title: HIC-library of CNG

city: Wuhan

first: Xiaojian

last: Cao

state: Hubei

address: No.1095 Jiefang Avenue

department: Department of Rehabilination Medicne

institute: Tongji Hospital

description: Library name: CNG

data_processing:
The Hic data was pre-processed by DLO-Hic tools[24], which produced the Hic Matrix. The TADs were calculated by HicFindTADs function of the hicexplorer[25]. The code for calculating the ratio of conserved, shifted, fused and separated TAD is developed and available at https://github.com/MSN-06s/TAD-ssf. The loop was calculated by hiccups function of juicertools[26]. PCA of the Hi-C data were calculated by hicPCA function of hicexplorer. Differential TAD were processed with hicDifferentialTADs function of hicexplorer, diffential Loop were processed with hiccupsdiff function of juicertools. The annotation of region file (TAD boundaries and loop anchors) wasonducted by chipseeker[27]. The motif discovery and visualization were done by Homer[28]. The matrix and region visualization were conducted by hicPlotMaxtrix and hicPlotTAD function of hicexplorer.
Assembly: hg19
Supplementary files format and content: mcool(multi-resolution HIC matrix)

growth_protocol: C2C12 Cells (mouse myoblast) were purchased from ATCC. Cells in DMEM (Gibco, Thermo Fisher Scientific Inc., USA) supplemented with antibiotics and 10% fetal bovine serum (FBS) were cultured in a 5% CO2 incubator at 37 °C. The medium was changed every 48 h, and cells could be digested and passaged when reaching 70%~80% confluency. Cells were plated 18 h before being placed under altered gravity conditions.

extract_protocol:
The DLO-Hic library was constructed following the protocol described in the previous study (Lin, D., P. Hong, S. Zhang, et al., Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture[J]. Nat Genet, 2018.50(5): 754-763)
The DLO-Hic library was constructed following the protocol described in the previous study (Lin, D., P. Hong, S. Zhang, et al., Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture[J]. Nat Genet, 2018.50(5): 754-763)

treatment_protocol: Two-dimensional (2D) clinostat developed and provided by China Astronaut Research and Training Center (CARTC) were utilized to simulate microgravity (MG). Myoblasts were incubated in 25 cm2 cell culture flasks with a concentration of 2×105 cells per flask filled with culture medium. To avoid the influence of shear stress, all culture flasks were filled with medium to eliminate air bubbles and hermetically closed during rotation. Cell samples in SMG group were randomly selected to be cultured in a clinostat, which were rotated around a horizontal axis at a speed of 30 rpm leading to randomization of the gravitational vector, equivalent to the gravity level of low earth orbit (about 10-2 g). Cells in control group were placed in the clinostat with identical culture environment but under 1 g normal gravity. 2D clinostat has been reported and described previously. After intervention, cells in flasks were dissociated with Trypsin for further assessments.

value: normal gravity


title: Colon, Day 0, replicate 3

status: Public on Apr 28 2026

type: SRA

city: Stockholm

first: Jennifer

last: Fransson

address: Karolinska Institutet

country: Sweden

institute: Karolinska Institutet

description:
D0dcRH5
Rag2_counts.tsv
Rag2_tpm.csv

library_source: transcriptomic

data_processing:
Read quality was inspected using FastQC and further processed for abundance estimation using Kallisto.
Read abundances and TPM values estimated with Kallisto were compiled into gene expression matrices and processed separately for each genotype.
Assembly: mm10
Supplementary files format and content: .csv-files with count and TPM matrices

molecule: polyA RNA

organism: Mus musculus

source_name: colon

extract_protocol:
Tissue biopsies (approximately 0.5 cm long) were collected from the distal colon and stored at -80°C in RNAlater (Invitrogen). To extract RNA, tissue was lysed in RLT Plus Buffer (QIAGEN) + 2% b-mercaptoethanol by bead-beating (Precellys). RNA was isolated with the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer's instructions and quantified using a Nanodrop spectrophotometer (ThermoFisher).
cDNA libraries were constructed by Novogene Co. Ltd (UK).
cDNA libraries were sequenced by Novogene Co. Ltd (UK) at a sequencing depth of 20 million reads per sample using paired-end 150 bp reads on a NovaSeq 6000 sequencer with a v1.0 reagent kit. Samples were sequenced using paired-end 150bp sequencing, aiming at a coverage of 20M reads.

tag: tissue

value: colon

tag: genotype

value: Rag2 KO

tag: treatment

value: CD45RBhi transfer

tag: time

tag: agent

tag: rin

tag: cage

value: H

tag: lipocalin feces_ng_g

tag: histological colitis_score


title: Colon, Day 0, replicate 1

description:
D0dcRH3
Rag2_counts.tsv
Rag2_tpm.csv


title: Colon, Day 0, replicate 2

description:
D0dcRH4
Rag2_counts.tsv
Rag2_tpm.csv


title: OE21 cells, STM3675, 24 h, rep1

city: Cambridge

first: Harry

last: Fischl

address: Babraham Research Campus

country: United Kingdom

institute: Storm Therapeutics

description:
Library name: OE21_STM3675_24h_rep1
rRNA depleted total RNA-seq

data_processing:
Unique molecular identifiers (UMIs) were extracted from single-end RNA-seq fastq files. Fastq files were then trimmed of adapters using cutadapt (Martin, 2011) according to Lexogen’s recommendations and aligned to the human GRCh38 genome using the STAR aligner (Dobin et al., 2013). Bam files were deduplicated using UMI tools (Smith et al., 2017) (--method=unique). Normalised bigwig tracks were generated by dividing the signal at each nucleotide by the total genome signal and multiplying by 1 billion.
Assembly: GRCh38
Supplementary files format and content: .bw files show normalized signal for positive and negative strands

molecule: total RNA

organism: Homo sapiens

extract_protocol:
RNA was extracted using Trizol according to the manufacturer's instructions
RNA was generated into RNA-seq libraries by Lexogen using Ribocop rRNA-depletion and CORALL Total RNA-seq library generation and sequenced to a depth of greater than 100 million SE100 reads.

treatment_protocol: A549, CAOV3, COV644, EFO21, OE21 and SKOV3 treated with DMSO and CAOV3 cells treated with 1 uM STM3675 for 24h

tag: cell line

tag: cell type

value: Oesophageal carcinoma


title: CUT-Tag_L-GMP_WT_DEK_3

city: Chongqing

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

country: China

institute: Chongqing Medical University

description: Library name: Sample5

library_source: genomic

data_processing:
The quality control of each sample was accomplished using FASTQC V0.11.5.
Clean reads were aligned to mouse reference genome (mm10) using Bowtie 2 version 2.2.9. MarkDuplicates was used to mark PCR duplicate and unmapped reads. Only unique mapped reads were used in further analysis.
Peak calling and annotation were performed using MACS2 and ChIPseeker package, respectively.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: Bone marrow

extract_protocol:
The CUT&Tag assay was performed using NovoNGS CUT&Tag 3.0 High-Sensitivity Kit (Novoprotein) according to the manufacturer’s protocol. 5,000-10,000 cells were harvested and resuspended in 45 µL wash buffer. Then 6 µL ConA beads were added to the sample and incubated at 37°C for 10 min. Then the supernatant was removed by magnet adsorption and the beads were resuspended in 50 µL antibody buffer (20 mM Hepes, pH 7.5, 150 mM Nacl, 0.5 mM Spermidine, 0.0125% Digitonin, 2 mM EDTA, 0.1% BSA, 1× PIC).
Then, 0.5 µL antibody was added to the sample and incubated at 4°C overnight. The supernatant was removed by magnet adsorption and the beads were resuspended in 50 µL secondary antibody buffer, containing 0.5 µL goat anti-rabbit IgG antibody. After incubation at 37°C for 60 min, the beads were resuspended in 50 µL ChiTag Buffer, containing 0.5 µL ChiTag transposome. After incubation at 37°C for 60 min, the beads were resuspended in 50 µL tagmentation buffer. Then, 1 µL 10% SDS was added to the sample and incubated at 55°C for 10 min, and DNA was extracted using 2×DNA clean beads (Vazyme) and amplified with i5 and i7 primers (Vazyme) by 17-20 PCR cycles. The libraries were purified by 1.2×DNA clean beads (Vazyme).

treatment_protocol: L-GMPs(Lin-Sca-1-c-Kit+CD16/32+CD34+) from MLL-AF9-driven Dek+/+, Dekfl/fl;Tie-Cre (Dek-cKO) and Dek-Ser306A/Ser308A/Ser311A/Ser312A(4S-A) AML mice were sorted, followed by DEK- and GABPA-CUT-Tag-seq. L-GMPs from MLL-AF9-driven Dekfl/fl and Dek-cKO AML mice were sorted, followed by PBX3-CUT-Tag-seq.

value: Bone marrow

value: Leukemia stem cell

value: Dek+/+


title: HIC-library of SMG

description: Library name: SMG

value: simulated gravity


title: EFO21 cells, STM3675, 24 h, rep1

description:
Library name: EFO21_STM3675_24h_rep1
rRNA depleted total RNA-seq

value: Ovarian carcinoma


title: CUT-Tag_L-GMP_KO_PBX3_2

description: Library name: Sample4


title: OE21 cells, DMSO, 24 h, rep2

description:
Library name: OE21_DMSO_24h_rep2
rRNA depleted total RNA-seq

value: DMSO 24h


title: CUT-Tag_L-GMP_FL_PBX3_2

description: Library name: Sample2

value: Dekfl/fl


title: CUT-Tag_L-GMP_KO_DEK_2

description: Library name: Sample7


title: OE21 cells, DMSO, 24 h, rep1

description:
Library name: OE21_DMSO_24h_rep1
rRNA depleted total RNA-seq


title: ATAC_L-GMP_4S-A_1

description: Library name: Sample3

data_processing:
Low-quality reads and adaptor sequences were removed by Trim Galore v0.4.4 with parameters “-q 10 -length 30 -stringency 5’.”
Paired-end reads were mapped to the mm10 reference genome using Bowtie2 version 2.2.9. Reads that aligned to the mitochondrial genome were filtered, and PCR duplicates were removed with picard MarkDuplicates.
To identify peaks, the bam files containing unique, nonchrM reads were used to call peaks with MACS2 using parameters ‘‘-nomodel-keep-dup all -q 0.01-shift -100-extsize 200-call-summits -g mm’’.
For differential coverage, corresponding bam files were merged to call peaks to get a union peak set. For each peak in the peak set, raw ATACseq reads were counted by featureCounts.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

extract_protocol:
About 5,000 cells were resuspended in 50 µL of lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween 20, 0.01% Digitonin) and incubated on ice for 5 min. After lysis, 950 µL wash buffer was added to the sample. The supernatant was removed by centrifugation (500 g, 10 min).
Then, 4 µLPBS, 0.4 µL 10% Tween 20, 0.4 µL 1% Digitonin, 13.6 µL ddH2O, 20 µl 2×TD buffer, and 1.6 µL Transposome Mix were added to the sample, which was mixed and incubated at 37°C for 30 min. The reaction was terminated by incubating with 10 µL stop buffer. Then the tagment DNA was extracted using 2×DNA Extract Beads (Novoprotein). Total 35 µL DNA was transferred to a 0.2 ml PCR tube, and 2.5 µL N5 primer, 2.5 µL N7 primer, and 10 µL 5×AmpliMix were added. PCR was performed to amplify the library for 13-16 cycles. After the PCR reaction, libraries were purified using the 1.2×DNA Clean Beads (Novoprotein).

treatment_protocol: L-GMPs(Lin-Sca-1-c-Kit+CD16/32+CD34+) from MLL-AF9-driven Dek+/+, Dekfl/fl;Tie2-Cre (Dek-cKO) and Dek-Ser306A/Ser308A/Ser311A/Ser312A(4S-A) AML mice were sorted, followed by ATAC-seq.


title: CUT-Tag_L-GMP_FL_PBX3_1

description: Library name: Sample1


title: EFO21 cells, DMSO, 24 h, rep2

description:
Library name: EFO21_DMSO_24h_rep2
rRNA depleted total RNA-seq


title: EFO21 cells, DMSO, 24 h, rep1

description:
Library name: EFO21_DMSO_24h_rep1
rRNA depleted total RNA-seq


title: CUT-Tag_L-GMP_KO_PBX3_1

description: Library name: Sample3


title: EFO21 cells, DMSO, 24 h, rep3

description:
Library name: EFO21_DMSO_24h_rep3
rRNA depleted total RNA-seq


title: snRNA-seq mouse brain pooled run L003

city: New York

first: Lindsey

last: Starr

state: NY

country: USA

institute: Columbia University

description: Library name: FMRP_L003

data_processing:
Raw BCL files were converted to FASTQ format using bcl2fastq without sample demultiplexing, resulting in pooled FASTQ files labeled as "Undetermined".
Sequencing reads were processed using the inDrops computational pipeline.
Reads were assigned to individual libraries based on index sequences specified in the YAML file
Filtering, barcode identification, and read sorting were performed using indrops.py.
Reads were aligned to the mouse reference genome and quantified at the gene level  to generate count matrices.
Assembly: mm10
Supplementary files format and content: count

molecule: nuclear RNA

source_name: brain

growth_protocol: Mouse brain tissue was collected from wild-type (WT) and Fmr1 knockout (KO) mice at postnatal day 7 under standard housing conditions.

