title: Embryo424_3_T

description:
Pooled RNA sequencing
RawGeneCounts.txt

value: Methionine-treated


title: FLIT mice day 3 rep2

status: Public on Feb 10 2023

type: SRA

city: Houston

first: Ziyi

last: Li

state: TX

address: 1400 Pressler Street

country: USA

institute: MD Anderson Cancer Center

library_source: transcriptomic

data_processing:
After qPCR and RNA sequencing, reads were mapped to the UCSC Mouse Reference Genome (mm9) using STAR (v2.7).48 Reads covering gene coding regions were counted with R/Bioconductor package GenomicRanges
Genome_build: mm9
Supplementary_files_format_and_content: csv file contains raw read counts for each gene

molecule: total RNA

organism: Mus musculus

source_name: Mice brain cortical tissue

growth_protocol: no in vitro growth

extract_protocol:
Qiagen RNA kit
RNA libraries were prepared for sequencing using standard Illumina protocols per Admera Inc

treatment_protocol: different pain models

tag: brain region

value: cortical

tag: age

value: Day 3

tag: model type

value: FLIT


title: Primary fetal cells - rep1

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description: female fetus

library_source: genomic

data_processing:
basecalls were generated by bcl2fastq v. 2.20.0.42
fastq files were trimmed using TrimGalore-0.5.0 with parameters --illumina --rrbs
Alignments were generated  bismark v0.22.1 and bowtie2 v2-2.3.5.1
MethylKit count files were generated using  R v 3.6.1 and methylKit v1.10.0
Genome_build: MesAur1.0
Supplementary_files_format_and_content: tab delimited with columns; chrBase,chr,base,strand,coverage,freqC,freqT

molecule: genomic DNA

organism: Mesocricetus auratus

source_name: Individual female SHF at 13.5 days of gestation

growth_protocol: This paragraph explains the growth of the primary fetal cells and of the MT2 cell line. Fetal primary cells were isolated at 13.5-days of gestation. Fetus were washed and transferred into sterile culture dishes containing wash solution, and the differentiated organs (head, viscera, and limbs) were discarded from each fetus.  The remainder of the fetus was minced, cells were dissociated by four rounds of enzymatic digestion (Dispase, 2 U/mL in calcium magnesium free phosphate buffered saline), washed and grown (DMEM, 15% FBS, 2% antibiotics (penicillin 5000 U/mL ; streptomycin 5000 µg/mL), pH 7.0 at 37°C, 10% CO2) for 24-48 h until 60-90% confluence. Cells were detached, counted and cryopreserved (DMEM pH 7.0, 10% FBS, 10% DMSO) until needed.  Being from fetuses, the collected cells are therefore a mixture of rapidly dividing cells at different stages of differentiation (stem, progenitor, and fully differentiated) of ectodermal (e.g. skin) and mesodermal (e.g. muscle, bone, cartilage) origin, and that grow in colonies in vitro.  The MT2 cell line used here was derived from benzo[a]pyrene induced morphologically transformed (MT) colony at Bioreliance (Dr. K Pant, Boston, MA, USA).  The cell line was then transferred to Dr. RF Newbold and Dr. JC Pickles (Brunel University London, UK.  See Pickles J.C. et al. 2016. Mutat.Res.Genet.Toxicol.Environ Mutagen. 802:50-58), who generously provided the cell line to us. Here at Health Canada (Ottawa, ON) the MT2 cell line was typed as "female" using kdm5c/d qPCR test.  It was maintained in DMEM, 20% FBS, 2% antibiotics (penicillin 5000 U/mL ; streptomycin 5000 µg/mL), pH 6.7 at 37°C, 10% CO2, until the experiment.

extract_protocol:
Cells were harvested using TryplE (thermofisher), resuspended 2x with dPBS, the frozen in cell pellet.  Genomic DNA was harvested following the Qiagen DNEasy kit.
Libraries were prepared from100ng genomic DNA using Diagenode's Premiere RRBS kit (catalogue number C02030032)

treatment_protocol: Four different stocks of female primary cells (biological replicates) were thawed and used without further culture as naïve cells for genomic DNA isolation (no treatment).  To test for effects of 5aCdR, a stock of MT2 cell line was thawed and seeded. Four plates received vehicle only (0.05% DMSO as final concentration), and four others were exposed to 5aCdR (5 uM, 48h).

tag: cell type

value: Primary fetal cells (see growth protocol)

tag: sh_cta treatment

value: no treatment

tag: days in culture

value: < 3 days, one passage

tag: adapter

value: GTAGAG


title: Embryo424_2_T

city: Madison

first: Hasan

last: Khatib

state: Wisconsin

address: 1675 Observatory Dr.

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

description:
Pooled RNA sequencing
RawGeneCounts.txt

data_processing:
The FASTQ files were demultiplexed with the bcl2fastq Conversion Software (v.2.20) and checked for reads quality with the FastQC software
To trim low-quality reads and bases and remove adapter sequences, Trimmomatic was used in each sample
The trimmed reads were then aligned to the sheep reference genome (Oar_rambouillet_v1.0) using the “--quantMode GeneCounts” option to obtain gene counts.
Assembly: Oar_rambouillet_v1.0
Supplementary files format and content: Matrix tables with gene counts for all genes and all sample

organism: Ovis aries

source_name: blastocyst

extract_protocol:
Total RNA was extracted from embryos using the RNAqueous-Micro Kit (Ambion, Austin, TX, USA). DNA removal and whole transcriptome amplification were performed using the REPLI-g WTA Single Cell Kit (Qiagen, Germantown, MD, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Embryos were grouped into 12 pools based on sire and dam information, of which six pools represent the treatment group and six pools the control group, each containing five embryos

tag: tissue

value: blastocyst

value: inner cell mass & trophectodetm

tag: treatment


title: Male_Pre_7

city: St. Louis

first: Joseph

last: Dougherty

state: MO

address: 660 S Euclid Ave, Campus Box 8232

department: Genetics

institute: Washington University in St. Louis

data_processing:
Barcode extraction from sample fastq - see bitbucket repository for script. Requires flanking 14 bp around barcode to be identical to design, plus a 10bp sequence to be found in between the flanks. All 10bp sequences extracted from Fastqs into text file.
Tabulation of barcode counts for each sample using table() in R. Subsequently, merging to a metadata table on designed barcodes to drop sequences that were not a perfect match to a designed barcode.
Filtering for low read counts, poor barcode representation across replicates, etc. Described at length in Supplementary Methods.
Calculation of log2(cpm RNA barcode) / log2(cpm DNA barcode) for each retained barcode in each sample.
Subtract the within-sample mean of "basal" (minimal-promoter-only) barcode expression from all other barcode expression values --> REML linear mixed model: expression ~ allele + sex + sex:allele + (1|BC), where BC is the unique barcode identifier to control for effects of barcode sequence.
Assembly: hg19-derived sequences (up to 126bp); see enclosed file "Reference-Barcode Sequences, their paired internal identifiers, and the corresponding sequence placed upstream of min promoter.txt" for each allele of each sequence and its paired reporter (RNA) barcodes
Supplementary files format and content: Tab-delimited text; barcode counts for each RNA sample and the DNA sample.

source_name: Hippocampus

growth_protocol: Ad libitum feeding in single-sex group housing on 12 hour light/dark cycle.

extract_protocol:
Hippocampus dissected away from rest of brain, homogenized with power drill in glass pestle with RNAse inhibitors and translation inhibitor cycloheximide, spun 2,000g, supernatant mixed with 10% NPC and 10% DHPC 20min on ice, 20,000g spin, part of supernatant added to trizol for "input" (total hippocampal) RNA and remainder used for immunoprecipitation of GFP+ ribosomes (i.e. TRAP). See methods in paper for full details.
Reporter-specific cDNA synthesis using a reverse-complementary primer, followed by PCR, digestion, adapter ligation, and index PCR. DNA from plasmid was prepared simultaneously, starting with the first PCR step. Each step was followed by a cleanup using size-selection beads (brands Ampure XP and Magbind).

treatment_protocol: Stereotactic delivery of AAV9 to 1 hippocampal coordinate at 2 depths per side, 2µL of AAV9 per site (4 sites/mouse) 28 days prior to tissue collection. Females received either ovariectomy surgery or sham surgery prior to AAV delivery during the same surgical session.

tag: tissue (trap fraction)

value: Total hippocampus

tag: material

value: RNA

tag: condition

value: Male


title: FLIT mice day 3 rep1


title: Sham mice day 0 rep 4

value: Day 0

value: Sham


title: Ram511_T

description:
Individual Reduced Representation Bisulfite Sequencing
MethylationCount.txt

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq Conversion Software (version 2.20, Illumina)
TrimGalore version was used to discard low-quality reads and bases and adapter sequences
Alignment to the sheep reference genome (Oar_rambouillet_v1.0) was performed using bowtie2 of the Bismark software, followed by deduplication to filter out duplicate reads and PCR errors
The CG methylation calling was performed using the “bismark_methylation_extractor” function
Assembly: Oar_rambouillet_v1.0
Supplementary files format and content: Matrix tables with methylation counts for every cytosine and every sample

source_name: Sperm

extract_protocol:
Genomic DNA was extracted from sperm using the Quick-DNA Miniprep Plus Kit (Zymo Research, Irvine, CA, USA) per the manufacturer’s protocol.
Reduced Representation Bisulfite Sequencing libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Six Polypay rams were selected, with three randomly assigned to the control diet and three to the treatment diet. The control diet was a general basal diet, and the treatment was the control diet plus a 0.22% addition (1.5g) top-dress of rumen-protected methionine (RPM Smartamine, Adisseo, Alpharetta, GA, United States).

value: Sperm


title: Donor 2, Septum, snRNA-seq

city: Chicago

first: Sebastian

last: Pott

state: IL

address: 920 E 58th St

institute: The University of Chicago

description:
10X Genomics
instrument model: Illumina NovaSeq 6000 or NextSeq 500
HeartAtlas_RNA_barcodes_03092023.tsv.gz
HeartAtlas_RNA_genes.tsv
HeartAtlas_RNA_counts.mtx

library_source: transcriptomic single cell

data_processing:
FastQ files were individually processed using an in-house scRNA-seq pipeline dropRunner. Briefly, dropRunner utilizes FastQC to obtain quality control metrics followed by fast and efficient alignment to human reference genome hg38 using STARsolo 2.6.197 in GeneFull mode with other parameters set to default. STARsolo performs alignment and quantification of gene expression in one package.
We quantified expression at the gene level using Gencode v29 gene annotations utilizing both intronic and exonic reads to improve clustering and downstream analyses of the snRNA-seq data. We extracted the raw gene-by-barcode expression matrices output by STARsolo for downstream analyses.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

organism: Homo sapiens

source_name: Interventricular septum

extract_protocol:
Single nuclei isolation was performed on the heart tissue aliquots as described in Litvinukova et al. 2020 (PMID:  32971526), with some modifications. Single heart aliquots were kept on dry ice until being transferred into a precooled 2 mL dounce homogenizer (Sigma) with 2 mL homogenization buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl, 1 mM dithiothreitol (DTT), 1x protease inhibitor, 0.4 U/µl, RNaseIn, 0.2 U/µl SUPERaseIn, 0.1% Triton X-100 in nuclease-free water). Samples were dounced 25 times with pestle A (loose) and 15 times with pestle B (tight), filtered through a 40-µm cell strainer, and centrifuged (500g, 5 minutes, 4ºC). Supernatant was discarded and the nuclei pellet was suspended in nuclei resuspension buffer (1x PBS, 1% BSA, 0.2 U/µL RnaseIn) and stained with NucBlue Live ReadyProbes Reagents (ThermoFisher). Hoechst-positive nuclei were enriched using fluorescence-activated cell sorting (FACS) on the FACSAria (BD Biosciences), obtaining between 172,500 and 350,000 nuclei while targeting a maximum of 350,000. Nuclei were sorted into 0.75 ml of resuspension buffer. Flow-sorted nuclei were counted in a C-Chip Disposable Hemocytometer, Neubauer Improved (INCYTO) before commencing with library preparation.
A portion of the sorted nuclei suspension was removed and brought to a concentration of between 700 and 1,200 nuclei per microliter. An appropriate number of nuclei were loaded on the Chromium controller (10X genomics) in order to target between 6,000-8,000 nuclei, according to V3 of the manufacturer’s instructions for the Chromium Next GEM Single Cell 3ʹ Reagent Kits (10X Genomics). 3’ gene expression libraries were amplified with 15 cycles during sample index PCR. QC was performed on 3’ gene expression cDNA and final libraries using a Qubit Fluorometer (ThermoFisher) and an Agilent 2100 Bioanalyzer (Agilent).
single nucleus RNA-seq library,  3' mRNA libraries (10x Genomics)

tag: individual

value: Donor 2

value: Interventricular septum

tag: Sex

tag: ancestry

value: White, European


title: Embryo423_2_C

description:
Pooled RNA sequencing
RawGeneCounts.txt

value: Control


title: Ram498_T

value: Methionine-treated


title: Sham mice day 0 rep 3

value: cortical


title: Male_IP_10


title: Male_IP_11


title: Ram444_C


title: Barcode decay_Day_15_1

city: Glasgow

first: Maximiliano

middle: M

last: PORTAL

address: Garscube Estate. Switchback road

country: United Kingdom

institute: Cancer Research UK Scotland Institute - The University of Glasgow

data_processing: Indexes for libraries demultiplexing: 0 days_1 - TTAGGC, 0 days_2 - TGACCA, 5 days_1 - ACAGTG, 5 days_2 - GCCAAT, 15 days_1 - ACTTGA, 15 days_2 - GATCAG.

