title: mock-corn oil rep3

city: Madison

first: Allan

last: Brasier

state: WI

address: 715 Highland

department: ICTR

institute: university of Wissconsin

description:
Library name: 203
10X Genomics

data_processing:
CellRanger v 8.0 was used to generate filtered barcode files.  The sequences were mapped to the Chromium_Mouse_Transcriptome_Probe_Set_v1.0.1_mm10-2020-A.csv. Cells captured are listed in the 'captured_cells.txt'.
STAR (version 2.5.2a) was used for mapping. Reads were aligned to the mm10 reference genome (provided by the Dropseq group, GSE63269).  For barcode filtering, we excluded barcodes with <200 detected genes. Cells with >10% mitochondrial reads, and >5000 UMIs were filtered from further analysis.  Downstream analysis was in ScanPy (Python).  Doublets were identified and removed using nearest-neighbor classifier (Scrublet)(38).  Batch effects were corrected using SciV.  Counts were normalized to median total counts, log transformed and PCA clustered.  Highly variable genes were identified using Seurat.  Nearest neighbor clustering was using Leiden.  Cell annotation followed best practices manually validated using PanglaoDB.  Differential gene expression was using pseudobulk correcting for multiple hypothesis using moderated estimation in DESEQ2.
Assembly: Chromium_Mouse_Transcriptome_Probe_Set_v1.0.1_mm10-2020-A.csv
Supplementary files format and content: features, barcodes and matrix as .tsv.gz files

source_name: lung

growth_protocol: mouse experiments described below

extract_protocol:
The right lung was digested in Dispase II (100mg/mL), Collagenase A (10mg/mL), DNAse I (1500 kU/mL), and CaCl2 (0.25M) into a single cell solution using a 40 mm filter to create a single cell solution. Half the cells were separated for Single Cell Sequencing.
Libraries were constructed according to the Chromium NextGEM Fixed RNA Profiling Reagent Kits user guide (10x Genomics). Cells frozen in 10X Genomics Quenching Buffer were thawed and resuspended in 0.5X PBS with 0.02% BSA. The total cell number was quantified on the Luna-FX7 automated cell counter (Logos Biosystems, Anyang, South Korea) using acridine orange/propidium iodide stain. Aliquots of less than two million cells were used as input for the probe hybridization reaction and incubated at 42C overnight (21 hours 16 minutes). Following overnight incubation, subsets of four samples with unique probe barcodes were pooled together and washed three times with 10X Genomics Post-Hyb Wash Buffer. Samples were filtered through 30 μm Celltrics filters (Sysmex, Kobe, Japan) and the appropriate volume of cells was loaded onto a Single Cell Chip Q required for recovery of [enter captured cell number] cells.  Following the completion of the Chromium run the GEMs were transferred to emulsion safe strip tubes for the cell and UMI barcoding reaction using an Eppendorf MasterCycler Pro thermocycler (Eppendorf, Hamburg, Germany). After the GEM incubation, GEMs were broken, and the barcoded probe products were amplified by PCR. A portion of the amplified probe products was put into a second PCR reaction to add unique dual indexes to each library. The final libraries were quantified on the Qubit v4 fluorometer (ThermoFisher Scientific) and profiled on the Agilent 4200 Tapestation (Agilent Technologies, Santa Clara, CA). These libraries were sequenced on a NovaSeq X+ sequencer with paired-end, 150bp sequencing. Data was processed with bcl2fastq.

treatment_protocol: Scgb1a1-Cre X RelAfl/fl mice were Mock (PBS) or RSV-infected 3-5 weeks after birth (107 PFU).  Three days post-infection, when inflammation/viral replication resolved, mice were randomized into corn oil (10% ethanol and 90% corn oil; RelA WT) or tamoxifen (TMX) treatment (20 mg/kg/d i.p.; Sigma Aldrich, St. Louis, MO; T5648; RelA CKO) for 10 doses.  Animals were then rested for an additional week (21d post-RSV infection) before they were euthanized and lungs collected.

value: lung

value: scgb1a1-Cre X RelA fl/fl

value: corn oil


title: R_E18_5_WT_1

status: Public on Apr 01 2026

type: SRA

city: zhejiang

first: Siyu

last: Chen

address: zhejiang

country: China

institute: zhejiang university

description: Library name: R_E18_5_WT_1

library_source: transcriptomic

data_processing:
Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm10) with STAR v2.7.11a and ERCC spike-in sequences using Hisat2 v2.2.1. Only uniquely mapped reads were assembled into transcripts using feature Counts v2.0.6. The expression level of each transcript was quantified to the normalized TPM and normalized to the ERCC spike-in. Only transcripts with TPM > 1 in at least one sample were considered in all analyses.
Assembly: mm10
Supplementary files format and content: TPM

molecule: total RNA

organism: Mus musculus

source_name: ovary

extract_protocol:
Single cells are obtained by lysing of ovaries from mice in Lysis Buffer (DMEM, 13 WU/ml Liberase™ DH, Dnase I).
Library construction was performed based on the well-established protocol using the Fast RNA-seq Lib Prep Kit V2 (ABclonal).

tag: tissue

value: ovary

tag: strain

tag: cell type

value: oocyte

tag: genotype

value: WT


title: E38_FU2 Alpha

city: Cambridge

first: Samuel

last: Wright

state: MA

address: 415 Main St.

country: USA

institute: Broad Institute of MIT and Harvard

description:
Library name: Sample 193
Illumina

data_processing:
The analysis pipeline described in Li et al., 2019 was used to obtain bulk TCR CDR3 sequences found in blood samples (Li et al., Nat. Protoc. 2019)
Assembly: Human GRCh38
Supplementary files format and content: csv files
Library strategy: TCR-Seq

organism: Homo sapiens

source_name: PBMCs

extract_protocol:
Matched peripheral blood was collected prior to initiation of treatment and at serial timepoints aligned with tumor samples as described in the protocol.
Concentration, 260/280 and 260/230nm ratios were measured with ND1000 spectrophotometer (Nanodrop Technologies, Thermo-Fisher Scientific) and then DNA/RNA was quantified using a Qubit fluorometer (Life Technologies).

value: PBMCs


title: PNKY_96h_rep1_RNAseq

city: Boulder

first: Mingfeng

last: Liu

state: CO

address: 709 Mohawk Dr

institute: University of Colorado

description: Library name: PNKY_96_1

data_processing:
Quality control, read mapping, and quantification were performed using nf-core/rnaseq v3.14.0 (Ewels et al. 2020).
Assembly: The cleaned reads were aligned to the GRCh38.p13 human reference genome and quantified using GENCODE v38 annotations.
Supplementary files format and content: .csv, raw gene counts and tpm

source_name: hiPSCs

extract_protocol:
RNA was harvested using Directzol RNA Miniprep kit (ZymoResearch). RNA integrity and quantity were assessed using Agilent 2100 Bioanalyzer and NanoDrop.
Ribosomal RNA was depleted from total RNA using a commercial rRNA depletion kit. Strand-specific sequencing libraries were constructed following standard Illumina-compatible protocols. Library quality was assessed, and paired-end sequencing was performed on an Illumina platform. All library construction and sequencing steps were conducted by Novogene Co., Ltd.

tag: cell line

value: hiPSCs


title: PNKY_24h_rep2_RNAseq

description: Library name: PNKY_24_2


title: mock-corn oil rep2

description:
Library name: 202
10X Genomics

library_source: transcriptomic single cell

tag: treatment


title: PNKY_24h_rep3_RNAseq

description: Library name: PNKY_24_3


title: E38_FU1 Beta

description:
Library name: Sample 192
Illumina


title: PNKY_48h_rep1_RNAseq

description: Library name: PNKY_48_1


title: mock-corn oil rep1

description:
Library name: 201
10X Genomics


title: E38_FU1 Alpha

description:
Library name: Sample 191
Illumina


title: PNKY_48h_rep2_RNAseq

description: Library name: PNKY_48_2


title: PNKY_24h_rep1_RNAseq

description: Library name: PNKY_24_1


title: PNKY_16h_rep3_RNAseq

description: Library name: PNKY_16_3


title: PNKY_16h_rep1_RNAseq

description: Library name: PNKY_16_1


title: PNKY_16h_rep2_RNAseq

description: Library name: PNKY_16_2


title: E38_B Beta

description:
Library name: Sample 190
Illumina


title: Control, whole bone

city: Farmington

first: Ernesto

last: Canalis

state: CT

address: 263 Farmington Avenue

department: Orthopaedic Surgery

institute: UConn Health

description:
Library name: Control
10X Genomics

data_processing:
Demultiplexing, barcode processing, gene counting done using Cell Ranger Multi (v9.0.1) software.
Assembly: Mouse (GRCm39) 2024-A
Supplementary files format and content: H5, filtered feature-barcode matrix

source_name: whole bone

extract_protocol:
scRNA-Seq was conducted in femoral bone samples from 5-month-old male LepR-Cre;Hes1∆/∆ and sex-matched controls. Intact femoral bones were excised, the marrow flushed, and bones digested with collagenase, dispace and DNase, incubated with ACK lysis buffer to remove red blood cells followed by immune and erythroid cell depletion by double negative (CD45−;TER119−) selection by fluorescence activated cell sorting.
Barcoded libraries were prepared using a ChromiumX instrument and a Chromium Single Cell GEM-X Universal 3' gene expression v4 4-plex library and a GEM-X OCM3' Chip v4 4-plex kit. cDNA amplification and library generation were performed according to manufacturer’s protocol. cDNAs from a single cell had the same barcode, allowing the sequencing reads to be mapped back to the cell of origin. Libraries were validated for length and adapter dimer removal using the Agilent TapeStation D1000 High Sensitivity assay, quantified and sequenced as one sample pool on an AVITI Platform using 2 x 7.5 high-output flow cell. Target read depth of 50,000 transcriptome reads per cell was achieved in each sample.

value: whole bone

value: Control


title: Proband_BM_AML

type: genomic

city: Perugia

first: Cristina

last: Mecucci

address: Piazzale Menghini n.9

department: Department of Medicine, Hematology and Bone Marrow Transplantation Unit

country: Italy

institute: University of Perugia

description: CytoScan HD Array GeneChip

hyb_protocol: DNA was restriction digested, ligated, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G

data_processing:
Protocol was supported by Affymetrix GeneChip Command Console (AGCC) software. Analysis was performed through Affymetrix Chromosome Analysis 4.3 (ChAS) software with filters set at 200 Kb for Copy Number Alterations (CNAs) and 50 Mb for copy neutral Loss Of Heterozygosity (cnLOH). Our data refer to NetAffx Build 20211122 (hg19) database
primary data description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

molecule: genomic DNA

source_name: Bone Marrow

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA were extracted from bone marrow cells of patients using All Prep DNA/RNA Mini Kit (Qiagen). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, Bioanalyzer and/or Tapestation visualization (Agilent 2100 Bioanalyzer) and agarose gel electrophoresis

value: FXN trinucleotide-GAA repeat expansion (1000±50); RUNX1 c.681dup, p.L228Tfs*33; MPO c.2031-2A>C; RTEL1 c.3437C>T; NF1 c.1019_1020insAAAATAGG

value: Bone Marrow


title: Healthy_Brother_PB

description: CytoScan HD Array GeneChip

source_name: Peripheral Blood

value: FXN trinucleotide-GAA repeat expansion

value: Peripheral Blood


title: LepRCre;Hes1, whole bone

description:
Library name: LepRCre_Hes1
10X Genomics

value: LepR-Cre;Hes1 delta/delta


title: PNKY_8h_rep1_RNAseq

description: Library name: PNKY_8_1


title: PNKY_8h_rep3_RNAseq

description: Library name: PNKY_8_3


title: Mother_PB

description: CytoScan HD Array GeneChip

value: FXN trinucleotide-GAA repeat expansion; RUNX1 c.681dup, p.L228Tfs*33; MPO c.2031-2A>C; RTEL1 c.3437C>T; TET2 C.4889C>A; TET2 c.238C>T ; TET2 c.4624C>T; DNMT3A c.2711C>A; FAT1 c.6463G>T


title: E38_B Alpha

description:
Library name: Sample 189
Illumina


title: PNKY_8h_rep2_RNAseq

description: Library name: PNKY_8_2


title: Proband_BM_ALL

description: CytoScan HD Array GeneChip

value: FXN trinucleotide-GAA repeat expansion (1000±50); RUNX1 c.681dup, p.L228Tfs*33; MPO c.2031-2A>C; RTEL1 c.3437C>T; NF1 c.1019_1020insAAAATAGG; NOTCH1 c.4754T>C; FBXW7 c.1040G>A


title: PNKY_4h_rep1_RNAseq

description: Library name: PNKY_4_1


title: PNKY_2h_rep3_RNAseq

description: Library name: PNKY_2_3


title: control 16

city: Cheonan

first: Keunsoo

last: Kang

state: Chungnam

address: Dandae-ro 119

department: Microbiology

country: South Korea

institute: Dankook University

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented, and hybridized to the Infinium MethylationEPIC v2.0 BeadChip following the standard Illumina user guide.

scan_protocol: Arrays were imaged using the Illumina iScan system with standard recommended settings.

