title: HNSCC_014_TUMOUR

description:
Library name: 014_TUMOUR
71 L


title: 15243X137_blastomere_83B_type_SCNT_cell_number_4

status: Public on Jun 01 2025

type: SRA

city: dallas

first: Edward

last: Grow

state: TEXAS

address: 7053 beltau lane

country: USA

institute: UTSW

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

molecule: genomic DNA

organism: Bos taurus

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.

tag: cell type

value: SCNT


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

city: tianjin

first: junying

last: ma

address: Heping District Meteorological Observatory Road

country: China

institute: Tianjin Medical University

library_source: transcriptomic

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.

molecule: cytoplasmic RNA

organism: Mus musculus

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. 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.

tag: cell line

value: B16-F10 cells


title: HNSCC_013_TME

city: Brisbane

first: Arutha

last: Kulasinghe

state: QLD

address: 37 kent st

country: Australia

institute: University of Queensland

description:
Library name: 013_TME
72 L

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

molecule: total RNA

organism: Homo sapiens

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

tag: tissue

value: Lung


title: 15243X149_blastomere_89B_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_013_TUMOUR

description:
Library name: 013_TUMOUR
72 L


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


title: 15243X136_blastomere_83A_type_SCNT_cell_number_4

description: cellnumber 4


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

molecule: nuclear RNA


title: HNSCC_011_TME

description:
Library name: 011_TME
74 L


title: 15243X145_blastomere_88B_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X133_blastomere_63B_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X138_blastomere_83C_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X132_blastomere_63A_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X134_blastomere_63C_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X131_blastomere_49D_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_011_TUMOUR

description:
Library name: 011_TUMOUR
74 L


title: 15243X139_blastomere_83D_type_SCNT_cell_number_4

description: cellnumber 4


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


title: 15243X129_blastomere_49B_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X128_blastomere_49A_type_SCNT_cell_number_4

description: cellnumber 4


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

molecule: polyA RNA


title: 15243X127_blastomere_48D_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_010_TUMOUR

description:
Library name: 010_TUMOUR
76 L


title: 15243X130_blastomere_49C_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_010_TME

description:
Library name: 010_TME
76 L


title: 15243X126_blastomere_48C_type_SCNT_cell_number_4

description: cellnumber 4


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


title: HNSCC_009_TUMOUR

description:
Library name: 009_TUMOUR
77 L


title: 15243X123_blastomere_47D_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X125_blastomere_48B_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X124_blastomere_48A_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_008_TME

description:
Library name: 008_TME
78 L


title: 15243X122_blastomere_47C_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X135_blastomere_63D_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X121_blastomere_47B_type_SCNT_cell_number_4

description: cellnumber 4


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


title: Carm1-knockout B16-F10 cells Nuclear, sgAlyref, rep2


title: 15243X120_blastomere_47A_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X119_blastomere_46D_type_SCNT_cell_number_4

description: cellnumber 4


title: Carm1-knockout B16-F10 cells Nuclear, sgAlyref, rep1


title: 15243X117_blastomere_46B_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X118_blastomere_46C_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_007_TME

description:
Library name: 007_TME
80 L


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


title: Carm1-knockout B16-F10 cells Nuclear, sgCtrl, rep4


title: 15243X115_blastomere_45D_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X116_blastomere_46A_type_SCNT_cell_number_4

description: cellnumber 4


title: Carm1-knockout B16-F10 cells Nuclear, sgCtrl, rep3


title: 15243X114_blastomere_45C_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_007_TUMOUR

description:
Library name: 007_TUMOUR
80 L


title: HNSCC_006_TME

description:
Library name: 006_TME
82 L


title: 15243X113_blastomere_45B_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_006_TUMOUR

description:
Library name: 006_TUMOUR
82 L


title: 15243X112_blastomere_45A_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_008_TUMOUR

description:
Library name: 008_TUMOUR
78 L


title: Carm1-knockout B16-F10 cells Cytoplasm, sgAlyref, rep1


title: HNSCC_009_TME

description:
Library name: 009_TME
77 L


title: 15243X110_blastomere_44C_type_SCNT_cell_number_4

description: cellnumber 4


title: Carm1-knockout B16-F10 cells Cytoplasm, sgCtrl, rep4


title: Carm1-knockout B16-F10 cells Cytoplasm, sgCtrl, rep3


title: 15243X108_blastomere_44A_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X106_blastomere_43C_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_005_TME

description:
Library name: 005_TME
83 L


title: Carm1-knockout B16-F10 cells Cytoplasm, sgAlyref, rep2


title: 15243X104_blastomere_43A_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X105_blastomere_43B_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X107_blastomere_43D_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_004_TUMOUR

description:
Library name: 004_TUMOUR
86 L


title: 15243X103_blastomere_42D_type_SCNT_cell_number_4

description: cellnumber 4


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


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


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


title: 15243X101_blastomere_42B_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_003_TME

description:
Library name: 003_TME
87 L


title: 15243X102_blastomere_42C_type_SCNT_cell_number_4

description: cellnumber 4


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


title: 15243X099_blastomere_41D_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X098_blastomere_41C_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_003_TUMOUR

description:
Library name: 003_TUMOUR
87 L


title: 15243X109_blastomere_44B_type_SCNT_cell_number_4

description: cellnumber 4


title: Carm1-knockout B16-F10 cells Nuclear, sgDdx39a, rep2


title: HNSCC_002_TME

description:
Library name: 002_TME
90 L


title: 15243X111_blastomere_44D_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X096_blastomere_41A_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X097_blastomere_41B_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_002_TUMOUR

description:
Library name: 002_TUMOUR
90 L


title: Carm1-knockout B16-F10 cells Nuclear, sgDdx39a, rep1


title: HNSCC_004_TME

description:
Library name: 004_TME
86 L


title: 15243X095_blastomere_38D_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_001_TME

description:
Library name: 001_TME
89 L


title: 15243X094_blastomere_38C_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X093_blastomere_38B_type_SCNT_cell_number_4

description: cellnumber 4


title: HNSCC_001_TUMOUR

description:
Library name: 001_TUMOUR
89 L


title: Carm1-knockout B16-F10 cells Nuclear, sgCtrl, rep2


title: 15243X092_blastomere_38A_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X091_blastomere_37D_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X100_blastomere_42A_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X090_blastomere_37C_type_SCNT_cell_number_4

description: cellnumber 4


title: Carm1-knockout B16-F10 cells Cytoplasm, sgDdx39a, rep2


title: HNSCC_005_TUMOUR

description:
Library name: 005_TUMOUR
83 L


title: 15243X089_blastomere_37B_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X088_blastomere_37A_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X087_blastomere_36D_type_SCNT_cell_number_4

description: cellnumber 4


title: Myometrium from testosterone treated patient (MyoT), patient MP565

city: Grand Rapids

first: Jose

middle: M

last: Teixeira

state: MI

address: 400 Monroe Ave NW

department: Ob/Gyn

institute: Michigan State University

description: Library name: MP565T

data_processing:
Reads were trimmed for quality and adapters using TrimGalore (version 0.6.5)
Trimmed reads were mapped to Homo sapiens (human) using STAR (version 2.7.9a)
Overlapping Ensembl annotations (version 99)
Analysis was performed using edgeR-robust
Assembly: GRCh38 (hg38)
Supplementary files format and content: txt file with the raw cout per gene

source_name: myometrium

extract_protocol:
RNA was isolated using trizol or colums from the Qiagen RNAeasy kit
paired-end (2 × 100 bp) RNA-sequencing on an Illumina NextSeq 6000 or paired-end (2 × 75 bp) RNA-sequencing on an Illumina NextSeq 500

value: myometrium

tag: race

value: C

tag: age

tag: treatment

tag: batch


title: Carm1-knockout B16-F10 cells Cytoplasm, sgDdx39a, rep1


title: Myometrium from testosterone treated patient (MyoT), patient MP562

description: Library name: MP562T

value: AA


title: Myometrium from testosterone treated patient (MyoT), patient MP554

description: Library name: MP554T


title: 15243X084_blastomere_36A_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X085_blastomere_36B_type_SCNT_cell_number_4

