title: HCC1954 cells, DMSO, 72 h

city: Yogyakarta

first: Adam

last: Hermawan

state: DI Yogyakarta

address: Sekip Utara II

department: Pharmacy

country: Indonesia

institute: Universitas Gadjah Mada

data_processing:
The qualities of cleaned reads were assessed using FastQC version 0.11.9 (https://github.com/s-andrews/FastQC)
the reports were compiled using MultiQC version 1.1 (https://multiqc.info).
The transcript were quantified using the pseudo-alignment method employing kallsito version 0.461
Supplementary files format and content: tab-delimited text files

source_name: Breast

growth_protocol: HCC1954 cells were culture using RPMI supplemented with 10% of FBS in 5% CO2 incubator

extract_protocol:
RNA was harvested using Bioline - Isolate II RNA Mini Kit.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: DMSO or PGB-0-ol, DMSO as control

tag: tissue

value: Breast

value: epithelial

value: WT

value: DMSO (as control)


title: HCC1954  cells, PGB-0-ol, 72 h

status: Public on Nov 26 2022

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: ESC_Day0_rep2_HiChIP

city: Salt Lake City

first: Dean

last: Tantin

state: UT

address: 15 North Medical Drive East

department: Department of Pathology

country: USA

institute: University of Utah

library_source: genomic

data_processing:
paired-end Illumina sequencing reads were aligned to the mouse Mm10 reference genome using HiC-Pro pipeline.
Hi-ChIP was analyzed using Hichipper to perform restriction site bias-aware modeling of the output from HiC-Pro and to call interaction loops.
Assembly: mm10
Supplementary files format and content: Paired end bed  (.bedpe) containing discovered loops
Library strategy: Hi-ChIP

molecule: genomic DNA

organism: Mus musculus

source_name: ESC

extract_protocol:
Chromatin was crosslinked with 1% formaldehyde in growth media and isolated using Hi-C lysis buffer supplemented with protease inhibitor.
Hi-ChIP as previously described by M. R. Mumbach et al.,.Nat Methods 13, 919-922 (2016).

value: ESC

value: Parental

tag: time

value: day 0


title: Experiment B JV5

city: Cambridge

first: Sophia

middle: Alisa

last: Wild

state: Cambridgshire

address: Robinson Way

department: School of Clinical Medicine

country: United Kingdom

institute: University of Cambridge and Cancer Research UK Cambridge Institute

library_source: transcriptomic single cell

data_processing:
10X Cell Ranger v3 was used to align transcriptomes to a custom index, including the mm9 mouse genome index and the barcode transcript
Sparse expression matrices for transcriptomes were produced using 10X Cell Ranger v3
Clonal annotation was produced by extracting barcodes from 10X data and enrichment PCRs using custom scripts
Assembly: Custom mm9 index with barcoding transcript.
Supplementary files format and content: .tsv files are tab seperated txt files and .mtx files are sparse expression matrices
Supplementary files format and content: .rds files are Seurat objects containing barcode annotation in metadata

molecule: polyA RNA

source_name: Tumor tissue

extract_protocol:
Tumours were harvested, dissociated into single cells using the tumor dissociation kit and the gentleMACS Octo dissociator from Miltenyi, and sorted for live-dead with propidium iodide. Sorted cells were resuspended in PBS + 0.04% BSA prior to counting with a hemocytometer. The final single cell suspension was diluted as required and prepared for sequencing using the Gene Expression 3' v3.1 dual index kit of 10X Genomics.
Libraries were prepared according to 10X Genomics instructions. After cdDNA amplification, 10 µL cDNA was split off for barcode enrichment PCRs. Transcriptimic library construction contiunued as in the 10X user guide instructions. Barcode enrichment PCRs were prepared using a custom targeted PCR with Illumina-indexed primers. Barcode libraries were purified using gel purification.

treatment_protocol: Seven days post implantation, tumor were treated with either DTX treatment 12.5 mg/kg for 3 times a week for two weeks) and JQ1 treatment at 75 mg/kg (5 days on, 2 days off until endpoint)

tag: strain

value: Balb/C

value: JQ1 vehicle treated


title: CoLa_seq_pladienolideB

city: Chicago

first: Jon

last: Staley

state: IL

institute: University of Chicago

data_processing:
Data were processed as follows: (1) 6 nt UMIs were trimmed from reads and attached to read names to maintain their association with reads using fastp (Chen et al., 2018a), (2) adaptors were trimmed using Cutadapt. Reads shorter than 15 nts were discarded, (3) the remaining reads were aligned to the human reference genome (hg38) with GENCODE transcriptome annotation (v26) using the STAR software (Dobin et al., 2013) with the following settings: --outSAMattributes NH HI AS nM NM MD jM jI XS --outFilterMultimapNmax 50 --outFilterMismatchNmax 15 --outSJfilterDistToOtherSJmin 10 0 5 10 --alignIntronMin 15 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 15 --outSAMtype BAM SortedByCoordinate --twopassMode Basic, (4) aligned read pairs were further filtered for unique mapping using samtools, (5) to remove RT mis-primed reads, raw reads were separately mapped without UMI trimming. If the UMI portion of a read was mapped to the genome without any mismatch, it is considered as a mis-primed read and removed from the reads that were mapped with UMI trimming. These RT mis-primed reads were removed using samtools and pysam, (6) PCR duplicates were removed using UMI-tools(Smith et al., 2017), (7) reads overlapping with ncRNAs (snRNAs, snoRNAs, miRNAs, rRNAs) were removed using samtools based on the GENCODE reference (v26). The remaining reads were used for downstream analyses.
Adaptors were removed by Cutadapt default setting. When applicable, UMIs are processed by fastp default setting.
Filtered reads were aligned using STAR.
Mapped reads were filtered for unique-mapping reads using samtools
Unique-mapping reads are deduplicated using either samtools or umi-tools when reads have UMIs
Bed files were generated using bedtools
Assembly: hg38
Supplementary files format and content: BED format; ELI and NLI reads identified in each dataset
Supplementary files format and content: tsv format; read abundance calculated by kallisto
Library strategy: CoLa-seq

growth_protocol: K562 cells were maintained with in RPMI + GlutaMAX (Life Technologies) supplemented with 10% (v/v) fetal bovine serum (Life Technologies). Cells were cultured at 37 C with 5% CO2

extract_protocol:
Chromatin RNA was isolated from K562 cells similar to previously described methods (Pandya-Jones and Black, 2009; Wuarin and Schibler, 1994; Werner and Ruthenburg, 2015), with modifications noted below. All the steps were performed with pre-chilled, ice-cold, freshly prepared RNase-free buffers using RNase-free equipment on ice or at 4 ˚C. Roughly 5% of subcellular fractions were saved for quality control (western and RNA fragment size analysis). Fifty million K562 cells were spun down at 100 x g for 3 minutes and washed twice with 15 mL of ice-cold 1X PBS (phosphate-buffered saline) and once with 1 mL of ice-cold 1X PBS. Washed cells were then gently resuspended in 1mL of 0.1% (v/v) Triton X-100-containing buffer A (10 mM HEPES (pH 7.5), 10 mM KCl, 10% glycerol, 0.116 g/mL sucrose, 1 mM DTT, 1x protease inhibitor, 2 mM EDTA) and lysed on ice for 9 min. After incubation, the lysed cells were centrifuged at 800 x g for 5 minutes at 4 ˚C. The supernatant corresponding to the cytoplasmic fraction was carefully removed. The remaining nuclei pellet was gently resuspended in 250 µL of NRB buffer (20 mM HEPES (pH 7.5), 75 mM NaCl, 50% glycerol, 0.5 mM EDTA, 1 mM DTT, 1x protease inhibitors). Then, 250 µL of NUN buffer (50 mM HEPES (pH 7.5), 300 mM NaCl, 0.2 mM EDTA, 1 M urea, 1 mM DTT, 1% NP-40) was slowly added and mixed by inversion. The resulting nuclei suspension was incubated on ice for 5 minutes and centrifuged at 800 x g for 5 minutes at 4 ˚C. The supernatant corresponding to the nucleoplasmic fraction was carefully removed. The chromatin pellet was washed once with 500 µL of premixed NRB/NUN buffer (1:1) and centrifuged at 800 x g for 5 minutes at 4 ˚C. The supernatant was carefully removed. The washed chromatin pellet was gently resuspended in 200 µL of NRB buffer. The chromatin pellet were extracted by Trizol (Invitrogen) followed by a second extraction with phenol:chloroform:isoamyl alcohol (25:24:1) and isopropanol precipitation. The isolated RNA was furthered treated with Turbo DNase (Invitrogen) to remove residual genomic DNA, followed by extraction with phenol:chloroform:isoamyl alcohol (25:24:1).  For each CoLa-seq library, chromatin-associated RNA from 200 million cells was used. To enrich for lariat RNA species (nascent lariat intermediates and excised lariat introns) from the chromatin-associated RNA, RNAs less than roughly 200 nts were removed using SPRI paramagnetic beads (Beckman Coulter) with a beads to sample ratio of 1:1.2. Note that this step also removes excised lariat introns derived from short introns and nascent lariat intermediates derived from short introns with short tails (i.e., short introns that form early during in-order splicing).  Next, ribosomal RNA was depleted using oligo-based Ribo-Zero Magnetic Gold Kit (Illumina) according to the manufacturer’s manual. During the optimization of CoLa-seq, we noticed abundant ncRNA reads in our libraries, similar to previous observations in mNET-seq (Mayer et al., 2015). To overcome this issue, biotinylated anti-sense oligos were designed to specifically target and deplete ncRNAs that were found to be abundant in our initial libraries (table S4). Briefly, for every g of rRNA-depleted RNA, a depletion reaction was assembled, containing 82.5 pmol of total depletion oligo mix (table S4), 2X SSC, and 5 mM EDTA. The depletion reaction was put through an oligo annealing cycle (5 min at 75 ˚C, cool down to 22˚C at 0.1 °C/sec), after which ncRNA bound biotinylated depletion oligos were pulled down using Dynabeads™ MyOne™ Streptavidin C1 beads (Invitrogen), according to the manufacturer’s manual. The RNA in the supernatant was purified using the RNA Clean and Concentrate kit (Zymo Research) and excess anti-sense oligos were removed by treatment with Turbo DNase (Invitrogen). Finally, according to the manufacturer’s instructions, purified RNA was treated with RppH (NEB) to decap linear RNA and then was degraded using Terminator 5’-3’ exonuclease (Lucigen). The resulting RNA was put through a size selection step to remove ≤200 nts RNA using SPRI paramagnetic beads (Beckman Coulter) with a beads to sample ratio of 1:1.2. The final RNA quantity is about 0.5-1% of the starting material.
Once the chromatin RNA was enriched for lariat species, ~500 ng of RNA was used for CoLa-seq library prep. The 3’ ends of RNA were ligated to a pre-adenylated 3’ end adapter (table S5), which includes a 6 nt UMI (unique molecule identifier) at the 5’ end to allow correction for PCR duplication and RT mis-priming. The ligation reaction contained 17.5% PEG-8000 (w/v), 1X T4 RNA ligase buffer (NEB), 1 µM of the pre-adenylated 3’ end adaptor, and 10 units/µL T4 RNA Ligase 2 (truncated K227Q, NEB). The ligation reaction was incubated for 3 hours at 22 ˚C. After the reaction excess adapters were removed by size selection using SPRI paramagnetic beads (Beckman Coulter) with a beads to sample ratio of 1.6:1. Then, the adapter-ligated RNA was used for cDNA synthesis using 0.25 µM of RT primer (table S5) and 10 units/µL of Superscript III (Invitrogen) at 50 ˚C for 1 hour, according to the manufacturer’s manual. Afterwards, to degrade excessive RT primer, 3.5 µL of ExoSAP-IT was added to the cDNA synthesis reaction and incubated for another 30 min at 37 ˚C. The reaction was stopped by adding 10 µL of 0.5M EDTA and RNA was degraded by adding 10 µL of 1 N NaOH. The resulting cDNA was cleaned up using Oligo Clean & Concentrator columns (Zymo Research) and was circularized with Circligase (Lucigen), according to the manufacturer’s manual. Final library amplification was performed on the circularized cDNA using Phusion polymerase (Thermo Fisher Scientific) with primers that add sequencing adaptor sequences and specific sequencing indices, which are located in the reverse primers (table S5). The number of PCR cycles was between 15 and 18 cycles. The amplified product was run on a 6% TBE gel and DNA fragments between 175 and 750 bps were gel purified and 3 nM of the library was sequenced in a 100 bp paired-end mode on an Illumina HiSeq 4000.

