title: SCNT-TE-RNAseq-rep2

city: Shanghai

first: Liao

last: Zhaodi

address: 500, Qiangye Road

department: Institute of Neuroscience

institute: Chinese Academy of Sciences

data_processing:
The raw sequencing reads were trimmed by using trim_galore with parameters of "-q 25 --phred33 --length 36 -e 0.1 --stringency 4" to remove low-quality bases and adapters in paired-end reads.
The remaining reads were mapped to the Macaca fascicularis genome (macFas5) using hisat2 with default parameters "--dta --no-mixed --no-discordant --no-softclip -p 12".
The sam files were converted to bam files using samtools, then the bam file were sorted and the index files were created.
Raw read counts were calculated by featureCounts.
Assembly: macFas5
Supplementary files format and content: a tab-delimited text file include count values for each Sample

organism: Macaca fascicularis

source_name: trophoblast

extract_protocol:
The RNA was extracted by following the instructions of NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® NEB #E6420S
1. RNA Extraction
2. Reverse Transcription and Adapter Ligation
3. cDNA Amplification
4. cDNA Fragmentation
5. cDNA Adapter Ligation
6. cDNA PCR Enrichment

value: trophoblast

value: embryo trophoblast cells

value: wild type

value: SCNT


title: PAPNAI (RNA-seq)

status: Public on Aug 01 2023

type: SRA

city: Jerusalem

first: Miriam

middle: I.

last: Rosenberg

address: Edmond Safra Campus

department: Genetics

country: Israel

institute: Hebrew University of Jerusalem, Givat Ram

description: RNAseq from fresh frozen tumor RNA

library_source: transcriptomic

data_processing:
Raw FASTQs from both the OMAS/LR/HR cohort and NCI TARGET (Pugh TJ et al 2013) datasets were processed using fastq-mcf (https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/ FastqMcf.md; parameters used were: http://expressionanalysis.github.io/ea-utils/; parameters: --max-ns 4 –qual-mean 25 -H -p 5 -q 7 -l 25).
[Alignment and isoform quantification] Clipped reads were aligned to the human reference genome hg19 using STAR v2.4 (Dobin et al 2013) and a UCSC reference transcriptome supplemented with lincRNAs from Ensembl. RSEM v1.2.14 (https://github.com/ExpressionAnalysis/STAR-SEQR) was used for both gene and isoform quantification
[RNA fusion event detection]  RNA fusion events were detected using STAR-SEQR v0.6.5  (Ritchie et al 2014) parameters: -m 1).
[Differential expression analysis]  Differential expression analysis was performed using Q2 Solutions’ ensemble two group comparisons suite. This method summarizes the differential expression p-values and classification probabilities from five tools—t-test, limma4, DESeq2 ((Ritchie et al 2014), edgeR (Anders and Huber, 2010) and EBSeq (Robinson MD, McCarthy DJ, Smyth GK 2010)—to produce a new p-value for differential expression.
[p-value calculation]  For any given gene, the p-values of each constituent model are input into a logistic regression model, which estimates the probability that the gene is differentially expressed. This probability is transformed into a p-value for differential expression by comparing it against its empirical cumulative distribution as estimated by bootstrap resampling of TCGA data from various cancer types.
Genome_build: hg19
Supplementary_files_format_and_content: RSEM files given for gene counts

molecule: total RNA

organism: Homo sapiens

source_name: Neuroblastoma tumor

growth_protocol: Tumor total RNA and tumor genomic DNA were prepared from fresh-frozen tumor collected during tumor resection or biopsy.

extract_protocol:
Fresh tumor was frozen on dry ice and stored until further processing. RNA was extracted using Trizol reagent as per manufacturer's instructions.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Access kit (now called TruSeq RNA Exome).  Briefly

tag: patient subgroup

value: OMAS

tag: disease state

value: neuroblastoma

tag: tissue

value: fresh frozen tumor


title: ABF1_A_ChEC-seq

city: SEATTLE

first: Lakshmi

last: Mahendrawada

state: WA

address: 1100 FAIRVIEW AVE N

department: Basic Sciences Division

country: USA

institute: Fred Hutchinson Cancer Center

library_source: genomic

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and D. melanogaster reference genome (release 6.06) with Bowtie2 (Langmead and Salzberg, 2012) using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
For each base pair in the genome, we counted the number of paired-end fragments aligned over it.
Signal per base pair was normalized by the number of all D. melanogaster reads mapped for the sample and multiplied by 10000 (arbitrarily chosen number).
Assembly: sacCer3 (S. cerevisiae), release 6.06 (D. melanogaster)
Supplementary files format and content: Processed data is provided in a bigwig format and contains spike-in normalized signal per base pair.
Library strategy: ChEC-seq

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 ABF1-MNase::TRP1

growth_protocol: 30 degrees in a synthetic complete (SC) medium to mid-log phase.

extract_protocol:
ChEC-seq was performed as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Sequencing libraries were constructed as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.

treatment_protocol: After reaching appropriate OD selected samples were treated with either DMSO or SM, Raffinose or Galactose.

tag: genotype

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 ABF1-MNase::TRP1


title: PANSDX (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: PANUTJ (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: F37 104885-001-038

city: Leiden

first: Anita

last: van den Hoek

state: Zuid-Holland

address: Zernikedreef 9

department: MHR

country: Netherlands

institute: TNO

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Assembly: Mus_musculus.GRCm38.gencode.vM19
Supplementary files format and content: The count files contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package.

organism: Mus musculus

source_name: liver

growth_protocol: Animal care and experimental procedures were approved by The Netherlands Central Authority for Scientific Procedures on Animals (CCD; project license AVD5010020172064) and an independent Animal Welfare Body of The Netherlands Organization for Applied Scientific Research (IvD TNO; TNO-489). Ldlr-/-.Leiden mice were bred and housed at the SPF animal facility at TNO (TNO Metabolic Health Research, Leiden, The Netherlands). Male mice were chosen because of their increased susceptibility for developing obesity and inflammation in comparison to female mice.

extract_protocol:
For next generation sequencing the RNA-Bee total-RNA isolation kit (Bio-Connect, Huissen, The Netherlands) was used to isolate total RNA from individual liver samples (lobus sinister lateralis) and RNA integrity was determined with the RNA 6000 Nano Lab-on-a-Chip kit and bioanalyzer 2100 (Agilent Technologies, Amstelveen, The Netherlands). Total RNA's were processed into tagged random sequence libraries.
Next Generation Sequencing was performed at Genome Scan (Leiden, the Netherlands). For this, strand-specific cDNA libraries were generated from total-RNA using oligo-dT magnetic beads, mRNA fragmentation, NEBNext Ultra Directional RNA Library Prep Kit from Illumina, NEB #E7760S/L resulting in 300–500 bp amplified libraries/sample. Libraries were multiplexed, clustered, and sequenced on a NovaSeq6000 v1.5 system (Illumina, New England Biolabs, Inc. Ipswich, MA, USA), with a paired-end, 150 bp sequencing protocol, 20-35 million reads per sample and indexing.
Clustering and DNA sequencing using the NovaSeq6000 v1.5 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: Mice (10-17 weeks old) were group-housed in a temperature-controlled room on a 12h light-dark cycle at 50-60% humidity and with free access to heat-sterilized water and food. Body weight, food intake per cage and clinical signs were monitored regularly. One group of mice (n=8) received the healthy grain-based chow diet (Ssniff Spezialdiäten GmbH, Soest, Germany) and a total of 45 mice received fast food diet (FFD) containing 41 kCal% fat from milk fat, 44 kCal% from carbohydrates (mainly fructose) and 14 kCal% casein (Research Diets, New Brunswick, NJ, USA) to induce advanced NASH and hepatic fibrosis. At t=0, after a 25-week run-in period on FFD, mice were matched on body weight, glucose, cholesterol and triglycerides into three groups of 15 mice each. Appropriate group sizes were calculated a priori by power analysis (GPower), with a minimal effect size of 30%, using a two-sided test with 95% confidence interval, power of 90% and α of 0.05. One group of n=15 mice served as FFD reference and was sacrificed at t=0 to indicate NASH and atherosclerosis severity at the start of the treatment. Comparison of semaglutide-treated mice with this reference group indicated whether semaglutide treatment could reduce NASH, hepatic fibrosis and atherosclerosis below levels at the start of treatment or blocked further progression. The second group (n=15) received daily subcutaneous saline injections for twelve weeks (FFD control). The third group (n=15) received daily subcutaneous semaglutide injections (100 µL, Ozempic®, Novo Nordisk, Bagsværd, Denmark) for twelve weeks. The dose was escalated over five days at a rate of 0.024 (20%), 0.048 (40%), 0.072 (60%), 0.096 (80%) mg/kg/day until the final dose of 0.120 mg/kg/day was reached and maintained until the study endpoint (based on weekly body weight measurement). Animals were sacrificed non-fasted by gradual-fill CO2 asphyxiation after the 25-week run-in period (t=0; FFD reference) or twelve weeks after the run-in period (t=12; other groups) and organs were collected for further analysis.

tag: treatmentperiod

tag: mousenr

value: m38 sema


title: F37 104885-001-036

value: m36 sema


title: F37 104885-001-035

value: m35 sema


title: S37 104885-001-041

value: m41 sema


title: S37 104885-001-040

value: m40 sema


title: S37 104885-001-044

value: m44 sema


title: S37 104885-001-039

value: m39 sema


title: S37 104885-001-043

value: m43 sema


title: F37 104885-001-037

value: m37 sema


title: ICSI-TE-RNAseq-rep2

country: China

value: trophoblast

tag: cell line

tag: cell type

tag: treatment

value: ICSI


title: S37 104885-001-042

value: m42 sema


title: PASPIH (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: Rep2 Ded1-RNA X-link grown with glucose depletion

city: Paris

first: N.

middle: Kyle

last: Tanner

state: Ile de France

address: 13 rue Pierre et Marie Curie

department: Microbial Gene Expression

country: France

institute: Université de Paris-Cité & CNRS

data_processing:
The Illumina adapters were de-multiplexed using the bcl2fastq2 tool (version 2.18.12)
Adapters were removed with Cutadapt (adapter trimming, version 1.15).
The quality of the reads was verified using the FastQC tool (version v0.11.5)
BWA tool (version 0.7.12) was usedto do a local alignment with the following parameter : bwa mem -t 40 –c 1000 index .fasta read-file.fastq > sample.sam.
Samtools tool (version 1.9) was used according to the following parameter: samtools view -bt index.fasta sample.sam - o sample.bam.
PCR duplications were eliminated using the following parameter: samtools rmdup -s sample.bam -o sample-rmdup.bam.
File sorted by genomic coordinates using the yeast genome in general feature format (GFF) available from SGD (genome.gff) using the following parameters: samtools sort sample-rmdup.bam > sample-rmdup-sorted.bam and samtools index sample-rmdup-sorted.bam.
The counting table of each reads was obtained using the Bedtools tool (version 2.3.0) according to the following parameters: bedtools multicov -S -D -bams sample- rmdup-sorted.bam -bed genome.gff > sens-counts.txt and bedtools multicov -s -D -bams sample-rmdup-sorted.bam -bed genome.gff > antisens-counts.txt.
Assembly: Yeast S. cerevisiae (S288C) genome was indexed (index.fasta).
Supplementary files format and content: *RMdup_bedtools.txt:
column 1: NCBI locus
column 2: keywords
column 3: Feature
column 4: coordinate start
column 5: coordinate end
column 6: ND
column 7: Orientation
column 8: Merged features
column 9: Identification
column 10: Reads

growth_protocol: The wild type BY4742 yeast strain with the DED1 gene under its own promoter and terminator in the YCplac111 plasmid was grown at 30°C in SD-LEU to an OD600 of ~0.4 (exponential phase). The cultures were then made 300 µM in 4-thiouracil. Cultures were incubated to an OD600 of 1.8-2.0 (~5 hours). Some cultures were subjected to glucose depletion by growing 10 min in medium lacking glucose prior to irradiation.

