title: 22_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_22


title: 25_1_Old_Veh

status: Public on May 01 2026

type: RNA

city: La Jolla

first: Kathryn

last: Lande

state: CA

address: 10010 N Torrey Pines Rd

department: IGC

country: USA

institute: Salk Institute

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_25

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

molecule: total RNA

organism: Mus musculus

source_name: whole liver

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: tissue

value: whole liver

tag: biological replicate

tag: Sex

value: Female

tag: genotype

value: Vehicle

tag: age

value: Old

tag: treatment

value: Veh

tag: fov notes

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


title: 11805 - EM-Seq

type: SRA

city: Indianapolis

first: Helen

last: Masson

address: 893 S Delaware St.

institute: Eli Lilly and Company

description: Library name: Sample 41

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

organism: Homo sapiens

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: SLE


title: 11604 - EM-Seq

description: Library name: Sample 40


title: 20_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_20


title: 17_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_17

value: Immune infiltrate


title: 11603 - EM-Seq

description: Library name: Sample 39


title: 19_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_19


title: 11506 - EM-Seq

description: Library name: Sample 35


title: 11807 - EM-Seq

description: Library name: Sample 42


title: 11514 - EM-Seq

description: Library name: Sample 37


title: 11601 - EM-Seq

description: Library name: Sample 38


title: 15_2_Old_HDM

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_15

value: HDM201 treatment

value: HDM


title: 11209 - EM-Seq

description: Library name: Sample 32


title: 11206 - EM-Seq

description: Library name: Sample 30


title: 18_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_18


title: 11508 - EM-Seq

description: Library name: Sample 36


title: 14_2_Old_HDM

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_14


title: 11502 - EM-Seq

description: Library name: Sample 34


title: 21_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_21


title: 12_2_Old_HDM

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_12


title: 13_2_Old_HDM

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_13


title: 16_2_Old_HDM

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_16


title: 10_2_Old_HDM

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_10


title: 11201 - EM-Seq

description: Library name: Sample 27


title: 11204 - EM-Seq

description: Library name: Sample 29


title: 10802 - EM-Seq

description: Library name: Sample 25


title: 8_1_Old_HDM

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_8


title: 7_1_Old_HDM

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_7


title: 11501 - EM-Seq

description: Library name: Sample 33


title: 11202 - EM-Seq

description: Library name: Sample 28


title: 11207 - EM-Seq

description: Library name: Sample 31


title: 6_1_Old_HDM

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_6


title: 10801 - EM-Seq

description: Library name: Sample 24


title: 9_2_Old_HDM

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_9


title: 11_2_Old_HDM

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_11


title: 10618 - EM-Seq

description: Library name: Sample 22


title: 10547 - EM-Seq

description: Library name: Sample 21


title: 2_1_Old_HDM

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_2


title: 10902 - EM-Seq

description: Library name: Sample 26


title: 10542 - EM-Seq

description: Library name: Sample 19


title: 45_2439_Rosa_Old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_45

value: Male


title: 5_1_Old_HDM

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_5


title: 4_1_Old_HDM

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_4


title: 10544 - EM-Seq

description: Library name: Sample 20


title: 1_1_Old_HDM

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_1


title: 10703 - EM-Seq

description: Library name: Sample 23


title: 3_1_Old_HDM

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_3


title: 10541 - EM-Seq

description: Library name: Sample 18


title: 10535 - EM-Seq

description: Library name: Sample 16


title: 10540 - EM-Seq

description: Library name: Sample 17


title: 43_2439_Rosa_Old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_43


title: 41_2439_Rosa_Old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_41


title: 10533 - EM-Seq

description: Library name: Sample 15


title: 40_2439_Rosa_Old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_40


title: 10532 - EM-Seq

description: Library name: Sample 14


title: 46_2439_Rosa_Old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_46


title: 44_2439_Rosa_Old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_44


title: 39_2437_Rosa26_Young

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_39

value: Young


title: 42_2439_Rosa_Old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_42


title: 10524 - EM-Seq

description: Library name: Sample 10


title: 10527 - EM-Seq

description: Library name: Sample 12


title: 37_2437_Rosa26_Young

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_37


title: 10531 - EM-Seq

description: Library name: Sample 13


title: 38_2437_Rosa26_Young

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_38


title: 10526 - EM-Seq

description: Library name: Sample 11


title: 10522 - EM-Seq

description: Library name: Sample 9


title: 10514 - EM-Seq

description: Library name: Sample 7


title: 33_2456_p53_KO_Old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_33


title: 35_2437_Rosa26_Young

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_35


title: 36_2437_Rosa26_Young

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_36


title: 34_2437_Rosa26_Young

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_34


title: 10202 - EM-Seq

description: Library name: Sample 4


title: 10104 - EM-Seq

description: Library name: Sample 3


title: 10517 - EM-Seq

description: Library name: Sample 8


title: 10505 - EM-Seq

description: Library name: Sample 5


title: 31_2456_p53_KO_Old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_31


title: 32_2456_p53_KO_Old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_32


title: 10103 - EM-Seq

description: Library name: Sample 2


title: 10102 - EM-Seq

description: Library name: Sample 1


title: 10510 - EM-Seq

description: Library name: Sample 6


title: 30_2456_p53_KO_Old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_30


title: 28_2456_p53_KO_Old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_28


title: 29_2456_p53_KO_Old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_29


title: 26_2456_p53_KO_Old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_26


title: 25_2456_p53_KO_Old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_25


title: 24_2450_p53_KO_Young

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_24


title: 965

description: Library name: Sample 804

library_source: transcriptomic

data_processing:
Data was processed using nf-core/rnaseq v3.14.0 of the nf-core collection of workflows, utilizing reproducible software environments from the Bioconda and Biocontainers projects. The pipeline was executed with Nextflow v23.10.1. Resulting count data was pre-processed using the edgeR packagein R, which included filtering out lowly-expressed genes using edgeR filterByExpr (min.count = 10) and performing quantile-normalized voom transformation.
Assembly: GRCh38
Supplementary files format and content: txt file includes normalized gene counts for each sample

molecule: polyA RNA

extract_protocol:
Whole blood RNA 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. RNA was extracted from one half of the suspension using the QIAsymphony PAXgene Blood RNA Kit (Qiagen). The other half of the suspension was used for DNA extraction. RNA concentration and integrity were assessed using the Ribogreen Assay (Thermo) and a Fragment Analyzer (Agilent), respectively.
Polyadenylated RNA was enriched using NEBNext Magnetic Oligo(dT)25 Beads and prepared into RNA-seq libraries using the NEBNext mRNA Library Prep Reagent Set for Illumina (New England BioLabs, Ipswich, MA, USA). Unique dual-index barcodes were incorporated as specified per manufacturer’s protocol. 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 Quantificaiton Kit (Roche). Paired-end sequencing (2 x 100 bp, 100 million reads per sample) was carried out on an Illumina NovaSeq 6000 platform (Illumina) following manufacturer’s recommended protocols.

