title: ChIP-seq ZBTB43 15.5 dpc mouse prospermatogonia 491K cells

city: Grand Rapids

first: Piroska

middle: E

last: Szabó

state: MI

address: 333 Bostwick ave NE

department: Epigenetics

institute: Van Andel Institute

description:
1IP43_vs_control_log2ratio.bw
igg_as_control_S1IP43.bed
input_as_control_S1IP43.bed

data_processing:
Deep sequencing: Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). 150 bp, paired end sequencing was performed on an Illumina NovaSeq sequencer using a 150 bp high-output sequencing kit (v2) (Illumina Inc., San Diego, CA, USA) to a minimum depth of 40 M reads/library. Base calling was done by Illumina NextSeq Control Software (NCS) v2.0 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.
Reads were trimmed using Trim Galore v0.6.0 (https://github.com/FelixKrueger/TrimGalore) then were aligned to the mm10 genome using bwa mem v0.7.17, using default parameters for both steps. Duplicate alignments were marked using SAMBLASTER v0.1.24 with the parameter, “--addMateTags”. Alignments were filtered using samtools view v1.9 with the parameters, “-q 30 -F 2828 -f 2” and removing mitochondrial alignments. Peaks were called using MACS2 v 2.2.7.1 with the parameters, “-f BAMPE -g mm -q 0.05 --keep-dup 1” and the corresponding input or IgG samples as control. Peaks overlapping ENCODE blacklist v2 regions were removed using bedtools intersect v2.29.2 with the “-v” option.
DeepTools v3.4.3 was used to generate bigWig files. For single-sample bigWig files, bamCoverage was run with the parameters, ‘--binSize 10 --normalizeUsing “CPM” --samFlagInclude 64 --extendReads’. For bigWig files comparing IP to IgG, bamCompare was run with the parameters ‘--extendReads --binSize 10 --samFlagExclude 1024 --samFlagInclude 64’ and specifying the ENCODE blacklist v2 19 using ‘--blackListFileName’.
Assembly: mm10
Supplementary files format and content: BigWig files using counts-per-million normalization.
Supplementary files format and content: BED files containing peaks called by MACS2.

source_name: prospermatogonia

extract_protocol:
ChIP-seq of prospermatogonia. Purification of fetal male germ cells and somatic cells of the testis: To obtain fetuses for germ cell purification, C57Bl/6J females were crossed with OG2 (Szabo et al., 2002) males (Oct4-EGFPTg/Tg; Zbtb43+/+). Testicles were dissected from the resulting male fetuses at 15.5 days post coitum (dpc), and were dissociated to single cell suspension using trypsin digestion and trituration as described earlier (Szabo et al., 2002). Up to 8 testes were digested in 150 µl 0.25% trypsin (including 0.5 % BSA) at 36 °C for 15 min, tapping gently every 5 min. The trypsin reaction was stopped by adding 450 µl 20 % FBS in M2 medium (Cat. No. M7167 Sigma). The EGFP+ germ cells were purified by flow cytometry using a Beckman Coulter MoFlo Astrios sorter.
Library preparation: The library was prepared with NEBNext® Ultra™ II DNA Library Prep Kit (New England Biolabs, Cat. No. E7645S) according to the manufacturer’s protocol as described online (dx.doi.org/10.17504/protocols.io.wvgfe3w). Briefly, end preparation, adapter ligation and PCR amplification with index primers was performed using the captured DNA. The library was cleaned up before sequencing using 1 X Ampure beads twice to remove the excess adaptors.

value: prospermatogonia

tag: antibody

value: Wild type

tag: dev stage

value: fetus


title: ChIP-seq Input 15.5 dpc mouse prospermatogonia 491K cells

status: Public on Apr 14 2022

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: tissue

tag: genotype

tag: Sex

value: male

tag: strain

tag: age


title: ChIP-seq ZBTB43 15.5 dpc mouse prospermatogonia 100K cells

description:
5IP43_vs_control_log2ratio.bw
igg_as_control_S5IP43.bed
input_as_control_S5IP43.bed


title: ChIP-seq Input 15.5 dpc mouse prospermatogonia 100K cells


title: CBS-/-(5) CBS5-1

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

library_source: transcriptomic

data_processing:
Read trimming (Trimmomatic)
Short read alignment (STAR)
Alignment file sorting and indexing (samtools)
Read counting (featureCounts)
Assembly: Dm6
Supplementary files format and content: First column: Flybase gene identifier, second column — counts per million (non-normalized gene expression value)

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: mixed

extract_protocol:
Three biological replicates of 5-day-old naive males were collected for each transcriptome analysis. For each replicate, total RNA was isolated from approximately 100 heads of naïve males collected by decapitation of Drosophila male on an ice-cooled surface. The extraction was made using RNAzol RT (Molecular Research Center, USA) according to the company’s protocol. The concentration and quality of RNA was determined via Qubit Fluorometer (Invitrogen) and an Agilent BioAnalyzer 2100 respectively using RNA 6000 nano kit. For each of three biological replicates taken for libraries 100 heads were collected. For libraries RNA with Integrity Number (RIN) no less than 8 was taken.
Illumina NEB Next Ultra II Directional RNA Library Prep Kit (NEB, USA) was used for mRNA libraries preparation. The sequencing was performed on the Illumina NextSeq 500 platform. For each library sequencing provided around 15-20 million reads.

tag: cell line

value: mixed

tag: cell type

value: bulk

tag: treatment

value: no

tag: time

value: Day 5


title: ChIP-seq IgG control15.5 dpc mouse prospermatogonia 415K cells

description:
1IP43_vs_control_log2ratio.bw
igg_as_control_S1IP43.bed

value: IgG


title: Affinity-seq MBP-ZBTB43 Zbtb43+/+ normally methylated sperm DNA

data_processing:
Deep sequencing and data analysis: Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.) and Promega QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), 50 bp, paired end sequencing was performed on an Illumina NovaSeq6000 sequencer using an S1, 100 bp sequencing kit (Illumina Inc., San Diego, CA, USA) to a minimum depth of 30 M reads/library. Base calling was done by Illumina RTA3 and output of NextSeq Control Software (NCS) v2.0 was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.DNA-Protein affinity sequencing assay
Reads were aligned to the mm10 genome using bwa mem v0.7.17 with default parameters. Peaks were called for Affinity-seq samples using MACS2 callpeak v2.2.7.1 with default parameters, combining duplicate samples and using the corresponding MBP background samples as controls.
DeepTools v3.4.3 was used to generate bigWig files; bamCoverage was run with the parameters, ‘--binSize 10 --normalizeUsing “CPM” --samFlagInclude 64 --extendReads’. For heatmaps showing read coverage at ZBTB43 ChIP-seq peaks, the input BAM files were additionally filtered for consistency, using samtools view v1.9 with the parameters, “-q 30 -F 2828 -f 2”.
Assembly: mm10
Supplementary files format and content: BigWig files using counts-per-million normalization.
Supplementary files format and content: BED files containing peaks called by MACS2.

source_name: spermatozoa

extract_protocol:
Affinity capture. His-MBP-ZBTB43 recombinant protein was purified from E.coli against His tag and stored in dialysis buffer (50 mM HEPES pH 7.4, 50 % glycerol, 5 mM 2-mercaptoethanol) at -80 °C. Unmethylated genomic DNA was purified from mouse TKO ES cells (Dnmt1-/- Dnmt3a-/- Dnmt3b-/-) ES (clone19) RBRC No.: AES0146 (Tsumura et al., 2006) with phenol-chloroform extraction and ethanol precipitation, and was sonicated to an average fragment size of 200 bp using a Covaris E220 Evolution ultrasound sonicator. Fully methylated DNA was prepared using M.SssI (NEB, Cat. No. M0226M) in fragmented mouse lung genomic DNA. Sperm DNA was prepared from WT and ZBTB43 mutant adulut mice. His-MBP-ZBTB43 protein (His-MBP as background control)  was preincubated with MBP-magnetic beads (NEB, Cat. No. E8037S) at 4 °C for 90 min. To capture the ZBTB43 fraction, the fragmented mouse genomic DNA was mixed with the preincubated beads in a 200 µl reaction volume of 1 X binding buffer (10 mM Tris-HCl pH 7.8, 100 mM NaCl, 10 mM MgCl2, 0.05% NP40, 25 ng/µl BSA, 1 mM DTT, 0.05 mM ZnCl2) at 37 °C for 2 h. After incubation, the beads were washed with 1 X binding buffer 3 times to remove the unbound DNA. The bound DNA was eluted in 1 X elution buffer (10 mM Tris-HCl pH 8.0, 10mM EDTA, 500 mM NaCl, % SDS, 10 mM maltose), and was collected by ethanol precipitation. The precipitated DNA was stored in -80 °C before library preparation.
Library preparation: the library was prepared with NEBNext® Ultra™ II DNA Library Prep Kit (NEB Cat. No. E7645S) according to the manufacturer’s instructions as described online (dx.doi.org/10.17504/protocols.io.wvgfe3w). Briefly, end preparation, adapter ligation and PCR amplification with index primers was performed using the captured DNA. The library was cleaned up before sequencing using 0.9 X Ampure beads to remove the excess adaptors.

value: spermatozoa

value: adult

value: 2 months old


title: Affinity-seq MBP-ZBTB43 Zbtb43-/- hypomethylated sperm DNA


title: HCC827/GS_rep3

city: Hangzhou

first: linying

last: Wu

address: qingchun road

country: China

institute: Zhejiang University

data_processing:
Cutadapt was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Then sequence quality was verified using FastQC
We used Bowtie2 and Tophat2 to map reads to the genome of Homo sapiens
The mapped reads of each sample were assembled using StringTie
After the final transcriptome was generated, StringTie and Ballgownwas used to estimate the expression levels of all transcripts.
Assembly: hg18
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: lung adenocarcinoma cell line

growth_protocol: HCC827 cells were grown in recommended medium at 37℃ with 5% CO2 in humidified incubator.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure.
Approximately 1 ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA). And then we performed the single-end sequencing (36bp or 50bp ) on an Illumina Hiseq 2500 at the LC-BIO (Hangzhou, China) following the vendor’s recommended protocol.

treatment_protocol: The gefitinib resistant HCC827/GR cells were established by gradient dose treatment for parental cells more than 6 months.

value: exon 19 del

tag: drug sensitivity

value: gefitinib sensitive


title: HCC827/GS_rep2


title: ChIP-seq IgG control15.5 dpc mouse prospermatogonia 100K cells

description:
5IP43_vs_control_log2ratio.bw
igg_as_control_S5IP43.bed


title: HCC827/GR_rep1

value: gefitinib resistant


title: Affinity-seq MBP-ZBTB43 SssI methylated lung DNA replicate 2

description: SSSi.bed

source_name: lung

value: lung


title: HCC827/GR_rep3


title: HCC827/GR_rep2


title: Affinity-seq MBP background Zbtb43+/+ normally methylated sperm DNA


title: Affinity-seq MBP-ZBTB43 SssI methylated lung DNA replicate 1

description: SSSi.bed


title: HK16_U133Plus_2_16_Sh-WT1-1

type: RNA

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were nomalized by RMA with Parteck Genomic Suit 6.6

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cancer cell lines were grown in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal calf serum (FCS), 2mM L-glutamine, and 50 units/ml and 50 ug/ml of penicillin G and streptomycin respectively (final concentration).  When the cells reached 80% confluency in 100 mm dish, cells were treated with N3 and were transfected ShWT1. Total RNA was then isolated at 48 hours after induction using Qiagen RNeasy Mini kit according to the recommended protocol and the final concentration of total RNA was about 0.5 -1.0 ug/ml for each sample as measured by spectrophotometry.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Stardand cell culture

value: desmoplastic small round cell tumors (DSRCT) cell line

tag: genotype/variation


title: Affinity-seq MBP-ZBTB43 unmethylated TKO ES DNA replicate 2

description: TKN.bed

source_name: ES cell

value: ES cell

value: TKO ES

value: not applicable


title: Day1

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive, DUMC 3382, CIEMAS 2177A, Duke University, SOM

department: Molecular Genetics and Microbiology

institute: Duke University

description: Single-cell suspensions were loaded on the 10x Genomics system, and mRNA was converted to cDNA library. Samples from 3 donors were aggregated for further data processing.

data_processing:
Alignment, counting, filtering, of aggregated single cell RNA-Seq from 3 donors of Day1  and Day15 RBCs, using 10X Cellranger v5.0 with default parameters and forcing cells to 5000 for each.
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: raw read counts in gene-barcode matrix
Supplementary_files_format_and_content: Gene-barcode matrix in Market Exchange Format (MEX). Columns correspond to individual cells(barcodes), while rows correspond to genes.
Supplementary_files_format_and_content: Barcode sequences that correspond to column indices in matrix.mtx.
Supplementary_files_format_and_content: Gene id information that corresponds to row indices in matrix.mtx

source_name: Whole Blood

growth_protocol: Typical blood storage conditions in AS1 at 4C.

extract_protocol:
The stored RBCs were separated to individual GEM in Chromium.
Single-cell suspensions were loaded on the 10x Genomics system, and mRNA was converted to cDNA library.
Single-cell libraries were sequenced on HiSeq 2500. Libraries were sequenced in single index mode with the following read lengths: 26x8x125.

