title: 15244X230_blastomere_14C_type_SCNT_cell_number_4

description: cellnumber 4

library_source: genomic single cell

data_processing:
RNA-seq reads were trimmed and filtered for quality using BBDuk and FastQC (version 0.10.1).
Processed reads were aligned to bostau7 with Bowtie2 (v2.2.6) with the following parameters: (--t --q --N1 --L 25 --X 2000 --no-mixed --no-discordant).
PCR duplicates were removed using bedtools
mitochondrial reads were removed using sed '/chrM/d'
counts for each ATACseq union region were generated using ‘Get datasets’ (https://metacpan.org/pod/distribution/Bio-ToolBox/scripts/get_datasets.pl).
Assembly: bostau7
Supplementary files format and content: 20230629-scATAC-seq-cell-ID-conversion.xls excel file containing sample ID and information
Supplementary files format and content: 20180822-scATAC-819-cells-vs-302830-regions.tabular count file for n=819 retained high quality scATACseq libraries in ATAC-seq peaks regions created as a union dataset, tabular format

source_name: SCNT

growth_protocol: Oocyte collection and in vitro maturation: Bovine ovaries were collected from a local abattoir (JBS, Hyrum, Utah) and transported in a cooler containing 0.9% saline solution to the laboratory. Because this research used discarded tissues to generate embryos that were then disposed of without implantation, approval of this work via the Institutional Animal Care and Use Committee was not required. The cumulus-oocyte complexes (COCs) were aspirated from 3-8 mm follicles using an 18-gauge needle and vacuum system. Only compact COCs with homogenous ooplasm and intact layers of cumulus cells were used for somatic cell nuclear transfer (SCNT) or in vitro fertilization (IVF). Following aspiration, COCs were cultured at 38.5°C with 5% CO2 for 22–24 h. The oocytes were cultured in TCM199 maturation medium containing Earles salts, L-glutamine, and sodium bicarbonate (Sigma M4530) supplemented with 10% (v/v) fetal bovine serum (FBS) (Hyclone, SH30070.03), 0.05 mg/ml of bovine follicle stimulating hormone (Sioux Biochemicals, Sioux city, IA), 5 mg/ml of bovine luteinizing hormone (Sioux Biochemicals, Sioux Center, Iowa), 100 U/ml of penicillin, and 100 mg/ml of streptomycin (Gibco 15070-063).  In vitro fertilization: Following 22–24 h of maturation, MII oocytes were fertilized by using the laboratory’s standard in vitro fertilization protocol [Reproduction, 2006, 131:45-51]. Briefly, one straw of cryopreserved bovine semen (Hoffman AI, Logan, Utah) was removed from the liquid nitrogen tank and placed into a 35°C water bath to thaw. Live sperm were isolated by centrifugation through a 45%/90% percoll gradient (MP Biomedical, Irvine, California), suspended (final concentration 1x106/ml) in Tyrodes albumin lactate pyruvate containing 10 μg/ml porcine heparin and used to fertilize the oocytes. Twenty to 22 h post-IVF, cumulus cells were removed by vortexing, and fertilized zygotes were washed in phosphate buffered saline with 0.32 mM sodium pyruvate, 5.55 mM glucose, and 3 mg/ml bovine serum albumin (PB1+). After washing, zygotes were cultured in 40 μl of synthetic oviductal fluid (SOFaa) [Human Reproduction 2000; 15:395-401] with 3% FBS (Hyclone, SH30070.03, Logan, Utah) overlaid with mineral oil. The embryos were cultured at 38.5°C in a humidified atmosphere with 5% CO2. Half of the SOFaa medium was removed and replaced with fresh, equilibrated medium every other day starting the day after in vitro culture. Historically, production of IVF embryos via these methods followed by blastocyst embryo transfers to cattle recipients has generated successful pregnancies at an approximate rate of 50% (number live births/number of embryo transfer procedures) by our research group (unpublished observations). The timing of embryo collection post-fertilization was approximately 24–36 h for 2-cell stage, 48–60 h for 8-cell stage, 156–168 h for morula stage, and 192–204 h for blastocyst stage. Embryos that were obviously dead or arrested by microscopic examination were removed from culture.  Somatic cell nuclear transfer (SCNT): Primary bovine fibroblast cultures were established from ear biopsy tissues from multiple donor Brahma Spanish bull crosses by using well-established procedures [PNAS USA; 2000; 97:990-995]. These cell lines have been previously employed on multiple projects to evaluate their efficiency to generate live calves via SCNT (unpublished observations). Frozen/thawed cells were grown to 80-100% confluence then passaged, with cells from passages 4-5 used as nuclear donors. Three days prior to a cloning session, donor fibroblast cells were thawed and propagated, and incubated in DMEM medium (Hyclone, Logan, Utah) supplemented with 15% (v/v) FBS at 39°C with 5% CO2. Bovine fibroblasts at 80-90% confluence were serum-starved by replacing culture medium with DMEM containing 0.5% (v/v) FBS 24 h prior to SCNT. Oocytes were matured for 18–20 h, then denuded by using 100 μl of 1% (v/v) hyaluronidase (Sigma H3506), incubated for 5 min at 38.5°C with 5% CO2, followed by gentle pipetting. The denuded oocytes were then rinsed with PB1+, and oocytes with polar bodies were selected and separated. SCNT was performed according to established protocols [Reproduction 2006; 131:45-51; Anim Reprod Sci 2006; 95:234-243; Mol Reprod Dev 2004; 68189-197]. Briefly, oocytes with polar bodies were incubated in 0.6 μg/ml demecolcine for 30–40 min and a metaphase plate and a polar body were removed by using a beveled pipette. Fibroblast cells were covered in 0.25% trypsin (Gibco, Carlsbad, CA) for 1 min, and then the trypsin was removed, and fibroblasts were incubated for another 6 min at 39°C with 5% CO2. Once fibroblast cells were detached, they were rinsed in warm medium and centrifuged at 150 × g for 6 min. The supernatant was removed, and the cellular pellet was resuspended in 100 μl of Hepes SOF medium [Hum Reprod 2000; 15:395-401]. One fibroblast cell was injected into the perivitelline space of the recipient oocyte and fused by using one direct pulse of 1.2 kV/cm for 22 μs by an Electro Cell Manipulator 2001 (BTX, San Diego, CA) in 0.28 M sorbitol, 0.05% (w/v) BSA, 0.1 mM CaCl2, 0.5 mM MgCl2, and 0.5 mM Hepes. Following fusion, embryos were washed through Hepes SOF, and incubated in embryo culture medium for 1 h. Activation was then performed, with successfully fused embryos cultured in 5 μM ionomycin for 5 min, followed by 4 h of incubation in activation medium composed of SOFaa medium with 10 μg/ml cyclohexamide and 1 mM 6-dimethylaminopyridine at 38.5°C with 5% CO2. Following activation, embryos were cultured in 40 μl drops of SOFaa with 3% (v/v) FBS overlaid with mineral oil. The embryos were cultured at 38.5°C in a humidified atmosphere with 5% CO2. Half of the SOFaa medium was removed and replaced with fresh, equilibrated medium every other day starting the day after in vitro culture. The timing of embryo collection was the same as for IVF embryos as described above. The rates of development for IVF and SCNT embryos were similar at each developmental stage.

extract_protocol:
ATAC-seq was performed using 2x Tris-DMF-tagmentation buffer (10mM Tris-pH=8.0, 5mM MgCl, 20% DMF). Add (batch-determined actitivty) 2 to 2.5 uL of Nextera Tn5 transposase (Cat# FC-121-1030, Illumina. Samples were incubated at 37C for 30 minutes in a PCR machine. The reactions were stopped with 0.5uL of 10% SDS, pipetted up and down, and placed on ice 5 min. 5x volume of PB buffer was added to the ATAC-seq reaction and purified using a ampure beads and eluted in 10mM Tris-pH=8.0 + 1mM EDTA.
Libraries were PCR amplified in 25uL reaction volumes using custom Nextera PCR primers from Buenrostro, et al. Nature 2015. PCR reaction conditions: ~10uL tagmented DNA, 12.5 uL of 2xphusion PCR mastermix (Phusion High-Fidelity PCR Master Mix with HF Buffer - 100 rxns, NEB, cat #M0531S), 0.625uL of 100uM F primer, 0.625uL of 100uM R primer. QS to 50uL total with H20. Do 5 cycles of “pre-amp” PCR. PCR cycling conditions: 72C incubation for 5 min. 5 cycles of the following: 95C for 30 sec, 72C for 90 sec. Remove 5uL of the “pre-PCR” reaction for qPCR. qPCR reaction conditions: 20uL qPCR reaction: 5uL of pre-amp PCR product, 10 ul of 2x syber (SsoAdvanced SYBR Green Supermix, Biorad catalog #1725275), 0.25uL of 100uM F primer, 0.25uL of 100uM R primer. Run 30-40 cycles of qPCR with the same cycling conditions as above. Select the additional number of PCR cycles to perform as per Buenrostro, et al. Nature Methods 2013. Ampure bead purification (Beckman Coulter, catalog # A63881) as per manufacturer’s instructions.
Nextera tagmentation

treatment_protocol: Each embryo was dissociated into single blastomeres in a single drop of Ca+2/Mg+2 free PBS+0.1% PVP-40 with gentle pipetting. Each individual blastomere of the embryo was pipetted into a PCR strip tube for lysis and ATAC-seq, retaining the embryo identity of each single-cell ATACseq library.

value: SCNT


title: 78_RSB036_V04

status: Public on Jun 01 2025

type: SRA

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

country: USA

institute: Stanford University

description: Library name: 78

library_source: transcriptomic

data_processing:
STAR alignment to human genome version GRCh38.p13
Assembly: GRCh38.p13
Supplementary files format and content: Count table, tab-delimited text file

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
Qiagen RNAeasy
NovaSeq PE150

tag: tissue

value: Peripheral blood

tag: description


title: iKO30_10

city: Davis

first: Gaurav

last: Sarode

address: 6404A GBSF, 451 E. Health Sciences Dr.

department: Internal Medicine

institute: University of California, Davis

data_processing:
Raw reads (FASTQ) were processed through fastp (0.20.0), removing reads containing adapter and poly-N sequences and low-quality reads while simultaneously calculating Q20, Q30, and GC content
Paired-end clean reads were aligned to the reference genome(grcm38) using the Spliced Transcripts Alignment to a Reference (STAR) software (v2.6.1d)
FeatureCounts(v1.5.0-p3) was used to count the reads mapped to each gene; RPKM of each gene was calculated based on the length of the gene and reads mapped to the gene.
Assembly: grcm38 (mm10)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: Liver

growth_protocol: Mice were anesthetized with isoflurane, then euthanized by cervical dislocation. The ventral incision site was wet with 70% ethanol and the abdominal cavity was opened. The small intestine was cut at the proximal end and gently pulled out of the abdominal cavity to unfurl it, removing the majority of pancreas and mesenteric fat in the process. The small intestine was released by cutting the distal end at the cecum and wet with ice-cold dissection buffer comprised of Hank’s Balanced Salt Solution without calcium/magnesium, 10 mM HEPES, and 5% FBS. Half the full length plus 2 cm of the small intestine was used for dissociation. In a glass petri dish with ice-cold dissection buffer, the intestine was cut into 4-5 smaller segments and each segment was thoroughly flushed with ice-cold dissection buffer. Each segment was then placed on a clean paper towel saturated with ice-cold dissection buffer; any remaining bits of pancreas and mesenteric fat were trimmed; any remaining lumenal content was removed by gently sliding a pair of blunt-tip surgical forceps along the segment (holding the forceps closed), and the segment was held in ice-cold dissection buffer until all segments were cleaned. Each segment was then cut open longitudinally, cut into ~0.5 cm pieces, and placed directly into a conical tube with 40 ml dissociation buffer (HBSS without calcium/magnesium, 10mM HEPES, 12.5 mM EDTA, 5% FBS, 1mM dithiothreitol), and dissociated for 30 minutes at 300 rpm and 37°C in a Corning LSE benchtop orbital shaking incubator (Corning, NY). The dissociated suspension was passed through a 70 µm cell strainer and centrifuged. The supernatant was removed and the cell pellet was washed in 25 ml ice-cold PBS (pH 7.2) with 0.5% FBS then centrifuged. The cells were washed a total of 3 times to remove as many non-IECs, e.g. lymphocytes, as possible. Live cells were counted and the cell suspension was divided across multiple aliquots. Aliquots were centrifuged, supernatant was removed, and cell pellets were flash-frozen and stored at -80°C for downstream analyses. All centrifugations were performed for 5 minutes at 300 x g and 4°C.

