title: H211-LSD1-Replicate 3

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes. Genes with adjusted p-values < 0.05 and absolute log2 fold changes > 1 were called as differentially expressed genes for each comparison. A gene ontology analysis was performed on the statistically significant set of genes by implementing the software GeneSCF
Transcript counts and abundances were quantified from RNA-seq reads using Salmon v1.1.0 (Patro, R, et al 2017). RNA-seq raw reads were mapped to 25-mer indexed hg38 genome by Salmon. With default settings, mapping validation (--validatemappings), bootstrapping with 30 re-samplings (--numBootstraps), sequence specific biases correction (--seqBias), coverage biases correction (--posBias) and GC biases correction (--gcBias) were also enabled. Transcript to gene mapping based on Ensembl 92 (Zerbino, DR, et al 2018), normalized by size factor at gene level, and differential gene expression analyses were processed on Salmon output files using Sleuth v0.30.0 in gene mode (Subramanian, A, et al 2015). Differentially expressed genes were identified using the Wald test. Genes were marked as significant if the False Discovery Rates, q, calculated using the Benjamini-Hochberg method, was less than 0.05, and beta (Sleuth-based estimation of log2 fold change) > 0.58, which approximately correlated to a log2 fold change of 1.5 in our data.
Gene set enrichment analysis (GSEA) was performed on full sets of differential gene expression results on the previously mentioned comparisons. Genes were ranked on p value scores computed as -log10(p value)*(sign of beta). Gene set annotations include all gene sets deposited in the Molecular Signatures Database (MSigDB v7.0.1) (Subramanian, A, et al 2005; Liberzon, A, et al 2011). The significance level of enrichment was evaluated using permutation test and the p value was adjusted by Benjamini-Hochberg procedure. Any enriched gene sets with adjusted p value ≤ 0.05 were regarded as significant. This analyses were executed with the R package ClusterProfiler v3.18.1 (Yu, G, et al 2012).
Pathways and gene sets of interest were procured from GSEA-msigdb database (https://www.gsea-msigdb.org/gsea/index.jsp) and Gene Ontology resources (http://geneontology.org/). Interested pathways were highlighted in H82 and H211 GSEA dot plots. The log of the normalized TPM values for significant genes within the interested pathways, were rescaled using a z-score transformation, and plotted in a heatmap using the ComplexHeatmap v2.7.10 (Gu, Z, et al, 2016) Library in R 4.0.4.
Assembly: hg38
Supplementary files format and content: GEO_Sleuth_TPM.txt

growth_protocol: H82 and H211 cell lines were grown in RPMI media supplemented with 10% FBS and 1% P/S. Cells were passaged every 3 days, STR-verified and routinely tested for mycoplasma.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on 2 flowcell lanes. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence  data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed  using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence  identification.

treatment_protocol: Treatment was performed with LSD1 inhibitor ORY-1001 (1𝝁M) or vehicle for 10 days

value: lung

value: small cell lung cancer

tag: genotype

value: WT

value: ORY-1001-7 days


title: sample_6

status: Public on Jun 13 2022

type: SRA

city: Milano

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

country: Italy

institute: IRCCS, Ospdale San Raffaele

description: kidney ephitelial cell line A498, treated with IL1β, 4 hours

library_source: transcriptomic

data_processing:
alignment with STAR_2.5.3a (--outFilterMismatchNmax 10)
counting reads with featureCounts
Differential Gene Expression with LIMMA
Assembly: Hg38; genome annotation: basic annotation Hg38 Gencode v31
Supplementary files format and content: xls with count data

molecule: total RNA

organism: Homo sapiens

source_name: kidney epithelial cell line A498, treated with IL1β, 4 hours

growth_protocol: Cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before addition of IL1β 30 ng/ml for 4h hours.  The supernatant was removed, cells were washed with PBS, trypsinized and harvested. Pellets were washed with PBS and resuspendend in RLT buffer (QIAGEN)

extract_protocol:
Total RNA was extracted using RNeasy plus mini kit  (Qiagen). RNA quantification was carried out using Qubit Fluorimetric Quantification (Life Technologies) and 100ng of RNA were used to prepare the library.
Illumina_TruSeq_stranded

treatment_protocol: A498 cells were grown in RPMI medium containing 10% FBS, and supplemented with penicillin (10000 units/ml), streptomycin (10 mg/ml), in a standard incubator (37°C, 5% CO2).

tag: cell line

tag: treatment

value: IL1Beta, 4 hours


title: pi-staining-and-freezing: pi_stained_frozen 4np (F38F7)

city: Oxford

first: Robert

middle: A

last: Beagrie

address: Headley Way

department: Molecular Haematology Unit

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

library_source: genomic

data_processing:
Library strategy: Genome Architecture Mapping
Reads were aligned to the mm9 build of the mouse genome using bowtie v2.1.
GAMtools (https://gam.tools) was used to discard poorly or non-uniquely mapped reads, remove PCR duplicates and call positive 40kb windows based on the level of read coverage. Samples with less than 15% of reads mapping to the Mouse genome were not taken forward for further analysis but can be found in a separate GEO submission under the same super-series.
Genome_build: mm9
Supplementary_files_format_and_content: GAM segregation table: Each row represents one 40kb window from the mouse genome, each column indicates one sequencing sample (containing three nuclear profiles). Values indicate whether the given window was present (1) or absent (0) from the given sample.

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse ES Cells

growth_protocol: Cells were grown at 37°C in a 5% CO2 incubator in Glasgow Modified Eagles Medium, supplemented with 10% fetal bovine serum, 2 ng/ml LIF and 1 mM 2-mercaptoethanol, on 0.1% gelatin-coated dishes. Cells were passaged every other day. After the last passage 24h before harvesting, ES cells were re-plated in serum-free ESGRO Complete Clonal Grade medium (Millipore Inc.)

extract_protocol:
220 nm cryosections were collected in sucrose droplets and transferred to steel frame PEN membrane slides. Slides were washed in 1x PBS (3 times, 5 min each), then with water (3 times, 5 min each). Staining was performed with propidium iodide (10 µg/ml in PBS) for 10 min, followed by 2 washes with water (30 s each) and air dryed for 15 minutes. Nuclear profiles were laser microdissected into adhesive 8-strip LCM collection caps, with four profiles dissected into each cap. Whole genome amplification was performed using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (13 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.1 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. Samples were then frozen and stored overnight at -20 ∞C. The next day, 4.32 µl library preparation mastermix (2.88 µl library preparation buffer, 1.44 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 1.4 µl library preparation enzyme was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 87.84 µl amplification master mix (10.8 µl amplification buffer, 69.84 µl H2O, 7.2 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 25 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines

tag: cell type

tag: strain


title: sample_4

description: kidney ephitelial cell line A498, untreated

source_name: kidney epithelial cell line A498, untreated

value: untreated


title: pi-staining-and-freezing: pi_stained_frozen 4np (F38E9)


title: H211-LSD1-Replicate 2

city: New York

state: NY

country: USA

source_name: lung

tag: tissue


title: H211-LSD1-Replicate 1


title: ChIP-Seq_Pol2_NTD_BRD2_BRD3_untreated_rep2

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

data_processing:
All libraries were sequenced using an Illumina Hiseq sequencer and 150 bp paired-end format.
The 150 bp paired-end reads were pre-processed by Cutadapt and then aligned to the mm10 mouse genome assembly using Bowtie2.
Unmapped reads, low quality mapped reads and PCR duplicates were discarded. Only uniquely mapped were retained for downstream analysis.
Peaks were called against input control using the MACS2 function callpeak on each replicate in default parameters and q-value threshold of 0.05 to ensure high confidence. Repeatable peaks between the replicates were detected by IDR software using IDR threshold of 0.05.
The ChIP reads at each genomic position were normalized and converted to bigwig format using bamCoverage from deeptools toolkit. Rloop datasets were normalized by the spike-in reads that mapped to the E.coli T7 genome.
Genome_build: mm10
Supplementary_files_format_and_content: The bigwig files of ChIP-seq data were generated using deepTools.

source_name: mouse embryonic stem cells

growth_protocol: For BRD2-degron cells and BRD2-degron_BRD3-knockout cells ChIP-seq, BRD2-mAID tagged mES (V6.5) cell lines and BRD2-mAID BRD3-knockout mES (V6.5) cell lines were cultured with 2i medium containing 15% FBS, leukaemia inhibiting factor (mLIF), L-glutamine, β-mercaptoethanol, non-essential amino acids, 3 μM CHIR99021, and 1 μM PD0325901 in ES-qualified Dulbecco’s modified Eagle’s medium (DMEM), incubated at 37 °C with 5% CO2. mES cells were cultured with mESC EB medium without mLIF to form embryonic bodies (EBs).

extract_protocol:
The crosslinked cells were isolated into chromatin and digested using MNase (15 min at 37 °C), and then, sonicated in Bioruptor Sonication Device (high energy for 30s on and 60s off, work on 16 cycles).  Lysates were centrifuged twice, 40 μl supernatant were sampled as input, and the rest supernatant were transferred into 2 new DNase free tubes, 2 μg of BRD2 abs (CST, D89B4), 2 μg of BRD3 abs (Proteintech, 11859-1-AP), 2 μg of BRD4 abs (Abcam, ab128874), 1 μg of CTCF abs (ABclonal, A1133), 1 μg of Smc1a abs (Bethyl, A300-055A), 1 μg of Rpb1NTD abs (CST, D8L4Y) , 1 μg of Rpb1 PSer2 abs (CST, E1Z3G), 2.5 μg of TAF1 abs (CST, D6J8B), 2.5 μg of TAF3 abs (Proteintech, 18901-1-AP), 2.5 μg of TBP abs (Proteintech, 22006-1-AP), 4 μg of XRN2 abs (Proteintech, 11267-1-AP), and 1 μl GFP abs (Abcam, ab290) were added for each ChIP reaction, respectively, and equal isotype IgG control (Millipore, 12-370, 12-371) and incubated overnight at 4 °C with low speed rotation, the antibody enriched DNA was extracted by Tris saturated equilibrium phenol (25:24:1) (pH8.0).
BRD2-degron mES, BRD2, BRD3, BRD4, GFP, CTCF, SMC1, Pol II-NTD, Pol II-S2P, TAF1, TAF3, TBP, and XRN2 ChIPed DNA were subjected for library construction using the NEBNext Ultra II DNA library prep kit, according to the manufacturer-supplied protocol, and then the 200~400 bps length amplified DNA were recovered and analyzed with Qubit assays and Fragment Analyzer, and finally subject to HiSeq Xten PE150 sequencing (Novogene, Beijing).

treatment_protocol: BRD2-degron mES cells for 4 days were treated with 1 μg/ml Doxycycline (Dox) for 18 hrs and 500 μM auxin (indole-3-acetic acid) for 3 hrs to induce the BRD2 degradation. Then, cells were harvested and crosslinked using 1% formaldehyde for 10 min at room temperature, finally, cells were subjected for ChIP.

