title: N323E2_NSC_46XY

city: Thuwal

first: Antonio

last: Adamo

state: Makkah

address: Thuwal 23955-6900 KAUST

department: iological, Environmental Sciences and Engineering

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

data_processing:
After FastQC quality control,sequence adapters were trimmedwith trimGalore v.0.06.
High quality reads were mapped against the reference genome (GRCh38/Ensembl release 101) using Bismark v.0.23.1
The CpG  extraction was done with MethylDackel v 0.6.1
Assembly: Ensembl GRCh38 v. 101
Supplementary files format and content: One BedGraph for each sample, containing information about methylation levels. Column 1: chromosome, Column 2: start position of CpG site (0-based),  Column 3: ending position of the CpG site (exclusive), Column 4: methylation percentage observed at the CpG site. Percentage is calculated as the proportion of methylated cytosines relative to the total number of cytosines sequenced at that position  (C/C+T *100), Column 5: Total number of reads covering CpG site, Column 6: Counts of methylated cytosines detected at each site.

source_name: NSC

growth_protocol: Fibroblasts were cultured and expanded in high glucose DMEM supplemented with 15% FBS, 1% non-essential amino acids and 1% penicillin-streptomycin. The established hiPSC lines were cultured on hESC-qualified Matrigel (Corning) coated 6-well-plates in E8 medium and passaged with Versene in E8 medium supplemented with 5 uM Rock Inhibitor (Y-27632). Human iPSC lines were incubated at 37°C in the presence of 5% CO2 and 5% O2. NSCs have been further expanded in Neural Expansion Media and collected at P2 for RNA extraction and immunostaining.

extract_protocol:
The gDNA was extracted using the DNeasy Blood & Tissue genomic DNA  Extraction Kit From Qiagen.
DNA libraries were generated  by Beijing Novogene Bioinformatics Technology, Co., Ltd. (Beijing, China). Target enrichment was performed to construct the exome library using the Agilent SureSelect Human All Exon V6 kit (Agilent Technologies, Inc., Santa Clara, CA, United States), according to manufacturer’s protocol, then DNA was sequenced using IluminaNovaseq6000/NovaseqX 2 x 150b or Novaseq 6000 as indicated in the table.

treatment_protocol: Fibroblasts were reprogrammed using the the Stemgent® StemRNA-NM Reprogramming Kit. Fibroblasts were transfected daily with synthetic NM-RNAs in presence of Essential 8 Media (E8) for four consecutive days. The differentiation of iPSCs into Neural stem cells was established using the PSC Neural Induction Kit from Thermo Fisher. Briefly, iPSCs were detached when reached 70-80% confluency in small clumps using Versene and seeded at a dilution 1:6-1:8 on Matrigel-coated dishes in the presence of E8 + 10 uM Y-27632. Twenty-four hours after seeding, the Neural Induction Media (Neurobasal Medium + 1X Neural Induction Supplement) was added and used for seven days. On day 7 of neural induction, NSCs that reached P0 were harvested using Accutase, seeded at 1.0*106 cells on Matrigel-coated 6-well plates and cultured in Neural Expansion Media (50% Neurobasal Medium + 50% Advanced DMEM/F12 media + 1X Neural Induction Supplement) for about five days, until they reached 90% confluency.

value: NSC

tag: condition

value: Healthy


title: 13LGS_NeuroD1_Biological_Rep2_technical_Rep2

status: Public on Apr 28 2025

type: SRA

city: Baltimore

first: Pin

last: Lyu

address: 400 N Broadway

country: USA

institute: JHU

description:
Library name: 13LGS_NeuroD1_B2_T2
13LGS_Neurod1_peaks.narrowPeak

library_source: genomic

data_processing:
Sequence reads were trimmed of low quality bases and adapters using cutadapt v3.5 76and Trim Galore v0.6.4_dev 77, using arguments ---paired --length 20 -e 0.1 --illumina -q 20 --stringency 3. Trimmed reads were aligned to mouse genome GRCm38 and 13LGS genome Itri_07Aug2017 using Bowtie2 78 with arguments -X 1000 --very-sensitive-local --no-mixed --no-discordant --no-dovetail. Unmapped reads with a MAPQ score of 30 or below were filtered from the analysis with SAMtools v1.12 79. Aligned reads were deduplicated using UMI-tools 80 dedup with parameters -chimeric-pairs="discard" --unpaired-reads="discard" --paired --ignore-umi. Technical replicates were collapsed into single biological replicates using samtools merge. For visualization, normalization was applied using deepTools bamCoverage v3.5.1 81 using arguments --binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 2311060300 (13LGS) or --effectiveGenomeSize 2651675564 (mouse). For each protein target, peaks were called jointly across replicates against IgG control using macs2 82 using arguments -f BAMPE --keep-dup all -q 0.05 -g 2311060300 (13LGS) or -g 2651675564 (mouse). For mouse samples, peaks on mitochondrial reads and blacklisted ENCODE regions 83 were filtered from analysis.
Assembly: GRCm38
Supplementary files format and content: txt for called peaks
Library strategy: CUT&Run

molecule: genomic DNA

organism: Ictidomys tridecemlineatus

source_name: P5 retina

extract_protocol:
Nuclei were isolated according to the described protocol 75, using a lysis buffer modified to contain 0.01% Tween-20 and 0.01% Nonidet P40, as well as 1X protease inhibitor cocktail (Roche, 11873580001) in all solutions. Samples were lysed for 5 minutes in the lysis buffer with gentle trituration throughout, as described. CUT&RUN was performed using the CUTANA™ ChIC/CUT&RUN Kit (Epicypher, 14-1048). For each reaction, either 500,000 13LGS nuclei or 385,000 mouse nuclei were used. The CUTANA protocol v4.0 protocol was followed with minor modifications. In brief, isolated nuclei were resuspended in CUT&RUN wash buffer and added directly to Concanavalin A beads. Then 0.5 µg of the following antibodies were added to each respective reaction: IgG control (EpiCypher, 13-0042), H3K4me1 (EpiCypher, 13-0057), H3K4me3 (EpiCypher, 13-0041), H3K27ac (EpiCypher, 13-0059), H3K27me3 (EpiCypher, 13-0055), NeuroD1 (Cell Signaling, 62953), Otx2 (R&D Systems, BAF1979), or Otx2 (Atlas Antibodies, HPA000633).  H3K9me3 (Abcam, ab8898) was used at 0.41 µg of antibody per reaction.
The total CUT&RUN DNA yield, up to 5 ng of total purified DNA, was used for library preparation, using reagents from CUTANA™ CUT&RUN Library Prep Kit (EpiCypher, 14-1001) or NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, E7645S). The EpiCypher CUTANA Library Prep Kit User Manual v1.3 was followed and indexing performed using NEBNext® Multiplex Oligos for Illumina® (NEB, E7395S) or Dual Index Kit TT Set A (10X Genomics, PN-1000215). Final libraries were sequenced at the Novogene sequencing core (Sacramento, CA, USA) on the NovaSeq X Plus (Illumina) to generate paired-end 150 base pair reads.

tag: tissue

value: P5 retina


title: 13LGS_NeuroD1_Biological_Rep2_technical_Rep1

description:
Library name: 13LGS_NeuroD1_B2_T1
13LGS_Neurod1_peaks.narrowPeak


title: primed HSCs [primed-11_L2_F0000551D87]

city: Guangzhou

first: chen

last: minqi

state: Guangdong

address: No.74, 2nd Zhongshan Road

country: China

institute: Sun Yat-sen University

library_source: transcriptomic

data_processing:
RNA seq reads were aligned to mouse genome GRCm38 and gene annotation from the Ensembl database. For read alignment and expression quantification, low quality reads were removed and the adaptor sequences were trimmed by Trim Galore (v0.5.0, Babraham Bioinformatics). The remaining pair-end reads were mapped to the reference genome by Salmon (v0.03.1, COMBINE-lab) with ENCODE options. The uniquely mapped reads were counted and transformed to transcripts per kilobase millionreads (TPM)
Assembly: GRCm38
Supplementary files format and content: merge.count.csv with raw counts matrices

molecule: total RNA

organism: Mus musculus

source_name: bone marrow

extract_protocol:
In brief, intact bone marrows from mice at the age of 6-8 weeks were flushed from mouse femora and tibiae. Bone marrow cells by pipetting with 1 mL syringe, and then underwent red blood cell lysis using 0.16 M ammonium chloride solution.
smart-seq2

tag: strain

value: bone marrow

tag: age

value: 6-8 weeks

tag: genotype

value: Cd4-cre;R26Tdtomato mice

tag: cell type

value: primed HSCs


title: P323E2_iPSC_46XY

organism: Homo sapiens

source_name: iPSC

value: iPSC


title: primed HSCs [primed-12_L2_Y0000740D87]


title: HD1, ADT

city: Bethesda

first: Laura

last: Dillon

state: Maryland

address: Room 10CRC 6-5142, 10 Center Drive

department: Hematology Branch

institute: National Heart Lung and Blood Institute, NIH

description: Healthy Donor 1 Single-cell

library_source: other

data_processing:
Reads were aligned to human genome assembly GRCh37/hg19 by HISAT2 (version 2.1.0) with default setting for paired-end reads. The aligned reads were converted to BAM files and sorted by SAMtools 1.9 with index files created. The sorted BAM files were processed in R (version 3.5; R Foundation for Statistical Computing, Vienna, Austria) with Bioconductor packages. The count matrix on gene level was generated by featureCounts in Rsubread function.
Assembly: GRCh37/hg19 for bulk RNAseq; Single-cell cellranger used the pre-built GRCh38 in the pipeline.
Supplementary files format and content: Gene raw count matrix in csv for bulk RNAseq; single-cell processed data contain the gene and protein expression matrices with cell barcodes.

molecule: protein

source_name: Bone marrow

growth_protocol: Bone marrow aspirate was collected from enrolled patients at different time points and healthy donors.

extract_protocol:
Bulk RNAseq: RNA was isolated from PAXgeneTM BM RNA tubes using the PAXgene BM RNA kit (PreAnalytiX). RNA quantity was measured using a Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA) and RNA quality was assessed using the TapeStation system (Agilent Technologies, Santa Clara, CA). All samples had RNA Integrity Numbers (RIN) of seven or higher. Single-cell: BM mononuclear cells (BMMCs) were purified from BM aspirate using density centrifugation, cryopreserved, and stored in liquid nitrogen.
Bulk RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina Inc., San Diego, CA) using 1 μg of total RNA input and paired-end 75-bp sequencing on a HiSeq 3000 (Illumina, San Diego, CA). The 10x Genomics 3’v3 Single Cell Immune profiling platform was used for scRNA-seq of BMMCs. cDNA amplification was performed according to manufacturer’s instructions with the addition of 1 ul 0.2 uM ADT additive primer per sample to amply ADT tags.

treatment_protocol: No treatment

value: Bone marrow


title: 13LGS_H3K27ac_Biological_Rep2

description:
Library name: 13LGS_H3K27ac_B2
13LGS_H3K27ac_peaks.narrowPeak


title: P807G_iPSC_46XY


title: primed HSCs [primed-10_L2_Y0000645D87]


title: 13LGS_H3K4me3_Biological_Rep2

description:
Library name: 13LGS_H3K4me3_B2
13LGS_H3K4me3_peaks.narrowPeak


title: NS4774_NSC_47XYY

data_processing:
RNA-Seq data validation, pairing and FastQC quality control was followed by adaptor sequence/low quality sequence trimming using BBDuk.
High quality reads were mapped against the reference genome (GRCh38/Ensembl release 101) using the STAR end-to-end alignment method
Read counts quantification was perfomed with FeatureCounts, lowly expressed genes were filtered out using HTSFilter
Assembly: Ensembl GRCh38 v. 101
Supplementary files format and content: Worksheet file containing Normalized counts (TMM). Columns represent samples and rows genes.

extract_protocol:
The total RNA extraction was performed using MagMAX mirVana Total RNA Isolation Kit (Applied Biosystems) following the manufacturer’s instructions. 250-500  ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were generated using the human mRNA TruSeq Stranded library preparation KIT from Illumina (Illumina) following the manufacturer's protocols.