data_processing: Raw IDAT files were processed using two independent pipelines to generate genome-wide DNA methylation profiles. For the file minfi_beta_with_detectionp.tsv, processing was performed using the minfi package with Noob-based normalization (preprocessNoob) for background correction and dye-bias adjustment. For the file sesame_beta_with_detectionp.tsv, processing was conducted using the SeSAMe package with the '0CDB' prep code (no masking, pOOBAH, Noob dye-bias, Noob background). Both files contain Beta values and detection p-values derived from their respective workflows, exported without additional probe or sample filtering.

label: Cy3 and Cy5

source_name: peripheral blood

label_protocol: Bisulfite conversion was performed using the standard Illumina Infinium HD Methylation protocol.

growth_protocol: Not applicable

extract_protocol: Whole blood (3 mL) was collected in citrate-coated tubes. Buffy coat was separated by centrifugation at 100 × g for 15 min and stored at -80°C. Genomic DNA was extracted from buffy coats using the DNeasy Blood & Tissue Kit (Qiagen, Cat. no. 69506) according to the manufacturer's instructions and stored at -20°C until use.

treatment_protocol: Not applicable

value: peripheral blood

tag: Sex

value: female

tag: hb


title: E37_FU2 Alpha

description:
Library name: Sample 187
Illumina


title: PNKY_4h_rep3_RNAseq

description: Library name: PNKY_4_3


title: PNKY_4h_rep2_RNAseq

description: Library name: PNKY_4_2


title: E37_FU2 Beta

description:
Library name: Sample 188
Illumina


title: PNKY_2h_rep1_RNAseq

description: Library name: PNKY_2_1


title: PNKY_2h_rep2_RNAseq

description: Library name: PNKY_2_2


title: E37_FU1 Beta

description:
Library name: Sample 186
Illumina


title: E37_FU1 Alpha

description:
Library name: Sample 185
Illumina


title: control 14

value: male


title: control 15


title: E37_EOT Beta

description:
Library name: Sample 184
Illumina


title: control 12


title: PNKY_0h_rep3_RNAseq

description: Library name: PNKY_0_3


title: control 13


title: PNKY_0h_rep2_RNAseq

description: Library name: PNKY_0_2


title: PNKY_0h_rep1_RNAseq

description: Library name: PNKY_0_1


title: LNCPRESS1_96h_rep3_RNAseq

description: Library name: LNCPRESS1_96_3


title: control 11


title: LNCPRESS1_96h_rep2_RNAseq

description: Library name: LNCPRESS1_96_2


title: LNCPRESS1_96h_rep1_RNAseq

description: Library name: LNCPRESS1_96_1


title: E37_EOT Alpha

description:
Library name: Sample 183
Illumina


title: E37_B Beta

description:
Library name: Sample 182
Illumina


title: all-SVD 16


title: E37_B Alpha

description:
Library name: Sample 181
Illumina


title: LNCPRESS1_24h_rep1_RNAseq

description: Library name: LNCPRESS1_24_1


title: LNCPRESS1_48h_rep2_RNAseq

description: Library name: LNCPRESS1_48_2


title: all-SVD 15


title: LNCPRESS1_48h_rep1_RNAseq

description: Library name: LNCPRESS1_48_1


title: control 10


title: LNCPRESS1_48h_rep3_RNAseq

description: Library name: LNCPRESS1_48_3


title: LNCPRESS1_16h_rep2_RNAseq

description: Library name: LNCPRESS1_16_2


title: LNCPRESS1_16h_rep3_RNAseq

description: Library name: LNCPRESS1_16_3


title: all-SVD 14


title: LNCPRESS1_24h_rep3_RNAseq

description: Library name: LNCPRESS1_24_3


title: E36_FU1 Beta

description:
Library name: Sample 180
Illumina


title: LNCPRESS1_24h_rep2_RNAseq

description: Library name: LNCPRESS1_24_2


title: E36_FU1 Alpha

description:
Library name: Sample 179
Illumina


title: LNCPRESS1_16h_rep1_RNAseq

description: Library name: LNCPRESS1_16_1


title: LNCPRESS1_8h_rep3_RNAseq

description: Library name: LNCPRESS1_8_3


title: E36_B Beta

description:
Library name: Sample 178
Illumina


title: all-SVD 13


title: LNCPRESS1_8h_rep1_RNAseq

description: Library name: LNCPRESS1_8_1


title: control 9


title: E36_B Alpha

description:
Library name: Sample 177
Illumina


title: all-SVD 12


title: all-SVD 11


title: LNCPRESS1_2h_rep3_RNAseq

description: Library name: LNCPRESS1_2_3


title: LNCPRESS1_4h_rep1_RNAseq

description: Library name: LNCPRESS1_4_1


title: E35_FU2 Beta

description:
Library name: Sample 176
Illumina


title: LNCPRESS1_2h_rep2_RNAseq

description: Library name: LNCPRESS1_2_2


title: E35_FU1 Alpha

description:
Library name: Sample 173
Illumina


title: LNCPRESS1_4h_rep2_RNAseq

description: Library name: LNCPRESS1_4_2


title: LNCPRESS1_8h_rep2_RNAseq

description: Library name: LNCPRESS1_8_2


title: E35_FU1 Beta

description:
Library name: Sample 174
Illumina


title: E35_FU2 Alpha

description:
Library name: Sample 175
Illumina


title: LNCPRESS1_0h_rep3_RNAseq

description: Library name: LNCPRESS1_0_3


title: LNCPRESS1_2h_rep1_RNAseq

description: Library name: LNCPRESS1_2_1


title: control 7


title: mock-corn oil rep4

description:
Library name: 204
10X Genomics

value: lung

value: scgb1a1-Cre X RelA fl/fl

value: corn oil


title: LNCPRESS1_0h_rep2_RNAseq

description: Library name: LNCPRESS1_0_2


title: LINCROR_48h_rep2_RNAseq

description: Library name: LINCROR_48_2


title: LNCPRESS1_4h_rep3_RNAseq

description: Library name: LNCPRESS1_4_3


title: E35_EOT Beta

description:
Library name: Sample 172
Illumina

value: PBMCs


title: control 6


title: all-SVD 10


title: LNCPRESS1_0h_rep1_RNAseq

description: Library name: LNCPRESS1_0_1

value: hiPSCs


title: all-SVD 9


title: E35_B Beta

description:
Library name: Sample 170
Illumina


title: control 5


title: LINCROR_16h_rep1_RNAseq

description: Library name: LINCROR_16_1


title: LINCROR_24h_rep2_RNAseq

description: Library name: LINCROR_24_2


title: E35_B Alpha

description:
Library name: Sample 169
Illumina


title: all-SVD 8


title: E35_EOT Alpha

description:
Library name: Sample 171
Illumina


title: control 8


title: LINCROR_16h_rep2_RNAseq

description: Library name: LINCROR_16_2


title: LINCROR_24h_rep3_RNAseq

description: Library name: LINCROR_24_3


title: LINCROR_8h_rep3_RNAseq

description: Library name: LINCROR_8_3


title: LINCROR_48h_rep1_RNAseq

description: Library name: LINCROR_48_1


title: LINCROR_24h_rep1_RNAseq

description: Library name: LINCROR_24_1


title: LINCROR_16h_rep3_RNAseq

description: Library name: LINCROR_16_3


title: RP11_0h_rep3_RNAseq

description: Library name: RP11_0_3


title: E34_FU2 Beta

description:
Library name: Sample 168
Illumina


title: E34_FU2 Alpha

description:
Library name: Sample 167
Illumina


title: all-SVD 7


title: LINCROR_8h_rep2_RNAseq

description: Library name: LINCROR_8_2


title: LINCROR_8h_rep1_RNAseq

description: Library name: LINCROR_8_1


title: control 3


title: LINCROR_4h_rep2_RNAseq

description: Library name: LINCROR_4_2


title: LINCROR_2h_rep3_RNAseq

description: Library name: LINCROR_2_3


title: E34_FU1 Beta

description:
Library name: Sample 166
Illumina


title: control 4


title: all-SVD 5


title: E34_B Alpha

description:
Library name: Sample 163
Illumina


title: LINCROR_4h_rep3_RNAseq

description: Library name: LINCROR_4_3


title: LINCROR_2h_rep1_RNAseq

description: Library name: LINCROR_2_1


title: control 2


title: LINCROR_4h_rep1_RNAseq

description: Library name: LINCROR_4_1


title: E34_FU1 Alpha

description:
Library name: Sample 165
Illumina


title: E33_FU2 Beta

description:
Library name: Sample 162
Illumina


title: all-SVD 6


title: LINCROR_0h_rep1_RNAseq

description: Library name: LINCROR_0_1


title: E34_B Beta

description:
Library name: Sample 164
Illumina


title: LINCROR_2h_rep2_RNAseq

description: Library name: LINCROR_2_2


title: LINCPINT_96h_rep3_RNAseq

description: Library name: LINCPINT_96_3


title: LINCROR_0h_rep3_RNAseq

description: Library name: LINCROR_0_3


title: E33_FU2 Alpha

description:
Library name: Sample 161
Illumina


title: LINCPINT_96h_rep2_RNAseq

description: Library name: LINCPINT_96_2


title: all-SVD 4


title: LINCPINT_96h_rep1_RNAseq

description: Library name: LINCPINT_96_1


title: LINCPINT_48h_rep3_RNAseq

description: Library name: LINCPINT_48_3


title: control 1


title: LINCROR_0h_rep2_RNAseq

description: Library name: LINCROR_0_2


title: E33_FU1 Beta

description:
Library name: Sample 160
Illumina


title: all-SVD 2


title: E31_FU2 Beta

description:
Library name: Sample 156
Illumina


title: LINCPINT_16h_rep1_RNAseq

description: Library name: LINCPINT_16_1


title: all-SVD 3


title: LINCPINT_8h_rep2_RNAseq

description: Library name: LINCPINT_8_2


title: Ovarian Sample 13; NPL

city: Ithaca

first: Laurie

last: Francoeur

state: NY

address: 507 Tower Rd

department: Animal Science

institute: Cornell University

description:
Library name: LF5-sample13_NPL
Column Name in RawCounts.txt: LF5-13

data_processing:
FastQ files were first processed through trim-galore (Barbraham Institute, Cambridge, UK) to trim adaptors and filter for low-quality reads as a quality control step.
Assembly: Galgal6
Supplementary files format and content: Text file includes raw counts for samples.

organism: Gallus gallus

growth_protocol: Single-comb White Leghorn hens (Shaver; n = 40) were reared in individual cages. Hens were given feed and water ad libitum and maintained on a 16L:8D cycle. Egg-laying data were collected daily from 16 to 76 weeks of age.

extract_protocol:
Total RNA was extracted from a ~10 mg sample of the ovarian body with follicles >1 mm removed using Trizol reagent (ThermoFisher Scientific, Waltham, MA, USA). Ovarian RNA was cleaned using an RNeasy Mini kit with optional on-column DNase treatment.
RNA libraries were consturcted using NEBNext Ultra II [Directional] RNA Library Prep Kit (New England Biolabs, Ipswich, MA).

treatment_protocol: Hens were reared until 76 weeks and were stratified into quartiles according to egg-laying efficiency, and were characterized as persistent laying (PL, n=3, egg-laying rate= 100%) or non-persistent laying (NPL, n=4, egg-laying rate ≤82%) based on upper and lower quartiles respectively.

value: ovary

tag: sample group

value: NPL


title: E33_B Beta

description:
Library name: Sample 158
Illumina


title: E33_B Alpha

description:
Library name: Sample 157
Illumina


title: E33_FU1 Alpha

description:
Library name: Sample 159
Illumina


title: LINCPINT_48h_rep2_RNAseq

description: Library name: LINCPINT_48_2


title: all-SVD 1


title: LINCPINT_48h_rep1_RNAseq

description: Library name: LINCPINT_48_1


title: LINCPINT_16h_rep2_RNAseq

description: Library name: LINCPINT_16_2


title: LINCPINT_16h_rep3_RNAseq

description: Library name: LINCPINT_16_3


title: Ovarian Sample 42; NPL

description:
Library name: LF7-sample42_NPL
Column Name in RawCounts.txt: LF7-42


title: LINCPINT_24h_rep1_RNAseq

description: Library name: LINCPINT_24_1


title: LINCPINT_24h_rep2_RNAseq

description: Library name: LINCPINT_24_2


title: LINCPINT_24h_rep3_RNAseq

description: Library name: LINCPINT_24_3


title: LINCPINT_8h_rep3_RNAseq

description: Library name: LINCPINT_8_3


title: LINCPINT_8h_rep1_RNAseq

description: Library name: LINCPINT_8_1


title: Ovarian Sample 12; NPL

description:
Library name: LF4-sample12_NPL
Column Name in RawCounts.txt: LF4-12


title: E31_FU2 Alpha

description:
Library name: Sample 155
Illumina


title: E31_FU1 Beta

description:
Library name: Sample 154
Illumina


title: LINCPINT_4h_rep3_RNAseq

description: Library name: LINCPINT_4_3


title: LINCPINT_4h_rep1_RNAseq

description: Library name: LINCPINT_4_1


title: Ovarian Sample 10; NPL

description:
Library name: LF3-sample10_NPL
Column Name in RawCounts.txt: LF3-10


title: LINCPINT_4h_rep2_RNAseq

description: Library name: LINCPINT_4_2


title: E31_FU1 Alpha

description:
Library name: Sample 153
Illumina


title: E31_B Beta

description:
Library name: Sample 152
Illumina


title: Ovarian Sample 20; PL

description:
Library name: LF6-sample20_PL
Column Name in RawCounts.txt: LF6-20

value: PL


title: LINCPINT_2h_rep3_RNAseq

description: Library name: LINCPINT_2_3


title: LINCPINT_0h_rep2_RNAseq

description: Library name: LINCPINT_0_2


title: LINCPINT_2h_rep2_RNAseq

description: Library name: LINCPINT_2_2


title: Ovarian Sample 9; PL

description:
Library name: LF2-sample9_PL
Column Name in RawCounts.txt: LF2-9


title: E31_B Alpha

description:
Library name: Sample 151
Illumina


title: Ovarian Sample 8; PL

description:
Library name: LF1-sample8_PL
Column Name in RawCounts.txt: LF1-8


title: E30_FU2 Alpha

description:
Library name: Sample 149
Illumina


title: E30_FU2 Beta

description:
Library name: Sample 150
Illumina


title: LINCPINT_0h_rep1_RNAseq

description: Library name: LINCPINT_0_1


title: LINC01547_96h_rep1_RNAseq

description: Library name: LINC01547_96_1


title: hALT_1

type: RNA

city: Yokohama City

first: Yasuharu

last: Ueno

state: Kanagawa

address: 3-9  Fuku-ura, Kanazawa-ku

department: Graduate School of Medicine

country: Japan

institute: Yokohama City University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays ( G4845A,  G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent High-Resolution Microarray Scanner using one color scan setting for micro array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 12.1.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
The raw signal intensities of samples were log2-transformed and normalised by the quantile algorithm.