molecule: polyA RNA

extract_protocol:
Total RNA was extracted using Trizol reagent.
Standard illumina libraries were generated using custom primers.
Target RNA was amplified from oligo dT generated cDNA using custom primers.

tag: cell line

tag: time point

value: Barcode decay_Day_15_1


title: Barcode decay_Day_15_2

value: Barcode decay_Day_15_2


title: Sham mice day 0 rep 2

tag: brain region


title: Ram424_T


title: Barcode decay_Day_5_2

value: Barcode decay_Day_5_2


title: Male_IP_8


title: Sham mice day 0 rep 1

tag: age


title: Barcode decay_Day_5_1

value: Barcode decay_Day_5_1


title: Barcode decay_Day_0_2

value: Barcode decay_Day_0_2


title: Embryo410_1_C

description:
Pooled RNA sequencing
RawGeneCounts.txt

value: blastocyst

value: inner cell mass & trophectodetm


title: Male_IP_7

value: RNA

value: Male


title: Donor 1, Septum, snRNA-seq

value: Donor 1


title: Ram410_C

value: Sperm


title: Male_IP_12

value: Total hippocampus


title: 22

city: Tomsk

first: Irina

last: Larionova

state: Tomsk oblast

address: Lenin Ave, 36, Tomsk, Tomsk Oblast, Russia

country: Russia

institute: Tomsk State University

data_processing:
Raw data quality control was performed using FastQC (FastQC, RRID:SCR_014583) and visualized by MultiQC (MultiQC, RRID:SCR_014982)
Read alignment was performed using STAR aligner (STAR, RRID:SCR_004463) with GRCh38 genome and Gencode annotations
The numbers of reads assigned to genomic features were calculated using featureCounts software (featureCounts, RRID:SCR_012919)
Subsequent analysis steps were performed using DESeq2 software (DESeq2, RRID:SCR_015687)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: ex vivo TAMs

growth_protocol: CD14+ Monocytes were isolated from the buffy coats of healthy donors by density gradients followed by positive magnetic selection using CD14+ MACS beads (no. 130-050-201, Miltenyi Biotech, Germany), resulting to 90–98% monocyte purity as confirmed by flow cytometry. Monocytes were cultured at the concentration of 106 cells/ml in serum-free X-VIVO medium (Lonza, Germany) supplemented with 10 ng/ml of macrophage colony-stimulating factor (M-CSF) (no. 300-25, Peprotech, Germany), 10−8 M of dexamethasone (no. D2915, Sigma-Aldrich, Germany) and 10 ng/ml of IL-4 (no. 200-04, Peprotech, Germany). Supernatants from MCF-7 cells were added to freshly isolated human primary monocytes at a final volume of 20% of a cultivation medium. Monocytes were differentiated to TAMs for 6 days in the presence of 7.5% CO2.

extract_protocol:
RNA isolation was performed with E.Z.N.A. Total RNA Kit (Omega Bio-Tek, USA) and RNeasy Plus Mini Kit (Qiagen, Germany). The cells were lysed in Lysis Buffer with beta-mercaptoethanol, and centrifuged on columns with wash buffers. RNA was eluted with RNAase-free DEPC-water. The concentration of RNA was measured on Qubit 3.0, the quality of RNA was determined by capillary electrophoresis on TapeStation (AgilentTechnologies, USA) and using R6K ScreenTape (Agilent Technologies, USA #5067-5367). RIN was 6,7-9,8.
RNA libraries were prepared with NEXT flex Rapid Directional qRNA-SeqKit using indexed barcodes NEXTflex-qRNA-8nt-Barcodes (NOVA-5198-02, Bioo Scientific, PerkinElmer Applied Genomics, USA) according manufacture`s protocols. Ribosomal RNA depletion was performed with NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (NEB #E7400, New England Biolabs Inc., USA).

treatment_protocol: Cisplatin (Cisplatin-Teva, Teva Pharmaceutical Industries, Ltd. L01XA01 injection solution) was used for chemotherapeutic treatment of TAMs in vitro. For ex vivo TAMs, cisplatin was used at the selected concentrations (20 μM, 40 μM, and 80 μM) to determine the optimal concentration for further analysis. The 20 μМ concentration of cisplatin was used for further analysis. Cisplatin was added on day 6 of macrophages differentiation and TAMs were incubated with cisplatin for 3 days.

value: ex vivo TAMs

tag: supernatants

value: MCF-7 cells

tag: donor

value: TAMs+cisplatin


title: Female_Pre_12


title: C9HRE_isogenicCTRL_iMN_2

city: Baltimore

first: Yang

last: Liu

state: MD

address: 615 N. Wolfe Street

department: Biochemistry and Molecular Biology

institute: Johns Hopkins University

data_processing:
Raw reads were processed with TrimGalore v0.6.7 (Felix Krueger, 2021) and controlled for quality with FastQC v.0.11.9.
The processed reads were mapped to the human genome (hg19) and GENCODE v19 annotated transcripts using Hisat2 (Kim et al., 2015) v2.2.1 and quantified with featureCounts (Liao et al., 2014) v2.0.1.
Supplementary files format and content: Raw gene counts were loaded into R to perform differential expression analysis with edgeR (Robinson et al., 2010) and generate plots and heatmaps.

source_name: human iPSCs-derived motor neurons

growth_protocol:
Human iPSCs were maintained in StemFlex medium (Gibco, A3349401), with medium exchange every other day.
Motor neuron differentiation: human iPSCs were seeded onto Matrigel-coated plates and differentiated into neuroepithelial progenitor cells (NEPCs) by culturing 6 days in neural medium (1:1 DMEM/F12:neurobasal medium, GlutaMax, N2 supplement, B27 supplement, and ascorbic acid) containing 3 μM CHIR99021, 2 μM SB431542, and 2 μM DMH-1. NEPCs were dissociated with dispase (1 U/ml) and split into new plates coated with Matrigel with a ratio of about 1:6. NEPCs were differentiated into motor neuron progenitor cells (MNPCs) using neural medium supplemented with 1 μM CHIR99021, 2 μM SB431542, 2 μM DMH-1, 0.1 μM retinoic acid (RA), and 0.5 μM purmorphamine. After culturing for 6 days, MNPCS were dissociated and cultured in suspension using neural medium containing 0.5 μM RA and 0.1 μM purmorphamine. Six days later, neural spheres were dissociated and plated onto a Matrigel-coated plate. Adherent neural spheres were cultured in neural medium supplemented with 0.5 μM RA, 0.1 μM purmorphamine, and 0.1 μM compound E. After 12 days, mature motor neurons were acquired for experiments. The medium was changed every other day during the entire differentiation period.

extract_protocol:
Total RNAs were extracted by an RNeasy Plus mini kit (Qiagen, 74136).
RNA libraries for sequencing were prepared using a commercial kit (Invitrogen, A39005096).

treatment_protocol: DAXX was knocked down by shRNAs using lentivirus infection

tag: cell type

value: human iPSCs-derived motor neurons

tag: genotype

value: isogenic control


title: scRNAseq_BdLTseq_HA1ER_clone_F12_1F8_1C9_HTO [scRNAseq_HA1ER_clone_F12_1F8_1C9]

description: 10x Genomics

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Indexes for libraries demultiplexing: Gene expression library index - CGTGACATGC (i7), TTTAGACCAT (i5), HTO library index - TAATGAGCG.
Samples demultiplexing using hashtag barcodes: HA1ER F12 - CTCCTCTGCAATTAC, HA1ER 1F8 - CAGTAGTCACGGTCA, HA1ER 1C9 - ATTGACCCGCGTTAG.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: protein

source_name: Cell line

extract_protocol:
Samples were multiplexed on a single lane of a Chromium Next GEM Chip G and processed using 10x Chromium controller (10x Genomics).
Chromium Next GEM Single Cell 3'Reagent Kits v3.1.
https://cdn.10xgenomics.com/image/upload/v1660261285/support-documents/CG000204_ChromiumNextGEMSingleCell3_v3.1_Rev_D.pdf

tag: library line

value: HTO


title: Female_Pre_11


title: C9HRE_isogenicCTRL_iMN_1


title: scRNAseq_BdLTseq_HA1ER_clone_F12_1F8_1C9_GEx [scRNAseq_HA1ER_clone_F12_1F8_1C9]

description: 10x Genomics

value: mRNA


title: 10


title: 10b


title: 21

treatment_protocol: Without cisplatin treatment

value: TAMs


title: Female_Pre_10


title: C9HRE_iMN_2_shDAXX

value: C9orf72 HRE Mutation

value: DAXX knockdown


title: Male_IP_9


title: Ram423_C

tag: tissue

value: Control


title: Female_Pre_9


title: 9b

tag: treatment


title: scRNAseq_BdLTseq_HA1E_E7clone_RAS_BdLTseq [scRNAseq_BdLTseq_HA1E_E7_clone_RAS]

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Indexes for libraries demultiplexing: Gene expression library indexes - TAACGCGTGA (i7), GAAGTTAGGG (i5), Hashtag library index - CGAGTAAT, BdLT-Seq library index CGTGAT, Oncogenes library index - TGGTCA.
Samples demultiplexing using hashtag barcodes: HA1E E7_ RAS_0days - TGTCTTTCCTGCCAG and CTCCTCTGCAATTAC, HA1E E7_ RAS_5days - CAGTAGTCACGGTCA and ATTGACCCGCGTTAG.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Samples were multiplexed on a single lane of a Chromium Next GEM Chip G and processed using 10x Chromium controller (10x Genomics).
Chromium Next GEM Single Cell 3'Reagent Kits v3.1. BdLTseq library was generated by capturing GFP cDNA using specific probes followed by library construction using custom primers.
https://cdn.10xgenomics.com/image/upload/v1660261285/support-documents/CG000204_ChromiumNextGEMSingleCell3_v3.1_Rev_D.pdf

value: polyA mCherry


title: Barcode decay_Day_0_1

value: Barcode decay_Day_0_1


title: scRNAseq_BdLTseq_HA1E_E7clone_RAS_Onc [scRNAseq_BdLTseq_HA1E_E7_clone_RAS]

description: 10x Genomics

value: polyA GFP


title: Female_Pre_8

tag: tissue (trap fraction)

value: RNA


title: C9HRE_iMN_2


title: 9


title: scRNAseq_BdLTseq_HA1E_E7clone_RAS_Gex [scRNAseq_BdLTseq_HA1E_E7_clone_RAS]

description: 10x Genomics


title: C9HRE_iMN_1


title: scRNAseq_BdLTseq_HA1ER_F12_clone_BdLTseq_HTO [scRNAseq_BdLTseq_HA1ER_F12_clone_1]

