title: synovium from rat (rat ID #8) with sham surgery 2 weeks post-surgery

value: Sham Surgery


title: THP6, CDC73, shControl, 1

status: Public on Aug 29 2023

type: SRA

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

country: USA

institute: University of Michigan

library_source: genomic

data_processing:
Data processing was performing using Chipseq ATACseq Pipelines 1.0.1 (https://github.com/russell-ryan-lab/ChIPseq_ATACseq_pipelines).
Paired-end reads were aligned to using BWA 0.7.17.
Read duplicates were removed using Picard 2.22.3 and multimapping reads were also removed.
Peak calling was performed using Homer 4.10 findPeaks (“style -factor” for human CDC73 amd "style -histone” for mouse H3K27ac). Peaks falling within ENCODE exclusion / problematic regions were removed (https://github.com/Boyle-Lab/Blacklist).
Coverage/signal files (bigWig) were produced using DeepTools 3.4.3 bamCoverage.
H2K120Ub1 was quantified over genes defined in the GENCODE M15 mouse annotation (basic GTF). Raw counts and RPKM-normalized counts were computed using Homer 4.10 analyzeRepeats.pl in a strand-insensitive manner using parameters: (-raw or -rpkm) -gid -count genes -strand both.
Assembly: mm10, hg19
Supplementary files format and content: H2K120Ub1 quantification files (read coverage over genes) are tab-delimited text files with headers and include gene annotations, raw counts (0.5 per read in paired-end data, as per Homer analyzeRepeats.pl), and RPKM.  Sample matrices fir counts and RPKM are also included for H2K120Ub1 data.

molecule: genomic DNA

organism: Homo sapiens

source_name: T-cell acute lymphoblastic leukemia

growth_protocol: T-ALL cell lines were grown in RPMI 1640 (Invitrogen) supplemented with 10% fetal bovine serum (Hyclone or Gibco), 2 mM L-glutamine, 2-mercaptoethanol (0.0005% (v/v), Sigma), penicillin and streptomycin.

extract_protocol:
Cells were crosslinked for most samples by addition of 1% formaldehyde to media at 37 C for 10 minutes, followed by glycine quenching and 2x washing in PBS. For Ets1. For H3K27ac and H2K120ub1, cells were crosslinked with 1% formaldehyde at room temperature. Nuclei were isolated by hypotonic buffer lysis, and chromatin was fragmented with a QSonica Q800 bath sonicator in 0.3% SDS-containing lysis buffer. Samples were diluted 1:3.3 and chromatin complexes containing the target of interest were isolated by immunoprecipitation, followed by reverse crosslinking and DNA purification by SPRI. For input samples (vehicle-treated only), 1:8 diluted sonicated chromatin (whole cell extract) was added directly to the reverse crosslinking step without immunoprecipitation.
Purified ChIP or input DNA was end-repaired and A-tailed. Illumina barcoded adaptors were ligated and PCR amplified. Final library was isolated by double SPRI purification (sequential reverse and forward SPRI) and paired-end sequenced on the Illumina NextSeq 550 (38 bp reads) or on the Illumina NovaSeq 6000 (151 bp reads) .

treatment_protocol: Murine T-ALL cells were treated with EtOH or OHT at 6nM for 30 hours prior to harvesting. THP-6 T-ALL cells were lentivirally transduced with pLKO.1-type shRNA for 2 days  and then selected with puromycin for 2 days prior to harvesting.

tag: tissue

value: T-cell acute lymphoblastic leukemia

tag: cell line

tag: chip-seq antibody

value: CDC73/Parafibromin (Bethyl A300-171A)

tag: genotype

tag: treatment

value: shControl


title: B_CD_220-F37-LIV-SW-44_S213_L003

city: Ås

first: Byron

last: Morales Lange

address: Arboretveien 6

country: Norway

institute: Norwegian University of Life Sciences

library_source: transcriptomic

data_processing:
nf-core rnaseq v3.3
Fragment mapping was counted using featureCounts (subread v1.5.1).
Differentially expressed genes (DEGs) were estimated using the SARTools R package (v1.7.3). Significant DEGs were determined when the adjusted p-value (padj) was < 0.05.
Assembly: SSAL_v3.1 (GenBank assembly accession: GCA_905237065.2).
Supplementary files format and content: Count files / Counts for each Sample.

molecule: total RNA

organism: Salmo salar

source_name: Liver

extract_protocol:
Total RNA was extracted from each sample using RNeasy Mini Kit (Qiagen) following the supplier’s instructions. Then, RNA samples were quantified using a NanoDrop™ 8000 spectrophotometer and RNA integrity was measured by Agilent Bioanalyzer 2100. All samples showed an RNA integrity number ≥ 7).
RNA libraries for RNA-seq were prepared by the Norwegian Sequencing Center (UiO, Norway).

value: Liver

tag: FISH group

value: B

tag: diet

value: Control Diet

value: Control

tag: water stage

value: Seawater


title: B_CD_219-F37-LIV-SW-43_S207_L003


title: LIV10_R2

city: New York

first: Meri

last: Rogava

state: New York

address: 650 W 168th St, New York, NY 10032

department: Hematology Oncology

institute: Columbia University

description: gDNA

data_processing:
data processing steps were performed as described previously (Doench et al., 2016). CRISPR–Cas9 screens were analyzed using software packages MAGeCK and MAGeCKFlute. MAGeCK allows to analyze CRISPR/Cas9 screen data, and performs quality control, read count generation and normalization, calculated beta score to evaluate gene selection performance. MAGeCK’s robust rank aggregation (RRA) method was used to identify significantly enriched or depleted CRISPR-screen hits in cells and tumors. MAGeCKFlute R package was used for data analysis and visualization.
For RNAseq data analysis the tximeta R package (Love et al. 2020) was used to import transcript-level quantification data quantified with Salmon package (Patro et al. 2017). Reads were mapped to mouse reference - Mus_musculus.GRCm38.97 and DESeq2 package was applied to generate normalized data.
Genome_build: Mus_musculus.GRCm38.97

organism: Mus musculus

source_name: mouse melanoma cell line

growth_protocol: Mouse melanoma cell line HCmel12 (gift from Prof. Thomas Tueting, Magdeburg, Germany) were grown in ‘complete’ RPMI-1640 medium (Gibson Bioscience) supplemented with 10%FBS (Gibco™ 10437028), 10mM non-essential amino acids, 1mM HEPES (all from Life Technologies), 20 µM 2-mercaptoethanol (Sigma), 100 IU per ml penicillin and 100 µg/ml-1 streptomycin (Invitrogen). Cell lines were routinely tested for mycoplasma contamination using Lonza MycoAlert Kit (Cat. # LT07-318).

extract_protocol:
Genomic DNA from cells (edited for 10, 14, 21, 28, 35, 42, 49 and 52 days) and mouse tissue (primary tumor, lung, liver, lymph node), was extracted using Qiagen kit for DNeasy Blood & Tissue Kit (69506,Qiagen).
The procedure of amplifying pooled sgRNA library was based on the protocol described previously (Doench et al., 2016). Sequencing libraries were constructed as previously described (Doench et al., 2016) and sequenced on an Illumina HiSeq2500 Instrument.
sgRNA enrichment sequencing

treatment_protocol: HCmel12-Cas9 melanoma cells were transduced at a MOI < 0.1 with lentivirus produced from a kinome-wide lentiviral mouse CRISPR knockout guide library containing 2,852 sgRNAs (Brie, Addgene # 75316) with at least 1000-fold representation (cells per construct) in each infection replicate. Spin-infected ~30 million HCmel12_Cas9 cells with the kinome CRISPR lentivirus library at MOI =0.1 in multiple 6-well plates at Day 0, and transferred the cells into T75 flasks at Day 2. Blasticidin selection (10 µg/ml) started at Day 2, and cells were harvested at Day 7. Puromycin selection stated at day 2 and lasted the entire experiment. On day 14 tumor cells were harvested and used for in vivo screening experiment. In parallel to in vivo screening experiment, cells were kept in culture and continued to edit for 21, 28, 35, 42, 49 and 52 days, the entire duration in parallel to in vivo editing. In vitro edited cells were palleted and used for downstream gDNA extraction and library preparations. For in vivo screening, 3x106 of library-transduced HCmel12-Cas9 cells were injected into the right flank or lateral tail vein of the mice. Tumor growth and signs of sickness was monitored over time. Mice were euthanized after 4 weeks and tumors, lungs, lymph node and liver were evaluated for metastasis presence, lesions dissected for gDNA isolation, amplification of the sgRNA region, and sequencing.

tag: pertubation/treatment

tag: sample origin

value: Liver Metastasis


title: meniscus from rat (rat ID #8) with sham surgery 2 weeks post-surgery

city: La Jolla

first: Padma

last: Natarajan

state: CA

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

data_processing:
The high throughput RNA-seq data was initially processed with in-house custom scripts using BBTools (https://sourceforge.net/ projects/bbmap/) to obtain demultiplexed reads for each sample based on the inline barcodes. The 5’-end 10-base barcodes and 3’-end 12-base UMI information from read1 fastq were first incorporated into read2 fastq as part of sequence ID using UMI-tools. The read2 sequences (from the pre-deduplicated dataset) were analyzed using nf-core/RNA-seq pipeline v1.4.2 (implemented on Nextflow v20.07.1), which is an open-source and available at https://github.com/nf-core/rnaseq as part of the nf-core project. Reads2s were trimmed for adapters using trimGalore! V0.6.4 (https://www.bioinformatics.babraham.ac.uk/projects/trim_ galore/) and aligned to the rat genome (Rattus norvegicus) ENSEMBL build Rnor 6.0 using STAR v2.6.1d. Gene-level assignment was then performed using featurecounts v1.6.4. The gene expression matrix with raw gene counts was then used for differential gene expression analysis using the Bioconductor DESeq2 R package v1.20.0. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate (FDR). Genes with an adjusted P-value (padj) < 0.05 found by DESeq2 were assigned as significantly differentially expressed genes (DEGs). The uniquely mapped alignments resulting from alignments to the reference genome were deduplicated removing the PCR duplicates. The transcript UMI for each gene was counted for each sample using UMI-tools.
Assembly: Rattus norvegicus (Rnor 6.0)
Supplementary files format and content: gene counts matrix, FPKM matrix, TPM matrix

organism: Rattus norvegicus

source_name: meniscus

extract_protocol:
Rats were euthanized 2 (n=8), 4 (n=8), or 6 (n=8) weeks after MMT. Cartilage from both the medial and lateral sides of tibial plateaus and femoral condyles, medial and lateral menisci, and synovium of both knees were collected. All visible synovium tissue was collected from the medial and lateral sides of the joint capsule and femoral condyles, distal to the meniscus and directly adjacent to the tibial plateau at all time points. Due to the very thin layer of synovium, it was not possible to collect exclusively the lining layer without some sub synovial adipose tissue. Tissues were homogenized with 350 uL TRIZOL using a homogenizer, for three 30 s intervals interrupted b y3 min breaks. The homogenized tissue was added to 70 uL ethanol. This mixture was vortexed, and the 100 uL supernatant was collected, centrifuged, and added to the mRNeasy Mini kit column (Qiagen) following manufacturer's instructions. Total RNA was eluted in 12 uL RNase-free water. The RNA integrity was determined using and Agilent Bioanalyzer and only samples with values >5 were used for RNA-seq.
The high throughput RNA-seq assay used was part of an early access kit from iGenomX Inc. Briefly, total RNA (50 ng) was placed in a solution containing 1.4X First Strand Buffer and barcode oligo dT primer and incubated at 80C for 10 min in 7 uL total volume, subsequently added was 4.5 mM DTT, barcoded template-switching oligonucleotide, 1.8 U/uL RNaseOUT (ThermoFisher), dNTP mix and Reverse Transcriptase in 11 uL final volume. Reactions were incubated 50 min at 42C, followed by 5 min at 85C. This was followed by addition of 2 uL reaction clean-up mix and incubated at 37C for 30 min and 80C for 20 min. Samples were pooled together, and cDNA products were purified by 1.2X SPRI bead clean-up procedure with SPRI bead mixture. cDNA products were taken directly into a PCR reaction containing 1X KAPA HiFi reaction mixture and 0.5 uM barcoded PCR primers of Illumina p5 and p7 sequences in 100 uL final volume. PCR products were first cleaned using 1X SPRI bead clean-up mix, and then separated on 2% agarose gels. Products approximately 350 bp-800 bp were excised and isolated using agarose gel dissolving buffer and clean-up and concentrator column (Zymo Research). Purified PCR products were quantified using Qubit dsDNA HS assay kit, analyzed on Agilent Tapestation, and sequenced on 100 cycle P2 flow cells with an Illumina NextSeq2000 sequencing instrument using paired-end sequencing (read1: 26 bases, read2: 94 bases, i5 and i8 indexes used 8 base reads).

