title: NMN-3 [T3]

first: Ji

last: Wu

address: No. 800, Dongchuan Road

institute: Shanghai Jiao Tong University

data_processing:
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic and the low quality reads were removed to obtain the clean reads.  Then the clean reads were mapped to reference genome using hisat. FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained by HTSeq-count.
Assembly: mm9
Supplementary files format and content: The spreadsheet file contains the raw counts for each sample.

source_name: FGSCs

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: FGSCs

value: female germline stem cells

value: NMN


title: macrophage, control, rep1

status: Public on Apr 23 2025

type: SRA

city: Westmead

first: Jianwei

last: Chen

state: NSW

address: 176 Hawkesbury Rd

department: CTRR

country: Australia

institute: The Westmead Institute for Medical

description: Sample 1

library_source: transcriptomic

data_processing:
Short-read sequencing was performed on the Novaseq X platform (Illumina) with 150bp pair-end reads. Library sequencing quality was determined using FastQC (Babraham Bioinformatics: www.bioinformatics.babraham.ac.uk/).
Illumina adaptor sequence and low quality read trimming (read pair removed if < 20 base pairs) was performed using Trim Galore (Babraham Bioinformatics). STAR was used to align reads to mouse genome mm10 using ENSEMBL gene annotations as a guide.
Read counts data corresponding to ENSEMBL gene annotations were generated the STAR flag --quantMode GeneCounts. Multiqc was used to verify quality metrics. All analyses were performed in the R Statistical Environment with tidyverse.
Briefly, counts data were background corrected and normalized for library size using edgeR. DGE was determined using the QLFtest (BH MTC p <0.05).
Gene lists were functionally annotated with Gene Ontology (GO), REACTOME and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways (adjusted p value <0.05) using the cluster Profiler package
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each Sample
Supplementary files format and content: Excel file includes matrix table for each Sample
Supplementary files format and content: Excel file includes logFC, pValue, FDR, ect for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow

growth_protocol: Bone marrow macrophages were maintained in DMEM supplemented with 10% Fetal bovine serum (FBS), 1X penicillin and streptomycin, 2mM glutamine, 1XNon-Essential Amino Acid (NEAA), and 10ng/ml macrophage colony-stimulating factor (M-CSF) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was isolated from mouse macrophages using Ambion 463 RiboPure RNA Purification Kit (AM1924, Thermo Fisher).
Poly-A selected mRNA libraries were generated using the Illumina stranded mRNA Prep Kit (20040534, Illumina) and validated with the Agilent Tapestation 4200 and qPCR before sequencing.

treatment_protocol: S1-4 are samples without any treatment. S5-8 are samples stimulatedbyLPS and IFN-r, S9-12 are samples stimulated by IL4 and IL13, S13-16 are samples transduced with the intact CAR, S17-20 are samples transduced with the intact CAR and stimulated by TNF-a, S21-24 are samples transduced with the truncated CAR, S21-28 are samples transduced with the truncated CAR and stimulated by TNF-a.

tag: tissue

value: Bone marrow

tag: cell type

value: macrophage

tag: treatment

value: No treatment


title: Zlike_1

city: 湖北省 / 武汉市 / 洪山区

first: 京明

last: 李

address: 狮子山街1号华中农业大学

country: China

institute: 华中农业大学

description:
Library name: Sample 7
column name in raw_counts_All_Sample.xlsx: Zlike_1
Slike vs Zlike fpkm1 degseqfc1 padj0.05.xlsx

data_processing:
Brassica_napus.ZS11.v0.genome.fa
Raw reads were processed using fastp.
Reads were aligned to brassica napus reference genome （Brassica_napus.ZS11.v0.genome.fa）using hisat2.
FeatureCounts was used to count the number of paired mapping reads for each gene.
Assembly: Brassica_napus.ZS11.v0.genome.fa
Supplementary files format and content: The tabular file contains the raw counts for each sample

organism: Brassica napus

source_name: apical meristems

growth_protocol: experimental station

extract_protocol: Toal RNA was extracted by using RNAprep Pure Plant Kit (Tiangen Biotech) from apical meristems with three replications

treatment_protocol: no treatment

value: apical meristems

tag: cell line

value: Zlike

tag: genotype

value: WT


title: 16H097

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 32 (based on Ensembl 98)
Expression values were also computed using RSEM version 1.3.2 based on Gencode version 32 transcript annotations, using both stranded and unstranded parameters
Strand orientation is reverse, that is R1 aligns on the reverse gene orientation.
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column), including expression values as expected counts, FPKM and TPM

organism: Homo sapiens

source_name: Blood

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
Stranded sequencing libraries were prepared from total RNA using the NEBNext PolyA mRNA Magnetic Isolation Module.

value: Blood

value: Acute myeloid leukemia


title: 16H129


title: sh-Hmgb1-2 [sh-1-2]

city: Shanghai

state: Shanghai

data_processing:
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic and the low quality reads were removed to obtain the clean reads.  Then the clean reads were mapped to reference genome using hisat2. FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained by HTSeq-count.
Assembly: mm9
Supplementary files format and content: The spreadsheet file contains the raw counts for each sample.

extract_protocol:
Total RNA was extracted using the KAPA Stranded mRNA-Seq Kit following the manufacturer’s protocol.
The libraries were constructed using KAPA Stranded mRNA-Seq Kit according to the manufacturer’s instructions.


title: macrophage, control, rep3

description: Sample 3


title: SX3_3

city: 湖北省 / 武汉市 / 洪山区

address: 狮子山街1号华中农业大学

description:
Library name: Sample 6
column name in raw_counts_All_Sample.xlsx: SX3_3
SX3_vs_ZS11_fpkm1_DESeqfc1_padj0 .05.xlsx

value: mutant


title: 17H008


title: 16H144


title: sh-Hmgb1-1 [sh-1-1]


title: 16H064


title: macrophage, control, rep2

description: Sample 2


title: SX3_2

city: 湖北省 / 武汉市 / 洪山区

address: 狮子山街1号华中农业大学

description:
Library name: Sample 5
column name in raw_counts_All_Sample.xlsx: SX3_2
SX3_vs_ZS11_fpkm1_DESeqfc1_padj0 .05.xlsx


title: NMN-2 [T2]


title: SX3_1

city: 湖北省 / 武汉市 / 洪山区

address: 狮子山街1号华中农业大学

description:
Library name: Sample 4
column name in raw_counts_All_Sample.xlsx: SX3_1
SX3_vs_ZS11_fpkm1_DESeqfc1_padj0 .05.xlsx


title: sh-Hmgb1-3 [sh-1-3]


title: ZS11_3

city: 湖北省 / 武汉市 / 洪山区

address: 狮子山街1号华中农业大学

description:
Library name: Sample 3
column name in raw_counts_All_Sample.xlsx: ZS11_3
SX3_vs_ZS11_fpkm1_DESeqfc1_padj0 .05.xlsx


title: ZS11_2

city: 湖北省 / 武汉市 / 洪山区

address: 狮子山街1号华中农业大学

description:
Library name: Sample 2
column name in raw_counts_All_Sample.xlsx: ZS11_2
SX3_vs_ZS11_fpkm1_DESeqfc1_padj0 .05.xlsx


title: 16H088


title: 16H073


title: sh-Control-1 [sh-NC1]

value: Control


title: Control-3 [C3]


title: ZS11_1

city: 湖北省 / 武汉市 / 洪山区

address: 狮子山街1号华中农业大学

description:
Library name: Sample 1
column name in raw_counts_All_Sample.xlsx: ZS11_1
SX3_vs_ZS11_fpkm1_DESeqfc1_padj0 .05.xlsx


title: sh-Control-3 [sh-NC3]


title: Control-2 [C2]


title: NMN-2-ChIP

library_source: genomic

data_processing:
For ChIP pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16), then aligned to the mm9 reference genome using bowtie2 (version 2.3.4.1)(Langmead and Salzberg, 2012) with default parameters. PCR duplicates were removed using Samtools (version 2.0.1) (Li et al., 2009) and generated normalized genome coverage tracks from uniquely mapping reads (MAPQ>10) using deepTools2 (version 3.1).
Assembly: mm9
Supplementary files format and content: bigwig file

molecule: genomic DNA

extract_protocol:
The cells were cross-linked with 1% PFA at room temperature for 10 minutes, followed by cross-linked with glycine solution for 5 minutes and then resuspended in lysis buffer.
ChiP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific.


title: HK-374 cells MXC-017 treated

city: Los Angeles

first: Frank

last: Pajonk

state: CA

address: 10833 Le Conte Ave

country: USA

institute: UC Los Angeles

description:
Library name: HK_374-MXC017_MXC017
10x Genomics

library_source: transcriptomic single cell

data_processing:
FASTQ files were aligned to a custom reference containing the human genome (GRCh38) and processed using the PIPseeker software, version 3.3.3 (Fluent Biosciences). Raw matrices were in processed in Seurat version 5 20. Cells with less than 500 genes were filtered out and cells with high mitochondrial gene count (>5%) were removed.
Assembly: human genome (hg38)
Supplementary files format and content: FASTQ and matrix files

source_name: Glioblastoma

growth_protocol: Patient-derived HK-374 gliomaspheres were cultured in serum-free conditions in ultra-low adhesion plates in DMEM/F12, supplemented with SM1 Neuronal Supplement, EGF, bFGF and heparin.

extract_protocol:
After two weeks, tumors were then harvested and dissociated into single cells using the Miltenyi Brain Tumor Dissociation Kit (#130-095-942), followed by mouse cell depletion (Mouse Cell Depletion Kit, #130-104-694, Miltenyi). Cells from 2-3 mice were pooled, passed through a 40-µm strainer and counted using a hemacytometer. After pelleting by centrifugation at 300 g for 5 minutes at 4°C, the cells were resuspended in the provided Cell Resuspension Buffer. Approximately 50,000 cells were then captured and processed for single-cell transcriptomics using the PIPseqTM T2 3’ Single Cell RNA Kit v5 (Fluent Biosciences).
Sequencing libraries were prepared according to PIPseq T2 instructions, with 12 cycles for cDNA amplification and 8 cycles for library amplification, depending on the DNA amount. The libraries were quantified using a Qubit 4 Fluorometer and a TapeStation 4200 and sequenced as per manufacturer recommendation on a NovaSeq X Plus – 25B 2 x150bp, with 3.25 billion reads in total for 8 samples.

treatment_protocol: Tumor engraftment was verified by bioluminescent imaging, after which mice received either a single 4 Gy dose of radiation alone or radiation followed by MXC-017 treatment (5 i.p. injections per week, 50 mg/kg) for two weeks.

