title: Bovine mammary epithelial cells,  miR-375 inhibitor, rep2

city: Yinchuan

first: Xing-Ping

state: Ningxia

address: No. 489, Helan Shanxi Road, Xixia District

department: College of animal science and technology

institute: Ningxia University

description: Bovine mammary epithelial cells transfected with miR-375 inhibitor

data_processing:
Illumina Novaseq 6000 used for basecalling.
Clean reads were obtained by removing the connector sequences and filtering out low-quality reads (the number of bases with a base mass value ≤ 25 accounted for over 60% of the total reads). The proportion of N (undetermined bases) was less than 5%. Finally, clean reads were used for subsequent analysis.
Clean reads were then compared to Mapped reads in the Bos taurus reference genome UMD3.1 (http://www.ensembl.org/Bos_taurus/Info/Index) using HiSAT2 software (http://daehwankimlab.github.io/hisat2/).
Gene expression was calculated by FeatureCounts (http://subread.sourceforge.net/) in the DESeq2 (http://bioconductor.org/packages/release/bioc/html/DESeq2.html) software for determining differentially expressed genes. The significantly differentially expressed genes were identified by the criteria of p-value < 0.05 and |log2FoldChange|>1.
Genome_build: UMD3.1
Supplementary_files_format_and_content: Matrix table with information of gene and gene count for each sample.

organism: Bos taurus

source_name: Bovine mammary epithelial cells

growth_protocol: Bovine mammary epithelial cells were thawed and cultured in DMEM/F12 medium supplemented with 10% fetal bovine serum at 37℃ under 5% CO2 and 100% humidity. The cells were seeded and cultured in 6-well plates. When the cells reached 60-70% confluence, they were transfected with miR-375 or negative control (NC) (final concentration 100nM). The experiment was performed in triplicate.

extract_protocol:
Total RNA was extracted from the transfected bovine mammary epithelial cells using the TriZol kit  following the manufacturer's protocol.
The sequencing library was constructed using the ABclonal mRNA-seq Lib Prep Kit (ABclonal, Wuhan, China), following the manufacturer's protocol.

treatment_protocol: Bovine mammary epithelial cells were transfected with NC inhibitor (100 nM) or miR-375 inhibitor (100 nM). The experiment was performed in triplicate. Continue culture for 48h and collecting cell, and stored at -80℃for further analysis.

tag: cell type

value: Bovine mammary epithelial cells

value: miR-375 inhibitor


title: WT-S-6-1

status: Public on Jun 15 2022

type: SRA

city: Jeddah

first: Haroon

last: Butt

state: Makkah

address: King Abdullah University of Science and Technology (KAUST) Thuwal, 23955-6900

department: BESE

country: Saudi Arabia

institute: KAUST

description: High-quality RNA samples with RNA integrity number (RIN) 7.0 were selected for library construction. The RNA-seq libraries were constructed using TruSeq mRNA stranded kit following the standard protocol

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.4
Trimming library adapters and quality controls with Trimmomatic using the following arguments; TrimmomaticPE - LEADING:25 TRAILING:25 CROP:120 MINLEN:120. Illumina adapters were removed and read pairs were trimmed to the same length
Alignement with STAR with the following arguments: --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --readFilesCommand zcat, --quantMode GeneCounts, --outFilterMultimapNmax 1.
bigwig files generated with deeptools BamCoverage
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: BIGWIG

molecule: polyA RNA

organism: Oryza sativa Japonica Group

source_name: Seedlings

growth_protocol: 7-day-old seedlings

extract_protocol:
Direct-zol RNA MiniPrep Plus (Zymo Research) according to the manufacturer’s instructions
The RNA-seq libraries were constructed using TruSeq mRNA stranded kit following the standard protocol and sequenced on the HiSeq-4000 platform to generate high-quality paired-end reads.

treatment_protocol: Three hours and six hours treatment with 200mM NaCl, 4ºC and mock

tag: background

value: Oryza sativa Japonica Group cv Nipponbare

tag: genotype

value: WT

tag: age

tag: treatment

value: 200mM NaCl, 6hours

tag: tissue

value: Seedlings


title: Normal_1_lnc

city: Hefei

first: Dahai

last: Zhao

state: Anhui

address: Furong Road, 678

department: Respiratory and Critical Care Medicine

country: China

institute: The Second Affiliated Hospital, Anhui Medical University

data_processing:
The Hisat2 and feature counts software were used to map clean reads to reference genome (grcm38) and calculate the gene expression level which was normalized to FPKM.
the find_circ software (v 1.2) was utilized to predict the junction of circRNAs.
Assembly: hg19
Supplementary files format and content: circRNA junction counts
Supplementary files format and content: raw counts

molecule: total RNA

organism: Homo sapiens

source_name: Human blood

extract_protocol:
The peripheral blood samples and TRizol reagent(Invitrogen, USA) are evenly mixed in a ratio of 1:3, total of 12 ml. Total RNA was extracted by using Trizol reagent according to the manufacturer’s instructions.
Whole transcriptome libraries were constructed by the TruSeq Ribo Profile Library Prep Kit (Illumina, United States), according to the manufacturer’s instructions. In brief, 10 mg total RNA was depleted rRNA with an Illumina Ribo-Zero Gold kit and purified for end repair and 50-adaptor ligation. Then, reverse transcription was performed with random primers containing 30 adaptor sequences and randomized hexamers. Finally, the cDNAs were purified and amplified with thermo cycler. The PCR products of 300–500 bp were purified, quantified and stored at -80℃ before sequencing. The libraries were subjected to 151 nt paired-end sequencing with an Illumina Novaseq 6000 system (Novogene, China).For small RNA (sRNA) sequencing, eight sRNA libraries were generated with TruSeq small RNA (Illumina, United States) according to the manufacturer’s instructions. Then the prepared libraries were sequenced with an Illumina Novaseq 6000 system (Novogene, China).

value: Normal human blood


title: Bovine mammary epithelial cells,  miR-375 inhibitor, rep3

last: Wang


title: WT-C-6-2

value: Mock, 6hours


title: WT-F-3-2

value: 4ºC, 3hours


title: WT, aux/dox, DMSO [KJ24]

city: Bunkyo-ku

first: Ryuichiro

last: Nakato

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

library_source: genomic

data_processing:
Sequenced paired-end 150-bp reads were mapped to the yeast genome using Juicer with default parameters.
Genome_build: Saccharomyces Genome Database (SGD), identical with sacCer3
Supplementary_files_format_and_content: hic files were generated by juicertools version 1.9.9 pre with "-r 1000" option . The total hic contact number of Hi-C samples was normalized.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: WT

growth_protocol: Cells were cultured in YEP medium (1 % yeast extract, 2 % peptone, 40 μg ml-1 adenine) supplemented with 2 % glucose (YEPD). For arrest in G2/M, benomyl (Sigma, 381586)-containing YEPD medium was added to cells growing logarithmically for a final concentration of 80 µg ml-1. Cell cultures were then incubated for 90 minutes at 30°C achieving complete G2/M-arrest. For synchronization in S-phase, 3 μg ml-1 α-factor mating pheromone (Sigma, custom peptide WHWLQLKPGQPMY) was added every hour (a total of three additions) to cells growing logarithmically at 25°C. Upon complete G1-arrest, cells were released into medium containing 0.2 M hydroxyurea (HU) (Sigma, H8627), and S-phase was allowed to progress at 25°C. The Schizosaccharomyces pombe strain (Table S1) used for spike-in normalization in RNA-seq was grown in YES medium (0.5 % yeast extract, 3 % glucose, 150 μg ml-1 adenine, 100 μg ml-1 uracil, 100 μg ml-1 leucine, 100 μg ml-1 lysine, 100 μg ml-1 histidine) at 32°C.

extract_protocol:
Our Hi-C protocol was adapted for S. cerevisiae from ref. (Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680, doi:10.1016/j.cell.2014.11.021 (2014)).  Fifty ml of cell culture (at an OD of 1.0) was fixed with 3 % formaldehyde for 20 minutes at 30°C, before the reaction was quenched by adding glycine to 0.125 M final concentration for 5 minutes at room temperature. Cells were washed once with 1 x PBS, before being resuspended in 5 ml pre-spheroplasting buffer (100mM PIPES (pH 9.4), 10mM DTT). The cells were incubated 5 minutes at room temperature and then pelleted (1500 g for 5 minutes at room temperature), before being resuspended in 5 ml spheroplasting buffer (50mM KH2PO4/K2HPO4 (pH 7.5), 1 M Sorbitol, 10 mM DTT). Twenty-five μl of 10 mg ml-1 100T Zymolyase (Nacalai Tesque, 07665-55) was added and cells were incubated for 15 minutes at 30°C. The spheroplasts were pelleted (500 g for 5 minutes at 4°C) and washed twice with ice-cold spheroplasting buffer (containing only 1 mM DTT). The spheroplasts were then resuspended in 250 μl of ice-cold Hi-C lysis buffer (10 mM Tris-HCl (pH 8.0), 10 mM NaCl, 0.2 % Igepal CA630) supplemented with 50 μl 6 x Complete (Roche) and 3 μl protease inhibitor (Sigma, P8215), and incubated on ice for 15 minutes. The spheroplasts were pelleted (1500 g for 5 minutes at 4°C) and washed twice with 500 μl of ice-cold Hi-C lysis buffer. After the last wash step the supernatant was discarded and the spheroplasts were incubated for 6 minutes at 62°C. Thereafter sodium dodecyl sulphate (SDS) was added to a final concentration of 0.2 % and the reaction was immediately and thoroughly mixed by inversion, and thereafter incubated at 62°C for 10 minutes. After addition of 80 μl H2O, 25 μl 10 % Triton X-100 was added to quench the SDS. The reaction was mixed by inversion and incubated at 37°C for 15 minutes. Thereafter, 28 μl 10 x NEB DpnII buffer and 500 units of DpnII (NEB, R0543M) was added, and the chromatin was digested overnight at 37°C. At the end of the incubation, the reaction was supplemented with 250 units of DpnII and incubated for 1 hour at 37°C. Then, the restriction enzyme was inactivated at 62°C for 20 minutes. The presence of intact and individual DNA masses throughout the spheroplasting, digestion and ligation steps was confirmed by DAPI (4′,6-diamidino-2-phenylindole)-staining and microscopy.
Marking and repairing DNA ends, proximity ligation, crosslink reversal, DNA shearing, size selection, biotin pull-down, preparation for Illumina sequencing, final amplification (15 cycles) and purification was performed as in ref. (Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680, doi:10.1016/j.cell.2014.11.021 (2014).

treatment_protocol: For transcription shut-off and degradation of Scc2 and Wpl1 in G2/M-arrest, auxin (3-indoleacetic acid, Sigma, I2886) and doxycycline (Sigma, D9891) were added for 1 hour at the final concentration of 1 mM and 5 μg ml-1, respectively. For transcription shut-off and degradation of Scc2 and Wpl1 in a synchronized S-phase, auxin and doxycycline were first added to G1-arrested cells for 30 minutes, and then for an additional hour in the HU-containing release medium at the same final concentrations as above. For transcription inhibition, thiolutin (Abcam, ab143556) was added to cell cultures for the final concentration of 20 µg ml-1 for 30 minutes. For inactivation of RNA pol II in G2/M-arrest, temperature-sensitive rpb1-1 cells were first arrested by benomyl for 2 hours at the permissive temperature of 25°C. Thereafter, the temperature was shifted to restrictive 37°C for 2 hours.

