title: FPKM.MET_40mM_3

city: Jinan

first: Weiting

last: Kang

state: Shandong

address: No. 324, Jingwu Road and Weiqi Road

department: Department of Urology

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

data_processing:
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million
Assembly: GRCH 38
Supplementary files format and content: tab-delimited text file includes fpkm and raw counts for all Samples

extract_protocol:
Using TRIzol (ThermoFisher, 15596018), the RNA of the total sample was isolated and purified according to the operating protocol provided by the manufacturer. Then, NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA) was used to control the quantity and purity of total RNA, and the integrity of RNA was detected by Bioanalyzer 2100 (Agilent, CA, USA); A concentration>50ng/μ L, RIN value>7.0, and total RNA>1 μ g are sufficient for downstream experiments.
Use oligo (dT) magnetic beads (Dynabeads Oligo (dT), cat. 25-61005, Thermo Fisher, USA) to specifically capture mRNA containing PolyA (polyadenylation) through two rounds of purification. The captured mRNA was fragmented using the NEBNextR Magnesium RNA Fragmentation Module (cat. E6150S, USA) under high temperature conditions at 94 ℃ for 5-7 minutes. CDNA was synthesized from fragmented RNA using reverse transcriptase (Invitrogen SuperScriptTM II Reverse Transcriptase, cat. 1896649, CA, USA). Then use E Coli DNA polymerase I (NEB, cat. m0209, USA) and RNase H (NEB, cat. m0297, USA) were subjected to double stranded synthesis, converting the complex double stranded DNA with RNA into DNA double stranded DNA. At the same time, dUTP Solution (Thermo Fisher, cat. R0133, CA, USA) was added to the double stranded DNA to fill the ends of the double stranded DNA to a flat end. Add an A base at each end to allow it to connect with a linker with a T base at the end, and use magnetic beads to screen and purify its fragment size. Use UDG enzyme (NEB, cat. m0280, MA, US) to digest the second strand, and then perform PCR pre denaturation at 95 ° C for 3 minutes, followed by 8 cycles of denaturation at 98 ° C for 15 seconds each time. After annealing to 60 ° C for 15 seconds, extend at 72 ° C for 30 seconds, and finally extend at 72 ° C for 5 minutes to form a library with a fragment size of 300bp ± 50bp (chain specific library). Finally, we performed double ended sequencing on Illumina NovaseqTM 6000 (LC Bio Technology CO., Ltd. Hangzhou, China) according to standard procedures using PE150 sequencing mode.

value: Metformin 40mM


title: MDA-MB-231_Leucine_depletion_1

status: Public on Dec 27 2024

type: SRA

city: Amsterdam

first: Pierre-Rene

last: Körner

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute (NKI)

library_source: transcriptomic

data_processing:
RiboSeq: Adaptors were removed from FASTQ files using cutadapt with parameters (-quality-base=33 -O 7 -e 0.15 -m 20 -q 5). Ribosomal RNA (rRNA) and tRNA contaminants were removed by aligning FASTQ reads with Bowtie2 and parameters ( -seed 42 -p1 -local) against a reference library (rRNA reference was obtained from GENCODE v19: rRNA, MT_RNA, rRNA_pseudogene, and tRNA reference data was obtained from GtRNAdb). Preprocessed FASTQ files were then aligned with TopHat2 and Bowtie2 against GRCh37/hg19 and GENCODE v19/BASIC transcripts with Ensembl coordinates using the parameters (seed 41 -n 2-m 1 -novel-juncs -- no-novel-indels –no-coverage-search –segment-length 25). Aligned reads were then filtered for minimum mapping quality of 10. Quality control of frames and periodicity of RPFs were performed using the RiboWaltz package.
HTSEQ was used to coun reads at exons of genes. Normalization was done using the TMM method from edgeR.
Assembly: hg19
Supplementary files format and content: Tab delimited text file containing readcounts normalized with TMM as decsribed in data processing steps
Library strategy: Ribo-Seq

molecule: total RNA

organism: Homo sapiens

source_name: Breast

growth_protocol: PC3 and MD55A3 cells were cultured in Roswell Park Memorial Institute 1640 Medium (RPMI 1640, Gibco) supplemented with 10% fetal bovine serum (Gibco), 100 U/ml penicillin–streptomycin (Gibco). MDA-MB-231 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco), supplemented with 10% fetal bovine serum and 100 U/ml penicillin–streptomycin. All cell lines were maintained in a humidified atmosphere containing 5% CO2 at 37 °C and were regularly tested by PCR analysis and were found negative for mycoplasma contamination.

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen), according to manufacturer’s instructions. Rapid gel extraction was used, followed by overnight precipitation at −20 °C for RNA extraction from the polyacrylamide gels. Ribosomal RNA depletion was not performed. Prepared RPF libraries were analyzed on a 2100 Bioanalyzer using a 7500 chip (Agilent, Santa Clara, CA) and quantified by qPCR (Cat.no. 07960140001, Roche, Switzerland) and subsequently diluted to a 10 nM concentration. Next, the libraries were pooled and loaded with 1.5 pM on a NextSeq550Dx system (RUO mode) and sequenced with 75-base single-read using a 75 Cycles High Output Kit v2.5 (Illumina Inc., San Diego).

treatment_protocol: Leucine-free medium was prepared by adding glucose (Gibco), sodium pyruvate (Sigma) and all amino acids except for L-Leucine to RPMI 1640 Medium without amino acids (US Biologicals). Etoposide (Selleckchem), was dissolved in DMSO and used at a final concentration of 10 μM, unless stated otherwise. For t-RNA expression samples, oligonucleotides coding for tRNA-Leu-CAA-6-1 or tRNA-Leu-TAA-1-1 were annealed and phosphorylated. Next, a ligation reaction was performed with the annealed oligos and the digested vector using T4 DNA ligase (Thermo Scientific) for 1 hour at room temperature. The ligation products were subsequently transformed to DH5α competent cells. All resulting plasmids were sequence verified by Sanger sequencing. pLKO.1-puro vectors for expression of tRNA-Leu-CAG-1-7, tRNA-Leu-CAG-1-7-to-TAA and tRNA-TAA-3-1 were a kind gift from Heidi Greulich (PMID: 36302897).

tag: tissue

value: Breast

tag: cell line

tag: cell type

value: Breast cancer

tag: genotype

value: WT

tag: treatment

value: Leucine depletion


title: CCL+IL_1b_1

type: RNA

city: Osaka

first: Minami

last: Hikida

state: Chuou-Ku

address: 1-17 Machikaneyama-tyo

country: Japan

institute: Medicine for Sports and Performing Arts, Dept. of Health and Sport Sciences, Osaka University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: human knee articular chondrocytes, 3D constructs, IL-1β10ng/mL stimulation and cyclic compressive loading (CCL), 40kPa 0.5Hz 1h, 12h after loading

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: human knee articular cartilage

value: knee articular chondrocytes

tag: disease state

value: OA


title: CCL_2

source_name: human knee articular chondrocytes, 3D constructs, cyclic compressive loading (CCL), 40kPa 0.5Hz 1h,  12h after loading


title: PA_sample55

city: Ithaca

first: Hao

last: Zhou

address: 200 Kimball Hall

country: USA

institute: Cornell University

description: Library name: DSP-1001660018950-B-A10_S112

data_processing:
The sequencing depth requirement was determined by aggregating the areas of illumination (measured in µm²) and multiplying the total area by a factor of 100, as recommended in the GeoMx DSP Library and Sequencing Guide (nanostring.com). Sequencing was executed using the NovaSeq 6000 System. The resultant FASTQ files were processed to Digital Count Conversion (DCC) files utilizing the GeoMxNGSPipeline v.2.3.3.10, a pipeline publicly available through NanoString Technologies. This pipeline facilitated individual probe alignment by identifying read tag sequences (RTS). Additionally, it eliminated duplicates in probe counts generated during the library preparation's polymerase chain reaction, through a meticulous analysis of the unique molecular identifiers (UMIs) associated with each probe.
Assembly: mm10
Supplementary files format and content: combined_dcc.zip
Supplementary files format and content: Mm_R_NGS_WTA_v1.0.pkc
Supplementary files format and content: Moderna_Pa02_v1.0.pkc
Library strategy: Spatial Transcriptomics

organism: Mus musculus

source_name: Cornea

growth_protocol: P. aeruginosa strains PAO1, PA14, PA14_30590_Tn (PA2590 transposon mutant) were grown in Luria–Bertoni broth (LB) broth (BD-Difco) overnight at 37°C with agitation (200rpm). Cultures were then passaged in fresh LB broth (BD-Difco) until an OD600 of 0.20 (midlog phase) was reached. The PAO1 strain was obtained from Dr. A. Rietsch (Case Western Reserve University). The PA14 and PA14_2590_Tn were generated during the PA14 transposon insertion mutant library generation ((http://ausubellab.mgh.harvard.edu/cgi-bin/pa14/home.cgi)) and obtained from Prof. G. Pier (BWH, HMS)48 . The PA2590 transposon mutant was sequence validated.

extract_protocol:
After imaging the corneas, eyes had 15µl of 4% formalin (ThermoFisher) dropped onto them and were left to fix at room temperature for 15 minutes. Eyes were then carefully resected and placed in 1ml of iced 4% formalin (ThermoFisher) and were fixed at 4°C for 48-72hrs. After fixation, formalin was removed, and tissue was washed twice with sterile 1x PBS. Samples were then placed in 2ml of 70% ethanol and were kept at 4°C until shipment to UMass Histopathology was complete. Tissue embedding was done by UMass Histopathology.  All tissues were processed using UMass Chan Medical School Morphology Core services following standard protocols.
Illumina i5 and i7 dual-indexing primers (Nanostring Technologies) were added to the collected barcodes during polymerase chain reaction (8 µl collected oligonucleotides/ROI) to uniquely index each ROI. Briefly, collected barcodes were re-suspended in 10 mL of nuclease-free water and incubated for 10min at room temperature. In a 96-well PCR plate, 2 mL of master mix (Nanostring Technologies), 4 mL of seq-code indexes (Nanostring Technologies) and 4 mL of re-suspended barcodes were mixed and placed in a thermocycler for PCR amplification using the following program. 1x UDG incubation for 30min at 37° C, 1x UDG deactivation for 10min at 50° C, 1x Initial denaturation for 3min at 95° C, 18x Denaturation for 15sec at 95° C > Anneal for 60sec at 65° C > Extend for 30sec at 68° C, Final extension for 5min at 68° C, Hold at 4° C.

value: Cornea


title: CCL_1

value: cyclic compressive loading (CCL), 40kPa 0.5Hz 1h,  12h after loading


title: CCL_3


title: MDA-MB-231_WT_2


title: FPKM.MET_40mM_2

country: China


title: FPKM.MET_40mM_1


title: MDA-MB-231_WT_1


title: IL_1b_3

source_name: human knee articular chondrocytes, 3D constructs, IL-1β10ng/mL stimulation,  13h after stimulation


title: FPKM.MET_20mM_3

value: Metformin 20mM


title: PA_sample52

description: Library name: DSP-1001660018950-B-A07_S109


title: IL_1b_2

value: IL-1β10ng/mL stimulation,  13h after stimulation


title: liver,CCl4+eplerenone,rep05

city: Halle

first: Alexander

last: Nolze

address: Magdeburger Strasse 6

country: Germany

institute: MLU Halle-Wittenberg

data_processing:
Alignment (HISAT2 2.1.0)
Counting (featureCounts - 2.0.0)
Assembly: rn6
Supplementary files format and content: txt files containing raw counts obtained after Counting with featureCounts

organism: Rattus norvegicus

source_name: liver

growth_protocol: see at experimental design

extract_protocol:
Total RNA was isolated with TriZol Reagent, following the manufacturer's instructions. Eventual gDNA contaminations were removed using Turbo DNAse (ambion, Life Technologies). RNAs were precipitated with sodium acetate, glycogen and ethanol.
mRNA were enriched using oligo(dT) beads and then fragmented randomly by adding fragmentation buffer. cDNA synthesis is done with random hexamers primers and is followed by second strand synthesis after sequencing adaptor ligation. Double-stranded cDNA libraries are then subjected to size selection (250-300bp) and PCR enrichment. Libraries were pooled before clustering on flowcell for sequencing.

