title: WT CPZ2

city: shanghai

first: yumeng

address: dongan road 130

institute: Fudan University

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

source_name: corpus callosum

extract_protocol:
Total RNA was extracted from mouse corpus callosum using the Qiagen RNeasy kit (Qiagen, Germany) according to the manufacturer protocol.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: corpus callosum

value: WT

tag: treatment

value: cuprizone


title: WT Ctrl3

status: Public on Aug 03 2022

type: SRA

last: wang

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype

value: Ctrl


title: WT Ctrl2


title: WT Ctrl1


title: WT CPZ3


title: WT CPZ1


title: AHR CKO CPZ2

value: AHR CKO


title: AHR CKO CPZ3


title: 18481T H3K27ac ChIP-seq

city: New York

first: Royce

last: Zhou

address: 1470 Madison Avenue

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: genomic

data_processing:
FastQC - quality control of sequenced reads to assess duplication levels for ChIP-seq and detect adapter contamination during library prep.
cutadapt - removal of adapter contamination within raw sequenced reads
bowtie - Reads were mapped to the hg19 human genome using bowtie under the following parameters: bowtie -k 1 -m 1 --best -S -n 2 -l 60 -q --chunkmbs 200.
Samtools - Duplicate reads were removed using samtools.
MACS2 - Peak calling was performed using MACS2 with the following parameters: –f BAM –g 2.7e9 –s 75 --nomodel --extsize 200 –B –-SPMR –p 1e-10. For H3K27ac, a p-value cutoff of 10-10 was used for peak calling
deeptools - Bigwig tracks were generated using deepTools bamCoverage using the parameters: -of bigwig --effectiveGenomeSize 2736124973 --normalizeUsing RPKM
bedtools - Blacklisted regions (Duke_Hg19SignalRepeatArtifactRegions.bed, downloaded from the Broad Institute) were excluded from called peaks using bedtools
Salmon - Sequenced reads were mapped to the hg38 transcriptome using Salmon quasi-mapping under the default parameters and expression output in TPM was extracted.
Genome_build: ChIP-seq - hg19. RNA-seq hg38.
Supplementary_files_format_and_content: ChIP-seq processed data files are in the bigwig format ready for easy viewing on a genome broswer such as IGV or UCSC. RNA-seq processed data files are Salmon output excel files with raw and normalized read counts for each gene/transcript (ENSEMBL ID).

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary CRC

extract_protocol:
Xenograft tumors and patient surgical specimens were digested with 1X collagenase/hyaluronidase (Stem Cell Technologies), minced, and passed through a 100μM filter. Cells were double crosslinked with 0.25M disuccinimidyl glutarate followed by 1% formaldehyde. ChIP-seq was performed as previously described3. Briefly, 2X crosslinked chromatin was sonicated on a Diagenode Bioruptor for 15 cycles 30s ON/30s OFF on the low power setting. Cells were precleared using 100μL of Magna-ChIP Protein A+G magnetic bead slurry (Millipore) before overnight incubation with 10μg ChIP antibody conjugated to100μL beads. Beads were washed once with IP Wash Buffer I, twice with High Salt Wash Buffer, once with IP Wash Buffer II, and twice with TE buffer. For buffer recipes refer to Fontanals-Cirera, Hasson et al3. Beads were eluted with 1% SDS at 65 degrees Celsius with agitation and reverse crosslinked overnight with high salt with RNase treatment (Roche). The next day, DNA underwent Proteinase K treatment at 42 degrees Celsius before elution using QIAquick PCR purification kit (QIAGEN).  DNA was run on an Agilent High Sensitivity DNA chip using an Agilent Technologies 2100 Bioanalyzer for quality control. H3K27ac ChIP-seq antibodies were purchased from abcam (#ab177178). Total RNA was extracted using the QIAGEN Rneasy Mini Kit. For ChIP-seq, antibody bound DNA was purified using the QIAGEN QIAquick PCR cleanup kit.
For ChIP-seq, DNA underwent end repair, poly-adenylation, and barcoding using enzymes from New England Biolabs. ChIP libraries were amplified 12-15 PCR cycles using the 2X KAPA HiFi DNA HotStart ReadyMix before quality assessment by running on a High Sensitivity chip using a Bioanalyzer 2100 (Agilent) followed by a Qubit fluorometer (Thermo Fisher). The Mount Sinai Oncological Sciences Sequencing Core Facility prepared poly-A-capture RNA-seq libraries using the TruSeq RNA Library Prep Kit v2 (Illumina) according to manufacturer’s instructions.

tag: cells/tissue

value: tissue

tag: chip-seq antibody


title: 17787T H3K27ac ChIP-seq


title: 18607T H3K27ac ChIP-seq


title: 18081T H3K27ac ChIP-seq


title: 760T, Biopsy, Tumor

type: genomic

city: Washington

first: Erin

middle: R

last: Bonner

state: DC

address: 7144 13th Place NW

department: Center for Genetic Medicine Research

institute: Children's National Hospital

hyb_protocol: Illumina EPIC DNA methylation array protocol

scan_protocol: Illumina iScan System

data_processing: IDAT files were uploaded to the molecularneuropathology.org portal (https://www.molecularneuropathology.org/mnp/) and Brain Classifier V11b4 workflow was applied to generate Copy Number Variation plots.

label: Cy5 and Cy3

source_name: Pontine tumor, diagnostic biopsy

extract_protocol: Gentra PureGene Tissue Kit (QIAGEN)

tag: age at diagnosis

value: 9 years

tag: gender

value: Male

value: Pontine tumor

tag: tumor location

value: Pons

tag: time

value: at initial diagnosis

tag: diagnosis

value: Diffuse midline glioma


title: AHR CKO CPZ1


title: 17753T H3K27ac ChIP-seq


title: 17753N H3K27ac ChIP-seq

source_name: Normal colon mucosa


title: 17627N H3K27ac ChIP-seq


title: AHR CKO Ctrl3


title: mTEC4_rep1

city: Rehovot

first: Jakub

last: Abramson

address: 234 Herzl st.

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
The Omics IT and Data Management Core Facility (ODCF; DKFZ, Heidelberg) processed the tWGBS data. Reads alignment was executed using an updated version of the previously published pipeline(Wang et al., 2013), implemented as a Roddy Workflow (https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows) in the automated One Touch Pipeline(Reisinger et al., 2017). Briefly, Trimmomatic v.0.30(Bolger et al., 2014) was used for trimming of adaptor sequences of raw reads, followed by in-silico bisulfite-convertion(Li, 2013) (C>T for the first read, G>A for the second). Converted reads were aligned to the in-silico bisulfite-converted reference genome mm10, which was augmented with the PhiX and lambda phage sequences, using the BWA-MEM v0.7.8(Li, 2013) software with default parameters. After alignment, reads with a mapping quality ≥25 and nucleotides with a Phred-scaled quality score ≥25 were converted back to their original state. Sambamba v0.4.6( https://lomereiter.github.io/sambamba/ ) was used for PCR duplication removal per library. Methylation calling and M-bias QC was executed using MethylDackel (Ryan, 2014) v0.4.0.
Methylation calls were imported into R statistical environment for further analysis and smoothing using BSSeq package v1.20.0(Hansen et al., 2012). BigWig files were exported via rtracklayer v1.46.0(Lawrence et al., 2009) and visualized using the IGV software.
Assembly: mm10
Supplementary files format and content: bigwig coverage tracks

source_name: thymus

extract_protocol:
DNA and RNA were isolated using TRIzol reagent (Sigma Aldrich, Darmstadt, Germany) and further AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) purification, following the manufacturer’s instructions. For RNA isolation (RNase-free DNAse set, Qiagen) DNAse I digestion was performed on the column. Proteinase K digestion was applied for RNA and DNA isolation (Puregene Proteinase K, Qiagen). Prior to library preparation, DNA and RNA quality was checked by Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and quantified by Qubit fluorimetry (Thermo Scientific, Wilmington, USA). All RNA samples reached an RNA integrity number (RIN) > 8.5.
Generation of tWGBS libraries was performed as previously published(Wang et al., 2013). Briefly, 20-30ng DNA from sorted adult mTEC populations was tagmented in a 20µl reaction mix at 55°C for 8min, followed by addition of 15µl 5M guanidinium thiocyanate and purification with HighPrep beads (Gaithersburg, MD, United States). Oligonucleotide replacement and gap repair were performed at 37°C for 30min in a 20µl mix, followed by another bead-mediated purification. Bisulfite treatment was done with the EZ DNA Methylation kit (Zymo, Irvine, CA, U.S.A.) using 16 cycles (60min at 50°C, 15sec at 95°C). Four differently barcoded tWGBS libraries per sample were generated under real-time conditions to monitor amplification using a program of initial melting at 95°C for 3min followed by cycling with 95°C for 20sec, 62°C for 15sec and 72°C for 40sec. After bead-mediated purification, libraries were quantified and pooled per sample in equimolar amounts with a final concentration of 10nM. Each pool was sequenced at the DKFZ Genomics and Proteomics Core Facility using paired-end, 125 bp, on one lane of the Illumina HiSeq2000 v4 platform.

tag: strain

value: thymus

tag: cell type

value: thymus epithelial cell type 4

tag: batch


title: AHR CKO Ctrl2


title: HCC#51, classical monocytes, Day0, NDB

city: Daejeon

first: Seung Hyuck

last: Jeon

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
Sequences were trimmed using BBDuk
Sequences were aligned to a human reference genome (hg19) using Bowtie2
Read count was calculated using Bedtools
Quantile normalization was performed using EdgeR
Assembly: hg19
Supplementary files format and content: tab-delimited text files include log2 normalized expression for each Sample

source_name: peripheral blood

extract_protocol:
Total RNA was extracted from the sorted cells using TRIZOL reagent (Thermo Fisher Scientific), and was assessed for quantity and quality using a Bioanalyzer 2100 (Agilent).
Libraries were generated using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen)

value: peripheral blood

tag: cell line

value: primary

value: classical monocyte

value: nivolumab

tag: time point

tag: group

value: NDB


title: HCC#51, classical monocytes, Day7, NDB


title: mTEC4_rep2


title: HCC#50, classical monocytes, Day7, NDB


title: HCC#36, classical monocytes, Day7, NDB


title: HCC#03, classical monocytes, Day7, NDB


title: HCC#03, classical monocytes, Day0, NDB


title: AHR CKO Ctrl1

value: corpus callosum


title: HCC#48, classical monocytes, Day7, DCB

value: DCB


title: mTEC1_rep1

value: thymus epithelial cell type 1


title: mTEC1_rep2


title: ATII_WT_1

source_name: lung

value: lung

value: type II airway epithelial cells


title: HCC#37, classical monocytes, Day0, DCB


title: ATII_WT_2


title: mTEC3_rep1

value: thymus epithelial cell type 3


title: mTEC3_rep2+B36


title: HCC#08, classical monocytes, Day0, DCB


title: HCC#36, classical monocytes, Day0, NDB


title: 17627T H3K27ac ChIP-seq

value: tissue


title: ATII_WT_3


title: HCC#37, classical monocytes, Day7, DCB


title: HCC#48, classical monocytes, Day0, DCB


title: HCC#50, classical monocytes, Day0, NDB


title: HCC#02, classical monocytes, Day7, DCB


title: OVCAR3_974_2

city: BLOOMINGTON

first: Kenneth

middle: P.

last: Nephew

state: IN

department: Medical Sciences

institute: Indiana University

data_processing:
The raw RNA-seq reads were cleaned using Trimmomatic version 0.38 (Bolger et al. 2014) setting the cutoff threshold for average base quality score at 20 over a window of 3 bases. Reads shorter than 20 bases post-trimming were excluded. (parameters: LEADING:20 TRAILING:20 SLIDINGWINDOW:3:20 MINLEN:20)
The cleaned reads were aligned to the human genome reference, GRCh38.p12 using STAR (version STAR_2.7.3a) (Dobin et al. 2013).
Individual gene expression was quantified by counting the number reads mapping to the exon regions of each of the annotated genes from gencode v.28 using featureCounts tool of subread package (version 2.0.0) (Liao et al. 2014). Those reads that mapped to antisense strand, or mapped to multiple regions on the genome or those reads that overlapped with multiple genes were excluded. (parameters: -s 2 -p -B -C)
Assembly: GRCh38.p12
Supplementary files format and content: Tab deliminted text files containing counts of reads overlapping with exon regions of the genes.

