title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 24 h, AR Ab, rep1

value: AR (Santa Cruz, # sc-816)


title: COHP_46932_484_TET_OFF_B_5wks

status: Public on Nov 02 2023

type: SRA

city: Duarte

first: Denis

last: OMeally

state: California

address: 1500 E Duarte Rd

department: Arthur Riggs Diabetes & Metabolism Research Institute

country: USA

institute: City of Hope

description: cml_mrna_processed_1tpm_in_5_samples.tsv.gz

library_source: transcriptomic

data_processing:
nf-core RNASeq pipeline version 3.7
Trimmed reads were mapped using STAR to the GRCm39 reference (Genbank accession GCA_000001635.9) amended with the human BCR-ABL1 fusion gene sequence (Genbank accession EF158045.1) using GENCODE annotation Release m28
Each library was subjected to extensive quality control, including estimation of library complexity, gene body coverage, and duplication rates, among other metrics detailed in the pipeline repository
Transcript abundance was estimated across genomic features using Salmon and merged into a matrix of pseudocounts per million transcripts (TPM) per gene for each sample. BCR-ABL1 transcript abundance was measured by counting reads that spanned the fusion boundary
Assembly: GCA_000001635.9
Supplementary files format and content: tab delimited file includes Salmon pseudocounts for each sample (TPM)

molecule: total RNA

organism: Mus musculus

source_name: PBMC

growth_protocol: Inducible transgenic SCLtTA/BCR-ABL mice of B6 background were maintained on tetracycline (tet) water at 0.5 g/L. Tet withdrawal (tet-off) results in expression of BCR-ABL and generation of a CML-like disease in these mice with a median survival of approximately 10 weeks after induction of BCR-ABL, which recapitulates human CP CML.

extract_protocol:
Total RNA was extracted from whole blood using the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany); quality and quantity were estimated using a BioAnalyser (Agilent, Santa Clara, CA). Samples with a RIN > 4.0 were included.
Sequencing libraries were constructed using the KapaHyper with RiboErase (Kapa Biosystems, Wilmington, MA) and are reverse stranded.

treatment_protocol: Six to eight weeks old male and female SCLtTA/BCR-ABL mice were randomly divided into 4 groups: control (Tet on, n=3 mice), CML (Tet off, n=6 mice), Tet Off-On (TOTO; Tet off 6 weeks then Tet on for 12 weeks, n=4 mice), TKI [Tet off 6 weeks then TKI (Nilotinib, 50mg/kg, oral gavage, daily) treatment 4 weeks, n=7 mice]. Blood was collected from these mice weekly, i.e., before BCR-ABL induction (t = 0) and weekly after induction up to 18 weeks (t = 1 to 18) or when the mouse developed leukemia and became moribund, whichever event occurred first.

tag: mouse id

tag: sample weeks

tag: batch

tag: tissue

value: PBMC

tag: strain

tag: Sex

value: M

tag: genotype

value: tTA+/-, BCR-ABL+/-

tag: treatment


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 12 h, AR Ab, rep2

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

library_source: genomic

data_processing:
Reads were mapped to the GRCh38 human genome reference using Bowtie2.
ChIP-Seq peak calling was performed with MACS v2.2.7.1. with default parameters.
Assembly: GRCh38
Supplementary files format and content: MACS output file containing peak locations and fold enrichment.

molecule: genomic DNA

organism: Homo sapiens

source_name: R1-AD1 FLAGHA-H3F3A, DAXX KO

growth_protocol: Cells were propogated in RPMI-1640 medium suplemented with 10% FBS, 1X penicillin/streptomycin at  5% CO2, 37C . Cells were plated in RPMI-1640 without phenol-red, suplemented with 10%CSS, 72 h before the experiment.

extract_protocol:
Cells were fixed with 1% formaldehyde in PBS for 10 min at RT, quenched with glycine (f.c. 0.125 M) for 5 min. After cell lysis chromatin was sheared by Diagenode Bioraptor Pico with peak enrichment at 200 bp.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs)

treatment_protocol: Cells were treated with 1 nM R1881 for 4, 12 or 24 hours

tag: cell line

value: R1-AD1 FLAGHA-H3F3A, DAXX KO

tag: cell type

value: Prostate cancer

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, DAXX KO

tag: chip antibody


title: 4H,rep2

city: La Jolla

first: Songpeng

last: Zu

state: CA

address: 9500 Gilman Dr

department: Department of Cellular and Molecular Medicine

institute: University of California San Diego

data_processing:
Paired-end sequencing reads were demultiplexed and the cell index transferred to the read name. Sequencing reads were aligned to mm10 reference genome using bwa.
We combined the sequencing reads to fragments with the function make_fragment_file in SnapATAC2. , and for each fragment we followed the quality controls: 1) Keep only fragments with quality scores MAPQ > 30; 2) remove PCR duplicates. Reads were also sorted based on cell barcodes in read names, and shifted +4 bp for positive strand and -5 bp for negative strand to correct the 9-bp duplication induced from Tn5 transposase.
We used the function filter_cells in SnapATAC2 to calculate TSSenrichment (TSSe). Nuclei with >=1,000 uniquely mapped fragments and TSSe >= 10 were filtered for each of 234 samples by following the ENCODE ATAC-seq data standards and process pipeline(https://www.encodeproject.org/atac-seq/). We used the function filter_cells in SnapATAC2 to filter out cells.
We applied a modified version of Scrublet to remove potential doublets for every sample independently using SnapATAC2. Firstly, we used the function of add_tile_matrix to add the 500-bp genomic bin features, then used the function of select_features to filter out the features with the frequencies along the samples lower than 0.5% or higher than 99.5%. Then applied the function of scrublet in SnapATAC2 to get the doublet scores. The parameter expected_doublet_rate is set to 0.08, which is based on our previous experiment on the snATAC-seq pipeline. Barcodes with the scrublet scores larger than 0.5 will be treated as potential doublets, and then removed from our analysis.
Assembly: Genome_build: mm10 (GRCm38)
Supplementary files format and content: SnapATAC2 HDF5 matrix files (cells with the raw fragments, 500bp bmat)

source_name: brain

extract_protocol:
Adult C57BL/6J male mice were purchased from Jackson Laboratories. Brains were extracted from 56-63 day old mice and sectioned into 600 µm coronal sections along the anterior-posterior axis in ice-cold dissection media. Specific brain regions were dissected according to the Allen Brain Reference Atlas (Wang, Q. et al. The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas. Cell (2020). https://doi.org:10.1016/j.cell.2020.04.007). For each region, dissected brain tissues were pooled from 2-31 male C57BL/6J mice  to obtain enough nuclei for single nucleus ATAC-seq for each biological replica, and two biological replicas were performed.
Brain nuclei were pelleted with a swinging bucket centrifuge (500g, 5 min, 4 °C; 5920R, Eppendorf). Nuclei pellets were resuspended in 1 ml nuclei permeabilization buffer (5% BSA, 0.2% IGEPAL-CA630, 1 mM DTT and cOmpleteTM, EDTA-free protease inhibitor cocktail (Roche) in PBS) and pelleted again (500g, 5 min, 4 °C; 5920R, Eppendorf). Nuclei were resuspended in 500 μl high-salt tagmentation buffer (36.3 mM Tris-acetate (pH 7.8), 72.6 mM potassium-acetate, 11 mM Mg-acetate, 17.6% dimethylformamide) and counted using a haemocytometer. Concentration was adjusted to 1,000–4,500 nuclei per 9 μl, and 1,000–4,500 nuclei were dispensed into each well of a 96-well plate. For tagmentation, 1 μl barcoded Tn5 transposomes26 were added using a BenchSmart 96 (Mettler Toledo), mixed five times, and incubated for 60 min at 37 °C with shaking (500 rpm). To inhibit the Tn5 reaction, 10 μl of 40 mM EDTA was added to each well with a BenchSmart 96 (Mettler Toledo) and the plate was incubated at 37 °C for 15 min with shaking (500 rpm). Next, 20 μl 2× sort buffer (2% BSA, 2 mM EDTA in PBS) were added using a BenchSmart 96 (Mettler Toledo). All wells were combined into a FACS tube and stained with 3 μM Draq7 (Cell Signaling). Using a SH800 (Sony), 20 nuclei were sorted per well into eight 96-well plates (total of 768 wells, 30,720 nuclei total, 15,360 nuclei per sample) containing 10.5 μl EB (25 pmol primer i7, 25 pmol primer i5, 200 ng BSA (Sigma). If processing two samples per day, tagmentation was performed with different sets of barcodes in separate 96 well plates. After tagmentation nuclei from individual plates were pooled together. Preparation of sort plates and all downstream pipetting steps were performed on a Biomek i7 Automated Workstation (Beckman Coulter). After the addition of 1 μl 0.2% SDS, samples were incubated at 55 °C for 7 min with shaking (500 rpm). Then, 1 μl 12.5% Triton X-100 was added to each well to quench the SDS. Next, 12.5 μl NEBNext High-Fidelity 2 × PCR Master Mix (NEB) were added and samples were amplified by PCR (72 °C 5 min, 98 °C 30 s, (98 °C 10 s, 63 °C 30 s, 72 °C 60 s) × 11 or 12 cycles, held at 12 °C). After PCR, all wells were combined. Libraries were purified according to the MinElute PCR Purification Kit manual (Qiagen) using a vacuum manifold (QIAvac 24 plus, Qiagen) and size selection was performed with SPRI Beads (Beckmann Coulter, 0.55x and 1.5x). Libraries were purified one more time with SPRI Beads (Beckmann Coulter, 1.5x). Libraries were quantified using a Qubit fluorimeter (Life Technologies) and the nucleosomal pattern was verified using a Tapestation (High Sensitivity D1000, Agilent). Libraries generated with indexing version 1 were sequenced on a HiSeq2500 sequencer (Illumina) using custom sequencing primers, 25% spike-in library and following read lengths: 50 + 43 + 37 + 50 (Read1 + Index1 + Index2 + Read2). Libraries generated with indexing version 2 were sequenced on a Libraries were sequenced on a HiSeq 4000 (Illumina) or a NovaSeq 6000 (Illumina) with these settings:  50 + 10 + 12 + 50 (Read1 + Index1 + Index2 + Read2).

value: brain

tag: tissue region

value: PAL

tag: number of_animals_pooled

value: Male

tag: age

value: 8-9 weeks old

tag: library type

value: ATAC-seq


title: COHP_46931_484_TET_OFF_B_4wks


title: MiE-5

city: Jacksonville

first: Yingxue

last: Ren

address: 4500 San Pablo Rd S

institute: Mayo Clinic

library_source: transcriptomic single cell

data_processing:
The single cell sequence preprocessing was performed using the standard 10x Genomics Cell Ranger Single Cell Software Suite (v3.0.0).
Raw sequencing data were demultiplexed, aligned to the mouse genome mm10, and the reads aligned to each gene were counted. Cell filtration, normalization, clustering and differential expression analyses were performed using Seurat v.4.0.
Assembly: mm10
Supplementary files format and content: matix files

source_name: cortex

extract_protocol:
Mice were transcardially perfused with PBS and the cortical tissues were quickly dissected and enzymatically digested using the Neural Tissue Dissociation kit (P) (Cat#130-092-628, Myltenyi Biotec) at 37˚C in the gentleMACS™ Octo Dissociator with Heaters (Myltenyi Biotec). The myelin was then removed using magnetic bead separation (Myelin Removal Beads II, Cat#130-096-733, Myltenyi Biotec). After myelin removal, samples were subjected to red blood cell removal (Cat.# 130-094-183, Miltenyi Biotec), followed by dead cell removal  (Cat. #130-090-101, Miltenyi Biotec) according to the manufacturer’s instructions. The final cell pellet was suspended in Ca/Mg-free PBS supplemented with 0.5% FBS for downstream analysis. In all samples, more than 90% of the cells were viable based on trypan blue examination.
Libraries were prepared using the Chromium platform (10x Genomics) with the 3′ gene expression (3′ GEX) V3 kit with a targeted input of ~ 6,000 cells per sample following the manufacturer’s instructions.

tag: group


title: MiE-4


title: 3E,rep1

value: OLF


title: 4H,rep1


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 4 h, AR Ab, rep 2


title: COHP_46930_484_TET_OFF_B_3wks


title: COHP_46929_484_TET_OFF_B_2wks


title: MiE-2


title: MiE-3


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 4 h, AR Ab, rep 1


title: MiE-1


title: R1-AD1 FLAGHAH3F3A cells, DAXX KO, AR Ab, rep2

value: EtOH


title: 5F,rep1

value: STR


title: 5F,rep2


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, AR Ab, rep1


title: COHP_46927_484_TET_OFF_B_0wks


title: MiE-6


title: COHP_46926_545_TET_OFF_ON_A_18wks

value: F


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 24 h, AR Ab, rep2

source_name: R1-AD1 FLAGHA-H3F3A

value: R1-AD1 FLAGHA-H3F3A

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene


title: mNGF_2 (biol rep 2)

city: Durham

first: Liuyang

last: Wang

state: NC

address: 213 Research Drive

institute: Duke University

data_processing:
RNA-seq data were processed using the fastp toolkit to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads with default parameter. Only bases with quality ≥20 and only reads that were ≥20nt after trimming were kept for further analysis.
Reads were mapped to mouse genome reference combining the GRCm38.  STAR software was used to align reads to reference genome. Reads were kept for subsequent analysis if they mapped to a single genomic location. Reads with mappiing quality <20 were excluded. Gene counts were measured using the featureCounts.
Assembly: GRCm38
Supplementary files format and content: Tao_NGF_featurecount_matrix.txt: Reads mapped to human GRCm38, featurecount was used to count reads per gene per sample, tab-delimited txt file

source_name: spleen of C57BL/6 mice

growth_protocol: CD8+ T cells were isolated by MACS from 6-8 week old C57BL/6 mice, and activated by plate-bound anti-CD3/28 antibodies. T cells were culutred in T cell specific media.

