title: 43551

description:
total RNA extract (Qiagen RNeasy Plus Minikit)
16p11_2_Dup2


title: ChIP-Seq_RPB1_RPB3_IAA_0h_rep1

status: Public on Feb 16 2023

type: SRA

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

country: China

institute: Peking University

library_source: genomic

data_processing:
ChIP-Seq raw data were processed using a custom pipeline that builds on published workflows with minor modifications. Briefly, raw reads after adapter trimming and quality control with cutadapt and RseQC were aligned to a concatenated genome comprised of mouse mm10 and fly dm6 assemblies using bowtie2 with options (-very-sensitive-local) as described in the ChIP-seq section.
Only properly paired and uniquely aligned reads were retained for subsequent processing. Reads mapped to the mouse genome were normalized to total reads originating from Human HEK293T spike-in cells, and the normalization factor was calculated as previously described (Jiang et al., 2020).
SAMtools (v 0.1.19) and sambamba (v0.7.0) were used to filter unmapped reads, multiple mapped reads, and potential PCR duplicates. The final BAM files were converted to bigwig and normalized to spike-in controls using bamCoverage from deeptools.
For visualization purposes, the bigWig format tracks from two biological replicates for each treatment were merged into an averaged signal using the mean operator from the WiggleTools (v1.2) package (Zerbino, Johnson, et al. 2014).
Assembly: mm10 and hg19
Supplementary files format and content: bigwig files

molecule: genomic DNA

organism: Mus musculus

source_name: mouse embryonic stem cells (V6.5)

growth_protocol: For ChIP-seq, dRPB3 or RPB3 degron cells were cultured in DMEM-KO (Thermo Fisher, Cat#10829018) supplemented with 15% FBS (Gibco, Cat#10099141C), 1× penicillin/ streptomycin (Gibco, Cat#15140122), 1 × L-glutamine (Gibco, Cat#25030081), 1 × non-essential amino acids (Gibco, Cat#11140050), 1 × nucleoside (Millipore, Cat#ES-008-D), 3 μM CHIR99021 (Selleck, Cat#S1263), 0.5 μM PD0325901 (Selleck, Cat#S1036), 143 μM 2-mercaptoethanol (Thermo Fisher, Cat#M3148) and maintained at 37℃ cell incubator with 5% CO2. The HEK293T cells were cultured in basic-DMEM (Thermo Fisher, Cat#C11995500BT) supplemented with 10% FBS (GIBCO, Cat#10099141C), and maintained at 37℃ cell incubator with 5% CO2.

extract_protocol:
Cross-linked cells were subjected to chromatin fraction isolation as reported (Ji et al., 2015), and the chromatin was pretreated with 40 U MNase (NEB, Cat#M0247), followed by sonication as previously described (Yongpeng et al., 2020). 1 μl RPB1 antibodies (Cell Signaling Technology, Cat#14958) and 30 μl Protein G beads (Thermo Fisher, Cat#10004D) were used to enrich Pol II subunit-DNA complexes.
ChIP DNA were subjected to library construction according to the instructions of the NEBNext Ultra II DNA Library Prep Kit (NEB, Cat#E7645S). 200bp-400bp DNA libraries were gel-selected, purified, and delivered to Novogene company for sequencing.

treatment_protocol: The degron cells were pretreated with 1 μg/ml Doxycycline for 12 h to induce TIR1 expression, then treated with or without 500 μM IAA for 1 h to induce target protein degradation. Then the cells were harvested and mixed with 10% HEK293T cells before cross-linking.

tag: cell line

tag: treatment

value: RPB3 degron mESCs treated with 1ug/ml Dox for 12 h

tag: chip antibody

value: RPB1 (Cell Signaling Technology, Cat#14958)


title: RNA-seq_DMSO_rep1

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

library_source: transcriptomic

data_processing:
Raw reads were mapped to the reference genome assembly mm10 using STAR mapping tool (Dobin et al, 2013l; PMID: 23104886).
Assembly: mm10
Supplementary files format and content: Differentially expressed genes were analyzed using Cufflinks tools (Trapnell et al, 2012; PMID: 22383036)

molecule: total RNA

source_name: murine AML cells

growth_protocol: Above cell lines were cultured in conditions as described in this study.

extract_protocol:
Total RNAs were extracted from ~ 1 million cells using Qiaizol reagent
Libraries were prepared using the NEXTflex Rapid Directional mRNA-seq kit (Cat# NOVA-5138-11; PerkinElmer) according to the manufacturer's instructions.

treatment_protocol: treated with drugs as indicated.

tag: strain

value: engineered murine acute myeloid leukemia cell line (MLL-AF9/NRAS G112D)

tag: biological replicate

value: DMSO


title: ChIP-Seq_RPB1_dRPB3_IAA_1h_rep2

value: dRPB3 degron mESCs treated with 1ug/ml Dox for 12 h, then treated with 500 uM IAA for 1h


title: Pol2Ser5_BBC1115

data_processing:
Raw reads were mapped to the reference mouse (mm9) genome assembly using Bowtie2 allowing two-mismatches for only unique alignment. To avoid clonal artifacts introduced in the library amplification steps, duplicated mapped reads were further discarded using SAMtools (http://samtools.sourceforge.net). HOMER suite (http://homer.salk.edu/homer/) was used for overall analysis. Details were described in the experimental procedues of this study.
Assembly: mm9
Supplementary files format and content: bigWig files were generated using makebigWig.pl script of HOMER suite.

growth_protocol: Mouse AML cell lines were cultured in conditions as described in this study.

extract_protocol:
Lysates were prepared from ~5 millon single cell dissociated of organoid cultures or monolayer cultures. Sonicated nuclei with Bioruptor were further proceeded to ChIP assay with apporiate antibodies.
Libraries were prepared using the NEXTflex ChIP-seq kit (Cat# NOVA-5143-02; PerkinElmer) according to the manufacturer's instructions.

treatment_protocol: Treated with DMSO or BBC1115 as indicated.

tag: antibody

value: RNA polymerase II CTD repeat YSPT[phospho]SPS (ab5408)


title: Pol2Ser5_OTX015


title: RNA-seq_OTX015_rep2


title: 43511

city: ILLKIRCH

first: Yann

last: HERAULT

address: 1 rue Laurent Fries

country: France

institute: IGBMC/PHENOMIN-ICS

description:
total RNA extract (Qiagen RNeasy Plus Minikit)
16p11_2_wt5

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
The raw sequenced reads were aligned by Hisat2 against the Rno6.v96. 32623 ENSEMBL Gene Ids were quantified aligning to the Rno6.v96 assembly. HTSeq-count was used to generate the raw counts.
The downstream analyses were carried on with in-house bash scripts and R version 3.6 scripts using FCROS and DESeq2 packages to identify the DEGs. Raw reads and normalized counts have been deposited in GEO
Assembly: rn6

molecule: polyA RNA

organism: Rattus norvegicus

source_name: hippocampus

extract_protocol: Total RNA-Seq libraries were generated from 1000 ng of total RNA using TruSeq Stranded Total RNA Library Prep Gold kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the depleted RNA was fragmented into small pieces using divalent cations at 94oC for --- minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis. The Whole genome expression sequencing was performed by the platform using Illumina Hiseq 4000 and generating single-end RNA-Seq reads of 50 bps length.

tag: genetic background

value: Sprague Dawley

tag: Sex

value: M

tag: genotype

value: Dup/+

tag: tissue

value: hippocampus


title: Pol2Ser5_RVX208


title: ChIP-Seq_RPB1_dRPB3_IAA_0h_rep2

value: dRPB3 degron mESCs treated with 1ug/ml Dox for 12 h


title: ChIP-Seq_RPB1_dRPB3_IAA_0h_rep1


title: Pol2Ser5_DMSO


title: 43550

description:
total RNA extract (Qiagen RNeasy Plus Minikit)
16p11_2_Dup1


title: 43509

description:
total RNA extract (Qiagen RNeasy Plus Minikit)
16p11_2_wt4

value: wt


title: ChIP-Seq_RPB1_dRPB3_IAA_1h_rep1


title: 43580

description:
total RNA extract (Qiagen RNeasy Plus Minikit)
16p11_2_wt2


title: 43499

description:
total RNA extract (Qiagen RNeasy Plus Minikit)
16p11_2_wt3


title: ChAR-Seq_dRPB11_IAA_3h_rep1

description: Ribosomal RNA depleted, strand-specific library

data_processing:
ChAR-seq raw data were processed using a custom pipeline that builds on published workflows with minor modifications. Briefly, ribosomal reads were first removed by mapping to one copy of the mouse rDNA sequence. After adapter trimming and quality control with cutadapt and RseQC separately, clean reads were then aligned to a concatenated genome comprised of mouse mm10 and fly dm6 assemblies using bowtie2 with options (-very-sensitive-local) as described in the ChIP-seq section.
Only reads that were properly paired and uniquely aligned were retained for subsequent processing. Reads that mapped to the mouse (or human) genome were normalized to total reads originating from Drosophila spike-in cells, and the normalization factor was calculated as previously described (Jiang et al., 2020).
Plus- and minus-strand were assigned to uniquely mapped reads using SAMtools, and the final BAM files were converted to bigwig, separated by strand, and normalized to spike-in controls using bamCoverage from deeptools. Finally, bigWig score tracks for visualization prepared for different biological replicates but for the same treatment were merged to an averaged signal using the mean operator from the WiggleTools (v1.2) package (Zerbino, Johnson, et al. 2014).
Then raw read counts were calculated per gene, in a strand-specific manner, based on annotations described in the Gene list definition section below, using featureCounts (Liao et al., 2014).
Assembly: mm10 or hg19
Supplementary files format and content: bigwig files
Library strategy: ChAR-Seq

growth_protocol: For ChAR-seq, the degron cells were cultured in DMEM-KO (Thermo Fisher, Cat#10829018) supplemented with 15% FBS (Gibco, Cat#10099141C), 1× penicillin/ streptomycin (Gibco, Cat#15140122), 1 × L-glutamine (Gibco, Cat#25030081), 1 × non-essential amino acids (Gibco, Cat#11140050), 1 × nucleoside (Millipore, Cat#ES-008-D), 3 μM CHIR99021 (Selleck, Cat#S1263), 0.5 μM PD0325901 (Selleck, Cat#S1036), 143 uM 2-mercaptoethanol (Thermo Fisher, Cat#M3148) and maintained at 37℃ cell incubator with 5% CO2. The Schneider 2 (S2) cells were cultured in complete Schneider’s Drosophila Medium (Invitrogen, Cat#21720024) supplemented with 10% FBS (CellMax, Cat#SA311.02) at room temperature.HEK293T cells were cultured in basic-DMEM containing 10% FBS (Gibco, Cat#10099141C) and maintained at 37℃ cell incubator with 5% CO2.

extract_protocol:
Cells were collected and mixed with 10% S2 cells. The chromatin-associated RNA were extracted as reported (Dev M. Bhatt et al., 2012).
Chromatin-associated RNA were delivered to Novogene Company. The concentration, purity, and integrity of RNA were examined and followed by ribosomal RNA depletion and strand-specific library construction.

treatment_protocol: The degron cells were pretreated with 1 μg/ml Doxycycline for 12 h to induce TIR1 expression, then treated with or without 500 μM IAA for 1 h or 3h to induce target protein degradation. For HEK293T cells ChAR-seq, the HEK293T cells were transfected with GFP or N137-GFP plasmids using PEI. After 24 h, the cells were treated with 5 μg/ml puromycin for another 24 h, and the cells were harvested.

