title: Skeletal muscle, Balbc_GR3

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

description:
mice_muscle_Balbc_GLR_RNA_seq_rpkm.txt
BGR4A

data_processing:
RNA-seq raw files (fastq, SE50) were aligned to the GRCm38/mm10 version of the mouse reference genome, using HISAT2 with default parameters. Read counts were imported by HOMER and analyzed using analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for four replicates per condition.  Differential gene expression was performed with DESeq2 using HOMER’s getDiffExpression.pl using default parameter. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
HISAT2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: GRCm38/mm10
Supplementary files format and content: Bedgraph files contain the gene expression tags counts and p-value.
Supplementary files format and content: The differential expression file was further provided (tab-delimited file).

source_name: Skeletal muscle

growth_protocol: Mice were maintained under standard housing conditions and received a regular diet.

extract_protocol:
Total cellular RNA was extracted using the RNA Rapid Extraction Kit (Vazyme, Nanjing, China) and total tissue RNA was extracted using Trizol (Vazyme), according to the reagent instructions.
The RNA-seq library preparation was followed by the instructions of LC Bio Technology CO., Ltd.

treatment_protocol: The mice were anesthetized with inhaled isoflurane, placed on the operating table in the prone position, and the skin was prepared in the surgical area of the right hind limb; a surgical incision of 6-8 mm in length was made in the middle of the right posterior femur to expose the biceps femoris muscle and the pyriformis muscle, and bluntly isolate and expose the sciatic nerve; the sciatic nerve was cut 1 cm below the lower edge of the pyriformis muscle, and a notch of 1.5 cm was prepared in each end; the two severed ends of the nerves were turned over by 180° and  sutured to the adjacent muscle tissue, and the muscle and skin were sutured layer by layer. In the sham-operated group, only the sciatic nerve was exposed, but no nerve amputation was performed. Two weeks after surgery, the gastrocnemius muscle was selected for the experiment.

value: Skeletal muscle

value: BALB/c

value: Male

value: neuron-denervated (Den); right leg muscles (Muscle atrophy)


title: Skeletal muscle, Balbc_GR2

status: Public on Oct 31 2024

type: SRA

city: Nanjing

country: China

institute: Nanjing University

description:
mice_muscle_Balbc_GLR_RNA_seq_rpkm.txt
BGR2A

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: strain

tag: Sex

tag: genotype

value: WT

tag: treatment


title: RNA.prefrontal cortex.WT.male.NQ3

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

country: USA

institute: The University of Pennsylvania

description:
NQ3PFC_S27
Counts.Males.txt

data_processing:
Alignment: sequencing data were aligned to mouse genome assembly GRCm38/mm10 using STAR v2.5.2a with command-line parameters --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --readFilesCommand zcat --outFilterMismatchNoverReadLmax 0.04. The STAR index was constructed GENCODE M25 annotation (ENSEMBL 100 assembly).
Filtering: aligned data were filtered for poor mapping tags using samtools v1.1 subcommand view -bS -q 255.
Pooling: filtered data from two flowcells (*FC1.*, *FC2.*, i.e., technical repeat samples from two flowcells) were combined using samtools merge and aligned tags were sorted by chromosome position and indexed using samtools sort and index, respectively.
Quantitation: HTseq v0.6.1 was used to quantify tag counts over exons with command-line parameters -f bam -r pos -s reverse -t exon -i gene_id --additional-attr=gene_name.
Analysis: differentially expressed genes (DEGs) between ACSS2 KO and WT samples were detected separately in each tissue and each sex using DESeq2 in R v4.0.2 with the FDR controlled at 0.1. Sexes were analyzed separately and so the uploaded gene counts tables are also separated by sex.
Assembly: GRCm38 / mm10
Supplementary files format and content: Counts.Males.txt and Counts.Females.txt contain the results of HTSeq run on all male or female samples, respectively.

molecule: total RNA

source_name: prefrontal cortex

growth_protocol: We used CRISPR/Cas9 technology to generate constitutive ACSS2 KO mice as previously described (Alexander et al, PNAS 2022, PMID: 35921439). Pairs of single-guide RNAs (sgRNA) targeting intronic regions of the Acss2 locus upstream of exon 3 and downstream of exon 7 were designed with the CRISPOR online tool (crispor.org) using the mm10 genome assembly as template. The resulting guides (5'[exon 3]) were selected to maximize specificity while retaining high on-target efficiency. sgRNAs were synthesized by in vitro transcrip- tion (T7 High Yield RNA Synthesis Kit; NEB, E2040S). Cas9 mRNA (100 ng/μL; Trilink, L-6125) and both sgRNAs (100 ng/μL each) were diluted in injection buffer (10 mM Tris, pH 7.5; 0.1 mM EDTA). This mix was injected into the cyto- plasm of single-cell C57Bl6/J mouse embryos. Resulting founder mice were screened for the desired deletion using primer pairs amplified across each cut site. Sanger sequencing confirmed sites of nonhomologous end joining. To reduce off-target effects, founder mice were backcrossed to C57Bl6/J mice (Jackson Laboratories) for three generations.

extract_protocol:
Briefly, total RNA was extracted using Trizol-chloroform. Total RNA quality was assessed on the Bioanalyzer platform using the RNA 6000 Nano assay (Agilent). mRNA was isolated from 300 ng total RNA using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490L).
Libraries were prepared using the NEBNext® UltraTM II RNA Library Prep Kit for Illumina® (E7770).

treatment_protocol: Single-housed adult mice of both sexes were allowed to voluntarily consume ethanol in the drinking-in-the-dark (DID) paradigm, an extensively used rodent model of binge-like drinking. During the habituation period, mice were acclimated to having two bottles (2BC) in the housing cage. Following the 1-week habituation period, ethanol intake was evaluated in the DID-2BC paradigm. For this, mice had access to 15% (v/v) ethanol and water for 2 h on days 1-3 and 4 h on day 4. The position of the bottles was alternated daily to avoid side preference. On the second week of DID, mice had access to 15% ethanol in a similar schedule, but water was not available during the drinking session (DID-1B). All drinking sessions started 1.0-1.5 h into the dark phase of the light cycle. Bottles were weighed to the nearest hundredth at the beginning and end of each DID session to determine fluid consumption. Mice were weighed at the beginning of each DID session to determine ethanol dose (g/kg). Ethanol consumption was calculated using r15_ethanol=0.97897 g/mL and r100_ethanol=0.789 g/mL. Ethanol preference was calculated as the ratio of ethanol to total fluid intake (mL ethanol solution/mL total fluid).

value: prefrontal cortex

value: male

value: DiD 2BC + 1B

tag: mouse id


title: Brain, glioblastoma, rep5

city: Debrecen

first: Zsuzsanna

last: Birkó

address: Egyetem tér 1.

department: Humangenetics

country: Hungary

institute: University of Debrecen

data_processing:
Fastq data were generated by BaseSpace (Illumina)
Raw sequencing data (fastq) was aligned to human reference genome version GRCh38 using Novoalign algorithm and BAM files were generated
Downstream analysis was performed using StrandNGS software (Deseq) where the FPKM values were generated
Assembly: GRCh38 human reference genome
Supplementary files format and content: FPKM values of each samples
Supplementary files format and content: tab-delimited matrix text file that include the FPKM values for each Sample

organism: Homo sapiens

source_name: Brain

extract_protocol:
Total RNA including small RNAs was isolated by the miRNeasy Mini Kit (Qiagen) according to the protocol provided by the manufacturer.
Library preparation was performed by the NEBNext Multiplex Small RNA Perp Set for Illumina (1-48) 96 rxn kit (New England BioLabs) according to the protocol provided by the manufacturer.

value: Brain

tag: disease state

value: glioblastoma


title: Tree Shrew Primary Neurons, PBS-4, 24h, rep4

city: Kunming City

first: shu wei

last: zhang

state: Yunnan Province

address: Chenggong District

department: School of Forensic Medicine

institute: Kunming Medical University

data_processing:
After constructing the library, a preliminary quantification was performed using Qubit 2.0, and the library was diluted to 2 ng/µL. The insert size of the library was then assessed with the Agilent 2100 Bioanalyzer. Once the insert size met the expected criteria, the effective concentration of the library was accurately quantified using qPCR (quantitative PCR). Ensuring that the effective concentration of the library is above 2 nM guarantees the quality of the library.
After the library passes quality control, different libraries should be pooled according to their effective concentrations and the desired sequencing data output. The pooled libraries are then subjected to sequencing using the Illumina HiSeq or MiSeq platforms.
The raw image data files generated from high-throughput sequencing platforms, such as the Illumina HiSeq 2500, are converted into sequencing reads through a process known as Base Calling. These sequencing reads are referred to as Raw Data or Raw Reads. The results are stored in the FASTQ (fq) file format, which includes both the sequence information of the reads and their corresponding quality scores.
The raw reads obtained from sequencing contain adapters and low-quality reads. To ensure the quality of downstream data analysis, it is essential to process the raw reads to obtain clean reads.
Assembly: ASM18137v1
Supplementary files format and content: Readcount_TPM txt files inlude readcount values for each sample

organism: Tupaia belangeri

source_name: brain

growth_protocol: Place the culture plates in a CO2 incubator set to 5% CO2, 37°C, and 95% humidity, and cultivate the cells using a complete neuronal medium. The composition of the complete medium includes Neurobasal-A, 15% fetal bovine serum, 2% penicillin/streptomycin, 2% B-27 supplement, and 2% L-glutamine.

extract_protocol:
Agarose gel electrophoresis was used to assess the degree of RNA degradation and potential contamination. The purity of the RNA (OD260/280 ratio) was measured using Nanodrop, while the RNA concentration was precisely quantified with Qubit. The integrity of the RNA was accurately evaluated using the Agilent 2100 Bioanalyzer.
Using the Smal RNA Sample Prep Kit, a library was constructed by leveraging the unique structures of the 3' and 5' ends of small RNA (with a complete phosphate group at the 5' end and a hydroxyl group at the 3' end). Starting with B RNA as the initial sample, adapters were directly added to both ends of the small RNA, followed by reverse transcription to synthesize DNA. The resulting DNA was then amplified by PCR, and the target DNA fragments were separated by PAGE gel electrophoresis. The desired cDNA library was obtained by excising and recovering the gel fragments.

treatment_protocol: When the primary neurons of the tree shrew reach 80% confluency, aspirate the culture medium from the flasks and rinse the cells 1-2 times with PBS. For the control group, add 1ml of complete neuronal medium per well. For the METH group, add 995μl of complete neuronal medium and 5μl of 100mmol METH per well. After 24 hours, collect the cells for further use.

value: brain

tag: cell line

value: primary cell

tag: cell type

value: primary neuron

value: PBS


title: Tree Shrew Primary Neurons, PBS-1, 24h, rep4


title: Skeletal muscle, Balbc_GR1

description:
mice_muscle_Balbc_GLR_RNA_seq_rpkm.txt
BGR1A


title: Brain, glioblastoma, rep3


title: Muscle biopsy, 32-0028R

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

description:
bilat_gene_counts.csv
bilat_dds.rda

data_processing:
trimming the Illumina universal adapters by Trimmomatic
alignment against genome built GRCh38(p13) by Rsubread
gene features were collected from GENCODE, version 35 and the gene counts were profiled by using the GenomicAlignment::summarizedOverlap() function with “IntersectionStrict” mode
Assembly: GRCh38.p13
Supplementary files format and content: bilat_dds.rda: DESeqDataSet instance containing gene counts, TPM gene annotation, and gene ranges
Supplementary files format and content: bilat_gene_counts.csv

source_name: tibialis anterior muscle biopsy

growth_protocol: needle muscle biopsy of both tibialis anterior muscles from 34 FSHD subjects

extract_protocol:
RNA was extracted from frozen crushed muscle biopsy material using TRIzol and single end 100 nt Illumina sequencing
RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep v2 Kit (Illumina, Inc., San Diego, CA, USA) and a Sciclone  NGSx Workstation (PerkinElmer, Waltham, MA, USA).