value: JS


title: F323_Fibroblast_46XY

source_name: Fibroblast

value: Fibroblast


title: primed HSCs [primed-9_L2_Y0000084D87]


title: 13LGS_H3K4me1_Biological_Rep2

description:
Library name: 13LGS_H3K4me1_B2
13LGS_H3K4me1_peaks.narrowPeak


title: primed HSCs [primed-7_L2_Y0000521D87]


title: primed HSCs [primed-8_L2_Y0000703D87]


title: 13LGS_IgG_Biological_Rep2

description: Library name: 13LGS_IgG_B2


title: NS4748_NSC_47XYY


title: NS4773_NSC_47XYY


title: 13LGS_Otx2_RD_Biological_Rep1_technical_Rep2

description:
Library name: 13LGS_Otx2_RD_B1_T2
13LGS_Otx2_peaks.narrowPeak


title: NS4772_NSC_47XYY


title: N807G_NSC_46XY


title: NS4747_NSC_47XYY


title: primed HSCs [primed-6_L2_F0000341D87]


title: 13LGS_Otx2_RD_Biological_Rep1_technical_Rep1

description:
Library name: 13LGS_Otx2_RD_B1_T1
13LGS_Otx2_peaks.narrowPeak


title: primed HSCs [primed-5_L2_Y0000739D87]


title: primed HSCs [primed-4_L2_Y0001488D87]


title: NS4746_NSC_47XYY


title: primed HSCs [primed-3_L2_Y0000653D87]


title: 13LGS_NeuroD1_Biological_Rep1_technical_Rep2

description:
Library name: 13LGS_NeuroD1_B1_T2
13LGS_Neurod1_peaks.narrowPeak


title: 13LGS_NeuroD1_Biological_Rep1_technical_Rep1

description:
Library name: 13LGS_NeuroD1_B1_T1
13LGS_Neurod1_peaks.narrowPeak


title: NS4745_NSC_47XYY


title: primed HSCs [primed-2_L2_Y0000644D87]


title: 13LGS_IgG_Biological_Rep1_technical_Rep2

description: Library name: 13LGS_IgG_B1_T2


title: NS4744_NSC_47XYY


title: 13LGS_IgG_Biological_Rep1_technical_Rep1

description: Library name: 13LGS_IgG_B1_T1


title: primed HSCs [primed-1_L2_Y0000082D87]


title: NS4743_NSC_47XYY


title: Control participant 329

type: genomic

city: Budapest

first: Zsolt

last: Radák

address: Alkotás Street 44, building L3

country: Hungary

institute: Research Center for Molecular Exercise Science, Hungarian University of Sports Science

description:
MethylationEPIC v2.0
OLY.C9.EPI.A

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing:
The raw methylation signal intensities were retrieved using the function read.metharray.exp of the minfi v1.40.0 R package, followed by linear dye bias correction and noob background correction to account for technical variation in background fluorescence signal. Specifically, the value was calculated from the intensity of the methylated and unmethylated sites, as the ratio of fluorescent signals.
*processed value definition: Average Beta

label: Cy3 and Cy5

source_name: Blood

label_protocol: standard protocol

extract_protocol: standard protocol

value: Blood

tag: project batch

tag: gender

value: female

tag: olympic champion

value: no

tag: sport

value: controll

tag: date of sampling

tag: age (days)


title: Control participant 328

description:
MethylationEPIC v2.0
OLY.C6.EPI.A

value: male


title: NS4579_NSC_47XYY


title: PC9/GR si-MYLK-AS1 repeat2

city: Nanjing

first: Erbao

last: Zhang

state: Jiangsu

address: longmian da dao

department: Department of Epidemiology

institute: Nanjing Medical University

description: Library name: Sample 5

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to  genome using Mapsplice v2.1.8 with  parameters -s 22 -p 15 --ins 6 --del 6 --non-canonical --bam -o
count counting
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA library using standard Ion proton RNA-Seq Kit v2.0 protocol

tag: cell line

value: lung cancer cells

value: MYLK-AS1 knockdown


title: PC9/GR si-MYLK-AS1 repeat3

description: Library name: Sample 6


title: NS4578_NSC_47XYY

value: NSC


title: PC9/GR si-MYLK-AS1 repeat1

description: Library name: Sample 4


title: Control participant 327

description:
MethylationEPIC v2.0
OLY.C5.EPI.A


title: Control participant 326

description:
MethylationEPIC v2.0
OLY.C4.EPI.A


title: Control participant 325

description:
MethylationEPIC v2.0
OLY.C34.EPI.A


title: NS4577_NSC_47XYY


title: PC9/GR si-NC repeat2

description: Library name: Sample 2

value: Control


title: PC9/GR si-NC repeat1

description: Library name: Sample 1


title: NS4556_NSC_47XYY


title: PC9/GR si-NC repeat3

description: Library name: Sample 3


title: NS4555_NSC_47XYY


title: Control participant 323

description:
MethylationEPIC v2.0
OLY.C32.EPI.A


title: Control participant 322

description:
MethylationEPIC v2.0
OLY.C30.A


title: NS4554_NSC_47XYY


title: NS4537_NSC_47XYY


title: hepatocyte m6A input

city: Shanghai

first: Jia

middle: Kai

last: W

address: 800 Xiangyin Road

institute: National Key Laboratory of Medical Immunology and Institute of Immunology

data_processing:
using the application Seqtk for filtering, the main steps are as follows: Remove the adaptor sequences, bases with a mass Q of less than 20 at the 3 'end, reads with a length less than 25, and ribosome RNA reads
Performed Hisat2 for genome mapping to mm10
using exomepeak R package for peak calling and annotation
Assembly: mm10
Supplementary files format and content: bed files include all peak calling for Sample

source_name: liver

growth_protocol: C57BL/6 mice were purchased from Joint Ventures Sipper BK Experimental Animal (Shanghai, China).

extract_protocol:
Primary hepatocytes seeded in a 15 cm dish at 85% confluence were cross-linked by ultraviolet light and harvested. For m6A RIP, the procedure was performed according to the instructions of Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit.
cDNA library was constructed and subjected to high throughput sequencing using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® kit
m6A RIP-seq

treatment_protocol: Primary hepatocytes were isolated according to the protocol

value: liver

value: hepatocyte


title: NS4536_NSC_47XYY


title: NS4538_NSC_47XYY


title: hepatocyte m6A RIP


title: Control participant 320

description:
MethylationEPIC v2.0
OLY.C29.EPI.A


title: Control participant 321

description:
MethylationEPIC v2.0
OLY.C3.EPI.A


title: eCLIP-seq, HepG2, PXR, IP, rep2

city: Pittsburgh

first: Min

state: PA

address: Salk Hall, 3501 Terrace St

institute: University of Pittsburgh

data_processing:
The data was processed using CLIP Tool Kit (CTK).
eCLIP-Seq data were firstly demultiplexed using fastx-toolkit. Then the adapters were trimmed using Cutadapt and the low-quality reads were dropped.
The exact PCR duplicates were collapsed. The trimmed read 2 sequences were mapped to the hg38 genome using bwa (Li and Durbin, 2009). Only uniquely mapped reads were retained. The two IP replicates were merged for futther analysis.
For IP sample, we separated the reads into plus and minus strand. Peaks were called using MACS2, and peaks from plus and minus strands were merged as the final peak list.
Bedgraph files were generated using CTK for visualization in the UCSC genome browser based on the bed files of processed reads.
Assembly: hg38, mm10
Supplementary files format and content: bedgraph and peak files from MACS2
Library strategy: eCLIP-Seq

source_name: Liver

growth_protocol: Wildtype and PXR knockout LS174T cells and HepG2 cells were maintained in EMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 °C.  Mouse livers were collected from humanized PXR mice.

extract_protocol:
RNA fragments were extracted using acid phenol:chloroform:isoamyl alcohol (25:24:1, pH 6.6) (Invitrogen) and cleaned up RNA Clean & Concentrator-5 columns (Zymo). After reverse transcription, qPCR was performed to determine the Ct value of the cDNA with Power SYBR Green Master Mix (Applied Biosystems).
DNA fragments were amplified with primers containing Illumina adapter sequences using Q5 High-Fidelity 2× Master Mix (NEB) for 9 to 18 cycles based on the Ct values, and PCR products were purified with Agencourt AMPureXP beads (Beckman Coulter). The DNA fragments ranging from 175 - 300 bp were selected via agarose gel electrophoresis. Fragments was excised and extracted using the MinElute Gel Extraction Kit (Qiagen) and libraries were validated using the 1× High Sensitivity DNA Kit (Invitrogen).

treatment_protocol: 20 million cells for each reaction were washed twice with ice-cold PBS, UV-crosslinked on ice with 254 nm at 400 mJ/cm2 with a UV crosslinker (XL-1000, Spectrolinker), lysed with iCLIP lysis buffer for 15 min on ice and digested with RNase I (Ambion) and Turbo DNase (Ambion) at 37°C on a ThermoMixer C (Eppendorf), and incubated with anti-PXR, anti-HA or anti-IgG antibodies overnight.

value: Liver

tag: disease

value: Hepatocellular carcinoma

tag: eclip antibody

value: HA


title: NS4535_NSC_47XYY + Chr6 (q21.5 gain 1,998 Kb)


title: eCLIP-seq, HepG2, PXR, IP, rep1


title: Control participant 319

description:
MethylationEPIC v2.0
OLY.C28.EPI.A


title: Control participant 318

description:
MethylationEPIC v2.0
OLY.C27.EPI.A


title: NS4534_NSC_47XYY + Chr6 (q21.5 gain 1,998 Kb)


title: Control participant 317

description:
MethylationEPIC v2.0
OLY.C25.EPI.A


title: NS4527_NSC_47XYY  +Chr11(q13.5 gain 1,218 Kb)


title: NS4533_NSC_47XYY + Chr6 (q21.5 gain 1,998 Kb)


title: eCLIP-seq, PXR knockout LS174T, PXR, IP

source_name: Colon

value: Colon

value: Colorectal Adenocarcinoma

value: PXR


title: Control participant 324

description:
MethylationEPIC v2.0
OLY.C33.EPI.A

value: Blood


title: eCLIP-seq, HepG2, input


title: Control participant 316

description:
MethylationEPIC v2.0
OLY.C20.EPI.A


title: DHX58 RIP

data_processing:
using the application Seqtk for filtering, the main steps are as follows: Remove the adaptor sequences, bases with a mass Q of less than 20 at the 3 'end, reads with a length less than 25, and ribosome RNA reads
Performed Hisat2 for genome mapping to mm10
Apply Stringtie (version: 1.3.0) to count the number of Fragments for each gene after Hisat2 alignment, then normalize using TMM (trimmed mean of M values) method, and finally calculate the FPKM value for each gene using Perl script
Using edgeR for inter sample differential gene analysis, obtain p-value, and perform multiple hypothesis testing correction
Assembly: mm10
Supplementary files format and content: xls files include count and FPKM values for LGP2 Sample

extract_protocol:
Primary hepatocytes seeded in a 15 cm dish at 85% confluence were cross-linked by ultraviolet light and harvested. RIP was performed using the Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit (Millipore) according to the manufacturer’s instructions.
cDNA library was constructed and subjected to high throughput sequencing using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® kit

tag: antibody

value: DHX58 antibody

tag: treatment

value: wild type


title: Control participant 315

description:
MethylationEPIC v2.0
OLY.C2.EPI.A

value: no

value: controll


title: NS4526_NSC_47XYY  +Chr11(q13.5 gain 1,218 Kb)

tag: condition

value: JS


title: eCLIP-seq, wildtype LS174T, input

tag: tissue


title: Control participant 314

description:
MethylationEPIC v2.0
OLY.C19.EPI.A

value: male


title: eCLIP-seq, wildtype LS174T, PXR, IP


title: FKBP-SETD1B

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.3.3.1.
Duplication reads were removed from aligned file by using picard-tools-2.18.2
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER v4.7 makeUCSCfile command and comberted to bigwig by bedGraphToBigWig. BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: MOLM-13 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol:
Cells were fixed with 2mM DSG and 1% formaldehyde, and samples from sonicated nuclear fraction were incubated with each antibody and histone-DNA complexes were isolated.
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) following the manufacturer’s protocol.

