title: Untreated HN9.10 cells, replicate 3 [1-1c_S580]


title: RUNX1_CUT_IP_A

status: Public on Jul 12 2023

type: SRA

city: Philadelphia

first: Alexandra

last: Zezulin

address: 421 Curie Blvd 544 BRB II/III

country: USA

institute: University of Pennsylvania

library_source: genomic

data_processing:
Sequencing reads were demultiplexed using Bcl2Fastq v2.20 then trimmed and filtered for quality using Trim Galore with the following settings: fastqc, paired, and trim1. Reads were then aligned to the mouse genome (mm10) or the E. coli K12 genome using bowtie 2.3.5.1. Only uniquely mapped reads with fewer than 2 mismatches and MAPQ equal or greater than 30 were used for downstream analyses. Samtools v.1.1 was used to convert SAM files to BAM files, and Sambamba v0.6.6 was used to filter out duplicates, multi-mappers, reads mapped to ChrM or blacklist regions, and unmapped reads. MACS2 2.1.4 was used for peak calling with the following parameters: narrow, q: 0.05. Merged replicates were used to create bigwig files for visualization using Deeptools v3.3.0. The following parameters were used: normalized to Bins Per Million mapped reads (BPM bin size: 50. IGV or UCSC genome browser was used for visualization.
Assembly: mm10
Supplementary files format and content: BigWig files provided are normalized tracks of merged replicates
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Mus musculus

source_name: BM GMPs

extract_protocol:
Cells were sorted from the bone marrow. CUT&RUN reactions were performed using 200,000 FACS-sorted cells.
Libraries were constructed using NEBNext Ultra II DNA Kit. Libraries were size-selected at 150-350 bp  by AMPure XP beads. Libraries were quantified with KAPA, qPCR, and bioanalyzer prior to paired-end sequencing.

treatment_protocol: Cells were harvested and were sorted on the same day as harvest

tag: isoloation markers

value: Lin- cKIT+Sca1-CD16/32+CD150-

tag: strain

tag: developmental stage

value: Adult (4-6 weeks old)

tag: tissue

value: Bone Marrow

tag: genotype

value: Control (Runx1f/f)

tag: chip antibody


title: M45_left-ear_control_0min

city: Saarbrücken

first: Annika

last: Engel

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

country: Germany

institute: Saarland University

description: Li M45 0h K

library_source: transcriptomic

data_processing:
We performed the pre-processing step according to our pipeline miRMaster 2.0 with standard parameter settings (https://doi.org/10.1093/nar/gkab268). Detection filtering was processed for at least in one ear type (left-ear_treatment, right-ear_treatment, left-ear_control and right-ear_control) 100% of the samples needed to be expressed.
Assembly: mm10
Supplementary files format and content: miRNA_expression_raw.tsv: Tab-separated file of raw feature counts per sample.

molecule: total RNA

source_name: ear skin

extract_protocol:
The ears were immersed in RNAlater for 12 hours at 4°C and subsequently frozen at -80°C. RNA was isolated using miRNeasy Mini kit (Qiagen, Hilden, Germany) after manufacturers recommendations. RNA quantity and quality was determined using Nanodrop (ThermoFisher Scientific, Waltham, MA, USA) and Bioanalyzer RNA Nano Chip Kit (Agilent Technologies, Santa Clara, CA, USA). Mean RNA Integrity Number (RIN) of the samples was 8.2 ± 0.9.
SmallRNA sequencing libraries were prepared using MGIEasy Small RNA Library Prep Kit on the high-throughput MGI SP-960 sample prep system (MGI Tech, Shenzhen, China). According to the manufacturer's protocols, the 3’- and 5’-adapters were ligated to the RNA. Afterwards, an RT primer including sample-specific barcodes was utilised to perform reverse transcription (RT). Amplification of the cDNA was achieved using a polymerase chain reaction (PCR) with 21 cycles. PCR products were subsequently size selected via AMPure Beads XP (Beckman Coulter, Brea, CA, USA). Size and 449 concentration of the purified PCR products were determined using an Agilent DNA 1000 Kit (Agilent Technologies, Santa Clara, CA, USA) and QubitTM 1X dsDNA High Sensitivity (HS) (ThermoFisher Scientific, Waltham, MA, USA), respectively. Fifteen samples and one performance control sample were pooled in an equimolar fashion in one sequencing library, which was circularized using the MGI Easy circularisation kit. In total, we prepared 8 libraries composed of a total of 120 samples
Samples were sequenced on DNBSEQ-G400RS with DNBSEQ-G400RS High-throughput Sequencing Set (Small RNA FCL SE50) by BGI in Wuhan, China.

value: ear skin

value: wild-type

tag: age

tag: Sex

value: female

tag: mouse id

tag: location

value: left

tag: group

value: control

tag: group 2

value: none experimental ear

tag: timepoint (min)


title: KO_LPS_PMN_H3K27ac_IP2

description: #REF!

data_processing:
Sequencing reads were demultiplexed using Bcl2Fastq v2.20 then trimmed and filtered for quality using Trim Galore (Martin 2011) with the following settings: fastqc, and trim1. Reads were then aligned to the mouse genome (mm10) using bowtie 2.3.5.1. Only uniquely mapped reads with fewer than 2 mismatches were used for downstream analyses. Samtools v.1.1 was used to convert SAM files to BAM files, and Sambamba v0.6.6 was used to filter out duplicates, multi-mappers, reads mapped to ChrM or blacklist regions, and unmapped reads. MACS2 2.1.4 was used for peak calling using the following parameters: narrow, q: 0.05. Control or Runx1ΔGMP specific differential peaks were called if the RPKM fold change between Control and Runx1ΔGMP peaks was greater than 2. Merged replicates were used to create bigwig files for visualization using Deeptools v3.3.0 (Ramírez et al. 2016). The following parameters were used: normalized to reads per genomic content (RPGC), effective genome size: 2,308,125,349 bp, ignore for normalization: ChrX, min fragment length: 20, bin size: 10.
Assembly: mm10
Supplementary files format and content: BigWig files provided are normalized tracks of merged replicates
Supplementary files format and content: Bed files provided are the output of merged Control and Runx1ΔGMP MACS2 peak calling:  Control or Runx1ΔGMP specific differential peaks were called if the RPKM fold change of between Control and Runx1ΔGMP peaks was greater than 2

source_name: BM Neutrophils

extract_protocol:
Cells were sorted from the bone marrow and stimulated with 100 ng/mL of LPS. ChIP reactions were performed using 50,000 FACS-sorted cells per IP. IP and IN DNA were purified with MinElute PCR Purification Kit.
Libraries were constructed using Rubicom ThruPLEX DNA-Seq Kit. Libraries were size-selected at 100-700 bp by AMPure XP beads. Libraries were quantified with KAPA qPCR and bioanalyzer prior to single-end sequencing.

value: Runx1f/f; Cebpa-Cre + (Runx1{delta}GMP)


title: Untreated HN9.10 cells, replicate 2 [1-1b_S579]

city: Udine

first: Emiliano

last: Dalla

state: UD

address: Piazzale Kolbe 4

department: Department of Medicine

country: Italy

institute: Università degli Studi di Udine

data_processing:
Quality control for raw sequencing reads was performed using the FastQC (v0.11.9) and MultiQC (v1.4)
Reads had very good quality and no correction was required. Cutadapt (ver 1.15) was used to remove the 3’adapter, primer and other types of unwanted sequences.
Alignment of reads was conducted with STAR (v2.5.3a) using the mouse genome assembly GRCm38 (mm10) with reference annotation; reads were assigned to a miRNA based on GENCODE annotations and via the STAR function “quantMode TranscriptomeSAM GeneCounts”.
Differential expression analysis was performed using gene raw counts, within the R/Bioconductor DESeq2 package; we estimated the dispersion parameter for each library using the biological group dispersion.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Immortalized hippocampal neurons HN9.10e were grown in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 100 IU/mL penicillin, 100 μg/mL streptomycin, and 2.5 μg/mL amphotericin B. Cells were maintained at 37 °C in a saturating humidity atmosphere containing 95% air and 5% CO2.

extract_protocol:
Exosome Isolation: Exosomes released in the culture medium from untreated HN9.10e cells (control sample) and Cer-treated HN9.10e cells (experimental sample) were isolated after 48 hours of treatment. The supernatant was centrifuged at 2000g x 30 min, filtered with 0.22µm filter unit (MILLEX-GS from Millipore, Molsheim, France), in order to remove larger extracellular vesicles and apoptotic bodies, and concentrated with Pierce™ Protein Concentrators PES, 100K MWCO from Thermo Scientific™. Then, the retained in the filter was used to isolate exosomes with “total exosome isolation” kit from Invitrogen-Thermo Fisher Scientific (Waltham, MA, USA) by following the instructions of the company. Exosomal miRNA Isolation: The exosomes-containing pellet was resuspended in 200ul of PBS buffer, quantified using the Exosome Quantitation Kit (System Biosciences) and stored at −80 °C until use. Total RNA was extracted from 5×1010 exosomes using mirVana miRNA Isolation kit (Life Technologies) and miRNA concentration was determined by Qubit microRNA assay kit (Invitrogen).
Sequencing libraries were prepared based on the QIAseq miRNA library kit (QIAGEN, Hilden, Germany), following the manufacturer’s instructions. Final libraries were checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent Bioanalyzer DNA assay or Caliper (PerkinElmer, Waltham, MA). Quantified libraries were mixed at an equimolar ratio and sequenced on single-end 150 bp mode on NovaSeq 6000 (Illumina, San Diego, CA).

treatment_protocol: To study the effect of ceramide on cell differentiation and exosome release, ceramide was added to the culture medium at the 100 nmol/L concentration corresponding to the amount of ceramide present in exosomes released under vitamin D3 treatment, as previously reported (Conte et al., 2021). To investigate the effect of exosomes released under ceramide treatment on cell differentiation, exosomes were added to the culture medium with increasing concentration of exosomes (protein concentration from 200 to 300 µg/106 cells), considering that 1x106 cells were able to release exosomes corresponding to 250 µg protein.

tag: cell line

tag: cell type

value: Immortalized hippocampal neurons

value: WT

tag: treatment

tag: molecule subtype

value: Exosomal miRNA


title: KO_LPS_PMN_H3K27ac_IP1

description: #REF!