treatment_protocol: Typical blood storage conditions in AS1 at 4C for one and fifteen days.

value: Red blood cells


title: HK15_U133Plus_2_15_Sh-Con3

source_name: Sh-Con

value: Sh-Con


title: HK18_U133Plus_2_18_Sh-WT1-3


title: Day15


title: Larson_pooled_screen_data

city: CAMBRIDGE

first: Nicholas

last: Haradhvala

state: MA

address: 75 Ames St

institute: Broad Institute

data_processing:
Library strategy: genome wide crispr KO screen
poolQ v3.2.10 with parameters  --row-matcher exact  --col-matcher exact  --row-barcode-policy PREFIX:CACCG@6  --col-barcode-policy FIXED:0 --skip-unexpected-sequence-report  --compat
poolQ counts the occurrence of sgRNA barcodes per sample from pooled crispr KO experiments
sgRNA identity is extracted in the read1 fastq Larson_et_al.1.fastq.gz, and sample identity in the sample barcode file Larson_et_al.barcode_1.fastq.gz
Supplementary_files_format_and_content: tsv of sgRNA counts

source_name: glioblastoma cell line U87

growth_protocol: U87 cells were grown in EMEM + 10% FBS + 1% Pen/Strep in 15cm dishes and replated at confluence (~3-5e6 cells)

extract_protocol: CAR T-cells were removed by aspiration and the tumor cells were gently rinsed 4 times with PBS to remove any remaining CAR T-cells. The tumor cells were then passaged so that any remaining dying cells would not survive. After a 2-day recovery period, the tumor cells were rinsed once with PBS and harvested. Their DNA was isolated (NucleoSpin Blood XL, Macherey-Nagel) and prepared for PCR (Onestep PCR Inhibitor, Zymo Research) prior to processing for guide PCR amplification and sequencing by the Genetic Perturbation Platform (GPP) facility at the Broad Institute based on Broad recommended preparation protocols.

treatment_protocol: CAR T cells were added at a 1:10 ratio of CAR:tumor for 18 hours

value: glioblastoma cell line U87


title: HK14_U133Plus_2_14_Sh-Con2


title: HK17_U133Plus_2_17_Sh-WT1-2


title: HK13_U133Plus_2_13_Sh-Con1


title: Affinity-seq MBP background SssI methylated lung DNA replicate 2

description: SSSi.bed

value: Wild type

value: male


title: Affinity-seq MBP background unmethylated TKO ES DNA replicate 1

description: TKN.bed


title: Affinity-seq MBP background  SssI methylated lung DNA replicate 1

description: SSSi.bed


title: Affinity-seq MBP background unmethylated TKO ES DNA replicate 2

description: TKN.bed


title: CD102-MHCII+CSF1R+ Female 4

city: Edinburgh

first: Stephen

last: Jenkins

address: 47, Little France Crescent

department: Centre For Inflammation Research

country: United Kingdom

institute: University of Edinburgh

data_processing:
Sequence reads were trimmed using Cutadapt (vesion cutadapt-1.9.dev2)
Reads were aligned to the reference genome using STAR
Generation of counts: featureCounts (version1.5.1)
Differential gene expression analysis, DESeq2
Assembly: Mus musculus genome from Ensemble assebbly GRCm38, annotation version 84
Supplementary files format and content: tab-delimited text files include count values for each Sample ...

source_name: Peritoneal exudate cells

extract_protocol:
For each population, 25,000 cells were sorted into 500μl RLT buffer (Qiagen) and snap frozen on dry ice. RNA was isolated using the RNeasy Plus Micro kit (Qiagen), at which point triplicates of 25,000 cells for each population were pooled. 10 ng of total RNA were amplified and converted to cDNA using Ovation RNASeq System V2 (Nugen).
Ovation RNASeq System V2 was used to amplify DNA
Preparation of Truseq DNA Nano gel free library and sequencing using the Illumina HiSeq 4000 system (75PE) was performed by Edinburgh Genomics.

treatment_protocol: Peritoneal cavities were lavaged with RPMI containing 2mM EDTA and 10mM HEPES according to PMID29761387. Cells were stained with antibodies according to PMID29761387 and live single CD45+ SiglecF- CD19- CD3- Ly6G- CD11b+ CD102- Ly6C- CSF1R+ cells were FACS-sorted to >98% purity.

tag: gating strategy

value: single CD45+ SiglecF- CD19- CD3- Ly6G- CD11b+ CD102- MHCII+ Ly6C- CSF1R+

value: Female

value: Peritoneal exudate cells


title: CD102-MHCII+CSF1R+ Female 3


title: CD102-MHCII+CSF1R+ Male 4

value: Male


title: CD102-MHCII+CSF1R+ Female 1


title: CD102-MHCII+CSF1R+ Male 1


title: Affinity-seq MBP background Zbtb43-/- hypomethylated sperm DNA

value: spermatozoa

value: adult

value: 2 months old


title: Affinity-seq MBP-ZBTB43 unmethylated TKO ES DNA replicate 1

description: TKN.bed


title: rat DRG_A2

city: Athens

first: Oshri

last: Avraham

state: GA

address: 120 Cedar St

department: Cellular Biology

institute: University of Georgia

description: single cell

data_processing:
A digital expression matrix was obtained using the 10X Genomics Cell Ranger pipeline.
Quantification and statistical analysis were done with Partek Flow package (https://www.partek.com/partek-flow/).
Genome_build: Rnor_6.0, hg19
Supplementary_files_format_and_content: txt, mtx files containing the UMI count matrix

organism: Rattus norvegicus

source_name: L4, L5 DRG

extract_protocol:
Whole DRG’s were dissociated from rat with enzyme mix (Papain, Collagenase) to a single cell suspension, washed in 1X PBS+0.2%BSA solution, passed through a 40-micron cell strainer and FACS sorted using live/dead staining. For human DRG sample L4 lumbar DRG was removed from a 44 year old Asian female. The tissue was immediately snap-frozen and stored at -80C. For nuclei isolation, the entire DRG was processed into smaller pieces by cryopulverization using the CryoPrep. Tissue was then homogenized using EZ Nuclei Lysis Buffer with 0.5% RNasin, 0.5% SUPERase-In and 1mM DTT  or with CST buffer (NaCl2 146 mM, Tris HCl pH 7,5 10 mM, CaCl2 1mM, MgCl2 21 mM, 0.49% CHAP, 0.01% BSA, 0.5% SUPERasin-in, 0.5% RNasin Plus). The homogenate was filtered through a 50-micron filter. The samples were  centrifuged at 500g, 4ºC for 5 mins. The supernatant was removed and the pellet was resuspended in 1 mL of Nuclei Resuspension Buffer (NRB) consisting of 1x PBS, 1% Bovine Serum Albumin and 1% SUPERas-In followed by centrifugation. The final pellet was resuspended in 0.5 mL of NRB containing 6 μM DAPI and filtered through a 20 μm filter. Fluorescence Activated Nuclear Sorting (FANS) was performed to purify nuclei from debris on a FACSAria II (BD).
single-cell RNA-Seq libraries were prepared using GemCode Single-Cell 3′ Gel Bead and Library Kit (10x Genomics). polyA selection based RNA capture as per the manufacturer's instructions provided by 10X genomics platform.  Libraries were prepared as per manufacturer's insturctions provided by 10X genomics platform (https://www.10xgenomics.com/single-cell/). libraries were then constructed using standard instrutions of the 10x plaform.

value: Dorsal root ganglion (L4,5)

value: Adult


title: rat DRG_A1

description: single cell

source_name: L4 L5 DRG


title: cotreated replicate C

city: High Point

first: Heather

middle: Bennett

last: Miller

address: One University Parkway

department: Chemistry

institute: High Point University

data_processing:
Quality control of resulting reads included removing adapter-containing reads, removing reads where “N” was > 10%, and removing low-quality reads where the quality value of over 50% of the bases was ≤ 5.
The remaining reads were mapped to the reference genome (ATCC 43300) using Bowtie2.
Gene expression levels were quantified as fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM) and averaged among biological triplicate samples.
Genome_build: ATCC 43300
Supplementary_files_format_and_content: *_DEG.txt: Tab-delimited text files for all treatment comparison groups that contain all replicates, gene information, read counts, fpkm, log2fold change and adjusted pvalues.

organism: Staphylococcus aureus

source_name: bacterial cell total RNA

growth_protocol: S. aureus 43300 was purchased from the American Type Culture Collection. Cultures were grown overnight in CAMHB at 37 °C with shaking. Mid-log-phase cultures were diluted to 5 × 10^5 CFU mL–1 in CAMHB.

extract_protocol:
Total RNA was purified from 3mL of culture using a Qiagen RNeasy kit and Thermo's Turbo DNase kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The cell suspension (3 mL) was aliquoted into sterile culture tubes, and compound 8 was added to the appropriate concentration (≤25% of the compound MIC = 25 uM). Oxacillin was added to a separate culture tube at 4 ug/mL. Cotreatment consisted of both oxacillin (4 ug/mL) and compound 8 (25uM). Untreated cultures served as negative controls. These treatments continued for 1 hour while in the shaking incubator.

value: oxacillin and compound 8


title: cotreated replicate B


title: oxacillin treated replicate B

value: oxacillin, 4 ug/mL


title: compound 8 treated replicate B

value: compound 8, 25 uM


title: oxacillin treated replicate C


title: untreated replicate B

value: untreated


title: SynCre + IL-4R fl/fl neurons rep2

city: Mainz

first: Samantha

last: Schmaul

address: Langenbeckstr 1

department: Neurology

country: Germany

institute: University Medical Centre Mainz

description: S4 FlowCell with PE150 bp (300 cycles)

data_processing:
Raw RNAseq data were filtered with the fastp program (Chen et al., 2018) for eliminating low-quality reads. Parameters -g -x -p were set for polyG tail trimming, polyX tail trimming, and overrepresented sequence analysis
The quality of trimmed data was verified with the fastqc program (Babraham Bioinformatics).
Afterwards, data were aligned to the latest reference genome (GRCm39) using the long-read STAR aligner (Dobin et al., 2013).
Low-quality alignments were filtered out using SAMtools (Li et al., 2009).
The remaining high-quality alignments were quantified using StringTie (Pertea et al., 2015).
Statistical analysis of the gene counts were carried out with DESeq2 (Love et al., 2014) in R.
Gene ontology (GO) analysis was performed with clusterProfiler and DOSE and visualized with Enrichplot (Yu et al., 2015).
The database org.Mm.eg.db was used in R for annotating purposes; heatmaps were created with pheatmap package in R.
Assembly: GRCm39
Supplementary files format and content: TSV, raw counts of sequencing reads with gene coordinates
Supplementary files format and content: TSV, normalized abundance measurements with gene coordinates

source_name: brain

extract_protocol:
Brains were dissociated using the Adult Brain Dissociation Kit and Gentle Macs Octo Dissociator with Heaters (Miltenyi) according to the manufacturer’s protocol. Non-neuronal cells were removed using the Neuron Isolation Kit (Miltenyi).
RNA was isolated from murine neurons using the RNeasy® Micro Kit (Qiagen) according to the manufacturer’s instructions. Quantity of total RNA was measured using a Qubit 2.0 Fluorimeter (Invitrogen) and quality was assessed using a RNA 6000 Nano chip on a Bioanalyzer 2100 (Agilent Genomics). Only samples with RNA integrity numbers (RIN) ≥ 7 were included in library preparation. Sequencing libraries were prepared from 10 ng total RNA using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (New England Biolabs), according to the manufacturer’s protocol for polyA mRNA workflow. Quality of the cDNA library preparation was checked using the Agilent High Sensitivity DNA assay (Agilent) on a Bioanalyzer 2100 platform.

