title: RNase H1-/- rep4

data_processing:
Sequenced paired-end reads were aligned to the mouse genome (mm10) with HISAT2 v2.10 using default parameters.
Properly paired, primary alignments were retained and read pairs aligned to the mitochondrial genome were realigned with the --no-spliced-alignment parameter enabled to remove spurious mitochondrial splice junctions.
Gene counts were produced with featureCounts v1.6.3 (-C -p -B -P -s 2) using the Ensembl GRCm38 v94 annotation combined with an in-house mitochondrial annotation.
Differential expression was analyzed with DESeq2 v1.18.1 in R v3.5.1.
Strand-specific coverage profiles were generated with samtools and bedtools genomecov, normalised to total reads mapped to mitochondria.
Assembly: mm10
Supplementary files format and content: wig files of per-strand normalised mitochondrial coverage

extract_protocol:
Total RNA was extracted form 24-week-old mouse heart tissues with Qiagen miRNeasy kit according to the kit instructions for transcriptome analysis.
An Illumina TruSeq RNA library was constructed according to manufacturers instructions.


title: RNase H1+/+ rep4

status: Public on Aug 16 2022

type: SRA

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: Heart tissue

growth_protocol: The tissue-specific conditional knockout of RNase H1 in heart and skeletal muscle was obtained by crossing Rnaseh1+/loxP with transgenic mice expressing Cre recombinase under the control of the muscle creatinine kinase promoter (Ckmm-cre). Animals were housed in a 12-hour light/dark cycle at 21°C and fed with a normal chow diet ad libitum.

tag: strain

tag: age

value: 24 weeks

tag: genotype/variation

value: wild type


title: RNase H1-/- rep2


title: RNase H1-/- rep3


title: RNase H1+/+ rep3


title: RNase H1-/- rep1


title: RNase H1+/+ rep2


title: naïve retina 4

city: Boston

first: Oleg

last: Butovsky

state: MA

address: 60 Fenwood Rd

department: Neurology

country: USA

institute: Brigham and Women's Hospital

description: naïve control

data_processing:
Samples were processed according to Smart-Seq2 protocol and sequenced on Illumina sequencers.
Reads in FASTQ were quantified at the transcript level using Salmon (v1.4.0) against the M. musculus Ensembl gene catalog (August 2020).
Differential expression analysis was conducted using R (v4.0.3) and DESeq2 (v1.30.1). Hypothesis testing was performed by using either DESeq2’s Wald test on appropriate variable contrasts or with a Likelihood Ratio Test (LRT) for models with greater than two variable conditions being tested.
Adjusted p-values were determined using the Benjamini-Hochberg procedure and significance cutoffs were set at 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: matrix table with raw gene counts for every sample

source_name: Microglia

extract_protocol:
Microglia isolation was performed according to previously described protocols. Briefly, mice were euthanized using CO2, eyes removed, and retinas dissected. Single-cell suspensions were prepared and centrifuged over a 37%/70% discontinuous Percoll gradient (GE Healthcare), and mononuclear cells were isolated from the interface. To distinguish resident microglia from recruited myeloid cells, we used a monoclonal antibody that recognizes Fcrls, which is expressed on microglia but not on infiltrating myeloid cells. Isolated cells were stained with anti-Fcrls [clone 4G11, 3 μg ml−1, Butovsky lab], CD11b-PeCy7 [clone M1/70, BD Biosciences, 2 μg ml−1] and Ly6c-PerCP/Cy5.5 [clone HK1.4, BioLegend, 2 μg ml−1] antibodies to specifically sort resident microglia as CD11b+, Ly6c–, and Fcrls+ cells. 100 to 600 cells were collected from each retina, normalized to 100 to 300 cells per 5 μl of TCL buffer, and submitted for RNAseq.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Retina

value: 12 weeks

tag: genotype

tag: cell line

tag: treatment


title: naïve retina 3

description: naïve control


title: naïve retina 2

description: naïve control


title: sham-injected retina 4

description: sham control

value: sham injection


title: sham-injected retina 3

description: sham control


title: sham-injected retina 2

description: sham control


title: contralateral retina 1

description: contralateral

value: contralateral to microbead injection


title: contralateral retina 2

description: contralateral


title: sham-injected retina 1

description: sham control


title: microbead-injected retina 3

description: glaucoma

value: microbead injection


title: microbead-injected retina 2

description: glaucoma


title: Apoe -/- microbead-injected retina 4

description: glaucoma model

data_processing:
Samples were processed according to Smart-Seq2 protocol and sequenced on Illumina sequencers.
Reads in FASTQ were quantified at the transcript level using Salmon (v1.4.0) against the M. musculus Ensembl gene catalog (August 2020).
Differential expression analysis was conducted using R (v4.0.3) and DESeq2 (v1.30.1). Hypothesis testing was performed by using either DESeq2’s Wald test on appropriate variable contrasts or with a Likelihood Ratio Test (LRT) for models with greater than two variable conditions being tested.
Adjusted p-values were determined using the Benjamini-Hochberg procedure and significance cutoffs were set at 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
Supplementary_files_format_and_content: matrix table with raw gene counts for every sample

value: Apoe -/-


title: microbead-injected retina 1

description: glaucoma


title: Apoe -/- microbead-injected retina 3

description: glaucoma model


title: Apoe -/- microbead-injected retina 2

description: glaucoma model


title: naïve retina 1

description: naïve control


title: Apoe -/- microbead-injected retina 1

description: glaucoma model


title: wildtype microbead-injected retina 2

description: glaucoma model

value: wildtype


title: Apoe -/- sham-injected retina 1

description: sham control


title: Apoe -/- sham-injected retina 3

description: sham control


title: Apoe -/- sham-injected retina 2

description: sham control


title: wildtype microbead-injected retina 1

description: glaucoma model


title: wildtype microbead-injected retina 3

description: glaucoma model


title: wildtype sham-injected retina 3

description: sham control


title: wildtype sham-injected retina 4

description: sham control


title: contralateral retina 3

description: contralateral


title: wildtype sham-injected retina 2

description: sham control


title: small RNase H1-/- rep2

data_processing:
Single-end reads were aligned to the mouse genome (mm10) with bowtie2 v2.3.4.1 using default parameters.
Gene counts were produced with featureCounts v1.6.3 (-s 1) using the Ensembl GRCm38 v94 annotation combined with an in-house mitochondrial annotation.
Differential expression was analyzed with DESeq2 v1.18.1 in R v3.5.1.
Strand-specific coverage profiles were generated with samtools and bedtools genomecov, normalised to total reads mapped to mitochondria.
Assembly: mm10
Supplementary files format and content: wig files of per-strand normalised mitochondrial coverage

extract_protocol:
Small RNA was extracted form 24-week-old mouse heart tissues with Qiagen miRNeasy kit according to the kit instructions for transcriptome analysis.
An Illumina small RNA library was constructed according to manufacturers instructions.


title: APOE E4 microbead-injected retina 2

description: glaucoma model

value: APOE E4

value: APOE E4/E4


title: APOE E3 microbead-injected retina 1

description: glaucoma model

value: APOE E3

value: APOE E3/E3


title: APOE E4 microbead-injected retina 3

description: glaucoma model


title: APOE E3 microbead-injected retina 2

description: glaucoma model


title: APOE E4 sham-injected retina 3

description: sham control


title: APOE E3 sham-injected retina 4

description: sham control


title: APOE E4 sham-injected retina 2

description: sham control


title: Apoe -/- sham-injected retina 4

description: sham control

value: sham-injection


title: APOE E4 sham-injected retina 4

description: sham control


title: APOE E4 sham-injected retina 1

description: sham control


title: APOE E3 sham-injected retina 2

description: sham control


title: Apoe -/- non-phagoctyic pooled sample 5

description: non-phagocytic microglia

extract_protocol:
Microglia were isolated as CD11b+/Ly6c–/Fcrls+ cells, and phagocytic versus non-phagocytic microglia were further sorted from the Fcrls+CD11b+ population by detection of Alexa488. 5-6 retinas were pooled per sample according to sex and genotype to increase yield. 100-500 phagocytic cells were collected per sample and normalized to 100 to 300 cells per 5 μl of TCL buffer for RNAseq.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Apoe KO

value: intravitreal injection of apoptotic neurons


title: Apoe -/- non-phagoctyic pooled sample 6

description: non-phagocytic microglia


title: Apoe -/- non-phagoctyic pooled sample 2

description: non-phagocytic microglia


title: Apoe -/- phagoctyic pooled sample 6

description: phagocytic microglia


title: Apoe -/- non-phagoctyic pooled sample 1

description: non-phagocytic microglia


title: APOE E3 sham-injected retina 1

description: sham control


title: Apoe -/- phagoctyic pooled sample 3

description: phagocytic microglia


title: wildtype sham-injected retina 1

description: sham control


title: Apoe -/- phagoctyic pooled sample 4

description: phagocytic microglia


title: APOE E4 microbead-injected retina 1

description: glaucoma model


title: APOE E3 microbead-injected retina 3

description: glaucoma model


title: Apoe -/- phagoctyic pooled sample 5

description: phagocytic microglia


title: AdPhactr1-3

city: Hefei

first: Ma

middle: Xiao

last: xuan

address: 443, Huangshan Rd

country: China

institute: University of Science and Technology of China

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database built by BGI (Beijing Genomic Institute in ShenZhen), in which known and novel, coding and noncoding transcripts were included
Expression level of gene was calculated by RSEM(v1.2.12).
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Homo sapiens

source_name: Human umbilical vein endothelial cells

growth_protocol: Cells were cultured in M200 media supplemented with 5% FBS and 1X ECGS.

extract_protocol:
Total RNA was harvested using RNAeasy Mini Kit from Qiagen.
RNA libraries were prepared for sequencing using rRNA Removal Library Construction Protocol.

treatment_protocol: cells were treated with Phactr1 Adenovirus (2.5×10E10 pfu/ml, WZ Biosciences) or control adenovirus for 24 hours.


title: wild type non-phagocytic pooled sample 5

description: non-phagocytic microglia


title: AdPhactr1-2


title: Apoe -/- phagoctyic pooled sample 2

description: phagocytic microglia


title: AdPhactr1-1


title: Apoe -/- non-phagoctyic pooled sample 3

description: non-phagocytic microglia


title: AdNC-2

value: AdNC


title: AdNC-3


title: AdNC-1


title: Apoe -/- non-phagoctyic pooled sample 4

description: non-phagocytic microglia


title: wild type non-phagocytic pooled sample 3

description: non-phagocytic microglia


title: Dermal_EC_rep2_plateB

city: Uppsala

first: Sofia

last: Nordling

address: Dag Hammarskölds väg 20

country: Sweden

institute: Uppsala University

library_source: transcriptomic single cell

data_processing:
Alignment to the GRCm38 reference genome was done with tophat (v.2.1.1).
Duplicated reads were filtered out with samtools (v.0.1.18).
Gene counts were generated with Subread (v.1.4.6-p5).
Assembly: mm10 (GRCm38)
Supplementary files format and content: csv files containing the read counts for each cell in the sample.

source_name: Ear dermis

growth_protocol: Mice were maintained until adulthood (12-26 weeks).

extract_protocol:
Ears were mechanically disrupted before enzymatic dissociation (10 mg/ml Collagenase IV, 0.2% FBS and 0.2 mg/ml DNase I in PBS) at 37 ˚C for 20 minutes. Cells were incubated with an anti-CD16/32 antibody (ThermoFischer Scientific, 14-0161-85), followed by staining with CD31-FITC (BD Biosciences, 553372), CD45-APC (BioLegend, 103112), Lyve1-eFluor 660 (ThermoFischer Scientific, 50-0443-82) and Live/Dead near IR cell stain (ThermoFischer Scientific, L10119). CD31+/CD45-/Lyve1- cells were sorted using a BD FACSAria III (100 μm nozzle size, 20 psi sheet pressure).
Single-cell libraries were prepared using SMART-seq2 methodology as described previously (Picelli et al., 2014). The libraries were sequenced on a HiSeq2500 with single 50-bp reads (dual indexing reads).

