title: 23P5 Non-injury matched DRG RNA-seq

description: Library name: 23P5 DRG L5

source_name: Dorsal Root Ganglia

extract_protocol:
For scRNA-seq: The NP and surrounding transition zone (n = 3 injured and 3 non-injured discs) were isolated and manually morselized to ~1mm^3 pieces. The tissue was then enzymatically digested for 1 hour at 37°C in 2 mg/mL of Pronase Protease (Millipore, Temecula, CA) in growth media containing 1% antibiotic-antimycotic solution (Gibco, Carlsbad, CA) and 10% fetal bovine serum (FBS, Gemini Bioproducts, West Sacramento, CA) in Dulbecco’s modified eagle media-F12 media (DMEM/F12, GIBCO, Carlsbad, CA), followed by an ~18 hours digestion at 37°C in 0.25 mg/mL of Collagenase Type 1S (Sigma Aldrich) in growth media. The resulting sample was pushed through a 70μm cell strainer, and cells were isolated via centrifugation at 300G for ten minutes. The pellet was resuspended in phosphate-buffered saline at a concentration of 1,500 cells/uL. For bulk RNA-seq (both DRGs and IVD): Total RNA for the nucleus pulposus and dorsal root ganglia were collected using a RNeasy Lipid Tissue Mini Kit (Qiagen, Hilden, Germany) following the manufacturer protocol. The isolated RNA was transcribed into cDNA using a high-capacity reverse transcription kit (Applied Biosystems, Waltham, MA). Pig Taqman gene expression assays (Thermo Fisher Scientific) as detailed in Supplemental materials were used for analysis (Supplemental Table 2). All assays were normalized to 18S housekeeping gene.
Single cell suspensions were stained with ViaStain AOPI Staining Solution (Nexcelom Bioscience, Lawrence, MA) and imaged on an EVOS M7000 Imaging System (Thermo Fisher Scientific, Waltham, CA) to determine cell suspension quality and cell viability.  Cell suspensions with a minimum viability of 70% were partitioned (10,000 target capture) into Gel Beads-in-emulsion (GEMs) on the Chromium X (10x Genomics, Pleasanton, CA) per the Chromium NextGEM Single Cell 3’ v3.1 Gene Expression kit user guide.  Following reverse transcription and cDNA amplification, single cell libraries were prepared on the Chromium Connect (10x Genomics) using the Automated Gene Expression Library Construction kit (10x Genomics).  Barcoded libraries were quantified by quantitative PCR using the Collibri Library Quantification Kit (Thermo Fisher Scientific) and library size was measured via the 4200 TapeStation (Agilent Technologies, Santa Clara, CA).  Libraries were sequenced on a NovaSeq 6000 or X Plus (Illumina, San Diego, CA) with sequencing configuration 28x10x10x90bp, and a sequencing depth of 50,000 reads/cell. Bulk RNA seq for DRGs: RNA integrity was analyzed on the 2100 Bioanalyzer using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA) and RNA quantified using the Qubit RNA HS Assay Kit (ThermoFisher Scientific, Waltham, MA).  Four hundred ng RNA was ribodepleted using the Lexogen RiboCop Depletion Kit Human/Mouse/Rat v2 kit (Lexogen Inc., Greenland, NH).  Stranded RNA-Seq library construction was performed using the IDT xGen Broad-Range RNA Library Prep Kit (Integrated DNA Technologies, Coralville, IA) with 11 cycles of PCR amplification.  Library concentration was measured via the Qubit 1X dsDNA HS Assay kit, and library size on the Agilent 4200 TapeStation (Agilent Technologies) with the Agilent HS D1000 ScreenTape.  Multiplexed libraries were pooled and sequenced on a NovaSeq 6000 (Illumina, San Diego, CA) using 1x75bp sequencing at 50M reads/sample. Bulk RNA-se2q for IVD: RNA integrity was analyzed on the 2100 Bioanalyzer using the Agilent RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA) and RNA quantified using the Qubit RNA HS Assay Kit (ThermoFisher Scientific, Waltham, MA).  Library construction was performed using the SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian kit (Takara Bio USA, Inc., Mountain View, CA).  Three ng of total RNA was used for library construction with 13 cycles of PCR amplification.  Final libraries were quantified via the Qubit 1X dsDNA HS Assay kit and analyzed for size on the 4200 TapeStation (Agilent Technologies) with the Agilent HS D1000 ScreenTape.  Multiplexed libraries were pooled and sequenced on a NovaSeq 6000 (Illumina, San Diego, CA) using 1x75bp sequencing at 50M reads/sample.

value: Dorsal Root Ganglia

value: Non-injury matched


title: OvSvK Day2 CUT&Tag-seq of Sox2 rep1

status: Public on Jan 01 2026

type: SRA

city: Guangzhou

first: Hui

last: Zheng

state: Guangdong

address: No.190 Kaiyuan Avenue, Science Park

country: China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description:
Library name: S3vFd2
MEF infected with Oct4-VP16, Sox2-VP16, Klf4 for 2 days, and changed into iCD1 medium for reprogammming

library_source: genomic

data_processing:
Raw CUT&Tag reads were trimmed and ﬁltered for quality control using Trim Galore v0.6.7.
Clean paired-end reads were ﬁrst mapped to mouse geneme mm10 using Bowtie2(v2.4.5)  with parameters  '--very-sensitive'.
PCR duplicates were removed with picard(v2.26.10).
For histone marks enriched in Narrow domains, the NarrowPeak  representation was used applying following settings : -f BAM --keepdup all -q 0.05 --bdg. For histone marks enriched in broad domains, the broadPeak representation was used applying following settings: -f BAM --keepdup all  -q 0.05 --broad --broad-cutoff 0.01.
bigwig files required for coverage tracks as well as heatmaps were generated using Deeptools v3.3.1
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: GSE222746
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse embryonic fibroblasts

growth_protocol: Cells were maintained in iCD1 reprogramming medium.

extract_protocol:
Cells were collected by trypsin digestion.
Libraries for CUT&Tag were prepared using Hyperactive Universal CUT&Tag Assay Kit for Illumina following manufacturer's protocols.

treatment_protocol: MEF cells were infected with different TF combinations or siRNA combinations.

tag: cell line

value: Mouse embryonic fibroblasts

tag: cell type

value: reprgramming cells

tag: genotype

tag: treatment

value: OvSvK CUT&Tag seq of Sox2

tag: batch


title: Patient1

city: Ningbo

first: Shibo

last: Wu

address: Ningbo Medical Center

institute: Department of Respiratory Medicine, Lihuili Hospital

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
For 10X data, Cell Ranger 3.1.0 was used to quantify gene expression level.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: cancer tumor tissues

extract_protocol:
Surgically resected fresh tumor tissues from six patients were cut into pieces of approximately 1-3 mm³ . Then, the pieces were transferred to the gentle MACS C Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany), with 5 mL of digestive enzyme included in Tumor Dissociation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany). Then the tissues were made into single-cell suspension using the gentleMACS Dissociator (Miltenyi Biotec, Bergisch Gladbach, Germany) for 60 min on a rotor at 37℃ according to the manufacturer’s instructions. After removing of red blood cells using erythrocyte lysis solution (Miltenyi Biotec, Bergisch Gladbach, Germany), the cells were filtered using a 40 µm strainer (BD Falcon, New York, USA). CD45+ cells were sorted by using the Human CD45 Microbeads Isolation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany).
Cell suspensions (700-1200 living cells/μL determined by trypan blue staining) were loaded on a 10x Genomics ChromiumTM Single Cell Controller Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell gel beads in emulsions (GEMs) by using Chromium Single Cell 5' Library & Gel Bead Kit v1.0 (10x Genomics, Cat# 1000006) and Single Cell A Chip Kit (10x Genomics, Cat# 1000152). Captured cells were lysed and the released RNA was barcoded through reverse transcription in individual GEM. Barcoded cDNAs were pooled and cleanup by using DynaBeads MyOne Silane Beads (Thermo Fisher, Cat# 37002D), and then amplified and cleanup for further next generation library construction.

tag: tissue

value: cancer tumor tissues

tag: group

value: EGFR-TKI resistance

value: All cells

tag: pathology

value: LUAD


title: hepG2-S2-rep3-rna

city: Minneapolis

first: Quinn

last: Dickinson

state: MN

address: 100 Church Street SE

country: USA

institute: University of Minnesota

description: Library name: S2-3-rna

library_source: transcriptomic

data_processing:
For repliseq data reads were trimmed with cutadapt and aligned with bwa
Alignments were filtered and duplicates removed with samtools
reads were counted within genomic bins of 50kb to create final bedgraphs
For RNA data reads were trimmed with trimmomatic and aligned with HISAT2
alignments were filtered and counts calculated with SAMtools.
TPM was calculated from raw counts in python
Assembly: hg38
Supplementary files format and content: G1-1-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: G1-2-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: G1-3-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: G2-1-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: G2-2-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: G2-3-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S1-1-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S1-2-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S1-3-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S2-1-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S2-2-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S2-3-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S3-1-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S3-2-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S3-3-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S4-1-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S4-2-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: S4-3-rt: genomic tab separated bedgraph file with the rpkm within each 50kb bin
Supplementary files format and content: bulk-r1-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: bulk-r2-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: bulk-r3-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: G1-2-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: G1-3-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: G2-2-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: G2-3-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: S1-2-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: S1-3-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: S2-2-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: S2-3-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: S3-2-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: S3-3-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: S4-2-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id
Supplementary files format and content: S4-3-rna: tab separated txt file with the calculated tpm for each gene labeled by ensembl id

molecule: nuclear RNA

extract_protocol:
DNA samples were processed using the optimized Repli-seq protocol as previously described (Rivera-Mulia et al., 2022). Briefly, purified DNA from sorted cells was directly processed using the KAPA HyperPlus library preparation kit (Roche Cat. No. 07958978001) according to the manufacturer instructions. PARTAGE RNA-seq: RNA samples were processed using the SMARTer Stranded Total RNA-Seq ultra-low inputs (Takara Cat. No. 634411) according to the manufacturer instructions. Bulk RNA samples were isolated from 0.5 million HepG2 cells using the RNeasy Plus Kit (Qiagen 74004)
Libraries were purified using the Zymo DNA Clean & Concentrator-5 kit and processed for BrdU-IP. Immunoprecipitated libraries were amplified using the KAPA HiFi HotStart from the KAPA HyperPlus kit according to the manufacturer instructions. Repli-seq libraries were sequenced on the Illumina NextSeq P2 platform at ~ 8 M reads per library and 100 bp of single-end sequencing. PARTAGE RNA-seq libraries were sequenced on the Illumina NovaSeqX platform at  ~ 40 M reads per library and 150 bp of pair-end sequencing. Bulk rna libraries were prepared with the TruSeq Stranded mRNA Library Prep (Illumina) according to the manufacturer instructions. Standard RNA-seq libraries were sequenced on the Illumina NovaSeq platform at  ~ 20 M reads per library and 150 bp of pair-end sequencing”


title: hepG2-S4-rep2-rna

description: Library name: S4-2-rna


title: OSK Day3 CUT&Tag-seq of H3K27ac rep2

description:
Library name: B3FAcB2
MEF infected with Oct4, Sox2, Klf4 for 2 days, and changed into iCD1 medium for reprogammming

value: OSK CUT&Tag seq of H3K27ac


title: hepG2-S3-rep3-rna

description: Library name: S3-3-rna


title: OvSvK Day2 CUT&Tag-seq of H3K27ac rep1

description:
Library name: B3vFAc
MEF infected with Oct4-VP16, Sox2-VP16, Klf4 for 2 days, and changed into iCD1 medium for reprogammming

value: OvSvK CUT&Tag seq of H3K27ac


title: hepG2-S2-rep2-rna

description: Library name: S2-2-rna


title: OSK Day3 CUT&Tag-seq of H3K27ac rep1

description:
Library name: B3FAc
MEF infected with Oct4, Sox2, Klf4 for 2 days, and changed into iCD1 medium for reprogammming