extract_protocol:
Total RNA was extrated using a kit from ZYMO RESEARCH (Direct-zol RNA miniprep, cat. No. R2052) according to the manufacturer’s instructions and dissolved in RNase-free water.
Sequencing libraries were prepared using the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s protocol. Libraries were sequenced using an Illumina HiSeq machine and paired-end reads were generated.

treatment_protocol: 72 hr after anti-CD3/28 stimulation, activated CD8+ T cells were further treated by 200 ng/ml recombinant murine NGF for another 24 hr. Cells were then collected for bulk RNA-seq.

value: spleen of C57BL/6 mice

value: primary T cell

value: CD8+T cells

value: WT

value: NGF treatment


title: mNGF_1 (biol rep 1)


title: 1C,rep1


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 12 h, AR Ab, rep1

value: R1-AD1 FLAGHA-H3F3A, DAXX KO

value: Prostate cancer

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, DAXX KO

value: AR (Santa Cruz, # sc-816)


title: C_3 (biol rep 3)

value: CD8 T cells

value: Control


title: COHP_46925_545_TET_OFF_ON_A_16wks

value: PBMC

value: tTA+/-, BCR-ABL+/-


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 24 h, AR Ab, rep1


title: 1C,rep2

value: brain

value: OLF

value: Male

value: 8-9 weeks old

value: ATAC-seq


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 12 h, AR Ab, rep2

value: R1-AD1 FLAGHA-H3F3A

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene


title: C_2 (biol rep 2)

value: spleen of C57BL/6 mice

value: primary T cell

value: CD8+T cells

value: WT


title: COHP_46924_545_TET_OFF_ON_A_12wks

value: F


title: COHP_46923_545_TET_OFF_ON_A_8wks


title: COHP_46928_484_TET_OFF_B_1wks

value: M


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 4 h, AR Ab, rep 2

value: Prostate cancer

value: AR (Santa Cruz, # sc-816)


title: COHP_46922_545_TET_OFF_ON_A_7wks

value: PBMC


title: COHP_46921_545_TET_OFF_ON_A_6wks

value: tTA+/-, BCR-ABL+/-


title: 5B,rep1

value: brain

value: Isocortex


title: mNGF_3 (biol rep 3)

value: NGF treatment


title: C_1 (biol rep 1)

value: Control


title: Nko4_1

source_name: Melanoma cell line

growth_protocol: B16F10 cells were subcutaneously injected into C57BL/6J mice. Total RNA was extracted from melanoma tissues on day 15 and analyzed by RNA-seq.

treatment_protocol: CRISPR/Cas9 technology was used to generate NGF knockout stable cell lines.

value: Melanoma cell line

value: Melanoma

value: NGF-/-

value: Total RNA from melanoma cells


title: 5B,rep2

value: Male

value: 8-9 weeks old

value: ATAC-seq


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 12 h, AR Ab, rep1

value: R1-AD1 FLAGHA-H3F3A

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 4 h, AR Ab, rep 1

value: Prostate cancer


title: Nko2_1


title: COHP_46919_545_TET_OFF_ON_A_4wks

value: F


title: Nko3_1


title: 2E,rep1

value: OLF


title: 5H,rep2

value: PAL


title: 5H,rep1

value: brain


title: R1-AD1 FLAGHAH3F3A cells, AR Ab, rep2

value: AR (Santa Cruz, # sc-816)

value: EtOH


title: R1-AD1 FLAGHA-H3F3A cells, AR Ab, rep1


title: Nko1_1


title: 4A,rep1

value: Isocortex


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 24 h, H3K27Ac Ab, rep2

source_name: R1-AD1 FLAGHA-H3F3A, HIRA KO

value: R1-AD1 FLAGHA-H3F3A, HIRA KO

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, HIRA KO


title: C4_1

value: Melanoma cell line

value: Melanoma

value: WT


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 24 h, H3K27Ac Ab, rep1


title: COHP_46916_545_TET_OFF_ON_A_1wks

value: PBMC

value: tTA+/-, BCR-ABL+/-


title: COHP_46917_545_TET_OFF_ON_A_2wks


title: 4A,rep2

value: Male

value: 8-9 weeks old

value: ATAC-seq


title: COHP_46918_545_TET_OFF_ON_A_3wks

value: F


title: C3_1

value: Total RNA from melanoma cells


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 12 h, H3K27Ac Ab, rep2

value: Prostate cancer


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 4 h, H3K27Ac Ab, rep 2


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 12 h, H3K27Ac Ab, rep1


title: C2_1


title: C1_1


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 4 h, H3K27Ac Ab, rep 1


title: Carboplatin_MC38_2

city: SOUTH SAN FRANCISCO

first: Kobe

last: Yuen

address: 1 DNA WAY

department: Oncology Biomarker Development

institute: Genentech

data_processing:
RNA-sequencing data were analyzed using HTSeqGenie in BioConductor.
Reads with low nucleotide qualities (70% of bases with quality <23) or rRNA and adapter contamination were removed
Filtered reads were aligned to the reference genomes GRCh38 (for human) and GRCm38 (for mouse) using GSNAP
Assembly: GRCh38; GRCm38
Supplementary files format and content: Tab delimited files with raw counts for each sample

growth_protocol: Cell lines were cultured with RPMI 1640 medium supplemented with 2mM L-Glutamine, 10% FBS and 1% PenStrep

extract_protocol:
Total RNA extracted using RNEasy mini kit (Qiagen) according to manufacturer instructions.
0.1 μg of total RNA was used as an input material for library preparation using TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA). Size of the libraries was confirmed using 4200 TapeStation and High Sensitivity D1K screen tape (Agilent Technologies, Santa Clare, CA) and their concentration was determined by a quantitative PCR-based method using Library quantification kit (KAPA Biosystems, Wilmington, MA). The libraries were multiplexed and sequenced on Illumina HiSeq4000 (Illumina, San Diego, CA) to generate 30 million single-end 50 base pair reads.

treatment_protocol: Cells were treated with various concentrations of cisplatin or carboplatin for 24 hours, with and without ATR inhibitor (VE-821, 1 µM)

value: Colon cacner

value: Carboplatin


title: Carboplatin_MC38_1


title: COHP_46913_483_TET_OFF_ON_A_16wks


title: COHP_46912_483_TET_OFF_ON_A_12wks


title: Cisplatin_MC38_2

value: Cisplatin


title: 4F,rep1

value: brain

value: OLF


title: R1-AD1 FLAGHAH3F3A cells, HIRA KO, H3K27Ac Ab, rep2

value: R1-AD1 FLAGHA-H3F3A, HIRA KO

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, HIRA KO

value: EtOH


title: 4F,rep2


title: COHP_46911_483_TET_OFF_ON_A_8wks


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, H3K27Ac Ab, rep1


title: Cisplatin_MC38_1


title: COHP_46910_483_TET_OFF_ON_A_7wks


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 24 h, H3K27Ac Ab, rep2

value: R1-AD1 FLAGHA-H3F3A, DAXX KO

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, DAXX KO


title: CD4 T cells, OT2-pMan-2-batch2

city: Chicago

first: Jeffrey

last: Hubbell

state: Illinois

address: 5640 S. Ellis Ave

institute: University of Chicago

description:
count_protein_coding_kallisto_batch2.txt
S16

data_processing:
Fastq files were generated using bcl2fastq
kallisto (v0.46.1) was used to quantify abundances of transcripts from the fastq files.
Count tables were generated using R package tximport to import transcript-level estimates from kallisto output and summarize them at gene level
Assembly: GRCm38.97
Supplementary files format and content: tab-delimited text file includes matrix table with raw gene count values for each sample

molecule: polyA RNA

source_name: CD4 T cells

extract_protocol:
Spleens and lymph nodes were pooled. OT-I and OT-II were sorted into Trizol using fluorescence activated cell sorting (FACS) and frozen at-80. RNA was extracted (Qiagen), and three mice were pooled per replicate.
Pooled samples were converted to cDNA using SmartSeq protocol

treatment_protocol: At 1 day post adoptive transfer of OTI and OTII cells, mice received either 5ug p(Man)-OVA, the molar equivalent of OVA,  or saline

value: OT-II

value: pMan

value: prophylactic batch 2


title: CD4 T cells, OT2-pMan-1-batch2

description:
count_protein_coding_kallisto_batch2.txt
S15


title: COHP_46920_545_TET_OFF_ON_A_5wks

value: PBMC

value: tTA+/-, BCR-ABL+/-


title: COHP_46909_483_TET_OFF_ON_A_6wks

value: F


title: COHP_46915_545_TET_OFF_ON_A_0wks


title: COHP_46908_483_TET_OFF_ON_A_5wks


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 12 h, H3K27Ac Ab, rep2

value: Prostate cancer


title: COHP_46907_483_TET_OFF_ON_A_4wks


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 24 h, H3K27Ac Ab, rep1


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 12 h, H3K27Ac Ab, rep1


title: CD4 T cells, OT2-OVA-2-batch2

description:
count_protein_coding_kallisto_batch2.txt
S12

value: OVA


title: CD4 T cells, OT2-OVA-1-batch2

description:
count_protein_coding_kallisto_batch2.txt
S11


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 4 h, H3K27Ac Ab, rep 2


title: KDF donor 3, 8kPa

city: London

first: John

last: Connelly

state: London

address: 4 Newark Street

department: Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

data_processing:
Sequencing reads were trimmed and aligned to the human genome (Hg19) using the Galaxy platform
Differential gene expression and principal components analysis was performed using DESEQ2 with Seqmonk
Assembly: hg19
Supplementary files format and content: comma separated file of raw feature counts for each sample

source_name: skin

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS and 1% pen-strep at 37C and 5% CO2

extract_protocol:
RNA was isolated using the Qiagen Rneasy micro kit
Library preparation was performed by Lexogen Gmbh, QuantSeq 3' mRNA Library Preparation kit

treatment_protocol: Cells were cultured on polyacrylamide gels of 8 or 214 kPa elastic moduli for 24 hours

tag: individual

value: donor 3

value: skin

value: dermal fibroblast

value: keloid

value: WT

value: 8 kPa gels


title: KDF donor 2, 214kPa

value: donor 2

value: 214 kPa gels


title: CD4 T cells, OT2-Saline-2-batch2

description:
count_protein_coding_kallisto_batch2.txt
S10

value: Saline


title: KDF donor 3, 214kPa


title: COHP_46906_483_TET_OFF_ON_A_3wks

tag: mouse id


title: COHP_46905_483_TET_OFF_ON_A_2wks

tag: sample weeks


title: R1-AD1 FLAGHAH3F3A cells, DAXX KO, H3K27Ac Ab, rep2

value: R1-AD1 FLAGHA-H3F3A, DAXX KO

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, DAXX KO

value: EtOH


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 4 h, H3K27Ac Ab, rep 1


title: KDF donor 1, 214kPa

value: donor 1


title: COHP_46904_483_TET_OFF_ON_A_1wks

tag: batch

value: PBMC

value: tTA+/-, BCR-ABL+/-


title: CD8 T cells, OT1-pMan-2-batch2

description:
count_protein_coding_kallisto_batch2.txt
S08

source_name: CD8 T cells

value: OT-I

value: pMan

value: prophylactic batch 2


title: COHP_46903_483_TET_OFF_ON_A_0wks

tag: tissue

value: F


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, H3K27Ac Ab, rep1

value: Prostate cancer


title: CD8 T cells, OT1-OVA-2-batch2

description:
count_protein_coding_kallisto_batch2.txt
S04

tag: strain

value: OVA


title: COHP_46902_482_TET_OFF_ON_A_18wks

tag: Sex


title: CD8 T cells, OT1-OVA-1-batch2

description:
count_protein_coding_kallisto_batch2.txt
S03


title: NDF donor 3, 214kPa

value: donor 3

value: skin

value: dermal fibroblast

value: normal

tag: genotype

value: WT


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, R1881, 24 h, H3K27Ac Ab, rep1