description: cellnumber 4


title: 15243X086_blastomere_36C_type_SCNT_cell_number_4

description: cellnumber 4


title: Myometrium from testosterone treated patient (MyoT), patient MP551

description: Library name: MP551T


title: Carm1-knockout B16-F10 cells Cytoplasm, sgCtrl, rep2


title: Carm1-knockout B16-F10 cells Cytoplasm, sgCtrl, rep1


title: 15243X082_blastomere_92D_type_SCNT_cell_number_5

description: cellnumber 5


title: Myometrium from testosterone treated patient (MyoT), patient MP550

description: Library name: MP550T


title: Carm1-knockout B16-F10 cells, sgDdx39a, rep2


title: 15243X081_blastomere_92C_type_SCNT_cell_number_5

description: cellnumber 5


title: 15243X083_blastomere_92E_type_SCNT_cell_number_5

description: cellnumber 5


title: 15243X080_blastomere_92B_type_SCNT_cell_number_5

description: cellnumber 5


title: Carm1-knockout B16-F10 cells Nuclear, sgCtrl, rep1


title: Myometrium from testosterone treated patient (MyoT), patient MP545

description: Library name: MP545T


title: 15243X079_blastomere_92A_type_SCNT_cell_number_5

description: cellnumber 5


title: Carm1-knockout B16-F10 cells, sgDdx39a, rep1


title: 15243X078_blastomere_91E_type_SCNT_cell_number_5

description: cellnumber 5


title: 15243X077_blastomere_91D_type_SCNT_cell_number_5

description: cellnumber 5


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


title: Myometrium from testosterone treated patient (MyoT), patient MP542

description: Library name: MP542T


title: 15243X076_blastomere_91C_type_SCNT_cell_number_5

description: cellnumber 5


title: Myometrium from fibroid patient (MyoF), patient MP411

description: Library name: MP411N

value: Myometrium from fibroid patient


title: 15243X075_blastomere_91B_type_SCNT_cell_number_5

description: cellnumber 5


title: Myometrium from fibroid patient (MyoF), patient MP541

description: Library name: MP541N


title: 15243X073_blastomere_51E_type_SCNT_cell_number_5

description: cellnumber 5


title: 15243X074_blastomere_91A_type_SCNT_cell_number_5

description: cellnumber 5


title: B16-F10 cells Nuclear, sgCarm1, rep2


title: 15243X072_blastomere_51D_type_SCNT_cell_number_5

description: cellnumber 5


title: 15243X071_blastomere_51C_type_SCNT_cell_number_5

description: cellnumber 5


title: Myometrium from fibroid patient (MyoF), patient MP521

description: Library name: MP521N


title: B16-F10 cells Nuclear, sgCarm1, rep1


title: 15243X069_blastomere_51A_type_SCNT_cell_number_5

description: cellnumber 5


title: 15243X068_blastomere_39E_type_SCNT_cell_number_5

description: cellnumber 5


title: Myometrium from fibroid patient (MyoF), patient MP456

description: Library name: MP456N

value: A


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


title: 15243X070_blastomere_51B_type_SCNT_cell_number_5

description: cellnumber 5


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


title: Myometrium from fibroid patient (MyoF), patient MP416

description: Library name: MP416N


title: 15243X066_blastomere_39A_type_SCNT_cell_number_5

description: cellnumber 5


title: 15243X065_blastomere_110C_type_SCNT_cell_number_3

description: cellnumber 3


title: 15243X064_blastomere_110B_type_SCNT_cell_number_3

description: cellnumber 3


title: B16-F10 cells Cytoplasm, sgCarm1, rep2


title: Myometrium from fibroid patient (MyoF), patient MP396

description: Library name: MP396N


title: 15243X063_blastomere_110A_type_SCNT_cell_number_3

description: cellnumber 3


title: 15243X062_blastomere_82C_type_SCNT_cell_number_3

description: cellnumber 3


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


title: Myometrium from fibroid patient (MyoF), patient MP380

description: Library name: MP380N


title: 15243X061_blastomere_82B_type_SCNT_cell_number_3

description: cellnumber 3


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


title: 15243X058_blastomere_103A_type_SCNT_cell_number_2

description: cellnumber 2


title: Myometrium from fibroid patient (MyoF), patient MP369

description: Library name: MP369N


title: 15243X057_blastomere_102B_type_SCNT_cell_number_2

description: cellnumber 2


title: B16-F10 cells, sgCarm1, rep2


title: 15243X067_blastomere_39C_type_SCNT_cell_number_5

description: cellnumber 5


title: 15243X060_blastomere_82A_type_SCNT_cell_number_3

description: cellnumber 3


title: 15243X055_blastomere_101B_type_SCNT_cell_number_2

description: cellnumber 2


title: Myometrium from fibroid patient (MyoF), patient MP523

description: Library name: MP423N


title: 15243X059_blastomere_103B_type_SCNT_cell_number_2

description: cellnumber 2


title: 15243X056_blastomere_102A_type_SCNT_cell_number_2

description: cellnumber 2


title: Myometrium from fibroid patient (MyoF), patient MP295

description: Library name: MP295N


title: B16-F10 cells, sgCarm1, rep1


title: 15243X054_blastomere_101A_type_SCNT_cell_number_2

description: cellnumber 2


title: 15243X053_blastomere_100B_type_SCNT_cell_number_2

description: cellnumber 2


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


title: Myometrium from fibroid patient (MyoF), patient MP291

description: Library name: MP291N


title: Myometrium from fibroid patient (MyoF), patient MP286

description: Library name: MP286N

value: H


title: 15243X051_blastomere_99B_type_SCNT_cell_number_2

description: cellnumber 2


title: 15243X050_blastomere_98A_type_SCNT_cell_number_2

description: cellnumber 2


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


title: Myometrium from fibroid patient (MyoF), patient MP282

description: Library name: MP282N


title: 15243X052_blastomere_100A_type_SCNT_cell_number_2

description: cellnumber 2


title: Myometrium from fibroid patient (MyoF), patient MP381

description: Library name: MP381N


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


title: 15243X049_blastomere_97B_type_SCNT_cell_number_2

description: cellnumber 2


title: B16-F10 cells, overexpressed exogenous Ddx39a, rep2


title: 15243X048_blastomere_97A_type_SCNT_cell_number_2

description: cellnumber 2


title: 15243X047_blastomere_96B_type_SCNT_cell_number_2

description: cellnumber 2


title: B16-F10 cells, overexpressed exogenous Ddx39a, rep1


title: Myometrium from fibroid patient (MyoF), patient MP278

description: Library name: MP278N


title: Myometrium from fibroid patient (MyoF), patient MP142

description: Library name: MP142N


title: 15243X045_blastomere_95B_type_SCNT_cell_number_2

description: cellnumber 2


title: Myometrium from fibroid patient (MyoF), patient MP136

description: Library name: MP136N


title: 15243X046_blastomere_96A_type_SCNT_cell_number_2

description: cellnumber 2


title: B16-F10 cells, transfection control, rep2


title: B16-F10 cells Cytoplasm, sgCarm1, rep1


title: 15243X043_blastomere_86A_type_SCNT_cell_number_2

description: cellnumber 2


title: 15243X042_blastomere_85B_type_SCNT_cell_number_2

description: cellnumber 2


title: Myometrium from fibroid patient (MyoF), patient MP61

description: Library name: MP61


title: 15243X044_blastomere_86B_type_SCNT_cell_number_2

description: cellnumber 2


title: B16-F10 cells, transfection control, rep1


title: Sorted B16-F10 cells, sgCarm1, rep2


title: 15243X041_blastomere_85A_type_SCNT_cell_number_2

description: cellnumber 2


title: 15243X039_blastomere_84A_type_SCNT_cell_number_2

description: cellnumber 2


title: 15243X038_blastomere_81B_type_SCNT_cell_number_2

description: cellnumber 2


title: Myometrium from fibroid patient (MyoF), patient HF29

description: Library name: HF29


title: Myometrium from fibroid patient (MyoF), patient HF33

description: Library name: HF33


title: Sorted B16-F10 cells, sgCarm1, rep1


title: 15243X040_blastomere_84B_type_SCNT_cell_number_2

description: cellnumber 2


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


title: 15243X036_blastomere_79B_type_SCNT_cell_number_2

description: cellnumber 2


title: 15243X034_blastomere_78B_type_SCNT_cell_number_2

description: cellnumber 2


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


title: 15243X035_blastomere_79A_type_SCNT_cell_number_2

description: cellnumber 2


title: Myometrium from fibroid patient (MyoF), patient HF27

description: Library name: HF27


title: 15243X033_blastomere_78A_type_SCNT_cell_number_2

description: cellnumber 2


title: Carm1-knockout B16-F10 cells, Input

library_source: genomic

data_processing:
In our ChIP-Rx paired-end sequencing protocol, we initially subjected the reads to an optimized trimming process using Trim Galore (v0.6.6). Following this, the trimmed reads were aligned to the mouse mm10 and human hg38 reference genomes using Bowtie2 (v2.4.3), strictly adhering to the default parameters. To maintain data integrity and quality, we meticulously filtered out unmapped reads, those with low mapping quality (MAPQ < 30), and PCR duplicates, employing SAMtools (v1.9) and Picard (v2.26.5) for this purpose. Peak calling was conducted with MACS2 (v2.2.7.1), setting the FDR threshold at 0.05. For normalization, we calculated the factor alpha (1e6/hg38_count) based on the count of spike-in hg38 reads as determined by SAMtools (v1.9). The culmination of our workflow entailed the generation of normalized bigWig files, a task adeptly accomplished with the aid of deepTools (version 3.5.0).
Assembly: mm10
Supplementary files format and content: bigWig files generated by deepTools (version 3.5.0).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
DNA libraries were prepared for sequencing according to standard Illumina protocols.