tag: strain

value: G2/M-arrest, auxin, doxycycline, DMSO


title: 1022_pA-RNA_1

city: Memphis

first: Mario

last: Halic

state: Tennessee

address: 262 Danny Thomas Place

department: Structural Biology

country: USA

institute: St. Jude Children’s Research Hospital

data_processing:
Sequencing reads obtained in the poly(A) RNA sequencing (pA RNA), Pol II ChIP, nascent RNA sequencing (Pol II RIP) and total RNA sequencing experiments were mapped to the S. pombe reference genome (PomBase, release 2018) using splice-aware alignment tool STAR version 2.7.3a (Dobin et al., 2013).  Alignment of RIP-seq and RNA-seq data was performed with STAR default parameters. Unspliced alignments of ChIP-seq data was enforced through parameters ‘--alignIntronMax 1’ and ‘--alignEndsType EndToEnd’. Reads mapping to ribosomal RNA have been removed from further analysis.
Genomic read counts were obtained using a custom script that extended basic htseq-count functionality with ‘--mode intersection-strict’ option. Additionally, for RNA assays pA RNA, Pol II RIP and total RNA, we used the ‘--stranded yes’ option to disambiguate which strand reads originated from. In short, reads mapping uniquely to protein-coding genes and reads that map less than 16 times were counted and normalized by gene length and sequencing depth (TPM, Transcripts Per Million). We chose 16 (dg/dh have in 12-13 copies) as multi-mapping threshold for heterochromatic genes to eliminate low-complexity reads without discarding reads originating from heterochromatic regions. In the read counting, we did not distinguish between individual gene copies but used one representative copy to collect all reads stemming from any one copy.
Assembly: PomBase, release 2018
Supplementary files format and content: tab-delimited text files include raw counts for each sample

organism: Schizosaccharomyces pombe

growth_protocol: Cells were grown in rich YES medium.

extract_protocol:
50 ml yeast cultures with an OD600 of 1.2 were cross-linked with 1% formaldehyde (Roth) for 15 min at room temperature. The reaction was quenched with 125 mM glycine for 5 min. The frozen pellet was resuspended in 500 µl lysis buffer (250 mM KCl, 1x Triton-X, 0.1% SDS, 0.1% Na-Desoxycholate, 50 mM HEPES pH 7.5, 2 mM EDTA, 2 mM EGTA, 5 mM MgCl2, 0.1% Nonidet P-40, 20% Glycerol) with 1 mM PMSF and Complete EDTA free Protease Inhibitor Cocktail (Roche). Lysis was performed with 0.25-0.5 mm glass beads (Roth) and the BioSpec FastPrep-24 bead beater (MP-Biomedicals), 8 cycles at 6.5 m/s for 30s and 3 min on ice. DNA was sheared by sonication (Bioruptor, Diagenode) 35 times for 30 s with a 30 s break. Cell debris was removed by centrifugation at 13 000 x g for 15 min. The crude lysate was normalized based on the RNA and Protein concentration (Nanodrop, Thermo Scientific) and incubated with 1.2 µg immobilized (Dynabeads Protein A, Thermo Scientific) antibody against Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody - ChIP Grade (ab5095, abcam) for at least 2 h at 4°C. The resin with immunoprecipitates was washed five times with each 1 ml of lysis buffer and eluted with 150 µl of elution buffer (50 mM Tris HCl pH 8.0, 10 mM EDTA, 1% SDS) at 65°C for 15 min. Cross-linking was reversed at 95°C for 15 min and subsequent RNase A (Thermo Scientific) digest for 30 min followed by Proteinase K (Roche) digest for at least 2 h at 37°C. DNA was recovered by phenol-chloroform-isoamylalcohol (25:24:1, Roth) extraction with subsequent ethanol precipitation.
For sequencing, a ChIP-seq library was made using the NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB).

tag: strain number

tag: target molecule

value: p(A) RNA

tag: ip antibody


title: COPD_2_lnc

value: Human blood with COPD


title: WT-C-6-1


title: Bovine mammary epithelial cells,  miR-375 inhibitor, rep1


title: COPD_3_lnc


title: Bovine mammary epithelial cells,  NC inhibitor, rep3

description: Bovine mammary epithelial cells transfected with NC inhibitor

value: NC inhibitor


title: COPD_1_lnc


title: Scc2-AID, HU, aux/dox [KJ22]

data_processing:
Sequenced paired-end 150-bp reads were mapped to the yeast genome using Juicer with default parameters.
Genome_build: Saccharomyces Genome Database (SGD), identical with sacCer3.
Supplementary_files_format_and_content: hic files were generated by juicertools version 1.9.9 pre with "-r 1000" option. The total hic contact number of Hi-C samples was normalized.

growth_protocol: Cells were cultured in YEP medium (1 % yeast extract, 2 % peptone, 40 μg ml-1 adenine) supplemented with 2 % glucose (YEPD). For arrest in G2/M, benomyl (Sigma, 381586)-containing YEPD medium was added to cells growing logarithmically for a final concentration of 80 µg ml-1. Cell cultures were then incubated for 90 minutes at 30°C achieving complete G2/M-arrest. For synchronization in S-phase, 3 μg ml-1 α-factor mating pheromone (Sigma, custom peptide WHWLQLKPGQPMY) was added every hour (a total of three additions) to cells growing logarithmically at 25°C. Upon complete G1-arrest, cells were released into medium containing 0.2 M hydroxyurea (HU) (Sigma, H8627), and S-phase was allowed to progress at 25°C. For transcription shut-off and degradation of Scc2 and Wpl1 in G2/M-arrest, auxin (3-indoleacetic acid, Sigma, I2886) and doxycycline (Sigma, D9891) were added for 1 hour at the final concentration of 1 mM and 5 μg ml-1, respectively.

extract_protocol:
Our Hi-C protocol was adapted for S. cerevisiae from ref. (Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680, doi:10.1016/j.cell.2014.11.021 (2014)). Fifty ml of cell culture (at an OD of 1.0) was fixed with 3 % formaldehyde for 20 minutes at 30°C, before the reaction was quenched by adding glycine to 0.125 M final concentration for 5 minutes at room temperature. Cells were washed once with 1 x PBS, before being resuspended in 5 ml pre-spheroplasting buffer (100mM PIPES (pH 9.4), 10mM DTT). The cells were incubated 5 minutes at room temperature and then pelleted (1500 g for 5 minutes at room temperature), before being resuspended in 5 ml spheroplasting buffer (50mM KH2PO4/K2HPO4 (pH 7.5), 1 M Sorbitol, 10 mM DTT). Twenty-five μl of 10 mg ml-1 100T Zymolyase (Nacalai Tesque, 07665-55) was added and cells were incubated for 15 minutes at 30°C. The spheroplasts were pelleted (500 g for 5 minutes at 4°C) and washed twice with ice-cold spheroplasting buffer (containing only 1 mM DTT). The spheroplasts were then resuspended in 250 μl of ice-cold Hi-C lysis buffer (10 mM Tris-HCl (pH 8.0), 10 mM NaCl, 0.2 % Igepal CA630) supplemented with 50 μl 6 x Complete (Roche) and 3 μl protease inhibitor (Sigma, P8215), and incubated on ice for 15 minutes. The spheroplasts were pelleted (1500 g for 5 minutes at 4°C) and washed twice with 500 μl of ice-cold Hi-C lysis buffer. After the last wash step the supernatant was discarded and the spheroplasts were incubated for 6 minutes at 62°C. Thereafter sodium dodecyl sulphate (SDS) was added to a final concentration of 0.2 % and the reaction was immediately and thoroughly mixed by inversion, and thereafter incubated at 62°C for 10 minutes. After addition of 80 μl H2O, 25 μl 10 % Triton X-100 was added to quench the SDS. The reaction was mixed by inversion and incubated at 37°C for 15 minutes. Thereafter, 28 μl 10 x NEB DpnII buffer and 500 units of DpnII (NEB, R0543M) was added, and the chromatin was digested overnight at 37°C. At the end of the incubation, the reaction was supplemented with 250 units of DpnII and incubated for 1 hour at 37°C. Then, the restriction enzyme was inactivated at 62°C for 20 minutes. The presence of intact and individual DNA masses throughout the spheroplasting, digestion and ligation steps was confirmed by DAPI (4′,6-diamidino-2-phenylindole)-staining and microscopy.
Marking and repairing DNA ends, proximity ligation, crosslink reversal, DNA shearing, size selection, biotin pull-down, preparation for Illumina sequencing, final amplification (15 cycles) and purification was performed as in ref. (Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680, doi:10.1016/j.cell.2014.11.021 (2014)).

treatment_protocol: For transcription shut-off and degradation of Scc2 and Wpl1 in a synchronized S-phase, auxin and doxycycline were first added to G1-arrested cells for 30 minutes, and then for an additional hour in the HU-containing release medium at the same final concentrations as above. For transcription inhibition, thiolutin (Abcam, ab143556) was added to cell cultures for the final concentration of 20 µg ml-1 for 30 minutes.

value: HU-arrest, auxin, doxycycline


title: Bovine mammary epithelial cells,  NC inhibitor, rep1


title: WT, HU [KJ20]

value: HU-arrest


title: Bovine mammary epithelial cells,  NC inhibitor, rep2


title: 33-F-6-2

value: 4ºC, 6hours


title: Normal_3_circ


title: 33-F-6-1


title: Scc2-AID, aux/dox, DMSO [KJ18]


title: Normal_1_circ


title: Normal_2_circ


title: W3: HONE-1 siWTAP_3

type: RNA

city: Guangzhou

first: Zhi-Xuan

last: Li

state: Guangdong

address: No. 651 Dongfeng east road, Yuexiu district, Guangzhou

institute: Sun Yat-sen University Cancer Center

description: Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities.

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer. The mixture was heated at 60 °C for 30 min. 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C). Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). Differentially m6A-methylated RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds.

source_name: siWTAP_3_Gene expression

label_protocol: Sample labeling was performed according to the Agilent Two-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, the total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Kit.

extract_protocol: Total RNA was extracted from the 6 tissues using QIAGEN FFPE RNeasy kit (QIANGEN, Hilden, Germany) according to the manufacturer’s instructions. mRNA was purified from the total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). RNA quantity and quality were measured by NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Scrambled control or si-WTAP was transfected into HONE-1 cells.

tag: cell line

source_name: siWTAP_3_m6A methylation


title: WT-F-3-1


title: Wpl1-AID, HU, aux/dox [KJ23]


title: W1: HONE-1 siWTAP_1

source_name: siWTAP_1_Gene expression

source_name: siWTAP_1_m6A methylation


title: Scc2-AID, aux/dox, thiolutin [KJ19]

value: G2/M-arrest, auxin, doxycycline, thiolutin


title: 33-S-6-2


title: W2: HONE-1 siWTAP_2

source_name: siWTAP_2_Gene expression

source_name: siWTAP_2_m6A methylation


title: 33-S-6-1


title: COPD_3_circ


title: Wpl1-AID, aux/dox, thiolutin [KJ17]


title: WT-S-3-1

value: 200mM NaCl, 3hours


title: WT-S-3-2


title: COPD_1_circ


title: COPD_2_circ


title: Patient 2 / Cnt_PR-A

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.5)
Single-cell sequencing FASTQ files were processed using Kallisto (v0.46.0) and BUStools (v0.39.2) for sample demultiplexing, barcode processing, pseudo-alignment to human transcriptome (Ensembl release 96) and UMI counting. The unfiltered output of Kallisto and BUStools is provided for each sample (genes.barcodes.txt, genes.genes.txt and genes.mtx files)
Quality controls were performed using the dropletUtils (version 1.14.2), scran (v1.22.1) and scatter (v1.22.0) Bioconductor packages, mostly following the steps of the OSCA book (http://bioconductor.org/books/release/OSCA/). Based on the observed distributions, cells with 0% or more than 25% of UMI counts attributed to the mitochondrial genes [15], with less than 631 UMI counts, or with less than 502 detected genes were excluded. The presence of doublet cells was investigated with the scDblFinder package (version 1.8.0), and suspicious cells were filtered out (score > 0.95).
After quality filtering, the resulting dataset consisted of 7,196 cells for patient 1 (DMEM), 887 cells for patient 2 (DMEM), 542 cells for patient 3 (DMEM), and 5,280 cells for patient 2 (CNT). The filtered UMI counts matrix for these genes and cells is provided in files UMIsMatrix_DMEM.txt.gz and UMIsMatrix_CNT.txt.gz
Assembly: hg38
Supplementary files format and content: TSV file (tab separated values) with UMI counts for ensembl release 96 gene models (after filtering out genes with low average expression level); columns correspond to: 1. ENSEMBL ID, 2. and remaining columns contain UMI counts for each cell; column headers include the cell barcode sequence and the sample ID separated by a dash (e.g., "AAAAAAAAAAAAAAAT_Patient_1")

