title: LiHe_MY3_1887

city: Saarbruecken

first: Gilles

last: Gasparoni

state: Saarland

address: Campus

department: Genetics Department

institute: Saarland University

description: RRBS with MspI restriction enzyme

data_processing:
after a quality control with FastQC (www.bioinformatics.bbsrc.ac.uk/projects/fastqc/), reads were adapter-trimmed (Q< 20) with Trim Galore! version 0.4.2 (www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
reads were aligned to mm10 assembly with the BWA (v0.6.2) wrapper methylCtools (v 0.9.2).
Samtools (v1.3) and Picard tools (v1.115) (http://broadinstitute.github.io/picard) were used for converting, merging, and indexing of the alignment files.
SNP aware realignment to identify single nucleotide polymorphisms (SNPs) for accurate identification of methylated cytosines and methylation calls were performed with the bisulfite SNP calling software Bis-SNP.
Assembly: mm10
Supplementary files format and content: bed file with CpG methylation values (chr, start, end, methylation, coverage, strand, start, end, qualityMetrics).

source_name: hepatocytes

extract_protocol:
liver hepatocytes isolated by perfusion.
RRBS protocol using restriction enzyme MspI
DNA was fragmented with MspI restriction enzyme. Fragments were end-repaired and A-tailed, followed by NGS adaptor (methylated) ligation using T4 ligase. Fragments were then bisulfite converted and amplified by PCR.

treatment_protocol: all animals were female C57Bl6/J mice of 10 weeks or 40 weeks age.

value: hepatocytes

tag: Sex

value: female

value: 10 weeks

value: hepatocytes from liver enriched by perfusion


title: T-cells HypoCpGs targeted dCAS9-DNMT3A Day 3 Replica 1

status: Public on Feb 11 2025

type: genomic

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

description:
DNMT3A_HypoCpGs_D10_R1
isolation after 10 days of culture

hyb_protocol: DNA was bisulfite converted, amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChips (Illumina)  according to the standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan)

data_processing:
dye bias correction, pOOBAH, ssnoob normalization, remove of non-CpG probes, remove of probes with SNP and remove of flagged probes in manifest b5 file
*processed value definition: normalized beta-value

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: primary T-cells

label_protocol: Standard Illumina protocol

growth_protocol: Human primary T-cells were then cultured in TexMacs medium (Miltenyi Biotec) with 10% FCS (Bio&Sell), IL-2 (50 IU/mL, GibcoTM) and Penicillin Streptomycin 100U/ml (GibcoTM) at 37°C / 5% CO2.

extract_protocol: Genomic DNA was isolated using the Macherey Nagel Tissue kit.

treatment_protocol: Transfection of T cells was performed using the NEON transfection system (Invitrogen). 5 million T cells were transfected with 5μg of plasmids for CRISPR-constructs and 5μg of gRNA plasmids inside of a NEON 100ul pipet tip with 1 pulse (20ms) at 2100V. After 24 hours, cells were resuspended in MACS buffer for flowcytometric sorting for double positive cells (BD FACSAriaTM fusion) and further cultured in TexMACS medium as indicated above for up to 21 days.

tag: tissue

value: primary T-cells

tag: treatment

value: guides HypoCpGs (AKAP8L, CSNK1D, IGSF11, MEIS1-AS3, COL1A1) + dCAS9-DNMT3A/3L


title: comp-wt-1

type: SRA

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

library_source: transcriptomic

data_processing:
In our sequencing strategy, 21nt read  R1 of pooled libraries contains two parts of UMI splitted by barcode. We move UMI sequences to be next to each other and remove additional nucleotide. For this we use awk command: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
Fastq files for 55nt read R2 of pooled libraries was demultiplexed into separate fastq files for each replica using BRBseqTools (v 1.6) and R1. Demultiplex with parameters -p UB -UMI 14 -n 1. Read R2 of each library was trimmed to remove potential contamination with poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then mapped using STAR (v 2.7.8a) with parameters --sjdbOverhang 54 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Finally, the deduplicated counts for each gene were obtained using BRBseqTools (v 1.6) CreateDGEMatrix with parameters -p UB -UMI 14 -s yes. Counts were used for differential gene expression analysis using DESeq2 R package.
Assembly: TAIR10
Supplementary files format and content: count text files

molecule: total RNA

organism: Arabidopsis thaliana

source_name: 21 day old seedlings

growth_protocol: Seeds were stratified for 2 days at 4ºC and grown on soil under a 16 h light/8 h dark (long-day) conditions.

extract_protocol:
Total plant RNA was isolated from 3-week-old plants grown using Trizol reagent (Sigma) according to manufacturer’s instructions.
500 ng of RNA was used in reverse transcription with 50 mM different barcoded oligo(dT) primers and SuperScript III. 0.25 of each reaction was pooled. cDNA pools were purified with Ampure beads (1.5x beads to sample volumes) and then eluted in 17 ul of water. 15 ul of recovered cDNA pools were mixed by pipetting with 15 ul of second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 uM dNTPs) and incubated overnight at 16°C. Reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 ul of water. 3 ul of recovered dsDNA samples were used for tagmentation using 3 ul 5x diluted B-loaded Tn5 enzyme (homemade) and 6 ul freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). Reactions were mixed by pipetting and incubated for 7 min at 55°C followed by 5 min at 80°C. Water was added up to 30 ul, samples were purified with Ampure beads (1.2x beads to sample volumes) and eluted with 11 ul of water. Illumina indexing PCRs were performed using 10 ul tagmented DNA in 50 ul reaction with Q5 2× PCR Master Mix (NEB) and 0.5 uM final concentration of primers. Libraries were Illumina Next-seq sequenced to obtain two reads: R1 (contain barcode and UMI) and R2 (contain mRNA sequence).
OTHER: 3'RNA-seq

value: 21 day old seedlings

tag: genotype


title: dxo1-4


title: ACLY_WT_survival_2

city: New Brunswick

first: Daniel

last: Herranz

state: New Jersey

address: 195 Little Albany St

country: USA

institute: Rutgers Cancer Institute of New Jersey

description:
Acly_KO_survival_vs_WT_survival_DESeqNormalizedCounts.csv
V2survival

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Gene abundance estimates were obtained for each sample using kallisto 0.46.0, with the Gencode GRCm39 (version M34) transcriptome as the reference
Assembly: GRCm39
Supplementary files format and content: comma-separated values file includes the DESeq normalized counts

molecule: polyA RNA

organism: Mus musculus

source_name: Leukemic spleen

growth_protocol: Acly conditional knockout T-ALLs were injected intravenously in sub-lethally Irradiated mice.

extract_protocol:
Leukemic spleens were removed, single-cell suspensions were obtained by pressing them through a 40μm filter, and subsequently subjected to red blood cell lysis. RNA was extracted using QIAGEN QIAshredder (#79656) and Rneasy Mini (#74106) kits. 1μg of Total RNA was used for the construction of sequencing libraries by Genewiz.
Strand-specific RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For acute experiments, mice were allowed to become overtly leukemic and then treated with vehicle only (control: corn oil, C8267, Sigma-Aldrich) or tamoxifen (T5648, Sigma-Aldrich; 3 mg per mouse in corn oil) administered by intraperitoneal injection, and leukemic spleens were collected 72h later. For surival experiments, 48h upon transplantation with Acly conditional knockout leukemic cells, mice were treated with vehicle only (control: corn oil, C8267, Sigma-Aldrich) or tamoxifen (T5648, Sigma-Aldrich; 3 mg per mouse in corn oil) administered by intraperitoneal injection, and their surivival was monitored afterwards. Samples were collected at the time of humane endpoint.

value: Leukemic spleen

value: Control

tag: group

value: survival


title: comp-mut-1


title: T-cells HypoCpGs targeted dCAS9-DNMT3A Day 3 Replica 3

description:
DNMT3A_HypoCpGs_D10_R3
isolation after 10 days of culture


title: LiHe_MY1_1885

description: RRBS with MspI restriction enzyme

library_source: genomic

tag: age


title: ACLY_KO_survival_2

description:
Acly_KO_survival_vs_WT_survival_DESeqNormalizedCounts.csv
T12survival

value: Acly deleted


title: ACLY_WT_survival_1

description:
Acly_KO_survival_vs_WT_survival_DESeqNormalizedCounts.csv
V1survival


title: dxo1-3


title: comp-wt-4


title: ACLY_KO_acute_4

description:
Acly_KO_acute_vs_WT_acute_DESeqNormalizedCounts.csv
T11acute

value: acute


title: LiHe_MO3_1891

description: RRBS with MspI restriction enzyme

value: 40 weeks


title: HEK293T HyperCpGs targeted dCAS9-DNMT3A Day 7 Replica 2

description:
HEK_HyperL_DNMT_R2
isolation after 7 days of culture

growth_protocol: HEK293T cells were cultured in Dulbecco's Modified Eagle Medium (GibcoTM) with 10% fetal calf serum (FCS; Bio&Sell) and Penicillin-Streptomycin (Life Technologies) at 37°C / 5% CO2, and passaged manually at 80 - 90% confluency

treatment_protocol: HEK293T cells were transfected with the TransIT®-LT1 transfection reagent (Mirus Bio) in 6-well plates with 1.25μg of plasmids for the CRISPR-construct and 1.25μg of plasmids for single gRNA. We either pooled two gRNAs targeting PDE4C or up to nine gRNAs for multiplexed editing. After 24 hours we selected the transfected cells either by puromycin treatment (2 ug/ml for 2 days) or flowcytometric sorting for double positive cells (BD FACSAriaTM fusion).

tag: cell line

value: guides HyperCpGs (PDE4C, FHL2, ELOVL2, KLF14, and TEAD1) + dCAS9-DNMT3A/3L


title: dxo1-1


title: ACLY_KO_survival_1

description:
Acly_KO_survival_vs_WT_survival_DESeqNormalizedCounts.csv
T11survival


title: ACLY_KO_acute_3

description:
Acly_KO_acute_vs_WT_acute_DESeqNormalizedCounts.csv
T10acute


title: T-cells HypoCpGs targeted dCAS9-DNMT3A Day 3 Replica 2

description:
DNMT3A_HypoCpGs_D10_R2
isolation after 10 days of culture


title: Col0-4


title: ACLY_WT_survival_5

description:
Acly_KO_survival_vs_WT_survival_DESeqNormalizedCounts.csv
V7survival


title: ACLY_KO_acute_2

description:
Acly_KO_acute_vs_WT_acute_DESeqNormalizedCounts.csv
T9acute


title: Q88.M5

city: Detroit

first: Oluwademilade

last: Nuga

state: MI

address: 540 E Canfield

department: Pharmacology

institute: Wayne State University School of Medicine

description: Library name: Sample 30

data_processing:
Trimmed and de-duplicated reads were then mapped to the Drosophila melanogaster BDGP6 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using ‘featureCounts’ from the Subread package v.1.5.2.
Assembly: Drosophila melanogaster BDGP6
Supplementary files format and content: Raw count matrix generated from "featureCounts" in ".csv" format

organism: Drosophila melanogaster

source_name: Whole Fly

extract_protocol:
Trizol extraction followed Invitrogen RNA Purellink Mini kit with on the column DNAase digestion.
Poly A selection and paired end 150bp read.

