufacturer’s protocol. Samples were decrosslinked by heating for 4 hours at 65°C. DNA was purified by using IPure kit (Diagenode) and quantified by using Qubit Assays (Thermo Fisher Scientific) according to the manufacturer's protocol. For ChIP-seq, purified DNA was used to prepare libraries and then sequenced by Arraystar (USA, http://www.arraystar.com/).
ChIP-Sequencing library preparation was performed according to Illumina’s protocol Preparing Samples for ChIP Sequencing of DNA. Library Preparation: 10 ng DNA of each sample was converted to phosphorylated blunt-ended with T4 DNA polymerase, Klenow polymerase and T4 polymerase (NEB); An ‘A’ base was added to the 3' end of the blunt phosphorylated DNA fragments using the polymerase activity of Klenow (exo minus) polymerase (NEB); Illumina's genomic adapters were ligated to the A tailed DNA fragments; PCR amplification was performed to enrich ligated fragments using Phusion High Fidelity PCR Master Mix with HF Buffer (Finnzymes Oy). The enriched product of ~200-700 bp was cut out from gel and purified. Sequencing:  The library was denatured with 0.1M NaOH to generate single-stranded DNA molecules, and loaded onto channels of the flow cell at 8pM concentration, amplified in situ using TruSeq Rapid SR cluster kit (#GD-402-4001, Illumina). Sequencing was carried out by running 100 cycles on Illumina HiSeq 4000 according to the manufacturer’s instructions.

treatment_protocol: HFF cells were grown to confluence and infected with RHKU80 SNF2h mAID HA strains. Genome-wide SNF2h and MORC occupancy profiles in RHKU80 SNF2h mAID HA left untreated (UT) and treated with IAA (indole-3-acetic acid) for 24 hours. Harvested intracellular parasites were crosslinked with formaldehyde (final concentration 1%) for 8 mins at room temperature and the crosslinking was stopped by addition of glycine (final concentration 0.125M) for 5 min at room temperature.

tag: chip antibody

value: MORC - Home made antibody (Farhat et al., 2020)


title: CG1, snRNAseq

description: ovary tissue from CG patient


title: Skin, biopy sampling, bulk, DLB-1681

value: skin

value: SLE


title: RNAseq_Molm13_sgCOX4I1#2


title: HA_1


title: Ctrl_2

value: control


title: SNF2h-KD-HA_HA-antibody_IAA24h

value: RH

value: HA antibody (Cell Signaling)


title: RNAseq_Molm13_sgCOX4I1#1


title: Ctrl_3


title: Skin, biopy sampling, bulk, DLB-1683

value: M


title: RNAseq_Molm13_sgCtrl#3

value: sgCtrl


title: SNF2h-KD-HA_MORC-antibody_UT

value: Intracellular tachyzoites


title: LSK_HTO

city: Parkville

first: Carolyn

last: de Graaf

state: VIC

address: 1G Royal Parade

country: Australia

institute: WEHI

description:
Cul5-/- LSK (Lin- Sca+ Kit+) cells from the bone marrow (enriched for haematopoietic stem cells)
10x Genomics

data_processing:
Read alignment and count summarization were performed using CellRanger v2.0 using the Illumina BCL files as input.
Assembly: mm10
Supplementary files format and content: matrix.mtx files contain genewise read counts for all cells in a space-efficient matrix market format; genes.tsv files contain Ensembl IDs and gene symbols as tab-delimited text; barcode.tsv files contain the 10X barcodes used to identify cells.

extract_protocol:
A 10X Genomics Chromium machine was used for 3,900-6,900 single cell capture and cDNA was prepared using the Single Cell 3’ Protocol recommended by the manufacturer.
The 10X Genomics Chromium machine partitions cells into Gel Bead-In-EMulsions (GEMs), where all generated cDNA share a common 10x Genomics barcode but uses a pool of  about 750,000 barcodes to separately index each cell’s transcriptome. The P7 and R2 primers were added during the GEM incubation and the P5, and R1 during library construction via end repair, A-tailing, adaptor ligation and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. The sequencing was carried out on an Illumina Nextseq 500 to achieve paired-end 75 bp reads.

value: Bone Marrow

value: Adult

value: multiplexed sample:Cul5+/+ or Cul5-/-


title: LSK_GEX

description:
wildype LSK (Lin- Sca+ Kit+) cells from the bone marrow (enriched for haematopoietic stem cells)
10x Genomics


title: Total LSK/Tom+ LSK cells, HTO

city: New York City

first: Boris

last: Reizis

state: New York

address: 550 1st Ave

department: Pathology

institute: NYU Grossman School of Medicine

description:
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz

library_source: other

data_processing:
fastqs aligned to mm10 and quantitated by Cellranger v6; hashtag demultiplexing perfromed with Seurat v4 HTODemux function; downstream processing performedb by iCellR, QC parameters: max mitochondrial percent < 5; max genes = 6000; min genes =200.
Assembly: mm10
Supplementary files format and content: gzipped counts matrix; corresponding cell barcodes and gene names
Library strategy: CITE-seq

molecule: protein

source_name: Bone marrow

extract_protocol:
Tom+ Lin- Sca-1+ c-Kit+ (LSK) cells from Kras reporter mice (n=2) or total LSK cells from WT reporter mice (n=2) were sorted. Single cells were encapsulated into emulsion droplets using Chromium Controller (10x Genomics) and subsequent scRNA-seq and Cell Surface Protein libraries were constructed using Chromium Single Cell 3′ v3.1 Reagent Kit according to the manufacturer’s protocol.
Briefly, cell populations were hashtagged using BioLegend Type B oligo-tagged antibodies and counted using a BioRad TC20 Automated Cell Counter. Cells were then pooled and placed in each channel of a Next GEM Chip, loaded onto the Chromium instrument and an emulsion was created. Reverse transcription and library preparation were performed on a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad). cDNA was amplified 11 cycles and evaluated on a Agilent BioAnalyzer 2100 using a High Sensitivity DNA Kit (Agilent Technologies). Final Gene Expression and Cell Surface Protein libraries were amplified 14 and 10 cycles respectively and visualized on an Agilent TapeStation 4200 using High Sensitivity D1000 ScreenTape (Agilent Technologies). Individual libraries were diluted to 2nM and pooled for sequencing. Pools were sequenced with an S2 100 cycle run kit (28bp Read1, 8bp Index1 and 91bp Read2) on the NovaSeq 6000 Sequencing System (Illumina).

value: Bone marrow

value: Pdzk1ip1-CreER R26Tom/Tom KrasG12D, Pdzk1ip1-CreER R26Tom/Tom KrasG12D

value: mixed sample (WT, Kras)

tag: library type

value: HTO

tag: hto

value: TotalSeqTM-B 0301 anti-mouse Hashtag 1, TotalSeqTM-B 0302 anti-mouse Hashtag 2, TotalSeqTM-B 0303 anti-mouse Hashtag 3, TotalSeqTM-B 0304 anti-mouse Hashtag 4


title: RNAseq_Molm13_sgCtrl#2

value: MLL-r leukemia


title: SNF2h-KD-HA_HA-antibody_UT

value: untreated sample


title: Total LSK/Tom+ LSK cells, GEX

value: mRNA


title: his-9/H3.1 reporter strain, rep 4, whole organism, starved, input

city: Indianapolis

first: Scott

middle: T

last: Aoki

state: Indiana

address: 635 Barnhill Drive MS-4071

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

description: Library name: H3.1_starved_rep_4_input

data_processing:
Fastq raw sequencing files were assessed for quality and filtered to remove adaptors by fastp. Filtered reads were aligned to the C. elegans genome using Bowtie 2 with WBcel235(ce11) as the reference genome. Read alignments were further processed using SAMtools to remove duplicate and mitochondrial reads and BEDtools to remove any “blacklisted” alignments found in the C. elegans genome (UCSC). DeepTools was used to generate bigwig files for visualization of enriched regions on genome browsers.
deepTools was used to normalize all bigWig files. All samples were normalized to themselves using the reads per genomic content (RPGC) method.
Assembly: ce11
Supplementary files format and content: bigWig

organism: Caenorhabditis elegans

source_name: Whole organism

growth_protocol: Large synchronized populations of his-58/H2B, his-9/H3.1, and N2 (WT) were generated by standard bleaching protocol and allowed to develop for 72 hours on NGM plates seeded with HB101 bacteria as a food source.

extract_protocol:
Frozen worms were lysed by a pre-chilled biopulverizer (Biospec, #59013N). Pulverized samples were moved to a pre-chilled mortar and grinded vigorously with mortar and pestle (Fisher, #FB961B; #FB961L). Sample powder was moved to tubes and reconstituted in Nuclei Preparation Buffer (NPB) (10 mM HEPES pH 7.5, 10 mM KCl, 1.5 mM MgCl2, 0.1% Triton X-100) containing protease inhibitors (Promega, #G6521). Samples were cross-linked in 1.1% PFA (Fisher, # 50-980-487) for 4 minutes and quenched for 10 minutes with 125 mM (final concentration) Glycine (VWR, # 97061-128). Samples were washed in NPB + protease inhibitors and resuspended in lysis buffer (50 mM Tris pH 8.1, 10 mM EDTA, 0.25% SDS) plus protease inhibitors. A Diagenode Bioruptor Plus sonicator (#B01020001) and TPX tubes (Diagenode, #NC0065146) were used to sonicate samples to generate 400-500 bp DNA fragments.
Input and IP sequencing libraries were generated using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, #E7645S) with barcodes unique to each of the samples (NEB, #E7335S; #E7500S).

treatment_protocol: Synchronized young adult worms were washed off plates with 1x PBS + Tween-20 and subsequently washed until bacteria was no longer present in supernatant. Worms from each strain were then split in half and moved to NGM plates that were either seeded with HB101 or contained no food source. Worms were either fed or starved for 6 hours. Worms were washed from plates again and subsequently washed to remove all traces of bacteria. Worms were snap frozen in liquid nitrogen and stored at -80°C until ChIP processing.