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Indexes for libraries demultiplexing: Gene expression library index - GAGCAAGA, TCTGTGAT, CGCAGTTC, ATATCCCG, HTO library index - ATTACTCG, BdLT-seq library index - CGTGAT.
Samples demultiplexing using hashtag barcodes: HA1ER F12_0days - GTCAACTCTTTAGCG, HA1ER F12_7days - TGATGGCCTATTGGG, HA1ER F12_14days - TTCCGCCTCTCTTTG.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files


title: Female_IP_12

tag: material


title: Female_Pre_7

tag: condition


title: human ref2, RNA-seq

description: genes.data.tsv

data_processing:
RRBS - FASTQ files were trimmed using TrimGalore-0.5.0 with parameters --illumina --rrbs
RRBS - basecalls were generated by bcl2fastq v. 2.20.0.42
RRBS - Alignments were generated  bismark v0.22.1 and bowtie2 v2-2.3.5.1
RRBS - MethylKit count files were generated using  R v 3.6.1 and methylKit v1.10.0
Assembly: MesAur1.0
RNA-seq - FASTQ files were pre-processed using fastp version 0.20.1 with parameters --cut_front --cut_front_window_size 1 --cut_front_mean_quality 3 --cut_tail --cut_tail_window_size 1 --cut_tail_mean_quality 3 --cut_right --cut_right_window_size 4 --cut_right_mean_quality 15 --length_required 36
RNA-seq - reads were aligned to the Golden Hamster genome using STAR version 2.7.4a
RNA-seq - read counts were estimated using RSEM (rsem-calculate-expression) version 1.3.1
RNA-seq - differentially expressed genes were called using DESeq2 v1.24.0 and were considered significant with a Wald test p-value cutoff of 0.05 and linear fold change of 1.5
Supplementary files format and content: RRBS data was processed into bedGraph format; RNASeq data was processed into a genes X counts matrix

source_name: human reference RNA -Takara bio

growth_protocol: The Syrian hamster fetal cells were plated and treated following a modified version of the SH-CTA assay at pH 6.7 (Pant, K. et al 2012. Mutat. Res.: 744:54-63).  Instead of culture on a feeder layer, cells were cultured in preconditioned media (Pant, K. et al. 2010. Mutat. Res.: 698:6-10).

extract_protocol:
Cells were rinsed with dPBS then  lifted using TryplE (Thermofisher), suspended in complete medium then washed twice by centrifugation /suspension in dPBS then divided into identical aliquots, pelleted and  frozen at -80C until use.  Genomic DNA and total RNA were isolated from cell pellets using DNEasy(Blood and Tissue) and RNEasy mini kits (Qiagen, Mississauga ON),  respectively.  DNA integrity was verified by 0.8% agarose electrophoresis.   RNA integrity was measured using Agilent's 2200 tapestation(Mississauga ON) and all RIN values exceeded 9.7
RRBS libraries were prepared from 100ng genomic DNA using the Premium RRBS kit from Diagenode (catalogue number C02030032).    RNA-seq libraries were prepared from 1µg total RNAusing Illumina's Truseq stranded mRNA kit (20020594 ) and labelled with TruSeq RNA CD Indexes (20019792)

treatment_protocol: Immortalized SHF cells were plated at 10^6 cells per 10cm plate and were grown for 24 hours before treatment.  Cells were then either left untreated (naïve) or treated with vehicle alone or with 1µM or 5µM of 5-Aza-2'-deoxycytidine (5aCdR) for 48 hours.

value: a collection of adult human tissues (https://www.takarabio.com/documents/Certificate%20of%20Analysis/636690/636690.pdf)

tag: days in culture

tag: catalog number

value: Takara Catalog number 636690

value: ATAGAGGC

value: GCCTCTAT


title: scRNAseq_BdLTseq_HA1E_E7_clone_BdLTseq [scRNAseq_BdLTseq_HA1E_E7_clone]

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Libraries demultiplexing: Gene expression library - GTAGCCCTGT (i7), ATAGATGCTC (i5), Hashtag library index - CGAGTAAT, BdLT-Seq library index - TGGTCA.
Samples demultiplexing using hashtag barcodes: HA1E E7_0days - CAGTAGTCACGGTCA, HA1E E7_5days - ATTGACCCGCGTTAG.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files


title: scRNAseq_BdLTseq_HA1E_E7_clone_HTO [scRNAseq_BdLTseq_HA1E_E7_clone]

description: 10x Genomics


title: Female_IP_10


title: scRNAseq_BdLTseq_HA1E_E7_clone_Gex [scRNAseq_BdLTseq_HA1E_E7_clone]

description: 10x Genomics


title: DAXX_ChIP_CTRL_B_lymphocytes_input

data_processing:
Raw reads were processed with TrimGalore v0.6.7 and controlled for quality with FastQC v.0.11.9.
The trimmed reads were aligned to the human genome (hg19) using Bowtie2 v2.3.5.1.Uniquely mapped reads were retained to identify DAXX-associated peaks using MACS2 v2.2.6 with standard parameters (q-value cutoff 0.05).
Assembly: hg19
Supplementary files format and content: Peaks were annotated and visualized with an R package, ChIPseeker

source_name: Human B lymphocytes

growth_protocol: human B lymphocytes were cultured in RPMI 1640 medium containing 15% FBS. Medium was exchanged every other day.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed by using a CHIP assay kit (Millipore Sigma, 17-295).
The ChIP-seq libraries were prepared using an NEBNext Ultra II FS DNA Library Prep kit (NEB, E6177S).

value: Human B lymphocytes

tag: disease state

value: healthy control

tag: chip antibody

value: none (input)


title: DAXX_ChIP_C9orf72ALS_B_lymphocyte_input2

tag: cell line

value: C9HRE ALS/FTD


title: DAXX_ChIP_CTRL_B_lymphocytes_IP

value: DAXX (Sigma, D7810)


title: Female_IP_9


title: DAXX_ChIP_CTRL_B_lymphocytes_IgGCTRL

value: anti-IgG


title: Female_IP_11


title: 501T DA737 IgG

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17

department: Wallenberg Neuroscience Center

country: Sweden

institute: Lund University

description: Illumina Hyperprep kit (KAPA)

data_processing:
Paired-end reads (2x150) were aligned to the hg38 genome using bowtie2 (--local–very-sensitive-local –no-mixed –no-discordant –phred33 -I 10 -X 700)
SAM files were converted to bam files with samtools (Langmead and Salzberg, 2012; Li et al., 2009).
Normalized bigwig coverage tracks were made with bamCoverage (deepTools)  (Ramirez et al., 2014), with RPKM normalization.
Assembly: GRCh38
Supplementary files format and content: Bigwigs of filtered (mapq10) and unfiltered alignments for genome browser visualization
Library strategy: CUT&RUN

source_name: adult cortex temporal lobe

extract_protocol:
Nuclei extraction: Protocol based on published nuclei isolation protocol (Södersten et al., 2018). Around 20 μg of -80 C-conserved tissue were thawed and dissociated in ice-cold lysis buffer (0.32M sucrose, 5 mM CaCl2, 3 mM MgAc, 0.1 mM Na2EDTA, 10 mM Tris-HCl pH 8.0, 1 mM DTT) using a 1 ml glass douncer (Wheaton). The homogenate was slowly and carefully layered in the centrifuge tubes on top of a sucrose layer (1.8 M sucrose, 3 mM MgAc, 10 mM Tris-HCl pH 8.0, 1 mM DTT) to create a gradient, and then centrifuged at 15500 rpm for 2 h 15 min. Following centrifugation, the supernatant was removed and the pellet softened for 10 minutes in 100 μl of nuclear storage buffer (15% sucrose, 10 mM Tris-HCl pH 7.2, 70 mM KCl, 2 mM MgCl2) prior resuspension in 300 μl of dilution buffer (10 mM Tris-HCl pH 7.2, 70 mM KCl, 2 mM MgCl2, Draq7 1:1000). The suspension was then filtered (70 μm cell strainer) and sorted via FACS (FACS Aria III, BD Biosciences) at 4° C with low flowrate, using a 100 μm nozzle (Pipette tips and Eppendorf tubes for transferring nuclei were pre-coated with 1% BSA). CUT&RUN: We followed the protocol detailed by the Henikoff lab  (Skene et al., 2018)  with some modifications. ConA-coated magnetic beads (Epicypher) were activated by washing twice in bead binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl, 1 mM MnCl2) and placed on ice until use. For fetal cortex samples, 300,000 or 600,000 single nuclei were sorted per frozen tissue piece. For adult neuron samples, 300,000 NeuN+ single nuclei were sorted per frozen tissue piece. Pipette tips for transferring nuclei were pre-coated with 1% BSA. Nuclei were pelleted and resuspended in ice-cold nuclear wash buffer (20 mM HEPES, 150 mM NaCl, 0.5 mM spermidine, 1x cOmplete protease inhibitors, 0.1% BSA) and 30 μL (10 μL per antibody treatment) of ConA-coated magnetic beads (Epicypher) added with gentle vortexing. Binding of nuclei to beads proceeded for 10 min at RT with gentle rotation, and then bead-bound nuclei were split into three equal volumes (corresponding to IgG control, H3K4me3 and H3K9me3 treatments). After removal of the wash buffer, nuclei were then resuspended in 100 μL cold nuclear antibody buffer (20 mM HEPES pH 7.5, 0.15 M NaCl, 0.5 mM Spermidine, 1x Roche complete protease inhibitors, 0.02% w/v digitonin, 0.1% BSA, 2 mM EDTA) containing primary antibody (rabbit anti-H3K9me3, Abcam ab8898, RRID:AB_306848; rabbit anti-H3K4me3 Active Motif 39159, RRID:AB_2615077; or goat  anti-rabbit   IgG,  Abcam  ab97047,  RRID:AB_10681025)  at  1:50  dilution  and incubated at 4 ºC overnight with gentle shaking. Nuclei were washed thoroughly with nuclear digitonin wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Roche cOmplete protease inhibitors, 0.02% digitonin, 0.1% BSA) on the magnetic stand. After the final wash, pA-MNase (a generous gift from Steve Henikoff) was added in nuclear digitonin wash buffer and incubated with the nuclei at 4 ºC for 1 h. Nuclei were washed twice, resuspended in 100 μL digitonin buffer, and chilled to 0-2 ºC in a metal block sitting in wet ice. Genome cleavage was stimulated by addition of 2 mM CaCl2 at 0 ºC for 30 min. The reaction was quenched by addition of 100 μL 2x stop buffer (0.35 M NaCl, 20 mM EDTA, 4mM EGTA, 0.02% digitonin, 50 ng/μL glycogen, 50 ng/μL RNase A, 10 fg/μL yeast spike-in DNA (a generous gift from Steve Henikoff)) and vortexing. After 30 min incubation at 37 ºC to release genomic fragments, bead-bound nuclei were placed on the magnet stand and fragments from the supernatant purified by a NucleoSpin clean-up kit (Macherey-Bagel).
Illumina sequencing libraries were prepared using the Hyperprep kit (KAPA) with unique dual-indexed   adapters   (KAPA),   pooled   and   sequenced   on   a Nextseq500   instrument (Illumina).

value: adult cortex temporal lobe

tag: Sex

value: M


title: scRNAseq_BdLTseq_HA1E_E7clone_RAS_HTO [scRNAseq_BdLTseq_HA1E_E7_clone_RAS]

description: 10x Genomics

value: HTO


title: Female_IP_8


title: scRNAseq_BdLTseq_HA1ER_F12clone_TRAIL_BdLTseq  [scRNAseq_BdLTseq_HA1ER_F12_clone_TRAIL]

