title: BT6B [S132]

description:
blue light:dark, time point 6, replicate B
Sample name in processed data file:
S132

source_name: whole-organism

value: whole organism


title: B6.bead.beadPos.24.AD60817

status: Public on Jun 12 2019

type: SRA

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

country: USA

institute: Seattle Children's Research Institute

library_source: transcriptomic

data_processing:
Stranded paired-end reads of length 76 were preprocessed: The first three nucleotides of R1 (v1 kit) or R2 (v2 kit) were removed as described in the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian User Manual (v1: 112215, v2: 063017) and read ends consisting of 50 or more of the same nucleotide were removed.
The remaining read pairs were aligned to the mouse genome (mm10) + Mtb H37Rv genome using the gsnap aligner (v. 2016-08-24) allowing for novel splicing. (gsnap options: -s Mus_musculus.GRCm38.78.splicesites --filter-chastity=either --max-middle-deletions=3 --max-middle-insertions=3 --query-unk-mismatch=1 )
Concordantly mapping read pairs (average 15-million / sample) that aligned uniquely were assigned to exons using the subRead program and gene definitions from Ensembl Mus_Musculus GRCm38.78 coding and non-coding genes.
Genome_build: mm10 + Mtb H37Rv
Supplementary_files_format_and_content: rawCounts.tsv contains the raw counts for each sample generated by subRead, tab-separated

molecule: total RNA

organism: Mus musculus

source_name: Alveolar macrophages

extract_protocol:
RNA isolation was performed using TRIzol (Invitrogen), two sequential chloroform extractions, Glycoblue carrier (Thermo Fisher), isopropanol precipitation, and washes with 75% ethanol.
cDNA libraries were constructed and amplified using the SMARTer Stranded Total RNA-Seq Kit (v1 or v2) - Pico Input Mammalian (Clontech) per the manufacturers instructions. Libraries were amplified and then sequenced on an Illumina NextSeq (2 x 75, paired-end).

tag: cell type

value: Alveolar macrophages

tag: strain/genotype

tag: infectious challenge

value: bead

tag: infection status

value: beadPos

tag: time infected (hrs)

tag: library version

tag: experiment label


title: 245_STEM_1h_5mM

type: RNA

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

description:
1h 5 mM
245_3

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: The data were analyzed with Bioconductor tools in R (version 3.1.0; http://www.r-project.org) using GC-RMA as normalization method.

label: biotin

organism: Homo sapiens

source_name: EpOCs from Ctrl (245), 1h incubation,  5 mM butyrate stimulation

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

growth_protocol: Crypts from descending/sigmoid colon samples were isolated by EDTA treatment. Crypt units were embedded in Matrigel, expanded for 3-4 days in stem medium and dissociated. Single epithelial cells were replated in fresh stem medium according to a 1:3 dilution to generate EpOCs. Part of the EpOCs was induced to differentiate (d-EpOCs) by the addition of fresh differentiation medium.

extract_protocol: Total RNA was extracted using Trizol+RNA Cleanup protocol by RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: At day 5 of in vitro expansion, EpOCs were stimulated with 0.5 mM and 5 mM butyrate during 1h, 3h, 6h or 24h and total RNA was isolated. d-EpOCs were stimulated with 0.5 mM and 5 mM butyrate during 1h, 3h, 6h or 24h and total RNA was isolated.

tag: patient id

value: Epithelial organoid cultures (EpOCs)


title: 243_DIFF_24h_0,5mM

description:
24h 0.5mM
243_23

source_name: d-EpOCs from Ctrl (243), 24h incubation, 0.5 mM butyrate stimulation

value: d-EpOCs


title: 245_STEM_1h_0,5mM

description:
1h 0.5mM
245_2

source_name: EpOCs from Ctrl (245), 1h incubation, 0.5 mM butyrate stimulation


title: RT6D [S130]

city: Charlotte

first: Whitney

middle: at

last: Leach

address: 9201 University City Blvd.

department: Biological Sciences

institute: University of North Carolina at Charlotte

description:
red light:dark, time point 6, replicate D
Sample name in processed data file:
S130

data_processing:
Sequenced reads were concatenated and renamed based on sample ID
Each Illumina read was trimmed of the adapter and PCR duplicates were removed
Quality filtering was performed using fastx_toolkit
Transcriptome mapping was performed using Bowtie2
Genome_build: genome Putnam et al. (2007) is available at:
https://figshare.com/articles/Nematostella_vectensis_transcriptome_and_gene_models_v2_0/807696
Supplementary_files_format_and_content: tab-delimited table of counts per gene for each sample

organism: Nematostella vectensis

growth_protocol: Animals were maintained as described in Hand et al. (1994)

extract_protocol:
Whole-organism RNA was extracted from animals (that were preserved in RNAlater and stored at -80) using Ambion RNAqueous extraction kit.
Libraries were prepared as in Meyer et al. (2011)

treatment_protocol: Animals were experimentally exposed to one of 4 light conditions: 1) red light:dark 2) blue light:dark 3) green light:dark or 4) dark:dark conditions for 1 month, then sampled every 4 hours for 1 day (24 hours) in replicates of 4

tag: tissue

tag: developmental stage

value: adult

tag: treatment

value: red light:dark

tag: time point

value: time point 6

tag: replicate

value: replicate D


title: BT6A [S131]

description:
blue light:dark, time point 6, replicate A
Sample name in processed data file:
S131

value: blue light:dark

value: replicate A


title: B6.bead.naive.24.AD60817

value: naive


title: 243_DIFF_24h_5mM

description:
24h 5 mM
243_24

source_name: d-EpOCs from Ctrl (243), 24h incubation,  5 mM butyrate stimulation


title: SAMPLE 32 TF-1 IDH mut rep1

type: genomic

city: Birmingham

first: Rui

last: Lu

state: AL

address: 1824 6th Ave S

institute: Univ of Alabama at Birmingham

description: SAMPLE 34

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using Illumina standard protocol.

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting.

data_processing: GenomeStudio software version V2011.1

label: Cy5 and Cy3

molecule: genomic DNA

source_name: TF-1 cells

label_protocol: Standard Illumina labelling protocol.

growth_protocol: The TF-1 human erythroleukemic cell line was obtained from ATCC and cultivated in the RPMI 1640 base medium (Invitrogen) supplemented with 10% of FBS and 2 ng/ml of recombinant human GM-CSF (R&D Systems).

extract_protocol: Genomic DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen), and 1µg genomic DNA was subject to bisulfite conversion using EZ DNA methylation gold kit (Zymo Research) according to manufacturer's instructions.

treatment_protocol: TF-1 cell lines with stable expression of wild-type (WT) or mutant DNMT3A were established by MSCV-based retrovirus packaged in HEK293 cells.

