title: GP muscle from control mice

description: 10x Genomics

data_processing:
10X Cell Ranger Arc (version 2.0.0) was used to perform sample demultiplexing for both the snRNA-seq and snATAC-seq data. Raw base call files (BCL) from the Nextseq 500 were demultiplexed with the Cell Ranger Arc mkfastq pipeline into FASTQ files. We used this command to demultiplex ATAC and GEX flow cells. FASTQ files were processed further using the Cell Ranger ARC count pipeline to perform alignment, filtering, barcode counting, peak calling and counting of ATAC and GEX molecules with the mouse mm10 (Sequence: GRCm38 Ensembl 93) genome used as the reference and default parameters. Further quality filtering was performed using the Seurat R package (version 4.0.4) and Signac (1.4.0) performed in R version (4.1.0). Any barcodes (nuclei) with between 25,000 and 400 reads from RNA (nCount_RNA) and between 70,000 and 400 reads from snATAC-seq were analyzed. Cells with >20% of the reads coming from mitochondrial genes were also filtered to remove potential dead cells from analysis.  We obtained 4899 nuclei from the cachexic samples and 3293 from the control samples. After performing unsupervised clustering analysis and integrating the snRNA-seq and snATAC-seq datasets and careful inspection with known cell markers, we annotated each cluster and merged clusters that did not show clear distinctions as the same cell type.
Assembly: mm10
Supplementary files format and content: .h5 file for 10X count data

extract_protocol:
Skeletal muscles were dissected, snap-frozen, and stored in liquid nitrogen until the single nucleus multi-ome procedure was performed. Three control and three KIC GP muscles were pooled together. Muscles were thawed for 5 min on ice and minced with scissors in 1 mL cold lysis buffer (10 mM Tris- HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NonidetTM P40, 1 mM DTT, 1 U/μl RNase inhibitor in Nuclease-Free Water). Cold lysis buffer was then added, and muscles were lysed for 5 min at 4 °C. Cold wash buffer (PBS, BSA 2%, and 0.2 U/μl RNase inhibitor from Roche) was added, and the lysate was dounced with a loose dounce homogenizer for 20 strokes. The homogenate was then filtered with 70 μm and 40 μm cell strainers. Nuclei were pelleted by centrifugation for 5 min at 500 x g at 4 °C. Nuclei were then resuspended in wash buffer and 2 μL of Nuclear Pore Complex antibody (Biolegend, 682203) to stain all nuclei. After 15 min, nuclei were pelleted by centrifugation for 5 min at 500 x g at 4 °C. Nuclei were then resuspended in wash buffer and filtered with 30 μm cell strainers.  Nuclei were FACS sorted to exclude debris with a BD FACSAria III and the BD FACSDIVA and Flowjo v10.8.1 software. Nuclear Pore Complex-positive nuclei were collected for each condition and pelleted by centrifugation for 10 min at 500 x g at 4 °C. Nuclei were then resuspended in ATAC lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.01% Tween-20, 0.01% NonidetTM P40, 0.001% Digitonin, 1% BSA, 1 mM DTT, 1U/μl RNase inhibitor in Nuclease- Free Water). After 2 min, ATAC wash buffer (10 mM Tris- HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1 mM DTT, 1% BSA, 1U/μl RNase inhibitor in Nuclease-Free Water) was added. Nuclei were then pelleted by centrifugation for 10 min at 500 x g at 4 °C and resuspended in diluted nuclei buffer from 10x Genomics.  Nuclei concentrations were quantified with an automatic hemocytometer, and were adjusted to 2000 nuclei/μL with wash buffer. We loaded ~ 5000 nuclei per condition into the 10x Chromium Chip. We used the Next GEM single-cell Multiome ATAC+ Gene expression kit according to manufacturer’s protocol.
ATAC library was generated and purified with the SPRIselect Reagent Kit. The fragment size estimation of the resulting ATAC libraries was assessed with Agilent TapeStation D1000 HS (Agilent) and quantified using the QubitTM double stranded DNA (dsDNA) High-Sensitivity HS assay (ThermoFisher Scientific). SnATAC-seq libraries were then sequenced by pair with a HighOutput flowcell using an Illumina Nextseq 500.


title: GP muscle from KIC mouse 2

status: Public on Jul 12 2024

type: SRA

city: Dallas

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

country: USA

institute: UTsouthwestern

library_source: transcriptomic

data_processing:
FastQC tool (version 0.11.8) was used for quality control of RNA-seq raw fastq data to evaluate low quality or adaptor portion of the reads for trimming. Read were trimmed with Trimmomatic (Version 0.39) and aligned to mm10 reference genome using HiSAT2 (Version 2.1.0) with default settings. The raw count matrix was generated using featureCounts (Version 1.6.2) with bam files as input.
Assembly: mm10
Supplementary files format and content: .txt RawCount

molecule: total RNA

organism: Mus musculus

source_name: GP

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
Samples are run on the Agilent Tapestation 4200 to determine level of degradation thus ensuring only high quality RNA is used (RIN Score 8 or higher).  The Qubit fluorimeter is used to determine the concentration prior to staring library prep. One microgram of total DNAse treated RNA is then prepared with the TruSeq Stranded mRNA Library Prep Kit from Illumina. Poly-A RNA is purified and fragmented before strand specific cDNA synthesis. cDNA are then a-tailed and indexed adapters are ligated. After adapter ligation, samples are PCR amplified and purified with AmpureXP beads, then validated again on the Agilent Tapestation 4200.

tag: tissue

value: GP

tag: strain

value: KIC, mixed background (C57BL/6 with FVB)

tag: age

value: 66 days

tag: genotype

tag: treatment

value: no treatment


title: GP muscle from KIC mouse 1


title: GP muscle from control mouse 3

value: control, mixed background (C57BL/6 with FVB)

value: Ink4afl/fl (Control)


title: GP muscle from control mouse 1


title: 2Gy+ICI

city: Madison

first: Zachary

middle: Scott

last: Morris

state: Wisconsin

address: 1111 Highland Ave., WIMR Tower 1, Room 3131

department: Human Oncology

institute: University of Wisconsin-Madison

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, and gene counting was performed using 10x Genomics Cell Ranger software v6.1.2
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix file of filtered feature counts data

molecule: polyA RNA

source_name: solid tumors

extract_protocol:
Tumors were dissected from mice, minced, and digested using the Miltenyi Biotec tumor dissociation kit. Cells were strained through a 70 µm filter and washed with FACS buffer. Red blood cells were lysed using ACK lysis buffer, washed again with FACS buffer, and strained through a 40 µm filter. Cells were then washed and stained for CD45+ FACS.
Sorted live CD45+ cells were loaded on a Chromium iX single cell instrument (10x Genomics) to generate single-cell beads in emulsion and scRNA-seq libraries were prepared using the Chromium Single Cell 3′ Reagent Kits (v3). Cells were sequenced to greater than 50,000 reads per cell over two lanes.

value: solid tumors

tag: cell type

value: tumor-infiltrating CD45+ cells

value: 2 Gy external beam radiation therapy+Immune checkpoint inhibitors


title: 8Gy+ICI

description: 10x Genomics

value: 8 Gy external beam radiation therapy+Immune checkpoint inhibitors


title: GP muscle from control mouse 2


title: ICI

description: 10x Genomics

value: Immune checkpoint inhibitors


title: BT

description: 10x Genomics

value: Brachytherapy


title: BT+ICI

description: 10x Genomics


title: PaKiT03 PR8 infected 24hpi

city: Shanghai

first: Yang

last: Li

address: 2005 Songhu Rd, Yangpu district

country: China

institute: Fudan university

description: 3’-adapters were trimmed  and sRNAs containing any N base or overwhelming 10% of total reads were removed. Trimmed reads were first mapped to genome of Pteropus Alecto with 0 mis match, mappable  reads were futher aligned to miRNAs (pal22-), tRNAs, rRNAs, snRNAs, snoRNAs of Pteropus alecto.  Reads unmapped to host genome were aligned to viral genome. Alignment was done by Bowtie 1.2.2. Reads mapped to positive and negative strands were used to define positive and negative vsRNAs separately. Characterization of vsRNAs were performed as previously described

data_processing:
3’-adapters were trimmed  and sRNAs containing any N base or overwhelming 10% of total reads were removed.
Trimmed reads were first mapped to genome of Pteropus Alecto with 0 mis match, mappable  reads were futher aligned to miRNAs (pal22-), tRNAs, rRNAs, snRNAs, snoRNAs of Pteropus alecto.
Reads unmapped to host genome were aligned to viral genome.
Characterization of vsRNAs were performed as previously described.
Assembly: Pteropus alecto (GCA_000325575.1), hg38
Supplementary files format and content: *.viralreads.xls for all perfect mapped virus-derived small RNA reads in each library (unnormalized)
Supplementary files format and content: *.miRNAreads.xls for all perfect mapped miRNA reads in each library (unnormalized)

organism: Pteropus alecto

growth_protocol: All cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were washed with PBS twice, TRIzol was then added to the cells, and total RNAs were extracted following the manufacturer's instructions.
Extracted total RNAs were used for the construction of small RNA libraries by the method that depends on the 5’ monophosphate of small RNAs as described previously with the TruSeq Small RNA Sample Preparation Kit of Illumina (San Diego, CA).

treatment_protocol: Cells were plated in 6 cm dishes the day before infection. Infection was done with following titer: PR8delNS1 MOI=1, NoV/NoV∆B2 10 copies of genomic RNA1 per cell, SINVGFP MOI=0.5. Cells infected with NoV∆B2 were cultured at 30℃ during infection. At defined time post infection cells were harvested and total RNAs were extracted by TRIzol reagent then used for further analysis.

tag: cell line

value: kidney cell

value: wildtype

value: infected with PR8


title: PaKiT03 NoV infected 48hpi

value: infected with NoV


title: PaKiT03 SINVGFP MOI=0.1 infected 24hpi

value: infected with SINVGFP


title: PaKiT03 dsRNA 37 degree treatment

value: dsRNA transfection heat treatment


title: Sham

description: 10x Genomics

value: untreated/mock treament


title: BT+ICI, day 3, rep 1

data_processing:
The demultiplexing, barcode processing, and gene counting was performed using 10x Genomics Space Ranger v2.0.0
Assembly: 10x Genomics Space Ranger mm10 reference
Supplementary files format and content: tab-separated files and matrix files represent raw counts matrix; tissue_positions.csv defines spot barcodes, spot row and column coordinates, spot pixel coordinates, and denotes tissue detection;  png image of tissue section on slide; json contains size and scaling factors between slide image and array spots

source_name: solid tumor

extract_protocol:
Tumor were harvested and formalin fixed and paraffin embedded. 10 μm thick tissue sections were cut and placed onto a Visium Gene Expression slide
Tissue permeabilization, reverse transcription, second strand synthesis, and cDNA amplification were performed according to Visium Spatial for FFPE Gene Expression Kit protocol
10x Genomics Visium spatial

value: solid tumor

tag: time

value: day 3


title: PaKiT03 dsRNA 42 degree treatment


title: GP muscle from KIC mice

description: 10x Genomics

value: GP

value: KIC, mixed background (C57BL/6 with FVB)

value: 66 days mouse age

value: no treatment


title: PaKiT03 NoV∆B2 infected 48hpi

source_name: cell line

value: cell line

value: infected with NoV∆B2


title: PaKiT03 SINVGFP infected 24hpi


title: PaKiT03 mock infected

value: mock infected


title: PaKiT03 PR8delNS1 infected 24hpi

value: infected with PR8delNS1


title: GP muscle from 48 hour fasted mouse 1

value: control, mixed background (C57BL/6 with FVB)

value: 66 days

value: Ink4afl/fl (Control)

value: 48 hours fasting (no food)


title: 20Gy+ICI

description: 10x Genomics

value: solid tumors

value: tumor-infiltrating CD45+ cells

value: 20 Gy external beam radiation therapy+Immune checkpoint inhibitors


title: 09 Control4

city: Kumamoto

first: Yoshihiro

last: Komohara

address: Honjo 1‐1‐1, Chuouku

department: Department of Cell Pathology

country: Japan

institute: Graduate School of Medical Sciences, Kumamoto University

data_processing:
illumina Local Run Manager v2.4.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim galore! v0.6.6
Trimmed sequence reads were mapped to UCSC hg19 using STAR v2.7.3a
Read count extraction and normalization were performed using RSEM v1.3.3
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Homo sapiens

source_name: blood

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using illumina TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

value: blood

value: macrophage

value: Control


title: 03 Control2

value: Control cocultured with control IgG


title: 05 anti-CD74(agonist)

value: Cocultured with anti-CD74 agonistic antibody


title: 04 anti-CD74(blocking)

value: Cocultured with anti-CD74 blocking antibody


title: 02 AGP

value: Cocultured with AGP


title: A549 SINVGFP infected 24hpi

description: 3’-adapters were trimmed  and sRNAs containing any N base or overwhelming 10% of total reads were removed. Trimmed reads were first mapped to genome of human(hg38).  Reads unmapped to host genome were aligned to viral genome. Alignment was done by Bowtie 1.2.2. Reads mapped to positive and negative strands were used to define positive and negative vsRNAs separately. Characterization of vsRNAs were performed as previously described

value: cell line

value: wildtype

value: infected with SINVGFP


title: 01 Control1


title: HeLa SINVGFP infected 24hpi

value: HeLa


title: Adult hermaphrodite 24hr+midL4, prg-1(∆PAZ-domain), rep 3

city: Houston

first: Jacob

middle: Manuel

last: Ortega

state: Texas

address: 6550 Bertner Ave

department: Genetics

institute: MD Anderson Cancer Center

description: Small RNA sample

data_processing:
Raw data were first analyzed for quality using FastQC (Version 0.12.0).
Adapter sequences were trimmed using CutAdapt (Version 3.7).
Reads were aligned to C. elegans piRNAs (piRNAdb.cel.v1_7_6.fa) and the C. elegans genome (ce11genome.fa) using a custom python script HQAlign (https://github.com/FireLabSoftware/HQAlign).
Aligned piRNA reads for each sample were normalized to total number of reads mapping to the C. elegans genome (per million).
Assembly: piRNAdb.cel.v1_7_6
Assembly: ce11genome
Supplementary files format and content: xlsx file includes includes raw counts of genome mapped reads and piRNA mapped reads
Supplementary files format and content: xlsx file includes normalization of piRNA reads to the total number of reads aligning to the C. elegans genome per million

organism: Caenorhabditis elegans

source_name: Whole Animal

growth_protocol: 20-30 hermaphrodite, mid-L4 stage animals were collected of each genotype from C. elegans stocks cultured at 25°C. These male animals were seperately cultured at 25°C until adulthood (24 hours past mid-L4 stage) at which point animals were collected for small RNA extraction.