value: Whole organism

value: starved


title: human HSCs transduced with NUP98b-KDM5A EGFP repeat 2

first: Isaac

middle: B

last: Hilton

address: 6500 Main St

department: Bioengineering

institute: Rice University

data_processing:
Reads were aligned to the GRCh38 transcriptome using HISAT2(2.2.1). Transcript abundance was calculated using feature Counts from the subread package (v2.0.3), and differential expression was determined in R studio (v2022.07.2, R 4.2.2) using the DESeq2 (v1.38.3) analysis package with default parameters. For ChIP-seq analysis, reads were aligned to the GRCh38 reference genome using Bowtie2 (v2.4.5) and peaks were called using MACS2 (v2.2.7.1) with a q-value ≤ 0.01. Resulting peaks were assessed and analyzed with deepTools (v3.5.4),  DiffBind (v3.8.4) and ChIPSeeker (v1.34.1)
Assembly: GRCh38
Supplementary files format and content: featurecount, narrowPeak, bdg

source_name: Hematopoietic stem cells

growth_protocol: CD34+ human hematopoietic stem cells (HSCs; StemCell, 70060) were cultured in StemSpan Leukemic Cell Culture Kit (StemCell, 09720) and Complete MethoCult Optimum media (StemCell, H4034). HEK293T cells (ATCC, CRL-11268) were cultured in Dulbecco's modified Eagle's medium (DMEM; Gibco, 31-053-028) supplemented with 10% FBS (Sigma, F2442) and 1% penicillin/streptomycin (Gibco, 15140).All cell lines were maintained at 37 °C with 5% CO2.

extract_protocol:
RNA was isolated from transduced CD34+ human hematopoietic stem cells using the RNeasy Plus mini kit (Qiagen, 74136). For ChIP-seq HEK293T Cells were harvested and washed with ice cold 1X PBS and suspended in Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40) supplemented with protease inhibitor (Thermo Scientific, A32965). Cells were then pelleted and resuspended in RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS) supplemented with protease inhibitor. Approximately 2.5e7 cells were used for each ChIP experiment. Chromatin in RIPA buffer was sheared to a median fragment size of around 250 bp using a Bioruptor XL (Diagenode).  2 μg of α-FLAG antibody (Sigma-Aldrich, F1804) was incubated with 50 μl Mouse IgG magnetic beads (Life Technologies, 11202D) for ~16 hours at 4 °C, respectively.  Antibody-linked magnetic beads were washed 3 times with PBS/BSA buffer (1X PBS and 5 mg/ml BSA) and sheared chromatin was incubated with corresponding antibody-linked magnetic beads at 4° C overnight and then washed 5 times with LiCl IP wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate). Cross-links were then reversed via overnight incubation at 65°C and DNA was purified using QIAquick PCR purification kit (Qiagen, 28106) for ChIP-seq. Input DNA was prepared from ~1.0e6 cells.
Total RNA samples were normalized to 10ng each, based on picogreen quantitation. RNA-seq libraries were constructed using the Takara SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara, 634485). The Switching Mechanism at 5’ end of RNA template (SMARTer) cDNA synthesis technology generates directionally identifiable ds-cDNA, incorporated with Illumina sequencing adapters and sample barcodes. Following cDNA synthesis and purification, ribosomal cDNA reduction is achieved by using probes (R-Probes v3) which target mammalian ribosomal cDNA and human mitochondrial ribosomal cDNA and ZapR v3 cleaves these fragments. Following amplification of the library using universal primers and a final purification using Takara NucleoMag NGS Clean-up and Size Select beads, the final library is ready for quantification and sequencing. Read 1 sequenced reads map to the antisense strand of the original RNA. The resulting libraries were quantitated by picogreen and fragment size assessed with the Agilent 2100 Bioanalyzer. ChIP DNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific) and the DNA integrity was checked with 4200 TapeStation (Agilent Technologies). ChIP-seq libraries were prepared using the NEB NextUltra DNA Library Preparation kit (NEB, 7645). Briefly, the ChIP DNA was end-repaired and adapters were ligated after adenylation of the 3’ ends. Adapter-ligated DNA was size-selected, followed by clean up, and limited cycle PCR enrichment. The ChIP library was validated using Agilent TapeStation (Agilent) and quantified using Qubit 2.0 Fluorometer as well as real time PCR (KAPA Biosystems). The sequencing libraries were multiplexed and clustered onto one lane of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq 4000 equivalent instrument. Sequencing was performed using a 2x150 Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software

treatment_protocol: 24-well plates were treated with 20 ug/ml RetroNectin (Takara Bio, T100B) as per manufacturer’s instruction. 2e6 CD34+ human HSCs (StemCell, 70060) were then mixed with 2e9 lentiviral particles and Lentiboost-P (1:100 dilution, Siron Biotech), and were then seeded onto the RetroNectin-treated plates. After centrifugation at 800g at 4°C for 90 mins, plates were placed at 37°C overnight. The cell medium was changed and cells were cultured for another ~48 hours. The transduced cells were imaged using a fluorescent microscope (Nikon ECLIPSE Ti2-E; 541094) and EGFP-positive cells were isolated using FACS cell sorting (Sony Biotechnology, MA900) and cultured in Complete MethoCult Optimum media (StemCell, H4034) for 2 weeks. HEK293T cells were co-transfected with indicated NUP98 fusions (10 μg ) or dCas9 fusion (7.5 μg) expression vectors and gRNA (2.5 μg) constructs in 10 cm plates in biological duplicates for each condition tested. ~72 hours post-transfection, cells were cross-linked for 10 min at RT using 1% formaldehyde (Sigma F8775-25ML) and then the reaction was stopped by the addition of glycine to a final concentration of 125 mM.

value: Hematopoietic stem cells

value: NUP98b-KDM5A EGFP

value: Tranduced with NUP98b-KDM5A EGFP


title: RNAseq_Molm13_sgCtrl#1

value: sgCtrl


title: Control_G7_Gas

city: Rehovot

first: FABIAN

middle: Simone

last: PASSINI

address: Herzl Street 234

country: Israel

institute: Weizmann Institute

description:
G7_Gas
Gastrocnemius muscle from control mouse

data_processing:
A user-friendly Transcriptome Analysis Pipeline (UTAP) version 1.10.2 was used for analysis. Gene expression was calculated and normalized using DESeq2 version 1.16.1, using only genes with a minimum of five reads in at least one sample. Raw p-values were adjusted for multiple testing. A gene was considered differentially expressed if it passed the following thresholds: minimum mean normalized expression of 5, adjusted p-value ≤0.05, and absolute value of log2 fold change ≥1.
Assembly: Reads were mapped to theM. musculusgenome (UCSC, mm10) using STAR (v2.5.2b) and GENECODE annotation. Only reads with unique mapping were considered for further analysis.
Supplementary files format and content: Deseq2 file (excel file)

source_name: Muscle

extract_protocol:
Muscle tissues were homogenized with Trizol reagent (15596018, Invitrogen) and RNA was isolated using MaXtract high density tubes (129056, Qiagen) following the manufacturer’s protocol.
Libraries were prepared using the INCPM-mRNA-seq protocol. Briefly, the polyA fraction (mRNA) was purified from 500 ng of total input RNA followed by fragmentation and the generation of double-stranded cDNA. After Agencourt Ampure XP beads cleanup (Beckman Coulter), end repair, A base addition, adapter ligation, and PCR amplification steps were performed.

value: Muscle


title: his-9/H3.1 reporter strain, rep 3, whole organism, starved, input

description: Library name: H3.1_starved_rep_3_input


title: CB, 14 DPI

city: Beijing

first: Zhijie

last: Bai

state: 北京Beijing

address: Taiping Road, Haidian District

institute: beijing institute of radiation

description: 10x Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were made using CellRanger software v4.0
Assembly: GRCm39
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: bone marrow

extract_protocol:
Bone marrow cells were obtained through flushing the femurs and stained with Lin and Kit as described above. Lin-Kit+, Lin-Kit- and Lin+ populations from three individual mice were then sorted and mixed with a ratio of 5:4:1 for 10x Genomics single-cell sample preparation. The single cells were centrifuged and resuspended before finally load to 10x chromium controller for Gel Beads-in-Emulsion (GEMs) generation.
cDNA library construction was performed following the standard protocol offered by 10x Genomics (single-cell, 3' V2).

value: bone marrow

value: BMNC

value: CBD treatment


title: his-9/H3.1 reporter strain, rep 2, whole organism, starved, input

description: Library name: H3.1_starved_rep_2_input


title: IR, 14 DPI

description: 10x Genomics

value: 6.0 Gy gamma-irradiation


title: human HSCs transduced with NUP98b-KDM5A EGFP repeat 1


title: Control_G6_Sol

description:
G6_Sol
Soleus muscle from control mouse


title: human HSCs transduced with NUP98b-HOXA9 EGFP repeat 2

value: NUP98b-HOXA9 EGFP

value: Tranduced with NUP98b-HOXA9 EGFP


title: his-9/H3.1 reporter strain, rep 1, whole organism, starved, input

description: Library name: H3.1_starved_rep_1_input


title: Ctrl, 14 DPI

description: 10x Genomics

value: control


title: Control_G6_Gas

description:
G6_Gas
Gastrocnemius muscle from control mouse


title: Ctrl_1

value: islet


title: his-9/H3.1 reporter strain, rep 3, whole organism, fed, input

description: Library name: H3.1_fed_rep_3_input

value: fed


title: his-9/H3.1 reporter strain, rep 2, whole organism, fed, input

description: Library name: H3.1_fed_rep_2_input


title: human HSCs transduced with NUP98b-HOXA9 EGFP repeat 1


title: Mutant_G5_Gas

description:
G5_Gas
Gastrocnemius muscle from mutant mouse


title: Mouse Parotid gland Male Wild Type Sample 3

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

data_processing:
Fastqc
Trimming of reads using trimmomatic V.0.36
Star (2.5.2a) alignment using Ensemble GRCm38
Raw Gene ocunt generation using htseq-count program (0.6.1p1)
Assembly: Ensembl Mus_musculus.GRCm38.95
Supplementary files format and content: htseq-Count text fiile

source_name: Parotid gland

growth_protocol: All mice were maintained on a C57BL/6 genetic background and used between 6 and 40 weeks of age. Animals were kept in specific-pathogen-free rooms in the vivarium of NYU College of Dentistry in normal light-dark cycles under the constant temperature of 22 ± 2°C and 60 ± 10% humidity. Animal studies were approved under the Institutional Animal Care and Use Committee (IACUC) protocol # IA16-00625.