value: Whole Fly


title: ACLY_WT_survival_4

description:
Acly_KO_survival_vs_WT_survival_DESeqNormalizedCounts.csv
V6survival


title: Col0-2


title: CD8+ T cell, Nae1WT, biol rep 3

city: Columbus

first: Gang

last: Xin

state: OH

address: 460 W 12th Ave

department: MI&I

institute: The Ohio State University

description: Library name: W4

data_processing:
bcl2fastq
HISAT2
DESeq2 v1.42.0
Assembly: mm10
Supplementary files format and content: csv file includes normalized counts

source_name: CD8+ T cell

extract_protocol:
Total RNA was extracted from flash frozen pelleted CD8+ T cells
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

tag: cell type

value: CD8+ T cell


title: HEK293T scramble guide dCAS9-DNMT3A Day 7 Replica 3

description:
HEK_scr_DNMT_R3
isolation after 7 days of culture

value: scramble guide + dCAS9-DNMT3A/3L


title: ACLY_WT_acute_6

description:
Acly_KO_acute_vs_WT_acute_DESeqNormalizedCounts.csv
V6acute


title: LiHe_MY2_1886

description: RRBS with MspI restriction enzyme

value: hepatocytes


title: ACLY_WT_survival_3

description:
Acly_KO_survival_vs_WT_survival_DESeqNormalizedCounts.csv
V3survival


title: Q88.M3

description: Library name: Sample 28


title: HEK293T scramble guide dCAS9-DNMT3A Day 7 Replica 2

description:
HEK_scr_DNMT_R2
isolation after 7 days of culture


title: Q88.M2

description: Library name: Sample 27


title: U2OS_CHR, Myc, ChIP

city: Hefei,

first: Qin

last: Zhou

state: Anhui

address: 111 Jiulong Road, Hefei, Anhui, China

country: China

institute: Anhui university

data_processing:
The filtering software SOAPnuke developed by BGI independently for raw data filtering: Remove low quality tags as well as contaminants to get clean reads. SOAPnuke Parameter: Clean Parameter: SOAPnuke filter -l 15 -q 0.5 -n 0.01 -Q 2 -c 21.
After filtering, SOAPaligner/SOAP2[2](v 2.21t), which allows up to two mismatches in the alignment, is used to align clean data to the reference genome. The unique mapped reads are used for downstream bioinformatic analysis. Parameter：Clean Parameter: soap_mm_gz -p 4 -v 2 -s 35
MACS (Model-based Analysis forChIP-Seq, version: MACS-1.4.2) : The candidatePeakregion was extended to be long enough for modeling. Dynamic Possion Distribution was used to calculated p-value of the specific region based on the unique mapped reads. The region would be defined as aPeakwhen p-value < le-05.MACS work well for the identification of the sharp peaks of most sequence-specific transcription factors.  Calling Parameter: macs14 -s 50 -g 3.25e9 -p 1e-5 -w --space 50 -m 10, 30
MAnorm(v1.1)[5] is used to build different enriched peaks of different samples. The significant regions are picked up if |M|≥1 and p-value≤10-5. The gene element annotation of peak or different enrichment peak from different samples is carried out by bedtools intersect mode with overlap 50%.
The interaction between DNA and transcription factor or histone modification is not random but displays specific sequence preference. By default, MEME (v4.10.1) is used to analyze motif. HOMER (v4.10.3) software will be used if the peak region is too large.
Assembly: hg38
Supplementary files format and content: wiggle, BED (except for Input sample)

source_name: Bone

extract_protocol:
Pipeline of  ChIP  Enrichment
(1) DNA-protein cross-linking by formaldehyde.
(2) Add Lysis Buffer to get whole cell lysate.
(3) Lysate sonication (100-500bp).
(4) Immunoprecipitation: Add primary antibody and beads to samples.
(5) Elution and reverse cross-links.
(6) qPCR for Quality Control.
(7) Ready for  ChIP -seq library construction.
1 Sample QC
The corresponding sample quality control protocol will be selected depending upon sample types and product requirements.
2 End Repair, add “A”, Adaptor Ligation
After the reaction system and program are configured and set up, DNA fragments obtained from ChIP are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the DNAs.
3 PCR
The PCR reaction system and program are configured and set up to amplify the product.
4 Library QC
The corresponding library quality control protocol will be selected depending upon product requirements.
5 Circularization
Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.
6 Sequencing
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: Bone

value: Human Osteosarcoma Cells

tag: chip antibody

value: Myc


title: ACLY_WT_acute_4

description:
Acly_KO_acute_vs_WT_acute_DESeqNormalizedCounts.csv
V4acute


title: U2OS_CHR, Myc, Input


title: HEK293T HyperCpGs targeted dCAS9-DNMT3A Day 7 Replica 3

description:
HEK_HyperL_DNMT_R3
isolation after 7 days of culture


title: ACLY_KO_acute_1

description:
Acly_KO_acute_vs_WT_acute_DESeqNormalizedCounts.csv
T8acute


title: HEK293T scramble guide dCAS9-DNMT3A Day 7 Replica 1

description:
HEK_scr_DNMT_R1
isolation after 7 days of culture


title: CD8+ T cell, Nae1T-KO, biol rep 2

description: Library name: K3


title: CD8+ T cell, Nae1WT, biol rep 1

description: Library name: W1


title: Col0-1


title: LiHe_MO2_1890

description: RRBS with MspI restriction enzyme

value: female

value: hepatocytes from liver enriched by perfusion


title: ACLY_WT_acute_5

description:
Acly_KO_acute_vs_WT_acute_DESeqNormalizedCounts.csv
V5acute


title: LiHe_MO4_1892

description: RRBS with MspI restriction enzyme


title: Q88.M1

description: Library name: Sample 26


title: CD8+ T cell, Nae1WT, biol rep 2

description: Library name: W2


title: ACLY_WT_acute_3

description:
Acly_KO_acute_vs_WT_acute_DESeqNormalizedCounts.csv
V3acute


title: Q88.M4

description: Library name: Sample 29


title: Q88.F5

description: Library name: Sample 25


title: U2OS_CHR, BMAL1, Input

value: treat with 200 nM dexamethasone and 4 h before the trough of PBMAL1::Luc oscillation, the collection was started every 4 h, labelled as time-points 0, 4, 8, 12, 16 and 20, The input DNA were mixed together.


title: M. yumanensis, rep/individu 4, 6 hours, universal type I IFN

city: Lyon

first: Lucie

last: Etienne

address: 46 Allée d'Italie

country: France

institute: Centre International de Recherche en Infectiologie

data_processing:
Raw data quality was assessed using FASTQC (version 0.12.0) and results were compiled using MultiQC (version v1.14)
The data were trimmed to remove adapters/UMI index and low quality reads using FASTP (version 0.23.1, with the parameter -min_len 40 and -q 20).
Transcriptome mapping was performed using a transcriptome index (Salmon 1.10.2) with the following options: --validateMappings,  --seqBias --allowDovetail,    --gcBias --posBias --writeUnmappedNames
Assembly: reference sequence used for read alignment
Supplementary files format and content: tar file of salmon outputs including plaint text quantification file (quant.sf), transcripts used for quantification, parameter settings, version of Salmon, and estimated bias parameters

organism: Myotis yumanensis

source_name: Wing biopsy

growth_protocol: All primary Myotis yumanensis cell lines were grown in  DMEM medium supplemented with 10% of FCS and 1% Penicylin-streptomycine antibiotic

extract_protocol:
RNA was extracted from frozen cell pellets according to RNA isolation Machery Nagel kit protocol. To maximise RNA extraction quality, DNAse incubation time was increase to 30 minutes
RNA libraries were generated using CORALL Total RNA-Seq Library Prep kit (UDI 12 nt set B1, Lexogen).

treatment_protocol: Cell were treated for 6 hour with poly I:C (0,5 mg/mL) or universal type I IFN (1000 U/ mL, PBL assay science) and incubated at 37°C

value: Wing biopsy

value: Primary cell lines

value: Fibroblast-like

value: IFN type I


title: CD8+ T cell, Nae1T-KO, biol rep 3

description: Library name: K4


title: M. yumanensis, rep/individu 4, 6 hours, poly I:C

value: poly I:C


title: iPSC-derived motor neurons, DNAJC7 WT homozygote replicate 3

city: Chicago

first: Evangelos

last: Kiskinis

state: IL

address: 303 E. Superior Street

department: Neurology

institute: Northwestern University Feinberg School of Medicine

description: Library name: WT_3

data_processing:
Raw reads were trimmed of Illumina adapters and low quality sequences (-q20,20) using cutadapt. Reads were removed if they were shorter than 25bp following trimming (-m25)
STAR was used to align trimmed reads to the GRCh38 genome using Gencode V38 gene builds. STAR was run in two-pass mode with additional ENCODE parameters as supplied in the STAR manual.
Gene-level counts were quantified using featureCounts against Gencode V38 gene models.
Assembly: GRCh38/hg38, Gencode V38
Supplementary files format and content: gene-level reads for all samples.

source_name: iPSC line CS0002

extract_protocol:
Cells were harvested in 1mL TRIzol Reagent (Thermo Fisher Scientific) per 1 million cells. 0.2mL of chloroform was mixed with the samples for 3 minutes prior to being centrifuged at 12,000g at 4ºC for 15 minutes. The RNA containing aqueous phase was then transferred to a new tube and 5 μg of Glycogen carrier (Thermo Fisher Scientific) was added to facilitate complete precipitation. Then, 0.5mL of isopropanol was added to the mixtures and left to incubate at room temperature for 25 minutes prior to being centrifuged for 10 minutes at 15,000g at 4ºC
RNA was sent to Novogene for QC, and library preparation (250~300 bp insert strand nonspecific library with polyA enrichment)

value: iPSC line CS0002

value: iPSC-derived lower motor neurons


title: LiHe_MY4_1888

description: RRBS with MspI restriction enzyme

value: 10 weeks


title: M. yumanensis, rep/individu 3, 6 hours, universal type I IFN


title: Q88.F1

description: Library name: Sample 21

value: Whole Fly


title: Q88.F2

description: Library name: Sample 22


title: M. yumanensis, rep/individu 3, 6 hours, poly I:C


title: ACLY_WT_acute_1

description:
Acly_KO_acute_vs_WT_acute_DESeqNormalizedCounts.csv
V1acute

value: Leukemic spleen

value: Control

value: acute


title: CTRL.M5

description: Library name: Sample 20


title: iPSC-derived motor neurons, DNAJC7 WT homozygote replicate 1

description: Library name: WT_1


title: dxo1-2

value: 21 day old seedlings


title: M. yumanensis, rep/individu 3, Control


title: iPSC-derived motor neurons, DNAJC7 R156X/+ heterozygote replicate 2

description: Library name: HET_2


title: CTRL.M3

description: Library name: Sample 18


title: U2OS_WT, BMAL1, 20h, ChIP

value: Bone

value: Human Osteosarcoma Cells

value: treat with 200 nM dexamethasone and 4 h before the trough of PBMAL1::Luc oscillation, the collection was started every 4 h, labelled as time-points 0, 4, 8, 12, 16 and 20

tag: time


title: M. yumanensis, rep/individu 2, Control


title: ACLY_WT_acute_2

description:
Acly_KO_acute_vs_WT_acute_DESeqNormalizedCounts.csv
V2acute


title: Col0-3


title: Q88.F3

description: Library name: Sample 23


title: U2OS_WT, BMAL1, 12h, ChIP


title: klk6 positive rep 3

city: Beer-Sheva

last: Levi

address: David Ben-Gurion Blvd. 1

department: Biotechnology engineering

country: Israel

institute: Ben Gurion university

description: Library name: klk6_positive3

library_source: other

data_processing:
The analysis was performed in MATLAB, version R2016a. The number of reads of each variant from each library was counted following the alignment of the DNA sequences and their amino acid translations to the sequence of APPI-3M.
Assembly: Human amyloid protein precursor inhibitor 3M (APPI-3M) reference sequence: EVCSEQAETGPCRAGFSRWYFDVTEGKCAPFVYGGCGGNRNNFDTEEYCMAVCGS
Supplementary files format and content: csv file that includes raw counts of each variant from each library.

molecule: other

organism: Saccharomyces cerevisiae

extract_protocol:
A YSD vector (pCTCON) containing the APPI gene was isolated from the naïve and sorted libraries by using the USB PrepEase Yeast Plasmid Isolation Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocol.
A naive library of mutated APPI-3M variants, generated using both site-directed random mutagenesis of the APPI-3M binding loop (residues 11–18, except invariant Cys-14) and error-prone PCR amplification of the entire coding sequence, was displayed on the yeast cell surface and presented to pairs of proteases. Each protease in the pair was labeled with a different fluorescent dye. Flow cytometry sorting was used to screen the library to isolate APPI-3M variants, with enhanced selectivity toward each of the serine proteases (mesotrypsin; KLK6). In each sort, two variant populations were collected inside gates, yielding sorted library populations of protease-selective APPI-3M variants.

tag: strain

tag: sorted population

value: KLK6 positive


title: U2OS_CHR, BMAL1, 16h, ChIP


title: iPSC-Neuron, Day 21, CROP-seq, rep1

city: Palo Alto

first: Steven

last: Boggess

state: California

address: 3181 Porter Dr

institute: Arc Institute

description: Library name: iPSC-Neuron CROP-seq

library_source: transcriptomic single cell

data_processing:
A kallisto index was generated from the human transcriptome using the ENSEMBL cDNA
reference (GRcH38). Introns were annotated using the GRCh38 version 112 genome annotation. The default k-mer size (k=31) was used in generation of the index. The gene expression library sequences were then pseudo-aligned to this index using kallisto-bustools. After pseudo-alignment, barcodes were then corrected and filtered against the 10X-v4 cell barcode whitelist.
A kallisto index was generated for the sgRNA library with a k-mer size of 15. The sgRNA enrichment PCR sequences were then pseudo-aligned to this index using kallisto bustools. After pseudo-alignment, barcodes were corrected and filtered against the 10X-v4 cell barcode whitelist. Cells were then assigned to guides using geomux (https://github.com/noamteyssier/geomux), which performs a hypergeometric test for each cell on its observed guide counts, then calculates a log2-odds ratio between the highest counts. Cells were assigned to their majority guide if their Benjamini-Hochberg corrected P-value was below 0.05, the log-odds ratio was above 1, and the total number of UMIs were greater than 5.
Cells were merged for the 10X sequence and the enrichment PCR by matching on cell-barcode and GEM library. Cells were filtered to only include those with a minimum count of 2000 and a minimum of 100 genes. 3000 of the most highly variable genes were selected with a minimum shared count of 10. Cells were further filtered to only include those with less and 8% and greater that 3% ribosomal gene content and less than 6.5% mitochondrial gene content. Cells were then normalized to a target sum of 1000 and log transformed. Principal component analysis was then performed using these highly variable genes. Clustering was performed using the Leiden algorithm, setting the resolution to 0.15. All single-cell filtering, transformation, and dimensionality reduction was performed using scanpy 1.10.3.
Assembly: Human GRCh38 version 112
Supplementary files format and content: H5AD file

extract_protocol:
These cells were dissociated using papain, then pelleted at 300 xg for 5 minutes. These were resuspended and washed in dPBS. The centrifugation and wash steps were repeated for a total of 4 washes to completely remove papain and cell debris. The resuspension was counted and diluted to target 20k cells for a single 10X Chromium GEM-X 3’ chip.
Cells were prepared according to 10x Genomics general sample preparation protocol. sgRNA enrichment was performed using three semi-nested PCR reactions.