tag: antibody

tag: genotype


title: 15243X032_blastomere_77B_type_SCNT_cell_number_2

description: cellnumber 2


title: Myometrium from fibroid patient (MyoF), patient HF25

description: Library name: HF25

value: Multi


title: 15243X031_blastomere_77A_type_SCNT_cell_number_2

description: cellnumber 2


title: Wild-type B16-F10 cells, Input

value: Wild-type


title: 15243X029_blastomere_75B_type_SCNT_cell_number_2

description: cellnumber 2


title: Carm1-knockout B16-F10 cells, H3K27ac


title: 15243X037_blastomere_80A_type_SCNT_cell_number_2

description: cellnumber 2


title: 15243X027_blastomere_74B_type_SCNT_cell_number_2

description: cellnumber 2


title: Myometrium from fibroid patient (MyoF), patient HF28

description: Library name: HF28


title: 15243X026_blastomere_74A_type_SCNT_cell_number_2

description: cellnumber 2


title: Carm1-knockout B16-F10 cells, H3K4me3


title: Myometrium from fibroid patient (MyoF), patient HF19

description: Library name: HF19


title: Wild-type B16-F10 cells, H3K27ac


title: 15243X025_blastomere_73B_type_SCNT_cell_number_2

description: cellnumber 2


title: Myometrium from fibroid patient (MyoF), patient HF18

description: Library name: HF18


title: 15243X024_blastomere_73A_type_SCNT_cell_number_2

description: cellnumber 2


title: 15243X022_blastomere_72A_type_SCNT_cell_number_2

description: cellnumber 2


title: Wild-type B16-F10 cells, H3K4me3


title: 15243X020_blastomere_70B_type_SCNT_cell_number_2

description: cellnumber 2


title: Myometrium from fibroid patient (MyoF), patient HF15

description: Library name: HF15


title: 15243X021_blastomere_71A_type_SCNT_cell_number_2

description: cellnumber 2


title: 15243X019_blastomere_70A_type_SCNT_cell_number_2

description: cellnumber 2


title: 15243X030_blastomere_76A_type_SCNT_cell_number_2

description: cellnumber 2


title: Sff_6

city: Ann Arbor

first: Karan

last: Bedi

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: TAM-induced gene deletion

value: colon


title: 15243X018_blastomere_69B_type_SCNT_cell_number_2

description: cellnumber 2


title: Myometrium from fibroid patient (MyoF), patient HF24

description: Library name: HF24


title: Myometrium from fibroid patient (MyoF), patient HF13

description: Library name: HF13


title: 15243X017_blastomere_69A_type_SCNT_cell_number_2

description: cellnumber 2


title: Myometrium from fibroid patient (MyoF), patient HF23

description: Library name: HF23


title: 15243X028_blastomere_75A_type_SCNT_cell_number_2

description: cellnumber 2


title: Sff_4


title: 15243X016_blastomere_68B_type_SCNT_cell_number_2

description: cellnumber 2


title: Myometrium from fibroid patient (MyoF), patient HF12

description: Library name: HF12


title: Sff_3


title: 15243X023_blastomere_72B_type_SCNT_cell_number_2

description: cellnumber 2


title: 15243X014_blastomere_35A_type_SCNT_cell_number_2

description: cellnumber 2


title: Myometrium from fibroid patient (MyoF), patient HF10

description: Library name: HF10


title: 15243X013_blastomere_34A_type_SCNT_cell_number_2

description: cellnumber 2


title: Sff_2


title: Sff_1


title: Myometrium from fibroid patient (MyoF), patient HFB

description: Library name: HFB


title: Myometrium from fibroid patient (MyoF), patient HF14

description: Library name: HF14


title: 15243X011_blastomere_32A_type_SCNT_cell_number_2

description: cellnumber 2


title: Sff_5


title: 15243X012_blastomere_33B_type_SCNT_cell_number_2

description: cellnumber 2


title: Myometrium from fibroid patient (MyoF), patient HF8

description: Library name: HF8


title: Myometrium from fibroid patient (MyoF), patient HF9

description: Library name: HF9


title: 15243X007_blastomere_30A_type_SCNT_cell_number_2

description: cellnumber 2


title: 15243X009_blastomere_31A_type_SCNT_cell_number_2

description: cellnumber 2


title: Control_6

value: Soxflox/+(no Cre)

value: No TAM treatment


title: Control_5


title: Myometrium from fibroid patient (MyoF), patient HF4

description: Library name: HF4


title: 15243X006_blastomere_29B_type_SCNT_cell_number_2

description: cellnumber 2


title: Control_4


title: Myometrium from fibroid patient (MyoF), patient HF2

description: Library name: HF2


title: 15243X003_blastomere_28A_type_SCNT_cell_number_2

description: cellnumber 2


title: 15243X005_blastomere_29A_type_SCNT_cell_number_2

description: cellnumber 2


title: 15243X004_blastomere_28B_type_SCNT_cell_number_2

description: cellnumber 2


title: Control_3

value: Apcflox/flox(no Cre)


title: 15243X002_blastomere_27B_type_SCNT_cell_number_2

description: cellnumber 2


title: 15243X001_blastomere_27A_type_SCNT_cell_number_2

description: cellnumber 2


title: Myometrium from fibroid patient (MyoF), patient HF1

description: Library name: HF1


title: 15243X010_blastomere_31B_type_SCNT_cell_number_2

description: cellnumber 2


title: 15243X015_blastomere_68A_type_SCNT_cell_number_2

description: cellnumber 2


title: Control_2


title: 2-cell_SCNT_ATAC-seq_rep2

data_processing:
reads were trimmed and filtered for quality using BBDuk and FastQC (version 0.10.1).
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 prior to peaks calling (over input DNA for ChIP-seq) with MACS2 'callpeak' (--f BAMPE --B --SPMR)
Assembly: bostau7
Supplementary files format and content: bigwig

source_name: SCNT embryo

growth_protocol: IVF or SCNT embryos were grown in SOF media and cultered under oil at 38.5C

extract_protocol:
mini-elute column (Qiagen MinElutePCR purification Kit , Cat # 28006).
Nextera

treatment_protocol: zona pelucida and polar bodies were removed by pronase treatement, lysed using lysis buffer (10mM Tris-pH=7.4, 10mM MgCl, 0.1% NP-40), and then subjected to Tn5 Tagmentation for 30 min at 37C

value: SCNT embryo

value: wildtype


title: Myometrium from fibroid-free patient (MyoN), patient MP561

description: Library name: MP561M

value: Control myometrium


title: 2-cell_SCNT_ATAC-seq_rep1


title: Aff.Sff_6


title: morula_SCNT_ATAC-seq_rep2

value: morula


title: Control_1


title: morula_SCNT_ATAC-seq_rep1


title: 8-cell_SCNT_ATAC-seq_rep2


title: 8-cell_SCNT_ATAC-seq_rep1


title: Myometrium from fibroid-free patient (MyoN), patient MP552

description: Library name: MP552M

value: myometrium


title: 15243X008_blastomere_30B_type_SCNT_cell_number_2

description: cellnumber 2

value: SCNT


title: 4-cell_SCNT_ATAC-seq_rep1


title: Aff.Sff_4


title: morula_SCNT_ATAC-seq_rep3


title: blast_SCNT_ATAC-seq_rep2

value: blast


title: Myometrium from fibroid-free patient (MyoN), patient MP500

description: Library name: MP500M

value: C


title: blast_SCNT_ATAC-seq_rep1


title: 2-cell_IVF_ATAC-seq_rep2

source_name: IVF embryo

value: IVF embryo


title: Aff.Sff_2


title: Myometrium from fibroid-free patient (MyoN), patient MP499

description: Library name: MP499M


title: 2-cell_IVF_ATAC-seq_rep1


title: Aff.Sff_1


title: blast_IVF_ATAC-seq_rep2


title: Aff_6


title: 4-cell_IVF_ATAC-seq_rep1


title: Myometrium from fibroid-free patient (MyoN), patient MP496

description: Library name: MP496M


title: Aff.Sff_5


title: morula_IVF_ATAC-seq_rep2


title: Aff_5


title: morula_IVF_ATAC-seq_rep1


title: Myometrium from fibroid-free patient (MyoN), patient MP495

description: Library name: MP495M


title: Aff.Sff_3


title: 8-cell_IVF_ATAC-seq_rep2


title: 8-cell_IVF_ATAC-seq_rep1


title: Myometrium from fibroid-free patient (MyoN), patient MP490

description: Library name: MP490M


title: Aff_4


title: 4-cell_IVF_ATAC-seq_rep2


title: blast_IVF_ATAC-seq_rep1


title: BEF_BEF_ATAC-seq_rep1

source_name: fibroblast

value: fibroblast


title: Myometrium from fibroid-free patient (MyoN), patient MP497

description: Library name: MP497M


title: Myometrium from fibroid-free patient (MyoN), patient MP485

description: Library name: MP485M

value: AA


title: Myometrium from fibroid-free patient (MyoN), patient MP502

description: Library name: MP502M


title: Aff_2


title: Aff_3


title: Myometrium from fibroid-free patient (MyoN), patient MP484

description: Library name: MP484M


title: BEF_BEF_ATAC-seq_rep2


title: Aff_1


title: Apcfl_flSox9fl_fl_4

source_name: organoid

value: Apc and Sox9 deletion

value: generated from TAM-treated mice

value: Colon organoid


title: PN_adult_biorep2

first: Eleanor

middle: Josephine

last: Clowney

address: 1105 North University, 4218

department: MCDB

description: gene expression profiling

data_processing:
Galaxy
Reads were groomed using FASTQ Groomer in Galaxy with Input FASTQ quality scores type "Sanger & Illumina 1.8+" and "basic" settings.
Single-end reads were aligned to dm6 using TopHat in Galaxy, with settings "preSet."
Expression of refSeq genes was quantified from TopHat "accepted hits" using Cufflinks, in Galaxy, with default settings.
Assembly: dm6
Supplementary files format and content: microsoft xlsx worksheet containing FPKM values for each sample
Supplementary files format and content: Gene names were mapped from refSeq IDs to refSeq "name2," and FPKM values compiled from each sample type. Values for adult samples are averaged from two biological replicates each.

organism: Drosophila melanogaster

source_name: brain

growth_protocol: Flies were raised on standard cornmeal-agarose with molasses at 25C on a 12 hour light/ dark cycle

extract_protocol:
Cells were sorted into Trizol-LS and stored at -80C until RNA isolation. For RNA extraction, we followed the standard Trizol-LS protocol until the aqueous phase was isolated. We then passed the aqueous phase over Arcturus Picopure columns, including a DNAse treatment on the column.
We quantified total RNA using a BioAnalyzer and aimed for 1ng starting material per library. As insect processing of rRNA makes the “RNA Integrity Number” irrelevant, we visually inspected total RNA profile to assess RNA quality. For each replicate, we matched the amount of total RNA used for library prep across the three cell types, i.e. we matched Kenyon cell and “double negative” RNA amounts to the amount we obtained for olfactory PNs. Total RNA was poly-A selected and libraries were prepared using SmartSeq V2 at the Rockefeller University Genomics Core and sequenced to a depth of 25 million reads using HiSeq 50 SR (adult samples) or NextSeq High Output 75SR (45h APF samples).