tag: isoloation markers


title: liver metastasis CRC55

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

institute: IRCCS San Raffaele Scientific Institute

data_processing:
Reads were quality filtered according to the Illumina pipeline, then were aligned to mouse genome build GRCh38/hg38  using using START version 2.5.3a. Only uniquely mapped reads were retained.
Gene expression counts were estimated using featureCounts (version 1.6.4) , summarized across all exons , with option “largestOverlap”.
Differentially expressed genes were identified using EdgeR R-package (version 4.0.5).
Assembly: GRCh38/hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: liver metastasis from colorectal cancer

extract_protocol:
RNA was extracted from OCT-embedded samples using AllPrep DNA/RNA Mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: disease state

value: metastasis


title: KO_LPS_PMN_H3K27ac_IN

description: #REF!

tag: strain

tag: developmental stage


title: Untreated HN9.10 cells, replicate 1 [1-1_S1]

tag: genotype


title: M40_right-ear_control_120min

description: Re M40 2h K

tag: tissue

value: right


title: liver metastasis CRC56


title: M26_right-ear_control_10min

description: Re M26 10' K gefällt

tag: age


title: M49_right-ear_control_10min

description: Re M49 10' K

tag: Sex


title: WT_LPS_PMN_H3K27ac_IP2

description: #REF!

tag: chip antibody


title: liver metastasis CRC53


title: WT

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

library_source: transcriptomic single cell

data_processing:
Illumina bcl2fastq2 Conversion Software 2.20. Quality score is encoded in a +33 offset ASCII (Sanger like)
The raw sequencing reads were filtered, demultiplexed and aligned to the mouse genome and transcriptome (mm10, refdata-gex-mm10-2020-A) using the 10x Genomics Cell Ranger pipeline (version 7.0.1). The cellranger count function was used with default parameters (i.e. --include-introns=TRUE).
Assembly: mm10
Supplementary files format and content: Output of cellranger count: for each sample, a matrix (mtx) file contains the raw counts per gene (in rows) per cell (in columns). The tab-separated values file features.tsv contains the corresponding row names of the mtx file, and the barcodes.tsv file contains the corresponding cell names of the mtx file

source_name: Spleen

extract_protocol:
Total P14 CD8+ T cells were flow sorted from the spleen on day 28 post-infection with LCMV clone 13 and encapsulated in droplets for scRNAseq analysis using the 10x Chromium controller
10x genomics Single Cell 3' v3 chemistry

value: Spleen

value: P14 T cells

value: CD8 T cells

value: 28 days post-infection with LCMV clone 13


title: liver metastasis CRC51


title: RUNX1_CUT_IP_B

value: Lin- cKIT+Sca1-CD16/32+CD150-

value: Adult (4-6 weeks old)

value: Bone Marrow

value: Control (Runx1f/f)


title: NFAT5_KO

value: B6;D2-Tg(TcrLCMV)327Sdz/JDvsJ x B6.Cg-Tg(Cd4-cre)1Cwi/BfluJ  x NFAT5 flox/flox


title: liver metastasis CRC50


title: M34_right-ear_control_10min

description: Re M34 10' K

value: ear skin

value: wild-type

value: female

tag: mouse id

tag: location

value: control

value: none experimental ear


title: HN9.10 cells treated with 100 nmol/L ceramide, replicate 2 [2-2b_S1]

value: Immortalized hippocampal neurons

value: WT

value: 100 nmol/L ceramide

value: Exosomal miRNA


title: WT_LPS_PMN_H3K27ac_IN

description: #REF!


title: KO_GMP_RNA_C

description: GMP_Differential_expression_analysis_table.csv

data_processing:
Sequencing and base calling was performed by GeneWiz (https://www.genewiz.com/). Raw sequence data (.bcl files) were converted into fastq files and de-multiplexed using Illumina Bcl2Fastq v2.20 software. One mis- match was allowed for index sequence identification. Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate P values and Log2 fold changes. Genes with adjusted P values < 0.05 and absolute log2 fold changes >1 were called as differentially expressed genes for each comparison. Merged replicates were used to create bigwig files for visualization using Deeptools v3.5.1 with the following parameters: normalized to Bins Per Million mapped reads (BPM), bin size: 50
Assembly: mm10
Supplementary files format and content: BigWig files provided are normalized tracks of merged replicates
Supplementary files format and content: CSV file provided is a summary of data analyzed using DESeq2:DESeq2 results summary was used to generate a CSV of base mean expression, P values and Log2 fold changes comparing control and Runx1ΔGMP expression.

extract_protocol:
Cells were sorted from BM. Total RNA samples were isolated using RNeasy Mini Kit (Qiagen).
Sample QC, library preparations, and sequencing reactions were conducted at GENEWIZ, LLC./Azenta US, Inc. ERCC RNA Spike-In Mix  was added to normalized cell number prior to library preparation. The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions. The  libraries were validated on the Agilent TapeStation, and quantified by using Qubit 2.0 Fluorometer. Libraries were sequenced on the NovaSeq 6000 using a 2x150bp Paired End (PE) configuration

value: BM GMPs

value: Runx1f/f; Cebpa-Cre + (Runx1{delta}GMP)


title: KO_GMP_RNA_B


title: M40_left-ear_control_120min

description: Li M40 2h K

value: left

tag: group

tag: group 2


title: liver metastasis CRC49

value: liver

value: metastasis


title: D3 MEFs

city: fuzhou

first: yangfan

last: zhang

address: Fujian Normal University Qishan Campus, College Town, Fuzhou, Fujian Province

country: China

institute: FJNU

data_processing:
Quality control of raw data using fastp
Download Mus musculus GRCm39 from ensamble. Building indexes with Hisat2
Matching the raw data after QC to the reference genome
Use featureCounts to count the expression of sample genes and obtain the expression matrix
Supplementary files format and content: Mus musculus GRCm39
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: MEFs

growth_protocol: Primary MEFs, spontaneously immortalized MEFs, in Dulbecco’s modified Eagle’s medium (DMEM) plus 10% (v/v) FBS, 2 mM L-glutamine, 10 mM HEPES and 1 mM sodium pyruvate (complete DMEM) with the addition of Pen-Strep and cultured at 37°C with 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell line

value: MEFs

value: Mouse embryonic fibroblasts

tag: time point

value: at 2 Passage


title: P212 1 MEFs

tag: cell type


title: P212 2 MEFs


title: liver metastasis CRC43


title: M48_left-ear_control_10min

description: Li M48 10' K

value: ear skin

tag: timepoint (min)


title: WT_GMP_RNA_C

tag: isoloation markers

value: Lin- cKIT+Sca1-CD16/32+CD150-

value: Adult (4-6 weeks old)

value: Bone Marrow

value: Control (Runx1f/f)


title: WT_GMP_RNA_B


title: M34_left-ear_control_10min

description: Li M34 10' K

value: wild-type

value: female

value: control

value: none experimental ear


title: M48_right-ear_control_10min

description: Re M48 10' K

value: right


title: M49_left-ear_control_10min

description: Li M49 10' K


title: KO_GMP_RNA_A

value: BM GMPs

value: Runx1f/f; Cebpa-Cre + (Runx1{delta}GMP)


title: liver metastasis CRC48

value: liver

tag: disease state


title: WT_LPS_PMN_H3K27ac_IP1

description: #REF!

tag: strain


title: M44_left-ear_control_0min

description: Li M44 0h K

value: left


title: D2 MEFs

value: MEFs


title: liver metastasis CRC40

value: metastasis


title: D1 MEFs

value: Mouse embryonic fibroblasts

value: at 2 Passage


title: liver metastasis CRC42


title: WT_GMP_RNA_A

value: Lin- cKIT+Sca1-CD16/32+CD150-

tag: developmental stage


title: KO_PMN_RNA_C

description: PMN_Differential_expression_analysis_table.csv

value: BM Neutrophils

value: Adult (4-6 weeks old)

tag: genotype


title: liver metastasis CRC38

tag: tissue


title: DK3 MEFs


title: M32_left-ear_control_120min

description: Li M32 2h K

value: ear skin

tag: age


title: M44_right-ear_control_0min

description: Re M44 0h K

value: wild-type

tag: Sex


title: DK2 MEFs


title: M6a_left-ear_treatment_10min_irradiated

description: RNA Mausohr 6 - 10min

value: female

value: treatment

value: experimental ear


title: DK1 MEFs


title: liver metastasis CRC37


title: liver metastasis CRC46


title: KO_PMN_RNA_A

value: Bone Marrow


title: M2a_left-ear_treatment_0min_irradiated

description: RNA Mausohr 2 -0h


title: WT_PMN_RNA_C

value: Control (Runx1f/f)


title: WT3 MEFs

value: WT


title: liver metastasis CRC34

value: liver


title: M17_right-ear_control_120min

description: Re M17 2h K

value: right

value: control

value: none experimental ear


title: WT1 MEFs

value: MEFs

value: Mouse embryonic fibroblasts


title: liver metastasis CRC31

value: metastasis


title: WT_PMN_RNA_A

value: BM Neutrophils


title: hPCSK9-/- (10-weeks-old)_5

city: Gothenburg

first: Muhammad

last: Arif

state: Västra Götaland

address: Blå Straket 5/WLAB

department: Department of Molecular and Clinical Medicine

country: Sweden

institute: University of Gothenburg

data_processing:
We quantified the raw RNA-sequencing data using Kallisto
The estimated count and TPM files were then mapped to mapping file retrieved from Ensembl Biomart to remove the non-protein coding genes and transcripts.
WE then summarized the transcripts into genes by summing transcripts that belong to the same gene.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited Raw counts for every gene and samples
Supplementary_files_format_and_content: Tab-delimited TPM counts for every gene and samples
Supplementary_files_format_and_content: Metadata Summary of each sample

source_name: heart

extract_protocol:
Samples were snap-frozen in liquid nitrogen and stored at -80°C until analysis. Total RNA was isolated from homogenized heart tissue using RNeasy Fibrous Tissue Kit or RNeasy Lipid Tissue Mini Kit (Qiagen).
RNA sequencing library were prepared with Illumina RNA-Seq with Poly-A selections

value: heart

value: 10 weeks

value: KO


title: WT_PMN_RNA_B

value: Adult (4-6 weeks old)


title: M25_right-ear_control_10min

description: Re M25 K

value: ear skin

value: wild-type

value: female


title: M27_right-ear_control_30min

description: Re M27 30' K


title: liver metastasis CRC29


title: M3a_right-ear_control_0min

description: Maus 3 unbestrahlt


title: KO_IP_rep_2b

description:
RNA pulled down from neutrophils with dsRNA-specific 9D5 dsRNA rabbit IgG mAb
DESeq2_TE_subFamily.txt

