title: Root_polyA_2_F

city: La Jolla

first: Joseph

last: Ecker

address: 1001 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: The Salk Institute

description: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the light for 7 days at 25 degrees C. An root tips were collected from Arabidopsis seedlings (7 days old) which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio-state.edu/~plantbio/Facilities/abrc/abrchome.htm).Total RNA was isolated from root tips using the Qiagen RNeasy kit (Valencia,CA) according to the manufacturerfs instructions with DNase I treatment step. The quality and quantity of RNA isolated was checked by both gel electrophoresis and spectrophotometry.Five micro g total RNA was converted into double-stranded cDNA using Affymetrix T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions, fragmented, and then approximately 15 micro g of fragmented cRNA were hybridized to the tiling arrays according to Affymetrix (Santa Clara, CA) instructions. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis by TileMap software.

hyb_protocol: Whole Genome Tiling Array  was hybridized for 16 hrs, washed and stained with a streptavidin-phycoerythrin conjugate on the Affymetrix Fluidics Station 400 according to the standard Affymetrix protocol.

scan_protocol: Whole Genome Tiling array were scanned on Affymetrix scanner G7

data_processing: Two biological replicates were performed for data processing using each genotype and tissues with the method below, and yielding very consistent results. The same TileMap algorithms(1) as DNA Methylation Data analysis can also be applied to analyze tiling microarray data measuring transcription activity. It can be applied to identify regions with significantly gene expression, such as a fraction of an exon, intergenic regions, or antisense transcripts. For identification of expressed regions, first, microarray feature intensities for all replicates were quantile normalized by TileMap. Next, we applied statistics method calculate the probe-level t-statistics to identify expressed region. Third, a two-state HMM was trained to assign probes as either expressed or non-expressed. These three steps was performed using the software package TileMap with the HMM option same as DNA methylation analysis. (1). Regions statistically different between two groups were identified using the Hidden Markov Models (HMM) option. 1. H. Ji and W. H. Wong, Bioinformatics 21, 3629-3636 (2005).

organism: Arabidopsis thaliana

source_name: Root tip (5 mm length)

label_protocol: The genomic DNA in the samples was 3'-end-labelled with dd-UTP (Roche) by the terminal transferase (TdT, Roche) reaction for 1 h at 37 degrees C.

extract_protocol: total RNA was isolated from Root tips using RNAeasy kit following instructions from the manufacturer (QIAGEN)

treatment_protocol: Untreated

tag: Strain;Wild type columbia, Tissue; Root tip (5 mm length), Age; 7 days, Growth; on MS medium under continuous light condition


title: colL_polyA_1_F

status: Public on Mar 11 2023

type: RNA

state: CA

country: USA

description: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the light for 40 days at 25 degrees C. A mature leaves were collected from mature Arabidopsis plants (40 days old) which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio-state.edu/~plantbio/Facilities/abrc/abrchome.htm).Total RNA was isolated from mature leaves using the Qiagen RNeasy kit (Valencia,CA) according to the manufacturerfs instructions with DNase I treatment step. The quality and quantity of RNA isolated was checked by both gel electrophoresis and spectrophotometry.Five micro g total RNA was converted into double-stranded cDNA using Affymetrix T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions, fragmented, and then approximately 15 micro g of fragmented cRNA were hybridized to the tiling arrays according to Affymetrix (Santa Clara, CA) instructions. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis by TileMap software.

label: biotin

molecule: total RNA

source_name: mature leaf

extract_protocol: total RNA was isolated from mature leaves using RNAeasy kit following instructions from the manufacturer (QIAGEN)

tag: Strain;Wild type columbia, Tissue; mature leaf, Age; 40days, Growth; on soil under continuous light condition


title: callus_polyA_2_F

description: Arabidopsis ecotype Columbia suspension-culture cells were obtained from hypocotyls of etiolated seedlings as described (Ferrando 2000). The cells were cultured at 25 ‹C in the dark with an orbital agitation at 130 rpm in 500-mL Erlenmeyer flasks containing 200 mL of culture medium. A 25-mL aliquot of suspension cells was transferred to fresh medium every week. All experiments were conducted on 7-d-old cells The growth medium contained Murashige-Skoog basal salts, Gamborg's B5 vitamins (Life Technologies, Inc.), 3% sucrose, and 1 mg/L 2,4- dichlorophenoxyacetic acid (2,4-D). The cells were harvested two-days after subculture.Total RNA was isolated from suspension-culture cells using the Qiagen RNeasy kit (Valencia,CA) according to the manufacturerfs instructions with DNase I treatment step. The quality and quantity of RNA isolated was checked by both gel electrophoresis and spectrophotometry.Five micro g total RNA was converted into double-stranded cDNA using Affymetrix T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions, fragmented, and then approximately 15 micro g of fragmented cRNA were hybridized to the tiling arrays according to Affymetrix (Santa Clara, CA) instructions. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis by TileMap software.

source_name: suspension-culture cells

extract_protocol: total RNA was isolated from suspension-culture cells using RNAeasy kit following instructions from the manufacturer (QIAGEN)

tag: Strain;Wild type columbia, Tissue; suspension cultured cells, Age; 7 days, Growth; in MS medium with 2,4-D


title: colL_polyA_2_F


title: callus_polyA_1_F


title: Root_polyA_1_F

tag: Strain;Wild type columbia , Tissue; Root tip (5 mm length), Age; 7 days, Growth; on MS medium under continuous light condition


title: met1L_polyA_1_F

tag: Strain;met1 mutant on colmbia back ground segregated from heterozygote, Tissue; mature leaf, Age; 40days, Growth; on soil under continuous light condition


title: ddcL_polyA_1_F

tag: Strain;drm1drm2cmt3 mutant on colmbia back ground segregated from heterozygote, Tissue; mature leaf, Age; 40days, Growth; on soil under continuous light condition


title: ddcL_polyA_2_F


title: ddcB_polyA_1_F

description: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the light for 40 days at 25 degrees C. An inflorescence buds were collected from mature Arabidopsis plants (40 days old) which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio-state.edu/~plantbio/Facilities/abrc/abrchome.htm).Total RNA was isolated from inflorescence buds using the Qiagen RNeasy kit (Valencia,CA) according to the manufacturerfs instructions with DNase I treatment step. The quality and quantity of RNA isolated was checked by both gel electrophoresis and spectrophotometry.Five micro g total RNA was converted into double-stranded cDNA using Affymetrix T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions, fragmented, and then approximately 15 micro g of fragmented cRNA were hybridized to the tiling arrays according to Affymetrix (Santa Clara, CA) instructions. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis by TileMap software.

source_name: inflorescence buds

extract_protocol: total RNA was isolated from inflorescence buds using RNAeasy kit following instructions from the manufacturer (QIAGEN)

tag: Strain;drm1drm2cmt3 mutant on colmbia back ground segregated from heterozygote, Tissue; inflorescence buds, Age; 40days, Growth; on soil under continuous light condition


title: met1B_polyA_2_F

tag: Strain;met1 mutant on colmbia back ground segregated from heterozygote, Tissue; inflorescence buds, Age; 40days, Growth; on soil under continuous light condition


title: ddcB_polyA_2_F


title: mock_2

type: genomic

description: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the light for 40 days at 25 degrees C. An inflorescence buds were collected from mature Arabidopsis plants (40 days old) which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio-state.edu/~plantbio/Facilities/abrc/abrchome.htm).DNA was extracted from the same tissues and at the same developmental stage as those used for methylome analyses using the Plant DNeasy Mini Kit (QIAGEN). The quality and quantity of isolated RNA and DNA was estimated by both gel electrophoresis and spectrophotometry.The methylcytosine immunoprecipitation (mCIP) method was described previously with slight modification (Zhang 2006). Immunoprecipitation was performed by incubating 5 ug of sonicated genomic DNA (approximately 300-500 bp length) with 10 ug mouse anti-methylcytosine monoclonal antibody (Calbiochem) using chromatin immunoprecipitation (ChIP) assay kit (Millipore) according to manufacturer's protocol. Then, eluted DNA was recovered by phenol-chloroform extraction and ethanol precipitation. The recovered DNA was examined real-time PCR to confirm methylated region of FWA promoter, AtSN1, and Ta3 and unmethylated region of actin8 in each fraction. The remaining DNA from the mock and elution fractions was amplified and used for microarray hybridization. Two biological replicates were performed for each genotype. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis by TileMap software.

data_processing: Two biological replicates were performed for data processing each genotype and tissues with the method below, and yielding very consistent results (Box plot). Raw tiling microarray data processing was performed in a manner similar to previously described (Zhang et al., 2006). Methylated regions are expected to show a significantly higher hybridization signal in IP fraction when mock fraction is used as probe compared to IP fraction. First, the two groups (IP fraction and mock fraction) were subjected to quantile normalization. Next, we applied statistics method calculate the probe-level t-statistics using an empirical Bayes shrinkage estimator (Ji and Wong, 2005), to identify methylated regions and compared the results. Third, a two-state hidden Markov model (HMM) was trained to assign probes as either methylated or unmethylated. These three steps was performed using the software package TileMap with the HMM option (Ji and Wong, 2005). For the method, DNA methylated probes were called by applying a cutoff (posterior probability > 0.1 for TileMap) and DNA methylated regions were then derived by combining neighboring methylated probes allowing a maximal gap of 200 bases.(1). Regions statistically different between two groups were identified using the Hidden Markov Models (HMM) option. 1. H. Ji and W. H. Wong, Bioinformatics 21, 3629-3636 (2005).

molecule: genomic DNA

extract_protocol: genomic DNA was isolated from inflorescence buds using DNAeasy kit following instructions from the manufacturer (QIAGEN) instruction

tag: Strain;met1 mutant on colmbia back ground segregated from heterozygote, Tissue; inflorescence buds, Age; 40days, Growth; on soil under continuous light condition (Enriched for methylated DNA at all sequenced contexts)


title: ddcB_mCIP_1

tag: Strain;drm1drm2cmt3 triple mutant on colmbia back ground segregated from heterozygote, Tissue; inflorescence buds, Age; 40days, Growth; on soil under continuous light condition (Enriched for methylated DNA at all sequenced contexts)


title: met1B_mCIP_2


title: ddcB_mCIP_2


title: met1L_mCIP_2

description: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the light for 40 days at 25 degrees C. A mature leaf were collected from mature Arabidopsis plants (40 days old) which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio-state.edu/~plantbio/Facilities/abrc/abrchome.htm).DNA was extracted from the same tissues and at the same developmental stage as those used for methylome analyses using the Plant DNeasy Mini Kit (QIAGEN). The quality and quantity of isolated RNA and DNA was estimated by both gel electrophoresis and spectrophotometry.The methylcytosine immunoprecipitation (mCIP) method was described previously with slight modification (Zhang 2006). Immunoprecipitation was performed by incubating 5 ug of sonicated genomic DNA (approximately 300-500 bp length) with 10 ug mouse anti-methylcytosine monoclonal antibody (Calbiochem) using chromatin immunoprecipitation (ChIP) assay kit (Millipore) according to manufacturerÕs protocol. Then, eluted DNA was recovered by phenol-chloroform extraction and ethanol precipitation. The recovered DNA was examined real-time PCR to confirm methylated region of FWA promoter, AtSN1, and Ta3 and unmethylated region of actin8 in each fraction. The remaining DNA from the mock and elution fractions was amplified and used for microarray hybridization. Two biological replicates were performed for each genotype. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis by TileMap software.