extract_protocol:
Total RNA was extracted from frozen mouse liver  using the AllPrep DNA/RNA Mini Kit (Cat. No- 80204 QIAGEN).
Sequencing libraries were generated using with 1 ug of total RNA by NEBNext Ultra RNA Library Prep Kit for Illumina (Cat. no-E7530LNew England Biolabs).

tag: cell line

value: Liver

tag: cell type

tag: genotype

value: iKO

tag: treatment

value: Intetsine Specific ATP7B KO

tag: time

value: 30 weeks


title: iKO30_1


title: Cumulus cell whole genome sequencing

city: dallas

first: Edward

last: Grow

state: TEXAS

address: 7053 beltau lane

institute: UTSW

library_source: genomic

data_processing:
WGS reads were trimmed and filtered for quality using BBDuk and FastQC (version 0.10.1).
Processed reads were aligned to bostau7 with Bowtie2 (v2.2.6) with the following parameters: (--t --q --N1 --L 25 --X 2000 --no-mixed --no-discordant).
PCR duplicates were removed using bedtools
VarScan.v2.4.2 to identify homozygous SNVs using command “--min-coverage 20 --min-var-freq 0.1  --p-value 0.05”.
Homozygous SNVs exclusively found in Dreamboy were identified using VarScan.v2.4.2.jar  compare
Assembly: Bostau7
Supplementary files format and content: VCF= Varscan output of SNVs found with indivated variant detected
Library strategy: whole genome sequencing

molecule: genomic DNA

organism: Bos taurus

source_name: cumulus cell pool from multiple donors

growth_protocol: Cells were maintained in DMEM-high glucose (Thermo-Fisher 11965118) + 10% FBS, 1X Non-essential amino acids, 1X glutamax, 1X penicillin/streptomycin at 20% oxygen, and passaged using trypsin every 2-5 days.

extract_protocol:
genomic DNA was extracted using phenol:chlorform:isoamyl alcohol and precipitated with sodium acetated and ethanol at -80C for 20 min
gDNA was tagmented using Nextera XT DNA Library Preparation Kit (Illumina catalog #FC-131-1024) and libraries were amplified by PCR

treatment_protocol: Cumulus cells were harvested with trypsinization from expanded COC complexes, semen genomic DNA was harvested directly from cryopreserved samples.

value: cumulus cell pool from multiple donors

value: female


title: 15244X229_blastomere_14B_type_SCNT_cell_number_4

description: cellnumber 4


title: 77_RSB036_V01

description: Library name: 77


title: Proliferative conditioned media_replicate3

city: Pittsburgh

first: Katherine

last: Aird

state: PA

address: 5051 Centre Ave.

institute: University of Pittsburgh School of Medicine

data_processing:
Demultiplexed and quality-filtered mRNA-Seq reads were then aligned to human reference genome (GRCh38) using STAR (v.2.6.1)
Differential expression analysis was done using DESeq2 (v2_1.6.3)
Assembly: GRCh38
Supplementary files format and content: Tab delimited text file includes FPKMs for all samples

molecule: polyA RNA

growth_protocol: Ovcar8 cells were cultured in RPMI 1640 + 5% FBS

extract_protocol:
RNA was harvested by Trizol followed by a Qiagen clean up column with a DNAse step.
The cDNA libraries were prepared using NEBNext Ultra 2 RNA Library Prep Kit for Illumina (New England Biolabs; Cat.# E7775)

treatment_protocol: Cells were cultured in ULA plates in conditioned media and RPMI 1640 + 5% in a 1:1 ratio

value: High grade serous ovarian cancer


title: I45

source_name: Intestinal epithelial cells

value: Intestinal epithelial cells

value: iWT

value: Intetsine Specific Wildtype

value: 16 weeks


title: 15244X226_blastomere_13C_type_SCNT_cell_number_4

description: cellnumber 4


title: I4


title: 76_RSB030_V13

description: Library name: 76


title: 15244X227_blastomere_13D_type_SCNT_cell_number_4

description: cellnumber 4


title: Fresh media_replicate3

value: Fresh media_replicate3


title: 75_RSB030_V12

description: Library name: 75


title: 15244X225_blastomere_13B_type_SCNT_cell_number_4

description: cellnumber 4


title: CRISPRa/i bulk screen gRNA library

city: Berlin

first: Dubravka

last: Vucicevic

address: Hannoversche Straße 28

department: Berliner Institut for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine in the Helmholtz Association

library_source: other

data_processing:
Described in the manuscript.Sequencing reads were assigned to sgRNA using a modified version of a script in (Sanjana, 2016). Mean guide-counts were obtained at each time-point and all time-points were combined in a single table. Normalization was performed using the following equation: counts = qi/Σ(q)jx106qi (where qi is reads mapped to a specific guide and Σ(q)j is total number of reads mapped to all guides). We employed a sliding window strategy to score each bin based on the information from the sgRNAs targeting it and the adjacent bins upstream and downstream. Each bin was analyzed using guides targeting a 300bp window centered on it. To assess guide enrichment or depletion within these windows, we utilized a mixed linear model (MLM) with random intercepts: The model was fitted using the ‘lme4’(v. 1.1.28) R package (REML = FALSE) (Bates et al., 2015). Hypothesis testing was done by comparing our full model to a reduced version that does not account for time using a maximum likelihood ratio via ANOVA (Kaufmann and Schering, 2014). Adjustment of the p-value for correction of multiple tests was performed using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995). After identifying significant windows, bedtools (v 2.30.0) (Quinlan and Hall, 2010) was used to merge significant bins within 500bp of each other into CaREs. If a significant bin was not within 500 bp of another significant bin, it was classified as a distinct CaRE. CaREs were scored by MLM using information from all guides targeting the genomic area defined by the merged CaRE. Scores were calculated as: -log10 (adjusted p-value).
CRISPRa_bulk_screen_CaREs_gRNAs_results.txt are the results of the CRISPRa at gRNA and CaRE level.
CRISPRi_gRNA_bulk_screen_results.txt are the results of the CRISPRi screen at the gRNA level.
Assembly: hg38
Supplementary files format and content: Tab deliminated files summarising the results.
Library strategy: bulkCRISPR-screen

molecule: other

organism: synthetic construct

source_name: CROP-seq vector

extract_protocol: Described in the manuscript.