source_name: Alveolar basal cells from peripheral lung tissue of IPF patient

growth_protocol:
DMEM supplemented with 10% FCS, 25 mM HEPES, 1× (vol/vol) sodium pyruvate, 1× (vol/vol) MEM vitamin-mix, and 1× (vol/vol) antibiotic-antimycotic, for 5 days
For the culture of alveolar basal cells, lung tissue was cut into small pieces and placed into flasks containing DMEM with 10% FCS, 25 mM HEPES and 2 mM l-glutamine, 1× (vol/vol) MEM vitamin-mix, 100 U/l penicillin, 100 μg/ml streptomycin, and 0.25 μg/ml amphotericin B and maintained in a humified atmosphere of 5% CO2 at 37°C. After five days, tissue pieces were removed and cells were harvested for down-stream analysis (Samples 1 to 3), or transferred to a Cnt-PR-A growth medium for five additional days (Sample 4)

extract_protocol:
Cells were collected in 2 batches (patient 1 on April 8th 2019, and patients 2 and 3 on May 27th 2019) for an expected recovery of 10,000 cells.
Cell suspensions from each patient were loaded into a single well of a 10× Genomics Chromium Single Cell Controller.
Single-cell capture and cDNA and library preparation were performed at the Genomics Facility Basel of the ETH Zurich, Basel, with a Single Cell 3’ v3 Reagent Kit (10× Genomics) according to manufacturer’s instructions.

tag: patient

value: mixed

tag: disease

value: idiopathic pulmonary fibrosis

tag: Sex

value: female


title: WT-C-3-2

value: Oryza sativa Japonica Group cv Nipponbare

value: WT

value: Mock, 3hours


title: NC2: HONE-1 Control_2

source_name: Control_2_Gene expression

source_name: Control_2_m6A methylation


title: Scc2-AID, aux/dox, thiolutin [KJ15]


title: Wpl1-AID, aux/dox, DMSO [KJ16]


title: NC3: HONE-1 Control_3

source_name: Control_3_Gene expression

source_name: Control_3_m6A methylation


title: Scc2-AID, aux/dox, DMSO [KJ14]


title: NC1: HONE-1 Control_1

source_name: Control_1_Gene expression

source_name: Control_1_m6A methylation


title: WT-C-3-1

value: Seedlings


title: Patient 2 / DMEM


title: METTL18KO_4bp_del_biol rep 2

first: Eriko

last: Matsuura

address: Yayoi

department: IQB

description: Ribosome Profiling.Only R1 file was used.

data_processing:
Library strategy: Ribosome profiling
Basecalling with RTA(Real-Time Analysis): ver2.7.7
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA and other non-coding RNA alignment with STAR
Alignment with STAR
Read quantitation using custom scripts
Assembly: hg38
Supplementary files format and content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

extract_protocol: RNase I footprinting, ribosome pelleting, RNA extraction

value: human leukemia cell

value: mettl18 4bp deletion mutant


title: 33-C-6-2

value: Mock, 6hours


title: WT, aux/dox, DMSO [KJ12]

value: G2/M-arrest, auxin, doxycycline, DMSO


title: Patient 3 / DMEM

value: male


title: WT, aux/dox, thiolutin [KJ13]


title: METTL18KO_4bp_del_biol rep 1


title: METTL18KO_2bp_del_biol rep 2

value: mettl18 2bp deletion mutant


title: WT, DMSO [KJ4]

value: G2/M-arrest, DMSO


title: Wpl1-AID, thiolutin [KJ5]

value: G2/M-arrest, thiolutin


title: GTE012

city: Beijing

first: Haoda

last: Wu

address: Lincui East Road

department: State Key Laboratory of Molecular Development Biology

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
Sequencing was performed on an Illumina NovaSeq6000 platform
We used 10x genomics cellranger count pipeline 3.1.0 to analyze the sequencing data and generated the single cell information, once for each individual sample.
Genome_build: hg19
Supplementary_files_format_and_content: UMI counts matrix file with gene and barcode annotations

source_name: Ependymoma

extract_protocol:
Fresh EPN tissue was excised by physicians from Beijing Tiantan Hospital and delivered on ice to Institute of Genetics and Developmental Biology of Chinese Academy of Sciences immediately. Microdissected tissues were transferred to a 24-well cell culture plate and digested by buffer comprising 20 U/mL Papain (Worthington, LK003178), 100 U/mL DNaseI (Worthington, LK003172), 10 U/L chondroitinase ABC (Sigma, C3667), 0.07% hyaluronidase (Rhawn, R006687), 1 XGlutamax (Life Technologies, 35050061), 0.05 mM (2R)-amino-5-phosphonovaleric acid (APV; Thermo Fisher Scientific, 010510), 0.01 mM Y27632 dihydrochloride (Sigma, T9531), and 0.2 XB27 supplement (Thermo Fisher Biosciences, 17504044) in Hibernate-E media (Life Technologies, A1247601) for 1-2 hrs at 37°C, and then pooled with Hibernate-E buffer containing 1×Glutamax, 0.05 mM APV, 0.2X B27, 0.01 mM Y27632 dihydrochloride. Tissues were gently triturated through Pasteur pipettes with finely-polished tips of 600, 300 and 200 μm diameters in order, and washed once with Hibernate-E buffer to generate single-cell suspensions. After filtration through a 40 μm strainer (Thermo Fisher Scientific, 130-101-812), 1 X red blood cell lysis solution (MACS Miltenyi Biotec, 130-094-183) was added to remove blood contamination during surgery followed by 1800 μL debris removal solution (MACS Miltenyi Biotec, 130-109-398). Subsequently, the dissociated cells were stained with DAPI (0.2 µg/mL) to identify dead cells.
scRNA-seq libraries were constructed under the manufacturer instructions provided by 10×Genomics accompanying single cell 3' Library and Gel Bead Kit V3 (10×Genomics, 1000075). A Chromium Single Cell Controller (10×Genomics) loaded cell suspensions (300-600 living cells per microliter determined by Count Star) to generate single-cell gel beads in the emulsion (GEM). Quality control was performed on the generated cDNA library using the Agilent 4200 and scRNA-seq was performed on the Illumina Novaseq6000 sequencer.

value: Female

tag: relapse

value: Primary


title: Patient 1 / DMEM

value: mixed


title: 33-F-3-2

source_name: Seedlings

value: 4ºC, 3hours


title: 33-S-3-2

value: 200mM NaCl, 3hours


title: GTE002

value: Male

value: Recurrent


title: Wpl1-AID, aux/dox [KJ3]

value: G2/M-arrest, auxin, doxycycline


title: Scc2-AID, aux/dox [KJ2]


title: METTL18KO_2bp_del_biol rep 1


title: 33-C-6-1

value: Oryza sativa Japonica Group cv Nipponbare

value: Seedlings


title: Naïve_HAP1_biol rep 2

value: human leukemia cell

value: Wild type


title: METTL18KO_1bp_del_biol rep 1

value: mettl18 1bp deletion mutant


title: 33-F-3-1


title: GTE009


title: 33-C-3-2

value: Mock, 3hours


title: WT, aux/dox [KJ1]


title: Human_lung_2

city: Seoul

first: Hongyoon

last: Choi

address: 101, Daehak-ro, Jongno-gu

department: Department of Nuclear Medicine

country: South Korea

institute: Seoul National University Hospital

data_processing:
Space Ranger v1.1.0 software was utilized
STAR v.2.5.1b was used for genome alignment
The genome alignment and generation of count matrix were implemented with ‘spaceranger count’ command with according FASTQ files, reference, Visium slide image, and slide information
Genome_build: Cell Ranger hg38 reference genome (GRCh38)
Supplementary_files_format_and_content: HDF5 file containing UMI counts, spatial barcodes, and feature information (*filtered_feature_bc_matrix.h5)
Scale factors for high and low resolution images and number of pixels in each spatial spot (*scalefactors_json.json)
A table for barcodes names, binary codes for differentiating the location of spots relative to the tissue (1: inside tissue, 0: outside tissue), row and column number of each spot, and row and column pixel coordinates (*tissue_positons_list.csv)
High and low resolution tissue images (*image.png)

source_name: Lung

extract_protocol:
Two normal lung samples were acquired from lung specimen from one patient who underwent surgical resection for lung cancer. We acquired samples and embedded them in OCT compound in the operating room, and stored at -80°C until cryosectioning. For cryosectioning, samples were equilibrated to -20°C with cryotome (Thermo Scientific, USA). Sections were imaged and processed for spatially resolved gene expression using the Visium Spatial Transcriptomic kit (10X Genomics, USA). The protocol of this study was reviewed and approved by the institutional review board of Seoul National University (Application number: H-2009-081-1158).
Visium Spatial Transcriptomics

value: Normal lung

tag: patient number


title: 33-S-3-1


title: eye_disc_tumor_late_scrna

city: Leuven

first: Stein

last: Aerts

state: Flemish-Brabant

address: Herestraat 49

department: Department of Human Genetics / VIB Center for Brain and Disease Research

country: Belgium

institute: VIB-KU Leuven

library_source: transcriptomic single cell

data_processing:
Sequencing data were processed with CellRanger (v5.0.1) with default parameters and FlyBase r6.35 reference genome
scRNA data was processed using the NextFlow pipeline VSN (Flerin et al., 2021). VSN processing includes the doublet filtering using scrublet (Wolock et al., 2019) and the correction for batch effects between the runs using Harmony (Korsunsky et al., 2019). We used the following filtering parameters : minimum of 200 detected genes per cell, maximum of 15% signal of mitochondrial origin, minimum of 3 cells expressing any targeted genes.
Assembly: dm6
Supplementary files format and content: CellRanger output for each scRNA sample (control and tumor) comprising GEX features are present as TSV (barcode and features) and matrix (raw counts) format.

organism: Drosophila melanogaster

source_name: eye-antennal imaginal disc

growth_protocol: Wild-type flies were raised at 18°C at a density of 50 larvae/vial. Flies with induced Ras/Scrib tumor were raised at 25°C on a yeast-based medium under a 12h-12h day-night light cycle.

extract_protocol:
Eye-antennal discs or wing discs were dissected and transferred to a tube containing 100 µl ice cold PBS. After centrifugation at 800 g for 5 min, the supernatant was replaced by 50 µl of dispase (3 mg/ml, Sigma-Aldrich_D4818-2mg) and 75 µl collagenase I (100 mg/ml, Invitrogen_17100-017). Discs were dissociated at 25°C in a Thermoshaker (Grant Bio PCMT) for 45 min at 25°C, 500 rpm. The enzymatic reaction was reinforced by pipette mixing every 15 min. Cells were washed with 1 ml ice cold PBS and resuspended in 400 µl PBS supplemented with 0.04% BSA. Cell suspensions were passed through a 10 µM pluriStrainer (ImTec Diagnostics-435001050). Cell viability and concentration were assessed by the LUNA-FL Dual Fluorescence Cell Counter.
Single-cell libraries were generated using the 10x Chromium Single-Cell Instrument and Single Cell 3’ Gene Expression (GEX) kit according to the manufacturer’s protocol. Briefly, single cells from eye-antennal discs or wing discs were suspended in 0.04% BSA-PBS. After generation of nanoliter-scale Gel bead-in-emulsions (GEMs), GEMs were reverse transcribed in a C1000 Touch Thermal Cycler (Bio Rad) programmed at 53°C for 45 min, 85°C for 5 min, and hold at 4°C. After reverse transcription, single-cell droplets were broken and the single-strand cDNA was isolated and cleaned with Cleanup Mix containing DynaBeads (Thermo Fisher Scientific). cDNA was then amplified by PCR: 98°C for 3 min; 12 cycles of 98°C for 15 s, 67°C for 20 s, 72°C for 1 min; 72°C for 1 min; and hold at 4°C. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed and index adaptor ligated, with SPRIselect cleanup in between steps. The final gene expression library was amplified by PCR: 98°C for 45 s; 14 cycles of 98°C for 20 s, 54°C for 30 s, 72°C for 20 s; 72°C for 1 min; and hold at 4°C. The sequencing-ready library was cleaned up with SPRIselect beads.

