title: Single fibroblast 5H8S3, PDL = 56


title: Single fibroblast 5G2S3, PDL = 56

status: Public on Jun 05 2025

type: SRA

city: Grand Rapids

first: Peter

middle: W

last: Laird

state: MI

address: 333 Bostwick Ave NE

department: Epigenetics

country: USA

institute: Van Andel Institute

library_source: genomic

data_processing:
Supplementary files format and content: CSV format with columns chr (chromosome), pos (1-based position of C on reference strand), strand (aligned strand), allele (assigned local microhaplotype), beta (beta value), coverage (number of reads covering C), phase_set (local microhaplotype ID), which_all_has_cg (which allele has a CpG, if this CpG is created or destroyed by a SNP used to distinguish between alleles), twosnp_cpg (is this CpG composed of two SNPs which are used to distinguish between alleles?)
Supplementary files format and content: BED format (no-header TSV, with columns chr [chromosome], start [0-based bin start], end [bin end], and n_reads [number of aligned reads in bin])
Supplementary files format and content: Biscuit BED (no-header TSV with columns chr [chromosome], start [0-based location of C], end [1-based location of G], beta, coverage, and support)
Adapter trimming with Cutadapt; alignment with Biscuit; deduplication with Dupsifter; quality control and filtering with Biscuit and Samtools; methylation calling with Biscuit; allele-resolved methylation analysis with custom tools (see publication methods).
Assembly: hg38

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Lysis in sodium bisulfite
sc-DEEP-mC

tag: cell line

tag: treatment


title: Single fibroblast 5G9S3, PDL = 56


title: Single fibroblast 5G10S3, PDL = 56


title: Single fibroblast 5G1S3, PDL = 56


title: Single fibroblast 5G4S3, PDL = 56


title: Single fibroblast 5G11S3, PDL = 56


title: Single fibroblast 5G5S3, PDL = 56


title: Single fibroblast 5G3S3, PDL = 56


title: Single fibroblast 5F4S3, PDL = 56


title: Single fibroblast 5F3S3, PDL = 56


title: Single fibroblast 5H5S3, PDL = 56


title: Single fibroblast 5G12S3, PDL = 56


title: Single fibroblast 5F6S3, PDL = 56


title: Single fibroblast 5F2S3, PDL = 56


title: Single fibroblast 5F10S3, PDL = 56


title: Single fibroblast 5F1S3, PDL = 56


title: Single fibroblast 5H4S3, PDL = 56


title: Single fibroblast 5F9S3, PDL = 56


title: Single fibroblast 5F7S3, PDL = 56


title: Single fibroblast 5E6S3, PDL = 56


title: Single fibroblast 5F5S3, PDL = 56


title: Single fibroblast 5E4S3, PDL = 56


title: Single fibroblast 5F8S3, PDL = 56


title: Single fibroblast 5E3S3, PDL = 56


title: Single fibroblast 5E2S3, PDL = 56


title: Single fibroblast 5E9S3, PDL = 56


title: Single fibroblast 5E10S3, PDL = 56


title: Single fibroblast 5E7S3, PDL = 56


title: Single fibroblast 5E1S3, PDL = 56


title: Single fibroblast 5E8S3, PDL = 56


title: Single fibroblast 5E5S3, PDL = 56


title: Single fibroblast 5D3S3, PDL = 56


title: Single fibroblast 5D4S3, PDL = 56


title: Single fibroblast 5D5S3, PDL = 56


title: Single fibroblast 5D9S3, PDL = 56


title: Single fibroblast 5F11S3, PDL = 56


title: Single fibroblast 5D8S3, PDL = 56


title: Single fibroblast 5D1S3, PDL = 56


title: Single fibroblast 5D12S3, PDL = 56


title: Single fibroblast 5D6S3, PDL = 56


title: Single fibroblast 5D7S3, PDL = 56


title: Single fibroblast 5C8S3, PDL = 56


title: Single fibroblast 5C6S3, PDL = 56


title: Single fibroblast 5D11S3, PDL = 56


title: Single fibroblast 5C9S3, PDL = 56


title: Single fibroblast 5C3S3, PDL = 56


title: Single fibroblast 5C7S3, PDL = 56


title: Single fibroblast 5C4S3, PDL = 56


title: Single fibroblast 5C10S3, PDL = 56


title: Single fibroblast 5E12S3, PDL = 56


title: Single fibroblast 5C1S3, PDL = 56


title: Single fibroblast 5C12S3, PDL = 56


title: Single fibroblast 5C2S3, PDL = 56


title: Single fibroblast 5B4S3, PDL = 56


title: Single fibroblast 5B9S3, PDL = 56


title: Single fibroblast 5B8S3, PDL = 56


title: Single fibroblast 5B6S3, PDL = 56


title: Single fibroblast 5C11S3, PDL = 56


title: Single fibroblast 5B7S3, PDL = 56


title: Single fibroblast 5D10S3, PDL = 56


title: Single fibroblast 5B2S3, PDL = 56


title: Single fibroblast 5B11S3, PDL = 56


title: Single fibroblast 5B10S3, PDL = 56


title: Single fibroblast 5A9S3, PDL = 56


title: Single fibroblast 5B3S3, PDL = 56


title: Single fibroblast 5B1S3, PDL = 56


title: Single fibroblast 5B12S3, PDL = 56


title: Single fibroblast 5A7S3, PDL = 56


title: Single fibroblast 5C5S3, PDL = 56


title: Single fibroblast 5A6S3, PDL = 56


title: Single fibroblast 5A5S3, PDL = 56


title: Single fibroblast 5A8S3, PDL = 56


title: Single fibroblast 5A3S3, PDL = 56


title: Single fibroblast 5A4S3, PDL = 56


title: Single fibroblast 5A12S3, PDL = 56


title: Single fibroblast 5A11S3, PDL = 56


title: Single fibroblast 5A10S3, PDL = 56


title: Single fibroblast 5A1S3, PDL = 56


title: Single fibroblast 5G8S2, PDL = 39


title: Single fibroblast 5G10S2, PDL = 39


title: Single fibroblast 5G12S2, PDL = 39


title: Single fibroblast 5F2S2, PDL = 39


title: Single fibroblast 5F5S2, PDL = 39


title: Single fibroblast 5D7S2, PDL = 39


title: Single fibroblast 5E7S2, PDL = 39


title: Single fibroblast 5D12S2, PDL = 39


title: Single fibroblast 5C7S2, PDL = 39


title: Single fibroblast 5C6S2, PDL = 39


title: Single fibroblast 5C11S2, PDL = 39


title: Single fibroblast 5C10S2, PDL = 39


title: Single fibroblast 5A6S2, PDL = 39


title: Single fibroblast 5B8S2, PDL = 39


title: Single fibroblast 5B1S2, PDL = 39


title: Single fibroblast 5A12S2, PDL = 39


title: Single fibroblast 5C5S2, PDL = 39


title: Single fibroblast 5A3S2, PDL = 39


title: Single fibroblast 5D2S2, PDL = 39


title: Single fibroblast 5H7S1, PDL = 20


title: Single fibroblast 5H9S1, PDL = 20


title: Single fibroblast 5H8S1, PDL = 20


title: Single fibroblast 5H4S1, PDL = 20


title: Single fibroblast 5H5S1, PDL = 20


title: Single fibroblast 5G4S2, PDL = 39


title: Single fibroblast 5F9S2, PDL = 39


title: Single fibroblast 5H2S1, PDL = 20


title: Single fibroblast 5E12S2, PDL = 39


title: Single fibroblast 5H10S1, PDL = 20


title: Single fibroblast 5H12S1, PDL = 20


title: Single fibroblast 5H1S1, PDL = 20


title: Single fibroblast 5A2S3, PDL = 56


title: Single fibroblast 5G7S1, PDL = 20


title: Single fibroblast 5G6S1, PDL = 20


title: Single fibroblast 5H3S1, PDL = 20


title: Single fibroblast 5B6S2, PDL = 39


title: Single fibroblast 5G5S1, PDL = 20


title: Single fibroblast 5G3S1, PDL = 20


title: Single fibroblast 5G12S1, PDL = 20


title: Single fibroblast 5G1S1, PDL = 20


title: Single fibroblast 5G10S1, PDL = 20


title: Single fibroblast 5F5S1, PDL = 20


title: Single fibroblast 5F8S1, PDL = 20


title: Single fibroblast 5F9S1, PDL = 20


title: Single fibroblast 5F4S1, PDL = 20


title: Single fibroblast 5F6S1, PDL = 20


title: Single fibroblast 5F11S1, PDL = 20


title: Single fibroblast 5F10S1, PDL = 20


title: Single fibroblast 5F1S1, PDL = 20


title: Single fibroblast 5F2S1, PDL = 20


title: Single fibroblast 5E6S1, PDL = 20


title: Single fibroblast 5E9S1, PDL = 20


title: Single fibroblast 5E8S1, PDL = 20


title: Single fibroblast 5E3S1, PDL = 20


title: Single fibroblast 5E2S1, PDL = 20


title: Single fibroblast 5E12S1, PDL = 20


title: Single fibroblast 5G9S1, PDL = 20


title: Single fibroblast 5E7S1, PDL = 20


title: Single fibroblast 5E1S1, PDL = 20


title: Single fibroblast 5G4S1, PDL = 20


title: Single fibroblast 5G11S1, PDL = 20


title: Single fibroblast 5F7S1, PDL = 20


title: Single fibroblast 5D8S1, PDL = 20


title: Single fibroblast 5D5S1, PDL = 20


title: Single fibroblast 5D6S1, PDL = 20


title: Single fibroblast 5D3S1, PDL = 20


title: Single fibroblast 5E4S1, PDL = 20


title: Single fibroblast 5D2S1, PDL = 20


title: Single fibroblast 5D10S1, PDL = 20


title: Single fibroblast 5C9S1, PDL = 20


title: Single fibroblast 5C8S1, PDL = 20


title: Single fibroblast 5C7S1, PDL = 20


title: Single fibroblast 5C6S1, PDL = 20


title: Single fibroblast 5C5S1, PDL = 20


title: Single fibroblast 5E10S1, PDL = 20


title: Single fibroblast 5C3S1, PDL = 20


title: Single fibroblast 5C4S1, PDL = 20


title: Single fibroblast 5E11S1, PDL = 20


title: Single fibroblast 5D9S1, PDL = 20


title: Single fibroblast 5C12S1, PDL = 20


title: Single fibroblast 5C2S1, PDL = 20


title: Single fibroblast 5C10S1, PDL = 20


title: Single fibroblast 5C1S1, PDL = 20


title: Single fibroblast 5B7S1, PDL = 20


title: Single fibroblast 5B9S1, PDL = 20


title: Single fibroblast 5B8S1, PDL = 20


title: Single fibroblast 5B5S1, PDL = 20


title: Single fibroblast 5B4S1, PDL = 20


title: Single fibroblast 5D7S1, PDL = 20


title: Single fibroblast 5B11S1, PDL = 20


title: Single fibroblast 5D4S1, PDL = 20


title: Single fibroblast 5D1S1, PDL = 20


title: Single fibroblast 5B10S1, PDL = 20


title: Single fibroblast 5B1S1, PDL = 20


title: Single fibroblast 5A8S1, PDL = 20


title: Single fibroblast 5A7S1, PDL = 20


title: Single fibroblast 5A5S1, PDL = 20


title: Single fibroblast 5A2S1, PDL = 20


title: Single fibroblast 5A10S1, PDL = 20


title: Single fibroblast 5A4S1, PDL = 20


title: SK-N-BE(2)-C_G1_phase_rep3

city: Cambridge

first: William

last: Beckman

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Reads were trimmed using TrimGalore with a Phred score cut- off of 20 and then mapped to hg19 using Bowtie2.
MACS2 was used to call peaks and DiffBind (EdgeR) for identifying differential peaks with reads in peaks library size normalisation. Bigwigs were generated using deeptools bamCoverage and scaled according to these TMM scaling factors.
Assembly: hg19
Supplementary files format and content: BigWig

growth_protocol: Cells were cultured at 5% CO2 at 37ºC in DMEM/F12 with L-glutamine and 15mM HEPES, and further supplemented with 10% FBS and 1% Penicillin-Streptomycin

extract_protocol:
ATAC-seq was performed using the Omni-ATAC protocol as previously described
Libraries were prepared using NEBNext 2x MasterMix and pooled at equimolar ratios before sequencing

treatment_protocol: Live cells were then stained with 3ug/ml Hoechst 33342 for 1 hour, before being trypsinised and collected. Cells were centrifuged for 5 minutes at 600g before being resuspended in FACS buffer (PBS with 5mM EDTA; 25mM HEPES: 0.1% BSA) and filtered with a 45μm filter. 50,000 G1 or G2M cells were sorted into 500μl FACS buffer using a FACSariaIII based on UV 355 signal. For ATAC-seq of asynchronous parental SK-N-BE(2)C cells and ASCL1 knockout cells, 50,000 live cells from the total population were sorted using a FACSariaIII