value: brain

value: neurons

value: Syn Cre+ x IL-4R fl/fl


title: SynCre + IL-4R fl/fl neurons rep3

description: S4 FlowCell with PE150 bp (300 cycles)


title: SynCre - IL-4R fl/fl neurons rep2

description: S4 FlowCell with PE150 bp (300 cycles)

value: Syn Cre- x IL-4R fl/fl


title: SynCre + IL-4R fl/fl neurons rep1

description: S4 FlowCell with PE150 bp (300 cycles)


title: cotreated replicate A


title: CD102-MHCII+CSF1R+ Male 3

value: single CD45+ SiglecF- CD19- CD3- Ly6G- CD11b+ CD102- MHCII+ Ly6C- CSF1R+


title: SynCre - IL-4R fl/fl neurons rep4

description: S4 FlowCell with PE150 bp (300 cycles)


title: untreated replicate A


title: SynCre - IL-4R fl/fl neurons rep3

description: S4 FlowCell with PE150 bp (300 cycles)


title: Male CD8 TILs, biological replicate 1, scRNAseq

city: Columbus

first: HYUNWOO

last: KWON

state: OH

address: 460 W 12th Ave

institute: The Ohio State University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Using the Cell Ranger software, we converted BCL files into FASTQ files, trimmed adapters and primer sequences, mapped reads to the mm10 reference genome, and quantified expression levels. In this step, to eliminate low-quality and dying cells, we filtered out cells with counts less than 200 and those with >5% mitochondrial counts. Then, we used the Seurat software for the downstream analysis, based on the count data obtained from Cell Ranger.
Assembly: mm10
Supplementary files format and content: CSV format, gene-cell raw count matrix and metadata for each cell

source_name: s.q. tumor

extract_protocol:
6 weeks old WT male and female C57BL/6 mice were inoculated subcutaneously with 5 x 10^5 MB49 tumor cells, which are a urothelial cell cancer cell line. On Day 10 post inoculation, single cell suspensions were prepared from the tumors after mechanical disruption and enzymatic digestion with 1 mg/mL Type IV Collagenase (Roche). Cells were strained through a 70 µM filter. Live tumor infiltrating CD8+ T cells (CD3+ CD8+ CD4-) were sorted on a BD FACSAria Ilu Cell Sorter and immediately processed for scRNA-seq.
Experimental procedures for scRNA-seq followed established techniques using the Chromium Single Cell 3’ Library V3 Kit (10x Genomics).  Briefly, FACS-sorted CD8+ T cells were loaded onto a 10X Genomics Chip A and emulsified with 3’ Single Cell GEM beads using a Chromium™ Controller. Libraries were constructed from the barcoded cDNAs

value: s.q. tumor

tag: injected cell line

value: Tumor-infiltrating CD8+ T cells

tag: host genotype

value: WT C57BL6

value: male

value: 6-8 weeks old


title: RAW_4C_seq_silencer_rp1

city: Nanjing

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

institute: Nanjing University

data_processing:
Library strategy: 4C-seq
4C-seq raw files (fastq, single-end) were first trimmed by the short reads. Then files were aligned to the NCBI37/mm9 version of the mouse reference genome, using bowtie2 with default parameters by pipe4C software.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Wig files contain the normalized tag counts in the specific chromosome.

source_name: RAW264.7 cells

growth_protocol: Mice RAW264.7 cells were maintained normal 10% FBS DMEM medium.

extract_protocol:
10^7 RAW 264.7 cells were re-suspended with 1ml lysis buffer for 10 minutes. Nuclei were re-suspended into 440 ul Milli-Q water and 60 ul of digestion buffer was added. The cell lysis mixture was then incubated at 37C for 2 hours in the shaker (900 rpm). 200U DpnII was added into the mixture three times. The lysis mixture was then incubated in the shaker overnight. The reaction mix was inactivated after overnight digestion by incubating at 65C for 20 min. The samples were then transferred to 50 ml Falcon tubes with 700 ul ligation buffer and 5.5 ml Milli-Q water. The samples were then supplemented with 100 U T4 ligase and incubated overnight at room temperature. After that, samples were de-crosslinked at 65C for 12 hours. The ligated DNA was then purified by the phenol-chloroform method, and further digested with NlaIII at 37C overnight. The restriction enzyme was then inactivated for 20 min at 65C. The DNA was further ligated at room temperature overnight. After the second ligation, the DNA was purified by QIAquick PCR purification kit.
4C-PCR products DNA was processed using Takara SMRTer ThruPLEX DNA-seq Kit. Briefly, DNA was end-repaired and ligated to stem-loop adaptors. Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.

treatment_protocol: RAW264.7 cells were harvested without any treatment.

value: Macrophage

value: BALB/c

tag: bait

value: Silencer

tag: sample type

value: Ctrl


title: RAW_4C_seq_silencer_rp2


title: Male CD8 TILs, biological replicate 3, scRNAseq

description: 10x Genomics


title: Male CD8 TILs, biological replicate 2, scRNAseq

description: 10x Genomics


title: compound 8 treated replicate C


title: SynCre - IL-4R fl/fl neurons rep1

description: S4 FlowCell with PE150 bp (300 cycles)


title: IgG_Ctrl_CutnRun

city: Cleveland

first: Evan

last: Deneris

state: Ohio

address: 2210 Circle Dr., Robbins E640

department: Neurosciences

institute: Case Western Reserve University

data_processing:
Library strategy: CUT&RUN
Illumina Casava 1.8.4 and 2.20 software used for basecalling.
ATAC-seq reads were filtered and mapped using the ENCODE uniform ATAC-seq processing pipeline
ChIPmentation reads were filtered and mapped using the ENCODE uniform ChIP-seq processing pipeline
CUT&RUN reads were filtered and mapped using the ENCODE uniform ChIP-seq processing pipeline. Peaks were called using SEACR.
ScATAC-seq and scRNA-seq datasets were processed using the 10X genomes cellranger pipeline and further processed using Seurat v4 and Signac.
Bam files were converted to bigWig files using deeptools bamCoverage normalizing to 1X genome coverage.
RNA-seq reads were filtered for low-quality sequence, then mapped to mm10 whole genome using hisat2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks and control samples were compared to DKO samples using cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: BED files are the consensus irreproducibility discovery rate (IDR) filtered peaks for each dataset. BigWig files are the filtered, uniquely mapped, and pooled reads that are normalized to 1X genome coverage. Mtx, barcodes, features, fragments for single cell data

source_name: hindbrain

growth_protocol: Brain tissue was taken from transgenic mice maintained under standard housing conditions.

extract_protocol:
CUT&RUN IgG purified DNA fragments were amplified using the NEB NEBNext Ultra II library kit.
Dissected tissue between the mid-hindbrain boundary to the spinal cord boundary of E11.5, E14.5, and E17.5 hindbrains from Pet1-Cre;Lmx1bfl/fl;Rosa-TdTomato, Pet1-Cre;Pet1fl/fl;Rosa-TdTomato, or Pet1-Cre;Pet1fl/fl;Lmx1bfl/fl;Rosa-TdTomato embryos. For ATAC-seq EYFP+ or tdTomato+ 5-HT neurons were sorted using a BD FACSAria I & SORP or Sony iCyt into PBS with 1% FBS. For RNA-seq, E17.5 tdTomato+ 5-HT  neurons from Pet1-Cre;Pet1fl/fl;Lmx1bfl/fl;Rosa-TdTomato (DKO) embryos were sorted using a BD FACSAria SORP into Trizol LS. For ChIPmentation, CUT&RUN, scATAC-seq, and scRNA-seq EYFP+ 5-HT  neurons from E14.5 Pet1-EYFP embryos were sorted using a BD FACSAria I & SORP into PBS with 1% FBS.

value: 5-HT neuron

value: wildtype; Pet1::EYFP


title: CD4+CD25highCD127low Treg SM + M rep2

city: Philadelphia

first: Ying

last: Shao

state: Pennsylvania

address: 3500 N Broad St, MERB1083A

institute: Temple University

data_processing:
FASTQC were used to check the quality of sequencing data. kallisto v0.44.0 and Rstudio were used to quantify abundances of transcripts.
Sequenced reads were mapped to Mus_musculus.GRCm38.cdna.all.fa using kallisto with parameters quant -i transcripts.idx -o output -b 100 reads_1.fq.gz.gz reads_2.fq.gz.gz reads_3 fq.gz reads_4.fq.gz.gz
Data were filtered using [rowSums(Txi_gene$counts)>=10,] as cutoff (done after DEG calculation).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include gene TPM (transcript per million) values for each Sample ...

source_name: spleen

extract_protocol:
Spleen singlet cell suspension were made, stained with anti-mouse CD4, CD25, CD127 antibodies, then CD4+CD25highCD127low cells were purified by Aria Cell Sorter directly into TRIzol, and RNA was harvested using miRNeasy Mini kit.
Total RNA libraries were prepared by RNA Library(T01), and Illumina sequencing PE150, 40M clean reads were generated for bioinformatic analysis.

tag: phenotype

value: wildtype

value: 8 weeks Smoke with 4 weeks morphine


title: untreated replicate C

value: untreated


title: CD4+CD25highCD127low Treg SM + M rep1


title: Female CD8 TILs, biological replicate 3, scRNAseq

description: 10x Genomics

tag: tissue

value: female


title: IgG_1_CutnRun

tag: genotype


title: compound 8 treated replicate A

value: compound 8, 25 uM


title: ChIPmentation_Input-3

data_processing:
Illumina Casava 1.8.4 and 2.20 software used for basecalling.
ATAC-seq reads were filtered and mapped using the ENCODE uniform ATAC-seq processing pipeline
ChIPmentation reads were filtered and mapped using the ENCODE uniform ChIP-seq processing pipeline
CUT&RUN reads were filtered and mapped using the ENCODE uniform ChIP-seq processing pipeline. Peaks were called using SEACR.
ScATAC-seq and scRNA-seq datasets were processed using the 10X genomes cellranger pipeline and further processed using Seurat v4 and Signac.
Bam files were converted to bigWig files using deeptools bamCoverage normalizing to 1X genome coverage.
RNA-seq reads were filtered for low-quality sequence, then mapped to mm10 whole genome using hisat2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks and control samples were compared to DKO samples using cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: BED files are the consensus irreproducibility discovery rate (IDR) filtered peaks for each dataset. BigWig files are the filtered, uniquely mapped, and pooled reads that are normalized to 1X genome coverage. Mtx, barcodes, features, fragments for single cell data

extract_protocol:
ChIP input DNA fragments were amplified into sequencing libraries using the ChIPmentation protocol that uses a Tn5 transposase mediated adapter ligation and amplification (Schmidl, et al. 2015).
Dissected tissue between the mid-hindbrain boundary to the spinal cord boundary of E11.5, E14.5, and E17.5 hindbrains from Pet1-Cre;Lmx1bfl/fl;Rosa-TdTomato, Pet1-Cre;Pet1fl/fl;Rosa-TdTomato, or Pet1-Cre;Pet1fl/fl;Lmx1bfl/fl;Rosa-TdTomato embryos. For ATAC-seq EYFP+ or tdTomato+ 5-HT neurons were sorted using a BD FACSAria I & SORP or Sony iCyt into PBS with 1% FBS. For RNA-seq, E17.5 tdTomato+ 5-HT  neurons from Pet1-Cre;Pet1fl/fl;Lmx1bfl/fl;Rosa-TdTomato (DKO) embryos were sorted using a BD FACSAria SORP into Trizol LS. For ChIPmentation, CUT&RUN, scATAC-seq, and scRNA-seq EYFP+ 5-HT  neurons from E14.5 Pet1-EYFP embryos were sorted using a BD FACSAria I & SORP into PBS with 1% FBS.


title: Female CD8 TILs, biological replicate 2, scRNAseq

description: 10x Genomics

tag: Sex


title: ChIPmentation_Input-1

tag: strain


title: CD4+CD25highCD127low Treg SM rep2

value: 8 weeks Smoke with 4 weeks PBS


title: oxacillin treated replicate A

value: oxacillin, 4 ug/mL


title: Female CD8 TILs, biological replicate 1, scRNAseq

description: 10x Genomics

value: s.q. tumor

value: Tumor-infiltrating CD8+ T cells

tag: age


title: 5HT_E14.5_WT_scATAC-seq

source_name: 5-HT neuron

extract_protocol:
single 5HT neurons were processed using the standard 10X Genomics scATAC-seq protocol (Chromium Single Cell ATAC Reagent Kit v1).
Dissected tissue between the mid-hindbrain boundary to the spinal cord boundary of E11.5, E14.5, and E17.5 hindbrains from Pet1-Cre;Lmx1bfl/fl;Rosa-TdTomato, Pet1-Cre;Pet1fl/fl;Rosa-TdTomato, or Pet1-Cre;Pet1fl/fl;Lmx1bfl/fl;Rosa-TdTomato embryos. For ATAC-seq EYFP+ or tdTomato+ 5-HT neurons were sorted using a BD FACSAria I & SORP or Sony iCyt into PBS with 1% FBS. For RNA-seq, E17.5 tdTomato+ 5-HT  neurons from Pet1-Cre;Pet1fl/fl;Lmx1bfl/fl;Rosa-TdTomato (DKO) embryos were sorted using a BD FACSAria SORP into Trizol LS. For ChIPmentation, CUT&RUN, scATAC-seq, and scRNA-seq EYFP+ 5-HT  neurons from E14.5 Pet1-EYFP embryos were sorted using a BD FACSAria I & SORP into PBS with 1% FBS.


title: 5HT_E17.5_Control_RNAseq_3

extract_protocol:
Purified total RNA was amplified with the TRIO RNA-seq kit (Nugen)
Dissected tissue between the mid-hindbrain boundary to the spinal cord boundary of E11.5, E14.5, and E17.5 hindbrains from Pet1-Cre;Lmx1bfl/fl;Rosa-TdTomato, Pet1-Cre;Pet1fl/fl;Rosa-TdTomato, or Pet1-Cre;Pet1fl/fl;Lmx1bfl/fl;Rosa-TdTomato embryos. For ATAC-seq EYFP+ or tdTomato+ 5-HT neurons were sorted using a BD FACSAria I & SORP or Sony iCyt into PBS with 1% FBS. For RNA-seq, E17.5 tdTomato+ 5-HT  neurons from Pet1-Cre;Pet1fl/fl;Lmx1bfl/fl;Rosa-TdTomato (DKO) embryos were sorted using a BD FACSAria SORP into Trizol LS. For ChIPmentation, CUT&RUN, scATAC-seq, and scRNA-seq EYFP+ 5-HT  neurons from E14.5 Pet1-EYFP embryos were sorted using a BD FACSAria I & SORP into PBS with 1% FBS.

