title: Induced cortical neurons, 5-Azacytidine, replicate 1

city: New York

first: Oliver

middle: H

last: Tam

address: 435 E 30th St

department: Institute for Systems Genetics

description:
Library name: i3N_5Aza
i3N_Ctrl_5Aza_hg38_minimap2

data_processing:
Circular consensus sequencing reads were generated from PacBio sequencing output using the CCS algorithm (version 8, Pacific Biosciences). Libraries were demultiplexed, refined and clustered using IsoSeq toolkit (version 4.0.0). FASTA files were generated and aligned to the hg38 genome using minimap2104 (version 2.24) with splice:hq preset (-x splice:hq) and GT-AG search on the transcript strand (-u f). Transcript discovery and quantification was performed using bambu105 (version 3.2.6), with the GENCODE106 gene annotation (version 47) as reference.
Assembly: hg38
Supplementary files format and content: Count table of detected genes in isoseq library
Supplementary files format and content: Count table of detected transcripts in isoseq library
Supplementary files format and content: Count table of "full length" transcripts in isoseq library
Supplementary files format and content: Count table of uniquely aligned transcripts in isoseq library
Supplementary files format and content: Counts per million reads of detected transcripts in isoseq library
Supplementary files format and content: GTF of detected transcripts

source_name: KOLF2.1J -derived

growth_protocol: A previously engineered CRISPRi-i3N-KOLF2.J1 iPSC line, obtained from The Jackson Laboratory (a gift from the NIH/INDi Consortium), was used for cortical neuron differentiation with minor modifications. This line expresses human NGN2 under a doxycycline-inducible promoter (2 µg/mL) and constitutively expresses a dCas9-BFP-KRAB CRISPRi construct. Prior to differentiation, iPSCs received lentiviral particles encoding either non-targeting (NT) or TDP-43-targeting sgRNAs. The Lentiblast™ transduction enhancer (1:1000; OZ Biosciences, Cat. no. LBPX1500) was added to improve transduction efficiency. Forty-eight hours post-transduction, transduced cells were selected with 2 µg/mL puromycin (InvivoGen, Cat. no. ant-pr-1) for five days. The resulting stable cell pools were expanded before initiating differentiation. To initiate differentiation, 7 × 10⁶ cells from the stable pools were dissociated using accutase (Innovative Cell Technologies, Inc., Cat. no. AT104), and seeded into AggreWell™800 plates (STEMCELL Technologies, Cat. no. 34815) using differentiation medium consisting of Neurobasal™ Plus Medium (Thermo Fisher Scientific, cat. no. A3582901), GlutaMAX™ (Thermo Fisher Scientific, cat. no. 35050061), BDNF (10 ng/mL; Thermo Fisher Scientific, cat. no. 450-02), NT-3 (10 ng/mL; Thermo Fisher Scientific, Cat. no. 450-03), doxycycline (2 µg/mL; Thermo Fisher Scientific, Cat.no.J67043.AD), and Gem21 NeuroPlex™ (without Vitamin A; Gemini Bio, Cat. no. 400-161-010), supplemented with 1X RevitaCell™ (Thermo Fisher Scientific, Cat. no. A2644501), to form spheroids98. After 24 hours, cell media was switched to fresh medium lacking RevitaCell, and changed daily. On day 8, neuronal spheroids were transferred and plated onto culture plates pre-coated with Geltrex™ (1:100; Thermo Fisher Scientific, Cat. no. A1413302) and Cultrex™ Stem Cell Qualified Laminin I (5 µg/mL; Bio-Techne, Cat. no. 3400-010-03).

extract_protocol:
RNA was extracted and purified from cultured cells using the Direct-zol™ RNA Miniprep Plus (R2071, Zymo Research, Irvine, CA, USA). RNA concentration was determined with the Qubit RNA BR Assay Kit (Q10210, ThermoFisher Scientific, Waltham, MA, USA) and Qubit 4 Fluorometer (Q33226, ThermoFisher Scientific, Waltham, MA, USA). RNA quality was assessed using the RNA 6000 Nano (5067-1511, Agilent, Santa Clara, CA, USA) on the Agilent 2100 Bioanalyzer (G2939BA, Agilent, Santa Clara, CA, USA).
CrypTE-seq read libraries were prepared from ~300ng total RNA per sample following a modified PacBio Iso-Seq v2 library protocol (103-071-500, PacBio, Menlo Park, CA, USA) and pooled using the SMRTbell Prep Kit 3.0 (102-182-700, PacBio, Menlo Park, CA, USA). Modifications include the use of post-primer annealing with first strand cDNA synthesis performed with MarathonRT (200035, RNAConnect, Branford, CT, USA) followed by Iso-seq RT and then addition of the template switch oligo. All other steps followed the Iso-seq v2 library protocol (103-071-500, PacBio, Menlo Park, CA, USA).

treatment_protocol: After overnight attachment, fresh medium was added, supplemented with 5 µM 5-Azacytidine, and the cells were incubated for 72 hours. Neuronal cultures were maintained in differentiation medium ± 5-azacytidine and harvested for analysis on either day 12 or day 15, depending on the specific downstream application.

value: KOLF2.1J -derived

value: induced cortical neurons (i3N)


title: MG_Control_2

status: Public on Jan 09 2026

type: SRA

city: Tokyo

first: Shiro

last: Yui

address: 1-5-45, Yushima, Bunkyo-ku

department: Center for stem cell and Regenerative medicine

country: Japan

institute: Institute of Science Tokyo

description: Library name: Sample 2

library_source: transcriptomic

data_processing:
Raw sequencing data were converted to FASTQ files using bcl2fastq2 v2.20. Reads were aligned to the mouse reference genome (GRCm39; GENCODE release M38) using the DRAGEN Bio-IT Platform v4.3.6, and gene-level read counts and TPM values were quantified.
Assembly: mm39
Supplementary files format and content: Tab-separated values files

molecule: polyA RNA

organism: Mus musculus

source_name: Small intestine

growth_protocol: Mouse small intestinal crypt–derived organoids were established and maintained as previously described (Yui et al., Cell Stem Cell, 2018). Briefly, small intestines from C57BL/6 wild-type mice were harvested, flushed with cold PBS (Nacalai Tesque, 14249-24), and opened longitudinally. The tissues were cut into 2–5 mm fragments and incubated in PBS containing 2 mM EDTA (Invitrogen, #AM9260G) at 4 °C for 30 minutes in a 50 mL conical tube (VIOLAMO, 1-3500-22) to dissociate the epithelial layer. Epithelial fractions were collected by vigorous shaking, passed through a 70 µm cell strainer (Falcon, #352350), and centrifuged at 500 × g for 3 minutes in a 15 mL conical tube (Falcon, #188271-013). Isolated crypts were resuspended in either Matrigel (Corning, 356231) or collagen type I (Cellmatrix Type I-A; Nitta Gelatin, 631-00651) and plated as 30 µL domes in pre-warmed 24-well plates (Corning, 3524). After polymerization at 37 °C for 30 minutes, Matrigel domes were overlaid with 500 µL ENR medium (MG). For collagen-embedded organoids, domes were overlaid with 500 µL ENRW medium (COL) for 5-FU treatment or 25% cWRNE medium (COL-cWRNE) for comparison with V-organoids. For V-organoid cultures, villi within 3 cm distal to the pylorus were gently scraped using a glass coverslip (MATSUNAMI, #MAS-01), washed in PBS, and centrifuged at 100 × g for 3 minutes to separate intact villi from single cells. Villi were washed by transferring a 70 µm cell strainer (Falcon, #353046) sequentially through wells of a 6-well plate filled with PBS and gently pipetting. After washing, villi remaining in the strainer were collected into a 15 mL tube, centrifuged at 500 × g for 3 minutes, resuspended in 20 µL collagen matrix, and plated in 24-well plates. Cultures were maintained in 25% cWRNE medium (VIL).  Medium Compositions ENR medium: Advanced DMEM/F12 supplemented with 1% penicillin/streptomycin, 1% GlutaMAX, 1× B27, 1× N2, EGF (50 ng/mL), Noggin (100 ng/mL), and R-spondin 1 (400 ng/mL). ENRW medium: ENR medium supplemented with Wnt3a (100 ng/mL), nicotinamide (10 mM), and 1% BSA. cWRNE medium: Advanced DMEM/F12 supplemented with 1% penicillin/streptomycin, 1% GlutaMAX, 1× B27, 1× N2, EGF (50 ng/mL), NAC (1 mM), and 25% L-WRN conditioned medium concentrated with a 10-kDa filter.

extract_protocol:
On day 6, organoids were released from the ECM and total RNA was extracted using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions.
Whole-transcriptome libraries were generated using the SMART-Seq mRNA kit (Takara Bio) based on the SMART (Switching Mechanism at the 5′ End of RNA Template) method. cDNA libraries were purified using AMPure XP beads (Beckman Coulter). Tagmentation and adapter ligation were performed using the Nextera XT DNA Library Prep Kit (Illumina) together with Illumina DNA-RNA UD Indexes. Pooled libraries were sequenced on an Illumina NovaSeq X Plus system.

treatment_protocol: For 5-FU treatment, 40 µM 5-fluorouracil (Selleck Chemicals, #S-1209) was added to the culture medium of MG- or COL-embedded crypt-derived organoids on days 4–6 of culture.

tag: tissue

value: Small intestine

tag: cell type

value: intestinal epithelial cells

tag: genotype

value: C57BL/6J WT

tag: treatment

value: non-treat


title: 4593_KPC-TN,scRNAseq,gene_exp

city: Woodbury

first: Jonathan

last: Preall

state: NEW YORK

address: 500 Sunnyside Blvd

country: USA

institute: Cold Spring Harbor Laboratory

description:
Library name: 4593_KPC-TN
10x Genomics
KPC_KC_annot.csv

library_source: transcriptomic single cell

data_processing:
Sequencing reads were demultiplexed with matrices using 10X Genomics' Cell Ranger mkfastq software v6.0.0.
Gene expression count matrices were generated with STARsolo version 2.7.11a using mouse reference genome 2.7.4a (gex-mm10-2020-A, 10X Genomics) with default parameters. Barcodes were filtered for cell-containing droplets with STAR. Ambient RNA was subtracted using Cellbender 0.2.0.
Scanpy version 1.9.1 was used for normalization, dimensionality reduction, clustering and projection. Cell types were assigned to clusters based on differential expression of a curated list of marker genes.
Assembly: GRCm38
Supplementary files format and content: Gene expression: Single cell 3' cell/gene matrices in .mtx format generated by STAR for individual samples. Aggregated, Cellbender-corrected count matrices representing fibroblast populations provided as .csv.gz files

source_name: Pancreas Tumor

extract_protocol:
For tumor digestion: Pancreatic tumors from KPC (Kras+/LSL-G12D; Trp53+/LSL-R172H; Pdx1-Cre),  from KC (Kras+/LSL-G12D; Pdx1-Cre) mice were minced and enzymatically digested in DMEM supplemented with Collagenase D,Liberase DL, DNase I  at 37°C for 40 minutes. KPC tumor suspensions were then stained for CD45,CD31, EPCAM, and FACS sorted. Fibroblasts were enriched by sorting viable (DAPI-) cells from the population negative for all three markers (triple-negative, "TN"). Alternatively, all viable cells were enriched from the DAPI- fraction ("DN").  KC pancreata were harvested for single-cell RNAseq without sorting.  For KC samples, (from KC (Kras+/LSL-G12D; Pdx1-Cre mice), pancreata were minced in mincing media and enzymatically digested in DMEM supplemented with Collagenase D,Liberase DL, DNase I, Soybean trypsin inhibitor and HEPES  at 37°C for 20 minutes with refreshed enzyme media at 20 minutes for a total of 40 minutes. Samples were then stained and sorted for 70% Live,CD45-, and 30% Live, CD45+ and submitted for single cell sequencing.
Single-cell RNA sequencing was performed using 10X Genomics NextGEM v3.1 3' Gene Expression kits by the Cold Spring Harbor Laboratory Single-Cell Biology Shared Resource. Cells were loaded into a 10x Genomics Chromium instrument and libraries prepared according to the manufacturer’s instructions. Unique dual-indexe libraries were paired end sequenced using the Illumina NextSeq2000 sequencing system with 28x10x10x90bp reads to a mean depth of ~40,000 reads per cell.