tag: Sex

value: Female

value: Adult

value: Ear dermis

tag: cell type

value: Blood vascular endothelial cells


title: wild type non-phagocytic pooled sample 4

description: non-phagocytic microglia

value: Retina

value: 12 weeks

value: wild type


title: APOE E3 sham-injected retina 3

description: sham control

value: sham injection


title: wild type non-phagocytic pooled sample 2

description: non-phagocytic microglia


title: wild type non-phagocytic pooled sample 1

description: non-phagocytic microglia


title: 27-3mo_1

city: Decatur

first: Akhilesh

last: Kaushal

state: GA

address: 1760 Haygood street

institute: Emory University

description: Multiple Myeloma Patient# 27 CITE-seq data at 3months after CAR T therapy (part1)

data_processing:
Reads were aligned to human reference sequence GRCh38/hg38, filtered, deduplicated and converted into a feature barcode matrix using Cell Ranger 6.0
Samples with low fraction reads (<70%), high reads mapped to antisense strand (>10%) and with problematic barcode rank plot were excluded. Final samples with feature barcode matrix containing data for genes and 55 surface proteins were analyzed using Seurat V3 (20).  Cells with fewer than 200 unique sequenced genes, more than 10% mitochondrial gene and more than 70,000 sequenced features were filtered to exclude dead cells and doublets. The data was batch corrected using canonical correlation analysis (CCA) method using Seurat V3 data integration pipeline.
Seurat V3 pipeline for multi-modal data was used for analysis. Batch correction was performed using CCA method in Seurat.
Assembly: GRCh38/hg38
Supplementary files format and content: 10x Genomics output files: HDF5 and BAM
Library strategy: CITE-Seq

extract_protocol:
Cells were fixed, permeabilized and washed in accordance with the fluidigm`s cell surface and nuclear staining protocol as described.
Gene expression and cell surface libraries were prepared according to the protocol from 10X Genomics

tag: disease state

value: Multiple Myeloma (MM)

tag: subject id

value: Patient# 27

tag: treatment group

value: 3 months after CAR T therapy (part1)

value: Bone Marrow Mononuclear cells

tag: sequencing method

value: CITE-Seq


title: wild type phagoctyic pooled sample 5

description: phagocytic microglia


title: 32-3mo

description: Multiple Myeloma Patient# 32 CITE-seq data at 3months after CAR T therapy

value: Patient# 32

value: at 3months after CAR T therapy


title: 33-d28

description: Multiple Myeloma Patient# 33 CITE-seq data at day 28 after CAR T therapy

value: Patient# 33

value: day 28 after CAR T therapy


title: 33-pre

description: Multiple Myeloma Patient# 33 CITE-seq data before CAR T therapy

value: before CAR T therapy


title: 33-3mo

description: Multiple Myeloma Patient# 33 CITE-seq data at 3months after CAR T therapy

value: 3 months after CAR T therapy


title: 27-3mo_2

description: Multiple Myeloma Patient# 27 CITE-seq data at 3months after CAR T therapy (part2)

value: 3 months after CAR T therapy (part2)


title: 32-pre

description: Multiple Myeloma Patient# 32 CITE-seq data before CAR T therapy


title: Apoe -/- phagoctyic pooled sample 1

description: phagocytic microglia

value: Apoe KO

value: Apoe -/-

value: intravitreal injection of apoptotic neurons


title: 25-3mo

description: Multiple Myeloma Patient# 25 CITE-seq data at 3months after CAR T therapy

value: Patient# 25


title: wild type phagoctyic pooled sample 3

description: phagocytic microglia

value: Retina

value: 12 weeks

value: wild type


title: wild type phagoctyic pooled sample 4

description: phagocytic microglia


title: 20-d28

description: Multiple Myeloma Patient# 20 CITE-seq data at Day 28 after CAR T therapy

value: Multiple Myeloma (MM)

value: Patient# 20

value: Day 28 after CAR T therapy


title: wild type phagoctyic pooled sample 2

description: phagocytic microglia


title: 19-3mo

description: Multiple Myeloma Patient# 19 CITE-seq data at 3months after CAR T therapy

value: Patient# 19

value: Bone Marrow Mononuclear cells

value: CITE-Seq


title: wild type phagoctyic pooled sample 1

description: phagocytic microglia


title: 19-pre

description: Multiple Myeloma Patient# 19 CITE-seq before CAR T therapy


title: 20-3mo

description: Multiple Myeloma Patient# 20 CITE-seq data at 3months after CAR T therapy


title: 19-d28

description: Multiple Myeloma Patient# 19 CITE-seq data at Day28 after CAR T therapy


title: Early disease DBA/2J animal 4 OS

value: 6 months

value: Gpnmb-/- Tyrp1b-/-


title: Myeloblast of patient LEU485

city: Hong Kong

first: Kathy

middle: YY

last: Chan

address: Rm84041, 6/F, Clinical Science Building, Prince of Wales Hospital, Shatin, N.T.

department: Paediatrics

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
Partek Flow version 10
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to hg38 whole genome using STAR-2.5.3a.
Count per million + 0.001 were calculated.
Assembly: hg38
Supplementary files format and content: Matrix table with gene counts for every gene and every sample

source_name: Bone marrow

extract_protocol:
RNA was isolated using Trizol reagent and Qiagen RNAeasy kit. NEBNext Ultra Directional RNA Library Prep Kit for Illumina(Cat No. 7420) was used with 1 ug RNA to construct sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tumor

value: Acute myeloid leukemia

value: Diagnosis


title: Early disease DBA/2J animal 5 OS


title: Myeloblast of patient LEU476

value: Relapse 1


title: 27-d28

description: Multiple Myeloma Patient# 27 CITE-seq data at Day 28 after CAR T therapy

value: Patient# 27


title: Early disease DBA/2J animal 3 OD


title: 25-3+mo

description: Multiple Myeloma Patient# 25 CITE-seq data at more than 3months after CAR T therapy

value: more than 3 months after CAR T therapy


title: ST28, sigE null mutant ST28, 24 hours, biol rep 3

city: Padova

first: Giacomo

last: Baruzzo

address: Via Gradenigo 6/a

department: Department of Information Engineering

country: Italy

institute: University of Padova

data_processing:
Reads were pre-processed with the FASTX Toolkit 0.0.13.2 (http://hannonlab.cshl.edu/fastx_toolkit): ‘fastx_clipper’ was used to remove adapter sequences, whereas ‘fastq_quality_trimmer’ was used to trim read ends with Phred-score lower than 20 and remove reads shorter than 70bp.
For each library, paired reads (i.e. read pairs passing data preprocessing) and singletons (i.e. reads whose mate was discarded by data pre-processing) was stored in separated files.
The reference for read mapping was built merging the M. tuberculosis H37Rv complete genome (GenBank: AL123456.3) with the FASTA sequences of the 92 ERCC RNAs. To build the GTF file of gene coordinates, we gathered the H37Rv annotations from TubercuList, selected the coding sequences (CDS), and merged them with the ERCC RNA annotations.
Paired reads and singletons were mapped separately to the reference using Bowtie 2 version 2.2.1, which is suited for un-spliced reads of 50-100bp in length with the options ‘--end-to-end’ and ‘--very-sensitive’. Finally, mapped paired reads and singletons were merged in a single BAM file with samtools.
Gene expression levels were quantified in two ways (i.e. maxcounts and totcounts) considering read strandness (-Ss option) using a patch to the bedtools suite (https://gitlab.com/sysbiobig/maxcounts). Gene expression level were normalized using the TMM normalization.
Assembly: AL123456.3
Supplementary files format and content: Tab-delimited text files include raw count data matrix quantified using maxcounts and totcounts, and TMM normalized count data matrix from maxcounts data.

organism: Mycobacterium tuberculosis

growth_protocol: The two strains of M. tuberculosis (i.e., the wild-type H37RV and a sigE-mutant ST28 in which the sigE gene was rendered unfunctional) were grown in triplicates in phosphate-rich substrate until time 0h. The strains were routinely grown in 7H9 medium supplemented with AND (Albumin 5%, 0.2% glucose, 0.85% sodium chloride, 0.05% Tween 80, 0.2% glycerol). For the RNA-seq the cells were grown in Modified 7H9 broth containing 20 mM MOPS pH 6.6, 25mM Pi (NaH2PO4) and supplemented with 0.05% Tween 80, 0.02% of glycerol and 0.2% glucose until OD600 0.6-0.9.

extract_protocol:
Total RNA was extracted from 35 mL cultures as previously described [10.1128/JB.00756-09]. Two or three DNase treatments were performed to remove DNA contamination from the samples. The DNA contamination was verified using 5ng of nucleic acids samples. RNA was quantified by spectrophotometer (Nanodrop) and its quality was verified by bioanalyzer (Agilent RNA 6000 Nano kit). Only samples with RIN values of 8/9 were used for the following steps.
Before sequencing, the Ambion ERCC Spike-In Control Mixes from Thermo Fisher Scientific were added to the M. tuberculosis RNAs following the manufacturer instructions. Tagged libraries were prepared with the Illumina TruSeq stranded protocol with depletion of ribosomal RNA (rRNA), pooled and subjected to 2x100 bp paired-end sequencing.

treatment_protocol: Then the cells were harvested, washed three times in Pi-free broth, and re-suspended in Pi-free modified Middlebrook 7H9 broth (20 mM MOPS pH 6.6, 1.46g sodium chloride, 0.05% Tween 80, 0.02% glycerol and 0.2% glucose). Cells were harvested and RNA extracted at 0h (in high-phosphate conditions), and at 6, 12 and 24h. Bacteria were cultured in triplicate and total 2x4x3=24 RNA samples were collected.

value: sigE null mutant

tag: condition

value: low phosphate

tag: time point

value: 24 hours


title: Myeloblast of patient LEU463


title: H37Rv, WT, 24 hours, biol rep 3

value: WT


title: H37Rv, WT, 24 hours, biol rep 2


title: 20-3+mo

description: Multiple Myeloma Patient# 20 CITE-seq data at more than 3months after CAR T therapy

value: Multiple Myeloma (MM)


title: ST28, sigE null mutant ST28, 24 hours, biol rep 2


title: DBA/2J Gpnmb+ animal 5 OS

value: DBA/2J Gpnmb+

value: Retina

value: 12 months

value: Gpnmb+/+ Tyrp1b-/-


title: Myeloblast of patient LEU470


title: Early disease DBA/2J animal 1 OD


title: DBA/2J Gpnmb+ animal 5 OD


title: RNase H1+/+ rep1

value: 24 weeks

value: wild type


title: H37Rv, WT, 24 hours, biol rep 1


title: Myeloblast of patient LEU433


title: ST28, sigE null mutant ST28, 24 hours, biol rep 1


title: Myeloblast of patient LEU501

source_name: Ascitic fluid


title: Myeloblast of patient LEU417


title: H37Rv, WT, 12 hours, biol rep 3

value: 12 hours


title: DBA/2J Gpnmb+ animal 4 OD


title: DBA/2J Gpnmb+ animal 3 OS


title: ST28, sigE null mutant ST28, 12 hours, biol rep 3


title: Myeloblast of patient LEU404

value: Acute myeloid leukemia


title: Myeloblast of patient LEU414

value: Myelodysplastic syndromes

value: Diagnosis


title: H37Rv, WT, 12 hours, biol rep 2


title: DBA/2J Gpnmb+ animal 3 OD


title: Myeloblast of patient LEU271


title: Myeloblast of patient LEU458


title: Myeloblast of patient LEU254

value: Relapse 1


title: DBA/2J Gpnmb+ animal 2 OS


title: Early disease DBA/2J animal 2 OS

value: 6 months

value: Gpnmb-/- Tyrp1b-/-


title: H37Rv, WT, 12 hours, biol rep 1

value: low phosphate


title: DBA/2J Gpnmb+ animal 2 OD


title: ST28, sigE null mutant ST28, 12 hours, biol rep 2

value: sigE null mutant


title: ST28, sigE null mutant ST28, 12 hours, biol rep 1


title: DBA/2J Gpnmb+ animal 1 OD


title: DBA/2J Gpnmb+ animal 1 OS


title: Myeloblast of patient LEU205


title: Myeloblast of patient LEU216


title: Myeloblast of patient LEU89


title: DBA/2J animal 5 OD

description: mild disease (NOE)


