title: Pt6_PBMC_I1D007_GEX

description:
Library name: Sample10
10x Genomics


title: Pt7_PBMC_I1D007_GEX

status: Public on May 01 2026

type: SRA

city: Seattle

first: Aude

last: Chapuis

address: 1100 Fairview Ave N

country: USA

institute: Fred Hutchinson Cancer Center

description:
Library name: Sample13
10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing reads were processed using Cell Ranger (v6.1.1) for alignment, barcode assignment, and UMI counting.
Assembly: GRCh38 (with appended TCRMCC1 and MCPyV sequences)
Supplementary files format and content: matrix.mtx.gz – raw gene expression counts (genes × cells)
Supplementary files format and content: features.tsv.gz – gene annotation file corresponding to rows of the count matrix
Supplementary files format and content: barcodes.tsv.gz – cell barcodes corresponding to columns of the count matrix

molecule: polyA RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Cryopreserved PBMCs were thawed and washed in PBS with 0.04% BSA. Tumor biopsies were enzymatically dissociated, washed, and subjected to dead cell removal. Cells were counted and resuspended for single-cell capture.
Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 5’ Reagent Kits v2 (Dual Index) following the manufacturer’s instructions.

tag: patient id

tag: infusion

tag: day

tag: tissue

value: PBMC

tag: collection site

value: Blood

tag: treatment group


title: Pt2_PBMC_I1D014_GEX

description:
Library name: Sample5
10x Genomics

value: SFRT


title: Pt4_PBMC_I2D014_GEX

description:
Library name: Sample8
10x Genomics

value: Flu/Cy


title: MOLM-14 cells, RX-5902, 6 hours, biological replicate #3

city: Boston

first: WEI

last: NI

state: MA

address: 450 Brookline Ave, Bldg MA-0543

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
Library name: sample 12
Column name in all_samples_RX5902_6hrs_counts.txt: RX-5902_3

library_source: transcriptomic

data_processing:
Reads were trimmed with Trim Galore (v0.6.7) to remove adapters and low-quality ends (Phred score < 30). The reference index for the human genome was built using STAR (v2.7.9a) with the GRCh38 primary assembly and its corresponding annotation file from GENCODE release 41 (https://www.gencodegenes.org/human/release_41.html). Reads were aligned to the reference genome using STAR (v2.7.9a), and alignment quality was assessed using Picard (v2.8.0). Uniquely aligned reads were summarized into gene-level counts using the featureCounts function from Subread (v2.0.3). The above steps were conducted on the O2 high-performance computing cluster at Harvard Medical School. Gene-level counts obtained from featureCounts were analyzed for differential expression locally in R (v4.4.2) using the DESeq2 package (v1.46.0), with metadata specifying the experimental groups. Normalized counts were generated through DESeq2’s internal factor-size estimation.
Assembly: Release 41 (GRCh38.p13)
Supplementary files format and content: tab-delimited text file includes raw counts for all samples in DDX5 knockdown experiment
Supplementary files format and content: tab-delimited text file includes raw counts for all samples in RX-5902 treatment experiemnt

molecule: total RNA

growth_protocol: MOLM-14 cells were cultured in RPMI-1640 medium (ThermoFisher Scientific) supplemented with 10% heat-inactivated fetal bovine serum (ThermoFisher Scientific) and 1% Penicillin-Streptomycin (ThermoFisher Scientific), at 37°C with 5% CO2.

extract_protocol:
RNA was extracted using Trizol reagent (ThermoFisher Scientific) with chloroform, and purified using Rneasy mini plus kit (Qiagen) with on-column genomic DNA removal by RNase-free DNase (Qiagen).
RNA libraries for RNA-seq were prepared using MGIEasy Fast RNA Library Prep Set following manufacturer's protocols.

treatment_protocol: For DDX5 knockdown experiment, MOLM-14 cells transduced with control shRNA (shControl) or DDX5-targeting shRNA (shDDX5) by spinoculation, and then cells were collected 96 hours post lentiviral infection. For RX-5902 treatment experiment, MOLM-14 cells treated with DMSO (0.1%) or RX-5902 (100 nM) for 6 hours, and then cells were harvested for RNA extraction.

tag: cell line

tag: cell type

value: human AML cell line

tag: treatment


title: Pt4_PBMC_I1D014_GEX

description:
Library name: Sample7
10x Genomics


title: Pt1_PBMC_I2D003_GEX

description:
Library name: Sample3
10x Genomics


title: Pt1_PBMC_I1D056_GEX

description:
Library name: Sample2
10x Genomics


title: Pt1_PBMC_I1D014_GEX

description:
Library name: Sample1
10x Genomics


title: C233_F

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: Library name: BRA6403A15

data_processing:
CellRanger v7.0.1 was used to demultiplex samples and generate raw matrices for input into CellBender v0.3.2, using force-cells to specify a lower limit for cell number per sample. Samples T017_B, C090_B, C074_F, C070_F were not multiplexed. The barcode and number of cells forced for each sample can be found in the demultiplexing_barcodes.csv file.
Scripts for analysis available at github.com/ogarralab/branchett_human_bal_tb_2026
Assembly: GRCh38, Homo sapiens
Supplementary files format and content: CellBender filtered matrices per sample
Supplementary files format and content: Data slot from anndata object integrated across all samples

source_name: Bronchoalveolar lavage

extract_protocol:
All sample processing, flow cytometry staining and preservation of samples for subsequent 525 analyses was performed on the day of bronchoscopy. Samples were filtered to remove mucus and debris by pipetting through 70 um 529 cell strainers, before pelleting by centrifugation at 500 x G for 7 minutes at 4oC and transferring 530 supernatants in aliquots to storage at -80oC for subsequent processing. All cell pellets were 531 briefly suspended in ammonium chloride potassium (ACK) lysing buffer (Thermo Fisher 532 Scientific) to lyse erythrocytes, before washing with RPMI 1640 supplemented with 10% foetal 533 bovine serum and 5% penicillin and streptomycin (all Thermo Fisher Scientific) and 534 centrifuging at 400 x G for 5 minutes at 4oC and suspending in supplemented RPMI.
Cell pellets containing 0.5-1 x 106 live cells were fixed and permeabilized using the Chromium 576 Next GEM Single Cell Fixed RNA Sample Preparation Kit (10X Genomics), as per 577 manufacturer’s instructions. Briefly, cell pellets were suspended in 0.04% Ultrapure BSA 578 (Thermo Fisher Scientific) in 1X PBS (Corning), then centrifuged at 400 x G for 5 minutes at 579  17 4oC, before suspending in 10X Genomics Fixation and Permeabilization buffer, supplemented 580 with 4% molecular biology grade formaldehyde, and fixing at 4 oC for 22 hours. Fixed cells 581 were pelleted by centrifugation at 900 x G for 5 minutes, suspended in 10X Genomics Quench 582 buffer and supplemented with 10X Genomics Enhancer solution and 50% molecular biology 583 grade glycerol (Sigma-Aldrich), to a final glycerol concentration of 10%, before storing at -584 80oC until subsequent batch processing. Sample were stored for between 7 and 574 days 585 before running scRNA-seq. Fixed samples were processed in pooled scRNA-seq runs of up 586 to 10 samples using the Chromium Fixed RNA Profiling Kits for Multiplexed Samples, splitting 587 each sample over one to three barcoded probe sets, to maximise cells recovered per sample 588 where input cell number was sufficient for splitting over multiple barcoded probe sets.

value: Bronchoalveolar lavage

tag: barcoding

value: Multiplex sample

tag: library type

value: mRNA

tag: kit

value: 10X Flex Gene


title: C189_B, P164_T

description: Library name: BRA6403A13


title: T146_B, T123_B, C155_B, C155_F, C106_F

description: Library name: BRA6403A5


title: T185_B, T219_B, T218_B, C231_B

description: Library name: BRA6403A12


title: T147_B, T127_B, T156_B

description: Library name: BRA6403A10


title: C220_B, C224_B, C223_B, C239_B, C233_B, P074_P, T196_B , T202_B

description: Library name: BRA6403A7


title: C089_B, C079_F, C075_F, C090_F, C128_B, C142_B, C091_B, C122_B

description: Library name: BRA6403A2


title: C182_B, T212_B, C211_B, C211_F

description: Library name: BRA6403A11


title: C140_B , T132_B, C134_B, C154_B, C103_F, C157_F, P103_P, C075_P

description: Library name: BRA6403A6


title: C070_F

description: Library name: BRA5853A4

value: Single sample


title: C074_F

description: Library name: BRA5853A3


title: C222_B, C224_F, C225_F

description: Library name: BRA6403A14


title: C090_B

description: Library name: BRA5853A2


title: P013_P, C034_B, C039_F, T096_B, C110_B, T137_B, P077_P, T158_B, C164_P, T166_B

description: Library name: BRA6403A3


title: T017_B

description: Library name: BRA5853A1


title: HCE-2 cells, hyperosmotic stress, replicate 3

city: Nanjing

first: Yun

last: Tang

address: 321 Zhongshan Road

country: China

institute: Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University

description: Library name: HN_3

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Homo sapiens reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: corneal epithelium

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: corneal epithelium

value: corneal epithelial cells

value: 90 mM NaCl, 24h


title: HCE-2 cells, hyperosmotic stress, replicate 2

description: Library name: HN_2


title: HCE-2 cells, untreated control, replicate 3

description: Library name: cont_3

value: untreated


title: T094_B, C077_F, T095_B, C098_B, T105_B ,C106_B, C107_B, C115_B

description: Library name: BRA6403A1


title: HCE-2 cells, hyperosmotic stress, replicate 1

description: Library name: HN_1


title: RECQL4 ChIP-seq, –MCM10, Rep2 (ChIP)

city: Mishima

first: Masato

last: Kanemaki

state: Shizuoka

address: Yata 1111

department: Department of Chromosome Science

country: Japan

institute: National Institute of Genetics

description: Library name: RECQL4 Rep2 Ligand ChIP

library_source: genomic

data_processing:
Initial assessment of raw FASTQ sequencing reads was performed using FastQC (v0.11.9). We utilized Trim Galore (v0.6.6) for adapter removal (Illumina sequence: AGATCGGAAGAGC) via the --illumina flag. The processed reads were mapped to the GRCh38 (NCBI) reference genome with Bowtie2 (v2.2.5), employing stringent alignment criteria (--end-to-end --very-sensitive --no-mixed --no-discordant -I 0 -X 1000). Following alignment, SAMtools (v1.12) was used to convert outputs to BAM format and enforce quality filters, including a MAPQ score ≥ 20 and a requirement for proper pairing. PCR duplicates were identified and discarded using the fixmate and markdup suites. Genomic signal tracks were generated with MACS2 (v2.2.7.1) and converted to bigWig files. Final normalization was achieved through deepTools (v3.5.5) bigwigCompare, which calculated the ChIP/Input ratio across 100 bp genomic windows (--operation ratio --pseudocount 0 -bs 100).
Assembly: GRCh38
Supplementary files format and content: bigwig (input normalized signal)

molecule: genomic DNA

growth_protocol: HCT116 cells were cultured in McCoy’s 5A, supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/mL streptomycin at 37 °C in a 5% CO2 incubator.

