title: shATF7IP-2_HepG2

city: tianjin

first: yijie

last: su

state: tianjin

address: Tianjin Medical University, No.22 Qixiangtai Road, Heping District, Tianjin City.

institute: Tianjin medical university

description:
Library name: Sample 3
gene_count.csv: shATF7IP2_HepG2

data_processing:
Reads were aligned to the human genome (UCSC hg38) using HISAT2 (v2.2.1) with the following parameters: --no-mixed --no-discordant
Gene expression levels were quantified by StringTie (v2.2.1).
DESeq2 (v1.34.0) was used to perform differential expression analysis.
Assembly: hg38
Supplementary files format and content: gene_count.csv: comma-separated table file includes raw count for each example

source_name: liver

growth_protocol: HepG2 cells were cultured in Dulbecco's modified Eagle’s medium supplemented with 10% fetal bovine serum at 37℃ in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard DNBSEQ-G400 protocols.

treatment_protocol: HepG2 cells were infected with lentiviruses expressing Control shRNA, ATF7IP shRNA or SETDB1 shRNA to establish Control, ATF7IP and SETDB1 knockdown HepG2 cells, followed by treatment with Sorafenib (10 μM) for 48 hours.

value: liver

value: human hepatocellular carcinoma cell

value: HepG2 cells were infected with lentiviruses expressing ATF7IP shRNA-2 to establish ATF7IP knockdown cells, followed by treatment with Sorafenib (10 μM) for 48 hours.


title: WT_Ly108_C_S19

status: Public on Apr 14 2025

type: SRA

city: Philadelphia

first: Gregory

last: Chen

address: 3400 Civic Center Blvd

country: USA

institute: University of Pennsylvania

description:
Mouse_LCMV_Tcell_RNA-Seq_ReadCounts_MGI.tsv
Mouse_LCMV_Tcell_RNA-Seq_TPM_MGI.tsv

library_source: transcriptomic

data_processing:
RNA-Seq alignment with STAR v 2.7.10a
RNA quantification with cufflinks v2.2.1
Read count quantification with Rsubread in R v4.0.2
ATAC-Seq alignment with bwa-mem
ATAC-Seq peak calling with MACS2
Assembly: mm39
Supplementary files format and content: Tab-delimited text file. First column is MGI Gene Symbol or Peak coordinate. Subsequent columns are sample names. The first row is a header. Subsequent rows represent a gene or peak

molecule: total RNA

organism: Mus musculus

growth_protocol: Recipient mice were intravenously infected with 4 × 10^6 PFU of LCMV clone 13

extract_protocol:
RNA was isolated using the Qiagen rNeasy Micro Kit
cDNA libraries were generated following the manufacturer’s instructions with the SMART-Seq v4 Ultra Low Input RNA Kit and Nextera XT DNA library kit

treatment_protocol: WT and TET2KO P14 cells were mixed at a 1:1 ratio, and a total of 500 P14 cells (250 WT and 250 TET2KO) were adoptively transferred intravenously into recipient mice of a third congenic background.

tag: cell type

value: T cells

tag: genotype

value: WT

tag: treatment

value: T cells in LCMV mouse experiment


title: WT_Negative_C_S20


title: WT Liver, MASLD, 16weeks, rep3

city: Eonyang-eup, Ulju-gun

first: Bukyung

last: Baik

state: Ulsan

department: Department of Biological Science

country: South Korea

institute: Ulsan National Institute of Science and Technology

data_processing:
Read trimming and quality filtering were performed using Cutadapt (version 4.2).
Trimmed fastq files were aligned to the mm39 mouse genome using STAR (version 2.7.10a) software.
Read count extraction was performed using GeneCounts options to quantMode parameter of STAR (version 2.7.10a) software.
Raw read counts of each sample are combined to generate a raw count matrix.
Assembly: mm39
Supplementary files format and content: Tab-delimited text files include gene read counts for each sample

source_name: Liver

extract_protocol:
Total mRNAs were isolated using TRIzol reagent purchased from Thermo Fisher Scientific. Reverse-transcription of the RNA (total RNA 1ug) was performed with ABI Reverse Transcription Kit
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: Liver

value: Wild-type

value: Diet:High fat-high fructose


title: FK75110

city: CLICHY

first: Camille

last: PIGNOLET

address: 100 Bd du Général Leclerc

department: CRI U1149

country: France

institute: INSERM

description: Library name: FK75110

data_processing:
Reads were aligned using STAR and gene expression counts obtained with FeatureCount
Assembly: GRCm38.75
Supplementary files format and content: tab_delimited text file includes raw counts for each Sample

source_name: cd4 T cells

extract_protocol:
Five µm-thick sections were cut from FFPE blocks. Total RNAs were further isolated using the Qiagen FFPE RNA extraction kit (RNeasy FFPE kit, Qiagen)
Gene expression was analysed using SMARTer Stranded Total RNA-Seq Kit.

value: cd4 T cells


title: Control_HepG2

country: China

description:
Library name: Sample 1
gene_count.csv: Control_HepG2

molecule: polyA RNA

organism: Homo sapiens

tag: cell line

value: HepG2 cells were infected with lentiviruses expressing Control shRNA to establish Control cells, followed by treatment with Sorafenib (10 μM)  for 48 hours.


title: SlowBKK, control, hindgut, rep1

city: Planegg-Martinsried

first: Vera

middle: Miyase

last: Yilmaz Bachmaier

state: Bavaria

address: Grosshaderner St. 2

department: Evolutionary Biology

country: Germany

institute: LMU Munich

description:
pooled 4 iso-female lines, 60 individuals
S_RT_Hg_1

data_processing:
quality control: FastQC (version 0.11.9)
mapping: NextGenMap (version 0.5.2)
Assembly: dana_r1.05_FB2016_01
Supplementary files format and content: tab-delimited text file includes counts for each sample

organism: Drosophila ananassae

source_name: hindgut

growth_protocol: Fly lines were kept on standard corn-molasses medium. The day after eclosure, treatment started.

extract_protocol:
Total RNA was extracted from the body samples using MasterPureTM RNA Purification Kit (Epicentre), from hindgut and malpighian tubules using RNeasy Mini Kit (Qiagen).
The libraries were constructed by Novogene using poly-A enrichment method.

treatment_protocol: The cold acclimation treatment started the day after eclosure (from pupa). Adult flies were kept at 10˚C for 4 days (96 hours), which was followed by 90-minute recovery. The control samples were kept at rearing temperature (22 ˚C ±1˚C) for 4 days.

value: hindgut

tag: population

value: Bangkok

tag: phenotype

value: sensitive

tag: Sex

value: male

value: control


title: TET2_KO_Ly108_C_S23


title: WT_Total_C_S18

source_name: Total

value: Total


title: SlowBKK, cold accl, body, rep4

description:
pooled 4 iso-female lines, 10 individuals
S_10_W_4

source_name: body

value: body

value: cold acclimation


title: WT Liver, MASLD, 16weeks, rep1


title: TET2_KO_Negative_B_S16


title: KO Liver, MASLD, 16weeks, rep4

value: miR-93 knockout


title: SlowBKK, cold accl, body, rep3

description:
pooled 4 iso-female lines, 10 individuals
S_10_W_3


title: WT_Naive_C_S17

source_name: Naive

value: T cells

value: Naive


title: SlowBKK, cold accl, body, rep1

description:
pooled 4 iso-female lines, 10 individuals
S_10_W_1


title: shSETDB1_HepG2

description:
Library name: Sample 4
gene_count.csv: shSETDB1_HepG2

value: liver

value: human hepatocellular carcinoma cell

value: HepG2 cells were infected with lentiviruses expressing SETDB1 shRNA to establish SETDB1 knockdown cells, followed by treatment with Sorafenib (10 μM) for 48 hours.


title: WT Liver, MASLD, 16weeks, rep2

value: Liver

value: Wild-type

value: Diet:High fat-high fructose


title: KO Liver, MASLD, 16weeks, rep3


title: TET2_KO_Ly108_B_S15

value: T cells in LCMV mouse experiment


title: TET2_KO_Total_B_S14


title: shATF7IP-1_HepG2

description:
Library name: Sample 2
gene_count.csv: shATF7IP1_HepG2

value: HepG2 cells were infected with lentiviruses expressing ATF7IP shRNA-1 to establish ATF7IP knockdown cells, followed by treatment with Sorafenib (10 μM) for 48 hours.


title: SlowBKK, cold accl, malpighiantubule, rep3

description:
pooled 4 iso-female lines, 60 individuals
S_10_Mt_3

source_name: malpighian tubule

value: malpighian tubule

value: Bangkok

value: sensitive


title: Control (C6)

type: RNA

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

hyb_protocol: cRNA was hybridized on an Agilent Human Gene Expression Microarray using the Agilent Gene Expression Hybridization kit according to the manufactorer's instructions.

scan_protocol: Arrays were scanned using an Agilent Microarray Scanner.

data_processing: Data was preprocessed using the R/Bioconductor marray package.  The ProcessedSignal values were loess normalized and Control probes were removed.

source_name: breast xenograft, saline

label_protocol: The cDNA reverse transcription and fluorescent labeling reactions were performed using the Invitrogen SuperScript Plus Direct cDNA Labeling System with Alexa Fluor S′‐Aminohexylacrylamido‐dUTP (Invitrogen).

growth_protocol: A xenograft model of DCIS (ductal carcinoma in situ) of the breast was used.

extract_protocol: Cancer cells were extracted by laser-capture microdissection from 8 um frozen sections of cancerous areas of fresh, unfixed xenograft sections.

treatment_protocol: Botox was reconstituted to a concentration of 1U/uL.  Ten units of Botox were used.

value: saline

source_name: universal reference

value: control (universal reference)


title: SlowBKK, cold accl, malpighiantubule, rep2

description:
pooled 4 iso-female lines, 60 individuals
S_10_Mt_2

value: male

value: cold acclimation


title: Control (C5)


title: WT_Negative_A_S12

value: T cells

value: WT


title: High-fat diet,Transcriptomics,MII-3

city: Zhengzhou

first: Lin-Li

last: Yang

state: Henan

address: No. 1, Jianshe East Road, Erqi District

department: department of obstetrics and gynecology

institute: The First Affiliated Hospital of Zhengzhou University

description: Library name: HFD-MII-RNA-3

data_processing:
library strategy: T&T seq(Transcriptomics)
Quality Control and Adapter Removal: Raw sequencing data was processed using Trim Galore to perform quality control and remove adapter sequences, low-quality bases, and adapter sequences. The quality control parameters were set with a quality score threshold of 20 (Phred+33), requiring at least 3 bases to perfectly match the adapter sequence, a minimum retained sequence length of 50 bp, and allowing a 10% error rate.
Alignment to Reference Genome: After quality control, cleaned reads were aligned to the reference genome (mouse genome mm39) using Hisat2. The alignment process was performed using 8 threads for parallel computation, generating alignment reports and SAM files.
SAM to BAM Conversion and Sorting: The aligned SAM files were converted to BAM format using Samtools and were then sorted and indexed for further analysis.
Gene Expression Quantification: Gene expression was quantified using featureCounts, with exons as the counting unit. Overlapping and multi-mapping reads were allowed. To accurately calculate gene lengths, the latest version of the mouse genome annotation (GRCm39) was used, and exon annotation information was downloaded from the Gencode database (Mus_musculus.GRCm39.113.gtf.gz).
Exon Processing and Gene Length Calculation: Exon information from the gene annotation was extracted, including chromosome, start position, end position, gene ID, and gene name. These exonic regions were converted into GRanges objects using the GenomicRanges package. To remove overlapping or adjacent exonic regions within the same gene, exons were grouped by gene ID, and the reduce function was applied to merge overlapping regions. For each gene, the total exon length was calculated by merging all exon lengths.Gene Name Consistency: If multiple gene names were associated with a single gene, the most frequent name was retained to ensure consistency in gene naming.Export            Gene Length Information: Finally, the merged gene length information was exported as a CSV file for subsequent analysis.
Assembly: GRCm39
Supplementary files format and content: csv files include FPKM or TPM for each sample

source_name: oocytes

growth_protocol: Eight-week-old female C57BL/6J mice were randomly assigned to either normal diet (ND, 10% fat calories) or high-fat diet (HFD, 60% fat calories) groups and maintained on these diets for 12 weeks prior to oocyte collection. For superovulation, mice received an intraperitoneal injection of 10 IU pregnant mare serum gonadotropin (PMSG; Sigma-Aldrich), and germinal vesicle (GV)-stage oocytes were collected from antral follicles 44-48 hours post-injection. The collected oocytes were cultured in M2 medium (Sigma-Aldrich, MR-015-D) and M16 medium (Sigma-Aldrich, M7292) under mineral oil (Sigma-Aldrich, M8410) at 37°C with 5% CO₂, with cumulus-oocyte complexes (COCs) being dissected from antral follicles and denuded using hyaluronidase treatment (Sigma-Aldrich, H3506) to remove granulosa cells, leaving denuded oocytes for subsequent experiments, while in specified cases, 2.5 μM milrinone (MedChemExpress, HY-14252) was added to the culture medium to prevent spontaneous germinal vesicle breakdown (GVBD).