data_processing:
Raw dsRNA-seq sequencing data (.bcl files) was converted into Fastq files and de-multiplexed using Bcl2Fastq v2.20 software. The data in fastq file format was processed with the toolkit SQuIRE. The raw reads were aligned to the mm10 reference genome and TEs were annotated using RepeatMasker. The SQuIRE call module was used to perform differential expression analysis of genes, or TE by family, or TE by sub-family between Control and Runx1ΔGMP cells.
Assembly: mm10
Supplementary files format and content: Txt file for RNA-seq samples is an output of the SQuIRE call module

extract_protocol:
Protein G Dynabeads and Protein A Dynabeads were washed and resuspended in NET-2 buffer. 9D5 dsRNA rabbit IgG mAb was bound to the beads for 1-2 hours. Cells were lysed in cytosolic lysis buffer. The cell lysate was centrifuged at 980 x g for 3 min at 4℃ (X3). The cytosolic supernatant was spun at 17,000 x g for 10 min. For IP, lysate was diluted to 1:4 with NET-2-TurboDNase buffer. 95D-Dynabeads were added to the lysate and end-to-end rotated for 2 hr at 4 °C. Following magnetic separation, beads were washed with high salt washing buffer and then NET-2 buffer. 95D-bound dsRNA was extracted with Trizol reagent and purified using Direct-zol™ RNA Miniprep Kit (Zymo Research). RNA samples were ribo-depleted with Ribominus™ Eukaryote v2 kit (Thermo Fisher Scientific).
Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. Libraries were sequenced on Illumina HiSeq 2500 sequencer in paired-end mode with read length of 75bp.

tag: cell type source

value: Peripheral Blood

value: Runx1f/f; Cebpa-Cre + (Runx1{delta}GMP)

tag: antibody

value: 9D5 dsRNA rabbit IgG mAb(Ab00458-23.0)


title: KO_IP_rep_1b

value: Bone Marrow


title: KO_PMN_RNA_B


title: hPCSK9-/- (10-weeks-old)_3


title: hPCSK9-/- (10-weeks-old)_4


title: liver metastasis CRC28

value: liver


title: liver metastasis CRC25


title: hPCSK9-/- (10-weeks-old)_2


title: liver metastasis CRC36


title: M43_right-ear_treatment_120min

description: Re M43 2h B

tag: mouse id

tag: location

value: right

value: treatment

value: none experimental ear


title: M18_right-ear_control_60min

description: Re M18 1h K

tag: group

value: control

tag: group 2


title: M10a_right-ear_treatment_60min

description: Maus 10 - 1h


title: liver metastasis CRC23

value: metastasis


title: KO_IP_rep_2a

value: BM Neutrophils


title: M8a_right-ear_treatment_30min

description: Maus 8 - 30 min


title: WT_IP_rep_2a

extract_protocol:
Protein G Dynabeads and Protein A Dynabeads were washed and resuspended in NET-2 buffer. 9D5 dsRNA rabbit IgG mAb was bound to the beads for 1-2 hours. Cells were lysed in cytosolic lysis buffer. The cell lysate was centrifuged at 980 x g for 3 min at 4℃ (X3). The cytosolic supernatant was spun at 17,000 x g for 10 min.  For IP, lysate was diluted to 1:4 with NET-2-TurboDNase buffer. 95D-Dynabeads were added to the lysate and end-to-end rotated for 2 hr at 4 °C. Following magnetic separation, beads were washed with high salt washing buffer and then NET-2 buffer. 95D-bound dsRNA was extracted with Trizol reagent and purified using Direct-zol™ RNA Miniprep Kit (Zymo Research). RNA samples were ribo-depleted with Ribominus™ Eukaryote v2 kit (Thermo Fisher Scientific).
Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. Libraries were sequenced on Illumina HiSeq 2500 sequencer in paired-end mode with read length of 75bp.

value: Control (Runx1f/f)


title: liver metastasis CRC32


title: liver metastasis CRC21


title: WT_IP_rep_2b


title: WT_IP_rep_1b


title: liver metastasis CRC16


title: liver metastasis CRC22


title: hPCSK9+/+ (10-weeks-old)_4

value: heart

value: 10 weeks

value: WT


title: M2a_righ-ear_treatment_0min

description: Maus 2 - 0 min

value: ear skin

value: wild-type


title: M6a_right-ear_treatment_10min

description: Maus 6 - 10 min

value: female


title: hPCSK9+/+ (10-weeks-old)_5


title: M43_left-ear_treatment_120min_irradiated

description: Li M43 2h B

value: left

value: experimental ear


title: WT_IP_rep_1a

value: Adult (4-6 weeks old)

value: Bone Marrow

value: 9D5 dsRNA rabbit IgG mAb(Ab00458-23.0)


title: hPCSK9+/+ (10-weeks-old)_3


title: hPCSK9+/+ (10-weeks-old)_2


title: KO_PMN_H3K27ac_IP2

extract_protocol:
Cells were sorted from mouse fetuses. ChIP reactions were performed using 50,000 FACS-sorted cells per IP. IPed and Input DNA were purified with MinElute PCR Purification Kit.
Libraries were constructed using Rubicom ThruPLEX DNA-Seq Kit. Libraries were size-selected at 100-700 bp by AMPure XP beads. Libraries were quantified with KAPA qPCR and bioanalyzer prior to single-end sequencing.

value: Runx1f/f; Cebpa-Cre + (Runx1{delta}GMP)

tag: chip antibody


title: liver metastasis CRC13

value: liver


title: hPCSK9+/+ (10-weeks-old)_1


title: liver metastasis CRC10


title: KO_PMN_H3K27ac_IP1

tag: cell type


title: KO_IP_rep_1a


title: hPCSK9-/- (10-weeks-old)_1

value: KO


title: hPCSK9-/- (28-weeks-old)_5

value: 28 week


title: M8a_left-ear_treatment_30min_irradiated

description: RNA Mausohr 8 - 30min

value: treatment

tag: timepoint (min)


title: liver metastasis CRC07

value: metastasis


title: WT_PMN_H3K27ac_IP2

tag: isoloation markers

value: BM Neutrophils

value: Control (Runx1f/f)


title: WT_PMN_H3K27ac_IP1


title: hPCSK9-/- (28-weeks-old)_4

value: heart


title: hPCSK9-/- (28-weeks-old)_3


title: C-5day-03 miRNA-Seq

city: Guangzhou

first: Danni

last: Lin

address: 388 Guangxin Road, Baiyun District

institute: Zhongkai University of Agriculture and Engineering

data_processing:
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Sequence quality was verified using FastQC, including the Q20, Q30 and GC-content of the clean data.
De novo assembly of the transcriptome was performed with Trinity 2.4.0.
All assembled Unigenes were aligned against the non-redundant (Nr) protein database,Gene ontology (GO), SwissProt, Kyoto Encyclopedia of Genes and Genomes (KEGG) and eggNOG databases using DIAMOND with a threshold of Evalue<0.00001.
Salmon was used to perform expression level for Unigenes by calculating TPM. The differentially expressed Unigenes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR.
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files

organism: Auxenochlorella pyrenoidosa

source_name: whole cells

extract_protocol:
Total RNA was extracted from C. pyrenoidesa and the co-culture system using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) with the manufacturer’s protocol.
The mRNA sequencing libraries were generated using the NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA), and the miRNA sequencing library was generated using the Next Ultra-small RNA Sample Library Prep Kit for Illumina (NEB, USA)
miRNA-Seq、mRNA-Seq

value: whole cells


title: liver metastasis CRC06

tag: disease state


title: hPCSK9-/- (28-weeks-old)_2

tag: strain


title: liver metastasis CRC04


title: C-5day-02 miRNA-Seq


title: M10a_left-ear_treatment_60min_irradiated

description: RNA Mausohr 10 - 1h

value: ear skin

value: wild-type


title: C-5day-01 miRNA-Seq


title: KO_GMP_ATAC_B

data_processing:
Sequencing reads were demultiplexed using Bcl2Fastq v2.20 then trimmed and filtered for quality using Trim Galore v0.6.4 with the following settings: fastqc, paired, and trim1. Reads were then aligned to the mouse genome (mm10) using bowtie 2.3.5.1. Only uniquely mapped reads with fewer than 2 mismatches were used for downstream analyses. Samtools v.1.1 was used to convert SAM files to BAM files, and Sambamba v0.6.6 was used to filter out duplicates, multi-mappers, reads mapped to ChrM or blacklist regions, and unmapped reads. MACS2 2.2.7.1 was used for peak calling using the following parameters: BAMPE, q: 0.05. Peaks from Control and Runx1ΔGMP were merged if there is at least 1bp overlap between two peaks. Reads Per Kilobase Million (RPKM) of a peak was then calculated using bedtools v2.25. Peaks with RPKM less than 0.5 in both Control and Runx1ΔGMP were filtered from downstream analysis. Control or Runx1ΔGMP specific peaks were called if the RPKM fold change between Control and Runx1ΔGMP peaks was greater than 2. Merged replicates were used to create bigwig files for visualization using Deeptools v3.3.0 and the  following parameters: normalized to Bins Per Million mapped reads (BPM), bin size: 50.
Assembly: mm10
Supplementary files format and content: BigWig files provided are normalized tracks of merged replicates
Supplementary files format and content: Bed files provided are the output of merged Control and Runx1ΔGMP MACS2 peak calling:  peaks with RPKM less than 0.5 in both Control and Runx1ΔGMP were filtered from downstream analysis. Control or Runx1ΔGMP specific peaks were called if the RPKM fold change of between Control and Runx1ΔGMP peaks was greater than 2.

extract_protocol:
50,000 cells were collected and washed with cold PBS. Cell pellets were resuspended in 50 µl of lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% Tween-20, 0.1% NP-40, 0.01% Digitonin, 1% BSA) and incubated on ice for 4 min. Lysis was halted with the addition of 50 uL of wash buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% Tween-20, 0.1%, 1% BSA). Samples were centrifuged at  500 x g, 4 °C for 5 min. Nuclei pellets were resuspended in 50 µl of wash buffer and centrifuged at  500 x g, 4 °C for 5 min.  Nuclei pellets were resuspended in 50 µl of transposition reaction mix (1× Tagment DNA Buffer, 2.5 µl of Tagment DNA Enzyme 1) and incubated for 30 min at 37 °C
Libraries were purified using a Qiagen MinElute Gel Purification kit and the concentrations were measured using both Qubit and KAPA qPCR. 2100 Bioanalyzer was used to check the quality of libraries. Libraries were sequenced on the Illumina NextSeq 250, with 75-bp paired-end reads.