value: Glioblastoma

value: patient-derived cell line


title: U118_resistant_RNA-seq_3

city: Chongqing

first: liao

last: bin

address: 118 Xingguang Avenue

institute: Chongqing General Hospital, Chongqing University

data_processing:
FastQC (version 0.11.2) was used for evaluating the quality of sequenced data. Raw reads were filtered by Trimmomatic (version 0.36).
Clean reads were mapped to the reference genome using HISAT2 (version 2.0) with default parameters. RSeQC (version 2.6.1) was used to quantify alignment results. Qualimap (version 2.2.1) was employed to check for uniform distribution and genomic structure. BEDTools (version 2.26.0) was used for statistical analysis of gene coverage.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes TPM values for each Sample

extract_protocol:
Total RNA was extracted using the Total RNA Extractor (Trizol) kit (B511311, Sangon, China) according to the manufacturer’s protocol. A total amount of 1 μg RNA per sample was used for the construction of the sequencing library .
Sequencing libraries were generated using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: phenotype

value: resistant


title: NMN-2-Input


title: 16H007


title: sh-Control-2 [sh-NC2]


title: Control-1 [C1]


title: HK-374 cells 0 Gy Control

description:
Library name: HK_374-MXC017_0Gy
10x Genomics

value: control


title: U118_sensitive_RNA-seq_1

value: sensitive


title: 16H045


title: NMN-1 [T1]

value: FGSCs

value: female germline stem cells


title: HK-374 cells RT + MXC-017 treated

description:
Library name: HK_374-MXC017_RT_MXC017
10x Genomics


title: U118_resistant_RNA-seq_1


title: 16H042


title: U118_sensitive_RNA-seq_3


title: 16H027

value: Bone marrow


title: 15H139


title: U118_resistant_RNA-seq_2


title: HK-374 cells irradiated

description:
Library name: HK_374-MXC017_RT
10x Genomics


title: U87_resistant_RNA-seq_1

source_name: U-87 MG

value: U-87 MG


title: U87_resistant_RNA-seq_3


title: 16H063


title: U118_sensitive_RNA-seq_2


title: Patient 10 CSF Low MOCA scRNAseq

city: New Haven

first: Kristopher

last: Kahle

state: Connecticut

address: 333 Cedar St

institute: Yale University Department of Neurosurgery

description:
Library name: Sample 19
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)"
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CSF

extract_protocol:
Animals were anesthetized with Ketamine/Xylazine and transcardially perfused with ice cold TBS before brain removal. Choroid plexi from bilateral lateral ventricles were microdissected in ice cold HBSS with 30uM Actinomycin D (ActD, Sigma, cat#A1410 ) and digested at 37oC for 20 min with Collagenases-I and -IV (10 U/mL, 400 U/mL final, Worthington, Cat# LS004194, and LS004184) and DNase I (30 U/mL, Roche, cat# 04716728001) and ActD (3uM). For Flow sorting, the cell suspension was blocked with CD16-CD32 antibodies (1:100, biolegend, cat#101302) and stained 30 min at 4oC with anti-rat CD45-PE/cy7 (1:100, biolegend, cat#202207) to and DAPI (50ug/mL). Cells were subsequently washed in FACS staining buffer (0.5% BSA, 2mM EDTA in PBS without Calcium/Magnesium) and centrifuged at 350 rcf for 5 minutes. Cells were resuspended in 300ul of FACS buffer and sorted by CD45 positivity on a BD ARIA instrument. CD45 positive and CD45 negative cells were collected in 0.4% BSA/PBS and 3uM ActD and sent for 10X 3prime library preparation and sequencing at Yale Center for Genome Analysis
Sequencing libraries were loaded on an Illumina HiSeq4000 flow cell with sequencing settings following the recommendations of 10x Genomics (read 1: 26 cycles; read 2: 98 cycles; index i7: eight cycles; index i5: no cycles; 2.1 pM loading concentration). The Cell Ranger pipeline was designed to perform sample demultiplexing and to generate FASTQ files for read 1, read 2 and the i7 sample index. Read 2, containing the cDNA, was mapped to the reference genome (mouse mm10) using STAR

value: CSF

value: Low MOCA


title: 15H144


title: U87_sensitive_RNA-seq_3


title: Control-2-Input


title: Patient 10 PBMC  Low MOCA scRNAseq

description:
Library name: Sample 20
10x Genomics

source_name: PBMC

value: PBMC


title: Patient 8 PBMC  Low MOCA scRNAseq

description:
Library name: Sample 16
10x Genomics


title: NMN-1-ChIP

value: NMN


title: U87_sensitive_RNA-seq_2


title: U87_resistant_RNA-seq_2


title: 15H105

value: Blood


title: Control-2-ChIP


title: Patient 9 PBMC  Low MOCA scRNAseq

description:
Library name: Sample 18
10x Genomics


title: Control-1-Input


title: U87_sensitive_RNA-seq_1


title: Control-1-ChIP


title: NMN-1-Input


title: 15H080

value: Acute myeloid leukemia


title: Patient 9 CSF Low MOCA scRNAseq

description:
Library name: Sample 17
10x Genomics


title: 15H058


title: 6M-T3

city: Hangzhou

first: Dengfeng

last: Ruan

state: China

address: 88 Jie Fang Road

department: Department of Orthopedic Surgery

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

description:
Library name: Sample 29
6-month-old

data_processing:
Illumina Casava software used for basecalling.
The RNA sequencing reads were aligned to GRCm39 Mus musculus reference genome with STAR(v2.7.10a) using a supplied set of known transcripts in GTF format (RefSeq GRCm39; Mus musculus, Ensembl).
Count of each gene was calculate by using featureCounts (v2.0.0).
Differentially expressed genes were calculated using DESeq2.
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample，

molecule: polyA RNA

source_name: tendon tissue

extract_protocol:
Total RNA was isolated by TRIzol Reagent (Thermo Fisher Scientific, USA), mRNA was purified using poly-T oligo-attached magnetic beads, fragmented and then reverse-transcribed into double-stranded cDNA.
 A sequencing library was generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB, USA) and the clustering of index-coded samples was generated using TruSeq PE Cluster Kit v3-cBot-HS (Illumia, USA).

treatment_protocol: The tendon is subjected to needle puncture injury, and then sampling is performed at different time points after the injury.

value: tendon tissue

value: wild type

value: normol tendon


title: 15H065


title: ATAC_seq_BCAS_hippocampus_4

first: Zengyu

last: Zhang

address: Dong'an Road

department: Neurology

institute: Fudan University

data_processing:
ATAC-seq: Raw data was first processed by FastQC for quality control, and cleaned using Trim-galore. Clean data were then aligned to the Mouse (mm10) reference genome using default settings of Bowtie2 v2.3.4.3. After removing duplications, Samtools v1.9 was used to sort and build the alignment file index. MACS2 was used for peak calling. Parameters were used as follows: --keep-dup 1 --shift -100 --extsize 200 –nomodel. Diffbind was used for differential analysis.
Assembly: mm10
Supplementary files format and content: ATAC-seq: ATAC_peak text files

source_name: the right hippocampus

growth_protocol: The mice were housed at 25°C and fed standard rodent chow and tap water

extract_protocol:
Nuclei was extracted from isolated hippocampus in 1 ml of lysis buffer (0.32M sucrose, 5 mM CaCl2, MgAce2, EDTA, Tris-HCl pH=8, w/o 0.1% NP-40), followed by washing in a sucrose buffer, and collected by centrifugation.
ATAC-seq library was generated using reagents from TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) according to the manuscript’s instruction with modifications.

treatment_protocol: The control group was exposed to sham operation. The experimental group was exposed to bilateral carotid artery stenosis (BCAS) operation

tag: strain

value: the right hippocampus


title: Patient 7 PBMC  Low MOCA scRNAseq

description:
Library name: Sample 14
10x Genomics


title: Patient 8 CSF Low MOCA scRNAseq

description:
Library name: Sample 15
10x Genomics


title: ATAC_seq_BCAS_hippocampus_3

value: bilateral carotid artery stenosis (BCAS) operation


title: 6M-T2

description:
Library name: Sample 28
6-month-old


title: 15H066


title: Patient 7 CSF Low MOCA scRNAseq

description:
Library name: Sample 13
10x Genomics


title: 15H061


title: ATAC_seq_BCAS_hippocampus_2


title: Patient 6 PBMC  Unknown MOCA scRNAseq

description:
Library name: Sample 12
10x Genomics

value: Unknown MOCA


title: 15H045


title: 15H038


title: 6M-T1

description:
Library name: Sample 27
6-month-old


title: Patient 6 CSF Unknown MOCA scRNAseq

description:
Library name: Sample 11
10x Genomics


title: d28_rep4

description:
Library name: Sample 25
8-week-old

value: The tendon on the twenty-eighth day after injury


title: 15H033


title: ATAC_seq_Sham_hippocampus_4

value: Sham operation


title: d28_rep3

description:
Library name: Sample 24
8-week-old


title: ATAC_seq_BCAS_hippocampus_1


title: Patient 5 CSF High MOCA scRNAseq

description:
Library name: Sample 9
10x Genomics

value: High MOCA


title: ATAC_seq_Sham_hippocampus_3


title: Patient 4 PBMC  High MOCA scRNAseq

description:
Library name: Sample 8
10x Genomics


title: Patient 5 PBMC  High MOCA scRNAseq

description:
Library name: Sample 10
10x Genomics


title: ATAC_seq_Sham_hippocampus_2


title: d28_rep2

description:
Library name: Sample 23
8-week-old


title: 15H027

value: Bone marrow


title: ATAC_seq_Sham_hippocampus_1


title: 15H003


title: d28_rep1

description:
Library name: Sample 22
8-week-old


title: d28_rep5

description:
Library name: Sample 26
8-week-old


title: Patient 4 CSF High MOCA scRNAseq

description:
Library name: Sample 7
10x Genomics


title: T3

city: Paris

first: Céline

last: Vallot

address: 26 Rue D'Ulm

country: France

institute: Institut Curie

data_processing:
The scRNA-seq sequencing files were preprocessed using the cellRanger pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/3-0). All the samples were aligned against the mm10 reference transcriptome whereas the juxta-tumor human samples were aligned against the hg19 reference transcriptome; and only cells identified as "not doublets" by DoubletFinder included in the CellRanger count were kept.
Assembly: mm10
Supplementary files format and content: The processed data files are the output from CellRanger count. For each sample,the file formats include:  ‘*barcodes.tsv’  files containing the cell barcode sequence ; the ‘*features.tsv’ files containing the features (gene symbols) and the ‘*matrix.mtx’ files containing the sparse (non-zero) matrix in .mtx format. These were further loaded on R library suits.

source_name: Mammary Gland

growth_protocol:
mammary gland/tumor cell dissociation protocol:
control and tumor samples were roughly cut  with dissecting scissors  2 scalpels for approximately 10 min. Cell dissociation was performed by enzymatic digestion with 3mg/ml collagenase I (Roche, 11088793001) and 100U/ml hyaluronidase (Sigma-Aldrich, H3506) in complete media (HBSS (24020117), 5% SVF) during 1h30 under agitation at 170 rpm at 37°C. Thi step was followed by a second round dissociation under PBS 0,25% Trypsin-Versen (Thermo Fisher Scientific, 15040-033) prewarmed at 37°C for 1min30s with pipetting for 45s. The cell suspension was then treated with dispase 5 mg/ml (Sigma-Aldrich, D4693) and DNase 0,1 mg/ml (Roche, 11284932001) in complete media for 5 min at 37°C. A treatment with Red Blood cell lysis buffer (Thermo Fisher Scientific, 00-4333-57) was carried out then the suspension was filtered at 40µM before counting and FACS staining. Cell suspensions were stained 20 min in dark at 4°C with anti-CD45-APC 1:100 (BioLegend, 103112), anti-CD31-APC 1:100 (BioLegend, 102510), anti-CD24-BV421 1:50 (BioLegend, 101826), anti-CD49f-PE 1:50 (BioLegend, 313622). Cells were resuspended in cytometry media (PBS, BSA, EDTA). For the mammary gland samples, we either recovered the total epithelium or the luminal and basal cells populations separately.

extract_protocol: Cell suspensions were resuspended in PBS 0,04% BSA according to Chromium 10X recommandations. Depending on the samples, approximately 3000 or 4000 cells were loaded on the Chromium Single Cell Controller Instrument (Chromium single cell 3’ v3 or 3’ NextGem, 10X Genomics, PN-1000075) in accordance with the manufacturer's protocol. Libraries were sequenced on a NovaSeq 6000 (Illumina) in PE8-8-91.