source_name: Ovarian cancer

growth_protocol: OVCAR3 cells were grown in RPMI medium with 10% FBS and 100mM Sodium pyruvate

extract_protocol: RNA was harvested from the cells using the RNAEasy kit (Qiagen,Catalog No; 74106).

treatment_protocol: Cells were treated with compound 974 (5uM for 48h) or DMSO.

value: Ovarian cancer

value: ovarian cancer cell

value: WT


title: OVCAR3_DMSO control_3


title: mTEC2_rep3

value: thymus

value: thymus epithelial cell type 2


title: OVCAR3_DMSO control_1


title: HCC#02, classical monocytes, Day0, DCB

value: peripheral blood


title: OVCAR3_DMSO control_2


title: OVCAR3_974_1


title: HCC#08, classical monocytes, Day7, DCB

value: primary


title: LUCAT1_CRISPRi_2

city: Marburg

first: Leon

middle: Nicolas

last: Schulte

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

country: Germany

institute: Philipps-Universität Marburg

description: THP1 cells transduced with LUCAT1 CRISPRi vector

data_processing:
RTA version 1.18.66.4 was used for basecalling
bcl2fastq version 1.8.4. was used for demultiplexing
Reads were mapped using the CLC genomics workbench version 10.01 and the GRCh38 human genome annotation with standard settings: mismatch cost = 2; insertion cost = 3; deletion cost = 3; length fraction = 0.8; similarity fraction = 0.8.
RPKMs were calculated based on uniqely mapped read numbers reported by the CLC genomics worbench version 10.01
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text-file including ENSEMBL gene ID, gene alias, chromosome, genomic position, unique gene reads, RPKM

molecule: polyA RNA

source_name: monocytic leukemia

growth_protocol: THP1 monocytes were cultured in RPMI 1640 medium (Thermo Fisher), containing 10 % FCS and 1% penicillin / streptomycin solution (Thermo Fisher).

extract_protocol:
Cells were washed once with PBS and RNA was extracted using the MirVana microRNA isolation kit (Ambion), following the total RNA isolation procedure. Obtained RNA was DNaseI digested, PCI extracted, precipitated with 30:1 ethanol / sodium-acetate and redissolved in water.
Libraries were prepared using the Vertis Biotech stranded mRNA in-house protocol
poly(A) RNA-Seq

treatment_protocol: Cells were activated with Salmonella typhimurium lipopolysaccharide (100 ng / ml) and poly I:C (10 µg / ml) for 4 h.

value: THP1 (monocytic cell line)

tag: precursor

value: monocyte

tag: donor

value: 1 year old male with acute monocytic leukemia

value: LUCAT1 CRISPRi vector


title: Control_CRISPRi_2

description: Control-transduced THP1 cells (containing empty CRISPRi vector)

tag: treatment

value: control


title: mTEC2_rep2

tag: tissue


title: CD4-Treated TAMs - biological repeat 4 - mAdbID:116696

type: RNA

city: Bethesda

first: Ainhoa

last: Perez-Diez

state: MD

address: 9000 Rockville Pike

institute: NIAID, NIH

description: mAdb experiment ID: 116696

hyb_protocol: Illumina Hybridization Protocol We applied 2 ug of conjugate to Illumina Mouse WG-6 v2.0 Expression BeadChip microarrays and hybridized at 48 degree Celsius for 16 hr, post-processed per manufacturer's instructions.

scan_protocol: Illumina Scanning Protocol Illumina Mouse WG-6 v2.0 Expression BeadChip microarrays were scanned using a HiScan (Illumina). Images were analyzed using Genome Studio software (Illumina).

data_processing:
BRB ArrayTool Data Processing
Calculation Method: Microarray data were analyzed using BRB Array Tools developed by the Biometric Research Branch of the National Cancer Institute under the direction of Dr. Richard Simon (http://linus.nci.nih.gov/BRB-ArrayTools.html). Array data were filtered to threshold the spot intensity of the probes at the minimum value if the spot intensity was <10, and a quantile normalization was applied.

label: biotin

source_name: CD4-treated TAMs

label_protocol:
NuGEN Biotinylation Protocol
RNA quality was verified by Bioanalyzer with RNA Integrity Number greater than 8.5 for all samples. Microarray target material was prepared by amplification of 50 ng total RNA using NuGEN WT-Ovation systems V2, followed by biotinylation with NuGEN Encore(TM) BiotinIL, using 4ug input of cDNA.

extract_protocol:
Qiagen miRNeasy Mini Kit Protocol
Sorted TAMs were lysed immediately post sort for RNA isolation using miRNeasy mini kit (Qiagen).

treatment_protocol: In-vivo treatment: Tumor bearing RAGKO mice were first challenged with 10(5) MB49 tumor cells s.c.. Five days later, half of the mice received Marilyn CD4 T cells i.p. All mice were euthanized 12 days after tumor challenge. The tumors were dissociated and cells stained with different antibodies to either compare the phenotype of Untreated versus CD4-treated TAMs or to compare their protein production. For the latter, between 10(5) and 1.25x10(5) TAMs sorted TAMs were plated in 200 uL of complete IMDM in 96 well-plates. Supernatants were collected 18 hours later and sent to Raybiotech, Inc. to measure cytokines and chemokines characteristic of M2 or M1 macrophages using a custom Cytokine array. Amount of protein in the supernatant was normalized to 10(5) cells. For the microarray experiments, sorted TAMs were lysed immediately post sort for RNA isolation. TAMs were sorted based on the markers CD11b+, MHC ClassII+, Gr-1neg and 7AADneg.

tag: strain backgroud

tag: genotype/variation

value: rag-/- (Rag KO)

value: Tumor Associated Macrophages (TAMs)


title: CD4-Treated TAMs - biological repeat 6 - mAdbID:116699

description: mAdb experiment ID: 116699


title: WT LMS_RNA_rep1

city: Wuhan

first: Xiaorong

last: Huang

address: Bayi Road

institute: College of Life Science, Wuhan university

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using hisat2 v2.1.0 with parameters -p 8 -t --no-unal --un-conc
Predicting new transcripts from the genome alignment using StingTie v1.3.5 with parameters -p 6 -G
Mapping the reads to the merged transcriptome set using bowtie2 and quantified the normalized expression level (FPKM) of each gene and transcript using RSEM v1.3.1 with parameters -p 4 --paired-end --bam
Genome_build: TAIR10
Supplementary_files_format_and_content: gene.fpkm_matrix.xls
Supplementary_files_format_and_content: isoform.fpkm_matrix.xls

organism: Arabidopsis thaliana

source_name: late microspore

growth_protocol: In greenhouse under long-day conditions (16 h light/8 h dark) at 22 °C

extract_protocol:
Total RNA of late microspore (about 100000 microspores per sample) was extracted using an RNeasy Plant Mini Kit (QIAGEN). Subsequent cDNA synthesis and amplification were performed using a SMART-Seq® HT Kit (Takara), and then purified using an Agencourt AMPure Purification Kit (Beckman Coulter). Purified cDNA was quantified by a Qubit 3.0 Fluorometer (Life Technologies) and validated using a Bioanalyzer 2100 system (Agilent Technologies).
Sequencing libraries were constructed using the VAHTS Universal V6 RNA-seq Library Kit for MGI (Vazyme) following the manufacturer's recommendations with unique index codes. The Library quantification and size was assessed using a Qubit 3.0 Fluorometer and Bioanalyzer 2100 system.

treatment_protocol: Unopened buds at late microspore stage were picked from plants and ground gently in ice-cold pollen buffer. The FACS of the late microspore (LMSs) on a BD FACSAria III cell sorter were preformed in standard configuration with a 100μm nozzle, and gate for microspores based on their green autofluorescence (488nm). Microspores also gate with a RFP (561nm) channel to allow the exclusion of unwished bicellular pollen. Microspores collected are maintained in ice and RNA was extracted immediately.

tag: ecotype

value: late microspore

tag: line


title: Untreated TAMs - biological repeat 6 - mAdbID:116700

description: mAdb experiment ID: 116700

source_name: Untreated TAMs

treatment_protocol: In-vivo treatment: Tumor bearing RAGKO mice were first challenged with 10(5) MB49 tumor cells s.c.. All mice were euthanized 12 days after tumor challenge. The tumors were dissociated and cells stained with different antibodies to either compare the phenotype of Untreated versus CD4-treated TAMs or to compare their protein production. For the latter, between 10(5) and 1.25x10(5) TAMs sorted TAMs were plated in 200 uL of complete IMDM in 96 well-plates. Supernatants were collected 18 hours later and sent to Raybiotech, Inc. to measure cytokines and chemokines characteristic of M2 or M1 macrophages using a custom Cytokine array. Amount of protein in the supernatant was normalized to 10(5) cells. For the microarray experiments, sorted TAMs were lysed immediately post sort for RNA isolation. TAMs were sorted based on the markers CD11b+, MHC ClassII+, Gr-1neg and 7AADneg.


title: OVCAR3_974_3

tag: genotype


title: CD4-Treated TAMs - biological repeat 5 - mAdbID:116697

description: mAdb experiment ID: 116697


title: Untreated TAMs - technical repeat 3 - mAdbID:116694

description: mAdb experiment ID: 116694


title: Untreated TAMs - technical repeat 5 - mAdbID:116698

description: mAdb experiment ID: 116698


title: CD4-Treated TAMs - technical repeat 3 - mAdbID:116693

description: mAdb experiment ID: 116693


title: Untreated TAMs - biological repeat 2 - mAdbID:116692

description: mAdb experiment ID: 116692


title: Untreated TAMs - biological repeat 1 - mAdbID:116690

description: mAdb experiment ID: 116690


title: Untreated TAMs - biological repeat 4 - mAdbID:116695

description: mAdb experiment ID: 116695


title: WT LMS_RNA_rep3


title: CD4-Treated TAMs - biological repeat 2 - mAdbID:116691

description: mAdb experiment ID: 116691


title: CD4-Treated TAMs - technical repeat 1 - mAdbID:116689

description: mAdb experiment ID: 116689


title: WT LMS_RNA_rep2


title: Control_CRISPRi_1


title: C42B_3

city: Frederick

first: Leah

middle: M

last: Cook

address: 1050 Boyles St, Room 21-89

institute: National Cancer Institute-Frederick

data_processing:
The original FASTQ format reads were trimmed by fqtrim tool (https://ccb.jhu.edu/software/fqtrim) to remove adapters, terminal unknown bases (Ns) and low quality 3’ regions (Phred score < 30).
For quality control (QC), the low quality 3’ regions were trimmed and only high quality reads with Phred score >=30 were retained.
The QC passed trimmed fastq files were mapped to hg38 reference genome using STAR 2.7.0f aligner and
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM and TPM values for each Sample …
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human bone marrow

extract_protocol:
Human bone marrow was purchased from Lonza and neutrophils were isolated using a modified Ficoll gradiant centrifugation protocol, as described1.  Isolated neutrophils were treated with either LNCaP or C42B prostate cancer cell conditioned media (CM) (n=3 biological replicates per CM) for 3 hours and RNA was isolated using Trizol reagent (Invitrogen).  RNA sequencing (RNA-seq) was performed on 6 total human neutrophil samples treated with CM.  Samples were analyzed with respect to purity and potential degradation in the UNMC Genomics Core Facility. Purity and concentration were assessed by measurement of the A260/280 ratios using a Nanodrop (Thermo Scientific, Nanodrop Products, Wilmington, DE) instrument and samples with values of 1.8 to 2.0 were processed.  Potential degradation of the sample was assessed by analysis of 200 ng of the RNA with an Advanced Analytical Technical Instruments Fragment Analyzer (AATI, Ames, IA) and only intact RNA samples were utilized to create sequencing libraries. Libraries were generated using 1 μg of total RNA from each sample.
TruSeq V2 RNA sequencing library kit from Illumina following recommended procedures (Illumina Inc., San Diego, CA)

value: neutrophils


title: V-Mt LMS_RNA_rep3

value: pLat52:REF6-GFP; pHTR10:HTR10-RFP


title: LNCaP_2

value: LNCaP


title: LNCaP_3


title: LNCaP_1


title: V-Mt LMS_RNA_rep2


title: C42B_1


title: V-Mt LMS_RNA_rep1


title: C42B_2


title: LUCAT1_CRISPRi_1


title: bb181sn_2_S18_2ndDS

city: Pavia

first: Ilaria

last: Palmieri

state: PV

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

data_processing:
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using Gencode Release m24 (GRCm38) as a reference, using the “-strandness forward” option. Differential expression analysis for mRNA and lncRNA was performed using R package DESeq2
Genome_build: HG19

source_name: substantia nigra

growth_protocol: Autoptic human brain samples were collected. Slices of basal ganglia, parietal lobe, hippocampus and substantia nigra were fresh cut into about 10 mm thickness and frozen at -80°C.