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Indexes for libraries demultiplexing: Gene expression library index - CGAAGTATAC (i7), CTCCAAGTTC (i5), Hashtag library index - AATGAGCG, BdLT-seq library index - GCCTAA.
Samples demultiplexing using hashtag barcodes: HA1ER F12_TRAIL_resistant - AAGTATCGTTTCGCA, HA1ER F12_TRAIL_withdrawal - GGTTGCCAGATGTCA, HA1ER 1F8_TRAIL_resistant - TGTCTTTCCTGCCAG, HA1ER 1F8_TRAIL_withdrawal - CTCCTCTGCAATTAC, HA1ER 1C9_TRAIL_resistant - CAGTAGTCACGGTCA, HA1ER 1C9_TRAIL_withdrawal - ATTGACCCGCGTTAG.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files


title: C9HRE_iMN_1_shDAXX

value: human iPSCs-derived motor neurons

value: C9orf72 HRE Mutation

value: DAXX knockdown


title: scRNAseq_BdLTseq_HA1ER_F12clone_TRAIL_HTO  [scRNAseq_BdLTseq_HA1ER_F12_clone_TRAIL]

description: 10x Genomics


title: DAXX_ChIP_C9orf72ALS_B_lymphocyte_IP2


title: 501T DA737 H3K4me3

description: Illumina Hyperprep kit (KAPA)

tag: age


title: scRNAseq_BdLTseq_HA1ER_F12_clone_GEx [scRNAseq_BdLTseq_HA1ER_F12_clone_1]

description: 10x Genomics

value: mRNA


title: DAXX_ChIP_C9orf72ALS_B_lymphocyte_IgGCTRL2


title: 501T DA737 H3K9me3

description: Illumina Hyperprep kit (KAPA)


title: 529T DA736 IgG

description: Illumina Hyperprep kit (KAPA)


title: human ref1, RNA-seq

description: genes.data.tsv

value: a collection of adult human tissues (https://www.takarabio.com/documents/Certificate%20of%20Analysis/636690/636690.pdf)

value: GGCTCTGA

value: TCAGAGCC


title: scRNAseq_BdLTseq_HA1ER_F12clone_TRAIL_Gex  [scRNAseq_BdLTseq_HA1ER_F12_clone_TRAIL]

description: 10x Genomics


title: DAXX_ChIP_C9orf72ALS_B_lymphocyte_input1


title: scRNAseq_BdLTseq_HA1ER_F12_clone_BdLTseq [scRNAseq_BdLTseq_HA1ER_F12_clone_3]

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Indexes for libraries demultiplexing: Gene expression library index - AAGTGGAGAG (i7),  GTAACAGGAA (i5), Hashtag library index - CGAGTAAT, BdLT-seq library index - CGTGAT.
Samples demultiplexing using hashtag barcodes: HA1ER F12_0days - TGTCTTTCCTGCCAG and CTCCTCTGCAATTAC, HA1ER F12_5days - CAGTAGTCACGGTCA and ATTGACCCGCGTTAG.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

value: polyA GFP


title: 529T DA736 H3K9me3

description: Illumina Hyperprep kit (KAPA)


title: PFC_WT_M, 10X single-nuclei RNA-seq

city: Charleston

first: Makoto

last: Taniguchi

state: SC

address: 173 Ashley ave, BSB410C

institute: Medical University of South Carolina

description: 10X single-nuclei RNA-seq

data_processing:
Raw sequencing data were processed with Cell Ranger (v6.1.2). Cellranger mkfastq command was used to demultiplex the different samples and cellranger count command was used to generate gene – cell expression matrices. Ambient RNA contamination was inferred and removed using CellBender (v0.232) with standard parameters. Mouse genome mm10 was used for the alignment and genecode vM25 was used for gene annotation and coordinates. We used the R package Seurat (v4.1.0) and customized R scripts for data analyses Data from different samples (SalineCPP, CocaineCPP, SalineNPAS4, CocaineNPAS4) were merged into a unique single cell object. Nuclei with > 250 genes, < 10000 UMIs, and < 5% mitochondrial transcripts were retained for downstream analysis. Genes located in the mitochondrial genome were removed. Doublets were removed using scDblFinder (v1.8.0) for a resultant expression matrix with 21,516 genes and 52,743 cells. The SCTransform workflow was used for count normalization and data integration using 30 principal components and resolution of 0.5 for Louvain clustering and UMAP. Cluster marker genes were identified using FindAllMarkers using Wilcoxon Rank Sum test with the standard parameters. After removing 4 clusters showing high expression of glutamatergic neuronal markers and subsequent re-clustering, we identified 20 final distinct clusters. Cell annotation was performed using two different approaches: 1) markers enrichment using a Nucleus Accumbens independent data by Fisher’s exact test and 2) a predictive machine learning model based on a Nucleus Accumbens atlas reference data using the R package scPred. Cell annotation then was manually curated to reflect both analyses. To identify differentially expressed genes between conditions (SalCPP vs CocCPP, CocCPP vs CocNPAS4) in each defined cell types, the R package LIBRA with option MAST was used to perform zero-inflated regression analysis. Genes were defined as significantly differentially expressed at Benjamini–Hochberg correction FDR < 0.05 and abs(log2(Fold Change)) > 0.2. We further confirmed these results using a Wilcoxon’s rank sum test.
Assembly: Mus musculus mm10
Supplementary files format and content: HDF5 Feature-Barcode Matrix

source_name: PFC

extract_protocol:
Control mice (Vgat-cre positive) were live-decapitated at eight weeks of age. Brains were rapidly extracted into a supplemented 4˚C Hibernate A medium, with GlutaMAX supplement (Fisher), B27 supplement (Fisher), and NxGen RNase inhibitor (0.2U/uL, Lucigen), and incubated for 30 seconds. The brain was sectioned into 1 mm sections using a brain matrix. The prefrontal cortex (PFC) was dissected with fine forceps, flash frozen on dry ice, and stored at -80oC. The nuclear isolation protocol was modified from Savell et al., 2020. On the day of nuclear dissociation, the frozen tissue was slowly thawed on ice and chopped with a scalpel blade 100 times in two orthogonal directions on a glass petri dish. The chopped tissue of three PFCs were pooled and transferred to a hypotonic lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL (Sigma) in Nuclease-Free Water). Supplemented Hibernate A medium was added, and the tissue was triturated ~30 times/sample using three glass pipettes of decreasing diameter. The tissue was then filtered using a 40 micron filter (Fisher). The nuclei were isolated using 500xg centrifugation and washed with 1x PBS+1.0% BSA and 0.2U/uL RNase inhibitor. Nuclei were incubated with 7-aminoactinomycin D (7-AAD) (Invitrogen) for five minutes and sorted for 7-AAD-positive single nuclei using fluorescence-activated nuclear sorting on the Aria II. Samples were counted and diluted to 1500 nuclei/uL before immediate processing on the 10x Genomics Single-Cell Protocol by the MUSC Translation Science Lab. Libraries were constructed using the Chromium Single Cell 3’ Library Construction Kit (10x Genomics, v3.1) and sequenced at Vanderbilt’s Next Gen Sequencing Core (Illumina NovaSeq 6000).
Droplet-based snRNA-seq libraries were prepared using the Chromium Single Cell 3’ v3.1 according to the manufacturer’s protocol. Libraries and sequencing were performed at the Translational Sequencing Core at MUSC.

tag: strain

value: 8 weeks old

value: PFC


title: SHAM, scRNAseq

first: Bo

state: WI

address: 1111 Highland Ave

institute: University of Wisconsin - Madison

description: 10x Genomics

data_processing:
Raw Illumina sequencing reads were aligned to mm10 (GENCODE vM23/Ensembl 98) reference genome and, subsequently, genes were quantified as UMI counts using Cell Ranger Count v6.1.2 pipeline (10x Genomics Cloud Analysis). Downstream analysis was performed on filtered feature counts generated by Cell Ranger using Seurat v4.1.0. Cells containing <800 genes or <1000 total number of RNA counts or >25% mitochondrial transcripts were considered as low quality cells and removed from the dataset.
Assembly: mm10
Supplementary files format and content: h5

source_name: Inferior vena cava

extract_protocol:
Mouse infrarenal IVCs were collected and sequentially digested in two digestion buffers (PBS containing 200 U/ml collagenase I (SCR103, Sigma Aldrich), 0.05 U/ml elastase (E1250, Sigma Aldrich), 5 U/ml neutral protease (LS02111, Worthington), and 0.3 U/ml deoxyribonuclease I (M6101, Promega) for 20 minutes, followed by DMEM containing 5 mg/ml collagenase type II [C6885, Sigma-Aldrich] and 0.5 mg/ml elastase [LS002292, Worthington Biochemistry]) for 2.5 minutes at 37°C). The tissue suspension was filtered with a 40um cell strainer, then centrifuged at 500 g for 5 minutes. Cells were resuspended with PBS containing 0.04% BSA. Single-cell suspensions from 5 DVT-adjacent IVCs or 8 sham-IVCs were pooled together as one sample.
8000 cells per sample were loaded on a Chromium Controller (10x Genomics). The scRNA-seq libraries were constructed using the Chromium Single Cell 3’ v3.1 Reagent Kit according to the manufacturer’s guidelines (10x Genomics). cDNA libraries were uniquely sample indexed and pooled for sequencing.

value: Inferior vena cava

value: Male

value: Sham surgery


title: DVT, scRNAseq

description: 10x Genomics

value: IVC ligation


title: Female_IP_7

data_processing:
Barcode extraction from sample fastq - see bitbucket repository for script. Requires flanking 14 bp around barcode to be identical to design, plus a 10bp sequence to be found in between the flanks. All 10bp sequences extracted from Fastqs into text file.
Tabulation of barcode counts for each sample using table() in R. Subsequently, merging to a metadata table on designed barcodes to drop sequences that were not a perfect match to a designed barcode.
Filtering for low read counts, poor barcode representation across replicates, etc. Described at length in Supplementary Methods.
Calculation of log2(cpm RNA barcode) / log2(cpm DNA barcode) for each retained barcode in each sample.
Subtract the within-sample mean of "basal" (minimal-promoter-only) barcode expression from all other barcode expression values --> REML linear mixed model: expression ~ allele + sex + sex:allele + (1|BC), where BC is the unique barcode identifier to control for effects of barcode sequence.
Assembly: hg19-derived sequences (up to 126bp); see enclosed file "Reference-Barcode Sequences, their paired internal identifiers, and the corresponding sequence placed upstream of min promoter.txt" for each allele of each sequence and its paired reporter (RNA) barcodes
Supplementary files format and content: Tab-delimited text; barcode counts for each RNA sample and the DNA sample.

value: RNA


title: PancOVA+Tc17 4

city: Marburg

first: Magdalena

last: Huber

address: Hans-Meerweinstr. 02

department: Mikrobiology

country: Germany

institute: University of Marburg

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v20.0 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome. Expression value=TPM
Assembly: GRCm38
Supplementary files format and content: txt

source_name: PancOVA cells

growth_protocol: Co-cultures of iCAF, Tc17 cells and labelled PancOVA cells (with Cell Proliferation Dye eFluor 670 (#65-0840-90 eBioscience)) were set up by seeding labeled PancOVA (2.5 × 105) cells alone, mixed with Tc17-iCAF (3.5 × 105) or mixed with (2.5 × 104) differentiated Tc17 cells were re-seeded in 70 µl of fresh matrigel and mixed at a 1:1 ratio with DMEM (10 % FCS) on a 3.5 cm suspension dish (Sarstedt). The matrigel-embedded PSC were covered with 0.5 % FCS-containing DMEM. After 48h, the matrigel droplets were harvested, dissolved by incubation with Collagenase D (5mg/ml, Roche) and DNAse 1 (10µg/ml, Roche) in HBSS at 37°C for 45 min. The cells were sorted into eFluor670+ fractions on a FACS ARIA II. The eFluor670+ tumor cell fraction was resuspended in Extraction Buffer (Thermo Fisher) followed by RNA Isolation (Arcturus PicoPure RNA Isolation Kit).

extract_protocol: RNA was isolated fibroblasts with the Arcturus PicoPure RNA Isolation Kit according to manufacturer’s protocol.