treatment_protocol: Expression of the oncogenic driver Ras/Scrib was induced by raising the flies at 25°C

value: eye-antennal imaginal disc

tag: developmental stage

value: thrid instar larvae

tag: condition

value: late tumor

value: y,w,eyFlp; act>y+>Gal4, UAS-GFP/UAS-RasV12; FRT82 tub-Gal80/FRT82 scrib-,e

value: Ras/Scrib induction


title: GTE001


title: Human_lung_1


title: 33-C-3-1

tag: background


title: Naïve_HAP1_biol rep 1

tag: cell type

tag: genotype


title: WT_P3

status: Public on Jun 14 2022

city: Xiamen

first: Yanchun You

last: YOU

state: Fujian

address: No. 422, Siming South Road

institute: Xiamen University

data_processing:
The sequencing data was filtered with SOAPnuke by removing reads containing sequencing adapter.
Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%.
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM (v1.2.12).
Assembly: ASM15095v2
Supplementary files format and content: Tab-delimited text files include gene_id, transcript_id(s), length, effective_length, expected_count, TPM, FPKM values for each Sample.

organism: Phaeodactylum tricornutum

source_name: cell

growth_protocol: Cultures were grown at 20 °C in 16 h: 8 h, light: dark diurnal cycles with a photon flux of 100 μE m-2 s -1.

extract_protocol:
Total RNA was extracted using the TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) and the RNeasy Plus Micro Kit (QIAGEN, Code: 74034, Germany).
The total RNA and isolated mRNA quality and quantity were checked using the Agilent 2100 Bioanalyzer and NanoDrop (Thermo Fisher Scientific, MA, USA). Libraries for RNAseq were created from 1µg of mRNA from each culture.

treatment_protocol: The standard f/2, phosphate-depleted and nitrate-depleted cultures are named HNHP, P-depleted (HNLP), and N-depleted (LNHP), respectively. Cells were pre-starvation following the steps: cultures were grown to mid-exponential phase on f/2 medium without nitrogen and sampled, transferred to fresh f/2 medium with 1 µM PO4- and without nitrogen, and grown to mid-exponential phase.

tag: Stage

value: day 5

value: wild type

value: P


title: WT_P2


title: WT_N2

value: N


title: WT_CK3

value: CK


title: WT_N1


title: M_P2

value: PtTryp2 ko


title: M_P3


title: WT_CK1


title: M_N3


title: WT_CK2


title: M_CK1


title: M_CK2


title: JZ2005_emb_rep1 [DJ70]

city: New York

first: Jun

last: Kim

state: NY

address: 100 Washington Square East 1009 Silver Center

department: Biology

institute: NYU

data_processing:
Hi-C:  data was mapped to ce10 (WS220) reference genome or its variant that corrosponds to the perturbation using default parameters of the Juicer pipeline version 1.5.7 (Durand et al., 2016).
processed data files format and content: Hi-C:  hic matrix files
Assembly: WS220 or its variants based on rex insertion or chromosome fusion

organism: Caenorhabditis elegans

source_name: whole worms

extract_protocol:
Hi-C: Crosslinked worms were resuspended in 20 ul of PBS per 50ul of worm pellet then dripped into liquid nitrogen containing mortar. The worms were grounded with pestle until fine powder. Grounded worms were crosslinked again in 2% formaldehyde using the TC buffer as described by the Arima Hi-C kit, which uses two 4-base cutters, DpnII and HinfI. The Arima manufacturer’s protocol was followed.
Hi-C:  Library preparation was performed using the KAPA Hyper Prep Kit using the protocol provided by Arima.

value: JZ2005 (dcas9 suntag, sgRNA); pySi[Pfib-1:NLS:scFv:sfGFP/unc-119(+) ] I; pySi[Pfib-1:NLS:dCas9:24xGCN4/unc-119(+) ] II; unc-119(ed3)?III; pyIs(pU6:sgRNA-X227/Punc-122:mcherry).

tag: tissue

value: whole worms

value: Embryo


title: JZ2005_emb_rep2 [DJ87]

tag: strain


title: ERC90_L3_rep2 [JK123]

value: ERC90 (super rex in II); ersIs62[superrex(rex40,rex8,rex35)x2],II:8420106]


title: M_CK3


title: WT_N3


title: ERC90_L3_rep1 [JK102]


title: METTL18KO_1bp_del_biol rep 2

value: human leukemia cell

value: mettl18 1bp deletion mutant


title: ERC63_L3_rep2 [JK53]


title: WT_P1


title: ERC61_L3_rep2 [JK52]

value: ERC61 (rex-8 in II); ersSi25[wt400bp_rex8, cb-unc-119(+)] II; unc-119(ed3) III


title: ERC80_emb_rep2 [DJ68]


title: ERC63_L3_rep1_1 [JK19_1]


title: ERC80_emb_rep3 [DJ69]


title: M_N1


title: ERC80_emb_rep1_2 [DJ61_2]


title: M_N2


title: ERC69_emb_rep2_2 [DJ66_2]


title: M_P1


title: ERC69_emb_rep1_1 [DJ65_1]


title: ypT47_L3_rep1 [JK85]

value: ypT47 (XV)


title: ERC69_emb_rep2_1 [DJ66_1]


title: ERC80_emb_rep1_1 [DJ61_1]


title: N2_emb_rep2 [DJ74]


title: N2_L3_rep2_2 [JK90]


title: N2_L3_rep1 [JK15]


title: N2_L3_rep2_1 [JK89]


title: ERC69_emb_rep1_2 [DJ65_2]


title: N2_emb_rep1 [DJ73]


title: ERC63_L3_rep1_2 [JK19_2]


title: A549 treated with TGF-β1 plus acetate 4

city: St. Petersburg

first: Jianhua

last: Xiong

state: Florida

address: 600 5th Street S

department: Medicine

institute: Johns Hopkins University

description: cancer cells

data_processing:
The fastq files were generated using the bcl2fastq software for further analysis. Data were analyzed as previously described with minor modifications. Briefly, quality confirmed RNA-seq reads from each library were aligned and mapped with HISAT2. Differential expression analysis was performed using open source Limma R package.
Genome_build: hg38
Supplementary_files_format_and_content: The processed data file was in txt format.

growth_protocol: The cells were cultured with Ham's F-12K (Kaighn's) Medium supplemented with 10% fetal bovine serum at 37°C with 5% CO2

extract_protocol:
The total RNA was extracted by RNAeasy plus mini kit.
The sequencing libraries were constructed from 100 ng – 500 ng of total RNA using the Illumina’s TruSeq Stranded Total RNA kit with Ribo-Zero following the manufacturer’s instruction. The fragment size of RNAseq libraries was verified using the Agilent 2100 Bioanalyzer (Agilent) and the concentrations were determined using Qubit instrument (Thermo Fisher Scientific). The libraries were loaded onto Illumina HiSeq 3000 (Illumina, San Diego, CA) for 2 × 75 bp paired end read sequencing.

treatment_protocol: A549 cells were seeded in 6 well plate and treated with 10 ng/mL TGF-β1 with or without 40 mM sodium acetate  for 2 days.

value: Lung Cancer Cell

tag: passages

tag: treatment

value: TGF-β1 plus acetate


title: A549 treated with TGF-β1 plus acetate 2

description: cancer cells


title: ypT47_L3_rep2 [JK103]


title: A549 treated with TGF-β1 4

description: cancer cells


title: ERC61_L3_rep1 [JK51]


title: A549 treated with TGF-β1 2

description: cancer cells


title: A549 treated with TGF-β1 1

description: cancer cells


title: A549 treated with TGF-β1 3

description: cancer cells


title: A549 control 4

description: cancer cells

value: Control


title: A549 control 3

description: cancer cells


title: A549 control 2

description: cancer cells


title: macrophages, wild-type, MSU treated, rep3

city: Boston

first: Mridul

last: Agrawal

address: 450 Brookline Ave.

institute: Dana-Farber Cancer Institute

data_processing:
Paired-end reads in FASTQ format were first processed through fastp.
Reads containing adapter and poly-N sequences and reads with low quality were removed. At the same time, Q20, Q30, and GC content of the clean data were calculated. All downstream analyses were based on the clean reads with high quality.
The reads were then aligned to the mouse reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
FeatureCounts was used to count the reads mapped to each gene.
Assembly: mm10
Supplementary files format and content: counts

organism: Mus musculus

source_name: macrophages

extract_protocol:
Total RNA extraction was performed using the RNeasy Plus Mini Kit (Qiagen, catalog# 74134) according to the manufacturer’s instructions.
For generation of sequencing libraries, the NEBNext Ultra RNALibrary Prep Kit for Illumina (NEB, USA) was used following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: macrophages

value: wild-type

value: MSU


title: macrophages, wild-type, MSU treated, rep1


title: macrophages, wild-type, MSU treated, rep2


title: A549 treated with TGF-β1 plus acetate 3

description: cancer cells


title: macrophages, Tet2 knockout, MSU treated, rep3

value: Tet2 knockout


title: A549 treated with TGF-β1 plus acetate 1

description: cancer cells


title: macrophages, Tet2 knockout, MSU treated, rep2


title: macrophages, Tet2 knockout, MSU treated, rep1


title: A549 control 1

description: cancer cells


title: organoid_d14_rat_transplant-4wk_scRNAseq_3

city: Cambridge

first: Eva

last: Fast

state: MA

address: 1 Portland st

institute: Pfizer

data_processing:
Demultiplexing, alignment, and estimation of cell-containing partitions and associated UMIs using Cell Ranger Version 3.0.2
Genome_build: GRCh38
Supplementary_files_format_and_content: For each sample countmatrixes (.mtx) and table files identifying cell barcodes and genes (.tsv)

organism:
Homo sapiens
Rattus norvegicus

source_name: IPSC

growth_protocol: High-throughput in vitro kidney organoid generation: For the development of a reproducible scalable protocol, we introduced several key modifications to published protocols5, 7, 13, 14. We started by dispersing iPSCs reaching 80 to 85% confluency into single cell suspensions using Accutase and seeding 275,000 cells per flask in hESC-qualified, matrigel-coated flasks with TeSR1 media plus Y-27632 (Tocris 1254, Bristol, United Kingdom). On the next day, the medium was changed to STEMdiff APEL2 (StemCell Technologies) supplemented with 10 M CHIR99021 (Tocris 4423). After 48 h, the medium was changed to STEMdiff APEL2 supplemented with 8 M CHIR99021. Subsequently, medium was switched to STEMdiff APEL2 with 200 ng/mL FGF9 (R&D Systems, Minneapolis, MN) and 1 g/mL heparin (StemCell Technologies) and changed every other day. On day 7, cells were passaged using Accutase and pelleted by centrifugation at 500,000 cells per pellet. The pellets were placed on transwell plates and STEMdiff APEL2 supplemented with 5 M CHIR99021 was added for 1 h before changing to STEMdiff APEL2 with 200 ng/mL FGF9 and 1 g/mL heparin. Medium was changed every other day for the next 4 days using STEMdiff APEL2 containing 200 ng/mL FGF9 and 1 g/mL heparin. On day 13, the medium was switched to STEMdiff APEL2 with 1 g/mL heparin. Thereafter, organoids were grown in STEMdiff APEL2 and medium was changed every other day.

