title: RPE1 H4K20me1-Dam (set11.samplenr_036) DamID

last: Kind

address: Uppsalalaan 8

institute: Hubrecht Institute


title: KO 2

status: Public on Apr 01 2022

type: SRA

city: NEW YORK

first: Jesus

middle: Maria

last: Gomez Salinero

state: NY

address: 1300 York Avenue

country: USA

institute: Weill Cornell Medicine

library_source: transcriptomic

data_processing:
FastQC (v0.11.5) to check FASTQ quality.
Skewer (v0.2.2) for adapter trimming
Minion from Kraken tool (reaper-13-100) for adapter diagnosis
STAR (v2.7.6a) for alignment and gene count quantification using --quantMode GeneCounts
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene count matrix

molecule: polyA RNA

organism: Mus musculus

source_name: Liver endothelium

extract_protocol:
ECs were isolated by fluorescence-activated cell sorting and subjected to RNA extraction using RNeasy Mini Kit from Qiagen.
RNA-seq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

tag: tissue

value: Liver

tag: genotype

value: c-Maf KO


title: KOPALM2

city: MADRID

last: VALDECANTOS

state: MADRID

address: C/ARTURO DUPERIER, 4

country: Spain

institute: IIB ALBERTO SOLS

data_processing:
RNA-Seq paired-end reads were mapped against the mouse reference genome using STAR (RRID:SCR_015899, version 2.5.2a) with ENCODE parameters for long RNA. Genes were quantified using RSEM (RRID:SCR_013027, version 1.2.2.8) and GENCODE (RRID:SCR_014966, version 24).
Mapping quality metrics were calculated with GEMtools (http://gemtools.github.io/) and RSeQC (RRID:SCR_005275).
Normalization and transformation of the expression data for plotting and analysis were done with the variance stabilizing transformation function of DESeq2 (RRID:SCR_015687). Only the protein coding genes from the normalized count matrix were selected for further analysis.
After low-expressed genes were filtered out (at least 1 count in 70% of samples) and genes with duplicated gene symbol were averaged by the median of their expression.
Finally, counts were log2 transformed for Limma analysis.
Assembly: RNA-Seq paired-end reads were mapped against the mouse reference genome using STAR (RRID:SCR_015899, version 2.5.2a) with ENCODE parameters for long RNA.
Supplementary files format and content: Processed data file are presented as normalized counts in microsoft excel  format

molecule: total RNA

source_name: Liver progenitor cells

growth_protocol: Cells were mantained in DMEM 10% with 10% FBS and passed twice a week

extract_protocol:
RNA was extracted using the miRNeasy Mini kit (QIAGEN 217004, Hilden, Germany) following the manufacturer’s instructions and assessed for quality. The starting input material for the construction of the RNA library was DNA-free total RNA from FFPE samples, obtained using the KAPA RNA HyperPrep Kit with RiboErase (HMR; Kapa Biosystems, Wilmington, MA, USA), according to the manufacturer´s protocol. Briefly, the ribosomal RNA (rRNA) was depleted from 0.8 to 1 μg of total RNA using RiboErase. rRNA-depleted RNA samples were fragmented in the presence of divalent ions at 65°C for 1 min due to the low quality of the initial total RNA. Following RNA fragmentation (first- and second-strand synthesis), the Illumina-compatible bar-coded adapters were ligated at a concentration of 1.5 μM.
The libraries were sequenced on HiSeq2000 (Illumina, San Diego, CA, USA) in paired-end mode with a read length of 2 × 76 bp using TruSeq SBS Kit v4. Each sample was sequenced in a fraction of a sequencing v4 flow cell lane, following the manufacturer's protocol.

treatment_protocol: Cells were treated with Palmitic Acid 400 µM in DMEM  supplemented with 5% FBS and 1% of BSA

tag: cell type

value: Hepatic progenitor cells

tag: agent

value: Palmitic acid 400 microM 8h


title: RPE1 H4K20me1-Dam (set11.samplenr_035) DamID

city: Utrecht

first: Jop

country: Netherlands

library_source: genomic

data_processing:
Library strategy: DamID-seq
Samples are demultiplexed based on the sample barcode present in R1, using custom pipelines (available at: https://github.com/KindLab/scDamAndTools).
DamID reads are aligned using bowtie2 (v. 2.3.3.1) with the following parameters: “--seed 42 --very-sensitive -N 1”.
Alignments with a MAPQ < 10 are removed.
Using our own custom pipeline (see KindLab GitHub), aligned reads are matched to known GATC positions in the genome to get the number of observations per (strand-specific) GATC position.
GATC-position counts are deduplicated using UMI information to allow a maximum of 64 unique UMIs per GATC position.
Unique GATC counts are summarized in genomic intervals at the desired resolution.
Genome_build: hg19
Supplementary_files_format_and_content: Hdf5 files contain per chromosome the observed number of UMI-unique counts within genomic intervals of a resolution indicated by the bin size.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Human hTERT-immortalized RPE-1 cells were grown in DMEM: F12 supplemented with 10% fetal bovine serum and 1% Pen/Strep (100 U/mL penicillin and 100 ug/mL streptomycin).

extract_protocol:
Cells were harvested by trypsinization, and genomic DNA was extracted by column purification.
DamID sequencing was performed as previously described (doi 10.1038/s41596-020-0314-8). Briefly, genomic DNA was digested with DpnI, followed by indexed adapter ligations, bead cleanup and amplification by T7 RNA polymerase. RNA sequencing libraries were prepared by reverse transcription, PCR-based amplification of cDNA, and single-ended size selection. Libraries were sequenced on the Illumina HiSeq 2500 or NextSeq 500.

treatment_protocol: hTERT-RPE1 cells grown in DMEM/F12 (Gibco) 10% FBS (Hyclone) and 1% Pen/Strep (Gibco) on 6 well to 30% confluency were transduced in 1500ul total volume with lentiviral amounts ranging between 0.1-40ul concentrated or 20-1500ul unconcentrated lentivirus in the presence of 10ug/ml of polybrene, and collected for gDNA isolation 48hrs after transduction.

tag: cell line

tag: dam-fusion protein

value: anti-H4K20me1 (mintbody)

tag: dam type

value: DamWT


title: KOCTRL1

value: CONTROL


title: KOCTRL4


title: KOCTRL3


title: Ctl 2

value: Control


title: KoCCE4

city: Brooklyn

first: Brahim

last: Chaqour

address: 450 Clarkson Avenue

department: Cell Biology

institute: SUNY Downstate Medical Center

data_processing:
Trim, filter, and map reads; perform advanced analysis
Genome_build: GENCODE mouse GRCm38
Supplementary_files_format_and_content: counts.txt, Differential_expression_analysis_table-1.csv, Significant-DEGs.csv

source_name: Retina

extract_protocol:
Eyes were enucleated at E18.5. Retinas were dissected,snap frozen in liquid nitrogen and RNA was extracted using  Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols on the Illumina® HiSeq4000 platform.

tag: strain

value: retina

tag: age

value: Embryonic day (E) 18.5

value: KoCCE


title: WTPALM3


title: WTPALM2


title: Ctl 1


title: RPE1 Dam-H3K9ac (set4.samplenr_011) DamID

value: anti-H3K9ac (mintbody)


title: KOPALM1


title: KoCCE3


title: WTCTRL4


title: RPE1 H4K20me1-Dam (set14.samplenr_033) DamID


title: WTPALM1


title: RPE1 H4K20me1-Dam (set14.samplenr_031) DamID


title: RPE1 Dam-H3K9ac (set2.samplenr_007) DamID


title: RPE1 Dam-H4K20me1 (set9.samplenr_013) DamID


title: KoCCE1


title: WTCTRL3


title: KOCTRL2


title: WTCTRL2


title: RPE1 Dam126-H3K27me3MUT (set5.samplenr_018) DamID

value: anti-H3K27me3-mutated (mintbody)


title: WTCTRL1


title: WTCCE3

value: WTCCE


title: RPE1 H3K27me3MUT-Dam (set2.samplenr_017) DamID


title: WTCCE2


title: RPE1 H3K27me3MUT-Dam (set2.samplenr_023) DamID


title: WTCCE1


title: RPE1 Dam-H3K9ac (set2.samplenr_001) DamID


title: RPE1 Dam-H3K27me3 (set4.samplenr_016) DamID

value: anti-H3K27me3 (mintbody)


title: Func120_T2

type: RNA

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

description: Tumor biopsy

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in BeadStudio 3.1.3.0. Gene expression profiles of the RNeasy derived samples were transformed by centring the median expression value of every probe to the median value of the miRNeasy samples. Transformation was based on a larger number of samples than provided here.

label: biotin

source_name: Prostate tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol

growth_protocol: 1-2 punch biopsies (T1 and/or T2) were collected from each patient at the time of surgery

extract_protocol: Total RNA was isolated from a piece of each biopsy (10 slices x 20μm), using RNeasy MiniKit (n=45) or miRNeasy MiniKit (n=96) (Qiagen, Hilden, Germany), according to the information given for each sample. All samples had an RNA integrity number (RIN) of 6 or above, as assessed by the Agilent 2100 Bioanalyzer (Agilent Technology, Santa Clara, CA, USA).

treatment_protocol: The samples were immediately snap-frozen in liquid nitrogen and stored at -80 C until used for analysis. Biopsies with more than 75% malignant glands and less than 50% stroma in HE stained sections from the specimen were used further.

tag: histology

value: Adeno carcinoma

tag: d'amico risk classification

tag: tumor gleason score pathology

tag: tumor isup grade group

tag: pathological tumor stage

tag: lymph node status

tag: rna isolation kit

value: miRNeasy


title: RPE1 Dam126-H3K27me3 (set4.samplenr_008) DamID


title: Molt-4 PRMT7 KO11 repl. 3

city: Tampere

first: Laura

last: Oksa

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: T-ALL cells

data_processing:
Base calling was mabe using CASAVA base recognition software and SecureCRT was used to data demultiplexin. These steps were performed by Novogene Europe (Cambridge, UK).
The quality of the raw reads was ensured with FastaQC (v0.11.08)
STAR software (version 2.5.3a) was used to map the reads to the human reference genome (hg19).
Tag directories were made from the alingment files and raw read counts were calculated using Homer tool kit ( v.4.11)
Assembly: hg19
Supplementary files format and content: Tab-delimited text file includes raw read counts of the samples and replicates.

source_name: Molt-4 cell line

growth_protocol: Cells were cultured in RPMI (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 2 mM L-glut, 100 U penicillin, 100 ug/ml streptomycin and 10% FBS (Gibco).

extract_protocol:
Total RNA extraction was performed with PureLink™ RNA Mini Kit and On-Column PureLink® DNase Treatment Protocol was used to avoid contamination by genomic DNA (Ambion® by Life Technologies and Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols (Hiseq-PE150)

treatment_protocol: Jurkat Cas9 cells  were transfected with 2µg of px321-GFP plasmid, containing PRMT7 KO gRNA (PRMT7 KO2 or PRMT7 KO33), targeting exon3 (PRMT7 KO2) and exon4 (PRMT7 KO33), containing the AdoMet MTase I binding site. After 24h, GFP positive cells were single cell sorted. Single cell clones were Sanger sequenced to confirm the mutations. PRMT7 knockout cells for the Molt-4 line were obtained from Synthego (Synthego Corporation, Menlo Park, CA, USA); the bulk cells were single-cell sorted. Single-cell clones were screened for mutations and two different genetic clones (Molt-4 KO11 and KO55) were selected. Western blot and Immunohistoshemistry were used to confirm the decreased level of PRMT7 protein. PRMT7 KO2 clone has 1 nucleotide deletion (chr16:68349960_68349960delC) and the amino acid change H27fs20* resulting an early stop codon. PRMT7 KO33 clone consists of cells having two different deltions of 1 nucleotide (chr16:68358662_68358662delA and chr16:68358663_68358663delC) and amino acid changes D70Afs*11 or D70Efs*11 respectively, resulting the early stop codons. Molt-4 KO11 clone consists of cells having insertion of 2 nucleotides and deletion of 1 nucleotide (chr16:68363063_68363064insGA and chr16:68363064_68363064delG) and amino acid changes T124Rfs*3 or T124Lfs*2 respectively, resulting the early stop codons. Molt-4 KO55 clone consists of cells having insertion of 8 nucleotides and deletion of 2 nucleotide (chr16:68363066_68363072insAGCCCCAG and chr16:68363066_68363067delCT) and amino acid changes V128Afs*4 or T127Sfs*6 respectively, resulting the early stop codons.