source_name: R1-AD1 FLAGHA-H3F3A, AR KO

value: R1-AD1 FLAGHA-H3F3A, AR KO

value: FLAG-HA knock-in 5' ORF of H3F3A gene, AR KO

tag: treatment


title: NDF donor 2, 214kPa

value: donor 2

tag: cell line

value: 214 kPa gels


title: COHP_46900_482_TET_OFF_ON_A_12wks

value: PBMC


title: CD8 T cells, OT1-Saline-2-batch2

description:
count_protein_coding_kallisto_batch2.txt
S02

tag: cell type

value: Saline


title: NDF donor 3, 8kPa

value: 8 kPa gels


title: CD4 T cells, OT2-Saline-1-batch2

description:
count_protein_coding_kallisto_batch2.txt
S09

value: OT-II


title: COHP_46899_482_TET_OFF_ON_A_8wks

value: tTA+/-, BCR-ABL+/-


title: CD8 T cells, OT1-pMan-2

description:
count_protein_coding_kallisto_batch1.txt
S35

value: OT-I

value: pMan

value: prophylactic batch 1


title: NDF donor 2, 8kPa


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, R1881, 12 h, H3K27Ac Ab, rep1

value: Prostate cancer

tag: chip antibody


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, R1881, 12 h, H3K27Ac Ab, rep2


title: CD4 T cells, OT2-pMan-3

description:
count_protein_coding_kallisto_batch1.txt
S36


title: KDF donor 2, 8kPa

value: skin

value: keloid


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, R1881, 4 h, H3K27Ac Ab, rep 2


title: COHP_46898_482_TET_OFF_ON_A_7wks

value: F


title: NDF donor 1, 214kPa

value: donor 1

value: dermal fibroblast

value: normal

value: WT


title: KDF donor 1, 8kPa


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, R1881, 24 h, H3K27Ac Ab, rep2

value: R1-AD1 FLAGHA-H3F3A, AR KO

value: FLAG-HA knock-in 5' ORF of H3F3A gene, AR KO


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, R1881, 4 h, H3K27Ac Ab, rep 1


title: COHP_46897_482_TET_OFF_ON_A_6wks

value: PBMC


title: COHP_46901_482_TET_OFF_ON_A_16wks


title: CD4 T cells, OT2-pMan-1

description:
count_protein_coding_kallisto_batch1.txt
S34


title: COHP_46896_482_TET_OFF_ON_A_5wks


title: CD4 T cells, OT2-OVA5-2

description:
count_protein_coding_kallisto_batch1.txt
S32

value: OVA


title: HepG2_R1_Late S Fraction

city: Minneapolis

first: Juan Carlos

last: Rivera-Mulia

state: MN

address: 420 Washington Ave SE

department: Department of Biochemistry, Molecular Biology and Biophysics

institute: University of Minnesota Medical School

data_processing:
Reads were mapped to corresponding genome (hg38) using BWA.
Coverage data are calculated from mapped reads using samtools and bedtools
Base 2 log of early to late coverage ratio was calculated in 10kb windows
Log 2 ratio data were quantile normalized using R package preprocessCore
Data were loess smoothed and binned into 10kb windows
Assembly: hg38
Supplementary files format and content: processed data are 10kb windows in hg38 genome build.
Library strategy: Repli-seq

source_name: HepG2 cell line

growth_protocol: HepG2 cells were cultured in Minimum Essential Medium (MEM) media (Sigma cat. No M5650-1L) supplemented with 10% FBS (Sigma cat. No F2442).

extract_protocol:
Genome-wide replication timing profiles were constructed as previously described (Rivera-Mulia et al., 2022). Briefly, cells were pulse labeled with BrdU, separated into early andlate S-phase fractions by flow cytometry based on DNA content (mesured by flurescence intensity of cell permeant dyes), and processed by NGS.
Sequencing libraries of BrdU-substituted DNA from early and late fractions were prepared by KAPA HyperPlus library preparation kit (Roche Cat. No.  07958978001).

value: HepG2 cell line

tag: s-phase fraction

value: Late S fraction

tag: replicate


title: COHP_46895_482_TET_OFF_ON_A_4wks

value: tTA+/-, BCR-ABL+/-


title: R1-AD1 FLAGHAH3F3A cells, AR KO, H3K27Ac Ab, rep2

value: EtOH


title: CD4 T cells, OT2-OVA5-3

description:
count_protein_coding_kallisto_batch1.txt
S33

value: OT-II

value: prophylactic batch 1


title: HepG2_R1_Early S Fraction

value: Early S fraction


title: CD4 T cells, OT2-saline-3

description:
count_protein_coding_kallisto_batch1.txt
S27

value: Saline


title: COHP_46894_482_TET_OFF_ON_A_3wks

description: cml_mrna_processed_1tpm_in_5_samples.tsv.gz

value: F


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 24 h, H3K27Ac Ab, rep2

value: R1-AD1 FLAGHA-H3F3A

value: Prostate cancer

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene


title: COHP_46893_482_TET_OFF_ON_A_2wks


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 24 h, H3K27Ac Ab, rep1


title: HMVEC NS rep 3

city: new york city

first: Carmen

last: Argmann

state: NY

address: 1425 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine

description:
BFX17_expr.txt
HMV-3

data_processing:
Raw reads were aligned to the human reference genome hg38 using TopHat2
rpkm gene expression was calculated for each replicate using Cufflinks.
HTSeq was used to count the gene features
DESeq2 to call differential genes between non-senescent and senescent samples.
Assembly: GRCh38
Supplementary files format and content: tab delimited text files containing RPKM values for each sample

source_name: microvaculature endothelial cells

growth_protocol: Human lung fibroblasts IMR-90 cells (ATCC, CCL-186) were cultured in DMEM medium (VWR VWRL0101-0500) supplemented with 10% fetal bovine serum (VWR). Human Umbilical Vein Endothelial Cells (HUVEC, Lonza C2519A) were cultured in EGM-2 Bulletkit (Lonza, CC-3162). Human Microvascular Endothelial Cells (HMVEC, Lonza CC-2527) were cultured in EGM-2 MV Bulletkit (Lonza, CC-3202). Renal Proximal Tubule Epithelial Cells (RPTEC, Lonza CC-2553) were cultured in REGM Bulletkit (Lonza, CC-3190). Adipose-derived Stem Cells (ADSC, Lonza PT-5006) were cultured in ADSC Bulletkit (Lonza, PT-4505). All cell culture media included 100 I.U./mL of penicillin streptomycin, and cells were maintained at 37°C in an atmosphere of 5% CO2 and 3% O2 (except where indicated as 20% O2). Senescence was induced by irradiation, chemicals, or transduction with an oncogene. Irradiation was used at 10 Gy (Precision X-Ray, X-RAD 320) and chemicals were added at the following concentrations: bleomycin (15 µg/mL, 24 hours), oligomycin (16 nM, 7 days), antimycin (80 nM, 7 days) and rotenone (100 nM, 14 days). All chemicals were obtained from SelleckChem, dissolved in DMSO, and added to the culture medium. DMSO vehicle control was used at 0.01 % v/v. Oncogene induced senescence was done in hTERT immortalized IMR-90 (IMR90) cells with lentiviral particles generated from the pLVX-TetOnePuro (Takara, 634847) with either GFP or RasV12 cloned into the EcoRI/BamHI sites. Cells were grown as described above with addition of 1 µg/ml doxycycline hyclate (Sigma, D9891) and daily media changes over 7 days. Cells were then incubated in media for three days, followed by media change to DMEM supplemented with 0.1% FBS and 10 µg/mL insulin (Thermo, 12585014). Control IMR90 hTERT cells were cultured in absence of puromycin. In all cases, replicates were cultured independently at senescence induction. One or more replicates were used for senescence induction assays. Three replicates were processed for RNA-seq in most cases. Five replicates were processed for RNA-seq in the case of treatment with bleomycin, oligomycin and antimycin as well as two of the four irradiated IMR-90 experiments.

extract_protocol:
Cells were washed and directly lysed in Trizol (Thermo, 15596018).
total RNA was incubated with mRNA capture beads in order to remove contaminating ribosomal RNA from the sample. The resulting poly(A)-captured mRNA was then fragmented. First-strand cDNA synthesis was performed using reverse transcriptase and random primers in the presence of Actinomycin D, followed by second-strand cDNA synthesis with DNA polymerase I and RNaseH. Double-stranded cDNA was end-repaired and A-tailed for subsequent adaptor ligation. Indexed adaptors were ligated to the A-tailed cDNA. Enrichment by PCR was performed to generate the final cDNA sequencing library.

treatment_protocol: For all IMR90 experiments, serum was reduced from 20 to 0.2% 48 hrs before collection

value: microvaculature endothelial cells

value: normal


title: CD4 T cells, OT2-saline-1

description:
count_protein_coding_kallisto_batch1.txt
S25


title: CD4 T cells, OT2-saline-2

description:
count_protein_coding_kallisto_batch1.txt
S26


title: HMVEC NS rep 2

description:
BFX17_expr.txt
HMV-2


title: HMVEC NS rep 1

description:
BFX17_expr.txt
HMV-1


title: NDF donor 1, 8kPa

value: donor 1

value: skin

value: dermal fibroblast

value: WT

value: 8 kPa gels


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 12 h, H3K27Ac Ab, rep2


title: COHP_46891_482_TET_OFF_ON_A_0wks

value: PBMC

value: tTA+/-, BCR-ABL+/-


title: COHP_46892_482_TET_OFF_ON_A_1wks


title: CD4 T cells, OT2-pMan-2

description:
count_protein_coding_kallisto_batch1.txt
S17

value: OT-II

value: pMan


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 12 h, H3K27Ac Ab, rep1


title: COHP_46889_476_TET_OFF_ON_A_16wks

value: M


title: HMVEC Sen IR rep 3

description:
BFX17_expr.txt
HMV-SnC-3

tag: agent

value: 10Gy ionising radiation 14 days prior collection


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, H3K27Ac Ab, rep1

value: R1-AD1 FLAGHA-H3F3A, AR KO

value: FLAG-HA knock-in 5' ORF of H3F3A gene, AR KO

value: EtOH


title: HMVEC Sen IR rep 1

description:
BFX17_expr.txt
HMV-SnC-1


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 4 h, H3K27Ac Ab, rep 1

value: R1-AD1 FLAGHA-H3F3A

value: Prostate cancer

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene


title: COHP_46888_476_TET_OFF_ON_A_12wks


title: HMVEC Sen IR rep 2

description:
BFX17_expr.txt
HMV-SnC-2

value: microvaculature endothelial cells

value: normal


title: CD8 T cells, OT1-OVA5-3

description:
count_protein_coding_kallisto_batch1.txt
S15

value: OT-I

value: OVA

value: prophylactic batch 1


title: CD8 T cells, OT1-OVA5-2

description:
count_protein_coding_kallisto_batch1.txt
S14


title: HUVEC NS rep 3

description:
BFX17_expr.txt
HUV-3

source_name: Umbilical Vascular endothelial cell

value: Umbilical Vascular endothelial cell


title: R1-AD1 FLAGHAH3F3A cells, H3K27Ac Ab, rep2


title: COHP_46887_476_TET_OFF_ON_A_8wks

value: PBMC

value: tTA+/-, BCR-ABL+/-


title: HUVEC NS rep 2

description:
BFX17_expr.txt
HUV-2


title: R1-AD1 FLAGHA-H3F3A cells, H3K27Ac Ab, rep1


title: CD8 T cells, OT1-pMan-3

description:
count_protein_coding_kallisto_batch1.txt
S18

value: pMan


title: HUVEC NS rep 1

description:
BFX17_expr.txt
HUV-1


title: COHP_46886_476_TET_OFF_ON_A_7wks

value: M


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 24 h, HA Ab, rep2

value: R1-AD1 FLAGHA-H3F3A, HIRA KO

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, HIRA KO

value: HA (BioLegend, # 901502)


title: CD8 T cells, OT1-saline-3

description:
count_protein_coding_kallisto_batch1.txt
S09

value: Saline


title: CD8 T cells, OT1-saline-2

description:
count_protein_coding_kallisto_batch1.txt
S08


title: COHP_46885_476_TET_OFF_ON_A_6wks


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 4 h, H3K27Ac Ab, rep 2

value: R1-AD1 FLAGHA-H3F3A


title: COHP_46890_476_TET_OFF_ON_A_18wks


title: CD8 T cells, OT1-pMan-1

description:
count_protein_coding_kallisto_batch1.txt
S16


title: HUVEC Sen IR rep 2

description:
BFX17_expr.txt
HUV-SnC-2

value: 10Gy ionising radiation 14 days prior collection


title: COHP_46884_476_TET_OFF_ON_A_5wks


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 12 h, HA Ab, rep2

value: Prostate cancer


title: HUVEC Sen IR rep 3

description:
BFX17_expr.txt
HUV-SnC-3


title: YW3-32

city: New York

first: Joseph

last: Castellano

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
Trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner (v.2.5.2b)
Gene hit counts were calculated by using featureCounts from the Subread package (v.1.5.2)
Assembly: mm10
Supplementary files format and content: comma separated values file includes raw counts for each sample