treatment_protocol: see at experimental design

value: liver


title: PC3_Etoposide_1

source_name: Prostate

value: Prostate

value: Prostate cancer

value: Etoposide treatment


title: PA_sample50

description: Library name: DSP-1001660018950-B-A05_S107


title: PA_sample51

description: Library name: DSP-1001660018950-B-A06_S108


title: IL_1b_1


title: control_3

source_name: human knee articular chondrocytes, 3D constructs, free-swelling, 13h

value: free-swelling, 13h


title: PA_sample54

description: Library name: DSP-1001660018950-B-A09_S111


title: PC3_Leucine_depletion_2


title: PC3_Leucine_depletion_1


title: FPKM.MET_0mM_3

value: Metformin 0mM


title: liver,CCl4+eplerenone,rep04


title: control_2


title: PA_sample49

description: Library name: DSP-1001660018950-B-A04_S106


title: PA_sample48

description: Library name: DSP-1001660018950-B-A03_S105


title: FPKM.MET_0mM_2


title: PC3_WT_2


title: PC3_Etoposide_2


title: PA_sample47

description: Library name: DSP-1001660018950-B-A02_S104


title: FPKM.MET_20mM_1


title: control_1


title: liver,CCl4+eplerenone,rep02


title: PC3_WT_1


title: PA_sample53

description: Library name: DSP-1001660018950-B-A08_S110


title: liver,CCl4+eplerenone,rep01


title: liver,CCl4+eplerenone,rep03


title: d28 biological replicate 4 non (control)  irradiated

city: Essen

first: Bettina

last: Budeus

address: Virchowstrasse 173

department: Institute for Cell Biology

institute: University Hospital Essen

data_processing:
Sequences were trimmed with TrimGalore and standard settings
Sequences were aligned with hisat2 (standard settings) on grch38
Reads were counted by summarizeOverlaps
Assembly: grch38
Supplementary files format and content: semicolon separated file contains the raw transcript counts

molecule: polyA RNA

source_name: lung

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
Libraries were construced with QuantSeq 3’ mRNA-Seq Library Prep Kit FWD

treatment_protocol: iPSC-derived lung organoids were cultured under standard conditions, irradiated and total RNA was isolated prior RNAseq, for scRNAseq lung organoids were enzymatically digested and sc analyses were perfomed (non-irradiated and irradiated condition) and

value: lung

value: iPSC

value: various lung cell types

value: unknown

value: control (d28)


title: liver,control,rep05

value: control


title: sch71 circRNA

city: Taiyuan

first: Sha

last: Liu

state: Shanxi

address: No. 56 Xinjian South Road, Yingze District, Taiyuan, Shanxi province

department: Department of Psychiatry

institute: First Hospital of Shanxi Medical University

data_processing:
For circRNAs, the quality control of raw data was conducted via Q30, followed by the removal of adapters and low-quality reads using the cutadapt software.
The reads were aligned to the reference genome/transcriptome based on the STAR software. CircRNAs were identified and annotated with DCC and CircBase. Subsequently, the data was normalized and DE circRNAs were filtered using the edgeR software.
Assembly: hg19
Supplementary files format and content: CircRNA Expression Profiling
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: Peripheral Blood

extract_protocol:
About 5 ml of plasma was isolated from 10 ml of peripheral blood. Total RNAs were pretreated with and then used to construct RNA libraries with a TruSeq Stranded Total RNA Library Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Peripheral Blood

value: early-onset schizophrenia


title: PA_sample46

description: Library name: DSP-1001660018950-B-A01_S103

value: Cornea


title: PA_sample45

description: Library name: DSP-1001660018892-E-D09_S45


title: d28 biological replicate 3 non (control)  irradiated


title: liver,control,rep04


title: FPKM.MET_20mM_2

value: WT

value: Metformin 20mM


title: PA_sample44

description: Library name: DSP-1001660018892-E-D08_S44


title: PA_sample43

description: Library name: DSP-1001660018892-E-D07_S43


title: liver,control,rep02

value: liver


title: liver,control,rep03


title: d28 biological replicate 2 non (control)  irradiated


title: sch63 circRNA


title: sch69 circRNA


title: sch58 circRNA


title: d28 biological replicate 1 non (control)  irradiated


title: d24 biological replicate 4 non (control)  irradiated

value: control (d24)


title: liver,control,rep01


title: PA_sample42

description: Library name: DSP-1001660018892-E-D06_S42


title: FPKM.MET_0mM_1


title: PA_sample41

description: Library name: DSP-1001660018892-E-D05_S41


title: d24 biological replicate 3 non (control)  irradiated


title: d24 biological replicate 2 non (control)  irradiated


title: PA_sample40

description: Library name: DSP-1001660018892-E-D04_S40


title: liver,CCl4,rep05


title: sch33 circRNA


title: PA_sample39

description: Library name: DSP-1001660018892-E-D03_S39


title: sch70 circRNA


title: liver,CCl4,rep04


title: liver,CCl4,rep03


title: PA_sample38

description: Library name: DSP-1001660018892-E-D02_S38


title: iPSC biological replicate 4 non (control)  irradiated

value: control (d0)


title: sch21 circRNA


title: liver,CCl4,rep02


title: sch20 circRNA


title: PA_sample37

description: Library name: DSP-1001660018892-E-D01_S37


title: PA_sample36

description: Library name: DSP-1001660018892-E-C12_S36


title: liver,CCl4,rep01


title: scon250 circRNA

value: healthy control


title: iPSC biological replicate 2 non (control)  irradiated


title: sch32 circRNA


title: LPS_S_4

city: Philadelphia

first: Stephanie

last: Daws

state: PA

address: 3500 N Broad St

institute: Temple University

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing  adapter and poly-N sequences and reads with low quality from raw data.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads  were mapped to the reference genome using HISAT2 software. HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome.
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes.
Assembly: rn6
Supplementary files format and content: RPKM of each gene was calculated  based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of  sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.

source_name: nucleus accumbens

extract_protocol:
Total RNA was isolated using the miRvana PARIS kit (AM1556) from Invitrogen according to the manufacturer's protocol.
RNA sequencing was performed on four biological replicates per group by Novogene America (Sacramento, CA, USA). Total RNA was assessed for quality before library preparation and RNA Integrity Numbers (RIN) were ≥ 7 with 28S/18S ≥ 1.3. A total amount of 300ng total RNA per sample was used as input material for the  RNA library. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP for directional library. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

treatment_protocol: Adult male Sprague Dawley rats were aged 8 weeks on arrival. For self-administration, animals were acclimited to the animal facility for 1 week then underwent jugular vein catheterization. Following 1 week of recovery, animals self-administered  heroin at a dosage of 0.075mg/kg/infusion, or saline, for 6 hours per day in 10 daily sessions. Following the last self-administration session, animals were euthanized immediately and their brains were frozen in ice cold isopentane. For experimenter administered substances, animals first received subchronic intraperitoneal (IP) injection of either 250ug/kg lipopolysaccharide (LPS) or saline intermittentently once per day over a two week period for a total of 5 injections. One week later, animals received either saline or heroin (IP) for five days in escalating doses of 1-5mg/kg per day. After the last injection, animals were euthanized 1 hour later. Nucleus accumbens tissue was dissected from each animal on dry ice then RNA extraction proceeded.

tag: strain

value: Sprague dawley

tag: Sex

value: male

tag: age

value: adult

value: intermittent LPS (IP) followed by saline (IP) for 5 days

value: nucleus accumbens


title: PA_sample35

description: Library name: DSP-1001660018892-E-C11_S35


title: scon249 circRNA


title: PA_sample34

description: Library name: DSP-1001660018892-E-C10_S34


title: LPS_S_3


title: sch22 circRNA


title: iPSC biological replicate 1 non (control)  irradiated

value: lung

value: iPSC

value: unknown


title: T4.A

data_processing:
Sequences were trimmed with TrimGalore and standard settings
Sequences were aligned with hisat2 (standard settings) on grcm38
Reads were counted by summarizeOverlaps
Libraries were construced with QuantSeq 3’ mRNA-Seq Library Prep Kit FWD
Assembly: grcm38
Supplementary files format and content: semicolon separated file contains the raw transcript counts

source_name: primary stromal cells

growth_protocol: RB medium is comprised of Dulbecco´s modified Eagle´s medium supplemented with 15% fetal bovine serum, 100 U penicillin/ml and 100 µg streptomycin/ml, 4 mM L-glutamine, 50 µM β-mercaptoethanol and 10 µg insulin/ml. MEGM medium was purchased (MEGM™ Mammary Epithelial Cell Growth Medium BulletKit, CC-3150, Lonza). Cells were cultivated at 37°C, 10% CO2 and 95% humidity.

extract_protocol:
RNA was harvested using the miRNeasy Kit (Qiagen). 20 ug of total RNA was used for the construction of sequencing libraries.
Libraries were construced with QuantSeq 3’ mRNA-Seq Library Prep Kit FWD

value: primary stromal cells

value: retinoblastoma tumor derived stromal cells

value: RB medium


title: T18.A

value: WT


title: scon244 circRNA

value: Peripheral Blood


title: scon241 circRNA


title: PA_sample32

description: Library name: DSP-1001660018892-E-C08_S32

value: Cornea


title: PA_sample33

description: Library name: DSP-1001660018892-E-C09_S33


title: LPS_S_1


title: T11.A


title: scon236 circRNA


title: T7

source_name: primary tumor cells

value: primary tumor cells

value: retinoblastoma tumor cells

value: RB1 Mutation

value: MEGM medium


title: iPSC biological replicate 3 non (control)  irradiated

value: control (d0)


title: T18


title: PA_sample31

description: Library name: DSP-1001660018892-E-C07_S31


title: PA_sample30

description: Library name: DSP-1001660018892-E-C06_S30


title: SS_3

value: Sprague dawley

value: male

value: adult

value: intermittent saline (IP) followed by saline (IP) for five days


title: SS_4

value: nucleus accumbens


title: SS_2


title: PA_sample29

description: Library name: DSP-1001660018892-E-C05_S29


title: T14

value: RB1 Mutation/MYCN amp


title: LPS_S_2

value: intermittent LPS (IP) followed by saline (IP) for 5 days


title: PA_sample28

description: Library name: DSP-1001660018892-E-C04_S28


title: T11


title: scon235 circRNA

value: healthy control


title: SH_4

value: intermittent saline (IP) followed by escalating heroin (IP)


title: T4_S

value: RB medium


title: scon243 circRNA

value: Peripheral Blood


title: PA_sample27

description: Library name: DSP-1001660018892-E-C03_S27

value: Cornea


title: SH_3


title: scon361 circRNA


title: T7_S

value: primary tumor cells


title: PA_sample26

description: Library name: DSP-1001660018892-E-C02_S26


title: sch71 miRNA

data_processing:
The initial processing of miRNAs raw data was similar to circRNAs, which required Q30 to perform quality control and cutadapt to remove low quality reads and retained the adaptor-trimmed-reads (≧15nt) for merging.
Novel miRNAs were predicted using miRDeep2, and the data was aligned to the human pre-miRNA database using Novoalign software with at most one mismatch. The data was normalized using TPM. DE miRNAs were filtered by fold change and p value.
Assembly: miRBase v21
Supplementary files format and content: miRNA_Expression
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