treatment_protocol: We produced a pool of lentiviruses containing the CROP-seq sgRNA library and transduced iPSCs at a low MOI (10% transduction efficiency) to minimize multiple infections in which a cell receives more than one sgRNA. Then, iPSCs were selected with puromycin, differentiated into neurons, and grown to day 21.

value: iPSC-neurons

value: sgRNA library


title: NUTF2, HA, 4OHT, Rep2, CUT&RUN

city: Jupiter

first: Jerome

last: Nwachukwu

state: Florida

address: 130 Scripps Way

department: Department of Immunology and Microbiology

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

description: Library name: HA_NUTF2_4OHT_Rep2

data_processing:
Sequences were analyzed using the nf-core cutandrun pipeline (v3.2.2, doi: 10.5281/zenodo.5653535)
After adaptor trimming, reads were aligned to the human genome (GRCh38) using Bowtie2
Sorting and indexing using SAMtools
Normalization by counts Per Million mapped reads
Peak calling using MACS2 with a q-value < 0.01.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for control samples)
Library strategy: CUT&RUN

source_name: Breast

growth_protocol: Phenol red-free DMEM + 10% charcoal-stripped FBS for 3 days

extract_protocol:
CUT&RUN using the CUTANA kit (EpiCypher, cat no. 14-1048)
Illumina standard library construction (New England Biolabs) by the University of Florida ICBR NextGen DNA Sequencing Core Facility, RRID:SCR_019152

treatment_protocol: DMSO (Vehicle), 10 nM 17β-estradiol (E2), or 1 µM 4-hydroxytamoxifen (4OHT) for 1 hour

value: Breast

value: Epithelial

tag: cut&run antibody

value: HA tag (C29F4) (Cell Signaling, cat no. 3724, 1:800)

value: 1 µM 4OHT


title: M. yumanensis, rep/individu 2, 6 hours, universal type I IFN

value: Wing biopsy

value: Primary cell lines

value: Fibroblast-like

value: IFN type I


title: klk6 positive rep 2

description: Library name: klk6_positive2


title: U2OS_CHR, BMAL1, 12h, ChIP


title: iPSC-derived motor neurons, DNAJC7 WT homozygote replicate 2

description: Library name: WT_2

value: iPSC line CS0002

value: iPSC-derived lower motor neurons


title: CTRL.F5

description: Library name: Sample 15

value: Whole Fly


title: U2OS_CHR, BMAL1, 8h, ChIP

value: Bone


title: CD8+ T cell, Nae1T-KO, biol rep 1

description: Library name: K2

value: CD8+ T cell


title: U2OS_CHR, BMAL1, 4h, ChIP

value: Human Osteosarcoma Cells

value: treat with 200 nM dexamethasone and 4 h before the trough of PBMAL1::Luc oscillation, the collection was started every 4 h, labelled as time-points 0, 4, 8, 12, 16 and 20


title: M. yumanensis, rep/individu 2, 6 hours, poly I:C

value: poly I:C


title: U2OS_WT, BMAL1, Input

value: treat with 200 nM dexamethasone and 4 h before the trough of PBMAL1::Luc oscillation, the collection was started every 4 h, labelled as time-points 0, 4, 8, 12, 16 and 20, The input DNA were mixed together.


title: iPSC-derived motor neurons, DNAJC7 R156X/+ heterozygote replicate 3

description: Library name: HET_3


title: U2OS_WT, BMAL1, 0h, ChIP


title: M. yumanensis, rep/individu 4, Control

value: Control


title: U2OS_CHR, BMAL1, 0h, ChIP


title: mesotrypsin positive rep 3

description: Library name: mesotrypsin_positive3

value: mesotrypsin positive


title: CTRL.M2

description: Library name: Sample 17


title: iPSC-derived motor neurons, DNAJC7 R156X/+ heterozygote replicate 1

description: Library name: HET_1


title: CTRL.M4

description: Library name: Sample 19


title: U2OS_WT, BMAL1, 16h, ChIP


title: Q88.F4

description: Library name: Sample 24


title: Wild Type, 12 weeks

city: Vari

first: George

last: Kollias

state: Attica

address: 34 Fleming Street

department: Institute for Bioinnovation/ Department of Physiology, School of Medicine

country: Greece

institute: BSRC "Alexander Fleming"/ National and Kapodistrian University of Athens

data_processing:
The initial steps of the analysis including read alignment and gene count summarization per cell, were performed using the 10X Genomics Cell Ranger pipeline (v 7.0.1)
Assembly: mm10
Supplementary files format and content: Output of cellranger (containing the files: matrix.mtx, features.tsv, barcodes.tsv) per sample
Supplementary files format and content: Raw count matrices (...raw_counts.txt) and metadata info (metadata_table.txt) for myeloid, lymphoid and stromal cells in each sample.

source_name: Ileum

extract_protocol:
Intestinal samples were digested using a mix of Collagenase XI/ Dnase/ Dispase II after removing epithelial cells.
10X Genomics Single Cell 3’ v3.1 kit

value: Ileum

value: TNF+/+

value: NO


title: CTRL.M1

description: Library name: Sample 16


title: WT.M5

description: Library name: Sample 10


title: HEK293T HyperCpGs targeted dCAS9-DNMT3A Day 7 Replica 1

description:
HEK_HyperL_DNMT_R1
isolation after 7 days of culture

value: guides HyperCpGs (PDE4C, FHL2, ELOVL2, KLF14, and TEAD1) + dCAS9-DNMT3A/3L


title: LiHe_MO1_1889

description: RRBS with MspI restriction enzyme

value: hepatocytes

value: female

value: 40 weeks

value: hepatocytes from liver enriched by perfusion


title: U2OS_CHR, BMAL1, 20h, ChIP


title: NUTF2, ERa, Veh, Rep2, CUT&RUN

description: Library name: ERa_NUTF2_Veh_Rep2

value: Breast

value: Epithelial

value: ERa (EpiCypher, cat no. 13-2011, 1:100)

value: DMSO


title: U2OS_WT, BMAL1, 8h, ChIP

value: Bone

value: Human Osteosarcoma Cells

value: treat with 200 nM dexamethasone and 4 h before the trough of PBMAL1::Luc oscillation, the collection was started every 4 h, labelled as time-points 0, 4, 8, 12, 16 and 20


title: CTRL.F4

description: Library name: Sample 14

value: Whole Fly


title: Control, IgG, Rep2, CUT&RUN

description: Library name: IgG_Rep2

value: normal rabbit IgG (EpiCypher, cat no. 13-0042, 1:50)


title: dxo1-2_xrn3-8_RNAseq_rep2

data_processing:
Reads were mapped with HISAT2 v2.0.4 with the additional command-line parameters: --fr --rnastrandness RF --known-splicesite-infile.
Mapped reads were counted with htseq-count v0.6.0 and the following commandline parameters: -a 0 -s reverse using Araport11 gene annotation release 201604.
RNA-seq alignments were split to separate read-pairs that originate from transcription on the forward and reverse strands using samtools v1.1. To isolate the forward strand alignments we use the bitflag filters -f 128 -F 16 for R2 reads and -f 64 -F 32 for their R1 pairs, producing two separate alignment files which were then merged (samtools). To isolate the reverse strand alignments we use the bitflag filters -f 144 for R2 reads and -f 96 for their R1 pairs, again producing two separate alignment files which were then merged (samtools).
Assembly: TAIR10
Supplementary files format and content: count text files

extract_protocol:
Total plant RNA was isolated from 3-week-old plants grown using Trizol reagent (Sigma) according to manufacturer’s instructions.
Illumina TruSeq Stranded Total RNA with Ribo-Zero Plant rRNA Removal (Plant Leaf).

value: 21 day old seedlings

value: dxo1-2 xrn3-8


title: U2OS_WT, BMAL1, 4h, ChIP


title: NUTF2, HA, Veh, Rep2, CUT&RUN

description: Library name: HA_NUTF2_Veh_Rep2

value: HA tag (C29F4) (Cell Signaling, cat no. 3724, 1:800)


title: klk6 positive rep 1

description: Library name: klk6_positive1

value: KLK6 positive


title: WT.M3

description: Library name: Sample 8


title: CTRL.F3

description: Library name: Sample 13


title: Control, HA, 4OHT, Rep2, CUT&RUN

description: Library name: HA_Empty_4OHT_Rep2

value: 1 µM 4OHT


title: Control, IgG, Rep1, CUT&RUN

description: Library name: IgG_Rep1


title: CTRL.F2

description: Library name: Sample 12


title: dxo1-2_RNAseq_rep3 (re-analyzed)


title: WT.M1

description: Library name: Sample 6


title: CTRL.F1

description: Library name: Sample 11


title: Control, HA, Veh, Rep2, CUT&RUN

description: Library name: HA_Empty_Veh_Rep2


title: TNFDARE, 12 weeks

value: Ileum

value: TNFDARE/+

value: NO


title: mesotrypsin positive rep 2

description: Library name: mesotrypsin_positive2

value: mesotrypsin positive


title: NUTF2, HA, 4OHT, Rep1, CUT&RUN

description: Library name: HA_NUTF2_4OHT_Rep1

value: Breast

value: Epithelial


title: NUTF2, ERa, 4OHT, Rep2, CUT&RUN

description: Library name: ERa_NUTF2_4OHT_Rep2

value: ERa (EpiCypher, cat no. 13-2011, 1:100)


title: mesotrypsin positive rep 1

description: Library name: mesotrypsin_positive1


title: dxo1-2_RNAseq_rep1 (re-analyzed)


title: dLsd1∆N/dLsd1∆N 2

city: Toulouse

first: Luisa

last: Di Stefano

address: 118 Route de Narbonne

institute: Centre de Biologie Intégrative (CBI)

data_processing:
the reads were trimmed with trimmomatic v.0.36 ( parameters SLIDINGWINDOW:5:28 MINLEN:50)
The alignment was processed using STAR (v2.5.2a) and reads were mapped to the FlyBase reference dm6
Differential expression between wild type and mutant samples was performed using TEtranscripts (v1.5.1) from TEToolkit and the R library Bioconductor:DESesq2
Assembly: dm6 (dmel-all-r6.12)

source_name: L3 wandering female wing discs

growth_protocol: Flies were grown on standard Drosophila medium and maintained at 25°C

extract_protocol:
Wing discs from L3 wandering female larvae from dLsd1∆N homozygous mutant and wild-type stocks were dissected in ice cold PBS. A total of 30 wing discs per sample were used to extract RNA using TriZol reagent (Invitrogen). Samples were protected from RNAses using RNAsecure (Ref AM7006 - Ambion). DNA contaminants were eliminated using DNA-free DNA Removal kit (Ref AM1906 - Invitrogen). RNA cleanup and purification were performed using RNeasy Mini Kit (Ref 74104 – QIAGEN) and RNA was resuspended in water.
Library preparation was performed using the standard Illumina TruSeq stranded mRNA Library preparation following manufactures instruction

treatment_protocol: Not applicable

value: L3 wandering female wing discs

value: dLSD1 loss of function


title: presort rep 1

description: Library name: presort1

value: presort


title: Control, HA, 4OHT, Rep1, CUT&RUN

description: Library name: HA_Empty_4OHT_Rep1


title: presort rep 3

description: Library name: presort3


title: WT.M4

description: Library name: Sample 9

value: Whole Fly


title: presort rep 2

description: Library name: presort2


title: Control, ERa, 4OHT, Rep2, CUT&RUN

description: Library name: ERa_Empty_4OHT_Rep2


title: WT.F3

description: Library name: Sample 3


title: WT.M2

description: Library name: Sample 7


title: Control, ERa, Veh, Rep2, CUT&RUN

description: Library name: ERa_Empty_Veh_Rep2

value: DMSO


title: dxo1-2_xrn3-8_RNAseq_rep1

value: 21 day old seedlings


title: WT.F1

description: Library name: Sample 1


title: dLsd1∆N/dLsd1∆N 1


title: xrn3-8_RNAseq_rep2 (re-analyzed)


title: dxo1-2_xrn3-8_RNAseq_rep3

value: dxo1-2 xrn3-8


title: NUTF2, ERa, 4OHT, Rep1, CUT&RUN

description: Library name: ERa_NUTF2_4OHT_Rep1


title: wildtype 1

value: wildtype


title: xrn3-8_RNAseq_rep3 (re-analyzed)


title: dxo1-2_RNAseq_rep2 (re-analyzed)