extract_protocol:
Small RNAs were extracted using a mirVana miRNA isolation kit (Ambion) following manufacturers protocol. Purified small RNA samples were treated with Acid Pyrophosphotase to allow for cloning of small RNAs bearing a 5' triphosphate.
Libraries were contructured using a TruSeq Small RNA Library Preparation Kit (Illumina).

value: Whole Animal


title: Adult hermaphrodite 24hr+midL4, prg-1(∆PAZ-domain), rep 1

description: Small RNA sample


title: Adult hermaphrodite 24hr+midL4, prg-1(∆PAZ-domain), rep 2

description: Small RNA sample


title: Adult hermaphrodite 24hr+midL4, prg-1(Rnase-dead), rep 1

description: Small RNA sample

value: prg-1(Rnase-dead) mutant


title: Adult hermaphrodite 24hr+midL4, prg-1(Rnase-dead), rep 2

description: Small RNA sample


title: Adult hermaphrodite 24hr+midL4, Wild Type, rep 2

description: Small RNA sample

value: Wild Type


title: Adult hermaphrodite 24hr+midL4, Wild Type, rep 1

description: Small RNA sample


title: Adult male 24hr+midL4, prg-1 null mutant, rep 5

description: Small RNA sample

growth_protocol: 20-30 male, mid-L4 stage animals were collected of each genotype from C. elegans stocks cultured at 25°C. These male animals were seperately cultured at 25°C until adulthood (24 hours past mid-L4 stage) at which point animals were collected for small RNA extraction.

value: prg-1 null mutant


title: Adult hermaphrodite 24hr+midL4, Wild Type, rep 3

description: Small RNA sample


title: Adult male 24hr+midL4, Wild Type, rep 4

description: Small RNA sample


title: 1e11_5months_mouse_4

city: Urbana

first: Pablo

last: Perez-Pinera

state: Illinois

address: 1406 W Green Street

institute: University of Illinois, Urbana-Champaign

library_source: genomic

data_processing:
Supplementary files format and content: Excel sheet containing editing data sorted by figure number
Crispresso2 utilized for base calling and base editing frequency quantification for all DNA NGS files. Sequences were filtered for 90% homology with a phred33 read qualitty of >30. Sequencecs were aligned to an inputted PCR amplicon with the gRNA region of interest
RNAstar utilized for exon junction analysis, creating bam and SJ outputs to visualize and quantify RNA splicing. 2-pass mapping was used with a MAPQ quality score of 60
Assembly: chr38

molecule: genomic DNA

source_name: striatum

extract_protocol:
Striatum extraction; DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and allele frequency
Samples for DNA editing were extracted using Qiagen's DNeasy DNA extraction kit
Samples for total RNA editing were extracted using Qiagen's RNeasy plus kit
For Illumina Miseq experiments, libraries were constructed with the nextera XT indexing primer kits as per manufacturer's instructions
Targeted genomic and exon high throughput sequencing with nextera indexing primers

value: striatum

value: neuron

value: transgenic

value: AAV9 injection with SpRY-ABE-HTT-4 sgRNA

tag: Sex

value: male


title: Adult male 24hr+midL4, Wild Type, rep 5

description: Small RNA sample


title: 11 CRP 24h

value: blood

value: macrophage

value: Cocultured with CRP for 24 hours


title: 10 CRP 6h

value: Cocultured with CRP for 6 hours


title: 1e10_5months_mouse_2

value: female


title: 1e11_5months_mouse_3


title: 1e11_5months_mouse_1


title: 1e9_5months_mouse_2


title: 1e9_5months_mouse_1


title: 1e10_5months_mouse_1


title: 1e10_mouse_2months_mouse_1


title: 1e11_mouse_2months_mouse_1


title: 1e9_mouse_2months_mouse_1


title: 1e11_mouse_2months_mouse_2


title: Adult hermaphrodite 24hr+midL4, prg-1(Rnase-dead), rep 3

description: Small RNA sample


title: 1e10_mouse_2months_mouse_2


title: SpRY-ABE-HTT-3_cDNA_mouse_5

extract_protocol:
Striatum extraction; RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment, splice junction quantification, sashimi plot analysis on IGV
Samples for DNA editing were extracted using Qiagen's DNeasy DNA extraction kit
Samples for total RNA editing were extracted using Qiagen's RNeasy plus kit
For Illumina Miseq experiments, libraries were constructed with the nextera XT indexing primer kits as per manufacturer's instructions
Targeted genomic and exon high throughput sequencing with nextera indexing primers


title: 1e9_mouse_2months_mouse_2


title: SpRY-ABE-HTT-3_cDNA_mouse_1


title: SpRY-ABE-HTT-3_cDNA_mouse_3


title: SpRY-ABE-mRosa26_cDNA_mouse_6

value: AAV9 control injection with SpRY-ABE-mRosa26 sgRNA


title: 1e11_5months_mouse_2


title: SpRY-ABE-mRosa26_cDNA_mouse_5


title: SpRY-ABE-mRosa26_cDNA_mouse_3


title: SpRY-ABE-HTT-3_cDNA_mouse_2


title: SpRY-ABE-mRosa26_cDNA_mouse_2


title: SpRY-ABE-HTT-3_gDNA_mouse_3


title: SpRY-ABE-HTT-3_gDNA_mouse_2


title: SpRY-ABE-HTT-3_gDNA_mouse_1


title: SpRY-ABE-HTT-3_gDNA_mouse_4


title: SpRY-ABE-mRosa26_gDNA_mouse_7


title: SpRY-ABE-mRosa26_gDNA_mouse_4


title: SpRY-ABE-mRosa26_gDNA_mouse_5


title: SpRY-ABE-mRosa26_gDNA_mouse_3


title: SpRY-ABE-mRosa26_gDNA_mouse_6


title: SpRY-ABE-HTT-3_cDNA_mouse_4


title: SpRY-ABE-HTT-3_gDNA_mouse_5


title: SpRY-ABE-mRosa26_gDNA_mouse_2


title: CBE-HTT-4_cDNA_mouse_10

value: AAV9 injection with CBE-HTT-4 sgRNA


title: SpRY-ABE-mRosa26_gDNA_mouse_1


title: CBE-HTT-4_cDNA_mouse_6


title: CBE-HTT-4_cDNA_mouse_9


title: CBE-HTT-4_cDNA_mouse_8


title: SpRY-ABE-mRosa26_cDNA_mouse_7


title: SpRY-ABE-mRosa26_cDNA_mouse_4


title: CBE-HTT-4_cDNA_mouse_7


title: SpRY-ABE-mRosa26_cDNA_mouse_1


title: CBE-HTT-4_cDNA_mouse_4


title: CBE-HTT-4_cDNA_mouse_5


title: CBE-HTT-4_cDNA_mouse_3


title: CBE-mRosa26_cDNA_mouse 4

value: AAV9 control injection with CBE-mRosa26 sgRNA


title: CBE-HTT-4_cDNA_mouse_2


title: CBE-mRosa26_cDNA_mouse 2


title: CBE-HTT-4_cDNA_mouse_1


title: CBE-mRosa26_cDNA_mouse 1


title: CBE-HTT-4_gDNA_mouse_10


title: CBE-mRosa26_cDNA_mouse 6


title: CBE-HTT-4_gDNA_mouse_8


title: CBE-mRosa26_cDNA_mouse 5


title: CBE-HTT-4_gDNA_mouse_4


title: CBE-mRosa26_gDNA_mouse 6


title: CBE-HTT-4_gDNA_mouse_3


title: CBE-mRosa26_gDNA_mouse 3


title: CBE-HTT-4_gDNA_mouse_6


title: CBE-HTT-4_gDNA_mouse_7


title: CBE-HTT-4_gDNA_mouse_5


title: CBE-mRosa26_gDNA_mouse 4


title: CBE-HTT-4_gDNA_mouse_1


title: CBE-mRosa26_gDNA_mouse 5


title: CBE-mRosa26_cDNA_mouse 3


title: CBE-mRosa26_gDNA_mouse 2


title: CBE-mRosa26_gDNA_mouse 1


title: 8C_mz_NrKO_13

city: Paris

first: Nicola

last: Festuccia

address: 25-28 Rue du Docteur Roux

department: Developmental and Stem Cell Biology

country: France

institute: Institut Pasteur

data_processing:
Fastq files that are part of this series, or obtained from the GEO series GSE66581 (Wu et al., Nature;2016), and GSE229740 (Lai et al., Cell Res; 2023) were trimmed using the cutadapt software, and aligned with Bowtie2 to the mm10 genome, with options --no-unal, and --no-mixed --no-discordant when relevant. Reads were then filtered based on the alignment score to allow a maximum of 2 mismatches in high quality positions running awk '(int(substr($12,6))>-15)', or awk '((int(substr($(NF-1),6))>-15) && (int(substr($12,6))>-15))' on single or paired-end bam files respectively, and retaining only reads with mates. Reads with MAPQ lower than 30 were then excluded, and duplicates removed. Experimental replicates for each stage were then merged before peak calling. Specifically: for ATAC data from GSE66581 or Cut&Run data from GSE229740 all experimental replicates were merged separately for the 8C or 2C stage; for data from this series obtained using single mz Nr5a2 KO or control 8C embryos, all samples were merged; for data from this series obtained using pools of inducible Nr5a2 KO embryos, treated and untreated samples were merged. Peaks were then called using MACS2 with options -q 0.2 -g 1.87e9. This defined NR5A2 bound regions. Accessible regions were instead retained if a peak was called in at least 2 out of 3 datasets: mzKO or inducible Nr5a2 KO from this series, and data from GSE66581. Accessible and bound regions were defined as the union of overlapping accessible and bound peaks. Blacklisted regions (Amemiya et al. Sci Rep; 2019) were excluded from all datasets. ATAC-seq regions were further classified as losing, or increasing in accessibility based on the mean of two ratios in ATAC signal: that between Nr5a2 mzKO / Nr5a2 mzHet and that between untreated / tamoxifen-treated samples (FC <>1.5).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include a list of NR5A2 bound and accessible or bound but not accessible regions in control and Nr5a2 KO 8-cell stage embryos. ATAC-seq and C&R coverage are also reported and expressed in RPKM. Regions are further classified as losing, maintaining or increasing acessibility in Nr5a2 KOs.

source_name: Embryo

growth_protocol: Analysis was performed ex-vivo on 8-cell stage embryos for mz_NrHet or mz_NrKO samples. Embryos from Inducible NrKO samples (iNrko) were dissected at the early 2C stage (30h post hCG), and kept in culture for additional 45h until they reached the 8C stage, treating or not with 750nM 4-hydroxytamoxifen for the first 24h.

extract_protocol:
Lysis was part of the tagmentation protocol (see below)
The method was adapted from (Corces et al. Nature Metods; 2017) and performed with the following variations. First, the zona pellucida was removed by treatment with acid Tyrode’s. After blocking in EmbryoMax FHM HEPES Buffered Medium w/o Phenol Red , embryos were transferred in acethylated BSA(1 mg/ml in 1X PBS), and lysed for 3 min in resuspension  buffer (RSB; 10 mM Tris-HCl pH 7.4 10 mM, 5M NaCl, 3mM MgCl2) supplemented with 0.1% NP40, 0.1% Tween-20 and 0.01% digitonin in Terasaki wells. Embryos were then washed 3min in RSB with 0.1%Tween, and tagmentation performed for 30 min at 37°C in 25 ul total volume of the following reaction buffer: 12.5ul TD buffer (20mMTris-HCl pH 7.6,10 mM MgCl2, 20 % dimethyl Formamide), 8.25 ul PBS, 5ul water, supplemented with 0.01% digitonin, 0.1% Tween-20, and 1ul of Tagment DNA Enzyme (Illumina, Cat# 20034210). 125 ul of buffer PB were added directly to stop the reaction, and the material loaded on MinElute PCR Purification columns (Quiagen, Cat# 28006), eluting in 17 ul of water. The eluted 14.5ul of transposed DNA, was then mixed with 1.5 µl of 25 µM Ad1.noMX primer, 2.5 µl of 25 µM Ad2 primer from (20), 1.5 ul of 10 µM genotyping primers, 19 ul of KAPA HiFi HotStart 2x master Mix (Roche; cat. KK2502) and 1ul of pre-diluted (1:10) of Quant-iT Picogreen dye (Invitrogen, P11496). The amplification was performed on a Roche LightCycler 480 II instrument using the following programme:72°C 5 min;98°C 30 sec;Followed by repetitions of:98°C 10 sec;63°C 30 sec;72°C 1 min until reaching mid-exponential phase. Amplified material was then purified on SPRI beads (1.4 sample/beads volume). 1ul was used to measure the DNA concentration with an Invitrogen Qubit 3 and dedicated reagents. 1 -5 ng of DNA were used to check fragment size with a D1000 High Sensitivity Screentape and appropriate  reagents on an Agilent 2200 Tapestation. Genotyping was performed on pre-amplified material.

