title: Strep-ALKBH5 Rep 3 (RIP-seq)

city: Chicago

first: Allen

last: Zhu

state: Illinois

address: 929 E 57th St, Room E331

institute: University of Chicago

data_processing:
Adapters of all raw RIP-seq data sets were removed by Cutadapt v1.18.
Then reads longer than 19 nt were mapped to the human genome (hg38) and the GENCODE v36 gene annotation using HISAT2 v2.1.0 with default parameters.
Raw reads on each gene were counted by featureCounts (-t exon -g gene_id -M -O --fraction -T 24 -s 2) from Subread v1.6.4.
For each gene, the differential enrichment of reads between IP and input samples were calculated by the edgeR v3.24.3 package.
Genes with the cutoff (log2FCIP/input > 1 and FDR < 0.05) were determined as candidate targets and used for further analysis.
genome_build: hg38
Supplementary_files_format_and_content: Fold changes of read abundance and p-values between IP and input groups in the plain txt format

source_name: Head&Neck SCC cells

growth_protocol: UM-SCC-1 cells were rountinely cultured in 10 cm dishes with DMEM mediun supplemented with p.s and FBS and cell passge was pefromed by 0.25% trypsin digestion when cell conflunece reaches 95%.

extract_protocol:
Lysates were obtained from lysis buffer containing 0.1% NP-40. RNA was purified and fragmented with the BioRuptor Pico.
Libraries were prepared at half scale according to the manufacturer's instructions accompanying the Takara SMARTER Stranded Total RNA-seq Kit v2 - Pico Input Mammalian (Cat # 634412). Libraries were then inspected with the Bioanalyzer machine. Libraries were sequencied on the Illumina NovaSeq 6000 according to manufacturer's instructions.

treatment_protocol: For the RNA-Seq and m6A-Seq assay, UM-SCC-1 cells were infected with si RNA scramble, ALKBH5 siRNA#1/2, RBM33 siRNA#1/#2 retrovirus and selected with10 ug/mL blasticidin for 4 days. For the RIP-Seq assay, UM-SCC-1 cells were infected with strep-Vec, strep-ALKBH5, and strep-RBM33 lenti-virus and selected with 1 ug/mL puromycin for 4 days. Then infect UM-SCC-1 cells stably expressing strep-ALKBH5 with RBM33 siRNA#1/#2 retrovirus and selected with blasticidin for another 4 days.

value: Head and neck squamous cell carcinoma (HNSC)

value: StrepTactin-XT RIP

tag: tag


title: wild type + ATMi + E2, 2 h, rep 1

status: Public on Jun 01 2023

type: SRA

city: Kyoto

first: Rifat

middle: Ara

last: Najnin

state: Kyoto

address: Yoshida Konoe, Sakyo-ku

department: Radiation Genetics

country: Japan

institute: Kyoto University

description: Nascent RNA

library_source: transcriptomic

data_processing:
CAGE libraries were sequenced using single-end reads of 75 nt on a NextSeq 500 instrument (Illumina). Obtained reads (CAGE tags) were mapped to the human hg38 genome using BWA (version 0.5.9) (https://arxiv.org/abs/1303.3997). Unmapped reads were then mapped by HISAT2 (version 2.0.5). CAGE tag count data were clustered through the CAGEr toolbox using Paraclu algorithm  with default parameters. Clusters with count per million (CPM) <0.2 were discarded. Differentially expressed genes at each timepoint were detected using DESeq2 (version 1.20.0).
Assembly: hg38
Supplementary files format and content: BigWig
Library strategy: NET-CAGE

molecule: total RNA

organism: Homo sapiens

source_name: Breast

growth_protocol: MCF-7 cells were cultured in a serum-free medium for 24–26 h before treatment with estrogen.

extract_protocol:
RNA was extracted as described previously (Hirabayashi et al.,PMID: 31477927).Briefly, fresh cells were lysed in the presence of α-amanitin, and the nuclear insoluble fraction was isolated. Following DNase treatment, RNA was purified using the miRNeasy Mini kit (Qiagen) according to the manufacturer’s instructions.
NET-CAGE library preparation, sequencing, mapping, and gene expression analysis were performed by DNAFORM (Kanagawa, Japan). In brief, the cDNAs were synthesized from total RNA using random primers. The ribose diols in the 5′ cap structures of RNAs were oxidized and then biotinylated. The biotinylated RNA/cDNAs were selected by streptavidin beads (cap-trapping). After RNA digestion by RNaseONE/H and adaptor ligation to both cDNA ends, double-stranded cDNA libraries (CAGE libraries) were constructed.

treatment_protocol: To assess the effect of ATM loss on the E2 response, 10 µM of ATMi was added to the medium together with E2 or ethanol; DMSO was added 30 min prior to the E2 treatment as a control. Three replicates of cells cultured in three 15-cm dishes (approximately 10 million cells per dish) were treated simultaneously and pooled for analysis. Replicates were processed simultaneously throughout to avoid potential batch effects.

tag: tissue

value: Breast

tag: cell line

tag: cell type

value: Breast cancer cell

tag: genotype

value: Wild-type

tag: treatment

value: ATMi ,Estrogen

tag: time


title: Strep-ALKBH5 Rep 1 (RIP-seq)

country: USA


title: Strep-ALKBH5 Rep 2 (RIP-seq)


title: N9 LPS replicate_2

city: Madison

first: Daniel

last: Shippy

address: 1111 Highland Avenue

institute: UW-Madison

description: Each processed file has all the groups in one file.

data_processing:
Library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Paired-end clean reads were aligned to the reference genome using HiStat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include gene counts for each sample.
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample.

organism: Mus musculus

growth_protocol: N9 microglial cells were routinely cultured in RPMI 1640 media with FBS (5%) and penicillin/streptomycin (1%).

extract_protocol:
RNA was extracted from cells using Qiagen Rneasy Plus Mini Kit.
RNA libraries were prepared for sequencing using standard protocols by Novogene.

treatment_protocol: N9 microglial cells were cultured in control media (glucose-free dmem, dialyzed serum (5%), glucose (3 mM) and fructose (5 mM)), high glucose media (control media with 15 mM glucose), and high fructose media (control media with 15 mM fructose) for 18 hours and stimulated with LPS (1 µg/ml) for an additional 6 hours.

value: Microglia

value: Control media + LPS


title: Strep-RBM33 Rep 2 (RIP-seq)


title: TDP2–/–, 1 h, replicate 1

description: Nascent RNA

value: TDP2 null mutant

value: Estrogen


title: SNU-449, TGFb, rep2

type: RNA

city: Rennes

first: Cedric

last: Coulouarn

address: CLCC Eugène Marquis, Rue de la Bataille Flandres Dunkerque, Bat D, 1er étage

country: France

institute: INSERM

description: SNU-449 cells treated with TGFb1 - Replicate 2

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µ of 2x Agilent hybridization buffer (HI-RPM) was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray C Scanner (G2565) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09_ssSurrogates and Grid: 028004_D_F_20110325). Gene expression data were further analyzed by using the GeneSpring software (Agilent Technologies).

source_name: SNU-449 cells treated with TGFb1

label_protocol: Total RNA was amplified and labeled with Cy3 fluorescent dye using Agilent one color low-input QuickAmp labeling kit following according to the manufacturer's instructions. Starting from 150 ng total RNA, amplification yield was 3.14 ± 0.49 µg cRNA and specific activity was 24.13 ± 3.02 pmol Cy3 per µg cRNA.

growth_protocol: PRC/PRF/5 and SNU-449 HCC cell lines were purchased from ATCC (www.lgcstandards-atcc.org) and cultured as previously described (PMID: 34825776). ATCC performed cell line authentication by STR DNA profiling. Cells were treated for 16 hours with 1 ng/mL recombinant human TGF-β1 (R&D Systems, Minneapolis, MN) and/or 10 μM LY2157299 (Sigma-Aldrich, St. Louis, MO) after overnight serum starvation. All cell cultures were conducted at 37 ◦C in a 5% CO2 atmosphere. Independent culture experiments were carried out in triplicate.

extract_protocol: Total RNA was extracted and purified using the RNAeasy kit (Qiagen, Valencia, CA, USA) following the manufacturer’s recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: All cell cultures were conducted at 37°C in a 5% CO2 atmosphere and then submitetd to RNA extration and gene expression profiling. Independent culture experiments were carried out in triplicate.


title: N9 LPS replicate_1


title: Strep-Vec-1 Rep 3 (RIP-seq)


title: N9 control replicate_3

value: Control media


title: TDP2–/–, 0 h, replicate 1

description: Nascent RNA

value: No treatment


title: SNU-449, TGFb, rep3

description: SNU-449 cells treated with TGFb1 - Replicate 3


title: TDP2–/– + Mock, 6 h, replicate 3

description: Nascent RNA

value: Empty vector overexpression into TDP2 null mutant


title: N9 control replicate_1


title: SNU-449, Galunisertib, rep1

description: SNU-449 cells treated with Galunisertib - Replicate 1

source_name: SNU-449 cells treated with Galunisertib

value: Galunisertib


title: TDP2–/– + Mock, 6 h, replicate 2

description: Nascent RNA


title: Strep-Vec-1 Rep 1 (RIP-seq)


title: Strep-RBM33 Rep 2 (RIP-seq, input)


title: SNU-449, control, rep2

description: Untreated control SNU-449 cells - Replicate 2

source_name: Untreated control SNU-449 cells

value: Control


title: SNU-449, control, rep3

description: Untreated control SNU-449 cells - Replicate 3


title: SNU-449, TGFb, rep1

description: SNU-449 cells treated with TGFb1 - Replicate 1


title: TDP2–/– + Mock, 6 h, replicate 1

description: Nascent RNA


title: Repro, Cry1KO, MEF, 2i, scRNAseq

city: College Station

first: Shogo

last: Sato

state: Texas

address: 3258 TAMU, Biological Science Building West (BSBW) 309

department: Biology

institute: Texas A&M University

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

library_source: transcriptomic single cell

data_processing:
FASTQ files for 10x Genomics 3’ gene expression assay were aligned utilizing 10x Genomics Cell Ranger 3.1.0.
Each sample’s library was aligned to the mm10 genome (10x Genomics, mm10-3.0.0) using Cell Ranger Count (10x Genomics, Cell Ranger 3.1.0).
Aggregation of aligned matrices to normalize for mean reads per cell was performed using Cell Ranger Aggr (10x Genomics, Cell Ranger 3.1.0).
Aggregated gene expression matrix was read into RStudio (R version 3.6.1/RStudio version 1.2.1) using the Seurat package (version 3.1.1).
Quality control trimming was performed to remove any genes not expressed in at least 3 cells, and any cells that fall outside the range of 2000 to 10,000 unique genes or containing more than 7% mitochondrial genes.
Cells in the expression matrix were labeled from each respective sample and labels were used to subset selected samples for analysis.
Selected samples were merged and batch-corrected using the Seurat Integration feature.
Assembly: mm10
Supplementary files format and content: tsv, mtx
Supplementary files format and content: In barcodes.tsv:
WT_iPSC_scRNAseq barcode-1
WT_MEF_scRNAseq barcode-2
Cry1KO_MEF_scRNAseq barcode-3
Repro_WT_MEF_scRNAseq barcode-4
Repro_WT_MEF_2i_scRNAseq barcode-5
Repro_Cry1KO_MEF_scRNAseq barcode-6
Repro_Cry1KO_MEF_2i_scRNAseq barcode-7

source_name: Reprogrammed cells derived from Cry1 KO MEFs

growth_protocol: Yamanaka 4F-overexpressed cells were trypsinized and transferred onto MEF feeder cells that mitotically inactivated with mitomycin C treatment (day 4). At day 5, cell culture medium was replaced into ESC medium (GMEM/high glucose containing 10% FBS, antibiotics, GlutaMAX, non-essential amino acids, sodium pyruvate, 2-mercaptoethanol, and LIF) followed by 2i treatment at day 9. Reprogrammed cells, as well as the reference cells (MEFs and iPSCs), were subjected to scRNA-seq before and after 2i treatment.

