title: PRO_dTAG-3h_INTS8-dTAG_vector_DLD1

description: treated with dTAG13 for 3 hours

data_processing:
The paired-end PRO-seq reads were trimmed by Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and fastp v0.21.0 (Chen et al., 2018b), and ribosomal RNA reads were removed using Bowtie v2.3.5.1 (Langmead and Salzberg, 2012).
Resulting reads were aligned to hg19 or mm10 genome using Bowtie v2.3.5.1 with “--local --sensitive-local” (Langmead and Salzberg, 2012), and PCR duplicates were removed by umi_tools v1.0.1 (Smith et al., 2017).
Removal of low mapping quality reads and duplicated reads and calculation of normalization factor were performed with SAMtools v1.9 (Li et al., 2009) and Picard v2.23.3 (https://broadinstitute.github.io/picard/).
Strand-specific PRO-seq signal normalized by spike-in reads was generated by deeptools v3.5.0 (Ramirez et al., 2016) with "--Offset 1" for single-base files and "--Offset None" for full-length files.
Assembly: hg19
Supplementary files format and content: bigWig files

source_name: INTS8-dTAG_vector DLD1

extract_protocol:
RNA was isolated with TRIzol.
Enriched RNA was ligated with RNA adapters. Reverse transcription (RT) was performed using the Superscript III enzyme (Invitrogen). The reverse transcription products were proceeded to library amplification by using the Q5 enzyme mix.  Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.
PRO-Seq

value: INTS8-dTAG_vector DLD1

value: INTS8 knock-in of a dTAG tag, then ectopic control vector expression

value: treated with dTAG13


title: ICP22-null infection, 12h p.i., replicate 2 [RNA-Seq]

status: Public on Apr 19 2023

type: SRA

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

description:
Total RNA prepared using Trizol
Delta_ICP22_12_hpi_2

library_source: transcriptomic

data_processing:
Reads were mapped against the human genome (GRCh37/hg19), HSV-1 genome (Human herpesvirus 1 strain 17, JN555585, terminal repeats masked) and rRNA sequences using ContextMap v2.7.9
Number of read fragments per gene were determined using featureCounts and gene annotations from Ensembl (version 87 for GRCh37). HSV-1 gene annotations were obtained from GenBank (GenBank accession code: JN555585).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: gene read counts

molecule: total RNA

organism: Homo sapiens

growth_protocol: Human fetal foreskin fibroblasts were cultured in DMEM supplements with 10% FBS and P/S. Cells were infected at 60-80% confluency 24h after the last split. T-HF cells were cultured in DMEM supplements with 10% FBS and P/S. Expression of HA-ICP22 and HA-ICP22 + V5-ICP27 was induced by adding 5 μg/ml doxycycline for 48h.

extract_protocol:
Total RNA was prepared using Trizol.
TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat
35bp paired-end, NextSeq 500 (Illumina)

treatment_protocol: HFFF cells were infected for 15 minutes with HSV-1 strain F or ICP22-null virus at an MOI of 10 followed by PBS wash and media replacement. 350 µg/ml PAA was added to indicated samples for 8 or 12 hours. 5 μg/mL DOX was added to indicated samples 48 hours prior to collecting RNA. 80 mM KCl (salt stress) was added to indicated samples for 2 hours prior to collecting RNA.

tag: cell type

value: human fetal foreskin fibroblasts

tag: time post infection

value: 12 hpi

tag: agent

value: ICP22-null mutant of herpes simplex virus 1, strain F

tag: treatment

value: no treatment


title: ICP22-null infection, 12h p.i., replicate 1 [RNA-Seq]

description:
Total RNA prepared using Trizol
Delta_ICP22_12hpi_1


title: PRO_dTAG-3h_INTS8-dTAG_INTS8-WT_DLD1

city: Shanghai

first: Linna

last: Peng

address: Dong'an Road

country: China

institute: Fudan University

description: treated with dTAG13 for 3 hours

source_name: INTS8-dTAG_INTS8-WT DLD1

growth_protocol: Colorectal adenocarcinoma cell line DLD1 cells were cultured in DMEM (Dulbecco’s Modified Eagle’s medium, Hyclone) supplemented with 10% fetal bovine serum (FBS, Biowest), nonessential amino acids (Gibco) at 37 °C and 5% CO2.

treatment_protocol: Cells were treated with dTAG 13 for 3h.

tag: cell line

value: INTS8-dTAG_INTS8-WT DLD1

value: colorectal adenocarcinoma cell lines

tag: genotype

value: INTS8 knock-in of a dTAG tag, then ectopic INTS8-WT expression

tag: time

value: 3 hours


title: 11A_M_1189

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain

tag: Sex

value: male


title: ICP22-null infection, 8h p.i.,replicate 2 [RNA-Seq]

description:
Total RNA prepared using Trizol
Delta_ICP22_8hpi_2

value: 8 hpi


title: 11A_M_1183


title: 11A_M_1185


title: PRO_dTAG-3h_INTS8-dTAG_DLD1_rep2

description: treated with dTAG13 for 3 hours

source_name: INTS8-dTAG DLD1

value: INTS8-dTAG DLD1

value: INTS8 knock-in of a dTAG tag


title: PRO_dTAG-3h_INTS8-dTAG_INTS8-N211del_DLD1

description: treated with dTAG13 for 3 hours

source_name: INTS8-dTAG_INTS8-N211del DLD1

value: INTS8-dTAG_INTS8-N211del DLD1

value: INTS8 knock-in of a dTAG tag, then ectopic INTS8-N211del expression


title: 11A_M_1182


title: 11A_M_1180


title: PRO_dTAG-3h_INTS11-dTAG_DLD1_rep2

description: treated with dTAG13 for 3 hours

source_name: INTS11-dTAG DLD1

value: INTS11-dTAG DLD1

value: INTS11 knock-in of a dTAG tag


title: PRO_dTAG-3h_INTS8-dTAG_DLD1_rep1

description: treated with dTAG13 for 3 hours

value: treated with dTAG13


title: 11A_M_1181


title: 11A_M_118


title: 11A_M_1179


title: PRO_DMSO-3h_INTS8-dTAG_vector_DLD1

description: untreated

value: INTS8-dTAG_vector DLD1

value: INTS8 knock-in of a dTAG tag, then ectopic control vector expression

value: treated with DMSO


title: 11A_M_1178


title: 11A_M_1177


title: PRO_DMSO-3h_INTS8-dTAG_INTS8-WT_DLD1

description: untreated


title: PRO_DMSO-3h_INTS8-dTAG_INTS8-N211del_DLD1

description: untreated


title: 11A_M_1176


title: PRO_DMSO-3h_INTS8-dTAG_DLD1_rep2

description: untreated


title: 11A_M_1175


title: PRO_dTAG-3h_INTS11-dTAG_DLD1_rep1

description: treated with dTAG13 for 3 hours


title: Cartillage_AES_2h_rep4

type: RNA

city: Uppsala

first: Maria

last: Löfgren

department: Department of Biomedical Sciences and Veterinary Public Health

country: Sweden

institute: Swedish University of Agricultural Sciences

hyb_protocol: GeneChip® Equine Gene 1.0 ST Arrays (Affymetrix Inc., Santa Clara, CA USA), containing 25923 probes sets were hybridized for 16 h in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual P/N 702731 Rev 3 (Affymetrix Inc.), the arrays were washed and stained using the Fluidics Station 450.

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix Inc.).

data_processing: The raw data from the microarray analysis were normalized in an Expression Console (Affymetrix Inc.,), using the robust multi-array average method first suggested by Li and Wong (Li & Wong 2001; Irizarry et al. 2003). Subsequent analysis of the gene expression data was carried out in the statistical computing language R (www.r-project.org) using packages available from the Bioconductor project (www.bioconductor.org). In order to search for the differentially expressed genes between the IL-1β stimulated pellets and the other groups (unstimlated, treated with AES, AES 24h or ACS), a paired empirical Bayes moderated t-test was applied using the ‘limma’ package (Smyth 2004; Smyth 2005). To address the problem with multiple testing, the p-values were adjusted using the method of Benjamini and Hochberg (Benjamini & Hochberg 1995).

label: biotin

organism: Equus caballus

label_protocol: 100 ng of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome, according to the GeneChip® WT PLUS Reagent Kit User Manual P/N 703174 Rev 1 (Affymetrix Inc., Santa Clara, CA USA).

growth_protocol: Chondrocytes isolated from equine cartilage cultured as 3D pellet cultures.

extract_protocol: In brief, one pellet from each group (unstimulated, IL-1β stimulated and treated with AES, AES 24h or ACS) was homogenized and RNA was extracted with a lysis reagent and chloroform followed by purification using RNeasy Mini Kit (Qiagen, Hilden, Germany) and RNase-Free DNase Set (Qiagen) according to the manufacturer’s instruction.

treatment_protocol: 48h pre-stimulation with 5 ng/ml recombinant equine IL-1β, controls without IL-1β. Thereafter treated in groups as follows: unstimulated control, IL-1β, IL-1β+AES, IL-1β+AES24h, IL-1β+ACS. Harvest after 2h and 48h.

value: 3D Chondrocyte pellets

value: AES

tag: time point


title: Cartillage_AES_48h_rep4


title: Cartilage_ACS_2h_rep4

value: ACS


title: Cartilage_ACS_48h_rep3


title: Cartilage_AES24h_48h_rep4


title: Cartilage_IL1b_48h_rep4


title: Cartilage_ACS_48h_rep4


title: Cartilage_IL1b_2h_rep4


title: Cartilage_control_48h_rep4

value: Control


title: Cartilage_AES24h_48h_rep3


title: Cartilage_AES24h_2h_rep4


title: Cartillage_AES_48h_rep3


title: Cartilage_ACS_2h_rep3


title: 11A_M_1174


title: Cartilage_IL1b_48h_rep3


title: Cartilage_control_48h_rep3


title: Cartilage_control_2h_rep4


title: Cartilage_IL1b_2h_rep3


title: PRO_DMSO-3h_INTS11-dTAG_DLD1_rep2

description: untreated

value: colorectal adenocarcinoma cell lines

value: 3 hours


title: 11A_M_1173

value: male


title: Cartillage_AES_2h_rep3


title: Cartilage_control_2h_rep3


title: Cartilage_ACS_48h_rep2


title: PRO_DMSO-3h_INTS8-dTAG_DLD1_rep1

description: untreated

value: INTS8-dTAG DLD1


title: PRO_DMSO-3h_INTS11-dTAG_DLD1_rep1

description: untreated


title: 11A_M_1172


title: Cartilage_AES24h_2h_rep3


title: 11A_M_1171


title: 11A_M_1170


title: Cartillage_AES_48h_rep2


title: ChIP-RPB1-pS5_dTAG-3h_INTS8-dTAG_INTS8-N211del_DLD1_rep2

description: treated with dTAG13 for 3 hours

data_processing:
Raw reads were processed with Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality reads with the parameter “-q 25” .
The remaining reads were aligned to the human hg19 and mouse mm10 assemblies using Bowtie v2.3.5.1 with default parameters (Langmead and Salzberg, 2012).
All unmapped reads, low mapping quality reads (MAPQ < 30) and PCR duplicates were removed using SAMtools v1.9 (Li et al., 2009) and Picard v2.23.3 (https://broadinstitute.github.io/picard/).
The number of spike-in mm10 reads was counted with SAMtools v1.9 and normalization factor alpha = 1e6/mm10_count was calculated (Li et al., 2009).
Normalized bigwig was generated with deeptools v3.5.0 and reads mapped to the ENCODE blacklist regions were removed using bedtools v2.29.2 (Amemiya et al., 2019; Quinlan and Hall, 2010; Ramirez et al., 2016).
Peaks were called using macs2 v2.2.6 with a q-value threshold of 0.05 and peak annotation was performed with ChIPseeker R package v1.24.0 (Yu et al., 2015; Zhang et al., 2008).
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
Lysates were clarified from sonicated cells and RBP1-DNA complexes were isolated with antibody.
Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Universal DNA Library Prep Kit (Vazyme ND607-02). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

tag: chip antibody

value: Phospho-Rpb1 CTD (Ser5) (CST, #13523)