value: healthy controls


title: 888921995

description: Library name: Sample 800


title: 955

description: Library name: Sample 803


title: 888949831

description: Library name: Sample 801


title: 888882695

description: Library name: Sample 799


title: 888992066

description: Library name: Sample 802


title: 27_2456_p53_KO_Old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_27


title: 888849255

description: Library name: Sample 798


title: 23_2450_p53_KO_Young

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_23


title: 22_2450_p53_KO_Young

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_22


title: 888647920

description: Library name: Sample 796


title: 21_2450_p53_KO_Young

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_21


title: 20_2450_p53_KO_Young

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_20


title: 19_2450_p53_KO_Young

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_19


title: 888713165

description: Library name: Sample 797


title: 888454783

description: Library name: Sample 795


title: 888364317

description: Library name: Sample 794


title: 888100344

description: Library name: Sample 791


title: 888247070

description: Library name: Sample 793


title: 15_2441_Pten_KO_old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_15

value: PtenKO


title: 521

description: Library name: Sample 790


title: 16_2441_Pten_KO_old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_16


title: 14_2441_Pten_KO_old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_14


title: 11_2441_Pten_KO_old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_11


title: 9_2441_Pten_KO_old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_9


title: 18_2450_p53_KO_Young

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_18


title: 17_2450_p53_KO_Young

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_17


title: 8_2434_Pten_KO_Young

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_8


title: 110046778

description: Library name: Sample 783


title: 110046733

description: Library name: Sample 782


title: 1627

description: Library name: Sample 787


title: 12_2441_Pten_KO_old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_12


title: 13_2441_Pten_KO_old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_13


title: 1703

description: Library name: Sample 789


title: 7_2434_Pten_KO_Young

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_7


title: 6_2434_Pten_KO_Young

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_6


title: 110046622

description: Library name: Sample 781


title: 1638

description: Library name: Sample 788


title: 5_2434_Pten_KO_Young

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_5


title: 3_2434_Pten_KO_Young

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_3


title: 2_2434_Pten_KO_Young

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_2


title: 110046231

description: Library name: Sample 778


title: 110046272

description: Library name: Sample 780


title: 110046264

description: Library name: Sample 779


title: 1_2434_Pten_KO_Young

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_1


title: 888236332

description: Library name: Sample 792


title: 50_2431_Rosa_Old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_50


title: 51_2431_Rosa_Old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_51


title: 46_2431_Rosa_Old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_46


title: 110046189

description: Library name: Sample 777


title: 110044887

description: Library name: Sample 774


title: 110046051

description: Library name: Sample 775


title: 110044838

description: Library name: Sample 771


title: 110044845

description: Library name: Sample 772


title: 47_2431_Rosa_Old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_47


title: 43_2431_Rosa_Old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_43


title: 48_2431_Rosa_Old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_48


title: 110044681

description: Library name: Sample 768


title: 45_2431_Rosa_Old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_45


title: 110044812

description: Library name: Sample 770


title: 49_2431_Rosa_Old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_49


title: 110044782

description: Library name: Sample 769


title: 42_2433_Rosa26_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_42


title: 110044658

description: Library name: Sample 767


title: 110044475

description: Library name: Sample 765


title: 44_2431_Rosa_Old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_44


title: 110044866

description: Library name: Sample 773


title: 41_2433_Rosa26_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_41


title: 39_2433_Rosa26_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_39


title: 40_2433_Rosa26_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_40


title: 37_2433_Rosa26_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_37


title: 110044358

description: Library name: Sample 763


title: 110044621

description: Library name: Sample 766


title: 110044290

description: Library name: Sample 762


title: 4_2434_Pten_KO_Young

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_4


title: 110044225

description: Library name: Sample 761


title: 36_2433_Rosa26_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_36


title: 38_2433_Rosa26_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_38


title: 110044374

description: Library name: Sample 764


title: 110042853

description: Library name: Sample 757


title: 35_2452_p53_KO_Old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_35


title: 32_2452_p53_KO_Old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_32


title: 34_2452_p53_KO_Old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_34


title: 110042972

description: Library name: Sample 760


title: 110042749

description: Library name: Sample 756


title: 110042893

description: Library name: Sample 759


title: 110042858

description: Library name: Sample 758


title: 110042731

description: Library name: Sample 755


title: 33_2452_p53_KO_Old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_33


title: 31_2452_p53_KO_Old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_31


title: 30_2452_p53_KO_Old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_30


title: 29_2452_p53_KO_Old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_29


title: 25_2446_p53_KO_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_25


title: 28_2452_p53_KO_Old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_28


title: 110042619

description: Library name: Sample 753


title: 110042555

description: Library name: Sample 751


title: 110042565

description: Library name: Sample 752


title: 26_2452_p53_KO_Old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_26


title: 110040856

description: Library name: Sample 749


title: 110042636

description: Library name: Sample 754


title: 27_2452_p53_KO_Old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_27


title: 110040939

description: Library name: Sample 750


title: 110040735

description: Library name: Sample 746


title: 24_2446_p53_KO_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_24


title: 110040764

description: Library name: Sample 747


title: 23_2446_p53_KO_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_23


title: 110040691

description: Library name: Sample 745


title: 20_2446_p53_KO_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_20


title: 110040777

description: Library name: Sample 748


title: 110040651

description: Library name: Sample 744


title: 19_2446_p53_KO_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_19


title: 21_2446_p53_KO_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_21


title: 110040592

description: Library name: Sample 743


title: 18_2446_p53_KO_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_18


title: 110040414

description: Library name: Sample 742


title: 110040327

description: Library name: Sample 740


title: 17_2428_Pten_KO_old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_17


title: 110040412

description: Library name: Sample 741


title: 110040247

description: Library name: Sample 739


title: 16_2428_Pten_KO_old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_16


title: 14_2428_Pten_KO_old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_14


title: 13_2428_Pten_KO_old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_13


title: 110040206

description: Library name: Sample 738


title: 110040194

description: Library name: Sample 737


title: 15_2428_Pten_KO_old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_15


title: 11_2428_Pten_KO_old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_11


title: 12_2428_Pten_KO_old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_12


title: 110040164

description: Library name: Sample 736


title: 110046143

description: Library name: Sample 776


title: 10_2428_Pten_KO_old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_10