extract_protocol:
About 5 ml of plasma was isolated from 10 ml of peripheral blood. Total RNAs were pretreated with and then used to construct RNA libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: early-onset schizophrenia


title: SH_2


title: sch70 miRNA


title: SH_1


title: PA_sample25

description: Library name: DSP-1001660018892-E-C01_S25


title: T18_S

value: retinoblastoma tumor cells

value: RB1 Mutation


title: PA_sample24

description: Library name: DSP-1001660018892-E-B12_S24


title: scon227 circRNA


title: T14_S


title: sch63 miRNA


title: S_SA_4

value: saline self-administration for 10 days


title: T11_S

value: WT


title: S_SA_3

value: Sprague dawley

value: male


title: PA_sample23

description: Library name: DSP-1001660018892-E-B11_S23


title: PA_sample22

description: Library name: DSP-1001660018892-E-B10_S22


title: S_SA_2

value: adult


title: sch58 miRNA


title: M130830_TGFb_MEKi_REP3 [A70]

city: Zurich

first: Lukas

last: Sommer

state: Zurich

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

data_processing:
FASTQ files were aligned to the human genome annotation (retrieved from Ensembl database) using STAR algorithm (version 2.7.10a)
Assembly: GRCh38 release 105
Supplementary files format and content: tab delimited text file including raw counts for each sample

growth_protocol: All melanoma cell lines were maintained in RPMI medium supplied with 10% FBS, 1% Pen/Strep and 4mM Glutamine in a humidified atmosphere with 5% CO2 and 37C

extract_protocol:
RNA isolation was performed using the NucleoSpin RNA Mini kit (740955, Macherey-Nagel) according to the manufacturer’s protocol.
Library preparation was done using the TruSeq RNA Library Prep Kit v2 (RS-122-2001/RS-122-2002, Illumina). Samples were sequenced by a NextSeq 550 instrument (Illumina) in the single read configuration for 75bp.

treatment_protocol: Human TGFB1 ligand (10ng/mL) and/or the MEKi trametinib (10nM) was added to the culture medium 20h before RNA was isolated from the cells.

value: melanoma

value: TGFb + MEKi


title: S_SA_1

value: nucleus accumbens


title: PA_sample21

description: Library name: DSP-1001660018892-E-B09_S21


title: scon359 circRNA

value: healthy control


title: sch33 miRNA


title: M130830_MEKi_REP3 [A69]

value: MEKi


title: M130830_TGFb_REP3 [A68]

value: TGFb


title: SS_1

value: intermittent saline (IP) followed by saline (IP) for five days


title: sch22 miRNA

value: Peripheral Blood


title: LPS_H_4

value: intermittent LPS (IP) followed by escalating heroin (IP) for 5 days


title: M130830_DMSO_REP3 [A67]

value: DMSO


title: d24 biological replicate 1 non (control)  irradiated

value: lung

value: iPSC

value: various lung cell types

value: unknown

value: control (d24)


title: PA_sample19

description: Library name: DSP-1001660018892-E-B07_S19

value: Cornea


title: sch69 miRNA

value: early-onset schizophrenia


title: sch21 miRNA


title: LPS_H_3

value: Sprague dawley

value: male

value: adult


title: PA_sample18

description: Library name: DSP-1001660018892-E-B06_S18


title: sch20 miRNA


title: LPS_H_2

value: nucleus accumbens


title: M170117_MEKi_REP3 [A65]

value: melanoma

value: MEKi


title: M170117_TGFb_MEKi_REP3 [A66]

value: TGFb + MEKi


title: scon250 miRNA

value: Peripheral Blood

value: healthy control


title: PA_sample17

description: Library name: DSP-1001660018892-E-B05_S17


title: LPS_H_1

value: intermittent LPS (IP) followed by escalating heroin (IP) for 5 days


title: scon249 miRNA


title: PA_sample16

description: Library name: DSP-1001660018892-E-B04_S16


title: M170117_TGFb_REP3 [A64]

value: TGFb


title: PA_sample20

description: Library name: DSP-1001660018892-E-B08_S20


title: scon244 miRNA


title: H_SA_4

value: heroin self-administration for 10 days


title: H_SA_3


title: PA_sample14

description: Library name: DSP-1001660018892-E-B02_S14


title: M130830_TGFb_MEKi_REP2 [A62]


title: M170117_DMSO_REP3 [A63]

value: DMSO


title: scon241 miRNA


title: M130830_MEKi_REP2 [A61]


title: H_SA_2


title: PA_sample15

description: Library name: DSP-1001660018892-E-B03_S15


title: H_SA_1


title: PA_sample12

description: Library name: DSP-1001660018892-E-A12_S12


title: M130830_TGFb_REP2 [A60]


title: scon236 miRNA


title: Arabidopsis thaliana; H3K27me1; atxr56; ZT16; Biological replicate 2

city: Madrid

first: Crisanto

last: Gutierrez

address: Nicolas Cabrera 1

department: Genome Dynamics and Function

country: Spain

institute: Centro de Biologia Molecular Severo Ochoa

library_source: genomic

data_processing:
ChIP-Seq raw reads were trimmed with Trimmomatic (v 0.39) to remove adapters and small sequences.
FastQC (v 0.11.9) was used to assess the quality control of the reads.
Trimmed reads were then aligned to the A. thaliana reference genome (TAIR10) using Bowtie2 (v 2.3.4.3) with default parameters.
Duplicate reads were removed with Picard MarkDuplicates (v 2.7.1)
Unmapped reads and unwanted regions (transposons, miRNA) were removed with SAMtools (v 1.9)
Narrow peaks were called with MACS2 (v 2.2.6, additional parameters -p 0.05 -s 150). DeepTools bamCompare (v 3.5.1) was used to normalize reads with CPM and against H3.
Read pileup plots were generated with deepTools.
Assembly: TAIR10
Supplementary files format and content: bigwig file for each sample

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Whole seedlings 14 DAS

growth_protocol: Arabidopsis thaliana seedlings were grown in Murashige and Skoog (MS) with 0,8% agar medium. Seedlings were synchronized in short days (8h light – 16h dark) at 22ºC.

extract_protocol:
Samples were fixed in 1% formaldehyde solution under vacuum (16% Formaldehyde (w/v), Methanol-free, ThermoFisher) for a total of 12 minutes. After nuclei extraction and lysis, soluble chromatin was incubated overnight at 4ºC with anti-H3K27me1 and anti-H3. Conjugates were immunoprecipitated for 4 hours at 4ºC with protein G Dynabeads™ (ThermoFisher).
Libraries were generated using the Ovation® Ultralow V2 DNA-Seq Library Preparation Kit (Tecan), following manufacturer´s instructions. Total ChIPed DNA was resuspended in 10 µL of nuclease-free water and quantified by Qubit HS dsDNA assay (ThermoScientific) before the amplification step. 7 to 16 amplification cycles were used after taking in consideration ChIPed DNA concentration.

treatment_protocol: Wild type and atxr5/6 seedlings were harvested at ZT4 and ZT16 time points, 14 days after sowing.

value: Whole seedlings 14 DAS

value: atxr5/6 double mutant

tag: time point

value: ZT16 (midnight)

tag: chip antibody

value: H3K27me1 (07448 Millipore)


title: PA_sample11

description: Library name: DSP-1001660018892-E-A11_S11

value: Cornea


title: M130830_DMSO_REP2 [A59]


title: Arabidopsis thaliana; H3K27me1; atxr56; ZT16; Biological replicate 1


title: scon235 miRNA


title: PA_sample10

description: Library name: DSP-1001660018892-E-A10_S10


title: M170117_TGFb_MEKi_REP2 [A58]


title: scon227 miRNA


title: M170117_MEKi_REP2 [A57]


title: scon361 miRNA


title: Arabidopsis thaliana; H3K27me1; atxr56; ZT4; Biological replicate 1

value: ZT4 (midday)


title: scon243 miRNA


title: Arabidopsis thaliana; H3K27me1; WT; ZT16; Biological replicate 2

value: WT


title: PA_sample9

description: Library name: DSP-1001660018892-E-A09_S9


title: PA_sample8

description: Library name: DSP-1001660018892-E-A08_S8


title: M130830_TGFb_MEKi_REP1 [A44]


title: PA_sample6

description: Library name: DSP-1001660018892-E-A06_S6


title: PA_sample7

description: Library name: DSP-1001660018892-E-A07_S7


title: M170117_DMSO_REP2 [A55]


title: scon359 miRNA


title: M170117_TGFb_REP2 [A56]


title: Arabidopsis thaliana; H3K27me1; WT; ZT4; Biological replicate 2


title: MDA-MD-231_Leu1

description:
7030_9_MDA-MB-231_Leu-1_CAAGGATCGA-GCAGACACAA_S17
merged_MDA231_RNA.tsv

data_processing:
RNAseq: pair ended reads were aligned to the GRCH37.p13 (hg19) genome file using STAR. Readcounts per gene were obtained using HTSeq. Reads were normalized using DESeq2.
Assembly: hg19
Supplementary files format and content: Tab delimited text file containing readcounts per gene normalized with DESeq2 as decsribed in data processing steps

growth_protocol: MDA-MB-231 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco), supplemented with 10% fetal bovine serum and 100 U/ml penicillin–streptomycin. All cell lines were maintained in a humidified atmosphere containing 5% CO2 at 37 °C and were regularly tested by PCR analysis and were found negative for mycoplasma contamination.

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen), according to manufacturer’s instructions. Rapid gel extraction was used, followed by overnight precipitation at −20 °C for RNA extraction from the polyacrylamide gels. Ribosomal RNA depletion was not performed. Prepared RPF libraries were analyzed on a 2100 Bioanalyzer using a 7500 chip (Agilent, Santa Clara, CA) and quantified by qPCR (Cat.no. 07960140001, Roche, Switzerland) and subsequently diluted to a 10 nM concentration. Next, the libraries were pooled and loaded with 1.5 pM on a NextSeq550Dx system (RUO mode) and sequenced with 75-base single-read using a 75 Cycles High Output Kit v2.5 (Illumina Inc., San Diego).
Total RNA was isolated using Trizol reagent (Invitrogen), according to manufacturer’s instructions. Rapid gel extraction was used, followed by overnight precipitation at −20 °C for RNA extraction from the polyacrylamide gels. Ribosomal RNA depletion was not performed. Prepared RPF libraries were analyzed on a 2100 Bioanalyzer using a 7500 chip (Agilent, Santa Clara, CA) and quantified by qPCR (Cat.no. 07960140001, Roche, Switzerland) and subsequently diluted to a 10 nM concentration. Next, the libraries were pooled and loaded with 1.5 pM on a NextSeq550Dx system (RUO mode) and sequenced with 75-base single-read using a 75 Cycles High Output Kit v2.5 (Illumina Inc., San Diego).

treatment_protocol: Leucine-free medium was prepared by adding glucose (Gibco), sodium pyruvate (Sigma) and all amino acids except for L-Leucine to RPMI 1640 Medium without amino acids (US Biologicals). Cells were treated either with leucine-less medium, or control medium. 48 hours after the start of treatment, cells were harvested in RLT buffer (Qiagen).