tag: gene expressed

value: DNMT3A IDH1 R132H


title: RT6C [S129]

description:
red light:dark, time point 6, replicate C
Sample name in processed data file:
S129

value: replicate C


title: 243_DIFF_24h_c-

description:
24h c-
243_22

source_name: d-EpOCs from Ctrl (243), 24h incubation, not stimulated

value: c-


title: B6.H37Rv.mEmPos.24.AD13

value: mEmPos


title: 243_DIFF_6h_5mM

description:
6h 5 mM
243_21

source_name: d-EpOCs from Ctrl (243), 6h incubation,  5 mM butyrate stimulation


title: RT6B [S128]

description:
red light:dark, time point 6, replicate B
Sample name in processed data file:
S128

value: whole organism

value: replicate B


title: SAMPLE 30 TF-1 R882H H rep 1

description: SAMPLE 30

value: DNMT3A R882H GFP high


title: SAMPLE 31 TF-1 R882H H rep 2

description: SAMPLE 31


title: B6.H37Rv.mEmNeg.24.AD13

value: Alveolar macrophages

value: mEmNeg


title: SAMPLE 33 TF-1 IDH mut rep2

description: SAMPLE 35


title: RT6A [S127]

description:
red light:dark, time point 6, replicate A
Sample name in processed data file:
S127


title: SAMPLE 28 TF-1 R882H M rep 1

description: SAMPLE 28

value: DNMT3A R882H GFP medium


title: DT5D [S126]

description:
dark:dark, time point 5, replicate D
Sample name in processed data file:
S126

value: adult

value: time point 5


title: 243_DIFF_6h_0,5mM

description:
6h 0.5mM
243_20

source_name: d-EpOCs from Ctrl (243), 6h incubation, 0.5 mM butyrate stimulation

value: d-EpOCs


title: B6.H37Rv.naive.24.AD13


title: DT5C [S125]

description:
dark:dark, time point 5, replicate C
Sample name in processed data file:
S125


title: 243_DIFF_6h_c-

description:
6h c-
243_19

source_name: d-EpOCs from Ctrl (243), 6h incubation, not stimulated


title: B6.bead.beadPos.24.AD51617

value: bead

value: beadPos


title: SAMPLE 29 TF-1 R882H M rep 2

description: SAMPLE 29


title: 243_DIFF_3h_0,5mM

description:
3h 0.5mM
243_17

source_name: d-EpOCs from Ctrl (243), 3h incubation, 0.5 mM butyrate stimulation


title: DT5B [S124]

description:
dark:dark, time point 5, replicate B
Sample name in processed data file:
S124


title: (miR-135aIP) AIP-3 (2015_015_018)

city: Utrecht

first: Ronald

middle: Jeroen

last: Pasterkamp

state: Utrecht

address: Universiteitsweg 100

department: Translational Neuroscience

country: Netherlands

institute: UMC Utrecht

description:
(miR-135aIP) AIP-3 (2015_015_018)
Immunoprecipitates

data_processing:
Single and paired end sequencing was performed using the NextSeq500 instrument according to the manufacturer’s instructions (Illumina).
Following trimming of low-quality bases and adapter sequences with FASTQ-MCF (version 0.0.13), processed reads were mapped to the GRCm38.p6 reference mouse genome (Ensembl) with TopHat2 (version 2.0.13).
‘fr-secondstrand’ option was chosen for the alignments of the total RNA sequencing data. Mapped counts were summarised for each gene using the python script htseq-count (Anders et al., 2015. Bioinformatics).
For differential expression analysis, count data for genes and transcripts were analysed for differential expression in R using the Bioconductor package EdgeR version 3.12.1 (Robinson et al., 2010. Bioinformatics) with the trimmed mean of M-values (TMM) normalisation method (Robinson and Oshlack, 2010. Genome Biology). Adjusted P values for multiple testing were calculated using the Benjamini-Hochberg false discovery rate (FDR) and only genes with an FDR < 0.05 were considered significantly differentially expressed.
Data visualisation was performed in R using the ggplot2 library (version 2.1.0). Enrichment analysis was performed using the R package goseq (Young et al., 2010. Genome Biology) to correct for bias due to transcript length.
Further, in silico prediction of miRNA signatures on target genes upregulated on the IP samples was performed using miRanda software version 3.3a. The following parameters were used in this study: match with a minimum threshold score of 150; target mRNA duplex with minimum folding free energy threshold -7kcal/mol; gap opening penalty -8; gap extension penalty -2; scaling parameter 4 for complementary nucleotide match score.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files contain read counts of inputs and IPs, list of significant genes, upregulated genes, predictied targets
Supplementary_files_format_and_content: INPUT_AIPvsNCIP_edgeR_counts.txt : Abundance measurements
Supplementary_files_format_and_content: INPUT_AIP_vs_NCIP_sigGenesFDR005.txt: significant genes
Supplementary_files_format_and_content: IP_AIPvsNCIP_edgeR_counts.txt: Abundance measurements
Supplementary_files_format_and_content: IP_AIP_vs_NCIP_sigGenesFDR005.txt: significant gene list
Supplementary_files_format_and_content: AIPvsNCIP_IP_up_genes.txt: Upregulated gene list
Supplementary_files_format_and_content: AIP_3UTRs_miranda_targets.txt: target site prediction
Supplementary_files_format_and_content: AIP_5UTRs_miranda_targets.txt: target site prediction
Supplementary_files_format_and_content: AIP_CDS_miranda_targets.txt: target site prediction

source_name: N2A cells

extract_protocol:
Beads used to perform immunoprecipitation were collected in Qiazol (Qiagen) and stored at -80oC until RNA isolation. Total RNA was extracted using miRNeasy kit (Qiagen), according to manufacturer’s protocol. Further details can be found on manuscripts methods section. Library preparation and sequencing was performed by the Biogazelle sequencing facility (Biogazelle NV Technologiepark 3, 9052 Zwijnaarde, Belgium) using standard illumina protocols.
Libraries for total RNA sequencing were prepared using the TruSeq Stranded Total RNA sample prep kit (Illumina).

tag: cell line

value: neuroblastoma


title: DT5A [S123]

description:
dark:dark, time point 5, replicate A
Sample name in processed data file:
S123

value: replicate A


title: SAMPLE 22 TF-1 RH Y735A rep 1

description: SAMPLE 22

value: DNMT3A R882H Y735A


title: 243_DIFF_3h_5mM

description:
3h 5 mM
243_18

source_name: d-EpOCs from Ctrl (243), 3h incubation,  5 mM butyrate stimulation


title: SAMPLE 26 TF-1 R882H L rep 1

description: SAMPLE 26

value: DNMT3A R882H GFP low


title: (miR-135aIP) AIP-1 (2015_015_002)

description:
(miR-135aIP) AIP-1 (2015_015_002)
Immunoprecipitates
AIP_5UTRs_miranda_targets.txt


title: GT5C [S121]

description:
green light:dark, time point 5, replicate C
Sample name in processed data file:
S121

value: green light:dark

value: replicate C


title: (miR-135aIP) AIP-2  (2015_015_010)

description:
(miR-135aIP) AIP-2  (2015_015_010)
Immunoprecipitates
AIP_CDS_miranda_targets.txt


title: SAMPLE 27 TF-1 R882H L rep 2

description: SAMPLE 27


title: 243_DIFF_1h_0,5mM

description:
1h 0.5mM
243_14

source_name: d-EpOCs from Ctrl (243), 1h incubation, 0.5 mM butyrate stimulation


title: GT5D [S122]