value: Pet1::Cre; Rosa-TdTomato


title: 5HT_E14.5_WT_scRNA-seq

extract_protocol:
single 5HT neurons were processed using the standard 10X Genomics scRNA-seq protocol (Single Cell 3' v3).
Dissected tissue between the mid-hindbrain boundary to the spinal cord boundary of E11.5, E14.5, and E17.5 hindbrains from Pet1-Cre;Lmx1bfl/fl;Rosa-TdTomato, Pet1-Cre;Pet1fl/fl;Rosa-TdTomato, or Pet1-Cre;Pet1fl/fl;Lmx1bfl/fl;Rosa-TdTomato embryos. For ATAC-seq EYFP+ or tdTomato+ 5-HT neurons were sorted using a BD FACSAria I & SORP or Sony iCyt into PBS with 1% FBS. For RNA-seq, E17.5 tdTomato+ 5-HT  neurons from Pet1-Cre;Pet1fl/fl;Lmx1bfl/fl;Rosa-TdTomato (DKO) embryos were sorted using a BD FACSAria SORP into Trizol LS. For ChIPmentation, CUT&RUN, scATAC-seq, and scRNA-seq EYFP+ 5-HT  neurons from E14.5 Pet1-EYFP embryos were sorted using a BD FACSAria I & SORP into PBS with 1% FBS.


title: 5HT_E17.5_Control_RNAseq_2


title: CD4+CD25highCD127low Treg M rep2

value: 8 weeks air with 4 weeks morphine


title: Gli1_TAC_28

city: Aachen

first: Fabian

last: Peisker

address: Pauwelsstraße 30

institute: Uniklinikum RWTH Aachen

data_processing:
The Cell Ranger Software (version 3.0.2) was used for processing sequencing information.
Seurat (version 3.2.2) was used to integrate the single cell RNA-seq data.
Genome_build: mm10 + tdtomato gene sequence
Supplementary_files_format_and_content: matrix: In hdf5 format. The top level of the file contains a single HDF5 group, called matrix, and metadata stored as HDF5 attributes. Within the matrix group are datasets containing the dimensions of the matrix, the matrix entries, as well as the features and cell-barcodes associated with the matrix rows and columns, respectively.
Supplementary_files_format_and_content: Molecule Info : The cellranger pipeline outputs an HDF5 file containing per-molecule information for all molecules that contain a valid barcode and valid UMI and were assigned with high confidence to a gene or Feature Barcode. This HDF5 file contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis.
Supplementary_files_format_and_content: Summary : The cellranger pipeline outputs a summary HTML file named web_summary.html that contains summary metrics and automated secondary analysis results. Rarely, an issue may also be detected during the pipeline run leading to an alert also appearing on this page, and more information about these is provided in the troubleshooting documentation.

source_name: heart cells

growth_protocol: GLI1CreER (Gli1tm3(cre/ERT2)Alj/J, JAX Stock #007913) were purchased from Jackson Laboratories (Bar Harbor, ME, USA). Cdh5(PAC)-CreERT2 (Taconic no. 13073) was a kind gift of Rui Benedito (Madrid). All Cre-driver lines were crossbred with Rosa26tdTomato (i.e. B6-Cg-Gt(ROSA)26Sort tm(CAG-tdTomato)Hze/J, JAX Stock #007909) also from Jackson Laboratories, to generate the according tamoxifen inducible fate tracing genotype.For inducible fate tracing mice (8 weeks of age) of all different strains were injected intraperitoneal four times with 3mg tamoxifen. For inducible fate tracing mice (8 weeks of age) of all different strains were injected intraperitoneal four times with 3mg tamoxifen.

extract_protocol:
Hearts were harvested 28 days after surgery and single cell solution was generated by enzymatic digestion (30min, 37°C) and mechanic dissociation (C-tube, gentleMACS). Tdtomato positive, DAPI negative cells were sorted and pooled from 3-5 mice per condition and genotype. Single cell solutions were then loaded on a Chromium Single Cell B Chip Kit following the manufacturer protocol.
All protocols to generate scRNA-seq data on the 10x Chromium platform, including sample prep, library prep, instrument and sequencing settings, are available here:https://support.10xgenomics.com/single-cell-gene-expression
Single Cell 3' v3.1

treatment_protocol: After a washout period of 21 days, transverse aortic constriction (TAC) was performed to induce cardiac hypertrophy or Sham surgery as control procedure.

tag: Stage

value: pressure overload induced cardiac remodeling

value: cardiac hypertrophy


title: 5HT_E17.5_DKO_RNAseq_2

value: Pet1 fl/fl; Lmx1b fl/fl; Pet1::Cre; Rosa-TdTomato


title: 5HT_E14.5_Lmx1b_CUT&RUN

extract_protocol:
CUT&RUN purified DNA fragments were amplified using the NEB NEBNext Ultra II library kit.
Dissected tissue between the mid-hindbrain boundary to the spinal cord boundary of E11.5, E14.5, and E17.5 hindbrains from Pet1-Cre;Lmx1bfl/fl;Rosa-TdTomato, Pet1-Cre;Pet1fl/fl;Rosa-TdTomato, or Pet1-Cre;Pet1fl/fl;Lmx1bfl/fl;Rosa-TdTomato embryos. For ATAC-seq EYFP+ or tdTomato+ 5-HT neurons were sorted using a BD FACSAria I & SORP or Sony iCyt into PBS with 1% FBS. For RNA-seq, E17.5 tdTomato+ 5-HT  neurons from Pet1-Cre;Pet1fl/fl;Lmx1bfl/fl;Rosa-TdTomato (DKO) embryos were sorted using a BD FACSAria SORP into Trizol LS. For ChIPmentation, CUT&RUN, scATAC-seq, and scRNA-seq EYFP+ 5-HT  neurons from E14.5 Pet1-EYFP embryos were sorted using a BD FACSAria I & SORP into PBS with 1% FBS.

tag: antibody


title: Cdh5_TAC_28

tag: treatment


title: Ng2_TAC

description: Treatment

data_processing:
The Cell Ranger Software (version 3.0.2) was used for processing sequencing information.
Seurat (version 3.2.2) was used to integrate the single cell RNA-seq data.
Genome_build: mm10 + tdtomato gene sequence
Supplementary_files_format_and_content: *_matrix.h5: In hdf5 format. The top level of the file contains a single HDF5 group, called matrix, and metadata stored as HDF5 attributes. Within the matrix group are datasets containing the dimensions of the matrix, the matrix entries, as well as the features and cell-barcodes associated with the matrix rows and columns, respectively.
Supplementary_files_format_and_content: *_molecule_info.h5: The cellranger pipeline outputs an HDF5 file containing per-molecule information for all molecules that contain a valid barcode and valid UMI and were assigned with high confidence to a gene or Feature Barcode. This HDF5 file contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis.

growth_protocol: PDGFRßCreERt2 (i.e.B6-Cg-Gt(Pdgfrß-cre/ERT2)6096Rha/J, JAX Stock #029684), NG2CreER (B6.Cg-Tg(Cspg4-cre/Esr1*)BAkik/J, JAX Stock #008538), GLI1CreER (Gli1tm3(cre/ERT2)Alj/J, JAX Stock #007913), MYH11CreER (B6.FVB-Tg(Myh11-cre/ERT2)1Soff/J, JAX Stock #019079) were purchased from Jackson Laboratories (Bar Harbor, ME, USA). C57Bl6/129SV-Collagen 1alpha1-GFP-CreERT2 was a kind gift of Ivica Grgic (Marburg). Cdh5(PAC)-CreERT2 (Taconic no. 13073) was a kind gift of Rui Benedito (Madrid). All Cre-driver lines were crossbred with Rosa26tdTomato (i.e. B6-Cg-Gt(ROSA)26Sort tm(CAG-tdTomato)Hze/J, JAX Stock #007909) also from Jackson Laboratories, to generate the according tamoxifen inducible fate tracing genotype. For inducible fate tracing, mice (8 weeks of age) of all different strains were injected intraperitoneal four times with 3mg tamoxifen.

extract_protocol:
Hearts were harvested and single cell solution was generated by enzymatic digestion (30min, 37°C) and mechanic dissociation (C-tube, gentleMACS). Tdtomato positive, DAPI negative cells were sorted and pooled from 3-5 mice per condition and genotype. Single cell solutions were then loaded on a Chromium Single Cell B Chip Kit following the manufacturer protocol.
All protocols to generate scRNA-seq data on the 10x Chromium platform, including sample prep, library prep, instrument and sequencing settings, are available here: https://support.10xgenomics.com/single-cell-gene-expression
Single Cell 3' v3.0.

tag: mouse line

value: TAC surgery

tag: cell type

value: tdTomato-positive heart cells

value: Pressure overload induced cardiac remodeling


title: CD4+CD25highCD127low Treg NS rep1

value: wildtype

value: 8 weeks air with 4 weeks PBS


title: CD4+CD25highCD127low Treg M rep1


title: CD4+CD25highCD127low Treg NS rep2


title: 5HT_E17.5_DKO_RNAseq_1

value: 5-HT neuron


title: 5HT_E14.5_H3K27me3_2_ChIPmentation

description:
E14.5_WT_5HT_H3K27me3_peaks.bed
E14.5_5HT_H3K27me3_pooled.sort.bw

extract_protocol:
Antibody-immunopurified DNA fragments were amplified into sequencing libraries using the ChIPmentation protocol that uses a Tn5 transposase mediated adapter ligation and amplification (Schmidl, et al. 2015).
Dissected tissue between the mid-hindbrain boundary to the spinal cord boundary of E11.5, E14.5, and E17.5 hindbrains from Pet1-Cre;Lmx1bfl/fl;Rosa-TdTomato, Pet1-Cre;Pet1fl/fl;Rosa-TdTomato, or Pet1-Cre;Pet1fl/fl;Lmx1bfl/fl;Rosa-TdTomato embryos. For ATAC-seq EYFP+ or tdTomato+ 5-HT neurons were sorted using a BD FACSAria I & SORP or Sony iCyt into PBS with 1% FBS. For RNA-seq, E17.5 tdTomato+ 5-HT  neurons from Pet1-Cre;Pet1fl/fl;Lmx1bfl/fl;Rosa-TdTomato (DKO) embryos were sorted using a BD FACSAria SORP into Trizol LS. For ChIPmentation, CUT&RUN, scATAC-seq, and scRNA-seq EYFP+ 5-HT  neurons from E14.5 Pet1-EYFP embryos were sorted using a BD FACSAria I & SORP into PBS with 1% FBS.

value: wildtype; Pet1::EYFP

value: Anti-H3K27me3, , Cat#


title: Ng2_Sham

description: Control

value: Sham surgery

value: Homeostasis


title: 5HT_E17.5_Control_RNAseq_1


title: 5HT_E14.5_Pet1_CUT&RUN

value: Anti-FEV, , Cat#


title: CD4+CD25highCD127low Treg SM rep1

value: 8 weeks Smoke with 4 weeks PBS


title: 5HT_E14.5_H3K27me3_1_ChIPmentation


title: P14 Sp-3

city: Heidelberg

first: Guoliang

last: Cui

address: Im Neuenheimer Feld 280

institute: German cancer research center (DKFZ)

data_processing:
base calling bcl2fastq 2.20.0.422
low quality bases were removed with Fastq_quality_filter from the FASTX Toolkit 0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/index.html) with 90% of the read needing a quality phred score > 20. Homertools 4.7 33 were used for PolyA-tail trimming, and reads with a length < 17 were removed.
With STAR 2.3 34, the filtered reads were mapped against mouse genome 38 (mm10) using default parameters
Count data were generated using featureCounts 35(parameters --minReadOverlap 3 -T 3 -M -O -s 0 ) for the genes annotated in the gencode.vM23.gtf file.
Genome_build: mm10
Supplementary_files_format_and_content: 1 raw count file (tab separated) for 6 samples

source_name: Mouse T cells

extract_protocol: SmarTer Ultra Low Input RNA and Illumina Trueseq Stranded RNA-Kit was used for library construction. libraries were pooled with six samples in each lane and sequenced (Illumina HiSeq 2000 v4 Single-Read 50 bp)

treatment_protocol: We smashed the B16-GP33-41 tumors into a single-cell suspension. Then, we performed the Percoll centrifugation to recover the total tumor-infiltrating leukocytes. We FACS-sort the donor P14 CD8+ T cell fraction from tumor-infiltrating leukocytes. As a control, we also smashed the spleen from the same tumor-bearing mice. We then FACS sort the donor P14 CD8+ T cells in the spleen as well for RNA extraction, library preparation, and sequencing.