extract_protocol:
Cells were lysed by vortexing in a FastPrep-24, clarified by centrifugation, and then bound to Protein A-Sepharose beads with Ded1 IgG, washed extensively and digested with nuclease S1
The 3' adapter was added directly to the Protein-Sepharose-bound Ded1-RNA complex, eluded, the 5' adapter was added, the Ded1-RNA complex was eluted, digested with protease K, the RNA was phenol/chloroform extracted, ethanol precipitated and then subjected to RT-PCR. The PCR products were combined and concentrated with a NucleoSpin Gel and PCR Clean-up kit amplification, purified on 6% PAGE and material migrating between ~120 and ~200 residues were recovered.

treatment_protocol: Cells with ~1.3% 4-thiouridine incorporated were concentrated to an OD600 of ~32 and irradiate 2X 10 min with UV light centered at 365 nm with a flux of ~7 Joules/cm^2 in a polystyrene petri dish with lid and on ice.

tag: strain

value: 15 min glucose depletion

tag: molecule subtype

value: Ded1 bound RNA


title: Rep3 Ded1-RNA X-link grown in SD+LEU medium

value: with the DED1 gene under its own promoter and terminator in the YCplac111 plasmid

value: Normal (WT) growth conditions


title: Rep3 Ded1-RNA X-link grown with glucose depletion


title: F37 104885-001-034

value: m34 sema


title: F37 104885-001-033

value: m33 sema


title: ICSI-TE-RNAseq-rep1

value: embryo trophoblast cells

value: wild type


title: leaf-shading-48 rep2

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

institute: HUJI

description: N

data_processing:
Raw reads were trimmed for quality and adaptor removal using Trim Galore default settings. Average raw reads library size per sample was 36 M
trimmed reads were mapped to Solanum lycopersicum genome ITAG 3.2 as downloaded from https://solgenomics.net/ using STAR mapper v. 2.6.0c within RSEM package for quantifying gene and isoform abundances. Average percent of alignable reads was 93.5% and out of those an average of 87% were aligned uniquely to a gene.
Expected counts of mapped reads to genes per sample table was subjected to differential expression analysis using DESeq2 R package. Differentially Expressed genes were defined as genes with FDR corrected p-value < 0.1
Assembly: Solanum lycopersicum genome ITAG 3.2 as downloaded from https://solgenomics.net/
Supplementary files format and content: tab-delimited text files include raw counts per gene values for each Sample

organism: Solanum lycopersicum

source_name: leaf

growth_protocol: Tomato (Solanum lycopersicum L. cv. M82) plants were sown in trays filled with 70% (w/w) coconut fiber, 30% (w/w) vent materials, fertilizer and nutrients in a temperature-controlled growth chamber. Day/night air temperatures were 25/18 ± 2oC, and light intensity was 180 µmol m-2 s-1. Photoperiod was set to 12 h. Seedlings (4 weeks old) were transferred to 1-L pots, and grown in a greenhouse at 28/20 ± 2oC (day/night, respectively) under natural sunlight.

extract_protocol:
Total RNA was extracted from the remaining and parallel control leaves using RNeasy® Plant Mini Kit (Qiagen, Germany) according to the manufacturer's protocol.
A TruSeq mRNA library was then created using TruSeq RNA Library Prep Kit v2 (Illumina, USA).

treatment_protocol: For partial shading, all leaves except for the youngest fully expanded leaf (number 4 or 5 from the top, with leaf number 1 being the first to reach a length of 3 cm) were covered with aluminum foil. For partial defoliation, all leaves except for the measured one were carefully cut near the stem with a sharp surgical knife. Both treatments were performed at the reproductive stage—1 week after anthesis of the first flowers.

value: leaf

value: Leaf Mesophyll

value: WT


title: leaf-shading-48 rep3

description: O


title: PAUPWX (RNA-seq)

description: RNAseq from fresh frozen tumor RNA

value: OMAS

value: neuroblastoma

value: fresh frozen tumor


title: F37 104885-001-032R

value: m32 sema


title: F37 104885-001-030

value: m30 sema


title: leaf-defoliation 48 rep3

description: L

value: defoliation 48


title: leaf-defoliation 48 rep2

description: K


title: F37 104885-001-029

value: m29 sema


title: leaf-control rep3

description: C

value: control


title: leaf-defoliation 48 rep1

description: J


title: Rep1 Ded1-RNA X-link grown with glucose depletion

value: with the DED1 gene under its own promoter and terminator in the YCplac111 plasmid

value: 15 min glucose depletion

value: Ded1 bound RNA


title: F37 104885-001-027

value: m27 sema


title: F37 104885-001-026

value: m26 sema


title: PAUWXL (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: F37 104885-001-028

value: m28 sema


title: F37 104885-001-025

value: m25 sema


title: leaf-control rep2

description: B

value: leaf

value: Leaf Mesophyll


title: leaf-control rep1

description: A

value: WT


title: F37 104885-001-024R

value: m24 sema


title: PAUHDK (RNA-seq)

description: RNAseq from fresh frozen tumor RNA

value: OMAS

value: neuroblastoma

value: fresh frozen tumor


title: PAUHXD (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: PATXKK (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: PAUKNU (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: PATTTS (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: PATRNS (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: F37 104885-001-031

value: m31 sema


title: PANNNX (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: F25 104885-001-023

value: m23 sema


title: F25 104885-001-022

value: m22 sema


title: SCNT-TE-RNAseq-rep1

value: trophoblast

value: embryo trophoblast cells

value: wild type

value: SCNT


title: PASLAE (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: leaf-shading-48 rep1

description: M


title: PATADI (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: PASGHN (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: PASIUC (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: PASDYT (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: PASJDC (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: HFD_CD34pos_rep1

type: RNA

city: Madison

first: Lisa

last: Arendt

state: WI

address: 2015 Linden Drive

department: Comparative Bioscience

institute: University of Wisconsin-Madison

description: mice were fed a high-fat diet (58Y1, Test Diet) for 16 weeks

hyb_protocol: The products of the Low input RNA amplification reactions was combined with the Reporter/Hybridization Buffer master mix and Capture ProbeSet and incubated for 16 hours at 65 degrees C according to manufacturer's instructions.

scan_protocol: The Nanostring fibrosis panel cartridge was scanned on an nCounter MAX at MAX FOV.

data_processing: Data was processed using Rosalind Nanostring software.  Counts for each gene were derived by dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization were selected based on the geNorm algorithm as implemented in the NormqPCR R library. P-value adjustment was performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR). Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library.

label: nCounter Low RNA input kit primers for Fibrosis V2 panel

source_name: CD11b+CD34+ cells

label_protocol: RNA was converted to cDNA and amplified with the NanoString Low RNA Input Amplification kit using low input primers for the Fibrosis V2 Panel according the manufacturer's instructions.

growth_protocol: Mice were randomized to receive diets starting at 3 weeks of age and weighed weekly.  After 16 weeks, mice were euthanized, and mammary glands were collected.  Mammary glands were collagenase digested for 1 hr prior to dissociation to single cells using trypsin.

extract_protocol: Cells were FACS sorted into Trizol, and RNA was extracted immediately after sorting using Qiagen microRNA kit.

treatment_protocol: The Fc receptor was blocked using CD16/32 antibodies on dissociated cells from the mammary glands.  Cells were stained with fixable live/dead and antibodies for CD45, CD11b, and CD34.  Live CD45+ cells were sorted for CD11b+CD34+ and CD11b+CD34- cell populations.

value: FVB/N

tag: gender

value: female

tag: organ

value: mammary gland

tag: diet

value: high-fat diet

tag: isolation method

value: FACS


title: PASCCV (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: HFD_CD34pos_rep3


title: F25 104885-001-020

value: m20 sema


title: F25 104885-001-015

value: m15 sema


title: F25 104885-001-018

value: m18 sema


title: F25 104885-001-019

value: m19 sema


title: HFD_CD34neg_rep3

source_name: CD11b+CD34- cells


title: HFD_CD34pos_rep2


title: F25 104885-001-016

value: m16 sema


title: HFD_CD34neg_rep1


title: HFD_CD34neg_rep2


title: PASAKL (RNA-seq)

description: RNAseq from fresh frozen tumor RNA

value: OMAS

value: neuroblastoma

value: fresh frozen tumor


title: LFD_CD34pos_rep3

description: mice were fed a low-fat diet (2920X, Teklad Global) for 16 weeks

value: low-fat diet


title: PASAHC (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: F25 104885-001-014

value: m14 sema


title: PARTZY (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: LFD_CD34neg_rep3


title: LFD_CD34pos_rep2


title: F25 104885-001-021

value: m21 sema


title: F25 104885-001-013

value: m13 sema


title: PARJPI (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: PATWIL (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: F25 104885-001-012

value: m12 sema


title: PANJHR (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: LFD_CD34neg_rep2

value: FVB/N

value: female


title: F25 104885-001-017

value: m17 sema


title: WGBS monkey_oocyte_MII_rep3

description:
monkey_oocyte_MII_rep3
oocyte

data_processing:
The raw sequencing reads were trimmed by fastp (version 0.23.2) with default parameters to remove low-quality bases and adapters in paired-end reads.
The remaining reads of oocytes and STB cells were aligned to the Macaca fascicularis genome (macFas5) using Bismark (version 0.23.1) with parameters “--non_directional”.
The WGBS datasets of placenta were aligned to macFas5 using Bismark with default parameters.
The methylation level and coverage depth of each cytosine were extracted from the aligned reads with bismark_methylation_extractor.
The bedGraph files resulted from bismark_methylation_extractor was converted to BW files using bedGraphToBigWig software.
Assembly: macFas5
Supplementary files format and content: The bw files containing the DNA methylation peaks of the corresponding samples.
Supplementary files format and content: The tab-delimited txt files containing the DNA methylation peaks of CpGs of the corresponding samples.

source_name: oocytes

growth_protocol: placenta, STB cells, single oocyte

extract_protocol:
For the placenta tissues, their whole genome was extracted with the TIANamp Genomic DNA Kit (DP304-03) under the manufactures construction. For the STBThe oocytes were lysed in the lysis buffer and then whole genome were
For the WGBS of placenta, 1 µg genomic DNA was fragmented to 200-300bp and purified using MiniElute PCR Purification Kit (QIAGEN). The resulted DNA was incubated at 20 ℃ with End Repair Mix and then purified. After end repair, the library was combined with A-Tailing Mix and incubated at 37 ℃ and then purified. Next, methylated adaptors were ligated to the Adenylate 3’Ends DNA and purified again. The above library was then undergoing bisulfite treatment and purified with Methylation-Gold kit (ZYMO). After that, fragments ranging from 320 to 420 bp were purified using agarose gel electrophoresis. The library was then amplified using PCR. Finally, the purified DNA products was qualified using the Agilent Technologies 2100 bioanalyzer and ABI StepOnePlus Real-Time PCR system. The library was sequenced in pair-end on the DNBseq platform.     STB cells were seeded into lysis buffer by mouth pipette and subjected to bisulfite conversion using the EZ DNA Methylation Direct Kit (Zymo Research, D5020). A small amount of unmethylated Lambda DNA (Promega, D152A) was added to each sample before bisulfite conversion to serve as spike-in controls for evaluating bisulfite conversion efficiency. After column-based purification, DNA was complemented with the random primer Preamp and Klenow polymerase (Enzymatics, P7010-HC-L). This random priming was repeated five times in total. Second strands were synthesized using another random primer, Adapter 2. Final libraries were generated after PCR amplification with the Illumina universal PCR primer and Illumina indexed primer, and were then purified using SPRI beads. Final libraries were subjected to paired-end 150 bp sequencing on a NovaSeq 6000 sequencer (Illumina) with PhiX spike-in control.     For the WGBS library construction of oocyte, a single oocyte was collected for each replication. A total of 2 GV oocytes and 3 MII oocytes were collected in this research. After cells were lysed using cell lysis buffer, bisulfite treatment was performed and the resultant DNA was purified using PureLink PCR Micro Kit (InvitrogenTM, K310050). The purified DNA was added with oligo1, followed by PCR. Then, the single strand DNA template was digested using polymerase, and the PCR products was purified using DynabeadsM-280 Streptavidin. The beads were resuspended in reaction mix with oligo2, the products were then purified again using Agencourt RNAClean XP beads. The purified DNA products were amplified using primers containing illumina specific primer and index. Finally, the amplified PCR products were further purified and eluted in elution buffer. The library was qualified using Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System (TaqMan Prob). The qualified DNA library sequenced using DNBseq platform.