value: embryonic stem cells

tag: genotype/variation

value: untreated BRD2-degron mES

tag: antibody

value: Pol2 ntd


title: ChIP-Seq_Pol2_NTD_BRD2_degron_3h_rep1

value: BRD2 degron 3h mES


title: sample_5


title: ChIP-Seq_Pol2_NTD_BRD2_BRD3_untreated_rep1


title: pi-staining-and-freezing: pi_stained_frozen 4np (F38E8)


title: pi-staining-and-freezing: pi_stained_frozen 4np (F38E7)


title: sample_1


title: pi-staining-and-freezing: pi_stained_frozen 4np (F38D8)


title: ChIP-Seq_Pol2_NTD_BRD2_BRD3_input

value: untreated mES


title: H211-Control-Replicate 3

value: PBS-7 days


title: ChIP-Seq_Pol2_NTD_BRD2_BRD3_BRD3_KO_rep1

value: BRD3 KO mES


title: pi-staining-and-freezing: pi_stained_frozen 4np (F38D9)


title: sample_2


title: ChIP-Seq_Pol2_NTD_BRD2_BRD3_BRD2_degron_rep2


title: pi-staining-and-freezing: pi_stained_frozen 4np (F38C9)


title: AB678 OIP5-AS1:MIR-7 TSB 48h-1

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: transfected  OIP5-AS1:MIR-7 TSB for 24h and further transfered into differentiated medium for 48 h human myoblast replicate-1

data_processing:
BCL files were de-multiplexed and converted to standard FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed for adapter sequences using Cutadapt version v1.18 and aligned to human genome hg19 Ensembl v82 using STAR software v2.4.0j.
featureCounts (v1.6.4) were used to create gene counts from the samples.
Assembly: hg19
Supplementary files format and content: text files containing counts

source_name: human myoblast

growth_protocol: Human myoblasts were cultured in growth medium (equal volume mixture of Hamm's F10 media with 20% FBS and Promocell Skeletal Muscle Cell Growth Medium).  Human myoblasts were induced to differentiate by growth to high density and replacement of the growth medium with differentiation medium (DMEM with 2% horse serum)

extract_protocol:
Total RNA from cultured cells was isolated using the Direct-zol™ RNA MiniPrep kit (Zymo Research), which includes a digestion step using DNase I.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human myoblasts were transfected with 50 nM TSB to block the interaction between OIP5-AS1 and miR-7 or with scrambled controls; 24 h later, the cells were replaced to frash growth medoium for 24h or induced to differentiate by replacement of the growth medium with differentiation medium for the indicated time points.

value: Human myoblast

tag: cell status

value: Differentiated for 48h

value: transfected  OIP5-AS1:MIR-7 TSB for 24h


title: H211-Control-Replicate 2


title: H82-LSD1i-Replicate 2


title: ChIP-Seq_Pol2_NTD_BRD2_BRD3_BRD3_KO_rep2


title: AB678 OIP5-AS1:MIR-7 TSB 48h-2

description: transfected  OIP5-AS1:MIR-7 TSB for 24h and further transfered into differentiated medium for 48h human myoblast replicate-2


title: H211-Control-Replicate 1


title: H82-LSD1i-Replicate 3


title: pi-staining-and-freezing: pi_stained_frozen 4np (F38C8)


title: H82-LSD1i-Replicate 1


title: pi-staining-and-freezing: pi_stained_frozen 4np (F38D7)


title: sample_3


title: pi-staining-and-freezing: pi_stained_frozen 4np (F38C7)


title: H82-Control-Replicate 3


title: ChIP-Seq_Pol2_NTD_BRD2_BRD3_BRD2_degron_BRD3_KO_rep1

value: BRD2 degron 3h & BRD3 KO mES


title: H82-Control-Replicate 2

value: lung


title: AB678 Ctrl TSB 48h-1

description: transfected Ctrl TSB for 24h and further transfered into differentiated medium for 48h human myoblast replicate-1

value: transfected Ctrl TSB for 24h


title: ChIP-Seq_Pol2_NTD_BRD2_BRD3_BRD2_degron_BRD3_KO_rep2


title: AB678  OIP5-AS1:MIR-7 TSB 24h-2

description: transfected  OIP5-AS1:MIR-7 TSB for 24h and further transfered into differentiated medium for 24h human myoblast replicate-2

value: Differentiated for 24h


title: ChIP-Seq_Pol2_NTD_BRD2_BRD3_BRD2_degron_rep1


title: ChIP-Seq_CTCF_BRD2_untreated_rep2

value: Ctcf


title: ChIP-Seq_CTCF_BRD2_untreated_rep1


title: pi-staining-and-freezing: pi_stained_frozen 4np (F38B9)


title: AB678 Ctrl TSB 24h-2

description: transfected Ctrl TSB for 24h and further transfered into differentiated medium for 24h human myoblast replicate-2


title: ChIP-Seq_CTCF_BRD2_untreated_input


title: eCLIP_4

city: Cologne

first: Leo

last: Kurian

address: Robert-Kochstr. 21

country: Germany

institute: University of Cologne

data_processing:
Data was analzed and processed according to the bioinformatic pipeline  (Van Nostrand et al., 2016)
Assembly: hg19
Supplementary files format and content: InputNormalized.rbpms1.bed.compressed
Supplementary files format and content: InputNormalized.rbpms2.bed.compressed
Supplementary files format and content: InputNormalized.rbpms3.bed.compressed
Supplementary files format and content: InputNormalized.rbpms4.bed.compressed

growth_protocol: Cells were cultivated in FTDA medium (Frank et al. (2012))

extract_protocol:
Lysate preparation was performed as in the eCLIP IP protocol (Van Nostrand et al., 2016)
Libraries were prepared according to the library preparation protocol (Van Nostrand et al., 2016), RNA adapters for all IP samples was X1A and X1B, PCR amplification of libraries was performed using Illumina TruSeq HT Kit primers
Paired-end sequencing on HiSeq 4000 with a read length of 75

treatment_protocol: Cell culture dishes containing around 20M hESCs were UV-crosslinked with (400 mJ/cm2 constant energy) to stabilize protein-RNA interaction. IP was performed with a RBPMS-specific antibody.

value: human embryonic stem cells

value: WT

value: control

tag: rip antibody

value: RBPMS-specific antibody


title: AB678 OIP5-AS1:MIR-7 TSB 24h-1

description: transfected  OIP5-AS1:MIR-7 TSB for 24h and further transfered into differentiated medium for 24h human myoblast replicate-1


title: Input_4


title: pi-staining-and-freezing: pi_stained_frozen 4np (F38A9)


title: H82-Control-Replicate 1

value: small cell lung cancer


title: pi-staining-and-freezing: pi_stained_frozen 4np (F38B8)


title: pi-staining-and-freezing: pi_stained_frozen 4np (F38A8)


title: eCLIP_3


title: Input_3


title: ChIP-Seq_CTCF_BRD2_degron_3h_rep1

value: embryonic stem cells

value: BRD2 degron 3h mES


title: ChIP-Seq_CTCF_BRD2_degron_3h_rep2


title: AB678 Ctrl TSB 24h-1

description: transfected Ctrl TSB for 24h and further transfered into differentiated medium for 24h human myoblast replicate-1


title: AB678 Ctrl TSB 48h-2

description: transfected Ctrl TSB for 24h and further transfered into differentiated medium for 48h human myoblast replicate-2


title: ChIP-Seq_BRD4_BRD2_untreated_rep2

value: untreated BRD2-degron mES


title: AB678 Ctrl TSB 0h-1

description: transfected Ctrl TSB for 24h and further transfered into Proliferation medium for 24h human myoblast replicate-1

value: Proliferating


title: eCLIP_2


title: AB678 OIP5-AS1:MIR-7 TSB 0h-1

description: transfected  OIP5-AS1:MIR-7 TSB for 24h and further transfered into Proliferation medium for 24h human myoblast replicate-1

value: Human myoblast


title: ChIP-Seq_CTCF_BRD2_degron_3h_input

value: untreated mES


title: pi-staining-and-freezing: pi_stained 4np (F38G5)

extract_protocol:
220 nm cryosections were collected in sucrose droplets and transferred to steel frame PEN membrane slides. Slides were washed in 1x PBS (3 times, 5 min each), then with water (3 times, 5 min each). Staining was performed with propidium iodide (10 µg/ml in PBS) for 10 min, followed by 2 washes with water (30 s each) and air dryed for 15 minutes. Nuclear profiles were laser microdissected into adhesive 8-strip LCM collection caps, with four profiles dissected into each cap. Whole genome amplification was performed using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (13 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.1 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. 4.32 µl library preparation mastermix (2.88 µl library preparation buffer, 1.44 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 1.4 µl library preparation enzyme was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 87.84 µl amplification master mix (10.8 µl amplification buffer, 69.84 µl H2O, 7.2 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 25 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines


title: AB678 Ctrl TSB 0h-2

description: transfected Ctrl TSB for 24h and further transfered into Proliferation medium for 24h human myoblast replicate-2


title: pi-staining-and-freezing: pi_stained 4np (F38H5)


title: AB678 OIP5-AS1:MIR-7 TSB 0h-2

description: transfected  OIP5-AS1:MIR-7 TSB for 24h and further transfered into Proliferation medium for 24h human myoblast replicate-2

value: transfected  OIP5-AS1:MIR-7 TSB for 24h


title: pi-staining-and-freezing: pi_stained_frozen 4np (F38A7)


title: pi-staining-and-freezing: pi_stained_frozen 4np (F38B7)


title: pi-staining-and-freezing: pi_stained 4np (F38G4)


title: ChIP-Seq_BRD4_BRD2_untreated_rep1


title: pi-staining-and-freezing: pi_stained 4np (F38H4)


title: ChIP-Seq_BRD4_BRD2_degron_3h_rep1


title: Input_2


title: eCLIP_1


title: CITE_HTO

city: Pittsburgh

first: Wei

last: Chen

address: 4401 Penn Ave, Rangos Research Building 9125

institute: UPMC Children's Hospital of Pittsburgh

description: HTO data of the CITE dataset

library_source: other

data_processing:
Standard 10X Genomics Cell Ranger and Cell Ranger ARC pipelines, as well as kallisto | bustools workflow for ADT and HTO libraries.
Assembly: GRCh38
Supplementary files format and content: For each sample, the filtered UMI count matrix and filtered peak count matrix from 10X Genomics pipelines are stored in a h5 file, with atac_fragments.tsv.gz provided. HTO and ADT count matrices from kallisto | bustools workflow are stored in csv files, with non-singlets filtered out.
Library strategy: CITE-seq