extract_protocol:
Samples were homogenized and total RNA was isolated by Trizol® reagent (Life Science Technologies, Italy) following the manufacturer’s specifications. RNAs were quantified using a Nanodrop ND-100 Spectrophotometer (Nanodrop Technologies, Wilmington, USA) and a 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit, Waldbronn, Germany); RNAs with a 260:280 ratio of ≥1.5 and an RNA integrity number of ≥2 were subjected to deep sequencing.
Sequencing libraries were prepared by the SENSE Total RNA-Seq Library Prep Kit for Illumina with RiboCop (Lexogen) using 500-ng total RNA. Qualities of sequencing libraries were assessed with 2100 Bioanalyzer (Agilent DNA 1000 Kit, Waldbronn, Germany). RNA processing has been carried out using Illumina NextSeq 500 Sequencing.

tag: disease

value: LBD


title: bb181sn_2_S18


title: bb181sn_1_S24


title: bb181lp_2_S15_2ndDS

source_name: parietal lobe


title: bb181lp_2_S15


title: bb181lp_1_S20


title: bb181ippo_2_S13

source_name: Hippocampus


title: bb181lp_1_S20_2ndDS


title: bb181ippo_2_S13_2ndDS


title: bb181ippo_1_S21


title: bb181ippo_1_S21_2ndDS


title: bb181sn_1_S24_2ndDS


title: scRNAseq C. elegans whole animals day 15, 1 technical replicate

city: South San Francisco

first: Han

last: Yuan

state: CA

address: 1170 Veterans Blvd

institute: Calico Life Sciences

description: 10x Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: CE11_WS268
Supplementary files format and content: Tab-separated values files and matrix files are CellRanger outputs in the filtered_feature_bc_matrix folder.

organism: Caenorhabditis elegans

source_name: all the tissues

growth_protocol: Worms were cultured on Nematode Growth Media (NGM) following standard methods, at 20°C or 25°C as indicated in OP50 E. coli (Brenner, 1974). Live E. coli colonize old worms leading to their premature death (Podshivalova et al., 2017). We chose to feed our population with killed OP50 to collect data during the geriatric period of the end of their life. For dead OP50, bacteria were treated with antibiotics, the only method we found to efficiently kill E. coli without altering their nutritive property. OP50 was grown in LB at 37°C overnight to saturation, then diluted in a large volume to OD 0.2 and cultured at 37°C until it reached OD 1 to 2. Gentamicin sulfate was then added to the culture at 200µg/mL and kept in the incubator for 5 hours. The resulting culture was centrifuged to pellet bacteria and resuspended in 1/75 the initial volume of LB gentamicin sulfate 16.7µg/mL. 2-layer agar plates were used to prevent worms from digging and to protect them from drying out. 15 mL autoclaved regular NGM containing 2% agar was poured in 10 cm plates. After 24 hours, 25 mL autoclaved NGM with 3% pure agarose was poured on top. Both layers contained gentamicin sulfate 16.7 µg/ml and carbenicillin 25 µg/ml, added in the solutions after autoclaving. After 24 hours, we added 0.5 mL dead bacteria solution under a sterile hood and we added another 0.5 ml when the lawn was dry. The plates were stored at 4°C. For an aging time course assay, a population of approximately 200,000 C. elegans was required. Twenty gon-2(q388) L4s larvae (P0) were sampled and transferred to 5 regular OP50 6cm plates (twenty per plate). The F1 eggs were collected in S-Basal-PEG without bleach according to (Roux et al., 2016) and transferred to new plates. 3 days later, the F2 eggs were collected from plates without males, and 300-500 of them were added to new plates. At the end of day-1 of adulthood, the F2s lay thousands of eggs per plate (we added a few drops of 50x concentrated OP50 to avoid starvation). At least 30,000 F2s eggs were collected in solution using the same method, they were used as parents of the last generation. They were washed 4 times in 12 mL S-basal-PEG and left overnight at 20°C to hatch. 2500 F2 L1s were transferred on each 10 10cm OP50 plate (25,000 L1s total). They were incubated 48 hours at 20°C until they reached the L4 stage. 300 µL of 50x concentrated OP50 were added on top of the bacterial loan to avoid starvation. They were then shifted to 25°C and incubated 24 hours. A total of 300,000-400,000 eggs were recovered. Parents were discarded by centrifugation and the eggs were treated for 30 seconds in bleaching solution, washed immediately 5 times in S-Basal-PEG and incubated in solution at 25°C for 12 hours to allow hatching (100% of them should hatch). We estimated the L1s concentration using a stereo-microscope. We transferred around 200,000 L1s into ‘2-layers’ 10cm-plate with 2500 L1s per plate. 0.5 mL of dead OP50 was added to the plates every day from day 4 to day 10. We closely monitored the plates to discard the contaminated ones. Most worms were gonad-less, but because q388 mutation in gon-2 is not fully penetrant at 25°C, some worms retained their fertility (about 1-2 eggs per 100 worms). For this reason, we kept the population at 25°C the entire aging time course to prevent the development of the fertile worms. Spontaneous apparition of rare males is tolerated, they represented around 1% of the last generation.

extract_protocol:
For a detail protocol please refer to Roux et al Biorxiv 2022 (https://doi.org/10.1101/2022.06.15.496201). Approximately 30,000 CF4596 worms were harvested per time point and washed 4 times in S-Basal/PEG 0.01%. Worms were pelleted in a 15mL tube. We added 3 times the volume of lysis buffer to the worm pellete (200 mM DTT, 0.25% SDS, 20 mM HEPES pH 8.0, 3% sucrose, stored at –20°C and used freshly thawed). The incubation time varied between 3 to 6 minutes. The worms were then quickly pelleted at around 200 rcf for 30 seconds. After pelleting the worms at 150 rcf for 20 seconds, the supernatant was removed and replaced with 1 mL freshly prepared pronase solution in L15 Leibovitz medium (L1518 Sigma adjusted to 340 m Osm with sucrose 28mM final; pronase 15mg/mL) as described in (Zhang et al., 2011). The pronase incubation was carried out at room temperature with gentle rocking for 5 to 15 minutes until about 5-30% of the worms broke open.  The debris and the unopened worms were separated from the cells at 150 rcf for 1 minute and the supernatant (cell suspension #1) was transferred to a new tube. 250uL L15-FBS 10% (FBS heat inactivated) was added to the 1 mL cell suspension #1 at 4°C to inactivate the pronase. The debris pellet was then treated again with 1 mL fresh pronase solution rocking at room temperature for an additional 3 minutes and returned on ice for a second mechanical cell extraction. The two cell suspensions were then pooled at 4°C and passed through a 35 µm nylon mesh (C. Murphy lab protocol), pre-wet with L15 340mOsm 2% inactivated FBS, to filter debris. We used a commercial cell strainer as the nylon mesh holder, after its original filter was cut out (Suppl. Notes 3A). The resulting cell suspension was centrifuged 7.5 minutes at 500 rcf 4°C. The resulting pellet was gently suspended in 3 mL 4°C egg buffer BSA (8 mM NaCl, 3 mM MgCl2-6H2O, 3 mM CaCl2, 5 mM HEPES, 48 mM KCl, pH 7.3, BSA added the same day 10 mg/mL). Hemocytometer C-Chip was used to estimate the cell concentration through a DIC microscope. The cell count was between a few million up to 20 million cells in total per isolation.
Single cell capture and library preparation followed 10X Genomics published protocols. Cells were processed into libraries using 10x Genomics Chromium Single Cell 3’ V3 Chemistry as directed by the manufacturer. 16,000 cells were loaded to aim for 10,000 cells per channel processed into a 10X Genomics Chromium chip, 3 channels per time point were used. cDNA was amplified for 12 cycles. Between 1/4 and 7/8 of the cDNA was moved forward into library construction, and the index PCR was cycled 12 times. Final libraries were brought to 2.4 nM and processed on an Illumina cBot and HiSeq4000 sequencer.

value: all the tissues

value: all the cell types

value: gon-2(q388) I; muIs274 [eft-3p:del:unc-54 3'UTR + Cbr-unc-119(+)] II; daf-2(mu465[daf-2::AID] III

tag: developmental stage

value: age day 15


title: scRNAseq C. elegans whole animals day 11, technical replicate 2

description: 10x Genomics

value: age day 11


title: bb118sn_2_S17

value: Helathy Control


title: bb181gb_2_S14_2ndDS

source_name: basal ganglia


title: bb181gb_1_S7


title: bb181gb_1_S7_2ndDS


title: bb181gb_2_S14


title: bb118sn_2_S17_2ndDS


title: bb118sn_1_S23


title: scRNAseq C. elegans whole animals day 3, technical replicate 2

description: 10x Genomics

value: age day 3


title: scRNAseq C. elegans whole animals day 5, technical replicate 2

description: 10x Genomics

value: age day 5


title: scRNAseq C. elegans whole animals day 1, technical replicate 2

description: 10x Genomics

value: age day 1


title: OPCs, siGPR17, 48h, rep2

city: Milano

first: Davide

last: Marangon

state: MI

address: Via Giuseppe Balzaretti 9

institute: Università degli studi di Milano

description: Gene expression in oligodendrocytes 48 h after transfection of siRNA for GPR17 transcript

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing Agilent fragmentation buffer and Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GE Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent  SurePrint G3 Rat Gene Expression v2 8x60K Microarray (G4858A-074036) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Rattus norvegicus

source_name: oligodendrocytes, 48h, siGPR17

label_protocol: Labelled cRNA was synthesized from 100 ng of total RNA using the Low Input Quick-Amp Labelling Kit, one colour (Agilent Technologies) in the presence of cyanine 3-CTP.

growth_protocol: Oligodendrocyte precursor cells were isolated from post-natal 2 rat cortices and plated in presence of bFGF and PDGF for 3 days to promote cell proliferation.

extract_protocol: Cells were lysed and RNA was extracted by means of RNeasy mini kit (Qiagen).

treatment_protocol: OPCs were transfected with 50 nM of GPR17 siRNA (or the negative control) by means of Lipofectamine RNAiMax by following manufacturer's protocol.

value: cortex

value: oligodendrocytes

tag: time

value: 2 Days in vitro (maturation)

value: GPR17 silencing


title: bb118sn_1_S23_2ndDS


title: OPCs, siNEG, 48h, rep1

description: Gene expression in oligodendrocytes 48 h after transfection of siRNA negative control

source_name: oligodendrocytes, 48h, siNEG

tag: cell type

value: control


title: OPCs, siGPR17, 48h, rep1


title: scRNAseq C. elegans whole animals day 11, technical replicate 1

description: 10x Genomics


title: OPCs, siNEG, 48h, rep2


title: bb118lp_2_S19_2ndDS


title: scRNAseq C. elegans whole animals day 8, technical replicate 1

description: 10x Genomics

value: age day 8


title: scRNAseq C. elegans whole animals day 8, technical replicate 2

description: 10x Genomics


title: scRNAseq C. elegans whole animals day 5, technical replicate 1

description: 10x Genomics


title: scRNAseq C. elegans whole animals day 3, technical replicate 1

description: 10x Genomics


title: bb118lp_1_S6_2ndDS


title: scRNAseq C. elegans whole animals day 1, technical replicate 1

description: 10x Genomics


title: Co_DL1_3

city: Columbus

first: Justin

middle: Ray

last: Kaspar

state: OH

address: 305 W 12th Ave

department: Biosciences

institute: The Ohio State University

description: repeat 3 of 3

data_processing:
Step 1: FASTQ Groomer
Step 2: FASTQ Quality Trimmer
Step 3: FastQC
Step 4: Map with Bowtie2
Step 5: sort
Step 6: featurecounts (see our publication for details)
Assembly: Streptococcus mutans: NC_004350.2
Assembly: Streptococcus gordonii: NC_009785.1
Assembly: Streptococcus sanguinis: NC_009009.1
Assembly: Streptococcus oralis: CP079724.1
Supplementary files format and content: Counts obtained from step 6: featurecounts, listed along side each open reading frame

organism:
Streptococcus gordonii
Streptococcus mutans

source_name: Whole cell lysate

growth_protocol: Bacterial cells used for extraction of RNA were grown in TYG medium, in the presence of 5% CO2 at 37°C without agitation, until they reached mid-exponential phase (OD600 ≈ 0.5)

extract_protocol:
Total RNA was extracted from bacterial cells using the RNeasy Mini kit (Qiagen), with chromosomal DNA removed using a DNase I kit (Qiagen).
cDNA libraries were constructed by MiGS
RNA-Seq: single-ended short reads were obtained from a set of bar-coded cDNA libraries

treatment_protocol: Cells were harvested by centrifugation at 4°C for 5 min, treated with bacterial RNAprotect Bacteria Reagent (Qiagen), and immediately stored at -80°C.