treatment_protocol: Male and female brains were dissected, optic lobes removed, and subjected to dissociation and flow cytometry

value: brain

tag: developmental stage

value: adult

tag: Sex

value: pooled male and female


title: PN_adult_biorep1

description: gene expression profiling


title: Myometrium from fibroid-free patient (MyoN), patient MP473

description: Library name: MP473M


title: KC_adult_biorep1

description: gene expression profiling


title: Apcfl_flSox9fl_fl_3


title: Apcfl_flSox9fl_fl_2


title: DN_adult_biorep2

description: gene expression profiling


title: Myometrium from fibroid-free patient (MyoN), patient MP472

description: Library name: MP472M


title: Apcfl_flSox9fl_fl_1


title: DN_adult_biorep1

description: gene expression profiling


title: HAE cells

city: Hannover

first: Chris

last: Lauber

address: Feodor-Lynen Str. 7

country: Germany

institute: TWINCORE Centre for Experimental and Clinical Infection Research

description: Library name: HAE_Mock_24

data_processing:
CLC Genomics Workbench
Assembly: human reference genome hg19
Supplementary files format and content: csv files contain raw counts, TPM, and RPKM values for each sample

source_name: human airway epithelial cells

extract_protocol:
Total RNA from cell lines was isolated using a NucleoSpin RNA kit (Macherey Nagel) according to the instructions of the manufacturer.
RNA quality was checked using an Agilent Bioanalyzer and sequencing libraries were generated using ScriptSeq v2 RNA library preparation kit (Illumina).

value: human airway epithelial cells


title: Hep-2 cells

description: Library name: Hep-2_S9


title: Calu-3 cells

description: Library name: Calu-3_p36_S61


title: Myometrium from fibroid-free patient (MyoN), patient MP459

description: Library name: MP459M


title: Apcfl_fl_4

value: Apc deletion


title: Myometrium from fibroid-free patient (MyoN), patient MP479

description: Library name: MP479M

value: Control myometrium


title: Myometrium from fibroid-free patient (MyoN), patient MP452

description: Library name: MP452M


title: KC_adult_biorep2

description: gene expression profiling


title: Myometrium from fibroid-free patient (MyoN), patient MP478

description: Library name: MP478M


title: A549 cells

description: Library name: A549_S11


title: Apcfl_fl_3


title: A427 cells

description: Library name: A427_S12


title: 16HBE140 cells

description: Library name: 16HBE140_S8


title: Apcfl_fl_2


title: SW1116 xenograft

city: Heidelberg

first: John

last: Mariadason

state: VIC

address: 145 Studley Road

institute: Olivia Newton-John Cancer Research Institute

description: Library name: SW1116x

data_processing:
Raw FASTQ RNA-Seq files were aligned to both the human (hg38) and mouse (mm10) reference genomes using STAR aligner (v2.7.0a). XenofilteR was applied to accurately distinguish RNA sequences of human and mouse origin. Gene-level read counts were then quantified using featureCounts (Subread v1.6.1).
Assembly: HG38 / GRCh38.93
Supplementary files format and content: gene level count data

source_name: Colorectal cancer

extract_protocol:
High Pure RNA isolation kit, Roche
Illumina TruSeq Stranded mRNA

treatment_protocol: Colorectal cancer cell lines were grown as xenografts in Balb/c nu/nu mice until the reached 1 cm3 in size.

value: Colorectal cancer

value: CRC cell line


title: SW620 xenograft

description: Library name: SW620x


title: Apcfl_fl_1


title: Myometrium from fibroid-free patient (MyoN), patient MP450

description: Library name: MP450M

value: myometrium


title: LIM2405 xenograft

description: Library name: LIM2405x


title: Myometrium from fibroid-free patient (MyoN), patient MP408

description: Library name: MP408M


title: IRK_3

city: Guangzhou

first: Xiaolong

last: Li

address: 1838 North Guangzhou Ave

department: Nanfang Hospital

institute: Southern Medical University

data_processing:
Quality control: clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
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)
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for each samples
Supplementary files format and content: tab-delimited text files includes FPKM for each samples

source_name: kidney

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer.

value: kidney

value: FAM5A knockout

value: IRI


title: Elo5_n9

type: RNA

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® ClariomS Rat (LifeTechnologies) at 45°C for 17 hours.  80 ng of total RNA is reverse transcribed following the Ovation PicoSl V2 kit (Tecan). Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Nugen protocol, 3,6 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Nugen). After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® MouseGene2.0 ST  (Affymetrix) at 45°C for 17 hours.

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. RMA normalization is performed using R with Version 18 of Entrezgene CDF brain array.

label: Biotin

source_name: embryonic heart E10.5

label_protocol: 20 ng of total RNA is reverse transcribed following the GeneChip® WT Plus Reagent Kit (Affymetrix) .  Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA polymerase (all these steps are included in the WT cDNA synthesis and amplification kit of Affymetrix). After purification according to Affymetrix protocol, 5.5 ug of Sens Target DNA are fragmented and biotin labelled.

extract_protocol: Trizol extraction

treatment_protocol: No treatment

value: Control

value: embryonic heart


title: Elo5_n2

value: KO


title: Elo5_n3


title: Elo5_n10


title: LS513 xenograft

description: Library name: LS513x


title: LIM1899 xenograft

description: Library name: LIM1899x


title: Myometrium from fibroid-free patient (MyoN), patient MP407

description: Library name: MP407M

value: C


title: Elo5_n6


title: IS2 xenograft

description: Library name: IS2x


title: IRK_2

value: FAM4A knockout


title: Myometrium from fibroid-free patient (MyoN), patient MP402

description: Library name: MP402M


title: Colo320 xenograft

description: Library name: Colo320x


title: Myometrium from fibroid-free patient (MyoN), patient MP399

description: Library name: MP399M


title: fetal liver, hypoxic, animal 6

city: Aurora

first: Molly

last: McGuckin

state: Colorado

address: 13243 East 23rd Avenue, Aurora, CO 80045-0508

institute: University of Colorado

description: Library name: Sample 15

data_processing:
STAR 2.7.10b
Sequences were mapped to the Ovis aries reference genome (ARS-UI_Ramb_v1.0) and Ovis aries rambouillet annotation file (Ensembl)
The genomic sequence around splice junctions was set to 100 bases to build the splice junction database. Reads that mapped to multiple locations were discarded to avoid ambiguity. Chimeric reads were required to have at least 12 bases in each segment, and the maximum intron length was set to 200,000 bases. The maximum gap between paired-end reads was set to 20,000 bases, with a minimum overhang of 10 bases for spliced alignments and 12 bases for chimeric junctions. A two-pass mapping approach was used: first aligning the reads without considering splice junctions, then re-aligning using the splice junctions identified in the first pass for improved accuracy.
Assembly: ARS-UI_Ramb_v1.0
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: raw_reads.txt

organism: Ovis aries

source_name: liver

extract_protocol:
Frozen fetal liver tissue was homogenized in TRIzol reagent (Qiagen)), and RNA was extracted using the RNeasy mini spin columns kit (Qiagen).
RNA libraries for RNAseq were prepared using Universal Plus mRNA library prep kit according to manufacturers instructions.

treatment_protocol: Welsh mountain ewes

value: liver

tag: breed

value: Welsh Mountain

value: Male

value: 0.9 gestation

value: hypoxia


title: fetal liver, hypoxic, animal 7

description: Library name: Sample 16

value: Female


title: IR_3

value: WT


title: Myometrium from fibroid-free patient (MyoN), patient MP451

description: Library name: MP451M

value: Control myometrium


title: fetal liver, hypoxic, animal 5

description: Library name: Sample 14


title: Myometrium from fibroid-free patient (MyoN), patient MP398

description: Library name: MP398M

value: myometrium


title: fetal liver, hypoxic, animal 4

description: Library name: Sample 13


title: fetal liver, hypoxic, animal 2

description: Library name: Sample 11


title: Myometrium from fibroid-free patient (MyoN), patient MP397

description: Library name: MP397M


title: IR_2

value: kidney


title: IR_1


title: HCT116 xenograft

description: Library name: HCT116x

value: Colorectal cancer

value: CRC cell line


title: fetal liver, hypoxic, animal 1

description: Library name: Sample 10


title: C_3

value: sham


title: Myometrium from fibroid-free patient (MyoN), patient MP363

description: Library name: MP363M


title: fetal liver, hypoxic, animal 3

description: Library name: Sample 12


title: fetal liver, control, animal 7

description: Library name: Sample 7

value: normoxia


title: Myometrium from fibroid-free patient (MyoN), patient MP365

description: Library name: MP365M


title: fetal liver, control, animal 6

description: Library name: Sample 6


title: C_2


title: IRK_1

value: FAM3A knockout

value: IRI


title: C_1


title: fetal liver, control, animal 5

description: Library name: Sample 5


title: Myometrium from fibroid-free patient (MyoN), patient MP362

description: Library name: MP362M

value: C


title: fetal liver, control, animal 4

description: Library name: Sample 4

value: liver


title: Myometrium from fibroid-free patient (MyoN), patient MP361

description: Library name: MP361M


title: Trib1_Cop1KO_4

city: Tokyo

first: Takuro

last: Nakamura

address: 6-1-1 Shinjuku, Shinjuku-ku

country: Japan

institute: Tokyo Medical University

data_processing:
Row reads were trimmed to remove adaptor sequences by trimmomatic ver 0.39.
FASTQ files were processed in the AltAnalyze ver 2.1.0.
Transcript permillion estimates were calculated in AltAnalyze through a built-in call to Kallisto for read pseudoalignment and transcript quantification (mm10).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include tpm values for each sample

growth_protocol: Mouse FT1CL AML cells were maintained in Iscove modified Dulbecco medium containing 10% fetal bovine serum and 5 ng/mL interleukin-3.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
The double strand cDNA fragments were processed for adaptor ligation, size selection for 200 bp inserts, and amplification to generate strand-specific libraries.

treatment_protocol: AML cells were treated with 4-hydroxy-tamoxifen for Cop1 knockout.