extract_protocol:
Organoids were rinsed with DPBS, collected into 1.5 ml conical tube containing 500 ml TrypLE Select and incubated for 5 min at 37°C, passed 3 to 4 times through a 27G needle, and incubated for 5 min at 37°C after adding additional 500 ml of TrypLE Select. Organoids were dissociated into single cell suspensions by passing 3 to 4 times through a 30G needle, followed by centrifugation at 600xg for 5 min. Supernatants were discarded, and cell pellets were resuspended in DPBS and filtered through a 40 mm cell strainer. Cell numbers were quantified on a Cellometer cell counter and adjusted to 1000 cells/ml in DPBS.
Single cell cDNA library preparation was performed following manufacturer's protocols (https://www.10xgenomics.com). Single cell suspension were loaded on a Chromium controller to generate single cell GEMS (Gel Beads-In-Emulsions). The scRNA-Seq library was prepared with chromium single cell 3’ reagent kit v3 (10x Genomics)

treatment_protocol: In vitro organoids from growth protocol were grown in parallel and compared to in vivo transplanted organoids. Organoid transplantation protocol:  Prior to initiating transplantation into rats for preclinical studies with stem cell derived organoids, persuasive evidence of promise in in vitro experimental models (Figure 2), were performed in accordance with International Society for Stem Cell Research (ISSCR) guidelines. Organoids differentiated as described above were transplanted into 3-4 weeks old athymic male nude rats (Crl:NIH-Foxn1rnu, Charles River Labs, Wilmington, MA) weighing approximately 100g each, acclimated for at least three days in conventional cage setting with rodent diet 5053 and ad libitum water, at_rat_Research test facility (Worcester, MA) in accordance with an approved IACUC study protocol. 45 rats divided randomly and equally into three experimental groups (Day 10, 12 and 14 differentiated) were anesthetized with ketamine/dexdomitor and an antibiotic (Cephazolin) as well as an analgesic (Buprenorphine-SR) was administered to facilitate post-surgical recovery. The kidneys were exposed by an incision in the abdominal wall. After creating an incision in the kidney capsule, a small niche was created under the kidney capsule to host the organoids. Organoids grown for 10, 12 or 14 days in vitro were aspirated into the tip of an 18-24G catheter (Instech, Plymouth, PA) and placed into the niche, the abdominal wall and skin were closed, and the animals were allowed to recover and followed up with routine cage side observations for general health. At 2 or 4 weeks after transplantation, 6-8 rats per experimental group were euthanized under CO2 as per IACUC approved study protocol, kidneys exposed by an incision in the abdominal wall and organoids (n≥3) were harvested for scRNA-Seq and NanoString mRNA analysis as well as analysis of graft tissue vascularization and functional connectivity in the PK/PD studies.  Organoid differentiation was also evaluated at the protein level by flow cytometry analysis of two podocyte surface proteins, nephrin30 and podocalyxin31. Cells from dissociated organoids were washed with DPBS, blocked in 1% mouse serum for 30 min at 4°C, incubated with anti-nephrin primary antibody (R&D Systems, AF4269) and APC-conjugated anti-podocalyxin antibodies (R&D Systems, FAB1658A) diluted in sorting buffer (HBSS containing 1% BSA and 0.035% NaHCO3). The cells were further incubated for 10 min in Alexa Fluor 488-conjugated donkey anti-sheep LgG (H+L) antibody (ThermoFisher Scientific, A-11015), washed and resuspended in sorting buffer. Unstained cells were utilized to establish background fluorescence. Data acquisition and analysis were performed on a SONY SH800 flow cytometer. Mean fluorescence in live cells was determined for each sample and is presented after subtraction of background fluorescence.

tag: type of organoid

value: in vivo organoid

tag: day of maturation

value: day 14 - 4wk transplant


title: organoid_d14_rat_transplant-4wk_scRNAseq_2


title: organoid_d14_rat_transplant-4wk_scRNAseq_1


title: tumor, RAS and iHPV, 6

city: Chicago

first: John

last: Bechill

state: IL

department: Radiation Oncology

institute: The University of Chicago

description: Gene expression data from RAS-HPV E6 expressing tumor

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Gene ST 2.0 exon array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: Affymetrix exon level data processed by rma quintile normalization using Partek software

label: biotin

source_name: KHR + tamoxifen

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Tumors were grown out of C57BL/6 × FVB F1 mice treated with intraperitoneal injections of tamoxifen

extract_protocol: RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

treatment_protocol: not applicable

value: tumor

value: C57BL/6 x FVB F1


title: tumor, RAS, 4

description: Gene expression data from RAS expressing tumor

source_name: KR + tamoxifen


title: Lung, BAL, MuHV-4, CCR2 KO

city: Liège

first: Bénédicte

last: Machiels

state: Liège

address: Avenue de Cureghem 7b, B43b

department: DMI

institute: Université de Liège

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung, BAL

extract_protocol:
After euthanasia, the trachea was catheterized and BAL was performed by two consecutive flushes of the lungs with 1 mL of ice-cold PBS containing cOmplete™ Protease Inhibitor Cocktail (Roche). One tablet of inhibitor cocktail was dissolved in 50 mL ice-cold PBS. Cell density in BALF was evaluated using a hemocytometer after Tuerk solution staining (Sigma-Aldrich). To harvest lung cells, mice were perfused with ice-cold PBS through the right ventricle. Then, lung lobes were collected into a C-Tube (Miltenyi) containing complete Hanks' Balanced Salt Solution (HBSS) medium, 1 mg/ml collagenase D (Roche) and 50 μg/ml DNase I (Roche). These lung lobes were processed with a gentleMACS dissociator (Miltenyi) and, finally, were incubated for 30 min at 37 °C. Cells were finally strained through a 70-μm filter. Cell density was evaluated using a hemocytometer after Trypan solution staining (Sigma-Aldrich).
Libraries preparations for single-cell immune profiling, sequencing, and post-processing of the raw data were performed at the GIGA-Genomics Core Facility (Belgium). Sorted cells were washed with 1X PBS (calcium and magnesium free) containing 0,04% weight/volume BSA (400 μg/mL). BALF and lung cells were pooled together within each condition after cell hashing with barcoded antibodies (BioLegend).We equalized numbers of cells between conditions for the scRNA-seq profiling and cell concentration was adjusted to 1.000 total cells/μL and 16.000 cells were loaded on Chromium Controller (10x Genomics). Samples were further processed for droplet-based RNA sequencing and libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3 according to manufacturer’s protocol (10x Genomics). Amplified cDNA quality controls were performed with an Agilent bioanalyzer (Agilent) and final library profile were checked on Qiaxcel (Qiagen). Sequencing libraries were loaded an Illumina Novaseq sequencer with NovaSeq SP 100 v1 kit (Illumina, CA, USA) using the following read lengths: 28 bp for Read1 (18 bp Barcode + 10 bp Randomer), 8 bp for Sample Index and 88 bp for Read2. Library quantification was processed with KAPA Library quantification kit (KAPA Biosystems). Gene counts were obtained by aligning reads to the mm10 genome using CellRanger software (10× Genomics).

value: Female

tag: age

value: 6 weeks old

value: Lung, BAL

value: MOs, CD4 T cells

value: MuHV-4, CCR2 KO


title: Lung, BAL, MuHV-4, WT (hash)

description: 10x Genomics

value: MuHV-4, WT


title: Lung, BAL, MuHV-4, WT

description: 10x Genomics


title: Lung, BAL, MuHV-4, CCR2 KO (hash)

description: 10x Genomics


title: tumor, RAS, 6


title: Lung, Mock, CCR2 KO

description: 10x Genomics

value: Lung

value: CCR2 KO


title: organoid_d12_rat_transplant-4wk_scRNAseq_3

value: day 12 - 4wk transplant


title: Lung, Mock, WT

description: 10x Genomics

value: WT


title: organoid_d12_rat_transplant-4wk_scRNAseq_2


title: organoid_d12_rat_transplant-4wk_scRNAseq_1


title: organoid_d10_rat_transplant-4wk_scRNAseq_3

value: day 10 - 4wk transplant


title: tumor, RAS and iHPV, 1


title: tumor, RAS and iHPV, 2


title: organoid_d10_rat_transplant-4wk_scRNAseq_2


title: TKO2 methylation

city: Rehovot

first: Markus

last: Mittnenzweig

state: Shfela

address: 234 Herzl St.

country: Israel

institute: Weizmann Institute of Science

description:
DNA methylation analysis of Tet-TKO mESCs-derived E8.5 cells using PBAT
tet_tko_s2

data_processing:
MARS-seq data was processed as detailed in the MARS-seq2.0 protocol (Keren-Shaul et al. 2019):
1. bcl2fastq/2.15.0.4
2. Pool_barcode (4 bps) and well_barcode (7 bps) plus UMI barcode (8 bps) were removed from Read 1 and Read 2 (respectively) and concatenated to the fastq header.
3. Read 1 sequences were mapped to the mm9 genome using bowtie2.
4. Demultiplexing and construction of mRNA count matrix were based on 4bp plate barcode, 7bp well barcode and 8bp UMI barcode
5. Header structure of labeled Read 1 fastq files: "ORIGINALHEADER_barcode=similar_oligo-pool_barcode_quality-well_barcode_quality-UMI_quality-pool_barcode-well_barcode-UMI". Concatenated entries are separated by "-"
6. well_barcode (7bp), pool_barcode (4bp) and external_barcode (8bp) of each single cell can be found in metadata.
PBAT data was processed as detailed (Meir et al., 2020): PE 150bp or 300bp reads were aligned to the mm9 reference genome using an in-house script based on Bowtie2. In cases where the two reads ends were not aligned in a concordant manner, the reads were discarded. Reads that were mapped to the same genome coordinates where marked as duplicates and were used only once. We subsample methylation of single-cells to have only one methylation call per CpG.
Assembly: mm9
Supplementary files format and content: Tab-separated text file for each 384-well plate containing UMI counts per gene per single cell. metadata_cells_scrna_sequencing.txt file contains metadata for each processed single cell.
Supplementary files format and content: Tab-separated text file for each sample, containing a row per genomic CpG with the following columns: 'chrom','start','end' - coordinates in 0-based form, 'cov' - # of times the CpG was covered, 'meth' # of times the CpG was methylated.

source_name: Sorted TKO2 cells from E8.5 mixed chimeras

growth_protocol: Control and mutant mESCs were cultured on irradiated mouse embryonic fibroblasts (MEFs) with standard serum medium for 2-3 days and replaced with 2i+LIF medium containing an additional 1 mM PD0325901 and 3 mM CHIR99021 for another growth of 10-12 hours.

extract_protocol:
Whole-embryo chimera, mixed chimera, and AAV-Cre treated embryos were dissected in ice-cold 1×PBS, followed by imaging in a drop of DMEM medium supplemented with 10% foetal bovine serum (FBS) under a Nikon Eclipse Ti2 inverted microscope. Embryos were then rinsed in ice-cold 1×PBS, transferred into an Eppendorf tube containing 35 µl 0.25% Trypsin/0.02% EDTA Solution A, and incubated at 37 °C for 5 min with 2-3 times pipetting. Trypsinization was stopped by adding 10% FBS/DMEM medium. Cell suspensions were filtered through a 35 µm strainer before sorting.
For MARS-seq analysis, single cells were index-sorted into a pre-barcoded 384-well capture plate that contains 2 µl of lysis solution and barcoded poly (T) reverse-transcription (RT) primers. In each plate, 12 wells at positions C1, C2, D1, D2, J6, J7, K6, K7, O23, O24, P23, and P24 were kept as non-cell controls. Immediately after sorting, each plate was sealed, spun down, snap-frozen on dry ice, and stored at -80 °C until library preparation.
For bisulfite sequencing, Tet-TKO1, Tet-TKO2, Ctrl1, and Ctrl2 cells were sorted from E8.5 chimera embryos respectively. Cell pellets were kept at -80 °C until library preparation. Genomic DNA was extract using commercial kit.
Single-cell cDNA libraries were prepared using the MARS-Seq method as described (Keren-Shaul et al., 2019). Briefly, reverse transcription was performed in individual wells of the sorted 384-well plate to get complementary DNA (cDNA). Subsequently, all liquid from each 384-well plate was pooled and converted to double-stranded DNA, transcribed using T7 RNA polymerase, and fragmented. A unique plate adaptor was added to each library to be sequenced together, and RNA::ssDNA (plate adaptor) ligation was performed. The purified ligates were applied to a second RT step with a primer complementary to the ligated adaptor, and the library is completed by cDNA enrichment through PCR amplification. Library concentration and profile were evaluated before sequencing.  Bulk PBAT library was performed as previously described (Meir et al., 2020). Briefly, genomic DNA was converted with bisulfate, and applied to the first and second strand synthesis. The product was treated by Klenow fragment and purified. A final PCR was performed using a universal primer and indexed primers. The final product was clean and sequenced.