value: PancOVA cells

value: cocultured with Tc17 cells


title: scRNAseq_BdLTseq_HA1ER_F12_clone_HTO [scRNAseq_BdLTseq_HA1ER_F12_clone_3]

description: 10x Genomics

value: HTO


title: DAXX_ChIP_C9orf72ALS_B_lymphocyte_IP1

value: Human B lymphocytes

value: C9HRE ALS/FTD

value: DAXX (Sigma, D7810)


title: PancOVA+Tc17 3


title: 529T DA736 H3K4me3

description: Illumina Hyperprep kit (KAPA)

value: adult cortex temporal lobe

value: M


title: scRNAseq_BdLTseq_HA1ER_F12_clone_Gex [scRNAseq_BdLTseq_HA1ER_F12_clone_3]

description: 10x Genomics

value: mRNA


title: 502F DA735 IgG

description: Illumina Hyperprep kit (KAPA)

source_name: adult cortex frontal lobe

value: adult cortex frontal lobe


title: scRNAseq_BdLTseq_HA1ER_F12_clone_BdLTseq  [scRNAseq_BdLTseq_HA1ER_F12_clone_2]

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Indexes for libraries demultiplexing: Gene expression library index - TATCAGCCTA (i7), AGGACGAAAC (i5), HTO library index - CGAGTAAT, BdLT-Seq library index - CGTGAT.
Samples demultiplexing using hashtag barcodes: HA1ER F12_0days - GTCAACTCTTTAGCG and TTCCGCCTCTCTTTG, HA1ER F12_5days - TGATGGCCTATTGGG and AGTAAGTTCAGCGTA.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

value: polyA GFP


title: scRNAseq_BdLTseq_HA1ER_F12_clone_HTO [scRNAseq_BdLTseq_HA1ER_F12_clone_2]

description: 10x Genomics


title: 502F DA735 H3K9me3

description: Illumina Hyperprep kit (KAPA)


title: 502F DA735 H3K4me3

description: Illumina Hyperprep kit (KAPA)


title: HiChIP_NoBlueActivation

data_processing:
Illumina and Nextera adapter sequences were removed using Trim Galore (version 0.6.6)
The raw reads were aligned to the human hg19 genome using HiC-Pro (version 2.11.4) with bin sizes of 5 kb, 50 kb, and 100 kb. The MboI restriction site, followed by fill-in, and the ligation was specified as GATCGATC.
Assembly: hg19
Supplementary files format and content: The processed data were analyzed, and contact maps were generated using the HiTC R package (Servant et al., 2012)
Library strategy: HiChIP-seq

source_name: HEK293 cells

growth_protocol: HEK293 cells were cultured in DMEM containing 10% FBS.

extract_protocol:
HEK293 cells were plated in 10-cm dishes 1 day before pHR-DAXX-mCherry-Cry2WT transfection, followed by a 2-day incubation. The plates with >80% of cells expressing Opto-DAXX were randomly divided into two groups, with each containing 1x107 cells. One group was activated by blue-light illumination for 10 min, and the other served as a negative control. Cells were detached, pelleted, resuspended at 1×106 cells/ml in freshly prepared 1% formaldehyde, and incubated at room temperature for 10 min with gentle rotation, with constant blue-light illumination for the activated group during this step. The formaldehyde was quenched with glycine at a final concentration of 125 mM for 5 min. Following three washes with ice-cold PBS, 1×107 cells were lysed in 500 μl ice-cold lysis buffer (10 mM Tris-HCl [pH 8.0], 10 mM NaCl, 0.2% NP-40, and Protease Inhibitor Cocktail [1:200, Millipore Sigma, P8340]), incubated at 4°C for 30 min, and centrifuged at 2,500 g for 5 min to collect nuclei. The nuclear pellets were washed once with 500 μl of ice-cold lysis buffer, suspended in 100 μl 0.5% SDS, and incubated at 62°C for 10 min. Triton X-100 (10%, 50 μl) was added into the pellets to quench the SDS, followed by the addition of 285 μl H2O and incubation at 37°C for 15 min. In situ chromatins were digested with 375 U of MboI restriction enzyme in 500 µl of 1× NEB buffer 2 at 37°C for 2 h before heat inactivation (65°C, 20 min). The overhangs of the cut DNA fragments were filled in with biotin-labeled dATP (Thermo, 19524016) using 5 U DNA polymerase I large (Klenow) fragment (NEB, M0210) at 37°C for 1 h. The blunt-ended DNA fragments were ligated with NEB T4 DNA ligase buffer, 10% Triton X-100, BSA, and T4 DNA ligase (NEB, M0202) at room temperature for 4 h with rotation. After the incubation, nuclei were pelleted at 2,500 g for 5 min and subjected to sonication (Diagenode Bioruptor: 30-sec cycles, high power for 15 min) in nuclear lysis buffer (50 mM Tris-HCl [pH 7.5], 10 mM EDTA, 1% SDS, and Protease Inhibitor Cocktail [1:200, Millipore Sigma, P8340]). The sonicated samples were centrifuged at 16,100 g for 15 min at 4°C and used for chromatin immunoprecipitation with an antibody against DAXX (Sigma, D7810), following the same protocol described in the section on chromatin immunoprecipitation qPCR below. A sample (150 ng) of the DNA pulled down from the ChIP was used to capture biotin-labeled DNAs using 5 μl of Streptavidin C-1 beads in 20 μl of 1× biotin binding buffer (5 mM Tris-HCl [pH 7.5], 0.5 mM EDTA, and 1 M NaCl) at room temperature for 15 min with rotation. Beads were washed twice with 500 μl Tween wash buffer (5 mM Tris-HCl [pH 7.5], 0.05% Tween-20, 0.5 mM EDTA, and 1 M NaCl) at 55°C for 2 min with shaking and once with 100 μl of 2× Tagment DNA buffer (20 mM Tris-HCl [pH 7.5], 10 mM MgCl2, and 20% dimethylformamide). The washed beads were added into 25 μl of 2× Tagment DNA buffer with 4 μl Tn5 Transposase (Illumina, FC-121-1030) and incubated at 55°C for 10 min. After the incubation, the beads were removed and washed twice in 50 mM EDTA at 50°C (first for 30 min and then 3 min), twice in Tween wash buffer at 55°C for 2 min, and once in 10 mM Tris.
To amplify the transposed DNA fragments, the DNA sample was mixed with PCR amplification buffer containing nuclease-free H2O, Nextera PCR Primer 1, Nextera PCR Primer 2 (barcode), and NEBNext High-Fidelity 2× PCR Master Mix (New England Labs, M0541), and then amplified by 1 cycle of 72°C incubation for 5 min and 98°C for 30 sec, followed by 5 cycles of 98°C for 10 sec, 63°C for 30 sec, and 72°C for 1 min. To avoid PCR saturation of a library and reduce the GC and size bias, 5 μl of the first PCR reaction were amplified in a side qPCR reaction to select an appropriate cycle number for the second-round PCR reaction, which was set to 1 cycle of 98°C incubation for 30 sec, followed by 20 cycles of 98°C for 10 sec, 63°C for 30 sec, and 72°C for 1 min. The cycle number corresponding to a quarter of the maximum fluorescence intensity was used in the final PCR amplification. After the final amplification, PCR products were purified using a Qiagen MinElute PCR Purification Kit (Cat. NO. 28204) and analyzed by deep sequencing.

treatment_protocol: HEK293 cells were transfected with DAXX-mCherry-Cry2 for 48 hours and exposed to blue light illumination for 10 min or not.

value: HEK293 cells

value: expressing DAXX-mCherry-Cry2

value: without blue light illumination


title: HiChIP_BlueActivation_REPLICATE2

value: with blue light illumination


title: PancOVA+Tc17 2


title: CVID patient with villous atrophy 8

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

data_processing:
Basecalls performed using RTA 2.7.3
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following paramters: HEADCROP:3 TRAILING:10 MINLEN:25
paired-end reads were aligned to the hg19 genome assembly using STAR (v2.5.2b), and read count per gene was subsequently estimated with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.05 i--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16  --quantMode GeneCounts
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited txt file including read count per gene for each sample

source_name: duodenal tissue

growth_protocol: ex vivo samples

extract_protocol:
RNA was extracted using RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions
Libraries were prepared from high quality total RNA samples (~200 ng/sample) using the Illumina TruSeq RNA Sample Preparation v2 Kit (Illumina) implemented on the liquid handling robot Beckman FXP2. Obtained libraries that passed the QC step were pooled in equimolar amounts; 1.8 pM solution of this pool was loaded on the Illumina sequencer NextSeq 500 and sequenced uni-directionally, generating ~500 million reads, each 85 bases long.

treatment_protocol: untreated samples

value: Duodenum

tag: health status

value: Common Variable Immunodeficiency, with enteropathy

tag: pathological stage

value: villous atrophy


title: DAXX_ChIP_C9orf72ALS_B_lymphocyte_IgGCTRL1

value: anti-IgG


title: HiChIP_BlueActivation_REPLICATE1

tag: genotype


title: CVID patient with villous atrophy 9


title: scRNAseq_BdLTseq_HA1ER_F12_clone_GEx  [scRNAseq_BdLTseq_HA1ER_F12_clone_2]

description: 10x Genomics

tag: library line


title: CVID patient with villous atrophy 4

description: was defined as outlier

tag: tissue


title: ATAC-seq for iPSCs-derived motor neurons from a ALS/FTD patient carrying the C9orf72 HRE mutation_1

data_processing:
Adapters were removed using Cutadapt
The quality of the reads was measured by FastQC.
The trimmed reads were sequentially mapped to the human reference genome (hg39 version) using Bowtie in an end-to-end model.
Duplicate fragments were removed with Picard MarkDuplicates.
MACS2 was used to find peak callings.
Assembly: hg39

source_name: iPSCs-derived motor neurons

growth_protocol:
human B lymphocytes were cultured in RPMI 1640 medium containing 15% FBS. Medium was exchanged every other day.
Human iPSCs were maintained in StemFlex medium (Gibco, A3349401), with medium exchange every other day.
Motor neuron differentiation: human iPSCs were seeded onto Matrigel-coated plates and differentiated into neuroepithelial progenitor cells (NEPCs) by culturing 6 days in neural medium (1:1 DMEM/F12:neurobasal medium, GlutaMax, N2 supplement, B27 supplement, and ascorbic acid) containing 3 μM CHIR99021, 2 μM SB431542, and 2 μM DMH-1. NEPCs were dissociated with dispase (1 U/ml) and split into new plates coated with Matrigel with a ratio of about 1:6. NEPCs were differentiated into motor neuron progenitor cells (MNPCs) using neural medium supplemented with 1 μM CHIR99021, 2 μM SB431542, 2 μM DMH-1, 0.1 μM retinoic acid (RA), and 0.5 μM purmorphamine. After culturing for 6 days, MNPCS were dissociated and cultured in suspension using neural medium containing 0.5 μM RA and 0.1 μM purmorphamine. Six days later, neural spheres were dissociated and plated onto a Matrigel-coated plate. Adherent neural spheres were cultured in neural medium supplemented with 0.5 μM RA, 0.1 μM purmorphamine, and 0.1 μM compound E. After 12 days, mature motor neurons were acquired for experiments. The medium was changed every other day during the entire differentiation period.

extract_protocol:
Human B lymphocytes (~1×105) or progenitor-differentiated motor neurons (~1.6×106) were used for ATAC-seq. Cells were pelleted in 1× PBS (500 g for 5 min, 4°C) and resuspended in 50 μl of cold lysis buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630) with gentle pipetting. Cell lysates were centrifuged (500×g for 10 min, 4°C) to pellet the nuclei, which were then incubated with 50 μl of transposition reaction buffer (25 μl of 2× Tagment DNA reaction buffer [Illumina FC-121-1030], 2.5 μl of Nextera Tn5 Transposase [Illumina FC-121-1030], and 22.5 μl of nuclease-free H2O) at 37°C for 30 min with gentle rotation. After the reaction, genomic DNA was purified with a Qiagen MinElute PCR Purification Kit (Qiagen, 28204) and eluted in 10 μl of elution buffer (10 mM Tris buffer [pH 8.0]).
To amplify the transposed DNA fragments, the DNA sample was mixed with PCR amplification buffer containing nuclease-free H2O, Nextera PCR Primer 1, Nextera PCR Primer 2 (barcode), and NEBNext High-Fidelity 2× PCR Master Mix (New England Labs, M0541), and then amplified by 1 cycle of 72°C incubation for 5 min and 98°C for 30 sec, followed by 5 cycles of 98°C for 10 sec, 63°C for 30 sec, and 72°C for 1 min. To avoid PCR saturation of a library and reduce the GC and size bias, 5 μl of the first PCR reaction were amplified in a side qPCR reaction to select an appropriate cycle number for the second-round PCR reaction, which was set to 1 cycle of 98°C incubation for 30 sec, followed by 20 cycles of 98°C for 10 sec, 63°C for 30 sec, and 72°C for 1 min. The cycle number corresponding to a quarter of the maximum fluorescence intensity was used in the final PCR amplification. After the final amplification, PCR products were purified using a Qiagen MinElute PCR Purification Kit (Cat. NO. 28204) and analyzed by deep sequencing.