tag: replicate

value: Molt-4  T-ALL

value: PRMT7 KO11


title: Molt-4 PRMT7 KO55 repl. 3

description: T-ALL cells

value: PRMT7 KO55


title: Molt-4 PRMT7 KO55 repl. 1

description: T-ALL cells


title: RPE1 Dam-H3K27me3MUT (set2.samplenr_016) DamID


title: Func119_T2

description: Tumor biopsy


title: Func115_T1

description: Tumor biopsy


title: RPE1 Dam126-H3K27me3 (set4.samplenr_009) DamID


title: 8x pooled E17 SCN, maternal SCN after sham surgery, ad libitum fed mother killed at time 6

city: Prague 4

first: Martin

last: Sládek

address: Videnska 1083

country: Czech Republic

institute: Institute of Physiology of the Czech Academy of Sciences

data_processing:
nf-core/rnaseq workflow pipeline
Reads were mapped to the latest UCSC rn6 (RGSC Rnor_6.0) rat genome assembly by HISAT2 v.2.1.0
FPKM were calculated by Salmon and Stringtie
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: comma-delimited csv file includes read counts for each sample

organism: Rattus norvegicus

source_name: 8x pooled E17 SCN

extract_protocol:
Fetal SCN samples collected at each of the 8 time points (time 0-21) were pooled from the same mother (n = 8 for Group A, n = 5-10 for Group B). RNA was isolated by RNeasy Micro Kit (Qiagen, Germany) according to manufacturer’s instructions, treated with On-Column DNAse I digestion set (Sigma) for 15 minutes at 37°C, then quantified by spectrophotometry. RNA integrity was tested by capillary electrophoresis (Agilent Tech., USA).
RNA libraries were prepared for sequencing by rRNA depletion, polyA RNA enrichment and using Smarter Stranded low input tot-RNA-Seq kit v2 (Takara, Japan).
Illumina NextSeq 500/550 High output kit v2 (150 cycles, SE)

value: Wistar

tag: tissue

value: suprachiasmatic nuclei (SCN)

tag: circadian time

value: 6 hr

tag: developmental stage

value: fetus

value: embryonic age 17

tag: mother treatment

value: SCN sham surgery, ad libitum feeding regime

tag: mother group

value: A


title: Molt-4 PRMT7 KO55 repl. 2

description: T-ALL cells

tag: cell type

tag: genotype


title: Func120_T1

description: Tumor biopsy


title: Func116_T1

description: Tumor biopsy


title: Molt-4 PRMT7 KO11 repl. 2

description: T-ALL cells


title: Molt-4 PRMT7 KO11 repl. 1

description: T-ALL cells


title: Func113_T2

description: Tumor biopsy


title: Func116_T2

description: Tumor biopsy


title: Func111_T1

description: Tumor biopsy


title: Func114_T1

description: Tumor biopsy


title: Func114_T2

description: Tumor biopsy


title: Func117_T2

description: Tumor biopsy


title: Func119_T1

description: Tumor biopsy


title: RPE1 H3K27me3-Dam (set2.samplenr_020) DamID

tag: cell line

tag: dam-fusion protein

tag: dam type

value: DamWT


title: Func113_T1

description: Tumor biopsy

tag: histology

tag: d'amico risk classification


title: Func109_T2

description: Tumor biopsy

tag: tumor gleason score pathology

tag: tumor isup grade group


title: RPE1 Dam-H3K27me3 (set2.samplenr_019) DamID


title: Func109_T1

description: Tumor biopsy

tag: pathological tumor stage

tag: lymph node status


title: Molt-4 PRMT7 WT repl. 2

description: T-ALL cells

tag: replicate

value: PRMT7 WT


title: RPE1 Dam126-H3K27me3 (set2.samplenr_015) DamID


title: Molt-4 PRMT7 WT repl. 1

description: T-ALL cells


title: RPE1 Dam-H3K27me3 (set2.samplenr_013) DamID


title: Func111_T2

description: Tumor biopsy

tag: rna isolation kit


title: Func108_T1

description: Tumor biopsy


title: Jurkat Cas9 PRMT7 KO33 repl. 3

description: T-ALL cells

source_name: Jurkat Cas9 cell line

value: Jurkat-Cas9 T-ALL

value: PRMT7 KO33


title: Func108_T2

description: Tumor biopsy


title: RPE1 Dam-H3K27me3 (set5.samplenr_030) DamID

value: anti-H3K27me3 (mintbody)


title: RPE1 H3K27me3-Dam (set9.samplenr_023) DamID


title: Molt-4 PRMT7 WT repl. 3

description: T-ALL cells


title: Func106_T1

description: Tumor biopsy

value: Adeno carcinoma


title: Func104_T1

description: Tumor biopsy

value: miRNeasy


title: Jurkat Cas9 PRMT7 KO33 repl. 1

description: T-ALL cells


title: Func105_T1

description: Tumor biopsy


title: Jurkat Cas9 PRMT7 KO33 repl. 2

description: T-ALL cells


title: Func104_T2

description: Tumor biopsy


title: Func100_T2

description: Tumor biopsy


title: RPE1 H3K27me3-Dam (set2.samplenr_014) DamID


title: Jurkat Cas9 PRMT7 KO2 repl. 3

description: T-ALL cells

value: PRMT7 KO2


title: RPE1 Dam-H3K27me3 (set8.samplenr_014) DamID


title: Func100_T1

description: Tumor biopsy


title: Func096_T1

description: Tumor biopsy


title: Func098_T1

description: Tumor biopsy


title: RPE1 Dam-H3K27me3 (set14.samplenr_005) DamID


title: Jurkat Cas9 PRMT7 KO2 repl. 2

description: T-ALL cells


title: RPE1 Dam-H3K27me3 (set8.samplenr_013) DamID


title: Func095_T1

description: Tumor biopsy


title: WTPALM4

value: Hepatic progenitor cells

tag: agent

value: Palmitic acid 400 microM 8h


title: Jurkat Cas9 PRMT7 KO2 repl. 1

description: T-ALL cells


title: RPE1 H3K27me3-Dam (set9.samplenr_022) DamID


title: Transwell

city: Austin

first: Song

last: Yi

state: TX

address: 1601 Trinity Street, Building B

institute: The University of Texas at Austin

data_processing:
Alignment and bc-umi counting using CellRanger 3.0.2
Assembly: GRCh38
Supplementary files format and content: filtered feature bc matrix (sparse matrix)

source_name: Caco-2 cell

growth_protocol: Caco-2 cells were cultured in a gut-on-a-chip for 7 days in DMEM supplmented with 20% fetal bovine serum and antibiotics (penicillin and streptomycin) under medium flow (50 µL/h) and stretching motion (10% strain and 0.15 Hz frequency). Caco-2 cells were cultured in Transwell inserts in the same culture medium under a static culture condition for 7 days.

extract_protocol: Single cell suspension were run through Chromium (10x Genomic) using the Single Cell 3' Reagent Kit v3, following the manufacturer's protocol

value: adenocarcinoma epithelium

tag: treatment

value: No treatment

tag: culture method

value: Transwell


title: Func093_T1

description: Tumor biopsy


title: RPE1 H3K27me3-Dam (set9.samplenr_024) DamID


title: Func099_T1

description: Tumor biopsy


title: Chip

value: Chip


title: Func091_T2

description: Tumor biopsy


title: Func088_T2

description: Tumor biopsy


title: Func094_T2

description: Tumor biopsy


title: U87-OE-2(MEOX2 OE-2)

city: suzhou

first: Ji

last: Wang

address: 1055 Sanxiang Road, Gusu District

country: China

institute: Soochow University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz.
Differential expression analysis of two conditions was performed using the DESeq2 R package (1.26.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include count and FPKM values for each Sample

source_name: human glioma cell line

growth_protocol: Cells were grown in Dulbecco's Modified Eagle's Medium (DMEM) with 10% fetal bovine serum (FBS) and kept at 37°C in a humidified condition with 5% CO2.

extract_protocol:
Total RNA was extracted by using TRIzol (Invitrogen) according to the manufacturer's instructions.
A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. MRNA was purified from total RNA using poly-T oligo-attached magnetic beads. The library preparations were sequenced on an Illumina HiSeq 4000 platform by Shanghai Life Genes Biotech Co. Ltd (Shanghai, China), and 150 bp paired-end reads were generated.

treatment_protocol: SNB19 cells were transfected with siRNA by Lipofectamine 3000; U87 cells were transfected with lentivirals by polybrene.

value: transfected with MEOX5 overexpression lentivirals


title: Func087_T2

description: Tumor biopsy


title: Func092_T1

description: Tumor biopsy


title: Func088_T1

description: Tumor biopsy


title: RPE1 Dam-H3K27me3 (set14.samplenr_004) DamID


title: RPE1 Dam126-only (set4.samplenr_013) DamID

value: untethered Dam


title: Func086_T1

description: Tumor biopsy


title: Func085_T1

description: Tumor biopsy


title: U87-OE-1(MEOX2 OE-2)

value: transfected with MEOX4 overexpression lentivirals


title: Func089_T1

description: Tumor biopsy


title: U87-EV-2(MEOX2 EV-2)

value: transfected with MEOX3 empty vector lentivirals


title: U87-EV-1(MEOX2 EV-1)

value: transfected with MEOX2 empty vector lentivirals


title: RPE1 Dam126-only (set4.samplenr_014) DamID


title: SNB19-m3-3(siMEOX2-3)

value: transfected with MEOX2 siRNA


title: RPE1 Dam-H3K27me3 (set14.samplenr_006) DamID

value: DamWT


title: RPE1 Dam-only (set5.samplenr_019) DamID


title: SNB19-m3-2(siMEOX2-2)


title: RPE1 Dam-only (set8.samplenr_016) DamID


title: Func085_T2

description: Tumor biopsy


title: SNB19-m3-1(siMEOX2-1)


title: RPE1 Dam-only (set14.samplenr_002) DamID


title: SNB19-NC-3(NC-3)

value: transfected with Scramble siRNA


title: RPE1 Dam-only (set11.samplenr_033) DamID


title: Func083_T2

description: Tumor biopsy

value: Adeno carcinoma


title: Func082_T1

description: Tumor biopsy

value: miRNeasy


title: Func076_T2

description: Tumor biopsy


title: SNB19-NC-2(NC-2)


title: Func078_T1

description: Tumor biopsy


title: Func072_T2

description: Tumor biopsy


title: RPE1 Dam-only (set11.samplenr_032) DamID


title: RPE1 Dam-only (set5.samplenr_021) DamID


title: Func080_T1

description: Tumor biopsy


title: Func078_T2

description: Tumor biopsy


title: Func082_T2

description: Tumor biopsy


title: Func081_T2

description: Tumor biopsy


title: Func068_T1

description: Tumor biopsy


title: Func069_T2

description: Tumor biopsy


title: Func079_T1

description: Tumor biopsy


title: Func071_T1

description: Tumor biopsy


title: Func076_T1

description: Tumor biopsy


title: Func075_T1

description: Tumor biopsy


title: Func062_T2

description: Tumor biopsy


title: Func081_T1

description: Tumor biopsy


title: RPE1 Dam-only (set8.samplenr_015) DamID


title: SNB19-NC-1(NC-1)


title: RPE1 Dam-only (set14.samplenr_003) DamID


title: RPE1 Dam-only (set11.samplenr_031) DamID


title: RPE1 Dam-Cbx7_3 (set3.samplenr_020) DamID

value: Cbx7 (chromodomain trimer)


title: Control, patient 16

city: Rochester

first: Tao

last: Ma

state: MN

address: 200 First St. SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by STAR (https://github.com/alexdobin/STAR)
Gene counts were generated using Subread featureCounts (http://subread.sourceforge.net/)
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include Raw counts and FPKM values for each gene per sample

source_name: Lymph node

extract_protocol:
Total RNA was extracted from cryosections of residual O.C.T.-embedded/fresh-frozen biopsy aliquots, using miRNeasy Mini Kit (Qiagen, Germantown, MD) and a QIAcube automated handler (Qiagen).
cDNA libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA). Libraries were amplified on an Illumina CBot automated cluster generator and sequenced as 100 X 2 paired end reads on an Illumina HiSeq 4000.