value: leukemia

tag: chip antibody

value: HA-Tag (Cell Signaling #3724)


title: NS4090_NSC_46XY

value: NSC

value: Healthy


title: Control participant 313

description:
MethylationEPIC v2.0
OLY.C18.EPI.A


title: N3263_NSC_46XY


title: Control participant 312

description:
MethylationEPIC v2.0
OLY.C16.EPI.A

value: female


title: liver_Cort, High Protein Diet, rep3

city: Baton Rouge

first: Jaroslaw

last: Staszkiewicz

state: LA

address: 6400 Perkins Rd

department: Genomics Core Facility

institute: Pennington Biomedical Research Center

description: Library name: liver_HP_Cort_3

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, R V4.0.3, Rstudio V1.3.1093 and biomaRt V2.46.3
Raw expression data was normalized by the TMM (trimmed mean of M-values) method
Potential outlier samples were detected via principal components analysis (PCA) via princomp package in R
Differential gene expression analysis was performed via limma package in R (v 3.46.0)
Assembly: Mouse – GRCm38.84  mm10
Supplementary files format and content: tab-delimited text containing raw counts

extract_protocol:
Liver and eWAT were removed, flash frozen on dry ice, and RNA was harvested using Rneasy kit from Qiagen
Quant-Seq  3' mRNA-Seq Library Prep Kit

value: Liver


title: liver_Cort, High Protein Diet, rep4

description: Library name: liver_HP_Cort_4


title: N3262_NSC_46XY


title: Control participant 311

description:
MethylationEPIC v2.0
OLY.C13.EPI.A


title: liver_Cort, High Protein Diet, rep2

description: Library name: liver_HP_Cort_2


title: N3257_NSC_46XY


title: N3258_NSC_46XY


title: liver_Cort, Normal Protein Diet, rep4

description: Library name: liver_NP_Cort_4


title: N3256_NSC_46XY


title: liver_Cort, Normal Protein Diet, rep3

description: Library name: liver_NP_Cort_3


title: Control participant 307

description:
MethylationEPIC v2.0
OLY.C1.EPI.A


title: liver_Cort, Normal Protein Diet, rep2

description: Library name: liver_NP_Cort_2


title: N3098_NSC_46XY


title: Control participant 306

description:
MethylationEPIC v2.0
OLY.C.26.EPIC.A


title: N3097_NSC_46XY


title: Control participant 308

description:
MethylationEPIC v2.0
OLY.C10.EPI.A


title: NS4525_NSC_47XYY  +Chr11(q13.5 gain 1,218 Kb)


title: liver_Cort, Normal Protein Diet, rep1

description: Library name: liver_NP_Cort_1


title: liver_Veh, High Protein Diet, rep4

description: Library name: liver_HP_Veh_4


title: liver_Veh, High Protein Diet, rep3

description: Library name: liver_HP_Veh_3


title: Control participant 305

description:
MethylationEPIC v2.0
OLY.C.24.EPIC.A


title: N3094_NSC_46XY


title: liver_Veh, High Protein Diet, rep2

description: Library name: liver_HP_Veh_2


title: N3095_NSC_46XY


title: Control participant 302

description:
MethylationEPIC v2.0
OLY.C.14.EPIC.A


title: N3093_NSC_46XY


title: Control participant 310

description:
MethylationEPIC v2.0
OLY.C12.EPI.A


title: liver_Cort, High Protein Diet, rep1

description: Library name: liver_HP_Cort_1


title: liver_Veh, Normal Protein Diet, rep4

description: Library name: liver_NP_Veh_4


title: Control participant 309

description:
MethylationEPIC v2.0
OLY.C11.EPI.A


title: Control participant 301

description:
MethylationEPIC v2.0
OLY.36.EPIC.A/C23


title: L_4744_NSC_47XYY


title: L_4536_NSC_47XYY


title: Control participant 300

description:
MethylationEPIC v2.0
C.8.EPIC.A


title: liver_Veh, Normal Protein Diet, rep3

description: Library name: liver_NP_Veh_3


title: N3096_NSC_46XY


title: Control participant 303

description:
MethylationEPIC v2.0
OLY.C.15.EPIC.A


title: Control participant 299

description:
MethylationEPIC v2.0
C.7.EPIC.A


title: L_3263_NSC_46XY


title: L_3257_NSC_46XY


title: Control participant 298

description:
MethylationEPIC v2.0
C.35..A


title: Control participant 297

description:
MethylationEPIC v2.0
C.22.A


title: liver_Veh, Normal Protein Diet, rep1

description: Library name: liver_NP_Veh_1


title: L_3105_NSC_46XY


title: liver_Veh, High Protein Diet, rep1

description: Library name: liver_HP_Veh_1


title: L_4525_NSC_47XYY  +Chr11(q13.5 gain 1,218 Kb)


title: liver_Veh, Normal Protein Diet, rep2

description: Library name: liver_NP_Veh_2


title: eWAT_Cort, High Protein Diet, rep3

description: Library name: eWAT_HP_Cort_3

source_name: epididymal adipose tissue (eWAT)

value: epididymal adipose tissue (eWAT)


title: eWAT_Cort, High Protein Diet, rep2

description: Library name: eWAT_HP_Cort_2


title: eWAT_Cort, High Protein Diet, rep4

description: Library name: eWAT_HP_Cort_4


title: G807_NS_NSC_46XY


title: JS3C1_NS_NSC_47XYY


title: eWAT_Cort, High Protein Diet, rep1

description: Library name: eWAT_HP_Cort_1


title: CKO-YOUNG_Rep2

city: Tianjin

first: Liangyu

last: Xing

address: 22nd Qixiangtai Road

institute: Tianjin Medical University

description: Library name: Sample 17

data_processing:
Sequencing quality was checked by fastqc.
Use trim-galore to filter the adapters.
Clean reads were aligned to the human genome (UCSC mm39) using Hisat2 with the following parameters:  --no-mixed --no-discordant
Assembly: mm39
Supplementary files format and content: Comma-Separated Values of quantitative counts

source_name: femur

growth_protocol: Osteoblasts were cultured in Dulbecco's modified Eagle’s medium supplemented with 10% fetal bovine serum at 37℃ in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was harvested using  kit (M050, New Cell & Molecular Biotech Co.,Ltd)
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: In Aging RNA-Seq，osteoblats isolated from femur of 3-month and 18-month mice(C57BL/6J).In CKO RNA-Seq,Kdm2b-CxxC domain conditional knockout osteoblats isolated and screening from femur of Kdm2bfl/fl Ocncre mice Ai14 (C57BL/6J), osteoblats isolated from Ocncre Ai14 mice as control.

value: femur

value: Osteoblast

value: mice femoral osteoblast


title: CKO-YOUNG_Rep1

description: Library name: Sample 16


title: Control participant 304

description:
MethylationEPIC v2.0
OLY.C.17.EPIC.A

value: Blood


title: eWAT_Cort, Normal Protein Diet, rep4

description: Library name: eWAT_NP_Cort_4


title: IPIPOOL06_CD45_enriched_2

city: San Francisco

first: Arja

last: Ray

state: California

address: 513 Parnassus Avenue

department: Pathology

institute: UCSF

description: Library name: IPIPOOL006_P1_sccite_CD45_enriched_S12_L003

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: .H5 Matrices
Library strategy: CITE-seq

source_name: Primary Head and Neck Tumor

extract_protocol:
Pooled 8:2 CD45+:CD45- cells were resuspended in Cell Staining Buffer (BioLegend) and stained with a pool of 137 TotalSeq-C antibodies (Table) according to the manufacturer’s protocol before loading onto the Chromium Controller (10X Genomics) for GEM generation.
The cDNA libraries were generated using all or a subset of Chromium Next GEM Single Cell 5′ Library Kit for gene expression (GEX), Chromium Single Cell V(D)J Enrichment kit (10X Genomics) for T cell receptor (TCR), and Chromium Single Cell 5′ Feature Barcode Library kit for antibody derived tag (ADT) according to the manufacturer’s instructions

value: Primary Head and Neck Tumor


title: P4520_iPSCs_47XYY

source_name: iPSCs

value: iPSCs


title: CON-YOUNG_Rep3

description: Library name: Sample 15


title: CON-YOUNG_Rep1

description: Library name: Sample 13


title: IPIPOOL06_CD45_enriched_1

description: Library name: IPIPOOL006_P1_sccite_CD45_enriched_S14_L003


title: P4460_iPSCs_47XYY


title: eWAT_Veh, High Protein Diet, rep4

description: Library name: eWAT_HP_Veh_4


title: eWAT_Cort, Normal Protein Diet, rep3

description: Library name: eWAT_NP_Cort_3


title: P4458_iPSCs_47XYY


title: eWAT_Cort, Normal Protein Diet, rep1

description: Library name: eWAT_NP_Cort_1


title: eWAT_Veh, High Protein Diet, rep2

description: Library name: eWAT_HP_Veh_2


title: CKO-OLD_Rep3

description: Library name: Sample 9


title: W_M_ADPPO_16

city: santiago

first: Jose

middle: Eduardo

last: Galgani

address: Avda. Libertador Bernardo O´Higgins 340

department: Nutrition, Diabetes and Metabolism

country: Chile

institute: PONTIFICIA UNIVERSIDAD CATOLICA DE CHILE

description: Library name: A9463PO

data_processing:
reads trimmed with cutadapt v.4.4; params: -a AAAAAAAAAAAAAAAAAAAA -m 20 -O 20 -n 1
reads trimmed with cutadapt v.4.4; params: -a AAAAAAAAAAAAAAAAAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -m 20 -O 3 -q 10
reads trimmed with cutadapt v.4.4; params: -a AAAAAAAAAAAAAAAAAA -m 20 -O 3
reads trimmed with cutadapt v.4.4; params: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -m 20 -O 20
reads aligned with STAR v.2.7.10b; params: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate
features counted with htseq v.2.0.3
genes annotated with biomaRt v.2.56.1, R v4.3.1
Raw counts were normalized using Trimmed Mean of M-values (TMM) method with edgeR v4.2.2, Rv4.4.1
Differential Expression Analysis with Limma v3.60..6, R v4.4.1
Pathway Enrichment Analysis with Fgsea v1.30.0, Rv4.4.1
Assembly: hg38
Supplementary files format and content: tab-delimited text file representing counts

source_name: abdominal subcutaneous adipose

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen), and cDNA synthesis was performed using iScript (Bio-Rad).
QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI, standard protocol

value: abdominal subcutaneous adipose

tag: race

value: White

value: Male

tag: bmi

value: normal

tag: study

value: EAT


title: P4459_iPSCs_47XYY

tag: cell type

tag: genotype

value: JS


title: CON-YOUNG_Rep2

description: Library name: Sample 14


title: P4518_iPSCs_47XYY


title: CON-OLD-iBP_Rep3

description: Library name: Sample 12


title: CON-OLD-iBP_Rep1

description: Library name: Sample 10


title: CON-OLD-iBP_Rep2

description: Library name: Sample 11


title: eWAT_Cort, Normal Protein Diet, rep2

description: Library name: eWAT_NP_Cort_2


title: eWAT_Veh, High Protein Diet, rep3

description: Library name: eWAT_HP_Veh_3


title: W_M_ADPBL_15

description: Library name: A9463BL

tag: gender


title: P4428_iPSCs_47XYY


title: W_M_ADPPO_22

description: Library name: A7916PO


title: A_M_ADPPO_31

description: Library name: A9629PO

value: African American

value: overweight

value: PROOF


title: A_M_ADPBL_30

description: Library name: A9629BL


title: eWAT_Veh, High Protein Diet, rep1

description: Library name: eWAT_HP_Veh_1


title: P4429_iPSCs_47XYY


title: W_M_ADPBL_21

description: Library name: A7916BL


title: CKO-OLD_Rep2

description: Library name: Sample 8


title: P4427_iPSCs_47XYY


title: W_M_ADPPO_26

description: Library name: A7381PO


title: CKO-OLD_Rep1

description: Library name: Sample 7


title: eWAT_Veh, Normal Protein Diet, rep4

description: Library name: eWAT_NP_Veh_4


title: eWAT_Veh, Normal Protein Diet, rep3

description: Library name: eWAT_NP_Veh_3


title: P4426_iPSCs_47XYY


title: eWAT_Veh, Normal Protein Diet, rep2

description: Library name: eWAT_NP_Veh_2


title: W_M_ADPBL_25

description: Library name: A7381BL


title: OLD_Rep2

description: Library name: Sample 5


title: P4425_iPSCs_47XYY


title: eWAT_Veh, Normal Protein Diet, rep1

description: Library name: eWAT_NP_Veh_1


title: W_M_ADPPO_27

description: Library name: A6841BL


title: YOUNG_Rep3

description: Library name: Sample 3


title: P4423_iPSCs_47XYY


title: OLD_Rep3

description: Library name: Sample 6


title: P4424_iPSCs_47XYY


title: W_M_ADPPO_28

description: Library name: A6841PO


title: P4422_iPSCs_47XYY


title: eCLIP-seq, hPXR mouse liver, hPXR, IP, rep2

value: Liver

value: liver tissue

value: Normal tissue

value: PXR


title: eCLIP-seq, hPXR mouse liver, hPXR, IP, rep1


title: OLD_Rep1

description: Library name: Sample 4

value: femur

value: Osteoblast

value: mice femoral osteoblast


title: YOUNG_Rep2

description: Library name: Sample 2


title: W_M_ADPBL_05

description: Library name: A5822BL


title: P4421_iPSCs_47XYY

value: iPSCs


title: eCLIP-seq, hPXR mouse liver, input


title: YOUNG_Rep1

description: Library name: Sample 1


title: W_M_ADPPO_20

description: Library name: A5140PO

value: abdominal subcutaneous adipose


title: P4420_iPSCs_47XYY


title: W_M_ADPPO_06

description: Library name: A5822PO

value: White


title: MA9_FLT3ITD_Setd1b_dSET_IL3_rep3

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values corrected by Spike-In for each Sample.