tag: strain

value: grown in coculture (TYG) to OD600 nm = 0.5


title: bb118ippo_2_S11_2ndDS


title: bb118lp_1_S6


title: bb118ippo_2_S11


title: Co_DL1_1

description: repeat 1 of 3


title: Co_DL1_2

description: repeat 2 of 3


title: WT SC_RNA_rep3

description:
MGISEQ-2000
gene.fpkm_matrix.txt
isoform.fpkm_matrix.txt

data_processing:
Data trimming: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. hisat2 v2.1.0 with parameters -p 8 -t --no-unal --un-conc
Alignment to genome: Maps data to TAIR10 whole genome. StringTie v1.3.5 with parameters -p 6 -G
New transcript prediction: Predict new transcripts based on RNAseq data. bowtie2 v2.3.5 with parameters -q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 4 -k 200
Alignment to transcript: Maps data to transcript sequences after prediction of new transcripts. RSEM v1.3.1 with parameters -p 4 --paired-end --bam
Expression level quantification: Quantify and normalized expression level (FPKM) of each gene and transcript.
Genome_build: TAIR10
Supplementary_files_format_and_content: gene.fpkm_matrix.txt: Normalized expression level (FPKM) for each gene in all samples; tab-delimited text.
Supplementary_files_format_and_content: isoform.fpkm_matrix.txt: Normalized expression level (FPKM) for each transcript in all samples; tab-delimited text.

source_name: sperm cell nuclei

growth_protocol: In greenhouse under long-day conditions (16 h light/8 h dark) at 22 °C.

extract_protocol:
mRNA was extracted from the FANS-isolated nuclei using a DynabeadsTM mRNA DIRECTTM Micro Purification Kit (Life Technologies). Subsequent cDNA synthesis and amplification were performed using a SMART-Seq® HT Kit (Takara), and then purified using an Agencourt AMPure Purification Kit (Beckman Coulter). Purified cDNA was quantified by a Qubit 3.0 Fluorometer (Life Technologies) and validated using a Bioanalyzer 2100 system (Agilent Technologies).
Sequencing libraries were constructed using the VAHTS Universal V6 RNA-seq Library Kit for MGI (Vazyme) following the manufacturer's recommendations with unique index codes. The library quantification and size were assessed using a Qubit 3.0 Fluorometer and Bioanalyzer 2100 system.

treatment_protocol: The collected pollen grains were re-suspended in Galbraith buffer (30mM Trisodium citrate dehydrate, 45mM MgCl2, 20mM MOPS, 0.1% (v/v) Triton X-100, adjust pH to 7.0) and then transferred to a 1.5 ml tube containing glass beads. Vortex continuously at 2000rpm for 3 min. Filter the sample through a 10μm nylon mesh in a 2ml tube to acquire the nucleus mixture. Fluorescence-activated SN and VN sorting were performed in a BD FACSAria III cell sorter. Use GFP (488nm) and RFP (561nm) to gate VN population (GFP-positive) and SN population (RFP-positive) respectively. Gate also for both VN and SN with a uniform side scatter (SSC) profile, which allowed the exclusion of debris and incomplete nuclei. The sorted nuclei were collected directly into Galbraith buffer and kept on ice for the subsequent experiments.

value: pACTIN11:H2B-GFP; pHTR10:HTR10-RFP

value: mature pollen

value: sperm cell


title: WT SC_RNA_rep2


title: bb118ippo_1_S4


title: bb118gb_2_S12


title: WT SC_RNA_rep1


title: bb118gb_1_S5_2ndDS


title: WT VC_RNA_rep3

source_name: vegetative cell nuclei

value: vegetative cell


title: WT VC_RNA_rep2


title: bb105sn_2_S16

value: AD


title: bb118ippo_1_S4_2ndDS


title: bb118gb_1_S5


title: WT VC_RNA_rep1


title: bb118lp_2_S19


title: V-Mt SC_RNA_rep3

value: pLat52:REF6-GFP; pHTR10:HTR15-RFP


title: bb105sn_1_S22


title: V-Mt SC_RNA_rep2

value: pLat52:REF6-GFP; pHTR10:HTR14-RFP


title: bb105sn_1_S22_2ndDS


title: V-Mt VC_RNA_rep3

value: pLat52:REF6-GFP; pHTR10:HTR12-RFP


title: V-Mt SC_RNA_rep1

value: pLat52:REF6-GFP; pHTR10:HTR13-RFP


title: bb118gb_2_S12_2ndDS

value: Helathy Control


title: bb105lp_1_S3


title: V-Mt VC_RNA_rep1

value: pLat52:REF6-GFP; pHTR10:HTR10-RFP


title: bb105lp_1_S3_2ndDS


title: bb105ippo_2_S8


title: bb105lp_2_S10_2ndDS


title: bb105ippo_2_S8_2ndDS


title: bb105ippo_1bis_S25_2ndDS


title: CD22#66

first: LIPEI

last: SHAO

address: 9000 Rockville Pike Bldg 10, 2C328

department: Center for Cellular Engineering

institute: National Institutes of Health

hyb_protocol: Hybridizations were performed per Nanostring manufacturer's protocol overnight for 65 degree, 18h in a thermocycler

scan_protocol: Cartridges were run on a Nanostring machine

data_processing: We used Partek Genomics Suite to do batch effect removal and normalization work. The normalization algorithm is built-in.

source_name: pre-infusion CAR T-cell product

label_protocol: Probe labeling was performed per Nanostring manufacturer's protocol

extract_protocol: Total RNA extracted from CAR T-cells using QIAGEN

value: CD3+ T cells

tag: crs grade

value: CRS grade 1


title: CD22#62

value: CRS grade 0


title: CD22#63

value: CRS grade 2


title: bb105ippo_2bis_S26_2ndDS


title: V-Mt VC_RNA_rep2

value: pLat52:REF6-GFP; pHTR10:HTR11-RFP


title: CD22#67


title: bb105gb_1_S2


title: BTZ_2nd_time_treated_cells_2nd_repeat

city: Szczecin

first: Tomasz

middle: K

last: Wojdacz

state: Zachodniopomorskie

address: Unii Lubelskiej 1

department: Independent Clinical Epigenetics Laboratory

country: Poland

institute: Pomeranian Medical University

description: DNA extracted from LUHMES cells treated with BTZ at second timepoint, 2nd repeat

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

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

data_processing: Data were processed in R, normalized using BMIQ normalization.

source_name: Cell Line

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from 1.5 × 106 dLUHMES cells using NucleoSpin TriPrep (Macherey Nagel, Düren, Germany) following the manufacturer's instructions.

tag: timepoint

value: Timepoint 2


title: bb105gb_2_S9_2ndDS


title: Control_at_1st_time_treated_cells_3rd_repeat

description: DNA extracted from non-treated LUHMES cells at first timepoint, 3rd repeat

value: Timepoint 1


title: CD22#55


title: LINC00211_ChIRP

description:
Eluate from ChIRP with LINC00211 antisense oligos
ChIRP_peaks.txt
Genomic DNA-Seq

data_processing:
Library strategy: ChIRP-Seq
RTA version 1.18.66.4 was used for basecalling
bcl2fastq version 1.8.4. was used for demultiplexing
Reads were mapped using the CLC genomics workbench version 10.01 and the GRCh38 human genome annotation with standard settings: mismatch cost = 2; insertion cost = 3; deletion cost = 3; length fraction = 0.8; similarity fraction = 0.8.
ChIRP peaks were identified using the CLC enomics worbench version 10.01 ChIP peak calling algorithm
Tab-delimited text-file including chromosome, genomic position, Center of peak, Length of peak, peak shape score, p-value
Genome_build: hg38

source_name: blood-derived CD14+ monocytes

growth_protocol: CD14+ monocytes from buffy coats were washed with PBS and crosslinked with Glutaraldehyde.

extract_protocol:
DNA was isolated the ChIRP method
Libraries were prepared using the Vertis Biotech stranded in-house ChIP protocol

treatment_protocol: Cells were left untreated

tag: cell line

value: CD14+ monocyte

value: common myeloid progenitor

value: healthy donor


title: BTZ_1st_time_treated_cells_2nd_repeat

description: DNA extracted from LUHMES cells treated with BTZ at first timepoint, 2nd repeat


title: Control_at_1st_time_treated_cells_1st_repeat

description: DNA extracted from non-treated LUHMES cells  at first timepoint, 1st repeat


title: CD22#54


title: Control_ChIRP

description:
Eluate from ChIRP with random antisense oligos
ChIRP_peaks.txt
Genomic DNA-Seq

tag: precursor


title: CLBGA 3AP prexasertib combination repl3

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

country: Belgium

institute: Ghent University

data_processing:
Adequate sequencing quality was confirmed using FastQC version 0.11.8 (Andrews, 2010).
To remove the “QuantSEQ FWD” adaptor sequence, the reads were trimmed using cutadapt version 1.18.
The trimmed reads were mapped to the human reference genome using the STAR aligning software v 2.6.0c.
The RSEM software, version v1.3.1, was used to generate count tables.
Genome_build: Homo sapiens GRCh38.89
Supplementary_files_format_and_content: tab-delimited text files include gene_id, transcirpt_id(s), gene length, effective_length, expected_counts, TPM an FPKM for each sample

source_name: CLBGA, 3AP_prexasertib_combination, 48h, replicate 3

extract_protocol:
RNA extraction was performed practicing the manufacturer’s instructions of miRNeasy kit (Qiagen) including on-column DNase treatment and nanodrop (Thermo Scientific) was used to determine the concentration.
Illumina mRNA sequencing libraries were made from 330 ng total RNA of each sample using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, Vienna, Austria) according to manufacturer's protocol. Fifteen PCR cycles were used during the enrichment PCR. The size distribution, purity (absence of free adaptors) and quantity of the resulting libraries were measured using a High Sensitivity DNA chip (Agilent Technologies, Santa Clara, CA, US). The libraries were equimolarly pooled and sequenced in an Illumina Nextseq 500 high throughput flow cell, generating single-end 75bp reads.

treatment_protocol: The adherent cell lines were seeded in a T-75 flask at density of 2x106 – 2.25x106 cells per flask, depending on the cell line. Cells were allowed to adhere for 48h, after which the medium was replaced by fresh medium and treated with either 3AP (IC15) or prexasertib alone or with the 3AP-prexasertib combination. After 48h of treatment the cells were scraped, centrifuged, for 5 minutes at 1200 rpm, and the pellet was washed twice with ice-cold PBS. During each wash, the cells were pelleted during 5 minutes at 1200 rpm.