title: WT.F5

description: Library name: Sample 5


title: wildtype 3


title: WT.F4

description: Library name: Sample 4


title: NUTF2, ERa, Veh, Rep1, CUT&RUN

description: Library name: ERa_NUTF2_Veh_Rep1


title: NUTF2, HA, Veh, Rep1, CUT&RUN

description: Library name: HA_NUTF2_Veh_Rep1

value: HA tag (C29F4) (Cell Signaling, cat no. 3724, 1:800)


title: dLsd1∆N/dLsd1∆N 3


title: Control, HA, Veh, Rep1, CUT&RUN

description: Library name: HA_Empty_Veh_Rep1


title: xrn3-8_RNAseq_rep1 (re-analyzed)


title: GFP+ cones, Pde6ccpfl1

city: North Coogee

first: Denise

last: Anderson

state: WA

address: 71 Caledonia Loop

country: Australia

institute: INSiGENe Pty Ltd

description: Library name: Pde6c-GFP

data_processing:
Reads were allocated to individual wells, and to the 3’ and 5’ end, via quality-filtering and being passed through a demultiplexing tool. Reads for single cells were demultiplexed using plate-ID (30 nucleotides) and cell barcode (6 nucleotides), and further demultiplexed as either 5’ or 3’ using primer sequence (30 nucleotides). The remainder 45 nucleotide sequences aligned to the GRCh38 Mus-Musculus reference genome (Ensembl rel. 97) using the CLC Genomics Workbench (CLC Bio) (v.11, QIAGEN Bioinformatics). PCR-duplicate reads were removed by using the eight nucleotide UMI tag and mapping coordinates. Gene-specific read counts were calculated via RSubread:featureCount using Gencode M17 (2018) annotations, and the 3' and 5' counts were totalled.
Assembly: GRCh38 Mus-Musculus reference genome (Ensembl rel. 97)
Supplementary files format and content: FASTQ files for each sample
Supplementary files format and content: CSV file of raw gene counts for all samples combined

source_name: Retina

extract_protocol:
Fresh retinas were dissected out of the mouse eyes and dissociated with a papain digestion. A papain/DNase solution (1:20, Worthington Biochemicals, LK003170/LK003176) was made to 100 µL/sample and activated at 37 ºC on a heat block for 30 mins before adding in the dissected retina. Samples were then incubated for 45 mins at 37 ºC and gently triturated with a pipette after to completely dissociate the tissue. 200 µL of inhibitor solution (Earle’s balanced salt solution [EBSS; Gibco, 24010-043], 9.5% v/v ovomucoid protease inhibitor [OMI; Worthington Biochemicals, LK003182], 5% v/v DNaseI [Worthington Biochemicals, LK003170]) was added to each sample and was incubated at 37 ºC for 10 mins. The sample was then spun at 1400 × rpm for 5 mins before being resuspended again in 300 µL resuspension solution (EBSS, 10% v/v DNaseI). eBioscience™ Fixable Viability Dye eFluor™ 660 (Invitrogen, 65-0864-14) was used as a dead cell stain and was added at a 1:1000 dilution after resuspension and samples and incubated on ice in the dark for 30 mins. FACS buffer (2% heat-inactivated foetal calf serum [HI-FCS; Fisher Biotec, WS-FBS-AU0-015], 1mM Ethylenediaminetetraacetic acid [EDTA], 1X PBS) was added at 1 mL/sample to wash off the cell stain after incubation and the sample was spun down at 1400 × rpm for 5 mins to collect the pellet. The pellet was resuspended in 500 µL FACS buffer and kept on ice before FACS were performed on the BD FACSMelody™ Cell Sorter to sort GFP+ cones into a 96-well plate for each mouse line. Each well contained 3 µL of lysis buffer and ribonuclease inhibitor. Sorted plates were stored at -80 °C until further processing.
After FACS samples were collected, the 96-well plates were sent to the Institute for Immunology and Infectious Diseases (Murdoch University, WA) for further processing. Sample preparation and sequencing was performed using an adapted approach of SMARTseq2 and MARS-seq following methods by Wanjalla et al [Single-cell analysis shows that adipose tissue of persons with both HIV and diabetes is enriched for clonal, cytotoxic, and CMV-specific CD4+ T cells. Cell Reports Medicine. 2021;2(2)]. Cell size, shape or number was not restricted by these approaches. Uniquely tagged primers for reverse transcription and template switching with a pre-amplification step were used in the assay to increase yield and transcript length of the single cell cDNA library. At the reverse transcription stage, cDNAs were tagged with barcodes coupled with a unique molecular identified (UMI) which allowed for multiplexing and increased samples throughput. UMIs also enabled quantification of individual gene expression levels within single cells, thereby reducing technical variability and bias introduced during amplification. Using the KAPA HiFi HotStart ReadyMix (Roche, Basel, Switzerland) as per the manufacturer’s instructions, samples were pooled and amplified. Purified amplicons from the 5’ and 3’ were combined to equimolar quantities. Indexed libraries were created for sequencing using Truseq adapters and quantification was done using the Kapa universal qPCR library quantification kit (Kapa Biosystems Inc., MA, USA) as per user instructions.

value: Retina

value: Cones

value: Postnatal day 12


title: wildtype 2


title: Col0_RNAseq_rep2 (re-analyzed)


title: GFP+ cones, Cnga3-/-

description: Library name: Cnga3-GFP


title: Control, ERa, Veh, Rep1, CUT&RUN

description: Library name: ERa_Empty_Veh_Rep1


title: MYCN-driven tp53-/- primary neuroblastoma, biological sample 3

status: Public on Feb 10 2025

city: Toronto

first: Madeline

middle: Nicole

last: Hayes

state: Ontario

address: 72 Elm St

department: DSCB

country: Canada

institute: Sickkids Research

description: Library name: tp53_3

data_processing:
Raw .fastq data was processed using Salmon quantification of transcripts. A “decoy-aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k-mers length of 23. Samples were quantified with the following arguments: -r, --seqBias, --mp -3, --validateMappings, --rangeFactorizationBins 4.
Assembly: GRCz11
Supplementary files format and content: Comma-separated values .csv file including raw non-normalized counts for all conditions generated by Salmon

organism: Danio rerio

source_name: GFP+ sorted neuroblastoma

growth_protocol: Zebrafish were reared and maintained according to standard husbandry procedure at the Zebrafish Genetics and Disease Modeling Core Facility at the Hospital for Sick Children.

extract_protocol:
Dissected neuroblastoma tumors were manually dissociated and processed to single-cell suspensions. GFP+ tumor cells were sorted from bulk tissue at the SickKids-UHN Flow Cytometry Core Facility on a Sony MA900 VBYR cell sorter, before pelleting and lysis using Qiagen RNeasy Mini Kit, as per manufacturer instructions. Sequence ready polyA-enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina (NEB, E7760).
Sequence ready polyA-enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina (NEB, E7760).

treatment_protocol: All animal monitoring and sample collection were performed in accordance with animal use protocols approved by the Hospital for Sick Children Animal Care Committee (#1000054111, #1000064586).

value: GFP+ sorted neuroblastoma

value: neuroblastoma


title: MYCN-driven brca2+/-;tp53-/- primary neuroblastoma, 4x serially passaged by transplant, biological sample 3

description:
Library name: brca2_4T_3
transplantion into prkdc(SCID) immune-deficient zebrafish


title: Control, ERa, 4OHT, Rep1, CUT&RUN

description: Library name: ERa_Empty_4OHT_Rep1

value: Breast

value: 1 µM 4OHT


title: MYCN-driven brca2+/-;tp53-/- primary neuroblastoma, 4x serially passaged by transplant, biological sample 2

description:
Library name: brca2_4T_2
transplantion into prkdc(SCID) immune-deficient zebrafish


title: Col0_RNAseq_rep3 (re-analyzed)


title: MYCN-driven brca2+/-;tp53-/- primary neuroblastoma, 4x serially passaged by transplant, biological sample 1

description:
Library name: brca2_4T_1
transplantion into prkdc(SCID) immune-deficient zebrafish


title: GFP+ cones, Wildtype

description: Library name: Chrnb4-GFP

value: Wildtype


title: Col0_RNAseq_rep1 (re-analyzed)


title: MYCN-driven atm+/-;tp53+/- primary neuroblastoma

description: Library name: atm_2


title: MYCN-driven tp53-/- primary neuroblastoma, biological sample 1

description: Library name: tp53_1


title: MYCN-driven brca2+/-;tp53-/- primary neuroblastoma, biological sample 3

description: Library name: brca2_3


title: BR4_0%_5VC

city: Vienna

first: Nadine

middle: Elpida

last: Tatto

address: Muthgasse 18

department: Department of Biotechnology

country: Austria

institute: University of Natural Resources and Life Sciences

description: sampling point 4 - biological replicate 4, 0%  oxygen at 5 volume changes

data_processing:
Sequencing at Vienna Biocenter Core Facilites
Basecalling by Vienna Biocenter Core Facilites
Merging and sorting of raw sequencing files with Samtools 1.9
Adapter and Quality Trimming with cutadapt (cutadapt 1.18)
alignment with BowTie2 2.3.4.1 againts the reference sequence of Komagataella phaffii CBS 7435 (FR839628.1–FR839632.1)
Abundance measurement with kallisto (kallisto-0.44.0-h7d86c95_2)
Differential Expression analysis using DESeq2  (R version 4.2.0 (2022-04-22), DESeq2 1.36.0, tximport 1.24.0)
Assembly: Komagataella phaffii FR839628.1–FR839632.1
Supplementary files format and content: kallisto count abundance in tsv format (tab seperated)

organism: Komagataella phaffii CBS 7435

source_name: cells

growth_protocol: Chemostat cultivations were performed in a 1 L DASGIP benchtop bioreactors (SR0700ODLS; Eppendorf AG, Germany) or 1.8 L DASGIP benchtop bioreactors (SR1500ODLS; Eppendorf AG, Germany). The media compositions used in batch and chemostat cultivation are described below. For the entire cultivation, the temperature was set at 25 o C and the pH was controlled at 5.5 by automated addition of 12.5% NH 4 OH. The bioreactors were inoculated to a starting OD 600 of 3.5. During the batch phase, the dissolved oxygen (DO) was kept above 30% by automated adjustment of the stirrer speed between 400 and 1200 rpm and the air flow between 9.5 and 30 sL h -1 . Glucose-limited chemostat cultivations were initiated after the batch-end was reached (indicated by sudden spike in DO) at a dilution rate of 0.075 h -1 . The chemostat working volume of 0.6 L was maintained by means of a level sensor. The stirrer speed was set between 690 to 710 rpm and air flow was set at 0.55 vvm.

extract_protocol:
Total RNA was isolated from cell pellets sampled during chemostat cultivations under normoxic and hypoxic conditions as described by Ata et al. (Ata Ö, Rebnegger C, Tatto NE, Valli M, Mairinger T, Hann S, et al. A single Gal4-like transcription factor activates the Crabtree effect in Komagataella phaffii. Nat Commun. 2018;9(1):4911).
rRNA depletion was conducted with Ribovanish a homemade kit of  Vienna Biocenter Core Facilites (NGS). Libary preparation was performed by the VBCF with NEB Ultra II directional RNA library  kit.

treatment_protocol: The different oxygenation conditions during chemostat cultivation were established by varying the oxygen concentration in the inlet air: a) hyperoxia (31% O 2 ), b) normoxia (21% O 2 ), c) oxygen-limited (14% O 2 ) and d) hypoxia (8% O 2 ). For the first 66 h of the chemostat phase (corresponding to 5 resident times), chemostats were operated under normoxia to establish base-line conditions. When two different oxygenation conditions were tested during the same chemostat cultivation, normoxic conditions were applied in-between the respective oxygenation conditions for 66 h in order to return  to base-line conditions. Four sampling points were selected for RNA-Seq analysis. The first sample was taken after 66 h (T0; 5 resident times) of cultivation at normoxic conditions and the remaining three samples were taken after the switch to hypoxic conditions, specifically after 5 h (T1; 0.5 resident times), 50 h (T2; 4.0 resident times) and 70 h (T3; 5.2 resident times) had passed, respectively.

value: cells

value: whole cells

value: wt

value: 0% 5 volume changes


title: BR4_0%_4VC

description: sampling point 3 - biological replicate 4, 0%  oxygen at 4.0 volume changes

value: 0% 4 volume changes


title: BR3_0%_4VC

description: sampling point 3 - biological replicate 3, 0%  oxygen at 4.0 volume changes


title: BR1_0%_4VC

description: sampling point 3 - biological replicate 1, 0%  oxygen at 4.0 volume changes


title: Microglia_8-mo-female

type: RNA

city: Fukuoka

first: Akiko

last: Mizokami

address: 3-1-1 Maidashi, Higashi-ku

department: Faculty of Dental Science

country: Japan

institute: Kyushu University

description: ND_f microglia

hyb_protocol: biotin labeled miRNA was hybridized toThermo Fisher GeneChip miRNA 4.0 array, washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner

data_processing: The data were analyzed with  with median polish summarization and quantile normalization by Thermo Fisher Transcriptome Analysis Console Software, and obtained normalized intensity values.