tag: group

value: Control lymph node

tag: disease subtype


title: Control, patient 17


title: Control, patient 19


title: Control, patient 18


title: RPE1 Dam-Cbx7_3 (set3.samplenr_002) DamID


title: Func069_T1

description: Tumor biopsy


title: Control, patient 15


title: Func062_T1

description: Tumor biopsy


title: RPE1 Dam-Cbx7_3 (set3.samplenr_019) DamID


title: RPE1 Dam-Cbx7_3 (set3.samplenr_001) DamID


title: Func066_T1

description: Tumor biopsy


title: Func059_T2

description: Tumor biopsy


title: Func058_T4

description: Tumor biopsy


title: Func061_T1

description: Tumor biopsy


title: Control, patient 11


title: Control, patient 13


title: RPE1 Dam-Cbx7_3 (set14.samplenr_017) DamID


title: Func057_T1

description: Tumor biopsy


title: Control, patient 14


title: Func056_T1

description: Tumor biopsy


title: Func057_T2

description: Tumor biopsy


title: Func052_T2

description: Tumor biopsy


title: Control, patient 12


title: Func050_T2

description: Tumor biopsy


title: Func056_T2

description: Tumor biopsy


title: Func051_T1 reanalysis

description:
Tumor biopsy
GSM1348792

value: RNeasy


title: RPE1 Dam-Cbx7_3 (set8.samplenr_001) DamID


title: Func052_T1 reanalysis

description:
Tumor biopsy
GSM1348793


title: Func050_T1 reanalysis

description:
Tumor biopsy
GSM1348791


title: Func053_T2 reanalysis

description:
Tumor biopsy
GSM1348794


title: Control, patient 10


title: Func061_T2

description: Tumor biopsy


title: RPE1 Dam-Cbx7_3 (set8.samplenr_002) DamID


title: RPE1 Dam-Cbx7_3 (set14.samplenr_018) DamID


title: Control, patient 9


title: RPE1 Dam-Cbx7_3 (set14.samplenr_016) DamID


title: Control, patient 7


title: RPE1 Cbx1_full-Dam (set14.samplenr_029) DamID

value: Cbx1 (full protein)


title: Control, patient 8


title: Func049_T1 reanalysis

description:
Tumor biopsy
GSM1348790


title: RPE1 Cbx1_full-Dam (set14.samplenr_030) DamID


title: Func047_T2

description: Tumor biopsy


title: Func047_T1 reanalysis

description:
Tumor biopsy
GSM1348788


title: Func046_T2

description: Tumor biopsy


title: Func046_T1

description: Tumor biopsy


title: Func048_T1 reanalysis

description:
Tumor biopsy
GSM1348789


title: Func045_T1 reanalysis

description:
Tumor biopsy
GSM1348787


title: Control, patient 6


title: Func044_T1 reanalysis

description:
Tumor biopsy
GSM1348786


title: Control, patient 5


title: RPE1 Cbx1_full-Dam (set14.samplenr_027) DamID


title: RPE1 Dam-Cbx1_3 (set10.samplenr_006) DamID

value: Cbx1 (chromodomain trimer)


title: Func043_T1 reanalysis

description:
Tumor biopsy
GSM1348785


title: Func043_T2

description: Tumor biopsy


title: Control, patient 4


title: Control, patient 3


title: RPE1 Dam-Cbx1_3 (set10.samplenr_004) DamID


title: RPE1 Dam-Cbx1_3 (set1.samplenr_011) DamID


title: Control, patient 2


title: Func042_T2

description: Tumor biopsy


title: Func039_T1 reanalysis

description:
Tumor biopsy
GSM1348782


title: Func040_T2 reanalysis

description:
Tumor biopsy
GSM1348783


title: Func042_T1 reanalysis

description:
Tumor biopsy
GSM1348784


title: Func037_T2 reanalysis

description:
Tumor biopsy
GSM1348780


title: Func036_T2 reanalysis

description:
Tumor biopsy
GSM1348779


title: Func038_T1 reanalysis

description:
Tumor biopsy
GSM1348781


title: RPE1 Dam-Cbx1_3 (set10.samplenr_005) DamID


title: RPE1 Dam-Cbx1_2 (set7.samplenr_015) DamID

value: Cbx1 (chromodomain dimer)


title: Func036_T1

description: Tumor biopsy


title: Control, patient 1


title: Unicentric Castleman, patient 19, sample 1

value: Castleman disease

value: Unicentric

value: Mixed


title: Func040_T1

description: Tumor biopsy


title: RPE1 Dam-Cbx1_2 (set14.samplenr_023) DamID


title: Func035_T1 reanalysis

description:
Tumor biopsy
GSM1348778


title: Unicentric Castleman, patient 22


title: RPE1 Dam-Cbx1_2 (set7.samplenr_014) DamID


title: Unicentric Castleman, patient 21

value: Hyaline-vascular


title: Func034_T2 reanalysis

description:
Tumor biopsy
GSM1348777


title: Func034_T1

description: Tumor biopsy


title: Func033_T1 reanalysis

description:
Tumor biopsy
GSM1348776


title: Func033_T2

description: Tumor biopsy


title: RPE1 Dam-Cbx1_2 (set14.samplenr_024) DamID


title: Func032_T2 reanalysis

description:
Tumor biopsy
GSM1348775


title: Unicentric Castleman, patient 20, sample 2


title: Func031_T2 reanalysis

description:
Tumor biopsy
GSM1348774


title: Unicentric Castleman, patient 20, sample 1


title: Func030_T2

description: Tumor biopsy


title: RPE1 Dam-Cbx1_2 (set14.samplenr_022) DamID


title: Unicentric Castleman, patient 19, sample 2


title: Func031_T1

description: Tumor biopsy


title: Func032_T1

description: Tumor biopsy


title: Unicentric Castleman, patient 18


title: Unicentric Castleman, patient 17


title: human RPE1 Input2 ChIP-seq

data_processing:
Reads were aligned using bowtie2  (v. 2.3.3.1) with the following parameters: “--seed 42 --very-sensitive -N 1”.
Indexes for the alignments were then generated using “samtools index” and genome coverage tracks were computed using the “bamCoverage” utility from DeepTools with the following parameters: “--ignoreDuplicates --minMappingQuality 10”.
For marks that exist in broad domains in the genome, domains were called using MUSIC according to the suggested workflow (https://github.com/gersteinlab/MUSIC). For marks that form narrow peaks in the genome, peaks were called using MACS2 (v. 2.1.1.20160309) using the “macs2 callpeak” utility with the following parameters: “-q 0.05”.
Genome_build: mm10 (mouse) / hg19 (human)
Supplementary_files_format_and_content: bedGraph files were generated using DeepTools and contain the unnormalized, deduplicated read counts across the genome at a resolution indicated by the bin size.
Supplementary_files_format_and_content: broadPeak files were generated using MUSIC and indicate domains of enriched signal for the given mark.
Supplementary_files_format_and_content: narrowPeak files were generated using MACS2 and indicate peaks of enriched signal for the given mark.

source_name: human RPE-1 cells

growth_protocol: Human hTERT-immortalized RPE-1 cells were grown in DMEM: F12 supplemented with 10% fetal bovine serum and 1% Pen/Strep (100 U/mL penicillin and 100 ug/mL streptomycin). Mouse embryonic stem cells were cultured on mouse embryonic fibroblasts and replated on 0.1% gelatin for two passages before harvest.

extract_protocol:
Cells were harvested by trypsinization, and chemically crosslinked with fresh formaldehyde solution (1% in PBS) for 8 minutes while rotating at room temperature. Crosslinking was quenched with glycine on ice. Cells were then lysed, sonicated, treated with RNase A and Proteinase K to reverse the crosslink, and cleared using DNA purification columns. Chromatin was incubated with antibodies, after which beads were added for antibody binding. After extensive washing, samples were cleared using purification columns and eluate was measured.
Libraries were prepared according to the Illumina TruSeq DNA LT kit and sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

tag: chip antibody


title: human RPE1 Input1 ChIP-seq

tag: cell line


title: human RPE1 H4K20me1 ChIP-seq

value: H4K20me1 (Abcam ab9051)


title: Unicentric Castleman, patient 16


title: human RPE1 H3K9me3 ChIP-seq

value: H3K9me3 (abcam ab8898)


title: Func029_T2

description: Tumor biopsy


title: Func027_T2 reanalysis

description:
Tumor biopsy
GSM1348770


title: Func029_T1 reanalysis

description:
Tumor biopsy
GSM1348772


title: Func026_T1

description: Tumor biopsy


title: Func028_T1

description: Tumor biopsy


title: Func024_T1

description: Tumor biopsy


title: Unicentric Castleman, patient 15


title: human RPE1 H3K9ac ChIP-seq

value: H3K9ac (Abcam ab4441)


title: Func028_T2 reanalysis

description:
Tumor biopsy
GSM1348771


title: Func037_T1

description: Tumor biopsy


title: Func026_T2 reanalysis

description:
Tumor biopsy
GSM1348769


title: Func030_T1 reanalysis

description:
Tumor biopsy
GSM1348773


title: Func022_T1

description: Tumor biopsy


title: Unicentric Castleman, patient 13


title: Func024_T2 reanalysis

description:
Tumor biopsy
GSM1348768


title: Unicentric Castleman, patient 14


title: Func023_T1 reanalysis

description:
Tumor biopsy
GSM1348767


title: human RPE1 H3K4me3 ChIP-seq

value: H3K4me3 (Abcam ab8580)


title: Unicentric Castleman, patient 11


title: Func020_T2 reanalysis

description:
Tumor biopsy
GSM1348764


title: human RPE1 H3K36me3 ChIP-seq

value: H3K36me3 (Active Motif 61902)


title: HEK_5_TT_Seq_alpha_amanitin

city: Oxford

first: Jane

last: Mellor

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

description: Sample 11

data_processing:
Paired-end sequencing reads were quality-checked with fastqc and then trimmed using Trim-Galore to remove sequences with a quality below a Q score of 20. Trimmed reads were then aligned to the human genome (hg38 assembly) with hisat2 (Kim et al., 2015) using the –no-mixed and the -no-discordant flags. Aligned files in the sam format were then filtered using samtools (Li et al., 2009) with the flags -q 40, -f 99, -F3852, -bS. Calibration of samples was achieved by calculating scaling factors of spike-in counts between samples based on counts tables generated by the bioconductor pack- age featureCounts. Bedgraph and bigwig files were generated from bam files using bedtools and wigTobigWig (UCSC Genome Browser), respectively
genome build: hg38
Supplementary_files_format_and_content: bw

source_name: Human Embryonic Kidney

growth_protocol: HeLa and HEK293 cells were cultured in DMEM supplemented with 10 % (v/v) FBS and 1 % (v/v) Penicillin-Streptomycin. The incubator was set at 37 ◦C at 5 % CO2. Cells were passaged 24 hours before harvesting for next-generation sequencing ex- periments at which point they were grown to 80 % confluency. Cells were counted on a Nexcelom Biosciences Auto 2000 Cell Counter