value: Breast

value: Breast cancer

value: Leucine depletion


title: PA_sample5

description: Library name: DSP-1001660018892-E-A05_S5


title: MDA-MD-231_Leu2

description:
7030_10_MDA-MB-231_Leu-2_TTACACCAAC-ATGAGTTAGG_S18
merged_MDA231_RNA.tsv


title: M130830_MEKi_REP1 [A43]

value: melanoma

value: MEKi


title: PA_sample4

description: Library name: DSP-1001660018892-E-A04_S4


title: MDA-MD-231_Ctrl2

description:
7030_8_MDA-MB-231_Ctrl-2_AGGCAGCCAT-GAGTGTCTAG_S16
merged_MDA231_RNA.tsv


title: Arabidopsis thaliana; H3; atxr56; ZT16; Biological replicate 1

value: H3 (ab1791 Abcam)


title: M130903_TGFb_MEKi_REP1 [A36]

value: TGFb + MEKi


title: M130830_TGFb_REP1 [A42]

value: TGFb


title: Arabidopsis thaliana; H3K27me1; WT; ZT4; Biological replicate 1


title: MDA-MD-231_Ctrl1

description:
7030_7_MDA-MB-231_Ctrl-1_GTACGCTCAA-ATTGATGGCG_S15
merged_MDA231_RNA.tsv


title: Arabidopsis thaliana; H3; atxr56; ZT16; Biological replicate 2


title: Arabidopsis thaliana; H3K27me1; WT; ZT16; Biological replicate 1


title: M130830_DMSO_REP1 [A41]


title: Arabidopsis thaliana; H3; atxr56; ZT4; Biological replicate 2


title: shTP53-rIgG-3

city: Beijing

first: Qizhi

last: Wang

address: Chaoyang District

institute: Chinese Academy of Sciences

data_processing:
Low quality sequencing reads and adapters were removed by Trim Galore
All clean reads were aligned to human hg38 genome using Bowtie2
Multiple mapped reads and PCR duplicates were removed to generate uniquely mapped reads by JAVA picard MarkDuplicates
Assembly: hg38
Supplementary files format and content: bw
Library strategy: CUT&Tag

extract_protocol:
For each sample, 1×105 cells were harvested and the nucleus were isolated with nuclear extraction buffer according to the manufacturer of Hyperactive Universal CUT&Tag Assay Kit of Illumina
Add N5 and N7 connectors, establish and amplify the library using PCR

tag: antibody

value: rIgG


title: shTP53-rIgG-1


title: PA_sample2

description: Library name: DSP-1001660018892-E-A02_S2


title: M130903_TGFb_REP1 [A34]


title: PA_sample13

description: Library name: DSP-1001660018892-E-B01_S13


title: shTP53-rIgG-2


title: M130903_DMSO_REP1 [A33]

value: DMSO


title: Arabidopsis thaliana; H3; WT; ZT16; Biological replicate 1

value: Whole seedlings 14 DAS


title: H3t_deletion-m980

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

data_processing:
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore, and reads were mapped to the GRCm38 reference using HISAT2. Read counts for each gene were obtained by featureCounts .
Assembly: GRCm38
Supplementary files format and content: gzipped tab delimited raw count matrix for each sample

source_name: testis

extract_protocol:
Cryo sliced testies sections were lysed in Trizol reagent and column purified by Direct-zol RNA Kit (ZYMO research).
TaKaRa SMART-Seq Stranded Kit(#Z4444N)

value: testis

value: H3t deletion


title: Arabidopsis thaliana; H3; atxr56; ZT4; Biological replicate 1

value: atxr5/6 double mutant


title: M130903_MEKi_REP1 [A35]


title: MM150543_TGFb_MEKi_REP1 [A28]


title: shTP53-TfR1-3


title: PA_sample3

description: Library name: DSP-1001660018892-E-A03_S3

value: Cornea


title: Arabidopsis thaliana; H3; WT; ZT16; Biological replicate 2

value: ZT16 (midnight)


title: Arabidopsis thaliana; H3K27me1; atxr56; ZT4; Biological replicate 2

value: ZT4 (midday)

value: H3K27me1 (07448 Millipore)


title: shTP53-TfR1-1


title: WT-m819

value: wild-type


title: Arabidopsis thaliana; H3; WT; ZT4; Biological replicate 2

value: WT


title: MM150543_TGFb_REP1 [A26]

value: melanoma


title: shscr-rIgG-2

description: shscr-rIgG.bw


title: shscr-rIgG-1

description: shscr-rIgG.bw


title: H3t_deletion_m818


title: WT-m900


title: PA_sample1

description: Library name: DSP-1001660018892-E-A01_S1


title: Arabidopsis thaliana; H3; WT; ZT4; Biological replicate 1


title: Seedlings; short days; WT; ZT16; Biological replicate 3

data_processing:
RNA-Seq raw reads were trimmed with Trimmomatic (v 0.39) to remove adapters and small sequences.
Quality control of the raw (151 bp, paired-end) and trimmed reads was assessed with FastQC (v.0.11.9)
Trimmed reads were aligned to the A. thaliana reference genome with HISAT2
Unmapped reads and secondary alignments were filtered out with SAMtools
Gene abundances (TPMs and FPKMs) were counted by StringTie (v 2.2.1) using the Araport 11 GFF annotation file
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include FPKM and TPM values for each sample

extract_protocol:
RNA was isolated with miRNeasy Mini Kit® (Qiagen) following the manufacturer´s instructions.
RNA libraries for RNA-seq were generated using TruSeq Stranded Total RNA kit with Ribo-Zero Plant (Illumina)

value: wild type (Col-0)

tag: timepoint


title: shTP53-TfR1-2


title: M161201_TGFb_MEKi_REP1 [A20]


title: H3tKO-leydig-rep01-03

data_processing:
Cell barcode and UMI in Read1 was extracted by using UMI-tools with following command “umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC”. Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore, and reads were mapped to the GRCm38 reference using HISAT2. Read counts for each gene were obtained by featureCounts and UMI duplications were removed by UMI-tools.
Assembly: GRCm38
Supplementary files format and content: gzipped tab delimited raw count matrix for each sample
Supplementary files format and content: gzipped tab delimited sample : Cell Barcode list.

extract_protocol:
Sliced tissue section(10um) was lysed with proK/PBS and purified cDNA with ZYMO DCC5 (ZYMO reserch).
PIC library preparation protocol (Honda et al.,2021)

value: H3t KO

value: PIC UV irradiated (only Leydig)


title: H3t_deletion-m979


title: Seedlings; short days; WT; ZT16; Biological replicate 2


title: shscr-TfR1-3


title: young-WT-leydig-rep01-03


title: MM150543_DMSO_REP1 [A25]


title: shscr-TfR1-2


title: Seedlings; short days; WT; ZT16; Biological replicate 1


title: Testis_IgG_3

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

data_processing:
Raw reads were cleaned by Trim Galore v0.6.7.
The clean reads were further mapped to the mouse genome (mm10) by STAR v2.7.10a.
Uniquely mapped reads were quantified by FeatureCounts v2.0.2.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes the read count list of each sample.
Library strategy: acRIP-seq

source_name: Testis

extract_protocol:
Polyadenylated RNAs were isolated from total RNAs by Oligo(dT)25 Dynabeads.
Libraries were constructed by following the Smart-seq2 procedure.

value: Testis

value: Male

value: IgG


title: Seedlings; short days; WT; ZT4; Biological replicate 3

value: Whole seedlings 14 DAS


title: MM150543_MEKi_REP1 [A27]

value: MEKi


title: shscr-rIgG-3

description: shscr-rIgG.bw

value: rIgG


title: M161201_MEKi_REP1 [A19]


title: M161201_TGFb_REP1 [A18]

value: TGFb


title: shscr-TfR1-1


title: Seedlings; short days; WT; ZT4; Biological replicate 2


title: WT-m981

value: testis


title: M161201_DMSO_REP1 [A17]

value: DMSO


title: Testis_IgG_2


title: Seedlings; short days; WT; ZT4; Biological replicate 1


title: HCT-116-mIgG-3

value: mIgG


title: Testis_IgG_1


title: M170117_TGFb_MEKi_REP1 [A12]

value: TGFb + MEKi


title: Testis_IP_3

value: IP


title: M170117_TGFb_REP1 [A10]


title: HCT-116-mIgG-1


title: HCT-116-rIgG-3


title: HCT-116-mIgG-2


title: Seedlings; short days; atxr56; ZT16; Biological replicate 3

value: atxr5;atxr6 double mutant


title: Seedlings; short days; atxr56; ZT16; Biological replicate 1


title: M170117_MEKi_REP1 [A11]

value: melanoma


title: Seedlings; short days; atxr56; ZT16; Biological replicate 2


title: Testis_IP_2

value: WT


title: Testis_IP_1


title: M170117_DMSO_REP1 [A9]


title: Seedlings; short days; atxr56; ZT4; Biological replicate 3


title: Testis_Input_3


title: HCT-116-rIgG-1


title: Seedlings; short days; atxr56; ZT4; Biological replicate 2


title: Testis_Input_2


title: M010817_MEKi_REP1 [A3]


title: HCT-116-p53-3


title: M010817_TGFb_REP1 [A2]


title: lon2-8 atg2-4 Rep 3 DM

city: Houston

first: Bonnie

last: Bartel

state: Texas

department: BioSciences

institute: Rice University

description: Sample 21

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Supplementary files format and content: File name: Pseq_all_comps. File type: .xlsx. Content: Contains the list of all genes identified from the RNA-seq including those that are not considered significantly differentially expressed. Includes gene ID, names, discription, fold change, pval and FDR and normalized FPKM values for each genotype compared to Col-0 (wild type), and the double mutant (lon2-8 atg2-4) compared to atg2-4.
Supplementary files format and content: File name DE_RNA     File type: xlsx.   Content: Contains the list of differentially expressed gene ID, names, discription, fold change, pval and FDR and normalized FPKM values for each genotype compared to Col-0 (wild type), and the double mutant (lon2-8 atg2-4) compared to atg2-4.

source_name: whole plant

growth_protocol: 8 day-old continuous light-grown

extract_protocol:
whole seedlings were collected and flash frozen in liquid nitrogen. Tissue was ground with mortar and pestel. RNA was extracted with Qaigen Rneasy plant kit
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.  Library preparation was performed with 5 to 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases

treatment_protocol: grown in  plant nutrient media (Haughn and Somerville, 1986)

value: whole plant

tag: ecotype

value: lon2-8 atg2-4

value: total RNA


title: lon2-8 atg2-4 Rep 2 DM

description: Sample 20


title: M010817_DMSO_REP1 [A1]


title: HCT-116-p53-1


title: PANC-1-EVvector_3

city: Guangzhou

first: Dingwen

last: Zhang

state: Guangdong

address: 106 Zhongshan 2nd Road, Guangzhou, Guangdong Province

department: Department of Pancreatic Surgery

institute: Guangdong Provincial People's Hospital

data_processing:
fastpe (v0.23.2)
We used fastpe (v0.23.2) to filter the raw reads, the filtering rules were as follows: 1) Removed reads containing adapters, 2) Removed reads with N ratio greater than 5%, 3) Removed low-quality reads (the number of bases with quality value Q<=15 accounts for more than 20% of the entire read).
We then performed gene expression profiling analysis using data obtained from RNA-seq of dorsal root ganglia cells induced with 50μg of PANC-1-EVcircPNIT and PANC-1-Evvector
Comparative gene expression profiling analysis of RNA-seq data for PANC-1-EVcircPNIT or PANC-1-EVvector induced dorsal root ganglia cells

source_name: dorsal root ganglia

growth_protocol: Dorsal root ganglia cells were maintatined in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37

extract_protocol:
RNA were harvested using Universal RNA Purification Kit (EZBioscience, China, EZB-RN4). 1.5μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: Dorsal root gangalion cells were induced with 50μg of PANC-1-EVcircPNIT and PANC-1-EVvector for 3 days

value: dorsal root ganglia

value: primary culture cell


title: HCT-116-TfR1-3


title: PANC-1-EVvector_2


title: PANC-1-EVvector_1


title: PANC-1-EVcircPNIT_3


title: atg2-4 Rep 3

description: Sample 18


title: lon2-8 atg2-4 Rep 1 DM

description: Sample 19


title: HCT-116-TfR1-2


title: HCT-116-rIgG-2


title: M010817_TGFb_MEKi_REP1 [A4]