title: H37Rv, WT, 6 hours, biol rep 3

value: WT

value: 6 hours


title: DBA/2J animal 5 OS

description: moderate disease


title: Myeloblast of patient LEU76


title: Myeloblast of patient LEU66


title: ST28, sigE null mutant ST28, 6 hours, biol rep 3


title: DBA/2J animal 4 OS

description: mild disease (NOE)


title: ST28, sigE null mutant ST28, 6 hours, biol rep 2


title: Myeloblast of patient LEU360

data_processing:
Partek Flow version 10
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to hg38 whole genome using STAR-2.5.3a.
Count per million + 0.001 were calculated.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with gene counts for every gene and every sample


title: ST28, sigE null mutant ST28, 6 hours, biol rep 1


title: H37Rv, WT, 6 hours, biol rep 1


title: DBA/2J animal 3 OS

description: severe disease


title: H37Rv, WT, 0 hours, biol rep 3

value: high phosphate

value: 0 hours


title: DBA/2J animal 3 OD

description: severe disease

value: Retina

value: 12 months


title: DBA/2J animal 2 OS

description: moderate disease


title: Myeloblast of patient LEU322


title: Myeloblast of patient LEU328


title: DBA/2J animal 2 OD

description: moderate disease


title: DBA/2J animal 1 OS

description: severe disease


title: Myeloblast of patient LEU293


title: H37Rv, WT, 6 hours, biol rep 2


title: Myeloblast of patient LEU350


title: H37Rv, WT, 0 hours, biol rep 2


title: ST28, sigE null mutant ST28, 0 hours, biol rep 3


title: DBA/2J animal 1 OD

description: moderate disease


title: Myeloblast of patient LEU306


title: Input from wild-type regenerating myofibers, replicate 1

city: Dallas

first: Prashant

last: Mishra

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

library_source: genomic

data_processing:
Reads were aligned against the mm10 reference genome with BWA (version 0.7.5).
Peak calling was performed using MACS14 using option -nomodel and p-value cutoff of 1e-5.
Bigwig files were generated from mapped reads using bamCoverage from deeptools (version 3.5.0) using a 10bp binsize and a smooth length of 50bp.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, peaks

molecule: genomic DNA

source_name: Myofibers

growth_protocol: Animals were maintained on standard chow diet, ad libitum, under a standard 12 hr light-dark cycle.

extract_protocol:
Minced myofibers were crosslinkd in 1% formaldehyde in PBS for 10 min at room temperature, and then quenched with 125mM glycine for 10minutes at room temperature. The tissue was then dounced in cold PBS, filtered through a 40uM cell strainer and washed twice with cold PBS. Chromatin was sonicated to approximatley 500bp, followed by extraction with NFAT1 antibody (Santa Cruz Biotechnology, sc-32758X) overnight at 4C. The mixture was incubated with protein A/G Dynabeads for 3hr at 4C. After washing, chromatin was eluted in 1% SDS buffer, followed by reverse crosslinking at 65C overnight. Pulldown DNA was incubated with RNaseA and proteinase K for 2 hr, and then purified with QIAquick spin column (Qiagen, 28004).
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina Kit (NEB, #E7645S) following the manufacturer's instructions.

treatment_protocol: Tamoxifen (75mg/kg, once per day x 5 days) was adminstered by intraperitoneal injection to mice containing the mito-Dendra2 allele drived by a Pax7-Cre(ERT2) driver. Two days after the last tamoxifen dose, muscle injury was induced by BaCl2 administration (50 uL of 1.2% solution) into the tibialis anterior muscle. Fourteen days after injury, regenerating Dendra2+ myofibers were dissected and flash frozen at -80C for further analysis.

value: Regenerating myofibers were isolated for the tibialis anterior muscle at 14 days post induction of injury.

value: wild-type

tag: chip antibody

value: none (input)


title: Myeloblast of patient LEU262

value: Acute myeloid leukemia


title: ST28, sigE null mutant ST28, 0 hours, biol rep 2

tag: strain


title: ST28, sigE null mutant ST28, 0 hours, biol rep 1


title: NFAT1-chipseq from Mfn2-/- regenerating myofibers, replicate 2

value: anti-NFAT1 (Santa Cruz Biotechnology, sc-32758X)


title: Myeloblast of patient LEU280

value: Diagnosis


title: Myeloblast of patient LEU257


title: Liver, AS treated, replicate 2

city: Edinburgh

first: Richard

middle: Sydney

last: Taylor

state: Midlothian

address: The University of Edinburgh, Easter Bush Campus

department: Roslin Institute

country: United Kingdom

institute: University of Edinburgh

description: 10X Chromium, 3’ v3.1 chemistry

data_processing:
Mapping of reads to the genome, assignment of reads to cellular barcodes, and collapsing of unique molecular identifiers (UMIs) was performed with StarSolo v2.7.7a. The genome index was generated with standard settings and “sjdbOverhang” set to 149. The reads were then mapped with the “STAR” command and following settings: “soloType=CB_UMI_Simple”, “outFilterMultimapNmax = 20”, “outMultimapperOrder=random”, “soloUMIdedup=1MM_Directional”, “soloFeatures GeneFull”, “soloBarcodeReadLength = 0”, “outFilterMatchNminOverLread = 0”, “soloCellFilter = TopCells 100000”. The top 100,000 cell barcodes ranked by UMI number were retained to ensure the capture of transcriptionally quiet nuclei
Assembly: Salmo Salar Ensembl 104 genome
Supplementary files format and content: Tab separated value (tsv) and matrix (mtx) format. Contains gene names (features.tsv), cell barcodes (barcodes.tsv) and UMI count (matrix.mtx)

molecule: nuclear RNA

organism: Salmo salar

source_name: Liver

extract_protocol:
Approximately 45mg of each frozen liver sample was placed in a 6-well tissue culture plate (Stem Cell Technologies) with 1 ml TST (2 mL of 2X ST buffer + 120 µL of 1% Tween-20 + 20 µL of 2% BSA brought up to 4 ml with nuclease-free water). The tissue was minced using Noyes Spring Scissors for 10 min on ice. The resulting homogenate was filtered through a 40 µm Falcon cell strainer, and a further 1 mL of TST was added to wash the well and filter. The volume was brought up to 5 mL using 3 mL of 1X ST buffer (diluted from 2xST buffer [292 µl of 146 mM NaCl, 100 µl of 10 mM Tris-HCl pH 7.5, 10 µl of 1 mM CaCl2, 210 µl of 21 mM MgCl2, brought up to 10ml with nuclease-free water]). The sample was centrifuged at 4°C for 5 min at 500g before the resulting pellet was re-suspended in 1 ml 1X ST buffer and the recovered nuclei were filtered through a 40 µm Falcon cell strainer, Hoechst stained, visually inspected under a fluorescent microscope, and counted using a Bio-Rad TC20
Liver nuclei were processed through the 10X Chromium Single Cell Platform using the ChromiumTM Single Cell 30 Library and Gel Bead Kit v3.1 and ChromiumTM Single Cell A Chip Kit (both 10X Genomics) as per the manufacturer’s protocol. For each sample, the nuclei were loaded into a channel of a Chromium 3’ Chip and partitioned into droplets using the Chromium controller before the captured RNA for each nucleus was barcoded and reverse transcribed. The resulting cDNA was PCR amplified for 14 cycles, fragmented, and size selected before Illumina sequencing adaptor and sample indexes were attached

treatment_protocol: Twenty fish were anaesthetized using 2-phenoxyethanol (2.5ml in 10L water/ 0.0025% v/v) and given an intraperitoneal injection of either PBS (0.5 mL) (n=10), or the pathogenic Hooke strain of A. salmonicida (2 × 105 colony-forming units / mL in PBS; 0.5 mL/fish) (n=10). Sampling was performed 24 h post-injection. The fish were killed using a Schedule 1 method following overdose anaesthetization using 2-phenoxyethanol (0.1% v/v) and destruction of the brain. Fish were immediately sampled, with liver samples (approx. 100mg) flash frozen on dry ice before storage at -80°C prior to snRNA-Seq library construction

value: Liver

value: Pathogenic Hooke strain of A. salmonicida (24 prior to sampling)


title: Myeloblast of patient LEU353

value: Relapse 2


title: Liver, AS treated, replicate 1

description: 10X Chromium, 3’ v3.1 chemistry


title: Myeloblast of patient LEU252

value: Relapse 1


title: DBA/2J animal 4 OD

description: mild disease (NOE)

tag: age

value: Gpnmb-/- Tyrp1b-/-


title: NFAT1-chipseq from Mfn2-/- regenerating myofibers, replicate 1


title: Liver, PBS treated, replicate 2

description: 10X Chromium, 3’ v3.1 chemistry

value: PBS


title: Myeloblast of patient LEU243

source_name: Peripheral Blood


title: NFAT1-chipseq from wild-type regenerating myofibers, replicate 1


title: Liver, PBS treated, replicate 1

description: 10X Chromium, 3’ v3.1 chemistry


title: H37Rv, WT, 0 hours, biol rep 1

value: WT


title: Input activated muscle stem cells, replicate 1

data_processing:
Reads were aligned against the mm10 reference genome with BWA (version 0.7.5).
Peak calling was performed using MACS14 using option -nomodel and p-value cutoff of 1e-5.
Bigwig files were generated from mapped reads using bamCoverage from deeptools (version 3.5.0) using a 10bp binsize and a smooth length of 50bp.
Genome_build: mm10

source_name: Activated muscle stem cells

extract_protocol:
Skeletal muscle was dissected and digested with Collagenase II and Dispase at 37C for 30 minutes. Mononucleated cells were collected through a 70micron cell strainer. Activatd stem cells were FACS purified as CD34-, Dendra2+, DAPI- populations. Quiescent stem cells were FACs purified as the CD34+, Dendra2+, DAPI- populations. Stem cells were crosslinked in 1% formaldehyde in PBS for 10min at room temperature, and then quenched with 125mM glycine for 10minutes at room temperature. Chromatin was sonicated to approximatley 500bp, followed by extraction with Myod antibody (Santa Cruz Biotechnology, sc-32758X) or Myog antibody (DSHB, #F5D) overnight at 4C. The mixture was incubated with protein A/G Dynabeads for 3hr at 4C. After washing, chromatin was eluted in 1% SDS buffer, followed by reverse crosslinking at 65C overnight. Pulldown DNA was incubated with RNaseA and proteinase K for 2 hr, and then purified with QIAquick spin column (Qiagen, 28004).
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina Kit (NEB, #E7645S) following the manufacturer's instructions.

treatment_protocol: Tamoxifen (75mg/kg, once per day x 5 days) was adminstered by intraperitoneal injection to mice containing the mito-Dendra2 allele drived by a Pax7-Cre(ERT2) driver. Two days after the last tamoxifen dose, muscle injury was induced by BaCl2 administration (50 uL of 1.2% solution) into the tibialis anterior muscle. As an uninjured control, saline was injected into the contralateral tibialis anterior muscle. Two days after injury, quiescent stem cells were purified from the uninjured tibialis anterior, and activated stem cells were purified from the injured tibialis anterior muscles.

value: Activated muscle stem cells purified from injured mouse tibialis anterior muscle.