value: Embryo

tag: date

tag: embryo n

tag: developmental stage


title: 8C_mz_NrKO_11


title: 8C_i_NrKO_1


title: 8C_mz_NrKO_10


title: 8C_i_Nrpp_1


title: 8C_mz_NrKO_6


title: 8C_mz_NrKO_5


title: 8C_mz_NrKO_8


title: CBE-HTT-4_gDNA_mouse_9


title: CBE-HTT-4_gDNA_mouse_2


title: 8C_mz_NrKO_4


title: 8C_mz_NrKO_12


title: 8C_mz_NrKO_3


title: 8C_mz_NrKO_7


title: 8C_mz_NrKO_2


title: 8C_mz_NrKO_1


title: 8C_mz_NrHet_6


title: 8C_mz_NrHet_4


title: 8C_mz_NrHet_2


title: 8C_mz_NrHet_5


title: UMI_E2C_m_NrKO_18

description:
Trimmed and de-duplicated
no processed data (The processed data tables for UMI reads do not include oocytes or early 2-cell stage embryo samples, since these analyses were not performed in the study related to this submission.)

data_processing:
Single-end sequences (50-85bp, using 50bp sequencing kits) were generated using an Illumina Next-seq 500 or 2000 instruments. After trimming Illumina adapter sequences with cutadapt (3) using options -b CTGTCTCTTATA --minimum-length=1, reads were split in UMI containing or not with Julia (J. Bezanson, A. Edelman, S. Karpinski, V. Shah, Julia: “A fresh approach to numerical computing.” https://arxiv.org/abs/1411.1607; 2015), trimming 11bp after the sequence “AAGCAGTGGTATCAACGCAGAGTACGATC”. For UMI, reads were further processed in Julia to remove the invariant adapter sequence, extract the identifier, and the UMI/ transcript sequence pairs used to remove duplicates. Conventional or UMI reads were then aligned to the mm10 genome using STAR (A. Dobin et al., “STAR: ultrafast universal RNA-seq aligner. Bioinformatics” 29, 15-21; 2013) and quantified by RSEM (B. Li, C. N. Dewey, “RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.” BMC Bioinformatics 12, 323; 2011) through the RSEM-STAR pipeline,  using gencode.v25 annotations and additional options “--seed 1618 --calc-pme --calc-ci --estimate-rspd --forward-prob 0.5” for conventional reads and “--seed 1618 --calc-pme --calc-ci --estimate-rspd --forward-prob 1” for UMI reads. RSEM estimated read counts per sample were rounded for use with DESeq2 (M. I. Love, W. Huber, S. Anders, “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biol 15, 550; 2014). Genes were considered as differentially expressed if their mean expression exceeded 10 TPM in at least one genotype for a given stage, and using a <> 1.5 fold change and <0.1 FDR cutoff.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each sample

growth_protocol: Ex-vivo

extract_protocol:
Extraction and library preparation were performed in one reaction (see below)
The protocol employed is derived from FLASH-seq (V. Hahaut et al., “Fast and highly sensitive full-length single-cell RNA sequencing using FLASH-seq.” Nat Biotechnol 40, 1447-1451; 2022), with two main modifications: 1/ Genotyping primers are added during the cDNA amplification step; 2/ A phosphate group is added to the 3’ of the template switching primer to exclude the possibility it might prime DNA synthesis during the cDNA amplification step, which would result in tagging single transcripts with multiple UMI barcodes. Embryos were isolated and directly transferred by mouth pipetting to PCR tubes in 5ul of the following lysis solution: 0.1   μL Triton X-100 (10% v/v, Sigma-Aldrich, T8787); 1.2   μL dNTP mix (25 mM each, ThermoFisher Scientific, R1121); 0.46 μL 5’Bio-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’, 100 μM (supplied by IDT). 0.46 μL 5’ Biotin-AGTGGTATCAACGCAGAGTAC G ATC NNNNNNNN rGrGrG-3′Phospate, 100 μM (supplied by IDT); 0.15 μL recombinant RNase Inhibitor (40 U/μL, ThermoFisher Scientific, AM2684); 0.06 μL Dithiothreitol (DTT, 100 mM; part of the Superscript IV kit, ThermoFisher Scientific, 18091050); 1       μL betaine (5M, Sigma-Aldrich, 61962-50G); 0.45 μL dCTP (100 mM, Sigma-Aldrich, DNTP100); Water to 5 μL final. Notes (AGTGGTATCAACGCAGAGTAC is an suppression PCR sequence. Random Ns form the UMI tag, and ATC is a 3bp barcode that can be varied if multiple samples are to be mixed before tagmentation, and only UMI reads are considered. rGrGrG are required for template switching. The 3’ Phosphate inhibits priming in following steps). Tubes were incubated 3 min at 72C in a thermocycler, and immediately transferred on ice. RT-pcr was performed by adding 20ul of the following mix to each sample:1.19 μL Dithiothreitol (DTT, 100 mM; part of the Superscript IV kit, ThermoFisher Scientific, 18091050); 4 μL betaine (5M, Sigma-Aldrich, 61962-50G); 0.23 μL magnesium chloride (1 M, ThermoFisher Scientific, AM9530G); 0.48 μL recombinant RNase Inhibitor (40 U/μL, ThermoFisher Scientific, AM2684); 0.25 uL Superscript IV Reverse Transcriptase (200 U/μL, ThermoFisher Scientific, 18091050); 12.5 μL KAPA HiFi Hot-Start ReadyMix (2x, Roche; cat. KK2502); Water to a final volume of 20 μL. Samples were incubated in a thermocycler set to execute the following programme: Hold at 50°C, and after placing tubes skip to 60 min at 50°C; 3 min at 90°C; Hold at 4°C. Tubes were transferred on ice and 0.5ul of a 100 uM solution of amplification primer (TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGAGCAGTGGTATCAACGCAGAGTAC G) were added to each sample. 1ul of a solution of genotyping primers (see embryo genotyping section) at 10uM each was also added in each tube. Tubes were then transferred to a thermocycler, set to the following programme: Hold at 4°C and after placing tubes skip to 20 sec 98°C; 20 sec 64°C; 6 min 72°C; Followed by 20 cycles of: (20 sec 98°C; 20 sec 67°C ;6 min 72°C, adding 12 seconds per cycle); then hold at 4°C. Amplification products were purified using 1x volume of SPRI magnetic beads, eluting in 15 ul water. 1ul was set aside to perform a nested PCR for genotyping. Fragment size distribution was checked on a Genomic DNA Screentpape (Agilent Technologies, 5067-5365/6), with a typical lengths ranging from less than 1Kb to more than 10kb. For tagmentation, each sample was diluted to 150 pg/ul. 2 ul of diluted cDNA were mixed with 2ul of Amplicon Tagment Mix (ATM) and 4 μL of Tagment DNA Buffer (TD) from an Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024), and incubated for 8 min at 55°C, in a thermocycler. Tn5 was released from DNA by adding 2μL of Neutralization Buffer (NT), followed by a 5 min RT. Enrichment of UMI containing fragments in the tagmented DNA was performed by adding 5 μL of Nextera PCR Master Mix (NPM) and 1ul of 5 uM amplification primer (TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG AAGCAGTGGTATCAACGCAGAGTAC G, as before). KAPA HiFi Hot-Start ReadyMix (2x, Roche; cat. KK2502) can substitute the Nextera PCR Master Mix, adapting volumes as required. Tubes were incubated as follows: 72°C for 3 min; 95°C for 30 sec; followed by 10 cycles of linear enrichment PCR: (95°C for 10 sec; 55°C for 30 sec; 72°C for 30 sec); then hold at 4°C. 4 ul of a 2.5uM solution of each of the following amplification primers were added on ice: Universal primer AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG; Indexed primer CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG. The 8 Ns are to be replaced with the Illumina index sequence of choice. Tubes were returned to the thermocycler held at 4°C and then subjected to 14 iterations of the cycle:( 95°C for 10 sec; 55°C for 30 sec; 72°C for 30 sec); Followed by 72°C for 5 mi and then hold at 4°C. Amplification products were purified using 1-1.4x volume of SPRI magnetic beads, eluting in 30 ul water. Fragment size distribution was checked on a DNA Hi Sensitivity D1000 HS Screentape (Agilent Technologies, 5067-5584/5).