label: biotin

source_name: Microglia isolated from hippocampus of five 8-month-old female mice

label_protocol: 130ng of total RNAs were labeled  using the FlashTag™ Biotin HSR RNA Labeling Kit (Affymetrix), following the manufacturer’s instructions (User manual of the FlashTag™ Biotin HSR RNA Labeling Kit, Thermo Fisher)

growth_protocol: Hippocampal microglia were isolated by a magnetic-activated cell sorting (MACS) system.

extract_protocol: Total RNAs including miRNAs were isolated and purified from cells using miRNeasy Mini Kit  (Qiagen)　according to the manufacturer's instructions.

value: Hippocampus

value: Microglia


title: Microglia_8-mo-male

description: ND_m microglia

source_name: Microglia isolated from hippocampus of five 8-month-old male mice


title: BR2_0%_4VC

description: sampling point 3 - biological replicate 2, 0%  oxygen at 4.0 volume changes


title: BR4_0%_0.4VC

description: sampling point 2 - biological replicate 4, 0%  oxygen at 0.4 volume changes

value: 0% 0.4 volume changes


title: BR3_0%_0.4VC

description: sampling point 2 - biological replicate 3, 0%  oxygen at 0.4 volume changes


title: MYCN-driven tp53-/- primary neuroblastoma, biological sample 2

description: Library name: tp53_2


title: MYCN-driven brca2+/-;tp53-/- primary neuroblastoma, biological sample 2

description: Library name: brca2_2


title: BR2_0%_0.4VC

description: sampling point 2 - biological replicate 2, 0%  oxygen at 0.4 volume changes


title: MYCN-driven brca2+/-;tp53-/- primary neuroblastoma, biological sample 1

description: Library name: brca2_1


title: MYCN-driven atm+/-;tp53-/- primary neuroblastoma

description: Library name: atm_1


title: BR3_30%_5VC

description: sampling point 1 - biological replicate 3, 30%  oxygen at 5 volume changes

value: 30% 5 volume changes


title: BR2_0%_5VC

description: sampling point 4 - biological replicate 2, 0%  oxygen at 5 volume changes


title: BR1_0%_5VC

description: sampling point 4 - biological replicate 1, 0%  oxygen at 5 volume changes


title: BR1_30%_5VC

description: sampling point 1 - biological replicate 1, 30% oxygen at 5 volume changes


title: 1h/LBM_B12_x_rep1, SVb3-43

city: Boston

first: Smriti

last: Verma

state: MA

address: 55 Fruit Street

department: Department of Infectious Diseases

institute: Massachusetts General Hospital

description: Library name: SVb3-Sample 17

data_processing:
Sequencing reads were mapped to V. cholerae O1 biovar El Tor strain N16961 chromosome I and II separately by using the program Rockhopper.
For differential expression analysis, we used EdgeR, and classified genes as differentially expressed based on the cutoffs of 1.5-fold change in expression value and false discovery rates (FDR) below 0.05.
Assembly: N16961_v2
Supplementary files format and content: text files include raw counts for each sample

organism: Vibrio cholerae C6706

source_name: bacterial

growth_protocol: Prio to exposure to antibody, V. cholerae El Tor O1 strain C6706 were grown in toxin-inducing-conditions in AKI media (1.5% Bacto-Peptone, 0.4% yeast extract, 0.5% NaCl) supplemented with sodium bicarbonate to a final concentration of 0.3% w/v without agitation at 37 ºC for four hours.

extract_protocol:
Bacterial cultures were then pelleted, and total RNA was isolated using Lysozyme and RNeasy (Qiagen) per manufacturer’s instructions.
RNA was depleted of ribosomal RNA using a ribosomal depletion kit (NEB) and RNA-seq libraries were constructed using NEBNext Ultra II Directional kit per manufacturer’s instructions.

treatment_protocol: Bacterial cultures were diluted to sub-agglutinating conditions of an optical density at 600 nm (O.D.600) of ≤ 0.1 in either LB or LB containing 1% w/v mucin (LBM) and exposed to human monoclonal immunoglobulin (Ig) G1 targeting V. cholerae O-specific polysaccharide component of LPS (clone G1 - CF21.2.G01) and flagellin (clone B12 -AT11.1.B12) for one hour at room temperature

value: bacterial

value: Wild type

value: LBMucin + 0.0125 µM anti-flagellin B12


title: 1h/LBM_G1_x-rep2, SVb3-36

description: Library name: SVb3-Sample 14

value: LBMucin + 0.0125 µM anti-OSP G1


title: BR4_30%_5VC

description: sampling point 1 - biological replicate 4, 30%  oxygen at 5 volume changes


title: 1h/LBM_G1_x-rep1, SVb3-34

description: Library name: SVb3-Sample 13


title: BR1_0%_0.4VC

description: sampling point 2 - biological replicate 1, 0%  oxygen at 0.4 volume changes


title: 1h/LBM_B12_xxx-rep2, SVb3-51

description: Library name: SVb3-Sample 20

value: LBMucin + 0.125 µM anti-flagellin B12


title: 1h/LBM_B12_x-rep2, SVb3-45

description: Library name: SVb3-Sample 18


title: BR2_30%_5VC

description: sampling point 1 - biological replicate 2, 30% oxygen at 5 volume changes


title: 1h/LB_B12_x-rep2, SVb3-15

description: Library name: SVb3-Sample 8

value: LB + 0.0125 µM anti-flagellin B12


title: 1h/LB_B12_xxx-rep1, SVb3-20

description: Library name: SVb3-Sample 9

value: LB + 0.125 µM anti-flagellin B12


title: 1h/LBM_G1_xxx-rep2, SVb3-42

description: Library name: SVb3-Sample 16

value: LBMucin + 0.125 µM anti-OSP G1


title: 1h/LB_G1_x-rep1, SVb3-5

description: Library name: SVb3-Sample 3

value: LB + 0.0125 µM anti-OSP G1


title: 1h/LBM_G1_xxx-rep1, SVb3-40

description: Library name: SVb3-Sample 15


title: 1h/LB_B12_x-rep1, SVb3-14

description: Library name: SVb3-Sample 7


title: 1h/LB_G1_x-rep2, SVb3-6

description: Library name: SVb3-Sample 4


title: 1h/LBM_B12_xxx-rep1, SVb3-50

description: Library name: SVb3-Sample 19


title: BR3_0%_5VC

description: sampling point 4 - biological replicate 3, 0%  oxygen at 5 volume changes

value: cells

value: whole cells


title: 1h/LBM-rep2, SVb3-33

description: Library name: SVb3-Sample 12

value: 1% w/v mucin in LB


title: KLRG1+Tregs, Old, Sample 3

city: Madrid

first: María

last: Mittelbrunn

state: Madrid

address: C/ Nicolás Cabrera, 1

country: Spain

institute: Centro de Biología Molecular Severo Ochoa

data_processing:
RNA-sequencing reads were mapped to the Mus musculus reference genome, GRCm39, using Hisat2 v2.2.1 software.
Reads were then preprocessed with SAMtools v1.13 to transform Sequence Alignment/Map files into Binary Alignment/Map files and sorted.
The number of reads covered by each gene is calculated by HTSeq-Count v1.99.2.
The normalized counts was obtained using DESeq2 v1.44.0.
Assembly: grcm39
Supplementary files format and content: comma-separated value file with the DESeq2 normalized counts for each sample
Supplementary files format and content: comma-separated value file the metadata for each sample

source_name: Spleen

extract_protocol:
RNA from FACS-sorted Treg subsets was purified using the RNeasy Micro Kit (QIAGEN)
Sample quality was measured using the Qubit 3.0 fluorimeter for sample concentration and Agilent 5400 for fragment analysis. SMART-Seq V4 Ultra Low Input RNA kit for Sequencing 480 Rxns (Takarabio) was used for efficient cDNA synthesis and library preparation. After amplification, cDNA was purified using AMPure XP beads to remove any contaminants and ensure high-quality cDNA. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection

value: Spleen

value: Treg KLRG1+

value: WT C57BL/6JRccHsd


title: 1h/LBM-rep1, SVb3-31

description: Library name: SVb3-Sample 11


title: 1h/LB_B12_xxx-rep2, SVb3-21

description: Library name: SVb3-Sample 10


title: KLRG1+Tregs, Old, Sample 2


title: RestingTregs, Old, Sample 2

value: Treg CD62L+ CD44-


title: 1h/LB-rep1, SVb3-2

description: Library name: SVb3-Sample 1

value: No treatment/control in LB


title: 1h/LB_G1_xxx-rep2, SVb3-12

description: Library name: SVb3-Sample 6

value: bacterial

value: LB + 0.125 µM anti-OSP G1


title: 1h/LB-rep2, SVb3-3

description: Library name: SVb3-Sample 2

value: Wild type


title: ActivatedTregs, Old, Sample 4

value: Treg CD62L- CD44+


title: RestingTregs, Old, Sample 1


title: RestingTregs, Old, Sample 4


title: RestingTregs, Old, Sample 3


title: RestingTregs, Young, Sample 4


title: RestingTregs, Young, Sample 3


title: ActivatedTregs, Young, Sample 2


title: KLRG1+Tregs, Old, Sample 4


title: ActivatedTregs, Old, Sample 1


title: KLRG1+Tregs, Young, Sample 3


title: KLRG1+Tregs, Old, Sample 1


title: 1h/LB_G1_xxx-rep1, SVb3-11

description: Library name: SVb3-Sample 5


title: ActivatedTregs, Old, Sample 2


title: RestingTregs, Young, Sample 1


title: Male Nprl3 homozygous mouse fetal liver 9 (S3)

city: Oxford

first: Robert

middle: A

last: Beagrie

address: Headley Way

department: Molecular Haematology Unit

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

data_processing:
RNA-seq reads were mapped to mm39 using STAR v2.7.9 with default parameters.
A read count matrix was assembled using featureCounts v1.6.4 and the Ensembl gene annotation v104.
Sample sex was assigned based on the number of reads mapping to genes located on chromosome Y.
RPKM normalised bigwig files were generated by Deeptools "bamCoverage" v3.3.1
Analysis scripts can be found at https://github.com/beagrie-lab/preston-rna-seq
Assembly: mm39
Supplementary files format and content: read_counts contains a matrix giving the number of sequencing reads from each fetal liver sample (columns) assigned to each gene (rows)

growth_protocol: S1/S3 erythroblasts were FACS sorted from E13.5 fetal liver, according to Ter119 and CD71 expression, using a BD FACS Aria Fusion cytometer. 10-30,000 erythroblasts were sorted directly into lysis solution from the RNAqueous™-Micro Total RNA Isolation Kit (Thermo Fisher Scientific; cat. no. AM1931).

extract_protocol:
RNA extraction was then performed with the RNAqueous™-Micro Total RNA Isolation Kit, according to the manufacturer’s instructions. RNA quality was assessed using an Agilent high sensitivity RNA ScreenTape (Agilent, 5067-5579) and a 4200 TapeStation system (Agilent, G2991BA).
The RNA was amplified by  Novogene using an in-house ‘SMARTer amplification’ pipeline, prior to mRNA library preparation (poly A enrichment).

value: Embryonic stem cells

value: homozygous


title: Male Nprl3 wildtype mouse fetal liver 8 (S3)

value: wildtype


title: KLRG1+Tregs, Young, Sample 4


title: Male Nprl3 heterozygous mouse fetal liver 3 (S3)

value: heterozygous


title: Male Nprl3 heterozygous mouse fetal liver 4 (S3)


title: Female Nprl3 homozygous mouse fetal liver 2 (S3)


title: Female Nprl3 wildtype mouse fetal liver 1 (S3)


title: Male Nprl3 homozygous mouse fetal liver 9 (S1)


title: Male Nprl3 wildtype mouse fetal liver 0 (S3)


title: ActivatedTregs, Young, Sample 3


title: Female Nprl3 wildtype mouse fetal liver 5 (S1)


title: KLRG1+Tregs, Young, Sample 2


title: Female Nprl3 wildtype mouse fetal liver 1 (S1)


title: RestingTregs, Young, Sample 2


title: Het (Q140) KI X Pms1-/- Striatum female 43-5-S

city: Princeton

first: Jeff

last: Aaronson

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

description:
Library name: Sample 93
Pm1Q 43-5-S

data_processing:
Libraries for RNA-seq were sequenced using an Illumina NovaSeq 6000 S4.
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR 2.7.5c with default parameter settings
Raw counts were obtained with Samtools 1.10 and HTSeq 0.12.3 using refSeq gene model (mm10) as reference. Only uniquely mapped reads were used for the subsequent analyses.
Assembly: Genome version Mouse GRCm38
Supplementary files format and content: txt files include FPKM and Count values for each Sample

source_name: Corpus Striatum

extract_protocol:
Brain cortical and striatal tissues were dissected from all mice at 6 months of age. RNA was extracted using a Qiagen RNeasy kit.
Libraries for RNA-seq were prepared using the Illumina TruSeq stranded library preparation protocol (Illumina Inc).