title: Myeloblast of patient LEU212

value: Mixed phenotype acute leukemia


title: Myog Chip-seq from activated muscle stem cells, replicate 3

value: anti-Myog (DSHB, #F5D)


title: Myeloblast of patient LEU200


title: Myeloblast of patient LEU183


title: Myod Chip-seq from activated muscle stem cells, replicate 3

value: anti-Myod (Santa Cruz Biotechnology, sc-32758X)


title: Myeloblast of patient LEU167


title: Myog Chip-seq from activated muscle stem cells, replicate 2


title: Myeloblast of patient LEU156


title: Myeloblast of patient LEU153


title: D4Y-100 rep3

city: guangzhou

first: ying

last: liu

address: wushan

institute: SCAU

data_processing:
Oligo (dT) magnetic beads are used to select mRNA with polyA tail.
Remove contaminated Reads (the number of bases contaminated with Reads is greater than 5 bp. For double-stranded sequencing, if one end is affected Connector contamination, then remove both ends of the Reads). Remove low-quality Reads (Quality Q ≤ 19 bases in Reads account for more than 50% of total bases. For double-stranded sequencing, If one end has low quality Reads, both ends will be removed). Remove Reads containing more than 5% of N (for double-ended sequencing, if the ratio of N at one end is greater than 5%, both ends will be removed Reads)
Bowtie2 v2.2.3 was used for building the genome index,and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Screening DEGs using DESeq2 v1.6.3.
Genome_build: Glycine max Wm82.a2.v1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

organism: Glycine max

source_name: Leaf

extract_protocol:
Total RNA of nodules was isolated using Trizol reagent (Invitrogen, USA) according to the manufacturer’s protocol. The quantity and purity of total RNA was checked using a Agilent 2100 RNA Nano 6000 Assay Kit (Agilent Technologies, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: manganese concentration

tag: developmental stage

value: Young leaf


title: D4Y-100 rep2


title: D2Y-100 rep2

value: Old leaf


title: D4Y-100 rep1


title: D2Y-100 rep3


title: Myog Chip-seq from activated muscle stem cells, replicate 1

tag: tissue

tag: genotype

value: wild-type


title: Myod Chip-seq from activated muscle stem cells, replicate 2


title: NFAT1-chipseq from wild-type regenerating myofibers, replicate 2

value: Regenerating myofibers were isolated for the tibialis anterior muscle at 14 days post induction of injury.


title: D4Y-5 rep3

value: 5 uM


title: D2Y-100 rep1


title: Myeloblast of patient LEU152

value: Acute myeloid leukemia

value: Diagnosis


title: D4Y-5 rep2


title: Myeloblast of patient LEU120


title: Myeloblast of patient LEU242


title: Myeloblast of patient LEU110


title: Input quiescent muscle stem cells, replicate 1

source_name: Quiescent muscle stem cells

value: Quiescent muscle stem cells purified from uninjured mouse tibialis anterior muscle.

value: none (input)


title: Myeloblast of patient LEU100


title: Myog Chip-seq from quiescent muscle stem cells, replicate 3


title: Myod Chip-seq from quiescent muscle stem cells, replicate 3


title: D2Y-5 rep3


title: Myod Chip-seq from activated muscle stem cells, replicate 1


title: Myog Chip-seq from quiescent muscle stem cells, replicate 2


title: Myeloblast of patient LEU81


title: D4Y-5 rep1


title: Myeloblast of patient LEU58


title: D2Y-5 rep1


title: wild-type regenerating myofibers, replicate 1

data_processing:
Reads were aligned against the mm10 reference genome with BWA (version 0.7.5).
Peak calling was performed using MACS14 using option -nomodel and p-value cutoff of 1e-5.
Bigwig files were generated from mapped reads using bamCoverage from deeptools (version 3.5.0) using a 10bp binsize and a smooth length of 50bp.
Genome_build: mm10
Supplementary_files_format_and_content: biigwig and peak

extract_protocol:
Minced myofibers were crosslinkd in 1% formaldehyde in PBS for 10 min at room temperature, and then quenched with 125mM glycine for 10minutes at room temperature. The tissue was then dounced in cold PBS, filtered through a 40uM cell strainer and washed twice with cold PBS. Chromatin was sonicated to approximatley 500bp, followed by extraction with H3K9me3 antibody (Abcam, #ab8898) or H3K27me3 antibody (Abcam, #ab6002) overnight at 4C. The mixture was incubated with protein A/G Dynabeads for 3hr at 4C. After washing, chromatin was eluted in 1% SDS buffer, followed by reverse crosslinking at 65C overnight. Pulldown DNA was incubated with RNaseA and proteinase K for 2 hr, and then purified with QIAquick spin column (Qiagen, 28004).
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina Kit (NEB, #E7645S) following the manufacturer's instructions.


title: D2Y-5 rep2


title: H3K27me3-ChipSeq from HIF1dPA regenerating myofibers, replicate 3


title: Msh6_input

city: Caserta

first: Francesco

last: Cecere

state: Caserta

address: Via A. Vivaldi, n. 43

department: DiStABiF

institute: University of Campania "Luigi Vanvitelli"

data_processing:
First, we checked the quality of the base call and the presence of the adapters in the raw data. There were no bad quality base calls and adapter contaminations, so, we aligned the reads against the Mus musculus genome (mm10) using Bowtie2 short read aligner v2.3.5.1 with default parameters (Langmead and Steven L. Salzberg, 2012). We removed duplicate reads using Picard MarkDuplicates v2.22.9 [http://broadinstitute.github.io/picard/] and we only used uniquely mapped reads for the rest of the analysis.
The DNA binding profiles of ZFP57 and KAP1 in the E14 ESCs were obtained from the GSE77744 dataset. The coordinates were converted into the mm10 genome by using CrossMap Python script (Zhao et al., 2014).
For the visualization in UCSC, we used tracks normalized by reads per milion (RPM) generated by the GenomeCoverageBed tools of the BEDtools suite v2.292 (Quinlan and Ira M. Hall, 2010). To define the enriched regions, we used MACS2 algorithm with PE and –broad parameters (Zhang et al., 2008).
We considered only the intersection of the peaks of the two replicates for the rest of the analysis, obtained using the intersectBed function of BEDtools suite v2.292.
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: mESCs were cultured under standard feeder-free conditions on gelatinized tissue culture dishes and maintained in DMEM (Gibco, Thermo Fisher Scientific) supplemented with 100 uM 2-mercaptoethanol (Sigma), 1 mM sodium pyruvate, 2 mM L-glutamine, 1x penicillin–streptomycin, 15% fetal calf serum (HyClone) and 103 U/ml leukemia inhibitory factor (LIF, Millipore).

extract_protocol:
ChIP for the analysis of biotin tagged-MSH2, MSH6, was performed on formaldehyde cross-linked chromatin isolated from cells grown on 10 cm dishes to ∼80% confluency. Briefly, the cells were detached by adding 0.05% trypsin at 37°C for 3 min. Formaldehyde was added to approximately 3 × 107  cells resuspended  in Phosphate buffered saline (PBS) at a final concentration of 1% and the cells were incubated at room temperature for 10 min with shaking. The reaction was stopped by addition of glycine to a final concentration of 0.125 M. Cells were washed twice in ice-cold PBS, centrifuged and resuspended in lysis buffer 1 (50 mM HEPES pH 8, 10 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40 and 0.25% Triton X-100) for 10 min at 4°C. Isolated nuclei were lysed in lysis buffer 2 (10 mMTris–HCl pH 8.0, 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA) for 10 min at 4°C. The chromatin was sheared in sonication buffer (10 mM Tris–HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate and 0.5% N-lauroylsarcosine) to an average size of 100–400 bp using the S220 Focused-ultrasonicator (Covaris). Sonicated chromatin were diluted in sonication buffer. Chromatin for MSH6, ChIP was pre-cleared with 30 μl protein A/G agarose beads (SantaCruz) for 4 h at 4°C on a rotating wheel. Streptavidin beads (Dynabeads MyOne streptavidin T1, ref 65601, Invitrogen), anti-MSH6 (Santa Cruz sc-137015) or rabbit/mouse IgG were added to the pre-cleared chromatin and incubated overnight at 4°C on a rotating wheel.Chromatin for MSH6 ChIP was precipitated with 30 μl protein A/G agarose beads for 4 h at 4°C with rotation. The beads were then washed five times with 500 μl RIPA buffer (10 mM Tris–HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 1% Triton X-100and 0.1% SDS) and once with each of the following buffers: WASH buffer (50 mM HEPES, 0.5% sodium deoxycholate, 1% Triton X-100, 1 mM EDTA, 500 mM NaCl and 0.2% NaN3), LiCl buffer (0.25 M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA and 10 mMTris pH 8) and TE buffer (10 mM Tris pH 8, 1 mM EDTA). The bound chromatin was eluted in 100 μl TE buffer. Cross-links were reversed by incubation at 1 h at 37°C after addition of 1 μl RNAse cocktail (Ambion) and O/N at 60°C after addition of 2.5 μl SDS 20% + 2.5 μl 20 mg/ml proteinase K (Sigma). The DNA was extracted by using the QIAquick Gel Extraction Kit (Qiagen). Immunoprecipitated or 1% input DNAs were analysed by real-time PCR using SBYR Green PCR Master Mix (Bio-Rad) on a CFXCONNECT Thermal Cycler (Bio-Rad).
For ChIP-seq analysis, two nanograms of DNA from immunoprecipitated and input chromatin were used for Illumina library preparation. Libraries were generated and sequenced at IGA Technology Services (Italy), by using the NuGen Ovation Ultralow Library System v2 Kit and 150 bp paired-end sequencing on the Illumina NovaSeq6000 platform (Illumina, San Diego, CA)

tag: cell line

value: mESCs


title: Myod Chip-seq from quiescent muscle stem cells, replicate 1


title: mESC_RRBS+UMI

data_processing:
We performed the trimming and quality step using TrimGalore v. 0.6.6 using the RRBS mode (--rrbs). We aligned the reads against the Mus musculs genome (mm10) using Bismark v.0.23.0  with default parameters.We removed the duplicate reads using UMI-tools v.1.1.1 with default parameters and then we use Bismark methylation extractor to obtain the methylation level of the CpGs covered.
Assembly: mm10
Supplementary files format and content: bedGraph containing the methylation profile of the CpGs

extract_protocol: we used 100–200 ng of genomic DNA according to Illumina's instructions. Libraries were generated and sequenced at IGA Technology Services (Italy), by using the NuGEN Ovation RRBS Methyl-Seq Library System and sequenced on paired-end 150 bp mode on NovaSeq6000 (Illumina, San Diego, CA)

value: mESC


title: Myeloblast of patient LEU34


title: H3K9me3-ChipSeq from HIF1dPA regenerating myofibers, replicate 3

value: H3K9me3 (Abcam, #ab8898)


title: Myeloblast of patient LEU55

value: Relapse 1


title: Myeloblast of patient LEU54

value: Myelodysplastic syndromes


title: Myeloblast of patient LEU57


title: Myeloblast of patient LEU31


title: Msh6_rep2

value: Msh6(Santa Cruz, sc-137015)


title: Msh2_control

value: Streptavidin beads for MSH2 Bio-Tag ChIP (Dynabeads MyOne streptavidin T1, ref 65601, Invitrogen)


title: Myog Chip-seq from quiescent muscle stem cells, replicate 1

value: anti-Myog (DSHB, #F5D)


title: Myod Chip-seq from quiescent muscle stem cells, replicate 2

value: anti-Myod (Santa Cruz Biotechnology, sc-32758X)


title: H3K27me3-ChipSeq from HIF1dPA regenerating myofibers, replicate 2


title: Msh2_rep2

value: Streptavidin beads for MSH2 Bio-Tag ChIP + MSH2 transfected (Dynabeads MyOne streptavidin T1, ref 65601, Invitrogen)


title: Myeloblast of patient LEU26


title: H3K9me3-ChipSeq from HIF1dPA regenerating myofibers, replicate 2


title: Msh2_rep1


title: Post-NACT-E

city: Hangzhou

first: Junfen

last: Xu

state: Other (Non U.S.)