value: tibialis anterior muscle biopsy

tag: condition

value: FSHD

tag: location

value: R


title: Brain, glioblastoma, rep2


title: RNA.dorsal striatum.WT.male.NQ3

description:
NQ3DS_S15
Counts.Males.txt

source_name: dorsal striatum

value: dorsal striatum


title: Muscle biopsy, 32-0029R

description:
bilat_gene_counts.csv
bilat_dds.rda


title: Muscle biopsy, 32-0027R

description:
bilat_gene_counts.csv
bilat_dds.rda


title: Muscle biopsy, 32-0029L

description:
bilat_gene_counts.csv
bilat_dds.rda

value: L


title: RNA.ventral hippocampus.WT.male.NQ3

description:
NQ3vHPC_S3
Counts.Males.txt

source_name: ventral hippocampus

value: ventral hippocampus


title: Brain, control, rep5

value: lower grade (Grade I-II.) glioma


title: Muscle biopsy, 32-0027L

description:
bilat_gene_counts.csv
bilat_dds.rda


title: Skeletal muscle, Balbc_GL3

description:
mice_muscle_Balbc_GLR_RNA_seq_rpkm.txt
BGL4A

value: Skeletal muscle

value: BALB/c

value: Male

value: WT

value: neuron-denervated (Den); left leg muscles (Healthy)


title: Brain, control, rep6

value: Brain


title: RNA.dorsal hippocampus.WT.male.NQ3

description:
NQ3dHPC_S3
Counts.Males.txt

source_name: dorsal hippocampus

value: dorsal hippocampus

value: male

value: DiD 2BC + 1B


title: RNA.amygdala.WT.male.NQ3

description:
NQ3Amygdala_S39
Counts.Males.txt

source_name: amygdala

value: amygdala


title: Muscle biopsy, 32-0026R

description:
bilat_gene_counts.csv
bilat_dds.rda

value: tibialis anterior muscle biopsy


title: Brain, glioblastoma, rep1

value: glioblastoma


title: RNA.ventral striatum.ACSS2 KO.male.NQ2

description:
NQ2VS_S26
Counts.Males.txt

source_name: ventral striatum

value: ventral striatum

value: ACSS2 KO


title: Skeletal muscle, Balbc_GL2

description:
mice_muscle_Balbc_GLR_RNA_seq_rpkm.txt
BGL2A


title: Skeletal muscle, Balbc_GL1

description:
mice_muscle_Balbc_GLR_RNA_seq_rpkm.txt
BGL1A


title: Brain, control, rep3


title: Skeletal muscle, C57_GR1

description:
mice_muscle_C57_LR_RNA_seq_rpkm.txt
CGR1A

value: neuron-denervated (Den); right leg muscles (Muscle atrophy)


title: Skeletal muscle, C57_GR3

description:
mice_muscle_C57_LR_RNA_seq_rpkm.txt
CGR3A


title: Skeletal muscle, C57_GR2

description:
mice_muscle_C57_LR_RNA_seq_rpkm.txt
CGR2A


title: RNA.ventral hippocampus.ACSS2 KO.male.NQ2

description:
NQ2vHPC_S2
Counts.Males.txt

value: ventral hippocampus


title: Brain, control, rep2

value: lower grade (Grade I-II.) glioma


title: Muscle biopsy, 32-0025R

description:
bilat_gene_counts.csv
bilat_dds.rda

value: FSHD

value: R


title: Muscle biopsy, 32-0024R

description:
bilat_gene_counts.csv
bilat_dds.rda


title: U937 Monocytes, SGF29 knockout, rep 3

city: La Jolla

first: Karina

middle: Ofelia

last: Barbosa Guerra

state: CA

address: 10901 North Torrey Pines Rd, Deshpande Lab RM6210B

department: Tumor Initiation & Maintenance Program

institute: Sanford Burnham Prebys Medical Discovery Institute

description:
U937_SGF29_KO_Rep3
U937_SGF29_TPM.txt.gz

data_processing:
Raw reads were preprocessed by trimming Illumina Truseq adapters, polyA, and polyT sequences using cutadapt v2.3 with parameters “cutadapt -j 4 -m 20 --interleaved -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT Fastq1 Fastq2 | cutadapt --interleaved -j 4 -m 20 -a "A{100}" -A "A{100}" - | cutadapt -j 4 -m 20 -a "T{100}" -A "T{100}" -”.
Trimmed reads were subsequently aligned to human genome version hg38 using STAR aligner  v2.7.0d_0221 with parameters according to ENCODE long RNA-seq pipeline.
Gene expression levels were quantified using RSEM v1.3.1. Ensembl v84 gene annotations were used for the alignment and quantification steps. RNA-seq sequence, alignment, and quantification qualities were assessed using FastQC v0.11.5 and MultiQC v1.8. Lowly expressed genes were filtered out by retaining genes with estimated counts (from RSEM) ≥ number of samples times 5.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum, 2mM Glutamine and 100 U/ml penicillin/streptomycin in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using the Rneasy Mini Kit (Qiagen) and 900ng of total RNA per sample were used for library preparation.
RNA library prep was performed with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) follownig the manufacturer's instructions.

treatment_protocol: Cells were transduced with CRISPR sgRNA lentivirus targeting SGF29 or non-targeting control. Puromycin (1ug/ul) was added 2 days after to select for transduced cells and removed from the culture upon selection completion. Cells were harvested by centrifugation 7 days after puromycin removal and washed with 1X PBS and protease inhibitors.

value: Monocytes

value: SGF29 knockout

value: CRISPR sgRNA lentiviral transduction


title: Muscle biopsy, 32-0025L

description:
bilat_gene_counts.csv
bilat_dds.rda

value: L


title: Brain, control, rep1

value: Brain


title: Skeletal muscle, C57_GL2

description:
mice_muscle_C57_LR_RNA_seq_rpkm.txt
CGL2A

value: Skeletal muscle

value: Male

value: WT

value: neuron-denervated (Den); left leg muscles (Healthy)


title: Brain, control, rep4


title: RNA.dorsal striatum.ACSS2 KO.male.NQ2

description:
NQ2DS_S14
Counts.Males.txt

value: dorsal striatum

value: male

value: DiD 2BC + 1B


title: Skeletal muscle, C57_GL3

description:
mice_muscle_C57_LR_RNA_seq_rpkm.txt
CGL3A


title: Muscle biopsy, 32-0026L

description:
bilat_gene_counts.csv
bilat_dds.rda

value: tibialis anterior muscle biopsy


title: Skeletal muscle, C57_GL1

description:
mice_muscle_C57_LR_RNA_seq_rpkm.txt
CGL1A


title: RNA.cortex.ACSS2 KO.male.NQ2

description:
NQ2ctx_S14
Counts.Males.txt

source_name: cortex

value: cortex

value: ACSS2 KO


title: Muscle biopsy, 32-0024L

description:
bilat_gene_counts.csv
bilat_dds.rda

value: FSHD


title: RNA.dorsal hippocampus.ACSS2 KO.male.NQ2

description:
NQ2dHPC_S2
Counts.Males.txt

value: dorsal hippocampus


title: Muscle biopsy, 32-0023R

description:
bilat_gene_counts.csv
bilat_dds.rda

value: R


title: U937 Monocytes, SGF29 knockout, rep 1

description:
U937_SGF29_KO_Rep1
U937_SGF29_TPM.txt.gz

value: Monocytes

value: SGF29 knockout


title: RNA.cortex.WT.male.NQ3

description:
NQ3ctx_S15
Counts.Males.txt


title: RNA.amygdala.ACSS2 KO.male.NQ2

description:
NQ2Amygdala_S38
Counts.Males.txt

value: amygdala


title: TA-/- CD8+ T

city: Guangzhou

first: Jie

last: Long

address: No.106 Zhongshan 2nd Road

institute: Guangdong Provincial People's Hospital

description:
gene expression
liver_cd8_rpkm.txt

data_processing:
For scRNA-seq and scTCR-seq, the BD Genomics Rhapsody Targeted Analysis pipeline was used to demultiplex cellular barcodes, map reads to the reference genome. For bulk RNA-seq, STAR-2.5.2b software was used to map reads to the reference genome.
Assembly: mm10
Supplementary files format and content: Matrix table with raw UMI counts for every gene and every cell
Supplementary files format and content: tab-delimited text files include FPKM values for bulk RNA-seq Samples

source_name: murine liver tissue

extract_protocol:
For bulk RNA sequencing, total RNA was extracted utilizing RNA iso Plus (TaKaRa, 9109) from liver tissues or 5×10^5 CD8+ T cells that were isolated using a FACS Aria II cell sorter
For single cell RNA-seq and BCR-seq, CD45+ cells from dnTGFβRII, Aire-/-, dnTGFβRII Aire+/- and dnTGFβRII Aire -/- mice (each sample mixed with hepatic cells from 2-3 mice) were sorted using the FACS Aria II cell sorter and dispensed into individual microwell plates following the manufacturer’s instruction of BD Rhapsody system,The transcriptome  was split to construct the TCR library and the targeted mRNA library; For bulk RNA-seq, RNA libraries were prepared for sequencing using standard Illumina protocols or BGI protocols.

tag: age

value: 2-4 weeks

value: TG Aire-/-

value: CD8+ T cells


title: U937 Monocytes, SGF29 knockout, rep 2

description:
U937_SGF29_KO_Rep2
U937_SGF29_TPM.txt.gz

value: CRISPR sgRNA lentiviral transduction


title: U937 Monocytes, non-targeting control, rep 3

description:
U937_NTC_Rep3
U937_SGF29_TPM.txt.gz

value: Non-targeting control


title: Muscle biopsy, 32-0023L

description:
bilat_gene_counts.csv
bilat_dds.rda

value: L


title: RNA.ventral hippocampus.WT.female.NQ24

description:
NQ24vHPC_S12
Counts.Females.txt

value: ventral hippocampus

value: female

value: WT


title: RNA.ventral striatum.WT.female.NQ24

description:
NQ24VS_S36
Counts.Females.txt

value: ventral striatum

value: DiD 2BC + 1B


title: Muscle biopsy, 32-0022R

description:
bilat_gene_counts.csv
bilat_dds.rda

value: tibialis anterior muscle biopsy

value: FSHD


title: U937 Monocytes, non-targeting control, rep 1

description:
U937_NTC_Rep1
U937_SGF29_TPM.txt.gz


title: A-/- CD8+ T

description:
gene expression
liver_cd8_rpkm.txt

value: Aire-/-


title: Muscle biopsy, 32-0022L

description:
bilat_gene_counts.csv
bilat_dds.rda


title: RNA.dorsal striatum.WT.female.NQ24

description:
NQ24DS_S24
Counts.Females.txt

value: dorsal striatum


title: OE_NC_3

city: Bengbu

first: Jingya

last: Chen

address: Donghai Road

institute: Bengbu Medical University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)  by Removing reads containing sequencing adapter; Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4) .
Bowtie2 (v2.2.5)  was applied to align the clean reads to the reference coding gene set， then expression level of gene was calculated by RSEM (v1.2.12) .
Assembly: GCF_000001450.39_GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: Gastric cancer cell

growth_protocol: MGC-803 cells were cultured in DMEM (GIBCO, USA) medium containing 10% fetal bovine serum (Wisent, St. Bruno, QC, Canada), 1% streptomycin and 1% penicillin (Invitrogen, Carlsbad, CA, USA) in a humidified atmosphere at 37℃ with 5% CO2.