title: ChIP-RPB1-pS5_dTAG-3h_INTS8-dTAG_INTS8-N211del_DLD1_rep1

description: treated with dTAG13 for 3 hours

value: INTS8-dTAG_INTS8-N211del DLD1


title: 11A_M_117


title: 11A_M_1169


title: ChIP-RPB1-pS5_dTAG-3h_INTS11-dTAG_DLD1_rep2

description: treated with dTAG13 for 3 hours


title: ChIP-RPB1-pS5_dTAG-3h_INTS11-dTAG_DLD1_rep1

description: treated with dTAG13 for 3 hours


title: ChIP-RPB1-pS5_DMSO-3h_INTS8-dTAG_INTS8-N211del_DLD1_rep2

description: untreated


title: 11A_M_1168


title: ChIP-RPB1-pS5_DMSO-3h_INTS8-dTAG_INTS8-N211del_DLD1_rep1

description: untreated


title: Cartilage_AES24h_2h_rep2


title: Cartillage_AES_2h_rep2


title: Cartilage_IL1b_2h_rep2


title: Cartilage_IL1b_48h_rep2


title: Cartilage_AES24h_48h_rep2


title: Cartilage_control_48h_rep2


title: 11A_M_1167


title: ChIP-RPB1-pS5_DMSO-3h_INTS11-dTAG_DLD1_rep2

description: untreated


title: Cartilage_AES24h_48h_rep1


title: Cartillage_AES_48h_rep1


title: Cartilage_control_2h_rep2


title: 11A_M_1166


title: Cartilage_control_48h_rep1


title: Cartilage_IL1b_48h_rep1


title: ChIP-RPB1-pS5_DMSO-3h_INTS11-dTAG_DLD1_rep1

description: untreated


title: Cartilage_ACS_2h_rep2


title: 11A_M_1165


title: ChIP-RPB1-pS2_dTAG-3h_INTS8-dTAG_INTS8-N211del_DLD1_rep2

description: treated with dTAG13 for 3 hours

value: Phospho-Rpb1 CTD (Ser2) (CST, #13499)


title: Cartilage_ACS_2h_rep1


title: 11A_M_1164


title: H3EYFP sRNA req2

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

description: HOT3-EYFP Seedling, rep2

data_processing:
Raw reads were trimmed by cutadapt v4.2 using 3' adapter sequence AGATCGGAAGAGC. Then, 18-42 nt trimmed reads were mapped to the Arabidopsis genome Araport11 using ShortStack v3.8.5 with parameters "--align_only --bowtie_m 1000 --ranmax 50 --mmap u --mismatches 0 --nohp".
18-26 nt reads were assigned to 100 bp non-overlapping windows on the genome according to the 5' end of the alignment, and read counts were summerized and normalized based on read lengthes and total mapped reads. Reads corresponding to genome features such as miRNA, coding gene, etc. were also counted using featureCounts v2.0.3.
Differential sRNAs were calculated by the R package DESeq2 v1.34.0.
Assembly: Araport11
Supplementary files format and content: tab-delimited txt files containing bin accession and raw read counts ranging from 18 to 26 nt for each bin

organism: Arabidopsis thaliana

source_name: 18-day-old seedling

growth_protocol: 16 hr light/8 hr dark, 23˚C

extract_protocol:
Total RNA was isolated from 18-day-old seedlings using TRI Reagent (MRC, TR118) according to the manufacturer’s instructions. 20ug total RNA was resolved on a 15% urea-polyacrylamide gel (Urea-PAGE) and small RNAs of 18~40 nucleotides (nt) were recovered from excised gel pieces corresponding to RNAs of this size range.
Small RNA libraries were constructed following instructions from the NEBNext Multiplex Small RNA Library Prep Set for Illumina (E7300).

tag: tissue

value: 18-day-old seedling

value: somatic cells

value: HOT3-EYFP hot3-2


title: Cartillage_AES_2h_rep1


title: Cartilage_ACS_48h_rep1


title: H3EYFP sRNA req1

description: HOT3-EYFP Seedling, rep1


title: Cartilage_IL1b_2h_rep1


title: h33 sRNA req2

description: hot3-3 Seedling, rep2


title: h33 sRNA req1

description: hot3-3 Seedling, rep1


title: ChIP-RPB1-pS2_dTAG-3h_INTS11-dTAG_DLD1_rep2

description: treated with dTAG13 for 3 hours

value: INTS11-dTAG DLD1


title: 11A_M_1160


title: h32 sRNA req2

description: hot3-2 Seedling, rep2


title: ChIP-RPB1-pS2_dTAG-3h_INTS11-dTAG_DLD1_rep1

description: treated with dTAG13 for 3 hours


title: ChIP-RPB1-pS2_dTAG-3h_INTS8-dTAG_INTS8-N211del_DLD1_rep1

description: treated with dTAG13 for 3 hours


title: WT sRNA req2

description: WT Seedling, rep2

value: WT


title: WT sRNA req1

description: WT Seedling, rep1


title: 11A_M_116


title: 11A_M_1158


title: h32d2d4 nonpolysome ENDrep4

description: hot3-2 dcl2 dcl4 Seedling, non-polysome RNA, rep4

data_processing:
Reads were trimmed by cutadapt v4.2 using adapter sequence GGATCAACCAGGTA and then mapped to the Arabidopsis rDNA using STAR v2.7.10b with parameters "--alignIntronMax 5000 --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 10000000000 --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outFilterMismatchNoverLmax 0.1".
Reads mapped to the negative strand of nucleotide 1886 ~ 1915 of rDNA were split into 5' "perfect match" bodies and 3' "soft clip" tails. Then these reads were grouped according to the position of 3' end of body and the length of tail and counted (tails longer than 10 nt were included in length 10 group).
Assembly: rDNA reference from Darriere, et al. RNA Biology 2022 (DOI: 10.1080/15476286.2022.2071517)
Supplementary files format and content: Tab-delimited txt files containing the position of 3' end of body, the length of tail, and raw read counts

extract_protocol:
Approximately 0.25g of frozen seedling or inflorescence was ground into fine powder in liquid nitrogen. One milliliter of polysome extraction buffer (PEB) (0.2M Tris-HCl pH8.0, 0.2M KCl, 35mM MgCl2, 25mM EGTA, 1% TritonX-100, 2% polyoxyethylene-10-tridecyl ether (PTE), 100mM 2-Mercaptoethanol, 25ug/ml cycloheximide (CHX), 100ug/ml chloramphenicol (CHL) and 0.5mg/ml heparin) was added and mixed thoroughly with the powder. After 10 minutes incubation on ice, cell debris was removed by centrifugation for 5 min at 12,000 rpm in a microcentrifuge at 4 °C. Sodium deoxycholate (DOC) was added to the supernatant to a final concentration of 0.5%, and the lysate was kept on ice for 5 min. After centrifugation for 15 min at 12,000 rpm in a microcentrifuge, the supernatant was transferred to a new 1.5ml RNase-free tube and marked as PEB-input.  0.5 ml of the PEB-input was loaded onto a 4.4-ml sucrose gradient (15-55% Sucrose in 40mM Tris-HCl pH8.0, 20mM KCl, 10mM MgCl2, 25ug/ml CHX, 100ug/ml CHL, 0.5mg/ml heparin). After ultracentrifugation in a Beckman SW-55Ti rotor at 45,000 rpm for 65 minutes at 4°C, density gradient fractionation (Brandel, SYN-202) was performed as described before (94, 95). The fluid speed was 1.5 ml/min, and collection time for each fraction was 19 seconds. Ethylenediamine tetraacetic acid (EDTA) and sodium dodecyl sulfate (SDS) were added to 20mM and 0.5%, respectively, into each fraction at room temperature. RNA was immediately extracted from each fraction using TRI-reagent (MRC, TR118) according to the manufacturer’s instructions. Pelleted RNA was resuspended in 25ul RNase-free ddH2O for library construction.
The 18S-ENDseq library construction pipeline was adapted from the circular RT–PCR assay with modifications. 1.5ug of RNA was used for RNA self-ligation followed by reverse-transcription with the RT-primer 18c2, using the RevertAid First Strand cDNA Synthesis Kit (Thermo Fisher, K1621). A custom-made universal primer and indexed primers were then employed to amplify 18S-END libraries, using the SYBR-Green qPCR Supermix (BioRad, 170-8882) in a CFX96 Real-Time system (BioRad, C1000 Touch) for 15 cycles. PCR products were size selected in an agarose gel and recovered by QIAEX II Gel Extraction Kit (150) (QIAGEN,20021), or directly purified with AMPure XP Beads (Beckman, A63881). After quality control and quantitation with a Bioanalyzer (Agilent, 2100), the barcoded libraries were pooled for single-end 150-bp sequencing in an Illumina Hiseq 2500 machine