title: UMI_E2C_m_NrKO_17


title: 8C_mz_NrHet_3


title: 8C_mz_NrHet_1


title: 8C_mz_NrKO_9


title: UMI_E2C_m_NrKO_16


title: UMI_E2C_m_NrKO_14


title: UMI_E2C_m_NrKO_15


title: UMI_E2C_m_NrKO_10


title: UMI_E2C_m_NrKO_13


title: UMI_E2C_m_NrKO_12


title: UMI_E2C_m_NrKO_9


title: UMI_E2C_m_NrKO_11


title: UMI_E2C_m_NrKO_8


title: UMI_E2C_m_NrKO_7


title: UMI_E2C_m_NrKO_5


title: UMI_E2C_z_NrKO_10


title: UMI_E2C_m_NrKO_6


title: UMI_E2C_z_NrKO_11


title: 8C_mz_NrHet_7


title: UMI_E2C_m_NrKO_1


title: UMI_E2C_m_NrKO_2


title: UMI_E2C_m_NrKO_4


title: UMI_E2C_m_NrKO_3


title: UMI_E2C_z_NrKO_12


title: UMI_E2C_z_NrKO_8


title: UMI_E2C_z_NrKO_9


title: UMI_E2C_z_NrKO_7


title: UMI_E2C_z_NrKO_6


title: UMI_E2C_z_NrKO_1


title: UMI_E2C_mz_NrKO_21


title: UMI_E2C_mz_NrKO_19


title: UMI_E2C_z_NrKO_3


title: UMI_E2C_z_NrKO_2


title: UMI_E2C_mz_NrKO_13


title: UMI_E2C_mz_NrKO_10


title: UMI_E2C_mz_NrKO_12


title: UMI_E2C_mz_NrKO_6


title: UMI_E2C_mz_NrKO_7


title: UMI_E2C_z_NrKO_5


title: UMI_E2C_mz_NrKO_22


title: UMI_E2C_mz_NrKO_5


title: UMI_E2C_mz_NrKO_17


title: UMI_E2C_mz_NrKO_20


title: UMI_E2C_mz_NrKO_18


title: UMI_E2C_mz_NrKO_3


title: UMI_E2C_mz_NrKO_15


title: UMI_E2C_mz_NrKO_14


title: UMI_E2C_mz_NrKO_1


title: UMI_E2C_mz_NrKO_8


title: UMI_E2C_mz_NrHet_26


title: UMI_E2C_mz_NrKO_4


title: UMI_E2C_mz_NrHet_25


title: UMI_E2C_z_NrKO_4


title: UMI_E2C_mz_NrHet_24


title: UMI_E2C_mz_NrKO_9


title: UMI_E2C_mz_NrHet_23


title: UMI_E2C_mz_NrHet_27


title: UMI_E2C_mz_NrHet_29


title: UMI_E2C_mz_NrHet_22


title: UMI_E2C_mz_NrKO_11


title: UMI_E2C_mz_NrHet_21


title: UMI_E2C_mz_NrHet_19


title: UMI_E2C_mz_NrHet_16


title: UMI_E2C_mz_NrHet_18


title: UMI_E2C_mz_NrHet_12


title: UMI_E2C_mz_NrHet_20


title: UMI_E2C_mz_NrHet_11


title: UMI_E2C_mz_NrHet_9


title: UMI_E2C_mz_NrHet_8


title: UMI_E2C_mz_NrHet_17


title: UMI_E2C_mz_NrHet_6


title: UMI_E2C_mz_NrHet_7


title: UMI_E2C_mz_NrHet_15


title: UMI_E2C_mz_NrHet_14


title: UMI_E2C_mz_NrHet_5


title: UMI_E2C_mz_NrHet_13


title: UMI_E2C_mz_NrHet_3


title: UMI_E2C_mz_NrHet_1


title: UMI_E2C_mz_Nrpp_19


title: UMI_E2C_mz_NrHet_10


title: UMI_E2C_mz_NrHet_28


title: UMI_E2C_mz_NrKO_2


title: UMI_E2C_mz_Nrpp_18


title: UMI_E2C_mz_Nrpp_16


title: UMI_E2C_mz_Nrpp_20


title: UMI_E2C_mz_NrHet_2


title: UMI_E2C_mz_Nrpp_21


title: UMI_E2C_mz_Nrpp_10


title: UMI_E2C_mz_Nrpp_14


title: UMI_E2C_mz_Nrpp_17


title: UMI_E2C_mz_Nrpp_13


title: UMI_E2C_mz_NrHet_4


title: UMI_E2C_mz_Nrpp_9


title: UMI_E2C_mz_Nrpp_12


title: UMI_E2C_mz_Nrpp_11


title: UMI_E2C_mz_Nrpp_6


title: UMI_E2C_mz_Nrpp_8


title: UMI_E2C_mz_Nrpp_7


title: UMI_E2C_mz_Nrpp_5


title: UMI_E2C_mz_Nrpp_4


title: UMI_E2C_mz_Nrpp_1


title: UMI_OoMII_NrKO_10

value: NrKO


title: UMI_E2C_mz_Nrpp_15


title: UMI_OoMII_NrKO_9


title: UMI_OoMII_NrKO_6


title: UMI_OoMII_NrKO_7


title: UMI_OoMII_NrKO_12


title: UMI_OoMII_NrKO_8


title: UMI_OoMII_NrKO_11


title: UMI_OoMII_NrKO_5


title: UMI_OoMII_NrKO_4


title: UMI_OoMII_NrKO_3


title: UMI_OoMII_NrKO_2


title: UMI_OoMII_NrHet_18

value: NrHet


title: UMI_OoMII_NrHet_17


title: UMI_OoMII_NrHet_16


title: UMI_OoMII_NrHet_15


title: UMI_E2C_mz_Nrpp_3


title: UMI_OoMII_NrHet_13


title: UMI_OoMII_NrKO_1


title: UMI_E2C_mz_Nrpp_2


title: UMI_OoMII_NrHet_14


title: UMI_OoMII_NrHet_11


title: UMI_OoMII_NrHet_8


title: UMI_OoMII_NrHet_9


title: UMI_OoMII_NrHet_12


title: UMI_OoMII_NrHet_10


title: UMI_OoMII_NrHet_7


title: UMI_OoMII_NrHet_6


title: UMI_OoMII_NrHet_4


title: UMI_OoMII_NrHet_3


title: UMI_OoMII_Nrpp_9

value: Nrpp


title: UMI_OoMII_Nrpp_8


title: UMI_OoMII_NrHet_1


title: UMI_OoMII_Nrpp_7


title: UMI_OoMII_NrHet_2


title: UMI_OoMII_Nrpp_5


title: UMI_OoMII_Nrpp_4


title: UMI_OoMII_Nrpp_2


title: E2C_m_NrKO_17

description:
Trimmed
Gene_expression_resubmission.tsv


title: E2C_m_NrKO_14


title: E2C_m_NrKO_15


title: E2C_m_NrKO_16


title: E2C_m_NrKO_12


title: UMI_OoMII_Nrpp_1


title: UMI_OoMII_NrHet_5


title: E2C_m_NrKO_13


title: E2C_m_NrKO_11


title: E2C_m_NrKO_8


title: E2C_m_NrKO_9


title: E2C_m_NrKO_10


title: E2C_m_NrKO_7


title: E2C_m_NrKO_4


title: E2C_m_NrKO_5


title: E2C_z_NrKO_11


title: E2C_z_NrKO_10


title: UMI_OoMII_Nrpp_6


title: 8C_mz_NrHet_8


title: E2C_m_NrKO_2


title: E2C_m_NrKO_6


title: E2C_m_NrKO_3


title: E2C_z_NrKO_12


title: E2C_m_NrKO_18


title: E2C_m_NrKO_1


title: E2C_z_NrKO_6


title: E2C_z_NrKO_5


title: E2C_z_NrKO_7


title: E2C_z_NrKO_9


title: UMI_OoMII_Nrpp_3


title: E2C_z_NrKO_4


title: E2C_z_NrKO_8


title: E2C_z_NrKO_3


title: E2C_z_NrKO_1


title: E2C_mz_NrKO_20


title: E2C_z_NrKO_2


title: E2C_mz_NrKO_18


title: E2C_mz_NrKO_22


title: E2C_mz_NrKO_21


title: E2C_mz_NrKO_19


title: E2C_mz_NrKO_17


title: E2C_mz_NrKO_15


title: E2C_mz_NrKO_14


title: E2C_mz_NrKO_10


title: E2C_mz_NrKO_16


title: E2C_mz_NrKO_7


title: E2C_mz_NrKO_8


title: E2C_mz_NrKO_6


title: E2C_mz_NrKO_11


title: E2C_mz_NrKO_9


title: E2C_mz_NrKO_5


title: UMI_E2C_mz_NrKO_16


title: E2C_mz_NrKO_3


title: E2C_mz_NrHet_29


title: E2C_mz_NrHet_27


title: E2C_mz_NrHet_28


title: E2C_mz_NrKO_4


title: E2C_mz_NrKO_1


title: E2C_mz_NrHet_25


title: E2C_mz_NrHet_24


title: E2C_mz_NrHet_23


title: E2C_mz_NrHet_21


title: E2C_mz_NrHet_18


title: E2C_mz_NrHet_19


title: E2C_mz_NrHet_20


title: E2C_mz_NrHet_17


title: E2C_mz_NrKO_13


title: E2C_mz_NrHet_22


title: E2C_mz_NrHet_15


title: E2C_mz_NrHet_16


title: E2C_mz_NrKO_12


title: E2C_mz_NrHet_13


title: E2C_mz_NrHet_11


title: E2C_mz_NrKO_2


title: E2C_mz_NrHet_26


title: E2C_mz_NrHet_6


title: E2C_mz_NrHet_8


title: E2C_mz_NrHet_9


title: E2C_mz_NrHet_7


title: E2C_mz_NrHet_5


title: E2C_mz_NrHet_3


title: E2C_mz_Nrpp_21


title: E2C_mz_NrHet_1


title: E2C_mz_NrHet_2


title: E2C_mz_Nrpp_20


title: E2C_mz_Nrpp_19


title: E2C_mz_Nrpp_15


title: E2C_mz_Nrpp_13


title: E2C_mz_NrHet_12


title: E2C_mz_Nrpp_17


title: E2C_mz_Nrpp_16


title: E2C_mz_NrHet_14


title: E2C_mz_Nrpp_14


title: E2C_mz_Nrpp_12


title: E2C_mz_NrHet_10


title: E2C_mz_Nrpp_8


title: E2C_mz_Nrpp_9


title: E2C_mz_Nrpp_5


title: E2C_mz_Nrpp_3


title: E2C_mz_Nrpp_1


title: E2C_mz_Nrpp_6


title: E2C_mz_Nrpp_4


title: OoMII_NrKO_11


title: E2C_mz_Nrpp_2


title: E2C_mz_Nrpp_18


title: OoMII_NrKO_8


title: OoMII_NrKO_12


title: OoMII_NrKO_6


title: E2C_mz_Nrpp_11


title: OoMII_NrKO_5


title: E2C_mz_Nrpp_10


title: OoMII_NrKO_9


title: OoMII_NrKO_7


title: OoMII_NrKO_4


title: OoMII_NrKO_2


title: OoMII_NrKO_3


title: OoMII_NrKO_1


title: E2C_mz_Nrpp_7


title: OoMII_NrHet_17


title: OoMII_NrHet_16


title: OoMII_NrHet_18


title: OoMII_NrHet_15


title: OoMII_NrHet_14


title: OoMII_NrHet_13


title: OoMII_NrKO_10


title: OoMII_NrHet_12


title: OoMII_NrHet_9


title: OoMII_NrHet_10


title: OoMII_NrHet_11


title: OoMII_NrHet_7


title: OoMII_NrHet_8


title: OoMII_NrHet_5


title: OoMII_NrHet_6


title: OoMII_NrHet_3


title: OoMII_NrHet_4


title: OoMII_NrHet_2


title: OoMII_Nrpp_8


title: OoMII_NrHet_1


title: OoMII_Nrpp_7


title: OoMII_Nrpp_5


title: OoMII_Nrpp_9


title: OoMII_Nrpp_4


title: OoMII_Nrpp_2


title: OoMII_Nrpp_1


title: UMI_8C_mz_DKO_9

description:
Trimmed and de-duplicated
Gene_expression_UMI_resubmission.tsv


title: UMI_8C_mz_DKO_8


title: UMI_8C_mz_DKO_7


title: UMI_8C_mz_DKO_1


title: UMI_8C_mz_DKO_2


title: UMI_8C_mz_DKO_4


title: UMI_8C_mz_DKO_3


title: UMI_8C_mz_DKO_5


title: UMI_8C_mz_NrKO_3


title: UMI_8C_mz_NrKO_2


title: UMI_8C_mz_NrKO_5


title: UMI_8C_mz_EKO_9


title: UMI_8C_mz_EKO_8


title: UMI_8C_mz_EKO_7


title: UMI_8C_mz_EKO_5


title: UMI_8C_mz_EKO_4


title: OoMII_Nrpp_3


title: OoMII_Nrpp_6


title: UMI_8C_mz_EKO_1


title: UMI_8C_mz_EKO_3


title: UMI_8C_mz_EKO_6


title: UMI_8C_mz_DHet_16


title: UMI_8C_mz_EKO_2


title: UMI_8C_mz_DKO_6


title: UMI_8C_mz_DHet_12


title: UMI_8C_mz_DHet_15


title: UMI_8C_mz_DHet_10


title: UMI_8C_mz_DHet_13


title: UMI_8C_mz_NrKO_4


title: UMI_8C_mz_DHet_8


title: UMI_8C_mz_DHet_5


title: UMI_8C_mz_DHet_6


title: UMI_8C_mz_NrKO_1


title: UMI_8C_mz_DHet_9


title: UMI_8C_mz_DHet_7


title: UMI_8C_mz_DHet_3


title: UMI_8C_mz_DHet_4


title: UMI_8C_mz_DHet_1


title: UMI_4C_mz_DKO_10


title: UMI_8C_mz_DHet_2


title: UMI_8C_mz_DHet_14


title: UMI_4C_mz_DKO_9


title: UMI_4C_mz_DKO_8


title: UMI_4C_mz_DKO_7


title: UMI_4C_mz_DKO_6


title: UMI_8C_mz_DHet_11


title: UMI_4C_mz_DKO_4


title: UMI_4C_mz_DKO_5


title: B4204DEHP

city: Chiayi County

first: Mita

last: Tran

address: 168 University Road

department: Biomedical Sciences

country: Taiwan

institute: National Chung Cheng University

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse (GRCm38/mm10) genomes using the Illumina Genome Analyzer Pipeline.
All reads mapping with two or fewer mismatches were retained and processed according to Rodriguez et al., BMC Genomics 2012
and MethylKit Package for DMR identification
Genome_build: mm10
Supplementary_files_format_and_content: MethylKit output

source_name: cDC mouse

growth_protocol: C57BL/6 female and male mice, 6-8 weeks of age, were obtained from the National Laboratory Animal Center and maintained by the Animal Center of the Kaohsiung Medical University in a pathogen-free environment. All animal experiments were performed according to the guidelines of the Institutional Animal Care and Use Committee of the Kaohsiung Medical University (IACUC: 99032).

extract_protocol:
Genomic DNA was isolated by standard methods or by the QIAamp DNA Mini Kit (Qiagen) following the manufacturer's protocol. Mice F1 including control and DEHP treatment were chosen for extract DNA. Genomic DNA was extracted from cDC and Spleen tissuses.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Female C57BL/6 mice are treated with DEHP (37μg/kg/day) or vehicle control for 10 days. These female mice were crossed with naïve male mice. F1 splenic CD11c DC  are then isolated for for global methylation analysis.

tag: generation

tag: immunization status

value: OVA

value: Splenic CD11c DC


title: UMI_4C_mz_DKO_3


title: UMI_4C_mz_DKO_2


title: UMI_4C_mz_DKO_1


title: B4200ctr

value: F0-corn oil


title: B4201ctr


title: UMI_4C_mz_NrKO_4


title: B4202DEHP


title: Couptf1_WT_2

city: San Francisco

first: Luciano

middle: Custo

last: Greig

state: CA

address: 490 Illinois St

department: Ophthalmology

institute: University of California, San Francisco

data_processing:
TopHat and Cufflinks
Assembly: mm10
Supplementary files format and content: tab-delimited text file

source_name: Cerebral Cortex

extract_protocol:
RNAeasy - Qiagen
Smartseq v4 Ultra Low Input - Takara

value: Cerebral Cortex

value: Superficial layer projection neurons

value: Couptf1 wild-type

value: RFP electroporation


title: Couptf1_null_2

value: Couptf1 null

value: Cre/GFP electroporation


title: Couptf1_null_3


title: Couptf1_null_1


title: Couptf1_WT_3


title: UMI_4C_mz_NrKO_5


title: B4199ctr

value: female


title: UMI_4C_mz_NrKO_2


title: DEHPB7


title: UMI_4C_mz_NrKO_1


title: UMI_4C_mz_NrKO_3


title: DEHPB8


title: UMI_4C_mz_EKO_3


title: ctrA5


title: B4203DEHP


title: UMI_4C_mz_EKO_2


title: ctrA6


title: UMI_4C_mz_EKO_4


title: SpRY-ABE-HTT-3_OT5_biorep_3

source_name: kidney

extract_protocol:
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency
Samples for DNA editing were extracted using Qiagen's DNeasy DNA extraction kit
Samples for total RNA editing were extracted using Qiagen's RNeasy plus kit
For Illumina Miseq experiments, libraries were constructed with the nextera XT indexing primer kits as per manufacturer's instructions
Targeted genomic and exon high throughput sequencing with nextera indexing primers

value: kidney

value: epithelial

value: Lipofectamine 2000 transfected split_SpRY-ABE-HTT-3 plasmid


title: UMI_4C_mz_EKO_1

value: Embryo


title: SpRY-ABE-HTT-3_OT5_biorep_2


title: UMI_4C_mz_DHet_6


title: SpRY-ABE-HTT-3_OT4_biorep_3


title: UMI_4C_mz_DHet_4


title: DEHPB6


title: SpRY-ABE-HTT-3_OT5_biorep_1


title: SpRY-ABE-HTT-3_OT3_biorep_3


title: UMI_L2C_z_NrKO_6


title: SpRY-ABE-HTT-3_OT4_biorep_2


title: UMI_4C_mz_DHet_1


title: SpRY-ABE-HTT-3_OT4_biorep_1


title: UMI_L2C_z_NrKO_5


title: Couptf1_WT_1


title: UMI_4C_mz_DHet_5


title: UMI_4C_mz_DHet_2


title: SpRY-ABE-HTT-3_OT3_biorep_2


title: SpRY-ABE-HTT-3_OT2_biorep_3


title: UMI_L2C_z_NrKO_2


title: UMI_L2C_z_NrKO_1


title: UMI_L2C_z_NrKO_3


title: UMI_L2C_z_NrKO_4


title: UMI_L2C_z_NrHet_7


title: SpRY-ABE-HTT-3_OT3_biorep_1


title: UMI_4C_mz_DHet_3


title: UMI_L2C_z_NrHet_6


title: UMI_L2C_z_NrHet_4


title: UMI_L2C_z_NrHet_3


title: KA5

city: Guiyang

first: Jiaqi

last: Tang

state: Guizhou

address: No. 9, Beijing Road, Guiyang City, Guizhou Province

institute: GUIZHOU MEDCIAL UNIVERSITY

data_processing:
The raw data obtained from data filtering sequencing is filtered using SOAPnuke (v1.5.6) to remove 1) reads containing connectors (connector contamination); 2) Reads with an unknown base N content greater than 5%; 3) Low quality reads (reads with a mass value less than 15 and a proportion greater than 20% of the total base of the reads are considered low-quality reads), resulting in clean data.
Use HISAT2 (v2.1.0) software to align clean data to the reference genome. Use Bowtie2 (v2.3.4.3) to align clean data to the reference gene set.
Use RSEM (v1.3.1) software for gene expression quantification, and use pheatmap (v1.0.8) to draw clustering heatmaps of gene expression levels in different samples. Use DESeq2 (v1.4.5) (or DEGseq or Poisson Dis) for differential gene detection, with Q value ≤ 0.05 or FDR ≤ 0.001.
KEGG and GO enrichment analysis further explores the gene functions related to phenotypic changes. Based on hypergeometric testing, we used Phyper（ https://en.wikipedia.org/wiki/Hypergeometric_distributionopen GO differential genes in a new window（ http://www.geneontology.org/open In new window and KEGG（ https://www.kegg.jp/open Enrichment analysis in new window, with Qvalue ≤ 0.05 as the threshold, is defined as significant enrichment in candidate genes that meet this condition.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: The file format is TXT file,and the content includes C (control, n=3), M (model, n=3), QU (quercetin, n=3), MY (myricetin, n=3), KA (kaempferol, n=3)

