title: LNCaP_24hr_si-A2_replicate-4

description:
LNCaP_1_7_7_siA2
Gene expression at 24h after TAPIR-2 knockdown (replicate 4)

hyb_protocol: 1.65 µg of Cy3-labelled cRNA (specific activity >15.0 pmol Cy3/µg cRNA) was fragmented using at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions (Agilent Gene Expression Hybridization Kit). On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent??? Microarrays??? (bitte ergänzen) (with an ozone barrier slide) for 17 hours at 65°C in SureHyb chambers using rotating an Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the SureScan Microarry Scanner System using one color scan setting (AgilentG3_GX_1Color) for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Tiff 20 bit and Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Differentially expressed probes were identified by using R v3.4.3 and the Bioconductor package limma v3.34.8. Quality control of arrays were performed by checking distribution of ``bright corner'', ``dark corner'' probes, and unsupervised clustering of raw intensities. One replicate of si-A2 at 48h had to be removed from downstream analyses due to too low foreground intensities. To retrieve a set of probes mapping to unique genomic positions in hg38 we used BLAT v35 with the parameter -minIdentity=95 allowing to detect probes spanning splice sites for all arrays. All probes mapping to more than one distinct genomic region were discarded. Remaining probes were annotated by known genes using Gencode v27. Normalization between arrays was done by using quantile normalization, and batch effects considered as additive covariates in the linear model. In order to reduce the number of univariate t-tests nonspecific filtering was applied as follows: The expression of a probe must be larger than background expression in at least three arrays. Background expression was defined by the mean intensity plus three times the standard deviation of negative control spots (Agilent's 3xSLv spots). In addition, a probe must exhibit a nonspecific change of expression, which was assessed by an interquartile range of at least 0.5. Finally, a linear model was fitted using limma to assess significant expression changes for the contrasts si-A1 (siRNA against TAPIR-1) versus si-SCRL (scramble siRNA) and si-A2 (siRNA against TAPIR-2) versus si-SCRL (scramble siRNA), respectively. Reliable variance estimates were obtained by Empirical Bayes moderated t-statistics. False discovery rate (FDR) was controlled by Benjamini-Hochberg adjustment. All genes with log2 fold change ≥ 0.5 and FDR < 0.01 were classified to be significantly regulated upon TAPIR-1 or TAPIR-2 knock-down.

source_name: LNCaP, 24hr, si-A2, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 µg total RNA using the One-Color Low RNA Input Amplification kit (Agilent) and QuickAmpLableling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer. The minimum concentration and labeling efficiency were 60 ng/µl and 15pmol Cy3/µg cRNA, respectively.

growth_protocol: LNCaP cells were obtained from ATCC and grown RPMI-1640 Medium (gibco), supplemented with 10% fetal bovine serum (FBS; gibco, 10270-106).

extract_protocol: Total RNA was isolated from LNCaP cells with TRIzol (ambion), following the manufacturers protocol.

treatment_protocol: Stealth RNAiTM siRNA Duplex (Invitrogen, cat#10620312) were designed using a siRNA target finder tool (Invitrogen, Block-iTTM RNAi Designer), to silence following target transcripts: TAPIR-1 (GeneBank accession no. AC141930.1, ENSG00000228613 Homo sapiens: GRCh37.p13 (GCF_000001405.25) Chr2 (NC_000002.11): 1,550,437-1,623,885) and TAPIR-2 (GeneBank accession no. AC144450.2 ENSG00000203635 Homo sapiens: GRCh38.p12 (GCF_000001405.38) Chr2 (NC_000002.12): 1,620,510-1,625,419). A BLAST search (http://www.ncbi.nlm.nih.gov/BLAST) for selected siRNA sequences was carried out to exclude any alignment with other sequences in the human genome. As negative control Stealth RNAiTM Negative Control Medium GC Duplex (Invitrogen, cat# 12935-300) with no significant homology to any known human mRNA was used for subsequent normalization. Transfection was carried out using the NEON™-Kit and the microporator MP100 Digitalbio (LIFE Technologies) according to the manufacturer’s instructions. Two pulses of 1250 V and 20ms were applied.

tag: cell line

value: LNCaP

tag: genotype

value: TAPIR-2 knockdown


title: RNAseq_Syn_WH7803_LL_UV_T1_D1

status: Public on Jun 17 2020

type: SRA

city: Roscoff

first: Laurence

last: Garczarek

address: Place Georges Teissier

department: UMR7144-Adaptation and Diversity in Marine Ecosystems

country: France

institute: Station Biologique (Sorbonne University and CNRS)

library_source: transcriptomic

data_processing:
Reads quality checks were performed with the FastQC tool.
Illumina adapters, found in 23.5 +/- 4.5 % of all reads, were removed using Cutadapt v1.8.3.
rRNA, constituting 5.0 +/- 5.9 % of all reads, were removed with Sortmerna v2.1.
Reads under 50 bp size and with a mean quality score lower than 25 were filtered out using Prinseq v0.20.4.
Remaining reads were then aligned on the reference genome of Synechococcus sp. WH7803 using Bowtie2 v2.2.9 software with ‘--non-deterministic --end-to-end –sensitive’ parameters and by selecting only the properly paired reads (i.e. SAM flagged as 99, 147, 163 or 83)
Read counts table were obtained using HTSeq Count v0.6.0 with following parameters: ‘--stranded=reverse -a 10 -m intersection-nonempty’.
Genes expression level between stress and control conditions as well as adjusted p-value based on the Benjamini-Hochberg procedure were determined using SARTools v1.4.0 with embedded DESeq2 v1.14.1.
Genome_build: NC_009481.1
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each sample, log2FC and  their associated pvalues and adjusted pvalues

molecule: total RNA

organism: Synechococcus sp. WH 7803

source_name: culture of Synechococcus sp. WH7803 cells

growth_protocol: Synechococcus sp. WH7803, an axenic strain retrieved from the Roscoff culture collection (RCC752; http://roscoff-culture-collection.org/), was grown in modified PCR-S11 culture medium with 1 mM sodium nitrate and 1 μg/L vitamin B12. Cultures were acclimated for at least two weeks at 22°C (hereafter medium temperature: MT) and 20 μmol photon.m-2.s-1 (LL and μE.m-2.s-1) or 250 μE.m-2.s-1 (HL) provided by multicolor (cool white: 6500K, blue: 470 nm, green: 530 nm) LED systems (Alpheus, France). For each growth irradiance, 9 L of exponentially growing culture were split in 500 mL aliquots in 1 L flasks (Nalgene, St. Louis, MO, USA) and left under their initial growth irradiance overnight before being submitted to light, UV or temperature stress conditions and sampled at different times for various parameters.

extract_protocol:
RNA extractions were performed from 150 mL of culture harvested by centrifugation for 7 min at 10,414 × g and 4°C in an Eppendorf 5804R, followed by 2 min centrifugation at 20,817 × g in Eppendorf tubes and 4°C in an Eppendorff 5417R centrifuge. Cell pellet was then resuspended in 1 mL Qiazol (Qiagen, Valencia, CA, USA) and quickly frozen in liquid nitrogen. After thawing the tubes at 65 °C, followed by and additional incubation of 5 min at this temperature, RNA was extracted using the Direct-Zol kit (Zymo Research Corp, Proteigene) as recommended by the manufacturer. Three successive DNase treatments were performed on the Zymo-Spin™-IIC Column using the Qiagen RNase-free DNase Set (Qiagen), followed by elution from the column in 30 L DEPC-treated water. RNA quantification and quality check were performed using a Qubit (Invitrogen) and a BioAnalyzer 2100 with the RNA 6000 Nano Kit (Agilent, Santa Clara, CA, USA), respectively. RNA samples were then frozen in liquid nitrogen and stored at -80°C.
Ribodepletion was performed at the Genotoul platform (Toulouse, France) from 5 µg of RNA using the Ribo-Zero Bacteria Magnetic Kits (Illumina) in presence of RiboGuard RNase Inhibitor (Epicentre) and treated RNA samples were purified and concentrated using RNA Clean & Concentrator™-5 columns (Zymo research). 0.5 µL of ribo-depleted RNA was then used for quantification (Qubit RNA HS Assay Kit) and quality check (Bioanalyzer RNA Pico kit or Labchip GX). Libraries were then prepared using 100 to 400 ng of RNA with the Illumina TruSeq Stranded mRNA kit and sequenced as 150 bp paired-end reads on Illumina HiSeq 3000 System (Illumina, San Diego, CA, USA) at Genotoul (Toulouse, France). 18.5 +/- 4.7·10^6 paired-end reads were generated per sample.

treatment_protocol: For shift experiments, High light (HL) stress was induced by a shift from LL acclimated conditions (LL, 20 μE m-2 s-1) to HL ((250 μE m-2 s-1). Cultures were then sampled after 20 min (T0.3), 1h (T1), 3h (T3) and 6h (T6). UV stress was induced by a shift from LL-acclimated conditions or HL-acclimated conditions to 3 W.m −2  of UV-A and 0.3 W.m −2  of UV-B. Cultures were then sampled after 20 min (T0.3), 1h (T1), 3h (T3) and 6h (T6). Low temperature (LT) stress was performed on LL- or HL-acclimated culture by shifting them from 22 °C to 13 °C. Cultures were then sampled after 12h (J0-5), 24h (J1), 48h (J2), 72h (J3) or after 4h (J0-17), 8h (J0-33), 16h (J0-67), 24h (J1), for LL and HL-acclimated cultures, respectively. High temperature (HT) stress was performed on LL- or HL-acclimated culture by shifting them from 22°C to 30 °C. Cultures were then sampled after 12h (J0-5), 1 day (J1), 2 days (J2), 3 days (J3) and after 4h (J0-17), 8h (J0-33), 14.5h (J0-67), 24h (J1), for LL and HL-acclimated cultures, respectively. UVA and UVB radiations, generated from UVA-351 and UVB-313 fluorescent bulbs (Q-Panel Lab products, Cleveland, OH, USA), were measured between 280–320 and 320–400 nm, respectively using a USB2000 spectroradiometer (Ocean Optics, Ew Duiven, The Netherlands). Temperature stress were performed in temperature-controlled chambers (Liebherr-Hausgeräte, Lienz, Austria).  For diel cycle experiments, run at two temperatures (21 and 27°C), a bell-shaped 12/12 h L/D cycle, triggering a good synchronization of cell division, was generated using the multicolor LED systems and the Ether software (Alpheus, France). The maximal irradiance (at virtual noon) was set at 669 μE.m-2.s-1. Two replicate cultures per temperature were acclimated to L/D cycles for at least 2 weeks prior to start monitoring the different parameters. During the experiment, two replicate cultures were grown with a continuous input of fresh medium, in order to maintain cells in exponential growth throughout the whole sampling period. To study the kinetics of the response of cells to light fluctuations, cultures were sampled at 6:00, 9:00, 12:00, 15:00, 18:00, 20:00, 22:00, and 2:00 over 3 days.

tag: strain

tag: acclimation condition

value: Low Light

tag: stress condition

value: UV exposition

tag: timepoint

value: 1 hour

tag: replicate


title: prostate_tissue-H+sf-replicate_RIB0034402

type: RNA

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

description: Gene expression of prostate RP tissue specimen (prostate cancer)

hyb_protocol: We used 1.65 µg of labeled cRNA for hybridization with the custom microarray following manufacturer's instructions.

scan_protocol: After hybridization the arrays were washed according to the manual and scanned using the Agilent G2565CA Microarray Scanner System with Agilent Scan Control Software (Version A851) and following settings for scanning: Profile: AgilentG3_GX_1Color; Channels: Green; Scan Region: Agilent HD (61x 21,6 mm); Resolution: 3 µm double pass; Tiff: 20 bit; Green PMT Gain: 100 %. We extracted the result tables after grid placement using Agilent Feature Extraction Software (Version 11.5.1.1).

data_processing: Three microarray were excluded from further processing due to scratches on array slides (data not included in GEO series). Quality control of remaining arrays (N=255) was performed by checking distribution of ``bright corner'', ``dark corner'' probes, and relative spike-in concentration versus normalized signal. Quality control confirmed high quality of the results and consequently all remaining microarray data were included in the downstream analysis. To retrieve a set of probes mapping to unique genomic positions in hg19 we used BLAT v35 with the parameter -minIdentity=95 allowing to detect probes spanning splice sites. All probes mapping to more than one distinct genomic region were discarded. Normalization between arrays was done by using quantile normalization. In order to reduce the number of univariate t-tests nonspecific filtering was applied as follows: The expression of a probe must be larger than background expression in at least 20 arrays. Background expression was defined by the mean intensity plus three times the standard deviation of negative control spots (Agilent's 3xSLv spots). In addition, a probe must exhibit a nonspecific change of expression, which was assessed by an interquartile range of at least 0.5. Finally, a linear model to detect expression variation between BPH and tumor specimens adjusted for array processing batches was fitted using limma v3.24.15 and reliable variance estimates were obtained by Empirical Bayes moderated t-statistics. False discovery rate (FDR) was controlled by Benjamini-Hochberg adjustment.