title: Rf-1_sIO_un-2

city: Daejeon

first: Dongbin

last: Park

address: 55, Expo-ro

country: South Korea

institute: Institute for Basic Science

description:
Library name: Rf-1_sIO_un-2
TruSeq Stranded mRNA Kit

data_processing:
STAR aligner (version 2.7.11b)
RSEM (version 1.3.3)
Assembly: Greater horseshoe bat genome (R. ferrumequinum; GCF_004115265.2), Big brown bat (E. fuscus; GCF_027574615.1), MRV, Shaanvirus-like, IAV (human H1N1), MERS-CoV, and SeoV
Supplementary files format and content: tsv files

organism: Rhinolophus ferrumequinum

source_name: Small intestine organoid

extract_protocol:
Trizol LS reagent (Ambion)
TruSeq Stranded mRNA Kit (illumina)

value: Small intestine organoid


title: Rf-1_sIO_un-1

description:
Library name: Rf-1_sIO_un-1
TruSeq Stranded mRNA Kit


title: OSK Day3 CUT&Tag-seq of Oct4 rep1

description:
Library name: O3Fd3
MEF infected with Oct4, Sox2, Klf4 for 2 days, and changed into iCD1 medium for reprogammming

value: OSK CUT&Tag seq of Oct4


title: 7361_liver_sbr_Male_2-U1

type: other

city: St Louis

first: Alla

last: Karpova

state: MO

address: 700 Rosedale avenue Campus Box 1000

institute: Washington University St Louis

description: Xenium panels used: MMTPS + custom Q6VTXC

hyb_protocol: After RNase treatment to release the RNA strand, a polishing step was performed, followed by overnight probe hybridization utilizing Xenium Prime 5K Mouse Pan Tissue & Pathways Panel (10x Genomics, 1000725) of probes for 5001 genes and an additional custom panel of probes for 100 genes (design ID: Q6VTXC). Probes were subsequently ligated and underwent rolling circle amplification, generating multiple copies of the gene-specific barcode for each RNA target.

scan_protocol: Cell segmentation reagents were applied during a staining workflow to label nuclei, membranes, and cytoplasmic regions for automated morphology-based segmentation. The background was quenched using an auto-fluorescence mixture, and nuclei were counterstained with DAPI to aid in sample tracking and cell boundary segmentation (10x Genomics, CG000760, Rev C). Xenium slides were then loaded onto the 10X Xenium Analyzer instrument (10x Genomics, 1000481) for imaging and initial data processing following manufacturer’s instructions (10x Genomics, CG000584, Rev F). Fluorescently labeled oligos bind to the amplified DNA probes, and iterative rounds of probe hybridization, imaging, and stripping generated optical signatures for each barcode, which were decoded to gene identities.

data_processing:
Nuclear segmentation and transcript assignment was performed on the Xenium instrument using Xenium's proprietary DAPI-based algorithm. In mouse samples Xenium's multimodal segmentation was used, in which three different markers were tested to determine the optimal method for cell segmentation. The best approach, as determined by a proprietary algorithm, combined markers for cell boundaries (epithelial markers : ATP1A1, E-Cadherin and pan-lymphocyte marker: CD45), cell interiors (18S rRNA), and nuclear expansion (DAPI). Segmentation quality was assessed using Xenium Q-Scores. Output files generated by the Xenium instrument were subsequently converted into HDF5, MEX, parquet, and CSV formats using Cell Ranger for downstream off-instrument analysis
Raw matrices represent individual transcript counts per gene per cell

molecule: other

source_name: Liver from SBR cohort at 2 wks

extract_protocol: Formalin-fixed paraffin-embedded (FFPE) blocks of interest were identified and screened by performing hematoxylin and eosin (H&E) staining. FFPE passed screening were sectioned at 5 µm and mounted onto Xenium slides following a modified version of the FFPE Tissue Preparation Guide (10x Genomics, CG000578, Rev D). Slides were deparaffinized with sequential xylene and ethanol washes, followed by decrosslinking using the FFPE Tissue Enhancer and diluted Perm Enzyme B (10x Genomics, CG000580, Rev E).

treatment_protocol: All animal studies were approved by Washington University in St. Louis Institutional Animal Care and Use Committee protocol  #(23-0421). All experiments were performed in accordance with relevant guidelines and regulations, including the ARRIVE guidelines (https://arriveguidelines.org/). 8-week-old male C57BL/6J mice (purchased from The Jackson Laboratory; Bar Harbor, ME) received sham or 75% proximal small bowel resection (SBR). Mice were randomized into 2-, 5-, 10-, 26-, and 52-week cohorts. The sham operation involves a transection of the small bowel 6 cm proximal to the cecum with primary end-to-end anastomosis with 9-0 nylon sutures placed in an interrupted fashion. For the 75% SBR operations, the small bowel is transected at two points: 1-2cm distal to the ligament of Treitz and 6cm proximal to the cecum. The intervening mesentery is tied off and the small bowel is resected. An end-to-end primary anastomosis is completed with 9-0 nylon sutures placed in an interrupted fashion. Postoperative care included no food for 24 hours and 1 week of incubator housing. All mice were fed a liquid enteral diet (LD101 #0007551, Test Diet; Richmond, IN) ad lib.

value: Liver

tag: Sex

value: Male

tag: cohort

value: sbr

tag: timepoint (weeks)


title: Rf-1_sIO_ShVl_2d_1

description:
Library name: Rf-1_sIO_ShVl_2d_1
TruSeq Stranded mRNA Kit


title: Rf-1_KiO_SeoV_2d_2

description:
Library name: Rf-1_KiO_SeoV_2d_2
TruSeq Stranded mRNA Kit

source_name: Kidney organoid

value: Kidney organoid


title: hepG2-S1-rep2-rna

description: Library name: S1-2-rna


title: Male 1 Single CLD2AD SVC Fraction

city: OKC

first: David

last: Sparling

state: OK

address: 1200 Children’s Avenue, Suite 4D

department: Section of Pediatric Diabetes and Endocrinology

institute: Oklahoma Children’s Hospital OU Health

description: Library name: Sample 2

data_processing:
The raw sequencing data were trimmed and aligned to the mouse transcriptome (Mouse (mm10) v3.0.0) using Cell Ranger v7.2.0 then the data was transferred to Partek Flow
Within the Partek Software, cells with low-quality cell barcodes or with high mitochondrial genome were excluded.  Qualified cells with detected gene number between 50 and 9,000 were selected for analysis.  The unique molecular identifier (UMI) number above 500 and below 75,000 and the percentage of mitochondrial genes below 20% were kept.  Data were normalized by counts per million, using add 1.0 and log 2.0, and features with a value of 0 in 99% of the samples were excluded
The top 100 principal components contributing to data variance were used for principal component analysis
. After these steps, cells were clustered by graph-based clustering and visualized by t-SNE. Cell type was identified using the biomarkers identified by the Gene Set ANOVA filter by the lowest average coverage of 1.0.
Assembly: (Mouse (mm10) v3.0.0)
Supplementary files format and content: a matrix.h5  for each sample- exported from Partek

molecule: polyA RNA

source_name: Adipose

extract_protocol:
Stromal vascular cells from 7 mos mice were isolated by collagenase digestion .  Cell viability was measured by trypan blue exclusion to confirm a viability of greater than 97%.  Cell suspensions were loaded into a 10x Genomics Chromium Next GEM Chips and encapsulated with Single Cell 3ʹ v3 barcoded gel bead using the 10x Genomics Chromium X according to the manufacturer’s instructions.
Single-cell libraries were then constructed according to the 10X Genomics' instructions. Dual Index Library Kit. 3.0

treatment_protocol: Gene Expression induced by doxycycline

value: Adipose

value: Stromal vascular cells

value: CLD2AD OverExpression, Single Tg

value: Induced with doxycycline


title: Male 2 Double CLD2AD SVC Fraction

description: Library name: Sample 3

value: CLD2AD OverExpression, Double Tg


title: 23P5 Injury matched DRG RNA-seq

city: Los Angeles

first: Dmitriy

last: Sheyn

address: 127 S San Vicente Blvd

institute: Cedars-Sinai Medical Center

description: Library name: 23P5 DRG L2

data_processing:
For scRNA-seq: Raw sequencing data was demultiplexed and converted to FASTQ format using bcl2fastq v2.20. Cell Ranger v7.1.0 (10X Genomics) was used for barcode identification, read alignment, and UMI quantification with default parameters and aligning to the pig reference genome Sscrofa11 with intron mode used. For bulk RNA-seq (both sample types): Raw reads obtained from RNA-Seq were aligned to the transcriptome using STAR (version 2.6.1) (Dobin A et al., 2013) / RSEM (version 1.2.28) (Li B and Dewey CN, 2011) with default parameters, using a custom pig Sscrofa11 transcriptome reference downloaded from https://useast.ensembl.org/, containing all protein-coding and long non-coding RNA genes based on Sscrofa11.1.104 annotation.
Assembly: For scRNA-seq: Sscrofa11. For bulk RNA-seq: custom pig Sscrofa11 transcriptome reference downloaded from https://useast.ensembl.org/, containing all protein-coding and long non-coding RNA genes based on Sscrofa11.1.104 annotation.
Supplementary files format and content: tsv and mtx files

organism: Sus scrofa

value: Dorsal Root Ganglia

value: Injury matched


title: Rf-1_KiO_SeoV_2d_1

description:
Library name: Rf-1_KiO_SeoV_2d_1
TruSeq Stranded mRNA Kit


title: Rf-1_sIO_ShVl_1d_3

description:
Library name: Rf-1_sIO_ShVl_1d_3
TruSeq Stranded mRNA Kit


title: Rf-1_sIO_un-3

description:
Library name: Rf-1_sIO_un-3
TruSeq Stranded mRNA Kit


title: 23P4 Injury matched DRG RNA-seq

description: Library name: 23P4 DRG L2


title: Male 1 Double CLD2AD SVC Fraction

description: Library name: Sample 1


title: 23P3 Injury matched DRG RNA-seq

description: Library name: 23P3 DRG L2


title: hepG2-G1-rep2-rna

description: Library name: G1-2-rna


title: PBS_3_D7

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

description: Library name: sample14

data_processing:
Qulity control by Fastqc
Paired-end aligned with mm10 throught Hisat2
count matrix generated by feature-count
Assembly: mm10
Supplementary files format and content: count matrix as csv

source_name: colon

growth_protocol: Mice were maintained under specific pathogen-free conditions. All animal protocols were reviewed and approved by the Institutional Animal Care and Use Committee of Xiamen University.

extract_protocol:
Total RNA was extracted from colon tissue previously washed from luminal content. Samples were homogenized in TRIZOL. Homogenized tissues were then added with chloroform in order to separate RNA from genomic DNA and proteins. RNA isolation and purification required isopropanol (RNA precipitation) and 70% ethanol (RNA wash). Total RNA was resuspended in Nuclease-free water.
Illumina standard protocol

treatment_protocol: Mice were i.p. injected with one dose of BG (1 mg) on day -7 (designated day0, D0 ), Then, Mice received 3% indicated DSS (36,000 to 50,000 molecular weight; MP Biomedicals) in their drinking water for 5 days, followed by 2 days(D7) or 7 days(Day12) of distilled water without DSS. Control animals received distilled water for the entire period.