molecule: other

source_name: Peripheral blood T cells

extract_protocol:
T cells were enriched from 30 ml of whole blood from healthy human subjects, ages 18-35, following the MACSxpress® Whole Blood Pan T Cell Isolation Kit, human (Miltenyi Biotec) protocol. Four aliquots of one million cells each per study subject were stimulated overnight for 12 hours in 1 ml X-VIVO™ 15 Serum-free Hematopoietic Cell Medium (Lonza) with 10 ul ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator (STEMCELL Technologies), 50 ng/ml IL-1B (R&D Systems), and 50 ng/ml IL-23 (R&D Systems), and either 1 uM Prostaglandin E2 (PGE2) (Sigma) or 3 ng/ml TGFB (R&D Systems), or both, for a total of four stimulation conditions per subject. After the overnight incubation, the cells were collected into 15 ml conical tubes through a 30-um strainer and washed with up to 14 ml of PBS/0.2% BSA, centrifuged at 400g for 5 minutes at 4°C, and resuspended in 50 ul Pharmingen Stain Buffer (BSA) (BD Biosciences).
For CITE-seq, a total of 30,000 cells were loaded into each of two wells of a Chromium Next GEM Chip G and run on the Chromium Controller (10X Genomics) for Gel Bead-in-emulsion (GEM) generation. The samples were processed according to the CG000204 Chromium Next GEM Single Cell 3’ v3.1 Rev. D protocol (10X Genomics) for RNA library construction while modifications for CITE-seq ADT and cell hashing HTO library preparation were performed according to the TotalSeq™-A Antibodies and Cell Hashing with 10x Single Cell 3' Reagent Kit v3 or v3.1 single index protocol (BioLegend). The modifications include the addition of ADT and HTO additive primers to a final concentration of 0.2 uM in the cDNA amplification reaction (step 2.2), and using Illumina TruSeq™ Small RNA RPIX (with custom indexes) and Illumina TruSeq™ D70X_short primers, respectively, together with the SI-PCR primer, in ADT and HTO sample index PCRs. The ADT and HTO sample index PCRs were performed on the purified fraction of the supernatant recovered from cDNA amplification cleanup.  For DOGMA-seq, the cells were processed according to the CG000338 Chromium Next GEM Multiome ATAC + Gene Expression Rev. D protocol (10X Genomics) for Gene Expression and ATAC library construction while modifications for DOGMA-seq were performed following the “Cell permeabilization with DIG” section of the DOGMA-seq protocol (NYGC Innovation Lab).  We first optimized the concentration of DIG that we would use for the DIG cell permeabilization step. We tested 0.0025%, 0.005%, 0.0075% and 0.01% DIG with about 230,000 cells each, and a DIG concentration of 0.0075% was chosen.  Approximately 600,000 cells were centrifuged at 400g for 5 minutes at 4°C and permeabilized in 100 ul chilled DIG lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 3 mM MgCl2, 0.0075% DIG and 2 U/ul Protector RNase inhibitor (Roche)) for 1 min on ice, followed by the addition of 1 ml of chilled DIG wash buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 3 mM MgCl2 and 1 U/ul RNase inhibitor) and pipette mixing, before centrifugation at 500g for 5 minutes at 4°C. The supernatant was discarded, the pellet was resuspended in a very small volume of about 17 ul of diluted Nuclei Buffer (10X Genomics) and 5 ul were used for cell counting.  In a separate experiment, we compared DOGMA-seq’s DIG and LLL protocols. Approximately 600,000 cells were permeabilized with DIG as described above and resuspended in 7.5 ul of Nuclei Buffer. Approximately 300,000 cells were fixed with 0.1% formaldehyde for 5 minutes at room temperature. Glycine was added as a quencher at 0.125M. The cells were washed twice with PBS/1% BSA/RNase inhibitor, centrifuged at 400g for 5 minutes at 4°C and permeabilized in 100 ul chilled LLL lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 1% BSA, 1 mM DTT and 2 U/ul RNase inhibitor) for 3 min on ice followed by the addition of 1 ml of chilled LLL wash buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 1 mM DTT and 1 U/ul RNase inhibitor) and pipette mixing, before centrifugation at 500g for 5 minutes at 4°C. The cells were resuspended in 7.5 ul of Nuclei Buffer. DIG and LLL-treated cells were also processed as described below. The cell recovery after DIG permeabilization was approximately 25-30 %, while the cell recovery after LLL permeabilization was approximately 50%.   Following the CG000338 Chromium Next GEM Multiome ATAC + Gene Expression Rev. D protocol, 30,000 cells were processed for each of two transposition reactions, which were then loaded into each of two wells of a Chromium Next GEM Chip J and run on the Chromium Controller (10X Genomics) for GEM generation.  During sample pre-amplification (step 4.2), ADT and HTO additive primers were added to a final concentration of 0.2 uM. After cleanup and elution in 100 ul, 30 ul were set aside for ADT and 10 ul were set aside for HTO sample index PCR reactions, that were performed using Illumina TruSeq™ Small RNA RPIX (with custom indexes) and Illumina TruSeq™ D70X_short primers, respectively, and the SI-PCR primer.  When generating the RNA library in the Chromium Next GEM Multiome ATAC + Gene Expression protocol, we chose to use the Single Index Plate T Set A instead of the Dual Index Plate TT Set A.

tag: molecule

value: HTO


title: CITE_RNA

description: RNA data of the CITE dataset

value: RNA


title: ChIP-Seq_BRD4_BRD2_degron_3h_rep2


title: ChIP-Seq_BRD3_BRD2_untreated_rep2


title: pi-staining-and-freezing: pi_stained 4np (F38F4)


title: KO_Polysome_2_2

data_processing:
Data was processed according via R using the kallisto
Differential gene expression was analysed via sleuth
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Library strategy: TS-seq

extract_protocol:
RNA was isolated using Trizol
The kit used was the illumina TruSeq stranded mRNA
Paired-end sequencing on HiSeq 4000 with a read lenght of 75

treatment_protocol: Before isolation of polysomes, cells were treated for 5 min with 100 ng/ml cycloheximide

value: RBPMS KO


title: ChIP-Seq_BRD3_BRD2_degron_3h_rep2


title: CITE_ADT

description: ADT data of the CITE dataset

value: ADT


title: pi-staining-and-freezing: pi_stained 4np (F38E6)


title: ChIP-Seq_BRD3_BRD2_untreated_rep1


title: Input_1


title: DOGMA_ATAC

description: ATAC data of the DOGMA dataset

data_processing:
Standard 10X Genomics Cell Ranger and Cell Ranger ARC pipelines, as well as kallisto | bustools workflow for ADT and HTO libraries.
Assembly: GRCh38
Supplementary files format and content: For each sample, the filtered UMI count matrix and filtered peak count matrix from 10X Genomics pipelines are stored in a h5 file, with atac_fragments.tsv.gz provided. HTO and ADT count matrices from kallisto | bustools workflow are stored in csv files, with non-singlets filtered out.
Library strategy: DOGMA-seq

tag: condition

value: DIG

value: ATAC


title: pi-staining-and-freezing: pi_stained 4np (F38F5)


title: pi-staining-and-freezing: pi_stained 4np (F38E4)


title: KO_Polysome_1_2

value: human embryonic stem cells


title: DOGMA_HTO

description: HTO data of the DOGMA dataset


title: pi-staining-and-freezing: pi_stained 4np (F38D6)


title: DOGMA_ADT

description: ADT data of the DOGMA dataset


title: pi-staining-and-freezing: pi_stained 4np (F38E5)


title: KO_Polysome_1_3

value: control


title: 4C_Myb_BRD2_untreated_rep2

data_processing:
Library strategy: 4C-seq
Reads were filtered and trimmed by enzyme sites using trimLinker of ChIA-PET2 software. Pair-end reads without a bait site were discarded by fastq-multx software.
Processed reverse reads were mapped to the mm10 mouse genome using Bowtie2 software in ‘very-sensitive-local’ mode with default parameters.
PCR duplicates, multihits, dangling-ends, self-religations and reads that longer than the library size were extruded.
Bigwig files were generated using bamCoverage from deepTools software.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated using deepTools. Scores represent the normalized RPGC signal.

growth_protocol: The V6.5 mouse ES (mES) cell line was cultured with 2i medium containing 15% FBS, leukaemia inhibiting factor (mLIF), L-glutamine, β-mercaptoethanol, non-essential amino acids, 3 μM CHIR99021, and 1 μM PD0325901 in ES-qualified Dulbecco’s modified Eagle’s medium (DMEM), incubated at 37 °C with 5% CO2.

extract_protocol:
We modified 4C-seq protocol based on 3C-HTGTS version (Jain et al., 2018). Briefly, After Nla III digestion and proximal ligation, target DNA was extracted with biotinyled bait primer.
Library were constructed via two rounds of PCR with truseq adaptor.

treatment_protocol: BRD2-degron mES cells were pre-treated with 1 μg/ml doxycycline for 18 hours and treated with or without 500 μM indole-3-acetic acid for 24 hours. Wild type mES cells were treated with BET bromodomain inhibitor, JQ1, 500 nM for 24 hours.

tag: restriction enzyme

value: AluI


title: KO_Polysome_2_3


title: 4C_Myb_BRD2_untreated_rep1


title: KO_Polysome_1_1


title: DOGMA_RNA

description: RNA data of the DOGMA dataset


title: KO_disome_3


title: KO_Polysome_2_1


title: pi-staining-and-freezing: pi_stained 4np (F38D4)


title: 4C_Myb_BRD2_degron_3h_rep1


title: ChIP-Seq_BRD3_BRD2_degron_3h_rep1


title: LLL_RNA

description: RNA data of the LLL dataset

value: LLL


title: KO_disome_2


title: LLL_ATAC

description: ATAC data of the LLL dataset


title: pi-staining-and-freezing: pi_stained 4np (F38C6)


title: 4C_Hoxd13_BRD2_untreated_rep2


title: LLL_HTO

description: HTO data of the LLL dataset


title: pi-staining-and-freezing: pi_stained 4np (F38C5)


title: KO_disome_1


title: LLL_ADT

description: ADT data of the LLL dataset


title: KO_80S_3


title: pi-staining-and-freezing: pi_stained 4np (F38D5)


title: pi-staining-and-freezing: pi_stained 4np (F38C4)


title: 4C_Hoxd13_BRD2_untreated_rep1


title: DIG_HTO

description: HTO data of the DIG dataset


title: 4C_Myb_BRD2_degron_3h_rep2


title: 4C_Hoxd13_BRD2_degron_3h_rep1


title: 4C_Hoxd13_BRD2_degron_3h_rep2


title: pi-staining-and-freezing: pi_stained 4np (F38B6)


title: pi-staining-and-freezing: pi_stained 4np (F38B5)


title: KO_80S_1


title: KO_40S_3


title: DIG_ADT

description: ADT data of the DIG dataset


title: EBD4-IAA-3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
After filtering out the reads mapped to mouse rRNA, cleaned reads were then mapped to the mm10 reference genome, guided by the GENCODE vM23 gene model using STAR aligner (v2.5.3a) with default settings.
Uniquely mapped reads were retained and then assigned to GENCODE gene annotation using featureCounts (v1.5.2) with parameters: -M --primary -p.
Differential expression testing was performed using DESeq2 bioconductor package (Love et al., 2014).
A threshold of  corrected p-value < 0.05 and log2(FC) > 1 was chosen to determine significantly changed gene expression after treatment.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq raw counts include DESeq2 annotated values of differentially expressed genes per sample in comma-separated values format.

source_name: Brd2 degron 24h EB-Day4

growth_protocol: The V6.5 mouse ES (mES) cell line was cultured with 2i medium containing 15% FBS, leukaemia inhibiting factor (mLIF), L-glutamine, β-mercaptoethanol, non-essential amino acids, 3 μM CHIR99021, and 1 μM PD0325901 in ES-qualified Dulbecco’s modified Eagle’s medium (DMEM), incubated at 37 °C with 5% CO2. mES cells were cultured with mESC EB medium without mLIF to form embryonic bodies (EBs).

extract_protocol:
Total RNA was isolated using TRIzol following manufacturer’s recommendations.
Sequencing libraries were generated by Novogene corporation with standard Illumina protocols.

treatment_protocol: BRD2-degron mES cells and EBs for 2, 3, 4 days were pre-treated with 1 μg/ml doxycycline for 18 hours and treated with or without 500 μM indole-3-acetic acid for 24 hours.