source_name: hippocampus, male, WT

extract_protocol:
RNA from frozen hippocampi was isolated using RNAeasy Mini Kit (Qiagen) and submitted to Genewiz for RIN/Qubit quality control who recommended isolation of 0.5-2ug RNA for downstream processing
Library preparation with paired-end 150 base pair sequencing on an Illumina HiSeq performed by GENEWIZ

value: hippocampus

value: male

value: WT


title: COHP_46883_476_TET_OFF_ON_A_4wks


title: HUVEC Sen IR rep 1

description:
BFX17_expr.txt
HUV-SnC-1

value: normal


title: COHP_46882_476_TET_OFF_ON_A_3wks


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 12 h, HA Ab, rep1


title: YW3-31


title: RPTEC NS rep 3

description:
BFX17_expr.txt
RPT-3

source_name: Renal proximal tubule epithelial cell

value: Renal proximal tubule epithelial cell


title: YW3-30

source_name: hippocampus, female, KO

value: female

value: KO


title: RPTEC NS rep 2

description:
BFX17_expr.txt
RPT-2


title: COHP_46881_476_TET_OFF_ON_A_2wks

source_name: PBMC

value: PBMC

value: tTA+/-, BCR-ABL+/-


title: YW3-28

source_name: hippocampus, female, WT


title: RPTEC NS rep 1

description:
BFX17_expr.txt
RPT-1


title: R1-AD1 FLAGHAH3F3A cells, HIRA KO, HA Ab, rep2

value: EtOH


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, HA Ab, rep1

value: R1-AD1 FLAGHA-H3F3A, HIRA KO


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 24 h, HA Ab, rep1

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, HIRA KO


title: RPTEC Sen IR rep 3

description:
BFX17_expr.txt
RPT-SnC-3


title: YW3-27


title: COHP_46879_476_TET_OFF_ON_A_0wks

value: M


title: COHP_46914_483_TET_OFF_ON_A_18wks

value: F


title: COHP_45015_541_TET_OFF_B_18wks


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 24 h, HA Ab, rep2

source_name: R1-AD1 FLAGHA-H3F3A, DAXX KO

value: R1-AD1 FLAGHA-H3F3A, DAXX KO

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, DAXX KO

value: HA (BioLegend, # 901502)


title: COHP_46880_476_TET_OFF_ON_A_1wks


title: CD8 T cells, OT1-saline-1

description:
count_protein_coding_kallisto_batch1.txt
S07

value: OT-I

value: Saline

value: prophylactic batch 1


title: RPTEC Sen IR rep 2

description:
BFX17_expr.txt
RPT-SnC-2

value: normal

value: 10Gy ionising radiation 14 days prior collection


title: YW3-26

value: hippocampus

value: male

value: WT


title: COHP_45014_541_TET_OFF_B_17wks

value: PBMC

value: tTA+/-, BCR-ABL+/-


title: RPTEC Sen IR rep 1

description:
BFX17_expr.txt
RPT-SnC-1

value: Renal proximal tubule epithelial cell


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 24 h, HA Ab, rep1

value: Prostate cancer


title: COHP_45013_541_TET_OFF_B_16wks


title: YW3-25

value: female

value: KO


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 4 h, HA Ab, rep 2

value: R1-AD1 FLAGHA-H3F3A, HIRA KO

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, HIRA KO


title: YW3-24


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 12 h, HA Ab, rep2

value: R1-AD1 FLAGHA-H3F3A, DAXX KO

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, DAXX KO

value: HA (BioLegend, # 901502)


title: ADSC NS rep 3

description:
BFX17_expr.txt
ADS-3

source_name: Adipose derived stem cell

value: Adipose derived stem cell


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 4 h, HA Ab, rep 1


title: COHP_45012_541_TET_OFF_B_15wks

value: F


title: YW3-29


title: ADSC NS rep 2

description:
BFX17_expr.txt
ADS-2

value: normal


title: YW3-23

value: hippocampus


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 12 h, HA Ab, rep1


title: ADSC NS rep 1

description:
BFX17_expr.txt
ADS-1


title: COHP_45011_541_TET_OFF_B_14wks


title: YW3-22

value: male


title: ADSC Sen IR rep 3

description:
BFX17_expr.txt
ADS-SnC-3

value: 10Gy ionising radiation 14 days prior collection


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 4 h, HA Ab, rep 2


title: YW3-21

value: WT


title: ADSC Sen IR rep 2

description:
BFX17_expr.txt
ADS-SnC-2


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 4 h, HA Ab, rep 1


title: YW3-20

source_name: hippocampus, male, KO


title: COHP_45010_541_TET_OFF_B_13wks

value: PBMC

value: tTA+/-, BCR-ABL+/-


title: COHP_45009_541_TET_OFF_B_12wks


title: COHP_45008_541_TET_OFF_B_11wks


title: R1-AD1 FLAGHAH3F3A cells, DAXX KO, HA Ab, rep2

value: Prostate cancer

value: EtOH


title: COHP_45007_541_TET_OFF_B_10wks


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, HA Ab, rep1


title: ADSC Sen IR rep 1

description:
BFX17_expr.txt
ADS-SnC-1


title: IMR90 NS DMSO rep 5

description:
BFX36_expr.txt
DMSO-5

source_name: Lung Fibroblast

value: Lung Fibroblast


title: COHP_45006_541_TET_OFF_B_9wks


title: IMR90 NS DMSO rep 4

description:
BFX36_expr.txt
DMSO-4


title: YW3-18

value: KO


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, R1881, 24 h, HA Ab, rep1

value: R1-AD1 FLAGHA-H3F3A, AR KO

value: FLAG-HA knock-in 5' ORF of H3F3A gene, AR KO


title: COHP_45005_541_TET_OFF_B_8wks


title: IMR90 NS DMSO rep 3

description:
BFX36_expr.txt
DMSO-3


title: YW3-16

value: female


title: YW3-15


title: IMR90 NS DMSO rep 2

description:
BFX36_expr.txt
DMSO-2


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, R1881, 12 h, HA Ab, rep2

value: HA (BioLegend, # 901502)


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, R1881, 12 h, HA Ab, rep1


title: COHP_45003_541_TET_OFF_B_6wks


title: IMR90 NS DMSO rep 1

description:
BFX36_expr.txt
DMSO-1


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, R1881, 4 h, HA Ab, rep 2


title: IMR90 NS Ras rep 3

description:
Control for Ras
BFX06_expr.txt
HS-D12-Ctl-neg-RNA-Rep-3

value: hTERT immortalised

tag: tag

value: stably transduced with inducible RasV12


title: YW3-12


title: YW3-11


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, R1881, 4 h, HA Ab, rep 1


title: COHP_45002_541_TET_OFF_B_5wks

value: F


title: YW3-19

value: hippocampus


title: IMR90 NS Ras rep 2

description:
Control for Ras
BFX06_expr.txt
HS-D12-Ctl-neg-RNA-Rep-2

tag: group


title: R1-AD1 FLAGHAH3F3A cells, AR KO, HA Ab, rep2


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, R1881, 24 h, HA Ab, rep2


title: COHP_45001_541_TET_OFF_B_4wks


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, HA Ab, rep1


title: IMR90 NS Ras rep 1

description:
Control for Ras
BFX06_expr.txt
HS-D12-Ctl-neg-RNA-Rep-1


title: COHP_45000_541_TET_OFF_B_3wks


title: YW3-9


title: IMR90 NS Qui Set E rep 3

description:
Control for rotenone and IR Set E
BFX02_expr.txt
IMR90-CTRL-1-R3

value: normal


title: COHP_45004_541_TET_OFF_B_7wks


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 24 h, HA Ab, rep2

source_name: R1-AD1 FLAGHA-H3F3A

value: R1-AD1 FLAGHA-H3F3A

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene


title: COHP_44999_541_TET_OFF_B_2wks

value: PBMC


title: YW3-8


title: IMR90 NS Qui Set E rep 2

description:
Control for rotenone and IR Set E
BFX02_expr.txt
IMR90-CTRL-1-R2


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 24 h, HA Ab, rep1


title: COHP_44998_541_TET_OFF_B_1wks

value: tTA+/-, BCR-ABL+/-


title: YW3-7

value: male

value: WT


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 12 h, HA Ab, rep2

value: Prostate cancer


title: YW3-14

value: KO


title: YW3-6


title: COHP_44997_541_TET_OFF_B_0wks


title: YW3-10


title: YW3-5


title: IMR90 NS Qui Set D rep 5

description:
Control for IR Set D
BFX36_expr.txt
NS-5

value: Lung Fibroblast


title: IMR90 NS Qui Set D rep 4

description:
Control for IR Set D
BFX36_expr.txt
NS-4


title: COHP_44995_490_TET_ON_C_17wks

description: cml_mrna_processed_1tpm_in_5_samples.tsv.gz

value: M


title: YW3-4

value: female


title: YW3-3


title: IMR90 NS Qui Set D rep 3

description:
Control for IR Set D
BFX36_expr.txt
NS-3


title: IMR90 NS Qui Set D rep 2

description:
Control for IR Set D
BFX36_expr.txt
NS-2


title: COHP_44994_490_TET_ON_C_16wks


title: YW3-2


title: COHP_44991_490_TET_ON_C_13wks


title: YW3-1


title: COHP_44992_490_TET_ON_C_14wks


title: COHP_44993_490_TET_ON_C_15wks


title: IMR90 NS Qui Set E rep 1

description:
Control for rotenone and IR Set E
BFX02_expr.txt
IMR90-CTRL-1-R1


title: POG-treated and POG-treated TSPCs from 18-month-old rats,biological rep2

type: RNA

city: Beijing

first: Yan

last: Liu

state: Beijing

address: No. 22 South Street, Zhongguan Street

department: Peking University School and Hospital of Stomatology

country: China

institute: Peking university

hyb_protocol: Following labeling, cDNA was hybridized on a GeneChip Rat Gene 2.0.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Command Console installed in the GeneChip® Scanner 3000 7G.

data_processing: The data was analyzed with the Robust Multichip Analysis (RMA) algorithm, using the Affymetrix default analysis settings.

label: biotin

organism: Rattus norvegicus

source_name: Rattus norvegicus tendon stem/progenitor cells

label_protocol: Biotinylated cDNA was prepared from 150 ng total RNA according to the manufacturer’s standard protocol (Affymetrix).

growth_protocol: The concentration of 20 μM POG was added to the culture medium of rTSPCs from 18-month-old rats. An equal amount of the vehicle control dimethyl sulfoxide (DMSO) was added in the control group to exclude the influence of solvent

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: TSPCs were collected for further total RNA extraction.

value: POG-treated TSPCs until Passage 12

value: tendon stem/progenitor cells


title: IMR90 NS Qui Set C rep 3

description:
Control for IR Set C
BFX17_expr.txt
IMR-LS-3


title: COHP_44996_490_TET_ON_C_18wks


title: IMR90 NS Qui Set D rep 1

description:
Control for IR Set D
BFX36_expr.txt
NS-1


title: IMR90 NS Qui Set C rep 2

description:
Control for IR Set C
BFX17_expr.txt
IMR-LS-2


title: DMSO-treated and POG-treated TSPCs from 18-month-old rats,biological rep1

value: DMSO-treated TSPCs until Passage 12


title: POG-treated and POG-treated TSPCs from 18-month-old rats,biological rep1


title: COHP_44990_490_TET_ON_C_12wks


title: IMR90 NS Qui Set C rep 1

description:
Control for IR Set C
BFX17_expr.txt
IMR-LS-1


title: COHP_44989_490_TET_ON_C_11wks


title: DMSO-treated and POG-treated TSPCs from 18-month-old rats,biological rep2


title: AF-TD-TED-2

first: Katia

last: Corano Scheri

state: IL

address: 300 E. Superior St.

department: Ophthalmology, Feinberg School of Medicine

institute: Northwestern University

description: 10x Genomics

data_processing:
Raw sequencing data, in base call format (.bcl) was demultiplexed using Cell Ranger (version 4.0.0) from 10x Genomics, converting the raw data into FASTQ format.
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Preretinal fibrovascular membrane

extract_protocol:
Post-surgery, PDR fibrovascular membranes were placed in balanced salt solution (BSS) and stored on ice for transportation. For dissociation, membranes were transferred to a 500µL solution of 0.22µm filter sterilized 1x Dulbecco’s Phosphate Buffered Saline (DPBS) with calcium and magnesium (Life Technologies, Carlsbad, CA) containing 2mg/mL Collagenase Type I (Worthington, Lakewood, NY). Samples were incubated at 370C for 30 minutes with gently trituration every 10 minutes. Samples were then spun down at 400g for 8 minutes at 40C and cell pellets were resuspended in 500µL 1X DPBS without calcium and magnesium (Life Technologies, Carlsbad, CA), 1% bovine serum albumen (BSA, citation), and 2mM EDTA and stored on ice until further processing.
Single cell libraries were generated using a Chromium Single Cell 3’ v3 kit (10x Genomics). RNA Quality and quantity were assessed using an Agilent Bio-analyzer. RNA-Seq libraries were prepared using Illumina mRNA TruSEQ kits following manufacturer’s instructions.