value: oocytes

value: pre-implantation

value: wild type


title: F25 104885-001-009

value: m09 sema


title: LFD_CD34pos_rep1

value: mammary gland

value: FACS


title: multiome GEX, mixed glial differentiation, ROSMAP Line 18

city: New York

first: Paul

last: Frazel

state: NY

address: 435 E 30th St

institute: NYU Langone Medical Center

data_processing:
After demultiplexing, cell calling was performed via Cellranger v6.0.1 or Cellranger ARC v4.0.5 for multiomic data.
Assembly: mm10, GRCh38-2020-A
Supplementary files format and content: Processed data type: h5 file for gene expression, atac fragments for snATACseq. Can be used for tertiary scRNAseq analysis

source_name: mixed glial differentiation

extract_protocol:
Single cell suspensions were generated with papain dissociation. Single nuclei generated with Sigma EZ Lysis buffer.
10X Genomics manufacturer's instructions (Illumina dual-index library)

value: mixed glial differentiation

value: nuclei


title: F25 104885-001-010

value: m10 sema


title: F25 104885-001-011

value: m11 sema


title: WGBS monkey_oocyte_MII_rep1

description:
monkey_oocyte_MII_rep1
oocyte


title: WGBS monkey_oocyte_MII_rep2

description:
monkey_oocyte_MII_rep2
oocyte


title: multiome GEX, mixed glial differentiation, ROSMAP Line 17


title: WGBS monkey_oocyte_GV_rep2

description:
monkey_oocyte_GV_rep2
oocyte


title: LFD_CD34neg_rep1

value: low-fat diet


title: WGBS monkey_oocyte_GV_rep1

description:
monkey_oocyte_GV_rep1
oocyte


title: C37 104885-001-006

value: m06 sema


title: C37 104885-001-007

value: m07 sema


title: C37 104885-001-008

value: m08 sema


title: multiome GEX, mixed glial differentiation, ROSMAP Line 16


title: multiome GEX, mixed glial differentiation, ROSMAP Line 14


title: C37 104885-001-005

value: m05 sema


title: multiome GEX, mixed glial differentiation, ROSMAP Line 19


title: multiome GEX, mixed glial differentiation, ROSMAP Line 13


title: multiome GEX, mixed glial differentiation, ROSMAP Line 12


title: C37 104885-001-004

value: m04 sema


title: WGBS STB_WGBS_SCNT_rep1

description:
STB_WGBS_SCNT_rep1
SCNT

source_name: placenta

value: placenta

value: syncytial trophoblast cells

value: day 82

value: SCNT


title: WGBS STB_WGBS_ICSI_rep2

description:
STB_WGBS_ICSI_rep2
ICSI

value: day 85

value: ICSI


title: C37 104885-001-003

value: m03 sema


title: multiome GEX, mixed glial differentiation, ROSMAP Line 11

value: mixed glial differentiation


title: C37 104885-001-002

value: m02 sema


title: WGBS STB_WGBS_ICSI_rep1

description:
STB_WGBS_ICSI_rep1
ICSI

value: day 80


title: multiome GEX, mixed glial differentiation, ROSMAP Line 8

molecule: polyA RNA

value: nuclei


title: C37 104885-001-001

value: m01 sema


title: multiome GEX, mixed glial differentiation, ROSMAP Line 9


title: multiome GEX, mixed glial differentiation, ROSMAP Line 15


title: WGBS IVC_WGBS_epiblast_SCNT_rep1

description:
IVC_WGBS_epiblast_SCNT_rep1
SCNT

source_name: in vitro cultured embryos

value: in vitro cultured embryos

value: post-implanted

value: embryo

value: wild type


title: WGBS IVC_WGBS_epiblast_ICSI_rep2

description:
IVC_WGBS_epiblast_ICSI_rep2
ICSI


title: WGBS IVC_WGBS_epiblast_SCNT_rep2

description:
IVC_WGBS_epiblast_SCNT_rep2
SCNT


title: intraTAD2_1xBorCTCF-E105-LB-Shh-cHiC 2

city: Berlin

first: Daniel

middle: Murad

last: Ibrahim

state: Berlin

address: Augustenburger Platz 1

department: Center for Regenerative Therapies

country: Germany

institute: Berlin Institute of Health

data_processing:
Basecalling with standard Illumina software
reads were trimmed to 50bp to make the mapping comparable to wildtype samples (GSM3502453 and GSM3502454)
Mapping and filtering of di-tags was performed with the HiCUP pipeline v0.5.8 (http://www.bioinformatics.babraham.ac.uk/projects/hicup/) (parameters: Nofill:1without any size selection). The pipeline used Bowtie2 v2.2.6 for mapping short reads to reference genome (NCBI37/mm9).
Filtered di-tags were further processed with Juicebox command line tools (https://github.com/theaidenlab/juicebox) to bin di-tags (10kb bins) and normalized by KR normalization (Only reads with MAPQ >= 30 were considered). The DNA-capturing step enriches genomic region chr11:109,010,001-114,878,000 on mm9 . Before binning and normalization, di-tags were filtered for the enriched region and mm9 coordinates were shifted by -109,010,000 bp (a custom chromosome file containing only the enriched region on chr11 (length 5,868,000 bp) was used). After binning and normalization, coordinates were shifted back to their original values.
Log2 ratios between different CHi-C maps were generated based on raw count maps, which were normalized individually by dividing contact counts by (‘genome wide contact counts’/10^6). A constant value of 0.001 was added to each bin to avoid division by zero prior to the computation of log2 ratios.
For visualization CHi-C maps of count values and log2 ratios were visualized with the WashU epigenome browser (epigenomegateway.wustl.edu/browser/).
Assembly: mm10 and custom mm10
Supplementary files format and content: BAM file of mapped and filtered di-tags/paired end reads
Supplementary files format and content: CHi-C map in WashU epigenome browser pairwise interaction format

source_name: limb bud

growth_protocol: E10.5 limb buds of embryos were dissected in cold PBS and subsequently fixed with 2% formaldehyde in 10%FCS-PBS at room temperature for 10 minutes and quenced with 125mM glycine and frozen until further use in liquid N2

extract_protocol:
Capture Hi-C libraries were prepared as described previously (van der Werken et al. 2012), i.e. crosslinking, cell lysis, DpnII digestion, ligation and de-crosslinking. Re-ligated products were then sheared using a Covaris sonicator (Duty cycle: 10%, Intensity:5, Cycles per Burst: 200, Time: 6 cycles of 60 sec each, Set Mode: Frequency sweeping, Temperature: 4° to 7°C).
Adaptors were added to the sheared DNA and amplified according to Agilent instructions for Illumina sequencing. The library was hybridized to the custom-designed sure-select beads and indexed for sequencing (75 or 100bp paired-end) following Agilent instructions.

value: limb bud

tag: developmental stage

value: intraTAD2-1xBorCTCF hom

tag: embryo generation

value: tetraploid aggregation


title: intraTAD2_2xBorCTCF-E105-LB-Shh-cHiC 1

value: intraTAD2-2xBorCTCF hom


title: multiome GEX, mixed glial differentiation, ROSMAP Line 6


title: intraTAD2_i4CTCF-E105-LB-Shh-cHiC

value: intraTAD2-i4CTCF hom

value: mating


title: multiome GEX, mixed glial differentiation, ROSMAP Line 7


title: intraTAD3-E105-LB-Shh-cHiC 2

value: intraTAD3 hom


title: WGBS STB_WGBS_SCNT_rep2

description:
STB_WGBS_SCNT_rep2
SCNT

value: placenta

value: syncytial trophoblast cells

value: day 74

value: SCNT


title: multiome GEX, mixed glial differentiation, ROSMAP Line 5

value: mixed glial differentiation

value: nuclei


title: WGBS Placenta_WGBS_SCNT_rep2

description:
Placenta_WGBS_SCNT_rep2
SCNT

value: placenta cell


title: WGBS Placenta_WGBS_SCNT_rep3

description:
Placenta_WGBS_SCNT_rep3
SCNT


title: multiome GEX, mixed glial differentiation, ROSMAP Line 4


title: intraTAD2-E105-LB-Shh-cHiC 1

value: IntraTAD2 hom


title: multiome GEX, mixed glial differentiation, ROSMAP Line 3


title: GF_S4, larynx, scRNAseq

first: Zijian

last: Ni

address: 425 Henry Mall

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files were aligned and quantified using cellranger-3.1.0 under default parameters.
Assembly: GRCm38
Supplementary files format and content: tar.gz containing all 10x Cell Ranger pipeline output files, except BAM files

source_name: larynx

extract_protocol:
Mouse larynges were collected from ConvR and GF mice and minced into 0.5 mm small pieces on a sterile petri dish under a dissection scope, then digested in a 1 ml modified dissociation solution for 40 min in a cold room (4 °C). Specifically, 1 ml of modified dissociation solution contained 5 mM CaCl¬2, 90 µl Accutase (Stem Cell Technologies, Cambridge, MA), 90 µl Accumax (Stem Cell Technologies, Cambridge, MA), 10 mg/ml Bacillus lichenformis protease (MilliporeSigma, Burlington, MA), and 125 U/ml DNase I (MilliporeSigma, Burlington, MA) dissolved in sterile calcium/magnesium-free PBS. Samples were gently triturated every 5 min using a wide-bore pipette tip during dissociation. Dissociation was performed for each larynx separately. Single-cell suspensions from three larynges per mouse group were pooled together as one sample. Pooled suspensions were added to 5 ml Ca/Mg-free PBS supplemented with 10% FBS, filtered with a 40 µm cell strainer (MilliporeSigma, Burlington, MA), then centrifuged at 300 g, for 10 min, at 4°C.  Cell pellet was resuspended in 30 µl ACK lysing buffer (Lonza, Bend, OR) briefly to remove erythrocytes, following manufacture’s instruction. ACK treated single cells were resuspended in 500 µl of Ca/Mg-free PBS supplemented with 2% FBS. Libraries were prepared according to Chromium Single Cell 3’ Reagent Kit v3.1.
single cell suspensions were transported on ice to the University of Wisconsin-Madison Biotechnology Center, where cell concentration and viability were quantified on the Countess II (Thermo Fisher Scientific, Waltham, MA) using 0.4% Trypan Blue (Invitrogen, Carlsbad, CA). Six thousand cells were added to each channel with an average recovery rate of over 4,000 cells. Cells were then partitioned into Gel Beads in Emulsion in the GemCode instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification, shearing and 5′ adaptor and sample index attachment. Libraries were quantified using the Qubit High Sensitivity DNA Kit (Thermo Fisher Scientific, Waltham, MA), uniquely indexed, pooled, balanced for the number of estimated reads per cell with a MiSeq (Illumina, San Diego, CA) sequencing run, and subsequently sequenced on a NovaSeq SP flowcell (Illumina, San Diego, CA using a 150 x 150 bp sequencing reaction targeting > 60,000 reads/cell, yielding a calculated depth of over 0.1 million reads per cell for both mouse groups. MiSeq balancing run was quality controlled using calculations based on UMI-tools101.