tag: cell type

value: Neuroblastoma


title: SK-N-BE(2)-C_G2M_phase_rep2


title: Single fibroblast 5A9S1, PDL = 20


title: SK-N-BE(2)-C_G2M_phase_rep1


title: Single fibroblast 5C11S1, PDL = 20


title: Single fibroblast 5A12S1, PDL = 20


title: SK-N-BE(2)-C_G1_phase_rep1


title: SK-N-BE(2)-C_G1_phase_rep2


city: Berkeley

first: Sharon

last: Greenblum

state: CA

address: 1 Cyclotron Road

institute: DOE Joint Genome Institute

description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi712H01-ORGi5010-96P247

data_processing:
Fastq files were quality filtered and adapters were trimmed using BBTools v38.96 bbduk.sh62 with parameters k=21 mink=11 ktrim=r tbo tpe qtrim=r trimq=6 maq=10, and then aligned to the corresponding reference genome using bowtie2 v2.4.2 and parameters --no-mixed --no-discordant. Bam files from negative control wells were merged using the samtools v1.15.1 merge command, to generate a single background file for each 96-well plate. The MACS3 v3.0.0a6 callpeak command was used to generate narrowPeak files, using the merged background as the control, with the parameters --call-summits --keep-dup 1 and –gsize with the total fasta genome size. Bigwig files were generated using deeptools v3.5.2 bamCoverage with parameters --extendReads --binSize 1 --ignoreDuplicates --maxFragmentLength 600 --normalizeUsing RPGC, and --effectiveGenomeSize with the total fasta genome assembly size of each species.
Assembly: Oryza sativa Nipponbare: MSU via Phytozome v7.0
Supplementary files format and content: narrowPeak are tab-delimited extended bed format files that contain peak regions identified by MACS3, using the matched negative controls on each 96 well plate to dentify regions that were enriched for by each transcription factor. The identified peaks represent putative transcription factor binding sites.
Supplementary files format and content: bigwig files show the genome coverage of each DAP-seq library. They can be used to compare coverage between different libraries and to view peaks in a genome browser. Note that they should be compared to the matched negative control libraries from the same plate.
Library strategy: DAP-seq

organism: Oryza sativa

source_name: plant

growth_protocol: Various growth protocols and tissues were used for gDNA extraction depending on the plant species, however gDNA libraries were PCR amplified upstream of DAP-seq to remove condition/tissue-specific DNA modifications.

extract_protocol:
CTAB protocol for gDNA extraction
Genomic DNA fragment libraries were constructed with an average shearing size at 150 bp. Different species were labeled by unique Illumina i5 index adapters to enable multiplexing following the multiDAP method. Upstream of the DAP-seq assay, fragment libraries were amplified for 10 cycles to remove any DNA modifications. After performing the DAP-seq enrichment in 96-well plates with each well containing a single in vitro expressed transcription factor, the libraries were amplified with i7 index primers to attach a unique i7 adapter corresponding to each well.

tag: tissue

value: plant

tag: genotype

value: Nipponbare

tag: tf id

tag: multidap sample_id

tag: 96 well_plate_id


title: Single fibroblast 5A11S1, PDL = 20


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi712H12-ORGi5010-96P247


title: lung, M3

city: 银川市

first: 天松

last: 王

state: 宁夏回族自治区

address: 兴庆区大新镇胜利街1160号

country: China

institute: 宁夏医科大学

library_source: transcriptomic

data_processing:
Trimmomatic software was first used for adpter removing, and then low-quality bases and N-bases or low-quality reads were filtered out.
HISAT2 was used to align clean reads to the reference genome of the experimental species, and RSeQC suite was used to calculate the proportion of various alignment types and evaluate the alignment results.
Stringtie software was used to assemble the reads aligned to genes, and the Single Transcripts of each sample were fused into a Merged Transcripts.
The Merged Transcripts were compared with the known reference gene models by Cuffcompare software
After alignment of clean reads to the transcription template (mRNA+novel lncRNA+known lncRNA or mRNA+candidate lncRNA) by Bowtie2 software, eXpress software was used for transcript quantification to obtain FPKM values and counts of mRNA and lncRNA
Assembly: 200 bp or more apart from the existing annotation gene;  and not less than 180 bp in length.
Supplementary files format and content: tab delimited text files include count and FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: lung

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.1.3 ug of tota RNA was used for the construction of sequencing libraries
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions.

value: lung

tag: strain

tag: Sex

value: Female

value: Asthma model treatment 12weeks


title: Single fibroblast 5A6S1, PDL = 20


title: Single fibroblast 5B12S1, PDL = 20


title: SK-N-BE(2)-C_G2M_phase_rep3


title: Single fibroblast 5B3S1, PDL = 20


title: ASCL1_KO_SK-N-BE(2)-C_rep4


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi712A12-ORGi5010-96P247


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi712A01-ORGi5010-96P247


title: lung, M2

address: 兴庆区大新镇胜利街1160号


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi712H12-ORGi5010-96P364


title: ASCL1_KO_SK-N-BE(2)-C_rep3


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi712H01-ORGi5010-96P364


title: Single fibroblast 5A3S1, PDL = 20


title: lung, M1

address: 兴庆区大新镇胜利街1160号


title: lung, E3

address: 兴庆区大新镇胜利街1160号

value: Asthma model 12weeks


title: ASCL1_KO_SK-N-BE(2)-C_rep2


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi712A12-ORGi5010-96P364


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi712A01-ORGi5010-96P364


title: lung, E2

address: 兴庆区大新镇胜利街1160号


title: Parental_SK-N-BE(2)-C_rep4


title: lung, E1

address: 兴庆区大新镇胜利街1160号


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi710H01-ORGi5010-96P358


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi710H12-ORGi5010-96P358


title: Parental_SK-N-BE(2)-C_rep2


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi711H01-ORGi5010-96P361


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi711A01-ORGi5010-96P361


title: lung, N3

address: 兴庆区大新镇胜利街1160号

value: Normal 12weeks


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi710A12-ORGi5010-96P358


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi710G12-ORGi5010-96P358


title: lung, N2

address: 兴庆区大新镇胜利街1160号


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi711H12-ORGi5010-96P361


title: Parental_SK-N-BE(2)-C_rep3


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi709H12-ORGi5010-96P354


title: ASCL1_KO_SK-N-BE(2)-C_rep1


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi710A01-ORGi5010-96P358


title: SK-N-BE(2)-C_ASCL1_KO_7days_pb_rep5

data_processing:
Reads were trimmed and quality filtered using TrimGalore with a minimum phred score of 20 then aligned to hg19 using STAR with quantMode to obtain read counts
Assembly: hg19
Supplementary files format and content: txt file of raw counts for each sample

molecule: polyA RNA

extract_protocol:
Cells were lysed in situ using RLT buffer and RNA was purified using the RNeasy mini kit (Qiagen) as per manufacturer’s instructions
Poly-A selection was performed, and libraries were made using NEBNext Ultra II directional RNA kit

treatment_protocol: Cells were treated with 1μM palbociclib for the stated duration, or vehicle control (DMSO).

value: palbociclib

tag: time point


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi709H01-ORGi5010-96P354


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi712G12-ORGi5010-96P364


title: Parental_SK-N-BE(2)-C_rep1


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi709A01-ORGi5010-96P354


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi712H12-ORGi5010-96P220


title: SK-N-BE(2)-C_ASCL1_KO_7days_pb_rep4


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi712H01-ORGi5010-96P220


title: SK-N-BE(2)-C_ASCL1_KO_7days_pb_rep3


title: N1

address: 兴庆区大新镇胜利街1160号

library_source: other

data_processing:
Trimmomatic software was first used for adpter removing, and then low-quality bases and N-bases or low-quality reads were filtered out.
HISAT2 was used to align clean reads to the reference genome of the experimental species, and RSeQC suite was used to calculate the proportion of various alignment types and evaluate the alignment results.
Stringtie software was used to assemble the reads aligned to genes, and the Single Transcripts of each sample were fused into a Merged Transcripts.
The Merged Transcripts were compared with the known reference gene models by Cuffcompare software
After alignment of clean reads to the transcription template (mRNA+novel lncRNA+known lncRNA or mRNA+candidate lncRNA) by Bowtie2 software, eXpress software was used for transcript quantification to obtain FPKM values and counts of mRNA and lncRNA
Assembly: 200 bp or more apart from the existing annotation gene;   and not less than 180 bp in length.
Supplementary files format and content: tabdelimited text files include RPKM values for each Sample

molecule: other

source_name: Mouse lung tissue

value: Mouse lung tissue

value: N1:Normal 12weeks

value: C57BL/6 Female mouse


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi712A12-ORGi5010-96P220


title: A3

address: 兴庆区大新镇胜利街1160号

value: A3:Asthma model  treatment 12weeks

value: Asthma model  treatment 12weeks


description: Library name: Control_TF_DNA_O_sativa_Nipponbare_DAPi712A01-ORGi5010-96P220


title: SK-N-BE(2)-C_ASCL1_KO_7days_pb_rep2


description: Library name: AL2G28980.t1_O_sativa_Nipponbare_DAPi712H11-ORGi5010-96P247

tag: tf family

value: HOMEOBOX

tag: tf source_species


title: lung, N1

address: 兴庆区大新镇胜利街1160号


title: M1

address: 兴庆区大新镇胜利街1160号

value: M1:Asthma model 12weeks


title: A2

address: 兴庆区大新镇胜利街1160号

value: A2:Asthma model  treatment 12weeks


description: Library name: Carub.0002s1959.1_O_sativa_Nipponbare_DAPi712H10-ORGi5010-96P247

value: MYBRELATED


description: Library name: AT2G46270_O_sativa_Nipponbare_DAPi712H11-ORGi5010-96P220

value: plant

value: BZIP


description: Library name: AT2G47070_O_sativa_Nipponbare_DAPi712H10-ORGi5010-96P220

value: Nipponbare

value: SBP


title: SK-N-BE(2)-C_ASCL1_KO_24hr_pb_rep5

value: Neuroblastoma


title: SK-N-BE(2)-C_ASCL1_KO_7days_pb_rep1


description: Library name: AL1G24970.t1_O_sativa_Nipponbare_DAPi712H09-ORGi5010-96P364

value: RAV


title: SK-N-BE(2)-C_ASCL1_KO_24hr_pb_rep4


description: Library name: Carub.0005s0095.1_O_sativa_Nipponbare_DAPi712H08-ORGi5010-96P364

value: BBRBPC


description: Library name: AT5G17300_O_sativa_Nipponbare_DAPi712H08-ORGi5010-96P220


title: A1

address: 兴庆区大新镇胜利街1160号

value: A1:Asthma model  treatment 12weeks


title: SK-N-BE(2)-C_ASCL1_KO_24hr_pb_rep3

value: palbociclib


title: M1-1

address: 兴庆区大新镇胜利街1160号

value: Mouse lung tissue

value: M1-1:Asthma model 12weeks

value: Asthma model 12weeks


description: Library name: LOC_Os01g17260.2_O_sativa_Nipponbare_DAPi712H07-ORGi5010-96P247


title: M3

address: 兴庆区大新镇胜利街1160号

value: M3:Asthma model 12weeks

value: C57BL/6 Female mouse


title: M2

address: 兴庆区大新镇胜利街1160号

value: M2:Asthma model 12weeks


title: SK-N-BE(2)-C_ASCL1_KO_24hr_pb_rep2


description: Library name: XP_013634112.1_O_sativa_Nipponbare_DAPi712H08-ORGi5010-96P247


title: N3

address: 兴庆区大新镇胜利街1160号

value: N3:Normal 12weeks

value: Normal 12weeks


description: Library name: AT3G50410_O_sativa_Nipponbare_DAPi712H06-ORGi5010-96P220

value: plant


description: Library name: AT5G18560_O_sativa_Nipponbare_DAPi712H07-ORGi5010-96P220


title: N2

address: 兴庆区大新镇胜利街1160号

value: N2:Normal 12weeks


description: Library name: AL4G45550.t1_O_sativa_Nipponbare_DAPi712H06-ORGi5010-96P247

value: Nipponbare

value: BZIP


title: SK-N-BE(2)-C_ASCL1_KO_24hr_pb_rep1

value: Neuroblastoma


description: Library name: XP_013635977.1_O_sativa_Nipponbare_DAPi712H05-ORGi5010-96P364

value: SBP


title: SK-N-BE(2)-C_ASCL1_KO_control_rep5

value: control


description: Library name: Solyc08g078340.3.1_O_sativa_Nipponbare_DAPi712H09-ORGi5010-96P247

value: MYBRELATED


description: Library name: AT1G01060_O_sativa_Nipponbare_DAPi712H05-ORGi5010-96P220


description: Library name: LOC_Os10g28340.1_O_sativa_Nipponbare_DAPi712H04-ORGi5010-96P364

value: HSF


description: Library name: Solyc01g102340.3.1_O_sativa_Nipponbare_DAPi712H04-ORGi5010-96P247

value: MYB


title: SK-N-BE(2)-C_ASCL1_KO_control_rep4


title: N1-1

address: 兴庆区大新镇胜利街1160号

value: Mouse lung tissue

value: N1-1:Normal 12weeks


title: Cortical tissue, all 4 groups mixed, 6562

city: Columbus

first: Jonathan

last: Godbout

state: OH

address: 460 Medical Center Drive

institute: The Ohio State University

description:
Library name: 6562
Parse Biosciences V1

library_source: transcriptomic single cell

data_processing:
All data processing was done via Parse Biosciences pipeline (https://www.parsebiosciences.com) utilizing the Ohio Super Computer. Data was transferred via Globus from University of Michigan following sequencing to The Ohio Supercomputer. It was then uploaded, aligned, filtered, and concatenated via Parse Biosciences Pipeline . Matrices and raw data files were output and read into Seurat.
Matrices were downloaded and manually filtered in RStudio using Seurat (v4.1.1) Low-quality nuclei and doublets were filtered using Seurat in R. Cell-type identification was done using previously established markers: endothelial cells (Flt1), astrocytes (Slc1a3), oligodendrocytes (Mag), microglia (Csf1r), and neurons (Syt1). Differential gene expression was performed using the FindMarkers feature of Seurat with non-parametric Wilcoxon rank sum test. Pathway and master regulators analyses were performed with Ingenuity Pathway Analysis (IPA; Qiagen).
Assembly: Mm39
Supplementary files format and content: .MTX files, and CSV files of cell_metadata for all libraries.