value: day 0

tag: genetic modification


title: 15244X224_blastomere_13A_type_SCNT_cell_number_4

description: cellnumber 4


title: 15244X223_blastomere_12B_type_SCNT_cell_number_2

description: cellnumber 2


title: I37


title: 73_RSB030_V09

description: Library name: 73


title: 74_RSB030_V10

description: Library name: 74


title: KO214

value: KO

value: Global ATP7B KO


title: I31


title: 15244X221_blastomere_11B_type_SCNT_cell_number_2

description: cellnumber 2

value: SCNT


title: 72_RSB030_V08

description: Library name: 72

value: Peripheral blood


title: I38


title: I30

value: Liver


title: 15244X219_blastomere_10B_type_SCNT_cell_number_2

description: cellnumber 2


title: 15244X216_blastomere_9A_type_SCNT_cell_number_2

description: cellnumber 2


title: 15244X218_blastomere_10A_type_SCNT_cell_number_2

description: cellnumber 2


title: 15244X228_blastomere_14A_type_SCNT_cell_number_4

description: cellnumber 4


title: 71_RSB030_V07

description: Library name: 71


title: I3

value: iKO


title: 15244X215_blastomere_8B_type_SCNT_cell_number_2

description: cellnumber 2


title: 15244X212_blastomere_7A_type_SCNT_cell_number_2

description: cellnumber 2


title: I24


title: 15244X211_blastomere_6B_type_SCNT_cell_number_2

description: cellnumber 2


title: 70_RSB030_V06

description: Library name: 70


title: 69_RSB030_V05

description: Library name: 69


title: 15244X220_blastomere_11A_type_SCNT_cell_number_2

description: cellnumber 2


title: 15244X213_blastomere_7B_type_SCNT_cell_number_2

description: cellnumber 2


title: 15244X214_blastomere_8A_type_SCNT_cell_number_2

description: cellnumber 2


title: 15244X210_blastomere_6A_type_SCNT_cell_number_2

description: cellnumber 2


title: 67_RSB030_V01

description: Library name: 67


title: 15244X209_blastomere_5B_type_SCNT_cell_number_2

description: cellnumber 2


title: I230


title: 68_RSB030_V04

description: Library name: 68


title: 15244X217_blastomere_9B_type_SCNT_cell_number_2

description: cellnumber 2


title: 15244X208_blastomere_5A_type_SCNT_cell_number_2

description: cellnumber 2


title: 15244X207_blastomere_4B_type_SCNT_cell_number_2

description: cellnumber 2


title: I228

value: Intetsine Specific ATP7B KO


title: 66_RSB028_V13

description: Library name: 66


title: I218

value: 30 weeks


title: 15244X205_blastomere_3B_type_SCNT_cell_number_2

description: cellnumber 2


title: 15244X204_blastomere_3A_type_SCNT_cell_number_2

description: cellnumber 2


title: 15244X203_blastomere_2B_type_SCNT_cell_number_2

description: cellnumber 2


title: 15244X206_blastomere_4A_type_SCNT_cell_number_2

description: cellnumber 2


title: 64_RSB028_V10

description: Library name: 64


title: I223


title: 65_RSB028_V12

description: Library name: 65


title: I213


title: I215


title: 63_RSB028_V09

description: Library name: 63


title: 15244X201_blastomere_1B_type_SCNT_cell_number_2

description: cellnumber 2


title: I212


title: 15244X199_blastomere_ZYGOTE2_type_SCNT_cell_number_1

description: cellnumber 1


title: I211


title: 62_RSB028_V08

description: Library name: 62


title: 15244X197_blastomere_114L_type_SCNT_cell_number_12

description: cellnumber 12


title: 15244X196_blastomere_114K_type_SCNT_cell_number_12

description: cellnumber 12


title: 15244X195_blastomere_114J_type_SCNT_cell_number_12

description: cellnumber 12


title: 60_RSB028_V06

description: Library name: 60


title: 15244X194_blastomere_114I_type_SCNT_cell_number_12

description: cellnumber 12


title: 15244X202_blastomere_2A_type_SCNT_cell_number_2

description: cellnumber 2


title: 15244X193_blastomere_114H_type_SCNT_cell_number_12

description: cellnumber 12


title: I210


title: 15244X192_blastomere_114G_type_SCNT_cell_number_12

description: cellnumber 12


title: 59_RSB028_V05

description: Library name: 59


title: 61_RSB028_V07

description: Library name: 61


title: 58_RSB028_V04

description: Library name: 58


title: 15244X191_blastomere_114F_type_SCNT_cell_number_12

description: cellnumber 12


title: 15244X189_blastomere_114D_type_SCNT_cell_number_12

description: cellnumber 12


title: 57_RSB028_V01

description: Library name: 57


title: I208


title: 15244X190_blastomere_114E_type_SCNT_cell_number_12

description: cellnumber 12


title: I207


title: 15244X188_blastomere_114C_type_SCNT_cell_number_12

description: cellnumber 12


title: 15244X198_blastomere_ZYGOTE1_type_SCNT_cell_number_1

description: cellnumber 1


title: I17


title: 15244X187_blastomere_114B_type_SCNT_cell_number_12

description: cellnumber 12


title: 15244X186_blastomere_114A_type_SCNT_cell_number_12

description: cellnumber 12


title: 56_RSB026_V08

description: Library name: 56


title: 15244X184_blastomere_104D_type_SCNT_cell_number_5

description: cellnumber 5


title: 15244X185_blastomere_104E_type_SCNT_cell_number_5

description: cellnumber 5


title: 55_RSB026_V07

description: Library name: 55


title: 15244X183_blastomere_104B_type_SCNT_cell_number_5

description: cellnumber 5


title: I200


title: 15244X182_blastomere_104A_type_SCNT_cell_number_5

description: cellnumber 5


title: 54_RSB026_V06

description: Library name: 54


title: 15244X181_blastomere_93F_type_SCNT_cell_number_6

description: cellnumber 6


title: 53_RSB026_V05

description: Library name: 53


title: I11


title: I19


title: 52_RSB026_V04

description: Library name: 52


title: 15244X180_blastomere_93E_type_SCNT_cell_number_6

description: cellnumber 6


title: 15244X177_blastomere_93B_type_SCNT_cell_number_6

description: cellnumber 6


title: 15244X178_blastomere_93C_type_SCNT_cell_number_6

description: cellnumber 6


title: H30_3

value: Het

value: Heterozygus


title: 51_RSB026_V01

description: Library name: 51


title: H30_4


title: 15244X179_blastomere_93D_type_SCNT_cell_number_6

description: cellnumber 6


title: 50_RSB023_V13

description: Library name: 50


title: 15244X175_blastomere_57F_type_SCNT_cell_number_6

description: cellnumber 6


title: 15244X176_blastomere_93A_type_SCNT_cell_number_6

description: cellnumber 6


title: I14


title: 15244X174_blastomere_57E_type_SCNT_cell_number_6

description: cellnumber 6


title: 49_RSB023_V12

description: Library name: 49


title: H30_2


title: 15244X172_blastomere_57B_type_SCNT_cell_number_6

description: cellnumber 6


title: H30_1


title: 15244X171_blastomere_57A_type_SCNT_cell_number_6

description: cellnumber 6


title: 48_RSB023_V10

description: Library name: 48


title: H30_5


title: 15244X170_blastomere_55D_type_SCNT_cell_number_6

description: cellnumber 6


title: 15244X169_blastomere_55C_type_SCNT_cell_number_6

description: cellnumber 6


title: colon, AShet, rep7

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

data_processing:
Sequencing was performed on a NovaSeq-6000 (Illumina, San Diego, CA) with 300 total cycles of paired-end sequencing (150 cycles per read) according to the manufacturer's protocol. Bcl2fastq2 Conversion Software (Illumina, San Diego, CA) was used to generate demultiplexed Fastq files.
Reads were trimmed using cutadapt v2.3 with the following parameters --nextseq-trim 13 -u 3 -m 20 --trim-n -a AGATCGGAAGAG -A AGATCGGAAGAG.
Paired-end alignments and gene level counts were obtained using RSEM v1.3.2 (Li and Dewey. BMC Bioinformatics. 2011). STAR v2.7.3a was the aligner called by RSEM and the default parameters were used (Dobin et al. Bioinformatics. 2013.)
Assembly: mm10
Supplementary files format and content: The columns of the counts.txt files are: (1) gene; (2) sample read count

source_name: Colon tissue

growth_protocol: The organoids derived from the colon of TAM-treated A mice or AS mice were cultured in Matrigel, overlaid with Wnt-withdrawn organoid medium containing advanced DMEM/F12 supplemented with 2 mM L-Glutamine, 16.7% Noggin conditioned-medium, 50 ng/ml mouse EGF, 20 ng/ml mouse HGF, 10 μM Y-27632, and antibiotics. The culture was maintained in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was extracted usingTrizol(Invitrogen) and purified with miRNeasy Mini Kit (Qiagen).
Libraries were prepared using the Illumina TruSeq stranded kit.

treatment_protocol: TAM-induced gene deletion: Cre-mediated deletion of the Apc or Sox9 gene was induced by administering intraperitoneal injections of TAM (Sigma) to the mice, with each mouse receiving two daily doses at 120 mg/kg weight per dose. After 30-40 days post TAM treatment, mouse colon tissues were harvested to obtain RNAs for RNA-seq. The organoids derived from the colon of TAM-treated A mice or AS mice were cultured in Wnt-withdrawn organoid medium for 3 days before being harvested for RNA analysis.

value: Colon tissue

value: CDX2P-CreERT2 Apcflox/flox Sox9flox/+

value: TAM-induced gene deletion


title: 46_RSB023_V08

description: Library name: 46


title: 15244X167_blastomere_55A_type_SCNT_cell_number_6

description: cellnumber 6


title: 15244X168_blastomere_55B_type_SCNT_cell_number_6

description: cellnumber 6


title: 47_RSB023_V09

description: Library name: 47


title: 15244X166_blastomere_50F_type_SCNT_cell_number_6

description: cellnumber 6


title: colon, AShet, rep6


title: 15244X163_blastomere_50C_type_SCNT_cell_number_6

description: cellnumber 6


title: colon, AShet, rep4


title: 15244X173_blastomere_57C_type_SCNT_cell_number_6

description: cellnumber 6


title: 15244X164_blastomere_50D_type_SCNT_cell_number_6

description: cellnumber 6


title: colon, AShet, rep5


title: 15244X162_blastomere_50B_type_SCNT_cell_number_6

description: cellnumber 6


title: 44_RSB023_V06

description: Library name: 44


title: 15244X200_blastomere_1A_type_SCNT_cell_number_2

description: cellnumber 2


title: 43_RSB023_V05

description: Library name: 43


title: 15244X161_blastomere_50A_type_SCNT_cell_number_6

description: cellnumber 6


title: 15244X160_blastomere_40C_type_SCNT_cell_number_6

description: cellnumber 6


title: 15244X159_blastomere_40A_type_SCNT_cell_number_6

description: cellnumber 6


title: colon, AShet, rep2


title: 15244X158_blastomere_113N_type_SCNT_cell_number_14

description: cellnumber 14


title: colon, AShet, rep1


title: 45_RSB023_V07

description: Library name: 45


title: 15244X165_blastomere_50E_type_SCNT_cell_number_6

description: cellnumber 6


title: 41_RSB023_V01

description: Library name: 41


title: 15244X155_blastomere_113K_type_SCNT_cell_number_14

description: cellnumber 14


title: 40_RSB021_V13

description: Library name: 40


title: 15244X154_blastomere_113J_type_SCNT_cell_number_14

description: cellnumber 14


title: 15244X156_blastomere_113L_type_SCNT_cell_number_14

description: cellnumber 14


title: 39_RSB021_V12

description: Library name: 39


title: 15244X222_blastomere_12A_type_SCNT_cell_number_2

description: cellnumber 2


title: 15244X153_blastomere_113I_type_SCNT_cell_number_14

description: cellnumber 14


title: p53-/-; Myc Hepatoblasts, drug, 7days, rep3

city: Milan

first: Pasquale

last: Tomaiuolo

state: Milan

address: via Balzaretti n.9

department: Department of Pharmacologic Sciences

country: Italy

institute: University of Milan

data_processing:
Reads were aligned to the Mouse Reference Genome (GRCm39) using STAR v2.7.1a.
The featureCounts v2.0.6 from Subread package was used to summarize and quantify the mapped reads.
Differential analyses of gene expression between specific experimental conditions  were conducted by means of the R package DESeq2 v1.40.2.
Assembly: mm39 (GRCm39)
Supplementary files format and content: Count matrix ofgene counts per sample.

source_name: Hepa p53 -/-,myc

extract_protocol:
RNA was isolated from cells using column-based methods with the NucleoSpin RNA kit (Macherey-Nagel) following the manufacturer's instructions. The RNA Integrity Number (RIN) was assessed using the TapeStation instrument (Agilent Technologies).
1000 ng of total RNA was used as the starting material. RNA-seq library preparation was performed using the Illumina Stranded mRNA Prep, Ligation kit and Illumina RNA UD Indexes Set A (Illumina, Cat). The quality of the prepared libraries was assessed using the TapeStation instrument (Agilent Technologies).