value: hot3-2 dcl2 dcl4


title: 11A_M_1157


title: ChIP-RPB1-pS2_DMSO-3h_INTS8-dTAG_INTS8-N211del_DLD1_rep1

description: untreated


title: ChIP-RPB1-pS2_DMSO-3h_INTS8-dTAG_INTS8-N211del_DLD1_rep2

description: untreated


title: Cartilage_AES24h_2h_rep1

value: 3D Chondrocyte pellets


title: h32d2d4 nonpolysome ENDrep2

description: hot3-2 dcl2 dcl4 Seedling, non-polysome RNA, rep2


title: h32d2d4 nonpolysome ENDrep1

description: hot3-2 dcl2 dcl4 Seedling, non-polysome RNA, rep1


title: h32d2d4 nonpolysome ENDrep3

description: hot3-2 dcl2 dcl4 Seedling, non-polysome RNA, rep3


title: 11A_M_1156


title: h32d2d4 polysome ENDrep4

description: hot3-2 dcl2 dcl4 Seedling, polysome RNA, rep4


title: ChIP-RPB1-pS2_DMSO-3h_INTS11-dTAG_DLD1_rep2

description: untreated


title: h32d2d4 polysome ENDrep2

description: hot3-2 dcl2 dcl4 Seedling, polysome RNA, rep2


title: ChIP-RPB1-pS2_DMSO-3h_INTS11-dTAG_DLD1_rep1

description: untreated


title: h32d2d4 polysome ENDrep1

description: hot3-2 dcl2 dcl4 Seedling, polysome RNA, rep1


title: ChIP-RPB1_dTAG-3h_INTS8-dTAG_INTS8-N211del_DLD1_rep2

description: treated with dTAG13 for 3 hours


title: h32 sRNA req1

description: hot3-2 Seedling, rep1


title: h32d2d4 total ENDrep3

description: hot3-2 dcl2 dcl4 Seedling, total RNA, rep3


title: Cartilage_control_2h_rep1


title: h32d2d4 total ENDrep2

description: hot3-2 dcl2 dcl4 Seedling, total RNA, rep2


title: ChIP-RPB1_dTAG-3h_INTS8-dTAG_INTS8-N211del_DLD1_rep1

description: treated with dTAG13 for 3 hours


title: h32 nonpolysome ENDrep4

description: hot3-2 Seedling, non-polysome RNA, rep4


title: ChIP-RPB1_dTAG-3h_INTS11-dTAG_DLD1_rep2

description: treated with dTAG13 for 3 hours


title: h32 nonpolysome ENDrep3

description: hot3-2 Seedling, non-polysome RNA, rep3


title: h32 nonpolysome ENDrep2

description: hot3-2 Seedling, non-polysome RNA, rep2


title: ChIP-RPB1_dTAG-3h_INTS11-dTAG_DLD1_rep1

description: treated with dTAG13 for 3 hours


title: h32 nonpolysome ENDrep1

description: hot3-2 Seedling, non-polysome RNA, rep1


title: 11A_M_1151


title: 11A_M_1150


title: h32 polysome ENDrep3

description: hot3-2 Seedling, polysome RNA, rep3


title: ChIP-RPB1_DMSO-3h_INTS8-dTAG_INTS8-N211del_DLD1_rep2

description: untreated


title: 11A_M_115


title: h32d2d4 polysome ENDrep3

description: hot3-2 dcl2 dcl4 Seedling, polysome RNA, rep3


title: ChIP-RPB1_DMSO-3h_INTS8-dTAG_INTS8-N211del_DLD1_rep1

description: untreated


title: h32 polysome ENDrep2

description: hot3-2 Seedling, polysome RNA, rep2


title: 11A_M_1155


title: 11A_M_1149


title: h32d2d4 total ENDrep4

description: hot3-2 dcl2 dcl4 Seedling, total RNA, rep4


title: 11A_M_1154


title: h32 polysome ENDrep1

description: hot3-2 Seedling, polysome RNA, rep1


title: ChIP-RPB1_DMSO-3h_INTS11-dTAG_DLD1_rep2

description: untreated


title: 11A_M_1153


title: 11A_M_1148


title: h32d2d4 total ENDrep1

description: hot3-2 dcl2 dcl4 Seedling, total RNA, rep1


title: h32 total ENDrep2

description: hot3-2 Seedling, total RNA, rep2


title: ChIP-RPB1_DMSO-3h_INTS11-dTAG_DLD1_rep1

description: untreated


title: h32 total ENDrep3

description: hot3-2 Seedling, total RNA, rep3


title: 11A_M_1152


title: h32 total ENDrep1

description: hot3-2 Seedling, total RNA, rep1


title: d2d4 nonpolysome ENDrep4

description: dcl2 dcl4 Seedling, non-polysome RNA, rep4

value: dcl2 dcl4


title: ChIP-input_dTAG-3h_INTS8-dTAG_INTS8-N211del_DLD1

description: treated with dTAG13 for 3 hours

value: input


title: 11A_M_1147


title: h32 polysome ENDrep4

description: hot3-2 Seedling, polysome RNA, rep4


title: d2d4 nonpolysome ENDrep2

description: dcl2 dcl4 Seedling, non-polysome RNA, rep2


title: d2d4 nonpolysome ENDrep3

description: dcl2 dcl4 Seedling, non-polysome RNA, rep3


title: 11A_M_1146


title: ChIP-input_dTAG-3h_INTS11-dTAG_DLD1

description: treated with dTAG13 for 3 hours


title: 11A_M_1145


title: ChIP-input_DMSO-3h_INTS8-dTAG_INTS8-N211del_DLD1

description: untreated


title: d2d4 polysome ENDrep4

description: dcl2 dcl4 Seedling, polysome RNA, rep4


title: d2d4 polysome ENDrep3

description: dcl2 dcl4 Seedling, polysome RNA, rep3


title: 11A_M_1144


title: d2d4 polysome ENDrep2

description: dcl2 dcl4 Seedling, polysome RNA, rep2


title: 11A_M_1143


title: h32 total ENDrep4

description: hot3-2 Seedling, total RNA, rep4


title: ChIP-input_DMSO-3h_INTS11-dTAG_DLD1

description: untreated


title: d2d4 polysome ENDrep1

description: dcl2 dcl4 Seedling, polysome RNA, rep1


title: d2d4 total ENDrep4

description: dcl2 dcl4 Seedling, total RNA, rep4


title: d2d4 total ENDrep3

description: dcl2 dcl4 Seedling, total RNA, rep3


title: 11A_M_1142


title: d2d4 total ENDrep1

description: dcl2 dcl4 Seedling, total RNA, rep1


title: d2d4 total ENDrep2

description: dcl2 dcl4 Seedling, total RNA, rep2


title: 11A_M_1141


title: WT nonpolysome ENDrep4

description: WT Seedling, non-polysome RNA, rep4


title: Patient 2, 4, 5, 6  Product Protein

city: Houston

first: Antonino

last: Montalbano

state: TX

address: 1102 Bates Ave

institute: Baylor School of Medicine

description:
Patient 2 labelled with hash1  Patient 4 labelled with hash8  Patient 5 labelled with hash9  Patient 6 labelled with hash10
processed_metadata.csv
rna_counts_cols.tsv.gz
rna_counts.mtx.gz
rna_counts_rows.tsv.gz
cite_counts_cols.tsv.gz
cite_counts.mtx.gz
cite_counts_rows.tsv.gz
hto_counts_cols.tsv.gz
hto_counts.mtx.gz
hto_counts_rows.tsv.gz

library_source: other

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, Feature and TCR barcode counts) was performed using the 10x genomics Cell Ranger pipeline with default settings (version 5.0.1) and aligning to a custom version based off of the human genome hg38 (cellranger_custom_hg38_ref_with_complete_car_all_ig_removed_2009.tar.gz).
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification,).
Supplementary files format and content: hg38
Supplementary files format and content: Processed data files contain count matrices and metadata (including patient number and response) of the integrated scRNA-seq data.

molecule: protein

source_name: NKTs

extract_protocol:
Frozen cells were thawed  in water bath at 37 C for 3 minutes. Cells were centrifuged at 500 x g for 5 minutes, and washed in RPMI + 10 % Fetal Bovine Serum. Finally, cell pellets were resuspended in PBS + BSA 0.04% and processed with the 10x Genomics single cell 5’ system according to manufacturer’s instructions.
scRNA-seq libraries were prepared with the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 as described by the manufacturer's instructions.
10x Genomics scRNA-seq 5' library construction kit

value: NKTs

tag: library type

value: HTO

tag: antibodies/tags

value: Patient 2 hashtag antibody:TotalSeqC-0251  Patient 4 hashtag antibody:TotalSeqC-0258  Patient 5 hashtag antibody:TotalSeqC-0259  Patient 6 hashtag antibody:TotalSeqC-0260


title: Patient 12 Product Protein

description:
Patient 12 labelled with hash1
processed_metadata.csv
rna_counts_cols.tsv.gz
rna_counts.mtx.gz
rna_counts_rows.tsv.gz
cite_counts_cols.tsv.gz
cite_counts.mtx.gz
cite_counts_rows.tsv.gz
hto_counts_cols.tsv.gz
hto_counts.mtx.gz
hto_counts_rows.tsv.gz

value: Patient 12 hashtag antibody:TotalSeqC-0251


title: Patient 7 Product Protein

description:
Patient 7 labelled with hash1  Patient 8 labelled with hash8  Patient 10 labelled with hash9  Patient 11 labelled with hash10
processed_metadata.csv
rna_counts_cols.tsv.gz
rna_counts.mtx.gz
rna_counts_rows.tsv.gz
cite_counts_cols.tsv.gz
cite_counts.mtx.gz
cite_counts_rows.tsv.gz
hto_counts_cols.tsv.gz
hto_counts.mtx.gz
hto_counts_rows.tsv.gz

value: Patient 7 hashtag antibody:TotalSeqC-0251  Patient 8 hashtag antibody:TotalSeqC-0258  Patient 10 hashtag antibody:TotalSeqC-0259  Patient 11 hashtag antibody:TotalSeqC-0260


title: WT nonpolysome ENDrep3

description: WT Seedling, non-polysome RNA, rep3


title: Patient 1, 2, 3 Product Protein

description:
Patient 1 labelled with hash1+hash2  Patient 2 labelled with hash3+hash5  Patient 3 labelled with hash6+hash7
processed_metadata.csv
rna_counts_cols.tsv.gz
rna_counts.mtx.gz
rna_counts_rows.tsv.gz
cite_counts_cols.tsv.gz
cite_counts.mtx.gz
cite_counts_rows.tsv.gz
hto_counts_cols.tsv.gz
hto_counts.mtx.gz
hto_counts_rows.tsv.gz

value: Patient 1 hashtag antibody:TotalSeqC-0251 + TotalSeqC-0252  Patient 2 hashtag antibody:TotalSeqC-0253 + TotalSeqC-0255  Patient 3 hashtag antibody:TotalSeqC-0256 + TotalSeqC-0257


title: WT nonpolysome ENDrep2

description: WT Seedling, non-polysome RNA, rep2


title: 11A_M_1140

value: male


title: WT nonpolysome ENDrep1

description: WT Seedling, non-polysome RNA, rep1


title: d2d4 nonpolysome ENDrep1

description: dcl2 dcl4 Seedling, non-polysome RNA, rep1


title: 11A_M_1139


title: 11A_M_114


title: WT polysome ENDrep4

description: WT Seedling, polysome RNA, rep4


title: Patient 12 Product TCR

molecule: other

value: TCR


title: Patient 7 Product TCR


title: 11A_M_1138


title: WT polysome ENDrep1

description: WT Seedling, polysome RNA, rep1

value: 18-day-old seedling


title: WT polysome ENDrep3

description: WT Seedling, polysome RNA, rep3

value: somatic cells


title: Patient 2, 4, 5, 6  Product TCR


title: WT total ENDrep3

description: WT Seedling, total RNA, rep3


title: 11A_M_1137


title: Patient 1, 2, 3 Product TCR


title: WT total ENDrep2

description: WT Seedling, total RNA, rep2


title: Patient 11 PB mRNA

description:
processed_metadata.csv
rna_counts_cols.tsv.gz
rna_counts.mtx.gz
rna_counts_rows.tsv.gz
cite_counts_cols.tsv.gz
cite_counts.mtx.gz
cite_counts_rows.tsv.gz
hto_counts_cols.tsv.gz
hto_counts.mtx.gz
hto_counts_rows.tsv.gz

library_source: transcriptomic single cell

molecule: polyA RNA

value: mRNA


title: 11A_M_1136


title: 11A_M_1135


title: Patient 10 PB mRNA


title: SC biol rep2

city: Zhengzhou

first: Lei

last: Zhang

state: Henan

address: No. 7, Weiwu Road

department: Reproductive Medicine Center

institute: Henan Provincial People’s Hospital

data_processing:
Firstly, Fastp (version 0.18.0) was used to remove the adaptor sequence and low-quality bases to obtain clean reads.
Bowtie2 (version 2.2.8) was used to remove ribosome RNA (rRNA) reads.
Then, mapped reads were obtained by comparing clean reads to the reference genome through Hisat2 (version 2.4).
The FPKM value of gene expression (fragment per kilobase of transcript per million mapped reads) was calculated by StringTie (version 1.3.1).
DEseq2 analyzed the gene expression differences between samples.  The screening criteria for differential genes were the following: the FPKM in at least one group was greater than 1; the differential fold change (FC) was greater than 2.5; and the false discovery rate (FDR) was less than 0.05.
Assembly: Ensembl_release100 (GRCm39)
Supplementary files format and content: gene_expression_anno.xls including FPKM values for each sample

source_name: Spleen

growth_protocol: For both the control group and the ART group, the feeding environment of mice was 12 h/12 h light/dark, the temperature was 25℃, and the humidity was 50%. Their offspring were raised to adulthood (8 weeks old) after birth. The feeding, management, and use of mice complied with the ‘3Rs’ of animal ethics.

extract_protocol:
The offspring mice were raised to adulthood (8W) after birth. After being killed by cervical dislocation, the liver and kidney tissues were retrieved and thoroughly washed with normal saline to remove the blood. Then, the tissue block was cut 0.5 cm×0.5 cm in size with sterile RNase-free surgical scissors, ground into a powder after adding liquid nitrogen, and collected in a sterile RNase-free EP tube. After TRIzol was added and fully lysed, the total RNA in the tissues was obtained for sequencing according to the conventional RNA extraction steps.
The library was built according to standard Illumina protocols, which mainly include the steps of rRNA removal, mRNA isolation and fragmentation, cDNA double-strand synthesis and purification, cDNA terminal repair, 3’ end plus A, adaptor ligation, screening cDNA fragments of around 200 bp, PCR library enrichment and purification, etc.

treatment_protocol: The control group was natural pregnancy. The ART group included the following operations: ovulation induction, vitrification and thawing, in vitro fertilization, embryo in vitro culture and transfer. The zygotes were cultured in KSOM medium for 24 hours, and the cleaved embryos were used for embryo transfer. The cleaved embryos were transferred into the fallopian tubes of pseudopregnant female mice by operation. Twenty embryos were transplanted into each female mouse and raised normally until the offspring mice were born.

value: CD-1 (ICR)

value: Spleen

tag: developmental stage

value: adult offspring

value: derived from natural pregnancy


title: ST biol rep2

value: derived from ART pregnancy


title: ST biol rep1


title: SC biol rep3


title: SC biol rep1


title: 11A_M_1134


title: HT biol rep3

source_name: Heart

value: Heart


title: 11A_M_1133


title: HT biol rep2


title: Patient 8 PB mRNA

tag: cell type

value: NKTs


title: WT polysome ENDrep2

description: WT Seedling, polysome RNA, rep2


title: HT biol rep1


title: HC biol rep3


title: Patient 7 PB mRNA


title: Patient 5 PB mRNA


title: WT total ENDrep4

description: WT Seedling, total RNA, rep4


title: HC biol rep1


title: 11A_M_1131


title: Patient 4 PB mRNA


title: ChIP_input_WT_1

city: birmingham

first: ildem

last: akerman

address: BR Tower, 3rd Floor, Room 333, Edgbaston,

department: IMSR

country: United Kingdom

institute: University of Birmingham

data_processing:
FastQ files were trimmed using bbduk and  aligned to mm10 using Bowtie (or STAR for RNA-seq)
Bam files were converted to bigwig, usinfg CPM normalisation in deeptools.
Assembly: mm10
Supplementary files format and content: Merged bigwig files for visualisation

source_name: Input Control DNA for ChIP-seq samples

extract_protocol:
Approximately 5 million mESCs from three independent cell cultures each of Ezh2WT and  Ezh2∆/∆ were collected for total RNA extraction using the RNeasy Kit (Qiagen).
Libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Preparation Kit

treatment_protocol: KO cells were treated with tamoxifen for 48 hours, then harvested at 96 hours from the start of treatment

value: mESC

value: stem cell

value: EZH2 WT


title: WT total ENDrep1

description: WT Seedling, total RNA, rep1


title: 11A_M_1130


title: ChIP_input_KO_1

value: EZH2 KO

value: tamoxifen


title: Patient 2 PB mRNA


title: 11A_M_1129

value: male


title: ChIP_input_KO_2


title: Patient 12 Repeat challenging mRNA


title: Patient 11 Repeat challenging mRNA


title: 11A_M_1128


title: BY4741 expressing NdeltaCit1-DS/AA-H/G, 8I-6

city: Nagoya

first: Kunio

last: Nakatsukasa

state: Aichi

address: Yamanohata 1, Mizuho-cho, Mizuho-ku

country: Japan

institute: Nagoya City University

data_processing:
Base calls were generated in real-time on the NovaSeq6000 instrument (RTA 3.4.4). Bcl2fastq2 v2 19 Conversion Software (Illumina) was used to generate demultiplexed Fastq files. Sequencing was performed on a NovaSeq-6000 (Illumina) with 300 total cycles of paired-end sequencing (150 cycles per read) according to the manufacturer's protocol.
Sequence reads were trimmed to remove possible adaptor sequences and nucleotides with poor quality using Cutadapt v.1.18.(parameters : -q 20  --pair-filter=any  --minimum-length 75  --max-n 0)
The trimmed reads were quantified in mapping-based mode using Salmon v.1.2.1, based on the Saccharomyces cerevisiae S288c reference transcripts available via ENSEMBL.(parameter : -l ISR)
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis.
A comparison of gene expression between 8A and 8I cells was performed using R v3.5.1. The version of the major R pacakge used Tag Count Comparison (TCC) v1.22.0.
Assembly: R64-1-1
Supplementary files format and content: tab-delimited text file includes TCC normalized count values for all samples. (AllEntity.txt)