value: acute myeloid leukemia

value: Cop1 ko/ko

value: Cells were treated with 4-hydroxytamoxifene to delete Cop1


title: fetal liver, control, animal 3

description: Library name: Sample 3

value: Welsh Mountain

value: Male

value: 0.9 gestation


title: fetal liver, control, animal 2

description: Library name: Sample 2

value: Female


title: Myometrium from fibroid-free patient (MyoN), patient MP358

description: Library name: MP358M

value: myometrium

value: Control myometrium


title: fetal liver, control, animal 1

description: Library name: Sample 1


title: Trib1_Cop1KO_3


title: fetal liver, control, animal 8

description: Library name: Sample 8


title: Aged Liver - SIRT7 KO Rep D

city: Philadelphia

first: Khoa

last: Tran

address: 3400 Civic Blvd

institute: University of Pennsylvania

description: Library name: Sample 14

data_processing:
Sequence reads were aligned to reference genome using STAR aligner
Reads for each gene with RefSeq annotations were counted using htseq-count
Counts were normalized and significant differences calculated with DESeq2
Assembly: mm9 (SIRT7 KO) and GRC27/hg19 (NUCKS1 KD)
Supplementary files format and content: .txt

source_name: Liver

growth_protocol: IMR90 cells were cultured in DMEM supplemented with 10% FBS and 1% pen/strep. IMR90 cells under PD 40 was used for the RNA-sequencing experiments.

extract_protocol:
Trizol extraction in conjunction with RNeasy Mini Kit
NEBNext Poly(A) mRNA Magnetic Isolation Module followed by NEBNext Ultra II Direction Prep Kit for Illumina

treatment_protocol: To induce senescence, cells control or NUCKS1 KD cells were treated with etoposide for 24 hours. Media was changed and cells were cultured for an additonal 11 days before harvesting for RNA-Seq.

value: Liver

value: SIRT7 KO

value: Aged


title: Myometrium from fibroid-free patient (MyoN), patient MP356

description: Library name: MP356M


title: Aged Liver - SIRT7 KO Rep C

description: Library name: Sample 13


title: Trib1_Cop1KO_2


title: Aged Liver - SIRT7 KO Rep B

description: Library name: Sample 12


title: RMS patient tumour tissue

city: SYDNEY

first: Diego

last: Chacon-Fajardo

state: NSW

address: 384 Victoria St

institute: Garvan Institute of Medical Research

description: Library name: LSRNA27

data_processing:
Sequence reads were trimmed to remove Illumina adapter and aligned to to human reference genomes using STAR.
Assembly: HG38
Supplementary files format and content: Text files include raw counts for each sample calculated using featureCounts.

source_name: tumour

growth_protocol: Patient tumour tissue was mechanically and enzymatically dissociated using Collagenase/Hyaluronidase (Stem Cell Technologies, Canada) and plated onto flask coated with 0.2mg/ml rat tail I collagen (BD Biosciences, US). Cells were maintained at 37°C in a humidified incubator with 5% CO2 in DMEM/F-12 medium (Thermo Fisher Scientific, AU) supplemented with 10% fetal bovine serum (FBS; HyClone), 15mM HEPES (Thermo Fisher Scientific), 400ng/mL hydrocortisone (Sigma-Aldrich, US), 10ng/mL human recombinant epidermal growth factor (Thermo Fisher Scientific), 0.1IU/mL insulin (Novo Nordisk, DK), and 1x MEM vitamins (Thermo Fisher Scientific).

extract_protocol:
RNA was extracted from fresh frozen RMS patient tumour tissue and TKCC-IORMS-01 PDCL using Qiagen AllPrep Kit (Qiagen, US) following the manufacturer's instructions
150bp paired-end

value: tumour

value: Tumour

value: Untreated


title: Trib1_Cop1WT_4


title: Aged Liver - SIRT7 KO Rep A

description: Library name: Sample 11


title: Trib1_Cop1WT_3


title: Trib1_Cop1KO_1


title: Young Liver - SIRT7 KO Rep C

description: Library name: Sample 6

value: Young


title: Aged Liver - SIRT7 WT Rep D

description: Library name: Sample 10

value: SIRT7 WT


title: Aged Liver - SIRT7 WT Rep C

description: Library name: Sample 9


title: RMS patient normal tissue

description: Library name: LSRNA8

source_name: normal tissue adjacent to the tumor

value: normal tissue adjacent to the tumor

value: WT


title: Aged Liver - SIRT7 WT Rep B

description: Library name: Sample 8


title: fetal liver, control, animal 9

description: Library name: Sample 9

value: liver

value: normoxia


title: Aged Liver - SIRT7 WT Rep A

description: Library name: Sample 7


title: Young Liver - SIRT7 WT Rep C

description: Library name: Sample 3


title: Trib1_Cop1WT_1

value: acute myeloid leukemia


title: 4-cell_SCNT_ATAC-seq_rep2

value: SCNT embryo

value: wildtype


title: Trib1_Cop1WT_2


title: RNAseq, E15.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep2

city: Ramat Gan

first: Isabelle

last: Stévant

address: Institute of Nanotechnology and Advanced Materials, Building 206

country: Israel

institute: University of Bar Ilan

data_processing:
nf-core/rnaseq pipeline v3.12.0
Assembly: mm10 from Gencode (M25)
Supplementary files format and content: Comma-delimited read count for each samples
Supplementary files format and content: Comma-delimited TPM for each samples

source_name: fetal gonads

extract_protocol:
Total RNA was isolated from ~40,000 sorted Sertoli or pre-granulosa cells of E11.5, E12.5, E13.5 and E15.5 gonads via FACS. RNA purification was performed using the RNeasy plus micro kit (Qiagen, 74034) according to the manufacturer instructions.
cDNA libraries were prepared using the NEB Next Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB, E6420) according to the manufacturer’s protocol. cDNAs were synthesized by reverse transcriptase enzyme, followed by cDNA amplification and cDNA clean-up using AMPure beads (Beckman coulter, Bc-a63881). cDNA was then fragmented, and adapters were ligated with unique indexes for each sample using the NEBNext® Multiplex Oligos for Illumina (NEB, E7335).

value: fetal gonads

value: Sertoli cells

value: male


title: iPS-endothelial cells, Day14_2

city: Suita-shi

first: Yukika

last: Tanabe

state: Osaka

address: 3-1 Yamada-ok

institute: Research Institute for Microbial Diseases, Osaka University

description: Library name: D14_2

data_processing:
featureCounts v2.0.0.
Assembly: hg19
Supplementary files format and content: F6454_v866_FPKM_for_iDEP.tsv

growth_protocol: UTA-SF2-2 (JCRB Cell Bank, Osaka, Japan), human iPSCs were maintained on iMatrix-511™ (Nippi, Tokyo, Japan) in StemFit® AK02N (Ajinomoto, Tokyo, Japan) supplemented with 10µM CultureSure®Y-27632(Wako, Settsu, Japan).

extract_protocol:
Total RNA was extracted using the miRNeasy Micro kit (Qiagen) following the protocol.
Library preparation was performed using the TruSeq stranded mRNA Library Prep kit (Illumina) according to the provided instructions.

treatment_protocol: For differentiation induction into endothelial cells, MiraCell® iPS Cell to Endothelial Cell Differentiation Kit (TaKaRa, Otsu, Japan) was utilized.

value: endothelial cells

value: differentiation induction Day14


title: Young Liver - SIRT7 KO Rep B

description: Library name: Sample 5

value: Liver

value: SIRT7 KO


title: Jurkat,dasatinib+dabrafenib biol rep2

city: guangzhou

first: Chen

last: Jun-Zhu

state: State...

address: 广州市越秀区中山二路58号中山大学附属第一医院

institute: Sun Yat-Sen University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base   quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown   base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored   in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5) [3] was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include fpkm, tpm, read count values for each Sample

source_name: Peripheral blood

growth_protocol: Jurkat cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was prepared from cells of triplicate samples using an RNA-Quick Purification Kit (#RN001, Esunbio, China).1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were treated with 100nM dasatinib, or 100nM dasatinib plus 1μM dabrafenib for 48h

value: Peripheral blood

value: Jurkat

value: Human T Lymphocyte Cells

value: dasatinib+dabrafenib


title: iPS-endothelial cells, Day24

description: Library name: D24_1

value: WT

value: differentiation induction Day24


title: Myometrium from fibroid-free patient (MyoN), patient MP506

description: Library name: MP506M

source_name: myometrium

value: myometrium

value: AA

value: Control myometrium


title: RNAseq, E15.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep3


title: Myometrium from fibroid-free patient (MyoN), patient MP516

description: Library name: MP516M

value: C


title: iPS-endothelial cells, Day24_2

description: Library name: D24_2


title: iPS-endothelial cells, Day11_2

description: Library name: D11_2

value: differentiation induction Day11


title: Jurkat,dasatinib+dabrafenib biol rep3

address: 广州市越秀区中山二路58号中山大学附属第一医院


title: iPS-endothelial cells, Day14

description: Library name: D14_1


title: RNAseq, E15.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep1

value: fetal gonads

value: Sertoli cells


title: RNAseq, E13.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep3

value: male


title: iPS-endothelial cells, Day11

description: Library name: D11_1

value: endothelial cells


title: Young Liver - SIRT7 KO Rep A

description: Library name: Sample 4

value: Liver

value: Young


title: RNAseq, E13.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep2


title: RNAseq, E13.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep1


title: HMGB3 Knock-out U2OS cells, Clone 6, replicate 4

city: Austin

first: Anna

last: Battenhouse

state: TX

address: 100 East 24th St., Stop A5000

department: Center for Biomedical Research Support

institute: The University of Texas at Austin

description: Library name: KO-Cl-6-rep4

data_processing:
FASTQ datasets were post-processed (TagSeq post-processing based on tag-based_RNAseq code as of August 2019) in order to collapse duplicates based on molecular tags.
Single-end pseudo-alignment was performed against the human transcriptome. using kallisto (v0.45.0). Kallisto’s estimated counts were used for differential expression analysis.
Downstream analysis of transcript abundance data was performed in R (v4.0.3) following protocols outlined in Bioconductor. The tximport package (v1.6.0) was first used to roll up transcript-level counts into gene-level counts provided to the DESeq257 package (v1.18.1). Before further analysis, count data matrices were filtered to remove genes with fewer than 1 read across all included samples. Three contrasts were analyzed to explore the relationship between each of the knockout clones and the WT (e.g. KO-Cl-2 vs. WT). A fourth model was analyzed comparing all knockout samples to the WT. Differentially expressed genes (DEGs) reported are those with maximum adjusted p-value 0.05 and log2 fold change greater than 1.0 or less than -1.0.
Assembly: GENCODE v42 transcrips and annotations for GRCh38 human genome
Supplementary files format and content: Per-sample raw transcript counts from kallisto