extract_protocol:
Yamanaka 4F-induced cells were trypsinized and transferred onto mitomycin-treated and SytoxBlue (Invitrogen)-stained MEF feeder cells. Cells were washed with PBS and digested with 0.05% trypsin to generate a single-cell suspension. Dead cells were stained with SytoxBlue dead cell stain and sorted by FACS. Flow cytometry-sorted cells were washed in PBS with 0.04% BSA and resuspended at a concentration of ~1000 cells/µl.
Library generation for 10X Genomics v3 chemistry was performed following the Chromium Single Cell 3ʹ Reagents Kits User Guide: CG000204 Rev D. Quantiﬁcation of cDNA libraries was performed using Qubit dsDNA HS Assay Kit (Life Technologies Q32851) and high-sensitivity DNA chips (Agilent. 50674626). Quantiﬁcation of library construction was performed using KAPA qPCR (Kapa Biosystems KK4824). The library was sequenced on the Illumina NovaSeq6000 platform to target an average of ~50,000 reads per cell.


title: Strep-RBM33 Rep 1 (RIP-seq, input)


title: TDP2–/– + Mock, 3 h, replicate 3

description: Nascent RNA


title: Strep-ALKBH5 Rep 3 (RIP-seq, input)


title: Strep-Vec-1 Rep 2 (RIP-seq)


title: Strep-ALKBH5 Rep 2 (RIP-seq, input)


title: N9 control replicate_2


title: TDP2–/– + Mock, 3 h, replicate 1

description: Nascent RNA


title: Repro, WT, MEF, scRNAseq

source_name: Reprogrammed cells derived from WT MEFs

value: Reprogrammed cells derived from WT MEFs

value: WT

value: control


title: PLC/PRF/5, TGFb + Galunisertib, rep3

description: PLC/PRF/5 cells cotreated with TGFb1 and Galunisertib - Replicate 3


title: PLC/PRF/5, TGFb + Galunisertib, rep2

description: PLC/PRF/5 cells cotreated with TGFb1 and Galunisertib - Replicate 2


title: Strep-ALKBH5 Rep 1 (RIP-seq, input)

value: Head and neck squamous cell carcinoma (HNSC)


title: PLC/PRF/5, TGFb + Galunisertib, rep1

description: PLC/PRF/5 cells cotreated with TGFb1 and Galunisertib - Replicate 1


title: TDP2–/– + Mock, 1 h, replicate 3

description: Nascent RNA

value: Breast


title: PLC/PRF/5, Galunisertib, rep2

description: PLC/PRF/5 cells treated with Galunisertib - Replicate 2


title: Repro, Cry1KO, MEF, scRNAseq

value: Reprogrammed cells derived from Cry1 KO MEFs


title: WT, iPSC, scRNAseq

source_name: iPSCs

value: induced pluripotent stem cells

value: reference cells


title: PLC/PRF/5, Galunisertib, rep3

description: PLC/PRF/5 cells treated with Galunisertib - Replicate 3


title: Strep-RBM33 Rep 1 (RIP-seq)

value: StrepTactin-XT RIP


title: SNU-449, control, rep1

description: Untreated control SNU-449 cells - Replicate 1


title: TDP2–/– + Mock, 1 h, replicate 2

description: Nascent RNA

value: Breast cancer cell


title: Strep-Vec-1 Rep 3 (RIP-seq, input)


title: Strep-Vec-1 Rep 2 (RIP-seq, input)


title: NeuDet-D2-3

city: Boston

first: Jiehui

last: Chen

state: MA

address: 320 Longwood Ave

institute: Boston Children’s Hospital

description:
NeuDet-D2-3
count1.csv

data_processing:
For data analysis, reference genome and gene annotation files were downloaded from GENECODE (hg38). Fastq files were pre-processed by Fastp (v0.12.1) (Chen et al., 2018) with default parameters. Cleaned data were then aligned to the reference genome via Hisat2 (v2.1.0) (Kim et al., 2015). FeatureCounts (v1.5.3) (Liao et al., 2014) was used to count the reads mapped to each gene.
RNA-seq data in this paper were compared with nmps (Verrier et al., 2018) after removing batch effects by the R package “combat” (Johnson et al., 2007). Principal Components Analysis (PCA) (Jolliffe, 2002) was used to show the correlation of these samples.
The ‘Developmental Transcriptome Dataset’ of BRAINSPAN (https://www.brainspan.org/static/download.html) was also downloaded. We merged the brain samples of same stage and calculated Pearson correlation coefficients between the merged samples and RNA-seq data in this paper.  Pseudo-bulk RNA-seq of human spinal cord, GSE171892 (Rayon et al., 2021), was conducted through the R package “scuttle” (McCarthy et al., 2017). After that, samples at same stages were merged and pearson correlation coefficients were calculated between the pseudo-bulk RNA-seq and RNA-seq data in this paper.
The SCENIC (Aibar et al., 2017) was used to infer the gene regulatory network (regulon). Binary regulon-activity matrix for all samples was used in principal components analysis. GO enrichment analysis of related target genes was carried out by Metascape (https://metascape.org/) with default parameters (Zhou et al., 2019).
Assembly: hg38
Supplementary files format and content: csv files include counts for each Sample.

source_name: cell line

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen).
RNA libraries were prepared for sequencing according to the manufacturer’s protocol (NEBNext® UltraTM RNA Library Prep Kit for Illumina®).

value: cell line

value: differentiating hSCNPCs

value: Neural differentiation


title: TDP2–/– + Mock, 1 h, replicate 1

description: Nascent RNA

value: Estrogen


title: TDP2–/– + Mock, 3 h, replicate 2

description: Nascent RNA

value: Empty vector overexpression into TDP2 null mutant


title: WT, MEF, scRNAseq

source_name: MEFs

value: Mouse embryonic fibroblasts


title: PLC/PRF/5, Galunisertib, rep1

description: PLC/PRF/5 cells treated with Galunisertib - Replicate 1

value: Galunisertib


title: Repro, WT, MEF, 2i, scRNAseq

value: Reprogrammed cells derived from WT MEFs


title: Strep-Vec-1 Rep 1 (RIP-seq, input)


title: ESC_IgG_ChIP

library_source: genomic

data_processing:
Raw sequencing reads were mapped to mouse reference genome GRCm38 (mm10) by bowtie2 (v2.2.7).
Mapped reads were filtered to only keep proper-paired and high mapping quality (> 30) reads.
Duplicate reads were removed using MarkDuplicates from Picard tools (v1.96).
The remaining reads were used for peak calling by MACS2 (v2.2.7.1) with a cutoff of q-value ≤ 0.05.
The peaks common to two replicates were applied for downstream analyses.
Peaks that were common to multiple cell types or specific to a cell type were identified using BEDtools (v2.29.2).
Binding peaks were assigned to the associated genes using R package ChIPseeker, which also performed GO Biological Process enrichment analysis of these genes and visualized the results.
The ChIP-seq reads density was determined based on CPM (Counts Per Million mapped reads) normalization method by deepTools (v3.5.0).
Heatmaps and aggregate lines were generated by deepTools based on the read density.
The visualized genomic regions were extracted based on GRCm38 Ensembl genes.
The findMotifsGenome.pl of HOMER (v4.11) was applied for motif searching at CRY1 binding peaks with the option of “-size 200,” which allows identification of motifs at the 400 bp region centered by peak midpoint.
Assembly: mm10
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: embryonic stem cells

growth_protocol: MEFs were cultured at 37oC in DMEM/high glucose (Sigma-Aldrich) containing 10% FBS and antibiotics (penicillin and streptomycin). PreiPSCs, iPSCs, and ESCs were cultured at 37oC in GMEM/high glucose (Sigma-Aldrich) containing 10% FBS, antibiotics (penicillin and streptomycin), GlutaMAX, non-essential amino acids, sodium pyruvate, 2-mercaptoethanol, and leukemia inhibitory factor (LIF). 2i (GSK3b inhibitor CHIR99021 and MEK/ERK inhibitor SB202190) was supplemented in iPSC culture medium for the maintenance of pluripotency.

extract_protocol:
Cells were cross-linked with 1% Formaldehyde for 10 min at room temperature. Collected cells were resuspended in cell lysis buffer (5 mM HEPES, pH 8.0, 85 mM KCL, 0.5% NP-40, and the same inhibitors as described in the Western blot section) and incubated for 10 min at 4oC. Samples were spun down and the pellets were resuspended in RIPA buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, pH 8.0, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, and the same inhibitors for cell lysis buffer) and incubated for 20 min at 4oC.  Nuclear samples were sonicated to fragment DNA to ~0.2 kb using Bioruptor (Diagenode). Sheared DNA was pre-cleared for 2 hr at 4oC with protein G or A sepharose beads (Sigma-Aldrich) and immunoprecipitated with anti-CRY1 antibody (MBL Life science, PM081), overnight at 4oC. Protein A beads were added and rocked for 3hr at 4oC. The beads were washed with low-salt RIPA (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, pH 8.0, 1% Triton X-100, 0.1% SDS, and 0.1% sodium deoxycholate), high-salt RIPA (50 mM Tris-HCl, pH 8.0, 500 mM NaCl, 1 mM EDTA, pH 8.0, 1% Triton X-100, 0.1% SDS, and 0.1% sodium deoxycholate), LiCl wash (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1 mM EDTA, pH 8.0, 0.5% NP-40, and 0.1% sodium deoxycholate), and TE buffer (10 mM Tris-HCl, pH 8.0 and 1 mM EDTA, pH 8.0). Samples were reverse-crosslinked in elution buffer (10 mM Tris-HCl, pH 8.0, 300 mM NaCl, 5 mM EDTA, pH 8.0, and 0.5% SDS) overnight at 65oC, followed by the treatment with RNase for 30 min at 37oC, and proteinase K for 1 hr at 55oC. DNA was purified by phenol/chloroform and eluted in water. Anti-guinea pig IgG (MBL Life science, PM067) antibody was used as a negative control.
Library construction was performed using the Perkin Elmer NEXTFLEX Rapid DNA-seq v2.0 and the Perkin Elmer NEXTFLEX Unique Dual Index barcodes. The DNA quantity was measured by Qubit DNA High Sensitivity and the fragment size was measured by Agilent Bioanalyzer 2100 High Sensitivity DNA chip assay. The input amount of DNA was 2ng. The ends of the DNA were repaired and adenylated. The reaction mixture was then cleaned up using AMPure XP magnetic beads and Illumina-compatible barcoded adapters were ligated onto the blunt-end/adenylated product. The adaptor-ligated product was cleaned using AMPure XP beads and then amplified for adaptor-ligated products using 11 cycles of PCR. The resulting library was cleaned with AMPure XP beads and quantified by qPCR with the Roche Kapa Universal/Illumina Library Quantification kit. The library size was determined by analysis using the Bioanalyzer 2100 DNA High Sensitivity Chip.