treatment_protocol: All animal procedures were approved by the Scripps Research Institutional Animal Care and Use Committee. Male Lewis rats (n=42 total) were assigned to the following groups: 24 rats with MMT surgery on the right and sham surgery (SS) on the left knee for knee tissue collection and RNA sequencing at 2, 4 and 6 weeks (n=8 animals per time point); 18 rats with MMT surgery on the right and sham surgery on the left knee for knee histology at 2, 4 and 6 weeks (n=6 animals per time point). Animals were anesthetized with ketamine/xylazine cocktail (50 mg/kg Ketaved – Henry Schein, and 5 mg/kg Xylazine – AniSed respectively) by intraperitoneal injection, administered appropriate analgesics (Flunixin, 5 mg/kg subcutaneous injection), and the surgical site shaved and disinfected. A small incision was made on the medial right hind knee to expose the collateral ligament. The collateral ligament was transected, and the joint capsule opened sufficiently to expose the medial meniscus. The meniscus was transected completely, then the skin incision was closed, and pressure applied to the wound to prevent hematoma development. Animals were allowed to recover on a heated blanket and were returned to their home cage. Sham procedures were carried out in a similar fashion except the medial meniscus was not cut.

value: meniscus

tag: timepoint

value: 2 weeks

tag: disease state


title: LIV10_R1

description: gDNA


title: A_L6_236-F37-LIV-SW-92_S238_L003

value: A

value: hydrolyzed Debaryomyces hansenii


title: LNG_R8

description: gDNA

value: Lung


title: GSK458_IgG

data_processing:
Reads were trimmed using TrimGalore v0.4.5 and CutAdapt v1.15 with the following parameters: –adapter AGATCGGAAGAGC -e 0.1 –stringency 6 –length 20 –nextseq 20.
Trimmed reads were aligned to hg19 using Bowtie2 v2.3.4.1 (Langmead and Salzberg, 2012) with the following parameters: -X 2000, and defaults multi-seed length of 20bp with 0 mismatches.
Duplicate reads were marked and removed with Picard v2.20.2. Alignments below a MAPQ threshold of 10 were removed using samtools v1.2 (Li et al., 2009)and the parameters: -q 10 -F 1024. Reads completely overlapping the ENCODE Problematic Regions (Amemiya et al., 2019) were removed with bedtools2 v2.28.0 (Quinlan and Hall, 2010).
DeepTools v3.3.0 (Ramírez et al., 2016) was used to calculate coverage (bigWig format) and IP efficiency plots.
Sample-wise peaks were called for anti-H3K27Ac and IgG ChIP using MACS2 v.2.1.2 (Zhang et al., 2008) (v2.1.2) in its default mode (narrow peaks) using treatment-matched input as control.  Parameters used: –format BAM –gsize hs.
Assembly: hg19
Supplementary files format and content: BigWig (coverage)
Supplementary files format and content: BED (MACS2 peaks)

source_name: brain stem

extract_protocol:
The cell lysate was sonicated. Protein concentrations of whole-cell lysates were determined using Lowry assays (Bio-Rad). Samples containing 750 µg of protein were used per immunoprecipitation (IP) reaction. Protein of interest was immunoprecipitated using Thermo Fisher Dynabead A kit (cat# 10006D), following the manufacturer’s instructions. For immunoprecipitation the H3K27ac antibody (Abcam cat# ab4729) and IgG included in the Diagenode kit was used. Following immunoprecipitation, half of the precipitate
Libraries were prepared with the Swift Accel-NGS 2S Plus DNA kit and 2S Combinatorial Dual Indexing kit, according to the manufacturer’s instructions. Each library was prepared with 3.9ng of DNA. The final library amplification was performed with 8 cycles of PCR amplification. The Qubit dsDNA HS Assay Kit and High Sensitivity D1000 ScreenTape assay were used for QC assessment. The KAPA Library Quanitification Kit for Illumina platforms (Roche) was used to obtain library concentrations and guide pooling. Libraries were sequenced on the NovaSeq 6000 (Illumina) using the S1 flow cell and paired-end 50-nucleotide chemistry.

treatment_protocol: Ten million SU-DIPG XIII cells were seeded 24 hours prior to treatment and incubated with GSK-458 for 2 hours at 10 µM. Cells were washed with PBS and incubated for 30 minutes in RIPA lysis buffer (Thermo Fisher) supplemented with protease inhibitors (Complete Protease Inhibitor Cocktail, Roche) and phosphatase inhibitors (PhosSTOP, Roche) to lyse the cells.

value: brain stem

value: SU-DIPG-XIII

tag: cell type

value: diffuse intrinsic pontine glioma cell line


title: LIV10_R4.2

description: gDNA


title: synovium from rat (rat ID #7) with medial meniscus transection surgery 2 weeks post-surgery

source_name: synovium

value: synovium

value: Medial Meniscus Transection


title: meniscus from rat (rat ID #7) with medial meniscus transection surgery 2 weeks post-surgery


title: LIV10_R4.1

description: gDNA


title: A_L6_235-F37-LIV-SW-91_S259_L003


title: LNG_R7

description: gDNA


title: A_L6_223-F37-LIV-SW-55_S265_L003


title: A_L6_224-F37-LIV-SW-56_S272_L003


title: LNG_R6

description: gDNA


title: GSK458_antiH3K27Ac


title: DMSO_IgG

value: DMSO


title: cartilage from rat (rat ID #7) with medial meniscus transection surgery 2 weeks post-surgery

source_name: cartilage

value: cartilage


title: DMSO_Input


title: LNG_R5

description: gDNA


title: synovium from rat (rat ID #7) with sham surgery 2 weeks post-surgery

value: Sham Surgery


title: DMSO_antiH3K27Ac


title: LNG_R4

description: gDNA


title: A_CD_212-F37-LIV-SW-20_S195_L003

value: Liver

value: Control Diet


title: AZA_TAK_3

city: Montpellier

first: Denis

last: Tempé

address: 1919 route de Mende

country: France

institute: CNRS

data_processing:
Libraries were sequenced using an Illumina Novaseq 6000 sequencer as paired-end 150 base reads.
Image analysis and base calling were performed using NovaSeq Control Software, Real‑Time Analysis 3 (RTA) and bcl2fastq.
RNA‑seq reads were mapped on the Human reference genome (hg38, GRCh38p12) using TopHat2 (2.1.1) based on the Bowtie2 (2.3.5.1) aligner.
Reads association to annotated genes was performed using HTseq‑count v0.11.1 with option "non-unique=all"
Differential expression analysis was performed using DESeq2 with normalization by sequencing depth and parametric negative binomial law to estimate the data dispersion. Genes with a fold change >2 or < 0.5 and an adjusted p‑value < 0.05 were considered as differentially expressed genes (DEGs).
Assembly: hg38/GRCh38p12
Supplementary files format and content: suppTable2_DESeq2.csv
Supplementary files format and content: Output from DESeq2 analysis : comma separated table containing mean counts for each treamtment condition and statistical analysis for each treatment comparison : AZA vs DMSO, TAK-981 vs DMSO, AZA+TAK-981 vs DMSO, TAK-981 vs AZA, AZA + TAK-981 vs AZA, AZA vs TAK-981, AZA + TAK-981 vs TAK-981

source_name: cell line

growth_protocol: Cells were cultured at 37°C in the presence of 5% CO2 in RPMI 1640 medium (Eurobio Scientific, CM1RPM08-01) supplemented with 10% heat-decomplemented (30 min at 56°C) fetal bovine serum (FBS), 100 IU/mL penicillin and 100 μg/mL streptomycin. After thawing, cells were seeded at 0.3 x 106/mL every 2 to 3 days for no more than 10 passages. Cells were seeded at 0.3 x 106/mL the day before treatment starts.

extract_protocol:
Total RNAs were purified using the GenElute Mammalian Total RNA kit (Sigma-Aldrich), treated with DNase I (4U, New England Biolabs) and RNasin (2,5U, Promega) and re‑purified. RNA quality was assessed using a BioAnalyzer Nano 6000 chip (Agilent).
TruSeq stranded total RNA Library kit from Illumina was used for both ribodepletion and library preparation.

treatment_protocol: TAK-981 was obtained from Takeda Development Center Americas and resuspended in DMSO and RPMI. Azacytidine (5-azacytidine - AZA) was from StemCell and resuspended in RPMI prior to each experiment. Cells were treated with either AZA, TAK-981 or both at a final concentration 10nM each. The treatment was renewed each day for 3 consecutive days.

value: cell line

value: AML

value: Azacitidine + TAK-981


title: A_CD_211-F37-LIV-SW-19_S277_L003

value: Control

value: Seawater


title: cartilage from rat (rat ID #8) with sham surgery 2 weeks post-surgery

value: 2 weeks


title: GSK458_Input


title: LNG_R3.2

description: gDNA

value: Lung


title: A_CD_206-F37-LIV-SW-2_S232_L003

value: A


title: cartilage from rat (rat ID #7) with sham surgery 2 weeks post-surgery


title: meniscus from rat (rat ID #7) with sham surgery 2 weeks post-surgery

value: meniscus


title: LNG_R3.1

description: gDNA


title: A_CD_205-F37-LIV-SW-1_S204_L003


title: AZA_3

value: Azacitidine


title: synovium from rat (rat ID #6) with medial meniscus transection surgery 2 weeks post-surgery

value: synovium


title: TAK_3


title: LNG_R2.2

description: gDNA


title: B_L6_276-F37-HK-SW-104_S287_L003

source_name: Head kidney

value: Head kidney

value: B

value: hydrolyzed Debaryomyces hansenii


title: meniscus from rat (rat ID #6) with medial meniscus transection surgery 2 weeks post-surgery

value: Medial Meniscus Transection


title: LNG_R2.1

description: gDNA


title: B_L6_275-F37-HK-SW-103_S244_L003


title: cartilage from rat (rat ID #6) with medial meniscus transection surgery 2 weeks post-surgery

value: cartilage


title: DMSO_3

value: DMSO


title: AZA_TAK_2

value: cell line


title: LNG_R1.2

description: gDNA


title: B_L6_274-F37-HK-SW-98_S237_L003


title: synovium from rat (rat ID #6) with sham surgery 2 weeks post-surgery

value: Sham Surgery


title: B_L6_273-F37-HK-SW-97_S209_L003


title: meniscus from rat (rat ID #6) with sham surgery 2 weeks post-surgery


title: AZA_2

value: AML


title: TAK_2


title: Mel_R8

description: gDNA

value: transplated tumor


title: cartilage from rat (rat ID #6) with sham surgery 2 weeks post-surgery


title: Mel_R7

description: gDNA


title: DMSO_2


title: B_CD_267-F37-HK-SW-79_S231_L003

value: Control Diet

value: Control

value: Seawater


title: AZA_TAK_1

value: Azacitidine + TAK-981


title: Mel_R6

description: gDNA


title: synovium from rat (rat ID #5) with medial meniscus transection surgery 2 weeks post-surgery

value: 2 weeks


title: Mel_R5

description: gDNA


title: meniscus from rat (rat ID #5) with medial meniscus transection surgery 2 weeks post-surgery

value: meniscus


title: B_CD_256-F37-HK-SW-44_S243_L003


title: TAK_1


title: A_L6_272-F37-HK-SW-92_S210_L003

value: A


title: cartilage from rat (rat ID #5) with medial meniscus transection surgery 2 weeks post-surgery