address: No.1 Xueshi Road

department: Department of Gynecologic Oncology

institute: Women’s Hospital, Zhejiang University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

molecule: polyA RNA

source_name: high-grade serous fallopian tube carcinoma

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3' Reagent Kit v3 (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

tag: tumor stage

value: IIIC

tag: tumor position

value: Post-NACT tumor sample from greater omentum


title: 1466_MGME1_Ctrl_TotalDNA

city: Gothenburg

first: Claes

middle: M

last: Gustafsson

address: Medcinaregatan 9A

department: Department of Medical biochemistry and cell biology

institute: Gothenburg University

data_processing:
Data were analyzed using Mitochondrial Structural Alterations (MitoSAlt) high-throughput computational pipeline with default parameters except: dna=yes, enriched=yes, nu_mt=no, o_mt=yes, i_del=yes, cn_mt=no, hplimit=0.01, breakthreshold=-2, cluster_threshold=2
Assembly: GRCm38
Supplementary files format and content: tsv. It is a tabular format that includes predicted deletions, duplications, estimated heteroplasmy, and potential repeat sequences at the boundary of breakpoint positions.

source_name: Brain

growth_protocol: All mice maintaining an inbred C57BL/6N nuclear background were housed in a 12-hour light/dark cycle at 21°C and fed with a normal chow diet ad libitum. Animal studies were approved by the animal welfare ethics committee and performed in compliance with National and European law.

extract_protocol:
Genomic DNA from mouse tissue was isolated by Gentra Puregene Tissue Kit according to kit instructions. Mitochondria isolation from mouse heart was performed as described previously (PMID: 31588022) and mtDNA was then isolated by Gentra Puregene Tissue Kit according to kit instructions.
Library construction was performed by using TruSeq Nano DNA Library Preparation Kit by GeneCore SU, University of Gothenburg

value: brain

value: 23-25 weeks

tag: gender

value: Female

value: Mgme1 +/+

tag: library prep

value: Total DNA


title: Msh6_rep1

tag: cell type

value: mESCs


title: H3K27me3-ChipSeq from HIF1dPA regenerating myofibers, replicate 1

value: Regenerating myofibers were isolated for the tibialis anterior muscle at 14 days post induction of injury.


title: 916_MGME1_KO_TotalDNA

value: Mgme1 -/-


title: H3K27me3-ChipSeq from vhl-/- regenerating myofibers, replicate 3

value: vhl-/-


title: Pre-NACT-C

value: Pre-NACT tumor sample from ascites

value: high-grade serous fallopian tube carcinoma


title: H3K9me3-ChipSeq from HIF1dPA regenerating myofibers, replicate 1

value: H3K9me3 (Abcam, #ab8898)


title: Post-NACT-F

value: Post-NACT tumor sample from lesser omentum


title: H3K27me3-ChipSeq from vhl-/- regenerating myofibers, replicate 2


title: 774_RH1_KO_TotalDNA

source_name: Heart

value: heart

value: 8 weeks


title: 923_MGME1_KO_TotalDNA

value: Male


title: 919_MGME1_Ctrl_TotalDNA


title: 771_RH1_Ctrl_TotalDNA

value: Rnaseh1 loxP/loxP


title: Post-NACT-D

value: IIIC

value: Post-NACT tumor sample from colon


title: Pre-NACT-A

value: Pre-NACT tumor sample from peritoneum


title: 837_RH1_KO_MitoDNA

molecule: other

value: Mitochondrial DNA


title: H3K9me3-ChipSeq from vhl-/- regenerating myofibers, replicate 3


title: Pre-NACT-B

value: Pre-NACT tumor sample from greater omentum


title: H3K9me3-ChipSeq from vhl-/- regenerating myofibers, replicate 2


title: H3K27me3-ChipSeq from vhl-/- regenerating myofibers, replicate 1


title: MDA-MB-468 shCK5-22 replicate 3

city: Aurora

first: Jessica

last: Finlay-Schultz

state: CO

department: Pathology

institute: University of Colorado Denver Anschutz Medical Campus

data_processing:
Adapter trimming was done for raw fastq files cutadapt
Alignment to the reference genome was done using STAR
The aligned bam files were indexed and sorted using samtools
Sorted bam files were used for gene expression quantification using cufflinks
Genome_build: GRCh38
Supplementary_files_format_and_content: txt; consists of raw counts of each gene

source_name: MDA-MB-468 cell line

growth_protocol: MDA-MB-468 cells were maintained in Dulbecco’s Modified Eagle Media supplemented with 10% fetal bovine serum.

extract_protocol:
Extraction of total RNA was performed using the Qiagen miRNeasy Mini Kit with DNase treatment according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols at the University of Colorado Denver Genomics and Microarray Core facility.

tag: shRNA


title: H3K9me3-ChipSeq from vhl-/- regenerating myofibers, replicate 1


title: MDA-MB-468 shCK5-22 replicate 2


title: 835_RH1_Ctrl_MitoDNA


title: MDA-MB-468 shCK5-22 replicate 1


title: MDA-MB-468 shControl replicate 3


title: H3K27me3-ChipSeq from mfn2-/- regenerating myofibers, replicate 3


title: H3K27me3-ChipSeq from mfn2-/- regenerating myofibers, replicate 2


title: MDA-MB-468 shControl replicate 1


title: OCT4 (CUT&RUN bisulfite) 2

city: Toronto

first: Michael

middle: M.

last: Hoffman

state: ON

address: 101 College St PMCRT 11-311

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

description: OCT4 CUT&RUN in mESCs (rep. 2), followed by WGBS. This is used as an indication of methylated binding.

data_processing:
Base calls were performed using Illumina Real-Time Analysis (RTA, version 3.4.4). BCLs are converted to FASTQs, via bcl2fastq (version 2.20).
We trimmed adapter sequences with fastp (version 0.19.4)
Then, we aligned reads to GRCm38/mm10 with Bismark (version 0.22.3; for converted sequences). Bismark used Bowtie  (version 2.4.1; and for unconverted sequences), SAMtools (version 1.10), and BedTools (version 2.29.2). We used Bowtie 2 as recommended, using their described parameters, excepting increasing alignment sensitivity, and specifying implied or default parameters. The parameters were therefore -D 20 -R 6 -N 1 -L 18 -i S,1,0.25, plus: --local --phred33 --no-unal --no-discordant --no-mixed -I 10 -X 700. As outlined in the protocol (Skene and Henikoff. Nat. Protoc. 13:1006–19, 2018), we do not permit dovetailing (off by default) nor overlaps, for alignments used for calculating the spike-in coefficient, adding: --no-overlap --no-dovetail. We used Bismark’s default parameters, save those controlling output destinations and use of multiple cores, excepting Bowtie 2 parameters, which were set as described. Sambamba (version 0.7.1) was used for post-processing, including marking duplicates.
We called peak summits using MACS 2 (version 2.1.2). We first filtered the input reads, with DeepTools (version 3.1.3) alignmentSieve, ensuring that only those with insert sizes ≤ 120 bp were included, as recommended (Skene and Henikoff). We used the standard MACS 2 callpeak command, specifying treatment and control inputs and outputs as usual. We also used the additional parameters, --buffer-size 1000000 --format 'BAMPE' --gsize 'mm' --qvalue 0.05 --call- summits --bdg --SPMR.
For bisulfite-converted data, we extracted and called peaks only upon methylated reads (filtering through Sambamba using Bismark’s added “XM:Z:” tag). All hmC-Seal-seq reads are presumed to be completely hydroxymethylated.
Assembly: GRCm38/mm10
Supplementary files format and content: Peak calls, in the form of MACS 2 narrowPeak files.

source_name: mouse embryonic stem cells (mESC)

growth_protocol: Male E14 murine embryonic stem cells were grown in feeder-free conditions on 10 cm plates gelatinized with 0.2% porcine skin gelatin type A (Sigma) at 37 °C and 5% CO2. Cells were cultured in N2B27+2i media (Mulas et al. Development 146:dev173146, 2019). Cells were passaged every 48 h using trypsin (Gibco) and split at a ratio of ≈ 1∶8 with fresh medium. Routine anti-mycoplasma cleaning was conducted (LookOut DNA Erase spray, Sigma) and cell lines were screened by PCR to confirm no mycoplasma presence.

extract_protocol:
We performed CUT&RUN as described elsewhere (Patty and Hainer, Nat. Protoc. 16:2633-66, 2021) using recombinant Protein A-micrococcal nuclease (pA-MN). Briefly, we extracted nuclei from ~ 4500000 embryonic stem cells using a nuclear extraction buffer and bound to 500 µl pre-washed lectin-coated concanavalin A magnetic beads (Polysciences). Then, we washed beads in binding buffer. We pre-blocked immobilized nuclei with blocking buffer and washed once in wash buffer. Following this, we incubated nuclei in wash buffer containing primary antibody for one hour at 4°C with rotation. We then incubated in wash buffer containing recombinant pA-MN for 30 min at 4°C with rotation. Using ice-water bath, we equilibrated samples to 0°C and added 3 mM CaCl2 to activate pA-MN cleavage. We then performed sub-optimal digestion, at 0°C for 30 min. Following this, we chelated digestion with 2× STOP+ buffer (including 1.5 pg MNase-digested saccharomyces cerevisiae mononucleosome-sized DNA spike-in control). We released and separated genomic fragments after RNase A treatment and centrifugation. Finally, we digested protein using proteinase K, and DNA was purified using PCl extraction, followed by ethanol precipitation.
We bisulfite-converted adapter-ligated CUT&RUN DNA using Zymo Research EZ DNA Methylation Kit (Zymo, cat. no. D5001) following the alternative protocol for the Illumina Infinium Methylation Assay. Briefly, we added 5 µl of M-Dilution buffer to purified adaptor-ligated DNA, and adjusted total sample volume to 50 µl with sterile, molecular grade, water. We incubated samples at 37°C for 15 min, prior to the addition of 100 µl of CT Conversion Reagent. We further incubated samples, prior to purification, at (95°C for 30 s, 50°C for 60 min) for 16 cycles, then at 4°C for at least 10 min (per manufacturer's protocol). Finally, we eluted samples in 23 µl molecular grade water.
We amplified the bisulfite-converted DNA using 2× KAPA HiFiSeq HS Uracil+ (KAPA, cat. no. KK2801), and unique dual index primers from NEB (cat. no. E6440S) in a final volume of 50 µl. This was performed using the following PCR program: 98°C for 45 s, followed by 17 cycles of: 98°C for 15 s, 65°C for 30 s, and 72°C for 30 s, and final extension at 72°C for 60 s. We purified and dual size selected amplified libraries using AMPure XP Beads at 0.6× to 1.0× bead ratio, eluted in a volume of 20 µl.

value: mESC

tag: cut&run antibody

value: OCT4 (Diagenode, C15410305, lot A2089P)

tag: Sex

value: male

tag: specific library preparation

value: bisulfite

tag: treatment

tag: i7 index

value: TATGGCAC

tag: i5 index

value: TCTCGCAA


title: OCT4 (CUT&RUN bisulfite) 1

description: OCT4 CUT&RUN in mESCs (rep. 1), followed by WGBS. This is used as an indication of methylated binding.

tag: strain

tag: age

value: AGCGAGAT

value: GATACTGG


title: H3K27me3-ChipSeq from mfn2-/- regenerating myofibers, replicate 1

tag: tissue

value: Regenerating myofibers were isolated for the tibialis anterior muscle at 14 days post induction of injury.

tag: chip antibody


title: H3K9me3-ChipSeq from mfn2-/- regenerating myofibers, replicate 3

tag: genotype

value: H3K9me3 (Abcam, #ab8898)


title: BT20 shCK5-22 replicate 3

source_name: BT20 cell line

growth_protocol: BT20 cells were maintained in DMEM/F12 1:1 medium with L-glutamine supplemented with 10% fetal bovine serum.


title: H3K9me3-ChipSeq from mfn2-/- regenerating myofibers, replicate 1


title: H3K9me3-ChipSeq from mfn2-/- regenerating myofibers, replicate 2


title: OCT4 (CUT&RUN hmC-Seal) 2

description: OCT4 CUT&RUN in mESCs (rep. 2), followed by hmC-Seal-seq. This is used as an indication of hydroxymethylated binding.