tag: cell

value: ESCs

value: embryonic stem cells

tag: chip antibody

value: IgG (MBL Life science, #PM067)


title: TDP2–/– + Mock, 0 h, replicate 3

description: Nascent RNA

value: Breast

value: No treatment


title: TDP2–/– + Mock, 0 h, replicate 2

description: Nascent RNA


title: PLC/PRF/5, TGFb, rep2

description: PLC/PRF/5 cells treated with TGFb1 - Replicate 2

source_name: PLC/PRF/5 cells treated with TGFb1


title: Cry1KO, MEF, scRNAseq


title: RBM33 shRNA-2 Rep 3 (m6A-seq)

data_processing:
Reads were aligned to the mycoplasma genome to check for contamination; aligned reads were removed
Input and IP reads were aligned to the hg38 genome using HISAT2
Differential gene expression analysis was performed with DESeq2
M6A peaks were called using the MeRIPtools and RADAR packages
genome_build: hg38
Supplementary_files_format_and_content: tables of DEG and DMG in txt, or csv format
Library strategy: m6A-seq

value: Head and neck squamous cell carcinoma (HNSC)

value: m6A antibody

value: RBM33 shRNA-2


title: iPSC_IgG_ChIP

source_name: induced pluripotent stem cells

value: iPSCs

value: induced pluripotent stem cells


title: PLC/PRF/5, TGFb, rep3

description: PLC/PRF/5 cells treated with TGFb1 - Replicate 3


title: PLC/PRF/5, TGFb, rep1

description: PLC/PRF/5 cells treated with TGFb1 - Replicate 1


title: RBM33 shRNA-2 Rep 2 (m6A-seq)


title: PLC/PRF/5, control, rep3

description: Untreated control PLC/PRF/5 cells - Replicate 3

source_name: Untreated control PLC/PRF/5 cells

value: Control


title: RBM33 shRNA-1 Rep 3 (m6A-seq)

value: RBM33 shRNA-1


title: PreiPSC_IgG_ChIP

source_name: Precursor-induced pluripotent stem cells

value: PreiPSCs


title: MEF_IgG_ChIP

source_name: Mouse embryonic fibroblasts

value: MEFs


title: TDP2–/– + Mock, 0.5 h, replicate 3

description: Nascent RNA

value: Breast cancer cell

value: Empty vector overexpression into TDP2 null mutant

value: Estrogen


title: ESC_CRY1_ChIP

value: ESCs

value: CRY1 (MBL Life science, #PM081)


title: RBM33 shRNA-1 Rep 2 (m6A-seq)


title: TDP2–/– + Mock, 0.5 h, replicate 1

description: Nascent RNA


title: TDP2–/– + Mock, 0 h, replicate 1

description: Nascent RNA


title: iPSC_CRY1_ChIP


title: TDP2–/– + Mock, 0.5 h, replicate 2

description: Nascent RNA


title: RBM33 shRNA-1 Rep 1 (m6A-seq)


title: TDP2–/– + dTDP2, 1 h, replicate 1

description: Nascent RNA

value: Catalytic-dead TDP2 overexpression into TDP2 null mutant


title: PLC/PRF/5, control, rep1

description: Untreated control PLC/PRF/5 cells - Replicate 1


title: shControl - RBM33 Scramble Rep 3 (m6A-seq)

value: shControl - RBM33 Scramble


title: RBM33 shRNA-2 Rep 1 (m6A-seq)


title: InVitro_ANBL-6_delta-C1orf112

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

description: Gene expression in C1orf112-KO ANBL-6 cells

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60℃ for 30 min according to the manufacturers instructions. After the fragmentation reaction, equal amount of Agilent hybridization buffer was added to the fragmentation mixture and hybridized to a SurePrint G3 Human GE microarray 8x60K Ver. 3.0 for 17 h at 65 ℃ in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), for 1 minute with 37℃ GE Wash buffer 2 (Agilent), and then dried for 1 minute at room temperature with acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 2 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: delta-C1orf112 ANBL-6, 48h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using  NucleoSpin RNA kit (TaKaRa Bio Inc., Shiga, Japan) following the manufacturer's recommendations.  RNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: The MM cell lines were incubated in a RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. Following 24h incubation, the cells were then incubated with either 0.1% DMSO or 10 μM of LEN of for 24 hours at 37 ºC

value: MM cell line

tag: gender

value: Female

tag: age


title: InVitro_ANBL-6_Control

description: Gene expression in control ANBL-6 cells

source_name: Control ANBL-6, 48h


title: shControl - RBM33 Scramble Rep 2 (m6A-seq)

source_name: Head&Neck SCC cells

value: Head and neck squamous cell carcinoma (HNSC)

value: m6A antibody


title: MEF_CRY1_ChIP

value: Mouse embryonic fibroblasts


title: PLC/PRF/5, control, rep2

description: Untreated control PLC/PRF/5 cells - Replicate 2


title: TRAF7_EChet, rep 7

city: Oklahoma City

first: Alla

last: Tsytsykova

state: OK

address: 1122 NE 13th Street

department: Neurosurgery

institute: OUHSC

data_processing:
Sequencing was done from both ends.
Post-sequence reads were quality-filtered for length and contaminants and were trimmed for Illumina adapters.
Resulting reads were pseudo-aligned to coding regions of the mouse reference genome mm10 using STAR.
Assembly: Mus musculus reference genome mm10.
Supplementary files format and content: Excel files with FPKM values (the rows are features/genes and the columns are samples).

source_name: Mouse embryo

extract_protocol:
Total RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN, 74034) and QIAshredder (QIAGEN, 79656) according to the manufacturer’s instructions.
Preparation of cDNA libraries and sequencing (Illumina platform) was conducted by Novogene Co., LTD.

treatment_protocol: WT and TRAF7_ko embryos at day E9.5 were extracted from yolk sacs and immediately placed in Invitrogen™ RNAlater™ Stabilization Solution (Fisher Scientific, AM7023). They were kept at 4 °C for 24 h and transferred to −80 °C for long-term storage before RNA extraction.

value: Mouse embryo

tag: developmental stage

value: Embryo E9.5

value: TRAF7_Endothelim-specific heterozygote


title: TDP2–/– + TDP2, 6 h, replicate 3

description: Nascent RNA

source_name: Breast

value: Breast

value: Intact TDP2 overexpression into TDP2 null mutant


title: PreiPSC_CRY1_ChIP

value: PreiPSCs

value: Precursor-induced pluripotent stem cells


title: shControl - RBM33 Scramble Rep 1 (m6A-seq)


title: TDP2–/– + TDP2, 6 h, replicate 2

description: Nascent RNA

value: Breast cancer cell

value: Estrogen


title: ALKBH5 shRNA-2 Rep 3 (m6A-seq)

value: ALKBH5 shRNA-2


title: TDP2–/– + TDP2, 6 h, replicate 1

description: Nascent RNA


title: 14S3

city: Cambridge

first: Hyunwoo

last: Yuk

email: hyunwoo@mit.edu, hyunwooyuk@gmail.com

address: 77 Massachusetts Ave.

institute: MIT

description: Abdominal wall treated with non-adhesive implant on day 14 post-imiplantation

data_processing:
The HiSeq Control Software (HCS) conducted image analysis and base calling. Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software.
Read quality was evaluated using FastQC and data were pre-processed with Cutadapt for adapter removal following best practices. Gene expression against the GRCm38 transcriptome (Ensembl 93 version) was quantified using STAR and featureCounts. Differential gene expression analysis was performed using DESeq2, while ClusterProfiler was utilized for downstream functional investigations. Genes with log2 | Fold Change | ≥1 and False Discovery Rate (FDR) ≤ 0.05 were considered statistically significant.
Assembly: GRCm38
Supplementary files format and content: gene count matrix

organism: Rattus norvegicus

source_name: abdominal wall

extract_protocol:
Total RNA was extracted from day 10 snap frozen wound samples using the Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
Extracted RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). All samples had RIN>7.8. RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

tag: strain

value: Sprague Dawley

tag: Sex

value: F

value: 12 weeks

value: Abdominal wall

tag: group

value: Non-adhesive implant


title: ALKBH5 shRNA-2 Rep 2 (m6A-seq)

value: Head and neck squamous cell carcinoma (HNSC)

value: m6A antibody


title: 14S4


title: TDP2–/– + TDP2, 3 h, replicate 3

description: Nascent RNA


title: TRAF7_EChet, rep 5

value: Mouse embryo


title: ALKBH5 shRNA-2 Rep 1 (m6A-seq)


title: 14S2


title: TRAF7_EChet, rep 3

value: Embryo E9.5


title: TRAF7_EChet, rep 4

value: TRAF7_Endothelim-specific heterozygote


title: ALKBH5 shRNA-1 Rep 3 (m6A-seq)

value: ALKBH5 shRNA-1


title: 14S1


title: TDP2–/– + dTDP2, 0 h, replicate 1

description: Nascent RNA

value: Breast

value: Catalytic-dead TDP2 overexpression into TDP2 null mutant

value: No treatment


title: InVitro_OPM-2_Control

description: Gene expression in control OPM-2 cells

source_name: Control OPM-2, 48h

value: MM cell line

value: Female


title: TDP2–/– + TDP2, 3 h, replicate 2

description: Nascent RNA

value: Breast cancer cell

value: Intact TDP2 overexpression into TDP2 null mutant

value: Estrogen


title: TDP2–/– + TDP2, 3 h, replicate 1

description: Nascent RNA


title: InVitro_KMS-11_delta-C1orf112

description: Gene expression in C1orf112-KO KMS-11 cells

source_name: delta-C1orf112 KMS-11, 48h


title: InVitro_KMS-11_Control

description: Gene expression in control KMS-11 cells

source_name: Control KMS-11, 48h


title: TRAF7_EChet, rep 1


title: TDP2–/– + TDP2, 1 h, replicate 2

description: Nascent RNA


title: TDP2–/– + TDP2, 1 h, replicate 3

description: Nascent RNA


title: 14P3

description: Abdominal wall treated with adhesive implant on day 14 post-imiplantation

value: Sprague Dawley

value: F

value: 12 weeks

value: Adhesive implant


title: ALKBH5 shRNA-1 Rep 1 (m6A-seq)

value: Head and neck squamous cell carcinoma (HNSC)

value: m6A antibody


title: InVitro_OPM-2_delta-C1orf112

description: Gene expression in C1orf112-KO OPM-2 cells

source_name: delta-C1orf112 OPM-2, 48h


title: 14P2

value: Abdominal wall


title: TRAF7_ECko, rep 7

value: Mouse embryo

value: Embryo E9.5

value: TRAF7_Endothelim-specific knockout


title: shControl - ALKBH5 Scramble Rep 3 (m6A-seq)

value: shControl - ALKBH5 Scramble


title: shControl - ALKBH5 Scramble Rep 2 (m6A-seq)


title: TRAF7_ECko, rep 6


title: 14P1


title: TRAF7_ECko, rep 5


title: TDP2–/– + TDP2, 0.5 h, replicate 3

description: Nascent RNA

value: Breast


title: TDP2–/– + TDP2, 1 h, replicate 1

description: Nascent RNA


title: TRAF7_EChet, rep 2

value: TRAF7_Endothelim-specific heterozygote


title: 4P1

description: Abdominal wall treated with adhesive implant on day 3 post-imiplantation


title: RBM33 shRNA-2 Rep 3 (RNA-seq)