title: AZA_1

value: Azacitidine


title: LNG_R1.1

description: gDNA

value: Lung


title: Mel_R4

description: gDNA


title: DIPG13, H3K27M-KO, IR5Gy, rep2

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Reads were trimmed using BBDuk (BB Tools v38.46). The bundled adapter sequences and following parameters were used. Single-end reads: ktrim=r, mink=5, minlength=20, hdist=1. The k parameter was set to 30 or the length of the smallest adapter sequence, whichever is larger. Paired-end reads: ktrim=r, mink=11, hdist=1, k=31.
Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2 (2.3.3).
Reads that did not align with rRNA, mitochondrial and EBV genomes were subsequently mapped to human genome build hg38/GRCh38 using STAR (v 2.5.3a) and a STAR index created from GENCODE annotation version 27.
Coverages were determined using bedtools 2 v2.28.0 as (1 / read length) for each base in the genome. These base coverages were used to obtain pseudo-read counts in strand-specific regions of interest using bedtools intersect. Reads Per Kilobase per Megabase of library size (RPKM) were calculated for meta-transcripts ("genes") defined by merging exons and intervening intronic spaces from all isoforms of a gene in the GENCODE v27 "basic" annotation. Genes were quantified by summing pseudo-counts falling within the features (exons and intronic spaces) and normalized by the effective gene length (sum of feature lengths) and by the size of the library (uniquely mapped read count).
Assembly: hg38
Supplementary files format and content: Per-library quantification files are tab-delimited text and header.  Columns: (1) chromosome; (2) start; (3) end; (4) Ensembl gene ID; (5) strand; (6) gene symbol; (7)  effective length; (8) pseudo-counts; (9) RPKM.
Supplementary files format and content: Library quantification matrices (counts and RPKM) are tab-delimited text files with headers.  First 7 columns are gene annotations: (1) chromosome; (2) start; (3) end; (4) Ensembl gene ID; (5) strand; (6) gene symbol; (7)  effective length.
Supplementary files format and content: Read depth file: tab-delimited text file with library name and number of uniquely-aligned reads (used to compute RPKM).
Library strategy: Bru-seq

growth_protocol: SU-DIPG-XIII cells were maintained in Tumor Stem Neurobasal-A medium mixed 1:1 with DMEM F-12 supplemented 10 mM HEPES, 100 mm Sodium Pyruvate, Non-essential Amino Acids, GlutaMAX-I supplement, 100X Antibiotic-Antimycotic, B27(-A) (Invitrogen), 20 ng/ml each of human-FGF (20ng/ml), human-EGF and human PDGF-AB (Shenandoah Biotech), and 10 ng/ml heparin (STEMCELL Technologies). Neurospheres were dissociated in TrypLE Express (Thermo Fisher) and 2D cultures with Trypsin-EDTA (Gibco). Cells were incubated at 37C in the presence of 5% CO2 and cultured for a period of ~ 2 months after which they were replaced by new thaws.

extract_protocol:
cells were lysed in TRIzol and total RNA isolated according to the TRIzol protocol (Invitrogen).
Ribosomal RNA was reduced via QiaSeq FastSelect (Qiagen) prior to first strand synthesis. These strand-specific libraries were made using a universal ligation adapter and dual-index, barcoded primers for PCR. Sequencing was performed on a NovaSeq 6000 (Illumina), yielding 150 bp, paired-ended reads.
RNA-seq (Bru-seq)

treatment_protocol: SU-DIPG-XIII cells were irradiated at 5 Gy using a C-320 Biological Irradiator (Kimtron Inc., Oxford, CT) or mock-irradiated ("untreated").  Bromouridine (2mM) was added to the condition media 1 h post-irradiation and incubated at 37C for 30 min prior to harvest.

value: brain stem

value: SU-DIPG-XIII

value: diffuse intrinsic pontine glioma cell line

value: H3.3K27M knockout

value: ionizing radiation (5 Gy)


title: DMSO_1

value: cell line

value: DMSO


title: synovium from rat (rat ID #5) with sham surgery 2 weeks post-surgery

value: synovium

value: Sham Surgery


title: meniscus from rat (rat ID #5) with sham surgery 2 weeks post-surgery


title: A_L6_260-F37-HK-SW-56_S279_L003

value: Head kidney

value: hydrolyzed Debaryomyces hansenii


title: cartilage from rat (rat ID #5) with sham surgery 2 weeks post-surgery

value: cartilage


title: Mel_R3.1

description: gDNA

value: transplated tumor


title: A_L6_271-F37-HK-SW-91_S206_L003

value: Seawater


title: A_L6_259-F37-HK-SW-55_S283_L003

value: A


title: synovium from rat (rat ID #4) with medial meniscus transection surgery 2 weeks post-surgery

value: 2 weeks

value: Medial Meniscus Transection


title: Mel_R2

description: gDNA


title: A_CD_248-F37-HK-SW-20_S196_L003

value: Control Diet

value: Control


title: Mel_R3.2

description: gDNA


title: meniscus from rat (rat ID #4) with medial meniscus transection surgery 2 weeks post-surgery

value: meniscus


title: B_CD_268-F37-HK-SW-80_S246_L003

value: B


title: Mel_R1

description: gDNA


title: B_CD_255-F37-HK-SW-43_S252_L003


title: cells_R8

description: gDNA

value: in vitro cells_edited for 52 days


title: DIPG13, H3K27M, IR5Gy, rep2

value: brain stem

value: SU-DIPG-XIII

value: diffuse intrinsic pontine glioma cell line

value: ionizing radiation (5 Gy)


title: DIPG13, H3K27M-KO, untreated, rep2

value: H3.3K27M knockout

value: untreated


title: A_CD_247-F37-HK-SW-19_S266_L003

value: Head kidney


title: DIPG13, H3K27M-KO, IR5Gy, rep1


title: cartilage from rat (rat ID #4) with medial meniscus transection surgery 2 weeks post-surgery

value: cartilage


title: cells_R7

description: gDNA

value: in vitro cells_edited for 49 days


title: A_CD_242-F37-HK-SW-2_S227_L003

value: A

value: Seawater


title: DIPG13, H3K27M, IR5Gy, rep1


title: A_CD_241-F37-HK-SW-1_S203_L003


title: cells_R6

description: gDNA

value: in vitro cells_edited for 42 days


title: DIPG13, H3K27M, untreated, rep2


title: meniscus from rat (rat ID #4) with sham surgery 2 weeks post-surgery

value: 2 weeks

value: Sham Surgery


title: cells_R5

description: gDNA

value: in vitro cells_edited for 35 days


title: cartilage from rat (rat ID #4) with sham surgery 2 weeks post-surgery


title: synovium from rat (rat ID #3) with medial meniscus transection surgery 2 weeks post-surgery

value: synovium

value: Medial Meniscus Transection


title: DIPG13, H3K27M, untreated, rep1

value: brain stem


title: TOF-ND2 - CAS

city: Hong Kong

first: Chun Ho

last: Chan

address: 5 Sassoon Road Pokfulam

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Raw sequencing reads filtered and aligned against GRCh38 genome with Cell Ranger 3.0
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix.mtx (RNA expression levels)
Supplementary_files_format_and_content: barcodes.tsv (Cell identification code)
Supplementary_files_format_and_content: features.tsv (List of genes)

molecule: polyA RNA

source_name: hiPSC-CMs

extract_protocol:
hiPSC-CPs and hiPSC-CMs cultured in monolayer were dissociated with 1X TrypLE at 37oC for 10-15 minutes. Dissociated cells were resuspended in RPMI/B27 for cell encapsulation.
Constructed with Chromium Single Cell 3' Reagent Kit v3.1 according to manufacturer's protocol

treatment_protocol: hiPSC-CMs were fabricated into CAS on Day11 post-differentiation and cultured for 10-11 days

tag: day post differentiation

value: TOF-ND

value: hiPSC-CMs


title: DIPG13, H3K27M-KO, untreated, rep1

value: SU-DIPG-XIII

value: diffuse intrinsic pontine glioma cell line


title: RNAseq_blastomere_Dux_KO_Obox4_KO_rep1

city: Shinjuku

first: Haruhiko

last: Siomi

state: Tokyo

address: 35 Shinanomachi

department: Department of Molecular Biology

country: Japan

institute: Keio University School of Medicine

description:
count_matrix_blastomere_KO_genes.csv
count_matrix_blastomere_KO_TEs.csv

data_processing:
Base calling was performed using bcl2fastq v2.20 to generate raw reads.
Quality control and adapter trimming was done using fastp (Chen et al., 2018) v0.23.2.
For RNA-seq, quality controlled reads were aligned to GRCm38.p6 reference genome using STAR (Dobin et al., 2013) v2.7.9a with default arguments. Reads were counted against GRCm38.p6 comprehensive gene annotation (Frankish et al., 2020) and mm10 repeats from UCSC RepeatMasker using FeatureCounts (Liao et al., 2014) v2.0.1 with multi mapping reads discard for non-TE features and count fractionally for TEs. For CUT&RUN-seq, quality controller reads were aligned to GRCm38.p6 reference genome using Bowtie2 (Langmead and Salzberg, 2012) v2.4.1 with default arguments.
For CUT&RUN, Peaks were called in each biological replicated using MACS3 (Zhang et al., 2008) v3.0.0a6 callpeak function (-f BAMPE). Quantitative histone modification analysis with replicated samples was performed using MAnorm2 (Tu et al., 2021) v1.2.0.
For visualization of CUT&RUN results, alignment tracks were generated using deepTools (Ramírez et al., 2016) v3.5.1 bamCoverage function (--binSize 10 --normalizeusing CPM --smoothLength 30). Visualization of genomic tracks was performed using trackplot (Pohl and Beato, 2014) v1.3.10.
Assembly: GRCm38.p6

source_name: embryo

growth_protocol: Eight-weeks old female and male B6D2F1 (BDF1) mice were purchased from the Japan SLC, Inc. All animal experiments were reviewed and approved by the Institutional Animal Care and Use Committee (protocol no. 09105-(10) and 11045-(6)) at Keio University, where mice were maintained and fed ad libitum with standard diet and water in a temperature- and light-controlled room (23℃±3℃, 14/10 hour light/dark cycle).

extract_protocol:
For RNA-seq of embryos, 30 middle-2C embryos were collected 20 hours after microinjection in each independent biological replicates. Zona pellucida was removed by treating the embryos with Acidic Tyrode’s solution. For RNA-seq of culture cells, total RNA was prepared using RNeasy Kit according to the manufacturer’s instruction. The RNA solution was subjected to TURBO DNase treatment according to the manufacturer’s instructions to remove genomic DNA carryover. For RNA-seq, rRNA-depleted total RNA was prepared.  For CUT&RUN, 1×10^5 culture cells freshly prepared by trypsin digestion were used to perform CUT&RUN assay with CUT&RUN Assay Kit (Cell Signaling Technology, 86652) according to the manufacturer’s instructions.
For RNA-seq of embryos, libraries were constructed with SMART-Seq Stranded Kit (TaKaRa, 634442) and indexed with SMARTer RNA Unique Dual Index Kit (TaKaRa, 634451) according to the manufacturer’s instructions. For RNA-seq of culture cells, libraries were constructed using 1µg total RNA with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760L) and indexed with NEBNext Multiplex Oligos for Illumina (NEB, E6440S) according to the manufacturer’s instructions. For CUT&RUN, enriched DNAs were subjected to library construction using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L) with the adapter ligation step performed at 50°C instead of 65°C to prevent denature of small DNA inserts. The libraries were indexed with NEBNext Multiplex Oligos for Illumina according to the manufacturer’s instructions.

treatment_protocol: 8-weeks-old BDF1 female mice were injected with 150µL CARD HyperOva (Kyudo Co., Ltd.). After 48 hours, the female mice were injected with 5IU hCG (ASKA Animal Health Co., Ltd.) and mated with BDF1 male mice. After 22 hours, PN3 zygotes were collected. Cumulus cells were removed by briefly culture the zygotes in KSOM medium (Merck, MR-101-D) supplemented with 0.3µg/µL hyaluronidase (Merck, H4272). Embryos were cultured in KSOM medium drops covered with liquid paraffin (Nacalai Tesque, 26137-85) under 5% CO2 at 37°C. After 4 hours, PBS containing either 40µM scramble ASO, 20µM anti-Dux ASO, 20µM anti-Obox4 ASO, 40µM equal molar anti-Dux/anti-Obox4 ASO mixture, or 40µM equal molar anti-Dux/anti-Obox4 ASO mixture with 100ng/μL codon-optimized Obox4 mRNA were microinjected into male pronuclei of zygotes using FemtoJet 4i microinjector (Eppendorf, 5252000013).