value: Preretinal fibrovascular membrane

tag: age

tag: treatments

value: Laser panretinal photocoagulation

tag: disease

value: Diabetes Mellitus 2


title: AF-TD-FAW-2

description: 10x Genomics

value: F

value: Preop anti-VEGF+ Laser panretinal photocoagulation

value: Diabetes Mellitus 1


title: AF-TTF-1

description: 10x Genomics


title: POG-treated Passage 12 TSPCs,biological rep2

growth_protocol: The concentration of 20 μM POG was added to the culture medium of rTSPCs in each passage from P3 to P12. An equal amount of the vehicle control dimethyl sulfoxide (DMSO) was added in the control group to exclude the influence of solvent


title: IMR90 NS Qui Set B rep 3

description:
Control for IR Set B
BFX17_expr.txt
IMR-3-3

value: normal


title: COHP_44988_490_TET_ON_C_10wks

tag: mouse id

tag: sample weeks

tag: batch

value: PBMC

value: tTA+/-, BCR-ABL+/-


title: AF-TD-FAW-1

description: 10x Genomics

tag: tissue

tag: Sex


title: IMR90 NS Qui Set B rep 2

description:
Control for IR Set B
BFX17_expr.txt
IMR-3-2


title: Animal C5 GFAP AOI 118

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description:
GeoMx DSP
AOI_118_GFAP_C5

data_processing:
library strategy: GeoMx DSP
Reads were trimmed, merged, and aligned to retrieve probe identity, and the unique molecular identifier of each read was used to remove PCR duplicates converting reads to digital counts for each target within an individual AOI
Supplementary files format and content: CountsROI_matrix.csv - ontains raw counts for the 94 samples that passed  min limit of quantification of 2
Supplementary files format and content: normROI_matrix.csv -  contains log2 Q3 normalized counts for 94 samples
Supplementary files format and content: countsAOI_matrix.csv - contains raw counts for the 18 samples that passed the minimum limit of quantification 2
Supplementary files format and content: normAOI_matrix.csv - contains log2 Q3 normalized counts for 18 samples

organism: Macaca nemestrina

source_name: Fetal brain

extract_protocol:
Unstained 5 µm-thick tissue sections cut from PFA-fixed, paraffin-embedded specimens were mounted on Colorfrost microscope slides
In situ hybridizations with the GeoMx Whole Transcriptome Atlas Panel (WTA, 18,676 total targets) were performed in Buffer R
Rabbit polyclonal anti-Olig2 antibody was incubated first at 1:100 in Buffer W, followed by Goat anti-rabbit AF647 for visualization. The remaining morphology markers were collectively diluted in Buffer W at the following concentrations: 1:50 RBFOX3 (NeuN), 1:400 GFAP, and STYO 83 for nuclei visualization
Each slide was scanned with a 20X objective and default scan parameters on a GeoMx Digitial Spatial Profiler
ROI placement: Geometric 500 µm diameter circle ROIs were placed in the subcortex (Superficial WM; n=3/section), WM tracts (Deep WM; n=3/section), and cortical layers IV-VI (GM; n=3/section). One maximum area (660 µm X 785 µm) ROI was placed at the GM/WM interface on each section
ALOI segmentation: Segmentation mask was applied to the GM/WM interface maximum area to select Olig2+, GFAP+, and NeuN+ areas of interest (AOI).
Sequencing libraries were generated by PCR from the photo-released indexing oligos and ROI-specific Illumina adapter sequences and unique i5 and i7 sample indices were added
Total target counts per DSP collection plate for sequencing were calculated from the total samples areas (µm2). For WTA libraries, the target sequencing depth was 100 counts/µm2. Pooled libraries were sequenced at 2×27 base pairs and with the dual-indexing workflow on an Illumina NovaSeq

value: Fetal brain

tag: brain reigion

value: GFAP

tag: zika infection

value: mock

tag: animal id

tag: region of interest (roi) identifer


title: DMSO-treated Passage 12 TSPCs,biological rep3

tag: treatment

tag: cell type


title: COHP_44986_490_TET_ON_C_8wks

tag: strain

value: M

tag: genotype


title: Carboplatin_5637_ATRi_3

tag: cell line

value: Bladder cancer

value: Cisplatin


title: IMR90 NS Qui Set B rep 1

description:
Control for IR Set B
BFX17_expr.txt
IMR-3-1

value: Lung Fibroblast

tag: group


title: Carboplatin_5637_ATRi_4


title: COHP_44985_490_TET_ON_C_7wks


title: DMSO-treated Passage 12 TSPCs,biological rep2

value: DMSO-treated TSPCs until Passage 12

value: tendon stem/progenitor cells


title: Animal C2 OLIG2 AOI 84

description:
GeoMx DSP
AOI_84_OLIG2_C2


title: POG-treated Passage 12 TSPCs,biological rep1

value: POG-treated TSPCs until Passage 12


title: COHP_44984_490_TET_ON_C_6wks


title: Animal C2 NEUN AOI 83

description:
GeoMx DSP
AOI_83_NEUN_C2

value: NEUN


title: DMSO-treated Passage 12 TSPCs,biological rep1


title: IMR90 Sen Oligo rep 2

description:
BFX36_expr.txt
Oligo-2

tag: agent

value: Oligomycin for 6 days on + 8 days off


title: IMR90 Sen Oligo rep 1

description:
BFX36_expr.txt
Oligo-1


title: IMR90 Sen Oligo rep 3

description:
BFX36_expr.txt
Oligo-3


title: Carboplatin_5637_ATRi_1


title: COHP_44987_490_TET_ON_C_9wks


title: COHP_44981_490_TET_ON_C_3wks


title: COHP_44982_490_TET_ON_C_4wks


title: Carboplatin_5637_Untreated_4


title: IMR90 Sen Oligo rep 4

description:
BFX36_expr.txt
Oligo-4


title: COHP_44983_490_TET_ON_C_5wks


title: Animal C2 GFAP AOI 82

description:
GeoMx DSP
AOI_82_GFAP_C2


title: Animal Z8 NEUN AOI 71

description:
GeoMx DSP
AOI_71_NEUN_Z8

value: ZIKV


title: Carboplatin_5637_Untreated_3


title: Animal C2 OLIG2 AOI 72

description:
GeoMx DSP
AOI_72_OLIG2_Z8


title: COHP_44980_490_TET_ON_C_2wks


title: Carboplatin_5637_Untreated_2


title: Animal Z8 GFAP AOI 70

description:
GeoMx DSP
AOI_70_GFAP_Z8


title: IMR90 Sen Ant rep 5

description:
BFX36_expr.txt
Anti-5

value: Antimycin A for 6 days on + 8 days off


title: Animal Z5 NEUN AOI 45

description:
GeoMx DSP
AOI_45_OLIG2_Z5


title: Carboplatin_5637_Untreated_1


title: COHP_44979_490_TET_ON_C_1wks


title: Animal Z5 GFAP AOI 44

description:
GeoMx DSP
AOI_44_GFAP_Z5


title: IMR90 Sen Oligo rep 5

description:
BFX36_expr.txt
Oligo-5

value: normal


title: Animal C3 OLIG2 AOI 34

description:
GeoMx DSP
AOI_34_OLIG2_C3


title: Cisplatin_5637_ATRi_3


title: Cisplatin_5637_ATRi_4


title: COHP_44978_490_TET_ON_C_0wks

value: PBMC


title: Carboplatin_5637_ATRi_2


title: IMR90 Sen Ant rep 3

description:
BFX36_expr.txt
Anti-3


title: IMR90 Sen Ant rep 2

description:
BFX36_expr.txt
Anti-2


title: Cisplatin_5637_ATRi_2


title: Animal C3 NEUN AOI 33

description:
GeoMx DSP
AOI_33_NEUN_C3


title: COHP_44976_489_TET_ON_C_17wks

value: F

value: tTA+/-, BCR-ABL+/-


title: Cisplatin_5637_ATRi_1


title: COHP_44977_489_TET_ON_C_18wks


title: IMR90 Sen Ant rep 4

description:
BFX36_expr.txt
Anti-4


title: COHP_44975_489_TET_ON_C_16wks


title: IMR90 Sen Rot rep 3

description:
BFX02_expr.txt
IMR90-Rotenone-R3

value: Rotenone for 14 days


title: IMR90 Sen Ant rep 1

description:
BFX36_expr.txt
Anti-1


title: Animal Z2 OLIG2 AOI 101

description:
GeoMx DSP
AOI_101_OLIG2_Z2

value: Fetal brain


title: Animal C3 GFAP AOI 32

description:
GeoMx DSP
AOI_32_GFAP_C3

value: GFAP

value: mock


title: Cisplatin_5637_Untreated_4

value: Bladder cancer

value: Cisplatin


title: Animal Z2 NEUN AOI 102

description:
GeoMx DSP
AOI_102_NEUN_Z2


title: COHP_44972_489_TET_ON_C_13wks


title: IMR90 Sen Rot rep 1

description:
BFX02_expr.txt
IMR90-Rotenone-R1

value: Lung Fibroblast


title: Animal Z2 GFAP AOI 100

description:
GeoMx DSP
AOI_100_GFAP_Z2


title: COHP_44973_489_TET_ON_C_14wks


title: Animal Z3 OLIG2 AOI 88

description:
GeoMx DSP
AOI_88_OLIG2_Z3


title: Cisplatin_5637_Untreated_3


title: IMR90 Sen Rot rep 2

description:
BFX02_expr.txt
IMR90-Rotenone-R2


title: Cisplatin_5637_Untreated_1


title: IMR90 Sen Bleo rep 5

description:
BFX36_expr.txt
Bleo-5

value: Bleomycin for 6 days on + 8 days off


title: COHP_44974_489_TET_ON_C_15wks


title: Cisplatin_5637_Untreated_2


title: COHP_44971_489_TET_ON_C_12wks


title: IMR90 Sen Bleo rep 4

description:
BFX36_expr.txt
Bleo-4


title: Animal Z3 NEUN AOI 89

description:
GeoMx DSP
AOI_89_NEUN_Z3


title: COHP_44970_489_TET_ON_C_11wks


title: Carboplatin_5637_3

value: Carboplatin


title: IMR90 Sen Bleo rep 3

description:
BFX36_expr.txt
Bleo-3


title: IMR90 Sen Bleo rep 2

description:
BFX36_expr.txt
Bleo-2


title: Animal Z3 GFAP AOI 87

description:
GeoMx DSP
AOI_87_GFAP_Z3


title: COHP_44969_489_TET_ON_C_10wks


title: Animal Z4 OLIG2 AOI 22

description:
GeoMx DSP
AOI_22_OLIG2_Z4


title: Carboplatin_5637_2


title: COHP_44968_489_TET_ON_C_9wks


title: Carboplatin_5637_1


title: IMR90 Sen Bleo rep 1

description:
BFX36_expr.txt
Bleo-1


title: Animal Z4 NEUN AOI 21

description:
GeoMx DSP
AOI_21_NEUN_Z4

value: NEUN


title: Cisplatin_5637_3


title: Cisplatin_5637_2


title: Animal Z4 GFAP AOI 20

description:
GeoMx DSP
AOI_20_GFAP_Z4


title: COHP_44967_489_TET_ON_C_8wks


title: Cisplatin_5637_1


title: Animal Z1 OLIG2 AOI 60

description:
GeoMx DSP
AOI_60_OLIG2_Z1


title: Carboplatin_RT112_3


title: COHP_44966_489_TET_ON_C_7wks


title: IMR90 Sen Ras rep 2

description:
BFX06_expr.txt
HS-D12-RasV12-pos-RNA-Rep-2

value: hTERT immortalised

tag: tag

value: stably transduced with inducible RasV12

value: DOX for 12 days


title: COHP_44965_489_TET_ON_C_6wks

tag: mouse id


title: Animal Z1 NEUN AOI 59

description:
GeoMx DSP
AOI_59_NEUN_Z1

value: ZIKV


title: IMR90 Sen Ras rep 1

description:
BFX06_expr.txt
HS-D12-RasV12-pos-RNA-Rep-1


title: COHP_44964_489_TET_ON_C_5wks

tag: sample weeks

value: PBMC


title: Carboplatin_RT112_2


title: Animal Z1 GFAP AOI 58

description:
GeoMx DSP
AOI_58_GFAP_Z1


title: COHP_44963_489_TET_ON_C_4wks

tag: batch

value: F


title: Animal C13 Gray Matter ROI 159

description:
GeoMx DSP
ROI_159_GM_C13

tag: tissue

value: GM


title: IMR90 Sen IR set E rep 3

description:
BFX02_expr.txt
IMR90-IR-R3_sequence

value: normal

value: 10Gy ionising radiation 14 days prior collection


title: IMR90 Sen IR set E rep 2

description:
BFX02_expr.txt
IMR90-IR-R2_sequence


title: IMR90 Sen Ras rep 3

description:
BFX06_expr.txt
HS-D12-RasV12-pos-RNA-Rep-3


title: COHP_44961_489_TET_ON_C_2wks

tag: Sex

value: tTA+/-, BCR-ABL+/-


title: Cisplatin_RT112_2


title: IMR90 Sen IR set D rep 5

description:
BFX36_expr.txt
IR-5


title: Animal C13 Gray Matter ROI 158

description:
GeoMx DSP
ROI_158_GM_C13

value: Fetal brain

tag: brain reigion

value: mock


title: COHP_44962_489_TET_ON_C_3wks


title: COHP_44960_489_TET_ON_C_1wks


title: IMR90 Sen IR set D rep 4

description:
BFX36_expr.txt
IR-4


title: COHP_44959_489_TET_ON_C_0wks


title: IMR90 Sen IR set D rep 3

description:
BFX36_expr.txt
IR-3


title: COHP_44958_480_TET_OFF_B_18wks

value: M


title: Animal C13 Gray Matter ROI 157

description:
GeoMx DSP
ROI_157_GM_C13

tag: zika infection


title: CART-14, scRNA-seq

last: Li

department: Pediatrics

institute: University of California, San Diego

data_processing:
Use Cell ranger to perform alignment, filtering, barcode counting, and UMI counting
Genome_build: hg38
Supplementary_files_format_and_content: all the zip files contain Features (Genes).tsv, Barcodes.tsv, and Matrix.mtx (set of 3 files)

