title: 15287X140_blastomere_616F_type_IVF_cell_number_8

description: cellnumber 8


title: DU145_RS_NT, rep5

status: Public on Jun 01 2025

type: SRA

city: Nantes

first: Delphine

last: Fradin

address: 8 quai Moncousu

country: France

institute: CRCI2NA, Inserm UMR1307, CNRS UMR6075

library_source: transcriptomic

data_processing:
Pipeline details have been published by Charpentier E et al. 2018 (10.21203/rs.3.pex-1336/v1)
Assembly: Hg38
Supplementary files format and content: Matrix table of raw gene counts for all genes in all samples

molecule: polyA RNA

organism: Homo sapiens

source_name: DU145 RS

growth_protocol: DU145 cells were grown in RPMI+10% SVF

extract_protocol:
miRNeasy kit (Qiagen)
Libraries were prepared according to NovaSeq 6000 Sequencing Sytem's instructions accompanying the NovaSeq 6000 SP Reagent Kit (Ref# 20028401). Libraries were sequenced on the NovaSeq 6000 following the manufacturer's protocols.
3' SRP

treatment_protocol: transfection with 66nM final of miRNA mimics

tag: cell line

tag: cell population

value: prostate cancer cell line

tag: phenotype

value: RS

tag: transfection

tag: replicate


title: DU145_RR_NT, rep5

source_name: DU145 RR

value: RR


title: 15287X139_blastomere_616E_type_IVF_cell_number_8

city: dallas

first: Edward

last: Grow

state: TEXAS

address: 7053 beltau lane

country: USA

institute: UTSW

description: cellnumber 8

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 indicus x Bos taurus

source_name: IVF

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: IVF


title: C_P_1

city: Nanchang

first: Biao

last: Chen

address: Zhimin street, Jingkai district

country: China

institute: Jiangxi Agricultural University

data_processing:
Cutadapt (https://cutadapt.readthedocs.io/en/stable/) was used to remove the reads containing adaptors and low-quality bases to make it suitable for analysis in next step.
HISAT2 (https://daehwankimlab.github.io/hisat2/, version: 2-2.0.4) was adopted to map the reads to duck genome (https://www.ncbi.nlm.nih.gov/genome/2793?genome_assembly_id=426073)
The mapped reads of each sample were then assembled by using StringTie (http://ccb.jhu.edu/software/stringtie/, version: stringtie-1.3.4d) with default parameters.
Then, a comprehensive transcriptome was reconstructed with the mapped reads from all samples using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version: gffcompare-0.9.8).
StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were employed to evaluate the expression levels of all transcripts and genes in each sample by calculating fragments per kilobase of exon model per Million mapped fragments (FPKM). The differentially expressed mRNAs (DEGs) and differentially expressed transcripts (DETs) were selected using the criteria |log2 fold change| ≥1 and p ≤0.05 by R package DESeq2 (http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: IASCAAS_PekingDuck_PBH1.5 (GCF_003850225.1)
Supplementary_files_format_and_content: Count, FPKM and differential expression analysis

molecule: total RNA

organism: Anas platyrhynchos

source_name: pituitary

growth_protocol: All ducks were kept at room temperature and fed with the commercial dietary produced by Nanchang Huada Group (Nanchang, Jiangxi, China). The 15 ducks raised in floor-water system (FW group) were maintained at natural illumination, while the ducks raised in cages (C group) were subjected to a standard light regimen of 16 h light. All the ducks remained in good health over the duration of the experiment.

extract_protocol:
Total RNAs of 16 samples were extracted and purified using Trizol reagent following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.  All samples were kept at -80 °C.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At the age of 110-day, fifteen ducks were randomly selected and raised in three cages (100 × 45 × 50 cm), the others were still fed in the floor-water system.

tag: tissue

value: pituitary

tag: strain

value: Shanma duck

tag: treatment

value: reared with multilayer cages

tag: age

tag: group


title: 15287X138_blastomere_616D_type_IVF_cell_number_8

description: cellnumber 8


title: DU145_RR_miR-neg, rep4

value: miR control


title: S2-Zld_A-485_Zld_Input1

city: Madison

first: Melissa

last: Harrison

state: Wisconsin

address: 6204B Biochemical Sciences Building, 440 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin- Madison

library_source: genomic

data_processing:
Reads were aligned to the Drosophila melanogaster genome (dm6) using bowtie2 v2.4.4. Reads mapped to mitochondrial or scaffold DNA, aligned multiple times, or were unmapped were discarded.
Assembly: dm6
Supplementary files format and content: bigwig files were formed from merged replicates and z-score normalized, except for bigwigs from the anti-GFP and H3K27ac (in S2 cells) ChIP-seq in which were spike-in normalized with mouse chromatin.

organism: Drosophila melanogaster

growth_protocol: Drosophila embryos were maintained at 25˚C on molasses agarose plates and processed for experimentation 2-3 hours after egg laying. S2 cells were cultured in Schneider’s medium with supplemented antibiotic/antimycotic and 10% FBS at 27 ˚C.

extract_protocol:
The ChIP protocol used on fixed embryos in this study was adapted from a published protocol (Blythe and Wieschaus, 2015). Embryos were collected 2-3hrs AEL, dechorionated in 50% bleach for 3 min, and followed by a 15min fixation in formaldehyde (.45% formaldehyde for Zld and H3K27ac, 1.8% for CBPGFP). Two replicates of 1000 stage five embryos per experiment were hand sorted under a dissecting scope to avoid contamination by older embryos. Sorted embryos were homogenized in 1mL of RIPA buffer (50 mM Tris-HCl pH 8.0, 0.1% SDS, 1% Triton X-100, 0.5% sodium deoxycholate, and 150 mM NaCl) and underwent 11 cycles of sonication for 20s at 20% output on full duty cycle. For CBPGFP ChIP, a spike-in of fixed and sonicated H3.3-GFP MEF chromatin was added before removing 2% input. IPs were incubated with 6µg antibody overnight at 4?C and purified using Protein A magnetic beads (Invitrogen). After washing and eluting purified IP, DNA from IPs and inputs were treated with 90µg of RNAseA for 30mins at 37˚C and decrosslinked by adding 100µg of Proteinase K overnight at 65˚C. DNA was purified using a phenol:chloroform extraction with an overnight ethanol precipitation step to concentrate samples. Libraries for inputs and IPs were prepared using the commercial NEB Next Ultra II kit. ChIP in S2 cells was performed as previously described (Gibson et al. 2023). 5x107 cells were fixed in .8% formaldehyde for 7 min. Fixed chromatin was sonicated on a Covaris S220 for five 120s rounds with 60s delay, peak power at 170, a duty factor of 10%, and 200 cycles per burst. A spike-in of 5% MEF chromatin was added to H3K27ac sonicated chromatin before separating IPs from 2% input. IPs were incubated with antibody at 4?C for 4 hours. IP purification, RNAse treatment, decrosslinking, and DNA concentration was performed identically to the embryo ChIP protocol stated above.
Libraries were contructed using the NEB Next II Ultra kit. Sequencing was completed between the Illumina NextSeq 500 using 75bp single end reads or the Illumina Hi-Seq4000 using 50bp single end reads.

treatment_protocol: S2 cells were induced to express Zld using CuSO4, and were treated either with control DMSO drug or a CBP catalytic inhibitor A485 for 4 hours.

tag: genotype

value: 0 uM CuSO4

tag: condition

tag: antibody


title: S2-Zld_A-485_Zld_IP2

value: Zld (Harrison et al., 2010)


title: S2-Zld_A-485_Zld_IP1


title: DU145_RR_miR-92a, rep4


title: 15287X137_blastomere_616C_type_IVF_cell_number_8

description: cellnumber 8


title: DU145_RR_miR-200c, rep4


title: FW_H_2

source_name: hypothalamus

value: hypothalamus

value: reared in water-floor combination system


title: S2-Zld_DMSO_Zld_Input2

value: DMSO


title: S2-Zld_DMSO_Zld_IP2


title: FW_H_3


title: 15287X136_blastomere_616B_type_IVF_cell_number_8

description: cellnumber 8


title: 15287X135_blastomere_616A_type_IVF_cell_number_8

description: cellnumber 8


title: DU145_RR_NT, rep4


title: S2-Zld_DMSO_Zld_Input1


title: C_P_2


title: FW_H_1


title: C_H_4


title: DU145_RS_NT, rep4


title: S2-Zld_DMSO_K27ac_Input1


title: Embryo_WT_H3K27ac_Input1

source_name: Stage 5 embryo

value: Stage 5 embryo


title: S2-Zld_DMSO_Zld_IP1


title: C_H_3


title: DU145_RR_miR-neg, rep3


title: 15287X133_blastomere_615G_type_IVF_cell_number_8

description: cellnumber 8


title: 15287X132_blastomere_615F_type_IVF_cell_number_8

description: cellnumber 8


title: C_H_2


title: H1975 siHHLA3-1

city: Guangzhou

first: Chunting

last: Zhang

address: Guangzhou Avenue North

institute: Southern Medical University

description:
Library name: Sample 2
K5_1

data_processing:
After obtaining the raw sequencing data (Raw Data), you first need to filter the data, remove the adapter sequence, and process low-quality reads, and then evaluate the sequencing quality to obtain high-quality data (Clean Data). And compare the Clean Data with the reference genome to get the BAM file.
Use the HISAT2 software to compare the sequencing data with the reference genome, and make a comprehensive evaluation of the coverage area and coverage depth of the sequencing data. HISAT2 is the successor of TopHat2/Bowtie2. It uses an improved BWT algorithm (FM index). HISAT uses a large number of FM indexes to cover the entire genome, and combines several comparison strategies to achieve an efficient and faster comparison of RNA-seq data.
In RNA sequencing, RPKM (expected number of Reads Per Kilobase of transcript sequence per Millions basepairs sequenced) is the number of reads from a gene per kilobase length per million reads, which also considers the sequence depth and gene length pair The influence of read count is currently the most commonly used method for estimating gene expression levels. Map the bam file obtained by sequencing to the gtf file of the reference species to obtain the gene expression level, and perform regional statistics on the gene expression level of the genome according to the statistical method to reflect the overall expression level of the sample.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include counts and TPM values for each Sample.

source_name: Lung cancer tissue

growth_protocol: H1975 were cultured in Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum and maintained at 37°C with 5% CO2 in a humidified atmosphere

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment. Then 1 ug of total RNA for the construction was used as sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with siNC or siHHLA3 with transfection reagent when the cells were about 70% confluency and then cells were incubate in non-serum 1640 at 37°C with 5% CO2 for 6 hour. After 6h change the medium with 10% serum 1640 and continuously incubate  24h.

value: Lung cancer tissue

value: lung adenocarcinoma cells

value: HHLA3-1 knockdown

tag: batch


title: H1975 siHHLA3-3

description:
Library name: Sample 3
K5_3

value: HHLA3-3 knockdown


title: DU145_RR_miR-200c, rep3

value: prostate cancer cell line


title: 15287X131_blastomere_615E_type_IVF_cell_number_8

description: cellnumber 8


title: H1975 siNC

description:
Library name: Sample 1
K5_NC

value: NC knockdown


title: DU145_RS_NT, rep3

value: RS


title: 15287X134_blastomere_615H_type_IVF_cell_number_8

description: cellnumber 8

value: IVF


title: Senescence - shNUCKS-3 Rep B

city: Philadelphia

first: Khoa

last: Tran

address: 3400 Civic Blvd

institute: University of Pennsylvania

description: Library name: Sample 30

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

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: NUCKS1 KD

value: Etoposide


title: 15287X129_blastomere_615C_type_IVF_cell_number_8

description: cellnumber 8


title: Day14, scRNA

city: 重庆Chongqing

first: Zeyu

last: Fu

state: 重庆Chongqing

address: 高滩岩正街

department: College of Preventive Medicine

institute: AMU

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Cellranger 8.0.1
Assembly: GRCh38
Supplementary files format and content: tab seprated vlaue files and matrix files

source_name: umbilical cord blood

extract_protocol:
We prepared the umbilical cord blood (UCB) single-cell suspension by collecting UCB samples, isolating mononuclear cells using density gradient centrifugation, gently dissociating the cells to ensure a single-cell suspension, filtering the suspension through a70 µm cell strainer to remove any clumps, centrifuging to pellet the cells, resuspending the pellet in an appropriate buffer, and assessing cell concentration and viability to ensure a high-quality single-cell suspension for downstream applications.
We performed single-cell library preparation by first isolating mononuclear cells from human umbilical cord blood (UCB) using density gradient centrifugation to enrich for specific cell populations. The isolated cells were then cultured in a serum-free medium supplemented with thrombopoietin (TPO) to induce differentiation into megakaryocytes. The cultured cell suspension was loaded onto a microfluidic device for single-cell capture, allowing individual cells to be encapsulated in droplets. Reverse transcription was conducted within each droplet to convert the mRNA from each cell into complementary DNA (cDNA), which was subsequently amplified to generate sufficient material for library preparation. The amplified cDNA was processed to construct the sequencing library, including the addition of sequencing adapters and barcodes for identification. Quality control was performed to ensure the constructed library met the required standards for sequencing. Finally, the library was sequenced using a high-throughput sequencing platform, enabling us to analyze the gene expression profiles of individual cells and gain insights into the differentiation dynamics of megakaryocyte development.