growth_protocol: mouse MLL-AF9 leukemia cells were grown in RPMI media supplemented with 10% FBS, penicillin/streptomycin, and 10 ng/ml rmIL-3.

extract_protocol:
Total RNA was collected using Rneasy Mini Kit with DNase (QIAGEN).
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

value: leukemia

value: Setd6b SET knockout

value: After wash with PBS, the cells were incubated with cytokines for 24 hr.


title: C10_hipp_M_5xFADHEMI_4mo_11631

city: Boston

first: Courtney

last: Benoit

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

description: Library name: AL150

data_processing:
Fastq files were assessed for quality using fastqc. Reads were pseudo-aligned using Salmon and imported into DESeq2 for differential expression analysis. Counts were normalized, filtered for low abundance transcripts, and batch effects were regressed using ComBat in the sva package. Principal component analysis (PCA) was performed on the batch-corrected, variance-stabilized expression matrix using the R function prcomp. Differential expression was assessed using the DESeq2 package in R. Gene set enrichment was calculated (queried against the M5 Gene Ontology pathway database) using the R package fgsea. Genes were ranked according to -log10(p-value)*sign of the log2 fold change. Heatmaps were produced for using the R package pheatmap with color palettes from the R package Seurat.
Assembly: Mouse mm39
Supplementary files format and content: Comma-separated count matrix (raw counts)
Supplementary files format and content: Comma-separated count matrix (normalized counts)
Supplementary files format and content: Comma-separated count matrix (variance-stabilized counts, batch-corrected for sex)

source_name: hippocampus

extract_protocol:
Frozen tissues were lysed and homogenized using the TissueLyser II (Qiagen, Germantown, MD). Total RNA was extracted with the RNeasy Mini Kit and treated with the RNase-Free DNase Set on the QIAcube (Qiagen) liquid handling platform. RNA integrity was assessed using the Qubit RNA IQ Assay (Life Technologies), and samples with an RNA integrity number (RIN) of ≥7.0 were selected for cDNA synthesis.
cDNA synthesis, amplification, library construction, and sequencing were performed by Novogene (Sacramento, CA) using Illumina NovaSeq and HiSeq platforms with paired-end 150 bp (PE 150) sequencing strategy.

value: hippocampus

tag: Sex

value: male

tag: age

value: 4 months old


title: P4419_iPSCs_47XYY

value: JS


title: MA9_FLT3ITD_Setd1b_dSET_IL3_rep2

value: Setd5b SET knockout


title: P4519_iPSCs_47XYY


title: A_M_ADPPO_12

description: Library name: A4812PO

value: African American

value: Male

value: normal

value: EAT


title: P4418_iPSCs_47XYY


title: C09_hipp_M_5xFADHEMI_4mo_11622

description: Library name: AL149


title: C08_hipp_M_5xFADHEMI_4mo_11621

description: Library name: AL148


title: A_M_ADPBL_11

description: Library name: A4812BL


title: C07_hipp_M_5xFADHEMI_4mo_11619

description: Library name: AL147


title: P4413_iPSCs_47XYY + Chr6 (q21.5 gain 1,998 Kb)


title: W_M_ADPBL_23

description: Library name: A4557BL


title: MA9_FLT3ITD_Setd1b_dSET_NC_rep2

value: Setd2b SET knockout

value: After wash with PBS, the cells were incubated without cytokines for 24 hr.


title: C06_hipp_M_5xFADHEMI_4mo_11611

description: Library name: AL146


title: P4412_iPSCs_47XYY + Chr6 (q21.5 gain 1,998 Kb)

value: iPSCs


title: MA9_FLT3ITD_Setd1b_dSET_NC_rep1

value: Setd1b SET knockout


title: P4403_iPSCs_47XYY


title: C05_hipp_F_5xFADHEMI_4mo_11626

description: Library name: AL145

value: female


title: CKO-YOUNG_Rep3

description: Library name: Sample 18

value: femur

value: Osteoblast

value: mice femoral osteoblast


title: MA9_FLT3ITD_Setd1b_WT_NC_rep3

value: leukemia

value: Setd2b SET wildtype


title: W_M_ADPBL_19

description: Library name: A5140BL

value: abdominal subcutaneous adipose

value: White


title: P4414_iPSCs_47XYY + Chr6 (q21.5 gain 1,998 Kb)

value: JS


title: W_M_ADPPO_24

description: Library name: A4557PO


title: A_M_ADPPO_10

description: Library name: A4365PO

value: African American

value: overweight


title: A_M_ADPBL_09

description: Library name: A4365BL

value: Male


title: MA9_FLT3ITD_Setd1b_dSET_NC_rep3

value: Setd3b SET knockout


title: C04_hipp_F_5xFADHEMI_4mo_11625

description: Library name: AL144

value: hippocampus

value: 4 months old


title: P4402_iPSCs_47XYY

value: iPSCs


title: MA9_FLT3ITD_Setd1b_WT_NC_rep2

value: Setd1b SET wildtype

value: After wash with PBS, the cells were incubated without cytokines for 24 hr.


title: C02_hipp_F_5xFADHEMI_4mo_11616

description: Library name: AL142

value: female


title: A_M_ADPBL_01

description: Library name: A1612BL

value: EAT


title: MA9_FLT3ITD_Setd1b_WT_NC_rep1


title: A_M_ADPPO_02

description: Library name: A1612PO


title: P4400_iPSCs_47XYY


title: MA9_FLT3ITD_Setd1b_dSET_IL3_H3K4me3

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.1.0.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
Duplication reads were removed from aligned file by using picard-tools-1.56.
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER v4.7 makeUCSCfile command and comberted to bigwig by bedGraphToBigWig. BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
Cells were fixed with 2mM DSG and 1% formaldehyde, and samples from sonicated nuclear fraction were incubated with each antibody and histone-DNA complexes were isolated. For histone modifications, DSG treatment was skipped.
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) following the manufacturer’s protocol.

value: Setd1b SET knockout

value: After wash with PBS, the cells were incubated with cytokines for 24 hr.

value: H3K4me3 (abcam Cat#ab8580)


title: C01_hipp_F_5xFADHEMI_4mo_11615

description: Library name: AL141


title: P4401_iPSCs_47XYY


title: B10_hipp_M_5xFADHEMI.CLUh2kbKIHO_4mo_12724

description: Library name: AL130

value: male


title: P4398_iPSCs_47XYY


title: C03_hipp_F_5xFADHEMI_4mo_11617

description: Library name: AL143


title: W_M_ADPBL_17

description: Library name: A1546BL

value: abdominal subcutaneous adipose

value: White

value: normal


title: MA9_FLT3ITD_Setd1b_WT_IL3_H3K4me3

value: leukemia


title: B09_hipp_M_5xFADHEMI.CLUh2kbKIHO_4mo_12717

description: Library name: AL129


title: MA9_FLT3ITD_Setd1b_dSET_NC_H3K4me3


title: RPE cells ,22-month-old mouse 3_right eye

city: bristol

first: Gongyu

last: Shi

address: Biomedical Sciences Building, University of Bristol, Tankard's Cl, University Walk

country: United Kingdom

institute: university of bristol

description: name in rowcounts: 22m_6

data_processing:
Galaxy software was used to assess the quality of reads via FastQC, followed by read trimming via Trimmomatic.
Reads were then aligned using HISAT2 and quantified using FeatureCounts to provide rawcounts.
Batch correction of the resulting counts from two independent experiments was performed using R Studio v2023.06.1 with ComBat-seq.
Following batch correction, the counts were normalized by DESeq2 package.
Assembly: mouse mm10
Supplementary files format and content: rawcounts in xlsx file contains all samples raw counts
Supplementary files format and content: batchcorrected counts in xlsx file contains all samples counts following batch correction
Supplementary files format and content: normalised counts in xlsx file contains all samples counts normalised by DESeq2 post batch correction

source_name: Retinal pigment epithelium

growth_protocol: C57BL/6J male mice with different ages were purchased from Charles River Laboratories and housed in the Animal Services Unit at University of Bristol, in accordance with the Home Office Regulations.

extract_protocol:
Murine RPE cells used for RNA-seq or cell culture were isolated following an established protocol (J. Liu et al., 2024; Scott et al., 2021).RNA of RPE cells was extracted using the RNeasy Mini kit (Qiagen).
Library preparation was conducted using Illumina Stranded Total RNA Prep with Ribo Zero Plus (Illumina), followed by sequencing using the Illumina NextSeq 550 platform with 2×75 bp by paired-end reads at a depth of 16 million reads.

value: Retinal pigment epithelium

value: WT

tag: batch


title: MA9_FLT3ITD_Setd1b_WT_NC_H3K4me3

tag: cell line


title: B08_hipp_M_5xFADHEMI.CLUh2kbKIHO_4mo_12715

description: Library name: AL128

value: hippocampus


title: RPE cells, 22-month-old mouse 3_left eye

description: name in rowcounts: 22m_5


title: P4394_iPSCs_47XYY  +Chr11(q13.5 gain 1,218 Kb)

value: JS


title: RPE cells, 22-month-old mouse 2_right eye

description: name in rowcounts: 22m_4


title: B07_hipp_M_5xFADHEMI.CLUh2kbKIHO_4mo_12708

description: Library name: AL127

value: 4 months old


title: P4393_iPSCs_47XYY  +Chr11(q13.5 gain 1,218 Kb)

value: iPSCs


title: Muscle Hindlimb, IR 56-days

city: Ottawa

first: Nicolas

last: Collao

state: ON

address: 75 Laurier Ave E.