source_name: Hu AL

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Purification kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Adult liver tissue


title: hALT_2


title: LINC01547_96h_rep3_RNAseq

description: Library name: LINC01547_96_3


title: LINCPINT_0h_rep3_RNAseq

description: Library name: LINCPINT_0_3


title: LINCPINT_2h_rep1_RNAseq

description: Library name: LINCPINT_2_1


title: LINC01547_48h_rep3_RNAseq

description: Library name: LINC01547_48_3


title: LINC01547_48h_rep2_RNAseq

description: Library name: LINC01547_48_2


title: LINC01547_96h_rep2_RNAseq

description: Library name: LINC01547_96_2


title: E30_FU1 Beta

description:
Library name: Sample 148
Illumina


title: hiPSC-LO d8

source_name: hiPSC-LO d8

value: hiPSC-LO d8


title: E30_FU1 Alpha

description:
Library name: Sample 147
Illumina


title: E30_B Beta

description:
Library name: Sample 146
Illumina


title: E30_B Alpha

description:
Library name: Sample 145
Illumina


title: hiPSC-LO d4

source_name: hiPSC-LO d4

value: hiPSC-LO d4


title: LINC01547_16h_rep3_RNAseq

description: Library name: LINC01547_16_3


title: LINC01547_24h_rep1_RNAseq

description: Library name: LINC01547_24_1


title: LINC01547_24h_rep2_RNAseq

description: Library name: LINC01547_24_2


title: LINC01547_8h_rep3_RNAseq

description: Library name: LINC01547_8_3


title: E29_FU2 Beta

description:
Library name: Sample 144
Illumina


title: LINC01547_8h_rep2_RNAseq

description: Library name: LINC01547_8_2


title: LINC01547_24h_rep3_RNAseq

description: Library name: LINC01547_24_3


title: hiPSC-LO d1

source_name: hiPSC-LO d1

value: hiPSC-LO d1


title: E29_FU2 Alpha

description:
Library name: Sample 143
Illumina


title: LINC01547_48h_rep1_RNAseq

description: Library name: LINC01547_48_1


title: LINC01547_16h_rep2_RNAseq

description: Library name: LINC01547_16_2


title: Immortalized hepatocyte cell line DeltaCN60

city: Aachen

first: Ralf

last: Weiskirchen

address: Pauwelsstr. 30

department: IFMPEGKC

country: Germany

institute: RWTH University Hospital Aachen

description: Library name: mRNA expression in DeltaCN60 cells, cultured under standard conditions

data_processing:
The data was processed with the nf-core/rnaseq pipeline (v3.12.0).
Assembly: GRCm39 v35
Supplementary files format and content: Raw sequencing data (FASTQ files: DeltaCN60_S1_R1_001.fastq.gz and DeltaCN60_S2_R2_001.fastq.gz) and processed transcript abundance tables can be found in this entry.

growth_protocol: The cells were routinely cultured in Dulbecco’s modified Eagle’s medium (DMEM, #D6171)) supplemented with 10% fetal bovine serum (FBS, #F7524), 2 mM L-glutamine (#G7513), 1 mM sodium pyruvate (#S8636), and 1× penicillin/streptomycin (#P0781). All reagents were obtained from Sigma-Aldrich (Taufkirchen, Germany).

extract_protocol:
Cells were cultured until they reached about 80% confluence before being lysed with guanidine thiocyanate for total RNA extraction using the cesium chloride cushion method.
All library preparation and sequencing were performed in a single batch, so no batch effects were present, and no batch correction was applied. Paired-end RNA sequencing was carried out on an Illumina MiSeq platform using a MiSeq Reagent Kit v2 (300 cycles).

treatment_protocol: no treatment

value: hepatocyte

value: no treatment


title: LINC01547_8h_rep1_RNAseq

description: Library name: LINC01547_8_1


title: saline_input_rep3

city: Chicago

first: Chuan

last: He

state: Illinois

address: 929 E 57th St, Room E319B

institute: University of Chicago

description: Library name: s.input.rep3

data_processing:
Adaptors trimmed with Cutadapt
Reads mapped to mm10 genome with STAR
Peaks called with CLIPPER package
Assembly: mm10
Supplementary files format and content: clipper_c_conf.csv, file summarizing peaks called from control (saline) samples
Supplementary files format and content: clipper_s_conf.csv, file summarizing peaks called from cocaine treated samples

source_name: striatum

extract_protocol:
RNAs were extracted by douncing the frozen brain tissue in ice-cold RIPA buffer (Thermo, 89901).
Both input and immunoprecipidated RNAs were end-repaired with T4 PNK  (Thermo, EK0031). Libraries were constructed with NEBNext® Small RNA Library Prep Set for Illumina®  (NEB, E7330S) according to manufacturer's instructions.

value: striatum

value: primary cells

value: striatal neurons

value: WT, C57BL/6J

value: Saline

tag: rip antibody


title: LINC01547_4h_rep3_RNAseq

description: Library name: LINC01547_4_3


title: E29_FU1 Beta

description:
Library name: Sample 142
Illumina


title: LINC01547_2h_rep3_RNAseq

description: Library name: LINC01547_2_3


title: saline_input_rep2

description: Library name: s.input.rep2


title: LINC01547_2h_rep2_RNAseq

description: Library name: LINC01547_2_2


title: LINC01547_0h_rep2_RNAseq

description: Library name: LINC01547_0_2


title: LINC01547_0h_rep3_RNAseq

description: Library name: LINC01547_0_3


title: LINC01547_16h_rep1_RNAseq

description: Library name: LINC01547_16_1


title: saline_input_rep1

description: Library name: s.input.rep1


title: LINC01547_4h_rep1_RNAseq

description: Library name: LINC01547_4_1


title: LINC00847_96h_rep2_RNAseq

description: Library name: LINC00847_96_2


title: LINC01547_2h_rep1_RNAseq

description: Library name: LINC01547_2_1


title: E29_EOT Beta

description:
Library name: Sample 140
Illumina


title: saline_clip_rep2

description: Library name: s.clip.rep2

value: monoclonal anti-YTHDF1 antibody (Abcam, ab220162)


title: LINC01547_4h_rep2_RNAseq

description: Library name: LINC01547_4_2


title: LINC01547_0h_rep1_RNAseq

description: Library name: LINC01547_0_1


title: E29_FU1 Alpha

description:
Library name: Sample 141
Illumina

value: PBMCs


title: E29_B Alpha

description:
Library name: Sample 137
Illumina


title: E29_EOT Alpha

description:
Library name: Sample 139
Illumina


title: E29_B Beta

description:
Library name: Sample 138
Illumina


title: saline_clip_rep1

description: Library name: s.clip.rep1


title: saline_clip_rep3

description: Library name: s.clip.rep3


title: cocaine_input_rep3

description: Library name: c.input.rep3

value: cocaine


title: LINC00847_96h_rep1_RNAseq

description: Library name: LINC00847_96_1

value: hiPSCs


title: cocaine_input_rep2

description: Library name: c.input.rep2


title: LINC00847_48h_rep3_RNAseq

description: Library name: LINC00847_48_3


title: cocaine_input_rep1

description: Library name: c.input.rep1


title: LINC00847_48h_rep1_RNAseq

description: Library name: LINC00847_48_1


title: cocaine_clip_rep3

description: Library name: c.clip.rep3


title: LINC00847_24h_rep3_RNAseq

description: Library name: LINC00847_24_3


title: E28_FU1 Alpha

description:
Library name: Sample 133
Illumina


title: LINC00847_96h_rep3_RNAseq

description: Library name: LINC00847_96_3


title: LINC00847_24h_rep2_RNAseq

description: Library name: LINC00847_24_2


title: LINC00847_16h_rep3_RNAseq

description: Library name: LINC00847_16_3


title: E28_FU2 Beta

description:
Library name: Sample 136
Illumina


title: LINC00847_48h_rep2_RNAseq

description: Library name: LINC00847_48_2


title: LINC00847_16h_rep2_RNAseq

description: Library name: LINC00847_16_2


title: E28_EOT Beta

description:
Library name: Sample 132
Illumina


title: LINC00847_24h_rep1_RNAseq

description: Library name: LINC00847_24_1


title: cocaine_clip_rep1

description: Library name: c.clip.rep1


title: LINC00847_8h_rep3_RNAseq

description: Library name: LINC00847_8_3


title: E28_FU1 Beta

description:
Library name: Sample 134
Illumina


title: LINC00847_4h_rep3_RNAseq

description: Library name: LINC00847_4_3


title: E28_FU2 Alpha

description:
Library name: Sample 135
Illumina


title: E28_EOT Alpha

description:
Library name: Sample 131
Illumina


title: LINC00847_8h_rep2_RNAseq

description: Library name: LINC00847_8_2


title: LINC00847_16h_rep1_RNAseq

description: Library name: LINC00847_16_1


title: E28_B Beta

description:
Library name: Sample 130
Illumina


title: LINC00847_0h_rep1_RNAseq

description: Library name: LINC00847_0_1


title: LINC00847_8h_rep1_RNAseq

description: Library name: LINC00847_8_1


title: LINC00847_0h_rep2_RNAseq

description: Library name: LINC00847_0_2


title: E28_B Alpha

description:
Library name: Sample 129
Illumina


title: LINC00847_4h_rep1_RNAseq

description: Library name: LINC00847_4_1


title: E27_FU2 Alpha

description:
Library name: Sample 127
Illumina


title: LINC00847_0h_rep3_RNAseq

description: Library name: LINC00847_0_3


title: LINC00847_4h_rep2_RNAseq

description: Library name: LINC00847_4_2


title: nSGOs, with growth factors, rep1, gene expression

city: Daejeon

first: Jong-Eun

last: Park

address: 291, Daehak-ro, Yuseong-gu

institute: Korea Advanced Institute of Science and Technology

description:
Library name: MnegGpos
10x Genomics

data_processing:
Raw sequencing reads were aligned to the mouse reference genome (mm10) and quantified using Cell Ranger v7.1.0 (10× Genomics). Ambient RNA contamination was corrected using CellBender v0.2.1. Subsequent analyses were performed in Python using Scanpy v1.9.1. Cells were filtered based on the following quality-control thresholds: minimum 2,000 total counts, minimum 800 detected genes, maximum 10% mitochondrial gene fraction, and Scrublet doublet score below 0.2. After filtering, count matrices were log-normalized and the top 2,000 highly variable genes were selected for downstream analysis.
Dimensionality reduction, clustering, and batch correction Principal component analysis was performed, and the top 50 components were retained for downstream analysis. Batch effects across samples were corrected using Harmony. A shared nearest-neighbor graph was constructed, and cells were clustered using the Leiden algorithm at multiple resolutions to identify the optimal granularity. Uniform manifold approximation and projection40 was used for two-dimensional visualization. Cell types were annotated based on canonical marker gene expression and comparison with a published developmental atlas of mouse salivary glands (GSE150327). Cell cycle scoring was performed using previously defined human cell cycle gene sets converted to mouse orthologs. Additional doublet detection was performed using the DouCLing method.
Assembly: mm10
Supplementary files format and content: h5ad file of integrated and processed single-cell RNA sequencing data from three organoid conditions (nSGOs with growth factors, nSGOs without growth factors, and cSGOs) samples; found in cSGO-Total.h5ad
Supplementary files format and content: h5ad file of integrated and processed single-cell RNA sequencing data from three organoid conditions (nSGOs with growth factors, nSGOs without growth factors, and cSGOs) samples, subsetted to epithelial cells; found in cSGO-Epithelial.h5ad
Supplementary files format and content: h5ad file of integrated and processed single-cell RNA sequencing data from two organoid conditions (cSGOs and Dexa-treated cSGOs) samples; found in cSGO-Dexa.h5ad