value: umbilical cord blood

value: TPO cultrued


title: 15287X130_blastomere_615D_type_IVF_cell_number_8

description: cellnumber 8


title: Senescence - shNUCKS-3 Rep A

description: Library name: Sample 29


title: 15287X128_blastomere_615B_type_IVF_cell_number_8

description: cellnumber 8


title: Senescence - shNUCKS-2 Rep B

description: Library name: Sample 28


title: Day7, scRNA

description: 10X Genomics


title: DU145_RR_miR-neg, rep2

value: RR

value: miR control


title: DU145_RR_miR-92a, rep3


title: 15287X127_blastomere_615A_type_IVF_cell_number_8

description: cellnumber 8


title: FW_H_4

value: hypothalamus

value: Shanma duck

value: reared in water-floor combination system


title: Senescence - shNUCKS-2 Rep A

description: Library name: Sample 27


title: DU145_RR_miR-92a, rep2


title: 15287X126_blastomere_614H_type_IVF_cell_number_8

description: cellnumber 8


title: C_H_1

value: reared with multilayer cages


title: Senescence - shNUCKS-1 Rep B

description: Library name: Sample 26


title: Day4, scRNA

description: 10X Genomics


title: 15287X125_blastomere_614G_type_IVF_cell_number_8

description: cellnumber 8


title: DU145_RR_NT, rep2


title: Day0, scRNA

description: 10X Genomics


title: IgG_L854F

city: Bronx

first: Matanel

last: Yheskel

state: NY

address: 1300 Morris Park

department: Genetics

institute: Albert Einstein College of Medicine

description:
Library name: IgG_L854F
CUT&RUN for IgG in L854F

data_processing:
Raw reads quality controlled and trimmed using rfastp (v 1.6.0) and were aligned using Rsubread (2.10.5) to the dm6 Drosophila melanogaster genome assembly
Assembly: dm6
Supplementary files format and content: merged bigwig files
Library strategy: CUT&RUN

source_name: Brain

extract_protocol:
Epicypher CUT & RUN Kit
Epicypher Library Prep Kit

value: Brain


title: IgG_JmjC

description:
Library name: IgG_JmjC
CUT&RUN for IgG in JmjC

value: JmjC


title: 15287X123_blastomere_614E_type_IVF_cell_number_8

description: cellnumber 8


title: DU145_RR_NT, rep3


title: IgG_WT

description:
Library name: IgG_WT
CUT&RUN for IgG in WT

value: WT


title: Senescence - shSC Rep A

description: Library name: Sample 23

value: NUCKS1 WT


title: DU145_RR_miR-neg, rep1

value: prostate cancer cell line


title: 15287X124_blastomere_614F_type_IVF_cell_number_8

description: cellnumber 8


title: DU145_RR_miR-92a, rep1


title: Proliferating - shNUCKS-3 Rep B

description: Library name: Sample 22

value: Proliferating


title: H3K4me3_L854F_3

description:
Library name: H3K4me3_L854F_3
CUT&RUN for H3K4me3 in L854F


title: DU145_RR_miR-200c, rep2


title: 15287X121_blastomere_614C_type_IVF_cell_number_8

description: cellnumber 8

value: IVF


title: Senescence - shSC Rep B

description: Library name: Sample 24


title: Proliferating - shNUCKS-3 Rep A

description: Library name: Sample 21

value: NUCKS1 KD


title: H3K4me3_L854F_2

description:
Library name: H3K4me3_L854F_2
CUT&RUN for H3K4me3 in L854F


title: Senescence - shNUCKS-1 Rep A

description: Library name: Sample 25

value: Etoposide


title: 15287X120_blastomere_614B_type_IVF_cell_number_8

description: cellnumber 8


title: 15287X119_blastomere_614A_type_IVF_cell_number_8

description: cellnumber 8


title: H3K4me3_L854F_1

description:
Library name: H3K4me3_L854F_1
CUT&RUN for H3K4me3 in L854F


title: Proliferating - shNUCKS-2 Rep B

description: Library name: Sample 20


title: H3K4me3_JmjC_3

description:
Library name: H3K4me3_JmjC_3
CUT&RUN for H3K4me3 in JmjC


title: Proliferating - shNUCKS-2 Rep A

description: Library name: Sample 19


title: DU145_RS_NT, rep2

value: RS


title: 15287X122_blastomere_614D_type_IVF_cell_number_8

description: cellnumber 8


title: ipsc_grna_4

city: San Francisco

first: David

last: Wu

state: California

address: 35 Medical Center Way

institute: UCSF

description:
Perturb-Seq of iPSCs, Rep4
sgrna_counts.mtx.gz

data_processing:
Pre-processing, alignment, and gene quantification using cellranger (3.1.0)
Genome_build: GRCh37.74
Supplementary_files_format_and_content: Counts matrix

source_name: iPSC WTC

growth_protocol: Essential 8 medium

extract_protocol:
10x Genomics Chromium 3' Assay v3
PE100

treatment_protocol: CRISPRi

value: iPSC

tag: time

tag: library type

value: CRISPR gRNA Capture


title: Proliferating - shNUCKS-1 Rep A

description: Library name: Sample 17

tag: cell line


title: Proliferating - shNUCKS-1 Rep B

description: Library name: Sample 18


title: 15287X117_blastomere_612G_type_IVF_cell_number_8

description: cellnumber 8


title: H3K4me3_JmjC_1

description:
Library name: H3K4me3_JmjC_1
CUT&RUN for H3K4me3 in JmjC


title: H3K4me3_JmjC_2

description:
Library name: H3K4me3_JmjC_2
CUT&RUN for H3K4me3 in JmjC


title: ipsc_grna_2

description:
Perturb-Seq of iPSCs, Rep2
sgrna_counts.mtx.gz


title: 15287X116_blastomere_612F_type_IVF_cell_number_8

description: cellnumber 8


title: ipsc_grna_3

description:
Perturb-Seq of iPSCs, Rep3
sgrna_counts.mtx.gz


title: 15287X115_blastomere_612E_type_IVF_cell_number_8

description: cellnumber 8


title: Proliferating - shSC Rep B

description: Library name: Sample 16


title: H3K4me3_WT_2

description:
Library name: H3K4me3_WT_2
CUT&RUN for H3K4me3 in WT


title: Proliferating - shSC Rep A

description: Library name: Sample 15


title: ipsc_grna_1

description:
Perturb-Seq of iPSCs, Rep1
sgrna_counts.mtx.gz


title: ipsc_gene_4

description:
Perturb-Seq of iPSCs, Rep4
perturbseq_counts.mtx.gz

value: Gene Expression


title: DU145_RS_NT, rep1

tag: cell population


title: H3K4me3_WT_1

description:
Library name: H3K4me3_WT_1
CUT&RUN for H3K4me3 in WT


title: ipsc_gene_3

description:
Perturb-Seq of iPSCs, Rep3
perturbseq_counts.mtx.gz


title: PN_45apf_pooled

city: Ann Arbor

first: Eleanor

middle: Josephine

last: Clowney

state: MI

address: 1105 North University, 4218

department: MCDB

institute: University of Michigan

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.

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: 45 h APF

tag: Sex

value: pooled male and female


title: Thymol_1_3_gastrocnemius

city: Lausanne

first: Philipp

last: Gut

address: route du Jorat 57

department: Nestlé Institute of Health Sciences

country: Switzerland

institute: Société des produits Nestlé SA

description: Library name: CL000044551_S83

data_processing:
Raw counts were mapped to mouse reference genome (GRCm38-101) using STAR (v.2.5.3) and counted using htseq-count (0.6.1). Data were checked for quality and no outliers were detected at PCA. A filter was applied to select only genes with a minimum of 30 reads in at least 6 samples (corresponding to a threshold of 3.809 on the CPM values) and non-annotated genes were discarded. 10697 features were kept with these filtering criteria. To account for composition bias between libraries, we applied Trimmed Mean of M-value (TMM) normalization
Assembly: Mus_musculus.GRCm38.101
Supplementary files format and content: cells_log2_norm_symbol.csv, comma delimited file containing filtered and log2 normalized counts for all samples

organism: Mus musculus

source_name: gastrocnemius

extract_protocol:
Total RNA from frozen tissue was extracted using the Agencourt RNAdvance Tissue Kit (Beckman Coulter)
75 ng of total RNA (8.9 < RQN<10) were used to generate the libraries using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, GmbH, Vienna, Austria) following 20 cycles of PCR amplification

treatment_protocol: SAMP8 mice at the age of 8 months received thymol (20 mg/kg body weight per day) or vehicle for 3 months.

value: gastrocnemius


title: 15287X113_blastomere_612C_type_IVF_cell_number_8

description: cellnumber 8


title: 15287X112_blastomere_612B_type_IVF_cell_number_8

description: cellnumber 8


title: Thymol_17_22_gastrocnemius

description: Library name: CL000044550_S82


title: ipsc_gene_2

description:
Perturb-Seq of iPSCs, Rep2
perturbseq_counts.mtx.gz


title: H3K4me3_WT_3

description:
Library name: H3K4me3_WT_3
CUT&RUN for H3K4me3 in WT

value: Brain


title: Day11, scRNA

description: 10X Genomics

value: umbilical cord blood

value: TPO cultrued


title: 15287X111_blastomere_612A_type_IVF_cell_number_8

description: cellnumber 8


title: KC_45apf_pooled

description: gene expression profiling


title: Thymol_16_21_gastrocnemius

description: Library name: CL000044549_S81


title: ipsc_gene_1

description:
Perturb-Seq of iPSCs, Rep1
perturbseq_counts.mtx.gz


title: 15287X114_blastomere_612D_type_IVF_cell_number_8

description: cellnumber 8


title: Thymol_15_20_gastrocnemius

description: Library name: CL000044548_S80


title: Heat Heat Selected_rep4_RNA

city: Antwerpen

first: Jesper

middle: Ruben

last: van Dijk

state: Antwerpen

address: Universiteitsplein 1, Building C

department: Biology

country: Belgium

institute: University of Antwerp

data_processing:
Sequences were checked for quality using FastQC (v0.11.4)
trimmed with Trimmomatic  (v0.35), LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
aligned to gene sequences of the Araport 11 reference genome and counted using STAR
Raw counts were normalized and significance for the effect of treatment, selection and interaction on expression levels was determined with DESeq2
Differentially expressed genes were clustered in MeV
Assembly: Araport 11
Supplementary files format and content: Counttable in tab-delimited text files

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: Plants were grown for 21 days and kept to developed seeds

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit
Library preparation was performed using TruSeq® Stranded mRNA sample preparation 96 rcx kit (Illumina™) and mRNA was purified using poly-A tail targeting beads.