extract_protocol:
Nuclei were isolated from mouse brain tissue using mechanical dissociation and filtration. Isolated nuclei were resuspended in buffer for downstream single-nucleus RNA sequencing.
Single-nucleus RNA-seq libraries were generated using the inDrops platform. Individual nuclei were encapsulated into droplets and barcoded using hydrogel beads. Reverse transcription was performed within droplets, followed by cDNA amplification and library preparation for Illumina sequencing.

treatment_protocol: No treatment applied.

value: brain


title: EFO21 cells, STM3675, 24 h, rep2

description:
Library name: EFO21_STM3675_24h_rep2
rRNA depleted total RNA-seq


title: snRNA-seq mouse brain pooled run L004

description: Library name: FMRP_L004


title: COV644 cells, STM3675, 24 h, rep2

description:
Library name: COV644_STM3675_24h_rep2
rRNA depleted total RNA-seq


title: COV644 cells, DMSO, 24 h, rep1

description:
Library name: COV644_DMSO_24h_rep1
rRNA depleted total RNA-seq


title: COV644 cells, DMSO, 24 h, rep3

description:
Library name: COV644_DMSO_24h_rep3
rRNA depleted total RNA-seq


title: ATAC_L-GMP_FL_3

description: Library name: Sample1


title: EFO21 cells, STM3675, 24 h, rep3

description:
Library name: EFO21_STM3675_24h_rep3
rRNA depleted total RNA-seq


title: COV644 cells, STM3675, 24 h, rep3

description:
Library name: COV644_STM3675_24h_rep3
rRNA depleted total RNA-seq


title: snRNA-seq mouse brain pooled run L001

description: Library name: FMRP_L001


title: ATAC_L-GMP_KO_3

description: Library name: Sample2


title: COV644 cells, STM3675, 24 h, rep1

description:
Library name: COV644_STM3675_24h_rep1
rRNA depleted total RNA-seq


title: COV644 cells, DMSO, 24 h, rep2

description:
Library name: COV644_DMSO_24h_rep2
rRNA depleted total RNA-seq


title: CAOV3 cells, STM3675, 24 h, rep3

description:
Library name: CAOV3_STM3675_24h_rep3
rRNA depleted total RNA-seq


title: snRNA-seq mouse brain pooled run L002

description: Library name: FMRP_L002


title: ATAC_L-GMP_4S-A_2

description: Library name: Sample4


title: Lung tissues colleceted from hDPP4 mouse3 infected with XBB.1.9.1 variant at dpi7

city: ChongQing

first: Yu

last: Zhang

address: Gaotan Street

institute: Army Medical University

description: Library name: M12

data_processing:
Raw data of fastq format were firstly processed through fastp software (v0.19.6) to obtain clean reads by removing contaminated reads for adapters and low-quality reads. Clean reads were aligned to the mouse genome (Mus_musculus GRCm38) using Hisat2 (v2.0.5). The number of reads mapped to each gene in each sample was counted by featureCounts software (v2.0.6) and then calculated to estimate the expression level of genes in each sample.
Assembly: mm10
Supplementary files format and content: raw counts for each Sample

source_name: lung

extract_protocol:
Lung tissue (~1 mg) from mice of hDPP4-KI_Delta and hDPP4-KI_XBB191 groups were collected for RNA extraction. The RNA quality was assessed using the 5300 Bioanalyser (Agilent) and quantified using the NanoDrop® ND-2000 spectrophotometer (Thermo Scientific Inc.). A total amount of 1 μg high-quality RNA was used to prepare the sequencing libraries.
RNA libraries for RNA-seq were prepared using the Illumina® Stranded mRNA Prep, Ligation Kit following manufacturer's protocols.

value: lung

tag: mouse

tag: sars-cov-2 variants

tag: day post_infecion

tag: sample group

value: hDPP4 mouse infected with XBB.1.9.1 variant at dpi7


title: CAOV3 cells, STM3675, 24 h, rep1

description:
Library name: CAOV3_STM3675_24h_rep1
rRNA depleted total RNA-seq


title: CAOV3 cells, STM3675, 24 h, rep2

description:
Library name: CAOV3_STM3675_24h_rep2
rRNA depleted total RNA-seq


title: Lung tissues colleceted from hDPP4 mouse2 infected with XBB.1.9.1 variant at dpi7

description: Library name: M11


title: Lung tissues colleceted from hDPP4 mouse1 infected with XBB.1.9.1 variant at dpi7

description: Library name: M10


title: CAOV3 cells, DMSO, 24 h, rep3

description:
Library name: CAOV3_DMSO_24h_rep3
rRNA depleted total RNA-seq


title: Lung tissues colleceted from hDPP4 mouse1 infected with XBB.1.9.1 variant at dpi5

description: Library name: M7

value: hDPP4 mouse infected with XBB.1.9.1 variant at dpi5


title: A549 cells, STM3675, 24 h, rep3

description:
Library name: A549_STM3675_24h_rep3
rRNA depleted total RNA-seq

value: Lung carcinoma


title: CAOV3 cells, DMSO, 24 h, rep1

description:
Library name: CAOV3_DMSO_24h_rep1
rRNA depleted total RNA-seq


title: Lung tissues colleceted from hDPP4 mouse3 infected with XBB.1.9.1 variant at dpi3

description: Library name: M6

value: hDPP4 mouse infected with XBB.1.9.1 variant at dpi3


title: Lung tissues colleceted from hDPP4 mouse2 infected with XBB.1.9.1 variant at dpi5

description: Library name: M8


title: A549 cells, STM3675, 24 h, rep2

description:
Library name: A549_STM3675_24h_rep2
rRNA depleted total RNA-seq


title: Lung tissues colleceted from hDPP4 mouse3 infected with XBB.1.9.1 variant at dpi5

description: Library name: M9


title: Lung tissues colleceted from hDPP4 mouse3 infected with Delta variant at dpi7

description: Library name: L12

value: Delta

value: hDPP4 mouse infected with Delta variant at dpi7


title: CUT-Tag_L-GMP_KO_DEK_1

description: Library name: Sample6


title: A549 cells, DMSO, 24 h, rep2

description:
Library name: A549_DMSO_24h_rep2
rRNA depleted total RNA-seq


title: A549 cells, DMSO, 24 h, rep3

description:
Library name: A549_DMSO_24h_rep3
rRNA depleted total RNA-seq


title: Lung tissues colleceted from hDPP4 mouse2 infected with XBB.1.9.1 variant at dpi3

description: Library name: M5


title: KO3

city: Shanghai

first: Tonglin

last: Pan

address: No. 12, Middle Urumqi Road, Jing'an District

institute: Fudan university affiliated Huashan hospital

description: Library name: Sample6

data_processing:
Raw reads were processed using the IsoSeq pipeline: Circular consensus sequences were generated, followed by primer removal, read classification, and clustering to obtain full-length non-chimeric reads. FLNC reads were then mapped to the reference genome using minimap. Transcripts were assembled and quantified using SQANTI3.
Assembly: GRCr8 (aka mRatBN7.2, GCF_036323735.1)
Supplementary files format and content: gene.counts.matrix.txt: The file contains raw counts for each sample

organism: Rattus norvegicus

source_name: abdominal aorta EC

growth_protocol: The resultant cells were plated on fibronectin-coated plates in endothelial cell medium (ECM, ScienCell, San Diego, CA) and cultured at 37 °C/5 % CO₂; medium was replenished twice weekly.

extract_protocol:
To extract total RNA from primary ECs, the R6834 Total RNA Kit was used. Cells were lysed in TRK Lysis Buffer containing 20µl β-mercaptoethanol, followed by centrifugation to remove insoluble debris. The supernatant was mixed with an equal volume of 70% ethanol and applied to an RNA binding column. After washing, RNA was eluted in Nuclease-free Water. The RNA quality was assessed using Nanodrop, Qubit, gel electrophoresis, or Agilent 2100.
For full-length transcriptome library construction, 500ng of high-quality total RNA was used for reverse transcription, low-cycle PCR amplification of full-length cDNA, followed by purification with AMPure beads.

treatment_protocol: Cultured endothelial cells (ECs) were transfected with 100 nM hsa-miR-337-3p inhibitor.

value: abdominal aorta EC

value: Primary rat abdominal aortic endothelial cells

value: Endothelium

value: miR-337-3p knockdown


title: A549 cells, DMSO, 24 h, rep1

description:
Library name: A549_DMSO_24h_rep1
rRNA depleted total RNA-seq


title: Lung tissues colleceted from hDPP4 mouse3 infected with Delta variant at dpi5

description: Library name: L9

value: hDPP4 mouse infected with Delta variant at dpi5


title: Lung tissues colleceted from hDPP4 mouse1 infected with XBB.1.9.1 variant at dpi3

description: Library name: M4


title: KO2

description: Library name: Sample5


title: Lung tissues colleceted from hDPP4 mouse2 infected with Delta variant at dpi5

description: Library name: L8


title: CAOV3 cells, DMSO, 24 h, rep2

description:
Library name: CAOV3_DMSO_24h_rep2
rRNA depleted total RNA-seq


title: KO1

description: Library name: Sample4


title: Lung tissues colleceted from hDPP4 mouse1 infected with Delta variant at dpi7

description: Library name: L10


title: Lung tissues colleceted from hDPP4 mouse2 infected with Delta variant at dpi7

description: Library name: L11


title: WT3

description: Library name: Sample3

value: WT


title: A549 cells, STM3675, 24 h, rep1

description:
Library name: A549_STM3675_24h_rep1
rRNA depleted total RNA-seq


title: Lung tissues colleceted from hDPP4 mouse1 infected with Delta variant at dpi5

description: Library name: L7


title: Lung tissues colleceted from hDPP4 mouse3 at dpi0

description: Library name: M2

value: PBS

value: hDPP4 mouse at dpi0


title: WT1

description: Library name: Sample1


title: Lung tissues colleceted from hDPP4 mouse2 infected with Delta variant at dpi3

description: Library name: L5

value: hDPP4 mouse infected with Delta variant at dpi3


title: Thy1p_T_96_2

city: Oxford

first: Sarah

last: Davidson

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

institute: University of Oxford

description:
Library name: CD34nThy1p_donor_3_rep2_TNF_IL1B
Column name in raw_counts: CD34nThy1p_T_96_2

data_processing:
Reads were processed using an in-house pipeline incorporating Trim Galore (v0.6.6 with default paramaters, quality score <20)  for adapter trimming and quality control, STAR62 for genome alignment (v2.7.3a,  spliced-alignment mode against the GRCh38 reference genome using Ensembl release 101) and featureCounts (v2.0.1) for read summarisation and count generation.
Assembly: GRCh38.101
Supplementary files format and content: Tab-separated values (TSV) file of raw counts, column names are sample names
Supplementary files format and content: Tab-separated values (TSV) file of sample meta data, row names are sample names

source_name: Foetal finger joint tissue

growth_protocol: Embryonic fibroblast populations were isolated from foetal fingers of n=3 independent donors (16-17pcw). Foetal material was provided by the Joint MRC/Wellcome Trust (grant# MR/X008304/1 and 226202/Z/22/Z) Human Developmental Biology Resource (www.hdbr.org). Skin was removed, leaving all tendon, ligaments, capsule and synovium intact, and DIP and PIP joints were excised and pooled for each donor individually. Tissue was enzymatically digested (0.1mg/ml of liberaseTL) in DMEM, at 37oC for 1h 30mins. Supernatant containing released cells was collected every 10-15 mins, and fresh enzyme applied to continue sample digestion. After digestion, the remaining tissue was manually dissociated, combined with collected supernatants and passed through a 70um filter. Once single cell suspensions were collected, cells were incubated with FC block (1:100) and a live/dead stain (Near-IR fluorescent reactive dye, 1:1000, Invitrogen, L10119A) in PBS for 20 mins at RT. After washing with PBS, cells were stained with antibodies in PBS 1% BSA for 20mins at 4°C and washed (PBS 1% BSA), before further filtering through 70um strainers. CD45-CD31-PDPN+ fibroblast populations were sorted into Thy1+CD34+ and Thy1+CD34- using the FACs Aria III (BD bioscience) and collected in neat FBS. Single cell suspensions were resuspended in DMEM + 4.5g/L Glucose and L-glutamine (11995-065), supplemented with penstrep and 10% FBS and cultured at 37oC in 5%CO2. After 24hs, cultures were washed with PBS and fresh media was applied to remove nonadherent cells.

extract_protocol:
Cells were lysed in RLT buffer (Qiagen) and RNA was extracted using Qiagen micro-kit, (74004).
RNA samples were shipped to Novogene (UK) for library preparation and paired-end sequencing on the Illumina PE150 platform.