value: colon

tag: treatment/time point


title: 23P4 Non-injury matched DRG RNA-seq

description: Library name: 23P4 DRG L5

value: Non-injury matched


title: Male 2 Single CLD2AD SVC Fraction

description: Library name: Sample 4


title: Rf-1_KiO_SeoV_1d_3

description:
Library name: Rf-1_KiO_SeoV_1d_3
TruSeq Stranded mRNA Kit


title: Rf-1_KiO_SeoV_2d_3

description:
Library name: Rf-1_KiO_SeoV_2d_3
TruSeq Stranded mRNA Kit


title: hepG2-G2-rep3-rna

description: Library name: G2-3-rna


title: 23P2 Injury matched DRG RNA-seq

description: Library name: 23P2 DRG L2


title: hepG2-bulk-rep2-rna

description: Library name: bulk-r2-rna


title: hepG2-S1-rep3-rna

description: Library name: S1-3-rna


title: 23P3 Non-injury matched DRG RNA-seq

description: Library name: 23P3 DRG L5


title: Rf-1_KiO_un-3

description:
Library name: Rf-1_KiO_un-3
TruSeq Stranded mRNA Kit


title: hepG2-G2-rep2-rna

description: Library name: G2-2-rna


title: 23P2 Non-injury matched DRG RNA-seq

description: Library name: 23P2 DRG L5


title: 23P3 L3-L4 injured RNA-seq

description: Library name: 23P3 L3-L4 injured

source_name: Nucleus Pulposus

value: Nucleus Pulposus

value: Needle injury


title: PBS_2_D12

description: Library name: sample11


title: 23P3  L1-L2 healthy RNA-seq

description: Library name: 23P3 L1-L2 healthy

value: Non-injured


title: PBS_3_D0

description: Library name: sample10


title: Rf-1_KiO_SeoV_1d_1

description:
Library name: Rf-1_KiO_SeoV_1d_1
TruSeq Stranded mRNA Kit


title: PBS_1_D7

description: Library name: sample13


title: 23P4 L3-L4 injured RNA-seq

description: Library name: 23P4 L3-L4 injured


title: PBS_3_D12

description: Library name: sample12


title: hepG2-G1-rep3-rna

description: Library name: G1-3-rna


title: hepG2-bulk-rep1-rna

description: Library name: bulk-r1-rna


title: Rf-1_KiO_un-1

description:
Library name: Rf-1_KiO_un-1
TruSeq Stranded mRNA Kit


title: 23P2 L3-L4 injured RNA-seq

description: Library name: 23P2 L3-L4 injured


title: hepG2-S4-rep2-rt

description: Library name: S4-2-rt


title: hepG2-bulk-rep3-rna

description: Library name: bulk-r3-rna


title: 23P4 L1-L2 healthy RNA-seq

description: Library name: 23P4 L1-L2 healthy


title: hepG2-S4-rep3-rt

description: Library name: S4-3-rt


title: 23P2 L1-L2 healthy RNA-seq

description: Library name: 23P2 L1-L2 healthy


title: Rf-1_KiO_SeoV_1d_2

description:
Library name: Rf-1_KiO_SeoV_1d_2
TruSeq Stranded mRNA Kit


title: Rf-1_KiO_un-2

description:
Library name: Rf-1_KiO_un-2
TruSeq Stranded mRNA Kit


title: glucan_3_D7

description: Library name: sample8


title: Rf-1T_MRV_2d_2

description:
Library name: Rf-1T_MRV_2d_2
TruSeq Stranded mRNA Kit

source_name: Trachea organoid

value: Trachea organoid


title: 22P70 L4-L5 injured RNA-seq

description: Library name: 22P70 L4-L5 injured


title: Rat urethral tissue sample E_3

city: Guiyang

first: Jian

last: Li

address: No. 206, Sixian Street, Baiyun District

department: Department of Sports Medicine

institute: Beijing Jishuitan Hospital Guizhou Hospital

description:
Library name: E_3_RNAseq
Urethral tissue collected from rats under the indicated experimental conditions for RNA sequencing.

data_processing:
Raw sequencing data were processed using standard bioinformatics pipelines.
Assembly: Rnor_6.0
Supplementary files format and content: Raw sequencing data are provided as paired-end FASTQ files (.fastq.gz), including Read 1 (R1) and Read 2 (R2) files for each sample.

organism: Rattus norvegicus

source_name: urethral tissue

extract_protocol:
Total RNA was extracted from rat urethral tissue using a commercial RNA extraction kit according to the manufacturer’s instructions. RNA quality and quantity were assessed prior to library preparation.
RNA-seq libraries were constructed using poly(A)-enriched RNA following standard Illumina library preparation protocols. Libraries were generated according to the manufacturer’s instructions.

value: urethral tissue

value: Urethral injury + TDN treatment


title: PBS_2_D0

description: Library name: sample9


title: Rf-1T_MRV_2d_1

description:
Library name: Rf-1T_MRV_2d_1
TruSeq Stranded mRNA Kit


title: Rf-1T_MRV_2d_3

description:
Library name: Rf-1T_MRV_2d_3
TruSeq Stranded mRNA Kit


title: hepG2-S3-rep3-rt

description: Library name: S3-3-rt


title: glucan_1_D7

description: Library name: sample7


title: hepG2-S4-rep1-rt

description: Library name: S4-1-rt


title: Rat urethral tissue sample E_1

description:
Library name: E_1_RNAseq
Urethral tissue collected from rats under the indicated experimental conditions for RNA sequencing.


title: Rf-1T_MRV_1d_2

description:
Library name: Rf-1T_MRV_1d_2
TruSeq Stranded mRNA Kit


title: glucan_3_D12

description: Library name: sample6


title: hepG2-S3-rep1-rt

description: Library name: S3-1-rt


title: glucan_2_D12

description: Library name: sample5


title: Rat urethral tissue sample E_2

description:
Library name: E_2_RNAseq
Urethral tissue collected from rats under the indicated experimental conditions for RNA sequencing.


title: hepG2-S3-rep2-rt

description: Library name: S3-2-rt


title: Rat urethral tissue sample D_3

description:
Library name: D_3_RNAseq
Urethral tissue collected from rats under the indicated experimental conditions for RNA sequencing.

value: Urethral injury + Rapamycin treatment


title: hepG2-S2-rep3-rt

description: Library name: S2-3-rt


title: Rf-1T_MERS_2d_3

description:
Library name: Rf-1T_MERS_2d_3
TruSeq Stranded mRNA Kit


title: Rf-1T_MRV_1d_3

description:
Library name: Rf-1T_MRV_1d_3
TruSeq Stranded mRNA Kit


title: Rf-1T_MRV_1d_1

description:
Library name: Rf-1T_MRV_1d_1
TruSeq Stranded mRNA Kit


title: hepG2-S2-rep1-rt

description: Library name: S2-1-rt


title: hepG2-S2-rep2-rt

description: Library name: S2-2-rt


title: glucan_1_D0

description: Library name: sample3


title: Ba/F3 cells,  WT_K118R

city: Hangzhou

first: Xuejing

last: Shao

address: 866, Yuhangtang Road

department: Zhejiang University

institute: College of Pharmaceutical Sciences

data_processing:
To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9)
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9).
After that, a total of G bp ofcleaned, paired-end reads were produced.
Reads of all samples were aligned to the reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
Assembly: Ensembl v101
Supplementary files format and content: text file includes raw counts for each Sample
Supplementary files format and content: text file includes FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure.
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.

value: Mouse original B cells


title: Rat urethral tissue sample B_3

description:
Library name: B_3_RNAseq
Urethral tissue collected from rats under the indicated experimental conditions for RNA sequencing.

value: Urethral injury


title: hepG2-S1-rep1-rt

description: Library name: S1-1-rt


title: Rat urethral tissue sample D_1

description:
Library name: D_1_RNAseq
Urethral tissue collected from rats under the indicated experimental conditions for RNA sequencing.


title: Rf-1T_MERS_2d_1

description:
Library name: Rf-1T_MERS_2d_1
TruSeq Stranded mRNA Kit


title: Rf-1T_MERS_1d_3

description:
Library name: Rf-1T_MERS_1d_3
TruSeq Stranded mRNA Kit


title: glucan_3_D0

description: Library name: sample4


title: Ba/F3 cells, S_PXT1_K118R


title: Rf-1T_MERS_2d_2

description:
Library name: Rf-1T_MERS_2d_2
TruSeq Stranded mRNA Kit


title: hepG2-S1-rep2-rt

description: Library name: S1-2-rt


title: hepG2-S1-rep3-rt

description: Library name: S1-3-rt


title: CTRL_2_D7

description: Library name: sample1


title: Ba/F3 cells,  WT


title: Rat urethral tissue sample A_3

description:
Library name: A_3_RNAseq
Urethral tissue collected from rats under the indicated experimental conditions for RNA sequencing.

value: Sham control (no urethral injury)


title: Rf-1T_MERS_1d_2

description:
Library name: Rf-1T_MERS_1d_2
TruSeq Stranded mRNA Kit


title: Rf-1T_IAV_2d_3

description:
Library name: Rf-1T_IAV_2d_3
TruSeq Stranded mRNA Kit


title: Rf-1T_MERS_1d_1

description:
Library name: Rf-1T_MERS_1d_1
TruSeq Stranded mRNA Kit


title: CTRL_3_D7

description: Library name: sample2


title: Rat urethral tissue sample A_2

description:
Library name: A_2_RNAseq
Urethral tissue collected from rats under the indicated experimental conditions for RNA sequencing.


title: Rat urethral tissue sample D_2

description:
Library name: D_2_RNAseq
Urethral tissue collected from rats under the indicated experimental conditions for RNA sequencing.


title: Rat urethral tissue sample B_2

description:
Library name: B_2_RNAseq
Urethral tissue collected from rats under the indicated experimental conditions for RNA sequencing.


title: Ba/F3 cells, S_PXT1


title: mycelium - Vea_KO_MEA - rep4

type: RNA

city: TOULOUSE

first: Olivier

last: PUEL

address: 180 chemin de Tournefeuille

department: TOXALIM UMR 1331

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Fungi_Pexp_Afla_Afum GE 8x60K (design 084703)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 084703_D_F_20170227). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);}. We firstly selected control probes and probes targeting Penicillium expansum transcripts (GeneNames begining by 'PEX1_') giving a dataset with 31803 entries. We next selected the spots with a minimal weight of 1 for 20 out of 24 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 28179 spots were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 9947 rows each corresponding to a unique ProbeName (provided as data Matrix).

organism: Penicillium expansum

source_name: mycelium

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: Strains were incubated for 5 days in the dark at 25°C in a incubator.

extract_protocol: Total RNA was isolated at the end of the growth period. The mycelium was transferred to lysing matrix D tubes (1.4 mm ceramic spheres), to which 760 µL of lysis buffer (10 μL of β-mercaptoethanol and 750 μL of RLT buffer) were added, and the tubes were placed in liquid nitrogen. The mycelium cells were broken down in a Precellys homogenizer with three grindings at a speed of 6,500 rpm for 15 s followed by 5 min incubation on ice, at 6,500 rpm for 25 s and 5 min on ice, and a final 6,500 rpm for 15 s. The samples were subsequently centrifuged at 16,000 g at 4 °C for 10 min. The supernatant was recovered in QIAshredder spin columns (QIAGEN) and the total RNA was purified using RNeasy spin minicolumns (QIAGEN).

treatment_protocol: Strains were centrally inoculated onto plates, either containing MEA medium alone or MEA medium supplemented with 400 μL (280 mM) DMSO covered with sterile cellophane sheets.

tag: medium

value: MEA


title: Rat urethral tissue sample A_1

description:
Library name: A_1_RNAseq
Urethral tissue collected from rats under the indicated experimental conditions for RNA sequencing.


title: Rf-1T_IAV_2d_2

description:
Library name: Rf-1T_IAV_2d_2
TruSeq Stranded mRNA Kit


title: Ba/F3 cells, PMSCV


title: Rat urethral tissue sample B_1

description:
Library name: B_1_RNAseq
Urethral tissue collected from rats under the indicated experimental conditions for RNA sequencing.