extract_protocol:
Total RNA from parotid glands was isolated using miRNeasy Mini Kit (1038703, Qiagen) for RNASeq and RNeasy mini kit (74106, Qiagen). A NanoDrop spectrophotometer (13400519, Thermo Scientific) was used to measure the 260/280 ratio.
Automated stranded RNA-seq library prep, polyA selection

value: Parotid gland

value: Male

value: Wild Type


title: human HSCs transduced with NUP98a-KDM5A EGFP repeat 2

value: Hematopoietic stem cells

value: NUP98a-KDM5A EGFP

value: Tranduced with NUP98a-KDM5A EGFP


title: Control_G7_Sol

description:
G7_Sol
Soleus muscle from control mouse


title: Mouse Parotid gland Male Wild Type Sample 2


title: Mouse Parotid gland Male Wild Type Sample 4


title: Mutant_G2_Gas

description:
G2_Gas
Gastrocnemius muscle from mutant mouse


title: Mutant_G5_Sol

description:
G5_Sol
Soleus muscle from mutant mouse


title: Mutant_G2_Sol

description:
G2_Sol
Soleus muscle from mutant mouse


title: human HSCs transduced with NUP98a-HOXA9 EGFP repeat 2

value: NUP98a-HOXA9 EGFP

value: Tranduced with NUP98a-HOXA9 EGFP


title: human HSCs transduced with NUP98a-HOXA9 EGFP repeat 1


title: his-58/H2B reporter strain, rep 3, whole organism, starved, input

description: Library name: H2B_starved_rep_3_input

value: Whole organism

value: starved


title: Mouse Parotid gland Male Knock out Sample 4

value: Knock out


title: his-58/H2B reporter strain, rep 2, whole organism, starved, input

description: Library name: H2B_starved_rep_2_input


title: human HSCs transduced with NUP98a-KDM5A EGFP repeat 1


title: his-9/H3.1 reporter strain, rep 1, whole organism, fed, input

description: Library name: H3.1_fed_rep_1_input


title: Mouse Parotid gland Male Knock out Sample 3


title: Control_F4_Gas

description:
F4_Gas
Gastrocnemius muscle from control mouse

value: Muscle


title: human HSCs transduced with EGFP repeat 2

value: EGFP

value: Tranduced with EGFP


title: human HSCs transduced with EGFP repeat 1


title: his-58/H2B reporter strain, rep 1, whole organism, starved, input

description: Library name: H2B_starved_rep_1_input


title: Mouse Parotid gland Male Knock out Sample 2


title: Mutant_F3_Sol

description:
F3_Sol
Soleus muscle from mutant mouse


title: his-58/H2B reporter strain, rep 3, whole organism, fed, input

description: Library name: H2B_fed_rep_3_input


title: Mouse Parotid gland Male Knock out Sample 1


title: Mutant_F3_Gas

description:
F3_Gas
Gastrocnemius muscle from mutant mouse


title: his-58/H2B reporter strain, rep 4, whole organism, starved, input

description: Library name: H2B_starved_rep_4_input


title: his-58/H2B reporter strain, rep 1, whole organism, fed, input

description: Library name: H2B_fed_rep_1_input


title: Mouse Parotid gland Male Wild Type Sample 1


title: Mutant_A5_Sol

description:
A5_Sol
Soleus muscle from mutant mouse


title: control 9 [LP 9]

city: changsha

first: ling

last: jie

state: hunan

address: xue shi

institute: Hunan university of Chinese medicine

data_processing:
Poly-N, adapter and low-quality were removed by in-house perl scripts ，Quality control analysis was performed by ng_qc.
Clean reads were aligned to the mus musculus ensembl 92 using bowtie (Langmead et al.,2009). bowtie was run with ‘-v 0 -k 1’, other parameters were set as default.
Processed reads of length at 18 to 35 nt for animals or 18-30 nt for plants were then mapped to their reference genome and analyzed using the bowtie package (no mismatch). To identify conserved miRNAs, the predicted miRNA hairpins were compared against miRNA precursor sequences from miRBase22.0 (Friedlander et al., 2011) using mirDeep2 and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. MirDeep2's quantifier.pl were used to obtain the miRNA counts, and custom scripts were used to obtain base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.
The characteristics of hairpin structure of miRNA precursor can be used to predict novel miRNA. The available software miREvo (Wen et al., 2012) and mirdeep2 (Friedlander et al., 2011) were integrated to predict novel miRNA through exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the small RNA reads unannotated in the former steps. At the same time, MirDeep2's quantifier.pl were used to obtain the miRNA counts, and custom scripts were used to obtain base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.
Genome_build: homo_sapiens_Ensembl_97
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: control

extract_protocol:
Breast tissue were removed,and RNA was harvested using Trizol reagent.Prep Kit for Illumina (NEB, USA)was used with 3 ug of total RNA for the construction of sequencing libraries.
small RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The normal tissue of volunteers was taken from the tissue next to the their fibroadenoma during breast fibormectomy.The GLM tissue was taken from lesion excision after pathological diagnosis is granulomatous mastitis.

tag: ethnicity

value: chinese

tag: subject status

value: healthy volunteer

tag: tissue type

value: tissue next to the bresat fibroadenoma

tag: molecule type

value: small RNA


title: Mouse Parotid gland Female Wild Type Sample 4

tag: tissue

value: Parotid gland

value: Female


title: his-58/H2B reporter strain, rep 2, whole organism, fed, input

description: Library name: H2B_fed_rep_2_input

value: fed


title: Control_F4_Sol

description:
F4_Sol
Soleus muscle from control mouse


title: Mouse Parotid gland Female Wild Type Sample 3

value: Wild Type


title: Mutant_A5_Gas

description:
A5_Gas
Gastrocnemius muscle from mutant mouse


title: Control_A3_Sol

description:
A3_Sol
Soleus muscle from control mouse


title: N2 (WT), ChIP negative control, rep 2, whole organism, starved, V5 ChIP

description: Library name: WT_control_rep_2_ChIP


title: Mouse Parotid gland Female Wild Type Sample 1


title: N2 (WT), ChIP negative control, rep 1, whole organism, starved, V5 ChIP

description: Library name: WT_control_rep_1_ChIP


title: control 8 [LP 8]


title: Control_A3_Gas

description:
A3_Gas
Gastrocnemius muscle from control mouse


title: control 7 [LP 7]


title: Mouse Parotid gland Female Knock out Sample 4


title: Mouse Parotid gland Female Knock out Sample 3


title: Mutant_A2_Sol

description:
A2_Sol
Soleus muscle from mutant mouse


title: control 6 [LP 6]


title: control 5 [LP 5]


title: his-9/H3.1 reporter strain, rep 4, whole organism, starved, V5 ChIP

description: Library name: H3.1_starved_rep_4_ChIP


title: his-9/H3.1 reporter strain, rep 3, whole organism, starved, V5 ChIP

description: Library name: H3.1_starved_rep_3_ChIP


title: Mouse Parotid gland Female Knock out Sample 2


title: control 10 [LP 10]


title: control 4 [LP 4]


title: his-9/H3.1 reporter strain, rep 2, whole organism, starved, V5 ChIP

description: Library name: H3.1_starved_rep_2_ChIP


title: Mutant_A2_Gas

description:
A2_Gas
Gastrocnemius muscle from mutant mouse


title: Mouse Parotid gland Female Knock out Sample 1


title: control 3 [LP 3]


title: control 2 [LP 2]


title: Control+tranilast4

city: Hefei

first: Weiwei

last: Qin

address: Huangshan road

institute: University of Science and Technology of China

data_processing:
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads
The enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).
The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).
.Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.
Assembly: Ensembl_release106
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Liver