growth_protocol: Human U2OS cells were obtained (Synthego), pre-treated with CRISPR-Cas9 targeting of HMGB3 or left untreated. The human U2OS knockout clones, and corresponding wild type (WT) cells, were grown in McCoy’s 5A media (Iwakata and Grace modified) with L. Glutamine, 10% FBS, and 1% Pen-Strep (Cat #10-050-CV, Corning), according to ATCC guidelines, in a 37°C incubator (5% CO2).

extract_protocol:
The three identified HMGB3 KO clones, along with the WT U2OS cells, were used for the TagSeq experiments. Cells of each type were maintained in three separate flasks prior to collection for replicate samples. RNA extraction was conducted using the Qiagen RNeasy micro kit (Cat: #74004), following the manufacturer’s protocol, with the exception of completing all of the centrifugation steps at 4°C. RNA concentrations were then measured using a Nanodrop and flash frozen, and stored at -80°C. Four cDNA libraries were constructed, each with 4 replicates: WT– wild-type human U2OS cells, KO1- CRISPR HMGB3 knockout clone #2, KO2- CRISPR HMGB3 knockout clone #5, KO3- CRISPR HMGB3 knockout clone #6.
Library preparation and sequencing for TagSeq, a form of 3’ RNA sequencing, were performed by the GSAF at the University of Texas at Austin. Total RNA was isolated from each sample (0.375 mL) by addition of Trizol (1.125 mL; Thermo Fisher) and the sample (1.4 mL) was transferred to a Phasemaker tube (Thermo Fisher). Total RNA was extracted following the protocol supplied by the manufacturer and further cleaned up using an RNeasy MinElute Cleanup Kit (QIAGEN). RNA integrity number (RIN) was measured using an Agilent Bioanalyzer and 100 ng of RNA was used for the Tag-Seq protocol. The fragmentation/RT mix was prepared then added to each RNA sample and then heated to 95°C for 2.5 minutes on a Thermocyler then immediately put on ice for 2 minutes. After cooling and the addition of the template switching oligo and SmartScribe RT the fragmented RNA reaction was incubated at 42°C for 1 hour, and at 65°C for 15 minutes. Next an AmPure bead clean-up was completed for the cDNA before it was amplified for 18 cycles, also incorporating the Illumina sequencing primer site, followed by another cleanup. The remaining portions of the Illumina adapter (the i5 and i7 indices) were then incorporated through an additional 4 cycles of PCR. Final libraries were quantified with PicoGreen then pooled equally for size selection using the Blue Pippin from 355-550 bp. The resulting libraries were sequenced using an Illumina Novaseq instrument (100-nucleotide single reads).

treatment_protocol: Individual cells were sorted into 96-well plates with a flow cytometer using the LIVE/DEAD Fixable Green Dead Cell Stain Kit (Cat L34969, Invitrogen). DNA was isolated from individual clones and sequenced at the University of Texas at Austin DNA Sequencing Facility using Synthego-designed primers (F: 5’-TGCTCTGAGAGGTGGAAGGT-3’; R: 5’-TCCTTCTTCTTCTTGCCTCCC-3’), which encompass the CRISPR-Cas9 gRNA sequence, 5’-GUUCUUUGCAGACGAUGUCC-3’, that was used by Synthego to knock out HMGB3. Clones that were identified as potential knockout clones were then tested for HMGB3 protein levels via western blot. Three HMGB3 KO clones were identified and used in subsequent experiments.

value: human osteosarcoma

value: HMGB3 Knock-out, Clone 6


title: Jurkat,dasatinib+dabrafenib biol rep1

address: 广州市越秀区中山二路58号中山大学附属第一医院

value: Peripheral blood

value: Jurkat

value: Human T Lymphocyte Cells


title: Jurkat,dasatinib biol rep3

address: 广州市越秀区中山二路58号中山大学附属第一医院

value: WT

value: dasatinib


title: RNAseq, E12.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep3


title: HMGB3 Knock-out U2OS cells, Clone 6, replicate 3

description: Library name: KO-Cl-6-rep3


title: Jurkat,dasatinib biol rep2

address: 广州市越秀区中山二路58号中山大学附属第一医院


title: RNAseq, E12.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep2


title: Young Liver - SIRT7 WT Rep A

description: Library name: Sample 1

value: SIRT7 WT


title: RNAseq, E11.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep3


title: RNAseq, E12.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep1


title: RNAseq, E11.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep2


title: Jurkat, CTL biol rep3

address: 广州市越秀区中山二路58号中山大学附属第一医院

value: DMSO


title: HMGB3 Knock-out U2OS cells, Clone 6, replicate 2

description: Library name: KO-Cl-6-rep2


title: RNAseq, E15.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep1

value: Pre-granulosa cells

value: female


title: HMGB3 Knock-out U2OS cells, Clone 6, replicate 1

description: Library name: KO-Cl-6-rep1


title: RNAseq, E15.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep2

value: fetal gonads


title: RNAseq, E15.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep3


title: Jurkat, CTL biol rep2

address: 广州市越秀区中山二路58号中山大学附属第一医院


title: Jurkat,dasatinib biol rep1

address: 广州市越秀区中山二路58号中山大学附属第一医院


title: RNAseq, E13.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep3


title: Jurkat, CTL biol rep1

address: 广州市越秀区中山二路58号中山大学附属第一医院


title: RNAseq, E11.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep1

value: Sertoli cells


title: HMGB3 Knock-out U2OS cells, Clone 5, replicate 4

description: Library name: KO-Cl-5-rep4

value: HMGB3 Knock-out, Clone 5


title: HMGB3 Knock-out U2OS cells, Clone 5, replicate 2

description: Library name: KO-Cl-5-rep2


title: HMGB3 Knock-out U2OS cells, Clone 5, replicate 3

description: Library name: KO-Cl-5-rep3


title: RNAseq, E13.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep1


title: Condition (Abx treated) Embryonic day 14 female biological rep 3, image 1

city: Boston

first: Brian

last: Kalish

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Boston Children's Hospital

description:
AbxF_5
mouse brain gene panel

hyb_protocol: A total of 500 genes were selected and assigned a 20-bit binary barcode which was used for generating MERFISH probes. Slides were prepared as per Vizgen protocol, briefly, slides were washed with 1x PBS followed by Sample Prep Wash Buffer (Vizgen, PN 20300001). Slides were incubated in Formamide Wash Buffer (Vizgen, PN 20300002) for 30 min at 37°C, then gene panel mix was spread on the section and incubated for 42-46 hr at 37°C in a humidified incubator. Slides were then incubated two times in Formamide Wash Buffer for 30 min each at 47°C, and washed with sample prep wash buffer for at least 2 min. Sections were coated in gel embedding solution (0.05% w/v ammonium persulfate, 0.05% v/v N,N,N’,N'-tetramethylethylenediamine in Gel Embedding Premix (Vizgen, PN 20300004)) and incubated at RT for 1.5 hr, tissue was cleared in 1:100 proteinase K in Clearing Premix (Vizgen, PN 20300003) at 37°C overnight or for a maximum of 7 days to clear lipids and proteins that may contribute to auto-fluorescence background noise. Prior to imaging, sections were washed two times with Sample Prep Wash Buffer, incubated in DAPI and PolyT Staining Reagent (Vizgen, PN 20300021) for 15 min on a rocking platform, incubated in Formamide Wash Buffer for 10 min, and washed again with Sample Prep Wash Buffer.

scan_protocol: Imaging was performed on the MERSCOPE platform (Vizgen, Cat: 10000001) according to manufacturer instructions.

data_processing: Transcript barcodes were read and matched assigned to the correct gene. MERFISH images were segmented using Vizgen's post-processing tool and Cellpose v2. DAPI and PolyT signals were used to delinate the cell boundaries. Individual RNA molecules were assigned to a cell based on whether they were positioned within the marked boundary. Anatomical segmentation was performed using the MERSCOPE Visualizer software. Cells for MERFISH were processed using the Seurat V5 package in R.

label: Gene targeting probes

source_name: Whole embryonic brain, Antibiotic treated (Abx)

label_protocol: Single-cell spatial RNA imaging  was performed using a gene panel targeting 500 transcripts.

extract_protocol: Fresh frozen brain were cryo-sectioned at 10 μm thickness at -21°C, and mounted onto MERSCOPE beaded slides. Sections were allowed to refreeze, and then fixed for 15 minutes in 4% paraformaldehyde prepared in 1x PBS, followed by 3 washings with 1x PBS for 5 minutes each and stored in 70% ethanol overnight.