extract_protocol:
We performed CUT&RUN as described elsewhere (Patty and Hainer, Nat. Protoc. 16:2633-66, 2021) using recombinant Protein A-micrococcal nuclease (pA-MN). Briefly, we extracted nuclei from ~ 4500000 embryonic stem cells using a nuclear extraction buffer and bound to 500 µl pre-washed lectin-coated concanavalin A magnetic beads (Polysciences). Then, we washed beads in binding buffer. We pre-blocked immobilized nuclei with blocking buffer and washed once in wash buffer. Following this, we incubated nuclei in wash buffer containing primary antibody for one hour at 4°C with rotation. We then incubated in wash buffer containing recombinant pA-MN for 30 min at 4°C with rotation. Using ice-water bath, we equilibrated samples to 0°C and added 3 mM CaCl2 to activate pA-MN cleavage. We then performed sub-optimal digestion, at 0°C for 30 min. Following this, we chelated digestion with 2X STOP+ buffer (including 1.5 pg MNase-digested Saccharomyces cerevisiae mononucleosome-sized DNA spike-in control). We released and separated genomic fragments after RNase A treatment and centrifugation. Finally, we digested protein using proteinase K, and DNA was purified using PCl extraction, followed by ethanol precipitation.
Library preparation using the NEB Ultra II Library Preparation Kit (New England Biolabs, Cat#: E7645L) was carried out on 30 ng of CUT&RUN DNA, as per the manufacturer's protocol with modifications described here. In brief, after end-repair and A-tailing, adaptor ligated DNA was purified using AMPure XP Beads at a 0.9X ratio and eluted in 11.5 µL of sterile water.
We added three spike-in DNA controls to the adapter ligated DNA to assess specific enrichment of modified DNA fragments. Controls consisted of 0.2ng/µl working stocks of unmethylated and methylated Arabidopsis DNA spike-in controls from the Diagenode DNA methylation control package (cat. no. C02040012). They also included the 5hmC spike-in control DNA (amplified from the APC promoter) from the Active Motif Methylated DNA standard kit (Active Motif, cat. no. 55008). We combined 0.3 ng of each spike-in DNA in a final volume of 4.5 µl per experimental sample. We mixed the adapter ligated DNA with the spike-in DNA mix. Then we aliquoted 1.6 µl of this mix into a separate PCR tube and stored it at -20°C, as an input control.
We 5hmC glucosylated the remaining 14.4 µl CUT&RUN DNA mixed with spike-in controls, as previously described (Han et al. Mol. Cell 63:711-19, 2016), with the below modifications. Briefly, we 1 µ1 diluted a 3 µM stock of N3-UDP- Glc (aka UDP-Azide-Glucose) from Active Motif (cat. no. 55020) in 1× phosphate-buffered saline (PBS) to establish a working stock of 1.5 µM for Mastermix preparation. We prepared a 20 µl glucosylation Mastermix per experimental sample consisting of the following: 14.4 µl CUT&RUN DNA mixed with spike-in controls, 50 µM HEPES (pH 8.0), 25 mM MgCl2 , 0.1 mM N3-UDP-Glc and 1 U of T4 Phage β-glucosyltransferase (NEB cat. no. M0357L). We incubated the mix for 1 h at 37°C, to promote glucosylation.
We then performed biotinylation of azide-labeled 5hmC residues of the glucosylated DNA fragments. We prepared 20mM DBCO-PEG4-Biotin Conjugate (Bioscience cat. no. CLK-A105P4-10) in sterile water and stored it (at -20°C), in one-time use aliquots to avoid freeze-thaw. We mixed 20 µl of glucosylated DNA with 1.8 µM DBCO-PEG4-Biotin in a final reaction volume of 22 µl, then incubated 2 h at 37°C to promote biotinylation. Then, we prepared BioRad MicroSpin P-30 Gel Columns (cat. no. 7326223), per manufacturer's protocol, and used them to purify total DNA fragments from reaction components. Briefly, we loaded the sample onto the column, then centrifuged 4 min at 1000 × g to elute purified DNA sample in 22 µl of Tris buffer.
To specifically capture biotinylated 5hmC DNA fragments, we prepared 2× binding and washing (B&W) buffer (10 mM Tris-HCl, 10 mM EDTA, 2 M NaCl). Using 20 µg of MyOne Streptavidin C1 Dynabeads (ThermoFisher, cat. no. 65001), we re-suspended in 0.2 ml of 1× B&W buffer per experimental sample to wash beads. We subjected beads to 3 total washes, then re-suspended to a final volume of 22 µl per sample in 2× B&W buffer. We added 22 µl of purified total DNA fragments to 22 µl of washed beads, then incubated 15 min under gentle rotation to promote streptavidin-biotin binding.
To isolate beads containing streptavidin-bound biotinylated DNA fragments, we incubated them on magnet for 3 min. Then, we washed the beads 3 times with 1× B&W buffer to remove non-biotinylated DNA fragments lacking 5hmC. Beads were re-suspended in 50 µl of low TE buffer.
We conducted reverse transcriptase qPCR (RT-qPCR) to compare enrichment of 5hmCspike- in after biotin enrichment relative to input sample stored earlier. RT-qPCR in the form of a 10µl reaction, consisted of 1× KAPA SYBR Fast qPCR Mastermix (KAPA, cat. no. KK4601), 1 µl of template DNA, and primers at a final concentration of 0.3 µM. We set up different reactions for each primer set to detect each spike-in control DNA separately. We used template-specific forward and reverse primers to detect the 5hmCspike-in DNA fragment from the Active Motif Methylated DNA standard kit, or the methylated- or unmethylated- Arabidopsis DNA spike-in controls from the Diagenode DNA Methylation Control package kit. We amplified with the following PCR program: 98°C for 30 s, followed by 40 cycles of 98°C for 15 s and 60°C for 15 s (with image capture), ending with melt curve analysis.
To generate bead-free template for library DNA amplification, we established a PCR reaction mix containing 0.3 µM of unique dual index primers (NEB cat. no. E6440S), 1× NEBUltra II Q5 MM, and DNA/bead template for a final volume of 100 µl per sample. We split samples into 2× 50 µl reactions and amplified using the following PCR program: 98°C for 30 s, followed by 5 cycles of 98°C for 10s, 60°C for 75s, ending with a hold at 4°C. We then transferred reaction tubes to a magnetic rack and transferred bead-free supernatant to new PCR tubes. To amplify DNA libraries for a maximum of 16 cycles total (including initial 5 cycles), we used the same PCR conditions for the bead-free template. We then dual size selected DNA libraries using AMPure XP beads at 0.7× to 1.0× ratio.

value: hmC-Seal

value: CGAGAGAA

value: TCTCTTCC


title: BT20 shCK5-22 replicate 1


title: H3K27me3-ChipSeq from wild-type regenerating myofibers, replicate 3

value: wild-type


title: OCT4 (CUT&RUN hmC-Seal) 1

description: OCT4 CUT&RUN in mESCs (rep. 1), followed by hmC-Seal-seq. This is used as an indication of hydroxymethylated binding.

value: GTAAGGTG

value: GCAATTCG


title: IgG (CUT&RUN bisulfite)

description: IgG CUT&RUN in mESCs, followed by WGBS. This is used as an indication of the modified background.

value: IgG (abcam, ab37415)

value: GAATCACC

value: CTTCGTTC


title: OCT4 (CUT&RUN conventional) 2

description: OCT4 CUT&RUN in mESCs (rep. 2), followed by conventional sequencing. This is used as an indication of unmodified binding.

extract_protocol:
We performed CUT&RUN as described elsewhere (Patty and Hainer, Nat. Protoc. 16:2633-66, 2021) using recombinant Protein A-micrococcal nuclease (pA-MN). Briefly, we extracted nuclei from ~ 4500000 embryonic stem cells using a nuclear extraction buffer and bound to 500 µl pre-washed lectin-coated concanavalin A magnetic beads (Polysciences). Then, we washed beads in binding buffer. We pre-blocked immobilized nuclei with blocking buffer and washed once in wash buffer. Following this, we incubated nuclei in wash buffer containing primary antibody for one hour at 4°C with rotation. We then incubated in wash buffer containing recombinant pA-MN for 30 min at 4°C with rotation. Using ice-water bath, we equilibrated samples to 0°C and added 3 mM CaCl2 to activate pA-MN cleavage. We then performed sub-optimal digestion, at 0°C for 30 min. Following this, we chelated digestion with 2XSTOP+ buffer (including 1.5 pg MNase-digested Saccharomyces cerevisiae mononucleosome-sized DNA spike-in control). We released and separated genomic fragments after RNase A treatment and centrifugation. Finally, we digested protein using proteinase K, and DNA was purified using PCl extraction, followed by ethanol precipitation.
We performed library preparation of 5 ng of CUT&RUN DNA, as per the NEB Ultra II Library Preparation Kit (cat. no. E7645L) manufacturer's protocol.

value: mESC

value: OCT4 (Diagenode, C15410305, lot A2089P)

value: male

value: TGCGTAAC

value: GATAGGCT


title: OCT4 (CUT&RUN conventional) 1

description: OCT4 CUT&RUN in mESCs (rep. 1), followed by conventional sequencing. This is used as an indication of unmodified binding.

value: TCTAGGAG

value: AGGTCACT


title: BT20 shControl replicate 2


title: IgG (CUT&RUN conventional)

description: IgG CUT&RUN in mESCs, followed by conventional sequencing. This is used as an indication of the unmodified background.

value: CTTGCTAG

value: GGAGATGA


title: H3K27me3-ChipSeq from wild-type regenerating myofibers, replicate 2

value: Regenerating myofibers were isolated for the tibialis anterior muscle at 14 days post induction of injury.


title: EtOH5_Female_placenta

city: Bryan

first: Rajesh

last: Miranda

address: 8447 Riverside Parkway

institute: Texas A&M University

data_processing:
Trimmomatic read trimmer was used to evaluate and trim all adapter sequences and low quality bases. Reads were scanned with a sliding window of 5, cutting when the average quality per base drops below 20, then trimming reads at the beginning and end if base quality drops below 25, and then if the read length is less than 35.
HISAT2 was used for read mapping
HTSeq generated transcript-wise counts
DESeq2 was used for normalizing counts, calculating fold change, and differential analysis.
Genome_build: mm10

source_name: Placenta (non-decidual)

growth_protocol: Adult C57BL/6J mice were purchased from Envigo and breeding was done in house to produce fetuses for experiments.

extract_protocol:
On gestational day 18, animals were anesthized using isoflurane vapor.  Placentas were removed and the nondecidual portion was microdissected, flash frozen in liquid nitrogen, and stored at -80 degrees Celcius. RNA was isolated using the Qiagen RNeasy Mini Kit.
RNA quantity was assessed using an Agilent TapeStation RNA assay.  Total RNA concentration was quantified via Qubit Fluorometric assay and subsequently all samples were normalized to an equivalent starting concentration. Sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Library Preparation kit (Illumina; San Diego, CA). Each sample was uniquely indexed (barcoded) to allow for pooling of all samples in a single sequencing run. Library size and quality were then assessed with an Agilent TapeStation D1000 DNA assay. Samples were normalized to ~4nM and pooled equally. Sequencing was performed on an Illumina NovaSeq S4 Flow Cell, XP running with a 150 cycle, paired‐end (2x150) sequencing run to generate approximately 50 million read pairs per sample.

treatment_protocol: Pregnant dams were distributed between treatment groups, ethanol or water as control, and received treatment by gavage on gestational day 10 while under isoflurane anesthesia.