organism: Homo sapiens

source_name: prostate

label_protocol: We prepared all samples assembled for expression analysis with the custom microarray using the Agilent Quick Amp Labeling Kit for single color following the manufacturer's instructions. Instead of the Oligo-dT/T7-primer delivered with the Quick Amp Labeling Kit, we used 120 pmol of a random N6/T7 primer synthesized by Metabion (Planegg, Germany) and used 200 ng RNA as input for the labeling procedure. cRNA quantity was checked using a NanoDrop ND-1000 UV-VIS Spectrophotometer, as enlisted in the manufacturer's instructions.

extract_protocol: Stacks of consecutive cryosections were generated from frozen RP tissue samples and immediately transferred to 1ml Qiazol (Qiagen, Hilden, Germany). A pathologist evaluated HE-stained cryosections flanking the stacks concerning tumor and stroma cell content (Supplementary Figure S1). Only PCa tissue stacks, which were flanked on either side by sections containing at least 50% tumor cells underwent RNA isolation. In case of insufficient RNA quantity, we combined multiple tissue stacks with suitable tumor cell content. We isolated total RNA using the miRNeasy Mini Kit on the QIAcube (Qiagen) followed by manual DNase I digestion. After determining the RNA concentration with a NanoDrop 1000 (Peqlab, Erlangen, Germany), we verified the RNA integrity on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). RNA samples with an RNA-Integrity-Number (RIN) of at least six passed for further processing.

tag: risk group

value: H+sf

tag: tissue

value: prostate

tag: gender

value: male

tag: gleason score

tag: diagnosis

value: prostate cancer


title: LNCaP_24hr_si-A1_replicate-4

description:
LNCaP_1_6_6_siA1
Gene expression at 24h after TAPIR-1 knockdown (replicate 4)

source_name: LNCaP, 24hr, si-A1, replicate 4

value: TAPIR-1 knockdown

tag: time


title: ANM_8

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

country: China

institute: Shanxi Medical University

description:
whole transcriptome sequencing
P_8

data_processing:
Basecalls performed using Perl package developed by Novogene.
Contaminant reads were filtered from the fq file and get the final clean reads. And then summarize the length distribution of these clean reads.
Raw data(raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using bowtie2 v2.2.8 and paired-end clean reads were aligned to the reference genome using HISAT2(Langmead, B.et al) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set as default. The mapped reads of each sample were assembled by StringTie (v1.3.1) (Mihaela Pertea.et al. 2016) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Then coding potential analysis was performed with CNCI, CPC, Pfam-sca, and phyloCSF, Transcripts predicted with coding potential by either/all of the four tools above were filtered out, and those without coding potential were candidate set of lncRNAs. Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Genome_build: hg19
Supplementary_files_format_and_content: txt file

source_name: adjacent normal mucosa tissue

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life  technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent  Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cancer and adjacent mormal mucosa tissues excised from LSCC patients after surgery were stored with RNAlater  (Cat#AM7020，Life  technologies, Carlsbad, CA, US) immediately following the manufacturer’s instructions.

tag: subject number

value: adjacent normal mucosa tissue

tag: tumor stage

value: Not Applicable

tag: tobacco smoking

tag: alcohol consumption


title: prostate_tissue-C-replicate_RIB0034824

description: Gene expression of prostate RP tissue specimen (benign prostate hyperplasia)

value: C

value: benign prostate hyperplasia


title: RNAseq_Syn_WH7803_LL_UV_T1_C1


title: LNCaP_24hr_scramble_replicate-4

description:
LNCaP_1_5_5_scr
Gene expression at 24h after scramble siRNA (replicate 4)

source_name: LNCaP, 24hr, scramble, replicate 4

tag: cell line

value: control


title: RNAseq_Syn_WH7803_LL_UV_T0-3_E1

value: 0.3 hours


title: ANM_10

description:
whole transcriptome sequencing
P10


title: RNAseq_Syn_WH7803_LL_UV_T0-3_C1


title: RNAseq_Syn_WH7803_LL_UV_T0-3_D1


title: PDGF 12

city: Moscow

first: Mikhail

last: Arbatsky

address: Lomonosovskiy 27 bld 10

country: Russia

institute: MSU IRM

hyb_protocol: Whole-genome gene expression was assessed using a direct hybridization approach. To amplify starting material, a single-round IVT amplification was carried out using the Illumina RNA Amplification Kit, manufactured by Ambion®, Inc.

scan_protocol: Illumina protocol

data_processing:
Lumi package is a very convenient tool for Illumina data preprocessing
The processing included following steps: Quality control of raw data; Background subtraction; Variance stabilization using algorithm VST, developed for Illumina data. Values after this processing step should be treated as log-transformed. Quantile normalization.
Enrichment Fold (1.3, 2)

label: biotin

source_name: Mesenchymal stem cells

label_protocol: Illumina protocol

growth_protocol: Cells were cultured in AdvanceSTEM™ Mesenchymal Stem Cell Media containing 10 % AdvanceSTEM™ Supplement (HyClone, USA), 1 % antibiotic–antimycotic solution (HyClone) at 37 °C in 5 % CO2 incubator.

extract_protocol: Total cellular RNA was isolated from cultured ADSCs using RNeasy Kit (Qiagen, cat # 74104) according to manufacturer instructions.

treatment_protocol: For assessment of transcriptome content ADSCs were cultured under standard conditions (5 % CO2 and 21 % O2) at 37 °C for 12 or 24 h with or without PDGF-BB.

tag: cell type

value: Human adipose-derived mesenchymal stem/stromal cells (ADSCs

tag: treatment

value: (5 % CO2 and 21 % O2) at 37 °C for 12 h with  PDGF-BB


title: LNCaP_24hr_si-A2_replicate-3

description:
LNCaP_1_3_3_siA2
Gene expression at 24h after TAPIR-2 knockdown (replicate 3)

source_name: LNCaP, 24hr, si-A2, replicate 3

value: LNCaP

tag: genotype

value: TAPIR-2 knockdown


title: LNCaP_24hr_si-A1_replicate-3

description:
LNCaP_1_2_2_siA1
Gene expression at 24h after TAPIR-1 knockdown (replicate 3)

source_name: LNCaP, 24hr, si-A1, replicate 3


title: prostate_tissue-H+sf-replicate_RIB0034835


title: ANM_6

description:
whole transcriptome sequencing
P_6


title: LNCaP_24hr_scramble_replicate-3

description:
LNCaP_1_1_1_scr
Gene expression at 24h after scramble siRNA (replicate 3)

source_name: LNCaP, 24hr, scramble, replicate 3


title: ANM_5

description:
whole transcriptome sequencing
P_5


title: ANM_4

description:
whole transcriptome sequencing
P_4


title: LNCaP_24hr_si-A1_replicate-2

description:
LNCaP_2_6_14_siA1
Gene expression at 24h after TAPIR-1 knockdown (replicate 2)

source_name: LNCaP, 24hr, si-A1, replicate 2


title: RNAseq_Syn_WH7803_LL_LT_J3_E1

tag: strain

tag: acclimation condition

value: Low Light

tag: stress condition

value: Low temperature

value: 72 hours


title: R740EB

type: genomic

city: Grand Rapids

first: Peter

middle: A

last: Jones

state: MI

address: 333 Bostwick Ave

department: Center for Epigenetics

country: USA

institute: Van Andel Research Institute

hyb_protocol: Using standard Illumina Infinium HumanMethylationEPIC BeadChip array hyb protocol.

data_processing:
Quality control, preprocessing and normalization process were performed using R package SeSAMe on Bioconductor.
Normalized Beta Value. The data was normalized according to R package SeSAMe user guide as published in Zhou W, Triche TJ, Laird PW, Shen H (2018). “SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions.” Nucleic Acids Research, gky691. doi: 10.1093/nar/gky691

label: Cy3, Cy5

molecule: genomic DNA

source_name: DKO8 cells expressing DNMT3B3 R740E

growth_protocol: Cells were cultured in McCoy’s 5A medium (Gibco) containing 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol: Genomic DNA was extracted using Phenol/Chloroform.

treatment_protocol: The lentiviral infection of DKO8 cells was performed in culture media with 8 μg/mL polybrene (Sigma H9268). Forty-eight hours after infection, cells were selected with 2 μg/mL puromycin until harvesting.

tag: expressing

value: DNMT3B3 R740E


title: LNCaP_24hr_scramble_replicate-2

description:
LNCaP_2_5_13_scr
Gene expression at 24h after scramble siRNA (replicate 2)

source_name: LNCaP, 24hr, scramble, replicate 2


title: LNCaP_24hr_si-A2_replicate-2

description:
LNCaP_2_7_15_siA2
Gene expression at 24h after TAPIR-2 knockdown (replicate 2)

source_name: LNCaP, 24hr, si-A2, replicate 2


title: ANM_9

description:
whole transcriptome sequencing
P_9

tag: tissue


title: prostate_tissue-H-sf-replicate_RIB0034889

tag: risk group

value: H-sf

value: prostate

tag: gender

value: male


title: ANM_3

description:
whole transcriptome sequencing
P_3

value: adjacent normal mucosa tissue


title: RNAseq_Syn_WH7803_LL_LT_J3_D2

tag: timepoint

tag: replicate


title: R740E

scan_protocol: Using standard Illumina Infinium HumanMethylationEPIC BeadChip array hyb protocol.


title: K745D

source_name: DKO8 cells expressing DNMT3B3 R745D

value: DNMT3B3 R745D


title: RNAseq_Syn_WH7803_LL_LT_J2_E1

value: 48 hours


title: RNAseq_Syn_WH7803_LL_LT_J2_D1


title: RNAseq_Syn_WH7803_LL_LT_J3_C1


title: LSCC_77

description:
whole transcriptome sequencing
C77

source_name: LSCC tissue

tag: subject number

value: LSCC tissue

value: Yes

value: No


title: ANM_2

description:
whole transcriptome sequencing
P_2

tag: tumor stage

value: Not Applicable


title: ANM_1

description:
whole transcriptome sequencing
P_1

tag: tobacco smoking


title: R743EB

source_name: DKO8 cells expressing DNMT3B3 R743E

value: DNMT3B3 R743E


title: prostate_tissue-C-replicate_RIB0034869

value: C

tag: gleason score

tag: diagnosis

value: benign prostate hyperplasia


title: prostate_tissue-H+sf-replicate_RIB0034838

value: H+sf

value: prostate cancer


title: ANM_7

description:
whole transcriptome sequencing
P_7

tag: alcohol consumption


title: RNAseq_Syn_WH7803_LL_LT_J2_C1

value: Low Light

value: Low temperature


title: R749EB

source_name: DKO8 cells expressing DNMT3B3 R749E

tag: cell line

value: DNMT3B3 R749E


title: RNAseq_Syn_WH7803_LL_LT_J1_E1

source_name: culture of Synechococcus sp. WH7803 cells

value: 24 hours


title: R749E


title: IFN3_L002

city: Shanghai

first: Junjun

last: CHENG

address: 371 Li Shizhen Road, Bldg 5  Pudong

department: Immunology, Infectious Diseases and Ophthalmology (I2O)

institute: Roche Innovation Center (Shanghai)

data_processing:
Illumina Hiseq2500 was used for base-calling
Raw sequence reads were aligned to the chicken genome. The sequence reads from first and second experiment were aligned to chicken genome Gallus_gallus4 and chicken genome Gallus_gallus6 (GRCg6a), respectively, using the Tophat algorithm
Genome_build: GRCg6a
Supplementary_files_format_and_content: FPKM

organism: Gallus gallus

source_name: Hepatocytes

growth_protocol: dstet5 cells were maintained in DMEM/F12 medium (Mediatech) supplemented with 10% fetal bovine serum, 100 U/ml of penicillin, 100 μg/ml of streptomycin, 1 μg/ml of tetracycline and 200 μg/ml of G-418.