extract_protocol: genomic DNA was isolated from mature leaf using DNAeasy kit following instructions from the manufacturer (QIAGEN) instruction

tag: Strain;met1 mutant on colmbia back ground segregated from heterozygote, Tissue; mature leaf, Age; 40days, Growth; on soil under continuous light condition (Enriched for methylated DNA at all sequenced contexts)


title: met1B_mCIP_1


title: ddcL_mCIP_2

tag: Strain;drm1drm2cmt3 triple mutant on colmbia back ground segregated from heterozygote, Tissue; mature leaf, Age; 40days, Growth; on soil under continuous light condition (Enriched for methylated DNA at all sequenced contexts)


title: met1L_mCIP_1


title: mock_1

tag: Strain;Wild type on colmbia back ground segregated from heterozygote, Tissue; inflorescence buds, Age; 40days, Growth; on soil under continuous light condition (Enriched for methylated DNA at all sequenced contexts)


title: M - Egr1cKO control  [4955]

type: SRA

city: Blacksburg

first: Hehuang

last: Xie

state: VA

address: 1015 Life Science Cir

department: Department of Biomedical Sciences and Pathobiology

institute: Virginia Tech

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore-3.8.2 (parameter --paired --phred33 --fastqc --illumina -q 30 --length 30)
Trimmed sequence reads were mapped to GRCm38 using STAR 2.7.9  (parameters- default settings)
Read count is extracted using STAR-2.7.9 --quant mode
Assembly: GRCm38
Supplementary files format and content: comma-delimited text files from the second column of STAR-2.7.9 quant output
Supplementary files format and content: sample information of the read count table

molecule: polyA RNA

organism: Mus musculus

source_name: pituitary

extract_protocol:
RNA extraction was performed using Rneasy mini kit (Qiagen). 1.5 ug of total RNA was used for non-stranded RNA-seq.
non-stranded RNA-seq

tag: tissue

value: pituitary

tag: cell line

value: Male

tag: cell type

value: endocrine

tag: genotype


title: met1L_polyA_2_F


title: met1B_polyA_1_F


title: biol rep 3, sample 2, hifFT cells, sorted for slow cycling

city: Philadelphia

first: Naveen

last: Jain

state: Pennsylvania

address: 415 Currie Boulevard

department: Bioengineering

institute: University of Pennsylvania

library_source: transcriptomic single cell

data_processing:
Base calling and preliminary quality scoreing was done in real time on a NextSeq 500, NextSeq 2000, or NovaSeq 6000 as indicated with RTA 2.0. The sequencing runs were stored on the Illumina BaseSpace website.
We mapped single cell RNA-sequencing reads to transcripts and cells using the cellranger pipeline v4.0.0 by 10x genomics. We used mkfastq with default parameters to demulitplex raw base call files into library-specific FASTQ files. We alligned FASTQ files to the human genome (hg38) and extracted gene expression count matrices using cellranger counts based on Gencode v32 annotation, filtering and correcting cell identifiers and unique molecular identifiers (UMIs) with default settings.
Assembly: GRCh38
Supplementary files format and content: *.matrix.mtx: Sparse gene expression matrix; rows are features/genes, columns are 10x barcodes (what we call "cellID")
Supplementary files format and content: *.barcodes.tsv: Barcodes
Supplementary files format and content: *.features.tsv: Features/genes

organism: Homo sapiens

source_name: BJ skin fibroblast

extract_protocol:
RNA was extracted as per the manufacter's protocol using a 10x Genomics v3 kit. We generated gel beads-in-emulsion (GEMs) using the 10X Chromium system and a Chromium Next GEM Single Cell 3' Reagent Kit v3.1 as per the manufecturer's protocol, aiming for 10,000 cells for recovery.
Single cellRNA-sequencing libraries were constructed as per the manufacter's protcol using a 10x Genomics single-cell RNA-sequencing kit v3. We extracted cDNA according to the post-GEM RT-cleanup instructions and used 10uL of amplified cDNA for fragmentation, end repair, poly A-tailing, adapter ligation, and 10x sample indexing.

value: BJ skin fibroblast

value: hiF-T

value: human fibroblast-like cells with inducible hTERT expression

value: WT

tag: treatment


title: biol rep 1, sample 1, iPS cells, DMSO

source_name: induced pluripotent stem cell

value: induced pluripotent stem cell

value: induced pluripotent stem cells derived from hiF-T cells cultured in doxycycline

value: DMSO


title: biol rep 1, sample 6, iPS cells, DOT1L inhibition

value: DOT1L inhibition


title: ddcL_mCIP_1


title: colL_mCIP_2

tag: Strain;Wild type colombia, Tissue; mature leaf, Age; 40days, Growth; on soil under continuous light condition (Enriched for methylated DNA at all sequenced contexts)


title: colR_mCIP_1

description: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the light for 7 days at 25 degrees C. An root tips were collected from Arabidopsis seedlings (7 days old) which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio-state.edu/~plantbio/Facilities/abrc/abrchome.htm).DNA was extracted from the same tissues and at the same developmental stage as those used for methylome analyses using the Plant DNeasy Mini Kit (QIAGEN). The quality and quantity of isolated RNA and DNA was estimated by both gel electrophoresis and spectrophotometry.The methylcytosine immunoprecipitation (mCIP) method was described previously with slight modification (Zhang 2006). Immunoprecipitation was performed by incubating 5 ug of sonicated genomic DNA (approximately 300-500 bp length) with 10 ug mouse anti-methylcytosine monoclonal antibody (Calbiochem) using chromatin immunoprecipitation (ChIP) assay kit (Millipore) according to manufacturerÕs protocol. Then, eluted DNA was recovered by phenol-chloroform extraction and ethanol precipitation. The recovered DNA was examined real-time PCR to confirm methylated region of FWA promoter, AtSN1, and Ta3 and unmethylated region of actin8 in each fraction. The remaining DNA from the mock and elution fractions was amplified and used for microarray hybridization. Two biological replicates were performed for each genotype. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis by TileMap software.

data_processing: Two biological replicates were performed for data processing each genotype and tissues with the method below, and yielding very consistent results (Box plot). Raw tiling microarray data processing was performed in a manner similar to previously described (Zhang et al., 2006). Methylated regions are expected to show a significantly higher hybridization signal in IP fraction when mock fraction is used as probe compared to IP fraction. First, the two groups (IP fraction and mock fraction) were subjected to quantile normalization. Next, we applied statistics method calculate the probe-level t-statistics using an empirical Bayes shrinkage estimator (Ji and Wong, 2005), to identify methylated regions and compared the results. Third, a two-state hidden Markov model (HMM) was trained to assign probes as either methylated or unmethylated. These three steps was performed using the software package TileMap with the HMM option (Ji and Wong, 2005). For the method, DNA methylated probes were called by applying a cutoff (posterior probability > 0.1 for TileMap) and DNA methylated regions were then derived by combining neighboring methylated probes allowing a maximal gap of 200 bases. (1). Regions statistically different between two groups were identified using the Hidden Markov Models (HMM) option. 1. H. Ji and W. H. Wong, Bioinformatics 21, 3629-3636 (2005).

extract_protocol: genomic DNA was isolated from root tip using DNAeasy kit following instructions from the manufacturer (QIAGEN) instruction

tag: Strain;Wild type colombia, Tissue; Root tip (5 mm length), Age; 7 days, Growth; on MS medium under continuous light condition, Growth; on soil under continuous light condition (Enriched for methylated DNA at all sequenced contexts)


title: biol rep 1, sample 4, iPS cells, LSD1 inhibition

value: LSD1 inhibition


title: colSC_mCIP_2

description: Arabidopsis ecotype Columbia suspension-culture cells were obtained from hypocotyls of etiolated seedlings as described (Ferrando 2000). The cells were cultured at 25 ‹C in the dark with an orbital agitation at 130 rpm in 500-mL Erlenmeyer flasks containing 200 mL of culture medium. A 25-mL aliquot of suspension cells was transferred to fresh medium every week. All experiments were conducted on 7-d-old cells The growth medium contained Murashige-Skoog basal salts, Gamborg's B5 vitamins (Life Technologies, Inc.), 3% sucrose, and 1 mg/L 2,4- dichlorophenoxyacetic acid (2,4-D). The cells were harvested two-days after subculture. DNA was extracted from the same tissues and at the same developmental stage as those used for methylome analyses using the Plant DNeasy Mini Kit (QIAGEN). The quality and quantity of isolated RNA and DNA was estimated by both gel electrophoresis and spectrophotometry.The methylcytosine immunoprecipitation (mCIP) method was described previously with slight modification (Zhang 2006). Immunoprecipitation was performed by incubating 5 ug of sonicated genomic DNA (approximately 300-500 bp length) with 10 ug mouse anti-methylcytosine monoclonal antibody (Calbiochem) using chromatin immunoprecipitation (ChIP) assay kit (Millipore) according to manufacturer's protocol. Then, eluted DNA was recovered by phenol-chloroform extraction and ethanol precipitation. The recovered DNA was examined real-time PCR to confirm methylated region of FWA promoter, AtSN1, and Ta3 and unmethylated region of actin8 in each fraction. The remaining DNA from the mock and elution fractions was amplified and used for microarray hybridization. Two biological replicates were performed for each genotype. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis by TileMap software.

extract_protocol: genomic DNA was isolated from suspension-culture cells using DNAeasy kit following instructions from the manufacturer (QIAGEN) instruction

tag: Strain;Wild type on colmbia back ground segregated from heterozygote, Tissue; suspension cultured cells, Age; 7 days, Growth; in MS medium with 2,4-D


title: biol rep 1, sample 5, iPS cells, DOT1L inhibition


title: biol rep 1, sample 3, iPS cells, LSD1 inhibition


title: biol rep 3, sample 1, hiFT cells, ungated


title: colR_mCIP_2


title: biol rep 2, sample 5, hiFT cells, ungated


title: biol rep 1, sample 2, hiFT cells, ungated


title: colL_mCIP_1


title: biol rep 1, sample 1, hiFT cells, ungated


title: colB_mCIP_2

tag: Strain;Wild type colombia, Tissue; inflorescence buds, Age; 40days, Growth; on soil under continuous light condition (Enriched for methylated DNA at all sequenced contexts)


title: biol rep 2, sample 4, hiFT cells, ungated


title: biol rep 1, hiFT cells, DMS0

data_processing:
Base calling and preliminary quality scoreing was done in real time on a NextSeq 500 with RTA 2.0. The sequencing runs were stored and demultiplexed automatically on the Illumina BaseSpace website.
We aligned RNA-sequencing reads to the human genome (hg38) via STAR and counted uniquely mapped reads via HTSeq to output a counts matrix. Normalized count values for each gene were obtained from the counts matrix using scripts provided at: https://github.com/arjunrajlaboratory/RajLabSeqTools/tree/master/LocalComputerScripts.
Assembly: GRCh38
Supplementary files format and content: *.htseq.stdout: Gene expression values; column 1 is gene names, column 2 is counts
Supplementary files format and content: *.meltedData.tsv: Melted, normalized gene expression values for all samples

extract_protocol:
RNA was extracted as per the manufacter's protocol using an RNeasy Micro kit (Qiagen #74004).
RNA-sequencing libraries were constructed as per the manufacter's protcol using a NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490L), NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770L), and NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) oligos (NEB #EE7600S).