extract_protocol:
ChIP-seq analysis was performed according to previously established methods (Zhu et al. 2025). Approximately 2 × 107 cells were trypsinised, washed twice with 10 ml PBS, and resuspended in 1 ml PBS for crosslinking. This was achieved by adding an equal volume of fresh 2% paraformaldehyde (10 min, room temperature), followed by quenching with 125 mM glycine for 5 min. After sequential washes with PBS, PBS/0.5% NP-40, and PBS/10% glycerol, cell pellets were either flash-frozen in liquid nitrogen for storage at -80 °C or lysed immediately. For lysis, cells were incubated on ice for 10 min in 1 ml ChIP lysis buffer (25 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5% Sarkosyl, 0.1% sodium deoxycholate, 0.5% Triton X-100, and Roche protease inhibitors). Chromatin fragmentation was performed using a Covaris S2 focused-ultrasonicator (5% duty factor, 100 cycles/burst, intensity 3) for 10 min. Following centrifugation (18,400 x g, 15 min, 4 °C), the supernatant was pre-cleared with 1.5 µg Protein G Dynabeads (Invitrogen, #10004D) for 1–2 h. A 2% input aliquot (20 µl) was reserved, while the remaining supernatant underwent immunoprecipitation overnight at 4 °C with 5 µg anti-FLAG M2 antibody (Sigma, #F1804) bound to Protein G Dynabeads. The beads were washed stringently with RIPA buffer, RIPA containing 300 mM NaCl, RIPA with 250 mM LiCl, and twice with TE buffer. DNA was eluted twice at 65 °C in TE + 1% SDS, and crosslinks were reversed at 65 °C for 4 h following RNase A and Proteinase K treatment. Finally, DNA was purified using the Takara NucleoSpin Gel and PCR Clean-up Kit.
Libraries were generated using the NEBNext Ultra II kit for 50 bp paired-end sequencing on an Illumina NovaSeq 6000.

treatment_protocol: To synchronise cells, nocodazole (Sigma, #M1404) was added to the culture medium at a final concentration of 50 ng/ml. After 14-16 h, the nocodazole-containing media was removed, and the cells were washed twice with fresh media. Following the nocodazole release, 1 µM 5-Ph-IAA (AID2 degradation inducer) and 0.5 µM AGB1 (BromoTag degradation inducer) were added for the desired period of time.

value: Colonic epithelial cells

tag: genotype

value: HCT116 CMV-OsTIR1 (F74G) Stag-3xFLAG-RECQL4 mAID-BromoTag-MCM10

value: Nocodazole for 15 hours and release for 6 hours, 5-Ph-IAA and AGB1 for 6 hours

tag: chip antibody

value: FLAG M2 (Sigma, F1804)


title: RECQL4 ChIP-seq, +MCM10, Rep2 (ChIP)

description: Library name: RECQL4 Rep2 DMSO ChIP

value: Nocodazole for 15 hours and release for 6 hours, DMSO for 6 hours


title: RECQL4 ChIP-seq, –MCM10, Rep1 (ChIP)

description: Library name: RECQL4 Rep1 Ligand ChIP


title: Irreversible pulpitis tissue sample 2

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

state: PA

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

description:
Library name: T06
10x Genomics Visium v2 FFPE

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files. Deconvolution was carried out using a public single cell reference using the RCTD algorithm.
Sequencing were aligned to hg38 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: hg38
Supplementary files format and content: Filtered feature matrices in H5 format
Supplementary files format and content: Spatial images in jpg, tiff and png formats
Library strategy: Spatial Transcriptomics

source_name: Dental pulp

extract_protocol:
Samples were assessed for RNA quality, and all FFPE samples had a DV200 score above the minimum threshold of ≥30%.
Spatial transcriptomic libraries were generated with the Visium v2 Human Transcriptome gene expression kit (10x Genomics: 1000443). Five-micron FFPE sections were placed on Superfrost Plus slides (FisherScientific) and processed through the 10x Visium v2 for FFPE protocol according to the manufacturer’s instructions (CG000518, CG000520, CG000495). H&E images were taken at 20x magnification using a Leica Aperio CS2 slide scanner (Leica Biosystems). Library QC was completed with an Agilent TapeStation 4150. Libraries were normalized and pooled to 2nM prior to loading on an Illumina NextSeq 2000, using a P4 100 flow cell with a target of a minimum of 120 million reads per sample for transcriptomic libraries.

value: Dental pulp

value: Irreversible pulpitis tissue sample 2


title: HCE-2 cells, untreated control, replicate 1

description: Library name: cont_1


title: Reversible pulpitis tissue

description:
Library name: T01
10x Genomics Visium v2 FFPE

value: Reversible pulpitis tissue


title: RECQL4 ChIP-seq, –MCM10, Rep1 (Input)

description: Library name: RECQL4 Rep1 Ligand Input


title: HCE-2 cells, untreated control, replicate 2

description: Library name: cont_2


title: RECQL4 ChIP-seq, +MCM10, Rep2 (Input)

description: Library name: RECQL4 Rep2 DMSO Input


title: Normal dental pulp tissue

description:
Library name: C10
10x Genomics Visium v2 FFPE

value: Normal dental pulp tissue


title: MCM10 ChIP-seq, +RECQL4, Rep2 (ChIP)

description: Library name: MCM10 Rep2 DMSO ChIP

value: HCT116 CMV-OsTIR1 (F74G) MCM10-Stag-3xFLAG mAID-BromoTag-RECQL4


title: RECQL4 ChIP-seq, +MCM10, Rep1 (ChIP)

description: Library name: RECQL4 Rep1 DMSO ChIP


title: RECQL4 ChIP-seq, +MCM10, Rep1 (Input)

description: Library name: RECQL4 Rep1 DMSO Input


title: MCM10 ChIP-seq, –RECQL4, Rep2 (ChIP)

description: Library name: MCM10 Rep2 Ligand ChIP


title: MCM10 ChIP-seq, –RECQL4, Rep2 (Input)

description: Library name: MCM10 Rep2 Ligand Input


title: RECQL4 ChIP-seq, –MCM10, Rep2 (Input)

description: Library name: RECQL4 Rep2 Ligand Input


title: MCM10 ChIP-seq, –RECQL4, Rep1 (Input)

description: Library name: MCM10 Rep1 Ligand Input


title: MCM10 ChIP-seq, –RECQL4, Rep1 (ChIP)

description: Library name: MCM10 Rep1 Ligand ChIP


title: MCM10 ChIP-seq, +RECQL4, Rep1 (ChIP)

description: Library name: MCM10 Rep1 DMSO ChIP


title: MCM10 ChIP-seq, +RECQL4, Rep2 (Input)

description: Library name: MCM10 Rep2 DMSO Input


title: 955 - EM-Seq

city: Indianapolis

first: Helen

last: Masson

address: 893 S Delaware St.

institute: Eli Lilly and Company

description: Library name: Sample 803

library_source: other

data_processing:
Data analysis was performed using nf-core/methylseq version 2.3.0 using the Bismark aligner with the GRCh38 human reference genome (GCA_000001405.15_GRCh38_no_alt fasta file with the hs38d1 decoy assembly). Most samples were deemed high quality with sufficient genome coverage > 20X. One sample was rejected as the sequencing data did not show an expected reduction in GC content observed in all other samples after sequencing, still averaging the pre-converted GC percentage of ~ 40%. The expected reduced GC content likely reflected the failure to enzymatically convert free cysteines. Decoy sequences were padded with NN to enable extraction of relevant methylation contexts (CG, CHH vs CHG). EMseq specific trimming was set with the flag em_seq = true. Methylation coverage files from Bismark were imported and individual samples smoothed in R using bsseq BSmooth as the sample size was too large to jointly smooth across all samples. A gtf file was provided to summarize the smoothed methylation signals using the bsseq getMeth command resulting in a summarized methylation signal across the regions provided. Gene promotors were calculated with the GenomicRanges promoters command using default parameters for 2000 bp upstream and 200 bp downstream of TSS. Individual samples were aggregated into two methylation matrices representing gene and promotor methylation separately.
Assembly: GRCh38
Supplementary files format and content: txt file includes summarized gene level methylation
Supplementary files format and content: txt file includes summarized promoter level methylation
Library strategy: EM-seq

molecule: other

source_name: whole blood

extract_protocol:
Whole blood DNA was extracted from PAXgene blood RNA tubes. Briefly, frozen tubes were thawed at room temperature and centrifuged according to the manufacturer’s protocol. The resulting pellet was then washed with nuclease free water, resuspended in sterile PBS, and split in half. DNA was extracted from one half of the suspension using the Mag-Bind Blood & Tissue DNA HDQ Kit (Omega Bio-Tek) on the Kingfisher Flex (Thermo) instrument. The other half of the suspension was used for RNA extraction. The concentration and integrity for DNA was evaluated by Picogreen Assay and Agarose Gel electrophoresis.
Whole genome methylation libraries were constructed using 200ng gDNA input with NEBNext® Enzymatic Methyl-seq Kit as per manufacturer instruction with minor modifications for automation. Library concentration was measured using the Quant-iT™ PicoGreen® dsDNA Reagent (Thermo), and library size distribution and quality were checked using a DNA chip on Caliper Gx Touch (Revity). Library quantification was further refined by qPCR using the KAPA Library Quantification Kit (Roche). Paired-end sequencing (2 × 150 bp, approximately 30X coverage per sample) was carried out on an Illumina NovaSeq 6000 Plus platform (Illumina) following the manufacturer’s recommended protocols.

value: whole blood

value: healthy controls


title: 888949831 - EM-Seq

description: Library name: Sample 801


title: C052_F, C093_B, C107_F, C118_B, C131_B, C135_B, C141_B, C141_F, T173_B

description: Library name: BRA6403A4

value: Bronchoalveolar lavage

value: Multiplex sample

value: mRNA

value: 10X Flex Gene


title: 888921995 - EM-Seq

description: Library name: Sample 800


title: 888849255 - EM-Seq

description: Library name: Sample 798


title: 888454783 - EM-Seq

description: Library name: Sample 795


title: 888247070 - EM-Seq

description: Library name: Sample 793


title: Irreversible pulpitis tissue sample 1

description:
Library name: T04
10x Genomics Visium v2 FFPE

value: Irreversible pulpitis tissue sample 1


title: 110048196 - EM-Seq

description: Library name: Sample 785


title: 1703 - EM-Seq

description: Library name: Sample 789


title: 521 - EM-Seq

description: Library name: Sample 790


title: 888100344 - EM-Seq

description: Library name: Sample 791


title: 110046778 - EM-Seq

description: Library name: Sample 783


title: 110046622 - EM-Seq

description: Library name: Sample 781


title: 1638 - EM-Seq

description: Library name: Sample 788


title: 110046733 - EM-Seq

description: Library name: Sample 782


title: 888992066 - EM-Seq

description: Library name: Sample 802


title: 110046051 - EM-Seq

description: Library name: Sample 775


title: 110048520 - EM-Seq

description: Library name: Sample 786


title: 110046143 - EM-Seq

description: Library name: Sample 776


title: 110044866 - EM-Seq

description: Library name: Sample 773


title: 110044838 - EM-Seq

description: Library name: Sample 771


title: 110044782 - EM-Seq

description: Library name: Sample 769


title: 110044887 - EM-Seq

description: Library name: Sample 774


title: 110044812 - EM-Seq

description: Library name: Sample 770


title: 110044681 - EM-Seq

description: Library name: Sample 768


title: 110044845 - EM-Seq

description: Library name: Sample 772


title: MCM10 ChIP-seq, +RECQL4, Rep1 (Input)