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA)
The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: Liver

value: WT

value: Treatment


title: his-9/H3.1 reporter strain, rep 1, whole organism, starved, V5 ChIP

description: Library name: H3.1_starved_rep_1_ChIP

value: Whole organism


title: his-9/H3.1 reporter strain, rep 3, whole organism, fed, V5 ChIP

description: Library name: H3.1_fed_rep_3_ChIP


title: Control+tranilast3


title: Control_A1_Sol

description:
A1_Sol
Soleus muscle from control mouse


title: Control_A1_Gas

description:
A1_Gas
Gastrocnemius muscle from control mouse


title: control 1 [LP 1]


title: Control+tranilast2


title: Control+tranilast1


title: his-9/H3.1 reporter strain, rep 1, whole organism, fed, V5 ChIP

description: Library name: H3.1_fed_rep_1_ChIP


title: granulomatous lobular mastitis 10 [RYZ 10]

source_name: granulomatous lobular mastitis

value: patient diagnosed with granulomatous lobular mastitis

value: Inflammatory mammary tissue


title: his-9/H3.1 reporter strain, rep 2, whole organism, fed, V5 ChIP

description: Library name: H3.1_fed_rep_2_ChIP


title: granulomatous lobular mastitis 9 [RYZ 9]


title: his-58/H2B reporter strain, rep 4, whole organism, starved, V5 ChIP

description: Library name: H2B_starved_rep_4_ChIP

value: starved


title: granulomatous lobular mastitis 8 [RYZ 8]


title: Control4

value: Control


title: his-58/H2B reporter strain, rep 3, whole organism, starved, V5 ChIP

description: Library name: H2B_starved_rep_3_ChIP


title: granulomatous lobular mastitis 7 [RYZ 7]


title: Control3


title: Control2


title: his-58/H2B reporter strain, rep 2, whole organism, starved, V5 ChIP

description: Library name: H2B_starved_rep_2_ChIP


title: granulomatous lobular mastitis 6 [RYZ 6]


title: his-58/H2B reporter strain, rep 1, whole organism, starved, V5 ChIP

description: Library name: H2B_starved_rep_1_ChIP


title: granulomatous lobular mastitis 5 [RYZ 5]


title: Control1


title: granulomatous lobular mastitis 4 [RYZ 4]


title: his-58/H2B reporter strain, rep 3, whole organism, fed, V5 ChIP

description: Library name: H2B_fed_rep_3_ChIP


title: Expt2_12w hom RFP r2

city: Cambridge

first: Joo-Hyeon

last: Lee

email: jhl62@cam.ac.uk, leej49@mskcc.org

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

description: 10x Genomics

data_processing:
Quality of fastq files was assessed with FastQC v0.11.3, MultiQC v1.8.
Alignment and protein-coding gene quantification was performed using 10x cellranger v3.1.0
Assembly: GRCm38
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Distal lung

extract_protocol:
Lungs were cleared of blood through perfusion and inflated with 2 mL of dispase solution via intratracheal injection and incubated on ice for 2 min. Individual lobes were separated from each lung and minced into small pieces (<1 mm in size). Cells were  washed down to the bottom of the tube using 3 mL of cold PBS and 60 μL of 100 mg/mL collagenase/dispase solution was added per tube. Samples were then placed in a shaking incubator set to 180 rpm at 37 °C  for 45 mins with 7.5 μL of 1% DNase I added to each sample in the final 10 min of incubation. Dissociated tissue cell suspensions were filtered sequentially through 100 μm and 40 μm cell strainers respectively and washed at each stage with 3 mL of 10% FBS in PBS (PF10) after each step to collect remaining cells. Tubes were then centrifuged at 800 rpm for 5 min at 4 °C, after which the supernatant was aspirated. Cell pellets were resuspended in 1 mL of red blood cell lysis buffer. Following a 90 second incubation at RT, cell lysis was inactivated with addition of 6 mL of DMEM/F-12, with 500 μL of FBS then added slowly to the bottom of each tube to collect live cells. After a second centrifugation step at 800 rpm for 5 min at 4 °C, the supernatant was aspirated, and the cell pellets were resuspended in PF10 and placed into separate Eppendorf tubes ready for FACS antibody staining, with a small fraction of cells set aside for unstained and single-stained antibody controls. EpCAM+RFP+ and EpCAM+YFP+ cells were isolated and submitted for library preparation and 10x Genomics sequencing. For each run, libraries were multiplexed and sequenced in the same lanes using NovaSeq 6000.
Library construction was performed according to manufacturers instructions (single cell 3' v2 chemstry, 10x Genomics)

value: Distal lung

value: Lineage-labelled AT2-derived

value: Il1r1-/-; Sftpc-CreERT2; Red2Kras


title: MDA231_ctl_rep2

city: Nottingham

first: Keith

last: Spriggs

state: Notts

address: University Park

department: Pharmacy

institute: University of Nottingham

data_processing:
trimming for adapters and quality with scythe and sickle respectively
mapping with TopHat
read counts with htseq-count
differential expression with DESeq
transcript assembly with Cufflinks and Cuffmerge.
Assembly: hg38
Supplementary files format and content: format = .csv; content = differential expression

source_name: MDA-MD-231 Fluc

growth_protocol: MDA-MB-231 Fluc were derived from MDA-MB-231 (CVCL_0062) cells by insertion of a luciferase gene which enables bioluminescence imaging of the cells once transplanted in vivo (Priddle et al. 2009; Kumari et al. 2007). These cells were kindly provided by Anna Grabowska and Philip Clarke from the Cancer Biology Unit, School of Medicine, University of Nottingham. They were seeded at a density of 3 million cells per 15 cm2 plate and incubated for 24 hours before treatment.

extract_protocol:
RNA was isolated using a Promega ReliaPrep kit with a prolonged DNase treatment (1 hour).
Illumina stranded RNA-seq libraries with ribo-depletion. 75 paired end, run on a NextSeq500

treatment_protocol: MDA-MB-231-Fluc cells were treated with 50 μM cordycepin or DMSO for 2 hours

value: MDA-MD-231 Fluc

value: vehicle control


title: NIH3T3-no-serum_control-rep2

type: RNA

hyb_protocol: Hybridised at 65C in a microarray hybridisation oven according to the manufacturer's protocol (Agilent).

scan_protocol: Agilent  Microarray Scanner, model number G2505C, scan control version A.8.4.1.

data_processing: Standard Agilent Feature Extraction normalization and background correction procedures

source_name: Serum starved NIH3T3 cells

label_protocol: Labelling was done with Agilent’s one-colour Low Input Quick Amp Labelling Kit (Cy3) according to the manufacturer's instructions. The level of dye incorporation was evaluated by spectrophotometry (Nanodrop ND1000, LabTech, Uckfield, UK). Labeled RNA was fragmented and diluted (v/v) in hybridization buffer.

growth_protocol: NIH-3T3 cells were grown in DMEM (2 mM glutamine) with 10% newborn bovine serum. Cells were seeded at 3 million per 15 cm plate. 24 hours later, the medium was replaced with DMEM 0.5% newborn bovine serum.

extract_protocol: Promega Reliaprep kits using the manufacturer’s instructions with a 1 hour DNase treatment.

treatment_protocol: 24 hours after medium replacement, 20 uM cordycepin in DMSO (cordycepin) or DMSO (0.1%) (control)  was added. 60 minutes after this treatment, 0.1 volume of newborn bovine serum was added to the indicated plates (serum) or not (no serum)

tag: male

value: male


title: his-58/H2B reporter strain, rep 1, whole organism, fed, V5 ChIP

description: Library name: H2B_fed_rep_1_ChIP


title: NIH3T3-no-serum_control-rep1


title: NIH3T3-serum_control-rep2

source_name: Serum starved NIH3T3 cells treated with vehicle for 90 mins and with serum 30 mins.


title: MDA231_C50_rep2

value: 50 μM cordycepin for 2 hours


title: granulomatous lobular mastitis 2 [RYZ 2]

value: chinese

value: small RNA


title: NIH3T3-cordycepin-90mins_rep2

source_name: Serum starved NIH3T3 cells treated with cordycepin for 90 mins and with serum 30 mins.


title: granulomatous lobular mastitis 3 [RYZ 3]


title: NIH3T3-cordycepin-90mins_rep3


title: NIH3T3-serum_control-rep1


title: MDA231_ctl_rep1


title: NIH3T3-cordycepin-90mins_rep1


title: NIH3T3-serum_control-rep3


title: granulomatous lobular mastitis 1 [RYZ 1]


title: MUT [JP1262]

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

data_processing:
Raw sequencing data was processed through 10X Genomics CellRanger v6.0.1 using default parameters to obtain the gene expression matrices.
Assembly: mm10
Supplementary files format and content: barcode, feature list and raw integer counts for the gene expression matrix

organism: Mus

source_name: kidney

extract_protocol:
Single-cell suspensions were processed through Chromium 10X to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: Rbpj c/- ; Foxd1cre/+

value: kidney


title: MUT [JP1261]


title: MDA231_C50_rep1


title: GRCF OE6

city: New York

first: Maria

middle: Victoria

last: Revuelta

address: 1300 York Avenue

department: Medicine

institute: Weill Cornell Medicine

description: vstnormcounts.txt

data_processing:
Raw sequencing reads (fastq files) were quality checked using Fastp and summarized with MultiQC.
Transcripts were quantified against Gencode v29 hg38 genome using Salmon.
Transcript abundances were summarized with tximport in R version 3.6.2.
DESeq2 was used for vst normalization and differential expression analyses
Illumina Casava-1.8.2 software used for basecalling
Genome_build: hg38

growth_protocol: cells were incubated in a 95% air and 5% CO2 humidified atmosphere at 37°C, and the medium was replaced every 48hrs. In logarithmic phase HT-29 cells were obtained and resuspended in DMEM medium (Gibco) supplemented with 10% FBS (Hyclone, Logan, UT, USA)

extract_protocol:
total RNA was isolated using Trizol reagent (Thermo Fisher Scientific). with Rneasy (Qiagen) 300ng/ul
RNA libraries were constructed using TruSeq RNA Library Prep Kit v2 (Illumina) and sequenced as 150 bp paired-end reads by Illumina NovaSeq.