value: CLBGA

tag: time point


title: COVID_scRNA-seq

description:
Peripheral blood mononuclear cells isolated from control and COVID-19 patients by density gradient centrifugation. Paired end dataset
scRNA-seq.txt
Targeted RNA panel

data_processing:
RTA version 1.18.66.4 was used for basecalling
bcl2fastq version 1.8.4. was used for demultiplexing
Read counts were loaded into the R (v3.6.3) environment and further analyzed using the Seurat package (v3.1.4)
Tab-delimited text-file including the columns "Cell Index", "Sample Tag" and "Sample name" (patient nr.), followed by columns with the respective HGNC gene ID as header. Gene ID columns contain molecule counts per cell. File contains scRNA-seq data from four patients (S14 = control 1, S16 = control 2, S2 = COVID-19_1, S7 = COVID-19_2)
Genome_build: hg38

source_name: peripheral blood mononuclear cells

growth_protocol: Whole PBMCs isolated from control and COVID-19 patient blood, stored in Vacutainer EDTA-tube

extract_protocol:
Single cell lysates were generated using a BD Rhapsody system
Libraries were prepared using the BD Rhapsody system with the immune response panel, combined with a custom lncRNA detection panel

value: peripheral blood mononuclear cells

value: hematopoietic stem cells

tag: donor

value: control patient w/o infection


title: BTZ_2nd_time_treated_cells_3rd_repeat

description: DNA extracted from LUHMES cells treated with BTZ at second timepoint, 3rd repeat


title: BTZ_2nd_time_treated_cells_1st_repeat

description: DNA extracted from LUHMES cells treated with BTZ at second timepoint, 1st repeat


title: CLBGA 3AP prexasertib combination repl4

source_name: CLBGA, 3AP_prexasertib_combination, 48h, replicate 4

tag: treatment


title: Control_at_2nd_time_treated_cells_2nd_repeat

description: DNA extracted from non-treated LUHMES cells at second timepoint, 2nd repeat


title: CD22#50

value: CRS grade 3


title: CD22#52


title: Control_at_2nd_time_treated_cells_1st_repeat

description: DNA extracted from non-treated LUHMES cells at second timepoint, 1st repeat


title: CD22#53


title: CD22#56


title: BTZ_1st_time_treated_cells_3rd_repeat

description: DNA extracted from LUHMES cells treated with BTZ at first timepoint, 3rd repeat


title: Control_at_1st_time_treated_cells_2nd_repeat

description: DNA extracted from non-treated LUHMES cells at first timepoint, 2nd repeat


title: CD22#49


title: CD22#48

value: CRS grade 4


title: Control_at_2nd_time_treated_cells_3rd_repeat

description: DNA extracted fromnon-treated LUHMES cells at second timepoint, 3rd repeat


title: bb105gb_2_S9

value: AD


title: BTZ_1st_time_treated_cells_1st_repeat

description: DNA extracted from LUHMES cells treated with BTZ at first timepoint, 1st repeat


title: CD22#61

value: CD3+ T cells


title: IMR32 3AP prexasertib combination repl2

source_name: IMR32, 3AP_prexasertib_combination, 48h, replicate 2


title: CD22#46

value: CRS grade 1


title: CLBGA prexasertib repl3

source_name: CLBGA, prexasertib, 48h, replicate 3

value: prexasertib


title: CD22#39


title: CLBGA prexasertib repl1

source_name: CLBGA, prexasertib, 48h, replicate 1


title: CLBGA 3AP prexasertib combination repl2

source_name: CLBGA, 3AP_prexasertib_combination, 48h, replicate 2


title: IMR32 prexasertib repl3

source_name: IMR32, prexasertib, 48h, replicate 3


title: CD22#36

value: CRS grade 2


title: CLBGA 3AP prexasertib combination repl1

source_name: CLBGA, 3AP_prexasertib_combination, 48h, replicate 1


title: CD22#34


title: IMR32 prexasertib repl1

source_name: IMR32, prexasertib, 48h, replicate 1


title: CD22#47


title: CLBGA 3AP repl3

source_name: CLBGA, 3AP, 48h, replicate 3


title: bb105gb_1_S2_2ndDS

source_name: basal ganglia


title: bb105sn_2_S16_2ndDS

source_name: substantia nigra


title: CLBGA 3AP repl1

source_name: CLBGA, 3AP, 48h, replicate 1


title: CD22#31

source_name: pre-infusion CAR T-cell product


title: CD22#57


title: IMR32 3AP prexasertib combination repl3

source_name: IMR32, 3AP_prexasertib_combination, 48h, replicate 3


title: CD22#26


title: bb105lp_2_S10

source_name: parietal lobe


title: IMR32 3AP repl2

source_name: IMR32, 3AP, 48h, replicate 2


title: IMR32 3AP repl1

source_name: IMR32, 3AP, 48h, replicate 1


title: CD22#29

value: CRS grade 0


title: CLBGA DMSO repl4

source_name: CLBGA, DMSO, 48h, replicate 4

value: DMSO


title: CLBGA DMSO repl3

source_name: CLBGA, DMSO, 48h, replicate 3


title: CLBGA 3AP repl2

source_name: CLBGA, 3AP, 48h, replicate 2


title: IMR32 3AP prexasertib combination repl1

source_name: IMR32, 3AP_prexasertib_combination, 48h, replicate 1


title: CD22#22


title: CD22#44


title: CD22#21


title: CLBGA prexasertib repl2

source_name: CLBGA, prexasertib, 48h, replicate 2


title: CLBGA prexasertib repl4

source_name: CLBGA, prexasertib, 48h, replicate 4


title: CD22#37


title: CD22#35


title: IMR32 prexasertib repl2

source_name: IMR32, prexasertib, 48h, replicate 2


title: CD22#23


title: CD22#19


title: CLBGA 3AP repl4

source_name: CLBGA, 3AP, 48h, replicate 4


title: CD22#33


title: IMR32 DMSO repl1

source_name: IMR32, DMSO, 48h, replicate 1


title: IMR32 3AP repl3

source_name: IMR32, 3AP, 48h, replicate 3


title: CD22#27


title: CLBGA DMSO repl2

source_name: CLBGA, DMSO, 48h, replicate 2


title: CD22#32


title: CD22#24


title: CD22#5


title: CD22#25


title: SHSY5Y_3AP_IC50_repl4

data_processing:
Adequate sequencing quality was confirmed using FastQC version 0.11.7 (Andrews, 2010).
To remove the “QuantSEQ FWD” adaptor sequence, the reads were trimmed using cutadapt version 1.15 (IMR32 and CLBGA cell lines) and 1.16 (SK-N-BE(2)-C and SHSY5Y cell lines).
The trimmed reads were mapped to the human reference genome using the STAR aligning software v 2.5.3a_modified (IMR32 and CLBGA cell lines) and  v 2.6.0c (SK-N-BE(2)-C and SHSY5Y cell lines).
The RSEM software, version v1.3.0 (IMR32 and CLBGA cell lines) and  v1.3.1 (SK-N-BE(2)-C and SHSY5Y cell lines) , was used to generate count tables.
Genome_build: Homo sapiens GRCh38.89
Supplementary_files_format_and_content: tab-delimited text files include gene_id, transcirpt_id(s), gene length, effective_length, expected_counts, TPM an FPKM for each sample

source_name: SHSY5Y, 3AP, IC50, 48h, repl4

extract_protocol:
RNA extraction was performed practicing the manufacturer’s instructions of miRNeasy kit (Qiagen) including on-column DNase treatment and nanodrop (Thermo Scientific) was used to determine the concentration.
Illumina mRNA sequencing libraries were made from 60 ng total RNA of the samples from the IMR32 and CLBGA cell lines and 200 ng total RNA of the samples from the SK-N-BE(2)-C and SHSY5Y cell lines using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, Vienna, Austria), with umi barcoding, according to manufacturer's protocol. Sixteen PCR cycles were used for the samples of the IMR32 and CLBGA cell lines and 15 PCR cycles were used for the samples of the SK-N-BE(2)-C and SHSY5Y cell lines during the enrichment PCR. The size distribution, purity (absence of free adaptors) and quantity of the resulting libraries were measured using a High Sensitivity DNA chip (Agilent Technologies, Santa Clara, CA, US). The libraries were equimolarly pooled and sequenced in an Illumina Nextseq 500 high throughput flow cell, generating single-end 75bp reads.

treatment_protocol: The adherent cell lines were seeded in a T-75 flask at density of 2x106 – 2.25x106 cells per flask, depending on the cell line. Cells were allowed to adhere for 48h, after which the medium was replaced by fresh medium and 3AP treatment was added. After 48h of treatment the cells were scraped, centrifuged, for 5 minutes at 1200 rpm, and the pellet was washed twice with ice-cold PBS. During each wash, the cells were pelleted during 5 minutes at 1200 rpm.

value: 3AP IC50


title: SHSY5Y_3AP_IC50_repl2

source_name: SHSY5Y, 3AP, IC50, 48h, repl2


title: tmRNA reverse mutant rep3

city: Shenzhen

first: Shanshan

last: Xu

address: Xueyuan Avenue, No. 1066

institute: Shenzhen University

description: Bacillus subtilis NCIB 3610

data_processing:
Illumina Casava1.7 software used for base-calling.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
HTSeq v0.6.1 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.
Assembly: CP020102
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

source_name: Bacteria

extract_protocol:
The growth status of samples in LBMG medium were analyzed and 36 hours was selected. The cells at the selected time point were collected and total RNA was extracted using the Total RNA Kit (OMEGA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: biofilm and planktonic bacteria

value: revertant strain (MB)

value: SsrA-


title: CD22#15

source_name: pre-infusion CAR T-cell product


title: CD22#2


title: CD22#16


title: tmRNA reverse mutant rep2

description: Bacillus subtilis NCIB 3610


title: tmRNA mutant rep3

description: Bacillus subtilis NCIB 3610

value: tmRNA mutant (TM)


title: CD22#9


title: CD22#7


title: tmRNA mutant rep2

description: Bacillus subtilis NCIB 3610


title: SHSY5Y_3AP_IC50_repl5

source_name: SHSY5Y, 3AP, IC50, 48h, repl5


title: CD22#8


title: SK-N-BE(2)-C_3AP_IC50_repl1


title: SK-N-BE(2)-C_3AP_IC50_repl2


title: CLBGA DMSO repl1

source_name: CLBGA, DMSO, 48h, replicate 1

value: CLBGA


title: CLBGA_3AP_IC50_repl3

source_name: CLBGA, 3AP, IC50, 48h, repl3


title: CLBGA_3AP_IC50_repl1

source_name: CLBGA, 3AP, IC50, 48h, repl1


title: SHSY5Y_3AP_IC50_repl3

source_name: SHSY5Y, 3AP, IC50, 48h, repl3


title: CD22#4


title: IMR32 DMSO repl2

source_name: IMR32, DMSO, 48h, replicate 2


title: SHSY5Y_3AP_IC50_repl1

source_name: SHSY5Y, 3AP, IC50, 48h, repl1


title: IMR32_3AP_IC50_repl3

source_name: IMR32, 3AP, IC50, 48h, repl3


title: SK-N-BE(2)-C_3AP_IC50_repl5


title: Co_So34_3

description: repeat 3 of 3

organism:
Streptococcus oralis
Streptococcus mutans

source_name: Whole cell lysate

value: grown in coculture (TYG) to OD600 nm = 0.5


title: tmRNA mutant rep1

description: Bacillus subtilis NCIB 3610


title: SK-N-BE(2)-C_3AP_IC50_repl3


title: wild-type rep3

description: Bacillus subtilis NCIB 3610

value: wild type (WT)

value: wild-type


title: CLBGA_3AP_IC50_repl4

source_name: CLBGA, 3AP, IC50, 48h, repl4


title: wild-type rep2

description: Bacillus subtilis NCIB 3610


title: Co_So34_2

description: repeat 2 of 3


title: IMR32_3AP_IC50_repl1

source_name: IMR32, 3AP, IC50, 48h, repl1


title: CLBGA_3AP_IC50_repl2

source_name: CLBGA, 3AP, IC50, 48h, repl2


title: wild-type rep1

description: Bacillus subtilis NCIB 3610


title: IMR32_3AP_IC50_repl4

source_name: IMR32, 3AP, IC50, 48h, repl4


title: tmRNA reverse mutant rep1

description: Bacillus subtilis NCIB 3610


title: SK-N-BE(2)-C_3AP_IC50_repl4


title: RPE-1_H3K27Ac_rep2

city: Amsterdam

first: Anoek

last: Friskes

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description: paired-end sequencing was performed but only the 'r1' read was used

data_processing:
54bp single-end reads. Mapped reads were filtered based on mapping quality of 20 using samtools version 0.1.19.
Reads were aligned to Hg38 using BWA (v0.7.17-r1188). Mapped reads were filtered for mapping quality using samtools (> 20)
Duplicates were marked with Picard MarkDupes function (v2.18) (http://broadinstitute.github.io/picard/).

growth_protocol: RPE-1 cells were grown in DMEMF12 with 6% FCS and 1%Pen/Strep. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
H3K27me3 (Millipore 07-449), H3K36me3 (Abcam 9050), H3K4me1 (Abcam 8895), H3K4me3 (Abcam 8580) ChIP-seq samples were used from (https://doi.org/10.1101/2021.02.02.429315). 65bp single-end reads were trimmed to 54bp reads and aligned to hg38 using BWA (v0.7.17-r1188). Mapped reads were filtered for mapping quality using samtools < MQ20.  samtools version 0.1.19.Only r1_were used.
H3K27ac, H3K9me3 and H2A.Z ChIP-seq samples were processed for library preparation (Part# 0801-03003, KAPA Biosystems kit) and sequenced with Illumina NovaSeq6000 54bp paired-end reads. Mapped reads were filtered based on mapping quality of 20 using samtools version 0.1.19. Only r1_were used.

treatment_protocol: Chromatin immunoprecipitations (ChIP) were performed as described (Stelloo et al. Oncogene 2018). For each ChIP 5 μg of specified antibody prebound to protein A beads were used.