treatment_protocol:
(1) To obtain whole-embryo and mixed chimeric embryos, mESCs were injected into diploid or tetraploid B6D2F x B6D2F1 E3.5 blastocysts and surgically implanted into E2.5 postcoitum pseudo-pregnant Hsd:ICR (CD-1) females following standard procedures. Females were sacrificed at embryonic day 7.5-9.5 based on the design of the experiment.
(2) To obtain AAV-Cre treated Tet knockout embryos, zygotes from Tet triple floxed mice were collected in M2 medium. Following acidic Tryode’s solution treatment, zygotes were rinsed in M2 medium and transferred to KSOM for incubation in a tissue culture incubator. Drops containing 35 µl KSOM medium were placed in 35 mm plates under mineral oil. 6e9 vg AAV1-Cre-GFP viral were added to each drop, followed by a 15 min incubation at 37 °C in the same tissue culture incubator. Subsequently, zygotes were transferred into the viral drop and cultured for 24 hrs. Qualified 2-cell embryos were rinsed in M2 medium and transferred into the oviduct of E0.5 pseudo-pregnant ICR females. Recipient females were allowed to carry the embryos and sacrificed at E7.5.

value: mESC-derived Tet TKO cells for clone TKO2

value: Bisulfite sequencing


title: tumor, RAS, 2


title: Ctrl1 methylation

description:
DNA methylation analysis of control mESCs-derived E8.5 cells using PBAT
control_s1

source_name: Sorted Ctrl1 cells from E8.5 mixed chimeras

value: mESC-derived Control cells for clone Ctrl1


title: tumor, RAS, 3


title: tumor, RAS and iHPV, 4


title: tumor, RAS and iHPV, 5


title: Tet1/2/3 AAV Cre TKO plate 10

description:
MARS-seq of whole-embryo Tet triple KOs
TetAAV_P19_2

source_name: E7.5 whole embryos

value: E7.5 whole embryos

value: Tet1/2/3 TKO

value: AAV Cre-delivered Tet1/2/3 triple KO


title: Tet1/2/3 AAV Cre TKO plate 9

description:
MARS-seq of whole-embryo Tet triple KOs
TetAAV_P13_2


title: Tet1/2/3 AAV Cre TKO plate 8

description:
MARS-seq of whole-embryo Tet triple KOs
TetAAV_P18


title: tumor, RAS and iHPV, 3

value: tumor

value: C57BL/6 x FVB F1


title: tumor, RAS, 1


title: organoid_d14_rat_transplant-2wk_scRNAseq_3

value: in vivo organoid

value: day 14 - 2wk transplant


title: Tet1/2/3 AAV Cre TKO plate 7

description:
MARS-seq of whole-embryo Tet triple KOs
TetAAV_P16


title: organoid_d12_rat_transplant-2wk_scRNAseq_3

value: day 12 - 2wk transplant


title: organoid_d14_rat_transplant-2wk_scRNAseq_1


title: organoid_d10_rat_transplant-4wk_scRNAseq_1


title: Ctrl2 methylation

description:
DNA methylation analysis of control mESCs-derived E8.5 cells using PBAT
control_s2

source_name: Sorted Ctrl2 cells from E8.5 mixed chimeras

value: mESC-derived Control cells for clone Ctrl2


title: TKO1 methylation

description:
DNA methylation analysis of Tet-TKO mESCs-derived E8.5 cells using PBAT
tet_tko_s1

source_name: Sorted TKO1 cells from E8.5 mixed chimeras

value: mESC-derived Tet TKO cells for clone TKO1


title: organoid_d14_rat_transplant-2wk_scRNAseq_2


title: Tet1/2/3 AAV Cre TKO plate 5

description:
MARS-seq of whole-embryo Tet triple KOs
TetAAV_P11


title: organoid_d12_rat_transplant-2wk_scRNAseq_2


title: Tet1/2/3 AAV Cre TKO plate 2

description:
MARS-seq of whole-embryo Tet triple KOs
TetAAV_P07


title: Tet1/2/3 AAV Cre TKO plate 4

description:
MARS-seq of whole-embryo Tet triple KOs
TetAAV_P10


title: organoid_d10_rat_transplant-2wk_scRNAseq_2

value: day 10 - 2wk transplant


title: Tet1/2/3 AAV Cre TKO plate 6

description:
MARS-seq of whole-embryo Tet triple KOs
TetAAV_P12


title: organoid_d10_rat_transplant-2wk_scRNAseq_3


title: Tet2/3 DKO chimera plate 12

description:
MARS-seq of chimera embryos injected with Tet2/3 double KO cells
Tet23DKO_3_0616

source_name: E7.5 chimera embryo

value: E7.5 chimera embryo

value: mESC-derived Tet2/3 DKO cells

value: Chimera assay


title: Tet1/2/3 AAV Cre TKO plate 3

description:
MARS-seq of whole-embryo Tet triple KOs
TetAAV_P08


title: organoid_d12_rat_transplant-2wk_scRNAseq_1


title: organoid_d10_rat_transplant-2wk_scRNAseq_1


title: Tet2/3 DKO chimera plate 13

description:
MARS-seq of chimera embryos injected with Tet2/3 double KO cells
Tet23DKO_4_0616


title: Tet2/3 DKO chimera plate 10

description:
MARS-seq of chimera embryos injected with Tet2/3 double KO cells
Tet23_DKO_1_0616


title: Tet2/3 DKO chimera plate 11

description:
MARS-seq of chimera embryos injected with Tet2/3 double KO cells
Tet23_DKO_2_0616


title: Tet1/2/3 AAV Cre TKO plate 1

description:
MARS-seq of whole-embryo Tet triple KOs
TetAAV_P01


title: tumor, RAS, 5

description: Gene expression data from RAS expressing tumor


title: Tet1/3 DKO chimera plate 11

description:
MARS-seq of chimera embryos injected with Tet1/3 double KO cells
Tet13_DKO_4

value: mESC-derived Tet1/3 DKO cells


title: Tet1/3 DKO chimera plate 12

description:
MARS-seq of chimera embryos injected with Tet1/3 double KO cells
Tet13_P05


title: IgG_JZ2005_emb_rep1 [JK33]

data_processing:
ChIP-seq: Bowtie2 version 2.4.2 was used to align 75 bp single-end reads to WS220 or its variants based on perturbation with default parameters (Langmead and Salzberg, 2012). Bam sorting and indexing was performed using samtools version 1.11 (Danecek et al., 2021). BamCompare tool in Deeptools version 3.5.0 was used to normalize for the sequencing depth using CPM and create ChIP-Input coverage and ChIP/Input ratios with a bin size of 10 bp and 200 bp read extension (Ramírez et al., 2016). Reads with a minimum mapping quality of 1 were used, and mitochondrial DNA, PCR duplicates, and blacklisted regions were removed (Amemiya et al., 2019). For DPY27 ChIP-seq data, the ratio values are used to rescale the data such that autosomes have mean of 0 and X-chromosome has mean of 1.
processed data files format and content: ChIP-seq: rescaled input normalized bigwigs
Assembly: WS220 or its variants based on rex insertion or chromosome fusion

extract_protocol:
ChIP-seq: embryos, L2/L3s and adult worms were dounce-homogenized in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) and sonicated in 0.1% sarkosyl to obtain chromatin fragments between 200 and 800 bp. 2 mg of protein extract and 3 to 10 ug of antibody was used per ChIP.
ChIP-seq: half of the ChIP DNA and 30 ng of input DNA were ligated to Illumina TruSeq adapters and amplified by PCR. Library DNA between 250 and 600 bp was gel purified.

value: JZ2005 (dcas9 suntag, sgRNA); pySi[Pfib-1:NLS:scFv:sfGFP/unc-119(+) ] I; pySi[Pfib-1:NLS:dCas9:24xGCN4/unc-119(+) ] II; unc-119(ed3)?III; pyIs(pU6:sgRNA-X227/Punc-122:mcherry).

value: whole worms

value: Embryo

tag: antibody target

value: IgG

tag: antibody (vendor, cat#, lot#)


title: protA_JZ2005_emb_rep2 [JK42]

value: protA


title: protG_JZ2005_emb_rep1 [JK43]

value: protG


title: IgG_JZ2005_emb_rep2 [JK37]


title: GFP_JZ2005_emb_rep2 [DJ83]

value: GFP


title: DPY27_protG_JZ2005_emb [JK46]


title: Tet1/3 DKO chimera plate 13

description:
MARS-seq of chimera embryos injected with Tet1/3 double KO cells
Tet13_P06


title: protG_JZ2005_emb_rep2 [JK45]


title: Tet1/3 DKO chimera plate 10

description:
MARS-seq of chimera embryos injected with Tet1/3 double KO cells
Tet13_DKO_3


title: protA_JZ2005_emb_rep1 [JK41]


title: Tet1/3 DKO chimera plate 9

description:
MARS-seq of chimera embryos injected with Tet1/3 double KO cells
Tet13_2_0613


title: DPY27_JZ2005_emb_rep1 [JK11]


title: DPY27_JZ2005_emb_rep2 [JK22]


title: input_JZ2005_emb_rep2 [JK36]

value: input


title: Tet1/3 DKO chimera plate 4

description:
MARS-seq of chimera embryos injected with Tet1/3 double KO cells
mTet13_P08


title: input_JZ2005_emb_rep1 [DJ79]


title: Tet1/3 DKO chimera plate 2

description:
MARS-seq of chimera embryos injected with Tet1/3 double KO cells
mTet13_P03


title: Tet1/2 DKO chimera plate 25

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12DKO_9

value: mESC-derived Tet1/2 DKO cells


title: input_JZ1973_emb [JK16]

value: JZ1973 (dcas9 suntag); pySi[Pfib-1:NLS:scFv:sfGFP/unc-119(+) ] I; pySi[Pfib-1:NLS:dCas9:24xGCN4/unc-119(+) ] II; unc-119(ed3) III


title: Tet1/3 DKO chimera plate 3

description:
MARS-seq of chimera embryos injected with Tet1/3 double KO cells
mTet13_P07


title: IgG_JZ1973_emb [JK29]


title: Tet2/3 DKO chimera plate 8

description:
MARS-seq of chimera embryos injected with Tet2/3 double KO cells
Tet23_7


title: Tet1/2 DKO chimera plate 23

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12DKO_7


title: DPY27_JZ1973_emb_rep1 [JK21]


title: Tet1/2 DKO chimera plate 22

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12DKO_15


title: Tet1/2 DKO chimera plate 24

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12DKO_8


title: input_ERC63_emb [LAS03]


title: DPY27_JZ1973_emb_rep2 [JK30]


title: DPY27_ERC63_emb_rep2 [LAS07]


title: input_ERC62_emb [LAS09]


title: DPY27_ERC63_emb_rep1 [LAS06]


title: DPY27_ERC62_emb_rep1 [LAS04]


title: GFP_JZ2005_emb_rep1 [DJ86]


title: DPY27_ERC62_emb_rep2 [LAS05]


title: Tet1/2 DKO chimera plate 16

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12_2_0616


title: Tet1/3 DKO chimera plate 1

description:
MARS-seq of chimera embryos injected with Tet1/3 double KO cells
mTet13_P01