value: Corpus Striatum

value: female

value: 6 months

value: Het (Q140) KI X Pms1-/-

tag: background


title: Pms1-/- Striatum male 44-3-S

description:
Library name: Sample 96
Pm1Q 44-3-S

value: male


title: Pms1-/- Striatum female 43-3-S

description:
Library name: Sample 92
Pm1Q 43-3-S


title: Het (Q140) KI X Pms1-/- Striatum male 44-1-S

description:
Library name: Sample 94
Pm1Q 44-1-S


title: Het (Q140) KI X Pms1-/- Striatum female 43-1-S

description:
Library name: Sample 91
Pm1Q 43-1-S


title: ActivatedTregs, Young, Sample 1

value: Spleen


title: KLRG1+Tregs, Young, Sample 1

value: Treg KLRG1+

value: WT C57BL/6JRccHsd


title: ActivatedTregs, Old, Sample 3


title: Wild type Striatum female 27-5-S

description:
Library name: Sample 89
Pm1Q 27-5-S


title: Het (Q140) KI X Pms1-/- Striatum female 27-3-S

description:
Library name: Sample 88
Pm1Q 27-3-S


title: Male Nprl3 wildtype mouse fetal liver 0 (S1)


title: Wild type Striatum female 27-2-S

description:
Library name: Sample 87
Pm1Q 27-2-S


title: Het (Q140) KI Striatum male 23-4-S

description:
Library name: Sample 85
Pm1Q 23-4-S

value: Het (Q140) KI


title: Pms1-/- Striatum female 22-3-S

description:
Library name: Sample 84
Pm1Q 22-3-S


title: Pms1-/- Striatum female 22-2-S

description:
Library name: Sample 83
Pm1Q 22-2-S


title: Female Nprl3 wildtype mouse fetal liver 5 (S3)


title: Male Nprl3 heterozygous mouse fetal liver 4 (S1)


title: Pms1-/- Striatum female 22-1-S

description:
Library name: Sample 82
Pm1Q 22-1-S


title: Het (Q140) KI X Pms1+/- Striatum male 20-2-S

description:
Library name: Sample 80
Pm1Q 20-2-S

value: Het (Q140) KI X Pms1+/-


title: ActivatedTregs, Young, Sample 4


title: Male Nprl3 wildtype mouse fetal liver 8 (S1)


title: Het (Q140) KI X Pms1+/- Striatum female 13-1-S

description:
Library name: Sample 69
Pm1Q 13-1-S


title: Het (Q140) KI Striatum female 15-1-S

description:
Library name: Sample 74
Pm1Q 15-1-S


title: Wild type Striatum male 14-2-S

description:
Library name: Sample 72
Pm1Q 14-2-S


title: Wild type Striatum male 14-4-S

description:
Library name: Sample 73
Pm1Q 14-4-S


title: Pms1-/- Striatum male 16-4-S

description:
Library name: Sample 75
Pm1Q 16-4-S


title: Pms1+/- Striatum female 13-2-S

description:
Library name: Sample 70
Pm1Q 13-2-S


title: Male Nprl3 heterozygous mouse fetal liver 3 (S1)


title: Wild type Striatum female 11-4-S

description:
Library name: Sample 66
Pm1Q 11-4-S


title: Pms1+/- Striatum female 11-1-S

description:
Library name: Sample 64
Pm1Q 11-1-S


title: Pms1+/- Striatum male 10-2-S

description:
Library name: Sample 63
Pm1Q 10-2-S


title: Het (Q140) KI X Pms1+/- Striatum female 9-4-S

description:
Library name: Sample 61
Pm1Q 9-4-S


title: Het (Q140) KI Striatum female 9-2-S

description:
Library name: Sample 59
Pm1Q 9-2-S


title: Het (Q140) KI X Pms1-/- Striatum male 28-4-S

description:
Library name: Sample 90
Pm1Q 28-4-S


title: Pms1-/- Striatum male 26-5-S

description:
Library name: Sample 86
Pm1Q 26-5-S


title: Het (Q140) KI Striatum male 8-2-S

description:
Library name: Sample 56
Pm1Q 8-2-S


title: Pms1-/- Striatum male 44-2-S

description:
Library name: Sample 95
Pm1Q 44-2-S


title: Het (Q140) KI X Pms1+/- Striatum female 5-2-S

description:
Library name: Sample 49
Pm1Q 5-2-S


title: Female Nprl3 homozygous mouse fetal liver 2 (S1)


title: Het (Q140) KI Striatum female 7-1-S

description:
Library name: Sample 53
Pm1Q 7-1-S


title: Pms1+/- Striatum female 5-3-S

description:
Library name: Sample 50
Pm1Q 5-3-S


title: Het (Q140) KI Striatum male 18-2-S

description:
Library name: Sample 78
Pm1Q 18-2-S


title: Pms1-/- Cortex male 44-3-C

description:
Library name: Sample 48
Pm1Q 44-3-C

source_name: Cerebral Cortex

value: Cerebral Cortex


title: Pms1-/- Cortex male 44-2-C

description:
Library name: Sample 47
Pm1Q 44-2-C


title: Het (Q140) KI X Pms1-/- Cortex female 43-5-C

description:
Library name: Sample 45
Pm1Q 43-5-C


title: Wild type Striatum male 8-4-S

description:
Library name: Sample 58
Pm1Q 8-4-S

value: Wild type


title: Het (Q140) KI X Pms1-/- Striatum male 18-1-S

description:
Library name: Sample 77
Pm1Q 18-1-S


title: Het (Q140) KI X Pms1-/- Cortex female 43-1-C

description:
Library name: Sample 43
Pm1Q 43-1-C


title: Het (Q140) KI X Pms1-/- Cortex male 28-4-C

description:
Library name: Sample 42
Pm1Q 28-4-C


title: Het (Q140) KI Striatum female 7-3-S

description:
Library name: Sample 54
Pm1Q 7-3-S


title: Het (Q140) KI X Pms1-/- Cortex female 27-3-C

description:
Library name: Sample 40
Pm1Q 27-3-C


title: Het (Q140) KI X Pms1-/- Cortex male 44-1-C

description:
Library name: Sample 46
Pm1Q 44-1-C


title: Pms1-/- Cortex female 22-2-C

description:
Library name: Sample 35
Pm1Q 22-2-C


title: Het (Q140) KI X Pms1-/- Striatum female 17-2-S

description:
Library name: Sample 76
Pm1Q 17-2-S


title: Pms1+/- Striatum female 13-4-S

description:
Library name: Sample 71
Pm1Q 13-4-S


title: Wild type Cortex female 27-5-C

description:
Library name: Sample 41
Pm1Q 27-5-C


title: Het (Q140) KI X Pms1+/- Cortex male 20-2-C

description:
Library name: Sample 32
Pm1Q 20-2-C


title: Wild type Cortex female 27-2-C

description:
Library name: Sample 39
Pm1Q 27-2-C


title: Wild type Striatum male 12-4-S

description:
Library name: Sample 68
Pm1Q 12-4-S


title: Wild type Striatum female 11-2-S

description:
Library name: Sample 65
Pm1Q 11-2-S


title: Het (Q140) KI X Pms1+/- Striatum male 12-1-S

description:
Library name: Sample 67
Pm1Q 12-1-S


title: Het (Q140) KI X Pms1-/- Striatum male 21-4-S

description:
Library name: Sample 81
Pm1Q 21-4-S


title: Pms1+/- Striatum male 10-1-S

description:
Library name: Sample 62
Pm1Q 10-1-S


title: Het (Q140) KI X Pms1+/- Striatum female 9-3-S

description:
Library name: Sample 60
Pm1Q 9-3-S


title: Het (Q140) KI X Pms1-/- Cortex female 17-2-C

description:
Library name: Sample 28
Pm1Q 17-2-C


title: Het (Q140) KI Striatum male 18-4-S

description:
Library name: Sample 79
Pm1Q 18-4-S


title: Wild type Cortex male 14-2-C

description:
Library name: Sample 24
Pm1Q 14-2-C


title: Het (Q140) KI X Pms1+/- Striatum male 8-3-S

description:
Library name: Sample 57
Pm1Q 8-3-S


title: Het (Q140) KI X Pms1+/- Striatum male 8-1-S

description:
Library name: Sample 55
Pm1Q 8-1-S


title: Pms1+/- Striatum male 6-1-S

description:
Library name: Sample 51
Pm1Q 6-1-S


title: Pms1-/- Cortex female 43-3-C

description:
Library name: Sample 44
Pm1Q 43-3-C


title: Pms1+/- Cortex female 13-2-C

description:
Library name: Sample 22
Pm1Q 13-2-C


title: Het (Q140) KI X Pms1+/- Cortex male 12-1-C

description:
Library name: Sample 19
Pm1Q 12-1-C


title: Wild type Cortex male 12-4-C

description:
Library name: Sample 20
Pm1Q 12-4-C


title: Wild type Cortex female 11-4-C

description:
Library name: Sample 18
Pm1Q 11-4-C


title: Wild type Cortex female 11-2-C

description:
Library name: Sample 17
Pm1Q 11-2-C


title: Pms1+/- Striatum male 6-2-S

description:
Library name: Sample 52
Pm1Q 6-2-S


title: Pms1-/- Cortex male 26-5-C

description:
Library name: Sample 38
Pm1Q 26-5-C


title: Pms1-/- Cortex female 22-3-C

description:
Library name: Sample 36
Pm1Q 22-3-C


title: Het (Q140) KI Cortex male 23-4-C

description:
Library name: Sample 37
Pm1Q 23-4-C


title: Pms1-/- Cortex female 22-1-C

description:
Library name: Sample 34
Pm1Q 22-1-C


title: Het (Q140) KI X Pms1+/- Cortex female 9-4-C

description:
Library name: Sample 13
Pm1Q 9-4-C


title: Het (Q140) KI X Pms1+/- Cortex male 8-3-C

description:
Library name: Sample 9
Pm1Q 8-3-C


title: Het (Q140) KI X Pms1+/- Cortex male 8-1-C

description:
Library name: Sample 7
Pm1Q 8-1-C


title: Het (Q140) KI Cortex male 8-2-C

description:
Library name: Sample 8
Pm1Q 8-2-C


title: Het (Q140) KI Cortex male 18-4-C

description:
Library name: Sample 31
Pm1Q 18-4-C


title: Het (Q140) KI Cortex male 18-2-C

description:
Library name: Sample 30
Pm1Q 18-2-C


title: Het (Q140) KI Cortex female 7-1-C

description:
Library name: Sample 5
Pm1Q 7-1-C


title: Het (Q140) KI X Pms1-/- Cortex male 18-1-C

description:
Library name: Sample 29
Pm1Q 18-1-C


title: Pms1-/- Cortex male 16-4-C

description:
Library name: Sample 27
Pm1Q 16-4-C


title: Pms1+/- Cortex female 5-3-C

description:
Library name: Sample 2
Pm1Q 5-3-C


title: Het (Q140) KI X Pms1+/- Cortex female 9-3-C

description:
Library name: Sample 12
Pm1Q 9-3-C


title: Sub-library 6

city: Ulm

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

department: Dermatology

institute: University of Ulm

description:
Library name: Sub-library 6
Parse Biosciences

data_processing:
The libraries were then sequenced in NovaSeq 6000 using S2 reagent kit with read 1 64 cycles, i7 index 1 8 cycles, i5 index 2 8 cycles and read 2 58 cycles. Read 1 contains the transcript sequence, while read 2 contains the 10bp polyN sequence and the three 8bp plate barcodes separated by two linker sequences. The demultiplex raw reads (fastq) were next used for genome alignment and transcript discovery, quantification and per identified barcode reporting. The fastq files from each sub-library were first aligned to mouse genome (GRCm39) using customized scripts (split-pipe, version 1.3.1), which call STAR aligner (2.7.11b) to align the fastq reads. The gene expression matrix (count matrix) and barcode list (cell_metadata) and gene information (all_genes) were finally generated by split-pipe scripts. Around 48000 quality filtered total cells were taken for analyses. The count matrix, cell_metadata (cell barcode information) and all_genes (gene annotation) were next loaded into RStudio environment (2004.04.2, build 764) for the data analyses using Seurat (version 5.1.0).
Assembly: GRCm39
Supplementary files format and content: comma separated value files and matrix file

source_name: Skin

extract_protocol:
The single cells were first fixed and permeabilized followed by cell barcoding and cDNA synthesis and library preparation. Single cells from each group was suspended in cell prefixation master mix, followed by addition of cell fixative and incubation of ice for 10 min to fix the cells. The fixed cells were then permeabilized by adding permeabilization solution. After washing the cells with fix and permeabilization stop buffer, the cells were  resuspended in cell storage master mix, containing 5% DMSO and then passed through 40 µm cell strainer and either processed directly for cell barcoding or stored at -80C.
After counting, the fixed and permeabilized cells, were in situ barcoded using four rounds of split-pool barcoding techniques. In the first barcoding reaction, cells were subjected to round 1 cell barcode mediated first strand cDNA synthesis (reverse transcription). After 1st barcoded reverse transcription (first strand of cDNA synthesis), cells were pooled and distributed into each well of a 96 well plate, containing unique 2nd round of barcode in each of the well. After second round of barcoding, cell were again pooled and distributed into another 96 well plate for 3rd round of barcoding. Following 3rd round of barcoding, the cells were again pooled and distributed equally into 8 strip PCR tubes (sub-libraries) to lyse and capture biotinylated cDNA using streptavidin beads. cDNA template switching were next performed to add an adapter to the 3’ end of the captured cDNA. cDNA amplification was next performed using template switch oligo specific primer and 5’ 3rd round of barcoding oligo specific primer. Purified amplified double stranded cDNA was next fragmented (~250 bp) and end repaired, followed by size selection using SPRI beads. The size selected fragmented, end-repaired cDNA was then used to add 5’ adapter with  Illumina Truseq R2  sequence, followed by round 4 barcoding reaction. Post barcoding, the library was purified and size selected and quantified using Qubit dsDNA HS assay kit (Thermo). The library was next subjected to quality control and to check size distribution using QIAxcel Advanced capillary electrophoresis system using high resolution kit.