source_name: PBMC from ALL patients

extract_protocol:
PBMCs were isolated from patient blood and processed for library generation for scRNA-Seq
[PBMC and BMMC extract protocol] PBMC or BMMC from the patients' blood or bone marrow were isloated by EasySep™ Direct Human PBMC Isolation Kit following the manufacturer’s instructions.
PBMC or BMMC were used for library construction using Chromium™ Single Cell 3’ Reagent Kits v2/v3
Libraries were generated by Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v2/v3 (10X Genomics)

treatment_protocol: ALL patients treated with CAR T cells at various time points

value: Human PBMC

tag: patient id

tag: age

tag: diagnosis

value: B-ALL

value: CAR T treatment Relapse

tag: time

value: Relapse CD22 Day 60

tag: therapy

value: CAR T


title: CART-13, scRNA-seq

tag: cell type

tag: treatment

value: Relapse CD22 Day 30


title: IMR90 Sen IR set E rep 1

description:
BFX02_expr.txt
IMR90-IR-R1_sequence

value: Lung Fibroblast

tag: group


title: IMR90 Sen IR set D rep 2

description:
BFX36_expr.txt
IR-2

tag: agent


title: Animal C13 Superficial White Matter ROI 154

description:
GeoMx DSP
ROI_154_SWM_C13

value: SWM

tag: animal id

tag: region of interest (roi) identifer


title: COHP_44957_480_TET_OFF_B_17wks

tag: mouse id

tag: sample weeks

value: PBMC

tag: strain

tag: genotype


title: IMR90 Sen IR set D rep 1

description:
BFX36_expr.txt
IR-1

tag: tissue


title: COHP_44956_480_TET_OFF_B_16wks

tag: batch

tag: Sex


title: IMR90 Sen IR set C rep 3

description:
BFX17_expr.txt
IMR-LS-SnC-3


title: Animal C13 Deep White Matter ROI 153

description:
GeoMx DSP
ROI_153_DWM_C13

tag: brain reigion

value: DWM

tag: zika infection


title: Animal C13 Deep White Matter ROI 152

description:
GeoMx DSP
ROI_152_DWM_C13


title: Cisplatin_RT112_3

tag: cell line

value: Bladder cancer

value: Cisplatin


title: CART-11, scRNA-seq

tag: patient id

tag: age

tag: diagnosis

value: 60 days of CAR T treatment

tag: time

value: Day 60

tag: therapy


title: CART-10, scRNA-seq

source_name: BMMC from ALL patients

extract_protocol:
BMMCs were isolated from patient blood and processed for library generation for scRNA-Seq
[PBMC and BMMC extract protocol] PBMC or BMMC from the patients' blood or bone marrow were isloated by EasySep™ Direct Human PBMC Isolation Kit following the manufacturer’s instructions.
PBMC or BMMC were used for library construction using Chromium™ Single Cell 3’ Reagent Kits v2/v3
Libraries were generated by Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v2/v3 (10X Genomics)

tag: cell type

value: Human BMMC

tag: treatment

value: 30 days of CAR T treatment

value: Day 30


title: Animal C13 Deep White Matter ROI 151

description:
GeoMx DSP
ROI_151_DWM_C13

value: Fetal brain

value: mock

tag: animal id

tag: region of interest (roi) identifer


title: Animal C13 Superficial White Matter ROI 156

description:
GeoMx DSP
ROI_156_SWM_C13


title: Cisplatin_RT112_1


title: IMR90 Sen IR set C rep 2

description:
BFX17_expr.txt
IMR-LS-SnC-2

tag: group

value: normal

tag: agent

value: 10Gy ionising radiation 14 days prior collection


title: COHP_44955_480_TET_OFF_B_15wks

tag: mouse id

tag: sample weeks

tag: tissue

tag: strain

value: M

tag: genotype

value: tTA+/-, BCR-ABL+/-


title: Animal C13 Superficial White Matter ROI 155

description:
GeoMx DSP
ROI_155_SWM_C13

tag: brain reigion

tag: zika infection


title: COHP_44954_480_TET_OFF_B_14wks

tag: batch

tag: Sex


title: COHP_44953_480_TET_OFF_B_13wks


title: CART-12, scRNA-seq

value: Human PBMC

tag: patient id

tag: age

tag: diagnosis

value: B-ALL

value: CAR T treatment Relapse

tag: time

value: Relapse CD19

value: CAR T


title: CART-9, scRNA-seq

tag: cell type

tag: treatment

tag: therapy


title: IMR90 Sen IR set B rep 3

description:
BFX17_expr.txt
IMR-3-SnC-3

value: Lung Fibroblast

tag: group

tag: agent


title: Animal C1 Gray Matter ROI 149

description:
GeoMx DSP
ROI_149_GM_C1

value: GM

tag: animal id

tag: region of interest (roi) identifer


title: IMR90 Sen IR set C rep 1

description:
BFX17_expr.txt
IMR-LS-SnC-1

tag: tissue


title: IMR90 Sen IR set B rep 1

description:
BFX17_expr.txt
IMR-3-SnC-1


title: CART-6, scRNA-seq

value: 180 days of CAR T treatment

value: Day 180


title: IMR90 Sen IR set B rep 2

description:
BFX17_expr.txt
IMR-3-SnC-2


title: CART-8, scRNA-seq

value: 15 days of CAR T treatment

value: Day 15


title: Animal C1 Gray Matter ROI 148

description:
GeoMx DSP
ROI_148_GM_C1

value: Fetal brain


title: Animal C1 Superficial White Matter ROI 146

description:
GeoMx DSP
ROI_146_SWM_C1

value: SWM

value: mock


title: COHP_44952_480_TET_OFF_B_12wks

tag: mouse id

tag: sample weeks

value: PBMC

tag: strain

tag: genotype


title: COHP_44950_480_TET_OFF_B_10wks

tag: batch

tag: Sex

value: M


title: IMR90 NS Qui Set A rep 5

description:
Control for IR Set A
BFX01_expr.txt
MCA_setE_Rep5

value: normal


title: Animal C1 Superficial White Matter ROI 145

description:
GeoMx DSP
ROI_145_SWM_C1

tag: brain reigion

tag: zika infection


title: CART-5, scRNA-seq

value: Human BMMC

tag: patient id

tag: age

tag: diagnosis

value: 30 days of CAR T treatment

tag: time

value: Day 30


title: CART-4, scRNA-seq

tag: cell type

value: Human PBMC

value: B-ALL

tag: treatment

tag: therapy


title: COHP_44949_480_TET_OFF_B_9wks

value: tTA+/-, BCR-ABL+/-


title: CART-3, scRNA-seq

value: CAR T


title: COHP_44948_480_TET_OFF_B_8wks


title: Animal C1 Deep White Matter ROI 143

description:
GeoMx DSP
ROI_143_DWM_C1

value: DWM

tag: animal id

tag: region of interest (roi) identifer


title: Carboplatin_RT112_1

tag: cell line

value: Bladder cancer

value: Carboplatin


title: COHP_44947_480_TET_OFF_B_7wks

tag: mouse id

tag: sample weeks

tag: tissue


title: Animal C1 Superficial White Matter ROI 144

description:
GeoMx DSP
ROI_144_SWM_C1


title: IMR90 NS Qui Set A rep 3

description:
Control for IR Set A
BFX01_expr.txt
MCA_setE_Rep3

value: Lung Fibroblast

tag: group


title: CART-2, scRNA-seq

value: Day of CART infusion

value: Day 0

value: bone marrow transplatation


title: IMR90 NS Qui Set A rep 4

description:
Control for IR Set A
BFX01_expr.txt
MCA_setE_Rep4


title: COHP_44951_480_TET_OFF_B_11wks

description: cml_mrna_processed_1tpm_in_5_samples.tsv.gz

tag: batch

value: PBMC

tag: strain

tag: Sex

tag: genotype


title: CART-1, scRNA-seq

tag: patient id

tag: age

value: B-ALL Prior CAR T treatment

value: Prior treatment


title: COHP_44945_480_TET_OFF_B_5wks

value: M


title: COHP_44946_480_TET_OFF_B_6wks


title: Animal C1 Deep White Matter ROI 142

description:
GeoMx DSP
ROI_142_DWM_C1

value: Fetal brain

tag: brain reigion

tag: zika infection

value: mock


title: Animal C1 Deep White Matter ROI 141

description:
GeoMx DSP
ROI_141_DWM_C1


title: IMR90 Sen IR set A rep 5

description:
BFX01_expr.txt
MCA_SetA_Rep5

value: normal

tag: agent

value: 10Gy ionising radiation 14 days prior collection


title: Animal C14 Gray Matter ROI 139

description:
GeoMx DSP
ROI_139_GM_C14

value: GM


title: COHP_44944_480_TET_OFF_B_4wks

value: tTA+/-, BCR-ABL+/-

tag: treatment


title: Animal C14 Gray Matter ROI 138

description:
GeoMx DSP
ROI_138_GM_C14

tag: animal id


title: Animal C1 Gray Matter ROI 147

description:
GeoMx DSP
ROI_147_GM_C1

tag: region of interest (roi) identifer


title: COHP_44943_480_TET_OFF_B_3wks


title: Animal C14 Gray Matter ROI 137

description:
GeoMx DSP
ROI_137_GM_C14


title: IMR90 Sen IR set A rep 3

description:
BFX01_expr.txt
MCA_SetA_Rep3


title: Slow_52_2_4

city: Helsinki

first: Sannakajsa

middle: Velmala

last: LUKE

address: Latokartanonkaari 9

country: Finland

institute: Natural resources Institute Finland Luke

hyb_protocol: Each microarray was hybridized with one sample labelled with one dye. The samples were mixed and the volume was reduced to ~10 µl by evaporating excess water in a DNA 120 speedvac (Thermo Fisher Scientific). Labelled aRNAs were fragmented for 15 minutes at 70°C using Ambion’s ”RNA Fragmentation Reagents“, placed on ice for 1 minute, denatured for 2 minutes at 95°C, put on ice for 2 min and resuspended in 120 µl hybridization buffer (50% formamide, 5X SSC, 0,1% SDS, 0,1 mg/mL Herring sperm DNA) preheated to 55°C. Samples were kept in a heating block at 50°C until hybridization. Hybridizations were performed in HS400Pro hybridization stations (Tecan Group Ltd., Männedorf, Switzerland). The slides were heated at 80°C for 10 minutes, then washed once at 37°C with 0.5X SSC, 0.1% SDS for 20 seconds and once at 50°C with 2X SSC, 0.5% SDS for 20 seconds, and prehybridized for 1 hour at 65°C in 5X SSC, 0.1% SDS, 0.1 mg/ml BSA, 0.1 mg/ml Herring Sperm DNA. Next the slides were washed at 55°C with 2X SSC, 0.5% SDS for 1 minute with a 30 seconds soak and washed again at 45°C for 1 minute with the same solution. The resuspended labelled targets were injected into the chambers and hybridized for 16 hours at 45°C with sample agitation. The slides were then washed as follows: 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 2X SSC, 0.5% SDS, 1 time 1 minute at 45° in 2X SSC, 0.5% SDS, 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 37°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 23°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute 30 seconds at 23°C with 30 seconds soaking in 0.1X SSC, 1 time 30 seconds at 23°C in 0.1X SSC and 2 times 30 seconds at 23°C in milliQ filtered water. Finally slides were dried for 2 minutes 30 seconds with nitrogen gaz.

scan_protocol: Microarray Scanner: PowerScanner (Tecan Group Ltd., Männedorf, Switzerland)  Image Analysis Program: ArrayPro Analyzer v. 6.3 (Media Cybernetics, Bethesda, MD, USA)  Slide scanning was performed at 5 micron resolution.