extract_protocol:
We collected GV and MII stage oocytes (n=4 per sample) from ND and HFD groups, lysing them in 10 µL ice-cold sample buffer (Vazyme N711 containing 0.2 µL 1:2500 ERCC spike-in [Invitrogen 4456740] and RNase inhibitor) for 10 minutes, then divided each lysate into 2.0 µL for transcriptomics and 8.0 µL for proteomics. For ribosome profiling, we functionalized RiboLace beads (Immagina RL001), resuspended them in the 8 µL lysate supplemented with binding buffer (100 µg/mL cycloheximide, 1 mM DTT, 5 mM MgCl₂, 150 mM NaCl, 20 mM Tris-HCl pH 8.0) and RNase inhibitor, then incubated at 4°C for 1 hour with 3 rpm rotation. After magnetic rack washing with W-buffer, we eluted ribosome-bound RNA in 12 µL RLT buffer (Qiagen 74004) containing β-mercaptoethanol and GlycoBlue, then purified using VAHTS RNA Clean Beads (Vazyme N411) with 2M LiCl precipitation following manufacturer protocols.
For ultra-sensitive T&T-seq library construction, total RNA (2 µL lysate) and ribosome-bound full-length RNA were reverse transcribed into cDNA and amplified for 18 PCR cycles using the Single Cell Full Length mRNA-Amplification Kit (Vazyme N711), followed by purification with VAHTS DNA Clean Beads (Vazyme N411), with cDNA concentration measured by Qubit (Invitrogen) and size distribution (~2000 bp) analyzed using Bioanalyzer 2100 (Agilent), then index libraries were prepared using TruePrep DNA Library Prep Kit V2 (Vazyme TD502) and size-selected (250-450 bp) with VAHTS DNA Clean Beads before quantification and paired-end sequencing (PE150) on Illumina Novaseq 6000 (Azenta Life Sciences). For RNA-seq library preparation, GV and MII stage oocytes (n=4/sample) from ND/HFD groups were lysed in sample buffer (Vazyme N711) containing 0.2 µL 1:2500 ERCC spike-in (Invitrogen 4456740), followed by cDNA synthesis using Oligo dT primers and Discover-sc reverse transcriptase for template switching adapter addition, PCR amplification of full-length cDNA, magnetic bead purification (Vazyme N411), library construction using TruePrep Kit V2 (Vazyme TD503) with 15 PCR cycles, size selection (250-450 bp), Qubit quantification, Bioanalyzer quality assessment, and PE150 sequencing on Illumina Novaseq 6000 (Azenta Life Sciences).

treatment_protocol: Fully matured oocytes were collected and maintained in M2 medium (Sigma-Aldrich, MR-015-D) containing 2.5 μM milrinone (MedChemExpress, HY-14252) to prevent spontaneous germinal vesicle breakdown (GVBD), followed by microinjection using an NTX-N4 micromanipulator system (Nikon) to deliver 5-10 picoliters (pl) of either 500 μg/ml mRNA or 20 μM siRNA per oocyte. After injection, oocytes were washed and cultured in M16 medium (Sigma-Aldrich, M7292) supplemented with 2.5 μM milrinone at 37°C under 5% CO₂ atmosphere to enable either translation of injected mRNA or target transcript knockdown by siRNA. Subsequently, oocytes were transferred to milrinone-free M16 medium (Sigma-Aldrich, M7292) for 14 hours before being processed for either confocal microscopy imaging or transcriptomic and proteomic library construction.

value: oocytes

value: MII oocytes

value: Obese

value: Oocyte maturation


title: SlowBKK, cold accl, hindgut, rep4

description:
pooled 4 iso-female lines, 60 individuals
S_10_Hg_4

value: hindgut


title: SlowBKK, cold accl, malpighiantubule, rep4

description:
pooled 4 iso-female lines, 60 individuals
S_10_Mt_4


title: KO Liver, MASLD, 16weeks, rep1

value: Liver

value: miR-93 knockout

value: Diet:High fat-high fructose


title: PyMT-Bad3SA 6

city: Edmonton

first: John Maringa

last: Githaka

state: AB

address: 5-73 Medical Sciences Building, University of Alberta

department: Biochemistry

country: Canada

institute: University of Alberta

data_processing:
Sequenced reads were pre-processed (i.e., adapter sequence trimming, quality control etc.) using fastp (version 0.23.1). The splice aware aligner, STAR (version 2.7.9a, latest version as of September 2021), was used to align the reads to the Mus musculus genome assembly GRCm38 (Ensembl release 102).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file has matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tabular file has DESeq2 output format matrix for differentially expressed genes

source_name: Breast tumor

extract_protocol:
PyMT tumor samples snap-frozen in RNAlater® solution (Sigma Aldrich cat#R0901) were thawed on ice. The tissue was retrieved with sterile forceps and excess RNAlater® Solution blotted away with an absorbent lab wipe. Tissue was then promptly lysed with a hand homogenizer (VWR Cat# 47747-370) and RNA extraction was carried out following the manufacturers protocol (QIAGEN’s RNAeasy plus mini kit cat#74134). Elution was done using RNase free water. Nanodrop (NanoDrop™ 2000/2000c model) was used to measure the RNA samples concentration and all samples were diluted to 100ng/μl RNA in RNase free water. Samples (20μl each) were packaged in dry ice and sent to Génome Québec for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Breast tumor

tag: mouse model of breast cancer

value: MMTV-PyMT

value: Bad 3SA

tag: end-point (wks)


title: WT_Ly108_B_S11

value: T cells in LCMV mouse experiment


title: WT_Total_B_S10

value: Total


title: PyMT-Bad3SA 5


title: SlowBKK, cold accl, hindgut, rep1

description:
pooled 4 iso-female lines, 60 individuals
S_10_Hg_1

value: Bangkok

value: sensitive

value: male


title: PyMT-Bad3SA 4


title: Control (C4)

value: saline

value: control (universal reference)


title: WT_Naive_B_S9

value: T cells

value: Naive

value: WT


title: TET2_KO_Naive_B_S13


title: KATH, control, body, rep4

description:
pooled 3 iso-female lines, 10 individuals
K_RT_W_4

value: body

value: Kathmandu

value: tolerant

value: control


title: Control (C3)


title: PyMT-Bad3SA 3

value: Breast tumor


title: Botox (B7)

source_name: breast xenograft, botox treated

value: botox


title: KO Liver, MASLD, 16weeks, rep2

value: Liver

value: miR-93 knockout

value: Diet:High fat-high fructose


title: Botox (B5)


title: Botox (B6)


title: KATH, control, body, rep2

description:
pooled 3 iso-female lines, 10 individuals
K_RT_W_2


title: 9 CS

city: Birmingham

first: Farah

middle: D

last: Lubin

state: AL

address: 1825 University Blvd

department: Neurobiology

institute: University of Alabama at Birmingham

library_source: genomic

data_processing:
Quality of reads was assessed using FastQC
Bases with Quality Scores < 20 and adapters were trimmed with Trim_Galore(v0.4.5)
Bowtie2(v2.3.4.2) alligned reads to genome with option "--very-sensitive-local" set
SAMtools(v.1.6) was used to sort and index BAM files which were then visualized using MultiQC(v1.6)
MEDIPS(v1.34.0) was used on a local RStudio session (R version: 3.5.3) for identification of differntially methylated regions using 2 criteria: 1. promoter (5000bp upstream of TSS) and entire gene body and 2. genome-wide using 500bp windows. Bsgenome.Rnorvegicus.UCSC.rn6 (v.1.4.1)  was used as reference.
DMR quantification across promoters and gene bodies: 'bed' files from UCSC of each region were implemented as the region of interest (ROI). MEDIPS.createROIset function was executed with the following parameters: "ROI=<promoter or gene-body references>, extend=0, shift=0, uniq= 1e-3 (to remove duplicates), paired=FALSE."
MEDIPS.meth was executed with the following parameters: "p.adj=”BH” (Benjamini-Hochberg method for p-value adjustment), diff.method="edgeR", MeDIP=TRUE, CNV=FALSE, minRowSum=10, diffnorm="quantile", CSet=CS (created with `MEDIPS.couplingVector(pattern = "CG")` with one of the control samples provided to `refObj`)".
For genome-wide DMRS, a MEDIPS dataset was created using the following parameters given to MEDIPS.createSet: "extend = 300, shift = 0, uniq = 1e-3, window size = 500 and paired = FALSE" differential methylated was computed with same method as promoters and gene bodies.
Genome-wide bigwigs were generated from bam files with deeptools (v3.5.1) with the parameters --binSize 500, --normalizeUsing CPM --ignoreDuplicates --extendReads 300 enabled (these bigwigs contain extension `ext.bw`).
Promoter and gene-body (ROIs) bigwigs were generated from normalized counts from MEDIPS quantification to the ROIs. MEDIPS outputs of normalized counts for each replicate were converted to bedGraph, then overlapping regions were merged with `bedtools merge -c 4 -o mean` and bigwigs were generated with UCSC tool `bedGraphToBigWig`  (these bigwigs contain extension `GB.bw` for gene body or `promoter.bw` and values for regions are thus reflective of normalized data from MEDIPS)
Assembly: rn6
Supplementary files format and content: Bigwigs with extension `ext.bw` were generated from BAMs with deeptools and normalzed by CPM. Bigwigs with extensions  `GB.bw` for gene body or `promoter.bw` were generated from normalized data from MEDIPS (quantile normalized) and are representative of the entire region quantified (promoter or gene-body) as opposed to genome-wide.

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Cornu Ammonis (CA) region of the Hippocampus

extract_protocol:
Samples were extracted fresh in ice cold oxygeneated artificial cerebral spinal fluid (ACSF) and frozen on dry ice. Tissue was homogenized in TE buffer. DNA was extracted using phenolchloroform/isoamyl alcohol and ethanol precipitiation. Samples were sheard to ~300bp using a Biorupter sonicator. Samples were immunuoprecipitated with 5-hmC antibody (Active Motive 39791). Samples were purified using phenolchloroform/isoamyl alcholor and ethanol precipitation.
Library was prepped using the ThruPLEX DNA-seq Kit (R400427, Rubicon Genomics)

value: Sprague Dawley

tag: group

value: Control

value: brain


title: Control (C2)

value: saline


title: KATH, control, body, rep1

description:
pooled 3 iso-female lines, 10 individuals
K_RT_W_1

value: male


title: Botox (B4)

value: control (universal reference)


title: TET2_KO_Negative_A_S8

value: T cells

value: T cells in LCMV mouse experiment


title: TET2_KO_Ly108_A_S7


title: PyMT-Bad3SA 2

value: MMTV-PyMT

value: Bad 3SA


title: SlowBKK, cold accl, hindgut, rep2

description:
pooled 4 iso-female lines, 60 individuals
S_10_Hg_2

value: hindgut

value: Bangkok

value: sensitive

value: cold acclimation


title: PyMT-Bad+/+ 5

value: Breast tumor

value: Bad wild-type


title: PyMT-Bad3SA 1


title: KATH, control, malpighiantubule, rep4

description:
pooled 3 iso-female lines, 60 individuals
K_RT_Mt_4

value: malpighian tubule

value: Kathmandu

value: tolerant

value: control


title: Botox (B2)

value: botox


title: 11 CS

value: Sprague Dawley

value: Control

value: brain


title: KATH, control, hindgut, rep5

description:
pooled 3 iso-female lines, 60 individuals
K_RT_Hg_5

value: male


title: PyMT-Bad+/+ 6

value: MMTV-PyMT


title: HC_Subject_sp

city: New Haven

first: Jeff

middle: R

last: Gehlhausen

state: CT

address: 333 Cedar St LCI 501

department: Yale Dermatology

institute: Yale School of Medicine

description: Library name: GSM16

data_processing:
For single-cell RNA-seq: Cell Ranger analysis pipelines were used for alignment, gene counts, and filtering. Analysis was performed using the Seurat package (version 4.3.0) in R (version 4.2.3). For quality control, cells with less than 200 or over 10,000 unique genes as well as cells with greater than 5% mitochondrial reads were removed. Samples were log-normalized and integrated using Seurat. Cells were clustered using a K-nearest neighbor graph-based approach. UMAP was used for visualization. For spatial transcriptomics: Space Ranger 2.0.0 (10x Genomics) was used to align CytAssist images with corresponding H&E stained images, perform quality control, and convert the data into spots x genes expression matrices. Cells that expressed less than 500 genes, had greater than 25% mitochondrial reads, or greater than 25% of genes representing hemoglobin were removed. SCTransform was used for sample normalization. Genome build: GRCh38/hg38
sequencing method: Libraries were sequenced using paired-end 150 base reads on an Illumina NovaSeq instrument.
Assembly: GRCh38/hg38
Supplementary files format and content: Spatial transcriptomics data in h5 format containing gene expression counts and spatial coordinates. TIFF images contain spatial visualization of gene expression.
Library strategy: Spatial Transcriptomics