value: Whole embryonic brain

value: Condition (Abx treated)

value: Embryonic day 14


title: RNAseq, E12.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep3


title: RNAseq, E12.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep2


title: RNAseq, E12.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep1


title: HMGB3 Knock-out U2OS cells, Clone 2, replicate 4

description: Library name: KO-Cl-2-rep4

value: human osteosarcoma

value: HMGB3 Knock-out, Clone 2


title: Condition (Abx treated) Embryonic day 14 female biological rep 2, image 2

description:
AbxF_4
mouse brain gene panel


title: RNAseq, E11.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep3


title: Condition (Abx treated) Embryonic day 14 female biological rep 2, image 1

description:
AbxF_3
mouse brain gene panel


title: Young Liver - SIRT7 WT Rep B

description: Library name: Sample 2

value: Liver

value: Young


title: RNAseq, E11.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep2


title: RNAseq, E13.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep2


title: HMGB3 Knock-out U2OS cells, Clone 2, replicate 3

description: Library name: KO-Cl-2-rep3


title: RNAseq, E11.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep1


title: Condition (Abx treated) Embryonic day 14 female biological rep 1, image 2

description:
AbxF_2
mouse brain gene panel


title: ATACseq, E15.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep3

data_processing:
nf-core/atacseq pipeline v2.1.2
Peaks called with MACS2 as narrowPeaks, with FDR<0.01, and found in at least two replicates.
Assembly: mm10 from Gencode (M25)
Supplementary files format and content: Comma-delimited read count per open chromatin regions for each samples
Supplementary files format and content: Bed files for peaks found in at least two of three replicate for each condition
Supplementary files format and content: Bed file for all the open chromatin regions combining all conditions
Supplementary files format and content: Normalized BigWig files for each samples

extract_protocol:
Sorted Sertoli and pre-granulosa cells (~60,000) were isolated from E11.5, E12.5, E13.5 and E15.5 gonads via FACS. ATAC-seq library preparation was performed using the Active Motif kit (Active Motif, cat. 53150) according to the manufacturer instructions.
ATAC-seq library preparation was performed using the Active Motif kit (Active Motif, cat. 53150) according to the manufacturer instructions.

value: male


title: HMGB3 Knock-out U2OS cells, Clone 2, replicate 1

description: Library name: KO-Cl-2-rep1


title: ATACseq, E13.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep3


title: HMGB3 Knock-out U2OS cells, Clone 2, replicate 2

description: Library name: KO-Cl-2-rep2


title: ATACseq, E15.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep1


title: Wild Type U2OS cells, replicate 4

description: Library name: WT-rep4

value: Wild type


title: Wild Type U2OS cells, replicate 3

description: Library name: WT-rep3


title: Condition (Abx treated) Embryonic day 14 female biological rep 1, image 1

description:
AbxF_1
mouse brain gene panel


title: ATACseq, E13.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep1


title: Condition (Abx treated) Embryonic day 14 male biological rep 3, image 1

description:
AbxM_5
mouse brain gene panel


title: ATACseq, E12.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep3


title: ATACseq, E12.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep2


title: Condition (Abx treated) Embryonic day 14 male biological rep 2, image 2

description:
AbxM_4
mouse brain gene panel


title: Condition (Abx treated) Embryonic day 14 male biological rep 1, image 2

description:
AbxM_2
mouse brain gene panel


title: ATACseq, E12.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep1


title: Condition (Abx treated) Embryonic day 14 male biological rep 2, image 1

description:
AbxM_3
mouse brain gene panel


title: ATACseq, E11.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep3


title: Wild Type U2OS cells, replicate 2

description: Library name: WT-rep2


title: ATACseq, E11.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep2


title: Wild Type U2OS cells, replicate 1

description: Library name: WT-rep1


title: ATACseq, E11.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep1


title: HMGB3 Knock-out U2OS cells, Clone 5, replicate 1

description: Library name: KO-Cl-5-rep1


title: Condition (Abx treated) Embryonic day 14 male biological rep 1, image 1

description:
AbxM_1
mouse brain gene panel


title: ATACseq, E15.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep2


title: ATACseq, E15.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep3


title: ATACseq, E13.5, sorted Sertoli cells, SOX9-IRES-GFP mouse line, rep2


title: NR_SK_9_003_Visit2_Involved_Nick_Reynolds_S81

city: Newcastle upon Tyne

first: Simon

middle: Joseph

last: Cockell

address: Framlington Place

department: School of Biomedical, Nutritional and Sport Sciences

country: United Kingdom

institute: Newcastle University

description: Library name: Sample_9

data_processing:
Reads were quantified to Ensembl (rel91) using Kallisto (v0.46.0)
Transcript level counts were aggrgated to the gene level using tximport.
Data was analysed using Limma
Assembly: GRCh38, Ensembl release 91
Supplementary files format and content: txt files with transcript-level counts

source_name: Involved

extract_protocol:
RNA was extracted following the Qiagen AllPrep kit’s protocol.  RNA concentration/integrity was checked using the Agilent Bioanalyzer 2100 with the RNA 6000 Nano assay (Agilent: 5067-1511); only samples with an RNA integrity number (RIN) of 8 or more were sequenced.
RNA library preparation from total RNA was conducted following the manufacturer’s protocol for the Kapa mRNA HyperPrep Kit.

treatment_protocol: The subject group were treated with oral methotrexate (10mg for the first week, 15mg/week thereafter, increased incrementally to maximum dose 25mg/week if suboptimal response).

value: skin biopsy

tag: patient

tag: visit

value: Involved

tag: easi


title: ATACseq, E15.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep2


title: NR_SK_8_003_Visit1_Involved_Nick_Reynolds_S80

description: Library name: Sample_8


title: Condition (MIA treated) Embryonic day 14 female biological rep 2, image 2

description:
MIAF_4
mouse brain gene panel

source_name: Whole embryonic brain, Maternal Immune activated (MIA)

value: Condition (MIA treated)


title: ATACseq, E13.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep2

value: Pre-granulosa cells


title: Condition (MIA treated) Embryonic day 14 female biological rep 2, image 1

description:
MIAF_3
mouse brain gene panel

value: female


title: ATACseq, E13.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep1

value: fetal gonads


title: ATACseq, E12.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep3


title: NR_SK_6_003_Baseline_Involved_Nick_Reynolds_S78

description: Library name: Sample_6

value: Baseline


title: Condition (MIA treated) Embryonic day 14 female biological rep 1, image 2

description:
MIAF_2
mouse brain gene panel


title: ATACseq, E12.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep1


title: NR_SK_5_002_Visit2_Uninvolved_Nick_Reynolds_S77

description: Library name: Sample_5

source_name: Uninvolved

value: Uninvolved


title: ATACseq, E11.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep3


title: NR_SK_44_010_Visitquery_Involved_Nick_Reynolds_S115

description: Library name: Sample_44


title: ATACseq, E12.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep2


title: Condition (MIA treated) Embryonic day 14 female biological rep 1, image 1

description:
MIAF_1
mouse brain gene panel

value: Whole embryonic brain


title: ATACseq, E11.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep1


title: Condition (MIA treated) Embryonic day 14 male biological rep 3, image 1

description:
MIAM_5
mouse brain gene panel


title: CD45+ cells from mouse bone metastasis sample, treated with IgG2a

city: 南京

first: shiji

last: ren

address: 南京鼓楼

institute: Nanjing University

description: Library name: Sample 2

library_source: transcriptomic single cell

data_processing:
For DNBelab C4 data, raw sequencing reads were filtered and demultiplexed using PISA (Version 0.2; https://github.com/shiquan/PISA). The filtered reads were aligned to mm10 transcriptome using STAR and sorted by sambamba (Version 0.7.0). Cell versus gene UMI count matrix was generated using PISA.
Assembly: mm10
Supplementary files format and content: standard cellranger output

source_name: tumor

extract_protocol:
Single cell suspensions were prepared from the bone metastasis samples immediately upon mouse sacrifice. In brief, bone marrow fluid was rinsed out with PBS from tibias and femurs of bone metastasis sites, and then filtered through 40-µm nylon cell strainers. Hind limbs (tibias and femurs) with bone metastasis were enzymatically dissociated with RMPI-1640 supplemented with 1 mg/ml collagenase IV and 100 U/ml DNase I and incubated at 37°C for 1 h. Then cells were filtered through 40-µm nylon cell strainers, and washed twice with PBS. Red blood cells were removed from single cell suspensions with red blood cell lysis buﬀer and washed twice with PBS. Single cells were then incubated with CD45 MicroBeads to isolate CD45+ immune cells.
Single cells were converted to barcoded scRNA-seq libraries through droplet encapsulation, emulsion breakage, mRNA captured beads collection, reverse transcription, cDNA amplification and purification. Indexed sequencing libraries were then constructed according to the manufacturer’s protocol. The sequencing library concentration was quantified by Qubit™ ssDNA Assay Kit (Thermo Fisher). DNA nanoballs (DNBs) were loaded into the patterned nano arrays and sequenced on the ultra‐high‐throughput DIPSEQ T1 sequencer using the following read length: 30 bp for read 1, inclusive of 10 bp cell barcode 1, 10 bp cell barcode 2, and 10 bp unique molecular identifier (UMI), 100 bp of transcript sequence for read 2, and 10 bp for sample index.