treatment_protocol: Plants were then either kept at control conditions, or placed in heat conditions for 10 days by which they were harvested

value: leaves

value: Heat selected line grown under Heat conditions


title: 15287X110_blastomere_611H_type_IVF_cell_number_8

description: cellnumber 8


title: 15287X109_blastomere_611G_type_IVF_cell_number_8

description: cellnumber 8


title: Embryo_WT_Zld_Input_R2

value: Stage 5 embryo


title: Heat Heat Selected_rep2_RNA


title: Control_13_15_gastrocnemius

description: Library name: CL000044547_S79


title: Embryo_WT_Zld_IP_R2

value: Zld (Harrison et al., 2010)


title: Heat Heat Selected_rep1_RNA


title: 15287X108_blastomere_611F_type_IVF_cell_number_8

description: cellnumber 8

value: IVF


title: Control_12_35_gastrocnemius

description: Library name: CL000044546_S78


title: Embryo_WT_Zld_Input_R1


title: Control Heat Selected_rep4_RNA

value: Heat selected line grown under Control conditions


title: Thymol_11_34_gastrocnemius

description: Library name: CL000044545_S77


title: Embryo_WT_Zld_IP_R1


title: DN_45apf_pooled

description: gene expression profiling


title: Control_18_18_gastrocnemius

description: Library name: CL000044552_S84


title: 15287X106_blastomere_611D_type_IVF_cell_number_8

description: cellnumber 8


title: 15287X118_blastomere_612H_type_IVF_cell_number_8

description: cellnumber 8


title: Control Heat Selected_rep3_RNA


title: Control_9_32_gastrocnemius

description: Library name: CL000044544_S76


title: chick_scRNA_cerebella_sublibrary2

city: Farmington

first: Nagham

last: Khouri-Farah

state: Connecticut

address: 400 Farmington Ave

department: Genetics and Genome Sciences

institute: UConn Health

data_processing:
The raw reads were processed to molecule counts using the Parse recommended pipeline with default setting
The raw UMI counts from Cell Ranger was processed by the Seurat R package.
The count matrix was uploaded.
Assembly: GRCg7b
Supplementary files format and content: count matrix in mtx format

organism: Gallus gallus

source_name: Cerebellum

extract_protocol:
Freshly disected cerebella from chicken embryos at stages E6, E7, E8 and E9 in ice-cold phosphate buffered saline. The dissected tissues were pooled and cut into pieces, smaller than 1 mm in dimension and processed according to 10X Genomics protocaol for scRNA-seq of embryonic mouse brain. Parse Biotechnology's Evercode WT Mini kit was used for scRNA extraction.
Parse Biotechnology's Evercode WT Mini kit was used to create libraries.
Evercode WT Mini kits from Parse Biosciences

value: Cerebellum

value: E6, E7, E8 and E9

value: wild type


title: 15287X105_blastomere_611C_type_IVF_cell_number_8

description: cellnumber 8


title: 15287X104_blastomere_611B_type_IVF_cell_number_8

description: cellnumber 8


title: chick_scRNA_cerebella_sublibrary1


title: Control Heat Selected_rep1_RNA


title: Control_8_31_gastrocnemius

description: Library name: CL000044543_S75


title: Thymol_8_30_gastrocnemius

description: Library name: CL000044542_S74


title: 15287X103_blastomere_611A_type_IVF_cell_number_8

description: cellnumber 8


title: Heat Control selected_rep4_RNA

value: Control line grown under Heat conditions


title: 15287X102_blastomere_610H_type_IVF_cell_number_8

description: cellnumber 8


title: 15287X107_blastomere_611E_type_IVF_cell_number_8

description: cellnumber 8


title: Thymol_7_26_gastrocnemius

description: Library name: CL000044541_S73


title: Thymol_7_28_gastrocnemius

description: Library name: CL000044540_S72


title: Heat Control selected_rep3_RNA


title: [DDB_PD_111]_[DDB35_ZnFeHigh]_[Fed-batch]_[24h]_[R2]

city: Kgs. Lyngby

first: Felix

last: Beulig

address: Kemitorvet 220

country: Denmark

institute: Novo Nordisk Center for Biosustainability

data_processing:
First, raw read trimming was performed using Trim Galore with default options, followed by FastQC on the trimmed reads. Next, reads were aligned to the E. coli K-12 MG1655 reference genome (NC_000913.3) using Bowtie. The read direction was inferred using RSeQC. Read counts were generated using featureCounts. All quality control metrics were compiled using MultiQC. Finally, the expression dataset was reported in units of log-transformed transcripts per million (log(TPM).
Assembly: Reference genome E. coli MG1655 (NC_000913.3)
Supplementary files format and content: Raw data files and comma-delimited text file reporting logtpm values for each sample

organism: Escherichia coli

source_name: Escherichia coli cells

growth_protocol: Batch-to-fed-batch fermentation experiments were performed in 0.25 L Ambr® fermenters (Sartorius) with 2 different media compositions (“High Metal” and “Low Metal” medium)

extract_protocol:
All transcriptome samples were collected and prepared in biological duplicates, whereby either 2 ml of culture (low cell density culture, batch phase) or 0.5 ml of culture (high cell density culture, fed batch phase) was added to 6 ml of Qiagen RNA-protect Bacteria Reagent immediately after sample collection. This solution was then vortexed for 30 seconds, incubated at room temperature for 5 minutes, and then centrifuged. The supernatant was then removed and the cell pellet was stored at -80° C. The RNeasy Mini Kit (Qiagen) was used to extract and purify RNA from the cell pellets per vendor protocol, including on-columns DNase treatment for 30 minutes at room temperature. RNA was quantified using qubit fluorometer (Thermofisher) and integrity was assessed using fragment analyzer (Agilent Technologies).
Ribosomal RNA was removed using QIAseq FastSelect –5S/16S/23S kit (Qiagen). Sequencing libraries were prepared with the KAPA Stranded RNA-Seq Library Preparation Kit (Kapa Biosystems) and assessed using fragment analyzer (Agilent Technologies). The libraries were then subjected to paired end sequencing on Illumina Nextseq using Nextseq Mid Output kit (Illumina) with a read length of 150 bp.

treatment_protocol: The “Low Metal” batch media contained base medium (22 g L-1 D-(+)-glucose monohydrate, 7.6 g L-1 (NH4)2SO4, 15.7 g L-1 KH2PO4, 0.241 g L-1 MgSO4, 100 mg L-1 thiamine hydrochloride, 0.5 mL L-1 Antifoam 204), and 1 mL L-1 of trace metal solution (0.48 g L-1 CuSO4·5H2O, 0.54 mg L-1 CoCl·7H2O, 0.54 g L-1 ZnSO4·7H2O, 2 g L-1 CaCl2·2H2O, 41.8 g L-1 FeCl3·6H2O, 0.3 g L-1 MnSO4·H2O, 33.4 g L-1 Na2EDTA, 0.5 g L-1 Na2MoO4·2H2O). The “High Metal” batch media contained the same base medium, 3.5 mL L-1 trace metal solution and was additionally supplemented with 1.86 g L-1 citric acid monohydrate and 41.8 mg L-1 FeCl3·6H2O, 21.6 mg L-1 ZnSO4·5H2O). Initial batch fermentations were performed with base medium until complete glucose consumption, marked by a 50% decline in the rate of CO2 formation, triggering an automatic switch to fed-batch operation with continuous supply of the feed medium (550 g L-1 D-(+)-glucose monohydrate, 13.7 g L-1 MgSO4·7H2O)

value: Escherichia coli cells


title: [DDB_PD_111]_[DDB35_ZnFeHigh]_[Fed-batch]_[20h]_[R2]


title: Heat Control selected_rep2_RNA


title: [DDB_PD_111]_[DDB35_ZnFeHigh]_[Fed-batch]_[20h]_[R1]


title: Control Heat Selected_rep2_RNA


title: 15287X099_blastomere_610E_type_IVF_cell_number_8

description: cellnumber 8


title: Thymol_6_24_gastrocnemius

description: Library name: CL000044538_S70


title: Control_6_23_gastrocnemius

description: Library name: CL000044537_S69


title: Control control selected_rep3_RNA

value: Control line grown under Control conditions


title: 15287X098_blastomere_610D_type_IVF_cell_number_8

description: cellnumber 8


title: [DDB_PD_111]_[DDB35_ZnFeHigh]_[Fed-batch]_[18h]_[R2]


title: [DDB_PD_111]_[DDB35_ZnFeHigh]_[Fed-batch]_[18h]_[R1]


title: 15287X097_blastomere_610C_type_IVF_cell_number_8

description: cellnumber 8


title: [DDB_PD_111]_[DDB35_ZnFeHigh]_[Fed-batch]_[15h]_[R2]


title: Heat Heat Selected_rep4_Bisulfite

description: 2x 50 bp

data_processing:
Sequences were checked for quality using FastQC
trimmed with Trim galore, aligned in paired-end mode with Bismark (v0.20.0) using Bowtie2 (v2.3.4.3) with Araport 11 as reference genome.
Output files were sorted and further analysed using methylKit
In addition, output files from Bismark were read into CGmapTools
Assembly: Araport 11
Supplementary files format and content: Bismark files, seperated by methylation context

extract_protocol:
DNA was isolated and converted using sodium bisulfite (EZ DNA Methylation-Gold Kits, Zymo Research, Irvine, U.S.A.)
library preparation (TruSeq Methyl Capture EPIC Library Prep Kit, Illumina)


title: Control control selected_rep2_RNA


title: [DDB_PD_111]_[DDB35_ZnFeHigh]_[Fed-batch]_[24h]_[R1]


title: Thymol_5_16_gastrocnemius

description: Library name: CL000044535_S67


title: 15287X096_blastomere_610B_type_IVF_cell_number_8

description: cellnumber 8


title: Heat Heat Selected_rep3_Bisulfite

description: 2x 50 bp


title: Control_5_14_gastrocnemius

description: Library name: CL000044534_S66


title: Control_7_27_gastrocnemius

description: Library name: CL000044539_S71


title: [DDB_PD_111]_[DDB35_ZnFeHigh]_[Fed-batch]_[12h]_[R2]


title: [DDB_PD_111]_[DDB35_ZnFeHigh]_[Fed-batch]_[15h]_[R1]


title: Control control selected_rep4_RNA


title: Heat Heat Selected_rep2_Bisulfite

description: 2x 50 bp


title: Thymol_4_11_gastrocnemius

description: Library name: CL000044533_S65


title: [DDB_PD_111]_[DDB35_ZnFeHigh]_[Fed-batch]_[12h]_[R1]


title: 15287X094_blastomere_585H_type_IVF_cell_number_8

description: cellnumber 8


title: Control_5_19_gastrocnemius

description: Library name: CL000044536_S68


title: [DDB_PD_111]_[DDB35_ZnFeHigh]_[Fed-batch]_[8h]_[R2]


title: Heat Heat Selected_rep1_Bisulfite

description: 2x 50 bp


title: Control Heat Selected_rep4_Bisulfite

description: 2x 50 bp


title: 15287X093_blastomere_585G_type_IVF_cell_number_8

description: cellnumber 8


title: [DDB_PD_111]_[DDB35_ZnFeHigh]_[Fed-batch]_[8h]_[R1]


title: Thymol_3_7_gastrocnemius

description: Library name: CL000044531_S63


title: 15287X101_blastomere_610G_type_IVF_cell_number_8

description: cellnumber 8


title: 15287X092_blastomere_585F_type_IVF_cell_number_8

description: cellnumber 8


title: [DDB_PD_111]_[DDB35_ZnFeHigh]_[Fed-batch]_[4h]_[R2]


title: 15287X091_blastomere_585E_type_IVF_cell_number_8

description: cellnumber 8


title: 15287X095_blastomere_610A_type_IVF_cell_number_8

description: cellnumber 8


title: Control Heat Selected_rep2_Bisulfite

description: 2x 50 bp


title: 15287X100_blastomere_610F_type_IVF_cell_number_8

description: cellnumber 8


title: Thymol_2_6_gastrocnemius

description: Library name: CL000044529_S61


title: 15287X090_blastomere_585D_type_IVF_cell_number_8

description: cellnumber 8


title: Control_1_1_gastrocnemius

description: Library name: CL000044528_S60


title: 15287X089_blastomere_585C_type_IVF_cell_number_8

description: cellnumber 8


title: [DDB_PD_111]_[DDB35_ZnFeHigh]_[Fed-batch]_[4h]_[R1]


title: Control Heat Selected_rep3_Bisulfite

description: 2x 50 bp


title: Heat Control selected_rep4_Bisulfite

description: 2x 50 bp


title: [DDB_PD_111]_[DDB35_ZnFeHigh]_[Batch]_[0h]_[R1]


title: DMSO-6

description: Library name: CL000044521_S53

source_name: MAFs

growth_protocol: Primary mouse adult fibroblasts (MAFs) were obtained from C57BL6/j. Biopsies were cut in small pieces with a scalpel blade and distributed on the surface of-coated dishes with 1.5 mL of Dulbecco's Modified Eagle Medium (DMEM) high glucose supplemented with 20% of Fetal Bovine Serum (FBS).