data_processing:
m6A-seq input samples were used for gene expression analysis.
Adapters of all raw m6A-seq input data sets were removed by Cutadapt v1.18.
Then reads longer than 19 nt were mapped to the human genome (hg38) and the GENCODE v36 gene annotation using HISAT2 v2.1.0 with default parameters.
Raw reads on each gene were counted by featureCounts (-t exon -g gene_id -M -O --fraction -T 24 -s 2) from Subread v1.6.4.
The trimmed mean of M-values (TMM) normalization method from edgeR v3.24.3 package was used for RNA abundance estimation.
Supplementary_files_format_and_content: Gene expression levels are represented by the Counts Per Million (CPM) values. DEGs were determined with the cutoff (|log2FCshRNA/shCtrl| > 0.5849625 and FDR < 0.05).
genome_build: hg38
Normalized gene expression levels and fold changes of gene expression levels and p-values between treatment and control groups in the plain txt format

value: RBM33 shRNA-2


title: 14P4


title: TDP2–/– + TDP2, 0.5 h, replicate 1

description: Nascent RNA

value: Breast cancer cell


title: TDP2–/– + TDP2, 0.5 h, replicate 2

description: Nascent RNA

value: Intact TDP2 overexpression into TDP2 null mutant


title: shControl - ALKBH5 Scramble Rep 1 (m6A-seq)


title: 4S1

description: Abdominal wall treated with non-adhesive implant on day 3 post-imiplantation

value: Non-adhesive implant


title: ALKBH5 shRNA-1 Rep 2 (m6A-seq)

value: ALKBH5 shRNA-1


title: RBM33 shRNA-2 Rep 2 (RNA-seq)


title: TRAF7_ECko, rep 4


title: 3S1

value: Sprague Dawley

value: F


title: TRAF7_ECko, rep 3


title: TRAF7_ECko, rep 2


title: TDP2–/– + TDP2, 0 h, replicate 3

description: Nascent RNA

value: No treatment


title: TDP2–/– + TDP2, 0 h, replicate 2

description: Nascent RNA


title: RBM33 shRNA-2 Rep 1 (RNA-seq)

value: Head and neck squamous cell carcinoma (HNSC)


title: TRAF7_ECko, rep 1


title: 2S1

value: 12 weeks


title: RBM33 shRNA-1 Rep 3 (RNA-seq)

value: RBM33 shRNA-1


title: WT, rep 6

value: Mouse embryo

value: Wild type


title: TRAF7_EChet, rep 6

value: Embryo E9.5


title: RBM33 shRNA-1 Rep 2 (RNA-seq)


title: WT, rep 4


title: WT, rep 5


title: shControl - RBM33 Scramble Rep 3 (RNA-seq)

value: shControl - RBM33 Scramble


title: 1S1

value: Abdominal wall


title: 1P1

value: Adhesive implant


title: shControl - RBM33 Scramble Rep 2 (RNA-seq)


title: WT, rep 3


title: STUDY, replicate 4, scRNAseq

city: Pittsburgh

first: Lillian

last: Tran

state: Pennsylvania

address: 200 Lothrop Street

department: Surgery

institute: University of Pittsburgh

description:
10x Genomics
DCREG_STUDY 004

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Filtered gene-barcode matrices generated using the 10X Genomics Cell Ranger analysis pipeline were pre-processed and analyzed with the R package Seurat version 4.0
Cells with detected gene number between 500 and 6000, mitochondrial gene percentage < 35%, and hemoglobin gene percentage < 0.5% were kept for further downstream analysis
Assembly: Hg38
Supplementary files format and content: matrix files

source_name: Liver allograft

extract_protocol:
Freshly collected 18g core biopsy of liver allograft tissue obtained 12 months post-transplant from 4 STUDY and 4 SOC living donor liver transplant patients was minced into small pieces and incubated with 1 mg/ml collagenase digestion solution at 37 °C for 8 minutes. The isolated liver cell suspensions were resuspended in 20%∆ FCS, 2mM EDTA, 1XPBS solution. Cells were washed and re-suspended in 4% Ultrapure BSA/1x DPBS
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: non-parenchymal, parenchymal

value: Liver allograft

value: Regulatory dendritic cell therapy

value: 12 months post-transplant


title: RBM33 shRNA-1 Rep 1 (RNA-seq)


title: TDP2–/– + TDP2, 0 h, replicate 1

description: Nascent RNA

value: Breast

value: Breast cancer cell

value: Intact TDP2 overexpression into TDP2 null mutant


title: SOC, replicate 4, scRNAseq

description:
10x Genomics
DCREG_SOC 004


title: 3P1

value: Sprague Dawley

value: F


title: SOC, replicate 3, scRNAseq

description:
10x Genomics
DCREG_SOC 003


title: WT, rep 2


title: TRAF7_GLOko, rep 6

value: TRAF7_Global knockout


title: shControl - RBM33 Scramble Rep 1 (RNA-seq)

value: Head and neck squamous cell carcinoma (HNSC)


title: WT, rep 1

value: Mouse embryo


title: ALKBH5 shRNA-2 Rep 3 (RNA-seq)

value: ALKBH5 shRNA-2


title: SOC, replicate 2, scRNAseq

description:
10x Genomics
DCREG_SOC 002


title: ALKBH5 shRNA-2 Rep 2 (RNA-seq)


title: SOC, replicate 1, scRNAseq

description:
10x Genomics
DCREG_SOC 001


title: TRAF7_GLOko, rep 5

value: Embryo E9.5


title: 2P1

value: 12 weeks


title: ALKBH5 shRNA-2 Rep 1 (RNA-seq)


title: STUDY, replicate 1, scRNAseq

description:
10x Genomics
DCREG_STUDY 001


title: TRAF7_GLOko, rep 4


title: ALKBH5 shRNA-1 Rep 3 (RNA-seq)

value: ALKBH5 shRNA-1


title: ALKBH5 shRNA-1 Rep 2 (RNA-seq)


title: TRAF7_GLOko, rep 2


title: HAM2_CD4(-)

city: Tokyo

first: Makoto

last: Yamagishi

address: 4-6-1, Shirokanedai, Minato-ku

department: Graduate School of Frontier Sciences

institute: The University of Tokyo

description: Gene expression in HAM CD4- cell

hyb_protocol: 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) for 1min and with GE Wash buffer 2 (Agilent) for 1min at 37°C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44K microarray slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel was set to Green, and No extended dynamic range was selected).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol : GE1-107_Sep09 and Grid: 026652_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HAM CD4-

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng total RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted using TriZol (Invitrogen) following the manufacturer's recommendations. The protocol includes DNaseI treatment to eliminate any genomic DNA contamination. The extracted total RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: HAM CD4-


title: TRAF7_GLOko, rep 3


title: TRAF7_GLOko, rep 1


title: HAM4_CD4(-)

description: Gene expression in HAM CD4- cell


title: ALKBH5 shRNA-1 Rep 1 (RNA-seq)


title: HAM3_CD4(-)

description: Gene expression in HAM CD4- cell


title: HAM1_CD4(-)

description: Gene expression in HAM CD4- cell


title: RNA-Seq BSC, Ctrl-LRT, rep3

first: Xingbin

last: Ai

address: 55 Fruit St

department: Pediatrics

institute: MASSACHUSETTS GENERAL HOSPITAL

data_processing:
The paired-end 42 bp sequencing reads are mapped to the human hg38 reference genome using the STAR algorithm with default settings.
The number of fragments overlapping predefined genomic genes is counted. Only read pairs that have both ends aligned are counted.
Read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands are discarded.
The gene annotations were obtained from Subread R package. These annotations were originally from NCBI RefSeq database and then adapted by merging overlapping exons from the same gene to form a set of disjoint exons for each gene.
Genes with the same Entrez gene identifiers were also merged into one gene.
Assembly: hg38
Supplementary files format and content: csv

source_name: Basal stem cell

extract_protocol:
Total RNA isolation using a RNeasy kit (QIAGEN, Cat# 74104).
For each sample, 2 µg of total RNA was used in library construction using TruSeq Stranded mRNA Library kit (Illumina, Cat# 20020594).

tag: source

value: Bronchiolar (lower respiratory trachea)

value: Basal stem cell

tag: disease state

value: Healthy


title: RNA-Seq BSC, CoV19, rep1

value: Tracheal aspirate


title: shControl - ALKBH5 Scramble Rep 3 (RNA-seq)

tag: tag

value: shControl - ALKBH5 Scramble


title: RNA-Seq BSC, Ctrl-LRT, rep2


title: HD4_CD4(-)

description: Gene expression in Healthy donor CD4- cell

source_name: Healthy donor CD4-

value: Healthy donor CD4-


title: RNA-Seq BSC, Ctrl-LRT, rep1


title: bilCLiP_3D_3

city: Philadelphia

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

data_processing:
Reads were mapped to GRCm39 mouse genome using the STAR aligner (version 2.7.10b).
Read counts were obtained using the featureCounts package (v2.0.1)
Read counts were imported to DESeq2, and normalization was performed using the "median of ratios normalization" method.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited normalized data including all the samples.

source_name: Liver

growth_protocol: hepCLiP_2D and bilCLiP_2D were maintained on collagen-coated plates using small hepatocyte medium (SHM) in the presence of 10% FBS and YAC (Y-27632, A83-01 and CHIR99021) (Katsuda et al. Cell Stem Cell 2017).

extract_protocol:
RNA was isolated with Nucleospin RNA kit (Takara)
Library was prepared by Novogene (Sacramento, CA)

treatment_protocol: For hepatic induction, spheroids were generated from hepCLiP_2D and bilCLiP_2D using an Aggrewell400 plate for 3 days in SHM+YAC medium in the absence of FBS. Then, the spheroids were transferred to an ultra-low attachable suspension culture plate, and cultured for 6-8 days in SHM+YAC with 10 ng/ml oncostatin M.

tag: tissue

value: Liver

value: bilCLiP

value: BEC-derived cells

value: RosaYFP

value: Maintained under 2D culture


title: shControl - ALKBH5 Scramble Rep 2 (RNA-seq)

tag: cell line

value: Head and neck squamous cell carcinoma (HNSC)


title: RNA-Seq BSC, Ctrl-TA, rep3

tag: cell type


title: shControl - ALKBH5 Scramble Rep 1 (RNA-seq)


title: HD3_CD4(-)


title: C694_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS

city: Houston

first: Jia

last: Li

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

data_processing:
For the WGBS analysis, raw FASTQ files were mapped to the NCBI Human Reference Genome Build GRCh37 (hg19) using BSMAP 53. Fastp was used to trim adaptor sequences from fastq data and remove 15 bp from the two ends of the reads based on Swift protocol. MCALL module in MOABS54 software was used to calculate DNA methylation ratio and coverage for each CpG site. Differentially methylated CpGs and regions were identified using the MCOMP module considering variance among samples (--withVariacne 1) in the MOABS software 54. Bisulfite conversion efficiencies were estimated using spike-in unmethylated lambda phage DNA. The output bedGraph files from MCALL include single base resolution DNA methylation ratios, which were transformed to a bigwig file format. The bigwig files were uploaded to the UCSC genome browser for visualization.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig; DNA methylation ratio in single CpG resolution

source_name: cerebrospnial fluid from pediatric medullablastoma patient

extract_protocol:
Total DNA containing cell-free tumor DNA (ctDNA) was isolated from 200-400 µL cerebral spinal fluid (CSF) using QIAamp Circulating Nucleic Acid Kit (Qiagen) according to manufacturer’s instructions. For MB tumor tissues, up to 20 mg of tumor tissues was snap frozen with liquid nitrogen and grinded. DNA was then isolated using an AllPrep DNA/RNA mini kit according to the manufacturer’s protocol. The isolated DNA concentration was measured by a Qubit 4 Fluorometer with the Qubit dsDNA high sensitivity assay kit (Thermo Fisher Scientific).
The whole genome bisulfite sequencing (WGBS) analysis was used to measure the genome-wide DNA methylation status. The ctDNA WGBS libraries were generated using SWIFT Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences). Briefly, adaptase was applied to the bisulfite-converted DNA, with adaptors as well as a low-complexity tail simultaneously ligated to the 3′ end of the DNA fragments. Following a primer extension, the bottom strand DNA was synthesized and the 3′ end was ligated with adaptor sequences. ctDNA was mixed with 0.1% unmethylated λ-bacteriophage DNA (NEB) .  Constructed libraries were run on 2% agarose gel to assess the size distribution and library concentration was measured by a Qubit 4 Fluorometer with a Qubit dsDNA high sensitivity assay kit (Thermo Fisher Scientific). Normalized libraries were then pooled in an equimolar ratio and sequenced on NextSeq 500 (Illumina) with a NextSeq 500/550 High Output Kit v2.5 (single-end reads, 75 Cycles) following the manufacturer’s protocols.   Enriched DNA fragments were purified using the conventional phenol/chloroform/isomyl-alcohol method, and amplified with random primers, followed by adaptor ligation and final amplification with Methyl-Seq Combinatorial Dual Indexing Kit (Swift Biosciences). DNA library sizes and concentrations were verified by Bioanalyzer. The DNA libraries were then sequenced in Novaseq S4 (pair-end reads, 150 Cycles) following the manufacturer’s protocols.