treatment_protocol: K562 cells at 90% confluency were treated for 2 hours with 10 µM of pladienolide B (Santa Cruz Biotechnology) in DMSO

value: pladienolide B

tag: protocol

value: CoLa-seq

tag: molecule subtype

value: Chromatin-associated RNA


title: chromation-associated-RNA-seq_rep1

data_processing:
Data were pre-processed as follows: (1) adaptors were trimmed using Cutadapt (Martin, 2011), with default parameters except discarding reads shorter than 15 nts, (2) remaining reads were aligned to the human reference genome (hg38) with GENCODE transcriptome annotation (v26) using the STAR software package (Dobin et al., 2013) with the following settings: --outSAMattributes NH HI AS nM NM MD jM jI XS, --outFilterMultimapNmax 50, --outFilterMismatchNmax 15, --outSJfilterDistToOtherSJmin 10 0 5 10 --alignIntronMin 15, --outSAMtype BAM SortedByCoordinate, --twopassMode Basic, (3) aligned reads were further filtered for unique mapping and proper alignment using samtools (Li et al., 2009). The resulting reads were used for downstream analyses. Separately, after the adapter removal step, reads were used for gene expression quantitation using Kallisto with default settings (Bray et al., 2016).
Adaptors were removed by Cutadapt default setting. When applicable, UMIs are processed by fastp default setting.
Filtered reads were aligned using STAR.
Mapped reads were filtered for unique-mapping reads using samtools
Unique-mapping reads are deduplicated using either samtools or umi-tools when reads have UMIs
Bed files were generated using bedtools
Assembly: hg38
Supplementary files format and content: BED format; ELI and NLI reads identified in each dataset
Supplementary files format and content: tsv format; read abundance calculated by kallisto

extract_protocol:
Chromatin RNA was isolated from K562 cells similar to previously described methods (Pandya-Jones and Black, 2009; Wuarin and Schibler, 1994; Werner and Ruthenburg, 2015), with modifications noted below. All the steps were performed with pre-chilled, ice-cold, freshly prepared RNase-free buffers using RNase-free equipment on ice or at 4 ˚C. Roughly 5% of subcellular fractions were saved for quality control (western and RNA fragment size analysis). Fifty million K562 cells were spun down at 100 x g for 3 minutes and washed twice with 15 mL of ice-cold 1X PBS (phosphate-buffered saline) and once with 1 mL of ice-cold 1X PBS. Washed cells were then gently resuspended in 1mL of 0.1% (v/v) Triton X-100-containing buffer A (10 mM HEPES (pH 7.5), 10 mM KCl, 10% glycerol, 0.116 g/mL sucrose, 1 mM DTT, 1x protease inhibitor, 2 mM EDTA) and lysed on ice for 9 min. After incubation, the lysed cells were centrifuged at 800 x g for 5 minutes at 4 ˚C. The supernatant corresponding to the cytoplasmic fraction was carefully removed. The remaining nuclei pellet was gently resuspended in 250 µL of NRB buffer (20 mM HEPES (pH 7.5), 75 mM NaCl, 50% glycerol, 0.5 mM EDTA, 1 mM DTT, 1x protease inhibitors). Then, 250 µL of NUN buffer (50 mM HEPES (pH 7.5), 300 mM NaCl, 0.2 mM EDTA, 1 M urea, 1 mM DTT, 1% NP-40) was slowly added and mixed by inversion. The resulting nuclei suspension was incubated on ice for 5 minutes and centrifuged at 800 x g for 5 minutes at 4 ˚C. The supernatant corresponding to the nucleoplasmic fraction was carefully removed. The chromatin pellet was washed once with 500 µL of premixed NRB/NUN buffer (1:1) and centrifuged at 800 x g for 5 minutes at 4 ˚C. The supernatant was carefully removed. The washed chromatin pellet was gently resuspended in 200 µL of NRB buffer. The chromatin pellet were extracted by Trizol (Invitrogen) followed by a second extraction with phenol:chloroform:isoamyl alcohol (25:24:1) and isopropanol precipitation. The isolated RNA was furthered treated with Turbo DNase (Invitrogen) to remove residual genomic DNA, followed by extraction with phenol:chloroform:isoamyl alcohol (25:24:1).
For each library, 10 µg chromatin-associated RNAs were depleted of ribosomal RNA depletion using Ribo-Zero Magnetic Gold Kit (human/mouse/rat; Illumina), according to the manufacturer’s instruction. Abundant ncRNAs were depleted as described in the section of enrichment for lariat RNA species (see methods). Then, 100 ng rRNA/ncRNA-depleted RNA was used to prepare an RNA-seq library using NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina, according to the manufacturer’s instruction. The final library was sequenced in a 100 bp paired-end mode on an Illumina HiSeq 4000.

value: RNA-seq


title: 18919X12: KO-6

data_processing:
Quality scores dipped towards the 3’ end of the reads, so reads were trimmed at 50 bases to eliminate poor-quality data.
The resulting 50-base reads were aligned to the mouse mm10 genome (GRCm38, December 2011) plus splice junctions using novoalign
Tests for differential gene expression were performed with DESeq2, version 1.10.0
Genome_build: mm10
Supplementary_files_format_and_content: raw reads counts in csv format

extract_protocol:
Cells suspensions were harvested by trypsinization and RNA was isolated using Trysol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: days of differentiation


title: 18919X10: KO-6


title: 18919X9: KO-3


title: ESC_Day0_rep1_HiChIP


title: lariat-seq_rep3

data_processing:
Data were processed according to previously described methods (Mercer et al., 2015; Pineda and Bradley, 2018).
Adaptors were removed by Cutadapt default setting. When applicable, UMIs are processed by fastp default setting.
Filtered reads were aligned using STAR.
Mapped reads were filtered for unique-mapping reads using samtools
Unique-mapping reads are deduplicated using either samtools or umi-tools when reads have UMIs
Bed files were generated using bedtools
Assembly: hg38
Supplementary files format and content: BED format; ELI and NLI reads identified in each dataset
Supplementary files format and content: tsv format; read abundance calculated by kallisto
Library strategy: Lariat-seq

extract_protocol:
Chromatin RNA was isolated from K562 cells similar to previously described methods (Pandya-Jones and Black, 2009; Wuarin and Schibler, 1994; Werner and Ruthenburg, 2015), with modifications noted below. All the steps were performed with pre-chilled, ice-cold, freshly prepared RNase-free buffers using RNase-free equipment on ice or at 4 ˚C. Roughly 5% of subcellular fractions were saved for quality control (western and RNA fragment size analysis). Fifty million K562 cells were spun down at 100 x g for 3 minutes and washed twice with 15 mL of ice-cold 1X PBS (phosphate-buffered saline) and once with 1 mL of ice-cold 1X PBS. Washed cells were then gently resuspended in 1mL of 0.1% (v/v) Triton X-100-containing buffer A (10 mM HEPES (pH 7.5), 10 mM KCl, 10% glycerol, 0.116 g/mL sucrose, 1 mM DTT, 1x protease inhibitor, 2 mM EDTA) and lysed on ice for 9 min. After incubation, the lysed cells were centrifuged at 800 x g for 5 minutes at 4 ˚C. The supernatant corresponding to the cytoplasmic fraction was carefully removed. The remaining nuclei pellet was gently resuspended in 250 µL of NRB buffer (20 mM HEPES (pH 7.5), 75 mM NaCl, 50% glycerol, 0.5 mM EDTA, 1 mM DTT, 1x protease inhibitors). Then, 250 µL of NUN buffer (50 mM HEPES (pH 7.5), 300 mM NaCl, 0.2 mM EDTA, 1 M urea, 1 mM DTT, 1% NP-40) was slowly added and mixed by inversion. The resulting nuclei suspension was incubated on ice for 5 minutes and centrifuged at 800 x g for 5 minutes at 4 ˚C. The supernatant corresponding to the nucleoplasmic fraction was carefully removed. The chromatin pellet was washed once with 500 µL of premixed NRB/NUN buffer (1:1) and centrifuged at 800 x g for 5 minutes at 4 ˚C. The supernatant was carefully removed. The washed chromatin pellet was gently resuspended in 200 µL of NRB buffer. The chromatin pellet were extracted by Trizol (Invitrogen) followed by a second extraction with phenol:chloroform:isoamyl alcohol (25:24:1) and isopropanol precipitation. The isolated RNA was furthered treated with Turbo DNase (Invitrogen) to remove residual genomic DNA, followed by extraction with phenol:chloroform:isoamyl alcohol (25:24:1).
10 µg chromatin-associated RNAs were depleted of ribosomal RNA depletion using Ribo-Zero Magnetic Gold Kit (human/mouse/rat; Illumina), according to the manufacturer’s instruction. To further enrich lariat RNA species, RNase R (Lucigen) digestion was performed to degrade linear RNA, according to the manufacturer’s instruction; treatment also trims tails of lariat RNA species. The resulting RNA was used to prepare an RNA-seq library using NEBNext Ultra™ Directional RNA Library Prep Kit from Illumina, according to the manufacturer’s instruction except for the RT step, during which 1 mM MnCl2 was included to facilitate reverse transcriptase go through the BP. The final library was sequenced in a 100 bp paired-end mode on an Illumina Hiseq 4000.

value: Lariat-seq

value: Rnase R treated Chromatin-associated RNA


title: 18919X11: KO-6


title: CoLa_seq_flavopirido

treatment_protocol: K562 cells at 90% confluency were treated for 2 hours with 1 µM of flavopiridol (Sigma)  in DMSO.

value: flavopirido


title: CoLa-seq_rep1


title: CoLa-seq_rep2


title: 117635 npl3-F245I (3) 37c

city: Würzburg

first: Kathi

last: Zarnack

address: Biocenter, Am Hubland

department: Theodor Boveri Institute

country: Germany

institute: University Würzburg

data_processing: For all genomic analyses, Saccharomyces cerevisiae S288c genome and gene annotation assembly (version R64-1-1) were downloaded from the EnsemblFungi database (https://fungi.ensembl.org/index.html). The annotation file was edited to replace all "transcript" entries with "Parent" and all "gene" entries with "ID". After initial quality control using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), RNA-seq reads were mapped using the splice-aware alignment tool STAR (version 2.7.2a) with the following parameters: --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.04. Reads were counted into exons using HTSeq-count from the HTSeq Python package. The following parameters were set: --stranded reverse --order pos --idattr ID --type exon.