extract_protocol:
Total RNA was extracted using the Agencourt RNAdvance Tissue Kit (Beckman Coulter)
75 ng of total RNA (8.9 < RQN<10) were used to generate the libraries using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, GmbH, Vienna, Austria) following 20 cycles of PCR amplification

treatment_protocol: Thymol was dissolved in DMSO and added to the cell growth medium for 24 h. As untreated condition, cells were cultured with an equal volume of DMSO in the growth medium.

value: MAFs

value: Primary mouse adult fibroblast

value: WT

value: DMSO


title: 15287X088_blastomere_585B_type_IVF_cell_number_8

description: cellnumber 8


title: [DDB_PD_111]_[DDB35_ZnFeHigh]_[Batch]_[0h]_[R2]


title: [DDB_PD_111]_[DDB35_ZnFeLow]_[Fed-batch]_[24h]_[R2]


title: Thymol_18_9_gastrocnemius

description: Library name: CL000044530_S62

value: gastrocnemius


title: Control Heat Selected_rep1_Bisulfite

description: 2x 50 bp

value: leaves


title: 15287X087_blastomere_585A_type_IVF_cell_number_8

description: cellnumber 8


title: Heat Control selected_rep2_Bisulfite

description: 2x 50 bp


title: Heat Control selected_rep3_Bisulfite

description: 2x 50 bp


title: [DDB_PD_111]_[DDB35_ZnFeLow]_[Fed-batch]_[24h]_[R1]


title: Heat Control selected_rep1_Bisulfite

description: 2x 50 bp


title: [DDB_PD_111]_[DDB35_ZnFeLow]_[Fed-batch]_[20h]_[R2]


title: 15287X085_blastomere_584G_type_IVF_cell_number_8

description: cellnumber 8


title: DMSO-2

description: Library name: CL000044519_S51


title: DMSO-3

description: Library name: CL000044517_S49


title: Control_4_10_Gastrocnemius

description: Library name: CL000044532_S64


title: Control control selected_rep4_Bisulfite

description: 2x 50 bp


title: [DDB_PD_111]_[DDB35_ZnFeLow]_[Fed-batch]_[20h]_[R1]


title: Control control selected_rep3_Bisulfite

description: 2x 50 bp


title: DMSO-1

description: Library name: CL000044516_S48


title: DU145_RR_miR-200c, rep1

value: prostate cancer cell line

tag: phenotype

value: RR

tag: transfection

tag: replicate


title: [DDB_PD_111]_[DDB35_ZnFeLow]_[Fed-batch]_[18h]_[R2]

tag: cell type

tag: strain


title: 15287X084_blastomere_584F_type_IVF_cell_number_8

description: cellnumber 8


title: Thymol100-6

description: Library name: CL000044515_S47

tag: treatment

value: Thymol


title: DMSO-4

description: Library name: CL000044520_S52


title: Control control selected_rep2_Bisulfite

description: 2x 50 bp

tag: tissue


title: 15287X082_blastomere_584D_type_IVF_cell_number_8

description: cellnumber 8

value: IVF


title: Control control selected_rep1_Bisulfite

description: 2x 50 bp

tag: genotype


title: [DDB_PD_111]_[DDB35_ZnFeLow]_[Fed-batch]_[15h]_[R2]


title: 15287X081_blastomere_584C_type_IVF_cell_number_8

description: cellnumber 8


title: 15287X086_blastomere_584H_type_IVF_cell_number_8

description: cellnumber 8


title: Thymol100-4

description: Library name: CL000044514_S46


title: DMSO-5

description: Library name: CL000044518_S50


title: mbd9-1 untreated seedling H2A.Z ChIP Rep 2

city: Atlanta

first: Roger

last: Deal

state: Georgia

address: 1510 Clifton Road NE, Room 2006

institute: Emory University

data_processing:
Reads were aligned to the Col-PEK genome assembly with Bowtie2  using --local --very-sensitive --no-mixed --no-discordant --phred33 parameters.  Samtools -view bS, -index, and -sort functions were used to process resulting alignment files  Picard MarkDuplicates function with REMOVE_DUPLICATES=T parameter was used to remove sequencing duplicates. deepTools2 bamCoverage function with parameters --normalizeUsing RPKM and --extendReads were used to create Read Per Kilobase Million (RPKM) normalized bigwig files for visualization.
Assembly: Col-PEK
Supplementary files format and content: Reads Per Kilobase Million (RPKM) normalized bigWig files showing enrichment of each protein across the entire Col-PEK genome

source_name: 7-day-old whole seedling

growth_protocol: Plants were grown horizontally on 1/2 MS plates sealed with medical tape in growth chambers at +20°C under a 16 hour-light/8-hour dark cycle for 7 days

extract_protocol:
Frozen tissue was ground in a mortar and pestle, homogenized into a slurry in 250 µl of Buffer S and moved directly to sonication. Post sonication, lysate was diluted 10x with Buffer F for use in pulldowns. 50 µl of diluted lysate was saved as input. αH2A.Z (2 μg/mL), αMBD9 (2 μg/mL) or αPIE1 (3 μg/mL) antibodies were added to diluted lysates and incubated overnight at 4°C on a nutator for end-over-end mixing. 20 µl of Protein G Dynabeads (Invitrogen) per replicate were washed in excess Buffer F, resuspended to their original volume and added to each pulldown. Samples were incubated with beads at 4°C on a nutator for 2 hours. ChIP DNA was extracted via the MinElute PCR Purification Kit (Qiagen)
Sequencing libraries were made using the ThruPLEX DNA-Seq Kit (Takara).

treatment_protocol: Plants were either untreated, or treated with 10uM (+) ABA for 4 hours or a Mock solution (DMSO in Water) for 4 hours, then tissue was collected, crosslinked, and frozen in liquid N2. All tissue collected around 1500 hours.

value: 7-day-old whole seedling


title: Thymol100-2

description: Library name: CL000044513_S45


title: [DDB_PD_111]_[DDB35_ZnFeLow]_[Fed-batch]_[15h]_[R1]


title: Thymol100-5

description: Library name: CL000044512_S44


title: DU145_RR_NT, rep1

extract_protocol:
miRNeasy kit (Qiagen)
Libraries were prepared according to NovaSeq 6000 Sequencing Sytem's instructions accompanying the NovaSeq 6000 SP Reagent Kit (Ref# 20028401). Libraries were sequenced on the NovaSeq 6000 following the manufacturer's protocols.
3' SRP


title: 15287X079_blastomere_584A_type_IVF_cell_number_8

description: cellnumber 8

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


title: 15287X083_blastomere_584E_type_IVF_cell_number_8

description: cellnumber 8


title: Thymol100-1

description: Library name: CL000044510_S42


title: D1209A untreated seedling PIE1 ChIP Rep 1


title: D1209A untreated seedling PIE1 ChIP Rep 2


title: [DDB_PD_111]_[DDB35_ZnFeLow]_[Fed-batch]_[18h]_[R1]


title: 15287X078_blastomere_526H_type_IVF_cell_number_8

description: cellnumber 8


title: 15287X077_blastomere_526G_type_IVF_cell_number_8

description: cellnumber 8


title: Thymol100-3

description: Library name: CL000044511_S43


title: [DDB_PD_111]_[DDB35_ZnFeLow]_[Fed-batch]_[12h]_[R1]


title: [DDB_PD_111]_[DDB35_ZnFeLow]_[Fed-batch]_[12h]_[R2]


title: D1209A untreated seedling MBD9 ChIP Rep 2


title: D1209A untreated seedling  MBD9 ChIP Rep 1


title: [DDB_PD_111]_[DDB35_ZnFeLow]_[Fed-batch]_[8h]_[R2]


title: [DDB_PD_111]_[DDB35_ZnFeLow]_[Fed-batch]_[8h]_[R1]


title: Org_USI_4mo_3p

city: Camden

first: Jean-Pierre

last: Issa

state: NJ

address: 403 Haddon Ave

institute: Coriell Institute for Medical Research

description:
Library name: YU_P2_145
Organoid Passage 2_mouse_145_4mo

data_processing:
Sequenced RRBS libraries were trimmed with TrimGalore, and reads aligned to the mm9 mouse genome using the Bismark Bisulfite Read Mapper and Methylation Caller, to call CpG methylation. Data were filtered for a minimum coverage of 20 reads per CpG. Differential methylation analysis was performed using the limma package in R. First, a design matrix was constructed to account for experimental conditions and potential confounders. The lmFit function was then applied to fit a linear model on the M-values for each CpG site, followed by the application of empirical Bayes moderation using the eBayes function to obtain moderated t-statistics and associated p-values.
Assembly: mm9

source_name: Upper small Intestine  epithelium

growth_protocol: Intestinal crypts, from Lgr5-EGFP-IRES-creERT2 (JAX Labs) mice aged 4 months and 24 months  , were isolated by dissecting the small intestine (upper small intestine and lower small intestine) and colon, following euthanasia. The intestine was cut longitudinally and washed with cold PBS, to remove debris. The tissue was then cut into 2–5 mm pieces and incubated in Gentle Cell Dissociation Reagent (STEMCELL Technologies, #100-1077), at room temperature for 30 min, on an orbital shaker, at 60 rpm. After incubation, the tissue was vortexed gently to release the crypts. The supernatant was filtered through a 70 µm cell strainer (Thermo Fisher, #22363548) and crypts collected by centrifugation at 250g, for 5 min, at room temperature. The crypt pellet was resuspended in Complete Mouse IntestiCultÔ  Organoid Growth Media (STEMCELL Technologies, # 06005), and Matrigel (Corning, #356231) added to a 1:1 ratio. The organoids were added as 50 µL droplets into a pre-warmed 24-well plate (CellTreat, #229123) and incubated at 37°C for 10–15 min, to solidify the Matrigel.Once the Matrigel solidified, 7500 µL of complete IntestiCult™ Organoid Growth Medium (Mouse) (STEMCELL) was added to each well, with 1% Primocin (InvivoGen, # ant-pm-1). Organoids were cultured in a 5% CO₂ humidified incubator at 37°C, with medium changes every 48 hr. Organoids were passaged every 7 days, when reaching 200–500 µm in diameter, by mechanically disrupting the Matrigel and organoids using room temperature Gentle Dissociation Reagent, followed by resuspension of the fragments in fresh IntestiCult organoid growth media, and Matrigel (1:1 ratio), and re-plating.

extract_protocol:
Cell pools from all organoids were lysed in 2% SDS and 25 mM EDTA, overnight. Ammonium acetate (10 M) was added to precipitate SDS with proteins, which were removed by centrifugation at 12,000 rpm. DNA was then precipitated with isopropanol, washed in 70% ethanol, and dissolved in LTET (10 mM Tris, 0.1 mM EDTA, 0.1% Tween 20). DNA concentration was measured using the Qubit dsDNA Broad Range kit (Thermo Fisher, #Q32850).
Two micrograms of DNA were digested with 100 U of MspI endonuclease (NEB, #R0106), at 37°C, for 3.5 h. The Klenow fragment (3′ > 5′ exo-  ) DNA polymerase (NEB, #M0212) was used to fill in 3′ recesses and generate 3′ dA overhangs. Size selection was performed using AMPure XP beads (Beckman, #A63881), with a 2X bead-to-DNA volume ratio. Methylated sequencing adapters (NEB, #E7535) were ligated to DNA fragments with T4 DNA ligase (NEB #M0202), at 16°C overnight. Adapters were cleaved by incubation with USER enzyme (NEB #M5505), at 37°C, for 15 min. Dual size selection with AMPure XP beads removed DNA fragments greater than 500 bp and less than 150 bp. Purified DNA fragments were bisulfite-converted using the EpiTect Bisulfite Conversion Kit (Qiagen, #59104). The bisulfite-converted fragments were cleaned using a 3X AMPure bead-to-DNA ratio. NEBNext Index i7 primers (NEB #7335, #7500) were used to amplify libraries with EpiMark Hot Start Taq (NEB, #M0490), for 15 cycles. Library concentrations were measured using the Qubit dsDNA High Sensitivity kit (Thermo Fisher, #Q32851). The Agilent Bioanalyzer determined size distribution and molarity using the Agilent High Sensitivity DNA kit (Agilent, #5067-4626). Libraries were pooled to a 10 nM concentration and spiked with 25% phiX (Illumina, #FC1103001) for sequence diversity. Sequencing occurred over several years at multiple facilities.