title: Tet1/2 DKO chimera plate 21

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12DKO_14


title: input_ERC61_emb_rep2 [JK98]

value: ERC61 (rex-8 in II); ersSi25[wt400bp_rex8, cb-unc-119(+)] II; unc-119(ed3) III


title: DPY27_ERC61_emb_rep2 [JK80]


title: Tet1/2 DKO chimera plate 19

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12DKO_12


title: input_ERC06_emb_rep2 [SE257]

value: ERC06 (rex-1 in II); knuSi254[DCC undisclosed, unc-119(+)] II; unc-119(ed3) III


title: Whole-embryo Tet TKO plate 47

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N29_13

source_name: E7.5 - E9.5 whole embryo

value: E7.5 - E9.5 whole embryo

value: mESC-derived Tet TKO cells

value: Tetraploid complementation assay


title: input_ERC61_emb_rep1 [JK76]


title: input_ERC90_L3_rep3 [JK101]

value: ERC90 (super rex in II); ersIs62[superrex(rex40,rex8,rex35)x2],II:8420106]


title: Tet1/2 DKO chimera plate 17

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12DKO_10

value: E7.5 chimera embryo

value: Chimera assay


title: Tet1/2 DKO chimera plate 20

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12DKO_13


title: Tet1/2 DKO chimera plate 15

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12_1_0616


title: input_ERC90_L3_rep2 [JK119]

value: whole worms


title: Tet1/2 DKO chimera plate 18

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12DKO_11


title: DPY27_ERC61_emb_rep1 [JK94]

value: Embryo


title: Whole-embryo Tet TKO plate 43

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N29_09


title: Whole-embryo Tet TKO plate 44

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N29_10


title: Whole-embryo Tet TKO plate 48

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N29_14


title: DPY27_ERC06_emb_rep1 [SE278]


title: DPY27_ERC90_L3_rep3 [JK97]


title: DPY27_ERC90_L3_rep1 [AKM365]


title: input_ERC90_L3_rep1 [AKM369]


title: Whole-embryo control plate 13

description:
MARS-seq of tetraploid complemented embryos injected with control cells
191125_P06_NOVA

source_name: E7.5 whole embryo

value: E7.5 whole embryo

value: mESC-derived Control cells


title: input_ERC06_emb_rep1 [LW17]


title: Whole-embryo Tet TKO plate 46

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N29_12


title: Whole-embryo Tet TKO plate 37

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N29_03


title: DPY27_ERC90_L3_rep2 [JK116]


title: input_ERC63_L3_rep2 [JK61]


title: Whole-embryo Tet TKO plate 38

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N29_04


title: input_ERC63_L3_rep1 [JK62]


title: Whole-embryo Tet TKO plate 45

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N29_11


title: DPY27_ERC06_emb_rep1 [LW13]


title: Whole-embryo Tet TKO plate 42

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N29_08


title: Whole-embryo Tet TKO plate 35

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N29_01


title: Whole-embryo Tet TKO plate 39

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N29_05


title: Whole-embryo Tet TKO plate 36

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N29_02


title: DPY27_ERC63_L3_rep1 [JK72]


title: input_ERC61_L3_rep3 [JK58]


title: Whole-embryo Tet TKO plate 31

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N_P11


title: Whole-embryo Tet TKO plate 34

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N_P14


title: Whole-embryo Tet TKO plate 41

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N29_07


title: input_ERC61_L3_rep2 [JK57]


title: Whole-embryo Tet TKO plate 33

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N_P13


title: Whole-embryo Tet TKO plate 40

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N29_06


title: input_ERC61_L3_rep1 [JK59]


title: input_ERC63_L3_rep3 [JK60]


title: Whole-embryo Tet TKO plate 30

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N_P10


title: DPY27_ERC61_L3_rep2 [JK67]


title: DPY27_ERC63_L3_rep2 [JK70]


title: Whole-embryo Tet TKO plate 28

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N_P05


title: input_N2_L3_rep3 [JK54]


title: DPY27_N2_L3_rep2 [JK65]


title: Whole-embryo Tet TKO plate 19

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N_P07


title: DPY27_ERC61_L3_rep1 [JK69]


title: Whole-embryo Tet TKO plate 16

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N26_06


title: DPY27_N2_L3_rep1 [JK66]


title: input_N2_L3_rep1 [JK56]


title: Whole-embryo Tet TKO plate 17

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N26_07


title: input_N2_L3_rep2 [JK55]


title: DPY27_ERC63_L3_rep3 [JK71]


title: Whole-embryo Tet TKO plate 27

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N_P04


title: Whole-embryo Tet TKO plate 15

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N26_05


title: DPY27_N2_L3_rep3 [JK64]


title: Whole-embryo Tet TKO plate 14

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N26_04


title: Whole-embryo Tet TKO plate 29

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N_P08


title: input_ERC80_emb_rep2 [JK18]


title: input_ERC80_emb_rep3 [JK19]


title: DPY27_ERC61_L3_rep3 [JK68]


title: Whole-embryo Tet TKO plate 32

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N_P12


title: Whole-embryo Tet TKO plate 12

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N26_02


title: Whole-embryo Tet TKO plate 18

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N26_08


title: input_ERC80_emb_rep1 [JK14]


title: DPY27_ERC80_emb_rep3 [JK24]


title: Whole-embryo Tet TKO plate 11

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N26_01


title: DPY27_ERC80_emb_rep2 [JK23]


title: Whole-embryo Tet TKO plate 10

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N_P06


title: Tet TKO chimera plate 95

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TKO23_P06

value: Host cells and injected mESC-derived Tet TKO cells


title: input_L3_ext344_rep2 [LAS50]


title: Whole-embryo Tet TKO plate 5

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
191125_P01_NOVA


title: DPY27_ERC69_emb_rep2 [DJ84]


title: Whole-embryo Tet TKO plate 9

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N_P01


title: input_ERC69_emb_rep2 [DJ80]


title: input_ERC69_emb_rep1 [LAS57]


title: DPY27_ERC80_emb_rep1 [JK12]


title: Tet TKO chimera plate 93

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TKO23_P04


title: Tet TKO chimera plate 92

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TKO23_P02


title: SDC3_L3_ext344_rep2 [LAS64]


title: Whole-embryo Tet TKO plate 13

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
4N26_03


title: Tet TKO chimera plate 86

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TetTKO23_P04


title: Tet TKO chimera plate 88

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TetTKO23_P06


title: Tet TKO chimera plate 90

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TetTKO23_P08


title: Tet TKO chimera plate 94

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TKO23_P05


title: Tet TKO chimera plate 84

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TetTKO23_P02


title: Tet TKO chimera plate 87

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TetTKO23_P05


title: Tet TKO chimera plate 89

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TetTKO23_P07


title: Tet TKO chimera plate 91

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TKO23_P01


title: Tet TKO chimera plate 83

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TetTKO23_P01


title: spinal cord, W-20 from CVB3-infected G85R mice-R#2

city: Vancouver

first: Honglin

last: Luo

state: British Columbia

address: Room 166, 1081 Burrard Street

country: Canada

institute: University of British Columbia

description: 500pfu_G85R_R#2_Week-20 (spinal cord)

hyb_protocol: Reporter-sample-capture mixtures were hybridized at 65C in a thermal cycler with the heated lid temperature set to 70C for 22 hrs. The hybridized mixture was loaded into Nanostring nCounter FLEX prep station (Nanostring Technologies, Seattle, WA) for robotic processing with high sensitivity detection setting.

scan_protocol: The cartridge the probe/RNA hybrids were hybridized on in the prep station were loaded onto Nanostring nCounter scanner (Nanostring Technologies, Seattle, WA) and a scan was performed at 555 FOVs per lane/sample.

data_processing: Data processing were performed by using NanoString nCounter Advanced Analysis Module

label: optical barcodes from Nanostring Technologies, Seattle, WA.

source_name: whole brain homogenates

label_protocol: 70uL of hybridization buffer was added to 70uL of Reporter Probe Set with optical barcodes (Nanostring Technologies, Seattle, WA) and 8uL of the mix was added to 5uL of 100ng RNA. 2 uL of Capture Probe set was added and the mixture was mixed by inversion.

growth_protocol: This study involved direct used of mice organs and hence, no growth protocol were involved.

extract_protocol: Whole brain and spinal cord were homogenized with steel beads and digested with proteinase K to remove protein residuals. Homogenates were then lysed with lysis buffer & subjected to RNA extraction.

treatment_protocol: This study involved direct used of mice organs and hence, no treatment protocol were involved.

tag: infection

value: spinal cord


title: Tet TKO chimera plate 85

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TetTKO23_P03


title: spinal cord, W-20 from CVB3-infected G85R mice-R#1

description: 500pfu_G85R_R#1_Week-20 (spinal cord)


title: spinal cord, W-20 from mock-infected G85R mice-R#2

description: DMEM_G85R_R#2_Week-20 (spinal cord)

value: mock-infected


title: SDC3_L3_ext99_rep1 [SEA189]


title: spinal cord, W-20 from mock-infected G85R mice-R#1

description: DMEM_G85R_R#1_Week-20 (spinal cord)


title: Tet TKO chimera plate 82

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TKO26_13_P15


title: spinal cord, W-20 from mock-infected G85R mice-R#3

description: DMEM_G85R_R#3_Week-20 (spinal cord)


title: Tet TKO chimera plate 80

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TKO26_13_P11


title: spinal cord, W-20 from CVB3-infected WT mice-R#3

description: 500pfu_WT_R#3_Week-20 (spinal cord)

value: WT


title: spinal cord, W-20 from CVB3-infected G85R mice-R#3

description: 500pfu_G85R_R#3_Week-20 (spinal cord)


title: DPY27_ERC69_emb_rep1 [LAS55]


title: Tet TKO chimera plate 81

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TKO26_13_P12


title: Tet TKO chimera plate 78

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TKO26_13_P09


title: spinal cord, W-20 from CVB3-infected WT mice-R#2

description: 500pfu_WT_R#2_Week-20 (spinal cord)


title: spinal cord, W-20 from CVB3-infected WT mice-R#1

description: 500pfu_WT_R#1_Week-20 (spinal cord)


title: spinal cord, W-20 from mock-infected WT mice-R#2

description: DMEM_WT_R#2_Week-20 (spinal cord)


title: Tet TKO chimera plate 71

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TKO26_13_P02


title: whole brain, W-60 from CVB3-infected G85R mice-R#3

description: 500pfu_G85R_R#3_Week-60 (whole brain)

value: whole brain


title: spinal cord, W-20 from mock-infected WT mice-R#1

description: DMEM_WT_R#1_Week-20 (spinal cord)


title: Tet TKO chimera plate 72

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TKO26_13_P03


title: spinal cord, W-20 from mock-infected WT mice-R#3

description: DMEM_WT_R#3_Week-20 (spinal cord)


title: Tet TKO chimera plate 79

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TKO26_13_P10


title: Tet TKO chimera plate 69

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
20200106_TKO26_P05_NOVA

value: Host cells and injected mESC-derived Control and Tet TKO cells


title: Tet TKO chimera plate 76

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TKO26_13_P07


title: whole brain, W-60 from mock-infected G85R mice-R#2

description: DMEM_G85R_R#2_Week-60 (whole brain)


title: whole brain, W-60 from CVB3-infected WT mice-R#3

description: 500pfu_WT_R#3_Week-60 (whole brain)


title: whole brain, W-60 from mock-infected G85R mice-R#1

description: DMEM_G85R_R#1_Week-60 (whole brain)


title: Tet TKO chimera plate 77

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TKO26_13_P08


title: whole brain, W-60 from CVB3-infected G85R mice-R#1

description: 500pfu_G85R_R#1_Week-60 (whole brain)


title: Tet TKO chimera plate 75

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TKO26_13_P06


title: whole brain, W-60 from CVB3-infected G85R mice-R#2

description: 500pfu_G85R_R#2_Week-60 (whole brain)