molecule: nuclear RNA

source_name: cortex

extract_protocol:
Parse Biosciences Nuclei Extraction
Parse Biosciences Library Preparation V1

value: cortex

value: WT (bl/6)

value: Veh, PLX, Veh TBI, PLX5622 TBI


description: Library name: XP_013629448.1_O_sativa_Nipponbare_DAPi712H03-ORGi5010-96P247


description: Library name: AT2G30250_O_sativa_Nipponbare_DAPi712H03-ORGi5010-96P220

value: WRKY


title: SK-N-BE(2)-C_ASCL1_KO_control_rep3


description: Library name: AT2G22430_O_sativa_Nipponbare_DAPi712H02-ORGi5010-96P220

value: HOMEOBOX


title: SK-N-BE(2)-C_ASCL1_KO_control_rep2


title: Cortical tissue, all 4 groups mixed, 6142

description:
Library name: 6142
Parse Biosciences V1


title: SK-N-BE(2)-C_ASCL1_KO_control_rep1


title: E15_RNA_Lhx2cKO_2

city: Shanghai

first: XIAOSU

last: LI

state: Shanghai

address: 131 Dongan Road

institute: Fudan University

description:
Library name: sample37
RNA-seq of E15 Lhx2cKO cortex

data_processing:
Trim Galore was used to remove low-quality bases and adapter sequences from the FastQ files.
The cleaned reads were mapping to mouse genome mm39 using Subread
Bam files were counted at gene levels using FeatureCounts.
differential expression analysis using EdgeR
Assembly: mm39
Supplementary files format and content: text and expression matrix

source_name: cerebral cortex

extract_protocol:
fresh brain
RNA-seq libraries were constructed using Hieff NGS® Ultima Dual-mode RNA Library Prep Kit (YEASEN, Cat#12309), following the manufacturer’s instructions.

value: cerebral cortex


description: Library name: AT5G09410_O_sativa_Nipponbare_DAPi712G11-ORGi5010-96P220

value: plant

value: CAMTA


title: E15_RNA_Lhx2cKO_1

description:
Library name: sample36
RNA-seq of E15 Lhx2cKO cortex


title: SK-N-BE(2)-C_parental_7days_pb_rep5

value: parental

value: palbociclib


description: Library name: Solyc03g116890.3.1_O_sativa_Nipponbare_DAPi712G11-ORGi5010-96P247

value: Nipponbare


description: Library name: XP_013609718.1_O_sativa_Nipponbare_DAPi712G12-ORGi5010-96P247


description: Library name: XP_013589913.1_O_sativa_Nipponbare_DAPi712G10-ORGi5010-96P247


description: Library name: AT5G45300_O_sativa_Nipponbare_DAPi712G10-ORGi5010-96P220


title: SK-N-BE(2)-C_parental_7days_pb_rep4

value: Neuroblastoma


description: Library name: LOC_Os10g41200.1_O_sativa_Nipponbare_DAPi712G09-ORGi5010-96P247

value: MYBRELATED


description: Library name: AT1G72740_O_sativa_Nipponbare_DAPi712G09-ORGi5010-96P220


description: Library name: AT3G02940_O_sativa_Nipponbare_DAPi712H04-ORGi5010-96P220


title: E15_RNA_WT_1

description:
Library name: sample34
RNA-seq of E15 control cortex


description: Library name: Carub.0002s2128.1_O_sativa_Nipponbare_DAPi712G10-ORGi5010-96P364

value: RWPRK


title: SK-N-BE(2)-C_parental_7days_pb_rep3


description: Library name: XP_013599843.1_O_sativa_Nipponbare_DAPi712G08-ORGi5010-96P364

value: BBRBPC


description: Library name: AL4G38490.t1_O_sativa_Nipponbare_DAPi712G08-ORGi5010-96P247

value: BZIP


title: SK-N-BE(2)-C_parental_7days_pb_rep1


description: Library name: Carub.0003s1161.1.p_O_sativa_Nipponbare_DAPi712G07-ORGi5010-96P247


description: Library name: AT5G19790_O_sativa_Nipponbare_DAPi712G07-ORGi5010-96P220


description: Library name: AT2G01940_O_sativa_Nipponbare_DAPi712G08-ORGi5010-96P220


title: SK-N-BE(2)-C_parental_24hr_pb_rep5


description: Library name: AT5G02320_O_sativa_Nipponbare_DAPi712G06-ORGi5010-96P220

value: MYB


description: Library name: Solyc10g018560.2.1_O_sativa_Nipponbare_DAPi712G06-ORGi5010-96P364


description: Library name: AL4G46570.t1_O_sativa_Nipponbare_DAPi712G05-ORGi5010-96P364

value: SBP


title: E15_RNA_WT_2

description:
Library name: sample35
RNA-seq of E15 control cortex


description: Library name: AT1G69180_O_sativa_Nipponbare_DAPi712G05-ORGi5010-96P220


title: Pten deficient mice (Rosa26CreERT2:Ptenfl/fl), in vitro induced-germinal center B cells, biol rep3

city: Chuncheon

first: Seongwon

last: Pak

address: 12-1, Bonguisan-gil 22beon-gil, Chuncheon-si, Gangwon-do, Republic of Korea

department: Biomedical science

country: South Korea

institute: Hallym university

description: Library name: Pt_GCB_3

data_processing:
Reads with Low quality and adapters were trimmed using Trimmomatic0.38.
Paired-end reads were equally controlled by Q30.
The percentages of Q30 bases were higher than 95%.
Trimmed reads were mapped to Mus Musculus mm10 reference genome by HISAT2 and assembled using StringTie.
Assembly: mm10
Supplementary files format and content: xlsx file of Read counts, FPKM, and TPM value for each sample

source_name: germinal center B cells

growth_protocol: CD40LB cells/B cells co-cultivation was maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin, 5 μg/ml of gentamycin in the cell incubator

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following manufacturer's protocols.

treatment_protocol: Germinal center B cells differentiation was induced by treatment of IL-4(from 0 day to 4 day) with CD40LB cells co-culture.

value: germinal center B cells

value: Cre positive; ptenfl/fl

value: 2nM IL-4


title: Pten/Rictor deficient mice (Rosa26CreERT2:Ptenfl/fl,Rictorfl/fl), in vitro induced-germinal center B cells, biol rep3

description: Library name: PtRc_GCB_3

value: Cre positive; ptenfl/fl; rictorfl/fl


title: Pten deficient mice (Rosa26CreERT2:Ptenfl/fl), in vitro induced-germinal center B cells, biol rep2

description: Library name: Pt_GCB_2


title: Pten/Rictor deficient mice (Rosa26CreERT2:Ptenfl/fl,Rictorfl/fl), in vitro induced-germinal center B cells, biol rep1

description: Library name: PtRc_GCB_1


title: Pten/Rictor deficient mice (Rosa26CreERT2:Ptenfl/fl,Rictorfl/fl), in vitro induced-germinal center B cells, biol rep2

description: Library name: PtRc_GCB_2


description: Library name: LOC_Os01g18240.1_O_sativa_Nipponbare_DAPi712G04-ORGi5010-96P247


title: SK-N-BE(2)-C_parental_24hr_pb_rep3


title: Pten deficient mice (Rosa26CreERT2:Ptenfl/fl), in vitro induced-germinal center B cells, biol rep1

description: Library name: Pt_GCB_1


description: Library name: AT3G50060_O_sativa_Nipponbare_DAPi712G02-ORGi5010-96P220


title: Control mice (Rosa26CreERT2), in vitro induced-germinal center B cells, biol rep3

description: Library name: Con_GCB_3

value: Cre positive


description: Library name: Carub.0005s0004.1_O_sativa_Nipponbare_DAPi712G01-ORGi5010-96P364

value: plant


title: SK-N-BE(2)-C_parental_24hr_pb_rep2


title: SK-N-BE(2)-C_parental_24hr_pb_rep1


title: SK-N-BE(2)-C_parental_7days_pb_rep2


description: Library name: LOC_Os09g25060.1_O_sativa_Nipponbare_DAPi712F11-ORGi5010-96P247

value: WRKY


description: Library name: AT1G18330_O_sativa_Nipponbare_DAPi712G01-ORGi5010-96P220


title: Control mice (Rosa26CreERT2), in vitro induced-germinal center B cells, biol rep2

description: Library name: Con_GCB_2


title: Control mice (Rosa26CreERT2), in vitro induced-germinal center B cells, biol rep1

description: Library name: Con_GCB_1


description: Library name: AT1G76880_O_sativa_Nipponbare_DAPi712F11-ORGi5010-96P220

value: TRIHELIX


title: SK-N-BE(2)-C_parental_control_rep5

value: parental

value: control


title: SK-N-BE(2)-C_parental_control_rep4

value: Neuroblastoma


title: SK-N-BE(2)-C_parental_24hr_pb_rep4

value: palbociclib


title: Control mice (Rosa26CreERT2), Naïve B cells, biol rep3

description: Library name: NaïveB_3

source_name: CD43 negative splenic cells

value: CD43 negative splenic cells


description: Library name: XP_013591813.1_O_sativa_Nipponbare_DAPi712F10-ORGi5010-96P364

value: Nipponbare

value: RWPRK


description: Library name: AT2G45480_O_sativa_Nipponbare_DAPi712F09-ORGi5010-96P220

value: GRF


description: Library name: AT1G80840_O_sativa_Nipponbare_DAPi712G03-ORGi5010-96P220


title: SK-N-BE(2)-C_parental_control_rep1


title: Control mice (Rosa26CreERT2), Naïve B cells, biol rep2

description: Library name: NaiveB_2


description: Library name: AL2G32420.t2_O_sativa_Nipponbare_DAPi712F10-ORGi5010-96P247

value: MYBRELATED


description: Library name: AT1G46768_O_sativa_Nipponbare_DAPi712G04-ORGi5010-96P220


title: SK-N-BE(2)-C_parental_control_rep3


description: Library name: AT4G14770_O_sativa_Nipponbare_DAPi712F10-ORGi5010-96P220

value: CPP


title: Control mice (Rosa26CreERT2), Naïve B cells, biol rep1

description: Library name: NaiveB_1


description: Library name: AL5G11070.t1_O_sativa_Nipponbare_DAPi712F08-ORGi5010-96P364

value: BBRBPC


title: SK-N-BE(2)-C_parental_control_rep2


description: Library name: AT2G02820_O_sativa_Nipponbare_DAPi712F08-ORGi5010-96P220

value: MYB


title: SK-N-BE(2)-C Input

data_processing:
Adapter sequences were then trimmed using fastp using default parameters and reads mapped to the hg19 genome using Bowtie2. Narrow peaks were called using MACS2 with the DMSO input sample as the control and peaks with an enrichment score of less than 4 were removed.
The input bigwig was generated using Deeptools bamCoverage with CPM normalisation. Sample bigwigs were generated using bamCoverage and scaled using DESeq2 reads in peak library size scaling factors.
Assembly: hg19
Supplementary files format and content: BigWig

growth_protocol: SK-N-BE(2)-C cells were cultured at 5% CO2 at 37ºC in DMEM/F12 with L-glutamine and 15mM HEPES, and further supplemented with 10% FBS and 1% Penicillin-Streptomycin

extract_protocol:
Cells were trypisinised and fixed in 1% formaldehyde for 10 minutes before quenching with 125mM glycine. Cells were rinsed with cold PBS plus protease inhibitor and lysed in 1ml of cold lysis buffer 1 (50mM HEPES-KOH; 140mM NaCl; 1mM EDTA; 10% glycerol; 0.5% Igepal CA-630; 0.25% triton X- 100) supplemented with cOmplete protease inhibitor then rotated at 4ºC for 10 minutes before being centrifuged at 2000g for 5 minutes at 4ºC. Pelleted nuclei were then resuspended in 1ml of cold lysis buffer 2 (10mM Tris-HCl; 200mM NaCl; 1mM EDTA; 0.5mM EGTA) supplemented with cOmplete protease inhibitor then rotated at 4ºC for 10 minutes before again centrifuging at 2000g for 5 minutes at 4ºC. Pelleted nuclei were then resuspended and lysed in 300μl of cold lysis buffer 3 (10mM Tris-HCl; 100mM NaCl; 1mM EDTA; 0.5mM EGTA; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine) supplemented with cOmplete protease inhibitor before being sonicated for 6 cycles in a Bioruptor 300 sonicator. 30μl of 10% Triton X-100 was then added to the lysate, and histone H2B and total mRNA added to final concentrations of 20ug/ml and 1ug/ml, respectively (acting as carrier). Lysate was centrifuged at 21000g for 10 minutes then supernatant was divided into 30μl for input, and 300μl for ASCL1 immunoprecipitation reaction.
Replicate input samples for vehicle treated cells were pooled at an equimolar ratio and all sample libraries were prepared using the NEBNext Ultra II library prep kit. Libraries were then pooled and sequenced paired end to 150bp on a NovaSeq 6000