data_processing: Data analyses were performed using customized scripts for R and Bioconductor (http://www.r-project.org and http://www.bioconductor.org). Spots that were flagged as presenting abnormal morphology during the image processing were replaced by mean value of the remaining spots of the same probe from the other slides from the same sample type. Background intensities were subtracted from the foreground intensities. Background-subtracted data were log2-transformed and normalized using quantile correction approach. A filtering step was applied to select positive genes to be used for further analysis. The mean intensity of spots containing buffer only was calculated for each row of sub-grids, and was taken as the minimum intensity of probes for that subgrid. Some genes on the array (1017 pcs.) were represented by more than one probe. The gene intensity values of redundant probes were corrected replacing the raw values with the geometric mean of corresponding probe intensities (analysis done based on the cluster-gene names) so that each gene was finally represented only once in the analyses. The slides were categorized by the age of saplings into two sets (five and 18-month-old), and a probe was considered positive if the signal intensity was detected above buffer intensity on at least three quarters of the slides in either of the sampling points.

label: AlexaFluor 647

organism: Picea abies

source_name: 5 month cutting

label_protocol: Total RNA (1 µg) or mRNA (10 ng) was transcribed in-vitro by using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion by Life Technologies, Austin, TX, USA), following the manufacturer’s instructions. The aaRNA (5 ug per sample) was labeled using Alexa 647 dyes (Invitrogen, Carlsbad, CA, USA), and purified as per the manufacturer’s instructions. Dye incorporation efficiency was determined by using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s instructions.

growth_protocol: Norway spruce (P. abies) seedlings were grown in the experimental nursery of Finnish Forest Research Institute for about one and a half years before sampling. They were grown in standard nursery growing media, light Sphagnum peat, and fertilized with mineral nutrients. Roots were washed under tap water to remove surrounding peat and approximately 1 cm of the root ends was collected for analysis. Between two and four biological samples comprised of several root ends were analysed for each of eight different genotypes. Sampling of Norway spruce  cutting roots representing eight genotypes was done in late September; for 1st year cuttings five months and the 2nd year cuttings 18 months after adventitious root initiation. The adventitious roots were washed carefully under tap water and the short roots were immediately detached from the cutting, wrapped in aluminium foil and finally frozen in liquid nitrogen. Samples were stored at -70°C degrees until RNA extraction.

extract_protocol: Total RNA was extracted from five replicates per clone per sampling point (5replicates x 8 clones x 2 time points) in a random order. The RNA was extracted by grinding the adventitious roots in liquid nitrogen from 62 samples as described in Chang et al. (1993) with modifications as described in Pavy et al. (2008). Quantification and quality check of messenger RNA (mRNA) was done on a Nanodrop 1000 (Thermo Scientific, MA, US) spectrophotometer and the integrity was verified on the Bioanalyzer 2100 (Agilent Technologies, CA, US).

value: adventitious roots

tag: age of trees


title: Slow_52_2_6b


title: COHP_44942_480_TET_OFF_B_2wks

extract_protocol:
Total RNA was extracted from whole blood using the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany); quality and quantity were estimated using a BioAnalyser (Agilent, Santa Clara, CA). Samples with a RIN > 4.0 were included.
Sequencing libraries were constructed using the KapaHyper with RiboErase (Kapa Biosystems, Wilmington, MA) and are reverse stranded.

tag: mouse id


title: IMR90 NS Qui Set A rep 2

description:
Control for IR Set A
BFX01_expr.txt
MCA_setE_Rep2


title: Animal C14 Superficial White Matter ROI 136

description:
GeoMx DSP
ROI_136_SWM_C14

value: SWM


title: IMR90 Sen IR set A rep 2

description:
BFX01_expr.txt
MCA_SetA_Rep2


title: IMR90 NS Qui Set A rep 1

description:
Control for IR Set A
BFX01_expr.txt
MCA_setE_Rep1


title: COHP_44941_480_TET_OFF_B_1wks

tag: sample weeks


title: Animal C14 Superficial White Matter ROI 134

description:
GeoMx DSP
ROI_134_SWM_C14

tag: tissue


title: BLEOR03 (rutin)

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

description:
BLEOR03
PE150 high throughout data

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human prostate tissue

growth_protocol: Normal human prostate stromal cells (PSC27) were routinely cultured in stromal complete media supplemented with 10% FBS, until a total number of approximately 1,000,000 was reached in each flask and subject to treatment by the chemotherapeutic agent bleomycin (BLEO) or BLEO combined with the phytochemical drug rutin.

extract_protocol:
Cells were lysed for RNA preparation using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To induce senescence, bleomycin (BLEO) was added to the media at 50 μg/ml, and cells were treated for 12 h before media change. Seven days later, to suppress the senescence-associated secretory phenotype (SASP) by a specific mechanism, the medicinal agent rutin was applied to the media at 100 µM.

tag: cell type

value: Normal human primary prostate stromal cells

tag: passage

tag: name


title: Animal C14 Superficial White Matter ROI 135

description:
GeoMx DSP
ROI_135_SWM_C14


title: BLEOR02 (rutin)

description:
BLEOR02
PE150 high throughout data


title: IMR90 Sen IR set A rep 4

description:
BFX01_expr.txt
MCA_SetA_Rep4

value: Lung Fibroblast

tag: group


title: 9099rh13

city: Nashville

first: Yinqiu

state: TN

address: 313 Harpeth view circle

department: medicine

institute: vumc

description: 10X genomics

data_processing:
RTA (version 2.4.11; Illumina) was used for base calling and analysis was completed using 10X Genomics Cell Ranger software v7.0.1.
Supplementary files format and content: mm10
Supplementary files format and content: Tap-seperated values files and matrix files

source_name: kidney

extract_protocol:
Nuclei were isolated using Nuclei EZ lysis buffer. Nuclei (>20,000 nuclei per sample) were submitted for processing using the 10X Genomics platform.
Libraries were prepared using P/N 1000121, 1000157, and 1000213 following the manufacturer's protocol.  The libraries were sequenced using the NovaSeq 6000 with 150 bp paired end reads.

value: kidney

tag: genotype

value: WT

value: uuo 1day


title: COHP_44940_480_TET_OFF_B_0wks

first: Denis

last: OMeally

institute: City of Hope

data_processing:
nf-core RNASeq pipeline version 3.7
Trimmed reads were mapped using STAR to the GRCm39 reference (Genbank accession GCA_000001635.9) amended with the human BCR-ABL1 fusion gene sequence (Genbank accession EF158045.1) using GENCODE annotation Release m28
Each library was subjected to extensive quality control, including estimation of library complexity, gene body coverage, and duplication rates, among other metrics detailed in the pipeline repository
Transcript abundance was estimated across genomic features using Salmon and merged into a matrix of pseudocounts per million transcripts (TPM) per gene for each sample. BCR-ABL1 transcript abundance was measured by counting reads that spanned the fusion boundary
Assembly: GCA_000001635.9
Supplementary files format and content: tab delimited file includes Salmon pseudocounts for each sample (TPM)

tag: batch

value: PBMC

tag: strain

tag: Sex


title: 9099rh14

description: 10X genomics

value: KO


title: Animal C14 Deep White Matter ROI 132

description:
GeoMx DSP
ROI_132_DWM_C14

tag: brain reigion

value: DWM

tag: zika infection


title: Slow_70_3_6

source_name: 18 month old cutting


title: Animal C14 Deep White Matter ROI 133

description:
GeoMx DSP
ROI_133_DWM_C14


title: 9099rh12

description: 10X genomics

tag: treatment

value: uuo 3days


title: BLEO03 (rutin)

description:
BLEO03
PE150 high throughout data


title: Slow_70_3_4


title: Fast_35_6_4


title: Fast_20_4_5


title: IMR90 Sen IR set A rep 1

description:
BFX01_expr.txt
MCA_SetA_Rep1

tag: agent


title: Slow_61_1_3


title: Animal C14 Deep White Matter ROI 131

description:
GeoMx DSP
ROI_131_DWM_C14

value: Fetal brain

tag: animal id

tag: region of interest (roi) identifer


title: BLEO02 (rutin)

description:
BLEO02
PE150 high throughout data


title: Slow_61_1_5

tag: age of trees


title: Animal C15 Gray Matter ROI 129

description:
GeoMx DSP
ROI_129_GM_C15

value: mock


title: BLEO01 (rutin)

description:
BLEO01
PE150 high throughout data


title: Animal C15 Gray Matter ROI 128

description:
GeoMx DSP
ROI_128_GM_C15


title: Slow_52_2_6a


title: 9099rh9

description: 10X genomics


title: BLEOR01 (rutin)

description:
BLEOR01
PE150 high throughout data


title: CTRL03 (rutin)

description:
CTRL03
PE150 high throughout data


title: Animal C15 Gray Matter ROI 127

description:
GeoMx DSP
ROI_127_GM_C15


title: RUNX3 restored cells [KRP16h]

city: Cheongju

first: Jung-Won

last: Lee

address: 1, Chungdae-ro

department: Department of Biochemistry, School of Medicine

country: South Korea

institute: Institute for Tumor Research

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Lung cancer

growth_protocol: KPR- and KPR_restored cells were maintained in Dulbecco’s modiﬁed Eagle’s medium (Gibco BRL, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (Gibco BRL) and 1% penicillin/streptomycin (Invitrogen, Carlsbad, CA, USA). Cells were incubated at 37°C with 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

treatment_protocol: Cells were cultured in 10% DMEM. Cells were treated with 10% serum and 1 μM 4-OHT (Sigma).

value: Lung cancer

tag: cell line

value: immortalized cell lines from KPRL/F-TAM(-) lung cancers (KPR-).

value: Mus musculus, mouse

value: RUNX3 -/+

value: 1 μM 4-OHT


title: Fast_35_3_5

tag: tissue

value: adventitious roots


title: Animal C15 Superficial White Matter ROI 126

description:
GeoMx DSP
ROI_126_SWM_C15

value: SWM


title: RUNX3 knock out cells [KRP0h]

description: KPR-

tag: cell type

value: RUNX3 -/-


title: Animal C15 Superficial White Matter ROI 125

description:
GeoMx DSP
ROI_125_SWM_C15


title: Fast_35_3_1


title: 11D

city: Hyderabad

first: Kumarswamy

last: Regalla

state: Telangana

address: Centre for Cellular and Molecular Biology (CSIR-CCMB), Habsiguda

country: India

institute: CCMB

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt v4.1 (quality cutoff:20 and min read length cutoff:50)
Trimmed sequence reads were mapped to GRCm38.p6 using HISAT2 v2.2.1
Gene and Isoform abundances were quantified using RSEM v1.3.3
Normalisation and RNA-seq differential expression was done in DESeq2
Assembly: GRCm38.p6
Supplementary files format and content: Tab-delimited text files includes gene counts, TPM and FPKM for each sample
Supplementary files format and content: Tab-delimited text files includes isoform counts, TPM and FPKM for each sample

source_name: HEART

growth_protocol: Animals were maintained in individually ventilated cages with ad libitum access to chow.

extract_protocol:
RNA was extracted using TRIZOL. DNA was depleted using DNaseI.
RNA libraries for RNA-seq were prepared using Illumina TrueSeq total RNA kit following manufacturer’s protocols.

treatment_protocol: C57BL6 male mice were administered with subcutaneous Isoproterenol for 4,8 and 11 days and saline as controls.

value: HEART

tag: gender

value: male

value: 11 DAY ISOPROTERNOL


title: 11C


title: 9099rh11

description: 10X genomics

value: kidney


title: Fast_20_2_5


title: Animal C15 Deep White Matter ROI 123

description:
GeoMx DSP
ROI_123_DWM_C15


title: Animal C15 Superficial White Matter ROI 124

description:
GeoMx DSP
ROI_124_SWM_C15


title: 11B


title: Fast_20_2_3


title: 11A


title: Animal C15 Deep White Matter ROI 122

description:
GeoMx DSP
ROI_122_DWM_C15


title: Slow_52_2_1


title: CTRL02 (rutin)

description:
CTRL02
PE150 high throughout data

value: Normal human primary prostate stromal cells

tag: passage

tag: name


title: Animal C15 Deep White Matter ROI 121

description:
GeoMx DSP
ROI_121_DWM_C15

value: DWM


title: 8C

value: 8 DAY ISOPROTERNOL


title: 8B


title: Animal C5 Gray Matter ROI 117

description:
GeoMx DSP
ROI_117_GM_C5

value: Fetal brain

value: GM


title: Fast_18_1_4

tag: genotype


title: Fast_18_1_3


title: Animal C5 Gray Matter ROI 116

description:
GeoMx DSP
ROI_116_GM_C5

value: mock


title: eIF4E1_IAA_RNAseq_3

city: Indianapolis

middle: James

last: Holmes

state: IN

address: 635 Barnhill Drive

department: Pharmacology & Toxicology

institute: Indiana University School of Medicine

data_processing:
sequencing adapters from read1 were removed with CutAdapt (5'adapt: AGTCCGACGATC, 3'adapt:NNNNNAGATCGGAAGAG); UMI extracted with UMI-tools (pattern "NNNNN" located at 3'end)
mapped with RNA-STAR to TgME49 genome (v58). Settings: –outFilterMultimapNmax=1,  –outFilterScoreMinOverLread=0.9, –outFilterMatchNminOverLread=0.9)
mapped reads deduplicated with UMI-tools
read counts from Htseq, filtered for coding genes only
differential expression with DESeq2, translational efficiency with Riborex
Assembly: Toxoplasma gondii (TGME49) v58 from toxodb.org
Supplementary files format and content: tabular files of mapped read counts
Library strategy: RIBO-seq

molecule: cytoplasmic RNA

organism: Toxoplasma gondii

source_name: RH::TIR1 parental strain

growth_protocol: parasites innoculated and grown in confluent human foreskin fibroblasts in DMEM+10%FBS (no antibiotic) for 48h prior to harvest

extract_protocol:
cytoplasmic lysate was collected and an aliquot was immediately stored in Trizol for RNA-seq samples.  The rest was digested with RNaseI and monosomes were collecte by ultracentrifugation on a sucrose gradient. Ribosome-protected fragments (RFP) were purified after gel electrophoresis
total RNA was fragmented by alkaline hydrolysis. Fragments were purfied by gel electrophoresis. fragments were dephosphorylated, ligated at 5' end with barcoded adapter, rRNA removal with sequential treatment of sample with riboPOOLs kit for human then Toxoplasma, phosphorylated, ligated at 3' end with SR-adapter, reverse transcribed & PCR with NEBnext barcoded adapters

treatment_protocol: treatment with 0.5% DMSO vehicle or 500uM indole-3-acetic acid (IAA) for 4 hours prior to harvest.