value: embryonic stem cells

value: IAA


title: pi-staining-and-freezing: pi_stained 4np (F38B4)


title: EBD4-IAA-2


title: MCF7-RBneg-birina, biol rep2

city: Buffalo

first: Jianxin

last: Wang

address: 665 Elm Street

department: Molecular and Cellular Biology

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Trim adapters
Alignment to GRCh37 using STAR
Produce raw read counts using RSEM
The entire data prcessing was done using nf-core/rnaseq pipeline, version 3.3
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include raw read count generated by RSEM

extract_protocol: TruSeq Stranded Total RNA, IDT-ILMN TruSeq RNA UD Indexes (96 Indexes)

value: breast adenocarcinoma

value: RB1 deletion

value: Birinapant

tag: time

value: 48 hours


title: MCF7-RBneg-birina, biol rep3


title: DIG_RNA

description: RNA data of the DIG dataset


title: KO_40S_2


title: KO_40S_1


title: pi-staining-and-freezing: pi_stained 4np (F38A6)


title: EBD4-IAA-1


title: KO_80S_2


title: MCF7-RBneg-birina, biol rep1


title: pi-staining-and-freezing: pi_stained 4np (F38A5)


title: KO_Input_2


title: KO_Input_3


title: DIG_ATAC

description: ATAC data of the DIG dataset


title: wga-reagent-volumes: protocol_c 4np (F37F5)

extract_protocol:
220 nm cryosections were collected in sucrose droplets and transferred to steel frame PEN membrane slides. Slides were washed in 1x PBS (3 times, 5 min each), then with water (3 times, 5 min each) and air dryed for 15 minutes. Nuclear profiles were laser microdissected into adhesive 8-strip LCM collection caps, with four profiles dissected into each cap. Caps were frozen and stored for up to two weeks. Whole genome amplification was performed using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (13 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.1 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. 5.35 µl library preparation mastermix (3.57 µl library preparation buffer, 1.78 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 5.35 µl library preparation enzyme (diluted 3x with H2O) was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 108.9 µl amplification master mix (13.4 µl amplification buffer, 86.6 µl H2O, 8.9 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 25 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines


title: MCF7-RBneg-DMSO, biol rep3

value: DMSO


title: EBD4-Dox-2

source_name: Untreated EB-Day4

value: Dox


title: WT_Polysome_2_3

value: WT


title: EBD4-Dox-3


title: MCF7-RBneg-DMSO, biol rep2


title: KO_Input_1

value: RBPMS KO


title: wga-reagent-volumes: protocol_c 4np (F37B5)


title: MCF7-RBpos-DMSO, biol rep2

value: RB1 wild type


title: EBD4-Dox-1


title: EBD3-IAA-2

source_name: Brd2 degron 24h EB-Day3


title: EBD3-IAA-3


title: wga-reagent-volumes: protocol_c 4np (F37A5)


title: MCF7-RBpos-birina, biol rep2


title: wga-reagent-volumes: protocol_a 4np (F37C2)

extract_protocol:
220 nm cryosections were collected in sucrose droplets and transferred to steel frame PEN membrane slides. Slides were washed in 1x PBS (3 times, 5 min each), then with water (3 times, 5 min each) and air dryed for 15 minutes. Nuclear profiles were laser microdissected into adhesive 8-strip LCM collection caps, with four profiles dissected into each cap. Caps were frozen and stored for up to two weeks. Whole genome amplification was performed using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (13 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.1 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. 4.32 µl library preparation mastermix (2.88 µl library preparation buffer, 1.44 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 1.4 µl library preparation enzyme was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 87.84 µl amplification master mix (10.8 µl amplification buffer, 69.84 µl H2O, 7.2 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 25 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines


title: pi-staining-and-freezing: pi_stained 4np (F38A4)


title: WT_Polysome_2_1


title: wga-reagent-volumes: protocol_a 4np (F37F1)


title: MCF7-RBpos-birina, biol rep3


title: WT_Polysome_1_2


title: WT_Polysome_1_3


title: EBD3-IAA-1


title: EBD3-Dox-3

source_name: Untreated EB-Day3


title: WT_Polysome_2_2


title: HECT_OVCAR3_4

city: Chapel Hill

first: Michael

middle: Ross

last: Kelly

state: NC

address: 120 Mason Farm Road

department: Bioinformatics and Genetics

institute: University of North Carolina at Chapel Hill

description: Hi-C-Seq

data_processing:
modified version of the Juicer Hi-C pipeline (https://github.com/EricSDavis/dietJuicer) with default parameters as previously described (Durand et al. 2016)
MboI was used as the restriction enzyme, and reads were aligned to the hg19 human reference genome with bwa (version 0.7.17). Four biological replicates were aligned and merged for a total of 2,922,558,308 Hi-C read pairs in OVCAR3 cells yielding 2,598,024,810 valid Hi-C contacts (88.90%).
Hi-C contact frequency was used to classify CRISPR-KO gene targets as direct or indirect. We compared the fold-change in observed over expected contact frequency between SE14 or SE60 and their respective gene targets with 100 permutations of distance-matched region-gene pairs as controls.
Genome_build: hg19
Supplementary_files_format_and_content: .hic files

source_name: OVCAR 3 Cell Line

growth_protocol: OVCAR3 cell lines were cultured in RPMI-1640 growth media (Gibco,11875093) supplemented with 10% FBS (Sigma) and 1% penicillin/streptomycin (Corning)

extract_protocol: In situ Hi-C was performed as previously described (Rao et al. 2014); see assocaited paper by Kelly et al. for more detail (methods section)

value: OVCAR 3

value: Wild Type

tag: replicate

value: Replicate 4


title: EBD3-Dox-2


title: EBD3-Dox-1


title: MCF7-RBneg-DMSO, biol rep1


title: EBD2-IAA-3

source_name: Brd2 degron 24h EB-Day2


title: WT_disome_2

value: human embryonic stem cells

value: control


title: T6

city: Harbin City

first: Chenghao

last: Li

state: HeiLongJiang Province

address: No. 51 HeXing Road,Xiangfang District

department: College of Forestry

institute: Northeast Forestry University

description:
Pu-miR172d-OE plants under drought treatment (4 days) conditions.
processed data file: fpkm.anno.txt
processed data file: total_fpkm.txt

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data).
The reference genomes and the annotation file were downloaded from the Populus genome (version3.0,https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa ). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Genome_build: Genome_build: Populus trichocarpa v3.0 (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa)
Supplementary_files_format_and_content: fpkm.anno.txt, total_fpkm.txt

organism: Populus ussuriensis

source_name: 7th and 8th leaves from shoot tips

growth_protocol: 4-week-old in vitro plants were transplanted in individual 300 ml pots with equal amounts of autoclaved soil and water for 70 days. All the plants were cultured on a greenhouse under a 16 h light/8 h dark photoperiod at 25°C.

extract_protocol:
The 7th and 8th leaves from shoot tips were harvested, flash frozen on dry ice, and RNA was isolated using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Drought treatment was applied to soil grown plants by withdrawing watering for 4 days.

value: 7th and 8th leaves from shoot tips

tag: age

value: 70-day-old plants transplanted in soil

value: Drought


title: T5


title: HECT_OVCAR3_2

description: Hi-C-Seq

value: Replicate 2


title: MCF7-RBpos-birina, biol rep1

value: breast adenocarcinoma


title: MCF7-RBpos-DMSO, biol rep1


title: WT_Polysome_1_1


title: WT_disome_1


title: EBD2-IAA-2

value: embryonic stem cells

value: IAA


title: wga-reagent-volumes: protocol_a 4np (F37E1)


title: WT_disome_3


title: T3

description:
Pu-miR172d-OE plants under well-watered (4 days) conditions.
processed data file: fpkm.anno.txt
processed data file: total_fpkm.txt

value: Well-watered


title: T1


title: EBD2-Dox-3

source_name: Untreated EB-Day2

value: Dox


title: HECT_OVCAR3_3

description: Hi-C-Seq

value: Replicate 3


title: T2


title: EBD2-Dox-2


title: EBD2-IAA-1


title: WT_80S_2

value: WT


title: WT_80S_3


title: T4


title: SE14KB_2

description: RNA-Seq

data_processing:
Alignment to GRCh38.p12 using STAR version 2.6.0.a
Counting was done on a gene level using htseq version 0.11.2
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: The processed data is the HTSEQ counts output for each sample, before normalization. These reads were input into DESEQ2 where the normalization was performed, as such there is no "normalized" count data.

source_name: CRISPR-dCas9-KRAB Modified OVCAR 3 Cell Line

extract_protocol:
RNA was harvested 72hrs after transfection of the sgRNA using the Zymo Quick-RNA Miniprep Kit (Cat#R1054) with on-column DNaseI treatment
RNA-seq libraries were prepared with the Illumina TruSeq mRNA Library Kit following the manufacturer's protocol

treatment_protocol: OVCAR3 cells that stably-expressed dCas9-KRAB were transfected with sgRNAs using Fugene 6 (Promega) following the manufacturer's protocol

value: OVCAR 3 (CRISPR-modified)

value: SE14 KRAB Targeting Rep 2


title: HECT_OVCAR3_1

description: Hi-C-Seq

value: OVCAR 3

value: Wild Type

value: Replicate 1


title: SE14KB_1

description: RNA-Seq

value: SE14 KRAB Targeting


title: EBD2-Dox-1


title: SE60KB_2

description: RNA-Seq

value: SE60 KRAB Targeting Rep 2


title: WT_40S_3

value: human embryonic stem cells

value: control


title: C5

description:
WT plants under drought treatment (4 days) conditions.
processed data file: fpkm.anno.txt
processed data file: total_fpkm.txt

value: 7th and 8th leaves from shoot tips

value: 70-day-old plants transplanted in soil

value: Drought


title: SE60KB_1

description: RNA-Seq

value: SE60 KRAB Targeting


title: C4


title: mES-IAA-2

source_name: Brd2 degron 24h mES

value: embryonic stem cells

value: IAA


title: C3

description:
WT plants under well-watered (4 days) conditions.
processed data file: fpkm.anno.txt
processed data file: total_fpkm.txt

value: Well-watered


title: SCRKB_2

description: RNA-Seq

value: Scramble Guide (non-targeting) Control Rep 2


title: mES-IAA-1


title: WT_40S_2

value: WT


title: WT_40S_1


title: C2


title: WT_Input_3


title: mES-Dox-3

source_name: Untreated mES

value: Dox


title: WT_Input_2


title: SCRKB_1

description: RNA-Seq

value: OVCAR 3 (CRISPR-modified)

value: Scramble Guide (non-targeting) Control


title: C1


title: mES-Dox-2


title: C6


title: OVCAR3_SE14KO4

description: RNA-SEQ

source_name: CRISPR Modified OVCAR 3 Cell Line

extract_protocol:
RNA was harvested from asynchronous cells using the Zymo Quick-RNA Miniprep Kit (Cat#R1054) with on-column DNaseI treatment
RNA-seq libraries were prepared with the Illumina TruSeq mRNA Library Kit following the manufacturer's protocol

treatment_protocol: Untreated

value: Super Enhancer 14 Deletion Clone 3


title: WT_80S_1


title: OVCAR3_SE14KO3

description: RNA-SEQ

value: Super Enhancer 14 Deletion Clone 2


title: WT_Input_1


title: OVCAR3_SE60KO4

description: RNA-SEQ

value: Super Enhancer 60 Deletion Clone 3 Rep 2


title: mES-Dox-1


title: mES-IAA-3


title: Brd2-mESCs_EBd4_GFP_ChIP_rep2

data_processing:
All libraries were sequenced using an Illumina Hiseq sequencer and 150 bp paired-end format.
The 150 bp paired-end reads were pre-processed by cutadapt (v2.10) and then aligned to the mm10 mouse genome assembly using Bowtie 2 (v2.3.2) with the default parameters “best -k 1 -m 1 and -l 18.”
Unmapped reads, low quality mapped reads and PCR duplicates were discarded. Only uniquely mapped were retained for downstream analysis.
Peaks were called against input control using the MACS2 function callpeak on each replicate with options ‘-f BAMPE -g mm --nomodel --shift 100 --extsize 200 -B –SPMR’ and q-value threshold of 10-5 to ensure high confidence. Common peaks between the replicates were used for downstream analysis.
The ChIP reads at each genomic position were normalized and converted to bigwig format using bamCoverage from deeptools toolkit (version 3.13).
For subsequent meta-gene analysis and browser visualization, replicates for each biological condition were merged into one bigwig track file.
Genome_build: mm10
Supplementary_files_format_and_content: The bigwig files of ChIP-seq data were generated using deepTools v3.13 with library size normalized to equal. 10 bp resolution with reads extended by 200bp

source_name: GFP tagged EB-Day4

extract_protocol:
Lysates were clarified from MNase digested and sonicated nuclei and protein-DNA complexes were isolated with specific antibody.
ChIP DNA were used to construct Illumina sequencing libraries using TELP method from (Peng et al., 2015).