treatment_protocol: Thymidine treated cells were exposed to 4mM thymidine for 24 hours, followed by a 12 hour release and a subsequent 24 hours of 4mM thymidine block. Palbociclib treated cells were exposed to 500nM palbociclib for 24 hours. Drugs were then washed out for 45 minutes prior to collection for ChIP-seq

value: Vehicle (DMSO)


description: Library name: Carub.0008s0039.1_O_sativa_Nipponbare_DAPi712F09-ORGi5010-96P247


description: Library name: XP_013586407.1_O_sativa_Nipponbare_DAPi712F07-ORGi5010-96P247

value: BZIP


title: SK-N-BE(2)-C Thymidine rep3

value: Thymidine


title: SK-N-BE(2)-C Thymidine rep2


description: Library name: AT5G52830_O_sativa_Nipponbare_DAPi712F07-ORGi5010-96P220

value: plant

value: WRKY


description: Library name: LOC_Os10g40810.1_O_sativa_Nipponbare_DAPi712F06-ORGi5010-96P364


description: Library name: AT2G45420_O_sativa_Nipponbare_DAPi712F06-ORGi5010-96P220


description: Library name: AT2G01060_O_sativa_Nipponbare_DAPi712F05-ORGi5010-96P220


description: Library name: AT1G33240_O_sativa_Nipponbare_DAPi712F03-ORGi5010-96P220

value: TRIHELIX


description: Library name: AT4G31800_O_sativa_Nipponbare_DAPi712F02-ORGi5010-96P220


title: Defeat3_good

city: Hangzhou

last: Liu

address: 866 Yuhangtang Road

institute: Zhejiang University

description: Library name: Defeat3

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Reads mapping to the reference genome: The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence (GRCm38). Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 2.0.4 tools soft were used to map with reference genome.
Novel transcripts Prediction: The StringTie v2.2.1 Reference Annotation Based Transcript (RABT) assembly method was used to construct and identify both known and novel transcripts from Hisat2 alignment results. The ASprofle software obtained the alternative splicing types and corresponding expression levels existing in each sample.
Gene functional annotation: Gene function was annotated using the DIAMOND 2.0.15. InterProScan 5.34-73.0 was used to analyze GO Orhology of new genes.
Quantification of gene expression levels: Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped. The formula is shown as follow: FPKM = {cDNA Fragments \over {Mapped Fragments(Millions) * Transcript Length(kb)}}
Differential expression analysis: For the samples with biological replicates: Differential expression analysis of two conditions/groups was performed using the DESeq2 1.30.1. DESeq2  provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value < 0.05 & Fold Change≥1.2 found by DESeq2 were assigned as differentially expressed.
GO enrichment analysis: Gene Ontology (GO) enrichment analysis of the differentially expressed genes (DEGs) was implemented by the clusterProfiler 4.4.4 packages based Wallenius non-central hyper-geometric distribution (Young et al, 2010),which can adjust for gene length bias in DEGs.
Assembly: GRCm38
Supplementary files format and content: tab-delimited txt file includes FPKM values for each Sample

source_name: brain

extract_protocol:
RNA was harvested according to the instruction manual of the TRlzol Reagent (Catalog Numbers 15596026 and 15596018). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: brain


title: Control2_good

description: Library name: Control2


title: Defeat2_good

description: Library name: Defeat2


title: Defeat1_good

description: Library name: Defeat1


title: Control3_good

description: Library name: Control3


title: SK-N-BE(2)-C Palbociclib rep3

value: Neuroblastoma

value: Palbociclib


title: Control1_good

description: Library name: Control1


description: Library name: Solyc04g078640.3.1_O_sativa_Nipponbare_DAPi712F01-ORGi5010-96P247


description: Library name: AT4G25480_O_sativa_Nipponbare_DAPi712F04-ORGi5010-96P220


title: SK-N-BE(2)-C Thymidine rep1


description: Library name: AT5G47390_O_sativa_Nipponbare_DAPi712F01-ORGi5010-96P220


description: Library name: Solyc08g079120.3.1_O_sativa_Nipponbare_DAPi712F03-ORGi5010-96P247

value: NAC


title: SK-N-BE(2)-C Palbociclib rep2


title: Chemerin knockout mouse placenta at embryonic day 18.5_smaple4

city: Shenzhen

first: Chen

last: Huang

state: Guangdong

address: 1068 Xueyuan Avenue, Shenzhen University Town

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

description: Library name: R21123295

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adaptor sequenc/low-quality sequence using CLC genomic benchwork (parameter- Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion const: 3 lengthe fration:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: placenta

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen). 1.3μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq library Prep Kit following manufactures's protocols.

value: placenta

value: chemerin knockout


title: SK-N-BE(2)-C Palbociclib rep1


description: Library name: LOC_Os08g44050.1_O_sativa_Nipponbare_DAPi712F02-ORGi5010-96P364

value: Nipponbare


description: Library name: XP_013620714.1_O_sativa_Nipponbare_DAPi712F01-ORGi5010-96P364


title: Chemerin knockout mouse placenta at embryonic day 18.5_sample3

description: Library name: R21123296


description: Library name: AT1G52880_O_sativa_Nipponbare_DAPi712E12-ORGi5010-96P220


description: Library name: Solyc01g091420.2.1_O_sativa_Nipponbare_DAPi712F05-ORGi5010-96P364


description: Library name: Carub.0002s2670.1_O_sativa_Nipponbare_DAPi712E11-ORGi5010-96P247


title: Chemerin knockout mouse placenta at embryonic day 18.5_smaple2

description: Library name: R21123297


title: SK-N-BE(2)-C DMSO rep3


description: Library name: Solyc10g005080.3.1_O_sativa_Nipponbare_DAPi712E10-ORGi5010-96P247

value: MYBRELATED


title: SK-N-BE(2)-C DMSO rep2


title: C57BL/6 mouse placenta at embryonic day 18.5_smaple4

description: Library name: R21134532

value: WT


description: Library name: AT1G20980_O_sativa_Nipponbare_DAPi712E11-ORGi5010-96P220

value: SBP


description: Library name: AT4G17980_O_sativa_Nipponbare_DAPi712E10-ORGi5010-96P220


title: SK-N-BE(2)-C DMSO rep1


title: Chemerin knockout mouse placenta at embryonic day 18.5_smaple1

description: Library name: CH831


description: Library name: AL3G23910.t2_O_sativa_Nipponbare_DAPi712E07-ORGi5010-96P247


title: GEMM Res2

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60).  GEMM mouse samples were mapped to mm10 and other samples were mapped to hg38 (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (  M22 for GEMM mouse samples; r31, GRCh38.p12 for other samples).
Assembly: GRCh38(hg38) or GRCm38(mm10)
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM txt files

source_name: Tumor

growth_protocol: PDX-NB14 tumor were established in CB17 severe combined immunodeficient mice (CB17 scid, Taconic). Transgenic TH-MYCN/ALKF1178L mouse model (GEMM) was provided by Peter Murray and breeded in lab.

extract_protocol:
Total RNA extraction from cells and tumor tissues was performed using the RNeasy Mini Kit according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.

treatment_protocol: PDX-NB14 mice and MYCN/ALKF1178L mice (GEMM) were treated with vehicle control or indisulam 25 mg/kg according the schedule in the paper. Some tumors from PDX and xenografts developed indisulam resistant. These tumors were isoldated for RNA-seq.

value: Tumor

value: indisulam 25mg/kg


title: C57BL/6 mouse placenta at embryonic day 18.5_sample3

description: Library name: R21123289


title: GEMM Res1


title: C57BL/6 mouse placenta at embryonic day 18.5_sample2

description: Library name: R21134533


description: Library name: AT5G14960_O_sativa_Nipponbare_DAPi712E08-ORGi5010-96P220


description: Library name: AL2G34360.t1_O_sativa_Nipponbare_DAPi712E10-ORGi5010-96P364

value: RWPRK


description: Library name: AT2G18550_O_sativa_Nipponbare_DAPi712E07-ORGi5010-96P220

value: HOMEOBOX


description: Library name: XP_013602065.1_O_sativa_Nipponbare_DAPi712E06-ORGi5010-96P364

value: plant


title: GEMM CTRL1

value: Vehicle  treatment


title: GEMM CTRL2


description: Library name: LOC_Os10g07510.1_O_sativa_Nipponbare_DAPi712E05-ORGi5010-96P364


description: Library name: Solyc05g007180.3.1_O_sativa_Nipponbare_DAPi712E12-ORGi5010-96P247


title: C57BL/6 mouse placenta at embryonic day 18.5_sample1

description: Library name: H181


description: Library name: AT5G56110_O_sativa_Nipponbare_DAPi712E06-ORGi5010-96P220

value: MYB


title: E12.5_SIS3_rep2, SIS3, 1 day

city: New Orleans

first: Qinghuang

last: Tang

state: LA

address: 2000 Percival Stern Hall

department: Cell and Molecular Biology

institute: Tulane University

description:
Library name: E12.5_SIS3_rep2
E12.5_SIS3.bw

data_processing:
Basecalls were performed using bcl-convert for Illumina NextSeq 500 and NovaSeq 6000 outputs.
The RNA-seq sequencing reads were mapped to the mm10 transcriptome using Salmon quant for quantification of gene expression at transcript level (Patro et al., 2017). Salmon quantification files were then imported into R with the tximport package (Soneson et al., 2015) to summarize gene-level expression.
RNA-seq reads were mapped to the mm10 transcriptome using Salmon quant (Patro et al., 2017), then imported into R with tximport (Soneson et al., 2015) for gene-level expression quantification.
Differentially expressed genes were identified using DESeq2 (Love et al., 2014).
For UCSC genome browser visualization, RNA-seq reads were aligned to the mouse reference genome (mm10) using Hisat2 (Kim et al., 2019), merged between replicates with samtools (Li et al., 2009), and converted to bigwig format using deepTools bamCoverage (Ramirez et al., 2016).
Assembly: mm10
Supplementary files format and content: Text files contain raw counts for each sample
Supplementary files format and content: BigWig files display RNA-seq read coverage signals for each group, showing RNA expression levels.

growth_protocol: The E12.5 and E13.5 molar tooth germs dissected from BRE-GFP mouse embryos were cultured in vitro in the DMEM supplemented with 10% FBS (Cytiva) and GlutaMAX™-1 (Gibco).

extract_protocol:
Total RNAs were extracted using the RNeasy Micro Plus Kit (Qiagen), quantified using a Qubit 2.0 Fluorometric Quantitation system (Life Technologies), and then subjected to RNA-seq library construction.
RNA-seq libraries were constructed using the SMARTer Universal Low Input RNA Kit (Takara Bio) and the TruSeq RNA Sample Preparation Kit v2 (Illumina) following the manufacturer's protocols.

treatment_protocol: The in vitro cultured molar tooth germs at indicated stages were treated with DMSO, SB431542 (Sigma-Aldrich) or SIS3 (Tocris Bioscience) for 1 day, and then were subjected to subsequent RNA-seq assays.

tag: library preparation

value: TruSeq RNA Sample Preparation Kit v2

value: BRE-GFP

tag: time

value: 1 day


description: Library name: LOC_Os02g42970.1_O_sativa_Nipponbare_DAPi712E03-ORGi5010-96P247

value: NAC


description: Library name: AT3G60530_O_sativa_Nipponbare_DAPi712E05-ORGi5010-96P220


description: Library name: AT5G62020_O_sativa_Nipponbare_DAPi712E04-ORGi5010-96P220

value: HSF


description: Library name: XP_013615900.1_O_sativa_Nipponbare_DAPi712E09-ORGi5010-96P247


title: NB14-IR2-H3K27ac-02

data_processing:
Raw reads were first trimmed low-quality ends using trim-galore (0.4.4; default parameter) and then aligned to the human reference genomes (hg38) using BWA (version 0.7.12; default parameter) and duplicated reads were then marked/removed with Picard (version 1.65). Only properly paired uniquely mapped reads were extracted by samtools (version 1.3.1 parameters used were -q 1 -f 2 -F 1804) for downstream analysis.
MACS2 (version 2.1.1 20160309) was used to call narrow peaks  using 'macs2 callpeak  -t cut_tag_file -f BEDPE -q 0.05 --keep-dup all' .
genomeCoverageBed (bedtools 2.25.0) was used to produce genome-wide coverage in BEDGRAPH file and then converted it to bigwig file by bedGraphToBigWig.
Assembly: GRCh38(hg38)
Supplementary files format and content: narrowPeak, bigwig
Library strategy: CUT&Tag

growth_protocol: SKNAS-naïve, IR1 and IR2 cells were rederived from SKNAS xenografe treated with vehicle and indisulam tumors and cultured in the RPMI complete medium. PDX-NB14 tumor were established in CB17 severe combined immunodeficient mice (CB17 scid, Taconic).