value: Skin

value: WT and db/db

value: PBS/Sodium butyrate


title: Sub-library 4

description:
Library name: Sub-library 4
Parse Biosciences


title: Sub-library 8

description:
Library name: Sub-library 8
Parse Biosciences


title: Sub-library 3

description:
Library name: Sub-library 3
Parse Biosciences


title: Sub-library 1

description:
Library name: Sub-library 1
Parse Biosciences


title: d120_SOD1_RIPK1i_B8

city: Cambridge

first: Timothy

middle: R

last: Hammond

address: 350 Water Street

institute: Sanofi

description: Library name: s11

data_processing:
cellranger-6.0.0
Assembly: mm10-2020-A
Supplementary files format and content: .h5 matrix files

source_name: SOD1G93A spinal cord

extract_protocol:
At 120 days of age, C57BL/6 mice along with vehicle and RIPK1i-treated SOD1G93A mice were sacrificed and perfused with HBSS supplemented with 5 µg/mL actinomycin D and 10 µM triptolide. Whole spinal cords were isolated, cut sagitally, and placed in 10 mL pre-incubation solution (HBSS (Gibco, 14025-092) supplemented with transcription/translation inhibitor cocktail: 5 µg/mL actinomycin D, 10 µM triptolide, and 27.1 µg/mL anisomycin) on ice and protected from light. Spinal cords were minced on ice with a razor blade then digested for 15 minutes on a shaker at 37 °C in 5 mL papain solution (300 U papain solution (Worthington, LS003126) was diluted in HBSS supplemented with 1:100 DNAse and the transcription/translation inhibitor cocktail). Every 5 minutes samples were triturated with a glass pipette and the papain reaction was quenched with 5 mL HBSS supplemented with 10% FBS. After filtering through a 70 µm strainer and pelleting cells for 5 minutes at 300 g and 4 °C, samples were resuspended in 3 mL HBSS with 10% FBS and 7 mL of 25% BSA solution in HBSS supplemented with the transcription and translation inhibitor cocktail. Cells were centrifuged for 10 minutes at 1200 g and the supernatant and myelin were aspirated prior to addition of 1 mL cold HBSS and a 2 minute spin at 500 g. Finally, the solution was decanted and cells were quantified after resuspending in 500 µL HBSS. Cells were loaded onto the 10x Genomics Next GEM Single Cell 3′ v3.1 sample chip and run following the manufacturerʼs protocols.
10x Genomics Next GEM Single Cell 3′ v3.1

value: SOD1G93A spinal cord


title: Het (Q140) KI X Pms1+/- Cortex female 5-2-C

description:
Library name: Sample 1
Pm1Q 5-2-C


title: Het (Q140) KI X Pms1-/- Cortex male 21-4-C

description:
Library name: Sample 33
Pm1Q 21-4-C


title: d120_SOD1_RIPK1i_B4

description: Library name: s6


title: Sub-library 5

description:
Library name: Sub-library 5
Parse Biosciences


title: Het (Q140) KI Cortex female 15-1-C

description:
Library name: Sample 26
Pm1Q 15-1-C


title: d120_WT_N9

description: Library name: s7


title: d120_SOD1_RIPK1i_B3

description: Library name: s5


title: d120_SOD1_veh_A5

description: Library name: s4


title: d120_WT_N8

description: Library name: s2


title: d120_SOD1_veh_A2

description: Library name: s3


title: Wild type Cortex male 14-4-C

description:
Library name: Sample 25
Pm1Q 14-4-C


title: Dnmt1tet/tet mESCs, Dnmt1 rescue embryoid bodies on day 10 (EB_RES_D10), replicate 2

city: Montreal

first: Serge

last: McGraw

state: Qc

address: 3175 Côte Sainte-Catherine, office 5.17.005

institute: CHU Ste-Justine Research Center/Université de Montréal

description:
Library name: EB_RES_D10-2
mRNAseq_Deconvolution_Embryoid_Bodies.txt

data_processing:
Raw reads were processed using the GenPipes RNA sequencing pipeline v3.1.4. First, Trimmomatic v0.36 was used for quality trimming of raw reads and removal of sequencing adapters and STAR v2.5.3a was used for aligning reads to the mouse reference genome assembly GRCm38/mm10. Then, several functions from Picard v2.9.0 were employed: MergeSamFiles for merging read alignment files of each sample, SortSam for sorting files by coordinate and MarkDuplicates for identifying read duplicates. Next, the HTSeq_count function from HTSeq v0.7.2 was used with Python v2.7.13 for calculating raw counts and StringTie v1.3.5 was used for transcript assembly. Finally, DESeq2 v1.18.1 was used with R v3.4.3 for generating normalized counts and conducting differential gene expression analysis between experimental conditions, producing an adjusted p-value and log2 fold change for each gene.
Raw mRNA-seq counts of embryoid bodies were deconvoluted from single-cell RNA-seq data of mouse gastrulation embryos obtained from the R package MouseGastrulationData v1.18.0, using only data from embryonic day 7.75 embryos and selecting only extraembryonic (ExE) endoderm, epiblast, primitive streak, rostral neurectoderm and forebrain/midbrain/hindbrain cell types. Rostral neurectoderm and forebrain/midbrain/hindbrain cell types were combined into one cell type category that we named neuroectoderm. Technical artifacts were filtered out of the single-cell data by removing doublets and cells with stripped nuclei. The deconvolution was performed with the function music2_prop_t_statistics from the R package MuSiC v1.0.0 using default function settings.
Assembly: GRCm38/mm10
Supplementary files format and content: Text file containing results from the deconvolution of embryoid body mRNA sequencing data

source_name: R1 mESCs

growth_protocol: Dnmt1tet/tet mESCs were maintained on gelatin-coated plates, free of mouse embryonic fibroblast feeder cells, in mESC culture medium in humidified atmosphere with 5% CO2 at 37 °C. Cell culture plates were coated with 0.1% solution of gelatin (Sigma-Aldrich, G1890) in DPBS 1X (Corning, 21-031-CV), then placed in the incubator for 30 minutes after which excess gelatin was removed. Culture medium for mESCs consisted of DMEM (Corning, 10-013-CV) supplemented with 15% ES cell qualified fetal bovine serum (Thermo Fisher, 16141079), 1% 2-mercaptoethanol 100X (Sigma-Aldrich, ES-007-E), 1% non-essential amino acids 100X (Thermo Fisher, 11140050), 1% L-Glutamine 200 mM (Corning, 25-005-CI), 1% nucleosides 100X (Sigma-Aldrich, ES-008-D), 1% penicillin-streptomycin 100X (Corning, 30-002-CI) and 103 units/mL of recombinant mouse LIF protein (Sigma-Aldrich, ESG1107), which was stored at 4 °C for up to 1 week. Culture medium was changed every day and cell confluency was maintained below 80%. Trypsin-EDTA 0.25% (Thermo Fisher, 25200056) was used for passaging cell cultures, typically every other day. The day before beginning differentiation protocols, mESCs were passaged using TrypLE™ Express Enzyme 1X (Thermo Fisher, 12604021) supplemented with 10 μM ROCK Inhibitor Y-27632 (STEMCELL Technologies, 72302) for detachment, re-seeding them with a density of 30,000 cells/cm2 in mESC culture medium in dishes coated with laminin from mouse Engelbreth-Holm-Swarm sarcoma (Roche, 11243217001). For laminin coating, 2.5 μg/cm2 of laminin diluted in DMEM (Corning, 10-013-CV) was added to cell culture dishes in a minimal volume to coat entire dish surface, after which excess laminin was removed and dishes were air dried for 45 minutes inside sterile cell culture hood. The next day, mESC cultures were rinsed twice with differentiation medium prior to starting differentiation protocols. Differentiations were conducted in triplicates, maintaining cultures in humidified atmosphere with 5% CO2 at 37 °C without passaging. Differentiation cultures were rinsed twice daily with differentiation medium prior to adding freshly prepared differentiation treatments to remove dead cells as a fair amount of cell death was expected. On the last day of differentiation protocols, differentiation cultures were sorted based on lineage-specific cell surface and viability markers using fluorescence-activated cell sorting (FACS). Differentiation cultures were rinsed twice with FACS buffer consisting of DPBS 1X (Corning, 21-031-CV) supplemented with 1% ES cell qualified fetal bovine serum (Thermo Fisher, 16141079). A minimal volume of FACS buffer was added to coat entire dish surface and cells were dissociated into single-cell suspension with a cell scraper and gentle pipetting and were transferred to conical tubes. Primary antibodies for cell surface markers were added to cell suspensions in the amount recommended by the manufacturer followed by an incubation of 45 minutes at 4°C, gently mixing every 10 mins. The primary antibodies used for endoderm, mesoderm and ectoderm were anti-CXCR4 (R&D Systems, MAB21651), anti-CDH2 (R&D Systems, AF6426) and anti-NCAM1 (R&D Systems, AF2408), respectively. Cell suspensions were then rinsed twice with FACS buffer and resuspended in FACS buffer containing the fluorophore-conjugated secondary antibody in the amount recommended by the manufacturer followed by an incubation of 45 minutes at 4°C, gently mixing every 10 mins. The secondary antibodies used for endoderm, mesoderm and ectoderm were APC-conjugated anti-Rat IgG (R&D Systems, F0113), APC-conjugated anti-Sheep IgG (R&D Systems, F0127) and Alexa Fluor™ 488-conjugated anti-Goat IgG (Thermo Fisher, A11055), respectively. Cell suspensions were rinsed twice with FACS buffer and resuspended in FACS buffer at a density of 2M cells/100 μL, transferring them to FACS tubes and adding 5 μL of propidium iodide 10 μg/mL (Thermo Fisher, P1304MP) per sample which was used for assessing viability. Cells were sorted with the BD FACSAria™ Fusion Flow Cytometer (BD Biosciences) and data was processed with the BD FACSDiva™ software v8.0.2. One unstained control sample per differentiation condition and one control sample of dead cells stained with propidium iodide were also sorted. The control sample of dead cells consisted of pooled differentiated cells heated at 65°C for 1 minute in a digital dry bath and then incubated on ice for 1 minute. After sorting, RNA was immediately extracted and stored at -80°C for subsequent mRNA sequencing.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (QIAGEN, 74104).
Libraries were prepared with the NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, E7765) in conjunction with the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490).