value: Spleen

value: P14 TCR transgenic

value: FACS-sorting


title: P14 Sp-2


title: Myh11_TAC

description: Treatment


title: 5HT_E14.5_H3K27ac_2_ChIPmentation

description:
E14.5_WT_5HT_H3K27ac_peaks.bed
E14.5_5HT_H3K27ac_pooled.sort.bw

value: Anti-H3K27ac, , Cat#


title: 5HT_E14.5_H3K27ac_1_ChIPmentation


title: 5HT_E14.5_H3K4me1_2_ChIPmentation

description:
E14.5_WT_5HT_H3K4me1_peaks.bed
E14.5_5HT_H3K4me1_pooled.sort.bw

value: Anti-H3K4me1, , Cat#


title: P14 Sp-1


title: Myh11_Sham

description: Control


title: 5HT_E14.5_H3K4me1_1_ChIPmentation


title: Cdh5_TAC

description: Treatment

value: TAC surgery


title: P14 TIL-3

value: tumor


title: 5HT_E14.5_H3K4me3_2_ChIPmentation

description:
E14.5_WT_5HT_H3K4me3_peaks.bed
E14.5_5HT_H3K4me3_pooled.sort.bw

value: Anti-H3K4me3, , Cat#


title: 5HT_E14.5_H3K4me3_3_ChIPmentation


title: P14 TIL-2


title: ChIPmentation_Input-2


title: Pet1neg_E14.5_WT_3_ATAC

source_name: Pet1-negative hindbrain cells

extract_protocol:
Adapter-ligated DNA fragments were purified using the NEB Monarch DNA & PCR cleanup kit , and subsequently PCR-amplified with the NEB NEBNext High-Fidelity 2x PCR Master Mix using the following conditions: (1) 5 minutes at 72°C, (2) 1 minute at 98°C, (3) 15 seconds at 98°C, (4) 30 seconds at 63°C, (5) one minute at 72°C, (6) Go to step 3 seven times, (7) hold at 10°C. All ATAC-seq libraries were sequenced on a Nextseq 550.
Dissected tissue between the mid-hindbrain boundary to the spinal cord boundary of E11.5, E14.5, and E17.5 hindbrains from Pet1-Cre;Lmx1bfl/fl;Rosa-TdTomato, Pet1-Cre;Pet1fl/fl;Rosa-TdTomato, or Pet1-Cre;Pet1fl/fl;Lmx1bfl/fl;Rosa-TdTomato embryos. For ATAC-seq EYFP+ or tdTomato+ 5-HT neurons were sorted using a BD FACSAria I & SORP or Sony iCyt into PBS with 1% FBS. For RNA-seq, E17.5 tdTomato+ 5-HT  neurons from Pet1-Cre;Pet1fl/fl;Lmx1bfl/fl;Rosa-TdTomato (DKO) embryos were sorted using a BD FACSAria SORP into Trizol LS. For ChIPmentation, CUT&RUN, scATAC-seq, and scRNA-seq EYFP+ 5-HT  neurons from E14.5 Pet1-EYFP embryos were sorted using a BD FACSAria I & SORP into PBS with 1% FBS.

value: Pet1-negative hindbrain cells


title: Pet1neg_E14.5_WT_2_ATAC


title: Cdh5_Sham

description: Control

value: tdTomato-positive heart cells


title: Gli1_TAC

description: Treatment

value: Pressure overload induced cardiac remodeling


title: P14 TIL-1


title: Col1a1_TAC

description: Treatment


title: 5HT_E14.5_H3K4me3_1_ChIPmentation

value: 5-HT neuron

value: wildtype; Pet1::EYFP


title: Col1a1_Sham

description: Control

value: Sham surgery


title: Pet1neg_E14.5_WT_1_ATAC


title: 5HT_E14.5_DKO_3_ATAC

description:
E14.5_DKO_5HT_ATAC_peaks.bed
E14.5_DKO_pooled.bw

value: Pet1 fl/fl; Lmx1b fl/fl; Pet1::Cre; Rosa-TdTomato


title: 5HT_E14.5_DKO_2_ATAC


title: MLL-AF9_WT_LSK_untreated_biorepl1

city: New York

first: Christopher

middle: Y.

last: Park

state: New York

address: 550 First Avenue

department: Pathology

institute: New York University

data_processing:
Raw fastq files were aligned to the mm10 reference genome. Read counts were extracted using HTSeq, and differentially expressed genes analyzed using DESeq2.
Assembly: mm10
Supplementary files format and content: HTSeq count file

source_name: Bone marrow

extract_protocol:
Samples were FACS-sorted into Trizol LS (Thermo Fisher, Rockford, Illinois).
Poly-A selected cDNA libraries were prepared using a SMARTer mRNA amplification kit (Clontech, Mountain View, California).

value: Bone marrow

tag: cell line

value: Double FACS-sorted Lin-Sca-1+c-Kit+ cells (LSK) with retroviral transduction with MLL-AF9

value: C57BL/6J WT

value: Untreated


title: MLL-AF9_WT_LSK_untreated_biorepl3


title: MLL-AF9_WT_LSK_untreated_biorepl2


title: 5HT_E14.5_DKO_1_ATAC


title: Pdgfrb_TAC

description: Treatment

value: Pdgfrb-CreER;tdTomato


title: MLL-AF9_Alox5-/-_LSK_untreated_biorepl3

value: C57BL/6J Alox5-/-


title: Gli1_Sham

description: Control

value: Homeostasis


title: HepaRG cells treated with SV-VD3 and OA/PA 3

city: Sansepolcro

first: Jacopo

last: Lucci

state: Arezzo

address: Loc. Aboca, 20

country: Italy

institute: Bios-Therapy, Physiological Systems For Health S.p.A

hyb_protocol: Fragmented and labeled cDNA was prepared according to the manufacturer's instructions and hybridized to a Human Clariom Go Screen 384-array plate for 17 h at 45°C on a GeneTitan MC Instrument (Applied Biosystems, ThermoFisher Scientific). Arrays were washed and stained on a GeneTitan MC Instrument (Applied Biosystems, ThermoFisher Scientific).

scan_protocol: Arrays were scanned using the GeneTitan MC Instrument (Applied Biosystems, ThermoFisher Scientific). Affymetrix GeneChip Command Console Software (AGCC, ThermoFisher Scientific) was used for GeneTitan MC Instrument control.

data_processing: Data analysis were performed using Transcriptomic Analysis Console Software (TAC, ThermoFisher Scientific) that provides quality control analysis, performs normalization and summarization, based on the Signal Space Transformation-Robust Multi-Chip Analysis (SST-RMA) analysis algorithm, and provides a list of differentially expressed genes (Limma Bioconductor package, pvalue<0,05) from the biological duplicates for WGO-VE_OA or triplicates of the other condition.

source_name: Treated with William E complete medium with a mix of oleic acid [200 µM] and palmitic acid [200 µM]+synthetic vitamin D3 [10 nM]

label_protocol: Biotinylated cRNA was prepared according to the standard ThermoFisher Scientific protocol from 6 ug total RNA (GeneChip™ 3’ IVT Pico Kit Manual Workflow).

growth_protocol: Cells were seeded at a density of 10,000 cells/well and kept at 37˚C in a humidified 5% CO2 cell culture incubator.

extract_protocol: Total RNA was extracted from cells lysates using an QIAsymphony RNA Kit (Qiagen,) with the QIAsymphony SP instrument (Qiagen) according to the manufacturer's instructions.

treatment_protocol: At 70% confluence, HepaRG cells were incubated for 24 hrs with either the vehicle or the three different sources of Vitamin D at final concentration of α-Tocopherol in the colture medium of 10 nM. Subsequently HepaRG were incubated with OA/PA mix at  the final concentration in the colture medium of 200 µM. Cell treatments with this OA/PA lasted for 48 hrs.

value: hepatic cell line

tag: features

value: Immortalized hepatic cell line terminally differentiated

value: Adult


title: MLL-AF9_Alox5-/-_LSK_untreated_biorepl1


title: HepaRG cells treated with SV-VD3 and OA/PA 2


title: 9VP5

city: Grand Rapids

first: Juozas

last: Gordevicius

state: Michigan

address: 333 Botswick Ave NE

institute: Van Andel Institute

data_processing:
Adapters from paired end sequencing reads were removed using TrimGalore (v 0.6.4_dev) and Cutadapt (v 2.8).
STAR (v 2.5.3a) aligner was used to align the reads and quantify the transcripts using ENSEMBL GRCm38 as reference genome and GENCODE mouse gene annotation M20.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: midbrain

extract_protocol:
Midbrain sections were kept on dry ice and RNA/DNA isolation was harvested using the Quick-DNA/RNA miniprep plus kit as directed by the manufacturer (Zymo Research, Irvine, CA). DNA digestion was done on the RNA columns for 15 minutes at room temperature to remove any contaminating DNA. RNA concentration and quality were checked on the nanodrop 2000 (Thermo Fisher, Waltham, MA).
Libraries were prepared by the Van Andel Genomics Core from 200 ng of total RNA using the KAPA mRNA Hyperprep kit (v4.17) (Kapa Biosystems, Wilmington, MA USA). RNA was sheared to 300-400 bp prior to PCR amplification, cDNA fragments were ligated to IDT for Illumina TruSeq UD Indexed adapters (Illumina Inc, San Diego CA, USA). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems).
Individually indexed libraries were pooled and 50 bp, paired end sequencing was performed on an Illumina NovaSeq6000 sequencer using an S1, 100 bp sequencing kit (Illumina Inc., San Diego, CA, USA) to an average depth of 40 million reads per sample. Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.

tag: damid

tag: pupid

tag: condition

value: PBS

value: M

tag: rin

tag: batch


title: NLRP3_8

city: Marburg

first: Veronika

last: Lutz

state: D

institute: Philipps-University of Marburg

data_processing:
de-multiplexed fastq files were tested with FastQC. Over-represented sequences and adapters were trimmed with the Qiagen CLC Workbench Software v. 10.0.1.
Reads were mapped with the Qiagen CLC Workbench Software v. 10.0.1., using the GRCm39.105 mouse reference genome using default mapping parameters
Differential gene expression analysis was performed using DESeq2 (v1.28.1)
Assembly: GRCm38
Supplementary files format and content: .txt

source_name: PancOVA

growth_protocol: Congenic CD45.1 (WT) or Nlrp3-/- mice were injected with 1x106 PancOVA cells s.c..

extract_protocol:
RNA preparation was carried out using the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer’s protocol
Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 Ico chip on Agilent's bioanalyzer. Barcoded mRNA seq libraries were prepared from 50 ng total RNA (RIN>8) using a NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to the manual. 13 cycles were run for final amplification of libraries. All quality controls were done using Invitrogen’s Qubit HS assay and average library size was determined on Agilent’s 2100 Bioanalyzer HS DNA assay.

treatment_protocol: On day 10 after tumor inoculation endogenous CD8+ T cells were isolated from the tumor and were analyzed ex vivo.

value: endogenous intratumoral CD8 T cell

value: untreated


title: NLRP3_3


title: Pdgfrb_Sham

description: Control

value: tdTomato-positive heart cells


title: NLRP3_9


title: 9VP1

value: F


title: 5HT_E14.5_Pet1CKO_1_ATAC

description:
E14.5_Pet1CKO_5HT_ATAC_peaks.bed
E14.5_PCKO_pooled.bw

tag: tissue

value: 5-HT neuron

value: Pet1 fl/fl; Pet1::Cre; Rosa-TdTomato


title: 5HT_E14.5_Pet1CKO_3_ATAC

tag: genotype


title: 8VP1

tag: Sex


title: HepaRG cells treated with SM-VD2 and OA/PA 2

source_name: Treated with William E complete medium with a mix of oleic acid [200 µM] and palmitic acid [200 µM]+vitamin D2-containing extract derived from Shitake mushroom [10 nM]


title: HepaRG cells treated with SV-VD3 and OA/PA 1


title: 5HT_E14.5_Lmx1bCKO_1_ATAC

description:
E14.5_Lmx1bCKO_5HT_ATAC_peaks.bed
E14_LCKO_atacseq.pooled.bw

tag: strain

value: Lmx1b fl/fl; Pet1::Cre; Rosa-TdTomato


title: 5HT_E14.5_Pet1CKO_2_ATAC

tag: age


title: HepaRG cells treated with SM-VD2 and OA/PA 3


title: 5HT_E14.5_Lmx1bCKO_3_ATAC


title: 7VP4


title: MLL-AF9_Alox5-/-_LSK_untreated_biorepl2

value: Bone marrow

value: Double FACS-sorted Lin-Sca-1+c-Kit+ cells (LSK) with retroviral transduction with MLL-AF9


title: NLRP3_10


title: 8VP4


title: 5HT_E17.5_Pet1KO_3_ATAC

description:
E17.5_Pet1KO_5HT_ATAC_peaks.bed
E17.5_5HT_Pet1KO_pooled.sort.bw

value: Pet1-/-; Pet1::EYFP


title: 5HT_E14.5_Lmx1bCKO_2_ATAC


title: HepaRG cells treated with 1,25(OH)D3 and OA/PA 2

source_name: Treated with William E complete medium with a mix of oleic acid [200 µM] and palmitic acid [200 µM]+1,25-dihydroxy vitamin D3 [10 nM]


title: WT_6

value: B6.SJL-Ptprca Pepcb/BoyJ


title: 7VP1


title: 5HT_E17.5_Pet1KO_2_ATAC


title: 6VP3


title: WT_5


title: 5HT_E17.5_Pet1KO_1_ATAC


title: HepaRG cells treated with 1,25(OH)D3 and OA/PA 1


title: WT_2


title: 6VP1


title: HepaRG cells pre-treated only with mix of oleic OA/PA 2

source_name: Treated with William E complete medium with a mix of oleic acid [200 µM] and palmitic acid [200 µM]


title: WT_7


title: HepaRG cells treated with SM-VD2 and OA/PA 1


title: 5HT_E14.5_Pet1KO_3_ATAC

description:
E14.5_Pet1KO_5HT_ATAC_peaks.bed
E14.5_5HT_Pet1KO_pooled.sort.bw


title: HepaRG cells pre-treated only with mix of oleic OA/PA 1


title: 5HT_E14.5_Pet1KO_1_ATAC


title: W18_KO1433_IL4_3

city: NEW YORK

first: WENHUO

last: HU

email: huwenhuo@gmail.com, huw@mskcc.org

state: NEW YORK

address: 1275 YORK AVENUE

department: HOPP

institute: MEMORIAL SLOAN KETTERING CANCER CENTER

description: 14-3-3eKO M2 macrophage Rep3

data_processing:
RSEM v1.3.1 (rsem-calculate-expression function w/ STAR aligning), GRCh38
DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab separated text file of genes x18 samples matrix

source_name: bone marrow derived macrophage

growth_protocol: Bone marrow cells were collected from the mice and cultured in α-MEM supplemented with 10% FBS and 10ng/ml M-CSF (Biolegend, San Diego, CA, USA) over 7 days for macrophage differentiation.