description: Library name: MCM10 Rep1 DMSO Input

value: Colonic epithelial cells


title: 110044621 - EM-Seq

description: Library name: Sample 766


title: 110044290 - EM-Seq

description: Library name: Sample 762


title: 110044475 - EM-Seq

description: Library name: Sample 765


title: 110044358 - EM-Seq

description: Library name: Sample 763


title: 110044225 - EM-Seq

description: Library name: Sample 761


title: 110044658 - EM-Seq

description: Library name: Sample 767


title: 110042893 - EM-Seq

description: Library name: Sample 759


title: 110042853 - EM-Seq

description: Library name: Sample 757


title: 110046231 - EM-Seq

description: Library name: Sample 778


title: 110042858 - EM-Seq

description: Library name: Sample 758


title: 110042749 - EM-Seq

description: Library name: Sample 756


title: 110042731 - EM-Seq

description: Library name: Sample 755


title: 110042619 - EM-Seq

description: Library name: Sample 753


title: 110042555 - EM-Seq

description: Library name: Sample 751


title: 110040939 - EM-Seq

description: Library name: Sample 750


title: 110042636 - EM-Seq

description: Library name: Sample 754


title: 888236332 - EM-Seq

description: Library name: Sample 792


title: 110040764 - EM-Seq

description: Library name: Sample 747


title: 110040777 - EM-Seq

description: Library name: Sample 748


title: 110040856 - EM-Seq

description: Library name: Sample 749


title: 110040691 - EM-Seq

description: Library name: Sample 745


title: 110040414 - EM-Seq

description: Library name: Sample 742


title: 110040735 - EM-Seq

description: Library name: Sample 746


title: 110040206 - EM-Seq

description: Library name: Sample 738


title: 110040412 - EM-Seq

description: Library name: Sample 741


title: 110040194 - EM-Seq

description: Library name: Sample 737


title: 110040164 - EM-Seq

description: Library name: Sample 736


title: 110040327 - EM-Seq

description: Library name: Sample 740


title: 110040592 - EM-Seq

description: Library name: Sample 743


title: 888713165 - EM-Seq

description: Library name: Sample 797


title: 110040001 - EM-Seq

description: Library name: Sample 733


title: 110039634 - EM-Seq

description: Library name: Sample 732


title: 110040045 - EM-Seq

description: Library name: Sample 734


title: 110039613 - EM-Seq

description: Library name: Sample 731


title: 110040247 - EM-Seq

description: Library name: Sample 739


title: 110039290 - EM-Seq

description: Library name: Sample 729


title: 110039591 - EM-Seq

description: Library name: Sample 730


title: 888364317 - EM-Seq

description: Library name: Sample 794


title: 110035347 - EM-Seq

description: Library name: Sample 726


title: 110032752 - EM-Seq

description: Library name: Sample 725


title: 110036411 - EM-Seq

description: Library name: Sample 728


title: 110046939 - EM-Seq

description: Library name: Sample 784


title: 110029997 - EM-Seq

description: Library name: Sample 724


title: 110029963 - EM-Seq

description: Library name: Sample 722


title: 110029969 - EM-Seq

description: Library name: Sample 723


title: 88702 - EM-Seq

description: Library name: Sample 720

value: SLE


title: 88701 - EM-Seq

description: Library name: Sample 719


title: 88601 - EM-Seq

description: Library name: Sample 718


title: 110042565 - EM-Seq

description: Library name: Sample 752


title: 88510 - EM-Seq

description: Library name: Sample 717


title: 1627 - EM-Seq

description: Library name: Sample 787


title: 965 - EM-Seq

description: Library name: Sample 804


title: 88508 - EM-Seq

description: Library name: Sample 716


title: 88507 - EM-Seq

description: Library name: Sample 715


title: 88506 - EM-Seq

description: Library name: Sample 714


title: 88503 - EM-Seq

description: Library name: Sample 713


title: 110040129 - EM-Seq

description: Library name: Sample 735


title: 88409 - EM-Seq

description: Library name: Sample 712


title: 88405 - EM-Seq

description: Library name: Sample 710


title: 88406 - EM-Seq

description: Library name: Sample 711


title: 88404 - EM-Seq

description: Library name: Sample 709


title: 110046189 - EM-Seq

description: Library name: Sample 777


title: 88310 - EM-Seq

description: Library name: Sample 707


title: 88401 - EM-Seq

description: Library name: Sample 708


title: 88302 - EM-Seq

description: Library name: Sample 704


title: 88308 - EM-Seq

description: Library name: Sample 706


title: 88211 - EM-Seq

description: Library name: Sample 702


title: 88102 - EM-Seq

description: Library name: Sample 699


title: 88304 - EM-Seq

description: Library name: Sample 705


title: 88201 - EM-Seq

description: Library name: Sample 700


title: 88204 - EM-Seq

description: Library name: Sample 701


title: 88301 - EM-Seq

description: Library name: Sample 703


title: 110036393 - EM-Seq

description: Library name: Sample 727


title: 87903 - EM-Seq

description: Library name: Sample 698


title: 87807 - EM-Seq

description: Library name: Sample 695


title: 87803 - EM-Seq

description: Library name: Sample 694


title: 87407 - EM-Seq

description: Library name: Sample 693


title: 87901 - EM-Seq

description: Library name: Sample 697


title: 87401 - EM-Seq

description: Library name: Sample 690


title: 888882695 - EM-Seq

description: Library name: Sample 799


title: 110029953 - EM-Seq

description: Library name: Sample 721


title: 110042972 - EM-Seq

description: Library name: Sample 760


title: 87402 - EM-Seq

description: Library name: Sample 691


title: 87307 - EM-Seq

description: Library name: Sample 689


title: 110044374 - EM-Seq

description: Library name: Sample 764


title: 87305 - EM-Seq

description: Library name: Sample 688


title: 87302 - EM-Seq

description: Library name: Sample 687


title: 87808 - EM-Seq

description: Library name: Sample 696


title: 86505 - EM-Seq

description: Library name: Sample 683


title: 86601 - EM-Seq

description: Library name: Sample 685


title: 86303 - EM-Seq

description: Library name: Sample 679


title: 86305 - EM-Seq

description: Library name: Sample 680


title: 86502 - EM-Seq

description: Library name: Sample 682


title: 86401 - EM-Seq

description: Library name: Sample 681


title: 86102 - EM-Seq

description: Library name: Sample 677


title: 86506 - EM-Seq

description: Library name: Sample 684


title: 85803 - EM-Seq

description: Library name: Sample 674


title: 86001 - EM-Seq

description: Library name: Sample 675


title: 86101 - EM-Seq

description: Library name: Sample 676


title: 85602 - EM-Seq

description: Library name: Sample 672


title: 85503 - EM-Seq

description: Library name: Sample 670


title: 87403 - EM-Seq

description: Library name: Sample 692


title: 85601 - EM-Seq

description: Library name: Sample 671


title: 85603 - EM-Seq

description: Library name: Sample 673


title: 110040651 - EM-Seq

description: Library name: Sample 744


title: 85203 - EM-Seq

description: Library name: Sample 667


title: 85201 - EM-Seq

description: Library name: Sample 665


title: 85105 - EM-Seq

description: Library name: Sample 664


title: 85103 - EM-Seq

description: Library name: Sample 663


title: 85501 - EM-Seq

description: Library name: Sample 668


title: 85202 - EM-Seq

description: Library name: Sample 666


title: 85502 - EM-Seq

description: Library name: Sample 669


title: 84605 - EM-Seq

description: Library name: Sample 662


title: 888647920 - EM-Seq

description: Library name: Sample 796


title: 84318 - EM-Seq

description: Library name: Sample 660


title: 84314 - EM-Seq

description: Library name: Sample 658


title: 84317 - EM-Seq

description: Library name: Sample 659


title: 84311 - EM-Seq

description: Library name: Sample 657


title: 84304 - EM-Seq

description: Library name: Sample 654


title: 110046272 - EM-Seq

description: Library name: Sample 780


title: 84403 - EM-Seq

description: Library name: Sample 661


title: 84307 - EM-Seq

description: Library name: Sample 656


title: 84217 - EM-Seq

description: Library name: Sample 650


title: 84306 - EM-Seq

description: Library name: Sample 655


title: 84228 - EM-Seq

description: Library name: Sample 652


title: 84210 - EM-Seq

description: Library name: Sample 647


title: 84234 - EM-Seq

description: Library name: Sample 653


title: 84213 - EM-Seq

description: Library name: Sample 648


title: 84202 - EM-Seq

description: Library name: Sample 644


title: 84206 - EM-Seq

description: Library name: Sample 645


title: 84224 - EM-Seq

description: Library name: Sample 651


title: 84209 - EM-Seq

description: Library name: Sample 646


title: 84216 - EM-Seq

description: Library name: Sample 649


title: 82506 - EM-Seq

description: Library name: Sample 637


title: 84102 - EM-Seq

description: Library name: Sample 641


title: 82604 - EM-Seq

description: Library name: Sample 639


title: 84101 - EM-Seq

description: Library name: Sample 640


title: 82601 - EM-Seq

description: Library name: Sample 638


title: 82503 - EM-Seq

description: Library name: Sample 634


title: 84201 - EM-Seq

description: Library name: Sample 643


title: 82505 - EM-Seq

description: Library name: Sample 636


title: 82504 - EM-Seq

description: Library name: Sample 635


title: 82405 - EM-Seq

description: Library name: Sample 630


title: 84104 - EM-Seq

description: Library name: Sample 642


title: 82412 - EM-Seq

description: Library name: Sample 632


title: 82502 - EM-Seq

description: Library name: Sample 633


title: 82320 - EM-Seq

description: Library name: Sample 628


title: 82314 - EM-Seq

description: Library name: Sample 625


title: 82319 - EM-Seq

description: Library name: Sample 627


title: 82410 - EM-Seq

description: Library name: Sample 631


title: 82312 - EM-Seq

description: Library name: Sample 623


title: 82403 - EM-Seq

description: Library name: Sample 629


title: 82308 - EM-Seq

description: Library name: Sample 622


title: 82301 - EM-Seq

description: Library name: Sample 620


title: 82120 - EM-Seq

description: Library name: Sample 618


title: 82119 - EM-Seq

description: Library name: Sample 617


title: 82302 - EM-Seq

description: Library name: Sample 621


title: 82315 - EM-Seq

description: Library name: Sample 626


title: 82101 - EM-Seq

description: Library name: Sample 611


title: 81407 - EM-Seq

description: Library name: Sample 607


title: 81414 - EM-Seq

description: Library name: Sample 610


title: 81403 - EM-Seq

description: Library name: Sample 605


title: 81408 - EM-Seq

description: Library name: Sample 608


title: 82110 - EM-Seq

description: Library name: Sample 614


title: 81402 - EM-Seq

description: Library name: Sample 604


title: 82112 - EM-Seq

description: Library name: Sample 615


title: 82103 - EM-Seq

description: Library name: Sample 612


title: 82113 - EM-Seq

description: Library name: Sample 616


title: 81316 - EM-Seq

description: Library name: Sample 603


title: 81315 - EM-Seq

description: Library name: Sample 602


title: 81412 - EM-Seq

description: Library name: Sample 609


title: 82201 - EM-Seq

description: Library name: Sample 619


title: 82313 - EM-Seq

description: Library name: Sample 624


title: 81301 - EM-Seq

description: Library name: Sample 598


title: 81405 - EM-Seq

description: Library name: Sample 606


title: 81304 - EM-Seq

description: Library name: Sample 599


title: 81211 - EM-Seq

description: Library name: Sample 597


title: 81207 - EM-Seq

description: Library name: Sample 595


title: 81209 - EM-Seq

description: Library name: Sample 596


title: 81204 - EM-Seq

description: Library name: Sample 594


title: 81314 - EM-Seq

description: Library name: Sample 601


title: 86801 - EM-Seq

description: Library name: Sample 686


title: 82104 - EM-Seq

description: Library name: Sample 613


title: 80603 - EM-Seq

description: Library name: Sample 582


title: 80801 - EM-Seq

description: Library name: Sample 583


title: 81103 - EM-Seq

description: Library name: Sample 589


title: 80502 - EM-Seq

description: Library name: Sample 580


title: 80504 - EM-Seq

description: Library name: Sample 581


title: 80346 - EM-Seq

description: Library name: Sample 575


title: 80334 - EM-Seq

description: Library name: Sample 571


title: 81007 - EM-Seq

description: Library name: Sample 588


title: 80807 - EM-Seq

description: Library name: Sample 585


title: 80404 - EM-Seq

description: Library name: Sample 579


title: 80403 - EM-Seq

description: Library name: Sample 578


title: 80338 - EM-Seq

description: Library name: Sample 572