extract_protocol:
Culture media were removed and cells were washed once with PBS. Total intracellular RNA were then extracted with TRIzol reagents
mRNA-seq library was made using the Truseq stranded mRNA library kit

treatment_protocol: dstet5 cells were seeded into 12-well plates. After 24 h incubation, the cells were mock-treated or treated with 10 ng/mL of rChIFN-α for 6 h.

tag: cell type

value: Hepatocytes

tag: treatment

value: 10 ng/mL of rChIFN-α for 6 h

tag: molecule subtype

value: Total intracellular RNA


title: LSCC_76

description:
whole transcriptome sequencing
C76


title: IFN3_L001


title: LSCC_75

description:
whole transcriptome sequencing
C75


title: RNAseq_Syn_WH7803_LL_LT_J1_D1

tag: strain

tag: acclimation condition

tag: stress condition


title: R743E

tag: expressing


title: LNCaP_24hr_si-A1_replicate-1

description:
LNCaP_2_2_10_siA1
Gene expression at 24h after TAPIR-1 knockdown (replicate 1)

source_name: LNCaP, 24hr, si-A1, replicate 1

value: LNCaP

tag: genotype

value: TAPIR-1 knockdown

tag: time


title: LSCC_74

description:
whole transcriptome sequencing
C74

tag: tissue

value: LSCC tissue

value: Yes


title: IFN2_L001


title: EVB

description: EVB

source_name: DKO8 cells expressing empty vector

value: empty vector


title: D3B3

source_name: DKO8 cells expressing DNMT3B3


title: IFN1_L002


title: RNAseq_Syn_WH7803_LL_LT_J0-5_E1

tag: timepoint

value: 12 hours

tag: replicate


title: RNAseq_Syn_WH7803_LL_LT_J1_C1


title: LSCC_66

description:
whole transcriptome sequencing
C66

tag: subject number

tag: tumor stage

tag: tobacco smoking


title: RNAseq_Syn_WH7803_LL_LT_J0-5_D1


title: prostate_tissue-C-replicate_RIB0034814

source_name: prostate

tag: risk group

value: C

value: prostate

tag: gender

value: male

tag: gleason score

tag: diagnosis


title: K745DB

tag: cell line

value: DNMT3B3 R745D


title: IFN1_L001

tag: cell type

tag: treatment

tag: molecule subtype


title: DKO8B

source_name: Colon cancer cell line DKO8


title: LSCC_65

description:
whole transcriptome sequencing
C65

tag: alcohol consumption

value: No


title: IFN2_L002


title: DKO8


title: NT3_L002

value: mock control


title: RNAseq_Syn_WH7803_LL_LT_J0-5_C1

tag: strain

tag: acclimation condition

value: Low Light

tag: stress condition

value: Low temperature


title: NT3_L001

value: Hepatocytes


title: RNAseq_Syn_WH7803_LL_HT_J3_E1

value: High temperature

tag: timepoint

value: 72 hours


title: LNCaP_24hr_si-A2_replicate-1

description:
LNCaP_2_3_11_siA2
Gene expression at 24h after TAPIR-2 knockdown (replicate 1)

source_name: LNCaP, 24hr, si-A2, replicate 1

value: LNCaP

tag: genotype

value: TAPIR-2 knockdown

tag: time


title: LSCC_64

description:
whole transcriptome sequencing
C64

tag: subject number

tag: tissue

value: LSCC tissue

tag: tumor stage


title: prostate_tissue-H-sf-replicate_RIB0034935

tag: risk group

value: H-sf

tag: gender

value: prostate cancer


title: RNAseq_Syn_WH7803_LL_HT_J3_C1

tag: replicate


title: LSCC_63

description:
whole transcriptome sequencing
C63

tag: tobacco smoking

value: Yes


title: NT2_L001

tag: cell line

tag: cell type

value: Total intracellular RNA


title: HCT116

source_name: Colon cancer cell line HCT116


title: EV

description: EV

tag: expressing

value: empty vector


title: NT2_L002

tag: treatment

tag: molecule subtype


title: RNAseq_Syn_WH7803_LL_HT_J2_E1

tag: strain

tag: acclimation condition

value: 48 hours


title: RNAseq_Syn_WH7803_LL_HT_J3_D1

tag: stress condition

tag: timepoint


title: LSCC_62

description:
whole transcriptome sequencing
C62

tag: alcohol consumption


title: prostate_tissue-C-replicate_RIB0034775

value: C

value: prostate

value: male

tag: gleason score

tag: diagnosis

value: benign prostate hyperplasia


title: NT1_L002

value: mock control


title: NT1_L001

value: Hepatocytes


title: LSCC_61

description:
whole transcriptome sequencing
C61

tag: subject number

tag: tissue

tag: tumor stage

value: No


title: LSCC_59

description:
whole transcriptome sequencing
C59


title: RNAseq_Syn_WH7803_LL_HT_J2_D1

value: Low Light

value: High temperature

tag: replicate


title: HCT116B


title: LSCC_60

description:
whole transcriptome sequencing
C60

tag: tobacco smoking


title: RNAseq_Syn_WH7803_LL_HT_J2_C1


title: RNAseq_Syn_WH7803_LL_HT_J1_E1

value: 24 hours


title: LSCC_58

description:
whole transcriptome sequencing
C58

value: LSCC tissue


title: LSCC_57

description:
whole transcriptome sequencing
C57


title: RNAseq_Syn_WH7803_LL_HT_J1_C1


title: RNAseq_Syn_WH7803_LL_HT_J1_D1


title: LSCC_56

description:
whole transcriptome sequencing
C56


title: ST05-DNMT5

library_source: genomic

data_processing:
Basecalling was performed using Illumina RTA 1.18.54.
Sequenced reads were trimmed for adaptor sequence using Cutadapt version: 1.18, and masked for low-complexity or low-quality sequence, then mapped to the NCP301 sequence using bwa 0.7.17.
For bisulfite sequencing, DNA methylation levels were called using BISulfite-seq CUI Toolkit (https://github.com/zhou-lab/biscuit).
Alignments were generated and visualized using Integrative Genomics Viewer.
DNA methylation level was extracted from VCF files using the betavalue (BT) from each CpG site.
Genome_build: NCP301.fa
Supplementary_files_format_and_content: .vcf files and .bw files

molecule: other

organism: synthetic construct

source_name: synthesized DNA, MNase digestion

extract_protocol:
DNA were extracted using phenol/chloroform after incubation with the complex.
Libraries were prepared by GENEWIZ company according to Illumina's amplicon sequencing instructions.
GENEWIZ Amplicon-EZ

value: MNase digestion

tag: sequence

value: 301 bp synthesized DNA

tag: sample type

value: MNase digested DNA fragment

tag: experimental replicates

value: 301bp-nucleosome and DNMT3A2/3B3 complex digested with MNase


title: ST8_R749K

source_name: synthesized DNA, Bisulfite treatment

tag: treatment

value: Bisulfite treatment

value: PCR product

value: DNA incubated with DNMT3A2/3B3 R749K protein


title: ST7_R749E

value: DNA incubated with DNMT3A2/3B3 K745R protein


title: ST02-NCP5

value: 301bp-nucleosome digested with MNase


title: ST6_K745R

value: DNA incubated with DNMT3A2/3B3 R743K protein


title: LSCC_54

description:
whole transcriptome sequencing
C54

value: Yes


title: LNCaP_24hr_scramble_replicate-1

description:
LNCaP_2_1_9_scr
Gene expression at 24h after scramble siRNA (replicate 1)

source_name: LNCaP, 24hr, scramble, replicate 1

tag: cell line

value: LNCaP

tag: genotype

value: control

tag: time


title: RNAseq_Syn_WH7803_LL_HT_J0-5_D1

tag: strain

tag: acclimation condition

value: Low Light

tag: stress condition

value: 12 hours


title: LSCC_55

description:
whole transcriptome sequencing
C55

tag: alcohol consumption

value: No


title: RNAseq_Syn_WH7803_LL_HT_J0-5_C2

value: High temperature

tag: timepoint


title: prostate_tissue-H-df-replicate_RIB0034903

tag: risk group

value: H-df

value: prostate

tag: gender

value: male

tag: gleason score

tag: diagnosis

value: prostate cancer


title: ST4_R743K

value: Bisulfite treatment

value: 301 bp synthesized DNA

value: DNA incubated with DNMT3A2/3B3 R749E protein


title: prostate_tissue-H-sf-replicate_RIB0034726

value: H-sf

tag: tissue


title: ST5_K745E

tag: sequence

value: PCR product

value: DNA incubated with DNMT3A2/3B3 R740K protein


title: RNAseq_Syn_WH7803_LL_HL_T6_D1

value: High light

value: 6 hours

tag: replicate


title: LSCC_52

description:
whole transcriptome sequencing
C52

tag: subject number

value: LSCC tissue

tag: tumor stage

tag: tobacco smoking

value: Yes


title: ST3_R743E

tag: treatment

tag: sample type

tag: experimental replicates

value: DNA incubated with DNMT3A2/3B3 K745E protein


title: ST2_R740K

value: DNA incubated with DNMT3A2/3B3 R743E protein


title: LSCC_50

description:
whole transcriptome sequencing
C50


title: RNAseq_Syn_WH7803_LL_HT_J0-5_E1

tag: strain

tag: acclimation condition

value: Low Light

value: High temperature

value: 12 hours


title: prostate_tissue-H-sf-replicate_RIB0034237

value: prostate

value: male


title: RNAseq_Syn_WH7803_LL_HL_T6_C1

tag: stress condition


title: ST10_WT

value: Bisulfite treatment

value: DNA incubated with DNMT3A2/3B3 WT protein


title: RNAseq_Syn_WH7803_LL_HL_T3_E1

tag: timepoint

value: 3 hours


title: LSCC_53

description:
whole transcriptome sequencing
C53

tag: alcohol consumption

value: No


title: RNAseq_Syn_WH7803_LL_HL_T3_D1


title: LSCC_37

description:
whole transcriptome sequencing
C37


title: LSCC_46

description:
whole transcriptome sequencing
C46


title: T8_R749K

value: 301 bp synthesized DNA

value: PCR product

value: DNA incubated with DNMT3A2/3B3 R749K protein


title: D3B3B

tag: cell line

tag: expressing


title: LSCC_73

description:
whole transcriptome sequencing
C73


title: RNAseq_Syn_WH7803_LL_HL_T6_E1

value: High light

value: 6 hours


title: LSCC_36

description:
whole transcriptome sequencing
C36

value: LSCC tissue

value: Yes


title: RNAseq_Syn_WH7803_LL_HL_T1_E1

value: 1 hour


title: T7_K745R

value: DNA incubated with DNMT3A2/3B3 K745R protein


title: T6_R743K

value: DNA incubated with DNMT3A2/3B3 R743K protein


title: RNAseq_Syn_WH7803_LL_HL_T1_D1

value: Low Light


title: T5_R740K

value: DNA incubated with DNMT3A2/3B3 R740K protein


title: LSCC_34

description:
whole transcriptome sequencing
C34


title: LSCC_35

description:
whole transcriptome sequencing
C35


title: RNAseq_Syn_WH7803_LL_HL_T1_C1


title: ST1_R740E

value: DNA incubated with DNMT3A2/3B3 R740E protein


title: T4_R749E

value: Bisulfite treatment

value: DNA incubated with DNMT3A2/3B3 R749E protein


title: T3_K745E

value: DNA incubated with DNMT3A2/3B3 K745E protein


title: RNAseq_Syn_WH7803_LL_HL_T0-3_E1

value: 0.3 hours


title: RNAseq_Syn_WH7803_LL_HL_T0-3_D1


title: T2_R743E

value: 301 bp synthesized DNA

value: DNA incubated with DNMT3A2/3B3 R743E protein


title: LSCC_28

description:
whole transcriptome sequencing
C28


title: LSCC_29

description:
whole transcriptome sequencing
C29


title: RNAseq_Syn_WH7803_LL_HL_T3_C1

value: 3 hours


title: T1_R740E

value: PCR product


title: LSCC_27

description:
whole transcriptome sequencing
C27


title: LSCC_31

description:
whole transcriptome sequencing
C31


title: T10_WT

value: DNA incubated with DNMT3A2/3B3 WT protein


title: LSCC_26

description:
whole transcriptome sequencing
C26

value: LSCC tissue


title: RNAseq_Syn_WH7803_LL_Ct_T0_E1

value: Control condition

value: 0 hour


title: LSCC_30

description:
whole transcriptome sequencing
C30

value: Yes


title: LSCC_25

description:
whole transcriptome sequencing
C25

value: No


title: RNAseq_Syn_WH7803_LL_Ct_T0_C1

value: Low Light


title: RNAseq_Syn_WH7803_LL_Ct_T0_D1


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J3-9h_A1

description:
WH7803_LD-Ref6h_norm_counts_FC.tsv
WH7803_LD-Ref21deg_norm_counts_FC.tsv

value: Light/dark cycle 12hours/12hours; 27 C

value: day 3, 9:00 solar time


title: LSCC_23

description:
whole transcriptome sequencing
C23


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J3-6h_A1

value: day 3, 6:00 solar time


title: LSCC_22

description:
whole transcriptome sequencing
C22


title: prostate_tissue-H+df-replicate_RIB0034256

tag: risk group

value: H+df

value: prostate

tag: gender

value: male

tag: gleason score

tag: diagnosis

value: prostate cancer


title: PO_iAs_1

city: Chicago

first: Lishi

last: Xie

state: IL

address: 909S Wolcott CMRB 5120

department: Department of Urology

institute: University of Illinois at Chicago

description:
replicate 1
SAMPLE 10

hyb_protocol: Standard Illumina hybridization protocol to the HumanHT-12 V4 BeadChip array

scan_protocol: Standard scanning protocol using the Bead Array Reader from Illumina

data_processing: The data were normalized using quantile normalization

label: Biotin

label_protocol: RNA was reverse transcripted, labled with biotin and amplified overnight using the Illumina TotalPrep RNA Amplification Kit (Life Technologies)

growth_protocol: Pooled primary human prostate epithelial cells from three disease-free young donors were grew in 3-D matrigel culture to form prostate spheres or organoids.