extract_protocol:
RNA was extracted from the isolated cells by Trizol (Thermo, MA, USA) according to the manufacturer's protocol and underwent transcript sequencing analysis
mRNA was enriched from total RNA and chain-specific transcriptional library was constructed and sequenced using DNBSEQ high-throughput platform.

treatment_protocol: MGC-803 cells were seeded and then transfected with expression vectors for MYBL2 or empty vector 24 h after seeding. At 48 h post-transfection, RNA sequencing analysis was performed.

value: Gastric cancer cell

value: Gastric adenocarcinoma cells

value: empty vector


title: Muscle biopsy, 32-0021R

description:
bilat_gene_counts.csv
bilat_dds.rda

value: R


title: OE_NC_2


title: RNA.cortex.WT.female.NQ24

description:
NQ24ctx_S24
Counts.Females.txt

value: cortex


title: Pcif1-KO HEK293T, PCF11

city: Shenzhen

first: Wee Siong Sho

last: Goh

state: Guangdong

address: Shenzhen Bay Laboratory, No. 5, Kelian Road, Goh Lab, A1819, Guangming District

department: Institute of Molecular Physiology

institute: Shenzhen Bay Laboratory

library_source: genomic

data_processing:
Basecalls performed using FASTQ Generation v1.0.0. for Nextseq output.
Fastq sequences were first trimmed of 5' and 3' adapter sequences and poly(A) tails using Cutadapt 3.7 --nextseq-trim -m 25 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
Reads were mapped to hg38 assembly transcriptome (Gencode v28 comprehensive gene annotations) using bowtie2 2.2.5 -N 1 --no-mixed --no-discordant.
Aligned pairs that had the same mapping coordinates and UMIs were filtered out as PCR duplicates using custom Python scripts.
Peaks were called uing MACS2 2.2.7.1 -f BAMPE -g hs --keep-dup all.
bigWig files were generated using bamCoverage --effectiveGenomeSize 2913022398 --normalizeUsing CPM -e. Metagene profiles of ChIP-seq were plotted using custom Python scripts, where enrichment fold-change and positions of the ChIP-seq peak summits relative to TSS or PAS of each gene were charted and binned into 500bp intervals. Mean enrichment fold-change was then calculated for plotting using Prism 9.5.0. ChIP-seq heatmaps were generated using Metagene2 with group_coverages normalization mode "log2_ratio". Density heatmaps of PCF11 ChIP-seq peak locations post PAS were calculated using the enrichment fold-change and positions of the ChIP-seq peak summits in the window ranging from PAS to 10kb downstream of PAS for each gene, and locating where the cumulative log2_ratio fold-change exceeds half of the sum of log2_ratio values within the window. Density heatmaps were then plotted using python package matplotlib.pyplot. For metagene analysis and peak density heatmaps generation, only genes not within 2kb of other genes, were included for analysis.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

growth_protocol: ATCC HEK293T CRL-3216 cells were cultivated in a sterile 5% CO2 incubator at 37°C, and in DMEM supplemented with 10% FBS. Cells within passage 3–25 were used for experiments. HEK293T cells were regularly subjected to MycoAlert Plus Mycoplasma kit (Lonza LT07) to verify that they were mycoplasma-free.

extract_protocol:
Cells were seeded in 150mm dishes and grown till 70-80% confluency. Media was aspirated and cells were washed with PBS and fixed with 10ml 1% formaldehyde (ThermoFisher 28906) in PBS at room temperature for 5min, with agitation every 2min. The fixing reaction was then quenched by adding 562ul of 2.5M glycine (Thermo J16407.A1) and incubated at room temperature for 5min, with agitation every 2min. The quenched solution was removed and fixed cells were washed twice with 10ml cold PBS. Cells were scraped in 10ml cold PBS+1%BSA and transferred to 50ml tubes pre-blocked with PBS+1%BSA. 5ml cold PBS+1%BSA was used to harvest and residual cells from plates. Cells were pelleted at 300rcf 4degC for 5min and resuspended in 1ml cold PBS+1%BSA. 2e7 cells were counted and transferred to a new cold LoBind tube before being washed twice by resuspending in 1ml cold PBS and centrifuging at 300rcf 4degC for 5min. Cells were resuspended in 0.9ml IP lysis buffer (50mM Tris pH 8, 100mM NaCl, 1.0% IGEPAL, 0.1% SDS, 0.5% sodium deoxycholate, 1mM EDTA 1x Complete protease inhibitor) and lysed on ice for 15min. Lysate was split into 3x300ul aliquots in pre-chilled LoBind tubes and sonicated at high setting for 15min (30s ON 30s OFF) using the Bioruptor Plus (Diagenode B01020001). SOnicated lysate was recombind and clarified via centrifuging at 13krpm 4degC for 10min. Meanwhile, 100ul Dynabead-Protein A (ThermoFisher 10001D) was washed twice in 1ml IP lysis buffer. Beads were resuspended in 200ul IP lysis buffer and split into 2 portions. 1 portion (“pre-clear beads”) was incubated with the clarified lysate at 4degC for 1hr to pre-clear the lysate. To the other portion, 10ug of anti-PCF11 antibody (Abcam ab134391) was added and mixed by tumbling at room temperature for 1hr (“IP beads”). IP beads were washed twice with 500ul IP lysis buffer. Both pre-clear beads and IP beads were magnetized and the pre-cleared lysate supernatant from the pre-clear beads was transferred to the decanted IP beads to be tumbled at 4degC overnight. 20ul of this mixture was set aside as “INPUT” and mixed with 80ul H2O and 100ul 2x elution buffer(). The remainder IP beads was washed once with 1ml low-salt buffer (50mM Tris pH 8, 100mM NaCl, 1% IGEPAL, 0.1% SDS, 0.5% sodium deoxycholate, 1mM EDTA), twice with 1ml mid-salt buffer (50mM Tris pH 8, 250mM NaCl, 1% IGEPAL, 0.1% SDS, 0.5% sodium deoxycholate, 1mM EDTA), twice with 1ml high-salt buffer (50mM Tris pH 8, 500mM NaCl, 1% IGEPAL, 0.1% SDS, 0.5% sodium deoxycholate, 1mM EDTA) and once again with 1ml low-salt buffer with a tube-change. Decanted beads were then eluted with 100ul 1x elution buffer (), shaking at 1krpm 30degC for 15min, before deads were magnetized and the elution supernatant was collected. A second elution was performed and the elutions were combined for a total of 200ul. 8ul 5M NaCl and 4ul 10mg/ml Rnase A (ThermoFisher EN0531) was added to both INPUT and IP elutions before shaking at 1krpm 65degC overnight. 4ul 20mg/ml proteinase K was added and the reactions shaken at 1krpm 60degC for 1hr before allowing them to cool to room temperature. DNA was purified with MinElute PCR cleanup kit (Qiagen 28004) and quantified with Qubit.
Illumina sequencing libraries were constructed using KAPA hyper-prep kit (Roche 07962347001), including a dual size selection step according to the manufacturer’s protocol. Libraries were quantified using KAPA library quantification (Roche KK4824), pooled and sequenced on Illumina Nextseq PE75.

value: Human embryonic kidney

tag: chip antibody

value: PCF11 (Abcam ab134391)


title: OE_NC_1


title: Muscle biopsy, 32-0020R

description:
bilat_gene_counts.csv
bilat_dds.rda


title: RNA.dorsal hippocampus.WT.female.NQ24

description:
NQ24dHPC_S12
Counts.Females.txt

value: dorsal hippocampus


title: RNA.ventral striatum.WT.female.NQ23

description:
NQ23VS_S35
Counts.Females.txt


title: TA+/- CD8+ T

description:
gene expression
liver_cd8_rpkm.txt

value: 2-4 weeks

value: TG Aire+/-

value: CD8+ T cells


title: WT HEK293T, Input

value: WT


title: WT HEK293T, PCF11


title: Muscle biopsy, 32-0020L

description:
bilat_gene_counts.csv
bilat_dds.rda

value: L


title: Muscle biopsy, 32-0021L

description:
bilat_gene_counts.csv
bilat_dds.rda

value: tibialis anterior muscle biopsy


title: Liver-21

city: Boston

first: Alan

middle: C.

last: Mullen

state: MA

address: 55 Fruit St.

department: Department of Medicine

institute: Massachusetts General Hospital

library_source: transcriptomic single cell

data_processing: The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)  Assembly: GRCh38 (human)  Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol: Frozen samples were dissociated on a GentleMACS in 1mL of TST buffer (https://www.nature.com/articles/s41591-020-0844-1). Nuclei were counted and resuspended in PBS+BSA+RNAse inhibitor before loading on a 10x 3' v3.1 channel.  Library construction was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, after nuclei loading and gel bead-in-emulsion (GEM) formation, the poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.  Libraries were pooled and sequenced on a NovaSeq S1 with the following parameters : Read 1, cell barcode and UMI, 28bp, i7 index, 10bp, i5 index, 10bp, Read 2, insert, 90bp

treatment_protocol: Samples were placed in cryo-tubes after removal of liquid by gently wiping it samples on the side of the container. Tubes were then covered in dry ice and transferred to −80 °C for long-term storage.

value: Liver


title: U937 Monocytes, non-targeting control, rep 2

description:
U937_NTC_Rep2
U937_SGF29_TPM.txt.gz

value: Monocytes

value: Non-targeting control

value: CRISPR sgRNA lentiviral transduction


title: Muscle biopsy, 13-0011R

description:
bilat_gene_counts.csv
bilat_dds.rda

value: FSHD


title: RNA.ventral hippocampus.WT.female.NQ23

description:
NQ23vHPC_S11
Counts.Females.txt

value: ventral hippocampus

value: female

value: DiD 2BC + 1B


title: Muscle biopsy, 13-0011L

description:
bilat_gene_counts.csv
bilat_dds.rda


title: MYBL2_1

value: Gastric cancer cell

value: Gastric adenocarcinoma cells

value: MYBL2 Overexpressed


title: Liver-23

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38 (human)
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Frozen samples were dissociated on a GentleMACS in 1mL of TST buffer (https://www.nature.com/articles/s41591-020-0844-1). Nuclei were counted and resuspended in PBS+BSA+RNAse inhibitor before loading on a 10x 3' v3.1 channel.
Library construction was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, after nuclei loading and gel bead-in-emulsion (GEM) formation, the poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
Libraries were pooled and sequenced on a NovaSeq S1 with the following parameters : Read 1, cell barcode and UMI, 28bp, i7 index, 10bp, i5 index, 10bp, Read 2, insert, 90bp