extract_protocol:
Cells were washed rapidly in PBS before adding 0.7 mL QIAZOL per 10 million cells. The cells were scraped off into 2mL Eppendorffs, vortexed for 10 s and placed on ice for 10 minutes. If required for comparative calibration, 2.4 ng of thio-labelled RNA spike-ins per 1 million cells were added at this stage. Total RNA was purified by adding 320 µL chloroform, vortexing for 10 s, incubating at room temperature for 3 minutes, and centrifugation at 4 ◦C for 15 minutes at 12000 rpm. The upper phase was transferred to a new Eppendorf with 800 uL isopropanol. The sample was left at room temperature for 5 minutes before centrifugation at 4 ◦C for 15 minutes at 15000 rpm. After removing the supernatant, the pellet was washed 3 times in 320 uL 75% ethanol (prepared freshly), with centrifugation at 4 ◦C for 15 minutes at 15000 rpm. The pellet was then air-dried for 10 minutes before dissolving in 160 µL RNAse-free water. At this stage samples were frozen at -80 ◦C. RNA amounts were checked with Nanodrop. 300 µg of total RNA in 400 µL water were chilled on ice for 10 minutes. Samples were sonicated in a Bioruptor at the ’HIGH’ setting for 1 cycle at 30s on / 30 s off. Samples were split equally into two Eppendorfs, incubated at 65 ◦C for 10 minutes, and then on ice for 5 minutes. After quick-spinning, 300 µL RNase-free water, 100 µL 10x Biotinylation Buffer (100 mM Tris pH 7.5, 1m mM EDTA pH 8.0), 200 µL DMF, and 200 mL EZ-link HPDP Biotin in DMF (1mg / mL, stored in the dark at 4 ◦C). Incubate in the dark at room temperature for 2 hours with shaking at 800 rpm. RNA was purified using Phase-Lock tubes and resuspended in 100 µL RNase-free water. Samples were pooled back together. For thio-labelled RNA separation, a wash buffer (100 mM Tris pH 7.5, 10 mM EDTA pH 8.0, 1 M NaCl, 0.1 % Tween-20) was prepared freshly – one kept at room temperature (RT-WB), and one at 65 ◦C (65-WB). 100 µL uMACS streptavidin beads were added to 200 µL RNA-Biotin and incubated in a thermomixer at 4 ◦C for 15 minutes at 800 rpm. During this time, the uMACS magnetic stand and rack were prepared alongside a drainer. uMACS columns were placed into the magnetic rack and equilibrated with 900 µL RT-WB for 10 minutes. The biotin-RNA-bead mix was added to the uMACS column. The flow-through was collected and re-loaded to the columns. The second flow-through was discarded. Columns were washed 3 times with 900 µL of 65-WB and then 3 times with 900 µL RT- WB. Elution of labelled RNA was carried out with 100 µL 100 mM DTT. After 5 minutes, elution was performed again with an additional 100 uL 100 mM DTT. Samples were then immediately carried through for RNA purification using the miRNeasy kit. RNA was eluted with 15 µL RNase-free water. Quality and quantity of thiolabelled RNA was checked using the Agilent Bioanalyzer with an RNA pico chip.
Sequencing libraries were prepared using the NEBNext rRNA Depletion kit for Hu- man Cells followed by the NEBNext II Ultra Directional RNA Library prep kit, following both kit instructions. Library quality was assessed using the Agilent Bioanalyzer with a DNA-High Sensitivity chip. Pooled libraries were sequenced on the Illumina NextSeq 500 platform using the High-Output Illumina Nextseq 500 kit.
Thiolabelled spike-ins were generated by amplifying 3 1000-bp long DNA frag- ments from genomic yeast DNA with a 42 % GC content, covering the genes bat2, hxt1, and gal1 using forward primers containing the T7 promoter sequence. The PCR product was purified and then transcribed in vitro following the MEGAscript T7 tran- scription kit instructions, using a thio-UTP to UTP ratio of 1:5.

treatment_protocol: For alpha-amanitin treatment, 60 million cells were incubated with or without 25 µg / mL alpha-amanitin for 6 hours at 37 ◦C before incubation with 500 µM 4sU for 5 minutes

value: alpha-amanitin treament to inhbit PolII not PolIII

tag: protocol

value: TT-Seq, 5 minute labelling after treatment with alpha-amanitin for 6 hours at 25ug/mL

tag: fraction

value: Nascent RNA


title: Func019_T2

description: Tumor biopsy

tag: histology

value: Adeno carcinoma

value: miRNeasy


title: Unicentric Castleman, patient 12


title: Func021_T2 reanalysis

description:
Tumor biopsy
GSM1348765

tag: d'amico risk classification

value: RNeasy


title: Func015_T2

description: Tumor biopsy

tag: tumor gleason score pathology


title: Func016_T1 reanalysis

description:
Tumor biopsy
GSM1348761

tag: tumor isup grade group


title: Unicentric Castleman, patient 9


title: Func020_T1

description: Tumor biopsy

tag: pathological tumor stage


title: Func019_T1 reanalysis

description:
Tumor biopsy
GSM1348763

tag: lymph node status


title: HEK_5_TT_Seq_untreated

description: Sample 10

value: Untreated Control

value: TT-Seq, 5 minute labelling after 6 hours control treatment a-amanitin for 6 hours at 25ug/mL


title: Unicentric Castleman, patient 10

value: Castleman disease


title: Func015_T1 reanalysis

description:
Tumor biopsy
GSM1348760


title: Func018_T1 reanalysis

description:
Tumor biopsy
GSM1348762


title: HEK_20_TT_Seq repeat 2

description: Sample 9

treatment_protocol: For TT-Seq labelling, 60 million cells per sample were incubated with 500 µM 4sU

value: Untreated

value: TT-Seq, 20 min labelling


title: Unicentric Castleman, patient 8

value: Unicentric

value: Hyaline-vascular


title: Unicentric Castleman, patient 7


title: HEK_20_TT_Seq repeat 1

description: Sample 8


title: HEK_15_TT_Seq repeat 2

description: Sample 7

value: TT-Seq, 15 min labelling


title: Func014_T1 reanalysis

description:
Tumor biopsy
GSM1348759


title: Func013_T1

description: Tumor biopsy


title: Func011_T2

description: Tumor biopsy


title: Func009_T1 reanalysis

description:
Tumor biopsy
GSM1348756


title: Func012_T2 reanalysis

description:
Tumor biopsy
GSM1348757


title: Func013_T2 reanalysis

description:
Tumor biopsy
GSM1348758


title: HEK_15_TT_Seq repeat 1

description: Sample 6


title: Func006_T2

description: Tumor biopsy


title: Func009_T2

description: Tumor biopsy


title: human RPE1 H3K27me3 ChIP-seq

value: H3K27me3 (Merck Millipore 07-449)


title: Func006_T1 reanalysis

description:
Tumor biopsy
GSM1348754


title: HEK_10_TT_Seq repeat2

description: Sample 5

extract_protocol:
Cells were washed rapidly in PBS before adding 0.7 mL QIAZOL per 10 million cells. The cells were scraped off into 2mL Eppendorffs, vortexed for 10 s and placed on ice for 10 minutes. If required for comparative calibration, 2.4 ng of thio-labelled RNA spike-ins per 1 million cells were added at this stage. Total RNA was purified by adding 320 µL chloroform, vortexing for 10 s, incubating at room temperature for 3 minutes, and centrifugation at 4 ◦C for 15 minutes at 12000 rpm. The upper phase was transferred to a new Eppendorf with 800 uL isopropanol. The sample was left at room temperature for 5 minutes before centrifugation at 4 ◦C for 15 minutes at 15000 rpm. After removing the supernatant, the pellet was washed 3 times in 320 uL 75% ethanol (prepared freshly), with centrifugation at 4 ◦C for 15 minutes at 15000 rpm. The pellet was then air-dried for 10 minutes before dissolving in 160 µL RNAse-free water. At this stage samples were frozen at -80 ◦C. RNA amounts were checked with Nanodrop. 300 µg of total RNA in 400 µL water were chilled on ice for 10 minutes. Samples were sonicated in a Bioruptor at the ’HIGH’ setting for 1 cycle at 30s on / 30 s off. Samples were split equally into two Eppendorfs, incubated at 65 ◦C for 10 minutes, and then on ice for 5 minutes. After quick-spinning, 300 µL RNase-free water, 100 µL 10x Biotinylation Buffer (100 mM Tris pH 7.5, 1m mM EDTA pH 8.0), 200 µL DMF, and 200 mL EZ-link HPDP Biotin in DMF (1mg / mL, stored in the dark at 4 ◦C). Incubate in the dark at room temperature for 2 hours with shaking at 800 rpm. RNA was purified using Phase-Lock tubes and resuspended in 100 µL RNase-free water. Samples were pooled back together. For thio-labelled RNA separation, a wash buffer (100 mM Tris pH 7.5, 10 mM EDTA pH 8.0, 1 M NaCl, 0.1 % Tween-20) was prepared freshly – one kept at room temperature (RT-WB), and one at 65 ◦C (65-WB). 100 µL uMACS streptavidin beads were added to 200 µL RNA-Biotin and incubated in a thermomixer at 4 ◦C for 15 minutes at 800 rpm. During this time, the uMACS magnetic stand and rack were prepared alongside a drainer. uMACS columns were placed into the magnetic rack and equilibrated with 900 µL RT-WB for 10 minutes. The biotin-RNA-bead mix was added to the uMACS column. The flow-through was collected and re-loaded to the columns. The second flow-through was discarded. Columns were washed 3 times with 900 µL of 65-WB and then 3 times with 900 µL RT- WB. Elution of labelled RNA was carried out with 100 µL 100 mM DTT. After 5 minutes, elution was performed again with an additional 100 uL 100 mM DTT. Samples were then immediately carried through for RNA purification using the miRNeasy kit. RNA was eluted with 15 µL RNase-free water. Quality and quantity of thiolabelled RNA was checked using the Agilent Bioanalyzer with an RNA pico chip.
Sequencing libraries were prepared using the NEBNext rRNA Depletion kit for Human Cells followed by the NEBNext II Ultra Directional RNA Library prep kit, following both kit instructions. Library quality was assessed using the Agilent Bioanalyzer with a DNA-High Sensitivity chip. Pooled libraries were sequenced on the Illumina NextSeq 500 platform using the High-Output Illumina Nextseq 500 kit.
Thiolabelled spike-ins were generated by amplifying 3 1000-bp long DNA frag- ments from genomic yeast DNA with a 42 % GC content, covering the genes bat2, hxt1, and gal1 using forward primers containing the T7 promoter sequence. The PCR product was purified and then transcribed in vitro following the MEGAscript T7 tran- scription kit instructions, using a thio-UTP to UTP ratio of 1:5.

value: TT-Seq, 10 min labelling


title: Func005_T2

description: Tumor biopsy


title: Unicentric Castleman, patient 5


title: Func004_T1 reanalysis

description:
Tumor biopsy
GSM1348752


title: Multicentric Castleman, patient 7

value: Multicentric

value: plasma cell


title: BM72

city: Dublin

first: Leonie

middle: S

last: Young

state: Dublin

address: York House, York Street,, Dublin 2

country: Ireland

institute: Royal College of Surgeons in Ireland

data_processing:
Salmon (v.0.91) was used to perform quasi-mapping of sequencing reads, with seqBias and gcBias corrections enabled, using a 31bp k-mer index of the GRCh38.p10 (GENCODE v.27) human reference transcripts, to estimate transcript abundance for each sample
Tximport package was used to import transcript abundance estimates from quant.sf files, generated by Salmon read mapping into R statistical programming environment for gene expression quantification. Transcript abundance estimates were collapsed to gene level gene expression counts. TXI data objects for MAYO and PITT-RCSI RNA-Seq cohort, containing unprocessed Salmon read counts, transcript per million (TPM) and gene length values were combined for subsequent downstream analysis.
Genes with little to no expression across all 90 samples were filtered if gene TPM < 0.5 in at least 10% of all samples (N=90)
Filtered gene level counts were normalized with edgeR calcNormFactors() and cpm() function, where counts per million (CPM): CPM = C * 106/N (counts (C) scaled by the library depth in million units). A log2 transformation was applied to CPM: log2(CPM +1), where 1 is a pseudocount added to prevent negative value counts. Filtered log2 CPM and TPM genes were annotated using biomaRt R package to identify protein coding genes using the ENSEMBL GRCh38 p.10 database.
In order to correct for between RNA-Seq cohort (MAYO, PITT-RCSI) batch driven effect, filtered protein coding gene expression counts were used as input to svaseq R package for batch effect assessment. A multiple linear regression model was fit for each surrogate variable (SV), with the following independent predictors: sequencing batch ID [1,5], disease status (primary breast (P) / brain metastases (M)), estrogen receptor (ER) IHC status (ER+/ER-) and primary tumor histological subtype (DCIS, IDC, ILC, Mixed ILC/IDC). A linear model fitted using SV1 was found to be significantly associated with sequencing batch (P < 0.05; R2 ~0.70).   As such, in order to correct for between RNA-Seq cohort (MAYO, PITT-RCSI) batch driven effect, removeBatchEffect() function in LIMMA package in R, was used with SV1, to adjust gene expression values to account for mean shifts in expression driven by the batch driven effect.
Genome_build: GRCh38.p10 (GENCODE v.27)
Supplementary_files_format_and_content: rna_seq_batch_corrected_log2_TMM_normalized_CPM_protein_coding_genes.xlsx  (Excel spread sheet containing batch corrected log2 TMM normalized CPM proteing coding gene expression values for all 90 samples)

source_name: Brain Metastatic Tumor

extract_protocol: 100 ng of RNA and Illumina’s TruSeq RNA Access Library Preparation protocol