extract_protocol:
CUT&Tag DNAs from SKNAS-naïve, IR1 and IR2 cells and PDX-NB14-ctrl and PDX-NB14-IR tumors were prepared by following the protocol as described previously (Kaya-Okur et al. 2019 and https://www.protocols.io/view/bench-top-cut-amp-tag-bcuhiwt6?step=1 ) with minor modifications. Briefly, for NB14-ctrl and NB14-IR tumor, nuclei extraction is following the protocol of isolate nuclei from frozen tissues (https://support.missionbio.com/hc/en-us/article_attachments/4421562098967 ). For SKNAS-naïve, IR1 and IR2 cells were washed with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail). Nuclei were isolated with cold NE1 buffer (20 mM HEPES–KOH, pH 7.9; 10 mM KCl 0.1%; Triton X-100; 20% Glycerol, 0.5 mM Spermidine; 1x Protease Inhibitor) for 10 min on ice. Nuclei were collected by 600 x g centrifuge and resuspended in 1ml washing buffer containing with 10 µL of activated concanavalin A-coated beads (Bangs laboratories, BP531) at RT for 10 min.  Bead-bound nuclei were collected with placing tube on magnet stand and removing clear liquid. The nuclei bound with bead were resuspended in 50 µL Dig-150 buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail; 0.05% Digitonin; 2 mM EDTA) and incubated with a 1:50 dilution of H3K27ac (Abcam, ab4729) overnight at 4 °C. The unbound primary antibody was removed by placing the tube on the magnet stand and withdrawing the liquid. The primary antibody bound nuclei bead was mixed with Dig-150 buffer 100uL containing guinea pig anti-Rabbit IgG antibody (Antibodies, ABIN101961) 1:100 dilution for 1 hour at RT. Beads bound nuclei were washed using the magnet stand 3× for 5 min in 1 mL Dig-150 buffer to remove unbound antibodies.  A 1:100 dilution of pA-Tn5 adapter complex was prepared in Dig-300 buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 0.05% Digitonin, 1× Protease inhibitor cocktail).  After removing the liquid on the magnet stand, 100 µL mixture of pA-Tn5 and Dig- 300 buffer was added to the nuclei bound beads with gentle vortex and incubated at RT for 1 h. After 3× 5 min in 1 mL Dig-300 buffer to remove unbound pA-Tn5 protein, nuclei were resuspended in 250 µL Tagmentation buffer (10 mM MgCl2 in Dig-300 buffer) and incubated at 37 °C for 1 h. EDTA 10 µL of 0.5 M, 3 µL of 10% SDS and 2.5 µL of 20 mg/mL Proteinase K were added to stop tagmentation and incubated at 55 °C for 1 hour. DNA libraries were then purified with SPRIselect beads (Beckman Coulter, B23318) following manufacture instruction and then dissolved in water.
Sequencing libraries were prepared using NEBNext HiFi 2× PCR Master Mix (NEB, M0541L) according to the manufacturer's instructions. The PCR products were cleaned up with SPRIselect beads and quantified using Qubit dsDNA HS assay kit (Agilent Technologies). The libraries were sequenced on a HiSeq2500 with paired-end 50-bp reads (Illumina).

treatment_protocol: SKNAS-naïve is from the tumor treated with vehicle. SKNAS-IR1 and IR2 are from indisulam resistant tumor (details in the manuscript). The PDX-NB14 mice were treate vehicle or indisulam 25mg/kg dosage and resistant indisulam treatment after a few treatment cycle.

tag: chip antibody

value: H3K27ac,  Rabbit, Abcam,4729

value: Indisulam resistan-PDX-NB14


title: E12.5_SIS3_rep1, SIS3, 1 day

description:
Library name: E12.5_SIS3_rep1
E12.5_SIS3.bw


description: Library name: AL5G10010.t1_O_sativa_Nipponbare_DAPi712E01-ORGi5010-96P364

value: Nipponbare


description: Library name: AT1G13260_O_sativa_Nipponbare_DAPi712E01-ORGi5010-96P220

value: RAV


description: Library name: AT5G64750_O_sativa_Nipponbare_DAPi712E03-ORGi5010-96P220


title: SKNAS-IR2-H3K27ac-02

value: Neuroblsatoma


title: E13.5_Molar, pSmad15_CUT&Run, rep2

description:
Library name: E13.5_Molar_pSmad15_rep2, CUT_Run
Peaks identified by SEACR are represented in a 6-column BED format including: chromosome, start coordinate, end coordinate, total signal within the region, maximum signal value, and the subregion containing the maximum signal.

data_processing:
Basecalls were performed using bcl-convert v3.7.4 for Illumina NovaSeq 6000 output.
The CUT&RUN data were processed following the pipeline described by Skene and Henikoff (2017). Breifly, paired-end sequencing reads were aligned to the mouse reference genome (mm10) using Bowtie2 (Langmead and Salzberg, 2012). The resulting BAM alignment files were processed with SAMtools (Li et al., 2009) to filter out low-quality reads, reads in ENCODE blacklist regions, unmapped mates, and PCR duplicates. The filtered BAM files were converted to bedGraph format using the bamtobed tool from BEDTools (Quinlan and Hall, 2010). These bedGraph files served as input for SEACR (Meers et al., 2019) to call peaks with the -non - stringent setting.
Common pSmad1/5 and pSmad3 peaks from two biological replicates were identified by intersection analysis using BEDTools (Quinlan and Hall, 2010).
Heatmaps of CUT&RUN signals centered on transcription start sites (TSSs) were generated using the plotHeatmap function of deepTools.
Motif discovery analysis was performed using the MEME Suite (Bailey et al., 2009) on sequences spanning ±100 bp from the summits of common pSmad1/5 and pSmad3 peaks (http://meme-suite.org).
For visualization in the UCSC Genome Browser, CUT&RUN sequencing reads from two biological replicates were merged using SAMtools, and redundant reads were subsequently removed using the intersect function of BEDTools (Quinlan and Hall, 2010). The filtered alignment files were then converted to bigWig format for display.
Assembly: mm10
Supplementary files format and content: BED, common peaks that identified by intersecting SEACR-called peaks from two biological replicates using BEDTools intersect.
Supplementary files format and content: BigWig, bins per million mapped reads (BPM) normalized coverage of DNA fragements at common pSmad1/5 and pSmad3 biding sites from two biological replicates.
Library strategy: CUT&Run

extract_protocol:
E13.5 molar tooth germs were harvested and enzymatically dissociated into a single-cell suspension. The cells were subsequently bound to concanavalin A-coated magnetic beads and permeabilized with Digitonin to facilitate entry of phosphorylated Smad1/5 or Smad3 antibodies for target binding. Following a brief washing step, the bead-bound cells were incubated with pA-MNase enzyme. The samples were then chilled to 0°C before adding CaCl₂ to activate MNase-mediated chromatin digestion for 30 minutes. The enzymatic reaction was terminated via chelation, and the released DNA fragments were extracted for Cut&Run sequencing library preparation.
CUT&RUN DNA libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, USA). The constructed libraries were sequenced on an Illumina NovaSeq 6000 platform using the NextSeq 500/550 High Output Kit v2 with 100 bp paired-end read configuration.

tag: cut&run antibody

value: pSmad1/5 (Cell signaling technology, #11971)

value: wildtype


description: Library name: LOC_Os06g07030.1_O_sativa_Nipponbare_DAPi712E01-ORGi5010-96P247


title: NB14-ctrl1-H3K27ac-02

value: Tumor

value: Vehicle  treatment-PDX-NB14


title: E13.5_Molar, pSmad15_CUT&Run, rep1

description: Library name: E13.5_Molar_pSmad15_rep1, CUT_Run


title: NB14-ctrl1-H3K27ac-01


title: E13.5_Molar, pSmad3_CUT&Run, rep1

description: Library name: E13.5_Molar_pSmad3_rep1, CUT_Run

value: pSmad3 (Abcam, #ab52903)


title: SKNAS-IR2-H3K27ac-01

tag: cell line


description: Library name: AT5G11260_O_sativa_Nipponbare_DAPi712D12-ORGi5010-96P220

value: plant

value: BZIP


description: Library name: AL8G10650.t1_O_sativa_Nipponbare_DAPi712D09-ORGi5010-96P247

value: MYBRELATED


description: Library name: LOC_Os08g06110.3_O_sativa_Nipponbare_DAPi712D10-ORGi5010-96P247


description: Library name: AT3G18990_O_sativa_Nipponbare_DAPi712D11-ORGi5010-96P220


title: p26688_28474/98

city: Zurich

first: Christelle

last: Le Foll

address: Winterthurerstrasse 260

department: Vetsuisse faculty

country: Switzerland

institute: Univeristy Of Zurich

description: Library name: Brain_region_98

data_processing:
Trimming performed with fastp v0.20
Transcript abundance estimation performed with kallisto v0.46.1
Assembly: GRCm39
Supplementary files format and content: tab-delimited transcript abundances

source_name: Brain tissue

extract_protocol:
mRNA was extracted from the brain punches with the reliaprep promega tissue kit (Z6212)
The quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Fragment Analyzer (Agilent, Santa Clara, California, USA). Only those samples with a 28S/18S ratio within 1.5–2 were further processed. The TruSeq Stranded mRNA (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were polyA enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples was fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR.  The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Fragment Analyzer (Agilent, Santa Clara, California, USA).  The product is a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20.

value: Brain tissue

value: ARC

tag: treatment

value: Vehicle


title: NB14-IR1-H3K27ac-01


description: Library name: Solyc06g051120.4.1_O_sativa_Nipponbare_DAPi712D07-ORGi5010-96P364

value: TRIHELIX


description: Library name: XP_013587997.1_O_sativa_Nipponbare_DAPi712D11-ORGi5010-96P247

value: WRKY


title: E13.5_Molar, pSmad3_CUT&Run, rep2

description:
Library name: E13.5_Molar_pSmad3_rep2, CUT_Run
Peaks identified by SEACR are represented in a 6-column BED format including: chromosome, start coordinate, end coordinate, total signal within the region, maximum signal value, and the subregion containing the maximum signal.


title: SKNAS-IR1-H3K27ac-02

tag: cell type

value: H3K27ac,  Rabbit, Abcam,4729


description: Library name: AT5G03150_O_sativa_Nipponbare_DAPi712D08-ORGi5010-96P220

tag: tissue

value: Nipponbare


description: Library name: LOC_Os10g26500.1_O_sativa_Nipponbare_DAPi712D12-ORGi5010-96P247

tag: genotype

value: HOMEOBOX


title: SKNAS-IR1-H3K27ac-01

value: Neuroblsatoma


title: p26688_28474/99

description: Library name: Brain_region_99


title: p26688_28474/97

description: Library name: Brain_region_97


description: Library name: Carub.0008s0285.1_O_sativa_Nipponbare_DAPi712D08-ORGi5010-96P247

tag: tf id


description: Library name: AL5G42830.t1_O_sativa_Nipponbare_DAPi712D06-ORGi5010-96P364

tag: multidap sample_id


title: p26688_28474/95

description: Library name: Brain_region_95


title: SKNAS-Naive-H3K27ac-01

source_name: SKNAS-Naive

value: SKNAS-Naive


description: Library name: Solyc01g095460.3.1_O_sativa_Nipponbare_DAPi712D07-ORGi5010-96P247

tag: 96 well_plate_id


title: Hypoxia knockout

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

data_processing:
The barcoded processing and gene counting were made using the Cell Ranger software v6.1.1 [Zheng2017] and post-alignment processing and visualisation was performed using Seurat v4.1.1 [Stuart2019]. Data was normalised using Sctransform [Hafemeister2019].
The clustering was performed using SLM; 8 clusters were determined in normoxia and 6 in hypoxia; the identification of markers was performed per cluster vs its complement, on 1 log2(FC) and <0.05 BH adjusted p-value.
The visualisation and community accessible overview were complied using ShinyCell [Ouyang2021]
Assembly: hg38 (GRCh38-3.1.0)
Supplementary files format and content: count matrix containing raw gene expression (csv)

source_name: hiPSC-derived Lung airways organoids

growth_protocol: hiPSC -derived Lung airways organoids derived from our differentiation protocol.

extract_protocol:
hiPSC were differentiated into AECs. Day60 ALIs were incubated with TRYPLE at 37 °C for 20 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended into PBS supplemented with 0.04% BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Cells were placed in an hypoxic chamber for 24h at 1% O2.