value: Dissociated single cells

value: Pancreas Tumor

tag: strain

value: KrasG12D/+;Trp53R172H/+;Pdx1-Cre (KPC)

tag: age

value: 6-14 weeks


title: OGO_Wnt7b-mut_5546F,scRNAseq,gene_exp

description:
Library name: OGO_Wnt7b-mut_5546F
10x Genomics
OGO_Wnt7b_annot.csv

source_name: Pancreas Orthotopic Tumor

value: Pancreas Orthotopic Tumor


title: MG_Control_3

description: Library name: Sample 3


title: WGBS, P8 testis, Daxx knockdown, biol rep1

status: Public on Jan 08 2026

city: Wuhan

first: shen

last: jin

state: Hubei

address: No. 299, Bayi Road, Wuchang District, Wuhan City

country: China

institute: Wuhan university

description:
Library name: SAMPLES3
Daxx_1

library_source: genomic

data_processing:
Adapters and low qualities bases were trimmed with Trim Galore (0.6.10)，the clean reads were aligned to the UCSC mm39 genome carried out with Bismark (v0.24.2)with the following set of parameters: –score_min L,0,-0.4, which incorporates Bowtie2(2.5.4). CpG methylation calls were extracted from the deduplicated mapping output using the Bismark methylation extractor. Only CpGs covered by a minimum of three reads were retained for downstream analyses in each replicate.
Assembly: UCSC mm39
Supplementary files format and content: bed file includes Methylation information at CpG sites

molecule: genomic DNA

source_name: testis

extract_protocol:
After samples DNA testing, positive control DNAs were added into the DNAs, and then they were fragmented into 200-400bp using Covaris S220 (Covaris, USA).
Next, ssDNA fragements were Bisulfite treated. After BS treatment, unmethylated Cytosine will change into Uracil, while methylated Cytosine will stay unchanged. Then, methylation sequencing adapters ligation, size selection and PCR amplification steps were performed to the DNA fragments. The library kit is Accel-NGS Methyl-Seq DNA Library Kit (Swift, USA, Catalog #:30096). Subsequently, library quality was assessed on the Agilent 5

value: testis

value: DAXX knockdown


title: WGBS, P8 testis, Daxx knockdown, biol rep2

description:
Library name: SAMPLES4
Daxx_2


title: OGO_Rosa_5550M,scRNAseq,gene_exp

description:
Library name: OGO_Rosa_5550M
10x Genomics
OGO_Wnt7b_annot.csv


title: 2hL2

city: BOSTON

first: Birol

last: Ay

state: Massachusetts

address: 50 BLOSSOM STREET

institute: MASSACHUSETTS GENERAL HOSPITAL

description: Library name: 2h-LPA-2

data_processing:
https://bioconductor.org/packages/release/workflows/vignettes/RNAseq123/inst/doc/limmaWorkflow.html
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: xlsx files include all results

molecule: total RNA

source_name: Bone

extract_protocol:
RNA was harvested by Rneasy mini plus kit (Qiagen).
DNBSEQ Fast RNA Library Prep Set was used to prepare libraries.

value: Bone

tag: cell line

value: Ocy454 cells

value: Osteocytic Cells


title: WGBS, P8 testis, Wild type, biol rep1

description:
Library name: SAMPLES1
Control_1

value: WT


title: CTL skin wound 1, Day 4 following injury

city: Zurich

first: Adrian

last: Salas-Bastos

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

description:
Library name: CTL skin wound 1
Sequencer model DNBSEQ-T10 4RS. Fresh frozen Spatial transcriptomics sequencing of day 4 skin wound.

data_processing:
The Stereo-seq Analysis Workflow (SAW; https://github.com/STOmics/SAW) was employed to process the spatial transcriptomics data. This included quality control of FASTQ files, read alignment to the mouse reference genome (GRCm38/mm10), image processing, cell segmentation, and generation of spatial gene expression matrices. All downstream analyses were conducted at the cellBin resolution.
Assembly: mm10
Supplementary files format and content: A03388F1.adjusted.cellbin.gef file is a Cellbin expression matrix with cell border expanding. A03388F1_swn_final_annotation_clean.h5ad file contains processed data and cell type annotations for the glia cells present in nerve bundles and other cells in the 150 microms radii around each nerve bundle.
Supplementary files format and content: A03388F1.barcodeToPos.h5 and A03388F1_ssDNA.tif files correspond to the barcode to positions and the nuclei staining image, respectively. Both files are required together with the raw Fastq files for running the SAW pipeline. The serial number of the Stereo-sep chip (SN code) is A03388F1
Library strategy: Spatial Transcriptomics

source_name: Regenerating skin wound

extract_protocol:
Day 4 skin wounds were processed with the spatial transcriptomic technique Stereo-seq. commercialised by STOmics. Briefly, fresh frozen day 4 skin wounds of PLP-CreERT2: tdTomato mice were sliced and mounted on a STOmics chip. Note that each chip contained two wound sections which then were processed together as single dataset.
Library preparation was performed following manufacturers protocol (STOmics, Stereo seq.)

treatment_protocol: Tamoxifen (Tmx) was administered to activate Cre-mediated recombination and induce tdTomato expression in Plp1-expressing peripheral glial cells.  Four circular full-thickness excisional wounds of 5 mm of diameter were generated on the lower back skin of each animal, two on each side, 1 cm of the midline of the animal and roughly 2 cm apart from each other.

value: Regenerating skin wound

value: 8-10 weeks old

value: female

value: Tmx intraperitoneal


title: 2hD3

description: Library name: 2h-1,25D-3


title: scRNAseq from day 16

city: Cincinnati

first: Kentaro

last: Iwasawa

state: OH

address: 3333 BURNET AVENUE

department: Division of Gastroenterology, Hepatology and Nutrition

institute: Cincinnati Children's Hospital Medical Center

description:
10x Genomics
integrated_counts.txt
integrated_metadata.txt

data_processing:
FASTQ files were first aligned against the human hg38 genome using Cellranger 3.0.2, outputting a counts matrix, estimated number of cells, number of reads and genes per cell, and flags for any quality issues detected.
SoupX v1.5.0 is used to further process the counts by correcting for ambient RNA.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

organism: Homo sapiens

source_name: highly hematopoietic human fetal liver organoids from iPSCs

extract_protocol:
FLOs on day 10 and hFLOs on days 13, 16 and 20 were singularized with Trypsin, cryopreserved in CellBanker and sent overnight to GENEWIZ/Azenta Life Sciences (New Jersey, USA).
In brief, at GENEWIZ the manufacturer's instructions for scRNA-sequencing were subsequently followed utilizing 10x Genomics Chromium; cells and barcoded gel beads were separated in partitioning oil droplets. Cell- and transcript-specific barcodes were added during reverse transcription. The Illumina platform was used to pool and sequence barcoded libraries.

value: cell line 72_3

value: human iPSC-derived

tag: time

value: day 16

value: No treatment


title: ChIP-Seq, round sperm, Daxx knockdown, biol rep1

description:
Library name: SAMPLES10
Daxx_1

data_processing:
Raw FASTQ files were processed using Trim Galore to remove adapter sequences and low-quality bases(parameters: --paired --length 25 –stringency 4). Clean paired-end reads were then aligned to the mouse reference genome (mm39) using Bowtie2(2.5.4) with default parameters. PCR duplicates were removed using Sambamba(version 1.0.1), and normalized genome-wide coverage tracks were generated with deepTools(3.5.6) bamCoverage using CPM normalization.
Assembly: UCSC mm39
Supplementary files format and content: bigWig files containing genome-wide normalized H3K9me3 ChIP-seq signal tracks.

extract_protocol:
For H3K9me3 ChIP-seq, the spermatocytes and RS were sorted by FACS and were crosslinked with 1 % formaldehyde in DMEM for 10 min at room temperature.
The ChIP experiments were performed with the ChIP-IT High Sensitivity Kit according to the manufacturers’ instructions. Libraries were prepared using the VAHTS Universal Pro DNA Library Prep Kit for Illumina from Vazyme following the manufacturer’s instructions. Libraries were sequenced a 150-bp paired-end mode on DNBSEQ-T7 platform.

value: round sperm


title: OGO_Rosa_5552F,scRNAseq,gene_exp

description:
Library name: OGO_Rosa_5552F
10x Genomics
OGO_Wnt7b_annot.csv

value: Dissociated single cells

value: 6-14 weeks


title: ChIP-Seq, round sperm, Wild type, biol rep3

description:
Library name: SAMPLES9
Control_3

value: testis


title: ChIP-Seq, round sperm, Wild type, biol rep2

description:
Library name: SAMPLES8
Control_2


title: DMSO_1uM_2_Days_2_VCaP

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: Library name: MR648

data_processing:
Raw fastq files were aligned using STAR v2.7.1. Raw counts were calculated by STAR, FPKM values were calculated by in-house perl script
Assembly: hg38
Supplementary files format and content: txt files of raw counts and FPKM values

source_name: Prostate

growth_protocol: VCaP and 22Rv1 prostate cancer cell line was maintained in Dulbecco’s modified Eagle’s medium (DMEM) and Roswell Park Memorial Institute Medium (RPMI), respectively, supplemented with 10% fetal bovine serum (FBS), penicillin sodium (100 U/mL), and streptomycin sulfate (100 µg/mL).

extract_protocol:
Total RNA was isolated from cells using NucleoSpin RNA isolation kit (Takara) following the manufacturer’s instructions.
RNA-seq libraries were prepared from 0.5 μg of high-quality DNA-free RNA using NEBNext Ultra RNA Library Prep Kit, according to the manufacturer’s instructions.

treatment_protocol: VCaP and 22Rv1 cells were treated with either DMSO, VHL-inactive control compound 6286 (1µM), EZH2 PROTAC degrader PROTAC-6272 (1µM), or EZH2 enzymatic inhibitor EPZ-6438 (1µM) for 48 hours and then collected for RNA analysis.

value: Prostate

value: VCaP

value: Prostate cancer cell

value: DMSO


title: MG_5FU_3

description: Library name: Sample 6

value: Small intestine

value: intestinal epithelial cells

value: C57BL/6J WT


title: ChIP-Seq, meiotic cells, Daxx knockdown, biol rep1

description:
Library name: SAMPLES4
Daxx_1

value: meiotic cells

value: DAXX knockdown


title: ChIP-Seq, meiotic cells, Wild type, biol rep3

description:
Library name: SAMPLES3
Control_3

value: WT


title: Induced cortical neurons, Control, replicate 1

state: New York

institute: NYU Grossman School of Medicine

description:
Library name: i3N_control
i3N_Ctrl_noAza_hg38_minimap2

value: KOLF2.1J -derived

value: induced cortical neurons (i3N)

value: Control


title: scRNAseq from day 13

value: highly hematopoietic human fetal liver organoids from iPSCs

value: cell line 72_3

value: human iPSC-derived

value: day 13

value: No treatment


title: scRNAseq from day 10

source_name: human fetal liver organoids from iPSCs

value: human fetal liver organoids from iPSCs

value: day 10


title: MG_5FU_1

description: Library name: Sample 4


title: SN12_S25_KC,scRNAseq,gene_exp

description:
Library name: SN12_S25_KC
10x Genomics
CP_Norm_annot.csv

source_name: Pancreas

value: Dissociated single cells

value: Pancreas

value: KrasG12D/+;Pdx1-Cre (KC)

value: 6-14 weeks


title: 2hVeh1

description: Library name: 2h-Veh-1

value: Bone

value: Ocy454 cells

value: Osteocytic Cells


title: Induced cortical neurons, TDP-43 CRISPRi, replicate 1

description:
Library name: i3N_TDP43KD
i3N_TDP43KD_noAza_hg38_minimap2

value: KOLF2.1J -derived

value: TDP-43 CRISPRi


title: ChIP-Seq, meiotic cells, Daxx knockdown, biol rep3

description:
Library name: SAMPLES6
Daxx_3

value: testis

value: meiotic cells

value: DAXX knockdown


title: MG_Control_1

description: Library name: Sample 1

value: Small intestine

value: intestinal epithelial cells

value: C57BL/6J WT

value: non-treat


title: thymus_gex

city: North York

first: Vinothkumar

last: Rajan

state: ON

address: 2075 Bayview Ave, Room # M7-413

department: Biological Sciences

country: Canada

institute: Sunnybrook Research Institute

description: Library name: GEX

data_processing:
Demultiplexed sequencing data were analyzed using CellRanger v8.0.0 with default parameters
Assembly: GRCm39-2024-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Thymus

extract_protocol:
Postnatal day 6 thymic tissues were minced into ~1 mm pieces and digested with a mixture of papain (0.5 mg/mL), collagenase IV (0.25 mg/mL), and DNase I (0.1 mg/mL) at 37°C for 30 minutes. Released cells were collected with fresh enzyme mixtures added after 15 minutes. CD45+ hematopoietic cells were depleted using CD45 MicroBeads and LS columns (Miltenyi Biotec). CD45– stromal cells were stained with APC-conjugated anti-EpCAM antibody (clone G8.8) and purified by fluorescence-activated cell sorting (FACS).
CD45–EpCAM+ TECs from three DKO and three control 6-day-old pups were independently labeled using TotalSeq™-A anti-mouse hashtag antibodies (BioLegend). Equal numbers of cells from each sample were pooled prior to encapsulation to minimize batch effects, targeting recovery of ~10,000 cells. An additive hashtag oligo (HTO) primer (5'-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT) was included in the cDNA amplification to enable efficient hashtag library preparation. Following cDNA cleanup, an HTO-specific library was generated by amplification with primers targeting Nextera Read 1 and Read 2. Libraries were pooled and sequenced using paired-end 2×150 bp reads, with a 10% PhiX spike-in, targeting a depth of 40,000 reads per cell for the cDNA library and 500 reads per cell for the HTO library.