tag: cohort

value: PITT-RCSI

tag: patientid

tag: tissue

value: brain metastatic tumor


title: BP7

source_name: Primary Breast Tumor

value: primary breast tumor


title: Func008_T2 reanalysis

description:
Tumor biopsy
GSM1348755

value: Adeno carcinoma

tag: rna isolation kit


title: Func002_T2 reanalysis

description:
Tumor biopsy
GSM1348750

value: RNeasy


title: Func005_T1 reanalysis

description:
Tumor biopsy
GSM1348753


title: Unicentric Castleman, patient 4


title: HEK_10_TT_Seq repeat1

description: Sample 4

data_processing:
Paired-end sequencing reads were quality-checked with fastqc and then trimmed using Trim-Galore to remove sequences with a quality below a Q score of 20. Trimmed reads were then aligned to the human genome (hg38 assembly) with hisat2 (Kim et al., 2015) using the –no-mixed and the -no-discordant flags. Aligned files in the sam format were then filtered using samtools (Li et al., 2009) with the flags -q 40, -f 99, -F3852, -bS. Calibration of samples was achieved by calculating scaling factors of spike-in counts between samples based on counts tables generated by the bioconductor package featureCounts. Bedgraph and bigwig files were generated from bam files using bedtools and wigTobigWig (UCSC Genome Browser), respectively.
genome build: hg38
Supplementary_files_format_and_content: bw

tag: treatment

value: Nascent RNA


title: Unicentric Castleman, patient 3

tag: group

value: Mixed


title: Unicentric Castleman, patient 6

value: Castleman disease

tag: disease subtype


title: Unicentric Castleman, patient 2


title: PL_size_selected_SNU_WT

description: Sample 3

data_processing:
Fastq files were quality-trimmed with Trim-Galore and aligned with bowtie2. Sorted bam files were generated from aligned sam files using samtools with a filtering step added to only retain reads that have a mapping quality score above 30 (-q 30). As above, 3’ end single basepair resolution was achieved by using the bedtools -bg -3 option when generating bedgraph files.
To generate TSS annotations from the size-selected SNU-Seq samples, 5’ end coverage was generated using the -bg -5 option (instead of -3) when generating bedgraphs from bam files in bedtools. To generate 5’end reads that only occur in nucleosome-depleted regions, ATAC-Seq data in HEK293 cells E-MTAB-6195) were used. The ATAC-Seq fastq files were trimmed with Trim-Galore, aligned with bowtie2, and converted to bam and bed files using samtools and bedtools, respectively.Subsequently, macs2 was used to call peaks (no model assumed). The intersect option in bedtools was then used to retain only those 5’end SNU-Seq (size-selected) signals that are located within ATAC-Seq peaks. The resulting bedgraph files were then used as an input to identify TSS cluster centres using Paraclu which identifies clusters in a sliding window, and a cluster value threshold of 30 was applied. Cluster-centres were calculated using the mean position of the cluster, and TSS candidates were verified in Matlab as follows: Only those TSS candidates were assigned as true TSSs where the summed TT-seq signal (using HEK WT 10 minute- labelled TT-Seq) in the 100 bp downstream of the candidate TSS was at least 5 times greater than in the 100 bp upstream of the candidate TSS. TSScall, a python code, was then used to identify annotated and un-annotated (novel) TSSs using the comprehensive Gencode (v29) annotation file which yielded 2955 previously annotated TSSs and 1428 novel transcription start sites. The read threshold for this was set to 5.
genome build: hg38
Supplementary_files_format_and_content: The four processed files report 5' end reads on the forward and reverse strand and 3' end reads on the forward and reverse strands from the short size selected thiolabelled nascent RNA.

extract_protocol:
Nascent, thio-labelled RNA was generated as described for SNU-Seq without size selection. The nascent RNA was then run on a 3.5 % TBE-Urea gel (8M urea). For this, 250 ng of nascent RNA was mixed with 2x loading dye and boiled for 2 minutes at 80 ◦C. The gel was kept on ice and pre-run for 10 minutes at 80 V, using ice-cold ultra-pure TBE (1x) as the running buffer. Wells of the gel were resuspended with TBE before loading samples. Samples were then run at 80 V for 90 minutes. The gel was transferred onto a square petri dish and incubated in 1x ultra-pure TBE with SYBR Gold (1/10,000 v/v) for 5 minutes. The gel was rinsed twice in 1x ultra-pure TBE before imaging.  For purification of the small nascent RNA fraction, the gel was incubated at -80◦C for 10 minutes. The small band of 70-100 bp size was cut using a razor blade. RNA was extracted from the gel slice using dialysis: The gel slice, along with 0.8 mL 10 mM Tris-HCl (pH 7), was placed into SnakeSkin dialysis membrane sealed by two Eppendorf caps. The dialysis was run for 35 minutes at 80 V. The RNA was then purified with isopropanol precipitation and eluted in 11 µL RNase-free water. Quality and size distribution of the size-selected RNA was checked on the Agilent Bioanalyzer using an RNA pico chip.   The size selected nascent RNA was treated with 5’ Pyrophosphohydrolase (NEB) in ThermoPolQR reaction buffer following the manufacturer’s instructions. The reaction was stopped with 1 µL 500 mM EDTA and heat-inactivated by incubation at 65 ◦C for 5 minutes. RNA was again purified with isopropanol precipitation and resuspended in 6 µL RNase-free water.
The NEBNext Small RNA Library kit for Illumina following the kit instructions. Library quality was assessed with the Agilent Bioanalyzer using a DNA High Sensitivity chip. Sequencing was performed on an Illumina NextSeq 500 platform.
Thiolabelled spike-ins were generated by amplifying 3 1000-bp long DNA frag- ments from genomic yeast DNA with a 42 % GC content, covering the genes bat2, hxt1, and gal1 using forward primers containing the T7 promoter sequence. The PCR product was purified and then transcribed in vitro following the MEGAscript T7 tran- scription kit instructions, using a thio-UTP to UTP ratio of 1:5.

treatment_protocol: For ssSNU-Seq, sufficient cells were incubated with 500 µM 4sU for 10 mins to enable purification of 250ng of nascent thiolabelled RNA.

value: Untreated

value: size-selected SNU-Seq


title: Multicentric Castleman, patient 6


title: Multicentric Castleman, patient 5


title: BP72


title: Multicentric Castleman, patient 4


title: BM68


title: BM7


title: Unicentric Castleman, patient 1

value: Unicentric


title: BP68


title: Multicentric Castleman, patient 3

source_name: Spleen


title: BP64


title: BP71


title: Multicentric Castleman, patient 2


title: BM64


title: Multicentric Castleman, patient 8


title: Multicentric Castleman, patient 1


title: BP62


title: Func001_T1 reanalysis

description:
Tumor biopsy
GSM1348749


title: Func003_T1 reanalysis

description:
Tumor biopsy
GSM1348751


title: Func003_T2

description: Tumor biopsy

value: miRNeasy


title: KMS11 cells_NSC12 12hrs-rep2

city: Brescia

first: Roberto

last: Ronca

address: viale Europa 11

department: Molecular and Translational medicine

country: Italy

institute: University of Brescia

description:
C12_12h_2
replicate 2

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: KMS-11 cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: MM cells were starved (1% FBS) for 24 hours before treatment

extract_protocol: Trizol reagent

treatment_protocol: MM cells were treated with DMSO or NSC12 6 uM for 6 or 12 hrs

tag: cell type

value: Multiple Myeloma cells

tag: agent

tag: time


title: MAYO_BP_9

extract_protocol: 100 ng of total RNA and a TruSeq Stranded Total RNA (Degraded RNA) v2 RNA Exome Library and TS RNA Access capture protocol (Illumina)

value: MAYO


title: KMS11 cells_DMSO 12hrs-rep3

description:
DMSO_12h_3
replicate 3

tag: cell line

value: DMSO


title: KMS11 cells_NSC12 6hrs-rep1

description:
C12_6h_1
replicate 1


title: KMS11 cells_NSC12 12hrs-rep3

description:
C12_12h_3
replicate 3


title: KMS11 cells_NSC12 12hrs-rep1

description:
C12_12h_1
replicate 1


title: KMS11 cells_DMSO 12hrs-rep1

description:
DMSO_12h_1
replicate 1


title: BM62


title: KMS11 cells_DMSO 12hrs-rep2

description:
DMSO_12h_2
replicate 2


title: plasma_exosome_control_rep3

city: Jinan

first: Xinhui

last: Fan

state: Shandong Province

address: 107 Wenhuaxi Road

institute: Qilu Hospital of Shandong University

description: Gene expression data from healthy control

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

source_name: plasma exosome, healthy control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

extract_protocol: Exosomes were isolated from plasma using a previously reported method (Wang et al., 2018). We collected venous blood (10 ml) from each participant using an EDTA-anticoagulated tube. Exosomes were isolated via differential centrifugation using ultracentrifuge (Beckman) and were stored at -80°C. Total RNA was isolated using TRIzol reagent (Life Technologies, Carlsbad, CA, USA) and purified with an RNeasy Mini Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Wistar rats were subjected to four cycles of remote ischemia, and each cycle consisted of 5-minute ischemia and 5-minute reperfusion.

tag: strain

value: Wistar

tag: gender

value: Male

value: plasma exosome

tag: condition

value: healthy control


title: TWSD_3

city: Portland

first: Brett

last: Davis

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

data_processing:
sample quality assessed with FastQC (v 0.11.8)
trimming of low-quality bases and adapter sequences with Trimmomatic (v 0.39)
align trimmed reads to Ensembl Mmul_10 reference genome with STAR (v2.7.0), specifying "quantMode GeneCounts" parameter and supplying Ensembl Mmul10.99 annotation gtf
Genome_build: Mmul10 (Ensembl)
Supplementary_files_format_and_content: raw_counts.txt contains the genes x samples raw counts after STAR alignment

organism: Macaca mulatta

source_name: Blastocyst

growth_protocol: Fresh semen from four adult male rhesus monkeys (aged 10-13 yrs old) with proven fertility, obtained through the ONPRC Assisted Reproductive Technologies (ART) Core, was used for IVF throughout this study. The semen was obtained on the same day as IVF, and the sperm prepared as previously described41 for use at a final concentration of 2x106 sperm/ml in TALP-Complete medium. IVF was performed the evening of the oocyte collection. In brief, sperm samples were treated with cyclic adenosine monophosphate (cAMP; 5 mg/ml) and caffeine (2 mg/ml) 15 minutes (min) before fertilization to induce hyperactivation. Activated sperm (1μl) were added to each well containing an oocyte. The IVF dishes were incubated in 5% CO2 at 37°C for 14-16 hr. Any remaining sperm were removed from fertilized oocytes by gentle micropipetting. Zygotes (N=12) identified by the presence of two pronuclei and/or two polar bodies were randomly selected and transferred to custom EevaTM 12-well polystyrene petri dishes (Progyny, Inc., San Francisco, CA) containing 100 μl of preequilibrated culture medium (IVF Bioscience, UK, BO-IVC) under mineral oil (SageTM, Trumbull, CT) for time-lapse monitoring (TLM) at 37°C with 6% CO2, 5% O2, and 89% N2. The remaining zygotes were transferred to a 10-well IVF dish (LifeGlobal, Guildford, CT) and cultured in the same media as the TLM dish. Media was changed at day 3 post-IVF and the embryos allowed to develop up to day 8 or until they reached the blastocyst stage.