value: hiPSC-derived Lung airways organoids

value: hypoxia

value: EHF knockout


description: Library name: Carub.0004s2803.1_O_sativa_Nipponbare_DAPi712D05-ORGi5010-96P364


description: Library name: AT2G01930_O_sativa_Nipponbare_DAPi712D05-ORGi5010-96P220

value: BBRBPC


description: Library name: Solyc05g009790.1.1_O_sativa_Nipponbare_DAPi712D10-ORGi5010-96P364

value: plant

value: RAV


title: Hypoxia wildtype

value: wildtype


description: Library name: AT1G74480_O_sativa_Nipponbare_DAPi712D07-ORGi5010-96P220

value: RWPRK


description: Library name: AT3G57920_O_sativa_Nipponbare_DAPi712D06-ORGi5010-96P220

value: SBP


title: p26688_28474/93

description: Library name: Brain_region_93

value: Brain tissue

value: ARC

value: Vehicle


title: p26688_28474/96

description: Library name: Brain_region_96


description: Library name: Carub.0001s1194.1_O_sativa_Nipponbare_DAPi712D03-ORGi5010-96P247

value: NAC


title: p26688_28474/92

description: Library name: Brain_region_92

value: LPBN

value: sCT 150 nmol/kg


description: Library name: Solyc02g094290.1.1_O_sativa_Nipponbare_DAPi712D04-ORGi5010-96P364

value: Nipponbare

value: TCP


description: Library name: AT5G65410_O_sativa_Nipponbare_DAPi712D03-ORGi5010-96P220

value: ZFHD


title: Normoxia wildtype

value: hiPSC-derived Lung airways organoids

value: normoxia


title: SKNAS-Naive-H3K27ac-02

value: SKNAS-Naive

value: Neuroblsatoma

value: H3K27ac,  Rabbit, Abcam,4729


description: Library name: AT3G50260_O_sativa_Nipponbare_DAPi712D02-ORGi5010-96P220

value: plant


title: p26688_28474/91

description: Library name: Brain_region_91


description: Library name: Solyc02g085630.3.1_O_sativa_Nipponbare_DAPi712D01-ORGi5010-96P364

value: HOMEOBOX


title: INPUT_Control_5.fastqsanger.gz

city: Athens

first: Spyros

last: Foutadakis

address: Soranou

country: Greece

institute: Biomedical Research Foundation Academy of Athens

data_processing:
The quality of sequencing reads was evaluated using FastQC (Galaxy Version 0.73+galaxy0)
Reads were aligned to the human genome using Bowtie2 with the very sensitive end to end option (Galaxy Version 2.4.2+galaxy0)
Duplicates were removed using the RmDup command from Samtools (Galaxy Version 2.0.1)
Peaks were called using the MACS2 callpeak command (Galaxy Version 2.1.1.20160309.6) using a qvalue of 0.05 as a cutoff
Bigwig files were prepared using the bamCoverage command (Galaxy Version 3.5.1.0.0) from deepTools
Assembly: hg19
Supplementary files format and content: 1 excel file containing the normalised sequencing count matrix, 1 excel file containing the DESeq2 results, 12 bed files containing the input corrected peaks and 24 bigwig files

source_name: Peripheral blood mononuclear cells from control

extract_protocol:
Samples were fixed with 1% formaldehyde for 30 minutes and chromatin was extracted and sonicated using a Covaris S220
ChIP-seq libraries were prepared with the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®

value: Peripheral blood mononuclear cells

tag: diagnosis

value: healthy control

value: none (input)


title: p26688_28474/94

description: Library name: Brain_region_94

value: Brain tissue

value: ARC

value: Vehicle


description: Library name: Carub.0001s3581.1.p_O_sativa_Nipponbare_DAPi712D01-ORGi5010-96P247

data_processing:
Fastq files were quality filtered and adapters were trimmed using BBTools v38.96 bbduk.sh62 with parameters k=21 mink=11 ktrim=r tbo tpe qtrim=r trimq=6 maq=10, and then aligned to the corresponding reference genome using bowtie2 v2.4.2 and parameters --no-mixed --no-discordant. Bam files from negative control wells were merged using the samtools v1.15.1 merge command, to generate a single background file for each 96-well plate. The MACS3 v3.0.0a6 callpeak command was used to generate narrowPeak files, using the merged background as the control, with the parameters --call-summits --keep-dup 1 and –gsize with the total fasta genome size. Bigwig files were generated using deeptools v3.5.2 bamCoverage with parameters --extendReads --binSize 1 --ignoreDuplicates --maxFragmentLength 600 --normalizeUsing RPGC, and --effectiveGenomeSize with the total fasta genome assembly size of each species.
Assembly: Oryza sativa Nipponbare: MSU via Phytozome v7.0
Supplementary files format and content: narrowPeak are tab-delimited extended bed format files that contain peak regions identified by MACS3, using the matched negative controls on each 96 well plate to dentify regions that were enriched for by each transcription factor. The identified peaks represent putative transcription factor binding sites.
Supplementary files format and content: bigwig files show the genome coverage of each DAP-seq library. They can be used to compare coverage between different libraries and to view peaks in a genome browser. Note that they should be compared to the matched negative control libraries from the same plate.
Library strategy: DAP-seq


title: INPUT_Control_4.fastqsanger.gz


title: p26688_28474/90

description: Library name: Brain_region_90

value: LPBN

value: sCT 150 nmol/kg


description: Library name: Carub.0002s1646.1_O_sativa_Nipponbare_DAPi712C12-ORGi5010-96P247

value: Nipponbare


description: Library name: AT4G00730_O_sativa_Nipponbare_DAPi712C11-ORGi5010-96P220


description: Library name: AL2G40550.t1_O_sativa_Nipponbare_DAPi712C11-ORGi5010-96P247

value: WRKY


title: p26688_28474/89

description: Library name: Brain_region_89


title: Normoxia knockout

value: hiPSC-derived Lung airways organoids

value: EHF knockout


description: Library name: LOC_Os01g49830.1_O_sativa_Nipponbare_DAPi712C10-ORGi5010-96P364

value: RAV


title: INPUT_Control_2.fastqsanger.gz


description: Library name: XP_013599228.1_O_sativa_Nipponbare_DAPi712D02-ORGi5010-96P364


description: Library name: AT1G76420_O_sativa_Nipponbare_DAPi712C09-ORGi5010-96P220

value: NAC


description: Library name: Solyc06g048630.3.1_O_sativa_Nipponbare_DAPi712C09-ORGi5010-96P247

value: BZIP


title: p26688_28474/88

description: Library name: Brain_region_88


description: Library name: AT5G62470_O_sativa_Nipponbare_DAPi712C08-ORGi5010-96P220

value: plant

value: MYB


description: Library name: XP_013613838.1_O_sativa_Nipponbare_DAPi712C08-ORGi5010-96P247


title: INPUT_Patient_7.fastqsanger.gz

source_name: Peripheral blood mononuclear cells from patient

value: Peripheral blood mononuclear cells

value: SARS-CoV-2 patient


title: INPUT_Patient_6.fastqsanger.gz

value: none (input)


description: Library name: AT1G12260_O_sativa_Nipponbare_DAPi712C12-ORGi5010-96P220


title: p26688_28474/9

description: Library name: Brain_region_9

value: Brain tissue

value: AP

value: AM833 0.3 nmol/kg


title: p26688_28474/84

description: Library name: Brain_region_84

value: LPBN


title: INPUT_Control_3.fastqsanger.gz

value: healthy control


title: p26688_28474/85

description: Library name: Brain_region_85

value: sCT 150 nmol/kg


description: Library name: Solyc05g053240.4.1_O_sativa_Nipponbare_DAPi712C06-ORGi5010-96P364

value: Nipponbare

value: SBP


description: Library name: AT5G60130_O_sativa_Nipponbare_DAPi712C07-ORGi5010-96P220


description: Library name: Solyc08g068320.3.1_O_sativa_Nipponbare_DAPi712C04-ORGi5010-96P247


title: INPUT_Patient_5.fastqsanger.gz


description: Library name: AT3G27010_O_sativa_Nipponbare_DAPi712C04-ORGi5010-96P220

value: TCP


title: p26688_28474/82

description: Library name: Brain_region_82


description: Library name: Carub.0001s0116.1_O_sativa_Nipponbare_DAPi712C10-ORGi5010-96P247

value: MYBRELATED


title: INPUT_Patient_3.fastqsanger.gz


description: Library name: LOC_Os01g69980.1_O_sativa_Nipponbare_DAPi712C04-ORGi5010-96P364


title: p26688_28474/81

description: Library name: Brain_region_81


description: Library name: AT5G03790_O_sativa_Nipponbare_DAPi712C06-ORGi5010-96P220

value: HOMEOBOX


title: INPUT_Patient_2.fastqsanger.gz


title: p26688_28474/87

description: Library name: Brain_region_87


description: Library name: LOC_Os01g46970.1_O_sativa_Nipponbare_DAPi712C07-ORGi5010-96P247

value: BZIP


title: p26688_28474/80

description: Library name: Brain_region_80


title: INPUT_Control_1.fastqsanger.gz


description: Library name: AT1G69690_O_sativa_Nipponbare_DAPi712C02-ORGi5010-96P220

value: plant


title: INPUT_Patient_1.fastqsanger.gz


description: Library name: LOC_Os03g10210.1_O_sativa_Nipponbare_DAPi712C01-ORGi5010-96P364


description: Library name: XP_013589953.1_O_sativa_Nipponbare_DAPi712B12-ORGi5010-96P247


title: p26688_28474/78

description: Library name: Brain_region_78


description: Library name: AT2G40620_O_sativa_Nipponbare_DAPi712B12-ORGi5010-96P220


title: p26688_28474/8

description: Library name: Brain_region_8


title: H3K27ac_ChIP-seq_Control_5.fastqsanger.gz


title: INPUT_Patient_4.fastqsanger.gz


title: p26688_28474/76

description: Library name: Brain_region_76

value: Vehicle


title: H3K27ac_ChIP-seq_Control_4.fastqsanger.gz

value: Peripheral blood mononuclear cells


description: Library name: XP_013602769.1_O_sativa_Nipponbare_DAPi712C03-ORGi5010-96P247

value: NAC


description: Library name: Solyc07g040920.2.1_O_sativa_Nipponbare_DAPi712B11-ORGi5010-96P247


description: Library name: Carub.0001s1299.1_O_sativa_Nipponbare_DAPi712B10-ORGi5010-96P364

value: RAV


title: H3K27ac_ChIP-seq_Control_3.fastqsanger.gz


description: Library name: AT1G20910_O_sativa_Nipponbare_DAPi712B10-ORGi5010-96P220

value: ARID


description: Library name: XP_013587350.1_O_sativa_Nipponbare_DAPi712B10-ORGi5010-96P247


title: p26688_28474/73

description: Library name: Brain_region_73

value: Brain tissue


description: Library name: Carub.0006s0445.1_O_sativa_Nipponbare_DAPi712B07-ORGi5010-96P364

value: TRIHELIX


description: Library name: AT1G79580_O_sativa_Nipponbare_DAPi712B09-ORGi5010-96P220


title: p26688_28474/70

description: Library name: Brain_region_70

value: LPBN


description: Library name: LOC_Os03g21800.1_O_sativa_Nipponbare_DAPi712B09-ORGi5010-96P247


title: H3K27ac_ChIP-seq_Control_1.fastqsanger.gz

value: healthy control


title: H3K27ac_ChIP-seq_Control_2.fastqsanger.gz


title: p26688_28474/72

description: Library name: Brain_region_72


description: Library name: AT1G27730_O_sativa_Nipponbare_DAPi712C01-ORGi5010-96P220


description: Library name: AL4G44590.t1_O_sativa_Nipponbare_DAPi712B05-ORGi5010-96P364


description: Library name: XP_013631649.1_O_sativa_Nipponbare_DAPi712B05-ORGi5010-96P247


title: H3K27ac_ChIP-seq_Patient_6.fastqsanger.gz

value: SARS-CoV-2 patient


title: H3K27ac_ChIP-seq_Patient_5.fastqsanger.gz


description: Library name: LOC_Os03g61760.1_O_sativa_Nipponbare_DAPi712B06-ORGi5010-96P364

value: Nipponbare


description: Library name: Carub.0004s2898.1.p_O_sativa_Nipponbare_DAPi712B07-ORGi5010-96P247


title: p26688_28474/69

description: Library name: Brain_region_69

value: sCT 150 nmol/kg


description: Library name: LOC_Os02g33430.1_O_sativa_Nipponbare_DAPi712D05-ORGi5010-96P247


title: p26688_28474/68

description: Library name: Brain_region_68


description: Library name: Carub.0005s0520.1_O_sativa_Nipponbare_DAPi712B04-ORGi5010-96P364

value: TCP


description: Library name: AT3G08500_O_sativa_Nipponbare_DAPi712B05-ORGi5010-96P220

value: MYB


title: p26688_28474/75

description: Library name: Brain_region_75


description: Library name: AL8G13510.t2_O_sativa_Nipponbare_DAPi712B08-ORGi5010-96P247


description: Library name: AT1G29160_O_sativa_Nipponbare_DAPi712B04-ORGi5010-96P220


title: H3K27ac_ChIP-seq_Patient_4.fastqsanger.gz


title: H3K27ac_ChIP-seq_Patient_7.fastqsanger.gz


title: p26688_28474/67

description: Library name: Brain_region_67


description: Library name: AT4G25470_O_sativa_Nipponbare_DAPi712B06-ORGi5010-96P220


description: Library name: Solyc11g022470.2.1_O_sativa_Nipponbare_DAPi712B02-ORGi5010-96P364


title: H3K27ac_ChIP-seq_Patient_3.fastqsanger.gz


description: Library name: AL1G23550.t1_O_sativa_Nipponbare_DAPi712B03-ORGi5010-96P247


title: p26688_28474/66

description: Library name: Brain_region_66


description: Library name: AT3G56400_O_sativa_Nipponbare_DAPi712B02-ORGi5010-96P220

value: WRKY


description: Library name: Carub.0003s3279.1_O_sativa_Nipponbare_DAPi712B01-ORGi5010-96P364

value: HOMEOBOX


title: H3K27ac_ChIP-seq_Patient_1.fastqsanger.gz


title: p26688_28474/7

description: Library name: Brain_region_7

value: AP


title: H3K27ac_ChIP-seq_Patient_2.fastqsanger.gz


description: Library name: AL1G53260.t1_O_sativa_Nipponbare_DAPi712B01-ORGi5010-96P247

value: plant


description: Library name: Solyc03g116010.3.1_O_sativa_Nipponbare_DAPi712A11-ORGi5010-96P364

value: RWPRK


title: p26688_28474/64

description: Library name: Brain_region_64


description: Library name: LOC_Os01g51154.1_O_sativa_Nipponbare_DAPi712A11-ORGi5010-96P247

value: MYBRELATED


description: Library name: XP_013637759.1_O_sativa_Nipponbare_DAPi712A10-ORGi5010-96P364

value: RAV


description: Library name: AL1G11460.t1_O_sativa_Nipponbare_DAPi712A10-ORGi5010-96P247


title: p26688_28474/62

description: Library name: Brain_region_62


description: Library name: AT5G05550_O_sativa_Nipponbare_DAPi712A10-ORGi5010-96P220


title: dMSC, menstrual fluid, rep3

city: Moscow

first: Roman

last: Eremichev

address: 27, b. 10, Lomonosovsky av.