tag: subtype


title: RNA-Seq BSC, Ctrl-TA, rep2


title: HD2_CD4(-)


title: bilCLiP_3D_1

tag: genotype

tag: treatment


title: HAM4_CD4+

description: Gene expression in HAM CD4+ T-cell

source_name: HAM CD4+

value: HAM CD4+


title: HD1_CD4(-)


title: C547_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: RNA-Seq BSC, Ctrl-TA, rep1


title: HAM1_CD4+

description: Gene expression in HAM CD4+ T-cell


title: HAM3_CD4+

description: Gene expression in HAM CD4+ T-cell


title: C2618C1-3_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS

value: SHH


title: bilCLiP_2D_2


title: HAM2_CD4+

description: Gene expression in HAM CD4+ T-cell


title: RNA-Seq BSC, Ctrl-URT, rep3

value: Bronchial (upper respiratory trachea)


title: RNA-Seq BSC, CoV19, rep2


title: C992_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: RNA-Seq BSC, Ctrl-URT, rep2


title: bilCLiP_2D_1


title: bilCLiP_3D_2


title: RNA-Seq BSC, Ctrl-URT, rep1


title: hepCLiP_2D_3

value: hepCLiP

value: Hepatocyte-derived cells

value: RosaConfetti

value: Hepatic induction under 3D culture


title: hepCLiP_3D_3


title: ATAC-Seq BSC, CoV19, rep2

data_processing:
The paired-end 42 bp sequencing reads are mapped to the human hg38 reference genome using the BWA v0.7.12 algorithm with default settings.
Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, duplicate reads are removed.
Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option.
Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Lung

extract_protocol:
BSCs were cryopreserved in 50% FBS/40% SAGM/10%DMSO solution prior to ATAC-seq by Active Motif (Carlsbad, CA, USA). Cells were thawed in a 37℃ water bath, pelleted, and tagmented using Nextera Library Prep Kit (Illuminutesa, Cat# FC-130-1064). Tagmented DNA was purified using the MinutesElute PCR purification kit (Qiagen, Cat# 13323).
The DNA was then amplified with 10 cycles of PCR, purified using Agencourt AMPure SPRI beads (Beckman Coulter).

value: Lung

value: Basal stem cell


title: bilCLiP_2D_3


title: KO clone  5

city: Bethesda

first: Lihe

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

data_processing:
Raw sequencing reads were aligned to the mouse reference genome (Ensembl genome 106) by STAR . Transcript per million (TPM) and expected counts were generated by RSEM. All samples are of high percentage of uniquely mapped reads (> 80%) and are included for downstream analysis. Unless otherwise specified, the computational analyses were performed on the National Institutes of Health Biowulf High-Performance Computing platform.
Assembly: Ensemble release 106
Supplementary files format and content: CamK2D_TPM.txt

source_name: Kidney

extract_protocol:
RNA was extracted from the mpkCCDs using Direct-zol RNA MicroPrep kit.
Trizol-extracted RNA was eluted in 35 µl DNA/RNA free water. First-strand cDNA was prepared from 50 ng of total RNA using SMART-Seq v4 Ultra Low Input RNA Kit, followed by cDNA amplification with 9 PCR cycles. 1 ng of the synthesized cDNA was fragmented and tagged with index primers using the Nextera XT DNA Sample Preparation Kit (Illumina) to generate sequencing libraries for high throughput sequencing. After the purification of libraries with AmPure XP magnetic beads (Beckman Coulter), each library was quantified using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). An equal amount of the index libraries were pooled, and the pooled libraries were sequenced on an Illumina platform (50-bp paired-end NovaSeq).

value: Kidney

value: Collecting duct

tag: strain background

value: Camk2d knockout


title: ATAC-Seq BSC, CoV19, rep1


title: KO clone  4


title: C964_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: C970_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS

value: Un


title: C913_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: KO clone 2


title: KO clone 3


title: ATAC-Seq CoV19 control BSC, Ctrl, rep3

value: Healthy


title: ATAC-Seq CoV19 control BSC, Ctrl, rep2


title: C809_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: C868_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: C896_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: KO clone 1


title: ATAC-Seq CoV19 control BSC, Ctrl, rep1


title: Intact clone 2_2

value: wild type; intact


title: ΔMMGT1, infected, replicate 3

first: Haroon

last: Kalam

address: 415 main st.

department: IDMP

institute: Broad Institute of MIT and Harvard University

data_processing:
Processing the raw RNA-seq reads by Trimmomatic to remove the adapter and obtain a high-quality base.
The sequencing data were aligned to the reference genome using STAR.
The raw read counts from STAR were subject to DESeq2 to identify differential expressed genes.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count for each Sample

source_name: cell line

extract_protocol:
RNA was harvested using Direct-Zol RNA kit (zymo research) followed by RNA-SPRI beads purification.
RNA-seq libraries were prepared using the Nextera XT DNA Library Preparation Kit and Nextera Multiplex Oligos for Illumina. 10 ng of RNA was used as starting material as input. Libraries were amplified using 21 cycles on the thermocycler. Post amplification libraries were size selected at 350bp in length using Agencourt AMPure XP beads from Beckman Coulter.

value: cell line

value: Macrophage

value: PMA treated, Mtb infected


title: C376_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS

value: SHH


title: C417_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: Intact clone 2_1


title: C273_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: Intact clone 1_2


title: ΔMMGT1, infected, replicate 1


title: ΔMMGT1, infected, replicate 2


title: Intact clone 1_1


title: ΔMMGT1, uninfected, replicate 3

value: PMA treated, Uninfected


title: Wild-type mpkCCD


title: C2613C1_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: C2602C1_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: HD3_CD4+

description: Gene expression in Healthy donor CD4+ T-cell

source_name: Healthy donor CD4+

value: Healthy donor CD4+


title: HAM3_PBMC

description: Gene expression in HAM PBMC

source_name: HAM PBMC

value: HAM PBMC


title: HAM4_PBMC

description: Gene expression in HAM PBMC


title: HD4_CD4+


title: C2582C1_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: HAM2_PBMC

description: Gene expression in HAM PBMC


title: ΔMMGT1, uninfected, replicate 1


title: HD4_PBMC

description: Gene expression in Healthy donor PBMC

source_name: Healthy donor PBMC

value: Healthy donor PBMC


title: HAM1_PBMC

description: Gene expression in HAM PBMC


title: HD1_CD4+


title: MLL34KO_Menin

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: MLL34KO cells

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC mm9 using bowtie/1.1.2.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg38 using STAR/2.5.2.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were nonstranded, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Assembly: mm9, hg38
Supplementary files format and content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

source_name: mouse embryonic stem cells

growth_protocol: Mouse ES cells were maintained serum free neurobasal+DMEM/F12 media supplemented with 2i+LIF; for colorectal cancer cells, RKO, HCT116, SW1417 were cultured in DMEM+10%FBS, DLD1 were cultured in RPM-1640 + 10% FBS, HT55 and Caco2 were cultured in DMEM+20% FBS

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

treatment_protocol: Cells were treated with DMSO or 1 uM LTX for 24 hours.

value: mouse embryonic stem cells

tag: passages

value: Low passages (6-10)

tag: chip antibody

value: anti-Menin antibody, cell signaling technology


title: HD2_CD4+


title: HD1_PBMC

description: Gene expression in Healthy donor PBMC


title: ΔMMGT1, uninfected, replicate 2


title: WT_Menin

description: wild type cells

value: wild type


title: C2551C3_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: HD2_PBMC

description: Gene expression in Healthy donor PBMC


title: THP1, Infected, replicate 2


title: C2548C1_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: MLL34KO_Set1A

description: MLL34KO cells

value: anti-SET1A antibody, generated in house


title: THP1, Infected, replicate 1


title: THP1, Uninfected, replicate 3


title: MLL34KO_Mll2C

description: MLL34KO cells

value: anti-MLL2C antibody, generated in house


title: WT_Set1A

description: wild type cells


title: C1510_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: THP1, Uninfected, replicate 2


title: C1507_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: THP1, Infected, replicate 3


title: WT_Mll2C

description: wild type cells


title: THP1, Uninfected, replicate 1


title: C1483_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS

value: Un


title: MLL34KO_Mll1C

description: MLL34KO cells

value: anti-MLL1C antibody, cell signaling technology


title: FLY WT S2 Sample 8

city: Bad Nauheim

first: Lei

last: Gu

state: MASSACHUSETTS

address: parkstreet 1

country: Germany

institute: Max Planck Institute for heart and lung research

description: FLY.counts.matrix

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19,mm10, dm6, sacCer1, GRCz11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: FLY

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

value: WT


title: HD3_PBMC

description: Gene expression in Healthy donor PBMC


title: EC7_Cisplatin_24h_with_SP600125_1

city: Yufu-city

first: Yoshiyuki

last: Tsukamoto

state: Oita

address: hasamacho idaigaoka 1-1

department: Molecular Pathology

institute: Oita university, Faculty of Medicine

hyb_protocol: Gene Expression Hybridization kit was used for hybridization in accordance with the manufacture's instructions (Agilent Technologies).

scan_protocol: Microarray images were obtained by using a laser confocal scanner G2565BA (Agilent Technologies).

data_processing: Feature Extraction software (Agilent Technologies) with the manufacturer’s recommended settings was applied for the microarray image analysis. Analysis of the raw data obtained from Feature Extraction software was performed with GeneSpring GX software(Aglrent). For comparison among multiple arrays, probe set data were median-normalized per chip.

source_name: 10uM Cisplatin, 24h, 40uM SP600125, replicate1

label_protocol: Cy3-labeled cRNA targets were generated by use of Quick Amp labeling Kit according to manufacture's instructions (Agilent Technologies).

extract_protocol: For each probe, the values were expressed as log2(normalized signal/median of normalized signals from Mock treated samples).