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Both strains were grown in synthetic complete medium containing galactose as a sole carbon source.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen #74104).
RNA sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Ipswich), following the manufacturer’s instructions.

value: yeast cells

value: expressing NdeltaCit1-DS/AA-H/G


title: H3K27ac_WT2

source_name: ChIP-seq against H3K27ac samples from WT and EZH2 KO mESCs


title: H3K27ac_KO2


title: 11A_M_1132


title: BY4741 expressing NdeltaCit1-DS/AA-H/G, 8I-5


title: BY4741 expressing NdeltaCit1-DS/AA-H/G, 8I-4


title: H3K27ac_WT1


title: Patient 10 Repeat challenging mRNA


title: 11A_M_1126


title: 11A_M_1127


title: 11A_M_1125


title: Patient 8 Repeat challenging mRNA


title: HC biol rep2


title: H3K27ac_KO1


title: H3K27me3_KO1

source_name: ChIP-seq against H3K27me3 samples from WT and EZH2 KO mESCs


title: BY4741 expressing NdeltaCit1-DS/AA, 8A-2

value: expressing NdeltaCit1-DS/AA


title: 11A_M_1124


title: BY4741 expressing NdeltaCit1-DS/AA, 8A-1


title: Patient 7 Repeat challenging mRNA

value: mRNA


title: ChIP_input_WT_2


title: H3K27me3_WT2


title: 11A_M_1123


title: Patient 6 Repeat challenging mRNA


title: 11A_M_1122


title: H3K27me3_KO2


title: Patient 5 Repeat challenging mRNA


title: HeLa WGS long reads

city: Guangzhou

first: yuyan

last: wang

address: Zhongshan 2nd Road, Yuexiu

institute: The First Affiliated Hospital, Sun Yat-sen University

description: Nanopore PromethION 48

data_processing:
RNA-seq: The raw RNA-seq reads were aligned with HISAT2 then assembled and merged with StringTie (1.3.3b). All the transcripts and abundance data were analyzed with Ballgown.
ChIP-seq: Raw sequencing data of ChIP-seq was evaluated with FastQC. Bowtie2 was used to map the ChIP-seq reads on the human GRCh38 genome. Reads with multiple hits were discarded to exclude false detection of non-specific repetitive sequences. Peak calling was carried out with MACS2 with a false discovery rate q-value of <0.01.
Hi-C: The clean reads from FastQC of each cell line were aligned to GRCh38 plus correspond HPV genome through HiC-Pro. All valid pairs were converted to .hic file by Juicebox.
WGS: We performed quality control on raw reads by FastQC in each cell line. The clean reads were aligned to GRCh38 plus correspond HPV genome by bwa and marked duplicates by picard.
RCA: The long-reads were corrected by short-reads by Filtlong and mapped to GRCh38 plus correspond HPV genome by minimap2.
Virus Capture: The virus integration were identified by VIPA pipeline using raw data.
WGBS: The clean data generated from FastQC were subject to bismark, and the methylation were extracted with --CX option
Assembly: hg38
Supplementary files format and content: RNA-seq_Processed: Reads counts, FPKM, and TPM table
Supplementary files format and content: ChIP-seq_Processed: H3K4me3 and H3K27Ac peak and bigwig file
Supplementary files format and content: Hi-C_Processed: The interaction matrices .hic file
Supplementary files format and content: WGBS_Processed: Genome-wide cytosine methylation reports
Library strategy: WGS

source_name: HeLa

extract_protocol:
Genome DNA were extracted using DNeasy Blood & Tissue Kit (69,506, Qiagen, Germany). The PCR reaction was conducted using Q5 Hot Start High-Fidelity 2X Master Mix (M0494S, NEW ENGLAND BioLabs, USA).
For short reads sequencing, PE100 bp read length sequencing was performed on the BGISEQ-500 sequencer after size selection by gel electrophoresis and 10 to 12 cycles of PCR. For long reads sequencing, size-select long DNA fragments used the BluePippin system and then libraries were constructed and sequenced following Nanopore standard protocol.

value: HeLa


title: 11A_M_1121


title: Patient 3 Repeat challenging mRNA


title: RNA_EZH2KO3

source_name: RNA-seq samples from WT and EZH2 KO mESCs


title: Patient 4 Repeat challenging mRNA


title: Patient 9 Repeat challenging mRNA


title: H3K27me3_WT1


title: RNA_EZH2KO2


title: S12 RCA long reads

description: Nanopore PromethION 48

data_processing:
RNA-seq: The raw RNA-seq reads were aligned with HISAT2 then assembled and merged with StringTie (1.3.3b). All the transcripts and abundance data were analyzed with Ballgown.
ChIP-seq: Raw sequencing data of ChIP-seq was evaluated with FastQC. Bowtie2 was used to map the ChIP-seq reads on the human GRCh38 genome. Reads with multiple hits were discarded to exclude false detection of non-specific repetitive sequences. Peak calling was carried out with MACS2 with a false discovery rate q-value of <0.01.
Hi-C: The clean reads from FastQC of each cell line were aligned to GRCh38 plus correspond HPV genome through HiC-Pro. All valid pairs were converted to .hic file by Juicebox.
WGS: We performed quality control on raw reads by FastQC in each cell line. The clean reads were aligned to GRCh38 plus correspond HPV genome by bwa and marked duplicates by picard.
RCA: The long-reads were corrected by short-reads by Filtlong and mapped to GRCh38 plus correspond HPV genome by minimap2.
Virus Capture: The virus integration were identified by VIPA pipeline using raw data.
WGBS: The clean data generated from FastQC were subject to bismark, and the methylation were extracted with --CX option
Assembly: hg38
Supplementary files format and content: RNA-seq_Processed: Reads counts, FPKM, and TPM table
Supplementary files format and content: ChIP-seq_Processed: H3K4me3 and H3K27Ac peak and bigwig file
Supplementary files format and content: Hi-C_Processed: The interaction matrices .hic file
Supplementary files format and content: WGBS_Processed: Genome-wide cytosine methylation reports
Library strategy: RCA

extract_protocol:
DNA isolation by column separation（Plasmid Mini AX; A&A Biotechnology）, removal of remaining linear DNA by exonuclease（Plasmid-Safe ATP-dependent DNase; Lucigen, PacI enzyme; NEB）, and rolling-circle amplification by random hexamer.
For short-reads, DNA were fragmented by sonication. For long-reads, DNA fragments were selected by the BluePippin system. Short-reads and long-reads libraries were constructed and sequenced following MGI’s and Nanopore standard protocol, respectively.

value: Rolling circle amplification


title: 11A_M_1119


title: 11A_M_1120


title: BY4741 expressing NdeltaCit1-DS/AA, 8A-3


title: HeLa RCA long reads

description: Nanopore PromethION 48


title: Patient 2 Repeat challenging mRNA


title: Ribo-ITP-K562-1cell-5

city: Austin

first: Can

last: Cenik

address: Moffett Molecular Biology Building 2.122 2500 Speedway

department: Molecular Biosciences

institute: The University of Texas at Austin

description: RNA from Ribosome Protected Footprint

data_processing:
Ribosome profiling data were processed using RiboFlow. We extracted the first 12 nucleotides from the 5’ end of the reads using UMI-tools version 1.1.1 with the following parameters: “umi_tools extract -p "^(?P<umi_1>.{12})(?P<discard_1>.{4}).+$" --extract-method=regex ”. The four nucleotides downstream of the UMIs are discarded as they are incorporated during the reverse transcription step.
We clipped the 3’ adapter AAAAAAAAAACAAAAAAAAAA from the Ribo-ITP data using cutadapt version 1.18 with the parameters “-a AAAAAAAAAACAAAAAAAAAA --overlap=4 --trimmed-only”. For conventional ribosome profiling data, we removed the poly-A tails and the first three nucleotides of the reads using “cutadapt -u 3 -a AAAAAAAAAA --overlap=4 --trimmed-only”
After UMI extraction and adapter trimming, reads were aligned to ribosomal and transfer RNAs using Bowtie2 version 2.3.4.3. The unaligned reads were mapped to a manually-curated transcriptome. We retained alignments with mapping quality greater than 2 followed by deduplication using UMI-tools. As the last step, .ribo files are created using RiboPy66 version 0.0.1
Assembly: A curated transcriptome of primary transcripts was used for alignment. Reference files for use with RiboFlow are located at https://github.com/ribosomeprofiling/references_for_riboflow
Supplementary files format and content: .ribo HDF5-formatted files contain ribosome occupancy at nucleotide resolution for lengths from 21 to 40. See https://ribopy.readthedocs.io/en/latest/ribo_file_format.html for a detailed description of the ribo format.
Library strategy: Ribo-ITP

growth_protocol: Human K562 cells were grown in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (Gibco) and 1% Pen-Strep (Gibco) and incubated at 37 °C with 5% CO2 to a density of ~250,000 cells per mL. Cells were regularly tested for Mycoplasma contamination. The identity of the K562 cell line was authenticated using STR profiling from ATCC