value: Mammary Gland

tag: age

value: CreP Tp53 fl/fl Brca1 fl/fl

tag: cre type

value: Cre+

tag: epithelial enrichment

value: yes


title: Patient 3 PBMC  High MOCA scRNAseq

description:
Library name: Sample 6
10x Genomics

value: PBMC


title: 15H002

value: Blood


title: T1


title: d14_rep5

description:
Library name: Sample 21
8-week-old

value: The tendon on the fourteenth day after injury


title: Patient 3 CSF High MOCA scRNAseq

description:
Library name: Sample 5
10x Genomics

value: CSF


title: 14H164

value: Acute myeloid leukemia


title: T2


title: d14_rep4

description:
Library name: Sample 20
8-week-old

value: tendon tissue

value: wild type


title: 14H156


title: Patient 2 PBMC  High MOCA scRNAseq

description:
Library name: Sample 4
10x Genomics


title: mmT_5.2m


title: 14H119


title: mmT_5.4m


title: d14_rep3

description:
Library name: Sample 19
8-week-old


title: d14_rep2

description:
Library name: Sample 18
8-week-old


title: 14H112


title: Patient 2 CSF High MOCA scRNAseq

description:
Library name: Sample 3
10x Genomics


title: Patient 1 PBMC  High MOCA scRNAseq

description:
Library name: Sample 2
10x Genomics


title: d14_rep1

description:
Library name: Sample 17
8-week-old


title: Patient 1 CSF High MOCA scRNAseq

description:
Library name: Sample 1
10x Genomics


title: CreP_3m


title: d7_rep4

description:
Library name: Sample 16
8-week-old


title: CreP_5m

value: no


title: 14H103


title: 14H102


title: d7_rep3

description:
Library name: Sample 15
8-week-old

value: The tendon on the seventh day after injury


title: CreP_2.7m


title: 14H095


title: D920_UTD_stim_rapa

city: Seattle

first: Jill

last: Rosenberg

state: WA

address: 188 E Blaine St

institute: Regeneron Pharmaceuticals

description: Library name: Sample62

data_processing:
Reads were filtered for quality and aligned to the Genome Resource Consortium hg38 human genome reference using STAR (2.5.4b).
Gene expression was quantified as transcripts per million (TPM) using RSEM (1.3.1).
Assembly: hg38
Supplementary files format and content: comma-delimited text file contains RSEM TPMs for each sample.
Supplementary files format and content: comma-delimited text file contains RSEM expected counts for each sample.

source_name: T cells

growth_protocol: To generate research scale CAR-T cell products, PBMCs were thawed (recorded as day 0 of culture) and resuspended in TCGM supplemented with 250 IU/ml recombinant human IL-2 (Stemcell, catalog 78220.3) prior to activation with 50ng/ml anti-CD3 (clone OKT3) and anti-CD28 (clone 15E8) antibodies (Miltenyi Biotec). Lentivirus supernatants were directly added to PBMC cultures 24 hours later (multiplicity of infection [MOI] = 10). On day 3 of culture (72 hours after activation), transduced PBMC were collected, washed, and resuspended in complete TCGM with human IL-2 at 0.5 x 10^6 cells/ml and transferred to gas permeable culture vessels (G-REX, WilsonWolf). Cultures were expanded for a total of 10 days until assays or cryopreservation.

extract_protocol:
Total RNA was isolated using the Qiagen 96-well RNeasy Prep Kit.
Libraries were generated using KAPA 148 Hyperprep Kit with RiboErase and KAPA Unique Dual-Indexed Adapter Kit (Roche).

treatment_protocol: Transduced and untransduced T cells generated from four donor PBMC samples were cultured with either media or media supplemented with 1 nM rapamycin and stimulated with A549 engineered to overexpress the antigen of interest (CD33 or MAGEA4-HLA-A:0201) or left unstimulated for 18 hours. T cells were then sorted to remove tumor cells using REAlease® CD4/CD8 (TIL) MicroBead Kit, human (Miltenyi).

value: T cells

tag: transgene

value: UTD

tag: donor

value: rapamycin

tag: stimulation

value: Stimulated


title: CreN_5m_b

value: Mammary Gland

value: CreN Tp53 +/+ Brca1 +/+

value: Cre-


title: d7_rep2

description:
Library name: Sample 14
8-week-old


title: 14H094

value: Bone marrow


title: D920_UTD_nostim_norapa

description: Library name: Sample60

value: media alone

value: Unstimulated


title: CreN_5m_a


title: d7_rep1

description:
Library name: Sample 13
8-week-old


title: D920_TCR_stim_rapa

description: Library name: Sample59

value: TCR


title: 14H059

value: Blood


title: CreN_6m


title: d3_rep3

description:
Library name: Sample 11
8-week-old

value: The tendon on the third day after injury


title: 14H053

value: Acute myeloid leukemia


title: 14H024


title: d3_rep4

description:
Library name: Sample 12
8-week-old

value: tendon tissue

value: wild type


title: D920_TCR_stim_norapa

description: Library name: Sample58


title: d3_rep1

description:
Library name: Sample 9
8-week-old


title: Sample set B, sample barcoding

city: Chicago

first: Peter

last: Savage

state: IL

department: Pathology

institute: University of Chicago

library_source: other

data_processing:
Gene expression libraries were demultiplexed with CellRanger count v4.0.2 against the mm10-2020-A reference genome from 10X.
Feature barcoding libraries were demultiplexed with CellRanger count v4.0.2 against the mm10-2020-A reference genome from 10X, and using the fbc_v2.csv feature reference file.
VDJ libraries were demultiplexed with CellRanger vdj v4.0.2 against the vdj-GRCm38-alts-ensembl-5.0.0 reference from 10X.
Cells were assigned to original Sample IDs and genotypes based on their sample set batch and hashtag, as listed in fbc.names.txt. For each cell, the distribution of protein counts in the feature barcoding data set was compared acorss all hashtags: cells with >80% of total feature barcoding counts coming from a single hashtag were assigned to the corresponding sample ID. Cells not meeting this criteria were discarded. Additionally, cells with fewer than 750 genes expressed, fewer than 2000 total UMI counts, or greater than 15% expression from mitochondrial genes were removed. The final combined cell set, including original sample IDs, genotypes, and final cluster assignments and cell types, is provided in gex-clustered-final_metadata.txt.
Assembly: mm10
Supplementary files format and content: fbc_v2.csv: Feature barcode reference file for CellRanger
Supplementary files format and content: fbc.names.txt: Metadata linking feature barcode IDs to original sample IDs and genotypes.
Supplementary files format and content: gex-clustered-final_metadata.txt: Final cell metadata for all cells used in downstream analysis.
Supplementary files format and content: *_matrix.mtx.gz: Sparse matrix files in MatrixMarket format
Supplementary files format and content: *_barcodes.tsv.gz: Cell barcode sequences for matrix files
Supplementary files format and content: *_features.tsv.gz: Gene annotations for matrix files
Supplementary files format and content: *_airr_rearrangement.tsv: Annotated contigs and consensus sequences of V(D)J rearrangements in the AIRR format.
Supplementary files format and content: *_all_contig_annotations.csv: High-level and detailed annotations of all contigs (from cell and background barcodes) in CSV format.
Supplementary files format and content: *_all_contig.fasta.gz: FASTA format sequence for each assembled contig in the V(D)J library.
Supplementary files format and content: *_clonotypes.csv: High-level descriptions of each clonotype.
Supplementary files format and content: *_consensus_annotations.csv: High-level and detailed annotations of each clonotype consensus sequence
Supplementary files format and content: *_filtered_contig_annotations.csv: High-level annotations of each high-confidence contigs from cell-associated barcodes.

molecule: protein

source_name: CD4+ T cells

growth_protocol: Cells were isolated from the spleens of male mice that were 8-12 weeks of age

extract_protocol:
To maximize cell viability, cell isolation, staining, enrichment, and FACS sorting was performed over a 12hr period directly before sequencing, and cells were kept cold or on ice whenever possible. Cells were isolated from the spleens of infected mice in two “batches”: the first consisting of 4 C4WT and 5 C4ΔTEC mice, and the second consisting of 5 C4WT and 5 C4ΔTEC mice. For each batch, individual spleens were first enriched for CD4+ T cells using CD4+ T cell negative selection kit (Miltenyi Biotec) following the manufacturers protocol. Individual samples were subsequently stained with C4/I-Ab tetramers as described above. Following tetramer staining, individual samples were incubated with anti-PE and anti-APC microbeads (Miltenyi Biotec) for 15 min on ice (100ul each antibody cocktail / ml), washed, and enriched over an autoMACS magnetic column. Following enrichment, the individual bound fractions were stained with separate surface marker antibody master mixes as described above in minimal staining buffer. Each surface stain master mix contained uniform surface markers common to all mixes, but contained 1 of 10 TotalseqTM-C030X hashing antibodies (Biolegend) used to identify cells derived from each mouse. Following surface staining, all samples within a batch were pooled and C4/I-Ab tetramer+ cells were sorted by FACS using a BD FACSAria Fusion 5-18 cytometer. Ultimately, two sorted samples (one per batch) containing C4/I-Ab tetramer+ cells from pooled and hashtagged mice resulted after isolation. These samples were resuspended in 45ul of sequencing buffer (0.04% BSA in PBS), and 40ul of each sample was loaded into one of two lanes of a sequencing chip and then subjected to Drop-seq (10X Genomics) to coencapsulate individual cells in reverse emulsion droplets in oil together with one uniquely barcoded mRNA-capture bead. Libraries were derived from single cells, then subjected to next-generation sequencing.
5' cDNA libraries were constructed for individual cells using a 10X Genomica Chromium Controller (gene expression, VDJ, and feature barcode). The two samples containing constructed libaries were sequenced across two lanes of a SP-100 flowcell.
scRNA-seq, plus feature barcoding (sample hashing) and VDJ sequencing of the TCR

treatment_protocol: Mice were infected intraveneously (retro-orbital) with 10^7 CFU Lm[C4], and cells were extracted from the spleen 4 days post-infection

tag: library type

value: Feature barcoding

value: CD4+ T cells

value: mixed

tag: sample pool

value: Pooled sample B


title: D920_RESET_stim_rapa

description: Library name: Sample56

value: T cells

value: RESET

value: rapamycin

value: Stimulated


title: D920_TCR_nostim_norapa

description: Library name: Sample57


title: Sample set B, TCR

value: VDJ sequencing


title: d3_rep2

description:
Library name: Sample 10
8-week-old


title: D920_UTD_nostim_rapa

description: Library name: Sample61

value: UTD


title: D920_RESET_nostim_rapa

description: Library name: Sample55

value: Unstimulated


title: 12H077

value: Bone marrow


title: 12H159


title: 12H019

value: Blood


title: 15H037


title: D920_RESET_nostim_norapa

description: Library name: Sample54

value: media alone


title: d1_rep4

description:
Library name: Sample 8
8-week-old

value: The tendon on the first day after injury


title: Sample set A, sample barcoding

value: Pooled sample A


title: Sample set B, gene expression

value: Gene expression


title: Sample set A, TCR


title: d1_rep3

description:
Library name: Sample 7
8-week-old

value: tendon tissue

value: wild type


title: D920_DARIC_stim_rapa

description: Library name: Sample53

value: DARIC


title: 11H194

value: Acute myeloid leukemia


title: Sample set A, gene expression

value: CD4+ T cells

value: mixed


title: d1_rep2

description:
Library name: Sample 6
8-week-old


title: 11H067


title: D920_DARIC_nostim_rapa

description: Library name: Sample52

value: T cells

value: rapamycin


title: Blastocyst Dis3L WT_1

city: Warszawa

first: Tomasz

middle: M.

last: Kuliński

state: Mazowieckie

address: ul. Ks. Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

data_processing:
Reads were mapped to the reference mouse genome (GRCm38) using the STAR short read aligner (version STAR 2.4.0b)
Quality control, read processing and filtering, visualization of the results was performed using custom scripts and elements of the RSeQC, BEDtools and SAMtools packages.
Reads were counted of reads for the Genecode v M6 basic annotation using featureCounts of the subread package (v2.0.1).
Differential expression analyses were performed using the DESeq2 (version 1.34.0) Bioconductor R package
Assembly: GRCm38
Supplementary files format and content: tab separated format. Contais count tables as well as DESeq2 differential annalisis output

source_name: Blastocyst

growth_protocol: Ovulation was artificially stimulated in females by intraperitoneal injection of 10 units of PMSG and hCG in 48h interval. Stimulated females were mated with males in the evening and terminated by cervical dislocation and dissected 96h after hCG injection to obtain blastocysts. ransferred to single wells of gelatin-coated culture plates with feeder layer of inactivated MEFs. After 3-4 days of culture blastocysts formed outgrowths which were disaggregated by 5 min incubation in 0.25% trypsin-EDTA followed by mechanical pipetting. Resulting cell suspension was transferred into a separate culture plate well onto fresh layer of inactivated MEFs and inspected daily for appearance of primary colonies. Established ESC lines were cultured in medium composed of KnockOut Dulbecco's modified Eagle's Medium supplemented with 15% heat inactivated FBS with addition of nonessential amino acids, L-glutamine, β-mercaptoethanol, penicillin and streptomycin, and 500 IU/ml LIF.