title: PANC-1-EVcircPNIT_2


title: atg2-4 Rep 2

description: Sample 17


title: HCT-116-TfR1-1


title: HCT-116-shTfR1-CDDP-RNA-seq 3

data_processing:
Low quality sequencing reads and adapters were removed by Cutadapt
All clean reads were mapped to the human hg38 genome by HISAT2
The gene counts were calculated with gene annotation from UCSC database using FeatureCounts
Assembly: hg38
Supplementary files format and content: txt count

extract_protocol:
HCT-116 cells transfected with shSCR or shTFRC were seeded in 100 mm dishes overnight. Cells were harvested after CDDP treatment and washed with PBS. TRIzolTM reagent (Thermo Scientific, 15596026) was used to extract total RNA from each sample.
After passing the detection of total RNA samples, purification is carried out based on the characteristics of mRNA from different sources. The end of eukaryotic mRNA3 has a polyA tail structure, and magnetic beads with Oligo (dT) were selected for enrichment and purification; Prokaryotic mRNA does not possess this characteristic, so a reagent kit was used to remove rRNA to obtain more effective information. Add Fragmentation Buffer to the purified mRNA to make its fragments short. Using the fragmented RNA as a template, reverse transcription was performed using random primers to synthesize the first strand of cDNA, and the second strand of cDNA was synthesized by adding the 2nd Strand Marking Buffer and 2nd Strand/End Repair Enzyme Mix. After end repair, addition of base A, sequencing adapter, magnetic bead screening to recover the target fragment, and PCR amplification, the entire library preparation work was completed.

value: CDDP treatment


title: Testis_Input_1

value: Testis

value: Male


title: atg2-4 Rep 1

description: Sample 16


title: PANC-1-EVcircPNIT_1


title: HCT-116-shTfR1-CDDP-RNA-seq 2


title: Seedlings; short days; atxr56; ZT4; Biological replicate 1

value: Whole seedlings 14 DAS


title: lon2-8 Rep 2

description: Sample 14


title: HCT-116-shscr-CDDP-RNA-seq 3

value: shscr


title: SG of OVX surgery group biological rep3

city: Yangsan-si

first: Yoojin

last: seo

state: Gyeongsangnam-do

address: 49, Pusandaehak-ro, Mulgeum-eup

country: South Korea

institute: School of Dentistry, Pusan National University

description: OVX 3

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing:
Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)
The data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Power Tools (APT).

label: biotin

source_name: submandibular gland from OVX group

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: 30 min egg collections of OreR and yw flies at 25C were aged at room temperature (RT) according to the different temporal classes T0-T4.

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

treatment_protocol: Mice underwent bilateral OVX or cham surgery

value: submandibular gland

value: balb/c

value: 14 weeks old

value: bilateral OVX

value: 8 wks after the surgery


title: lon2-8 Rep 1

description: Sample 13


title: SG of Sham surgery group biological rep3

description: Cont 3

source_name: submandibular gland from sham group

value: sham surgery


title: SG of OVX surgery group biological rep2

description: OVX 2


title: KAT6B_KO_d6_rep1

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

country: United Kingdom

institute: The Babraham Institute

data_processing:
Reads were mapped to the GRCm39 genome assemby using gene models from Ensembl v103 using hisat2 with options --no-softclip --no-discordant --no-mixed
Raw counts were calculated from merged mRNA isoforms in SeqMonk v1.48.1 using the RNA-Seq quantitation in opposing strand specific mode
Assembly: Mus musculus GRCm39
Supplementary files format and content: Tab delimited file of raw per gene exon overlap counts

growth_protocol: E14 embryonic stem cells (ESCs) were grown on plates coated with gelatin (0.1%, Sigma) in DMEM containing 4.5 g/l glucose (Gibco) supplemented with 15% fetal bovine serum (Gibco, South American, A3160802), 2 mM l-glutamine, 1 mM pyruvate, 1x MEM nonessential amino acids, 50 units/ml penicillin and 50 µg/ml streptomycin (all Gibco), 0.2 mM β-mercaptoethanol (Sigma), and heterologously expressed recombinant LIF (made in-house and batch-tested for maintenance of self-renewal) at 37°C and 5% CO2.

extract_protocol:
Cells were resuspended in 1 ml TriPure isolation reagent (Roche) per 10-cm plate of ESCs or EBs (or per 2x 6-cm plate for plated neural cells). RNA was extracted following the manufacturer’s instructions and resuspended in BTE (10 mM Bis-Tris pH 6.7, 1 mM EDTA). Extracted RNA was treated with Turbo DNAse (Ambion) for 30 min at 37°C. RNA extraction was repeated using TriPure and purified RNA was resuspended in 50 μl BTE. Integrity of RNA was assessed using RNA 6000 Nano chips on a Bioanalyzer (Agilent).
Ribosomal RNA was depleted from 1 µg of RNA using the NEBNExt rRNA depletion kit v2 (NEB). Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) and single index NEBNext multiplex oligos for Illumina (NEB). Following library preparation, library fragment size was determined using an Agilent Bioanalyzer 2100. Library concentration was assessed by qPCR using the NEBNext Library Quant kit for Illumina (NEB). Samples were sequenced on an S4 flow cell on an Illumina NovaSeq 6000 instrument as 150 bp paired-end reads (Novogene UK).

treatment_protocol: Neuronal differentiation was performed as previously described (Bibel et al., 2007). First, embryoid body (EB) formation was induced by removal of LIF. ESCs were plated onto non-adherent bacterial plates (Greiner) in 10 ml EB medium (ESC medium described above but without LIF and with 10% FBS instead of 15%) at a density of 4 x 10^6 cells per 10-cm plate. On day 2, the media was changed by gently transferring EBs to a 15-ml conical tube (Sarstedt), allowing EBs to settle for 5 min, then carefully aspirating the supernatant. EBs were then gently resuspended in 13 ml of fresh EB media using a 5-ml serological pipette (Sarstedt) and transferred to a fresh plate. On day 4 and day 6, media was changed in the same manner to 15 ml EB medium with 10 μM all-trans retinoic acid (Sigma). On day 8, EBs were washed 3 x in 20 ml PBS, trypsinised (Sigma, prepared at 0.5 mg/ml in 0.05% v/v EDTA/PBS) for approximately 3 min at 37°C with agitation and then quenched in 10 ml EB medium. Dissociated neural progenitor cells were then centrifuged for 5 min at 300 g, resuspended in 10 ml EB medium and passed through a 40-μm cell strainer (Thermo Fisher Scientific). Cells were counted, centrifuged again and resuspended in Advanced DMEM/F12 (Gibco) with 1x N2 supplement (Gibco) before being plated onto poly-D-lysine (Sigma) and laminin (Sigma) coated 6-cm dishes at a density of 3 x 10^6 cells/plate. On day 9, half of the media was replaced with Neurobasal medium (Gibco) containing 1x B27 supplement (Gibco). This was repeated on day 12.

value: embryonic stem cell (E14 line)

value: KAT6B-/- KO

value: EB differentiation and all-trans retinoic acid


title: HCT-116-p53-2


title: HCT-116-shTfR1-CDDP-RNA-seq 1


title: SG of OVX surgery group biological rep1

description: OVX 1


title: lon2-8 Rep 3

description: Sample 15

value: whole plant

value: total RNA


title: Col-0 Rep 3

description: Sample 12

value: wild type


title: HCT-116-shscr-CDDP-RNA-seq 2

value: CDDP treatment


title: KAT6B_KO_d6_rep3


title: KAT6B_KO_d6_rep2


title: Col-0 Rep 2

description: Sample 11


title: SG of Sham surgery group biological rep1

description: Cont 1


title: KAT6B_KO_d2_rep2

value: EB differentiation


title: RA-FLS 3

city: Wenzhou

first: Wu

last: Gan

address: Chashan Street, Ouhai District

institute: Wenzhou Medical University

description:
Library name: RA3
FPKM.RA3

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: hg38
Supplementary files format and content: excel file include FPKM value of each sample

source_name: fibroblast-like synoviocytes

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
The poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: fibroblast-like synoviocytes

value: rheumatoid arthritis (RA)


title: RA-FLS 1

description:
Library name: RA1
FPKM.RA1


title: RA-FLS 2

description:
Library name: RA2
FPKM.RA2


title: KAT6B_KO_d2_rep3


title: Col-0 Rep 1

description: Sample 10


title: HCT-116-shTfR1-RNA-seq 3


title: HCT-116-shscr-CDDP-RNA-seq 1

value: shscr


title: SG of Sham surgery group biological rep2

description: Cont 2

value: submandibular gland


title: HCT-116-shTfR1-RNA-seq 2


title: HC-FLS 3

description:
Library name: HC3
FPKM.HC3

value: healthy control


title: KAT6B_KO_d15_rep1

value: NPCs cultured in Advanced DMEM/F12 with N2 and B27 supplement


title: Control, RPF, Biol Replicate 1

city: Indianapolis

first: Jeffery

middle: M

last: Tharp

state: Indiana

address: 635 Barnhill Drive

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

data_processing:
Merge paired-end sequences: Samtoosl; Adapter trimming: ReadKnead v0.1.2 (minimum global alignment score = 40);
Read 1 was aligned to the Ensemble 108 GRCh38 genome assembly using STAR v2.7.1a with the following nondefault paramters: --alignEndsType EndToEnd, --sjdbScore 2, --outFilterMultimapNmax 1000, --outMultimapperOrder Random, --limitOutSAMoneReadBytes 600000
Duplicates were removed with rmdup v1.3 and profile counts generated with GeneAbacus v0.2.2 with a minimum read overlap of 10
Ribosome readthrough scores (RRTS) were calculated as described previously (PMID: 31971508)
Assembly: NA
Supplementary files format and content: Calculated RRTS provided as .csv files.
Library strategy: Ribo-Seq

source_name: Cultured Cells

growth_protocol: HEK 293 cells were grown in Dulbecco's Modified Essential Medium (DMEM) with 10% fetal bovine serum at 37 degrees with a 5% CO2 atmosphere.

extract_protocol:
48 h after transfection cells were lysed in buffer (20 mM Tris pH 7.4, 100 mM NaCl, 10 mM MgCl2, 100 ug/mL cycloheximide, 1% (w/v) Triton X-100, 25 U/ml Turbo DNase I) and passaged through a 25-gauge needle six times. Insoluble material was removed by centrifugation and total RNA was extracted from the soluble material using miRNeasy Kit (Qiagen). Ribosome protected fragments were prepared using a sucrose cushion following RNAse I digestion as described previously (PMID: 33377062).
Libraries were prepared as described previously (PMID: 26876183)

treatment_protocol: Cells in a 10 cm dish were transfected with 10 ug of a sup-tRNA expressing plasmid or a control empty vector using Fugene6 according to the manufacturer's protocol.