value: tumor


title: Condition (MIA treated) Embryonic day 14 female biological rep 3, image 1

description:
MIAF_5
mouse brain gene panel

value: Embryonic day 14


title: Condition (MIA treated) Embryonic day 14 male biological rep 2, image 2

description:
MIAM_4
mouse brain gene panel


title: ATACseq, E15.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep1


title: CD45+ cells from mouse bone metastasis sample, treated with mDKN-01

description: Library name: Sample 1


title: ATACseq, E13.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep3


title: NR_SK_42_010_Baseline_Involved_Nick_Reynolds_S113

description: Library name: Sample_42


title: Brain stem, uninfected, rep5

city: Aarhus

first: Soren

last: Paludan

address: CF Møllers Alle 6, Building 1115

department: Biomedicine

country: Denmark

institute: Aarhus university

description:
Library name: Sample20
10x Genomics

data_processing:
Reads demultiplexed from the DNBSEQ-G400 were mapped to a composite reference genome consisting of the mouse genome (GRCm39) and the HSV-1 genome (JX142173) using Cell Ranger v6.1 from 10x Genomics.
Assembly: GRCm39
Supplementary files format and content: gene expression value in HDF5 files

source_name: Brain stem

extract_protocol:
Brain stems were harvested from animals sedated with ketamine and xylazine and thoroughly perfused with a minimum of 25 ml of PBS. Brain stems were cut into pieces and digested for 40 min at 37 °C with 5% CO2 in PBS supplemented with 1.6 IU ml-1 Collagenase/Dispase (Roche) and 0.5 mg ml-1 DNase I (Sigma-Aldrich). 20 μl of sterile EDTA was added to each sample and incubated at 37°C for another 5 min. Tissues were then mechanically disrupted through a 70um cell strainer into a single-cell suspension. Single-cell suspensions were washed with 25ml 2% FCS-HBSS (Thermo Fisher Scientific), centrifuged, and resuspended in a mixture of PBS with 0.5% BSA (VWR) and Debris Removal Solution (Miltenyi Biotec). After overlaying PBS with 0.5% BSA, suspensions were centrifuged, resuspended, and adjust the cell count to 106 cells ml-1.
Single cell suspensions were converted to barcoded scRNAseq libraries following the manufacturer’s instructions of Chromium Single Cell 3’ Library, Gel bead & index kit and Chip G Kit (v3.1, 10x Genomics), aiming for recovering 10,000 cells per library. Quality control of libraries were performed with Tapestation 4200. After QC, libraries were sequenced on an MGI DNBSEQ-G400 sequencer.

value: Brain stem

value: Uninfected


title: NR_SK_41_007_Visit1_Involved_Nick_Reynolds_S112

description: Library name: Sample_41


title: Brain stem, uninfected, rep4

description:
Library name: Sample19
10x Genomics


title: NR_SK_7_003_Baseline_Uninvolved_Nick_Reynolds_S79

description: Library name: Sample_7


title: Condition (MIA treated) Embryonic day 14 male biological rep 2, image 1

description:
MIAM_3
mouse brain gene panel


title: Condition (MIA treated) Embryonic day 14 male biological rep 1, image 2

description:
MIAM_2
mouse brain gene panel


title: Brain stem, uninfected, rep2

description:
Library name: Sample17
10x Genomics


title: Brain stem, uninfected, rep1

description:
Library name: Sample16
10x Genomics


title: NR_SK_4_002_Visit2_Involved_Nick_Reynolds_S76

description: Library name: Sample_4


title: NR_SK_40_007_Baseline_Uninvolved_Nick_Reynolds_S111

description: Library name: Sample_40


title: NR_SK_43_010_Baseline_Uninvolved_Nick_Reynolds_S114

description: Library name: Sample_43


title: Brain stem, D8 post-infection, rep3

description:
Library name: Sample14
10x Genomics

value: Infected


title: Control (PBS treated) Embryonic day 14 female biological rep 3, image 1

description:
E14F_5
mouse brain gene panel

source_name: Whole embryonic brain, Control (PBS)

value: Control (PBS treated)


title: Condition (MIA treated) Embryonic day 14 male biological rep 1, image 1

description:
MIAM_1
mouse brain gene panel

value: male


title: Brain stem, D8 post-infection, rep4

description:
Library name: Sample15
10x Genomics


title: Brain stem, D8 post-infection, rep2

description:
Library name: Sample13
10x Genomics


title: Control (PBS treated) Embryonic day 14 female biological rep 2, image 2

description:
E14F_4
mouse brain gene panel


title: Brain stem, D6 post-infection, rep4

description:
Library name: Sample10
10x Genomics


title: NR_SK_39_007_Baseline_Involved_Nick_Reynolds_S110

description: Library name: Sample_39


title: Brain stem, D8 post-infection, rep1

description:
Library name: Sample12
10x Genomics


title: Brain stem, D6 post-infection, rep5

description:
Library name: Sample11
10x Genomics


title: ATACseq, E11.5, sorted pre-granulosa cells, Tg(Enh8-mCherry) mouse line, rep2


title: NR_SK_38_004_Visit1_Involved_Nick_Reynolds_S109

description: Library name: Sample_38


title: Brain stem, D6 post-infection, rep3

description:
Library name: Sample9
10x Genomics


title: Brain stem, uninfected, rep3

description:
Library name: Sample18
10x Genomics


title: NR_SK_37_004_Baseline_Uninvolved_Nick_Reynolds_S108

description: Library name: Sample_37


title: Brain stem, D6 post-infection, rep1

description:
Library name: Sample7
10x Genomics


title: Control (PBS treated) Embryonic day 14 female biological rep 2, image 1

description:
E14F_3
mouse brain gene panel


title: Brain stem, D6 post-infection, rep2

description:
Library name: Sample8
10x Genomics


title: NR_SK_36_004_Baseline_Involved_Nick_Reynolds_S107

description: Library name: Sample_36


title: Control (PBS treated) Embryonic day 14 female biological rep 1, image 2

description:
E14F_2
mouse brain gene panel


title: Brain stem, D4 post-infection, rep6

description:
Library name: Sample6
10x Genomics


title: Control (PBS treated) Embryonic day 14 female biological rep 1, image 1

description:
E14F_1
mouse brain gene panel


title: Brain stem, D4 post-infection, rep5

description:
Library name: Sample5
10x Genomics


title: NR_SK_35_001_Visit1_Involved_Nick_Reynolds_S106

description: Library name: Sample_35


title: Brain stem, D4 post-infection, rep4

description:
Library name: Sample4
10x Genomics


title: NR_SK_34_006_Visit2_Uninvolved_Nick_Reynolds_S105

description: Library name: Sample_34


title: HC, replicate3, scRNAseq

city: GuangZhou

first: bian

last: zhenhua

state: GuangDong

address: Panyu University Town

institute: South China University of Technology

data_processing:
The raw sequencing data of gene expression were aligned with the Macaca fascicularis reference genome (Macaca6), and subjected to barcodes assignment and unique molecular identifier (UMI) counting using the CellRanger V6.1.2 pipeline (10X genomics).
To acquire the dataset, genes with low detected cell number (less than 3) and cells with low detected genes (less than 200) were excluded with Seurat package (V4.0.0). Also, single cells with 200-4000 genes and less than 20000 reads counts were retained to ensure the quality of datasets and most of the heterogeneous cell types were included for downstream analyses. The transcriptome expression matrix were firstly natural-log transformed as log1p values. The top 2000 highly variable genes were selected for downstream principal component analysis. To integrated the six samples together, we used harmony package to remove the batch effects. The top 30 harmony principal components were used for cluster (resolution for 0.2), UAMP projection and visualization. The cluster-specific expressed genes were extracted for each cluster to annotate the cell types.
Assembly: Macaca fascicularis 6
Supplementary files format and content: h5

organism: Macaca fascicularis

source_name: Bone marrow

extract_protocol:
First, 3 mL of Ficoll solution (Lymphoprep, Stemcell Technology) was added to a 15 mL centrifuge tube. The centrifuge tube was tilted, and the bone marrow (less than 3 mL) was transferred to the top of the Ficoll solution against the wall of the centrifuge tube. Next, the centrifuge tube was centrifuged at 800 × g for 20 minutes (acceleration 6, brake 2) at room temperature. Finally, the BMMC at the interface were carefully harvested.
The isolation BMMC were captured by the 10X genomics chromium Single Cell 5’ solution. Then, reverse transcription was performed on drops and the cDNA was amplified following multiple amplification schemes from 10X genomics, including extension, purification, adapter connection. Sequencing libraries were quantified using the Qubit High Sensitivity DNA assay and NGS3K assay. The library was sequenced by Novaseq illumina (Illumina, San Diego, CA) on a 150 bp paired-end run. All the single cell library preparation was according to the 10X genomics Chromium Next GEM Single Cell 5’ Reagent Kits v2 (Dual Index).

value: Bone marrow

value: immune cells

tag: disease state

value: healthy control

value: 15.9 years


title: Brain stem, D4 post-infection, rep1

description:
Library name: Sample1
10x Genomics


title: Brain stem, D4 post-infection, rep2

description:
Library name: Sample2
10x Genomics


title: Control (PBS treated) Embryonic day 14 male biological rep 2, image 2

description:
E14M_4
mouse brain gene panel


title: HC, replicate2, scRNAseq

value: 8.1 years


title: NR_SK_33_006_Visit2_Involved_Nick_Reynolds_S104

description: Library name: Sample_33

value: skin biopsy

value: Involved


title: Control (PBS treated) Embryonic day 14 male biological rep 2, image 1

description:
E14M_3
mouse brain gene panel


title: NR_SK_32_006_Visit1_Involved_Nick_Reynolds_S103

description: Library name: Sample_32


title: Control (PBS treated) Embryonic day 14 male biological rep 3, image 1

description:
E14M_5
mouse brain gene panel


title: AS, replicate2, scRNAseq

value: Ankylosing Spondylitis-like disease

value: 11.1 years


title: HC, replicate1, scRNAseq

value: 12.7 years


title: NR_SK_31_006_Baseline_Uninvolved_Nick_Reynolds_S102

description: Library name: Sample_31

value: Baseline

value: Uninvolved


title: Control (PBS treated) Embryonic day 14 male biological rep 1, image 1

description:
E14M_1
mouse brain gene panel

value: Whole embryonic brain

value: Embryonic day 14