treatment_protocol: To inactivate Dnmt1, Dnmt1tet/tet mESCs were treated with 2 μg/mL doxycycline hyclate (Sigma-Aldrich, D9891), a tetracycline derivative, which was added to the culture medium for 6 days. Then, doxycycline treatment was stopped, and cells were maintained for 21 days. Samples were collected prior to doxycycline treatment (Dnmt1 control, CTL), immediately following doxycycline treatment (Dnmt1 inactive, INV), and after the 21-day period of recovery from doxycycline treatment (Dnmt1 rescue, RES).For endoderm differentiation, the differentiation medium consisted of RPMI (Thermo Fisher, 11875093) supplemented with 10% KnockOut™ Serum Replacement (Thermo Fisher, 10828028), 2% B-27™ minus insulin 50X (Thermo Fisher, A1895601), 1.5% HEPES 1M (Thermo Fisher, 15630106), 1% 2-mercaptoethanol 100X (Sigma-Aldrich, ES-007-E), 1% non-essential amino acids 100X (Thermo Fisher, 11140050), 1% L-Glutamine 200 mM (Corning, 25-005-CI), 1% nucleosides 100X (Sigma-Aldrich, ES-008-D) and 1% penicillin-streptomycin 100X (Corning, 30-002-CI). Cells were treated with 3 μM CHIR99021 (Sigma-Aldrich, SML1046) and 50 ng/mL Activin A (R&D Systems, 338-AC) for 1 day followed by 50 ng/mL Activin A (R&D Systems, 338-AC) and 100 nM LDN193189 (STEMCELL Technologies, 72147) for 2 days. For mesoderm differentiation, the differentiation medium consisted of EMEM (Corning, 10009CV), 10% KnockOut™ Serum Replacement (Thermo Fisher, 10828028), 1% sodium pyruvate 100 mM (Thermo Fisher, 11360070), 1% 2-mercaptoethanol 100X (Sigma-Aldrich, ES-007-E), 1% non-essential amino acids 100X (Thermo Fisher, 11140050), 1% L-Glutamine 200 mM (Corning, 25-005-CI), 1% nucleosides 100X (Sigma-Aldrich, ES-008-D) and 1% penicillin-streptomycin 100X (Corning, 30-002-CI). Cells were treated with 5 μM CHIR99021 (Sigma-Aldrich, SML1046) and 21 ng/mL BMP-4 (R&D Systems, 5020-BP) for 3 days. For ectoderm differentiation, the differentiation medium was the same as the mESC culture medium but without recombinant mouse LIF protein. Cells were treated with 1 μM of retinoic acid (Sigma-Aldrich, R2625) for 3 days. For embryoid body differentiation, Dnmt1 control, Dnmt1 inactive and Dnmt1 rescue mESCs were detached with TrypLE™ Express Enzyme 1X (Thermo Fisher, 12604021) supplemented with 10 μM ROCK Inhibitor Y-27632 (STEMCELL Technologies, 72302) and counted with a hemocytometer. mESCs were seeded into 96-well round bottom ultra-low attachment plates (Corning, 7007) at 1000 cells per well in 150 μL of culture medium, centrifuged at 100g for 3 minutes and left undisturbed for 2 days. The culture medium used for the first 2 days of embryoid body formation was the same as the mESC culture medium but without nucleosides and with 10 μM ROCK Inhibitor Y-27632. From day 2 to day 4, the embryoid body culture medium was the same as the mESC medium but without LIF and nucleosides. From day 4 to day 10, the embryoid body culture medium was the same as the mESC medium but without LIF and nucleosides and with DMEM/F12 (Thermo Fisher, 11330032) instead of DMEM. Culture medium was changed daily by replacing two thirds with fresh medium. Doxycycline hyclate (2 μg/mL; Sigma-Aldrich, D9891) was added to the embryoid body culture medium from day 0 (seeding) to day 10 for the Dnmt1 inactive condition, or from day 0 to day 5 for the post-differentiation Dnmt1 rescue condition. For post-differentiation Dnmt1 rescue, embryoid bodies were rinsed three times on day 5 with culture medium to remove doxycycline.

value: R1 mESCs

value: Embryonic stem cell

value: mESCs treated with doxycycline (2 μg/mL) for 6 days followed by a 21-day recovery period, then differentiated into embryoid bodies for 10 days


title: Dnmt1tet/tet mESCs, Dnmt1 rescue embryoid bodies on day 10 (EB_RES_D10), replicate 1

description:
Library name: EB_RES_D10-1
mRNAseq_Deconvolution_Embryoid_Bodies.txt


title: Dnmt1tet/tet mESCs, Dnmt1 inactive embryoid bodies on day 10 (EB_INV_D10), replicate 1

description:
Library name: EB_INV_D10-1
mRNAseq_Deconvolution_Embryoid_Bodies.txt

value: mESCs treated with doxycycline (2 μg/mL) for 6 days, then differentiated into embryoid bodies for 10 days while maintaining doxycyline treatment


title: Dnmt1tet/tet mESCs, Dnmt1 control embryoid bodies on day 10 (EB_CTL_D10), replicate 3

description:
Library name: EB_CTL_D10-3
mRNAseq_Deconvolution_Embryoid_Bodies.txt

value: Untreated mESCs differentiated into embryoid bodies for 10 days


title: Dnmt1tet/tet mESCs, Dnmt1 control embryoid bodies on day 10 (EB_CTL_D10), replicate 2

description:
Library name: EB_CTL_D10-2
mRNAseq_Deconvolution_Embryoid_Bodies.txt


title: Dnmt1tet/tet mESCs, Dnmt1 control embryoid bodies on day 10 (EB_CTL_D10), replicate 1

description:
Library name: EB_CTL_D10-1
mRNAseq_Deconvolution_Embryoid_Bodies.txt


title: Pms1+/- Cortex female 13-4-C

description:
Library name: Sample 23
Pm1Q 13-4-C

value: female

value: 6 months


title: Het (Q140) KI X Pms1+/- Cortex female 13-1-C

description:
Library name: Sample 21
Pm1Q 13-1-C


title: Dnmt1tet/tet mESCs, Dnmt1 rescue embryoid bodies on day 5 (EB_RES_D5), replicate 1

description:
Library name: EB_RES_D5-1
mRNAseq_Deconvolution_Embryoid_Bodies.txt

value: mESCs treated with doxycycline (2 μg/mL) for 6 days followed by a 21-day recovery period, then differentiated into embryoid bodies for 5 days


title: Dnmt1tet/tet mESCs, Dnmt1 inactive embryoid bodies on day 5 (EB_INV_D5), replicate 1

description:
Library name: EB_INV_D5-1
mRNAseq_Deconvolution_Embryoid_Bodies.txt

value: mESCs treated with doxycycline (2 μg/mL) for 6 days, then differentiated into embryoid bodies for 5 days while maintaining doxycyline treatment


title: Pms1+/- Cortex female 11-1-C

description:
Library name: Sample 16
Pm1Q 11-1-C


title: Pms1+/- Cortex male 10-2-C

description:
Library name: Sample 15
Pm1Q 10-2-C

value: male


title: Pms1+/- Cortex male 10-1-C

description:
Library name: Sample 14
Pm1Q 10-1-C


title: Het (Q140) KI Cortex female 9-2-C

description:
Library name: Sample 11
Pm1Q 9-2-C

value: Het (Q140) KI


title: Wild type Cortex male 8-4-C

description:
Library name: Sample 10
Pm1Q 8-4-C

value: Cerebral Cortex


title: Testes Knockout Replicate 5

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

description: Library name: KO_T_5

data_processing:
16 totalRNA-Seq samples were pooled and sequenced on NovaSeq 6000 S1 using Illumina® Stranded Total RNA Prep. Ligation was done with Ribo-Zero Plus and paired-end sequencing
RNA-Seq FASTQ files were aligned to the reference genome using STAR using the 2-pass setting.
Raw counts were produced using RSEM.
Assembly: mm10 with the GENCODE_M21 GTF
Supplementary files format and content: Tab-delimited file containing RSEM raw counts for the Liver & Cerebellum samples used in this study.

source_name: Testes

growth_protocol: Mice were housed at 25 ˚C in a 12 h light and 12 h dark cycle.

extract_protocol:
Mice were 6-12 weeks of age and of either sex, with age-matched littermates used as controls unless noted otherwise. Following euthanasia, tissues were isolated, flash-frozen in RNAlater using liquid nitrogen, and stored at −80 ˚C prior to Trizol extraction.
Total RNA from mouse tissues in which THUMPD1 gene has been knocked out (THUMPD1 KO) vs control (WT) were isolated by Trizol extraction and sequenced on NovaSeq 6000 S1 using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus and paired-end sequencing.

value: Testes

value: Knockout


title: Testes Knockout Replicate 6

description: Library name: KO_T_6


title: Het (Q140) KI Cortex female 7-3-C

description:
Library name: Sample 6
Pm1Q 7-3-C


title: Testes Wildtype Replicate 4

description: Library name: WT_T_4

value: Wildtype


title: Pms1+/- Cortex male 6-2-C

description:
Library name: Sample 4
Pm1Q 6-2-C


title: Dnmt1tet/tet mESCs, Dnmt1 control embryoid bodies on day 5 (EB_CTL_D5), replicate 1

description:
Library name: EB_CTL_D5-1
mRNAseq_Deconvolution_Embryoid_Bodies.txt

value: Untreated mESCs differentiated into embryoid bodies for 5 days


title: Pms1+/- Cortex male 6-1-C

description:
Library name: Sample 3
Pm1Q 6-1-C


title: Sub-library 7

description:
Library name: Sub-library 7
Parse Biosciences

value: Skin

value: WT and db/db

value: PBS/Sodium butyrate


title: Sub-library 2

description:
Library name: Sub-library 2
Parse Biosciences


title: d120_SOD1_RIPK1i_B12

description: Library name: s12

value: SOD1G93A spinal cord


title: d120_SOD1_veh_A11

description: Library name: s10


title: Cerebellum Knockout Replicate 8

description: Library name: KO_C_8

source_name: Cerebellum

value: Cerebellum


title: Cerebellum Knockout Replicate 6

description: Library name: KO_C_6


title: Cerebellum Knockout Replicate 7

description: Library name: KO_C_7


title: d120_SOD1_veh_A7

description: Library name: s9


title: Cerebellum Knockout Replicate 5

description: Library name: KO_C_5


title: Dnmt1tet/tet mESCs, post-differentiation Dnmt1 rescue embryoid bodies on day 10 (EB_PostDiff_D10), replicate 2

description:
Library name: EB_PostDiff_D10-2
mRNAseq_Deconvolution_Embryoid_Bodies.txt

value: R1 mESCs

value: Embryonic stem cell

value: mESCs treated with doxycycline (2 μg/mL) for 6 days, then differentiated into embryoid bodies for 5 days while maintaining doxycyline treatment and 5 more days without doxycycline treatment


title: Dnmt1tet/tet mESCs, post-differentiation Dnmt1 rescue embryoid bodies on day 10 (EB_PostDiff_D10), replicate 3

description:
Library name: EB_PostDiff_D10-3
mRNAseq_Deconvolution_Embryoid_Bodies.txt


title: d120_WT_N4

description: Library name: s1


title: Cerebellum Wildtype Replicate 2

description: Library name: WT_C_2


title: Dnmt1tet/tet mESCs, post-differentiation Dnmt1 rescue embryoid bodies on day 10 (EB_PostDiff_D10), replicate 1

description:
Library name: EB_PostDiff_D10-1
mRNAseq_Deconvolution_Embryoid_Bodies.txt


title: Dnmt1tet/tet mESCs, Dnmt1 rescue embryoid bodies on day 10 (EB_RES_D10), replicate 3

description:
Library name: EB_RES_D10-3
mRNAseq_Deconvolution_Embryoid_Bodies.txt

value: mESCs treated with doxycycline (2 μg/mL) for 6 days followed by a 21-day recovery period, then differentiated into embryoid bodies for 10 days


title: d120_WT_N10

description: Library name: s8


title: Dnmt1tet/tet mESCs, Dnmt1 inactive embryoid bodies on day 10 (EB_INV_D10), replicate 3

description:
Library name: EB_INV_D10-3
mRNAseq_Deconvolution_Embryoid_Bodies.txt

value: mESCs treated with doxycycline (2 μg/mL) for 6 days, then differentiated into embryoid bodies for 10 days while maintaining doxycyline treatment


title: Cerebellum Wildtype Replicate 1

description: Library name: WT_C_1


title: Dnmt1tet/tet mESCs, Dnmt1 inactive embryoid bodies on day 10 (EB_INV_D10), replicate 2

description:
Library name: EB_INV_D10-2
mRNAseq_Deconvolution_Embryoid_Bodies.txt


title: Dnmt1tet/tet mESCs, Dnmt1 rescue embryoid bodies on day 5 (EB_RES_D5), replicate 3

description:
Library name: EB_RES_D5-3
mRNAseq_Deconvolution_Embryoid_Bodies.txt

value: mESCs treated with doxycycline (2 μg/mL) for 6 days followed by a 21-day recovery period, then differentiated into embryoid bodies for 5 days


title: Dnmt1tet/tet mESCs, Dnmt1 rescue embryoid bodies on day 5 (EB_RES_D5), replicate 2

description:
Library name: EB_RES_D5-2
mRNAseq_Deconvolution_Embryoid_Bodies.txt


title: Cerebellum Wildtype Replicate 3

description: Library name: WT_C_3


title: Liver Wildtype Replicate 3

description: Library name: WT_L_3

source_name: Liver

value: Liver


title: Dnmt1tet/tet mESCs, Dnmt1 inactive embryoid bodies on day 5 (EB_INV_D5), replicate 3

description:
Library name: EB_INV_D5-3
mRNAseq_Deconvolution_Embryoid_Bodies.txt

value: mESCs treated with doxycycline (2 μg/mL) for 6 days, then differentiated into embryoid bodies for 5 days while maintaining doxycyline treatment


title: Testes Knockout Replicate 8

description: Library name: KO_T_8

value: Testes


title: Dnmt1tet/tet mESCs, Dnmt1 control embryoid bodies on day 5 (EB_CTL_D5), replicate 2

description:
Library name: EB_CTL_D5-2
mRNAseq_Deconvolution_Embryoid_Bodies.txt


title: Dnmt1tet/tet mESCs, Dnmt1 control embryoid bodies on day 5 (EB_CTL_D5), replicate 3

description:
Library name: EB_CTL_D5-3
mRNAseq_Deconvolution_Embryoid_Bodies.txt


title: Dnmt1tet/tet mESCs, Dnmt1 inactive embryoid bodies on day 5 (EB_INV_D5), replicate 2

description:
Library name: EB_INV_D5-2
mRNAseq_Deconvolution_Embryoid_Bodies.txt


title: Cerebellum Wildtype Replicate 4

description: Library name: WT_C_4


title: Testes Knockout Replicate 7

description: Library name: KO_T_7

value: Knockout