value: Cultured Cells

value: HEK 293

value: epithelial

value: WT

value: transfected with empty vector


title: HCT-116-shTfR1-RNA-seq 1


title: HCT-116-shscr-RNA-seq 2


title: KAT6B_KO_d2_rep1

value: embryonic stem cell (E14 line)

value: KAT6B-/- KO


title: HC-FLS 2

description:
Library name: HC2
FPKM.HC2


title: KAT6B_KO_d15_rep3


title: HC-FLS 1

description:
Library name: HC1
FPKM.HC1


title: Control, RPF, Biol Replicate 2


title: HCT-116-shscr-RNA-seq 3


title: T4

city: New Delhi

first: Tanveer

last: Ahmad

state: Delhi

address: 110025, Jamia Millia Islamia, Jamia Nagar, Okhla

department: Multidisciplinary Centre for Advanced Research and Studies (MCARS)

country: India

institute: Jamia Millia Islamia

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimgalore (Phred score threshold of 20)
Trimmed sequence reads were mapped to GRCh38 using STAR aligner.
Read count extraction was done using Salmon and normalization were performed using Voom.
Assembly: GRCh38
Supplementary files format and content: Tab delimited text file includes normalized counts for each sample

source_name: Oral mucosal tissue

extract_protocol:
Oral mucosal tissue was put in RNA later. The tissue was homogenised in Trizol and RNA was isolated according to manufacturer's protocol
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Oral mucosal tissue

value: OSCC 10


title: T6

value: OSCC 12


title: KAT6B_KO_d0_rep3


title: sup-tRNA, RPF, Biol Replicate 2

value: transfected with sup-tRNA


title: Ctrl _1 [WGBS_seq]

city: Xi'an

first: Wenhao

last: Shi

state: Shaanxi

address: Houzai Gate 73#

department: The assisted Reproduction Center

institute: Northwest Women’s and Children’s Hospital

data_processing:
Raw data filtration  Low quality bases and adapter sequences were trimmed by using trimmomatic (v0.38, Bolger, A. M. et al., 2014). The parameter settings used was “ SLIDINGWINDOW:5:15 HEADCROP:3 AVGQUAL:15 LEADING:5 TRAILING:5 MINLEN:35”. Sequence alignment and detection of cytosines methylation level  The cleaned reads were mapped back to reference genome using BSMAP software version 2.90 (Xi & Li, 2009). The parameter settings used was “-v 0.08 -g 1 -p 48”. Methylation ratios were extracted from BSMAP output (SAM) using a Python script (methratio.py) which is distributed with the BSMAP package. In brief, The methylation level was calculated based on the methylated cytosine (mC) percentage in the whole genome as site methylation level = 100× (number of sequences with methylated cytosines (mC)/total number of valid sequences). The global average methylation levels were displayed by ViolinPlot using R package. The various gene elements average methylation levels were calculated by genome gff file and were visualized by barplot using R package.  DMC and DMR detection  Differentially methylated cytosines (DMCs) were detected using MethylKit (v1.20, Akalin A et al.,2012) in de-novo mode among CpG sites with at least 10x coverage. The parameter settings used was “--mincov 10 --m_cutoff 0.1 --q_cutoff 0.05”. Differentially methylated regions (DMRs) were detected using metilene (Jühling et al., 2016) in de-novo mode among CpG sites with at least 10x coverage. The parameter settings used was “--mincpgs 3 --minMethDiff 0.2 --mode 1 -mtc 2”. Then detected DMR were filtered according to the standard: (1) Q-value must be less than 0.05; (2) methylation level difference must be greater than 0.2; (3) CpG number contained in DMR must be greater than 5; (4) the length of the DMR must be greater than 50bp. The related Elements and genes of DMCs and DMRs were located in genome by genome gff file. The genome GO and KEGG annotation was performed using emapper based on EGGNOG database. The above related hyper-methylated genes were then subjected to enrichment analysis of GO and KEGG by Allenricher (v1.0).
Assembly: hg38
Supplementary files format and content: bedgraph

source_name: ovary

extract_protocol:
Genomic DNA was extracted by QIAamp DNA Micro Kit (Qiagen) and quantified by Quant-iT dsDNA HS Assay Kit with Invitrogen Qubit fluorometer according to the manufacturer’s protocols.
Low input DNA whole genome bisulfite sequencing libraries were constructed by E-GENE Co. Ltd. as previously described(ref). Briefly, genomic DNA was bisulfite converted using a ZYMO EZ DNA Methylation-Gold Kit (ZYMO), following the manufacturer’s instructions. The purified DNA was eluted in 10 mM Tris-Cl (pH 8.5). The following post bisulfite extension was carried out with 0.4 mM dNTPs, 0.4 μM oligo 1 (Biotin-CTACACGACGCTCTTCCGATCTNN NNNNNNN) and 1× Blue Buffer in a final volume of 24 μl. After incubated at 65 °C for 3 min and 4 °C pause. 50 U of Klenow exo– (Enzymatics) were added and the samples incubated at 4 °C for 5 min, +1 °C/15 s to 37 °C, 37 °C for 30 min. After the first-strand synthesis, 40U exonuclease I (NEB) was added and incubated for 1h at 37 °C followed by DNA purification and amplified DNA capturing using streptavidin beads.
The second-strand synthesis was carried out as above described with 0.8mM dNTPs and 4 μM oligo 2 (TGCTGAACCGCTCTTCCGAT CTNNNNNNNNN). The final libraries were generated by PCR amplification using KAPA HiFi HotStart DNA Polymerase (KAPA Biosystems). The final libraries were analyzed by an Agilent Bioanalyzer (Agilent Technologies) and quantified by real time PCR and then sequenced by Illumina Nova 6000.

value: ovary

tag: group

value: Ctrl

value: cumulus cells


title: HCT-116-shscr-RNA-seq 1

value: shscr


title: T5

value: OSCC 11


title: KAT6AB_KO_d6_rep2

value: KAT6A-/-; KAT6B-/- dKO

value: EB differentiation and all-trans retinoic acid


title: T9

value: OSCC 15


title: sup-tRNA, RPF, Biol Replicate 1

value: Cultured Cells

value: HEK 293

value: epithelial


title: KAT6AB_KO_d6_rep3

value: embryonic stem cell (E14 line)


title: sup-tRNA, Total RNA, Biol Replicate 2

data_processing:
Merge paired-end sequences: Samtoosl; Adapter trimming: ReadKnead v0.1.2 (minimum global alignment score = 40);
Read 1 was aligned to the Ensemble 108 GRCh38 genome assembly using STAR v2.7.1a with the following nondefault paramters: --alignEndsType EndToEnd, --sjdbScore 2, --outFilterMultimapNmax 1000, --outMultimapperOrder Random, --limitOutSAMoneReadBytes 600000
Duplicates were removed with rmdup v1.3 and profile counts generated with GeneAbacus v0.2.2 with a minimum read overlap of 10
Differential expression analysis was performed with DEseq2 v1.40.1 with a parametric fit and custom R script.
Assembly: Ensemble 108 GRCh38
Supplementary files format and content: log2FoldChange

value: WT


title: KAT6AB_KO_d6_rep1


title: KAT6B_KO_d0_rep2

value: KAT6B-/- KO


title: POI_2 [WGBS_seq]

value: POI


title: KAT6B_KO_d15_rep2

value: NPCs cultured in Advanced DMEM/F12 with N2 and B27 supplement


title: KAT6AB_KO_d2_rep3

value: EB differentiation


title: T8

value: Oral mucosal tissue

value: OSCC 14


title: Ctrl _3 [WGBS_seq]

value: ovary

value: Ctrl

value: cumulus cells


title: Polyps sample-2

city: Kaohsiung

first: Yi-Fang

last: Yang

address: No. 386, Dajhong 1st Rd., Zuoying Dist., Kaohsiung City 813414, Taiwan.

department: Medical Education and Research

country: Taiwan

institute: Kaohsiung Veterans General Hospital

data_processing:
The bases with low quality and sequences from adapters in raw data were removed using program fastp (version 0.20.0)
The filtered reads were aligned to the reference genomes using HISAT2 (version 2.1.0)
The software FeatureCounts (v2.0.1) in Subread package was applied for the quantification of the gene abundance
Differentially expressed genes (DEGs) were identified by DESeq2
Assembly: HG38

source_name: Sinonasal inverted papilloma tissue

extract_protocol:
In preparation for the RNA extraction, 50 mg of tissue was added to 500 μl TRIzol (Thermo Fisher Scientific) in which contained steel beads (the ratio of tissue, TRIzol and steel beads were 1:1:2~3). Samples were homogenized by using TissueLyser II (Qiagen, Hilden, Germany) for two cycles of two minutes at 20 Hz. After homogenization, Proteinase K (Worthington Biochemical Corp.) was added to remove protein contamination. For phase separation, the homogenized samples were added to BCP solution to separate into an interphase and upper aqueous phase. The upper aqueous phase was then carefully transferred into a fresh tube, and 100% ethanol was added for RNA precipitation. The procedures of RNA washing were performed using miRNeasy Mini Kit (Qiagen, Hilden, Germany), following the manufacturer’s recommendations. The RNA was qualified by Fragment Analyzer 5200 (Agilent, Santa Clara, USA) and quantified by NanoDrop (Thermo Scientific, Waltham, MA, USA).
The purified RNA was used for the preparation of the sequencing library by TruSeq RNA Exome Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer’s recommendations. Briefly, total RNA (120 ng) was fragmented into small pieces with divalent cation under elevated temperature. The first-strand cDNA was synthesized by reverse transcriptase and random primers. After the generation of double-strand cDNA and adenylation on 3’ ends of blunt fragments, the adaptors were ligated and purified with AMPure XP system (Beckman Coulter, Beverly, USA). The purified libraries were hybridized with probes as biotinylated coding exome oligos. The streptavidin-coated magnetic beads were used to capture hybridized probes on the targeted regions of interest. The captured libraries were amplified by a second PCR. The quality of libraries was assessed on the Agilent Bioanalyzer 2100 system. The qualified libraries were then sequenced on Illumina NovaSeq 6000 platform with 150 bp paired-end reads generated by Genomics, BioSci & Tech Co., New Taipei City, Taiwan.

value: Sinonasal inverted papilloma tissue


title: Control, Total RNA, Biol Replicate 2

value: transfected with empty vector


title: KAT6B_KO_d0_rep1


title: T3

value: OSCC 9


title: Ctrl _2 [WGBS_seq]


title: T13

value: OSCC 5


title: Control, Total RNA, Biol Replicate 1

value: Cultured Cells

value: HEK 293


title: T7

value: OSCC 13


title: Control sample-1

source_name: Normal nasal mucosal tissue

value: Normal nasal mucosal tissue


title: T2

value: OSCC 8


title: POI_3 [WGBS_seq]

value: POI


title: sup-tRNA, Total RNA, Biol Replicate 1

value: epithelial

value: WT

value: transfected with sup-tRNA


title: T14

value: Oral mucosal tissue

value: OSCC 6


title: T10

value: OSCC 2


title: T15_3

value: OSCC 7


title: KAT6AB_KO_d15_rep2

value: embryonic stem cell (E14 line)

value: KAT6A-/-; KAT6B-/- dKO

value: NPCs cultured in Advanced DMEM/F12 with N2 and B27 supplement


title: POI_3 [RNA-Seq]

data_processing:
Data analysis Quality control of raw reads was performed using FastQC (version 0.11.5) , and clean reads were obtained following the removal of low‑quality reads with Trimmomatic (version 0.38) software. The parameter settings used was “HEADCROP:8 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”. Hisat2 (v2.2.1)  was employed for performing read mapping to Petuniahybrida genome reference (v1.6.2). Gene expression profiling was based on the number of reads. TPM (Transcripts Per Kilobase of exon model per Million mapped reads) values were calculated by StringTie (v2.1.7) [4], and were used to estimate the expressed values. DEGs were obtained using DEseq2 (v1.34.0) with an p value cutoff < 0.05 and an absolute log2(fold-change) of > 1. KEGG and GO enrichment analysis was performed on the clusterProfiler R package (v4.2.2).
Assembly: hg38
Supplementary files format and content: read count & gene_TPM

extract_protocol:
The total RNA of each sample was extracted using Invitrogen TRIzol® Reagent or the (single) cells were lysed with 4ul of 0.2% Triton X-100 solution containing 0.5ul of RNase inhibitor.
The cell lysis or the extracted total RNA was mixed with 1ul of 10uM Oligo-dT primer and 1ul of 10uM dNTP reagent and then incubated at 72℃ for 3min. The reverse transcription reaction was performed in 1X Super Script II first-strand buffer system with 200U of Super Script II reverse transcriptase，0.1ul  of TSO （100uM），20U RNAse Inhibitor，0.75ul of DTT（100mM），3ul of Betaine（5M）and 0.09ul of MgCl2（1M）. The full length cDNA was synthesized at 42℃ for 90min and then with 10 cycles of 50℃ for 2min and 42℃ for 2min. Finally, the product was incubated at 70℃ for 15min to inactive the enzyme activation. After amplified the synthesized cDNA with 10 to15 cycles of PCR amplification, the product was purified and used for library construction.
After analyzed by Agilent Bioanalyzer and quantified by real time PCR, the library was sequenced with Illumina Novaseq platform.