value: Hepa p53 -/-,myc

value: HCC

value: tumor stage


title: 15244X157_blastomere_113M_type_SCNT_cell_number_14

description: cellnumber 14


title: 15244X152_blastomere_113H_type_SCNT_cell_number_14

description: cellnumber 14


title: 15244X149_blastomere_113E_type_SCNT_cell_number_14

description: cellnumber 14


title: 15244X150_blastomere_113F_type_SCNT_cell_number_14

description: cellnumber 14


title: colon, AShet, rep3


title: 15244X151_blastomere_113G_type_SCNT_cell_number_14

description: cellnumber 14


title: p53-/-; Myc Hepatoblasts, drug, 7days, rep2


title: 38_RSB021_V10

description: Library name: 38


title: 15244X148_blastomere_113D_type_SCNT_cell_number_14

description: cellnumber 14


title: 37_RSB021_V09

description: Library name: 37


title: p53-/-; Myc Hepatoblasts, drug, 7days, rep1


title: 42_RSB023_V04

description: Library name: 42


title: p53-/-; Myc Hepatoblasts, control, 7days, rep4


title: 15244X147_blastomere_113C_type_SCNT_cell_number_14

description: cellnumber 14


title: 36_RSB021_V08

description: Library name: 36


title: p53-/-; Myc Hepatoblasts, drug, 7days, rep4


title: p53-/-; Myc Hepatoblasts, control, 7days, rep3


title: 15244X145_blastomere_113A_type_SCNT_cell_number_14

description: cellnumber 14


title: 15244X144_blastomere_112N_type_SCNT_cell_number_14

description: cellnumber 14


title: 35_RSB021_V07

description: Library name: 35


title: p53-/-; Myc Hepatoblasts, control, 7days, rep2


title: 15244X146_blastomere_113B_type_SCNT_cell_number_14

description: cellnumber 14


title: 34_RSB021_V06

description: Library name: 34


title: 15244X141_blastomere_112K_type_SCNT_cell_number_14

description: cellnumber 14


title: 15244X143_blastomere_112M_type_SCNT_cell_number_14

description: cellnumber 14


title: 33_RSB021_V05

description: Library name: 33


title: 15244X139_blastomere_112H_type_SCNT_cell_number_14

description: cellnumber 14


title: p53-/-; Myc Hepatoblasts, drug, 48h, rep4


title: p53-/-; Myc Hepatoblasts, control, 7days, rep1


title: 15244X140_blastomere_112J_type_SCNT_cell_number_14

description: cellnumber 14


title: 31_RSB021_V01

description: Library name: 31


title: 32_RSB021_V04

description: Library name: 32


title: 30_RSB020_V13

description: Library name: 30


title: 15244X138_blastomere_112F_type_SCNT_cell_number_14

description: cellnumber 14


title: 15244X136_blastomere_112C_type_SCNT_cell_number_14

description: cellnumber 14


title: p53-/-; Myc Hepatoblasts, drug, 48h, rep2


title: p53-/-; Myc Hepatoblasts, drug, 48h, rep1


title: 15244X134_blastomere_112A_type_SCNT_cell_number_14

description: cellnumber 14


title: 15244X133_blastomere_111P_type_SCNT_cell_number_16

description: cellnumber 16


title: 29_RSB020_V12

description: Library name: 29


title: p53-/-; Myc Hepatoblasts, control, 48h, rep4


title: 28_RSB020_V10

description: Library name: 28


title: 15244X142_blastomere_112L_type_SCNT_cell_number_14

description: cellnumber 14


title: p53-/-; Myc Hepatoblasts, control, 48h, rep3


title: 15244X130_blastomere_111L_type_SCNT_cell_number_16

description: cellnumber 16


title: 15244X131_blastomere_111M_type_SCNT_cell_number_16

description: cellnumber 16


title: p53-/-; Myc Hepatoblasts, drug, 48h, rep3


title: p53-/-; Myc Hepatoblasts, control, 48h, rep2


title: 15244X128_blastomere_111J_type_SCNT_cell_number_16

description: cellnumber 16


title: 26_RSB020_V08

description: Library name: 26


title: 15244X127_blastomere_111I_type_SCNT_cell_number_16

description: cellnumber 16


title: 15244X126_blastomere_111H_type_SCNT_cell_number_16

description: cellnumber 16


title: 25_RSB020_V07

description: Library name: 25


title: 15244X125_blastomere_111G_type_SCNT_cell_number_16

description: cellnumber 16


title: 15244X132_blastomere_111N_type_SCNT_cell_number_16

description: cellnumber 16


title: 15244X129_blastomere_111K_type_SCNT_cell_number_16

description: cellnumber 16


title: 15244X124_blastomere_111F_type_SCNT_cell_number_16

description: cellnumber 16


title: 27_RSB020_V09

description: Library name: 27


title: 24_RSB020_V06

description: Library name: 24


title: 15244X122_blastomere_111D_type_SCNT_cell_number_16

description: cellnumber 16


title: B16-F10 cells, sgExosc1, rep1

city: tianjin

first: junying

last: ma

address: Heping District Meteorological Observatory Road

country: China

institute: Tianjin Medical University

data_processing:
Paired-end sequencing reads were meticulously trimmed and filtered using fastp (v0.23.4) employing its default settings. Subsequently, these reads were aligned to the mouse mm10 reference genome utilizing STAR (v2.7.5c), with the parameters set to "--outSAMtype BAM SortedByCoordinate --twopassMode Basic --outFilterMismatchNmax 2 --outFilterMultimapNmax 1". Gene expression quantification was accurately calculated using featureCounts from the Rsubread package (v2.0.1).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw count of each gene for each sample.

source_name: B16-F10 cells

extract_protocol:
Total RNA was extracted using the Trizol method, followed by purification and concentration with an RNA Clean & Concentrator kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: B16-F10 cells


title: 23_RSB020_V05

description: Library name: 23


title: 15244X123_blastomere_111E_type_SCNT_cell_number_16

description: cellnumber 16


title: 15244X120_blastomere_111B_type_SCNT_cell_number_16

description: cellnumber 16


title: 15244X121_blastomere_111C_type_SCNT_cell_number_16

description: cellnumber 16


title: 22_RSB020_V04

description: Library name: 22


title: 15244X119_blastomere_111A_type_SCNT_cell_number_16

description: cellnumber 16


title: 15244X117_blastomere_67K_type_SCNT_cell_number_12

description: cellnumber 12


title: p53-/-; Myc Hepatoblasts, control, 48h, rep1


title: 21_RSB020_V01

description: Library name: 21


title: 15244X116_blastomere_67J_type_SCNT_cell_number_12

description: cellnumber 12


title: 15244X118_blastomere_67L_type_SCNT_cell_number_12

description: cellnumber 12


title: B16-F10 cells, sgDis3, rep2


title: 15244X115_blastomere_67I_type_SCNT_cell_number_12

description: cellnumber 12


title: B16-F10 cells, sgDis3, rep1


title: B16-F10 cells, sgExosc1, rep2


title: 15244X113_blastomere_67G_type_SCNT_cell_number_12

description: cellnumber 12


title: B16-F10 cells, sgCtrl, rep1


title: 20_RSB019_V13

description: Library name: 20


title: B16-F10 cells, sgCtrl, rep2


title: 15244X114_blastomere_67H_type_SCNT_cell_number_12

description: cellnumber 12


title: 19_RSB019_V12

description: Library name: 19


title: 15244X111_blastomere_67D_type_SCNT_cell_number_12

description: cellnumber 12


title: 15244X110_blastomere_67C_type_SCNT_cell_number_12

description: cellnumber 12


title: 18_RSB019_V10

description: Library name: 18


title: B16-F10 cells, Carm1-knockout, RIG-I, rep2

data_processing:
Paired-end sequencing reads were meticulously trimmed and filtered using fastp (v0.23.4) employing its default settings. Subsequently, these reads were aligned to the mouse mm10 reference genome utilizing STAR (v2.7.5c), with the parameters set to "--winAnchorMultimapNmax 500 --outFilterMultimapNmax 500". Gene expression quantification was accurately calculated using featureCounts from the Rsubread package (v2.0.1).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw count of each gene for each sample.

molecule: cytoplasmic RNA

extract_protocol:
Cytoplasmic total RNA or RNA bound to specific proteins was extracted using the Trizol method, followed by purification and concentration with an RNA Clean & Concentrator kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: 15244X112_blastomere_67F_type_SCNT_cell_number_12

description: cellnumber 12


title: 15244X109_blastomere_67B_type_SCNT_cell_number_12

description: cellnumber 12


title: B16-F10 cells, Carm1-knockout, RIG-I, rep1


title: B16-F10 cells, wild-type, RIG-I, rep2


title: 17_RSB019_V09

description: Library name: 17


title: 15244X107_blastomere_66P_type_SCNT_cell_number_14

description: cellnumber 14


title: 15244X108_blastomere_67A_type_SCNT_cell_number_12

description: cellnumber 12


title: 15244X106_blastomere_66O_type_SCNT_cell_number_14

description: cellnumber 14


title: 16_RSB019_V08

description: Library name: 16


title: 15244X105_blastomere_66K_type_SCNT_cell_number_14

description: cellnumber 14


title: B16-F10 cells, wild-type, RIG-I, rep1


title: 15_RSB019_V07

description: Library name: 15


title: 15244X102_blastomere_64N_type_SCNT_cell_number_14

description: cellnumber 14


title: B16-F10 cells, Carm1-knockout, MDA5, rep2


title: 15244X104_blastomere_66J_type_SCNT_cell_number_14

description: cellnumber 14


title: 15244X103_blastomere_66I_type_SCNT_cell_number_14

description: cellnumber 14


title: 13_RSB019_V05

description: Library name: 13


title: B16-F10 cells, wild-type, MDA5, rep2


title: 15244X099_blastomere_64G_type_SCNT_cell_number_14

description: cellnumber 14


title: 14_RSB019_V06

description: Library name: 14


title: B16-F10 cells, Carm1-knockout, MDA5, rep1


title: 15244X100_blastomere_64K_type_SCNT_cell_number_14

description: cellnumber 14


title: 15244X098_blastomere_64F_type_SCNT_cell_number_14

description: cellnumber 14


title: B16-F10 cells, wild-type, MDA5, rep1


title: 12_RSB019_V04

description: Library name: 12


title: B16-F10 cells, Carm1-knockout, input, rep4


title: 11_RSB019_V01

description: Library name: 11


title: 10_RSB018_V13

description: Library name: 10


title: 15244X094_blastomere_64B_type_SCNT_cell_number_14

description: cellnumber 14


title: 15244X093_blastomere_64A_type_SCNT_cell_number_14

description: cellnumber 14


title: 15244X101_blastomere_64M_type_SCNT_cell_number_14

description: cellnumber 14


title: 15244X096_blastomere_64D_type_SCNT_cell_number_14

description: cellnumber 14


title: 15244X092_blastomere_94G_type_SCNT_cell_number_7

description: cellnumber 7


title: 9_RSB018_V12

description: Library name: 9


title: B16-F10 cells, Carm1-knockout, input, rep3


title: 15244X091_blastomere_94F_type_SCNT_cell_number_7

description: cellnumber 7


title: B16-F10 cells, wild-type, input, rep4


title: 15244X090_blastomere_94E_type_SCNT_cell_number_7

description: cellnumber 7


title: 8_RSB018_V10

description: Library name: 8


title: 15244X089_blastomere_94D_type_SCNT_cell_number_7

description: cellnumber 7


title: 15244X088_blastomere_94C_type_SCNT_cell_number_7

description: cellnumber 7


title: B16-F10 cells, Carm1-knockout, J2, rep2


title: 6_RSB018_V08

description: Library name: 6


title: 7_RSB018_V09

description: Library name: 7


title: 15244X095_blastomere_64C_type_SCNT_cell_number_14

description: cellnumber 14


title: 15244X097_blastomere_64E_type_SCNT_cell_number_14

description: cellnumber 14


title: 15244X087_blastomere_94B_type_SCNT_cell_number_7

description: cellnumber 7


title: 15244X086_blastomere_94A_type_SCNT_cell_number_7

description: cellnumber 7


title: 5_RSB018_V07

description: Library name: 5


title: 15244X085_blastomere_58G_type_SCNT_cell_number_7

description: cellnumber 7


title: 15244X084_blastomere_58F_type_SCNT_cell_number_7

description: cellnumber 7


title: 15244X083_blastomere_58E_type_SCNT_cell_number_7

description: cellnumber 7


title: 4_RSB018_V06

description: Library name: 4


title: 3_RSB018_V05

description: Library name: 3


title: B16-F10 cells, wild-type, J2, rep1


title: B16-F10 cells, Carm1-knockout, input, rep2


title: 15244X079_blastomere_58A_type_SCNT_cell_number_7

description: cellnumber 7


title: 15244X081_blastomere_58C_type_SCNT_cell_number_7

description: cellnumber 7


title: 2_RSB018_V04

description: Library name: 2


title: 15244X078_blastomere_22G_type_SCNT_cell_number_7

description: cellnumber 7


title: 1_RSB018_V01

description: Library name: 1


title: B16-F10 cells, wild-type, J2, rep2


title: 15244X072_blastomere_22A_type_SCNT_cell_number_7

description: cellnumber 7


title: 15244X077_blastomere_22F_type_SCNT_cell_number_7

description: cellnumber 7


title: Blast siERH biol rep3

city: Seattle

first: Ryan

middle: Lehman

last: McCarthy

state: WA

address: 1900 9th Ave

department: Pediatrics

institute: University of Washington

data_processing:
RNA-seq reads (paired-end) were mapped to the mm10 or hg38 genome for mouse and human experiments respectively using STAR (2.7.10b). The mapped reads to genes were counted using featureCounts.
Assembly: hg38, mm39
Supplementary files format and content: bigwig

source_name: blastocyst

growth_protocol: Mouse embryo work Mouse embryo experimentation was approved by the Biological Resource Center Institutional Animal Care and Use Committee (IACUC), Agency for Science, Technology and Research (IACUC Protocol 806983). C57BL/6 wild-type 3–4-week-old female mice were superovulated using 5 IU of pregnant mare serum (PMS, National Hormone and Peptide Program) gonadotropin given intraperitoneally and 5 IU of recombinant chorionic gonadotrophin (CG, National Hormone and Peptide Program) given 48 h after and immediately before mating, according to animal ethics guidelines of the University of Pennsylvania. Embryos were flushed from oviducts of plugged females using M2 medium (Merck) and cultured in KSOM+AA (Merck) covered by mineral oil (Sigma, M-5310), at 37 °C and 5% CO2. Cell lines culture and condition Human H1 ES cells were obtained from WiCell (WA01), grown on Matrigel coated wells and cultured in mTeSR1 (Stem Cell Tech, 85850) medium at 37oC and 5% CO¬2. Medium was changed daily. Human BJ foreskin fibroblasts were obtained from ATCC (CRL-2522) and cultured in Eagle’s Minimum Essential Medium (EMEM, Sigma-Aldrich M2279) supplemented with 10% fetal bovine serum (FBS, Hyclone SH30071) and 2mM Glutamax (ThermoFisher 35050061) at 37oC and 5% CO¬2.