title: 80342 - EM-Seq

description: Library name: Sample 573


title: 80328 - EM-Seq

description: Library name: Sample 569


title: 80345 - EM-Seq

description: Library name: Sample 574


title: 80802 - EM-Seq

description: Library name: Sample 584


title: 81006 - EM-Seq

description: Library name: Sample 587


title: 81104 - EM-Seq

description: Library name: Sample 590


title: 80401 - EM-Seq

description: Library name: Sample 576


title: 81203 - EM-Seq

description: Library name: Sample 593


title: 80329 - EM-Seq

description: Library name: Sample 570


title: 80327 - EM-Seq

description: Library name: Sample 568


title: 80324 - EM-Seq

description: Library name: Sample 567


title: 80402 - EM-Seq

description: Library name: Sample 577


title: 80322 - EM-Seq

description: Library name: Sample 565


title: 80323 - EM-Seq

description: Library name: Sample 566


title: 80313 - EM-Seq

description: Library name: Sample 561


title: 110046264 - EM-Seq

description: Library name: Sample 779


title: 80310 - EM-Seq

description: Library name: Sample 560


title: 80215 - EM-Seq

description: Library name: Sample 558


title: 80216 - EM-Seq

description: Library name: Sample 559


title: 80316 - EM-Seq

description: Library name: Sample 562


title: 80204 - EM-Seq

description: Library name: Sample 554


title: 80214 - EM-Seq

description: Library name: Sample 557


title: 80207 - EM-Seq

description: Library name: Sample 555


title: 80101 - EM-Seq

description: Library name: Sample 548


title: 80108 - EM-Seq

description: Library name: Sample 551


title: 76803 - EM-Seq

description: Library name: Sample 546


title: 80106 - EM-Seq

description: Library name: Sample 550


title: 80109 - EM-Seq

description: Library name: Sample 552


title: 80111 - EM-Seq

description: Library name: Sample 553


title: 76507 - EM-Seq

description: Library name: Sample 543


title: 80213 - EM-Seq

description: Library name: Sample 556


title: 76902 - EM-Seq

description: Library name: Sample 547


title: 80320 - EM-Seq

description: Library name: Sample 564


title: 76801 - EM-Seq

description: Library name: Sample 545


title: 80318 - EM-Seq

description: Library name: Sample 563


title: 80104 - EM-Seq

description: Library name: Sample 549


title: 81311 - EM-Seq

description: Library name: Sample 600


title: 76419 - EM-Seq

description: Library name: Sample 540


title: 76506 - EM-Seq

description: Library name: Sample 542


title: 76501 - EM-Seq

description: Library name: Sample 541


title: 76508 - EM-Seq

description: Library name: Sample 544


title: 76410 - EM-Seq

description: Library name: Sample 537


title: 76417 - EM-Seq

description: Library name: Sample 539


title: 76415 - EM-Seq

description: Library name: Sample 538


title: 76313 - EM-Seq

description: Library name: Sample 534


title: 76403 - EM-Seq

description: Library name: Sample 535


title: 76405 - EM-Seq

description: Library name: Sample 536


title: 76305 - EM-Seq

description: Library name: Sample 531


title: 76107 - EM-Seq

description: Library name: Sample 525


title: 76204 - EM-Seq

description: Library name: Sample 530


title: 76109 - EM-Seq

description: Library name: Sample 526


title: 76311 - EM-Seq

description: Library name: Sample 533


title: 76203 - EM-Seq

description: Library name: Sample 529


title: 76106 - EM-Seq

description: Library name: Sample 524


title: 76111 - EM-Seq

description: Library name: Sample 527


title: 76112 - EM-Seq

description: Library name: Sample 528


title: 76308 - EM-Seq

description: Library name: Sample 532


title: 76002 - EM-Seq

description: Library name: Sample 521


title: 76011 - EM-Seq

description: Library name: Sample 523


title: 76007 - EM-Seq

description: Library name: Sample 522


title: 76001 - EM-Seq

description: Library name: Sample 520


title: 73605 - EM-Seq

description: Library name: Sample 519


title: 73506 - EM-Seq

description: Library name: Sample 518


title: 73415 - EM-Seq

description: Library name: Sample 516


title: 73413 - EM-Seq

description: Library name: Sample 515


title: 73410 - EM-Seq

description: Library name: Sample 513


title: 73412 - EM-Seq

description: Library name: Sample 514


title: 73504 - EM-Seq

description: Library name: Sample 517


title: 73409 - EM-Seq

description: Library name: Sample 512


title: 73401 - EM-Seq

description: Library name: Sample 511


title: 73302 - EM-Seq

description: Library name: Sample 510


title: 73201 - EM-Seq

description: Library name: Sample 509


title: 81202 - EM-Seq

description: Library name: Sample 592


title: 73003 - EM-Seq

description: Library name: Sample 507


title: 71101 - EM-Seq

description: Library name: Sample 505


title: 73002 - EM-Seq

description: Library name: Sample 506


title: 71011 - EM-Seq

description: Library name: Sample 502


title: 71001 - EM-Seq

description: Library name: Sample 496


title: 71012 - EM-Seq

description: Library name: Sample 503


title: 71008 - EM-Seq

description: Library name: Sample 501


title: 71014 - EM-Seq

description: Library name: Sample 504


title: 71007 - EM-Seq

description: Library name: Sample 500


title: 70911 - EM-Seq

description: Library name: Sample 495


title: 71003 - EM-Seq

description: Library name: Sample 497


title: 71006 - EM-Seq

description: Library name: Sample 499


title: 70822 - EM-Seq

description: Library name: Sample 490


title: 86302 - EM-Seq

description: Library name: Sample 678


title: 81201 - EM-Seq

description: Library name: Sample 591


title: 71005 - EM-Seq

description: Library name: Sample 498


title: 73005 - EM-Seq

description: Library name: Sample 508


title: 70901 - EM-Seq

description: Library name: Sample 493


title: 70821 - EM-Seq

description: Library name: Sample 489


title: 70827 - EM-Seq

description: Library name: Sample 492


title: 70811 - EM-Seq

description: Library name: Sample 486


title: 70904 - EM-Seq

description: Library name: Sample 494


title: 70814 - EM-Seq

description: Library name: Sample 487


title: 70815 - EM-Seq

description: Library name: Sample 488


title: 70810 - EM-Seq

description: Library name: Sample 485


title: 70708 - EM-Seq

description: Library name: Sample 479


title: 70808 - EM-Seq

description: Library name: Sample 483


title: 70809 - EM-Seq

description: Library name: Sample 484


title: 70802 - EM-Seq

description: Library name: Sample 481


title: 70825 - EM-Seq

description: Library name: Sample 491


title: 70610 - EM-Seq

description: Library name: Sample 476


title: 70806 - EM-Seq

description: Library name: Sample 482


title: 70702 - EM-Seq

description: Library name: Sample 477


title: 70603 - EM-Seq

description: Library name: Sample 472


title: 70711 - EM-Seq

description: Library name: Sample 480


title: 70204 - EM-Seq

description: Library name: Sample 465


title: 70406 - EM-Seq

description: Library name: Sample 468


title: 70705 - EM-Seq

description: Library name: Sample 478


title: 70202 - EM-Seq

description: Library name: Sample 464


title: 70413 - EM-Seq

description: Library name: Sample 469


title: 70501 - EM-Seq

description: Library name: Sample 470


title: 70605 - EM-Seq

description: Library name: Sample 474


title: 70118 - EM-Seq

description: Library name: Sample 462


title: 70110 - EM-Seq

description: Library name: Sample 460


title: 70107 - EM-Seq

description: Library name: Sample 459


title: 70502 - EM-Seq

description: Library name: Sample 471


title: 70111 - EM-Seq

description: Library name: Sample 461


title: 70208 - EM-Seq

description: Library name: Sample 466


title: 70608 - EM-Seq

description: Library name: Sample 475


title: 70102 - EM-Seq

description: Library name: Sample 457


title: 70604 - EM-Seq

description: Library name: Sample 473


title: 66311 - EM-Seq

description: Library name: Sample 456


title: 66310 - EM-Seq

description: Library name: Sample 455


title: 70201 - EM-Seq

description: Library name: Sample 463


title: 65904 - EM-Seq

description: Library name: Sample 452


title: 81003 - EM-Seq

description: Library name: Sample 586


title: 70404 - EM-Seq

description: Library name: Sample 467


title: 65903 - EM-Seq

description: Library name: Sample 451


title: 66309 - EM-Seq

description: Library name: Sample 454


title: 65725 - EM-Seq

description: Library name: Sample 446


title: 65729 - EM-Seq

description: Library name: Sample 447


title: 65716 - EM-Seq

description: Library name: Sample 442


title: 65724 - EM-Seq

description: Library name: Sample 445


title: 70103 - EM-Seq

description: Library name: Sample 458


title: 65901 - EM-Seq

description: Library name: Sample 450


title: 65723 - EM-Seq

description: Library name: Sample 444


title: 66202 - EM-Seq

description: Library name: Sample 453


title: 65601 - EM-Seq

description: Library name: Sample 434


title: 65706 - EM-Seq

description: Library name: Sample 439


title: 65715 - EM-Seq

description: Library name: Sample 441


title: 65718 - EM-Seq

description: Library name: Sample 443


title: 65713 - EM-Seq

description: Library name: Sample 440


title: 65509 - EM-Seq

description: Library name: Sample 432


title: 65512 - EM-Seq

description: Library name: Sample 433


title: 65701 - EM-Seq

description: Library name: Sample 435


title: 65705 - EM-Seq

description: Library name: Sample 438


title: 65702 - EM-Seq

description: Library name: Sample 436


title: 65804 - EM-Seq

description: Library name: Sample 449


title: 65504 - EM-Seq

description: Library name: Sample 429


title: 65507 - EM-Seq

description: Library name: Sample 431


title: 65503 - EM-Seq

description: Library name: Sample 428


title: 65704 - EM-Seq

description: Library name: Sample 437


title: 65007 - EM-Seq

description: Library name: Sample 425


title: 65305 - EM-Seq

description: Library name: Sample 426


title: 65506 - EM-Seq

description: Library name: Sample 430


title: 64804 - EM-Seq

description: Library name: Sample 423


title: 65002 - EM-Seq

description: Library name: Sample 424


title: 64802 - EM-Seq

description: Library name: Sample 422


title: 65308 - EM-Seq

description: Library name: Sample 427


title: 64502 - EM-Seq

description: Library name: Sample 419


title: 64303 - EM-Seq

description: Library name: Sample 417


title: 64704 - EM-Seq

description: Library name: Sample 421


title: 64208 - EM-Seq

description: Library name: Sample 416


title: 64207 - EM-Seq

description: Library name: Sample 415


title: 64010 - EM-Seq

description: Library name: Sample 408


title: 64304 - EM-Seq

description: Library name: Sample 418


title: 62301 - EM-Seq

description: Library name: Sample 402


title: 64201 - EM-Seq

description: Library name: Sample 414


title: 64101 - EM-Seq

description: Library name: Sample 413


title: 62216 - EM-Seq

description: Library name: Sample 401


title: 62703 - EM-Seq

description: Library name: Sample 406


title: 64015 - EM-Seq

description: Library name: Sample 411


title: 64011 - EM-Seq

description: Library name: Sample 409


title: 64013 - EM-Seq

description: Library name: Sample 410


title: 62406 - EM-Seq

description: Library name: Sample 405


title: 62403 - EM-Seq

description: Library name: Sample 404


title: 64701 - EM-Seq

description: Library name: Sample 420


title: 62211 - EM-Seq

description: Library name: Sample 400


title: 62205 - EM-Seq

description: Library name: Sample 397


title: 62401 - EM-Seq

description: Library name: Sample 403


title: 62209 - EM-Seq

description: Library name: Sample 398


title: 64016 - EM-Seq

description: Library name: Sample 412


title: 62210 - EM-Seq

description: Library name: Sample 399


title: 62203 - EM-Seq

description: Library name: Sample 395


title: 62202 - EM-Seq

description: Library name: Sample 394


title: 62704 - EM-Seq

description: Library name: Sample 407


title: 62004 - EM-Seq

description: Library name: Sample 387


title: 62010 - EM-Seq

description: Library name: Sample 392


title: 60506 - EM-Seq

description: Library name: Sample 378


title: 62204 - EM-Seq

description: Library name: Sample 396


title: 61501 - EM-Seq

description: Library name: Sample 384


title: 62008 - EM-Seq

description: Library name: Sample 390


title: 55611 - EM-Seq

description: Library name: Sample 374


title: 62001 - EM-Seq

description: Library name: Sample 385


title: 61105 - EM-Seq

description: Library name: Sample 381


title: 62007 - EM-Seq

description: Library name: Sample 389


title: 60301 - EM-Seq

description: Library name: Sample 376