molecule: polyA RNA

source_name: Submandibular gland

growth_protocol: Submandibular glands were dissected from PN1 ICR mice and digested with 0.5 mg/mL collagenase II (Gibco) and 0.5 mg/mL hyaluronidase (Sigma-Aldrich) in DMEM/F12 at 37°C for 30 min with gentle pipetting. Digested tissue was further dissociated using TrypLE Express (Gibco) at 37°C for 10 min. The resulting single-cell suspension was passed through a 40 μm cell strainer. Cells were resuspended in growth-factor-reduced Matrigel (Corning) and seeded at a density of 2,000 cells per 40 μL dome in 24-well plates. After solidification at 37°C for 20 min, domes were overlaid with organoid culture medium consisting of Advanced DMEM/F12 (Gibco) supplemented with 1× B27 (Gibco), 1.25 mM N-acetylcysteine (Sigma-Aldrich), 10 mM nicotinamide (Sigma-Aldrich), 10 μM Y-27632 (Tocris) for the first 48 h, 37.5 ng/mL NRG1 (PeproTech), 1 nM FGF-acidic (PeproTech), 5 nM FGF-7 (PeproTech), 100 ng/mL Noggin (PeproTech), 100 ng/mL R-Spondin-1 (PeproTech), 500 nM A83-01 (Tocris), 10 μM SB202190 (Sigma-Aldrich), and 50 ng/mL EGF (PeproTech). Medium was refreshed every 2–3 days, and organoids were passaged every 7–10 days by mechanical dissociation. Submandibular glands from E13 mouse embryos were microdissected and digested enzymatically with 1.6 U/mL Dispase II (Roche) and Accutase (Innovative Cell Technologies) at 37°C for 15 min. The mesenchymal fraction was separated from the epithelial rudiment by sequential enzymatic treatment and manual removal of epithelial buds. Mesenchymal cells were expanded in DMEM containing 10% FBS (Gibco) and 100 U/mL penicillin-streptomycin (Gibco) for up to 3 passages before use. To generate chimeric organoids (cSGOs), PN1-derived epithelial organoids were dissociated into single cells using TrypLE Express. Epithelial cells were mixed with E13-derived mesenchymal cells at defined ratios and resuspended in growth-factor-reduced Matrigel at a density of 20,000 stromal cells per 10 μL extracellular matrix. The cell-Matrigel mixture was deposited as domes in 24-well plates and allowed to solidify at 37°C for 20 min. Chimeric organoids were cultured in growth-factor-depleted medium (organoid culture medium without NRG1, FGF-acidic, FGF-7, Noggin, R-Spondin-1, A83-01, SB202190, and EGF) to assess stromal-dependent epithelial growth and differentiation. For glucocorticoid experiments, cSGOs were treated with 100 nM dexamethasone (Sigma-Aldrich) from the time of plating. For NFκB inhibition, 10 μM BAY11-7082 (Sigma-Aldrich) was added at plating. For TNFα rescue experiments, 10 ng/mL recombinant mouse TNFα (PeproTech) was added with or without dexamethasone. For cholinergic stimulation, 10 nM carbachol (Sigma-Aldrich) was applied acutely, and 1 μM atropine (Sigma-Aldrich) was used to confirm muscarinic receptor dependence. All pharmacological agents were refreshed with each medium change.

extract_protocol:
Organoids from three conditions (nSGOs with growth factors, nSGOs without growth factors, and cSGOs) and Dexa-treated versus untreated cSGOs were dissociated into single-cell suspensions using TrypLE Express at 37°C for 10 min with gentle pipetting. Cell viability was confirmed to exceed 85% by trypan blue exclusion.
Approximately 10,000 cells per condition were loaded onto a 10× Genomics Chromium Controller using the Chromium Next GEM Single Cell 3' Reagent Kit v3.1. Libraries were prepared following the manufacturer's protocol and sequenced on an Illumina NovaSeq 6000 platform targeting approximately 400 million reads per library.

value: Submandibular gland


title: cSGOs, with Dexamethasone, rep1, gene expression

description:
Library name: MposGnegDpos
10x Genomics


title: cSGOs, without Dexamethasone, rep1, gene expression

description:
Library name: MposGneg
10x Genomics


title: LINC00667c2_96h_rep3_RNAseq

description: Library name: LINC00667c2_B1_96_3


title: 5-week retina, miR-9-2 enhancer knockout, biol rep 2

city: Seattle

first: Timothy

middle: Joel

last: Cherry

state: WA

department: Pediatrics

institute: University of Washington/Seattle Children's Research Institute

description:
Library name: eKO2
10X Genomics
enh.rds

data_processing:
Cell Ranger from 10X Genomics was used align sequencing reads, demultiplex samples, and generate feature-barcode matrices. Raw feature-barcode matrices from Cell Ranger were input into Cellbender to remove ambient RNA and generate filtered feature-barcode matrices. Resulting matrices were used as input into Seurat snRNA-sequencing analysis pipeline.
Assembly: mm10
Supplementary files format and content: .h5; filtered count matrix output from Cellbender processing
Supplementary files format and content: .rds; individual Seurat objects for each timepoint, including RNA/SCT-normalized assays, annotated celltypes, and PCA/UMAP/HarmonyUMAP dimensional reductions.

molecule: nuclear RNA

source_name: Retina

extract_protocol:
Nuclei were isolated from flash frozen retinal tissue by adapting the 10X Protocol for Nuclei Isolation from Mouse Brain Tissue for Single Cell ATAC Sequencing. Briefly, for modifications, tissue was broken up by dounce before transfer to tube, and digitonin was not included in buffers for samples used with the Chromium Next GEM Single Cell 3ʹ v3.1 kit.
Single-nuclei RNA-sequencing libraries were constructed according to 10X Genomics protocols for the  Chromium Next GEM Single Cell 3ʹ v3.1 kit (E16.5, P0, enhancer KO) or the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (3-weeks), targeting 10,000 cells.

treatment_protocol: miR-9-2 knockout mice were generated by crossing Mir9-2 tm1Mtm/Mmjax mice with ROSA26::FLPe knock in and E2a-Cre mice to create a animals with a constitutive germline knockout of the miR-9-2 hairpin loop. miR-9-2 enhancer KO mice were generated by CRISPR targeting a ~300bp region corresponding to accessibility for the putative miR-9-2 enhancer.