source_name: skin

extract_protocol:
For single-cell RNA-seq: 4 or 5 mm punch biopsies were bisected into four pieces and digested with Dispase II (10 mg/mL) in RPMI supplemented with 10% FBS, 1% L-Glutamine, and 1% Penicillin/Streptomycin for 45 minutes. The tissue was then cut into finer pieces with a razor and placed in 0.5 mL/mL Liberase TH with 40 ug/mL DNase I for another 45 minutes. Tissue and media were passed through a 70 uM strainer, counted, and suspended in 0.04% BSA and PBS.
For spatial transcriptomics: FFPE tissues were sectioned onto glass slides. Deparaffinization, H&E staining, imaging, and decrosslinking were conducted following the 10x Genomics protocol CG000520. The Visium assay was performed using CytAssist technology according to protocol CG000495. Library construction protocol: For single-cell RNA-seq: 10x Genomics 5'v2 kit was used for library preparation. Samples were sequenced at a minimum depth of 20,000 read pairs per cell. For spatial transcriptomics: Following the transfer of gene expression probes from tissue to the Visium slide using CytAssist, the probes were extended, amplified, and made into libraries for sequencing. Sequencing protocol: Single-cell libraries were sequenced on an Illumina platform to a minimum depth of 20,000 read pairs per cell. Spatial transcriptomics libraries were sequenced using paired-end 150 base reads on an Illumina NovaSeq instrument.

treatment_protocol: Skin biopsies were obtained from subjects with cutaneous lupus erythematosus (CLE) and healthy controls. For CLE patients, both lesional and non-lesional skin biopsies were collected. 4-5mm punch biopsies were taken from the specified sites. The study was approved by Yale Human Research Protection Program Institutional Review Boards (protocol ID 2000027571 and 2000022585).

value: skin

value: HC

tag: sle

value: no

tag: site

value: distal arm


title: KATH, control, malpighiantubule, rep5

description:
pooled 3 iso-female lines, 60 individuals
K_RT_Mt_5


title: WT_Ly108_A_S3

description:
Mouse_LCMV_Tcell_RNA-Seq_ReadCounts_MGI.tsv
Mouse_LCMV_Tcell_RNA-Seq_TPM_MGI.tsv

value: T cells

value: WT

value: T cells in LCMV mouse experiment


title: WT_Total_A_S2

value: Total


title: TET2_KO_Naive_A_S5

value: Naive


title: 14 ES

value: Epileptic


title: WT_Negative_A_S4


title: 12 ES


title: PyMT-Bad+/+ 2

value: Breast tumor

value: Bad wild-type


title: SCLE_posttreatment_sp

description: Library name: GSM14

value: CLE-lesional

value: HCQ 200 BID + Prednisone 5 daily + Anifrolumab 300 mg q4w

value: yes


title: PyMT-Bad+/+ 4


title: KATH, control, malpighiantubule, rep1

description:
pooled 3 iso-female lines, 60 individuals
K_RT_Mt_1

value: malpighian tubule

value: Kathmandu

value: tolerant

value: male

value: control


title: PyMT-Bad+/+ 3

value: MMTV-PyMT


title: DLE_Patient _sp

description: Library name: GSM15

value: skin

value: no

value: thigh


title: KATH, control, hindgut, rep4

description:
pooled 3 iso-female lines, 60 individuals
K_RT_Hg_4

value: hindgut


title: TET2_KO_Total_A_S6

value: T cells

value: Total

value: T cells in LCMV mouse experiment


title: KATH, cold accl, body, rep3

description:
pooled 3 iso-female lines, 10 individuals
K_10_W_3

value: body

value: cold acclimation


title: Eye, wh5, Male 4

city: Corvallis

first: Dante

last: Perone

state: Oregon

institute: Oregon State University

data_processing:
quality trimmimg and adapter removal was performed using fastp with defualt settings
reads were mapped to the GRCz11 primary assembly using the STAR aligner
The Lawson Lab published a zebrafish annotation (Lawson et al., 2020). Both the genome assembly file and the annotation gtf file (v. 4.3.2) were downloaded from their website (https://www.umassmed.edu/lawson-lab/reagents/zebrafish-transcriptome). The arguments used in the mapping step included --alignIntronMin 15, --alignIntronMax 250000 and --quantMode GeneCounts
DESeq2 (v. 1.32.0) was used to explore the overall clustering of the brain and eye samples
DESeq2 (v. 1.32.0) was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = ~ Sex + Group, where the groups included brain KO (wh5), brain WT, eye KO (wh5), and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30,921 genes. Variance stabilizing transformation (blind = FALSE) was applied to the data and used for the generation of the PCA (including all filtered genes), MDS and heatmap plots. Sample10 (brain, WT, male) was an outlier in all three plots. In addition, Sample3 (brain, WT, female) appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples, it could be seen that both samples appeared to be outliers on the brain sample plots.
Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface
Of the 36,351 features in the table 25,411 (69%) could be matched to gene-level (Entrez) expression and low abundance features (counts < 4) and low variance feature (variance percentile rank < 15) were removed
DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p-value ≤ 0.05 and log2(fold change) ≥ |1| were considered DEGs
Assembly: GRCz11
Supplementary files format and content: .xlsx, raw counts of all samples and types
Supplementary files format and content: .csv, separate DEG analysis results table for eye and brain with sample 3 and 10 removed

organism: Danio rerio

source_name: brain

extract_protocol:
RNA extraction was performed using the Zymo Quick-RNA Miniprep kit with in-column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System.
Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a Poly(A) mRNA isolation kit

value: brain


title: Eye, wh5, Male 5


title: PyMT-Bad+/+ 1

value: Breast tumor

value: Bad wild-type


title: HC_Subject2

description: Library name: GSM11

library_source: transcriptomic single cell

data_processing:
For single-cell RNA-seq: Cell Ranger analysis pipelines were used for alignment, gene counts, and filtering. Analysis was performed using the Seurat package (version 4.3.0) in R (version 4.2.3). For quality control, cells with less than 200 or over 10,000 unique genes as well as cells with greater than 5% mitochondrial reads were removed. Samples were log-normalized and integrated using Seurat. Cells were clustered using a K-nearest neighbor graph-based approach. UMAP was used for visualization. For spatial transcriptomics: Space Ranger 2.0.0 (10x Genomics) was used to align CytAssist images with corresponding H&E stained images, perform quality control, and convert the data into spots x genes expression matrices. Cells that expressed less than 500 genes, had greater than 25% mitochondrial reads, or greater than 25% of genes representing hemoglobin were removed. SCTransform was used for sample normalization. Genome build: GRCh38/hg38
sequencing method: Libraries were sequenced using paired-end 150 base reads on an Illumina NovaSeq instrument.
Assembly: GRCh38/hg38
Supplementary files format and content: Spatial transcriptomics data in h5 format containing gene expression counts and spatial coordinates. TIFF images contain spatial visualization of gene expression.

value: HC

value: lower back


title: Eye, wh5, Male 3


title: KATH, control, hindgut, rep1

description:
pooled 3 iso-female lines, 60 individuals
K_RT_Hg_1

value: Kathmandu

value: tolerant

value: male


title: KATH, cold accl, body, rep4

description:
pooled 3 iso-female lines, 10 individuals
K_10_W_4


title: HC_Subject1

description: Library name: GSM10

value: skin


title: KATH, cold accl, body, rep2

description:
pooled 3 iso-female lines, 10 individuals
K_10_W_2


title: HC_Subject3

description: Library name: GSM12

value: no


title: SCLE_pretreatment_sp

description: Library name: GSM13

value: CLE-lesional

value: HCQ 200 BID + Prednisone 5 daily + Lenalidomide 5 mg qod

value: yes

value: distal arm


title: e16-5M3KO-2-IP

city: Dallas

first: Vishal

last: Patel

state: Texas

address: 5323 Harry Hines Blvd, RM F5.206, MC8856

department: Internal Medicine Nephrology

institute: UTSW

description: Library name: e16-5M3KO-2-IP

data_processing:
*library strategy: MeRIP-seq
Raw data were recorded in a FASTQ file which contains sequenced reads and corresponding information on sequencing quality
Peak annonation, metagene analysis, and diffpeak analysis were performed.
DESeq2 algorithm was applied to filter the differentially expressed genes between the control and Mettl3KO samples
Assembly: HiSAT2 was used to map to the reference Genome
Supplementary files format and content: BW files are attached

source_name: kidney

extract_protocol:
total RNA including non-coding RNA was extracted using the Qiagen miRNeasy isolation kit
Library was constructed using the mRNA sequencing kit (Illumina)

value: kidney

value: Six2:eGFPTGC/+; Mettl3F/F


title: WT_Naive_A_S1

value: T cells

value: Naive

value: WT

value: T cells in LCMV mouse experiment


title: Eye, wh5, Male 2

value: brain


title: e16-5M3KO-2-Input

description: Library name: e16-5M3KO-2-Input


title: CLE_Patient5_non-lesional

description: Library name: GSM9

value: CLE-nonlesional

value: Topical Clobetasol 0.05% ointment, MTX 15 mg weekly, ILK

value: lower back


title: KATH, cold accl, malpighiantubule, rep4

description:
pooled 3 iso-female lines, 60 individuals
K_10_Mt_4

value: malpighian tubule

value: Kathmandu

value: tolerant

value: male

value: cold acclimation


title: KO

city: Nanjing

first: HONGWEI

last: LIANG

state: Jiangsu Province

address: Qixia District, Xianlin Road No.163

institute: Nanjing University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: PNPT1 knockout A549 cell

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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.

growth_protocol: Cell lines were cultured in Dulbecco’s modified Eagle medium (DMEM, Thermo Fisher, USA) supplemented with 10% FBS (Gibco, Australia). All these cell lines were supplemented with penicillin and streptomycin (100 U/mL, Thermo Fisher, USA) and maintained at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol: Total RNA was extracted from cells via TRIzol reagent (Thermo Fisher Scientific) and stored at −80°C according to the manufacturer’s protocol.

treatment_protocol: PNPT1 knockout A549 cell and wild type A549 cells


title: Eye, wh5, Female 5


title: WT

source_name: wild type A549 cells


title: e16-5M3KO-1-IP

description: Library name: e16-5M3KO-1-IP


title: Eye, wh5, Male 1


title: KATH, cold accl, malpighiantubule, rep3

description:
pooled 3 iso-female lines, 60 individuals
K_10_Mt_3


title: CLE_Patient5_lesional

description: Library name: GSM8

value: skin

value: CLE-lesional

value: no

value: upper back


title: CLE_Patient4_non-lesional

description: Library name: GSM7

value: HCQ 200 mg BID + MMF 2500 daily

value: yes


title: e16-5Ctl-2-IP

description: Library name: e16-5Ctl-2-IP

value: kidney


title: Eye, wh5, Female 4


title: KATH, cold accl, hindgut, rep3

description:
pooled 3 iso-female lines, 60 individuals
K_10_Hg_3

value: hindgut


title: Eye, wh5, Female 3

value: brain


title: KATH, cold accl, hindgut, rep4

description:
pooled 3 iso-female lines, 60 individuals
K_10_Hg_4


title: e16-5Ctl-1-IP

description: Library name: e16-5Ctl-1-IP


title: CLE_Patient2_non-lesional

description: Library name: GSM4

value: CLE-nonlesional

value: HCQ 200 mg BID


title: Eye, wh5, Female 2


title: CLE_Patient3_non-lesional

description: Library name: GSM6

value: lower back


title: KATH, cold accl, hindgut, rep1

description:
pooled 3 iso-female lines, 60 individuals
K_10_Hg_1


title: Eye, wh5, Female 1


title: e16-5Ctl-1-Input

description: Library name: e16-5Ctl-1-Input


title: FastBKK, control, body, rep4

description:
pooled 4 iso-female lines, 10 individuals
F_RT_W_4

value: body

value: Bangkok

value: control


title: e16-5M3KO-1-Input

description: Library name: e16-5M3KO-1-Input

value: Six2:eGFPTGC/+; Mettl3F/F


title: CLE_Patient2_lesional

description: Library name: GSM3

value: proximal arm


title: EV_WI-38_IR_3

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
Fastq files were extracted using bcl2fastq2 (v2.20)
reads were trimmed with cutadapt (v1.18)
Trimmed sequence reads were aligned to hg19 genome and Ensmbl v82 annotation with STAR (v2.4.0j)
FeatureCounts (v1.6.3) were used to create gene counts
Assembly: hg19
Supplementary files format and content: text files of gene counts

growth_protocol: WI-38 fibroblasts were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
EVs were extracted by ultracentrifugation and total RNA was isolated from IR-treated cells and EVs with RNeasy Mini Kit and exoRNeasy Serum/Plasma Maxi kits (QIAGEN).  RNA-Seq libraries were prepared using the KAPA RNA Hyper Prep kit with RiboErase (HMR) to yield 200-300 bp insert size (Roche, Wilmington, MA).  The fragmented cDNA was ligated with adapters (Integrated DNA Technologies, Inc.), and amplified with KAPA HiFi HotStart ReadyMix (2X) and primers (10X) for 17 cycles.  Clean-up after amplification was performed with 1× KAPA Pure Beads.  Finally, the quality and quantity of the cDNA library were analyzed by Agilent Tapestation 4200 and Qubit 3.0 Fluorometer (Thermo Fisher Scientific Inc, Waltham, MA).
The final libraries were subjected to 150 bp PE (paired-end) sequencing on an Illumina HiSeq sequencer (Illumina Inc., San Diego, CA).