tag: cell type

value: iPSCs-derived motor neurons

value: C9orf72 HRE mutation


title: ASAP16 Ctl PT231 PFCTX 5'

description: Chromium Next GEM Single Cell 5’ Kit

data_processing:
Raw base calls were demultiplexed to obtained sample specific FastQ files using mkfastq in default parameters (10x Genomics), and reads were aligned to GRCh38 genome assembly using the Cell Ranger pipeline (10x Genomics, Cellranger count v6) with default parameters (--include-introns was used for nuclei mapping)
Assembly: GRCh38
Supplementary files format and content: Cellranger count output matrices

source_name: adult prefrontal cortex

extract_protocol:
Postmortem brain tissue from controls with no known history of neurological or neuropsychiatric symptoms was acquired from the Cambridge Brain Bank (ethical approval from the London-Bloomsbury Research Ethics Committee, REC reference:16/LO/0508). Brains were bisected in the sagittal plane with one half flash-frozen and stored at -80 °C and the other half fixed in 10% neutral buffered formalin for 2–3 weeks. From the flash-frozen blocks, 50-100mg were sampled from the dorsolateral prefrontal cortex (Brodmann area 46) and stored at -80 °C until use.
Nuclei was isolated as previously described with minor modifications42. Around 20 μg of -80 C-conserved tissue were thawed and dissociated in ice-cold lysis buffer (0.32M sucrose, 5 mM CaCl2, 3 mM MgAc, 0.1 mM Na2EDTA, 10 mM Tris-HCl pH 8.0, 1 mM DTT) using a 1 ml glass douncer (Wheaton). The homogenate was slowly and carefully layered in the centrifuge tubes on top of a sucrose layer (1.8 M sucrose, 3 mM MgAc, 10 mM Tris-HCl pH 8.0, 1 mM DTT) to create a gradient, and then centrifuged at 15500 rpm for 2 h 15 min. After centrifugation, the supernatant was removed, and the pellet softened for 10 minutes in 100 μl of nuclear storage buffer (15% sucrose, 10 mM Tris-HCl pH 7.2, 70 mM KCl, 2 mM MgCl2) before resuspension in 300 μl of dilution buffer (10 mM Tris-HCl pH 7.2, 70 mM KCl, 2 mM MgCl2, Draq7 1:1000). The suspension was then filtered (70 μm cell strainer) and sorted via FACS (FACS Aria III, BD Biosciences) at 4° C with low flowrate, using a 100 μm nozzle (Pipette tips and Eppendorf tubes for transferring nuclei were pre-coated with 1% BSA). 8500 nuclei were sorted for single-nuclei RNA-sequencing and then loaded onto the Chromium Next GEM Single Cell 5’ Kit (10x Genomics, PN-1000263).
Sequencing libraries were generated with unique dual indices (TT set A) and pooled for sequencing on a Novaseq6000 using a 100-cycle kit and 28-10-10-90 reads.

value: adult prefrontal cortex


title: CVID patient with villous atrophy 19


title: ATAC-seq for iPSCs-derived motor neurons from a healthy people_1

value: wt


title: ATAC-seq for C9HRE B lymphocytes from a ALS/FTD patient

source_name: B lymphocytes

value: B lymphocytes


title: ATAC-seq for iPSCs-derived motor neurons from a ALS/FTD patient carrying the C9orf72 HRE mutation_2


title: ASAP13 Ctl NP16-161 PFCTX 5' (1)

description: Chromium Next GEM Single Cell 5’ Kit

value: M


title: PancOVA+iCAF 4

value: PancOVA cells

tag: treatment

value: cocultured with Tc17 conditioned media treated iCAFS


title: PancOVA+iCAF 1


title: ASAP15 Ctl NP16-21 PFCTX 5'

description: Chromium Next GEM Single Cell 5’ Kit


title: PancOVA+iCAF 3


title: PDX 65

city: San Francisco

first: Rex

middle: Hayden

last: Lee

state: CA

address: 1450 Third Street

department: Otolaryngology

institute: UCSF

data_processing:
After initial sequencing, the unaligned reads were derived from a combination of sources including human, mouse, viral, and ostensibly other sequences. Reads were classified to a probable source prior to mapping to the human reference and expression counting. Adapters were trimmed and reads failing QC removed using fastp (v0.20.0).  Xenome (v1.0.0), a k-mer index based pseudoaligner, classified reads as "human," "mouse," "both," "neither," or "ambiguous"
Reads identified as uniquely human were advanced to the human expression pipeline. rRNA matches were removed by aligning against a ribosomal reference with bwa. The remaining reads  were mapped against an Ensembl GRCh38.90 reference, and expression counts were estimated using RSEM (v1.3.1).
Library sizes were adjusted using the weighted trimmed mean of M-values method from the Bioconductor edgeR package and data were transformed to log counts per million. Genes with median count less than 10 were excluded.
Assembly: Ensembl GRCh38.90 reference
Supplementary files format and content: .txt file; log counts per million (LCPM)

source_name: head and neck cancer patient-derived xenograft

growth_protocol: PDXs were grown in NOD-SCID gamma mice as previously described (Li H et al., Mol Cancer Res., 2016. PMID: 26685214)

extract_protocol:
Total RNA was extracted using the RNAeasy kit from Qiagen.
Standard library preps were created by QB3-Berkeley Genomics core.


title: ATAC-seq for iPSCs-derived motor neurons from a healthy people_2


title: ATAC-seq for B lymphocytes from a healthy people


title: PancOVA+iCAF 2


title: PancOVA 3

value: untreated


title: CVID patient with villous atrophy 17


title: PancOVA+Tc17 1

value: cocultured with Tc17 cells


title: ASAP13 Ctl NP16-161 PFCTX 5' (2)

description: Chromium Next GEM Single Cell 5’ Kit


title: CVID patient with villous atrophy 11

description: was defined as outlier


title: PDX 66

value: head and neck cancer patient-derived xenograft


title: PancOVA 4


title: 4L-shIso2-replicate C

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the human genome using the splice-aware STAR aligner.
Likely PCR duplicates were removed with Picard MarkDuplicates tool.
Htseq package was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Genome_build: hg19
Supplementary_files_format_and_content: CSV files contain raw and normalized counts for all genes and samples.

source_name: Melanoma cell line

extract_protocol: RNAeasy Mini Kit (Qiagen), according to the manufacturer's instructions.

value: WM239-derived 113/6-4L melanoma cell line


title: 4L-shIso2-replicate B


title: PancOVA 2


title: CVID patient without villous atrophy 18

value: no villous atrophy


title: PDX 64


title: CVID patient without villous atrophy 20

value: Duodenum


title: 4L-shIso2-replicate A


title: PDX 60


title: PDX 63


title: CVID patient without villous atrophy 22

value: Common Variable Immunodeficiency, with enteropathy


title: CVID patient without villous atrophy 16


title: UDP0072-UDP0072=63

city: Cincinnati

first: Jeffery

middle: D

last: Molkentin

state: Ohio

address: 240 Albert Sabin Way MLC 7020

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description:
Ventricular tissue was processed to isolate RNA associated with polysomal fraction.
RNA associated with Rpl3L-deficient polysomal fraction

data_processing:
Sequence reads were aligned using Strand NGS Software (Ver. 2.6) against Mouse mm10 (UCSC) using Ensembl transcript annotations ((2013.04.03)
Fold Change Analysis was carried out using Strand NGS Software and identifies genes with ratio between experimental and control conditions, above an assigned threshold. Our analysis had two conditions; wild-type samples were chosen as the reference (control condition) against which the fold change for the Rpl3L-null samples (experimental condition) was computed. As per Strand NGS manual, the exact fold change is computed as follows:  1. For each gene and condition, the average of the normalized signal values (in log-scale) is calculated.  2. Log Fold Change (Log FC) for a given gene, between the two conditions, is then the difference between their respective averages.  3. Fold change (FC) is then computed as (sign of Log FC) x 2ǀlogFCǀ; absolute FC is ǀFCǀ.
Assembly: Mouse mm10 (UCSC)

source_name: Cardiac ventricular muscle

growth_protocol: Mice were bred in-house and hearts harvested and flash-frozen as per approved protocols

extract_protocol:
Total RNA was extracted from monosome+polysome fraction using Trizol/chloroform extraction protocol. RNA quality and yield were determined using Agilent Bioanalyzer and submitted for RNA-seq analysis.
Ribozero + Tru Seq stranded; 40M reads per sample

treatment_protocol: Ribosomal fractions were generated using established, centrifugation-based sucrose gradient protocols.

tag: genetic modification

value: Rpl3L gene deletion; Homozygous knock-out

value: Rpl3L is constitutively knocked out


title: UDP0071-UDP0071=52


title: 4L-SCR-replicate C


title: CVID patient without villous atrophy 12


title: 4L-SCR-replicate B


title: PancOVA 1


title: PDX 59


title: CVID patient without villous atrophy 7


title: PDX 58


title: CVID patient without villous atrophy 10


title: PDX 62


title: CVID patient without villous atrophy 3


title: 4L-SCR-replicate A


title: UDP0068-UDP0068=400

description:
Ventricular tissue was processed to isolate RNA associated with polysomal fraction.
RNA associated with wild-type polysomal fraction

value: Rpl3L is expressed at wild-type levels


title: PDX 57


title: UDP0069-UDP0069=404


title: 4L-shIso2_NR2F2 ChIPseq

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Reads were aligned to the human genome (build hg19/GRCh37) with Bowtie 2 using local alignment.
Likely PCR duplicates were removed with Picard MarkDuplicates tool.
MACS was utilized to perform peak calling for each replicate.
Genome_build: hg19
Supplementary_files_format_and_content: BED files of peaks

extract_protocol: ChIP-IT High Sensitivity Kit (Active Motif), according the manufacturer recommendations.

value: NR2F2 antibody (Active Motif, Cat. 61214)


title: 4L-shIso2_Input

value: none (input)


title: CVID patient without villous atrophy 2


title: 4L-SCR_NR2F2 ChIPseq


title: PDX 56


title: UDP0067-UDP0067=57


title: PDX 55


title: healthy control 15

description: was defined as outlier

value: Healthy Control, no enteropathy


title: UDP0066-UDP0066=527


title: healthy control 14


title: healthy control 13


title: Control_Atria_PCM1+_4 [ATAC]

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

description: PCM1 sorted nuclei

data_processing:
Reads were mapped to mm10 build of the mouse genome using BWA (Li et al., 2009) using default settings.
The BEDTools suite (Quinlan et al., 2010) was used to distribute the genome wide signal into sliding window bins of 500bp. Differential peak calling was performed on bins using DESeq2 (Love et al., 2014)
BED files (peaks called differential or stable between G125R heterozygous and control mice).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file (containing differential peaks)

source_name: atrial cardiomyocyte nuclei

growth_protocol: Animal care and experiments conform to the Directive 2010/63/EU of the European Parliament. All animal work was approved by the Animal Experimental Committee of the Academic Medical Center, Amsterdam, and was carried out in compliance with the Dutch government guidelines.