value: Retina

value: miR-9-2 enhancer knockout

tag: developmental stage

value: 5 weeks

value: female

tag: batch


title: nSGOs, without growth factors, rep1, gene expression

description:
Library name: MnegGneg
10x Genomics


title: E27_FU2 Beta

description:
Library name: Sample 128
Illumina


title: LINC00847_2h_rep3_RNAseq

description: Library name: LINC00847_2_3


title: LINC00847_2h_rep2_RNAseq

description: Library name: LINC00847_2_2


title: LINC00847_2h_rep1_RNAseq

description: Library name: LINC00847_2_1


title: 5-week retina, miR-9-2 enhancer knockout, biol rep 1

description:
Library name: eKO1
10X Genomics
enh.rds

value: male


title: E26_FU2 Alpha

description:
Library name: Sample 125
Illumina


title: E26_FU1 Beta

description:
Library name: Sample 124
Illumina


title: LINC00667c2_96h_rep2_RNAseq

description: Library name: LINC00667c2_B1_96_2


title: LINC00667c2_48h_rep1_RNAseq

description: Library name: LINC00667c2_B1_48_1


title: 5-week retina, miR-9-2 enhancer knockout, biol rep 3

description:
Library name: eKO3
10X Genomics
enh.rds


title: E26_FU1 Alpha

description:
Library name: Sample 123
Illumina


title: E26_FU2 Beta

description:
Library name: Sample 126
Illumina


title: LINC00667c2_24h_rep1_RNAseq

description: Library name: LINC00667c2_B1_24_1


title: 5-week retina, wildtype, biol rep 3

description:
Library name: eWT3
10X Genomics
enh.rds

value: WT


title: 5-week retina, wildtype, biol rep 2

description:
Library name: eWT2
10X Genomics
enh.rds


title: LINC00667c2_24h_rep3_RNAseq

description: Library name: LINC00667c2_B1_24_3


title: LINC00667c2_96h_rep1_RNAseq

description: Library name: LINC00667c2_B1_96_1


title: LINC00667c2_48h_rep2_RNAseq

description: Library name: LINC00667c2_B1_48_2


title: LINC00667c2_48h_rep3_RNAseq

description: Library name: LINC00667c2_B1_48_3


title: cocaine_clip_rep2

description: Library name: c.clip.rep2


title: LINC00667c2_24h_rep2_RNAseq

description: Library name: LINC00667c2_B1_24_2


title: 5-week retina, wildtype, biol rep 1

description:
Library name: eWT1
10X Genomics
enh.rds


title: E26_EOT Beta

description:
Library name: Sample 122
Illumina


title: 3-week retina, miR-9-2 knockout, biol rep 5

description:
Library name: KO3WF3
10X Genomics
wk3.rds

value: miR-9-2 knockout

value: 3 weeks


title: E26_B Beta

description:
Library name: Sample 120
Illumina


title: LINC00667c2_8h_rep3_RNAseq

description: Library name: LINC00667c2_B1_8_3


title: LINC00667c2_16h_rep1_RNAseq

description: Library name: LINC00667c2_B1_16_1


title: E26_B Alpha

description:
Library name: Sample 119
Illumina


title: LINC00667c2_16h_rep2_RNAseq

description: Library name: LINC00667c2_B1_16_2


title: 3-week retina, miR-9-2 knockout, biol rep 1

description:
Library name: KO3WM1
10X Genomics
wk3.rds


title: LINC00667c2_4h_rep3_RNAseq

description: Library name: LINC00667c2_B1_4_3


title: E26_EOT Alpha

description:
Library name: Sample 121
Illumina


title: 3-week retina, miR-9-2 knockout, biol rep 4

description:
Library name: KO3WF2
10X Genomics
wk3.rds


title: E25_FU1 Beta

description:
Library name: Sample 116
Illumina


title: LINC00667c2_8h_rep2_RNAseq

description: Library name: LINC00667c2_B1_8_2


title: E25_FU2 Beta

description:
Library name: Sample 118
Illumina


title: E25_FU2 Alpha

description:
Library name: Sample 117
Illumina


title: LINC00667c2_2h_rep1_RNAseq

description: Library name: LINC00667c2_B1_2_1


title: LINC00667c2_4h_rep2_RNAseq

description: Library name: LINC00667c2_B1_4_2


title: 3-week retina, miR-9-2 knockout, biol rep 2

description:
Library name: KO3WM3
10X Genomics
wk3.rds


title: LINC00667c2_0h_rep3_RNAseq

description: Library name: LINC00667c2_B1_0_3


title: LINC00667c2_8h_rep1_RNAseq

description: Library name: LINC00667c2_B1_8_1


title: LINC00667c2_4h_rep1_RNAseq

description: Library name: LINC00667c2_B1_4_1


title: E25_EOT Alpha

description:
Library name: Sample 113
Illumina


title: LINC00667c2_0h_rep2_RNAseq

description: Library name: LINC00667c2_B1_0_2


title: 3-week retina, wildtype, biol rep 5

description:
Library name: WT3WF3
10X Genomics
wk3.rds


title: LINC00667c2_0h_rep1_RNAseq

description: Library name: LINC00667c2_B1_0_1


title: E25_EOT Beta

description:
Library name: Sample 114
Illumina


title: LINC00667c2_2h_rep2_RNAseq

description: Library name: LINC00667c2_B1_2_2


title: 3-week retina, wildtype, biol rep 4

description:
Library name: WT3WF2
10X Genomics
wk3.rds


title: LINC00667c1_96h_rep1_RNAseq

description: Library name: LINC00667c1_B1_96_1


title: LINC00667c2_2h_rep3_RNAseq

description: Library name: LINC00667c2_B1_2_3


title: E25_FU1 Alpha

description:
Library name: Sample 115
Illumina


title: 3-week retina, wildtype, biol rep 3

description:
Library name: WT3WF1
10X Genomics
wk3.rds


title: LINC00667c1_96h_rep3_RNAseq

description: Library name: LINC00667c1_B1_96_3


title: 3-week retina, wildtype, biol rep 2

description:
Library name: WT3WM3
10X Genomics
wk3.rds


title: LINC00667c1_96h_rep2_RNAseq

description: Library name: LINC00667c1_B1_96_2


title: E24_FU2 Beta

description:
Library name: Sample 112
Illumina


title: E24_FU1 Beta

description:
Library name: Sample 110
Illumina


title: E24_FU2 Alpha

description:
Library name: Sample 111
Illumina


title: LINC00667c1_48h_rep2_RNAseq

description: Library name: LINC00667c1_B1_48_2


title: P0 retina, miR-9-2 knockout, biol rep 4

description:
Library name: KOP0F2
10X Genomics
p0.rds


title: LINC00667c1_16h_rep3_RNAseq

description: Library name: LINC00667c1_B1_16_3


title: LINC00667c1_48h_rep1_RNAseq

description: Library name: LINC00667c1_B1_48_1


title: P0 retina, miR-9-2 knockout, biol rep 1

description:
Library name: KOP0M1
10X Genomics
p0.rds


title: LINC00667c1_16h_rep1_RNAseq

description: Library name: LINC00667c1_B1_16_1


title: 3-week retina, wildtype, biol rep 1

description:
Library name: WT3WM1
10X Genomics
wk3.rds


title: LINC00667c1_48h_rep3_RNAseq

description: Library name: LINC00667c1_B1_48_3


title: LINC00667c1_24h_rep2_RNAseq

description: Library name: LINC00667c1_B1_24_2


title: P0 retina, miR-9-2 knockout, biol rep 2

description:
Library name: KOP0M2
10X Genomics
p0.rds


title: P0 retina, miR-9-2 knockout, biol rep 3

description:
Library name: KOP0F1
10X Genomics
p0.rds


title: LINC00667c1_24h_rep1_RNAseq

description: Library name: LINC00667c1_B1_24_1


title: E24_FU1 Alpha

description:
Library name: Sample 109
Illumina


title: LINC00667c1_24h_rep3_RNAseq

description: Library name: LINC00667c1_B1_24_3


title: LINC00667c1_16h_rep2_RNAseq

description: Library name: LINC00667c1_B1_16_2


title: E24_B Beta

description:
Library name: Sample 106
Illumina


title: P0 retina, wildtype, biol rep 4

description:
Library name: WTP0F2
10X Genomics
p0.rds


title: E24_B Alpha

description:
Library name: Sample 105
Illumina


title: E24_EOT Alpha

description:
Library name: Sample 107
Illumina


title: E24_EOT Beta

description:
Library name: Sample 108
Illumina


title: LINC00667c1_8h_rep1_RNAseq

description: Library name: LINC00667c1_B1_8_1


title: LINC00667c1_4h_rep2_RNAseq

description: Library name: LINC00667c1_B1_4_2


title: LINC00667c1_4h_rep3_RNAseq

description: Library name: LINC00667c1_B1_4_3


title: LINC00667c1_8h_rep3_RNAseq

description: Library name: LINC00667c1_B1_8_3


title: LINC00667c1_8h_rep2_RNAseq

description: Library name: LINC00667c1_B1_8_2


title: P0 retina, wildtype, biol rep 3

description:
Library name: WTP0F1
10X Genomics
p0.rds


title: E16.5 retina, miR-9-2 knockout, biol rep 4

description:
Library name: KOE16F2
10X Genomics
e16.rds


title: P0 retina, wildtype, biol rep 2

description:
Library name: WTP0M2
10X Genomics
p0.rds


title: LINC00667c1_2h_rep2_RNAseq

description: Library name: LINC00667c1_B1_2_2


title: P0 retina, wildtype, biol rep 1

description:
Library name: WTP0M1
10X Genomics
p0.rds


title: E23_FU2 Beta

description:
Library name: Sample 104
Illumina


title: LINC00667c1_4h_rep1_RNAseq

description: Library name: LINC00667c1_B1_4_1


title: LINC00667c1_0h_rep2_RNAseq

description: Library name: LINC00667c1_B1_0_2


title: LINC00667c1_0h_rep3_RNAseq

description: Library name: LINC00667c1_B1_0_3


title: E23_FU2 Alpha

description:
Library name: Sample 103
Illumina


title: LINC00667c1_2h_rep3_RNAseq

description: Library name: LINC00667c1_B1_2_3


title: LINC00667c5_96h_rep3_RNAseq

description: Library name: LINC00667c5_B1_96_3


title: E23_EOT Alpha

description:
Library name: Sample 99
Illumina


title: E23_B Beta

description:
Library name: Sample 98
Illumina


title: LINC00667c1_0h_rep1_RNAseq

description: Library name: LINC00667c1_B1_0_1


title: E23_FU1 Alpha

description:
Library name: Sample 101
Illumina


title: E16.5 retina, miR-9-2 knockout, biol rep 1

description:
Library name: KOE16M1
10X Genomics
e16.rds


title: LINC00667c5_96h_rep1_RNAseq

description: Library name: LINC00667c5_B1_96_1


title: LINC00667c1_2h_rep1_RNAseq

description: Library name: LINC00667c1_B1_2_1


title: LINC00667c5_96h_rep2_RNAseq

description: Library name: LINC00667c5_B1_96_2


title: LINC00667c5_24h_rep2_RNAseq

description: Library name: LINC00667c5_B1_24_2


title: Rb1/p53-null mammary tumor #5

status: Public on Apr 06 2026

city: Boston

first: Zhe

last: Li

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

description: Library name: PRb-5

data_processing:
Visualization Pipeline for RNAseq (Viper) analysis tool developed by Center for Functional Cancer Epigenetics (CFCE) at Dana-Farber Cancer Institute was used to generate standard outputs.
Assembly: mm10
Supplementary files format and content: tab-delimited csv file include normalized TPM matrices for each sample.

source_name: mammary tumor

extract_protocol:
Total RNA was extracted by Zymo RNA extraction kit with Dnase I treatment to remove the genomic DNA
Libraries were prepared using Roche Kapa Biosystems RNA HyperPrep sample preparation reagents on a Beckman Coulter Biomek i7. Finished dsDNA libraries were quantified by Qubit fluorometer and Agilent TapeStation 4200. Uniquely dual indexed libraries were pooled in an equimolar ratio and shallowly sequenced on an Illumina MiSeq to further evaluate library quality and pool balance.

value: mammary tumor

value: total tumor cells

value: Rb1 L/L;Trp53L/L;Rosa26-LSL-YFP

value: Tumorigenesis induced by intraductal injection of Ad-K8-Cre


title: E16.5 retina, miR-9-2 knockout, biol rep 3

description:
Library name: KOE16F1
10X Genomics
e16.rds


title: E16.5 retina, wildtype, biol rep 4

description:
Library name: WTE16F2
10X Genomics
e16.rds


title: E23_EOT Beta

description:
Library name: Sample 100
Illumina


title: LINC00667c5_48h_rep1_RNAseq

description: Library name: LINC00667c5_B1_48_1


title: E16.5 retina, wildtype, biol rep 3

description:
Library name: WTE16F1
10X Genomics
e16.rds


title: LINC00667c5_48h_rep3_RNAseq

description: Library name: LINC00667c5_B1_48_3


title: LINC00667c5_48h_rep2_RNAseq

description: Library name: LINC00667c5_B1_48_2


title: E16.5 retina, wildtype, biol rep 2

description:
Library name: WTE16M2
10X Genomics
e16.rds


title: LINC00667c5_24h_rep3_RNAseq

description: Library name: LINC00667c5_B1_24_3


title: LINC00667c5_16h_rep3_RNAseq

description: Library name: LINC00667c5_B1_16_3


title: LINC00667c5_16h_rep2_RNAseq

description: Library name: LINC00667c5_B1_16_2


title: E23_FU1 Beta

description:
Library name: Sample 102
Illumina


title: E23_B Alpha

description:
Library name: Sample 97
Illumina


title: LINC00667c5_24h_rep1_RNAseq

description: Library name: LINC00667c5_B1_24_1


title: E16.5 retina, miR-9-2 knockout, biol rep 2

description:
Library name: KOE16M2
10X Genomics
e16.rds


title: E21_FU2 Beta

description:
Library name: Sample 96
Illumina


title: Mouse heart Immtfl/fl-Myh6-MCM 2

city: Cincinnati

first: Yasuhide

last: Kuwabara

state: Ohio

address: 240 Albert Sabin Way, Building S

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description: Library name: MitoKO2

data_processing:
1. FastQ generation and demux with BCL Convert v4.3.6 and fqtk v0.3.1.
2. Read-filtering using FastP v0.24.0: poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp.
3. Alignment to the appropriate reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads.
4. Coordinate sorting of BAM files using samtools v1.22.1.
5. UMI based de-duplication: Removal of PCR and optical duplicates using UMICollapse v1.1.0.
6. Mapping QC: Alignment quality metrics, strand specificity, and read distribution across genomic features using RSeQC v5.0.4 and Qualimap v2.3.
7. Gene-expression quantification using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file.
8. Differential expression using edgeR v4.0.16 with filtering for low-expressed genes with edgeR::filterByExpr with default values.
Assembly: GRCm39_114
Supplementary files format and content: A xlsx file contains expression data of each gene. The xlsx file also contains logFC, Pvalue, and FDR of each gene.

source_name: Heart

extract_protocol:
Total RNA was extracted from hearts using Trizol according to the manufacture's protocol.
1. Poly-A mRNA capture and reverse transcription for cDNA synthesis: oligo-dT primer to capture just the mRNA (contains sample barcode, UMI, and Read 1 sequences).2. Second strand synthesis and tagmentation: double stranded-cDNA is generated. Tagmentation creates fragments and incorporates Read 2 sequence. 3. Illumina library amplification: adds unique dual indices (UDI = i5, i7) and P5/P7 sequences.

value: Heart

value: Tamoxifen injection

value: 10 weeks after tamoxifien injection


title: LINC00667c5_16h_rep1_RNAseq

description: Library name: LINC00667c5_B1_16_1

value: hiPSCs


title: E16.5 retina, wildtype, biol rep 1

description:
Library name: WTE16M1
10X Genomics
e16.rds


title: LINC00667c5_8h_rep2_RNAseq

description: Library name: LINC00667c5_B1_8_2


title: LINC00667c5_8h_rep1_RNAseq

description: Library name: LINC00667c5_B1_8_1


title: E21_FU2 Alpha

description:
Library name: Sample 95
Illumina

value: PBMCs


title: E21_FU1 Alpha

description:
Library name: Sample 93
Illumina


title: Mouse heart Immt+/+-Myh6-Cre 3

description: Library name: MitoCTRL3


title: E21_FU1 Beta

description:
Library name: Sample 94
Illumina


title: LINC00667c5_0h_rep2_RNAseq

description: Library name: LINC00667c5_B1_0_2


title: LINC00667c5_0h_rep1_RNAseq

description: Library name: LINC00667c5_B1_0_1


title: Mouse heart Immtfl/fl-Myh6-MCM 1

description: Library name: MitoKO1


title: LINC00667c5_8h_rep3_RNAseq

description: Library name: LINC00667c5_B1_8_3


title: Mouse heart Immt+/+-Myh6-Cre 2

description: Library name: MitoCTRL2


title: LINC00667c5_0h_rep3_RNAseq

description: Library name: LINC00667c5_B1_0_3


title: LINC00667c4_BioRep2_96h_rep2_RNAseq

description: Library name: LINC00667c4_B2_96_2


title: LINC00667c4_BioRep2_96h_rep3_RNAseq

description: Library name: LINC00667c4_B2_96_3


title: LINC00667c4_BioRep2_96h_rep1_RNAseq

description: Library name: LINC00667c4_B2_96_1


title: E21_B Beta

description:
Library name: Sample 92
Illumina


title: E21_B Alpha

description:
Library name: Sample 91
Illumina


title: Mouse heart Immt+/+-Myh6-Cre 1

description: Library name: MitoCTRL1


title: LINC00667c4_BioRep2_48h_rep1_RNAseq

description: Library name: LINC00667c4_B2_48_1


title: LINC00667c4_BioRep2_48h_rep3_RNAseq

description: Library name: LINC00667c4_B2_48_3


title: LINC00667c4_BioRep2_48h_rep2_RNAseq

description: Library name: LINC00667c4_B2_48_2


title: Lin- cells, SETBP1D868N mutant, H3K14ac antibody, rep3

city: Portland

first: Julia

last: Maxson

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

description: Library name: mouse_batch2_SETBP1-D868N_H3K14ac_3

library_source: genomic

data_processing:
Paired-end reads were trimmed using Fastp with adapter detection and poly-G trimming.
Trimmed reads from K562 samples were aligned to the human genome (GRCh38/hg38) and trimmed reads from mouse Lin- samples were aligned to the mouse genome (GRCm38/mm10) using Bowtie2 with parameters “--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700”.
Duplicates were marked using the Sambamba “markdup” subcommand.
Peaks were called with GoPeaks using IgG samples as negative controls.
K562 CUT&RUN samples were sequenced across multiple batches. Samples from Batch 3 use an in-batch IgG control (K562_noDOX_IgG_3) for peak calling. K562 CUT&RUN samples from Batch 2 use the IgG control (K562_noDOX_IgG_1) from Batch 1 for peak calling. The IgG from Batch 2 yielded insufficient read depth to reliably model background signal and was therefore not used. The Batch 1 IgG sample used for peak calling was prepared using the same cell line and protocols as the experimental samples, allowing for consistent background estimation and peak calling when in-batch controls were not usable.
Mouse lineage-negative CUT&RUN samples were sequenced across multiple batches. Batch 1 samples (KAT7 and KMT2A samples) used the Batch 1 IgG control (mouse_batch1_LUC_IgG) for peak calling, which had similarly high read depth as the experimental samples in that batch, making it suitable for background modeling. Batches 2-3 used the Batch 4 IgG control (mouse_batch4_LUC_IgG) for peak calling. Batch 2 (sequenced on NovaSeq 6000) did not originally include an IgG control, and Batch 3 included an IgG control that had insufficient read depth and could not be used to reliably model background signal. The Batch 4 IgG control had read depth similar to samples in Batches 2-3, allowing for consistent background estimation and peak calling when in-batch controls were not usable.
Spike-in DNA from E. coli K-12 MG1655 was provided in the Epicypher CUT&RUN kit and used according to the manufacturer's protocols. To determine normalization factors for signal visualization, reads were aligned to host and E. coli reference genomes, and uniquely aligned reads were retained. Spike-in percentages were calculated as the proportion of reads mapping to E. coli relative to reads mapping to the host genome. Normalization factors were then calculated based on the relative spike-in percentages, scaled to the sample with the lowest spike-in recovery within each antibody target, consistent with Epicypher guidelines. Spike-in normalization was applied to the histone mark samples (H3K14ac, H3K23ac), as these samples had consistent spike-in recovery across replicates within each condition. BigWig coverage tracks for these samples were generated using spike-in derived scale factors with deepTools bamCoverage (--binSize 10 --smoothLength 50 --scaleFactor <sample-specific value>). Other antibody targets were not spike-in normalized due to variable spike-in recovery across replicates. For these samples, counts-per-million (CPM) normalized bigWig tracks were generated using deepTools bamCoverage with parameters “--binSize 10 --smoothLength 50 --normalizeUsing CPM”.
Assembly: GRCh38 (hg38) for samples from K562 cells, GRCm38 (mm10) for samples from mouse lineage-negative bone marrow cells
Supplementary files format and content: BigWig files include either spike-in normalized (for histone marks) or CPM-normalized (for other antibody targets) read signal for each sample.
Library strategy: CUT&Run

source_name: Bone marrow

growth_protocol: K562 cells were grown in IMDM medium with 10% FBS, 2mM glutamine, 1x penicillin/streptomycin. Mouse lineage-negative (Lin-) bone marrow primary cells were grown in IMDM medium with 15% FBS, 2mM glutamine, 1x penicillin/streptomycin in the presence of SCF, IL6, and IL3.