value: esophageal squamous cell carcinoma


title: C1456_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: WT_Mll1C

description: wild type cells


title: THP1, CRISPR lib transduced, Infected, Stressed non-replicating, rep 3

data_processing:
The sequencing data were aligned to the reference sgRNA using PoolQ.
The raw read counts from PoolQ were subject to edgeR and STARS to evaluate genetic perturbation.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count for each Sample
Library strategy: CRISPR screen

extract_protocol:
DNA was harvested using Qiagen DNeasy blood  kit followed by DNA-SPRI beads purification.
gDNAs were used in a total of 3 ug of DNA per PCR reaction, which consisted of 25 cycles using HiFi hotstart polymerase (KAPA Biosystems) with Illumina sequencing-compatiable primers. The final PCR product was run on a gel, and the right size fragment (354 base pairs) was gel extracted and sequenced on a NextSeq (Illumina).

value: cell line

value: Macrophage


title: EC7_Cisplatin_24h_with_SP600125_3

source_name: 10uM Cisplatin, 24h, 40uM SP600125, replicate3


title: C1444_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: C1575_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: EC7_Cisplatin_24h_with_SP600125_2

source_name: 10uM Cisplatin, 24h, 40uM SP600125, replicate2


title: EC7_Cisplatin_24h_3

source_name: 10uM Cisplatin, 24h, replicate3


title: MLL34KO_H3K4me3

description: MLL34KO cells

value: anti-H3K4me3 antibody, cell signaling technology


title: FLY KO S2 Sample 6

description: FLY.counts.matrix

value: KO


title: THP1, CRISPR lib transduced, Infected, Stressed non-replicating, rep 1

value: PMA treated, Mtb infected


title: C1431_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: THP1, CRISPR lib transduced, Infected, Active replication, rep 3


title: WT_H3K4me3

description: wild type cells


title: C1364_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: EC7_MOCK_24h_1

source_name: Mock, 24h, replicate1


title: EC7_MOCK_24h_2

source_name: Mock, 24h, replicate2


title: EC7_MOCK_24h_3

source_name: Mock, 24h, replicate3


title: EC7_Cisplatin_24h_2

source_name: 10uM Cisplatin, 24h, replicate2


title: Lin_neg_12mo_Tet2_KO

city: New York

first: Meelad

middle: M

last: Dawlaty

state: New York

address: 1301 Morris Park Ave, Price 419, Bronx

department: Genetics

institute: Albert Einstein College of Medicine

data_processing:
For RNA-seq RNA was extracted using Qaigen RNeasy Total RNA kit I. Library preparation and mRNA sequencing were performed at Novogene using their Illumina Novoseq 6000 platform. Adaptors were trimmed using trim galore (v0.6.5) and clean reads were mapped to the mouse genome (mm10) using STAR (v2.7.3a) with default parameters. Gene counts were extracted from mapped reads using featureCounts with --largestOverlap parameter. Raw counts were used to identify differentially expressed genes with edgeR (FDR <0.05 and fold-change >1.0), following the standard package documentation.
For WGBS, DNA was extracted by Quick-DNA miniprep kit (Zymo, D3024) following the manufacturer’s instructions. Bisulfite conversion and sequencing were performed at BGI Genomics (https://en.genomics.cn/). Lamda DNA spike-in confirmed a >99.4% bisulfite conversion efficiency. The libraries were subjected to 100 bp pair-end sequencing on a HiSeq 4000 Illumina platform. The raw reads were filtered by SOAPnuke (v1.5.5) (https://github.com/BGI-flexlab/SOAPnuke) with the parameters -n 0.001 -l 20 -q 0.4 -A 0.25 -Q 2 -G to remove adaptors and filter out low-quality reads. Clean reads were mapped to mouse genome mm10 using Bismark (v0.22.3) with default parameters. Duplicated reads were removed using deduplicate_bismark and methylation status of each cytosine extracted with bismark_methylation_extractor.
Assembly: mm10

growth_protocol: Bone marrow was harvested and LSK (Lin-, Sca1+, cKit+) and Lin– (lineage negative) cells sorted by FACS.

extract_protocol:
For RNA-seq, RNA extraction was performed using Qaigen RNeasy Total RNA kit. For WGBS, DNA extraction was performed using Zymo Quick-DNA Miniprep Kit.
RNA-seq libraries were prepared by Novogene (https://en.novogene.com/). WGBS libraries were prepared by BGI company (https://en.genomics.cn/).

value: Mixed 129/C57BL/6

tag: age


title: BRI_160

city: Birmingham

first: Changde

last: Cheng

state: AL

address: 1824 6th Ave S, Wallace Tumor Institute 520A

department: Medicine

institute: University of Alabama at Birmingham

data_processing:
Cell Ranger Single-Cell Software Suite (version 2.1.1, 10X Genomics) was used to processing the single-cell expression data.
Assembly: GRCh38
Supplementary files format and content: h5 files containing transcript counts for each sample

source_name: Blood

extract_protocol:
Peripheral blood was collected in a blood collection tube containing ethylenediaminetetraacetic acid [EDTA] (Becton, Dickinson and Company). Plasma was isolated by centrifugation at 2,000 × g for 20 min and stored at -80ºC. Peripheral blood mononuclear cells (PBMC) were isolated using the density gradient centrifugation method (GE Healthcare, STEMCELL Technology).
Prepared using 10X Genomics protocols

value: Poor

tag: time


title: C1339_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS

source_name: cerebrospnial fluid from pediatric medullablastoma patient


title: THP1, CRISPR lib transduced, Infected, Active replication, rep 2


title: Lin_neg_12mo_Tet2_Mut

tag: strain


title: EC7_Cisplatin_24h_1

source_name: 10uM Cisplatin, 24h, replicate1


title: BRI_159


title: C1334_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS

value: SHH


title: BRI_158


title: FLY WT S2 Sample 7

description: FLY.counts.matrix


title: Lin_neg_12mo_Tet2_WT


title: LSK_12mo_Tet2_KO

source_name: LSK

value: LSK


title: C1332_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: FLY KO S2 Sample 5

description: FLY.counts.matrix


title: THP1, CRISPR lib transduced, Uninfected, rep 2

source_name: cell line

value: PMA treated, Uninfected


title: THP1, CRISPR lib transduced, Infected, Stressed non-replicating, rep 2


title: C1278_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: LSK_12mo_Tet2_WT


title: THP1, CRISPR lib transduced, Uninfected, rep 1


title: 131

city: Berlin

first: Raik

last: Otto

state: Berlin

address: Rudower Chaussee 25

department: Computer Sciences

institute: Humboldt-Universität zu Berlin

description:
20180404_K12_130_10
Nanostring nCounter HSNCC Custom Panel

hyb_protocol: For mRNA expression analyses 400 ng (concentration 100 ng/µl) isolated RNA per sample were hybridized on a nCounter Analysis System using a customized NanoString panel consisting of 231 genes according to manufacturer’s instructions (NanoString Technologies, Seattle, WA).

scan_protocol: Slides were scanned on a slide scanner (Aperio AT2, Leica Biosystems GmbH, Nussloch, Germany) and evaluated on a standard monitor (Fujitsu B24T-7, Fujitsu Limited, Tokyo, Japan, resolution 1920 x 1080) utilizing Aperio ImageScope x64 (version 12.4.0.7018; Leica Biosystems GmbH, Nussloch, Germany). One digitized high-power field (HPF) comprised 97464 µm2 which corresponded to a field diameter of 0.35 mm in light microscopy.

data_processing: Dataset normalization was conducted with the ‘NanoStringNorm’ R-package, version 1.2.1 (36). The ‘stringR’ and ‘ggplot2’ packages in conjunction with the ‘pheatmap’ R-package (RRID:SCR_016418) were utilized for visualization and string manipulation (37,38). For differential expression analyses, the ‘LIMMA’ R-package was utilized (39,40). For computational analysis R (version 4.1.3) (41) and SPSS v25 (International Business Machines Corporation (IBM), Armonk, NY)  were used.

label: NanoString

source_name: Tumor tissue

label_protocol: Labels are artificial numbers without semantical meaning

growth_protocol: Direct in-vivo biopsy

extract_protocol: RNA extraction and NanoString analyses were conducted as previously described (35). In short, H&E stained slides of HNSCC cases were examined to identify tumor regions and to estimate tumor cell content. FFPE material with a minimal tumor cell content of 20 % (median 65 %)  was used for subsequent microdissection of RNA from 3 µm thick sections. RNA was then extracted according to manufacturer’s instructions on a Maxwell extraction system (Promega, Madison, WI) and quantified by Qubit (Thermo Fisher Scientific, Waltham, MA).

value: MS

tag: histotyp

value: non-keratinizing

tag: keratinization

tag: tumor_cell_budding (2 tier)

value: high

tag: cell_nest_size (2 tier)

value: small

tag: mitotic_count (2 tier)

value: low

tag: nuclear_size (2 tier)

value: big

tag: stroma_content (2 tier)

tag: necrosis

tag: necrosis (2 tier)

tag: inflammatory_infiltrate (2 tier)

tag: lymphangiosis

tag: Sex

tag: dcr

value: PR

value: Oral cavity


title: C1220_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS

tag: subtype


title: THP1, Infected, Stressed non-replicating, rep 2

tag: cell line

tag: cell type

value: Macrophage

tag: treatment


title: Lin_neg_9mo_Tet2_KO

tag: strain

tag: genotype

tag: age


title: C1242_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS

value: Un


title: THP1, Infected, Stressed non-replicating, rep 3


title: THP1, CRISPR lib transduced, Infected, Active replication, rep 1

tag: tissue

value: cell line


title: THP1, CRISPR lib transduced, Uninfected, rep 3


title: Lin_neg_9mo_Tet2_WT


title: THP1, Infected, Stressed non-replicating, rep 1

value: PMA treated, Mtb infected


title: C1154_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: 130

description:
20180404_K12_129_09
Nanostring nCounter HSNCC Custom Panel

value: BA

tag: histotyp

tag: keratinization

tag: tumor_cell_budding (2 tier)

tag: cell_nest_size (2 tier)

tag: mitotic_count (2 tier)

value: Oropharynx


title: BRI_155

tag: group

value: Healthy

tag: time


title: C1304_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: THP1, Infected, Active replication, rep 3


title: LSK_12mo_Tet2_Mut

value: LSK

value: Mixed 129/C57BL/6


title: 127

description:
20180404_K12_126_06
Nanostring nCounter HSNCC Custom Panel

value: keratinizing

tag: nuclear_size (2 tier)

tag: stroma_content (2 tier)

tag: necrosis

tag: necrosis (2 tier)

tag: inflammatory_infiltrate (2 tier)

tag: lymphangiosis

tag: Sex

value: PD

value: Tongue


title: LSK_9mo_Tet2_KO

tag: cell type

tag: strain

tag: genotype


title: 126

description:
20180404_K12_125_05
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: MS

tag: histotyp

value: small

value: high

tag: dcr


title: C1136_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: Lin_neg_9mo_Tet2_Mut

tag: age


title: 125

description:
20180404_K12_124_04
Nanostring nCounter HSNCC Custom Panel

value: CL

value: Unknown


title: THP1, Infected, Active replication, rep 2

tag: cell line

value: Macrophage

tag: treatment


title: LSK_9mo_Tet2_Mut


title: 124

description:
20180404_K12_123_03
Nanostring nCounter HSNCC Custom Panel

value: non-keratinizing

tag: keratinization

tag: tumor_cell_budding (2 tier)

value: low

tag: cell_nest_size (2 tier)

tag: mitotic_count (2 tier)