department: Health Science

country: Canada

institute: University of Ottawa

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The FASTQ sequencing reads were mapped to the mouse genome (mm10), barcode processed, UMI counted, and converted to digital gene expression matrices using the CellRanger v5.0.0 Software (10x Genomics).
Assembly: mm10
Supplementary files format and content: CellRanger output files

source_name: Muscle Hindlimb

extract_protocol:
Briefly, the IR or the CON limb was removed at 24-hours post the final dose of radiation or 56-days post-IR (CON 24-hours, IR 24-hours, CON 56-days, and IR 56-days). Mechanical and enzymatic dissociation were used as previously described16 to generate a single-cell suspension from the IR or the CON hindlimb at the different time points. Briefly, the IR and the CON limb were dissected and processed separately. The connective and fat tissue was removed, and the dissected limb was subsequently transferred to a Miltenyi GentleMACS C tube (Cat# 130-093-237, Miltenyi Biotec), which contained an enzymatic solution comprised of Collagenase B (1.5U/ml, Cat# 11088831001; Roche® Life Science Products,) and Dispase II (2U/ml, Cat# 42613-33-2; Sigma Aldrich) resuspended in Ham’s F10 media (Cat# 318-050-CL, Wisent Inc, St-Bruno, Canada). Using the gentleMACS Octo Dissociator (Cat# 130-096-427, Miltenyi Biotec), the muscle homogenate was passed through a 100 µm strainer (Cat# 22-363-549, Fisher Scientific). The resulting cell suspension was centrifuged at 600 x g at 4°C for 10 minutes. The cell pellet was treated with Red Blood Cell Lysing Buffer (Hydri-MaxTM; Cat# R7767; Sigma-Aldrich) and centrifuged at 600 x g at 4°C for 5 minutes. The cell pellet was then resuspended in 1 ml ice-cold FACS buffer, which consisted of 10% FBS and 3 mM EDTA in 1xPBS. For FACS, cell suspension from three limbs were pooled then were labelled with a live cell nuclei stain (NucBlue™ Live ReadyProbes™ Reagent (Hoechst 33342), Cat# R37605, Thermo Fisher Scientific), and SYTOX™ AADvanced™ (Cat# S10349, Thermo Fisher Scientific) for dead cells (Figure S7A). A minimum of 10,000 live, mononucleated cells were sorted in the Cell Sorting Facility at the Ottawa Hospital Research Institute using the Beckman Coulter MoFlo XDP cell sorter (32-bit high resolution digital system with five excitation laser lines (UV, 405nm, 488nm, 561nm, and 640nm) for further scRNA-seq.
Library preparation were conducted by the manufacter's instructions (single cell 3', 10x Genomics)

treatment_protocol: A fractionated dose of in vivo irradiation (in vivo-IR) of 8.2 Gy/dose (X-RAD 320, Precision X-Ray Irradiation, North Branford, CT) was administered for three days (Monday, Wednesday, and Friday) to one hindlimb at age five weeks (IR).9 The rest of the body was lead-shielded, and the contralateral limb was used as a non-IR control (CON).

value: Muscle Hindlimb

value: 5 weeks old

value: Irradiated hindlimb


title: W_M_ADPPO_18

description: Library name: A1546PO

value: Male

value: EAT


title: Muscle Hindlimb, CON 56-days

description: 10x Genomics

value: Control hindlimb


title: L_4420_iPSCs_47XYY


title: P4399_iPSCs_47XYY


title: L_4398_iPSCs_47XYY


title: RPE cells, 22-month-old mouse 1_right eye

description: name in rowcounts: 22m_2


title: B04_hipp_F_5xFADHEMI.CLUh2kbKIHO_4mo_12659

description: Library name: AL124

value: female


title: B05_hipp_F_5xFADHEMI.CLUh2kbKIHO_4mo_12669

description: Library name: AL125


title: Muscle Hindlimb, CON 24-hours

description: 10x Genomics

value: male


title: L_4393_iPSCs_47XYY  +Chr11(q13.5 gain 1,218 Kb)


title: RPE cells, 22-month-old mouse 1_left eye

description: name in rowcounts: 22m_1


title: RPE cells ,5-month-old mouse 3_right eye

description: name in rowcounts: 5m_6


title: B02_hipp_F_5xFADHEMI.CLUh2kbKIHO_4mo_12646

description: Library name: AL123


title: Zea mays B73, root tips (0-1mm), Repli-seq, late S phase, biorep 3

city: Raleigh

first: Emily

last: Markham

state: NC

address: 851 Main Campus Dr

institute: NCSU

description: Library name: B73_repliseq_L_br3

data_processing:
Sequenced reads were trimmed using trimmomatic v0.39, with the parameters -phred33 -validatePairs and ILLUMINACLIP:/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa:2:30:10:2:True LEADING:5 TRAILING:5 MINLEN:20
Trimmed reads were mapped to the genome assembly using bowtie2 v2.5.1, with the parameter --very-sensitive
Duplicate reads were removed using sambamba v1.0.0, with default parameters. Reads that were not properly paired or had a MAPQ value less than 6 were removed using samtools v1.9, with parameters -bf 0x2 and-q 6. Reads that mapped to scaffolds or plastids were also removed.
Spikes in the data were removed by calculating coverage in non-overlapping 10kb bins and the 0.25% highest coverage bins were removed. A low-mappability drop list was created to remove regions of the genome with low read coverage due to poor inherent refrence genome mappability.
Bam files were processed using the Repliscan program to create normalized profiles of each S phase stage as described (Zynda et al. 2017; Mickelson-Young et al. 2022; Github link: https://github.com/lconcia/repliscan; Link to software container: https://zenodo.org/records/13937103) The following parameter modifications were used: (1) read densities were aggregated in 10-kb static windows across the genome ( --window 10000) and (2) a segmentation threshold of 1.0 ( --threshold value, --value 1.0). The Repliscan program merges the bioreps from each S phase gate into one signal file for each gate in bedgraph format. KentUtils was used to convert bedgraph files to bigwig format. Repliscan also produces a segmentation track in gff3 format, assigning each window (defined by --window parameter) at replication timing class.
Assembly: B73v5, Zm-B73-REFERENCE-NAM-5.0, see https://maizegdb.org/NAM_project
Supplementary files format and content: bigWig
Supplementary files format and content: gff3

organism: Zea mays

source_name: terminal 1 mm of root tip

growth_protocol: B73 seeds were surface sterilized in absolute ethanol for 5 min and then in 1% NaClO; 0.05% Tween-20, imbibed overnight with stirring and aeration, and surface sterilized again but this time in 0.5% NaClO; 0.05% Tween-20. Seeds were germinated in 6.5x10 inch glass dishes with a clear sealing lid (Rubbermaid Brilliance) with 6 single layers of paper towels dampened with autoclaved dH2O (75 mL per dish). Seedlings were grown in a growth chamber for 3 days with constant dim LED light at 28 C.

extract_protocol:
A phenol:cholorform:IAA DNA extraction was used to isolate DNA from each sorted nuclei population.
DNA-seq libraries were made using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645S) in combination with NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs, NEB #E6440S). The libraries were constructed using 0.5 ng DNA input; the adapter dilution was 1:25 and there was no size selection performed. The libraries were amplified using 11 PCR cycles. The final average library size ranged from 390-436 bp (240-286 bp sequenceable insert + 150 bp adapters). The libraries were sequenced using the Illumina Novaseq 6000, 150 bp paired end.

treatment_protocol: The 3-day old seedlings were labeled in 25 uM 5-Ethynyl-2'-deoxyuridine (EdU) for 20 minutes to allow actively replicating DNA to incorporate the EdU. Then seedlings were rinsed and placed in 100 uM Thymidine to stop label incorporation.

value: terminal 1 mm of root tip

value: Flow sorted EdU-labeled late S phase

value: 25 uM EdU pulse for 20 min

value: Alexa Fluor 488 polyclonal antibody, Invitrogen #A-11094, lot 2551344


title: JS3C1_P2_iPSCs_47XYY

city: Thuwal

first: Antonio

address: Thuwal 23955-6900 KAUST

institute: King Abdullah University of Science and Technology

data_processing:
RNA-Seq data validation, pairing and FastQC quality control was followed by adaptor sequence/low quality sequence trimming using BBDuk.
High quality reads were mapped against the reference genome (GRCh38/Ensembl release 101) using the STAR end-to-end alignment method
Read counts quantification was perfomed with FeatureCounts, lowly expressed genes were filtered out using HTSFilter
Assembly: Ensembl GRCh38 v. 101
Supplementary files format and content: Worksheet file containing Normalized counts (TMM). Columns represent samples and rows genes.

extract_protocol:
The total RNA extraction was performed using MagMAX mirVana Total RNA Isolation Kit (Applied Biosystems) following the manufacturer’s instructions. 250-500  ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were generated using the human mRNA TruSeq Stranded library preparation KIT from Illumina (Illumina) following the manufacturer's protocols.


title: B01_hipp_F_5xFADHEMI.CLUh2kbKIHO_4mo_12517

description: Library name: AL122


title: P4395_iPSCs_47XYY  +Chr11(q13.5 gain 1,218 Kb)


title: RPE cells, 5-month-old mouse 3_left eye

description: name in rowcounts: 5m_5

value: Retinal pigment epithelium

value: WT


title: JS3C1_P1_iPSCs_47XYY

value: JS


title: Zea mays B73, root tips (0-1mm), Repli-seq, late S phase, biorep 1

description: Library name: B73_repliseq_L_br1


title: Zea mays B73, root tips (0-1mm), Repli-seq, late S phase, biorep 2

description: Library name: B73_repliseq_L_br2


title: B06_hipp_M_5xFADHEMI.CLUh2kbKIHO_4mo_12705

description: Library name: AL126

value: hippocampus

value: 4 months old


title: JS2B2_P2_iPSCs_47XYY + Chr6 (q21.5 gain 1,998 Kb)

value: iPSCs


title: DSSL1.0W6

city: Taipei

first: Feng-Yi

last: Yang

state: Taiwan

address: No. 155, Sec. 2, Li-Nong St.

department: Department of Biomedical Imaging and Radiological Sciences

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
Data processing involves circular consensus sequence (CCS) determination with a minimum predicted accuracy of 0.9 and a minimum number of passes set to 3 using PacBio's official workflow through the SMRT Link software. After demultiplexing, the CCS reads are further processed with DADA2 to obtain amplicons with single-nucleotide resolution.
Assembly: N/A
Supplementary files format and content: ASV analysis
Supplementary files format and content: The processed data files contain circular consensus sequence (CCS) reads and amplicons with single-nucleotide resolution obtained from DADA2 processing. Taxonomy classification based on the NCBI database, alpha and beta diversity analysis results, including observed-species, Chao1, ACE, Shannon, Simpson, PD whole tree, and Good-coverage indices, rarefaction curve, UniFrac distances, principal component analysis (PCA), principal coordinate analysis (PCoA), non-metric multidimensional scaling (NMDS), supervised partial-least-squares discriminant analysis (PLS-DA) results, differential abundance analysis results, and functional predictions of microbial communities are included.

organism: mouse gut metagenome

source_name: stool

growth_protocol: The study utilized 8-week-old male C57BL/6J mice sourced from BioLASCO, Taiwan Co., Ltd. Adhering to the Institutional Animal Care and Use Committee (IACUC) guidelines of National Yang-Ming Chiao Tung University, we ensured compliance with regulations for animal welfare. Monitoring the housing environment, we maintained temperatures (20-22°C) and humidity (30-70%) with a 12-hour light-dark cycle (08:00 lights on, 20:00 lights off). Animals had unrestricted access to food and water. Housing employed individually ventilated cage (IVC) systems, ensuring specific pathogen-free (SPF) conditions, with a maximum of 5 animals per cage to uphold comfort and health standards.

extract_protocol:
Total genomic DNA is extracted from samples using a column-based method, such as the QIAamp PowerFecal DNA Kit by Qiagen. DNA concentration is determined using a Qubit 4.0 Fluorometer and adjusted to 1 ng/μl for subsequent processing.
PCR amplification of full-length 16S genes (V1-V9 regions) is performed using barcoded 16S gene-specific primers. The PCR products are purified and pooled, and 500-1000 ng of pooled amplicon sample is used for SMRTbell library construction. The library construction involves DNA damage repairing, end-repair/A-tailing, ligation of universal hairpin adapters, purification, and primer annealing followed by sequencing on a PacBio Sequel IIe instrument.
The library strategy involves PCR amplification of full-length 16S genes with barcoded primers, followed by SMRTbell library construction for sequencing on a PacBio Sequel IIe instrument.