treatment_protocol: Around PDL25, WI-38 fibroblasts were irradiated with 10Gy ionizing radiation

tag: Stage

tag: treatment group

value: IR

tag: irradition (gy)


title: Eye, WT, Male 5

value: WT


title: FastBKK, control, body, rep3

description:
pooled 4 iso-female lines, 10 individuals
F_RT_W_3

value: tolerant

value: male


title: CLE_Patient1_non-lesional

description: Library name: GSM2

value: skin

value: HCQ 200 mg BID + Belimumab 200 mg/ml weekly


title: KATH, cold accl, malpighiantubule, rep1

description:
pooled 3 iso-female lines, 60 individuals
K_10_Mt_1

value: malpighian tubule

value: Kathmandu

value: cold acclimation


title: EV_WI-38_IR_2

tag: cell type


title: Eye, WT, Male 4

value: brain

tag: genotype


title: FastBKK, control, body, rep1

description:
pooled 4 iso-female lines, 10 individuals
F_RT_W_1

tag: treatment


title: CLE_Patient1_lesional

description: Library name: GSM1

tag: tissue

value: CLE-lesional

value: yes

value: distal arm


title: Eye, WT, Male 3


title: EV_WI-38_IR_1

tag: cell line


title: FastBKK, control, malpighiantubule, rep4

description:
pooled 4 iso-female lines, 60 individuals
F_RT_Mt_4

tag: population

value: Bangkok


title: e16-5Ctl-2-Input

description: Library name: e16-5Ctl-2-Input

value: kidney


title: CLE_Patient3_lesional

description: Library name: GSM5

value: no

value: face


title: DLD-1 cell,shNC-3

city: Xi'an

first: Xiaotian

last: Song

address: Changle west road

institute: xijing hospital

description: Library name: LN3

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Homo sapiens reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: DLD-1 cell

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: DLD-1 cell

value: control


title: Eye, WT, Male 2

value: WT


title: FastBKK, control, malpighiantubule, rep3

description:
pooled 4 iso-female lines, 60 individuals
F_RT_Mt_3

tag: phenotype

value: tolerant

value: male


title: DLD-1 cell,shNC-2

description: Library name: LN2


title: EV_WI-38_CTR_2

value: CTR


title: Eye, WT, Male 1


title: EV_WI-38_CTR_3


title: EV_WI-38_CTR_1


title: DLD-1 cell,shLCN2-3

description: Library name: LK3

value: Knockdown of LCN2 expression


title: WI-38_IR_3

value: Fibroblast

value: IR


title: FastBKK, control, hindgut, rep4

description:
pooled 4 iso-female lines, 60 individuals
F_RT_Hg_4

source_name: hindgut

value: hindgut

tag: Sex


title: Eye, WT, Female 5

value: brain


title: FastBKK, control, hindgut, rep3

description:
pooled 4 iso-female lines, 60 individuals
F_RT_Hg_3


title: DLD-1 cell,shNC-1

description: Library name: LN1


title: WI-38_IR_2


title: Eye, WT, Female 4


title: Eye, WT, Female 3


title: FastBKK, control, hindgut, rep1

description:
pooled 4 iso-female lines, 60 individuals
F_RT_Hg_1


title: WI-38_IR_1


title: DLD-1 cell,shLCN2-1

description: Library name: LK1


title: Eye, WT, Female 1


title: WI-38_CTR_2


title: RNA-seq_WT-R1

city: Panjin

first: Yubo

last: Liu

address: Dagong Lu

institute: Dalian University of Technology

description: Library name: RNA-seq_WT-R1

data_processing:
Base-calling: in-house Illumina software.
STAR (v2.7.11a) was used to align clean reads to the reference genome.
FeatureCounts (v2.0.3) was used to quantify the reads mapped to genomic features.
The differentially expressed genes were determined by DESeq2 (v1.42.1).
Assembly: hg19
Supplementary files format and content: bigwig
Supplementary files format and content: txt

growth_protocol: All cells were cultured in the complete medium composed of 90% RPMI-1640 medium and 10% fetal bovine serum. MCF-7 and MCF-7/DOX cells were grown in 10-cm culture dishes at 37 °C with 5% (v/v) CO2.

extract_protocol:
Approximately 2.5×10e6 cells were used as a standardized experimental unit to ensure reproducibility for COCA-seq assay. O-GlcNAz chromatin DNAs enriched by Streptavidin-magnetic beads were purified with the MiniBEST DNA Fragment Purification Kit Ver.4.0 (Takara) and the MiniBEST Agarose Gel DNA Extraction Kit Ver.4.0 (Takara). For RNA-seq, total RNA was extracted from the MCF-7 and MCF-7/DOX cells using Trizol reagent (Invitrogen). RNA quality was checked.
DNA-end repair, 3'-dA overhang and ligation of methylated sequencing adaptor. PCR amplification and size selection. Qualified library for sequencing. RNA-seq libraries were constructed using SMARTer cDNA library construction kit.

treatment_protocol: MCF-7 cells were grown in drug-free medium, while MCF-7/DOX cells were maintained in 1 μM doxorubicin to preserve drug resistance. For metabolic labeling, the medium was aspirated, followed by two washes with 1×PBS. The DMSO stock solution of 1,6-Pr2GalNAz was added to achieve the final treatment conditions, and cells were incubated for 48 h under standard culture conditions.

value: epithelial type of breast cancer cell

value: untreated


title: FastBKK, cold accl, body, rep4

description:
pooled 4 iso-female lines, 10 individuals
F_10_W_4

value: body

value: Bangkok

value: cold acclimation


title: FastBKK, cold accl, body, rep2

description:
pooled 4 iso-female lines, 10 individuals
F_10_W_2


title: RNA-seq_WT-R2

description: Library name: RNA-seq_WT-R2


title: Brain, wh5, Male 5

source_name: eye

value: eye


title: WI-38_CTR_3


title: FastBKK, control, malpighiantubule, rep2

description:
pooled 4 iso-female lines, 60 individuals
F_RT_Mt_2

value: malpighian tubule


title: DLD-1 cell,shLCN2-2

description: Library name: LK2

value: DLD-1 cell


title: FastBKK, cold accl, body, rep1

description:
pooled 4 iso-female lines, 10 individuals
F_10_W_1

source_name: body


title: RNA-seq_DOX-R2

description: Library name: RNA-seq_DOX-R2

value: treated with 1 μM doxorubicin


title: WI-38_CTR_1


title: Brain, wh5, Male 2


title: COCA-seq_WT-R2

description: Library name: COCA-seq_WT-R2

data_processing:
Base-calling: in-house Illumina software.
BWA (v0.7.18) was used to map clean reads to the reference genome.
Peak-calling: MACS2 (v2.2.9.1) for COCA-Seq.
DeepTools (v3.5.4) was used for generating bigwig files. ChIPseeker (v1.38.0) for the annotation of peaks.
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
Approximately 2.5×10e6 cells were used as a standardized experimental unit to ensure reproducibility for COCA-seq assay. O-GlcNAz chromatin DNA enriched by Streptavidin-magnetic beads was purified with the MiniBEST DNA Fragment Purification Kit Ver.4.0 (Takara) and the MiniBEST Agarose Gel DNA Extraction Kit Ver.4.0 (Takara). For RNA-seq, total RNA was extracted from the MCF-7 and MCF-7/DOX cells using Trizol reagent (Invitrogen). RNA quality was checked.
DNA-end repair, 3'-dA overhang and ligation of methylated sequencing adaptor. PCR amplification and size selection. Qualified library for sequencing. RNA-seq libraries were constructed using SMARTer cDNA library construction kit.


title: Brain, wh5, Male 4


title: FastBKK, cold accl, malpighiantubule, rep4

description:
pooled 4 iso-female lines, 60 individuals
F_10_Mt_4

value: tolerant


title: bulkrna seq of tumor biopsy, patient P-100

city: Berlin

first: Damian

middle: Tobias

last: Rieke

address: Charitéplatz 1

department: Comprehensive Cancer Center

institute: Charité – Universitätsmedizin Berlin

description: Library name: P-100

data_processing:
Generation of the count matrix and TPM matrix from raw data (fastq files) was performed with salmon (version 1.4.0)
Assembly: GRCh38, GENCODE 33
Supplementary files format and content: Count matrix and TPM matrix in *.tsv format

source_name: tumor

extract_protocol:
RNA from tumor were isolated using AllPrep Mini or Universal Kits (Qiagen). After library preparation (TruSeq RNA Sample Preparation kit V2, Illumina), RNA-paired-end sequencing (2 × 151 bp; 2 × 101 bp) was performed with various HiSeq instruments (e.g HiSeq 4000 and NovaSeq 6000; Illumina).
bulk mRNA sequencing; TruSeq RNA Sample Preparation kit V2

value: tumor

tag: pid

value: male

tag: age

tag: entity long

value: Basal Cell Carcinoma

tag: site 1_biopsy

tag: prior therapy

value: FALSE


title: SlowBKK, control, hindgut, rep2

description:
pooled 4 iso-female lines, 60 individuals
S_RT_Hg_2

value: sensitive

value: control


title: bulkrna seq of tumor biopsy, patient P-104

description: Library name: P-104

value: female

value: Adenoid Cystic Carcinoma

value: TRUE


title: COCA-seq_DOX-R2

description: Library name: COCA-seq_DOX-R2

value: epithelial type of breast cancer cell


title: RNA-seq_DOX-R1

description: Library name: RNA-seq_DOX-R1


title: bulkrna seq of tumor biopsy, patient P-103

description: Library name: P-103

value: lung


title: Eye, WT, Female 2

value: brain

value: WT


title: Brain, wh5, Male 3

value: eye


title: FastBKK, cold accl, malpighiantubule, rep1

description:
pooled 4 iso-female lines, 60 individuals
F_10_Mt_1

source_name: malpighian tubule

value: malpighian tubule

value: Bangkok

value: cold acclimation


title: COCA-seq_DOX-R1

description: Library name: COCA-seq_DOX-R1

value: treated with 1 μM doxorubicin


title: FastBKK, cold accl, hindgut, rep4

description:
pooled 4 iso-female lines, 60 individuals
F_10_Hg_4

value: hindgut

value: tolerant

value: male


title: bulkrna seq of tumor biopsy, patient P-97

description: Library name: P-97

value: tumor


title: bulkrna seq of tumor biopsy, patient P-98

description: Library name: P-98


title: COCA-seq_WT-R1

description: Library name: COCA-seq_WT-R1

value: untreated


title: Brain, wh5, Female 3


title: Brain, wh5, Female 5


title: FastBKK, cold accl, hindgut, rep3

description:
pooled 4 iso-female lines, 60 individuals
F_10_Hg_3


title: Brain, wh5, Male 1


title: Brain, wh5, Female 4


title: CPIP2

city: Hangzhou

first: Boyu

address: Binwen Road

institute: Zhejiang Chinese Medical University

description: Library name: Sample4

data_processing:
All libraries were sequenced by DNBSEQ-T7 Sequencer (MGI, China) on a 150 bp paired-end run.
Data analysis was performed by NovelBio Co.,Ltd. (China) with NovelBrain Cloud Analysis Platform.
Assembly: Rnor6.0, ensembl annotation version 100
Supplementary files format and content: Tab-separated values files and matrix files

source_name: L4-L6 DRG

growth_protocol: Rats were randomly allocated, and 5 rats were housed per cage(12 hour light–dark cycles and 24 ± 2 ℃). Food and water were provided ad libitum.