value: Thymus

value: thymic epithelial cells

value: mixed sample (WT & KO)

tag: hto

value: TotalSeq™-A0301 anti-mouse Hashtag 1 Antibody (KO), TotalSeq™-A0301 anti-mouse Hashtag 2 Antibody (KO), TotalSeq™-A0301 anti-mouse Hashtag 3 Antibody (WT), TotalSeq™-A0301 anti-mouse Hashtag 4 Antibody (KO), TotalSeq™-A0301 anti-mouse Hashtag 5 Antibody (WT), TotalSeq™-A0301 anti-mouse Hashtag 6 Antibody (WT)


title: WGBS, P8 testis, Wild type, biol rep2

description:
Library name: SAMPLES2
Control_2

value: WT


title: S14-03d-D

city: Los Angeles

first: Joshua

middle: Evan

last: Burda

state: CA

address: 127 S San Vicente Blvd

department: Biomedical Sciences, Center for Neural Science and Medicine

institute: Cedars Sinai Medical Center

description:
Library name: Sample 31
WT_Thoracic spinal cord3 days post ISCI

data_processing:
genome alignment by cellranger-v6.0.2, data normalization and clustering by Scanpy
Assembly: mm10 2020-A
Supplementary files format and content: .h5, count matrix

molecule: nuclear RNA

extract_protocol:
iSCI mice were perfused with ice-cold PBS with heparin at 3, 7 or 28 dpi, spinal cords dissected out and 4 mm of spinal cord rostral (T9-T11) and caudal (L1-L3) to the lesion epicenter were then rapidly removed, snap-frozen in dry ice and stored at -80°C. An anatomically equivalent region of spinal cord (T11-L1) was isolated from age- and genotype-matched healthy controls. Frozen tissue was homogenized in Homogenization buffer (320 mM Sucrose, 0.1mM EDTA, 0.1% IGAPAL, 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris, Roche Protector RNAse Inhibitor, Complete Roche Protease Inhibitor Version 12, 0.016mM PMSF, 0.166mM b-Mercaptoethanol; pH=7.8). Nuclei were isolated from the homogenate by iodixanol gradient and resuspended in 1% BSA solution before proceeding immediatly to 10x single cell RNA-sequencing
snRNA-Seq libraries were prepared using 10x Chromium Next GEMSingle Cell 3 (v3.1) per manufacturer's instructions. Samples were loaded to capture 10,000 nuclei per sample. During library preparation, the initial cDNA amplification was run for 13 cycles, which was found to be optimal for 10,000 nuclei. Sequencing: 2x150 reads base pairs (bps) , ~40,000 reads/cell

value: Thoracic spinal cord

tag: batch

value: 3 days post ISCI


title: S13-00d-D

description:
Library name: Sample 30
WT_Thoracic spinal corduninjured

value: uninjured


title: COL_Control_1

description: Library name: Sample 7


title: S10-28d-E

description:
Library name: Sample 27
WT_Lumbar spinal cord28 days post ISCI

value: Lumbar spinal cord

value: 28 days post ISCI


title: Induced cortical neurons, 5-Azacytidine + TDP-43 CRISPRi, replicate 1

description:
Library name: i3N_5Aza_TDP43KD
i3N_TDP43KD_5Aza_hg38_minimap2

value: KOLF2.1J -derived

value: induced cortical neurons (i3N)

value: 5-Azacytidine & TDP-43 CRISPRi


title: ChIP-Seq, round sperm, Daxx knockdown, biol rep3

description:
Library name: SAMPLES12
Daxx_3

value: testis

value: round sperm

value: DAXX knockdown


title: 8hD1

description: Library name: 8h-1,25D-1

value: Bone

value: Ocy454 cells

value: Osteocytic Cells


title: S04-07d-D

description:
Library name: Sample 21
WT_Thoracic spinal cord7 days post ISCI

value: 7 days post ISCI


title: S05-28d-E

description:
Library name: Sample 22
WT_Lumbar spinal cord28 days post ISCI


title: S12-28d-E

description:
Library name: Sample 29
WT_Lumbar spinal cord28 days post ISCI


title: S07-00d-E

description:
Library name: Sample 24
WT_Lumbar spinal corduninjured


title: K15-03d-D

description:
Library name: Sample 14
WT_Thoracic spinal cord3 days post ISCI


title: ChIP-Seq, meiotic cells, Daxx knockdown, biol rep2

description:
Library name: SAMPLES5
Daxx_2

value: meiotic cells


title: S16-28d-D

description:
Library name: Sample 33
WT_Thoracic spinal cord28 days post ISCI

value: WT


title: K18-28d-D

description:
Library name: Sample 17
WT_Thoracic spinal cord28 days post ISCI

value: Thoracic spinal cord


title: ChIP-Seq, round sperm, Daxx knockdown, biol rep2

description:
Library name: SAMPLES11
Daxx_2


title: K13-03d-D

description:
Library name: Sample 12
WT_Thoracic spinal cord3 days post ISCI

value: 3 days post ISCI


title: ChIP-Seq, round sperm, Wild type, biol rep1

description:
Library name: SAMPLES7
Control_1


title: S15-03d-D

description:
Library name: Sample 32
WT_Thoracic spinal cord3 days post ISCI


title: S18-28d-D

description:
Library name: Sample 35
WT_Thoracic spinal cord28 days post ISCI


title: K10-07d-E

description:
Library name: Sample 9
WT_Lumbar spinal cord7 days post ISCI


title: scRNAseq from day 20

description:
10x Genomics
integrated_counts.txt
integrated_metadata.txt

value: highly hematopoietic human fetal liver organoids from iPSCs

value: cell line 72_3

value: human iPSC-derived

value: day 20

value: No treatment


title: K08-03d-E

description:
Library name: Sample 7
WT_Lumbar spinal cord3 days post ISCI

value: Lumbar spinal cord


title: S17-00d-D

description:
Library name: Sample 34
WT_Thoracic spinal corduninjured

value: uninjured


title: K07-00d-E

description:
Library name: Sample 6
WT_Lumbar spinal corduninjured


title: S09-03d-E

description:
Library name: Sample 26
WT_Lumbar spinal cord3 days post ISCI


title: K03-28d-D

description:
Library name: Sample 3
WT_Thoracic spinal cord28 days post ISCI

value: 28 days post ISCI


title: S06-03d-E

description:
Library name: Sample 23
WT_Lumbar spinal cord3 days post ISCI


title: S03-28d-D

description:
Library name: Sample 20
WT_Thoracic spinal cord28 days post ISCI


title: ChIP-Seq, meiotic cells, Wild type, biol rep1

description:
Library name: SAMPLES1
Control_1

value: testis


title: K01-00d-D

description:
Library name: Sample 1
WT_Thoracic spinal corduninjured


title: S11-00d-E

description:
Library name: Sample 28
WT_Lumbar spinal corduninjured


title: S08-07d-E

description:
Library name: Sample 25
WT_Lumbar spinal cord7 days post ISCI


title: S02-07d-D

description:
Library name: Sample 19
WT_Thoracic spinal cord7 days post ISCI


title: K16-07d-D

description:
Library name: Sample 15
WT_Thoracic spinal cord7 days post ISCI


title: Die-5xFAD_4

city: Rochester

first: Lia

last: Calcines Rodriguez

state: NY

address: 17 S Goodman St, Apt. 2

department: Neuroscience

institute: University of Rochester

description:
Library name: 82DR
Female Die-5xFAD

data_processing:
Raw reads generated from the Illumina basecalls were demultiplexed using bcl-convert version 4.1.7.
Quality filtering and adapter removal are performed using FastP version 0.23.1 with the following parameters:  "--length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y –r"
Processed/cleaned reads were then mapped to the GRCm39/gencode M31 reference using STAR_2.7.9a with the following parameters: "—twopass Mode Basic --runMode alignReads --outSAMtype BAM Unsorted – outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical –outReadsUnmapped Fastx"
Genelevel read quantification was derived using the subread-2.0.1 package (featureCounts) with a GTF annotation file (GRCm39/gencode M31) and the following parameters for unstranded RNA libraries  "--s 0 -t exon -g gene_name" for unstranded libraries.
Assembly: GRCm39/gencode M31
Supplementary files format and content: Tab-delimited text file with raw counts for each sample.
Supplementary files format and content: Tab-delimited text file with normalized counts for each sample.

source_name: Brain

extract_protocol:
RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, Valencia, CA). The concentration of RNA was determined using the NanoDrop One spectrophotometer (NanoDrop, Wilmington, DE), and RNA quality was assessed with the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). Pre-amplification of 1 ng of RNA was performed with the SMART-seq v4 Ultra-Low mRNA Input kit (Clontech, Mountain View, CA) per manufacturer’s instructions. The quantity and quality of the cDNA were determined using Qubit Fluorometer (Life Technologies, Carlsbad, CA) and the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA).
A total of 150 pg of cDNA was used to generate Illumina-compatible sequencing libraries with the NexteraXT library preparation kit (Illumina, San Diego, CA) per manufacturer’s instructions.

value: Brain

value: Microglia

tag: sample group

value: Die


title: Die-5xFAD_3

description:
Library name: 80B
Female Die-5xFAD


title: ChIP-Seq, meiotic cells, Wild type, biol rep2

description:
Library name: SAMPLES2
Control_2


title: S01-00d-D

description:
Library name: Sample 18
WT_Thoracic spinal corduninjured


title: K17-07d-D

description:
Library name: Sample 16
WT_Thoracic spinal cord7 days post ISCI

value: 7 days post ISCI


title: K12-07d-E

description:
Library name: Sample 11
WT_Lumbar spinal cord7 days post ISCI


title: K14-28d-D

description:
Library name: Sample 13
WT_Thoracic spinal cord28 days post ISCI


title: K02-07d-D

description:
Library name: Sample 2
WT_Thoracic spinal cord7 days post ISCI


title: Pro-5xFAD_3

description:
Library name: 80DL
Female Pro-5xFAD

value: Pro


title: Males-5xFAD_2

description:
Library name: 77L
Males-5xFAD

value: Males


title: Pro-BL6_3

description:
Library name: 76DR
Female Pro-BL6


title: Die-BL6_4

description:
Library name: 82L
Female Die-BL6


title: K11-03d-E

description:
Library name: Sample 10
WT_Lumbar spinal cord3 days post ISCI

value: WT


title: Males-BL6_4

description:
Library name: 77R
Males-BL6


title: Males-5xFAD_4

description:
Library name: 79L
Males-5xFAD


title: K05-07d-E

description:
Library name: Sample 5
WT_Lumbar spinal cord7 days post ISCI


title: K04-00d-D

description:
Library name: Sample 4
WT_Thoracic spinal corduninjured

value: Thoracic spinal cord


title: Pro-5xFAD_1

description:
Library name: 83B
Female Pro-5xFAD


title: Males-BL6_3

description:
Library name: 81L
Males-BL6


title: Males-5xFAD_3

description:
Library name: 81R
Males-5xFAD


title: Males-BL6_1

description:
Library name: 84B
Males-BL6


title: Die-BL6_2

description:
Library name: 75DR
Female Die-BL6


title: Pro-5xFAD_2

description:
Library name: 80R
Female Pro-5xFAD


title: Die-BL6_3

description:
Library name: 80L
Female Die-BL6


title: Males-BL6_2

description:
Library name: 79B
Males-BL6


title: Die-5xFAD_1

description:
Library name: 64R
Female Die-5xFAD


title: Ga13 primary lung fibroblasts, Unstimulated_Cre, rep 3

city: Boston

first: Mikel

last: Garcia-Marcos

state: MA

address: East Concord Street

institute: Boston University

description: Library name: Ga13_UNS_CreV_3

data_processing:
Raw sequence reads were preprocessed using fastp to trim adapter sequences and filter out low-quality data.
Adapter-trimmed forward and reversed strand fq.gz files were mapped and aligned to the primary assembly of the mouse reference genome GRCm39 from GENCODE using the Subread package.
The feature Counts function of the Subread package was used to quantify the total number of fragments mapped to a particular gene, and generate a count matrix with integer-based reads.
Assembly: GRCm39
Supplementary files format and content: Processed data files are tab-delimited text files with raw counts for each sample

source_name: Lungs

growth_protocol: Mouse astroglial cells were isolated from mice heterozygous for the Gαs*-BERKY3 allele and seeded in wells of a glass bottom 12-well plate precoated with 0.1 mg/ml poly-L-lysine hydrobromide (overnight incubation followed by 3 washes with Hanks' Balanced Salts solution) in 750 µl of complete neuro DMEM (430,000 cells seeded per well). Mouse lung fibroblasts were isolated from mice heterozygous for either the Gαi*- BERKY3, Gαq*- BERKY3, or the Gα13*-BERKY3 allele and seeded in wells of a glass bottom 12-well plate precoated with 0.1% gelatin (5 min incubation at room temperature followed by aspiration) in 750 µl of fibroblast growth medium-2 (160,000 cells seeded per well).