treatment_protocol: DSS group animals were treated with 3% DSS for 7 days; DSS+LIPUS groups were treated with 3% DSS for 7 days and treated with LIPUS(0.5W/1.0W) for 4 days

value: stool

tag: strain


title: RPE cells, 5-month-old mouse 2_right eye

description: name in rowcounts: 5m_4


title: DSSL1.0W5


title: Muscle Hindlimb, IR 24-hours

description: 10x Genomics

value: Muscle Hindlimb

value: 5 weeks old

value: Irradiated hindlimb


title: JS2B2_P1_iPSCs_47XYY + Chr6 (q21.5 gain 1,998 Kb)

last: Adamo


title: RPE cells, 22-month-old mouse 2_left eye

description: name in rowcounts: 22m_3


title: Zea mays B73, root tips (0-1mm), Repli-seq, mid S phase, biorep 3

description: Library name: B73_repliseq_M_br3

value: Flow sorted EdU-labeled mid S phase


title: RPE cells, 5-month-old mouse 2_left eye

description: name in rowcounts: 5m_3


title: DSSL1.0W4


title: DSSL1.0W3


title: RPE cells, 5-month-old mouse 1_right eye

description: name in rowcounts: 5m_2


title: L_4827_Fibroblasts_47XYY

source_name: Fibroblasts

value: Fibroblasts


title: Zea mays B73, root tips (0-1mm), Repli-seq, mid S phase, biorep 2

description: Library name: B73_repliseq_M_br2


title: RPE cells, 5-month-old mouse 1_left eye

description: name in rowcounts: 5m_1


title: L_4823_Fibroblasts_47XYY


title: Zea mays B73, root tips (0-1mm), Repli-seq, mid S phase, biorep 1

description: Library name: B73_repliseq_M_br1


title: Zea mays B73, root tips (0-1mm), Repli-seq, early S phase, biorep 3

description: Library name: B73_repliseq_E_br3

value: Flow sorted EdU-labeled early S phase


title: DSSL1.0W2

value: male


title: L_4259_Fibroblasts_47XYY


title: multiome1unselected_RNA

city: Philadelphia

first: Eoin

middle: Christopher

last: Whelan

address: 3800 Spruce St

department: Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

description:
3' single-cell multiome RNA. h5 file contains both modalities
Multiome5merge_filtered_feature_bc_matrix.h5

data_processing:
CellRanger was used to align reads to the Mus musculus reference (GENCODE vM23/Ensembl 98) and the Rattus norvegicus 6.0 DNA primary assembly along with the corresponding GTF file (v6.0.85) from Ensembl70. Gene counts were analyzed with Seurat v471 for clustering, integration and differential gene expression and Monocle version 372 for clustering and pseudotime. Filtering cutoffs were set as follows: minimum genes per cell = 500, maximum genes = 5000, minimum UMIs per cell was set on a per-sample basis after inspecting a rank plot of UMI/cell. Cells with over 20% mitochondrial reads were also excluded. Differentially-expressed genes were identified via Seurat’s FindMarker function with default parameters. Samples were integrated using Seurat’s integration anchors and the first 30 principle components were used for integration and UMAP creation. Clusters were found using monocle (cluster_cells, resolution = 5 10-5, k = 8, partition_qval = 0.05). Psudotime was generated using Monocle’s learn_graph (default parameters). For ATAC analysis, peaks were called using Signac with MACS2, and gene activity scores were calculated with Signac.
Assembly: Mus musculus reference (GENCODE vM23/Ensembl 98)
Supplementary files format and content: filtered_feature_bc_matrix.h5 files
Supplementary files format and content: atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi
Supplementary files format and content: featurereference.csv
Assembly: Rattus norvegicus 6.0 DNA primary assembly along with the corresponding GTF file (v6.0.85)
Supplementary files format and content: Contain mRNA+ADT or mRNA + ATAC counts as appropriate
Supplementary files format and content: ATAC fragment files
Supplementary files format and content: Contain ADT antibodies used & barcode sequences
Library strategy: single-cell multiome RNA + ATAC

source_name: testis

extract_protocol:
Rat cells were isolated from the testes of 3- to 4-month-old Sprague Dawley rats transgenic for the LacZ gene under the metallothionine promoter67. Mouse cells were isolated from C57BL/6 inbred mice also 3-4 months old. Tissue was chopped into fine pieces and incubated in collagenase (Sigma) at a concentration of 1mg/ml in HBSS (Gibco) for 15 minutes at 37C. Cells were spun down for 1 minute at 600 rcf, then resuspended in warm Trypsin (Gibco, 0.25%) with 20% DNase solution (Sigma, 7mg/ml dissolved in HBSS). Tissue was pipetted for 2 minutes with a 10 ml pipette and incubated at 37C for 5 minutes. Then tissue was pipetted for another 2 minutes and incubated at 37C for 3 minutes. FBS (Sigma F2442) was added to stop the digestion. Additional DNase was added until no turbidity was visible. Cells were washed in PBS-S twice (PBS [Gibco] with 1% FBS, 10 mM HEPES [Sigma Aldrich], 1 mg/ml glucose [Sigma Aldrich], 1 mM pyruvate [Gibco], 50 units/ml penicillin [Gibco], 50 ug/ml streptomycin [Gibco] prepared as described in 68). All centrifugation steps were 5 minutes at 600 rcf.   Cells were processed both as unselected samples and enriched for EPCAM as described below. Each biological replicate was then used for either encapsulation of cells with antibody treatment or further processed as nuclei for GEX+ATAC assay.
Cells were encapsulated and libraries generated for GEX+CITE using a Chromium Next GEM Single Cells 3’ Kit v3.1 with Feature Barcoding (10X Genomics) per manufacturer’s protocol. Prepared nuclei were encapsulated with the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit following manufacturer’s instructions. Each biological replicate was encapsulated individually. Libraries were sequenced on a NextSeq2000 sequencer (Illumina) using a 100-cycle sequencing kits to a minimum depth of 30k reads per cell.

value: testis

tag: Stage

value: Adult

tag: selection

value: unselected

tag: library type

value: mRNA


title: multiome1unselected_ATAC

description:
3' single-cell multiome ATAC. h5 file contains both modalities
Multiome5merge_atac_fragments.tsv.gz
Multiome5merge_atac_fragments.tsv.gz.tbi

value: ATAC DNA


title: DSSL1.0W1

tag: treatment


title: Zea mays B73, root tips (0-1mm), Repli-seq, early S phase, biorep 2

description: Library name: B73_repliseq_E_br2

tag: tissue

value: terminal 1 mm of root tip

value: 25 uM EdU pulse for 20 min

tag: antibody

value: Alexa Fluor 488 polyclonal antibody, Invitrogen #A-11094, lot 2551344


title: F4828_Fibroblasts_47XYY

tag: condition

value: JS


title: DSSL0.5W6

value: stool


title: Zea mays B73, root tips (0-1mm), Repli-seq, early S phase, biorep 1

description: Library name: B73_repliseq_E_br1


title: Whole skin, IMQ-mice, quinpirole_5

city: Yufu-shi

first: Takashi

last: Sakai

state: Oita

address: 1-1, Idaigaoka, Hasama-machi

department: Dermatology

institute: Oita University

data_processing:
MGI DNBseq-G400 FAST was used to perform the amplicons deep sequencing following the standard operation protocol. The sequence format was 150bp pair read for all samples.
All sequencing reads were trimmed low-quality bases and adapters with Trimmomatic (v.0.38) .
Raw counts for each gene were estimated in each sample using RSEM version 1.3.0 and Bowtie 2. Calculation of the log fold-change (log FC) and p-value were performed using edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

source_name: whole skin

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

value: whole skin

value: BALB/c

value: Female

value: quinpirole


title: F4827_Fibroblasts_47XYY

value: Fibroblasts


title: DSSL0.5W5


title: Whole skin, IMQ-mice, quinpirole_4


title: Whole skin, IMQ-mice, quinpirole_3


title: DSSL0.5W4


title: Zea mays B73, root tips (0-1mm), Repli-seq, G1 phase, biorep 2

description: Library name: B73_repliseq_G1_br2

value: Flow sorted G1 phase

value: no IP


title: Zea mays B73, root tips (0-1mm), Repli-seq, G1 phase, biorep 3

description: Library name: B73_repliseq_G1_br3


title: F4825_Fibroblasts_47XYY


title: F4826_Fibroblasts_47XYY


title: DSSL0.5W3

value: male


title: DSSL0.5W2


title: Zea mays B73, root tips (0-1mm), Repli-seq, G1 phase, biorep 1

description: Library name: B73_repliseq_G1_br1


title: F4823_Fibroblasts_47XYY


title: Zea mays B73, root tips (0-1mm), DNA copy number, G1 phase, biorep 2

description: Library name: B73_G1_BR2

data_processing:
Sequenced reads were trimmed using trimmomatic v0.39, with the parameters -phred33 -validatePairs and ILLUMINACLIP:/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa:2:30:10:2:True LEADING:5 TRAILING:5 MINLEN:20
Trimmed reads were mapped to the genome assembly using bowtie2 v2.5.1, with the parameter --very-sensitive
Duplicate reads were removed using sambamba v1.0.0, with default parameters. Reads that were not properly paired or had a MAPQ value less than 6 were removed using samtools v1.9, with parameters -bf 0x2 and-q 6. Reads that mapped to scaffolds or plastids were also removed.
Spikes in the data were removed by calculating coverage in non-overlapping 10kb bins and removing the 0.25% highest coverage bins. A low-mappability drop list was created to remove regions of the genome where low read coverage could be due to poor inherent refrence genome mappability.
Read coverage was calculated in the remaining non-overlapping 10kb bins and normalized to 1X reads per genomic content (RPGC) using DeepTools bamCoverage with parameters -of bedgraph -bs 10000 --effectiveGenomeSize 2071945143 --normalizeUsing RPGC --ignoreDuplicates --extendReads, and with a --blackListFileName bed file that included the 0.25% spikes in coverage and low mappability regions from previous step. The effective genome size was calculated by subtracting the number of bp in the --blackListFileName file from the number of bp in the chromosomal fasta file.
The ratio of S coverage to G1 coverage for each biological replicate was calculated for each bin.
The S/G1 ratio data in non-overlapping 10kb bins was haar wavelet smoothed at level 2.
Assembly: B73v5, Zm-B73-REFERENCE-NAM-5.0, see https://maizegdb.org/NAM_project
Supplementary files format and content: bigWig

growth_protocol: B73 seeds were surface sterilized in 1% NaClO; 0.05% Tween-20, imbibed overnight with stirring and aeration, and surface sterilized again but this time in 0.5% NaClO; 0.05% Tween-20. Seeds were germinated in 6.5x10 inch glass dishes with a clear sealing lid (Rubbermaid Brilliance) with 6 single layers of paper towels dampened with autoclaved dH2O (75 mL per dish). Seedlings were grown in a growth chamber for 3 days with constant dim LED light at 28 C.

extract_protocol:
A phenol:cholorform:IAA DNA extraction was used to isolate DNA from each sorted nuclei population.
DNA-seq libraries were made using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645S) in combination with the NEBNext Multiplex Oligos for Illumina (NEB #E6440S). The libraries were constructed using 100 ng of DNA input; the adapter dilution was 1:10 and the size selection protocol for obtaining 300-400 bp sequenceable inserts was followed. The  libraries were amplified using 7 PCR cycles. The final average library size ranged from 472-492 bp (352-372 bp sequenceable insert + 120 bp adapters). The libraries were sequenced using the Illumina Novaseq 6000, 150 bp paired end.