value: big

value: SD

value: Tonsil


title: THP1, Infected, Active replication, rep 1

value: PMA treated, Mtb infected


title: LSK_9mo_Tet2_WT

value: LSK


title: 129

description:
20180404_K12_128_08
Nanostring nCounter HSNCC Custom Panel

value: BA

tag: nuclear_size (2 tier)

tag: stroma_content (2 tier)

tag: necrosis

tag: necrosis (2 tier)

value: Oral cavity


title: C1055_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: THP1, Uninfected, rep 3

tag: cell type

value: PMA treated, Uninfected


title: Lin_neg_6mo_Tet2_Mut

tag: strain

value: Mixed 129/C57BL/6


title: C1123_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: C1050_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: THP1, Uninfected, rep 1


title: C1041_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: THP1, Uninfected, rep 2


title: 122

description:
20180404_K12_121_01
Nanostring nCounter HSNCC Custom Panel

value: keratinizing

tag: inflammatory_infiltrate (2 tier)

tag: lymphangiosis

tag: Sex

value: Larynx


title: 120

description:
20180404_K11_120_12
Nanostring nCounter HSNCC Custom Panel

tag: subtype

tag: histotyp

value: high

value: small

tag: dcr

value: NE


title: LSK_6mo_Tet2_KO

tag: genotype

tag: age


title: C1016_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: C1109_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: ACE2NB_VDJ

city: Baltimore

first: Srinivasan

last: Yegnasubramanian

address: 1661 Orleans St

institute: Johns Hopkins SOM

data_processing:
The cDNA libraries were sequenced (150 bp paired-end) on the Illumina HiSeqX platform.
Each sequenced library was demultiplexed to FASTQ files using Cell Ranger (10x Genomics).
Cell Ranger (version 2.2.0) count pipeline was used to align reads to the human transcriptome and create a gene by cell count matrix.
Seurat was used for downstream analysis
Genome_build: Hg37
Genome_build: Supplementary_files_format_and_content: For each library preparation includes the following files: matrix.mtx, barcodes.tsv, genes.tsv

source_name: Pooled B cells non-reactive with ACE2 peptides from 7 patients

extract_protocol:
B-cells isolated from 7 COVID-19 patient's peripheral blood were seperated into ACE2 reactive and non-reactive population using ACE2 peptides. Each of these patient's B-cells were labelled with Hashtag oligo linked to antibody, which allowed to barcode each patient with unique DNA oligo sequence. Then ACE2 reactive B cells from 7 patients were pooled together and loaded on 10x Genomics Chip G using 5'DGE kit to interogate single cell 5DGE (Digital gene expression) and VDJ sequence in B-cells. Similarly, ACE2 non-reactive cells were pooled together.
10x Genomics

value: B-cells isolated from PBMC

tag: ace2 reactive status

value: ACE2 non-reactive

tag: sequence

value: VDJ sequence of B-cells

tag: disease state

value: COVID-19 patients


title: LSK_6mo_Tet2_WT


title: ACE2PB_VDJ

source_name: Pooled B cells reactive with ACE2 peptides from 7 patients

value: ACE2 reactive


title: 333-18T

city: Montréal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on annotations from Gencode version 37
Expression values were also computed using RSEM version 1.2.28 based on Gencode version 37 transcript annotations
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned

molecule: polyA RNA

source_name: Primary breast cancer

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

value: breast cancer

value: Invasive ductal carcinoma

tag: tissue

value: Neoplastic mammary epithelial tisssue

tag: breast cancer type

value: Triple negative


title: 1305-19T

value: Hormone-receptor positive


title: LSK_6mo_Tet2_Mut

value: LSK


title: Lin_neg_6mo_Tet2_KO

value: Mixed 129/C57BL/6


title: 928-19T


title: 123

description:
20180404_K12_122_02
Nanostring nCounter HSNCC Custom Panel

value: CL

value: non-keratinizing

tag: keratinization

tag: tumor_cell_budding (2 tier)

tag: cell_nest_size (2 tier)

tag: mitotic_count (2 tier)

value: low

tag: nuclear_size (2 tier)

value: big

tag: stroma_content (2 tier)

tag: necrosis

value: SD


title: Lin_neg_3mo_Tet2_KO

tag: cell type

tag: strain


title: 116

description:
20180404_K11_116_08
Nanostring nCounter HSNCC Custom Panel

tag: subtype

tag: histotyp

value: keratinizing

value: high

value: small

tag: necrosis (2 tier)

tag: inflammatory_infiltrate (2 tier)

tag: lymphangiosis

tag: Sex

tag: dcr

value: Hypopharynx


title: ACE2PB_HASHTAG

value: B-cells isolated from PBMC

tag: ace2 reactive status

value: ACE2 reactive

tag: sequence

value: Hashtag information of each patient

tag: disease state

value: COVID-19 patients


title: 820-19T

value: breast cancer

value: Invasive ductal carcinoma

tag: tissue

value: Neoplastic mammary epithelial tisssue

tag: breast cancer type


title: ACE2NB_HASHTAG

value: ACE2 non-reactive


title: Lin_neg_6mo_Tet2_WT

value: Mixed 129/C57BL/6

tag: genotype

tag: age


title: 119

description:
20180404_K11_119_11
Nanostring nCounter HSNCC Custom Panel

value: BA

value: non-keratinizing

tag: keratinization

tag: tumor_cell_budding (2 tier)

tag: cell_nest_size (2 tier)

tag: mitotic_count (2 tier)

tag: nuclear_size (2 tier)

tag: stroma_content (2 tier)

tag: necrosis

value: PD

value: Larynx


title: 115

description:
20180404_K11_115_07
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: MS

tag: histotyp

value: basaloid

value: low

value: big

tag: necrosis (2 tier)

tag: inflammatory_infiltrate (2 tier)

tag: lymphangiosis


title: 790-18T

tag: disease state

tag: cell type

value: Hormone-receptor positive


title: Lin_neg_3mo_Tet2_Mut

tag: strain


title: Lin_neg_3mo_Tet2_WT

tag: genotype


title: 2189-18T

tag: tissue

tag: breast cancer type

value: Triple negative


title: ACE2NB_5DGE

value: B-cells isolated from PBMC

tag: ace2 reactive status

tag: sequence

value: single cell gene expression


title: 113

description:
20180404_K11_113_05
Nanostring nCounter HSNCC Custom Panel

tag: keratinization

tag: tumor_cell_budding (2 tier)

value: high

tag: cell_nest_size (2 tier)

value: small

tag: mitotic_count (2 tier)

tag: Sex

tag: dcr

value: SD


title: 117

description:
20180404_K11_117_09
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: Unknown

value: PR

value: Tonsil


title: Sample 53: HepG2_polyA_RNA_siFTSJ3_Treated_rep3

city: Chicago

first: Li-Sheng

last: Zhang

address: 929 E 57th St Rm E313

department: Department of Chemistry

institute: The University of Chicago

data_processing:
The sequencing data was all trimmed with cutadapt tool to remove adapters and low-quality reads. PCR duplicates were removed with BBMap tool (https://sourceforge.net/projects/bbmap/), 5-mer random barcodes at reads ends were trimmed, and low-quality or short reads (less than 20 nt) were removed using cutadapt tool. Remaining reads were aligned to hg38 genome using Tophat2 (version 2.1.1) and bowtie2 (version 2.3.5.1) allowing at most three mismatches. The generated .bam files were split into positive and negative strands and sorted using Samtools (http://samtools.sourceforge.net/). Sequence variants were identified by measuring the base composition at each position using fine-tuned bam-readcount (https://github.com/genome/bam-readcount). The generated bam-readcount results were parsed and analyzed by in-house scripts. A to T or C to T or G to T mutation ratio at each Nm candidate site were calculated by data output from bam-readcount pipeline and confirmed by direct visualization through IGV software (https://software.broadinstitute.org/software/igv/).  The input of Nm-Mut-seq is equivalent to regular RNA-seq, therefore we quantified the gene-level read counts of input samples that aligned to hg38 for differential gene expression analysis. Cufflinks and Cuffdiff were used to make inferential tests where differentially expressed genes were identified at FDR < 0.05 cut-off. Gene ontology analysis was performed using the online analysis software DAVID v6.8 (https://david.ncifcrf.gov) and REViGO tool (http://revigo.irb.hr).
Genome_build: hg38
Supplementary_files_format_and_content: xlsx (excel)

source_name: cell culture

growth_protocol: HepG2 were used for Nm analysis in this study were purchased from the American Type Culture Collection (ATCC). HepG2 was maintained in a low glucose DMEM medium (1g/L glucose) supplemented with 10% v/v FBS and 1% penicillin/streptomycin (GIBCO). Cells were cultured at 37 °C with 5.0% CO2 in a Heracell™ VIOS 160i incubator (Thermo Scientific).

extract_protocol:
Cellular total RNA was isolated with TRIzol reagent (Invitrogen) following manufacturer’s protocol by isopropanol precipitation. When extracting polyA+ RNA for sequencing Nm in RNA, Dynabeads™ mRNA DIRECT™ Purification Kit (Invitrogen™) was used for polyA+ RNA enrichment.
For purified total RNA, after DNase I treatment for cellular DNA removal, we removed small RNA species by MEGAclear Transcription Cleanup Kit (Invitrogen). We next performed two-rounds of polyA+ RNA enrichment with 50 μg total RNA harvested from the last step, using Dynabeads™ mRNA DIRECT™ Purification Kit (Invitrogen™). The yield of polyA+ RNA in this step is roughly 0.5~1 μg. Then the eluted polyA+ RNA or total RNA  was fragmented into 50-80 nt length using Na2CO3/NaHCO3 buffer (pH 9.2) and heated at 95 °C for 8 min, followed by purification with RNA Clean & Concentrator (Zymo Research). 50-100 ng of RNA was used for 3’-/5’-adaptor ligation. Starting with the 3’-adaptor ligation, the RNA oligos were incubated with 0.5 μL (12 μM) customized adaptors 5’App-NNNNN ATCACGAGATCGGAAGAGCACACGTCT-3SpC3 (containing five randomized nucleotides sequence (NNNNN) together with a 6-mer in-line barcode) at 70 °C for 2 mins and immediately placed on ice. 10 µL 3´ Ligation Reaction Buffer (2X) (NEB) and 3 µL 3´ Ligation Enzyme Mix (NEB) were added to the RNA-adapter mixture. The reaction was incubated at 25 °C for 2 hrs. Then 1.0 µL SR RT Primer for Illumina (NEB) was added to the mixture, followed by 5 minutes at 75°C, 15 minutes at 37°C, 15 minutes at 25°C, and then on ice. The denatured 0.5 µL 5’-Adaptor (5’-GUUCAGAGUUCUACAGUCCGACGAUCNNNNN-3’) was added into the mixture, together with 1.0 µL 5´ Ligation Reaction Buffer (10X) (NEB) and 2.5 µL 5´ Ligation Enzyme Mix (NEB). The reaction was incubated at 25 °C for 2 hrs followed by 16 °C for 4 hrs, followed by RNA Clean & Concentrator purification.  The purified RNA was eluted with 20 μL RNase-free water and subjected to reverse transcription. Two independent RT reactions (10 μL RNA for each reaction) were conducted with evolved RT 41B4 under two dNTP conditions: one RT reaction (as “input”) incubated with 1.0 mM dNTP without generating mutations on Nm sites; the other RT reaction (as “Nm-Mut-seq”) with 2 μM dNTP + 1 mM dATP would reveal mutations on Am, Cm and Gm sites. The RT reactions were performed at 37°C for 1 hour, followed by 80°C inactivation for 10 min. The libraries were amplified using the SR Primer for Illumina (NEB) and indexed primers (from NEBNext Multiplex Oligos for Illumina).
RNA-Seq. All libraries were sequenced on Illumina NovaSeq 6000 with single-end 100 bp read length.