extract_protocol: RNA was extracted with Direct-zol RNA MiniPrep Kit (Zymo Research,CA, USA)

treatment_protocol: Prostate spheres/organoids were cultured -/+ 1 uM inorganic arsenic (iAs) for 14 days.

tag: culture condition

value: Organoid

tag: agent

value: 1 uM inorganic arsenic (iAs)


title: LSCC_20

description:
whole transcriptome sequencing
C20

tag: subject number

tag: tissue

tag: tumor stage

tag: tobacco smoking


title: RNAseq_Syn_WH7803_LL_HL_T0-3_C1

tag: strain

value: High light

value: 0.3 hours

tag: replicate


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J3-2h_A1

tag: acclimation condition

tag: stress condition

value: day 3, 2:00 solar time


title: PO_iAs_3

description:
replicate 3
SAMPLE 12


title: PO_iAs_2

description:
replicate 2
SAMPLE 11


title: prostate_tissue-H-sf-replicate_RIB0034421

value: H-sf


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J3-22h_A1

tag: timepoint

value: day 3, 22:00 solar time


title: LSCC_19

description:
whole transcriptome sequencing
C19

value: LSCC tissue

value: Yes

tag: alcohol consumption


title: LSCC_24

description:
whole transcriptome sequencing
C24


title: prostate_tissue-C-replicate_RIB0034465

value: C

value: benign prostate hyperplasia


title: PO_Veh-3

description:
replicate 3
SAMPLE 9

value: Vehicle


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J3-18h_A1

value: Light/dark cycle 12hours/12hours; 27 C

value: day 3, 18:00 solar time


title: LSCC_18

description:
whole transcriptome sequencing
C18

value: No


title: LSCC_17

description:
whole transcriptome sequencing
C17


title: PO_Veh-2

description:
replicate 2
SAMPLE 8


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J3-15h_A1

value: day 3, 15:00 solar time


title: PO_Veh-1

description:
replicate 1
SAMPLE 7


title: LSCC_16

description:
whole transcriptome sequencing
C16


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J3-20h_A1

value: day 3, 20:00 solar time


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J3-12h_A1

value: day 3, 12:00 solar time


title: LSCC_15

description:
whole transcriptome sequencing
C15


title: prostate_tissue-H-sf-replicate_RIB0034859

value: prostate

value: male

value: prostate cancer


title: LSCC_14

description:
whole transcriptome sequencing
C14


title: LSCC_13

description:
whole transcriptome sequencing
C13


title: PS_iAs-3

description:
replicate 3
SAMPLE 6

value: Sphere

value: 1 uM inorganic arsenic (iAs)


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J2-2h_C1

value: day 2, 2:00 solar time


title: PS_iAs-1

description:
replicate 1
SAMPLE 4


title: PS_iAs-2

description:
replicate 2
SAMPLE 5


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J2-22h_C1

value: day 2, 22:00 solar time


title: PS_Veh-2

description:
replicate 2
SAMPLE 2


title: LSCC_12

description:
whole transcriptome sequencing
C12

value: LSCC tissue

value: Yes


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J2-20h_C1

value: day 2, 20:00 solar time


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J2-9h_C1

value: day 2, 9:00 solar time


title: LSCC_11

description:
whole transcriptome sequencing
C11


title: prostate_tissue-C-replicate_RIB0035000

value: C

value: benign prostate hyperplasia


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J2-6h_C1

value: Light/dark cycle 12hours/12hours; 27 C

value: day 2, 6:00 solar time


title: LSCC_10

description:
whole transcriptome sequencing
C10


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J2-18h_C1

value: day 2, 18:00 solar time


title: LSCC_9

description:
whole transcriptome sequencing
C_9

value: No


title: PS_Veh-1

description:
replicate 1
SAMPLE 1

value: Vehicle


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J2-15h_C1

value: day 2, 15:00 solar time


title: prostate_tissue-C-replicate_RIB0034975

value: prostate

value: male


title: prostate_tissue-C-replicate_RIB0034862


title: wt_ctrl_570: Cebpa WT untreated Rep 3

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

description: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]  35,557 rows

hyb_protocol: Affymetrix Mouse Gene 1.0 ST Array (Cat No. 901169); Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip® fluidics station 450: protocol FS450_0007 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC 3.1.1)

data_processing: Affymetrix Geneexpression Console v.1.1, Affymetrix (Expression Console  EC1.1.2) using Affymetrix default analysis settings for generation of CEL-files.

organism: Mus musculus

source_name: bone marrow HSPC from WT mice

label_protocol: 1ng total RNA for NuGEN PicoSL_WTA v2 M01226v2 (Cat No. 3312), NuGEN Encore_Biotin M01111v5 (Cat No. 4200)

growth_protocol: We isolated bone marrow cells from the Cebpa WT and KO mice, subjected them to lineage depletion followed by enrichment using FACS double sorting for cKit+ FLT3+ populations. The lin- cKit+ FLT3+ HSPCs were then immediately analysed or set in culture for 4 hours with  FLT3L . The RNA was isolated from these cells and hybridised on  Affymetrix Chips.

extract_protocol: RNeasy Micro Kit inclusive DNase digest (Qiagen; Hilden, Germany; Cat No. 74004)

value: bone marrow hematopoietic stem and progenitor cells

tag: genotype/variation

value: Cebpa F/F


title: wt_ctrl_606: Cebpa WT untreated Rep 4


title: PS_Veh-3

description:
replicate 3
SAMPLE 3

value: Sphere


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J2-12h_C1

value: day 2, 12:00 solar time


title: wt_ctrl_567: Cebpa WT untreated Rep 2


title: LSCC_7

description:
whole transcriptome sequencing
C_7

value: LSCC tissue

value: Yes


title: LSCC_51

description:
whole transcriptome sequencing
C51


title: LSCC_8

description:
whole transcriptome sequencing
C_8


title: LSCC_6

description:
whole transcriptome sequencing
C_6


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J1-9h_C1

value: day 1, 9:00 solar time


title: LSCC_4

description:
whole transcriptome sequencing
C_4


title: LSCC_5

description:
whole transcriptome sequencing
C_5


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J1-6h_C1

value: day 1, 6:00 solar time


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J1-6h_A2


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J1-9h_A1


title: LSCC_3

description:
whole transcriptome sequencing
C_3


title: wt_ctrl_536: Cebpa WT untreated Rep 1


title: wt_4h treated_570_2: Cebpa WT 4h FLT3L treated Rep 3


title: LSCC_2

description:
whole transcriptome sequencing
C_2


title: LSCC_1

description:
whole transcriptome sequencing
C_1


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J1-2h_C1

value: day 1, 2:00 solar time


title: 100 ug/mL H2A (Replicate 3)

city: Irvine

first: Albert

last: Siryaporn

state: CA

address: 4129 Reines Hall

institute: University of California Irvine

description:
mRNA
exp24
processed data file: hist3-counted.xlsx

data_processing:
Custom script - barcode identification.
Custom script - remove primer adapters.
Bowtie2 alignment using MG1655 genome U00096.3.
Custom script - count reads.
Custom script - normalizing and averaging.
Genome_build: MG1655 genome U00096.3
Supplementary_files_format_and_content: hist3-counted.xlsx: RAW counts for each experiment, averaged counts from triplicate experiments.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Bacterial culture

growth_protocol: MG1655 cultured to mid-exponential phase in minimal medium A at 37 degrees C in shaker at 225 rpm.

extract_protocol:
Hot phenol
DNase, Illumina RiboZero, NEBNext Ultra Directional Library kit.

treatment_protocol: Samples were untreated or treated with H2A, and harvested after 30 minutes. Experiments performed in biological triplicate.

tag: growth phase

value: Mid-exponential culture

tag: treatment

value: H2A, 100 ug/mL


title: wt_4h treated_606: Cebpa WT 4h FLT3L treated Rep 4


title: ko_ctrl_584: Cebpa KO untreated rep 3

source_name: bone marrow HSPC from KO mice

value: Cebpa F/F Mx1-Cre


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J1-22h_C1

value: Light/dark cycle 12hours/12hours; 27 C

value: day 1, 22:00 solar time


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J1-2h_A1


title: ko_ctrl_581: Cebpa KO untreated rep 2


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J1-22h_A1


title: ko_ctrl_515: Cebpa KO untreated rep 1


title: 100 ug/mL H2A (Replicate 2)

description:
mRNA
exp23
processed data file: hist3-counted.xlsx


title: prostate_tissue-H-sf-replicate_RIB0034437

description: Gene expression of prostate RP tissue specimen (prostate cancer)

tag: risk group

value: H-sf

tag: gender

tag: gleason score

value: prostate cancer


title: wt_4h treated_567: Cebpa WT 4h FLT3L treated Rep 2


title: ko_ctrl_608: Cebpa KO untreated rep 4


title: wt_4h treated_536: Cebpa WT 4h FLT3L treated Rep 1


title: ko_4h treated_608_2: Cebpa KO 4h FLT3L treated Rep 4


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J1-20h_C1

value: day 1, 20:00 solar time


title: 100 ug/mL H2A (Replicate 1)

description:
mRNA
exp22
processed data file: hist3-counted.xlsx


title: prostate_tissue-C-replicate_RIB0034487

description: Gene expression of prostate RP tissue specimen (benign prostate hyperplasia)

value: C

value: prostate

value: male

tag: diagnosis

value: benign prostate hyperplasia


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J1-20h_A1


title: 50 ug/mL H2A (Replicate 3)

description:
mRNA
exp21
processed data file: hist3-counted.xlsx

value: H2A, 50 ug/mL


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J1-18h_C1

value: day 1, 18:00 solar time


title: 50 ug/mL H2A (Replicate 2)

description:
mRNA
exp20
processed data file: hist3-counted.xlsx


title: ko_4h treated_581: Cebpa KO 4h FLT3L treated Rep 2

value: bone marrow hematopoietic stem and progenitor cells


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J1-18h_A1


title: D32 MAT VCM

city: Toronto

first: Gordon

last: Keller

state: Ontario

address: 101 College St

department: Medicine

country: Canada

institute: McEwen Stem Cell Institute

description: D32 MAT VCM

data_processing:
Raw data consisted of CellRanger-processed, filtered feature matrices
Datasets were read in and concatenated using scanpy.read_10x_mtx
Genome_build: hg38
Supplementary_files_format_and_content: .mtx, .txt (x2). Standard for 10x Prepreprocessing pipeline (Cell Ranger 3.0)

source_name: Day 32 PPDT Treatment

growth_protocol: For ventricular differentiation, we used a modified version of our embryoid body (EB)-based protocol

extract_protocol:
10x Genomics Microfluidic Platform
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Three groups; Day 20 No treatment, Day 32 No treatment, Day 32 PPDT Treatment

tag: cell type

value: ES-derived ventricular cardiomyocytes

tag: condition

value: Treated with PPDT/PAL

tag: day


title: prostate_tissue-C-replicate_RIB0034420

tag: tissue


title: D32 IM VCM

description: D32 IM VCM

source_name: Day 32 No treatment

value: HG Time matched control


title: 50 ug/mL H2A (Replicate 1)

description:
mRNA
exp19
processed data file: hist3-counted.xlsx

value: Mid-exponential culture


title: prostate_tissue-H-df-replicate_RIB0034427

value: H-df


title: ko_4h treated_515: Cebpa KO 4h FLT3L treated Rep 1

value: Cebpa F/F Mx1-Cre


title: 10 ug/mL H2A (Replicate 2)

description:
mRNA
exp17
processed data file: hist3-counted.xlsx

value: H2A, 10 ug/mL


title: 10 ug/mL H2A (Replicate 3)

description:
mRNA
exp18
processed data file: hist3-counted.xlsx


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J1-15h_C1

source_name: culture of Synechococcus sp. WH7803 cells

tag: strain

value: Light/dark cycle 12hours/12hours; 27 C

value: day 1, 15:00 solar time


title: GC3b_Ab

city: New York

first: Riccardo

last: Dalla-Favera

state: NY

address: 1130 St Nicholas Avenue

institute: Columbia University

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8. The _i.fastq.gz files contain sample barcodes, the _1.fastq.gz files contain feature barcodes and the _2.fastq.gz files contain reads. The data can be de-multiplexed using 10X Genomics CellRanger software.
RNA reads were mapped to the human genome (GRCh38) using 10x Genomics Cell Ranger v2.1
Antibody tags and cell barcodes were extracted using the feature barcoding function of 10x Genomics Cell Ranger v3.0. The feature references for mapping feature barcodes to antibody names are provided in the processed data files.
Genome_build: grch38
Supplementary_files_format_and_content: Tab delimited text files with cell barcodes, transcript counts and antibody tag counts. Antibody feature references are provided as CSV files for compatability with CellRanger.