value: colon

tag: morphology

value: epithelial

tag: geneotype

value: CHD2 overexpression


title: GRCF OE5

description: vstnormcounts.txt


title: Expt2_2w hom RFP r1

description: 10x Genomics

tag: cell type


title: Liver, N_7

city: Xi'an

first: Shuoyi

last: Ma

address: No. 127, Changle West Road, Xincheng District

institute: Xijing Hospital of Digestive Diseases, Fourth Military Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly(Mus_musculus_Ensemble_96). Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: Mus_musculus_Ensemble_96
Supplementary files format and content: tab-delimited text file includes read count values for each Sample

source_name: liver tissues

extract_protocol:
1.RNA degradation and contamination was monitored on 1% agarose gels.2.RNA purity was checked using the NanoPhotometer®spectrophotometer(IMPLEN, CA, USA) .3.RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: liver tissues

tag: group

value: N


title: his-58/H2B reporter strain, rep 2, whole organism, fed, V5 ChIP

description: Library name: H2B_fed_rep_2_ChIP

value: Whole organism

tag: treatment

value: fed


title: Expt2_12w hom RFP r1

description: 10x Genomics

value: Distal lung

value: Lineage-labelled AT2-derived

tag: genotype


title: Expt2_2w het RFP r2

description: 10x Genomics

value: Il1r1+/-; Sftpc-CreERT2; Red2Kras


title: Liver, N_6


title: Expt2_12w het RFP r2

description: 10x Genomics


title: K562, WT, 2, VP:Enhancer

city: Utrecht

first: Peter

last: Krijger

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
FastQ files were demultiplexed and processed using pipe4C (https://github.com/deLaatLab/pipe4C). Reads were mapped against hg38.  Blind fragments were omitted. Read counts were normalized to one-million mapped intra chromosomal reads (normalized reads) excluding the two highest covered fragments and 21 fragment end rolling mean scores were calculated for every fragment end.
Assembly: hg38
Supplementary files format and content: Wig files.
Library strategy: 4C-seq

molecule: other

growth_protocol: Human erythroleukemia K562 cells were grown at 37°C at 5% CO2 in RPMI 1640 (Gibco, cat. no. 11875093) supplemented with 10% FBS (Sigma, cat. no. F7524) and 1% Penicillin-Streptomycin (Gibco, cat. no. 15140122). Cells were maintained at a density below 1 million per ml and were routinely tested for mycoplasma.

extract_protocol:
4C template preparation was performed as previously described in PMID: 31351925. In brief, ten million cells per sample were cross-linked in 2% formaldehyde. Chromatin was digested in situ with DpnII (NEB, cat. no. R0543) followed by dilution and ligation. Subsequently, crosslinks were removed by Proteinase K treatment, followed by template trimming using Csp6I (CviQI, second cutter, Thermo Scientific, cat. no. ER0211) and re-ligation.
Indexed Illumina sequencing adapters were introduced to ligation fragments of interest with a two-step PCR strategy using ELT PCR System (Roche, cat. no. 11681842001).

treatment_protocol: RAD21 depletion in K562 cells was induced by adding 1µM 5-Ph-IAA (MedChemExpress, cat. no. HY-134653) to cell cultures two-hour before crosslink.

tag: cell line

value: WT

tag: replicate

tag: vp

value: Enhancer


title: GRCF OE4

description: vstnormcounts.txt


title: Expt2_12w het RFP r1

description: 10x Genomics


title: Expt2_2w het RFP r1

description: 10x Genomics


title: K562, WT, 2, VP:CTCF_4


title: Liver, N_4


title: Expt2_Confetti RFP r2

description: 10x Genomics

value: Sftpc-CreERT2; R26R-Confetti


title: Expt2_2w hom RFP r2

description: 10x Genomics

value: Il1r1-/-; Sftpc-CreERT2; Red2Kras


title: GRCF OE2

description: vstnormcounts.txt


title: Liver, N_5


title: K562, WT, 2, VP:CTCF_1


title: Liver, N_3


title: K562, WT, 2, VP:MYEOV

value: MYEOV


title: GRCF OE1

description: vstnormcounts.txt


title: K562, WT, 2, VP:CCND1


title: Liver, N_2


title: K562, WT, 2, VP:CTCF_2


title: GRCF OE3

description: vstnormcounts.txt


title: GRCF WT6

description: vstnormcounts.txt

value: CHD2 WildType


title: Liver, N_1


title: GRCF WT4

description: vstnormcounts.txt


title: K562, WT, 1, VP:Enhancer


title: Expt1_2w YFP r1

description: 10x Genomics

value: Sftpc-CreERT2; Red2Kras


title: Liver, M_7

value: M


title: K562, WT, 1, VP:MYEOV


title: Expt1_2w RFP r2

description: 10x Genomics


title: Expt1_2w RFP r1

description: 10x Genomics


title: Liver, M_6


title: GRCF WT3

description: vstnormcounts.txt

value: colon

value: epithelial


title: K562, WT, 1, VP:CTCF_4


title: Expt2_Confetti RFP r1

description: 10x Genomics


title: Liver, M_5

value: liver tissues


title: Expt1_4d YFP r2

description: 10x Genomics


title: K562, WT, 1, VP:CTCF_2


title: GRCF WT2

description: vstnormcounts.txt


title: Liver, M_4


title: Expt1_2w YFP r2

description: 10x Genomics


title: K562, WT, 1, VP:CTCF_1


title: GRCF WT1

description: vstnormcounts.txt


title: K562, WT, 1, VP:CCND1


title: Expt1_4d RFP r2

description: 10x Genomics


title: K562, MYEOV-del, clone2, VP:Enhancer

value: MYEOV-del


title: GRCF WT5

description: vstnormcounts.txt


title: Expt1_4d RFP r1

description: 10x Genomics


title: Liver, M_2


title: GRCF KD5

description: vstnormcounts.txt

value: CHD2 knockdown


title: GRCF KD4

description: vstnormcounts.txt


title: K562, MYEOV-del, clone1, VP:Enhancer


title: K562, MYEOV-del, clone2, VP:CTCF_2


title: Expt1_Confetti RFP

description: 10x Genomics


title: GRCF KD3

description: vstnormcounts.txt


title: Sample19

type: protein

first: Joseph

last: Castellano

state: NY

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description: Plasma protein data is reported as SOMAmer reagent abundance in relative fluorescence units (RFU) with reagent abundance indicating protein concentration within the sample

hyb_protocol: Raw data were processed for hybridization normalization to adjust for individual sample variance according to manufacturer recommendations.

data_processing: Median signal normalization was performed to adjust sample-to-sample differences in RFU brightness. Calibration normalization was applied to all samples in the plate to remove variance due to assay run according to manufacturer recommendations.

label: Slow Offrate Modified Aptamer (SOMAmer) reagents

source_name: plasma

extract_protocol: Whole blood samples were drawn from fasted subjects into 10 mL syringes pre-coated with 0.5 M EDTA and transferred to 15 mL polypropylene tubes containing 120 µL of 0.5 M EDTA. Samples were kept on ice until centrifugation (<2 hours) at 2,000 g x 17 minutes, allowing separation of plasma from the cellular fraction. Plasma was pooled and aliquoted into new polypropylene tubes (300-500 µL) prior to storage at -80°C.

tag: Sex

value: positive

tag: age

tag: subarray


title: GRCF KD2

description: vstnormcounts.txt


title: Expt1_4d YFP r1

description: 10x Genomics

value: Distal lung


title: Zscan4-H3K27me3_2

city: Tianjin

first: Jie

last: Li

address: Wei Jin Road Nankai District No. 94

department: Department of Cell Biology and Genetics

institute: Nankai University

data_processing:
CUT&Tag reads were aligned to the mm10 and genome and BDGP6 genomeCUT&Tag reads were aligned to the mm10 and genome and BDGP6 genome using bowtie2 with the default options.
Bam files were got using SAMtools (v.1.9). Bam files were got using SAMtools (v.1.9).
We normalized the mouse profiles to the number of drosophilid reads (Zscan4+/Zscan4-H3K27me3 data).
Scatterplots, correlation plots, and heatmaps are displayed using deepTools .
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&TAG

extract_protocol:
Histone-DNA complexes were isolated from cell lysates using H2AK119ub or H3K27me3  antibody.
The library was prepared according to TruePrep DNA Library Prep Kit V2 for Illumina(TD502) and Hyperactive pA-Tn5 Transposase for CUT&Tag kit (Vazyme, S603-01).The library quality was assessed on the Agilent Bioanalyzer 2100 system and the library preparations sequenced on an Illumina Hiseq platform.

value: mouse embryonic stem cell

value: Zscan4 negative

tag: chip antibody


title: GRCF KD1

description: vstnormcounts.txt


title: Sample24


title: K562, MYEOV-del, clone1, VP:CTCF_2


title: GRCF KD6

description: vstnormcounts.txt


title: K562, Enhancer-del, clone2, VP:CTCF_2

value: Enhancer-del


title: Brain cortex, wild type control, n5

first: Yumei

last: Liang

address: Changchun Street 45

department: Xuanwu hospital

institute: Capital Medical University

data_processing:
Real-Time Analysis software on Illumina sequencing system for base calling.
Raw reads were trimmed for adaptor sequence and low-quality sequence using Trim Galore software.
Trimmed sequence reads were mapped to mm39 using STAR software.
Assembly: mm39
Supplementary files format and content: comma-separated values file include raw counts for all samples
Supplementary files format and content: comma-separated values file include FPKM values for all samples

source_name: Brain cortex

growth_protocol: All mice were kept in a specific pathogen-free facility with a constant temperature of 22 ± 1℃ and relative humidity of 50 ± 10%, and were artificially provided with a 12 h light/dark cycle. Mice were fed with standard food and water ad libitum.

extract_protocol:
RNA was harvested using TruSeq RNA sample Preparation kit V2 (Illumina). 2 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture’s protocals.

treatment_protocol: The mice groups were intraperitoneally administered with different compounds once daily for three months: (a) WT group (vehicle), (b) control group (vehicle), (c) (-)-Vestitol group ((-)-Vestitol 5 mg/kg), (d) Salviolone group (Salviolone 5 mg/kg), (e) combination group ((-)-Vestitol 2.5 mg/kg and Salviolone 2.5 mg/kg), and (f) standard drug group (Donepezil 1 mg/kg).