treatment_protocol: Organoids were treated with 50 ng/mL decitabine (DAC) beginning 24 hr after plating. DAC was replenished every 48 hr during media changes, and organoids were passaged on day 7. After each cycle of DAC treatment, organoids were passaged twice without DAC exposure, allowing for a rest period  . This treatment and rest cycle was repeated for a total of 21 days.

value: Upper small Intestine  epithelium

value: Organoid


title: 15287X080_blastomere_584B_type_IVF_cell_number_8

description: cellnumber 8


title: Org_USI_4mo_14p

description:
Library name: YU_P13_145
Organoid Passage 13_mouse_145_4mo


title: 15287X075_blastomere_526E_type_IVF_cell_number_8

description: cellnumber 8


title: D1209A untreated seedling H2A.Z ChIP Rep 2


title: Org_LSI_4mo_3p

description:
Library name: YL_P2_145
Organoid Passage 2_mouse_145_4mo

source_name: Lower small Intestine  epithelium

value: Lower small Intestine  epithelium


title: [DDB_PD_111]_[DDB35_ZnFeLow]_[Fed-batch]_[4h]_[R1]


title: D1209A untreated seedling H2A.Z ChIP Rep 1


title: [DDB_PD_111]_[DDB35_ZnFeLow]_[Fed-batch]_[4h]_[R2]


title: 15287X074_blastomere_526D_type_IVF_cell_number_8

description: cellnumber 8

source_name: IVF


title: [DDB_PD_111]_[DDB35_ZnFeLow]_[Batch]_[0h]_[R2]


title: 15287X073_blastomere_526C_type_IVF_cell_number_8

description: cellnumber 8


title: WT untreated seedling PIE1 ChIP Rep 2


title: Org_LSI_4mo_14p

description:
Library name: YL_P13_145
Organoid Passage 13_mouse_145_4mo


title: [DDB_PD_111]_[DDB35_ZnFeLow]_[Batch]_[0h]_[R1]


title: WT untreated seedling PIE1 ChIP Rep 1


title: 15287X072_blastomere_526B_type_IVF_cell_number_8

description: cellnumber 8


title: Org_COL_4mo_14p

description:
Library name: YC_P13_145
Organoid Passage 13_mouse_145_4mo

source_name: Colon  epithelium

value: Colon  epithelium


title: [DDB_PD_110]_[SDT551_ZnFeHigh]_[Fed-batch]_[24h]_[R2]

value: Escherichia coli cells


title: 15287X076_blastomere_526F_type_IVF_cell_number_8

description: cellnumber 8


title: Org_COL_4mo_3p

description:
Library name: YC_P2_145
Organoid Passage 2_mouse_145_4mo


title: [DDB_PD_110]_[SDT551_ZnFeHigh]_[Fed-batch]_[24h]_[R1]


title: WT untreated seedling MBD9 ChIP Rep 2


title: P5_283_ctrl

description:
Library name: OU_P5_283
Organoid Passage 5_mouse_283_24mo


title: WT untreated seedling  MBD9 ChIP Rep 1


title: [DDB_PD_110]_[SDT551_ZnFeHigh]_[Fed-batch]_[20h]_[R2]


title: P5_285_ctrl

description:
Library name: OU_P5_285
Organoid Passage 5_mouse_285_24mo


title: mbd9-1 untreated seedling H2A.Z ChIP Rep 1


title: 15287X070_blastomere_525F_type_IVF_cell_number_8

description: cellnumber 8


title: 15287X069_blastomere_525E_type_IVF_cell_number_8

description: cellnumber 8


title: WT untreated seedling H2A.Z ChIP Rep 2


title: [DDB_PD_110]_[SDT551_ZnFeHigh]_[Fed-batch]_[20h]_[R1]


title: P4_283_ctrl

description:
Library name: OU_P3_283
Organoid Passage 3_mouse_283_24mo


title: 15287X067_blastomere_525C_type_IVF_cell_number_8

description: cellnumber 8


title: 91d_ANT1_ND6_IN

first: Joseph

middle: W

last: Guarnieri

state: PA

address: 3501 Civic Center Blvd

department: Center for Mitochondrial and Epigenomic Medicine

institute: Children's Hosptial of Philadelphia

description:
IonCode_0212
IonCode_205-212.txt

data_processing:
Sequencing data was aligned using the Ion Torrent S5 ampliSeqRNA and coverageAnalysis plugins.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: Heart

extract_protocol:
RNA was collected using TRIzol™ Reagent (Invitrogen, 15596026) from heart samples.
The RNA was assessed by NanoDrop spectrophotometer (ThermoFisher Scientific) and quantified by Qubit Flex (Thermofisher Scientific) using the Qubit RNA HS Assay Kit (Thermofisher Scientific, Q32855).
The RNA was diluted to 1.43 ng/ul and reverse transcribed into cDNA using the Ion Torrent™ NGS Reverse Transcription Kit (Cat. No. A45003). The RNA library was prepared using the Ion Torrent S5 Chef and Ion AmpliSeq Kit for Chef DL8 (Thermofisher Scientific, A29024) and sequenced using the Ion Torrent S5 Sequencer and Ion 540 Kit (Thermofisher Scientific, A30011).
For snRNA-seq, isolated nuclei were processed using the Chromium Single Cell 3ʹ Reagent V3.1 kit from 10X Genomics. A total of 8,000 nuclei per sample were loaded into a Chip G. Barcoding, cDNA amplification, and library construction were performed according to the Chromium 3ʹ V3.1 protocol. Sequencing was performed on a DNBSEQ-T7 platform targeting 20,000 reads per nucleus.

treatment_protocol: Bulk RNA sequencing and single nucleus RNA Sequencing (snRNA-seq) analysis on C57BL/6JEiJ, C57BL/6JEiJ Ant1-/-, and C57BL/6JEiJ Ant1-/- ND6P25L mice (WT, ANT1, ANT1 ND6), pericardially injected with 2.5x10^11 vg AAV2/9Des-Gfp-mAnt1 or 2.5x10^11 vg AAV2/9Des-Gfp .

value: Heart

value: C57BL/6JEiJ ANT1 -/- ND6 P25L

value: 2.5x10^11 vg AAV2/9Des-Gfp


title: [DDB_PD_110]_[SDT551_ZnFeHigh]_[Fed-batch]_[18h]_[R2]


title: P4_285_ctrl

description:
Library name: OU_P3_285
Organoid Passage 3_mouse_285_24mo


title: P3_285_ctrl

description:
Library name: OU_P2_285
Organoid Passage 2_mouse_285_24mo


title: P3_4mo

description:
Library name: YU_P2_202
Organoid Passage 2_mouse_202_24mo


title: 91c_ANT1_ND6_IN

description:
IonCode_0211
IonCode_205-212.txt


title: 15287X071_blastomere_526A_type_IVF_cell_number_8

description: cellnumber 8

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


title: 15287X066_blastomere_525B_type_IVF_cell_number_8

description: cellnumber 8


title: 61d_ANT1_ND6_IN

description:
IonCode_0210
IonCode_205-212.txt


title: 15287X064_blastomere_521H_type_IVF_cell_number_8

description: cellnumber 8


title: P3_283_ctrl

description:
Library name: OU_P2_283
Organoid Passage 2_mouse_283_24mo


title: [DDB_PD_110]_[SDT551_ZnFeHigh]_[Fed-batch]_[15h]_[R2]


title: 15287X065_blastomere_525A_type_IVF_cell_number_8

description: cellnumber 8


title: [DDB_PD_110]_[SDT551_ZnFeHigh]_[Fed-batch]_[15h]_[R1]


title: [DDB_PD_110]_[SDT551_ZnFeHigh]_[Fed-batch]_[18h]_[R1]


title: 61c_ANT1_ND6_IN

description:
IonCode_0209
IonCode_205-212.txt


title: 22d_ANT1_ND6_NI

description:
IonCode_0208
IonCode_205-212.txt


title: 15287X068_blastomere_525D_type_IVF_cell_number_8

description: cellnumber 8


title: [DDB_PD_110]_[SDT551_ZnFeHigh]_[Fed-batch]_[12h]_[R2]


title: 15287X062_blastomere_521F_type_IVF_cell_number_8

description: cellnumber 8


title: P3_24mo

description:
Library name: OU_P2_196
Organoid Passage 2_mouse_196_24mo


title: 15287X063_blastomere_521G_type_IVF_cell_number_8

description: cellnumber 8


title: WT untreated seedling H2A.Z ChIP Rep 1

value: WT


title: [DDB_PD_110]_[SDT551_ZnFeHigh]_[Fed-batch]_[12h]_[R1]


title: Org_USI_P28_4mo

description:
Library name: YU_P27_202
Organoid Passage 27_mouse_202_4mo


title: 22c_ANT1_ND6_NI

description:
IonCode_0207
IonCode_205-212.txt


title: [DDB_PD_110]_[SDT551_ZnFeHigh]_[Fed-batch]_[8h]_[R1]


title: P28_283_24mo

description:
Library name: OU_P27_283
Organoid Passage 27_mouse_283_24mo


title: [DDB_PD_110]_[SDT551_ZnFeHigh]_[Fed-batch]_[8h]_[R2]


title: P28_285_24mo

description:
Library name: OU_P27_285
Organoid Passage 27_mouse_285_24mo


title: 70d_B6ME_NI

description:
IonCode_0206
IonCode_205-212.txt


title: Org_USI_P28_4mo_1

description:
Library name: YU_P27_202_1
Organoid Passage 27_mouse_202_4mo


title: Org_USI_P28_24mo_1

description:
Library name: OU_P27_196_1
Organoid Passage 27_mouse_196_24mo


title: 70c_B6ME_NI

description:
IonCode_0205
IonCode_205-212.txt


title: 15287X057_blastomere_521A_type_IVF_cell_number_8

description: cellnumber 8


title: 15287X061_blastomere_521E_type_IVF_cell_number_8

description: cellnumber 8


title: [DDB_PD_110]_[SDT551_ZnFeHigh]_[Batch]_[0h]_[R2]


title: [DDB_PD_110]_[SDT551_ZnFeHigh]_[Fed-batch]_[4h]_[R1]


title: [DDB_PD_110]_[SDT551_ZnFeHigh]_[Fed-batch]_[4h]_[R2]


title: [DDB_PD_110]_[SDT551_ZnFeHigh]_[Batch]_[0h]_[R1]


title: 15287X059_blastomere_521C_type_IVF_cell_number_8

description: cellnumber 8


title: Org_USI_P28_24mo

description:
Library name: OU_P27_196
Organoid Passage 27_mouse_196_24mo


title: 15287X058_blastomere_521B_type_IVF_cell_number_8

description: cellnumber 8


title: 91a_ANT1_ND6_IN

description:
IonCode_0203
IonCode_197-204.txt


title: 15287X055_blastomere_550C_type_IVF_cell_number_4

description: cellnumber 4


title: 61b_ANT1_ND6_IN

description:
IonCode_0202
IonCode_197-204.txt


title: 15287X056_blastomere_550D_type_IVF_cell_number_4

description: cellnumber 4


title: 61a_ANT1_ND6_IN

description:
IonCode_0201
IonCode_197-204.txt


title: 22b_ANT1_ND6_NI

description:
IonCode_0200
IonCode_197-204.txt


title: 15287X060_blastomere_521D_type_IVF_cell_number_8

description: cellnumber 8


title: [DDB_PD_110]_[SDT551_ZnFeLow]_[Fed-batch]_[24h]_[R2]


title: P25_24mo

description:
Library name: OU_P24_196
Organoid Passage 24_mouse_196_24mo


title: P25_4mo

description:
Library name: YU_P24_202
Organoid Passage 24_mouse_202_4mo


title: 15287X053_blastomere_550A_type_IVF_cell_number_4

description: cellnumber 4


title: 70b_B6ME_NI

description:
IonCode_0198
IonCode_197-204.txt


title: [DDB_PD_110]_[SDT551_ZnFeLow]_[Fed-batch]_[20h]_[R2]