extract_protocol:
RNA was isolated using the RNAqueous isolation kit (Invitrogen, cat# AM1931) by following the manufacturer’s instructions for guanidinium-based lysis/denaturant and glass fiber filter separation technology.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. (Done by Novogene Co)

treatment_protocol: Approximately 18 h after seeding, cells were transduced by replacing the media with 750 µl of fresh media supplemented with 6 μg/ml polybrene and either an adeno-associated virus for the expression of Cre recombinase (AAV2/1-CMV-Cre; University of Iowa Viral vector Core, cat# VVC-U of Iowa-237) or a control empty adeno-associated virus (AAV2/1-CMV-empty; University of Iowa Viral vector Core, cat# VVC-U of Iowa-4223) at a 1:500 dilution (for astrocytes) or 1:1000 dilution (for lung fibroblasts). 90 min prior to RNA isolation, cell media were replaced with fresh media with or without agonist (i.e., 1 µM isoproterenol or 100 µM TRAP-6 for astroglial cells and lung fibroblasts, respectively).

value: Lungs

value: Fibroblasts

value: Primary


title: Ga13 primary lung fibroblasts, Stimulated_Cre, rep 3

description: Library name: Ga13_S_CreV_3


title: Pro-BL6_1

description:
Library name: 64L
Female Pro-BL6


title: Ga13 primary lung fibroblasts, Stimulated_control, rep 1

description: Library name: Ga13_S_EmptyV_1


title: Die-BL6_1

description:
Library name: 64B
Female Die-BL6


title: Pro-5xFAD_4

description:
Library name: 82B
Female Pro-5xFAD


title: Ga13 primary lung fibroblasts, Stimulated_Cre, rep 2

description: Library name: Ga13_S_CreV_2


title: Die-5xFAD_2

description:
Library name: 64DR
Female Die-5xFAD


title: Pro-BL6_2

description:
Library name: 64DL
Female Pro-BL6


title: Ga13 primary lung fibroblasts, Stimulated_control, rep 3

description: Library name: Ga13_S_EmptyV_3


title: Males-5xFAD_1

description:
Library name: 84R
Males-5xFAD


title: Ga13 primary lung fibroblasts, Unstimulated_control, rep 2

description: Library name: Ga13_UNS_EmptyV_2


title: Pro-BL6_4

description:
Library name: 80DR
Female Pro-BL6


title: Gaq primary lung fibroblasts, Unstimulated_Cre, rep 3

description: Library name: Gaq_UNS_CreV_3


title: Ga13 primary lung fibroblasts, Stimulated_control, rep 2

description: Library name: Ga13_S_EmptyV_2


title: Gaq primary lung fibroblasts, Stimulated_control, rep 3

description: Library name: Gaq_S_EmptyV_3


title: Gaq primary lung fibroblasts, Stimulated_Cre, rep 3

description: Library name: Gaq_S_CreV_3


title: Gaq primary lung fibroblasts, Unstimulated_control, rep 3

description: Library name: Gaq_UNS_EmptyV_3


title: Gaq primary lung fibroblasts, Unstimulated_Cre, rep 2

description: Library name: Gaq_UNS_CreV_2


title: Gaq primary lung fibroblasts, Stimulated_Cre, rep 2

description: Library name: Gaq_S_CreV_2


title: Ga13 primary lung fibroblasts, Unstimulated_Cre, rep 1

description: Library name: Ga13_UNS_CreV_1


title: Gaq primary lung fibroblasts, Stimulated_control, rep 1

description: Library name: Gaq_S_EmptyV_1


title: Gaq primary lung fibroblasts, Unstimulated_control, rep 2

description: Library name: Gaq_UNS_EmptyV_2


title: Ga13 primary lung fibroblasts, Unstimulated_Cre, rep 2

description: Library name: Ga13_UNS_CreV_2


title: Ga13 primary lung fibroblasts, Unstimulated_control, rep 1

description: Library name: Ga13_UNS_EmptyV_1


title: Gaq primary lung fibroblasts, Unstimulated_Cre, rep 1

description: Library name: Gaq_UNS_CreV_1


title: Ga13 primary lung fibroblasts, Stimulated_Cre, rep 1

description: Library name: Ga13_S_CreV_1


title: Ga13 primary lung fibroblasts, Unstimulated_control, rep 3

description: Library name: Ga13_UNS_EmptyV_3


title: Gaq primary lung fibroblasts, Stimulated_Cre, rep 1

description: Library name: Gaq_S_CreV_1


title: Gaq primary lung fibroblasts, Stimulated_control, rep 2

description: Library name: Gaq_S_EmptyV_2


title: Gai primary lung fibroblasts, Unstimulated_control, rep 3

description: Library name: Gai_UNS_EmptyV_3


title: Gaq primary lung fibroblasts, Unstimulated_control, rep 1

description: Library name: Gaq_UNS_EmptyV_1


title: Gai primary lung fibroblasts, Unstimulated_Cre, rep 3

description: Library name: Gai_UNS_CreV_3


title: Gai primary lung fibroblasts, Stimulated_control, rep 2

description: Library name: Gai_S_EmptyV_2


title: Gai primary lung fibroblasts, Unstimulated_Cre, rep 1

description: Library name: Gai_UNS_CreV_1


title: Gai primary lung fibroblasts, Stimulated_Cre, rep 3

description: Library name: Gai_S_CreV_3


title: Gai primary lung fibroblasts, Stimulated_Cre, rep 2

description: Library name: Gai_S_CreV_2


title: Gas primary astrocytes, Stimulated_Cre, rep 3

description: Library name: Gas_S_CreV_3

value: Astrocytes


title: Gai primary lung fibroblasts, Unstimulated_control, rep 2

description: Library name: Gai_UNS_EmptyV_2


title: Gas primary astrocytes, Stimulated_control, rep 3

description: Library name: Gas_S_EmptyV_3


title: Gai primary lung fibroblasts, Stimulated_control, rep 1

description: Library name: Gai_S_EmptyV_1


title: Gas primary astrocytes, Unstimulated_Cre, rep 1

description: Library name: Gas_UNS_CreV_1


title: Gai primary lung fibroblasts, Unstimulated_control, rep 1

description: Library name: Gai_UNS_EmptyV_1


title: Gas primary astrocytes, Unstimulated_Cre, rep 2

description: Library name: Gas_UNS_CreV_2


title: Gas primary astrocytes, Stimulated_control, rep 2

description: Library name: Gas_S_EmptyV_2


title: Gas primary astrocytes, Unstimulated_control, rep 1

description: Library name: Gas_UNS_EmptyV_1


title: Gai primary lung fibroblasts, Stimulated_control, rep 3

description: Library name: Gai_S_EmptyV_3


title: Gai primary lung fibroblasts, Unstimulated_Cre, rep 2

description: Library name: Gai_UNS_CreV_2


title: Gas primary astrocytes, Unstimulated_Cre, rep 3

description: Library name: Gas_UNS_CreV_3


title: Gas primary astrocytes, Stimulated_Cre, rep 1

description: Library name: Gas_S_CreV_1


title: Gas primary astrocytes, Unstimulated_control, rep 2

description: Library name: Gas_UNS_EmptyV_2


title: deltaD19B_ovary_rep1_1

city: Bunkyo-ku

first: Raku

last: Saito

state: Tokyo-to

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

institute: The University of Tokyo

description: Library name: Sample63

data_processing:
Raw sequence reads were trimmed by fastp.
Trimmed reads were mapped to drosophila dm6 (BDGP6) genome by bowtie2.
Uniquely mapped reads were extracted by samtools.
Matrix bigwig files were produced by deeptools.
Peak calling were performed by MACS2.
Assembly: dm6
Supplementary files format and content: general bigwig, narrowPeak file format

organism: Drosophila melanogaster

source_name: ovary

extract_protocol:
nc14 (2h10min-2h40min) early embryo for ChIP and adult ovary for RNA-seq
Prepared by manufacturer's protocol of NEBNext Ultra II DNA Library Prep Kit for Illumina

value: ovary

value: adult ovary

value: deltaD19B (used for RNA-seq)


title: yw_ovary_rep1_2

description: Library name: Sample62

value: yw (used for RNA-seq)


title: Gas primary astrocytes, Stimulated_Cre, rep 2

description: Library name: Gas_S_CreV_2


title: Gai primary lung fibroblasts, Stimulated_Cre, rep 1

description: Library name: Gai_S_CreV_1


title: JHEM3

city: San Antonio

first: Lacy

middle: J

last: Barton

state: Texas

address: 1 UTSA Circle

department: Neuroscience, Developmental and Regenerative Biology

institute: University of Texas at San Antonio

description:
Library name: Sample 24
Column name in htseq-counts_ALL.csv: JHEM_3

data_processing:
Demultiplexed .fastq files were aligned to BDGP dm6 using HISAT v 2.2.1, converted to .bam, sorted and indexed using SAMtools 1.21 view, sort and index commands with default flags, and visualized as .bigwig using deepTools 3.5.6 bamCoverage “--binSize 1” flag. Read quality and alignment statistics were summarized with FastQC and multiQC. Read counts were summarized from sorted .bam files using HTSeq 2.0.3 “htseq-count” command using BDGP dm6.46 113 release .gtf reference.
Differentially expressed genes were identified using DESeq 2, with thresholds of fold change >1.5 and p value <0.05 adjusted for multiple testing using Benjamini-Hochberg correction. Normalized counts adjusted for differences in sequencing depth across samples were extracted from DESeq2 analysis results.
Assembly: dm6.46.113
Supplementary files format and content: htseq-counts_ALL.csv : CSV (Comma-Separated Values) file with raw counts generated from HTseq for each sample.
Supplementary files format and content: normal.counts.female.csv : CSV (Comma-Separated Values) file with normalized counts from DESeq2 for each sample.
Supplementary files format and content: .bw : BigWig binary format files with reads mapped to each position in the genome.

source_name: whole prepupae

growth_protocol: Stocks used in this study were reared on a molasses/cornmeal medium with methyl 4-hydroxybenzoate (Tegosept) as a mold inhibitor. Embryo collections were conducted using cages with removable apple juice plates. The apple juice plates were made of 25% apple juice, 2.5% sucrose, 2.25% Bacto-agar, and 0.15% Tegosept.Experiments were carried out at 25°C, 70% humidity with a 12-hour day-night cycle unless otherwise specified.

extract_protocol:
As prepupae were collected, they were homogenized in TRIzol (Invitrogen, ThermoFisher #15596018) and stored at -80°C for later RNA extraction. RNA was isolated from three biological replicates, each containing five white prepupa, by TRIzol extraction followed by isopropanol precipitation. Seven micrograms of total RNA from each replicate were DNaseI-treated and cleaned up using Monarch Total RNA Miniprep Kit (NEB T2010S). One microgram of total RNA was used for RNA-Seq library preparation, using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760) with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490).
Individual libraries were sized and quantified using Tapestation 4200 and High Sensitivity D1000 ScreenTape (Agilent 5067-5584), and Qubit fluorometer with dsDNA HS Assay kit (Thermo Q32854). Equimolar amounts of individual libraries were combined in one pool and sequenced by a commercial provider (Azenta Inc.) using 150 bp paired-end chemistry on NovaSeq X Plus with 5% phiX spike-in.