extract_protocol:
RNA from ES cells was extracted by lysis of 1 million cells using TRI Reagent, following manufacturers protocol. RNA from blastocysts was extracted using PicoPure RNA Isolation Kit following manufacturers protocol.
For ES cells’ RNA sequencing, total DNA-free RNA was ribodepleted using Ribo-Zero Gold rRNA-removal kit (Illumina). rRNA-free RNA samples were clean-up by precipitation with 3M NaAc. Sequencing libraries were prepared using KAPA Stranded RNA-Seq Library Preparation Kit (KAPA Biosystems). Between each step samples were cleaned up using AMPure XP Reagent magnetics beads. Library quality and fragment size distribution was verified by electrophoresis in Agilent 2100 Bioanalyzer (Agilent Technologies Inc.).     RNA-seq libraries from single blastocysts DNA-free RNA samples were prepared by tagmentation reaction following published protocols (24,25) with various steps and amount of enzyme optimized for use of homemade batch of Tn5 transposase produced in our laboratory. Briefly: Tn5 (0,25 mg/ml) was loaded with linker oliguncleotides Tn5ME-A/Tn5Merev and Tn5ME-B/Tn5Merev by mixing of 10 ul Tn5 with 0,5 ul of both linkers (0,35 uM) and incubating for 45 min in 23oC with shaking at 350 rpm. Right before the reaction setup loaded Tn5 was diluted 10 times with nuclease-free water. 10 ul of freshly prepared tagmentation buffer (20 mM Tris-HCl ph 7,5; 20 mM MgCl2; 50% dimethylformamide (Sigma-Aldritch)  were mixed with 5 ul of diluted Tn5 and 5 ul od cDNA, incubated for 3 min at 55oC in preheated thermocycler and cooled to 10oC for 1 min. Reaction was inactivated by addition of 5 ul 0,2% SDS (Sigma-Aldrich and incubation for 5 min at RT. Tagmented cDNA was purified in 1,25 volume of AMPure XP Reagent magnetic beads.     For library amplification (15 cycles) KAPA HiFi HotStart ReadyMix PCR Kit (Roche) with addition of 5% DMSO was used. Number of cycles yielding best results was determined experimentally and was further individually adjusted for each batch of prepared cDNA. Library quality and fragment size distribution was verified by electrophoresis in Agilent 2100 Bioanalyzer.  Illumina NovaSeq or NextSeq sequencing platform in the 100-nt or 75-nt pair-end mode was used for sequencing.

value: Blastocyst

value: Dis3L WT


title: d0_rep4

description:
Library name: Sample 4
8-week-old

value: normol tendon


title: Blastocyst Dis3L KO_3

value: Dis3L KO


title: D920_CAR_stim_norapa

description: Library name: Sample49

value: CAR

value: Stimulated


title: D920_CAR_stim_rapa

description: Library name: Sample50


title: D920_CAR_nostim_rapa

description: Library name: Sample48

value: Unstimulated


title: D920_DARIC_nostim_norapa

description: Library name: Sample51

value: media alone


title: 11H015

value: Bone marrow


title: d0_rep3

description:
Library name: Sample 3
8-week-old

value: tendon tissue


title: 10H044


title: 10H114


title: 11H001

value: Blood


title: d0_rep1

description:
Library name: Sample 1
8-week-old

value: wild type


title: 10H125

value: Acute myeloid leukemia


title: d1_rep1

description:
Library name: Sample 5
8-week-old

value: The tendon on the first day after injury


title: Blastocyst Dis3L KO_1


title: D320_UTD_stim_rapa

description: Library name: Sample46

value: UTD


title: d0_rep2

description:
Library name: Sample 2
8-week-old


title: Blastocyst Dis3L WT_3


title: Blastocyst Dis3L KO_2


title: Blastocyst Dis3L WT_2


title: I7D

description: Library name: I7D

data_processing:
Illumina Casava software used for basecalling.
Quality control, read mapping, gene counts and unique molecular identifier (UMI) counts were processed as described in 2.3 by the celescope pipeline of singleronbio. Matrix files were generated based on gene counts and UMI count.
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample，

extract_protocol:
Upon the euthanasia of mice, the mice were perfused with normal saline and tendons were dissected and placed in Dulbecco’s modified Eagle’s medium (low glucose; Thermo Fisher Scientific, USA) with 10% (vol/vol) fetal bovine serum (FBS, Gibco, USA) and 1% (vol/vol) penicillin-streptomycin (Thermo Fisher Scientific, USA). The specimens were rinsed twice with phosphate buffered saline (PBS) and minced, then subjected to pre-warmed dissociation solution (3 mg/mL Collagenase I (Gibco, USA) and 4 mg/mL Dispase II (Roche, Swiss) at 37 °C, 5%CO2 cell incubator for 2 hours. Every 30 minutes the tissues were gently blown by pipette. After digestion, 40-micron sterile strainers (Biosharp, China) were used to filter residue and the samples were centrifuged at 1,200 rpm for 5 min. To obtain single cell suspension, supernatant was discarded and 0.5mL PBS were added to resuspend the sediment.
Single-cell suspensions (1×10^5 cells/mL) with PBS were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding beads collection, mRNA transcription, PCR amplification, fragmentation, ligation and library construction were conduct as per manufacture’s protocol (GEXSCOPE® Single Cell RNA Library Kits, Singleron, China).

value: tendon injury

tag: time point

value: on the seventh day after injury


title: D920_CAR_nostim_norapa

description: Library name: Sample47

value: T cells


title: 08H116


title: I30D

description: Library name: I30D

value: on the twenty-eighth day after injury


title: 08H080


title: 08H092

value: Myelodysplastic syndrome


title: D320_UTD_nostim_rapa

description: Library name: Sample45

value: rapamycin


title: I1D

description: Library name: I1D

value: on the first day after injury


title: D320_UTD_nostim_norapa

description: Library name: Sample44


title: D320_TCR_stim_rapa

description: Library name: Sample43

value: TCR

value: Stimulated


title: WT

description: Library name: WT

value: normol tendon


title: D320_RESET_stim_rapa

description: Library name: Sample40

value: RESET


title: D320_TCR_stim_norapa

description: Library name: Sample42

value: media alone


title: D320_RESET_nostim_rapa

description: Library name: Sample39

value: Unstimulated


title: Anti-NSUN7 CLIP-Seq of WT mice (with UV) - control - WT_UV

city: Vienna

first: Sergey

last: Isaev

address: Spitalgasse, 4

department: Department of Neuroimmunology

country: Austria

institute: Medical University of Vienna

data_processing:
library strategy: CLIP-seq
CLIP-Seq reads were firstly trimmed with Trim Galore tool and after aligned onto the mm39 mouse genome with STAR prohibiting novel splice junctions within the alignment. Resulting bam files were deduplicated and concatenated together to perform peak calling with Piranha. Coordinates of each peak were extracted and used to calculate the coverage of each peak in each sample with featureCounts tool.
Assembly: mm39
Supplementary files format and content: tsv-files with amount of reads per each annotated peak

source_name: Testis

extract_protocol:
Testis were obtained from 30 mice of wild type and 30 HA-Nsun7 mice. Testis were decapsulated in PBS and irradiated twice with 400 mJ/sm2 UV (GS Gene Linker UV Chamber Biorad). After that seminiferous tubules were lysed in PXL buffer (0.1% SDS, 0.5% deoxycholate, 0.5% NP-40 in PBS without Ca and Mg) and exposed to 5 cycles of 8 seconds ultrasonication with 70% amplitude. Then samples were incubated with Rnase T1 0.01 u/μl (Thermofisher) for 10 minutes at 37 C with shaking 1000 rpm. For immunoprecipitation were used Pierce™ Anti-HA Magnetic Beads (Thermofisher). Before elution RNA-protein conjugates, which were bound to magnetic beads, were exposed ro dephosphorylation with СIAP (0,5 U/мкл) (2386334, Invitrogen) for 15 minutes at 37 C with shaking 1000 rpm, which was followed by phosphorylation with T4 PNK (Thermofisher) 30 minutes at 37 C with shaking 1000 rpm. RNA was eluted from the magnetic beads with proteinase K (Thermofisher) for 20 minutes at 37 C with shaking 1000 rpm.
RNA libraries were prepared with the NEBNext® Small RNA Library Prep Set for Illumina® (Multiplex Compatible, E7330S) in accordance with the manufacturer's recommendations, omitting the size-select step at the final stage of the protocol.

value: Testis

value: 2-4 months

value: WT


title: 06H122

value: Blood

value: Acute myeloid leukemia


title: 07H073

value: Bone marrow


title: 014N

city: Baltimore

first: Mahashweta

last: Basu

state: MD

address: 670 W. Baltimore Street

institute: Institute for Genome Sciences

description: Library name: 014N

data_processing:
Samples were sequenced across 4 channels using the 75 base pair paired-end protocol on an Illumina HiSeq 4000 sequencer, targeting 50 million read pairs per sample
An average of 64–100 million reads were obtained for each sample.
Sequencing reads were aligned to the Rattus norvegicus genome (Rnor v7.2) using HISAT2
The number of reads that aligned to the predicted coding regions was determined using HTSeq.
Assembly: Rnor v7.2
Supplementary files format and content: Raw counts file (without normalization)
Supplementary files format and content: File is in text format with first column as gene ensemble IDs and second its counts.

organism: Rattus norvegicus

source_name: 30-day-old amygdala

extract_protocol:
RNA was extracted using the RNeasy Kit (Qiagen, Hilden, Germany), following the manufacturer’s instructions, including column treatment with DNase I (Qiagen) to remove contaminating DNA
Libraries were prepared using a NEBNext Ultra Directional RNA prep kit (New England Biolabs, Ipswich, MA) using the manufacturer’s protocol

treatment_protocol: On P30 (~24 hours after the final play bout), juveniles (n=6 per group) were deeply anesthetized with Fatal Plus (Vortech Pharmaceuticals, Dearborn, MI) and decapitated. Brains were removed and placed on ice, and the amygdala of both hemispheres was dissected out and immediately flash frozen. Tissue was stored at -80°C until it was prepared for RNA extraction.