title: 70a_B6ME_NI

description:
IonCode_0197
IonCode_197-204.txt


title: 15287X052_blastomere_554F_type_IVF_cell_number_6

description: cellnumber 6


title: P14_4mo

description:
Library name: YU_P13_202
Organoid Passage 13_mouse_202_4mo


title: [DDB_PD_110]_[SDT551_ZnFeLow]_[Fed-batch]_[20h]_[R1]


title: 22a_ANT1_ND6_NI

description:
IonCode_0199
IonCode_197-204.txt


title: [DDB_PD_110]_[SDT551_ZnFeLow]_[Fed-batch]_[24h]_[R1]


title: P14_285_ctrl

description:
Library name: OU_P13_285
Organoid Passage 13_mouse_285_24mo


title: 91b_ANT1_ND6_IN

description:
IonCode_0204
IonCode_197-204.txt


title: 15287X054_blastomere_550B_type_IVF_cell_number_4

description: cellnumber 4


title: P13_285_ctrl

description:
Library name: OU_P12_285
Organoid Passage 12_mouse_285_24mo


title: P13_283_ctrl

description:
Library name: OU_P12_283
Organoid Passage 12_mouse_283_24mo


title: P14_283_ctrl

description:
Library name: OU_P13_283
Organoid Passage 13_mouse_283_24mo


title: [DDB_PD_110]_[SDT551_ZnFeLow]_[Fed-batch]_[18h]_[R2]


title: 15287X051_blastomere_554E_type_IVF_cell_number_6

description: cellnumber 6


title: P14_24mo

description:
Library name: OU_P13_196
Organoid Passage 13_mouse_196_24mo


title: [DDB_PD_110]_[SDT551_ZnFeLow]_[Fed-batch]_[15h]_[R2]


title: 15287X050_blastomere_554D_type_IVF_cell_number_6

description: cellnumber 6


title: 8d_ANT1_ND6_IN

description:
IonCode_0196
IonCode_189-196.txt

value: 2.5x10^11 vg AAV2/9Des-Gfp-mAnt1


title: [DDB_PD_110]_[SDT551_ZnFeLow]_[Fed-batch]_[18h]_[R1]


title: [DDB_PD_110]_[SDT551_ZnFeLow]_[Fed-batch]_[15h]_[R1]


title: [DDB_PD_110]_[SDT551_ZnFeLow]_[Fed-batch]_[12h]_[R2]


title: 8c_ANT1_ND6_IN

description:
IonCode_0195
IonCode_189-196.txt


title: 15287X049_blastomere_554C_type_IVF_cell_number_6

description: cellnumber 6


title: P12_285_ctrl

description:
Library name: OU_P11_285
Organoid Passage 11_mouse_285_24mo


title: 15287X047_blastomere_554A_type_IVF_cell_number_6

description: cellnumber 6


title: 15287X048_blastomere_554B_type_IVF_cell_number_6

description: cellnumber 6


title: 5c_ANT1_ND6_IN

description:
IonCode_0193
IonCode_189-196.txt


title: 22d_ANT1_IN

description:
IonCode_0192
IonCode_189-196.txt

value: C57BL/6JEiJ ANT1 -/-


title: P11CT285

description:
Library name: OU_P10_285
Organoid Passage 10_mouse_285_24mo


title: P12_283_ctrl

description:
Library name: OU_P11_283
Organoid Passage 11_mouse_283_24mo


title: 22c_ANT1_IN

description:
IonCode_0191
IonCode_189-196.txt


title: 21d_ANT1_IN

description:
IonCode_0190
IonCode_189-196.txt


title: Org_USI_P0_4mo

description:
Library name: YU_P0_202
Organoid Passage 0_mouse_202_4mo


title: [DDB_PD_110]_[SDT551_ZnFeLow]_[Fed-batch]_[8h]_[R1]


title: 5d_ANT1_ND6_IN

description:
IonCode_0194
IonCode_189-196.txt


title: P11CT283

description:
Library name: OU_P10_283
Organoid Passage 10_mouse_283_24mo


title: 15287X044_blastomere_524D_type_IVF_cell_number_6

description: cellnumber 6


title: Org_USI_P0_4mo_1

description:
Library name: YU_P0_202_1
Organoid Passage 0_mouse_202_4mo


title: [DDB_PD_110]_[SDT551_ZnFeLow]_[Fed-batch]_[4h]_[R2]


title: 20d_ANT1_IN

description:
IonCode_0188
IonCode_181-188.txt


title: 15287X043_blastomere_524C_type_IVF_cell_number_6

description: cellnumber 6


title: [DDB_PD_110]_[SDT551_ZnFeLow]_[Fed-batch]_[4h]_[R1]


title: Org_USI_P0_24mo

description:
Library name: OU_P0_196
Organoid Passage 0_mouse_196_24mo


title: 20c_ANT1_IN

description:
IonCode_0187
IonCode_181-188.txt


title: [DDB_PD_110]_[SDT551_ZnFeLow]_[Batch]_[0h]_[R2]


title: 15287X042_blastomere_524B_type_IVF_cell_number_6

description: cellnumber 6


title: 15287X041_blastomere_524A_type_IVF_cell_number_6

description: cellnumber 6


title: Org_USI_24mo_3p

description:
Library name: OU_P2_112
Organoid Passage 2_mouse_112_24mo


title: 83d_B6ME_IN

description:
IonCode_0186
IonCode_181-188.txt


title: [DDB_PD_110]_[SDT551_ZnFeLow]_[Fed-batch]_[8h]_[R2]


title: 15287X045_blastomere_524E_type_IVF_cell_number_6

description: cellnumber 6


title: [DDB_PD_110]_[SDT551_ZnFeLow]_[Batch]_[0h]_[R1]


title: 15287X046_blastomere_524F_type_IVF_cell_number_6

description: cellnumber 6


title: 15287X040_blastomere_523F_type_IVF_cell_number_6

description: cellnumber 6


title: 81d_B6ME_IN

description:
IonCode_0184
IonCode_181-188.txt


title: Org_USI_P0_24mo_1

description:
Library name: OU_P0_196_1
Organoid Passage 0_mouse_196_24mo


title: Org_USI_24mo_14p

description:
Library name: OU_P13_112
Organoid Passage 13_mouse_112_24mo


title: [DDB_PD_107]_[HMP3427_ZnFeHigh]_[Fed-batch]_[24h]_[R2]


title: 21c_ANT1_IN

description:
IonCode_0189
IonCode_189-196.txt


title: 15287X038_blastomere_523D_type_IVF_cell_number_6

description: cellnumber 6


title: 15287X039_blastomere_523E_type_IVF_cell_number_6

description: cellnumber 6


title: 81c_B6ME_IN

description:
IonCode_0183
IonCode_181-188.txt


title: [DDB_PD_107]_[HMP3427_ZnFeHigh]_[Fed-batch]_[20h]_[R2]


title: [DDB_PD_107]_[HMP3427_ZnFeHigh]_[Fed-batch]_[24h]_[R1]


title: OUorg3p_conca

description:
Library name: OU_P2_112_1
Organoid Passage 2_mouse_112_24mo


title: YLorg3p_concat

description:
Library name: YL_P2_145_1
Organoid Passage 2_mouse_145_4mo


title: 80d_B6ME_IN

description:
IonCode_0182
IonCode_181-188.txt


title: [DDB_PD_107]_[HMP3427_ZnFeHigh]_[Fed-batch]_[20h]_[R1]


title: 15287X036_blastomere_523B_type_IVF_cell_number_6

description: cellnumber 6


title: 15287X037_blastomere_523C_type_IVF_cell_number_6

description: cellnumber 6


title: 80c_B6ME_IN

description:
IonCode_0181
IonCode_181-188.txt


title: 83c_B6ME_IN

description:
IonCode_0185
IonCode_181-188.txt


title: OLorg3p_concat

description:
Library name: OL_P2_112_1
Organoid Passage 2_mouse_112_24moL


title: 15287X035_blastomere_523A_type_IVF_cell_number_6

description: cellnumber 6


title: [DDB_PD_107]_[HMP3427_ZnFeHigh]_[Fed-batch]_[18h]_[R2]


title: YCorg3p_concat

description:
Library name: YC_P2_145_1
Organoid Passage 2_mouse_145_4mo


title: [DDB_PD_110]_[SDT551_ZnFeLow]_[Fed-batch]_[12h]_[R1]


title: [DDB_PD_107]_[HMP3427_ZnFeHigh]_[Fed-batch]_[18h]_[R1]


title: 8b_ANT1_ND6_IN

description:
IonCode_0180
IonCode_173-180.txt


title: 15287X034_blastomere_522F_type_IVF_cell_number_6

description: cellnumber 6


title: 8a_ANT1_ND6_IN

description:
IonCode_0179
IonCode_173-180.txt


title: YUorg3p_concat

description:
Library name: YU_P2_145_1
Organoid Passage 2_mouse_145_4mo


title: [DDB_PD_107]_[HMP3427_ZnFeHigh]_[Fed-batch]_[15h]_[R2]


title: 15287X033_blastomere_522E_type_IVF_cell_number_6

description: cellnumber 6


title: 5b_ANT1_ND6_IN

description:
IonCode_0178
IonCode_173-180.txt


title: Org_LSI_24mo_3p

description:
Library name: OL_P2_112
Organoid Passage 2_mouse_112_24moL


title: [DDB_PD_107]_[HMP3427_ZnFeHigh]_[Fed-batch]_[15h]_[R1]


title: 15287X032_blastomere_522D_type_IVF_cell_number_6

description: cellnumber 6


title: Org_LSI_24mo_14p

description:
Library name: OL_P13_112
Organoid Passage 13_mouse_112_24moL


title: 5a_ANT1_ND6_IN

description:
IonCode_0177
IonCode_173-180.txt


title: [DDB_PD_107]_[HMP3427_ZnFeHigh]_[Fed-batch]_[12h]_[R2]


title: 22b_ANT1_IN

description:
IonCode_0176
IonCode_173-180.txt


title: 22a_ANT1_IN

description:
IonCode_0175
IonCode_173-180.txt


title: 15287X031_blastomere_522C_type_IVF_cell_number_6

description: cellnumber 6


title: Org_COL_24mo_3p

description:
Library name: OC_P2_112
Organoid Passage 2_mouse_112_24moC


title: 15287X030_blastomere_522B_type_IVF_cell_number_6

description: cellnumber 6


title: [DDB_PD_107]_[HMP3427_ZnFeHigh]_[Fed-batch]_[12h]_[R1]


title: 15287X029_blastomere_522A_type_IVF_cell_number_6

description: cellnumber 6


title: 21b_ANT1_IN

description:
IonCode_0174
IonCode_173-180.txt


title: [DDB_PD_107]_[HMP3427_ZnFeHigh]_[Fed-batch]_[4h]_[R2]


title: Org_USI_P25_285_1

description:
Library name: OU_P24_285_1
Organoid Passage 24_mouse_285_24mo


title: [DDB_PD_107]_[HMP3427_ZnFeHigh]_[Fed-batch]_[8h]_[R2]


title: [DDB_PD_107]_[HMP3427_ZnFeHigh]_[Fed-batch]_[8h]_[R1]


title: Org_USI_P25_285

description:
Library name: OU_P24_285
Organoid Passage 24_mouse_285_24mo


title: 21a_ANT1_IN

description:
IonCode_0173
IonCode_173-180.txt


title: 15287X028_blastomere_520E_type_IVF_cell_number_5

description: cellnumber 5


title: [DDB_PD_107]_[HMP3427_ZnFeHigh]_[Fed-batch]_[4h]_[R1]