source_name: liver

extract_protocol:
2.1 Sample crushing and fragmentation 2.1.1 Grinding machine crushing 2.1.1.1 Take an appropriate amount of tissue sample into the corresponding numbered grinding and fragmentation tube. 2.1.1.2 Add 1.5mL of TRIzol lysis solution, put it into a tissue grinder, grind for 30 seconds, take it out and let it stand for 5 minutes to fully lyse the tissue cells. 2.1.2 Liquid nitrogen grinding and crushing 2.1.2.1 Divide 1.5mL TRIzol cracking solution into 2mL EP tubes. 2.1.2.2 Take an appropriate amount of tissue sample and grind it into powder under liquid nitrogen protection, then transfer it into the lysis solution. Let it stand flat for 5 minutes to fully lyse the tissue cells. 2.2 Sample Extraction and Purification 2.2.1 Centrifuge the ground and crushed tissue samples (cell samples do not require centrifugation) at 4 ° C and 12000 × g for 5 minutes. 2.2.2 Transfer the supernatant into an EP tube containing 300 µ L chloroform/isoamyl alcohol (24:1), invert and shake vigorously to mix well; 2.2.3 Centrifuge at 4 ℃ and 12000 × g for 8 minutes. If the middle layer is thick and the aqueous phase is turbid, the supernatant volume of chloroform/isoamyl alcohol (24:1) can be used for another extraction. 2.2.4 Suck the supernatant into a new 1.5 mL centrifuge tube, add 2/3 of the volume of the supernatant isopropanol (trace tissue or trace cell samples, 2 µ L 5mg/mL glycogen assisted precipitation can be added during precipitation), gently invert and mix, and place in a -20 ℃ refrigerator for more than 2 hours. 2.2.5 Centrifuge at 17500 × g for 25 minutes at 4 ℃, discard the supernatant, wash with 0.9 mL of 75% ethanol, invert the suspension and precipitate, and centrifuge at 17500 × g for 3 minutes at 4 ℃ (depending on the precipitation situation, wash again with 75% ethanol and centrifuge at 17500 × g for 3 minutes at 4 ℃). 2.2.7 Discard the supernatant, centrifuge briefly, then remove any residual liquid and let it dry for 3-5 minutes. Dissolve the precipitate in 20-200 μ L DEPC water or RNase free water.
2.1 Sample testing: Select the corresponding testing method for quality inspection based on the requirements of the sample and product. 2.2 mRNA isolation: Take a certain amount of RNA sample, denature it at appropriate temperature to open its secondary structure, and enrich mRNA using oligo (dT) magnetic beads. 2.3 mRNA Interruption: Add a disruption reagent to the mRNA obtained in the previous step, react at appropriate temperature for a certain period of time, and fragment the mRNA. 2.4 cDNA synthesis: Prepare a one strand synthesis reaction system and set up a reaction program to synthesize one strand of cDNA; Prepare a double stranded synthesis reaction system and set up a reaction program to synthesize double stranded cDNA. 2.5 End repair, addition of "A" and adapter connection to prepare a reaction system, and setting up a reaction program to repair the double stranded cDNA end, and adding an A base at the 3 'end; Prepare a connector connection reaction system and set up a reaction program to connect the connector to cDNA. 2.6 Prepare a PCR reaction system and set up a reaction program to amplify the product. 2.7 Library inspection: Select the corresponding testing method according to product requirements to conduct quality inspection on the library. 2.8 Cyclization: After denaturing the PCR product into a single strand, a cyclization reaction system is prepared and the reaction program is set to obtain a single stranded circular product. The linear DNA molecules that have not been cyclized are digested. 2.9 On machine sequencing: Single stranded circular DNA molecules replicate through rolling rings to form a DNA nanosphere (DNB) containing multiple copies. The obtained DNBs were subjected to high-density DNA nanochip technology and added to the network of small pores on the chip for sequencing using a combined probe anchored polymerization technique (cPAS).

value: liver

value: WT

value: Mice were fed a high-fat diet for 6 weeks and kaempferol(KA) at 100 mg/kg/day via oral gavage


title: KA8


title: UMI_L2C_z_NrHet_2


title: MY7

value: Mice were fed a high-fat diet for 6 weeks and myricetin(MY) at 75 mg/kg/day via oral gavage


title: KA3


title: UMI_L2C_z_NrHet_5


title: UMI_L2C_mz_DKO_5


title: SpRY-ABE-HTT-3_OT2_biorep_2


title: MY8


title: SpRY-ABE-HTT-3_OT2_biorep_1


title: E2C_mz_NrHet_4


title: QU5

value: Mice  were fed a high-fat diet for 6 weeks and quercetin(QU) at 200 mg/kg/day via oral gavage


title: MY5


title: UMI_L2C_z_NrHet_1


title: UMI_L2C_mz_DKO_6


title: QU8


title: UMI_L2C_mz_DKO_4


title: UMI_L2C_mz_DKO_2


title: UMI_L2C_mz_DKO_3


title: CBE-HTT-4_OT8_biorep_3

value: Lipofectamine 2000 transfected split_CBE-HTT-4 plasmid


title: SpRY-ABE-HTT-3_OT1_biorep_1


title: SpRY-ABE-HTT-3_OT1_biorep_3


title: QU2


title: SpRY-ABE-HTT-3_OT1_biorep_2


title: UMI_L2C_mz_DKO_1


title: M5

value: Mice were fed a high-fat diet (HFD) for 6 weeks, consisting of 10% lard, 10% egg yolk powder, 1% cholesterol, 0.2% sodium cholate, and 78.8% standard feed components


title: CBE-HTT-4_OT8_biorep_2


title: UMI_L2C_mz_NrKO_10


title: M2


title: UMI_L2C_mz_NrKO_9


title: UMI_L2C_mz_NrKO_7


title: M1


title: CBE-HTT-4_OT8_biorep_1


title: UMI_L2C_mz_NrKO_8


title: UMI_L2C_mz_NrKO_5


title: UMI_L2C_mz_NrKO_4


title: CBE-HTT-4_OT7_biorep_2


title: UMI_L2C_mz_NrKO_6


title: UMI_L2C_mz_NrKO_2


title: C2

value: Mice were fed a normal diet with standard feed for 6 weeks


title: UMI_L2C_mz_NrKO_3


title: UMI_L2C_mz_NrKO_1


title: CBE-HTT-4_OT7_biorep_1


title: C1


title: UMI_L2C_mz_EKO_10


title: CBE-HTT-4_OT6_biorep_3


title: UMI_L2C_mz_EKO_7


title: UMI_L2C_mz_EKO_8


title: CBE-HTT-4_OT7_biorep_3


title: UMI_L2C_mz_EKO_6


title: CBE-HTT-4_OT6_biorep_2


title: C3


title: CBE-HTT-4_OT6_biorep_1


title: UMI_L2C_mz_EKO_4


title: UMI_L2C_mz_EKO_5


title: UMI_L2C_mz_EKO_3


title: psmb1 mutants, 72hpf, biological replicate 4, cranial mylz2+ cells

city: Boston

first: Bess

last: Miller

state: MA

address: 77 Avenue Louis Pasteur

institute: BWH

description:
mylz2 M4
mylz2_raw_counts.txt

data_processing:
Reads were aligned to the GRCz11 reference assembly using STAR (Dobin et al., 2013) and differential gene expression analysis was performed with DESeq2 (Love et al., 2014).
Assembly: GRCz11
Supplementary files format and content: text file with raw counts for each sample for sox10 samples
Supplementary files format and content: text file with raw counts for each sample for mylz2 samples

organism: Danio rerio

source_name: cranial mylz2+ cells (muscle)

growth_protocol: Embryos were raised in E3 at 28.5C until 72hpf.

extract_protocol:
20-25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase (Sigma-Aldrich 05401119001), and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation, samples were pipetted 20-25 times every 8-10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β-mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit (Qiagen 74004). For RNA-seq on sox10:kaede+ cells, 7000 cells were sorted per sample. For RNA-seq on mylz2+ cells, 1500 cells were sorted per sample.
The SMART-Seq HT kit was used for full-length cDNA synthesis and amplification (Takara, San Jose, CA, USA), and the Illumina Nextera XT kit (Illumina, San Diego, CA, USA) was used for sequencing library preparation.

value: cranial mylz2+ cells (muscle)


title: CBE-HTT-4_OT5_biorep_2


title: CBE-HTT-4_OT5_biorep_1


title: UMI_L2C_mz_EKO_1


title: psmb1 mutants, 72hpf, biological replicate 3, cranial mylz2+ cells

description:
mylz2 M2
mylz2_raw_counts.txt


title: UMI_L2C_mz_EKO_2


title: UMI_L2C_mz_DHet_7


title: UMI_L2C_mz_EKO_9


title: CBE-HTT-4_OT4_biorep_3


title: psmb1 wild-type/heterozygous 72hpf, biological replicate 4, cranial mylz2+ cells

description:
mylz2 WH4
mylz2_raw_counts.txt


title: 23 -dox TC71 3

type: RNA

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

country: Germany

institute: German Cancer Research Center (DKFZ)

description:
TC71shEF1#3
Dox_no

hyb_protocol: Affymetrix Clariom D Array one-color based hybridization protocol, cDNA samples were hybridized at 45°C for 16 h on separate Affymetrix Human Clariom D™ Arrays

scan_protocol: Affymetrix GeneChip 3000 Scanner

data_processing:
Data were processed with Transcriptome Analysis Console (version 4.0) using the SST-RMA analysis algorithm
Clariom_D_Human.r1.pgf
Clariom_D_Human.r1.mps

label: biotin

source_name: Ewing sarcoma cell line

label_protocol: Affymetrix GeneChip WT PLUS Reagent Kit, according to the manufacturer's protocol

growth_protocol: For refined culture conditions, all cell lines were cultured in HPLMax, supplemented with 7% FCS tested to be dox-free (Sigma-Aldrich, Germany), and penicillin and streptomycin (final concentrations 100 units/mL and 100 μg/mL, respectively; Merck, Germany) in tissue culture flasks and plates (Sarstedt, Germany) that were previously coated with high gel-strength agar (Serva) to generate ultra-low attachment conditions for spheroid formation20. Agar was prepared at a 1,5% concentration, autoclaved and stored at 4°C. For agar coating, the agar solution was heated until boiling in a microwave and then mixed in a 1:1 dilution with HPLMax Medium. T-25 culture flasks (Sarstedt, Germany) were filled with 2 ml of this dilution and solidified for 2 h at room temperature (RT). Coated flasks were either directly used or stored at 4°C for max 2 weeks.   In both culture conditions, cells were incubated at 37°C and 5% CO2 in a fully humidified environment. Cells were subcultured in ratios 1:2 to 1:8 after detachment with trypsin/EDTA (Biochrom) and spinning down the detached cells. Mycoplasma contamination was ruled out regularly by nested PCR with cell supernatant of each experiment.

extract_protocol: For RNA extraction, the NucleoSpin RNA kit from Macherey-Nagel (Duren, Germany) was used following the manufacturer’s protocol.

treatment_protocol: 96h Dox or no Dox

value: physiologic condition (HPLMmax, 3D, 7% FCS)


title: 22 +dox TC71 2

description:
TC71shEF1#3
Dox_yes


title: 20 +dox TC71 1

description:
TC71shEF1#3
Dox_yes


title: 21 -dox TC71 2

description:
TC71shEF1#3
Dox_no


title: 24 +dox TC71 3

description:
TC71shEF1#3
Dox_yes


title: CBE-HTT-4_OT4_biorep_2


title: 19 -dox TC71 1

description:
TC71shEF1#3
Dox_no


title: psmb1 wild-type/heterozygous 72hpf, biological replicate 3, cranial mylz2+ cells

description:
mylz2 WH3
mylz2_raw_counts.txt


title: CBE-HTT-4_OT4_biorep_1


title: UMI_L2C_mz_DHet_5


title: UMI_L2C_mz_DHet_6


title: 18 +dox TC106 3

description:
TC106shEE
Dox_yes


title: CBE-HTT-4_OT3_biorep_3


title: psmb1 wild-type/heterozygous 72hpf, biological replicate 2, cranial mylz2+ cells

description:
mylz2 WH2
mylz2_raw_counts.txt


title: UMI_L2C_mz_DHet_4


title: psmb1 wild-type/heterozygous 72hpf, biological replicate 1, cranial mylz2+ cells