source_name: Germinal Center B cells

growth_protocol: Surgically removed tonsil tissue was immediately processed to isolate mononuclear cells by Ficoll.

extract_protocol:
Single cells were captured and analyzed in the Chromium Controller using the Chromium Single Cell 3' kit v3 (10X Genomics) according to the manufacturer's instructions.
Antibody-Derived Tags (ADT) libraries were prepared as detailed in the TotalSeq-A Antibodies Hashing with 10x Single Cell 3' Reagent kit v3 protocol (BioLegend).

treatment_protocol: Tonsillar germinal center B cells were sorted based on established surface markers: CD3-; IgD-; CD38+. After sorting cells were incubated with TotalSeq-A Antibody cocktail (BioLegend) including the following: CXCR4 (clone 12G5, BioLegend), CD83 (clone HB15e, BioLegend), CD9 (clone HI9a, BioLegend), CCR6 (clone G034E3, BioLegend), CD69 (clone FN50, BioLegend), CD44 (clone IM7, BioLegend).

value: Tonsil

value: Germinal Center B cells


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J1-12h_C1

value: day 1, 12:00 solar time

tag: replicate


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J1-15h_A1

tag: acclimation condition


title: RNAseq_Syn_WH7803_LD-27deg_LD-27deg_J1-12h_A1

tag: stress condition


title: ko_4h treated_584: Cebpa KO 4h FLT3L treated Rep 3


title: 10 ug/mL H2A (Replicate 1)

description:
mRNA
exp16
processed data file: hist3-counted.xlsx


title: Untreated (Replicate 3)

description:
mRNA
exp15
processed data file: hist3-counted.xlsx

value: Untreated


title: GC3b

extract_protocol:
Single cells were captured and analyzed in the Chromium Controller using the Chromium Single Cell 3' kit v3 (10X Genomics) according to the manufacturer's instructions.
Libraries were prepared using the Chromium Single Cell 3' Library and Gel Bead Kit v3 (10X Genomics).

treatment_protocol: Tonsillar germinal center B cells were sorted based on established surface markers: CD3-; IgD-; CD38+


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J5-9h_A1

value: Light/dark cycle 12hours/12hours; 21 C

tag: timepoint

value: day 5, 9:00 solar time


title: GC3a


title: prostate_tissue-H+df-replicate_RIB0034296

value: H+df

value: prostate

value: male

value: prostate cancer


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J5-6h_A1

value: day 5, 6:00 solar time


title: D20 VCM

description: D20 VCM

source_name: Day 20 No treatment

value: ES-derived ventricular cardiomyocytes

value: D20 VCM standard Keller Protocol


title: LZ2

source_name: Light zone germinal center B cells

extract_protocol:
Single cells were captured and analyzed in the Chromium Controller using the Chromium Single Cell 3' kit v2 (10X Genomics) according to the manufacturer's instructions.
Libraries were prepared using the Chromium Single Cell 3' Library and Gel Bead Kit v2 (10X Genomics).

treatment_protocol: Tonsillar dark zone (CD3-; IgD-; CD38+; CXCR4high; CD83low), light zone (CD3-; IgD-; CD38+; CXCR4low; CD83high) and total (CD3-; IgD-; CD38+) germinal center B cells were isolated by cytofluorimetric cell sorting.


title: Untreated (Replicate 1)

description:
mRNA
exp13
processed data file: hist3-counted.xlsx

value: Mid-exponential culture


title: GC3a_Ab


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J5-2h_A1

value: day 5, 2:00 solar time


title: DZ2

source_name: Dark zone germinal center B cells


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J5-22h_A1

value: day 5, 22:00 solar time


title: GC2


title: S3-wo

city: London

first: Enrique

last: Martinez-Perez

address: L Block - Level 2, Du Cane Road

country: United Kingdom

institute: MRC London Institute of Medical Sciences (LMS)

data_processing:
Paired end 100bp libraries were sequenced on Illumina Hiseq 2500 and Raw basecall files were converted to fastq files using Illumina’s bcl2fastq (version 2.1.7).
Reads were aligned to the Caenorhabditis elegans genome (ce10) using Tophat2 version 2.0.11 (Kim et al., 2013) with default parameters.
Mapped reads that fell on genes were counted using featureCounts from Rsubread package (Liao et al., 2019).
Generated count data were then used to identify differentially expressed genes using DESeq2 (Love et al., 2014).
Genes with very low read counts were excluded.
Genome_build: ce10
Supplementary_files_format_and_content: bigwig, xls

organism: Caenorhabditis elegans

source_name: Whole worm RNA

growth_protocol: All C. elegans strains were grown on E. coli (OP50) seeded NG agar plates at 20 °C

extract_protocol: Adult worms were collected into 400 µl of M9 salt buffer in RNase-free tubes. After the worms settled to the bottom, the majority of the M9 was removed. 1 ml of Trizol and 100 µl of 0.5 mm of glass beads were added to each tube and immediately frozen at -80 C. Samples were thawed in ice and bead-beaten with a FastPrep-24 5G instrument  with the following settings: speed 4 m/s, 3 cycles, and run time of 20 seconds. After the beads settled at the bottom of the tube, the solution was transferred to a new RNase-free tube. 200 µl of chloroform was added and tubes were vigorously mixed by hand for 15 sec. Samples were then centrifuged at 12000 g for 15 minutes at 4 C and the resulting clear upper-phase was transferred to a new tube, where 500 µl of isopropanol and 1 µl of glycogen were added prior to storing the sample overnight at -20 C. Next, samples were spun at 12000 g for 10 minutes at 4 C, the supernatant was discarded and the pellet washed with 1 ml of fresh 75% ethanol. After 5 minutes centrifugation at 7500 g and 4 C, ethanol was discarded, pellet briefly air-dried and resuspended with 15 µl of RNase-free water.

treatment_protocol: Auxin treatment was performed by placing young adult worms (18-24 hours post L4)  in NG agar plates seeded with OP50 E. coli and containing 4 mM auxin for 4 hours.

value: control


title: S2-wo


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J5-20h_A1

value: day 5, 20:00 solar time


title: S4-wo


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J5-18h_A1

value: day 5, 18:00 solar time


title: HS683-O-3

type: protein

city: Santa Monica

first: Dave

last: Hoon

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

data_processing: Raw data was obtained by CCSG-supported RPPA Core Facility at the University of Texas MD Anderson Cancer Center. RPPA data was processed in order to obtain differentially expressed genes when comparing control-empty vector and KPC1-overexpression LN18 and HS683 cells, respectively. Only genes commonly deregulated in both cell lines were considered.

molecule: protein

source_name: Glioblastoma

growth_protocol: Glioblastoma cell lines were cultured in DMEM supplemented with 10mM HEPES, 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin-streptomycin. Cells were dettached using non-enzimatic solution and cell pellet were frozen at -80ºC until protein extraction.

extract_protocol: Protein extraction was performed as recommended by CCSG-supported RPPA Core Facility at the University of Texas MD Anderson Cancer Center.

treatment_protocol: Each glioblastoma cell line was transiently transfected with control empty vector or KPC1-vector. Cell lines were selected and positive clones for KPC1-overexpression were confirmed by WB and RT-qPCR.

value: Glioblastoma

tag: cell line


title: S1-wo

tag: genotype/variation


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J5-15h_A1

value: day 5, 15:00 solar time


title: HS683-O-2


title: Untreated (Replicate 2)

description:
mRNA
exp14
processed data file: hist3-counted.xlsx

tag: growth phase

value: Untreated


title: prostate_tissue-H+sf-replicate_RIB0034394

source_name: prostate

value: H+sf


title: HS683-O-1


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J5-12h_A1

value: Light/dark cycle 12hours/12hours; 21 C

value: day 5, 12:00 solar time


title: prostate_tissue-H+sf-replicate_RIB0034280

value: prostate

value: male


title: HS683-3

value: control vector


title: prostate_tissue-H+sf-replicate_RIB0034792

value: prostate cancer


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J4-9h_A1

value: day 4, 9:00 solar time


title: S2-IAA

tag: treatment

value: IAA


title: S1-IAA


title: S3-IAA


title: HS683-2


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J4-6h_A1

value: day 4, 6:00 solar time


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J4-2h_A1

value: day 4, 2:00 solar time


title: N2-4-wo

value: N2 wild type

value: control


title: S4-IAA


title: N2-3-wo


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J4-22h_A1

value: day 4, 22:00 solar time


title: LN18-O-3

value: Glioblastoma


title: N2-2-wo


title: prostate_tissue-H+sf-replicate_RIB0034721

tag: risk group


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J4-18h_A1

value: day 4, 18:00 solar time


title: HS683-1


title: LN18-O-2


title: LN18-O-1


title: N2-1-wo


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J4-20h_A1

value: day 4, 20:00 solar time


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J4-15h_A1

value: day 4, 15:00 solar time


title: LN18-3


title: LN18-2


title: N2-4-IAA


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J4-12h_A1

value: Light/dark cycle 12hours/12hours; 21 C

value: day 4, 12:00 solar time


title: N2-3-IAA


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J3-9h_C1

value: day 3, 9:00 solar time


title: LN18-1


title: N2-2-IAA


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J3-6h_C2

value: day 3, 6:00 solar time


title: Triple Mutant RNAseq

city: Omaha

first: Adam

middle: R.

last: Karpf

state: Nebraska

address: 985950 Nebraska Medical Center

department: Eppley Institute for Research in Cancer

institute: University of Nebraska Medical Center

data_processing:
10X Genomics R2 read fastq files were analyzed as single end bulk RNA-seq analysis based on the following steps.
Adaptor sequences and low quality (Phred score: 20) ends were trimmed from sequences using the Trim Galore software package (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Resulting fastq files were aligned to the mouse genome (GRCm38/mm10) using the software TopHat (v2.0.8) (http://ccb.jhu.edu/software/tophat/index/shtml/).
The software Cufflinks (v2.1.1) (http://cole-trapnell-lab.github.io/cufflinks/) was used to estimate the expression values and Cuffdiff (V2.1.1) was used to determine differential expression.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each sample plus gene, log2 fold change, pvalue and qvalue

source_name: S. aureus infected orthopedic implant-associated tissue

extract_protocol: For scRNA-seq, Live, CD45+ leukocytes were isolated from implant-associated tissues at day 14 post-infection and libraries were created using standard 10X Genomics protocols.

value: CD45+ leukocytes

tag: age

value: 10-12 weeks

tag: infected with

value: Triple mutant S. aureus

tag: s. aureus background strain and genotype

value: USA300 LAC13c


title: 202242410170_R06C01

city: San Francisco

first: Harish

last: Vasudevan

address: 555 Mission Bay Blvd South, Room 452H

department: Radiation Oncology

institute: University of California San Francisco

description:
Primary human meningioma methylation profile
M13-3
Run2

hyb_protocol: Methylation analysis was performed according to the manufacturer’s instructions on the Illumina Methylation EPIC Beadchip