value: embryo

value: blastomere

tag: developmental stage

value: 2C embryo

value: Obox4/Dux double KO

tag: background strain


title: RNAseq_blastomere_Dux_KO_Obox4_KO_rep2


title: RNAseq_blastomere_Dux_KO_Obox4_Het_rep1

value: Obox4 Het/Dux KO


title: cells_R4

description: gDNA

value: in vitro cells_edited for 28 days


title: cells_R3

description: gDNA

value: in vitro cells_edited for 21 days


title: RNAseq_blastomere_Dux_KO_Obox4_Het_rep2


title: cells_R2

description: gDNA

value: in vitro cells_edited for 14 days


title: TOF-DG2 - CAS

value: TOF-DG


title: cartilage from rat (rat ID #3) with medial meniscus transection surgery 2 weeks post-surgery

value: cartilage

value: 2 weeks


title: TOF-ND1 - CAS


title: meniscus from rat (rat ID #3) with medial meniscus transection surgery 2 weeks post-surgery

value: meniscus

value: Medial Meniscus Transection


title: TOF-DG1 - CAS


title: cells_R1

description: gDNA

value: in vitro cells_editied for 10 days


title: synovium from rat (rat ID #3) with sham surgery 2 weeks post-surgery

value: synovium

value: Sham Surgery


title: RNAseq_blastomere_Dux_KO_Obox4_WT_rep2

value: Obox4 WT/Dux KO


title: synovium from rat (rat ID #4) with sham surgery 2 weeks post-surgery


title: RNAseq_blastomere_Dux_KO_Obox4_WT_rep1

value: embryo


title: meniscus from rat (rat ID #3) with sham surgery 2 weeks post-surgery


title: cartilage from rat (rat ID #3) with sham surgery 2 weeks post-surgery


title: RNAseq_ESC_Obox4_OE_48hr_rep3

data_processing: Base calling was performed using bcl2fastq v2.20 to generate raw reads.  Quality control and adapter trimming was done using fastp (Chen et al., 2018) v0.23.2.  For RNA-seq, quality controlled reads were aligned to GRCm38.p6 reference genome using STAR (Dobin et al., 2013) v2.7.9a with default arguments. Reads were counted against GRCm38.p6 comprehensive gene annotation (Frankish et al., 2020) and mm10 repeats from UCSC RepeatMasker using FeatureCounts (Liao et al., 2014) v2.0.1 with multi mapping reads discard for non-TE features and count fractionally for TEs. For CUT&RUN-seq, quality controller reads were aligned to GRCm38.p6 reference genome using Bowtie2 (Langmead and Salzberg, 2012) v2.4.1 with default arguments.  For CUT&RUN, Peaks were called in each biological replicated using MACS3 (Zhang et al., 2008) v3.0.0a6 callpeak function (-f BAMPE). Quantitative histone modification analysis with replicated samples was performed using MAnorm2 (Tu et al., 2021) v1.2.0.  For visualization of CUT&RUN results, alignment tracks were generated using deepTools (Ramírez et al., 2016) v3.5.1 bamCoverage function (--binSize 10 --normalizeusing CPM --smoothLength 30). Visualization of genomic tracks was performed using trackplot (Pohl and Beato, 2014) v1.3.10.

source_name: culture cell

extract_protocol:
For RNA-seq of embryos, 30 middle-2C embryos were collected 20 hours after microinjection in each independent biological replicates. Zona pellucida was removed by treating the embryos with Acidic Tyrode’s solution. For RNA-seq of culture cells, total RNA was prepared using RNeasy Kit according to the manufacturer’s instruction. The RNA solution was subjected to TURBO DNase treatment according to the manufacturer’s instructions to remove genomic DNA carryover. For CUT&RUN, 1×105 culture cells freshly prepared by trypsin digestion were used to perform CUT&RUN assay with CUT&RUN Assay Kit (Cell Signaling Technology, 86652) according to the manufacturer’s instructions.
For RNA-seq of embryos, libraries were constructed with SMART-Seq Stranded Kit (TaKaRa, 634442) and indexed with SMARTer RNA Unique Dual Index Kit (TaKaRa, 634451) according to the manufacturer’s instructions. For RNA-seq of culture cells, libraries were constructed using 1µg total RNA with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760L) and indexed with NEBNext Multiplex Oligos for Illumina (NEB, E6440S) according to the manufacturer’s instructions. For CUT&RUN, enriched DNAs were subjected to library construction using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L) with the adapter ligation step performed at 50°C instead of 65°C to prevent denature of small DNA inserts. The libraries were indexed with NEBNext Multiplex Oligos for Illumina according to the manufacturer’s instructions.

value: culture cell

value: ESC

value: doxycycline


title: Control1 - CAS

value: healthy

value: hiPSC-CMs


title: ATAC_mTOR_WT (re-analyzed)

city: Cincinnati

first: Yi

last: Zheng

state: OH

address: 3333 Burnet Ave MLC7013

department: Experimental Hematology and Cancer Biology

institute: CINCINNATI CHILDRENS HOSP MED CTR

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Peak calling was performed using MACS1.4 with a default p value cut off.
Genome_build: mm10
Supplementary_files_format_and_content: bed file generated by MACS1.4

source_name: mTOR WT Control HSC cells

extract_protocol:
50,000 sorted HSC cells from poly(I:C)-treated WT control and mTOR KO mice were lysed in a cold lysis buffer. Transposase reaction were performed for 30 min at 37 °C immediately after the nuclei preparation. The samples were purified using a Qiagen MinElute kit.
The ATAC-seq libraries were amplified using NEBnext PCR master mix followed by purified using Qiagen MinElute PCR Purification Kit (Qiagen, 28004), and then run on the Illumina sequencer HiSeq 2500.

value: HSC cells

value: Adult


title: RNAseq__mTOR_KO_4 (re-analyzed)

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to mm10 whole genome by Tophat with default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file.
Genome_build: mm10
Supplementary_files_format_and_content: bed file generated by MACS1.4

source_name: mTOR KO HSC cells

extract_protocol:
HSC cells from poly(I:C)-treated WT control and mTOR KO mice were sorted by FACS. RNA were extracted using miRNeasy Micro Kit (Qiagen, 217084).
RNA-seq libraries were prepared using Illumina TruSeq Stranded Total RNA Sample Preparation Kit (Illumina, 20020597)


title: RNAseq_ESC_Obox4_OE_48hr_rep2


title: TOF-ND1 - Day11

source_name: hiPSC-CPs

value: TOF-ND

value: hiPSC-CPs


title: meniscus from rat (rat ID #2) with medial meniscus transection surgery 2 weeks post-surgery

value: 2 weeks


title: RNAseq_ESC_Obox4_OE_48hr_rep1


title: RNAseq__mTOR_KO_3 (re-analyzed)


title: synovium from rat (rat ID #2) with medial meniscus transection surgery 2 weeks post-surgery


title: TOF-ND1 - Day8


title: RNAseq__mTOR_KO_2 (re-analyzed)


title: TOF-ND1 - Day7


title: RNAseq__mTOR_KO_1 (re-analyzed)


title: meniscus from rat (rat ID #2) with sham surgery 2 weeks post-surgery

value: meniscus


title: RNAseq_ESC_Obox4_OE_12hr_rep2


title: RNAseq_ESC_Obox4_OE_12hr_rep1


title: ATAC_mTOR_KO (re-analyzed)


title: RNAseq_Ctr_mTOR_WT_4 (re-analyzed)


title: synovium from rat (rat ID #2) with sham surgery 2 weeks post-surgery


title: Control2 - CAS


title: cartilage from rat (rat ID #2) with sham surgery 2 weeks post-surgery

value: cartilage


title: RNAseq_Ctr_mTOR_WT_3 (re-analyzed)


title: RNAseq_Ctr_mTOR_WT_2 (re-analyzed)


title: synovium from rat (rat ID #1) with medial meniscus transection surgery 2 weeks post-surgery

value: Medial Meniscus Transection


title: RNAseq_ESC_Obox4_OE_0hr_rep2


title: RNAseq_ESC_Obox4_OE_0hr_rep3


title: TOF-DG1 - Day7

value: TOF-DG


title: Control2 - Day11


title: RNAseq_Ctr_mTOR_WT_1 (re-analyzed)


title: cartilage from rat (rat ID #2) with medial meniscus transection surgery 2 weeks post-surgery


title: meniscus from rat (rat ID #1) with medial meniscus transection surgery 2 weeks post-surgery


title: RNAseq_ESC_Obox4_OE_12hr_rep3


title: Control2 - Day8


title: mESC_TRE_3FLAG_Obox4_FLAG_rep3

description: CUT&RUN-enriched DNA

data_processing:
Library strategy: CTU&RUN
Base calling was performed using bcl2fastq v2.20 to generate raw reads.
Quality control and adapter trimming was done using fastp (Chen et al., 2018) v0.23.2.
For RNA-seq, quality controlled reads were aligned to GRCm38.p6 reference genome using STAR (Dobin et al., 2013) v2.7.9a with default arguments. Reads were counted against GRCm38.p6 comprehensive gene annotation (Frankish et al., 2020) and mm10 repeats from UCSC RepeatMasker using FeatureCounts (Liao et al., 2014) v2.0.1 with multi mapping reads discard for non-TE features and count fractionally for TEs.  For CUT&RUN-seq, quality controller reads were aligned to GRCm38.p6 reference genome using Bowtie2 (Langmead and Salzberg, 2012) v2.4.1 with default arguments.
For CUT&RUN, Peaks were called in each biological replicated using MACS3 (Zhang et al., 2008) v3.0.0a6 callpeak function (-f BAMPE). Quantitative histone modification analysis with replicated samples was performed using MAnorm2 (Tu et al., 2021) v1.2.0.
For visualization of CUT&RUN results, alignment tracks were generated using deepTools (Ramírez et al., 2016) v3.5.1 bamCoverage function (--binSize 10 --normalizeusing CPM --smoothLength 30). Visualization of genomic tracks was performed using trackplot (Pohl and Beato, 2014) v1.3.10.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq reads (.csv)
Supplementary_files_format_and_content: CUT&RUN peaks (.narrowPeak or .broadPeak)
Supplementary_files_format_and_content: CUT&RUN read coverage (.bigwig)

source_name: Obox4 inducible mESC

extract_protocol:
For RNA-seq of embryos, 30 middle-2C embryos were collected 20 hours after microinjection in each independent biological replicates. Zona pellucida was removed by treating the embryos with Acidic Tyrode’s solution.  For RNA-seq of culture cells, total RNA was prepared using RNeasy Kit according to the manufacturer’s instruction. The RNA solution was subjected to TURBO DNase treatment according to the manufacturer’s instructions to remove genomic DNA carryover.  For CUT&RUN, 1×105 culture cells freshly prepared by trypsin digestion were used to perform CUT&RUN assay with CUT&RUN Assay Kit (Cell Signaling Technology, 86652) according to the manufacturer’s instructions.
For RNA-seq of embryos, libraries were constructed with SMART-Seq Stranded Kit (TaKaRa, 634442) and indexed with SMARTer RNA Unique Dual Index Kit (TaKaRa, 634451) according to the manufacturer’s instructions.  For RNA-seq of culture cells, libraries were constructed using 1µg total RNA with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760L) and indexed with NEBNext Multiplex Oligos for Illumina (NEB, E6440S) according to the manufacturer’s instructions.  For CUT&RUN,  enriched DNAs were subjected to library construction using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L) with the adapter ligation step performed at 50°C instead of 65°C to prevent denature of small DNA inserts. The libraries were indexed with NEBNext Multiplex Oligos for Illumina according to the manufacturer’s instructions.

value: culture cell (ESC)


title: ATAC_mTOR_KI

source_name: mTOR KI HSC cells

extract_protocol:
50,000 sorted HSC cells from poly(I:C)-treated WT control, mTOR KO and KI mice were lysed in a cold lysis buffer. Transposase reaction were performed for 30 min at 37 °C immediately after the nuclei preparation. The samples were purified using a Qiagen MinElute kit.
The ATAC-seq libraries were amplified using NEBnext PCR master mix followed by purified using Qiagen MinElute PCR Purification Kit (Qiagen, 28004), and then run on the Illumina sequencer HiSeq 2500.


title: TOF-DG1 - Day11


title: RNAseq_mTOR_KI_4

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to mm10 whole genome by Tophat with default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file.
Genome_build: mm10
Supplementary_files_format_and_content: fpkm_tracking  (contains the estimated expression values produced by Cufflinks)

extract_protocol:
HSC cells from poly(I:C)-treated WT control, mTOR KO and KI mice were sorted by FACS. RNA were extracted using miRNeasy Micro Kit (Qiagen, 217084).
RNA-seq libraries were prepared using Illumina TruSeq Stranded Total RNA Sample Preparation Kit.


title: TOF-DG1 - Day8


title: synovium from rat (rat ID #1) with sham surgery 2 weeks post-surgery

value: synovium

value: Sham Surgery


title: Control2 - Day7


title: Control1 - Day8


title: meniscus from rat (rat ID #1) with sham surgery 2 weeks post-surgery


title: RNAseq_mTOR_KI_3


title: mESC_TRE_3FLAG_Obox4_FLAG_rep1

description: CUT&RUN-enriched DNA


title: RNAseq_mTOR_KI_2


title: mESC_TRE_3FLAG_Obox4_FLAG_rep2

description: CUT&RUN-enriched DNA


title: mESC_TRE_3FLAG_Obox4_IgG

description: CUT&RUN-enriched DNA


title: Control1 - Day11


title: Control1 - Day7


title: Fibers, 15DPA3

status: Public on Aug 28 2023

city: Zhengzhou

first: yanyong

last: cao

state: henan

address: No. 116, Huayuan Road

country: China

institute: Henan Academy of Agricultural Sciences

data_processing:
Using the Illumina paired-end RNA-seq approach
we aligned reads of  all samples to the TM-1 reference genome (http://mascotton.njau.edu.cn/info/1054/1118.htm) using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Genome_build: TM-1
Supplementary_files_format_and_content: Excel file includes read counts and FPKM values for each Sample

organism: Gossypium hirsutum

source_name: 15DPA fibers

growth_protocol: We used Gossypium hirsutum strain 63, a standard system for genetics provided by the National Cotton Breeding Center of the Cotton Research Institute of the Chinese Academy of Agricultural Sciences (Zhengzhou, China).