value: dRPB11-mAID-GFP degron mESCs treated with 1ug/ml Dox for 12 h, then treated with 500 uM IAA for 3h


title: ChAR-Seq_dRPB11_IAA_3h_rep2


title: BRD4_OTX015


title: 43496

description:
total RNA extract (Qiagen RNeasy Plus Minikit)
16p11_2_wt1


title: KV_B7_20200130

city: Baltimore

first: Suvarna

last: Nadendla

state: MD

address: 670 W.Baltimore Street

department: Institute for Genome Sciences

country: USA

institute: University of Maryland School of Medicine

description: Total RNAs extracted from PMNs from this donor D31 were of lower quality (lower RNA integrity [RIN] values), affecting overall RNA-seq data quality

data_processing:
Streptococcus pnemoniae : Sequence reads were trimmed for adaptor sequence and mapped to the EF3030 using bowtie v1.0 with parameters -mode=v --num_mismatches=2 --file-type=fastq --seedlen=28 --minins=0 --maxins=600 --library-type=fr  --args='--sam' --v --gzip
Homo sapiens: Sequenced reads were trimmedfor adaptor sequence and mapped to the 2018 GRCh38 Human genome assembly using HISAT v2.0 with parameters -mismatch-penalties=6,2 --softclip-penalties=2,1 --read-gap-penalties=5,3 --ref-gap-penalties=5,3 --min-intronlen=20 --max-intronlen=500000 --score-min=L,0,-0.2 --pen-cansplice=0 --num-threads=1 --pen-noncansplice=12 --pen-canintronlen=G,-8,1 --pen-noncanintronlen=G,-8,1 --rna-strandness=RF --dta-cufflinks=1 --num-alignments=5 --minins=0 --maxins=600 --no-unal=1 --args='' --v
Streptococcus pneumoniae: Transcripts Per Million values for gene features were calculated as described in D'Mello et al. Proceedings of the National Academy of Sciences of the United States of America vol. 117,52 (2020): 33507-33518. doi:10.1073/pnas.2010428117
Homo sapiens: Transcripts Per Million values for exon features were calculated as described in D'Mello et al. Proceedings of the National Academy of Sciences of the United States of America vol. 117,52 (2020): 33507-33518. doi:10.1073/pnas.2010428117
Assembly: Streptococcus pnemoniae:EF3030 accession NZ_CP035897.1 ;  Human: 2018 GRCh38 Human genome assembly GCA_000001405.15

organism: Streptococcus pneumoniae

source_name: Deep sequencing of cDNA from Streptococcus pneumoniae EF3030 bacteria and normalized human broncial epithelial cells (nHBEC), alone, together, and after coincubation with Influenza A virus pH1N1.

growth_protocol: Primary human bronchial epithelial cells were obtained from human lung tissue through the tissue donation program by the International Institute for the Advancement of Medicine . Cells were harvested from the human tracheobronchial tissues and plated onto collagen-coated 100-mm plates (Biocoat; Becton Dickinson), in BEGM medium to ~80% confluency, followed by passaging onto 6.5-mm Transwell inserts (0.4-μm pore size) with FNC coating (0407, AthenaES) and differentiated at an Air-Liquid Interface (ALI) using Lonza tissue culture reagents. Differentiation was further enhanced by adding 10 nM recombinant human neuregulin-1α/epidermal growth factor-like domain of heregulin-α (296-HR-050, R&D Systems) to the basolateral ALI media . Cells were incubated for approximately two weeks until appearance of ciliated cells and mucus production was seen.

extract_protocol:
On the day of RNA isolation, transwell samples were thawed and the membranes cut out using a scalpel. RNAprotect and isolated membranes were centrifuged at 10,000 rpm, to pellet the membrane and any dislodged cells, and the supernatant discarded. Pellets were then incubated in 100 μL of lysis buffer (10 μL of mutanolysin, 20 μL of proteinase K, 30 μL of lysozyme, 40 μL of TE buffer) for 10 minutes. Followed by mechanical disruption in 600 μL RLT buffer (RNeasy Mini Kit, Qiagen) containing 1% ß-mercaptoethanol, using a motorized pestle for 30 seconds. RNA was then captured on the RNeasy Mini Kit columns with DNase treatment on column (Qiagen protocol).
Strand specific RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Following culture of differentiated human bronchial epithelial cells on transwells, cells were infected with pH1N1 or mock infected (no pH1N1 controls) for 72 h (~50% of cells infected with IAV). pH1N1 infected cells were then exposed to 1000 CFUs of Streptococcus pneumoniae strain EF3030 for 6 h. For pneumococcal EF3030 control samples, ~50,000 CFUs of EF3030 were cultured in ALI media for 6 hours. 1ml of RNA protect was then added to all transwells and then stored in 5ml of RNAprotect Bacteria Reagent in 50 ml falcon tubes at -80C.

tag: treatment condition

value: Bacteria alone

tag: human cell type

tag: incubation time

tag: s. pneumoniae strain


title: ChAR-Seq_dRPB11_IAA_0h_rep2

value: dRPB11-mAID-GFP degron mESCs treated with 1ug/ml Dox for 12 h


title: BRD4_RVX208


title: ChAR-Seq_dRPB11_IAA_0h_rep1


title: 43552

description:
total RNA extract (Qiagen RNeasy Plus Minikit)
16p11_2_Dup3


title: ChAR-Seq_dRPB10_IAA_3h_rep2

value: dRPB10-mAID-GFP degron mESCs treated with 1ug/ml Dox for 12 h, then treated with 500 uM IAA for 3h


title: BRD4_DMSO


title: KV_B6_20200130


title: ChAR-Seq_dRPB10_IAA_3h_rep1


title: ChAR-Seq_dRPB10_IAA_0h_rep2

value: dRPB10-mAID-GFP degron mESCs treated with 1ug/ml Dox for 12 h


title: h4.IL21_Cd40.3.GCBC

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

data_processing:
Raw reads quality and adapter sequences were checked using fastqc (v. 0.11.7).
Filtered adaptor and poor quality sequences respectively, using trimgalore(v.0.6.5 )
The reference genome (mm10) based alignment of clean reads were performed using STAR (v.2.6.1a) (Dobin et al., 2013).
Gene-level counts were determined using featureCounts packgae by subread/2.0.1 (Liao et al. 2014).
Raw counts were analyzed for differential expression using the “voom” method (Law et al. 2014) in the “limma” R package (Ritchie et al. 2015).
Genome_build: Mus musculus reference genome (mm10).
Supplementary_files_format_and_content: tab-delimited text files include log2 normalized expression values for each Sample.

source_name: spleen

extract_protocol:
RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols, using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takata Cat# 634894).

treatment_protocol: GC B cells were beads-purified and stimulated

value: IgM B1-8 BCR transgenic BALB/c (MEG)

value: spleen

tag: cell type

value: GC B cell

value: 4h IL-21 + a-CD40 stimulation


title: H3K27ac_DMSO

value: engineered murine acute myeloid leukemia cell line (MLL-AF9/NRAS G112D)

value: H3K27ac (ab4729, Abcam)

value: DMSO


title: BRD4_BBC1115


title: h4.IL21_Cd40.2.NBC

value: Naive B cell


title: H3K9me3_ICM_rep2

city: Davis

first: Chuan

last: Zhou

state: CA

address: Meyer Hall, 450 Bioletti Way

department: Animal Science

institute: University of California, Davis

data_processing:
Raw reads were trimmed with Trim Galore (v0.4.0) and Cutadapt (v1.8.3) to remove adaptor sequences and low-quality reads (q < 20).
Trimmed reads were then mapped to the cattle reference genome (ARS-UCD1.2) using BWA (v0.7.9a) with the 'mem' mode and default parameters.
Duplicate reads were removed using Picard Tools (v2.26.10) and low-quality mapped reads were removed using SAMtools (version 1.9) to generate the final informative reads which were used for downstream analyses.
Peaks were called from each library with Epic2 using the parameters '--effective-genome-fraction 0.7 -bin 50 -g 1 -e 1' for H3K4me3, H3K27ac and ATAC-seq, and the parameters '--effective-genome-fraction 0.7 -bin 200 -g 5 -e 1' for H3K9me3 and H3K27me3.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: BED files show regions of histone modification or ATAC-seq signal enrichment (peaks).

organism: Bos taurus

source_name: In vitro produced embryo

growth_protocol: Bovine ovaries were collected from a local slaughterhouse and transported to the laboratory in 0.9% NaCl solution. Cumulus-oocyte complexes (COCs) were aspirated from antral follicles (2-10 mm in diameter) with a 10 ml syringe and then washed in M199 (Sigma, M7653) containing 2% (v/v) fetal bovine serum (FBS, Hyclone). Only COCs containing at least three layers of compact cumulus and evenly granulated cytoplasm were selected for maturation in vitro. After washing three times in M199 supplemented with 2% (v/v) FBS, COCs were cultured for 22-24 hours in BO-IVM media (IVF Bioscience, 71001) in an atmosphere of 5% CO2 in air at 38.5 °C. After maturation in vitro, MII oocytes were washed three times in SOF-IVF medium (107.7 mM NaCl, 25.07 mM NaHCO3, 7.16 mM KCl, 1.19 mM KH2PO4, 1.17 mM CaCl2, 0.49 mM MgCl2, 5.3 mM sodium lactate, 0.20 mM sodium pyruvate, 10 ?g/ml heparin, 0.5 mM fructose, 1X nonessential amino acids, 6 mg/ml BSA, 5 ?g/ml gentamicin), and then transferred to drops of SOF-IVF medium covered with mineral oil (Vitrolife, 10029). Frozen semen was thawed and 10 ul 2X106 sperm/ml were added to the drop. After incubation for 6 h in the incubator in an atmosphere of 5% CO2 in air at 38.5 °C, cumulus cells were removed by vortexing for 5 min and zygotes were cultured in BO-IVC media (IVF Bioscience, 71005).