value: Placenta (non-decidual)

value: Gestational Day 18

value: Ethanol Gavage

value: Female


title: H3K9me3-ChipSeq from wild-type regenerating myofibers, replicate 3

value: wild-type

value: H3K9me3 (Abcam, #ab8898)


title: BT20 shControl replicate 1


title: MDA-MB-468 shControl replicate 2


title: EtOH5_Male_placenta

value: Male


title: BT20 shCK5-22 replicate 2


title: epithelium co-cultivated with macrophages and  dendritic cells+UPM_72_16

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

data_processing:
Trimmomatic, version 0.39, parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:50
hisat2
htseq-count, version 0.6.0, parameters: --stranded=reverse --secondary-alignments=ignore
removal of features with less then 32 counts based on the sum of normalized counts across all samples
DESeq2, version 1.26.0, vst normalization
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2 normalized count matrix

source_name: primary nasal epithalial cells

growth_protocol: Nasal epithelial cells obtained from patients were cultured in air-liquid interface (ALI) conditions for 21 days. Macrophages and DCs were obtained from peripheral blood monocytes (PBMC) isolated from a blood sample by Lymphoprep. Monocyte derived macrophages were specialized by 20 ng/ml M-CSF  stimulation for 10 days and monocyte derived DCs by cultivation in combination of 40 ng/ml GM-CSF, 20 ng/ml IL-4 for 8 days and 50 ng/ml TNF-α and 50 ng/ml IL-1β, in 6th  day of specialization.

extract_protocol:
Total RNA were then isolated by TRIzol method and further purified on collumns. 250 ng of intact total RNA was subjected to heat fragmentation (94°C, 5 min or  85°C, 6 min for partially degraded samples) and TruSeq Unique dual index adapters (Illumina, USA) were used.
Twelve cycles of library amplification was applied. Size distribution of final libraries were validated using Agilent Bioanalyzer 2100 and High Sensitivity DNA kit (Agilent, USA). Final library concentration was determined by qPCR using Kapa Library Quantification kit (Roche, Switzerland).

treatment_protocol: Macrophages were treated with UPM (200µg/ml) into the culture medium for 24 hours before the preparation of tri-culture. Co-cultures were additionally exposed to 100 μg/ml of UPM suspension for 24 hours.

tag: disease

value: control

tag: culture

value: triple co-culture

tag: agent

value: Urban Particulate Matter treated


title: EtOH4_Female_placenta


title: H3K27me3-ChipSeq from wild-type regenerating myofibers, replicate 1


title: H3K9me3-ChipSeq from wild-type regenerating myofibers, replicate 1


title: epithelium co-cultivated with  macrophages and  dendritic cells_72_15

value: untreated


title: epithelium+UPM_72_14

value: monoculture


title: P_24h_2

city: Harbin City

first: Chenghao

last: Li

state: HeiLongJiang Province

address: No. 51 HeXing Road,Xiangfang District

department: College of Forestry

institute: Northeast Forestry University

description: Basal ends of stem cuttings cultured in medium containing 200 μM KH2PO4

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
The reference genomes and the annotation file were downloaded from  the Populus genome (version3.0,https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa ). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Genome_build: Populus trichocarpa v3.0 (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa)

organism: Populus ussuriensis

source_name: basal ends of stem cuttings

growth_protocol: New cuttings from 3-week-old in vivo plants were cultured on the solid Woody Plant Medium (WPM) containing 20 g/L sucrose and 3 g/L Gelrite (Duchefa) for 5 days in a plant culture room with 16 h-light/8 h-darkness cycling, 25℃ and 46 μmol photons m−2s−1 light intensity condition. When root prmordium formed, root primordium-formed cuttings were transferred to modified liquid WPM containing 200 μM or 10 μM KH2PO4.

extract_protocol:
The basal ends of stem cuttings containing root primordium with its surrounding tissues were cut out with 11# scalpel and immerged in the Sample Protector for RNA (Takara) immediately to prevent tissue degradation and Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Root primordium-formed cuttings were transferred to modified liquid WPM containing 200 μM or 10 μM KH2PO4.

value: 200 uM KH2PO4


title: P_24h_1


title: EtOH4_Male_placenta


title: EtOH3_Female_placenta


title: EtOH2_Female_placenta


title: EtOH3_Male_placenta


title: epithelium+UPM_68_14


title: EtOH1_Female_placenta


title: BT20 shControl replicate 3


title: EtOH2_Male_placenta


title: P_8h_2


title: P_8h_1


title: epithelium_68_13


title: H3K9me3-ChipSeq from wild-type regenerating myofibers, replicate 2


title: EtOH1_Male_placenta


title: P_4h_2


title: epithelium co-cultivated with macrophages and  dendritic cells+UPM_65_16


title: epithelium_72_13


title: Control6_Female_placenta

value: Water Gavage (control)


title: epithelium co-cultivated with  macrophages and  dendritic cells_65_15


title: P_4h_1


title: epithelium+UPM_65_14


title: Control6_Male_placenta


title: epithelium co-cultivated with macrophages and  dendritic cells+UPM_68_16


title: epithelium co-cultivated with  macrophages and  dendritic cells_68_15


title: P_12h_2


title: Control5_Female_placenta


title: P_2h_2


title: epithelium co-cultivated with  macrophages and  dendritic cells_63_15

value: COPD


title: epithelium co-cultivated with macrophages and  dendritic cells+UPM_63_16


title: LP_24h_1

description: Basal ends of stem cuttings cultured in medium containing 10 μM KH2PO4

value: 10 uM KH2PO4


title: P_2h_1


title: LP_24h_2


title: Control4_Female_placenta


title: Control4_Male_placenta


title: epithelium+UPM_63_14


title: LP_12h_2


title: Control3_Female_placenta


title: epithelium_63_13


title: epithelium co-cultivated with macrophages and  dendritic cells+UPM_60_16


title: LP_12h_1


title: Control3_Male_placenta


title: Control2_Female_placenta


title: epithelium co-cultivated with  macrophages and  dendritic cells_60_15


title: LP_8h_1


title: LP_8h_2


title: epithelium+UPM_60_14


title: LP_4h_2


title: Control2_Male_placenta


title: Control1_Female_placenta


title: epithelium_60_13


title: epithelium_65_13


title: LP_4h_1


title: Control1_Male_placenta


title: LP_2h_2


title: Control5_Male_placenta


title: epithelium co-cultivated with  macrophages and  dendritic cells_58_15

value: asthma


title: KO3_3hr

city: Kunigami-gun

first: Mohieldin

last: Youssef

state: Okinawa

address: 1919-1 Tancha

department: Cell Signal Unit

country: Japan

institute: Okinawa Institute of Science and Technology

description: KO 3hr after fear conditioning

data_processing:
fastq files were analyzed by RNA-seq analysis pipeline nf-core 2.0, alignment by STAR 2.6.1d
Counting by Htseq 0.9.0 using OmicsBox 1.4.11
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited .txt file containing raw gene counts for different time points and two genotypes (WT and Tob KO) in triplicates

extract_protocol:
Total RNA was purified from mouse hippocampi tissues using Isogen II reagent (Nippon Gene).
Intact poly(A) RNA was purified from 1 µg of total RNA using an NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, USA) and following the manufacturer’s protocol. Library preparation was performed using NEBNext® Ultra II Directional RNA Library Prep Kits for Illumina (New England Biolabs, USA), according to the manufacturer’s protocol with 8 PCR cycles. Library sizes were checked using microfluidic-based electrophoresis LabChip GX Touch (Perkin Elmer, USA) and concentrations were checked using Qubit 1X dsDNA HS (ThermoFisher, USA) and then pooled after concentration adjustment. 150-bp paired-end RNA sequencing was performed using a NovaSeq 6000 SP flow cell (Illumina, USA).

value: Brain

value: Tob KO

tag: protocol

value: 3hr after fear conditioning


title: KO2_3hr

description: KO 3hr after fear conditioning


title: epithelium_58_13


title: epithelium co-cultivated with  macrophages and  dendritic cells_52_15


title: PatuS-GATA4-mab2606, 2

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

country: Spain

institute: CNIO

data_processing:
Data were analyzed using cut and run nfcore pipeline: https://nf-co.re/cutandrun
Peaks were called by SEACR  in target data by selecting the top 5% of regions by AUC.
Consensus peaks were called by common peaks in the 4 replicates by homer mergePeaks function.
Assembly: UCSC hg19
Supplementary files format and content: Bigwig files of each replicate and bed file containing common peaks between the 4 replicates
Library strategy: CUT&RUN

source_name: Pancreatic adenocarcinoma

growth_protocol: DMEM supplemented with 10% FBS, 2?mmol/L l-glutamine, 100?U/mL penicillin, and 100?mg/mL streptomycin

extract_protocol:
500,000 cells/sample were harvested and bound to concanavalin Acoated magnetic beads. Cells were permeabilized with 5% digitonin. After overnight incubation with anti-human GATA4 antibodies (10ug) (MAB2606, R&D systems), beads were washed and incubated with pAG-MNase produced at CNIO (Protein Production Unit). Cells were chilled to 0 °C and digestion was initiated by adding Ca2+. Reactions were stopped by chelation including spike-in DNA and the DNA fragments released by cleavage were extracted from the supernatant.
Library preparation and paired-end sequencing were performed at the CNIO Genomics Unit.
DNA samples (average 35ng, range 5-62ng) were processed through subsequent enzymatic treatments for end-repair, dA-tailing, and ligation to adapters with "NEBNext Ultra II DNA Library Prep Kit for Illumina" (NEB ref.E7645). Adapter-ligated libraries were completed by a limited-cycle PCR, with 63º T(ann/ext) for 10s, and extracted with a [single] double-sided SPRI size selection. Resulting average fragment size is 325 bp from which 120 bp correspond to adaptor sequences. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument by following manufacturer's recommendations.

value: Pancreatic adenocarcinoma

tag: cell line

tag: cell type

value: Cancer cell

tag: antibody

value: GATA4-MAB2606 (R&D systems)

tag: antibody amount


title: PatuS-GATA4-mab2606, 1


title: epithelium+UPM_58_14


title: PatuS-GATA4-mab2606, 4


title: KO1_3hr

description: KO 3hr after fear conditioning


title: epithelium+UPM_52_14


title: KO1_1hr

description: KO 1hr after fear conditioning

value: 1hr after fear conditioning


title: epithelium co-cultivated with macrophages and  dendritic cells+UPM_58_16


title: KO3_15min

description: KO 15min after fear conditioning

value: 15min after fear conditioning


title: P_12h_1


title: epithelium co-cultivated with macrophages and  dendritic cells+UPM_48_16

value: control

value: triple co-culture


title: KO2_1hr

description: KO 1hr after fear conditioning


title: epithelium_52_13

value: untreated


title: KO2_15min

description: KO 15min after fear conditioning


title: E14-Input

city: Camperdown

first: Pengyi

last: Yang

address: The University of Sydney

institute: The University of Sydney

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using STAR (v2.5.4b) with following parameters: --outFilterMultimapNmax 1 --alignEndsType EndToEnd --outFilterMismatchNmax 3 --alignIntronMax 1. Bowtie output were converted into Bed format.  Genome_build: mm9  Supplementary_files_format_and_content: The bed file contains chromosom name, start coordinate on the chromosome, end coordinate on the chromosome and the DNA strand orientation.
Genome_build: mm9
Supplementary_files_format_and_content: The bed file contains chromosom name, start coordinate on the chromosome, end coordinate on the chromosom and the DNA strand orientation.

source_name: embryonic stem cell

growth_protocol: Embryonic stem cells were cultured at 37°C, 5% CO2, in DMEM (GIBCO) with supplemented with 15% ESC-qualified fetal bovine serum (GIBCO), 0.1 mM 2-mercaptoethanol, 1mM nonessential amino acids, and 1,000 U/ml of LIF (Millipore). For cell maintenance, ESCs were cultured in the serum-free ESGRO medium (Millipore).