treatment_protocol: After 1 or 2 passages, cells were stimulated +/- TNF (10ng/ml) and IL1b (1ng/ml) for 24h

value: Foetal finger joint tissue

value: Primary fibroblasts

value: fibroblasts


title: Lung tissues colleceted from hDPP4 mouse1 at dpi0

description: Library name: L1

value: lung


title: Thy1p_T_952b

description:
Library name: CD34nThy1p_donor_2_rep2_TNF_IL1B
Column name in raw_counts: CD34nThy1p_T_952b


title: Lung tissues colleceted from hDPP4 mouse1 infected with Delta variant at dpi3

description: Library name: L4


title: WT2

description: Library name: Sample2


title: Thy1p_T_61_2

description:
Library name: CD34nThy1p_donor_1_rep2_TNF_IL1B
Column name in raw_counts: CD34nThy1p_T_61_2


title: Lung tissues colleceted from hDPP4 mouse3 infected with Delta variant at dpi3

description: Library name: L6


title: Thy1p_T_95_1

description:
Library name: CD34nThy1p_donor_2_rep1_TNF_IL1B
Column name in raw_counts: CD34nThy1p_T_95_1


title: Lung tissues colleceted from hDPP4 mouse2 at dpi0

description: Library name: M1


title: SNI+Transplant1

city: University of Sydney

first: Lipin

last: Loo

state: New South Wales

address: CHARLES PERKINS CENTRE D-17,

department: Charles Perkins Centre and School of Life & Environmental Sciences

country: Australia

institute: The University of Sydney

description:
Library name: sample 7
10X Genomics

library_source: transcriptomic single cell

data_processing:
10X Genomics raw sequencing data were processed using Cell Ranger (v7.1.0) with default parameters for alignment to the mouse reference genome (mm10).
Assembly: mm10
Supplementary files format and content: tab-separated value files and matrix files

source_name: Lumbar spinal cord

extract_protocol:
At day-28 post-surgery, nuclei were extracted using the detergent-based chemical lysis method from PMC8964935 using 0.5% Triton X-100, RNase inhibitors, and DTT to disrupt cell membranes and preserve RNA in the nuclei. These nuclei were stained with NeuN and Hoecsht before FANS.
Following FANS, nuclei were counted and  assessed using trypan blue inclusion.. Approximately 25,000 nuclei for each condition Sham, SNI and SNI+Transplant (3 biological replicates for Sham/SNI, 2 for Tranplant; all males) were captured in the 10X Genomics Chromium Controller using the Single Cell 3’ Gene Expression kit (v3.1). Gel bead-in-emulsion (GEM) generation, reverse transcription, and cDNA amplification were performed according to the manufacturer’s protocol. Libraries were constructed with their respective library preparation kits and quantified by Bioanalyzer. Sequencing was performed on an Illumina NovaSeq 6000 platform to achieve a minimum depth of ~60,000 reads per cell.

value: Lumbar spinal cord

value: Neurons  and non-neuronal nuclei

value: SNI+Transplant

tag: batch


title: Thy1p_T_61_1

description:
Library name: CD34nThy1p_donor_1_rep1_TNF_IL1B
Column name in raw_counts: CD34nThy1p_T_61_1


title: SNI+Transplant2

description:
Library name: sample 8
10X Genomics


title: Thy1p_T_961b

description:
Library name: CD34nThy1p_donor_3_rep1_TNF_IL1B
Column name in raw_counts: CD34nThy1p_T_961b


title: SNI3

description:
Library name: sample 6
10X Genomics

value: SNI


title: Thy1p_96_1

description:
Library name: CD34nThy1p_donor_3_rep1
Column name in raw_counts: CD34nThy1p_96_1

value: Control


title: SNI2

description:
Library name: sample 5
10X Genomics


title: Thy1p_95_1

description:
Library name: CD34nThy1p_donor_2_rep1
Column name in raw_counts: CD34nThy1p_95_1


title: Thy1p_96_2b

description:
Library name: CD34nThy1p_donor_3_rep2
Column name in raw_counts: CD34nThy1p_96_2b


title: Sham3

description:
Library name: sample 3
10X Genomics

value: Sham


title: Thy1p_61_1

description:
Library name: CD34nThy1p_donor_1_rep1
Column name in raw_counts: CD34nThy1p_61_1


title: Sham2

description:
Library name: sample 2
10X Genomics


title: CD34p_T_96_2

description:
Library name: CD34pThy1p_donor_3_rep2_TNF_IL1B
Column name in raw_counts: CD34pThy1p_T_96_2


title: SNI1

description:
Library name: sample 4
10X Genomics


title: AstroCSF1KO_SCI_4

city: Lexington

first: Meifan

state: Kentucky

address: 741 S. Limestone St, BBSRB B457

department: SCoBIRC

institute: University of Kentucky

description: Library name: AstroCSF1KO_SCI_4

data_processing:
Raw sequencing data were generated using Illumina platforms and processed by CASAVA (v1.8) for base calling. Low-quality reads were filtered by removing adapter-contaminated reads, reads with >10% Ns, and reads with >50% bases of Q<5. Clean reads were aligned to the reference genome using HISAT2, and gene expression levels were quantified using FPKM.
Assembly: mm39
Supplementary files format and content: xlsx file containing FPKM for all samples.

source_name: spinal cord

extract_protocol:
Total RNA from spinal cord tissues, either containing injury site from mice with SCI or collected from corresponding segments from uninjured mice, was isolated using the RNA isolation kit (Takara Bio).
Libraries were constructed using a standard Illumina protocol with poly(A) selection for mRNA enrichment. After end repair and adapter ligation (P5/P7), libraries were PCR-amplified and sequenced using Illumina sequencing-by-synthesis in paired-end mode (~150 bp). The libraries were non-strand-specific.

treatment_protocol: See paper for details.

value: spinal cord

value: CSF1 deletion in astrocytes with SCI


title: Thy1p_95_2b

description:
Library name: CD34nThy1p_donor_2_rep2
Column name in raw_counts: CD34nThy1p_95_2b


title: Sham1

description:
Library name: sample 1
10X Genomics


title: AstroCSF1KO_SCI_2

description: Library name: AstroCSF1KO_SCI_2


title: CD34p_T_96_1

description:
Library name: CD34pThy1p_donor_3_rep1_TNF_IL1B
Column name in raw_counts: CD34pThy1p_T_96_1


title: CD34p_T_95_2

description:
Library name: CD34pThy1p_donor_2_rep2_TNF_IL1B
Column name in raw_counts: CD34pThy1p_T_95_2


title: AstroCSF1KO_SCI_3

description: Library name: AstroCSF1KO_SCI_3


title: AstroCSF1KO_uninjured_2

description: Library name: AstroCSF1KO_uninjured_2

value: naïve CSF1 deletion in astrocytes


title: Thy1p_61_2

description:
Library name: CD34nThy1p_donor_1_rep2
Column name in raw_counts: CD34nThy1p_61_2


title: CD34p_T_95_1

description:
Library name: CD34pThy1p_donor_2_rep1_TNF_IL1B
Column name in raw_counts: CD34p_T_95_1


title: CD34p_96_2

description:
Library name: CD34pThy1p_donor_3_rep2
Column name in raw_counts: CD34pThy1p_96_2


title: AstroCSF1KO_uninjured_1

description: Library name: AstroCSF1KO_uninjured_1


title: AstroCSF1KO_SCI_1

description: Library name: AstroCSF1KO_SCI_1


title: CD34p_T_61_2

description:
Library name: CD34pThy1p_donor_1_rep2_TNF_IL1B
Column name in raw_counts: CD34pThy1p_T_61_2


title: CD34p_96_1b

description:
Library name: CD34pThy1p_donor_3_rep1
Column name in raw_counts: CD34pThy1p_96_1b


title: CD34p_T_61_1

description:
Library name: CD34pThy1p_donor_1_rep1_TNF_IL1B
Column name in raw_counts: CD34pThy1p_T_61_1


title: Control_SCI_2

description: Library name: Control_SCI_2

value: controls with SCI


title: CD34p_95_2b

description:
Library name: CD34pThy1p_donor_2_rep2
Column name in raw_counts: CD34pThy1p_95_2b


title: AstroCSF1KO_uninjured_3

description: Library name: AstroCSF1KO_uninjured_3


title: Control_SCI_1

description: Library name: Control_SCI_1


title: Control_SCI_3

description: Library name: Control_SCI_3


title: CD34p_61_2

description:
Library name: CD34pThy1p_donor_1_rep2
Column name in raw_counts and meta_data: CD34pThy1p_61_2


title: H9 ESCs, STAg ,96 h，replicate 3

city: Nanjing

last: LAB

address: Longmian Street num101

institute: nanjingmedicaluniversity

description: Library name: ST3

data_processing:
Data filter: Trim Smart-seq2 public primer sequence from the Reads；Remove the contaminated reads for adapters；Remove the low quality readsRemove the reads whose N base more than 5% for total bases
reads alignment : HISAT2
Transcript assembly and quantification : StringTie
Differential Expression Analysis :DEGseq
Assembly: Homo sapiens.cRch38.99.chr
Supplementary files format and content: fpkm.xls,which contained gene expression quantification

source_name: H9 ESCs

extract_protocol:
RNA purity was checked using the kaiaoK5500®Spectrophotometer (Kaiao,Beijing, China).RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair,A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed.

value: H9 ESCs

value: human embryonic stem

value: STAg treatment


title: Control_SCI_4

description: Library name: Control_SCI_4


title: H9 ESCs, STAg ,96 h，replicate 2

description: Library name: ST2


title: CD34p_61_1

description:
Library name: CD34pThy1p_donor_1_rep1
Column name in raw_counts: CD34pThy1p_61_1

value: Foetal finger joint tissue


title: Control_uninjured_2

description: Library name: Control_uninjured_2

value: naïve controls


title: CD34p_95_1

description:
Library name: CD34pThy1p_donor_2_rep1
Column name in raw_counts: CD34pThy1p_95_1

value: Primary fibroblasts

value: fibroblasts


title: Control_uninjured_3

description: Library name: Control_uninjured_3


title: Control_uninjured_1

description: Library name: Control_uninjured_1


title: H9 ESCs, STAg ,96 h，replicate 1

description: Library name: ST1


title: Mouse_Sham4

description:
Library name: sample4
10X Genomics

data_processing:
Generated sequences were aligned with 10X Genomics Space Ranger version 2.0.0 with mm10-2020-A as reference, before downstream analysis with Seurat and RCTD.
Assembly: mm10
Supplementary files format and content: tab-separated value files and matrix files
Library strategy: Spatial Transcriptomics

extract_protocol:
Sham lumbar spinal cord were obtained from mice and snap frozen in liquid nitrogen before embedding in OCT. Embedded tissues were sectioned at 10um before placement within fiducial frames of 6.5mm x 6.5mm capture areas on a Visium Spatial glass slide. These sections then undergo H&E staining (MethanolFixationandHEStaining_RevB), followed by imaging on a Leica DM6B and at 10x magnification.
Imaged sections are permeabilized, reverse-transcribed before denaturation. The collected cDNA are further amplified and indexed before sequencing to achieve 75 million reads, which equated to approximately 42,501 reads per spot for the presented data.