value: 30-day-old amygdala

tag: animal sex

value: F

tag: play level

value: high

tag: group

value: FHI


title: Anti-NSUN7 CLIP-Seq of WT mice (with UV) - control - WT2

tag: tissue


title: Anti-NSUN7 CLIP-Seq of NSUN7-HA mice (without UV) - control - HA_noUV


title: 116Y

description: Library name: 116Y

value: low

value: FLO


title: 08H060

tag: cell type


title: D320_RESET_nostim_norapa

description: Library name: Sample38

value: T cells

tag: treatment


title: 07H061


title: Anti-NSUN7 CLIP-Seq of WT mice (with UV) - control - WT1

tag: genotype


title: 112Y

description: Library name: 112Y

value: M

value: MHI


title: 06H063


title: D320_TCR_nostim_norapa

description: Library name: Sample41

value: TCR

value: media alone


title: Anti-NSUN7 CLIP-Seq of NSUN7-HA mice (with UV) - HA_UV

value: Testis

tag: strain


title: 110Y

description: Library name: 110Y


title: 06H112


title: D320_DARIC_stim_rapa

description: Library name: Sample37

value: DARIC

value: rapamycin

value: Stimulated


title: 19N

description: Library name: 19N

value: MLO


title: Anti-NSUN7 CLIP-Seq of WT mice (without UV) - control - WT_noUV

tag: age

value: 2-4 months

value: WT


title: Anti-NSUN7 CLIP-Seq of NSUN7-HA mice (with UV) - HA2


title: 07H142

value: Blood

value: Acute myeloid leukemia


title: 115N

description: Library name: 115N

value: 30-day-old amygdala

value: F


title: 05H176

value: Bone marrow


title: 111N

description: Library name: 111N

value: low


title: 05H141


title: 016N

description: Library name: 016N

value: high

value: FHI


title: D320_DARIC_nostim_norapa

description: Library name: Sample35

value: T cells

value: Unstimulated


title: 012N

description: Library name: 012N

value: M


title: D320_CAR_stim_norapa

description: Library name: Sample33

value: CAR

value: media alone


title: Nsun7-/- mouse 2

data_processing:
Analysis of BS-RNA-Seq was performed with methylseq (v2.4.0) nf-core pipeline using mm39 version of the mouse genome. Briefly, in this pipeline Bismark is used to prepare the reference with C-to-T substitutions in both orientations of DNA strands, and alignment itself is done via splicing-robust method HISAT2. Reads with the same start and end are removed from the alignment, and methylation in each position is calculated as a fraction of non-converted cytosines. Only positions that are covered with at least 10 reads in total in each group of comparison (mutants and wild types) were kept for further analysis.
Assembly: mm39
Supplementary files format and content: tsv-files with methylation coverage
Library strategy: BS-RNA-Seq

extract_protocol:
Testes were decapsulated and incubated with collagenase type IV (2 mg/ml, Gibco) at 37C for 20 minutes. After that seminiferous tubules were applied to the 5% percoll solution and incubated on ice for 15 minutes. Seminiferous tubules, which had drowned, were homogenized with Dounce homogenizer type A. The obtained cell suspension was twice filtered through a 40 mkm cell strainer (Greiner Bio-One). After that cells were centrifuged (5 minutes, 800 g), dissolved in 3 ml of PBS and fixed on ice for 15 minutes with 3 volumes of ethanol 100% supplied with 0.8 mM EDTA. Then cells were stained with SYTO16 (Invitrogen) on ice for 30 minutes. Cell sorting was performed on a 4-Laser (405 nm - violet, 488 nm - blue, 561 nm - yellow-green, 633 nm - red) 20-parameter BD FACSAria III and the BD FACSDiva 6.1.3 software is used to visualize and analyze the data. Laser delay was set to 0 for the blue, -77.39 for the red, 37.33 for the violet and -39.85 for the yellow-green lasers. Areas scaling was set to 1.14 for the blue, 1.0 for the red, 0.75 for the violet and 0.96 for the yellow-green lasers. Window extension was set to 2.00 µs and the FSC Area scaling to 1.00. A sample filter line of 50 µm was placed at the end of the sample line to avoid clumping.  Cells on 10-16 steps of spermatogenesis (elongated spermatids) were collected in falcons covered with FBS. From fractions of elongated spermatids was purified RNA using ExtractRNA reagent (evrogen) according to the manufacturer's protocol. rRNA depletion (RiboMinus™ Eukaryote Kit v2, Invitrogen) and bisulfite conversion (Abcam) were conducted under manufacture recommendations with an additional thermal cycle of bisulfite conversion.
RNA libraries were prepared with the NEBNext® Small RNA Library Prep Set for Illumina® (Multiplex Compatible, E7330S) in accordance with the manufacturer's recommendations, omitting the size-select step at the final stage of the protocol.

value: Testis


title: 05H127


title: Nsun7-/- mouse 1


title: 05H004


title: D320_CAR_nostim_rapa

description: Library name: Sample32

value: rapamycin


title: 013Y

description: Library name: 013Y

value: FLO


title: WT mouse 3 — control

value: 2-4 months

value: WT


title: D320_CAR_nostim_norapa

description: Library name: Sample31


title: 011Y

description: Library name: 011Y

value: MLO


title: OA2

city: Shenzhen

first: Shimin

last: Wang

address: 3025# Shennan Road

institute: The Eighth Affiliated Hospital, Sun Yat-sen University

description: one sample from testicular tissue of one OA patient

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:
- MT% < 40%;
- Cell Gene Number < Median Gene Number * 2;
- Cell Gene Number > 200.
PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: GRCh38
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: OA patient 2 testis

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3' Reagent Kit v3 (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

value: testis

tag: disease state

value: Obstructive azoospermia (OA)


title: OA1

source_name: OA patient 1 testis


title: WT mouse 2 — control


title: 18Y

description: Library name: 18Y

value: 30-day-old amygdala

value: F


title: WT mouse 1 — control


title: 17N

description: Library name: 17N

value: high


title: D315_UTD_stim_rapa

description: Library name: Sample30

value: UTD

value: Stimulated


title: D320_DARIC_nostim_rapa

description: Library name: Sample36

value: T cells

value: DARIC

value: Unstimulated


title: NOA3

description: one sample from testicular tissue of one NOA patient

source_name: NOA patient 3 testis

value: Non-obstructive azoospermia (NOA)


title: Anti-NSUN7 CLIP-Seq of NSUN7-HA mice (with UV) - HA1

value: Testis


title: Nsun7-/- mouse 3


title: 015Y

description: Library name: 015Y

value: FHI


title: D320_CAR_stim_rapa

description: Library name: Sample34

value: CAR

value: rapamycin


title: D315_UTD_nostim_rapa

description: Library name: Sample29


title: HuH7-NTCP_ND_3

city: Strasbourg

last: Jühling

address: 3 Rue Koeberlé

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

description: Library name: 7-ND-3

data_processing:
Raw data acquisition (HiSeq Control Software, HCS, HD 3.4.0.38) and base calling (Real-Time Analysis Software, RTA, 2.7.7) was performed on-instrument
Base calls were converted into lane-specific, multiplexed, unaligned BAM files suitable for long-term archival (IlluminaBasecallsToMultiplexSam, 2.19.2-CeMM).
Archive BAM files were demultiplexed into sample-specific, unaligned BAM files (Illumi-naSamDemux, 2.19.2-CeMM).
NGS reads were mapped to the Genome Reference Consortium GRCh38 assembly via “Spliced Transcripts Alignment to a Reference” (STAR, 2.7.5a) utilizing the “basic” ensembl transcript annotation from version e100 (April 2020) as reference transcriptome.
STAR was run with options recommended by the ENCODE project. NGS read alignments overlapping ensembl transcript features were counted with the Bioconductor (3.12) Genomic Alignments (1.26.0) package. Transcript-level counts were aggregated to gene-level counts and the Bioconductor DESeq2 (1.30.0) package was used to test for differential expression based on a model using the negative binomial distribution.
Assembly: hg38
Supplementary files format and content: tab-separated file includes normalized counts of protein-coding genes for each sample

growth_protocol: 10% FCS-supplemented DMEM

extract_protocol:
Total intracellular RNAs were extracted with the “Monarch, nucleic acid purification kit” according to the manufacturer’s instructions (New England Biolabs)
RNA-seq libraries were prepared with the NEB-Next® Ultra™ II Directional RNA sample preparation kit (New England Biolabs, Inc., Ipswich, MA, USA)

treatment_protocol: Both cell lines were differentiated with 2% of DMSO for 1 week without splitting the cells

tag: cell line

value: Mock


title: NOA2

source_name: NOA patient 2 testis


title: 14Y

description: Library name: 14Y

value: M

value: low

value: MLO


title: HuH7-NTCP_ND_1

description: Library name: 7-ND-1


title: 12Y

description: Library name: 12Y

value: 30-day-old amygdala

value: MHI


title: HeLa 7SK KO RNA-Seq Rep 3

city: Iowa City

first: David

last: Price

state: IA

address: 500 Newton Road, 260 EMRB

department: Biochemistry

institute: University of Iowa

data_processing:
Adapter trimming using trim_galore 0.4.4.
Alignment of trimmed reads to concatenated hg38 (human), and JQCY02.1 (SF21 moth) genome assemblies for PRO-Seq using Bowtie. Alignment of trimmed reads to hg38 using HISAT2 for RNA-Seq datasets.
Deduplication of mapped reads according to unique molecular identifiers using dedup (https://github.com/P-TEFb/dedup) for PRO-Seq datasets.
Reads were parsed out based on the genome to which they aligned.
Bedgraphs were generated using bedTools genomecov 2.26 and data were normalized by library size and spike-in reads accorind to Ball et. al. (2019, PMID: 30743000).
Bigwigs were generated using kentUtils bedgraphtobigwig.
Assembly: hg38 (human), JQCY02.1 (Spodoptera).
bigwigs contain PRO-Seq pileups.

source_name: HeLa 7SK KO cells

growth_protocol: WT HAP1, HAP1 7SK KO, and HAP1 LARP7 KO cells were cultured in IMDM supplemented with 10% FBS to 80% confluence. WT HeLa and HeLa 7SK KO cells were cultured in DMEM supplemented with 10% FBS to 80% confluence.

extract_protocol:
Nuclei isolation was carried out as described in Parida et. al. (2019, PMID: 30755505) and Li et. al. (2020, PMID: 32251483) .
PRO-Seq library preparation to extract and sequence nascent RNAs is carefully detailed in the manuscript and was carried out as previously described by  Li et. al. (2020, PMID: 32251483), with noted modifications. RNA-Seq library preparation was carried out by the University of Iowa Genomics Division using the Illumina TruSeq Stranded Total RNA Library Prep kit and Ribo-Zero Gold rRNA Depletion Kit according to manufacturer's instructions.

treatment_protocol: Flavo treated samples were incubated with 1 µM flavopiridol for 1 hour prior to isolation of nuclei. Samples without flavopiridol were incubated with a vehicle control (DMSO) for the 1 hour prior to nuclei isolation.

value: HeLa

value: 7SK KO


title: NOA1

source_name: NOA patient 1 testis

value: testis


title: D315_TCR_nostim_norapa

description: Library name: Sample26

value: T cells

tag: transgene

value: TCR

value: media alone


title: 04H141

data_processing:
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 32 (based on Ensembl 98)
Expression values were also computed using RSEM version 1.3.2 based on Gencode version 32 transcript annotations, using both stranded and unstranded parameters
Strand orientation is reverse, that is R1 aligns on the reverse gene orientation.
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column), including expression values as expected counts, FPKM and TPM

source_name: Bone marrow

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
Stranded sequencing libraries were prepared from total RNA using the NEBNext PolyA mRNA Magnetic Isolation Module.