extract_protocol:
Total RNA was extracted from BMDMs with RNeasy Mini Kit (Qiagen, Germantown, MD, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Differentiated BMDMs were stimulated with 100ng/ml LPS (Sigma-Aldrich) + 20ng/ml IFNy (Peprotech) or 20ng/ml IL-4 (Peprotech, Rocky Hill, NJ, USA) for 18h to polarize cells to M1 or M2 macrophage, respectively.

value: bone marrow derived macrophage

value: Myeloid 14-3-3e knockout

value: treat with 20ng/ml IL-4 for 18 hrs


title: HepaRG cells pre-treated only with mix of oleic OA/PA 3

value: hepatic cell line

value: Immortalized hepatic cell line terminally differentiated

value: Adult


title: 5VP1

value: CMV


title: 5VP6

value: M


title: 5VP4


title: W17_KO1433_IL4_2

description: 14-3-3eKO M2 macrophage Rep2


title: 5HT_E11.5_Pet1KO_3_ATAC

description:
E11.5_Pet1KO_5HT_ATAC_peaks.bed
E11.5_5HT_Pet1KO_pooled.sort.bw


title: Hca his: Panarchaea - rep2

city: Durham

first: Amy

middle: K

last: Schmid

address: 125 Science Dr.

department: Biology

institute: Duke University

description:
Total RNA depleted using siTools Panarchaea kit
HAH_pyrE_pan_2
ΔpyrF

data_processing:
50bp paired reads were quality checked using FastQC, adapter sequences trimmed using Trim Galore and Cutadapt.
Result sequences were aligned to the Hbt sal genome (GCF_000006805.1), Hfx vol (GCF_000025685.1_ASM2568v1), Hca his (GCF_000223905.1_ASM22390v1), or Hfx med (GCF_000306765.2_ASM30676v2) genomes (as appropriate) using Bowtie2.
BAM files were generated using samtools, they were inputs to generate count files using HTSeq (count files associated with each sample are included in this GEO dataset). Note that these BAM files are sorted by name, not by read.
Counts mapping to rRNA genes as a percentage of counts mapping to all genes were obtained and reported.
Supplementary files format and content: *.count: Tab-delimited text files include raw counts.

organism: Haloarcula hispanica

source_name: Archaeal cells

growth_protocol: Cells (3-4 biological replicates) were precultured to stationary phase, and then diluted back to a starting OD. These cultures were then grown to mid-log phase in appropriate rich media.

extract_protocol:
~3-5mL of cells in mid-log phase were flash-frozen in Liq N2 and stored at -80C. Total RNA was extracted from cell pellets using the Agilent Absolutely RNA Miniprep kit. RNA was measured using Nanodrop and quality-checked using Bioanalyzer.
1-10ng of total RNA was used as input for rRNA removal by the various kits tested here. The kit protocol included creation of a dsDNA library from the depleted RNA as template. This library was quality-checked using DNA High Sensitivity chip on the Bioanalyzer.

value: <delta>pyrF


title: Hca his: Panarchaea - rep1

description:
Total RNA depleted using siTools Panarchaea kit
HAH_pyrE_pan_1
ΔpyrF


title: Hca his: Panarchaea - rep3

description:
Total RNA depleted using siTools Panarchaea kit
HAH_pyrE_pan_3
ΔpyrF


title: HepaRG cells untreated (vehicle) 2

source_name: Treated with William’s E complete medium with DMSO [0.001%]


title: 5HT_E11.5_Pet1KO_2_ATAC


title: W16_KO1433_IL4_1

description: 14-3-3eKO M2 macrophage Rep1


title: HepaRG cells untreated (vehicle) 1


title: HepaRG cells untreated (vehicle) 3


title: 3VP3

value: F


title: 5HT_E14.5_Pet1KO_2_ATAC

value: 5-HT neuron


title: 3VP1


title: Hbt sal: Panarchaea - rep4

description:
Total RNA depleted using siTools Panarchaea kit
HBT_ura3_pan_4
Δura3

organism: Halobacterium salinarum


title: 3VP4


title: W14_KOPGRN_IL4_2

description: PGRN KO M2 macrophage Rep2

value: PGRN knockout


title: 5HT_E11.5_Pet1KO_1_ATAC


title: 26VP1

value: PBS


title: Hbt sal: Panarchaea - rep1

description:
Total RNA depleted using siTools Panarchaea kit
HBT_ura3_pan_1
Δura3


title: 5HT_E17.5_WT_2_ATAC

description:
E17.5_WT_5HT_ATAC_peaks.bed
E17.5_5HT_WT_pooled.sort.bw

value: wildtype; Pet1::EYFP


title: Hbt sal: Panarchaea - rep2

description:
Total RNA depleted using siTools Panarchaea kit
HBT_ura3_pan_2
Δura3


title: 25VP6


title: W13_KOPGRN_IL4_1

description: PGRN KO M2 macrophage Rep1


title: 25VP1


title: 5HT_E17.5_WT_1_ATAC


title: W12_WT_IL4_3

description: WT M2 macrophage Rep3

value: wild-type


title: 5HT_E14.5_WT_5_ATAC

description:
E14.5_WT_5HT_ATAC_peaks.bed
E14.5_5HT_WT_pooled.sort.bw


title: W11_WT_IL4_2

description: WT M2 macrophage Rep2


title: Hbt sal: NEBHvo_30 - rep3

description:
Total RNA depleted using NEBNext Core Depletion set with 30 minutes of RNase digestion
HBT_ura3_NEBHVO30_3
Δura3


title: W15_KOPGRN_IL4_3

description: PGRN KO M2 macrophage Rep3


title: Hbt sal: NEBHvo_30 - rep2

description:
Total RNA depleted using NEBNext Core Depletion set with 30 minutes of RNase digestion
HBT_ura3_NEBHVO30_2
Δura3


title: W9_KO1433_LPS_3

description: 14-3-3eKO M1 macrophage Rep3

value: treat with100ng/ml LPS + 20ng/ml IFNy for 18hrs


title: 5HT_E17.5_WT_3_ATAC


title: W8_KO1433_LPS_2

description: 14-3-3eKO M1 macrophage Rep2


title: 24VP3


title: Hbt sal: NEBHvo_60 - rep3

description:
Total RNA depleted using NEBNext Core Depletion set with 60 minutes of RNase digestion
HBT_ura3_NEBHVO60_3
Δura3


title: 24VP1


title: 5HT_E14.5_WT_4_ATAC


title: 5HT_E14.5_WT_3_ATAC


title: 24VP6


title: 5HT_E14.5_WT_2_ATAC


title: Hbt sal: NEBHvo_60 - rep2

description:
Total RNA depleted using NEBNext Core Depletion set with 60 minutes of RNase digestion
HBT_ura3_NEBHVO60_2
Δura3


title: W10_WT_IL4_1

description: WT M2 macrophage Rep1


title: Hbt sal: Panarchaea - rep3

description:
Total RNA depleted using siTools Panarchaea kit
HBT_ura3_pan_3
Δura3


title: W5_KOPGRN_LPS_2

description: PGRN KO M1 macrophage Rep2


title: W6_KOPGRN_LPS_3

description: PGRN KO M1 macrophage Rep3


title: 22VP4


title: 22VP1


title: 5HT_E11.5_WT_3_ATAC

description:
E11.5_WT_5HT_ATAC_peaks.bed
E11.5_5HT_WT_pooled.sort.bw


title: Hbt sal: NEBHvo_120 - rep3

description:
Total RNA depleted using NEBNext Core Depletion set with 120 minutes of RNase digestion
HBT_ura3_NEBHVO120_3
Δura3


title: 5HT_E11.5_WT_2_ATAC


title: Hbt sal: NEBHvo_30 - rep1

description:
Total RNA depleted using NEBNext Core Depletion set with 30 minutes of RNase digestion
HBT_ura3_NEBHVO30_1
Δura3


title: Hbt sal: NEBHvo_60 - rep1

description:
Total RNA depleted using NEBNext Core Depletion set with 60 minutes of RNase digestion
HBT_ura3_NEBHVO60_1
Δura3


title: 5HT_E11.5_WT_1_ATAC


title: Hbt sal: NEBHvo_120 - rep2

description:
Total RNA depleted using NEBNext Core Depletion set with 120 minutes of RNase digestion
HBT_ura3_NEBHVO120_2
Δura3


title: W7_KO1433_LPS_1

description: 14-3-3eKO M1 macrophage Rep1


title: W3_WT_LPS_3

description: WT M1 macrophage Rep3


title: Hbt sal: control - rep 3

description:
Total RNA, not rRNA-depleted
HBT_ura3_control_3
Δura3


title: W2_WT_LPS_2

description: WT M1 macrophage Rep2


title: 5HT_E14.5_WT_1_ATAC


title: Hfx med: Panarchaea - rep2

description:
Total RNA depleted using siTools Panarchaea kit
HFX_pyrE_pan_2
ΔpyrE

organism: Haloferax mediterranei

value: <delta>pyrE


title: Hfx med: Panarchaea - rep3

description:
Total RNA depleted using siTools Panarchaea kit
HFX_pyrE_pan_3
ΔpyrE


title: 1VP7


title: 1VP1


title: 21VP1


title: Hfx med: Panarchaea - rep1

description:
Total RNA depleted using siTools Panarchaea kit
HFX_pyrE_pan_1
ΔpyrE


title: Hbt sal: control - rep 2

description:
Total RNA, not rRNA-depleted
HBT_ura3_control_2
Δura3


title: W1_WT_LPS_1

description: WT M1 macrophage Rep1

value: bone marrow derived macrophage


title: W4_KOPGRN_LPS_1

description: PGRN KO M1 macrophage Rep1


title: 21VP2


title: 18VP6


title: Hfx vol: RiboPool - rep3

description:
Total RNA depleted using siTools RiboPool kit
HVO_pyrE_Rpool_3
ΔpyrE

organism: Haloferax volcanii


title: 18VP4


title: Hfx vol: RiboPool - rep2

description:
Total RNA depleted using siTools RiboPool kit
HVO_pyrE_Rpool_2
ΔpyrE


title: fKO2

city: Ann Arbor

first: Clair

last: Harris

address: 3710 Med Sci II 1241 Catherine St

department: Human Genetics

institute: University of Michigan

data_processing:
Full length reads were mapped to mm9 using TopHat2 (v2.1.0) with Bowtie2 (v2.2.6.0) allowing up to one mismatch. Only uniquely mapping reads were analyzed further.
BAM files were converted to BigWig files in a strand specific manner. Bigwigs were normalized to 10 million non-rRNA and non-mitochondrial reads.
DESeq was used to call differential gene expression between genotypes. Cuffdiff was used to calculate FPKM values.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files represent genome coverage by the reads in a strand specific manner after normalizing to 10 million non-rRNA non-mtRNA reads. DESeq files represent differential gene expression between genotypes (incorporating technical replicates).

source_name: mouse epiblast like cells

growth_protocol: Three independent mouse ESC lines were differentiated into EpiLCs for each genotype. Mouse ES cells were derived and grown as described in PMID: 17487198. To convert ESCs to EpiLCs, ESC lines were grown in 2i culture conditions (N2B27 medium consisting 50% DMEM/F12, 50% neurobasal media, 2 mM L-glutamine (GIBCO, #25030), 0.1 mM 2-mercaptoethanol (Sigma, #M7522), N2 supplement (Invitrogen #17502048), B27 supplement (Invitrogen #17504-044), supplemented with 1 μM GSK3 inhibitor CHIR99021 (Stemgent #04-0004), 1 μM MEK inhibitor PD0325901 (Stemgent #04-0006), and 1000 U/ml LIF (Millipore #ESG1106) in gelatin-coated tissue culture dishes for 4 passages.

extract_protocol:
Cells were homogenized in TRI Reagent BD (Sigma) and subjected to total RNA isolation using RNEasy Mini Kit (Qiagen). Ribosomal RNA was depleted using RiboMinus Eukaryotic Kit v2 (Life Technologies).
Libraries were prepared using Direct Ligation of Adapters to First-strand cDNA as described in PMID: 25607527

treatment_protocol: To achieve EpiLC differentiation, cells were cultured in N2B27 medium supplemented with 10 ng/ml FGF2 (R&D Systems, #233-FB) and 20 ng/ml Activin A (R&D Systems, #338-AC) in Fibronectin (15 μg/ml) (Sigma#F1141)-coated tissue culture dishes for 48 hrs.