value: RH::TIR1 parental strain

value: tachyzoites


title: eIF4E1_IAA_RNAseq_2


title: 4D

value: 4 DAY ISOPROTERNOL


title: eIF4E1_IAA_RNAseq_1


title: Animal C5 Gray Matter ROI 115

description:
GeoMx DSP
ROI_115_GM_C5


title: IleumSingleCells - iPGC1a-/-_CHOW - Rep1

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 20 out of 24 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 35743 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 33095 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: IleumSingleCells

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: RNA was extracted using Qiazol reagent, following the protocol.B2

treatment_protocol: For ileum section, the isolation of single cells was performed by a modification of Weiser method, as previously described 27,28. Briefly, the ileum was harvested, washed with cold saline solution and cut longitudinally. To remove luminal content, ileum was transferred into Hank’s balanced salt solution with 0.5mM-DTT. Then, ileum was placed into 20 ml of Chelating Buffer (Na2PO4 5mM, NaCl 96mm, Na Citrate27mM, KH2PO4 8mM, KCl 1.5 mm, D-Sorbitol 55mM, Sucrose 44mM, DTT 0.5 mM), and incubated at 4˚C with constant stirring for 20 minutes and supernatant was collected. After, ileum was transferred into a 50ml tube with 15 ml of Chelating buffer, gently shaken by hand (30 inversions) and supernatant was collected. This operation was repeated eight time. All collected supernatant were centrifuged at 1000g, washed with cold saline buffer and then stored at -80°C.

tag: diet

value: CHOW


title: Slow_76_1_4

value: adventitious roots


title: 4C

tag: strain


title: CTRL01 (rutin)

description:
CTRL01
PE150 high throughout data


title: IleumSingleCells - iPGC1afl/fl_CHOW - Rep2


title: Animal C5 Superficial White Matter ROI 114

description:
GeoMx DSP
ROI_114_SWM_C5

value: SWM


title: IleumSingleCells - iPGC1a-/-_HFD - Rep1

value: HFD


title: eIF4E1_control_RNAseq_3


title: 4B

value: HEART


title: Fast_15_2_3


title: IleumSingleCells - iPGC1afl/fl_HFD - Rep4


title: IleumSingleCells - iPGC1afl/fl_CHOW - Rep4


title: eIF4E1_control_RNAseq_2


title: Slow_76_1_1


title: 4A

value: male


title: IleumSingleCells - iPGC1afl/fl_HFD - Rep6


title: 8A


title: IleumSingleCells - iPGC1a-/-_HFD - Rep3


title: Animal C5 Superficial White Matter ROI 112

description:
GeoMx DSP
ROI_112_SWM_C5


title: IleumSingleCells - iPGC1a-/-_CHOW - Rep4


title: eIF4E1_control_RNAseq_1


title: Animal C5 Deep White Matter ROI 111

description:
GeoMx DSP
ROI_111_DWM_C5


title: SalineD

value: SALINE


title: eIF4E1_IAA_RIBOseq_3


title: IleumSingleCells - iPGC1a-/-_HFD - Rep4


title: IleumSingleCells - iPGC1a-/-_CHOW - Rep3


title: Animal C5 Deep White Matter ROI 110

description:
GeoMx DSP
ROI_110_DWM_C5


title: eIF4E1_IAA_RIBOseq_2


title: eIF4E1_IAA_RIBOseq_1


title: Animal C5 Deep White Matter ROI 109

description:
GeoMx DSP
ROI_109_DWM_C5


title: SalineA


title: Animal C2 Gray Matter ROI 81

description:
GeoMx DSP
ROI_81_GM_C2


title: IleumSingleCells - iPGC1afl/fl_HFD - Rep1


title: Animal C5 Superficial White Matter ROI 113

description:
GeoMx DSP
ROI_113_SWM_C5


title: eIF4E1_control_RIBOseq_3


title: eIF4E1_control_RIBOseq_2


title: Animal C2 Gray Matter ROI 80

description:
GeoMx DSP
ROI_80_GM_C2


title: B16 Control

first: Liuyang

last: Wang

institute: Duke University

description: 10x Genomics

data_processing:
Sequences were generated using paired end sequencing (one end to generate cell specific, barcoded sequence and the other to generate sequence of the expressed poly-A tailed mRNA) on an Illumina sequencing platform.
CellRanger v3.3.0 was used to process raw short reads, demultiplex cell barcodes, and map reads to the GRCm38 reference genome. Seurat v4.076 was used for normalization, dimension reduction, cell clustering, and DEGs analysis. Cells with less than 200 unique genes and genes expressed in less than 5 cells were excluded from all subsequent analyses.
Assembly: GRCm38
Supplementary files format and content: Tab format values and matrix from Cellranger pipeline
Supplementary files format and content: comma-separate excel csv file: B16_NGF_scRNAseq_SeuratMetadata.csv

source_name: melanoma

growth_protocol: 1,000,000 B16 cells with Ctrl or NGF sgRNA were subcutaneously injected into C57BL/6J mice.

extract_protocol:
Each prep was titered to contain 10,000 cells per library construction. Cells were combined with master mix containing reverse transcription (RT) reagents. Then the cell RT reaction mix, gel beads carrying the Illumina TruSeq Read 1 sequencing primer, a 16 bp 10x barcode, a 12 bp unique molecular identifier (UMI), and a poly-dT primer together with oil for the emulsion reaction were loaded onto the 10x Chromium Chip G. The Chromium Controller partitions the cells into nanoliter-scale gel beads in emulsion (GEMS) within which reverse-transcription occurs. All cDNAs within a GEM, i.e. from one cell, shared a common barcode. After the RT reaction, GEMs were broken and full length cDNAs were cleaned with Silane Dynabeads. cDNAs were then amplified and purified using SPRI beads. After purification, cDNAs were assayed on an Agilent 4200 TapeStation High Sensitivity D5000 ScreenTape (Agilent Technologies, Santa Clara, CA) for qualitative and quantitative analysis. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. Illumina P5 and P7 sequences (Illumina, San Diego, CA), a sample index, and TruSeq read 2 primer sequence were added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contained P5 and P7 primers used in Illumina bridge amplification.
Libraries were constructed at the Molecular Genomics Core of Duke University. Libraries were prepared following the 10x Genomics Single Cell 3’ v3.1 protocol (10x Genomics, Pleasanton, CA).

treatment_protocol: Melanoma tissues were harvested on day 10 and CD45+ cells from melanoma tissues were sorted by FACS for single cell RNA-seq. FACS sorting purity was around 85%.

value: melanoma

value: CD45+ cells

value: WT

value: control sgRNA


title: B16 Knockout

description: 10x Genomics

value: NGF sgRNA


title: eIF4E1_control_RIBOseq_1


title: Animal C2 Gray Matter ROI 79

description:
GeoMx DSP
ROI_79_GM_C2

value: Fetal brain

value: GM


title: Animal C2 Superficial White Matter ROI 78

description:
GeoMx DSP
ROI_78_SWM_C2

value: mock


title: Input_Aged_Rep2

city: Shantou

first: Chengyang

middle: Peter

last: Huang

address: 22 Xinling Street

institute: Shantou University Medical College

data_processing:
ChIP-Seq reads were aligned to the mm10 genome using Bowtie software (for single-end) or Bowtie2 (for paired-end) with default settings. Only uniquely mapping reads with at most two mismatches were retained. The reads of repeated samples were merged in the BAM file for peak calling analysis. Peaks were called using MACS2 with default settings. Bedgraph (Bdg) files were generated using MACS2.
Assembly: mm10
Supplementary files format and content: Bedgraph files with peaks (except for input samples)

source_name: Neural stem cells

growth_protocol: Primary NSCs were isolated from the brain SVZs of young (2 months) and aged (18 months) mice, respectively (Nat Protoc. 2012 Nov; 7(11):2005-2012). Briefly, microdissection of the brain SVZ was performed on ice. The tissue pieces of SVZ from 6 mice were pooled and dissociated into single cells using Neural Tissue Dissociation kit (Miltenyi Biotec). The NSCs were maintained in the initial proliferation medium at 37°C at 5% CO2.

extract_protocol:
NSCs were fixed with 1% formaldehyde for 10 min and quenched with glycine solution for 20 min at room temperature. The fixed NSCs were lysed in ChIP lysis buffer on ice. Chromatin was released during cell lysis and sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-Seq libraries were prepared based on the protocol of KAPA HyperPrep Kit (Roche) complemented with the NEXTflex DNA Barcodes (Bioo Scientific).

value: Neural stem cells

tag: tissue type

value: Brain SVZ

tag: antibody

value: none (input)

tag: condition

value: Aged


title: SalineC

tag: treatment


title: SalineB


title: Animal C2 Superficial White Matter ROI 77

description:
GeoMx DSP
ROI_77_SWM_C2

tag: brain reigion

value: SWM

tag: zika infection


title: eIF4E2_input_rep3

data_processing:
sequencing adapters from read2 were removed with CutAdapt (5'adapt: CTCTTCCGATCT, 3'adapt:GATCGTCGGACT); UMI extracted with UMI-tools (pattern "NNNNNNNNNN" located at 3'end)
mapped with RNA-STAR to TgME49 genome (v58). Settings: –outFilterMismatchNoverLmax=0.1, –outFilterScoreMinOverLread=0.75, –outFilterMatchNminOverLread=0.75, –alignIntronMin50, –alignIntronMax=5000
mapped reads deduplicated with UMI-tools
peaks called with Peakachu (options -adaptive mode; -min_cluster_expr_frac = 10-6, -min_block_overlap = 0.8; -min_max_block_expr = 0.8; -mad_multiplier) = 0; -fc_cutoff = 1; -padj_threshold = 0.05)
Assembly: Toxoplasma gondii (TGME49) v58 from toxodb.org
Supplementary files format and content: eIF4E1 & 2 binding profiles across genome (bigwig)
Supplementary files format and content: eIF4E1 & 2 enriched peaks (bed)

extract_protocol:
monolayers were rinsed with PBS, UV-crosslinked 2x 175mJ/cm2 with 254nm.  Monolayers were syringe lysed and parasites were pelleted twice with PBS washes. Parasites were lysed in (50mM Tris pH7.4, 100mM NaCl, 1% NP40, 0.1% SDS, 0.5% sodium deoxycholate) and HA tag was immunoprecipated for 6h after saving an aliquot for size-matched input
library was generated according to eCLIP protocol PMID: 27018577
eCLIP

value: RH::TIR1 parental strain

value: tachyzoites


title: eIF4E2_input_rep2


title: Wdr5_Aged_Rep2

value: Wdr5 (Proteintech, 15544-1-AP)


title: IleumSingleCells - iPGC1afl/fl_CHOW - Rep6

value: CHOW


title: IleumSingleCells - iPGC1afl/fl_HFD - Rep3

value: HFD


title: Animal C2 Superficial White Matter ROI 76

description:
GeoMx DSP
ROI_76_SWM_C2

tag: animal id

tag: region of interest (roi) identifer


title: eIF4E2_input_rep1

tag: cell line


title: IleumSingleCells - iPGC1afl/fl_CHOW - Rep5


title: Wdr5_Young_Rep2

value: Young


title: IleumSingleCells - iPGC1afl/fl_CHOW - Rep3


title: IleumSingleCells - iPGC1a-/-_HFD - Rep6


title: Animal C2 Deep White Matter ROI 75

description:
GeoMx DSP
ROI_75_DWM_C2

tag: tissue

value: DWM


title: Rbbp5_Aged_Rep2

tag: cell type

value: Rbbp5 (Cell Signaling, D316P)


title: Animal C2 Deep White Matter ROI 74

description:
GeoMx DSP
ROI_74_DWM_C2