title: 15287X026_blastomere_520C_type_IVF_cell_number_5

description: cellnumber 5


title: 15287X027_blastomere_520D_type_IVF_cell_number_5

description: cellnumber 5


title: 15287X025_blastomere_520B_type_IVF_cell_number_5

description: cellnumber 5


title: Org_USI_P0_285_1

description:
Library name: OU_P0_285_1
Organoid Passage 0_mouse_285_24mo


title: 83b_B6ME_IN

description:
IonCode_0170
IonCode_165-172.txt


title: Org_COL_24mo_14p

description:
Library name: OC_P13_112
Organoid Passage 13_mouse_112_24moC


title: 20a_ANT1_IN

description:
IonCode_0171
IonCode_165-172.txt


title: 20b_ANT1_IN

description:
IonCode_0172
IonCode_165-172.txt


title: 15287X023_blastomere_592B_type_IVF_cell_number_2

description: cellnumber 2


title: Org_USI_P25_283_1

description:
Library name: OU_P24_283_1
Organoid Passage 24_mouse_283_24mo


title: [DDB_PD_107]_[HMP3427_ZnFeHigh]_[Batch]_[0h]_[R2]


title: Org_USI_P0_283_1

description:
Library name: OU_P0_283_1
Organoid Passage 0_mouse_283_24mo


title: OCorg3P_concat

description:
Library name: OC_P2_112_1
Organoid Passage 2_mouse_112_24moC


title: [DDB_PD_107]_[HMP3427_ZnFeLow]_[Fed-batch]_[24h]_[R2]


title: 83a_B6ME_IN

description:
IonCode_0169
IonCode_165-172.txt


title: [DDB_PD_107]_[HMP3427_ZnFeHigh]_[Batch]_[0h]_[R1]


title: [DDB_PD_107]_[HMP3427_ZnFeLow]_[Fed-batch]_[24h]_[R1]


title: 81b_B6ME_IN

description:
IonCode_0168
IonCode_165-172.txt


title: 15287X021_blastomere_519E_type_IVF_cell_number_5

description: cellnumber 5


title: D4P2_285

description:
Library name: OU_P13_285_DAC
Organoid Passage 13_mouse_285_24mo


title: 80a_B6ME_IN

description:
IonCode_0165
IonCode_165-172.txt


title: Org_USI_P0_285

description:
Library name: OU_P0_285
Organoid Passage 0_mouse_285_24mo


title: 15287X022_blastomere_592A_type_IVF_cell_number_2

description: cellnumber 2


title: 81a_B6ME_IN

description:
IonCode_0167
IonCode_165-172.txt


title: D4P1_285

description:
Library name: OU_P12_285_DAC
Organoid Passage 12_mouse_285_24mo


title: 21f_ANT1_ND6_NI

description:
IonCode_0164
IonCode_157-164.txt


title: 15287X020_blastomere_519D_type_IVF_cell_number_5

description: cellnumber 5


title: Org_USI_P25_283

description:
Library name: OU_P24_283
Organoid Passage 24_mouse_283_24mo


title: [DDB_PD_107]_[HMP3427_ZnFeLow]_[Fed-batch]_[20h]_[R2]


title: 15287X024_blastomere_520A_type_IVF_cell_number_5

description: cellnumber 5


title: [DDB_PD_107]_[HMP3427_ZnFeLow]_[Fed-batch]_[18h]_[R1]


title: [DDB_PD_107]_[HMP3427_ZnFeLow]_[Fed-batch]_[20h]_[R1]


title: 15287X019_blastomere_519C_type_IVF_cell_number_5

description: cellnumber 5


title: 21e_ANT1_ND6_NI

description:
IonCode_0163
IonCode_157-164.txt


title: D4P2_283

description:
Library name: OU_P13_283_DAC
Organoid Passage 13_mouse_283_24mo


title: D4P1_283

description:
Library name: OU_P12_283_DAC
Organoid Passage 12_mouse_283_24mo


title: [DDB_PD_107]_[HMP3427_ZnFeLow]_[Fed-batch]_[18h]_[R2]


title: 20f_ANT1_ND6_NI

description:
IonCode_0162
IonCode_157-164.txt


title: 15287X016_blastomere_591B_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_107]_[HMP3427_ZnFeLow]_[Fed-batch]_[15h]_[R2]


title: 80b_B6ME_IN

description:
IonCode_0166
IonCode_165-172.txt


title: 15287X017_blastomere_519A_type_IVF_cell_number_5

description: cellnumber 5


title: 15287X018_blastomere_519B_type_IVF_cell_number_5

description: cellnumber 5


title: Org_USI_P0_283

description:
Library name: OU_P0_283
Organoid Passage 0_mouse_283_24mo


title: D4_285

description:
Library name: OU_P11_285_DAC
Organoid Passage 11_mouse_285_24mo_DAC

value: Decitabine (50ng/ml)


title: 20e_ANT1_ND6_NI

description:
IonCode_0161
IonCode_157-164.txt


title: [DDB_PD_107]_[HMP3427_ZnFeLow]_[Fed-batch]_[15h]_[R1]


title: 38f_ANT1_NI

description:
IonCode_0160
IonCode_157-164.txt


title: 15287X015_blastomere_591A_type_IVF_cell_number_2

description: cellnumber 2


title: D3P2M285

description:
Library name: OU_P10_285_DAC
Organoid Passage 10_mouse_285_24mo


title: [DDB_PD_107]_[HMP3427_ZnFeLow]_[Fed-batch]_[12h]_[R1]


title: 15287X014_blastomere_579B_type_IVF_cell_number_2

description: cellnumber 2


title: 15287X013_blastomere_579A_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_107]_[HMP3427_ZnFeLow]_[Fed-batch]_[8h]_[R2]


title: [DDB_PD_107]_[HMP3427_ZnFeLow]_[Fed-batch]_[8h]_[R1]


title: 35f_ANT1_NI

description:
IonCode_0156
IonCode_149-156.txt


title: 38e_ANT1_NI

description:
IonCode_0159
IonCode_157-164.txt


title: D1P2_285

description:
Library name: OU_P4_285_DAC
Organoid Passage 4_mouse_285_24mo


title: D3P2M283

description:
Library name: OU_P10_283_DAC
Organoid Passage 10_mouse_283_24mo


title: D1P2_283

description:
Library name: OU_P4_283_DAC
Organoid Passage 4_mouse_283_24mo


title: 15287X012_blastomere_590D_type_IVF_cell_number_4

description: cellnumber 4


title: D1P1_285

description:
Library name: OU_P3_285_DAC
Organoid Passage 3_mouse_285_24mo


title: [DDB_PD_107]_[HMP3427_ZnFeLow]_[Fed-batch]_[4h]_[R2]


title: 35e_ANT1_NI

description:
IonCode_0155
IonCode_149-156.txt


title: 15287X011_blastomere_590C_type_IVF_cell_number_4

description: cellnumber 4


title: 15287X010_blastomere_590B_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_107]_[HMP3427_ZnFeLow]_[Fed-batch]_[4h]_[R1]


title: 15287X009_blastomere_590A_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_107]_[HMP3427_ZnFeLow]_[Fed-batch]_[12h]_[R2]


title: D4_283

description:
Library name: OU_P11_283_DAC
Organoid Passage 11_mouse_283_24mo_DAC


title: D1_285

description:
Library name: OU_P2_285_DAC
Organoid Passage 2_mouse_285_24mo_DAC


title: D1P1_283

description:
Library name: OU_P3_283_DAC
Organoid Passage 3_mouse_283_24mo


title: [DDB_PD_107]_[HMP3427_ZnFeLow]_[Batch]_[0h]_[R2]


title: 25f_B6ME_NI

description:
IonCode_0154
IonCode_149-156.txt


title: [DDB_PD_107]_[HMP3427_ZnFeLow]_[Batch]_[0h]_[R1]


title: 25e_B6ME_NI

description:
IonCode_0153
IonCode_149-156.txt


title: 36e_ANT1_NI

description:
IonCode_0157
IonCode_157-164.txt


title: D1_283

description:
Library name: OU_P2_283_DAC
Organoid Passage 2_mouse_283_24mo_DAC


title: 36f_ANT1_NI

description:
IonCode_0158
IonCode_157-164.txt


title: 15287X007_blastomere_589C_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_107]_[HMP3071_ZnFeHigh]_[Fed-batch]_[24h]_[R2]


title: [DDB_PD_107]_[HMP3071_ZnFeHigh]_[Fed-batch]_[24h]_[R1]


title: 24f_B6ME_NI

description:
IonCode_0152
IonCode_149-156.txt


title: [DDB_PD_107]_[HMP3071_ZnFeHigh]_[Fed-batch]_[20h]_[R2]


title: 24e_B6ME_NI

description:
IonCode_0151
IonCode_149-156.txt


title: Passage4_mouse283

description:
Library name: OU_P4_283
Orgnoid passage 4_mouse_283

data_processing:
RNA libraries were trimmed using Trimmomatic, aligned to the mm9 genome, and gene counts obtained using STAR.
Assembly: mm9
Supplementary files format and content: tab delimited text files contains counts for each sample

source_name: Small intestine epithelium

extract_protocol:
Organoids were collected, pelleted, and stored in RNAlater (Thermo Fisher, #AM7020) at -20°C. Pellets were lysed in 1 mL TRIzol (Thermo Fisher, #15596026), with the addition of 100 µL bromo-chlorophenol (Fisher, #AC173530050). Phase separation was achieved by centrifugation at 12,000 g, for 15 min, at 4 °C, and the RNA-containing supernatant collected. RNA was precipitated with an equal volume of isopropanol, followed by a wash with 1 mL 75% ethanol. The RNA pellet was collected by centrifugation at 7,500 g, for 5 min, and dissolved in 30 µL nuclease-free water. RNA concentrations were measured using the Qubit RNA Broad Range kit (Thermo Fisher, #Q10210), and RNA integrity (RIN) determined using an Agilent RNA 6000 Nano kit (Agilent, #56067-1511).
RNA was sent to BGI   Genomics for library preparation and sequencing

value: Small intestine epithelium


title: Passage4_mouse285

description:
Library name: OU_P4_285
Orgnoid passage 4_mouse_285


title: 15287X005_blastomere_589A_type_IVF_cell_number_4

description: cellnumber 4


title: 15287X003_blastomere_588C_type_IVF_cell_number_4

description: cellnumber 4


title: Passage3_mouse_283

description:
Library name: OU_P3_283
Orgnoid passage 3_mouse_283


title: 15287X004_blastomere_588D_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_107]_[HMP3071_ZnFeHigh]_[Fed-batch]_[20h]_[R1]


title: [DDB_PD_107]_[HMP3071_ZnFeHigh]_[Fed-batch]_[18h]_[R1]


title: Passage2_mouse_283

description:
Library name: OU_P2_283
Orgnoid passage 2_mouse_283


title: 37h_ANT1_ND6_IN

description:
IonCode_0148
IonCode_141-148.txt


title: 15287X002_blastomere_588B_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_107]_[HMP3071_ZnFeHigh]_[Fed-batch]_[15h]_[R2]


title: [DDB_PD_107]_[HMP3071_ZnFeHigh]_[Fed-batch]_[18h]_[R2]


title: 37e_ANT1_ND6_IN

description:
IonCode_0145
IonCode_141-148.txt


title: 15287X001_blastomere_588A_type_IVF_cell_number_4

description: cellnumber 4


title: 37f_ANT1_ND6_IN

description:
IonCode_0146
IonCode_141-148.txt


title: Passage13_mouse_283

description:
Library name: OU_P13_283
Orgnoid passage 13_mouse_283


title: 37g_ANT1_ND6_IN

description:
IonCode_0147
IonCode_141-148.txt


title: 15287X006_blastomere_589B_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_107]_[HMP3071_ZnFeHigh]_[Fed-batch]_[15h]_[R1]


title: 23f_B6ME_NI

description:
IonCode_0150
IonCode_149-156.txt


title: [DDB_PD_107]_[HMP3071_ZnFeHigh]_[Fed-batch]_[12h]_[R2]


title: Passage12_mouse285

description:
Library name: OU_P12_285
Orgnoid passage 12_mouse_285


title: Passage2_mouse285

description:
Library name: OU_P2_285
Orgnoid passage 2_mouse_285


title: Passage12_mouse_283

description:
Library name: OU_P12_283
Orgnoid passage 12_mouse_283


title: [DDB_PD_107]_[HMP3071_ZnFeHigh]_[Fed-batch]_[12h]_[R1]