extract_protocol:
Cells were harvested following the EpiCypher CUT&RUN kit protocol (EpiCypher CUTANA 14-1048).
CUT&RUN libraries were prepared using the New England Biolabs NEBNext Ultra II DNA Library Prep Kit for Illumina.

treatment_protocol: K562 cells were either induced with 250ng/mL of doxycycline or not induced with any doxycycline for 24 hours. For mouse lineage-negative (Lin-) CUT&RUN, lentivirus were generated by co-transfecting psPAX2 (Addgene: 12260), pMD2.G (Addgene: 12259), and pSMAL_Luciferase (control) or pSMAL_SETBP1D868N into LentiX cells (Takara) with Fugene 6 (Promega E2691), according to the manufacturer's instructions. Mouse lineage-negative bone marrow cells were lentivirally transduced with either a control (luciferase) or SETBP1D868N mutant and then GFP-sorted.

value: Bone marrow

value: lineage-negative bone marrow primary cells

value: wild-type

value: lentiviral transduction with SETBP1D868N mutant

tag: cutrun antibody

value: H3K14ac (Cell Signaling Technology, 7627)

tag: genome assembly

value: GRCm38 (mm10)

tag: sequencing batch


title: E20_FU2 Beta

description:
Library name: Sample 90
Illumina


title: LINC00667c4_BioRep2_24h_rep3_RNAseq

description: Library name: LINC00667c4_B2_24_3


title: Lin- cells, SETBP1D868N mutant, H3K14ac antibody, rep2

description: Library name: mouse_batch2_SETBP1-D868N_H3K14ac_2


title: E20_FU2 Alpha

description:
Library name: Sample 89
Illumina


title: LINC00667c4_BioRep2_24h_rep2_RNAseq

description: Library name: LINC00667c4_B2_24_2


title: LINC00667c4_BioRep2_24h_rep1_RNAseq

description: Library name: LINC00667c4_B2_24_1


title: Lin- cells, SETBP1D868N mutant, H3K14ac antibody, rep1

description: Library name: mouse_batch2_SETBP1-D868N_H3K14ac_1


title: E20_FU1 Beta

description:
Library name: Sample 88
Illumina


title: LINC00667c4_BioRep2_16h_rep3_RNAseq

description: Library name: LINC00667c4_B2_16_3


title: LINC00667c4_BioRep2_16h_rep1_RNAseq

description: Library name: LINC00667c4_B2_16_1


title: E20_EOT Beta

description:
Library name: Sample 86
Illumina


title: LINC00667c4_BioRep2_16h_rep2_RNAseq

description: Library name: LINC00667c4_B2_16_2


title: Lin- cells, Luciferase control, H3K14ac antibody, rep1

description: Library name: mouse_batch2_LUC_H3K14ac_1

value: lentiviral transduction with control (luciferase)


title: E20_EOT Alpha

description:
Library name: Sample 85
Illumina


title: Lin- cells, Luciferase control, H3K14ac antibody, rep2

description: Library name: mouse_batch2_LUC_H3K14ac_2


title: LINC00667c4_BioRep2_8h_rep2_RNAseq

description: Library name: LINC00667c4_B2_8_2


title: LINC00667c4_BioRep2_8h_rep3_RNAseq

description: Library name: LINC00667c4_B2_8_3


title: LINC00667c4_BioRep2_8h_rep1_RNAseq

description: Library name: LINC00667c4_B2_8_1


title: LINC00667c4_BioRep2_0h_rep2_RNAseq

description: Library name: LINC00667c4_B2_0_2


title: E20_B Beta

description:
Library name: Sample 84
Illumina


title: Lin- cells, Luciferase control, H3K14ac antibody, rep3

description: Library name: mouse_batch2_LUC_H3K14ac_3


title: LINC00667c4_BioRep2_0h_rep1_RNAseq

description: Library name: LINC00667c4_B2_0_1


title: LINC00667c4_BioRep2_0h_rep3_RNAseq

description: Library name: LINC00667c4_B2_0_3


title: LINC00667c4_BioRep1_96h_rep3_RNAseq

description: Library name: LINC00667c4_B1_96_3


title: Tissue_010_Week 4_MI

city: Tucson

first: Jordan

middle: M

last: Fink

state: AZ

address: 1501 N Campbell Ave

department: Sarver Heart Center

institute: University of Arizona

description: Library name: DSP-1012340083302-B-E03

data_processing:
FASTQs were processed into .dcc files as per Nanostring's pipeline
.dcc files were combined, normalized, and batch adjusted to generate the combined count matrix
Assembly: mm10
Supplementary files format and content: Compiled_Count_Matrix.csv contains  metadata and counts
Supplementary files format and content: pkc file needed for processing the data
Library strategy: Spatial Transcriptomics

source_name: Cardiac

extract_protocol:
Nanostring UV cleaving of molecular probes and collection
DNA probes were processed according to nanostring's protocols