value: Lumbar spinal cord

value: WT


title: H9 ESCs, 100 nM FA, day 10 to day 15; STAg, day 11 to day 15，replicate 3

description: Library name: FS3

value: FA+STAg treatment


title: Mouse_Sham3

description:
Library name: sample3
10X Genomics

value: Neurons  and non-neuronal nuclei


title: H9 ESCs, 100 nM FA, day 10 to day 15; STAg, day 11 to day 15，replicate 2

description: Library name: FS2


title: H9 ESCs, 100 nM FA, day 10 to day 15; STAg, day 11 to day 15，replicate 1

description: Library name: FS1


title: H9 ESCs, 100 nM FA, day 10 to day 15，replicate 3

description: Library name: FA3

value: FA treatment


title: Mouse_Sham2

description:
Library name: sample2
10X Genomics

value: Sham


title: H9 ESCs, 100 nM FA, day 10 to day 15，replicate 2

description: Library name: FA2


title: H9 ESCs, 100 nM FA, day 10 to day 15，replicate 1

description: Library name: FA1


title: H9 ESCs, no special treatment，replicate 3

description: Library name: C3


title: Old MDSPCs, O1-1, biol rep 1

city: Chicago

first: Seth

middle: David

last: Thompson

state: IL

address: 355 E Erie St

department: Physical Medicine and Rehabilitation

institute: Northwestern University

description:
Library name: Sample 4
10x genomics

data_processing:
Single-cell RNA sequencing was performed at the Northwestern University Sequencing (NUSeq) Core facility, using the Illumina Novaseq 6000 machine. Filtered matrix files for each sample (young Y1-Y3 and old O1-O3) were generated by CellRanger (v7.2.0) at the NUSeq core. All downstream analyses were conducted on these filtered matrices using Seurat v5.134. A total of 62331 cells were captured across six samples. Cells were filtered out if they met any or all of the following criteria- more than 25% mitochondrial content, fewer than 250 expressed genes, transcript count more than 2 standard deviations from the mean, fewer than 500 detected transcripts, or a complexity (log10 genes per UMI) below the 80th percentile. Additionally, genes expressed in fewer than 10 cells or zero counts were excluded.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Muscle-derived stem/progenitor cells

extract_protocol:
Skeletal muscle tissue was enzymatically dissociated with collagenase type-XI, dispase, and trypsin to generate a single-cell suspension. Cells were sequentially plated onto collagen type I-coated flasks, and non-adherent cells were serially transferred to fresh flasks for a total of six preplateing steps over five days to enrich for the slowly adhering MDSPC population. MDSPCs were cultured in collagen type-1 coated flasks containing proliferation media (DMEM supplemented with 10% fetal bovine serum, 10% horse serum, 1% penicillin/streptomycin, and 0.05% chick embryo extract).
Cell number and viability were analyzed using Nexcelom Cellometer Auto2000 with AOPI fluorescent staining method. Sixteen thousand cells were loaded into the Chromium iX Controller (10X Genomics, PN-1000328) on a Chromium Next GEM Chip G (10X Genomics, PN-1000120) and processed to generate single cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol. The cDNA and library were generated using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics, PN-1000286) and Dual Index Kit TT Set A (10X Genomics, PN-1000215) according to the manufacturer’s manual. Quality control for constructed library was performed by Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) and Qubit DNA HS assay kit for qualitative and quantitative analysis, respectively. The multiplexed libraries were pooled and sequenced on Illumina Novaseq 6000 sequencer with 100 cycle kits using the following read length: 28 bp Read1 for cell barcode and UMI, and 90 bp Read2 for transcript.

value: Muscle-derived stem/progenitor cells


title: Old MDSPCs, NA-f2, biol rep 2

description:
Library name: Sample 5
10x genomics


title: Young MDSPCs, Y1-1, biol rep 1

description:
Library name: Sample 1
10x genomics


title: Mouse_Sham1

description:
Library name: sample1
10X Genomics


title: H9 ESCs, no special treatment，replicate 2

description: Library name: C2


title: Young MDSPCs, PtC5, biol rep 2

description:
Library name: Sample 2
10x genomics


title: MAB04-2-Mutant

first: Bertie

last: Gottgens

email: bg200@cam.ac.uk, nkw22@cam.ac.uk

address: Jeffrey Cheah Biomedical Centre

institute: University of Cambridge

description: Library name: MAB04-2-Mutant

data_processing:
Barcode processing, mapping and gene counting were performed using the Cell Ranger pipeline v6.0.1
Assembly: mm10
Supplementary files format and content: adata_meta.h5ad is the adata object containing all the processed data and the metadata for the 2 samples used in this work

source_name: bone marrow

extract_protocol:
To isolate lineage negative ckit positive cells (Lin-ckit+) for single-cell RNA-seq experiments, bone marrow was flushed from femur and tibia into PFP (PBS, 10% FBS, 1% Penicillin-Streptomycin), red blood cells lysed with ACK lysing buffer (Gibco, A1049201 or IOTest 3 Lysing Solution, Beckman Coulter, A07799) and cells manually counted. Cell suspensions were stained for 25 min at 4 °C in the dark with the following LSK SLAM panel antibodies: CD3 PE (1:1,000; Biolegend 100205), B220 PE (1:1,000; 1663 BD Biosciences 553089), Gr1 PE (1:1,000; BD Biosciences 553128), Ter119 PE (1:1,000; BD Biosciences 553673), CD11b PE (1:1,000; BD Biosciences 553311), NK1.1 AF700 (1:1,000; Biolegend 108730), Sca1 PeCy (1:250; eBioscience 25-5981-81), CD48 AF700 (1:250; Biolegend 103425), c-Kit BV421 (1:250; BD Biosciences 562609), CD150 BV605 (1:100; Biolegend 115927). Cells were washed with PFP, and Lineage- c-Kit+ isolated using FACS on a 5-laser LSRFortessa SORP Cell Analyzer (BD Biosciences). Dead cell exclusion was by Hoechst 33342. Sorted cells were collected and processed for scRNA-Seq.
Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10X Genomics) following manufacturer’s protocols

value: bone marrow

value: Lin- cKit+

value: Dnmt3a W326R/+


title: NEUDW867LF9_SCC_10.sl3_PRO

first: David

last: Gate

address: 745 N Fairbanks Ct

department: Neurology

description:
Library name: NEUDW867LF9_SCC_10.sl3_PRO
NEUDW867LF9_SCC_10.sl3_PRO

library_source: other

data_processing:
FASTQs were processed using 10X SpaceRanger v2.1.1 and saved as Seurat objects for analysis
ST spots with more than 20% of reads attributed to mitochondrial genes in the mRNA assay were removed.
ST spots with extreme low and high UMI counts in the mRNA assay were omitted on a per-sample basis
ST spots with extreme low and high mRNA Feature counts were removed on a per-sample basis
ST spots not located on cortical spinal cord tissue are removed
Raw mRNA counts were lognormalized using Seurat's NormalizeData()
Raw mRNA counts were transformed using SCTransform
Assembly: GrCh38-2020-A
Supplementary files format and content: The .rds processed data files are Seurat objects containing count matrices, transformed data matrices, and metadata
Supplementary files format and content: Also included are the SpaceRanger output files for each sample: aligned fiducials, scale factors, hires image, lowres image, detected tissue image, tissue positions list, and barcode fluorescence intensity from the spatial output folder, and the barcode, features, and matrix matrices from the filtered_feature_bc_matrix output folder, as well as .rds objects for each sample
Library strategy: Spatial Proteogenomics

molecule: protein

source_name: Cervical spinal cord

extract_protocol:
Formalin-fixed, paraffin-embedded samples were processed according to the Visium CytAssist Spatial Gene and Protein Expression for FFPE – Deparaffinization, Decrosslinking, Immunofluorescence Staining & Imaging (CG000659, Rev B, 10x Genomics) protocol
Libraries were constructed according to the user guide for Visium CytAssist Spatial Gene and Protein Expression Reagent Kits (CG000494; Rev B; 10x Genomics).

value: Cervical spinal cord


title: Young MDSPCs, FT-QU, biol rep 3

description:
Library name: Sample 3
10x genomics


title: NEUHD481VCL_SCC_19.sl14_PRO

description:
Library name: NEUHD481VCL_SCC_19.sl14_PRO
NEUHD481VCL_SCC_19.sl14_PRO


title: Ehd1-KO scRNA

city: Los Angeles

first: Bishuang

last: Cai

state: CA

address: 675 Charles E. Young Dr South, Rm 1220

department: Medicine

institute: University of California, Los Angeles

description:
Library name: BF002
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2
The scRNA-seq filtered raw counts matrices were analyzed using Seurat (v5.0.1) in R (v4.3.2).
Assembly: mm10-2020-A
Supplementary files format and content: cell barcodes (barcodes.tsv), genes (genes.tsv),  and count matrix (matrix.mtx)

source_name: Aortic

extract_protocol:
Aortic CD45+ cells were isolated as previously described (PMID: 33731931). Briefly, aortas from male Ldlr-/- mice (n = 7) fed a high-fat diet for 12 weeks were pooled and digested with an enzyme mixture. Aortic single cells were stained with anti-CD45 antibody and DAPI. DAPI-/CD45+ cells were sorted by FACS and collected for scRNA-seq.
scRNA-seq libraries were prepared using a Chromium Single Cell 3’ Reagent kit (10x Genomics) according to the manufacturer’s instructions.

value: Aortic

tag: strain

tag: Sex

value: Male

tag: age

value: 26 weeks

value: Ehd1 KO


title: NEUUJ189PPH_SSC_2.5_PRO

description:
Library name: NEUUJ189PPH_SSC_2.5_PRO
NEUUJ189PPH_SSC_2.5_PRO

tag: tissue


title: MILLERMI.AU.87.sl5_PRO

description:
Library name: MILLERMI.AU.87.sl5_PRO
MILLERMI.AU.87.sl5_PRO


title: MAB04-1-WT

description: Library name: MAB04-1-WT

tag: genotype


title: H9 ESCs, no special treatment，replicate 1

description: Library name: C1

value: H9 ESCs

value: human embryonic stem

tag: treatment


title: TP_H3K4me3_Rep2

city: New York City

first: Dan

last: Li

department: HOPP

institute: Memorial Sloan-Kettering Cancer Center

description:
Library name: TP_H3K4me3_Rep2_TZ-971-4_IGO_14046_EF_21
ChIPseq

data_processing:
"trim_galore" was used to trim the adapters, "bowtie2" was used to map the reads to reference genome, using the command: "bowtie2 -p 20 --local --very-sensitive-local --no-mixed --no-discordant -x Bowtie2_index/mm10_ecoli_drosophila -1 trim_galore/val_1.fq.gz -2 trim_galore/val_2.fq.gz | samblaster | samtools sort -o bam/mm10.bam" -O BAM -" and bigwig files were generated using "bamCoverage --normalizeUsing RPGC --effectiveGenomeSize 2451960000 -bs=10 -e -b bam/mm10.bam -o bigwig/mm10.bw" command.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: primary stomach epithelial cells

extract_protocol:
ChIPseq was performed using standard ChIP protocol (Shipra Shukla, et al. Cancer Cell, 16 November, 2017).
ChIPseqwere prepared using KAPA HTP Library Preparation Kit (Kapa Biosystems KK8234) according to the manufacturer’s instructions.

treatment_protocol: In ChIPseq: we performed ChIP-seq of H3K4me1 and H3K4me3 in TP and TPCD cells, . In each experiment, 1μg antibodies against H3K4me1 (5326, Cell Signaling Technology) and H3K4me3 (130060, EpiCypher). The library preparation and next-generation sequencing were performed by the MSKCC IGO core facility using Illumina NovaSeq 6000 with paired-end 100bp for 30-40 million reads.

value: primary stomach epithelial cells

value: TP

tag: chip antibody


title: MILLERMINEUWM_344ZLM.sl10_PRO

description:
Library name: MILLERMINEUWM_344ZLM.sl10_PRO
MILLERMINEUWM_344ZLM.sl10_PRO


title: Old MDSPCs, NA-f3, biol rep 3

description:
Library name: Sample 6
10x genomics


title: WT scRNA

description:
Library name: BF001
10x Genomics

value: WT


title: TP_H3K4me3_Rep1

description:
Library name: TP_H3K4me3_Rep1_TZ-971-3_IGO_14046_EF_20
ChIPseq


title: GWF_19.47_10B_sl13_PRO

description:
Library name: GWF_19.47_10B_sl13_PRO
GWF_19.47_10B_sl13_PRO


title: GWF_19.35_10C.sl9_PRO

description:
Library name: GWF_19.35_10C.sl9_PRO
GWF_19.35_10C.sl9_PRO


title: TP_Input

description:
Library name: TP_Input_TZ-971-17_IGO_14046_EF_34
ChIPseq

value: Input


title: TPCD_H3K4me3_Rep2

description:
Library name: TPCD_H3K4me3_Rep2_TZ-971-16_IGO_14046_EF_33
ChIPseq

value: TPCD


title: GWF.20.50.10B.sl5_PRO

description:
Library name: GWF.20.50.10B.sl5_PRO
GWF.20.50.10B.sl5_PRO


title: MILLERMI.N14.280.CSC_PRO

description:
Library name: MILLERMI.N14.280.CSC_PRO
MILLERMI.N14.280.CSC_PRO


title: GWF.19.37.10B.sl10_PRO

description:
Library name: GWF.19.37.10B.sl10_PRO
GWF.19.37.10B.sl10_PRO


title: TPCD_H3K4me3_Rep1

description:
Library name: TPCD_H3K4me3_Rep1_TZ-971-15_IGO_14046_EF_32
ChIPseq


title: GWF.18.33.10B.sl11_PRO

description:
Library name: GWF.18.33.10B.sl11_PRO
GWF.18.33.10B.sl11_PRO


title: TPCD_Input

description:
Library name: TPCD_Input_TZ-971-20_IGO_14046_EF_37
ChIPseq


title: TPCD_Input_EJ-1004-12_IGO_16980_AU_12

description:
Library name: ChIP_mStomach_TPCD3_Input_EJ-1004-12_IGO_16980_AU_12
ChIPseq


title: TPCD_H3K4me1_Rep2

description:
Library name: ChIP_mStomach_TPCD3_H3K4me1_CST_5326_rep2_EJ-1004-8_IGO_16980_AU_8
ChIPseq


title: TPCD_H3K4me1_Rep1

description:
Library name: ChIP_mStomach_TPCD3_H3K4me1_CST_5326_rep1_EJ-1004-7_IGO_16980_AU_7
ChIPseq