extract_protocol:
COS protocols were performed. Briefly, recombinant human gonadotropins, follicle-stimulating hormone (FSH) and luteinizing hormone (LH), were administered to promote the development of multiple ovarian follicles. Female rhesus macaques were anesthetized for laparoscopic follicular aspirations 36 hours (hr) after a bolus of human chorionic gonadotropin (hCG) was administered to induce events necessary for the re-initiation of meiosis. Two individual follicle aspirates per ovary (N=4 each animal) were collected manually using a low dead space 3ml syringe with a 22-gauge X 1.5inch needle (Ulticare, UltaMed Inc., Excelsior, MN). Individual follicle aspirates were centrifuged to separate the follicular fluid (FF) from the cumulus oocyte complexes (COCs) and the granulosa cells (GCs). FF was stored at -80°C until analysis and the oocytes from the individual aspirates were denuded from the surrounding cumulus cells (CCs) of the COCs by gentle micropipetting. The remaining follicles were aspirated in bulk using a (Ulticare, UltaMed Inc., Excelsior, MN) connected to a vacuum system. Bulk aspirated COCs were collected in Tyrode’s albumin lactate in pyruvate (TALP)-HEPES medium with 0.3% bovine serum albumin (BSA; Sigma-Aldrich, St. Louis, MO) and 1% Heparin sodium salt solution at 37°C. Oocytes from the bulk aspirates were denuded by gentle micropipeting in TALP-HEPES medium containing 0.3% BSA and 3% hyaluronidase (Sigma-Aldrich). The developmental stage of each oocyte was recorded and categorized as either immature germinal vesicle (GV), maturing metaphase I (MI), mature metaphase MII (MII), or degenerated. Individual oocytes were placed in pre-equilibrated 100 μL TALP complete drops in a 10-well IVF dish (LifeGlobal, Guildford, CT) in 5% CO2 at 37°C until IVF.
Blastocysts were collected from all 4 treatment groups, the zona pellucida removed, washed with Ca2+ and Mg2+-free PBS, and frozen at -80°C until RNA isolation. To analyze the effect of the treatments rather than embryo morphology, 38 blastocysts (N=12 C, N=12 T, N=10 WSD, and N=4 T+WSD) that did not exhibit cellular fragmentation or asymmetrical/multipolar divisions were chosen for RNA-seq analysis. RNA was extracted from the blastocysts using the ARCTURUS PicoPure RNA Isolation Kit (ThermoFisher Scientific KIT0204, Waltham, MA), cDNA prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for sequencing (TakaraBio, Shiga, Japan) and the amplified cDNA purified using the Agencourt AMPure XP Kit (Beckman Coulter, Brea, CA), all according to the manufacturer’s instructions. cDNA was then sheared to approximately 250 base pairs in length using a Covaris M220 sonicator.  Sheared cDNA was resuspended in Tru-Seq Resuspension Buffer and libraries prepared using a Tru-Seq Nano kit (Illumina, San Diego, CA) according to the manufacturer’s instructions, except that 16 cycles of amplification were performed to account for low input samples. Fragment size was measured using a Fragment Analyzer 5200 and samples quantified with quantitative PCR and pooled at equimolar concentration. Multiplexed samples were sequenced across seven lanes of a single-read, 75 cycle run on an Illumina HiSeq 4000 sequencer.

treatment_protocol: All protocols involving animals were approved by the Oregon National Primate Research Center (ONPRC) Institutional Animal Care and Use Committee and conducted in accordance with the National Institutes of Health Guidelines for the Care and Use of Laboratory Animals. The housing and general care of rhesus macaques (Macaca mulatta) has been previously described39. At the onset of the study, a cohort of 40 female rhesus macaques were equally divided into 4 treatment groups (N=10/group) at ~2.5 yrs of age just prior to puberty, including control (C), testosterone (T), Western-style diet (WSD), and T+WSD. Control animals consumed a standard chow diet (SCD: 15% fat, 59% carbohydrate, 26% protein) and received cholesterol implants. Females in the T group received T implants to maintain their circulating blood T levels up to 3-5 times the normal circulating T concentration and fed SCD. The WSD group was fed an obesogenic high-fat diet (36% fat, 46% carbohydrate, 18% protein). The T+WSD group received both T implants and the obesogenic diet . All 10 C animals underwent COS protocols, whereas 7 T, 6 WSD, and 3 T+WSD females were able to undergo a COS protocol after 5-6 yrs of treatment due to health issues, primarily endometriosis, that prevented further reproductive testing.

value: Blastocyst

value: Testosterone + Western Style Diet


title: plasma_exosome_RIC_rep1

description: Gene expression data from RIC-exosomes

source_name: plasma exosome, RIC

value: remote ischemic conditioning (RIC)


title: MAYO_BM_9

value: brain metastatic tumor


title: 6P_RCS

extract_protocol: 100 ng of RNA and Illumina’s TruSeq DSN library & TruSeq RNA Access Library Preparation protocol

value: PITT-RCSI

value: primary breast tumor


title: BM71


title: plasma_exosome_RIC_rep5

description: Gene expression data from RIC-exosomes


title: plasma_exosome_control_rep5


title: plasma_exosome_RIC_rep3

description: Gene expression data from RIC-exosomes


title: TWSD_2


title: plasma_exosome_control_rep2


title: plasma_exosome_RIC_rep2

description: Gene expression data from RIC-exosomes


title: MAYO_BP_8


title: plasma_exosome_RIC_rep4

description: Gene expression data from RIC-exosomes


title: 6M_RCS


title: WSD_9

value: Western Style Diet


title: BP6


title: plasma_exosome_control_rep4


title: KMS11 cells_DMSO 6hrs-rep3

description:
DMSO_6h_3
replicate 3


title: MAYO_BP_7


title: WSD_4


title: KMS11 cells_DMSO 6hrs-rep2

description:
DMSO_6h_2
replicate 2


title: KMS11 cells_NSC12 6hrs-rep2

description:
C12_6h_2
replicate 2


title: plasma_exosome_control_rep1


title: MAYO_BM_7


title: KMS11 cells_DMSO 6hrs-rep1

description:
DMSO_6h_1
replicate 1


title: KMS11 cells_NSC12 6hrs-rep3

description:
C12_6h_3
replicate 3


title: BP52


title: WSD_1


title: BM52


title: MAYO_BP_5


title: T_9

value: Testosterone


title: T_7


title: T_5


title: WSD_3


title: T_4


title: MAYO_BP_6


title: T_3


title: MAYO_BP_4


title: BM6


title: BP51


title: C_12

value: Control


title: MAYO_BM_8


title: 5M_RCS


title: T_8


title: BM51


title: T_6


title: C_8


title: MAYO_BP_3


title: BM47


title: WSD_8


title: WSD_7


title: WSD_6


title: MAYO_BM_3


title: T_10


title: DMR363_t90_induced

city: Lausanne

first: Anna

last: Anchimiuk

state: Vaud

address: UNIL-Sorge District

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

description: sporulation_1kb_ChIPseq_DMR312_314_363.txt

data_processing:
End trimming using trimmomatic Version 0.39
Reads were mapped using bowtie2 (--very sensitive-local mode)
Downstream data analysis was conducted using SeqMonk (Babraham Institute), with a bin size of 1 kb. Data was visualized using R.
Genome_build: NC_000964.3
Supplementary_files_format_and_content: txt format for read count in 1 kb bins

organism: Bacillus subtilis

source_name: anti-ScpB ChIP-seq of Bs cells with wt Soj conducted 90 min after re-suspension in sporulation salts + xylose

growth_protocol: For the single time point ChIP-seq, 10 ml overnight cultures of strains DMR178, DMR179 and DMR181 grown in CH media were diluted to OD600 = 0.1 in 50 ml fresh CH. For the time-course ChIP-seq, 10 ml overnight cultures of strains DMR312, DMR314 and DMR363 grown in CH media were diluted to OD600 = 0.1 in 100 ml fresh CH. Each strain was then grown at 30°C or 37°C until the OD600 reached 0.8. Cultures were then pelleted and resuspended into an equal volume of A+B sporulation salts, which marked t0 of sporulation. All subsequent time points for sporulation (in min or h) are measured similarly (e.g. t90 min marks 90 minutes after re-suspension in sporulation salts). For the time-course ChIP-seq,upon re-suspension in A+B sporulation salts, each sample was split into 2x 50 ml samples, with expression of the ectopic copy of soj being induced in one of each pair by the addition of 0.5 % (final) xylose.

extract_protocol:
To purify the DNA, 500 μl phenol:chloroform:isoamyl alcohol mix (Sigma) was added to the IP and WCE tubes, mixed vigorously and centrifuged for 10 min at 13,000 rpm (at room temperature). 450 μl of aqueous phase was collected and precipitated with 1 ml 100 % ethanol in the presence of 45 μl NaOAc (Sigma) and 1.2 μl of Glycoblue (Invitrogen) for 20 min at −20°C. DNA pellets were collected by centrifugation and resuspended in 100 μl EB (Qiagen) by vigorous shaking for 10 min at 55°C. Final purification was performed using a PCR purification kit (Qiagen), eluting the DNA in 50 μl EB. Prior to deep sequencing, the success of the IP was verified with qPCR.
For deep sequencing, the DNA libraries were prepared by the Genomic Facility at CIG, UNIL, Lausanne. Briefly, the DNA was fragmented by sonication (Covaris S2) until the DNA was sheared to 220-250 bp. The Ovation Ultralow Library Systems V2 kit (NuGEN) including 15 cycles of PCR amplification was used to prepare the DNA libraries. 12-15 million sequence reads per sample were obtained on a HiSeq4000 (Illumina) with 150 bp read length.

treatment_protocol: At respective time points the samples were crosslinked with formaldehyde (1 % final) for 30 min at room temperature with shaking every 10 mins. Each sample pellet was washed twice in PBS, prior to rapid freezing and storage at −80°C until further processing. Each sample pellet was resuspended in 2 ml cold PBS and adjusted to 4 OD600 units (4 ml at OD600=1). Adjusted sample pellets were resuspended in TSEMS buffer (50 mM Tris pH 7.4, 50 mM NaCl, 10 mM EDTA pH 8.0, 0.5 M sucrose and PIC (Sigma)) supplemented with 10 mg/ml lysozyme from chicken egg white (Sigma) and incubated for 30 min at 37°C with vigorous shaking. Resulting protoplasts were collected by centrifugation, washed twice with TSEMS, resuspended in 1 ml TSEMS and split into 3 aliquots. Pelleted samples were rapidly frozen in liquid nitrogen for storage at −80°C until further processing. For immunoprecipitation (IP), the sample pellets were resuspended in 2 ml buffer L (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 1 % (v/v) Triton X-100, 0.1 % (w/v) Na-deoxycholate, 0.1 mg/ml RNaseA and PIC (Sigma)) and transferred to 50 ml round bottom tubes. Sonication was performed using a Bandelin Sonoplus with an MS72 tip (90 % pulse and 35 % power output) for 3 rounds of 20 sec. Lysates were transferred to 2 ml tubes and, after centrifugation for 10 min at 21,000 g at 4°C, 800 μl of the supernatant was collected for IP and 200 μl was kept as whole-cell extract (WCE) at −20°C.    Prior to IP, the anti-scpB antibody serum (Gruber Lab) was incubated with Protein G coupled Dynabeads (Invitrogen) in a 1:1 ratio for 2.5-3.5 hrs at 4°C with rotation. The antibody-bead mixture was then washed and resuspended in buffer L, prior to adding 50 μl to each IP sample, which were incubated for 2.5-3 hrs at 4°C with rotation. Next, the samples were washed with the following buffers: buffer L, buffer L5 (buffer L containing 500 mM NaCl), buffer W (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5 % (v/v) NP-40, 0.5 % (w/v) Na-deoxycholate, 1 mM EDTA pH 8.0), and buffer TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0). Finally, for crosslink reversal, the IP samples were resuspended in 520 μl buffer TES (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1 % (w/v) SDS) and transferred to 1.5 ml screw-cap tubes. WCE samples were thawed and 300 μl of TES and 20 μl of 10 % SDS were added. Both tubes were incubated overnight at 65°C with vigorous shaking.