organism: Saccharomyces cerevisiae

source_name: whole cell RNA extract

growth_protocol: overnight cultures were diluted to OD600 = 0.2 and kept growing in YPD at 30°C for ~4 hours till they reached mid-log phase. Cells with treatment were shifted to a shaking water bath at 37°C for 1 hour when reached mid-log phase before 10 ml culture was pelleted

extract_protocol:
total RNA was extraced from cell pellet of 10 ml mid-log phase grown cells using Trizol reagent (Invitrogen) and used according to manufactures protocol
Illumina TruSeq mRNA stranded; handled according to the manufacturer’s protocol

value: W303, npl3-shuffle, pRS315-npl3-F245I

value: 37°C 1 hour


title: 117633 npl3-F245I (1) 37c


title: 18919X8: KO-3


title: 18919X7: KO-3


title: CoLa-seq_DMSO_for_pladienolideB

treatment_protocol: K562 cells at 90% confluency were treated for 2 hours with DMSO  as a control for pladienolide B treatment.


title: 16141X12: KO-0


title: 117631 npl3-F245I (3) 30c

value: untreated


title: 117629 npl3-F245I (2) 30c


title: 16141X11: KO-0


title: 16141X10: KO-0


title: 117627 npl3-F245I (1) 30c


title: CoLa-seq_DMSO_for_flavopirido

treatment_protocol: K562 cells at 90% confluency were treated for 2 hours with DMSO as a control for flavipridol treatment.

value: DMSO


title: 18919X6: WT-6


title: 18919X5: WT-6


title: 117625 npl3-F162Y (3) 37c

value: W303, npl3-shuffle, pRS315-npl3-F162Y


title: 18919X4: WT-6

value: ESC


title: 117623 npl3-F162Y (1) 37c


title: 117621 npl3-F162Y (3) 30c


title: 18919X3: WT-3

value: Parental


title: 117619 npl3-F162Y (2) 30c


title: 18919X2: WT-3


title: 16141X3: WT-0


title: 18919X1: WT-3


title: PC3_GFP-_3

city: New York

first: Naitao

last: Wang

state: NY

address: 1275 York Avenue

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

description: processed data file: log2_normalized_counts_RNAseq.csv

data_processing:
Extracted RNA was processed by Beijing Berry Genomics. The libraries were sequenced on Illumina HiSeq X TEN platform with 150 bp paired-end reads to obtain a minimum yield of 40 million.
Reads aligned to peak regions were counted using STAR. Read count normalization and differential accessible peaks were called with DESeq2. Normalized abundance was shown as TPM.
Genome_build: not provided
Supplementary_files_format_and_content: log2_normalized_counts_RNAseq.csv: Comma-separated text file includes log2_normalized_counts of all samples.

source_name: Human prostate cancer cell PC3

growth_protocol: DMEM + 10% FBS.

extract_protocol:
Total RNA was extracted with RNeasy Plus Mini Kit from Qiagen.
DNA and RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Based on the GFP intensity, we sorted out top 10% and bottom 10% cells as Wnt/β-catenin signaling active and inactive cells, respectively.

value: Sorted GFP- cells


title: PC3_GFP-_2


title: 117617 npl3-F162Y (1) 30c


title: 117615 npl3-P196D-A197D (3) 37c


title: 16141X1: WT-0


title: 16141X2: WT-0


title: 117613 npl3-P196D-A197D (3) 30c


title: 18932X3: H3K27me3

data_processing:
paired-end Illumina sequencing reads were aligned to the mouse Mm10 reference genome using Novocraft novoalign v3.8.2
ChIP was analyzed using the MultiRepMacsChIPSeq pipeline v12.2 using options “--pe --optdist 10000 --dupfrac 0.15 --mapq 10 --cutoff 2 --tdep 10 --peaksize 500 --peakgap 100 --species mouse --chrskip ‘chrM|PhiX’ --blacklist mm10.blacklist.bed”
Genome_build: mm10
Supplementary_files_format_and_content: Signal tracks (.bw) and narrow peak lists (.bed)

extract_protocol:
Chromatin was crosslinked with 1% formaldehyde and isolated sing Farnaham and RIPA buffer.
NovaSeq 2X50 bp Sequencing_100M read-pairs
NEBNext ChIP-seq Library Prep with Unique Dual Index primers

tag: antibody


title: 117611 npl3-P196D-A197D (1) 37c


title: 18932X2: Utx

source_name: Utx


title: 17425X4

data_processing:
Fastq files were demultiplexed with cellranger mkfastq version 3.1.0 to create the I1 sample index, R1 cell barcode and UMI, R2 RNA sequence
Reads were aligned to the refdata-cellranger-mm10-3.0.0 reference from 10x Genomics
Barcodes and UMIs were counted using cellranger count with expected-cells=6000
Genome_build: mm10
Supplementary_files_format_and_content: Filtered feature-barcode matrices in TSV and MEX format from cellranger count.

extract_protocol:
Single cells suspensions were harvested by trypsinization
10X Genomics Single Cell 5' Gene Expression library prep

value: differentiated toward mesodermal lineage

tag: differentiation day


title: PC3_GFP-_1


title: PC3_GFP+_3

value: Sorted GFP+ cells


title: 18932X1: Input

source_name: Input


title: 17425X3


title: 117609 npl3-P196D-A197D (2) 30c


title: 17425X1


title: PC3_GFP+_2


title: PC3_GFP+_1


title: 17425X2


title: 117605 NPL3 (3) 37c

value: W303, npl3-shuffle, pRS315-NPL3


title: DU145_GFP-_3

source_name: Human prostate cancer cell DU145


title: 117607 npl3-P196D-A197D (1) 30c


title: 17418X1

source_name: ESCs


title: ChIP-seq_16292X11

value: ESC differentiated toward mesodermal lineage

tag: chip antibody


title: 17418X2


title: 117603 NPL3 (1) 37c


title: ChIP-seq_16292X10

value: none (input)


title: DU145_GFP-_2


title: DU145_GFP-_1


title: ChIP-seq_16292X8


title: 117599 NPL3 (2) 30c


title: ChIP-seq_16292X3


title: DU145_GFP+_3


title: ChIP-seq_16292X2


title: 117597 NPL3 (1) 30c


title: 111419 npl3- F245I (2) 37c


title: DU145_GFP+_2


title: ChIP-seq_16292X1


title: 16141X17

value: ESCs differentiated using RA differentatiation protocol


title: 16141X16


title: 16141X18


title: 16141X15


title: 111417 npl3-F162Y (2) 37c


title: 16141X14


title: 111413 NPL3 (2) 37c


title: wildtype nephrectomy, sample 3, snRNAseq

city: leipzig

first: silke

last: zimmermann

state: Sachsen

institute: Universitätsklinikum Leipzig

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: build mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
brains were extracted followed by isolation of nuclei using FACS.
For experiments utilizing the 10x Genomics platform, the following reagents were used: Chromium Next GEM Single Cell 3′ Library kit v3.1 (PN-1000158), Chromium Next GEM Single Cell 3′ GEM Kit v3.1 (PN-1000130), Chromium Next GEM Single Cell 3’ Gel Bead Kit v3.1 (PN-1000129) and Dynabeads MyOne SILANE (PN-2000048) and were used according to the manufacturer’s instructions in the Chromium Single Cell 3′ Reagents Kits V3.1 User Guide. Single nuclei droplets were generated using 10X Genomics Droplet generator and in total 10,000 nuclei per sample were targeted.
Sequencing and read mapping: Generated libraries were sequenced on an Illumina NextSeq 500 at the Next Generation Sequencing Facility[ZS1]  of the Max Planck Institute of Biochemistry  with >50 x 103 reads per nucleus followed by de-multiplexing and mapping to the mouse genome (build mm10) using CellRanger v3.0 (10x Genomics) with standard settings and inclusion of introns for nuclear transcripts. Count matrixes were further analyzed with Seurat V4.2.0 R package

treatment_protocol: sham surgery versus 5/6 nephrectomy 6 weeks prior to harvest of tissue

value: brain

value: wildtype

value: 5/6 nephrectomy


title: wildtype nephrectomy, sample 1, snRNAseq


title: wildtype nephrectomy, sample 2, snRNAseq


title: 16141X12

value: ESCs


title: MDA-MB-231 cells, Vector Control

city: 淮北市

first: Zou

last: Deng

state: 安徽

address: 相山区

country: China

institute: Huaibei Normal University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

growth_protocol: MDA-MB-231 mesenchymal cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),

value: breat cancer cells

value: Vector Control


title: 117601 NPL3 (3) 30c

value: untreated


title: YCO19

city: SEOUL

first: Hee Seung

last: Lee

state: --- Select ---

address: SEOUL

country: South Korea

institute: Yonsei University

data_processing:
RNA sequencing was performed using a TruSeq Stranded mRNA Sample Prep Kit (Illumina). Adapter sequences and ends of reads with a Phred quality score less than 20 were trimmed, and reads shorter than 50 bp were simultaneously removed using cutadapt v.2.8. Filtered reads were mapped to the species reference genome using the aligner, STAR v.2.7.1a, following ENCODE standard options, with application of the "quantMode TranscriptomeSAM" option for estimation of transcriptome expression level. Gene expression levels were estimated using RSEM v.1.3.1.
Assembly: UCSC hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Tumor organoid developed from cholangiocarcinoma epithelial cell

extract_protocol:
Samples separated by duct type (SD-type and LD-type) were used for RNA sequencing. RNA sequencing was performed using a TruSeq Stranded mRNA Sample Prep Kit (Illumina).
RNA libraries for RNA-seq were prepared using Truseq Stranded mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: ICCA organoid, large duct type

tag: disease state

value: cholangiocarcinoma


title: YCO18


title: YCO15


title: wildtype sham, sample 3, snRNAseq

value: sham


title: DU145_GFP+_1


title: wildtype sham, sample 2, snRNAseq


title: 16141X11


title: LysM-DKO/ApoE-/- aorta on western diet [scRNA-seq]

city: Boston

first: Xinlei

last: Gao

state: MA

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

description: 10x Genomics

data_processing:
The raw scRNA-seq data were processed using Cell Ranger (version 6.1.2) (10x Genomics). The reads were mapped to the prebuilt mouse mm10 genome.
The resulted gene expression matrix in individual single cells was processed by the R package Seurat (version 4.1.0). Low-quality cells with number of expressed genes less than 200 or larger than 5000 or with percentage of mitochondria reads greater than 10% were dropped out. Rarely expressed genes which were detected in less than 3 cells were removed. Mitochondria genes and ribosomal protein coding genes were removed from the expression matrix before normalization.
The high-quality data after these filtering steps was then used at additional processing steps including log normalization, data scaling, principal component analysis (PCA), cell clustering, and UMAP visualization. The cell clusters were visualized by the DimPlot function. Differentially expressed genes among cell clusters were identified by FindAllMarkers function using the default Wilcoxon test method, with minimal percentage of expressed cells as 25% and minimal log2 fold change as 0.25. Next, marker genes in each cell clusters were used to annotate cell types based on known marker genes in PanglaoDB database and literatures. The marker gene expressions were visualized by DotPlot and VlnPlot function. Trajectory analysis was conducted by Monocle3.
The metabolite-sensor cell-cell communication was analyzed by MEBOCOST. The data was analyzed following the tutorial on the MEBOCOST website (https://github.com/zhengrongbin/MEBOCOST). scRNA-seq expression data was used to estimate metabolite abundance and calculate communication score for each condition. Next, results of two conditions were combined to compare the communications. The differences in communication scores between two conditions were calculated. The prediction of sender-metabolite-sensor-receiver communication events were visualized by barplot, flow plot and circle plot. The metabolite abundance and sensor expression levels were exhibited by violin plot. Index of dispersion (IOD) was calculated using communication scores across conditions as described in the MEBOCOST paper. The top 100 most variable communications were selected for further investigation.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: aorta

extract_protocol:
WT and DKO mice were euthanized by CO2 inhalation. The aortas were isolated after perfusion with 30 mL of PBS through left ventricular and quickly transferred to cold DMEM medium. Aortas from the two groups were cut into about small pieces and digested with an enzyme solution (5mg/mL collagenase type I, 5mg/mL collagenase type IV, and 5mg/mL liberase) for 90min at 37 °C on a shaker. The digested cell suspension was filtered through a 40 μm strainer and washed twice with PBS. The cells were resuspended and ready for sequencing in PBS with 0.04% bovine serum albumin, and their viability was over 90%.
Single-cell RNA-Seq library construction was performed using the protocol provided by 10X Genomics. In brief, the single-cell suspensions from both groups, reagents, gel beads and partitioning oil were loaded to 10X Chromium Chip G to generate single-cell Gel Beads-in-emulsion (GEMs, Single cell 3’ Reagent Kits v3.1, 10X Genomics). scRNA was barcoded through reverse transcription in individual GEMs followed by a post GEM-RT cleanup and cDNA amplification. Then, a 3’-gene expression library construction was performed. Finally, the library was sent for sequencing.