value: larynx

tag: age

value: 8-10 week

value: multiple

value: wildtype

value: GF


title: WGBS Placenta_WGBS_ICSI_rep2

description:
Placenta_WGBS_ICSI_rep2
ICSI

value: wild type

value: ICSI


title: WGBS Placenta_WGBS_SCNT_rep1

description:
Placenta_WGBS_SCNT_rep1
SCNT


title: multiome GEX, mixed glial differentiation, ROSMAP Line 2


title: ConvR_S2, larynx, scRNAseq

description: 10x Genomics

value: ConvR


title: GF_S3, larynx, scRNAseq

description: 10x Genomics


title: multiome GEX, mixed glial differentiation, ROSMAP Line 1


title: mixed glial differentiation, iPSC, 50days, rep2

value: cells


title: 9 day treatment with CNTF at 10ug/mL [RNA]

data_processing:
10xGenomics Multiomics libraries were processed using CellRanger ARC (v4.0.5)
Assembly: mm10
Supplementary files format and content: processed files include 10X genomics h5 gene expression file, fragment file (CellRanger outputs)

source_name: mouse stem cell-derived astrocytes

extract_protocol:
Trypsinization with TrypLE, nuclei extraction with EZ lysis
snRNAseq: Dual Index Illumina libraries were prepared following 10xGenomics Multiome instructions; snATACseq: Single Index Illumina libraries were prepared following 10xGenomics Multiome instructions

treatment_protocol: BMP4/FGF1 or CNTF (10ug/mL for all) treatment for 5,7,9 days

value: CNTF at 10ug/mL


title: mixed glial differentiation, iPSC, 50days, rep1


title: mixed glial differentiation, iPSC, 30days, rep2


title: WGBS IVC_WGBS_epiblast_ICSI_rep1

description:
IVC_WGBS_epiblast_ICSI_rep1
ICSI

value: in vitro cultured embryos

value: post-implanted

value: embryo


title: ConvR_S1, larynx, scRNAseq

description: 10x Genomics


title: hrde-2(qe20), replicate 2

city: Los Angeles

first: Carolyn

middle: Marie

last: Phillips

state: CA

address: 1050 Childs Way, RRI 201

department: Biological Sciences

institute: University of Southern California

data_processing:
mRNA libraries sequenced on the Illumina NextSeq2000 100-cycle (SE 75-bp reads) platform.
Adapter sequences were trimmed using Trimmomatic (version 0.39)
Reads were mapped to the C. elegans genome, WS258, using HISAT2 (version 2.2.1)
Mapped reads for genomic features were counted using featureCounts which is part of the Subread package (version 2.0.1)
Assembly: WS258
Supplementary files format and content: Processed data files are tab-delimited text files including total reads mapping to each gene generated by featureCounts.

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: 50,000 synchronized adult animals (~68 h at 20 °C after L1 arrest) were collected, in biological triplicates.

extract_protocol:
Worms were resuspended in 1 ml Trizol reagent and freeze-thawed on dry ice followed by vortexing. RNA isolation was performed by chloroform extraction and isopropanol precipitation.
RNA samples were normalized to 7.5μg per 10μL, followed by polyA selection using the Dynabead mRNA Purification Kit. 100ng of polyA selected mRNA samples were treated using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manual, using NEBNext multiplex oligos for Illumina.

value: Whole worm

value: FD53 - hrde-2/enri-3(qe20) V

tag: Stage

value: 1-day-old adult

tag: temperature

tag: fraction

value: Whole worm lysate


title: mixed glial differentiation, iPSC, 30days, rep1

tag: tissue

value: mixed glial differentiation


title: 7 day treatment with CNTF at 10ug/mL [RNA]


title: hrde-1(tm1200) , replicate 3

value: USC661 -hrde-1(tm1200) III


title: hrde-2(qe20), replicate 3


title: hrde-1(tm1200), replicate 1


title: 7 day treatment with BMP4/FGF1 at 10ug/mL [RNA]

value: BMP4/FGF1 at 10ug/mL


title: wild-type, replicate 3

value: N2 - wild-type


title: 9 day treatment with BMP4/FGF1 at 10ug/mL [RNA]


title: hrde-2(qe20), replicate 1


title: 5 day treatment with BMP4/FGF1 at 10ug/mL [RNA]


title: WGBS Placenta_WGBS_ICSI_rep1

description:
Placenta_WGBS_ICSI_rep1
ICSI

value: placenta

value: placenta cell

tag: genotype


title: Subject_6 Oligodendrocyte Precursor Cells RNA-seq

city: Bronx

first: Stella

last: Dracheva

state: New York

address: James J. Peters VA Medical Center,130 W Kingsbridge Rd

department: Dept. of Psychiatry

institute: Icahn School of Medicine at Mount Sinai

data_processing:
RNA-seq FASTQ files were trimmed to remove sequencing adapters and low-quality sequences using Scythe (github.com/vsbuffalo/scythe) and Sickle (github.com/najoshi/sickle) software tools. The first 3 bp of Read 2 were removed with seqtk (github.com/lh3/seqtk), according to the instructions for the SMARTer® Stranded Total RNA-Seq v2 Kit.
Trimmed reads were then mapped to the hg38 genome and annotated transcriptome GTF_ENSEMBL_v92 with STAR (github.com/alexdobin/STAR).
Read counts per gene were calculated using the featureCounts command in the “subread” software tool (subread.sourceforge.net). Only the reads that mapped to exons were included.
Differentially expressed genes were then called with the R package DESeq2 (Love, Huber, & Anders, 2014). The genes with low read counts were excluded with the “independent filtering” option during the DESeq2 analysis. Differentially expressed (DE) genes were defined using the settings: Fold Change > 2, FDR < 0.05.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include raw counts values for each sample.

molecule: nuclear RNA

source_name: dorsolateral prefrontal cortex

extract_protocol:
A novel method to isolate OPC and MO nuclei by FANS from frozen postmortem brain tissue was used. The protocol includes the following steps: (1) tissue specimens are homogenized at 4C in 4 ml of lysis buffer with a glass Douncer, (2) the homogenates are underlaid with a 4.5 ml layer of high sucrose buffer, and centrifuged at 24,000 rpm for 1 hour, (3) nuclear pellets are resuspended in 300 ul of blocking buffer and incubated with primary antibodies for 1.5 hours while rotating at 4C, (4) another centrifugation step for 30 min through a layer of high sucrose buffer is performed, (5) nuclear pellets are resuspended in blocking buffer and incubated with secondary antibodies for 1 hour, (6) after diluting the samples 5x times, a DNA dye (DAPI) is added, and the samples are separated by FANS on a flow cytometer. The following reagents, parameters and modifications to the basic protocol were employed. Primary antibodies were against the targets: NeuN (also known as RBFOX3) – a well-established marker of neuronal nuclei, SOX10 – a marker of oligodendroglial lineage, and SOX6 – a marker of OPCs. For anti-SOX10 antibodies (goat polyclonal, R&D Systems, AF2864), custom-made direct conjugates with the AF647 fluorophore were prepared and used at 1:150 dilution. For anti-NeuN antibodies, commercially available direct conjugates with the phycoerythrin (PE) fluorophore were used (mouse monoclonal anti-NeuN-PE, Millipore, FCMAB317PE, at 1:1000 dilution). For anti-SOX6 antibodies [guinea pig polyclonal antibodies, 1:1000 dilution (Stolt et al., 2006)], anti-guinea pig AF488-conjugated secondary antibodies (Jackson ImmunoResearch, 706-546-148) were used at a 1:250 dilution during the second incubation step. The use of the flow cytometer instrument BD Influx with four lasers (355nm, 488nm, 561nm and 640nm) allowed for separation between sorted populations with no need to perform compensation. The details of the gating steps in the flow cytometry protocol are provided in the Results section (see also Fig. 1). In the experiments aimed at obtaining OPC and MO nuclei for RNA isolation, RNase inhibitors were added to all buffers during the nuclei preparation protocol (Recombinant RNase Inhibitors, Takara; 1:40 dilution).
For RNA-seq library construction, Pico Input Mammalian SMARTer® Stranded Total RNA-Seq Kit v2 (Takara) was used, with 10 ng RNA as input material and 12 cycles of PCR amplification. The SMARTer® Total RNA-Seq protocol includes a ribosomal cDNA depletion step. Libraries were sequenced on a NovaSeq S4 instrument (Illumina) using the paired-end 100-cycle (PE100) protocol to the average depth of ~50 million reads per sample.

value: dorsolateral prefrontal cortex

value: Oligodendrocyte Precursor Cells

tag: donor id

tag: disease

value: control

tag: Sex

value: Male


title: Subject_7 Mature Oligodendrocytes RNA-seq

tag: cell type

value: Mature Oligodendrocytes

value: Female


title: Subject_7 Oligodendrocyte Precursor Cells RNA-seq


title: wild-type, replicate 2

tag: strain


title: 9 day treatment with CNTF at 10ug/mL [ATAC]

tag: cell line

tag: treatment

value: CNTF at 10ug/mL


title: Subject_6 Mature Oligodendrocytes RNA-seq


title: Subject_3 Oligodendrocyte Precursor Cells RNA-seq


title: wild-type, replicate 1

value: Whole worm


title: 7 day treatment with CNTF at 10ug/mL [ATAC]


title: hrde-2(qe20) - H3K9me3, replicate 3

description: tagmented DNA

data_processing:
CUT&Tag libraries were sequenced on the Illumina NextSeq2000 100-cycle (PE 50-bp reads) platform.
Reads were mapped to the C. elegans genome, WS258, using bowtie2 (version 2.5.0)   (options: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700 -p 8)
Mapped reads for genomic features were counted using featureCounts which is part of the Subread package (version 2.0.1)
Bedtools (version 2.30.0) was used to generate the density plots.
SEACR (version 1.3) was used to call peaks.
DiffBind (version 3.17) was used for differential expression analysis.
Assembly: WS258
Supplementary files format and content: Processed data files are tab-delimited text files including total reads mapping to each gene generated by FeatureCounts.
Library strategy: CUT&Tag

source_name: whole worm

growth_protocol: 50,000 synchronized adult animals (∼68 h at 20°C after L1) were collected, in biological triplicates.

extract_protocol:
Worms were washed off plates and lightly crosslinked in 0.1% formaldehyde (ThermoFisher 28908) for 2min, then quenched in a 1 M Tris (pH 7.5) wash. Next, worms were washed in M9 media and pre-chilled Nuclei Purification Buffer+ (50 mM HEPES pH 7.5, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.1% Tween-20, 0.5 mM PMSF, 0.2 mM DTT, 0.5 mM spermidine, 0.25 mM spermine, cOmplete protease inhibitor cocktail (Millipore Sigma 11873580001)). Worms were resuspended in 7 ml pre-chilled Nuclei Purification Buffer+ and dounced on ice in a Wheaton dura-grind stainless steel dounce tissue grinder (VWR 62400-675) for 12 strokes. After every 5 strokes, the samples were incubated on ice for 5 min. After grinding, samples were vortexed for 30 s then incubated on ice for 5 min to release the germline nuclei twice. The nuclei were passed through six 40 μm cell strainers (Fisherbrand 22-363-547) then passed through four 20 μm cell strainers (Pluriselect NC1004201) to remove worm debris. Isolated nuclei were pelleted at 4100 rpm at 4°C for 4 min and resuspended in Nuclei Purification Buffer+, transferred to a nonstick 2 ml tube (Ambion AM12475) and an aliquot was DAPI-stained and counted to calculate the number of nuclei extracted using Hausser Scientific hemacytometer (VWR 15170-263). The remainder of the nuclei were pelleted, the supernatant was removed, and the nuclei were resuspended in NE1 buffer (1 ml 1M HEPES-KOH pH 7.9, 500 μL 1M KCl, 25 μL 1 M spermidine, 500 µL 10% Triton X-100, and 10 ml glycerol in 38 ml dH2O, 1 Roche Complete Protease Inhibitor EDTA-Free (Millipore Sigma 11873580001)), followed by slow freezing and storage at −80°C.
CUT&Tag-seq was performed following the protocol (Kaya-Okur et al. 2019). 50,000 isolated C. elegans germline nuclei were thawed at 37°C and resuspended in 50 ml NE1 buffer, ConA beads were washed in binding buffer (200 μL 1M HEPES pH 7.9, 100 μL 1M KCl, 10 μL 1M CaCl2 and 10 μL 1M MnCl2, in 10 mL final volume of dH2O). 10ul ConA beads were added into 50,000 nuclei for each sample. anti-H3K27me3 antibody (Cell Signaling 9733T) was used at 1:50 for positive control, no primary antibody was used for negative control. anti-H3K9me3 antibody (Abcam ab8898) were used at 1:100 for the experiment. Samples were incubated at 4°C overnight. Anti-Rabbit IgG (Antibodies-online ABIN101961) antibody was added 1:100 to samples as the secondary antibody and incubated at room temperature for 30 mins. 2ul pA-Tn5 (EpiCypher 15-1017) was added to each sample and tagmentation was performed. DNA was isolated using Phenol:Chloroform:Isoamyl Alcohol (ThermoFisher 15593031) and chloroform. After PCR amplification using NEBNext High-Fidelity 2 × PCR Master Mix (VWR 102500-096) and post-PCR cleanup using SPRI beads (Beckman Coulter A63880).