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number > 7.0.
Approximately 10 μ g of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, using divalent cations, the poly (A) - or poly (A) + RNA fractions were fragmented into small pieces under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to the final cDNA library according to the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp ( ± 50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following of the merchant's recommended protocol.
The paired-end libraries was 300 bp ( ± 50 bp)

treatment_protocol: New roots, stems, young leaves, flowers (during the flowering period) and different stages of fibers during development were frozen in liquid nitrogen and stored at -80 °C until RNA was extracted for tissue expression analysis. The flowering day of cotton was labeled as 0 day and the next was labeled as 1st day, and so on. Samples of cotton fiber was obtained at the same position of cotton plant depending on the flowering time. The cotton tissues (80 mg leaves or flower tissue) were quickly frozen in liquid nitrogen immediately after collection and ground into fine powder with a mortar and pestle.

tag: strain

value: fibers

value: 15days post-anthesis (DPA)


title: RNAseq_ESC_Obox4_OE_0hr_rep1

tag: tissue

value: culture cell

value: ESC


title: RNAseq_mTOR_KI_1


title: Fibers, 5DPA2

source_name: 5DPA fibers

value: 5days post-anthesis (DPA)


title: Fibers, 15DPA2


title: cartilage from rat (rat ID #1) with medial meniscus transection surgery 2 weeks post-surgery


title: Fibers, 5DPA3


title: Fibers, 15DPA1


title: Fibers, 5DPA1


title: cartilage from rat (rat ID #1) with sham surgery 2 weeks post-surgery


title: F38, spleen, Triploid, Day3

city: Waterloo

first: Ivan

middle: Gregory

last: Cadonic

state: Ontario

address: 200 University Ave W, B1-171B

department: Biology

country: Canada

institute: University of Waterloo

data_processing:
Raw read files were initially run through Cutadapt (version 3.4 in Python 3.6.7) to remove the sequencing adapter (NEBnext 3SR adaptor for Illumina) and trim low-quality bases and reads. The Novaseq 6000 instrument uses two colour chemistry when encoding bases, so the cutadapt function “nextseq-trim” was used in place of the quality option with a cut-off of 28. Simultaneously, read lengths were filtered so that only reads between 18 and 35 bp (after adapter removal) remained.
Quality trimmed reads were then analyzed using the miARma-seq pipeline (v1.7.2) to generate read counts for each miRNA gene. Bowtie1 (version 1.1.2) was used to generate an index for the Ensembl genome (Ensembl release 105, Otsh_v1.0) that reads were aligned to with a seed length of 15 bases, 0 mismatches in the seed alignment and the optional parameters to report the best alignment (--best) and prevent rounding of phred scores (--nomaqround).
FeatureCounts (version 1.5.0-pl) was then used to generate a read count matrix containing the number of reads at each miRNA-gene loci for each individual sample.
Assembly: Ensembl Otsh_v1.0(GCA_002872995.1)
Supplementary files format and content: Cutadapt trimmed files are fastq format and contain reads after adaptor and quality trimming
Supplementary files format and content: FeatureCounts files (hg, hk, and sp) are tab separated file format and contain number of reads associated with each annotated Chinook salmon miRNA gene

organism: Oncorhynchus tshawytscha

source_name: spleen

growth_protocol: Full-sibling diploid  and triploid fish were transferred to separate 200 L tanks (8°C) and allowed to acclimate for 4 weeks prior to the start of the trial. Fish were handfed to satiety twice daily (Taplow Feeds) and maintained on a 12hr light:dark cycle.

extract_protocol:
Total RNA was extracted from each tissue using the mirVana miRNA isolation kit (Ambion, AM1560/1561). Flash-frozen tissues were ground over liquid nitrogen before following manufacturer's protocol without deviation.
The NEBNext Small RNA Library Prep (New England Biolabs, E7330) was used to generate libraries for each sample with RNA inputs depending on sample concentration (300 ng for hindgut and 100 ng for spleen/head kidney).

treatment_protocol: Ten fish for each ploidy were sampled to collect tissues (head kidney, spleen, and hindgut) prior to infection. The rest of the cohort of fish were then exposed to the pathogen to simulate an outbreak of Vibrio anguillarum . Individuals were sedated using diluted clove oil (0.1 mL/L of water) and received a 100 µL intraperitoneal injection (IP) of 4.0 × 10^5 CFU/mL of V. anguillarum  resuspended in sterile phosphate buffered saline (PBS). Fish were then moved to a recovery bath of aerated hatchery water (10°C) before transfer back to the original barrels. After 3 days of infection, another ten fish for each ploidy were sampled. Diluted clove oil (0.4 mL/L of water; Sigma-Aldritch, C8392) was used to terminally anesthetize all fish prior to tissue collection.

value: spleen

value: triploid

value: Day3 - Vibrio infected


title: Ctrl_6dpMI

city: Shanghai

first: Min

last: Zhang

state: Shanghai

address: 1678 Dongfang Road

department: Shanghai Children's Medical Center

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
CellRanger toolkit v2.1.0 was used to process the raw sequencing data. Reads were aligned to the mm10 genome build.
Genome_build: mm10
Supplementary_files_format_and_content: h5 files contain cell gene matrices

source_name: control_pooled endothelial cells and immune cells

extract_protocol:
The pooled endothelial cells and immune cells were loaded into the 10X Genomics Chromium system for library construction.
Each set of cell suspension was subjected to the GemCode Single Cell Instrument to generate single-cell gel beads in emulsion (GEMs), targeting for 8,000 cell yield. Following the lysis step, cDNA was synthesized and amplified using the Chromium Single Cell 3’ Reagent Kits v2 (10× Genomics, USA), as per the standard protocols provided by the manufacturer

tag: disease model

value: myocardial infarction

value: two-month-old

tag: genotype/variation

value: Control

value: heart

value: enriched CD31+ endothelial cells and CD45+ leucocytes


title: Tbx1cko_6dpMI

source_name: Tbx1cko_pooled endothelial cells and immune cells


title: F30, spleen, Diploid, Day3

tag: genotype

value: diploid


title: F28, spleen, Diploid, Day3

tag: treatment


title: F19, spleen, Triploid, Day0

value: Day0 - uninfected


title: F23, spleen, Diploid, Day3


title: F31, spleen, Triploid, Day3


title: F9, spleen, Diploid, Day0


title: F16, spleen, Triploid, Day0


title: F8, spleen, Diploid, Day0


title: F14, spleen, Triploid, Day0


title: F21, spleen, Diploid, Day3


title: F4, spleen, Diploid, Day0


title: F5, spleen, Diploid, Day0


title: F11, spleen, Triploid, Day0


title: F36, head kidney, Triploid, Day3

source_name: head kidney

value: head kidney


title: F38, head kidney, Triploid, Day3


title: F31, head kidney, Triploid, Day3


title: F30, head kidney, Diploid, Day3


title: F28, head kidney, Diploid, Day3


title: F23, head kidney, Diploid, Day3


title: F21, head kidney, Diploid, Day3


title: F36, spleen, Triploid, Day3


title: F32, spleen, Triploid, Day3


title: F14, head kidney, Triploid, Day0


title: F11, head kidney, Triploid, Day0


title: F9, head kidney, Diploid, Day0


title: F8, head kidney, Diploid, Day0


title: F5, head kidney, Diploid, Day0


title: F4, head kidney, Diploid, Day0


title: F36, hindgut, Triploid, Day3

source_name: hindgut

value: hindgut


title: F33, hindgut, Triploid, Day3


title: F38, hindgut, Triploid, Day3


title: F32, hindgut, Triploid, Day3


title: F34, hindgut, Triploid, Day3


title: F29, hindgut, Diploid, Day3


title: F32, head kidney, Triploid, Day3


title: F30, hindgut, Diploid, Day3


title: F28, hindgut, Diploid, Day3


title: F16, head kidney, Triploid, Day0


title: F19, hindgut, Triploid, Day0


title: F14, hindgut, Triploid, Day0


title: F24, hindgut, Diploid, Day3


title: F16, hindgut, Triploid, Day0


title: F19, head kidney, Triploid, Day0


title: F12, hindgut, Triploid, Day0


title: F23, hindgut, Diploid, Day3


title: F21, hindgut, Diploid, Day3


title: F10, hindgut, Diploid, Day0


title: F9, hindgut, Diploid, Day0


title: F8, hindgut, Diploid, Day0


title: F11, hindgut, Triploid, Day0


title: F5, hindgut, Diploid, Day0


title: F4, hindgut, Diploid, Day0


title: F1, hindgut, Diploid, Day0


title: F31, hindgut, Triploid, Day3


title: 73.12 GFAP P63 - RiboTag 5

city: Boston

first: Timothy

middle: M

last: O'Shea

state: MA

address: 44 Cummington Mall, ERB Room 521

department: Biomedical Engineering

institute: Boston University

data_processing:
The R1 and R2 FASTQ files from lanes 1 and 2 that were obtained directly from the Illumina NovaSeq S2 run were concatenated and cleaned-up using the Trimmomatic tool with default parameters in Galaxy.
Data was then aligned to the M. musculus (mm10) reference genome using the HISAT2 tool applying default parameters in Galaxy
Gene counts from the aligned datasets was performed using the featureCounts tool applying default parameters in Galaxy
Differential expressed gene (DEG) analysis on raw gene count data was conducted using Edge-R in Galaxy applying Benjamini and Hochberg p-value adjustment and TMM normalization
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw gene counts for every gene and every sample

source_name: Spinal Cord

extract_protocol:
spinal cord tissue samples were homogenized in supplemented homogenization buffer (50 mM Tris pH 7.4, 100 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM Dithiothreitol (DTT), 1X Protease inhibitors, 200 U/ml RNAsin, 100 mg/ml Cyclohexamide, 1 mg/ml Heparin) using 2mL glass Dounce tissue grinders (D8938-1SET, Sigma). Tissue homogenates were centrifuged to remove tissue debris before being incubated with Anti-HA.11 Epitope Tag Antibody (Biolegend, Cat# 901515) for 4 hours in a microcentrifuge tube on a microtube rotator kept at 4°C. At the end of 4 hours, IP solutions were combined with Pierce A/G Magnetic Beads (Thermofisher, #PI88803) and incubated overnight on a microtube rotator at 4°C. On the second day, magnetic beads were washed three times with high salt solution (50 mM Tris pH 7.4, 300 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM Dithiothreitol (DTT), 100 mg/ml Cyclohexamide). Unpurified RNA was collected from the magnetic beads by addition of RLT Plus buffer with BME and vigorous vortexing. RNA was then purified using RNeasy Plus Mini (for in vitro cell pellets) or Micro Kits (for spinal cord tissue) (QIAGEN Cat# 74134 and 74034). Total mRNA derived from the RiboTag IP was quantified using an automated electrophoresis bioanalyzer. RNA samples with RNA integrity numbers (RIN) greater than seven were processed for RNA-Sequencing. Sequencing was performed on poly-A selected libraries using Illumina NovaSeq S2 (housed in the UCLA Technology Center for Genomics & Bioinformatics) using pair end reads (2x50 – 50bp length) with an average of 50-100M reads per sample.
The workflow for library construction involved poly(A) RNA selection, RNA fragmentation and double-stranded cDNA synthesis using a mixture of random and oligo(dT) priming, followed by end repair to generate blunt ends, adaptor ligation, strand selection, and PCR amplification to produce the final library.
RNA-Seq (2x50 read length)