extract_protocol:
Isolated nuclei from both atria pooled together per individual were stained for PCM1 (pericentreolar material 1). Samples were FACS sorted and gated in such a way that debris, nuclei clumps, and nuclei with no cardiomyocyte origin were excluded. Nuclei were collected and successively washed with PBS and used as input for ATAC-seq using Illumina Tagment DNA enzyme and buffer (20034197) according to protocol. Libraries were sequenced paired end 150bp on an Illumina Hiseq4000.
Illumina Tagment DNA enzyme and buffer (20034197) according to protocol

value: 8-12 week

value: left and right atrium

value: control


title: 4L-SCR_Input


title: PDX 52


title: UDP0070-UDP0070=406


title: Control_Atria_PCM1+_3_r2 [ATAC]

description: PCM1 sorted nuclei


title: PDX 54


title: UDP0065-UDP0065=522


title: Control_Atria_PCM1+_3_r1 [ATAC]

description: PCM1 sorted nuclei


title: healthy control 6


title: PDX 51


title: Control_Atria_PCM1+_2 [ATAC]

description: PCM1 sorted nuclei


title: healthy control 5


title: healthy control 1


title: PDX 50


title: PDX 49


title: Control_Atria_PCM1+_1_r2 [ATAC]

description: PCM1 sorted nuclei


title: C3 [RNA-seq]

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Sequencing adapter contaminations were removed using cutadapt, discarding those reads that were shorter than 30 nt after trimming.
Resulting reads were aligned against the GRCm38_76 mouse transcriptome, with RSEM v1.3.1, to obtain expression estimates at gene level.
Assembly: GRCm38_76
Supplementary files format and content: Estimated counts for 41,214 genes (coding, small non coding, and long non coding genes, and pseudogenes) described in the GRCm38_76 primary assembly.

source_name: Naïve B cells from spleen

extract_protocol:
RNA was extracted with the Qiagen RNeasy kit and was treated with DNase.
Total RNA (500 ng) was used to generate libraries with the TruSeq RNA sample preparation kit v2 (Illumina). Libraries were sequenced in a HiSeq2500 next-generation sequencer (Illumina) to generate 60-base single reads.

treatment_protocol: Naïve B cells were isolated from the spleen. Spleens were meshed through 70 μm pore nylon cell strainers (BD Falcon) in complete RPMI medium supplemented with 10% FBS and penicillin (50 U/ml) and streptomycin (50 μg/ml). Erythrocytes were lysed by incubating the cell suspension in erythrocyte lysis buffer (ACK Lysing Buffer, BioWhittaker) for 4 minutes at room temperature. After washing with cold complete RPMI, B cells were isolated by immunomagnetic depletion using anti-CD43 beads (Miltenyi Biotec).

value: Spleen

value: B cells

value: CTCFfl/+; CD19-Creki/+


title: PDX 48

value: head and neck cancer patient-derived xenograft


title: Control_Atria_PCM1+_1_r1 [ATAC]

description: PCM1 sorted nuclei


title: C2 [RNA-seq]


title: Atria_Tbx5_REint_PCM1+_4 [ATAC]

description: PCM1 sorted nuclei


title: Atria_Tbx5_REint_PCM1+_3 [ATAC]

description: PCM1 sorted nuclei


title: PDX 47


title: C1 [RNA-seq]


title: PDX 46


title: Atria_Tbx5_REint_PCM1+_2 [ATAC]

description: PCM1 sorted nuclei


title: PDX 53


title: InputNaive

description: Input sample

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Illumina adapter contaminations were removed from reads using Cutadapt.
Processed reads were mapped with BWA, against a human-mouse chimeric reference genome obtained by combining GRCh38 and GRCm38 assemblies.
Alignments were filtered with samtools to retain only properly mapped, non duplicate reads, with mapping quality above 0, not aligning to unlocalized or unassembled contigs, the mitochondrial genome, or chromosome Y.
ChIPSeq peaks were called against input using MACS2, with “-q 0.1”.
Peaks were filtered to remove those overlapping with human or mouse blacklisted regions.
Assembly: Combined GRCh38-GRCm38
Supplementary files format and content: ENCODE narrow peak files (extended bed format) including coordinates, score, pvalue and qvalue for ChIPSeq peaks called for each sample against input, using MACS2, filtered to eliminate those overlapping with human or mouse blacklisted regions.

growth_protocol: Conditional CTCF-deficient mice (CTCFfl/fl; CD19-Creki/+) were obtained by breeding CTCFfl/fl mice  with CD19-Creki/+ mice

extract_protocol:
ChIP was performed according to the Diagenode protocol (iDeal ChIP-seq Kit for Transcription Factors C01010055)
Immunoprecipitated chromatin was eluted and decrosslinked for 8 hours. DNA was purified and quantified with an Invitrogen Qubit Fluorometer. Finally, 3-4 ng of DNA were used to prepare libraries using the Illumina NEBNext Ultra II DNA Library Prep Kit. ChIP-seq and input control libraries from three biological replicates per genotype were sequenced in a Illumina HiSeq 2500 next-generation sequencer.


title: FL3

description: ChIP sample

value: CTCFfl/fl; CD19-Creki/+


title: Atria_Tbx5_REint_PCM1+_1 [ATAC]

description: PCM1 sorted nuclei


title: PDX 45


title: 4x4_Tbx5(int);Prrx1(RE)_Adult_LA_4

description: 4x4_Tbx5(REint)Prrx1(RE)_LA_RNAseq_DEG_NC.xlsx

data_processing:
Reads were mapped to mm10 build of the mouse transcriptome using STAR (Dobin et al. 2013).
Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love, Huber, and Anders 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with differential expression analysis (DESeq2) and normalized counts (NC)

source_name: Whole dissected left atrium

extract_protocol:
Tissue was homogenized and RNA was extracted using ReliaPrep RNA Miniprep System (Promega) and used as input for library preparation according to protocol. Libraries were sequenced on an Illumina Hiseq4000.
Truseq RNA library Prep Kit v2 (Part# 15031048 Rev.E, Illumina) input 500ng

treatment_protocol: Whole left atria were dissected from ~8 week old mice

value: adult ~8 weeks

value: Left atrium

tag: genotype/variation


title: FL2

description: ChIP sample


title: 4x4_Tbx5(int);Prrx1(RE)_Adult_LA_3


title: FL1

description: ChIP sample


title: PDX 43


title: 4x4_Tbx5(int);Prrx1(RE)_Adult_LA_2


title: PDX 41


title: PDX 42


title: C3

description: ChIP sample


title: 4x4_Tbx5(int);Prrx1(RE)_Adult_LA_1


title: C2

description: ChIP sample


title: PDX 40


title: PDX 39


title: 4x4_Tbx5(int)_Adult_LA_3


title: C1

description: ChIP sample


title: 4x4_Tbx5(int)_Adult_LA_2


title: LT_M rep2

city: Harbin

first: Qingyu

last: Xu

state: Heilongjiang

address: Changjiang Road,Xiangfang district

department: College of Agronomy

country: China

institute: Northeast Agricultural University

description:
LT_Me2
Seed adversity treatment 2h sampling

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (ZmB73RefGenv4),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam)
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64)
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam)
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs
Genome_build: Zea mays NCBI B73 RefGen_v4
Supplementary_files_format_and_content: FPKM

organism: Zea mays

source_name: LT_M_seed embryo

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel
Poly (A) RNA is purified from 5μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min
Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp
At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: low temperature sensitive line Mo17

tag: developmental stage

value: Germination period

value: low temperature condition (10℃)

value: Embryo


title: PDX 38


title: PDX 37


title: PDX 36


title: LT_B rep3

description:
LT_Be3
Seed adversity treatment 2h sampling

source_name: LT_B_seed embryo

value: low temperature resistant lines B73


title: LT_M rep3

description:
LT_Me3
Seed adversity treatment 2h sampling


title: 4x4_Tbx5(down)_Adult_LA_2


title: 4x4_Tbx5(down)_Adult_LA_3


title: LT_M rep1

description:
LT_Me1
Seed adversity treatment 2h sampling


title: PDX 44


title: PDX 35


title: LT_B rep1

description:
LT_Be1
Seed adversity treatment 2h sampling


title: 4x4_Tbx5(down)_Adult_LA_1


title: PDX 34


title: PDX 33


title: 4x4_Control_Adult_LA_4

description:
4x4_Tbx5(REdown)_LA_RNAseq_DEG_NC.xlsx
4x4_Tbx5(REint)_LA_RNAseq_DEG_NC.xlsx
4x4_Tbx5(REint)Prrx1(RE)_LA_RNAseq_DEG_NC.xlsx


title: 4x4_Control_Adult_LA_5


title: 4x4_Tbx5(int)_Adult_LA_1


title: PDX 32


title: 4x4_Control_Adult_LA_3


title: PDX 30


title: CK_M rep2

description:
CK_Me2
Seed adversity treatment 2h sampling

source_name: CK_M_seed embryo

value: normal condition (25℃)


title: LT_B rep2

description:
LT_Be2
Seed adversity treatment 2h sampling


title: CK_M rep1

description:
CK_Me1
Seed adversity treatment 2h sampling


title: 4x4_Control_Adult_LA_2


title: Tbx5(REint)_E14-5_Ventricles_5

description: total RNA

data_processing:
Reads were mapped to mm10 build of the mouse transcriptome using STAR (Dobin et al. 2013).
Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love, Huber, and Anders 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Tbx5RE_E14-5_Vent_RNA_DEG_NC.xlsx (Excel file with differential expression analysis (DESeq2) and normalized counts (NC)).

source_name: Whole dissected ventricles

treatment_protocol: Whole ventricles were dissected from E14.5 mice

value: right and left ventricles


title: PDX 29


title: PDX 28


title: CK_B rep2

description:
CK_Be2
Seed adversity treatment 2h sampling

source_name: CK_B_seed embryo


title: PDX 31


title: Tbx5(REint)_E14-5_Ventricles_4

description: total RNA


title: CK_M rep3

description:
CK_Me3
Seed adversity treatment 2h sampling


title: CK_B rep1

description:
CK_Be1
Seed adversity treatment 2h sampling


title: P10_A44

data_processing:
Barcode extraction from sample fastq - see bitbucket repository for script. Requires flanking 14 bp around barcode to be identical to design, plus a 10bp sequence to be found in between the flanks. All 10bp sequences extracted from Fastqs into text file.
Tabulation of barcode counts for each sample using table() in R. Subsequently, merging to a metadata table on designed barcodes to drop sequences that were not a perfect match to a designed barcode.
For samples prepared and sequenced multiple times (e.g., A8_p0p10coprep and A8_prep1, AAV DNAs), CPM values were calculated for each sample individually and then averaged to get a single CPM value per biological sample.
Filtering for low read counts, poor barcode representation across replicates, etc. Described at length in Supplementary Methods.
Calculation of log2(cpm RNA barcode) / log2(cpm DNA barcode) for each retained barcode in each sample.
Subtract the within-sample mean of "basal" (minimal-promoter-only) barcode expression from all other barcode expression values --> REML linear mixed model: expression ~ allele + sex + sex:allele + (1|BC), where BC is the unique barcode identifier to control for effects of barcode sequence.
Genome_build: hg19-derived sequences (up to 126bp); see enclosed file "Reference-Barcode Sequences, their paired internal identifiers, and the corresponding sequence placed upstream of min promoter.txt" for each allele of each sequence and its paired reporter (RNA) barcodes
Supplementary_files_format_and_content: Tab-delimited text; barcode counts for each RNA sample and the DNA sample.

source_name: Whole brain

extract_protocol:
Brain dry frozen at -80°C overnight, lysed in 500µL (P0) or 1mL Trizol, the following day, returned to -80. At time of RNA prep,addition of 200uL chloroform and cleanup of the aqueous phase using the Zymo Clean and Concentrator 5 kit per manufacturer instructions. Turbo DNAse-free kit was used to remove incidental DNA
Reporter-specific cDNA synthesis using a reverse-complementary primer, followed by PCR, digestion, adapter ligation, and index PCR. DNA from plasmid was prepared simultaneously, starting with the first PCR step. Each step was followed by a cleanup using size-selection beads (brands Ampure XP and Magbind).