treatment_protocol: BRD2-degron mES cells and EBs for 4 days were untreated with doxycycline or indole-3-acetic acid.

value: GFP (Abcam, ab290)


title: PP_A5_KO_input_rep1

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: 3 Qingchun East Rd.

department: Sir Run-Run Shaw Hospital

institute: Zhejiang University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were first trimmed by fastp (Chen et al., 2018) to remove adapter sequence and reads with low sequencing quality.
Clean data were aligned to human reference genome version 38 (GRCh38) using hisat2 (Kim et al., 2015) with parameters: --rna-strandness=FR -k 1 --no-unal.
The m6A peaks were called using R package exomePeak2 (Wei, 2020) (IP/input > 1.5, p value < 10-5), the longest isoform was retained if a gene has more than one isoform.
The differential m6A peaks were calculated using R package exomePeak2 with parameters: |log2 FC| > 1, adjust p value < 0.05.
Motif enrichment was done using HOMER (Heinz et al., 2010) selecting a motif length of 5,6 and 7 nucleotides.
Genome_build: hg38
Supplementary_files_format_and_content: m6A peak text files

source_name: MEL1 hESC line

growth_protocol: Undifferentiated MEL1 human embryonic stem cells were cultured in hPSC medium: DMEM/F12 (Life Technologies) supplemented with 20% KnockOut Serum Replacement (KSR) (Life Technologies), 1× Non-Essential Amino Acids (NEAA) (Life Technologies), 1× Penicillin/Streptomycin, 0.055 mM 2-Mercaptoethanol (Sigma), and 10 ng/ml bFGF (Peprotech). hPSCs were maintained on CF1 feeder cells in humidified incubator at 37°C and 5% CO2.  hPSCs were seeded into 10-cm dishes and cultured for four days before differentiation. The medium was changed every day. Then, hPSCs were washed by DPBS (Life Technologies) followed by dissociated into single cells using Accutase. hPSCs were seeded into 12-well plates at a density of 5×105 per well and the differentiation was initiated 24 hours after seeding. hPSCs were quickly washed by DPBS (Life Technologies) and exposed to differentiation media. Here is the detailed media: Day 1: RPMI (Life Technologies), 1× Penicillin/Streptomycin, 100 ng ml-1 activin A, and 3 μM CHIR99021 (TargetMol). Day 2: RPMI, 0.2% FBS, 1× Penicillin/Streptomycin, and 100 ng ml-1 activin A. Day 3: RPMI, 2% FBS, 1× Penicillin/Streptomycin, and 100 ng ml-1 activin A. Day 4-6: RPMI, 0.5X B27, 0.5X N2, 0.05% BSA (Yeasen), 1× Penicillin/Streptomycin, and 50 ng ml-1 KGF (Peprotech). Day 7-8: DMEM, 1X B27 (Gibco), 0.05% BSA, 1× Penicillin/Streptomycin, 0.25 mM vitamin C, 50 ng ml-1 KGF, 0.1 μM LDN-193189 (Tocris), 0.1 μM GDC-0449 (Selleck), and 2 μM retinoic acid (Sigma). Day 9-14: DMEM, 1X B27, 0.05% BSA, 1× Penicillin/Streptomycin, 0.25 mM vitamin C, 0.1 μM LDN-193189, and 50 ng ml-1 EGF (Peprotech). Then, cells were suspended to form aggregates, and differentiated into hILO stage using medium modified from our previous protocol. Day 15-22 (R6 medium): DMEM, 1:50 B27, 0.05% BSA, 1× Penicillin/Streptomycin, 10 μM zinc sulfate (Sigma), 10 μg ml-1 heparin (Sigma), 10 μM 616452 (TargetMol), 1 μM T3 (Sigma), 0.1 μM LDN-193189, 0.1 μM compound E (MedChem Express), and 0.25 mM vitamin C. Day 23-30 (R7 medium): DMEM, 1:50 B27, 0.05% BSA, 1× Penicillin/Streptomycin, 10 μM zinc sulfate, 10 μg ml-1 heparin, 10 μM 616452, 1 μM T3, 1 mM N-acetyl cysteine (Sigma), 1 μM trolox (Sigma), and 0.25 mM vitamin C.

extract_protocol:
Total RNAs were extracted with TRIzol™ Reagent (Invitrogen, cat. 15596018), and mRNAs were further enriched by GenElute mRNA Miniprep Kit (Sigma, cat. MRN10–1KT).
For samples from hPSC, DE, PP and hILO stages, mRNAs were fragmented into about 100 nt and immunoprecipitated (IP) with m6A antibody (SYSY, cat. 202003), both input and IP products were subjected to library construction (Illumina). For samples from WT and A5-KO PP cells, total RNAs were extracted, fragmented and subjected to immunoprecipitation directly due to limited materials. rRNAs in input fragments were first depleted by rRNA Depletion Kit (NEB, cat. E7400L), then both input and IP fragments were subjected to library preparation using SMARTer® Stranded Total RNA-Seq Kit v2 (Takara).

value: MEL1 hESC line

value: hPSC-derived pancreatic progenitor cells

tag: batch


title: PP_A5_KO_m6A_rep2

tag: genotype

value: m6A (Millipore)


title: PP_WT_input_rep2

tag: cell line


title: Brd2-mESCs_EBd4_GFP_ChIP_rep1


title: PP_A5_KO_m6A_rep1


title: OVCAR3_SE60KO3

description: RNA-SEQ

value: Super Enhancer 60 Deletion Clone 3 Rep 1


title: HiC_16HD_3h_rep2

city: La Jolla

first: Amir

last: Gamliel

state: CA

address: 9500 Gilman Dr.

department: Medicine

institute: University of California San Diego

data_processing:
Basecalling was performed using Illumina RTA (v1.18.66 or  v2.7.3  for HiSeq4000, v3.4.4  for NovaSeq6000)
Read pairs obtained by sequencing Hi-C libraries were mapped to the human reference genome assembly hg19 using bowtie2 62 version 2.3.0 with the following parameters: --end-to-end --very-sensitive -L 30 --score-min L,-0.6,-0.2 --mp 6,2. For each pair, each 100-base read was mapped independently. Reads aligning to multiple genomic locations were discarded. Reads that could not be aligned to any genomic location were further processed. The 8-base sequence (GATCGATC), expected for the junction resulting from ligation of the blunt ends of two MboI restriction fragments, was searched within the read sequence, allowing for a single base mismatch. If the searched junction sequence was found at one or two locations, the read sequence was split at the midpoint of each junction, and the resulting sub-sequences were mapped independently to the reference genome. If the junction sequence was not found, then the read sequence was processed in the iterative mapping procedure as described by Imakaev et al. (Nat Meth 9, 999-1003, 2012)
Sequence pairs aligned to genomic locations closer than 1000 bp were classified as “same strand” and “outward” pairs and hence discarded. The remaining aligned sequence pairs were used to generate raw contact maps, i.e., symmetric matrices of raw contact counts for all possible pairs of genomic bins  (Lajoie, B.R., Dekker, Methods 72, 65-75 , 2015), with one matrix per chromosome and either 40 kb or 250 kb per bin. The contact maps were inspected to identify rows and columns that contained too many zero entries for all of the analyzed Hi-C libraries. The minimum acceptable number of non-zero entries was arbitrarily set to 25% of the median number of non-zero entries in each row. The identified rows and columns were omitted from subsequent analysis steps.
To remove experimental biases in the matrices , each raw contact map was processed using an iterative matrix-balancing procedure (Yaffe, E. & Tanay,, Nat Genet 43, 1059-1065, 2011) that yields a matrix with approximately constant row, and column sum
The reproducibility of the Hi-C experiments was assessed through a modified calculation of the “stratum-adjusted correlation coefficient” (SCC) (Yang, T. et al, Genome Research 27, 1939-1949, 2017).
Genome_build: hg19
Supplementary_files_format_and_content: fastq

source_name: human embryonic stem cells

growth_protocol: RUES1 cells were cultured in mTeSR1 (StemCell Technologies, catalog #05850), plated in Corning Matrigel hESC-qualified Matrix (Corning, catalog #354277) in a humidified incubator with 5% CO2 at 37 degrees Celcius.

extract_protocol:
In situ Hi-C was essentially performed as described  (Rao, S.S. et al, Cell 159, 1665-80 , 2014), using the restriction enzymes  MboI for Hexanediol Hi-C, or DpnII for flavopiridol and triptolide Hi-C.
Hi-C DNA was purified on Dynabeads MyOne Streptavidin T1 beads (Thermo Fisher), and sequencing libraries were prepared using the KAPA HTP/LTP Library Preparation Kits.

treatment_protocol: Cells were treated with 7% 1,6-Hexanediol (1,6-HD) (Sigma, Cat#240117), 2,5-Hexanediol (2,5-HD) (Sigma, Cat # H11904) for 5 minutes. The chemical was washed away with mTeSR1 and was incubated for additional time points as indicated at 37 degrees Celcius .For transcription inhibition experiments, RUES1 cells were treated with either 5uM flavopiridol hydrochloride (F3055 Sigma) or 1uM triptolide (T3652 Sigma), for 15 minutes, 1 hour and 3 hours. Cells were then washed with PBS, cross-linked with 1% formaldehyde in PBS at room temperature for 10 min and neutralized with 0.125M glycine.

tag: treatment

value: 7% 1,6-Hexanediol for 5 minutes, wash, incubate with fresh media for 3 hours at 37 deg C.


title: HiC_16HD_3h_rep1


title: HiC_TRP_3h_rep2

value: Triptolide 3 hours


title: Brd2-mESCs_EBd4_Input

tag: cell type

value: embryonic stem cells

value: none (input)


title: HiC_16HD_30min_rep2

value: 7% 1,6-Hexanediol for 5 minutes, wash, incubate with fresh media for 30 minutes at 37 deg C.


title: HiC_16HD_30min_rep1


title: HiC_TRP_3h_rep1


title: HiC_16HD_5min_rep2

value: 7% 1,6-Hexanediol for 5 minutes, wash, incubate with fresh media for 5 minutes at 37 deg C.


title: HiC_TRP_1h_rep2

value: Triptolide 1 hour


title: Brd2-mESCs_GFP_ChIP_rep2

source_name: GFP tagged mES


title: PP_A5_KO_input_rep2


title: PP_WT_input_rep1

value: WT


title: PP_WT_m6A_rep2


title: HiC_TRP_1h_rep1


title: Brd2-mESCs_GFP_ChIP_rep1


title: HiC_16HD_5min_rep1


title: hILO_input_rep2

value: hPSC-derived islet-like organoids


title: untreated_Sox2_4C_rep2

data_processing:
Library strategy: 4C-seq
Reads were filtered and trimmed by enzyme sites using trimLinker of ChIA-PET2 software. Pair-end reads without a bait site were discarded by fastq-multx software.
Processed reverse reads were mapped to the mm10 mouse genome using Bowtie2 software in ‘very-sensitive-local’ mode with default parameters.
PCR duplicates, multihits, dangling-ends, self-religations and reads that longer than the library size were extruded.
Replicates and treatments of the same gene were sampled to the same depth, and then normalized by trans reads number using deepTools. Samples were quantile normalized by the R package preprossesCore.
Bigwig files were converted from mm10 to mm9 using CrossMap and visualized with UCSC genome browser.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated using deepTools. Scores represent the normalized RPGC signal.