value: Lin- cKIT+Sca1-CD16/32+CD150-

value: BM GMPs

tag: developmental stage


title: liver metastasis CRC03


title: liver metastasis CRC05


title: KO_GMP_ATAC_A

value: Adult (4-6 weeks old)

tag: genotype


title: hPCSK9-/- (28-weeks-old)_1

tag: tissue


title: KO_PMN_H3K27ac_IN

value: Bone Marrow


title: hPCSK9+/+ (28-weeks-old)_5

tag: age

value: WT


title: WT_GMP_ATAC_B


title: C-3day-02 miRNA-Seq


title: hPCSK9+/+ (28-weeks-old)_4


title: liver metastasis CRC08


title: C-3day-03 miRNA-Seq


title: liver metastasis CRC02


title: WT_PMN_H3K27ac_IN

extract_protocol:
Cells were sorted from the bone marrow. ChIP reactions were performed using 50,000 FACS-sorted cells per IP. IP and IN DNA were purified with MinElute PCR Purification Kit.
Libraries were constructed using Rubicom ThruPLEX DNA-Seq Kit. Libraries were size-selected at 100-700 bp by AMPure XP beads. Libraries were quantified with KAPA qPCR and bioanalyzer prior to single-end sequencing.


title: WT_GMP_ATAC_A


title: MOLT-4 - Vehicle - 3h

type: RNA

city: Haifa

first: Elazar

last: Besser

address: Kiryat Hatechnion

country: Israel

institute: Technion

hyb_protocol: ll reactions and hybridizations were carried out according to the manufacturer's protocol (Affymetrix; Thermo Fisher Scientific). Affymetrix GeneChip Human Clariom S arrays (Thermo Fisher Scientific) were washed using the GeneChip® Fludics Station 450 (Thermo Fisher Scientific)

scan_protocol: Affymetrix GeneChip Human Clariom S arrays were scanned with the GeneChip Scanner 3000 (Thermo Fisher Scientific).

data_processing:
Raw data were processed to perform gene-level normalization and quality control using Affymetrix Expression Console Software (Thermo Fisher Scientific). RMA expression value derived from Expression Console software Transcriptome Analysis Console (TAC) 4.0.1 (Applied Biosystems).
Clariom_S_Human.r1.na36.hg38.a1.transcript.csv
Gene-Level Fold Change < -2 or > 2 Total number of genes: 21448
Anova Method: ebayes
A Probeset (Gene/Exon) is considered expressed if ≥ 50% samples have DABG values below DABG Threshold.
DABG < 0.05

label: biotin

source_name: MOLT-4 - Vehicle - 3h

label_protocol: GeneChip® WT Plus Reagent Kit were used for generating biotinylated ss-cDNA for hybridization.

growth_protocol: Molt-4 cell line grown in RPMI 1640 media, and kept at 37 ºC in a 5% carbon dioxide (CO2) incubator. Unless otherwise stated, all culture media were supplemented with fetal bovine serum (FBS, 10%), penicillin (100 U/mL) and streptomycin (100 mg/mL).

extract_protocol: Total RNA was isolated from cells (1,000,000 cells/sample) using Trizol® and a RNeasy kit according to the manufacturer's instructions. Sample quality was assessed by both spectrophotometer (Nanodrop Technologies®) and agarose gels (1%).

treatment_protocol: Cells were cultured in 12-well plates at 1,000,000 cells/well with media containing 0.5% FBS and DMSO (vehicle) or Cannabis extracts at a concentration of 3 µg/mL and incubated for 3 h

value: T-cell acute lymphoblastic leukemia (T-ALL)

tag: cell line

tag: treatment

value: Vehicle


title: hPCSK9+/+ (28-weeks-old)_3


title: C-3day-01 miRNA-Seq


title: hPCSK9+/+ (28-weeks-old)_2


title: C-5day-03 RNA-Seq


title: KO_PMN_ATAC_A

value: Runx1f/f; Cebpa-Cre + (Runx1{delta}GMP)


title: hPCSK9+/+ (28-weeks-old)_1

value: 28 week


title: MOLT-4 - Cannabis extract - 3h

source_name: MOLT-4 - Cannabis extract - 3h

value: Cannabis extract


title: C-5day-02 RNA-Seq


title: WT_PMN_ATAC_B


title: FTO_OE_meRIP_rep1

city: Yiwu

first: Qiang

last: Sun

state: Zhejiang

address: No. N1, Shangcheng Avenue

institute: Zhejiang University

data_processing:
Basecalls performed using CASAVA version 1.4
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.20.1). In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data.
m6A-seq reads were aligned to the hg38 genome assembly using HISAT2 2.0.1 with default parameters.
peaks were called using R exomePeak package. Only the peaks with FDR<0.05 are retained for further analysis.
The m6A peaks were annotated using an ad hoc perl script. The RNA-Seq reads were normalized using TPM method. DESeq2 was used to find differentially expressed genes.
Genome_build: hg38
Supplementary_files_format_and_content: peak bigwig files

molecule: polyA RNA

source_name: HMC cell

growth_protocol: Cells were cultured in RPMI+10% FBS at 37C 5% CO2

extract_protocol:
RNA was extracted by Trizol. Polyadenylated RNA was extracted using FastTrack MAC Maxi mRNA isolation kit (Invitrogen)
Fragmented RNA (~100 nt) was incubated for 2 hr at 4oC with anti-m6A polyclonal antibody (Merk Millipore) in the immunoprecipitation experiment. Then, immunoprecipitated RNAs or Input was used for library construction with Ovation SoLo RNA-Seq System Core Kit (NuGEN).

value: HMC cell line

value: Human kidney glomerular mesangial cells

tag: antibody

value: FTO overexpression


title: C-5day-01 RNA-Seq


title: HFD 3 dpi

city: Daejeon

first: Heung Kyu

last: Lee

address: 291 Daehak-ro, Yuseong-gu

department: Graduate School of Medical Science and Engineering

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description: 10x Genomics

data_processing:
Cell Ranger (10X Genomics) was used.
Samples were aligned using mm10 (10X Genomics).
Further analysis was done by Seurat package.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Vagina

growth_protocol: C57BL/6J mice were housed in specific pathogen free (SPF) facility in KAIST.

extract_protocol:
At 0 or 3 dpi, vaginal cells were isolated. By FACS Aria II, 7-AAD- live cells were sorted.
Library was performed according to the manufacter’s instructions (10x Genomics)

treatment_protocol: SCD or 60%kcal HFD were fed to mice for 10 weeks. At 9 weeks of feeding, MPA were subcutaneously injected. At 10 weeks of feeding, 10^4 pfu of HSV-2 WT were injected intravaginally.

value: 7-AAD- live cells

value: Vagina

value: 15-16 weeks old

tag: diet

value: 60%kcal HFD for 10 weeks


title: Ctrl_meRIP_rep2


title: FTO_OE_input_rep1

value: input


title: FTO_OE_input_rep2


title: WT_PMN_ATAC_A

value: BM Neutrophils

value: Control (Runx1f/f)


title: SCD 3 dpi

description: 10x Genomics

value: SCD


title: FTO_OE_meRIP_rep2


title: C-3day-03 RNA-Seq

value: whole cells


title: Ctrl_input_rep2

value: WT


title: C-3day-02 RNA-Seq


title: Ctrl_meRIP_rep1


title: HFD 0 dpi

description: 10x Genomics


title: Small intestine endothelial cells, FICZ-60k

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
The data was de-multiplexed and analysed using CellRanger v4.0.0 and bcl2fastq v2.17.1.14.
Briefly, libraries were de-multiplexed using CellRanger mkfastq based on sample indices.
CellRanger count pipeline was used to perform alignment against mouse genome mm10 (using STAR), filtering and counting UMIs.
Assembly: mm10
Supplementary files format and content: tsv and matrix files

source_name: Small intestine

extract_protocol: Cells were partitioned using the 10X chromium controller and the resulting GEMs  converted into scRNA-seq libraries using the 10x Single Cell 3' v3 kit

treatment_protocol: Mice injected with 10mg/Kg 6-Formylindolo(3,2-b)carbazole (FICZ) or corn-oil vehicle control intraperitoneally, 3h prior to culling

value: Small intestine endothelial cells

value: Small intestine

value: 6.9 wks

value: FICZ


title: C-3day-01 RNA-Seq


title: SCD 0 dpi

description: 10x Genomics


title: KO_PMN_ATAC_B

value: Adult (4-6 weeks old)

value: Bone Marrow

value: Runx1f/f; Cebpa-Cre + (Runx1{delta}GMP)


title: Ctrl_input_rep1

value: HMC cell line

value: Human kidney glomerular mesangial cells


title: Small intestine endothelial cells, FICZ-15k


title: mst2Depe1D biological replicate 1 rep2

status: Public on Jul 11 2023

city: Waltham

first: Ajay

last: Larkin

state: MA

address: 415 South St

department: MCB

institute: Brandeis University

data_processing:
sequences were trimmed with Trimmomatic, then aligned and quantified by STAR
downstream diff. expression quantification was performed with USEQ DRDS
Assembly: ASM294v2.29
Supplementary files format and content: Excel xlsx files contain raw transcript count matricies

organism: Schizosaccharomyces pombe

source_name: mst2D epe1D bioRep 1 rep2

growth_protocol: EMMC, grown to log phase at 32C

extract_protocol:
Hot phenol extraction followed by DNAse I treatment and Qiagen RNeasy Column Cleanup
RNAseq libraries were prepared by Novogene Corporation Inc.