title: COS-2,SD rat, 20 months old, sciatic nerve

city: XuZhou

first: Bin

last: Pan

state: JiangSu

address: 99 Huaihai West Road,Quanshan District

institute: The Affiliated Hospital of Xuzhou Medical University

description: Library name: COS-2

data_processing:
The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest. Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K-means algorithm and graph-based algorithm, respectively.The other clustering method is Seurat 3.0(R package). Cells whose gene number was less than 200, or gene number ranked in the top 1%, or mitochondrial gene ratio was more than 25% were regarded as abnormal and filtered out. Dimensionality reduction was performed using PCA, and visualization was realized by TSNE and UMAP.GO enrichment, KEGG enrichment, Reactome enrichment and Disease enrichment (human only) of cluster markers were performed using KOBAS software with Benjamini-Hochberg multiple testing adjustment, using top 20 markers gene of cluster. The results were visualized using R package.
Assembly: Rattus_norvegicus_107
Supplementary files format and content: barcodes tsv.gz list of spatial barcodes
Supplementary files format and content: features.tsv.gz. list of gene lDs
Supplementary files format and content: matrix.mtx.gz. gene expresion count data in Matrix Market Exchange Format

source_name: sciatic nerve

extract_protocol:
Using single cell 3 'Library and Gel Bead Kit V3.1(10x Genomics, 1000121) and Chromium Single Cell G Chip Kit (10x Genomics, 1000120), the cell suspension (300-600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, single cells were suspended in PBS containing 0.04% BSA.Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs.Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 min, followed by 85°C for 5 min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200.
According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp(PE150) strategy.

value: sciatic nerve

value: Schwann Cells


title: hepG2-G2-rep3-rt

description: Library name: G2-3-rt


title: Rf-1T_IAV_2d_1

description:
Library name: Rf-1T_IAV_2d_1
TruSeq Stranded mRNA Kit


title: POU2F3_Library3_DMS_Screen

city: Cold Spring Harbor

first: Damianos

last: Skopelitis

state: NY

address: One Bungtown Rd

department: Cancer Biology

institute: Cold Spring Harbor Laboratory

description:
Library name: POU2F3_Library3_DMS_Screen
300 cycles P2 chip

data_processing:
OCAT1 paired end reads were converted into full length sequences by combining the r1 and r2 files from NGS sequencing.
Raw reads from each sample were filtered and deconvoluted from multiplexed reads by requiring that they had 100% matches to the following sequeces-
OCAT1_Library: P0_Rep1: ATCACGGTGGAAAGGACGAAACACC and CGGCGAACCTGGCAT
OCAT1_Library: P0_Rep2: ACAGTGGTGGAAAGGACGAAACACC and CGGCGAACCTGGCAT
OCAT1_Library: P10_Rep1: TGACCAGTGGAAAGGACGAAACACC and CGGCGAACCTGGCAT
OCAT1_Library: P10_Rep2: GCCAATGTGGAAAGGACGAAACACC and CGGCGAACCTGGCAT
POU2F3_Library_1: P0_Rep1: CGATGTGTGGAAAGGACGAAACACC and AGCTTCAAGAACATGTG
POU2F3_Library_1: P0_Rep2: TTAGGCGTGGAAAGGACGAAACACC and AGCTTCAAGAACATGTG
POU2F3_Library_1: P10_Rep1: TGACCAGTGGAAAGGACGAAACACC and AGCTTCAAGAACATGTG
POU2F3_Library_1: P10_Rep2: ACAGTGGTGGAAAGGACGAAACACC and AGCTTCAAGAACATGTG
POU2F3_Library_2: P0_Rep1: CGATGTGTGGAAAGGACGAAACACC and AACCCAAAACCCAGCTC
POU2F3_Library_2: P0_Rep2: TTAGGCGTGGAAAGGACGAAACACC and AACCCAAAACCCAGCTC
POU2F3_Library_2: P10_Rep1: TGACCAGTGGAAAGGACGAAACACC and AACCCAAAACCCAGCTC
POU2F3_Library_2: P10_Rep2: ACAGTGGTGGAAAGGACGAAACACC and AACCCAAAACCCAGCTC
POU2F3_Library_3: P0_Rep1: CGATGTGTGGAAAGGACGAAACACC and TCCCGGCTGGTATCTCC
POU2F3_Library_3: P0_Rep2: TTAGGCGTGGAAAGGACGAAACACC and TCCCGGCTGGTATCTCC
POU2F3_Library_3: P10_Rep1: TGACCAGTGGAAAGGACGAAACACC and TCCCGGCTGGTATCTCC
POU2F3_Library_3: P10_Rep2: ACAGTGGTGGAAAGGACGAAACACC and TCCCGGCTGGTATCTCC
Reads were then clipped to only include the sequences between the filter sequences and to remove POU2F3-specific 5' flanking sequences (POU2F3 Library 1:CCAGCTCTGGAGGGGCC,  POU2F3 Library_2: GACCACCATCTCACGATTT) and POU2F3 Library_3: CGCCTCACCCTCGAGAAG) that are not included in the mutagenesis window. For OCAT1 libraries, they were also clipped at 76 nucleotide for read 1 and 77 nucleotides for read 2 so that the reads could be concatenated into a full length cDNA variant with no overlap.
Clipped reads with the same nucleotide sequence were counted and counts were matched to a variant id by requiring a 100% match between the read sequence and the library design reference sequence.
Assembly: DNA sequences used for alignment are in the supplemental files OCA-T1_library_design.csv, POU2F3_library_1_design.csv, POU2F3_library_2_design.csv, and POU2F3_library_3_design.csv in column 3: Mutagenesis_windows_nucleotide_sequence. Each library uses the sequences in the file with the corresponding name.
Supplementary files format and content: Comma Seperated Value format (csv). Column 1: Amino acid substitution Column 2 and 3:  Position of substitution in the original protein and the DMS library column 4: Id of each variant column 5-end: Raw counts of variants at initial and final collection time point for both replicates for each DMS screen.

growth_protocol: NCI-H211 Cas9+ cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin. Cells were maintained at 37 °C in a humidified incubator with 5% CO₂.

extract_protocol:
Genomic DNA isolated from cells using ~1mL extraction buffer (10mM  Tris-HCl (pH8), 150mM NaCl, 10mM  EDTA, 0.1% SDS and 0.2 mg/mL Proteinase K. Samples were incubated at  56C for 48-hours and  purified with Phenol followed by EtOH/NaOAc precipitation.  DNA pellets were resuspended in water.
DMS libraries were generated from genomic DNA extracted from the initial (P0) and final (P10) time points of each screen using a two-step PCR amplification strategy. In the first PCR step, the total cDNA variant population was amplified using primers flanking the mutagenized region of each DMS library. Each forward primer contained a universal 5′ adapter sequence (5′-GTGGAAAGGACGAAACACC-3′), and each reverse primer contained the corresponding reverse universal adapter (5′-AGTTCTTGAGAGGCCATGTTTATCG-3′). In the second PCR step, products were barcoded using a set of stacked P5/P7 Illumina-compatible primers. Barcodes used for each library and replicate were as follows:             OCA-T1 library (P0 Replicate1:ATCACG P10 Replicate1:TGACCA P0 Replicate 2: ACAGTG P10 Replicate 2:GCCAAT)                                                                                POU2F3 library 1 (P0 Replicate1:CGATGT P10 Replicate1:TGACCA P0 Replicate 2: TTAGGC P10 Replicate 2:ACAGTG)                                                                                POU2F3 library 2 (P0 Replicate1:CGATGT P10 Replicate1:TGACCA P0 Replicate 2: TTAGGC P10 Replicate 2:ACAGTG)                                                                                POU2F3 library 3 (P0 Replicate1:CGATGT P10 Replicate1:TGACCA P0 Replicate 2: TTAGGC P10 Replicate 2:ACAGTG).                                                                                Libraries from each screen were multiplexed and sequenced on Illumina Nextseq 2000 platform. OCA-T1 screen was sequenced as Paired-end a50 (PE150 ) while all POU2F3 libraries were sequenced in Single-end 300 (SE300).

treatment_protocol: NCI-H211 Cas9+ were transduced at low Multiplicity of Infection (~MOI: 0.1 - 0.15) with DMS (OCA-T1 or POU2F3) lentiviral libraries and cells were cultured for 10 doublings. Cells were collected at initial and final timepoint for library preparation.

value: SCLC

value: Deep Mutagenesis Scan library

value: 10 doublings


title: COD,SD rat, 20 months old,dorsal root ganglia

description: Library name: COD

source_name: dorsal root ganglia

value: dorsal root ganglia

value: Neurons


title: CAS-2,SD rat, 3 months old, sciatic nerve

description: Library name: CAS-2


title: DN2091, DCZ, Male

city: New York

first: Daniele

last: Neri

address: 630 West 168th Street

description:
Library name: DL024
column name in all_samples_raw.txt: DL024

data_processing:
Libraries were sequenced using Element AVITI
Samples were multiplexed in each lane to yield a targeted number of paired-end 75bp reads for each sample
Bases2fastq version 1.4.0.833301531 was used to convert BCL to the fastq format, coupled with adaptor trimming
Pseudoalignment to a kallisto index created from the transcriptome (Ensembl v96, Mouse:GRCm38.p6) by kallisto (0.44.0).
Assembly: Ensembl v96, Mouse:GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: interscapular brown adipose tissue

extract_protocol:
RNA from iBAT was extracted using Tri-Isolate RNA Pure Kit (IBI Scientific, IB47631) following the manufacturer’s directions
RNA samples were tested for RIN and sequenced by the Genome Center Core at Columbia University Irving Medical Center. Poly-A pull-down method was used to enrich mRNAs from total RNA samples followed by library construction using Illumina TruSeq chemistry. The final PCR step was modified using the KAPA HiFi HotStart Ready Mix.

value: interscapular brown adipose tissue

value: Male

tag: age

value: 6-8 months

value: B6.129X1- Tht1(cre)Te/Kieg

value: DCZ


title: CAD,SD rat, 3 months old, dorsal root ganglia

description: Library name: CAD


title: DN2086, Saline, Female

institute: Columbia University Irving Medical Center

description:
Library name: DL022
column name in all_samples_raw.txt: DL022

value: Female

value: Saline


title: DN2089, Saline, Male

description:
Library name: DL023
column name in all_samples_raw.txt: DL023


title: Rf-1T_IAV_1d_3

description:
Library name: Rf-1T_IAV_1d_3
TruSeq Stranded mRNA Kit

value: Trachea organoid


title: DN2097, DCZ, Male

description:
Library name: DL021
column name in all_samples_raw.txt: DL021


title: COS-1,SD rat, 20 months old, sciatic nerve

description: Library name: COS-1


title: CAS-1,SD rat, 3 months old, sciatic nerve

description: Library name: CAS-1


title: DN2094, Saline, Female

description:
Library name: DL020
column name in all_samples_raw.txt: DL020


title: Rf-1T_IAV_1d_1

description:
Library name: Rf-1T_IAV_1d_1
TruSeq Stranded mRNA Kit


title: Rf-1T-3

description:
Library name: Rf-1T-3
TruSeq Stranded mRNA Kit


title: Whole bone marrow cell, DEIX, rep3

city: Jeonbuk

first: JungChae

last: Lee

address: 567, Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, Republic of Korea

institute: Jeonbuk National University

description: Library name: 4-III

data_processing:
Skewer ver 0.2.2 was used for trmming adaptor sequence.
Trimmed sequence reads were mapped to mm10 using STAR aligner ver 2.6
Read count extraction and normalization were performed using Cufflinks ver 2.2.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: Whole bone marrow cells from B6 mice

extract_protocol:
The 1 ug of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.
RNA libraries for RNA-seq were prepared using MGIEasy RNA Directional Library Prep Kit following manufacture's protocols.