value: ovary

value: cumulus cells


title: KAT6AB_KO_d15_rep1


title: POI_1 [WGBS_seq]


title: Ctrl _3 [RNA-Seq]

value: Ctrl


title: KAT6AB_KO_d2_rep2

value: EB differentiation


title: KAT6AB_KO_d2_rep1


title: Polyps sample-1

value: Sinonasal inverted papilloma tissue


title: mitochondrial DRIP-seq KO RnaseH-treated

city: Debrecen

first: Lorant

last: Szekvolgyi

address: Egyetem ter 1.

department: Department of Pharmacy

country: Hungary

institute: University of Debrecen

description: Library name: drip_endoG_KO_ip_rnaseh.fastq

data_processing:
Raw reads were aligned to the M. musculus mitochondrial reference genome (NCBI Reference Sequence: NC_005089.1) using the default parameters of Burrows-Wheeler Aligner (BWA MEM) algorithm
Low mapping quality reads (MAPQ < 10) and PCR duplicates were removed. Processed alignments were subjected to bamCoverage to generate signal files.
RPKM (Reads Per Kilobase Million) values were calculated for 20 bp binds for each sample and smoothed using a 45 bp sliding window (--binSize 15 –smoothLength 45 –normalizeUsing RPKM).
The generated signal files were visualized in R 3.4.2, using the ggplot2 (https://ggplot2.tidyverse.org) and ggbio.
Assembly: mitochondrion Mus musculus (house mouse) /  NC_005089
Supplementary files format and content: bigwig files from IP and input, without and with Rnase H treatment.
Supplementary files format and content: Final bigwig files were background corrected with the Rnase H signal.

source_name: liver

growth_protocol: Ob/ob mice in C57 background were purchased from Jackson Laboratory (000632). EndoG KO mouse was a generous gift from Dr. Michael Lieber, University of Southern California.

extract_protocol:
Nucleic acid isolation from mitochondria enriched pellets Mitochondria were isolated from the liver of two wild type and two EndoG knock-out animals (Liu JC, et al. Cell Rep. 2016; 16 (6): 1561- 1573). Mitochondrion-enriched samples were resuspended with freshly made 1% formaldehyde in phosphate buffered saline (PBS, 136 mM NaCl, 2.6 mM KCl, 12.4 mM Na2HPO4, 1.7 mM KH2PO4, pH=7.4) supplemented with 5 mM EDTA. Mitochondria were fixed for 10 minutes at room temperature, with shaking (Biosan TS-100 shake; Biosan, Riga, Latvia). Formaldehyde fixation was quenched with the addition of glycine to a final concentration of 0.667 M for 5 minutes at room temperature. Samples were then centrifuged at 10000xg for 10 minutes at 4oC using Eppendorf 5424 centrifuge (Eppendorf, Hamburg Germany). Supernatants were discarded, and pellets were washed in PBS. Lysis was performed using a DRIP-lysis buffer (50 mM TRIS-HCl, 10 mM EDTA, 1% SDS and 0.333 mg/ul Proteinase K (Bioline, Alexandria, NSW, Australia) at 37oC, overnight. Lysates were extracted in phase-lock tubes (5 Prime GmbH, Hilden, Germany) by phenol (50%)-chloroform (48%)-isoamylalcohol (2%) and the nucleic acid content was precipitated by 2.5V 100% ethanol and 10% 3.5 M sodium acetate at -20oC for 45 minutes. After centrifugation with 20000xg for 20 minutes at 5oC, pellets were washed with 70 V/V% ethanol and centrifuged again for 5 minutes at 20000xg. Nucleic acid pellets were dissolved in 10 mM TRIS-Cl pH 7.5. DNA concentration was measured by a NanoDrop-1000 photometer (Thermo Scientific, Waltham, Massachusetts, USA). Isolated nucleic acid samples were fragmented by sonication (Bioruptur Plus; Diagenode, Belgium; 10 cycles: 30 s “on” followed by 30 s “off”) to an average fragment size of 300-500 bp. 2% of the sonicated material was kept as ‘input’. The remaining samples were divided into two aliquots that were or were not treated with E. coli RNaseH New England Biolabs, Ipswich, Massachusetts, USA). RNaseH digestion (was performed at 37oC, overnight by adding 7U of enzyme for 1ug of measured DNA content. RNaseH-treated samples were then PCR cleanup purified (Macherey-Nagel, Düren, Germany) and eluted in 5 mM TRIS-Cl pH 7.5 solution. RNA-DNA hybrid immunoprecipitation was performed using the S9.6 mouse monoclonal antibody (HB-8730, ATCC). Nucleic acid content of the IP and input samples was measured by a Qubit fluorometer (Thermo Fisher Scientific).
DRIP ‘IP’ and ‘input’ samples and RNaseH1-treated (negative control) DRIP samples were concentrated to less than 30 l volume with Eppendorf Concentrator Plus (Eppendorf, Hamburg Germany) at 30oC for 30 minutes. Illumina compatible sequencing libraries were generated from fragmented 1 – 10ng of dsDNA using Ovation® Ultralow System V2 (Nugen, San Carlos, CA, USA) library preparation kit according to the manufacturer’s protocol. Briefly, fragmented dsDNA samples were end-repaired and A-tailed, then Illumina compatible indexed adaptor were ligated. Adaptor ligated dsDNA were amplified, and the products were purified using MagSi-DNA NGSPREP Plus (MagnaMedics GmbH, Aachen, Germany) magnetic beads. Sequencing libraries were quantified using Qubit fluorometer (Thermo Fisher Scientific), the fragment size distributions were analyzed on Agilent BioAnalyzer 2100 using DNA High Sensitivity assay (Agilent Technologies, Santa Clara, CA, USA). Sequencing libraries were normalized to the same molar concentration and pooled together. Library pool was sequenced on NextSeq500 instrument (Illumina, San Diego, CA, USA) generating single read 75bp long sequencing reads. Fastq files were generated automatically after the sequencing run by Illumina BaseSapce. The library preparations and the sequencing run were performed by Genomic Medicine and Bioinformatics Core Facility of Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary.

treatment_protocol: EndoG KO mice were backcrossed to C57BL/6J (Jackson Laboratory, 000664) for 13 generations to generate congenic WT and KO littermates. Mice were housed with a 12/12 – light/ dark cycle with free access to food and water. Unless indicated otherwise, mice were fed NIH-31 open formula mouse/rat diet (sterilizable).

value: liver


title: mitochondrial DRIP-seq  KO IP

description: Library name: drip_endoG_KO_ip.fastq


title: KAT6AB_KO_d15_rep3


title: Ctrl _2 [RNA-Seq]


title: POI_1 [RNA-Seq]

value: POI


title: Ctrl _1 [RNA-Seq]


title: mitochondrial DRIP-seq KO input

description: Library name: drip_endoG_KO_input.fastq


title: KAT6AB_KO_d0_rep2


title: T15

value: OSMF-IV 2


title: mitochondrial DRIP-seq IP RnaseH-treated

description: Library name: drip_wt_ip_rnaseh.fastq


title: POI_2 [RNA-Seq]


title: T15_2

value: OSMF-IV 5


title: KAT6AB_KO_d0_rep3


title: T1_2

value: OSCC 1


title: Control sample-2

value: Normal nasal mucosal tissue


title: KAT6A_KO_d6_rep3

value: KAT6A-/- KO

value: EB differentiation and all-trans retinoic acid


title: T1

value: Oral mucosal tissue

value: OSMF-III 5


title: S2

value: OSMF-IV 1


title: E14,SA,ADR,H3K27Ac,ChIP

city: Seoul

first: Han-Teo

last: Lee

address: Daehakro 103, Jongro

department: College of Medicine

institute: Hong-Duk Youn

data_processing:
Quality of raw data were checked (FastQC, version 0.11.9). Adapter sequences were trimmed (Cutadapt, version 4.0) and aligned to mouse reference genome (mm9) (Bowtie2, version 2.5.0) with default setting. Output datasets were sorted by coordinate order (SortSam, version 2.18.2). Duplicated reads were identified and removed (MarkDuplicates, version 2.18.2). Narrow peaks of each alignment result files were called with q-value 0.05 cutoff (MACS2, version 2.2.7.1). Histone broad peak regions were detected from bedgraph output generated using MACS2 with default option (Cutoff 2.0, minimum length 200, maximum gap 30, maximum liking 800, MACS2, version 2.2.7.1).
Assembly: mm9
Supplementary files format and content: bedgraph, narrow peaks or broad peaks (except for Input sample)

growth_protocol: DMEM, 15% fetal bovine serum, 2mM L-glutamine, 1% non-essential amino acids, 100U/ml penicillin, 100ug/ml streptomycin, 55uM beta-mercaptoethanol, 1000U/ml ESGRO leukemia inhibitory factor (LIF)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10min, room temperature and quenched using 125mM glycine solution. Cells were lysed and nuclei were collected. Chromatin was sheared by diagenode bioruptor sonicator
ChIP-seq library was prepared using TruSeq ChIP Sample Preparation kit (Illumina). Libraries were validated using Bioanalyzer DNA 1000 Chip (Agilent Technolgies).