treatment_protocol: +TN cultures were treated with 15mM thiamine and 500mM 1-napthaleneacetic acid


title: mst2D epe1-deg,+TN 48hrs, rep2

source_name: mst2D epe1-deg 48hr rep2

value: +TN


title: mst2Depe1D biological replicate 2 rep3

source_name: mst2D epe1D bioRep 2 rep3


title: mst2D epe1-deg,+TN 48hrs, rep3

source_name: mst2D epe1-deg 48hr rep3


title: mst2Depe1D biological replicate 1 rep1

source_name: mst2D epe1D bioRep 1 rep1


title: mst2D epe1-deg,+TN 24hrs, rep2

source_name: mst2D epe1-deg 24hr rep2


title: mst2D epe1-deg,+TN 120hrs, rep2

source_name: mst2D epe1-deg 120hr rep2


title: mst2D epe1-deg,+TN 72hrs, rep3

source_name: mst2D epe1-deg 72hr rep3


title: mst2D epe1-deg,+TN 72hrs, rep1

source_name: mst2D epe1-deg 72hr rep1


title: mst2D epe1-deg,+TN 120hrs, rep1

source_name: mst2D epe1-deg 120hr rep1


title: mst2Depe1D biological replicate 2 rep1

source_name: mst2D epe1D bioRep 2 rep1


title: mst2D epe1-deg,+TN 48hrs, rep1

source_name: mst2D epe1-deg 48hr rep1


title: mst2D epe1-deg,+TN 96hrs, rep1

source_name: mst2D epe1-deg 96hr rep1


title: mst2Depe1D biological replicate 1 rep3

source_name: mst2D epe1D bioRep 1 rep3


title: mst2D epe1-deg,+TN 72hrs, rep2

source_name: mst2D epe1-deg 72hr rep2


title: mst2D epe1-deg,+TN 24hrs, rep3

source_name: mst2D epe1-deg 24hr rep3


title: mst2D epe1-deg,+TN 120hrs, rep3

source_name: mst2D epe1-deg 120hr rep3


title: Small intestine endothelial cells, Vehicle-15k

source_name: Small intestine

value: Vehicle


title: mst2D epe1-deg,-TN, rep3

source_name: mst2D epe1-deg 0hr rep3


title: mst2D epe1-deg,-TN, rep2

source_name: mst2D epe1-deg 0hr rep2


title: mst2D epe1-deg,-TN, rep1

source_name: mst2D epe1-deg 0hr rep1


title: mst2D epe1-deg,+TN 24hrs, rep1

source_name: mst2D epe1-deg 24hr rep1


title: mst2Depe1D biological replicate 2 rep2

source_name: mst2D epe1D bioRep 2 rep2


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 085

city: Tsu-shi

first: Rawin

last: Poonperm

state: Mie

address: 1577 Kurimamachiya

department: Graduate School of Bioresources

country: Japan

institute: Mie University

description:
mm9
haplotype-resolved

data_processing:
Two-step adapter trimming was performed to first remove the Illumina adapter and the SEQXE adapter.
Trimmed fastq files were aligned to mm9 and a constructed B6/JF1 specific diploid genome (Sakata et al., 2017) for non-haplotype and haplotype-resolved analysis, respectively.
Genome coordinates of allele-specific uniquely mapped reads (MAPQ >16) were converted to mm9 by liftOver tool (UCSC Genome Browser). Duplicated reads were filtered out.
Single-cell non-haplotype resolved analysis was performed as described (Takahashi et al., 2019; Miura et al., 2020). First, we counted the reads in non-overlapping 100-kb windows, and used the AneuFinder’s correctMappability command for normalizing mid-S data (Mappability corrected Mid-S reads) based on the merged G1 control. Binarization was performed using the Mappability corrected 25per-S (25% S-phase) , Mid-S (50% S-phase), 75per-S (75% S-phase) reads described above by using the findCNVs command in AneuFinder [2-HMM; options for 25per-S: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="1-somy"; options for Mid-S, 75per-S: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="2-somy"; 1-somy, unreplicated; 2-somy, replicated]. In the processed data files, replicated bin was shown as 1, unrelicated bin was shown as -1, and no-data was shown as 0. “Repliscore” was calculated as a percentage of replicated bins in the total number of replicated and unreplicated bins.
Single-cell haplotype-resolved data was performed as described (Takahashi et al., 2019). After the specific filtering steps for haplotype-resolved data, we counted the reads in non-overlapping 400-kb windows, and used the AneuFinder’s correctMappability command for normalizing S data (Mappability corrected S reads) based on the filtered merged G1 control. Binarization was performed as described above by using the findCNVs command in AneuFinder [2-HMM; options for early-S: method="HMM", max.iter=5000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="1-somy" ; options for mid and late-S: method="HMM", max.iter=5000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="2-somy" ].
Assembly: mm9
Supplementary files format and content: bedgraph
Library strategy: Single-cell Repli-seq

source_name: embryonic stem cell

growth_protocol: Neural stem cells (NSCs) were derived from wild-type and SmcHD1-mutant JB4/EI7HZ2 mESCs and cultured as described (Pollard et al., 2006). NSCs were cultured in NSC maintenance media [(DMEM/F12 (nacalai tesque, #11581-15); 1× N2 supplement (Thermo Fisher, 17502048); 2 mM L-Glutamine (Nacalai tesque, #16948-08); 1× Pen/strep (Nacalai tesque, 09367-34); 75 µg/ml BSA (sigma, A3311-10G); 25 µg/ml Insulin (sigma, I1882-100MG); 10 ng/ml FGF2 (Peprotech 100-18B); 10 ng/ml EGF (Funakoshi, 2028-EG-200)] on 0.2% gelatin coated plate.

extract_protocol:
Single cells were sorted with a Sony SH800 cell sorter. Sample preparations were performed as described (Miura et al., 2020).
DNA samples were subject to whole-genome amplification (WGA) with a SeqPlex kit (Sigma, SEQXE). NGS libraries were constructed WGA DNA with an NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions

value: embryonic stem cell

value: neural stem cells (NSCs)

value: SmcHD1 knockout

tag: Sex

value: female


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 083

description:
mm9
haplotype-resolved


title: mst2D epe1-deg,+TN 96hrs, rep3

source_name: mst2D epe1-deg 96hr rep3


title: mst2D epe1-deg,+TN 96hrs, rep2

source_name: mst2D epe1-deg 96hr rep2


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 084

description:
mm9
haplotype-resolved


title: gRNA_library

city: Frankfurt am Main

first: Martin

last: Wegner

state: Hessen

address: Theodor-Stern-Kai 7

department: Institute of Biochemistry II

institute: University Hospital Frankfurt am Main, Germany

data_processing:
NextSeq Control Software 2.0.0
Adapter trimming: cutadapt v1.15 --pair-filter=any --minimum-length 20 --discard-untrimmed --max-n 0 --nextseq-trim=20 -e 0.1 -g TTGGGTACCTCG -G GACGAAACACCG
gRNA alignment: bowtie2 2.3.0 ..local -L11 -N 1 -i S,1.0,0.75
Supplementary files format and content: MTH01_DFPlow_R1.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_OAhigh_R3.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_OAhigh_R2.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_DFPhigh_R1.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_Library.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_D0_R2.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_D14_R1.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_D0_R1.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_DFPhigh_R3.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_OAlow_R1.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_DFPlow_R2.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_D0_R3.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_D14_R2.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_DFPlow_R3.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_OAlow_R3.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_OAlow_R2.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_DFPhigh_R2.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_D14_R3.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_OAhigh_R1.csv table containing gRNA pairs and their abundance

organism: Escherichia coli

source_name: bacteria

extract_protocol: custom protocol for gDNA Isolation and PCR for amplification and barcoding

treatment_protocol: Mitophagy was induced at Day 14 by deferiprone (DFP) treatment or oligomycin/antimycin A (OA) treatment

value: bacteria


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 082

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 081

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 064

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 067

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 080

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 065

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 056

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 062

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 076

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 069

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 075

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 079

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 071

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 073

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 072

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 057

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 059

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 060

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 058

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 061

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 066

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 063

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 055

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 078

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 074

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 077

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 070

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 068

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 052

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 054

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 051

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 050

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 045

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 047

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 048

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 037

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 043

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 028

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 033

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 038

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 032

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 040

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 049

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 046

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 036

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 029

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 041

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 042

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 031

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 044

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 039

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 034

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 030

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 053

description:
mm9
haplotype-resolved


title: WT2 MEFs

source_name: MEFs

value: MEFs

value: Mouse embryonic fibroblasts

value: WT

tag: time point

value: at 2 Passage


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 027

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 025

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 035

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 026

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 022

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 018

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 016

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 011

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 013

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 014

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 019

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 020

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 012

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 023

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 024

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 021

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 010

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 009

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 006

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 008

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 007

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 015

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 017

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, G1 003

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, G1 002

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, G1 004

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 005

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, G1 001

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 004

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 001

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 094

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 093

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 003

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs, scRepli-seq, S 002

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 092

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 090

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 091

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 088

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 086

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 082

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 083

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 089

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 084

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 085

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 087

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 075

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 077

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 074

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 076

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 079

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 078

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 068

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 069

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 067

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 066

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 071

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 072

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 073

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 065

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 063

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 081

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 080

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 062

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 061

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 060

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 059

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 057

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 070

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 055

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 058

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 052

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 056

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 054

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 053

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 047

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 051

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 045

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 044

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 043

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 046

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 042

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 048

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 040

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 039

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 041

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 038

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 037

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 035

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 036

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 034

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 032

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 033

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 064

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 050

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 027

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 030

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 029

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 049

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 026

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 025

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 017

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 023

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 018

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 021

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 022

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 019

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 015

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 016

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 013

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 012

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 011

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 010

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 014

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 007

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 028

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 005

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 009

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 006

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 020

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 002

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, G1 002


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 003

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 031

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 001

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 008

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, G1 003


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 004

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, G1 001


title: WT B6 MEFs Replicate 1, BrdU-IP Early

description:
mm9
non-haplotype resolved
B6_MEF_WT_male_mm9_1_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.noX.qnorm.bedGraph

data_processing:
Two-step adapter trimming was performed to first remove the Illumina adapter and the SEQXE adapter.
Trimmed fastq files were aligned to mm9 and a constructed B6/JF1 specific diploid genome (Sakata et al., 2017) for non-haplotype and haplotype-resolved analysis, respectively.
Genome coordinates of allele-specific uniquely mapped reads (MAPQ >16) were converted to mm9 by liftOver tool (UCSC Genome Browser). Duplicated reads were filtered out.
Reads per million (rpm) normalization were calculated for early- and late-S-phase BrdU-IP samples in sliding windows of 200-kb at 80-kb intervals and a nonoverlapping 400-kb bins for non-haplotype and haplotype-resolved analysis, respectively.
Then the ratio of early-S-phase to total read counts [(early-S reads)/(early-S reads + late-S reads)] was calculated for each bin, and their distribution was converted to fit within a ±1 scale. We filtered out bins whose total read counts were within the bottom 5% of all bins.
Assembly: mm9
Supplementary files format and content: bedGraph
Library strategy: BrdU-IP Repli-seq