extract_protocol:
Ipsilateral L4-L6 DRG of CPIP model and sham rats were surgically removed and enzymatically digested with an enzyme solution containing 2 mg/mL dispase (#17105-041, Thermo Fisher, USA), 1 mg/mL collagenase Type I (#17100-017, Thermo Fisher, USA) and 0.1mg/mL DNase (#MB3069-1, MeilunBio, China) in DMEM at 37 °C for 50 min. Samples from 3 rats were pooled for one biological replicate. Two biological replicates were included in sham or CPIP model group. Samples were centrifuged at 1,000 g for 5 min at room temperature and supernatant were discarded followed by 1 mg/mL papain (#HY-P1645, MCE, USA) in DMEM at 37 °C for 10 min. Digestion was terminated with DMEM containing 10 % FBS and filtered with a 40 μm cell strainer.
BD Rhapsody system was used to capture the transcriptomic information of the single cells (BD, USA). Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell. The cells were lysed in the microwell to hybridize mRNA molecules to barcoded capture oligos on the beads. Beads were collected into a single tube for reverse transcription and ExoI digestion. Upon cDNA synthesis, each cDNA molecule was tagged on the 5scription and ExoId Ea mRNA transcript) with a unique molecular identifier (UMI) and cell barcode indicating its cell of origin. Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification (WTA) workflow including random priming and extension (RPE), RPE amplification PCR and WTA index PCR. The libraries were quantified using a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent, USA) and Qubit High Sensitivity DNA assay (Thermo Fisher, USA).

value: L4-L6 DRG


title: bulkrna seq of tumor biopsy, patient P-99

description: Library name: P-99

value: Adenoid Cystic Carcinoma


title: FastBKK, cold accl, hindgut, rep1

description:
pooled 4 iso-female lines, 60 individuals
F_10_Hg_1


title: single nuclei RNA seq of tumor biopsy, Patient 85

description:
Library name: P85
10x 3´GEX

data_processing:
*library strategy: Single nuclei RNAseq
Generation of count matrices from raw data was performed with CellRanger version 7.1.0. Barcodes were filtered with Cellbender.0.1.0
Assembly: GRCh38
Supplementary files format and content: Filtered count matrix in *.h5 format
Supplementary files format and content: Filtered cell barcodes in *.csv fotmat

molecule: nuclear RNA

extract_protocol:
Each sample of fresh frozen tumor tissue was suspended in NP-40 lysis buffer  in a 1.5ml Eppendorf tube and disrupted with a plastic pestle. The suspension was incubated on ice for 5 minutes, filtered through a 70 µm pre-separation strainer and centrifuged at 4°C. The supernatant was removed and the nuclei were resuspended in nuclei wash buffer. 3.5 µl DAPI were added, followed by incubation on ice. The mixture was filtered through a 40 µm Flowmi cell strainer and sorted with a 100 µm nozzle in an Eppendorf tube containing 200 µL sort buffer
Single nuclei libraries were generated according to the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) user guide (CG0003154) by 10x Genomics.

tag: biopsy site

tag: tumor entity

value: Adenoid cystic carcinoma


title: FastBKK, cold accl, malpighiantubule, rep3

description:
pooled 4 iso-female lines, 60 individuals
F_10_Mt_3

data_processing:
quality control: FastQC (version 0.11.9)
mapping: NextGenMap (version 0.5.2)
Assembly: dana_r1.05_FB2016_01
Supplementary files format and content: tab-delimited text file includes counts for each sample


title: bulkrna seq of tumor biopsy, patient P-95

description: Library name: P-95

value: female

value: Adenocarcinoma NOS

value: TRUE


title: single nuclei RNA seq of tumor biopsy, Patient 103

description:
Library name: P103
10x 3´GEX

value: lung


title: Brain, wh5, Female 2

value: eye


title: CPIP1

description: Library name: Sample3


title: single nuclei RNA seq of tumor biopsy, Patient 79

description:
Library name: P79
10x 3´GEX

value: skin


title: Brain, wh5, Female 1


title: bulkrna seq of tumor biopsy, patient P-91

description: Library name: P-91

value: FALSE


title: single nuclei RNA seq of tumor biopsy, Patient 66, technical replicate 2

description:
Library name: P66_2
10x 3´GEX

value: lymphnode

value: Basal cell carcinoma


title: Sham1

description: Library name: Sample1


title: Sham2

description: Library name: Sample2


title: Brain, WT, Male 4

value: WT


title: single nuclei RNA seq of tumor biopsy, Patient 74

description:
Library name: P74
10x 3´GEX

value: primary

value: Mucoepidermoid carcinoma


title: Fungus cells, Glucose medium, rep3

city: Auckland

first: Yapeng

last: Lai

address: 55 Wellesley Street East,  Auckland Central

department: School of Science

country: New Zealand

institute: Auckland University of Technology

data_processing:
Clean reads were obtained from the raw reads by removing the adaptor sequences, low quality sequences and reads containing poly-N with Trimmomatic software.
The clean reads were aligned to the reference genome using the software Hisat2
Gene expression calculation was performed by StringTie software. Gene expression profiling was based on the number of reads. FPKM (fragments per kb of exon model per million mapped reads) values were used to estimate the expressed values and transcript levels
DESeq2 was selected to identifying differentially expressed genes (DEGs).Genes with an adjusted Pvalue (padj) < 0.05 and abs(log2(fold change)) >1 were assigned as DEGs.
Assembly: The Reference genome is ASM22609v1
Supplementary files format and content: xlsx file includes FPKM values for each sample

organism: Thermothelomyces thermophilus ATCC 42464

source_name: Fungus cells

growth_protocol: Fresh spores of M. thermophila were inoculated into 50 mL liquid minimal medium with 2% (w/v) glucose or 2% (w/v) Avicel as the sole carbon source at 45°C for 36 h, respectively.

extract_protocol:
Total fungal RNA were extracted from fresh mycelia harvested from respective liquid medium through vacuum filtration.Total RNA was isolated using an RNA extraction kit TransZol Up (TransGen Biotech, Beijing, China) following the manufacturer’s protocols, and RNA extracts were assessed by electrophoresis and quantified using the NanoDrop 2000 Spectrophotometer (Thermo Scientific, Waltham, MA, USA).
After total RNA was obtained, the mRNA for each samples were enriched by Oligo (dT) beads and reversely transcribed into cDNA via the aid of NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA).

value: Fungus cells

value: Glucose


title: single nuclei RNA seq of tumor biopsy, Patient 66, technical replicate 1

description:
Library name: P66_1
10x 3´GEX

value: tumor


title: bulkrna seq of tumor biopsy, patient P-90

description: Library name: P-90

value: Adenoid Cystic Carcinoma


title: bulkrna seq of tumor biopsy, patient P-89

description: Library name: P-89

value: male

value: Mucoepidermoid Carcinoma


title: Fungus cells, Glucose medium, rep2


title: single nuclei RNA seq of tumor biopsy, Patient 46, technical replicate 2

description:
Library name: P46_2
10x 3´GEX


title: Brain, WT, Male 3


title: Brain, WT, Male 2


title: single nuclei RNA seq of tumor biopsy, Patient 46, technical replicate 1

description:
Library name: P46_1
10x 3´GEX


title: Fungus cells, Glucose medium, rep1


title: bulkrna seq of tumor biopsy, patient P-88

description: Library name: P-88

value: female


title: single nuclei RNA seq of tumor biopsy, Patient 42

description:
Library name: P42
10x 3´GEX

value: Adenoid cystic carcinoma


title: bulkrna seq of tumor biopsy, patient P-94

description: Library name: P-94

value: metastasis


title: Brain, WT, Female 5

value: eye


title: bulkrna seq of tumor biopsy, patient P-92

description: Library name: P-92

value: TRUE


title: bulkrna seq of tumor biopsy, patient P-87

description: Library name: P-87

value: FALSE


title: Fungus cells, Avicel medium, rep2

value: Avicel


title: single nuclei RNA seq of tumor biopsy, Patient 33

description:
Library name: P33
10x 3´GEX

value: skin


title: Brain, WT, Male 1

value: WT


title: bulkrna seq of tumor biopsy, patient P-85

description: Library name: P-85

value: lung


title: single nuclei RNA seq of tumor biopsy, Patient 32

description:
Library name: P32
10x 3´GEX

value: primary


title: bulkrna seq of tumor biopsy, patient P-84

description: Library name: P-84


title: single nuclei RNA seq of tumor biopsy, Patient 31, technical replicate 2

description:
Library name: P31_2
10x 3´GEX

value: Carcinoma ex-pleomorphic adenoma


title: Brain, WT, Male 5


title: bulkrna seq of tumor biopsy, patient P-83

description: Library name: P-83

value: Adenocarcinoma NOS


title: Brain, WT, Female 4


title: single nuclei RNA seq of tumor biopsy, Patient 31, technical replicate 1

description:
Library name: P31_1
10x 3´GEX

value: tumor


title: Brain, WT, Female 2


title: Fungus cells, Avicel medium, rep3

value: Fungus cells


title: bulkrna seq of tumor biopsy, patient P-82

description: Library name: P-82

value: Adenoid Cystic Carcinoma


title: Disease_C_Lib_Tad-CBE(CCA2)

city: CHICAGO

first: Yuan

last: Wu

state: Illinois

address: 929 E 57th St, GCIS E535

department: Chemistry

institute: University of Chicago

description: Library name: sample 38

data_processing:
Paired-end reads were trimmed, demultiplexed using BCL convert software v2.2.0, and mapped to the designed library cassette in Python v3.8. Reads are considered if (1) the R1 read contains ‘GTTTTAGAGC’, the first 10 nucleotides of the gRNA backbone; (2) the 20-nt spacer 5’ of the gRNA backbone matches a designed sequence; (3) the protospacer matches the spacer and carries only C-to-N and A-to-G mutations; and (4) an NGG PAM can be located at the 3’ end of the protospacer. Target sites with sequencing depths >20 are included in downstream analysis. Conversion rates are calculated as 〖Reads〗_G/(Total Reads) at A positions and as 〖Reads〗_T/(Total Reads) at C positions.
Supplementary files format and content: excel
Supplementary files format and content: All the mapped reads were output to excel with the corresponding information in Clinvar. Editing were showed as mismatched.

extract_protocol:
Transfected cells were incubated for an additional 3 days before harvesting. Genomic DNA was extracted using a Quick-DNA Miniprep Plus Kit (Zymo, D4069) following the manufacture’s protocol. HEK293T cells were seeded into two 6 cm tissue culture dishes at a density of 1 x 106 cells per dish, and infected 18 h post-seeding with 2.5 mL lentiviral library at low multiplicity of infection (MOI) using 10 μg/mL polybrene. Cells were trypsinized 24 h post-infection, transferred into two 10 cm tissue culture dishes, and grown in DMEM medium supplemented with 10% FBS and 2 μg/mL puromycin. Cells were cultured and selected with 2 μg/mL puromycin for an additional 14 days. To maintain the diversity of the paired sgRNA-target library, cells were split and passaged at a minimum density of 1 x 107 cells per passage.
The paired sgRNA-target cassette was amplified and barcoded via two rounds of PCR, following a protocol similar to that described in “Targeted deep sequencing”. Initial amplification was set up with 20 μg of purified genomic DNA, 1 μL of 50 μM forward primers (a 1:1:1:1 mixture of YX1451-YX1454) and reverse primer YX1381, 200 μM of dNTPs, and 5 U Taq polymerase in 100 μL of 1× standard Taq reaction buffer using the following PCR program: denaturing (95 oC, 3 min); 25 cycles of amplification (95 oC, 30 s; 60 oC, 30 s; 72 oC, 30 s); and final extension (72 oC, 5 min). A 50 μL second-round barcoding PCR was set up with 2.5 μL of the first-round PCR mixture, 0.5 μM of forward and reverse barcoding primers, and 2.5 U Taq DNA Polymerase in 1× standard Taq reaction buffer. Second-round PCR was conducted as follows: initial denaturing (95 oC, 3 min); 8 cycles of amplification (95 oC, 30 s; 60 oC, 30 s; 68 oC, 45 s); and final extension (68 oC, 5 min). PCR products were pooled, resolved by gel electrophoresis, and purified with the Zymoclean Gel Recovery Kit. The library concentration was quantified using the KAPA Library Quantification Kit before sequencing on an Illumina NextSeq Instrument.