description:
mylz2 WH1
mylz2_raw_counts.txt


title: psmb1 mutants, 72hpf, biological replicate 1, cranial mylz2+ cells

description:
mylz2 M1
mylz2_raw_counts.txt


title: UMI_L2C_mz_DHet_3


title: CBE-HTT-4_OT3_biorep_2


title: CBE-HTT-4_OT5_biorep_3


title: e0082798-51f8-4ecb-b7b1-c701d8ee6843

city: La Jolla

first: Timothy

middle: D

last: Arthur

address: 9500 Gilman Drive #0761

department: Pediatrics

institute: UCSD

description: RNA-seq for UDID148

data_processing:
RNA-seq: To measure gene expression in the 8 CVPC samples, we obtained raw counts in transcript per million bp (TPM) as previously described. Briefly, FASTQ files were aligned to the hg19 reference human genome using with STAR v.2.7.3 and GencodeV.34lift37 with parameters: --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --alignIntronMin 20  --alignIntronMax 1000000 --alignMatesGapMax 1000000. Next, the BAM files were sorted and indexed using sambamba v0.6.7, and duplicates were marked using bammarkduplicates from the biobambam software. To quantify gene expression (TPM), we used RSEM version 1.2.20  with the following parameters: rsem-calculate-expression –bam --estimate-rspd --paired-end --forward-prob 0. RNA-seq sample quality was analyzed with samtools stats, idxstats, and Picard RNA Metrics.
ATAC-seq: The 16 FASTQ files were aligned to the hg19 reference genome with STAR using the following parameters; --outFilterMultimapNmax 20, -- outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --seedSearchStartLmax 20, -- outFilterScoreMinOverLread 0.1, outFilterMatchNminOverLread 0.1. Sample mate coordinates were filled using samtools fixmate and duplicates were marked using samtools markdup. We then removed poorly mapped reads, fragments < 38bp,  fragments  > 2,000 bp, and reads that did not map to autosomal or sex chromosomes with samtools view. Finally, we removed reads in the blacklisted regions (https://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg19-human/wgEncodeHg19ConsensusSignalArtifactRegions.bed.gz) using bedtools intersect with the v parameter. Narrow peaks were called using MACS2 on each of the 8 BAM files individually, using the following parameters; -f BAMPE -g hs --nomodel --shift -100 --extsize 200 --call-summits –q 0.01. We merged the peak bed files from the 8 ATAC-seq samples, then removed peaks that were only present in one sample which resulted in 119,794 reference peaks. For each sample, we counted the number of reads in the reference peaks using featureCounts.
Assembly: hg19
Supplementary files format and content: RNA-seq: RSEM TPM measurements
Supplementary files format and content: ATAC-seq: Counts for reference narrow peaks

source_name: iPSC-derived cardiovascular progenitors

growth_protocol: iPSC lines from four unrelated individuals recruited as part of the iPSCORE project were previously differentiated into iPSC-CVPCs using small molecules and enriched using metabolic selection with lactate (Table S1). The CVPCs were harvested at day 25, which we and others have previously shown represent fetal cardiac cells, and cryopreserved at -80° C. The cryopreserved CVPCs (day 25) were then thawed, plated at a density of 2.5x105/cm2 cells on Matrigel (Corning) coated 6-well plates, and allowed 72 hours for recovery and expansion.

extract_protocol:
RNA-seq: We extracted total RNA from lysed pellets frozen in RLT Plus buffer (collected on day 29) using the Quick-RNA™ MiniPrep Kit (Zymo Research), assessed quality to make sure RNA Integrity number (RIN) was 7.5 or greater. ATAC-seq: ATAC-seq samples were processed as previously described in detail25. Briefly, frozen nuclear pellets of 1x105 CVPC were thawed on ice and tagmented in total volume of 25μl in permeabilization buffer containing digitonin (10mM Tris-HCl pH 7.5, 10mM NaCl, 3mM MgCl2, 0.01% digitonin) and 2.5μl of Tn5 from Nextera DNA Library Preparation Kit (Illumina) for 45-75min at 37°C in a thermomixer (500 RPM shaking).
RNA-seq: We prepared indexed libraries using the Illumina TruSeq stranded mRNA kit and sequenced with 150 bp paired-end reads on an Illumina HiSeq 4000 (mean = 91.4M reads). ATAC-seq: To eliminate confounding effects due to index hopping, all libraries within a pool were indexed with unique pairs of i7 and i5 barcodes. Libraries were amplified for 12 cycles using NEBNext® High-Fidelity 2X PCR Master Mix (NEB) in total volume of 25µl in the presence of 800nM of barcoded primers (400nM each) custom synthesized by Integrated DNA Technologies (IDT) and sequenced with 150-bp paired end reads on a HiSeq4000 (mean = 112.9M reads).
One RNA-seq and ATAC-seq library was generated for each sample. Four CVPCs with 2 treatments = 8 RNA-seq and 8 ATAC-seq samples.

treatment_protocol: On day 28 (three days after thawing), CVPCs were treated with 100 nM human recombinant IFN-γ (ThermoFisher) for 24h. On day 29, control and IFN-γ-treated CVPC samples (eight in total) were harvested.

value: iPSC-derived cardiovascular progenitors

value: IFNg


title: 17 -dox TC106 3

description:
TC106shEE
Dox_no


title: CBE-HTT-4_OT3_biorep_1


title: UMI_L2C_mz_DHet_2


title: 16 +dox TC106 2

description:
TC106shEE
Dox_yes


title: e2660158-529f-4812-9a4f-82e46eb0fe82

description: RNA-seq for UDID148

value: Untreated Control


title: 15 -dox TC106 2

description:
TC106shEE
Dox_no


title: CBE-HTT-4_OT2_biorep_3

value: kidney


title: 14 +dox TC106 1

description:
TC106shEE
Dox_yes


title: CBE-HTT-4_OT2_biorep_2

value: epithelial


title: CBE-HTT-4_OT2_biorep_1


title: 13 -dox TC106 1

description:
TC106shEE
Dox_no


title: 0f449a51-5eb0-4bb4-ba7a-288fef87cf1a

description: RNA-seq for UDID088


title: 8C_mz_DKO_9


title: 8C_mz_DKO_10


title: ed95483f-22c2-47d5-830f-609dcb78d80f

description: RNA-seq for UDID088


title: 85c676f7-a023-4149-8798-3de51fdf7645

description: RNA-seq for UDID076


title: 8C_mz_DKO_8


title: 7b7436b8-7a7a-43cf-b8a0-1ecda20e7553

description: RNA-seq for UDID076


title: 002cdced-2528-4506-a8a9-11228a93355c

description: RNA-seq for UDID006


title: CBE-HTT-4_OT1_biorep_2


title: 8C_mz_DKO_6


title: 10 +dox SKNMC 2

description:
SKNMCshEF1#4
Dox_yes


title: 95cbd7c7-778b-4feb-8cd5-4e1291e6ff20

description: RNA-seq for UDID006


title: 9 -dox SKNMC 2

description:
SKNMCshEF1#4
Dox_no


title: split_SpRY-ABE-HTT-3_cDNA_biorep_4

extract_protocol:
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment, splice junction quantification, sashimi plot analysis on IGV
Samples for DNA editing were extracted using Qiagen's DNeasy DNA extraction kit
Samples for total RNA editing were extracted using Qiagen's RNeasy plus kit
For Illumina Miseq experiments, libraries were constructed with the nextera XT indexing primer kits as per manufacturer's instructions
Targeted genomic and exon high throughput sequencing with nextera indexing primers

value: Lipofectamine 2000 transfected full length_SpRY-ABE-HTT-3 plasmid


title: 11 -dox SKNMC 3

description:
SKNMCshEF1#4
Dox_no


title: UMI_L2C_mz_DHet_1

value: Embryo


title: 8 +dox SKNMC 1

description:
SKNMCshEF1#4
Dox_yes


title: 8C_mz_DKO_5


title: ae4183e9-563b-4187-98a5-ce920183a94d

description: ATAC-seq for UDID148


title: full-length_SpRY-ABE-HTT-3_cDNA_biorep_2


title: 7 -dox SKNMC 1

description:
SKNMCshEF1#4
Dox_no


title: 8C_mz_DKO_4


title: full-length_SpRY-ABE-HTT-3_cDNA_biorep_1


title: 12 +dox SKNMC 3

description:
SKNMCshEF1#4
Dox_yes


title: 8C_mz_DKO_3


title: 6 +dox MHH 3

description:
MHHES1shEF1#8
Dox_yes


title: ctrA4

value: F0-corn oil

value: female

value: OVA

value: Splenic CD11c DC


title: 6cb549ee-a086-427a-a58a-b38f8e5164ac

description: ATAC-seq for UDID006


title: 5 -dox MHH 3

description:
MHHES1shEF1#8
Dox_no


title: 8C_mz_DKO_2


title: 8C_mz_DKO_7


title: CBE-HTT-4_OT1_biorep_1


title: 73813519-84f0-446a-8e78-68c3e96cd4dc

description: ATAC-seq for UDID076


title: 8C_mz_DKO_1


title: 6d96d550-39b9-4ee7-b6e4-ad5692232305

description: ATAC-seq for UDID148


title: 8C_mz_NrKO_10


title: 6638a01a-73be-486f-9d0e-1e9ff7c3dcc1

description: ATAC-seq for UDID006


title: 6b36c7f9-4084-4763-b6ca-a54bb9dfc6c6

description: ATAC-seq for UDID088


title: 3 -dox MHH 2

description:
MHHES1shEF1#8
Dox_no


title: CBE-HTT-4_OT1_biorep_3


title: 4a9408b0-453b-4fe7-8f59-72c3e1312153

description: ATAC-seq for UDID088


title: 4 +dox MHH 2

description:
MHHES1shEF1#8
Dox_yes


title: split_SpRY-ABE-HTT-3_cDNA_biorep_2

value: Lipofectamine 2000 transfected split_SpRY-ABE-HTT-3 plasmid


title: 8C_mz_NrKO_8


title: split_SpRY-ABE-HTT-3_cDNA_biorep_1


title: 8C_mz_NrKO_7


title: Liver mac, CDAA-tdTnegtive-rep1, RNAseq

first: zixin

last: liu

address: 320 Yueyang road, Life Science Research Building A2112

institute: Center for Excellence in Molecular Cell Science

description: BGI

data_processing:
1. RNAseq: Filtered reads were aligned against the Ensembl mouse genome version mm10 (GRCm38) using Hisat2 (v0.1.6-beta) with default parameters. The number of reads aligning to genes was counted with the HTSeq (v2.0.1) tool. Only reads mapping at least partially inside exons were included and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
2. scRNAseq: Each single-cell RNA sequencing (scRNA-seq) dataset underwent processing using the CellRanger pipeline (v6.1.1). This included alignment to the customized mouse reference genome (mm10), alignment filtering, barcode counting, and UMI counting.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol:
After killing the mice, 30 ml of HBSS (Invitrogen, 14175103) was perfused through the portal vein, and then a portion of the liver tissue was placed in cold HBSS containing 0.4 mg/ml pronase (Roche, 10165921001) and 1 mg/ml collagenase type IV (Worthington, LS004188). The livers were then cut into small pieces and incubated in cold HBSS (Invitrogen, 14026126) containing 0.5 mg/ml pronase, 1 mg/ml collagenase type I (Gibco, 17100017), 1 mg/ml collagenase type IV and 50μg/ml DNase I (Worthington, LS002139) in 10 ml HBSS digested at 37 °C with shaking for 30 min. Liver samples were filtered through a 70 μm cell strainer. Nonsubstantial cells were then isolated by gradient centrifugation (1500 g, 20 min) between two density pads of 25% and 50% Percoll (Sigma, P4937-500ML). After isolation and centrifugation at 4 °C, 1 ml of erythrocyte lysis buffer (eBioscience, 00-4333-57) was added and centrifuged for 5 min at room temperature. To stop the reaction, 9 ml of cold PBS was added and centrifuged at 700 g for 5 min at 4 °C and the supernatant was discarded. After lysis of erythrocytes, the cells were washed twice with PBS for the next step. Dissociated hepatic nonparenchymal cells were resuspended in an appropriate amount of buffer containing 1% Fc block (Catalog No. 14-0161, eBioscience) and incubated for 5 minutes at room temperature to block non-specific antigens on the cell surface. Cells were then stained with fluorescence-conjugated antibodies for 30 min at 4 °C. All antibodies are commercially available: CD45-FITC (eBioscience, Cat# 11-0451, 1:200); CD45-APC (eBioscience, Cat# 17-0451-82, 1:200); CD31-FITC (eBioscience, Cat# 11-0311-82, 1:40); CD31-APC (eBioscience, Cat# 170311-82, 1:40); F4/80 PE-Cy7 (biolegend, Cat# 123114, 1:200); F4/80-APC (eBioscience, Cat# 17-4801-82, 1:200); CD11b PE-Cy7 (eBioscience, Cat# 25-0112-82, 1:200); CD11b-APC (eBioscience, Cat# 17-0112-81, 1:200). After staining, cells were washed with PBS to elute excess antibody and then centrifuged at 700 g for 5 min at 4 °C to obtain cells; cell pellets were resuspended in 1 ml of PBS with 1 μl of DAPI and 1 μl of DNase I. DAPI was used to differentiate between dead and live cells, and DNase I was used to avoiding cell adhesion. Flow cytometry analysis was performed using a Beckman CytoFLEX LX, and cell sorting was performed using a SonyMA900, with individual cells collected in a collection buffer (2% FBS in DMEM).
1.RNAseq: The extraction of total RNA from isolated cells was conducted using the RNeasy Micro kit (QIAGEN, GER) following the manufacturer's instructions. Briefly, cells underwent treatment with Buffer RL and 70% ethanol. The resulting mixture was then transferred to a RNeasy MinElute spin column and centrifuged at ≥ 8,000 g for 15 seconds. Subsequent steps involved the addition of Buffer RW1, DNase I, Buffer RPE, and 80% ethanol, followed by additional centrifugation. The RNA-containing RNeasy MinElute spin column was placed in a new 2 ml collection tube, centrifuged with the lid open at full speed for 5 minutes to dry the membrane, and then transferred to a new 1.5 ml tube with RNase-free water. Finally, tubes were centrifuged for 1 minute at full speed to elute the RNA. Qualification and quantification of total RNA were performed using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA). High-quality RNA was employed for mRNA library construction. For mRNA library construction, limited RNA (more than 200 pg, high-quality) underwent amplification with oligo-dT and dNTPs. After incubation at 72 ℃ and immediate cooling on ice, reverse transcription to cDNA based on polyA tail was performed. The template was switched to the 5' end of the RNA, and full-length cDNA was generated by PCR. The average molecule length of the PCR product was determined using the Agilent 2100 bioanalyzer instrument. Purified cDNA was fragmented into small pieces with fragment buffer by PCR, and the product was purified and selected by the Agencourt AMPure XPMedium kit (Thermo Fisher Scientific, USA). cDNA quantification was conducted using the Agilent Technologies 2100 bioanalyzer. The double-stranded PCR product, post-QC, was heat denatured and circularized by the splint oligo sequence. The single-strand circle DNA (ssCir DNA) constituted the final library. To ensure the high quality of the sequencing data, two methods were employed for library quantification: determination of the average molecule length using the Agilent 2100 bioanalyzer instrument and quantification of the library using real-time quantitative PCR (qRT-PCR). The final library was amplified with phi29 (Thermo Fisher Scientific, MA, USA) to produce DNA nanoballs (DNB), each containing more than 300 copies of one molecular. DNBs were loaded into the patterned nanoarray, and single-end 50 bases reads were generated on the MGISEQ-2000RS platform (BGI-Shenzhen, China). 2. scRNAseq: Hepatic non-parenchymal cells, isolated from indicated p16-tdT, SnEC-gTracer, or SnMø-cTracer mice, were individually loaded into the 10x Chromium controller to generate GEMs. Subsequently, these GEMs were processed into single-cell 5ʹ gene expression libraries using the Chromium Single Cell 5ʹ Library Kit (v2 Chemistry). All samples were pooled for sequencing on the Illumina NovaSeq 6000 PE150 platform.