tag: chip antibody

value: anti-ScpB


title: MAYO_BM_24


title: MAYO_BM_6


title: 4M_RCS


title: DMR363_t60_uninduced

source_name: anti-ScpB ChIP-seq of Bs cells with wt Soj conducted 60 min after re-suspension in sporulation salts w/o xylose


title: 3P_RCS


title: DMR363_t0_induced

source_name: anti-ScpB ChIP-seq of Bs cells with wt Soj conducted at the moment of re-suspension in sporulation salts + xylose


title: MAYO_BM_4


title: T_11


title: MAYO_BP_23


title: C_1


title: MAYO_BM_5


title: 5P_RCS


title: T_1


title: C_11


title: C_2


title: DMR363_t60_induced

source_name: anti-ScpB ChIP-seq of Bs cells with wt Soj conducted 60 min after re-suspension in sporulation salts + xylose


title: 4P_RCS


title: MAYO_BM_22


title: DMR363_t90_uninduced

source_name: anti-ScpB ChIP-seq of Bs cells with wt Soj conducted 90 min after re-suspension in sporulation salts w/o xylose


title: DMR314_t0_induced

source_name: anti-ScpB ChIP-seq of Bs cells carrying an inducible version of Apo-Soj conducted at the moment of re-suspension in sporulation salts + xylose


title: MAYO_BM_23


title: 3M_RCS


title: MAYO_BP_24


title: BM29


title: DMR312_t90_induced

source_name: anti-ScpB ChIP-seq of Bs cells carrying an inducible version of ATP-Soj conducted 90 min after re-suspension in sporulation salts + xylose


title: BP25


title: DMR314_t60_induced

source_name: anti-ScpB ChIP-seq of Bs cells carrying an inducible version of Apo-Soj conducted 60 min after re-suspension in sporulation salts + xylose


title: BP29


title: DMR314_t90_uninduced

source_name: anti-ScpB ChIP-seq of Bs cells carrying an inducible version of Apo-Soj conducted 90 min after re-suspension in sporulation salts w/o xylose


title: MAYO_BM_21


title: WSD_10


title: DMR314_t60_uninduced

source_name: anti-ScpB ChIP-seq of Bs cells carrying an inducible version of Apo-Soj conducted 60 min after re-suspension in sporulation salts w/o xylose


title: BM25

source_name: Brain Metastatic Tumor


title: DMR314_t0_uninduced

source_name: anti-ScpB ChIP-seq of Bs cells carrying an inducible version of Apo-Soj conducted at the moment of re-suspension in sporulation salts w/o xylose


title: DMR312_t60_induced

source_name: anti-ScpB ChIP-seq of Bs cells carrying an inducible version of ATP-Soj conducted 60 min after re-suspension in sporulation salts + xylose


title: DMR312_t90_uninduced

source_name: anti-ScpB ChIP-seq of Bs cells carrying an inducible version of ATP-Soj conducted 90 min after re-suspension in sporulation salts w/o xylose


title: DMR312_t60_uninduced

source_name: anti-ScpB ChIP-seq of Bs cells carrying an inducible version of ATP-Soj conducted 60 min after re-suspension in sporulation salts w/o xylose


title: DMR312_t0_induced

source_name: anti-ScpB ChIP-seq of Bs cells carrying an inducible version of ATP-Soj conducted at the moment of re-suspension in sporulation salts + xylose


title: DMR312_t0_uninduced

source_name: anti-ScpB ChIP-seq of Bs cells carrying an inducible version of ATP-Soj conducted at the moment of re-suspension in sporulation salts w/o xylose


title: 2M_RCS


title: 2P_RCS

source_name: Primary Breast Tumor


title: MAYO_BM_20


title: MAYO_BP_21


title: MAYO_BP_20


title: MAYO_BP_2


title: DMR314_t90_induced

source_name: anti-ScpB ChIP-seq of Bs cells carrying an inducible version of Apo-Soj conducted 90 min after re-suspension in sporulation salts + xylose


title: Clp1 KO rep 2

city: Cambridge

first: Jimmy

last: Ly

state: Massachusetts

address: 455 main street

department: Biology

institute: Whitehead Institute

data_processing:
Samples were demultiplexed with bcl2fastq v2.20 to generate fastq files.
Poly(A) tracks were removed using Cutadapt v3.7
Reads were aligned using STAR v2.7.1.a
Transcript counts were quantified using htseq-count (0.11.0)
DESeq2 was used for normalization and differential expression analysis
Assembly: hg38, Gencode release 25 annotations. Nano and Firefly Lucifease CDS (spike-in mRNA) was included.
Supplementary files format and content: Transcript counts are stored in tab-delimited files with one row per transcript. ENSG00000000001.1 represents Nano luciferase and ENSG00000000002.2 represents Firefly luciferase. Quantification done using htseq-count.

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum and 100 U/mL penicillin/streptomycin

extract_protocol:
Cells were collected using mitotic shake-off to enrich for mitotic cells, washed once in PBS, then snap frozen for later processing. RNA was extracted using TRIzol reagent (Life Technologies).
KAPA mRNA HyperPrep kit with poly(A) selection was used for library preparation.

treatment_protocol: Cas9 expression was induced with 1 ug/mL doxycycline for 3 days and mitotically enriched cells were harvested on day 5 by shake-off. For control and ZNF335 knockout cells, cells were additionally treated with 10μM STLC for 12 h prior to harvest.

value: HeLa

tag: gene target

tag: genotype

value: Clp1 KO

tag: replicate


title: ZNF335 KO rep 1

value: ZNF335 KO


title: ZNF335 KO rep 2


title: MAYO_BM_19

tag: cohort

value: MAYO

tag: patientid


title: LIN52 KO rep 1

value: LIN52 KO


title: BM17

tag: tissue


title: BP19-2


title: HS1 control rep 1

value: negative control intergenic sgRNA

value: HS1 control


title: MAYO_BP_19


title: MAYO_BM_2


title: LZE8T

city: Beijing

first: Chen

last: Wu

state: Beijing

address: 17 Panjiayuan Nanli

department: Department of Etiology

institute: CAMS Cancer Hospital

data_processing:
Raw sequencing data was processed using the cell-ranger pipeline (version 2.1.0, 10X Genomics) with default parameters and mapped to GRCh38 reference genome to generate matrices of gene counts by cell barcodes. Gene count matrices were analyzed with Seurat package (version 3.1.5, 100) in R (version 3.6.3, The R Foundation)
Filtering genes and cells: Cells had to express a minimum of 200 genes with a mitochondrial fraction less than 20%. Suspected doublets were annotated using DoubletFinder package (version 2.0.3) and removed. We removed ribosomal genes and retained genes that were expressed in at least 0.1% of all cells.
Identification of epithelial cell: Raw unique molecular identifier (UMI) counts were normalized using SCTransform function with default parameters. Batch effect was adjusted by implementing Harmony package (version 1.0; 101). Dimension reduction was performed using principal-component analysis (PCA) and the optimal number of principal components (PCs) selected using ElbowPlot function. The same PCs are also applied in cell cluster identification with modularity optimization using kNN graph algorithm as input. Cell clusters were visualized using UMAP algorithm 102. And with resolution of 0.3 we obtained nine distinct cell clusters. These clusters were annotated based on the expression of known markers. For epithelial cells, the marker genes included EPCAM, SFN, KRT5, and KRT14, resulting in 5,070 epithelial cells, including 215 from tissue of normal or inflammatory esophageal epithelium, 44 from LGIN, 1,456 from HGIN, and 3,355 from ICA (657, 1,540, 1,137, and 21 for stage I, II, III, and IV, respectively)
Extract count matrix: Using cell barcode to extract original cell count by  gene matrix for 5070 epithelial cells.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include UMI counts for each gene and each cell barcode
Supplementary files format and content: scTDN_UMI_matrix_epithelial_cell.txt.gz: raw counts

source_name: Tumor tissue of esophageal carcinoma

extract_protocol:
Fresh tissues were rinsed with cold 10% FBS PBS, cut into small pieces on ice, and digested in RPMI-1640 medium containing 2 mg/ml collagenase IV (Gibco, Cat:17104-019) and 0.5 mg/ml hyaluronidase (Sigma Aldrich, Cat:7326-33-3 ) for 1 hour at 37 degree centigrade. The digested cell suspension was subsequently filtered through a 70-μm cell strainer (Falcon, Cat:352350) before centrifuging at 560 rcf for 6 minutes at 4°C. Cells were treated with 2ml of 1x red blood cell lysis buffer (BD Biosciences, Cat: 555899) for 5 min following centrifuging of the same parameter. The remaining cells were suspended in 50 μl of 1% FBS PBS after washing once with the same medium. Single-cell suspension was stained with 4',6-diamidino-2-phenylindole (DAPI, Solarbio, Cat:C0065) prior to fluorescence-activated cell sorting (FACS) on a BD FACSAria II flow cytometer (BD Biosciences) to remove dead cells and debris. The number and viability cells were examined using cell pellet by staining trypan blue (20μl mix of 10μl suspension and 10ul 0.4% trypan solution, Thermo Fisher Scientific, Cat: 15250061), following centrifuging at 500g for 5 minutes at 4°C immediately after FACS. We targeted for ~4,000 cells recovered from each channel.
Libraries were prepared using Chromium Single Cell 5’ Reagent Kits (V1, 10X Genomics, Pleasanton, CA, Cat# PN-1000006, PN-1000020) and sequencing was accomplished with an Illumina NovaSeq 6000 (Illumina, Inc., San Diego, CA) with 2 × 150 bp paired-end mode.

treatment_protocol: Tissue samples were placed in RPMI-1640 medium (Corning, Cat:10-040-CV) with 20% fetal bovine serum (FBS, Cell technologies, Cat:30070.03) immediately after surgical resection. Tissue was processed for single cell RNA sequencing (scRNA-seq) with a portion being cryo-sectioned and hematoxylin-eosin (H&E) stained to confirm the histological staging.

tag: patient

value: esophagus

value: epithelial cell


title: BM19-2


title: RNPC3 KO rep 2

value: RNPC3 KO


title: MAYO_BP_22

value: brain metastatic tumor


title: LZE8D2

source_name: Low-grade intraepithelial neoplasia of esophagus


title: LZE8D1

source_name: Non-tumor esophgeal epithelium


title: BP12

value: PITT-RCSI


title: HS1 control rep 2


title: LIN52 KO rep 2


title: RNPC3 KO rep 1


title: 1P_RCS

value: primary breast tumor


title: MAYO_BM_18


title: LZE7N


title: BM12


title: LZE7T


title: MAYO_BP_18


title: MAYO_BP_17


title: Clp1 KO rep 1


title: LZE7D1


title: BP17


title: MAYO_BP_16


title: MAYO_BM_17


title: LZE7D2


title: LZE8N


title: LZE6N


title: 1M_RCS


title: 65 9 months

city: PORTLAND

first: JUNGSUN

last: KIM

state: OR

address: KCRB 5001.51, 2720 SW Moody Ave

institute: Oregon Health & Science University

description: 9 months

data_processing:
NextSeq 500 sequencer was used to sequence pooled 16 cDNA libraries (330 clusterings).
Reads were trimmed to 35 nucleotides and aligned into the hg19 genome using Spliced Transcripts Alignment to Reference (STAR)4 with the following parameters; Max number of multiple alignments allowed for a read was 20. OutfilterType is set for BySJout to detect and weed out "spurious" splice junctions inferred from overlapping tag data. The minimum eight tags had to be spread across each side for inferring novel splice junctions, and the minimum one tag had to be spread across each side when aligning to annotated splice junctions. The minimum and maximum number of intron length allowed when inferring splicing junctions set to 20 and 1000000.
The quantification of tags over genes was presented as HTSeq count using the HTSeq package.
The HTSeq counts were normalized by library size differences using estimated size factors from the DESeq2 package5.
Genome_build: hg19 genome
Supplementary_files_format_and_content: Matrix table with DESeq2-normalized counts with Likelihood ratio test (LRT)

growth_protocol: human pluripotent ES culture condition (+doxycycline 50 ng/ml) for day 0 samples. Each 10-22 cell tagged with KiR-EG was subcutaneously transplanted into 4-6 weeks old female NOD-SCID-IL2Rgc null (NSG) mice and harvested 1 week, 2 weeks, 3 months, 6 months, and 9 months.

extract_protocol:
RNA was extracted from FACSorted cell populations using PicoPure RNA extraction kit. RNA quality was tested using the Bioanalyzer 2100 (Agilent) and concentration was determined using the Life Technologies Qubit.
Ovation single-cell RNA-Seq was used to generate cDNA libraries from total RNA (100-300 pg)

treatment_protocol: day 0, 1 week, 2 weeks, 3 months, 6 months, and 9 months

value: human PDAC-derived iPS-like cell

tag: potential contaminated strain

value: NSG

value: 9 months


title: LZE6D3


title: LZE5T


title: 36 6 months

description: 6 months

value: 6 months


title: DMR363_t0_uninduced

source_name: anti-ScpB ChIP-seq of Bs cells with wt Soj conducted at the moment of re-suspension in sporulation salts w/o xylose

value: anti-ScpB


title: BP47


title: 62 9 months

description: 9 months

value: 10 months


title: LZE6D1


title: MAYO_BM_16


title: MAYO_BP_15


title: LZE5D2


title: LZE5N


title: 57 6 months

description: 6 months

value: 7 months


title: MAYO_BM_15

value: MAYO


title: 79 6 months

description: 6 months


title: MAYO_BP_14


title: LZE5D1


title: LZE4T


title: LZE6T


title: LZE4N


title: MAYO_BM_14


title: 18 3 months

description: 3 months

value: 3 months


title: LZE4D

source_name: High-grade intraepithelial neoplasia of esophagus


title: LZE2T


title: 39 3 months

description: 3 months


title: LZE3D


title: LZE3N


title: 47 2 weeks

description: 2 weeks

value: 18 days


title: 15 3 months

description: 3 months

value: 2 months


title: MAYO_BP_12


title: LZE2D

value: esophagus


title: MAYO_BM_13


title: LZE24T

value: epithelial cell


title: C24_2

city: Tianjin

first: Mengxu

last: Li

state: China

address: Tianjin University, School of Chemical Engineering and Technology, 321, 54 building, Tianjin Univ., Peiyang Park Campus: No.135 Yaguan Road, Haihe Education Park

institute: Tianjin University

description: Total RNA excluding rRNA.