value: paired sgRNA-target library harboring HEK293T


title: bulkrna seq of tumor biopsy, patient P-81

description: Library name: P-81

value: female

value: NUT Carcinoma


title: Disease_C_Lib_Tad-CBE(TCC1)

description: Library name: sample 37


title: Brain, WT, Female 1


title: Disease_C_Lib_Tad-CBE(ACT4)

description: Library name: sample 36


title: bulkrna seq of tumor biopsy, patient P-78

description: Library name: P-78

value: male

value: Myoepithelial Carcinoma


title: bulkrna seq of tumor biopsy, patient P-96

description: Library name: P-96

value: TRUE


title: single nuclei RNA seq of tumor biopsy, Patient 6

description:
Library name: P6
10x 3´GEX

value: Carcinosarcoma


title: single nuclei RNA seq of tumor biopsy, Patient 14

description:
Library name: P14
10x 3´GEX


title: Disease_C_Lib_Tad-CBE(GCA1)

description: Library name: sample 34


title: bulkrna seq of tumor biopsy, patient P-80

description: Library name: P-80

value: FALSE


title: bulkrna seq of tumor biopsy, patient P-79

description: Library name: P-79

value: skin


title: bulkrna seq of tumor biopsy, patient P-73

description: Library name: P-73


title: Fungus cells, Avicel medium, rep1

value: WT

value: Avicel


title: Disease_C_Lib_Tad-CBE(TCG2)

description: Library name: sample 35


title: bulkrna seq of tumor biopsy, patient P-46

description: Library name: P-46

value: Basal Cell Carcinoma

value: lung


title: Disease_C_Lib_Tad-CBE(GCG1)

description: Library name: sample 39


title: bulkrna seq of tumor biopsy, patient P-77

description: Library name: P-77

value: metastasis


title: bulkrna seq of tumor biopsy, patient P-44

description: Library name: P-44

value: tumor

value: Mucoepidermoid Carcinoma


title: bulkrna seq of tumor biopsy, patient P-77, biological replicate 2

description: Library name: P-77-1

value: Adenoid Cystic Carcinoma


title: Disease_C_Lib_Tad-CBE(CCG3)

description: Library name: sample 32

value: paired sgRNA-target library harboring HEK293T


title: bulkrna seq of tumor biopsy, patient P-66

description: Library name: P-66


title: bulkrna seq of tumor biopsy, patient P-75

description: Library name: P-75


title: Disease_C_Lib_Tad-CBE(ACG1)

description: Library name: sample 33


title: Brain, WT, Female 3

value: eye


title: 279.Coombes.Pre

city: STORRS MANSFIELD

first: Grace

last: Vaziri

address: 77 Forest Rd., Apt A

institute: University of Connecticut

data_processing:
We used Trimmomatic  to trim R1 reads to 28 bp to retain the 14 bp barcode and 14 bp UMI for each sample (all genomic sequencing data were contained in the R2 read).
Following the Alithea Genomics User Guide: BRB-seq Library Preparation kit (https://25700946.fs1.hubspotusercontent-eu1.net/hubfs/25700946/MERCURIUS-BRBseq-kit-PN-10813-10814-11013-11014-User-Guide-v0.7.1.revB.pdf ) we used the “solo” mode in the STAR aligner (Dobin et al., 2013) to simultaneously align reads and produce read count matrices.
We aligned R2 reads to the wood frog genome (GenBank Accession: JAQSEC000000000.1) and used barcode and UMI data from R1 to demultiplex and deduplicate samples and read counts, respectively.
Assembly: GenBank Accession: JAQSEC000000000.1
Supplementary files format and content: matrix file with three columns, the first column denoting the identity of the transcript, the second denoting the identity of the sample, and the third denoting the counts of each transcript per sample

organism: Lithobates sylvaticus

source_name: ventral skin

extract_protocol:
RNeasy Mini Kit (Qiagen)
Mercurius BRB-Seq (Alithea Genomics)
Tag-seq

value: ventral skin


title: bulkrna seq of tumor biopsy, patient P-45

description: Library name: P-45

value: female


title: bulkrna seq of tumor biopsy, patient P-62

description: Library name: P-62

value: Adenocarcinoma NOS

value: liver


title: bulkrna seq of tumor biopsy, patient P-76

description: Library name: P-76

value: Acinic Cell Carcinoma

value: TRUE


title: bulkrna seq of tumor biopsy, patient P-72

description: Library name: P-72

value: skullcap

value: FALSE


title: bulkrna seq of tumor biopsy, patient P-50

description: Library name: P-50


title: bulkrna seq of tumor biopsy, patient P-74

description: Library name: P-74

value: male


title: 16.CC.M


title: bulkrna seq of tumor biopsy, patient P-29

description: Library name: P-29

value: Salivary Duct Carcinoma


title: bulkrna seq of tumor biopsy, patient P-71

description: Library name: P-71


title: Disease_C_Lib_Tad-CBE(TCA3)

description: Library name: sample 31


title: Disease_C_Lib_Tad-CBE(ACC3)

description: Library name: sample 29


title: bulkrna seq of tumor biopsy, patient P-18

description: Library name: P-18


title: 52.ORI.M


title: Disease_C_Lib_Tad-CBE(CCT2)

description: Library name: sample 28


title: Disease_C_Lib_Tad-CBE3.1

description: Library name: sample 27


title: 40.Burke.H


title: bulkrna seq of tumor biopsy, patient P-9

description: Library name: P-9


title: 246.Woodstock.M


title: bulkrna seq of tumor biopsy, patient P-42

description: Library name: P-42

value: lung


title: single nuclei RNA seq of tumor biopsy, Patient 18

description:
Library name: P18
10x 3´GEX

value: lymphnode

value: Salivary duct carcinoma


title: bulkrna seq of tumor biopsy, patient P-69

description: Library name: P-69

value: tumor


title: Disease_C_Lib_Tad-CBE(CCC5)

description: Library name: sample 26


title: bulkrna seq of tumor biopsy, patient P-70

description: Library name: P-70

value: Adenoid Cystic Carcinoma


title: Disease_C_Lib_Tad-CBE(GCC3)

description: Library name: sample 30

value: paired sgRNA-target library harboring HEK293T


title: Disease_C_Lib_Tad-CBE(TCT1)

description: Library name: sample 25


title: 105.Barr.H


title: bulkrna seq of tumor biopsy, patient P-68

description: Library name: P-68


title: D1

city: Chongqing

first: Yaqi

last: Sui

state: --- Select One ---

address: Chongqing

institute: Chongqing University

description: Library name: Sample 10

data_processing:
ATAC-Seq high throughput sequencing and subsequent bioinformatics analysis were all done by Cloud-Seq Biotech (Shanghai, China). Briefly, raw data were generated after sequencing, image analysis, base calling, and quality filtering on the sequencer. Use fastp software (v 0.23.4) to remove joints and low-quality reads to obtain high-quality clean reads; And clean reads alignment to the reference genome using bowtie2 software (v2.2.4); The reads aligned to the chrM were removed using the samtools software (v1.9). PCR duplicates were removed using getki-picard software (v4); open chromatin regions (Peak Calling) using MACS2 software (v2.1.1); differential enriched regions were identified using diffReps software; and enrichment peaks were annotated using ChIPseeker software (v1.2.6). GO and KEGG pathway analysis were performed for genes associated with differentially enriched peaks.
Data processing: removing connectors, removing low-quality reads
Match genomes to obtain expression profile data
Differential analysis
GO, KEGG analysis
Assembly: HG38
Supplementary files format and content: xlsx files includes raw counts for each sample

extract_protocol:
ATAC sequencing service was provided by CloudSeq Biotech (Shanghai, China) with GenSeq® ATAC kit (GenSeq Inc.). Briefly, cells were lysed using cold lysis buffer. After lysis, nuclei were collected by centrifuging at 500 g for 10 min at 4℃. The pellet was transposed with transposome and add tags on the both sides of fragmented genomic DNA according to the manufacturer’s instruction. After tagmentation, the purified tagged DNA was used for PCR amplification with Genseq® 2×HiFi PCR Mix (GenSeq Inc.). The libraries were quantified using Qubit fluorometric assay (ThermoFisher) and then sequenced. in a NovaSeq platform (Illumina).
ATAC-seq


title: Disease_C_Lib_Tad-CBE(ACA1)

description: Library name: sample 24


title: D3

description: Library name: Sample 12


title: bulkrna seq of tumor biopsy, patient P-67

description: Library name: P-67

value: other


title: Disease_C_Lib_Tad-CBE2.4

description: Library name: sample 23


title: bulkrna seq of tumor biopsy, patient P-65

description: Library name: P-65


title: C2

description: Library name: Sample 8


title: 19.CC.H

value: ventral skin


title: 347.Coombes.Pre


title: bulkrna seq of tumor biopsy, patient P-64

description: Library name: P-64


title: Disease_C_Lib_Tad-CBE(GCT1)

description: Library name: sample 22


title: Disease_C_Lib_rAPOBEC1-BE4

description: Library name: sample 21


title: C1

description: Library name: Sample 7


title: D2

description: Library name: Sample 11


title: bulkrna seq of tumor biopsy, patient P-63

description: Library name: P-63

value: Carcinoma Ex-Pleomorphic Adenoma

value: metastasis


title: Disease_C_Lib_TadCBEd

description: Library name: sample 20


title: 260.Victory.M


title: bulkrna seq of tumor biopsy, patient P-61

description: Library name: P-61


title: 253.Victory.H


title: B2

description: Library name: Sample 5

value: siCtrl+BHB


title: bulkrna seq of tumor biopsy, patient P-60

description: Library name: P-60

value: Squamous Cell Carcinoma


title: B1

description: Library name: Sample 4


title: 319.Victory.Pre


title: 147.Barr.Pre


title: C3

description: Library name: Sample 9


title: Disease_C_Lib_Tad-CBE(GCC3)_UGI_minus

description: Library name: sample 18


title: bulkrna seq of tumor biopsy, patient P-59

description: Library name: P-59

value: TRUE


title: A3

description: Library name: Sample 3

value: siCtrl


title: A2

description: Library name: Sample 2


title: Disease_C_Lib_Tad-CBE(CCT2)_UGI_minus

description: Library name: sample 17


title: bulkrna seq of tumor biopsy, patient P-58, biological replicate 2

description: Library name: P-58-1

value: female


title: 313.Coombes.M


title: 294.Coombes.H


title: 121.Burke.Pre


title: Disease_C_Lib_Tad-CBE(TCG2)_UGI_minus

description: Library name: sample 15


title: bulkrna seq of tumor biopsy, patient P-58

description: Library name: P-58


title: bulkrna seq of tumor biopsy, patient P-57

description: Library name: P-57


title: A1

description: Library name: Sample 1


title: U937 6h IFNg rep4

city: Durham

first: Jörn

last: Coers

state: NC

address: 3 Genome Ct

institute: Duke University

description:
Library name: Sample 40
40-U937-IFN-4

data_processing:
RNA-seq data was processed using the fastp toolkit to trim low-quality bases and sequencing adapters from the 3’ end of reads, then mapped to GRCh38 (downloaded from Ensembl, version 106) using the STAR RNA-seq alignment tool. Reads aligning to a single genomic location were summarized across genes.
Assembly: GRCh38 (downloaded from Ensembl, version 106)
Supplementary files format and content: csv file with raw counts for each sample