title: 15286X211_blastomere_587C_type_IVF_cell_number_4

description: cellnumber 4


title: 27h_ANT1_IN

description:
IonCode_0144
IonCode_141-148.txt


title: 23e_B6ME_NI

description:
IonCode_0149
IonCode_149-156.txt


title: Passage13_mouse285

description:
Library name: OU_P13_285
Orgnoid passage 13_mouse_285


title: 15286X212_blastomere_587D_type_IVF_cell_number_4

description: cellnumber 4


title: 15286X210_blastomere_587B_type_IVF_cell_number_4

description: cellnumber 4


title: 27g_ANT1_IN

description:
IonCode_0143
IonCode_141-148.txt


title: [DDB_PD_107]_[HMP3071_ZnFeHigh]_[Fed-batch]_[8h]_[R1]


title: Passage11_mouse285

description:
Library name: OU_P11_285
Orgnoid passage 11_mouse_285


title: [DDB_PD_107]_[HMP3071_ZnFeHigh]_[Fed-batch]_[8h]_[R2]


title: Passage11_mouse_283

description:
Library name: OU_P11_283
Orgnoid passage 11_mouse_283


title: 27f_ANT1_IN

description:
IonCode_0142
IonCode_141-148.txt


title: 27e_ANT1_IN

description:
IonCode_0141
IonCode_141-148.txt


title: scRNAseq capture rxn #2

city: Seattle

first: Julie

last: Boiko

state: Washington

address: 1101 Fairview Ave N

institute: Fred Hutchinson Cancer Center

description: Library name: Sample 2

data_processing:
Cell Ranger
Assembly: GRCm38
Supplementary files format and content: Seurat object in RDS format; combines all samples

source_name: Peripheral blood

extract_protocol:
10X Genomics 3' dual-index protocol
10X Genomics 3' dual-index protocol

value: Peripheral blood


title: 37d_ANT1_ND6_IN

description:
IonCode_0140
IonCode_133-140.txt


title: [DDB_PD_107]_[HMP3071_ZnFeHigh]_[Fed-batch]_[4h]_[R2]


title: scRNAseq capture rxn #1

description: Library name: Sample 1


title: [DDB_PD_107]_[HMP3071_ZnFeHigh]_[Fed-batch]_[4h]_[R1]


title: 15286X206_blastomere_583B_type_IVF_cell_number_4

first: Edward

last: Grow

address: 7053 beltau lane

institute: UTSW

description: cellnumber 4


title: 37c_ANT1_ND6_IN

description:
IonCode_0139
IonCode_133-140.txt


title: [DDB_PD_107]_[HMP3071_ZnFeHigh]_[Batch]_[0h]_[R2]


title: 15286X205_blastomere_583A_type_IVF_cell_number_4

description: cellnumber 4


title: 37b_ANT1_ND6_IN

description:
IonCode_0138
IonCode_133-140.txt


title: 15286X204_blastomere_580D_type_IVF_cell_number_4

description: cellnumber 4


title: 15286X203_blastomere_580C_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_107]_[HMP3071_ZnFeHigh]_[Batch]_[0h]_[R1]


title: [DDB_PD_107]_[HMP3071_ZnFeLow]_[Fed-batch]_[24h]_[R1]


title: WA09-RO Transplanted Set3

first: Raghavi

last: Sudharsan

address: 3900 Delancey Street

description:
Library name: WA09ROT_S3
10X Genomics

data_processing:
Sequencing data were processed using the Cell Ranger pipeline.
Assembly: Homo sapeins (human) genome assembly GRCh38 (hg38)
Supplementary files format and content: Compressed Tab-separated value files and matrix market exchange format files

source_name: Retinal organoid

growth_protocol: As described in PMC6340149 and PMC5823737

extract_protocol:
RO fragments were dissociated into single cells using Miltenyi Biotec Neural Tissue Dissociation kit - Postnatal neurons. Cells were washed and resuspended in PBS supplemented with 0.5% BSA.
Libraries were prepared using the 10X Single Cell 3' v3.1 following manufacterer's protocol.

treatment_protocol: As described in PMC9391525

value: Retinal organoid

value: WA09 CRX-tdTomato hESC

value: Tranplanted


title: 15286X207_blastomere_583C_type_IVF_cell_number_4

description: cellnumber 4

value: IVF


title: Wilms tumor_CMCW81

city: Dallas

first: Keri

last: Drake

state: Texas

address: 5323 Harry Hines Boulevard

department: Pediatric Nephrology

description:
Library name: Sample 2
10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were made using Cell Ranger software (Version 5.0.1).
Assembly: Human GRCh38
Supplementary files format and content: tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Tumor

extract_protocol:
Nuclei were isolated as previously reported from paired kidneys with Nuclei EZ Lysis buffer supplemented with protease inhibitor and RNase inhibitor. Samples were homogenized using a Dounce homogenizer in 2ml of ice-cold Nuclei EZ Lysis buffer first with a loose pestle, then passed through a 200 µm strainer into 50 ml conical tube and followed by homogenization with a tight pestle which was then filtered through a 40-µm cell strainer and incubated on ice for 5 minutes. The suspension was centrifuged at 500 g x for 5 min at 4 ºC with the pellet resuspended and washed with 4 ml of the buffer and incubated on ice for 5 min. After another centrifugation, the pellet was resuspended with Nuclei Suspension Buffer (1x PBS, 0.07% BSA, 0.1% RNase inhibitor) and filtered through a 5-µm cell strainer into a conical tube. The nuclei were counted with a disposable hemacytometer and diluted to a concentration of 700-1200 cells per µL.
Library was performed according to the manufacturer’s instructions (single cell 3’ GEX kit).

value: Tumor


title: 15286X209_blastomere_587A_type_IVF_cell_number_4

city: dallas

description: cellnumber 4


title: 27c_ANT1_IN

description:
IonCode_0135
IonCode_133-140.txt


title: 37a_ANT1_ND6_IN

description:
IonCode_0137
IonCode_133-140.txt


title: [DDB_PD_107]_[HMP3071_ZnFeLow]_[Fed-batch]_[20h]_[R2]


title: [DDB_PD_107]_[HMP3071_ZnFeLow]_[Fed-batch]_[24h]_[R2]


title: Wilms tumor_CMCW17

description:
Library name: Sample 1
10x Genomics


title: WA09-RO Transplanted Set2

description:
Library name: WA09ROT_S2
10X Genomics


title: 15286X200_blastomere_556D_type_IVF_cell_number_4

description: cellnumber 4


title: 15286X208_blastomere_583D_type_IVF_cell_number_4

description: cellnumber 4


title: 15286X202_blastomere_580B_type_IVF_cell_number_4

description: cellnumber 4


title: WA09-RO Cultured Set2

description:
Library name: WA09ROC_S2
10X Genomics

value: Cultured


title: 15286X199_blastomere_556C_type_IVF_cell_number_4

description: cellnumber 4


title: 21d_ANT1_ND6_NI

description:
IonCode_0132
IonCode_125-132.txt


title: 15286X198_blastomere_556B_type_IVF_cell_number_4

description: cellnumber 4


title: WA09-RO Cultured Set3

description:
Library name: WA09ROC_S3
10X Genomics


title: WA09-RO Transplanted Set1

description:
Library name: WA09ROT_S1
10X Genomics


title: 21c_ANT1_ND6_NI

description:
IonCode_0131
IonCode_125-132.txt


title: 27b_ANT1_IN

description:
IonCode_0134
IonCode_133-140.txt


title: [DDB_PD_107]_[HMP3071_ZnFeLow]_[Fed-batch]_[20h]_[R1]


title: WA09-RO Cultured Set1

description:
Library name: WA09ROC_S1
10X Genomics


title: Wilms tumor_CMCW69

description:
Library name: Sample 3
10x Genomics


title: [DDB_PD_107]_[HMP3071_ZnFeLow]_[Fed-batch]_[18h]_[R2]


title: 15286X197_blastomere_556A_type_IVF_cell_number_4

description: cellnumber 4


title: 27a_ANT1_IN

description:
IonCode_0133
IonCode_133-140.txt


title: 27d_ANT1_IN

description:
IonCode_0136
IonCode_133-140.txt


title: Myometrium from fibroid patient (MyoF), patient NW206

city: Grand Rapids

first: Jose

middle: M

last: Teixeira

address: 400 Monroe Ave NW

department: Ob/Gyn

institute: Michigan State University

description: Library name: NW206N

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: AA

tag: age

value: Myometrium from fibroid patient


title: 15286X201_blastomere_580A_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_107]_[HMP3071_ZnFeLow]_[Fed-batch]_[15h]_[R1]

value: Escherichia coli cells


title: 15286X196_blastomere_555D_type_IVF_cell_number_4

description: cellnumber 4


title: Myometrium from fibroid patient (MyoF), patient MP366

description: Library name: MP366N

tag: batch


title: 20d_ANT1_ND6_NI

description:
IonCode_0130
IonCode_125-132.txt

value: Heart

value: C57BL/6JEiJ ANT1 -/- ND6 P25L

value: 2.5x10^11 vg AAV2/9Des-Gfp


title: [DDB_PD_107]_[HMP3071_ZnFeLow]_[Fed-batch]_[15h]_[R2]


title: 15286X195_blastomere_555C_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_107]_[HMP3071_ZnFeLow]_[Fed-batch]_[12h]_[R2]


title: Myometrium from fibroid patient (MyoF), patient MP364

description: Library name: MP364N

value: C


title: 36d_ANT1_NI

description:
IonCode_0126
IonCode_125-132.txt

value: C57BL/6JEiJ ANT1 -/-


title: Myometrium from fibroid patient (MyoF), patient MP355

description: Library name: MP355N


title: [DDB_PD_107]_[HMP3071_ZnFeLow]_[Fed-batch]_[12h]_[R1]


title: 15286X194_blastomere_555B_type_IVF_cell_number_4

description: cellnumber 4


title: 38c_ANT1_NI

description:
IonCode_0127
IonCode_125-132.txt


title: 15286X193_blastomere_555A_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_107]_[HMP3071_ZnFeLow]_[Fed-batch]_[8h]_[R2]


title: 38d_ANT1_NI

description:
IonCode_0128
IonCode_125-132.txt


title: [DDB_PD_107]_[HMP3071_ZnFeLow]_[Fed-batch]_[4h]_[R2]


title: [DDB_PD_107]_[HMP3071_ZnFeLow]_[Fed-batch]_[8h]_[R1]


title: 15286X192_blastomere_553D_type_IVF_cell_number_4

description: cellnumber 4


title: 36c_ANT1_NI

description:
IonCode_0125
IonCode_125-132.txt


title: 15286X191_blastomere_553C_type_IVF_cell_number_4

description: cellnumber 4


title: Myometrium from fibroid patient (MyoF), patient MP353

description: Library name: MP353N


title: Myometrium from fibroid patient (MyoF), patient MP351

description: Library name: MP351N


title: 35d_ANT1_NI

description:
IonCode_0124
IonCode_117-124.txt


title: 20c_ANT1_ND6_NI

description:
IonCode_0129
IonCode_125-132.txt


title: [DDB_PD_107]_[HMP3071_ZnFeLow]_[Fed-batch]_[4h]_[R1]


title: 35c_ANT1_NI

description:
IonCode_0123
IonCode_117-124.txt


title: 25d_B6ME_NI

description:
IonCode_0122
IonCode_117-124.txt


title: [DDB_PD_107]_[HMP3071_ZnFeLow]_[Batch]_[0h]_[R2]


title: [DDB_PD_107]_[HMP3071_ZnFeLow]_[Fed-batch]_[18h]_[R1]


title: [DDB_PD_107]_[HMP3071_ZnFeLow]_[Batch]_[0h]_[R1]


title: 15286X188_blastomere_548D_type_IVF_cell_number_4

description: cellnumber 4


title: 15286X190_blastomere_553B_type_IVF_cell_number_4

description: cellnumber 4


title: Myometrium from fibroid patient (MyoF), patient MP348

description: Library name: MP348N


title: 15286X189_blastomere_553A_type_IVF_cell_number_4

description: cellnumber 4


title: Myometrium from fibroid patient (MyoF), patient MP346

description: Library name: MP346N


title: Myometrium from fibroid patient (MyoF), patient MP359

description: Library name: MP359N


title: 25c_B6ME_NI

description:
IonCode_0121
IonCode_117-124.txt


title: 15286X187_blastomere_548C_type_IVF_cell_number_4

description: cellnumber 4


title: 24d_B6ME_NI

description:
IonCode_0120
IonCode_117-124.txt