treatment_protocol: 500nM Adriamycin

value: Mouse embryonic stem cells

value: Adriamycin


title: E14,SA,DMSO,H3K27Ac,ChIP

value: DMSO


title: T12

value: OSCC 4


title: T11

value: OSCC 3


title: mitochondrial DRIP-seq wt IP

description: Library name: drip_wt_ip.fastq


title: KAT6A_KO_d6_rep1

value: embryonic stem cell (E14 line)


title: T15N

value: OSMF-IV 3


title: S4

value: OSMF-IV 4


title: Ctrl _2

data_processing:
Raw data filtration Low quality bases andadapter sequenceswere trimmed by using trimmomatic(v0.38, Bolger, A. M. et al., 2014). The parameter settings used was “ SLIDINGWINDOW:5:15 HEADCROP:3 AVGQUAL:15 LEADING:5 TRAILING:5 MINLEN:80”.  Sequence alignmentand detection ofcytosinesmethylation level The cleaned reads were mapped back to reference genome using BSMAP software version 2.90(Xi & Li, 2009). The parameter settings used was “-v 0.08 -g 1 -n 1 -p 48”. Hydroxymethylation ratios were extracted from BSMAP output (SAM) using a Python script (methratio.py) which isdistributed with the BSMAP package. In brief, The hydroxymethylation level was calculated basedon the hydroxymethylated cytosine (hmC) percentage in the whole genome assite hydroxymethylation level = 100× (number of sequences with hydroxymethylatedcytosines (hmC)/total number of valid sequences).The global average hydroxymethylation levels were displayed by ViolinPlot using R package. The various gene elements average hydroxymethylation levels werecalculatedby genome gff file and were visualized by barplot using R package.  DhMC andDhMR detection Differentially hydroxymethylated cytosines (DhMCs) were detected using MethylKit(v1.20, Akalin Aet al.,2012)in de-novo mode among CpG sites with at least 5x coverage. The parameter settings used was “--mincov5--m_cutoff0.1 --p_cutoff 0.01”.Differentially hydroxymethylated regions (DhMRs) were detected using metilene(Jühling et al., 2016)in de-novo mode among CpG sites with at least 5x coverage. The parameter settings used was “--mincpgs 3 --minMethDiff 0.1--mode 1-mtc 2”. Then detected DhMR were filtered according to the standard: (1) corrected MWU-test P-value must be less than 0.05; (2) hydroxymethylation level difference must be greater than 0.1; (3) CpG number contained in DhMR must be greater than 5; (4) the length of the DhMR must be greater than 50bp.The related Elements and genes of DhMCs and DhMRs were located in genome by genome gff file. The genome GO and KEGG annotation was performed using emapper based on EGGNOG database. The above related hyper-hydroxymethylatedgenes were then subjected to enrichment analysis of GO and KEGG by Allenricher (v1.0).
Assembly: hg38
Supplementary files format and content: bedgraph
Library strategy: ACE-seq

value: ovary

value: cumulus cells


title: KAT6AB_KO_d0_rep1

value: KAT6A-/-; KAT6B-/- dKO


title: KAT6A_KO_d2_rep2

value: EB differentiation


title: POI_1


title: E14,SE,DMSO,H3K27Ac,ChIP


title: Ctrl _1


title: ORG6BA_domes-2

city: Boston

first: Kung-Chi

last: Chang

state: MA

address: 240 Longwood Avenue, Building C/Rom 501

department: Cell Department

institute: Harvard medical School

description:
Sample 27
BS7301_100
sample13-27count_matrix

data_processing:
Data was processed and analyzed at Partek.com using Partek Flow Genomic Analysis Software
Alignment using STAR; hg38 for assembly (whole genome)
Quantify to an annotation model (Partek E/M)
Noise reduction for low expression genes by applying fliter exclude features where maximum <= 50.0.
DESeq2 (Median ratio DESeq2 only) for normalization
Assembly: hg38
Supplementary files format and content: matrix table text files include sample reads and gene counts

source_name: Breast

growth_protocol: Organoid culture medium from dekker et. Al, 2021 (PMID: 33692550)

extract_protocol:
RNA was extracted using Trizol/Chloroform method and isopropanol precipitation
RNA samples were sent to Novogene co. for library preparation

treatment_protocol:
Cells isolated from human breast organoids
Hormone sensing (HS) treated w/wo Estrogen 1nM for 7 days
luminal adaptive secretory precursor fate (LASP), Basal (BA)

value: Breast

value: Primary epithelial cells

value: BA

value: WT

value: No


title: KAT6A_KO_d6_rep2

value: KAT6A-/- KO

value: EB differentiation and all-trans retinoic acid


title: POI_2


title: N1

value: Oral mucosal tissue

value: OSMF-III 4


title: POI_3


title: Ctrl _3


title: E14,WT,ADR,H3K27Ac,ChIP

value: Mouse embryonic stem cells

value: Adriamycin


title: KAT6A_KO_d2_rep3

value: embryonic stem cell (E14 line)


title: ORG6BA_domes-1

description:
Sample 26
BA37301
sample13-27count_matrix


title: S1

value: OSMF-III 3


title: E14,SE,ADR,H3K27Ac,ChIP


title: N2N

value: Normal 5


title: KAT6A_KO_d15_rep2

value: NPCs cultured in Advanced DMEM/F12 with N2 and B27 supplement


title: N2

value: Normal 4


title: KAT6A_KO_d15_rep1


title: S3

value: OSMF-III 2


title: mitochondrial DRIP-seq wt input

description: Library name: drip_wt_input.fastq

value: liver


title: KAT6A_KO_d2_rep1

value: EB differentiation


title: N4

value: OSMF-III 1


title: N22

value: Normal 3


title: E14,WT,DMSO,H3K27Ac,ChIP

value: DMSO


title: KAT6A_KO_d0_rep2

value: KAT6A-/- KO


title: E14,Input


title: N22N

value: Normal 2


title: KAT6A_KO_d15_rep3


title: E14,SA,Input


title: ORG6BA_suspension-2

description:
Sample 25
BA7301_5
sample13-27count_matrix

value: Breast

value: Primary epithelial cells

value: BA

value: WT

value: No


title: ORG6LASP_suspension-2

description:
Sample 21
AV7301_5
sample13-27count_matrix

value: LASP


title: E14,SA,ADR,Ctbp2,ChIP

value: Mouse embryonic stem cells

value: Adriamycin


title: E14_d6_rep3

value: embryonic stem cell (E14 line)

value: E14 wildtype

value: EB differentiation and all-trans retinoic acid


title: ORG6LASP_domes-2

description:
Sample 23
AV7301_100
sample13-27count_matrix


title: ORG6HS_domes-2

description:
Sample 19
HS37301
sample13-27count_matrix

value: HS


title: KAT6A_KO_d0_rep3


title: E14,SA,DMSO,Ctbp2,ChIP


title: ORG6LASP_domes-1

description:
Sample 22
AV7_7301
sample13-27count_matrix


title: E14,SE,ADR,Ctbp2,ChIP


title: E14_d6_rep2


title: E14_d6_rep1


title: N3

value: Oral mucosal tissue

value: Normal 1


title: KAT6A_KO_d0_rep1


title: E14,WT,ADR,Ctbp2,ChIP


title: ORG6LASP_suspension-1

description:
Sample 20
AV47301
sample13-27count_matrix


title: 31

city: Grenoble

first: Anouk

last: Emadali

address: Allée des Alpes, Site Santé La Tronche, BP170, Cedex 9

department: Institute for Advanced Biosciences

country: France

institute: Grenoble University Hospital

data_processing:
Reads were quality-checked using FastQC. (Dobin 226 et al., 2013).
Reads were then aligned to H. sapiens genome build hg38 using STAR 2.7.1a
Raw read counts for each gene were calculated using HTSeqCount 0.11.2.
Read counts were normalized using log2 of RPM normalization
Assembly: hg38
Supplementary files format and content: Normalized counts (log2 RPM) for each sample

growth_protocol: NUDUL-1, OCI-Ly18, RAMOS cell lines were 143 cultured in RPMI 1640 medium supplemented with 20% fetal bovine serum (FBS), 1% 144 glutamine, 100 mg/mL penicillin/streptomycin. SUDHL-4, SUDHL-6, HT, B593 and RAJI cell 145 lines were cultured in RPMI Glutamax supplemented with 20% FBS, 1 mM sodium pyruvate, 146 1% minimum essential medium non-essential amino acids (MEM NEAA) and 100 mg/mL 147 penicillin/streptomycin. OCI-Ly1 cell line was grown in IMDM medium with 20 % FBS and 100 148 mg/mL penicillin/streptomycin.

extract_protocol:
RNA was extracted from 3 million cells with NucleoSpin 210 RNA extraction kit (Macherey-Nagel) according to manufacturer's instructions.
(Samples 1-36) RNA-Seq libraries were generated according to manufacturer's instructions from 500 ng of total RNA using the Illumina Stranded mRNA Prep, Ligation kit and IDT for Illumina RNA UD Indexes Ligation (Illumina, San Diego, USA). Briefly, Oligo(dT) magnetic beads were used to purify and capture the mRNA molecules containing polyA tails.The purified mRNA were then fragmented at 94oC for 8 min and copied into first strand complementary DNA (cDNA) using reverse transcriptase and random primers. Second strand cDNA synthesis further generated blunt-ended double-stranded cDNA and incorporated dUTP in place of dTTP to achieve strand specificity by quenching the second strand during amplification. Following A-tailing of DNA fragments and ligation of pre-index anchors, PCR amplification was used to add indexes and primer sequences and to enrich DNA libraries (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x12cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France) and the final libraries were checked for quality and quantified using capillary electrophoresis. (Samples 37-60) Librairies were prepared according to BGI procedures.

treatment_protocol: Cells cere treated for 24h with 500 nM JQ1 and compared to DMS0-treated counterparts.

value: High-grade B-Cell Lymphoma

value: DMSO replicat 2


title: 35

value: JQ1 replicat 3


title: E14_d2_rep3

value: EB differentiation


title: ORG6BA_suspension-1

description:
Sample 24
BA47301
sample13-27count_matrix

value: Breast

value: Primary epithelial cells


title: E14,SE,DMSO,Ctbp2,ChIP

value: DMSO


title: 34

value: DMSO replicat 3


title: E14,SE,Input


title: ORG6HS_7dculture-3

description:
Sample 15
HS7301_0_2
sample13-27count_matrix

value: WT

value: No


title: ORG6HS_domes-1

description:
Sample 18
HS7301_100
sample13-27count_matrix


title: 28

value: DMSO replicat 1


title: 32

value: JQ1 replicat 2


title: 26


title: E14_d15_rep3

value: embryonic stem cell (E14 line)

value: E14 wildtype

value: NPCs cultured in Advanced DMEM/F12 with N2 and B27 supplement


title: PDOVCA_146

city: Padova

first: Daniele

last: Boso

address: Via Gattamelata, 64

department: Basic and Translational Oncology Unit

country: Italy

institute: Veneto Institute of Oncology IOV - IRCCS

data_processing:
data quality: FastQC and MultiQC(1.14)
trimming of the raw reads was carried out using cutadapt(1.18) with specific adapter sequences (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT), and reads below a minimum length of 100 bases were discarded.
alignment and quantification of the high-quality human reads against the Gencode GRCh38.p13 reference genome were performed using Salmon(1.4.0)
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample

source_name: Ovarian cancer ascites

growth_protocol: Ovarian cancer PDX were propagated by injecting 1 million tumor cells intra-peritoneally into 8-week-old female NOD/SCID mice. Then, cells were harvested from developed ascites and used for RNAseq

extract_protocol:
RNA was harvested using Trizol® protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit (NEB)

treatment_protocol: Ascites-derived cells were maintained in PBS until cell count was done and 1 million pellets were kept at -80°C until RNA extraction was performed

value: Ovarian cancer ascites

value: Ovarian cancer patient derived xenografts (PDX)


title: ORG6HS_suspension-2

description:
Sample 17
HS47301
sample13-27count_matrix

value: HS


title: E14_d15_rep2


title: ORG6HS_7dculture-1

description:
Sample 13
HS73010
sample13-27count_matrix


title: PDOVCA_128


title: E14,WT,DMSO,Ctbp2,ChIP

value: Mouse embryonic stem cells


title: 29

value: High-grade B-Cell Lymphoma

value: JQ1 replicat 1


title: ORG11HS_E21nM-2

description:
Sample 12
HS7149E27_2
sample1-12_count_matrix

value: Breast

value: Estrogen 1nM 7days


title: E14_d2_rep2

value: EB differentiation


title: 23


title: E14,WT,Input


title: E14_d2_rep1


title: ORG6HS_suspension-1

description:
Sample 16
HS7301_5
sample13-27count_matrix

value: Primary epithelial cells


title: E14_d15_rep1


title: 22

value: DMSO replicat 2


title: ORG11HS-control-2

description:
Sample 10
HS71490_2
sample1-12_count_matrix

value: WT


title: ORG6HS_7dculture-2

description:
Sample 14
hS7301_0
sample13-27count_matrix

value: No


title: PDOVCA_145


title: ORG11HS_E21nM-1

description:
Sample 11
HS7149E27
sample1-12_count_matrix

value: Control


title: E14_d0_rep3

value: embryonic stem cell (E14 line)


title: 25

value: DMSO replicat 3


title: 19

value: DMSO replicat 1


title: PDOVCA_126

value: Ovarian cancer ascites