department: Centre for Regenerative Medicine

country: Russia

institute: Lomonosov Moscow State University

description: Library name: dMSC_MF_3

data_processing:
Quality control of sequencing data was performed in the FastQC program and then visualized with MultiQC. RNA sequencing raw fastq files were quantified using Salmon.
Assembly: GRCh38
Supplementary files format and content: csv file includes raw counts for each sample

source_name: dermis

growth_protocol: dMSC and eMSC were obtained from 3 healthy donors each.

extract_protocol:
Samples were lysed at passage 3-4 in Trizol reagent (Sigma-Aldrich, Burlington, MA, USA) according to the manufacturer’s instructions. The RNA sample quality was controlled using BioAnalyser and the RNaA 6000 Nano Kit (both Agilent Technologies, Santa Clara, CA, USA). PolyA RNA was purified with the Dynabeads®® mRNA Purification Kit (Ambion, Waltham, MA, USA).
An Illumina library was made from polyA RNA with NEBNext® Ultra™ II RNA Library Prep (New England Biolabs, Ipswich, MA, USA), according to the manufacturer’s instructions. Concentrations of nucleic acids in the obtained libraries were analyzed by the Qubit dsDNA HS Assay Kit using Qbit 2.0 equipment (Thermo Fisher Scientific, Waltham, MA, USA). The distribution of library fragment lengths was assessed using the Agilent High-Sensitivity DNA Kit (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Samples for RNA extraction and subsequent RNA-sequencing were collected before and 24h after MF treatment.

value: dermis

value: mesenchymal stromal cells

value: menstrual fluid


description: Library name: Carub.0004s2291.1_O_sativa_Nipponbare_DAPi712A09-ORGi5010-96P247

extract_protocol:
CTAB protocol for gDNA extraction
Genomic DNA fragment libraries were constructed with an average shearing size at 150 bp. Different species were labeled by unique Illumina i5 index adapters to enable multiplexing following the multiDAP method. Upstream of the DAP-seq assay, fragment libraries were amplified for 10 cycles to remove any DNA modifications. After performing the DAP-seq enrichment in 96-well plates with each well containing a single in vitro expressed transcription factor, the libraries were amplified with i7 index primers to attach a unique i7 adapter corresponding to each well.

value: BZIP


title: dMSC, menstrual fluid, rep2

description: Library name: dMSC_MF_2


description: Library name: LOC_Os10g02584.3_O_sativa_Nipponbare_DAPi712A09-ORGi5010-96P364

value: BBRBPC


title: p26688_28474/61

description: Library name: Brain_region_61

value: Brain tissue

value: LPBN

value: AM833 0.3 nmol/kg


title: dMSC, baseline, rep3

description: Library name: dMSC_BL_3

value: baseline


description: Library name: AT4G25490_O_sativa_Nipponbare_DAPi712A08-ORGi5010-96P220

value: Nipponbare


title: dMSC, menstrual fluid, rep1

description: Library name: dMSC_MF_1


title: dMSC, baseline, rep2

description: Library name: dMSC_BL_2


description: Library name: XP_013631386.1_O_sativa_Nipponbare_DAPi712A07-ORGi5010-96P247


title: p26688_28474/60

description: Library name: Brain_region_60


title: p26688_28474/59

description: Library name: Brain_region_59


description: Library name: Solyc11g064950.3.1_O_sativa_Nipponbare_DAPi712A08-ORGi5010-96P247


description: Library name: LOC_Os08g37970.1_O_sativa_Nipponbare_DAPi712A06-ORGi5010-96P247

value: MYB


description: Library name: AT5G62940_O_sativa_Nipponbare_DAPi712A05-ORGi5010-96P220


title: eMSC, menstrual fluid, rep3

description: Library name: eMSC_MF_3

source_name: endometrium

value: endometrium


description: Library name: XP_013593496.1_O_sativa_Nipponbare_DAPi712A04-ORGi5010-96P364

source_name: plant

value: TCP


title: dMSC, baseline, rep1

description: Library name: dMSC_BL_1


description: Library name: AT3G12250_O_sativa_Nipponbare_DAPi712A07-ORGi5010-96P220

value: plant


description: Library name: Carub.0004s2981.1_O_sativa_Nipponbare_DAPi712A06-ORGi5010-96P364

value: SBP


title: p26688_28474/57

description: Library name: Brain_region_57


title: p26688_28474/58

description: Library name: Brain_region_58


description: Library name: AT1G69780_O_sativa_Nipponbare_DAPi712A03-ORGi5010-96P220

value: HOMEOBOX


title: eMSC, menstrual fluid, rep1

description: Library name: eMSC_MF_1


title: eMSC, menstrual fluid, rep2

description: Library name: eMSC_MF_2


description: Library name: AT1G49480_O_sativa_Nipponbare_DAPi712A04-ORGi5010-96P220

value: REM


title: p26688_28474/56

description: Library name: Brain_region_56


title: p26688_28474/6

description: Library name: Brain_region_6

value: AP

value: Vehicle


description: Library name: LOC_Os09g12770.1_O_sativa_Nipponbare_DAPi712A02-ORGi5010-96P364


description: Library name: AL2G28980.t1_O_sativa_Nipponbare_DAPi711H11-ORGi5010-96P361


title: eMSC, baseline, rep3

description: Library name: eMSC_BL_3

value: mesenchymal stromal cells


title: p26688_28474/55

description: Library name: Brain_region_55


description: Library name: AT5G39760_O_sativa_Nipponbare_DAPi712A02-ORGi5010-96P220

value: ZFHD


description: Library name: AT5G67300_O_sativa_Nipponbare_DAPi712B01-ORGi5010-96P220


title: p26688_28474/65

description: Library name: Brain_region_65

value: sCT 150 nmol/kg


title: p26688_28474/54

description: Library name: Brain_region_54

value: Brain tissue


description: Library name: Carub.0002s1959.1_O_sativa_Nipponbare_DAPi711H10-ORGi5010-96P361

value: MYBRELATED


description: Library name: Solyc08g078340.3.1_O_sativa_Nipponbare_DAPi711H09-ORGi5010-96P361


title: eMSC, baseline, rep2

description: Library name: eMSC_BL_2


description: Library name: XP_013634112.1_O_sativa_Nipponbare_DAPi711H08-ORGi5010-96P361

value: BZIP


title: p26688_28474/53

description: Library name: Brain_region_53

value: LPBN


description: Library name: LOC_Os01g17260.2_O_sativa_Nipponbare_DAPi711H07-ORGi5010-96P361

value: Nipponbare


title: eMSC, baseline, rep1

description: Library name: eMSC_BL_1

value: baseline


title: Whole heart tissue,cSirt4-Tg-Sham-Vehicle, rep 6

city: Birmingham

first: Sayan

last: Bakshi

state: Alabama

department: Department of Pathology

institute: University of Alabama at Birmingham

data_processing:
Prior to alignment to the reference mouse genome, each sequence in the raw FASTQ files was trimmed on base call quality and sequencing adapter contamination using the Trim Galore! wrapper tool. Reads shorter than 20 base pairs were removed from the FASTQ files.
Trimmed reads were aligned to the reference genome using the open source short read aligner STAR with settings according to log file.
Pre-filtering was performed to keep only rows that have at least 10 reads total.
Gene annotation was performed using the R package “bioMaRt”.
Assembly: mm39
Supplementary files format and content: tab-delimited text file include normalized count values for all samples

source_name: Whole heart tissue

extract_protocol:
Whole hearts were excised and were snap frozen in liquid nitrogen and stored at - 80 °C until subjected to further analysis.
RNA was isolated using Rneasy Fibrous Tissue Mini Kit (Qiagen). 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEB NEXT Ultra II Directional Library Prep Kit following manufacturer's protocols.

value: Whole heart tissue

value: Sham


title: p26688_28474/52

description: Library name: Brain_region_52


title: Whole heart tissue,Control-Sham-Vehicle, rep 6

value: Control


description: Library name: XP_013629448.1_O_sativa_Nipponbare_DAPi711H03-ORGi5010-96P361

value: plant

value: MYB


description: Library name: XP_013609718.1_O_sativa_Nipponbare_DAPi711G12-ORGi5010-96P361

value: HOMEOBOX


description: Library name: Solyc03g116890.3.1_O_sativa_Nipponbare_DAPi711G11-ORGi5010-96P361

value: WRKY


title: p26688_28474/51

description: Library name: Brain_region_51

value: Vehicle


description: Library name: XP_013589913.1_O_sativa_Nipponbare_DAPi711G10-ORGi5010-96P361


description: Library name: AL4G45550.t1_O_sativa_Nipponbare_DAPi711H06-ORGi5010-96P361


title: Whole heart tissue,Control-Sham-Vehicle, rep 5


description: Library name: AT5G10030_O_sativa_Nipponbare_DAPi712A06-ORGi5010-96P220


title: p26688_28474/50

description: Library name: Brain_region_50


title: p26688_28474/49

description: Library name: Brain_region_49


title: Whole heart tissue,cSirt4-Tg-Sham-Vehicle, rep 4


description: Library name: LOC_Os10g41200.1_O_sativa_Nipponbare_DAPi711G09-ORGi5010-96P361


description: Library name: AL4G38490.t1_O_sativa_Nipponbare_DAPi711G08-ORGi5010-96P361


description: Library name: AL3G51890.t2_O_sativa_Nipponbare_DAPi711F12-ORGi5010-96P361


description: Library name: AL7G19010.t1_O_sativa_Nipponbare_DAPi711G03-ORGi5010-96P361


description: Library name: Carub.0003s1161.1.p_O_sativa_Nipponbare_DAPi711G07-ORGi5010-96P361


title: p26688_28474/5

description: Library name: Brain_region_5

value: AP


title: p26688_28474/48

description: Library name: Brain_region_48


title: Whole heart tissue,Control-Sham-Vehicle, rep 4


title: Whole heart tissue,cSirt4-Tg-Sham-Vehicle, rep 5


title: p26688_28474/47

description: Library name: Brain_region_47


description: Library name: LOC_Os09g25060.1_O_sativa_Nipponbare_DAPi711F11-ORGi5010-96P361


description: Library name: AL2G32420.t2_O_sativa_Nipponbare_DAPi711F10-ORGi5010-96P361


title: Whole heart tissue,cSirt4-Tg-TAC-Vehicle, rep 6

value: TAC


title: Whole heart tissue,cSirt4-Tg-TAC-MitoQ, rep 6

value: MitoQ


description: Library name: Solyc08g079120.3.1_O_sativa_Nipponbare_DAPi711F03-ORGi5010-96P361

value: NAC


description: Library name: Solyc04g078640.3.1_O_sativa_Nipponbare_DAPi711F01-ORGi5010-96P361


title: Whole heart tissue,cSirt4-Tg-TAC-MitoQ, rep 5


title: p26688_28474/46

description: Library name: Brain_region_46

value: Brain tissue

value: sCT 150 nmol/kg


description: Library name: XP_013586407.1_O_sativa_Nipponbare_DAPi711F07-ORGi5010-96P361

value: BZIP


description: Library name: Solyc05g007180.3.1_O_sativa_Nipponbare_DAPi711E12-ORGi5010-96P361

value: Nipponbare


description: Library name: Carub.0002s2670.1_O_sativa_Nipponbare_DAPi711E11-ORGi5010-96P361


title: p26688_28474/45

description: Library name: Brain_region_45


description: Library name: XP_013615900.1_O_sativa_Nipponbare_DAPi711E09-ORGi5010-96P361

value: MYBRELATED


title: p26688_28474/43

description: Library name: Brain_region_43


description: Library name: Solyc10g005080.3.1_O_sativa_Nipponbare_DAPi711E10-ORGi5010-96P361


description: Library name: AL3G23910.t2_O_sativa_Nipponbare_DAPi711E07-ORGi5010-96P361


title: p26688_28474/44

description: Library name: Brain_region_44


description: Library name: Carub.0008s0039.1_O_sativa_Nipponbare_DAPi711F09-ORGi5010-96P361