value: aorta

value: LysM-DKO/ApoE-/-

value: western diet


title: 16141X10


title: WT/ApoE-/- aorta on western diet [scRNA-seq]

description: 10x Genomics

value: WT/ApoE-/-


title: LysM-DKO aorta on normal diet [scRNA-seq]

description: 10x Genomics

value: LysM-DKO

value: normal diet


title: 16141X13

value: ESCs differentiated using RA differentatiation protocol


title: 111415 npl3-P196D-A197D (2) 37c

value: 37°C 1 hour


title: MDA-MB-231 cells, OE-YWHAB

value: OE-YWHAB


title: 16141X9

value: Parental


title: wildtype sham, sample 1, snRNAseq

value: brain

value: wildtype


title: WT aorta on normal diet [scRNA-seq]

description: 10x Genomics

value: WT


title: YCO13


title: 16141X8


title: ABCG1KO macrophage, replicate 2

description: ABCG1KO macrophage, replicate 2

data_processing:
The raw reads of RNA sequencing data were mapped to the mouse genome (version mm10) using STAR (version 2.7.9a) or TopHat (version v2.1.1).
The read count was calculated for each gene by htseq-count (version 0.11.2).
For differential expression analysis of epsin deficient and wild type macrophage dataset, the read count matrix produced by htseq-count was imported into the R package DESeq2 (version 1.30.1).
For the ABCG1 knock out dataset, we first performed a batch effect removal on the log10 transformed TPM expression matrix using ComBat in the R package sva (version 3.38.0). Then, the R package limma was used to do differential expression analysis for the batch effect removed expression matrix.
Assembly: mm10
Supplementary files format and content: Tab separated text files containing read counts

source_name: macrophage

extract_protocol:
Total RNA was extracted from primary macrophages with Qiagen RNeasy Mini Kit based on manufacturer’s instruction including the optional step to eliminate genomic DNA.
For RNA sequencing, extracted RNA from primary macrophages with Qiagen RNeasy Mini Kit based on manufacturer’s instruction were sent to BGI Genomics Company (San Jose, USA) for RNA sequencing.

value: macrophage


title: YCO11

value: ICCA organoid, small duct type


title: YCO10

value: cholangiocarcinoma


title: 16141X7


title: ABCG1KO macrophage, replicate 1

description: ABCG1KO macrophage, replicate 1


title: 16141X6


title: ChIP-seq_16292X9

value: ESC differentiated toward mesodermal lineage


title: YCO9


title: YCO14

value: ICCA organoid, large duct type


title: YCO8


title: LysM-DKO macrophage, replicate 2

description: LysM-DKO macrophage, replicate 2


title: 16141X5


title: 16141X3

value: ESCs


title: YCO7


title: 16141X2


title: YCO4


title: Input DNA

city: Beijing

first: Yu

last: Zhang

address: Xueyuan Road

institute: Peking University Health Science Center

data_processing:
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. Low-quality reads include two types, and the reads meeting any one of the two conditions will be removed: 1) Unknown bases are more than 10%; 2) The ratio of bases whose quality was less than 20 was over 10%.
After filtering, the remaining reads are called "clean reads" and stored as FASTQ format. The clean data was mapped to the reference genome by BOWTIE, and the duplication reads were further removed. The peak positions were then determined by MACS using aligned bam file as input.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Bedgraph files record reads coverage.

source_name: R1 cells

extract_protocol:
For ChIP-seq, the crosslinked protein-DNA complex was extracted from the sonicated nuclei and isolated with antibody.
Enriched DNA for ChIP-seq, sequencing was end polished with T4 DNA polymerase and kinase. An 'A' base was added to the polished DNA fragments, followed by the Qiaquick column clean up. Sequencing adaptors were ligated to the DNA fragments and enriched by 15 cycles of PCR amplification. 200-300 bp size fractions were selectively isolated from the 1% agarose gel and eluted by the Qiagen gel extraction kit. The extracted DNA was quantified by Qubit 2.0 and subjected to HiSeq 2500 sequencing according to the manufacturer’s instructions.

value: Embryonic stem cells


title: WT macrophage, replicate 3

description: WT macrophage, replicate 3


title: WT macrophage, replicate 1

description: WT macrophage, replicate 1


title: WT macrophage, replicate 2

description: WT macrophage, replicate 2


title: YCO3


title: PDLSCs_osteogenic medium_PA_14 days_rep2

type: RNA

city: Xi’an

first: Honglei

last: Qu

address: 145, Changlexi Road

department: Department of Periodontology

institute: School of Stomatology, Fourth Military Medical University

description: Gene expression in PDLSCs after incubation in osteogenic medium with PA for 14 days

hyb_protocol: The hybridization was conducted with Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242). Cy3-labelled cRNA (yield > 1.65 μg and specific activity > 9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. The hybridization reaction was performed for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%). Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: The scanned images were analyzed with  Agilent Feature Extraction (FE) software.  Add the images (.tif) to be extracted to the FE Project. Save the FE Project (.fep) by selecting File > Save As and browse for desired location. Select Project > Start Extracting and export data to txt.

source_name: PDLSCs, osteogenic medium, PA, 14 days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  The specific activity (pmol dyes per μg cRNA) of the labeled RNA Dye incorporation and cRNA yield were determined by using the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Three groups of PA-exposed PDLSCs and paired BSA-exposed PDLSCs were collected and lysed, and total RNA was extracted using the TRIzol® Reagent (Invitrogen life technologies) following the manufacturer's recommendations.RNA quantification and quality were assured by NanoDrop ND-1000. RNA Integrity and gDNA contamination were tested by Denaturing Agarose Gel Electrophoresis.

treatment_protocol: PDLSCs were incubated in osteogenic medium (a-MEM containing 10% FBS, 0.1 mmol/L dexamethasone, 10 mmol/L b-sodium glycerophosphate, and 50 mg/mL ascorbic acid)  with the presence of palmitic acid (PA) or osteogenic medium with the presence of fatty acid-free bovine serum albumin (BSA) for 14 days.

tag: cell

value: periodontal ligament stem cells

tag: gender

value: female

tag: age


title: PDLSCs_osteogenic medium_PA_14 days_rep3

value: male


title: YCO5

tag: tissue


title: PDLSCs_osteogenic medium_BSA_14 days_rep3

description: Gene expression in PDLSCs after incubation in osteogenic medium with BSA for 14 days

source_name: PDLSCs, osteogenic medium, BSA, 14 days


title: DK19150_155

status: Public on Nov 25 2022

city: Chiba

first: Hidekazu

last: Nagano

state: Chiba

address: 1-8-1 Inohana

country: Japan

institute: Chiba University

data_processing:
Sequencing was performed on the Illumina NextSeq 500 using NextSeq 500/550 High Output Kit v2.5.
Analyzed using bclfastq ver 2.17.
Assembly: hg38
Supplementary files format and content: bam, count, rpm

source_name: pituitary adenoma

extract_protocol:
Total RNA was extracted from all tumor tissues using P/GTC.
QuantSeq 3’mRNA-Seq Library Prep Kit for Illumina

value: pituitary gland

tag: tumor type

value: GH-producing pituitary adenoma


title: DK19150_156


title: DK19150_157


title: PDLSCs_osteogenic medium_PA_14 days_rep1


title: PDLSCs_osteogenic medium_BSA_14 days_rep2


title: LysM-DKO macrophage, replicate 3

description: LysM-DKO macrophage, replicate 3

tag: cell type

value: LysM-DKO

value: normal diet


title: DK19150_159

value: Nonfunctional pituitary adenoma


title: DK19150_154


title: 16141X4

tag: genotype

value: Parental

value: ESCs differentiated using RA differentatiation protocol


title: LysM-DKO macrophage, replicate 1

description: LysM-DKO macrophage, replicate 1

value: macrophage

tag: treatment


title: DK19150_105


title: DK19150_103


title: DK19150_102


title: DK19150_100


title: 16141X1


title: DK19150_158


title: DK19150_096


title: DK19150_098


title: Uhrf2_ChIPSeq

tag: cell line


title: DK19150_101


title: DK19150_099


title: DK19150_095


title: PDLSCs_osteogenic medium_BSA_14 days_rep1


title: DK19150_093


title: DK19150_091


title: DK19150_090


title: DK19150_092


title: DK19150_083


title: DK19150_084


title: DK19150_089


title: DK19150_087


title: DK19150_088


title: DK19150_085


title: DK19150_082


title: DK19150_081


title: DK19150_078


title: DK19150_080


title: DK19150_079


title: DK19150_077


title: DK19150_073


title: DK19150_071


title: DK19150_094


title: DK19150_072


title: DK19150_076


title: DK19150_068


title: DK19150_069


title: DK19150_074


title: DK19150_070


title: DK19150_067


title: DK19150_065


title: DK19150_097


title: DK19150_064


title: DK19150_062


title: DK19150_061


title: DK19150_059


title: DK19150_060


title: DK19150_057


title: DK19150_058


title: DK19150_075


title: DK19150_056


title: DK19150_054


title: DK19150_055


title: DK19150_053


title: DK19150_051


title: DK19150_047


title: DK19150_050


title: DK19150_066


title: DK19150_046


title: DK19150_048


title: DK19150_049


title: DK19150_052


title: DK19150_044


title: DK19150_063


title: DK19150_045


title: DK19150_043


title: DK19150_040


title: DK19150_042


title: DK19150_041


title: DK19150_036


title: DK19150_031


title: DK19150_034


title: DK19150_152


title: DK19150_029


title: DK19150_028


title: DK19150_033


title: DK19150_027


title: DK19150_026


title: DK19150_023


title: DK19150_022


title: DK19150_025


title: DK19150_039


title: DK19150_020


title: DK19150_018


title: DK19150_017


title: DK19150_016


title: DK19150_037


title: DK19150_021


title: DK19150_038


title: DK19150_019


title: DK19150_011


title: DK19150_010


title: DK19150_013


title: DK19150_009


title: DK19150_012


title: DK19150_006


title: DK19150_007


title: DK19150_003


title: DK19150_002


title: DK19150_015


title: Nudt7-/-  Knockout, Female, Western Diet - 3

city: Morgantown

first: Quincy

middle: Alexander

last: Hathaway

state: WV

address: 1 Medical Center Drive

institute: West Virginia University

description: For RNASeq experiments, RNA was isolated from mouse liver as described above and sequenced by the West Virginia University Genomics Core Facility. Total RNA was used for library construction using the KAPA mRNA HyperPrep Kit (Roche) and run on the HiSeq 2500 (Illumina) in 50bp paired end reads

data_processing:
Fastq files were aligned and mapped using Salmon (v1.3.0)
Briefly, a decoy-aware index was prepared using the Mus musculus primary genome assembly (Ensembl v101). Salmon was run using quantification mode, with no other parameter alterations. Tximport (v1.16.1) and tximeta (v1.6.3) were implemented to import transcript-level abundance and estimated counts, apply gene level information, and collate the quantification data.
Differential expression analysis was performed using DESeq2 (v1.28.1) and data were filtered for low abundance transcripts using "keep <- rowSums(counts(dds) >= 10) >= x", with a minimum read count of 10 for at least half of the samples within the dataset being analyzed.
Read count extraction and normalization were performed using CLC genomic benchwork
Pathway analyses was performed using Kyoto Encyclopedia of Genes and Genomes (KEGG v1.1.1) nd were visualized using pathfindR (v1.6.1)
Assembly: GRCm38 – mm10
Supplementary files format and content: Salmon (v1.3.0) qunatification files (.sf)

source_name: Liver

growth_protocol: Mice were housed at a room temperature of 22.2 ± 0.2 °C, room humidity of 40% ± 2%, and a 12-h light/12-h dark cycle, with the dark cycle starting at 6:00 PM.