value: whole worm

tag: antibody

value: H3K9me3 (Abcam ab8898)

value: FD53 - hrde-2/enri-3(qe20) V

value: Purified germline nuclei


title: Subject_3 Mature Oligodendrocytes RNA-seq


title: 5 day treatment with CNTF at 10ug/mL [ATAC]


title: hrde-2(qe20) - H3K9me3, replicate 2

description: tagmented DNA

value: 1-day-old adult


title: 9 day treatment with BMP4/FGF1 at 10ug/mL [ATAC]

value: BMP4/FGF1 at 10ug/mL


title: 5 day treatment with CNTF at 10ug/mL [RNA]


title: Subject_25 Mature Oligodendrocytes RNA-seq


title: 7 day treatment with BMP4/FGF1 at 10ug/mL [ATAC]


title: hrde-1(tm1200), replicate 2

value: USC661 -hrde-1(tm1200) III

value: Whole worm lysate


title: hrde-2(qe20) - H3K9me3, replicate 1

description: tagmented DNA


title: hrde-2(qe20) - IgG

description: tagmented DNA

value: IgG (Antibodies-online ABIN101961)


title: hrde-1(tm1200) - H3K9me3, replicate 2

description: tagmented DNA


title: 5 day treatment with BMP4/FGF1 at 10ug/mL [ATAC]


title: kidney, cisplatin+CBLB502, 72h, rep2

city: Beijing

first: Changhui

last: Ge

email: chge502@163.com, chge88@sina.com

address: 27 Taiping Rd., Haidian Dist.

department: Department of Experimental Hematology and Biochemistry

institute: Beijing institute of Radiation Medicine

description: mouse was treated with 20mg/kg Cisplatin and 0.2mg/kg CBLB502, then collect kidney at 72h

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as  follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Supplementary files format and content: tab-delimited text files include FPKM values

source_name: kidney

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

value: 20mg/kg Cisplatin + 0.2mg/kg CBLB502 i.p.


title: kidney, cisplatin+CBLB502, 72h, rep3


title: hrde-1(tm1200) - H3K9me3, replicate 1

description: tagmented DNA


title: kidney, cisplatin+CBLB502, 72h, rep1


title: Subject_23 Oligodendrocyte Precursor Cells RNA-seq

value: dorsolateral prefrontal cortex

value: Oligodendrocyte Precursor Cells

value: control


title: Subject_22 Oligodendrocyte Precursor Cells RNA-seq

value: Female


title: Subject_23 Mature Oligodendrocytes RNA-seq

value: Mature Oligodendrocytes

value: Male


title: Subject_25 Oligodendrocyte Precursor Cells RNA-seq


title: Subject_22 Mature Oligodendrocytes RNA-seq


title: liver, cisplatin+CBLB502, 72h, rep3

description: mouse was treated with 20mg/kg Cisplatin and 0.2mg/kg CBLB502, then collect liver at 72h

source_name: Liver

value: Liver


title: hrde-1(tm1200) - IgG

description: tagmented DNA

value: whole worm


title: wild-type - H3K9me3, replicate 3

description: tagmented DNA

value: H3K9me3 (Abcam ab8898)

value: N2 - wild-type


title: wild-type - IgG

description: tagmented DNA

value: 1-day-old adult

value: Purified germline nuclei


title: liver, cisplatin+CBLB502, 72h, rep2


title: Subject_21 Oligodendrocyte Precursor Cells RNA-seq


title: hrde-1(tm1200) - H3K9me3, replicate 3

description: tagmented DNA

value: USC661 -hrde-1(tm1200) III


title: liver, cisplatin+CBLB502, 72h, rep1


title: Subject_24 Oligodendrocyte Precursor Cells RNA-seq


title: Subject_21 Mature Oligodendrocytes RNA-seq


title: kidney, cisplatin, 72h, rep3

description: mouse was treated with 20mg/kg Cisplatin, then collect kidney at 72h

value: 20mg/kg Cisplatin i.p.


title: wild-type - H3K9me3, replicate 2

description: tagmented DNA


title: Subject_20 Oligodendrocyte Precursor Cells RNA-seq


title: liver, cisplatin, 72h, rep3

description: mouse was treated with 20mg/kg Cisplatin, then collect liver at 72h


title: kidney, cisplatin, 72h, rep2


title: Subject_24 Mature Oligodendrocytes RNA-seq


title: Subject_20 Mature Oligodendrocytes RNA-seq


title: WT pMSP3535-PnisA-6his-ftsH(H456Y) 3

city: Singapore

first: Zeus

middle: Jaren

last: Nair

address: 60 Nanyang Dr

country: Singapore

institute: Singapore Centre for Environmental Life Sciences Engineering

description: rRNA depleted from total RNA using Ribo-Zero™ Magnetic Kits (Lucigen, USA) prior to cDNA conversion

data_processing:
Illumina Casava software used for basecalling.
Demultiplexed sequencing reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to respective bacterial genome using BWA (version 0.5.9) with default parameters.
Reads were counted with predicted open reading frames to each reference genome using HTSeq and subjected to differential analysis using EdgeR
Assembly: NC_017316.1
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample

organism: Enterococcus faecalis OG1RF

growth_protocol: WT pMSP3535-PnisA-6his-ftsH(H456Y) and WT pMSP3535-PnisA-6his-ftsH were grown to mid-log phase and expression induced with nisin at 125 ng/mL.

extract_protocol:
Cultures were treated with RNA protect followed by lysozyme and subjected to RNA extraction in Trizol.  Dnase treatment was performed and remaining RNA was depleted of ribosomal RNA before subjected to first and second strand synthesis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Grown to mid-log, induced 16-18 hr at 125 ng/mL nisin


title: Subject_2 Oligodendrocyte Precursor Cells RNA-seq


title: Subject_2 Mature Oligodendrocytes RNA-seq


title: WT pMSP3535-PnisA-6his-ftsH(H456Y) 2


title: WT pMSP3535-PnisA-6his-ftsH(H456Y) 1


title: wild-type - H3K9me3, replicate 1

description: tagmented DNA


title: liver, cisplatin, 72h, rep2


title: liver, cisplatin, 72h, rep1


title: kidney, CBLB502, 72h, rep2

description: mouse was treated with 0.2mg/kg CBLB502, then collect kidney at 72h

value: kidney

value: 0.2mg/kg CBLB502 i.p.


title: WT pMSP3535-PnisA-6his-ftsH 3

value: Wildtype, pMSP3535-PnisA-6his-ftsH


title: Subject_19 Oligodendrocyte Precursor Cells RNA-seq

value: dorsolateral prefrontal cortex

value: Oligodendrocyte Precursor Cells


title: kidney, CBLB502, 72h, rep1


title: kidney, cisplatin, 72h, rep1


title: WGBS Placenta_WGBS_TR_rep1

description:
Placenta_WGBS_TR_rep1
TR

organism: Macaca mulatta

value: placenta

value: placenta cell

value: wild type

value: TR


title: WT pMSP3535-PnisA-6his-ftsH 2


title: Subject_17 Oligodendrocyte Precursor Cells RNA-seq

value: control

value: Male


title: liver, CBLB502, 72h, rep3

description: mouse was treated with 0.2mg/kg CBLB502, then collect liver at 72h

value: Liver


title: WGBS Placenta_WGBS_ICSI_rep3

description:
Placenta_WGBS_ICSI_rep3
ICSI

value: ICSI


title: liver, CBLB502, 72h, rep2


title: S48h_2

city: Baoding

first: yajing

last: Liu

address: Le Kai Nan StreetBaoding

department: College of Horticulture

institute: Hebei  Agricultural University

data_processing:
Quality of the RNA-seq reads were evaluated using the FastQC software.
Raw data (raw reads) in the fastq format were processed and cleaned (clean reads). The clean data were mapped to the eggplant reference genome database (http://eggplant-hq.cn/Eggplant/home/index).
HTSeq v0.6.1 was used to count the read numbers mapped to each gene, and the FPKM (Fragments Per Kilobase of transcript sequence per Million base pairs sequenced) of each gene was calculated based on the length of the gene and read counts mapped to this gene35.
Assembly: Solanum melongena reference genome was obtained from http://eggplant-hq.cn/Eggplant/home/index
Supplementary files format and content: tab-delimited text files with raw gene counts for individual samples

organism: Solanum virginianum

growth_protocol: All seeds were sown in pots in a greenhouse with a 16:8 h (L:D) photoperiod, 26–28°C day temperature and 15°C night temperature and 90% humidity.All samples were collected one week after transplanting.

extract_protocol:
RNA extraction was conducted using a total RNA extraction kit LS1040 (Promega, Shanghai) and according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: three biological replicates for thrip-resistant and -susceptible eggplants after feeding at 0 h, 4 h, 8 h, 12 h, 24 h and 48 h

value: leaf

value: thrip-susceptible

value: thrips feeding

tag: timepoint


title: Subject_19 Mature Oligodendrocytes RNA-seq

value: Mature Oligodendrocytes

value: Female


title: Subject_18 Mature Oligodendrocytes RNA-seq


title: Subject_18 Oligodendrocyte Precursor Cells RNA-seq


title: WT pMSP3535-PnisA-6his-ftsH 1

value: Grown to mid-log, induced 16-18 hr at 125 ng/mL nisin


title: kidney, CBLB502, 72h, rep3

value: kidney

value: 0.2mg/kg CBLB502 i.p.


title: Subject_17 Mature Oligodendrocytes RNA-seq

value: dorsolateral prefrontal cortex


title: liver, CBLB502, 72h, rep1


title: Subject_15 Oligodendrocyte Precursor Cells RNA-seq

value: Oligodendrocyte Precursor Cells


title: Subject_13 Oligodendrocyte Precursor Cells RNA-seq


title: kidney, control, rep2

description: kidney from normal mouse

value: no treatment


title: S48h_1


title: S24h_3


title: S24h_1


title: kidney, control, rep1

description: kidney from normal mouse


title: liver, control, rep3

description: Liver from normal mouse


title: Subject_13 Mature Oligodendrocytes RNA-seq


title: S12h_3


title: S48h_3


title: liver, control, rep2

description: Liver from normal mouse


title: S24h_2


title: Subject_12 Oligodendrocyte Precursor Cells RNA-seq


title: Subject_12 Mature Oligodendrocytes RNA-seq


title: Subject_16 Oligodendrocyte Precursor Cells RNA-seq


title: Subject_11 Oligodendrocyte Precursor Cells RNA-seq


title: S12h_2


title: Trim71_3

city: Baltimore

first: Angelika

last: Doetzlhofer

state: MD

address: 855 North Wolfe St

department: Neuroscience

institute: Johns Hopkins University School of Medicine

data_processing:
psuedoalignment and quantification using kallisto
QC and differential testing using Sleuth
Assembly: Ensembl v96 reference transcriptome
Supplementary files format and content: h5 abundance files

source_name: cochlear organoid culture

growth_protocol: The expansion medium was prepared with DMEM/F12 , N2 supplement , B-27 supplement, EGF, FGF2, CHIR99021, 616452, VPA, and penicillin.