value: Healthy

value: F


title: Pcif1-KO HEK293T, Input

value: Human embryonic kidney


title: Muscle biopsy, 13-0010R

description:
bilat_gene_counts.csv
bilat_dds.rda

value: R


title: MYBL2_3


title: Muscle biopsy, 13-0010L

description:
bilat_gene_counts.csv
bilat_dds.rda

value: L


title: RNA.amygdala.WT.female.NQ24

description:
NQ24Amygdala_S47
Counts.Females.txt

value: amygdala

value: WT


title: Liver-22

description: 10x Genomics

value: M

value: Liver


title: MYBL2_2


title: RNA.dorsal hippocampus.WT.female.NQ23

description:
NQ23dHPC_S11
Counts.Females.txt

value: dorsal hippocampus


title: Liver-20

description: 10x Genomics


title: RNA.amygdala.WT.female.NQ23

description:
NQ23Amygdala_S46
Counts.Females.txt


title: Muscle biopsy, 13-0009R

description:
bilat_gene_counts.csv
bilat_dds.rda

value: tibialis anterior muscle biopsy

value: FSHD


title: Muscle biopsy, 13-0009L

description:
bilat_gene_counts.csv
bilat_dds.rda


title: Liver-19

description: 10x Genomics


title: Muscle biopsy, 13-0007R

description:
bilat_gene_counts.csv
bilat_dds.rda


title: RNA.prefrontal cortex.WT.female.NQ23

description:
NQ23PFC_S34
Counts.Females.txt

value: prefrontal cortex

value: female


title: Liver-18

description: 10x Genomics


title: RNA.ventral striatum.ACSS2 KO.male.NQ1

description:
NQ1VS_S25
Counts.Males.txt

value: ventral striatum

value: male

value: ACSS2 KO

value: DiD 2BC + 1B


title: Arabidopsis resette_erfVII_Botrytis_48h

type: RNA

city: San Giuliano Terme

first: Simone

last: Castellana

state: PIsa

address: Via Giovanni Guidiccioni, 8/10

department: Istitute of Plant Science

country: Italy

institute: Scuola Superiore Sant'Anna

hyb_protocol: GeneChip Hybridization, Wash, and Stain Kit

scan_protocol: GeneChip Scanner 3000 7G

data_processing: Microarray Suite 5.0

label: biotin

organism: Arabidopsis thaliana

source_name: Arabidopsis resette_erfVII_Botrytis_48h

label_protocol: GeneChip  3' IVT PLUS Reagent Kit

growth_protocol: Arabidopsis plants grown in pots with soil

extract_protocol: Total RNA was extracted as described (Perata et al., Plant Cell, 1997) with a minor modiﬁcation (omission of aurintricarboxylic acid)

treatment_protocol: Plants were infected with Botrytis cinerea (~1x106 conidia/mL) for 48 hours at high umidity

value: 4 weeks

value: Leaves

value: Botrytis cinerea


title: Liver-24

description: 10x Genomics

value: Healthy

value: F


title: RNA.ventral hippocampus.ACSS2 KO.male.NQ1

description:
NQ1vHPC_S1
Counts.Males.txt

value: ventral hippocampus


title: Muscle biopsy, 13-0007L

description:
bilat_gene_counts.csv
bilat_dds.rda

value: L


title: RNA.prefrontal cortex.ACSS2 KO.male.NQ1

description:
NQ1PFC_S25
Counts.Males.txt


title: Liver-17

description: 10x Genomics

value: M

value: Liver


title: RNA.dorsal striatum.WT.female.NQ23

description:
NQ23DS_S23
Counts.Females.txt

value: dorsal striatum

value: WT


title: scnasRNA-seq of SI, 72h post salmonella infection

city: Beijing

first: Zhen

last: Xiong

address: 15 Datun Road, Beijing 100101, China

department: Institute of Biophysics

institute: Chinese Academy of Sciences

description:
total RNA and nascent RNA
SI_S.T_72h

data_processing:
Data were processed to generate gene expression profiles using scnasRNA-seq pipeline (https://github.com/singleron-RD/CeleScope/blob/master/doc/assay/multi_dynaseq.md). Briefly, raw reads were processed with fastQC and fastp to remove low quality reads, such as those without poly T tails, cell barcode and UMI. Adapters and poly A tails were trimmed by Cutadapt before aligning paired reads to the mouse reference genome (GRCm38 with ensemble version 92 gene annotation) using STAR (version 2.5.3a). We then acquired gene counts and UMI counts by assigning uniquely mapped reads to genomic features with FeatureCounts (version 1.6.2). To quantify S4U labeled and unlabeled reads, we got T-to-C substitutions in each read. After excluding background T-to-C substitutions (presenting in control samples without metabolic labeling), we distinguished nascent RNA from old RNA based on whether reads contained T-to-C substitutions. Reads with the same cell barcode, UMI and gene were grouped together to count numbers of labeled and unlabeled UMIs for each gene per cell. Finally, we obtained two gene expression matrices (nascent RNA count and old RNA count matrix) for each sample. Total RNA count matrix is the sum of nascent RNA count matrx and old RNA count matrix.
Assembly: GRCm38
Supplementary files format and content: tsv file includes raw counts of new RNA for each Sample
Supplementary files format and content: tsv file includes raw counts of old RNA for each Sample

source_name: small intestine

extract_protocol:
Single-cell suspension was loaded onto microwell chips for single cell partition, followed with bead loading and cell lysis. After 20 min incubation at room temperature (RT), mRNA in each well was captured on a magnetic bead coated with oligonucleotides, each containing a primer sequence, a cell barcode, a unique molecular identifier (UMI), and a poly-T tail.
We used DynaSCOPETM Single Cell Dynamic RNA Library Kit (Singleron Biotechnologies) to construct scnasRNA-seq libraries. After collecting all beads that captured mRNA, S4U integrated on nascent RNA was converted into cytidine analogs. mRNA was incubated with conversion reagent at 25°C for 60 min. Mutations were inserted at the indicated sites on reverse transcription. For reference control samples, mRNA was incubated in the same condition but without conversion reagent. The reverse transcription reaction was incubated at 42°C for 90 min. cDNA amplification was performed by PCR using 13 cycles. PCR amplification products were purified using AMPure XP beads. After cDNA fragmentation and adaptor ligation, products were purified and amplified by PCR. After size selection, libraries were sequenced.

treatment_protocol: 8 to10 week-old mice were deprived of food and water for 4 h. Then mice were gavaged with 20 mg streptomycin sulfate in 200 ml PBS. 24 h later, mice were again deprived of food and water for 4 h, and then were gavaged with 10^8 CFUs of Salmonella. Bone marrow and small intestinal cells were collected at the indicated time point. Nacent RNA was labeled with S4U (1% of body weight) through tail vein injection

value: small intestine

value: salmonella


title: Liver-16

description: 10x Genomics


title: RNA.dorsal striatum.ACSS2 KO.male.NQ1

description:
NQ1DS_S13
Counts.Males.txt


title: Liver-15

description: 10x Genomics


title: RNA.dorsal hippocampus.ACSS2 KO.male.NQ1

description:
NQ1dHPC_S1
Counts.Males.txt

value: dorsal hippocampus


title: scnasRNA-seq of SI, 2h post salmonella infection

description:
total RNA and nascent RNA
SI_S.T_2h


title: Arabidopsis resette_Col-0_Botrytis_48h

source_name: Arabidopsis resette_Col-0_Botrytis_48h


title: SI_Reference

description:
Reference
SI_Ref


title: scnasRNA-seq of SI, 0h post salmonella infection

description:
total RNA and nascent RNA
SI_S.T_0h


title: Arabidopsis resette_erfVII_mock

source_name: Arabidopsis resette_erfVII_mock

value: control


title: Muscle biopsy, 13-0005L

description:
bilat_gene_counts.csv
bilat_dds.rda

value: tibialis anterior muscle biopsy

value: FSHD


title: Arabidopsis resette_Col-0_mock

source_name: Arabidopsis resette_Col-0_mock

value: 4 weeks


title: RNA.cortex.ACSS2 KO.male.NQ1

description:
NQ1ctx_S13
Counts.Males.txt

value: cortex

value: male

value: ACSS2 KO

value: DiD 2BC + 1B


title: Liver-14

description: 10x Genomics

value: Healthy


title: Liver-13

description: 10x Genomics

value: F


title: aorta, Apoe-knockout mouse, rep4 [Apoe_ko_C4]

first: Benrong

last: Liu

address: 250 Changgang Dong Road

institute: Guangzhou Institute of Cardiovascular Disease,the Second Affiliated Hospital, Guangzhou Medical University

data_processing:
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:：  Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Supplementary files format and content: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: aorta

growth_protocol: Normal chaw diet

extract_protocol:
The aorta were dissected and aortic tissues were stored in liquid nitrogen and stored in low temperature.Total RNA was extracted with Trizol (Tiangen, Beijing, China). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer’s instructions.

value: aorta

value: Apoe-knockout

value: Normal chaw diets

value: 7-8 weeks


title: aorta, Apoe-knockout mouse, rep3 [Apoe_ko_C3]


title: Muscle biopsy, 13-0004R

description:
bilat_gene_counts.csv
bilat_dds.rda

value: R


title: Muscle biopsy, 13-0004L

description:
bilat_gene_counts.csv
bilat_dds.rda

value: L


title: RNA.ventral striatum.WT.male.NQ13

description:
NQ13VS_S34
Counts.Males.txt

value: ventral striatum

value: WT


title: scnasRNA-seq of SI, 6h post salmonella infection

description:
total RNA and nascent RNA
SI_S.T_6h

value: small intestine

value: salmonella


title: Muscle biopsy, 13-0003R

description:
bilat_gene_counts.csv
bilat_dds.rda

value: tibialis anterior muscle biopsy

value: FSHD


title: Liver-10

description: 10x Genomics

value: M

value: Liver


title: aorta, Apoe-knockout mouse, rep2 [Apoe_ko_C2]

value: male


title: aorta, Apoe-knockout mouse, rep1 [Apoe_ko_C1]


title: Muscle biopsy, 13-0003L

description:
bilat_gene_counts.csv
bilat_dds.rda


title: Liver-9

description: 10x Genomics

value: Healthy


title: Muscle biopsy, 13-0005R

description:
bilat_gene_counts.csv
bilat_dds.rda


title: RNA.dorsal striatum.WT.male.NQ13

description:
NQ13DS_S22
Counts.Males.txt

value: dorsal striatum

value: DiD 2BC + 1B


title: RNA.amygdala.ACSS2 KO.male.NQ1

description:
NQ1Amygdala_S37
Counts.Males.txt

value: amygdala

value: ACSS2 KO


title: Muscle biopsy, 13-0002R

description:
bilat_gene_counts.csv
bilat_dds.rda


title: Liver-8

description: 10x Genomics


title: aorta, C57BL/6J mouse, rep5 [WT_A5]

value: aorta

value: wild type

value: Normal chaw diets

value: 7-8 weeks


title: RNA.dorsal hippocampus.WT.male.NQ13

description:
NQ13dHPC_S10
Counts.Males.txt

value: dorsal hippocampus

value: WT


title: Muscle biopsy, 13-0006L

description:
bilat_gene_counts.csv
bilat_dds.rda

value: L


title: aorta, C57BL/6J mouse, rep4 [WT_A4]


title: Muscle biopsy, 13-0002L

description:
bilat_gene_counts.csv
bilat_dds.rda

value: tibialis anterior muscle biopsy


title: Liver-7

description: 10x Genomics

value: F


title: Liver-11

description: 10x Genomics


title: aorta, C57BL/6J mouse, rep3 [WT_A3]


title: RNA.amygdala.WT.male.NQ13

description:
NQ13Amygdala_S45
Counts.Males.txt


title: Liver-6

description: 10x Genomics


title: RNA.ventral hippocampus.WT.male.NQ13

description:
NQ13vHPC_S10
Counts.Males.txt

value: ventral hippocampus


title: Muscle biopsy, 13-0001R

description:
bilat_gene_counts.csv
bilat_dds.rda

value: FSHD

value: R


title: aorta, C57BL/6J mouse, rep1 [WT_A1]