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

data_processing:
BeadStudio software v3.2, raw data uploaded as IDAT; processed beta values obtained using the 'preprocessFunnorm()' function as part of the Minfi bioconductor package
Beta Values obtained using minfi package function "getBeta" from normalized data as noted above
BetaValues_MeningiomaMethylation_Run*.txt files represent raw beta values.

label: Cy5 and Cy3

source_name: Meningioma

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from primary tumor samples using Qiagen AllPrep Kit according to standard instructions

tag: individual

tag: disease state

value: Meningioma

tag: gender

value: M

tag: site

value: Intracranial


title: 202242410170_R05C01

description:
Primary human meningioma methylation profile
M13-2
Run2


title: 202242410170_R08C01

description:
Primary human meningioma methylation profile
M13-5
Run2


title: 202242410201_R01C01

description:
Primary human meningioma methylation profile
M13-6
Run2


title: 202242410201_R02C01

description:
Primary human meningioma methylation profile
M13-7
Run2


title: 202242410170_R07C01

description:
Primary human meningioma methylation profile
M13-4
Run2


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J3-20h_C1

description:
WH7803_LD-Ref6h_norm_counts_FC.tsv
WH7803_LD-Ref21deg_norm_counts_FC.tsv

extract_protocol:
RNA extractions were performed from 150 mL of culture harvested by centrifugation for 7 min at 10,414 × g and 4°C in an Eppendorf 5804R, followed by 2 min centrifugation at 20,817 × g in Eppendorf tubes and 4°C in an Eppendorff 5417R centrifuge. Cell pellet was then resuspended in 1 mL Qiazol (Qiagen, Valencia, CA, USA) and quickly frozen in liquid nitrogen. After thawing the tubes at 65 °C, followed by and additional incubation of 5 min at this temperature, RNA was extracted using the Direct-Zol kit (Zymo Research Corp, Proteigene) as recommended by the manufacturer. Three successive DNase treatments were performed on the Zymo-Spin™-IIC Column using the Qiagen RNase-free DNase Set (Qiagen), followed by elution from the column in 30 L DEPC-treated water. RNA quantification and quality check were performed using a Qubit (Invitrogen) and a BioAnalyzer 2100 with the RNA 6000 Nano Kit (Agilent, Santa Clara, CA, USA), respectively. RNA samples were then frozen in liquid nitrogen and stored at -80°C.
Ribodepletion was performed at the Genotoul platform (Toulouse, France) from 5 µg of RNA using the Ribo-Zero Bacteria Magnetic Kits (Illumina) in presence of RiboGuard RNase Inhibitor (Epicentre) and treated RNA samples were purified and concentrated using RNA Clean & Concentrator™-5 columns (Zymo research). 0.5 µL of ribo-depleted RNA was then used for quantification (Qubit RNA HS Assay Kit) and quality check (Bioanalyzer RNA Pico kit or Labchip GX). Libraries were then prepared using 100 to 400 ng of RNA with the Illumina TruSeq Stranded mRNA kit and sequenced as 150 bp paired-end reads on Illumina HiSeq 3000 System (Illumina, San Diego, CA, USA) at Genotoul (Toulouse, France). 18.5 +/- 4.7·10^6 paired-end reads were generated per sample.

tag: strain

value: day 3, 20:00 solar time


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J3-22h_C2

value: day 3, 22:00 solar time

tag: replicate


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J3-18h_C1

tag: acclimation condition

value: day 3, 18:00 solar time


title: 202242410170_R04C01

description:
Primary human meningioma methylation profile
M13-1
Run2


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J3-15h_C1

tag: stress condition

value: day 3, 15:00 solar time


title: prostate_tissue-C-replicate_RIB0034970

description: Gene expression of prostate RP tissue specimen (benign prostate hyperplasia)

extract_protocol: Stacks of consecutive cryosections were generated from frozen RP tissue samples and immediately transferred to 1ml Qiazol (Qiagen, Hilden, Germany). A pathologist evaluated HE-stained cryosections flanking the stacks concerning tumor and stroma cell content (Supplementary Figure S1). Only PCa tissue stacks, which were flanked on either side by sections containing at least 50% tumor cells underwent RNA isolation. In case of insufficient RNA quantity, we combined multiple tissue stacks with suitable tumor cell content. We isolated total RNA using the miRNeasy Mini Kit on the QIAcube (Qiagen) followed by manual DNase I digestion. After determining the RNA concentration with a NanoDrop 1000 (Peqlab, Erlangen, Germany), we verified the RNA integrity on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). RNA samples with an RNA-Integrity-Number (RIN) of at least six passed for further processing.

value: C

tag: tissue

value: prostate

value: male

tag: gleason score

tag: diagnosis

value: benign prostate hyperplasia


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J3-2h_C2

value: Light/dark cycle 12hours/12hours; 21 C

tag: timepoint

value: day 3, 2:00 solar time


title: N2-1-IAA

tag: genotype/variation

value: N2 wild type

tag: treatment

value: IAA


title: 202242410170_R03C01

description:
Primary human meningioma methylation profile
M12-LivMet
Run3

tag: age

value: F

value: Liver


title: prostate_tissue-C-replicate_RIB0034281

tag: risk group


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J2-9h_C1

value: day 2, 9:00 solar time


title: WT RNAseq

tag: cell type

value: CD45+ leukocytes

value: 10-12 weeks

tag: infected with

value: WT S. aureus

tag: s. aureus background strain and genotype

value: USA300 LAC13c


title: LNCaP_48hr_scramble_replicate-4

description:
LNCaP_2_5_13_scr
Gene expression at 48h after scramble siRNA (replicate 4)

data_processing: Differentially expressed probes were identified by using R v3.4.3 and the Bioconductor package limma v3.34.8. Quality control of arrays were performed by checking distribution of ``bright corner'', ``dark corner'' probes, and unsupervised clustering of raw intensities. One replicate of si-A2 at 48h had to be removed from downstream analyses due to too low foreground intensities. To retrieve a set of probes mapping to unique genomic positions in hg38 we used BLAT v35 with the parameter -minIdentity=95 allowing to detect probes spanning splice sites for all arrays. All probes mapping to more than one distinct genomic region were discarded. Remaining probes were annotated by known genes using Gencode v27. Normalization between arrays was done by using quantile normalization, and batch effects considered as additive covariates in the linear model. In order to reduce the number of univariate t-tests nonspecific filtering was applied as follows: The expression of a probe must be larger than background expression in at least three arrays. Background expression was defined by the mean intensity plus three times the standard deviation of negative control spots (Agilent's 3xSLv spots). In addition, a probe must exhibit a nonspecific change of expression, which was assessed by an interquartile range of at least 0.5. Finally, a linear model was fitted using limma to assess significant expression changes for the contrasts si-A1 (siRNA against TAPIR-1) versus si-SCRL (scramble siRNA) and si-A2 (siRNA against TAPIR-2) versus si-SCRL (scramble siRNA), respectively. Reliable variance estimates were obtained by Empirical Bayes moderated t-statistics. False discovery rate (FDR) was controlled by Benjamini-Hochberg adjustment. All genes with log2 fold change ≥ 0.5 and FDR < 0.01 were classified to be significantly regulated upon TAPIR-1 or TAPIR-2 knock-down.

source_name: LNCaP, 48hr, scramble, replicate 4

extract_protocol: Total RNA was isolated from LNCaP cells with TRIzol (ambion), following the manufacturers protocol.

tag: cell line

value: LNCaP

tag: genotype

value: control

tag: time


title: LNCaP_48hr_si-A1_replicate-4

description:
LNCaP_2_6_14_siA1
Gene expression at 48h after TAPIR-1 knockdown (replicate 4)

source_name: LNCaP, 48hr, si-A1, replicate 4

value: TAPIR-1 knockdown


title: LNCaP_48hr_si-A2_replicate-4

description:
LNCaP_2_7_15_siA2
Gene expression at 48h after TAPIR-2 knockdown (replicate 4)

source_name: LNCaP, 48hr, si-A2, replicate 4

value: TAPIR-2 knockdown


title: 202242410170_R02C01

description:
Primary human meningioma methylation profile
M12-7
Run2

tag: individual

tag: disease state

value: Meningioma

tag: gender

tag: site

value: Intracranial


title: prostate_tissue-C-replicate_RIB0034294

value: C

tag: tissue

value: prostate

value: male

tag: gleason score

value: benign prostate hyperplasia


title: prostate_tissue-H-sf-replicate_RIB0034332

description: Gene expression of prostate RP tissue specimen (prostate cancer)

value: H-sf

tag: diagnosis

value: prostate cancer


title: 202242410103_R08C01

description:
Primary human meningioma methylation profile
M12-5
Run2

value: F


title: 202242410170_R01C01

description:
Primary human meningioma methylation profile
M12-6
Run2


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J2-6h_C1

data_processing:
Reads quality checks were performed with the FastQC tool.
Illumina adapters, found in 23.5 +/- 4.5 % of all reads, were removed using Cutadapt v1.8.3.
rRNA, constituting 5.0 +/- 5.9 % of all reads, were removed with Sortmerna v2.1.
Reads under 50 bp size and with a mean quality score lower than 25 were filtered out using Prinseq v0.20.4.
Remaining reads were then aligned on the reference genome of Synechococcus sp. WH7803 using Bowtie2 v2.2.9 software with ‘--non-deterministic --end-to-end –sensitive’ parameters and by selecting only the properly paired reads (i.e. SAM flagged as 99, 147, 163 or 83)
Read counts table were obtained using HTSeq Count v0.6.0 with following parameters: ‘--stranded=reverse -a 10 -m intersection-nonempty’.
Genes expression level between stress and control conditions as well as adjusted p-value based on the Benjamini-Hochberg procedure were determined using SARTools v1.4.0 with embedded DESeq2 v1.14.1.
Genome_build: NC_009481.1
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each sample, log2FC and  their associated pvalues and adjusted pvalues

tag: strain

tag: acclimation condition

value: Light/dark cycle 12hours/12hours; 21 C

tag: stress condition

tag: timepoint

value: day 2, 6:00 solar time

tag: replicate


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J2-2h_C1

value: day 2, 2:00 solar time


title: 202242410103_R07C01

description:
Primary human meningioma methylation profile
M12-4
Run2

tag: age


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J2-22h_C1

value: day 2, 22:00 solar time


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J3-12h_C1

value: day 3, 12:00 solar time


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J2-20h_C1

value: day 2, 20:00 solar time


title: 202242410103_R06C01

description:
Primary human meningioma methylation profile
M12-3
Run2


title: LNCaP_48hr_si-A2_replicate-3

description:
LNCaP_2_3_11_siA2
Gene expression at 48h after TAPIR-2 knockdown (replicate 3)

source_name: LNCaP, 48hr, si-A2, replicate 3

value: LNCaP


title: 202242410103_R05C01

description:
Primary human meningioma methylation profile
M12-2
Run2


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J2-18h_C1

value: day 2, 18:00 solar time


title: LNCaP_48hr_si-A1_replicate-3

description:
LNCaP_2_2_10_siA1
Gene expression at 48h after TAPIR-1 knockdown (replicate 3)

source_name: LNCaP, 48hr, si-A1, replicate 3

value: TAPIR-1 knockdown


title: LNCaP_48hr_si-A2_replicate-2

description:
LNCaP_1_7_7_siA2
Gene expression at 48h after TAPIR-2 knockdown (replicate 2)

source_name: LNCaP, 48hr, si-A2, replicate 2

value: TAPIR-2 knockdown


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J2-15h_C1

description:
WH7803_LD-Ref6h_norm_counts_FC.tsv
WH7803_LD-Ref21deg_norm_counts_FC.tsv

value: day 2, 15:00 solar time


title: LNCaP_48hr_scramble_replicate-2

description:
LNCaP_1_5_5_scr
Gene expression at 48h after scramble siRNA (replicate 2)

source_name: LNCaP, 48hr, scramble, replicate 2

value: control


title: 202242410103_R04C01

description:
Primary human meningioma methylation profile
M11-10
Run2

value: Meningioma

value: Intracranial


title: prostate_tissue-H-sf-replicate_RIB0034212

data_processing: Three microarray were excluded from further processing due to scratches on array slides (data not included in GEO series). Quality control of remaining arrays (N=255) was performed by checking distribution of ``bright corner'', ``dark corner'' probes, and relative spike-in concentration versus normalized signal. Quality control confirmed high quality of the results and consequently all remaining microarray data were included in the downstream analysis. To retrieve a set of probes mapping to unique genomic positions in hg19 we used BLAT v35 with the parameter -minIdentity=95 allowing to detect probes spanning splice sites. All probes mapping to more than one distinct genomic region were discarded. Normalization between arrays was done by using quantile normalization. In order to reduce the number of univariate t-tests nonspecific filtering was applied as follows: The expression of a probe must be larger than background expression in at least 20 arrays. Background expression was defined by the mean intensity plus three times the standard deviation of negative control spots (Agilent's 3xSLv spots). In addition, a probe must exhibit a nonspecific change of expression, which was assessed by an interquartile range of at least 0.5. Finally, a linear model to detect expression variation between BPH and tumor specimens adjusted for array processing batches was fitted using limma v3.24.15 and reliable variance estimates were obtained by Empirical Bayes moderated t-statistics. False discovery rate (FDR) was controlled by Benjamini-Hochberg adjustment.