value: Bone marrow

value: Acute myeloid leukemia


title: HuH7-NTCP_Dif_3

description: Library name: 7-Dif-3

value: DMSO


title: D315_TCR_stim_norapa

description: Library name: Sample27

tag: donor

value: Stimulated


title: 08N (L8)

description: Library name: 08N (L8)

value: F

value: FLO


title: 08N (L7)

description: Library name: 08N (L7)


title: HuH7-NTCP_Dif_2

description: Library name: 7-Dif-2


title: D315_RESET_stim_rapa

description: Library name: Sample25

value: RESET

value: rapamycin

tag: stimulation


title: HeLa 7SK KO RNA-Seq Rep 2


title: HeLa 7SK KO RNA-Seq Rep 1


title: HuH7-NTCP_Dif_1

description: Library name: 7-Dif-1


title: WT HeLa RNA-Seq Rep 3

source_name: HeLa cells

value: WT


title: HuH7.5-NTCP_ND_3

description: Library name: 75-ND-3

value: Mock


title: 08N (L6)

description: Library name: 08N (L6)

value: 30-day-old amygdala

value: low


title: D315_RESET_nostim_rapa

description: Library name: Sample24

value: Unstimulated


title: 15N

description: Library name: 15N

value: high

value: FHI


title: D315_RESET_nostim_norapa

description: Library name: Sample23

value: T cells


title: D315_DARIC_stim_rapa

description: Library name: Sample22

value: DARIC


title: HuH7-NTCP_ND_2

description: Library name: 7-ND-2


title: HuH7.5-NTCP_ND_2

description: Library name: 75-ND-2


title: WT HeLa RNA-Seq Rep 2

value: HeLa


title: D315_UTD_nostim_norapa

description: Library name: Sample28

value: UTD

value: media alone


title: 06N

description: Library name: 06N


title: D315_DARIC_nostim_rapa

description: Library name: Sample21


title: WT HeLa RNA-Seq Rep 1


title: HuH7.5-NTCP_ND_1

description: Library name: 75-ND-1


title: 04N

description: Library name: 04N

value: M

value: MHI


title: HAP1 LARP7 KO RNA-Seq Rep 3

source_name: HAP1 LARP7 KO cells

value: LARP7 KO


title: 03Y

description: Library name: 03Y


title: HuH7.5-NTCP_Dif_3

description: Library name: 75-Dif-3

value: DMSO


title: D315_CAR_stim_rapa

description: Library name: Sample19

value: CAR

value: rapamycin

value: Stimulated


title: HuH7.5-NTCP_Dif_2

description: Library name: 75-Dif-2


title: 22N

description: Library name: 22N

value: 30-day-old amygdala

value: MLO


title: 07Y

description: Library name: 07Y

value: F

value: low

value: FLO


title: 01Y

description: Library name: 01Y

value: high


title: D315_CAR_nostim_rapa

description: Library name: Sample18

value: T cells

value: Unstimulated


title: HuH7.5-NTCP_Dif_1

description: Library name: 75-Dif-1


title: HAP1 7SK KO RNA-Seq Rep 3

source_name: HAP1 7SK KO cells

value: 7SK KO


title: hiPSCCM_Nit_2_2

city: Dover

middle: C

last: Zebrowski

state: DE

address: 1151 Walker Rd

institute: GenKardia Inc.

data_processing:
Raw sequence reads were mapped to the RAT genome (RN6) and human genome (hg38) using Tophat2 with Bowtie2 option where adaptor sequences were removed using trim_galore before read mapping.
BAM files containing the alignment results were sorted according to the mapping position. Raw read counts for each gene were calculated using featureCounts from Subread package.
Differential expression analysis was performed using DEseq2, with raw counts as input. The differentially expressed genes were identified by adjusted p value for multiple testing using Benjamini-Hochberg correction with False Discovery Rate (FDR) values less than 0.1.
Assembly: rat genome (RN6) and human genome (hg38)
Supplementary files format and content: Excel file includes results from differential expression analysis and normalized counts per gene and sample

source_name: iPS-cells

growth_protocol: Neonatal Rat Ventricular Cardiomyocyte Isolation and Culture: Ventricular cardiomyocytes were isolated from 6-day old neonatal Sprague-Dawley rats as described previously (18). Cardiomyocytes were seeded and cultured in DMEM/F-12, GlutamaxTM-I (ThermoFisher Scientific, catalogue number: 10565018) + Penicillin (100 U/ml)/Streptomycin (100 µg/ml) (Pen/Step) (ThermoFisher Scientific, catalogue number: 15140122) for 2 days prior to experimentation.Cells were plated in 24-well plates on glass coverslips (ThermoScientific. Menzel-Gläser. 13mm #0, catalogue number: 17274914) coated with Fibronectin for at least 2 hours at RT prior to seeding. Treatment of NRVMs with Nitrendipine and 1-NA-PP1 was done in the presence of 5%HS and 10%FBS for 2 days prior to fixation or RNA-isolation. Human iPSC-derived Cardiomyocytes and Culture: Human induced-PSC-derived cardiomyocytes (hiPSC-CMs) were acquired from Fujifilm Cellular Dynamics International, Inc. (CDI) (iCell Cardiomyocytes, catalogue number: CMC-100-010-001). hiPSC-CMs from CDI were seeded and cultured according to manufacture´s directions (https://cellulardynamics.com/assets/CDI_iCellCardiomyocytes_UG.pdf). CDI iCell Cardiomyocyte lot numbers used in this study: #1833511, #1099441, #1098841. In brief, hiPSC-CMs were thawed and cultured in plating medium (CDI, catalogue number: M1003) for 2 days and then cultured in maintenance medium (CDI, catalogue number: M1001) for 4 days. Afterwards, hiPSC-CMs were treated with compounds for 2 days prior to fixation or RNA isolation. hiPSC-CMs were plated in 24-well plates on glass coverslips (Thermo Fisher Scientific. Menzel-Gläser. 13mm #0, catalogue number: 17274914) coated with Matrigel (Corning, catalogue number: 356255) for at least 2 hours at RT.

extract_protocol:
P6-NRVMs and CDI-CMs were treated with Nitrendipine or 1-NA-PP1 for 2 days prior to RNA extraction. In addition, both P6-NRVMs and CDI-CMs during treatment with Nitrendipine or 1-NA-PP1 were cultured in the presence of araC. AraC was used to reduce overgrowth of contaminating cardiac fibroblasts (which generally amount to ~3% of cultured cells in primary cardiomyocyte isolation procedure). RNA was extracted from sub-confluent 10-cm plates using Qiagen RNeasy mini kit. RNA quality (RNA integrity number, RIN) and quantity was measured in a Bioanalyzer 2100 (Agilent) using the Agilent RNA 6000 Nano Kit (part number 5067-1511). The sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760S, New England Biolabs), starting with 200 ng of total RNA. In brief, mRNA was isolated and fragmented using the NEBNext poly(A) mRNA magnetic isolation module (E7490S, New England Biolabs), with the first and second strands of cDNA synthesized and purified using AmPure XP SPRI beads (A63880, Beckman Coulter). Then adaptor ligation and size selection wereperformed according to the manufacturer’s protocol. Next, the adaptor ligated cDNA was PCR enriched to incorporate an Illumina compatible index sequence (NEBNext Oligos for Illumina, Dual Index Primers Set1 (E7600S, New England Biolabs). All libraries were purified using AmPure XP SPRI beads, and the size distribution of the libraries was analyzed at the Bioanalyzer 2100 using the Agilent High Sensitivity DNA Kit (part number 5067-4626). Subsequently, the quantification of the libraries was performed with the Qubit® 2.0 Fluorometer (ThermoFisher Scientific) and QubitTMdsDNA HS Assay Kits (Q32851, Invitrogen). Finally, all 19 libraries were pooled and diluted to 3.5 nM for sequencing on one lane of a Hiseq 3000 sequencer (Illumina), using a single read 50 bp and dual indexed sequencing strategy.
The sequencing libraries for RNA-seq were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacture's protocols.

treatment_protocol: Treatment of NRVMs with Nitrendipine and 1-NA-PP1 was done in the presence of 5%HS and 10%FBS for 2 days prior to fixation or RNA-isolation. Treatment of CDI cardiomyocytes with Nitrendipine and 1-NA-PP1 was done in the presence of CDI culture medium for 2 days prior to fixation or RNA-isolation.

value: iPS-cells

value: cardiomyocytes

tag: developmental stage

value: mature

value: Nitrendipine, 48 hours

tag: time


title: D315_CAR_nostim_norapa

description: Library name: Sample17

value: media alone


title: hiPSCCM_Nit_2_1


title: D180_UTD_stim_rapa

description: Library name: Sample16

value: UTD


title: HAP1 7SK KO RNA-Seq Rep 2


title: HAP1 7SK KO RNA-Seq Rep 1


title: hiPSCCM_Nit_2_0


title: Muscle39

city: Måløv

first: Jens

last: Halling

address: Novo Nordisk Park 1

country: Denmark

institute: Novo Nordisk

description: Library name: Muscle39

data_processing:
Trimming of sequence reads to remove potential adapter sequences and low-quality nucleotides using fastp v.0.23.1
UMI-based de-duplication was carried out using fastp v.0.23.1
Assembly: Rattus norvegicus Rnor6.0 reference genome - aligned using the STAR aligner v.2.5.2b
Supplementary files format and content: Raw counts csv file containing counts for each sample

source_name: Quadriceps

extract_protocol:
RNeasy Minikit
Twist UMI system

value: Quadriceps

value: WT

value: CagriSema


title: Muscle40

description: Library name: Muscle40


title: hiPSCCM_Nit_1_2


title: D315_DARIC_nostim_norapa

description: Library name: Sample20

source_name: T cells

value: DARIC


title: WT HAP1 RNA-Seq Rep 3

source_name: HAP1 cells


title: D180_UTD_nostim_norapa

description: Library name: Sample14


title: D180_UTD_nostim_rapa

description: Library name: Sample15

value: rapamycin


title: HAP1 LARP7 KO RNA-Seq Rep 2

value: LARP7 KO


title: Muscle37

description: Library name: Muscle37


title: Muscle38

description: Library name: Muscle38


title: D180_TCR_stim_rapa

description: Library name: Sample13

value: TCR

value: Stimulated


title: WT HAP1 RNA-Seq Rep 2


title: WT HAP1 RNA-Seq Rep 1


title: hiPSCCM_Nit_1_1


title: Muscle36

description: Library name: Muscle36


title: HAP1 LARP7 KO RNA-Seq Rep 1


title: hiPSCCM_Nit_1_0


title: D180_TCR_stim_norapa

description: Library name: Sample12

value: T cells


title: D180_TCR_nostim_norapa

description: Library name: Sample11

value: Unstimulated


title: hiPSCCM_Ctrl_2_2

value: DMSO, 48 hours


title: Muscle35

description: Library name: Muscle35


title: Muscle34

description: Library name: Muscle34


title: HeLa 7SK KO Flavo Rep 1

description: nascent RNA

data_processing:
Adapter trimming using trim_galore 0.4.4.
Alignment of trimmed reads to concatenated hg38 (human), and JQCY02.1 (SF21 moth) genome assemblies for PRO-Seq using Bowtie. Alignment of trimmed reads to hg38 using HISAT2 for RNA-Seq datasets.
Deduplication of mapped reads according to unique molecular identifiers using dedup (https://github.com/P-TEFb/dedup) for PRO-Seq datasets.
Reads were parsed out based on the genome to which they aligned.
Bedgraphs were generated using bedTools genomecov 2.26 and data were normalized by library size and spike-in reads accorind to Ball et. al. (2019, PMID: 30743000).
Bigwigs were generated using kentUtils bedgraphtobigwig.
Assembly: hg38 (human), JQCY02.1 (Spodoptera).
bigwigs contain PRO-Seq pileups.
Library strategy: PRO-Seq

value: HeLa

value: 7SK KO


title: D180_RESET_stim_rapa

description: Library name: Sample10

value: RESET


title: HeLa 7SK KO Flavo Rep 2

description: nascent RNA


title: hiPSCCM_Ctrl_2_1

value: iPS-cells

value: cardiomyocytes

value: mature


title: Muscle33

description: Library name: Muscle33

value: Quadriceps


title: HeLa 7SK KO Rep 2

description: nascent RNA


title: hiPSCCM_Ctrl_2_0


title: D180_RESET_nostim_rapa

description: Library name: Sample9


title: hiPSCCM_Ctrl_1_2


title: D180_RESET_nostim_norapa

description: Library name: Sample8

value: media alone


title: Muscle32

description: Library name: Muscle32

value: WT

value: Weight matched


title: HeLa 7SK KO Rep 1

description: nascent RNA


title: Muscle31

description: Library name: Muscle31


title: D180_DARIC_stim_rapa

description: Library name: Sample7

value: DARIC

value: rapamycin


title: hiPSCCM_Ctrl_1_0


title: WT HeLa Flavo Rep 2

description: nascent RNA


title: D180_DARIC_nostim_rapa

description: Library name: Sample6


title: hiPSCCM_Ctrl_1_1


title: WT HeLa Flavo Rep 1

description: nascent RNA


title: Muscle30

description: Library name: Muscle30


title: hiPSCCM_PP1_2_2

value: 1-NA-PP1, 48 hours


title: D180_DARIC_nostim_norapa

description: Library name: Sample5


title: WT HeLa Rep 1

description: nascent RNA


title: hiPSCCM_PP1_2_1


title: WT HeLa Rep 2

description: nascent RNA


title: D180_CAR_stim_rapa

description: Library name: Sample4

value: CAR

value: Stimulated


title: hiPSCCM_PP1_2_0


title: D180_CAR_stim_norapa

description: Library name: Sample3

value: T cells


title: HAP1 7SK KO Rep 2

description: nascent RNA


title: Muscle27

description: Library name: Muscle27


title: HAP1 7SK KO Rep 1

description: nascent RNA


title: D180_CAR_nostim_rapa

description: Library name: Sample2

value: Unstimulated


title: hiPSCCM_PP1_1_2


title: Muscle25

description: Library name: Muscle25


title: WT HAP1 Flavo Rep 2

description: nascent RNA


title: hiPSCCM_PP1_1_1


title: D180_CAR_nostim_norapa

description: Library name: Sample1


title: ICGC_PA56_NextSeq500

city: Heidelberg

first: Konstantin

last: Okonechnikov

state: Germany

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center

data_processing:
10X data: reads aligned, assigned to cells and gene expression counts computed with CellRanger v2.1.0
DROP-seq,C1 data: reads aligned with STAR, gene expression counts per cell computed with FeatureCount
Filtering of low quality cells performed with Seurat
Assembly: hg19, mm10
Supplementary files format and content: Gene expression matrix (raw)