value: male


title: RNA.ventral striatum.WT.male.NQ12

description:
NQ12VS_S33
Counts.Males.txt

value: ventral striatum


title: Liver-4

description: 10x Genomics

value: Healthy

value: Liver


title: Muscle biopsy, 01-0031R

description:
bilat_gene_counts.csv
bilat_dds.rda


title: RNA.ventral hippocampus.WT.male.NQ12

description:
NQ12vHPC_S9
Counts.Males.txt

value: DiD 2BC + 1B


title: aorta, C57BL/6J mouse, rep2 [WT_A2]

value: aorta


title: Liver-3

description: 10x Genomics

value: M


title: Muscle biopsy, 01-0031L

description:
bilat_gene_counts.csv
bilat_dds.rda


title: RNA.prefrontal cortex.WT.male.NQ12

description:
NQ12PFC_S32
Counts.Males.txt

source_name: prefrontal cortex

value: prefrontal cortex


title: RNA.cortex.WT.male.NQ13

description:
NQ13ctx_S22
Counts.Males.txt

value: cortex


title: Muscle biopsy, 01-0030R

description:
bilat_gene_counts.csv
bilat_dds.rda

source_name: tibialis anterior muscle biopsy


title: Liver-2

description: 10x Genomics


title: RNA.dorsal striatum.WT.male.NQ12

description:
NQ12DS_S21
Counts.Males.txt

source_name: dorsal striatum

value: dorsal striatum


title: RNA-seq, wild-type/tmc5, Day-4, L4 stage, replicate-2

city: Austin

first: ELIF

last: SARINAY CENIK

state: TX

address: 2415 Speedway

institute: University of Texas at Austin

data_processing:
RiboFlow and RiboR was used for data processing. https://pubmed.ncbi.nlm.nih.gov/31930375/
Assembly: Transcriptome mapping reads were mapped using  WBcel235 assembly
Supplementary files format and content: CSV format transcriptome mapping counts

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: 16C on NGM OP-50 until L4 stage

extract_protocol:
Flash freezing and lysis foro Riboseq, Trizol extraction for RNAseq. Details will be provided with the manuscript.
Diagenode small RNA kit for Ribo-Seq and Smarter Stranded RNAseq kit for RNA-Seq libraries

treatment_protocol: no treatment

value: whole body


title: RNA-seq, wild-type/tmc5, Day-3, L4 stage, replicate-2


title: Muscle biopsy, 01-0030L

description:
bilat_gene_counts.csv
bilat_dds.rda

value: L


title: Liver-1

description: 10x Genomics


title: RNA-seq, rps-23(0)/tmc5, Day-4, L4 stage, replicate-2


title: RNA-seq, wild-type/tmc20, Day-3, L4 stage, replicate-2


title: RNA-seq, wild-type/tmc20, Day-4, L4 stage, replicate-2


title: Muscle biopsy, 01-0029R

description:
bilat_gene_counts.csv
bilat_dds.rda

value: tibialis anterior muscle biopsy


title: RNA.dorsal hippocampus.WT.male.NQ12

description:
NQ12dHPC_S9
Counts.Males.txt

source_name: dorsal hippocampus

value: dorsal hippocampus

value: WT


title: Liver-5

description: 10x Genomics


title: RNA.cortex.WT.male.NQ12

description:
NQ12ctx_S21
Counts.Males.txt


title: 2nd 4sU-PUGNAc

city: Bethesda

first: Brian

middle: A

last: Lewis

state: Maryland

address: 9000 Rockville Pike, Building 10 Room 2N105

department: CCR/Laboratory of Pathology

institute: NCI

data_processing:
Library strategy: 4sU-seq
cutadapt: adaptor removal
fastx_reverse_complement: reverse complement of one set of paired reads
cat: combining the reverse complement of R1 with R2
slamdunk map; slamdunk filter; slamdunk snp
alleyoop rates:  calculated T>C conversion rates: alleyoop read-separator: separates T>C reads from unincorporated reads
deeptools bamCoverage: CPM normalization
deeptools computeMatrix: calculates matrices for TSS metagene plots
deeptools plotProfile: output is the actual metagene plot
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files of T>C converted reads normalized by CPM

source_name: Hela cells S3

growth_protocol: 10%FCS/DMEM/high glucose +glutamine

extract_protocol:
Rnazol RNA isolation as per manufacturer's instructions
We used the Total RNA seq library protocol from Illumina. This protocol involves the removal of ribosomal RNA (rRNA) using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. The RNA is fragmented into small pieces and the cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The resulting double-strand cDNA is used as the input to a standard Illumina library prep with end-repair, adapter ligation and PCR amplification. The final purified product is then quantitated by qPCR before cluster generation and sequencing.

treatment_protocol:
Hela cells were grown to 50% confluency and treated with either DMSO, FP, or PUGNAc for 24 hours, followed by a 10 minute treatment with 4sU
24 hour incubation with inhibitors; 10 minute treatment with 4sU

value: HeLa S3

tag: rna population

value: nascent RNA

value: PUGNAc


title: Muscle biopsy, 13-0001L

description:
bilat_gene_counts.csv
bilat_dds.rda

value: FSHD


title: 2nd 4sU-Flavopiridol

value: Flavopiridol


title: RNA-seq, rps-10(0)/tmc20, Day-4, L4 stage,  replicate-2


title: RNA.amygdala.WT.male.NQ12

description:
NQ12Amygdala_S44
Counts.Males.txt

source_name: amygdala

value: amygdala

value: male


title: Muscle biopsy, 01-0029L

description:
bilat_gene_counts.csv
bilat_dds.rda


title: 1st 4sU-PUGNAc


title: RNA.ventral striatum.WT.female.NQ11

description:
NQ11VS_S32
Counts.Females.txt

source_name: ventral striatum

value: ventral striatum

value: female

value: DiD 2BC + 1B


title: Muscle biopsy, 01-0028R

description:
bilat_gene_counts.csv
bilat_dds.rda

value: R


title: 1st 4sU-Flavopiridol


title: 2nd 4sU-DMSO

value: DMSO


title: Muscle biopsy, 01-0028L

description:
bilat_gene_counts.csv
bilat_dds.rda


title: RNA-seq, wild-type/mc6, Day-4, pregravid adults, replicate-2

value: whole body


title: Muscle biopsy, 01-0026R

description:
bilat_gene_counts.csv
bilat_dds.rda


title: RNA.ventral hippocampus.WT.female.NQ11

description:
NQ11vHPC_S8
Counts.Females.txt

source_name: ventral hippocampus

value: ventral hippocampus


title: RNA.prefrontal cortex.WT.female.NQ11

description:
NQ11PFC_S31
Counts.Females.txt

value: prefrontal cortex


title: 1st 4sU-DMSO


title: Muscle biopsy, 01-0026L

description:
bilat_gene_counts.csv
bilat_dds.rda

value: tibialis anterior muscle biopsy

value: L


title: RNA.dorsal striatum.WT.female.NQ11

description:
NQ11DS_S20
Counts.Females.txt

value: dorsal striatum

value: WT


title: RNA-seq, wild-type/mc6, Day-3, L4 stage, replicate-2


title: RNA-seq, rpl-5(0)/mc6, Day-4, L4 stage, replicate-2


title: RNA-seq, rpl-33(0)/mc6, Day-4, L4 stage, replicate-2


title: RNA.dorsal hippocampus.WT.female.NQ11

description:
NQ11dHPC_S8
Counts.Females.txt

value: dorsal hippocampus


title: Muscle biopsy, 01-0025L

description:
bilat_gene_counts.csv
bilat_dds.rda

value: FSHD


title: Muscle biopsy, 01-0025R

description:
bilat_gene_counts.csv
bilat_dds.rda


title: RNA-seq, wild-type/tmc5, Day-4, pregravid adults, replicate-1


title: RNA-seq, wild-type/tmc5, Day-3,  L4 stage, replicate-1


title: TGC-3

city: Shanghai

first: Junpeng

last: Dong

address: 145 Guangyuan Rd, Xuhui District

department: School of Medicine, Shanghai Jiao Tong University

institute: The International Peace Maternity and Child Health Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to mm10 using hisat2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Supplementary files format and content: mm10

source_name: trophoblast stem cells

growth_protocol: mTSCs were nurtured in a stem cell medium (SCM) specifically designed for their growth. This medium was comprised of 30% standard medium (Roswell Park Memorial Institute (RPMI) 1640 (Gibco, Grand Island, NY, USA) enhanced with 20% fetal bovine serum (FBS) (Gibco), 25 ng/ml Fibroblast Growth Factor 4 (FGF4) (Peprotech, Cranbury, NJ, USA), 1 mg/ml heparin (Sigma, St. Louis, MO, USA), 100 mM 2-mercaptoethanol (Gibco), 2 mM L-glutamine (Gibco), and 2 mM sodium pyruvate (Gibco)), along with 70% mouse embryonic fibroblast-feeder conditioned medium (FCM). The differentiation of mTSCs into TGCs were enabled using a specialized differentiation medium (DM). This medium was essentially SCM without the components of FGF4 and heparin.

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyze. RNA libraries were prepared for sequencing using standard Illumina protocols.
The libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer’ s instructions.

value: TGC


title: TGC-1


title: RNA.cortex.WT.female.NQ11

description:
NQ11ctx_S20
Counts.Females.txt

source_name: cortex

value: cortex


title: TGC-2


title: Muscle biopsy, 01-0024R

description:
bilat_gene_counts.csv
bilat_dds.rda


title: RNA.ventral striatum.ACSS2 KO.male.NQ10

description:
NQ10VS_S31
Counts.Males.txt

value: male

value: ACSS2 KO


title: mTSC-3

value: mTSC


title: Muscle biopsy, 01-0024L

description:
bilat_gene_counts.csv
bilat_dds.rda


title: RNA-seq, rps-23(0)/tmc5, Day-4,  L4 stage, replicate-1


title: RNA-seq, wild-type/tmc20, Day-4,  pregravid adults, replicate-1


title: mTSC-2


title: RNA.ventral hippocampus.ACSS2 KO.male.NQ10

description:
NQ10vHPC_S7
Counts.Males.txt

value: DiD 2BC + 1B


title: RNA.dorsal hippocampus.ACSS2 KO.male.NQ10

description:
NQ10dHPC_S7
Counts.Males.txt


title: RNA-seq, wild-type/tmc20, Day-3,  L4 stage, replicate-1,


title: RNA.dorsal striatum.ACSS2 KO.male.NQ10

description:
NQ10DS_S19
Counts.Males.txt


title: RNA-seq, rps-10(0)/tmc20, Day-4,  L4 stage, replicate-1


title: RNA-seq, wild-type/mc6, Day-4, pregravid adults, replicate-1


title: RNA.cortex.ACSS2 KO.male.NQ10

description:
NQ10ctx_S19
Counts.Males.txt


title: Muscle biopsy, 01-0022R

description:
bilat_gene_counts.csv
bilat_dds.rda

value: R


title: C884PyMT-Ctl rep3

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

data_processing:
RNAseqraw data (fastq or fasq.gz files) quality were checked using FastQC (v0.11.9), and adapter trimming on raw data was performed using Cutadapt (v3.5). Reads with low quality (quality score < 33, error rate > 10%) or length are too short (<25 bp) after trimming were removed before alignment.
The reference genome was downloaded from Ensembl GRCm38 release 102, and the reference index was built using Star (v2.7.9a) software
Paired-end trimmed reads alignment and raw read count calculation were performed using RSEM software (v1.3.1).
Statistical analysis was performed using the DESeq2 package (v1.36.0) in R (v4.1).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes expected counts, TPM and FPKM for each sample