extract_protocol:
RNA was isolated from flash frozen tissue using the TRI Reagent, as per manufacturer’s instructions. Following the removal of genomic DNA with Turbo DNA-free kit (Thermo Fisher Scientific), mRNA levels were quantified by RT-PCR using the Quantitect SYBR Green RT-PCR kit (Qiagen).
Total RNA was used for library construction using the KAPA mRNA HyperPrep Kit (Roche)

treatment_protocol:
Whole-body Nudt7-/- mice were generated by CRISPR/Cas9 genome editing, which resulted in the deletion of exons 3 and 4 in the process of flanking this DNA region with LoxP sites. Single guide RNAs (5g, 5’-TCCCAACCCAACATAGTGGAAGG-3’ and 3g, 5’-TGGAATTACTCCCTAACCCCAGG-3’, protospacer adjacent motif sequences underlined) were selected and provided in a microinjection cocktail by Applied StemCell. The microinjection cocktail, which also included Cas9 mRNA and single-stranded donor oligonucleotides containing LoxP sequences and NdeI restriction sites, was injected into FVB mouse zygotes by the WVU Transgenic Core Facility.
A western diet (WD, Research Diets D12079B, 41% kcal from fat, and 0.2% cholesterol,) or low fat control diet (CD, Research Diets 98121701, 10% kcal from fat, 0% cholesterol) were fed to the Nudt7-/- and wild type mice starting at 6 weeks of age until they were sacrificed between 17 and 20 weeks of age. Aged-matched male and female mice were used in all experiments. Mice were either harvested in the fed state at 7:00 AM, or in the fasted state after being placed on cages with grids without food for 24 h prior to harvest.

value: Liver

tag: strain

value: Nudt7-/- CRISPR/Cas9 Knockout

value: Western Diet

tag: Sex

value: Female


title: Wildtype, Female, Western Diet - 4

value: WT


title: Nudt7-/-  Knockout, Female, Western Diet - 2


title: Nudt7-/-  Knockout, Female, Western Diet - 1


title: Wildtype, Female, Western Diet - 2


title: DK19150_008


title: Nudt7-/-  Knockout, Female, Control Diet - 3

value: Control Diet


title: Nudt7-/-  Knockout, Female, Control Diet - 2


title: Wildtype, Female, Western Diet - 1


title: DK19150_005


title: Nudt7-/-  Knockout, Female, Control Diet - 1


title: Nudt7-/-  Knockout, Female, Control Diet - 4


title: Wildtype, Female, Control Diet - 4


title: Wildtype, Female, Control Diet - 3


title: Wildtype, Female, Control Diet - 1


title: Wildtype, Female, Control Diet - 2


title: Nudt7-/-  Knockout, Male, Western Diet - 4

value: Male


title: Nudt7-/-  Knockout, Male, Western Diet - 3


title: DK19150_004


title: Wildtype, Male, Western Diet - 2


title: Nudt7-/-  Knockout, Male, Western Diet - 2


title: DK19150_001


title: Nudt7-/-  Knockout, Male, Western Diet - 1


title: Nudt7-/-  Knockout, Female, Western Diet - 4


title: Wildtype, Male, Western Diet - 4


title: Wildtype, Male, Western Diet - 3


title: Wildtype, Female, Western Diet - 3


title: Nudt7-/-  Knockout, Male, Control Diet - 4


title: Nudt7-/-  Knockout, Male, Control Diet - 2


title: Nudt7-/-  Knockout, Male, Control Diet - 3


title: Wildtype, Male, Control Diet - 4


title: Wildtype, Male, Control Diet - 3


title: Wildtype, Male, Control Diet - 2


title: Wildtype, Male, Control Diet - 1


title: lact_3

city: Marburg

first: Wilhelm

last: Bertrams

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps University 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 mouse reference genome using default mapping parameters
Mapped total reads were analysed with the R package DeSeq2 v. 1.22.2 in R version 3.5.1, and the contrasts Lactate vs. Control and IPA vs. Control were calculated
The DeSeq2 output, namely the contrasts Lactate vs. Control and IPA vs. Control, is provided as excel file processed_results.xlsx
Genome_build: GRCm39
Supplementary_files_format_and_content: processed_results.xlsx, DeSeq2 contrast of Lactate vs. Control and IPA vs. Control

source_name: murine T cells

extract_protocol:
CD4+ T  cells were obtained from lymph nodes and spleens and total RNA was isolated with the EXTRACT ME total RNA kit (blirt).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Murine CD4+ T cells were purified from spleens and lymph nodes and differentiated for 48 hours under Th17-polarizing conditions in the presence or absence of lactate and IPA, respectively.

value: female

value: CD4+ T cells

value: spleen and lymph nodes

value: lactate (25 mM)


title: ipa_1

value: IPA (50 µM)


title: lact_2


title: ipa_2


title: ctrl_1


title: lact_1


title: ipa_3


title: Embryo Hi-C data 12

city: Rehovot

first: Nimrod

last: Rappoport

state: Shfela

address: 234 Herzl St.

country: Israel

institute: Weizmann Institute of Science

description:
genomic_bin_a_score_per_cell.txt
genomic_bin_coverage_per_cell.txt

data_processing:
scRNA-seq:
.Read_1 files were mapped into mm9 using bowtie2, using default parameters.
.Demultiplexing and UMI counting (UMI and cell barcodes are in read 2) was performed using the pipeline described in Jaitin et al. 2014 (10.1126/science.1247651).
UMI counts were analyzed using the metacell package as described in Baran et al. 2019 (https://doi.org/10.1186/s13059-019-1812-2), and the results of the analysis are in metacell_expression.txt
scHiC: Standard Illumina base-calling pipeline.
Sequence processing pipeline Paired-end reads of sequencing batches were de-multiplexed to single cell datasets based on the two 8 bp unique identification tags attached to each cell during the Tn5-transposase tagmentation. Reads lacking a perfect match were discarded. Reads were broken down to segments on their matches to the MboI recognition site (GATC), concatenating segments shorter than 16 bp with their adjacent segment. Each segment was independently mapped to the Mus Musculus genome (assembly mm9) using Bowtie2 in end-to-end alignment mode. The uniquely mapped (MAPQ > 36) segments from each paired-end read were consolidated into a chain of segments by merging segments mapped to overlapping genomic regions. Next, the segments chain was translated to a chain of fragment-ends (fends) by associating each segment with its downstream fend. Finally, adjacent fend pairs from all chains were used to comprise the contact map of the cell. All the analysis following used the distinct contacts, ignoring the number of times each contact appeared in the map.
Fends were then mapped to 40kb genomic bins. The genomic_bin_coverage_per_cell counts the number of fends mapped to every genomic bin.
Parts of the genome were designated as strict-A and strict-B regions, and for every 40kb genomic bin the numbers of contacts between the bin and strict-A or strict-B regions were counted (in the genomic_bin_a_score_per_cell files).
Genome_build: mm9

source_name: Mouse embryos

extract_protocol:
Pregnant C57BL/6 mice were sacrificed at day 9.5 post-coitum and embryos were dissected under a microscope. The yolk sack was mechanically removed from each embryo, leaving the embryo proper only, and the embryo morphology was validated to match that of a wildtype embryo of the appropriate age. To create single-cells suspension, each embryo was moved to a 1.5ml tube containing 200µl of trypsin-EDTA (0.05% trypsin, 0.02% EDTA) and incubated at 37ºC for 5 minutes. 800µl of cold MEF medium was then added to each tube to inactivate the trypsin.
Cell suspensions of all embryos were combined and MEF medium at room temperature was added to a final volume of 21ml. 3ml of 16% formaldehyde were added (2% formaldehyde final concentration) and the mixture was incubated for 10 minutes at room temperature, followed by quenching with 127mM glycine for 5 minutes on ice and washing with cold PBS + 0.001% BSA. Cells were then permeabilized in 10 mM Tris-Cl pH 8, 10 mM NaCl, 0.2% IGEPAL CA-630 and cOmplete EDTA-free protease inhibitor cocktail (Roche) for 30 min on ice with intermittent agitation, and spun to collect a nuclei pellet.  The nuclei were washed with 1.24x NEBuffer 3 (New England Biolabs) and suspended in 400µl of that buffer. 6µl of 20% SDS and then 40µl of 20% Triton X-100 were added to the suspension, with an incubation of 60 minutes at 37ºC with constant agitation following the addition of each of these detergents. Next 50µl of 25U/µl MboI (New England Biolabs) was added and the suspension incubated at 37ºC overnight with constant agitation.  To label the digested DNA ends, dCTP, dGTP, dTTP and biotin-14-dATP (Thermo fisher) were added to the suspension (final concentration of 28.36µM per nucleoside triphosphate) along with DNA polymerase I, large (Klenow) fragment (New England Biolabs, final concentration 0.095U/µl) and the sample incubated at 37ºC for 60 minutes with occasional mixing. The sample was then spun and the supernatant partially removed, leaving a volume of 50µl, followed by the addition of 100µl 10x T4 DNA ligase reaction buffer (New England Biolabs), 10µl 100x BSA (New England Biolabs), 10µl of 1U/µl T4 DNA ligase (Thermo Fisher) and water to a final volume of 1 ml, and incubated at 16ºC overnight. Finally, the nuclei were filtered through a 30µm cell strainer and single nuclei were sorted into individual empty wells in 384 well plates using an BD Influx cell sorter. The plates were sealed and stored at -80ºC until further processing.  To prepare single-cell Hi-C libraries from single nuclei in plate wells, 2.5µl of PBS was added to each well and the plate was sealed and incubated at 65ºC overnight. DNA was then tagmented using the Nextera XT kit (Illumina) by adding 5µl of TD and 2.5µl of ATM per well and incubating at 55ºC for 5 minutes, followed by cooling to 10ºC and adding of 2.5µl of NT per well. Hi-C ligation junctions were then captured by Dynabeads M-280 streptavidin beads (Thermo Fisher; 10µl of original suspension per well). Beads were prepared by washing with 1x BW buffer (5mM Tris-Cl pH 7.5, 0.5 mM EDTA, 1M NaCl), resuspended in 4x BW buffer (20mM Tris-Cl pH 7.5, 2mM EDTA, 4M NaCl; 4µl per sample), and then mixed with the 12.5µl per-well sample and incubated at room temperature overnight with gentle agitation. The beads were then washed four times with 40µl of 1x BW buffer, washed twice with 40µl of 10mM Tris-Cl pH 7.5 and resuspended in 12.5µl of 10mM Tris-Cl pH 7.5. Single-cell Hi-C libraries were amplified from the beads by adding 7.5µl of Nextera PCR Master Mix, 2.5µl of Index 1 primer and 2.5µl of Index 2 primer (a different combination of index 1 and index 2 per well) followed by 12 PCR cycles. The beads were then magnetically removed and the supernatant from all 384 wells combined. The combined supernatant was purified using AMPure XP beads (Beckman Coulter; 0.6 times volume of the supernatant) according to the manufacturer's instructions and resuspended in 100µl of 10mM Tris-Cl pH 7.5. Finally, the sample was purified again using AMPure XP beads (1.0 times volume of supernatant) and resuspended in 11µl of 10mM Tris-Cl pH 7.5.