title: 61304 - EM-Seq

description: Library name: Sample 382


title: 60101 - EM-Seq

description: Library name: Sample 375


title: 62009 - EM-Seq

description: Library name: Sample 391


title: 60702 - EM-Seq

description: Library name: Sample 379


title: 62005 - EM-Seq

description: Library name: Sample 388


title: 61003 - EM-Seq

description: Library name: Sample 380


title: 55602 - EM-Seq

description: Library name: Sample 373


title: 55505 - EM-Seq

description: Library name: Sample 371


title: 55502 - EM-Seq

description: Library name: Sample 370


title: 55301 - EM-Seq

description: Library name: Sample 368


title: 62003 - EM-Seq

description: Library name: Sample 386


title: 55104 - EM-Seq

description: Library name: Sample 367


title: 55102 - EM-Seq

description: Library name: Sample 365


title: 60503 - EM-Seq

description: Library name: Sample 377


title: 61401 - EM-Seq

description: Library name: Sample 383


title: 55103 - EM-Seq

description: Library name: Sample 366


title: 54125 - EM-Seq

description: Library name: Sample 362


title: 54110 - EM-Seq

description: Library name: Sample 360


title: 54119 - EM-Seq

description: Library name: Sample 361


title: 55101 - EM-Seq

description: Library name: Sample 364


title: 55601 - EM-Seq

description: Library name: Sample 372


title: 65732 - EM-Seq

description: Library name: Sample 448


title: 55302 - EM-Seq

description: Library name: Sample 369


title: 53805 - EM-Seq

description: Library name: Sample 356


title: 53907 - EM-Seq

description: Library name: Sample 359


title: 53807 - EM-Seq

description: Library name: Sample 357


title: 53005 - EM-Seq

description: Library name: Sample 353


title: 53803 - EM-Seq

description: Library name: Sample 355


title: 53810 - EM-Seq

description: Library name: Sample 358


title: 53001 - EM-Seq

description: Library name: Sample 352


title: 52910 - EM-Seq

description: Library name: Sample 351


title: 52709 - EM-Seq

description: Library name: Sample 349


title: 52702 - EM-Seq

description: Library name: Sample 347


title: 54206 - EM-Seq

description: Library name: Sample 363


title: 52710 - EM-Seq

description: Library name: Sample 350


title: 52504 - EM-Seq

description: Library name: Sample 344


title: 52708 - EM-Seq

description: Library name: Sample 348


title: 52508 - EM-Seq

description: Library name: Sample 346


title: 53601 - EM-Seq

description: Library name: Sample 354


title: 52501 - EM-Seq

description: Library name: Sample 343


title: 52505 - EM-Seq

description: Library name: Sample 345


title: 51902 - EM-Seq

description: Library name: Sample 339


title: 51706 - EM-Seq

description: Library name: Sample 338


title: 52406 - EM-Seq

description: Library name: Sample 342


title: 52001 - EM-Seq

description: Library name: Sample 341


title: 51703 - EM-Seq

description: Library name: Sample 337


title: 51904 - EM-Seq

description: Library name: Sample 340


title: 51403 - EM-Seq

description: Library name: Sample 329


title: 51602 - EM-Seq

description: Library name: Sample 333


title: 51404 - EM-Seq

description: Library name: Sample 330


title: 51610 - EM-Seq

description: Library name: Sample 335


title: 51608 - EM-Seq

description: Library name: Sample 334


title: 50609 - EM-Seq

description: Library name: Sample 326


title: 50510 - EM-Seq

description: Library name: Sample 323


title: 50707 - EM-Seq

description: Library name: Sample 327


title: 51408 - EM-Seq

description: Library name: Sample 332


title: 50606 - EM-Seq

description: Library name: Sample 324


title: 51407 - EM-Seq

description: Library name: Sample 331


title: 50608 - EM-Seq

description: Library name: Sample 325


title: 50107 - EM-Seq

description: Library name: Sample 316


title: 49809 - EM-Seq

description: Library name: Sample 312


title: 49808 - EM-Seq

description: Library name: Sample 311


title: 49807 - EM-Seq

description: Library name: Sample 310


title: 49408 - EM-Seq

description: Library name: Sample 304


title: 50111 - EM-Seq

description: Library name: Sample 317


title: 50305 - EM-Seq

description: Library name: Sample 320


title: 50207 - EM-Seq

description: Library name: Sample 319


title: 50103 - EM-Seq

description: Library name: Sample 314


title: 49805 - EM-Seq

description: Library name: Sample 308


title: 51103 - EM-Seq

description: Library name: Sample 328


title: 50507 - EM-Seq

description: Library name: Sample 321


title: 50508 - EM-Seq

description: Library name: Sample 322


title: 49806 - EM-Seq

description: Library name: Sample 309


title: 51612 - EM-Seq

description: Library name: Sample 336


title: 50203 - EM-Seq

description: Library name: Sample 318


title: 49407 - EM-Seq

description: Library name: Sample 303


title: 50104 - EM-Seq

description: Library name: Sample 315


title: 49306 - EM-Seq

description: Library name: Sample 299


title: 50101 - EM-Seq

description: Library name: Sample 313


title: 49703 - EM-Seq

description: Library name: Sample 307


title: 49601 - EM-Seq

description: Library name: Sample 305


title: 49405 - EM-Seq

description: Library name: Sample 301


title: 49205 - EM-Seq

description: Library name: Sample 298


title: 49406 - EM-Seq

description: Library name: Sample 302


title: 49115 - EM-Seq

description: Library name: Sample 296


title: 49202 - EM-Seq

description: Library name: Sample 297


title: 49404 - EM-Seq

description: Library name: Sample 300


title: 49112 - EM-Seq

description: Library name: Sample 295


title: 49105 - EM-Seq

description: Library name: Sample 293


title: 44503 - EM-Seq

description: Library name: Sample 286


title: 49104 - EM-Seq

description: Library name: Sample 292


title: 44103 - EM-Seq

description: Library name: Sample 285


title: 43906 - EM-Seq

description: Library name: Sample 278


title: 44001 - EM-Seq

description: Library name: Sample 283


title: 43601 - EM-Seq

description: Library name: Sample 273


title: 44004 - EM-Seq

description: Library name: Sample 284


title: 43914 - EM-Seq

description: Library name: Sample 281


title: 49101 - EM-Seq

description: Library name: Sample 290


title: 44903 - EM-Seq

description: Library name: Sample 289


title: 42402 - EM-Seq

description: Library name: Sample 271


title: 44601 - EM-Seq

description: Library name: Sample 288


title: 43917 - EM-Seq

description: Library name: Sample 282


title: 49106 - EM-Seq

description: Library name: Sample 294


title: 43809 - EM-Seq

description: Library name: Sample 276


title: 44506 - EM-Seq

description: Library name: Sample 287


title: 43811 - EM-Seq

description: Library name: Sample 277


title: 43413 - EM-Seq

description: Library name: Sample 272


title: 43907 - EM-Seq

description: Library name: Sample 279


title: 49103 - EM-Seq

description: Library name: Sample 291


title: 40701 - EM-Seq

description: Library name: Sample 269


title: 43913 - EM-Seq

description: Library name: Sample 280


title: 43801 - EM-Seq

description: Library name: Sample 275


title: 43710 - EM-Seq

description: Library name: Sample 274


title: 42102 - EM-Seq

description: Library name: Sample 270


title: 40404 - EM-Seq

description: Library name: Sample 266


title: 40304 - EM-Seq

description: Library name: Sample 264


title: 40309 - EM-Seq

description: Library name: Sample 265


title: 40602 - EM-Seq

description: Library name: Sample 268


title: 40243 - EM-Seq

description: Library name: Sample 262


title: 40107 - EM-Seq

description: Library name: Sample 256


title: 40406 - EM-Seq

description: Library name: Sample 267


title: 40104 - EM-Seq

description: Library name: Sample 255


title: 40205 - EM-Seq

description: Library name: Sample 258


title: 36304 - EM-Seq

description: Library name: Sample 250


title: 40113 - EM-Seq

description: Library name: Sample 257


title: 40227 - EM-Seq

description: Library name: Sample 260


title: 40301 - EM-Seq

description: Library name: Sample 263


title: 36207 - EM-Seq

description: Library name: Sample 246


title: 40212 - EM-Seq

description: Library name: Sample 259


title: 36206 - EM-Seq

description: Library name: Sample 245


title: 36204 - EM-Seq

description: Library name: Sample 244


title: 36308 - EM-Seq

description: Library name: Sample 252


title: 36303 - EM-Seq

description: Library name: Sample 249


title: 40232 - EM-Seq

description: Library name: Sample 261


title: 40103 - EM-Seq

description: Library name: Sample 254


title: 36209 - EM-Seq

description: Library name: Sample 247


title: 36307 - EM-Seq

description: Library name: Sample 251


title: 40101 - EM-Seq

description: Library name: Sample 253


title: 36302 - EM-Seq

description: Library name: Sample 248


title: 36107 - EM-Seq

description: Library name: Sample 241


title: 36201 - EM-Seq

description: Library name: Sample 242


title: 36104 - EM-Seq

description: Library name: Sample 240


title: 36015 - EM-Seq

description: Library name: Sample 238


title: 36102 - EM-Seq

description: Library name: Sample 239


title: 36203 - EM-Seq

description: Library name: Sample 243


title: 36014 - EM-Seq

description: Library name: Sample 237


title: 36005 - EM-Seq

description: Library name: Sample 235


title: 36001 - EM-Seq

description: Library name: Sample 234


title: 36006 - EM-Seq

description: Library name: Sample 236


title: 35901 - EM-Seq

description: Library name: Sample 232


title: 35903 - EM-Seq

description: Library name: Sample 233


title: 35804 - EM-Seq

description: Library name: Sample 231


title: 35614 - EM-Seq

description: Library name: Sample 225


title: 35709 - EM-Seq

description: Library name: Sample 229


title: 35617 - EM-Seq

description: Library name: Sample 226


title: 35605 - EM-Seq

description: Library name: Sample 220


title: 35708 - EM-Seq

description: Library name: Sample 228


title: 35611 - EM-Seq

description: Library name: Sample 223


title: 62011 - EM-Seq

description: Library name: Sample 393


title: 35609 - EM-Seq

description: Library name: Sample 222


title: 35607 - EM-Seq

description: Library name: Sample 221


title: 35513 - EM-Seq

description: Library name: Sample 217


title: 35604 - EM-Seq

description: Library name: Sample 219


title: 35702 - EM-Seq

description: Library name: Sample 227


title: 35501 - EM-Seq

description: Library name: Sample 212


title: 35410 - EM-Seq

description: Library name: Sample 210


title: 35507 - EM-Seq

description: Library name: Sample 213


title: 35406 - EM-Seq

description: Library name: Sample 209


title: 35612 - EM-Seq

description: Library name: Sample 224


title: 35511 - EM-Seq

description: Library name: Sample 216


title: 35802 - EM-Seq

description: Library name: Sample 230


title: 35601 - EM-Seq

description: Library name: Sample 218


title: 35413 - EM-Seq

description: Library name: Sample 211


title: 35316 - EM-Seq

description: Library name: Sample 207


title: 35311 - EM-Seq

description: Library name: Sample 205


title: 35510 - EM-Seq

description: Library name: Sample 215


title: 35508 - EM-Seq

description: Library name: Sample 214


title: 35313 - EM-Seq

description: Library name: Sample 206


title: 35404 - EM-Seq

description: Library name: Sample 208


title: 35309 - EM-Seq

description: Library name: Sample 204


title: 35308 - EM-Seq

description: Library name: Sample 203


title: 35209 - EM-Seq

description: Library name: Sample 201


title: 35212 - EM-Seq

description: Library name: Sample 202


title: 35206 - EM-Seq

description: Library name: Sample 199


title: Mtb_rv0998_comp_pH_5.7_biol_rep_3

first: Gerald

last: Larrouy-Maumus

address: South Kensington Campus, Exhibition Road

department: Life Sciences

institute: Imperial College London

description: Library name: Sample 18

data_processing:
https://imperial-genomics-facility.github.io/igf-pipeline-help/alignment_qc.html#qc-of-transcriptomic-data:~:text=Go%20to%20Top-,QC%20of%20transcriptomic%20data,-Sequencing%20data%20for
Assembly: Mycobacterium tuberculosis H37Rv (GenBank: AL123456.3)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Mycobacterium tuberculosis

source_name: Bacterial cell culture

growth_protocol: Bacterial strains were grown in 7H9 media supplemented with 0.2% w/v dextrose, 0.5% w/v bovine serum albumin Fraction V, 0.08% w/v NaCl and 0.05% w/v tyloxapol, with pH of the media adjusted according to experimental design prior to inoculation. Bacterial strains were grown in a static 37°C incubator until mid-exponential phase (OD600 approximately 1).