title: biol rep 4, hiFT cells, midlow accumulation dye

tag: agent

value: midlow accumulation dye


title: biol rep 2, hiFT cells, no drug


title: biol rep 2, hiFT cells, LSD1 inhibition


title: biol rep 4, hiFT cells, midhigh accumulation dye

value: midhigh accumulation dye


title: biol rep 3, sample 2, hiFT cells, sorted for fast cycling


title: biol rep 4, hiFT cells, high accumulation dye

value: high accumulation dye


title: biol rep 1, hiFT cells, DOT1L inhibition


title: CF_RNA_72hrTGFB-s2

city: Cambridge

first: Matthew

middle: C

last: Hill

state: MA

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

description:
Hum_CF_TGFB_RNAseq_CountsTable.csv
t72tg2

data_processing:
Sequenced RNA reads were aligned to the human genome (GRCh38) using Salmon (version 1.8.0)(PMID: 28263959). Differential expression analysis was performed with DESeq2 (1.30.1)(PMID: 25516281).
ATAC-seq reads were mapped to the human genome (GRCh38) using Bowtie2 with default paired-end settings (version 2.3.4.3)(PMID: 22388286). Next, all non-nuclear and unmapped paired reads were discarded. Duplicated reads were removed with the picard MarkDuplicates function, default settings. Visualization of ATAC-seq signals was done with Homer (version 4.10)(PMID: 20513432), and all reads were normalized by read count where scores represent read count per bp per 1 x 10^7 reads. Motif enrichment analysis was performed with Homer using the findMotifsGenome.pl function with default parameters. Peak calling was carried out with MACS2 (callpeak–nomodel–broad)( version 2.2.6) using all ATAC-seq libraries as input. Reads were counted for each condition from the comprehensive peak file by using bedtools (multicov module) (version v2.26.0)( PMID: 25199790). Quantile normalization of ATAC-seq data sets was performed with CQN (version 1.36.0)( PMID: 22285995), and offsets were fed into DESeq2 to quantify differential accessibility.
Assembly: hg38
Supplementary files format and content: RNA-seq raw counts provided as Genecounts table. Mapped ATAC-seq bigWig files output from Homer are provided.

source_name: Cardiac Fibroblasts

growth_protocol: We used primary human cardiac fibroblasts (ACBRI5118, Cell Systems) for all in vitro experiments. Cells were cultured in Lonza FGM-3 Cardiac Fibroblast Growth Medium (CC-4525). The cardiac fibroblast activation assay was initiated by performing a media exchange for starvation media (CC-4525 without FBS and supplements) containing TGFβ1 (Sigma T7039) at 10 ng/ml. Controls were given starvation media only.

extract_protocol:
Total RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo Research, R2051).  50,000 cardiac fibroblasts were used as input for ATAC-seq, following the OMNI-ATAC-seq protocol (PMID: 28846090). Transposed DNA was purified with a Qiagen PCR MinElute kit (Qiagen 28004).
Standard RNA-seq libraries were generated and sequenced by Genewiz on an Illumina NovaSeq. And final ATAC-seq libraries were purified with a 1.8X SPRI purification using SPRISelect beads (Beckman Coulter) following PCR amplification. Libraries were sequenced on an Illumina Nextseq 500.
TruSeq and ATAC-seq.

value: Primary

value: Cardiac Fibroblasts

value: Wildtype


title: colB_mCIP_1

description: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the light for 40 days at 25 degrees C. An inflorescence buds were collected from mature Arabidopsis plants (40 days old) which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio-state.edu/~plantbio/Facilities/abrc/abrchome.htm).DNA was extracted from the same tissues and at the same developmental stage as those used for methylome analyses using the Plant DNeasy Mini Kit (QIAGEN). The quality and quantity of isolated RNA and DNA was estimated by both gel electrophoresis and spectrophotometry.The methylcytosine immunoprecipitation (mCIP) method was described previously with slight modification (Zhang 2006). Immunoprecipitation was performed by incubating 5 ug of sonicated genomic DNA (approximately 300-500 bp length) with 10 ug mouse anti-methylcytosine monoclonal antibody (Calbiochem) using chromatin immunoprecipitation (ChIP) assay kit (Millipore) according to manufacturerÕs protocol. Then, eluted DNA was recovered by phenol-chloroform extraction and ethanol precipitation. The recovered DNA was examined real-time PCR to confirm methylated region of FWA promoter, AtSN1, and Ta3 and unmethylated region of actin8 in each fraction. The remaining DNA from the mock and elution fractions was amplified and used for microarray hybridization. Two biological replicates were performed for each genotype. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis by TileMap software.

tag: Strain;Wild type colmbia, Tissue; inflorescence buds, Age; 40days, Growth; on soil under continuous light condition (Enriched for methylated DNA at all sequenced contexts)


title: biol rep 4, hiFT cells, low accumulation dye

value: low accumulation dye


title: CF_RNA_72hrTGFB-s1

description:
Hum_CF_TGFB_RNAseq_CountsTable.csv
t72tg1


title: biol rep 1, sample 2, iPS cells, DMSO


title: colSC_mCIP_1

tag: Strain;Wild type colombia, Tissue; suspension cultured cells, Age; 7 days, Growth; in MS medium with 2,4-D


title: CF_RNA_72hrTGFB-s3

description:
Hum_CF_TGFB_RNAseq_CountsTable.csv
t72tg3


title: biol rep 4, hiFT cells, ungated

value: ungated


title: colB_polyA_2_F

tag: Strain;Wild type columbia, Tissue; inflorescence buds, Age; 40days, Growth; on soil under continuous light condition


title: biol rep 3, hiFT cells, midlow accumulation dye

value: BJ skin fibroblast


title: biol rep 3, hiFT cells, low accumulation dye

value: hiF-T


title: CF_RNA_72hr-s3

description:
Hum_CF_TGFB_RNAseq_CountsTable.csv
t72_3


title: ddcL_polyA_2_R

tag: Strain;drm1drm2cmt3 mutant on colmbia back ground segregated from heterozygote, Tissue; mature leaf, Age; 40days, Growth; on soil under continuous light condition


title: CF_RNA_72hr-s2

description:
Hum_CF_TGFB_RNAseq_CountsTable.csv
t72_2


title: biol rep 3, hiFT cells, ungated

value: human fibroblast-like cells with inducible hTERT expression


title: colB_polyA_1_F


title: biol rep 3, hiFT cells, high accumulation dye

value: WT


title: ddcL_polyA_1_R


title: biol rep 3, hiFT cells, midhigh accumulation dye


title: CF_RNA_72hr-s1

description:
Hum_CF_TGFB_RNAseq_CountsTable.csv
t72_1


title: CF_RNA_48hrTGFB-s3

description:
Hum_CF_TGFB_RNAseq_CountsTable.csv
t48tg3


title: biol rep 2, hiFT cells, low accumulation dye


title: Root_polyA_2_R

tag: Strain;Wild type columbia, Tissue; Root tip (5 mm length), Age; 7 days, Growth; on MS medium under continuous light condition


title: biol rep 2, hiFT cells, high accumulation dye


title: biol rep 2, hiFT cells, midlow accumulation dye


title: biol rep 2, hiFT cells, midhigh accumulation dye


title: biol rep 2, hiFT cells, ungated


title: CF_RNA_48hrTGFB-s2

description:
Hum_CF_TGFB_RNAseq_CountsTable.csv
t48tg2


title: Root_polyA_1_R

description: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the light for 7 days at 25 degrees C. An root tips were collected from Arabidopsis seedlings (7 days old) which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio-state.edu/~plantbio/Facilities/abrc/abrchome.htm).Total RNA was isolated from root tips using the Qiagen RNeasy kit (Valencia,CA) according to the manufacturerfs instructions with DNase I treatment step. The quality and quantity of RNA isolated was checked by both gel electrophoresis and spectrophotometry.Five micro g total RNA was converted into double-stranded cDNA using Affymetrix T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions, fragmented, and then approximately 15 micro g of fragmented cRNA were hybridized to the tiling arrays according to Affymetrix (Santa Clara, CA) instructions. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis by TileMap software.


title: biol rep 1, hiFT cells, midlow accumulation dye


title: biol rep 1, hiFT cells, midhigh accumulation dye


title: CF_RNA_48hrTGFB-s1

description:
Hum_CF_TGFB_RNAseq_CountsTable.csv
t48tg1


title: met1L_polyA_2_R

description: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the light for 40 days at 25 degrees C. A mature leaves were collected from mature Arabidopsis plants (40 days old) which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio-state.edu/~plantbio/Facilities/abrc/abrchome.htm).Total RNA was isolated from mature leaves using the Qiagen RNeasy kit (Valencia,CA) according to the manufacturerfs instructions with DNase I treatment step. The quality and quantity of RNA isolated was checked by both gel electrophoresis and spectrophotometry.Five micro g total RNA was converted into double-stranded cDNA using Affymetrix T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions, fragmented, and then approximately 15 micro g of fragmented cRNA were hybridized to the tiling arrays according to Affymetrix (Santa Clara, CA) instructions. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis by TileMap software.

tag: Strain;met1 mutant on colmbia back ground segregated from heterozygote, Tissue; mature leaf, Age; 40days, Growth; on soil under continuous light condition


title: biol rep 1, hiFT cells, low accumulation dye


title: met1L_polyA_1_R


title: CF_RNA_48hr-s3

description:
Hum_CF_TGFB_RNAseq_CountsTable.csv
t48_3


title: biol rep 1, hiFT cells, high accumulation dye


title: biol rep 1, hiFT cells, ungated


title: met1B_polyA_1_R

description: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the light for 40 days at 25 degrees C. An inflorescence buds were collected from mature Arabidopsis plants (40 days old) which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio-state.edu/~plantbio/Facilities/abrc/abrchome.htm).Total RNA was isolated from inflorescence buds using the Qiagen RNeasy kit (Valencia,CA) according to the manufacturerfs instructions with DNase I treatment step. The quality and quantity of RNA isolated was checked by both gel electrophoresis and spectrophotometry.Five micro g total RNA was converted into double-stranded cDNA using Affymetrix T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions, fragmented, and then approximately 15 micro g of fragmented cRNA were hybridized to the tiling arrays according to Affymetrix (Santa Clara, CA) instructions. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis by TileMap software.

tag: Strain;met1 mutant on colmbia back ground segregated from heterozygote, Tissue; inflorescence buds, Age; 40days, Growth; on soil under continuous light condition


title: met1B_polyA_2_R


title: CF_RNA_48hr-s1

description:
Hum_CF_TGFB_RNAseq_CountsTable.csv
t48_1


title: CF_ATAC_6hrTGFB-s3

library_source: genomic


title: CF_ATAC_6hrTGFB-s2


title: CF_ATAC_72hrTGFB-s2


title: colL_polyA_1_R

tag: Strain;Wild type columbia, Tissue; mature leaf, Age; 40days, Growth; on soil under continuous light condition


title: CF_ATAC_72hrTGFB-s3

tag: cell line


title: colL_polyA_2_R


title: CF_RNA_24hrTGFB-s2

description:
Hum_CF_TGFB_RNAseq_CountsTable.csv
t24tg2

tag: cell type


title: CF_RNA_24hrTGFB-s3

description:
Hum_CF_TGFB_RNAseq_CountsTable.csv
t24tg3

tag: genotype


title: CF_RNA_24hrTGFB-s1

description:
Hum_CF_TGFB_RNAseq_CountsTable.csv
t24tg1

tag: treatment


title: CF_ATAC_48hrTGFB-s2


title: CF_ATAC_24hrTGFB-s3


title: callus_polyA_2_R

description: Arabidopsis ecotype Columbia suspension-culture cells were obtained from hypocotyls of etiolated seedlings as described (Ferrando 2000). The cells were cultured at 25 ‹C in the dark with an orbital agitation at 130 rpm in 500-mL Erlenmeyer flasks containing 200 mL of culture medium. A 25-mL aliquot of suspension cells was transferred to fresh medium every week. All experiments were conducted on 7-d-old cells The growth medium contained Murashige-Skoog basal salts, Gamborg's B5 vitamins (Life Technologies, Inc.), 3% sucrose, and 1 mg/L 2,4- dichlorophenoxyacetic acid (2,4-D). The cells were harvested two-days after subculture.Total RNA was isolated from suspension-culture cells using the Qiagen RNeasy kit (Valencia,CA) according to the manufacturerfs instructions with DNase I treatment step. The quality and quantity of RNA isolated was checked by both gel electrophoresis and spectrophotometry.Five micro g total RNA was converted into double-stranded cDNA using Affymetrix T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions, fragmented, and then approximately 15 micro g of fragmented cRNA were hybridized to the tiling arrays according to Affymetrix (Santa Clara, CA) instructions. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis by TileMap software.