extract_protocol:
Lentivirus transduced ESCs were fixed using 1% formaldehyde for 10 min, and 0.125 M glycine was added to stop the fixation. Cells were then harvested, and DNA was fragmented to 300–500 base pairs (bp) by sonication with Scientz08-III sonicator (SCIENTZ). Immunoprecipitation was performed with antibodies (Pol II, Santa Cruz, sc-47701) conjugated to Dynabeads protein A/G beads (Pierce). The ChIPped DNA was eluted, reverse-cross-linked, extracted by AMPure XP beads (Beckman).
Libraries were prepared according to the instructions accompanying the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). Briefly, DNA was end-repaired and treated with Klenow fragment to yield a protruding 3- 'A' tail for ligation of Illumina's adapters.Then, DNA was amplified with Illumina primers for 13 cycles using PCR. PCR products were purified with AMPure XP beads (Beckman). The libraries were sequenced on the Illumina NovaSeq 6000  following the manufacturer's protocols.

treatment_protocol: For virus production, shRNA constructs were cotransfected with the envelope plasmid pMD2.G (Addgene) and the packing vector psPAX2 (Addgene) using lipofiter reagents (Hanbio). Viruses were harvested 48 h after transfection and tittered by colony formation assay. Then, the viruses were used to transduce E14 ESCs.

value: mouse embryonic stem cell line

value: none (input)

value: nontarget shRNA Virus transduced


title: Z-138_MSI2ADAR_GSK591_Ro_rep2

city: new york

last: Kharas

state: New York

address: 417 68th street

department: Molecular Pharmacology Program

institute: Mamorial Sloan Kettering Cancer Center

data_processing:
The paired-end RNA-seq reads to human (hg19) genome using STAR aligner (Dobin et al., 2013)
All mutations (SNP) were identified for each RNA-seq library using the GATK (Van der Auwera et al., 2013) workflow for calling variants in RNA-seq
The mutations were then restricted to annotated mRNA transcripts, as well as restricted to A-to-G mutations in transcripts encoded by the forward strand and T-to-C mutations in transcripts encoded by the reverse strand.
Data were then filtered using mutations found in the dbSNP database since they are most likely DNA-level mutations.
The filtered sets of RNA editing events from all RNA-seq libraries of the same experiment were combined, and counted the number of reads containing reference (A/T) and alternative (G/C) alleles from each library at each site
Genome_build: hg19
Supplementary_files_format_and_content: "MSI2ADAR-samples-vs.over_Sample_MSI2ADAR-Control-_snp_counts_significance_fpkm.csv" files includes also difference frequency (editing frequency of a site in MSI2_ADA sample subtracted to the average of editing frequency of the site in MIG sample), p value, adjusted p value, number of edit sites

source_name: Z-138 cells

growth_protocol: Z-138 cells (obtained from ATCC) were cultured in IMDM 10% Horse serum 1%L-Glutamine PenStrep.

extract_protocol:
0.5 million of sorted cells per sample were harvested and frozen in TRIzol reagent. RNA was extracted using Phenol-Chloroform
After PicoGreen quantification and quality control by Agilent BioAnalyzer, 1ug RNA input was used for library preparation (TrueSeq Stranded mRNA LT Sample Prep Kit)

treatment_protocol: Cells were infected with virus expressing MSI2-HyperADAR (MSI2-ADA) at 1:1 ratio (v/v) cell: virus at 0.5 million and treated with 5uM Ro or GSK-591 or combination for 24h

value: Z-138 cells

value: Mantle cell lymphoma cell line

tag: overexpression

value: Overexpressing MSI2-HyperADAR fusion

tag: time point

value: 48hr after transduction

value: Treated with 5µM GSK591 and 5µM Ro for 24hr


title: LP_2h_1

tag: treatment

value: 10 uM KH2PO4


title: Z-138_MSI2ADAR_GSK591_Ro_rep1


title: H18

city: Richmond

first: Suyun

last: Huang

state: VA

address: 401 College Street

institute: Virginia Commonwealth University

data_processing:
The ChIP-seq reads were first trimmed by Trim Galore (v0.6.5), a wrapper around two tools: cutadapt v2.8 and FastQC v0.11.5
ChIP-seq reads were mapped to the human genome (GRCh38), using Bowtie2 (v2.4.1). The resulting sorted BAM files were converted into bedGraph and bigWig formats using BEDTools (v2.24.0) and UCSC bedGraphToBigWig (v4).
The ChIP-seq peaks were identified by MACS2 (v2.1.2) with the parameters “macs2 callpeak -t ChIP.bam -c INPUT.bam -g hs --outdir output -n NAME 2> NAME.callpeak.log”.
BETA (v1.0.7) was used to annotate the peaks that are associated with genes of interest.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: DMEM/F12, 10 ng/mL EGF and bFGF, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
2x10^6 cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated by Sonicator 3000。
NEBNext Ultra II DNA Library Prep kit for ChIP-seq library preparation

value: GBM


title: H20


title: H19


title: epithelium co-cultivated with  macrophages and  dendritic cells_48_15


title: epithelium co-cultivated with macrophages and  dendritic cells+UPM_52_16

value: asthma

value: Urban Particulate Matter treated


title: PatuS-GATA4-mab2606, 3

value: Pancreatic adenocarcinoma

value: Cancer cell

value: GATA4-MAB2606 (R&D systems)


title: KO3_1hr

description: KO 1hr after fear conditioning

value: Brain

value: Tob KO

value: 1hr after fear conditioning


title: KO1_15min

description: KO 15min after fear conditioning

value: 15min after fear conditioning


title: H17


title: epithelium+UPM_48_14

value: control

value: monoculture


title: KO3_No

description: KO without fear conditioing


title: H16


title: epithelium_48_13

value: untreated


title: Z-138_MSI2ADAR_GSK591_rep2

value: Z-138 cells

value: Mantle cell lymphoma cell line

value: Overexpressing MSI2-HyperADAR fusion

value: Treated with 5µM GSK591 for 24hr


title: H15

value: GBM


title: Z-138_MSI2ADAR_GSK591_rep1

value: 48hr after transduction


title: Z-138_MSI2ADAR_GSK591_Ro_rep3

value: Treated with 5µM GSK591 and 5µM Ro for 24hr


title: KO2_No

description: KO without fear conditioing


title: epithelium co-cultivated with macrophages and  dendritic cells+UPM_45_16

value: COPD

value: triple co-culture

value: Urban Particulate Matter treated


title: KO1_No

description: KO without fear conditioing

value: Brain


title: Z-138_MSI2ADAR_Ro_rep3

value: Treated with 5µM Ro for 24hr


title: H8


title: epithelium+UPM_45_14


title: Z-138_MSI2ADAR_Ro_rep2


title: H6


title: WT3_3hr

description: WT 3hr after fear conditioning

value: WT

value: 3hr after fear conditioning


title: H7


title: Z-138_MSI2ADAR_Ro_rep1


title: WT1_3hr

description: WT 3hr after fear conditioning


title: WT2_3hr

description: WT 3hr after fear conditioning


title: Z-138_MSI2ADAR_Control_rep2

value: Treated with DMSO for 24hr


title: epithelium co-cultivated with macrophages and  dendritic cells+UPM_40_16

value: asthma


title: epithelium_45_13

value: monoculture

value: untreated


title: H4


title: WT3_1hr

description: WT 1hr after fear conditioning

value: 1hr after fear conditioning


title: Z-138_MSI2ADAR_Control_rep1

value: Z-138 cells

value: Mantle cell lymphoma cell line

value: Overexpressing MSI2-HyperADAR fusion


title: Z-138_MIGR1_GSK591_Ro_rep3

data_processing:
The paired-end RNA-seq reads to human (hg19) genome using STAR aligner (Dobin et al., 2013)
All mutations (SNP) were identified for each RNA-seq library using the GATK (Van der Auwera et al., 2013) workflow for calling variants in RNA-seq
The mutations were then restricted to annotated mRNA transcripts, as well as restricted to A-to-G mutations in transcripts encoded by the forward strand and T-to-C mutations in transcripts encoded by the reverse strand.
Data were then filtered using mutations found in the dbSNP database since they are most likely DNA-level mutations.
The filtered sets of RNA editing events from all RNA-seq libraries of the same experiment were combined, and counted the number of reads containing reference (A/T) and alternative (G/C) alleles from each library at each site
Genome_build: hg19
Supplementary_files_format_and_content: Sample_MIGR1-GSK591-_vs.over_Sample_MIGR1-Control-_snp_counts_significance, Sample_MIGR1-GSK591Ro-_vs.over_Sample_MIGR1-Control-_snp_counts_significance and Sample_MIGR1-Ro-_vs.over_Sample_MIGR1-Control-_snp_counts_significance files include strand, entrez id, gene symbol, annotation, reference nucleotide, alternative nucleotide (edited nucleotide) for each RNA-seq library and p value, adjusted p value, number of edit sites per gene, fpkm in each sample for edited genes

treatment_protocol: Cells were infected with virus expressing MIG (empty vector) at 1:1 ratio (v/v) cell: virus at 0.5 million and treated with 5uM Ro or GSK-591 or combination for 24h

value: Overexpressing empty vector

value: 48hr after retrovirus transduction


title: WT2_1hr

description: WT 1hr after fear conditioning


title: epithelium co-cultivated with  macrophages and  dendritic cells_40_15


title: WT1_1hr

description: WT 1hr after fear conditioning


title: epithelium+UPM_40_14


title: Z-138_MIGR1_GSK591_Ro_rep1

value: Treated with 5µM GSK591 and 5µM Ro for 24hr


title: epithelium_40_13


title: epithelium co-cultivated with  macrophages and  dendritic cells_45_15

value: COPD

value: triple co-culture


title: H1, Input

value: GBM


title: epithelium co-cultivated with macrophages and  dendritic cells+UPM_38_16

value: Urban Particulate Matter treated


title: WT3_15min

description: WT 15min after fear conditioning

value: Brain

value: WT

value: 15min after fear conditioning


title: Z-138_MIGR1_Ro_rep3

value: Treated with 5µM Ro for 24hr


title: WT2_15min

description: WT 15min after fear conditioning


title: H5


title: Z-138_MIGR1_Ro_rep2


title: epithelium co-cultivated with  macrophages and  dendritic cells_38_15


title: epithelium+UPM_38_14

value: monoculture


title: WT1_15min

description: WT 15min after fear conditioning


title: Z-138_MIGR1_GSK591_rep3

value: Treated with 5µM GSK591 for 24hr


title: Z-138_MIGR1_Ro_rep1


title: WT3_No

description: WT without fear conditioing


title: epithelium_38_13

value: untreated


title: Z-138_MIGR1_GSK591_rep2

value: Z-138 cells


title: WT2_No

description: WT without fear conditioing


title: Z-138_MIGR1_GSK591_Ro_rep2

value: Mantle cell lymphoma cell line


title: epithelium co-cultivated with macrophages and  dendritic cells+UPM_36_16

value: asthma


title: H3


title: epithelium co-cultivated with  macrophages and  dendritic cells_36_15


title: Z-138_MIGR1_GSK591_rep1

value: Overexpressing empty vector


title: E14-shLsd1 rep2

extract_protocol:
Lentivirus transduced ESCs were fixed using 1% formaldehyde for 10 min, and 0.125 M glycine was added to stop the fixation. Cells were then harvested, and DNA was fragmented to 300–500 base pairs (bp) by sonication with Scientz08-III sonicator (SCIENTZ). Immunoprecipitation was performed with antibodies (Pol II, Santa Cruz, sc-47701) conjugated to Dynabeads protein A/G beads (Pierce). The ChIPped DNA was eluted, reverse-cross-linked, extracted by AMPure XP beads (Beckman).
Libraries were prepared according to the instructions accompanying the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). Briefly, DNA was end-repaired and treated with Klenow fragment to yield a protruding 3- 'A' tail for ligation of Illumina's adapters.Then, DNA was amplified with Illumina primers for 13 cycles using PCR. PCR products were purified with AMPure XP beads (Beckman). The libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

value: mouse embryonic stem cell line

value: Anti-Pol II Antibody (CTD4H8):sc-47701

value: shLsd1 Virus transduced


title: epithelium+UPM_36_14


title: Z-138_MIGR1_Control_rep2

value: 48hr after retrovirus transduction

value: Treated with DMSO for 24hr


title: E14-shLsd1 rep1