source_name: embryonic fibroblast

growth_protocol: JB4/EI7HZ2 mESCs were grown in serum containing medium + 2i/LIF [MEK and GSK3 inhibitors (2i) and leukemia inhibitory factor (LIF)] (DMEM (Nacalai , 08458-45 500 ml, or sigma, cat#D6429-500ML); 15% FBS (gibco 10270-106, lot# 42Q6272K); 1× Pen/strep (Nacalai, 09367-34); 1× Non-essential amino acid (Nacalai, 06344-56); 0.1 mM β-mercaptoethanol (Gibco, 21985-023); 1000 U/ml LIF (Nacalai USA, NU0012-2); 1 µM PD0325901 (Wako, 162-25291); 3 µM CHIR99021 (Wako, 034-23103)) on culture plate coated with 0.2% gelatin. Medium also contained 0.2 mg/ml G418 (invivogen, ant-gn-1) and 25 µg/mL Zeocin (invivogen, ant-zn-1) in order to maintain two X chromosomes state. Wild-type and SmcHD1-mutant JB4/EI7HZ2 mESCs were differentiated to neuroectoderm for 7 or 9 days as described (Miura et al., 2019). Neural stem cells (NSCs) were derived from wild-type and SmcHD1-mutant JB4/EI7HZ2 mESCs and cultured as described (Pollard et al., 2006). NSCs were cultured in NSC maintenance media [(DMEM/F12 (nacalai tesque, #11581-15); 1× N2 supplement (Thermo Fisher, 17502048); 2 mM L-Glutamine (Nacalai tesque, #16948-08); 1× Pen/strep (Nacalai tesque, 09367-34); 75 µg/ml BSA (sigma, A3311-10G); 25 µg/ml Insulin (sigma, I1882-100MG); 10 ng/ml FGF2 (Peprotech 100-18B); 10 ng/ml EGF (Funakoshi, 2028-EG-200)] on 0.2% gelatin coated plate.

extract_protocol:
We followed the BrdU-IP-based protocol as described (Ryba et al., 2011). 75% ethanol fixed cells were stained with Propidium iodide (Nacalai tesque, 29037), then early- and late-S phase cell population (at least 10,000 cells/fraction) were sorted by a Sony SH800 cell sorter (ultra-purity mode). Extracted DNA was sonicated by a Bioruptor UCD-250 (Sonic Bio). BrdU-incorporated DNA was immunoprecipitated using anti-BrdU antibody (BD Biosciences Pharmingen, #555627).
BrdU-immunoprecipitated DNA samples were subject to whole-genome amplification (WGA) with a SeqPlex kit (Sigma, SEQXE). NGS libraries were constructed from early- and late-replicating DNA after WGA with an NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions

value: embryonic fibroblast

value: epiblast stem cell

value: male


title: WT EpiSCs Replicate 2, BrdU-IP Early

description:
mm9
non-haplotype resolved
B6JF1_EpiSC_WT_mm9_Rep2_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.noX.qnorm.bedGraph

source_name: epiblast stem cells (EpiSCs)

value: epiblast stem cells (EpiSCs)


title: WT B6 MEFs Replicate 1, BrdU-IP Late


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 2, BrdU-IP Early

description:
mm9
haplotype-resolved
KO_b6_NSC_rep2.qnorm.bedGraph
KO_jf1_NSC_rep2.qnorm.bedGraph

value: differentiation to neural stem cells


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 1, BrdU-IP Late

description:
mm9
haplotype-resolved
KO_b6_NSC_rep1.qnorm.bedGraph
KO_jf1_NSC_rep1.qnorm.bedGraph


title: WT EpiSCs Replicate 1, BrdU-IP Early

description:
mm9
non-haplotype resolved
B6JF1_EpiSC_WT_mm9_Rep1_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.noX.qnorm.bedGraph


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 1, BrdU-IP Early


title: WT JB4/EI7HZ2 NSCs Replicate 2, BrdU-IP Late

description:
mm9
haplotype-resolved
WT_b6_NSC_rep2.qnorm.bedGraph
WT_jf1_NSC_rep2.qnorm.bedGraph


title: WT EpiSCs Replicate 2, BrdU-IP Late


title: WTEpiSCs Replicate 1, BrdU-IP Late


title: WT JB4/EI7HZ2 NSCs Replicate 2, BrdU-IP Early


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 2, BrdU-IP Late

description:
mm9
haplotype-resolved
KO_b6_Day9_rep2.qnorm.bedGraph
KO_jf1_Day9_rep2.qnorm.bedGraph

value: day-9 differentiated ESCs

value: differentiation to embryoid body


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 3, BrdU-IP Late

description:
mm9
haplotype-resolved
KO_b6_Day9_rep3.qnorm.bedGraph
KO_jf1_Day9_rep3.qnorm.bedGraph


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 3, BrdU-IP Early


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 2, BrdU-IP Early


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 1, BrdU-IP Late

description:
mm9
haplotype-resolved
KO_b6_Day9_rep1.qnorm.bedGraph
KO_jf1_Day9_rep1.qnorm.bedGraph


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 1, BrdU-IP Early


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, G1 004


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 2, BrdU-IP Late


title: WT JB4/EI7HZ2 Day 9 Replicate 2, BrdU-IP Early

description:
mm9
haplotype-resolved
WT_b6_Day9_rep2.qnorm.bedGraph
WT_jf1_Day9_rep2.qnorm.bedGraph


title: WT JB4/EI7HZ2 Day 9 Replicate 1, BrdU-IP Early

description:
mm9
haplotype-resolved
WT_b6_Day9_rep1.qnorm.bedGraph
WT_jf1_Day9_rep1.qnorm.bedGraph


title: WT JB4/EI7HZ2 Day 9 Replicate 2, BrdU-IP Late


title: WT JB4/EI7HZ2 Day 9 Replicate 1, BrdU-IP Late


title: WT JB4/EI7HZ2 Day 9 Replicate 3, BrdU-IP Early

description:
mm9
haplotype-resolved
WT_b6_Day9_rep3.qnorm.bedGraph
WT_jf1_Day9_rep3.qnorm.bedGraph


title: WT JB4/EI7HZ2 NSCs Replicate 1, BrdU-IP Late

description:
mm9
haplotype-resolved
WT_b6_NSC_rep1.qnorm.bedGraph
WT_jf1_NSC_rep1.qnorm.bedGraph


title: WT JB4/EI7HZ2 Day 9 Replicate 3, BrdU-IP Late


title: WT JB4/EI7HZ2 NSCs Replicate 1, BrdU-IP Early


title: WT JB4/EI7HZ2 NSCs, scRepli-seq, S 024

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 Day 7 Replicate 2, BrdU-IP Late

description:
mm9
haplotype-resolved
KO_b6_Day7_rep2.qnorm.bedGraph
KO_jf1_Day7_rep2.qnorm.bedGraph

value: day-7 differentiated ESCs


title: SmcHD1-KO JB4/EI7HZ2 Day 7 Replicate 3, BrdU-IP Late

description:
mm9
haplotype-resolved
KO_b6_Day7_rep3.qnorm.bedGraph
KO_jf1_Day7_rep3.qnorm.bedGraph

value: embryonic stem cell


title: SmcHD1-KO JB4/EI7HZ2 Day 7 Replicate 2, BrdU-IP Early


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 2, BrdU-IP Early

description:
mm9
haplotype-resolved
KO_b6_mESC_rep2.qnorm.bedGraph
KO_jf1_mESC_rep2.qnorm.bedGraph

value: embryonic stem cells


title: WT JB4/EI7HZ2 Day 7 Replicate 3, BrdU-IP Late

description:
mm9
haplotype-resolved
WT_b6_Day7_rep3.qnorm.bedGraph
WT_jf1_Day7_rep3.qnorm.bedGraph


title: WT JB4/EI7HZ2 Day 7 Replicate 2, BrdU-IP Early

description:
mm9
haplotype-resolved
WT_b6_Day7_rep2.qnorm.bedGraph
WT_jf1_Day7_rep2.qnorm.bedGraph


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 2, BrdU-IP Late

value: SmcHD1 knockout


title: WT JB4/EI7HZ2 Day 7 Replicate 1, BrdU-IP Early

description:
mm9
haplotype-resolved
WT_b6_Day7_rep1.qnorm.bedGraph
WT_jf1_Day7_rep1.qnorm.bedGraph

value: female


title: WT JB4/EI7HZ2 Day 7 Replicate 1, BrdU-IP Late


title: SmcHD1-KO JB4/EI7HZ2 Day 7 Replicate 1, BrdU-IP Early

description:
mm9
haplotype-resolved
KO_b6_Day7_rep1.qnorm.bedGraph
KO_jf1_Day7_rep1.qnorm.bedGraph


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 1, BrdU-IP Late

description:
mm9
haplotype-resolved
KO_b6_mESC_rep1.qnorm.bedGraph
KO_jf1_mESC_rep1.qnorm.bedGraph


title: WT JB4/EI7HZ2 Day 7 Replicate 3, BrdU-IP Early


title: SmcHD1-KO JB4/EI7HZ2 Day 7 Replicate 1, BrdU-IP Late


title: WT JB4/EI7HZ2 Day 7 Replicate 2, BrdU-IP Late


title: WT JB4/EI7HZ2 mESCs Replicate 2, BrdU-IP Early

description:
mm9
haplotype-resolved
WT_b6_mESC_rep2.qnorm.bedGraph
WT_jf1_mESC_rep2.qnorm.bedGraph


title: WT JB4/EI7HZ2 mESCs Replicate 1, BrdU-IP Late

description:
mm9
haplotype-resolved
WT_b6_mESC_rep1.qnorm.bedGraph
WT_jf1_mESC_rep1.qnorm.bedGraph


title: WT JB4/EI7HZ2 mESCs Replicate 2, BrdU-IP Late


title: WT JB4/EI7HZ2 mESCs Replicate 1, BrdU-IP Early


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 2, 4C-seq, VP148Mb

description:
mm9
haplotype-resolved

data_processing:
Adapter trimming was performed to remove the Illumina adapter sequence.
4C-seq reads were first separated specifically to B6 or JF1 based on SNPs in read 2 (from P7) using cutadapt. Only reads with 0% mismatches to the expected sequence and SNPs were kept
P5 reads of each assigned allele were mapped to mouse mm9 genome as single-end alignment and analyzed using an R pipeline from Krijger et al., 2020 with analysis mode: all, w201
Assembly: mm9
Supplementary files format and content: wig
Library strategy: 4C-seq