title: 110040129

description: Library name: Sample 735


title: 9_2428_Pten_KO_old

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_9


title: 110040045

description: Library name: Sample 734


title: 8_2430_Pten_KO_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_8


title: 110039634

description: Library name: Sample 732


title: 7_2430_Pten_KO_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_7


title: 110040001

description: Library name: Sample 733


title: 110039613

description: Library name: Sample 731


title: 6_2430_Pten_KO_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_6


title: 5_2430_Pten_KO_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_5


title: 3_2430_Pten_KO_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_3


title: 110039290

description: Library name: Sample 729


title: 110036393

description: Library name: Sample 727


title: 110035347

description: Library name: Sample 726


title: 2_2430_Pten_KO_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_2


title: 110036411

description: Library name: Sample 728


title: 1_2430_Pten_KO_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_1


title: 110039591

description: Library name: Sample 730


title: 53_2423_Rosa_Old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_53


title: 110032752

description: Library name: Sample 725


title: 110029997

description: Library name: Sample 724


title: 52_2423_Rosa_Old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_52


title: 88702

description: Library name: Sample 720


title: 110029969

description: Library name: Sample 723


title: 110029963

description: Library name: Sample 722


title: 49_2423_Rosa_Old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_49


title: 48_2423_Rosa_Old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_48


title: 50_2423_Rosa_Old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_50


title: 51_2423_Rosa_Old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_51


title: 110029953

description: Library name: Sample 721


title: 47_2423_Rosa_Old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_47


title: 88701

description: Library name: Sample 719


title: 45_2423_Rosa_Old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_45


title: 4_2430_Pten_KO_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_4


title: 88601

description: Library name: Sample 718


title: 42_2421_Rosa26_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_42


title: 88508

description: Library name: Sample 716


title: 46_2423_Rosa_Old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_46


title: 88510

description: Library name: Sample 717


title: 88506

description: Library name: Sample 714


title: 88507

description: Library name: Sample 715


title: 88409

description: Library name: Sample 712


title: 40_2421_Rosa26_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_40


title: 44_2423_Rosa_Old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_44


title: 43_2421_Rosa26_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_43


title: Sample_ISM247539-2

city: New York

first: yu

last: liu

state: NY

address: 1428 Madison Ave

institute: Mount Sinai

data_processing:
The PacBio Iso-Seq pipeline was used for preparing full-length non-concatemer (FLNC) reads from the raw sequencing data. First, subreads were intramolecular error-corrected and polished using the circular consensus sequencing (CCS) algorithm to produce highly accurate CCS reads. The polished CCS reads were then passed to the lima tool to remove barcodes, SMART-Seq primers and template-switching oligo sequences and orient the isoforms into the correct 5’ to 3’ direction. The refine command was then used to remove polyA tails and concatemers to generate FLNC reads ready for downstream analysis.  The FLNC reads were then mapped to the GRCh38 genome assembly using the splice-aware aligner, GMAP. Then, TAMA was used to collapse isoseq transcripts down to unique isoform. Lastly, SQANTI2 was used to classify isoforms in the GTF file to identification of known and novel isoforms with the provided human polyA motif list.
Assembly: GRCh38
Supplementary files format and content: gtf, gene structure inferred from all six samples.
Library strategy: SMRT-seq

source_name: IEC

extract_protocol:
RNA was extracted from tissue using TRIzol (Invitrogen, Waltham MA) according to manufacturer’s instructions, followed by addition of chloroform and centrifugation to separate the solution into aqueous and organic phases. Finally, RNA was precipitated, washed, solubilized and quantified via Bioanalyzer (Agilent, Santa Clara CA) where an RNA Integrity Number (RIN) score of 7 was set as the quality threshold.
Starting with Total RNA, the library constructed by following PacBio protocol. Briefly, it starts with first-strand synthesis, then, pool the diluted first-strand reactions for large-scale amplification. Performing cycle number optimizations to minimize PCR bias following the PCR cycle optimization protocol. The determined cycle number is used to generate a sufficient amount of double-stranded cDNA product for SMRTbell library construction.
AMPure methods (1X and 0.40X ) are used for purification, then pooled the fraction 1 (1X) and fraction 2 (0.40X) for SMRTbell template preparation. At least 1 μg of pooled cDNA for library construction. The steps include repair DNA damage, repair ends, prepare blunt ligation reaction, adding exonuclease to remove failed ligation products, and purifying SMRTbell templates. Finaly, anneal and bind non-size selected SMRTbell templates.
A combined procedure to construct and pool a non-size selected Iso-Seq library with a size selected Iso-Seq library for sequencing on the Sequel System. Incorporating a size selection step using BluePippinTM enables one to increase the sequencing yield of >4 kb transcripts. Using the Clontech SMARTer PCR cDNA Synthesis Kit, RNA is synthesized to cDNA and subsequently amplified to generate double-stranded cDNA. One portion of the amplified cDNA product is used directly to construct a non-size selected SMRTbell library as summarized above. A second portion of the amplified cDNA product can be size-selected using either BluePippinTM, and then the size-fractionated cDNA is used to construct a size-selected SMRTbell library. Finally, the non-size selected SMRTbell library and the size-selected SMRTbell library are separately annealed and bound, and then pooled together for sequencing on the Sequel System.

tag: disease status

value: control

tag: cell type

value: IEC

tag: sample source

value: Surgical


title: 38_2421_Rosa26_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_38

value: whole liver


title: 41_2421_Rosa26_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_41


title: 88503

description: Library name: Sample 713


title: Sample_ISM247561-2

value: CD


title: 88405

description: Library name: Sample 710


title: 37_2421_Rosa26_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_37


title: 39_2421_Rosa26_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_39


title: 88406

description: Library name: Sample 711


title: Sample_ISM247601-2

source_name: LPL CD3-

value: UC

value: LPL CD3-


title: Sample_ISM247626-2

source_name: LPL

value: LPL

value: Biopsy


title: 88404

description: Library name: Sample 709

value: whole blood

value: SLE


title: 36_2442_p53_KO_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_36


title: Sample_ISM247555-2


title: 88401

description: Library name: Sample 708


title: Sample_ISM247622-2

source_name: LPL CD3+

value: LPL CD3+


title: 35_2442_p53_KO_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_35


title: 110048520

description: Library name: Sample 786


title: 88308

description: Library name: Sample 706


title: 110048196

description: Library name: Sample 785


title: 88310

description: Library name: Sample 707


title: 10_2441_Pten_KO_old

description:
R6272_E7_Liver_exprMat_file.csv
R6272_E7_Liver_fov_positions_file.csv
R6272_E7_Liver_metadata_file.csv
R6272_E7_Liver-polygons.csv
R6272_E7_Liver_tx_file.csv
R6272_E7_Liver_tx_file.csv
Slide 7
E7_10

value: Old


title: 88304

description: Library name: Sample 705


title: 34_2442_p53_KO_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_34

value: Male


title: 33_2442_p53_KO_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_33

value: Young


title: 32_2442_p53_KO_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_32


title: 88302

description: Library name: Sample 704


title: 31_2442_p53_KO_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_31


title: 88301

description: Library name: Sample 703


title: SOD2i replicate 2

city: Pune

first: Richa

last: Rikhy

state: Maharashtra

address: IISER, Dr. Homi Bhabha Road, Pashan

department: Biology

country: India

institute: Indian Institute of Science Education and Research (IISER) Pune, India