extract_protocol:
Cell processing: Cells were pelleted at 300 x g for 5 minutes. The cells were washed with 1x PBS and resuspended to achieve approximetly one million cells in 1 mL of PBS containing 0.1% BSA (Sigma) with 1 µg/ml of DAPI . The cells were passed through a strained cap to attain a single cell suspension and sorted with the Sony MA9000 Cell Sorter or BD FACSAria Fusion Flow Cytometer into Eppendorf LoBind 96-well plates containing 5 µL of cold lysis buffer with cycloheximide. Singlet cells were defined by gating on FSC-A/SSC-A, SSA-H/SSC-W, FSC-A/FSC-H, and FSC-A/Histogram. Live cells were selected using DAPI-negative gating. The plates were sealed and flash frozen in liquid nitrogen immediately after the sort was completed. The lysate was incubated at 37 °C with 1 µL of a 1:150 dilution of MNase stock (2,000 gel units/µL, NEB) for 30 minutes or 1 µL of a 1:300 dilution of RNase I (100 U/µL, Ambion) for 15 minutes. The MNase digestion was stopped by adding EGTA to a final concentration of 10 mM. SDS was added to a final concentration of 0.1% to samples digested with RNase I. The lysates were held on ice until processing through Ribo-ITP. Polydimethylsiloxane (PDMS) chip fabrication: Molds were 3D-printed by Proto Labs with WaterShed XC 11122 at high resolution (Fig. S1). Reusable molds were assembled by taping 3D-printed molds to glass slides (5” by 4”; Ted Pella). Sylgard 184 PDMS monomer and curing agent (Ellsworth Adhesives 4019862) were mixed at a 10:1 (w/w) ratio. The mixture was degassed using a desiccator connected to a vacuum pump, poured over the mold, and degassed again until there were no air bubbles. The mold was incubated for at least 16 h at 50°C. Individual PDMS chips were cut along the lines that form the outer rectangle on the design in Extended Data Fig. 1a. The 5 mm-diameter elution well, TE-, and LE-reservoirs were made with a biopsy punch (Extended Data Fig. 1b). Prior to the plasma treatment, glass slides (4’’ by 3’’; Ted Pella) and the feature-side of the PDMS slabs were thoroughly cleaned with tape to remove any dust particles. PDMS chips and glass slides were plasma cleaned with a 115V Expanded Plasma Cleaner (Harrick Plasma) connected to a Dry Scroll Pump (Agilent) for 2 minutes at high RF level. The plasma-treated surfaces of the glass and PDMS slabs were immediately brought together to form a covalent bond. Bonded chips were heated at 80°C on a heat block for at least two hours to enhance bonding. PDMS chip preparation for Ribo-ITP experiments: To ensure clean, RNAse-free chips, we pre-treated the channels and reservoirs of the Ribo-ITP chip by sequential treatment with the following solutions: RNaseZap (100% concentrate), nuclease-free water, 1 M NaOH, nuclease-free water, 1 M HCl, nuclease-free water, 10% (w/v) benzophenone in acetone (for 10 minutes, replenishing channels as needed to avoid bubble accumulation), methanol, and 0.1% Triton X-100. The channel was completely dried after final treatment by fully vacuuming out any remaining liquid in the channel. After securing the chips to a ProteinSimple 302/365nm UV Transilluminator with tape, we added 10% polyacrylamide (PA) prepolymer mix (Supplementary Table 6) to the size-selection channel through the elution well. Similarly, 5% PA prepolymer mix was loaded into the extraction channel through branch channel 2. To catalyze the polymerization of polyacrylamide on chip, we used a photoactivatable azo-initiator, 2,2'-Azobis[2-methyl-N-(2-hydroxyethyl)propionamide] (Wako Chemicals VA-086), at 0.5% final concentration in the prepolymer mixes. UV-driven polymerization (365 nm wavelength) was performed for one minute followed by a 30 second break. This on/off UV cycle was repeated two more times for a total UV exposure time of 3 minutes. UV intensity was measured as ~8.9 mW/cm2 using a G&R Labs Model 200 UV Light meter with a 365 nm probe. To avoid dehydration of the polyacrylamide gels after polymerization, we filled any open channels and reservoirs with storage buffer (Supplementary Table 6) until use. The chips were protected from light and used within six hours of preparation. Isotachophoresis setup: The prepared ITP chip was placed on a Dark Reader blue light transilluminator (Clare Chemical) and secured with tape. Storage buffer was removed from the channels and reservoirs using a vacuum. Leading electrolyte pluronic solution (LEp) and MOPS trailing electrolyte pluronic solution (TEp) (Supplementary Table 6) were kept on ice throughout the loading procedure. 200 µL pipet tips were kept at -20°C until the time of the experiment to facilitate manipulation of the pluronic-containing LEp and TEp solutions, which solidify within a minute above 4°C. 80 µL of LEp was loaded in LE reservoir 3, filling the reservoir to the top as well as the small section of the channel between the elution well and LE reservoir 3 (Extended Data Fig. 1b). LE reservoir 2 was filled with 30 µL LEp, ensuring contact with the polyacrylamide gel present in branch channel 2. The elution well was filled with 20 µL of RB. Fluorescent marker oligonucleotides containing a 5’ ATTO fluorophore and 3’ ddC blocking modification (Supplementary Table 7) were added to the sample followed by dilution with sample dilution buffer (SDB). The mixture was loaded into the lysate channel through LE reservoir 1. Finally, LE reservoir 1 was filled with 30 µL LEp and 70 µl TEp was added to the TE reservoir. The negative electrode was placed in the TE reservoir and the positive electrode in the LE reservoir. Positive and negative electrodes were placed in LE reservoir 3 and the TE reservoir, respectively. A constant current of 300 mA with a maximum voltage of 1.1 kV (Keithley 2410 Sourcemeter) was applied to the channel. Once the trailing end of the fluorescent markers entered the 5% PA gel, the branch channel electrode–with a lower current output due to a 510 kΩ (Xikon) resistor on a custom circuit board–was manually applied in LE reservoir 1 for ~10 seconds. When the leading edge of the shorter fluorescent marker reached the end of the size-selection channel, the current was suspended. The elution reservoir was thoroughly washed twice with 30 µL nuclease-free water and refilled with 10 µL dephosphorylation buffer (Supplementary Table 6). Current was applied again until the longer fluorescent marker began to enter the elution well. Finally, the purified sample with a 10 µL volume was collected from the elution well into a low-bind PCR tube and immediately stored at -80 °C.
D-Plex Small RNA-seq Kit (Diagenode C05030001) with minor modifications was used as detailed below. The dephosphorylation reaction was supplemented with 0.5 µL T4 PNK (NEB) and the reaction was incubated for 25 minutes. For reverse transcription, the template switching oligo (TSO) was diluted 1:2 in nuclease-free water. Samples were processed using the unique dual index (UDI) module. Half of the cDNA was amplified for 17 PCR cycles and a 1:4 dilution of the resulting library was assessed by Agilent Bioanalyzer High Sensitivity DNA kit. The concentrations of the target peaks were used to pool samples with approximately equimolar representation. AMPure XP bead cleanup (1.8x) was performed followed by size-selection using 3% agarose, dye-free gel cassettes with internal standards (Sage Science BDQ3010) on the BluePippin platform. Tight parameter settings of 173-207 bp range were used for samples prepared with the SDI module. Tight parameter settings of 183-217 bp range were used for MNase digested libraries. For the RNase I digested single cell libraries final size selection was performed by PAGE purification of 200 bp products.

value: Chronic myelogenous leukemia

value: 13.33 gel-units Mnase


title: Patient 1 Repeat challenging mRNA


title: RNA_EZH2KO1


title: RNA_EZH2WT3


title: 11A_M_1117


title: Patient 12 Product mRNA

value: Patient 12 hashtag antibody:TotalSeqC-0251


title: 11A_M_1115


title: Ribo-ITP-K562-1cell-4

description: RNA from Ribosome Protected Footprint


title: RNA_EZH2WT2


title: P2016063_pa RNA

data_processing:
RNA-seq: The raw RNA-seq reads were aligned with HISAT2 then assembled and merged with StringTie (1.3.3b). All the transcripts and abundance data were analyzed with Ballgown.
ChIP-seq: Raw sequencing data of ChIP-seq was evaluated with FastQC. Bowtie2 was used to map the ChIP-seq reads on the human GRCh38 genome. Reads with multiple hits were discarded to exclude false detection of non-specific repetitive sequences. Peak calling was carried out with MACS2 with a false discovery rate q-value of <0.01.
Hi-C: The clean reads from FastQC of each cell line were aligned to GRCh38 plus correspond HPV genome through HiC-Pro. All valid pairs were converted to .hic file by Juicebox.
WGS: We performed quality control on raw reads by FastQC in each cell line. The clean reads were aligned to GRCh38 plus correspond HPV genome by bwa and marked duplicates by picard.
RCA: The long-reads were corrected by short-reads by Filtlong and mapped to GRCh38 plus correspond HPV genome by minimap2.
Virus Capture: The virus integration were identified by VIPA pipeline using raw data.
WGBS: The clean data generated from FastQC were subject to bismark, and the methylation were extracted with --CX option
Assembly: hg38
Supplementary files format and content: RNA-seq_Processed: Reads counts, FPKM, and TPM table
Supplementary files format and content: ChIP-seq_Processed: H3K4me3 and H3K27Ac peak and bigwig file
Supplementary files format and content: Hi-C_Processed: The interaction matrices .hic file
Supplementary files format and content: WGBS_Processed: Genome-wide cytosine methylation reports

source_name: Cervical tissue

extract_protocol:
Total RNA was extracted from cells according to manufacturer’s instructions, and subjected to library preparation.
Libraries were sequenced following Illumina’s standard protocol.

value: Cervical tissue

value: Epithelial cell

value: poly-A enrichment


title: Patient 7, 8, 10, 11 Product mRNA

value: NKTs

value: Patient 7 hashtag antibody:TotalSeqC-0251  Patient 8 hashtag antibody:TotalSeqC-0258  Patient 10 hashtag antibody:TotalSeqC-0259  Patient 11 hashtag antibody:TotalSeqC-0260


title: Patient 2, 4, 5, 6  Product mRNA

value: Patient 2 hashtag antibody:TotalSeqC-0251  Patient 4 hashtag antibody:TotalSeqC-0258  Patient 5 hashtag antibody:TotalSeqC-0259  Patient 6 hashtag antibody:TotalSeqC-0260


title: RNA_EZH2WT1

value: mESC

value: stem cell

value: EZH2 WT


title: 11A_M_1114

value: male


title: P2016051_pa RNA


title: 11A_M_1113


title: SNS_EZH2WT3

data_processing:
FastQ files were trimmed using bbduk and  aligned to mm10 using Bowtie (or STAR for RNA-seq)
Bam files were converted to bigwig, usinfg CPM normalisation in deeptools.
Assembly: mm10
Supplementary files format and content: Merged bigwig files for visualisation
Library strategy: SNS-seq

source_name: SNS-seq samples from WT and EZH2 KO mESCs


title: Patient 1, 2, 3 Product mRNA

value: Patient 1 hashtag antibody:TotalSeqC-0251 + TotalSeqC-0252  Patient 2 hashtag antibody:TotalSeqC-0253 + TotalSeqC-0255  Patient 3 hashtag antibody:TotalSeqC-0256 + TotalSeqC-0257


title: 11A_M_1112


title: P2016041_pa RNA


title: SNS_EZH2WT1


title: 11A_M_1111


title: P2016036_pa RNA


title: sgCtrl_3_to_sgUFM1

city: Dongguan

first: Zhou

last: Junzhi

state: Guangdong

address: Xincheng Road 1#, Songshan Lake

institute: Guangdong Medicine University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed by fastp v0.20.1 for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR v2.7.7a with default parameters.Annotation file of Ensembl release 76 (GRCh38) transcriptome gff file was provided to STAR as gene model.
raw reads count aligned to each gene were calculated by FeatureCount v2.0.0
Supplementary files format and content: Matrix table with raw gene counts for each gene by every sample
Supplementary files format and content: FPKM values for each gene by everySample

source_name: breast cancer cell line

extract_protocol:
RNA was isolated from 1-2x10^6 cells stored in TRIzol reagent following manufacturer's instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: sgUFL1, sgUFM1, and sgCtrl

value: sgCtrl

value: breast cancer cell line


title: sgCtrl_3_to_sgUFL1


title: SNS_EZH2KO3

value: EZH2 KO

value: tamoxifen


title: sgCtrl_2_to_sgUFM1


title: SNS_EZH2WT2


title: P2016048_pa RNA


title: P2016035_pa RNA


title: 11A_M_111

source_name: C57BL/6J Male P56 Mouse Brain


title: 11A_M_1110


title: SNS_EZH2KO2


title: 11A_M_1118


title: sgCtrl_2_to_sgUFL1


title: P2016032_pa RNA


title: 11A_M_1109


title: SNS_EZH2KO1


title: sgCtrl_1_to_sgUFM1


title: 11A_M_1108


title: SNS_EZH2_WT_RNASE_CONTROL


title: P2016030_pa RNA


title: sgCtrl_1_to_sgUFL1


title: P2016028_pa RNA


title: 11A_M_1107


title: sgUFM1_3


title: sgUFM1_2


title: 11A_M_1106


title: HEK293T RNA


title: SRBI+/+

city: Cincinnati

middle: Frank

last: Huang

state: Ohio

address: 2600 Clifton Ave

institute: Uiversity of Cincinnati

data_processing:
.fastq files of each sample were aligned to mm10 reference genome
expression matrices and cell barcodes were extracted from alignments by cellranger 4.0.0
Genome_build: mm10

source_name: splenocytes

extract_protocol:
10x Genomics Demonstrated Protocols available on the 10x Genomics Support site support.10xgenomics.com.
Libraries were prepared according to 10x Genomics Single Cell libraries (10x Chromium Single Cell Gene Expression) :https://www.10xgenomics.com/products/single-cell-gene-expression;

treatment_protocol: 20h anti-CD3 treatment

value: Wild Type

value: 20h post anti-CD3 treatment


title: 11A_M_1105


title: 11A_M_1104


title: sgUFM1_1


title: SRBI-/-

value: SRBI-/-


title: HEK293T ChIP-seq Input

extract_protocol:
Cells were cross-linked with formaldehyde and collected with trypsin and the chromatin was extracted.
Extracted chromatin was sonicated to an average size of 200‐ 500 bp. Chromatin immunoprecipitation was performed following the Diagenode iDeal histone ChIP‐seq protocol. Finally, pair-end data was generated on an Illumina HiSeq 2500 platform.