source_name: untreated Brd2-degron mES

value: mouse embryonic stem cells

value: AluI

value: untreated


title: HiC_TRP_15min_rep2

value: Triptolide 15 minutes


title: Brd2-mESCs_Input


title: HiC_TRP_15min_rep1


title: HiC_25HD_5min_rep2

value: 7% 2,5-Hexanediol for 5 minutes, wash, incubate with fresh media for 5 minutes at 37 deg C.


title: PP_WT_m6A_rep1

value: MEL1 hESC line

value: hPSC-derived pancreatic progenitor cells


title: HiC_25HD_5min_rep1


title: untreated_Sox2_4C_rep1


title: HiC_Ctrl_TRP_rep2

value: sham (Ethanol) treated


title: untreated_Sall4_bait2_4C_rep2


title: hILO_input_rep1


title: untreated_Sall4_bait2_4C_rep1


title: hILO_m6A_rep2


title: HiC_Ctrl_TRP_rep1


title: PP_input_rep2


title: HiC_FP_3h_rep2

value: Flavopiridol 3 hours


title: PRO_25HD_5min_rep2

description: nascent nuclear RNA

data_processing:
Basecalling was performed using Illumina RTA (v2.7.6)
Quality control: FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TRIMMOMATIC (http://www.usadellab.org/cms/?page=trimmomatic) were used to inspect the quality of the sequencing reads, and to trim the sequencing adaptors, if necessary.
Read alignment: Bowtie2 (Langmead et al., Nature Methods 2012)  (version 2.2.6) was employed to align PRO-seq samples to hg19 genome using --very-sensitive setting. Tag directories were then generated using HOMER (version 4.10.3), keeping only unique aligned reads per genome position, but allowing up to 3 unique reads per position (-tbp 3).
Read counting: The HOMER script analyzeRepeats.pl was used in order to estimate the raw counts per gene in  PRO-seq data, and to compute the Pausing Ratio. For gene expression counting, the aligned reads were counted over the RefSeq gene bodies (after excluding a TSS 400bp-proximal region downstream of TSS up to 13Kb of the gene body). EdgeR (http://www.bioconductor.org/) was used to compute the significance of the differential gene expression (FC≥1.5, FDR≤0.05).
Generation of bedgraph files: we have used the HOMER scripts makeUCSCfile and makeMultiWigHub.pl in order to generate bedgraph files for visualization in the UCSC genome browser.
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph

extract_protocol:
Precision Run-on sequencing (PRO-seq) experiments were performed as previously described (Mahat, D. B. et al, Nat Protoc 11, 1455-1476, 2016) with modification. Briefly, for nuclei isolation, RUES1 cells were incubated with swelling buffer (10 mM Tris-HCl pH7.5, 2 mM MgCl2, 3 mM CaCl2) for 5min on ice and then incubated with lysis buffer (swelling buffer with 0.5% NP-40 and 10% glycerol) for 5 min on ice, before being re-suspended in 100μl of freezing buffer (50 mM Tris-Cl pH8.0, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA). For Run-on assay, an equal volume of reaction buffer (10 mM Tris-Cl pH 8.0, 5 mM MgCl2, 300 mM KCl, 1 mM DTT, 20 units of SuperaseIn, 1% sarkosyl, 500 μM ATP, GTP, bio-UTP and bio-CTP) was added into each sample before incubation at 30°C for 5 min. The nuclear run-on RNA was then extracted with TRIzol LS reagent (Invitrogen) and subjected to hydrolysis, buffer exchange and purification by streptavidin beads (Thermo Fisher). Purified RNA was treated with PNK before being used for cDNA synthesis by using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® Kit (NEB). Obtained cDNA template was amplified by PCR using the LongAmp® Taq 2X Master Mix (NEB) for deep sequencing.
Purified RNA was treated with PNK before being used for cDNA synthesis by using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® Kit (NEB). Obtained cDNA template was amplified by PCR using the LongAmp® Taq 2X Master Mix (NEB) for deep sequencing.
PRO-seq

treatment_protocol: Cells were treated with 7% 1,6-Hexanediol (1,6-HD) (Sigma, Cat#240117), 2,5-Hexanediol (2,5-HD) (Sigma, Cat # H11904) for 5 minutes. The chemical was washed away with mTeSR1 and was incubated for additional time points as indicated at 37 degrees Celcius before isolating nuclei for PRO-seq.


title: PRO_16HD_5min_rep2

description: nascent nuclear RNA


title: hILO_m6A_rep1


title: untreated_Sall4_bait1_4C_rep1


title: PRO_16HD_5min_rep1

description: nascent nuclear RNA


title: GRO_16HD_3h_rep2

description: nascent nuclear RNA

data_processing:
Basecalling was performed using Illumina RTA (v1.18.66 or v2.7.3)
Quality control: FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TRIMMOMATIC (http://www.usadellab.org/cms/?page=trimmomatic) were used to inspect the quality of the sequencing reads, and to trim the sequencing adaptors, if necessary.
Read alignment: Bowtie2 (Langmead et al., Nature Methods 2012)  (version 2.2.6) was employed to align GRO-seq samples to hg19 genome using --very-sensitive setting. Tag directories were then generated using HOMER (version 4.10.3), keeping only unique aligned reads per genome position, but allowing up to 3 unique reads per position (-tbp 3).
Read counting: The HOMER script analyzeRepeats.pl was used in order to estimate the raw counts per gene in  GRO-seq data, and to compute the Pausing Ratio. For gene expression counting, the aligned reads were counted over the RefSeq gene bodies (after excluding a TSS 400bp-proximal region downstream of TSS up to 13Kb of the gene body). EdgeR (http://www.bioconductor.org/) was used to compute the significance of the differential gene expression (FC≥1.5, FDR≤0.05).
Generation of bedgraph files: we have used the HOMER scripts makeUCSCfile and makeMultiWigHub.pl in order to generate bedgraph files for visualization in the UCSC genome browser.
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph

extract_protocol:
GRO-Seq experiments were performed as previously reported (Oh, S. et al. Nature s41586-021-03577-1 ,2021) with modification. Briefly, ~10  million RUES1 cells were washed 3 times with cold PBS and then sequentially swelled in swelling buffer (10mM Tris-Cl pH7.5, 2mM MgCl2, 3mM CaCl2) for 5 min on ice, harvested, and lysed in lysis buffer (swelling buffer plus 0.5% NP-40 and 10% glycerol). The resultant nuclei were washed one more time with 10mL lysis buffer and finally re-suspended in 100uL of freezing buffer (50mM Tris-Cl pH8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA). For the run-on assay, re-suspended nuclei were mixed with an equal volume of reaction buffer (10mM Tris-Cl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 20 units of SUPERase-IN, 1% sarkosyl, 500uM ATP, GTP, and Br-UTP, 2uM CTP) and incubated for 5 min at 30°C. The resultant nuclear-run-on RNA (NRO-RNA) was then extracted with TRIzol LS reagent (Invitrogen) following manufacturer’s instructions. NRO-RNA was fragmented to ~300-500nt by alkaline base hydrolysis on ice and followed by treatment with DNase I and Antarctic phosphatase. These fragmented Br-UTP labeled nascent RNA was then immunoprecipitated with an anti-BrdU agarose beads (Sc32323ac, Santa Cruz Biotechnology) in binding buffer (0.5XSSPE, 1mM EDTA, 0.05% tween) for 3 hrs at 4°C with rotation. Purified RNA was treated with PNK before being used for cDNA synthesis by using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® Kit (NEB). Obtained cDNA template was amplified by PCR using the LongAmp® Taq 2X Master Mix (NEB) for deep sequencing.
Purified RNA was treated with PNK before being used for cDNA synthesis by using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® Kit (NEB). Obtained cDNA template was amplified by PCR using the LongAmp® Taq 2X Master Mix (NEB) for deep sequencing.
GRO-Seq

treatment_protocol: Cells were treated with 7% 1,6-Hexanediol (1,6-HD) (Sigma, Cat#240117), 2,5-Hexanediol (2,5-HD) (Sigma, Cat # H11904) for 5 minutes. The chemical was washed away with mTeSR1 and was incubated for additional time points as indicated at 37 degrees Celcius before isolating nuclei for GRO-seq.

value: 7% 1,6-Hexanediol for 5 minutes, wash, incubate with fresh media for 3 hours at 37 deg C.


title: PP_m6A_rep1


title: HiC_FP_3h_rep1


title: PP_input_rep1


title: PRO_25HD_5min_rep1

description: nascent nuclear RNA


title: DE_input_rep2

value: hPSC-derived definitive endoderm cells


title: PP_m6A_rep2


title: HiC_FP_1h_rep1

value: Flavopiridol 1 hour


title: untreated_Sall4_bait1_4C_rep2


title: HiC_FP_1h_rep2


title: untreated_Phc1_4C_rep2


title: JQ1_Sox2_4C_rep1

source_name: JQ1 treated wild type mES


title: DE_input_rep1


title: GRO_16HD_3h_rep1

description: nascent nuclear RNA


title: HiC_FP_15min_rep2

value: Flavopiridol 15 minutes


title: HiC_Ctrl_FP_rep2


title: JQ1_Sox2_4C_rep2


title: untreated_Phc1_4C_rep1


title: HiC_Ctrl_FP_rep1


title: GRO_16HD_30min_rep1

description: nascent nuclear RNA

value: 7% 1,6-Hexanediol for 5 minutes, wash, incubate with fresh media for 30 minutes at 37 deg C.


title: GRO_16HD_5min_rep1

description: nascent nuclear RNA

value: 7% 1,6-Hexanediol for 5 minutes, wash, incubate with fresh media for 5 minutes at 37 deg C.


title: JQ1_Sall4_bait2_4C_rep2


title: HiC_FP_15min_rep1


title: JQ1_Sall4_bait1_4C_rep1


title: DE_m6A_rep2


title: GRO_16HD_30min_rep2

description: nascent nuclear RNA


title: hPSC_input_rep1

value: hESC


title: PP_A5-KO_3h_rep2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing reads were trimmed by fastp to remove adapter sequence and reads with low sequencing quality.
Sequencing reads were mapped to the human hg38 reference genome assembly using HISAT2(v2.1.0)(Kim et al., 2015) with the default parameter settings.
Gene expression based on GENCODE v34 annotations (Harrow et al., 2012) was determined using stringrie (Pertea et al. 2015) with the default parameter settings.
Gene expression was converted to attomoles by linear fitting of the RNA ERCC spike-ins.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with normalized gene CPM for every gene and every sample

growth_protocol: Undifferentiated hPSCs were cultured in hPSC medium: DMEM/F12 (Life Technologies), 20% KnockOut Serum Replacement (KSR) (Life Technologies), 1× Non-Essential Amino Acids (NEAA) (Life Technologies), 0.055 mM 2-mercaptoethanol (Sigma), 1× Penicillin/Streptomycin, and 10 ng ml-1 bFGF (Peprotech). hPSCs were maintained on CF1 feeder cells at 37°C and 5% CO2. hPSCs were isolated by Accutase (Life Technologies) as 1:3 to 1:6 every 3-6 days. 0.5 μM thiazovivin (TargetMol) were used during the first 24 hours when passaging or thawing cells. hPSCs were seeded into 12-well plates at a density of 5×10e5 per well and the differentiation was initiated 48 hours after seeding. hPSCs were quickly washed by DPBS (Life Technologies) and exposed to differentiation media. Here is the detailed media: Day 1: RPMI (Life Technologies), 1× Penicillin/Streptomycin, 100 ng ml-1 activin A, and 3 μM CHIR99021 (TargetMol). Day 2: RPMI, 0.2% FBS, 1× Penicillin/Streptomycin, and 100 ng ml-1 activin A. Day 3: RPMI, 2% FBS, 1× Penicillin/Streptomycin, and 100 ng ml-1 activin A. Day 4-6: RPMI, 0.5X B27 (Gibco), 0.5X N2 (Gibco), 0.05% BSA (Yeasen), 1× Penicillin/Streptomycin, and 50 ng ml-1 KGF (Peprotech). Day 7-8: DMEM, 1X B27, 0.05% BSA, 1× Penicillin/Streptomycin, 0.25 mM vitamin C, 50 ng ml-1 KGF, 0.1 μM LDN-193189 (Tocris), 0.1 μM GDC-0449 (Selleck), and 2 μM retinoic acid (Sigma). Day 9-14: DMEM, 1X B27, 0.05% BSA, 1× Penicillin/Streptomycin, 0.25 mM vitamin C, 0.1 μM LDN-193189, and 50 ng ml-1 EGF (Peprotech).