source_name: mammary tumor

growth_protocol: tumor measurement LxW

extract_protocol:
RNA was extracted using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA purity was assessed by the integrity of 18S and 28S rRNA using an Agilent microfluidic chip.
Standard Azenta RNAseq library construction protocol

treatment_protocol: oral administration in Medigel cups continuously from 6 weeks of age

value: mammary tumor

value: Vehicle


title: C884PyMT-Ctl rep2


title: Muscle biopsy, 01-0022L

description:
bilat_gene_counts.csv
bilat_dds.rda


title: RNA.amygdala.ACSS2 KO.male.NQ10

description:
NQ10Amygdala_S43
Counts.Males.txt

data_processing:
Alignment: sequencing data were aligned to mouse genome assembly GRCm38/mm10 using STAR v2.5.2a with command-line parameters --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --readFilesCommand zcat --outFilterMismatchNoverReadLmax 0.04. The STAR index was constructed GENCODE M25 annotation (ENSEMBL 100 assembly).
Filtering: aligned data were filtered for poor mapping tags using samtools v1.1 subcommand view -bS -q 255.
Pooling: filtered data from two flowcells (*FC1.*, *FC2.*, i.e., technical repeat samples from two flowcells) were combined using samtools merge and aligned tags were sorted by chromosome position and indexed using samtools sort and index, respectively.
Quantitation: HTseq v0.6.1 was used to quantify tag counts over exons with command-line parameters -f bam -r pos -s reverse -t exon -i gene_id --additional-attr=gene_name.
Analysis: differentially expressed genes (DEGs) between ACSS2 KO and WT samples were detected separately in each tissue and each sex using DESeq2 in R v4.0.2 with the FDR controlled at 0.1. Sexes were analyzed separately and so the uploaded gene counts tables are also separated by sex.
Assembly: GRCm38 / mm10
Supplementary files format and content: Counts.Males.txt and Counts.Females.txt contain the results of HTSeq run on all male or female samples, respectively.

extract_protocol:
Briefly, total RNA was extracted using Trizol-chloroform. Total RNA quality was assessed on the Bioanalyzer platform using the RNA 6000 Nano assay (Agilent). mRNA was isolated from 300 ng total RNA using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490L).
Libraries were prepared using the NEBNext® UltraTM II RNA Library Prep Kit for Illumina® (E7770).

value: amygdala


title: Muscle biopsy, 01-0021R

description:
bilat_gene_counts.csv
bilat_dds.rda


title: RNA-seq, wild-type/mc6, Day-3,  L4 stage, replicate-1

value: whole body


title: C884PyMT-Ctl rep1


title: heat plant 6

city: Acton

first: Peng

last: Zhang

state: ACT

address: 134 Linnaeus Way

country: Australia

institute: The Australian National University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (parameter: LEADING: 10 TRAILING: 10 SLIDINGWINDOW: 4:15 MINLEN: 50)
Trimmed sequence reads were mapped to the genomic sequence of Setaria italica (v 2.1) using Tophat2 with the default setting allowing 2 mismatches.
The alignments were counted to exons using HT-Seq with mode set to union.
Count normalization and differential expression analysis were carried out in DESEQ.
Assembly: Setaria italica v 2.1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Setaria viridis

source_name: leaf

growth_protocol: Setaria viridis seeds are germinated in soil in a Conviron growth chamber set under 16h/8h day/night cycle. The temperature was set at 28 ºC during the day, and 20 ºC at night, and the humidity was 40-60%, CO2 level of 380 ppm, irradiance at 1000 𝛍mol quanta m-2s-1. Two weeks after germination, plants in the treatment group were transferred in to a different growth chamber with all identical grwoth conditions, except the day temperature was set at 42 ºC and night temperature was set at 32 ºC.

extract_protocol:
RNA extracted using TRIzol™
RNA libraries for RNA-seq were prepared using Illumina TruSeq RNA Sample Preparation kit version 2 following the manufacture instructions.

treatment_protocol: Two-week-old plants were transferred in to a different growth chamber with all identical grwoth conditions, except the day temperature was set at 42 ºC and night temperature was set at 32 ºC. Treatment was applied for two weeks. Leaves were harvested at the end of treatment for RNA extraction.

value: leaf

value: WT. A10

tag: time

value: Day 28


title: RNA-seq, rpl-5(0)/mc6, Day-4, replicate-1


title: heat plant 5


title: Muscle biopsy, 01-0021L

description:
bilat_gene_counts.csv
bilat_dds.rda

value: tibialis anterior muscle biopsy

value: L


title: heat plant 4


title: RNA-seq, rpl-33(0)/mc6, Day-4, replicate-1


title: C816PyMT-DMHCA rep1

value: LXR agonist


title: Muscle biopsy, 01-0020L

description:
bilat_gene_counts.csv
bilat_dds.rda

value: FSHD


title: C816PyMT-DMHCA rep2


title: Muscle biopsy, 01-0023L

description:
bilat_gene_counts.csv
bilat_dds.rda


title: Muscle biopsy, 01-0020R

description:
bilat_gene_counts.csv
bilat_dds.rda


title: Muscle biopsy, 01-0023R

description:
bilat_gene_counts.csv
bilat_dds.rda


title: Ribo-Seq, rpl-33(0)/mc6, 4 days old, L4 stage, replicate-2

data_processing:
RiboFlow and RiboR was used for data processing. https://pubmed.ncbi.nlm.nih.gov/31930375/
Assembly: Transcriptome mapping reads were mapped using  WBcel235 assembly
Supplementary files format and content: CSV format transcriptome mapping counts
Library strategy: Ribo-seq


title: mTSC-1


title: heat plant 2


title: Ribo-Seq, rpl-5(0)/mc6, 4 days old, L4 stage,  replicate-2


title: C816PyMT-DMHCA rep3


title: Muscle biopsy, 01-0019L

description:
bilat_gene_counts.csv
bilat_dds.rda

data_processing:
trimming the Illumina universal adapters by Trimmomatic
alignment against genome built GRCh38(p13) by Rsubread
gene features were collected from GENCODE, version 35 and the gene counts were profiled by using the GenomicAlignment::summarizedOverlap() function with “IntersectionStrict” mode
Assembly: GRCh38.p13
Supplementary files format and content: bilat_dds.rda: DESeqDataSet instance containing gene counts, TPM gene annotation, and gene ranges
Supplementary files format and content: bilat_gene_counts.csv


title: Atria_rep2_SYNE2_GATC_GTAC

city: Geneva

first: Raquel

last: ROUCO GARCIA

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

data_processing:
Library strategy: 4C
Demultiplexing: different samples were demultiplexed using the primer sequences
Mapping: reads were mapped to the Mus musculus (mm9 assembly) genome using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: only those reads that mapped within fragments with a DpnII at one end and a NlaIII or Csp6I at the other end were kept. Fragments smaller than 40 bp, or within a window of 10 kilobase (kb) around the viewpoint were filtered out.
Mapped reads were then converted to reads per first enzyme fragment ends and smoothened using a 30-fragment mean running window algorithm. Smoothened scores of each experiment were then normalized by the total number or reads
For contact estimation, the reference genome was digested in silico according to the first and second restriction enzymes (NlaIII or Csp6I). Then, processed reads were assigned to their corresponding first cutter (DpnII) digested genome fragment, filtering out reads on fragments located 5kb around the viewpoint. Quantification was performed considering each fragment end as one captured site if one or more sequences mapped to it. The number of captured sites was summarized per 30 fragments window (max of 60 captured sites per window). The frequency of captured sites per window was used to fit a distance decreasing monotone function and Z-scores were calculated from its residuals using a modified version of FourCSeq (Klein et al. 2015). Significant contacts were considered in cases where the Z-score was >2 in both replicates and deviated significantly (adjusted p value <0.05) from its normal cumulative distribution in at least one of the replicates. After data analysis, processed reads and interactions were visualized at the WashU EpiGenome Browser Mouse genome (mm9).
Individual viewpoint fastq files were reconstructed form the individual viewpoint sorted.bam files using BEDtools toolset (https://bedtools.readthedocs.io/en/latest/)
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files contain smoothed and normalized data for each replicate. These processed files can be directly uploaded to UCSC or WashU Browsers for visualization.
Supplementary_files_format_and_content: bed file contains the coordinates of significative interactions. These processed files can be directly uploaded to WashU Browser for visualization.
Supplementary_files_format_and_content: txt file contains paired interactions between the viewpoint and the genome. These processed files can be directly uploaded to WashU Browser for visualization.

source_name: Adult mouse atria

extract_protocol:
Heart were dissected and atria tissue were micro-dissected. Pools of 20 atria were dissociated to obtain single cells preparations with collagenase. Chromatin was fixed with 2% formaldehyde for 10 min at room temperature and the reaction was quenched on ice with glycine. After fixation, pools were lysed in 50mM Tris-HCl pH7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% TX-100 and 1x complete protease inhibitor (Roche), digested first with DpnII (New England Biolabs, Cat. No. R0543M), ligated with T4 DNA ligase (Promega) followed by either NlaIII (New England Biolabs, Cat. No. R0125L) or Csp6I (Fermentas, cat.no. ER0211) digestion, depending on the initial design of the 4C viewpoint, and re-ligated with T4 DNA ligase (Promega).
500ng of 4C templates were amplified using Expand Long Template Polymerase enzyme (Roche) and inverse PCR primers flanked with barcodes allowing multiplexing. The Illumina adaptors used were 5'-AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCT-3' for the reading primers and 5'-CAAGCAGAAGACGGCATACGA-3' for the non-reading. Specific primer information for each viewpoint is displayed in the related publication.

value: atria

value: 8 weeks

tag: gentoype

value: Wild type


title: heat plant 1


title: Atria_rep1_SYNE2_GATC_GTAC

value: male


title: Ribo-Seq, wild-type/mc6, 3 days old, L4 stage replicate-2


title: Ribo-Seq, wild-type/mc6, 4 days old, pre-gravid adults, replicate-2


title: Atria_rep2_CAV1_GATC_CATG


title: Muscle biopsy, 01-0019R

description:
bilat_gene_counts.csv
bilat_dds.rda

extract_protocol:
RNA was extracted from frozen crushed muscle biopsy material using TRIzol and single end 100 nt Illumina sequencing
RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep v2 Kit (Illumina, Inc., San Diego, CA, USA) and a Sciclone  NGSx Workstation (PerkinElmer, Waltham, MA, USA).


title: Ribo-Seq, wild-type/tmc5, 3 days old, L4 stage, replicate 2


title: control plant 5


title: control plant 4


title: Atria_rep1_CAV1_GATC_CATG


title: Tcell_Culture_ATAC

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

library_source: genomic single cell

data_processing:
Fastqs were generated using CellRanger-ATAC mkfastq v2.0
Per-cell chromatin accessibility in peaks was determined using CellRanger-ATAC count v2.0
Per-cell antibody derived tags were computed via kallisto v0.4.4
Assembly: hg38
Supplementary files format and content: Per-cell chromatin accessibility in peaks, per-cell antibody derived tags

source_name: peripheral blood mononuclear cells

extract_protocol:
NP40 lysis, see method sections for full details
10x Genomics scATAC-seq
Customized scATAC-seq (mtscATAC-seq & ASAP) workflow as described in https://www.nature.com/articles/s41587-020-0645-6 and https://www.biorxiv.org/content/10.1101/2020.09.08.286914v1

treatment_protocol: Thawed cryopreserved PBMCs were resuspended to 1M/ml density in either complete medium supplemented with complete medium supplemented with IL2 and ImmunoCult Human CD3/CD28 T cell activation then profiled 9 days after the initial culture.