tag: risk group

value: H-sf

value: prostate

value: male


title: 202242410103_R03C01

description:
Primary human meningioma methylation profile
M11-9
Run2

value: F


title: RNAseq_Syn_WH7803_LD-21deg_LD-21deg_J2-12h_C1

source_name: culture of Synechococcus sp. WH7803 cells

value: Light/dark cycle 12hours/12hours; 21 C

value: day 2, 12:00 solar time


title: 202242410103_R02C01

description:
Primary human meningioma methylation profile
M11-8
Run2


title: prostate_tissue-C-replicate_RIB0034887

description: Gene expression of prostate RP tissue specimen (benign prostate hyperplasia)

value: C

value: benign prostate hyperplasia


title: LNCaP_48hr_scramble_replicate-3

description:
LNCaP_2_1_9_scr
Gene expression at 48h after scramble siRNA (replicate 3)

source_name: LNCaP, 48hr, scramble, replicate 3

tag: cell line


title: RNAseq_Syn_WH7803_HL_UV_T6_F1

value: High light

value: UV exposition

value: 6 hours


title: 202242410103_R01C01

description:
Primary human meningioma methylation profile
M11-7
Run2


title: RNAseq_Syn_WH7803_HL_UV_T6_D1


title: RNAseq_Syn_WH7803_HL_UV_T6_C1


title: LNCaP_48hr_si-A2_replicate-1

description:
LNCaP_1_3_3_siA2
Gene expression at 48h after TAPIR-2 knockdown (replicate 1)

source_name: LNCaP, 48hr, si-A2, replicate 1

value: LNCaP

tag: genotype


title: 202242410022_R08C01

description:
Primary human meningioma methylation profile
M11-6
Run2


title: RNAseq_Syn_WH7803_HL_UV_T3_F1

value: 3 hours


title: E16_RNAseq_Tex15KO_1

city: Edinburgh

first: Yuka

last: Kabayama

address: 5 Little France Drive

institute: University of Edinburgh

description: rRNA depleted total RNA

data_processing:
For analysis of differentially expressed genes, paired-end reads were mapped to GRCm38 genome_tran (release 84) using HISAT2 '--no-mixed --no-discordant --qc-filter --trim5 3'.
Mapped reads per gene were counted with htseq-count (HTSeq 0.11.1) providing GTF file.
Differentially expressed genes were analysed using DESeq2 (1.26.0).
Genome_build: UCSC mm10, GRCm38
Supplementary_files_format_and_content: The processed RNA-seq data are raw read count from htseq-count and raw read count mapped to transposable elements (rodrep_hit).

source_name: E16.5 gonocytes

extract_protocol:
Total RNA was extracted from sorted spermatogonia from E16.5 testis using QIAzol reagent following the manufacturer’s instructions.
RiboGone and the SMARTer Stranded RNA-seq kit from Clontech

value: mixed B6CBAF1/Crl; C57BL/6N

tag: developmental stage

value: gonocytes


title: E16_RNAseq_Tex15KO_3

description: rRNA depleted total RNA


title: E16_RNAseq_Tex15KO_2

description: rRNA depleted total RNA


title: LNCaP_48hr_si-A1_replicate-1

description:
LNCaP_1_2_2_siA1
Gene expression at 48h after TAPIR-1 knockdown (replicate 1)

source_name: LNCaP, 48hr, si-A1, replicate 1

value: TAPIR-1 knockdown

tag: time


title: LNCaP_48hr_si-A1_replicate-2

description:
LNCaP_1_6_6_siA1
Gene expression at 48h after TAPIR-1 knockdown (replicate 2)

source_name: LNCaP, 48hr, si-A1, replicate 2


title: E16_RNAseq_control_3

description: rRNA depleted total RNA


title: prostate_tissue-C-replicate_RIB0034267


title: prostate_tissue-H+df-replicate_RIB0034831

description: Gene expression of prostate RP tissue specimen (prostate cancer)

value: H+df

value: prostate cancer


title: 202242410022_R07C01

description:
Primary human meningioma methylation profile
M11-5
Run2

tag: individual

tag: disease state

value: Meningioma

value: Intracranial


title: 202242410022_R06C01

description:
Primary human meningioma methylation profile
M11-4
Run2

tag: gender

value: F

tag: site


title: E16_RNAseq_control_2

description: rRNA depleted total RNA

tag: tissue


title: 202242410022_R05C01

description:
Primary human meningioma methylation profile
M11-2
Run2


title: RNAseq_Syn_WH7803_HL_UV_T3_C1


title: RNAseq_Syn_WH7803_HL_UV_T3_D1


title: E16_RNAseq_control_1

description: rRNA depleted total RNA


title: RNAseq_Syn_WH7803_HL_UV_T1_F1

value: 1 hour


title: 202242410022_R04C01

description:
Primary human meningioma methylation profile
M10-7
Run2


title: 202242410022_R03C01

description:
Primary human meningioma methylation profile
M10-6
Run2


title: RNAseq_Syn_WH7803_HL_UV_T1_D1


title: LNCaP_48hr_scramble_replicate-1

description:
LNCaP_1_1_1_scr
Gene expression at 48h after scramble siRNA (replicate 1)

source_name: LNCaP, 48hr, scramble, replicate 1

value: control


title: sod rac astros 3

city: Stanford

first: Julien

last: Couthouis

address: 279 Campus Dr

department: Genetics

institute: Stanford University

description:
processed data file:
wt_rac_astro_vs_sod_rac_astro-ExpDiff.csv

data_processing:
RNAseq analysis
illumina basecalling
STAR alignment
RSEM counts
DESeq2 normalization and analyzis
Full pipeline with settings used available on https://github.com/emc2cube/Bioinformatics/blob/master/sh_RNAseq.sh
Genome_build: mm10
Supplementary_files_format_and_content: comma separated value text files with normalized abundance measurements (output from DESeq2)

source_name: Acrtivated Sod1 Astrocytes

growth_protocol: Astrocytes were cultured in defined, serum-free medium containing 50% neurobasal, 50% DMEM, 100 U/mL penicillin, 100 μg/mL streptomycin, 1 mM sodium pyruvate, 292 μg/mL L-glutamine, 1× SATO, 5 μg/mL of N acetyl cysteine, and 5ng/mL HBEGF (Peptrotech, 100-47). Microglia were cultured in a minimal, serum-free media consisting of DMEM/F12 (Gibco, 21041025) supplemented with 100 units/mL penicillin, 100 μg/mL streptomycin, 2mM glutamine, 5 μg/mL N-acetyl cysteine, 100 μg/mL apo-transferrin, 100 ng/mL sodium selenite, TGF-β2 (2 ng/mL, Peprotech), murine IL-34 (100 ng/mL, R&D Systems), ovine wool cholesterol (1.5 μg/mL, Avanti Polar Lipids), and heparan sulfate (1 μg/mL, Galen Laboratory Supplies).

extract_protocol:
RNA extracted using the Rneasy Mini Kit by Qiagen
polyA enriched mRNA libraries (SureSelect Automated Strand-Specific RNA Library Prep, mRNA Library Prep for Illumina Paired-End Multiplexed Sequencing)

treatment_protocol: Astrocytes were treated with PBS (control) or treated with 3ng/ml Il-1a, 30ng/ml TFNa, and 400ng/ml C1q (IL-1a (3ng/ml), TNFa (30ng/ml), and C1q (400ng/ml)). Microglia were treated with PBS  (control) or with 50ng/ml LPS (50ng/ml LPS).

tag: genotype/variation

tag: cell type

value: Primary Postnatal Cortical Astrocytes

tag: treatment


title: sod rac astros 2

value: IL-1a (3ng/ml), TNFa (30ng/ml), and C1q (400ng/ml)


title: RNAseq_Syn_WH7803_HL_UV_T1_C1

city: Roscoff

first: Laurence

last: Garczarek

address: Place Georges Teissier

institute: Station Biologique (Sorbonne University and CNRS)

tag: strain

tag: acclimation condition

value: High light

tag: stress condition


title: prostate_tissue-H-sf-replicate_RIB0034262

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

institute: Fraunhofer Institute for Cell Therapy and Immunology

source_name: prostate

value: H-sf

value: prostate

value: male

tag: gleason score

tag: diagnosis


title: 202242410022_R02C01

description:
Primary human meningioma methylation profile
M10-4
Run2

source_name: Meningioma

tag: age


title: 202242410022_R01C01

description:
Primary human meningioma methylation profile
M10-3
Run2


title: wt rac astro 2

description:
processed data file:
wt_rac_astro_vs_sod_rac_astro-ExpDiff.csv
wt_astro_vs_wt_rac_astro-ExpDiff.csv

source_name: Acrtivated Astrocytes

value: wild type


title: RNAseq_Syn_WH7803_HL_UV_T0-3_C1

value: UV exposition

tag: timepoint

value: 0.3 hours

tag: replicate


title: 202226400180_R07C01

description:
Primary human meningioma methylation profile
M9-7
Run2


title: 202226400180_R06C01

description:
Primary human meningioma methylation profile
M9-6
Run2


title: prostate_tissue-H+sf-replicate_RIB0034246

tag: risk group

value: H+sf


title: prostate_tissue-H-sf-replicate_RIB0034443


title: wt rac astro 1


title: 202226400180_R05C01

description:
Primary human meningioma methylation profile
M9-5
Run2

tag: individual


title: wt rac astro 3


title: sod astros 3

description:
processed data file:
wt_astro_vs_sod_astro-ExpDiff.csv

source_name: Quiescent Sod1 Astrocytes

value: Control


title: RNAseq_Syn_WH7803_HL_LT_J1_F1

value: Low temperature

value: 24 hours


title: RNAseq_Syn_WH7803_HL_LT_J1_D1


title: 202226400180_R04C01

description:
Primary human meningioma methylation profile
M9-4
Run2

tag: disease state

value: Meningioma

value: Intracranial


title: sod astros 2


title: RNAseq_Syn_WH7803_HL_UV_T0-3_D1


title: 202226400180_R03C01

description:
Primary human meningioma methylation profile
M9-3
Run2

tag: gender

value: F


title: sod astros 1


title: wt astro 3

description:
processed data file:
wt_astro_vs_sod_astro-ExpDiff.csv
wt_astro_vs_wt_rac_astro-ExpDiff.csv

source_name: Quiescent Astrocytes


title: RNAseq_Syn_WH7803_HL_LT_J0-67_F1

value: 16 hours


title: RNAseq_Syn_WH7803_HL_LT_J0-67_D1


title: wt astro 2

value: Primary Postnatal Cortical Astrocytes


title: 202226400180_R02C01

description:
Primary human meningioma methylation profile
M9-2
Run2

tag: site


title: RNAseq_Syn_WH7803_HL_LT_J1_C1


title: RNAseq_Syn_WH7803_HL_LT_J0-67_C1


title: prostate_tissue-C-replicate_RIB0034341

description: Gene expression of prostate RP tissue specimen (benign prostate hyperplasia)

value: C

tag: tissue

value: benign prostate hyperplasia


title: prostate_tissue-H-df-replicate_RIB0034473

description: Gene expression of prostate RP tissue specimen (prostate cancer)