title: TP_Input_EJ-1004-9_IGO_16980_AU_9

description:
Library name: ChIP_mStomach_TP2_Input_EJ-1004-9_IGO_16980_AU_9
ChIPseq


title: GBB21.03.A12.sl5_PRO

description:
Library name: GBB21.03.A12.sl5_PRO
GBB21.03.A12.sl5_PRO


title: GWF.17.23_PRO

description:
Library name: GWF.17.23_PRO
GWF.17.23_PRO


title: TP_H3K4me1_Rep2

description:
Library name: ChIP_mStomach_TP2_H3K4me1_CST_5326_rep2_EJ-1004-2_IGO_16980_AU_2
ChIPseq


title: GBB19.13.A13.sl5_PRO

description:
Library name: GBB19.13.A13.sl5_PRO
GBB19.13.A13.sl5_PRO


title: GBB.17.21.B10.CNS.sl4_PRO

description:
Library name: GBB.17.21.B10.CNS.sl4_PRO
GBB.17.21.B10.CNS.sl4_PRO


title: GWF.17.24.10B.sl10_PRO

description:
Library name: GWF.17.24.10B.sl10_PRO
GWF.17.24.10B.sl10_PRO


title: NEUUJ189PPH_SSC_2.5

description:
Library name: NEUUJ189PPH_SSC_2.5
NEUUJ189PPH_SSC_2.5


title: TY_Rapa_Rep1

description:
Library name: Sample_TY_2_Rapa_Rep1_IGO_16602_19
polyA RNA

data_processing:
Data was processed using (v3.10) of the nf-core collection of workflows. The pipeline was executed with Nextflow v23.04.3 with the following command: nextflow run nf-core/rnaseq -r 3.12.0 --input samplesheet.csv --genome GRCm38 -profile singularity. Briefly, raw FASTQ files were aligned to the GRCm38 (mm10) reference genome and quantified using salmon (v 1.10.0). Differential gene expression was performed in R with DESeq2 (1.46.0) and iDEP.
Assembly: mm10
Supplementary files format and content: Counts_raw_reads_normalized.txt

extract_protocol:
In RNAseq, total RNA was extracted with Trizol reagent following the manufacture's instruction.
RNAseq libraries were prepared using standard Illumina polyA library preparation protocol (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102, 8 cycles of PCR). ChIPseqwere prepared using KAPA HTP Library Preparation Kit (Kapa Biosystems KK8234) according to the manufacturer’s instructions.

treatment_protocol: In RNAseq: mouse stomach epithelial TY, TP, and TPCD cells were treated with DMSO or rapamycin (10nM) for 24 hours. Total RNA was extracted suing TRIzol reagent. RNA-seq libraries were prepared using poly-A capture protocol. Next-generation sequencing was performed by the MSKCC Integrated Genomics Operation (IGO) on Illumina NovaSeq 6000 with paired-end 100bp for 30-40 million reads.

value: TY

value: Rapa


title: GBB20.16.A13.sl10_PRO

description:
Library name: GBB20.16.A13.sl10_PRO
GBB20.16.A13.sl10_PRO


title: NEUDW867LF9_SCC_10.sl3

description:
Library name: NEUDW867LF9_SCC_10.sl3
NEUDW867LF9_SCC_10.sl3


title: TP_H3K4me1_Rep1

description:
Library name: ChIP_mStomach_TP2_H3K4me1_CST_5326_rep1_EJ-1004-1_IGO_16980_AU_1
ChIPseq


title: NEUHD481VCL_SCC_19.sl14

description:
Library name: NEUHD481VCL_SCC_19.sl14
NEUHD481VCL_SCC_19.sl14


title: GBB.18.01.A9.sl12_PRO

description:
Library name: GBB.18.01.A9.sl12_PRO
GBB.18.01.A9.sl12_PRO


title: MILLERMINEUWM_344ZLM.sl10

description:
Library name: MILLERMINEUWM_344ZLM.sl10
MILLERMINEUWM_344ZLM.sl10


title: TP_Rapa_Rep1

description:
Library name: Sample_TP_2_Rapa_Rep1_IGO_16602_27
polyA RNA


title: TY_Rapa_Rep2

description:
Library name: Sample_TY_2_Rapa_Rep2_IGO_16602_20
polyA RNA


title: TY_DMSO_Rep2

description:
Library name: Sample_TY_2_Ctrl_Rep2_IGO_16602_4
polyA RNA

value: DMSO


title: TP_DMSO_Rep2

description:
Library name: Sample_TP_2_Ctrl_Rep2_IGO_16602_12
polyA RNA


title: MILLERMI.N14.280.CSC

description:
Library name: MILLERMI.N14.280.CSC
MILLERMI.N14.280.CSC


title: TP_Rapa_Rep2

description:
Library name: Sample_TP_2_Rapa_Rep2_IGO_16602_28
polyA RNA


title: TY_DMSO_Rep1

description:
Library name: Sample_TY_2_Ctrl_Rep1_IGO_16602_3
polyA RNA


title: TP_DMSO_Rep1

description:
Library name: Sample_TP_2_Ctrl_Rep1_IGO_16602_11
polyA RNA


title: GWF_19.47_10B_sl13

description:
Library name: GWF_19.47_10B_sl13
GWF_19.47_10B_sl13


title: GWF_19.35_10C.sl9

description:
Library name: GWF_19.35_10C.sl9
GWF_19.35_10C.sl9


title: MILLERMI.AU.87.sl5

description:
Library name: MILLERMI.AU.87.sl5
MILLERMI.AU.87.sl5


title: TPCD_Rapa_Rep2

description:
Library name: Sample_TPCD_2_Rapa_Rep2_IGO_16602_32
polyA RNA


title: TPCD_Rapa_Rep1

description:
Library name: Sample_TPCD_2_Rapa_Rep1_IGO_16602_31
polyA RNA


title: GWF.18.33.10B.sl11

description:
Library name: GWF.18.33.10B.sl11
GWF.18.33.10B.sl11


title: TPCD_DMSO_Rep2

description:
Library name: Sample_TPCD_2_Ctrl_Rep2_IGO_16602_16
polyA RNA


title: GWF.17.23

description:
Library name: GWF.17.23
GWF.17.23


title: SO3-m

city: Zhuhai

first: Biao

last: Liu

address: meihuadong road

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

description: Library name: sample9

data_processing:
Reads were aligned to the human Ensemble genome GRCh38 using Hisat2 aligner.
Assembly: GRCh38
Supplementary files format and content: tab delimited text files include fpkm values for each Sample

source_name: penis

extract_protocol:
RNA was harvested using Rneasy mini plus kit. 1.3ug of total RNA was used for the construction of sequencing libraries.
The concentration of total RNA was measured by Qubit RNA HS assay kit. EpiTM mRNA Library Fast Kit was used for library preparation according to the instructions.

value: penis

value: primary human cavernous fibroblasts


title: TPCD_DMSO_Rep1

description:
Library name: Sample_TPCD_2_Ctrl_Rep1_IGO_16602_15
polyA RNA


title: GWF.19.37.10B.sl10

description:
Library name: GWF.19.37.10B.sl10
GWF.19.37.10B.sl10

value: Cervical spinal cord


title: GWF.17.24.10B.sl10

description:
Library name: GWF.17.24.10B.sl10
GWF.17.24.10B.sl10


title: MD3-m

description: Library name: sample6


title: GBB19.13.A13.sl5

description:
Library name: GBB19.13.A13.sl5
GBB19.13.A13.sl5


title: GBB21.03.A12.sl5

description:
Library name: GBB21.03.A12.sl5
GBB21.03.A12.sl5


title: MD2-m

description: Library name: sample5


title: DOXO granulosa cell [DS14]

city: Pitscataway

first: Shuo

last: Xiao

state: NJ

address: 170 Frelinghuysen Rd, Room 404

department: Pharmacology & Toxicology

institute: Rutgers University

description:
Library name: DS14
paired-endIllumina NovaSeq 6058

data_processing:
Sequenced reads were uploaded into Partek Flow software for data analyses. We first filtered out potential rDNA and mtDNA contaminants using Bowtie 2. Next,  filtered reads were aligned to the whole mouse genome assembly-mm10 using the HISAT 2 aligner. Raw read counts were obtained by quantifying aligned reads to Ensembl Transcripts release 99 using the Partek EM algorithm. Raw read counts were then normalized based on the Transcripts Per Million (TPM) method, and differential expression analysis was performed by using the DESeq2(R).
Assembly: mm10
Supplementary files format and content: csv file with raw counts for each sample

source_name: granulosa

extract_protocol:
SMART-seq v4 Ultra-low input RNA kit
The single-cell SMART-seq2 RNA-seq libraries were constructed using a modified single-cell tagged reverse transcription sequencing protocol. Briefly, mRNA from each single cell was extracted into the lysis buffer provided by the SMART-seq v4 Ultra-low input RNA kit (634891, TaKaRa, San Jose, CA, USA). mRNAs were then reversed transcribed into complementary DNA（cDNA), which was then pre-amplified and purified. Single-cell transcriptomes were subsequently tagged with unique barcodes using the Nextera XT DNA library preparation kit (FC-131-1096, Illumina, San Diego, CA, USA) and the Nextera XT Index kit v2 setA (TG-131-2001, Illumina).

value: granulosa

value: DOXO


title: GWF.20.50.10B.sl5

description:
Library name: GWF.20.50.10B.sl5
GWF.20.50.10B.sl5


title: DOXO granulosa cell [DS15]

description:
Library name: DS15
paired-endIllumina NovaSeq 6059


title: GBB.17.21.B10.CNS.sl4

description:
Library name: GBB.17.21.B10.CNS.sl4
GBB.17.21.B10.CNS.sl4


title: SO1-m

description: Library name: sample7


title: GBB20.16.A13.sl10

description:
Library name: GBB20.16.A13.sl10
GBB20.16.A13.sl10


title: MD1-m

description: Library name: sample4


title: SO2-m

description: Library name: sample8


title: DOXO granulosa cell [DS13]

description:
Library name: DS13
paired-endIllumina NovaSeq 6057


title: DOXO granulosa cell [DS16]

description:
Library name: DS16
paired-endIllumina NovaSeq 6060


title: U87-CP-24, replicate1, bulk-RNA-seq

city: Haidian

first: Pengcheng

last: Tan

address: 30 Shuangqing Rd

institute: Tsinghua University

data_processing:
TrimGalore software (with Cutadapt v1.18) was used to trim the adaptor and first 10 bp of both reads. STAR (version 2.7.10b) was used for the alignment to the hg38 reference genome and htseq-count (v2.0.3) was used to obtain the gene expression count matrix using hg38 RefSeq gene annotation downloaded from UCSC table browser.
Assembly: Genome was built by STAR (version 2.7.10b).
Supplementary files format and content: Raw count matrix in csv file.

growth_protocol: U87 cells were cultured in DMEM supplemented with 10% Fetal Bovine Serum, 1% Penicillin/Streptomycin, and 1% non-essential amino acids.

extract_protocol:
Cells were harvested and lysed in 1 mL Trizol (Gibco, 15596018), followed by adding 0.2 mL CHCl3. Then solution was vortex for 15~30 s and set at room temperature for 2~3 minutes, followed by centrifugation for 15 minutes at 12,000g under 4°C. After centrifugation, the water layer was transferred into a new 1.5ml tube with 0.5 mL isopropanol (IPA) and set at -80°C overnight for RNA precipitation. The RNA pellet was obtained by centrifugation for 10 minutes at 12,000g under 4°C followed by removing the liquid. RNA pellet was washed using cold 75% ethanol, and was centrifuged for 5 minutes at 12,000g under 4°C. After removing liquid, RNA pellet was resuspended in 20ul DEPC-water for further experiments.
The RNA-seq libraries were constructed using the using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® according to manufacturer’s instructions. Briefly, total RNA samples were enriched for eukaryotic mRNA by Oligo(dT) magnetic beads followed by fragmentation and cDNA synthesis and purification. Purified double-stranded cDNA was subjected to end repair, adaptor ligation, and PCR amplification to obtain cDNA libraries.

treatment_protocol: U87 cells were treated with DMSO, 5 μM Osimertinib, or 40 μM CP-24 24 h before RNA extraction.