extract_protocol:
BJ fibroblasts grown in a 6-well dish were washed twice with cold PBS, followed by addition of 1 mL TRIzol reagent (ThermoFisher 15596026) and transferred to a chilled 1.5 mL tube using a cell scraper. The cells were homogenized by pipetting through a 25G needle attached to a 2 mL syringe 10 times. 200 µl of chloroform was added to the cells and vortexed for 15 seconds, followed by a room temperature incubation of 3 minutes. Phase separation of nucleic acids and protein was performed by centrifugation at 12,000 x g for 15 minutes at 4C. The upper aqueous phase containing RNA was then transferred to a fresh chilled tube. RNA was precipitated from the aqueous phase by adding an equal volume of isopropyl alcohol, followed by a 10 minute incubation at room temperature. The RNA was pelleted by centrifugation at 12,000 x g for 10 minutes at 4C. After removal of supernatant, the pellet was washed twice with 1 mL 75% ethanol, and resuspended in nuclease free water. RNA quality was verified using a high-sensitivity RNA screentape (Agilent 5067-5576).
1ug of total RNA was sent to Novogene, who assembled and sequenced bulk RNA-seq libraries.

treatment_protocol: Mouse embryo siRNA injection experiments Microinjections were performed using a FemtoJet (Eppendorf). For ERH knockdown experiments, mouse embryos were injected with two siRNAs (Qiagen, S104403294 & S104403287) against ERH at a total concentration of 400 nM. For knockdown experiments AllStars negative control siRNA (Qiagen, 1027281) was injected in embryos at a concentration of 400nM.  Differentiation of hESCs Prior to differentiation, for samples to be analyzed by RNA-seq, cells grown to a density of 80% were digested with Accutase (Stem Cell Technologies, 07920) for 7 min. Then, DMEM/F12 was added and gently pipetted to generate a cell suspension. After centrifugation, cells were resuspended in mTeSR1 medium with 5uM ROCK inhibitor Y-27632 (Cayman Chemical, 10005583) and seeded at 8X105-1X106 cells per well in a 6 well plate coated with Matrigel (Millipore Sigma, CLS354277) 24 hours prior to differentiation treatment. For definitive endoderm differentiation of hESCs, mTeSR1 medium was removed and cells were cultured in DMEM/F12 (Thermo Fisher, 11320033) supplemented with 10% (v/v) Fetal Bovine Serum (Hyclone, SH30071) with 100ng/ml Activin A (Peprotech, 120-14P) and 3uM CHIR99021 (Cayman Chemical, 13122). For ectoderm differentiation of hESCs, mTeSR medium was removed and cells were cultured in DMEM/F12 with 5uM Retinoic Acid (Cayman Chemical, 11017).  Cell culture siRNA transfection experiments All ERH knockdown experiments were performed with two cycles of siRNA transfection (Silencer Select siRNA, Thermo Fisher, s4815), three days apart. Transfections were performed in fibroblasts using 5nM final concentration of siRNA and in hESCs using a 10nM final concentration of siRNA and 2.5ul/ml final concentration of Lipofectamine RNAiMAX (Thermo Fisher #31985070).

value: blastocyst

value: embryo

value: siERH


title: B16-F10 cells, Carm1-knockout, J2, rep1


title: 15244X075_blastomere_22D_type_SCNT_cell_number_7

description: cellnumber 7

value: SCNT


title: 15244X071_blastomere_115H_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_069_TUMOUR

city: Brisbane

first: Arutha

last: Kulasinghe

state: QLD

address: 37 kent st

country: Australia

institute: University of Queensland

description:
Library name: 069_TUMOUR
1 OC

data_processing:
Adapter trimming with trim galore,  trimGaloreOpts = " --hardtrim5 26 --dont_gzip"
If paired-end, merge overlapping R1 and R2 with flash2, flash2Opts = " -m 26 -e 26 -f 26 -s 1 -r 27”
Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN"
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1“
Quality control of the data was conducted based on previously established pipeline for spatial data (standR, Liu et al, Nucleic Acids Research. 2023) using the probe normalised (probeQC) counts. Low expressing genes with less than 5 counts per sample in more than 90% of the samples were removed. Sample QC filters out low expression FOVs based on gene expression depth (> 200,000 per FOW) and nuclei count (> 100 cells per FOV), removing 4 FOVs from the TME segments. The filtered data is normalised using the "relative log expression” (RLE) scaling factor method. One FOV was assessed to be an outlier with extremely small normalization factor and consequently removed. This result in a final normalised dataset of 117 FOVs from 61 cores used for downstream analyses. The normalised/scaled log2-transformed counts per million (logCPM) of the data is provided as inputs.
Assembly: Sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform
Supplementary files format and content: Processed data files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: Initial: uncollapsed probe counts, QC: collapsed probe counts, norm: quartile normalised data, "relative log expression” (RLE) normalised log2-transformed counts per million (logCPM) of the the QC filtered data is provided. 122 column entries with filtered FOVs (5 columns) having blank entries.
Library strategy: Spatial Transcriptomics

source_name: Lung

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

treatment_protocol: Samples were fixed in formalin and paraffin embedded (FFPE) for GeoMx processing

value: Lung


title: 15244X082_blastomere_58D_type_SCNT_cell_number_7

description: cellnumber 7


title: HNSCC_068_TME

description:
Library name: 068_TME
2 OC


title: B16-F10 cells, Carm1-knockout, input, rep1


title: B16-F10 cells, wild-type, input, rep1


title: 15244X074_blastomere_22C_type_SCNT_cell_number_7

description: cellnumber 7


title: 15244X080_blastomere_58B_type_SCNT_cell_number_7

description: cellnumber 7


title: 15244X070_blastomere_115G_type_SCNT_cell_number_8

description: cellnumber 8


title: Blast siERH biol rep2


title: HNSCC_068_TUMOUR

description:
Library name: 068_TUMOUR
2 OC


title: 15244X068_blastomere_115E_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X073_blastomere_22B_type_SCNT_cell_number_7

description: cellnumber 7


title: HNSCC_069_TME

description:
Library name: 069_TME
1 OC


title: 15244X137_blastomere_112E_type_SCNT_cell_number_14

description: cellnumber 14


title: HNSCC_067_TME

description:
Library name: 067_TME
3 OC


title: Blast siERH biol rep1


title: 15244X066_blastomere_115C_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X067_blastomere_115D_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X065_blastomere_115B_type_SCNT_cell_number_8

description: cellnumber 8


title: Blast siControl biol rep3

value: siControl


title: Blast siControl biol rep2


title: 15244X063_blastomere_65H_type_SCNT_cell_number_8

description: cellnumber 8


title: Blast siControl biol rep1


title: 15244X062_blastomere_65G_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X064_blastomere_115A_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X061_blastomere_65F_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X135_blastomere_112B_type_SCNT_cell_number_14

description: cellnumber 14


title: 15244X060_blastomere_65E_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X069_blastomere_115F_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X059_blastomere_65D_type_SCNT_cell_number_8

description: cellnumber 8


title: trauma_spatial_1

city: Shanghai

first: Wei

last: Zuo

state: Shanghai

address: No. 500 Zhennan Road, Putuo District, Shanghai

institute: University

description: Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseg coding genes were quantified using Space Ranger's default settings
Assembly: mm10 and EGFP
Supplementary files format and content: filtered_feature_bc_matrix.h5
Library strategy: Spatial Transcriptomics

source_name: Mus musculus

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10um frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to  manufacturer's construction

value: kidney


title: HNSCC_066_TUMOUR

description:
Library name: 066_TUMOUR
4 OC


title: HNSCC_065_TME

description:
Library name: 065_TME
5 OC


title: 15244X058_blastomere_65C_type_SCNT_cell_number_8

description: cellnumber 8


title: B16-F10 cells, wild-type, input, rep2


title: M_D_miPSC, MD2, Day1

city: Dallas

first: Leijie

last: Li

state: Texas

address: 5323 Harry Hines Blvd.

department: Molecular Biology

institute: UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER

data_processing:
Hisat2 v 2.1.0 and Stringtie v 2.1.7 pipeline
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore v 0.6.10
Trimmed sequence reads were mapped to GRCh38/GRCm39 genomics by using Hisat2 v 2.1.0
Read count extraction using StringTie v 2.1.7
Assembly: GRCh38 for human; GRCm39 for mouse
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: mESCs

growth_protocol: PRKN-overexpressing mouse embryonic stem cells (PRKN-mESCs) were maintained in 2iL media and grown on Matrigel-coated plates, with 5% CO2 at 37C. PRKN-overexpressing human H9 embryonic stem cells (PRKN-hESCs) were grown in mTeSR Plus (STEMCELL) medium on Matrigel-coated (Corning) plates, with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using the RNeasy Mini Plus Kit (Qiagen).
RNA libraries for RNA-seq were prepared using the SMARTer mRNA-Seq Library Prep Kit following the manufacturer's protocols.

treatment_protocol:
Mitochondria-depletion was carried out by treating PRKN-mESCs with 1 uM oligomycin A (Sigma) and antimycin A (Sigma) (A/O) for 72 hours in 2iL medium. For mitochondria-depletion of PRKN-hESCs, cells were treated with 1 uM A/O for 48 hours in mTeSR Plus. After A/O treatment, cells were washed three times with complete medium, then cultured for an additional 48 hours. After A/O treatment, washes, and 48-hour culture, cells were collected as Day 1 mitochondria-depleted cells. Medium was refreshed every day.
For Day 7 and Day 14 samples, mitochondria-depletion was carried out the same way, except after the washes, cells were cultured for only an additional 24 hours. Then, cells were grown in complete medium supplemented with 10% FBS (Gibco) and 1x CEPT (Tocris). Medium was changed every day for the first 7 days, then half of the medium was refreshed every day for the next 7 days.

value: mESCs

value: pluripotent stem cells

value: WT

value: Mitochondria depletion


title: 15244X057_blastomere_65B_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_065_TUMOUR

description:
Library name: 065_TUMOUR
5 OC


title: M_D_miPSC, MD1, Day1


title: 15244X056_blastomere_65A_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_067_TUMOUR

description:
Library name: 067_TUMOUR
3 OC


title: 15244X055_blastomere_62H_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_064_TME

description:
Library name: 064_TME
6 OC


title: M_D_miPSC, Control2, Day0

value: Control


title: 15244X054_blastomere_62G_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_066_TME

description:
Library name: 066_TME
4 OC


title: 15244X052_blastomere_62E_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_064_TUMOUR

description:
Library name: 064_TUMOUR
6 OC


title: M_D_miPSC, Control1, Day0


title: HNSCC_063_TME

description:
Library name: 063_TME
7 OC


title: S6

city: Guangzhou

first: Xiaofei

last: He

state: Guangdong

address: 600 Tianhe Road

department: Department of Rehabilitation Medicine

institute: The Third Affiliated Hospital of Sun Yat-sen University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using GLC genomics bench work (Parameter-Quality: 0.05)
Assembly: mm10
Supplementary files format and content: Tab-delimited text file include RPKM values for each sample
Supplementary files format and content: Tab-delimited text file include raw count for each sample

source_name: Brain

growth_protocol: The mice were housed in a 12:12 h light:dark cycle (light on from 07:00−19:00 h), with controlled temperature of 22-24 °C, humidity of 40%~67%, and food and water provided ad libitum.