value: Spinal Cord

tag: Sex

value: Female

value: astrocytes

value: 73.12 GFAP Cre -RiboTag

tag: age


title: 73.12 GFAP P63 - Flow 5

value: flow


title: 73.12 GFAP P63 - Flow 4


title: F13, hindgut, Triploid, Day0


title: 73.12 GFAP P63 - Flow 3

value: Male


title: 73.12 GFAP P63 - RiboTag 1


title: 73.12 GFAP P63 - RiboTag 4


title: 73.12 GFAP P63 - Flow 2


title: 73.12 GFAP P63 - RiboTag 2


title: 73.12 GFAP P63 - Flow 1


title: 73.12 GFAP P35 - RiboTag 1


title: 73.12 GFAP P21 - RiboTag 2


title: 73.12 GFAP P14 - RiboTag 4


title: 73.12 GFAP P21 - RiboTag 4


title: Day 7 Parasites_HFF, scRNA seq

city: Riverside

first: Edward

last: Vizcarra

state: California

address: 900 University Ave

institute: UC Riverside

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: ME49 Toxoplasma Reference Genome
Supplementary files format and content: Tab-separated values files and matrix files

organism: Toxoplasma gondii

source_name: Purified from human foreskin fibroblast

extract_protocol:
Toxoplasma tissue cysts were purified from brain homogenate using a percoll density gradient. Tissue cysts were treated with pepsin-HCl mixture to excyst bradyzoites; Parasites that were cultured in human foreskin fibroblast or primary murine astrocytes were needle passed and run through a 3 μm filter on indicated timepoint. All parasites were used for scRNA seq.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, parasites were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: cell line

value: Purified from human foreskin fibroblast

value: parasite

value: ME49EW Strain


title: 73.12 GFAP P14 - RiboTag 3


title: DeltaUBP8_3READS_Rep2

city: Chapel Hill

first: Alexandra

last: Khitun

state: North Carolina

address: 250 Bell Tower Drive, 3244Genome Sciences Building

department: Chemistry

institute: UNC Chapel Hill

description: ubp8_2reps_3reads_RelativeCountsByPosition 1 to 400.txt

data_processing:
3'READS:
3' READS data was pre-processed and analyzed as reported in Geisberg et al., 2020. Reads were preprocessed to remove read adapters, and quantify initial Ts that could correspond to the poly(A) tail. Trimmed reads were mapped to the genome using Bowtie (Langmead et al., 2009) with a requirement for a perfect and unique sequence match.
Polyadenylation sites were identified where initial Ts in a mapped read (quantified in the previous steps) did not align to the genomic sequence. Polyadenylation sites up to 400nt after each ORF end were quantified.
NET-seq:
Data processing was performed according to the parameters and custom scripts outlined in Couvillion et al., 2022. The adapter sequence (ATCTCGTATGCCGTCTTCTGCTTG) was trimmed with cutadapt with the arguments: -O 3 -m 1 --length-tag ‘length=’. PrinSeq (http://prinseq.sourceforge.net/) was used to filter fastq files with the arguments: -no_qual_header -min_len 7 -min_qual_mean 20 -trim_right 1 -trim_ns_right 1 -trim_qual_right 20 -trim_qual_type mean -trim_qual_window 5 -trim_qual_step 1. Random hexamer linker  at the 5’ end of the read were trimmed before alignment to the genome, but were kept associated with the read for downstream analyses.
TopHat2 was used to align reads back to the SacCer3 genome (Kim et al., 2013) with the arguments: --read-mismatches 3 --read-gap-length 2 --read-edit-dist 3 --min-anchor-length 8 --splice-mismatches 1 --min-intron-length 50 --max-intron-length 1200 --max-insertion-length 3 --max-deletion-length 3 --num-threads --max-multihits 100 --library-type fr-firststrand --segment-mismatches 3 --no-coverage-search --segment-length 20 --min-coverage-intron 50 --max-coverage-intron 100000 --min-segment-intron 50 --max-segment-intron 500000 --b2-sensitive.  If molecular barcode sequences matched exactly to the genomic sequence next to the aligned read, the read was filtered out as a likely reverse transcription mispriming artifact. Pol II positions were mapped using a custom script described in Couvillion et al., 2022.
Assembly: SacCer3
Supplementary files format and content: tab-delimited text files,  polyadenylation positions for every nucleotide in the first 400 nt after yeast open reading frames
Supplementary files format and content: bigWig, read starts corresponding to Pol II position

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol:
3'READS: Yeast were grown in YPD at 30°C in a shaking incubator from an OD of 0.05 to mid-log phase  (OD of 0.6-0.8).
NET-seq:Yeast were grown in YPD at 30°C in a shaking incubator from an OD of 0.05 to mid-log phase  (OD of 0.6-0.8).

extract_protocol:
3'READS: Polyadenylation sites were detected using the 3'READS method (Jin, Y. et al., 2015). RNA was extracted  by hot acid phenol followed by Qiagen RNeasy purification.
3' READS libraries were prepared as previously described with 25µg total input RNA (Jin, Y. et al., 2015).
NET-seq: NET-seq samples were prepared as described previously (Churchman and Weissman,2012). Yeast grown to mid-log phase were isolated by filtration, and flash-frozen in liquid nitrogen. Frozen cell pellets were cryogenically lysed by six three-minute cycles of grinding in a cryomill . Pol II-RNA complexes were affinity purified using anti-FLAG agarose slurry.  .
NET-seq:  Isolation of nascent RNA and library construction for NET-seq samples was performed as described in Couvillion et al., (2022). Library concentration and size distribution was determined using a 2100 Agilent Bioanalyzer and qPCR quantitation with library-specific primer (TCCGACGATCATTGATGGTGCCTACAG).

value: yeast

value: RPB3::RPB3-3xFLAG NAT, UBP8::HIS3


title: DeltaRPB4_3READS_Rep2

description: rpb4_2reps_3reads_RelativeCountsByPosition 1 to 400.txt

value: RPB3::RPB3-3xFLAG NAT, RPB4::HIS3


title: DeltaRPB4_3READS_Rep1


title: DeltaUBP8_3READS_Rep1


title: Day 5 Parasites_HFF, scRNA seq

description: 10x Genomics


title: 73.12 GFAP P14 - RiboTag 2


title: 73.12 GFAP P63 - RiboTag 3


title: 73.12 GFAP P35 - RiboTag 2


title: Day 2 Parasites_HFF, scRNA seq

description: 10x Genomics


title: 73.12 GFAP P14 - RiboTag 1


title: Day 7 Parasites_Astrocyte, scRNA seq

description: 10x Genomics

source_name: Purified from primary murine astrocytes

value: Purified from primary murine astrocytes


title: 73.12 GFAP P7 - RiboTag 2


title: Day 5 Parasites_Astrocyte, scRNA seq

description: 10x Genomics


title: 73.12 GFAP P21 - RiboTag 1


title: 73.12 GFAP P3 - RiboTag 3


title: 73.12 GFAP P21 - RiboTag 3


title: Day 2 Parasites_Astrocyte, scRNA seq

description: 10x Genomics


title: 73.12 GFAP P7 - RiboTag 3


title: 73.12 GFAP P7 - RiboTag 1


title: 73.12 GFAP P3 - RiboTag 1


title: 73.12 GFAP P3 - RiboTag 2


title: 73.12 GFAP P0 - RiboTag 4


title: 73.12 GFAP P0 - RiboTag 3


title: 73.12 GFAP P0 - RiboTag 1


title: 73.12 GFAP P0 - RiboTag 2


title: 73.12 GFAP P35 - RiboTag 3


title: 73.12 GFAP P14 - RiboTag 5


title: 73.12 GFAP P35 - RiboTag 4


title: NTN_3M

city: Seoul

first: Donghwan

last: YUN

state: Jongno-gu

address: 103 Daehakro

country: South Korea

institute: Seoul National University Hospital

description: 10X Genomics

data_processing:
The purified libraries were quantified using quantitative PCR (qPCR) according to the manufacturer’s protocol (Sigma-Aldrich) and were qualified using the Agilent 4200 TapeStation (Agilent Technologies) and sequenced using HiSeqX (Illumina) with a read length of 28 bp for read 1 (cell barcode and UMI), an 10 bp index read (sample barcode), and a read length of 90 bp for read 2 (RNA read). The Cell Ranger pipeline (version 3.1.0; 10× Genomics) was used to process the raw data set.
Assembly: m10
Supplementary files format and content: h5 format

source_name: Kidney

extract_protocol:
After digesting kidneys with 0.2 mg/ml liberase (Roche) and 4 mg/ml DNase I at 37°C for 25 minutes in a shaking incubator, cells were filtered through a 70-μm and 40-μm strainer. Isolated cells were re-suspended in DMEM consist of 10% FBS.
Libraries were prepared using the chromium controller according to the 10× Chromium Next GEM Single Cell 3′ protocol (version 3.1; 10× Genomics).

treatment_protocol: For the NTN model, mice were preimmunized with 200 μg of sheep immunoglobulin G in Freund’s complete adjuvant via the intraperitoneal route, followed by 5 μL/g sheep nephrotoxic serum (Probetex Inc.) via intravenous injection 4 days later.  The mice were sacrificed at the indicated time points after reperfusion.

value: Kidney

value: 23 weeks

value: male

value: nephrotoxic nephritis model


title: 73.12 GFAP 14d SCI - Flow 5

value: Spinal Cord

value: SCI

tag: time


title: 73.12 GFAP 14d SCI - Flow 4

value: Female


title: 73.12 GFAP 14d SCI - RiboTag 5

value: astrocytes

value: 73.12 GFAP Cre -RiboTag


title: BoC122_CT6_primary resistant

type: RNA

city: Bochum

first: Stephan

middle: A

last: Hahn

address: Universitaetsstrasse 150

department: MGO

country: Germany

institute: Ruhr-University Bochum

description: mRNA expression

hyb_protocol: Samples were hybridized using Agilent 10x blocking agent and 25x fragmentation buffer, and 2xGEx hybridization buffer according to the manufacturer's instructions  for 17 hours at 65C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using standard settings

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE2_107_Sep09 and Grid: 026652_D_F_20100430) to obtain background subtracted and spatially detrended Processed Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: patient derived colon cancer xenograft tissue

label_protocol: 100 ng of total RNA were labeled using the QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, using T7 priming and MMLV-RT to generate cDNA. cRNA is then prepared using T7 RNA Polymerase according to the manufacturer's instructions, and labeled with  cyanine-5-CTP (Cy5)

growth_protocol: Three 1-3 mm tumor pieces of early passage xenograft tumors soaked in matrigel were implanted via standard technology subcutaneously on the dorsal flanks of nude mice (two implantation sites per mouse; nu/nu NMRI) to establish treatment and control tumor cohorts.

extract_protocol: Total RNA isolation from 25-30 (20mm) frozen xenograft tumor sections were isolates using the mirVana™ PARIS™ Kit (Applied Biosystems) according to the manufacture`s protocol. RNA integrity was analysed using standard RNA-gel electrophoresis. Total-RNA concentration and purity of total-RNA samples was measured with the NanoDrop 1000 spectrophotometer (NanoDrop Technologies/Thermo Scientific).