extract_protocol:
Cells were havested and total RNA was isolated using Fast Pure Cell Total RNA Isolation Kit (Vazyme).
1 μg RNA per sample were used as input material for the RNA sample preparations. Each RNA sample was spiked in with an appropriate amount of either Mix1 or Mix2 according to Life Technologies’ guidelines. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: WT and A5-KO PPs were treated with actinomycin D (Sigma, cat. ab141058) at a final concentration of 1 μg mL-1 and collected at indicated time points.

value: actinomycin D


title: JQ1_Sall4_bait2_4C_rep1

value: mouse embryonic stem cells


title: RAD21_25HD_rep1

description: chromatin immunoprecipitation

data_processing:
Basecalling was performed using Illumina RTA (v2.7.6)
Quality control: FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TRIMMOMATIC (http://www.usadellab.org/cms/?page=trimmomatic) were used to inspect the quality of the sequencing reads, and to trim the sequencing adaptors, if necessary.
Read alignment: Bowtie2 (Langmead et al., Nature Methods 2012)  (version 2.2.6) using --very-sensitive setting was employed to align ChIP-seq samples to hg19 genome. Tag directories were then generated using HOMER (version 4.10.3), keeping only unique alligned reads per genome position,  allowing 1 unique read per position (-tbp 1).
Peak finding: ChIP-seq peaks were called using HOMER findPeaks subroutine (Heinz et al., 2010, http://homer.ucsd.edu/homer/) with the default settings (-style factor -o auto).
Generation of bedgraph files: The  HOMER scripts makeUCSCfile and makeMultiWigHub.pl were used  in order to generate bedgraph and BigWig files for visualization in the UCSC genome browser.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

extract_protocol:
Briefly, approximately 10 million cells were cross-linked with 1% formaldehyde in PBS at room temperature for 10 min and neutralized with 0.125M glycine. After sonication, ~50µg soluble chromatin was incubated with 1-5μg of antibody at 40C overnight. Immunoprecipitated complexes were collected using Dynabeads A/G (Invitrogen). Subsequently, immuno-complexes were washed, DNA extracted, and purified by QIAquick Spin columns (Qiagen). For ChIP-seq, the extracted DNA was ligated to Illumina UDI adaptors followed by deep sequencing with Illumina’s HiSeq 4000 according to the manufacturer’s instructions.
ChIP enriched DNA was purified, and 10 ng used to prepare sequencing libraries with the KAPA HTP/LTP Library Preparation Kits

treatment_protocol: Cells were treated with 7% 1,6-Hexanediol (1,6-HD) (Sigma, Cat#240117), 2,5-Hexanediol (2,5-HD) (Sigma, Cat # H11904) for 5 minutes. The chemical was washed away with mTeSR1 and was incubated for additional time points as indicated at 37 degrees Celcius before fixing with 1% formaldehyde in PBS for ChIP-seq.

tag: chip antibody

value: RAD21 GenTex (#gtx106012)


title: GRO_25HD_5min_rep2

description: nascent nuclear RNA


title: JQ1_Sall4_bait1_4C_rep2

value: AluI


title: hPSC_input_rep2


title: GRO_25HD_5min_rep1

description: nascent nuclear RNA


title: PP_A5-KO_3h_rep1


title: DE_m6A_rep1


title: IAA_Sox2_4C_rep2


title: PP_A5-KO_2h_rep2


title: RAD21_25HD_inp

description: DNA input for chromatin immunoprecipitation


title: RAD21_16HD_rep2

description: chromatin immunoprecipitation


title: JQ1_Phc1_4C_rep2


title: hPSC_m6A_rep2


title: GRO_16HD_5min_rep2

description: nascent nuclear RNA


title: CTCF_16HD_rep2

description: chromatin immunoprecipitation

value: CTCF Active Motif (#61311, Lot 34614003)


title: IAA_Sall4_bait2_4C_rep2

value: IAA


title: PP_A5-KO_2h_rep1

value: MEL1 hESC line


title: JQ1_Phc1_4C_rep1


title: PP_A5-KO_0h_rep1

value: hPSC-derived pancreatic progenitor cells

value: control


title: hPSC_m6A_rep1


title: IAA_Sall4_bait1_4C_rep2


title: PP_A5-KO_1h_rep2


title: IAA_Sall4_bait1_4C_rep1


title: PP_A5-KO_1h_rep1


title: IAA_Sox2_4C_rep1


title: PP_A5-KO_0h_rep2


title: PP_WT_2h_rep2

value: WT


title: RAD21_16HD_inp


title: IAA_Phc1_4C_rep2


title: CTCF_16HD_rep1

description: chromatin immunoprecipitation


title: IAA_Sall4_bait2_4C_rep1


title: PP_WT_3h_rep2


title: Pan02-Mutant 4

type: RNA

city: Gifu City

first: Ayumi

last: Niwa

address: 1-1 Yanagido

country: Japan

institute: Gifu University

description: transplanted Pan02 cells to mouse subcutaneous tissue and then extracted RNA

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus

source_name: Pan02 transplanted to Mutant

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: All the Pan02 pancreatic cancer cells were transplanted to mouse subcutaneous tissue of Control(wild type) and Mutant(Ext1 flox/flox; S100a4-Cre) mice. Subcutaneous tumors were removed from the mice 36 to 40 days later and then extraced RNA.

extract_protocol: Total RNA was extracted using the Maxwell RSC simplyRNA Tissue Kit (Promega Corp., Fitchburg, Wisconsin, USA).

tag: tissue

value: subcutaneous tumor

value: pancreatic cancer cell

tag: source

value: obtained from B6 (Ext1 flox/flox; S100a4-Cre mice) subcutaneous tumor


title: CTCF_25HD_rep2

description: chromatin immunoprecipitation

value: 7% 2,5-Hexanediol for 5 minutes, wash, incubate with fresh media for 5 minutes at 37 deg C.


title: Pan02-Mutant 2


title: ubp12ubp13, biol replicate #1

city: Cold Spring Harbor

first: Ullas

middle: V.

last: Pedmale

address: 1 Bungtown RD

department: Pedmale

institute: Cold Spring Harbor Laboratory

data_processing:
The sequencing reads were mapped to the Arabidopsis thaliana Col-0 reference genome (TAIR10) using the STAR aligner
Differential gene expression analysis was performed using Cufflinks version 2.1.1.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include FPKM values

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Seedlings were grown for 4 days under 1 µmol m-2 s-1 constant blue light and frozen in liquid nitrogen prior to RNA extraction

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini kit (Qiagen) and quantified using a Flurometer (Qubit 2.0, Thermo Fisher).
500 ng of total RNA was used to isolate poly(A)-mRNA using the NEBNext poly(A) mRNA Isolation Module (NEB) and the purified mRNA was used to construct sequencing libraries using the Ultra II Directional RNA library Prep Kit for Illumina (NEB)

tag: ecotype

value: Columbia (Col-0)

value: whole seedlings

value: blue light (1 umol m-2 s-1)

value: 4 days


title: PP_WT_3h_rep1

value: actinomycin D


title: Pan02-Mutant 1


title: Pan02-Mutant 3


title: CTCF_25HD_rep1

description: chromatin immunoprecipitation


title: PP_WT_1h_rep1


title: DMSO_Sox2_4C_rep1

source_name: DMSO treated wild type mES

extract_protocol:
We modified 4C-seq protocol based on 3C-HTGTS version (Jain et al., 2018). Briefly, After Nla III digestion and proximal ligation, target DNA was extracted with biotinyled bait primer.
Library were constructed via two rounds of PCR with truseq adaptor.

value: mouse embryonic stem cells

value: DMSO


title: Pan02-Control 1

source_name: Pan02 transplanted to Control

value: obtained from B6 (Control) subcutaneous tumor


title: Pan02-Control 4


title: Pan02-Control 3


title: ubp12ubp13, biol replicate #2


title: IAA_Phc1_4C_rep1

value: AluI

value: IAA


title: PP_WT_1h_rep2

value: MEL1 hESC line

value: hPSC-derived pancreatic progenitor cells


title: UBP13oe, biol replicate #2


title: DMSO_Sall4_bait2_4C_rep2


title: UBP13oe, biol replicate #1


title: CRY2oe, biol replicate #1


title: PP_WT_0h_rep2

value: WT

value: control


title: Pan02-Control 2

value: subcutaneous tumor

value: pancreatic cancer cell


title: MC38-Ext1S100a4Cre 4

description: transplanted MC38 cells to mouse subcutaneous tissue and then extracted RNA

source_name: MC38 transplanted to S100a4Cre

growth_protocol: All the MC38 colon cancer cells were transplanted to mouse subcutaneous tissue of WT(wild type) and Ext1S100a4Cre(Ext1 flox/flox; S100a4-Cre) mice. Subcutaneous tumors were removed from the mice 25 to 30 days later and then extraced RNA.

value: colon cancer cell

value: obtained from B6 (S100a4Cre) subcutaneous tumor


title: cry2-1, biol replicate #2

value: Columbia (Col-0)

value: whole seedlings


title: PP_WT_2h_rep1


title: hILO_A5_KO_rep2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and removed low-complexity or low-quality sequence.
Sequencing reads were mapped to the human hg38 reference genome assembly using HISAT2(v2.1.0)(Kim et al., 2015) with the default parameter settings.
Gene expression based on GENCODE v34 annotations (Harrow et al., 2012) was determined using stringrie (Pertea et al. 2015) with the default parameter settings.Transcripts per million reads (TPM) were calculated for represented the expression of each gene.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene TPM for every gene and every sample

extract_protocol:
Cells were havested and total RNA was isolated using Quick-RNA MiniPrep Kit (ZYMO).
3 μg RNA per sample were used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: hPSC-derived islet-like organoids


title: CRY2oe, biol replicate #2

value: blue light (1 umol m-2 s-1)

value: 4 days


title: PP_WT_0h_rep1


title: DMSO_Sall4_bait2_4C_rep1

value: mouse embryonic stem cells

value: DMSO


title: DMSO_Sall4_bait1_4C_rep2

value: AluI


title: hILO_WT_rep2


title: cry2-1, biol replicate #1


title: Col-0 (WT), biol replicate #2

value: Col-0 (WT)


title: DMSO_Sall4_bait1_4C_rep1


title: DMSO_Phc1_4C_rep2


title: DMSO_Phc1_4C_rep1


title: hILO_WT_rep1

value: MEL1 hESC line


title: MC38-Ext1S100a4Cre 3


title: Col-0 (WT), biol replicate #1


title: MC38-Ext1S100a4Cre 2


title: MC38-WT 3

source_name: MC38 transplanted to WT

value: obtained from B6 (WT) subcutaneous tumor


title: MC38-Ext1S100a4Cre 1


title: 21d-Case-rep3

status: Public on Jun 12 2022

city: Nantong

first: hualin

last: sun

state: jiangsu

address: suzhou

institute: Nantong University

hyb_protocol: microarray hybridization and washing were performed based on the manufacturer’s standard protocols.