extract_protocol:
Mice were anesthetized with chloral hydrate (4.2%, 0.01 mL/g) and underwent transcardial perfusion with 40 mL of pre-cooled 0.9% NaCl, right hippocampus were isolated. Total RNA was extracted and mRNA was isolated using magnetic beads with oligo-dT, the mRNA was then segmented, the cDNA were synthesized and end repaired. A base was added to the 3’end and the segment was connected to the sequencing connector, which was then purified and amplified, the sequencing library was purified by magnetic beads. Qubit was used to detect the library concentration, and agilent fragment analyzer was used to detect the library fragment length.
RNA-Libraries for RNA-Seq were prepared using SMARTER mRNA-Seq Libraries prep kit following manufacture’s protocols

treatment_protocol: Transient middle cerebral artery occlusion (tMCAO) was performed as described [20]. In brief, mice were anesthetized with isoflurane delivered in a mixture of 30% O2 and 70% N2O, which was controlled by an anesthesia apparatus. For this purpose, an incision was made in the midline neck region and the common carotid artery, using a silicone-coated monofilament (210−230 µm tip diameter; Doccol, Sharon, MA, USA) inserted into the right internal carotid artery. After 50 min of occlusion, the filament was removed. For the survival period, the mice were kept in their home cages with free access to water and food. The body temperature was maintained throughout surgery using a heating pad.

value: Brain

tag: Sex

value: Male

value: tMCAO


title: 15244X049_blastomere_62B_type_SCNT_cell_number_8

description: cellnumber 8


title: S5


title: 15244X050_blastomere_62C_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X048_blastomere_62A_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_062_TME

description:
Library name: 062_TME
8 OC


title: 15244X051_blastomere_62D_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_063_TUMOUR

description:
Library name: 063_TUMOUR
7 OC


title: 15244X047_blastomere_61H_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X076_blastomere_22E_type_SCNT_cell_number_7

description: cellnumber 7


title: 15244X046_blastomere_61G_type_SCNT_cell_number_8

description: cellnumber 8


title: S4


title: HNSCC_062_TUMOUR

description:
Library name: 062_TUMOUR
8 OC


title: 15244X045_blastomere_61F_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X042_blastomere_61C_type_SCNT_cell_number_8

description: cellnumber 8


title: S3

value: Sham


title: 15244X043_blastomere_61D_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_061_TUMOUR

description:
Library name: 061_TUMOUR
9 OC


title: S2


title: B16-F10 cells, wild-type, input, rep3

value: B16-F10 cells


title: 15244X053_blastomere_62F_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X044_blastomere_61E_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X041_blastomere_61B_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_059_TME

description:
Library name: 059_TME
11 OC


title: HNSCC_061_TME

description:
Library name: 061_TME
9 OC


title: 15244X039_blastomere_60H_type_SCNT_cell_number_8

description: cellnumber 8


title: Mouse liver RNAseq data_KO RD 35days only - 8573_KOS_RD

city: Toronto

first: Gaia

last: Andreoletti

state: ON

address: 686 Bay St

country: Canada

institute: Sick Kids

data_processing:
Paired-end FASTQ files for each sample underwent quality control (QC) analysis using multiQC (version 0.1.12) to obtain general QC metrics.
Adapters were trimmed from the FASTQ files using Trim Galore (version 0.6.6).
Transcript expression quantification from RNA-seq data was performed using Salmon (version 1.4.0) in an in-house developed alignment-free pipeline. Adapter-trimmed reads were used as input, and the genome index built from the Mus musculus reference genome (mm10) with associated transcript annotations (GRCm38) was utilized.
Differential gene expression analysis was conducted using the R package DESeq2 (v.1.24.0) with default settings. Genes with at least 5 reads in 80% of the samples were retained. Replicates were used as covariates within the DESeq2 model, and statistical significance was set at 5% False Discovery Rate (FDR) using the Benjamini-Hochberg method.
Gene set enrichment analysis (GSEA) was performed using the Bioconductor package fgsea (v 1.10.1 R package) with mouse ortholog-mapped hallmark gene sets from the Molecular Signatures Database (MSigDB).
Assembly: mm10
Supplementary files format and content: quant files - tab delimited includes raw counts, included in tar archive

growth_protocol: All animal procedures were conducted in accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care. Mice were housed and bred at the Toronto Centre for Phenogenomics. The study involved Mtm1 multiparous carrier females being time-bred to WT C57BL/6J mice and individually housed throughout pregnancy and lactation. Post-natal day 14 pups were genotyped and identified by ear tagging. At post-natal day 21, WT and Mtm1 KO male pups were weighed and weaned. Weaned mice were monitored daily, and body weight and food intake were recorded every 48 hours. The study also involved investigating the effect of diet as a precipitate of cholestasis. Two dietary interventions were administered to the mice, and the study was terminated at post-natal day 35.

extract_protocol:
RNA was extracted from the liver lobes of wild-type (WT) and Mtm1 knockout (KO) mice at postnatal day 21 (PND 21) and postnatal day 35 (PND 35). The extraction followed the Qiagen RNeasy kit protocol and was quantified using a NanoDropTM2000 Spectrophotometer. The RNA quality was assessed using the Agilent 2100 BioAnalyzer and RNA 6000 Nano Kit at The Centre for Applied Genomics (TCAG).
Whole-transcriptome analysis was conducted through RNA sequencing at TCAG using the NEB Ultra II Directional poly(A) mRNA library prep kit, followed by paired-end sequencing on a NovaSeq 6000 system.

treatment_protocol: Two dietary interventions were employed: a standard laboratory chow diet and a semi-purified AIN93G diet. Mice were fed ad libitum until they reached postnatal day 35, after which they were euthanized, consistent with the median survival of Mtm1 KO mice on the C57BL6/J background strain.

value: Liver

value: KOS

value: RD


title: 15244X036_blastomere_60E_type_SCNT_cell_number_8

description: cellnumber 8

value: SCNT


title: HNSCC_058_TME

description:
Library name: 058_TME
12 OC

value: Lung


title: 15244X034_blastomere_60C_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X035_blastomere_60D_type_SCNT_cell_number_8

description: cellnumber 8


title: Mouse liver RNAseq data_KO RD 35days only - 5_KO_RD


title: Mouse liver RNAseq data_WT RD 35days only - 4_WT_RD


title: HNSCC_059_TUMOUR

description:
Library name: 059_TUMOUR
11 OC


title: 15244X033_blastomere_60B_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X031_blastomere_59H_type_SCNT_cell_number_8

description: cellnumber 8


title: Mouse liver RNAseq data_WT and KO Chow 35days only - 4_WT_CHOW

value: CHOW


title: HNSCC_058_TUMOUR

description:
Library name: 058_TUMOUR
12 OC


title: 15244X030_blastomere_59G_type_SCNT_cell_number_8

description: cellnumber 8


title: Mouse liver RNAseq data_WT and KO Chow 21 days - 4 WT


title: 15244X038_blastomere_60G_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X029_blastomere_59F_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_057_TUMOUR

description:
Library name: 057_TUMOUR
13 OC


title: HNSCC_056_TME

description:
Library name: 056_TME
14 OC


title: 15244X028_blastomere_59E_type_SCNT_cell_number_8

description: cellnumber 8


title: Mouse liver RNAseq data_KO RD 35days only - 4_KO_RD


title: 15244X026_blastomere_59C_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X027_blastomere_59D_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X025_blastomere_59B_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X040_blastomere_61A_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X037_blastomere_60F_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_056_TUMOUR

description:
Library name: 056_TUMOUR
14 OC


title: Mouse liver RNAseq data_WT and KO Chow 35days only - 4_KO_CHOW

value: KO


title: Mouse liver RNAseq data_WT and KO Chow 21 days - 4 KO


title: 15244X023_blastomere_56H_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X032_blastomere_60A_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X024_blastomere_59A_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_055_TME

description:
Library name: 055_TME
15 OC


title: Mouse liver RNAseq data_WT RD 35days only - 3_WT_CHOW - 3_WT_RD


title: S1


title: 15244X022_blastomere_56G_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X019_blastomere_56D_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X021_blastomere_56F_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X020_blastomere_56E_type_SCNT_cell_number_8

description: cellnumber 8


title: Mouse liver RNAseq data_WT RD 35days only - 3_WT_CHOW


title: HNSCC_054_TME

description:
Library name: 054_TME
16 OC


title: HNSCC_057_TME

description:
Library name: 057_TME
13 OC


title: 15244X018_blastomere_56C_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_054_TUMOUR

description:
Library name: 054_TUMOUR
16 OC


title: 15244X015_blastomere_54H_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X013_blastomere_54F_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X014_blastomere_54G_type_SCNT_cell_number_8

description: cellnumber 8


title: Mouse liver RNAseq data_WT and KO Chow 21 days - 3 WT


title: 15244X017_blastomere_56B_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_053_TME

description:
Library name: 053_TME
17 OC


title: Mouse liver RNAseq data_WT and KO Chow 21 days - 3 KO


title: 15244X012_blastomere_54E_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X011_blastomere_54D_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_055_TUMOUR

description:
Library name: 055_TUMOUR
15 OC


title: Mouse liver RNAseq data_ remaining 21 - 3_KO_RD


title: HNSCC_053_TUMOUR

description:
Library name: 053_TUMOUR
17 OC


title: HNSCC_052_TME

description:
Library name: 052_TME
19 OC


title: HNSCC_052_TUMOUR

description:
Library name: 052_TUMOUR
19 OC


title: 15244X009_blastomere_54B_type_SCNT_cell_number_8

description: cellnumber 8


title: Mouse liver RNAseq data_WT and KO Chow 35days only - 2_WT_CHOW


title: Mouse liver RNAseq data_WT and KO Chow 35days only - 2 KO RD


title: HNSCC_050_TME

description:
Library name: 050_TME
21 OC


title: 15244X016_blastomere_56A_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X007_blastomere_53H_type_SCNT_cell_number_8

description: cellnumber 8


title: Mouse liver RNAseq data_WT and KO Chow 21 days - 1


title: 15244X004_blastomere_53D_type_SCNT_cell_number_8

description: cellnumber 8


title: 15244X006_blastomere_53G_type_SCNT_cell_number_8

description: cellnumber 8


title: Mouse liver RNAseq data_KO RD 35days only - 2_KO_RD


title: HNSCC_050_TUMOUR

description:
Library name: 050_TUMOUR
21 OC


title: HNSCC_049_TME

description:
Library name: 049_TME
22 OC


title: 15244X003_blastomere_53C_type_SCNT_cell_number_8

description: cellnumber 8


title: Mouse liver RNAseq data_KO RD 35days only - 3_KO_CHOW


title: 15244X002_blastomere_53B_type_SCNT_cell_number_8

description: cellnumber 8


title: Mouse liver RNAseq data_KO RD 35days only - 2_KO_CHOW


title: 15244X010_blastomere_54C_type_SCNT_cell_number_8

description: cellnumber 8


title: Mouse liver RNAseq data_WT and KO Chow 21 days - 2 KO


title: 15243X259_blastomere_52H_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X258_blastomere_52G_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X257_blastomere_52F_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_049_TUMOUR