value: Whole bone marrow cells from B6 mice


title: POU2F3_Library2_DMS_Screen

description:
Library name: POU2F3_Library2_DMS_Screen
300 cycles P2 chip


title: DN2075, DCZ, Female

description:
Library name: DL019
column name in all_samples_raw.txt: DL019


title: Rf-1B_MERS_2d_3

description:
Library name: Rf-1B_MERS_2d_3
TruSeq Stranded mRNA Kit

source_name: Bronchioalveolar organoid

value: Bronchioalveolar organoid


title: OCAT1_DMS_Screen

description:
Library name: OCAT1_DMS_Screen
150 cycles P3 chip


title: Rf-1T_IAV_1d_2

description:
Library name: Rf-1T_IAV_1d_2
TruSeq Stranded mRNA Kit


title: Rf-1B_MERS_2d_2

description:
Library name: Rf-1B_MERS_2d_2
TruSeq Stranded mRNA Kit


title: POU2F3_Library1_DMS_Screen

description:
Library name: POU2F3_Library1_DMS_Screen
300 cycles P1 chip


title: Rf-1T-2

description:
Library name: Rf-1T-2
TruSeq Stranded mRNA Kit


title: Rf-1T-1

description:
Library name: Rf-1T-1
TruSeq Stranded mRNA Kit


title: DN2201, Saline, Female

description:
Library name: DL014
column name in all_samples_raw.txt: DL014


title: Rf-1B_MERS_2d_1

description:
Library name: Rf-1B_MERS_2d_1
TruSeq Stranded mRNA Kit


title: hepG2-G2-rep2-rt

description: Library name: G2-2-rt


title: hepG2-G1-rep2-rt

description: Library name: G1-2-rt


title: hepG2-G1-rep3-rt

description: Library name: G1-3-rt


title: hepG2-G2-rep1-rt

description: Library name: G2-1-rt


title: hepG2-G1-rep1-rt

description: Library name: G1-1-rt


title: Whole bone marrow cell, TBI+DEIX, rep1

description: Library name: 3-I


title: DN2072, DCZ, Male

description:
Library name: DL013
column name in all_samples_raw.txt: DL013


title: Rf-1B_MERS_1d_2

description:
Library name: Rf-1B_MERS_1d_2
TruSeq Stranded mRNA Kit


title: Whole bone marrow cell, DEIX, rep2

description: Library name: 4-II


title: WT12, Saline, Female

description:
Library name: DL012
column name in all_samples_raw.txt: DL012


title: DN2205, DCZ, Female

description:
Library name: DL015
column name in all_samples_raw.txt: DL015


title: DN2207, DCZ, Female

description:
Library name: DL018
column name in all_samples_raw.txt: DL018


title: Whole bone marrow cell, TBI+DEIX, rep3

description: Library name: 3-III


title: H211_L191_IgG

description: Library name: H211_L191_IgG

data_processing:
Sequencing reads were aligned to the human genome (hg38) using Bowtie2. SAM files were converted to sorted and indexed BAM format using SAMtools (v1.9)
Peaks were called with MACS2 (v2.2.x) using matched IgG controls and a q-value threshold of 0.01
Peaks were filtered to remove chrM, ENCODE blacklist regions, and non-standard chromosomes
bigWig files were generated using deepTools (v3.5.2) with CPM normalization
Assembly: hg38
Supplementary files format and content: bigWig files .bw
Library strategy: CUT&Run

growth_protocol: NCI-H211 cells stably expressing wild-type POU2F3 or the α1-helix mutant POU2F3L191A (3×FLAG-tagged) were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin. Cells were maintained at 37 °C in a humidified incubator with 5% CO₂.

extract_protocol:
Approximately 500,000 cells were processed per sample using the CUTANA™ ChIC/CUT&RUN Kit (EpiCypher, 14-1048) per the manufacturer’s protocol. Cells were bound to ConA beads, permeabilized with digitonin, and incubated overnight at 4 °C with 0.1 µg of anti-FLAG or IgG antibody. The next day, samples were treated with 2.5 µL pAG-MNase, and digestion was initiated with CaCl₂ for 2 hours at 4 °C. DNA was purified using SPRI beads and eluted in 0.1× TE buffer.
Libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645) following the manufacturer’s protocol. DNA was end-repaired, A-tailed, and adaptor-ligated, then purified with AMPure XP beads (0.9×). Libraries were PCR-amplified (14 cycles) with NEBNext Ultra II Q5 Master Mix using universal i5 and sample-specific i7 primers. Final libraries were cleaned, quantified by Qubit, size-checked by Bioanalyzer, and sequenced as paired-end 75 bp reads on an Illumina NextSeq.

tag: antibody

value: IgG IP


title: H211_WT_IgG

description: Library name: H211_WT_IgG


title: Rf-1B_MERS_1d_3

description:
Library name: Rf-1B_MERS_1d_3
TruSeq Stranded mRNA Kit


title: H211_EV_IgG

description: Library name: H211_EV_IgG

value: EV


title: H211_EV_FLAG

description: Library name: H211_EV_FLAG

value: SCLC

value: FLAG IP


title: Rf-RNA_oh-3_BAO

description:
Library name: Rf-RNA_oh-3_BAO
TruSeq Stranded mRNA Kit


title: DN2099, Saline, Male

description:
Library name: DL016
column name in all_samples_raw.txt: DL016


title: Whole bone marrow cell, TBI+DEIX, rep2

description: Library name: 3-II


title: DN2087, Saline, Male

description:
Library name: DL017
column name in all_samples_raw.txt: DL017


title: WT9, Saline, Male

description:
Library name: DL009
column name in all_samples_raw.txt: DL009


title: Whole bone marrow cell, control , rep3

description: Library name: 1-III


title: H211, WT, sgRosa, d5, Rep1

description: Library name: WT_sgRosa_1

data_processing:
Single-end 76 bp raw sequencing reads were pseudoaligned to the human transcriptome (hg38) using Kallisto with 100 bootstrap iterations.
Genes with low expression (maximum read count below 20 across all conditions) were filtered out.
Counts from all experimental groups were normalized and used to calculate log2 fold change (LFC) values.
These LFC values were  transformed and subjected to z-score calculation.
Heatmaps were generated using the z-scores of normalized LFC values to visualize the top 1000 differentially expressed genes, employing the ComplexHeatmap R package.
Assembly: hg38
Supplementary files format and content: H211_TPMs.csv

growth_protocol: NCI-H211 cells stably expressing POU2F3(WT), POU2F3(L191A) or an empty control were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin. Cells were maintained at 37 °C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted from each sample using 1mL TRIzol reagent following the manufacturer’s instructions. RNA was resuspended in RNase-free water.
RNA-seq libraries were prepared using 2 µg of total RNA using the TruSeq Sample Prep Kit v2 (Illumina), according to the standard protocol.

treatment_protocol: Cells were infected in triplicate with a lentivirus expressing either a non-targeting control sgRNA (sgROSA) or sgPOU2F3 in >95% mCherry-positivity. Samples were collected five days post-infection for RNA-seq analysis.

value: WT, sgRosa


title: Rf-RNA_oh-2_BAO

description:
Library name: Rf-RNA_oh-2_BAO
TruSeq Stranded mRNA Kit


title: H211_WT_FLAG

description: Library name: H211_WT_FLAG


title: WT10, DCZ, Female

description:
Library name: DL010
column name in all_samples_raw.txt: DL010


title: Whole bone marrow cell, TBI, rep3

description: Library name: 2-III


title: H211, WT, sgPOU2F3, d5, Rep3

description: Library name: WT_sgPOU2F3_3

value: WT, sgPOU2F3


title: WT8, Saline, Female

description:
Library name: DL008
column name in all_samples_raw.txt: DL008


title: H211_L191_FLAG

description: Library name: H211_L191_FLAG


title: Whole bone marrow cell, DEIX, rep1

description: Library name: 4-I


title: H211, WT, sgRosa, d5, Rep3

description: Library name: WT_sgRosa_3


title: Rf-1B_MERS_1d_1

description:
Library name: Rf-1B_MERS_1d_1
TruSeq Stranded mRNA Kit


title: Whole bone marrow cell, TBI, rep1

description: Library name: 2-I


title: Whole bone marrow cell, TBI, rep2

description: Library name: 2-II


title: WT11, Saline, Male

description:
Library name: DL011
column name in all_samples_raw.txt: DL011


title: H211, WT, sgRosa, d5, Rep2

description: Library name: WT_sgRosa_2


title: Post-transplantation_CMO

city: Seoul

first: Yuji

state: Soul-t'ukpyolsi

address: #308, Convergence building, Seoul National University College of Medicine, 103 D

institute: Seoul National University

description:
Library name: Primates_Post_CMO
single-cell RNA-sequencing

data_processing:
Sequenced fastq files were aligned, filtered, barcoded, demultiplexed and UMI counted using Cell Ranger Chromium Single Cell RNA-seq version 7.1.0, by 10X Genomics with the Macaca mulatta genome reference. Cells without a CMO tag or multiple tags were filtered out
Assembly: Macaca mulatta Mmul_10
Supplementary files format and content: Tab-seperated values files and matrix files.

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
A total of eight samples, including both pre- and post-transplantation samples (N=4), were utilized. Following careful thawing of the PBMCs, eight distinct cell multiplexing oligos were applied for demultiplexing. Single-cell capturing and library construction for scRNA-seq analysis were conducted according to the manufacturer's instructions (10X Genomics, Pleasanton, CA; Chromium Next GEM Single Cell 3’ HT Reagent Kits v3.1, CG000419).
PBMC samples and gel beads were combined on the Chromium Next GEM Chip M to produce gel bead-in-emulsions (GEMs). During the polymerase chain reaction (PCR), complementary DNA (cDNA) from poly-adenylated mRNA and DNA from cell multiplexing oligos were synthesized simultaneously. The resulting full-length cDNA underwent a cleanup process with a Cleanup Mix solution containing Dynabeads MyOne SILANE (PN 2000048, 10X Genomics) for each sample. Post-cleanup, cDNA was amplified to create libraries for gene expression and cell multiplexing oligo libraries.

value: PBMC

value: Post-transplantation


title: Pre-transplantation_CMO

description:
Library name: Primates_Pre_CMO
single-cell RNA-sequencing

value: Pre-transplantation


title: Pre-transplantation_GEX

description:
Library name: Pre_GEX
single-cell RNA-sequencing


title: Post-transplantation_GEX

description:
Library name: Post_GEX
single-cell RNA-sequencing


title: H211, WT, sgPOU2F3, d5, Rep2

description: Library name: WT_sgPOU2F3_2


title: CC_WT_axon_2

first: Ki-Jun

last: Yoon

address: 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

institute: Korea Advanced Institute of Science and Technology

data_processing:
Raw sequencing outputs were automatically converted to FASTQ files by the sequencer's built-in software.
Raw FASTQ files were de-multiplexed into relative FASTQ files for each samples with truncated index sequence through splitBarcode version 0.1.6 provided by MGI Tech.
The expression level was calculated by the RSEM (v1.3.3) and STAR (v2.7.10b) with default parameters.
do rsem-calculate-expression --star -p 8  --star-gzipped-read-file --paired-end $i"_1.fastq.gz" $i"_2.fastq.gz"
Assembly: mm10
Supplementary files format and content: tab-seperated text file include TPM and FPKM values

source_name: Corpus callosal axon

extract_protocol:
The corpus callosum (CC) region was manually microdissected and collected in TRIzol (Invitrogen) and stored at -80°C overnight. Total RNA was isolated from each sample, and further RNA cleanup was performed using the RNeasy Mini Kit (Qiagen). The Dynabeads mRNA DIRECT Purification Kit (Invitrogen) was used to isolate mRNA from the samples.
The NEBNext Ultra™ RNA Library Prep Kit for Illumina (New England Biolabs) was used, and the recommended protocol was followed to generate the library.

treatment_protocol: The P4 brain from a B6 mouse was isolated and frozen in OCT, and 60 µm thick sections were cut using a cryostat.