value: peripheral blood mononuclear cells

tag: sorted cell type

value: T cells


title: Tcell_Culture_ASAP

library_source: other

data_processing:
Fastqs were generated using CellRanger-ATAC mkfastq v2.0
Per-cell chromatin accessibility in peaks was determined using CellRanger-ATAC count v2.0
Per-cell antibody derived tags were computed via kallisto v0.4.4
Assembly: hg38
Supplementary files format and content: Per-cell chromatin accessibility in peaks, per-cell antibody derived tags
Library strategy: ASAP-seq

molecule: protein


title: heat plant 3


title: Ribo-Seq, rps-23(0)/tmc5, 4 days old, L4 stage, replicate 2

tag: tissue


title: Tcell_GeneExpression

data_processing:
Fastqs were generated using CellRanger mkfastq v6.0
TCR sequences were assembled using the CellRanger vdj v6.0
Gene expression counts were computed using CellRanger count v6.0
Per-cell mtDNA genotypes were determined using the mgatk package v0.6.6
Assembly: hg38
Supplementary files format and content: Per-cell mtDNA genotypes, TCR sequences, and gene expression counts

extract_protocol: 10x Genomics vdj scRNA-seq


title: Ribo-Seq, rpl-5(0)/mc6, 4 days old, L4 stage, replicate 1


title: control plant 3


title: control plant 2


title: control plant 1


title: A549 cells, shFXR, 3 days after ionizing radiation2 [D2]

first: Li

last: Xinyan

address: No.17, Panjiayuan Nanli, Chaoyang District, Beijing

institute: Cancer Hospital Chinese Academy of Medical Sciences

data_processing:
DESeq2 R package (1.20.0)
Assembly: hg38
Supplementary files format and content: xls file includes raw counts for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used was used for the construction of sequencing libraries
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magneticbeads. Fragmentation was carried out using divalent cations under elevated temperature inFirst Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized usingrandom hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strandcDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.Remaining overhangs were converted into blunt ends via exonuclease/polymerase activitiesAfter adenylation of 3’ends of DNA fragments, Adaptor with hairpin loop structure wereligated to prepare for hybridization.In order to select cDNA fragments of preferentially370~420 bp in length, the library fragments were purified with AMPure XP system(Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-FidelityDNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products werepurified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer2100 system.

value: non-small cell lung cancer cell lines

value: FXR knockdown

value: ionizing radiation


title: A549 cells, shFXR, 3 days after ionizing radiation1 [D1]


title: A549 cells, shFXR, sham irradiation3 [C3]

value: sham irradiation


title: A549 cells, shFXR, 3 days after ionizing radiation3 [D3]


title: PBMCs_Draw_20210329

data_processing:
Fastqs were generated using CellRanger-ATAC mkfastq v2.0
Raw reads were aligned to the hg38 reference using CellRanger-ATAC count
mtDNA genotypes were assigned using the mgatk package
Per-cell cell state annotations were performed using the Seurat bridge projection and annotation
Assembly: hg38
Supplementary files format and content: Cell type annotations from bridge reference projection for PBMCs

extract_protocol:
NP40 lysis, see method sections for full details
10x Genomics scATAC-seq
Customized scATAC-seq (mtscATAC-seq) workflow as described in https://www.nature.com/articles/s41587-020-0645-6

tag: date


title: PBMCs_Draw_20210511


title: Ribo-Seq, rpl-33(0)/mc6, 4 days old, L4 stage, replicate 1

value: whole body


title: Ribo-Seq, rps-10(0)/tmc20, 4 days old, L4 stage, replicate 2


title: PBMCs_Draw_20210218


title: Cardiomyocytes, HFD, rep3

first: Kaixin

last: Ge

address: 180 Fenglin Rd

department: Department of Cardiovascular Surgery

institute: Zhongshan Hospital, Fudan University

data_processing:
The sequencing data was filtered with SOAPnuke by Removing reads containing sequencing adapter
Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format
Bowtie2was applied to align the clean reads to the gene set and expression level of gene was calculated by RSEM (v1.3.1)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files includes raw TPM values for each Sample

source_name: heart

extract_protocol:
RNA was harvested using Magzol reagent (Magen, R480102). 1 ug of total RNA used for the construction of sequencing libraries.
RNA-Seq (Quantification) uses a new generation of high-throughput sequencing technology to study the gene expression pattern of eukaryotic cells and provide accurate digital expression profile detection by sequencing and comparing transcripts. The experimental procedure includes: 1. sample QC, 2. mRNA isolation, 3. mRNA fragmentation, 4. cDNA synthesis, 5. end repair,add A and adaptor ligation, 6. PCR, 7. library QC.

treatment_protocol: Pregnant female mice were randomly fed with a normal diet (ND), slight high-fat diet (sHFD), or high-fat diet (HFD) from fertilization to delivery and cardiomyocytes of the offspring were isolated at P0.

value: heart

value: Cardiomyocytes

tag: strain

value: WT

value: high fat diet


title: Ribo-Seq, wild-type/tmc5, 4 days old, pre-gravid adults, replicate 2

tag: genotype


title: A549 cells, shFXR, sham irradiation1 [C1]

tag: treatment


title: Ribo-Seq, wild-type/mc6, 4 days old, pregravid adults, replicate 1


title: Cardiomyocytes, HFD, rep1


title: PBMCs_Draw_20210115


title: Cardiomyocytes, HFD, rep2


title: Tcell_TCRs

data_processing:
Fastqs were generated using CellRanger mkfastq v6.0
TCR sequences were assembled using the CellRanger vdj v6.0
Gene expression counts were computed using CellRanger count v6.0
Per-cell mtDNA genotypes were determined using the mgatk package v0.6.6
Assembly: hg38
Supplementary files format and content: Per-cell mtDNA genotypes, TCR sequences, and gene expression counts
Library strategy: scTCR-seq


title: Ribo-Seq, wild-type/mc6, 3 days old, L4 stage, replicate 1


title: Ribo-Seq, wild-type/tmc20, 4 days old, pregravid adults, replicate 2


title: PBMCs_Draw_20201211


title: Cardiomyocytes, sHFD, rep3

value: slight high fat diet


title: A549 cells, shControl, 3 days after ionizing radiation2 [B2]


title: bB958-ZHT_HT_24h

city: Ann Arbor

first: Elliott

middle: Daniel

last: SoRelle

state: MI

address: 1137 Catherine St.

department: Microbiology & Immunology

institute: The University of Michigan

description: 10x Genomics; Site: Duke

data_processing:
Read assembly, demultiplexing, barcode processing, and counting were performed using the cellranger pipeline (v3) from 10x Genomics
Assembly: hg38 + NC007605 (EBV Type 1) or hg38 + NC009338 (EBV type 2), depending on viral strain. P3HR1 line is infected with a Type 2 EBV strain. Akata and B958 lines are infected with Type 1 EBV strains
Supplementary files format and content: Tab-separated values (tsv) and matrix (.mtx) files

organism: Saguinus oedipus

growth_protocol: All cell lines grown in R10 (RPMI + 10% heat inactivated FBS)

extract_protocol:
Cells were harvested from culture at specified times after specified treatments and enriched to >90% viability by Ficoll gradient prior to single-cell library preparation
Library preparation was performed according to manufacturer's protocol -- 10x Genomics v2 3' Gene Expression Kit

treatment_protocol: Treatments in culture as described above

value: B cell

value: 25 nM 4-hydroxytamoxifen, 24h


title: Cardiomyocytes, sHFD, rep2


title: A549 cells, shControl, 3 days after ionizing radiation1 [B1]


title: Ribo-Seq, wild-type/tmc20, 3 days old L4 stage, replicate 2


title: A549 cells, shControl, 3 days after ionizing radiation3 [B3]


title: Ribo-Seq wild-type/tmc20, 4 days old pregravid adult, , rpelicate 1


title: B958-ZHT_Unstim

description: 10x Genomics; Site: Duke

value: Untreated


title: A549 cells, shFXR, sham irradiation2 [C2]


title: Cardiomyocytes, sHFD, rep1


title: A549 cells, shControl, sham irradiation3 [A3]


title: Ribo-Seq wild-type/tmc20, 3 days old, L4 stage, , rpelicate 1


title: 6_PC_U

city: Godollo

first: Eva

last: Varallyay

address: 4 Szent-Györgyi Albert Street

department: Institute of Plant Protection

institute: Hungarian University of Agriculture and Life Sciences

data_processing:
The quality check of the sequenced small RNA libraries was done by FastQC program, embedded in CLC
Trimming of raw reads was performed using the CLC
Removing redundant reads using CLC
Supplementary files format and content: trimmed redundant list, each read with its number of repeats

organism: Prunus cerasus

extract_protocol:
CTAB method (Gambino, 2008: https://doi.org/10.1002/pca.1078 )
modified Illumina Trueseq small RNA kit protocol: https://doi.org/10.1007/978-1-4939-7683-6_9

value: leaf

tag: cultivar

value: pool of 13 cultivars

tag: grow type

value: isolator house

tag: library type

value: small RNA


title: 4_PC_E4

value: pool of 11 cultivars

value: open field


title: Ribo-Seq rps-10(0)/tmc20, 4 days old L4 stage, , rpelicate 1


title: 3_PC_E3

value: pool of 9 cultivars


title: A549 cells, shControl, sham irradiation1 [A1]

tag: cell line

tag: cell type

value: non-small cell lung cancer cell lines

value: sham irradiation


title: Cardiomyocytes, ND, rep3

value: heart

value: normal diet


title: A549 cells, shControl, sham irradiation2 [A2]

value: WT


title: Cardiomyocytes, ND, rep1

value: Cardiomyocytes


title: Ribo-Seq wild-type/tmc5, 4 days old pre-gravid adult, , rpelicate 1

value: whole body


title: Pcif1-KO_PCIF1-CD-rescue_anabolicSLAM_series2

data_processing:
Basecalling was performed using Illumina RTA, with further demultiplexing performed by Illumina bcl2fastq 2.20.
Fastq sequences were first trimmed of 5' and 3' adapter sequences and poly(A) tails using Cutadapt 3.7 -q 20 -m 30 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AAAAAAAAAAAAAAAAAAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
Reads were mapped to hg38 assembly transcriptome (Gencode v28 comprehensive gene annotations) using STAR 2.7.10a --outMultimapperOrder Random --outSAMmultNmax 1. T to C conversion in the reverse complement of read1 was counted and nascent reads were defined as reads with T to C conversion count >= 2.
Bedgraphs (in RPM) of the reverse complement of the first nucleotide of read 1 were constructed using custom Python scripts.
Reads were counted using htseq-count 2.0.1 -s reverse -t UTR, with gencode.v28.chr_patch_hapl_scaff.annotation.gtf obtained from gencodesgenes.org. Read counts were subjected to DESeq2 1.30.1 with lfcshrink to quantify differential transcriptional output. Cumulative log2fold-change plots and box-and-whiskers plots were generated with custom Python scripts.
Assembly: hg38
Supplementary files format and content: bedgraph

extract_protocol:
48hr later, cells were harvested by scraping and nuclei was enriched using Nuclei EZ (Sigma NUC-101). Nuclei were homogenized in Trizol-LS and nuclear RNA was isolated using Phase-Lock (HEAVY) tubes according to manufacturer’s protocol. Residual genomic DNA was removed using RQ1 RNase-free DNAse (Promega M6101) before RNA was purified with RNA concentrator (Zymo R1015).
RNA-seq library was prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit-REV (Lexogen 016).