value: Liver

value: Macrophage

value: CDAA


title: SpRY-ABE_GFP_cDNA_biorep_2

value: Lipofectamine 2000 transfected GFP plasmid


title: 8C_mz_NrKO_6


title: 2 +dox MHH 1

description:
MHHES1shEF1#8
Dox_yes

value: physiologic condition (HPLMmax, 3D, 7% FCS)


title: 1 - dox MHH 1

description:
MHHES1shEF1#8
Dox_no


title: Liver mac, CDAA-tdTnegtive-rep3, RNAseq

description: BGI


title: split_SpRY-ABE-HTT-3_cDNA_biorep_3


title: SpRY-ABE_GFP_cDNA_biorep_1


title: Homosapiens,adultnasalmucosa, male, S00242459, baseline

city: Oxford

first: Andre

last: Goncalves

address: Old Road Campus, Roosevelt Dr, Headington

department: Department of Paediatrics

country: United Kingdom

institute: University of Oxford

data_processing:
Quality control of raw sequencing data was done using FastQC tool. Mapping to a human reference genome assembly (GRCh38) was done using STAR 2.5.0a(71). Read counts from the resulting binary alignment map (BAM) files were obtained with featureCounts(72) using a general transfer format (GTF) gene annotation from the Ensembl database(73)The R/Bioconductor package DESeq2 (version 1.34.0) was used to identify differentially expressed genes among the samples after removing absent features (zero counts in more than 75% of samples). Genes with a p-value of < 0.05 and an absolute fold-change of > 2.0 were identified as differentially expressed.
Assembly: GRCh38
Supplementary files format and content: log2cpm_expression; raw_expression

source_name: nasal cells

extract_protocol:
Nasal cells were collected in RLT (QIAGEN) and stored at -80°C until extraction. RNA extraction (RNeasy; QIAGEN), sample integrity assessment (Bioanalyzer; Agilent 2100)
Library preparation and RNA sequencing (BGISEQ-500RS) were performed at the Beijing Genome Institute.

value: nasal cells

value: male

tag: timepoint

value: baseline

tag: carriage status

value: POS

tag: smorkers

value: N

tag: htn

value: Y

tag: renal disease

tag: previous malignancy

tag: statin

tag: charlson index


title: Liver mac, CDAA-tdTnegtive-rep2, RNAseq

description: BGI

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: 144b90ad-4280-44f8-8a5d-c973a064c406

description: ATAC-seq for UDID076

value: iPSC-derived cardiovascular progenitors

value: Untreated Control


title: full-length_SpRY-ABE-HTT-3_gDNA_biorep_2

value: kidney

tag: cell line

value: epithelial

value: Lipofectamine 2000 transfected full length_SpRY-ABE-HTT-3 plasmid


title: Homosapiens,adultnasalmucosa, female, S00246155, D9

tag: age

tag: Sex

value: female


title: Homosapiens,adultnasalmucosa, female, S00245236, D2


title: Liver mac, CDAA-tdTpositive-rep3, RNAseq

description: BGI

value: Liver


title: split_SpRY-ABE-HTT-3_gDNA_biorep_3

value: Lipofectamine 2000 transfected split_SpRY-ABE-HTT-3 plasmid


title: 8C_mz_NrKO_5

value: Embryo

tag: date

tag: developmental stage


title: Homosapiens,adultnasalmucosa, female, S00245067, baseline

tag: timepoint


title: Homosapiens,adultnasalmucosa, male, S00245069, D9

tag: carriage status


title: SpRY-ABE_GFP_gDNA_biorep_1

value: Lipofectamine 2000 transfected GFP plasmid


title: 8C_mz_NrKO_9


title: 8C_mz_NrKO_1


title: split_SpRY-ABE-HTT-3_gDNA_biorep_2


title: Liver mac, CDAA-tdTpositive-rep2, RNAseq

description: BGI

value: Macrophage

value: CDAA


title: Liver mac, CCl4-tdTnegtive-rep2, RNAseq

description: BGI


title: Homosapiens,adultnasalmucosa, male, S00244393, D2

value: nasal cells

value: male

tag: smorkers


title: 8C_mz_NrKO_4


title: Liver mac, CCl4-tdTnegtive-rep1, RNAseq

description: BGI


title: Homosapiens,adultnasalmucosa, male, S00243388, D9

value: POS

tag: htn


title: Liver mac, CDAA-tdTpositive-rep1, RNAseq

description: BGI


title: Liver mac, CCl4-tdTnegtive-rep3, RNAseq

description: BGI


title: 8C_mz_NrKO_3


title: full-length_SpRY-ABE-HTT-3_gDNA_biorep_1


title: SpRY-ABE_GFP_gDNA_biorep_2


title: Homosapiens,adultnasalmucosa, male, S00243686, baseline

value: baseline

value: N

tag: renal disease


title: 8C_mz_NrKO_2


title: 8C_mz_EKO_9


title: split_SpRY-ABE-HTT-3_gDNA_biorep_1


title: 8C_mz_EKO_8


title: 8C_mz_EKO_10


title: Liver mac, CCl4-tdTpositive-rep3, RNAseq

description: BGI


title: Homosapiens,adultnasalmucosa, female, S00244392, D2

tag: previous malignancy


title: Clone_CBE-HTT-4_cDNA_biorep_1

value: Lipofectamine 2000 transfected and puromycin selected  clone of CBE-HTT-4 plasmid


title: WT293T_cDNA_biorep_2

value: native HEK293T cells


title: full-length_CBE-HTT-4_cDNA-biorep_3

value: kidney

value: Lipofectamine 2000 transfected full length_CBE-HTT-4 plasmid


title: Liver endo, CDAA-tdTnegtive-rep3, RNAseq

description: BGI

value: Endothelial cell


title: Liver mac, CCl4-tdTpositive-rep2, RNAseq

description: BGI


title: Homosapiens,adultnasalmucosa, female, S00243685, baseline

value: female

tag: statin


title: Liver mac, CCl4-tdTpositive-rep1, RNAseq

description: BGI

value: Liver


title: 8C_mz_EKO_5


title: Homosapiens,adultnasalmucosa, male, S00243383, D2

value: Y

tag: charlson index


title: Homosapiens,adultnasalmucosa, male, S00242981, baseline


title: WT293T_cDNA_biorep_1

tag: tissue

value: epithelial


title: Liver endo, CDAA-tdTnegtive-rep2, RNAseq

description: BGI

tag: cell type


title: full-length_CBE-HTT-4_cDNA-biorep_2

tag: genotype


title: Homosapiens,adultnasalmucosa, female, S00243387, D9


title: full-length_CBE-HTT-4_cDNA-biorep_1

tag: treatment


title: Homosapiens,adultnasalmucosa, female, S00245068, D9


title: 8C_mz_EKO_4

value: Embryo


title: Liver endo, CDAA-tdTpositive-rep3, RNAseq

description: BGI


title: Homosapiens,adultnasalmucosa, female, S00242467, baseline


title: Clone_CBE-HTT-4_cDNA_biorep_2

tag: cell line


title: split_CBE-HTT-4_cDNA_biorep_3

value: Lipofectamine 2000 transfected split_CBE-HTT-4 plasmid


title: Liver endo, CDAA-tdTnegtive-rep1, RNAseq

description: BGI

value: CDAA


title: Liver endo, CDAA-tdTpositive-rep2, RNAseq

description: BGI


title: 8C_mz_EKO_3


title: 8C_mz_EKO_6


title: 8C_mz_EKO_7


title: Homosapiens,adultnasalmucosa, female, S00237294, D9

value: nasal cells

tag: age

value: NEG


title: Liver endo, CDAA-tdTpositive-rep1, RNAseq

description: BGI


title: split_CBE-HTT-4_cDNA_biorep_2


title: 8C_mz_EKO_1


title: Liver endo, CCl4-tdTnegtive-rep3, RNAseq

description: BGI


title: 8C_mz_DHet_21


title: CBE_GFP control_ cDNA_biorep_2

value: Lipofectamine 2000 transfected GFP plasmid


title: Liver endo, CCl4-tdTnegtive-rep2, RNAseq

description: BGI


title: split_CBE-HTT-4_cDNA_biorep_1


title: Homosapiens,adultnasalmucosa, female, S00236426, D2

tag: Sex


title: Homosapiens,adultnasalmucosa, female, S00235875, baseline

value: baseline


title: CBE_GFP control_ cDNA_biorep_1


title: full-length_CBE-HTT-4_gDNA_biorep_3


title: Homosapiens,adultnasalmucosa, male, S00238316, D2

value: male

value: N


title: Liver endo, CCl4-tdTpositive-rep3, RNAseq

description: BGI


title: 8C_mz_DHet_19

tag: date


title: 8C_mz_EKO_2

tag: developmental stage


title: full-length_CBE-HTT-4_gDNA_biorep_2


title: Liver endo, CCl4-tdTpositive-rep2, RNAseq

description: BGI


title: full-length_CBE-HTT-4_gDNA_biorep_1


title: 8C_mz_DHet_18


title: Homosapiens,adultnasalmucosa, male, S00237731, baseline

tag: timepoint


title: Liver endo, CCl4-tdTpositive-rep1, RNAseq

description: BGI


title: 8C_mz_DHet_17


title: Homosapiens,adultnasalmucosa, male, S00237298, D9

tag: carriage status


title: 8C_mz_DHet_16


title: Homosapiens,adultnasalmucosa, male, S00236425, D2

tag: smorkers


title: split_CBE-HTT-4_gDNA_biorep_3


title: 8C_mz_DHet_14


title: Biliary epithelial cells PC depleted rep 3

city: Edinburgh

first: Stuart

last: Forbes

address: 5 Little France Drive

department: Centre for Regenerative Medicine

institute: The University of Edinburgh

description: PC depleted

data_processing:
The normalization and data analysis were performed according to the manufacturers instructions using R
Normalization uses the average expression of the housekeeping genes B2m and Gapdh. Housekeeping genes were chosen by the RT2 Profiler PCR Array software (GeneGlobe; Qiagen)
Target gene signals were normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control (i.e., PC depleted/Control) ratios.

label: SYBR Green

source_name: Mouse biliary epithelial cells

extract_protocol: Mouse livers were perfused with saline, dissected down to approximately 2-4 mm3 portions and covered with a mix of 0.125 mg/ml Collagenase (Sigma-Aldrich) and Dispase (Life Technologies) in 2% FCS Advanced DMEM/F-12 (Thermo Fisher). This mix was incubated 1 hour at 37ºC and individual bile ducts were manually picked up, cleaned twice with 5%FCS DMEM/F-12 (Thermo Fisher) and transferred to Matrigel (Corning) for subsequent culture. Bile ducts were grown as three-dimensional organoids for 4 to 5 passages and then transferred to a two-dimensional culture in plates covered with 1mg/ml collagen (Sigma).

value: Biliary epithelial cells


title: Homosapiens,adultnasalmucosa, female, S00237297, D9

tag: htn


title: split_CBE-HTT-4_gDNA_biorep_1

value: kidney


title: Homosapiens,adultnasalmucosa, male, S00234871, baseline

tag: renal disease


title: 8C_mz_DHet_20


title: Homosapiens,adultnasalmucosa, male, S00240140, D9

tag: previous malignancy


title: Liver endo, CCl4-tdTnegtive-rep1, RNAseq

description: BGI


title: split_CBE-HTT-4_gDNA_biorep_2


title: 8C_mz_DHet_15


title: Biliary epithelial cells PC depleted rep 2

description: PC depleted


title: Homosapiens,adultnasalmucosa, female, S00236427, D2

tag: statin


title: Biliary epithelial cells PC depleted rep 1

description: PC depleted


title: 8C_mz_DHet_12


title: Homosapiens,adultnasalmucosa, female, S00234870, baseline

tag: charlson index


title: CBE_GFP control_ gDNA_biorep_2

tag: tissue


title: CBE_GFP control_ gDNA_biorep_1

tag: cell type


title: Biliary epithelial cells PC competent rep 3

description: Control


title: Homosapiens,adultnasalmucosa, male, S00238222, D9

value: POS


title: 8C_mz_DHet_10

tag: genotype


title: Homosapiens,adultnasalmucosa, male, S00237122, D2


title: 8C_mz_DHet_11


title: Biliary epithelial cells PC competent rep 2

description: Control

tag: treatment


title: Biliary epithelial cells PC competent rep 1

description: Control


title: CBE_GFP control_ gDNA_biorep_3

tag: cell line


title: psmb1 mutants, 72hpf, biological replicate 4, cranial sox10+ cells

description:
sox 10 M4
sox10_raw_counts.txt

source_name: cranial sox10+ cells (neural crest/chondrocytes)


title: CeD6_NT_Control2d_BCR

city: Stanford

first: Antonio

last: Santos

state: California

address: 265 Campus Dr.