description:
green light:dark, time point 5, replicate D
Sample name in processed data file:
S122

value: whole organism

value: replicate D


title: 243_DIFF_1h_c-

description:
1h c-
243_13

source_name: d-EpOCs from Ctrl (243), 1h incubation, not stimulated

value: c-


title: 243_DIFF_3h_c-

description:
3h c-
243_16

source_name: d-EpOCs from Ctrl (243), 3h incubation, not stimulated


title: 243_DIFF_1h_5mM

description:
1h 5 mM
243_15

source_name: d-EpOCs from Ctrl (243), 1h incubation,  5 mM butyrate stimulation


title: SAMPLE 21 TF-1 RH DDAA rep 3

description: SAMPLE 21

value: DNMT3A R882H D529A D531A


title: SAMPLE 24 TF-1 parental

description: SAMPLE 24


description:
(Negative control IP) NcIP-2 (2015_015_014)
Immunoprecipitates
AIPvsNCIP_IP_up_genes.txt


title: GT5A [S119]

description:
green light:dark, time point 5, replicate A
Sample name in processed data file:
S119

source_name: whole-organism


title: GT5B [S120]

description:
green light:dark, time point 5, replicate B
Sample name in processed data file:
S120

value: replicate B


title: SAMPLE 25 TF-1 parental

description: SAMPLE 25


title: (miR-135ain) Ain-3 (2015_015_017)

description:
(miR-135ain) Ain-3 (2015_015_017)
Input samples


title: SAMPLE 23 TF-1 RH Y735A rep 2

description: SAMPLE 23


title: BT5C [S117]

description:
blue light:dark, time point 5, replicate C
Sample name in processed data file:
S117

value: blue light:dark


title: 243_STEM_24h_c-

description:
24h c-
243_10

source_name: EpOCs from Ctrl (243), 24h incubation, not stimulated

value: Epithelial organoid cultures (EpOCs)


title: SAMPLE 20 TF-1 RH DDAA rep 2

description: SAMPLE 20


title: SAMPLE 19 TF-1 RH DDAA rep 1

description: SAMPLE 19


title: SAMPLE 16 TF-1 RH D333A rep 1

description: SAMPLE 16

value: DNMT3A R882H D333A


title: 243_STEM_24h_0,5mM

description:
24h 0.5mM
243_11

source_name: EpOCs from Ctrl (243), 24h incubation, 0.5 mM butyrate stimulation


title: 243_STEM_6h_5mM

description:
6h 5 mM
243_9

source_name: EpOCs from Ctrl (243), 6h incubation,  5 mM butyrate stimulation


title: (miR-135ain) Ain-2 (2015_015_009)

description:
(miR-135ain) Ain-2 (2015_015_009)
Input samples


description:
(Negative control IP) NcIP-1 (2015_015_006)
Immunoprecipitates
CTL_vs_AIP_IP_sigGenesFDR005.txt


title: SAMPLE 17 TF-1 RH D333A rep 2

description: SAMPLE 17


title: (miR-135ain) Ain-1 (2015_015_001)

description:
(miR-135ain) Ain-1 (2015_015_001)
Input samples


title: BT5A [S115]

description:
blue light:dark, time point 5, replicate A
Sample name in processed data file:
S115

value: adult

value: time point 5


title: SAMPLE 18 TF-1 RH D333A rep 3

description: SAMPLE 18


description:
(Negative control) Ncin-3 (2015_015_021)
Input samples


title: BT5B [S116]

description:
blue light:dark, time point 5, replicate B
Sample name in processed data file:
S116


title: B6.bead.naive.24.AD51617

source_name: Alveolar macrophages

value: Alveolar macrophages

value: bead

value: naive


title: 243_STEM_6h_0,5mM

description:
6h 0.5mM
243_8

source_name: EpOCs from Ctrl (243), 6h incubation, 0.5 mM butyrate stimulation


title: SAMPLE 13 TF-1 RHdPWWP rep 1

description: SAMPLE 13

source_name: TF-1 cells

value: DNMT3A R882H PWWP deletion


description:
(Negative control IP) NcIP-3 (2015_015_022)
Immunoprecipitates
AIP_3UTRs_miranda_targets.txt

value: neuroblastoma


title: RT5D [S114]

description:
red light:dark, time point 5, replicate D
Sample name in processed data file:
S114

value: red light:dark


title: SAMPLE 15 TF-1 RHdPWWP rep 3

description: SAMPLE 15


title: SAMPLE 14 TF-1 RHdPWWP rep 2

description: SAMPLE 14


title: SAMPLE 11 TF-1 RHdNTD rep 2

description: SAMPLE 11

value: DNMT3A R882H NTD deletion


title: RT5C [S113]

description:
red light:dark, time point 5, replicate C
Sample name in processed data file:
S113

value: whole organism

value: replicate C


description:
(Negative control) Ncin-1 (2015_015_005)
Input samples
CTL_vs_AIP_INPUT_sigGenesFDR005.txt


title: 243_STEM_3h_5mM

description:
3h 5 mM
243_6

source_name: EpOCs from Ctrl (243), 3h incubation,  5 mM butyrate stimulation


description:
(Negative control) Ncin-2 (2015_015_013)
Input samples


title: RT5B [S112]

description:
red light:dark, time point 5, replicate B
Sample name in processed data file:
S112


title: 243_STEM_6h_c-

description:
6h c-
243_7

source_name: EpOCs from Ctrl (243), 6h incubation, not stimulated

value: c-


title: BT5D [S118]

description:
blue light:dark, time point 5, replicate D
Sample name in processed data file:
S118

value: replicate D


title: SAMPLE 12 TF-1 RHdNTD rep 3

description: SAMPLE 12


title: 243_STEM_3h_c-

description:
3h c-
243_4

source_name: EpOCs from Ctrl (243), 3h incubation, not stimulated


title: 243_STEM_1h_5mM

description:
1h 5 mM
243_3

source_name: EpOCs from Ctrl (243), 1h incubation,  5 mM butyrate stimulation


title: RT5A [S111]

description:
red light:dark, time point 5, replicate A
Sample name in processed data file:
S111

value: replicate A


title: DT4D [S110]

description:
dark:dark, time point 4, replicate D
Sample name in processed data file:
S110

value: time point 4


title: CD34_ETO_rep2

city: Mainz

first: Vassilis

last: Roukos

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology gGmbH

library_source: genomic

data_processing:
Library strategy: BLISS-seq
Reads were mapped to the human genome (GRCh37/hg19) using BWA-MEM and only reads with mapping quality scores greater than 30 were retained.
PCR duplicates were filtered out by searching for proximal reads with at most two mismatches in the UMI sequence.
Bed files were generated containing a list of double-strand break (DSB) genomic locations associated with the number of unique UMIs identified.
BEDtools suite was used to generate bigwig files from bed files. First, one entry was created per UMI-DSB in the BED file and then each UMI-DSB was extended +/- 100bp.
Genome_build: hg19
Supplementary_files_format_and_content: bed files containing a list of genomic locations associated with unique UMIs. BigWig files were generated using BEDtools suite.