tag: strain

value: wild type

value: 6 month old

value: male

value: Brain cortex

value: vehicle

tag: time


title: Zscan4-H3K27me3_1


title: Liver, M_1

tag: tissue


title: Liver, M_3


title: Zscan4+H3K27me3_2

value: Zscan4 positive


title: Brain cortex, wild type control, n4


title: KD9-H3K27me3_2

description: KD9-H3K27me3 _2

value: Usp17l Knockdown


title: Zscan4+H3K27me3_1


title: Brain cortex, wild type control, n3


title: Expt1_Confetti YFP

description: 10x Genomics

value: Lineage-labelled AT2-derived

value: Sftpc-CreERT2; R26R-Confetti


title: Sample49

value: M


title: K562, Enhancer-del, clone2, VP:MYEOV

value: MYEOV


title: Sample18


title: Sample39


title: KD9-H3K27me3_1

description: KD9-H3K27me3 _1


title: K562, Enhancer-del, clone2, VP:CCND1


title: K562, Enhancer-del, clone2, VP:CTCF_4


title: Sample12

value: F


title: Control-H3K27me3

description: Control -H3K27me3

value: control


title: Brain cortex, wild type control, n1


title: K562, Enhancer-del, clone1, VP:MYEOV


title: Sample50

value: positive


title: K562, Enhancer-del, clone1, VP:CTCF_4


title: Sample2


title: K562, Enhancer-del, clone2, VP:CTCF_1


title: K562, Enhancer-del, clone1, VP:CTCF_2


title: Brain cortex, (-)-Vestitol and Salviolone, n5

value: APPswe, PSEN1dE9

value: (-)-Vestitol, 2.5 mg/kg and Salviolone, 2.5 mg/kg


title: KD9-H2AK119ub_2

description: KD9-H2AK119ub _2

source_name: ESC,H2AK119ub, CST

value: mouse embryonic stem cell


title: Control-H2AK119ub_2

description: Control-H2AK119ub _2

source_name: ESC, H2AK119ub, CST


title: KD9-H2AK119ub_1

description: KD9-H2AK119ub _1_


title: Brain cortex, (-)-Vestitol and Salviolone, n3


title: Brain cortex, (-)-Vestitol and Salviolone, n4


title: K562, Enhancer-del, clone1, VP:CTCF_1

value: Enhancer-del


title: Brain cortex, wild type control, n2

value: wild type

value: 6 month old


title: K562, Enhancer-del, clone1, VP:CCND1


title: Brain cortex, (-)-Vestitol and Salviolone, n2

value: male

value: Brain cortex


title: K562, CTCF2-del, clone1, VP:CTCF_4


title: Control-H2AK119ub_1

description: Control-H2AK119ub _1


title: Brain cortex, (-)-Vestitol and Salviolone, n1


title: WTG3

city: Qingdao 266237

first: Kexuan

state: China

address: No. 72 Binhai Road

department: State Key Laboratory of Microbial Technology

institute: Shandong University

description: Library name: WT_G_3

data_processing:
3' adaptor sequences were first removed from the sequencing reads to produce 50-nt long tags.
Then low quality tags, one copy tags and tags which are not 50-nt long were removed to generate clean tags.
Reference 50-nt tag databases were created from predicted Penicillium oxalicum transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Assembly: Whole Genome Shotgun project in GenBank under the accession number AGIH00000000.1
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Penicillium oxalicum

source_name: strain

growth_protocol: The germination of Penicillium oxalicum were inoculated in modifeid vogel's culture medium with 2% glucose as carbon resource for 24 h at 30℃ as the pre-culture, and then mycelia were transferred and grown in the modified Mendal’s medium with 2% glucose or 1% bran + 1% microcrystalline cellulose as carbon resources for 18h. Total RNA was extracted for DGE analysis.

extract_protocol:
Total RNA was extracted, and oligo (dT) beads were used to purify mRNA and guide double-stranded cDNA synthesis. The enzyme NlaIII was used to cut the cDNA at CATG sites. After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 50bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: strain

value: 114-2(wild type)

value: Modified Mendal’s medium with 2% glucose as carbon resource


title: Sample47


title: Sample3


title: Sample35


title: K562, CTCF2-del, clone1, VP:MYEOV


title: Brain cortex, Salviolone, n5

value: Salviolone, 5 mg/kg


title: Sample20


title: Sample37


title: WTG1

description: Library name: WT_G_1


title: WTG2

description: Library name: WT_G_2


title: K562, CTCF2-del, clone1, VP:Enhancer

value: Enhancer


title: Sample53


title: WTCW3

description: Library name: WT_FP_3

value: Modified Mendal’s medium with 1percent bran + 1percent microcrystalline cellulose as carbon resource


title: Brain cortex, Salviolone, n3


title: Sample22

value: F


title: K562, CTCF2-del, clone1, VP:CTCF_1


title: Brain cortex, Salviolone, n4


title: WTCW2

description: Library name: WT_FP_2


title: K562, CTCF2-del, clone1, VP:CCND1


title: Brain cortex, Salviolone, n2


title: Sample51


title: WTCW1

description: Library name: WT_FP_1


title: Sample45


title: Brain cortex, Salviolone, n1


title: K562, CCND1-del, clone1, VP:MYEOV

value: MYEOV


title: DRsc1G3

description: Library name: DRsc1_G_3

value: Rsc1 deletion strain


title: Brain cortex, (-)-Vestitol, n5

value: APPswe, PSEN1dE9

value: (-)-Vestitol, 5 mg/kg


title: TC-71_siDHX9_3 [T12]

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Count on FAST DB gene annotations (GenoSplice) and normalization using Deseq
Assembly: hg19
Supplementary files format and content: Tab-delimited text file includes deseq normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2018_1 were also provided

growth_protocol: TC-71 Ewing sarcoma Cells were maintained in culture in Iscove's modified Dulbecco's medium (IMDM, GIBCO), supplemented with 10% fetal bovine serum, and penicillin and streptomycin (Gibco) and maintained at 37 °C in humidified 5% CO2 atmosphere.

extract_protocol: RNA from three biological replicates of either control (DMSO or scrambled) or YK-4-279 treated TC-71 cells or siDHX9 transfected cells was purified using RNeasy Mini kit (Qiagen) and digested with DNase RNase free (Qiagen).

treatment_protocol: TC-71 Ewing sarcoma cells were treated for 16 hours with either DMSO or YK-4-279 (Cayman Chemical) 2mM. Lipofectamine RNAiMax reagent (ThermoFisher) was used for siRNAs and transfections. Briefly, 2 × 104 TC-71 cells were subjected to double pulse of reverse-transfection by using 4 μl of Lipofectamine RNAiMAX and collected at 48 h after the  of transfection.

value: Ewing sarcoma cells

value: DHX9 knockdown


title: TC-71_siDHX9_2 [T11]


title: Brain cortex, (-)-Vestitol, n4


title: Sample8

value: negative


title: Sample15


title: DRsc1G1

description: Library name: DRsc1_G_1


title: TC-71_siDHX9_1 [T10]


title: Brain cortex, (-)-Vestitol, n3

value: 6 month old


title: Sample5

value: positive


title: TC-71_scrambled_3 [T9]

value: scrambled knockdown


title: Sample17


title: DRsc1CW3

description: Library name: DRsc1_FP_3

value: strain


title: Sample38


title: DRsc1CW2

description: Library name: DRsc1_FP_2


title: Sample44


title: Brain cortex, disease model control, n5

value: male

value: Brain cortex

value: vehicle


title: TC-71_scrambled_1 [T7]


title: TC-71_scrambled_2 [T8]


title: Sample42


title: DRsc1G2

description: Library name: DRsc1_G_2

value: Modified Mendal’s medium with 2% glucose as carbon resource


title: Brain cortex, disease model control, n4


title: Brain cortex, (-)-Vestitol, n2


title: TC-71_YK4279_3 [T6]

value: WT


title: TC-71_YK4279_2 [T5]


title: DRsc1CW1

description: Library name: DRsc1_FP_1

value: Modified Mendal’s medium with 1percent bran + 1percent microcrystalline cellulose as carbon resource


title: TC-71_YK4279_1 [T4]


title: Brain cortex, disease model control, n2


title: Sample23

value: F


title: TC-71_DMSO_3 [T3]

value: DMSO


title: Brain cortex, disease model control, n1

value: APPswe, PSEN1dE9


title: Sample36


title: TC-71_DMSO_2 [T2]


title: Sample31


title: Embryonic day 18.5 fetal mouse leg muscle RNA-seq KO rep3

city: wuhan

first: wei

last: jiang

address: No.1, Shizishan Street, Hongshan District, Wuhan, China

institute: Huazhong Agricultural University

data_processing:
Raw reads were processed using Trim Galore (v0.6.6) to eliminate low-quality reads and adapter sequences.
Paired-end reads were then mapped to the mm10 genome using Hisat2 (v2.2.1)
To quantify differences in gene expression and obtain raw count data, Feature Counts (v 2.0.1) was employed.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw gene counts for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Leg muscle

growth_protocol: Mating of mice with the same genotype was performed, and vaginal plugs were checked at 7 a.m. daily. After a gestation period of 18.5 days, embryos were harvested, and leg muscle samples from the fetuses were collected. RNA was extracted and subjected to RNA-seq analysis.