tag: sample type

value: mouse embryos

tag: embryonic day


title: Embryo Hi-C data 11


title: Embryo Hi-C data 3


title: pEry Hi-C data

description:
genomic_bin_a_score_per_cell_pery.txt
genomic_bin_coverage_per_cell_pery.txt

source_name: CD71+, Ter119+ Mouse embryo cells

extract_protocol:
Day 10.5 embryos were placed in DMEM-high glucose, 10% FBS, 2mM L-glutamine, 1X MEM-Eagle non-essential amino acids and 12ug/mL heparin. Embryos were decapitated and circulating peripheral blood was allowed to flow into the droplet of the room temperature media from the severed vitelline and umbilical veins. Media was collected and fixed in 2% paraformaldehyde. Cells were stained for CD71 and Ter119, and Hi-C was performed on double positive cells.
Single cell libraries were constructed following established protocol (Nagano et al., 2017) using Illumuna Nextera XT kit.


title: ctrl_2


title: Embryo Hi-C data 6


title: Embryo Hi-C data 9


title: Embryo Hi-C data 2


title: ctrl_3


title: Embryo Hi-C data 1


title: Embryo Hi-C data 4


title: Embryo Hi-C data 8


title: Embryo Hi-C data 10


title: Nudt7-/-  Knockout, Male, Control Diet - 1


title: Embryo Hi-C data 5


title: Wildtype, Male, Western Diet - 1


title: POLR3A input in MDA-LM2 rep 1

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

data_processing:
FASTQ reads were trimmed using cutadapy (v1.8) and with -m 15 -q 15 parameters
FASTQ reads were mapped to the human genome (hg19) using Bowtie2 (v2.2)
ChIPseeqer (v2.0) was used to call peaks for every ChIP vs input samples with -t 10 -fold_t 1.5 parameters
Peaks were then sorted and combined using mergeBed into a single annotation (with -d 50)
Package DESeq was then used to compare the read counts in each peak between the MDA-231 and MDA-LM2 cells
Genome_build: hg19
Supplementary_files_format_and_content: ChIPseeqer target files (text)

growth_protocol: MDA-MB-231 and its highly metastatic derivative LM2 cells were cultured with  DMEM media supplemented with 10% FBS, sodium pyruvate, and L glutamine.

extract_protocol:
400 uL Lysis buffer (1% SDS, 50 mM Tris Hcl pH 8.0 20 mM EDTA, protease inhibitors (Roche)) and incubated on ice for 10 minutes. Lysates were then sonicated to produce DNA fragments between 200 – 1000 bp with settings Amplitude 70, 10 sec on 30 sec rest for three repetitions on Sonicator S-4000 (Branson) with Microtip and Ultrasonic Liquid Processor (Misonix)
Samples were PCR amplified with Illumina barcodes to construct a multiplexed library.
50 SR HiSeq at the Rockefeller Genomics Resource Center

treatment_protocol: For cross-linking, 1% formaldehyde was added to cells at 37oC for 10 minutes, and quenched with glycine at a final concentration of 0.14 M for 30 minutes at room temperature

tag: rep


title: POLR3A input in MDA-231 rep 1


title: POLR3A ChIPseq in MDA-LM2 rep 1

description: ChIP-seq

tag: antibody


title: POLR3A ChIPseq in MDA-LM2 rep 2

description: ChIP-seq


title: Embryo Hi-C data 7


title: POLR3A ChIPseq in MDA-231 rep 1

description: ChIP-seq


title: POLR3A ChIPseq in MDA-231 rep 2

description: ChIP-seq


title: POLR3A input in MDA-231 rep 2


title: Single 2 cell embryo. Sample 9 ex1 Condition: SR1848_NR5A2OE

city: Munich

first: Pavel

middle: Andreevich

last: Kravchenko

state: Planegg

address: Am Klopferspitz 18

department: Totipotency

institute: Max-Planck-Institute of Biochemistry

data_processing:
Base calling was performed using bcl2fastq Conversion Software by the Department of Totipotency, MPIB
Low quality reads were trimmed out using TrimGalore (version 0.6.2) using parameters: --nextera --trim-n --paired --quality 20 --nextera
Reads have been checked for contamination with BBMap (version 38.90) using parameters: ref=mm10,hg19 ambig2=all
Read pseudoalignment was done using Kallisto (version 0.46.1) using parameters: -b 100. All reads were aligned to mm10 genome index file.
Count tables have been created in R (version 3.5.1) with tximport (version 1.20.0). Differential expression was assesed with DESeq2 (version 1.32.0).
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: single embryo

growth_protocol: Mouse zygotes  were isolated at 5 hours post fertilization and cultured. Due to the hydrophobic nature of the inhibitor, embryos were cultured in wet chambers without oil.

extract_protocol:
Single embryo SmartSeq2 protocol with oligo dT priming
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: From 6 hpf, 10 uM SR1848 (Sigma) or 0.1% DMSO was added to the KSOM in which the embryos were cultured.

tag: developmental stage

value: 2 cell

value: 10 uM SR 1848 + 500 ng/µl NR5A2 mRNA


title: Single 2 cell embryo. Sample 9 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 8 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 7 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 6 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 4 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 4 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 40 ex2 Condition: SR1848_NR5A2OE


title: POLR3A input in MDA-LM2 rep 2


title: Single 2 cell embryo. Sample 38 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 35 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 5 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 36 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 6 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 3 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 33 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 39 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 5 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 32 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 3 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 37 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 30 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 34 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 31 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 2 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 7 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 8 ex2 Condition: SR1848_NR5A2OE


title: Pheochromocytoma sample 2 carrying co-occurrent mutations in NF1 and DLST

city: Madrid

first: Alberto

last: Cascón

address: Melchor Fernández Almagro 3

department: Human Cancer Genetics Program

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

data_processing:
HTSeq-Counts from CNIO series were generated with BlueBee® Genomics Platform (Lexogen, 090-094), from FASTQ files obtained from QuantSeq platform
STAR v2.5.2a algorithms were used to map the reads respectively to the reference genome GRCh38
The sample was integrated with previous samples, and batch effects due to the different platforms were corrected using ComBat from R/Bioconductor package sva v3.26.0
DESeq2 normalization and log2 transformation was performed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include DESeq2 values for the sample

source_name: Pheochromocytoma

extract_protocol:
Total RNA extraction was performed from FFPE specimens using Maxwell RSC RNA FFPE Kit (Promega), following manufacturers’ protocol. 500 ng of total RNA was used as starting material
Libraries were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, 015) with a UMI Second Strand Synthesis Module for QuantSeq FWD (Lexogen, 081), according to vendor’s protocol

value: Pheochromocytoma

value: Primary tumor


title: Pheochromocytoma sample 1 carrying co-occurrent mutations in NF1 and DLST


title: Single 2 cell embryo. Sample 2 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 29 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 27 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 28 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 27 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 26 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 26 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 25 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 25 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 24 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 21 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 22 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 20 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 23 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 24 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 1 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 22 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 17 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 18 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 21 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 23 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 18 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 20 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 1 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 19 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 17 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 19 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 16 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 15 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 16 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 13 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 14 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 13 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 15 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 12 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 11 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 11 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 10 ex2 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 14 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 12 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 10 ex1 Condition: SR1848_NR5A2OE


title: Single 2 cell embryo. Sample 8 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 9 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 9 ex1 Condition: SR1848


title: Single 2 cell embryo. Sample 5 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 8 ex1 Condition: SR1848


title: Single 2 cell embryo. Sample 4 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 5 ex1 Condition: SR1848


title: Single 2 cell embryo. Sample 7 ex1 Condition: SR1848


title: Single 2 cell embryo. Sample 7 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 6 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 3 ex1 Condition: SR1848


title: Single 2 cell embryo. Sample 4 ex1 Condition: SR1848


title: Single 2 cell embryo. Sample 24 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 23 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 21 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 2 ex1 Condition: SR1848


title: Single 2 cell embryo. Sample 3 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 2 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 1 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 22 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 1 ex1 Condition: SR1848


title: Single 2 cell embryo. Sample 19 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 17 ex1 Condition: SR1848


title: Single 2 cell embryo. Sample 16 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 18 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 6 ex1 Condition: SR1848


title: Single 2 cell embryo. Sample 15 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 16 ex1 Condition: SR1848


title: Single 2 cell embryo. Sample 15 ex1 Condition: SR1848


title: Single 2 cell embryo. Sample 14 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 14 ex1 Condition: SR1848


title: Single 2 cell embryo. Sample 20 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 13 ex1 Condition: SR1848


title: Single 2 cell embryo. Sample 11 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 12 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 10 ex1 Condition: SR1848


title: Single 2 cell embryo. Sample 11 ex1 Condition: SR1848


title: Single 2 cell embryo. Sample 17 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 7 ex1 Condition: DMSO

value: 0.1% DMSO

value: DMSO


title: Single 2 cell embryo. Sample 8 ex2 Condition: DMSO


title: Single 2 cell embryo. Sample 8 ex1 Condition: DMSO


title: Single 2 cell embryo. Sample 6 ex2 Condition: DMSO


title: Single 2 cell embryo. Sample 7 ex2 Condition: DMSO


title: Single 2 cell embryo. Sample 9 ex1 Condition: DMSO


title: Single 2 cell embryo. Sample 4 ex1 Condition: DMSO


title: Single 2 cell embryo. Sample 3 ex1 Condition: DMSO


title: Single 2 cell embryo. Sample 3 ex2 Condition: DMSO


title: Single 2 cell embryo. Sample 9 ex2 Condition: DMSO


title: Single 2 cell embryo. Sample 5 ex1 Condition: DMSO


title: Single 2 cell embryo. Sample 5 ex2 Condition: DMSO


title: Single 2 cell embryo. Sample 12 ex1 Condition: SR1848


title: Single 2 cell embryo. Sample 13 ex2 Condition: SR1848


title: Single 2 cell embryo. Sample 2 ex2 Condition: DMSO


title: Single 2 cell embryo. Sample 1 ex2 Condition: DMSO


title: Single 2 cell embryo. Sample 1 ex1 Condition: DMSO


title: Single 2 cell embryo. Sample 2 ex1 Condition: DMSO


title: Single 2 cell embryo. Sample 19 ex1 Condition: DMSO


title: Single 2 cell embryo. Sample 17 ex1 Condition: DMSO


title: Single 2 cell embryo. Sample 14 ex1 Condition: DMSO


title: Single 2 cell embryo. Sample 18 ex1 Condition: DMSO


title: Single 2 cell embryo. Sample 4 ex2 Condition: DMSO


title: Single 2 cell embryo. Sample 15 ex1 Condition: DMSO


title: Single 2 cell embryo. Sample 6 ex1 Condition: DMSO


title: Single 2 cell embryo. Sample 13 ex1 Condition: DMSO


title: Single 2 cell embryo. Sample 11 ex1 Condition: DMSO


title: Single 2 cell embryo. Sample 12 ex1 Condition: DMSO


title: Single 2 cell embryo. Sample 10 ex1 Condition: DMSO


title: PBS-treated Mouse 6 ILC2 sample

first: Gregory

last: Putzel

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

data_processing:
Raw sequence reads were mapped to the mm10 genome assembly using STAR aligner version 2.5.3
Reads per gene were counted using the Rsubread R package.
Assembly: mm10
Supplementary files format and content: gene_counts.tsv
Supplementary files format and content: Sample names followed by 3 rows of sample metadata, followed by raw counts for each gene (GeneID is NCBI Gene identifier)

source_name: colonic lamina propria

extract_protocol:
Nmur1-eGFP + ILC2s, Nmur1-eGFP + CD4 + T cells and Nmur1-eGFP – CD4 + T cells were purified by fluorescence-activated cell sorting (ILC2: CD45 + Lin – CD90.2 + CD127 + KLRG1 + , CD4 + T cells: CD45 + CD3 + CD5 + CD4 + ) from Nmur1 iCre-eGFP mice exposed to 3% DSS. RNA was extracted using the RNeasy Micro Kit (Qiagen).
RNA libraries were prepared using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (New England Biolabs).