scan_protocol: After washing, the arrays were scanned by the Agilent Scanner G2505C(Agilent Technologies)

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring(version13.1,Agilent Technologies)were employed to finish the basic analysis with the raw data,the raw data was normalized with the quantile algorithm

organism: Rattus norvegicus

label_protocol: The sample labeling were performed based on the manufacturer’s standard protocols.Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

extract_protocol:
Fresh muscle was obtained from each group, and NanoDrop ND-2000 was used to extract  total RNA.
Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100

value: muscle

tag: gender

value: male

value: Denervation 21d


title: 21d-Case-rep2


title: 21d-Ctrl-rep3

value: Control 21d


title: 21d-Ctrl-rep2


title: MC38-WT 2

value: subcutaneous tumor

value: colon cancer cell


title: MC38-WT 1


title: MC38-WT 4


title: 14d-Case-rep3

value: Denervation 14d


title: 7d-Case-rep2

value: Denervation 7d


title: 14d-Case-rep1


title: 14d-Case-rep2


title: 14d-Ctrl-rep2

value: Control 14d


title: 14d-Ctrl-rep1


title: 7d-Ctrl-rep2

value: Control 7d


title: 21d-Case-rep1


title: 7d-Case-rep3


title: 7d-Case-rep1


title: 3d-Case-rep2

value: Denervation 3d


title: 7d-Ctrl-rep1


title: 14d-Ctrl-rep3


title: 3d-Case-rep3


title: 3d-Case-rep1


title: 3d-Ctrl-rep3

value: Control 3d


title: 7d-Ctrl-rep3


title: 3d-Ctrl-rep1


title: 21d-Ctrl-rep1


title: hILO_A5_KO_rep1

value: hPSC-derived islet-like organoids


title: 24h-Case-rep3

value: Denervation 24h


title: 24h-Case-rep2


title: 24h-Ctrl-rep3

value: Control 24h


title: TES7 input

city: Lanzhou

first: Xingdong

address: The west lake street

institute: CAAS

description: 5-year-old cattle-yak

data_processing:
Raw data (raw reads) of fastq format were firstly processed using the Trimmomatic software.
HISAT2 2.0.4 software was used to compare the reference genome of valid data after preprocessing.
The m6A-enriched peaks in each m6A immunoprecipitation sample were identified by MeTDiff peak calling software with the corresponding input sample serving as control.
MeTDiff was run with options (FRAGMENT_LENGTH-200, PEAK_CUTOFF_PVALUE =0.01, PEAK_CUTOFF_FDR =0.05) for peak detection.
Called peaks were annotated by intersection with gene architecture using ChlPseeker
Assembly: LU_Bosgru_v3.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample …

organism: Bos grunniens

source_name: testis

growth_protocol: The testis tissues of 3 healthy cattle-yak (5 years old)  were collected in Xiahe County, Gannan Tibetan Autonomous Prefecture

extract_protocol:
The total RNA was isolated and purified using the TRIzol reagent . Bioanalyzer 2100 (Agilent, CA, USA) and NanoDrop 2000 (Thermo Scientific) with RIN number > 7.0 were used to evaluate the total RNA quality and quantity.
poly (A) mRNA fractions are broken using divalent cations at high temperatures (RNA solution at 94°C for exactly 5 minutes using a thermocycler). Then, the fragmentation of broken RNA were incubated with m6A-Dynabeads (Anti-m6A, Synaptic Systems, Cat. No 202003) in an m6A-binding buffer (50 mM Tris-HCl pH7.4, 150 mM NaCl2, 1%NP-40, 2 mM EDTA), Allow the fragmented RNA to bind to the m6A-Dynabeads. Then washing of m6A-Dynabeads, Elution of m6A-positive RNA. Extraction and Cleanup of the RIP, Collecting m6A “enriched RNA”. We have generally utilized 100 ng of RNA (100 ng of input and 100 ng of post m6A-IP positive fraction) for library construction utilizing Illumina TrueSeq Stranded mRNA. Afterwards, we implemented the paired-end sequencing on an Illumina HiSeq X10 system, using a suggested protocol from the manufacturer.

treatment_protocol: The testicular tissue is immediately stored in liquid nitrogen for RNA isolation. Testicular samples were obtained by castration

value: testis

value: 5 year old


title: TES7 IP

description: 5-year-old cattle-yak


title: TES5 input

description: 5-year-old cattle-yak


title: TES5 IP

description: 5-year-old cattle-yak


title: 24h-Case-rep1

value: muscle


title: 12h-Ctrl-rep2

value: male

value: Control 12h


title: 12h-Case-rep3

value: Denervation 12h


title: 24h-Ctrl-rep1


title: 6h-Case-rep2

value: Denervation 6h


title: 12h-Ctrl-rep1


title: 12h-Ctrl-rep3


title: 24h-Ctrl-rep2


title: 12h-Case-rep2


title: 6h-Ctrl-rep1

value: Control 6h


title: TES6 input

description: 5-year-old cattle-yak


title: 3d-Ctrl-rep2


title: TES6 IP

description: 5-year-old cattle-yak


title: 6h-Case-rep1


title: 6h-Ctrl-rep3


title: renal biopsy, ALD/HCV pt. 45 cel 29

city: Tucson

first: Nathan

last: Cherrington

state: Arizona

address: 1703 E. Mabel Street

department: Pharmacology & Toxicology

institute: University of Arizona

description: Gene expression data from kidney biopsy

hyb_protocol: Once the labeling reaction was completed, 60uL was combined with the hybridization solution, then hybridized overnight for 17 hours on a Mouse Gene 1.0ST array in an Affymetrix GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA).

scan_protocol: arrays were scanned using the GeneChip Scanner 3000 with 7G upgrade (Thermo Scientific, Wilmington, DE)

data_processing: The image generated was analyzed using the GeneChip Expression Console (Affymetrix, Santa Clara, CA) were .DAT (image), .CEL (cell intensity data), .CHP (probe analysis data) files were generated.

label: biotin

source_name: kidney FFPE neddgle biopsy

label_protocol: 10 ng of total RNA labeled according to GeneChip WT Pico Kit manufacturer's instructions

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions.

value: Kidney

tag: disease state

value: ALD/HCV


title: 3h-Case-rep3

value: Denervation 3h


title: 12h-Case-rep1


title: renal biopsy, ALD/HCV pt. 30 cel 27

description: Gene expression data from kidney biopsy


title: 6h-Case-rep3


title: renal biopsy, ALD/HCV pt. 9 cel 14

description: Gene expression data from kidney biopsy


title: renal biopsy, ALD/HCV pt. 40 cel 22

description: Gene expression data from kidney biopsy


title: 3h-Case-rep2


title: 3h-Case-rep1


title: renal biopsy, ALD/HCV pt. 1 cel 6

description: Gene expression data from kidney biopsy


title: 6h-Ctrl-rep2


title: renal biopsy, HCV pt. 67 cel 43

description: Gene expression data from kidney biopsy

value: HCV


title: 3h-Ctrl-rep3

value: Control 3h


title: renal biopsy, ALD/HCV pt. 46 cel 35

description: Gene expression data from kidney biopsy


title: renal biopsy, HCV pt. 47 cel 34

description: Gene expression data from kidney biopsy


title: renal biopsy, HCV pt. 62 cel21

description: Gene expression data from kidney biopsy


title: renal biopsy, HCV pt. 11 cel 13

description: Gene expression data from kidney biopsy


title: 3h-Ctrl-rep2


title: 0.5h-Ctrl-rep3

value: Control 30min


title: 0.5h-Case-rep2

value: Denervation 30min


title: 0.5h-Case-rep3


title: renal biopsy, ALD pt. 68 cel 16

description: Gene expression data from kidney biopsy

value: ALD


title: renal biopsy, HCV pt. 10 cel 5

description: Gene expression data from kidney biopsy


title: 0.5h-Ctrl-rep2


title: 3h-Ctrl-rep1


title: DMSO_Sox2_4C_rep2

value: mouse embryonic stem cells

value: AluI

value: DMSO


title: 0.25h-Case-rep3

value: muscle

value: Denervation 15min


title: renal biopsy, ALD pt. 63 cel 8

description: Gene expression data from kidney biopsy


title: renal biopsy, HCV pt. 15 cel 20

description: Gene expression data from kidney biopsy


title: 0.5h-Case-rep1

value: male


title: renal biopsy, ALD pt. 48 cel 36

description: Gene expression data from kidney biopsy


title: renal biopsy, ALD pt. 49 cel 37

description: Gene expression data from kidney biopsy


title: 0.25h-Case-rep2


title: NKD180900311

city: Perth

first: Wee Loong

last: Chin

address: Level 5, Qq Block, Qeii Medical Centre 6 Verdun St, Nedlands

country: Australia

institute: National Centre For Asbestos Related Diseases

data_processing:
cellranger: --expect-cells 60000
Supplementary_files_format_and_content: cellranger3 output - cellranger3 filtered matrices, containing cell barcodes, genes (feature), and count matrices in mtx format

source_name: tumour

growth_protocol: Subcutaneous tumour

extract_protocol:
gentleMACS system (Miltenyi Biotec)
Chromium Single Cell 3′ Libraries

treatment_protocol: MIce were treated 1 hour AFTER sample collected: 100ug anti-CTLA4 + anti-PDL1 i.p.

value: tumour

value: 8-9 weeks

value: f

tag: group

value: RS

tag: tumour type

tag: strain

value: balb/c

tag: timepoint


title: renal biopsy, ALD pt. 39 cel 30

description: Gene expression data from kidney biopsy

value: Kidney


title: 0.25h-Ctrl-rep3

value: Control 15min


title: renal biopsy, ALD pt. 3 cel 7

description: Gene expression data from kidney biopsy


title: NKD180900309

value: NR

value: Renca


title: NKD180900307


title: renal biopsy, NASH pt. 65 cel 26

description: Gene expression data from kidney biopsy

value: NASH


title: renal biopsy, NASH pt. 66 cel 33

description: Gene expression data from kidney biopsy


title: NKD180900308


title: 0.25h-Case-rep1


title: 0.25h-Ctrl-rep1


title: 0.5h-Ctrl-rep1

value: Control 30min


title: 0.25h-Ctrl-rep2


title: NKD180900306


title: renal biopsy, NASH pt. 59 cel 19

description: Gene expression data from kidney biopsy


title: renal biopsy, NAFLD pt. 78 cel 6584

description: Gene expression data from kidney biopsy

value: NAFLD


title: NKD180900305


title: renal biopsy, NASH pt. 58 cel 12

description: Gene expression data from kidney biopsy


title: NKD180900304


title: renal biopsy, NAFLD pt. 77 cel 12086

description: Gene expression data from kidney biopsy


title: NKD180900303


title: renal biopsy, NAFLD pt. 23 cel 25

description: Gene expression data from kidney biopsy


title: NKD180900310


title: renal biopsy, NAFLD pt. 20 cel 18

description: Gene expression data from kidney biopsy


title: renal biopsy, NAFLD pt. 13 cel 8679

description: Gene expression data from kidney biopsy


title: NKD180900302


title: NKD180900301


title: NKD180900300


title: renal biopsy, NAFLD pt. 2 cel 2

description: Gene expression data from kidney biopsy


title: renal biopsy, NASH pt. 50 cel 3

description: Gene expression data from kidney biopsy