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM (v1.2.12).
The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression indifferent samples. Essentially, differential expression analysis was performed using the DESeq2 (v1.4.5) with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expressed gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test.
Assembly: ASM252v1
Supplementary files format and content: fpkm.csv: Comma-separated text file includes FPKM values for each sample.

organism: Yarrowia lipolytica CLIB122

source_name: Yarrowia lipolytica CLIB122

growth_protocol: Y. lipolytica cells cultured at 24 h on the initial logarithmic phase were collected for RNA isolation.

extract_protocol:
Fungi RNA was extracted using the TRIzol® method following the manufacturer's protocol. Bulk cells or filamentous fungus are grounded to a powder using liquid nitrogen, and the powder was transferred into the 2ml tube contains 1.5ml Trizol reagent. The mix was shaked for 3min, and kept for 5min at room temperature, then was Centrifuged at 10,000×g for 5min at 4°C. The supernatant was added 200uL of chloroform/isoamyl alcohol (24:1) with 1ml lysis reagents. After centrifuged at 10,000×g for 10min at 4°C, the supernatant was transferred into another new tube with equal volume of isopropanol and put in the refrigerator at -20°C for 1h. After centrifuged at 13600×g for 20min at 4°C, the supernatant was precipitated by 1 mL of 75% ethanol and let dry for 3-5min. The RNA pellet was dissolved with 30-100uL of DEPC water or RNase-free water. The concentration of the extracted RNA samples was determined using a Nanodrop system (NanoDrop, Madison, USA), and the integrity of the RNA was examined by the RNA integrity number (RIN) using an Agilent 2100 bioanalyzer (Agilent, Santa Clara, USA).
DNase I was used to digest double-stranded and single-stranded DNA in total RNA, then, magnetic beads were purified to recover the reaction products, RNase H method (Illumina, USA) was used to remove the rRNA. Purified mRNA from previous steps was fragmented into small pieces with fragment buffer at appropriate temperature. Then, First-strand cDNA was generated in First Strand Reaction System by PCR, and the second-strand cDNA was generated as well. The reaction product was purified by magnetic beads, afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to carry out end repair. The cDNA fragments with adapters were amplified by PCR, and the products were purified by Ampure XP Beads. Library was validating on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products above were heated denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29(Thermo Fisher Scientific, MA, USA) to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGISEQ500 platform (BGI-Shenzhen, China).

treatment_protocol: Y. lipolytica cells were collected by centrifugation at 5000 rpm for 2 min, washed with PBS three times and then quick-frozen by liquid nitrogen and stored at -80 °C tentatively.

tag: growth phase

value: initial logarithmic phase


title: C24_3

description: Total RNA excluding rRNA.


title: C24_1

description: Total RNA excluding rRNA.


title: 27 1 week

description: 1 week

tag: cell type

value: 9 days


title: MAYO_BM_12

value: brain metastatic tumor


title: MAYO_BP_11

value: primary breast tumor


title: MAYO_BP_13


title: LZE2N


title: LZE3T


title: MAYO_BM_11


title: 44 1 week

description: 1 week

value: human PDAC-derived iPS-like cell


title: LZE24D3


title: MAYO_BP_10


title: A24_3

description: Total RNA excluding rRNA.


title: A24_2

description: Total RNA excluding rRNA.


title: LZE24D1


title: 6 1 week

description: 1 week

value: NSG


title: 12 2 weeks

description: 2 weeks

value: 14 days


title: 54 day 0

description: day 0

value: MEF

value: day 0


title: MAYO_BP_1


title: A24_1

description: Total RNA excluding rRNA.


title: LZE22T


title: LZE22N


title: LZE22D3


title: MAYO_BM_10


title: 67 day 0

description: day 0


title: LZE24N


title: MAYO_BM_1


title: 66 day 0

description: day 0


title: Whole blood (WB)

city: Durban

first: Christen

last: Erasmus

state: KwaZulu-Natal

address: 719 Umbilo Road, Durban

department: Medical Biochemistry

country: South Africa

institute: University of KwaZulu-Natal

data_processing: Thermocycler conditions were as follows: initial denaturation (95°C, 8 min), followed by 40 cycles of denaturation (95°C, 15 s), annealing (Table 1, 40 s), and extension (72°C, 30 s). GAPDH served as the endogenous control to normalize mRNA expression. The relative change in mRNA expression was calculated using the comparative threshold cycle (2−ΔCt) method.

label: SYBR Green

source_name: blood

label_protocol: qRT-PCR was performed using the PowerUp™ SYBR™ Green Master Mix (Thermo-Fisher Scientific, A25742) and the CFX96 touch real time PCR system (BIO-RAD).

extract_protocol: The VAT and WB samples were thawed on ice. Under laminar flow conditions, the VAT was homogenized together with the TRIzol™ reagent and centrifuged (10,000 xg, 4°C, 10 min). The supernatant was then removed for each VAT sample and added to a new labelled Eppendorf tube. The WB samples were each vortexed for 10 seconds and transferred into a new labelled Eppendorf tube. Each sample was centrifuged (12,000 xg, 4°C, 15 min) and isopropanol (500 µl) was added to the aqueous phase followed by overnight incubation at −80°C. The samples were centrifuged (12,000 xg, 4°C, 20 min), supernatants were removed, and RNA pellets were washed in 75% ethanol (500 µl). Samples were centrifuged (7,400 xg, 4°C, 15 min), RNA pellets were air-dried (30 min, room temperature (RT)), and resuspended in nuclease-free water (15 µl). RNA concentration and purity were assessed with the Nanodrop2000 spectrophotometer (Thermo-Fisher Scientific). Samples with A260/A280 ratios of 1.9–2.1 were considered pure and used for all subsequent assays. RNA concentration was adjusted as required for the respective assays. Total RNA (standardized to 1,000 ng) for each sample was reverse transcribed into complementary DNA (cDNA) using the Maxima H Minus First Strand cDNA Synthesis Kit (Thermo-Fisher Scientific, K1652).

value: whole blood

tag: Sex

value: female

tag: pregnancy status

value: pregnant


title: PC3-shHOXB13-2

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

data_processing:
Sequenced reads were mapped to hg38 human genome using STAR
raw counts were calculated by STAR, RPKM/FPKM values were calculated by perl script
Genome_build: hg38
Supplementary_files_format_and_content: txt file of RPKM/FPKM values for each Sample

source_name: prostate tumor

growth_protocol: LNCaP and PC3 cells were maintained in RPMI supplemented with 10% FBS and 1% penicillin and streptomycin

extract_protocol:
Total RNA was isolated from cells using the nucleospin RNA kit (Takara) according to the manufacturer's recommended protocol.
RNA-seq libraries were prepared from 0.5 μg high-quality DNA-free total RNA by using NEBNext® Ultra RNA Library Prep Kit, according to the manufacturer’s instructions. The libraries passing quality control (equal size distribution between 250-400 bp, no adapter contamination peaks, no degradation peaks) were quantified using the Library Quantification Kit from Illiumina (Kapa Biosystems, KK4603).using the Illumina provided protocol.
RNA-Seq samples were sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

treatment_protocol: LNCaP or PC3 cells were infected with control shRNA (pGIPZ) or shRNA targeting HOXB13 (shHOXB13) lentiviruses for 7 days. LNCaP cells with HOXB13 knockdown were rescued by HOXB13-WT or G84E .  LNCaP cells were co-infected with shRNA virus targeting HDAC1 (shHDAC1) and HDAC3 (shHDAC3) with or without concomittant HOXB13 overexpression for 7 days.

tag: cell line

tag: treatment/infection

value: WT


title: MY24_2

city: Houston

first: Charles

middle: Yang

last: Lin

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: RNA-Seq for MM1S treated with YKL-5-124 (98 nM) - 24Hr

data_processing:
The RNA-Seq data was first preprocessed with BBDuk for single end samples
All RNA-seq datasets were aligned with HISAT2 and quantified via Cuffquant 2.2 with the hg19 ERCC annotation
Cuffnorm was utilized to normalize data
Top 3 replicates (based on correlation) were used
Inactive genes (no samples with FPKM > 10) were filtered out prior to additional analysis
Genome_build: hg19 ERCC
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: MM1S MM Cell Line

growth_protocol: Cells were grown in 12 well plates in 1 mL of RPMI media with 10% FBS

extract_protocol:
Samples (~2.5x10^5 cells) were lysed with trizol and RNA was extracted via the Zymo Directzol RNA extraction kit
RNA-Seq libraries were prepared for sequencing using standard Quantseq 3' library prep protocols

treatment_protocol: Treatment with DMSO or YKL for 6 or 24 Hr

value: multiple myeloma

tag: treatment

tag: treatment time


title: MY24_1


title: T32_1

city: Zhengzhou

first: Liushuai

last: Hua

state: Henan

address: No.22 Huayuan Road

department: Institute of Animal Husbandry and Veterinary Science

institute: Henan Academy of Agricultural Sciences

data_processing:
Quality control. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Transcriptome assembly. The left files (read1 files) from all libraries/samples were pooled into one big left.fq file, and right files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity (Grabherr et al, 2011) with min_kmer_cov set to 2 by default and all other parameters set default.
Quantification of gene expression levels. Gene expression levels were estimated by RSEM (Li et al, 2011) for each sample, 1) clean data were mapped back onto the assembled transcriptome, 2) the readcount for each gene was obtained from the mapping results, 3) The readcount for each gene was normalized to FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced), 4) the expression levels of each gene were estimated by PFKM
Differential expression analysis. Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.10.1). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Supplementary_files_format_and_content: Differentially_expressed_genes, FPKM

organism: Mauremys reevesii

source_name: adrenal-kidney-gonad complexes

growth_protocol: Four hundred and fifty freshly laid Chinese pond turtle eggs were obtained from LVCA Company (Guangzhou Guangdong, China).

extract_protocol:
Eggs were incubated until they reached Greenbaum’s embryonic stage 16, at which point the embryonic gonads become responsive to ambient temperature. The AKG complexes, with three replicates at each incubation temperature, were collected using a stereoscopic microscope, and stored in liquid nitrogen for subsequent RNA extraction
Total RNA was isolated from the frozen AKG complexes samples using Trizol reagent (TaKaRa, Dalian, China). The quantity and quality of the RNA were determined using a NanoPhotometer spectrometer (Implen Inc., Westlake Village, CA, USA). Then the RNAs were used to constructing Illumina-indexed transcriptome analysis libraries.

treatment_protocol: The eggs were randomly allocated into plastic containers filled with moist vermiculite. Then the containers were put into one of three incubators, in which the temperatures were set at 26, 29 and 32°C, respectively.

tag: incubatioin temperature

tag: Stage

value: Greenbaum’s embryonic stage 16


title: T32_3


title: LZE21N

value: esophagus


title: Visceral adipose tissue (VAT)

source_name: adipose tissue

value: visceral adipose tissue


title: LZE21T

value: epithelial cell


title: T29_2


title: MD24_3

description: RNA-Seq for MM1S treated with DMSO (98 nM) - 24Hr

value: DMSO (98 nM)


title: T29_1


title: LZE20N


title: PC3-shHOXB13-1

tag: genotype


title: HY24_3

description: RNA-Seq for H929 treated with YKL-5-124 (83 nM) - 24Hr

source_name: H929 MM Cell Line


title: MY24_3


title: T26_3


title: MD24_2


title: LZE21D1


title: T32_2


title: LZE20T