treatment_protocol: JH esterase double knockout (DKO) and Jheh1,2,3 triple knockout (TKO) animals were generated by non-homologous end joining of CRISPR-mediated breakpoints flanking jhe and jheh loci. Guide RNAs were designed based on sequencing relevant PAM sites in the vas-Cas9 injection stock (Bloomington Stock Center #51323). For each knockout, two guides were injected per PAM site for a total of four injected guides each for jhe,jheDup and jheh1,2,3 deletion.

value: whole prepupae

tag: Sex

value: male

value: Jhe, JheDup double knockout

value: CRISPR


title: deltaD19B_ovary_rep1_2

description: Library name: Sample64


title: Gas primary astrocytes, Unstimulated_control, rep 3

description: Library name: Gas_UNS_EmptyV_3

value: Brain


title: yw_ovary_rep1_1

description: Library name: Sample61


title: Gas primary astrocytes, Stimulated_control, rep 1

description: Library name: Gas_S_EmptyV_1


title: JHEHM3

description:
Library name: Sample 19
Column name in htseq-counts_ALL.csv: JHEHM_3

value: Jheh1,2,3 triple knockout


title: JHEHF2

description:
Library name: Sample 21
Column name in htseq-counts_ALL.csv: JHEHF_2

value: female


title: OWM2

description:
Library name: Sample 14
Column name in htseq-counts_ALL.csv: orWTM_2

value: Oregon R x white 1118


title: OWF2

description:
Library name: Sample 11
Column name in htseq-counts_ALL.csv: orWTF_2


title: JHEF3

description:
Library name: Sample 9
Column name in htseq-counts_ALL.csv: JHEF_3


title: JHEF2

description:
Library name: Sample 8
Column name in htseq-counts_ALL.csv: JHEF_2


title: JHEHF3

description:
Library name: Sample 22
Column name in htseq-counts_ALL.csv: JHEHF_3


title: JHEHF1

description:
Library name: Sample 20
Column name in htseq-counts_ALL.csv: JHEHF_1


title: JHEM2

description:
Library name: Sample 23
Column name in htseq-counts_ALL.csv: JHEM_2


title: WF2

description:
Library name: Sample 2
Column name in htseq-counts_ALL.csv: wWTF_2

value: white 1118


title: JHEF1

description:
Library name: Sample 7
Column name in htseq-counts_ALL.csv: JHEF_1


title: WF1

description:
Library name: Sample 1
Column name in htseq-counts_ALL.csv: wWTF_1


title: WM2

description:
Library name: Sample 5
Column name in htseq-counts_ALL.csv: wWTM_2


title: WF3

description:
Library name: Sample 3
Column name in htseq-counts_ALL.csv: wWTF_3


title: JHEHM2

description:
Library name: Sample 18
Column name in htseq-counts_ALL.csv: JHEHM_2


title: JHEHM1

description:
Library name: Sample 16
Column name in htseq-counts_ALL.csv: JHEHM_1


title: T. monococcum Mon8 Heat Rep1

city: Valdivia

first: Javier

last: Canales

state: Los Ríos

address: Campus Isla Teja s/n

department: Instituto de Bioquimica y Microbiologia

country: Chile

institute: Universidad Austral de Chile

description: Library name: TA2MON

data_processing:
Raw sequencing reads were pseudo-aligned and quantified using Kallisto (v0.50.1) with a k-mer size of 31. The following reference transcriptomes were used: Triticum aestivum (IWGSC RefSeq v2.1) , Triticum turgidum (Svevo v1) , and Triticum monococcum (TA10622 v1.1). Differential expression analysis was performed using DESeq2 v1.42 in R.
Assembly: IWGSC RefSeq v2.1 for T.aestivum, Svevo v1 for T.turgidum, TA10622 v1.1 for T.monococcum
Supplementary files format and content: tsv files includes raw counts and tpm

organism: Triticum monococcum

source_name: Wheat grain

growth_protocol: Field experiments were conducted at the Experimental Station of the Universidad Austral de Chile (UACh) in Valdivia (39° 47' S, 73° 14' W), Chile. The crops were grown under typical temperate conditions with supplemental irrigation to prevent water stress. Plots were fertilized with 150 kg/ha N and 300 kg/ha P2O5 at sowing, with an additional 150 kg/ha N during mid-tillering.

extract_protocol:
Total RNA was isolated from complete caryopses (harvested from central spikelets) using a modified CTAB-based protocol. RNA quality was assessed using a Nanoquant Infinite M200 spectrophotometer(A260/A280 ratios between 1.8-2.0)
Illumina RNA-seq libraries were constructed using the Illumina TruSeq Stranded Total RNA Sample Prep Kit following the manufacturer's protocol. Unique barcodes were incorporated for multiplexing.

treatment_protocol: Thermal treatments were applied during the early grain-filling period (10-14 days after anthesis) using temperature-controlled polyethylene chambers. The experiment compared a Control (ambient temperature) against a severe Heat Stress treatment (TT2, up to 32°C mean temperature). Grain samples for RNA-seq were collected 3 hours after imposing the heat stress treatment on day 10 after anthesis.

value: Wheat grain

value: Diploid

value: 10 DAA (3h post-stress)

value: Heat (TT2)

value: replicate 1


title: K09-00d-E

description:
Library name: Sample 8
WT_Lumbar spinal corduninjured

value: Lumbar spinal cord

value: WT

value: uninjured


title: T. monococcum Mon8 Control Rep1

description: Library name: CAMON

value: Control


title: 0CUG (str2) 2 days old adults stage_1

city: Helsinki

first: Susana

last: Garcia

address: Viikinkaari 5D

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

description: Library name: R0CUGSG362DA1

data_processing:
Sequencing reads were mapped to the C. elegans reference transcriptome (WBcel235 assembly) using HISAT2. The software used for differential gene expression analysis and for alternative splicing analysis were DESeq2 and rMATS, respectively, and statistical significance was obtained by applying Wald test with a cutoff of 0.05.
Assembly: Sequencing reads were mapped to the C. elegans reference transcriptome (WBcel235 assembly) using HISAT2.
Supplementary files format and content: .fq files containing raw counts for each sample

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Strains were synchronized by NaOCl treatment and eggs were plated on RNAi plates seeded with empty vector. Animals were collected at two different stages: L4 and 2-day old adults.

extract_protocol:
Total RNA was extracted with TRIzol Reagent followed by chloroform extraction and isopropanol precipitation
RNA libraries from RNA-seq were prepared using the kit provided by Illumina and followiwng manusfacturers instructions,

treatment_protocol: Animals were grown on HT115 bacteria containing empty RNAi vector and colleceted at two different stages of development.

value: whole organism

value: Bristol strain

tag: developmental stage

value: 2 days old adults stage

value: aging


title: 0CUG (str2) 2 days old adults stage_3

description: Library name: R0CUGSG362DA3


title: 0CUG (str1) 2 days old adults stage_2

description: Library name: R0CUGSG262DA2


title: 0CUG (str1) 2 days old adults stage_3

description: Library name: R0CUGSG262DA3


title: JHEM1

description:
Library name: Sample 17
Column name in htseq-counts_ALL.csv: JHEM_1

value: whole prepupae

value: male

value: Jhe, JheDup double knockout

value: CRISPR


title: 123CUG (str2) 2 days old adults stage_2

description: Library name: R123CUGSG352DA2


title: 123CUG (str2) 2 days old adults stage_3

description: Library name: R123CUGSG352DA3


title: OWF1

description:
Library name: Sample 10
Column name in htseq-counts_ALL.csv: orWTF_1

value: female

value: Oregon R x white 1118


title: 123CUG (str1) 2 days old adults stage_2

description: Library name: R123CUGSG22DA2


title: 0CUG (str2) 2 days old adults stage_2

description: Library name: R0CUGSG362DA2


title: OWM1

description:
Library name: Sample 13
Column name in htseq-counts_ALL.csv: orWTM_1


title: 0CUG (str2) L4 stage_2

description: Library name: R0CUGSG36L42

value: L4 developmental stage


title: WM1

description:
Library name: Sample 4
Column name in htseq-counts_ALL.csv: wWTM_1

value: white 1118


title: WM3

description:
Library name: Sample 6
Column name in htseq-counts_ALL.csv: wWTM_3


title: 0CUG (str1) L4 stage_1

description: Library name: R0CUGSG26L41


title: OWM3

description:
Library name: Sample 15
Column name in htseq-counts_ALL.csv: orWTM_3


title: OWF3

description:
Library name: Sample 12
Column name in htseq-counts_ALL.csv: orWTF_3


title: T. monococcum Mon8 Heat Rep3

description: Library name: TC2MON

value: Wheat grain

value: Diploid

value: 10 DAA (3h post-stress)

value: Heat (TT2)

value: replicate 3


title: 123CUG (str2) L4 stage_2

description: Library name: R12335_L4_2

value: whole organism


title: 123CUG (str2) L4 stage_1

description: Library name: R123CUGSG35L41

value: Bristol strain


title: T. monococcum Mon8 Heat Rep2

description: Library name: TB2MON

value: replicate 2


title: 0CUG (str1) L4 stage_2

description: Library name: R0CUGSG26L42

value: aging


title: 123CUG (str1) 2 days old adults stage_1

description: Library name: R123CUGSG22DA1

value: 2 days old adults stage


title: T. monococcum Mon8 Control Rep2

description: Library name: CBMON

value: Control


title: T. monococcum Mon8 Control Rep3

description: Library name: CCMON


title: 123CUG (str2) 2 days old adults stage_1

description: Library name: R12335_2DA_1


title: mbl-1(tm1563) 2 days old adults stage_1

description: Library name: m_1_2DA_1


title: 0CUG (str1) L4 stage_3

description: Library name: R0_26_L4_3


title: N2 2 days old adults stage_1

description: Library name: wt_2DA_1

value: wt


title: 0CUG (str2) L4 stage_3

description: Library name: R0CUGSG36L43


title: 123CUG (str1) 2 days old adults stage_3

description: Library name: R123CUGSG22DA3


title: N2 2 days old adults stage_3

description: Library name: wt_2DA_3


title: 0CUG (str2) L4 stage_1

description: Library name: R0CUGSG36L41


title: mbl-1(tm1563) 2 days old adults stage_2

description: Library name: m_1_2DA_2


title: 123CUG (str1) L4 stage_2

description: Library name: R123CUGSG2L42


title: 123CUG (str1) L4 stage_1

description: Library name: R123CUGSG2L41


title: 0CUG (str1) 2 days old adults stage_1

description: Library name: R0CUGSG262DA1


title: N2 2 days old adults stage_2

description: Library name: wt_2DA_2


title: N2 L4 stage_1

description: Library name: wt_L4_1


title: mbl-1(tm1563) L4 stage_3

description: Library name: m_1_L4_3


title: mbl-1(tm1563) L4 stage_1

description: Library name: m_1_L4_1


title: N2 L4 stage_2

description: Library name: wt_L4_2


title: cococulture - 72 h of differentiation - sample 2

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

country: Poland

institute: National Research Institute of Animal Production

description:
Library name: s20065FL_07_02_04_CKDL240001622-1A_HJLL3CCX2_L7
02_4 : 2 : 72 : coculture

data_processing:
The raw sequences were quality controlled using FastQC.
Fastp software was used to remove Illumina adapters and poly-A sequences. Reads shorter than 36 bp and reads with a quality lower thanthe default of 20 were removed from the dataset.
Cleaned sequences were aligned to the Bos taurus genome with reference annotation containing more than 27,607 genes listed in the Ensembl database.
Alignment and estimation of gene expression level were made using the RSEM package supported by STAR aligner.
Differentially expressed genes and their corresponding p-values were determined using the statistical methods DESeq2
Assembly: ARS.UCD 1.2
Supplementary files format and content: raw.csv.gz
Supplementary files format and content: res_time0.tsv.gz
Supplementary files format and content: res_time24.tsv.gz
Supplementary files format and content: res_time72.tsv.gz

organism: Bos taurus

source_name: primary cell line

growth_protocol: Fibroblasts were cultured in High Glucose DMEM with the addition of 10% Fetal Bovine Serum and antibiotic Primocin in a humidified atmosphere with the 5% CO2 at 37 C .  Bovine muscle satellite cells were cultured in Low Glucose DMEM with the addition of 20% Fetal Bovine Serum and antibiotic Primocin in a humidified atmosphere with the 5% CO2 at 37 C.