extract_protocol:
GV oocytes were collected prior to maturation in vitro. Embryos at the 2-, 4-, 8-cell (cultured in the presence or absence of 50 μg/mL alpha-amanitin (Sigma, A2263)), morula, and blastocyst stages were collected at 32, 44, 56, 122, and 172 h post-insemination, respectively. For ICM separation, blastocysts were collected and subjected to immunosurgery with anti-bovine serum antibody (Sigma, B8270) and guinea pig complement serum (Innovative Research, IGP-COMPL-21249). For TE separation, blastocysts were collected and subjected to surgery under a microscope, cutting with a micro scalpel (Feather, 72046-30). GV oocytes and embryos were treated with 0.5% pronase to remove the zona pellucida, and then used for library construction of CUT&Tag or ATAC-seq. Approximately 500 oocytes or 1,000-1,500 blastomeres were collected for each CUT&Tag or ATAC-seq library.
CUT&Tag was performed following the manufacturer’s instructions (Hyperactive In-Situ ChIP Library Prep Kit, TD901, Vazyme) with modifications. In brief, bovine oocytes and embryos were incubated with concanavalin-coated magnetic beads for 20 min on a thermomixer at 400 rpm at room temperature (RT). The samples then were incubated with a primary antibody (1:50 dilution) overnight at 4 °C on a nutator, then with the secondary antibody (1:100 dilution, ABIN101961, Antibodies-online) for 1 h on a nutator at RT, then with hypoactive pA-Tn5 transposon for 1 h on a nutator at RT. To perform targeted digestion, 300 µL tagmentation buffer was then added, and samples were incubated at 37 °C for 1 h. The reaction was terminated by adding 10 µL of 0.5 M EDTA, 3 µL of 10% SDS and 2.5 µL of 20 mg/mL proteinase K to each tube, which were then incubated at 50 °C for 1 h. DNA extraction was performed by adding 300 µL of PCI (Phenol: Chloroform: Isoamyl alcohol = 25:24:1) to each tube and mixed by full-speed vortexing, after which the sample was transferred to a phase-lock tube (1038987, Qiagen) and centrifuged for 3 min at RT at 16,000 x g. Three hundred µL of chloroform was then added followed by centrifugation for 3 min at RT at 16,000 x g. The aqueous phase was removed and transferred to a 1.5 mL tube to which 750 µL of 100% ethanol was added, the tube inverted 10 times, and then centrifuged for 30 min at 4 °C at 16,000 x g. The supernatant was removed and 1 mL of 100% ethanol added, followed by centrifugation for 5 min at 4 °C at 16,000 x g. The supernatant was removed and the tube then allowed to dry in air. TE buffer (20 µL) was added and PCR was performed using NEB Next HiFi 2× PCR Master mix (New England Biolabs, M0541) as follows: 58 °C for 5 min, 72 °C for 5 min, 98 °C for 45 s, followed by 14 cycles of 98 °C for 15 s and 60 °C for 10 s, with a final extension at 72 °C for 1 min. Purification of PCR products was performed using Ampure XP beads (Bechman Coulter, A63881) and libraries were pooled for sequencing on the Illumina NextSeq platform to generate 40 bp paired-end reads.
For ATAC-seq library construction, pools of zona-free blastocysts, ICM and TE were collected for ATAC-seq library construction from three separate collections, respectively, and transferred to cold lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630). The samples were incubated on ice for 5 min, and then centrifuged for 10 min at 500 rcf, at 4°C. The supernatant was removed and the pellet was resuspended in 50 μl of transposition reaction mix (25 μl 2x TD buffer (Nextera DNA Library Prep Kit, Illumina), 2.5 μl TDE1 enzyme (Nextera DNA Library Prep Kit, Illumina), 22.5 μl ddH2O) by pipetting up and down three times. Transposition reactions were incubated at 37 °C for 60 min in a thermomixer at 300 rpm. Reaction products were purified with a MinElute PCR purification kit (Qiagen, Germany) and eluted in 20 μl EB buffer. Transposed DNA was amplified with NEB Next HiFi 2x PCR Master mix (New England Biolabs, M0541): 58 °C for 5 min, 72 °C for 5 min, 98 °C for 45 s, followed by 12 cycles of thermocycling (98 °C for 15 s and 60 °C for 10 s), and 72 °C for 1 min. Libraries were purified with Ampure XP beads (Bechman Coulter, A63881) and were pooled for sequencing on the Illumina NextSeq platform to generate 40 bp paired-end reads.

treatment_protocol: Embryos were cultured in the presence of α-amanitin (50 μg/ml).

tag: developmental stage

value: Inner cell mass

value: Control


title: H3K9me3_TE_rep2

value: Trophectoderm


title: H3K9me3_ICM_rep1


title: AMZ20_SA

type: genomic

city: Eiheiji-cho, Yoshida-gun

first: Shota

last: Nishitani

state: Fukui

address: 23-3 Matsuoka-Shimoaizuki

department: Research Center for Child Mental Development

country: Japan

institute: University of Fukui

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio Software v2.0.5; The beta values are preprocessed by noob (https://rdrr.io/bioc/minfi/man/preprocessNoob.html).

label: Cy5 and Cy3

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: Brain DNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) after disrupted and homogenized 10 mg RNAlater® preserved brain tissues by a rotor–stator (Speed: 6.5 m/sec, Running time: 45 sec, FastPrep FP120J-100, Savant Instruments, Inc.) with tissue homogenization beads (Lysing Matrix D, 2 mL, MP biomedicals, LLC). We followed the instruction in RiboPureTM RNA Purification Kit (Thermo Fisher Scientific, Inc.) for preprocessing for DNA extraction using RNAlater® preserved blood samples, although this preprocessing was originally for RNA extraction. Briefly, the RNAlater® preserved blood samples (720 L) were centrifuged 1 min at 16,000 x g and were removed supernatant. Then, 200 L of PBS were added and mixed by pipetting, and we repeated the centrifuge and supernatant removal. Finally, 200 L of PBS were added and mixed by pipetting and used for DNA extraction. Blood and buccal DNA were extracted using QIAamp DNA Mini kit (Qiagen) following the respective protocols for each tissue type. Saliva DNA was extracted using prepIT®•L2P reagent (DNA Genotek). DNA yield was quantified with the QubitTM dsDNA High Sensitivity Assay Kit (Thermo Fisher Scientific).

value: saliva

tag: gender

value: female

tag: age

tag: desease state

value: internal carotid‐posterior communicating aneurysm

tag: race

value: Japanese


title: ChAR-Seq_dRPB3_IAA_3h_rep2

tag: cell line

tag: treatment

value: dRPB3-mAID-GFP degron mESCs treated with 1ug/ml Dox for 12 h, then treated with 500 uM IAA for 3h


title: AMZ20_BL

value: blood


title: h4.IL21_Cd40.2.GCBC

tag: strain

value: IgM B1-8 BCR transgenic BALB/c (MEG)


title: H3K9me3_BL_rep2

value: Blastocyst


title: AMZ20_EP

value: buccal


title: h4.IL21_Cd40.1.NBC

value: spleen

value: 4h IL-21 + a-CD40 stimulation


title: ChAR-Seq_dRPB3_IAA_3h_rep1


title: AMZ19_BR

value: brain

value: Subarachnoid hemorrhage, moyamoya disease

tag: brodmann areas

value: angular gyrus

tag: hemisphere

value: right


title: ChAR-Seq_dRPB3_IAA_1h_rep2

value: dRPB3-mAID-GFP degron mESCs treated with 1ug/ml Dox for 12 h, then treated with 500 uM IAA for 1h


title: H3K9me3_TE_rep1

value: Trophectoderm

value: Control


title: h4.IL21_Cd40.1.GCBC

value: GC B cell


title: H3K9me3_MO_rep2

value: Morula


title: ChAR-Seq_dRPB3_IAA_1h_rep1


title: h4.Il21.3.NBC

value: Naive B cell

value: 4h IL-21 stimulation


title: H3K9me3_BL_rep1


title: H3K9me3_MO_rep1


title: AMZ20_BR

value: female

value: internal carotid‐posterior communicating aneurysm

value: Japanese

value: temporal pole


title: AMZ19_BL

value: blood


title: h4.IL21_Cd40.3.NBC

value: IgM B1-8 BCR transgenic BALB/c (MEG)

value: spleen

value: 4h IL-21 + a-CD40 stimulation


title: ChAR-Seq_dRPB3_IAA_0h_rep2

value: dRPB3-mAID-GFP degron mESCs treated with 1ug/ml Dox for 12 h


title: ChAR-Seq_dRPB10_IAA_0h_rep1

value: dRPB10-mAID-GFP degron mESCs treated with 1ug/ml Dox for 12 h


title: AMZ19_SA

value: saliva

value: Subarachnoid hemorrhage, moyamoya disease


title: H3K9me3_8C_rep2

value: 8-cell embryo

value: Control


title: ChAR-Seq_dRPB3_IAA_0h_rep1


title: AMZ19_EP

value: buccal


title: h4.Il21.2.NBC

value: Naive B cell


title: H3K9me3_8C_rep1


title: TT-Seq_RPB3_IAA_3h_rep2

description: Strand-specific library

data_processing:
TT-seq raw data were processed using a custom pipeline that builds on published workflows with minor modifications. Briefly, ribosomal reads were first removed by mapping to one copy of the mouse rDNA sequence. After adapter trimming and quality control with cutadapt and RseQC separately, clean reads were then aligned to a concatenated genome comprised of mouse mm10 and fly dm6 assemblies using bowtie2 with options (-very-sensitive-local) as described in the ChIP-seq section.
Only reads that were properly paired and uniquely aligned were retained for subsequent processing. Reads that mapped to the mouse genome were normalized to total reads originating from Drosophila spike-in cells, and the normalization factor was calculated as previously described (Jiang et al., 2020).
Plus- and minus-strand were assigned to uniquely mapped reads using SAMtools, and the final BAM files were converted to bigwig, separated by strand, and normalized to spike-in controls using bamCoverage from deeptools. Finally, bigWig score tracks for visualization prepared for different biological replicates but for the same treatment were merged to an averaged signal using the mean operator from the WiggleTools (v1.2) package (Zerbino, Johnson, et al. 2014).
Then raw read counts were calculated per gene, in a strand-specific manner, based on annotations described in the Gene list definition section below, using featureCounts (Liao et al., 2014).
Assembly: mm10
Supplementary files format and content: bigwig files
Library strategy: TT-Seq

growth_protocol: For TT-seq, dRPB3 and RPB3 degron cells were cultured in DMEM-KO (Thermo Fisher, Cat#10829018) supplemented with 15% FBS (Gibco, Cat#10099141C), 1× penicillin/ streptomycin (Gibco, Cat#15140122), 1 × L-glutamine (Gibco, Cat#25030081), 1 × non-essential amino acids (Gibco, Cat#11140050), 1 × nucleoside (Millipore, Cat#ES-008-D), 3 μM CHIR99021 (Selleck, Cat#S1263), 0.5 μM PD0325901 (Selleck, Cat#S1036), 143 uM 2-mercaptoethanol (Thermo Fisher, Cat#M3148) and maintained at 37℃ cell incubator with 5% CO2. The Schneider 2 (S2) cells were cultured in complete Schneider’s Drosophila Medium (Invitrogen, Cat#21720024) supplemented with 10% FBS (CellMax, Cat#SA311.02) at room temperature.

extract_protocol:
Nascent RNA samples were prepared as described previously with some modifications (Schwalb et al., 2016). Total RNA was extracted using TRIzol reagent according to the manufacturer’s instruction. The RNA was fragmentated with sonication, and the nascent fragmented RNA was biotinylated with 200 ug/mL Biotin-HPDP (Macklin, Cat#B871617). Biotinylated RNA was enriched with M280 streptavidin beads (Thermo Fisher Scientific, Cat#11205D) following the manufacturer's instruction and the enriched RNA was extracted with TRIzol reagent.
The purified nascent RNA was subjected to library construction following manufacturer's instruction (Vazyme, Cat#NR605). 300-500 bp library bands were gel-selected and delivered to Novogene company for sequencing.

treatment_protocol: The degron cells were pretreated with 1 μg/ml Doxycycline for 12 h to induce TIR1 expression, then treated with or without 500 μM IAA for 3h to induce target protein degradation. After degradation, cells are treated with 1 mM 4sU (Macklin, Cat#T820213) to metabolically label nascent RNA for 30 min, and the cells were harvested and mixed with 10% Drosophila S2 cells pretreated with 100 μM 4sU for 12 h.