treatment_protocol: MI_alone with no treatment; treated with biologic

value: Cardiac

tag: tissue type

value: Formalin Fixed Tissue


title: E20_FU1 Alpha

description:
Library name: Sample 87
Illumina

source_name: PBMCs


title: E20_B Alpha

description:
Library name: Sample 83
Illumina


title: LINC00667c4_BioRep1_96h_rep2_RNAseq

description: Library name: LINC00667c4_B1_96_2

source_name: hiPSCs


title: LINC00667c4_BioRep1_48h_rep3_RNAseq

description: Library name: LINC00667c4_B1_48_3


title: LINC00667c4_BioRep1_96h_rep1_RNAseq

description: Library name: LINC00667c4_B1_96_1


title: E19_FU1 Beta

description:
Library name: Sample 82
Illumina


title: Tissue_009_Week 4_MI

description: Library name: DSP-1012340083302-B-E01


title: LINC00667c4_BioRep1_48h_rep2_RNAseq

description: Library name: LINC00667c4_B1_48_2


title: Desmin_010_Week 4_MI

description: Library name: DSP-1012340083302-B-E02


title: LINC00667c4_BioRep1_48h_rep1_RNAseq

description: Library name: LINC00667c4_B1_48_1


title: E19_FU1 Alpha

description:
Library name: Sample 81
Illumina


title: LINC00667c4_BioRep1_24h_rep3_RNAseq

description: Library name: LINC00667c4_B1_24_3


title: Tissue_008_Week 4_MI

description: Library name: DSP-1012340083302-B-D11


title: E19_B Beta

description:
Library name: Sample 80
Illumina


title: LINC00667c4_BioRep1_24h_rep2_RNAseq

description: Library name: LINC00667c4_B1_24_2


title: E19_B Alpha

description:
Library name: Sample 79
Illumina


title: Desmin_009_Week 4_MI

description: Library name: DSP-1012340083302-B-D12


title: Desmin_008_Week 4_MI

description: Library name: DSP-1012340083302-B-D10


title: LINC00667c4_BioRep1_16h_rep3_RNAseq

description: Library name: LINC00667c4_B1_16_3


title: LINC00667c4_BioRep1_24h_rep1_RNAseq

description: Library name: LINC00667c4_B1_24_1


title: Tissue_007_Week 4_MI

description: Library name: DSP-1012340083302-B-D09


title: LINC00667c4_BioRep1_16h_rep1_RNAseq

description: Library name: LINC00667c4_B1_16_1


title: LINC00667c4_BioRep1_8h_rep3_RNAseq

description: Library name: LINC00667c4_B1_8_3


title: E18_FU2 Alpha

description:
Library name: Sample 77
Illumina


title: LINC00667c4_BioRep1_16h_rep2_RNAseq

description: Library name: LINC00667c4_B1_16_2


title: Desmin_007_Week 4_MI

description: Library name: DSP-1012340083302-B-D08


title: LINC00667c4_BioRep1_4h_rep3_RNAseq

description: Library name: LINC00667c4_B1_4_3


title: LINC00667c4_BioRep1_4h_rep2_RNAseq

description: Library name: LINC00667c4_B1_4_2


title: Tissue_006_Week 4_MI

description: Library name: DSP-1012340083302-B-D07


title: LINC00667c4_BioRep1_8h_rep2_RNAseq

description: Library name: LINC00667c4_B1_8_2


title: LINC00667c4_BioRep1_4h_rep1_RNAseq

description: Library name: LINC00667c4_B1_4_1


title: Desmin_006_Week 4_MI

description: Library name: DSP-1012340083302-B-D06


title: LINC00667c4_BioRep1_2h_rep3_RNAseq

description: Library name: LINC00667c4_B1_2_3


title: E18_EOT Beta

description:
Library name: Sample 74
Illumina


title: LINC00667c4_BioRep1_8h_rep1_RNAseq

description: Library name: LINC00667c4_B1_8_1


title: LINC00667c4_BioRep1_2h_rep2_RNAseq

description: Library name: LINC00667c4_B1_2_2


title: LINC00667c4_BioRep1_2h_rep1_RNAseq

description: Library name: LINC00667c4_B1_2_1


title: Tissue_005_Week 4_MI

description: Library name: DSP-1012340083302-B-D05


title: E18_FU1 Beta

description:
Library name: Sample 76
Illumina


title: E18_EOT Alpha

description:
Library name: Sample 73
Illumina


title: Desmin_005_Week 4_MI

description: Library name: DSP-1012340083302-B-D04


title: E18_FU1 Alpha

description:
Library name: Sample 75
Illumina


title: LINC00667c4_BioRep1_0h_rep2_RNAseq

description: Library name: LINC00667c4_B1_0_2


title: LINC00667c4_BioRep1_0h_rep3_RNAseq

description: Library name: LINC00667c4_B1_0_3


title: E18_FU2 Beta

description:
Library name: Sample 78
Illumina


title: E18_B Beta

description:
Library name: Sample 72
Illumina


title: Tissue_004_Week 4_MI

description: Library name: DSP-1012340083302-B-D03


title: HULC_96h_rep3_RNAseq

description: Library name: HULC_96_3


title: E18_B Alpha

description:
Library name: Sample 71
Illumina


title: Desmin_004_Week 4_MI

description: Library name: DSP-1012340083302-B-D02


title: HULC_96h_rep2_RNAseq

description: Library name: HULC_96_2


title: HULC_48h_rep3_RNAseq

description: Library name: HULC_48_3


title: Tissue_003_Week 4_MI

description: Library name: DSP-1012340083302-B-D01


title: LINC00667c4_BioRep1_0h_rep1_RNAseq

description: Library name: LINC00667c4_B1_0_1


title: E17_FU2 Beta

description:
Library name: Sample 70
Illumina


title: Desmin_003_Week 4_MI

description: Library name: DSP-1012340083302-B-C12


title: HULC_48h_rep1_RNAseq

description: Library name: HULC_48_1


title: E17_FU2 Alpha

description:
Library name: Sample 69
Illumina


title: HULC_96h_rep1_RNAseq

description: Library name: HULC_96_1


title: Tissue_002_Week 4_MI

description: Library name: DSP-1012340083302-B-C11


title: E17_FU1 Beta

description:
Library name: Sample 68
Illumina


title: HULC_24h_rep1_RNAseq

description: Library name: HULC_24_1


title: HULC_24h_rep3_RNAseq

description: Library name: HULC_24_3


title: HULC_24h_rep2_RNAseq

description: Library name: HULC_24_2


title: Tissue_001_Week 4_MI

description: Library name: DSP-1012340083302-B-C09


title: HULC_16h_rep2_RNAseq

description: Library name: HULC_16_2


title: Desmin_002_Week 4_MI

description: Library name: DSP-1012340083302-B-C10


title: Desmin_001_Week 4_MI

description: Library name: DSP-1012340083302-B-C08


title: HULC_16h_rep1_RNAseq

description: Library name: HULC_16_1


title: HULC_8h_rep3_RNAseq

description: Library name: HULC_8_3


title: HULC_48h_rep2_RNAseq

description: Library name: HULC_48_2


title: LINC00667c2_16h_rep3_RNAseq

description: Library name: LINC00667c2_B1_16_3


title: HULC_8h_rep2_RNAseq

description: Library name: HULC_8_2


title: HULC_8h_rep1_RNAseq

description: Library name: HULC_8_1


title: HULC_4h_rep2_RNAseq

description: Library name: HULC_4_2


title: E17_B Beta

description:
Library name: Sample 64
Illumina


title: E17_EOT Beta

description:
Library name: Sample 66
Illumina


title: HULC_16h_rep3_RNAseq

description: Library name: HULC_16_3


title: Tissue_015_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-C07

value: Biologic


title: E17_FU1 Alpha

description:
Library name: Sample 67
Illumina


title: E17_EOT Alpha

description:
Library name: Sample 65
Illumina


title: HULC_4h_rep1_RNAseq

description: Library name: HULC_4_1


title: Tissue_014_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-C05


title: E17_B Alpha

description:
Library name: Sample 63
Illumina


title: HULC_2h_rep3_RNAseq

description: Library name: HULC_2_3


title: E16_FU2 Beta

description:
Library name: Sample 62
Illumina


title: HULC_2h_rep2_RNAseq

description: Library name: HULC_2_2


title: E16_FU2 Alpha

description:
Library name: Sample 61
Illumina


title: HULC_2h_rep1_RNAseq

description: Library name: HULC_2_1


title: Tissue_013_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-C04


title: HULC_4h_rep3_RNAseq

description: Library name: HULC_4_3


title: CD45_015_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-C06


title: Desmin_013_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-C03


title: WT_96h_rep3_RNAseq

description: Library name: WT_96_3


title: HULC_0h_rep2_RNAseq

description: Library name: HULC_0_2


title: HULC_0h_rep1_RNAseq

description: Library name: HULC_0_1


title: Tissue_012_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-C02


title: E16_FU1 Alpha

description:
Library name: Sample 59
Illumina


title: WT_96h_rep2_RNAseq

description: Library name: WT_96_2


title: Desmin_012_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-C01


title: HULC_0h_rep3_RNAseq

description: Library name: HULC_0_3


title: E16_B Beta

description:
Library name: Sample 58
Illumina


title: WT_96h_rep1_RNAseq

description: Library name: WT_96_1


title: WT_48h_rep3_RNAseq

description: Library name: WT_48_3


title: WT_48h_rep2_RNAseq

description: Library name: WT_48_2


title: E16_FU1 Beta

description:
Library name: Sample 60
Illumina


title: CD45_012_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-B12


title: E16_B Alpha

description:
Library name: Sample 57
Illumina


title: WT_48h_rep1_RNAseq

description: Library name: WT_48_1


title: WT_24h_rep3_RNAseq

description: Library name: WT_24_3


title: Tissue_011_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-B11


title: E15_FU2 Alpha

description:
Library name: Sample 55
Illumina


title: WT_24h_rep2_RNAseq

description: Library name: WT_24_2


title: E15_FU2 Beta

description:
Library name: Sample 56
Illumina


title: Desmin_011_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-B10


title: WT_24h_rep1_RNAseq

description: Library name: WT_24_1


title: WT_16h_rep3_RNAseq

description: Library name: WT_16_3


title: Tissue_010_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-B09


title: WT_16h_rep1_RNAseq

description: Library name: WT_16_1


title: WT_16h_rep2_RNAseq

description: Library name: WT_16_2


title: WT_8h_rep3_RNAseq

description: Library name: WT_8_3


title: E15_FU1 Beta

description:
Library name: Sample 54
Illumina


title: CD45_010_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-B08


title: E15_FU1 Alpha

description:
Library name: Sample 53
Illumina


title: Tissue_009_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-B07


title: WT_4h_rep1_RNAseq

description: Library name: WT_4_1


title: WT_8h_rep1_RNAseq

description: Library name: WT_8_1


title: WT_4h_rep3_RNAseq

description: Library name: WT_4_3


title: CD45_009_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-B06


title: E15_EOT Alpha

description:
Library name: Sample 51
Illumina


title: E15_EOT Beta

description:
Library name: Sample 52
Illumina


title: WT_8h_rep2_RNAseq

description: Library name: WT_8_2


title: WT_4h_rep2_RNAseq

description: Library name: WT_4_2


title: Tissue_008_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-B05


title: E15_B Beta

description:
Library name: Sample 50
Illumina


title: WT_2h_rep2_RNAseq

description: Library name: WT_2_2


title: CD45_008_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-B04


title: Tissue_007_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-B03


title: WT_2h_rep3_RNAseq

description: Library name: WT_2_3


title: E15_B Alpha

description:
Library name: Sample 49
Illumina


title: WT_2h_rep1_RNAseq

description: Library name: WT_2_1


title: WT_0h_rep3_RNAseq

description: Library name: WT_0_3


title: E14_FU2 Beta

description:
Library name: Sample 48
Illumina


title: WT_0h_rep1_RNAseq

description: Library name: WT_0_1


title: HEIH_96h_rep2_RNAseq

description: Library name: HEIH_96_2


title: E14_FU2 Alpha

description:
Library name: Sample 47
Illumina


title: Desmin_007_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-B02


title: HEIH_96h_rep1_RNAseq

description: Library name: HEIH_96_1


title: WT_0h_rep2_RNAseq

description: Library name: WT_0_2


title: HEIH_48h_rep2_RNAseq

description: Library name: HEIH_48_2


title: HEIH_48h_rep3_RNAseq

description: Library name: HEIH_48_3


title: Tissue_006_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-B01


title: Desmin_006_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-A12


title: HEIH_96h_rep3_RNAseq

description: Library name: HEIH_96_3


title: E14_FU1 Beta

description:
Library name: Sample 46
Illumina


title: Tissue_005_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-A11


title: E14_FU1 Alpha

description:
Library name: Sample 45
Illumina


title: HEIH_48h_rep1_RNAseq

description: Library name: HEIH_48_1


title: HEIH_24h_rep2_RNAseq

description: Library name: HEIH_24_2


title: E14_B Beta

description:
Library name: Sample 44
Illumina


title: HEIH_24h_rep1_RNAseq

description: Library name: HEIH_24_1


title: HEIH_24h_rep3_RNAseq

description: Library name: HEIH_24_3


title: E14_B Alpha

description:
Library name: Sample 43
Illumina


title: Desmin_005_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-A10


title: HEIH_16h_rep2_RNAseq

description: Library name: HEIH_16_2


title: HEIH_16h_rep3_RNAseq

description: Library name: HEIH_16_3


title: Tissue_004_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-A09


title: Desmin_004_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-A08


title: HEIH_16h_rep1_RNAseq

description: Library name: HEIH_16_1


title: E12_FU2 Beta

description:
Library name: Sample 42
Illumina


title: E12_FU2 Alpha

description:
Library name: Sample 41
Illumina


title: HEIH_8h_rep1_RNAseq

description: Library name: HEIH_8_1


title: HEIH_8h_rep3_RNAseq

description: Library name: HEIH_8_3


title: HEIH_8h_rep2_RNAseq

description: Library name: HEIH_8_2


title: Tissue_003_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-A07


title: E12_FU1 Beta

description:
Library name: Sample 40
Illumina


title: HEIH_4h_rep3_RNAseq

description: Library name: HEIH_4_3


title: HEIH_4h_rep2_RNAseq

description: Library name: HEIH_4_2


title: E12_FU1 Alpha

description:
Library name: Sample 39
Illumina


title: HEIH_2h_rep3_RNAseq

description: Library name: HEIH_2_3


title: HEIH_4h_rep1_RNAseq

description: Library name: HEIH_4_1


title: HEIH_2h_rep1_RNAseq

description: Library name: HEIH_2_1


title: Tissue_002_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-A05


title: E12_EOT Beta

description:
Library name: Sample 38
Illumina


title: Desmin_003_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-A06


title: HEIH_2h_rep2_RNAseq

description: Library name: HEIH_2_2


title: Desmin_002_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-A04


title: HAGLR_96h_rep3_RNAseq

description: Library name: HAGLR_96_3


title: Tissue_001_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-A03


title: E12_B Beta

description:
Library name: Sample 36
Illumina


title: E12_EOT Alpha

description:
Library name: Sample 37
Illumina


title: Desmin_001_Week 4_MI-PATCH

description: Library name: DSP-1012340083302-B-A02


title: HEIH_0h_rep3_RNAseq

description: Library name: HEIH_0_3


title: HAGLR_96h_rep1_RNAseq

description: Library name: HAGLR_96_1


title: HAGLR_96h_rep2_RNAseq

description: Library name: HAGLR_96_2


title: HAGLR_48h_rep2_RNAseq

description: Library name: HAGLR_48_2


title: HAGLR_48h_rep3_RNAseq

description: Library name: HAGLR_48_3


title: HAGLR_24h_rep3_RNAseq

description: Library name: HAGLR_24_3


title: HAGLR_48h_rep1_RNAseq

description: Library name: HAGLR_48_1


title: E11_FU1 Alpha

description:
Library name: Sample 33
Illumina


title: No Template Control_Week_4

description: Library name: DSP-1012340083302-B-A01


title: HAGLR_24h_rep2_RNAseq

description: Library name: HAGLR_24_2


title: Tissue_016_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-E01


title: E11_FU1 Beta