extract_protocol:
RNA isolation was performed using PureLink RNA Mini Kit (Thermo Fisher Scientific) and PureLink™ DNase Set (Thermo Fisher Scientific). 400 ng of total RNA was used for the construction of sequencing libraries.
Vazyme VAHTS Universal V8 RNA-Seq Library Prep Kit for IlluminaTM systems was used to create RNA-seq libraries. The libraries were prepared according to the manufacturer's protocol.

treatment_protocol: A mix of three satellite cell lines (3rd passage since isolation) and fibroblasts (10th passage since isolation) were plated in the 6-well multiwell plate and 0.4 μm pore size co-culture plates (Thermo Fisher Scientific) at density 8000 cells/cm2, in High Glucose DMEM with the addition of 20% Fetal Bovine Serum. After five days of culture, the differentiation process was initiated by changing the medium to High Glucose DMEM with the addition of 10% Horse Serum (HS).

value: musculus longissimus dorsi

value: muscle satellite cell

value: WT

value: coculture


title: mbl-1(tm1563) 2 days old adults stage_3

description: Library name: m_1_2DA_3


title: cococulture - 72 h of differentiation - sample 3

description:
Library name: s20065FL_07_02_05_CKDL240001622-1A_HJLL3CCX2_L7
02_5 : 2 : 72 : coculture


title: N2 L4 stage_3

description: Library name: wt_L4_3

value: L4 developmental stage


title: cococulture - 24 h of differentiation - sample 4

description:
Library name: s20065FL_07_02_02_CKDL240001622-1A_HJLL3CCX2_L7
02_2 : 2 :24 : coculture


title: 123CUG (str2) L4 stage_3

description: Library name: R123CUGSG35L43


title: cococulture - 24 h of differentiation - sample 2

description:
Library name: s20065FL_07_01_18_CKDL240001621-1A_HJLL3CCX2_L6
01_18 : 2 : 24: coculture


title: cococulture - 24 h of differentiation - sample 3

description:
Library name: s20065FL_07_02_01_CKDL240001622-1A_HJLL3CCX2_L7
02_1 : 2 :24 : coculture


title: cococulture -  proliferation - sample 4

description:
Library name: s20065FL_07_01_16_CKDL240001621-1A_HJLL3CCX2_L6
01_16: 2 :0: coculture


title: cococulture - 24 h of differentiation - sample 1

description:
Library name: s20065FL_07_01_17_CKDL240001621-1A_HJLL3CCX2_L6
01_17 : 2 : 24: coculture


title: cococulture -  proliferation - sample 2

description:
Library name: s20065FL_07_01_14_CKDL240001621-1A_HJLL3CCX2_L6
01_14: 2 :0: coculture


title: 123CUG (str1) L4 stage_3

description: Library name: R0123CUGSG2L43


title: cococulture - 72 h of differentiation - sample 4

description:
Library name: s20065FL_07_02_06_CKDL240001622-1A_HJLL3CCX2_L7
02_6 : 2 : 72 : coculture


title: monoculture - 24 h of differentiation - sample 3

description:
Library name: s20065FL_07_01_07_CKDL240001621-1A_HJLL3CCX2_L6
01_07 : 1: 24: monoculture

value: monoculture


title: cococulture - 72 h of differentiation - sample 1

description:
Library name: s20065FL_07_02_03_CKDL240001622-1A_HJLL3CCX2_L7
02_3 : 2 : 72 : coculture


title: monoculture - 72 h of differentiation - sample 4

description:
Library name: s20065FL_07_01_12_CKDL240001621-1A_HJLL3CCX2_L6
01_12 : 1: 72: monoculture


title: monoculture - 24 h of differentiation - sample 2

description:
Library name: s20065FL_07_01_06_CKDL240001621-1A_HJLL3CCX2_L6
01_06 : 1: 24: monoculture


title: monoculture - 24 h of differentiation - sample 1

description:
Library name: s20065FL_07_01_05_CKDL240001621-1A_HJLL3CCX2_L6
01_05 : 1: 24: monoculture


title: mbl-1(tm1563) L4 stage_2

description: Library name: m_1_L4_2


title: cococulture -  proliferation - sample 1

description:
Library name: s20065FL_07_01_13_CKDL240001621-1A_HJLL3CCX2_L6
01_13: 2 :0: coculture


title: monoculture -  proliferation - sample 4

description:
Library name: s20065FL_07_01_04_CKDL240001621-1A_HJLL3CCX2_L6
01_04: 2: 0 : monoculture


title: cococulture -  proliferation - sample 3

description:
Library name: s20065FL_07_01_15_CKDL240001621-1A_HJLL3CCX2_L6
01_15: 2 :0: coculture


title: monoculture - 24 h of differentiation - sample 4

description:
Library name: s20065FL_07_01_08_CKDL240001621-1A_HJLL3CCX2_L6
01_08 : 1: 24: monoculture


title: E12.5 Mouse Placenta FGR 9

city: Aurora

first: JAMES

middle: R

last: BARDILL

state: CO

department: Surgery

institute: UNIVERSITY OF COLORADO-ANSCHUTZ MED

description:
Library name: Sample 9
column name in E12.5_mouse_RNAseq_FPKM_matrix.txt:  FGR_9

data_processing:
Raw reads were processed and filtered using Cutadapt (version 1.9, https://cutadapt.readthedocs.io/en/stable/), followed by quality verification of the sequences using FastQC.
RNA-seq reads from all samples were aligned to the <research species> reference genome using HISAT2 (version 2.0.4; https://daehwankimlab.github.io/hisat2/). Reads were mapped allowing up to two mismatches per read, and up to 20 multiple alignments per read (default HISAT2 settings). HISAT2 uses a graph-based index incorporating known and novel splice junctions to align spliced reads. Gene-level expression values were calculated and reported as FPKM. Raw FASTQ files are provided; raw read count matrices were not retained
Assembly: mm39
Supplementary files format and content: E12.5_mouse_RNAseq_FPKM_matrix.txt
Supplementary files format and content: E12.5_mouse_RNAseq_FPKM_matrix.txt contains FPKM values

source_name: Whole Placenta

growth_protocol: Pregnant C57BL/6 mice were provided ad libitum access to food between E1-E8.5. Beginning at E8.5 and continuing until tissue harvest, pregnant dams were divided into two groups as previously described.  Control dams continued to have ad libitum access to food.

extract_protocol:
Total RNA was extracted from mouse placenta samples (with intact decidua layer) using a bead homogenizer and Trizol LS reagent (ThermoFisher, 10-296-028) /chloroform method. RNA concentration was measured using the NanoDrop 2000c spectrophotometer (Thermofisher Scientific). If necessary, an RNA clean and concentrator kit (Zymo Research R1019) was used to remove any contaminating DNA, phenol, and concentrate samples to improve 260/280 (1.9-2.0) and 260/230 ratios (2.0-2.2).
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.

treatment_protocol: The FGR group received a 50% caloric restricted diet, which was calculated from a predetermined average ad libitum intake. This caloric restriction equated to approximately 1.5-2.0 grams of food provided daily

value: Whole Placenta

value: FGR


title: E12.5 Mouse Placenta FGR 6

description:
Library name: Sample 6
column name in E12.5_mouse_RNAseq_FPKM_matrix.txt:  FGR_6


title: E12.5 Mouse Placenta FGR 8

description:
Library name: Sample 8
column name in E12.5_mouse_RNAseq_FPKM_matrix.txt:  FGR_8


title: monoculture -  proliferation - sample 3

description:
Library name: s20065FL_07_01_03_CKDL240001621-1A_HJLL3CCX2_L6
01_03: 2: 0 : monoculture


title: E12.5 Mouse Placenta Control 3

description:
Library name: Sample 3
column name in E12.5_mouse_RNAseq_FPKM_matrix.txt:  Control_3


title: monoculture -  proliferation - sample 2

description:
Library name: s20065FL_07_01_02_CKDL240001621-1A_HJLL3CCX2_L6
01_02: 2: 0 : monoculture


title: monoculture - 72 h of differentiation - sample 3

description:
Library name: s20065FL_07_01_11_CKDL240001621-1A_HJLL3CCX2_L6
01_11 : 1: 72: monoculture


title: E12.5 Mouse Placenta FGR 10

description:
Library name: Sample 10
column name in E12.5_mouse_RNAseq_FPKM_matrix.txt:  FGR_10


title: monoculture - 72 h of differentiation - sample 2

description:
Library name: s20065FL_07_01_10_CKDL240001621-1A_HJLL3CCX2_L6
01_10 : 1: 72: monoculture


title: C57BL/6J, Lung, CD8, IPF-LC, CD4-depleted

city: Kashihara-shi

first: Toshihiro

last: Ito

state: Nara

address: 840, Shijocho

department: Immunology

institute: Nara Medical University

description: Library name: Sample 2

data_processing:
Adapter sequences and low-quality bases were removed using fastp (v0.23.4)
The trimmed reads were mapped to the mouse reference genome GRCm39 (mm39) using STAR (v2.7.11a)
Transcript abundance was quantified using RSEM (v1.3.3)
The quality of the sequence data and mapped data was checked using MultiQC (v1.25.2)
Assembly: GRCm39 (mm39)
Supplementary files format and content: tab-delimited text file including gene ID, transcript IDs, TPM and FPKM for each sample

source_name: Lung

extract_protocol:
CD8+ T cells were sorted as CD3+CD8+ cells from lungs. RNA was extracted using RNeasy Micro Kit (QIAGEN)
Extracted RNA was reverse-transcribed using a SMART-Seq v4 Ultra Low Input Kit (Takara-Bio) and RNA-seq libraries were prepared using a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs).

value: Lung

tag: model

value: IPF-LC

value: CD8+ T cells

value: anti CD4-depleting antibody


title: C57BL/6J, Lung, CD8, IPF-LC, control

description: Library name: Sample 1

value: isotype antibody


title: E12.5 Mouse Placenta Control 5

description:
Library name: Sample 5
column name in E12.5_mouse_RNAseq_FPKM_matrix.txt:  Control_5


title: monoculture -  proliferation - sample 1

description:
Library name: s20065FL_07_01_01_CKDL240001621-1A_HJLL3CCX2_L6
01_01: 2: 0 : monoculture


title: slide117A

description:
Library name: Sample 13
transverse spinal cord  section

data_processing:
Genome alignment by spaceranger-v1.3.0. Data normalization and clustering by Scanpy.
Assembly: mm10 2020-A
Supplementary files format and content: .h5-count matrix, .jpg-histology image, .csv-capture array coordinates
Library strategy: Spatial Transcriptomics

source_name: Lumbar spinal cord

extract_protocol:
Mouse spinal cord spatial transcriptomics was performed by Visium (10x Genomics). iSCI mice were perfused with ice-cold PBS with heparin at 3, 7, or 28 dpi, spinal cords dissected out and rostral and caudal blocks were rapidly embedded in OTC, snap frozen on dry ice and stored at - 80°C until sectioning. Visium slides were pre-chilled in a cryostat (Leica) for 30 minutes at the time of sectioning. Two 10um sections were taken from lesion-remote rostral (T9-T11) and caudal (L1-L3) blocks, equivalent to samples analyzed by snRNA-Seq. 4 tissue sections were placed onto each square, with uninjured on the top left, 3dpi on the top right, 7dpi on the bottom left, and 28dpi on the bottom right.
Samples were processed using the Visium Spatial Gene Expression Reagent Kit (10X Genomics) as per manufacturer’s established protocol. cDNA libraries were pooled in a NovaSeq6000 SP v1.0 flowcell and paired-end sequencing was performed on an Illumina NovaSeq6000 sequencer.