extract_protocol:
To extract RNA for RNA-seq, organoids were washed with PBS for one time and resuspened with Cell recovery solution to dissove matrigel. Then the cells were pelleted and used for RNA extraction by following the miRNeasy Micro Kit(Qiagen, no. 217084).
These samples were processed using Illumina's TruSeq stranded Total RNA kit, per manufacturer's recommendations, using the UDI indexes.  The samples were sequenced on the Illumina NovaSeq 6000, paired end, 2x50 bp reads

treatment_protocol: cells were infected with lentiviral constructs containing mCHerry and either HA (control) or human Trim71 transcript

value: cochlear organoid culture

value: Lentiviral Trim71 overexpression


title: Subject_11 Mature Oligodendrocytes RNA-seq

value: control


title: S12h_1


title: Trim71_2


title: Subject_10 Oligodendrocyte Precursor Cells RNA-seq


title: S8h_3


title: S8h_2


title: Subject_14 Oligodendrocyte Precursor Cells RNA-seq

value: Male


title: Trim71_1


title: kidney, control, rep3

description: kidney from normal mouse


title: S8h_1


title: S4h_3


title: Subject_10 Mature Oligodendrocytes RNA-seq


title: Subject_1 Mature Oligodendrocytes RNA-seq


title: 3HA_Control_1

value: Lentiviral HA overexpression


title: Subject_9 H3K27ac ChIP-seq Oligodendrocyte Precursor Cells

data_processing:
Raw sequencing data were pre-processed to remove adapters and low-quality sequences with the HTStream tool.
Reads were mapped to the human hg38 genome build with BWA-MEM2 and filtered to remove multi-mapping reads and low-quality alignments using Samtools.
Reads mapping to ENCODE-blacklisted genomic regions were excluded using BEDTools.
H3K27ac-enriched peaks were detected using MACS2, including input controls for each cell type and age group. Consensus peak sets were then constructed for each cell type and age group.
Differential peaks between infant and adult subjects in OPCs or MOs separately, and between OPCs and MOs in adult subjects, were identified using DESeq2.
Assembly: hg38
Supplementary files format and content: bigWig files (bw), H3K27ac signal normalized to 1 million reads. (Except for input samples)
Supplementary files format and content: spreadsheet table files (xlsx), with read counts within consenusus H3K27ac peaks. (Separate files for adult-infant and OPC-MO comparisons)

extract_protocol:
A novel method to isolate OPC and MO nuclei by FANS from frozen postmortem brain tissue was used. The protocol includes the following steps: (1) tissue specimens are homogenized at 4C in 4 ml of lysis buffer with a glass Douncer, (2) the homogenates are underlaid with a 4.5 ml layer of high sucrose buffer, and centrifuged at 24,000 rpm for 1 hour, (3) nuclear pellets are resuspended in 300 ul of blocking buffer and incubated with primary antibodies for 1.5 hours while rotating at 4C, (4) another centrifugation step for 30 min through a layer of high sucrose buffer is performed, (5) nuclear pellets are resuspended in blocking buffer and incubated with secondary antibodies for 1 hour, (6) after diluting the samples 5x times, a DNA dye (DAPI) is added, and the samples are separated by FANS on a flow cytometer. The following reagents, parameters and modifications to the basic protocol were employed. Primary antibodies were against the targets: NeuN (also known as RBFOX3) – a well-established marker of neuronal nuclei, SOX10 – a marker of oligodendroglial lineage, and SOX6 – a marker of OPCs. For anti-SOX10 antibodies (goat polyclonal, R&D Systems, AF2864), custom-made direct conjugates with the AF647 fluorophore were prepared and used at 1:150 dilution. For anti-NeuN antibodies, commercially available direct conjugates with the phycoerythrin (PE) fluorophore were used (mouse monoclonal anti-NeuN-PE, Millipore, FCMAB317PE, at 1:1000 dilution). For anti-SOX6 antibodies [guinea pig polyclonal antibodies, 1:1000 dilution (Stolt et al., 2006)], anti-guinea pig AF488-conjugated secondary antibodies (Jackson ImmunoResearch, 706-546-148) were used at a 1:250 dilution during the second incubation step. The use of the flow cytometer instrument BD Influx with four lasers (355nm, 488nm, 561nm and 640nm) allowed for separation between sorted populations with no need to perform compensation. The details of the gating steps in the flow cytometry protocol are provided in the Results section (see also Fig. 1). In the experiments aimed at obtaining nuclei for ChIP, protease inhibitors (benzamidine (Sigma) and PMSF (Thermofisher Scientific) at 1:1000 dilutions from 0.1 M stocks) were added to the lysis buffer.
We employed the native ChIP protocol (N-ChIP) in which chromatin fragmentation is performed using micrococcal nuclease (MNase) without crosslinking proteins to DNA (Sci Adv. 2018). We used anti-H3K27ac antibodies from Active Motif (Cat# 39133; rabbit polyclonal, 3 µg per sample). ChIP-Seq libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, Cat. # E7645). The resulting libraries were sequenced on a NovaSeq 6000 instrument (Illumina), using paired-end 100 cycles protocol.

tag: chip antibody

value: H3K27ac (Active Motif #39133)


title: S4h_1

value: leaf


title: S0h_3

value: thrip-susceptible


title: liver, control, rep1

description: Liver from normal mouse

value: Liver


title: Bone-bulkRNAseq-Sedentary-rep1

first: Ruici

last: Yang

address: 320 Yue Yang Road

institute: Center for Excellence in Molecular Cell Science, CAS

data_processing:
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 mouse genome using STAR (for RNA-seq).
For RNA-seq data, aligned reads with high quality were quantified by HTSeq.
For RNA-seq data, counts per million reads (CPM) were calculated.
For RNA-seq data, unique molecular identifiers (UMIs) were extracted from Read2. Raw gene counts were calculated by UMI number to get rmdup.count file.
Assembly: mm10
Supplementary files format and content: For RNA-seq data, we provided tab-delimited text files including raw count values for each sample.

source_name: bone

extract_protocol:
Bones of 13-week-old  exercised and sedentary mice after bone marrow was flushed were collected and ground with liquid nitrogen to extract the RNA.
RNA-seq libraries were constructed by a modified Smartseq2 method with UMI barcodes (Nature 533:487, 2016).

tag: cre line

value: Wild Type

tag: group

value: Sedentary


title: Subject_8 H3K27ac ChIP-seq Oligodendrocyte Precursor Cells


title: Subject_9 H3K27ac ChIP-seq Mature Oligodendrocytes

value: Mature Oligodendrocytes

value: Female


title: S4h_2

source_name: leaf

value: thrips feeding


title: Bone-bulkRNAseq-Sedentary-rep2

tag: age


title: Bone-bulkRNAseq-Exercise-rep2

value: Exercise


title: Subject_7 H3K27ac ChIP-seq Oligodendrocyte Precursor Cells

value: dorsolateral prefrontal cortex

value: Oligodendrocyte Precursor Cells


title: S0h_2


title: Subject_6 H3K27ac ChIP-seq Oligodendrocyte Precursor Cells


title: Bone-bulkRNAseq-Exercise-rep1


title: 3HA_Control_2

value: cochlear organoid culture


title: Subject_7 H3K27ac ChIP-seq Mature Oligodendrocytes


title: GF, larynx, scRNAseq

description: 10x Genomics

value: larynx

value: 8-10 week

value: multiple

value: wildtype

value: GF


title: Te15Neo7

city: Grand Rapids

first: Piroska

last: Szabó

state: MI

address: 333 Bostwick Ave NE

department: Department of Epigenetics

institute: Van Andel Insitute

data_processing:
Adaptor sequences and low-quality reads were trimmed using Trim Galore (v0.6.0; Martin, 2011). Trimmed reads were aligned to the mm10 reference genome using STAR (v2.7.8; Dobin et al., 2013) with --quantMode GeneCounts.
bigwig files were generated from bam files using deepTools "bamCoverage".
Assembly: mm10
Supplementary files format and content: normalized CPM in one txt file (exported from edgeR)
Supplementary files format and content: bigwig file of eahc sample
Supplementary files format and content: norm_forward.bw: stranded bigwig files (forward)
Supplementary files format and content: norm_reverse.bw: stranded bigwig files (reverse)

source_name: 15 dpc prospermatogonia

extract_protocol:
Total RNA was isolated using RNA-Bee reagent (Tel-Test) from FACS sorted 15.5 dpc male germ cells followed by DNase I treatment.
Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA RNA HyperPrep Kit (Kapa Biosystems, Wilmington, MA USA). Ribosomal RNA material was reduced using the QIAseq FastSelect -rRNA HMR Kit (Qiagen, Germantown, MD, USA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to IDT for Illumina TruSeq UD indexed adapters (Illumina Inc, San Diego, CA) and amplified with 8 cycles of PCR. Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.) and QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA). Individually indexed libraries were pooled and 50 bp, paired end sequencing was performed on an Illumina NovaSeq6000 sequencer to an average depth of 100M raw paired-reads per transcriptome. Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.

value: germ cells


title: Subject_8 H3K27ac ChIP-seq Mature Oligodendrocytes

value: control

value: Male

value: H3K27ac (Active Motif #39133)


title: R48h_3

value: leaf

value: thrip-resistant


title: 3HA_Control_3

value: Lentiviral HA overexpression


title: ConvR, larynx, scRNAseq

description: 10x Genomics

value: ConvR


title: R4h_1

value: thrips feeding


title: Subject_1 Oligodendrocyte Precursor Cells RNA-seq

value: dorsolateral prefrontal cortex

value: Female


title: R48h_1


title: Subject_6 H3K27ac ChIP-seq Mature Oligodendrocytes

value: Mature Oligodendrocytes


title: R48h_2


title: R24h_3


title: R24h_1


title: Te15Neo6


title: Te15MGC4


title: R12h_3


title: R24h_2


title: Subject_5 H3K27ac ChIP-seq Oligodendrocyte Precursor Cells

value: Oligodendrocyte Precursor Cells


title: S0h_1

value: thrip-susceptible


title: Subject_4 H3K27ac ChIP-seq Oligodendrocyte Precursor Cells


title: Subject_5 H3K27ac ChIP-seq Mature Oligodendrocytes


title: Te15MGC3


title: WT15MGC2

value: Wild type


title: Te15Neo5


title: R12h_2


title: WT15MGC1


title: Subject_4 H3K27ac ChIP-seq Mature Oligodendrocytes


title: subject_13 H3K27ac ChIP-seq Oligodendrocyte Precursor Cells


title: R12h_1


title: R8h_2


title: Subject_4 Oligodendrocyte Precursor Cells H3K27ac ChIP-seq Input

value: input


title: R8h_3


title: subject_12 H3K27ac ChIP-seq Oligodendrocyte Precursor Cells


title: subject_13 H3K27ac ChIP-seq Mature Oligodendrocytes


title: Neural stem cell line KN1

city: Takatsuki

first: Hisato

last: Kondoh

state: Osaka

address: 1-1 Murasaki-cho

country: Japan

institute: Biohistory Research Hall

data_processing:
To show that a significant fraction of cells simultaneously express genes representing different CNS regions, the reads per cell spreadsheet data (RPC.csv) were directly analyzed
To show that the cells in a cell line form an inseparable cell group in the UMAP projection of the data, data were processed in the following way. Transcript reads of ribosomal and mitochondrial proteins were omitted from the analysis because the cells were nearly homogeneous, and the reads of these transcripts were found to erroneously contribute to sub-clustering the cells. Then 4000 cells for each line were randomly selected, normalized, and scaled according to the standard procedure of Seurat (v. 4.3.0) (Satija et al., 2015).
Assembly: mm10
Supplementary files format and content: RPC.csv
Supplementary files format and content: normalized.csv
Supplementary files format and content: scaled.csv

growth_protocol: The basic culture medium: 50% DMEM/50% Neurobasal Medium, 0.004% BSA, with 2 mM L-glutamine, and 0.5´ N-2 and 0.5´ B-27 supplements. Additions for different culture conditions: Cell lines with prefix X, 10 ng/ml EGF, 10 ng/ml FGF2, and 10 µM XAV939; K, 10 ng/ml EGF and 10 ng/ml FGF2; C, 10 ng/ml EGF, 10 ng/ml FGF2, and 2 µM CHIR99021.