tag: Strain;Wild type columbia, Tissue; suspension cultured cells, Age; 7 days, Growth; in MS medium with 2,4-D


title: CF_ATAC_48hrTGFB-s3


title: CF_ATAC_48hrTGFB-s1


title: CF_RNA_24hr-s3

description:
Hum_CF_TGFB_RNAseq_CountsTable.csv
t24_3


title: callus_polyA_1_R


title: CF_ATAC_24hrTGFB-s1


title: CF_RNA_48hr-s2

description:
Hum_CF_TGFB_RNAseq_CountsTable.csv
t48_2


title: CF_ATAC_24hrTGFB-s2


title: CF_RNA_24hr-s2

description:
Hum_CF_TGFB_RNAseq_CountsTable.csv
t24_2


title: CF_ATAC_72hrTGFB-s1


title: CF_ATAC_ctrl-3

value: Ctrl


title: ddcB_polyA_2_R

tag: Strain;drm1drm2cmt3 mutant on colmbia back ground segregated from heterozygote, Tissue; inflorescence buds, Age; 40days, Growth; on soil under continuous light condition


title: CF_ATAC_ctrl-2


title: CF_RNA_24hr-s1

description:
Hum_CF_TGFB_RNAseq_CountsTable.csv
t24_1


title: colB_polyA_2_R

tag: Strain;Wild type Columbia, Tissue; inflorescence buds, Age; 40days, Growth; on soil under continuous light condition


title: CF_ATAC_ctrl-1


title: CF_ATAC_6hrTGFB-s1


title: CF_RNA_ctrl-3

description:
Hum_CF_TGFB_RNAseq_CountsTable.csv
zero6


title: 293T, L7AE, 24h, rep3

city: New York

first: Justin

middle: J

last: Frere

state: NY

address: Alexandria Center for Life Sciences, West Tower, 430 E 29th St.

department: Microbiology

institute: NYU Langone Health

data_processing:
Base calling and sample deconvolution was performed by Illumina BaseSpace.
Reads were aligned to the human genome using Salmon as performed in the BaseSpace 'RNA-seq Alignment' application. Salmon files were then processed via DESeq2 for differential expression analysis.
FASTQ files for each sample were aligned to the hg18 Homo Sapiens genome, and reads were quantified utilizing Salmon as made available through the BaseSpace 'RNA-sequencing Alignment' application; raw and normalized read counts are available for each gene in '.quant.genes.sf' salmon output files
Assembly: hg18
Supplementary files format and content: .quant.genes.sf files (salmon output)
Supplementary files format and content: CSV format differential expression analysis output from DESeq2 shows differential expression of genes in the L7AE-transfected group (experimental) compared to the eGFP-transfected group (control).

extract_protocol:
total RNA was poly-A enriched and prepared using Truseq stranded mRNA library Prep Kit (Illumina); L7AE is represented as a experimental group in differential expression dataset
Total RNA was harvested 24 hours post-transfection using Trizol phenol chloroform extraction
RNA was Dnase-treated using Dnase I recombinant. RNA was then poly-A enriched and prepared using Truseq stranded mRNA Library Prep Kit (Illumina) per manufacturer instructions. cDNA libraries were sequenced using an Illumina NextSeq500 platform.

treatment_protocol: Confluent 293T were transfected with pCAGGs-eGFP or pCAGGs-L7ae using Lipofectamine 2000 and harvested at 24 hours post transfection into Trizol reagent

value: Human Embryonic Kidney Cell

value: transfected with pCAGGs-L7ae; harvested 24 hours post-transfection


title: 293T, L7AE, 24h, rep2


title: CF_RNA_ctrl-2

description:
Hum_CF_TGFB_RNAseq_CountsTable.csv
zero5


title: 293T, L7AE, 24h, rep1


title: CF_RNA_ctrl-1

description:
Hum_CF_TGFB_RNAseq_CountsTable.csv
zero4


title: colB_polyA_1_R


title: 293T, eGFP, 24h, rep3

extract_protocol:
total RNA was poly-A enriched and prepared using Truseq stranded mRNA library Prep Kit (Illumina); eGFP is represented as a control group in differential expression dataset
Total RNA was harvested 24 hours post-transfection using Trizol phenol chloroform extraction
RNA was Dnase-treated using Dnase I recombinant. RNA was then poly-A enriched and prepared using Truseq stranded mRNA Library Prep Kit (Illumina) per manufacturer instructions. cDNA libraries were sequenced using an Illumina NextSeq500 platform.

value: transfected with pCAGGs-eGFP; harvested 24 hours post-transfection


title: TA_7A

status: Public on Mar 10 2023

city: Saarbruecken

first: Viktoria

last: Wagner

country: Germany

institute: Universität des Saarlandes

description:
Done by BGI: BGISEQ500RS (BGI) using single-end sequencing.
Para_rpmm_norm_complete_filtered_global_GEO_18012023.csv

data_processing:
We performed the primary data analysis using a stand-alone version of our web-based tool miRMaster, version 2.0. We carried out all analyses using the standard parameter settings as in the online version, allowing one mismatch in the quantification of ncRNAs. The following ncRNA databases are included in our analysis: miRBase version 22.1, Ensembl ncRNA version 100, RNACentral version 15 and GtRNAdb version 18.1.
Adapters at the 3′ end were trimmed, while allowing an error of maximum one base and requiring a minimum overlap with the read of 10 bases. Reads were quality trimmed when the average quality dropped below 20 in a window of four consecutive bases to ensure a high quality of reads used for the downstream processing. All reads shorter than 17 bases after trimming were discarded from all further analyses.
MiRNAs were quantified with up to one mismatch and a variability of two bases allowed at the 5′ end and five bases at the 3′ end.
Assembly: mm10
Supplementary files format and content: For each sample rpmm counts are provided.

extract_protocol:
After dissection, organs were frozen on dry ice. Total RNA was isolated with the miRNeasy Micro kit (Qiagen). RNA quantity and quality were assessed by Agilent 2100 Bioanalyzer (Agilent Technologies) on randomized samples.
Small RNA library preparation was performed using the MGIEasy Small RNA Library Prep Kit and the high-throughput MGI SP-960 sample prep system according to the manufacturer's protocols. In brief, 3’- and 5’-adapters were ligated to the RNA, and reverse transcription (RT) was performed using an RT primer, in which sample-specific barcodes were incorporated. The resulting cDNA was amplified in a polymerase chain reaction (PCR) with 21 cycles. The amplification product was size selected and purified using AMPure Beads XP (Beckman Coulter, Germany). The size of the purified PCR products was checked using an Agilent DNA 1000 Kit (Agilent Technologies), and the concentration was determined using Qubit™ 1X dsDNA High Sensitivity (HS) (Thermo Fisher Scientific). For each library, 16 samples, barcoded with barcodes 1-4, 13-16 and 25-32, were pooled in an equimolar fashion at a concentration of 4.56 ng/µl. Pooled libraries were circularized and sent for sequencing. A total of 65 libraries consisting of 947 samples were analysed in the project.

treatment_protocol: Suturing together the peritoneum of adjacent flanks of two mice, forming a continuous peritoneal cavity, accomplished the aging intervention parabiosis via the peritoneal method. To enable coordinated movement after surgery, adjacent knee joints and elbow joints were joined with nylon monofilament sutures, as well as skin with surgical autoclips.

tag: experiment batch

tag: age

tag: Sex

value: m

tag: experimental group

value: Parabiosis

tag: cell compartment

value: Whole cell


title: TA_6B


title: TA_9A


title: TA_9B


title: 293T, eGFP, 24h, rep1


title: TA_6A


title: TA_2B


title: TA_5A


title: ddcB_polyA_1_R


title: TA_5B


title: TA_20B


title: TA_20A


title: TA_1B


title: TA_2A


title: TA_19B


title: TA_1A


title: TA_19A


title: 293T, eGFP, 24h, rep2


title: TA_17A


title: TA_16A


title: TA_7B


title: TA_15A


title: TA_14B


title: TA_12B


title: TA_10B


title: TA_11A


title: TA_11B


title: TA_10A


title: MAT_9A

source_name: MAT


title: TA_16B


title: TA_15B


title: TA_12A


title: MAT_7B


title: MAT_7A


title: MAT_6B


title: MAT_5A


title: MAT_6A


title: MAT_2B


title: TA_17B


title: MAT_2A


title: MAT_1B


title: MAT_19B


title: MAT_20B


title: MAT_19A


title: MAT_5B


title: MAT_20A


title: MAT_1A


title: MAT_17B


title: MAT_14B


title: MAT_15B


title: MAT_16B


title: L_7B

source_name: Liver


title: MAT_17A


title: L_7A


title: MAT_16A


title: MAT_15A


title: MAT_11B


title: MAT_11A


title: MAT_12A


title: L_6A


title: L_6B


title: L_5B


title: L_5A


title: L_2B


title: L_2A


title: L_20B


title: L_1A


title: L_20A


title: L_1B


title: L_19A


title: MAT_10B


title: L_9A


title: MAT_10A


title: L_17B


title: L_9B


title: L_16A


title: L_14A


title: L_15A


title: L_17A


title: L_14B


title: L_12B


title: L_15B


title: L_16B


title: L_10B


title: K_9A

source_name: Kidney


title: L_11B


title: L_10A


title: K_7B


title: K_7A


title: K_6B


title: L_19B


title: K_6A


title: biol rep 1, hiFT cells, LSD1 inhibition

tag: tissue

value: LSD1 inhibition


title: K_5A


title: K_2B


title: K_5B


title: K_20B


title: K_1B


title: K_20A


title: K_1A


title: L_12A


title: K_19B


title: L_11A


title: K_17A


title: K_17B


title: K_9B


title: K_15B


title: K_19A


title: K_16A


title: K_14B


title: K_16B


title: K_15A


title: K_11B


title: K_12A


title: K_14A


title: K_12B


title: K_10B


title: K_11A


title: H_9B

source_name: Heart


title: K_10A


title: H_6B


title: H_7A


title: H_9A


title: H_7B


title: H_6A


title: H_2B


title: H_5B


title: H_5A


title: H_2A


title: H_20B


title: H_20A


title: H_1B


title: H_19B


title: H_17B


title: H_19A


title: H_1A


title: H_17A


title: H_15B


title: H_12B


title: H_14A


title: H_14B


title: H_16B


title: H_12A


title: H_10A


title: H_16A


title: H_10B


title: H_11A


title: H_11B


title: GAT_9A

source_name: GAT


title: GAT_7B


title: GAT_6A


title: GAT_6B


title: GAT_5B


title: GAT_5A


title: GAT_2B


title: GAT_20B


title: GAT_20A


title: H_15A


title: GAT_1B


title: GAT_1A


title: GAT_2A


title: GAT_19A


title: GAT_19B


title: GAT_17A


title: GAT_16B


title: GAT_15B


title: GAT_16A


title: GAT_14B


title: GAT_15A


title: GAT_14A


title: GAT_11B


title: GAT_12A


title: GAT_11A


title: GAT_9B


title: GAT_7A


title: GAT_10B


title: GAT_10A


title: Liver_41

description:
Done by BGI: BGISEQ500RS (BGI) using single-end sequencing.
MS_rpmm_Complete_Filtered_global_GEO_18012023.csv