extract_protocol:
Cells were fixed with 1% formaldehyde. 4C-DNA was prepared as described (Splinter et al., 2012; Krijger et al., 2020) using HindIII and DpnII as the first and second restriction enzyme, respectively.
4C-library was preparing by 2-step inversed PCR as described (Krijger et al., 2020)

value: neural stem cells (NSCs)


title: SmcHD1-KO JB4/EI7HZ2 Day 7 Replicate 3, BrdU-IP Early


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 1, 4C-seq, VP148Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs Replicate 2, 4C-seq, VP148Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 1, 4C-seq, VP148Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 2, 4C-seq, VP148Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 Day 9 Replicate 2, 4C-seq, VP148Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 Day 9 Replicate 1, 4C-seq, VP148Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs Replicate 1, 4C-seq, VP148Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 2, 4C-seq, VP148Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 1, 4C-seq, VP148Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 1, BrdU-IP Early


title: WT JB4/EI7HZ2 mESCs Replicate 2, 4C-seq, VP148Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 mESCs Replicate 1, 4C-seq, VP148Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 1, 4C-seq, VP100Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs Replicate 2, 4C-seq, VP100Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 2, 4C-seq, VP100Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs Replicate 1, 4C-seq, VP100Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 mESCs Replicate 1, 4C-seq, VP100Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 1, 4C-seq, VP98Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 Day 9 Replicate 1, 4C-seq, VP100Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 1, 4C-seq, VP98Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs Replicate 1, 4C-seq, VP98Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 2, 4C-seq, VP98Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 Day 9 Replicate 2, 4C-seq, VP100Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 2, 4C-seq, VP98Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 2, 4C-seq, VP100Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 Day 9 Replicate 1, 4C-seq, VP98Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 2, 4C-seq, VP98Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 1, 4C-seq, VP98Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 1, 4C-seq, VP100Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 mESCs Replicate 2, 4C-seq, VP98Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 mESCs Replicate 1, 4C-seq, VP98Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 1, 4C-seq, VP96Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 2, 4C-seq, VP96Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 2, 4C-seq, VP100Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 mESCs Replicate 2, 4C-seq, VP100Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 1, 4C-seq, VP100Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 1, 4C-seq, VP96Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs Replicate 1, 4C-seq, VP96Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 2, 4C-seq, VP96Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 2, 4C-seq, VP96Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs Replicate 2, 4C-seq, VP96Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 Day 9 Replicate 1, 4C-seq, VP96Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 1, 4C-seq, VP96Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs Replicate 2, 4C-seq, VP98Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 Day 9 Replicate 2, 4C-seq, VP96Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 Day 9 Replicate 2, 4C-seq, VP98Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 1, 4C-seq, VP84Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 2, 4C-seq, VP84Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs Replicate 1, 4C-seq, VP84Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 1, 4C-seq, VP84Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 mESCs Replicate 2, 4C-seq, VP96Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs Replicate 2, 4C-seq, VP84Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 1, 4C-seq, VP84Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 2, 4C-seq, VP84Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 Day 9 Replicate 2, 4C-seq, VP84Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 Day 9 Replicate 1, 4C-seq, VP84Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs Replicate 2, 4C-seq, VP56Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 1, 4C-seq, VP56Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs Replicate 1, 4C-seq, VP56Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 mESCs Replicate 1, 4C-seq, VP84Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 mESCs Replicate 2, 4C-seq, VP84Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 1, 4C-seq, VP56Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 2, 4C-seq, VP56Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 mESCs Replicate 1, 4C-seq, VP96Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 1, 4C-seq, VP56Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs Replicate 2, 4C-seq, VP45Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 Day 9 Replicate 2, 4C-seq, VP56Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 Day 9 Replicate 1, 4C-seq, VP56Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 2, 4C-seq, VP45Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 2, 4C-seq, VP84Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 2, 4C-seq, VP45Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 1, 4C-seq, VP45Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 mESCs Replicate 1, 4C-seq, VP56Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 mESCs Replicate 2, 4C-seq, VP56Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 2, 4C-seq, VP56Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs Replicate 1, 4C-seq, VP45Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 mESCs Replicate 1, 4C-seq, VP45Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 mESCs Replicate 2, 4C-seq, VP45Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 1, 4C-seq, VP45Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 Day 9 Replicate 1, 4C-seq, VP45Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 2, 4C-seq, VP45Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 1, 4C-seq, VP45Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 2, 4C-seq, VP34Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 1, 4C-seq, VP34Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs Replicate 2, 4C-seq, VP34Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs Replicate 1, 4C-seq, VP34Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 2, 4C-seq, VP34Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 1, 4C-seq, VP34Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 Day 9 Replicate 2, 4C-seq, VP45Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 2, 4C-seq, VP56Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 Day 9 Replicate 1, 4C-seq, VP34Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 2, 4C-seq, VP34Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 1, 4C-seq, VP34Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 mESCs Replicate 2, 4C-seq, VP34Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 2, 4C-seq, VP20Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 1, 4C-seq, VP20Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs Replicate 1, 4C-seq, VP20Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 NSCs Replicate 2, 4C-seq, VP20Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 mESCs Replicate 1, 4C-seq, VP34Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 1, 4C-seq, VP20Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 Day 9 Replicate 1, 4C-seq, VP20Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 Day 9 Replicate 2, 4C-seq, VP20Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 2, 4C-seq, VP20Mb

description:
mm9
haplotype-resolved


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 1, 4C-seq, VP20Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 Day 9 Replicate 2, 4C-seq, VP34Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 mESCs Replicate 1, 4C-seq, VP20Mb

description:
mm9
haplotype-resolved


title: WT JB4/EI7HZ2 mESCs Replicate 2, 4C-seq, VP20Mb

description:
mm9
haplotype-resolved


title: mouse olfactory bulb, 2D amino-modified slides [MOB-50-2D]

city: shanghai

first: di

last: sun

address: pujian road 160

department: institute of molecular medicine

institute: Renji Hospital, School of Medicine, Shanghai Jiao Tong University

description: barcode.txt

data_processing:
*library strategy: Spatial transcriptomic sequencing
The H&E image was used to accurately distinguish between tissues and backgrounds, with spots outside the tissue being removed. Spots with fewer than 50 observed genes (UMI > 2) were filtered out. And genes with counts in less than 10 spatial spots were discarded. Mitochondrial and ribosomal genes were also removed.
Giotto suite was used to perform spatial gene expression normalization, plotting, dimensionality reduction, spatial domains detection, and differential gene expression analysis. To incorporate spatial information into clustering, we utilized a hidden Markov random field (HMRF) model integrated with Giotto and allocated each cell to one of k spatial domains based on the accepted beta parameter. Furthermore, Giotto's findScanMarkers function was employed to annotate each spatial domain using identified markers.
Assembly: mm10, hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: mouse olfactory bulb

extract_protocol:
Spatial transcriptomic sequencing by Decoder-seq, details in Methods "Dendrimeric DNA coordinate barcoding arrays capture spatial mRNAs of tissues with high efficiency"
Spatial transcriptomic sequencing by Decoder-seq, details in Methods "Amplification, library construction, and sequencing"