source_name: primary CD34+ bone marrow  cells

extract_protocol:
Cells and nuclei were lysed with mild buffers. After blunting of DSBs and BLISS adapter ligation, DNA was extracted using DNA extraction buffer and proteinase K, followed by phenol/chloroform extraction and ethanol precipitation.
After DNA sonication, genomic DSB ends were amplified with in vitro transcription, after which generated RNA was subjected to an Illumina small RNA-like library preparation protocol (similar to described for BLISS in Yan, Mirzazadeh et al, Nature Communications 2017).

value: CD34+ bone marrow cells

value: ETO


title: CD34_DMSO_rep2

value: DMSO


title: CD34_ETO_rep1


title: SAMPLE 8 TF-1 R882S rep 1

description: SAMPLE 8

value: DNMT3A R882S


title: DT4B [S108]

description:
dark:dark, time point 4, replicate B
Sample name in processed data file:
S108

value: adult

value: replicate B


title: DT4C [S109]

description:
dark:dark, time point 4, replicate C
Sample name in processed data file:
S109


title: 243_STEM_1h_0,5mM

description:
1h 0.5mM
243_2

source_name: EpOCs from Ctrl (243), 1h incubation, 0.5 mM butyrate stimulation

value: Epithelial organoid cultures (EpOCs)


title: SAMPLE 9 TF-1 R882S rep 2

description: SAMPLE 9


title: 243_STEM_1h_c-

description:
1h c-
243_1

source_name: EpOCs from Ctrl (243), 1h incubation, not stimulated


title: TK6_untr_ETO_rep2

value: lymphoblastoid cells


title: CD34_DMSO_rep1


title: 243_STEM_24h_5mM

description:
24h 5 mM
243_12

source_name: EpOCs from Ctrl (243), 24h incubation,  5 mM butyrate stimulation


title: DT4A [S107]

description:
dark:dark, time point 4, replicate A
Sample name in processed data file:
S107


title: 241_DIFF_24h_5mM

description:
24h 5 mM
241_24

source_name: d-EpOCs from Ctrl (241), 24h incubation,  5 mM butyrate stimulation

value: d-EpOCs


title: 241_DIFF_24h_0,5mM

description:
24h 0.5mM
241_23

source_name: d-EpOCs from Ctrl (241), 24h incubation, 0.5 mM butyrate stimulation


title: SAMPLE 6 TF-1 R882C rep 1

description: SAMPLE 6

value: DNMT3A R882C


title: SAMPLE 7 TF-1 R882C rep 2

description: SAMPLE 7


title: gPUCHI-GR_NAA+DEX+CHX_rep2

city: Kobe

first: Hidehiro

last: Fukaki

state: Hyogo

address: Rokko-dai 1-1

country: Japan

institute: Kobe University

description: Gene expression data from 5-day-old gPUCHI-GR roots NAA DEX CHX treatment (4h) rep2

hyb_protocol: Hybridization, washing, staining procedures were run on Fluidics Station 450 (Affymetrix) with GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: GeneChips were scanned with GeneChip Scanner 3000 7G.

data_processing: Data procession was performed with Expression Console Version 1.3 (Affymetrix).

organism: Arabidopsis thaliana

source_name: Arabidopsis 5-day-old root

label_protocol: Biotinylated cRNA was prepared from total RNA with GeneChip 3' IVT Expression Kit (Affymetrix).

growth_protocol: Arabidopsis seedlings of gPUCHI-GR puchi-1 were grown for 5 days on 1x MS agar plate under continuous light condition.

extract_protocol: Total RNA was extracted with RNeasy Plant Mini Kit (QIAGEN).

treatment_protocol: 5-day-old seedlins of gPUCHI-GR puchi-1 were treated with/without 2 µM DEX, 10 µM CHX and 1µM NAA for 4 hours

tag: genotype

value: gPUCHI:GR, puchi-1

value: 5-day-old root

value: 1 µM NAA, 2 µM DEX and 10 µM CHX treatment for 4 hours


title: 241_DIFF_6h_5mM

description:
6h 5 mM
241_21

source_name: d-EpOCs from Ctrl (241), 6h incubation,  5 mM butyrate stimulation


title: GT4D [S106]

description:
green light:dark, time point 4, replicate D
Sample name in processed data file:
S106

source_name: whole-organism

value: whole organism

value: green light:dark


title: TK6_untr_DMSO_rep2


title: gPUCHI-GR_NAA+DEX+CHX_rep1

description: Gene expression data from 5-day-old gPUCHI-GR roots NAA DEX CHX treatment (4h) rep1


title: TK6_DRB_ETO_rep2


title: 241_DIFF_24h_c-

description:
24h c-
241_22

source_name: d-EpOCs from Ctrl (241), 24h incubation, not stimulated

value: c-


title: gPUCHI-GR_NAA+CHX_rep2

description: Gene expression data from 5-day-old gPUCHI-GR roots NAA CHX treatment (4h) rep2

value: 1 µM NAA and 10 µM CHX treatment for 4 hours


title: GT4C [S105]

description:
green light:dark, time point 4, replicate C
Sample name in processed data file:
S105

value: time point 4

value: replicate C


title: GT4B [S104]

description:
green light:dark, time point 4, replicate B
Sample name in processed data file:
S104


title: SAMPLE 4 TF-1 R882H rep 4

description: SAMPLE 4

value: DNMT3A R882H


title: TK6_untr_ETO_rep1


title: GT4A [S103]

description:
green light:dark, time point 4, replicate A
Sample name in processed data file:
S103

value: replicate A


title: SAMPLE 5 TF-1 R882H rep 5

description: SAMPLE 5


title: 241_DIFF_6h_0,5mM

description:
6h 0.5mM
241_20

source_name: d-EpOCs from Ctrl (241), 6h incubation, 0.5 mM butyrate stimulation


title: TK6_DRB_ETO_rep1


title: TK6_DRB_DMSO_rep2


title: gPUCHI-GR_NAA+CHX_rep1

description: Gene expression data from 5-day-old gPUCHI-GR roots NAA CHX treatment (4h) rep1


title: gPUCHI-GR_NAA+DEX_rep1

description: Gene expression data from 5-day-old gPUCHI-GR roots NAA DEX treatment (4h) rep1

value: 1 µM NAA and 2 µM DEX treatment for 4 hours


title: gPUCHI-GR_NAA+DEX_rep2

description: Gene expression data from 5-day-old gPUCHI-GR roots NAA DEX treatment (4h) rep2


title: TK6_untr_DMSO_rep1


title: 241_DIFF_3h_5mM

description:
3h 5 mM
241_18

source_name: d-EpOCs from Ctrl (241), 3h incubation,  5 mM butyrate stimulation


title: BT4C [S101]

description:
blue light:dark, time point 4, replicate C
Sample name in processed data file:
S101