value: Not immuno-precipitated


title: sgUFL1_3


title: U2OS, p53(AD/AD), Etoposide, rep2

city: New York

first: Joshua

last: Choe

state: NY

address: 816 Fairchild Center, MC 2422

department: Department of Biological Sciences

institute: Columbia University

description:
HOM.ETOPO.2
U2OS_RNAseq_countData.xlsx
res_hom_vs_par_etopo.csv
hom_vs_ko_etopo.csv
nomalized_expression_matrix_2.csv

data_processing:
fastq files were trimmed by "Cutadapt" and mapped to human reference genome hg38 by "HISAT2". The mapped reads were then counted by "featureCounts"
In order to perform integrated analysis of expression data from two separate library preps (RNA-seq #1 and RNA-seq #2) of U2OS cells, ComBat-Seq was utilized to correct for batch effect
Assembly: hg38
Supplementary files format and content: microsoft excel workbook containing raw counts of genes
Supplementary files format and content: Comma-separated value file of differentially expressed genes (DESeq2)
Supplementary files format and content: Comma-separate value file of RPKM values for each sample (U2OS)

growth_protocol:
Osteoblasts were cultured in osteogenic differentiation medium (α-MEM supplemented with 10% FBS, 10 mM β-glycerol phosphate, 200 μM ascorbic acid, and 0.1 μM dexamethasone). U2OS were cultured in Dulbecco’s Modified Eagle Medium (DMEM) containing 10% fetal bovine serum (FBS) at 37°C in a humidified 5% CO2 environment.  673 bovine serum (FBS) at 37°C in a humidified 5% CO2 environment
U2OS osteosarcoma cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Bulk RNA was extracted from cells using Trizol (Invitrogen)
library construction was performed using NEBNext Ultra II RNA Library Prep Kit following manufacturer’s instructions

treatment_protocol: U2OS cells varying in p53 status were treated with either DMSO or 20 µM etoposide (Sigma) for 24 hr

value: Osteosarcoma

value: Etoposide, 20 uM

value: 24 hr


title: 11A_M_1103

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: U2OS, p53(AD/AD), DMSO, rep2

description:
HOM.DMSO.2
U2OS_RNAseq_countData.xlsx
res_hom_vs_par_dmso.csv
hom_vs_ko_dmso.csv
nomalized_expression_matrix_2.csv

value: DMSO


title: HEK293T ChIP-seq H3K27ac

value: H3K27ac antibody


title: U2OS, p53(AD/AD), Etoposide, rep1

description:
HOM.ETOPO.1
U2OS_RNAseq_countData.xlsx
res_hom_vs_par_etopo.csv
hom_vs_ko_etopo.csv
nomalized_expression_matrix_2.csv


title: sgUFL1_2


title: 11A_M_1102


title: C666-1 ChIP-seq Input


title: sgUFL1_1


title: 11A_M_1101


title: Raji Virus Capture

data_processing:
RNA-seq: The raw RNA-seq reads were aligned with HISAT2 then assembled and merged with StringTie (1.3.3b). All the transcripts and abundance data were analyzed with Ballgown.
ChIP-seq: Raw sequencing data of ChIP-seq was evaluated with FastQC. Bowtie2 was used to map the ChIP-seq reads on the human GRCh38 genome. Reads with multiple hits were discarded to exclude false detection of non-specific repetitive sequences. Peak calling was carried out with MACS2 with a false discovery rate q-value of <0.01.
Hi-C: The clean reads from FastQC of each cell line were aligned to GRCh38 plus correspond HPV genome through HiC-Pro. All valid pairs were converted to .hic file by Juicebox.
WGS: We performed quality control on raw reads by FastQC in each cell line. The clean reads were aligned to GRCh38 plus correspond HPV genome by bwa and marked duplicates by picard.
RCA: The long-reads were corrected by short-reads by Filtlong and mapped to GRCh38 plus correspond HPV genome by minimap2.
Virus Capture: The virus integration were identified by VIPA pipeline using raw data.
WGBS: The clean data generated from FastQC were subject to bismark, and the methylation were extracted with --CX option
Assembly: hg38
Supplementary files format and content: RNA-seq_Processed: Reads counts, FPKM, and TPM table
Supplementary files format and content: ChIP-seq_Processed: H3K4me3 and H3K27Ac peak and bigwig file
Supplementary files format and content: Hi-C_Processed: The interaction matrices .hic file
Supplementary files format and content: WGBS_Processed: Genome-wide cytosine methylation reports
Library strategy: Virus Capture

source_name: Raji

extract_protocol:
The NC_007605.1 genome was used to design the PCR probes to capture EBV.
Libraries construction was following Illumina’s standard protocol. The sequencing was performed on the Illumina NovaSeq 6000.

value: Raji

value: EBV probes capture


title: 11A_M_1100

value: male


title: SNS_EZH2_KO_RNASE_CONTROL

value: mESC

value: stem cell


title: U2OS, p53(AD/AD), DMSO, rep1

description:
HOM.DMSO.1
U2OS_RNAseq_countData.xlsx
res_hom_vs_par_dmso.csv
hom_vs_ko_dmso.csv
nomalized_expression_matrix_2.csv


title: U2OS, p53(+/+), Etoposide, rep2

description:
PAR.ETOPO.2
U2OS_RNAseq_countData.xlsx
res_ko_vs_etopo.csv
nomalized_expression_matrix_2.csv

value: p53 WT/WT


title: Raji Hi-C

extract_protocol:
Cells are fixed with formaldehyde and digested by the HindIII or MboI restriction enzyme. The overhangs are filled in with biotin and ligated. Finally, the ligation product with biotin maker were pulled-down with streptavidin beads and sheared.
Libraries construction was following Illumina’s standard protocol. The sequencing was performed on the Illumina HiSeq X10 platform.

value: MboI digestion


title: C666-1 ChIP-seq H3K4me3

tag: antibody

value: H3K4me3 antibody


title: C666-1 ChIP-seq H3K27ac


title: U2OS, p53(+/+), Etoposide, rep1

description:
PAR.ETOPO.1
U2OS_RNAseq_countData.xlsx
res_ko_vs_etopo.csv
nomalized_expression_matrix_2.csv


title: C666-1 RNA

value: poly-A enrichment


title: 11A_M_110


title: HEK293T Hi-C


title: 11A_M_11


title: P2016026_pa RNA

value: Cervical tissue

value: Epithelial cell


title: 11A_M_1099


title: C666-1 Hi-C


title: U2OS, p53(+/+), DMSO, rep1

description:
PAR.DMSO.1
U2OS_RNAseq_countData.xlsx
res_ko_vs_par_dmso.csv
nomalized_expression_matrix_2.csv


title: Raji ChIP Input

description: Raji ChIP Input clean read

data_processing:
The raw RNA-seq reads were aligned with HISAT2 then assembled  and merged with StringTie (1.3.3b). All the transcripts and abundance data were analyzed with Ballgown.
Raw sequencing data of ChIP-seq was evaluated with FastQC. Bowtie2 was used to map the ChIP-seq reads on the human GRCh38 genome. Reads with multiple hits were discarded to exclude false detection of non-specific repetitive sequences. Peak calling was carried out with MACS2 with a false discovery rate q-value of <0.01.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with gene TPM for every gene and every sample
Supplementary_files_format_and_content: H3K4me3 and H3K27Ac peak.txt files for every sample with none antibody ChIP-Seq as control

source_name: Raji cell

growth_protocol: Ca Ski were maintained in RPMI-1640 supplemented with 10% fetal bovine serum. SiHa, HeLa and C33A were cultured in DMEM supplemented with 10% fetal bovine serum (10270-106, Gibco, USA). S12 were maintained in DF12 medium according to a previous study5. Raji were maintained in suspension culture in RPMI-1640 supplemented with 10% fetal bovine serum (10270-106, Gibco, USA). All cells were cultured in a humidified 37 °C incubator set at 5% CO2 and passaged 2–3 times weekly as recommended by ATCC.

extract_protocol:
Genome DNA were extracted using kit (69,506, Qiagen, Germany). The PCR reaction was conducted using Q5 Hot Start High-Fidelity 2X Master Mix (M0494S, NEW ENGLAND BioLabs, USA).
Cells were cross-linked with formaldehyde and collected with trypsin and the chromatin was extracted. Extracted chromatin was sonicated to an average size of 200‐ 500 bp. Chromatin immunoprecipitation was performed following the Diagenode iDeal histone ChIP‐seq protocol. Finally, pair-end data was generated on an Illumina HiSeq 2500 platform.


title: Raji ChIP H3K27Ac

description: Raji ChIP H3K27Ac clean read


title: U2OS, p53(+/+), DMSO, rep2

description:
PAR.DMSO.2
U2OS_RNAseq_countData.xlsx
res_ko_vs_par_dmso.csv
nomalized_expression_matrix_2.csv


title: 11A_M_1098


title: Raji ChIP H3K4me3

description: Raji ChIP H3K4me3 clean read


title: U2OS, p53 KO, Etoposide, rep1

description:
KO.ETOPO.1
U2OS_RNAseq_countData.xlsx
res_ko_vs_etopo.csv
nomalized_expression_matrix_2.csv

value: p53 KO


title: U2OS, p53 KO, Etoposide, rep2

description:
KO.ETOPO.2
U2OS_RNAseq_countData.xlsx
res_ko_vs_etopo.csv
nomalized_expression_matrix_2.csv

value: Osteosarcoma


title: 11A_M_1097


title: MCF7:CLDN4-/-_rep2

city: Fukushima

first: Hideki

last: Chiba

address: 1 Hikarigaoka

institute: Fukushima Medical University

description: CLDN4 knockout

data_processing:
RNA sequencing and mapping were performed by RIKEN. For mapping, the index trimmed singleend 100 bp reads were aligned to the human reference genome (GRCh38 v90) to generate bam files.
The mapped bam files were imported to SeqMonk software (Babraham Bioinformatics; https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) as single ended RNA-Seq data.
Quantification was performed by using the default RNA-Seq quantitation pipeline.
P-value was calculated from the intensity difference and representative genes of showing significant change (P<0.05)
Assembly: GRCh38 v90
Supplementary files format and content: Matrix table with gene expression ratio for every gene

growth_protocol: Dulbecco's Modified Eagle medium supplimented with 10% Fetal bovine serum and 1% penicillin streptomycin

extract_protocol:
Total RNA isolaton was performed using TRIzol reagent (Thermo Fisher) and its standard protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 416 bp of CLDN4 CDS region including the translation start site was removed by transient expression of Cas9 and a pair of CRISPR gRNA.

value: Breast cancer

value: CLDN4 -/-


title: iPSC-derived neural progenitors, karyotypically normal, GDNF transduced

city: Los Angeles

first: Shaughn

last: Bell

address: 8700 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

description: 10x Genomics

data_processing:
Sample demultiplexing was performed by the Cedars-Sinai Applied Genomics, Computation and Translational Core.  Raw data were delivered as multiple gzipped fastq files.
Demultiplexed fastq files were run via CellRanger v6.1.2 using the "cellranger count" command with the "--include-introns" option using the 10x-provided human reference sequence v2020-A.
Cellranger output filtered_feature_bc_matrix files (barcodes.tsv.gz, features.tsv.gz & matrix.mtx.gz) were loaded into R v4.2.1 and combined into one matrix file per sample.  The matrix file was then processed by summing all Ensmbl IDs with the same gene symbol to the gene symbol level via standard R matrix prossessing functions.
Assembly: Homo_sapiens.GRCh38 & gencode.v32 (10x-provided human reference version 2020-A)
Supplementary files format and content: Comma separated count matricies with gene symbols as rows and cell ID as columns

molecule: nuclear RNA

source_name: iPSC-derived neural progenitor cells

extract_protocol:
All steps were performed on ice.  Wide-bore Rainin LTS pipette tips were used exclusively throughout. Frozen cell pellets were thawed on ice, resuspended in cold homogenization buffer (5mM MgCl2, 3mM Mg(Ac)2, 10mM Tris pH7.8, 0.017 mM PMSF, 0.17 mM b-mercaptoethanol, 320 mM Sucrose, 0.1 mM EDTA, 0.1% NP40, RNAse inhibitors, and Protease inhibitors), and transferred to a 2 ml glass dounce.  The cells were manually lysed with 50 strokes each of the "A" and "B" pestles.  Homogenate was filtered using 70 um Flowmi pipette tip filters and gently mixed 1:1 with a 50% Iodixanol solution (5mM MgCl2, 3mM Mg(Ac)2, 10mM Tris pH7.8, 0.017 mM PMSF, 0.17 mM b-mercaptoethanol, RNAse inhibitors, Protease inhibitors, and 50% Iodixanol).  A centrifugation gradient was set up using 600 ul 40% Iodixanol solution (5mM MgCl2, 3mM Mg(Ac)2, 10mM Tris pH7.8, 0.017 mM PMSF, 0.17 mM b-mercaptoethanol, RNAse inhibitors, Protease inhibitors, 160 mM Sucrose, 0.2 ug/ul OrangeG, and 40% Iodixanol), 600 ul 29% Iodixanol solution (5mM MgCl2, 3mM Mg(Ac)2, 10mM Tris pH7.8, 0.017 mM PMSF, 0.17 mM b-mercaptoethanol, RNAse inhibitors, Protease inhibitors, 160 mM Sucrose, and 29% Iodixanol) and 800 ul of the 50% Iodixanol + Sample mixture (25% Iodixanol final concentration).  This was centrifuged at 3000 x g for 1 hour with the breaks disengaged.  Any debris on the top surface was removed, and 200 ul of the thin cloudy layer containing the nuclei was extracted, mixed with 1.8 ml PBS + 1% BSA solution, and centrifuged at 500 x g for 10 minutes with breaks engaged.  1.8 ml supernatant was removed and the remaining 200 ul plus nuclei pellet was resuspended in 1.8 ml PBS + 1% BSA solution.  The nuclei suspension was counted via hemocytometer and checked for nucleus quality.  A portion of this suspension was then diluted to achieve the correct nuclei concentration for the 10x Chromium NextGEM 3' protocol with a target of ~4,000 nuclei per sample.
Standard 10x protocol found in "Chromium NextGEM Single Cell 3' Reagent Kits v3.1 User Guide, Rev D" (single index)