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen)
RNA libraries were prepared using KAPA mRNA HyperPrep


title: B3

description: Library name: Sample 6


title: Disease_C_Lib_Tad-CBE(ACG1)_UGI_minus

description: Library name: sample 19


title: 84.Barr.M


title: U937 untreated rep4

description:
Library name: Sample 39
39-U937-4


title: Disease_C_Lib_Tad-CBE(GCT1)_UGI_minus

description: Library name: sample 13


title: bulkrna seq of tumor biopsy, patient P-56

description: Library name: P-56

value: FALSE


title: Disease_C_Lib_Tad-CBE(TCC1)_UGI_minus

description: Library name: sample 14


title: bulkrna seq of tumor biopsy, patient P-55

description: Library name: P-55


title: U937 6h IFNg rep3

description:
Library name: Sample 38
38-U937-IFN-3


title: 72.ORI.M


title: 71.ORI.H


title: bulkrna seq of tumor biopsy, patient P-54

description: Library name: P-54


title: U937 untreated rep3

description:
Library name: Sample 37
37-U937-3


title: Disease_C_Lib_Tad-CBE(GCG1)_UGI_minus

description: Library name: sample 12


title: 146.Barr.Pre


title: Disease_C_Lib_Tad-CBE3.1_UGI_minus

description: Library name: sample 16


title: Disease_C_Lib_Tad-CBE(TCT1)_UGI_minus

description: Library name: sample 11


title: 108.ORI.Pre


title: U937 6h IFNg rep2

description:
Library name: Sample 36
36-U937-IFN-2


title: bulkrna seq of tumor biopsy, patient P-51

description: Library name: P-51

value: male

value: Epitheloid Sarcoma


title: Disease_C_Lib_Tad-CBE(ACC3)_UGI_minus

description: Library name: sample 10


title: 327.Victory.Pre


title: U937 untreated rep2

description:
Library name: Sample 35
35-U937-2


title: 206.Woodstock.M


title: U937 6h IFNg rep1

description:
Library name: Sample 34
34-U937-IFN-1


title: Disease_C_Lib_Tad-CBE(GCA1)_UGI_minus

description: Library name: sample 9


title: bulkrna seq of tumor biopsy, patient P-49

description: Library name: P-49

value: Adenocarcinoma NOS

value: skin


title: 11.CC.H


title: U937 untreated rep1

description:
Library name: Sample 33
33-U937-1


title: bulkrna seq of tumor biopsy, patient P-48

description: Library name: P-48

value: tumor


title: Disease_C_Lib_Tad-CBE2.4_UGI_minus

description: Library name: sample 8


title: 119.Burke.Pre


title: Disease_C_Lib_Tad-CBE(CCC5)_UGI_minus

description: Library name: sample 7


title: THP1 6h IFNg rep4

description:
Library name: Sample 32
32-THP1-IFN-4


title: Disease_C_Lib_Tad-CBE(CCG3)_UGI_minus

description: Library name: sample 6


title: bulkrna seq of tumor biopsy, patient P-43

description: Library name: P-43

value: Salivary Duct Carcinoma

value: lung


title: THP1 untreated rep4

description:
Library name: Sample 31
31-THP1-4


title: 312.Coombes.H


title: Disease_C_Lib_Tad-CBE(TCA3)_UGI_minus

description: Library name: sample 5

value: paired sgRNA-target library harboring HEK293T


title: bulkrna seq of tumor biopsy, patient P-52

description: Library name: P-52

value: Adenoid Cystic Carcinoma


title: THP1 6h IFNg rep3

description:
Library name: Sample 30
30-THP1-IFN-3


title: bulkrna seq of tumor biopsy, patient P-41

description: Library name: P-41


title: 251.Woodstock.H

value: ventral skin


title: bulkrna seq of tumor biopsy, patient P-40

description: Library name: P-40


title: Disease_C_Lib_Tad-CBE(ACT4)_UGI_minus

description: Library name: sample 4


title: THP1 untreated rep3

description:
Library name: Sample 29
29-THP1-3


title: 137.CC.Pre


title: Disease_C_Lib_Tad-CBE(ACA1)_UGI_minus

description: Library name: sample 3


title: 259.Victory.Pre


title: THP1 6h IFNg rep2

description:
Library name: Sample 28
28-THP1-IFN-2


title: Disease_C_Lib_BE4_UGI_minus

description: Library name: sample 2


title: bulkrna seq of tumor biopsy, patient P-38

description: Library name: P-38

value: Mucoepidermoid Carcinoma


title: THP1 untreated rep2

description:
Library name: Sample 27
27-THP1-2


title: bulkrna seq of tumor biopsy, patient P-47

description: Library name: P-47

value: metastasis


title: 222.Coombes.M


title: Disease_C_Lib_Tad-CBE(CCA2)_UGI_minus

description: Library name: sample 1


title: 83.Barr.H


title: bulkrna seq of tumor biopsy, patient P-36

description: Library name: P-36


title: THP1 6h IFNg rep1

description:
Library name: Sample 26
26-THP1-IFN-1


title: THP1 untreated rep1

description:
Library name: Sample 25
25-THP1-1


title: 25.CC.H


title: Disease_C_Lib_TadCBEd_UGI_minus

description: Library name: sample 0


title: 59.ORI.H


title: PBMC, SARS-CoV-2, UNC0642, m6A-IP, rep 1

city: Chapel Hill

first: John

last: Wrobel

address: 120 Mason Farm Rd

department: Department of Biochemistry and Biophysics

institute: University of North Carolina

description:
Library name: ip_ps6_UNC0642
ip_ps6_UNC0642

data_processing:
Raw sequencing data were de-multiplexed using bcl2fastq2 v2.17.1.14 (Illumina) and adapters were removed using Trimmomatic-0.32 software. Then the Input and m6A-IP reads were mapped to a combined reference genome consisting of human (GRCh38/hg38) and Ensembl SARS-CoV-2 isolate Wuhan-Hu-1 genomes (Genome Assembly: ASM985889v3, Accession: GCA_009858895.3; Sequence: MN908947.3) using STAR v.2.7.6a. Only uniquely mapping reads at the exon level for each gene were quantified and summarized to gene counts. Differential gene expression analysis was performed using DESeq2 v.1.32.0. Resulting bam files were sorted and indexed using SAMtools v.1.1, and MACS2 v.2.2.7.1 was used for m6A peak calling using the bam files for each m6A-IP/input pair.
Assembly: GRCh38/hg38
Supplementary files format and content: Space-delimited text file for gene expression matrix (A549_rawcount.txt). Tab-delimited text files for gene expression matrix (PBMC_salmon_gene.matrix.txt) and m6A peaks (macs2).

source_name: PBMCs

extract_protocol:
The m6A/MeRIP-Seq was performed as described with some modifications [Neuron 97, 313-325.e6 (2018)]. Briefly, total RNA was extracted from A549-hACE2 and patient PBMCs using TRIzol (Life Technologies) followed by purification using illustra RNA spin Mini kit (GE Healthcare, UK). mRNA was isolated from 10 μg total RNA using Dynabeads Oligo (dT)25 (Thermo Fisher; 61006) according to manufacturer’s instructions. Ten percent of a total of 150 ng mRNA was used as input, while the rest was incubated with 3 ug anti-m6A polyclonal antibody (Synaptic Systems; 202003) that was pre-conjugated to Dynabeads Protein A (Thermo Fisher; 10001D) in 500 uL IP buffer (50 mM Tris, pH 7.4, 150 mM NaCl, 0.1% Igepal CA-630) for 2 hours at 4°C. After washing the beads twice with IP-buffer and twice with high-salt wash buffer (50 mM Tris pH 7.4, 500 mM NaCl, 0.1% Igepal CA-630) for 5 minutes each, the m6A-tagged mRNA was eluted using 100 uL IP-buffer containing 6.7 mM N6-Methyladenosine (Sigma-Aldrich; M2780) and 40 U RNase Inhibitor (NEB, M0314S) and then recovered with RNA Clean and Concentrator-5 spin columns (Zymo; R1015).
The input and m6A-IPed mRNA were subjected to library generation using the SMART-seq protocol as described [Nature Protocols 9, 171-181 (2014)]. For first strand cDNA synthesis, the mRNA was mixed with 0.25 µL RNase inhibitor and 1 µL CDS primer (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’) and heated to 70 °C for 2 min. Then the mixture containing 0.5 µL of 100 mM DTT, 0.3 µL of 200 mM MgCl2, 1 µL of 10 mM dNTPs, 0.25 µL RNase inhibitor, 1 µL of 10 µM TSO primer (5’-AAGCAGTGGTATCAACGCAGAGTACATrGrGrG-3’), 2 µL of 5X SMARTScribe RT buffer and 0.5 µL SMARTScribe reverse transcriptase (Takara, 639536) was added to perform reverse transcription. The cDNA was then amplified by Advantage Polymerase Mix (TAKARA, 639201) with IS primer (5’-AAGCAGTGGTATCAACGCAGAGT-3’). After purification with 0.8X AMPure XP beads (Fisher Scientific, A63880), the fragmentation of 100 pg cDNA was performed with EZ Tn5 Transposase (Lucigen, TNP92110). Fragments of cDNA were amplified by KAPA HiFi hotstart readymix (EMSCO/FISHER, KK2601) with the Nextera i7 primer and Nextera i5 primer. The DNA was purified with 0.8X AMPure XP beads and quantified by qPCR with KAPA Library Quantification Kit (Fisher, NC0078468). The DNA from different samples was pooled at equal molar amounts, and the final sequencing library was loaded at concentrations of 2.7 pM and sequenced on a NextSeq 550 (Illumina) for single-end sequencing.

value: PBMCs

tag: infection

tag: m6a ip

value: IP

tag: rip antibody

tag: replicate


title: T24 6h IFNg rep4

description:
Library name: Sample 24
24-T24-IFN-4


title: bulkrna seq of tumor biopsy, patient P-34

description: Library name: P-34


title: bulkrna seq of tumor biopsy, patient P-35

description: Library name: P-35

value: TRUE


title: 277.Coombes.Pre


title: bulkrna seq of tumor biopsy, patient P-33

description: Library name: P-33


title: PBMC, SARS-CoV-2, UNC0642, Input, rep 1

description:
Library name: input_ps6_UNC0642
input_ps6_UNC0642

tag: cell type

tag: treatment

value: input


title: T24 6h IFNg rep3

description:
Library name: Sample 22
22-T24-IFN-3

tag: cell line


title: T24 untreated rep4

description:
Library name: Sample 23
23-T24-4


title: 350.Coombes.M

tag: tissue


title: T24 untreated rep3

description:
Library name: Sample 21
21-T24-3


title: bulkrna seq of tumor biopsy, patient P-28

description: Library name: P-28


title: 266.Woodstock.H


title: bulkrna seq of tumor biopsy, patient P-32

description: Library name: P-32

value: female

value: FALSE


title: PBMC, SARS-CoV-2, no treatment, m6A-IP, rep 1

description:
Library name: ip_ps6_ctrl
ip_ps6_ctrl

value: anti-m6A polyclonal antibody (Synaptic Systems; 202003)


title: A549-hACE2, SARS-CoV-2, UNC0642, Input, rep 2

description:
Library name: SARS_UNC2_Input
SARS_UNC2_Input


title: 139.Barr.Pre


title: 249.Woodstock.H


title: T24 untreated rep1

description:
Library name: Sample 17
17-T24-1


title: bulkrna seq of tumor biopsy, patient P-37

description: Library name: P-37

value: male

value: Rhabdomyosarcoma


title: PBMC, SARS-CoV-2, no treatment, Input, rep 1

description:
Library name: input_ps6_ctrl
input_ps6_ctrl


title: bulkrna seq of tumor biopsy, patient P-23

description: Library name: P-23

value: tumor

value: Basal Cell Carcinoma


title: bulkrna seq of tumor biopsy, patient P-30

description: Library name: P-30

value: Acinic Cell Carcinoma

value: other


title: T24 6h IFNg rep2

description:
Library name: Sample 20
20-T24-IFN-2


title: A549-hACE2, SARS-CoV-2, UNC0642, m6A-IP, rep 2

description:
Library name: SARS_UNC2_IP
SARS_UNC2_IP


title: 64.ORI.M


title: HeLa untreated rep4

description:
Library name: Sample 15
15-HeLa-4

source_name: HeLa

value: HeLa


title: 134.CC.Pre

value: ventral skin


title: bulkrna seq of tumor biopsy, patient P-27

description: Library name: P-27

value: Mucoepidermoid Carcinoma


title: bulkrna seq of tumor biopsy, patient P-26

description: Library name: P-26

value: metastasis


title: T24 untreated rep2

description:
Library name: Sample 19
19-T24-2


title: A549-hACE2, SARS-CoV-2, no treatment, Input, rep 1

description:
Library name: SARS_ctrl1_Input
SARS_ctrl1_Input


title: 106.Barr.M


title: A549-hACE2, SARS-CoV-2, UNC0642, Input, rep 1

description:
Library name: SARS_UNC1_Input
SARS_UNC1_Input


title: T24 6h IFNg rep1

description:
Library name: Sample 18
18-T24-IFN-1


title: bulkrna seq of tumor biopsy, patient P-24

description: Library name: P-24

value: Adenoid Cystic Carcinoma


title: A549-hACE2, SARS-CoV-2, UNC0642, m6A-IP, rep 1

description:
Library name: SARS_UNC1_IP
SARS_UNC1_IP

value: IP


title: HeLa 6h IFNg rep4

description:
Library name: Sample 16
16-HeLa-IFN-4


title: HeLa untreated rep3

description:
Library name: Sample 13
13-HeLa-3


title: A549-hACE2, SARS-CoV-2, no treatment, m6A-IP, rep 2

description:
Library name: SARS_ctrl2_IP
SARS_ctrl2_IP


title: bulkrna seq of tumor biopsy, patient P-19

description: Library name: P-19

value: TRUE


title: 269.Woodstock.M


title: 57.ORI.H


title: A549-hACE2, SARS-CoV-2, no treatment, Input, rep 2

description:
Library name: SARS_ctrl2_Input
SARS_ctrl2_Input

value: input


title: 6.CC.M


title: bulkrna seq of tumor biopsy, patient P-20

description: Library name: P-20

value: female


title: 316.Victory.M


title: HeLa 6h IFNg rep3

description:
Library name: Sample 14
14-HeLa-IFN-3


title: A549-hACE2, mock, UNC0642, m6A-IP, rep 2

description:
Library name: Mock_UNC2_IP
Mock_UNC2_IP

value: mock


title: bulkrna seq of tumor biopsy, patient P-16

description: Library name: P-16


title: HeLa 6h IFNg rep2

description:
Library name: Sample 12
12-HeLa-IFN-2


title: 274.Victory.M


title: A549-hACE2, mock, UNC0642, m6A-IP, rep 1

description:
Library name: Mock_UNC1_IP
Mock_UNC1_IP

value: anti-m6A polyclonal antibody (Synaptic Systems; 202003)