value: RPB3 degron mESCs treated with 1ug/ml Dox for 12 h, then treated with 500 uM IAA for 3h


title: h4.Il21.2.GCBC

value: GC B cell

value: 4h IL-21 stimulation


title: AMZ18_BR

value: brain

value: male

value: internal carotid artery stenosis

value: Japanese

value: straight gyrus

value: right


title: H3K9me3_amanitin_8C_rep2

value: Transcription inhibition


title: AMZ18_BL

value: blood


title: h4.Il21.1.NBC

value: IgM B1-8 BCR transgenic BALB/c (MEG)

value: spleen


title: H3K9me3_amanitin_8C_rep1

value: 8-cell embryo


title: TT-Seq_RPB3_IAA_0h_rep2

description: Strand-specific library

value: RPB3 degron mESCs treated with 1ug/ml Dox for 12 h


title: H3K9me3_4C_rep2

value: 4-cell embryo

value: Control


title: AMZ18_SA

value: saliva


title: TT-Seq_RPB3_IAA_0h_rep1

description: Strand-specific library


title: H3K9me3_4C_rep1


title: h4.IgM_Cd40.2.NBC

value: Naive B cell

value: 4h a-IgM + a-CD40 stimulation


title: h4.Il21.1.GCBC

value: GC B cell

value: 4h IL-21 stimulation


title: TT-Seq_dRPB3_IAA_3h_rep2

description: Strand-specific library

value: dRPB3 degron mESCs treated with 1ug/ml Dox for 12 h, then treated with 500 uM IAA for 3h


title: AMZ17_BR

value: brain

value: male

value: temporal lobe epilepsy

value: Japanese

value: middle temporal gyrus


title: h4.IgM_Cd40.2.GCBC

value: IgM B1-8 BCR transgenic BALB/c (MEG)


title: AMZ18_EP

value: buccal

value: internal carotid artery stenosis


title: H3K9me3_2C_rep2

value: 2-cell embryo


title: TT-Seq_dRPB3_IAA_3h_rep1

description: Strand-specific library


title: h4.Il21.3.GCBC

value: spleen


title: AMZ17_BL

value: blood


title: h4.IgM_Cd40.1.NBC


title: TT-Seq_dRPB3_IAA_0h_rep2

description: Strand-specific library

value: dRPB3 degron mESCs treated with 1ug/ml Dox for 12 h


title: H3K9me3_2C_rep1

value: Control


title: H3K9me3_GV_rep2

source_name: Oocyte

value: GV oocyte


title: TT-Seq_RPB3_IAA_3h_rep1

description: Strand-specific library

value: RPB3 degron mESCs treated with 1ug/ml Dox for 12 h, then treated with 500 uM IAA for 3h


title: TT-Seq_dRPB3_IAA_0h_rep1

description: Strand-specific library


title: h4.IgM_Cd40.1.GCBC

value: GC B cell

value: 4h a-IgM + a-CD40 stimulation


title: h4.IgM.2.NBC

value: Naive B cell

value: 4h a-IgM stimulation


title: H3K9me3_GV_rep1


title: h4.IgM.2.GCBC


title: H3K27me3_TE_rep2

value: Trophectoderm


title: AMZ16_BR

value: brain

value: male

value: frontal lobe meningioma, epilepsy

value: Japanese

value: frontal eye field

value: right


title: AMZ16_BL


title: h4.IgM.1.NBC

value: IgM B1-8 BCR transgenic BALB/c (MEG)

value: spleen


title: H3K27me3_TE_rep1


title: AMZ16_SA

value: saliva


title: AMZ16_EP

value: buccal


title: h4.Ctl.2.NBC

value: 4h no stimulation control


title: H3K27me3_ICM_rep1

value: Inner cell mass

value: Control


title: Mouse,LV-MBD5,rep5

city: Chongqing

first: Feng-lin

last: Tang

address: No. 1, Youyi Road, Yuzhong District, Chongqing

department: Chongqing Key Laboratory of Neurology

institute: The First Affiliated Hospital of Chongqing Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the mus musculus（ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/） reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: hippocampus

tag: injection

value: Kainic acid model after MBD5 lentivirus infection one month


title: AMZ15_BR

tag: tissue

value: female

value: temporal lobe epilepsy, glioma

value: temporal pole

value: left


title: Mouse,LV-MBD5,rep4


title: AMZ17_SA

value: male

value: temporal lobe epilepsy


title: h4.IgM.1.GCBC

value: GC B cell

value: 4h a-IgM stimulation


title: AMZ15_BL

value: blood

value: Japanese


title: H3K27me3_BL_rep1

value: Blastocyst


title: H3K27me3_BL_rep2


title: AMZ17_EP

value: buccal


title: H3K27me3_MO_rep2

value: Morula


title: AMZ15_SA

value: saliva


title: h4.Ctl.1.GCBC

value: IgM B1-8 BCR transgenic BALB/c (MEG)

value: spleen

value: 4h no stimulation control


title: h4.CD40.5.NBC

value: Naive B cell

value: 4h a-CD40 stimulation


title: h4.Ctl.1.NBC


title: Mouse,LV-MBD5,rep2

value: hippocampus

value: Kainic acid model after MBD5 lentivirus infection one month


title: AMZ14_BR

value: brain

value: female

value: middle cerebral artery aneurysm

value: dorsal entorhinal cortex

value: right


title: AMZ15_EP

value: temporal lobe epilepsy, glioma

value: Japanese


title: H3K27me3_8C_rep2

value: 8-cell embryo

value: Control


title: Mouse,LV-MBD5,rep1


title: Mouse,LV-Control, rep5

value: LV-control


title: H3K27me3_ICM_rep2

value: Inner cell mass


title: h4.CD40.4.NBC

value: IgM B1-8 BCR transgenic BALB/c (MEG)

value: spleen


title: H3K27me3_MO_rep1

value: Morula


title: AMZ14_BL

value: blood


title: h4.Ctl.2.GCBC

value: GC B cell

value: 4h no stimulation control


title: H3K27me3_amanitin_8C_rep2

value: Transcription inhibition


title: h4.CD40.4.GCBC

value: 4h a-CD40 stimulation


title: AMZ14_EP

value: buccal

value: female

value: middle cerebral artery aneurysm


title: Mouse,LV-Control, rep3

value: hippocampus

value: Kainic acid model after MBD5 lentivirus infection one month


title: Mouse,LV-MBD5,rep3


title: h4.Cd40.3.NBC

value: Naive B cell


title: Mouse,LV-Control, rep2


title: AMZ13_BR

value: brain

value: male

value: internal carotid artery-posterior communicating artery aneurysm

value: Japanese

value: insula

value: right


title: h4.Cd40.2.NBC

value: IgM B1-8 BCR transgenic BALB/c (MEG)

value: spleen


title: Mouse,LV-Control, rep1

value: LV-control


title: H3K27me3_4C_rep2

value: 4-cell embryo

value: Control


title: h4.Cd40.3.GCBC

value: GC B cell

value: 4h a-CD40 stimulation


title: AMZ13_BL

value: blood


title: h4.CD40.5.GCBC


title: H3K27me3_4C_rep1


title: h4.Cd40.2.GCBC


title: AMZ13_EP

value: buccal


title: H3K27me3_8C_rep1

value: 8-cell embryo


title: h4.Cd40.1.NBC

value: Naive B cell


title: AMZ12_BR

value: brain

value: tentorial meningioma

value: middle temporal gyrus


title: H3K27me3_2C_rep2

value: 2-cell embryo


title: h4.Cd40.1.GCBC


title: Mouse,LV-Control, rep4

value: hippocampus

value: Kainic acid model after MBD5 lentivirus infection one month


title: AMZ14_SA

value: saliva

value: female

value: middle cerebral artery aneurysm

value: Japanese


title: h2.IL21_Cd40.3.NBC

value: IgM B1-8 BCR transgenic BALB/c (MEG)

value: spleen

value: 2h IL-21 + a-CD40 stimulation


title: H3K27me3_2C_rep1

value: Control


title: H3K27me3_GV_rep2

value: GV oocyte


title: AMZ12_BL

value: blood

value: male


title: h2.IL21_Cd40.3.GCBC

value: GC B cell


title: H3K27me3_GV_rep1


title: h2.IL21_Cd40.2.NBC

value: Naive B cell


title: AMZ12_SA

value: tentorial meningioma


title: AMZ12_EP

value: buccal


title: H3K27ac_TE_rep2

value: Trophectoderm


title: H3K27ac_ICM_rep2

value: Inner cell mass


title: AMZ11_BL

value: internal carotid artery-posterior communicating artery aneurysm


title: h2.IL21_Cd40.2.GCBC


title: H3K27ac_ICM_rep1


title: H3K27ac_TE_rep1


title: h2.IL21_Cd40.1.NBC


title: AMZ11_BR

value: brain

value: female

value: orbitofrontal cortex

value: left


title: h2.IL21_Cd40.1.GCBC

value: IgM B1-8 BCR transgenic BALB/c (MEG)

value: spleen


title: AMZ13_SA

value: saliva

value: Japanese


title: AMZ11_SA


title: AMZ11_EP


title: AMZ10_EP

value: anterior communicating artery aneurysm


title: h2.Il21.2.NBC

value: 2h IL-21 stimulation


title: H3K27ac_BL_rep2

value: Blastocyst

value: Control


title: H3K27ac_MO_rep2

value: Morula


title: AMZ10_SA


title: H3K27ac_BL_rep1


title: H3K27ac_MO_rep1


title: AMZ10_BL

value: blood


title: h2.Il21.2.GCBC

value: GC B cell


title: h2.Il21.1.NBC

value: Naive B cell


title: AMZ10_BR

value: right


title: h2.Il21.1.GCBC


title: H3K27ac_8C_rep2

value: 8-cell embryo


title: AMZ09_EP

value: buccal

value: female

value: internal carotid artery stenosis


title: H3K27ac_8C_rep1


title: h2.IgM_Cd40.2.NBC

value: IgM B1-8 BCR transgenic BALB/c (MEG)

value: 2h a-IgM + a-CD40 stimulation


title: AMZ09_SA

value: saliva


title: AMZ09_BL

value: Japanese


title: h2.IgM_Cd40.2.GCBC

value: spleen


title: H3K27ac_amanitin_8C_rep1

value: Transcription inhibition


title: h2.Il21.3.GCBC

value: 2h IL-21 stimulation


title: h2.IgM_Cd40.1.GCBC


title: h2.IgM_Cd40.1.NBC


title: AMZ09_BR

value: brain

value: temporal pole

value: left


title: H3K27ac_amanitin_8C_rep2


title: H3K27ac_4C_rep2

value: 4-cell embryo

value: Control


title: E21K_3_D7

first: He

last: Mengjiao

institute: Academy of Military Medical Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then mapped to mm8 whole genome using bowtie v0.12.2 with parameters.
Reads Per Kilobase of exon per Megabase of library size(RPKM) were calculated using a protocol from Chepelev et al.,Nucleic Acids Research, 2009. In short,exons from all isoforms.
Assembly: mm8
Supplementary files format and content: table-delimited text files inclide RPKM values for each Sample ......

source_name: brain

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit(Cat#FC-122-1001) was used with 1 ug of total RNA for the construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: E21K infected

tag: timepoint

value: 7 dpi


title: E21K_2_D7


title: H3K27ac_4C_rep1


title: E21K_1_D7


title: AMZ08_SA

value: male

value: frontal lobe tumor


title: AMZ08_EP

value: buccal


title: H3K27ac_2C_rep2

value: 2-cell embryo


title: E21K_3_D3

value: 3 dpi


title: H3K27ac_2C_rep1


title: E21K_2_D3


title: h2.IgM.1.NBC

value: IgM B1-8 BCR transgenic BALB/c (MEG)

value: Naive B cell

value: 2h a-IgM stimulation


title: E21K_1_D3


title: H3K27ac_GV_rep2

value: GV oocyte


title: h2.IgM.1.GCBC

value: spleen

value: GC B cell


title: AMZ08_BR

value: brain

value: Japanese

value: dlPFC

value: right


title: AMZ08_BL

value: blood


title: H3K27ac_GV_rep1

value: Control


title: h2.Ctl.2.NBC

value: 2h no stimulation control


title: WT_3_D7

value: WT infected

value: 7 dpi


title: H3K4me3_TE_rep2

value: Trophectoderm


title: WT_2_D7


title: WT_1_D7


title: h2.Ctl.2.GCBC


title: h2.Ctl.1.NBC


title: h2.IgM.2.GCBC


title: AMZ07_BL

value: male

value: internal carotid artery stenosis


title: h2.IgM.2.NBC

value: IgM B1-8 BCR transgenic BALB/c (MEG)