treatment_protocol: Nude mice were treated with cetuximab (25 mg/kg, twice weekly, i.p., Merck) and trametinib (0.5 mg/kg, five subsequent days per week, p.o., Hycultec) , treatment was initiated when tumor size reached approx. 100-200 mm³

tag: reponse

value: primary resistant


title: 73.12 GFAP 14d SCI - RiboTag 3


title: 73.12 GFAP 14d SCI - Flow 3

value: flow


title: 73.12 GFAP 14d SCI - RiboTag 4


title: BoC122_K3_untreated control

description: mRNA expression


title: BoC122_5dCT2_5 days cetuximab and trametinib

description: mRNA expression


title: BoC122_CT5_primary resistant

description: mRNA expression


title: BoC117F_CT6_primary resistant

description: mRNA expression


title: BoC117_CT7_primary resistant

description: mRNA expression


title: BoC117_5dCT2_5 days cetuximab and trametinib

description: mRNA expression


title: BoC109_CT6_primary resistant

description: mRNA expression


title: BoC109_K5_untreated control

description: mRNA expression


title: BoC137_K5_untreated control

description: mRNA expression

value: partial response


title: BoC117_K7_untreated control

description: mRNA expression


title: BoC109_CT2_primary resistant

description: mRNA expression


title: 73.12 GFAP 14d SCI - Flow 1


title: BoC122_5dCT1_5 days cetuximab and trametinib

description: mRNA expression


title: 73.12 GFAP 14d SCI - Flow 2


title: BoC109_5dCT2_5 days cetuximab and trametinib

description: mRNA expression


title: 73.12 GFAP 14d SCI - RiboTag 1


title: Aldh1l1 70d SCI - Flow 4

value: Aldh1l1-CreERT2 -RiboTag


title: Aldh1l1 70d SCI - RiboTag 4


title: Aldh1l1 70d SCI - RiboTag 3


title: Aldh1l1 70d SCI - Flow 3


title: Aldh1l1 70d SCI - Flow 2


title: BoC64_K1_untreated control

description: mRNA expression


title: BoC117_5dCT3_5 days cetuximab and trametinib

description: mRNA expression


title: Aldh1l1 70d SCI - Flow 1


title: Aldh1l1 70d SCI - RiboTag 2


title: BoC56_CT4_2_secondary resistant

description: mRNA expression

value: stable disease


title: 73.12 GFAP 14d SCI - RiboTag 2


title: BoC56_CT4_1_secondary resistant

description: mRNA expression


title: Aldh1l1 42d SCI - Flow 4


title: Aldh1l1 42d SCI - RiboTag 4


title: Aldh1l1 42d SCI - Flow 3


title: BoC51_CT6_primary resistant

description: mRNA expression


title: BoC56_5dCT1_5 days cetuximab and trametinib

description: mRNA expression


title: BoC51_5dCT1_1_5 days cetuximab and trametinib

description: mRNA expression


title: BoC51_CT5_primary resistant

description: mRNA expression


title: BoC51_5dCT1_2_5 days cetuximab and trametinib

description: mRNA expression


title: Aldh1l1 42d SCI - Flow 2


title: Aldh1l1 42d SCI - RiboTag 3


title: Aldh1l1 70d SCI - RiboTag 1


title: BoC2_CT6_secondary resistant

description: mRNA expression


title: BoC47_K7_untreated control

description: mRNA expression


title: BoC2_CT5_secondary resistant

description: mRNA expression


title: BoC56_5dCT2_5 days cetuximab and trametinib

description: mRNA expression


title: BoC2_K3_untreated control

description: mRNA expression


title: BoC51_K1_untreated control

description: mRNA expression


title: Aldh1l1 28d SCI - Flow 4


title: Aldh1l1 42d SCI - Flow 1


title: Aldh1l1 42d SCI - RiboTag 1


title: Aldh1l1 28d SCI - Flow 3


title: BoC2_5dCT1_5 days cetuximab and trametinib

description: mRNA expression


title: Aldh1l1 28d SCI - RiboTag 3


title: Aldh1l1 42d SCI - RiboTag 2


title: BoC2_5dCT2_ 5 days cetuximab and trametinib

description: mRNA expression


title: Aldh1l1 28d SCI - RiboTag 2


title: Aldh1l1 28d SCI - Flow 2


title: Aldh1l1 28d SCI - Flow 1


title: Aldh1l1 28d SCI - RiboTag 4


title: blood and endothelial cells, prior hospitalization, after venous stress test, patient 12 of this kind

first: Richard

last: Friedman

state: NY

address: 1130 St. Nicholas Av

department: Medicine

institute: Columbia University Irving  Medical Center

description: gene expression from blood and venous endothelial cells

hyb_protocol: According to manufacturer's protocol

scan_protocol: Arrays were washed, stained and scanned by GeneChip Scanner 300 7G according to the Affymetrix Expression Analysis technical manual. Affymetrix GCOS 1.4 was used as the image acquisition software. The signal, which represents the intensity of each gene, was extracted from the image. The target intensity value from each chip was scaled to 500.

data_processing: Normalization was performed with GCRMA

label: biotin

source_name: blood and venous endothelial cells

label_protocol: Biotin labeling of 10 micrograms of amplified RNA was performed using the TrueLabeling Kit (SuperArray Bioscience, Frederick, MD) according to the manufacturer's instructions.

extract_protocol: RNA was isolated with RNAqueous Micro Kit (Ambion Life Technologies, Grand Island, NY).

tag: prior hospitalization

value: yes

value: after


title: blood and endothelial cells, prior hospitalization, before venous stress test, patient 12 of this kind

value: before


title: Aldh1l1 28d SCI - RiboTag 1


title: blood and endothelial cells, no prior hospitalization, before venous stress test, patient 11 of this kind

value: no


title: blood and endothelial cells, no prior hospitalization, after venous stress test, patient 10 of this kind


title: blood and endothelial cells, no prior hospitalization, after venous stress test, patient 11 of this kind


title: blood and endothelial cells, no prior hospitalization, before venous stress test, patient 10 of this kind


title: blood and endothelial cells, no prior hospitalization, after venous stress test, patient 9 of this kind


title: Aldh1l1 14d SCI - RiboTag Male 4

value: Male


title: Aldh1l1 14d SCI - Flow Male 2


title: Aldh1l1 14d SCI - RiboTag Male 3


title: Aldh1l1 14d SCI - Flow Male 3


title: blood and endothelial cells, prior hospitalization, after venous stress test, patient 11 of this kind

value: female


title: Aldh1l1 14d SCI - Flow Male 1


title: Aldh1l1 14d SCI - RiboTag Male 2


title: blood and endothelial cells, no prior hospitalization, before venous stress test, patient 9 of this kind

value: male


title: Aldh1l1 14d SCI - Flow Male 4

value: Spinal Cord


title: Aldh1l1 14d SCI - RiboTag Male 1

value: SCI


title: Aldh1l1 14d SCI - RiboTag 4

value: Female


title: Aldh1l1 14d SCI - Flow 4


title: blood and endothelial cells, prior hospitalization, before venous stress test, patient 11 of this kind


title: blood and endothelial cells, prior hospitalization, before venous stress test, patient 10 of this kind


title: blood and endothelial cells, prior hospitalization, after venous stress test, patient 10 of this kind


title: blood and endothelial cells, no prior hospitalization, after venous stress test, patient 8 of this kind


title: Aldh1l1 14d SCI - Flow 3


title: blood and endothelial cells, no prior hospitalization, after venous stress test, patient 7 of this kind


title: blood and endothelial cells, no prior hospitalization, before venous stress test, patient 7 of this kind


title: Aldh1l1 14d SCI - RiboTag 3

value: astrocytes


title: Aldh1l1 14d SCI - Flow 2


title: Aldh1l1 14d SCI - RiboTag 2


title: Aldh1l1 14d SCI - Flow 1


title: blood and endothelial cells, no prior hospitalization, before venous stress test, patient 6 of this kind


title: Aldh1l1 5d SCI - RiboTag Male 4


title: blood and endothelial cells, prior hospitalization, after venous stress test, patient 9 of this kind


title: Aldh1l1 14d SCI - RiboTag 1


title: blood and endothelial cells, no prior hospitalization, after venous stress test, patient 6 of this kind


title: Aldh1l1 5d SCI - Flow Male 4


title: blood and endothelial cells, prior hospitalization, before venous stress test, patient 9 of this kind


title: blood and endothelial cells, no prior hospitalization, after venous stress test, patient 5 of this kind


title: blood and endothelial cells, no prior hospitalization, before venous stress test, patient 5 of this kind


title: Aldh1l1 5d SCI - Flow Male 3


title: blood and endothelial cells, no prior hospitalization, after venous stress test, patient 4 of this kind


title: Aldh1l1 5d SCI - RiboTag Male 3


title: blood and endothelial cells, no prior hospitalization, before venous stress test, patient 4 of this kind


title: blood and endothelial cells, no prior hospitalization, before venous stress test, patient 8 of this kind


title: Aldh1l1 5d SCI - Flow Male 2


title: Aldh1l1 5d SCI - RiboTag Male 2


title: blood and endothelial cells, prior hospitalization, after venous stress test, patient 8 of this kind


title: Aldh1l1 5d SCI - Flow Male 1


title: Aldh1l1 5d SCI - RiboTag Male 1


title: blood and endothelial cells, prior hospitalization, after venous stress test, patient 7 of this kind


title: blood and endothelial cells, prior hospitalization, before venous stress test, patient 8 of this kind


title: Aldh1l1 5d SCI - Flow 3


title: Aldh1l1 5d SCI - Flow 4


title: Aldh1l1 5d SCI - RiboTag 4


title: blood and endothelial cells, prior hospitalization, after venous stress test, patient 6 of this kind


title: blood and endothelial cells, prior hospitalization, before venous stress test, patient 6 of this kind


title: blood and endothelial cells, prior hospitalization, after venous stress test, patient 5 of this kind


title: blood and endothelial cells, prior hospitalization, before venous stress test, patient 5 of this kind


title: Aldh1l1 5d SCI - Flow 2


title: Aldh1l1 5d SCI - RiboTag 3


title: blood and endothelial cells, no prior hospitalization, after venous stress test, patient 3 of this kind


title: blood and endothelial cells, no prior hospitalization, before venous stress test, patient 3 of this kind


title: Aldh1l1 5d SCI - RiboTag 2


title: blood and endothelial cells, prior hospitalization, before venous stress test, patient 4 of this kind


title: Aldh1l1 5d SCI - Flow 1


title: Aldh1l1 5d SCI - RiboTag 1


title: blood and endothelial cells, prior hospitalization, before venous stress test, patient 7 of this kind


title: blood and endothelial cells, prior hospitalization, after venous stress test, patient 3 of this kind


title: Aldh1l1 2d SCI - Flow 4


title: Aldh1l1 2d SCI - RiboTag 5


title: Aldh1l1 2d SCI - Flow 3


title: blood and endothelial cells, prior hospitalization, before venous stress test, patient 3 of this kind


title: Aldh1l1 2d SCI - RiboTag 4


title: Aldh1l1 2d SCI - RiboTag 3


title: Aldh1l1 2d SCI - Flow 5


title: Faster_Netseq_Rep2

library_source: other

data_processing:
library strategy: NET-seq
3'READS:
3' READS data was pre-processed and analyzed as reported in Geisberg et al., 2020. Reads were preprocessed to remove read adapters, and quantify initial Ts that could correspond to the poly(A) tail. Trimmed reads were mapped to the genome using Bowtie (Langmead et al., 2009) with a requirement for a perfect and unique sequence match.
Polyadenylation sites were identified where initial Ts in a mapped read (quantified in the previous steps) did not align to the genomic sequence. Polyadenylation sites up to 400nt after each ORF end were quantified.
NET-seq:
Data processing was performed according to the parameters and custom scripts outlined in Couvillion et al., 2022. The adapter sequence (ATCTCGTATGCCGTCTTCTGCTTG) was trimmed with cutadapt with the arguments: -O 3 -m 1 --length-tag ‘length=’. PrinSeq (http://prinseq.sourceforge.net/) was used to filter fastq files with the arguments: -no_qual_header -min_len 7 -min_qual_mean 20 -trim_right 1 -trim_ns_right 1 -trim_qual_right 20 -trim_qual_type mean -trim_qual_window 5 -trim_qual_step 1. Random hexamer linker  at the 5’ end of the read were trimmed before alignment to the genome, but were kept associated with the read for downstream analyses.
TopHat2 was used to align reads back to the SacCer3 genome (Kim et al., 2013) with the arguments: --read-mismatches 3 --read-gap-length 2 --read-edit-dist 3 --min-anchor-length 8 --splice-mismatches 1 --min-intron-length 50 --max-intron-length 1200 --max-insertion-length 3 --max-deletion-length 3 --num-threads --max-multihits 100 --library-type fr-firststrand --segment-mismatches 3 --no-coverage-search --segment-length 20 --min-coverage-intron 50 --max-coverage-intron 100000 --min-segment-intron 50 --max-segment-intron 500000 --b2-sensitive.  If molecular barcode sequences matched exactly to the genomic sequence next to the aligned read, the read was filtered out as a likely reverse transcription mispriming artifact. Pol II positions were mapped using a custom script described in Couvillion et al., 2022.
Assembly: SacCer3
Supplementary files format and content: tab-delimited text files,  polyadenylation positions for every nucleotide in the first 400 nt after yeast open reading frames
Supplementary files format and content: bigWig, read starts corresponding to Pol II position