value: Corpus callosal axon

value: WT


title: WT2, Saline, Female

description:
Library name: DL002
column name in all_samples_raw.txt: DL002

value: interscapular brown adipose tissue

value: 6-8 months


title: CC_WT_axon_3


title: WT7, Saline, Male

description:
Library name: DL007
column name in all_samples_raw.txt: DL007

value: Male

value: Saline


title: CC_cKO_axon_1

value: Mettl14 cKO


title: Whole bone marrow cell, control, rep1

description: Library name: 1-I

value: Whole bone marrow cells from B6 mice


title: H211, L191A, sgRosa, d5, Rep2

description: Library name: L191A_sgRosa_2

value: L191A, sgRosa


title: H211, L191A, sgPOU2F3, d5, Rep2

description: Library name: L191A_sgPOU2F3_2

value: L191A, sgPOU2F3


title: H211, WT, sgPOU2F3, d5, Rep1

description: Library name: WT_sgPOU2F3_1


title: Rf-RNA_oh-1_BAO

description:
Library name: Rf-RNA_oh-1_BAO
TruSeq Stranded mRNA Kit

value: Bronchioalveolar organoid


title: WT5, DCZ, Male

description:
Library name: DL005
column name in all_samples_raw.txt: DL005

value: DCZ


title: sni445-HTTP

city: Toulouse

first: Hussein

last: HAMZE

address: 118 Route de Narbonne  31062 TOULOUSE Cedex France

institute: Toulouse university - cnrs

description:
Library name: Sample 2
cDNA librairies obtained after reverse transcription and PCR amplification of associated RNAs after digestion (RNase it)

data_processing:
CRAC-seq data processing was performed using the pyCRAC toolkit (version 1.5.1) (https://sandergranneman.bio.ed.ac.uk/pycrac-software), a suite of Python-based tools specifically designed for the analysis of Crosslinking and Analysis of cDNAs (CRAC) data. The analysis pipeline was implemented using Snakemake (version 8.5.5), ensuring workflow reproducibility, modularity, and scalability. Each step of the pipeline was encapsulated within dedicated conda environments, guaranteeing consistent software dependencies across executions. - Raw reads were first demultiplexed using pyCRAC’s `pyBarcodeFilter.py` with 1 mismatch allowed. - Raw reads were quality-checked using FastQC (v0.12.1) and aligned to the _Saccharomyces cerevisiae_ pyCRAC’s reference genome (Saccharomyces_cerevisiae.EF2.59.1.0.fa) using Novoalign (v3.09.00) with the `-r Random` parameter to randomly assign multimapping reads. Both `.sam` and `.novo` output files were retained to support downstream analyses: `.sam` files were used to generate CPM-normalized BigWig coverage tracks using **samtools** (v1.14) for sorting and indexing, and **deepTools** (v3.4.3) for coverage computation (`bamCoverage`); `.novo` files were used as input for pyCRAC's internal tools requiring alignment metadata. - The pyCRAC’s reference GTF annotation file (Saccharomyces_cerevisiae.EF2.59.1.3.gtf) was first checked using PyCRAC’s `pyCheckGTFfile.py`. Gene name information was extracted using PyCRAC’s `pyGetGeneNamesFromGTF.py`, and a tabular genome file required by pyCRAC was generated from the reference FASTA using a custom Python script. - PyCRAC’s pyReadCounters.py was used to quantify the number of crosslinking events per transcript. The tool was run without the `--blocks` option, using various values for the `--readLength` parameter, in this study we generated data at 30 and 1000 bp read lengths. All hits were analyzed without limitation applicated. - Pileup profiles of crosslink events were generated using PyCRAC’s pypileup.py. This tool was run with default parameters with pyreadCounter output gtf as input.
Assembly: _Saccharomyces cerevisiae_ pyCRAC’s reference genome (Saccharomyces_cerevisiae.EF2.59.1.0.fa)
Supplementary files format and content: hittable reads: the number of crosslinking events per transcript. The tool was run without the `--blocks` option, using 30 for the `--readLength` paramete. All hits were analyzed without limitation applicated.     Pileup profiles of crosslink events were generated using PyCRAC’s pypileup.py. This tool was run with default parameters with pyreadCounter output gtf as input.

organism: Saccharomyces cerevisiae

growth_protocol: Yeast were gorwn in YNB, -trp + glucose, until final OD=0.6

extract_protocol:
Cell lysis was perfomed using Zirconium beads (5x 1minutes, with 1 minutes intervals on ice). Complex was isolated by two succesive IPs.
Library was constructed by linking to digested RNA illumina compatible 5' Adaptaters and 3' linkers. Then, those modified RNA were extracted and a Reverse Transcription was performed using Superscript III followed by a final moderate PCR enrichement (16 cycles). This was then analyzed on MiSeq plateform from illumina.

treatment_protocol: Protein were corss-linked to RNA using Megatron

tag: protocol

value: HTP (His-Tev-ProtA)

value: Megatron (100 secondes)


title: CC_WT_axon_1


title: H211, L191A, sgRosa, d5, Rep1

description: Library name: L191A_sgRosa_1


title: Cortical nuclei, 2 pooled samples, 1 female het/ 1 male wt, biol rep 2

city: Davis

first: Stephanie

middle: A

last: Lozano

state: CA

address: 1544 Newton Ct

institute: University of California, Davis

description:
Library name: snRNA-seq_ctx6_FHET_MWT
10X Genomics 3' GEX v3.1

data_processing:
Demultiplexed FASTQ files were passed through the Cell Ranger count pipeline for alignment to the mouse mm10 genome, filtering, and creation of feature-barcode matrices. Ambient RNA removal was performed using SoupX (version 1.6.1), and Seurat objects were generated using Seurat (version 4.3.0). These Seurat objects were subjected to initial clustering, and each resulting cluster was filtered based on cluster-specific thresholds for UMI count, feature count, and percentage of mitochondrial reads, which were determined using standard deviation criteria. Mitochondrial genes were then removed from all objects. The DoubletFinder package (version 2.0.4) was used to assign nuclei as ‘Singlet’ or ‘Doublet’.  Predicted doublets were removed before proceeding with downstream analyses. Nuclei were next assigned as ‘male’ or ‘female’ using the sxreveal package (version 0.2.0), which uses X- and Y-linked marker gene expression to predict sex.  Chd8 genotype was assigned based on the predicted sex and pool-specific metadata. Because each pool consisted of only one male and one female of opposite genotype, all female nuclei in a pool were assumed to be one genotype and all males were assumed to be the other.  Seurat objects for each of the 5 samples were individually passed through SCTransform to normalize counts, then all 5 were integrated using IntegrateData. The ‘RNA’ assay of the integrated object was normalized and scaled using NormalizeData and ScaleData. Principal Components Analysis was performed on the ‘Integrated’ assay of the integrated data to identify top variable genes, and FindNeighbors was used to construct a KNN graph based on their euclidean distance in PCA space. The data were then passed through FindClusters to group cells into clusters using the Louvain algorithm. Clusters were visualized with uniform manifold approximation and projection (UMAP).  FindAllMarkers was used to identify cluster marker genes. Modules of cell type marker genes described in published scRNA-seq datasets from adult mouse cortex were constructed. Canonical marker genes were added to these modules, then AddModuleScore was used to calculate relative expression of each module in each cluster. The cell type associated with the marker gene module that had the highest expression in each cluster was assigned as that cluster’s identity.  All nuclei were assigned identities at 3 levels of classification, with ‘Cell_Type_1’ being the most specific and ‘Cell_Type_3’ the broadest.  Clusters that were poorly clustered, had a high percentage of mitochondrial reads relative to other clusters, or had ambiguous marker genes (i.e. markers for multiple distinct cell types) were removed before subsequent analysis. The filtered Seurat object was then re-normalized, re-scaled, and re-clustered as described previously.
Assembly: Mouse mm10
Supplementary files format and content: Filtered and quality-controlled Seurat object (.rds) containing single-nucleus gene expression matrices, cell-level metadata, dimensionality reductions (PCA, UMAP), and cluster cell type assignments. All samples have been integrated into one object.

source_name: P60 cortex

extract_protocol:
Frozen issue from the first 6 samples was processed into nuclei using 2mL glass dounce homogenizers containing 2mL of EZ Prep lysis buffer each. Tissue for 3 samples was dounced over ice, 25 times with pestle A and 35 times with pestle B. Each solution was transferred to a 15 mL conical tube, then the same douncing process was repeated for the second set of 3 samples. Solutions from the latter 3 samples were pooled with those of the first 3 such that each pool contained one male and one female of opposite genotype. An additional 6 mL of EZ Prep lysis buffer was added to each conical tube and the tubes were incubated on ice for 5 minutes. Homogenates were centrifuged at 500xg for 5 minutes at 4°C, the supernatant was discarded, and the pellet was washed twice in NSB (1X PBS with 0.01% BSA and 0.1% RNAse inhibitor). The final pellet was resuspended in 1mL NSB then passed through a 20uM cell strainer. Nuclei were counted using a LUNA-FL cell counter and Acridine Orange/ Propidium Iodide stain. The 10X Genomics nuclei isolation kit, with protocol as described, was used to isolate nuclei for the final 4 samples. These samples were combined into 2 pools, each containing one male and one female of opposite genotype, then nuclei were counted as described previously. Nuclei suspensions had concentrations adjusted to target 10,000 nuclei for sequencing per pool, then used as input for the 10X Genomics 3’ Gene Expression Assay.
Library preparation was performed according to the manufacturer’s instructions (Next GEM Single Cell 3' Gene Expression v3.1 protocol, 10X Genomics). Briefly, nuclei were resuspended in a reverse transcription master mix and loaded into a Chromium Next GEM Chip G along with barcoded gel beads and partitioning oil. The chip was run on a Chromium controller to generate Gel Beads-in-Emulsion (GEMs). Within each GEM, reverse transcription occurred, producing cDNA tagged with a cell barcode, UMI, and an Illumina Read 1 primer sequence. GEMs were then broken and the barcoded cDNA was purified using Dynabeads, amplified by PCR, and cleaned using SPRIselect beads. During library construction, cDNA was fragmented, end-repaired, A-tailed, and ligated to sequencing adapters that include the Illumina Read 2 primer binding site. After adapter ligation and SPRIselect cleanup, sample index PCR was performed to incorporate P5 and P7 sequences and sample indices, followed by a final SPRIselect cleanup. Libraries were QCed and sequenced on an Agilent BioAnalyzer, batches 1, 2, and 4 were sequenced on an Illumina NovaSeq 6000 and batches 5 and 6 were sequenced on an Element Biosciences AVITI.