treatment_protocol: Intrauterine AAV9 into brain

value: brain without cerebellum

tag: sequencing prep and run

value: M


title: Tbx5(REint)_E14-5_Ventricles_3

description: total RNA


title: PDX 27


title: 9_Spindle

city: Rehovot

first: Bavat

last: Bornstein

address: pob 26

country: Israel

institute: Weizmann Institute of Science

data_processing:
A user-friendly Transcriptome Analysis Pipeline (UTAP) version 1.10.1 was used for analysis (Kohen et al., 2019). Reads were mapped to the Mus musculus genome (Genome Reference Consortium Mouse Build 38 (GRCm38), version M25 Ensembl 100) using STAR (v2.4.2a) (Dobin et al., 2013) and GENECODE annotation. Only reads with unique mapping were considered for further analysis. Gene expression was calculated and normalized using DESeq2 version 1.16.1  (Love et al., 2014), using only genes with a minimum of 5 reads in at least one sample. Raw p-values were adjusted for multiple testing (Benjamini and Hochberg, 1995). A gene was considered differentially expressed if it passed the following thresholds: minimum mean normalized expression of 5, adjusted p value ≤0.05 and absolute value of log2 fold-change ≥1.
Assembly: GRCm38
Supplementary files format and content: file includes raw counts for each Sample and DESeq2 statistics

source_name: Spindle

extract_protocol:
Total RNA was purified using Qiazol followed by chloroform phase separation and application of micro RNA using RNAeasy kit  (Qiagen). RNA quality and concentration was measured by NanoDrop and TapeStation.
RNA-seq libraries were prepared at the Crown Genomics institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science. Libraries were prepared using the INCPM-mRNA-seq protocol. Briefly, the polyA fraction (mRNA) was purified from 500 ng of total input RNA followed by fragmentation and generation of double-stranded cDNA. After Agencourt Ampure XP beads cleanup (Beckman Coulter), end repair, A base addition, adapter ligation and PCR amplification steps were performed. Libraries were quantified by Qubit (Thermo Fisher Scientific) and TapeStation (Agilent).
Sequencing was done on a Nextseq instrument (Illumina) using a single end 84 cycles high output kit, allocating ~20M reads or more per sample (single read sequencing).

value: Spindle


title: Tbx5(REint)_E14-5_Ventricles_2

description: total RNA


title: P10_A41

first: Joseph

address: 660 S Euclid Ave, Campus Box 8232

institute: Washington University in St. Louis

value: F


title: PDX 26


title: 9_Muscle

source_name: Muscle

value: Muscle


title: P10_A43


title: Tbx5(REint)_E14-5_Ventricles_1

description: total RNA


title: PDX 25


title: P10_A40


title: Control_E14-5_Ventricles_5

description: total RNA

value: Control


title: 16_Muscle


title: P10_A39


title: 16_Spindle


title: CK_B rep3

description:
CK_Be3
Seed adversity treatment 2h sampling


title: Control_E14-5_Ventricles_4

description: total RNA


title: P10_A38


title: 13_Spindle


title: Control_E14-5_Ventricles_3

description: total RNA


title: PDX 22

value: head and neck cancer patient-derived xenograft


title: P10_A42


title: Control_E14-5_Ventricles_2

description: total RNA


title: 12_Spindle


title: 13_Muscle


title: PDX 21


title: P10_A36


title: Control_E14-5_Ventricles_1

description: total RNA


title: PDX 20


title: 11_Muscle


title: PDX 19


title: P10_A35


title: PDX 24


title: 12_Muscle


title: P10_A34


title: 10_Spindle


title: TBIN #9, day9 [TBIN9_9d_s128]

city: Kuopio

first: Mette

last: Heiskanen

address: Neulaniementie 2, P.O.B. 1627

department: A.I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

data_processing:
Read quality of the raw data was assessed using FastQC v11.8 software produced by the Babraham Institute (Babraham, Cambridgeshire, UK) and the Trimmomatic v0.36 was used to filter low-quality base calls and any adapter contamination. Low-quality leading and trailing bases were removed from each read, and a sliding window trimming using a window of 4 and a phred33 score threshold of 15 was used to assess the quality of the read body. Any reads <17 nucleotides were discarded.
After quality control the replicates for each sample were merged and aligned to the rat reference genome (Rno6) using Bowtie2 using --very-sensitive-local settings. Using the featureCounts program from the Subread package, the number of reads aligned with the known rat miRNAs in accordance with miRBase22 was calculated.
Assembly: Rno6, miRBase22
Supplementary files format and content: compiled matrix table with raw counts for every miRNA in every sample

organism: Rattus norvegicus

source_name: plasma

extract_protocol:
Whole blood was drawn from the lateral tail vein into Microtainer K2 EDTA-tubes. To obtain plasma, tubes were centrifuged at 1300xg for 10 min at 4 °C within 1 hour after blood sampling. RNA was extracted from 200 μl plasma using miRNeasy Mini Kit (#217004, QIAGEN).
Small RNA library preparation was performed using the Illumina TruSeq Small RNA Sample Prep Kit. Briefly, small RNA was isolated from purified RNA by size selection after adapter ligation. The excised product was used for PCR amplification of the resulting product. The quality and yield after sample preparation were measured with a Fragment Analyzer. The size of the resulting products was consistent with the expected size of approximately 150 bp. Single-read sequencing with a read length of 51 nts was performed on a Illumina HiSeq 4000. To increase read depth each sample was sequenced on two flow-cells giving two replicates for each sample.

value: plasma

value: Sprague-Dawley

value: adult

value: male

tag: time

value: Day 9

tag: group

value: traumatic brain injury

tag: outcome

value: no epilepsy


title: P10_A33

city: St. Louis

last: Dougherty

tag: Sex


title: TBIN #7, day9 [TBIN7_9d_s146]

tag: age


title: 10_Muscle


title: P10_A37


title: TBIN #6, day9 [TBIN6_9d_s140]

tag: strain


title: PDX 23


title: PDX 16


title: P0_A22_2


title: TBIN #5, day9 [TBIN5_9d_s134]


title: 20 Ly6C low

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc.
Reads were mapped using STAR_2.4.0.
Count on FAST DB gene annotations (GenoSplice) and normalization using DESeq.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Deseq_normalized_gene_expression_with_annotations.txt: Tab-delimited text file includes DESeq normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2018_1 were also provided.

source_name: Macrophages

extract_protocol:
Non-parenchymal cells were isolated from mice liver and Ly6C high and Ly6C low macrophages were sorted by flow cytometry cell sorter (BD FACSAria III) in RLT lysis buffer. RNAs were isolated using RNeasy Microkit (QIAgen, #74004).
RNA libraries were prepared for sequencing using NEBNext Single Cell/Low Input RNA Library Prep from New england Biolabs. cDNA and final libraries were controlled with AGILENT Tapestation 2200 on High Sensitivity DNA chip. Final equimolar pooled library prep were sequenced on Nextseq 500 ILLUMINA with HighOutPut cartridge (2x400Millions of 75 bases reads). Corresponding to 2x20Millions of reads per sample after demultiplexing.

value: sorted intrahepatic Ly6C low macrophages F4/80+CD11b+

tag: treatment 1

value: 4 weeks CCl4 treatment :fibrotic liver

tag: treatment 2


title: TBIN #8, day9 [TBIN8_9d_s152]


title: PDX 15


title: P0_A22_1


title: P0_A19


title: 18 Ly6C low


title: TBIN #4, day9 [TBIN4_9d_s127]


title: PDX 13


title: TBIN #3, day9 [TBIN3_9d_s119]


title: 17 Ly6C low


title: PDX 18


title: PDX 12


title: TBIN #2, day9 [TBIN2_9d_s111]


title: 19 Ly6C low


title: PDX 17


title: 16 Ly6C low


title: PDX 11


title: TBIN #1, day9 [TBIN1_9d_s103]


title: TBIN #9, day2 [TBIN9_2d_s177]

value: Day 2


title: PDX 10


title: P0_A18_1

value: brain without cerebellum


title: PDX 9


title: 14 Ly6C low

value: vehicle


title: 13 Ly6C low


title: TBIN #8, day2 [TBIN8_2d_s170]


title: P0_A16_2

value: M


title: P0_A18_2


title: TBIN #7, day2 [TBIN7_2d_s163]


title: TBIN #6, day2 [TBIN6_2d_s156]


title: 12 Ly6C low


title: PDX 6


title: PDX 7


title: P0_A16_1


title: TBIN #5, day2 [TBIN5_2d_s150]


title: 15 Ly6C low


title: 11 Ly6C low


title: P0_A17_2

value: F


title: 20 Ly6C hi

value: sorted intrahepatic Ly6C hi macrophages F4/80+CD11b+


title: 19 Ly6C hi


title: TBIN #4, day2 [TBIN4_2d_s144]


title: P0_A12_1


title: TBIN #3, day2 [TBIN3_2d_s138]


title: PDX 4


title: PDX 3


title: P0_A17_1


title: 18 Ly6C hi


title: PDX 8


title: TBIN #2, day2 [TBIN2_2d_s132]


title: P0_A10_1


title: PDX 2


title: PDX 1


title: Control [273]

city: Guelph

first: Samantha

last: Dixon

address: 50 Stone Rd E

department: Animal Biosciences

institute: University of Guelph

description: DESeqControlvsHigh; DESeqControlvsLow

data_processing:
RNA-Seq analysis was performed using the CLC genomics workbench software, version 12 (CLC Bio, Aarhus, Denmark). Quality control analysis, including guanine-cytosine (GC) content, ambiguous base content, Phred score, base coverage, nucleotide contributions and over-represented sequences parameters, was performed on fastq files
Sequence reads were aligned to the annotated Oar_v3.1 ovine reference genome (release 95).
Counts per gene were transformed using a Log10 transformation and normalized to reads per kilo base per million mapped reads (RPKM) values
Assembly: Oar_v3.1
Supplementary files format and content: DESeq log2FoldChange

source_name: liver

extract_protocol:
A representative sample of tissue (30 mg) from the center of the right liver lobe was ground using a mortar and pestle with liquid nitrogen and homogenized using a hand-held homogenizer. Total RNA was extracted following the manufacturer’s instructions using Qiagen RNeasy Mini Prep Kit (Qiagen, Calif., USA).
The NEBNext Ultra RNA Library Prep kit for Illumina (New England Biolabs, Mass., USA) was used for library preparation with Poly-A selection, according to the manufacturer’s recommendations

value: liver

value: Control (no exposure)


title: P0_A12_2


title: TBIN #1, day2 [TBIN1_2d_s151]

value: plasma


title: P0_A9_1


title: P0_A14


title: Control [262]

description: DESeqControlvsHigh; DESeqControlvsLow


title: 14 Ly6C hi


title: TBIE #7, day9 [TBIE7_9d_s120]

value: Sprague-Dawley

value: epilepsy


title: Control [243]

description: DESeqControlvsHigh; DESeqControlvsLow


title: P0_A10_2


title: 17 Ly6C hi


title: P0_A8_1


title: 16 Ly6C hi


title: TBIE #6, day9 [TBIE6_9d_s112]

value: adult

value: male


title: PDX 5

source_name: head and neck cancer patient-derived xenograft


title: P0_A9_2


title: TBIE #4, day9 [TBIE4_9d_s179]

value: Day 9

value: traumatic brain injury


title: TBIE #3, day9 [TBIE3_9d_s172]


title: P0_A7


title: 11 Ly6C hi


title: 13 Ly6C hi


title: P0_A8_2


title: TBIE #2, day9 [TBIE2_9d_s165]


title: 12 Ly6C hi


title: TBIE #5, day9 [TBIE5_9d_s104]


title: TBIE #1, day9 [TBIE1_9d_s158]


title: P0_A6_2


title: 15 Ly6C hi


title: Control [206]

description: DESeqControlvsHigh; DESeqControlvsLow


title: HPB [1131]

description: DESeqControlvsHigh

value: GIN-exposed


title: HPB [1234]

description: DESeqControlvsHigh


title: LPB [1117]

description: DESeqControlvsLow


title: LPB [1186]

description: DESeqControlvsLow


title: HPB [1205]

description: DESeqControlvsHigh


title: TBIE #6, day2 [TBIE6_2d_s139]


title: TBIE #5, day2 [TBIE5_2d_s133]


title: TBIE #4, day2 [TBIE4_2d_s126]


title: TBIE #3, day2 [TBIE3_2d_s118]


title: LPB [1031]

description: DESeqControlvsLow


title: P0_A6_1