value: Naive B cell


title: H3K4me3_TE_rep1


title: h2.Ctl.1.GCBC


title: WT_2_D3

value: 3 dpi


title: AMZ07_BR

value: temporal pole


title: H3K4me3_ICM_rep1

value: Inner cell mass


title: WT_3_D3

value: brain


title: h2.CD40.5.NBC

value: spleen

value: 2h a-CD40 stimulation


title: H3K4me3_ICM_rep2


title: PBS_3_D7

value: mock


title: AMZ07_EP

value: buccal

value: Japanese


title: h2.CD40.4.NBC


title: h2.CD40.5.GCBC

value: GC B cell


title: H3K4me3_BL_rep2

value: Blastocyst

value: Control


title: AMZ06_BL

value: blood

value: anterior communicating artery aneurysm


title: H3K4me3_BL_rep1


title: h2.CD40.4.GCBC


title: AMZ07_SA

value: saliva

value: male

value: internal carotid artery stenosis


title: AMZ06_BR

value: straight gyrus

value: left


title: PBS_1_D7

value: 7 dpi


title: PBS_2_D7

value: brain


title: h2.Cd40.3.NBC

value: IgM B1-8 BCR transgenic BALB/c (MEG)

value: spleen

value: Naive B cell


title: AMZ04_EP

value: buccal

value: female

value: metastatic brain tumor (breast cancer)


title: PBS_3_D3

value: mock

value: 3 dpi


title: H3K4me3_MO_rep1

value: Morula

value: Control


title: H3K4me3_8C_rep2

value: 8-cell embryo


title: h2.Cd40.2.NBC

value: 2h a-CD40 stimulation


title: WT_1_D3

value: WT infected


title: AMZ06_EP

value: male

value: anterior communicating artery aneurysm

value: Japanese


title: H3K4me3_8C_rep1


title: AMZ04_BL

value: blood


title: PBS_2_D3

value: brain


title: h2.Cd40.2.GCBC

value: IgM B1-8 BCR transgenic BALB/c (MEG)

value: spleen

value: GC B cell


title: AMZ06_SA

value: saliva


title: PBS_1_D3


title: H3K4me3_amanitin_8C_rep2

value: Transcription inhibition


title: H3K27me3_amanitin_8C_rep1


title: h2.Cd40.1.NBC

value: Naive B cell


title: H3K4me3_amanitin_8C_rep1


title: TOM+_multiplexed_capture2_HTO

city: Darlinghurst

first: Tri

middle: Giang

last: Phan

state: New South Wales

address: 384 Victoria St

department: Immunology Division

country: Australia

institute: Garvan Institute

description:
10X capture 2
Hashtag-derived oligonucleotide (HTO)
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

library_source: transcriptomic single cell

data_processing:
CellRanger v4.0.0. count and aggr functions to aggregate reads across sequencing lanes into a single set of  barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz
Cell barcodes from CellRanger output were used as whitelist to quantify ADTs and HTOs using CITE-seq-Count (v1.4.5)
Assembly: mm10
Supplementary files format and content: CellRanger aggr output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CITE-seq-Count umi-count files: adt_barcodes.tsv.gz, adt_features.tsv.gz, adt_matrix.tsv.gz
Supplementary files format and content: CITE-seq-Count umi-count files: hto_barcodes.tsv.gz, hto_features.tsv.gz, hto_matrix.tsv.gz

source_name: lymph nodes

extract_protocol:
CD11b hi TOM pos cells sorted from 2 unimmunized 2 immunized mice. Single cells were encapsulated in  Gel-Beads-in emulsion (GEMs) using the 10X Controller with a Chromium Single Cell 3’ GEM Library and Gel Bead kit (Garvan Weizmann Centre for Cellular Genomics).
The CITE-seq and hashing protocol described by Stoeckius et al was used to generate an antibody-derived tag (ADT) sequencing library, a hashtag oligo (HTO) library and a 3’ gene expression library for each capture reaction (Stoeckius et al.,2017) https://citeseq.files.wordpress.com/2019/02/cite-seq_and_hashing_protocol_190213.pdf

value: lymph nodes

value: CD11b hi TOM +

tag: library type

value: HTO

tag: antibodies

value: TotalSeq-A0301 anti-mouse Hashtag 1 (unimmunized), TotalSeq-A0302 anti-mouse Hashtag 2 (unimmunized), TotalSeq-A0303 anti-mouse Hashtag 3 (immunized), TotalSeq-A0304 anti-mouse Hashtag 4 (immunized)


title: h2.Cd40.1.GCBC

value: 2h a-CD40 stimulation


title: H3K4me3_4C_rep2

value: 4-cell embryo

value: Control


title: TOM+_multiplexed_capture2_ADT

description:
10X capture 2
Antibody-derived oligonucleotide (ADT)
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

value: ADT

value: TotalSeq-A0106 anti-mouse CD11c, TotalSeq-A0015 anti-mouse Ly-6G, TotalSeq-A0013 anti-mouse Ly-6C, TotalSeq-A0440 anti-mouse CD169 (Siglec-1), TotalSeq-A0560 anti-mouse CD68, TotalSeq-A0114 anti-mouse F4/80


title: AMZ04_BR

value: female

value: metastatic brain tumor (breast cancer)

value: Japanese

value: visual cortex

value: left


title: B6: high protein low carbohydrate(HPLC) diet rep5

city: Shenzhen

first: li

last: anqi

address: No. 66, Gongchang Road, Guangming District

institute: School of Pharmaceutical Sciences (Shenzhen)

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to dmel-all-r6.39 whole genome using hisat2 with parameters -p 6 -q -x genome_tran -1.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: dmel-all-r6.39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: Brain

extract_protocol:
Brains were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Wild-type (W1118)

value: brain

tag: Sex

value: male

value: HPLC diet (P:C=1:2,360g/L)


title: H3K4me3_MO_rep2

tag: developmental stage

value: Morula


title: AMZ03_SA

value: saliva

tag: gender

value: internal carotid artery-posterior communicating artery aneurysm


title: AMZ03_BL

value: blood

tag: age


title: B5: high protein low carbohydrate(HPLC) diet rep4


title: TOM+_multiplexed_capture1_HTO

description:
10X capture 1
Hashtag-derived oligonucleotide (HTO)
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: lymph nodes

tag: cell type

value: CD11b hi TOM +

value: HTO

value: TotalSeq-A0301 anti-mouse Hashtag 1 (unimmunized), TotalSeq-A0302 anti-mouse Hashtag 2 (unimmunized), TotalSeq-A0303 anti-mouse Hashtag 3 (immunized), TotalSeq-A0304 anti-mouse Hashtag 4 (immunized)


title: H3K4me3_4C_rep1

value: 4-cell embryo

value: Control


title: AMZ04_SA

value: female

tag: desease state

value: metastatic brain tumor (breast cancer)

tag: race

value: Japanese


title: AMZ03_BR

value: temporal pole

value: left


title: B4: high protein low carbohydrate(HPLC) diet rep3

value: Wild-type (W1118)

value: brain

value: male

tag: treatment


title: H3K4me3_2C_rep2

value: 2-cell embryo


title: B3: high protein low carbohydrate(HPLC) diet rep2

value: HPLC diet (P:C=1:2,360g/L)


title: TOM+_multiplexed_capture1_ADT

description:
10X capture 1
Antibody-derived oligonucleotide (ADT)
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

value: ADT

value: TotalSeq-A0106 anti-mouse CD11c, TotalSeq-A0015 anti-mouse Ly-6G, TotalSeq-A0013 anti-mouse Ly-6C, TotalSeq-A0440 anti-mouse CD169 (Siglec-1), TotalSeq-A0560 anti-mouse CD68, TotalSeq-A0114 anti-mouse F4/80


title: H3K4me3_2C_rep1


title: B2: high protein low carbohydrate(HPLC) diet rep1


title: AMZ02_SA

value: saliva

value: falx meningioma


title: H3K4me3_GV_rep1

value: GV oocyte


title: AMZ03_EP

value: buccal

value: internal carotid artery-posterior communicating artery aneurysm


title: WT.3

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

data_processing:
Reads were aligned to Mouse genome GRCm38 with HISAT2.
counts generated for GRCm38 v102 with featureCounts from the subread package.
Counts were normalized with voom and differential expression tested with limma.
Genome_build: GRCm38
Supplementary_files_format_and_content: Text file of voom normalized expression for each gene and each sample

source_name: lung

extract_protocol:
Lungs were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
cDNA libraries were generated using NEBNext® Ultra™ II Directional (stranded) RNA Library Prep Kit for Illumina (NEB #E7760L). Ribosomal RNA was removed using NEBNext rRNA Depletion Kit (human, mouse, rat) (E #E6310X). Libraries were indexed using NEBNext Multiplex Oligos for Illumina Unique Dual Index Primer Pairs (NEB #644OS/L). Library prep generated cDNA was quantified and analyzed using Agilent DNA chip and Qubit DNA dye. Ribo-depleted total transcriptome libraries were sequenced on an Illumina NovaSeq SP flow cell (paired-end 150bp format; 35-40 million clusters, equivalent to 70-80 million reads). Library preparation, QC, and sequencing was carried out at Nationwide Children’s Hospital genomic core.

tag: knockout group

value: WT

value: 16 week old mouse


title: A7: low protein high carbohydrate(LPHC) diet rep5

value: LPHC diet (P:C=0:1,360g/L)


title: AMZ02_BL

value: blood

value: female

value: Japanese


title: ATAC_TE_rep3

value: Trophectoderm

value: Control


title: WT.2


title: A6: low protein high carbohydrate(LPHC) diet rep4

value: Wild-type (W1118)

value: brain

value: male


title: AMZ02_BR

tag: brodmann areas

value: frontal pole

value: right


title: ATAC_TE_rep2


title: WT.1


title: TOM+_multiplexed_capture2_mRNA

description:
10X capture 2
poly A RNA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: lymph nodes

value: CD11b hi TOM +

value: mRNA


title: AMZ01_EP

value: buccal

value: primary central nervous system vasculitis


title: ATAC_TE_rep1


title: A4: low protein high carbohydrate(LPHC) diet rep3


title: A3: low protein high carbohydrate(LPHC) diet rep2


title: AMZ01_SA

value: saliva


title: GSDM.2

value: GSDM

value: 16 week old mouse


title: AMZ01_BL

value: blood


title: A1: low protein high carbohydrate(LPHC) diet rep1

value: LPHC diet (P:C=0:1,360g/L)


title: TOM+_multiplexed_capture1_mRNA

description:
10X capture 1
poly A RNA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: H3K4me3_GV_rep2

value: GV oocyte


title: ATAC_ICM_rep3

value: Inner cell mass

value: Control


title: ATAC_ICM_rep2


title: AMZ01_BR

value: brain

value: Japanese

value: dlPFC

tag: hemisphere


title: GSDM.1


title: ATAC_ICM_rep1


title: ChAR-Seq_N137_Overexpress_rep2

source_name: HEK293T cells

tag: cell line

value: HEK293T cells transfected with N137-GFP plasmids using PEI; after 24 h, cells treated with 5 ug/ml puromycin for another 24 h


title: CSP11.3


title: KV_HB4_20200130

organism:
Streptococcus pneumoniae
Homo sapiens

tag: treatment condition

value: Co-culture

tag: human cell type

value: nHBEC

tag: incubation time

tag: s. pneumoniae strain


title: ChAR-Seq_N137_Overexpress_rep1


title: CSP11.2


title: ChAR-Seq_GFP_rep2

value: HEK293T cells transfected with GFP plasmids using PEI; after 24 h, cells treated with 5 ug/ml puromycin for another 24 h


title: ATAC_BL_rep2

value: Blastocyst


title: CSP11.1


title: ChAR-Seq_GFP_rep1


title: KV_HB1_20191114


title: KV_HB3_20200130


title: GSDM.3


title: ATAC_BL_rep1


title: ST-C2 WGBS

status: Public on Feb 15 2023

city: Gautam Buddha Nagar

first: Rohini

last: Garg

state: UP

address: Shiv Nadar University, NH - 91, Tehsil Dadri

country: India

institute: Shiv Nadar University

description:
ST-C2
BS-seq

data_processing:
The FASTQ files obtained from BS-sequencing were pre-processed using NGS QC Toolkit (v2.3) to remove adapters and low-quality reads below 20 Phred score.
Filtered high-quality reads were mapped on the Kabuli chickpea genome (v1.0) using Bismark (v0.14.3).
Identification of methylated cytosines in different sequence context was determined using Methylkit (v1.5.3) with minimum read coverage of ≥ 3 and P-value ≤ 0.0001.
Assembly: Kabuli chickpea genome (v1.0) (https://data.legumeinfo.org/Cicer/arietinum/genomes/CDCFrontier.gnm1.GkHc/) (BIOPROJECT:PRJNA175619)

organism: Cicer arietinum

source_name: root

growth_protocol: Cicer arietinum ICCV2 and JG62 seedlings were grown in growth chamber

extract_protocol:
Genomic DNA was extracted from all the samples using Qiagen DNeasy kit. The extracted DNA were quantified using Qubit 2.0 Fluorometer and quality was accessed in Bioanalyzer.
DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Salinity stress was given to 12 days old seedlings with 80mM NaCl for 6 days on alternate days. The roots were harvested from 18 day old plants from both stressed and control samples.