value: colonic lamina propria

value: sorted ILC2s

value: PBS


title: PBS-treated Mouse 7 NMUR1+ CD4 sample

value: sorted NMUR1+ CD4 T cells


title: PBS-treated Mouse 8 NMUR1+ CD4 sample


title: PBS-treated Mouse 7 NMUR1- CD4 sample

value: sorted NMUR1- CD4 T cells


title: PBS-treated Mouse 8 NMUR1- CD4 sample


title: PBS-treated Mouse 6 NMUR1+ CD4 sample


title: PBS-treated Mouse 5 ILC2 sample


title: PBS-treated Mouse 7 ILC2 sample


title: PBS-treated Mouse 5 NMUR1+ CD4 sample


title: PBS-treated Mouse 5 NMUR1- CD4 sample


title: NMU-treated Mouse 4 NMUR1+ CD4 sample

value: NMU


title: NMU-treated Mouse 4 ILC2 sample


title: NMU-treated Mouse 3 ILC2 sample


title: Single 2 cell embryo. Sample 10 ex2 Condition: SR1848


title: NMU-treated Mouse 4 NMUR1- CD4 sample


title: NMU-treated Mouse 3 NMUR1+ CD4 sample


title: NMU-treated Mouse 3 NMUR1- CD4 sample


title: NMU-treated Mouse 2 NMUR1- CD4 sample


title: NMU-treated Mouse 2 NMUR1+ CD4 sample


title: NMU-treated Mouse 1 ILC2 sample


title: NMU-treated Mouse 1 NMUR1- CD4 sample


title: NMU-treated Mouse 2 ILC2 sample


title: Single 2 cell embryo. Sample 16 ex1 Condition: DMSO


title: PBS-treated Mouse 8 ILC2 sample


title: Single 2 cell embryo. Sample 10 ex2 Condition: DMSO


title: 82KO, Pcc-infected

city: Oeiras

first: Rui

last: Martins

address: Rua da Quinta Grande 6

department: Inflammation

country: Portugal

institute: Gulbenkian Institute for Molecular Medicine

data_processing:
Primary data analysis, including base calling and quality scoring is performed by real-time analysis (RTA) on the instrument during the sequencing run. The NextSeq 500 uses a new implementation of RTA called RTA 2.0
RNAseq reads were aligned to the mm39 genome using the GENCODE vM27 annotation to extract splice junction information. Alignment performed using STAR (v.2.5.2a) with parameters: --alignIntronMax 500000 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${SAMPLE} --sjdbOverhang 99 --sjdbGTFfile ~/All/GRCm39/gencode.vM27.primary_assembly.annotation.gtf --runThreadN 8
Read summarization was performed by assigning uniquely mapped reads to genomic features using FeatureCounts (v.1.5.0-p1), with following parameters: -a ~/All/GRCm39/gencode.vM27.primary_assembly.annotation.gtf -o -Q20 --primary --ignoreDup -T 4
Gene expression tables were imported into the R programming language and environment (v.4.1.0) and normalized gene expression counts were obtained using the DESEq2 R package (v.1.32) package with the function counts using the option normalized = TRUE.
Genome_build: mm39
Supplementary_files_format_and_content: Tab-delimited feature counts table with raw gene counts for every gene; one file per sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: TRAP mRNA from kidney

extract_protocol:
Translating Ribosome Affinity Purification (TRAP).  The approach used was adapted Dr. McMahon (University of South California, USA)60 and Dr. N. Heintz (Rockefeller University, NYC, USA). For affinity matrix preparation: Streptavidin MyOne T1 Dynabeads (150µl, Thermo fisher, 65602) were added per kidney in RNAse-free 1.5 or 2ml tube. Beads were washed (1x in PBS) and collected on magnet (>1 min.) discarding supernatant. Use 500µl 1*PBS (AM9625, Thermofisher, diluted with RNAse-free water (AM9939, Thermofisher)) to resuspend. Thaw Protein L on ice, add 60µl of Protein L per kidney into Beads suspension. Incubate the beads at room temperature in a tube rotator for 25 min.. Collect beads on magnet for at least 1 minute, remove supernatant. Wash beads with 1*PBS with 3% BSA (REF) 4 times. Transfer washed beads into a fresh tube. Resuspend beads in 500µl low salt buffer per kidney (1ml 1M HEPES-KOH (REF), 3.75ml 2M KCl (AM9640G, Thermofisher), 500µl MgCl2 (AM9530G, Thermofisher), 5ml NP-40 (P-1505, Hölzel Diagnostika Handels GmbH), 39.75ml RNAse-free water to prepare 50ml low salt buffer. 1µl 100mg/ml Cycloheximide (C7698-1G, Sigma) per 1ml low slat buffer and 0.5µl 1M DTT (DL-Dithiothreitol, Sigma, D9779) per 1ml low slat buffer were added freshly for usage). Add 25µg/per kidney of each Monoclonal anti-GFP antibody (Core Facility, Memorial Sloan-Kettering Cancer Center, New York, USA.  clone number 19F7 and 19C8). Incubate the beads with antibodies at 4°C for 1 hour in a tube rotator. Collect beads on Magnet at least 1minute, and then remove the supernatant. Wash beads with low salt buffer for 3 times. Resuspend beads in 200µl low salt buffer per kidney for further use.  Tissue homogenates preparation: Briefly, Egfp-L10Pepck and Slc40a1PepckΔ/ΔEgfp-L10Pepck mice were sacrificed and perfused (10mL, ice-cold PBS) and kidneys were harvested, minced on ice in 2ml dissection buffer per kidney (10mL, 10x HBSS, Thermofisher #14065056), 250µl 1M HEPES-KOH (REF), 3.5ml 1M D-Glucose (Sigma, G7528), 400µl NaHCO3 (SODIUM BICARBONATE BIOXTRA, Sial, S6297), 85.85ml RNAse-free water to prepare 100ml dissection buffer, 1µl 100mg/ml Cycloheximide per 1ml dissection buffer was added freshly for usage). Slices were transferred and homogenized in 1ml lysis buffer per kidney (1ml 1M HEPES-KOH (REF), 3.75ml 2M KCl (AM9640G, Thermofisher), 500µl MgCl2 (AM9530G, Thermofisher), 44.75ml RNAse-free water to prepare 50ml Lysis buffer. 1µl 100mg/ml Cycloheximide (C7698-1G, Sigma) per 1ml Lysis buffer, 1 tab of Protease inhibitors (cOmplete™, Mini, EDTA-free Protease Inhibitor Cocktail, #11836170001, Roche) per 10ml Lysis buffer, 10µl RNasin RNase inhibitor (PROMN2515, Promega) and 10µl Superasin RNase inhibitor (AM2696, Thermofisher) were added freshly for usage). Centrifuge lysate at 2000*G, 4°C for 10 min., and transfer supernatant to fresh cold 1.5ml tube.  Add 100µl NP-40 (P-1505, Hölzel Diagnostika Handels GmbH) per 1ml of supernatant, and gently mix by inverting. Then add 100µl DHPC (prepared at 300mM, Avanti Polar Lipids, 850306P) per 1ml of supernatant, and gently mix by inverting. Incubate the mixture on ice for 5 min.. Centrifuge lysate at 20,000*G 4°C for 15 min.. Transfer the supernatant to a fresh cold 1.5ml tube for further use.  Immunoprecipitation: Add 200 µL of affinity matrix per kidney lysate (1mL). Incubate the mixture in rotator (4oC, 30 min.). Mixture was placed on pre-chilled Magnet  (1 min.) and the  supernatant was removed. Beads  were washed (50mL High salt buffer stock: 1 mL 1M HEPES-KO, 8.75 mL 2M KCl, 500 µL MgCl2, 5mL NP-40, 34.75 mL RNAse-free water) by gentle pipetting (5x) ….1µl 100mg/ml Cycloheximide (C7698-1G, Sigma) per 1ml low slat buffer and 0.5µl 1M DTT (DL-Dithiothreitol, Sigma, D9779) per 1ml high slat buffer were added freshly for usage). Remove the tube from magnet, place at room temperature for 5 min.. Resuspended beads in 100µl RNA extract lysis buffer (containing 20µl 2M DTT per 1ml lysis buffer) provided in QIAGEN RNeasy Micro Kit (Qiagen, #50974004). Vortex the beads and buffer for at least 5 seconds at high speed. Porceed with RNA extraction with QIAGEN RNeasy Micro Kit (Qiagen, #50974004) following the instructions .
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were infected with Plasmodium chabaudi chabaudi (Pcc) AS (PcAS) by intra-peritoneal (i.p.) inoculation of blood from infected mice infected (2x10^6 infected RBC; iRBC).

value: Kidney

value: 17.6 week old

tag: infection

value: Pcc infected for 7 days


title: 24WT, Pcc-infected

value: 11 week old


title: 7WT, Pcc-infected

value: 13.7 week old


title: 74WT, Pcc-infected

value: 19 week old


title: 60KO, uninfected

value: 17.9 week old


title: 68WT, uninfected

value: 14.3 week old


title: 13KO, Pcc-infected

value: 15 week old


title: 63KO, uninfected


title: 61KO, uninfected


title: Single 2 cell embryo. Sample W56 Condition: NT

description:
txi.kallisto_counts_normalized.csv
txi.kallisto_counts_raw.csv
CmpS_RNA-Seq_DESeq2.csv

data_processing:
Base calling was performed using bcl2fastq Conversion Software by the Department of Totipotency, MPIB
Low quality reads were trimmed out using TrimGalore (version 0.6.2) using parameters: --nextera --trim-n --paired --quality 20 --nextera
Reads have been checked for contamination with BBMap (version 38.90) using parameters: ref=mm10,hg19 ambig2=all
Read pseudoalignment was done using Kallisto (version 0.46.1) using parameters: -b 100. All reads were aligned to mm10 genome index file.
Count tables have been created in R (version 3.5.1) with tximport (version 1.20.0). Differential expression was assesed with DESeq2 (version 1.32.0).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