value: mouse olfactory bulb


title: 7D_M_2995

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region


title: 7D_M_2990


title: 7D_M_3000


title: 7D_M_2991


title: 7D_M_2999


title: 7D_M_2997


title: 7D_M_2989


title: 7D_M_2993


title: 7D_M_2992


title: 7D_M_2996


title: 7D_M_3002


title: 7D_M_2994


title: 7D_M_2998


title: 7D_M_3001


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 2, 4C-seq, VP20Mb

description:
mm9
haplotype-resolved


title: 7D_M_2988


title: 7D_M_2987


title: 7D_M_2986


title: 7D_M_2985


title: 7D_M_2983


title: 7D_M_2984


title: 7D_M_2982


title: 7D_M_2981


title: 7D_M_2979


title: 7D_M_2978


title: 7D_M_2977


title: 7D_M_2975


title: 7D_M_2976


title: 7D_M_2973


title: 7D_M_2961


title: 7D_M_2970


title: 7D_M_2962


title: 7D_M_2959


title: 7D_M_2967


title: 7D_M_2968


title: 7D_M_2966


title: 7D_M_2965


title: 7D_M_2972


title: 7D_M_2969


title: 7D_M_2963


title: 7D_M_2964


title: 7D_M_2957


title: 7D_M_2953


title: 7D_M_2956


title: 7D_M_2954


title: 7D_M_2951


title: 7D_M_2950


title: 7D_M_2949


title: 7D_M_2980


title: 7D_M_2971


title: 7D_M_2948


title: 7D_M_2952


title: 7D_M_2974


title: 7D_M_2955


title: 7D_M_2946


title: 7D_M_2947


title: 7D_M_2958


title: 7D_M_2960


title: 7D_M_2945


title: 7D_M_2944


title: 7D_M_2943


title: 7D_M_2942


title: 7D_M_2941


title: 7D_M_2939


title: 7D_M_2870


title: 7D_M_2940


title: 7D_M_2873


title: 7D_M_2871


title: 7D_M_2868


title: 7D_M_2869


title: 7D_M_2874


title: 7D_M_2872


title: 7D_M_2858


title: 7D_M_2864


title: 7D_M_2867


title: 7D_M_2854


title: 7D_M_2863


title: 7D_M_2866


title: 7D_M_2861


title: 7D_M_2860


title: 7D_M_2859


title: 7D_M_2857


title: 7D_M_2862


title: 7D_M_2852


title: 7D_M_2850


title: 7D_M_2856


title: 7D_M_2853


title: 7D_M_2851


title: 7D_M_2848


title: 7D_M_2847


title: 7D_M_2849


title: 7D_M_2865


title: 7D_M_2845


title: 7D_M_2843


title: 7D_M_2846


title: 7D_M_2839


title: 7D_M_2844


title: 7D_M_2837


title: 7D_M_2840


title: 7D_M_2855


title: 7D_M_2842


title: 7D_M_2835


title: 7D_M_2838


title: 7D_M_2836


title: 7D_M_2831


title: 7D_M_2829


title: 7D_M_2830


title: 7D_M_2828


title: 7D_M_2833


title: 7D_M_2827


title: 7D_M_2832


title: 7D_M_2841


title: 7D_M_2825


title: 7D_M_2822


title: 7D_M_2826


title: 7D_M_2823


title: 7D_M_2820


title: 7D_M_2818


title: 7D_M_2824


title: 7D_M_2814


title: 7D_M_2811


title: 7D_M_2819


title: 7D_M_2817


title: 7D_M_2815


title: 7D_M_2812


title: 7D_M_2813


title: 7D_M_2816


title: 7D_M_2808


title: 7D_M_2834


title: 7D_M_2805


title: 7D_M_2804


title: 7D_M_2800


title: 7D_M_2821


title: 7D_M_2810


title: 7D_M_2802


title: 7D_M_2798


title: 7D_M_2807


title: 7D_M_2799


title: 7D_M_2806


title: 7D_M_2809


title: 7D_M_2796


title: 7D_M_2801


title: 7D_M_2792


title: 7D_M_2797


title: 7D_M_2789


title: 7D_M_2788


title: 7D_M_2794


title: 7D_M_2795


title: 7D_M_2793


title: 7D_M_2784


title: 7D_M_2781


title: 7D_M_2791


title: 7D_M_2790


title: 7D_M_2803


title: 7D_M_2782


title: 7D_M_2785


title: 7D_M_2783


title: 7D_M_2778


title: 7D_M_2780


title: 7D_M_2779


title: 7D_M_2777


title: 7D_M_2771


title: 7D_M_2776


title: 7D_M_2786


title: 7D_M_2769


title: 7D_M_2775


title: 7D_M_2774


title: 7D_M_2768


title: 7D_M_2772


title: 7D_M_2773


title: 7D_M_2767


title: 7D_M_2787


title: 7D_M_2758


title: 7D_M_2759


title: 7D_M_2756


title: 7D_M_2763


title: 7D_M_2764


title: 7D_M_2761


title: 7D_M_2762


title: 7D_M_2760


title: 7D_M_2753


title: 7D_M_2754


title: 7D_M_2770


title: 7D_M_2750


title: 7D_M_2751


title: 7D_M_2752


title: 7D_M_2749


title: 7D_M_2765


title: 7D_M_2618


title: 7D_M_2766


title: 7D_M_2747


title: 7D_M_2616


title: 7D_M_2615


title: 7D_M_2617


title: 7D_M_2613


title: 7D_M_2611


title: 7D_M_2614


title: 7D_M_2612


title: 7D_M_2610


title: 7D_M_2755


title: 7D_M_2609


title: 7D_M_2606


title: 7D_M_2757


title: 7D_M_2603


title: 7D_M_2605


title: 7D_M_2602


title: 7D_M_2607


title: 7D_M_2608


title: 7D_M_2596


title: 7D_M_2601


title: 7D_M_2600


title: 7D_M_2599


title: 7D_M_2604


title: 7D_M_2748


title: 7D_M_2592


title: 7D_M_2591


title: 7D_M_2597


title: 7D_M_2598


title: 7D_M_2595


title: 7D_M_2590


title: 7D_M_2594


title: 7D_M_2593


title: 7D_M_2589


title: 7D_M_2584


title: 7D_M_2585


title: 7D_M_2586


title: 7D_M_2583


title: 7D_M_2580


title: 7D_M_2578


title: 7D_M_2582


title: 7D_M_2581


title: 7D_M_2579


title: 7D_M_2576


title: 7D_M_2572


title: 7D_M_2575


title: 7D_M_2574


title: 7D_M_2570


title: 7D_M_2569


title: 7D_M_2568


title: 7D_M_2588


title: 7D_M_2587


title: 7D_M_2566


title: 7D_M_2567


title: 7D_M_2565


title: 7D_M_2563


title: 7D_M_2564


title: 7D_M_2560


title: 7D_M_2559


title: 7D_M_2558


title: 7D_M_2556


title: 7D_M_2555


title: 7D_M_2577


title: 7D_M_2427


title: 7D_M_2571


title: 7D_M_2573


title: 7D_M_2562


title: 7D_M_2426


title: 7D_M_2422


title: 7D_M_2424


title: 7D_M_2423


title: 7D_M_2425


title: 7D_M_2420


title: 7D_M_2419


title: 7D_M_2418


title: 7D_M_2414


title: 7D_M_2415


title: 7D_M_2417


title: 7D_M_2413


title: 7D_M_2416


title: 7D_M_2557


title: 7D_M_2412


title: 7D_M_2408


title: 7D_M_2410


title: 7D_M_2407


title: 7D_M_2406


title: 7D_M_2409


title: 7D_M_2411


title: 7D_M_2405


title: 7D_M_2421


title: 7D_M_2403


title: 7D_M_2400


title: 7D_M_2398


title: 7D_M_2401


title: 7D_M_2402


title: 7D_M_2399


title: 7D_M_2396


title: 7D_M_2395


title: 7D_M_2393


title: 7D_M_2397


title: 7D_M_2391


title: 7D_M_2389


title: 7D_M_2388


title: 7D_M_2387


title: 7D_M_2390


title: 7D_M_2386


title: 7D_M_2385


title: 7D_M_2384


title: 7D_M_2404


title: 7D_M_2383


title: 7D_M_2377


title: 7D_M_2378


title: 7D_M_2380


title: 7D_M_2381


title: 7D_M_2379


title: 7D_M_2375


title: 7D_M_2376


title: 7D_M_2369


title: 7D_M_2394


title: 7D_M_2372


title: 7D_M_2370


title: 7D_M_2371


title: 7D_M_2374


title: 7D_M_2367


title: 7D_M_2373


title: 7D_M_2392


title: 7D_M_2368


title: 7D_M_2365


title: 7D_M_2171


title: 7D_M_2170


title: 7D_M_2168


title: 7D_M_2366


title: 7D_M_2364


title: 7D_M_2167


title: 7D_M_2169


title: 7D_M_2165


title: 7D_M_2382


title: 7D_M_2164


title: 7D_M_2163


title: 7D_M_2161


title: 7D_M_2162


title: 7D_M_2157


title: 7D_M_2158


title: 7D_M_2159


title: 7D_M_2160


title: 7D_M_2156


title: 7D_M_2150


title: 7D_M_2154


title: 7D_M_2153


title: 7D_M_2155


title: 7D_M_2148


title: 7D_M_2151


title: 7D_M_2152


title: 7D_M_2149


title: 7D_M_2146


title: 7D_M_2147


title: 7D_M_2144


title: 7D_M_2145


title: 7D_M_2166


title: 7D_M_2143


title: 7D_M_2139


title: 7D_M_2142


title: 7D_M_2136


title: 7D_M_2140


title: 7D_M_2141


title: 7D_M_2138


title: 7D_M_2135


title: 7D_M_2137


title: 7D_M_2134


title: 7D_M_2133


title: 7D_M_2129


title: 7D_M_2131


title: 7D_M_2127


title: 7D_M_2126


title: 7D_M_2120


title: 7D_M_2119


title: 7D_M_2125


title: 7D_M_2118


title: 7D_M_2117


title: 7D_M_2124


title: 7D_M_2121


title: 7D_M_2116


title: 7D_M_2122


title: 7D_M_2110


title: 7D_M_2112


title: 7D_M_2111


title: 7D_M_2113


title: 7D_M_2115


title: 7D_M_2109


title: 7D_M_2042


title: 7D_M_2041


title: 7D_M_2108


title: 7D_M_2040


title: 7D_M_2128


title: 7D_M_2038


title: 7D_M_2037


title: 7D_M_2036


title: 7D_M_2039


title: 7D_M_2034


title: 7D_M_2035


title: 7D_M_2123


title: 7D_M_2114


title: 7D_M_2030


title: 7D_M_2033


title: 7D_M_2032


title: 7D_M_2029


title: 7D_M_2043


title: 7D_M_2027


title: 7D_M_2132


title: 7D_M_2026


title: 7D_M_2028


title: 7D_M_2025


title: 7D_M_2023


title: 7D_M_2024


title: 7D_M_2020


title: 7D_M_2021


title: 7D_M_2018


title: 7D_M_2022


title: 7D_M_2016


title: 7D_M_2017


title: 7D_M_2019


title: 7D_M_2014


title: 7D_M_2013


title: 7D_M_2012


title: 7D_M_2011


title: 7D_M_2015


title: 7D_M_2008


title: 7D_M_2007


title: 7D_M_2031


title: 7D_M_2005


title: 7D_M_2003


title: 7D_M_1998


title: 7D_M_2001


title: 7D_M_1999


title: 7D_M_1997


title: 7D_M_2002


title: 7D_M_1996


title: 7D_M_1992


title: 7D_M_1991


title: 7D_M_1995


title: 7D_M_1988


title: 7D_M_1990


title: 7D_M_1993


title: 7D_M_1989


title: 7D_M_1987


title: 7D_M_2006


title: 7D_M_2009


title: 7D_M_1986


title: 7D_M_1983


title: 7D_M_1984


title: 7D_M_2004


title: 7D_M_1982


title: 7D_M_1981


title: 7D_M_1980


title: 7D_M_2000


title: 7D_M_1979


title: 7D_M_1994


title: 7D_M_1977


title: 7D_M_1972


title: 7D_M_1971


title: 7D_M_1985


title: 7D_M_1966


title: 7D_M_1975


title: 7D_M_1976


title: 7D_M_1969


title: 7D_M_1978


title: 7D_M_1973


title: 7D_M_1970


title: 7D_M_1968


title: 7D_M_1960


title: 7D_M_1962


title: 7D_M_1963


title: 7D_M_1974


title: 7D_M_1955


title: 7D_M_1961


title: 7D_M_1956


title: 7D_M_1965


title: 7D_M_1952


title: 7D_M_1967


title: 7D_M_1959


title: 7D_M_1957


title: 7D_M_1953


title: 7D_M_1954


title: 7D_M_1950


title: 7D_M_1951


title: 7D_M_1964


title: 7D_M_1947


title: 7D_M_1949


title: 7D_M_1958


title: 7D_M_1945


title: 7D_M_1946


title: 7D_M_1944


title: 7D_M_1948


title: 7D_M_1938


title: 7D_M_1941


title: 7D_M_1942


title: 7D_M_1937


title: 7D_M_1936


title: 7D_M_1939


title: 7D_M_1935


title: 7D_M_1933


title: 7D_M_1940


title: 7D_M_1930


title: 7D_M_1932


title: 7D_M_1928


title: 7D_M_1929


title: 7D_M_1926


title: 7D_M_1925


title: 7D_M_1931


title: 7D_M_1924


title: 7D_M_1923


title: 7D_M_1922


title: 7D_M_1943


title: 7D_M_1921


title: 7D_M_1917


title: 7D_M_1918


title: 7D_M_1919


title: 7D_M_1723


title: 7D_M_1916


title: 7D_M_1934


title: 7D_M_1722


title: 7D_M_1721


title: 7D_M_1719