description: Library name: Sample 8

data_processing:
The following parameters were checked from fastq file - Base quality score distribution, Sequence quality score distribution, Average base content per read, GC distribution in the reads, PCR amplification issue, Check for over-represented sequences and Adapter trimming. Based on the quality report of fastq files, sequence reads were trimmed where necessary to only retain high quality sequence for further analysis. In addition, the low-quality sequence reads were excluded from the analysis. The adapter trimming was performed using Trimmomatic (v-0.36). For the RNA-Seq analysis, the unwanted sequences were removed, especially nonpolyA tailed RNAs from the sample (assuming that poly-A tailed RNAs are sequenced). The unwanted sequences include - mitochondrial genome sequences, ribosomal RNAs, transfer RNAs, adapter sequences and others. Contamination removal was performed using Bowtie2 (2.2.4). The paired-end reads were aligned to the reference Drosophila melanogaster genome using HISAT2 (2.1.0) to quantify reads mapped to each transcript. Alignment percentage of reads were in the range of 91-95 percent for all the samples. The aligned reads were used for estimating expression of the genes. The raw read counts were estimated using FeatureCount (1.5.2). The raw read counts were normalized using DESeq2. The ratio of normalized read counts for treated over control was taken as the fold change. Genes were first filtered based on the p-value (≤ 0.05). A distribution of these log2 (foldchange) values were found to be normally distributed. Those genes which were found to have -1≤ log2(foldchange) ≥1 were considered as statistically significant.
Assembly: Drosophila melanogaster genome
Supplementary files format and content: Each processed data file is an excel worksheet (.xlsx). Each mutant genotype (Drp1SG, SOD2i and Drp1SG;SOD2i) is compared to the control genotype and the processed files are named accordingly such as Control_vs_Drp, Control_vs_SOD and Control_vs_DrpSOD.

organism: Drosophila melanogaster

source_name: Embryos

extract_protocol:
For sample preparation for RNA sequencing, embryos were manually sorted to avoid non developing embryos and to select for only cellularizing and gastrulating embryos. Firstly, egg laying was synchronised by discarding the first 2hr collection. For genotypes which laid enough embryos, 1hr collection was taken and aged for 1.5-2 hrs whereas for mutants which did not lay enough embryos 2.5-3 hr collection was taken directly after synchronisation from cages at 28 C. Embryos were dechorionated using bleach and washed with distilled water. Then around 50-60 embryos were taken, using a brush, on a slide and around 20-30ul 1X PBS was added on top of the embryos. Embryos of desired stages were then sorted using a single haired brush under a stereo microscope. These embryos were taken in an MCT and crushed in TriZol (Qiagen) using a homogeniser gun, snap frozen in liquid nitrogen and then stored at -80C. Multiple embryo collections were pooled such that there were 70-100 embryos (equal proportion of cellularizing and gastrulating embryos) per each replicate. RNA was isolated using the TRIZOL method. The concentration of RNA was measured using Qubit RNA BR Assay (Invitrogen, Cat# Q10211). RNA purity was checked using QIAxpert and RNA integrity was checked on TapeStation using RNA ScreenTapes (Agilent, Cat# 50675579).
KAPA RNA HyperPrep Kit (cat #0000141759) protocol was used to prepare libraries for mRNA sequencing. An initial Concentration of 200ng of total RNA was taken for the assay. mRNA molecules are captured using magnetic oligo Poly(T) beads (KAPA mRNA capture kit, Cat# 7962240001). Following purification, the enriched mRNA were fragmented using divalent cations under elevated temperatures (94 degrees for 6 minutes). The cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase and random priming. Combined 2nd strand synthesis and A-tailing is done, which converts the cDNA:RNA hybrid to double-stranded cDNA (dscDNA), incorporates dUTP into the second cDNA strand, and adds dAMP to the 3' ends of the resulting dscDNA. This is followed by Adapter Ligation, in which dsDNA indexing adapters with 3' dTMP overhangs are ligated to library insert fragments. The adapter-ligated products were then purified and enriched carrying appropriate adapter sequences at both ends using high-fidelity, low-bias PCR ( The strand marked with dUTP is not amplified, allowing strand-specific sequencing) using the following thermal conditions: initial denaturation 98°C for 45sec; 13 cycles of - 98°C for 15sec, 60°C for 30sec, 72°C for 30sec; final extension of 72°C for 1mins. PCR products are then purified and checked for fragment size distribution on Fragment Analyzer using HS NGS Fragment Kit (1-6000bp) (Agilent, Cat# DNF-474-1000). Prepared libraries were quantified using Qubit HS Assay (Invitrogen, Cat# Q32854). The obtained libraries were pooled and diluted to final optimal loading concentration. The pooled libraries were then loaded on to Illumina NovaSeq V1.5 instrument to generate 40M, 150bp paired-end reads/sample.

value: Embryos


title: Drp1SG replicate 3

description: Library name: Sample 6


title: Drp1SG;SOD2i replicate 3

description: Library name: Sample 12


title: Drp1SG replicate 2

description: Library name: Sample 5


title: 22_2446_p53_KO_Young

description:
R6272_E6_Liver_exprMat_file.csv
R6272_E6_Liver_fov_positions_file.csv
R6272_E6_Liver_metadata_file.csv
R6272_E6_Liver-polygons.csv
R6272_E6_Liver_tx_file.csv
R6272_E6_Liver_tx_file.csv
Slide 6
E6_22


title: Drp1SG replicate 1

description: Library name: Sample 4


title: Drp1SG;SOD2i replicate 1

description: Library name: Sample 10


title: Control replicate 1

description: Library name: Sample 1

value: Control


title: SOD2i replicate 3

description: Library name: Sample 9


title: SOD2i replicate 1

description: Library name: Sample 7


title: Drp1SG;SOD2i replicate 2

description: Library name: Sample 11


title: Control replicate 3

description: Library name: Sample 3


title: Control replicate 2

description: Library name: Sample 2


title: 29_2442_p53_KO_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_29


title: 88204

description: Library name: Sample 701


title: 30_2442_p53_KO_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_30


title: CFPAC-1 (shKLF4#1)

city: Guangzhou

first: bei

last: Jin

address: Jinsui street

country: China

institute: Zhongshan Ophthalmic Center

description: Library name: CFPAC_shKLF4#1_ATAC

library_source: genomic

data_processing:
RNA-seq：HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. ChIP-seq：Reads were mapped to the reference genome using BWA v0.7.12 and BWA mem v0.7.12. Wiggle files for gene tracks were generated using MACS2, and peaks were visualized in Integrative Genomics Viewer. ChIP-seq reads were first processed to remove adapter sequences using Cutadapt (v2.5) and then aligned to the human genome (hg38) using bowtie2 (v2.3.5.1) with default parameters. Significant H3K27ac enrichment peaks were identified using MACS2 (v2.1.2), generating narrowPeak files. Peaks overlapping blacklist regions were removed based on the ENCODE blacklist database. The remaining peaks were analyzed using the ROSE algorithm to identify active enhancers and super-enhancers. Enhancers were stitched, and super-enhancers were ranked based on input-subtracted H3K27ac signal. Typical enhancers were defined as peaks within 2.5 kb of transcription start sites (TSS), while super-enhancers were distinguished by an inflection point in the rank versus signal curve. ATAC-seq：Library DNA was sequenced in paired-end mode with 150 bp reads on an Illumina HiSeq X Ten platform.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data include gene expression matrices in XLS format containing FPKM values for each gene across samples.Processed data include TDF files representing genome-wide ChIP-seq and ATAC signal tracks for visualization in IGV.