value: retinal pigment epithelial cells

tag: chip antibody

value: H3K27Ac, Actif Motif #39133


title: IMR32_3AP_IC50_repl2

source_name: IMR32, 3AP, IC50, 48h, repl2


title: SHSY5Y_3AP_IC30_repl5

source_name: SHSY5Y, 3AP, IC30, 48h, repl5

value: 3AP IC30


title: IMR32 DMSO repl3

source_name: IMR32, DMSO, 48h, replicate 3


title: SHSY5Y_3AP_IC30_repl4

source_name: SHSY5Y, 3AP, IC30, 48h, repl4


title: RPE-1_H2A.Z_rep2


title: SK-N-BE(2)-C_3AP_IC30_repl5


title: RPE-1_H3K9me3_rep2


title: SK-N-BE(2)-C_3AP_IC30_repl4


title: RPE-1_H2A.Z_rep1


title: SK-N-BE(2)-C_3AP_IC30_repl1


title: MCF7, ac4C palmitate loaded with NAT10 siRNA_2

city: Jeddah

first: Mohammad

middle: Imran

last: Khan

state: Makkah

address: King Abdullah Road

department: Biochemistry

country: Saudi Arabia

institute: King Abdulaziz University

data_processing:
Raw data were recorded of fastq file which is then trimmed using Skewer 0.1.126
Mapping of different genome characters with BWA 0.7.12
The peak calling is done using MACS2 (threshold p value ≤ 0.05)
MEME and Dreme softwares were used to detect significant motif sequence in the peak
Differentially analysis of peaks was performed using diffbind followed by GO enrichment analysis using GOseq/top GO Bioconductor 2.13
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cell lysates were Iped by ac4C and IgG antibodies and total RNA was extracted using TRI reagent (Ambion)
acRIP-seq library construction was initially quantified using Qubit 2.0. Followed by the accurate library concentration quantified by q-PCR (library effective concentration >2nM) to ensure standard library quality.

treatment_protocol: Cells were treated with 25µM palmitate followed by transfection using NAT10 siRNA

value: Breast cancer

tag: rip antibody


title: CD22#51

source_name: pre-infusion CAR T-cell product

value: CD3+ T cells

value: CRS grade 3


title: CLBGA_3AP_IC30_repl3

source_name: CLBGA, 3AP, IC30, 48h, replicate 3


title: Co_So34_1

description: repeat 1 of 3


title: SHSY5Y_3AP_IC30_repl3

source_name: SHSY5Y, 3AP, IC30, 48h, repl3


title: PM exposure/control 3

first: Minhyeok

last: Lee

address: 158, Gwanjeodong-ro, Seo-gu

department: Department of Internal Medicine

institute: Konyang university hospital

hyb_protocol: DNA was hybridized to chip by Agilent’s ChiP-on-chip/aCGH Hybridization Kit.

scan_protocol: Scanned on an Agilent Technologies G2505C DNA Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version 11.5.1.1).

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Rat tendon_PM_rep3

label_protocol: Llabelled Cy3 for control group and Cy5 for particulate matter group

growth_protocol: sexually mature male Sprague–Dawley rats weighing 250 to 300 g (8-week-old) had tenotomy.

extract_protocol: DNA extracted using Qiaquick blood DNA mini kit following manufacturer's instructions. 1.0 μg of genomic DNA was fragmented by sonification (10s on/10s-off, 24 times, 40%). The fragmented DNA was incubated with MBD2bt protein for enrichment and nickel-coated magnetic bead were applied to purification. The enriched DNA fragments were amplified by WGA kit (Sigma, WGA2).

treatment_protocol: PM group was exposed to PM2.5 for 3 times a week for 6 weeks

value: Sprague-Dawley

tag: molecule

value: genomic DNA of tendon with tenotomy and repair

value: Exposured PM 2.5 inhalation

source_name: Rat tendon_control_rep3

tag: sample group

value: Not exposured PM 2.5 inhalation


title: SHSY5Y_3AP_IC30_repl2

source_name: SHSY5Y, 3AP, IC30, 48h, repl2


title: PM exposure/control 2

source_name: Rat tendon_PM_rep2

source_name: Rat tendon_control_rep2


title: SK-N-BE(2)-C_3AP_IC30_repl3


title: MCF7, IgG palmitate loaded with NAT10 siRNA_2

value: IgG (Cell signaling, ##2729S)


title: RPE-1_H3K9me3_rep1


title: RPE-1_Input_rep2


title: RPE-1_Input_rep1


title: S. aureus_single biofilm [SA5-N0790]

city: Braga

first: Ângela

last: França

address: Campus de Gualtar

department: Biological Engineering

country: Portugal

institute: University of Minho

description: S. aureus_single vs dual-species

data_processing:
Bcl2fastq version 2 (Illumina) was used for base calling and to convert data to FASTQ files.
CLC Genomics Workbench version 21 (QIAGEN) was used for quality, ambiguity and length trimming, using default settings. In addition, CLC was used for alignment, normalization of the reads (to Transcripts Per Million – TPM) and for the analysis of differential gene expression in single- vs dual-species biofilms. In the case of dual-species biofilms, reads were aligned with either S. aureus or P. aeruginosa genomes. Fold-change was calculated using single-species biofilms as control. Baggerley's test was applied to identify statistically significant alterations.
In the case of genes whose sequences were not detected (TPM = 0), TPM was replaced with 1 in order to be able to determined the minimum expression value for that particular gene.
Genome_build: CP009361 (S. aureus)
Genome_build: NZ_CP034244 (P. aeruginosa)
Supplementary_files_format_and_content: Processed data files are tab-delimited text files that contain (i) the gene locus tag, (ii) expression values (TPM) for each sample (in duplicates), (iii) mean of expression values (TPM) for each sample and, finaly, (iv) expression fold-change (using single species biofilms as a control). The list of genes presented was defined considering fold-change values greater than 2 and p-values less than 0.05.

organism: Staphylococcus aureus

source_name: S. aureus_single biofilm

growth_protocol: Single- and dual-species biofilms were grown as described in Magalhaes et al., 2021, Environmental Microbiology, 23(9), 5639-5649. In brief, overnight cultures of each species, grown in Tryptic Soy Broth (TSB) at 37ºC and 120 rpm in air conditions, were washed in sterile water and diluted in fresh TSB to obtain 1x10E7 CFU/mL. For dual-species cultures, a combination of 50% of the suspended inoculum of each species was used. Bacterial suspensions were further transferred to 24-well polystyrene plates (Orange Scientific, Braine- l’Alleud, Belgium) and incubated at 37ºC on a horizontal shaker (120 rpm) for 24h. This assay was performed six independent times.

extract_protocol:
Total RNA was extracted using RNeasy mini kit (QIAGEN) and as described in França et al., 2012, PLoS One 7 (5): e37480. In brief, cells were suspended in 600 µL of the lysis buffer provided by the kit, plus 500 µL of phenol and 12 µL of β-mercaptoethanol. This suspension was transferred to a safe lock tube (2 mL) with 0.4 g of acid-washed 150–212 mm glass beads (Sigma) and, using a BeadBugTM 6 (Benchmark Scientific) cells disruptor, the cells were lysed (4× 4500 rpm for 35 seconds, with 5 minutes intervals on ice between cycles). Finally, the tubes were centrifuged, and the suspension was transferred into a new tube. An equal volume of 70% of ethanol was added, the suspensions transferred into the RNeasy mini kit columns and the manufacturer's instructions were strictly followed. RNA quality was determined using Agilent TapeStation 4200 (Agilent) and RNA quality indicators were above 8 for all samples. Thereafter, total RNA obtained from three independent experiments were mixed and treated with TURBO DNase (Ambion) to degrade genomic DNA. Additionally, before the library construction, a NEBNext rRNA Depletion Kit (Bacteria) (NEB) was used to remove bacterial ribosomal RNA.
RNA libraries were prepared by strictly following the instructions of the kit KAPA HyperPrep (Roche). Libraries quality was determined using Agilent TapeStation 4200 and data were generated using Illumina NovaSeq 6000 (Illumina) from paired-end read (2 × 150 bp).

treatment_protocol: Biofilms cells (24h-old) were then collected and suspended in 1 mL of RNA protect bacteria reagent (Qiagen), diluted 2:1 in RNase-free water, as indicated by the manufacturer. After 5 minutes of incubation at room temperature, biofilm cells were harvested by centrifugation (3132 g, 20 minutes) and RNA isolation was performed.

value: Biofilm cells (24h)


title: SK-N-BE(2)-C_3AP_IC30_repl2


title: PM exposure/control 1

source_name: Rat tendon_PM_rep1

source_name: Rat tendon_control_rep1


title: MCF7, ac4C palmitate loaded with NAT10 siRNA_3


title: MCF7, ac4C palmitate loaded with NAT10 siRNA_1


title: CLBGA_3AP_IC30_repl1

source_name: CLBGA, 3AP, IC30, 48h, replicate 1


title: MCF7, Input palmitate loaded with NAT10 siRNA_2


title: RPE-1_H3K27Ac_rep1


title: MCF7, ac4C palmitate loaded scramble_3


title: MCF7, ac4C palmitate loaded scramble_2


title: IMR32_3AP_IC30_repl4

source_name: IMR32, 3AP, IC30, 48h, replicate 4


title: MCF7, IgG palmitate loaded with NAT10 siRNA_3


title: SHSY5Y_3AP_IC30_repl1

source_name: SHSY5Y, 3AP, IC30, 48h, repl1


title: CLBGA_3AP_IC30_repl4

source_name: CLBGA, 3AP, IC30, 48h, replicate 4


title: S. aureus_single biofilm [SA6-N0791]

description: S. aureus_single vs dual-species


title: CLBGA_3AP_IC30_repl2

source_name: CLBGA, 3AP, IC30, 48h, replicate 2


title: MCF7, IgG palmitate loaded with NAT10 siRNA_1


title: ChIP IP H3K4me1 Phalange Rep2

city: Rotterdam

first: Karol

last: Nowosad

address: Doctor Molewaterplein 40

institute: Erasmus MC

description: Transient_Cartilage_H3K4me1_IP_rep2_macs2_broad_peaks.broadPeak

data_processing:
In the ChIPseq primary analysis, the quality of reads was checked by FASTQC followed by removal of adapters using Trimmomatic tool.
Reads were mapped to the Gallus Gallus 6 reference genome using Bowtie2 followed by removal of PCR duplicates with Picard tool.
Peaks were called with MACS2.
In the RNAseq primary analysis, the quality of reads was validated with FASTQC and adapters were removed using Trimmomatic tool.
Reads were aligned to the  Gallus Gallus 6 reference genome using using STAR
Reads were counted by gene using FeatureCounts
Identification of differentially expressed genes was performed using DESeq2
Assembly: gg6
Supplementary files format and content: (RNA-seq) DESeq2 normalized abundance measurements ouput
Supplementary files format and content: (ChIP-seq) MACS2 narrow peaks files

organism: Gallus gallus

source_name: ChIP IP H3K4me1 Phalange

growth_protocol: Chick White Leghorn embryonated eggs were incubated at 38.5ºC in fixed humidity for 7.5 days, followed by evaluation of developmental stage based on the Hamilton Hamburger classification (HH). The joint interzones and adjacent phalange samples were microdissected from hindlimb digit-3

extract_protocol:
For the preparation of ChIPseq libraries, the histone-DNA complexes were immunoprecipitated with antibody.
For each sample, 100 specimens were collected from the 3rd hindlimb digit of developing chicken ebmryo (HH32) and pooled together. Further, samples were dissociated using Collagenase-II and passed through a 40-m cell strainer. The 1mln of cells were cross-linked and after series of washes the cell nuclei were further isolated. Subsequently, the nuclei were treated with SDS-containing lysis buffer, and chromatin was sheard obtaining the average size of 150 bp. For ChIP, 500 ng of sonicated chromatin was immunoprecipitated with 7.5 g of antibody. Input sample was collected prior to immunoprecipitation reaction. ChIP-seq libraries were prepared using QIAseq Ultra Low Input Library Kit (QIAGEN, Hilden, Germany). Briefly, DNA was end-repaired, adenosines were added to the 3 ends of dsDNA and adapters were ligated. Adapters containing DNA fragments were amplified by PCR using NEB starters. Mean library size was 300 bp. Libraries were run in the rapid run flow cell and were single-end sequenced (65 bp) on HiSeq 1500 (Illumina, San Diego, CA 92122 USA).