description:
Library name: Sample 34
Illumina


title: HAGLR_24h_rep1_RNAseq

description: Library name: HAGLR_24_1


title: E11_B Beta

description:
Library name: Sample 32
Illumina


title: HAGLR_16h_rep3_RNAseq

description: Library name: HAGLR_16_3


title: E12_B Alpha

description:
Library name: Sample 35
Illumina


title: E11_B Alpha

description:
Library name: Sample 31
Illumina


title: HAGLR_16h_rep2_RNAseq

description: Library name: HAGLR_16_2


title: Tissue_015_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-D11


title: Desmin_015_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-D10


title: HEIH_0h_rep2_RNAseq

description: Library name: HEIH_0_2


title: HAGLR_8h_rep3_RNAseq

description: Library name: HAGLR_8_3


title: CD45_016_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-D12


title: HAGLR_8h_rep2_RNAseq

description: Library name: HAGLR_8_2


title: HAGLR_16h_rep1_RNAseq

description: Library name: HAGLR_16_1


title: HAGLR_4h_rep3_RNAseq

description: Library name: HAGLR_4_3


title: Tissue_014_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-D09


title: E10_B Beta

description:
Library name: Sample 30
Illumina


title: E09_FU2 Beta

description:
Library name: Sample 28
Illumina


title: CD45_014_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-D08


title: E09_FU2 Alpha

description:
Library name: Sample 27
Illumina


title: HAGLR_4h_rep1_RNAseq

description: Library name: HAGLR_4_1


title: Tissue_013_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-D07


title: HAGLR_4h_rep2_RNAseq

description: Library name: HAGLR_4_2


title: HAGLR_2h_rep3_RNAseq

description: Library name: HAGLR_2_3


title: HAGLR_2h_rep1_RNAseq

description: Library name: HAGLR_2_1


title: E09_FU1 Beta

description:
Library name: Sample 26
Illumina


title: HAGLR_0h_rep2_RNAseq

description: Library name: HAGLR_0_2


title: CD45_013_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-D06


title: E09_FU1 Alpha

description:
Library name: Sample 25
Illumina


title: Tissue_012_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-D05


title: E10_B Alpha

description:
Library name: Sample 29
Illumina


title: HAGLR_0h_rep3_RNAseq

description: Library name: HAGLR_0_3


title: Desmin_012_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-D04


title: GFPc5_BioRep3_96h_rep2_RNAseq

description: Library name: GFPc5_B3_96_2


title: HAGLR_0h_rep1_RNAseq

description: Library name: HAGLR_0_1


title: HAGLR_2h_rep2_RNAseq

description: Library name: HAGLR_2_2


title: E09_B Beta

description:
Library name: Sample 24
Illumina


title: Tissue_011_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-D03


title: E09_B Alpha

description:
Library name: Sample 23
Illumina


title: GFPc5_BioRep3_96h_rep1_RNAseq

description: Library name: GFPc5_B3_96_1


title: GFPc5_BioRep3_96h_rep3_RNAseq

description: Library name: GFPc5_B3_96_3


title: GFPc5_BioRep3_48h_rep3_RNAseq

description: Library name: GFPc5_B3_48_3


title: E06_FU2 Beta

description:
Library name: Sample 22
Illumina


title: GFPc5_BioRep3_48h_rep2_RNAseq

description: Library name: GFPc5_B3_48_2


title: GFPc5_BioRep3_24h_rep3_RNAseq

description: Library name: GFPc5_B3_24_3


title: CD45_011_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-D02


title: E06_FU2 Alpha

description:
Library name: Sample 21
Illumina


title: GFPc5_BioRep3_48h_rep1_RNAseq

description: Library name: GFPc5_B3_48_1


title: Tissue_010_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-D01


title: Desmin_010_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-C12


title: E06_FU1 Alpha

description:
Library name: Sample 19
Illumina


title: GFPc5_BioRep3_24h_rep2_RNAseq

description: Library name: GFPc5_B3_24_2


title: GFPc5_BioRep3_24h_rep1_RNAseq

description: Library name: GFPc5_B3_24_1


title: GFPc5_BioRep3_16h_rep2_RNAseq

description: Library name: GFPc5_B3_16_2


title: E06_EOT Beta

description:
Library name: Sample 18
Illumina


title: Tissue_009_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-C11


title: CD45_009_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-C10


title: E06_FU1 Beta

description:
Library name: Sample 20
Illumina


title: GFPc5_BioRep3_8h_rep2_RNAseq

description: Library name: GFPc5_B3_8_2


title: E06_EOT Alpha

description:
Library name: Sample 17
Illumina


title: Tissue_008_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-C09


title: GFPc5_BioRep3_16h_rep3_RNAseq

description: Library name: GFPc5_B3_16_3


title: GFPc5_BioRep3_8h_rep1_RNAseq

description: Library name: GFPc5_B3_8_1


title: CD45_008_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-C08


title: GFPc5_BioRep3_8h_rep3_RNAseq

description: Library name: GFPc5_B3_8_3


title: GFPc5_BioRep3_0h_rep2_RNAseq

description: Library name: GFPc5_B3_0_2


title: GFPc5_BioRep3_0h_rep3_RNAseq

description: Library name: GFPc5_B3_0_3


title: GFPc5_BioRep3_16h_rep1_RNAseq

description: Library name: GFPc5_B3_16_1


title: E06_B Beta

description:
Library name: Sample 16
Illumina


title: GFPc5_BioRep3_0h_rep1_RNAseq

description: Library name: GFPc5_B3_0_1


title: Desmin_007_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-C06


title: GFPc4_96h_rep3_RNAseq

description: Library name: GFPc4_B1_96_3


title: E06_B Alpha

description:
Library name: Sample 15
Illumina


title: GFPc4_96h_rep1_RNAseq

description: Library name: GFPc4_B1_96_1


title: GFPc4_96h_rep2_RNAseq

description: Library name: GFPc4_B1_96_2


title: GFPc4_48h_rep2_RNAseq

description: Library name: GFPc4_B1_48_2


title: GFPc4_48h_rep3_RNAseq

description: Library name: GFPc4_B1_48_3


title: CD45_006_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-C04


title: E04_FU1 Beta

description:
Library name: Sample 14
Illumina


title: Tissue_005_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-C03


title: Tissue_006_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-C05


title: GFPc4_24h_rep2_RNAseq

description: Library name: GFPc4_B1_24_2


title: GFPc4_48h_rep1_RNAseq

description: Library name: GFPc4_B1_48_1


title: Tissue_007_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-C07


title: GFPc4_24h_rep3_RNAseq

description: Library name: GFPc4_B1_24_3


title: GFPc4_24h_rep1_RNAseq

description: Library name: GFPc4_B1_24_1


title: E04_FU1 Alpha

description:
Library name: Sample 13
Illumina


title: E03_FU2 Beta

description:
Library name: Sample 10
Illumina


title: E04_B Alpha

description:
Library name: Sample 11
Illumina


title: GFPc4_16h_rep3_RNAseq

description: Library name: GFPc4_B1_16_3


title: GFPc4_8h_rep3_RNAseq

description: Library name: GFPc4_B1_8_3


title: E04_B Beta

description:
Library name: Sample 12
Illumina


title: GFPc4_16h_rep2_RNAseq

description: Library name: GFPc4_B1_16_2


title: GFPc4_16h_rep1_RNAseq

description: Library name: GFPc4_B1_16_1


title: CD45_005_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-C02


title: Tissue_004_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-C01


title: Tissue_003_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-B11


title: E03_FU2 Alpha

description:
Library name: Sample 9
Illumina


title: GFPc4_8h_rep2_RNAseq

description: Library name: GFPc4_B1_8_2


title: Desmin_004_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-B12


title: GFPc4_0h_rep3_RNAseq

description: Library name: GFPc4_B1_0_3


title: GFPc4_8h_rep1_RNAseq

description: Library name: GFPc4_B1_8_1


title: E03_B Beta

description:
Library name: Sample 8
Illumina


title: GFPc4_0h_rep1_RNAseq

description: Library name: GFPc4_B1_0_1


title: GFPc4_0h_rep2_RNAseq

description: Library name: GFPc4_B1_0_2


title: Tissue_002_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-B09


title: E02_B Alpha

description:
Library name: Sample 5
Illumina


title: E03_B Alpha

description:
Library name: Sample 7
Illumina


title: Desmin_003_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-B10


title: E01_FU1 Beta

description:
Library name: Sample 4
Illumina


title: GFPc5_BioRep2_96h_rep2_RNAseq

description: Library name: GFPc5_B2_96_2


title: GFPc5_BioRep2_48h_rep2_RNAseq

description: Library name: GFPc5_B2_48_2


title: GFPc5_BioRep2_96h_rep3_RNAseq

description: Library name: GFPc5_B2_96_3


title: Desmin_002_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-B08


title: GFPc5_BioRep2_48h_rep1_RNAseq

description: Library name: GFPc5_B2_48_1


title: GFPc5_BioRep2_48h_rep3_RNAseq

description: Library name: GFPc5_B2_48_3


title: GFPc5_BioRep2_96h_rep1_RNAseq

description: Library name: GFPc5_B2_96_1


title: E02_B Beta

description:
Library name: Sample 6
Illumina


title: E01_FU1 Alpha

description:
Library name: Sample 3
Illumina


title: GFPc5_BioRep2_24h_rep3_RNAseq

description: Library name: GFPc5_B2_24_3


title: E01_B Beta

description:
Library name: Sample 2
Illumina


title: CD45_001_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-B06


title: Tissue_008_Week 2_MI

description: Library name: DSP-1012340083301-A-B05


title: GFPc5_BioRep2_16h_rep2_RNAseq

description: Library name: GFPc5_B2_16_2


title: GFPc5_BioRep2_24h_rep2_RNAseq

description: Library name: GFPc5_B2_24_2


title: GFPc5_BioRep2_16h_rep1_RNAseq

description: Library name: GFPc5_B2_16_1


title: GFPc5_BioRep2_16h_rep3_RNAseq

description: Library name: GFPc5_B2_16_3


title: GFPc5_BioRep2_8h_rep3_RNAseq

description: Library name: GFPc5_B2_8_3


title: Tissue_001_Week 2_MI-PATCH

description: Library name: DSP-1012340083301-A-B07


title: E01_B Alpha

description:
Library name: Sample 1
Illumina


title: E49_FU2 Beta

description:
Library name: Sample 268
Illumina


title: GFPc5_BioRep2_8h_rep2_RNAseq

description: Library name: GFPc5_B2_8_2


title: Tissue_007_Week 2_MI

description: Library name: DSP-1012340083301-A-B03


title: Desmin_008_Week 2_MI

description: Library name: DSP-1012340083301-A-B04


title: GFPc5_BioRep2_8h_rep1_RNAseq

description: Library name: GFPc5_B2_8_1


title: GFPc5_BioRep2_24h_rep1_RNAseq

description: Library name: GFPc5_B2_24_1


title: GFPc5_BioRep2_4h_rep2_RNAseq

description: Library name: GFPc5_B2_4_2


title: E49_FU1 Beta

description:
Library name: Sample 266
Illumina


title: GFPc5_BioRep2_4h_rep1_RNAseq

description: Library name: GFPc5_B2_4_1


title: Tissue_006_Week 2_MI

description: Library name: DSP-1012340083301-A-B01


title: Desmin_007_Week 2_MI

description: Library name: DSP-1012340083301-A-B02


title: GFPc5_BioRep2_4h_rep3_RNAseq

description: Library name: GFPc5_B2_4_3


title: GFPc5_BioRep2_2h_rep3_RNAseq

description: Library name: GFPc5_B2_2_3


title: E49_FU1 Alpha

description:
Library name: Sample 265
Illumina


title: E49_FU2 Alpha

description:
Library name: Sample 267
Illumina


title: GFPc5_BioRep2_2h_rep1_RNAseq

description: Library name: GFPc5_B2_2_1


title: GFPc5_BioRep2_2h_rep2_RNAseq

description: Library name: GFPc5_B2_2_2


title: Desmin_006_Week 2_MI

description: Library name: DSP-1012340083301-A-A12


title: E49_EOT Beta

description:
Library name: Sample 264
Illumina


title: Tissue_005_Week 2_MI

description: Library name: DSP-1012340083301-A-A11


title: GFPc5_BioRep2_0h_rep3_RNAseq

description: Library name: GFPc5_B2_0_3


title: Desmin_005_Week 2_MI

description: Library name: DSP-1012340083301-A-A10


title: GFPc5_BioRep2_0h_rep1_RNAseq

description: Library name: GFPc5_B2_0_1


title: GFPc5_BioRep1_5.5h_rep2_RNAseq

description: Library name: GFPc5_B1_5.5_2


title: GFPc5_BioRep1_5.5h_rep1_RNAseq

description: Library name: GFPc5_B1_5.5_1


title: E49_B Alpha

description:
Library name: Sample 261
Illumina


title: GFPc5_BioRep1_5h_rep1_RNAseq

description: Library name: GFPc5_B1_5_1


title: GFPc5_BioRep2_0h_rep2_RNAseq

description: Library name: GFPc5_B2_0_2


title: GFPc5_BioRep1_4.5h_rep2_RNAseq

description: Library name: GFPc5_B1_4.5_2


title: E48_FU1 Beta

description:
Library name: Sample 260
Illumina


title: Tissue_004_Week 2_MI

description: Library name: DSP-1012340083301-A-A09


title: GFPc5_BioRep1_4.5h_rep1_RNAseq

description: Library name: GFPc5_B1_4.5_1


title: E49_EOT Alpha

description:
Library name: Sample 263
Illumina


title: E48_FU1 Alpha

description:
Library name: Sample 259
Illumina


title: E49_B Beta

description:
Library name: Sample 262
Illumina


title: GFPc5_BioRep1_4h_rep1_RNAseq

description: Library name: GFPc5_B1_4_1


title: Desmin_003_Week 2_MI

description: Library name: DSP-1012340083301-A-A06


title: GFPc5_BioRep1_5h_rep2_RNAseq

description: Library name: GFPc5_B1_5_2


title: Tissue_003_Week 2_MI

description: Library name: DSP-1012340083301-A-A07


title: GFPc5_BioRep1_3.5h_rep1_RNAseq

description: Library name: GFPc5_B1_3.5_1


title: Tissue_002_Week 2_MI

description: Library name: DSP-1012340083301-A-A05


title: Desmin_004_Week 2_MI

description: Library name: DSP-1012340083301-A-A08


title: GFPc5_BioRep1_4h_rep2_RNAseq

description: Library name: GFPc5_B1_4_2


title: E48_B Beta

description:
Library name: Sample 258
Illumina


title: E47_FU2 Beta

description:
Library name: Sample 256
Illumina


title: GFPc5_BioRep1_2.5h_rep2_RNAseq

description: Library name: GFPc5_B1_2.5_2


title: GFPc5_BioRep1_3h_rep1_RNAseq

description: Library name: GFPc5_B1_3_1


title: GFPc5_BioRep1_3.5h_rep2_RNAseq

description: Library name: GFPc5_B1_3.5_2


title: E48_B Alpha

description:
Library name: Sample 257
Illumina


title: Desmin_001_Week 2_MI

description: Library name: DSP-1012340083301-A-A02


title: GFPc5_BioRep1_2h_rep1_RNAseq

description: Library name: GFPc5_B1_2_1


title: GFPc5_BioRep1_2.5h_rep1_RNAseq

description: Library name: GFPc5_B1_2.5_1


title: GFPc5_BioRep1_2h_rep2_RNAseq

description: Library name: GFPc5_B1_2_2


title: Tissue_001_Week 2_MI

description: Library name: DSP-1012340083301-A-A03


title: GFPc5_BioRep1_1h_rep2_RNAseq

description: Library name: GFPc5_B1_1_2


title: E47_FU1 Beta

description:
Library name: Sample 254
Illumina


title: E47_FU2 Alpha

description:
Library name: Sample 255
Illumina


title: GFPc5_BioRep1_3h_rep2_RNAseq

description: Library name: GFPc5_B1_3_2


title: GFPc5_BioRep1_1.5h_rep1_RNAseq

description: Library name: GFPc5_B1_1.5_1


title: Tissue_011_Week 1_MI-PAtch

description: Library name: DSP-1012340076101-H-D01


title: E47_B Beta

description:
Library name: Sample 252
Illumina


title: GFPc5_BioRep1_1h_rep1_RNAseq

description: Library name: GFPc5_B1_1_1


title: No Template Control_Week_2

description: Library name: DSP-1012340083301-A-A01


title: GFPc5_BioRep1_1.5h_rep2_RNAseq

description: Library name: GFPc5_B1_1.5_2


title: E47_B Alpha

description:
Library name: Sample 251
Illumina


title: GFPc5_BioRep1_0.5h_rep1_RNAseq

description: Library name: GFPc5_B1_0.5_1


title: E47_FU1 Alpha

description:
Library name: Sample 253
Illumina


title: Desmin_002_Week 2_MI

description: Library name: DSP-1012340083301-A-A04


title: GFPc5_BioRep1_0.5h_rep2_RNAseq

description: Library name: GFPc5_B1_0.5_2


title: Tissue_010_Week 1_MI-PAtch

description: Library name: DSP-1012340076101-H-C11