tag: condition

tag: genotype

value: 18 days old


title: ST-S2 small RNA-Seq

description:
ST-S2
total RNA

data_processing:
The FASTQ files obtained from small RNA sequencing were processed to remove adapters and low-quality reads.
After quality control, the reads were collapsed into a unique read and read count for each sequence was calculated.
Unique reads were mapped to the Kabuli chickpea genome.
Assembly: Kabuli chickpea genome (v1.0) (https://data.legumeinfo.org/Cicer/arietinum/genomes/CDCFrontier.gnm1.GkHc/) (BIOPROJECT:PRJNA175619)

extract_protocol:
Total RNA was isolated using TRI reagent and small RNA library was prepared using TruSeq small RNA sample Prep Kit  according to manufacturer’s instruction.
Small RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Salinity stress was given on 12 day old plants with 80mM NaCl for 6 days on alternate days. The roots were harvested from both stress and control samples from 18 days old seedlings.

value: Stress


title: ST-C1 WGBS

description:
ST-C1
BS-seq


title: SS-S1 WGBS

description:
SS-S1
BS-seq


title: SS-S2 WGBS

description:
SS-S2
BS-seq


title: ST-C1 small RNA-Seq

description:
ST-C1
total RNA


title: ST-S2 WGBS

description:
ST-S2
BS-seq


title: ST-S1 WGBS

description:
ST-S1
BS-seq


title: SS-C1 small RNA-Seq

description:
SS-C1
total RNA


title: ST-S2 RNA-Seq

description:
ST-S2
transcriptome

data_processing:
The FASTQ files obtained were pre-processed using NGS QC Toolkit (v2.3.3) to remove adapters and low-quality reads. Low-quality reads with Phred score >20 were filtered.
Filtered high-quality reads were mapped on the Kabuli chickpea genome (v1.0) using TopHat2 pipeline (v2.1.1).
A consensus reference-guided assembly of the transcriptome data was generated using Cufflinks (v2.2.1).
Differential expression of genes was determined by Cuffdiff (v2.2.1).
Assembly: Kabuli chickpea genome (v1.0) (https://data.legumeinfo.org/Cicer/arietinum/genomes/CDCFrontier.gnm1.GkHc/) (BIOPROJECT:PRJNA175619)
Supplementary files format and content: Tab-delimited text file including FPKM values for genes in the stress sensitive and stress tolerant under control and salinity stress conditions.

growth_protocol: Cicer arietinum ICCV2 and JG62 genotype seedlings were grown in growth chamber

extract_protocol:
Total RNA was extracted using TRI Reagent. RNA quantification was performed and quality was assessed using Agilent Bioanalyzer. cDNA libraries were prepared and RNA-sequencing was performed on Illumina platform.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Salinity stress was given on 12 day old seedlings with 80mM NaCl on alternate days for 6 days. The roots were harvested from both stressed and control samples from 18 days old plants.

tag: tissue

value: salinity


title: ST-S1 RNA-Seq

description:
ST-S1
transcriptome


title: SS-S2 small RNA-Seq

description:
SS-S2
total RNA


title: ATAC_BL_rep3

tag: developmental stage


title: ST-C1 RNA-Seq

description:
ST-C1
transcriptome

tag: age


title: ST-C2 RNA-Seq

description:
ST-C2
transcriptome


title: SS-S1 RNA-Seq

description:
SS-S1
transcriptome


title: SS-C1 RNA-Seq

description:
SS-C1
transcriptome


title: SS-C2 WGBS

description:
SS-C2
BS-seq


title: SS-S2 RNA-Seq

description:
SS-S2
transcriptome


title: SS-C1 WGBS

description:
SS-C1
BS-seq


title: SS-C2 RNA-Seq

description:
SS-C2
transcriptome


title: AMZ02_EP

value: buccal

tag: gender

value: female

value: falx meningioma


title: 133013

type: RNA

city: Berlin

first: Arndt

last: Stahler

address: Chariteplatz 1

department: Medical Department of Hematology, Oncology and Cancer Immunology

country: Germany

institute: Charite Universitaetsmedizin Berlin

description: RNA derived from FFPE tissue sample which was obtained prior to treatment start

hyb_protocol: 130 ng of RNA (controlled for quality and quantity by spectrophotometry and bioanalyzer) were hybridized with reporter and capture probes for 16 to 48 h

scan_protocol: The Nanostring nCounter SPRINT Profiler platform was used for scanning according to manual.

data_processing: Normalization and log2 transformation of .RCC data was performed using the Nanostring nSolver Analysis software.

label: fluorescent barcode

source_name: metastatic colorectal cancer

extract_protocol: mRNA was isolated from tumor slides following the instructions of the RNeasy FFPE tissue kit (Qiagen, Hilden, Germany)

value: metastatic colorectal cancer

tag: Stage

value: IV

tag: Sex

value: male


title: 133015


title: 133012


title: 133008


title: 133016


title: 133010


title: 133011


title: 133009


title: 133017


title: 130001


title: 133002


title: 133006


title: 133001


title: 123005


title: 133003


title: 123003


title: 123004


title: 123001


title: 121008


title: 121005


title: 121006


title: 121009


title: 121002


title: 121003


title: 121001


title: 133005


title: 118007


title: 114012


title: 114013


title: 114011


title: 121004


title: 114008


title: 114009


title: 114010


title: 114005


title: 114006


title: 114004


title: 114003


title: 114002


title: 114001


title: 111007


title: 111005


title: 111002


title: 111006


title: 111001


title: 105001


title: 101002


title: 102001


title: 111004


title: 103002


title: 101005


title: 103001


title: 101001


title: 100026


title: 100027


title: 100024


title: 100023


title: 111003


title: 100022


title: 100021


title: 100020


title: 100012


title: 100010


title: 100015


title: 100001


title: 98001


title: 100017


title: 100002


title: 95004


title: 100006


title: 96002


title: 95002


title: 93005


title: 95001


title: 93004


title: 93001


title: 93003


title: 92004


title: 92003


title: 93002


title: 92002


title: 100019


title: 100016


title: 100013


title: 90002


title: 87010


title: 90001


title: 87008


title: 95003


title: 92007


title: 87003


title: 87007


title: 87006


title: 87009


title: 87002


title: 87001


title: 85007


title: 85008


title: 84005


title: 85002


title: 85003


title: 85001


title: 84004


title: 85005


title: 83003


title: 84001


title: 80006


title: 80005


title: 80004


title: 81003


title: 81001


title: 83001


title: 80003


title: 85004


title: 80002


title: 84002


title: 83002


title: 75001


title: 75003


title: 75004


title: 75007


title: 77001


title: 79002


title: 74008


title: 74007


title: 74006


title: 75006


title: 74003


title: 74005


title: 73003


title: 72004


title: 74001


title: 74002


title: 73001


title: 75005


title: 71005


title: 71002


title: 71003


title: 72003


title: 71004


title: 71001


title: 69003


title: 69001


title: 68006


title: 68008


title: 75002


title: 68003


title: 63003


title: 68001


title: 63002


title: 64002


title: 65001


title: 63001


title: 60005


title: 60003


title: 60004


title: 57005


title: 57004


title: 60002


title: 57003


title: 57001


title: 60001


title: 56001


title: 56004


title: 55003


title: 60006


title: 55007


title: 55011


title: 56002


title: 55006


title: 55010


title: 55009


title: 55001


title: 55004


title: 55005


title: 55002


title: 54005


title: 54004


title: 54003


title: 54002


title: 53005


title: 55008


title: 53001


title: 54001


title: 52005


title: 53002


title: 52007


title: 53007


title: 52002


title: 47005


title: 53004


title: 45001


title: 47001


title: 47003


title: 42007


title: 44003


title: 42006


title: 42005


title: 44002


title: 52006


title: 44001


title: 52003


title: 40002


title: 42002


title: 52001


title: 42004


title: 40003


title: 53003


title: 42003


title: 39005


title: 39002


title: 40004


title: 39006


title: 40001


title: 30017


title: 38001


title: 30015


title: WT1_ATAC

city: Madrid

first: Mercedes

last: Ricote

address: Darwin 3

country: Spain

institute: CNB-CSIC

data_processing:
Illumina Casava software used for basecalling and bcl2fastq for demultiplexing.
Illumina and Nextera adapter contaminations were removed from reads using Cutadapt.
Processed reads were mapped against mm10 whole genome using bowtie2.
Alignments were filtered with samtools to retain only properly mapped, non duplicate reads, with mapping quality above 0, not aligning to unlocalized or unassembled contigs, the mitochondrial genome, or chromosome Y.
Peaks were called with MACS2, using parameters "--nomodel --shift -100 --extsize 200 -p 0.001".
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: ENCODE narrow peak files (extended bed format) including coordinates, score, pvalue and qvalue for ATAC-seq peaks, generated by MACS2.

source_name: Perinatal heart

extract_protocol:
Cardiac nuclei DNA from P0 hearts of wild type (WT) and cardiomyocyte-specific RXRab-/- newborns were extracted and tagmented using Tn5 (Illumina).
Libraries were prepared according to Buenrostro et al. (2015, Curr Protoc Mol Biol) with minor modifications. Briefly, nuclei DNA was tagmented and extracted. Then, a size selection (0.65x) was applied. Libraries were barcoded with Illumina sequencing indexes. Sequencing was performed on 2×50 HiSeq 3000 (Illumina) and with an average of 25 million paired-end reads per sample.

value: Total heart

tag: strain

value: WT


title: 30013


title: 30011


title: KO1_ATAC

value: edKO


title: 30008


title: 30007


title: 30006


title: 30004


title: 30003


title: 39004


title: KO2_ATAC


title: IPKO3_input

description:
Input sample
IPKO3.mm10_peaks.narrowPeak

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Illumina adapter contaminations were removed from reads using Cutadapt.
Processed reads were mapped against mm10 whole genome using BWA ALN / BWA SAMSE; samtools was used to generate output files in bam format.
Alignments were filtered with samtools to retain only properly mapped, non duplicate reads, with mapping quality above 0, not aligning to unlocalized or unassembled contigs, the mitochondrial genome, or chromosome Y.
ChIPSeq peaks were called against input using MACS2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: ENCODE narrow peak files (extended bed format) including coordinates, score, pvalue and qvalue for ChIPSeq peaks called for each sample against input, using MACS2.