title: Whole heart tissue,cSirt4-Tg-TAC-MitoQ, rep 3

value: Whole heart tissue


description: Library name: LOC_Os06g07030.1_O_sativa_Nipponbare_DAPi711E01-ORGi5010-96P361


title: p26688_28474/41

description: Library name: Brain_region_41


title: p26688_28474/42

description: Library name: Brain_region_42


description: Library name: LOC_Os10g26500.1_O_sativa_Nipponbare_DAPi711D12-ORGi5010-96P361


title: Whole heart tissue,cSirt4-Tg-TAC-MitoQ, rep 2


description: Library name: XP_013587997.1_O_sativa_Nipponbare_DAPi711D11-ORGi5010-96P361


title: Whole heart tissue,cSirt4-Tg-TAC-MitoQ, rep 4


title: Whole heart tissue,Control-TAC-MitoQ, rep 5


description: Library name: LOC_Os08g06110.3_O_sativa_Nipponbare_DAPi711D10-ORGi5010-96P361


description: Library name: AL8G10650.t1_O_sativa_Nipponbare_DAPi711D09-ORGi5010-96P361


title: p26688_28474/40

description: Library name: Brain_region_40


title: Whole heart tissue,Control-TAC-MitoQ, rep 6


description: Library name: Carub.0008s0285.1_O_sativa_Nipponbare_DAPi711D08-ORGi5010-96P361


title: p26688_28474/4

description: Library name: Brain_region_4


description: Library name: Solyc01g095460.3.1_O_sativa_Nipponbare_DAPi711D07-ORGi5010-96P361


title: Whole heart tissue,Control-TAC-MitoQ, rep 4


description: Library name: LOC_Os02g42970.1_O_sativa_Nipponbare_DAPi711E03-ORGi5010-96P361


description: Library name: Carub.0001s1194.1_O_sativa_Nipponbare_DAPi711D03-ORGi5010-96P361


title: Whole heart tissue,cSirt4-Tg-TAC-MitoQ, rep 1


description: Library name: LOC_Os02g33430.1_O_sativa_Nipponbare_DAPi711D05-ORGi5010-96P361


title: p26688_28474/39

description: Library name: Brain_region_39


title: p26688_28474/38

description: Library name: Brain_region_38

value: AM833 0.3 nmol/kg


title: p26688_28474/36

description: Library name: Brain_region_36


description: Library name: Carub.0001s0116.1_O_sativa_Nipponbare_DAPi711C10-ORGi5010-96P361


title: Whole heart tissue,Control-TAC-MitoQ, rep 1

value: Control


title: Whole heart tissue,Control-TAC-MitoQ, rep 3


description: Library name: Carub.0001s3581.1.p_O_sativa_Nipponbare_DAPi711D01-ORGi5010-96P361

value: plant


description: Library name: LOC_Os01g46970.1_O_sativa_Nipponbare_DAPi711C07-ORGi5010-96P361


description: Library name: AL2G40550.t1_O_sativa_Nipponbare_DAPi711C11-ORGi5010-96P361


description: Library name: Solyc08g068320.3.1_O_sativa_Nipponbare_DAPi711C04-ORGi5010-96P361

value: MYB


description: Library name: XP_013589953.1_O_sativa_Nipponbare_DAPi711B12-ORGi5010-96P361

value: HOMEOBOX


title: p26688_28474/33

description: Library name: Brain_region_33


title: Whole heart tissue,Control-TAC-Vehicle, rep 6


title: Whole heart tissue,Control-TAC-MitoQ, rep 2


title: Whole heart tissue,Control-Sham-Vehicle, rep 3

value: Sham


description: Library name: Solyc07g040920.2.1_O_sativa_Nipponbare_DAPi711B11-ORGi5010-96P361


description: Library name: XP_013587350.1_O_sativa_Nipponbare_DAPi711B10-ORGi5010-96P361


title: p26688_28474/30

description: Library name: Brain_region_30

value: Vehicle


description: Library name: XP_013613838.1_O_sativa_Nipponbare_DAPi711C08-ORGi5010-96P361


title: Whole heart tissue,cSirt4-Tg-TAC-Vehicle, rep 5


title: p26688_28474/35

description: Library name: Brain_region_35

value: AP


description: Library name: LOC_Os03g21800.1_O_sativa_Nipponbare_DAPi711B09-ORGi5010-96P361


description: Library name: Carub.0002s1646.1_O_sativa_Nipponbare_DAPi711C12-ORGi5010-96P361


title: p26688_28474/34

description: Library name: Brain_region_34


description: Library name: AL8G13510.t2_O_sativa_Nipponbare_DAPi711B08-ORGi5010-96P361


title: p26688_28474/3

description: Library name: Brain_region_3


title: Whole heart tissue,Control-TAC-Vehicle, rep 5

value: TAC


description: Library name: Carub.0004s2898.1.p_O_sativa_Nipponbare_DAPi711B07-ORGi5010-96P361


description: Library name: AL1G53260.t1_O_sativa_Nipponbare_DAPi711B01-ORGi5010-96P361


description: Library name: AL1G23550.t1_O_sativa_Nipponbare_DAPi711B03-ORGi5010-96P361


description: Library name: XP_013602769.1_O_sativa_Nipponbare_DAPi711C03-ORGi5010-96P361


title: Whole heart tissue,Control-TAC-Vehicle, rep 4


title: p26688_28474/29

description: Library name: Brain_region_29


description: Library name: AL1G11460.t1_O_sativa_Nipponbare_DAPi711A10-ORGi5010-96P361


description: Library name: XP_013631386.1_O_sativa_Nipponbare_DAPi711A07-ORGi5010-96P361


description: Library name: LOC_Os01g51154.1_O_sativa_Nipponbare_DAPi711A11-ORGi5010-96P361


title: p26688_28474/27

description: Library name: Brain_region_27


title: Whole heart tissue,Control-TAC-Vehicle, rep 3


description: Library name: Carub.0004s2291.1_O_sativa_Nipponbare_DAPi711A09-ORGi5010-96P361


description: Library name: AL1G24970.t1_O_sativa_Nipponbare_DAPi710H09-ORGi5010-96P358

value: RAV


title: p26688_28474/26

description: Library name: Brain_region_26


description: Library name: Solyc11g064950.3.1_O_sativa_Nipponbare_DAPi711A08-ORGi5010-96P361


title: p26688_28474/24

description: Library name: Brain_region_24


description: Library name: Carub.0005s0095.1_O_sativa_Nipponbare_DAPi710H08-ORGi5010-96P358

value: BBRBPC


description: Library name: LOC_Os08g37970.1_O_sativa_Nipponbare_DAPi711A06-ORGi5010-96P361


title: Whole heart tissue,cSirt4-Tg-TAC-Vehicle, rep 3


title: Whole heart tissue,cSirt4-Tg-TAC-Vehicle, rep 4


description: Library name: LOC_Os10g28340.1_O_sativa_Nipponbare_DAPi710H04-ORGi5010-96P358

value: HSF


description: Library name: Carub.0007s0775.1_O_sativa_Nipponbare_DAPi711A04-ORGi5010-96P361


title: Whole heart tissue,cSirt4-Tg-Sham-Vehicle, rep 3


title: p26688_28474/23

description: Library name: Brain_region_23

value: Brain tissue

value: sCT 150 nmol/kg


description: Library name: Carub.0002s2128.1_O_sativa_Nipponbare_DAPi710G10-ORGi5010-96P358

value: Nipponbare

value: RWPRK


title: Whole heart tissue,Control-TAC-Vehicle, rep 2

value: Whole heart tissue


title: p26688_28474/21

description: Library name: Brain_region_21


title: p26688_28474/16

description: Library name: Brain_region_16


description: Library name: XP_013635977.1_O_sativa_Nipponbare_DAPi710H05-ORGi5010-96P358

value: SBP


description: Library name: Solyc10g018560.2.1_O_sativa_Nipponbare_DAPi710G06-ORGi5010-96P358


description: Library name: Carub.0005s0004.1_O_sativa_Nipponbare_DAPi710G01-ORGi5010-96P358


title: Whole heart tissue,Control-Sham-Vehicle, rep 2

value: Control


description: Library name: XP_013591813.1_O_sativa_Nipponbare_DAPi710F10-ORGi5010-96P358

value: plant


title: Whole heart tissue,Control-Sham-Vehicle, rep 1


title: p26688_28474/18

description: Library name: Brain_region_18


title: Whole heart tissue,cSirt4-Tg-Sham-Vehicle, rep 1


title: Whole heart tissue,cSirt4-Tg-Sham-Vehicle, rep 2


title: p26688_28474/15

description: Library name: Brain_region_15

value: AM833 0.3 nmol/kg


description: Library name: LOC_Os10g40810.1_O_sativa_Nipponbare_DAPi710F06-ORGi5010-96P358


title: Whole heart tissue,Control-TAC-Vehicle, rep 1


title: p26688_28474/14

description: Library name: Brain_region_14


title: Whole heart tissue,cSirt4-Tg-TAC-Vehicle, rep 2


title: p26688_28474/20

description: Library name: Brain_region_20


description: Library name: XP_013599843.1_O_sativa_Nipponbare_DAPi710G08-ORGi5010-96P358


title: p26688_28474/137

description: Library name: Brain_region_137

value: ARC


title: p26688_28474/138

description: Library name: Brain_region_138


description: Library name: AL2G34360.t1_O_sativa_Nipponbare_DAPi710E10-ORGi5010-96P358


description: Library name: AL4G46570.t1_O_sativa_Nipponbare_DAPi710G05-ORGi5010-96P358


title: Whole heart tissue,cSirt4-Tg-TAC-Vehicle, rep 1


description: Library name: LOC_Os08g44050.1_O_sativa_Nipponbare_DAPi710F02-ORGi5010-96P358


description: Library name: XP_013602065.1_O_sativa_Nipponbare_DAPi710E06-ORGi5010-96P358


title: p26688_28474/135

description: Library name: Brain_region_135


description: Library name: LOC_Os10g07510.1_O_sativa_Nipponbare_DAPi710E05-ORGi5010-96P358


description: Library name: AL5G10010.t1_O_sativa_Nipponbare_DAPi710E01-ORGi5010-96P358


description: Library name: AL5G11070.t1_O_sativa_Nipponbare_DAPi710F08-ORGi5010-96P358


title: MSR-dCas9-Activator MEF, timecourse, post-induction 24h, rep2

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
Library name: vpr_24_2
Illumina HiSeq 3000

data_processing:
Unprocessed reads were first quality and adapter trimmed using cutadapt55 version 1.8.1 using a quality threshold of 20. Reads were then aligned to the GRCm38 genome from Ensembl using STAR56 version 2.5.2b, with settings as recommended by TEtranscripts57. Both repeats and genes were then quantified using TEtranscripts version 2.0.3
Assembly: mm10
Supplementary files format and content: countData.tsv

source_name: mouse embryonic fibroblast

growth_protocol: Cells were maintained in high glucose DMEM containing 10% tet-free FBS, 2 mM L-glutamine, 0.1 mM b-mercaptoethanol, 1x non-essential amino acids, 1 mM sodium pyruvate, and 400 mg/ml hygromycin in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using TRI Reagent and ethanol precipitated. 10 ug of total RNA was further processed to remove the remaining DNA with TURBO DNase and column purified prior to library construction.
Total RNA libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold (Illumina, 20020598) following manufacturer's protocol.

treatment_protocol: MSR-dCas9-Activator MEF cells were treated with 10 ng/ml doxycycline for 6 hrs, MSR-dCas9-Repressor MEF cells were treated with 100 ng/ml doxycycline for 24 hrs, and MSR-dCas9-Control MEF cells were treated with 10 ng/ml doxycycline for 24 hrs.

value: mouse embryonic fibroblast

value: inducible expression of MSR-dCas9-Activator

value: post-induction, fresh media, 24 hr


description: Library name: Solyc06g051120.4.1_O_sativa_Nipponbare_DAPi710D07-ORGi5010-96P358

value: TRIHELIX


description: Library name: Solyc05g009790.1.1_O_sativa_Nipponbare_DAPi710D10-ORGi5010-96P358

value: RAV


title: p26688_28474/136

description: Library name: Brain_region_136


title: MSR-dCas9-Activator MEF, timecourse, post-induction 24h, rep3

description:
Library name: vpr_24_3
Illumina HiSeq 3000


description: Library name: Solyc01g091420.2.1_O_sativa_Nipponbare_DAPi710F05-ORGi5010-96P358


description: Library name: XP_013620714.1_O_sativa_Nipponbare_DAPi710F01-ORGi5010-96P358


description: Library name: Carub.0004s2803.1_O_sativa_Nipponbare_DAPi710D05-ORGi5010-96P358


title: p26688_28474/134

description: Library name: Brain_region_134


title: MSR-dCas9-Activator MEF, timecourse, post-induction 24h, rep1

description:
Library name: vpr_24_1
Illumina HiSeq 3000


description: Library name: Solyc02g094290.1.1_O_sativa_Nipponbare_DAPi710D04-ORGi5010-96P358

value: TCP


title: p26688_28474/133

description: Library name: Brain_region_133


description: Library name: XP_013599228.1_O_sativa_Nipponbare_DAPi710D02-ORGi5010-96P358


title: p26688_28474/130

description: Library name: Brain_region_130