value: adult

value: blue light:dark


title: TK6_DRB_DMSO_rep1

value: lymphoblastoid cells


title: 241_DIFF_6h_c-

description:
6h c-
241_19

source_name: d-EpOCs from Ctrl (241), 6h incubation, not stimulated

value: d-EpOCs


title: SAMPLE 3 TF-1 R882H rep 3

description: SAMPLE 3

source_name: TF-1 cells


title: BT4B [S100]

description:
blue light:dark, time point 4, replicate B
Sample name in processed data file:
S100

value: replicate B


title: gPUCHI-GR_NAA_rep2

description: Gene expression data from 5-day-old gPUCHI-GR roots NAA treatment (4h) rep2

value: gPUCHI:GR, puchi-1

value: 1 µM NAA treatment for 4 hours


title: SAMPLE 2 TF-1 R882H rep 2

description: SAMPLE 2


title: BT4D [S102]

description:
blue light:dark, time point 4, replicate D
Sample name in processed data file:
S102

value: replicate D


title: K562_ETO

value: erythroleukemia cells

value: ETO


title: SAMPLE 1 TF-1 R882H rep 1

description: SAMPLE 1


title: BT4A [S99]

description:
blue light:dark, time point 4, replicate A
Sample name in processed data file:
S99

value: whole organism


title: 241_DIFF_3h_c-

description:
3h c-
241_16

source_name: d-EpOCs from Ctrl (241), 3h incubation, not stimulated

value: c-


title: K562_DMSO

value: DMSO


title: gPUCHI-GR_NAA_rep1

description: Gene expression data from 5-day-old gPUCHI-GR roots NAA treatment (4h) rep1

value: 5-day-old root


title: 241_DIFF_3h_0,5mM

description:
3h 0.5mM
241_17

source_name: d-EpOCs from Ctrl (241), 3h incubation, 0.5 mM butyrate stimulation


title: RT4D [S98]

description:
red light:dark, time point 4, replicate D
Sample name in processed data file:
S98

value: red light:dark

value: time point 4


title: 241_DIFF_1h_5mM

description:
1h 5 mM
241_15

source_name: d-EpOCs from Ctrl (241), 1h incubation,  5 mM butyrate stimulation


title: TK6_ETO_rep2


title: RT4C [S97]

description:
red light:dark, time point 4, replicate C
Sample name in processed data file:
S97

value: replicate C


title: TK6_DMSO_rep2


title: gPUCHI-GR_DEX+CHX_rep2

description: Gene expression data from 5-day-old gPUCHI-GR roots DEX+CHX treatment (4h) rep2

value: 2 µM DEX and 10 µM CHX treatment for 4 hours


title: TK6_ETO_rep1


title: RT4A [S95]

description:
red light:dark, time point 4, replicate A
Sample name in processed data file:
S95

value: adult

value: replicate A


title: 241_DIFF_1h_0,5mM

description:
1h 0.5mM
241_14

source_name: d-EpOCs from Ctrl (241), 1h incubation, 0.5 mM butyrate stimulation

value: d-EpOCs


title: SAMPLE 10 TF-1 RHdNTD rep 1

description: SAMPLE 10

value: DNMT3A R882H NTD deletion


title: TK6_DMSO_rep1

value: lymphoblastoid cells


title: 241_STEM_24h_5mM

description:
24h 5 mM
241_12

source_name: EpOCs from Ctrl (241), 24h incubation,  5 mM butyrate stimulation

value: Epithelial organoid cultures (EpOCs)


title: DT3D [S94]

description:
dark:dark, time point 3, replicate D
Sample name in processed data file:
S94

value: time point 3

value: replicate D


title: gPUCHI-GR_DEX_rep2

description: Gene expression data from 5-day-old gPUCHI-GR roots DEX treatment (4h) rep2

value: gPUCHI:GR, puchi-1

value: 2 µM DEX treatment for 4 hours


title: gPUCHI-GR_CHX_rep1

description: Gene expression data from 5-day-old gPUCHI-GR roots CHX treatment (4h) rep1

value: 10 µM CHX treatment for 4 hours


title: DT3C [S93]

description:
dark:dark, time point 3, replicate C
Sample name in processed data file:
S93

value: whole organism


title: 241_STEM_24h_0,5mM

description:
24h 0.5mM
241_11

source_name: EpOCs from Ctrl (241), 24h incubation, 0.5 mM butyrate stimulation


title: gPUCHI-GR_CHX_rep2

description: Gene expression data from 5-day-old gPUCHI-GR roots CHX treatment (4h) rep2

value: 5-day-old root


title: DT3B [S92]

description:
dark:dark, time point 3, replicate B
Sample name in processed data file:
S92

value: replicate B


title: Liver, FR F1_rep2

city: Wuhan

first: Jing-Jing

last: Zhang

state: Hubei

address: 1 Lion Rock Street

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction

country: China

institute: Huazhong Agricultural University

data_processing:
Reads of RNA-seq were mapped to the mouse genome (mm10) with STAR
Mapped reads were subsequently assembled into transcripts guided by the reference annotation (GENCODE gene models) with Stringtie
Gene differential expression analysis using DESeq2 based on the reads count file obtained by HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: counts

molecule: polyA RNA

source_name: liver

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Libraries were constructed with TruSeq DNA library preparation kit (Illumina)

tag: strain

value: ICR

value: liver of F1 males

tag: age

value: 8 wk of age

tag: stress

value: paternal famine


title: gPUCHI-GR_DEX+CHX_rep1

description: Gene expression data from 5-day-old gPUCHI-GR roots DEX+CHX treatment (4h) rep1

value: 2 µM DEX and 10 µM CHX treatment for 4 hours


title: VUB03_BcL_XL_5

city: Brussels

first: Claudia

last: Spits

address: Laarbeeklaan 103

department: Research Group of Reproduction and Genetics

country: Belgium

institute: Vrije Universiteit Brussel

data_processing:
mapping sequences:
STAR 2.5.3
STAR --runThreadN 8 --runMode alignReads \  --quantMode  TranscriptomeSAM \ --twopassMode Basic \  --outSAMtype BAM SortedByCoordinate
count tables:
RSEM 1.3.0
rsem-calculate-expression -p 8 \ --alignments Aligned.toTranscriptome.out.ba
RNA seq analysis:
edgeR and DESeq2
Genome_build: GRCh38.p10/hg19
Supplementary_files_format_and_content: expression.genes.results and expression.isoforms.results  for each sample containing: gene_id transcript_id(s) length effective_length expected_count TPM FPKM

growth_protocol: hESC cultured on Laminin-521 with Nutristem medium, refreshed every day. Passaged once a week in a 1:20 ratio

extract_protocol:
Total RNA was extracted using the QIAGEN Rneasy Mini kit, following manufacturers instructions
Illumina sequencing library preparation using the QuantSeq 3' mRNA-Seq Library Prep Kits (Lexogen) according to manufacturer's protocol

value: hESC

tag: karyotype


title: 241_DIFF_1h_c-

description:
1h c-
241_13

source_name: d-EpOCs from Ctrl (241), 1h incubation, not stimulated

value: d-EpOCs

value: c-


title: 241_STEM_6h_5mM

description:
6h 5 mM
241_9

source_name: EpOCs from Ctrl (241), 6h incubation,  5 mM butyrate stimulation

value: Epithelial organoid cultures (EpOCs)