value: epiblast like cells

value: Smcx knockout


title: fKO3


title: Hbt sal: NEBHvo_120 - rep1

description:
Total RNA depleted using NEBNext Core Depletion set with 120 minutes of RNase digestion
HBT_ura3_NEBHVO120_1
Δura3


title: fKO1


title: 18VP3


title: Hbt sal: RiboZero Plus - rep 3

description:
Total RNA was depleted using the RiboZero Plus kit at the Duke Genomics and Sequencing Center
HBT_ura3_rzplus_3
Δura3


title: Hbt sal: RiboZero Plus - rep 2

description:
Total RNA was depleted using the RiboZero Plus kit at the Duke Genomics and Sequencing Center
HBT_ura3_rzplus_2
Δura3


title: 18VP1


title: Hfx vol: RiboPool - rep1

description:
Total RNA depleted using siTools RiboPool kit
HVO_pyrE_Rpool_1
ΔpyrE


title: fWT3

value: Smcx wild type


title: 16VP6


title: Hbt sal: RiboZero Plus - rep 1

description:
Total RNA was depleted using the RiboZero Plus kit at the Duke Genomics and Sequencing Center
HBT_ura3_rzplus_1
Δura3


title: Hfx vol: Panarchaea - rep3

description:
Total RNA depleted using siTools Panarchaea kit
HVO_pyrE_pan_3
ΔpyrE


title: fWT2


title: 16VP3


title: Hfx vol: Panarchaea - rep2

description:
Total RNA depleted using siTools Panarchaea kit
HVO_pyrE_pan_2
ΔpyrE


title: fWT1


title: D109 CTRL

city: Indianapolis

first: Eri

last: Hashino

state: IN

address: 980 West Walnut Street

department: Otolaryngology—Head and Neck Surgery

institute: Indiana University School of Medicine

data_processing:
Illumina’s CellRanger v4.0.0 program was used to generate BCL files, which were de-mutiplexed and converted to FASTQ files via bcl2fastq Conversion Software (Illumina).
The FASTQ files were then aligned to the GRCh38-3.0.0 reference genome using the STAR (Spliced Transcripts Alignment to a Reference) aligner
The  filtered count matrices were preprocessed individually for each dataset in Seurat v3.2, removing cells where the number of mitochondrial gene counts exceeded 12.5 percent of the total number of molecules detected.
Cells with log-transformed RPL27 expression ± 2 standard deviations away from the mean were removed
After preprocessing, datasets were merged and normalized using the SCTransform function in Seurat
Assembly: GRCh38-3.0.0
Supplementary files format and content: gz file of filtered gene-barcode matrices

source_name: hESC aggregate

extract_protocol:
PAX2nG+ (D20 samples) or POU4F3nT+ (D80 and -109 samples) cells were isolated and used for scRNA-seq analyses. Thirty to 45 aggregates per condition were washed with 0.5 mM EDTA (Thermo Fisher) in DPBS, then incubated with 1.1 mM EDTA in 1X TrypLE (Life Technologies) in DPBS on an orbital shaker at 37°C for 30 min followed by 40-50 min without shaking. During incubation, the samples were mechanically dissociated on Nunclon Sphera 24-well plates (Thermo Fisher) with shaking and occasional gentle pipetting with P1000 tips. After confirming that most cells, especially those with reporter expression, were completely dissociated, they were filtered sequentially through a 100-µm and a 40-µm cell strainer (Falcon) and then transferred into 2-ml tubes (Eppendorf). After spinning down at 100 × g for 5 min, dissociated cells were resuspended in FACS buffer consisting of 2% fetal bovine serum (Thermo Fisher) in 1X DPBS. Cells were again filtered through a 40-µm cell strainer and collected into a 5-ml round-bottom polypropylene tube (Falcon). Dead cells were stained with propidium iodide (PI, Invitrogen) diluted at 1:500. Simultaneously, size control cells without PI staining were prepared using aggregates made from wild-type hESCs using the above protocol.  Cells were stored on ice and protected from light prior to sorting. PI-negative and GFP (or tdTomato)-positive populations were collected and cleaned using a SORP Aria (BD Biosciences).
scRNA-seq for all samples was performed using the 10X Genomics Chromium 3’ v3 platform for cDNA library construction and the NovaSeq 6000 system (Illumina) for sequencing.  For each sample, between 12,000 and 18,000 cells were added to the single cell master mix, following the Chromium NextGEM Single Cell 3’ Reagent Kits User Guide. The single cell master mix, along with the single-cell gel beads and partitioning oil, was dispensed onto a Single Cell Chip G and the chip was loaded into the Chromium Controller for barcoding and cDNA synthesis. The resulting cDNA library was sequenced with the NovaSeq 6000 system running a custom program for 28-bp plus 91-bp paired-end sequencing, resulting in a read depth of more than 40,000 reads per cell.
Illumina’s CellRanger v4.0.0 program was used to generate BCL files, which were de-mutiplexed and converted to FASTQ files via bcl2fastq Conversion Software (Illumina). The FASTQ files were then aligned to the GRCh38-3.0.0 reference genome using the STAR (Spliced Transcripts Alignment to a Reference) aligner. Mapped reads were grouped by cell barcode, single-cell gene expression was quantified using unique molecular identifiers (UMIs), and the resulting filtered gene-barcode (count) matrices were used as input for downstream analysis.

treatment_protocol: PAX2-2A-nGFP/POU4F3-2A-ntdTomat hESCs (passages 22–50) were maintained and passaged in Essential 8 Flex Medium (Thermo Fisher, A2858501) supplemented with 100 μg/ml Normocin (E8fn) on recombinant human Vitronectin-N (Thermo Fisher, A14700)-coated 6-well plates. Human inner ear organoids were derived from hESCs based on our previous protocol 5,10 with major modifications. Briefly, hESCs were dissociated with StemPro Accutase (Thermo Fisher, A1110501) and distributed at 3500 cells per well onto low-adhesion 96-well U-bottom plates in 100 µL E8fn containing 20 μM Y-27632 (Stemgent, 04-0012-02) and forcibly aggregated at 120 g for 5 minutes. 100 µL of E8fn was added to each well after >4h of incubation. Induction of non-neural epithelium occurred following 48 h of aggregation, marking differentiation day 0, as follows: aggregates were washed extensively in DMEM:F12 with HEPES buffer (DFH) (Thermo Fisher, 11320033) and transferred to new 96-well U-bottom plates in 100 µL of E6 medium (Thermo Fisher, A1516401) with Normocin (E6n) containing 4 ng mL−1 FGF-2 (StemCell Technologies, 780003), 10 µM SB-431542 (Stemgent, 04-0010-05), and 2% growth factor reduced (GFR) Matrigel (Corning, 354230). On day 3 of differentiation, 25 µL of E6n containing 50 ng/mL FGF-2 and 200 nM LDN-193189 (Stemgent, 04-0074-02) was added to each well.  Culture medium was changed on days 7 and 9 with E6n containing 3 µM CHIR 99021 (Reprocell, 04-0004-10), 200 nM LDN, and 50 ng/mL FGF-2. On day 11, aggregates were washed and transferred to a Nunc Delta surface 6-well culture dish in Organoid Maturation Medium (OMM) containing 1% GFR Matrigel and 3 µM CHIR99021. OMM consists of a 50:50 mixture of Advanced DMEM:F12 (Thermo Fisher, 12634028) and Neurobasal Medium (Thermo Fisher, 21103049) supplemented with 0.5× N2 Supplement (Thermo Fisher, 17502048), 0.5× B27 minus Vitamin A (Thermo Fisher, 12587010), 1× GlutaMAX (Thermo Fisher, 35050061), 0.1 mM β-Mercaptoethanol (Thermo Fisher, 21985023), and Normocin. Control cultures were maintained in OMM + 3 µM CHIR99021 until day 18 with media changes on days 13 and 15, then OMM for the remainder of the culture. Treatment cultures were supplemented with 1 µM Purmorphamine (Stemgent, 04-0009) from days 13-22, and IWP-2 (Tocris, 3533) from days 18-22, with media changes on days 15,18, and 20, then maintained in OMM for the remainder of the culture.

tag: timepoint

value: Day 109

tag: sort strategy

value: POU4F3nT Positive


title: Hbt sal: control - rep 1

description:
Total RNA, not rRNA-depleted
HBT_ura3_control_1
Δura3


title: mKO3


title: D109 PUR+IWP2


title: 16VP1


title: D80 CTRL

value: Day 80


title: Hfx vol: NEBHvo_30 - rep4

description:
Total RNA depleted using NEBNext Core Depletion set with 30 minutes of RNase digestion
HVO_pyrE_NEBHVO30_4
ΔpyrE


title: 15VP5

value: CMV

value: M


title: mKO2


title: Hfx vol: NEBHvo_30 - rep3

description:
Total RNA depleted using NEBNext Core Depletion set with 30 minutes of RNase digestion
HVO_pyrE_NEBHVO30_3
ΔpyrE


title: D80 PUR+IWP2

value: PAX2nG Positive


title: mWT3


title: 15VP1

value: F


title: D20 CTRL

value: Day 20


title: 15VP3


title: mKO1


title: 14VP1

value: PBS


title: D20 PUR


title: Hfx vol: NEBHvo_30 - rep2

description:
Total RNA depleted using NEBNext Core Depletion set with 30 minutes of RNase digestion
HVO_pyrE_NEBHVO30_2
ΔpyrE


title: Hfx vol: Panarchaea - rep1

description:
Total RNA depleted using siTools Panarchaea kit
HVO_pyrE_pan_1
ΔpyrE


title: Hfx vol: NEBHvo_30 - rep1

description:
Total RNA depleted using NEBNext Core Depletion set with 30 minutes of RNase digestion
HVO_pyrE_NEBHVO30_1
ΔpyrE


title: mWT1


title: mWT2


title: D20 PUR+IWP2


title: Hfx vol: NEBHvo_120 - rep3

description:
Total RNA depleted using NEBNext Core Depletion set with 120 minutes of RNase digestion
HVO_pyrE_NEBHVO120_3
ΔpyrE


title: 12VP4


title: 14PV5


title: Hfx vol: NEBHvo_120 - rep2

description:
Total RNA depleted using NEBNext Core Depletion set with 120 minutes of RNase digestion
HVO_pyrE_NEBHVO120_2
ΔpyrE


title: Human DRG Donor 4

city: Athens

first: Oshri

last: Avraham

institute: University of Georgia

description: single nuclei

data_processing:
A digital expression matrix was obtained using the 10X Genomics Cell Ranger pipeline.
Quantification and statistical analysis were done with Partek Flow package (https://www.partek.com/partek-flow/).
Genome_build: Rnor_6.0, hg19
Supplementary_files_format_and_content: csv files containing the UMI count matrix

source_name: L4,5 DRG

extract_protocol:
Whole DRG’s were dissociated from rat with enzyme mix (Papain, Collagenase) to a single cell suspension, washed in 1X PBS+0.2%BSA solution, passed through a 40-micron cell strainer and FACS sorted using live/dead staining. For human DRG sample L4 lumbar DRG was removed from a 44 year old Asian female. The tissue was immediately snap-frozen and stored at -80C. For nuclei isolation, the entire DRG was processed into smaller pieces by cryopulverization using the CryoPrep. Tissue was then homogenized using EZ Nuclei Lysis Buffer with 0.5% RNasin, 0.5% SUPERase-In and 1mM DTT  or with CST buffer (NaCl2 146 mM, Tris HCl pH 7,5 10 mM, CaCl2 1mM, MgCl2 21 mM, 0.49% CHAP, 0.01% BSA, 0.5% SUPERasin-in, 0.5% RNasin Plus). The homogenate was filtered through a 50-micron filter. The samples were  centrifuged at 500g, 4ºC for 5 mins. The supernatant was removed and the pellet was resuspended in 1 mL of Nuclei Resuspension Buffer (NRB) consisting of 1x PBS, 1% Bovine Serum Albumin and 1% SUPERas-In followed by centrifugation. The final pellet was resuspended in 0.5 mL of NRB containing 6 μM DAPI and filtered through a 20 μm filter. Fluorescence Activated Nuclear Sorting (FANS) was performed to purify nuclei from debris on a FACSAria II (BD).
single-cell RNA-Seq libraries were prepared using GemCode Single-Cell 3′ Gel Bead and Library Kit (10x Genomics). polyA selection based RNA capture as per the manufacturer's instructions provided by 10X genomics platform.  Libraries were prepared as per manufacturer's insturctions provided by 10X genomics platform (https://www.10xgenomics.com/single-cell/). libraries were then constructed using standard instrutions of the 10x plaform.