value: iPSC-derived neural progenitor cells

tag: passage

value: transduction with GDNF lentivirus


title: SiHa ChIP H3K27Ac

description: SiHa ChIP H3K27Ac clean read

source_name: SiHa cell

value: SiHa


title: 11A_M_1096


title: U2OS, p53 KO, DMSO, rep2

description:
KO.DMSO.2
U2OS_RNAseq_countData.xlsx
res_ko_vs_par_dmso.csv
nomalized_expression_matrix_2.csv

tag: treatment

value: DMSO

value: 24 hr


title: MCF7:CLDN4-/-_rep1

description: CLDN4 knockout

tag: cell line


title: SiHa ChIP H3K4me3

description: SiHa ChIP H3K4me3 clean read


title: 11A_M_1095

value: male


title: S12 ChIP Input

description: S12 ChIP Input clean read

source_name: S12 cell


title: MCF7_rep2

description: No treatment

tag: genotype

value: WT


title: 11A_M_1094


title: OB, LFS3

description:
LFS3
OB_RNAseq_countData.xlsx
res_osteoblast_lfs_vs_wt.csv

source_name: Osteoblast

value: Osteoblast

value: osteogenic differentiation

tag: time

value: Day 15


title: OB, LFS2

description:
LFS2
OB_RNAseq_countData.xlsx
res_osteoblast_lfs_vs_wt.csv


title: MCF7_rep1

description: No treatment


title: 11A_M_1093

tag: brain region


title: S12 ChIP H3K27Ac

description: S12 ChIP H3K27Ac clean read


title: T47D:CLDN4-/-_rep2

description: CLDN4 knockout


title: OB, LFS1

description:
LFS1
OB_RNAseq_countData.xlsx
res_osteoblast_lfs_vs_wt.csv


title: SiHa ChIP Input

description: SiHa ChIP Input clean read


title: T47D_rep2

description: No treatment


title: OB, WT3

description:
WT3
OB_RNAseq_countData.xlsx
res_osteoblast_lfs_vs_wt.csv

value: p53 WT/WT


title: Fetal-derived neural progenitors, GDNF transduced

description: 10x Genomics

source_name: fetal-derived neural progenitor cells

value: fetal-derived neural progenitor cells


title: 11A_M_1092

tag: age


title: T47D:CLDN4-/-_rep1

description: CLDN4 knockout


title: 11A_M_1091

tag: strain


title: HeLa ChIP H3K4me3

description: HeLa ChIP H3K4me3 clean read

source_name: HeLa cell

value: HeLa


title: HeLa ChIP H3K27Ac

description: HeLa ChIP H3K27Ac clean read


title: 11A_M_1090

tag: Sex


title: OB, WT2

description:
WT2
OB_RNAseq_countData.xlsx
res_osteoblast_lfs_vs_wt.csv


title: 11A_M_109


title: T47D_rep1

description: No treatment


title: OB, WT1

description:
WT1
OB_RNAseq_countData.xlsx
res_osteoblast_lfs_vs_wt.csv


title: CaSki ChIP Input

description: CaSki ChIP Input clean read

source_name: CaSki cell

value: CaSki


title: S33208_emd_24h_B

city: Cairo

first: Amal Kamal

last: Abdel-Aziz

address: African Union Organization St. Abbassia,

department: Pharmacology and Toxicology

country: Egypt

institute: Ain Shams University

data_processing:
FastX-toolkits and FastQC tools were used to filter reads and control the quality of all raw data
Paired-end reads were aligned to the hg38 reference genome using STAR.
Library size normalization and differential gene expression for EMD37 versus DMSO was carried out using DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count and Deseq2 output for each sample

source_name: Triple negative breast cancer MDA-MB-231

growth_protocol: MDA-MB-231 cells were cultured in DMEM media supplemented with 2mM L-glutamine, 10% FBS and 1% penicillin-streptomycin

extract_protocol:
RNA was then extracted from MBA-MB-231 cells using RNA extraction kit (Direct-zol™ RNA kit, Zymo research Corp). RNA quantity was evaluated using Qubit RNA HS Assay Kit. RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit, reagents and supplies.
1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.

treatment_protocol: MDA-MB-231 cells were treated with either DMSO or EMD37 (0.5 μM) for 12 and 24 hours.

value: Triple negative breast cancer


title: U2OS, p53 KO, DMSO, rep1

description:
KO.DMSO.1
U2OS_RNAseq_countData.xlsx
res_ko_vs_par_dmso.csv
nomalized_expression_matrix_2.csv

value: Osteosarcoma

value: p53 KO


title: S33207_emd_24h_A


title: OB, LFS2, p53ChIP

data_processing:
ChIP-seq reads were trimmed by Trim Galore! with default settings.
ChIP-seq reads were aligned to the UCSC hg19 genome using Bowtie2.
PCR duplicates were removed by SAMtools RmDup.
bigWig files were generated using deepTools bamCoverage with RPKM normalization.
Peaks were called uing MACS2 with the significance cut-off q-value <=0.01
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: Osteoblasts were cultured in osteogenic differentiation medium (α-MEM supplemented with 10% FBS, 10 mM β-glycerol phosphate, 200 μM ascorbic acid, and 0.1 μM dexamethasone). U2OS were cultured in Dulbecco’s Modified Eagle Medium (DMEM) containing 10% fetal bovine serum (FBS) at 37°C in a humidified 5% CO2 environment.  673 bovine serum (FBS) at 37°C in a humidified 5% CO2 environment

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature. After quenching and cell lysis, chromatin was sonicated using Branson Sonifier 450.
ChIP-seq library construction was performed using KAPA Hyper Prep Kit (KK8500) according to manufacturer's conditions. Post amplification libraries were size selected at around 200-500bp in length using KAPA Pure Beads beads from Roche.

value: p53 (Santa Cruz, sc-126)


title: CaSki ChIP H3K27Ac

description: CaSki ChIP H3K27Ac clean read


title: OB, LFS1, p53ChIP


title: CaSki ChIP H3K4me3

description: CaSki ChIP H3K4me3 clean read


title: 11A_M_1088


title: 11A_M_1087


title: S33206_veh_24h_B

value: DMSO - 24h


title: HeLa ChIP Input

description: HeLa ChIP Input clean read


title: OB, WT2, p53ChIP


title: S33205_veh_24h_A


title: C33A ChIP Input

description: C33A ChIP Input clean read

source_name: C33A cell


title: S12 ChIP H3K4me3

description: S12 ChIP H3K4me3 clean read


title: 11A_M_1086


title: C33A ChIP H3K27Ac

description: C33A ChIP H3K27Ac clean read


title: S33204_emd_12h_B


title: OB, WT1, p53ChIP


title: C33A ChIP H3K4me3

description: C33A ChIP H3K4me3 clean read


title: OB, WT, input


title: OB, LFS, input


title: 11A_M_1083


title: S33201_veh_12h_A

value: DMSO - 12h


title: S33203_emd_12h_A


title: 11A_M_1085


title: 11A_M_1084


title: 11A_M_1089


title: SiHa RNA-seq

description: SiHa RNA-seq clean read

value: SiHa


title: U2OS, p53(AD/AD), p53ChIP, Etoposide, rep2


title: Raji RNA-seq

description: Raji RNA-seq clean read

value: Raji


title: 11A_M_1082

value: male


title: U2OS, p53(AD/AD), p53ChIP, Etoposide, rep1


title: S2-VP10_xenograft_ROR1low-3

city: Kumamoto city

first: Masaya

last: Yamazaki

address: 1-1-1, Honjyo, Chuo-ku

institute: Kumamoto university

data_processing:
Basecalls and conversion to FASTQ files were performed using Basesapce online (Illumina).
Sequencing reads were trimmed for adaptor sequence, and aligned to human transcriptome (GRCh37) and quantified with Salmon (version 1.3.0) with default settings.
Differential expression testing was performed with DESeq2 (version 1.28.1).
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for every gene and every sample.
Supplementary_files_format_and_content: Tab-delimited text files include p-value and q-value for every genes.

source_name: Pancreatic adenocarcinoma

extract_protocol:
RNA was extracted from sorted ROR1high and ROR1low cells using MagMAX-96 Total RNA Isolation Kit (Thermo Fisher Scientific), and 1 ng of RNA was used for the reverse transcription reaction using SMART-seq HT (Takara).
RNA-seq library was prepared using Nextera XT Library Prep Kit (Illumina).

value: S2-VP10 (human pancreatic adenocarcinoma)

tag: model

value: xenograft

tag: sorted cell


title: S12 RNA-seq

description: S12 RNA-seq clean read


title: S2-VP10_xenograft_ROR1high-3


title: U2OS, p53(AD/AD), p53ChIP, DMSO, rep2

tag: chip antibody


title: HeLa RNA-seq

description: HeLa RNA-seq clean read


title: 11A_M_1080


title: 11A_M_1081


title: U2OS, p53(AD/AD), p53ChIP, DMSO, rep1


title: 11A_M_108


title: CaSki RNA-seq

description: CaSki RNA-seq clean read


title: U2OS, p53(+/+), p53ChIP, Etoposide, rep2


title: S2-VP10_xenograft_ROR1low-2


title: S2-VP10_xenograft_ROR1high-2


title: C33A RNA-seq

description: C33A RNA-seq clean read


title: U2OS, p53(+/+), p53ChIP, Etoposide, rep1


title: 11A_M_1079


title: S2-VP10_xenograft_ROR1low-1


title: S33202_veh_12h_B


title: U2OS, p53(+/+), p53ChIP, DMSO, rep2


title: S2-VP10_xenograft_ROR1high-1


title: U2OS, p53(+/+), p53ChIP, DMSO, rep1


title: RNAseq_22Rv1_3hours_KB05_Replicate_3

city: South San Francisco

first: Simon

middle: J

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

description:
RNAseq_counts_raw.csv
KB05-2h-3

data_processing:
Transcript abundance was quantified using Salmon (v1.3.0) with Hg38/GRCh38.p13 GENCODE v37 annotation.
Gene level quantification was performed using tximeta (v1.8.4).
Differential gene expression was analyzed by DESeq2 (v1.30.1).
Log2 fold expression changes were estimated using apeglm (v1.12.0) and p values were adjusted using the Benjamini-Hochberg procedure to control for multiple hypothesis testing.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Raw gene expresion counts table in CSV format

source_name: Prostate carcinoma

growth_protocol: Cells were grown in vitro under standard culture conditions

extract_protocol:
Rneasy Plus Mini Kit following manufacturer’s instructions
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: Samples were treated in biological triplicate in the presence of compounds, as indicated.

tag: timepoint

value: 3 hours

tag: agent

tag: dose


title: 11A_M_1076

last: Ecker


title: 11A_M_1075


title: U2OS, p53(-/-), p53ChIP, DMSO

tag: cell type


title: RNAseq_22Rv1_3hours_KB05_Replicate_1

description:
RNAseq_counts_raw.csv
KB05-2h-1


title: RNAseq_22Rv1_3hours_KB02_Replicate_3

description:
RNAseq_counts_raw.csv
KB02-2h-3


title: A4110_8: Adipose_8wks_12AM

city: San Diego

first: April

middle: Elizabeth

last: Williams

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

data_processing:
Basecalls were generated using CASAVA v1.8
Data quality was assessed using FastQC v0.11.8
Sequenced reads were aligned to the hg19 genome assembly using STAR v2.5.3a
Reads were annotated to genes using Homer v4.10
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes the raw counts for each sample.