title: GBB.18.01.A9.sl12

description:
Library name: GBB.18.01.A9.sl12
GBB.18.01.A9.sl12


title: U87-CP-24, replicate2, bulk-RNA-seq


title: U87-Osimertinib, replicate2, bulk-RNA-seq

value: Osimertinib


title: DOXO granulosa cell [DS12]

description:
Library name: DS12
paired-endIllumina NovaSeq 6056


title: U87-Osimertinib, replicate1, bulk-RNA-seq


title: HD2-m

description: Library name: sample2


title: HD3-m

description: Library name: sample3


title: U87-DMSO, replicate2, bulk-RNA-seq


title: U87-DMSO, replicate1, bulk-RNA-seq


title: DOXO granulosa cell [DS10]

description:
Library name: DS10
paired-endIllumina NovaSeq 6055


title: HD1-m

description: Library name: sample1


title: Foot regenerating fragment, 96hpa

city: Basel

first: Panagiotis

last: Papasaikas

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute

description:
Library name: 3271F1_96h
All cells, enriched for epithelial cells

data_processing:
Quantification of the generated single cell libraries was performed using the Salmon-Alevin software suite (Salmon version 1.8.0) against the NCBI Hydra vulgaris high contiguity assembly Hydra_vulgaris_105_v3  (GCF_022113875.1) and associated transcriptome. Example command: salmon alevin -l ISR -1 $R1  -2 $R2 --chromiumV3 -i $reference -p $threads -o OUTDIR --tgMap $tx2genemap --dumpFeatures --numCellBootstraps 50 --expectCells 5000
Post-alignment quality control employed alevinQC v1.8.0 within R/Bioconductor  providing barcode knee plots, mapping summaries, and other standard metrics for each sample. Gene- and cell-level quality control was carried out in R /Bioconductor  on the Hydra libraries. Cells were retained if they expressed 850–7000 genes (empirically chosen to exclude low-complexity droplets and potential multiplets).
Assembly: NCBI Hydra vulgaris Release Hydra_vulgaris_105_v3  (GCF_022113875.1)
Supplementary files format and content: tab-delimited files with raw (not normalized) UMI counts for each filtering-cleared cell (columns) and Hydra gene (row) as reported by Salmon-Alevin

organism: Hydra vulgaris

source_name: Whole tissue

growth_protocol: Animals are maintained in Hydra medium solution [1 mM CaCl2, 0.2 mM NaHCO3, 0.02 mM KCl, 0.02 mM MgCl2, and 0.2 mM tris-HCl (pH 7.4)] at 18°C and fed three times per week with freshly hatched Artemia nauplii.

extract_protocol:
Samples were incubated in Pronase E solution (7.5 mg/mL of pronase E diluted in dissociation medium [6 mM CaCI2, 1.2 mM MgSO4, 3.6 mM KCl, 12.5 mM N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid, 6 mM sodium pyruvate, 6 mM sodium citrate, 4 mM glucose; pH 6.9]) for 1h at 24°C, 300rpm, protected from light. Animals were dissociated into single cells mechanically by pipetting up and down. Cells were strained through a sterile CellTrics® 30µm cell strainer, collected in a centrifuge tube and spin 5min, 300xg at room temperature (RT). Supernatant was removed and cells were resuspended in dissociation medium + 0.01% Bovin serum albumin (BSA). Cells were centrifuged again and resuspended in dissociation medium + 0.01% BSA. Cells were strained and collected in a FACS tube. Dead cells were stained with DRAQ7 and excluded from the FACS sort. Cells were collected in a PBS + 0.04% BSA, without Cacl2 and MgCl2, solution.
FACS-sorted cells (16K) were immediately processed for scRNA-seq using 10X genomics Chromium Single Cell 3’ Reagents v3.1 with UDI indexes, according to the manufacturer’s protocol.

treatment_protocol: We bisected Hydras and collected samples at 0, 3, 6, 12, 24, 48, 72 and 96 hours after bisection separately for head and foot animal regeneration

value: Whole tissue

value: icells, ectodermal, gastrodermal

value: Body bisection

tag: time after_bisection

value: 96 hours

tag: regeneration type

value: Foot


title: DOXO granulosa cell [DS9]

description:
Library name: DS9
paired-endIllumina NovaSeq 6054

value: WT


title: Foot regenerating fragment, 48hpa

description:
Library name: 3357F1_48h
All cells, enriched for epithelial cells

value: 48 hours


title: Foot regenerating fragment, 72hpa

description:
Library name: 3746F2_72h
All cells, enriched for epithelial cells

value: 72 hours


title: Foot regenerating fragment, 12hpa

description:
Library name: 3271F3_12h
All cells, enriched for epithelial cells

value: 12 hours


title: DOXO granulosa cell [DS8]

description:
Library name: DS8
paired-endIllumina NovaSeq 6053


title: SO1-a

description: Library name: sample5

data_processing:
For data processing, adapter sequences were removed from the raw sequencing data using cutadapt software.
Assembly: GRCh38
Supplementary files format and content: FPKM
Library strategy: Ribo-Seq

molecule: other

source_name: primary human cavernous fibroblasts

extract_protocol:
Primary corpus cavernosum fibroblasts were cultured on Matrigel-coated dishes with pre-adjusted stiffness for 48 hours. For ribosome profiling, cells from each experimental group (n = 2 independent biological replicates) were treated with 100 μg/ml cycloheximide at 37°C for 8 minutes to arrest elongating ribosomes prior to lysis and RNA extraction. Cells were then lysed on ice for 10 minutes using a lysis buffer containing 20 mM Tris–HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl₂, 1 mM DTT, 100 μg/ml cycloheximide, and 1% Triton X-100. The lysate was centrifuged at 12,000 × g for 10 minutes at 4°C, and the supernatant was collected.
The absorbance of the supernatant at 260 nm was measured to standardize the ribosome content across groups. Lysates with equal A260 values were subjected to RNase 1 digestion (15 units per 1 OD of lysate) at 22°C for 40 minutes with gentle mixing to generate ribosome-protected fragments (RPFs). The digested fragments were purified using MicroSpin™ S-400 columns, followed by RNA extraction using the Zymo Research RNA Clean & Concentrator-25 kit. The purified RPFs were size-selected on a 15% polyacrylamide TBE-urea gel, and fragments between 25–34 nucleotides were excised and recovered using the ZR small-RNA™ PAGE Recovery Kit. The recovered RNA was treated with polynucleotide kinase (PNK) and used to construct sequencing libraries with the VAHTS™ Small RNA Library Prep Kit for Illumina®.

value: SO


title: Foot regenerating fragment, 24hpa

description:
Library name: 3271F2_24h
All cells, enriched for epithelial cells

value: 24 hours


title: SO2-a

description: Library name: sample6


title: Foot regenerating fragment, 0hpa

description:
Library name: 3271F5_0h
All cells, enriched for epithelial cells

value: 0 hour


title: DOXO granulosa cell [DS6]

description:
Library name: DS6
paired-endIllumina NovaSeq 6051


title: DOXO granulosa cell [DS7]

description:
Library name: DS7
paired-endIllumina NovaSeq 6052


title: MD2-a

description: Library name: sample4

value: primary human cavernous fibroblasts

value: MD


title: MD1-a

description: Library name: sample3


title: DOXO granulosa cell [DS4]

description:
Library name: DS4
paired-endIllumina NovaSeq 6050

value: granulosa


title: Head regenerating fragment, 48hpa

description:
Library name: 3357F2_48h
All cells, enriched for epithelial cells

value: Head


title: Foot regenerating fragment, 3hpa

description:
Library name: 3746F4_3h
All cells, enriched for epithelial cells

value: 3 hours


title: HD2-a

description: Library name: sample2

value: HD


title: Head regenerating fragment, 12hpa

description:
Library name: 3113F3_12h
All cells, enriched for epithelial cells

value: Whole tissue

value: icells, ectodermal, gastrodermal


title: DOXO granulosa cell [DS2]

description:
Library name: DS2
paired-endIllumina NovaSeq 6049

value: DOXO


title: Head regenerating fragment, 72hpa

description:
Library name: 3746F1_72h
All cells, enriched for epithelial cells

value: Body bisection


title: Head regenerating fragment, 24hpa

description:
Library name: 3113F4_24h
All cells, enriched for epithelial cells


title: Head regenerating fragment, 3hpa

description:
Library name: 3746F3_3h
All cells, enriched for epithelial cells


title: Head regenerating fragment, 6hpa

description:
Library name: 3113F2_6h
All cells, enriched for epithelial cells

value: 6 hours


title: Foot regenerating fragment, 6hpa

description:
Library name: 3271F4_6h
All cells, enriched for epithelial cells

value: Foot


title: DOXO granulosa cell [DS1]

description:
Library name: DS1
paired-endIllumina NovaSeq 6048

value: WT


title: Head regenerating fragment, 0hpa

description:
Library name: 3113F1_0h
All cells, enriched for epithelial cells


title: DOXO oocyte [DO16]

description:
Library name: DO16
paired-endIllumina NovaSeq 6047

source_name: oocyte

value: oocyte


title: Head regenerating tip,47hpa, repA

description: Library name: 1984F95_47A

data_processing:
Reads were aligned against the NCBI Hydra vulgaris NCBI  high contiguity assembly Hydra_vulgaris_105_v3  (GCF_022113875.1) using the STAR software (v2.7.10a). Command prototype: STAR --genomeDir INDEXDIR --sjdbGTFfile GTF --readFilesIn fqpath --outSJfilterReads Unique --outFilterType BySJout --outFilterMultimapNmax 5 --alignSJoverhangMin 8 --alignSJDBoverhangMin 4 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --seedSearchStartLmax 50  --quantMode GeneCounts --sjdbGTFtagExonParentTranscript transcript_id --sjdbGTFtagExonParentGene gene_id --genomeChrBinNbits 12 --genomeSAsparseD 2
Genes were quantified using the STAR software (v2.7.10a) GeneCounts quantification mode (--quantMode).
Assembly: NCBI Hydra vulgaris Release Hydra_vulgaris_105_v3  (GCF_022113875.1)
Supplementary files format and content: tab-delimited file with raw (not normalized) counts for each biological sample (96 columns) and Hydra gene feature (28608 rows).

extract_protocol:
RNA was purified using the Norgen Biotek Single Cell RNA Purification kit according to the manufacturer's protocol. RNA quality was assessed using an Agilent Bioanalyzer.
5ng of RNA was used as input to generate RNA sequencing libraries using SmartSeq2 .

treatment_protocol: We bisected Hydras and collected samples from the oral end of regenerating Hydras at one-hour intervals over a 48-hour period.

value: 47 hours


title: Head regenerating tip,47hpa, repB

description: Library name: 1984F96_47B


title: GABPA_CUT-Tag_MOLM13_4S-A_2

description: Library name: Sample12

data_processing:
The quality control of each sample was accomplished using FASTQC V0.11.5.
Clean reads were aligned to mouse reference genome (mm10) using Bowtie 2 version 2.2.9. MarkDuplicates was used to mark PCR duplicate and unmapped reads. Only unique mapped reads were used in further analysis.
Peak calling and annotation were performed using MACS2 and ChIPseeker package, respectively.
Assembly: GRCh38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

source_name: AML cell line

extract_protocol:
The CUT&Tag assay was performed using NovoNGS CUT&Tag 3.0 High-Sensitivity Kit (Novoprotein) according to the manufacturer’s protocol. 5,000-10,000 cells were harvested and resuspended in 45 µL wash buffer. Then 6 µL ConA beads were added to the sample and incubated at 37°C for 10 min. Then the supernatant was removed by magnet adsorption and the beads were resuspended in 50 µL antibody buffer (20 mM Hepes, pH 7.5, 150 mM Nacl, 0.5 mM Spermidine, 0.0125% Digitonin, 2 mM EDTA, 0.1% BSA, 1× PIC).
Then, 0.5 µL antibody was added to the sample and incubated at 4°C overnight. The supernatant was removed by magnet adsorption and the beads were resuspended in 50 µL secondary antibody buffer, containing 0.5 µL goat anti-rabbit IgG antibody. After incubation at 37°C for 60 min, the beads were resuspended in 50 µL ChiTag Buffer, containing 0.5 µL ChiTag transposome. After incubation at 37°C for 60 min, the beads were resuspended in 50 µL tagmentation buffer. Then, 1 µL 10% SDS was added to the sample and incubated at 55°C for 10 min, and DNA was extracted using 2×DNA clean beads (Vazyme) and amplified with i5 and i7 primers (Vazyme) by 17-20 PCR cycles. The libraries were purified by 1.2×DNA clean beads (Vazyme).

treatment_protocol: GFP⁺ MOLM-13 cells expressing shControl, shDEK-1, or shDEK-1 rescued with DEK-4S-A were similarly sorted for DEK and GABPA-CUT-Tag-seq.