title: Tet TKO chimera plate 70

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TKO26_13_P01


title: Tet TKO chimera plate 74

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TKO26_13_P05


title: Tet TKO chimera plate 65

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
20200106_TKO26_P01_NOVA


title: Tet TKO chimera plate 56

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
1106TKO29_15


title: Tet TKO chimera plate 67

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
20200106_TKO26_P03_NOVA


title: Tet TKO chimera plate 68

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
20200106_TKO26_P04_NOVA


title: Tet TKO chimera plate 66

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
20200106_TKO26_P02_NOVA


title: Tet TKO chimera plate 73

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
TKO26_13_P04


title: whole brain, W-60 from mock-infected WT mice-R#3

description: DMEM_WT_R#3_Week-60 (whole brain)


title: whole brain, W-60 from mock-infected WT mice-R#2

description: DMEM_WT_R#2_Week-60 (whole brain)


title: whole brain, W-20 from CVB3-infected G85R mice-R#2

description: 500pfu_G85R_R#2_Week-20 (whole brain)


title: whole brain, W-20 from CVB3-infected G85R mice-R#3

description: 500pfu_G85R_R#3_Week-20 (whole brain)


title: Tet TKO chimera plate 55

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
1106TKO29_14


title: Tet TKO chimera plate 53

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
1106TKO29_12


title: whole brain, W-60 from CVB3-infected WT mice-R#1

description: 500pfu_WT_R#1_Week-60 (whole brain)


title: Tet TKO chimera plate 51

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
1106TKO29_10


title: Tet TKO chimera plate 50

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
1106TKO29_09


title: Tet TKO chimera plate 52

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
1106TKO29_11


title: whole brain, W-60 from mock-infected G85R mice-R#3

description: DMEM_G85R_R#3_Week-60 (whole brain)


title: whole brain, W-20 from mock-infected G85R mice-R#2

description: DMEM_G85R_R#2_Week-20 (whole brain)


title: whole brain, W-20 from mock-infected G85R mice-R#1

description: DMEM_G85R_R#1_Week-20 (whole brain)


title: Tet TKO chimera plate 54

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
1106TKO29_13


title: Tet TKO chimera plate 49

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
1106TKO29_08


title: whole brain, W-60 from CVB3-infected WT mice-R#2

description: 500pfu_WT_R#2_Week-60 (whole brain)


title: whole brain, W-60 from mock-infected WT mice-R#1

description: DMEM_WT_R#1_Week-60 (whole brain)


title: whole brain, W-20 from mock-infected G85R mice-R#3

description: DMEM_G85R_R#3_Week-20 (whole brain)


title: Tet TKO chimera plate 48

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
1106TKO29_07


title: whole brain, W-20 from CVB3-infected G85R mice-R#1

description: 500pfu_G85R_R#1_Week-20 (whole brain)


title: whole brain, W-20 from CVB3-infected WT mice-R#3

description: 500pfu_WT_R#3_Week-20 (whole brain)


title: Tet TKO chimera plate 47

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
1106TKO29_06


title: Tet TKO chimera plate 46

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
1106TKO29_05


title: whole brain, W-20 from CVB3-infected WT mice-R#1

description: 500pfu_WT_R#1_Week-20 (whole brain)


title: whole brain, W-20 from CVB3-infected WT mice-R#2

description: 500pfu_WT_R#2_Week-20 (whole brain)


title: whole brain, W-20 from mock-infected WT mice-R#3

description: DMEM_WT_R#3_Week-20 (whole brain)


title: whole brain, W-20 from mock-infected WT mice-R#2

description: DMEM_WT_R#2_Week-20 (whole brain)


title: Tet TKO chimera plate 42

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
1106TKO29_01


title: Primary human CD34 RBM12 IP rep2

city: Philadelphia

first: Aoi

last: Wakabayashi

state: Pennsylvania

address: 3615 Civic Center Blvd, Abramson Research Center Rm 315A

department: Hematology/Oncology

institute: Children's Hospital of Philadelphia

data_processing:
Sequence reads were processed using the ENCODE3 eCLIP-Seq processing pipeline (https://www.encodeproject.org/documents/3b1b2762-269a-4978-902e-0e1f91615782/@@download/attachment/eCLIP_analysisSOP_v2.0.pdf)
Peaks were called using CLIPper (Lovci et al., 2012)
Reproducibility was assayed by standard Irreproducibility Rate (IDR) analysis (Li et al., 2011)
Assembly: hg38
Supplementary files format and content: .bed and .bigwig

source_name: Hematopoietic Stem and Progenitor Cells

growth_protocol: Primary human CD34+ HSPCs were cultured in vitro using a 3 phase erythroid differentiation system.

extract_protocol:
RBP-RNA interactions were captured and processed using the ENCODE eCLIP-Seq SOP (https://www.encodeproject.org/documents/842f7424-5396-424a-a1a3-3f18707c3222/@@download/attachment/eCLIP_SOP_v1.P_110915.pdf)
Libraries were prepared following the ENCODE eCLIP-Seq SOP (https://www.encodeproject.org/documents/842f7424-5396-424a-a1a3-3f18707c3222/@@download/attachment/eCLIP_SOP_v1.P_110915.pdf)

treatment_protocol: Cells were UV crosslinked and cell pellets were flash frozen at day 8 of differentiation.

value: human CD34+ HSPCs

tag: day of differentiation

value: day 8 of erythroid differentiation

tag: clip antibody

value: RBM12 (Santa Cruz, sc-514259)


title: Tet TKO chimera plate 45

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
1106TKO29_04

tag: developmental stage


title: Tet TKO chimera plate 43

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
1106TKO29_02


title: whole brain, W-20 from mock-infected WT mice-R#1

description: DMEM_WT_R#1_Week-20 (whole brain)


title: Primary human CD34 RBM12 IP rep1


title: Primary human CD34 sgNT rep3

data_processing:
Sequence reads were processed using the ENCODE3 long RNA-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL002LPE/)
Gene set Gencode v29 was used for mapping the reads to the human genome (hg38 assembly) using STAR
Gene quantification was done via RSEM workflow
Assembly: hg38
Supplementary files format and content: .tsv

extract_protocol:
Cells were lysed in buffer RLT plus BME and RNA was column-purified using the Qiagen RNEasy kit.
Libraries were prepared following Illumina's TruSeq Stranded mRNA kit protocol.

treatment_protocol: HSPCs were electroporated with either an RBM12 targeting or non-targeting sgRNA that is in complex with Cas9 protein at day 0 of differentiation.

value: day 7 of erythroid differentiation

value: targeted with NT sgRNA


title: Primary human CD34 sgNT rep2


title: Tet TKO chimera plate 20

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190325_P07

value: E7.5 chimera embryo


title: Tet TKO chimera plate 21

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190325_P08

value: Chimera assay


title: Primary human CD34 sgNT rep1


title: Primary human CD34 Input


title: Primary human CD34 sgRBM12 rep1

value: targeted with RBM12 sgRNA


title: week-10_H3K9me3_rep3

city: Wuhan

first: Min

state: Hubei

address: Room 5005, Life Science College, Wuhan University

department: College of Life Science and Technology of Huazhong Agricultural University

institute: Wuhan universioty

description:
10weeks-3-H3K9me3_combined
processed data file: 10weeks-H3K9me3_Input_peaks.broadPeak

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
ChIP-seq clean data were obtained by removing adaptor from raw fastq with Cutadapt (version 1.16, http://cutadapt.readthedocs.io/en/stable/guide.html, parameters were “-u 4 -u 35 -U 4 -U 35 -m 30”)
Cleaned reads were aligned in paired-end mode to mouse reference genome mm10 with BWA mem (version 0.7.15, http://bio-bwa.sourceforge.net )
Duplicate reads were removed by Picard MarkDuplicate (http://picard.sourceforge.net/). Only unique mapped reads were used in following work.
Peaks were called by MACS2 (version 2.1.1, https://github.com/taoliu/MACS, with parameters “--nomodel --keep-dup all -p 1E-10 --broad --broad-cutoff 1E-10 --extsize 147” ) at false discovery rate (FDR) < 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files

growth_protocol: The 8-week-old Wild-type C57BL/6J mice were purchased from Beijing HFK Bioscience Co. Ltd.

extract_protocol:
DNA were clarified from nuclei treated with micrococcal nuclease and histone-DNA complexes were isolated with antibody. Briefly, around 30 milligrams of each tissue were cut into 1 mm3 pieces in PBS with protease inhibitor. Tissue pieces were cross-linked for 10min at room temperature with 1% formaldehyde and then quenched with 0.125 M of glycine for 5 min. Cross-linked tissues were triturated in tissue grinding instrument for 60s at 60 Hz, and then centrifuged at 12000 rpm, 4 °C for 10 min. Supernatant with massive oil was discarded and the precipitates were lysed with 1 mL lysis buffer (50 mM Tris-HCl pH 8.0, 0.1% SDS, 5 mM EDTA) for 4 min with gentle rotation. After centrifugation at 12000 rpm, 4 °C for 2 min, the pellet was washed once with digestion buffer (50 mM Tris-HCl pH8.0, 1 mM CaCl2, 0.2% Triton X-100), incubated in 630-μL digestion buffer with 1 μL MNase (NEB, M0247S) at 37°C for 20min and quenched with 8 μL 0.5M EDTA. The resulted mixture was sonicated and the pellet was discarded after centrifugation. 30 μL supernatant was taken for checking the efficiency of digestion. Immunoprecipitation was performed with 150 μL sheared chromatin, 2 μg antibody, 50 μL Protein G beads and 800 μL dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS) overnight at 4 °C. Next day, the beads were washed once with Wash buffer I (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), once with Wash buffer II (20mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), once with Wash buffer III (10mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% Na-deoxycholate, 1% NP-40) and twice with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). The beads were eluted twice with 100 μL elution buffer (1% SDS, 0.1M NaHCO3, 20mg/mL Proteinase K) at room temperature. The elution was incubated at 65 °C for 6 h and then purified with DNA purification kit (TIANGEN DP214-03).
ChIP-seq libraries were constructed with ChIP and input DNA using VATHS Universal DNA Library Prep Kit for Illumina (Vazyme ND606). Briefly, 10 ng DNA was end-repaired for dA tailing, followed by adaptor ligation. Each adaptor was marked with a barcode of 8 bp DNA. Adaptor-ligated DNA was purified by AMPure XP beads (1:1) and then amplified by PCR of 10 cycles with the primer matching with adaptor universal part. Amplified DNA was purified again using AMPure XP beads (1:1) in 35 μL EB elution buffer. For multiplexing, libraries with different barcode were mixed with equal molar quantities (30-50 million reads per library). Libraries were sequenced by Illumina Nova-seq platform with pair-end reads of 150 bp.

treatment_protocol: The mice were randomly divided into four experimental groups (2 weeks, 4 weeks, 7 weeks, 10 weeks) and one control group (n = 5 per group). The mice in the experimental groups were given a single intraperitoneal injection of AOM (10 mg/kg body weight). Seven days after the AOM injection, the mice were given 2.5% DSS (w/v) in their drinking water for 7 days. The 2weeks group mice were sacrificed. The other three experimental group mice fed with distilled water for 14 days and then 4 weeks group mice were sacrificed. After that, the remained two experimental group mice were given 2.5% DSS (w/v) in their drinking water for 7 days and next distilled water for 14 days. The 7 weeks group mice were sacrificed. Afterwards the last 10 weeks group mice were given 2.5% DSS (w/v) in their drinking water for 7 days and then distilled water for 14 days and sacrificed. The control group (0 week) mice were fed with distilled water for 70 days and sacrificed. The colorectum of all mice were collected for RNA-seq and ChIP-seq.

tag: time point

value: Colon

tag: chip antibody


title: week-10_H3K9me3_rep2

description:
10weeks-2-H3K9me3_combined
processed data file: 10weeks-H3K9me3_Input_peaks.broadPeak


title: Tet TKO chimera plate 18

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190325_P04

tag: genotype