value: H-df

value: prostate cancer


title: 202226400180_R01C01

description:
Primary human meningioma methylation profile
M9-1
Run2


title: 202226400174_R08C01

description:
Primary human meningioma methylation profile
M8-8
Run2

value: M


title: RNAseq_Syn_WH7803_HL_LT_J0-33_F1

value: High light

value: 8 hours


title: RNAseq_Syn_WH7803_HL_LT_J0-33_D1


title: prostate_tissue-C-replicate_RIB0034346

value: prostate

value: male


title: 202226400174_R07C01

description:
Primary human meningioma methylation profile
M8-7
Run2


title: wt astro 1

tag: genotype/variation

value: wild type

value: Control


title: 202226400174_R06C01

description:
Primary human meningioma methylation profile
M8-6
Run2


title: sod lps 3

description:
processed data file:
wt_lps_vs_sod_lps-ExpDiff.csv

source_name: Activated Sod1 Microglia

tag: cell type

value: Primary Postnatal Microglia

value: 50ng/ml LPS


title: sod lps 2

tag: treatment


title: RNAseq_Syn_WH7803_HL_LT_J0-33_C1

tag: strain

value: Low temperature


title: sod lps 1


title: RNAseq_Syn_WH7803_HL_LT_J0-17_F1

tag: acclimation condition

value: 4 hours


title: wt lps 3

description:
processed data file:
wt_lps_vs_sod_lps-ExpDiff.csv
wt_vs_wt_lps-ExpDiff.csv

source_name: Activated Microglia


title: RNAseq_Syn_WH7803_HL_LT_J0-17_D1

tag: stress condition


title: wt lps 2


title: 202226400174_R04C01

description:
Primary human meningioma methylation profile
M8-4
Run2

value: Meningioma

value: Intracranial


title: 202226400174_R03C01

description:
Primary human meningioma methylation profile
M8-3
Run2


title: RNAseq_Syn_WH7803_HL_LT_J0-17_C1


title: RNAseq_Syn_WH7803_HL_HT_J1_F1

value: High temperature

value: 24 hours


title: wt lps 1


title: prostate_tissue-H-df-replicate_RIB0034316

value: H-df

tag: gleason score


title: 202226400174_R02C01

description:
Primary human meningioma methylation profile
M8-2
Run2


title: 202226400174_R01C01

description:
Primary human meningioma methylation profile
M8-1
Run2


title: 202226400155_R08C01

description:
Primary human meningioma methylation profile
M5-6
Run2

value: F


title: sod 3

description:
processed data file:
wt_vs_sod-ExpDiff.csv

source_name: Quiescent Sod1 Microglia


title: sod 1


title: RNAseq_Syn_WH7803_HL_HT_J1_C1


title: sod 2


title: RNAseq_Syn_WH7803_HL_HT_J0-67_F1

value: 16 hours


title: 202226400155_R07C01

description:
Primary human meningioma methylation profile
M5-5
Run2


title: wt 3

description:
processed data file:
wt_vs_sod-ExpDiff.csv
wt_vs_wt_lps-ExpDiff.csv

source_name: Quiescent Microglia


title: RNAseq_Syn_WH7803_HL_HT_J1_D1

source_name: culture of Synechococcus sp. WH7803 cells

value: High light


title: 202226400155_R05C01

description:
Primary human meningioma methylation profile
M5-3
Run2


title: wt 1


title: RNAseq_Syn_WH7803_HL_HT_J0-67_C1


title: 202226400155_R04C01

description:
Primary human meningioma methylation profile
M5-1
Run2


title: 202226400155_R06C01

description:
Primary human meningioma methylation profile
M5-4
Run2


title: wt 2


title: RNAseq_Syn_WH7803_HL_HT_J0-33_D1

value: 8 hours


title: RNA-seq_E16_spocd1_KO_4

first: Ansgar

last: Zoch

department: MRC Centre for Regenerative Medicine

description:
rRNA depleted total RNA
Spocd1-/-; Miwi2+/Tom

data_processing:
For analysis of small RNA, adapter sequence 'AGATCGGAAGA' was removed from fastq file using cutadapt version 1.16 with option '-m 16 --trimmed-only'.
Processed reads were mapped with bowtie (1.2.1.1) to known miRNAs, non-coding RNAs, repeatmasker track (UCSC mm10), and mouse genome (UCSC mm10).
Up to 3 mismatches were allowed when reads are mapped to genomic retrotransposon sequences.
For analysis of differentially expressed genes, paired-end reads were mapped to GRCm38 genome_tran (release 84) using HISAT2 '--no-mixed --no-discordant --qc-filter --trim5 3'.
Mapped reads per gene were counted with htseq-count (HTSeq 0.11.1) providing GTF file.
Differentially expressed genes were analysed using DESeq2.
For analysis of differentially expressed TEs, single- or paired-end reads were mapped to consensus sequences from Repbase using bowtie2 (2.3.4.3).
Mapped reads per TE were counted by home made pipeline.
Differentially expressed TEs were analysed using DESeq2.
Genome_build: UCSC mm10, GRCm38
Supplementary_files_format_and_content: The processed data file is the tab-delimited txt file that contains the sequence, length, count, annotation, sample ID, and condition of small RNAs identified in this study.

value: mixed B6CBAF1/Crl; C57BL/6N

value: gonocytes

tag: developmental stage

tag: genotype

value: Spocd1-/-; Miwi2+/Tom


title: prostate_tissue-H+df-replicate_RIB0034923

description: Gene expression of prostate RP tissue specimen (prostate cancer)

value: H+df

value: prostate

value: male

tag: diagnosis

value: prostate cancer


title: prostate_tissue-H-sf-replicate_RIB0034992

value: H-sf


title: RNAseq_Syn_WH7803_HL_HT_J0-67_D1

tag: timepoint

tag: replicate


title: prostate_tissue-H+df-replicate_RIB0034945

tag: risk group


title: 202226400174_R05C01

description:
Primary human meningioma methylation profile
M8-5
Run2

tag: individual

tag: disease state

value: Meningioma

tag: age

value: M


title: RNA-seq_E16_spocd1_KO_2

tag: tissue


title: 202226400155_R01C01

description:
Primary human meningioma methylation profile
M4-5
Run1

tag: gender

tag: site

value: Intracranial


title: sod rac astros 1

description:
processed data file:
wt_rac_astro_vs_sod_rac_astro-ExpDiff.csv

tag: genotype/variation

tag: cell type

value: Primary Postnatal Cortical Astrocytes

tag: treatment

value: IL-1a (3ng/ml), TNFa (30ng/ml), and C1q (400ng/ml)


title: RNAseq_Syn_WH7803_HL_HT_J0-17_F1

tag: strain

tag: acclimation condition

tag: stress condition

value: High temperature

value: 4 hours


title: RNAseq_Syn_WH7803_HL_HT_J0-33_F1

value: High light


title: prostate_tissue-H+sf-replicate_RIB0034991

value: H+sf

tag: gleason score


title: RNA-seq_E16_spocd1_KO_1

value: mixed B6CBAF1/Crl; C57BL/6N

tag: developmental stage

tag: genotype


title: RNAseq_Syn_WH7803_HL_HT_J0-17_D1

tag: timepoint

tag: replicate


title: RNA-seq_E16_control_2

description:
rRNA depleted total RNA
Spocd1+/-; Miwi2+/Tom

value: gonocytes

value: Spocd1+/-; Miwi2+/Tom


title: 202226400139_R07C01

description:
Primary human meningioma methylation profile
M4-3
Run1

tag: individual


title: RNA-seq_E16_control_3


title: 202226400139_R08C01

description:
Primary human meningioma methylation profile
M4-4
Run1

tag: disease state


title: RNA-seq_E16_spocd1_KO_3

value: Spocd1-/-; Miwi2+/Tom


title: 202226400155_R03C01

description:
Primary human meningioma methylation profile
M4-7
Run2

tag: age


title: 202226400139_R06C01

description:
Primary human meningioma methylation profile
M4-2
Run1


title: RNAseq_Syn_WH7803_HL_Ct_T0_F1

value: Control condition

value: 0 hour


title: RNA-seq_E16_control_1

tag: tissue


title: RNAseq_Syn_WH7803_HL_HT_J0-17_C1


title: RNAseq_Syn_WH7803_HL_HT_J0-33_C1

value: 8 hours


title: RNAseq_Syn_WH7803_HL_Ct_T0_D1


title: 202226400155_R02C01

description:
Primary human meningioma methylation profile
M4-6
Run2

tag: gender


title: 202226400139_R05C01

description:
Primary human meningioma methylation profile
M4-1
Run1

tag: site


title: 202226400180_R08C01

description:
Primary human meningioma methylation profile
M10-2
Run2

value: F


title: 202226400139_R03C01

description:
Primary human meningioma methylation profile
M11-6
Run1

value: Meningioma


title: prostate_tissue-H+sf-replicate_RIB0034449

tag: risk group

value: prostate

value: male

tag: diagnosis

value: prostate cancer


title: 202226400139_R04C01

description:
Primary human meningioma methylation profile
M11-7
Run1

value: Intracranial


title: TyM-I

city: Ribeirão Preto

first: Rubens

middle: Daniel Miserani

last: Magalhães

state: SP

address: Av. Bandeirantes 3900

department: Department of Cellular and Molecular Biology and Pathogenic Bioagents

country: Brazil

institute: Ribeirão Preto Medical School

data_processing:
First step was the avaluation of quality of the reads sequenced using FASTQC tool.
ChIP-seq reads were aligned to the T cruzi CL-Brener Esmeraldo-like genome (TriTrypDB, release 9) using BWA v 0.7.15-1140, "bwa aln" default parameters. Bwa SAMPE was used to group the files containing the pairs of reads and Samtools was used to obtain the final file properly filled in BAM format.
A Phred mapping quality filter (MAPQ) of 30 was implemented to select the uniquely mapped reads in the T. cruzi genome.
Peaks were called using MACS v2.2 with two distinct sets of parameters for identification of narrow and broad regions. The parameter "--keep-dup auto", using cutoff value of 1e-5 was used to remove part of duplicated reads. The GEM-Mappability Calculator was used to calculate the effective genome size used in MACS2.
The DiffBind v2.2.12 was used to determine the differential profiles of enrichment in each treatment, TY and MTY considering "False Discovery Rate" (FDR) lower than 5%. The statistical analysis is done using DESeq 2 model.
Genome_build: T. cruzi CL-Brener Esmeraldo-like (TritrypDB, release 9)
Supplementary_files_format_and_content: Bedgraph files was generate from MACS2 (Treat and lambda control).

organism: Trypanosoma cruzi

source_name: Parasite cell culture

growth_protocol: Cell culture of T. cruzi trypomastigotes (Y strain) were maintained by infection of LLC-MK2 cells in Minimum Essential Medium (MEM – GIBCO®) containing 2% of Fetal Bovine Serum (FBS), under 5% CO2 and 37oC. Five days after infection of the host cell, culture supernatants containing the trypomastigotes were centrifuged and purified.

extract_protocol:
After cell lysis in 3 steps, the samples were clarified from sonicated nuclei and Protein-DNA complexes were isolated with antibody.
The libraries of the immunoprecipitated DNA fragments from each sample and the corresponding INPUTs were constructed using the TruSeq ChIP Sample Prep Kit (Illumina, IP-202-1012), following the manufacturer's recommendations.

treatment_protocol: The commercially available extracellular matrix (Geltrex ™ LDEV-Free Reduced Growth Factor Basement Membrane Matrix, Gibco, 150 μl ECM per sample) was used to incubate part of the T cruzi trypomastigotes (5 x 10^8 cells). After incubation, the parasites were collected and used for chromatin extraction (Sample named MTy). As a control, 5 x 10^8 trypomastigotes from the same culture were subjected to the same conditions mentioned above in the absence of ECM (sample named Ty). The samples were frozen at -80°C for further use.

value: Y strain

tag: cell type

value: T.cruzi Trypomastigotes

tag: treatment

value: incubated with ECM

tag: chip antibody


title: 202226400139_R02C01

description:
Primary human meningioma methylation profile
M11-5
Run1


title: Ty-I

tag: strain

value: control


title: 202226400139_R01C01

description:
Primary human meningioma methylation profile
M11-4
Run1


title: 202226400129_R08C01

description:
Primary human meningioma methylation profile
M11-3
Run1


title: Ty

value: Anti-Nitroturosine, clone 1A6 (Millipore 05-233,Lot2325108)


title: 202226400129_R07C01

description:
Primary human meningioma methylation profile
M11-2
Run1


title: 202226400129_R05C01

description:
Primary human meningioma methylation profile
M10-6
Run1

value: M


title: RNAseq_Syn_WH7803_HL_UV_T0-3_F1

tag: acclimation condition

value: High light

tag: stress condition

value: UV exposition

value: 0.3 hours