value: Control


title: Pancreas_35

source_name: Pancreas


title: Heart_02


title: Bone_12

source_name: Bone


title: SCAT_27

source_name: SCAT


title: GAT_54


title: GAT_29


title: GAT_17B


title: Bone_45


title: Skin_29

source_name: Skin

value: f


title: Limb_Muscle_52


title: Marrow_56

source_name: Marrow


title: GAT_12B


title: Bone_35


title: Pancreas_08


title: Pancreas_10


title: Marrow_47


title: GAT_50


title: MAT_31


title: Bone_50


title: Limb_Muscle_28


title: Limb_Muscle_50


title: Limb_Muscle_18


title: Kidney_54


title: Pancreas_06


title: GAT_14


title: Skin_25


title: SCAT_43


title: MAT_56


title: MAT_32


title: Lung_03

source_name: Lung


title: BAT_36

source_name: BAT


title: Kidney_23


title: Spleen_38

source_name: Spleen


title: GAT_26


title: SCAT_31


title: Pancreas_01


title: Kidney_26


title: SCAT_52


title: TA_14A


title: Spleen_48


title: Lung_07


title: BAT_07


title: Heart_47


title: Liver_36


title: Limb_Muscle_42


title: GAT_23


title: Brain_25

source_name: Brain


title: GAT_09


title: Kidney_08


title: MAT_43


title: Heart_51


title: Pancreas_09


title: SCAT_19


title: Skin_19


title: Skin_52


title: GAT_16


title: Small_Intestine_24


title: Spleen_30


title: Lung_02


title: Heart_13


title: BAT_23


title: MAT_30


title: Liver_04


title: Limb_Muscle_10


title: MAT_17


title: Brain_12


title: Brain_14


title: Lung_18


title: Marrow_39


title: Bone_10


title: GAT_12


title: SCAT_20


title: Spleen_29


title: Small_Intestine_25


title: MAT_19


title: Skin_17


title: Marrow_40


title: Kidney_04


title: Liver_02


title: BAT_22


title: Limb_Muscle_09


title: Kidney_17


title: Kidney_07


title: Spleen_27


title: Brain_13


title: Heart_14


title: Small_Intestine_28


title: MAT_20


title: Limb_Muscle_30


title: SCAT_21


title: Marrow_38


title: Skin_16


title: Lung_19


title: Pancreas_54


title: BAT_18


title: Limb_Muscle_08


title: Kidney_11


title: BAT_17


title: Small_Intestine_27


title: Spleen_33


title: Brain_15


title: Heart_15


title: Skin_15


title: MAT_21


title: Lung_20


title: SCAT_23


title: GAT_10


title: Heart_17


title: Kidney_09


title: Liver_01


title: MAT_06


title: Pancreas_11


title: Pancreas_55


title: Marrow_03


title: Brain_52


title: Kidney_47


title: GAT_11


title: Limb_Muscle_54


title: Small_Intestine_03


title: GAT_21


title: Bone_07


title: Lung_11


title: SCAT_03


title: Heart_27


title: Liver_16


title: Marrow_37


title: Pancreas_12


title: BAT_03


title: Lung_06


title: Heart_26


title: Bone_16


title: Liver_15


title: Kidney_48


title: Marrow_04


title: Small_Intestine_04


title: Spleen_05


title: SCAT_04


title: GAT_20


title: Brain_51


title: Skin_03


title: Limb_Muscle_53


title: Bone_17


title: Heart_25


title: Brain_50


title: Small_Intestine_05


title: GAT_19


title: SCAT_06


title: Spleen_06


title: BAT_02


title: Marrow_05


title: Pancreas_13


title: Limb_Muscle_51


title: Skin_04


title: Kidney_50


title: Bone_14


title: BAT_04


title: Skin_02


title: Brain_49


title: MAT_04


title: Small_Intestine_06


title: Spleen_07


title: Skin_01


title: Lung_04


title: Marrow_07


title: MAT_01


title: SCAT_07


title: Pancreas_14


title: Liver_13


title: BAT_01


title: Heart_24


title: Kidney_51


title: Limb_Muscle_49


title: Small_Intestine_56


title: Heart_23


title: Brain_48


title: Skin_50


title: Lung_05


title: Liver_42


title: Spleen_12


title: GAT_28


title: Lung_55


title: Limb_Muscle_48


title: Kidney_42


title: MAT_52


title: Marrow_55


title: Pancreas_56


title: SCAT_56


title: Spleen_53


title: Bone_13


title: Heart_52


title: Pancreas_48


title: MAT_51


title: Brain_20


title: Small_Intestine_54


title: Skin_54


title: Kidney_56


title: BAT_33


title: Bone_56


title: SCAT_48


title: Spleen_52


title: GAT_53


title: Lung_52


title: Kidney_53


title: Skin_53


title: BAT_32


title: Liver_54


title: Brain_18


title: Brain_19


title: Small_Intestine_53


title: Marrow_51


title: Pancreas_47


title: SCAT_49


title: Lung_53


title: Small_Intestine_52


title: Heart_53


title: MAT_50


title: Liver_55


title: Limb_Muscle_41


title: GAT_55


title: Bone_54


title: Marrow_52


title: Lung_51


title: Kidney_52


title: Pancreas_23


title: Skin_51


title: Heart_54


title: Limb_Muscle_43


title: Limb_Muscle_45


title: Liver_53


title: Spleen_51


title: BAT_12


title: Brain_09


title: GAT_01


title: Small_Intestine_12


title: Marrow_12


title: Lung_17


title: Kidney_41


title: Limb_Muscle_01


title: Heart_03


title: Pancreas_16


title: Marrow_11


title: Limb_Muscle_02


title: Lung_16


title: Bone_52


title: SCAT_15


title: Liver_25


title: MAT_14


title: Bone_02


title: Heart_05


title: BAT_13


title: Kidney_40


title: Brain_10


title: Spleen_04


title: Pancreas_17


title: BAT_31


title: GAT_52


title: Skin_08


title: Small_Intestine_11


title: Spleen_08


title: SCAT_16


title: BAT_11


title: Marrow_10


title: GAT_03


title: Bone_03


title: Liver_26


title: Lung_15


title: Limb_Muscle_03


title: SCAT_13


title: Pancreas_18


title: Lung_14


title: Brain_07


title: MAT_12


title: Spleen_09


title: Skin_09


title: Kidney_39


title: Marrow_09


title: Skin_11


title: Kidney_38


title: GAT_04


title: Heart_06


title: Pancreas_19


title: Bone_04


title: Brain_06


title: SCAT_11


title: BAT_10


title: Small_Intestine_47


title: MAT_11


title: Spleen_41


title: MAT_44


title: Brain_33


title: Marrow_32


title: Bone_36


title: Skin_43


title: Small_Intestine_37


title: Brain_40


title: Heart_36


title: Liver_40


title: Spleen_39


title: Marrow_31


title: Spleen_40


title: Small_Intestine_44


title: Limb_Muscle_04


title: Brain_41


title: Bone_39


title: Liver_27


title: Skin_40


title: Small_Intestine_46


title: Brain_34


title: Bone_41


title: Heart_35


title: Small_Intestine_09


title: Spleen_37


title: Lung_35


title: Marrow_29


title: Pancreas_42


title: Heart_49


title: Spleen_25


title: Brain_39


title: Lung_37


title: Pancreas_37


title: Small_Intestine_38


title: Lung_47


title: Brain_36


title: Skin_46


title: Liver_38


title: Spleen_42


title: Bone_34


title: Marrow_36


title: Small_Intestine_41


title: Pancreas_39


title: Skin_37


title: Bone_32


title: Liver_45


title: Skin_38


title: Brain_37


title: Lung_39


title: Marrow_35


title: Limb_Muscle_37


title: Marrow_33


title: Heart_37


title: Bone_31


title: Spleen_24


title: Skin_45


title: Marrow_28


title: Small_Intestine_42


title: Lung_41


title: Spleen_23


title: Limb_Muscle_38


title: Heart_39


title: Bone_29


title: Liver_44


title: Lung_42


title: Marrow_27


title: Small_Intestine_43


title: Brain_38


title: Skin_35


title: Limb_Muscle_36


title: Pancreas_41


title: Marrow_34


title: Marrow_26


title: Limb_Muscle_29


title: Kidney_21


title: Bone_28


title: Pancreas_40


title: Pancreas_30


title: Liver_20


title: Heart_32


title: Small_Intestine_19


title: Pancreas_43


title: Lung_48


title: Marrow_19


title: Skin_34


title: Brain_46


title: Kidney_24


title: SCAT_41


title: MAT_41


title: Marrow_20


title: Spleen_22


title: Limb_Muscle_26


title: Spleen_21


title: Bone_27


title: Lung_33


title: MAT_46


title: Lung_32


title: Brain_28


title: Brain_27


title: Heart_33


title: Limb_Muscle_25


title: Liver_31


title: Bone_26


title: Spleen_20


title: Lung_30


title: Marrow_46


title: Pancreas_32


title: Pancreas_31


title: Small_Intestine_32


title: SCAT_42


title: Marrow_21


title: MAT_40


title: Pancreas_44


title: Liver_32


title: Kidney_25


title: Marrow_44


title: Kidney_27


title: Brain_29


title: Brain_30


title: Marrow_22


title: Liver_33


title: Kidney_31


title: Limb_Muscle_23


title: Spleen_19


title: Heart_34


title: BAT_54


title: Lung_46


title: Lung_29


title: Skin_32


title: SCAT_44


title: Kidney_28


title: MAT_38


title: Small_Intestine_33


title: Skin_30


title: Liver_47


title: SCAT_45


title: Brain_31


title: Liver_34


title: MAT_37


title: Lung_28


title: Liver_37


title: Heart_42


title: Brain_32


title: Spleen_18


title: Small_Intestine_36


title: Skin_28


title: Marrow_23


title: Spleen_17


title: SCAT_46


title: Limb_Muscle_22


title: Marrow_25


title: Pancreas_34


title: BAT_50


title: Limb_Muscle_33


title: Kidney_30


title: Small_Intestine_34


title: Limb_Muscle_21


title: GAT_30


title: Liver_35


title: Skin_21


title: Small_Intestine_18


title: Spleen_13


title: Kidney_13


title: Pancreas_24


title: MAT_34


title: Heart_31


title: Marrow_13


title: Pancreas_36


title: Liver_07


title: GAT_22


title: Lung_26


title: SCAT_50


title: Marrow_06


title: MAT_35


title: Limb_Muscle_19


title: MAT_55


title: Marrow_49


title: Heart_16


title: Heart_41


title: Brain_08


title: Kidney_44


title: Kidney_29


title: MAT_07


title: Limb_Muscle_06


title: SCAT_05


title: MAT_02


title: Bone_25


title: Marrow_24


title: Liver_43


title: MAT_54


title: SCAT_40


title: Heart_12


title: Skin_49


title: Pancreas_20


title: Kidney_33


title: SCAT_14


title: Kidney_36


title: Liver_39


title: Liver_19


title: Small_Intestine_21


title: Small_Intestine_40


title: Kidney_12


title: Kidney_10


title: Small_Intestine_26


title: Spleen_26


title: Spleen_35


title: Lung_56


title: Lung_43


title: Lung_54


title: MAT_15


title: MAT_22


title: SCAT_54


title: Liver_03


title: Spleen_36


title: Lung_31


title: MAT_23


title: SCAT_35


title: GAT_51


title: Spleen_28


title: GAT_15


title: SCAT_51


title: Liver_22


title: Small_Intestine_29


title: Liver_21


title: Lung_38


title: Lung_40


title: Spleen_55


title: MAT_24


title: Heart_50


title: Limb_Muscle_40


title: MAT_53


title: Liver_56


title: Marrow_50


title: Skin_55


title: Spleen_54


title: Small_Intestine_55


title: Kidney_55


title: SCAT_47


title: Kidney_34


title: BAT_34


title: Bone_55


title: Brain_21


title: Marrow_45


title: Heart_43


title: SCAT_09


title: Heart_46


title: Brain_42


title: Brain_45


title: Small_Intestine_48


title: Lung_45


title: Liver_49


title: Heart_45


title: Spleen_47


title: Spleen_45


title: Spleen_56


title: Bone_48


title: Spleen_43


title: Skin_07


title: Skin_44


title: GAT_56


title: Small_Intestine_49


title: Bone_38


title: Small_Intestine_45


title: Spleen_34


title: Small_Intestine_39


title: Marrow_30


title: Bone_33


title: Limb_Muscle_39


title: Skin_39


title: Lung_36


title: Pancreas_38


title: Liver_46


title: Bone_44


title: Heart_40


title: Heart_48


title: Lung_44


title: Small_Intestine_50


title: Spleen_46


title: Bone_46


title: Bone_42


title: Marrow_48


title: Spleen_44


title: Liver_50


title: Brain_35


title: Spleen_50


title: Marrow_43


title: Brain_44


title: SCAT_53


title: Bone_53