molecule: genomic DNA

extract_protocol:
RNA-seq：1) For THZ1 treatment, Mel270 cells were incubated in medium containing THZ1 at the indicated.concentrations or DMSO for 6 h, RNA was isolated with Rneasy Micro Kit (Qiagen). 2) For exosomal RNA-Seq, RNA extraceted from HUVEC exosomes was treated with terminator 5’-Phosphate-Dependent Exonuclease (Epicenter, Madsion, WI) to degrade 5’-monophosphate RNA in exosomal RNA, and subsequently treated with 5’ polyphosphatase (Epicenter, Madsion, WI) to convert 5’ppp to 5’p, yielding specifically ligated RNA adaptor P5_RNA to RNAs that originally have 5’ppp. ChIP-seq：EZ-ChIP Kit (EMD Millipore, Burlington, MA) was used for ChIP according to our previous reports⁹. In brief, Mel270 cells (1×10⁷) were crosslinked in 1% formaldehyde for 10 min at room temperature and quenched unreacted formaldehyde with glycine. The cell lysates were sonicated to shear DNA to length of 200–500 bp and centrifuged at 12,000 g at 4 °C for 10 min. Protein G agarose (60 μL) was added to each tube to preclear the chromatin before immunoprecipitated with anti-H3K27ac antibodies (5 μg), anti-ELK-1 antibodies (5 μg), anti-STAT1 antibodies (5 μg) or rabbit IgG (negative Parental) overnight at 4 °C with rotation. The protein-DNA complexes underwent reverse crosslinks overnight. RNase A and Proteinase K were used to digest RNA and protein, respectively. DNA was then purified with spin columns. ATAC-seq: CFPAC-1 (pTSB-Vector or pTSB-KLF4; Scramble, shKLF4#1 or shKLF4#2) cells were digested with 0.25% Trypsin. After washing with PBS, 5 × 10^4 cells were lysed in ice-cold lysis buffer (10 mmol/L Tris-HCl pH 7.5, 10 mmol/L NaCl, 3 mmol/L MgCl2, 0.5% IGEPAL CA-630, and 0.1% Tween-20) for 10 min. After nuclei were collected by centrifuging at 500 g for 5 min, Tn5 transposase reactions (#TD501, Vazyme Biotech, Nanjing, China) were immediately performed at 37°C for 30 min. The transposed DNA fragments were purified with VAHTS DNA Clean Beads (#N411, Vazyme Biotech, Nanjing, China).
RNA-seq：Sequencing libraries were generated using NEBNext® UltraTMRNA Library Prep Kit.for Illumina® (New England Biolabs, Ipswich, MA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. ChIP-seq： Illumina sequencing libraries were generated using TruSeq PE Cluster Kit v3-cBot-HS and sequenced on an Illumina HiSeq platform. ATAC-seq：The purified DNA fragments were amplified using TruePrep Index Kit V2 for Illumina (#TD202, Vazyme Biotech, Nanjing, China) according to the manufacturer’s instructions.

tag: cell line

value: Pancreatic Ductal Adenocarcinoma

value: WT

value: CFPAC-1 (shKLF4#1)


title: 88211

description: Library name: Sample 702


title: CFPAC-1 (pTSB-KLF4)

description: Library name: CFPAC_KLF4_ATAC

value: CFPAC-1 (pTSB-KLF4)


title: CFPAC-1 (Scramble)

description: Library name: CFPAC_SCR_ATAC

value: CFPAC-1 (Scramble)


title: 88201

description: Library name: Sample 700


title: 28_2444_p53_KO_Old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_28

value: whole liver


title: CFPAC-1 (pTSB-Vector )

description: Library name: CFPAC_PTSB_ATAC

value: CFPAC-1 (pTSB-Vector )


title: 88102

description: Library name: Sample 699


title: 27_2444_p53_KO_Old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_27


title: hVIC,CA3,Day5

city: Hangzhou

first: dilin

last: xu

state: 默认

address: 88 Jiefang Road, Shangcheng District

institute: zhejiang university

data_processing:
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic and the low quality reads were removed to obtain the clean reads.
Assembly: The clean reads were mapped to the human genome (GRCh38) using HISAT2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: aortic valve

growth_protocol: human valvular interstitial cells were maitained in DMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol.
Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: aortic valve

value: primary valvular interstitial cells

value: interstitial cells

value: osteogenic medium


title: 87903

description: Library name: Sample 698

value: whole blood

value: SLE


title: hVIC,NC3,Day5

value: control medium


title: 87808

description: Library name: Sample 696


title: 87807

description: Library name: Sample 695


title: hVIC,CA2,Day5


title: hVIC,CA1,Day5


title: hVIC,NC2,Day5


title: 26_2444_p53_KO_Old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_26

value: Male

value: Old


title: 25_2444_p53_KO_Old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_25


title: HCMV-12hpi HELF cells CAGE-seq

city: Shenyang

first: Yang

last: Li

address: No. 36. Sanhao street, Heping District

description:
Library name: HELF_12h
HCMV infected HELF cells were collected at 12 hours post-infection (hpi).

data_processing:
Quality control and adapter/low-quality trimming were performed.
Trimmed reads were aligned to the human reference genome GRCh38/hg38 (unique mappers retained; multi-mappers discarded).
The 5′ ends of aligned reads were extracted to define CAGE transcription start sites (CTSSs); per-sample CTSSs were merged to form transcript clusters (TCs).
CTSS/TC tag counts were generated and normalized as tags-per-million (TPM); consensus clusters across samples were computed for differential TSS-usage analysis between HCMV-infected and mock groups.
Assembly: GRCh38/hg38
Supplementary files format and content: BED6 file of CAGE transcript clusters (TCs) detected
Supplementary files format and content: Tab-delimited table with per-TC quantification and annotation

source_name: embryonic lung

growth_protocol: HELF (human embryonic lung fibroblast) cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified 5%CO₂ atmosphere at 37°C.

extract_protocol:
Total RNA was isolated from each condition using a column-based purification with on-column DNase treatment; 1 µg total RNA per sample was used to construct CAGE-seq libraries.
For CAGE-seq, 1 µg total RNA was treated with T4 polynucleotide kinase and Terminator 5′-phosphate-dependent exonuclease to enrich capped transcripts. Reverse transcription was primed with a randomized hexamer carrying the 3′ adaptor, followed by template switching to append the 5′ adaptor. cDNA was PCR-amplified and size-selected (≈250–500 bp). Libraries were sequenced on an Illumina HiSeq X Ten with 150-nt paired-end reads.