value: Lumbar spinal cord

value: NA - Tissue

value: uninjured/3/7/28 days post injury


title: slide117B

description:
Library name: Sample 14
transverse spinal cord  section

source_name: Thoracic spinal cord

value: Thoracic spinal cord


title: slide116D

description:
Library name: Sample 12
transverse spinal cord  section


title: E12.5 Mouse Placenta Control 4

description:
Library name: Sample 4
column name in E12.5_mouse_RNAseq_FPKM_matrix.txt:  Control_4

value: Control


title: slide115C

description:
Library name: Sample 7
transverse spinal cord  section


title: E12.5 Mouse Placenta FGR 7

description:
Library name: Sample 7
column name in E12.5_mouse_RNAseq_FPKM_matrix.txt:  FGR_7


title: slide116A

description:
Library name: Sample 9
transverse spinal cord  section


title: slide115A

description:
Library name: Sample 5
transverse spinal cord  section


title: monoculture - 72 h of differentiation - sample 1

description:
Library name: s20065FL_07_01_09_CKDL240001621-1A_HJLL3CCX2_L6
01_09 : 1: 72: monoculture

value: musculus longissimus dorsi

value: muscle satellite cell


title: C57BL/6J, Lung, CD8, LC, control

description: Library name: Sample 3

value: LC


title: C57BL/6J, Lung, CD8, LC, CD4-depleted

description: Library name: Sample 4


title: slide116B

description:
Library name: Sample 10
transverse spinal cord  section

value: WT


title: E12.5 Mouse Placenta Control 2

description:
Library name: Sample 2
column name in E12.5_mouse_RNAseq_FPKM_matrix.txt:  Control_2


title: slide117D

description:
Library name: Sample 16
transverse spinal cord  section


title: E12.5 Mouse Placenta Control 1

description:
Library name: Sample 1
column name in E12.5_mouse_RNAseq_FPKM_matrix.txt:  Control_1


title: slide114A

description:
Library name: Sample 1
transverse spinal cord  section


title: slide117C

description:
Library name: Sample 15
transverse spinal cord  section


title: slide115D

description:
Library name: Sample 8
transverse spinal cord  section


title: 7341-HA

description: Library name: Sample 195

data_processing:
data normalization and differential expression by EdgeR (v.3.28.0). Read counting by HT-seq (v.0.6.0). genome alignment by STAR aligner (v.2.4.0j).
Assembly: mm10
Supplementary files format and content: .cvs, Gene ID; Log2FC; raw and normalized read counts

source_name: spinal cord

extract_protocol:
In brief, WT(mGfap-cre-RiboTag) and Stat3cKO (mGfap-cre-Ribotag-Stat3-loxP) mice were perfused with ice-cold PBS with heparin and spinal cords were dissected out. 3 mm of spinal cord rostral (T9- T11) and caudal (L1-L3) to the lesion epicenter were then rapidly removed, snap-frozen in dry ice and stored at -80C until processing for RiboTag RNA-Seq. Spinal cords were collected at 3,7, 14 and 28 dpi and anatomically equivalent regions of spinal cord were isolated from age- and genotype-matched healthy controls.
Astrocyte RNA Integrity was analysed by a 2100 Bioanalyzer (Agilent) using the RNA Pico chip, RIN ≥ 8.9 for all samples. cDNA was generated from 10 ng of RNA using the Universal plus mRNA-Seq Kit (Nugen).

tag: spinal cord_region

value: thoracic

tag: sample class

value: HA

value: spinal cord

value: Tissue

value: mGFAP-Cre+ x RIboTag-Homo

value: Uninjured


title: slide115B

description:
Library name: Sample 6
transverse spinal cord  section


title: 7337-INP

description: Library name: Sample 194

value: input


title: slide114B

description:
Library name: Sample 2
transverse spinal cord  section


title: slide114D

description:
Library name: Sample 4
transverse spinal cord  section


title: 7337-HA

description: Library name: Sample 193


title: 7345-INP

description: Library name: Sample 198


title: 7202-INP

description: Library name: Sample 192

value: mGFAP-Cre+ x stat3lox/lox x RiboTag-homo


title: 7341-INP

description: Library name: Sample 196


title: slide114C

description:
Library name: Sample 3
transverse spinal cord  section


title: 7142-HA

description: Library name: Sample 189


title: 7142-INP

description: Library name: Sample 190


title: 7118-INP

description: Library name: Sample 184


title: 7202-HA

description: Library name: Sample 191


title: 7139-HA

description: Library name: Sample 185


title: slide116C

description:
Library name: Sample 11
transverse spinal cord  section

value: Lumbar spinal cord


title: 7141-INP

description: Library name: Sample 188


title: 7141-HA

description: Library name: Sample 187


title: 7117I-NP

description: Library name: Sample 182


title: 7118-HA

description: Library name: Sample 183


title: 6388R-INP

description: Library name: Sample 180

value: mGFAP-Cre+ x RiboTag-homo

value: 14 days post ISCI


title: 6388R-HA

description: Library name: Sample 179


title: 7345-HA

description: Library name: Sample 197


title: 6388C-INP

description: Library name: Sample 178

value: lumbar


title: 7139-INP

description: Library name: Sample 186


title: 6373R-INP

description: Library name: Sample 172

value: 3 days post ISCI


title: 6377C-INP

description: Library name: Sample 174


title: 6388C-HA

description: Library name: Sample 177


title: 6373C-INP

description: Library name: Sample 170


title: 6373R-HA

description: Library name: Sample 171


title: 6304C-INP

description: Library name: Sample 166

value: 7 days post ISCI


title: 6304R-HA

description: Library name: Sample 167


title: 5962R-HA

description: Library name: Sample 163


title: 5962R-INP

description: Library name: Sample 164


title: 6304R-INP

description: Library name: Sample 168


title: 6304C-HA

description: Library name: Sample 165


title: 5962C-HA

description: Library name: Sample 161


title: 6373C-HA

description: Library name: Sample 169


title: 7117-HA

description: Library name: Sample 181


title: 5962C-INP

description: Library name: Sample 162


title: 5960R-INP

description: Library name: Sample 160

value: 28 days post ISCI


title: 5959R-INP

description: Library name: Sample 156


title: 5959C-INP

description: Library name: Sample 154


title: 5959C-HA

description: Library name: Sample 153


title: 5960R-HA

description: Library name: Sample 159


title: 5960C-INP

description: Library name: Sample 158


title: 6377R-HA

description: Library name: Sample 175


title: 5959R-HA

description: Library name: Sample 155


title: 5960C-HA

description: Library name: Sample 157


title: 6377C-HA

description: Library name: Sample 173


title: 5955R-INP

description: Library name: Sample 144


title: 5956R-INP

description: Library name: Sample 148


title: 5957C-HA

description: Library name: Sample 149


title: 5957R-INP

description: Library name: Sample 152


title: 6377R-INP

description: Library name: Sample 176


title: 5957R-HA

description: Library name: Sample 151


title: 5956R-HA

description: Library name: Sample 147


title: 5955C-INP

description: Library name: Sample 142


title: 5955R-HA

description: Library name: Sample 143


title: 5957C-INP

description: Library name: Sample 150


title: 5956C-HA

description: Library name: Sample 145


title: 5956C-INP

description: Library name: Sample 146


title: 5955C-HA

description: Library name: Sample 141


title: 5947C-INP

description: Library name: Sample 138


title: 5947C-HA

description: Library name: Sample 137


title: 5947R-INP

description: Library name: Sample 140


title: 5947R-HA

description: Library name: Sample 139


title: 5917R-INP

description: Library name: Sample 132


title: 5919R-HA

description: Library name: Sample 135


title: 5917C-INP

description: Library name: Sample 130


title: 5919C-INP

description: Library name: Sample 134


title: 5919R-INP

description: Library name: Sample 136


title: 5917R-HA

description: Library name: Sample 131


title: 5914R-INP

description: Library name: Sample 128


title: 5914R-HA

description: Library name: Sample 127


title: 5914C-INP

description: Library name: Sample 126


title: 5913R-INP

description: Library name: Sample 124


title: 5913C-INP

description: Library name: Sample 122


title: 5913R-HA

description: Library name: Sample 123


title: 5913C-HA

description: Library name: Sample 121


title: 5917C-HA

description: Library name: Sample 129


title: 5919C-HA

description: Library name: Sample 133


title: 5909C-INP

description: Library name: Sample 118


title: 5909R-INP

description: Library name: Sample 120


title: 5907R-INP

description: Library name: Sample 112


title: 5909R-HA

description: Library name: Sample 119


title: 5905R-HA

description: Library name: Sample 107


title: 5907C-INP

description: Library name: Sample 110


title: 5903R-HA

description: Library name: Sample 103


title: 5909C-HA

description: Library name: Sample 117


title: 5903R-INP

description: Library name: Sample 104


title: 5905C-HA

description: Library name: Sample 105


title: 5907R-HA

description: Library name: Sample 111


title: 5903C-HA

description: Library name: Sample 101


title: 5908C-HA

description: Library name: Sample 113


title: 5902R-INP

description: Library name: Sample 100


title: 5908R-HA

description: Library name: Sample 115


title: 5914C-HA

description: Library name: Sample 125


title: 5907C-HA

description: Library name: Sample 109


title: 5902C-HA

description: Library name: Sample 97


title: 5908R-INP

description: Library name: Sample 116


title: 5705R-HA

description: Library name: Sample 95


title: 5908C-INP

description: Library name: Sample 114


title: 5705C-INP

description: Library name: Sample 94


title: 5699C-INP

description: Library name: Sample 90


title: 5705C-HA

description: Library name: Sample 93


title: 5705R-INP

description: Library name: Sample 96


title: 5905C-INP

description: Library name: Sample 106


title: 5905R-INP

description: Library name: Sample 108


title: 5902R-HA

description: Library name: Sample 99


title: 5699R-INP

description: Library name: Sample 92


title: 5699R-HA

description: Library name: Sample 91


title: 5686R-HA

description: Library name: Sample 79


title: 5467R-INP

description: Library name: Sample 76


title: 5687C-HA

description: Library name: Sample 81


title: 5687C-INP

description: Library name: Sample 82


title: 5686C-INP

description: Library name: Sample 78


title: 5698C-INP

description: Library name: Sample 86


title: 5698C-HA

description: Library name: Sample 85


title: 5448R-INP

description: Library name: Sample 72


title: 5687R-INP

description: Library name: Sample 84


title: 5687R-HA

description: Library name: Sample 83


title: 5698R-INP

description: Library name: Sample 88


title: 5448R-HA

description: Library name: Sample 71


title: 5448C-HA

description: Library name: Sample 69


title: 5467C-INP

description: Library name: Sample 74


title: 5448C-INP

description: Library name: Sample 70


title: 5698R-HA

description: Library name: Sample 87


title: 5375R-HA

description: Library name: Sample 63


title: 5902C-INP

description: Library name: Sample 98


title: 5375R-INP

description: Library name: Sample 64


title: 5699C-HA

description: Library name: Sample 89


title: 5447R-INP

description: Library name: Sample 68


title: 5447R-HA

description: Library name: Sample 67


title: 5686C-HA

description: Library name: Sample 77


title: 5375C-INP

description: Library name: Sample 62


title: 5240R-INP

description: Library name: Sample 56


title: 5686R-INP

description: Library name: Sample 80


title: 5447C-HA

description: Library name: Sample 65


title: 5242R-HA

description: Library name: Sample 59


title: 5242C-INP

description: Library name: Sample 58


title: 5242R-INP

description: Library name: Sample 60


title: 5242C-HA

description: Library name: Sample 57


title: 5375C-HA

description: Library name: Sample 61


title: 5169C-INP

description: Library name: Sample 50


title: 5447C-INP

description: Library name: Sample 66


title: 5467R-HA

description: Library name: Sample 75


title: 5088C-INP

description: Library name: Sample 42


title: 5240C-HA

description: Library name: Sample 53


title: 5088C-HA

description: Library name: Sample 41


title: 5168C-INP

description: Library name: Sample 46


title: 5240C-INP

description: Library name: Sample 54


title: 5169C-HA

description: Library name: Sample 49


title: 5088R-INP

description: Library name: Sample 44


title: 5085R-INP

description: Library name: Sample 40


title: 5169R-HA

description: Library name: Sample 51


title: 5085C-HA

description: Library name: Sample 37


title: 5467C-HA

description: Library name: Sample 73


title: 5070C-HA

description: Library name: Sample 33


title: 5169R-INP

description: Library name: Sample 52


title: 5168C-HA

description: Library name: Sample 45


title: 5085C-INP

description: Library name: Sample 38


title: 5240R-HA

description: Library name: Sample 55


title: 5070C-INP

description: Library name: Sample 34


title: 5088R-HA

description: Library name: Sample 43


title: 4999R-HA

description: Library name: Sample 31


title: 5085R-HA

description: Library name: Sample 39


title: 5168R-INP

description: Library name: Sample 48


title: 4998C-HA

description: Library name: Sample 25


title: 4999R-INP

description: Library name: Sample 32


title: 4999C-HA

description: Library name: Sample 29


title: 5903C-INP

description: Library name: Sample 102


title: 5070R-INP

description: Library name: Sample 36


title: 4998R-HA

description: Library name: Sample 27


title: 4815C-INP

description: Library name: Sample 22


title: 5168R-HA

description: Library name: Sample 47


title: 4998C-INP

description: Library name: Sample 26


title: 4815C-HA

description: Library name: Sample 21


title: 4814R-INP

description: Library name: Sample 20


title: 4998R-INP

description: Library name: Sample 28


title: 4814R-HA

description: Library name: Sample 19


title: 4815R-INP

description: Library name: Sample 24


title: 5070R-HA

description: Library name: Sample 35


title: 4999C-INP

description: Library name: Sample 30


title: 4815R-HA

description: Library name: Sample 23


title: 4813R-HA

description: Library name: Sample 15


title: 4813R-INP

description: Library name: Sample 16


title: 4796R-HA

description: Library name: Sample 7


title: con2

city: Jinan

first: Hongjie

last: Du

address: No. 324, Jingwu Road, Huaiyin District

department: Shandong Provincial Hospital

institute: Shandong First Medical University

description:
Library name: sample 2
control group, replicate biosample 2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DM 1-3 516 R44 (v6.1)  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes different expression gene for control samples and ECRSwNP samples