title: Heart_38


title: Brain_43


title: Kidney_35


title: GAT_49


title: Lung_50


title: Pancreas_46


title: Small_Intestine_51


title: Brain_17


title: Liver_52


title: MAT_49


title: Marrow_53


title: BAT_30


title: Kidney_32


title: Liver_51


title: Limb_Muscle_46


title: Heart_55


title: Limb_Muscle_47


title: Skin_20


title: Small_Intestine_22


title: Lung_27


title: SCAT_17


title: Marrow_42


title: Bone_15


title: Pancreas_50


title: GAT_17


title: Kidney_03


title: Liver_05


title: Limb_Muscle_12


title: Bone_11


title: Lung_01


title: Liver_06


title: Marrow_41


title: SCAT_55


title: Skin_47


title: Spleen_32


title: Lung_49


title: Spleen_31


title: Marrow_54


title: GAT_36


title: MAT_18


title: Kidney_01


title: Small_Intestine_23


title: Spleen_49


title: Bone_51


title: Heart_10


title: Heart_56


title: Brain_16


title: Pancreas_51


title: SCAT_18


title: GAT_13


title: Limb_Muscle_11


title: Heart_11


title: Skin_18


title: Brain_11


title: Heart_30


title: Limb_Muscle_17


title: Bone_20


title: Lung_08


title: Brain_22


title: Marrow_14


title: SCAT_39


title: Skin_22


title: GAT_31


title: Bone_21


title: BAT_46


title: Pancreas_26


title: Kidney_15


title: Liver_08


title: Limb_Muscle_16


title: MAT_33


title: Lung_24


title: Kidney_14


title: Brain_23


title: GAT_35


title: Marrow_15


title: Skin_23


title: Lung_25


title: Heart_21


title: Small_Intestine_17


title: Spleen_14


title: BAT_45


title: Small_Intestine_16


title: Bone_37


title: MAT_29


title: Pancreas_25


title: Liver_09


title: Brain_26


title: Bone_24


title: Marrow_17


title: Small_Intestine_14


title: Skin_26


title: Spleen_15


title: MAT_45


title: MAT_26


title: SCAT_26


title: Spleen_16


title: Kidney_19


title: Limb_Muscle_14


title: Liver_10


title: Pancreas_28


title: GAT_33


title: Small_Intestine_13


title: Heart_19


title: Heart_18


title: Liver_14


title: Lung_22


title: BAT_35


title: BAT_38


title: MAT_25


title: SCAT_28


title: Limb_Muscle_13


title: Marrow_18


title: Skin_27


title: Kidney_20


title: Lung_13


title: Lung_21


title: Pancreas_29


title: Kidney_37


title: Heart_07


title: Pancreas_21


title: Bone_05


title: Small_Intestine_08


title: BAT_09


title: MAT_05


title: Liver_29


title: Pancreas_22


title: Heart_08


title: Limb_Muscle_05


title: Bone_06


title: BAT_08


title: Small_Intestine_07


title: MAT_10


title: Marrow_08


title: Lung_12


title: GAT_08


title: Spleen_11


title: Skin_06


title: Liver_28


title: MAT_09


title: GAT_05


title: Heart_29


title: Spleen_10


title: Brain_03


title: Lung_09


title: Limb_Muscle_56


title: Spleen_01


title: Bone_19


title: Pancreas_02


title: MAT_08


title: BAT_06


title: Liver_18


title: Heart_28


title: Kidney_46


title: Skin_12


title: Brain_05


title: Limb_Muscle_55


title: SCAT_02


title: Brain_53


title: Skin_14


title: Marrow_02


title: SCAT_08


title: Marrow_01


title: GAT_24


title: Skin_05


title: BAT_05


title: Bone_18


title: Small_Intestine_02


title: BAT_43


title: GAT_25


title: SCAT_01


title: SCAT_30


title: Marrow_16


title: Small_Intestine_15


title: Skin_24


title: Brain_24


title: Small_Intestine_01


title: Liver_17


title: MAT_28


title: Lung_23


title: Bone_22


title: Lung_10


title: Brain_02


title: Kidney_18


title: Limb_Muscle_15


title: Liver_12


title: Heart_20


title: Spleen_03


title: Kidney_22


title: Liver_23


title: Brain_01


title: Kidney_16


title: Kidney_43


title: Small_Intestine_30


title: BAT_19


title: Heart_09


title: miRNA-seq_Panc-1, treatment, rep3, 24h

city: hongkong

first: Yangchao

last: Chen

state: State...

address: Lo Kwee-Seong Integrated Biomedical Sciences Bld , hongkong

department: School of Biomedical Science

country: Hong Kong

institute: Chinese University of Hongkong

data_processing:
The raw sequencing data are called raw tags. The raw tags were processed using the following steps: remove low quality tags; remove tags with 5 primer contaminants; remove tags without 3 primer; remove tags without insertion; remove tags with poly A;remove tags shorter than 18 nt. After filtering, the clean tags were mapped to the reference genome and other sRNA database including miRbase, siRNA, piRNA and snoRNA with Bowtie2. Particularly, cmsearch was performed for Rfam mapping.The software miRDeep2 was used to predict novel miRNA by exploring the secondary structure, and Piano was used to predict piRNAs. RNAhybrid, miRanda and TargetScan were used to predict target genes of miRNAs. The small RNA expression level is calculated by counting absolute numbers of molecules using unique molecular identifiers. Differential expression analysis was performed using the DEGseq, Q value less than 0.001 and the absolute value of Log2Ratio more than 1 as the default threshold to judge the significance of expression difference. To annotate gene functions, all target genes were aligned against the Kyoto Encyclopedia of Genes (KEGG) and Gene Ontology (GO) database. GO enrichment analysis and KEGG enrichment analysis of target genes were performed using phyper, a function of R. The P-value was corrected using the Bonferroni method, and a corrected P-value less than 0.05 was taken as a threshold. GO terms or KEGG terms fulfilling this condition were defined as significantly enriched terms.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Pancreatic Cancer

growth_protocol: Panc-1 in the control group was grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 50 units/ml penicillin-streptomycin (HyClone, USA) and 10% fetal bovine serum (FBS) (Gibco, USA)  in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
TRIZOL Reagent was used to isolate RNA from the whole-cell lysate.
Library was prepared with 1 μg total RNA for each sample. Total RNA was purified by electrophoretic separation on a 15% urea denaturing polyacrylamide gel electrophoresis (PAGE) gel and small RNA regions corresponding to the 18–30 nt bands in the marker lane (14-30 ssRNA Ladder Marker, TAKARA) were excised and recovered. Then the 18–30 nt small RNAs were ligated to a 5′-adaptor and a 3′-adaptor. The adapter-ligated small RNAs were subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen, USA) and then several rounds of PCR amplification with PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments. The PCR products were selected by agarose gel electrophoresis with target fragments 100~120 bp, and then purified by QIAquick Gel and then several rounds of PCR amplification with PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments. The PCR products were selected by agarose gel electrophoresis with target fragments 100~120 bp, and then purified by QIAquick Gel
Extraction Kit (QIAGEN, Valencia, CA). The library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe). The final ligation PCR products were sequenced using the BGISEQ-500 platform (BGI-Shenzhen, China).

treatment_protocol: Panc-1 in the treatment group was grown in DMEM (high glucose, no glutamine, no methionine, no cystine) (Thermo, 21013024) added with standard amount of L-Glutamine (Thermo 25030149) and methionine (Beyotime ST1465) with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C in humidified atmosphere with 5% CO2 at 37C.

value: Pancreatic Cancer

value: Pancreatic ductal adenocarcinoma

value: cystine depletion for 24h


title: miRNA-seq_Panc-1, treatment, rep2, 24h


title: miRNA-seq_Panc-1, treatment, rep1, 24h


title: Bone_49


title: lncRNA_Panc-1, treatment, rep2, 24h

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) [1] by Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) atio 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). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to detect fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5)  was applied to align the clean reads to the gene set, a database built by BGI (Beijing Genomic Institute in ShenZhen), in which known and novel, coding and noncoding transcripts were included, then expression level of gene was calculated by RSEM(v1.2.12). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value less than 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric
The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value less than0.05) by Bonferroni.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
TRIZOL Reagent was used to isolate RNA from the whole-cell lysate.
Approximately 1µg total RNA per sample was treated with Ribo-Zero™ Magnetic Kit(Epicentre) to deplete rRNA. The retrieved RNA was fragmented by adding First Strand Master Mix(Invitrogen). First-strand cDNA was generated using random primers reverse transcription,followed by a second-strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adapters were ligated to the ends of these 3’ adenylated cDNA fragments. Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix are performed to enrich the cDNA fragments. Then the PCR products are purified with Ampure XP Beads. The final library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe). The Qualified libraries were sequenced pair end on the Hiseq 4000 or Hiseq X-ten platform (BGI-Shenzhen, China).


title: miRNA-seq_Panc-1, control, rep3, 24h


title: lncRNA_Panc-1, treatment, rep1, 24h


title: miRNA-seq_Panc-1, control, rep1, 24h


title: lncRNA_Panc-1, treatment, rep3, 24h


title: miRNA-seq_Panc-1, control, rep2, 24h


title: lncRNA_Panc-1, control, rep1, 24h


title: lncRNA_Panc-1, control, rep3, 24h


title: lncRNA_Panc-1, control, rep2, 24h


title: Panc-1, control, rep2, 24h

data_processing:
Reads were mapped onto hg19 with STAR (v2.7) and quantified with featureCounts (v2.0.0) using gencode annotations (v28lift37 for hg19). CircRNAs were predicted and quantified using ciri2 v2.0.6 and find_circ v1.2 adhering to default settings Quantseq reads were mapped onto hg19 using STAR (v2.7). The resulting bam-files were merged and divided into plus and minus-strand alignments. Then, using MACS2 peakcall  (v2.2.6, https://github.com/macs3-project/MACS) with parameters [--nomodel --shift 0 –g 2.9e9], quantseq peaks were extracted. Each peak was then subsequently quantified using featureCounts (v2.0.0).
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
TRIZOL Reagent was used to isolate RNA from the whole-cell lysate.
5μg of total RNA was treated with DNase I which degraded double-stranded and single-stranded DNA presenting in RNA samples. Instead of purifying poly-A RNA using poly-dT primer beads, we removed ribosomal RNA using the Ribo-Zero™ rRNA Removal Kit (Illumina, Inc.). Linear RNA was removed using RNase R (Epicentre, lnc). Purification was performed using Agencourt RNAClean XP magnetic beads. All other steps were performed according to the manufacturer's protocols. The library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe). Finally, the Qualified libraries were sequenced pair end on the Hiseq 4000 or Hiseq X-ten platform (BGI-Shenzhen, China).