extract_protocol:
Bacteria were harvested by 10-minute centrifugation at 4,000 x g, 4°C. Total RNA was extracted using a FastRNA Pro Blue kit (MP) according to the manufacturer’s instructions.
The samples were treated with RNase-free Dnase (Promega) for 1 hour at 37°C to remove contamination of genomic DNA. The samples were purified with RNAeasy columns (Qiagen) according to the manufacturer’s instructions. The quantity and quality of RNA were assessed using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific) and an Agilent 2100 Bioanalyzer with an RNA 6000 Nano LabChip kit (Agilent). RNA sequencing was performed using an Illumina HiSeq4000 sequencer in the Imperial BRC Genomics Facility at Imperial College London.

value: Bacterial cell culture

value: Mycobacterium tuberculosis H37Rv

value: bacterial cells

value: rv0998 complemented

value: 7H9 growth medium, pH 5.7


title: Mtb_rv0998_comp_pH_5.7_biol_rep_2

description: Library name: Sample 17


title: Mtb_Δrv0998_pH_5.7_biol_rep_3

description: Library name: Sample 15

value: rv0998 deleted


title: 35111 - EM-Seq

description: Library name: Sample 196


title: Mtb_rv0998_comp_pH_5.7_biol_rep_1

description: Library name: Sample 16


title: 35110 - EM-Seq

description: Library name: Sample 195


title: Mtb_parental_pH_5.7_biol_rep_3

description: Library name: Sample 12

value: parental


title: 35202 - EM-Seq

description: Library name: Sample 197


title: 35011 - EM-Seq

description: Library name: Sample 192


title: Mtb_Δrv0998_pH_5.7_biol_rep_2

description: Library name: Sample 14


title: 35208 - EM-Seq

description: Library name: Sample 200


title: Mtb_Δrv0998_pH_5.7_biol_rep_1

description: Library name: Sample 13


title: 35103 - EM-Seq

description: Library name: Sample 194


title: 35204 - EM-Seq

description: Library name: Sample 198


title: 35101 - EM-Seq

description: Library name: Sample 193


title: Mtb_parental_pH_5.7_biol_rep_1

description: Library name: Sample 10


title: 35009 - EM-Seq

description: Library name: Sample 191


title: Mtb_parental_pH_5.7_biol_rep_2

description: Library name: Sample 11


title: Mtb_rv0998_comp_pH_6.8_biol_rep_3

description: Library name: Sample 9

value: 7H9 growth medium, pH 6.8


title: 35003 - EM-Seq

description: Library name: Sample 188

value: whole blood


title: Mtb_rv0998_comp_pH_6.8_biol_rep_1

description: Library name: Sample 7


title: Mtb_rv0998_comp_pH_6.8_biol_rep_2

description: Library name: Sample 8


title: 35004 - EM-Seq

description: Library name: Sample 189


title: 35006 - EM-Seq

description: Library name: Sample 190


title: 35002 - EM-Seq

description: Library name: Sample 187


title: Mtb_Δrv0998_pH_6.8_biol_rep_3

description: Library name: Sample 6


title: Mtb_Δrv0998_pH_6.8_biol_rep_2

description: Library name: Sample 5


title: Mtb_Δrv0998_pH_6.8_biol_rep_1

description: Library name: Sample 4


title: 30918 - EM-Seq

description: Library name: Sample 186


title: Mtb_parental_pH_6.8_biol_rep_1

description: Library name: Sample 1


title: Mtb_parental_pH_6.8_biol_rep_3

description: Library name: Sample 3


title: 30916 - EM-Seq

description: Library name: Sample 185


title: 30913 - EM-Seq

description: Library name: Sample 183


title: 30914 - EM-Seq

description: Library name: Sample 184


title: Mtb_parental_pH_6.8_biol_rep_2

description: Library name: Sample 2


title: 30911 - EM-Seq

description: Library name: Sample 182


title: 30902 - EM-Seq

description: Library name: Sample 181


title: 30828 - EM-Seq

description: Library name: Sample 176


title: 30835 - EM-Seq

description: Library name: Sample 179


title: 30834 - EM-Seq

description: Library name: Sample 178


title: 30825 - EM-Seq

description: Library name: Sample 175


title: 30832 - EM-Seq

description: Library name: Sample 177


title: 30901 - EM-Seq

description: Library name: Sample 180


title: Old_Trp53KO_2456

city: La Jolla

first: Kathryn

last: Lande

state: CA

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute

description: Library name: 2456

data_processing:
Alignment to GrCM38/mm10 using STAR aligner, tag counting using HOMER.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: txt files include raw count values for each Sample

organism: Mus musculus

source_name: liver

extract_protocol:
Flash frozen liver tissues were used to extract RNA using Quick-RNA Miniprep Plus Kit (Zymo) following manufacturer's protocols.
RNAseq polyA RNA isolation and library preparation was performed with the Watchmaker mRNA Library Prep Kit (Watchmaker Genomics: 7BK0001 ) with xGEN Stubby adaptors (IDT, Cat: 336338420) and xGEN 10nt UDIs (IDT, Cat: 336338436). Libraries were sequenced with the Element Biosciences AVITI Sequencing platform using the AVITI 2x75 High Output Cloudbreak Freestyle Kit (Element Biosciences, Cat: 860-00015).