extract_protocol:
Cells were lysed in the BD Rhapsody cartridge and polyA RNAs were captured on the beads.
Single-cell RNA sequencing libraries were prepared for each NSC line using a BD Rhapsody WTA Amplification kit (633801) using the manufacturer-supplied protocol.

treatment_protocol: The NSC lines in a growing phase, were dissociated using Accutase, passed through a 20 µm cell strainer, suspended in 10x volumes of CellCover (Anacyte Laboratories), and stored at 4º C, up to 2 weeks, until cells were processed for the single-cell transcriptome library preparation.

value: Neural stem cell line

value: 129/Sv, EpiSC-derived


title: Neural stem cell line CN4


title: subject_11 H3K27ac ChIP-seq Mature Oligodendrocytes

value: control


title: R8h_1


title: subject_10 Mature Oligodendrocytes H3K27ac ChIP-seq Input


title: Neural stem cell line XN1


title: R4h_2


title: WT larval CNS, replicate 1, scATAC-seq

city: Lausanne

first: Maria Cristina

last: Gambetta

address: Genopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

description: 10x Genomics

data_processing:
The demultiplexing, read filtering and alignment, identification of transposase cut sites, detection of accessible chromatin peaks, cell calling and count matrix generation for peaks were made using the Cell Ranger ATAC software v1.2.0. Custom reference using FlyBase version FB2020_05, dmel_r6.36 (dm6) genome assembly was used.
Assembly: dm6
Supplementary files format and content: Filtered peak-barcode matrix in HDF5 (.h5) format
Supplementary files format and content: Fragments file, where each line represents a unique ATAC-seq fragment captured by the assay, in tab-separated (.tsv) format
Supplementary files format and content: Peaks file in BED (.bed) format
Supplementary files format and content: Per barcode QC, ATAC signal, and cell calling table, in comma-separated (.csv) format

organism: Drosophila melanogaster

source_name: central nervous system

growth_protocol: standard Drosophila culture at 25°C

extract_protocol:
20 wandering third instar larvae were dissected in ice-cold Schneider’s medium supplemented with 10% fetal bovine serum, washed in Rinaldini solution (0.36 mM NaH2PO4*H2O, 11.9 mM NaHCO3, 137 mM NaCl, 2.7 mM KCl, 5.6 mM glucose*H2O), dissociated in 0.5 µg/µl collagenase I (Sigma C2674) for 1 hour at room temperature, washed in Schneider’s medium, and dissociated into single cells by pipeting up and down several times with wide-bore tips. The cell suspension was passed through a 40 µm cell strainer, washed in PBS with 0.04% (w/v) BSA, and counted. Nuclei were extracted in 0.1x lysis buffer (1 mM Tris-HCl pH 7.4, 1 mM NaCl, 0.3 mM MgCl2, 0.01% Tween20, 0.01% NP-40, 0.001% digitonin, 0.1% BSA) for 5 minutes on ice, washed in cold wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween20, 1% BSA), resuspended in 1x nuclei buffer (provided by the manufacturer), counted, and diluted to 2500 nuclei/µl. 20000 nuclei were then loaded and processed according to the instructions of 10x Genomics Chromium single cell ATAC reagent kits solution v1.0 (CG000168 revB January 2019).
Library preparation was performed according to the manufacturer’s instructions. 10x Genomics Chromium single cell ATAC reagent kits solution v1.0 (CG000168 RevB January 2019) was used.

value: central nervous system

value: third instar larva

value: wildtype


title: SF1Rep3

city: Aurora

first: Matthew

last: Taliaferro

state: CO

address: 12801 E 17th Ave, RC1 South Room 10403D

department: Biology

institute: University of Colorado Anschutz Medical Campus

data_processing:
Reads were aligned to the dm6 transcriptome using STAR (BDGP6, Ensembl 88)
Alternative splicing was analyzed using rMATS
Genome_build: dm6, DBGP6, Ensembl 88
Supplementary_files_format_and_content: Tab separated plain text, kallisto transcript quantification measurements

source_name: S2 cells

growth_protocol: Copper-inducible genes encoding LS2 mutants were integrated into S2 cells, and integrated were selected using a hygromycin gene on the LS2-containing plasmid.

extract_protocol:
RNA was isolated using a Qiagen Rneasy Mini kit
polyA RNA was selected using OligodT, and standard Illumina sequencing libraries were constructed

treatment_protocol: Cells were treated with 500 micromolar copper sulfate for 53 hours to induce LS2 expression.

tag: ls2 mutant

value: S2 cells


title: SF1Rep2


title: Subject_10 H3K27ac ChIP-seq Mature Oligodendrocytes

value: H3K27ac (Active Motif #39133)


title: subject_12 H3K27ac ChIP-seq Mature Oligodendrocytes

value: Male


title: R4h_3

value: leaf

value: thrip-resistant

value: thrips feeding


title: WTRep3

value: Wildtype


title: subject_11 H3K27ac ChIP-seq Oligodendrocyte Precursor Cells

value: dorsolateral prefrontal cortex

value: Oligodendrocyte Precursor Cells

value: Female


title: RRM2Rep3


title: R0h_3


title: subject_10 Oligodendrocyte Precursor Cells H3K27ac ChIP-seq Input

value: input


title: P11_Astrocytoma

city: HONG KONG

first: Jiguang

last: WANG

address: clear water bay, HKUST

institute: HKUST

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0
Assembly: hg38
Supplementary files format and content: Seurat object with gene matrix

source_name: tumor

extract_protocol:
After the operation ice-cold Dulbecco's phosphate-buffered saline (DPBS, D8537, Sigma-Aldrich, St. Louis, MO) was used to wash GB tissues immediately. Briefly, the GB specimens were dissociated using type IV collagenase (17104019, GIBCO, Gaithersburg, MD) (10 minutes at 37°C). The specimens were then washed with Dulbecco’s Modified Eagle’s Medium (DMEM, D5796, Sigma-Aldrich, St. Louis, MO) and centrifuged (4 minutes at 300 g with minimal braking). A 70 µm cell strainer were used to filter the specimens in DPBS. The filtered cell suspension was washed with red blood cell (RBC) lysis buffer (555899, BD Biosciences, Franklin Lakes, NJ) and with DPBS. The resulting cell pellet was then resuspended in 1 mL staining buffer (DPBS containing 5% fetal bovine serum, FBS; 0500, ScienCell, Carlsbad, CA) and washed one more time.Peripheral blood was collected into ethylenediaminetetraacetic acid anticoagulation coated tubes. The specimens were first centrifuged (5 minutes at 800 g with minimal braking) to remove plasma. Then, the specimens were transferred into SepMate PBMC isolation tubes containing Ficoll (86450, STEMCELL Technologies, Vancouver, Canada) and centrifuged (10 minutes at 1200 g with minimal braking). Pelleted cells were then washed with RBC lysis buffer. The blood cell pellet was resuspended in 1 mL staining buffer followed by washing to remove excessive stain. Single-cell specimens were prepared for CyTOF examination or single-cell RNA Sequencing.
The GB or peripheral blood cell suspension was loaded into Chromium microfluidic chips with 3’ (v3) chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ (v3) reagent kit (10X Genomics) according to the manufacturer’s recommendations. Sequencing was performed with Illumina (NovaSeq) according to the manufacturer’s recommendations (Illumina).

value: tumor

value: immune


title: WTRep1


title: WTRep2


title: R0h_2


title: Subject_10 H3K27ac ChIP-seq Oligodendrocyte Precursor Cells

value: control


title: R0h_1


title: Subject_4 Mature Oligodendrocytes H3K27ac ChIP-seq Input

value: Mature Oligodendrocytes


title: RRM2Rep2


title: FNV_SL_rep2

city: hong kong

first: Haoqing

last: Hu

address: No.21 Pokflam road, L412

institute: The University of Hong Kong

data_processing:
Raw reads in fastq format were aligned to the mm10 transcriptome using RSEM (Bo Li et al., 2011) and bowtie 2.0 (Langmead et al., 2012) (with options: rsem-calculate-expression --bowtie2 --bowtie2-sensitivity-level very_sensitive --no-bam-output --estimate-rspd --paired-end).
Gene level alignment results of samples were merged and annotated using glbase3 (Hutchins et al., 2014).
Read counts per genes were calculated using RSEM and normalized to GC content using EDAseq (Risso et al., 2011). GC-normalized read counts no less than 20 in at least two samples were kept, leading to a final read count table.
The table was used to inspect individual gene expression, generate correlation heatmaps, perform principal components analysis (PCA) and analyze differentially expressed genes (DEGs).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files. The first column is the ensemble gene ID(ensg). The second column contains the official gene names(name). The rest of the columns contain the normalized RNA expression gene counts.

organism: Mus

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, #15596018) following the user guide quantified using a Nanodrop One spectrophotometer (Thermo Scientific).
mRNA is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, a ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment. ffective concentration of library was determined by Q-PCR. Finally, the qualified libraries are fed into Illumina sequencers after pooling according to its effective concentration and expected data volume.

value: Embryonic stem cell

value: SOX17FNV_lentivirus transduced with endogenous SOX2 silienced

value: DOX


title: P10_Astrocytoma

description: 10x Genomics


title: P9_GB

description: 10x Genomics


title: NTC_SL_rep1

value: WT


title: P8_GB

description: 10x Genomics


title: GSlinkerRep2

value: H197-P233 replaced with GGS motifs

value: S2 cells


title: SOX2_SL_rep2

value: SOX2_lentivirus transduced with endogeouns SOX2 silienced


title: Epilepsy

description: 10x Genomics

source_name: epilepsy

value: epilepsy


title: Neural stem cell line XN4

value: Neural stem cell line

value: 129/Sv, EpiSC-derived


title: FNV_SL_rep1


title: SF1Rep1


title: SOX2_SL_rep1


title: SOX2_2i_rep2


title: NTC_SL_rep2


title: GFPRep1

value: No LS2, just GFP


title: NTC_2i_rep2


title: RRM2Rep1


title: FNV_2i_rep1


title: GSlinkerRep1


title: GSlinkerRep3


title: P11_PBMC

description: 10x Genomics

source_name: blood

value: blood


title: FNV_2i_rep2


title: SOX2_2i_rep1


title: GFPRep3


title: NTC_2i_rep1


title: P10_PBMC

description: 10x Genomics


title: d38Rep2


title: OVCAR3 Olaparib, Rep4

city: Innsbruck

first: Leonie

last: Madersbacher

address: Innrain 80/82

country: Austria

institute: Medical University of Innsbruck

data_processing:
Sequence reads were trimmed for adaptor and low quality sequences using BBDuk with parameters recommended by Lexogen (k=13 ktrim=r useshortkmers=t mink=5 qtrim=t trimq=10 minlength=20).
Trimmed sequence reads were mapped to GRCh38 (v38) using STAR aligner (version 2.7.9a).
Read count extraction was done using featureCounts (v2.0.0) with GENCODE annotation (v38).
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts of each sample

growth_protocol: UWB1.289 cells were maintained in 47.5% MEGM Bulletkit medium, 47.5% RPMI1640 and 3%FBS, OVCAR 3 cells in RPMI1640 with 20% FBS and 0.01mg/ml bovine insuline

extract_protocol:
RNA was harvested using the Rneasy Mini Kit (Qiagen). 500 ng of total RNA per sample were used for the library construction.
RNA libraries for RNA-Seq were prepared using the QuantSeq 3'-mRNA Kit (Lexogen) following the manufacturer's protocols.