tag: tissue

value: phalange


title: MCF7, IgG palmitate loaded scramble_3


title: MCF7, IgG palmitate loaded scramble_1


title: ChIP Input H3K4me1 Phalange Rep1

description: Transient_Cartilage_H3K4me1_IP_rep1_macs2_broad_peaks.broadPeak

source_name: ChIP Input H3K4me1 Phalange


title: IMR32_3AP_IC30_repl1

source_name: IMR32, 3AP, IC30, 48h, replicate 1


title: ChIP Input H3K4me1 Phalange Rep2


title: ChIP IP H3K4me1 Phalange Rep1


title: MCF7, Input palmitate loaded with NAT10 siRNA_1


title: ChIP Input H3K4me1 Interzone Rep2

description: Interzone_H3K4me1_IP_rep2_macs2_broad_peaks.broadPeak

source_name: ChIP Input H3K4me1 Interzone

value: interzone


title: IMR32_3AP_IC30_repl3

source_name: IMR32, 3AP, IC30, 48h, replicate 3


title: MCF7, Input palmitate loaded with NAT10 siRNA_3


title: HeLA-KMT2B-3

city: Shanghai

first: Yu

last: Gan

address: 25/Ln. 2200 Xietu Road

institute: Shanghai Cancer Institute

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

source_name: HeLa

growth_protocol: HeLa cell line was cultured in DMEM containing 10% FBS and maintained at 37°C in 5% CO2.

extract_protocol:
The total RNA of HeLs cells was extracted with Trizol (Invitrogen) under the manufacturer’s guiding.
The cDNA libraries were constructed for each pooled RNA sample using the NEBNext® UltraTM Directional RNA library Prep Kit for Illumina according to the manufacturer’s instructions.

treatment_protocol: We established KMT2B-overexpression stable clones in HeLa cell by CRISPR/dCas9 synergistic activation mediator system.

value: HeLa

value: epithelial cell

tag: genotype

value: KMT2B stable overexpression

value: KMT2B overexpression


title: IMR32_3AP_IC30_repl2

source_name: IMR32, 3AP, IC30, 48h, replicate 2


title: ChIP IP H3K4me1 Interzone Rep2

source_name: ChIP IP H3K4me1 Interzone

tag: developmental stage


title: MCF7, Input palmitate loaded scramble_3


title: MCF7, ac4C palmitate loaded scramble_1


title: ChIP Input H3K4me1 Interzone Rep1

description: Interzone_H3K4me1_IP_rep1_macs2_broad_peaks.broadPeak


title: MCF7, Input palmitate loaded scramble_2


title: ChIP Input H3K27ac Phalange Rep3

description: Transient_Cartilage_H3K27ac_IP_rep3_macs2_broad_peaks.broadPeak

source_name: ChIP Input H3K27ac Phalange


title: MCF7, Input palmitate loaded scramble_1


title: HeLa-VC-2

value: wild type

value: control


title: HeLa-VC-3


title: SHSY5Y_DMSO_repl4

source_name: SHSY5Y, DMSO, 48h, replicate 4

value: DMSO

tag: time


title: HeLA-KMT2B-2

tag: cell type


title: SHSY5Y_DMSO_repl5

source_name: SHSY5Y, DMSO, 48h, replicate 5


title: HeLa-VC-1


title: ChIP Input H3K27ac Phalange Rep2

description: Transient_Cartilage_H3K27ac_IP_rep2_macs2_broad_peaks.broadPeak


title: HeLA-KMT2B-4


title: TP-472 -SK-UT-1 RNA rep3

city: Chicago

first: Qiwei

last: Yang

address: 5841 S. Maryland Avenue

department: Obstetrics and Gynecology

institute: University of Chicago

data_processing:
Quasi-mapping and quantification: salmon 1.4.0
Assembly: GRCh38
Supplementary files format and content: gene level raw abdunance in TSV format

source_name: uterine leiomyosarcoma cell line

growth_protocol: The uterine leiomyosarcoma cell line (SK-UT-1) was cultured and maintained in ATCC-formulated Eagle’s Minimum Essential Medium with 10% of fetal bovine serum

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

treatment_protocol: The SK-UT-1 cell line was treated with  TP-472 (5 uM) for 48 hours or vehicle control.

value: BRD9/7 inhibitor


title: SHSY5Y_DMSO_repl3

source_name: SHSY5Y, DMSO, 48h, replicate 3


title: ChIP Input H3K27ac Phalange Rep1

description: Transient_Cartilage_H3K27ac_IP_rep1_macs2_broad_peaks.broadPeak


title: TP-472 -SK-UT-1 RNA rep2


title: HeLA-KMT2B-1


title: HeLa-VC-4


title: ChIP IP H3K4me1 Interzone Rep1


title: VEH-SK-UT-1 RNA rep3

value: DMSO (VEH)


title: MCF7, IgG palmitate loaded scramble_2

value: Breast cancer


title: TP-472 -SK-UT-1 RNA rep4


title: ChIP IP H3K27ac Phalange Rep3

source_name: ChIP IP H3K27ac Phalange


title: SHSY5Y_DMSO_repl1

source_name: SHSY5Y, DMSO, 48h, replicate 1


title: SHSY5Y_DMSO_repl2

source_name: SHSY5Y, DMSO, 48h, replicate 2


title: SK-N-BE(2)-C_DMSO_repl3

source_name: SK-N-BE(2)-C, DMSO, 48h, replicate 3


title: SK-N-BE(2)-C_DMSO_repl4

source_name: SK-N-BE(2)-C, DMSO, 48h, replicate 4


title: SK-N-BE(2)-C_DMSO_repl2

source_name: SK-N-BE(2)-C, DMSO, 48h, replicate 2


title: SK-N-BE(2)-C_DMSO_repl1

source_name: SK-N-BE(2)-C, DMSO, 48h, replicate 1


title: ChIP Input H3K27ac Interzone Rep3

description: Interzone_H3K27ac_IP_rep3_macs2_broad_peaks.broadPeak

source_name: ChIP Input H3K27ac Interzone


title: TP-472 -SK-UT-1 RNA rep1


title: VEH-SK-UT-1 RNA rep4


title: ChIP Input H3K27ac Interzone Rep2

description: Interzone_H3K27ac_IP_rep2_macs2_broad_peaks.broadPeak


title: Gliadel responding patient2

city: Udine

first: Emiliano

last: Dalla

state: UD

address: Piazzale Kolbe 4

department: Department of Medicine

institute: Università degli Studi di Udine

description:
Gliadel responding patient
S432 GASC

data_processing:
Quality control for raw sequencing reads was performed using the FastQC (v0.11.9) and MultiQC (v1.09)
Quality, adapters and contamination filtering were performed using the Trimmomatic command-line tool
Processed reads were aligned to the NCBI GRCh38 human reference using STAR (v2.7.1a)
Transcript assembly and the number of reads per gene were determined using Stringtie (RNA-seq)
Differentially expressed genes were identified using the DESeq2 R/Bioconductor package. Extended gene annotations (including HGNC gene symbol, description and transcript type) were obtained using the biomaRt R/Bioconductor package
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample (RNA-seq)

source_name: Glioblastoma multiforme tissue

growth_protocol: Glioma-associated stem cells (GASC) were isolated from surgical samples of removed tumor, before GW implantation, and maintained, in vitro, applying, with minor modifications, a protocol optimized for culturing multipotent adult stem cells from normal and neoplastic human tissues. Briefly, GBM fragments were first mechanically disaggregated with scalpels and then enzymatically dissociated, in a 0.025% Collagenase type II solution in Joklik modified Eagle’s Medium, for 5 min at 37 °C. Collagenase activity was stopped by adding 10% Fetal Bovine Serum in Joklik modified Eagle’s Medium. Cell suspension was centrifuged at 500× g for 10 min after being filtered through a sieve to select a population less than 40 μm in diameter.

extract_protocol:
Universal Plus mRNA-Seq kit (Tecan Genomics, Redwood City, CA) was used for library preparation following the manufacturer’s instructions (library type: fr-secondstrand)
Libraries were prepared for sequencing using standard Illumina protocols and sequenced on single-end 150 bp mode on NovaSeq 6000  (Illumina, San Diego, CA).

treatment_protocol: 2.0 × 106 freshly isolated human cells were plated onto 100 mm diameter, human fibronectin-coated dishes, in an expansion medium composed as follows: 60% low glucose DMEM, 40% MCDB-201, 1 mg/mL linoleic acid-BSA, 10−9 M dexamethasone, 10−4 M ascorbic acid-2 phosphate, 1× insulin-transferrin-sodium selenite, 2% foetal bovine serum, 10 ng/mL human PDGF-BB, 10 ng/mL human EGF.

value: brain

tag: gender

value: Female

tag: group

value: Gliadel responding

tag: # of passage

tag: days in culture


title: VEH-SK-UT-1 RNA rep1

tag: cell line


title: ChIP IP H3K27ac Phalange Rep2


title: ChIP IP H3K27ac Phalange Rep1


title: Gliadel responding patient3

description:
Gliadel responding patient
S464 GASC

value: Male


title: CLBGA_DMSO_repl3

source_name: CLBGA, DMSO, 48h, replicate 3

value: CLBGA


title: Gliadel responding patient1

description:
Gliadel responding patient
S431 GASC


title: CLBGA_DMSO_repl4

source_name: CLBGA, DMSO, 48h, replicate 4


title: SK-N-BE(2)-C_DMSO_repl5

source_name: SK-N-BE(2)-C, DMSO, 48h, replicate 5


title: hFFs, dox-IFN, rep3

city: Ulm

first: Thomas

last: Stamminger

address: Albert-Einstein-Allee 11

department: Institute of Virology

institute: Ulm University Medical Center

data_processing:
Samples were aligned to the human genome version hg19 using bowtie2 (version 2.3.3.1)
Alignments were sorted using samtools (version 1.9)
Readcounting was performed using htseq-count (version 0.9.1) and required hg19 gtf file
Genome_build: hg19
Supplementary_files_format_and_content: readcounts were generated using Homo_sapiens.GRCh37.75.gtf

source_name: hFFs, dox-IFN

growth_protocol: Cells were maintained in MEM (Gibco™/Thermo Fisher Scientific) supplemented with 10% tetracycline-free FCS (v/v), 1× GlutaMAX™ Supplement (Gibco™/Thermo Fisher Scientific), 10 μg/ml gentamicin, and 1 μg/ml puromycin

extract_protocol:
Cells were lysed with TRIzol Reagent, and total RNAs were isolated using the Direct-zol RNA Miniprep Kit (Zymo Research; R2052)
RNA libraries were prepared at Macrogen using standard Illumina protocols

treatment_protocol: Cells were treated with doxycycline (500 ng/ml) for 14 d to induce an ATRX knockdown, followed by stimulation with IFN-β for 24 h

value: dox-induced ATRX knockdown

value: dox-treated and stimulated with IFN-β

value: human foreskin fibroblasts (hFFs)


title: ChIP Input H3K27ac Interzone Rep1

description: Interzone_H3K27ac_IP_rep1_macs2_broad_peaks.broadPeak

value: interzone


title: hFFs, dox-IFN, rep2


title: hFFs, dox-IFN, rep1


title: ChIP IP H3K27ac Interzone Rep2

source_name: ChIP IP H3K27ac Interzone


title: CLBGA_DMSO_repl1

source_name: CLBGA, DMSO, 48h, replicate 1


title: Gliadel non-responding patient 1

description:
Gliadel non-responding patient
S471 GASC

value: Gliadel non-responding


title: VEH-SK-UT-1 RNA rep2

source_name: uterine leiomyosarcoma cell line


title: hFFs, dox, rep3

source_name: hFFs, dox

value: dox-treated


title: ChIP IP H3K27ac Interzone Rep3


title: IMR32_DMSO_repl4

source_name: IMR32, DMSO, 48h, replicate 4


title: Kidney- p49_snRNA-seq

city: New Haven

first: Nenad

last: Sestan

state: CT

address: 333 Cedar Street

department: Neuroscience

institute: Yale University

data_processing:
The cellranger version 5.0.1 commercial software was utilized to conduct the initial data processes.
Seurat and some in-house customized scripts were used to manage the single nuclei transcriptomic datasets.
For detailed snRNAseq analysis methods see Supplementary Information.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: .Rdata file includes counts for every gene in each cell and meta information for every cell