tag: strain

value: liver

tag: age months

tag: Sex

value: M

tag: cull date

tag: dob

tag: ko percent


title: Old_Trp53KO_2444

description: Library name: 2444

tag: tissue


title: 30822 - EM-Seq

description: Library name: Sample 174


title: Old_Trp53KO_2460

description: Library name: 2460


title: Yng_Trp53KO_2454

description: Library name: 2454


title: Yng_Trp53KO_2442

description: Library name: 2442


title: Old_Trp53KO_2448

description: Library name: 2448


title: 30819 - EM-Seq

description: Library name: Sample 173


title: Old_Trp53KO_2452

description: Library name: 2452


title: 30818 - EM-Seq

description: Library name: Sample 172


title: Yng_Trp53KO_2450

description: Library name: 2450


title: Old_PTENKO_2441

description: Library name: 2441

value: PTENKO


title: Yng_Trp53KO_2458

description: Library name: 2458


title: Yng_Trp53KO_2446

description: Library name: 2446


title: Old_PTENKO_2440

description: Library name: 2440


title: 30810 - EM-Seq

description: Library name: Sample 171


title: 30808 - EM-Seq

description: Library name: Sample 169


title: Yng_PTENKO_2438

description: Library name: 2438


title: 30806 - EM-Seq

description: Library name: Sample 168


title: Old_Rosa26KO_2439

description: Library name: 2439


title: 49701 - EM-Seq

description: Library name: Sample 306


title: 30809 - EM-Seq

description: Library name: Sample 170


title: Yng_Rosa26KO_2437

description: Library name: 2437


title: Old_Rosa26KO_2435

description: Library name: 2435


title: 30805 - EM-Seq

description: Library name: Sample 167


title: 30705 - EM-Seq

description: Library name: Sample 162


title: Old_PTENKO_2436

description: Library name: 2436


title: Yng_PTENKO_2430

description: Library name: 2430


title: Yng_Rosa26KO_2433

description: Library name: 2433


title: Yng_Rosa26KO_2429

description: Library name: 2429


title: Yng_PTENKO_2434

description: Library name: 2434


title: 30804 - EM-Seq

description: Library name: Sample 166


title: 30803 - EM-Seq

description: Library name: Sample 165


title: Yng_Rosa26KO_2425

description: Library name: 2425


title: Old_PTENKO_2432

description: Library name: 2432


title: 30709 - EM-Seq

description: Library name: Sample 164


title: Old_Rosa26KO_2431

description: Library name: 2431


title: Old_PTENKO_2424

description: Library name: 2424


title: Old_Rosa26KO_2427

description: Library name: 2427


title: 30708 - EM-Seq

description: Library name: Sample 163


title: Old_Rosa26KO_2423

description: Library name: 2423


title: Old_PTENKO_2428

description: Library name: 2428


title: 30701 - EM-Seq

description: Library name: Sample 160


title: 30606 - EM-Seq

description: Library name: Sample 158


title: 30608 - EM-Seq

description: Library name: Sample 159


title: 30604 - EM-Seq

description: Library name: Sample 156


title: 30605 - EM-Seq

description: Library name: Sample 157


title: 30703 - EM-Seq

description: Library name: Sample 161


title: Yng_PTENKO_2426

description: Library name: 2426


title: 30504 - EM-Seq

description: Library name: Sample 155


title: 30409 - EM-Seq

description: Library name: Sample 153


title: 30405 - EM-Seq

description: Library name: Sample 152


title: 30410 - EM-Seq

description: Library name: Sample 154


title: Yng_Rosa26KO_2421

description: Library name: 2421


title: Yng_PTENKO_2422

description: Library name: 2422


title: 30324 - EM-Seq

description: Library name: Sample 150


title: HFD_p53KO_5

description: Library name: 1963

tag: diet

value: HFD

tag: age

value: male


title: HFD_p53KO_6

description: Library name: 1964


title: Control_p53KO_5

description: Library name: 1961

value: ControlDiet


title: HFD_Rosa26KO_5

description: Library name: 1959


title: Control_p53KO_6

description: Library name: 1962


title: 30317 - EM-Seq

description: Library name: Sample 145


title: 30318 - EM-Seq

description: Library name: Sample 146


title: HFD_Rosa26KO_6

description: Library name: 1960


title: HFD_p53KO_7

description: Library name: 1965


title: 30403 - EM-Seq

description: Library name: Sample 151


title: Control_Rosa26KO_5

description: Library name: 1957


title: 30322 - EM-Seq

description: Library name: Sample 148


title: 30323 - EM-Seq

description: Library name: Sample 149


title: 30316 - EM-Seq

description: Library name: Sample 144


title: HFD_p53KO_4

description: Library name: 1956


title: HFD_p53KO_3

description: Library name: 1955


title: 30319 - EM-Seq

description: Library name: Sample 147


title: Control_Rosa26KO_6

description: Library name: 1958


title: Control_p53KO_3

description: Library name: 1953


title: 30315 - EM-Seq

description: Library name: Sample 143


title: 30305 - EM-Seq

description: Library name: Sample 139


title: 30310 - EM-Seq

description: Library name: Sample 141


title: 30303 - EM-Seq

description: Library name: Sample 137


title: HFD_Rosa26KO_4

description: Library name: 1952


title: 30311 - EM-Seq

description: Library name: Sample 142


title: 30306 - EM-Seq

description: Library name: Sample 140


title: Control_p53KO_4

description: Library name: 1954


title: 30304 - EM-Seq

description: Library name: Sample 138


title: 30103 - EM-Seq

description: Library name: Sample 134


title: 29403 - EM-Seq

description: Library name: Sample 132


title: HFD_Rosa26KO_3

description: Library name: 1951


title: 29401 - EM-Seq

description: Library name: Sample 131


title: Control_Rosa26KO_4

description: Library name: 1950


title: 30302 - EM-Seq

description: Library name: Sample 136


title: Control_Rosa26KO_3

description: Library name: 1949


title: Control_Rosa26KO_2

description: Library name: 1942


title: 30105 - EM-Seq

description: Library name: Sample 135


title: HFD_p53KO_1

description: Library name: 1947


title: 29003 - EM-Seq

description: Library name: Sample 129


title: HFD_Rosa26KO_2

description: Library name: 1944


title: HFD_p53KO_2

description: Library name: 1948


title: Control_p53KO_1

description: Library name: 1945


title: HFD_Rosa26KO_1

description: Library name: 1943


title: 30102 - EM-Seq

description: Library name: Sample 133


title: 29302 - EM-Seq

description: Library name: Sample 130


title: Control_p53KO_2

description: Library name: 1946


title: 26003 - EM-Seq

description: Library name: Sample 126


title: 27218 - EM-Seq

description: Library name: Sample 127


title: 25408 - EM-Seq

description: Library name: Sample 125


title: 25406 - EM-Seq

description: Library name: Sample 124


title: 869_old_Myc_Ruxolitinib

description:
Library name: 869
First sequencing batch

data_processing:
Alignment to GrCM38/mm10 using STAR aligner, tag counting using HOMER.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: whole liver

extract_protocol:
RNA was isolated using trizol-chloroform with ethanol precipitation protocol.
polyA RNA isolation and library preparation were performed with the Watchmaker Genomics mRNA Library Prep Kit (Watchmaker Genomics) and Elevate Long UDI Adapters (Element Biosciences). RNA libraries were pooled, and sequenced (2x75bp) on the Element Biosciences AVITI sequencer with the 2x75 Cloudbreak kit.

value: whole liver

tag: age (months)


title: 870_old_Myc_Vehicle

description:
Library name: 870
First sequencing batch


title: 25205 - EM-Seq

description: Library name: Sample 122

value: SLE


title: 868_old_Myc_Ruxolitinib

description:
Library name: 868
First sequencing batch


title: 871_old_Myc_Vehicle

description:
Library name: 871
First sequencing batch


title: 29002 - EM-Seq

description: Library name: Sample 128


title: 25309 - EM-Seq

description: Library name: Sample 123


title: 866_old_Myc_Vehicle

description:
Library name: 866
First sequencing batch


title: 25203 - EM-Seq

description: Library name: Sample 121


title: 25202 - EM-Seq

description: Library name: Sample 120


title: 865_old_mApple_Ruxolitinib

description:
Library name: 865
First sequencing batch


title: Control_Rosa26KO_1

description: Library name: 1941


title: 25102 - EM-Seq

description: Library name: Sample 118


title: 864_old_mApple_Ruxolitinib

description:
Library name: 864
First sequencing batch


title: 25030 - EM-Seq

description: Library name: Sample 117


title: 867_old_Myc_Vehicle

description:
Library name: 867
First sequencing batch


title: 25201 - EM-Seq

description: Library name: Sample 119


title: 863_old_mApple_Vehicle

description:
Library name: 863
First sequencing batch


title: 862_old_mApple_Vehicle

description:
Library name: 862
First sequencing batch


title: 861_old_Myc_Ruxolitinib

description:
Library name: 861
First sequencing batch


title: 25026 - EM-Seq

description: Library name: Sample 116


title: 25025 - EM-Seq

description: Library name: Sample 115


title: 860_old_Myc_Ruxolitinib

description:
Library name: 860
First sequencing batch


title: 858_old_Myc_Vehicle

description:
Library name: 858
First sequencing batch


title: 25024 - EM-Seq

description: Library name: Sample 114


title: 25009 - EM-Seq

description: Library name: Sample 112


title: 25005 - EM-Seq

description: Library name: Sample 111


title: 25017 - EM-Seq

description: Library name: Sample 113


title: 859_old_Myc_Vehicle

description:
Library name: 859
First sequencing batch


title: 1158_old_Myc_Ruxolitinib

description:
Library name: 1158
Second sequencing batch


title: 1157_old_Myc_Ruxolitinib

description:
Library name: 1157
Second sequencing batch


title: 25004 - EM-Seq

description: Library name: Sample 110


title: 24204 - EM-Seq

description: Library name: Sample 107


title: 856_old_mApple_Ruxolitinib

description:
Library name: 856
First sequencing batch


title: 25003 - EM-Seq

description: Library name: Sample 109


title: 857_old_mApple_Ruxolitinib

description:
Library name: 857
First sequencing batch


title: 1156_old_Myc_Ruxolitinib

description:
Library name: 1156
Second sequencing batch


title: 854_old_mApple_Vehicle

description:
Library name: 854
First sequencing batch


title: 24101 - EM-Seq

description: Library name: Sample 106


title: 24014 - EM-Seq

description: Library name: Sample 105


title: 25002 - EM-Seq

description: Library name: Sample 108


title: 1154_old_Myc_Ruxolitinib

description:
Library name: 1154
Second sequencing batch


title: 855_old_mApple_Vehicle

description:
Library name: 855
First sequencing batch


title: 23903 - EM-Seq

description: Library name: Sample 102


title: 24011 - EM-Seq

description: Library name: Sample 104


title: 1152_old_Myc_Ruxolitinib

description:
Library name: 1152
Second sequencing batch


title: 24005 - EM-Seq

description: Library name: Sample 103


title: 1155_old_Myc_Ruxolitinib

description:
Library name: 1155
Second sequencing batch


title: 1151_old_Myc_Ruxolitinib

description:
Library name: 1151
Second sequencing batch


title: 23217 - EM-Seq

description: Library name: Sample 99


title: 1153_old_Myc_Ruxolitinib

description:
Library name: 1153
Second sequencing batch


title: 23701 - EM-Seq

description: Library name: Sample 100


title: 1150_old_Myc_Ruxolitinib

description:
Library name: 1150
Second sequencing batch


title: 23802 - EM-Seq

description: Library name: Sample 101


title: 23203 - EM-Seq

description: Library name: Sample 97


title: 23206 - EM-Seq

description: Library name: Sample 98


title: 1146_old_Myc_Vehicle

description:
Library name: 1146
Second sequencing batch


title: 23125 - EM-Seq

description: Library name: Sample 96


title: 1144_old_Myc_Vehicle

description:
Library name: 1144
Second sequencing batch


title: 1148_old_Myc_Vehicle

description:
Library name: 1148
Second sequencing batch


title: 1147_old_Myc_Vehicle

description:
Library name: 1147
Second sequencing batch


title: 23001 - EM-Seq

description: Library name: Sample 93


title: 1145_old_Myc_Vehicle

description:
Library name: 1145
Second sequencing batch


title: 1149_old_Myc_Ruxolitinib

description:
Library name: 1149
Second sequencing batch


title: 23101 - EM-Seq

description: Library name: Sample 94


title: 1143_old_mApple_Ruxolitinib

description:
Library name: 1143
Second sequencing batch


title: 19104 - EM-Seq

description: Library name: Sample 91


title: 1140_old_mApple_Ruxolitinib

description:
Library name: 1140
Second sequencing batch


title: 1141_old_mApple_Ruxolitinib

description:
Library name: 1141
Second sequencing batch


title: 1142_old_mApple_Ruxolitinib

description:
Library name: 1142
Second sequencing batch


title: 19208 - EM-Seq

description: Library name: Sample 92


title: 23122 - EM-Seq

description: Library name: Sample 95


title: 19103 - EM-Seq

description: Library name: Sample 90


title: 19003 - EM-Seq

description: Library name: Sample 88


title: 1139_old_mApple_Ruxolitinib

description:
Library name: 1139
Second sequencing batch


title: 19002 - EM-Seq

description: Library name: Sample 87


title: 1136_old_mApple_Vehicle

description:
Library name: 1136
Second sequencing batch


title: 1137_old_mApple_Vehicle

description:
Library name: 1137
Second sequencing batch


title: 1138_old_mApple_Vehicle

description:
Library name: 1138
Second sequencing batch


title: 18001 - EM-Seq

description: Library name: Sample 85


title: 18101 - EM-Seq

description: Library name: Sample 86


title: 1134_young_mApple_Vehicle

description:
Library name: 1134
Second sequencing batch


title: 1133_young_mApple_Vehicle

description:
Library name: 1133
Second sequencing batch


title: 17801 - EM-Seq

description: Library name: Sample 84


title: 17301 - EM-Seq

description: Library name: Sample 82


title: 19102 - EM-Seq

description: Library name: Sample 89


title: 17300 - EM-Seq

description: Library name: Sample 81


title: 1135_old_mApple_Vehicle

description:
Library name: 1135
Second sequencing batch


title: 16701 - EM-Seq

description: Library name: Sample 79


title: 17501 - EM-Seq

description: Library name: Sample 83


title: 1129_young_mApple_Vehicle

description:
Library name: 1129
Second sequencing batch


title: 1131_young_mApple_Vehicle

description:
Library name: 1131
Second sequencing batch


title: 1132_young_mApple_Vehicle

description:
Library name: 1132
Second sequencing batch


title: 16902 - EM-Seq

description: Library name: Sample 80


title: 1127_young_Myc_Ruxolitinib

description:
Library name: 1127
Second sequencing batch


title: 1130_young_mApple_Vehicle

description:
Library name: 1130
Second sequencing batch


title: 16503 - EM-Seq

description: Library name: Sample 78


title: 1126_young_Myc_Ruxolitinib

description:
Library name: 1126
Second sequencing batch


title: 1128_young_Myc_Ruxolitinib

description:
Library name: 1128
Second sequencing batch


title: 16401 - EM-Seq

description: Library name: Sample 75


title: 16112 - EM-Seq

description: Library name: Sample 73


title: 16402 - EM-Seq

description: Library name: Sample 76


title: 1125_young_Myc_Ruxolitinib

description:
Library name: 1125
Second sequencing batch


title: 16111 - EM-Seq

description: Library name: Sample 72


title: 1124_young_Myc_Ruxolitinib

description:
Library name: 1124
Second sequencing batch


title: 16501 - EM-Seq

description: Library name: Sample 77


title: 1123_young_Myc_Ruxolitinib

description:
Library name: 1123
Second sequencing batch


title: 16202 - EM-Seq

description: Library name: Sample 74


title: 16110 - EM-Seq

description: Library name: Sample 71


title: 1122_young_Myc_Ruxolitinib

description:
Library name: 1122
Second sequencing batch


title: 15901 - EM-Seq

description: Library name: Sample 68


title: 1121_young_Myc_Ruxolitinib

description:
Library name: 1121
Second sequencing batch


title: 1119_young_Myc_Ruxolitinib

description:
Library name: 1119
Second sequencing batch


title: 15404 - EM-Seq

description: Library name: Sample 66


title: 1120_young_Myc_Ruxolitinib

description:
Library name: 1120
Second sequencing batch


title: 16106 - EM-Seq

description: Library name: Sample 69


title: 15101 - EM-Seq

description: Library name: Sample 64


title: 15803 - EM-Seq

description: Library name: Sample 67


title: 15401 - EM-Seq

description: Library name: Sample 65


title: 46_2_Young_Veh

type: RNA

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_46

hyb_protocol: RNA ISH probes (Mouse Universal Cell Characterization Panel, 1000-plex) were denatured at 95°C for 2 min and then placed on ice before preparing the ISH probe mix (1nM ISH probes, 1x Buffer R, 0.2 U/μL SUPERaseIn™ in DEPC H2O). 150 μL ISH probe mix was pipetted into the incubation frame of each slide, then incubation frame covers were applied to help move the hybridization solution across the tissue. Hybridization was performed at 37°C overnight (16-18 h) in a hybridization chamber to prevent evaporation. Following overnight hybridization, incubation frame covers were removed, and samples were washed twice with 50% formamide (VWR) in 2x SSC at 37°C for 25 min, rinsed twice with 2X SSC for 2 min at RT, then blocked with 200 μL Blocking Buffer (BSB) containing DAPI at 1:40 dilution for 15 min at RT. Samples were then incubated with a fluorophore-conjugated antibody cocktail against CD298/B2M, PanCK, CD45, and CD68 proteins at RT for 1 hr. After antibody staining, the samples were washed three times with 1x PBS for 5 min each at RT, then flow cells were assembled on the slide using the Flow Cell Assembly Tool and Kit (BSB).