treatment_protocol: Cells were infected with human cytomegalovirus (HCMV) HAN strain (moi=3) and harvested at 12 or 72 hours post-infection (hpi).

value: embryonic lung

value: human embryonic lung fibroblasts

value: HELF cells were infected with HCMV clinical strain HAN, which was isolated from a urine sample of a 5-month-old infant hospitalized in Shengjing Hospital of China Medical University, at a multiplicity of infection (MOI) of 3.


title: 87901

description: Library name: Sample 697


title: 23_2444_p53_KO_Old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_23


title: 87803

description: Library name: Sample 694


title: 21_2424_Pten_KO_old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_21

value: PtenKO


title: 24_2444_p53_KO_Old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_24


title: 87407

description: Library name: Sample 693


title: CON6CON7

city: New Haven, CT

first: Bhaskar

last: Roy

state: CT

address: 15 York Street

department: Neurology

institute: Yale University School of Medicine

description:
Library name: Sample3
10x genomics

library_source: transcriptomic single cell

data_processing:
We have used standard Seurat platform for data processing. Removal of poor quality data, and then doublet removal.
Assembly: human
Supplementary files format and content: tab separated value files and matrix files

source_name: blood

extract_protocol:
PBMC samples were thawed, dead cells were removed using Annexin V from Stemcell Technologies, B cells were enriched using Pan B cell enrichment kit (Stemcell Technologies) if indicated.
Library was prepared according to manufacter's instruction (Single Cell 5P, V2 and V3)

value: blood

value: PBMC


title: NF155AIN4+

description:
Library name: Sample2
10x genomics


title: CON4CON5

description:
Library name: Sample1
10x genomics


title: 87403

description: Library name: Sample 692


title: 22_2444_p53_KO_Old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_22

value: whole liver


title: Treated1

city: Braga

first: Jonas

last: Campos

state: Minho

address: Campus de Gualtar, Universidade do Minho

department: School of Medicine

country: Portugal

institute: ICVS - Life and Health Sciences Research Institute

description:
Library name: Sample4
Column E

data_processing:
Raw data was subjected to quality control to remove adapters contamination, reads containing N>10% and reads Qscore of over 50% bases below 5. Alignment to the reference genome was performed with HISAT2
Assembly: GRCh38.p14
Supplementary files format and content: TXT file organized into 15 columns, with column 1 being the Ensembl gene ID, followed by six sample columns (Control 1,2,3 and Treatment 1,2.3). The following columns are: gene name, gene chromosome, gene start, gene end, gene strand, gene length, gene biotype, and gene description.
Supplementary files format and content: CSV files for each sample is also provided

source_name: Adipose tissue

growth_protocol: Standard incubator conditions (36.5C, 5%CO2), grown in AlphaMem media supplmented with 10%FBS

extract_protocol:
Extracted using miRNeasy Micro kit (Qiagen) according to manufacturer’s instructions
mRNA library preparation with poly A enrichment using NEBNext® UltraTM RNA Library Prep Kit

treatment_protocol: Treated with DHA at 40micromolar concentration complexed with albumin

value: Adipose tissue

value: Primary

value: Mesenchymal Stromal Cell

value: Experiment


title: Treated3

description:
Library name: Sample6
Column G


title: Control2

description:
Library name: Sample2
Column C

value: Control


title: Treated2

description:
Library name: Sample5
Column F


title: Control3

description:
Library name: Sample3
Column D


title: Control1

description:
Library name: Sample1
Column B


title: 20_2424_Pten_KO_old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_20


title: 17_2424_Pten_KO_old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_17


title: 87402

description: Library name: Sample 691

value: whole blood


title: 16_2424_Pten_KO_old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_16


title: CON2CON3

description:
Library name: Sample3
10x genomics


title: AIN1CON1

description:
Library name: Sample1
10x genomics


title: 15_2424_Pten_KO_old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_15


title: NF155AIN2AIN3

description:
Library name: Sample2
10x genomics


title: 87307

description: Library name: Sample 689

value: SLE


title: 87305

description: Library name: Sample 688


title: 18_2424_Pten_KO_old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_18


title: 19_2424_Pten_KO_old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_19


title: B0

city: Graz

first: Sally

last: Connolly

state: Steiermark

address: Otto Loewi Forschungszentrum - Immunologie und Pathophysiologie Medizinische Universität Graz Heinrichstraße 31a A-8010 Graz

country: Austria

description: Library name: B_D0

data_processing:
Raw sequencing data were filtered to remove adapter contamination and low-quality reads. Clean reads were mapped to the reference genome, and gene expression levels were quantified based on gene annotation. Data processing and primary analysis were performed by Novogene.
Assembly: hg38
Supplementary files format and content: xlsx file includes fpkm amd raw counts for all samples

growth_protocol: CD34 cells were isolated and cultured in FLT3L, SCF, TPO and GM-CSF in DC grow media +10% FCS, 1% Glutamax for 4 days. During this period, cells were subject to lentiviral particles contaning shBHLHE40 or shControl. Transduced cells were subcultured in RPMI +10% FCS+ 1% Glutamax, TNFa, GM-CSF and TGFB1. 0h is prior to subculture, 24 hr is post subculture with TGFB1.

extract_protocol:
RNA was isolated using PureLink™ RNA Mini Kit (ThermoFisher) as per manufacturer’s instructions
mRNA was enriched from total RNA using poly(A) selection with oligo(dT) magnetic beads. The purified mRNA was fragmented under elevated temperature and converted into first-strand cDNA using random hexamer primers and reverse transcriptase. Second-strand cDNA synthesis was subsequently performed to generate double-stranded cDNA. The cDNA fragments were end-repaired, A-tailed, and ligated with Illumina sequencing adapters. Adapter-ligated fragments were PCR amplified and purified to construct the final sequencing libraries. Library quality and concentration were assessed prior to paired-end sequencing

value: TGF-B1 LC differentiation


title: D0KD

institute: Otto Loewi Forschungszentrum - Immunologie und Pathophysiologie Medizinische Universität Graz

description: Library name: D_S0


title: D24

description: Library name: D_D24


title: D24KD

description: Library name: D_S24


title: 14_2424_Pten_KO_old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_14

value: Male


title: B0KD

description: Library name: B_S0


title: 86801

description: Library name: Sample 686


title: 86601

description: Library name: Sample 685


title: A24

description: Library name: A_D24


title: B24

description: Library name: B_D24


title: D0

description: Library name: D_D0


title: 87302

description: Library name: Sample 687


title: A0

description: Library name: A_D0


title: B24KD

description: Library name: B_S24


title: 87401

description: Library name: Sample 690


title: A24KD

description: Library name: A_S24


title: 13_2424_Pten_KO_old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_13