description:
Library name: 049_TUMOUR
22 OC


title: HNSCC_048_TUMOUR

description:
Library name: 048_TUMOUR
23 OC


title: HNSCC_048_TME

description:
Library name: 048_TME
23 OC


title: 15244X008_blastomere_54A_type_SCNT_cell_number_8

description: cellnumber 8


title: Mouse liver RNAseq data_WT and KO Chow 21 days - 1 WT


title: 15243X256_blastomere_52E_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X255_blastomere_52D_type_SCNT_cell_number_8

description: cellnumber 8


title: Mouse liver RNAseq data_WT RD 35days only - 1_WT_RD


title: HNSCC_047_TME

description:
Library name: 047_TME
24 OC


title: 15243X254_blastomere_52C_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X253_blastomere_52B_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X252_blastomere_52A_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_047_TUMOUR

description:
Library name: 047_TUMOUR
24 OC


title: 15243X251_blastomere_26H_type_SCNT_cell_number_8

description: cellnumber 8


title: Mouse liver RNAseq data_WT RD 35days only - 1_WT_CHOW


title: 15244X001_blastomere_53A_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X250_blastomere_26G_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X249_blastomere_26F_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X248_blastomere_26E_type_SCNT_cell_number_8

description: cellnumber 8


title: Mouse liver RNAseq data_WT and KO Chow 35days only - 1 KO RD


title: Mouse liver RNAseq data_KO RD 35days only - 1 KO Chow


title: Mouse liver RNAseq data_WT and KO Chow 21 days - 1 KO


title: 15243X246_blastomere_26C_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_046_TUMOUR

description:
Library name: 046_TUMOUR
25 OC


title: 15243X247_blastomere_26D_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X245_blastomere_26B_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_045_TME

description:
Library name: 045_TME
26 OC


title: 15243X244_blastomere_26A_type_SCNT_cell_number_8

description: cellnumber 8


title: GSM_LC_55_3

first: Xiaoshen

last: Zhang

address: 1239 siping road

institute: Tongji University

library_source: transcriptomic single cell

data_processing:
Results from Illumina sequencing offline were converted to FASTQ format using bcl2fastq software (v5.0.1). The scRNA-seq sequencing data were compared to reference genome using CellRanger (v7.1.0). The output CellRanger expression profile matrix was loaded into Seurat (version 4.1.0), followed by the application of quality control and cell filtering. The thresholds for filtering low-quality cells required the removal of multiple cells if the number of genes expressed per cell was >500 or mitochondrial genes were expressed in <25% of cells
Assembly: mm9
Supplementary files format and content: data matrix

source_name: Ascites

extract_protocol:
RNA extraction and single-cell labeling
10X Genomics Chromium Single-Cell 3' kit (V3)

value: Ascites


title: 15243X243_blastomere_24H_type_SCNT_cell_number_8

description: cellnumber 8

data_processing:
RNA-seq reads were trimmed and filtered for quality using BBDuk and FastQC (version 0.10.1).
Processed reads were aligned to bostau7 with Bowtie2 (v2.2.6) with the following parameters: (--t --q --N1 --L 25 --X 2000 --no-mixed --no-discordant).
PCR duplicates were removed using bedtools
mitochondrial reads were removed using sed '/chrM/d'
counts for each ATACseq union region were generated using ‘Get datasets’ (https://metacpan.org/pod/distribution/Bio-ToolBox/scripts/get_datasets.pl).
Assembly: bostau7
Supplementary files format and content: 20230629-scATAC-seq-cell-ID-conversion.xls excel file containing sample ID and information
Supplementary files format and content: 20180822-scATAC-819-cells-vs-302830-regions.tabular count file for n=819 retained high quality scATACseq libraries in ATAC-seq peaks regions created as a union dataset, tabular format

extract_protocol:
ATAC-seq was performed using 2x Tris-DMF-tagmentation buffer (10mM Tris-pH=8.0, 5mM MgCl, 20% DMF). Add (batch-determined actitivty) 2 to 2.5 uL of Nextera Tn5 transposase (Cat# FC-121-1030, Illumina. Samples were incubated at 37C for 30 minutes in a PCR machine. The reactions were stopped with 0.5uL of 10% SDS, pipetted up and down, and placed on ice 5 min. 5x volume of PB buffer was added to the ATAC-seq reaction and purified using a ampure beads and eluted in 10mM Tris-pH=8.0 + 1mM EDTA.
Libraries were PCR amplified in 25uL reaction volumes using custom Nextera PCR primers from Buenrostro, et al. Nature 2015. PCR reaction conditions: ~10uL tagmented DNA, 12.5 uL of 2xphusion PCR mastermix (Phusion High-Fidelity PCR Master Mix with HF Buffer - 100 rxns, NEB, cat #M0531S), 0.625uL of 100uM F primer, 0.625uL of 100uM R primer. QS to 50uL total with H20. Do 5 cycles of “pre-amp” PCR. PCR cycling conditions: 72C incubation for 5 min. 5 cycles of the following: 95C for 30 sec, 72C for 90 sec. Remove 5uL of the “pre-PCR” reaction for qPCR. qPCR reaction conditions: 20uL qPCR reaction: 5uL of pre-amp PCR product, 10 ul of 2x syber (SsoAdvanced SYBR Green Supermix, Biorad catalog #1725275), 0.25uL of 100uM F primer, 0.25uL of 100uM R primer. Run 30-40 cycles of qPCR with the same cycling conditions as above. Select the additional number of PCR cycles to perform as per Buenrostro, et al. Nature Methods 2013. Ampure bead purification (Beckman Coulter, catalog # A63881) as per manufacturer’s instructions.
Nextera tagmentation


title: GSM_LC_45_55_2


title: HNSCC_045_TUMOUR

description:
Library name: 045_TUMOUR
26 OC


title: 15243X241_blastomere_25F_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_043_TME

description:
Library name: 043_TME
29 OC


title: 15243X242_blastomere_25G_type_SCNT_cell_number_8

description: cellnumber 8


title: GSM_LC_45_4


title: HNSCC_043_TUMOUR

description:
Library name: 043_TUMOUR
29 OC


title: 15243X240_blastomere_25E_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_046_TME

description:
Library name: 046_TME
25 OC


title: 15244X005_blastomere_53F_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X238_blastomere_25C_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X237_blastomere_25B_type_SCNT_cell_number_8

description: cellnumber 8


title: GSM_LC_3T3_5


title: HNSCC_041_TME

description:
Library name: 041_TME
31 F


title: 15243X236_blastomere_25A_type_SCNT_cell_number_8

description: cellnumber 8


title: GSM_LC_3T3_3


title: 15243X235_blastomere_24G_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X233_blastomere_24E_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X232_blastomere_24D_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X234_blastomere_24F_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_040_TME

description:
Library name: 040_TME
33 F


title: 15243X231_blastomere_24C_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_040_TUMOUR

description:
Library name: 040_TUMOUR
33 F


title: Raw264.7 cells, Samsn1 konckout, E.coli treated3

city: Chengdu

first: Yao

state: Sichuan province

address: No. 37 Guoxue Lane, Wuhou District

department: critical care medicine

institute: West China Hospital of Sichuan University

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm 10
Supplementary files format and content: gene count for each sample

growth_protocol: Raw264.7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the constrction of sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

treatment_protocol: E. coli was added to the cells in a 10:1 ratio and treated for 1h

value: murine macrophage cell line

value: Samsn1 knockout

value: E.coli treated


title: Raw264.7 cells, Samsn1 konckout, E.coli treated2


title: 15243X230_blastomere_24B_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_039_TME

description:
Library name: 039_TME
34 F


title: Raw264.7 cells, Samsn1 konckout, E.coli treated1


title: 15243X228_blastomere_23G_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X227_blastomere_23F_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X226_blastomere_23E_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_038_TME

description:
Library name: 038_TME
35 F


title: 15243X225_blastomere_23D_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X224_blastomere_23C_type_SCNT_cell_number_8

description: cellnumber 8


title: Raw264.7 cells, Samsn1 konckout, untreated2

value: untreated


title: HNSCC_041_TUMOUR

description:
Library name: 041_TUMOUR
31 F


title: 15243X223_blastomere_23B_type_SCNT_cell_number_8

description: cellnumber 8


title: Raw264.7 cells, Samsn1 konckout, untreated1


title: HNSCC_038_TUMOUR

description:
Library name: 038_TUMOUR
35 F


title: HNSCC_037_TME

description:
Library name: 037_TME
37 F


title: 15243X221_blastomere_21G_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X222_blastomere_23A_type_SCNT_cell_number_8

description: cellnumber 8


title: Raw264.7 cells, Samsn1 konckout, untreated3


title: 15243X219_blastomere_21E_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X220_blastomere_21F_type_SCNT_cell_number_8

description: cellnumber 8


title: Raw264.7 cells, wild type, E.coli treated2

value: WT


title: 15243X218_blastomere_21D_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X217_blastomere_21B_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_037_TUMOUR

description:
Library name: 037_TUMOUR
37 F


title: HNSCC_039_TUMOUR

description:
Library name: 039_TUMOUR
34 F


title: GSM_ctrl_3


title: 15243X216_blastomere_20H_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_036_TUMOUR

description:
Library name: 036_TUMOUR
38 F


title: HNSCC_036_TME

description:
Library name: 036_TME
38 F


title: Raw264.7 cells, wild type, E.coli treated3


title: Raw264.7 cells, wild type, E.coli treated1


title: 15243X215_blastomere_20G_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X214_blastomere_20F_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_035_TME

description:
Library name: 035_TME
39 F


title: Raw264.7 cells, wild type, untreated3


title: 15243X213_blastomere_20E_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X212_blastomere_20D_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_035_TUMOUR

description:
Library name: 035_TUMOUR
39 F


title: Raw264.7 cells, wild type, untreated2


title: 15243X211_blastomere_20C_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X210_blastomere_19H_type_SCNT_cell_number_8

description: cellnumber 8


title: Raw264.7 cells, wild type, untreated1


title: 15243X209_blastomere_19G_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_033_TME

description:
Library name: 033_TME
41 F


title: GlaKO hippocampus

city: Innsbruck

first: Kai

last: Kummer

address: Schoepfstrasse 41/Eg

department: Institute of Physiology

country: Austria

institute: Medical University of Innsbruck

description: 10x Genomics - Chromium Single Cell 3` Library v3.1

data_processing:
Quality control of sequenced reads was performed using Fast QC (Babraham Institute). Sequenced samples were processed using Cell Ranger V.6.0.1 pipeline (10x Genomics) and aligned to the mouse reference genome mm10 (cellranger reference 3.0.0, Ensembl v93 gene annotation). 9’630 (wt) and 8’865 (GlaKO) high quality cells were retrieved, mean reads per cell were 54’848 (wt) and 72’551 (GlaKO), median genes per cell were 1’533 (wt) and 1’426 (GlaKO). Single-cell RNA-seq data were further analyzed in R v.4.1.3 using Seurat V4 r-package (46). Filtering parameters were min.cells = 3; min.features = 200; expression = nFeature_RNA > 1000, percent.mt < 5. Data normalization was based on global-scaling method “LogNormalize”, scale.factor = 10’000. Populations labeled as singlets by DoubletFinder were used in the downstream analysis. Datasets were integrated with the mouse brain atlas (51). Epithelial-related cells that did not integrate to the mouse brain atlas database were excluded from downstream analysis (Fig. S1A). After filtering, a total of 2’821 wt and 3’758 GlaKO cells were further analyzed. Both datasets were merged and highly variable genes were detected using FindVariableFeatures (selection.method = "vst", nfeatures = 2000). Thirteen clusters were detected by a shared nearest neighbor clustering algorithm in FindClusters function, using the 20 first PCA dimensions and resolution of 0.5. Top 100 markers of each cluster were used to identify cell populations based on previous scRNA-seq datasets (47-50) (Fig. S1B and S1C). Neuronal clusters identification was based on the mouse brain atlas (51) (Fig. S1D). Differential expression analysis (DEA) was used to compare cell populations between wt and GlaKO, using MAST (134) test on normalized counts. Pathway and enrichment analysis of significant dysregulated genes (p_val_adj<0.1) was performed using clusterProfiler R package (135).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain, hippocampus