extract_protocol:
Cardiac nuclei chromatin from P0 hearts of wild type (WT) and cardiomyocyte-specific RXRab-/- newborns were extracted and sheared using a Covaris S220 sonicator (Covaris). IP was performed with H3K27ac antibody (#39135, ActiveMotif).
Libraries (IP and input) were prepared according to standard procedures and sequenced on 2×50 HiSeq 3000 (Illumina), with an average of 20 million single-end reads per sample.

tag: chip antibody


title: 30010


title: IPC3_input

description:
Input sample
IPC3.mm10_peaks.narrowPeak


title: 39003


title: WT2_ATAC


title: 39001


title: IPKO6_input

description:
Input sample
IPKO6.mm10_peaks.narrowPeak


title: IPKO1_input

description:
Input sample
IPKO1.mm10_peaks.narrowPeak


title: 30001


title: 30005


title: IPKO1_IP

description:
ChIP sample
IPKO1.mm10_peaks.narrowPeak


title: 29004


title: IPC4_IP

description:
ChIP sample
IPC4.mm10_peaks.narrowPeak


title: 29002


title: IPC4_input

description:
Input sample
IPC4.mm10_peaks.narrowPeak


title: 29001


title: IPKO6_IP

description:
ChIP sample
IPKO6.mm10_peaks.narrowPeak


title: IPC1_input

description:
Input sample
IPC1.mm10_peaks.narrowPeak


title: 30002


title: 30009


title: IPKO3_IP

description:
ChIP sample
IPKO3.mm10_peaks.narrowPeak


title: 29006


title: 29003


title: 3D4/21, GSK126 treated for 48h, RNA-Seq, rep2 [rRNA-deplete.48h_r2]

city: yangzhou

first: Z

last: LL

address: shuangqiaojiedao

institute: yangzhouaxue

data_processing:
Raw reads were trimmed with Trim Galore v0.6.4. Transcript Per Million (TPM) values were calculated with RSEM v1.3.2 with default settings.
Assembly: Sscrofa11
Supplementary files format and content: tab-delimited text files include TPM and FPKM values for each sample

organism: Sus scrofa

growth_protocol: Porcine 3D4/21 alveolar macrophages were cultured in 1640 medium with 10% fetal bovine serum and 1% penicillin-streptomycin (100×), incubated in a constant temperature incubator with 37 ℃, 5% CO2 and saturated humidity.

extract_protocol:
Total RNA for porcine alveolar macrophage was extracted using the FastPure® Cell/Issue Total RNA Isolation Kit BOX2 Kit(Vazyme).
RNA-Seq library is constructed by BGI company using the rRNA-depletion protocol.

treatment_protocol: GSK126 was added to RPMI 1640 medium to make its final concentration as 5 μmol/L. The same volume of DMSO was added for the untreated control group. The control group and GSK126 treated group are collected for subsequent experiments.

value: Wild-type

tag: treatment

value: GSK126 treated for 48h

tag: molecule type

value: polyA-deplete RNA


title: 3D4/21, GSK126 treated for 48h, RNA-Seq, rep1 [rRNA-deplete.48h_r1]

tag: cell line


title: 3D4/21, untreated, RNA-Seq, rep2 [rRNA-deplete.00h_r2]

value: none; untreated


title: WT4_input

description:
Input sample
WT4.mm10_peaks.narrowPeak

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Illumina adapter contaminations were removed from reads using Cutadapt.
Processed reads were mapped against mm10 whole genome using BWA ALN / BWA SAMSE; samtools was used to generate output files in bam format.
Alignments were filtered with samtools to retain only properly mapped, non duplicate reads, with mapping quality above 0, not aligning to unlocalized or unassembled contigs, the mitochondrial genome, or chromosome Y.
ChIPSeq peaks were called against input using MACS3.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: ENCODE narrow peak files (extended bed format) including coordinates, score, pvalue and qvalue for ChIPSeq peaks called for each sample against input, using MACS3.

extract_protocol:
Cardiac nuclei chromatin from P0 hearts of wild type (WT) and cardiomyocyte-specific RXRab-/- newborns were extracted and sheared using a Covaris S220 sonicator (Covaris). IP was performed with RXR antibody (#21218-1-AP, ProteinTech)
Libraries (IP and Input) were prepared according standard procedures and sequenced on 2×50 HiSeq 3000 (Illumina) and with an average of 20 million single-end reads per sample.


title: 3D4/21, untreated, RNA-Seq, rep1 [rRNA-deplete.00h_r1]


title: IPC1_IP

description:
ChIP sample
IPC1.mm10_peaks.narrowPeak


title: 28004


title: 28005


title: WT3_input

description:
Input sample
WT3.mm10_peaks.narrowPeak


title: IPC3_IP

description:
ChIP sample
IPC3.mm10_peaks.narrowPeak


title: KO4_input

description:
Input sample
KO4.mm10_peaks.narrowPeak


title: 3D4/21, GSK126 treated for 12h, RNA-Seq, rep1 [PolyA-enrich.12h_r1]

extract_protocol:
Total RNA for porcine alveolar macrophage was extracted using the FastPure® Cell/Issue Total RNA Isolation Kit BOX2 Kit(Vazyme).
RNA-Seq library is constructed by BGI company using the PolyA-enrichment protocol.

value: GSK126 treated for 12h


title: 3D4/21, GSK126 treated for 24h, RNA-Seq, rep1 [PolyA-enrich.24h_r1]

value: GSK126 treated for 24h


title: 3D4/21, GSK126 treated for 12h, RNA-Seq, rep2 [PolyA-enrich.12h_r2]


title: 3D4/21, GSK126 treated for 3h, RNA-Seq, rep2 [PolyA-enrich.03h_r2]

value: GSK126 treated for 3h


title: 26006


title: 28001


title: KO3_input

description:
Input sample
KO3.mm10_peaks.narrowPeak


title: 3D4/21, GSK126 treated for 3h, RNA-Seq, rep1 [PolyA-enrich.03h_r1]


title: 3D4/21, GSK126 treated for 48h, RNA-Seq, rep2 [PolyA-enrich.48h_r2]


title: 3D4/21, untreated, RNA-Seq, rep2 [PolyA-enrich.00h_r2]


title: 26005


title: WT4_IP

description:
ChIP sample
WT4.mm10_peaks.narrowPeak

value: RXR


title: 28002


title: 3D4/21, GSK126 treated for 24h, RNA-Seq, rep2 [PolyA-enrich.24h_r2]


title: 3D4/21, untreated, RNA-Seq, rep1 [PolyA-enrich.00h_r1]


title: WT3_IP

description:
ChIP sample
WT3.mm10_peaks.narrowPeak


title: 3D4/21, GSK126 treated for 48h, Input [Input_48h]

data_processing:
Reads were trimmed with TrimGalore v0.6.4 and then aligned to the corresponding reference genome (Sscrofa11.1.108) using Bowtie v2.3.5 with default settings. PCR duplicates were removed using the rmdup function of samtools v1.13. After confirming the data reproducibility, reads from biological replicates were pooled together for further analysis. Peak calling was performed with MACS v2.2.6 with default settings.
Assembly: Sscrofa11
Supplementary files format and content: narrowPeak (except for Input sample)

extract_protocol:
ChIP-Seq for porcine alveolar macrophage was performed following our previous study (Sun et al. 2021, PMID: 34320657).
Chromatin fragmentation was performed using Diagenode Bioruptor Plus Sonicator. The antibody for H3K27ac (Abcam, ab4729) is used. The amount of chromatin is 20 μg per reaction.

tag: antibody


title: 3D4/21, GSK126 treated for 48h, RNA-Seq, rep1 [PolyA-enrich.48h_r1]


title: 3D4/21, untreated, Input [Input_00h]


title: 26004


title: KO4_IP

description:
ChIP sample
KO4.mm10_peaks.narrowPeak


title: 3D4/21, GSK126 treated for 48h, H3K27ac, rep2 [H3K27ac_48h_r2]

value: Abcam, ab4729


title: 3D4/21, GSK126 treated for 48h, H3K27ac, rep1 [H3K27ac_48h_r1]


title: 3D4/21, untreated, H3K27ac, rep1 [H3K27ac_00h_r1]


title: 3D4/21, untreated, H3K27ac, rep2 [H3K27ac_00h_r2]


title: KO3_IP

description:
ChIP sample
KO3.mm10_peaks.narrowPeak


title: 24005


title: 26002


title: 24004


title: D5135CA1, hippocampal CA1, male,  control

city: Boston

first: Serkan

last: Erdin

state: MA

address: 185 Cambridge Street

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

description:
Unstranded
RK3_112012_D5135CA1_CAGATC_L004

data_processing:
RNAseq data was processed using a standard workflow, which includes quality assessment of fastq reads using FastQc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Each bulk RNAseq library of mouse sample was aligned to mouse reference genome GRCm38 version 75 using GSNAP aligner. Expression counts for each unstranded RNAseq sample was generated applying bedtools multicov to uniquely mapped reads. Expression cound for each strand specific RNAseq library was generated similarly requiring same strandedness.
Quality assessment of alignments were obtained using RNASeQC, RSeQC and SamTools.
Assembly: Mouse reference genome for bulk RNAseq GRCm38 v75.
Supplementary files format and content: raw counts

source_name: Hippocampal CA1

growth_protocol: Forebrain-specific Dicer conditional knock out mice were generated by crossing floxed Dicer mice with Camk2a-Cre transgenic mice.

extract_protocol:
Total RNA was isolated from the neocortex and hippocampal CA1 region using TRIzol reagent (Invitrogen).
RNA-sequencing libraries per each mouse tissue with conditional Dicer knockout or control were prepared from 500 ng of total RNA using a TruSeq stranded mRNA Sample Prep Kit for neocortex samples and unstranded mRNA Sample Prep Kit for hippocampal CA1 region. Each neocortex library included 1 ul of a 1:10 dilution of ERCC RNA Control Spike-Ins (Ambion) containing the same 92 synthetic RNA standards of known concentration and sequence to estimate the expression threshold to detect the expression threshold.

treatment_protocol: Camk2a-Cre;Dicer flox/flox mice were used for the experiments.

value: Hippocampal CA1

value: Control

value: M

value: 13-14 weeks


title: D5138CA1, hippocampal CA1, female, control

description:
Unstranded
RK5_112012_D5138CA1_ACAGTG_L004

value: F


title: 24003

value: metastatic colorectal cancer

value: IV

value: male


title: 24001

value: female


title: SCZ,CA_3,Day14

city: HeFei

first: Yaohua

last: Cheng

address: Changjiang West Road 130

institute: Anhui  Agricultural University

description: Camellia. sinensis var. ‘Shuchazao’

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10

organism: Camellia sinensis

source_name: tissue culture of tea seedlings(height of 4-5 cm)