title: bulkrna seq of tumor biopsy, patient P-14

description: Library name: P-14

value: male

value: Adenocarcinoma NOS

value: lung


title: 42.Burke.H


title: A549-hACE2, mock, UNC0642, Input, rep 2

description:
Library name: Mock_UNC2_Input
Mock_UNC2_Input


title: A549-hACE2, mock, UNC0642, Input, rep 1

description:
Library name: Mock_UNC1_Input
Mock_UNC1_Input


title: bulkrna seq of tumor biopsy, patient P-22

description: Library name: P-22

value: tumor


title: HeLa untreated rep2

description:
Library name: Sample 11
11-HeLa-2


title: bulkrna seq of tumor biopsy, patient P-12

description: Library name: P-12

value: FALSE


title: 104.Barr.M


title: A549-hACE2, SARS-CoV-2, no treatment, m6A-IP, rep 1

description:
Library name: SARS_ctrl1_IP
SARS_ctrl1_IP


title: HeLa 6h IFNg rep1

description:
Library name: Sample 10
10-HeLa-IFN-1


title: 2.CC.M


title: 203.Woodstock.Pre


title: bulkrna seq of tumor biopsy, patient P-15

description: Library name: P-15


title: HeLa untreated rep1

description:
Library name: Sample 9
9-HeLa-1


title: A549 6h IFNg rep4

description:
Library name: Sample 8
8-A549-IFN-4


title: bulkrna seq of tumor biopsy, patient P-13

description: Library name: P-13

value: Salivary Duct Carcinoma


title: A549 untreated rep4

description:
Library name: Sample 7
7-A549-4


title: A549 6h IFNg rep3

description:
Library name: Sample 6
6-A549-IFN-3


title: A549-hACE2, mock, no treatment, Input, rep 2

description:
Library name: Mock_ctrl2_Input
Mock_ctrl2_Input


title: bulkrna seq of tumor biopsy, patient P-8

description: Library name: P-8


title: bulkrna seq of tumor biopsy, patient P-11

description: Library name: P-11

value: Adeno-neuroendocrine Carcinoma


title: A549-hACE2, mock, no treatment, m6A-IP, rep 1

description:
Library name: Mock_ctrl1_IP
Mock_ctrl1_IP


title: bulkrna seq of tumor biopsy, patient P-10

description: Library name: P-10


title: 218.Coombes.M

value: ventral skin


title: A549-hACE2, mock, no treatment, Input, rep 1

description:
Library name: Mock_ctrl1_Input
Mock_ctrl1_Input


title: A549-hACE2, mock, no treatment, m6A-IP, rep 2

description:
Library name: Mock_ctrl2_IP
Mock_ctrl2_IP


title: A549 untreated rep3

description:
Library name: Sample 5
5-A549-3


title: A549 untreated rep2

description:
Library name: Sample 3
3-A549-2


title: bulkrna seq of tumor biopsy, patient P-6

description: Library name: P-6

value: Carcinosarcoma


title: skMt_GSDIII_Patient4_GM2523_n3

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

institute: I-Stem

data_processing:
QC: FastQC ( v0.11.9 )
Filters: cutadapt ( 1.18 ), PRINSEQ-lite ( 0.20.4 )
Mapping & QC: STAR ( 2.7.6a ), samtools ( 0.1.18 )
Counting: HTSeq-count ( 0.12.4 ), DEG R (4.3) DESeq2
Assembly: EnsEMBL Human GRCh97.87
Supplementary files format and content: Differential gene expression ( RNAseq82_hipsc_DE.xlsx )

source_name: hIPSC derived Myotubes

growth_protocol: Myoblasts (SkMb) were thawed on collagen I-coated plates in skeletal myoblast medium (#SKM02, AMSBIO, United Kingdom) and incubated at confluence with skeletal muscle differentiation medium (#SKM03, AMSBIO, United Kingdom) for three supplementary days to obtain myotubes (skMt).

extract_protocol:
Human skMt were lysed with RLT Plus buffer (#1030963, Qiagen, Germany). Mouse triceps biopsies were lysed with bead lysis tubes (#740814.50, Macherey-Nagel, Germany) using Qiazol (#79306, Qiagen, The Netherlands) and chloroform (#102444, Sigma-Aldrich, USA) reagents. Total RNA was isolated using an RNeasy Plus Mini extraction kit (#74134, Qiagen, Germany) according to the manufacturer’s instructions. DNase I digestion (Invitrogen, USA) was performed to degrade DNA in the sample.  RNA levels and quality were checked using the NanoDrop® spectrophotometer (ThermoFisher Scientific, United States).
For each sample, 100 ng of total RNA was used to perform the QuantSeq 3' mRNA-Seq Library Prep FWD for Illumina (Lexogene, Vienna, Austria) resulting in NGS libraries which originate from the 3' end of polyadenylated RNA. Briefly, library generation was started by oligo(dT) priming with primers. After first strand synthesis, the RNA was removed before the second strand synthesis was initiated by random primers. Libraries were PCR amplified and barcoded in 17 cycles and were quantified using Agilent High Sensitivity DNA kit (Agilent). 2nM of pooled libraries were denatured and 1.8pM was used for cluster generation before single-end sequencing on an Illumina Nextseq550 (Illumina, US).
strategy: 3’-seq

treatment_protocol: Myotubes (skMt) were then incubated with glucose-free DMEM (#11966-025, ThermoFisher Scientific, United States) supplemented with 10% Fetal Bovine Serum (#F7524, Sigma-Aldrich, United States) for 2,5 supplementary days.

value: hIPSC derived Myotubes

tag: genotype

value: GSDIII


title: bulkrna seq of tumor biopsy, patient P-7

description: Library name: P-7

tag: Sex

value: Acinic Cell Carcinoma

value: metastasis


title: A549 6h IFNg rep2

description:
Library name: Sample 4
4-A549-IFN-2


title: 219.Coombes.H


title: skMt_GSDIII_Patient4_GM2523_n1


title: 262.Woodstock.M


title: 267.Woodstock.Pre


title: A549 6h IFNg rep1

description:
Library name: Sample 2
2-A549-IFN-1


title: skMt_GSDIII_Patient4_GM2523_n2


title: A549 untreated rep1

description:
Library name: Sample 1
1-A549-1


title: bulkrna seq of tumor biopsy, patient P-5

description: Library name: P-5

tag: pid

value: Adenoid Cystic Carcinoma

value: TRUE


title: 62.ORI.M


title: bulkrna seq of tumor biopsy, patient P-4

description: Library name: P-4

value: female

tag: age


title: 132.CC.Pre


title: skMt_GSDIII_Patient3_GM0303_n2


title: bulkrna seq of tumor biopsy, patient P-3

description: Library name: P-3

tag: entity long


title: 204.Woodstock.Pre


title: H3K27me3 loss sample7

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description: Library name: H3K27me3 loss sample7 -293388

data_processing:
Amplified, target-enriched libraries were pooled equimolarly and sequenced on an Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA), employing a 2x 100-cycle paired-end sequencing strategy
FASTQ files were generated using Illumina’s bclconvert v3.10.5 and trimmed with Agilent Locatit v3.0
The RNA sequencing reads were aligned to the Gencode GRCh38.primary_assembly reference genome using STAR29 (v2.7.7a).
Gene-level quantification was conducted with HTSeq30 (v0.11.0) using Gencode V39 primary assembly annotations.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw values for each Sample.

source_name: FFPE

growth_protocol: Total RNA was extracted from formalin-fixed, paraffin-embedded (FFPE) tissue samples using the Maxwell RSC RNA FFPE Kit (Promega, Madison, WI, USA) on the automated Maxwell RSC 48 instrument (Promega)

extract_protocol:
RNA-seq libraries were prepared from total RNA using the TruSeq Stranded mRNA kit (Illumina, Inc., San Diego, CA, USA). Library size distribution was validated using an Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA, USA).  Additional library QC, blending of pooled indexed libraries, and cluster optimization was performed using Life Technologies’ Invitrogen Qubit® 2.0 Fluorometer (Life Technologies-Invitrogen, Carlsbad, CA, USA).
RNA-seq libraries were pooled (70-plex) and clustered onto an P2-100 flow cell.

treatment_protocol: untreated

value: FFPE

value: H3K27me3 loss


title: bulkrna seq of tumor biopsy, patient P-1

description: Library name: P-1

value: male

tag: site 1_biopsy


title: H3K27me3 loss sample6

description: Library name: H3K27me3 loss sample6 -293386


title: 110.ORI.Pre


title: skMt_GSDIII_Patient3_GM0303_n1


title: H3K27me3 loss sample5

description: Library name: H3K27me3 loss sample5 -293368


title: 41.Burke.M


title: skMt_GSDIII_Patient2_GM3390_n3


title: skMt_GSDIII_Patient2_GM3390_n2


title: MapID-tRNA-seq, "+AlkB", replicate2, MCF7

city: Chestnut Hill

first: Huiqing

last: Zhou

state: Massachusetts

address: 2609 Beacon St.

institute: Boston College

library_source: other

data_processing:
PCR dupilcates were removed by the Raw data (R2 reads of the pair-end data) were first processed with the “clumpify.sh” program in the BBMap package (BBMap-Bushnell B.-sourceforge.net/projects/bbmap/) with the option “dedupe subs=0” to remove PCR duplicates.
Adaptors were trimmed by the “cutadapt” program
Reads were aligned to the hg19 human tRNA genome, with intron removal and added CCA end, using bowtie2 aligner
Single base reads counting were performed with bam-readcount and expression are quantified by salmon
Assembly: hg19
Supplementary files format and content: .sf files containing read counts per tRNA

molecule: other

source_name: MCF7 cells

extract_protocol:
RNA samples were extracted from MCF10A, MCF7 and MDA-MB-231 cells using the TRIzol reagent and standard protocol; tRNA 5s and 5.8srRNA were purified by denaturing PAGE.
Libraries were constructed using ligation-based library construction approach incoporating the evolved RT, RT-1306, in the current work.

value: MCF7 cells


title: 256.Victory.M


title: MapID-tRNA-seq, "+AlkB", replicate1, MCF7


title: skMt_GSDIII_Patient2_GM3390_n1


title: 92.Barr.M


title: H3K27me3 loss sample3

description: Library name: H3K27me3 loss sample3 -293358


title: H3K27me3 loss sample2

description: Library name: H3K27me3 loss sample2 -87182


title: skMt_GSDIII_Patient3_GM0303_n3


title: MapID-tRNA-seq, "-AlkB", replicate2, MCF7


title: skMt_GSDIII_Patient1_GM0576_n3


title: skMt_GSDIII_Patient1_GM0576_n2


title: MapID-tRNA-seq, "-AlkB", replicate1, MCF7


title: 300.Victory.H


title: MapID-tRNA-seq, "+AlkB", replicate2, MDA-BA-231

source_name: MDA-MB-231 cells

value: MDA-MB-231 cells


title: 37.Burke.H


title: 271.Victory.H


title: MapID-tRNA-seq, "+AlkB", replicate1, MDA-BA-231


title: skMt_CTRL2_iCas9_n3

value: WT


title: BAP1 sample12

description: Library name: BAP1 sample12 -131814


title: 45.Burke.M


title: 142.Barr.Pre


title: MapID-tRNA-seq, "-AlkB", replicate2, MDA-BA-231