source_name: obese male

extract_protocol:
RNA were extracted following the protocol from Rneasy Lipid Tissue Mini kit (Qiagen) and RNA intergrity number were measured through Agilent 2200 TapeStation system
Libraries were pooled and sequenced using an Illumina HiSeq 2500 with 50-bp single-read chemistry

tag: tissue

value: Adipose

tag: gender

value: wild type


title: 11A_M_1074

city: La Jolla

first: Joseph

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute


title: 11A_M_1073


title: A4109_8: Adipose_8wks_12AM


title: U2OS, p53KO, p53ChIP

data_processing:
ChIP-seq reads were trimmed using Trim Galore! --quality 15 --stringency 3
Trimed reads were aligned to the UCSC hg19 genome using Bowtie2
Peaks were called uing MACS2 -q 0.01 using input as control
Unique peaks were identified by bedtools intersect
Peak annotation and motif prediction were performed by Homer software
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
Cells were fixed in 1% formaldehyde at room temperature for 10 min, quenched by 125mM glycine,and sonicated in ChIP lysis buffer on ice
ChIP-seq libraries were prepared using KAPA Hyper Prep Kit (KK8502) according to the manufacture's instruction

tag: antibody


title: 11A_M_1072


title: A4108_8: Adipose_8wks_12AM


title: RNAseq_22Rv1_3hours_KB02_Replicate_1

description:
RNAseq_counts_raw.csv
KB02-2h-1

tag: cell line


title: A4115_8: Adipose_8wks_12AM

tag: genotype


title: RNAseq_22Rv1_3hours_DMSO_Replicate_3

description:
RNAseq_counts_raw.csv
DMSO-2h-3

value: DMSO


title: 11A_M_1078


title: 11A_M_1071


title: A4114_8: Adipose_8wks_12AM


title: 11A_M_1077


title: A4106_8: Adipose_8wks_12AM


title: A4113_8: Adipose_8wks_12AM


title: U2OS, p53(+/AD), p53ChIP, rep2


title: U2OS, p53(-/-), p53ChIP, Etoposide


title: 11A_M_1070


title: RNAseq_22Rv1_3hours_KB05_Replicate_2

description:
RNAseq_counts_raw.csv
KB05-2h-2


title: A4112_8: Adipose_8wks_12AM


title: RNAseq_22Rv1_3hours_DMSO_Replicate_2

description:
RNAseq_counts_raw.csv
DMSO-2h-2


title: U2OS, p53(+/AD), p53ChIP, rep1


title: RNAseq_22Rv1_3hours_DMSO_Replicate_1

description:
RNAseq_counts_raw.csv
DMSO-2h-1


title: A4102_8: Adipose_8wks_12AM


title: 11A_M_1069


title: 11A_M_107


title: U2OS, p53(+/+), p53ChIP, rep2

value: p53 WT/WT


title: Total_RNAseq_22Rv1_8hours_WX-02-43_5uM_Replicate3

data_processing:
FASTQ files were first trimmed using Trim_galore (v0.6.4) to remove sequencing adapters and low quality (Q<15) reads.
Trimmed sequencing reads were aligned to the human Hg19 reference genome (GENCODE, GRCh37.p13) using STAR (v2.7.5).
SAM files were subsequently converted to BAM files, sorted, and indexed using samtools (v1.9).
BAM files were used to generate bigwig files using bamCoverage (part of the Deeptools package; v3.3.1).
Genome_build: HG19
Supplementary_files_format_and_content: bigWig

extract_protocol:
RNA was extracted using the Rneasy Plus Mini Kit (Qiagen) following manufacturer’s instructions
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: Samples were treated in biological triplicate in the presence of small molecule inhibitors, as indicated, for 8 hours prior to collection.

tag: time point

value: 8 hours


title: RNAseq_22Rv1_3hours_KB02_Replicate_2

description:
RNAseq_counts_raw.csv
KB02-2h-2


title: A4101_8: Adipose_8wks_12AM


title: U2OS, p53(+/+), p53ChIP, rep1


title: 11A_M_1068

tag: brain region


title: Total_RNAseq_22Rv1_8hours_WX-02-43_5uM_Replicate2


title: A4107_8: Adipose_8wks_12AM


title: A4115_7: Adipose_8wks_6PM


title: A4114_7: Adipose_8wks_6PM


title: Total_RNAseq_22Rv1_8hours_WX-02-43_5uM_Replicate1


title: 11A_M_1066

tag: age


title: 11A_M_1067

tag: strain


title: Total_RNAseq_22Rv1_8hours_WX-02-23_5uM_Replicate3


title: A4113_7: Adipose_8wks_6PM


title: 11A_M_1065

tag: Sex


title: Total_RNAseq_22Rv1_8hours_WX-02-23_5uM_Replicate2


title: S2 cell, WT, CrolN, rep2

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

data_processing:
Reads were trimmed using Trim Galore v0.6.5 and then aligned to the reference genome (dm3) using Bowtie v2.3.5 with default parameters. The PCR duplicates for each dataset were removed using the rmdup function of samtools v1.13. The data reproducibility between biological replicates was confirmed, then reads from replicates were pooled together for further analysis. Peak calling was performed with MACS v2.2.5 with parameters: -g dm -q 0.05 --nomodel --extsize 300. H3K27me3 and H3K27ac were called as broad peaks, while all other factors were called as narrow peaks. Differential binding analysis was performed using DiffBind2, with summit set as 250. Overlap of peaks were performed using the window function from BEDTools v2.29.2. ChIP-seq tracks were visualized using IGV, and heatmaps were created using DeepTools v3.5.1.
Assembly: dm3
Supplementary files format and content: narrowPeak (except for Input sample)

organism: Drosophila melanogaster

source_name: 3rd instar larval imaginal discs and brains

extract_protocol:
Chromatin immunoprecipitation (X-ChIP) was prepared as describe previously (Erokhin et al., BMC Biol, 2021). For each experiment, 150-200 mg of 3rd instar larvae or embryos were collected. The material was homogenized in 5 ml of buffer A1 (15 mM HEPES, pH 7.6; 60 mM KCl, 15 mM NaCl, 4 mM MgCl2, 0.5% Triton X-100, 0.5 mM DTT, Roche cOmplete protease inhibitor) supplemented with the EDTA-free protease inhibitor cocktail (Roche, Switzerland) and formaldehyde as a crosslinking agent (final concentration 1.8%). The reaction was stopped by adding glycine (final concentration 225 mM). The homogenate was cleared by passing through 100-µm nylon cell strainer (BD Falcon) and pelleted by centrifugation at 4000 g, 4°C for 5 min. After twice washing in buffer A1 at 4°C, the pellet was treated with 0.5 ml of complete lysis buffer (15 mM HEPES, pH 7.6; 140 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 1%Triton X-100, 0.5 mM DTT, 0.1% sodium deoxycholate, 0.1% SDS, 0.5 % N-lauroylsarcosine, Roche cOmplete protease inhibitor) and sonicated to break chromatin into fragments with an average length of  200-600 bp. The material was pelleted by centrifugation at 18 000 g for 5 min, and the supernatant fluid was transferred to a new tube. The pellet was treated with the second 0.5-ml portion of lysis buffer, and the preparation was centrifuged at 18 000 g for 5 min. The two portions of the supernatant fluid were pooled, cleared by centrifuging twice at 18 000 g for 10 min, and the resultant chromatin extract (1 ml) was used for ChIP experiments. 9 ml of ChIP dilution buffer (15 mM HEPES, pH 7.6; 140 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 1%Triton X-100, 0.5 mM DTT, Roche cOmplete protease inhibitor), was added to the sheared chromatin together with 50 ul of prewashed Protein A Sepharose beads (GE Healthcare). The samples were incubated at 4 oC for 1 hour on a rotating platform. The samples were spun at 10,000g to remove the beads and the supernatant was transferred to a fresh tube. One aliquot (1/10 volume) of chromatin extract after preincubation with Sepharose was kept as a control sample (Input).
DNA concentration of 5ul was measured using a Qubit 3.0 fluorometer (Invitrogen). 1.5ng of starting material/sample was used to make each library. ChIP-seq libraries were obtained using the NEBNext Ultra™ II DNA library preparation kit (New England Biolabs) or with the Thruplex DNA-seq and single index kits (Takara) following the manufacturer’s instructions. Samples were sequenced by 50bp or 100bp single-end sequencing with HiSeq2500 (Illumina) or with NovaSeq6000 sequencer.

value: Wild-type

value: CrolN, 1-188 aa of Crol, isoform A


title: S2 cell, WT, CrolN, rep1

value: 3rd instar larval imaginal discs and brains


title: A4112_7: Adipose_8wks_6PM


title: 11A_M_1064

source_name: C57BL/6J Male P56 Mouse Brain


title: 3rd instar larval imaginal discs and brains, WT, CrolN, rep 2


title: A4110_7: Adipose_8wks_6PM


title: 11A_M_1063


title: Total_RNAseq_22Rv1_8hours_WX-02-23_1uM_Replicate3


title: A4105_8: Adipose_8wks_12AM


title: 11A_M_1062


title: 3rd instar larval imaginal discs and brains, CrolKO, CrolN, rep2

value: CrolKO


title: 3rd instar larval imaginal discs and brains, WT, CrolN, rep 1


title: A4108_7: Adipose_8wks_6PM


title: 3rd instar larval imaginal discs and brains, CrolKO, CrolN, rep1


title: 3rd instar larval imaginal discs and brains, WT, Cg, rep2


title: 11A_M_1061


title: 11A_M_1060


title: A4107_7: Adipose_8wks_6PM


title: 11A_M_106


title: A4106_7: Adipose_8wks_6PM


title: 3rd instar larval imaginal discs and brains, WT, Cg, rep1


title: Total_RNAseq_22Rv1_8hours_PladienolideB_Replicate3

value: Pladienolide B


title: Total_RNAseq_22Rv1_8hours_WX-02-23_1uM_Replicate1


title: A4105_7: Adipose_8wks_6PM


title: 11A_M_1059


title: 3rd instar larval imaginal discs and brains, CrolKO, Cg, rep2


title: Total_RNAseq_22Rv1_8hours_PladienolideB_Replicate1


title: Total_RNAseq_22Rv1_8hours_PladienolideB_Replicate2


title: 11A_M_1058


title: A4101_7: Adipose_8wks_6PM


title: Total_RNAseq_22Rv1_8hours_WX-02-23_5uM_Replicate1


title: 3rd instar larval imaginal discs and brains, CrolKO, Cg, rep1


title: Total_RNAseq_22Rv1_8hours_DMSO_Replicate3


title: 11A_M_1057


title: A4109_7: Adipose_8wks_6PM


title: Total_RNAseq_22Rv1_8hours_DMSO_Replicate2


title: 3rd instar larval imaginal discs and brains, WT, Input, rep3

source_name: larval imaginal discs and brains

tag: developmental stage

value: 3rd instar

value: larval imaginal discs and brains


title: Total_RNAseq_22Rv1_8hours_WX-02-23_1uM_Replicate2


title: 3rd instar larval imaginal discs and brains, WT, Input, rep2


title: 11A_M_1056


title: A4114_6: Adipose_8wks_12PM


title: 11A_M_1055


title: A4113_6: Adipose_8wks_12PM


title: Total_RNAseq_22Rv1_8hours_DMSO_Replicate1


title: 3rd instar larval imaginal discs and brains, WT, Input, rep1


title: 11A_M_1054


title: PANC1-2SP-2

city: beijing

first: Yanhong

last: Wang

address: Dong dan san tiao No.5

institute: Institute of Basic Medical Sciences Chinese Academy of Medical Sciences，School of Basic Medicine Peking Union Medical College

data_processing:
RNA-seq was performed using Illunina hiseq 6000
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using HISAT
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using a protocol from DEseq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

growth_protocol: Cells lines were plated in ultralow attachment six well plates at a density of 5000 viable cells per well. Cells were grown in spheroid medium consisting of DMEM/F12 supplemented with, 20 ng/ml basic fibroblast growth factor-2, 20 ng/ml epidermal growth factor, B27 serum-free supplement (1:50) and penicillin-streptomycin at 37 °C in 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. VAHTS Universal V6 RNA-seq Library Prep Kit for Illuminaa was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Gemcitabine-resistant SW1990 cells were derived from original parental cell line by continuous exposure to stepwise increasing concentrations of gemcitabine. Initially, the exponentially growing cells were exposed 1 μM gemcitabine for 2-3 passages. The surviving cells were then exposed to gradually increasing concentrations of gemcitabine during every passage and this development period was persisting about 9 months. The final concentration of gemcitabine is 40 μM.

value: pancreatic cancer cell

tag: type

value: Secondary  spheroid formation cells


title: A4112_6: Adipose_8wks_12PM

value: male


title: PANC1-2SP-3


title: 11A_M_1053


title: 3rd instar larval imaginal discs and brains, CrolKO, Input, rep1

tag: chip antibody


title: PANC1-2SP-1


title: A4102_7: Adipose_8wks_6PM


title: 11A_M_1052


title: PANC1-WT-3

value: Wild type cell


title: A4109_6: Adipose_8wks_12PM


title: A4110_6: Adipose_8wks_12PM


title: 11A_M_1051


title: 3rd instar larval imaginal discs and brains, WT, Ph, rep2

value: a gift from Donna Arndt-Jovin, Buchenau et al.,  J Cell Biol, 1998


title: 3rd instar larval imaginal discs and brains, WT, Ph, rep1


title: PANC1-WT-2