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

tag: cultivar

value: SCZ

value: Low temperature (10 °C during the day and 4 °C at night) treatment for 7 days. Subsequently, freezing acclimation was performed by 4°C daytime, 0°C night exposure for 7 days (CA-treated)


title: SCZ,DA_1,Day21

description: Camellia. sinensis var. ‘Shuchazao’

value: tissue culture of tea seedlings(height of 4-5 cm)

value: CA-treated plants were exposed to normal temperature (25°C daytime, 20°C night)for 7 days


title: SCZ,CA_2,Day14

description: Camellia. sinensis var. ‘Shuchazao’


title: SCZ,DA_3,Day21

description: Camellia. sinensis var. ‘Shuchazao’


title: SCZ,NA_3,Day0

description: Camellia. sinensis var. ‘Shuchazao’

value: normal temperature (25°C daytime, 20°C night)


title: D5130CA1, hippocampal CA1, male, KO

description:
Unstranded
RK2_112012_D5130CA1_TGACCA_L004

value: KO


title: SCZ,NA_2,Day0

description: Camellia. sinensis var. ‘Shuchazao’


title: 26003


title: SCZ,NA_1,Day0

description: Camellia. sinensis var. ‘Shuchazao’


title: 23017


title: D5134CA1, hippocampal CA1, male, control

description:
Unstranded
RK1_112012_D5134CA1_CGATGT_L004


title: induced MCF10A YAP5SA cells YAP

city: Wuerzburg

first: Carsten

middle: P

last: Ade

address: Am Hubland

department: Lehrstuhl Biochemie und Molekularbiologie

institute: University of Wuerzburg

data_processing:
Base calling was performed with Illumina’s CASAVA software or FASTQ Generation software v1.0.0 and overall sequencing quality was tested using the FastQC script.
Galaxy was used to analyze NGS data (https://usegalaxy.org). Reads were mapped to the human genome (hg19 assembly) using Bowtie2 for Cut&Run-seq and ChIP-seq samples. Differential peak analysis was performed within Galaxy with Limma-voom (Liu et al., 2015).
To create heat maps and density profiles of ATACseq, ChIPseq and CUT&RUN data, DeepTools 2 was used (Ram.rez et al., 2016).
Normalized bigWig files were created using bamcoverage with a bin size of 10 and normalizing to counts per million (CPM). BigWig files were used to compute reads centered on ATAC-seq peak summits (called with Genrich), YAP peak summits or on the TSS of MMB-target genes (Fischer et al., 2016) using computeMatrix.
Heatmaps and profiles were created with the plotHeatmap and plotProfile tools. Metagene plots of PolII enrichment across MMB target genes were created with plotProfiles. ChIPseq data were visualized with the Integrated Genome Viewer (Robinson et al., 2011).
Assembly: hg19
Supplementary files format and content: For Cut&Run-seq and ChIP-seq, the provided processed files are bigWig files for data display in a genome browser.
Library strategy: CUT&RUN-seq

growth_protocol: MCF10A stably expressing doxycycline inducible YAP5SA were grown and cultured in DMEM/F-12 supplemented with 5% horse serum, 1% penicillin/ streptomycin, 10 µg/ml insulin, 500 ng/ml hydrocortisone, 20 ng/ml EGF and 100 ng/ml cholera toxin.

extract_protocol:
For CUT&RUN-seq, 500000 cells were harvested and washed twice with wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl and 0.5 mM spermidine containing protease inhibitor) and captured with 20 μl conacavallin A magnetic beads (Polyscience). Cells were resuspended with antibody buffer (wash buffer with 0.005% digitonin and 2 mM EDTA) and incubated with 2 μg of YAP-antibody (Novus Biologicals, NB110-58358) for 2 hours at room temperature.
Samples were then washed twice with wash buffer containing 0.005% digitonin and incubated with 700 ng/ml of purified protein-A/G-MNase fusion (pA/G-MNase) on a shaker at 4°C for 1 h followed by two more washes in digitonin wash buffer and once in low salt rinse buffer [20mM HEPES pH7.5, 0.5mM Spermidine, 0.005% Digitonin].
To activate protein A-MNase, incubation buffer (3.5mM HEPES, 10mMCaCl2, 0.005% digitonin) was added and the DNA was digested for 30min on ice. The incubation buffer was discarded and the reaction was stopped by resuspension in STOP buffer (170 mM NaCl, 20 mM EDTA, 0.005% Digitonin, 50μg/ml RNaseA, 25μg/ml Glycogen).
The protein-DNA complex was released by incubation at 37°C for 30min, the supernatant was transferred to a fresh tube and then digested by proteinase K at 50°C for 1 hours. DNA was extracted by ethanol precipitation.
Libraries were made with 6 ng of CUT&RUN DNA fragments using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645S). The end prep was performed at 20°C for 30min followed by 50°C for 1h. The adaptor was used at a concentration of 0.5 μM. 15 PCR cycles were performed at the following conditions: Initial denaturation: 98°C for 30sec. Denaturation 98°C for 10sec; Annealing/Extension 65°C for 10sec and final Extension 65°C for 5min. Library quality was analyzed using the Fragment Analyzer (Advanced Analytical). Libraries were sequenced on the NextSeq 2000 platform (Illumina).

treatment_protocol:
ATAC-seq and ChIP-seq: YAP5SA was induced with 0.5µg/ml doxycycline for 48 hours.
RNA-seq: Cells were induced with 0.5 µg/ml doxycycline for 45 hours and with 1µM OHT for 14h.

tag: dox-treatment (yap5sa)

value: induced

value: YAP1 (Novus Biologicals, NB110-58358)


title: 23016


title: induced MCF10A YAP5SA cells control

value: IgG control


title: 23015


title: D5135, neocortex, male, control

description:
Strand specific
4_140220_AC3JVRACXX_IlluminaRNA18

source_name: Neocortex

value: Neocortex

value: Control


title: EIF5A2_3rd

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Qvalue <=0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: neuroblastoma cells

growth_protocol: The human neuroblastoma cells (SH-SY5Y cell line, Procell Life Science & Technology Co., Ltd., Wuhan, China) were seeded into a 96-well microtiter plate at a density of 2–2.5 × 106 per well, and cultured at 37ºC, with 5% CO2 in DMEM/F12 medium (Sigma Aldrich, St.Louis, MO) supplemented with 10% fetal bovine serum (FBS; Sigma Aldrich, St.Louis, MO ), 100 IU/ml penicillin (Sigma Aldrich, St.Louis, MO), 100 µg/ml streptomycin (Sigma Aldrich, St.Louis, MO) and glutamine (2 mM) (Sigma Aldrich, St.Louis, MO) for 24 h. The transfection of SH-SY5Y cells with an EIF5A2-overexpressing plasmid was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.

extract_protocol:
Total RNA was extracted with TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: EIF5A2 group was infected with EIF5A2 overexpression plasmid

value: EIF5A2 overexpression in SH-SY5Y cell


title: D5133CA1, hippocampal CA1, male, KO

description:
Unstranded
RK6_112012_D5133CA1_GCCAAT_L004

value: Hippocampal CA1

value: M

value: 13-14 weeks


title: SCZ,DA_2,Day21

description: Camellia. sinensis var. ‘Shuchazao’


title: D5134, neocortex, male, control

description:
Strand specific
4_140220_AC3JVRACXX_IlluminaRNA16


title: EIF5A2_1st


title: EIF5A2_2nd


title: SCZ,CA_1,Day14

description: Camellia. sinensis var. ‘Shuchazao’


title: 23014

value: metastatic colorectal cancer

value: IV

value: male


title: 23013


title: Ctrl_3rd (EIF5A2 control)

value: EIF5A2 overexpression in SH-SY5Y cell (control plasmid)


title: D5133, neocortex, male, KO

description:
Strand specific
4_140220_AC3JVRACXX_IlluminaRNA15


title: Ctrl_2nd (EIF5A2 control)


title: Ctrl_1st (EIF5A2 control)


title: D5132, neocortex, male, KO

description:
Strand specific
4_140220_AC3JVRACXX_IlluminaRNA14


title: D5130, neocortex, male, KO

description:
Strand specific
4_140220_AC3JVRACXX_IlluminaRNA13


title: 23012


title: D5129, neocortex, male, control

description:
Strand specific
4_140220_AC3JVRACXX_IlluminaRNA12


title: AK58_DAP15_RNA-seq_rep1

city: Beijing

first: Zefu

last: Lu

state: Haidian

address: No.12 Zhongguancun South St.,Haidian District, Beijing, P.R.China

institute: Institute of Crop Sciences

data_processing:
Raw reads were trimmed with Trimmomatic v0.334 with default parameters. The remaining reads were aligned to the International Wheat Genome Sequencing Consortium (IWGSC) reference genome (version 1.0) using HISAT2 v2.0.5. Gene expression values were computed using StringTie v1.3.3b.
Assembly: IWGSC RefSeq v1.0
Supplementary files format and content: TPM values for each sample

organism: Triticum aestivum

source_name: Triticum aestivum seed at 15 days after fertilization

growth_protocol: 16h light  22°C, 8h dark 19°C

extract_protocol:
total RNA
For each sample, total RNA was prepared for sequencing with the Illumina Truseq mRNA Stranded Library Kit (Illumina, San Diego, CA) following the manufacturer’s instructions.

treatment_protocol: The three tissues of wheat, including leaves, roots and shoot apices, were obtained after 2 weeks of growth. The 2-week-old seeding were vernalized at 4°C under 16h light/8h dark conditions for 30 days and 1.0 - 2.0 cm axillary buds were obtained from these vernalized seedings.

value: Seed

tag: time point

value: at 15 days after fertilization


title: AK58_DAP15_RNA-seq_rep2


title: AK58_DAP20_RNA-seq_rep1

source_name: Triticum aestivum seed at 20 days after fertilization

value: at 20 days after fertilization


title: AK58_DAP20_RNA-seq_rep2


title: 23011

value: female


title: AK58_DAP9_RNA-seq_rep2

source_name: Triticum aestivum endosperm at nine days after fertilization

value: Endosperm

value: at nine days after fertilization


title: 23009


title: 23008


title: Induced pluripotent stem cell line of pediatric  brain tumour patient 2

city: Sevilla

first: Yolanda

last: Aguilera

address: Avda Americo Vespucio, 24

institute: Cabimer

description: reprogrammed using non-integrative Sendai virus vectors encoding the Yamanaka factors KLF4, OCT3/4, SOX2 and CMYC.

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: ChAS console from Affymetrix was used to assess genome wide copy number frequencies. Log2 Ratio copy number values with associated chromosome positions are available on the series record.

label: Biotin

source_name: urine

label_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from iPS culture obtained from urine using the Qiagen DNeasy Blood & Tissue kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: cell type

value: Induced pluripotent stem cell


title: AK58_DAP9_RNA-seq_rep1


title: AK58_DAP20_ATAC-seq_rep2

data_processing:
Raw reads were trimmed with Trimmomatic v0.36, clean sequencing reads were mapped to the International Wheat Genome Sequencing Consortium (IWGSC) reference genome (version 1.0) using Bowtie2. Peak calling was performed using MACS2. A black list was first generated by using the control samples as input.The raw peaks were first called with MACS2 with the following parameter “--keep-dup all --nomodel --extsizes 150 --shift -75”; then split into 150bp bins with 50bp overlapping; bins passed filtering by a Tn5 integration site density cutoff were selected and merged with bedtools with “-d 150”; peaks overlapped with the blacklist peaks, or homologous to plant orgenella DNA (NCBI) were discard  and the rest  were considered as high-quality ACRs.
Assembly: IWGSC RefSeq v1.0
Supplementary files format and content: peak files

extract_protocol: ATAC-seq libraries were prepared following the ATAC-seq protocol as previously described in (Lu et al. 2016)

treatment_protocol: Wheat endosperm was excised by removing the seed embryo at 5 and 9 days after fertilization. Wheat seed was collected at 15 and 20 days after fertilization.


title: AK58_DAP5_RNA-seq_rep1

source_name: Triticum aestivum endosperm at five days after fertilization

value: at five days after fertilization


title: Induced pluripotent stem cell line of pediatric  brain tumour patient 1


title: AK58_DAP20_ATAC-seq_rep1


title: AK58_DAP15_ATAC-seq_rep2


title: Induced pluripotent stem cell line of pediatric non-tumour patient 2


title: AK58_DAP15_ATAC-seq_rep1


title: Induced pluripotent stem cell line of pediatric non-tumour patient 1


title: 23006


title: 23007


title: 23005


title: AK58_DAP9_ATAC-seq_rep2


title: 23004