scan_protocol: Target RNA readout on SMI instrument was performed following published protocols (He et al, 2022). Briefly, assembled flow cells were loaded onto the SMI instrument and samples were washed with Reporter Wash Buffer to rinse the samples and remove any air bubbles from the flow cell. Once loaded and washed, the entire flow cell was scanned, and field of views (FOVs) were placed on each slide for RNA readout. Prior to assay initiation, a 5-channel Z-stack image (4 antibodies and DAPI) was collected for each FOV. These images were used to perform single cell segmentation. Assay cycling was then initiated. The first RNA readout cycle was initiated by flowing 100 µL of Reporter Pool 1 into the flow cell and incubating for 15 min. After incubation, 1 mL of Reporter Wash Buffer was flowed across the flow cell to wash out any unbound reporter probes. The Reporter Wash Buffer was then replaced with Imaging Buffer. Eight Z-stack images (0.8 μm step size) of each FOV were acquired and then fluorophores on the reporter probes were UV-cleaved and washed out with Strip Wash Buffer. This fluidic and imaging procedure was then repeated for the remaining 15 reporter pools, and the 16 cycles of reporter hybridization-imaging was repeated 7 additional times to increase RNA detection sensitivity. Raw image processing and feature extraction were performed using an in-house SMI data processing pipeline (He et al, 2022) which includes registration, feature detection, and localization. First, 3D rigid image registration was made using fiducials embedded in the samples matched with the fixed image reference established at the beginning of SMI run to correct for any shift. Next, RNA image analysis algorithm was used to identify reporter signature locations in X, Y, and Z axes along with an assigned confidence. The reporter signature locations and the associated features were collated into a single list. Lastly, the XYZ location information of individual target transcripts were extracted and recorded in a table by a secondary analysis algorithm, as described in He et al, 2022.

data_processing: The 5-channel Z-stack images of immunostaining + DAPI were used for drawing cell boundaries on the samples. A cell segmentation pipeline using a machine learning algorithm (Stringer et al, Pachitariu and Stringer) was used to accurately assign transcripts to cell locations and subcellular compartments. The transcript profile of individual cells was generated by combining target transcript location and cell segmentation boundaries. Raw files were read into Seurat and SCTransform normalized.

label: SMI imaging barcodes

label_protocol: To prepare samples, the protocol provided in CosMx® SMI Manual Slide Preparation for RNA Assays (Manual MAN-10184-06) was followed. Briefly, slides were baked vertically at 60°C overnight prior to commencing deparaffinization, heat-induced epitope retrieval (HIER), and proteinase digestion. To deparaffinize tissue, slides were put through two 5 min incubations with xylene, followed by two 2 min washes with 100% ethanol. HIER was then carried out at 100°C for 15 min in Target Retrieval Buffer (BSB) and proteinase digestion was performed at 40°C for 30 min with digestion buffer (3 ug/mL Proteinase K in 1x PBS). The samples were then rinsed with fresh DEPC-treated water twice and incubated with 0.001% fiducials (BSB) for 5 min at RT. Fiducials were diluted in 2x saline sodium citrate, 0.001% Tween 20 (2x SSC-T) prior to use. Excess fiducials were removed by rinsing with 1x PBS, followed by fixation with 10% NBF for 1 min at RT. Fixed samples were rinsed with Tris-glycine buffer (0.1M glycine, 0.1M Tris-base in DEPC H2O) twice for 5 min each at RT and then once with 1X PBS for 5 min. Next, samples were blocked using 100 mM N-succinimidyl acetate (NHS-acetate, ThermoFisher) in NHS-acetate buffer (0.1M NaP, 0.1% Tween pH 8 in DEPC H2O). Blocking lasted 15 min at RT. Prepared samples were rinsed twice with 2x saline sodium citrate (SSC) for 5 min each before proceeding to the in-situ hybridization step.

extract_protocol: FFPE mouse liver sections.

tag: biological replicate

value: Female

value: Vehicle

value: Young

value: Veh


title: 16109 - EM-Seq

description: Library name: Sample 70


title: 44_2_Young_Veh

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_44

tag: treatment


title: 15009 - EM-Seq

description: Library name: Sample 62


title: 42_2_Young_Veh

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_42


title: 15002 - EM-Seq

description: Library name: Sample 60


title: 43_2_Young_Veh

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_43


title: 45_2_Young_Veh

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_45


title: Sample2, Crataegus scabrifolia, leaf Protoplasts

city: Kunming

first: Guigang

last: Zhao

state: Yunnan

address: #21 Qingsong Road

institute: Kunming Institute of Zoology

description:
Library name: Sample2
BD Rhapsody

data_processing:
Raw sequencing data were first processed individually  using 10X Genomics Cell Ranger (version 8.0.1) and BD Rhapsody CWL-runner software (version 2.2.1). These pipelines include processing of raw fastq data to align reads and generate gene-cell matrices. After the low-quality barcode and UMI data were filtered out, the processed data were aligned to the C. scabrifolia genome.The snRNA-seq/scRNA-seq gene-cell matrices for each sample were imported into Seurat (v5.2.1) for downstream analysis. Each dataset was subsequently normalized and integrated via the IntegrateData function.
Assembly: Crataegus scabrifolia genome:Genome-wide survey of Crataegus scabrifolia provides new insights into its genetic evolution and adaptation mechanisms.
Supplementary files format and content: Tab-separated values fles and matrix fles.

organism: Crataegus scabrifolia

source_name: leaves

extract_protocol:
Protoplasts were isolated from cleaned hawthorn leaf material via an enzymatic digestion method. Five milliliters of enzymatic digestion solution (20 mM KCl, 10 mM CaCl₂, 0.1% bovine serum albumin, 20 mM MES, 0.6 M mannitol, 1% cellulase R10, 0.5% snailase, 0.5% macerozyme R-10) was added to the cleaned plant material fragments. The mixture was incubated at 25°C on a shaker at 40 rpm for 4–5 h to release protoplasts from the leaves. The protoplasts were filtered through a 40 µm cell sieve, centrifuged at 200 × g for 3 minutes, and washed with 2 mL of washing solution (5 mM KCl, 125 mM CaCl₂, 154 mM NaCl, 0.1% bovine serum albumin, 20 mM MES). An aliquot was stained with trypan blue and analyzed on a LUNA-FL Cell Counter to determine protoplast count and viability. Hawthorn leaf nuclei were isolated following protocol. Briefly, 1 mL of ice-cold NIB buffer (20 mM HEPES, pH 8.0, 250 mM sucrose, 1 mM MgCl₂, 5 mM KCl, 0.25% Triton X-100, 40% glycerol, 0.5 mM spermine, 0.5 mM spermidine, 0.1% 2-ME) was added to the cleaned plant material fragments, and the tissue was gently chopped with a razor for 5 min until it could be pipetted ,with 1 mL wide-bore tip. The homogenate was filtered through a 40 µm cell sieve into a chilled 50 mL conical tube. The filtrate was collected and washed with the remaining buffer to recover the nuclei. The mixture was incubated on ice for 10 min, centrifuged at 50 × g for 5 min at 4°C to remove bulk impurities, and then centrifuged at 1,100 × g for 10 min at 4°C. After the supernatant was removed, the nuclei were resuspended in 500 µL of NIB buffer, and the quality and count of the nuclei were validated via the Countstar Rigel S6 system with AOPI staining.
Single protoplasts were captured via the BD Rhapsody HT single-cell analysis system, and scRNA libraries were constructed via the WTA Amplification Kit (BD). For snRNA library construction, single nuclei were captured via a 10X Genomics GemCode single-cell instrument with the Chromium Next GEM Single Cell 3' Reagent Kit (v3.1). The snRNA-seq and scRNA-seq libraries were constructed according to the protocols of each platform. Briefly, single protoplasts or nuclei were encapsulated in droplets or wells via HT Xpress chips (BD Rhapsody) or Chromium Next GEM Chip (10X Genomics) to create independent environments. mRNA was captured via magnetic beads, followed by protoplast/nuclear lysis, reverse transcription, cDNA amplification, purification, and conversion into single-cell/nuclear RNA-seq libraries with barcode sequences. Indexed sequencing libraries were prepared following the Illumina user guide, with each library assigned a unique index.

value: leaves


title: Sample3, Crataegus scabrifolia, leaf nuclei

description:
Library name: Sample3
10x Genomics

organism: Crataegus pinnatifida


title: 15005 - EM-Seq

description: Library name: Sample 61


title: Sample1, Crataegus pinnatifida, leaf Protoplasts

description:
Library name: Sample1
BD Rhapsody


title: 40_2_Young_Veh

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_40


title: Sample4, Crataegus scabrifolia, leaf nuclei

description:
Library name: Sample4
10x Genomics


title: 15010 - EM-Seq

description: Library name: Sample 63


title: 14608 - EM-Seq

description: Library name: Sample 58


title: 15001 - EM-Seq

description: Library name: Sample 59


title: 14607 - EM-Seq

description: Library name: Sample 57


title: 39_1_Young_Veh

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_39


title: 41_2_Young_Veh

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_41


title: 14606 - EM-Seq

description: Library name: Sample 56


title: 34_1_Young_Veh

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_34


title: 14012 - EM-Seq

description: Library name: Sample 52


title: 14501 - EM-Seq

description: Library name: Sample 54


title: 14602 - EM-Seq

description: Library name: Sample 55


title: 36_1_Young_Veh

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_36


title: 14008 - EM-Seq

description: Library name: Sample 51


title: 14005 - EM-Seq

description: Library name: Sample 50


title: 35_1_Young_Veh

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_35


title: 33_1_Old_Veh

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_33

value: Old


title: 37_1_Young_Veh

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_37


title: 32_1_Old_Veh

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_32


title: 12411 - EM-Seq

description: Library name: Sample 46


title: 14017 - EM-Seq

description: Library name: Sample 53


title: 13403 - EM-Seq

description: Library name: Sample 49


title: 30_1_Old_Veh

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_30


title: 31_1_Old_Veh

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_31


title: 12202 - EM-Seq

description: Library name: Sample 44


title: 12508 - EM-Seq

description: Library name: Sample 47


title: 12510 - EM-Seq

description: Library name: Sample 48


title: 29_1_Old_Veh

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_29


title: 12207 - EM-Seq

description: Library name: Sample 45


title: 26_1_Old_Veh

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_26

tag: fov notes

value: Different location from planned FOV, and different from R6289


title: 28_1_Old_Veh

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_28


title: 27_1_Old_Veh

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_27


title: 24_2_Old_Veh

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_24


title: 11810 - EM-Seq

description: Library name: Sample 43


title: 23_2_Old_Veh

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_23