molecule: other

value: yeast

value: RPB3::RPB3-3xFLAG NAT, RPO21-E1103G


title: blood and endothelial cells, no prior hospitalization, before venous stress test, patient 2 of this kind


title: blood and endothelial cells, no prior hospitalization, after venous stress test, patient 1 of this kind


title: BoC56_K1_untreated control

description: mRNA expression


title: blood and endothelial cells, no prior hospitalization, after venous stress test, patient 2 of this kind


title: Faster_Netseq_Rep1


title: blood and endothelial cells, no prior hospitalization, before venous stress test, patient 1 of this kind


title: blood and endothelial cells, prior hospitalization, after venous stress test, patient 2 of this kind


title: BoC109_5dCT1_5 days cetuximab and trametinib

description: mRNA expression

value: primary resistant


title: Aldh1l1 2d SCI - Flow 2

value: flow


title: blood and endothelial cells, prior hospitalization, after venous stress test, patient 4 of this kind


title: Aldh1l1 2d SCI - RiboTag 2

value: Aldh1l1-CreERT2 -RiboTag


title: blood and endothelial cells, prior hospitalization, before venous stress test, patient 2 of this kind


title: blood and endothelial cells, prior hospitalization, before venous stress test, patient 1 of this kind


title: blood and endothelial cells, prior hospitalization, after venous stress test, patient 1 of this kind


title: Fast_Netseq_Rep2

value: RPB3::RPB3-3xFLAG NAT, RPO21-L1101S


title: Slow_Netseq_Rep2

value: RPB3::RPB3-3xFLAG NAT, RPO21-F1086S


title: Fast_Netseq_Rep1


title: Aldh1l1 Uninjured - Flow 4

value: Uninjured


title: Aldh1l1 2d SCI - RiboTag 1


title: Slow_Netseq_Rep1


title: Aldh1l1 Uninjured - RiboTag 4


title: BatchC_CD140- population from human fetal brain H [July2014_hfCD140-5n]

city: Rochester

first: Steven

last: Goldman

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

data_processing:
Raw FASTQ files were aligned to GRCh38 using Ensembl 95 gene annotations with STAR 2.5.4b in 2-pass mode across all samples
Reads were quantified with RSEM 1.3.1
Genome_build: GRCh38
Supplementary_files_format_and_content: gene count matrix - output from RSEM

extract_protocol:
Human brain samples were obtained under approved Institutional Review Board protocols from consenting patients at Strong Memorial Hospital at the University of Rochester.  Brain tissue was obtained from normal GW 18-24 cortical and/or VZ/SVZ dissections or adult white matter/cortex epileptic resections (18,19, and 27 years old for mRNA, 8, 20, 43, and 54 years old for miRNA).  Fetal GPC acquisition, dissociation and immunomagnetic sorting of A2B5+/PSA-NCAM- cells were as described (Windrem et al., 2004). GPCs were isolated from dissociated tissue using a dual immunomagnetic sorting strategy: depleting mouse anti-PSA-NCAM+ (Millipore, DSHB) cells, using microbead tagged rat anti-mouse IgM (Miltenyi Biotech), then selecting A2B5+ (clone 105; ATCC, Manassas, VA) cells from the PSA-NCAM- pool, as described (Windrem et al., 2004; Windrem et al., 2008). After sorting, cells were maintained for 1-14 days in DMEM-F12/N1 with 10 ng/ml bFGF and 20 ng/ml PDGF-AA. Alternatively  CD140a/PDGFRA-defined GPCs were isolated and sorted using MACS as described (Sim et al., 2011b), yielding an enriched population of CD140+ glial progenitor cells.
RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop) and RNA quality assessed with the Agilent Bioanalyzer 2100 (Agilent). For batch B, libraries were constructed with the SMART-Seq Ultra Low kit (Clontech) followed by the NexteraXT library preparation kit (Illumina). For batch C, libraries were constructed with the TruSeq RNA Library Prep Kit v2 (Illumina).

value: human fetal brain

tag: batch

value: BatchC

tag: cell type/population

value: CD140- population


title: WT_Netseq_Rep1

tag: cell type

value: RPB3::RPB3-3xFLAG NAT


title: Aldh1l1 2d SCI - Flow 1


title: Aldh1l1 Uninjured - Flow 3


title: BatchC_CD140- population from human fetal brain G [July2014_hfCD140-4n]


title: Aldh1l1 Uninjured - RiboTag 3


title: BatchC_CD140- population from human fetal brain F [July2014_hfCD140-3n]


title: Aldh1l1 Uninjured - RiboTag 1


title: Tet2_ChIP_INPUT

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

data_processing:
Preprocessing with PRINSEQ-lite (version 0.20.4)
Alignment to the mouse reference genome sequence (mm10) using BWA (version 0.7.17-r1188)
Processing with samtools (version 1.13)
Peak calling with MACS2 (version 2.1.0.20140616)
Normalized to CPM with bamCoverage from deeptools (version 3.5.1)
Assembly: mm10
Supplementary files format and content: BigWig: normalized coverage
Supplementary files format and content: Bed: called peaks

source_name: cell line

growth_protocol: RPMI + 10%FCS + P/S + Glu; 5 ng/ml mIL-3, 2 ug/ml Puro, 300 ug/ml G418

extract_protocol:
Monarch PCR & DNA Cleanup Kit (Cat#T1030L)
Libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB). The fragment size of the libraries was assessed using the NGS HS analysis kit and a fragment analyzer system (Agilent). The library concentrations were quantified with a KAPA Kit (Roche).

treatment_protocol: Doxycycline 1 µg/ml (48 h)

value: cell line

value: murine Cebpap30/p30

value: Doxycycline 1 µg/ml (48 h)


title: Aldh1l1 Uninjured - Flow 1

value: Spinal Cord

value: Female


title: Tet2_ChIP_2


title: Pancreas, CP

first: Jie

last: Tong

address: Siping road

institute: Tongji University

description: singlecellRNA-Seq

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:
 MT% < 20%;
 Cell Gene Number < Median Gene Number * 2;
 Cell Gene Number > 200.
PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mm10
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: Pancreas

extract_protocol: Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

value: Pancreas

value: Mouse pancreatic cell

tag: condition

value: Cae-induced acute pancreatitis

value: Cae treated


title: Tet2_ChIP_3


title: Pancreas, CP+EVs

description: singlecellRNA-Seq

value: Cae+EVs treated


title: BatchC_CD140- population from human fetal brain E [July2014_hfCD140-2n]


title: BatchC_CD140- population from human fetal brain D [July2014_hfCD140-1n]


title: Tet2_ChIP_1


title: WT_Netseq_Rep2

value: yeast


title: Aldh1l1 Uninjured - RiboTag 2

value: astrocytes

value: Aldh1l1-CreERT2 -RiboTag


title: Mutant SSCs

city: Sacramento

middle: H

last: Ambrosi

address: 2700 Stockton Blvd

institute: UC Davis

description:
SmartSeq2
gRDS_genlist.csv

data_processing:
demultiplexing using bcl2fastq2 2.18 (Illumina)
raw reads were further processed using skewer11 for 3′ quality-trimming, 3′ adaptor-trimming, and removal of degenerate reads (Jiang et al., 2014).
trimmed reads were then mapped to the human genome GRCm38.p6.gencode.vM20 using STAR 2.4 (Dobin et al., 2013)
When aligning female data the entire Y chromosome was masked, while only the PAR regions on the Y chromosome were masked for male data. If sex was unknown PAR-masking was used.
counts for gene and transcript reads were calculated using RSEM 1.2.21 (Li and Dewey, 2011)
Assembly: GRCm38.p6.gencode.vM20
Supplementary files format and content: gRDS_genlist.csv (raw gene counts)

source_name: long bone

growth_protocol: freshly purified cells without prior in vitro culture

extract_protocol:
Bone tissue with mechanically and enzymatically digested, stained with antibodies, and cell populations purified via FACS.
SmartSeq2 pipeline (Picelli et al.)
SmartSeq2 single cell RNA sequencing

treatment_protocol: no treatment

value: SSC

value: long bone

value: 7 weeks


title: Wild type SSCs

description:
SmartSeq2
gRDS_genlist.csv


title: BatchC_CD140+ population from human fetal brain G [July2014_hfCD140-4p]

value: human fetal brain

value: BatchC

value: CD140+ population


title: WGBS Cebpa-/p30 Tet2-/- s7

city: Copenhagen

first: Bo

last: Porse

address: Ole Maaløes Vej 5, 4

department: Finsen Laboratory and BRIC

country: Denmark

institute: University of Copenhagen

data_processing:
Raw reads were quality-assessed using FastQC v0.11.7, then trimmed and filtered with Trim Galore v0.4.3 with default parameters.
Trimmed reads were aligned to mouse genome assembly GRCm38 (mm10) using Bismark v0.19.1 with option --non_directional (other parameter left at default values; this used Bowtie2 and the in silico bisulfite converted reference genomes with -q --score-min L,0,-0.2 --ignore-quals).
Alignments were deduplicating using deduplicate_bismark.
Methylation information for individual cytosines was extracted using bismark_methylation_extractor (--cytosine_report --comprehensive --gzip).
Assembly: GRCm38/mm10
Supplementary files format and content: Bismark's genome-wide cytosine methylation output, tab-delimited with the following columns: <chromosome>  <position>  <strand>  <count methylated>  <count non-methylated>  <C-context>  <trinucleotide context>

source_name: AML blasts

extract_protocol:
DNA was isolated from 1*10^6 sorted cells using DNeasy Blood and tissue kit (#69504 Qiagen) according to the manufacturer’s instructions and fractionated using a Bioruptor. Bisulfite conversion of DNA was done according to manufacturers’ instructions using EZ-DNA Methylation gold Kit (#D5005 Zymo Research). Quality of bisulfite treated DNA was assessed by RNA 6000 Pico Kit (#5067-1513 Agilent) on a Bioanalyzer 2100 (Agilent).
Libraries of bisulfite converted DNA were prepared using Pico Methyl-Seq Library Prep Kit (#D5455 Zymo Research) according to manufacturer’s instructions and the final concentration and quality of the libraries was assessed using Qubit™ dsDNA HS Assay Kit (#Q32854 Thermo Fisher Scientific) and High Sensitivity DNA Analysis Kit (#5067-4626 Agilent) on a Bioanalyzer. Duplexed libraries were sequenced on a NextSeq 500 (Illumina) using NextSeq 500 High Output v2 Kit (75 cycles; #FC-404-2005 Illumina).

value: AML blasts from bone marrow


title: Aldh1l1 Uninjured - Flow 2

value: Spinal Cord

value: flow

value: Uninjured


title: 1745-MC-31

city: Toledo

first: Jennifer

last: Nguyen

address: 3000 Arlington Ave

department: Neuroscience

institute: University of Toledo

data_processing:
MultiQC
Trimmomatic - 0.36
hisat2
samtools
Assembly: GRCm38
Supplementary files format and content: raw counts as csv

source_name: brain

extract_protocol:
RNA extraction was performed on homogenized half brain tissue aliquots using the (QIAGEN, Germantown, MD) RNeasy Plus Micro Kit.
The Total RNA Library was prepared using the (Illumina, San Diego, CA)  Illumina NovaSeq (S4) 300 cycle flow cell and reagent kit.

value: brain

tag: agent

value: control


title: 1745-MC-29

value: deltamethrin


title: 1745-MC-27


title: 1745-MC-28


title: BatchC_CD140+ population from human fetal brain F [July2014_hfCD140-3p]


title: WGBS Cebpa-/p30 Tet2-/- s8

tag: strain


title: 1745-MC-26

tag: tissue


title: BatchC_CD140+ population from human fetal brain H [July2014_hfCD140-5p]


title: WGBS Cebpa-/p30 Tet2-/- s5


title: 1745-MC-25


title: 1745-MC-24


title: WGBS Cebpa-/p30 Tet2+/+ s24


title: 1745-MC-23


title: BatchC_CD140+ population from human fetal brain D [July2014_hfCD140-1p]


title: 1745-MC-22


title: BatchB_A2B5+ population from human fetal brain 3 [fP_A_Plus_3]

value: BatchB

value: A2B5+ population


title: WGBS Cebpa-/p30 Tet2+/+ s23


title: 1745-MC-30


title: 1745-MC-21


title: 1745-MC-20


title: 1745-MC-19


title: BatchB_A2B5+ population from human fetal brain 2 [fP_A_Plus_2]