department: Hematology

institute: Stanford University

description: 10X Genomics

data_processing:
Sequences from scRNA-seq were processed with Cell Ranger (v.3.0.2) software (10X Genomics) with demultiplexing, UMI (unique molecular identifier) collapsing and alignment to the GRCh38 human transcriptome. scRNA-seq data from CLIP versus gliadin treatment were loaded into Seurat objects following their standard pipeline
Assembly: GRCh38
Supplementary files format and content: mtx
Supplementary files format and content: clonotypes, contig_annotations

source_name: organoid

extract_protocol:
Organoids were dissociated in 2030 units ml-1 collagenase IV (Worthington, LS004212) at 37°C for 40 min, washed twice in PBS, and digested in 400 μg ml-1 Liberase-TL (Roche, 5401020001) and 416 units ml-1 DNase I (Worthington, LS006328) at 37°C for 30 min with intermittent shaking. Samples were washed twice in FACS buffer (0.6 mM EDTA (Invitrogen, AM9261), 5% FBS, in PBS)
FACS-isolated organoid cells were subjected to droplet based scRNA-seq with the 10X Genomics Chromium single cell 5’ platform, with or without single-cell TCR/Ig V(D)J library, per the manufacturer’s protocol using Chromium Next GEM Single Cell 5' Kit v2 (PN-1000263), Library Construction Kit (PN-1000190), Chromium Single Cell Human TCR Amplification Kit (PN-1000252) and Chromium Single Cell Human BCR Amplification Kit (PN-1000253). Cell capture, library construction, and sequencing were performed as previously described

tag: patient

tag: batch

tag: stimulation

value: CLIP 2d

value: organoid

tag: culture medium

value: WENR

value: EpCAM+ and CD45+


title: 8C_mz_DHet_8

tag: date

tag: developmental stage


title: psmb1 mutants, 72hpf, biological replicate 1, cranial sox10+ cells

description:
sox 10 M1
sox10_raw_counts.txt

value: cranial sox10+ cells (neural crest/chondrocytes)


title: 8C_mz_DHet_13

value: Embryo


title: Homosapiens,adultnasalmucosa, female, S00237295, D9

tag: age

tag: Sex

value: female

tag: timepoint

tag: carriage status

tag: smorkers

value: Y


title: CeD6_D2_Gliadin2d_BCR

description: 10X Genomics

value: Gliadin 2d


title: 8C_mz_DHet_7


title: CeD6_D2_Gliadin2d_TCR

description: 10X Genomics


title: 8C_mz_DHet_9


title: Homosapiens,adultnasalmucosa, female, S00236424, D2

value: nasal cells

value: NEG

tag: htn

tag: renal disease

tag: previous malignancy

tag: statin

tag: charlson index


title: 8C_mz_DHet_6

tag: tissue

tag: genotype


title: psmb1 mutants, 72hpf, biological replicate 3, cranial sox10+ cells

description:
sox 10 M3
sox10_raw_counts.txt


title: psmb1 wild-type/heterozygous 72hpf, biological replicate 3, cranial sox10+ cells

description:
sox 10 WH3
sox10_raw_counts.txt


title: Homosapiens,adultnasalmucosa, female, S00234869, baseline

tag: cell type

value: baseline


title: Homosapiens,adultnasalmucosa, female, S00236148, D9


title: 8C_mz_DHet_5


title: CeD5_NT_Control2d_TCR

description: 10X Genomics

tag: patient

tag: batch

tag: stimulation

value: control


title: psmb1 wild-type/heterozygous 72hpf, biological replicate 2, cranial sox10+ cells

description:
sox 10 WH2
sox10_raw_counts.txt


title: CeD5_NT_Control2d_BCR

description: 10X Genomics

tag: culture medium


title: CeD5_D2_Gliadin2d_BCR

description: 10X Genomics


title: 8C_mz_DHet_4

tag: date

tag: developmental stage


title: Homosapiens,adultnasalmucosa, male, S00236150, baseline

tag: age

tag: Sex

value: male

tag: timepoint

value: N


title: CeD5_D2_Gliadin2d_TCR

description: 10X Genomics


title: psmb1 wild-type/heterozygous 72hpf, biological replicate 1, cranial sox10+ cells

description:
sox 10 WH1
sox10_raw_counts.txt


title: Homosapiens,adultnasalmucosa, female, S00234376, baseline

tag: carriage status

tag: smorkers

tag: htn


title: cardiomyocytes, AKG3

city: chong qing

first: Miao

last: Tian

address: Changjiang zhilu

institute: daping hospital

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quaility sequence using fastep 0.18.0(-q 20 -u 50 -N 15 -l 50)
Trimmed sequence reads were mapped to Ensembl_release111 using HISAT2 v2.1.0, parameter set to "-rna-strandness RF" and the remaining parameters are default.
Read count extraction and normalization were performed using RSEM 1.2.19.
RNAs differential expression analysis was performed by DESeq2 software(v1.20.0).
Assembly: Ensembl_release109
Supplementary files format and content: The C-vs-A.all.annot.xls.txt file includes raw counts for each Sample
Supplementary files format and content: The C-vs-A.all.annot.xls.txt file includes FPKM values for each Sample

source_name: cardiomyocytes

growth_protocol: The cardiomyocytes were isolated from P21 mice hearts using Langendorff’s method.

extract_protocol:
RNA was harvested using Trizol.
RNA libraries for RNA-seq were prepared using Hieff NGS® Ultima Dual mode mRNA Library Prep Kit （12309ES YeasenYeasen）following manufacture's protocols.

treatment_protocol: P21 mice have received daily α-KG injection(300 mg/kg/d) (Sigma)or PBS (Control) for 2 weeks.

value: cardiomyocytes

value: WT

tag: treatment

value: alpha-KG injection


title: CeD6_NT_Control2d_TCR

description: 10X Genomics

value: CLIP 2d

value: organoid


title: 8C_mz_DHet_3


title: psmb1 wild-type/heterozygous 72hpf, biological replicate 4, cranial sox10+ cells

description:
sox 10 WH4
sox10_raw_counts.txt


title: 8C_mz_DHet_2


title: cardiomyocytes, AKG2


title: 8C_mz_DHet_1


title: CeD4_GL2D_Gliadin2d_TCR

description: 10X Genomics

value: WENR


title: cardiomyocytes, AKG1


title: CeD4_GL2D_Gliadin2d_BCR

description: 10X Genomics


title: Homosapiens,adultnasalmucosa, male, S00234317, D9

value: POS

tag: renal disease

tag: previous malignancy

tag: statin

tag: charlson index


title: Homosapiens,adultnasalmucosa, male, S00232387, baseline

tag: cell type


title: CeD4_CA2D_CLIP2d_BCR

description: 10X Genomics

tag: patient

tag: batch

tag: tissue


title: Homosapiens,adultnasalmucosa, male, S00240139, D9


title: cardiomyocytes, Control3

tag: genotype

value: PBS injection


title: 4C_mz_DKO_10

value: Embryo

tag: date

tag: developmental stage


title: 4C_mz_DKO_9


title: CeD4_CA2D_CLIP2d_TCR

description: 10X Genomics

tag: stimulation

tag: culture medium


title: Homosapiens,adultnasalmucosa, male, S00238315, D2

tag: age

tag: Sex

tag: timepoint

tag: carriage status

value: Y


title: cardiomyocytes, Control2

tag: treatment


title: Homosapiens,adultnasalmucosa, male, S00237730, baseline

tag: smorkers

tag: htn

tag: renal disease

tag: previous malignancy


title: Homosapiens,adultnasalmucosa, female, S00235272, D2

tag: cell type

value: female

tag: statin

tag: charlson index


title: CeD3_AS9_TCR

description: 10X Genomics

tag: patient

tag: batch

tag: tissue


title: 4C_mz_DKO_8

tag: date

tag: genotype

tag: developmental stage


title: CeD2_AS8_TCR

description: 10X Genomics

tag: stimulation

tag: culture medium


title: cardiomyocytes, Control1


title: 4C_mz_DKO_7


title: Liver, MacTracer-DT, scRNAseq

description:
SnMø-cTracer
10X Genomics

value: Liver

value: non-parenchymal cells

value: SnMo-cTracer

value: DT


title: Homosapiens,adultnasalmucosa, female, S00234308, D9

value: nasal cells

tag: age

tag: Sex

tag: timepoint

tag: carriage status

value: NEG


title: Liver, MacTracer-PBS, scRNAseq

description:
SnMø-cTracer
10X Genomics

tag: treatment

value: PBS


title: Homosapiens,adultnasalmucosa, female, S00233464, D2

tag: smorkers

value: N

tag: htn

tag: renal disease

tag: previous malignancy


title: 4C_mz_DKO_6


title: 4C_mz_DKO_5


title: Homosapiens,adultnasalmucosa, female, S00232388, baseline

tag: cell type

value: baseline

tag: statin

tag: charlson index


title: CeD1_Sample5_Gliadin2d_TCR

description: 10X Genomics

tag: patient

tag: batch

value: Gliadin 2d

tag: tissue

value: Live single cells


title: CeD1_Sample3_CLIP2d_TCR

description: 10X Genomics

tag: stimulation

value: CLIP 2d

value: organoid

value: WENR


title: 4C_mz_DKO_4

value: Embryo

tag: date

tag: genotype

tag: developmental stage


title: Liver, ECTracer-PBS, scRNAseq

description: 10X Genomics

value: SnEC-gTracer


title: CeD1_Sample1_freshtissue_TCR

description: 10X Genomics

source_name: fresh tissue

value: fresh tissue

tag: culture medium


title: Homosapiens,adultnasalmucosa, female, S00233467, D9

tag: age

tag: Sex

value: female

tag: timepoint

tag: carriage status


title: 4C_mz_DKO_3


title: Homosapiens,adultnasalmucosa, female, S00231885, baseline

tag: smorkers

tag: htn

tag: renal disease


title: Homosapiens,adultnasalmucosa, female, S00232654, D2

tag: cell type

tag: previous malignancy

tag: statin


title: Liver, CDAA, scRNAseq

description: 10X Genomics

value: Liver

value: non-parenchymal cells

tag: treatment

value: CDAA


title: 4C_mz_DKO_2

tag: tissue


title: Late_NoMo_rep_D

city: Bozeman

first: Eric

last: Boyd

address: 1 Montana State University

institute: Montana State University

data_processing:
RNA paired-end reads were processed to remove adapter sequences and filter reads before reads were aligned to the reference MmS2 genome using Bowtie2 to generate transcriptional profiles using the HT-Seq software program.
Assembly: ASM1158v1
Supplementary files format and content: tab-delimited text files for each sample contain raw count numbers for genes

organism: Methanococcus maripaludis

source_name: Methanogens

growth_protocol: MmS2 was grown under N2-fixing conditions in defined basal medium as described in Payne et al. 2023 (Communications Biology)

extract_protocol:
Cultures of MmS2 were harvested during late log phase (24 hrs. for molybdate and molybdenite conditions, 30 hrs. for the no Mo condition) of growth for RNA extraction. Cultures were brought into an anaerobic chamber and were vacuum-filtered over 0.2 µm Supor membrane filters that were then transferred into 2 mL microcentrifuge tubes. The tubes and their contents were immediately flash frozen in liquid nitrogen and stored at -80 °C. Total RNA was extracted from the filters using the Trizol method. DNA contamination was checked by performing PCR amplification using archaeal-specific 16S rRNA primers.
rRNA depletion was conducted using custom Methanococcus-specific oligonucleotides, and sequenced on the Illumina NovaSeq platform with 2x150 bp paired-end reads at the University of Wisconsin sequencing center.

treatment_protocol: MmS2 was provided with 0.4% w/v sodium formate, 10 mM acetate, and Wolfe’s vitamins. However, the composition of our trace metals solution was modified to exclude molybdate and ferrous iron; sodium molybdate was added separately to a final concentration of 5 µM. Ferrous iron was added in the form of synthetic mackinawite to a final concentration of 10 µM. In the case of MoS2 experiments, Fe was provided as FeCl2 to a final concentration of 25 µM . Where specified, HS- was added to a final concentration of 1 mM or a mixture of sodium thiosulfate and L-cysteine was added as S source to final concentrations of 1 mM each. All cultures were incubated at 37 °C and over-pressurized with 2.04 atm of 80:20 N2:CO2. MmS2 was passaged five times (2% v/v inoculum; ~3x10^8 total cells in 75 mL) in medium without Mo to induce Mo limitation prior to use as an inoculum.

value: Methanogens


title: Liver, CSAA, scRNAseq

description: 10X Genomics

value: CSAA


title: 4C_mz_DKO_1


title: Late_NoMo_rep_C


title: CeD2_AS7_TCR

description: 10X Genomics

tag: patient

tag: batch

tag: stimulation


title: Late_NoMo_rep_B


title: Liver, oil, scRNAseq

description: 10X Genomics

tag: genotype

value: Oil


title: 4C_mz_NrKO_4

tag: date

tag: developmental stage


title: Homosapiens,adultnasalmucosa, female, S00233469, D2

value: nasal cells

tag: age

tag: Sex

value: NEG

value: N

tag: charlson index


title: Homosapiens,adultnasalmucosa, female, S00232389, baseline

tag: timepoint

value: baseline

tag: carriage status

tag: smorkers


title: Liver, CCl4, scRNAseq

description: 10X Genomics

tag: cell type


title: Liver, ECTracer-DT, scRNAseq

description: 10X Genomics

value: DT


title: Late_MoS4_rep_D


title: 4C_mz_NrKO_5


title: 4C_mz_NrKO_3


title: Homosapiens,adultnasalmucosa, female, S00235277, D9

value: POS

tag: htn

tag: renal disease

tag: previous malignancy


title: Late_MoS4_rep_C


title: 4C_mz_NrKO_2

tag: tissue


title: 4C_mz_NrKO_1


title: Late_MoS4_rep_B


title: Homosapiens,adultnasalmucosa, female, S00234312, D2

tag: statin


title: Late_NoMo_rep_A


title: Homosapiens,adultnasalmucosa, female, S00233190, baseline


title: Homosapiens,adultnasalmucosa, male, S00227838, D9

value: male

value: Y


title: Homosapiens,adultnasalmucosa, female, S00234309, D9