value: Old


title: 12_2424_Pten_KO_old

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_12


title: 86506

description: Library name: Sample 684


title: 86505

description: Library name: Sample 683


title: A0KD

description: Library name: A_S0


title: 11_2422_Pten_KO_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_11

value: Young


title: 10_2422_Pten_KO_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_10


title: 86502

description: Library name: Sample 682


title: 110046939

description: Library name: Sample 784

value: healthy controls


title: 9_2422_Pten_KO_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_9


title: 8_2422_Pten_KO_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_8


title: 86305

description: Library name: Sample 680


title: cc_hepg2_bmal1_u_wellG_GTAC_SR008094

city: St. Louis

first: India

last: Reiss

state: Missouri

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University in St. Louis

description:
Library name: cc_hepg2_bmal1_u_wellG
Calling Cards Lib Prep, rep3

data_processing:
Calling Cards FASTQ reads were processed with a custom bash pipeline to generate per-sample insertion files for peak calling. Briefly, reads were first adapter-trimmed and demultiplexed by requiring an exact 5′ match to the OM-piggyBac transposon sequence using cutadapt with zero mismatches/indels and discarding untrimmed reads, then SRT barcodes were extracted with umi_tools extract, followed by an additional exact-match trim of the transposon sequence and trimming of trailing Nextera adapters (cutadapt).  Trimmed reads were aligned to the reference genome with Bowtie2 and converted to BAM; mapped reads were retained, then sorted and indexed. Transposon insertion sites were then computed per read by assigning the insertion point to the alignment start (forward reads) or end (reverse reads), correcting for soft clipping, and encoding the genomic interval immediately preceding the insertion. For piggyBac, reads were optionally filtered to those matching the expected “TTAA” insertion motif.  Finally, unique insertions were aggregated into an insertion table (“qbed” file)  by counting identical insertion sites; these insertion files were then used as input for downstream peak calling.
Differential Calling Cards peak sets were generated using a custom pipeline that (i) defines a unified candidate peak set and (ii) classifies those peaks as condition-enriched (CLN3-specific/WT-specific) or shared. For each condition, peaks were called with PyCallingCards using the MACCs (“cctools”) framework with the parameters  pvalue_cutoffbg=0.05, window_size=800, step_size=400, pvalue_cutoffTTAA=0.005, lam_win_size=1,000,000, pseudocounts=0.4. Peaks from the two TF conditions were then concatenated and collapsed into a nonredundant “union” peak set by sorting and merging intervals with bedtools merge using a 1 kb merge distance (-d 1000).  To call differential peaks, we quantified insertions from the two TF qbed files across the union peak set using pycallingcards.pp.make_Anndata, then tested TF_C1 vs TF_C2 per peak with Fisher’s exact test and ranked peaks by multiple-testing–adjusted p-values. Peaks with adjusted p < 0.05 enriched in TF_C1 were designated CLN3-specific peaks, and peaks enriched in TF_C2 were designated WT-specific peaks (written as separate BED files). Finally, “shared” peaks were defined as the remaining union peaks not assigned to either differential class, implemented with bedtools intersect -v against the condition-specific BED files.
Paired-end MNase-seq FASTQ files were aligned to the mm10 reference genome using Bowtie2 v2.3.5. Alignments were performed in paired-end mode with an expected insert-size range of 110-210 bp (-I 110 -X 210), requiring properly paired reads, and reads were trimmed to 40 bp prior to alignment. SAM files were converted to BAM and unmapped reads were removed, followed by coordinate sorting and indexing. To restrict analyses to canonical chromosomes, BAMs were filtered to chr1-chr19, chrX, chrY, name-sorted, and processed with samtools fixmate.  BAMs were then coordinate-sorted and PCR duplicates were removed with samtools markdup -r.
To generate genome-browser tracks, processed replicate BAMs for each condition were supplied to DANPOS3 for differential analysis using the standard danpos.py. DANPOS3 outputs included pooled per-condition WIG tracks (normalized/smoothed signal) and a differential WIG track (Poisson-based difference). Finally, WIG files were converted to bigWig format using the UCSC wigToBigWig utility. This produced bigWig tracks for each condition’s normalized/smoothed MNase signal and for the DANPOS differential signal.
RNA-seq counts tables produced by GTAC.
Assembly: mm10, hg38
Supplementary files format and content: Calling Cards: qBED, BED. Mnase-seq: bigWig. RNA-seq: counts  csv and metadata csv

growth_protocol: Hepg2 cells were maintained in DMEM+10% FBS, 1x Penstrep in 6 well plates.

extract_protocol:
For MNase-seq, MNase digestion was performed immediately following astrocyte isolation. Cells were fixed for 10 minutes in 1% formaldehyde and the reaction was quenched for 5 minutes with 2.5 M glycine, added to a final concentration of 0.125 M. The cells were then washed twice in 1x PBS. Nuclei were prepared by adding 100 μl of Nuclei Prep Buffer (Zymo EZ Nucleosome DNA Prep Kit, D5220) per 1 million cells. After centrifugation, the cells were resuspended in 1x Takara MNase Digestion Buffer. Chromatin was digested with 4 units of Takara MNase (2910A) per 1,000,000 cells. The reaction was stopped by adding 5x MN stop buffer from the EZ kit. Subsequently, 4.8 μl of 5 M NaCl and 2 μl of proteinase K were added per 1 million cells, and samples were incubated at 65°C overnight. The following day, DNA was isolated using the EZ kit according to the manufacturer’s instructions. For Calling Cards and RNA-seq, total RNA extraction after MACS was done using the Qiagen RNeasy Plus Mini Kit (Cat no. 74134) according to the manufacturer's protocol. All of the total RNA was used for reverse transcription.
For Calling Cards, First-strand cDNA was generated by oligo(dT) priming with the SMART_dT18VN primer and Maxima H Minus reverse transcriptase in the presence of RNase inhibitor, followed by heat inactivation and RNase H treatment to remove the RNA strand, yielding cDNA for downstream library construction. Self-reporting transposon (SRT) transcripts were then PCR-amplified from cDNA using KAPA HiFi HotStart with a reporter specific primer (tdtomato or puromycin) and SMART reverse primers (cycle number minimized/optimized to avoid over-amplification; typical program uses ~20 cycles with 98°C denaturation, 65°C annealing, and long 72°C extension), and amplicons were size-selected/cleaned with a 0.6× AMPure XP bead cleanup and QC’d by Qubit. Purified SRT PCR products were converted into sequencing-ready libraries by Nextera XT tagmentation (ATM + TD buffer at 55°C), neutralization, and an indexing PCR using a barcoded piggyBac (OM-PB) primer together with a Nextera N7 index primer to enable multiplexing, followed by a final 0.6× bead cleanup and fragment distribution QC prior to pooling and Illumina sequencing. A fraction of the samples were checked for sequencing quality using WashU’s DNA Sequencing Innovation Lab (DSIL)’s spike in program with the Illumina MiSeq or Illumina Miniseq. All samples were then submitted to the the Washington University Genome Technology Access Center (GTAC) to be deeply sequenced with the Illumina NovaSeq X Plus. All sequencing data was combined at the end for each sample. MNase-seq libraries were prepared using the NEBNext Ultra end repair and A-tailing module (NEBNext End Prep, E7442), followed by adapter ligation using the NEBNext Ultra Ligation Module with Quick Ligation (E7445). Libraries were purified using Agencourt AMPure XP beads (Beckman Coulter, A63880). Adapter-ligated DNA was PCR-amplified using Phusion High-Fidelity DNA Polymerase with NEB primers (NEB, E6440S), followed by a second cleanup with Agencourt AMPure XP beads. All samples were then submitted to the the Washington University Genome Technology Access Center (GTAC) to be deeply sequenced with the Illumina NovaSeq X Plus. RNA-seq libraries were prepared in-house from total RNA using the NEBNext UltraExpress® RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions. Indexes used from NEBNext Multiplex Oligos for Illumina® (E6440S).  Final libraries were quantified, pooled, and submitted to the Washington University Genome Technology Access Center (GTAC) for sequencing. GTAC performed sequencing on the Illumina NovaSeq X Plus (paired end reads extending 150 bases) and generated gene-level RNA-seq count tables from the resulting sequencing data using their standard RNA-seq processing workflow; these GTAC-provided count tables were used to assemble the final count matrix for downstream analyses.