extract_protocol:
Total RNA was extracted from the leg muscles of 18.5-day-old KO and WT mice during the embryonic stage. DNase I treatment was performed to remove genomic DNA from the total RNA.
For library construction, we used a protocol as described before.(Zhou et al., 2015) The purified library products were evaluated using a Bioanalyzer (Agilent) and SYBR qPCR and sequenced on an Illumina Hi-seq 2000 sequencer

value: Leg muscle

value: SYISL KO


title: Sample43


title: Embryonic day 18.5 fetal mouse leg muscle RNA-seq KO rep2


title: TC-71_DMSO_1 [T1]

value: Ewing sarcoma cells


title: Brain cortex, (-)-Vestitol, n1

value: (-)-Vestitol, 5 mg/kg


title: HA_2

city: Jinan

first: Shourui

last: Hu

address: wenhuaxi road 44

data_processing:
To get high quality clean reads, raw reads were filtered according to the following rules: 1） removing reads containing more than 10% of unknown nucleotides (N); 2） removing low quality reads containing more than 40% of low quality (Q-value ≤ 20) bases.
The obtained clean reads were mapped to the species reference genome using BSMAP software (version: 2.90) by default. Then a custom Perl script was used to call methylated cytosines and the methylated cytosines were tested with the correction algorithm described in Lister R.et al (2009)
Assembly: Ensembl_release110
Supplementary files format and content: Igv file with methylated cytosine percentage in  the whole genome

source_name: sperm

extract_protocol:
1 μg of genomic DNA was subjected to library synthesis using TIANamp Genomic DNA Kit (TIANGEN, Beijing, China)
After genomic DNAs were extracted from the samples, DNA concentration and  integrity were detected by NanoDrop spectrophotometer and Agarose Gel  Electrophoresis respectively. The DNA libraries for Enzymatic Methylation  sequencing were prepared as described previously. Briefly, genomic DNAs were  fragmented into 100-300bp by Sonication (Covaris) and purified with MiniElute PCR  Purification Kit（QIAGEN）. Purified DNA is enzymatically converted using a  EpiArt®DNA Enzymatic Methylation Kit.The fragmented DNAs were end repaired  and a single “A” nucleotide was added to the 3’ end of the blunt fragments. Then the  genomic fragments were ligated to methylated sequencing adapters.

value: sperm


title: Sample29

value: negative


title: Sample21


title: Embryonic day 18.5 fetal mouse leg muscle RNA-seq KO rep1


title: Sample30


title: Brain cortex, disease model control, n3

value: 6 month old


title: HA_1


title: Embryonic day 18.5 fetal mouse leg muscle RNA-seq WT rep2

value: wild type


title: Sample4


title: Embryonic day 18.5 fetal mouse leg muscle RNA-seq WT rep3


title: DFif2G3

description: Library name: D1580_G_3

value: strain

value: Fif2 deletion strain


title: Ctrl_1


title: Sample25

value: M

value: positive


title: Sample46


title: Embryonic day 18.5 fetal mouse leg muscle RNA-seq WT rep1


title: Nanopore-SNF2h-KD-IAA

city: La Tronche

first: Christopher

last: Swale

address: Batiment Jean Roger

institute: INSERM

data_processing:
Nanopore: All datasets were subsequently basecalled (high accuracy basecalling) with Dorado base-caller with a Q score cutoff of >7. Long read alignment was performed by Minimap2. Sam files were converted to bam and sorted using Samtools 1.4.
Illumina: The quality of the raw sequencing reads was assessed using FastQC (www.bioinformatics. babraham.ac.uk/projects/fastqc/) and MultiQC. For the expression data quantification and normalization, the FASTQ reads were aligned to the ToxoDB-49 build of the T. gondii ME49 genome using Subread version 2.0.1 with the following options ‘subread-align -d 50 -D 600 --sortReadsByCoordinates’. Read counts for each gene were calculated using featureCounts from the Subread package. Transcripts were quantified and normalized using TPMCalculator.
Assembly: Toxoplasma gondii genome (ME49 strain)
Supplementary files format and content: Nanopore: No processed data files, only quality filetered fastq files. | Illumina: excel file with subread raw counts and TPMCalculator normalized counts

source_name: RH

extract_protocol:
Total RNAs were extracted and purified using TRIzol (Invitrogen, Carlsbad, CA, USA) and RNeasy Plus Mini Kit (Qiagen).
Nanopore: the mRNA library preparation followed the SQK-RNA004 kit (Oxford Nanopore)–recommended protocol, the only modification was the input mRNA quantity increased from 500 to 900 ng (300ng from each replicate), and all other consumables and parameters were standard. | Illumina: RNA sequencing was performed following standard Illumina protocols, by Novogene (Cambridge, United Kingdom).

treatment_protocol: HFF cells were grown to confluence and infected with RHKu80 SNF2h KD or RHKu80 RFTS KD strains.Transcriptome profiles in each strain left untreated (UT) and treated with IAA (indole-3-acetic acid) for 24 hours.

value: RH

value: Intracellular tachyzoites

value: IAA treated for 24h


title: BALB/c 4T1 tumor, SerRS AA, rep3

city: La Jolla

first: Justin

last: Wang

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

data_processing:
Processing was performed by the Scripps Research Center for Computational Biology and Bioinformatics
Reads were trimmed using TrimGalore (v 0.6.4) and mapped to the full mouse genome (GRCm38) using STAR (v 2.6.1d) to generate gene counts.
Counts were passed into DESeq2 (v 1.20.0) to perform differential expression analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing raw read counts for each sample

source_name: mammary fat pad primary tumor

extract_protocol:
Primary tumors resected from tetracycline-inducible mSerRS-expressing BALB/c mice were processed for RNA-seq. Tumors were dissociated and RNA was extracted using TRIzol Reagent (ThermoFisher Scientific). RNA purity was measured by the NanoDrop 1000 (Thermo Fisher Scientific).
Libraries were produced by the Scripps Research Genomics Core following their protocol.

value: mammary fat pad primary tumor

value: breast cancer cells


title: Sample52


title: DFif2G1

description: Library name: D1580_G_1

value: Modified Mendal’s medium with 2% glucose as carbon resource


title: BALB/c 4T1 tumor, SerRS AA, rep1


title: DFif2CW3

description: Library name: D1580_FP_3

value: Modified Mendal’s medium with 1percent bran + 1percent microcrystalline cellulose as carbon resource


title: BALB/c 4T1 tumor, SerRS AA, rep2


title: Nanopore-SNF2h-KD-UT

value: untreated sample


title: Sample14


title: DFif2CW2

description: Library name: D1580_FP_2


title: BALB/c 4T1 tumor, SerRS WT, rep3


title: Magnolia_obovata_Pistil

city: Chiba

first: Mami

last: Yamazaki

state: Chiba

address: 1-8-1 Inohana, Chuo-ku, Chiba City Pharmaceutical Research Building II

department: Department of Molecular Biology and Biotechnology

country: Japan

institute: Chiba University

description: Plant Material ID MY_Magnolia_obovata#01 in Chiba University, Japan

data_processing:
We pre-processed raw reads, and removed adapter sequences, empty reads, reads with ambiguous ‘N’ bases > 5%, raw reads of low quality (Q<20), and raw reads with an average length less than 30 bases. Filtering of raw reads was performed using Trimmomatic program (Bolger et al., 2014), resulting into paired end raw reads, and unpaired reads which lost its corresponding sequence partner due to quality control.
Assembly: For generation of the de novo transcriptome assembly, three popular assemblers were used, CLC genomics workbench (https://www.qiagenbioinformatics.com/ ), and Trinity (Grabherr et al., 2011) with their default parameters and SoAPdeNOVO -TRANS (Xi et al., 2014)  with six different k-mer sizes, namely 31, 41, 51, 63, 71, and 91, of which k-mer 31 having best assembly statistics was selected for further use . The SOAPdeNOVO assembly with k-mer size 31 was concatenated with individual assembly obtained from Trinity  and CLC genomics workbench  to obtain the final assembly of M. obovata. The final assembly obtained was further processed using CD-HIT  (Li and Godzik 2006) to remove any sequence redundancy. Our final assembly resulting in 284,165 unigenes with N50 value as 1,280 bp. We then processed these contigs for read alignment and abundance estimation using Bowtie2.0 (Langmead et al., 2009) and RSEM (Li et al., 2011), respectively. To calculate unigene expression, we used Fragments per Kilobase exon per Million mapped fragments (FPKM) method. FASTA file is available on the series record.
Supplementary files format and content: Young_Leaf_Mo_FPKM.csv
Supplementary files format and content: Mature_Leaf_Mo_FPKM.csv
Supplementary files format and content: Stem_Mo_FPKM.csv
Supplementary files format and content: Bark_Mo_FPKM.csv
Supplementary files format and content: Central_Cylinder_Mo_FPKM.csv
Supplementary files format and content: Floral_Bud_Mo_FPKM.csv
Supplementary files format and content: Pistil_Mo_FPKM.csv
Supplementary files format and content: Magnolia_obovata_all_tissues_FPKM_values

organism: Magnolia obovata

source_name: Pistil

growth_protocol: All seven tissues, namely young leaf, mature leaf,  stem, bark, central cylinder, floral bud, and pistil were harvested from M. obovata growing in the natural conditions at Medicinal garden, Graduate School of Pharmaceutical Sciences, Chiba University

extract_protocol:
Frozen samples of M. obovata were powdered using a Multi Beads Shocker (Yasui Kikai, Japan) for subsequent RNA extraction. Total RNA for each of the seven tissues was extracted using RNeasy Plant Mini Kit (Qiagen, USA), according to the manufacturer’s instruction.
cDNA library was then prepared using SureSelect Strand Specific RNA Library kit (Agilent 150 Technologies, USA) according to the manufacturer’s specifications. mRNA was isolated from total RNA of each tissue using beads containing oligo(dt), which was then added with fragmentation buffer to shear mRNA into short fragments and used as a template for the synthesis of first strand cDNA synthesis using random hexamer primers. The cDNA library for Illumina sequencing was prepared using SureSelect Strand Specific RNA Library kit (Agilent, USA) according to the manufacturer’s instruction.