organism: Sus scrofa

source_name: Kidney

extract_protocol:
After administered anesthesia, circulatory collapse was induced with ventricular fibrillation to pigs 3-4 months of age for each experimental group (0h WIT, 1h WIT, 7h WIT, ECMO and OrganEx). Following the appropriate experimental condition, regions of interest were extracted from each organ and frozen at -80 ºC. Nuclei isolation from each organ (brain, heart, liver, kidney) were treated the same according to our already established protocol. The procedures/ dissections were performed in chilled RNAase-free PBS with RNase-free sterilized instruments under RNase-free conditions. Nuclei from injured and control frozen cerebral tissues were isolated by Dounce homogenization and centrifugation. Extracted nuclei samples were placed on ice and taken to the Yale Center for Genome Analysis core facility and processed within 15 minutes for single nucleus RNA sequencing. For more detail see Supplementary Information.
RNA libraries were prepared for sequencing using standard manufacturer (Illumina) protocols

value: Kidney

tag: age

value: 3-4 months

tag: condition

value: OrganEx


title: Kidney- p48_snRNA-seq


title: ChIP IP H3K27ac Interzone Rep1


title: Kidney- p46_snRNA-seq


title: Gliadel non-responding patient 2

description:
Gliadel non-responding patient
S419 GASC


title: hFFs, dox, rep2

tag: treatment


title: Kidney- p28_snRNA-seq

value: Ecmo


title: IMR32_DMSO_repl2

source_name: IMR32, DMSO, 48h, replicate 2

value: DMSO


title: hFFs, dox, rep1


title: CLBGA_DMSO_repl2

source_name: CLBGA, DMSO, 48h, replicate 2


title: hFFs, wt-IFN, rep1

source_name: hFFs, wt-IFN

value: control

value: stimulated with IFN-β


title: Kidney- p27_snRNA-seq


title: CLBGA_siRNA_RRM2_si62_repl3

data_processing:
Adequate sequencing quality was confirmed using FastQC version 0.11.8 (Andrews, 2010).
To remove the “QuantSEQ FWD” adaptor sequence, the reads were trimmed using cutadapt version 1.18.
The trimmed reads were mapped to the human reference genome using the STAR aligning software v 2.6.0c.
UMI-Tools version 1.0.1 was used to remove the PCR duplicates based on the UMI sequence.
The RSEM software, version v1.3.1, was used to generate count tables.
Genome_build: Homo sapiens GRCh38.89
Supplementary_files_format_and_content: tab-delimited text files include gene_id, transcirpt_id(s), gene length, effective_length, expected_counts, TPM an FPKM for each sample

source_name: CLBGA, RRM2 siRNA, si62, 72h, replicate 3

growth_protocol: Human neuroblastoma cell lines IMR32 and CLBGA were grown in RPMI 1640 medium supplemented with 10% fetal calf serum (FCS), 100 IU/mL penicillin/streptomycin and 2mM L-glutamine.

extract_protocol:
RNA was collected 72h post-transfection. RNA extraction was performed according to  the manufacturer’s instructions of miRNeasy kit (Qiagen) including on-column DNase treatment and nanodrop (Thermo Scientific) was used to determine the concentration.
Illumina mRNA sequencing libraries were made from 220 ng total RNA of each sample using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, Vienna, Austria), with umi barcoding, according to manufacturer's protocol. Thirteen PCR cycles were used during the enrichment PCR. The size distribution, purity (absence of free adaptors) and quantity of the resulting libraries were measured using a High Sensitivity DNA chip (Agilent Technologies, Santa Clara, CA, US). The libraries were equimolarly pooled and sequenced in an Illumina Nextseq 500 high throughput flow cell, generating single-end 75bp reads.

treatment_protocol: IMR32 and CLBGA neuroblastoma cells were transfected with 100 nM of two independent RRM2 targeting siRNAs (s12361 and s12362, Ambion, Thermo Fischer Scientific) or a control siRNA  (#AM4635, Ambion, Thermo Fischer Scientific) using the Neon transfection Kit (Cat. No. MPK10096).

value: RRM2 siRNA, si62

value: 72h post electroporation


title: hFFs, wt-IFN, rep2


title: CLBGA_siRNA_RRM2_si62_repl2

source_name: CLBGA, RRM2 siRNA, si62, 72h, replicate 2


title: Kidney- p50_snRNA-seq


title: IMR32_DMSO_repl3

source_name: IMR32, DMSO, 48h, replicate 3


title: IMR32_DMSO_repl1

source_name: IMR32, DMSO, 48h, replicate 1


title: Kidney- p32_snRNA-seq

value: 7h PMI


title: hFFs, wt-IFN, rep3


title: CLBGA_siRNA_RRM2_si62_repl1

source_name: CLBGA, RRM2 siRNA, si62, 72h, replicate 1

value: CLBGA


title: hFFs, wt, rep 3

source_name: hFFs, wt

value: untreated


title: Kidney- p33_snRNA-seq


title: hFFs, siATRX-IFN, rep 2

data_processing:
Trimming of the adaptors was   performed with either cutadapt or Trim_Galore!
Reads were aligned to hg38 using BWA software v.0.7.5a
Samples were   filtered for regions blacklisted by the ENCODE project
PCR duplicates and multimapping reads were removed using samtools
Alignment coordinates were converted to BED format using BEDTools v.2.17 and peak calling was performed using Epic2
Genome_build: hg38
Supplementary_files_format_and_content: NARROWPEAK files with the positions of the peaks

source_name: hFFs, siATRX-IFN

growth_protocol: Cells were maintained in MEM (Gibco™/Thermo Fisher Scientific) supplemented with 10% FCS (v/v), 1× GlutaMAX™ Supplement (Gibco™/Thermo Fisher Scientific), 1× penicillin-streptomycin, and 1 μg/ml puromycin

extract_protocol:
Isolation of nuclei was carried out by Diagenode SA (Seraing (Ougrée), Belgium) utilizing the ATAC-seq service (Assay for Transposase-Accessible Chromatin) (Diagenode Cat# G02060000). Nuclei were isolated with a concentration of 0.4% of Igepal CA-630 in the lysis buffer.
Library preparation was carried out by Diagenode SA (Seraing (Ougrée), Belgium) utilizing the ATAC-seq service (Assay for Transposase-Accessible Chromatin) (Diagenode Cat# G02060000). Lysed nuclei were transposed for 30 minutes at 37°C using the prokaryotic Tn5 transposase system (Nextera DNA library kit, Illumina, FC-121–1030), purified on Diapure columns (Diagenode, C03040001), and libraries were prepared using NEBNext High-Fidelity PCR MasterMix (NEB, M0541) and Illumina indexing primers

treatment_protocol: Cells were treated with IFN-β for 24h

value: ATRX knockdown


title: hFFs, siATRX-IFN, rep1

value: human foreskin fibroblasts (hFFs)


title: IMR32_siRNA_RRM2_si62_repl1

source_name: IMR32, RRM2 siRNA, si62, 72h, replicate 1


title: IMR32_siRNA_RRM2_si62_repl2

source_name: IMR32, RRM2 siRNA, si62, 72h, replicate 2


title: Kidney- p40_snRNA-seq

value: 1h PMI


title: Kidney- p26_snRNA-seq


title: Kidney- p38_snRNA-seq


title: IMR32_siRNA_RRM2_si62_repl3

source_name: IMR32, RRM2 siRNA, si62, 72h, replicate 3


title: hFFs, siATRX, rep2

source_name: hFFs, siATRX


title: CLBGA_siRNA_RRM2_si61_repl3

source_name: CLBGA, RRM2 siRNA, si61, 72h, replicate 3

value: RRM2 siRNA, si61


title: Kidney- p43_snRNA-seq

value: 0h PMI


title: hFFs, wt, rep2


title: hFFs, wt, rep1


title: hFFs, siC-IFN, rep 2

source_name: hFFs, siC-IFN


title: Kidney- p42_snRNA-seq

source_name: Kidney

value: Kidney


title: CLBGA_siRNA_RRM2_si61_repl1

source_name: CLBGA, RRM2 siRNA, si61, 72h, replicate 1


title: hFFs, siATRX, rep1


title: IMR32_siRNA_RRM2_si61_repl3

source_name: IMR32, RRM2 siRNA, si61, 72h, replicate 3


title: IMR32_iRNA_RRM2_si61_repl2

source_name: IMR32, RRM2 siRNA, si61, 72h, replicate 2


title: hFFs, siC, rep2

source_name: hFFs, siC


title: Liver- p48_snRNA-seq

source_name: Liver

value: Liver

value: 3-4 months


title: IMR32_siRNA_RRM2_si61_repl1

source_name: IMR32, RRM2 siRNA, si61, 72h, replicate 1


title: hFFs, siC, rep1


title: Kidney- p39_snRNA-seq


title: Liver- p46_snRNA-seq

value: OrganEx


title: CLBGA_control_siRNA_repl3

source_name: CLBGA, control siRNA, 72h, replicate 3

value: control siRNA


title: i-Omomyc-ONS76 Sample 18

city: Omaha

first: Jordan

last: Rowley

state: NE

address: 3828 Jones St, Apt 202

institute: University of Nebraska Medical Center

data_processing:
Reads were aligned and mapped to reference genome hg38 using STAR 2.7.3a
Peaks from bigwig flies were visualized using IGV
TPM values were calculated using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: ONS76, LNCaP, and DU145 and derived cell lines engineered for the inducible overexpression of SOX2: i-SOX2-ONS76, i-SOX2-LNCaP, and i-SOX2-DU145 have been described previously (21, 22). UW228 cells were obtained from Sutapa Ray (UNMC, Omaha, NE). HCT116 cells were obtained from American Type Culture Collection (Manassas, VA). All cells, including i-SOX2-derived lines, were cultured in Dulbecco’s Modified Eagle (DME) Medium supplemented with 10% fetal bovine serum. Doxycycline (Dox, Clontech, Mountain View, CA) was suspended in phosphate buffered  saline (PBS).

extract_protocol:
RNA isolation was performed using the RNeasy kit (Qiagen, Germantown, MD). Cells were lysed using RLT buffer and Qiashredder columns (Qiagen, Germantown, MD) as outlined in the manufacturer’s protocols.
i-SOX2-ONS76, i-SOX2-LNCaP, and i-Omomyc-ONS76 cells were cultured in the presence or absence of Dox for 4 days. mRNA was harvested as outlined above. RNA samples were assessed for purity and quality. Library preparation and transcriptome sequencing on an Illumina NovaSeq 6000 platform were performed by Novogene (Beijing, China).

treatment_protocol: SOX2 overexpression was induced by adding Dox to the culture medium at the times and concentrations indicated. Tamoxifen (4-OHT, Sigma, St. Louis, MO) was dissolved in ethanol. MYC-ER nuclear translocation was induced by adding 4-OHT to the culture medium at the indicated times and concentrations. Cell proliferation was assessed by MTT assays performed on triplicate samples as described previously (19-22). Statistical significance was determined using a two-tailed students t-test with a significance threshold of p=.05. Cell lines not obtained from American Type Culture Collection were verified by genetic analysis performed by the UNMC Molecular Diagnostics Laboratory. All cell lines were tested for the presence of mycoplasma and found to be negative.


title: i-Omomyc-ONS76 Sample 17


title: CLBGA_control_siRNA_repl1

source_name: CLBGA, control siRNA, 72h, replicate 1


title: CLBGA_control_siRNA_repl2

source_name: CLBGA, control siRNA, 72h, replicate 2


title: Liver- p50_snRNA-seq

value: Ecmo


title: Liver- p27_snRNA-seq


title: IMR32_control_siRNA_repl3

source_name: IMR32, control siRNA, 72h, replicate 3


title: Liver- p33_snRNA-seq


title: IMR32_control_siRNA_repl2

source_name: IMR32, control siRNA, 72h, replicate 2


title: Liver- p28_snRNA-seq


title: CLBGA_siRNA_RRM2_si61_repl2

source_name: CLBGA, RRM2 siRNA, si61, 72h, replicate 2


title: i-Omomyc-ONS76 Sample 14


title: Liver- p32_snRNA-seq


title: i-Omomyc-ONS76 Sample 15


title: hFFs, siC-IFN, rep1

value: control

value: stimulated with IFN-β


title: i-Omomyc-ONS76 Sample 16


title: Liver- p26_snRNA-seq


title: i-SOX2-ONS76 Sample 12


title: Liver- p49_snRNA-seq


title: IMR32_control_siRNA_repl1

source_name: IMR32, control siRNA, 72h, replicate 1

value: 72h post electroporation


title: i-SOX2-ONS76 Sample 11


title: Liver- p40_snRNA-seq


title: Liver- p39_snRNA-seq


title: i-SOX2-ONS76 Sample 9


title: Kidney- p41_snRNA-seq


title: i-SOX2-ONS76 Sample 10


title: Liver- p38_snRNA-seq