tag: cultivar


title: Whole skin, IMQ-mice, quinpirole_1


title: DSSL0.5W1


title: F4824_Fibroblasts_47XYY


title: F4261_Fibroblasts_47XYY


title: Whole skin, IMQ-mice, vehicle_5

value: vehicle


title: Zea mays B73, root tips (0-1mm), DNA copy number, G1 phase, biorep 1

description: Library name: B73_G1_BR1


title: F4260_Fibroblasts_47XYY


title: Whole skin, IMQ-mice, vehicle_4


title: DSS6

value: DSS


title: Zea mays B73, root tips (0-1mm), DNA copy number, EdU labeled S phase, biorep 3

description: Library name: B73_EdU_S_BR3

value: Flow sorted EdU-labeled S phase


title: DSS5


title: Zea mays B73, root tips (0-1mm), DNA copy number, EdU labeled S phase, biorep 2

description: Library name: B73_EdU_S_BR2


title: Whole skin, IMQ-mice, vehicle_2


title: Whole skin, IMQ-mice, vehicle_3


title: Whole skin, IMQ-mice, quinpirole_2


title: DSS4


title: Zea mays B73, root tips (0-1mm), DNA copy number, G1 phase, biorep 3

description: Library name: B73_G1_BR3


title: F4259_Fibroblasts_47XYY


title: DSS3


title: Zea mays B73, root tips (0-1mm), DNA copy number, EdU labeled S phase, biorep 1

description: Library name: B73_EdU_S_BR1


title: DSS2


title: F4257_Fibroblasts_47XYY


title: F4258_Fibroblasts_47XYY


title: CD9neg.rat.9.CS

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_rat18CD9neg_filtered_feature_bc_matrix.h5
rat18_featurereference.csv

data_processing:
CellRanger was used to align reads to the Mus musculus reference (GENCODE vM23/Ensembl 98) and the Rattus norvegicus 6.0 DNA primary assembly along with the corresponding GTF file (v6.0.85) from Ensembl70. Gene counts were analyzed with Seurat v471 for clustering, integration and differential gene expression and Monocle version 372 for clustering and pseudotime. Filtering cutoffs were set as follows: minimum genes per cell = 500, maximum genes = 5000, minimum UMIs per cell was set on a per-sample basis after inspecting a rank plot of UMI/cell. Cells with over 20% mitochondrial reads were also excluded. Differentially-expressed genes were identified via Seurat’s FindMarker function with default parameters. Samples were integrated using Seurat’s integration anchors and the first 30 principle components were used for integration and UMAP creation. Clusters were found using monocle (cluster_cells, resolution = 5 10-5, k = 8, partition_qval = 0.05). Psudotime was generated using Monocle’s learn_graph (default parameters). For ATAC analysis, peaks were called using Signac with MACS2, and gene activity scores were calculated with Signac.
Assembly: Mus musculus reference (GENCODE vM23/Ensembl 98)
Supplementary files format and content: filtered_feature_bc_matrix.h5 files
Supplementary files format and content: atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi
Supplementary files format and content: featurereference.csv
Assembly: Rattus norvegicus 6.0 DNA primary assembly along with the corresponding GTF file (v6.0.85)
Supplementary files format and content: Contain mRNA+ADT or mRNA + ATAC counts as appropriate
Supplementary files format and content: ATAC fragment files
Supplementary files format and content: Contain ADT antibodies used & barcode sequences
Library strategy: CITE-Seq

organism: Rattus norvegicus

value: testis

value: Adult

value: ADT


title: Whole skin, IMQ-mice, vehicle_1


title: DSS1


title: F4256_Fibroblasts_47XYY


title: Sham6

value: Sham


title: F4246_Fibroblasts_47XYY

value: JS


title: F4247_Fibroblasts_47XYY


title: CD9neg.rat.9

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_rat18CD9neg_filtered_feature_bc_matrix.h5

value: mRNA


title: Sham5

value: stool


title: CD9low.rat.9.CS

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_rat18CD9low_filtered_feature_bc_matrix.h5
rat18_featurereference.csv

value: CD9 low


title: CD9low.rat.9

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_rat18CD9low_filtered_feature_bc_matrix.h5


title: F4245_Fibroblasts_47XYY


title: CD9mid.rat.9.CS

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_rat18CD9mid_filtered_feature_bc_matrix.h5
rat18_featurereference.csv

value: CD9 mid


title: Sham4


title: Sham3


title: 3_2_2

first: Zhaorong

last: Li

institute: Dana Farber Cancer Institute

description: Single cell RNA-Seq samples generated by inDrop v3 protocol

data_processing:
The raw sequences from all the samples were aligned to the GRCh38 reference genome using STARSolo, and then the quantification of these samples was done using DropEst.
Assembly: GRCh38
Supplementary files format and content: RDS files of count matrix. The rows of count matrix are gene names and columns of count matrix are cell names

source_name: Tumor

extract_protocol:
Human GBM fresh tumor tissue specimens were allocated by the Neuropathology Division and the Tissue and Blood Repository at Brigham and Women’s Hospital in accordance with prospective consent to a tissue procurement IRB protocol for CNS disorders or IRB waiver of consent. Tissue was immediately placed in Hibernate A (Gibco) media using aseptic technique. Fragments of tissue were gently cut into ~2mm3 pieces for cultures on Millicell transwell membranes (Millipore Sigma) in neurobasal A media supplanted with B27 (Gibco). The transwell system contained 1mL media below the membrane, fitted into a 6 well tissue culture plate, with the slice resting on the membrane, covered with a thin film of media (roughly 5 mL) for optimal oxygen diffusion. The liquid film was maintained by pipetting 5 mL media onto slices from the lower chamber daily. Media in the lower well was replaced every 48 hours. The EF1a promoter was cloned into the pBOB-SynP-HTB plasmid, which contains a lentiviral backbone and was a gift from Edward Callaway & Liqun Luo (Addgene plasmid # 30195; http://n2t.net/addgene:30195 ; RRID:Addgene_30195). Lentivirus was produced from newly cloned pBOB-EF1a-HTB using previously described methods. On the first day of culture, each piece of tissue was lentivirally transduced with TVA and G under the EF1a promoter, which was pipetted on top of cultures in a volume 5 mL at a concentration of 106 infectious units. One day later, tissue was gently rinsed with PBS, which was removed to leave a thin liquid film on the top of each slice. After five days, tissues were injected with 1 mL barcoded, pseudotyped rabies virus (EnvA-RABDG) at a concentration of 10,000 infectious units per mL. One day later, tissue was gently rinsed with PBS, which was removed to leave a thin liquid film on the top of each slice. After five days, tissue was digested using papain, followed by trituration using fire polished glass Pasteur pipettes. Cells then underwent myelin removal using the Myelin removal kit from Miltenyi. Filtered cell suspensions then underwent FACS sorting for mCherry+ cells. Sorted mCherry+ cells then underwent single cell droplet encapsulation using Indrop v3 switch drops, followed by cDNA library preparation at the Single Cell Core at Harvard Medical School. Prior to sequencing, mCherry barcodes were amplified using 3’cDNA primers in addition to a primer to mCherry as described previously.
Cells then underwent myelin removal using the Myelin removal kit from Miltenyi. Filtered cell suspensions then underwent FACS sorting for mCherry+ cells. Sorted mCherry+ cells then underwent single cell droplet encapsulation using Indrop v3 switch drops, followed by cDNA library preparation at the Single Cell Core at Harvard Medical School. Prior to sequencing, mCherry barcodes were amplified using 3’cDNA primers in addition to a primer to mCherry as described previously.

tag: subject status

value: GBM patient

value: Tumor


title: CD9mid.rat.9

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_rat18CD9mid_filtered_feature_bc_matrix.h5


title: 3_2_1


title: Sham2


title: 3_1_1


title: CD9high.rat.9

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_rat18CD9high_filtered_feature_bc_matrix.h5

value: CD9 high


title: 3_1_2


title: Sham1


title: 2_2


title: Uterovaginal junction of breeder hens under heat stress (36°C for 6 h) condition biological replicate 3

city: Muang District

first: Satoshi

last: Kubota

state: Nakhon Ratchasima

address: 111 University Avenue, Suranaree Sub-District,

country: Thailand

institute: Suranaree University of Technology

description: Library name: HSC3

data_processing:
Raw data of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.
Paired-end clean reads were mapped to the reference genome using HISAT2 (v2.0.5) software with parameter "--dta --phred33".
Featurecounts (v1.5.0-p3) with default parameters was used to count the number of reads mapped to each gene.
Assembly: GRCg6a
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each Sample

organism: Gallus gallus

source_name: Uterovaginal junction

extract_protocol:
Total RNA was extracted from 24 uterovaginal junction tissue samples with RNeasy Mini Kit (Qiagen, Hilden, Germany).
The RNAs extracted from the uterovaginal junctions of 4 hens were pooled for one library. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP. It was ready after end repair, A-tailing, adapter ligation, size selection, enzyme digestion, amplification, and purification. Library preparation and subsequent RNA-seq were conducted by Novogene Biotechnology Company (Novogene, Beijing, China).

value: Uterovaginal junction


title: Uterovaginal junction of breeder hens under heat stress (36°C for 6 h) condition biological replicate 1

description: Library name: HSC1


title: Uterovaginal junction of breeder hens under heat stress (36°C for 6 h) condition biological replicate 2

description: Library name: HSC2


title: 1_5_b


title: EpCAM.rat.8.CS

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_rat17_epcam_filtered_feature_bc_matrix.h5
rat17_featurereference.csv

value: EpCAM+


title: CD9vhigh.rat.9.CS

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_rat18CD9vhigh_filtered_feature_bc_matrix.h5
rat18_featurereference.csv

value: CD9 very high


title: EpCAM.rat.8

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_rat17_epcam_filtered_feature_bc_matrix.h5


title: 1_5_a


title: Uterovaginal junction of breeder hens under thermoneutral (23°C) condition biological replicate 3

description: Library name: TC3


title: CD9vhigh.rat.9

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_rat18CD9vhigh_filtered_feature_bc_matrix.h5


title: Uterovaginal junction of breeder hens under thermoneutral (23°C) condition biological replicate 1

description: Library name: TC1


title: EpCAM.rat.7

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_rat16_epcam_filtered_feature_bc_matrix.h5


title: AML_10_c2_S38

city: Bethesda

first: Laura

last: Dillon

address: Room 10CRC 6-5142, 10 Center Drive

institute: National Heart Lung and Blood Institute, NIH

description:
Patient 10 end of cycle 2 bulk RNA-seq
S38

data_processing:
Reads were aligned to human genome assembly GRCh37/hg19 by HISAT2 (version 2.1.0) with default setting for paired-end reads. The aligned reads were converted to BAM files and sorted by SAMtools 1.9 with index files created. The sorted BAM files were processed in R (version 3.5; R Foundation for Statistical Computing, Vienna, Austria) with Bioconductor packages. The count matrix on gene level was generated by featureCounts in Rsubread function.
Assembly: GRCh37/hg19 for bulk RNAseq; Single-cell cellranger used the pre-built GRCh38 in the pipeline.
Supplementary files format and content: Gene raw count matrix in csv for bulk RNAseq; single-cell processed data contain the gene and protein expression matrices with cell barcodes.

source_name: Bone marrow

extract_protocol:
Bulk RNAseq: RNA was isolated from PAXgeneTM BM RNA tubes using the PAXgene BM RNA kit (PreAnalytiX). RNA quantity was measured using a Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA) and RNA quality was assessed using the TapeStation system (Agilent Technologies, Santa Clara, CA). All samples had RNA Integrity Numbers (RIN) of seven or higher. Single-cell: BM mononuclear cells (BMMCs) were purified from BM aspirate using density centrifugation, cryopreserved, and stored in liquid nitrogen.
Bulk RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina Inc., San Diego, CA) using 1 μg of total RNA input and paired-end 75-bp sequencing on a HiSeq 3000 (Illumina, San Diego, CA). The 10x Genomics 3’v3 Single Cell Immune profiling platform was used for scRNA-seq of BMMCs. cDNA amplification was performed according to manufacturer’s instructions with the addition of 1 ul 0.2 uM ADT additive primer per sample to amply ADT tags.

value: Bone marrow

value: Male


title: 2_1


title: 1_3


title: EpCAM.rat.6.CS

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_rat15_epcam_filtered_feature_bc_matrix.h5
rat15_featurereference.csv

value: testis


title: 1_2


title: AML_10_c1d8_S37

description:
Patient 10 cycle 1 day 8 bulk RNA-seq
S37


title: 1_4


title: EpCAM.rat.7.CS

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_rat16_epcam_filtered_feature_bc_matrix.h5
rat16_featurereference.csv

value: Adult


title: EpCAM.rat.6

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_rat15_epcam_filtered_feature_bc_matrix.h5


title: 1_1


title: EpCAM.rat.5.CS

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_rat14_epcam_filtered_feature_bc_matrix.h5
rat14_featurereference.csv

value: ADT


title: AML_9_c2_S35

description:
Patient 9 end of cycle 2 bulk RNA-seq
S35

value: Female


title: RNAseq, PXR knockout LS174T, rif, ActD 4h

first: Min

last: Zhang

institute: University of Pittsburgh

data_processing:
Sequenced reads were mapped to whole genome using STAR
Read counts were calculated using RSEM
Assembly: GRCh38
Supplementary files format and content: gene expression quantification from RSEM

source_name: Colon

growth_protocol: Wildtype and PXR knockout LS174T cells were maintained in EMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Total RNA from cultured cells were isolated using TRIzol (ThermoFisher), purified using RNA purification kit (ZYMO) as per the manufacturer’s instructions and RNA libraries were prepared for sequencing.
RNA libraries for RNA-seq were prepared using KAPA RNA Hyper RiboErase HMR (96 rxn) KK8581/8098140702 according to manufacturer's protocols.