extract_protocol:
Prior to hippocampal collection, animals (57 weeks old GlaKO and littermate controls) were anesthetized using a mix of xylazine 10 mg/kg and ketamine 100 mg/kg and transcardially perfused with PBS to washout the blood. Hippocampi were dissected in PBS on ice and dissociated using the Adult Dissociation Kit (130-107-677, Miltenyi Biotec). Briefly, hippocampi were transferred into a gentleMACS C tube containing 1900 μl of buffer Z and 50 μl of enzyme P. Before attaching the C tube to the gentleMACS Octo Dissociator, 20 μl of buffer Y and 10 μl of enzyme Z were added. The suspension was passed through a MACS SmartStrainer (70 μm) placed on a 50 mL tube on ice. Cells were centrifuged at 300xg for 10 min at 4°C and resuspended in 1550 μl of cold PBS. To remove cell debris after dissociation, 450 μL of Debri Removal Solution were added to prepare a density gradient, overlaid with 2 mL of cold PBS. After centrifugation at 3000xg and 4°C for 10 min, the two top layers were discarded and the pellet was washed and resuspended in Dounce buffer [15 mM HEPES, 0.6% (w/v) Glucose in Hank’s Balance Salt Solution, H8264, Sigma). Viable cells exclusion was performed by FACS cell sorting (FACSAria, BD Biosciences) using 7-AAD dye (1 μg/mL, V35123, Invitrogen).
Cell suspensions were processed to generate stable cDNA libraries. For every sample, 10’000 cells were loaded into a Chromium Single Cell A Chip (10x Genomics) and processed according to the manufacturer’s instructions. The sequencing library was generated with the 10x Genomics Chromium and Single Cell 3` Library v3.1 technology was used for single cell barcoding. Sequencing of the library pool was performed on the Illumina NovaSeq 6000 next generation sequencing system with asymmetric paired-end reads. Demultiplexing of the Illumina sequencer's base call files (BCLs) into FASTQ files was performed using the 10x Genomics package Cell Ranger V.4.0 with the mkfastq pipeline.

value: brain, hippocampus

value: GlaKO


title: 15243X208_blastomere_19F_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X239_blastomere_25D_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X205_blastomere_19C_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_032_TME

description:
Library name: 032_TME
42 F


title: MC38 cells Nuclear, sgAlyref, rep2

molecule: nuclear RNA

source_name: MC38 cells

extract_protocol:
Total RNA was extracted using the Trizol method, followed by purification and concentration with an RNA Clean & Concentrator kit. mRNA was isolated from total RNA using poly-T oligo-attached magnetic beads, ensuring enrichment of polyadenylated mRNA transcripts.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: MC38 cells


title: 15243X206_blastomere_19D_type_SCNT_cell_number_8

description: cellnumber 8

source_name: SCNT


title: wt hippocampus

value: wt


title: HNSCC_033_TUMOUR

description:
Library name: 033_TUMOUR
41 F


title: 15243X204_blastomere_19B_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X202_blastomere_18H_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X203_blastomere_19A_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X201_blastomere_18G_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_031_TME

description:
Library name: 031_TME
44 F


title: 15243X200_blastomere_18F_type_SCNT_cell_number_8

description: cellnumber 8


title: MC38 cells Nuclear, sgAlyref, rep1


title: MC38 cells Nuclear, sgDdx39a, rep2


title: HNSCC_031_TUMOUR

description:
Library name: 031_TUMOUR
44 F


title: MC38 cells Nuclear, sgDdx39a, rep1


title: 15243X198_blastomere_18D_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X199_blastomere_18E_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X196_blastomere_18B_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X195_blastomere_18A_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_030_TUMOUR

description:
Library name: 030_TUMOUR
45 F


title: 15243X197_blastomere_18C_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X207_blastomere_19E_type_SCNT_cell_number_8

description: cellnumber 8


title: MC38 cells Nuclear, sgCtrl, rep1


title: HNSCC_029_TUMOUR

description:
Library name: 029_TUMOUR
46 F


title: HNSCC_029_TME

description:
Library name: 029_TME
46 F


title: 15243X192_blastomere_17C_type_SCNT_cell_number_8

description: cellnumber 8


title: MC38 cells Cytoplasm, sgAlyref, rep2


title: 15243X190_blastomere_16H_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_028_TME

description:
Library name: 028_TME
49 F


title: MC38 cells Nuclear, sgCtrl, rep2


title: 15243X188_blastomere_16F_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_030_TME

description:
Library name: 030_TME
45 F


title: 15243X194_blastomere_17E_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_028_TUMOUR

description:
Library name: 028_TUMOUR
49 F


title: HNSCC_032_TUMOUR

description:
Library name: 032_TUMOUR
42 F


title: MC38 cells Cytoplasm, sgDdx39a, rep1


title: MC38 cells Cytoplasm, sgAlyref, rep1


title: HNSCC_026_TME

description:
Library name: 026_TME
51 F


title: 15243X186_blastomere_16D_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X187_blastomere_16E_type_SCNT_cell_number_8

description: cellnumber 8


title: MC38 cells Cytoplasm, sgCtrl, rep2


title: 15243X193_blastomere_17D_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_026_TUMOUR

description:
Library name: 026_TUMOUR
51 F


title: MC38 cells Cytoplasm, sgCtrl, rep1


title: 15243X182_blastomere_15G_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X191_blastomere_17B_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X184_blastomere_16B_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X181_blastomere_15F_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X180_blastomere_15E_type_SCNT_cell_number_8

description: cellnumber 8


title: MC38 cells, sgAlyref, rep2


title: 15243X185_blastomere_16C_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_025_TME

description:
Library name: 025_TME
52 F


title: MC38 cells Cytoplasm, sgDdx39a, rep2


title: HNSCC_025_TUMOUR

description:
Library name: 025_TUMOUR
52 F


title: 15243X189_blastomere_16G_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_024_TME

description:
Library name: 024_TME
54 F


title: 15243X177_blastomere_15B_type_SCNT_cell_number_8

description: cellnumber 8


title: MC38 cells, sgAlyref, rep1


title: 15243X178_blastomere_15C_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X176_blastomere_15A_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X175_blastomere_109D_type_SCNT_cell_number_4

description: cellnumber 4


title: MC38 cells, sgDdx39a, rep2


title: MC38 cells, sgDdx39a, rep1


title: 15243X174_blastomere_109C_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X183_blastomere_16A_type_SCNT_cell_number_8

description: cellnumber 8


title: HNSCC_023_TUMOUR

description:
Library name: 023_TUMOUR
55 F


title: MC38 cells, sgCtrl, rep2


title: 15243X229_blastomere_24A_type_SCNT_cell_number_8

description: cellnumber 8


title: 15243X172_blastomere_109A_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X179_blastomere_15D_type_SCNT_cell_number_8

description: cellnumber 8


title: MC38 cells, sgCtrl, rep1


title: HNSCC_023_TME

description:
Library name: 023_TME
55 F


title: HNSCC_022_TME

description:
Library name: 022_TME
57 F


title: B16-F10 cells Nuclear, sgAlyref treated with Decitabine, rep2

value: B16-F10 cells


title: 15243X168_blastomere_108A_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_022_TUMOUR

description:
Library name: 022_TUMOUR
57 F


title: 15243X169_blastomere_108B_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_021_TME

description:
Library name: 021_TME
60 F


title: B16-F10 cells Nuclear, sgAlyref treated with Decitabine, rep1


title: 15243X165_blastomere_107B_type_SCNT_cell_number_4

description: cellnumber 4


title: B16-F10 cells Nuclear, sgCtrl treated with Decitabine, rep4


title: 15243X164_blastomere_107A_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X166_blastomere_107C_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_024_TUMOUR

description:
Library name: 024_TUMOUR
54 F


title: 15243X170_blastomere_108C_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_021_TUMOUR

description:
Library name: 021_TUMOUR
60 F


title: 15243X173_blastomere_109B_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X163_blastomere_106D_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_019_TME

description:
Library name: 019_TME
63 L


title: 15243X162_blastomere_106C_type_SCNT_cell_number_4

description: cellnumber 4


title: B16-F10 cells Nuclear, sgCtrl treated with Decitabine, rep3


title: 15243X171_blastomere_108D_type_SCNT_cell_number_4

description: cellnumber 4


title: B16-F10 cells Cytoplasm, sgAlyref treated with Decitabine, rep2


title: 15243X167_blastomere_107D_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X159_blastomere_105D_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X157_blastomere_105B_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X158_blastomere_105C_type_SCNT_cell_number_4

description: cellnumber 4


title: B16-F10 cells Cytoplasm, sgAlyref treated with Decitabine, rep1


title: 15243X160_blastomere_106A_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_018_TUMOUR

description:
Library name: 018_TUMOUR
67 L


title: HNSCC_019_TUMOUR

description:
Library name: 019_TUMOUR
63 L


title: 15243X155_blastomere_90D_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X156_blastomere_105A_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_018_TME

description:
Library name: 018_TME
67 L


title: 15243X153_blastomere_90B_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_017_TME

description:
Library name: 017_TME
68 L


title: B16-F10 cells Cytoplasm, sgCtrl treated with Decitabine, rep4


title: B16-F10 cells Cytoplasm, sgCtrl treated with Decitabine, rep3


title: 15243X154_blastomere_90C_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X152_blastomere_90A_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X151_blastomere_89D_type_SCNT_cell_number_4

description: cellnumber 4


title: B16-F10 cells, sgAlyref treated with Decitabine, rep1


title: B16-F10 cells, sgAlyref treated with Decitabine, rep2


title: 15243X150_blastomere_89C_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X161_blastomere_106B_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_017_TUMOUR

description:
Library name: 017_TUMOUR
68 L


title: HNSCC_016_TME

description:
Library name: 016_TME
69 L


title: B16-F10 cells, sgCtrl treated with Decitabine, rep4


title: 15243X148_blastomere_89A_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X147_blastomere_88D_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_016_TUMOUR

description:
Library name: 016_TUMOUR
69 L


title: B16-F10 cells, sgCtrl treated with Decitabine, rep3


title: 15243X146_blastomere_88C_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_015_TME

description:
Library name: 015_TME
70 L


title: 15243X144_blastomere_88A_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_015_TUMOUR

description:
Library name: 015_TUMOUR
70 L


title: B16-F10 cells Nuclear, sgDdx39a treated with Decitabine, rep2


title: 15243X142_blastomere_87C_type_SCNT_cell_number_4

description: cellnumber 4


title: B16-F10 cells Nuclear, sgCtrl treated with Decitabine, rep2


title: 15243X140_blastomere_87A_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X141_blastomere_87B_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X143_blastomere_87D_type_SCNT_cell_number_4

description: cellnumber 4


title: B16-F10 cells Nuclear, sgDdx39a treated with Decitabine, rep1


title: HNSCC_014_TME

description:
Library name: 014_TME
71 L