treatment_protocol: HepG2 cells were transfected using siRNAs purchased from Qiagen, targeting FBL (ATCGAGGATGCTCGACACCCA) or FTSJ3(AAGTTCGGTGTTGGAGCGATA) or non-targeting sequence (AllStars Neg. Control, SI03650318, Qiagen). To prepare siRNA/lipofectamine (Lipofectamine RNAiMAX Reagent, Invitrogen) mixture for one 15-cm plate, 400 pmol of siRNAs were diluted in 1.75 mL of Opti-MEM I Reduced Serum Media (Gibco) and 40 μL of lipofectamine was diluted in 1.75 mL of the same media in a separate tube. The siRNA and lipofectamine were mixed together and incubated at room temperature for 15 min. The combined 3.5 mL transfection solution was added into HepG2 cells which have already grown for 12 hours. Cellular total RNA was extracted for further analysis at 48 hrs or 72 hrs after the transfection.

value: HepG2 cells


title: 684-19T

value: breast cancer

value: Invasive ductal carcinoma

value: Neoplastic mammary epithelial tisssue


title: LSK_3mo_Tet2_KO

value: LSK

value: Mixed 129/C57BL/6

tag: age


title: LSK_3mo_Tet2_Mut


title: 112

description:
20180404_K11_112_04
Nanostring nCounter HSNCC Custom Panel

value: BA

tag: histotyp

value: non-keratinizing

value: low

tag: nuclear_size (2 tier)

value: big

tag: stroma_content (2 tier)

tag: necrosis

tag: necrosis (2 tier)

tag: inflammatory_infiltrate (2 tier)

tag: lymphangiosis

value: PD

value: Oral cavity


title: 118

description:
20180404_K11_118_10
Nanostring nCounter HSNCC Custom Panel

value: CL

value: high

value: NE


title: Sample 52: HepG2_polyA_RNA_siFTSJ3_Treated_rep2

tag: tissue


title: ACE2PB_5DGE

tag: cell type

value: B-cells isolated from PBMC

tag: ace2 reactive status

value: ACE2 reactive

tag: sequence

value: single cell gene expression

tag: disease state

value: COVID-19 patients


title: 513-20T

value: breast cancer

value: Invasive ductal carcinoma

tag: breast cancer type

value: Triple negative


title: 111

description:
20180404_K11_111_03
Nanostring nCounter HSNCC Custom Panel

tag: keratinization

tag: tumor_cell_budding (2 tier)

tag: cell_nest_size (2 tier)

value: small

tag: mitotic_count (2 tier)

tag: Sex

value: Oropharynx


title: Sample 51: HepG2_polyA_RNA_siFTSJ3_Treated_rep1

value: HepG2 cells


title: LSK_3mo_Tet2_WT

value: LSK

tag: strain

value: Mixed 129/C57BL/6

tag: genotype

tag: age


title: 110

description:
20180404_K11_110_02
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: BA

tag: histotyp

value: keratinizing

value: low

tag: nuclear_size (2 tier)

tag: stroma_content (2 tier)

tag: necrosis

tag: necrosis (2 tier)

tag: dcr

value: SD


title: 2179-18T

tag: disease state

tag: cell type

tag: tissue

value: Neoplastic mammary epithelial tisssue

value: Hormone-receptor positive


title: 109

description:
20180404_K11_109_01
Nanostring nCounter HSNCC Custom Panel

value: CL

tag: keratinization

tag: tumor_cell_budding (2 tier)

value: high

tag: inflammatory_infiltrate (2 tier)

tag: lymphangiosis

value: PD

value: Hypopharynx


title: 2339-19T

value: breast cancer

value: Invasive ductal carcinoma

tag: breast cancer type


title: 1945-18T


title: 1208-18T


title: NEK2 knockout 5TGM1, scRNAseq

city: Little Rock

first: Yan

state: Arkansas

address: 4301 W. Markham St.

department: Internal Medicine

institute: University of Arkansas for Medical Sciences

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow cells

extract_protocol:
Mouse tibia and femur were harvested. Bone marrow cells were obtained by flushing using a 25-gauge needle with ice-cold PBS buffer. Debrics were removed by passing through a 70 μm nylon cell strainer and cells were collected in a 50 mL Falcon conical tube. Cells were centrifuged at 300g for 5 minutes and cell pellet was resuspended with 500 μL RBC lysis buffer at room temperature for 2 minutes, and neutralize the lysis buffer by adding 5 mL DMEM complete medium. Then cells were centrifuged at 300g for 5 minutes and resuspended with frozen medium (60% DMEM, 30% FBS, 10% DMSO) and stored at -80°C freezer. On the day for scRNA-seq analysis, frozen cells were recovered in 37°C water bath and washed twice with PBS buffer. Dead cells were removed using Dead cell removal kit (130-090-101, Miltenyi Biotec). Samples with viability higher than 95% were processed for 10x genomics scRNA-seq. Approximately 10,000 cells were targeted, and single-cell emulsions were generated with the Chromium Controller (10x Genomics, Pleasanton, CA, USA) using the Chromium Next GEM Chip G (Part Number 1000120, 10x Genomics) with the Chromium NextGEM Single Cell 3’ v3.1 kit (Part Number 1000121, 10x Genomics) following the standard protocol.
Libraries were assessed for mass concentration using the Qubit 1X dsDNA HS Assay Kit (catalog # Q33231; Invitrogen, Waltham MA, USA) and the Qubit 4 fluorometer (catalog # Q33238; Invitrogen, Waltham MA, USA). Library fragment size was assessed with the High Sensitivity NGS Fragment Analysis Kit (catalog # DNF-474-0500; Agilent, Santa Clara CA, USA) on the Fragment Analyzer System (catalog # M5310AA; Agilent, Santa Clara CA, USA). Libraries were functionally validated with the KAPA Universal Library Quantification Kit (catalog # 07960140001; Roche, Basel CH).

value: Bone marrow cells

tag: strain

tag: genotype

value: NEK2 knockout

tag: treatment

value: 5TGM1 MM cells injection


title: WT 5TGM1, scRNAseq

description: 10x Genomics

value: WT


title: NEK2 knockout, scRNAseq

description: 10x Genomics

value: PBS injection


title: Sample 48: HepG2_polyA_RNA_siFBL_Treated_rep1

value: HepG2 cells


title: Sample 50: HepG2_polyA_RNA_siFBL_Treated_rep3


title: 977-19T

value: Triple negative


title: WT, scRNAseq

description: 10x Genomics


title: 825-29T


title: 108

description:
20180327_K10_99_03
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: BA

tag: histotyp

value: keratinizing

tag: cell_nest_size (2 tier)

value: small

tag: mitotic_count (2 tier)

value: low

value: big

tag: Sex

value: NE

value: Larynx


title: 107

description:
20180327_K10_98_02
Nanostring nCounter HSNCC Custom Panel

value: non-keratinizing

value: high

tag: nuclear_size (2 tier)

tag: stroma_content (2 tier)

tag: necrosis

tag: necrosis (2 tier)

tag: dcr

value: PD

value: Oral cavity


title: homozygotes_2

data_processing:
Firstly, we removed the reads mapped to rRNAs and get rawdata, then we filter the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads.
Then we map those clean reads onto reference genome, followed with novel gene prediction, SNP & INDEL calling and gene splicing detection.
Finally, we identify DEGs (differentially expressed genes) between samples and do clustering analysis and functional annotations.
Genes that have no or nearly no expression (average count less than 1 ) were not removed, all genes were kept.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: spleen

extract_protocol:
Total RNA from CD19-selected spleen cells was extracted via RNeasy Plus Mini Kit (QIAGEN). RNA concentration, RNI value, 28S/18S and the fragment length distribution were detected via Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: tissue

value: spleen

tag: cell type

value: CD19-selected spleen B cells

tag: age

value: 6-8 weeks


title: Sample 46: HepG2_polyA_RNA_siControl_Treated_rep2


title: 2060-19T

tag: disease state

value: breast cancer

value: Invasive ductal carcinoma

value: Neoplastic mammary epithelial tisssue

tag: breast cancer type


title: 103

description:
20180327_K10_106_10
Nanostring nCounter HSNCC Custom Panel

value: MS

tag: keratinization

tag: tumor_cell_budding (2 tier)

tag: inflammatory_infiltrate (2 tier)

tag: lymphangiosis

value: SD

value: Oropharynx


title: homozygotes_1

tag: genotype


title: 102

description:
20180327_K10_105_09
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: BA

tag: histotyp

value: low

tag: cell_nest_size (2 tier)

tag: mitotic_count (2 tier)

value: PR


title: heterozygotes_3


title: 1097-19T

value: Triple negative


title: 106

description:
20180327_K10_97_01
Nanostring nCounter HSNCC Custom Panel

value: keratinizing

value: small

tag: nuclear_size (2 tier)

tag: stroma_content (2 tier)

tag: necrosis

tag: Sex


title: Sample 44: HepG2_Total_RNA_siFBL_Treated_rep3

tag: tissue

value: HepG2 cells


title: 1949-16T

tag: cell type


title: heterozygotes_2

tag: age


title: Sample 49: HepG2_polyA_RNA_siFBL_Treated_rep2


title: Sample 43: HepG2_Total_RNA_siFBL_Treated_rep2


title: 100

description:
20180327_K10_103_07
Nanostring nCounter HSNCC Custom Panel

value: CL

value: Unknown

tag: dcr

value: Tongue


title: 101

description:
20180327_K10_104_08
Nanostring nCounter HSNCC Custom Panel

value: non-keratinizing

tag: keratinization

tag: necrosis (2 tier)

value: high

value: Hypopharynx


title: 1478-18T

tag: disease state

value: breast cancer

value: Invasive ductal carcinoma

value: Neoplastic mammary epithelial tisssue

tag: breast cancer type


title: heterozygotes_1

value: spleen

value: CD19-selected spleen B cells

value: 6-8 weeks

tag: genotype


title: Sample 42: HepG2_Total_RNA_siFBL_Treated_rep1


title: 1192-17T

value: Hormone-receptor positive


title: wild type_2


title: Sample 40: HepG2_Total_RNA_siControl_Treated_rep2


title: wild type_1


title: Sample 45: HepG2_polyA_RNA_siControl_Treated_rep1


title: 1137-18T

value: Triple negative


title: Macrophage, B6AJ2

city: Irvine

first: S.

middle: Armando

last: Villalta

state: California

address: 843 Health Sciences Rd

institute: University of California Irvine

description: Integrated_B6_B10_MDX_B6AJ_SFigure10.rds

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: rms files

source_name: Muscle

extract_protocol:
WT C57BL/6, WT C57BL/10, mdx, B6A/J mice were humanely euthanized, perfused to clear circulating immune cells, and hind limb lymph nodes removed. Single-cell suspensions were prepared from healthy and dystrophic muscle by mechanical dissociation and enzymatic digestion with collagenase and DNase. Cell suspensions were washed and filtered sequentially through 70- and 40-micron cell strainers. Live muscle macrophages were FACS-sorted based on their expression of F4/80 and CD11b, and single-cell libraries constructed with the 10X Genomics platform.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 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: Muscle

value: Macrophage