value: 2 cell

value: 0.1% DMSO


title: 36WT, uninfected

value: 10 week old


title: Single 2 cell embryo. Sample W55 Condition: NT


title: Single 2 cell embryo. Sample W53 Condition: NT


title: Single 2 cell embryo. Sample W52 Condition: NT


title: Single 2 cell embryo. Sample W54 Condition: NT


title: Single 2 cell embryo. Sample W51 Condition: NT


title: Single 2 cell embryo. Sample W50 Condition: NT


title: Single 2 cell embryo. Sample W47 Condition: NT


title: Single 2 cell embryo. Sample W46 Condition: NT


title: Single 2 cell embryo. Sample W45 Condition: NT


title: 37KO, Pcc-infected

value: 10.9 week old


title: Single 2 cell embryo. Sample W43 Condition: NT


title: Single 2 cell embryo. Sample W42 Condition: NT


title: Single 2 cell embryo. Sample W44 Condition: NT


title: Single 2 cell embryo. Sample W41 Condition: NT


title: 45WT, uninfected

value: 10.7 week old


title: Single 2 cell embryo. Sample W39 Condition: NT


title: Single 2 cell embryo. Sample W40 Condition: NT


title: Single 2 cell embryo. Sample W31 Condition: NT


title: Single 2 cell embryo. Sample W37 Condition: NT


title: PBS-treated Mouse 6 NMUR1- CD4 sample

value: colonic lamina propria

value: PBS


title: Single 2 cell embryo. Sample W28 Condition: NT


title: Single 2 cell embryo. Sample W34 Condition: NT


title: Single 2 cell embryo. Sample W30 Condition: NT


title: Single 2 cell embryo. Sample W26 Condition: NT


title: Single 2 cell embryo. Sample W32 Condition: NT


title: Single 2 cell embryo. Sample W38 Condition: NT


title: Single 2 cell embryo. Sample W48 Condition: NT


title: Single 2 cell embryo. Sample W23 Condition: NT


title: Single 2 cell embryo. Sample W22 Condition: NT


title: Single 2 cell embryo. Sample W20 Condition: NT


title: Single 2 cell embryo. Sample W21 Condition: NT


title: Single 2 cell embryo. Sample W14 Condition: NT


title: Single 2 cell embryo. Sample W19 Condition: NT


title: Single 2 cell embryo. Sample W18 Condition: NT


title: Single 2 cell embryo. Sample W36 Condition: NT


title: Single 2 cell embryo. Sample W13 Condition: NT


title: Single 2 cell embryo. Sample W12 Condition: NT


title: Single 2 cell embryo. Sample W7 Condition: NT


title: Single 2 cell embryo. Sample W33 Condition: NT


title: Single 2 cell embryo. Sample W24 Condition: NT


title: Single 2 cell embryo. Sample W10 Condition: NT


title: Single 2 cell embryo. Sample W17 Condition: NT


title: Single 2 cell embryo. Sample S79 Condition: SR1848


title: Single 2 cell embryo. Sample W1 Condition: NT


title: Single 2 cell embryo. Sample W15 Condition: NT


title: Single 2 cell embryo. Sample W35 Condition: NT


title: Single 2 cell embryo. Sample W11 Condition: NT


title: Single 2 cell embryo. Sample W9 Condition: NT


title: Single 2 cell embryo. Sample W3 Condition: NT


title: Single 2 cell embryo. Sample W6 Condition: NT


title: Single 2 cell embryo. Sample W2 Condition: NT


title: Single 2 cell embryo. Sample S77 Condition: SR1848


title: Single 2 cell embryo. Sample S75 Condition: SR1848


title: Single 2 cell embryo. Sample S74 Condition: SR1848


title: Single 2 cell embryo. Sample S78 Condition: SR1848


title: Single 2 cell embryo. Sample S76 Condition: SR1848


title: Single 2 cell embryo. Sample S71 Condition: SR1848


title: Single 2 cell embryo. Sample S69 Condition: SR1848


title: Single 2 cell embryo. Sample W5 Condition: NT


title: Single 2 cell embryo. Sample S70 Condition: SR1848


title: Single 2 cell embryo. Sample S72 Condition: SR1848


title: Single 2 cell embryo. Sample S67 Condition: SR1848


title: Single 2 cell embryo. Sample S68 Condition: SR1848


title: Single 2 cell embryo. Sample S66 Condition: SR1848


title: Single 2 cell embryo. Sample W4 Condition: NT


title: Single 2 cell embryo. Sample S80 Condition: SR1848


title: Single 2 cell embryo. Sample S65 Condition: SR1848


title: Single 2 cell embryo. Sample S62 Condition: SR1848


title: Single 2 cell embryo. Sample S63 Condition: SR1848


title: Single 2 cell embryo. Sample S58 Condition: SR1848


title: Single 2 cell embryo. Sample S61 Condition: SR1848


title: Single 2 cell embryo. Sample S60 Condition: SR1848


title: Single 2 cell embryo. Sample S59 Condition: SR1848


title: Single 2 cell embryo. Sample S55 Condition: SR1848


title: Single 2 cell embryo. Sample S57 Condition: SR1848


title: Single 2 cell embryo. Sample S56 Condition: SR1848


title: Single 2 cell embryo. Sample S53 Condition: SR1848


title: Single 2 cell embryo. Sample S50 Condition: SR1848


title: Single 2 cell embryo. Sample S73 Condition: SR1848


title: Single 2 cell embryo. Sample S64 Condition: SR1848


title: Single 2 cell embryo. Sample S51 Condition: SR1848


title: Single 2 cell embryo. Sample S45 Condition: SR1848


title: Single 2 cell embryo. Sample S46 Condition: SR1848


title: Single 2 cell embryo. Sample S44 Condition: SR1848


title: Single 2 cell embryo. Sample S41 Condition: SR1848


title: Single 2 cell embryo. Sample S40 Condition: SR1848


title: Single 2 cell embryo. Sample S48 Condition: SR1848


title: Single 2 cell embryo. Sample S42 Condition: SR1848


title: Single 2 cell embryo. Sample S37 Condition: SR1848


title: Single 2 cell embryo. Sample S39 Condition: SR1848


title: Single 2 cell embryo. Sample S36 Condition: SR1848


title: Single 2 cell embryo. Sample S38 Condition: SR1848


title: Single 2 cell embryo. Sample S54 Condition: SR1848


title: Single 2 cell embryo. Sample S34 Condition: SR1848


title: Single 2 cell embryo. Sample S33 Condition: SR1848


title: Single 2 cell embryo. Sample S32 Condition: SR1848


title: Single 2 cell embryo. Sample S35 Condition: SR1848


title: Single 2 cell embryo. Sample S30 Condition: SR1848


title: Single 2 cell embryo. Sample S28 Condition: SR1848


title: Single 2 cell embryo. Sample S52 Condition: SR1848


title: Single 2 cell embryo. Sample S31 Condition: SR1848


title: Single 2 cell embryo. Sample S49 Condition: SR1848


title: Single 2 cell embryo. Sample S27 Condition: SR1848


title: Single 2 cell embryo. Sample S47 Condition: SR1848


title: Single 2 cell embryo. Sample S26 Condition: SR1848


title: Single 2 cell embryo. Sample S29 Condition: SR1848


title: Single 2 cell embryo. Sample S25 Condition: SR1848


title: Single 2 cell embryo. Sample S23 Condition: SR1848


title: Single 2 cell embryo. Sample S43 Condition: SR1848


title: Single 2 cell embryo. Sample S24 Condition: SR1848


title: Single 2 cell embryo. Sample S21 Condition: SR1848


title: Single 2 cell embryo. Sample S22 Condition: SR1848


title: Single 2 cell embryo. Sample S20 Condition: SR1848


title: Single 2 cell embryo. Sample S19 Condition: SR1848


title: Single 2 cell embryo. Sample S16 Condition: SR1848


title: Single 2 cell embryo. Sample S18 Condition: SR1848


title: Single 2 cell embryo. Sample S15 Condition: SR1848


title: Single 2 cell embryo. Sample S14 Condition: SR1848


title: Single 2 cell embryo. Sample S17 Condition: SR1848


title: Single 2 cell embryo. Sample S12 Condition: SR1848


title: Single 2 cell embryo. Sample S11 Condition: SR1848


title: Single 2 cell embryo. Sample S9 Condition: SR1848


title: Single 2 cell embryo. Sample S8 Condition: SR1848


title: Single 2 cell embryo. Sample S7 Condition: SR1848


title: Single 2 cell embryo. Sample S6 Condition: SR1848


title: NMU-treated Mouse 1 NMUR1+ CD4 sample

value: sorted NMUR1+ CD4 T cells

value: NMU


title: Single 2 cell embryo. Sample S5 Condition: SR1848


title: Single 2 cell embryo. Sample S4 Condition: SR1848


title: Single 2 cell embryo. Sample S3 Condition: SR1848


title: Single 2 cell embryo. Sample S2 Condition: SR1848


title: Single 2 cell embryo Exp3 NT 9

description:
txi.kallisto_counts_normalized.csv
txi.kallisto_counts_batchcorrected_counts.csv
txi.kallisto_counts_raw.csv
C88_KD_RNA-Seq_DESeq2_all.csv
C88_KD_RNA-Seq_DESeq2_10th_percentile_th.csv

data_processing:
Base calling was performed using bcl2fastq Conversion Software by the Department of Totipotency, MPIB
Low quality reads were trimmed out using TrimGalore (version 0.6.2) using parameters: --nextera --trim-n --paired --quality 20 --nextera
Reads have been checked for contamination with BBMap (version 38.90) using parameters: ref=mm10,hg19 ambig2=all
Read pseudoalignment was done using Kallisto (version 0.46.1) using parameters: -b 100. All reads were aligned to mm10 genome index file.
Count tables have been created in R (version 3.5.1) with tximport (version 1.20.0). Batch correction have been done with BatchCorrectedCounts from CountClust (version 1.18.0). Differential expression was assesed with DESeq2 (version 1.32.0).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Isolated mouse oocytes were cultured in microdrops under 5% O2, 5% CO2, 90% N2. Oocytes were isolated in M2 medium supplemented with dbcAMP (Sigma, 300 mM) and FBS (20%), microinjected and further cultured for 5 hours in M16 supplemented with dbcAMP. Oocytes were released from dbcAMP and cultured for 12 hours in M16, followed by in vitro fertilization (In Vitro Fert, Cooks; supplemented with GSH (Sigma)). Fertilized embryos were cultured in KSOM

treatment_protocol: Isolated GV oocytes were microinjected with sets of two siRNAs against targets (20µM each) or control. As a control of successful injection 150 ng/µl H2B-EGFP (for control) or 150 ng/µl H2B-rsEGFP (for target) was co-injected.

value: negative control


title: JMO_stim3

first: Jonathan

middle: M

last: Dreyfuss

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
The reads were trimmed for adapters and filtered by sequencing Phred quality (>= Q15) using fastp. The count table was generated by aligning reads to the mouse transcriptome (Ensembl version 98) using kallisto and converting transcript counts to gene counts using tximport.
Assembly: mouse transcriptome (Ensembl version 98)
Supplementary files format and content: A CSV file of counts

source_name: Brown preadipocytes

extract_protocol:
Total RNA was isolated from cells using TRIzol reagent (Thermo Fisher Scientific). The KAPA mRNA HyperPrep kit for Illumina sequencing was used.
mRNA was pulled down using oligo-dT beads, and the resulting mRNA was converted into cDNA. The resulting cDNA then became a library through adapter ligation and post-PCR Cleanup.

value: Brown preadipocytes

value: JMO

value: stimulated with insulin


title: Single 2 cell embryo Exp3 NT 7


title: Single 2 cell embryo Exp3 NT 8


title: JMO_stim2


title: Single 2 cell embryo. Sample S10 Condition: SR1848


title: Single 2 cell embryo. Sample S1 Condition: SR1848


title: Single 2 cell embryo. Sample S13 Condition: SR1848


title: JMO_stim1


title: Single 2 cell embryo Exp3 NT 6