title: VUB03_BcL_XL_4


title: RT4B [S96]

description:
red light:dark, time point 4, replicate B
Sample name in processed data file:
S96

value: adult

value: red light:dark

value: time point 4


title: gPUCHI-GR_mock_rep2

description: Gene expression data from 5-day-old gPUCHI-GR roots mock treatment (4h) rep2

source_name: Arabidopsis 5-day-old root

value: gPUCHI:GR, puchi-1

value: Mock (0.1% DMSO) treatment for 4 hours


title: VUB03_BcL_XL_3


title: 241_STEM_24h_c-

description:
24h c-
241_10

source_name: EpOCs from Ctrl (241), 24h incubation, not stimulated


title: gPUCHIGR_DEX_rep1

description: Gene expression data from 5-day-old gPUCHI-GR roots DEX treatment (4h) rep1

value: 2 µM DEX treatment for 4 hours


title: DT3A [S91]

description:
dark:dark, time point 3, replicate A
Sample name in processed data file:
S91

source_name: whole-organism

value: whole organism

value: time point 3

value: replicate A


title: gPUCHI-GR_mock_rep1

description: Gene expression data from 5-day-old gPUCHI-GR roots mock treatment (4h) rep1

value: 5-day-old root


title: Liver, FR F1_rep1

value: ICR

value: liver of F1 males

value: 8 wk of age


title: VUB03_BcL_XL_2

value: hESC


title: 241_STEM_6h_0,5mM

description:
6h 0.5mM
241_8

source_name: EpOCs from Ctrl (241), 6h incubation, 0.5 mM butyrate stimulation


title: GT3D [S90]

description:
green light:dark, time point 3, replicate D
Sample name in processed data file:
S90

value: green light:dark

value: replicate D


title: Liver, control F1_rep3

value: control


title: Liver, FR F1_rep3

value: paternal famine


title: 241_STEM_3h_5mM

description:
3h 5 mM
241_6

source_name: EpOCs from Ctrl (241), 3h incubation,  5 mM butyrate stimulation

value: Epithelial organoid cultures (EpOCs)


title: GT3C [S89]

description:
green light:dark, time point 3, replicate C
Sample name in processed data file:
S89

value: adult

value: replicate C


title: Liver, control F1_rep2


title: GT3B [S88]

description:
green light:dark, time point 3, replicate B
Sample name in processed data file:
S88

value: replicate B


title: Liver, control F1_rep1


title: VUB03_mt_2


title: VUB02_mt_2_5


title: acd6-1 lux-1 ZT13 rep2

city: Baltimore

first: HUA

last: LU

state: MD

address: 1000 Hilltop Circle

department: Biology

institute: University of Maryland Baltimore County

data_processing:
The CASAVA Software performs off-line image analysis and base calling,
Sequenced reads were trimmed for adaptor sequence and then mapped to Arabidopsis whole genome using CLC Genomics Workbench (Qiagen, Inc)
Genome_build: TAIR10
Supplementary_files_format_and_content: excel with RPKM values for each gene.

organism: Arabidopsis

source_name: acd6-1 lux-1 ZT13

growth_protocol: Plants were grown in growth chambers with a light intensity at 180 µmol m−2 s−1, 60% humidity and 22°C either in 12 h light/12 h dark (LD) cycle.

extract_protocol:
Genomic DNA extraction with CTAB.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: acd6-1 lux-1

value: whole plants

value: 25 day old

tag: collection time


title: VUB03_mt_1


title: VUB02_mt_2_4


title: BT3D [S86]

description:
blue light:dark, time point 3, replicate D
Sample name in processed data file:
S86

value: whole organism

value: blue light:dark

value: time point 3


title: 241_STEM_3h_0,5mM

description:
3h 0.5mM
241_5

source_name: EpOCs from Ctrl (241), 3h incubation, 0.5 mM butyrate stimulation


title: GT3A [S87]

description:
green light:dark, time point 3, replicate A
Sample name in processed data file:
S87

value: replicate A


title: VUB02_mt_2_3


title: BT3C [S85]

description:
blue light:dark, time point 3, replicate C
Sample name in processed data file:
S85


title: VUB03_BcL_XL_1


title: acd6-1 lux-1 ZT13 rep1


title: 241_STEM_3h_c-

description:
3h c-
241_4

source_name: EpOCs from Ctrl (241), 3h incubation, not stimulated

value: c-


title: VUB02_mt_2_2

value: hESC


title: 241_STEM_1h_5mM

description:
1h 5 mM
241_3

source_name: EpOCs from Ctrl (241), 1h incubation,  5 mM butyrate stimulation


title: BT3B [S84]

description:
blue light:dark, time point 3, replicate B
Sample name in processed data file:
S84


title: BT3A [S83]

description:
blue light:dark, time point 3, replicate A
Sample name in processed data file:
S83


title: 241_STEM_6h_c-

description:
6h c-
241_7

source_name: EpOCs from Ctrl (241), 6h incubation, not stimulated


title: VUB02_mt_2_1


title: acd6-1-0 ZT13 rep1


title: RT3D [S82]

description:
red light:dark, time point 3, replicate D
Sample name in processed data file:
S82

value: red light:dark


title: 237_DIFF_24h_0,5mM

description:
24h 0.5mM
237_23

source_name: d-EpOCs from Ctrl (237), 24h incubation, 0.5 mM butyrate stimulation

value: d-EpOCs


title: 241_STEM_1h_c-

description:
1h c-
241_1

source_name: EpOCs from Ctrl (241), 1h incubation, not stimulated


title: VUB02_mt_1_2


title: 237_DIFF_24h_5mM

description:
24h 5 mM
237_24

source_name: d-EpOCs from Ctrl (237), 24h incubation,  5 mM butyrate stimulation


title: acd6-1-0 ZT13 rep2


title: 241_STEM_1h_0,5mM

description:
1h 0.5mM
241_2

source_name: EpOCs from Ctrl (241), 1h incubation, 0.5 mM butyrate stimulation


title: RT3C [S81]

description:
red light:dark, time point 3, replicate C
Sample name in processed data file:
S81


title: lux-1 ZT13 rep1

source_name: lux-1 ZT13


title: VUB02_mt_1_1


title: lux-1 ZT13 rep2


title: Col-0 ZT13 rep3

source_name: Col-0 ZT13

value: wildtype


title: VUB01_mt_2


title: 237_DIFF_6h_5mM

description:
6h 5 mM
237_21

source_name: d-EpOCs from Ctrl (237), 6h incubation,  5 mM butyrate stimulation


title: 237_DIFF_24h_c-

description:
24h c-
237_22

source_name: d-EpOCs from Ctrl (237), 24h incubation, not stimulated


title: RT3A [S79]

description:
red light:dark, time point 3, replicate A
Sample name in processed data file:
S79


title: lux-1 ZT13 rep3


title: VUB01_mt_1


title: DT2D [S78]