value: P60 cortex

value: mixed nuclei

tag: genotype sex_1

tag: genotype sex_2


title: WT4, DCZ, Female

description:
Library name: DL004
column name in all_samples_raw.txt: DL004

value: Female


title: CC_cKO_axon_3

value: Corpus callosal axon


title: CC_cKO_axon_2


title: H211, L191A, sgRosa, d5, Rep3

description: Library name: L191A_sgRosa_3

tag: cell line


title: BY_CONTROL

description:
Library name: Sample 1
cDNA librairies obtained after reverse transcription and PCR amplification of associated RNAs after digestion (RNase it)

value: no Tag

tag: cell type


title: Whole bone marrow cell, control , rep2

description: Library name: 1-II


title: CornishLiver,10weeks,rep5

city: Mbarara

first: Andrew

middle: Wange

last: Bugenyi

address: N/A, N/A

department: Animal Resources Research Program

country: Uganda

institute: National Agricultural Research Organisation

description: Library name: C5Lwk10

data_processing:
Preprocessed them using tools availed through the Galaxy, public web server
Quality checking was done using FastQC and MultiQC
Read alignment was done using RNA STAR
Mapped reads were then quantified using featureCounts
Assembly: Read alignment was done using the most recent reference chicken genome, at the time, “bGalGal1.mat.broiler.GRCg7b” available in Ensembl (https://www.ensembl.org) using RNA STAR
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Gallus gallus

source_name: Liver

extract_protocol:
Total RNA was extracted from the liver samples using the RNAeasy Mini Kit (Qiagen, CA, USA)
High-quality RNA, stranded libraries were prepared using the ‘TruSeq Stranded Total RNA with Ribo-Zero Globin’ kit (Illumina®, CA, USA) following the manufacturer’s protocol

value: Liver

tag: breed

value: Cornish


title: H211, Empty Vector, sgRosa, d5, Rep2

description: Library name: Empty_vector_sgRosa_2

tag: genotype

value: Empty Vector, sgRosa


title: H211, L191A, sgPOU2F3, d5, Rep3

description: Library name: L191A_sgPOU2F3_3


title: CornishLiver,10weeks,rep4

description: Library name: C4Lwk10

tag: tissue


title: Spleen, KLHL3-KI, 2

city: Itabashi

first: Shigeru

last: Shibata

country: Japan

institute: Teikyo University

description:
Library name: Sample 4
KI_Sp_3

data_processing:
MGI DNBseq-G400 FAST was used to perform the amplicons deep sequencing following the standard operation protocol. The sequence format was 150bp pair read for all samples.
All sequencing reads were trimmed low-quality bases and adapters with Trimmomatic (v.0.38) .
Raw counts for each gene were estimated in each sample using RSEM version 1.3.0 and Bowtie 2. Calculation of the log fold-change (log FC) and p-value were performed using edgeR.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

source_name: Spleen

extract_protocol:
The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using MGIEasy rRNA Depletion Kit and MGIEasy RNA Directional Library Prep Set  according protocols

value: Spleen

tag: strain

tag: treatment

value: baseline


title: H211, Empty Vector, sgRosa, d5, Rep1

description: Library name: Empty_vector_sgRosa_1


title: H211, Empty Vector, sgPOU2F3, d5, Rep3

description: Library name: Empty_vector_sgPOU2F3_3

value: Empty Vector, sgPOU2F3


title: Spleen, wild-type, 1

description:
Library name: Sample 1
WT_Sp_2


title: WT3, DCZ, Male

description:
Library name: DL003
column name in all_samples_raw.txt: DL003

value: interscapular brown adipose tissue

tag: Sex

value: Male

value: 6-8 months


title: REO-treated tuber at day 40, rep3

city: Shenyang

first: Baodong

last: Wei

state: Liaoning

address: Dongling Street

institute: Shenyang Agricultural University

description:
Library name: Treatment.40d3
Column name in GEO_submission_count_matrix.txt:Treatment.40d3

data_processing:
Raw sequencing reads were quality-controlled and adapter-trimmed using Fastp (v0.20.0).
Clean reads were aligned to the potato reference genome (DM_v6.1) using HISAT2 (v2.1.0).
Transcript expression levels were quantified and normalized as FPKM.
Differential expression analysis was performed using DESeq2.
Assembly: DM_v6.1
Supplementary files format and content: Tab-delimited text file includes raw counts for all samples.
Supplementary files format and content: Tab-delimited text file includes FPKM values for all samples.

organism: Solanum tuberosum

source_name: tuber

growth_protocol: Not applicable. Commercially procured mature potato tubers were used directly for storage experiments.

extract_protocol:
Cryopreserved potato tuber tissues were homogenized in liquid nitrogen. Total RNA was extracted using TRIzol™ Reagent (Invitrogen). Extracted RNA was treated with DNase I (Thermo Fisher Scientific) to remove genomic DNA contamination. RNA quality was assessed by NanoDrop 2000 and Agilent 2100 Bioanalyzer.
Libraries were constructed from qualified RNA. Briefly, mRNA was enriched using oligo(dT) beads, fragmented, and reverse transcribed into cDNA with random hexamers. The cDNA underwent end repair, A-tailing, adapter ligation, size selection, and PCR amplification. Library quality was confirmed by Qubit, Agilent 2100, and qPCR.

treatment_protocol: Tubers were divided into control and REO fumigation treatment groups at the beginning of a 100-day storage period. All tubers were stored under identical controlled conditions (sealed environment, specific temperature and humidity). Transcriptomic analysis was performed on samples collected at day 40 of storage.

value: tuber

tag: cultivar

value: Keshan

value: REO fumigation

tag: storage time

value: 40 days


title: H3K4me3_ChIP mcm2_G221V rep2

first: zhiguo

last: zhang

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

description: synchronized to G2 ending, nascent DNA on S10 min

data_processing:
mapped to pombe reference genome by Bowtie2
Read coverage in a bin of 1bp was calculated from filtered bam files by deepTools2 and then normalized with total filtered reads number into reads per million (RPM).
Origins were called by MACS2 from BrdU-IP
Assembly: pombe, ASM294v2
Supplementary files format and content: bw, bigwig format, contains the read density at each genomic position
Library strategy: eSPAN-seq

organism: Schizosaccharomyces pombe

growth_protocol: Strains containing the cdc25-22 temperature-sensitive mutant were first grown at permissive temperature (25°C) until the early-mid log phase (OD 0.2~0.4). Cultures were then incubated at 36°C for 4 hours to arrest cells at the G2 phase of the cell cycle. Cells were then shifted to 25°C to allow them to enter the S phase synchronously.

extract_protocol:
Cells were crosslinked at 60 minutes after temperature shift with the addition of 1% formaldehyde and incubated for 20 minutes with shaking at 25°C. Immunoprecipitation was performed as described in ChIP. Crosslinking was reversed by Chelex-100. Briefly, total and ChIP DNA were incubated at 100°C for 5 minutes and then immediately cooled on ice for 5 minutes. DNA was diluted ten times with BrdU IP buffer (PBS, 0.0625% Triton X-100(v/v)), and incubated with BrdU antibody (BD Bioscience 555627) for two hours at 4°C. Next, Sepharose Protein G beads (Cytiva 17-0618-01) were added and incubated for an additional one hour at 4°C. The beads were then washed three times with BrdU IP buffer and once with TE. Finally, DNA was eluted with TES and purified with the QIAGEN MinElute PCR Purification kit (Qiagen 28004).
AccelNGS 1S Plus DNA library kit (Swift Bioscience, 10096).

treatment_protocol: BrdU was added to a final concentration of 650 μM at 25minutes after the temperature shift.

tag: sample type

value: fission yeast

tag: chip antibody


title: BrdU mcm2_G221V rep2

value: anti-BrdU

value: BrdU


title: H3K4me3_eSPAN mcm2_G221V rep2


title: H3K4me3_eSPAN mrc1_D827_880 rep1


title: H211, L191A, sgPOU2F3, d5, Rep1

description: Library name: L191A_sgPOU2F3_1

value: L191A, sgPOU2F3


title: Spleen, KLHL3-KI, 1

description:
Library name: Sample 3
KI_Sp_1


title: H3K4me3_ChIP mrc1_D827_880 rep1


title: H211, Empty Vector, sgRosa, d5, Rep3

description: Library name: Empty_vector_sgRosa_3


title: WT1, DCZ, Male

description:
Library name: DL001
column name in all_samples_raw.txt: DL001

tag: age

value: DCZ


title: Spleen, wild-type, 2

description:
Library name: Sample 2
WT_Sp_3


title: BrdU mrc1_D827_880 rep1


title: H211, Empty Vector, sgPOU2F3, d5, Rep2

description: Library name: Empty_vector_sgPOU2F3_2


title: Input mcm2_G221V rep2

value: none(input)

value: Input


title: CornishLiver,10weeks,rep3

description: Library name: C3Lwk10

value: Liver

value: Cornish


title: REO-treated tuber at day 40, rep2

description:
Library name: Treatment.40d2
Column name in GEO_submission_count_matrix.txt:Treatment.40d2


title: Cortical nuclei, 2 pooled samples, 1 male het/ 1 female wt, biol rep 3

description:
Library name: snRNA-seq_ctx5_MHET_FWT
10X Genomics 3' GEX v3.1

value: P60 cortex

value: mixed nuclei

tag: batch


title: Input mrc1_D827_880 rep1


title: REO-treated tuber at day 40, rep1

description:
Library name: Treatment.40d1
Column name in GEO_submission_count_matrix.txt:Treatment.40d1


title: 501M_shLENT_Heavy_3

city: Illkirch-Graffenstaden

first: Guillaume

last: Davidson

address: 1 Rue Laurent Fries

institute: I.G.B.M.C. - Institut de génétique et de biologie moléculaire et cellulaire

description:
501M Heavy fraction silenced by Dox-inducible shLENT
LRHR49

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed in order to remove adapter and low-quality sequences (Phred quality score below 20) using cutadapt version 1.10.
Reads were mapped to rRNA sequences using bowtie version 2.2.8, and reads mapping to rRNA sequences were removed for further analysis. Reads were mapped to spike sequences using bowtie2 version 2.2.8, and reads mapping to spike sequences were removed for further analysis.
Sequence reads were mapped to reference genome hg19 using Tophat v2.0.10 51 and the bowtie2 v2.1.0 aligner. Only uniquely aligned reads were retained for further analyses.
Gene expression quantification was performed from uniquely aligned reads using htseq-count version v0.6.1 with annotations from Ensembl version 75.
Data normalization and quantification of gene expression was performed using the DESeq2 Bioconductor package. Significantly deregulated genes were selected using a log2 fold change >1 and <1 and adjusted p-value cutoff of 0.05.
Assembly: hg19
Supplementary files format and content: Excel file containing raw read counts, normalized counts (by sequencing depth and median gene length) and log2(fold-change) with adjusted p-values for comparisons of interest. The file contains 3 distinct sheets for RNA-seq (501M whole extracts and fractions) and RIP-seq.

source_name: Skin

growth_protocol: 501mel were grown in RPMI1640 w/o HEPES medium supplemented with 10 % fetal calf serum (FCS) and gentamycin (40 µg/mL).

extract_protocol:
Total mRNA isolation was performed using Trizol (TR 118) and isopropanol precipitation. RNA was then treated with DNAseI following the TurboDNAse kit instructions (AM1907 – ThermoFisher) and 1µg of RNA was reversed transcribed using SuperScript IV (18090050 – ThermoFisher) following manufacturer instructions.
Library preparation was performed at the GenomEast platform at the Institute of Genetics and Molecular and Cellular Biology using RiboPOOL Kit Manual + Modified Truseq Stranded Total RNA Reference Guide - PN 1000000040499 . Total RNA-Seq libraries were generated from 100 ng of total RNA. Before cDNA synthesis, cytoplasmic and mitochondrial ribosomal RNA (rRNA) were removed using a biotin-streptavidin magnetic bead-based procedure with the riboPOOL kit targeting h/m/r ribosomal rRNA (siTOOLs Biotech, Planegg/Martinsried, DE) according to manufacturer’s instructions. Ribodepleted RNAs were purified using Agencourt RNAClean XP (Beckman-Coulter, Villepinte, France) and eluted in 8,5 μ l ELB buffer (Illumina, San Diego, USA). Purified RNAs were then processed using Illumina TruSeq Stranded Total RNA Library Prep Gold and IDT for Illumina - TruSeq RNA UD Indexes, omitting the ribodepletion step and starting directly from the fragmentation step. RNAs were fragmented at 94oC for 8 minutes. DNA library were amplified using 13 cycles of PCR. Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter) and the final libraries were checked for quality and quantified using Bioanalyzer 2100 system (Agilent technologies, Les Ulis, France).

treatment_protocol: 501M were silenced using doxycycline-inducible LENT shRNA (shLENT) or a scrambled control (shCTRL) that were cloned in LT3GEPIR (a gift from Johannes Zuber; Addgene plasmid #111177; http://n2t.net/addgene:111177; RRID: Addgene_111177).