value: Dorsal root ganglion (L4,5)

value: 45 yo male


title: Human DRG Donor 5

description: single nuclei

source_name: L5 DRG

value: Dorsal root ganglion (L5)

value: 51 yo female


title: Hfx vol: NEBHvo_120 - rep1

description:
Total RNA depleted using NEBNext Core Depletion set with 120 minutes of RNase digestion
HVO_pyrE_NEBHVO120_1
ΔpyrE

value: <delta>pyrE


title: 12VP2


title: Human DRG Donor 3

description: single nuclei

value: 23 to male


title: 12VP1


title: Human DRG Donor 2

description: single nuclei

value: 56 yo female


title: 24VP8


title: 11VP5


title: IgG

city: Rome

first: Irene

last: Bozzoni

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

institute: Sapienza University of Rome

description: IgG immunoprecipitate used as specificity control

data_processing:
Trimmomatic with parameters ILLUMINACLIP:path/to/adapter:2:30:10:8:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:18
Bowtie2 software was used to identify and discard reads mapping to human ribosomal RNAs
STAR software was used with following parameters: with parameters --outFilterIntronMotifs RemoveNoncanonical --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04
Alignment BAM files were further processed by filtering out reads mapping to mitochondrial genome, unlocalized and unplaced sequences and alternate loci using SAMtools and removing PCR duplicates using Picard Mark Duplicates
Calculation of transcript-level FPKM and log2 fold change (log2FC) values was performed using Cuffdiff versionv 2.2.1 with parameters -c 8 --library-norm-method quartile --dispersion-method blind -u --library-type fr-unstranded -b path/to/genome -M path/to/maskfile, the mask file being a GTF file containing the coordinates of rRNA and tRNA loci. Other steps of filtering are described in methods.
Genome_build: Genome build: GRCh38; Annotation: Ensembl release 90
Supplementary_files_format_and_content: tsv file containing for each enriched transcript its FPKM value in INPUT, IP and IgG samples and IP/INPUT and IP/IgG log2FC.

source_name: human myoblast DM1

growth_protocol: Human myoblasts were cultured in Human skeletal muscle growth medium (PromoCell) and differentiated using human skeletal muscle differentiation medium (PromoCell).

extract_protocol:
RNA extraction was performed using QIAzol reagent and miRNEasy spin columns (QIAGEN), following manufacturer’s instructions, and reverse transcription was performed with the Superscript VILO cDNA Synthesis Kit (Life Technologies)
Ovation RNA v2 followed by Ovation Ultralow v2 kit was used to prepare cDNA libraries. Sequencing reaction were perfomred by Illumina NovaSeq 6000 Sequencing system.

value: skeletal muscle

value: differentiating myoblast

tag: antibody

value: IgG


title: 11VP3


title: Hfx vol: NEBHvo_120 - rep4

description:
Total RNA depleted using NEBNext Core Depletion set with 120 minutes of RNase digestion
HVO_pyrE_NEBHVO120_4
ΔpyrE


title: IPDHX36

description: DHX36 immunoprecipitate


title: Control_rep2 [iCaM_2]

city: Wuhan

first: Yanqin

last: Zhou

state: Hubei province

address: No.1, Shizishan Street, Hongshan District

institute: Huazhong agricultural university

description: Control group. Rep2

data_processing:
Illumina Casava 1.8 software was used for basecalling
Clean reads were obtained by removing low quality reads and reads containing adapter. The clean reads were aligned to toxoplasma gondii TgGT1 genome  through HISAT2 v2.0.5.
Genome_build: TgGT1 reference genome for alignment: https://toxodb.org/common/downloads/release-43/TgondiiGT1/fasta/data/
Supplementary_files_format_and_content: Tab-delimited text files include read counts values for each sample.

organism: Toxoplasma gondii

source_name: TATI strain

growth_protocol: T. gondii strains were maintained in human foreskin fibroblasts (HFFs) cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 2% fetal bovine serum, 4 mM glutamine, and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted individually from tachyzoite samples using Transzol UP Reagent (TransGen Biotech) according to the manufacturer’s protocol.
The RNA library was generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB, USA).

treatment_protocol: The iCaM strain was inoculated into HFF cells, and treated with or without ATc for 40 h in 37℃ and 5% CO₂. Tachyzoites were harvested and filtered through 3.0 um membrane filters (Whatman). Each experimental group had 3 biological replicates.

tag: host cell type

value: human foreskin fibroblast cells (HFF)

tag: treatment

value: Control


title: 11VP1

value: CMV


title: Control_rep1 [iCaM_1]

description: Control group. Rep1


title: INPUT

description: Input sample

tag: cell type


title: Smcx_IP_delTsix_wtSmcx_day2

state: MI

description:
Tsix-del, Kdm5c-WT EpiLCs
Smcx_IP_wtSmcx_Merged.bw

data_processing:
Full length reads were mapped to mm9 and dm6 using Bowtie (v1.1.2). PCR-duplicates were removed. Technical duplicate BAM files were merged for further processing steps. All of the input BAM files (across all genotypes) were merged together. Smcx_IP_delTsix_koSmcx_rep2.fastq.gz was excluded because of a sample error.
Drosophila spike-in normalization factors were calculated based upon the number of reads that uniquely mapped to the Drosophila genome (after removal of PCR duplicates), as described in PMID: 25437568
For conversion to bigwig files, reads were extended to a total length of 180 bases from the first sequenced base. Libraries were normalized to the Drosophila correction factor.
Peaks were called using MACS2 software (version 2.1.0.20140616) using input bam files for normalization, with filters for a q-value < 0.1 and a fold enrichment greater than 1. Call line: macs2 callpeak -f BAM -g 1.87e9 -q 0.1 -m 1 150  -s 250 -t "IP File 1" "IP File 2" -c "Input File 1" "Input File 2".
Genome_build: mm9, dm6
Supplementary_files_format_and_content: Bigwig files represent genome coverage after normalizing using the Drosophila correction factor (Reads per Reference genome Per Million)

growth_protocol: Mouse ES cells were derived and grown as described in PMID: 17487198. To convert ESC to EpiLC, ESC lines were grown in 2i culture conditions (N2B27 medium consisting 50% DMEM/F12, 50% neurobasal media, 2 mM L-glutamine (GIBCO, #25030), 0.1 mM 2-mercaptoethanol (Sigma, #M7522), N2 supplement (Invitrogen #17502048), B27 supplement (Invitrogen #17504-044), supplemented with 1 μM GSK3 inhibitor CHIR99021 (Stemgent #04-0004), 1 μM MEK inhibitor PD0325901 (Stemgent #04-0006), and 1000 U/ml LIF (Millipore #ESG1106) in gelatin-coated tissue culture dishes for 4 passages.  To achieve EpiLC differentiation, cells were cultured in N2B27 medium supplemented with 10 ng/ml FGF2 (R&D Systems, #233-FB) and 20 ng/ml Activin A (R&D Systems, #338-AC) in Fibronectin (15 μg/ml) (Sigma#F1141)-coated tissue culture dishes for 48 hrs.

extract_protocol:
Sonicated chromatin was immunoprecipitated overnight with antibodies immobilized on Dynabeads Protein G.
Illumina TruSeq DNA Library Prep
ChIP-DNA was deproteinized, treated with Rnase-A, 3' end-repaired with T4 DNA polymerase and T4 Polynucleotide Kinase, 3' dA-tailed, ligated to adaptors, size selected and PCR amplified. Libraries were pooled and 280-600 bp were gel purified for sequencing.

treatment_protocol: ChIP was performed as described in PMID: 26804915, with a minor modification where we sonicated chromatin using truChIP sonicator (Covaris).

value: mouse epiblast like cells

value: wtSmcx

tag: chip antibody


title: Smcx_Input_delTsix_wtSMCX_day2

description:
Tsix-del, Kdm5c-WT EpiLCs
Smcx_merged_Input.bw


title: 10VP8

tag: damid

value: M


title: Smcx_IP_delTsix_koSmcx_day2

description:
Tsix-del, Kdm5c-KO EpiLCs
Smcx_IP_koSMCX.bw

value: koSmcx


title: DNA methylation-MIRAseq of Zbtb43+/+ adult sperm DNA replicate 2

first: Piroska

last: Szabó

address: 333 Bostwick ave NE

data_processing:
MIRA library: Libraries were prepared by the Van Andel Genomics Core form 2.5 ng of input material using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems, Wilmington, MA USA). Prior to PCR amplification, end repaired and A-tailed DNA fragments were ligated to Bioo Scientific NEXTflex Adapters (Bioo Scientific, Austin, TX, USA).  Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). 75 bp, single end sequencing was performed on an Illumina NextSeq 500 sequencer using a 75 bp mid-output sequencing kit (v2) (Illumina Inc., San Diego, CA, USA).  Base calling was done by Illumina NextSeq Control Software (NCS) v2.0 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.
Reads were aligned to the mm10 genome using bwa mem v0.7.17 with default parameters.
DeepTools v3.4.3 was used to generate bigWig files; bamCoverage was run with the parameters, ‘--binSize 10 --normalizeUsing “CPM” --extendReads 200’.
Assembly: mm10
Supplementary files format and content: BigWig files using counts-per-million normalization.
Supplementary files format and content: BED files containing peaks called by MACS2.

source_name: spermatozoa

extract_protocol:
DNA methylation MIRA-seq. Sperm collection by swim-up and DNA preparation: adult male mice were sacrificed at 3 months of age by CO2 asphyxiation and pairs of cauda epididymis were dissected and cleaned from fat tissue in 1 X PBS under microscope. Caudae were placed into 1 ml of M16 buffer, nicked with a blade three times, and were transferred with the buffer into a round bottom tube. 4 ml of additional M16 buffer was gently layered over the caudae. The samples were incubated, lid open, in a cell culture incubator at 37 °C with 5 % CO2 for 2 h. The top 4 ml was transferred into 15 ml tube without touching the bottom and the cell number was counted. The motile spermatozoa were pelleted down at 3000 RPM for 6 min. The sperm pellet was then suspended in 1ml sperm lysis buffer (0.1 M DTT and 2 mg/ml Proteinase K in 10 mM Tris-HCL pH 8.0, 10 mM EDTA and 1 % SDS) per cauda and was incubated at 55 °C overnight. The DNA was isolated with phenol-chloroform extraction and ethanol precipitation and was sonicated to an average fragment size of 200 bp using a Covaris E220 Evolution ultrasound sonicator.
MIRA-seq was carried out according to Jung (Jung et al., 2015). GST-MBD2b and His-MBD3L1 preparation: GST-MBD2b and His-MBD3L1 was purified from E. coli against GST, and His tags respectively. Both proteins were stored in salt-dialysis buffer (50 mM HEPES pH 7.4, 50 % glycerol, 5 mM 2-mercaptoethanol, and 150 mM NaCl) at -20 °C for no more than 6 months. MIRA reaction: MIRA proteins, 1 µg of GST-MBD2b and 1 µg His-MBD3L1, and the MagneGST beads (REF V8611, Promega) were preblocked with 500 ng unmethylated E.Coli genomic DNA in 1 X MIRA binding buffer (10 mM Tris-HCl pH 7.9, 50 mM NaCl, 1 mM DTT, 10 mM MgCl2, and 0.1 % Triton-X-100) at 4 °C for 20 min. 500 ng fragmented sperm DNA was combined with the with preblocked MBD2b and MBD3L1 proteins and the binding reaction was carried out at 4 °C, overnight with rotation. Next day, 5 µl preblocked MagneGST beads (REF V8611, Promega) were added to each MIRA rection and the bound fraction was captured by incubating at 4 °C for 1 h with rotation. The beads were collected using a magnetic stand. They were washed three times using 900 µl prechilled MIRA wash buffer (10 mM Tris-HCl pH 7.5, 400 mM NaCl, and 0.1 % Triton-X-100). After washing, the beads were captured using a magnetic stand and DNA was collected by adding 500 µl buffer PB from the Qiagen PCR purification kit (Catalog number: 28105) and DNA was isolated according to the kit’s instructions.

value: spermatozoa

value: Wild type

value: male

tag: dev stage

value: adult

value: 3 months old


title: CaM indirect knockout with Atc_rep3 [iCaM_ATC_3]

description: CaM was indirectly knocked out after adding Atc for 40 h. Rep3

value: CaM indirect knockout with Atc


title: DNA methylation-MIRAseq of Zbtb43+/+ adult sperm DNA replicate 1


title: DNA methylation-MIRAseq of Zbtb43-/- adult sperm DNA replicate 2


title: 10VP4

tag: pupid

tag: condition

value: F


title: DNA methylation-MIRAseq of Zbtb43-/- adult sperm DNA replicate 1


title: CaM indirect knockout with Atc_rep2 [iCaM_ATC_2]

description: CaM was indirectly knocked out after adding Atc for 40 h. Rep2


title: Human DRG_2A

address: 120 Cedar St

description: single nuclei

data_processing:
A digital expression matrix was obtained using the 10X Genomics Cell Ranger pipeline.
Quantification and statistical analysis were done with Partek Flow package (https://www.partek.com/partek-flow/).
Genome_build: Rnor_6.0, hg19
Supplementary_files_format_and_content: txt, mtx files containing the UMI count matrix

source_name: L4 DRG

value: Dorsal root ganglion (L4)

value: 44 yo female


title: human DRG_1A

description: single nuclei


title: CaM indirect knockout with Atc_rep1 [iCaM_ATC_1]

description: CaM was indirectly knocked out after adding Atc for 40 h. Rep1


title: Control_rep3 [iCaM_3]

description: Control group. Rep3


title: 10VP1

tag: rin

tag: batch


title: Smcx_Input_delTsix_koSmcx_day2

description:
Tsix-del, Kdm5c-KO EpiLCs
Smcx_merged_Input.bw

tag: genotype