description:
dark:dark, time point 2, replicate D
Sample name in processed data file:
S78

value: time point 2

value: replicate D


title: RT3B [S80]

description:
red light:dark, time point 3, replicate B
Sample name in processed data file:
S80

value: adult


title: DT2C [S77]

description:
dark:dark, time point 2, replicate C
Sample name in processed data file:
S77

value: replicate C


title: acd6-1 lux-1 ZT1 rep3

source_name: acd6-1 lux-1 ZT1


title: 237_DIFF_6h_0,5mM

description:
6h 0.5mM
237_20

source_name: d-EpOCs from Ctrl (237), 6h incubation, 0.5 mM butyrate stimulation


title: 237_DIFF_6h_c-

description:
6h c-
237_19

source_name: d-EpOCs from Ctrl (237), 6h incubation, not stimulated


title: 237_DIFF_3h_5mM

description:
3h 5 mM
237_18

source_name: d-EpOCs from Ctrl (237), 3h incubation,  5 mM butyrate stimulation


title: acd6-1 lux-1 ZT1 rep2


title: DT2B [S76]

description:
dark:dark, time point 2, replicate B
Sample name in processed data file:
S76

source_name: whole-organism

value: replicate B


title: DT2A [S75]

description:
dark:dark, time point 2, replicate A
Sample name in processed data file:
S75


title: acd6-1 lux-1 ZT1 rep1

value: acd6-1 lux-1


title: acd6-1-0 ZT1 rep3

value: whole plants


title: 237_DIFF_3h_c-

description:
3h c-
237_16

source_name: d-EpOCs from Ctrl (237), 3h incubation, not stimulated


title: 237_DIFF_1h_5mM

description:
1h 5 mM
237_15

source_name: d-EpOCs from Ctrl (237), 1h incubation,  5 mM butyrate stimulation


title: 237_DIFF_3h_0,5mM

description:
3h 0.5mM
237_17

source_name: d-EpOCs from Ctrl (237), 3h incubation, 0.5 mM butyrate stimulation


title: GT2D [S74]

description:
green light:dark, time point 2, replicate D
Sample name in processed data file:
S74

value: green light:dark


title: acd6-1-0 ZT1 rep2

value: 25 day old


title: GT2C [S73]

description:
green light:dark, time point 2, replicate C
Sample name in processed data file:
S73

value: whole organism


title: Col-0 ZT13 rep1


title: Col-0 ZT13 rep2


title: 237_DIFF_1h_0,5mM

description:
1h 0.5mM
237_14

source_name: d-EpOCs from Ctrl (237), 1h incubation, 0.5 mM butyrate stimulation


title: GT2A [S71]

description:
green light:dark, time point 2, replicate A
Sample name in processed data file:
S71


title: lux-1 ZT1 rep3

source_name: lux-1 ZT1


title: lux-1 ZT1 rep2


title: 237_DIFF_1h_c-

description:
1h c-
237_13

source_name: d-EpOCs from Ctrl (237), 1h incubation, not stimulated


title: BT2C [S69]

description:
blue light:dark, time point 2, replicate C
Sample name in processed data file:
S69

value: blue light:dark


title: Col-0 ZT1 rep3

source_name: Col-0 ZT1


title: lux-1 ZT1 rep1


title: BT2B [S68]

description:
blue light:dark, time point 2, replicate B
Sample name in processed data file:
S68


title: BT2D [S70]

description:
blue light:dark, time point 2, replicate D
Sample name in processed data file:
S70


title: 237_STEM_24h_5mM

description:
24h 5 mM
237_12

source_name: EpOCs from Ctrl (237), 24h incubation,  5 mM butyrate stimulation

value: Epithelial organoid cultures (EpOCs)


title: 237_STEM_24h_0,5mM

description:
24h 0.5mM
237_11

source_name: EpOCs from Ctrl (237), 24h incubation, 0.5 mM butyrate stimulation


title: acd6-1-0 ZT1 rep1


title: Col-0 ZT1 rep2


title: GT2B [S72]

description:
green light:dark, time point 2, replicate B
Sample name in processed data file:
S72


title: Col-0 ZT1 rep1


title: RT2C [S65]

description:
red light:dark, time point 2, replicate C
Sample name in processed data file:
S65


title: RT2D [S66]

description:
red light:dark, time point 2, replicate D
Sample name in processed data file:
S66


title: 237_STEM_6h_0,5mM

description:
6h 0.5mM
237_8

source_name: EpOCs from Ctrl (237), 6h incubation, 0.5 mM butyrate stimulation


title: 237_STEM_6h_c-

description:
6h c-
237_7

source_name: EpOCs from Ctrl (237), 6h incubation, not stimulated

value: c-


title: 237_STEM_3h_5mM

description:
3h 5 mM
237_6

source_name: EpOCs from Ctrl (237), 3h incubation,  5 mM butyrate stimulation


title: PNET_FFPE_10 RNA

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
RNA-seq reads were mapped to the hg19 reference genome using STAR 2.5.2 and GENCODE v19 annotations; reads with mapping scores <10 were discarded. Reads were counted by HTSeq-0.6.1.
Genome_build: hg19

source_name: pancreatic neuroendocrine tumors

extract_protocol:
We deparaffinized four 10-μm sections, rehydrated these in an ethanol/water series, and extracted RNA using AllPrep DNA/RNA FFPE kits (Qiagen). We measured concentrations using the Quant-iT RiboGreen RNA assay (Thermo Fisher) and assessed quality on an Agilent 2100 Bioanalyzer using the Agilent RNA 6000 Nano kit. Ribosomal and mitochondrial RNAs were removed using biotinylated, target-specific oligonucleotides combined with Ribo-Zero rRNA removal beads and the TruSeq Stranded Total RNA kit (Illumina).
We used 150 ng RNA to prepare libraries with TruSeq Stranded Total RNA kits (Illumina, cat #RS-122-2301).

tag: pnet subtype

value: A


title: 237_STEM_6h_5mM

description:
6h 5 mM
237_9

source_name: EpOCs from Ctrl (237), 6h incubation,  5 mM butyrate stimulation


title: RT2B [S64]

description:
red light:dark, time point 2, replicate B
Sample name in processed data file:
S64

value: red light:dark


title: RT2A [S63]

description:
red light:dark, time point 2, replicate A
Sample name in processed data file:
S63

value: replicate A


title: 237_STEM_24h_c-

description:
24h c-
237_10

source_name: EpOCs from Ctrl (237), 24h incubation, not stimulated


title: PNET_FFPE_9 RNA


title: PNET_FFPE_8 RNA


title: BT2A [S67]

description:
blue light:dark, time point 2, replicate A
Sample name in processed data file:
S67


title: mbn1

city: Fukuoka

first: Tetsuya

last: Sato

address: 3-1-1, Maidashi Higashi-ku

institute: Kyushu University

description: lymph gland tumor phenotye

data_processing:
Read quality was checked for each sample using FASTQC  (version 0.11.5).
Filterd reads were aligned to the reference D. melanogaster genome sequence (BDGP5) using the TopHat program version 2.0.6 with default parameters.
Cufflinks was employed with default parameters for transcript assembly. The expression level of each gene was quantified as FPKMs (fragments per kilo base of exon per million mapped fragments).
Genome_build: BDGP5
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each sample