title: Panc-1, control, rep1, 24h


title: Panc-1, treatment, rep1, 24h


title: Panc-1, control, rep3, 24h


title: S30P

city: Gainesville

first: Chu

last: Hsiao

state: FL

address: 2033 Mowry Rd

department: Anthropology

institute: University of Florida

description: S30 Placenta

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Clariom D array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Command Console

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) 4.0.2 software using the Signal Space Transformation-Robust Multi-chip Analysis (SST-RMA) for adjustment of background noise, normalization, and summarization. The detected above background (DABG) threshold was set to the default 0.05.

source_name: P

label_protocol: Biotinylated cRNA were prepared according to the GeneChip WT PLUS Reagent kit protocol from 6 ug total RNA

extract_protocol: Total RNA fom peripheral blood samples (mothers, newborns) were extracted using the Ribopure blood kit and eluted in the kit's elution solution with post extraction dnase treatment. Total RNA from placentas were extracted using a trizol and Qiagen RNeasy kit protocol and eluted in H2O with on-column dnase treatment.

tag: recruitment site

value: S

tag: rin


title: S49Bb

description: S49 Newborn

source_name: Bb


title: S73P

description: S73 Placenta


title: S37M

description: S37 Mother

source_name: M


title: C43P

description: C43 Placenta

value: C


title: S2M

description: S2 Mother


title: S18P

description: S18 Placenta


title: C90P

description: C90 Placenta


title: C95P

description: C95 Placenta


title: S36Bb

description: S36 Newborn


title: S46M

description: S46 Mother


title: Heart_04


title: S25P

description: S25 Placenta


title: S5P

description: S5 Placenta


title: Panc-1, treatment, rep3, 24h


title: S67P

description: S67 Placenta


title: S73Bb

description: S73 Newborn


title: C67M

description: C67 Mother


title: S15Bb

description: S15 Newborn


title: S28Bb

description: S28 Newborn


title: Panc-1, treatment, rep2, 24h


title: S35Bb

description: S35 Newborn


title: S63Bb

description: S63 Newborn


title: C7P

description: C7 Placenta


title: C93M

description: C93 Mother


title: S32Bb

description: S32 Newborn


title: C23M

description: C23 Mother


title: S21M

description: S21 Mother


title: S61M

description: S61 Mother


title: S14Bb

description: S14 Newborn


title: C63M

description: C63 Mother


title: S69P

description: S69 Placenta


title: C39P

description: C39 Placenta


title: S49M

description: S49 Mother


title: C53P

description: C53 Placenta


title: S72P

description: S72 Placenta


title: C9M

description: C9 Mother


title: S73M

description: S73 Mother


title: S61P

description: S61 Placenta


title: S51Bb

description: S51 Newborn


title: C5Bb

description: C5 Newborn


title: S33P

description: S33 Placenta


title: S58Bb

description: S58 Newborn


title: C80Bb

description: C80 Newborn


title: S11P

description: S11 Placenta


title: S62P

description: S62 Placenta


title: S21P

description: S21 Placenta


title: C74P

description: C74 Placenta


title: S50Bb

description: S50 Newborn


title: C8M

description: C8 Mother


title: S53P

description: S53 Placenta


title: S37Bb

description: S37 Newborn


title: C81P

description: C81 Placenta


title: S49P

description: S49 Placenta


title: S3P

description: S3 Placenta


title: C80M

description: C80 Mother


title: S33M

description: S33 Mother


title: C9Bb

description: C9 Newborn


title: C7M

description: C7 Mother


title: S8M

description: S8 Mother


title: S33Bb

description: S33 Newborn


title: C51P

description: C51 Placenta


title: S20Bb

description: S20 Newborn


title: C50M

description: C50 Mother


title: S5Bb

description: S5 Newborn


title: S28P

description: S28 Placenta


title: S5M

description: S5 Mother


title: C56Bb

description: C56 Newborn


title: S15P

description: S15 Placenta


title: C80P

description: C80 Placenta


title: S30Bb

description: S30 Newborn


title: S27Bb

description: S27 Newborn


title: C85M

description: C85 Mother


title: C66P

description: C66 Placenta


title: C39M

description: C39 Mother


title: S58M

description: S58 Mother


title: C59M

description: C59 Mother


title: C95Bb

description: C95 Newborn


title: C37P

description: C37 Placenta


title: C95M

description: C95 Mother


title: C51M

description: C51 Mother


title: S72Bb

description: S72 Newborn


title: C71Bb

description: C71 Newborn


title: S22M

description: S22 Mother


title: C12P

description: C12 Placenta


title: S18M

description: S18 Mother


title: S66Bb

description: S66 Newborn


title: C81M

description: C81 Mother


title: C8P

description: C8 Placenta


title: S2P

description: S2 Placenta


title: S20M

description: S20 Mother


title: S27M

description: S27 Mother


title: C12Bb

description: C12 Newborn


title: S52Bb

description: S52 Newborn


title: C71P

description: C71 Placenta


title: S71P

description: S71 Placenta


title: S27P

description: S27 Placenta


title: S14M

description: S14 Mother


title: S21Bb

description: S21 Newborn


title: S26M

description: S26 Mother


title: C61M

description: C61 Mother


title: S66M

description: S66 Mother


title: C56P

description: C56 Placenta


title: C55P

description: C55 Placenta


title: S51M

description: S51 Mother


title: S61Bb

description: S61 Newborn


title: S35P

description: S35 Placenta


title: C86M

description: C86 Mother


title: C10M

description: C10 Mother


title: C89M

description: C89 Mother


title: C89P

description: C89 Placenta


title: C86Bb

description: C86 Newborn


title: C52M

description: C52 Mother


title: C66M

description: C66 Mother


title: S69M

description: S69 Mother


title: C52P

description: C52 Placenta


title: S67Bb

description: S67 Newborn


title: S46P

description: S46 Placenta


title: S8P

description: S8 Placenta


title: S9Bb

description: S9 Newborn


title: S68P

description: S68 Placenta


title: S9M

description: S9 Mother


title: C54P

description: C54 Placenta


title: S28M

description: S28 Mother


title: C55Bb

description: C55 Newborn


title: C9P

description: C9 Placenta


title: C91P

description: C91 Placenta


title: S30M

description: S30 Mother


title: C43Bb

description: C43 Newborn


title: C68M

description: C68 Mother


title: S72M

description: S72 Mother


title: C68P

description: C68 Placenta


title: C8Bb

description: C8 Newborn


title: S67M

description: S67 Mother


title: S75Bb

description: S75 Newborn


title: C5P

description: C5 Placenta


title: C50Bb

description: C50 Newborn


title: C54M

description: C54 Mother


title: S71M

description: S71 Mother


title: C52Bb

description: C52 Newborn


title: S53Bb

description: S53 Newborn


title: C59P

description: C59 Placenta


title: S12P

description: S12 Placenta


title: S26P

description: S26 Placenta


title: C85Bb

description: C85 Newborn


title: C55M

description: C55 Mother


title: S66P

description: S66 Placenta


title: S43M

description: S43 Mother


title: C86P

description: C86 Placenta


title: C39Bb

description: C39 Newborn


title: S43P

description: S43 Placenta


title: C57M

description: C57 Mother


title: C89Bb

description: C89 Newborn


title: S12M

description: S12 Mother


title: S22P

description: S22 Placenta


title: S68Bb

description: S68 Newborn


title: C61Bb

description: C61 Newborn


title: C53M

description: C53 Mother


title: C23Bb

description: C23 Newborn


title: C90Bb

description: C90 Newborn


title: S68M

description: S68 Mother


title: C84Bb

description: C84 Newborn


title: S52P

description: S52 Placenta


title: S34Bb

description: S34 Newborn


title: S34M

description: S34 Mother


title: S17P

description: S17 Placenta


title: S57M

description: S57 Mother


title: C93P

description: C93 Placenta


title: S9P

description: S9 Placenta


title: C53Bb

description: C53 Newborn


title: C50P

description: C50 Placenta


title: S63P

description: S63 Placenta


title: S62M

description: S62 Mother


title: S51P

description: S51 Placenta


title: S63M

description: S63 Mother


title: C63Bb

description: C63 Newborn


title: S53M

description: S53 Mother


title: S76P

description: S76 Placenta


title: S76Bb

description: S76 Newborn


title: S48P

description: S48 Placenta


title: S57Bb

description: S57 Newborn


title: C43M

description: C43 Mother


title: S2Bb

description: S2 Newborn


title: C67Bb

description: C67 Newborn


title: S46Bb

description: S46 Newborn


title: C84M

description: C84 Mother


title: C74Bb

description: C74 Newborn


title: S52M

description: S52 Mother


title: S26Bb

description: S26 Newborn


title: C37Bb

description: C37 Newborn


title: C63P

description: C63 Placenta


title: S57P

description: S57 Placenta


title: C61P

description: C61 Placenta


title: C12M

description: C12 Mother


title: C91Bb

description: C91 Newborn


title: C57P

description: C57 Placenta


title: S17M

description: S17 Mother


title: S25M

description: S25 Mother


title: C84P

description: C84 Placenta


title: C54Bb

description: C54 Newborn


title: C57Bb

description: C57 Newborn


title: C93Bb

description: C93 Newborn


title: S14P

description: S14 Placenta


title: S3Bb

description: S3 Newborn


title: S71Bb

description: S71 Newborn


title: S22Bb

description: S22 Newborn


title: S32P

description: S32 Placenta


title: C66Bb

description: C66 Newborn


title: S32M

description: S32 Mother


title: S15M

description: S15 Mother


title: S11M

description: S11 Mother


title: C7Bb

description: C7 Newborn


title: S20P

description: S20 Placenta


title: S36M

description: S36 Mother


title: S50P

description: S50 Placenta


title: C81Bb

description: C81 Newborn


title: S50M

description: S50 Mother


title: C10P

description: C10 Placenta


title: S18Bb

description: S18 Newborn


title: S3M

description: S3 Mother


title: S36P

description: S36 Placenta


title: C37M

description: C37 Mother


title: S37P

description: S37 Placenta


title: S12Bb

description: S12 Newborn


title: S62Bb

description: S62 Newborn


title: S35M

description: S35 Mother


title: C59Bb

description: C59 Newborn


title: S43Bb

description: S43 Newborn


title: C74M

description: C74 Mother


title: C67P

description: C67 Placenta


title: S69Bb

description: S69 Newborn


title: C23P

description: C23 Placenta


title: S76M

description: S76 Mother


title: S11Bb

description: S11 Newborn


title: C91M

description: C91 Mother


title: S48M

description: S48 Mother


title: C68Bb

description: C68 Newborn


title: C56M

description: C56 Mother


title: S25Bb

description: S25 Newborn


title: S58P

description: S58 Placenta


title: C85P

description: C85 Placenta


title: C10Bb

description: C10 Newborn


title: S75M

description: S75 Mother


title: C90M

description: C90 Mother


title: S48Bb

description: S48 Newborn


title: S34P

description: S34 Placenta


title: S75P

description: S75 Placenta


title: S29Bb

description: S29 Newborn


title: S77P

description: S77 Placenta


title: C5M

description: C5 Mother


title: S29P

description: S29 Placenta


title: C51Bb

description: C51 Newborn


title: S42Bb

description: S42 Newborn


title: C71M

description: C71 Mother


title: C3M

description: C3 Mother


title: S17Bb

description: S17 Newborn


title: S16M

description: S16 Mother


title: C46P

description: C46 Placenta


title: S13P

description: S13 Placenta


title: C46M

description: C46 Mother


title: S6Bb

description: S6 Newborn


title: C17M

description: C17 Mother


title: S65Bb

description: S65 Newborn


title: C3Bb

description: C3 Newborn


title: S8Bb

description: S8 Newborn


title: S16P

description: S16 Placenta


title: C3P

description: C3 Placenta


title: S77M

description: S77 Mother


title: S42P

description: S42 Placenta


title: S16Bb

description: S16 Newborn


title: S65P

description: S65 Placenta


title: S29M

description: S29 Mother


title: S6M

description: S6 Mother


title: C46Bb

description: C46 Newborn


title: E140-M

city: Beijing

first: Xiangxiang

last: Jiang

state: Beijing

address: 1 Beichen West Road, Chaoyang District

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Raw fastq files were processed with Cell Ranger 3.1.0 with default mapping arguments.
Reads were mapped to the Macaca_fascicularis_5.0 genome
The cellranger aggr command was executed to adjust the sequencing depth of different samples to the same level.
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: MF217404.tar.gz: raw counts and metadata
Supplementary_files_format_and_content: MF-filtered.tar: raw counts data filtered by cellranger