value: AML cell line


title: HD1-a

description: Library name: sample1


title: Head regenerating tip, 35hpa, repB

description: Library name: 1984F94_35B

value: 35 hours


title: GABPA_CUT-Tag_MOLM13_4S-A_1

description: Library name: Sample11


title: Head regenerating tip, 35hpa, repA

description: Library name: 1984F93_35A


title: DOXO oocyte [DO15]

description:
Library name: DO15
paired-endIllumina NovaSeq 6046


title: Head regenerating tip, 46hpa, repB

description: Library name: 1984F92_46B

value: 46 hours


title: GABPA_CUT-Tag_MOLM13_shDEK_1

description: Library name: Sample9


title: DOXO oocyte [DO14]

description:
Library name: DO14
paired-endIllumina NovaSeq 6045


title: Head regenerating tip, 46hpa, repA

description: Library name: 1984F91_46A


title: DOXO oocyte [DO13]

description:
Library name: DO13
paired-endIllumina NovaSeq 6044


title: Head regenerating tip, 34hpa, repB

description: Library name: 1984F90_34B

value: 34 hours


title: Head regenerating tip, 34hpa, repA

description: Library name: 1984F89_34A


title: Head regenerating tip, 45hpa, repB

description: Library name: 1984F88_45B

value: 45 hours


title: GABPA_CUT-Tag_MOLM13_shControl_1

description: Library name: Sample7


title: GABPA_CUT-Tag_MOLM13_shControl_2

description: Library name: Sample8


title: Head regenerating tip, 45hpa, repA

description: Library name: 1984F87_45A


title: Head regenerating tip, 33hpa, repB

description: Library name: 1984F86_33B

value: 33 hours


title: GABPA_CUT-Tag_MOLM13_shDEK_2

description: Library name: Sample10


title: DOXO oocyte [DO12]

description:
Library name: DO12
paired-endIllumina NovaSeq 6043


title: naivezt20d_rep2

city: Kingston

first: Amanda

middle: M

last: Zacharias

state: Ontario

address: 99 University Avenue

country: Canada

institute: Queen's University

description: Library name: 17

data_processing:
BGI used SOAPnuke v1.5.274 with the parameters “-l 15 -q 0.2 -n 0.05” to clean raw-sequencing reads.
Reads were aligned to the mouse genome (GENCODE release M24) with Hisat2 v2.2.1 using parameters "--dta --sensitive --no-discordant --no-mixed".
Gene expression was quantified with StringTie v2.1.5, R v4.2.180, and IsoformSwitchAnalyzeR v1.17.04.
Assembly: Gencode GRCm38.p6
Supplementary files format and content: CSV file including raw gene counts for each Sample.

source_name: DRG

extract_protocol:
DRG tissues (L1 - L6) were dissected and flash-frozen for storage at −80°C after mouse euthanasia at either ZT2, 8, 14, or 20. RNA was extracted using the RNeasy mini kit (Qiagen 74004). Pelleted and washed RNA was resuspended in RNase-free water and quantified using the NanoDrop system (Thermo Fisher, Waltham, MA). MA). The concentration of each total RNA sample was standardized to 50 ng/µl.
Library preparation was performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). RNA was taken to prepare the reaction system. The mRNA removed RNA samples were denatured at suitable temperature to open the secondary structure, and mRNA was enriched by oligo (dT) attached magnetic beads. After reacting at a suitable temperature for a fixed time period, the enriched mRNA was fragmented with fragmentation reaction. Then the first-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Related, the synthesized double strand cDNA was subject to end repairment reaction. After cDNA end repairment, a single ?A? nucleotide was added to the 3? ends of the blunt fragments through a tailing reaction. Then the adaptors were connected to the double stranded cDNA with adaptor ligation reaction. Finally, the library products were amplified through PCR reaction and subjected to quality control.
Next, the single-stranded library products were produced via denaturation. The reaction system for circularization was set up to get the single-stranded circularized DNA products. Any single stranded linear DNA molecules will be digested. The final single strand circularized library was amplified with phi29 and rolling circle amplification (RCA) to make DNA nanoball (DNB) which carries more than 300 copies of the initial single stranded circularized library molecule. The DNBs were loaded into the patterned nanoarray and sequencing reads of PE 150 bases length were generated on G400 platform (BGI-Shenzhen, China).

value: DRG

value: male

value: 6-12 weeks old

tag: zt time


title: DOXO oocyte [DO10]

description:
Library name: DO10
paired-endIllumina NovaSeq 6041


title: DOXO oocyte [DO11]

description:
Library name: DO11
paired-endIllumina NovaSeq 6042


title: Head regenerating tip, 44hpa, repB

description: Library name: 1984F84_44B

value: Whole tissue

value: 44 hours


title: DEK_CUT-Tag_MOLM13_4S-A_2

first: Zhe

last: Chen

institute: Chongqing Medical University

description: Library name: Sample6

tag: cell line


title: naivezt20d_rep1

description: Library name: 16


title: naivezt14d_rep3

description: Library name: 13


title: DOXO oocyte [DO8]

description:
Library name: DO8
paired-endIllumina NovaSeq 6039

tag: cell type

value: DOXO


title: DEK_CUT-Tag_MOLM13_4S-A_1

description: Library name: Sample5


title: naivezt20d_rep3

description: Library name: 18


title: DEK_CUT-Tag_MOLM13_shDEK_2

description: Library name: Sample4


title: DEK_CUT-Tag_MOLM13_shDEK_1

description: Library name: Sample3


title: DOXO oocyte [DO7]

description:
Library name: DO7
paired-endIllumina NovaSeq 6038


title: DOXO oocyte [DO9]

description:
Library name: DO9
paired-endIllumina NovaSeq 6040


title: DEK_CUT-Tag_MOLM13_shControl_2

description: Library name: Sample2


title: naivezt14d_rep1

description: Library name: 11


title: Head regenerating tip, 44hpa, repA

description: Library name: 1984F83_44A


title: Head regenerating tip, 33hpa, repA

description: Library name: 1984F85_33A


title: Head regenerating tip, 32hpa, repA

description: Library name: 1984F81_32A

value: 32 hours


title: naivezt14d_rep2

description: Library name: 12


title: naivezt8d_rep3

description: Library name: 8


title: DOXO oocyte [DO5]

description:
Library name: DO5
paired-endIllumina NovaSeq 6036


title: Head regenerating tip, 32hpa, repB

description: Library name: 1984F82_32B


title: DOXO oocyte [DO6]

description:
Library name: DO6
paired-endIllumina NovaSeq 6037


title: DEK_CUT-Tag_MOLM13_shControl_1

description: Library name: Sample1


title: Head regenerating tip, 43hpa, repB

description: Library name: 1984F80_43B

value: 43 hours


title: ATAC_MOLM13_4S-A_1

description: Library name: Sample5

data_processing:
Low-quality reads and adaptor sequences were removed by Trim Galore v0.4.4 with parameters “-q 10 -length 30 -stringency 5’.”
Paired-end reads were mapped to the mm10 reference genome using Bowtie2 version 2.2.9. Reads that aligned to the mitochondrial genome were filtered, and PCR duplicates were removed with picard MarkDuplicates.
To identify peaks, the bam files containing unique, nonchrM reads were used to call peaks with MACS2 using parameters ‘‘-nomodel-keep-dup all -q 0.01-shift -100-extsize 200-call-summits -g mm’’.
For differential coverage, corresponding bam files were merged to call peaks to get a union peak set. For each peak in the peak set, raw ATACseq reads were counted by featureCounts.
Assembly: GRCh38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

extract_protocol:
About 5,000 cells were resuspended in 50 µL of lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween 20, 0.01% Digitonin) and incubated on ice for 5 min. After lysis, 950 µL wash buffer was added to the sample. The supernatant was removed by centrifugation (500 g, 10 min).
Then, 4 µLPBS, 0.4 µL 10% Tween 20, 0.4 µL 1% Digitonin, 13.6 µL ddH2O, 20 µl 2×TD buffer, and 1.6 µL Transposome Mix were added to the sample, which was mixed and incubated at 37°C for 30 min. The reaction was terminated by incubating with 10 µL stop buffer. Then the tagment DNA was extracted using 2×DNA Extract Beads (Novoprotein). Total 35 µL DNA was transferred to a 0.2 ml PCR tube, and 2.5 µL N5 primer, 2.5 µL N7 primer, and 10 µL 5×AmpliMix were added. PCR was performed to amplify the library for 13-16 cycles. After the PCR reaction, libraries were purified using the 1.2×DNA Clean Beads (Novoprotein).

treatment_protocol: GFP⁺ MOLM-13 cells expressing shControl, shDEK-1, or shDEK-1 rescued with DEK-4S-A were sorted for ATAC-seq.


title: DOXO oocyte [DO4]

description:
Library name: DO4
paired-endIllumina NovaSeq 6035

value: WT


title: ATAC_MOLM13_4S-A_2

description: Library name: Sample6


title: naivezt8d_rep2

description: Library name: 7


title: Head regenerating tip, 43hpa, repA

description: Library name: 1984F79_43A


title: DOXO oocyte [DO3]

description:
Library name: DO3
paired-endIllumina NovaSeq 6034

value: oocyte


title: Head regenerating tip, 31hpa, repB

description: Library name: 1984F78_31B

value: 31 hours


title: naivezt8d_rep1

description: Library name: 6


title: naivezt2d_rep3

description: Library name: 5


title: DOXO oocyte [DO2]

description:
Library name: DO2
paired-endIllumina NovaSeq 6033


title: ATAC_MOLM13_shDEK_2

description: Library name: Sample4

value: AML cell line


title: Head regenerating tip, 31hpa, repA

description: Library name: 1984F77_31A


title: naivezt2d_rep2

description: Library name: 4


title: DOXO oocyte [DO1]

description:
Library name: DO1
paired-endIllumina NovaSeq 6032


title: Head regenerating tip, 42hpa, repB

description: Library name: 1984F76_42B

value: 42 hours


title: ATAC_MOLM13_shControl_1

description: Library name: Sample1


title: ATAC_MOLM13_shControl_2

description: Library name: Sample2


title: ATAC_MOLM13_shDEK_1

description: Library name: Sample3


title: control granulosa cell [CS15]

description:
Library name: CS15
paired-endIllumina NovaSeq 6030

value: granulosa

value: vehicle


title: SNI2_3

type: RNA

description: mouse SNI spinal cord 2, capture area 3

hyb_protocol: A total of 300 gene probes were used. 10 um sections were overlaid on Xenium slides before deparaffinization, decrosslinking and probe hybridisation with the predesigned custom standalone probe panels. The DNA probes are flanked by two regions that independently hybridize to the target RNA and also contain a gene specific barcode sequence. The probes hybridized to their complementary target RNA in an overnight incubation.    The following day, excess unbound probes were washed away in the post hybridization wash step. After removal of unbound probes, a ligase was added to seal the junction between the probe regions that have hybridized to RNA. Ligation of the probe ends on the targeted RNA region generates a circular DNA probe. This ligation ensures a unique level of probe specificity to the target region. The ligation products were enzymatically amplified to generate hundreds of copies of the gene-specific barcodes. Autofluorescence quenching was conducted to diminish unwanted autofluorescence and enhance signal-to-noise ratio in the treated FFPE tissue sections. Next, nuclei were stained with DAPI (derived from Xenium Nuclei Staining Buffer) to assist in identification of tissue or regions of interest during an instrument overview scan. Finally, tissue sections on Xenium slides assembled into Xenium Cassettes were loaded into the Xenium Analyzer for imaging and decoding.

scan_protocol: Imaging processing and analysis was conducted on Xenium processor.

data_processing: The output was analysed with Seurat.

label: Xenium probe set

source_name: mouse lumbar spinal cord

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: Samples were prepared via FFPE following dissection according to 10X Genomics protocol

value: mouse lumbar spinal cord

tag: tissue preservation method

value: FFPE

value: SNI


title: control granulosa cell [CS16]

description:
Library name: CS16
paired-endIllumina NovaSeq 6031


title: SHED_1_OSR2

first: Liwen

last: Fan

address: Hanzhong Road 140

institute: Nanjing Medical University

description: Library name: Sample 2

data_processing:
Raw reads were processed using Trimmomatic to remove adapter sequences and low-quality reads. Clean reads were used for subsequent alignment.Clean reads were aligned to the human reference genome hg19 using BWA-MEM algorithm. Alignment statistics including mapped rate and unique mapped rate were calculated.
Peak calling was performed using MACS2. Peaks with qvalue < 0.05 were considered significantly enriched.
Bigwig files were generated using deeptools for visualization of read coverage across the genome. IgG control sample was processed similarly to assess background signal.
The bigwig files include genome-wide coverage tracks for each Sample.
Assembly: GRCh37 (hg19)
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: Dental pulp

extract_protocol:
Following CUT&Tag reaction, DNA was extracted using phenol-chloroform and ethanol precipitation. DNA fragments were purified and quantified for library preparation.
CUT&Tag libraries were prepared using the Cleavage Under Targets and Tagmentation (CUT&Tag) method as described (Kaya-Okur et al., Nat Commun 2019). Libraries were constructed without the need for sonication or chromatin immunoprecipitation, using pG-Tn5 transposase to fragment and tag DNA adjacent to OSR2-bound loci.

treatment_protocol: SHED cells (stem cells from human exfoliated deciduous teeth) were cultured in α-MEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C in a humidified atmosphere with 5% CO2. Cells at passages 2-4 were used for experiments.For the OSR2 antibody group, SHED cells at passage 3 were collected and subjected to CUT&Tag assay using anti-OSR2 primary antibody (sc-393516X, Santa Cruz). For the control group, a matched IgG sample (SHED_IgG) was processed in parallel using non-specific IgG antibody instead of anti-OSR2 primary antibody. No other treatment was applied.