molecule: nuclear RNA

source_name: Tumor

extract_protocol:
Nuclei from frozen tissue were isolated using the optimized protocol described on the original article.
See protocol column per each sample.
snRNA-seq

value: Tumor

tag: tumor class

value: PA

tag: protocol

tag: Sex

value: male

tag: tumor location

value: Cerebellum


title: Muscle29

description: Library name: Muscle29

tag: tissue


title: Muscle8

description: Library name: Muscle8

value: Vehicle


title: WT HAP1 Flavo Rep 1

description: nascent RNA


title: Muscle6

description: Library name: Muscle6


title: Muscle28

description: Library name: Muscle28


title: WT HAP1 Rep 1

description: nascent RNA


title: mrps-5 RNAi sample-6

city: Amsterdam

first: Man

middle: Iman

last: Hu

address: Meibergdreef 9

department: Laboratory Genetic Metabolic Diseases

country: Netherlands

institute: Amsterdam UMC Location University of Amsterdam

description: N2 worms treated with mrps-5 RNAi sample-6

data_processing:
Reads were subjected to quality control FastQC and trimmed using fastp (version 0.23.2) and aligned to the C. elegans genome obtained from Ensembl (wbcel235), using STAR2 (version 2.5.4)
Assembly: Ensembl (wbcel235)
Supplementary files format and content: table delimited row counts

organism: Caenorhabditis elegans

source_name: Whole body

growth_protocol: N2 worms were synchronized by hypochlorite treatment, then plated on NGMi plates (NGM plates with 2 mM IPTG and 25 mg/mL carbenicillin) with a bacterial lawn of either E. coli HT115 (RNAi control strain, containing an empty vector), mrps-5, C32E8.9, or mrps-5 + C32E8.9.

extract_protocol:
Total RNA was extracted as described above in the “RNA Isolation” section. Contaminating genomic DNA was removed using RNaseFree DNase (QIAGEN). RNA was quantified with a NanoDrop 2000 spectrophotometer (Thermo Scientific; Breda, The Netherlands). The qualities of RNA samples were checked with TapeStation (Agilent, CA, USA).
Sequencing libraries were constructed by using KAPA mRNA HyperPrep Kit (Roche, Switzerland)
Paired-end sequencing of Illumina NovaSeq was performed (Macrogen, Seoul, South Korea)

value: Whole body

value: mrps-5 RNAi


title: mrps-5 RNAi sample-5

description: N2 worms treated with mrps-5 RNAi sample-5


title: MesHMLE_sRNA_replicate_5

city: Adelaide

first: Katherine

middle: Anne

last: Pillman

state: SA

address: North Terrace

department: Centre for Cancer Biology

institute: Adelaide University

data_processing:
Illumina bcl2fastq Conversion Software v2.20 used for basecalling
Raw reads were adapter trimmed using cutadapt v2.8. adapter sequence = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, minimum length = 28, error rate = 0.2, overlap - 5
Reads derived from PCR duplicates were collapsed based on UMIs using UMI-tools v1.0.1m using the "extract" method to cut UMIs from the 3' end of reads
A 3' spacer sequence was removed using cutadapt v2.8. adapter: AACTGTAGGCACCATCAAT, minimum length: 18, error rate: 0.2, overlap: 5
Reads were mapped against the human reference genome (build hg19) using the BWA v0.7.17 alignment algorithm (~84% alignment rate)
PCR duplicate reads were collapsed using the UMI-tools ‘dedup’ method (using --method=percentile)
Annotation obtained from miRBase was used to obtain miR-level read counts using python scripts described in https://doi.org/10.1038/s41598-020-71323-0
Counts were TMM and log2 transformed using edgeR (version 3.34.0)
Genome_build: hg19
Supplementary_files_format_and_content: microrna deduplicated read count files

source_name: Human mammary epithelial cells

growth_protocol: HMLE cells were grown in HuMEC Ready Media (HuMEC Basal Serum-Free Medium (Gibco, #12753018) supplemented with HuMEC Supplement Kit (Gibco, #12755013)) at 37°C with 5% CO2.

extract_protocol:
RNA was extracted using Trizol (Ambion, #15596018) according to the manufacturer's protocol
The quantity and quality of the RNA samples were checked using nanodrop Qubit HS RNA (Invitrogen, # Q32852) and Bioanalyzer small RNA assay (Agilent, #5067-1548). Libraries were generated using 1 ug of the total RNA via QIAseq miRNA kit (Qiagen, # 331502) with 14 cycles of amplification. Amplified barcoded libraries were then size selected using auto gel-purification Pippin prep 3% agarose (SAGE science) which targets ranges from 100-250bp. Libraries (size between 180-190bp) were then confirmed by Qubit HS DNA and Bioanalyzer HS DNA assay for size and concentration.

treatment_protocol: A HMLE subline with a mesenchymal phenotype (mesHMLE) was achieved by culturing in DMEM:F12 media (Gibco, #11320033) supplemented with 10 mg/ml insulin (Actrapid HM 100IU/ml Penfill), 20 ng/ml EGF (R&D systems, #RDS236EG01M), 0.5 mg/ml hydrocortisone (Sigma Aldrich, # H0888), and 5% fetal Bovine serum (Hyclone, #SH300084) and treatment with 2.5 ng/ml of recombinant Human TGF-β 1 Protein (R&D systems, #RDS240B002) for maximum of 18 days. MesHMLEs were then maintained in this supplemented media without TGFβ1.

value: HMLE

tag: cell type

value: mammary epithelial cells

value: 2.5 ng/mL TGF-Beta, 18 days

tag: cellular fraction

value: Whole cell

tag: ip antibody


title: Muscle5

description: Library name: Muscle5

value: Quadriceps

tag: genotype

value: WT

tag: treatment


title: MesHMLE_sRNA_replicate_4


title: mrps-5 RNAi sample-4

description: N2 worms treated with mrps-5 RNAi sample-4


title: Muscle4

description: Library name: Muscle4


title: mrps-5 RNAi sample-3

description: N2 worms treated with mrps-5 RNAi sample-3


title: Muscle26

description: Library name: Muscle26

value: Weight matched


title: Raw264.7,Con-2

city: ChangChun

first: Dongxia

last: Gou

address: Changchun University, No.8326 Weixing Street

institute: Changchun university

description: Library name: Sample 5

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use fastp(0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis .
Assembly: The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0).
Supplementary files format and content: Expression analysis:we used Use HTSeq (v0.9.1) to statistically compare the Read Count values on each gene as the original expression level of the gene. In order to make gene expression levels comparable between different genes and samples, TPM is used to standardize expression levels. TPM is a normalized expression method that divides the expression level of each gene by the total number of transcripts and multiplies it by a normalization factor, usually 1000000 (calculated as follows: TPM for Gene A=(1000 * 1000/3000) * 1000000/(9000000)=37.04). Firstly, length normalization was performed on the two reads of Pair End sequencing, and instead of using the total read count as the size normalization, the sum of length standardized transcription values was used as the size indicator. Differential expression analysis: Then difference expression of genes was analyzed by DESeq (v1.38.3) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05. At the same time, we used R language Pheatmap (v1.0.12) software package to perform bi-directional clustering analysis of all different genes of samples. We geted heatmap according to the expression level of the same gene in different samples and the expression patterns of different genes in the same sample with Euclidean method to calculate the distance and Complete Linkage method to cluster. Enrichment analysis: we mapped all the genes to Terms in the Gene Ontology database and calculated the numbers of differentially enriched genes in each Term. Using topGO (v2.50.0) to perform GO enrichment analysis on the differential genes (all DEGs / up DEGs / down DEGs), calculate P-value by hypergeometric distribution method (the standard of significant enrichment is P-value <0.05), and find the GO term with significantly enriched differential genes to determine  the  main  biological  functions  performed  by  differential  genes.  ClusterProfiler (v4.6.0) software was used to carry out the enrichment analysis of the KEGG pathway of differential genes, focusing on the significant enrichment pathway with P-value <0.05. Gene Set Enrichment Analysis (GSEA) (v4.1.0) tool was used for GSEA enrichment analysis of all genes, and GSEA enrichment analysis pathway map was drawn.

extract_protocol:
This project enriched the total RNA by Oligo (dT) magnetic beads, with mRNA with polyA structure, to interrupt the RNA to about 300bp. A fragment of 300bp is selected because the joint length is fixed. If the broken segment length is shorter, the proportion of the effective data; if the broken fragment length is longer, it is not conducive to the generation of clusters during computer sequencing. The first strand cDNA was synthesized using 6-base random primers and reverse transcriptase and the second strand cDNA was synthesized using the first strand cDNA as the template.
After library construction, library fragment enrichment was performed by PCR amplification, followed by library selection based on fragment size at 450bp. Then, the library was inspected by Agilent 2100 Bioanalyzer, and then the total concentration and the effective concentration of the library were tested. Then, according to the effective concentration of the library and the amount of data required for the library, the libraries containing different Index sequences (different samples plus different Index, and finally to distinguish the data data of each sample according to Index) are mixed in proportion. Mixed libraries were uniformly diluted to 2 nM by base denaturation to form a single-stranded library.