organism: Macaca fascicularis

source_name: placenta

extract_protocol:
Single cells were added to the 10x Chip channels. Captured cells were lysed and the released RNA was barcoded through reverse transcription in individual GEMs.
RNA libraries were prepared for sequencing using 10x Single Cell 3' Library & Gel Bead Kit v2  protocol

treatment_protocol: no treatment

tag: developmental stage

value: day 140


title: S13M

description: S13 Mother


title: C17Bb

description: C17 Newborn


title: S42M

description: S42 Mother


title: S13Bb

description: S13 Newborn


title: E140-S


title: S6P

description: S6 Placenta


title: E90-M

value: day 90


title: C17P

description: C17 Placenta


title: E84-S

value: day 84


title: E84-M


title: E35-V1

value: day 35


title: E45-M

value: day 45


title: E62-M

value: day 62


title: E62-S


title: E29-D1

source_name: decidua

value: day 29


title: E45-S


title: E26-D1

value: day 26


title: E23-V1

value: day 23


title: S65M

description: S65 Mother


title: E35-V2


title: E20-V1

value: day 20


title: HGNET CIC fusion-positive case 11

city: Heidelberg

first: Daniel

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

institute: University Hospital Heidelberg, Intitute of Pathology

description:
HGNET CIC fusion-positive
SAMPLE_11

hyb_protocol: Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta
Processed data file includes: Average Beta

label: Cy3, Cy5

source_name: HGNET CIC fusion-positive

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

treatment_protocol: An automated extraction was done with a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

value: pediatric CNS tumor

tag: tissue preparation

value: Frozen


title: HGNET CIC fusion-positive case 1

description:
HGNET CIC fusion-positive
SAMPLE_1

value: FFPE


title: HGNET CIC fusion-positive case 7

description:
HGNET CIC fusion-positive
SAMPLE_7


title: E35-D2


title: E35-D1


title: Screen_Hygro50_sequencing

city: Paris

first: Pierre-Antoine

last: Defossez

address: 35 rue Hélène Brion

country: France

institute: Epigenetics and Cell Fate Unit

data_processing:
RNA-seq data: Trimmomatic (Bolger et al., 2014) (v0.39) and parameters: ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36.
Read pairs that survived trimming were aligned to the mouse reference genome (build mm10) using STAR (Dobin et al., 2013) (v2.7.5c) and default single-pass parameters.
PCR duplicate read alignments were flagged using Picard-tools (2019) MarkDuplicates (v2.23.4).
Uniquely aligned, non-PCR-duplicate reads were kept for downstream analysis using Samtools (Li et al., 2009) view (v1.10) and parameters: -q 255 -F 1540.
Bigwig files were generated using deeptools (Ramírez et al., 2016) bamCoverage (v3.3.0) and visualized in IGV (Thorvaldsdottir et al., 2013) (v2.8.9).
CRISPR Screen : The sgRNA distribution and enrichment at different time points were analyzed with the MAGeCK workflow (Doench et al, 2016)
ChIP-seq data : FASTQ reads were trimmed using Trimmomatic (v0.39) and parameters:ILLUMINACLIP:illumina_adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36. Trimmed reads were aligned using Bowtie2 (v2.4.1) in --local mode. Following alignment, Picard (v2.23.4) CleanSam, SamFormatConverter, SortSam and Markduplicates were used to generate a duplicate-marked bam file. The resulting bam files were converted to bigwig using deeptools (v3.3.0) Bamcoverage and options –ignoreDuplicates –normalizeUsing CPM –minMappingQuality 10 –ignoreForNormalization chrX chrY chrM.
WGBS data : As described in Miura et al 2019 NAR, the sequenced reads were mapped with BMap and summarized with an in-house pipeline, with custom scripts archived using GitHub (https://github.com/FumihitoMiura/Project-2).
Assembly: mm10
Supplementary files format and content: All processed files are in bigWig format. RNA-seq: genomic coverage counts, WGBS: percent methylation over CpGs covered by at least 5 reads, ChIP-seq/CUT&RUN-seq: signal coverage
Library strategy: CRISPR screen

extract_protocol:
Genomic DNA was extracted from the cells with QIAmp DNA Mini kit (Qiagen), according to the manufacturer’s instructions. Genomic regions of interest were amplified by PCR.
Libraries were sequenced on an Illumina HiSeq 1500 in single end (SE) 100 bp output mode.

tag: cell line

value: mouse embryonic stem cells

value: WT


title: Screen_HygroSca-_sequencing

tag: cell type


title: Screen_HygroSca+_sequencing

tag: genotype


title: Emx1-cre(+/-)::MDMD::Axin2(+/+) cell et E11.5_rep12

first: Zhenhua

state: China

address: West Beichen Road, Olympic Village, Beijing

department: State Key Laboratory of Molecular Development Biology

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

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR(2.7.0a) with with default parameter settings.
Fastq reads were filtered using Trimmomatic to discard low-quality reads and trim poor-quality bases.The remaining clean reads were aligned to GRCm38 (mm10) genome. STAR with default parameter settings was used for alignment to generate  BAM files. Gene-counting tools, featureCounts were used to generate TPM(transcripts per million) gene counts per cell/sample.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with  gene TPM for every gene and every sample

source_name: Neural progenitor cells

extract_protocol:
Emx1-CreERT2::MADM-11::Axin2LacZ/+ mice were breed and medial cortex were dissociated at E11.5.Axin2+/+ and Axin2-/- cells were separated for single cell rna-seq.Dosal diencephalon and ventral diencephalon were collected for Bulk RNA-seq at E10.5 wild type mice.
RNA libraries were prepared for sequencing using standard Illumina protocols and smart-seq2 protocals


title: Screen_Puro+_sequencing


title: S77Bb

description: S77 Newborn

value: S


title: E26-V1


title: Emx1-cre(+/-)::MDMD::Axin2(+/+) cell et E11.5_rep11


title: E90-S


title: E23-V2


title: Emx1-cre(+/-)::MDMD::Axin2(+/+) cell et E11.5_rep9


title: E29-V1


title: E26-V2


title: Emx1-cre(+/-)::MDMD::Axin2(+/+) cell et E11.5_rep8


title: Emx1-cre(+/-)::MDMD::Axin2(+/+) cell et E11.5_rep10


title: Emx1-cre(+/-)::MDMD::Axin2(+/+) cell et E11.5_rep7


title: E23-D1


title: Emx1-cre(+/-)::MDMD::Axin2(+/+) cell et E11.5_rep6


title: Emx1-cre(+/-)::MDMD::Axin2(+/+) cell et E11.5_rep3


title: Emx1-cre(+/-)::MDMD::Axin2(+/+) cell et E11.5_rep2


title: Emx1-cre(+/-)::MDMD::Axin2(-/-) cell et E11.5_rep11


title: Screen_Hygro125_sequencing


title: Emx1-cre(+/-)::MDMD::Axin2(-/-) cell et E11.5_rep10


title: Screen_Library_sequencing


title: Emx1-cre(+/-)::MDMD::Axin2(-/-) cell et E11.5_rep1


title: Emx1-cre(+/-)::MDMD::Axin2(+/+) cell et E11.5_rep5


title: Ventral diencephalon_at_E10.5_rep1

value: Ventral diencephalon


title: Ventral diencephalon_at_E10.5_rep2


title: Emx1-cre(+/-)::MDMD::Axin2(+/+) cell et E11.5_rep1


title: Emx1-cre(+/-)::MDMD::Axin2(-/-) cell et E11.5_rep13


title: Emx1-cre(+/-)::MDMD::Axin2(-/-) cell et E11.5_rep9


title: Emx1-cre(+/-)::MDMD::Axin2(-/-) cell et E11.5_rep12


title: Emx1-cre(+/-)::MDMD::Axin2(-/-) cell et E11.5_rep8


title: Emx1-cre(+/-)::MDMD::Axin2(-/-) cell et E11.5_rep6


title: Dosal diencephalon_at_E10.5_rep2

value: Dosal diencephalon


title: Emx1-cre(+/-)::MDMD::Axin2(-/-) cell et E11.5_rep5


title: Emx1-cre(+/-)::MDMD::Axin2(-/-) cell et E11.5_rep4


title: Emx1-cre(+/-)::MDMD::Axin2(-/-) cell et E11.5_rep3


title: Zbtb14_RNA_clone2

data_processing:
RNA-seq data: Trimmomatic (Bolger et al., 2014) (v0.39) and parameters: ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36.
Read pairs that survived trimming were aligned to the mouse reference genome (build mm10) using STAR (Dobin et al., 2013) (v2.7.5c) and default single-pass parameters.
PCR duplicate read alignments were flagged using Picard-tools (2019) MarkDuplicates (v2.23.4).
Uniquely aligned, non-PCR-duplicate reads were kept for downstream analysis using Samtools (Li et al., 2009) view (v1.10) and parameters: -q 255 -F 1540.
Bigwig files were generated using deeptools (Ramírez et al., 2016) bamCoverage (v3.3.0) and visualized in IGV (Thorvaldsdottir et al., 2013) (v2.8.9).
CRISPR Screen : The sgRNA distribution and enrichment at different time points were analyzed with the MAGeCK workflow (Doench et al, 2016)
ChIP-seq data : FASTQ reads were trimmed using Trimmomatic (v0.39) and parameters:ILLUMINACLIP:illumina_adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36. Trimmed reads were aligned using Bowtie2 (v2.4.1) in --local mode. Following alignment, Picard (v2.23.4) CleanSam, SamFormatConverter, SortSam and Markduplicates were used to generate a duplicate-marked bam file. The resulting bam files were converted to bigwig using deeptools (v3.3.0) Bamcoverage and options –ignoreDuplicates –normalizeUsing CPM –minMappingQuality 10 –ignoreForNormalization chrX chrY chrM.
WGBS data : As described in Miura et al 2019 NAR, the sequenced reads were mapped with BMap and summarized with an in-house pipeline, with custom scripts archived using GitHub (https://github.com/FumihitoMiura/Project-2).
Assembly: mm10
Supplementary files format and content: All processed files are in bigWig format. RNA-seq: genomic coverage counts, WGBS: percent methylation over CpGs covered by at least 5 reads, ChIP-seq/CUT&RUN-seq: signal coverage

extract_protocol:
Total RNA was extracted from the cells with RNEasy Plus Mini kit (Qiagen), according to the manufacturer’s instructions.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNALibrary Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: Zbtb14 KO


title: Spop_RNA_clone3

value: Spop KO


title: Zbtb14_RNA_clone3


title: Emx1-cre(+/-)::MDMD::Axin2(-/-) cell et E11.5_rep2


title: Dosal diencephalon_at_E10.5_rep3


title: Dosal diencephalon_at_E10.5_rep1


title: Mcm3ap_RNA_clone3

value: Mcm3ap KO


title: Spop_RNA_clone1


title: Ventral diencephalon_at_E10.5_rep3


title: Mcm3ap_RNA_clone2


title: Emx1-cre(+/-)::MDMD::Axin2(+/+) cell et E11.5_rep4