value: Dental pulp

value: Stem cells from human exfoliated deciduous teeth

value: Mesenchymal Stem Cells

value: OSR2 (sc-393516X, Santa Cruz)


title: Head regenerating tip, 30hpa, repB

description: Library name: 1984F74_30B

value: Whole tissue

value: 30 hours


title: Head regenerating tip, 30hpa, repA

description: Library name: 1984F73_30A


title: naivezt2d_rep1

description: Library name: 3

value: DRG

value: male

value: 6-12 weeks old


title: SNI2_2

description: mouse SNI spinal cord 2, capture area 2


title: SNI2_1

description: mouse SNI spinal cord 2, capture area 1


title: control granulosa cell [CS14]

description:
Library name: CS14
paired-endIllumina NovaSeq 6029

value: WT


title: control granulosa cell [CS13]

description:
Library name: CS13
paired-endIllumina NovaSeq 6028


title: SHED_1_IgG

description: Library name: Sample 1

growth_protocol: SHED cells (stem cells from human exfoliated deciduous teeth) were cultured in α-MEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C in a humidified atmosphere with 5% CO2. Cells at passages 2-4 were used for experiments.

value: IgG (sc-515946, Santa Cruz)


title: Head regenerating tip, 42hpa, repA

description: Library name: 1984F75_42A

value: 42 hours


title: control granulosa cell [CS12]

description:
Library name: CS12
paired-endIllumina NovaSeq 6027

value: granulosa


title: Head regenerating tip, 41hpa, repB

description: Library name: 1984F72_41B

value: 41 hours


title: SNI1_3

description: mouse SNI spinal cord 1, capture area 3

value: mouse lumbar spinal cord


title: monocytes from rheumatoid arthritis donor RA6, M2-like, LPS

city: Schlieren

first: Bojana

last: Müller-Durovic

state: Zurich

address: Wagistrasse 14

department: Department of Rheumatology

institute: University of Zurich

description: Library name: BSSE_QGF_223522

data_processing:
Base calling and demultiplexing were performed using bcl2fastq (v2.20.0.422) allowing one mismatch in index reads.
Raw sequencing reads were assessed for quality using FastQC, and summary quality metrics across samples were compiled using MultiQC.
cDNA reads were aligned to the human genome (UCSC version hg38) with STAR (v2.7.10a) using default parameters except allowing up to 10 hits in the genome (outFilterMultimapNmax 10), reporting only one alignment per multi-mapping read (outSAMmultNmax 1), and filtering reads without evidence in the splice junction table (outFilterType "BySJout").
Alignments were sorted and indexed with samtools (v1.11).
Gene-level read counts were generated using featureCounts from the Subread package (v2.0.1), counting read 5′ ends overlapping exons using the exon union model, with parameters -O, -M, --read2pos=5, --primary, -s 2, -p, -B. Gene annotation was based on Ensembl release 104.
Assembly: UCSC version hg38
Supplementary files format and content: csv file includes raw counts for each sample

source_name: blood

growth_protocol: Isolation of peripheral blood mononuclear cells (PBMCs) was done by standard density-gradient centrifugation (Lymphoprep, Fresenus Kabi, Norway). Positive selection of monocytes (M0) using CD14 Microbeads (Miltenyi Biotec, Germany) was performed according to manufacturer’s instructions. Isolated monocytes were cultured in R10 media (complete medium (RPMI 1640 (Gibco) with 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin- streptomycin supplemented with 2% GlutaMAX (all from GIBCO, ThermoFisher Scientific).

extract_protocol:
Cells were washed twice in ice-cold PBS and pelleted by centrifugation (4°C, 400xg, 5min). RNA extraction and on-column DNA digestion was performed using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.
Total RNA libraries were prepared using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) from 200 ng total RNA, including poly(A) selection and strand-specific library construction.

treatment_protocol: Differentiation of CD14+ monocytes into classically and alternatively activated macrophages was achieved by supplementing the culture with 20 ng/mL LPS/IFNγ or 20 ng/mL IL-4, respectively, on a three-times-per-week basis for 8 to 11 days. For macrophage activation, a 24-hour stimulation with 100 ng/mL LPS was used.

value: blood

value: primary cells

value: monocytes

tag: disease

value: rheumatoid arthritis

tag: donor id

tag: macrophage differentiation

tag: lps treatment

value: LPS


title: monocytes from rheumatoid arthritis donor RA6, M2-like, Vehicle

description: Library name: BSSE_QGF_223521

value: Vehicle


title: SNI1_2

description: mouse SNI spinal cord 1, capture area 2

value: FFPE

value: SNI


title: Head regenerating tip, 41hpa, repA

description: Library name: 1984F71_41A

value: Whole tissue

tag: strain


title: control granulosa cell [CS11]

description:
Library name: CS11
paired-endIllumina NovaSeq 6026

value: vehicle

tag: batch


title: Head regenerating tip, 29hpa, repB

description: Library name: 1984F70_29B

value: 29 hours


title: monocytes from rheumatoid arthritis donor RA6, M1-like, Vehicle

description: Library name: BSSE_QGF_223519


title: Head regenerating tip, 29hpa, repA

description: Library name: 1984F69_29A


title: SNI1_1

description: mouse SNI spinal cord 1, capture area 1


title: control granulosa cell [CS10]

description:
Library name: CS10
paired-endIllumina NovaSeq 6025

value: WT


title: monocytes from rheumatoid arthritis donor RA6, M1-like, LPS

description: Library name: BSSE_QGF_223520


title: Head regenerating tip, 40hpa, repB

description: Library name: 1984F68_40B

value: 40 hours


title: monocytes from rheumatoid arthritis donor RA6, undifferentiated M0, LPS

description: Library name: BSSE_QGF_223518

value: undifferentiated M0


title: Head regenerating tip, 40hpa, repA

description: Library name: 1984F67_40A


title: monocytes from rheumatoid arthritis donor RA6, undifferentiated M0, Vehicle

description: Library name: BSSE_QGF_223517


title: monocytes from rheumatoid arthritis donor RA5, M2-like, LPS

description: Library name: BSSE_QGF_223516


title: control granulosa cell [CS9]

description:
Library name: CS9
paired-endIllumina NovaSeq 6024

value: granulosa


title: Sham2_2

description: mouse Sham spinal cord 2, capture area 2

value: Sham


title: control granulosa cell [CS8]

description:
Library name: CS8
paired-endIllumina NovaSeq 6023


title: control granulosa cell [CS6]

description:
Library name: CS6
paired-endIllumina NovaSeq 6021


title: Sham2_1

description: mouse Sham spinal cord 2, capture area 1

value: mouse lumbar spinal cord


title: monocytes from rheumatoid arthritis donor RA5, M2-like, Vehicle

description: Library name: BSSE_QGF_223515

value: blood


title: Sham2_3

description: mouse Sham spinal cord 2, capture area 3


title: Head regenerating tip, 28hpa, repB

description: Library name: 1984F66_28B

value: 28 hours


title: Sham1_2

description: mouse Sham spinal cord 1, capture area 2


title: monocytes from rheumatoid arthritis donor RA5, M1-like, LPS

description: Library name: BSSE_QGF_223514

value: primary cells

value: monocytes


title: Head regenerating tip, 39hpa, repB

description: Library name: 1984F64_39B

value: 39 hours


title: control granulosa cell [CS4]

description:
Library name: CS4
paired-endIllumina NovaSeq 6019


title: control granulosa cell [CS7]

description:
Library name: CS7
paired-endIllumina NovaSeq 6022


title: Sham1_3

description: mouse Sham spinal cord 1, capture area 3


title: Sham1_1

description: mouse Sham spinal cord 1, capture area 1


title: control granulosa cell [CS3]

description:
Library name: CS3
paired-endIllumina NovaSeq 6018


title: control granulosa cell [CS5]

description:
Library name: CS5
paired-endIllumina NovaSeq 6020


title: Head regenerating tip, 39hpa, repA

description: Library name: 1984F63_39A


title: monocytes from rheumatoid arthritis donor RA5, M1-like, Vehicle

description: Library name: BSSE_QGF_223513

value: rheumatoid arthritis

value: Vehicle


title: monocytes from rheumatoid arthritis donor RA5, undifferentiated M0, LPS

description: Library name: BSSE_QGF_223512

value: LPS


title: Head regenerating tip, 27hpa, repB

description: Library name: 1984F62_27B

value: Whole tissue

value: 27 hours


title: Colon, D50, Immune fraction, gene expression

city: Stockholm

first: Jennifer

last: Fransson

address: Karolinska Institutet

institute: Karolinska Institutet

data_processing:
Reads were analyzed using CellRanger v 6.0.2 (10X Genomics). The first run did not capture the feature barcodes of some samples due to a mistake, for which reason .tsv-files containing the feature barcode counts for those samples.
Gene expression matrices were analyzed using the Seurat 4.1.1 pipeline
Assembly: mm10
Supplementary files format and content: .h5-files for each sample and .tsv-files with feature barcode counts for some samples.

source_name: colon

extract_protocol:
Colonic cells were isolated as previously described with minor alterations (Villablanca et al., 2011). Briefly, colonic tissue was cleaned from fat, opened longitudinally and cut into 1 cm pieces. Tissues from mice from the same treatment group and time point were pooled. Tissues were incubated for 30 min at 37 °C in 20 ml HBSS with 5% FCS, 5 mM EDTA, 1 mM DTT and 15 mM HEPES while shaking gently. The epithelium-enriched supernatant was then filtered through a 100 µm strainer, washed in PBS with 5% FCS and 1 mM EDTA, and cells were recovered at the interface of a 44-67% Percoll gradient. The remaining tissue was washed twice in PBS and digested in 10 ml of serum-free HBSS with Liberase TL (0.15 mg/ml, Roche) and 0.1 mg/ml DNase I (Roche) at 37 °C at 600 rpm for 60 min. After filtration through a 100 μm cell strainer, lamina propria-enriched cells were washed with PBS with 5% FCS and 1 mM EDTA and separated on a 44-67% Percoll gradient. Both epithelium-enriched and lamina propria-enriched fractions were stained with TER-119 Pacific Blue, CD45.2 PE/Cyanine7 and EpCAM FITC surface antibodies (BioLegend) for cell type assignment. Cells from the lamina propria were additionally labeled with TotalSeq antibodies (BioLegend) targeting CD90.2, CD3, CD4, KLRG1, CD127, Ly-6C, CD64, CD11b, CD11c, CD103 and Ly-6G according to manufacturer’s instructions. After additional staining with DAPI for live/dead cell identification, cells were sorted using Sony SH800 Cell Sorter into 15mL tubes filled with complete RPMI medium with 10% FCS. Epithelial cells were sorted from the epithelium-enriched fraction by gating EpCAM+/CD45- cells. Immune and stromal cells were sorted from the lamina propria-enriched fraction, by gating EpCAM-/CD45+ and EpCAM-/CD45- cells, respectively. Approximately 16000 cells per sample were loaded onto the 10X Genomics Chromium Controller and processed with the Chromium Next GEM Single Cell 3ʹ v3.1 (Dual Index) with Feature Barcode technology for Cell Surface Protein (10X Genomics).
Libraries were constructed following the manufacturer’s guidelines (Chromium Next GEM Single Cell 3ʹ v3.1 (Dual Index) with Feature Barcode technology for Cell Surface Protein (10X Genomics)), with TotalSeq-derived barcodes being retained only for the immune cell fractions.
Sequencing was performed by Novogene Co. Ltd (UK) (Rag2-/- samples) or NGI Sweden (SCID samples) on NovaSeq 6000 sequencers with a targeted sequencing depth of 300M reads per gene expression sample and 50M reads per TotalSeq-derived sample. Read length was PE150 (Novogene) or 28-10-10-150 for gene expression samples and 28-10-10-25 (NGI) for TotalSeq-derived samples.

value: colon

value: Immune

value: Rag2 KO

value: CD45RBhi transfer

tag: time

value: no


title: Head regenerating tip, 28hpa, repA

description: Library name: 1984F65_28A

tag: tissue


title: M1-siEHD1-2

description:
Library name: BMDM11
bulk RNA-seq

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality. Reads were pre-processed by Trim Galore (v.0.6.3) and Cutadapt programs.
Reads were aligned to the mouse genome mm10 using STAR (v2.7.6a) with the default settings.
Transcript assembly and differential expression analysis were performed using the Rsubread package (featureCounts, v2.20.0) and the DESeq2 package (v1.46.0) in R (v4.4.2).
Assembly: mm10
Supplementary files format and content: comma-delimited csv files containing feature counts values

source_name: Bone marrow-derived macrophages

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) according to the manufacturer’s instructions
RNA-seq library construction was performed at Innomics Inc. with a standard polyA-enrichment protocol.

treatment_protocol: Mouse bone marrow-derived macrophages (BMDMs) were treated with siEhd1 and incubated with lipopolysaccharide (LPS).

value: Bone marrow-derived macrophages

value: BMDM

tag: Sex

value: Male

tag: age

value: 8 weeks

value: BMDMs with siEhd1 and LPS treatment (M1)