treatment_protocol: UWB1.289 cells were treated for 96h with either 3.5µM Olaparib (in DMSO) or DMSO (vehicle control), OVCAR3 cells were treated for 96h with either 7.5µM Olaparib (in DMSO) or DMSO (vehicle control)

value: serous ovarian carcinoma cells

value: Olaparib


title: _-CsChrimson_10min2

city: Sai Kung

first: Yukinori

last: Hirano

address: Clear water bay

department: LIFS

country: Hong Kong

institute: The Hong Kong University of Science and Technology

data_processing:
The adaptors were trimmed via Trimommatic, followed by mapping to the Drosophila reference genome, dm6 from UCSC using STAR.
The reads with low mapping quality below 8 and the non-primary mapped reads were eliminated.
The filtered reads were analyzed with HTSeq-count to obtain numbers of the reads mapped on exons, which was further analyzed on R using DESeq2
Assembly: dm6
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: tab-delimited text files include statistical results and fold enrichment comparing to naive samples

source_name: mushroom body

growth_protocol: Flies were raised under a 12 h:12 h, light:dark cycle, at 25℃ and 60% humidity.

extract_protocol:
Heads were collected and homogenized in crosslinking buffer. The nuclei were dissolved in extraction buffer, sonicated to dissociate the individual nuclei, and precipitated with ANTI-FLAG M2 Affinity Gel. The precipitates were rinsed 4 times in extraction buffer, with 5 min nutation at 4℃ between washes, and subjected to ChIP analysis or RNA extraction for RNA-seq.
The library for nuclear RNA-seq was prepared by Oligo d(T)25 Magnetic Beads (New England Biolabs inc. Ipswich, MA, USA), and NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs inc. Ipswich, MA, USA), according to the manufacturer’s instructions.

treatment_protocol: Flies were subjected to optogenetic activation by expressing CsChrimson with red-light illumination.

value: mushroom body

value: 5-min optogenetic activation followed by 10-min rest


title: _-CsChrimson_10min3


title: GFPRep2


title: OVCAR3 Olaparib, Rep2


title: P6_GB

description: 10x Genomics

value: tumor

value: immune


title: P8_PBMC

description: 10x Genomics


title: Beta5Rep3


title: Beta5Rep2


title: P6_PBMC

description: 10x Genomics


title: OVCAR3 Olaparib, Rep1


title: d38Rep1


title: d38Rep3


title: OVCAR3 Olaparib, Rep3


title: Beta5Rep1


title: _-CsChrimson_10min1


title: P9_PBMC

description: 10x Genomics


title: _-CsChrimson_naive3

value: naive


title: MB477_Kdm4B_RNAi_naive3


title: _-CsChrimson_naive2


title: _-CsChrimson_naive1


title: OVCAR3 DMSO, Rep4

value: DMSO


title: OVCAR3 DMSO, Rep3


title: MB477_Kdm4B_RNAi_10min3


title: OVCAR3 DMSO, Rep2


title: MB477_Kdm4B_RNAi_10min2


title: MB477_Kdm4B_RNAi_10min1


title: MB477_10min3


title: UWB1.289 DMSO, Rep4


title: OVCAR3 DMSO, Rep1


title: UWB1.289 Olaparib, Rep3


title: 24_5W-NH4NO3-5_rep2

city: Kibichuo

first: Kenji

last: Henmi

state: Okayama

address: 7549-1 Yoshikawa

institute: Okayama Prefectural Technology Center for Agriculture, Forestry and Fisheries, Research Institute for Biological Sciences

hyb_protocol: Each 12.5 µg of labelled aRNA was hybridized for 16 h to Affymetrix GeneChip Arabidopsis ATH1 Genome Array, containing 22,810 probe sets. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The raw data were analyzed with Affymetrix GeneChip Command Console (AGCC) Software and Affymetrix Expression Console. The normalization between chips was performed using GeneSpring software.

label: biotin

organism: Arabidopsis thaliana

source_name: leaf blades of NH4NO3-fed Col-0 plants 5 weeks after sowing

label_protocol: Biotinylated aRNA were prepared from 100 ng of total RNA by 3’ IVT Express kit (Affymetrix Inc.).

growth_protocol: Wild-type Arabidopsis (ecotype Columbia-0) plants were grown three plants in square plastic pots (6.5 x 6.5 x 5 cm) filled with 10 g of vermiculite at the bottom, 30 g of Kureha soil in the middle, and 5 g of vermiculite on the top layer. They were cultivated in an air-conditioned room for 16 h in the light period and 8 h in the dark at 22 °C.

extract_protocol: Total RNA extraction from leaves or aerial parts including meristem was performed using an RNeasy Plant Mini Kit (Qiagen Inc.).

treatment_protocol: From the first week to the fifth week after sowing, a 25 ml of 1 mM oxidized glutathione (GSSG), 2 mM reduced glutathione (GSH) and 3 mM NH3NO4 aqueous solution per pot were applied by subirrigation once a week. Plants grown by water were used as control. The aerial parts including the shoot apical were harvested 3 weeks after sowing, and the second and third leaf blades from the top of the fully expanded leaves were harvested 4 and 5 weeks after sowing.

tag: ecotype

value: Columbia

tag: developmental stage

value: 5 weeks after sowing


title: UWB1.289 Olaparib, Rep4


title: MB477_Kdm4B_RNAi_naive2

tag: tissue


title: 21_5W-Control-5_rep2

source_name: leaf blades of Col-0 plants under control condition 5 weeks after sowing

value: the second and third leaf blades from the top of the fully expanded leaves

value: None (Control)


title: 19_5W-GSH-4_rep1

source_name: leaf blades of GSH-fed Col-0 plants 5 weeks after sowing

value: GSH


title: 22_5W-GSSG-5_rep2

source_name: leaf blades of GSSG-fed Col-0 plants 5 weeks after sowing

value: GSSG


title: 23_5W-GSH-5_rep2


title: 20_5W-NH4NO3-4_rep1


title: keratoconus-rep5 [KC5_Sup]

city: qingdao

first: HUIJIN

state: shandong province

address: yanerdao road

institute: Qingdao Eye Hospital of  Shandong First Medical University

hyb_protocol: Cy3 and Cy5 labeled cRNAs were combined together and hybridized to Arraystar Human mRNA&lncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 4 out of 8 samples were retained as “All Targets Value” in the Excel sheet for further “m6A methylation level” and “m6A quantity” and “expression level” analyses. “m6A methylation level” was calculated for the percentage of modification based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. “expression level” was calculated based on the total of IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities.
Differentially m6A-methylated RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds.

label_protocol: The total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Kit.

growth_protocol: cornea in both keratoconus patients (Trial group)  and non-keratoconus patients (Control group) was surgically obtained and preserved in −80℃liquid nitrogen tanks.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: subject status

value: keratoconus patient

tag: gender

value: male

tag: sample type

value: supernant


title: keratoconus-rep4 [KC4_Sup]


title: keratoconus-rep3 [KC3_Sup]

value: female


title: UWB1.289 Olaparib, Rep2

tag: cell type

value: serous ovarian carcinoma cells

value: Olaparib


title: MB477_naive3

tag: strain

value: mushroom body


title: MB477_Kdm4B_RNAi_naive1


title: UWB1.289 DMSO, Rep1

tag: cell line


title: UWB1.289 Olaparib, Rep1

tag: treatment


title: MB477_naive2


title: keratoconus-rep1 [KC1_Sup]


title: 18_5W-GSSG-4_rep1


title: RRMM21_T1

city: Heidelberg

first: Alexandra

middle: M

last: Poos

address: Im Neuenheimer Feld 410

institute: University Hospital Heidelberg

description: 10X Genomics

library_source: other

data_processing:
CellRanger ATAC version 1.2
Assembly: hg38
Supplementary files format and content: For each sample the fragments.tsv.gz, raw_peak_bc_matrix.h5 and singlecell.csv have been uploaded.

molecule: other

source_name: bone marrow

extract_protocol:
Viably frozenCD138+-enriched or CD138+-depleted (RRMM7) BMMCswere thawed at 37 ºC, resuspended in RPMI with 10% FBS and washed once in ice-cold PBS with cells being collected by centrifugation at 500 g for 5 min.
Library was performed according to the manufactur's instructions (scATAC-seq, v1.0 protocol, 10X Genomics)

value: bone marrow

value: CD138-positive fraction

value: pre


title: normal cornea-rep5 [SP5_Sup]

source_name: normal cornea_supernatant

value: non-keratoconus patient


title: MB131_Kdm4B_RNAi_10min3

value: 5-min optogenetic activation followed by 10-min rest


title: 17_5W-Control-4_rep1

value: Columbia

value: 5 weeks after sowing


title: 15_4W-GSH-4_rep2

source_name: leaf blades of GSH-fed Col-0 plants 4 weeks after sowing

value: the second and third leaf blades from the top of the fully expanded leaves

value: 4 weeks after sowing


title: MB477_10min2


title: UWB1.289 DMSO, Rep3

value: DMSO


title: MB477_10min1


title: UWB1.289 DMSO, Rep2


title: RRMM20_T1

description: 10X Genomics


title: 12_4W-NH4NO3-3_rep1

source_name: leaf blades of NH4NO3-fed Col-0 plants 4 weeks after sowing


title: MB131_Kdm4B_RNAi_10min2


title: 11_4W-GSH-3_rep1

value: GSH


title: normal cornea-rep4 [SP4_Sup]


title: 16_4W-NH4NO3-4_rep2


title: keratoconus-rep2 [KC2_Sup]

value: keratoconus patient

value: male


title: RRMM21_T2

description: 10X Genomics

value: post


title: 14_4W-GSSG-4_rep2

source_name: leaf blades of GSSG-fed Col-0 plants 4 weeks after sowing

value: GSSG


title: MB131_Kdm4B_RNAi_naive3

value: naive


title: MB477_naive1

value: mushroom body


title: RRMM20_T2

description: 10X Genomics

value: bone marrow


title: RRMM19_T1

description: 10X Genomics

value: CD138-positive fraction


title: keratoconus-rep5 [KC5_IP]

value: IP with anti-N6-methyadenosine (m6A) antibody


title: MB131_Kdm4B_RNAi_10min1


title: MB131_Kdm4B_RNAi_naive2


title: MB131_Kdm4B_RNAi_naive1


title: 13_4W-Control-4_rep2

source_name: leaf blades of Col-0 plants under control condition 4 weeks after sowing

value: None (Control)


title: MB131_10min3

value: 5-min optogenetic activation followed by 10-min rest


title: 09_4W-Control-3_rep1

value: Columbia


title: RRMM18_T1

description: 10X Genomics

value: pre


title: 10_4W-GSSG-3_rep1

value: the second and third leaf blades from the top of the fully expanded leaves


title: 07_3W-GSH-5_rep2

source_name: aerial parts of GSH-fed Col-0 plants 3 weeks after sowing

value: aerial parts including the shoot apical

value: 3 weeks after sowing


title: 06_3W-GSSG-5_rep2

source_name: aerial parts of GSSG-fed Col-0 plants 3 weeks after sowing


title: normal cornea-rep2 [SP2_Sup]

value: non-keratoconus patient

value: female

value: supernant


title: normal cornea-rep3 [SP3_Sup]

value: male


title: RRMM18_T2

description: 10X Genomics

value: post


title: normal cornea-rep1 [SP1_Sup]


title: keratoconus-rep3 [KC3_IP]

value: keratoconus patient


title: keratoconus-rep4 [KC4_IP]


title: 08_3W-NH4NO3-5_rep2

source_name: aerial parts of NH4NO3-fed Col-0 plants 3 weeks after sowing


title: MB131_10min1

value: mushroom body


title: RRMM17_T2

description: 10X Genomics

value: bone marrow


title: 05_3W-Control-5_rep2

source_name: aerial parts of Col-0 plants under control condition 3 weeks after sowing


title: MB131_naive3

value: naive


title: keratoconus-rep1 [KC1_IP]

value: IP with anti-N6-methyadenosine (m6A) antibody


title: MB131_10min2


title: keratoconus-rep2 [KC2_IP]


title: normal cornea-rep5 [SP5_IP]

source_name: normal cornea_IP


title: MB131_naive2