treatment_protocol: Wildtype and PXR knockout LS174T cells were cultured in MEM with charcoal-stripped FBS and antibiotics for 24 h, then treated with DMSO or rifampicin for 24 h, and then treated with actinomycin D for 2 or 4 h.

value: Colon

tag: cell type

value: colorectal cancer

value: PXR KO

value: rifampicin treated for 24 h, actinomycin D treated for 4 h


title: AML_9_c1d8_S34

description:
Patient 9 cycle 1 day 8 bulk RNA-seq
S34


title: EpCAM.rat.5

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_rat14_epcam_filtered_feature_bc_matrix.h5

value: mRNA


title: Uterovaginal junction of breeder hens under thermoneutral (23°C) condition biological replicate 2

description: Library name: TC2


title: RNAseq, PXR knockout LS174T, Ctrl, ActD 4h

tag: genotype

value: DMSO treated for 24 h, actinomycin D treated for 4 h


title: AML_8_c4_S32

description:
Patient 8 end of cycle 4 bulk RNA-seq
S32

tag: gender


title: unselected.rat.8.CS

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_rat17_unselected_filtered_feature_bc_matrix.h5
rat17_featurereference.csv

value: unselected


title: AML_8_c2_S31

description:
Patient 8 end of cycle 2 bulk RNA-seq
S31


title: RNAseq, wildtype LS174T, rif, ActD 4h

value: PXR WT


title: RNAseq, wildtype LS174T, Ctrl, ActD 4h


title: AML_8_c1d8_S30

description:
Patient 8 cycle 1 day 8 bulk RNA-seq
S30


title: unselected.rat.8

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_rat17_unselected_filtered_feature_bc_matrix.h5


title: RNAseq, PXR knockout LS174T, rif, ActD 2h

value: rifampicin treated for 24 h, actinomycin D treated for 2 h


title: AML_7_c2_S27

description:
Patient 7 end of cycle 2 bulk RNA-seq
S27


title: AML_7_c6_S28

description:
Patient 7 end of cycle 6 bulk RNA-seq
S28


title: RNAseq, PXR knockout LS174T, Ctrl, ActD 2h

value: DMSO treated for 24 h, actinomycin D treated for 2 h


title: unselected.rat.7

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_rat16_unselected_filtered_feature_bc_matrix.h5


title: AML_7_c1d8_S26

description:
Patient 7 cycle 1 day 8 bulk RNA-seq
S26


title: unselected.rat.6

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_rat15_unselected_filtered_feature_bc_matrix.h5


title: JS2E7_NS_NSC_47XYY

data_processing:
After FastQC quality control,sequence adapters were trimmedwith trimGalore v.0.06.
High quality reads were mapped against the reference genome (GRCh38/Ensembl release 101) using Bismark v.0.23.1
The CpG  extraction was done with MethylDackel v 0.6.1
Assembly: Ensembl GRCh38 v. 101
Supplementary files format and content: One BedGraph for each sample, containing information about methylation levels. Column 1: chromosome, Column 2: start position of CpG site (0-based),  Column 3: ending position of the CpG site (exclusive), Column 4: methylation percentage observed at the CpG site. Percentage is calculated as the proportion of methylated cytosines relative to the total number of cytosines sequenced at that position  (C/C+T *100), Column 5: Total number of reads covering CpG site, Column 6: Counts of methylated cytosines detected at each site.

source_name: NSC

extract_protocol:
The gDNA was extracted using the DNeasy Blood & Tissue genomic DNA  Extraction Kit From Qiagen.
DNA libraries were generated  by Beijing Novogene Bioinformatics Technology, Co., Ltd. (Beijing, China). Target enrichment was performed to construct the exome library using the Agilent SureSelect Human All Exon V6 kit (Agilent Technologies, Inc., Santa Clara, CA, United States), according to manufacturer’s protocol, then DNA was sequenced using IluminaNovaseq6000/NovaseqX 2 x 150b or Novaseq 6000 as indicated in the table.

value: NSC

value: JS


title: RNAseq, wildtype LS174T, Ctrl, ActD 2h


title: unselected.rat.6.CS

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_rat15_unselected_filtered_feature_bc_matrix.h5
rat15_featurereference.csv


title: unselected.rat.5.CS

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_rat14_unselected_filtered_feature_bc_matrix.h5
rat14_featurereference.csv


title: AML_6_c2_S24

description:
Patient 6 end of cycle 2 bulk RNA-seq
S24

value: Bone marrow


title: RNAseq, PXR knockout LS174T, rif, ActD 0h

value: rifampicin treated for 24 h


title: unselected.rat.5

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_rat14_unselected_filtered_feature_bc_matrix.h5

value: testis

value: Adult


title: unselected.rat.7.CS

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_rat16_unselected_filtered_feature_bc_matrix.h5
rat16_featurereference.csv

value: ADT


title: RNAseq, PXR knockout LS174T, Ctrl, ActD 0h

value: Colon

value: DMSO treated for 24 h


title: JS1E1_NS_NSC_47XYY


title: AML_5_c10_S21

description:
Patient 5 end of cycle 10 bulk RNA-seq
S21

value: Male


title: AML_6_c1d8_S23

description:
Patient 6 cycle 1 day 8 bulk RNA-seq
S23

value: Female


title: RNAseq, wildtype LS174T, rif, ActD 0h

value: colorectal cancer


title: JS2B2_NS_NSC_47XYY


title: AML_5_c6_S19

description:
Patient 5 end of cycle 6 bulk RNA-seq
S19


title: 326E1_NS_NSC_47XYY


title: RNAseq, wildtype LS174T, rif, ActD 2h


title: CD9high.rat.9.CS

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_rat18CD9high_filtered_feature_bc_matrix.h5
rat18_featurereference.csv

value: CD9 high


title: AML_5_c4_S18

description:
Patient 5 end of cycle 4 bulk RNA-seq
S18


title: JS3E1_NS_NSC_47XYY


title: Human ALI from small airway treated with IL13

first: Brian

last: Lin

address: 136 Harrison Avenue

department: DMCB

institute: Tufts University

data_processing:
FASTQ files were aligned using Cellranger 7.0.1 to GRCh38-3.0.0
Splice counts were modeled using velocyto 0.17
Downstream analysis was performed using Scanpy v1.6.0 and leidenalg 0.8.3
Assembly: GRCh38-3.0.0
Supplementary files format and content: A fully annotated and processed Scanpy adata file in h5ad format, and the splice count loom file output from velocyto. For timecourse data, all samples are combined in a single processed scanpy anndata object as an h5ad file.

source_name: small airway

growth_protocol: Human airway basal cells were expanded in PneumacultEx Plus in dual smad inhibition and rock-inhibitor on 804G coated plastic.

extract_protocol:
ALI membranes were cut out using a scalpel. Washed in PBS twice, incubated with TrypLE Express for 5 minutes at 37C with rotation. Dissociation was stopped with PBS containing 10% FBS and 5 uM Rock inhibitor, filtered through a 40 um filter before loading for 10x processing.
RNA libraries were made according to 10x single cell RNAseq protocols

treatment_protocol:
Basal cells were seeded onto 804G coated Corning transwell membranes and switched to Pneumacult ALI media to induce differentiation
Transwells were treated with 10 ng/ml recombinant human IL13 or PBS as a control.

value: small airway

value: airway

tag: culture

value: in-vitro, air-liquid interface culture


title: thallus, sample L

city: Vienna

first: Chloe

last: Casey

address: Zimmermannplatz 10

country: Austria

institute: St Anna Children's Cancer Research Institute

description: Library name: sample_47

data_processing:
Trimmomatic v0.38
Raw reads were trimmed to remove Illumina adaptors and low-quality reads using Trimmomatic v0.38. Parameters -  ILLUMINACLIP:all_adaptors.fasta:2:30:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:5:15 MINLEN:25
Salmon v1.5.2
Read counts were quantified using Salmon v1.5.2 in quasi-mapping-based mode against a salmon transcriptome index built from the MpTak_v6.1 transcriptome. Parameters for indexing -k 21; Parameters for read count quantification - --threads 12 --validateMappings
R v4.2.0; tximport v1.26.1
Transcript-level Salmon quantification files were imported and gene-level summarization was performed using tximport v1.26.1. Gene-level TPM values (transcripts per million) were extracted with tximport using a transcript to gene (tx2gene) mapping file constructed from the MpTak_v6.1 transcriptome.
R v4.2.0; DESeq2 v1.38.3
To identify genes that were differentially expressed between inactive and active meristems at each of the three stages, differential gene expression analysis was carried out using DESeq2 v1.38.3. The design formula “ ~ pair + activity ” was used to identify genes differentially expressed between inactive and active meristems while controlling for variability between sample pairs. Significantly differentially expressed genes were defined to have a Log2 Fold Change < -2 or > 2, and a padj < 0.05.
Assembly: MpTak_v6.1
Supplementary files format and content: Transcript-level Salmon quantification files (quant.sf) for each sample

organism: Marchantia polymorpha

source_name: thallus

extract_protocol:
The RNeasy® Plant Mini Kit was used to extract RNA from homogenised samples. 500 ng of total RNA was used for the construction of sequencing libraries.
Poly-A mRNA was isolated with the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490). Enriched poly-A mRNA sequencing libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® following the kit instructions. The fragment size of the libraries was assessed using the NGS HS analysis kit on an Agilent fragment analyzer system. The library concentrations were quantified with a Roche KAPA Kit by qPCR.

value: thallus

value: WT; Tak-1


title: stage 3, inactive meristem, pair H

description: Library name: sample_45

source_name: inactive meristem

value: inactive meristem


title: Human ALI Timecourse, PBS and IL13

description:
Human ALI from primary bronchus treated with IL13_d2, IL13_D2_SM-J4BUB_SI-TT-D2_S2.loom
Human ALI from primary bronchus treated with IL13_d2, IL13_D3_SM-J4BSA_SI-TT-F2_S6.loom
Human ALI from primary bronchus treated with IL13_d2, IL13_D5_SM-J4BSY_SI-TT-H2_S4.loom
Human ALI from primary bronchus treated with PBS_d2, PBS_D2_SM-J4BTY_SI-TT-C2_S3.loom
Human ALI from primary bronchus treated with PBS_d3, PBS_D3_SM-J4BUN_SI-TT-E2_S1.loom
Human ALI from primary bronchus treated with PBS_d5, PBS_D5_SM-J4BSM_SI-TT-G2_S5.loom

source_name: primary bronchus

value: primary bronchus

value: PBS, IL13

tag: time


title: JS3C1_NS_NSC_47XYY

value: NSC

value: JS


title: JS2C1_NS_NSC_47XYY


title: JS1C5_NS_NSC_47XYY


title: AML_5_c1d8_S16

description:
Patient 5 cycle 1 day 8 bulk RNA-seq
S16

value: Bone marrow

tag: age


title: Human ALI from small airway treated with PBS

value: PBS


title: stage 3, active meristem, pair G

description: Library name: sample_44

source_name: active meristem

value: active meristem


title: AML_5_c8_S20

description:
Patient 5 end of cycle 8 bulk RNA-seq
S20

value: Male


title: thallus, sample N

description: Library name: sample_49


title: Human ALI from primary bronchus treated with PBS


title: stage 3, inactive meristem, pair G

description: Library name: sample_43


title: RNAseq, wildtype LS174T, Ctrl, ActD 0h

city: Pittsburgh

address: Salk Hall, 3501 Terrace St

value: Colon

tag: cell line

value: PXR WT

value: DMSO treated for 24 h


title: Human ALI from primary bronchus treated with IL13


title: JS2C1_PS_iPSC_47XYY

source_name: iPSC

value: iPSC


title: AML_4_c2_S14

description:
Patient 4 end of cycle 2 bulk RNA-seq
S14


title: thallus, sample M

description: Library name: sample_48


title: stage 2, active meristem, pair E

description: Library name: sample_42


title: stage 3, active meristem, pair H

description: Library name: sample_46


title: JS3B1_PS_iPSC_47XYY


title: AML_5_c2_S17

description:
Patient 5 end of cycle 2 bulk RNA-seq
S17