source_name: cell culture

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: cell culture

value: Epithelial cells


title: 4811C-HA

description: Library name: Sample 9


title: 4813C-HA

description: Library name: Sample 13


title: 4814C-HA

description: Library name: Sample 17


title: con3

description:
Library name: sample 3
control group, replicate biosample 3


title: ECRSwNP1

description:
Library name: sample 4
ECRSwNP group, replicate biosample 1


title: ECRSwNP3

description:
Library name: sample 6
ECRSwNP group, replicate biosample 3


title: 4796C-INP

description: Library name: Sample 6


title: 4814C-INP

description: Library name: Sample 18


title: 4811R-INP

description: Library name: Sample 12

value: thoracic


title: 4794R-INP

description: Library name: Sample 4


title: ECRSwNP2

description:
Library name: sample 5
ECRSwNP group, replicate biosample 2


title: 4813C-INP

description: Library name: Sample 14


title: 4811C-INP

description: Library name: Sample 10


title: T0322090-6_res

city: Okayama

first: Shuta

last: Tomida

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Center for Comprehensive Genomic Medicine

institute: Okayama University Hospital

description:
Library name: DSP-1001660021518-D-H05
FFPE sample Spatial transcriptome sequencing

data_processing:
FASTQ files for GeoMx were aggregated into count matrices using GeoMx NGS pipeline.
Hs_R_NGS_WTA_v1.0.zip file include probe information, which was used for transform from fastq to dcc.
Assembly: GRCh38
Supplementary files format and content: DCC files which contain raw read counts along with RTS_IDs (probe barcodes).
Library strategy: Spatial Transcriptomics

extract_protocol:
Formalin-fixed, paraffin-embedde (FFPE) tissues (5 µm) were baked at 60 °C for 30 min, deparaffinized, rehydrated, and processed using a Leica BOND Rx system according to the manufacturer’s protocol.
The GeoMx Human Whole Transcriptome Atlas Human RNA for Illumina Systems (GMX-RNA-NGSHuWTA-4) was used in this study. All tumor samples were processed and stained according to the manufacturer’s protocol. Single 5-μm formalin-fixed, paraffin-embedded (FFPE) tissue sections were deparaffinized and subjected to antigen retrieval procedures.

value: Lung

value: responder


title: 4811R-HA

description: Library name: Sample 11

value: HA

value: spinal cord

value: Tissue


title: T0326937-1_res

description:
Library name: DSP-1001660021595-E-A03
FFPE sample Spatial transcriptome sequencing


title: T0322090-5_res

description:
Library name: DSP-1001660021518-D-H03
FFPE sample Spatial transcriptome sequencing


title: T0326937-4_res

description:
Library name: DSP-1001660021595-E-A09
FFPE sample Spatial transcriptome sequencing


title: T0326937-2_res

description:
Library name: DSP-1001660021595-E-A05
FFPE sample Spatial transcriptome sequencing


title: 4796R-INP

description: Library name: Sample 8

value: input


title: 4796C-HA

description: Library name: Sample 5

value: mGFAP-Cre+ x stat3lox/lox x RiboTag-homo


title: T0326937-3_res

description:
Library name: DSP-1001660021595-E-A07
FFPE sample Spatial transcriptome sequencing


title: 4794C-INP

description: Library name: Sample 2


title: 4794R-HA

description: Library name: Sample 3


title: T0322090-2_res

description:
Library name: DSP-1001660021518-D-G09
FFPE sample Spatial transcriptome sequencing


title: T0322090-4_res

description:
Library name: DSP-1001660021518-D-H01
FFPE sample Spatial transcriptome sequencing


title: con1

description:
Library name: sample 1
control group, replicate biosample 1


title: 4794C-HA

description: Library name: Sample 1


title: T0290847-5_res

description:
Library name: DSP-1001660021518-D-F03
FFPE sample Spatial transcriptome sequencing

source_name: Abdominal wall

value: Abdominal wall


title: T0290847-1_res

description:
Library name: DSP-1001660021518-D-E08
FFPE sample Spatial transcriptome sequencing


title: Il33 Maintained

city: Philadelphia

first: Kang

last: Ko

state: Pennsylvania

address: 240 S. 40th Street

department: Department of Periodontics

institute: University of Pennsylvania

description:
Library name: Control
10x genomics

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were fabricated using cellranger-6.1.2 software
Assembly: mm10
Supplementary files format and content: tab separated matrix and value files

source_name: oral palate

extract_protocol:
Oral wound samples were collected after 2 d of healing as above, from bilateral sites such that control group had 14 wounds whereas experimental group had 16 wounds pooled together. Single cells were prepared as above and sorted on FACSAria II SORPinstrument such that 1-to-1 ratio of FSClow SSClow CD45+ DAPI- lymphoid cells and FSCmid-hi SSCmid-hi CD45+ DAPI- myeloid/granulocytes were collected prior to single cell barcode capture
library was prepared according to manufacturer's instrutions (Single Cell 3' v3)

treatment_protocol: tamoxifen injection (1 mg/ 25g daily for 5 days) or corn oil injection with oral wound induced with 1 mm^2 biopsy punch.

value: oral palate

value: CD45+ leukocytes

value: Corn Oil

value: batch 1


title: T0268363-7_res

description:
Library name: DSP-1001660021518-D-D04
FFPE sample Spatial transcriptome sequencing

source_name: Lymph node

value: Lymph node


title: T0268363-8_res

description:
Library name: DSP-1001660021518-D-D06
FFPE sample Spatial transcriptome sequencing


title: Pou3f4_KO_2

first: Jing

last: Cai

state: Shandong

address: 4 Duanxing West Road

department: Shandong Provincial ENT Hospital

institute: Shandong University

description:
Library name: Sample 5
Pou3f4_KO_2

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Assembly: mm10
Supplementary files format and content: tab-delimted files include read count for each sample

source_name: inner ear cells

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

value: inner ear cells

value: interstitial cells

value: all the cells

value: identify


title: Pou3f4_KO_3

description:
Library name: Sample 6
Pou3f4_KO_3


title: WT 2

description:
Library name: Sample 2
WT_2

value: WT


title: T0322090-1_res

description:
Library name: DSP-1001660021518-D-G07
FFPE sample Spatial transcriptome sequencing

value: Lung

value: responder


title: Pou3f4_KO_1

description:
Library name: Sample 4
Pou3f4_KO_1


title: T0322090-3_res

description:
Library name: DSP-1001660021518-D-G11
FFPE sample Spatial transcriptome sequencing


title: T0268363-1_res

description:
Library name: DSP-1001660021518-D-C06
FFPE sample Spatial transcriptome sequencing


title: AKPS P5 3d MRTX1133 mouse #32_rep4

city: South San Francisco

first: Robert

last: Piskol

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

description:
Library name: SAM24462142
EpCam+ cells sorted from AKPS P5 tumor treated for 3d MRTX1133 mouse #32_rep4

data_processing:
RNA-sequencing data were analyzed using HTSeqGenie in BioConductor as follows: first, reads with low nucleotide qualities (70% of bases with quality <23) or matches to rRNA and adapter sequences were removed. The remaining reads were aligned to the mouse reference genome (GRCm38.p5) using GSNAP version ‘2013-10-10-v2’, allowing maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap'). Transcript annotation was based on the Gencode genes database (mouse: GENCODE M15). To quantify gene expression levels, the number of reads mapping unambiguously to the exons of each gene was calculated.
Trimmed mean of M-values (TMM) normalization was performed on the read counts using the "edgeR" package (Robinson et al., 2010), then the normalized counts were transformed to log counts per million (log-CPM) values.
Differential expression analysis on the normalized and transformed count data was performed using the “limma” R package (Ritchie et al., 2015) by contrasting MRTX1133 treated samples respectively with vehicle samples.
Assembly: mouse genome (GRCm38)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes log-CPM values for each sample

source_name: Colon tumor

extract_protocol:
RNA from sorted tumor epithelial cells from in vivo colon tumors was extracted using the RNeasy Plus Micro kit (Qiagen, 74034 ) with on column DNAse digestion (Qiagen 12023460) according to manufacturer’s instructions
Total RNA was quantified with Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and quality was assessed using RNA ScreenTape on TapeStation 4200 (Agilent Technologies). For low-input RNA-sequencing library generation (2 nanograms), the cDNA library was using Smart-Seq V4 Ultra Low Input RNA Kit (Takara). 150 picograms of cDNA were used to make sequencing libraries by Nextera XT DNA Sample Preparation Kit (Illumina). Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on TapeStation 4200 (Agilent Technologies). Libraries were pooled and sequenced on NovaSeq 6000 (Illumina) to generate 30 million single-end 50-base pair reads for each sample.

value: Colon tumor

value: Epithelial cell

value: MRTX1133_3 days


title: WT 1

description:
Library name: Sample 1
WT_1


title: T0290847-4_res

description:
Library name: DSP-1001660021518-D-F01
FFPE sample Spatial transcriptome sequencing


title: T0290847-2_res

description:
Library name: DSP-1001660021518-D-E10
FFPE sample Spatial transcriptome sequencing


title: HFSC_Jun

city: Chicago

first: Rui

last: Yi

state: IL

address: 303 E. Chicago Ave

institute: Northwestern University

description: Library name: HFSC_Jun

data_processing:
Raw reads were aligned to mouse genome version mm10 using Bowtie2.
Peak calling were performed using MACS2 with  -f BAMPE option.
Assembly: mm10
Supplementary files format and content: MACS2 called narrow peaks
Supplementary files format and content: igvtools generated tdf file
Library strategy: Cut&Run

source_name: Back skin

extract_protocol:
Hair follicle stem cells were sorted from telogen mouse back skin with a regime of K14H2BGFP+/Cd34+/Itga6+/Sca-1-
Sorted cells were subject to Jun Cut&Run based protocol for genomic DNA pull down. Pull-downed DNA were constructed into sequencing library using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®.

value: Back skin

value: Hair follicle stem cells

value: epithelial cells

value: wild-type

value: No

tag: chip antibody

value: Jun


title: AKPS P5 16d MRTX1133 mouse #34_rep1

description:
Library name: SAM24462143
EpCam+ cells sorted from AKPS P5 tumor treated for 16d MRTX1133 mouse #34_rep1

tag: tissue

value: MRTX1133_16 days


title: WT 3

description:
Library name: Sample 3
WT_3

value: inner ear cells

tag: cell type


title: T0268363-3_res

description:
Library name: DSP-1001660021518-D-C10
FFPE sample Spatial transcriptome sequencing

value: Lymph node


title: T0268363-9_res

description:
Library name: DSP-1001660021518-D-D08
FFPE sample Spatial transcriptome sequencing


title: AKPS P5 16d MRTX1133 mouse #40_rep4

description:
Library name: SAM24462146
EpCam+ cells sorted from AKPS P5 tumor treated for 16d MRTX1133 mouse #40_rep4


title: AKPS P5 3d MRTX1133 mouse #27_rep1

description:
Library name: SAM24462139
EpCam+ cells sorted from AKPS P5 tumor treated for 3d MRTX1133 mouse #27_rep1


title: T0268363-6_res

description:
Library name: DSP-1001660021518-D-D02
FFPE sample Spatial transcriptome sequencing


title: T0330339-01_non-res

description:
Library name: DSP-1001660021595-E-B02
FFPE sample Spatial transcriptome sequencing

value: non-responder


title: T0330339-04_non-res

description:
Library name: DSP-1001660021595-E-B08
FFPE sample Spatial transcriptome sequencing