treatment_protocol: AAV injections were performed as described in (Yen et al. 2023). Viral titers (viral genomes [vg] per milliliter) were ∼1.0 × 10. Neonatal mice (P0-P1) received intracerebroventricular (ICV) injections of Calling Cards AAVs encoding the piggyBac transposase (unfused or BMAL1 fusion) and donor/self-reporting transposon. AAV stocks were mixed 1:1 immediately prior to injection (6 µL total per pup). Pups were anesthetized by hypothermia on ice (5-8 min; ≤15 min maximum) and injected bilaterally using a Hamilton syringe fitted with a depth guard to ensure a consistent 2 mm insertion depth. Virus was delivered at 1 µL per site at three sites per hemisphere (1 µL/s); after each injection, the needle was held in place for 5 s before withdrawal to minimize backflow. Following injection, pups were placed on a low warming pad for recovery (5-10 min) and returned to the home cage with the dam. For HepG2 cells, calling card constructs (with puro as the marker gene) transfected through neon electroporation (2*10^6 cells/well). Puro selection performed with 3ug/mL puro. Puro selection done over 5 days to allow for cells without insertions to die off, a non-transfected well was used to determine that all cells without insertions had died at that point.

value: transfected with bmal1 cc plasmids


title: cc_hepg2_bmal1_u_wellE_GTAC_SR008094

description:
Library name: cc_hepg2_bmal1_u_wellE
Calling Cards Lib Prep, rep1


title: 7_2422_Pten_KO_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_7

value: PtenKO


title: cc_hepg2_unfused_u_wellB_GTAC_SR008094

description:
Library name: cc_hepg2_unfused_u_wellB
Calling Cards Lib Prep, rep2

value: transfected with unfused cc plasmids


title: 86401

description: Library name: Sample 681


title: cc_hepg2_bmal1_d_wellC_GTAC_SR008094

description:
Library name: cc_hepg2_bmal1_d_wellC
Calling Cards Lib Prep, rep2


title: cc_hepg2_bmal1_u_wellF_GTAC_SR008094

description:
Library name: cc_hepg2_bmal1_u_wellF
Calling Cards Lib Prep, rep2


title: cc_hepg2_unfused_u_wellA_GTAC_SR008094

description:
Library name: cc_hepg2_unfused_u_wellA
Calling Cards Lib Prep, rep1


title: cc_hepg2_unfused_d_wellJ_GTAC_SR008094

description:
Library name: cc_hepg2_unfused_d_wellJ
Calling Cards Lib Prep, rep1


title: cc_hepg2_unfused_d_wellK_GTAC_SR008094

description:
Library name: cc_hepg2_unfused_d_wellK
Calling Cards Lib Prep, rep2


title: cc_hepg2_bmal1_d_wellB_GTAC_SR008094

description:
Library name: cc_hepg2_bmal1_d_wellB
Calling Cards Lib Prep, rep1


title: cc_hepg2_unfused_u_wellC_GTAC_SR008094

description:
Library name: cc_hepg2_unfused_u_wellC
Calling Cards Lib Prep, rep3


title: 86303

description: Library name: Sample 679


title: 6_2422_Pten_KO_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_6


title: 86302

description: Library name: Sample 678


title: 86102

description: Library name: Sample 677


title: 5_2422_Pten_KO_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_5


title: 86101

description: Library name: Sample 676


title: HacaT cell, high glucose, C-FOS, ChIP

city: Wenzhou

first: Zhiming

last: Zhang

address: Chashan Campus of Wenzhou Medical University

institute: Department of Cardiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China

description: Library name: HacaT, HG, CHIP

data_processing:
Sequencing Run: Load the final purified DNA library onto an Illumina NovaSeq X Plus sequencer for sequencing.
Instrument Operation: The sequencing run is completed in approximately 2 days.
Data Processing: After the run, convert the raw sequencing data (.bcl format) into standard Fastq format files for downstream analysis.
Assembly: Homo sapiens GRCh38

source_name: skin

extract_protocol:
The ChIP assays were performed using the SimpleChIP Plus Enzymatic Chromatin IP Kit (Magnetic Beads) (Cell Signaling Technology, 9005) following the manufacturer's instructions. Briefly, HaCaT cells were cross-linked with 1% formaldehyde at room temperature for 10 minutes and then incubated in 2 ml of 10x glycine for 5 minutes. Cells were harvested in SDS lysis buffer and DNA fragments were digested to 150-900 bp fragments by Micrococcal Nuclease treatment. Then, samples were incubated overnight at 4°C with shaking with c-Fos antibody(Cat#31254S,Cell Signaling Technology) and normal IgG antibody as a control, followed by incubation with Magnetic Beads at 4°C with shaking for 2 hours the next day. After washing, chromatin was eluted from the beads using elution buffer and incubated with 5M NaCl and proteinase K at 65°C for 2 hours.
The ChIP-seq library construction was performed as follows: The ChIP-enriched DNA fragments were first assessed for quality by quantification using a Qubit 4.0 Fluorometer and integrity analysis via agarose gel electrophoresis. Qualified DNA samples (20-100 ng) underwent end repair and dA-tailing (30°C for 20 min, 72°C for 20 min). Sequencing adapters were then ligated using Fast T4 DNA Ligase at 20°C for 15 min. The ligation product was purified with magnetic beads (0.6X ratio) to remove free adapters. The library was then amplified by 7 cycles of PCR (98°C for 10 sec, 60°C for 30 sec, 72°C for 30 sec) using index primers for enrichment, followed by another round of purification with magnetic beads (0.9X ratio).

value: skin

value: HacaT

value: keratinocyte

tag: antibody

value: high glucose (33mM)


title: 4_2422_Pten_KO_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_4

value: whole liver