treatment_protocol: Not applicable

value: Pistil


title: Sample34


title: Sample10


title: BALB/c 4T1 tumor, SerRS WT, rep2


title: DFif2CW1

description: Library name: D1580_FP_1


title: Magnolia_obovata_Floral_Bud


title: Ctrl_2

value: sperm


title: DFif2G2

description: Library name: D1580_G_2


title: Magnolia_obovata_Central_Cylinder


title: HCT116_LIG4_KO_AID_RAD21_4OHT_MRE11_ChIP_seq_EDF5g_replicate 2

city: Bethesda

first: Christophe

middle: E

last: Redon

address: 37 Convent Drive

institute: NIH

data_processing:
BAM files were filtered using alignmentSieve to remove reads shorter than 40bp
For peak calling the MACS2 algorithm was used.
Nascent strand reads were called by comparison to genomic DNA.
Peaks were filtered to accept the top 40% by q-value based on the raw output
Assembly: hg19
Supplementary files format and content: Bed file format showing: AsiSI TADs and random TADs AsiSI cut sites in U2OS NS-seq peaks AsiSI cut sites in LIG4-/- AID RAD21 AsiSI-HCT116 replication timing in U2OS
Supplementary files format and content: BigWig file format of BrdU-seq NS-seq and ChIP-seq

source_name: Colon

growth_protocol: AsiSI-U2OS cells were grown in DMEM medium 10% FBS. AID RAD21 HCT116 and AID RAD21 AsiSI HCT116 are grown in McCoy's 5A medium with 10% FBS

extract_protocol:
DNA from cell cultures was isolated size fractionated and subject to exunuclease digestion as described in Aladjem et al. Science 281 1005 1998. and Wang et al. Molecular and Cellular Biology 24:3373-86 2004. For ChipSeq DNA molecules were enriched using antibodies against proteins of interest. For BrdU seq extraction was performed using a protocol modified from Marchal et al. 2018
Samples were eluted and then purified by Monarch PCR & DNA Cleanup Kit (NEBT1030S). 100 ng of samples were used to generate the library. The kits used for the library were NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7805S) and NEBNext Multiplex Oligos for Il-lumina (Index Primers Set 1 and Set 2) (NEB E7335S and E7500S).

treatment_protocol: 4OHT was added at a concentration of 300 nM for 4h to induce DNA DSBs. Where relevant WEE1i was added at a concentration of 10 uM for 1h.

value: Colon

value: colorectal carcinoma

value: HCT116 LIG4 KO


title: Magnolia_obovata_Bark

source_name: Bark

value: Bark


title: BALB/c 4T1 tumor, SerRS WT, rep1


title: Magnolia_obovata_Stem

source_name: Stem

value: Stem


title: HCT116_LIG4_KO_AID_RAD21_4OHT_MRE11_ChIP_seq_EDF5g_replicate 1


title: Sample32

value: M

value: negative


title: BALB/c 4T1 tumor, vector, rep2


title: SK-MEL-28siLINC00622

city: Guangzhou

first: can

last: li

address: Southern Medical University

institute: Southern Medical University

data_processing:
After obtaining the raw sequencing data (Raw Data), you first need to filter the data, remove the adapter sequence, and process low-quality reads, and then evaluate the sequencing quality to obtain high-quality data (Clean Data). And compare the Clean Data with the reference genome to get the BAM file.
Use the HISAT2 software to compare the sequencing data with the reference genome, and make a comprehensive evaluation of the coverage area and coverage depth of the sequencing data. HISAT2 is the successor of TopHat2/Bowtie2. It uses an improved BWT algorithm (FM index). HISAT uses a large number of FM indexes to cover the entire genome, and combines several comparison strategies to achieve an efficient and faster comparison of RNA-seq data.
In RNA sequencing, RPKM (expected number of Reads Per Kilobase of transcript sequence per Millions basepairs sequenced) is the number of reads from a gene per kilobase length per million reads, which also considers the sequence depth and gene length pair The influence of read count is currently the most commonly used method for estimating gene expression levels. Map the bam file obtained by sequencing to the gtf file of the reference species to obtain the gene expression level, and perform regional statistics on the gene expression level of the genome according to the statistical method to reflect the overall expression level of the sample.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include counts and TPM values for each Sample.

source_name: melanoma tissues

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment. Then 1 ug of total RNA for the construction was used as sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A375 and SK-MEL-28 cells were treated with siNC or siLINC00622 with transfection reagent when the cells were about 70% confluency and then cells were incubate in non-serum DMEM at 37°C with 5% CO2 for 6 hour，respectly. After 6h change the medium with 10% serum DMEM and continuously incubate  24h.

value: melanoma tissues


title: BALB/c 4T1 tumor, vector, rep3


title: Magnolia_obovata_Mature_Leaf


title: Sample48


title: BALB/c 4T1 tumor, vector, rep1


title: Sample40

value: positive


title: Magnolia_obovata_Young_Leaf


title: A375siLINC00622


title: MLO-Y4 cells, HICA2, 24h

city: Suzhou

first: Yujiang

last: Liu

address: Yangsu Road No.18

institute: Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine

data_processing:
The raw data were processed using an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexities, common RNA families (rRNA, tRNA, snRNA, snoRNA) (http://rfam.sanger.ac.uk/), repeats (http://www.girinst.org/repbase), and sequences <18 nt or >26 nt in length.
Subsequently, the unique sequences with a length of 18~26 nt were mapped to miRNA sequences in miRBase 22.0 (http://www.mirbase.org/). Mapping was also performed on pre-miRNA against mice genomic data (https://www.ncbi.nlm.nih.gov/genome/52?genome_assembly_id=992563).
The unique sequences that aligned to the known miRNAs sequences in miRBase 22.0 were identified as known miRNA. Secondary structure of pre-miRNAs was presented as a hairpin, including 5p- and 3p- derived miRNA.
The unique sequences mapping to the other arm of the pre-miRNAs sequences, which were not annotated in the miRBase 22.0, were considered to be 5p- or 3p- derived miRNA candidates. The remaining unmapped sequences were matched to the mice genomic sequences in search of candidate novel miRNAs.
To identify the results of putative miRNAs in mice, all the obtained miRNAs were used to predict the secondary structures using RNAfold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi).
Assembly: mmu10
Supplementary files format and content: tab-delimited text files include FRKM and count values for eachi Sample

source_name: MLO-Y4 cells

extract_protocol:
Total RNA was extracted from the exosomes using an Exosome RNA Purification Kit (System Biosciences Inc., Mountain View, CA, USA) according to the manufacturer’s protocol. The concentration and integrity of isolated RNA were evaluated with a Bioanalyzer 2100 instrument (Agilent Technologies, Santa Clara, CA, USA). Total exosome RNAs extracted were polyadenylated and reverse-transcribed with a poly (T) adapter into cDNAs. Only high-quality RNA sample (OD260/280 = 1.8∼2.2, OD260/230 ≥ 2.0, RIN ≥ 6.5, 28S:18S ≥ 1.0, >10 μg) was used to construct sequencing library.
RNA-seq transcriptome library was prepared following TruSeq RNA sample preparation kit from Illumina (San Diego, CA, USA) using 5 μg of total RNA. And then we performed the single-end sequencing (1x50bp) on an Illumina Hiseq2500 at the LC-BIO (Hangzhou, China) following the vendor’s recommended protocol.

value: MLO-Y4 cells

value: osteocyte-like cells

value: 10 uM ICA(HICA) for 24h


title: MLO-Y4 cells, HICA3, 24h


title: A375siNC

value: siNC


title: G12V1-m6AIP

city: Milwaukee

first: Tongjun

last: Gu

address: 8727 W Watertown Plank Rd

institute: VERSITI WISCONSIN, INC.

data_processing:
The library was sequenced by using Nova-seq X with a paired-end 150bp. 126 millions reads has been collected.
RNA reads were aligned to hg38 human genome using STAR V2.7.11b and quantified using Salmon V1.10.2.
m6A reads were aligned to hg38 human genome using Hisat2 V2.2.1 and peaks were called using Macs2 V2.2.7.1.
Assembly: hg38
Supplementary files format and content: The processed data for RNAseq are in the format of txt file and contains the gene expression values in the format of raw counts and TPM (Transcription per Million).
Supplementary files format and content: The processed data for m6A are in the format of txt and contains the narrow peaks for each m6A region called by Macs2 V2.2.7.1

source_name: human lung cancer cell line

growth_protocol: NCI-H522 cells stably expressing pCDH-Vector and pCDH-strep-KRAS G12V were cultured in RPMI-1640 mediun supplemented with 10% FBS+ 1% P.S. + 1 ug/mL puromycin

extract_protocol:
Total RNAs were extracted by Trizol reagent
The libraries for RNA-seq and m6A-seq were constructed by using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina® (NEB, Cat#E7760L).
The libraries for both RNA-seq and m6A-seq were sequenced by using Nova-seq X with 150 bp of paired-end.

treatment_protocol:
NCI-H522 cells were infected with pCDH-Flag-KRAS G12V lenti-virus twice. The infected cells were selected by using a final concentration of 1 ug/mL puromycin for three days.
1 mg/mL puromycin, 1:1000 dilution
NCI-H522 cells stably expressing pCDH-Vector and pCDH-strep-KRAS G12V were selected by 1 ug/mL puromycin (Final concentration).

value: lung cancer cell line

value: KRAS mutant


title: G12V2-m6AIP

data_processing:
The library was sequenced by using Nova-seq X with a paired-end 150bp. 91.6 millions reads has been collected.
RNA reads were aligned to hg38 human genome using STAR V2.7.11b and quantified using Salmon V1.10.2.
m6A reads were aligned to hg38 human genome using Hisat2 V2.2.1 and peaks were called using Macs2 V2.2.7.1.
Assembly: hg38
Supplementary files format and content: The processed data for RNAseq are in the format of txt file and contains the gene expression values in the format of raw counts and TPM (Transcription per Million).
Supplementary files format and content: The processed data for m6A are in the format of txt and contains the narrow peaks for each m6A region called by Macs2 V2.2.7.1