treatment_protocol: Cells were seeded in 6-well plates 24hr prior to transfection. Cells were then transfected with 5pmol siRNA against Dis3 (Silencer Select S229660), against scrambled control (Silencer Select 4390843) and/or against PCF11 (Silencer Select S28362); using Lipofectamine RNAimax (Invitrogen 13778030) according to manufacturer’s instructions.

value: Human embryonic kidney

value: PCIF1-CD overexpression


title: 7_PA_Paulus

organism: Prunus avium

value: cultivar "Paulus"

value: 2017 Augustus + 2019 July


title: 2_PC_E2

value: leaf


title: 5_PA_E


title: Ribo-Seq wild-type/tmc5, 3 days old L4 stagee, , rpelicate 1


title: Pcif1-KO_EGFP-rescue_anabolicSLAM

value: EGFP overexoression


title: Ribo-Seq rps-23 (0)/tmc5 4 days old , L4 stage, rpelicate 1


title: 1_PC_E1

value: small RNA


title: Cardiomyocytes, ND, rep2


title: TB + custom 9x NA rep 2

status: Public on Oct 30 2024

city: Calgary

first: Shawn

last: Lewenza

state: AB

address: 3330 Hospital Drive NW

department: Microbiology, Immunology & Infectious Diseases

country: Canada

institute: University of Calgary

data_processing:
Reads were mapped to Pseudomonas OST1909 genome using SHRiMP v2.2.3
.sam files were converted to fasta with Samtools (v 1.19.2)
Reads were assigned to transcripts via pseudoalignment with Kallisto v0.46.1-0.
Sleuth (v 0.30.0) in R (4.3.3) was used to do modeling and statistical analysis of transcriptome data.
Assembly: CP063780.1
Supplementary files format and content: TSV of counts and TPMs
Supplementary files format and content: Excel file of statistics

organism: Pseudomonas sp. OST1909

source_name: bacteria cultures

growth_protocol: Mig-log bacterial cultures were grown with or without exogenous naphthenic acids.

extract_protocol:
Total RNA was harvested with the RNeasy kit (Qiagen), DNAse treated, and ribosomal RNA was depleted with Ribo-Zero (Illumina)
cDNA sequencing libraries were prepared with the SOLiD Total RNA-Seq kit (Life Technologies)
Libraries were added to SOLiD sequencing beads using emulsion PCR, and sequences in a SOLiD 5500xl DNA sequencing for 75bp sequencing.

value: bacteria cultures

value: custom 9x NA


title: TB + acyclic Sigma NA rep 2

value: acyclic commercial (Sigma) NA


title: TB + OSPW-extracted NA rep 1

value: OSPW-extracted NA


title: TB + custom 9X NA rep 1


title: TB + OSPW-extracted NA rep 2


title: TAS51_mrna, replicate 2_Male ALL-Lymphosarcoma

city: Kansas City

first: Huzaifa

last: Hassan

state: MO

institute: Stowers Institute for Medical Research

data_processing:
Samples were sequenced by CSHL on a PacBio Sequel II sequencer. Pacbio long reads were analyzed using Iso-Seq (v 3) starting with the generation of consensus sequences from subreads. Subsequently, poly-A tails were trimmed, and the resulting full-length isoforms were then clustered to generate unpolished isoforms, which were further polished using subreads. The polished isoforms were aligned to the hg38 reference genome using pbmm2 (v 1.7.0) and collapsed based on genomic alignments
The transcripts generated from Iso-Seq were characterized using SQANTI (v3.4.2) with gene models retrieved from Ensembl release 102. Unannotated isoforms, Isoforms mapped to Antisense strand of an annotated gene, fusion genes and novel genes were removed for downstream analysis.
Assembly: hg38
Supplementary files format and content: SQANTI Annotations of pacbio Isoforms in TSV format

source_name: lymphoblastoid cell lines

growth_protocol: LCLs were cultured in Roswell Park Memorial Institute Medium 1640 with 2mM L-glutamine or equivalent, 15 % fetal bovine serum (Heat Inactivated) at 37C under 5% CO2.

extract_protocol:
Total RNA was extrcated using TRIzol (Invitrogen).
For polyA tail Iso-sequencing, total RNA was treated with ribosomal RNA depletion. SMRTbell Express Template Prep Kit 2.0 (PacBio, Cat# 100-938-900) was used for library construction. For nomal Iso-sequencing,  (without ribosomal RNA depletion), SMRTbell Express Template Prep Kit 2.0 (PacBio, Cat# 100-938-900) was used for library construction.
RNA-sequencing using Sequel II Sequencing Kit 2.0 (PacBio#101-820-200).

value: lymphoblastoid cell lines

value: B-cells

tag: Sex

value: male

tag: disease state

value: ALL-Lymphosarcoma

value: affected


title: TB DMSO control rep1

value: WT

value: DMSO


title: TB + acyclic Sigma NA rep 1


title: TAS51_mrna, replicate 1_Male ALL-Lymphosarcoma


title: TAS49_mrna, replicate 2_Female ALL

value: female

value: ALL


title: TAS50_mrna, replicate 2_Female ALL-Lymphosarcoma


title: TAS50_mrna, replicate 1_Female ALL-Lymphosarcoma


title: TAS43_mrna, replicate 1_Female Healthy

value: healthy donor

value: Apparently healthy


title: TAS49_mrna, replicate 1_Female ALL


title: TAS42_mrna, replicate 1_Male Healthy


title: TAS48_mrna, replicate 1_Male ALL


title: TAS41_mrna, replicate 2_Male Healthy


title: TAS39_mrna, replicate 2_Male FXD

value: FXD


title: TAS42_mrna, replicate 2_Male Healthy


title: TAS43_mrna, replicate 2_Female Healthy


title: TAS48_mrna, replicate 2_Male ALL


title: TAS39_mrna, replicate 1_Male FXD


title: TAS41_mrna, replicate 1_Male Healthy


title: TAS36_mrna, replicate 2_Male FXD


title: TAS29_mrna, replicate 2_Fale FXD

value: No data


title: TAS30_mrna, replicate 1_Female Healthy


title: TAS30_mrna, replicate 2_Female Healthy


title: TAS36_mrna, replicate 1_Male FXD


title: TAS29_mrna, replicate 1_Fale FXD


title: TAS23_mrna, replicate 1_Male Healthy


title: TAS22_mrna, replicate 1_Female Healthy


title: TAS21_mrna, eplicate 2_Fale FXD


title: TAS23_mrna, replicate 2_Male Healthy


title: TB DMSO control rep2

value: bacteria cultures


title: TAS21_mrna, replicate 1_Fale FXD


title: TAS22_mrna, replicate 2_Female Healthy


title: TAS20_mrna, replicate 1_Male FXD


title: TAS20_mrna, replicate 2_Male FXD


title: TAS19_mrna, replicate 2_Fale FXD


title: TAS18_mrna, replicate 2_Male FXD


title: TAS18_mrna, replicate 1_Male FXD


title: TAS11_mrna, replicate 1_Female Healthy


title: TAS10_mrna, replicate 1_Male Healthy


title: TAS2_mrna, replicate 2_Fale FXD


title: TAS11_mrna, replicate 2_Female Healthy


title: TAS1_mrna, replicate 2_Male FXD


title: TAS1_mrna, replicate 1_Male FXD


title: TAS51_total, replicate 1_Male ALL-Lymphosarcoma


title: TAS51_total, replicate 2_Male ALL-Lymphosarcoma


title: TAS50_total, replicate 1_Female ALL-Lymphosarcoma


title: TAS49_total, replicate 1_Female ALL


title: TAS2_mrna, replicate 1_Fale FXD


title: TAS50_total, replicate 2_Female ALL-Lymphosarcoma


title: TAS48_total, replicate 2_Male ALL


title: TAS48_total, replicate 1_Male ALL


title: TAS43_total, replicate 2_Female Healthy


title: TAS19_mrna, replicate 1_Fale FXD


title: TAS42_total, replicate 2_Male Healthy


title: TAS39_total, replicate 2_Male FXD


title: TAS43_total, replicate 1_Female Healthy


title: TAS42_total, replicate 1_Male Healthy


title: TAS36_total, replicate 2_Male FXD


title: TAS39_total, replicate 1_Male FXD


title: TAS10_mrna,replicate 1_Male Healthy


title: TAS41_total, replicate 1_Male Healthy


title: TAS30_total, replicate 1_Female Healthy


title: TAS29_total, replicate 2_Fale FXD


title: TAS23_total, replicate 2_Male Healthy


title: TAS36_total, replicate 1_Male FXD


title: TAS30_total, replicate 2_Female Healthy


title: TAS22_total, replicate 1_Female Healthy


title: TAS22_total, replicate 2_Female Healthy


title: TAS29_total, replicate 1_Fale FXD


title: TAS21_total, replicate 1_Fale FXD


title: TAS21_total, replicate 2_Fale FXD


title: TAS49_total, replicate 2_Female ALL


title: TAS19_total, replicate 2_Fale FXD


title: TAS18_total, replicate 1_Male FXD


title: TAS18_total, replicate 2_Male FXD


title: TAS11_total, replicate 2_Female Healthy


title: TAS41_total, replicate 2_Male Healthy


title: TAS11_total, replicate 1_Female Healthy


title: TAS10_total, replicate 2_Male Healthy


title: TAS10_total, replicate 1_Male Healthy


title: TAS1_total,replicate 2_Male FXD


title: TAS2_total, replicate 1_Fale FXD


title: TAS2_total, replicate 2_Fale FXD


title: TAS51 replicate 1_Male ALL-Lymphosarcoma, Ribosomal RNA depletion

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.20. Reads were aligned to UCSC genome hg38 with STAR aligner (version 2.7.3a ), using Ensembl 102 gene models. TPM values were generated using RSEM (version v1.3.0 )
Assembly: hg38
Supplementary files format and content: star_count.txt: Text file of Gene read counts, RSEM_TPM_table.txt: Text file of Transcripts per Million (TPM) of each gene

extract_protocol:
Total RNA was extrcated using TRIzol (Invitrogen).
Total RNA was used for library  construction. Library construction was performed using TruSeq Stranded RNA LT Kit Ribo-Zero Gold (48) (illumina, Cat # RS-122-2302 ).


title: TAS23_total, replicate 1_Male Healthy


title: TAS49 replicate 3_Female ALL, Ribosomal RNA depletion


title: TAS51 replicate 2_Male ALL-Lymphosarcoma, Ribosomal RNA depletion


title: TAS50 replicate 3_Female ALL-Lymphosarcoma, Ribosomal RNA depletion


title: TAS50 replicate 2_Female ALL-Lymphosarcoma, Ribosomal RNA depletion


title: TAS20_total, replicate 2_Male FXD


title: TAS20_total,replicate 1_Male FXD


title: TAS51 replicate 3_Male ALL-Lymphosarcoma, Ribosomal RNA depletion


title: TAS50 replicate 1_Female ALL-Lymphosarcoma, Ribosomal RNA depletion