value: Skin

value: shLENT


title: H3K4me3_eSPAN mrc1_D782_879 rep1


title: WT6, DCZ, Female

description:
Library name: DL006
column name in all_samples_raw.txt: DL006

value: interscapular brown adipose tissue

value: Female

value: 6-8 months


title: H3K4me3_ChIP mrc1_D782_879 rep1


title: CornishLiver,10weeks,rep2

description: Library name: C2Lwk10


title: 501M_shLENT_80S_3

description:
501M 80S fraction silenced by Dox-inducible shLENT
LRHR47


title: Control tuber at day 40, rep1

description:
Library name: CK.40d1
Column name in GEO_submission_count_matrix.txt: CK.40d1

value: tuber

value: Keshan

value: control

value: 40 days


title: H211, Empty Vector, sgPOU2F3, d5, Rep1

description: Library name: Empty_vector_sgPOU2F3_1

value: Empty Vector, sgPOU2F3


title: CornishLiver,10weeks,rep1

description: Library name: C1Lwk10


title: Input mrc1_D782_879 rep1

value: fission yeast


title: 501M_shLENT_Light_3

description:
501M Light fraction silenced by Dox-inducible shLENT
LRHR48


title: BrdU mrc1_D782_879 rep1

value: anti-BrdU

value: BrdU


title: OgyeLiver,10weeks,rep4

description: Library name: O4Lwk10

value: Liver

value: Ogye


title: Control tuber at day 40, rep2

description:
Library name: CK.40d2
Column name in GEO_submission_count_matrix.txt: CK.40d2


title: Control tuber at day 40, rep3

description:
Library name: CK.40d3
Column name in GEO_submission_count_matrix.txt: CK.40d3


title: OgyeLiver,10weeks,rep3

description: Library name: O3Lwk10


title: OgyeLiver,10weeks,rep2

description: Library name: O2Lwk10


title: OgyeLiver,10weeks,rep1

description: Library name: O1Lwk10


title: 501M_shLENT_Light_2

description:
501M Light fraction silenced by Dox-inducible shLENT
LRHR44


title: H3K4me3_eSPAN mcm2_G221V rep1


title: Control tuber at day 0, rep2

description:
Library name: CK.0d2
Column name in GEO_submission_count_matrix.txt: CK.0d2

value: 0 days


title: Control tuber at day 0, rep3

description:
Library name: CK.0d3
Column name in GEO_submission_count_matrix.txt: CK.0d3


title: CornishLiver,5weeks,rep5

description: Library name: C5Lwk05

value: Cornish


title: 501M_shLENT_Heavy_2

description:
501M Heavy fraction silenced by Dox-inducible shLENT
LRHR45

value: Skin


title: OgyeLiver,10weeks,rep5

description: Library name: O5Lwk10


title: CornishLiver,5weeks,rep3

description: Library name: C3Lwk05


title: H3K4me3_ChIP mcm2_G221V rep1


title: Input mcm2_G221V rep1

value: none(input)

value: Input


title: Control tuber at day 0, rep1

description:
Library name: CK.0d1
Column name in GEO_submission_count_matrix.txt: CK.0d1


title: BrdU mcm2_G221V rep1

description: synchronized to G2 ending, nascent DNA on S10 min


title: CornishLiver,5weeks,rep2

description: Library name: C2Lwk05


title: CornishLiver,5weeks,rep4

description: Library name: C4Lwk05


title: 501M_shLENT_80S_2

description:
501M 80S fraction silenced by Dox-inducible shLENT
LRHR43

value: shLENT


title: H3K4me3_eSPAN mrc1_F835A rep1


title: 501M_shCtrl_Heavy_3

description:
501M Heavy fraction silenced by Dox-inducible shCtrl
LRHR37

value: shCtrl


title: 501M_shLENT_80S_1

description:
501M 80S fraction silenced by Dox-inducible shLENT
LRHR39


title: BrdU mrc1_F835A rep1


title: 501M_shLENT_Heavy_1

description:
501M Heavy fraction silenced by Dox-inducible shLENT
LRHR41


title: 501M_shCtrl_Light_3

description:
501M Light fraction silenced by Dox-inducible shCtrl
LRHR36


title: H3K4me3_ChIP mrc1_F835A rep1


title: 501M_shCtrl_80S_3

description:
501M 80S fraction silenced by Dox-inducible shCtrl
LRHR35


title: 501M_shLENT_Light_1

description:
501M Light fraction silenced by Dox-inducible shLENT
LRHR40


title: H3K4me3_eSPAN mcm22A_mrc1D rep2

data_processing:
mapped to pombe reference genome by Bowtie2
Read coverage in a bin of 1bp was calculated from filtered bam files by deepTools2 and then normalized with total filtered reads number into reads per million (RPM).
Origins were called by MACS2 from BrdU-IP
Assembly: pombe
Supplementary files format and content: bw, bigwig format, contains the read density at each genomic position
Library strategy: eSPAN-seq

source_name: fission yeast

value: anti-BrdU and anti-H3K4me3

value: mcm2-2A mrc1delta


title: OgyeLiver,5weeks,rep5

description: Library name: O5Lwk05


title: Input mrc1_F835A rep1


title: CornishLiver,5weeks,rep1

description: Library name: C1Lwk05


title: H3K4me3_ChIP mcm22A_mrc1D rep2


title: OgyeLiver,5weeks,rep2

description: Library name: O2Lwk05


title: BrdU mcm22A_mrc1D rep2


title: 501M_shCtrl_Heavy_2

description:
501M Heavy fraction silenced by Dox-inducible shCtrl
LRHR33


title: OgyeLiver,5weeks,rep1

description: Library name: O1Lwk05


title: 501M_shCtrl_Heavy_1

description:
501M Heavy fraction silenced by Dox-inducible shCtrl
LRHR29


title: 501M_shCtrl_Light_1

description:
501M Light fraction silenced by Dox-inducible shCtrl
LRHR28


title: 501M_shCtrl_Light_2

description:
501M Light fraction silenced by Dox-inducible shCtrl
LRHR32


title: OgyeLiver,5weeks,rep4

description: Library name: O4Lwk05


title: H3K4me3_ChIP mcm22A_mrc1D rep1

value: mcm2-2A mrc1[delta]


title: WT_7d NAA and release for 24h_Bio1

city: ghent

first: Wei

last: Xiao

address: Technologiepark-Zwijnaarde 71 - 9052 Ghent - Belgium

country: Belgium

institute: VIB-UGent Center for Plant Systems Biology

description: Library name: WT_7d NAA and release for 24h_1

data_processing:
using Galaxy Belgium platform
Trimmomatic to remove adaptors
Salmon quant to align reads
tximport to count read
Deseq2 to differentially expressed gened
Assembly: TAIR10 on Galaxy (for Arabidopsis thaliana), Genome Selaginella moellendorffii v1.0 (for Selaginella moellendorffii)
Supplementary files format and content: tab-delimited file of count read for each sample

organism: Selaginella moellendorffii

source_name: Root

growth_protocol: 1/2 MS  plates 22°C constant light 4d old root of Arabidopsis thaliana, and 14d old root of Selaginella moellendorffii

extract_protocol:
ReliaPrep™ RNA Miniprep Systems
BGI RNA Library Prep Kit protocol

treatment_protocol: 0.2 cm of the root tip of the root. Rna extraction with ReliaPrep RNA Miniprep Systems kit (Z6112)

value: Root

value: WT

value: 1μM NAA for 7d, and release for 24h


title: WT_7d NAA and release for 24h_Bio3

description: Library name: WT_7d NAA and release for 24h_3


title: 501M_shCtrl_80S_2

description:
501M 80S fraction silenced by Dox-inducible shCtrl
LRHR31


title: OgyeLiver,5weeks,rep3

description: Library name: O3Lwk05


title: WT_7d NAA and release for 12h_Bio3

description: Library name: WT_7d NAA and release for 12h_3

value: 1μM NAA for 7d, and release for 12h


title: Input mcm22A_mrc1D rep1

value: fission yeast


title: Input mcm22A_mrc1D rep2


title: H3K4me3_eSPAN mcm22A_mrc1D rep1

value: anti-BrdU and anti-H3K4me4


title: 501M_shCtrl_80S_1

description:
501M 80S fraction silenced by Dox-inducible shCtrl
LRHR27


title: 501M_shLENT_DHX_2

description:
501M silenced by Dox-inducible shLENT and immunoprecipitated with DHX36-antibody
LRHR22

extract_protocol:
Cells were grown in 15 cm petri dishes, harvested by scraping, resuspended in lysis buffer (20 mM Tris-HCl pH 8, 200 mM NaCl, 2.5 mM MgCl2, 0.05 % Triton, DEPC water) supplemented with DTT (1 mM), protease/phosphatase inhibitor cocktail (Thermo Fisher Scientific) and RNAsin (Thermo Fisher Scientific) and kept on ice for 15 minutes, pipetting every 3 minutes. Membranes were pelleted 10 minutes at 10,000 g at 4 °C and the supernatant precleared 1 hour at 4 °C with protein G magnetic beads (Invitrogen). Lysate was quantified by Bradford protein quantification assay (Bio-Rad) and incubated overnight on a rotating wheel at 4 °C with 5 µg of the indicated antibodies. Then, 50 µL of resuspended Protein G magnetic beads were added for 3 hours to isolate RNA - protein complexes and washed five times in lysis buffer. After final wash, RNA was purified by TRI Reagent + isopropanol precipitation and proteins eluted by boiling beads at 95 °C for 15 minutes in Laemmli buffer. Ribosomal RNAs were depleted with the Ribo-Zero Plus rRNA depletion kit (Illumina) prior to library preparation.
Library preparation was performed at the GenomEast platform at the Institute of Genetics and Molecular and Cellular Biology using Clontech SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing User Manual - PN 091817 + Illumina Nextera XT DNA Library Prep Kit Reference Guide - PN 15031942. Full length cDNA were generated from 100 to 500 pg of total RNA using SMART-SeqX v4 UltraX Low Input RNA Kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer’s instructions with 15 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, USA) followed by 12 cycles of library amplification. Following purification with SPRIselect beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

tag: antibody for_rip-seq


title: WT_7d NAA and release for 24h_Bio2

description: Library name: WT_7d NAA and release for 24h_2


title: CCI_DAY3_3

city: Tainan

first: Chunwei

last: Lin

address: No. 1, Daxue Rd., East Dist.

country: Taiwan

institute: National Cheng Kung University

description: Rat dorsal root ganglia underwent CCI, and then released after 7day. mRNA sample was havested on post releasing Day 3

hyb_protocol: Followed manufacturer's protocol

scan_protocol: Samles were loaded onto a nCounter cartridge and ran on a nCounter SPRINT

data_processing: Sample gene transcript counts were normalized before downstream analysis by geoNorm algorithm in NanoString’s nSolver software Version 4.0 to figure out stable housekeeping genes and positive control for normalization.

source_name: rat dorsal root ganglia

label_protocol: Followed manufacturer's protocol

growth_protocol: Animal housing and care, were approved by the Laboratory Animal Center and Institutional Animal Care and Use Committee (IACUC; Protocol No. 108032) of National Cheng Kung University in Tainan, Taiwan.

extract_protocol: The rat dorsal root ganglion RNA were extracted via Trizol, and RNA sample quality was confirmed by spectrophotometry (SpectraMax QuickDrop) to determine concentration and chemical purity (A260/230 and A260/280 ratios) and with a Bioanalyzer (model 2100, Agilent Technologies) to determine RNA integrity and degraded samples were re-placed with an alternative sample if available.

treatment_protocol: The left sciatic nerve was dissected from the surrounding tissues and exposed at the mid-thigh level. The area proximal to the trifurcation of the sciatic nerve was cleared of any adhering tissue. Four ligatures made of 5–0 nylon (Ethicon US, Bridgewater, NJ) were tied around the sciatic nerve, with approximately 1 mm of space between each ligature. After 7 days, the CCI rats underwent a second surgery for decompression.

tag: days post never compression releasing

value: 3 day

value: rat dorsal root ganglia