tag: strain

value: BALB/c mice

value: macrophage cell

value: control


title: MesHMLE_sRNA_replicate_3

tag: cell line


title: Muscle2

description: Library name: Muscle2


title: Raw264.7,Con-1

description: Library name: Sample 4


title: mrps-5 RNAi sample-2

description: N2 worms treated with mrps-5 RNAi sample-2


title: hiPSCCM_PP1_1_0

value: iPS-cells

value: cardiomyocytes

value: mature

value: 1-NA-PP1, 48 hours


title: Muscle1

description: Library name: Muscle1

value: Vehicle


title: Raw 264.7,ASPS-A3

description: Library name: Sample 3


title: mrps-5 RNAi sample-1

description: N2 worms treated with mrps-5 RNAi sample-1

value: Whole body


title: HMLE_sRNA_replicate_1

value: Untreated


title: Liver40

description: Library name: Liver40

source_name: Liver

value: Liver

value: CagriSema


title: ICGC_GBM61_NextSeq500

value: Tumor

value: GBM

value: female

value: Hemispheric


title: Raw 264.7,ASPS-A2

description: Library name: Sample 2


title: WT HAP1 Rep 2

description: nascent RNA

value: WT


title: Muscle7

description: Library name: Muscle7

value: Quadriceps


title: C32E8.9 RNAi sample-6

description: N2 worms treated with C32E8.9 RNAi sample-6

value: C32E8.9 RNAi


title: C32E8.9 RNAi sample-5

description: N2 worms treated with C32E8.9 RNAi sample-5


title: MesHMLE_HITS-CLIP_sRNA_replicate_5

data_processing:
Library strategy: HITS-CLIP small RNA-seq
Illumina bcl2fastq Conversion Software v2.20 used for basecalling
Raw reads were adapter trimmed using cutadapt v2.8. adapter sequence = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, minimum length = 28, error rate = 0.2, overlap - 5
Reads derived from PCR duplicates were collapsed based on UMIs using UMI-tools v1.0.1m using the "extract" method to cut UMIs from the 3' end of reads
A 3' spacer sequence was removed using cutadapt v2.8. adapter: AACTGTAGGCACCATCAAT, minimum length: 18, error rate: 0.2, overlap: 5
Reads were mapped against the human reference genome (build hg19) using the BWA v0.7.17 alignment algorithm (~84% alignment rate)
PCR duplicate reads were collapsed using the UMI-tools ‘dedup’ method (using --method=percentile)
Annotation obtained from miRBase was used to obtain miR-level read counts using python scripts described in https://doi.org/10.1038/s41598-020-71323-0
Counts were TMM and log2 transformed using edgeR (version 3.34.0)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file of raw counts for all microRNAs for 1 sample
Supplementary_files_format_and_content: microrna deduplicated read count files

extract_protocol:
Cells were suspended in ice-cold PBS before UV crosslinking at 254 nM (Stratalinker). Cell pellets were then lysed on ice for 10 min using lysis buffer containing 0.1% SDS, 0.5% deoxycholate, 0.5% NP-40 and protease inhibitors (Roche) followed by RQ1 DNase (Promega) treatment at 37C for 15 min on shaker. RNase A/T1 (Ambion) was then added for a further 8 min flowed by addition of 30 mM ethylenediaminetetraacetic acid (EDTA) and a centrifuge at 30000 rpm. The lysate was then subjected to immunoprecipitation for 2 h with a pan-anti-Ago antibody (2A8) conjugated to protein-A dynabeads (Invitrogen) using bridging rabbit anti-mouse IgG (Jackson Immunoblots).
After washing the pellets (0.1% SDS, 0.5% deoxycholate, 0.5% NP40 in 1 × PBS; 0.1% SDS, 0.5% deoxycholate, 0.5% NP40 in 5xPBS; 50 mM Tris pH 7.5, 10 mM MgCl2, 0.5% NP40), on-bead phosphatase treatment performed for 30 min with Antarctic phosphatase (New England Biolabs) and SUPERaseIn RNase inhibitor (Ambion). After labelling the 39 RNA linker (CAGACGACGAGCGGG) with P32 using T4-PNK (NEB), it was ligated on beads for 1 h at 16C using T4 Ligase (Fermentas).
Following a wash, beads were treated with PNK to ligate the 59 RNA linker (AGGGAGGACGAUGCGGxxxG, with ‘‘X’’ representing different nucleotides for barcoding) and resuspended in 4x LDS Novex loading buffer with 4% B-mercaptoethanol, incubated at 70uC for 10 mins and the supernatant loaded on Novex NuPAGE 4-12% Bis-Tris acrylamide gels (Biorad). After the gel run, the Ago-RNA complexes were then transferred to nitrocellulose and exposed to film at 280uC for 3 days.
Complexes at 110 kDa were excited and resuspended in a solution containing 100 mM Tris pH 7.5, 50 mM NaCl, 10 mM EDTA and 4 mg/ml proteinase K for 20 min at 37C. After adding 3.5 M urea the samples were incubated for 20 min and RNA was isolated by a phenol-chloroform extraction method.
Samples were then run on a 10% denaturing (1:19) polyacrylamide gel and exposed to film with an intensifying screen at 280C for 5 d. The band corresponding to miRNAs was excised, crushed and eluted at 37C for 1 h in elution buffer containing 1 M NaOAc, pH 5.2 and 1 mM EDTA. After overnight ethanol precipitation, RNA was centrifuged, dried and resuspended in 8 mL RNase-free H2O.
First primer added (5’-TCCCGCTCGTCGTCTG-3’) and reverse transcription performed using SuperScriptIII (Invitrogen) and then PCR was performed for 25 cycles by adding the second primer (5’-ACGGAGGACGATGCGG-3’). PCR products were then run on a 10% native (1:29) polyacrylamide gel, stained with Sybr Gold (Qiagen) and bands excised over a UV light box.
After DNA precipitation using with isopropanol, additional 10 cycle PCR was performed by adding 2 primers :5’-AATGATACGGCGACCACCGACTATGGATACTTAGTCAGGGAGGACGATGCGG-3’ and 5’-CAAGCAGAAGACGGCATACGATCCCGCTCGTCGTCTG-3’. After running products on a 2% metaphor agarose/TBE gels and bands at 115 bp excised corresponding to the linker sequence + miRNA CLIP tag. Finally, samples were purified using quick-spin columns (Qiagen).

treatment_protocol: Briefly, HMLE cells were grown in (20 x 10 cm dishes) and were treated with TGFB1 for at least 18 days to form mesHMLE cells.

value: HMLE

value: mammary epithelial cells

value: 2.5 ng/mL TGF-Beta, 18 days

value: Whole cell

value: Pan-anti-Ago antibody (4F9, https://doi.org/10.1016/j.jim.2006.09.010)


title: MesHMLE_HITS-CLIP_sRNA_replicate_4


title: Liver38

description: Library name: Liver38


title: WT-drug_9607

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

data_processing:
Partek Flow platform used for data processing
Low quality sequence trimmed; 7-9% of sequences had an average of 2 bp trimmed.
Tophat 2 was used to align reads to the mm10 genome build
Reads were quantified to mm10 using the Partek E/M annotation model
Reads were normalized to counts per million (CPM) with 0.0001 added to the result.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file including CPM for each sample (in columns) and gene (in rows)

source_name: whole lung

extract_protocol:
Lungs were removed immediately upon sacrifice, and RNA extracted using a Qiagen RNEasy kit immediately. RNA was stored at -80° C until use.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

tag: drug treatment

value: Mas agonist

tag: age

value: 200 days

value: male


title: Raw264.7,Con-3

description: Library name: Sample 6

value: BALB/c mice

value: macrophage cell

value: control


title: C32E8.9 RNAi sample-4

description: N2 worms treated with C32E8.9 RNAi sample-4

value: Whole body


title: MesHMLE_HITS-CLIP_sRNA_replicate_3


title: Liver39

description: Library name: Liver39

value: Liver

value: CagriSema


title: WT-drug_8864

value: WT


title: Liver36

description: Library name: Liver36


title: C32E8.9 RNAi sample-3

description: N2 worms treated with C32E8.9 RNAi sample-3

value: C32E8.9 RNAi


title: HMLE_HITS-CLIP_sRNA_replicate_5

value: HMLE

value: Untreated


title: Liver35

description: Library name: Liver35


title: HMLE_sRNA_replicate_5

value: mammary epithelial cells


title: WT-drug_8863


title: HMLE_HITS-CLIP_sRNA_replicate_1

value: Whole cell


title: C32E8.9 RNAi sample-2

description: N2 worms treated with C32E8.9 RNAi sample-2


title: Liver34

description: Library name: Liver34


title: WT-ctl_9620

value: Inert control


title: Day_18_Nuclear_fraction_replicate_3

description: Fractionation method: https://doi.org/10.1038/nprot.2014.135

data_processing:
Illumina bcl2fastq Conversion Software v2.20 used for basecalling
Raw reads were adapter trimmed using cutadapt v2.8. adapter sequence = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, minimum length = 28, error rate = 0.2, overlap - 5
A 12 base UMI sequence was removed from the 3' end of the each read using UMI-tools v1.0.1m "extract" method.
A 3' spacer sequence was removed using cutadapt v2.8. Adapter: AACTGTAGGCACCATCAAT, minimum length: 18, error rate: 0.2, overlap: 5
Reads were mapped against the human reference genome (build hg19) using the BWA v0.7.17 alignment algorithm (~84% alignment rate)
PCR duplicate reads were collapsed based on the 12 nt UMI using the UMI-tools ‘dedup’ method (using --method=percentile)
Annotation obtained from miRBase was used to obtain miR-level read counts using python scripts described in https://doi.org/10.1038/s41598-020-71323-0
Counts were TMM and log2 transformed using edgeR (version 3.34.0)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file of raw counts for all microRNAs for 1 sample
Supplementary_files_format_and_content: Comma-delimited matrix table with raw gene counts for every microRNA and every sample

extract_protocol:
RNA was extracted using Trizol (Ambion, #15596018) according to the manufacturer's protocol
The quantity and quality of the RNA samples were checked using nanodrop Qubit HS RNA (Invitrogen, # Q32852) and Bioanalyzer small RNA assay (Agilent, #5067-1548). Libraries were generated using 1 ug of the total RNA via QIAseq miRNA kit (Qiagen, # 331502) with 14 cycles of amplification. Amplified barcoded libraries were then size selected using auto gel-purification Pippin prep 3% agarose (SAGE science) which targets ranges from 100-250bp. Libraries (size between 180-190bp) were then confirmed by Qubit HS DNA and Bioanalyzer HS DNA assay for size and concentration.
small RNA, 1x75 bp sequencing (Illumina NextSeq 500)

value: 2.5 ng/mL TGF-Beta

tag: time point

value: 18 days

value: Nucleus


title: Liver33

description: Library name: Liver33


title: C32E8.9 RNAi sample-1

description: N2 worms treated with C32E8.9 RNAi sample-1


title: WT-ctl_9606

value: lung

value: 200 days

value: male


title: HT115 RNAi sample-6

description: N2 worms treated with HT115 RNAi sample-6

value: HT115 RNAi


title: Day_18_Nuclear_fraction_replicate_2


title: Liver32

description: Library name: Liver32

value: Weight matched


title: Raw 264.7,ASPS-A1

description: Library name: Sample 1

value: BALB/c mice

value: macrophage cell


title: WT-ctl_9605

value: WT


title: Day_18_Nuclear_fraction_replicate_1


title: HT115 RNAi sample-5

description: N2 worms treated with HT115 RNAi sample-5

value: Whole body


title: Liver31

description: Library name: Liver31

value: Liver


title: Day_18_Cytoplasmic_fraction_replicate_3

description: Fractionation method: https://doi.org/10.1038/nprot.2014.136

value: HMLE

value: Cytoplasm


title: mas-drug_8878

value: Mas-/-

value: Mas agonist


title: HT115 RNAi sample-4

description: N2 worms treated with HT115 RNAi sample-4


title: Liver30

description: Library name: Liver30


title: Mas-drug_8873


title: mas-drug_8874


title: Day_18_Cytoplasmic_fraction_replicate_1

value: 2.5 ng/mL TGF-Beta


title: Day_18_Cytoplasmic_fraction_replicate_2

value: 18 days


title: HT115 RNAi sample-3

description: N2 worms treated with HT115 RNAi sample-3


title: Liver28

description: Library name: Liver28


title: mas-ctl_8879

value: Inert control


title: HT115 RNAi sample-2

description: N2 worms treated with HT115 RNAi sample-2


title: Liver29

description: Library name: Liver29


title: Day_2_Nuclear_fraction_replicate_3

description: Fractionation method: https://doi.org/10.1038/nprot.2014.141

value: 2 days

value: Nucleus


title: mas-ctl_8876

value: lung

value: 200 days

value: male


title: Liver27

description: Library name: Liver27

value: Weight matched


title: Liver26

description: Library name: Liver26


title: Day_2_Nuclear_fraction_replicate_2

description: Fractionation method: https://doi.org/10.1038/nprot.2014.140


title: mrps-5 + C32E8.9 RNAi sample-6

description: N2 worms treated with mrps-5 + C32E8.9 RNAi sample-6

value: mrps-5 + C32E8.9 RNAi


title: Liver25

description: Library name: Liver25

value: WT


title: Day_2_Nuclear_fraction_replicate_1

description: Fractionation method: https://doi.org/10.1038/nprot.2014.139


title: HT115 RNAi sample-1

description: N2 worms treated with HT115 RNAi sample-1

value: Whole body

value: HT115 RNAi


title: mas-ctl_8875