organism: Drosophila melanogaster

source_name: 3rd instar larvae whole body

extract_protocol:
Total RNA was extracted from 3rd instar larvae using the Trizol reagent (Invitrogen, Carlsbad, CA, USA). The isolated RNAs were used for the construction of single-end mRNA-seq libraries, using a NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MS, USA) according to the manufacturer's recommendations. mRNA-seq was performed on an Illumina Hi-seq 1000 instrument (Illumina, San Diego, CA, USA) using 51-bp single-end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: gender

value: male

value: 3rd instar larvae

value: whole body


title: DT1D [S62]

description:
dark:dark, time point 1, replicate D
Sample name in processed data file:
S62

source_name: whole-organism

value: adult

value: time point 1

value: replicate D


title: DT1C [S61]

description:
dark:dark, time point 1, replicate C
Sample name in processed data file:
S61

value: replicate C


title: PNET_FFPE_7 RNA

value: B


title: G43

description: hypomorphic allele not displaying any tumor phenotype


title: DT1B [S60]

description:
dark:dark, time point 1, replicate B
Sample name in processed data file:
S60

value: replicate B


title: 237_STEM_1h_5mM

description:
1h 5 mM
237_3

source_name: EpOCs from Ctrl (237), 1h incubation,  5 mM butyrate stimulation


title: 237_STEM_1h_0,5mM

description:
1h 0.5mM
237_2

source_name: EpOCs from Ctrl (237), 1h incubation, 0.5 mM butyrate stimulation


title: 237_STEM_3h_0,5mM

description:
3h 0.5mM
237_5

source_name: EpOCs from Ctrl (237), 3h incubation, 0.5 mM butyrate stimulation


title: PNET_FFPE_5 RNA


title: DT1A [S59]

description:
dark:dark, time point 1, replicate A
Sample name in processed data file:
S59


title: CantonS

description: wild type

value: Canton S


title: 237_STEM_1h_c-

description:
1h c-
237_1

source_name: EpOCs from Ctrl (237), 1h incubation, not stimulated


title: PNET_FFPE_3 RNA


title: GT1D [S58]

description:
green light:dark, time point 1, replicate D
Sample name in processed data file:
S58

value: whole organism

value: green light:dark


title: 237_STEM_3h_c-

description:
3h c-
237_4

source_name: EpOCs from Ctrl (237), 3h incubation, not stimulated

value: Epithelial organoid cultures (EpOCs)


title: TS3LL

city: Oklahoma City

first: William

middle: Michael

last: McShan

state: OK

address: 1110 N. Stonewall Ave.

department: Pharmaceutical Sciences

institute: University of Oklahoma Health Sciences Center

description: TIGR4(SpnCI), Biological replicate 3

data_processing:
Raw data for each sample was analyzed using CLC Genomics Workbench version 11.0.1
Raw sequence reads were mapped to the TIGR4 Streptococcus pneumoniae genome (Accession AE005672.3)
Pairwise comparison of the expression results were performed using the total mapping results for TIGR4 SpnCI∆strA vs TIGR4
Differential gene lists were created with 3-fold expression cutoff and significant p values of less than or equal to 0.05 with a false discovery rate of 0.05 or less to identify genes that were up- or down-regulated under each condition.
RNA sequencing data was compiled from triplicate biological repeats.
Genome_build: Streptococcus pneumoniae TIGR4
Supplementary_files_format_and_content: Excel spreadsheet comparing TIGR4 with TIGR4(SpnCI)

organism: Streptococcus pneumoniae

source_name: Whole bacterial cell

growth_protocol: Incubator with 5% CO2

extract_protocol:
Trizol reagent (Life Technologies)
RNA libraries were prepared for sequencing using standard Illumina protocols with TruSeq V2 chemistry and methods.

treatment_protocol: Cells stored in RNA-Later until RNA extraction

tag: growth state

value: Late logarithmic

tag: temperature

value: 37 degreeC

tag: growth medium

value: Todd Hewitt Broth +lysed horse blood


title: PNET_FFPE_2 RNA

value: A


title: GT1C [S57]

description:
green light:dark, time point 1, replicate C
Sample name in processed data file:
S57

tag: tissue

tag: developmental stage


title: Leaves from combined stress treated gbf3 mutant, biological rep 2

city: New Delhi

first: Senthil-Kumar

last: Muthappa

address: Aruna Asaf Ali Road

country: India

institute: National Institute of Plant Genome Research

description: Gene expression data of leaves from combined  combined drought and P. syringae stressed Atgbf3 mutant plants

hyb_protocol: Suitable amount of fragmented and biotin-labeled ss-cDNA was mixed with hybridization master mix and was loaded onto array (GeneChip® Gene 1.0 ST, Cat # 901915, Affymetrix, USA). Loaded array was hybridized for 16 hr at 45C using Affymetrix GeneChip Hybridization oven 645. Hybridized chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Hybridized chips were scanned using Affymetrix GeneChip Scanner 7G.

data_processing: Raw intensity files (.CEL) were processed with using algorithm with Expression Console software (Affymetrix)

label_protocol: The ss-cDNA2 was purified and fragmented at dUTP residues and was terminally labelled with biotin using GeneChip® WT PLUS reagent kit (Cat # 902281, Affymetrix, USA) as per manufacturer instructions.

growth_protocol: Plants were grown in growth chamber (PGR15, Conviron, Canada) maintained at 12-h-light/12-h-dark photoperiod, 155 μE m−2s−1 light intensity, 20±1 °C temperature and 70% relative humidity. Plants were irrigated with water thrice in a week and fertilized with Hoagland solution (Cat # TS1094, Hi-media) though bottom once in a week.

extract_protocol: Isolation of leaf total RNA using RNeasy plant mini kit (Cat # 74904, Qiagen) following manufacturer's guidelines

treatment_protocol: Arabidopsis thaliana Col-0 plants (31-d-old) were exposed to progressive drought by withholding water. The soil moisture level (field capacity, FC) was monitored by gravimetric method. Gravimetric approach involved weighing of potted plants once in a day. Upon attaining 40% FC, plants were infiltrated with P. syringae pv. tomato DC3000 through abaxial side of leaves. Even after inoculation, water withholding was continued for plants to experience progressive drought stress. Leaf samples were collected at 24 hpi.

value: Leaves

tag: treatment


title: PNET_FFPE_1 RNA

value: C


title: Leaves from combined stress treated gbf3 mutant, biological rep 3

value: combined drought and P. syringae stressed


title: Leaves from combined stress treated Col-0, biological rep 3

description: Gene expression data of leaves from combined drought and P. syringae stressed Col-0 plants


title: Leaves from combined stress treated gbf3 mutant, biological rep 1


title: Leaves from combined stress treated Col-0, biological rep 2


title: PNET_12 RNA

extract_protocol:
A small piece of each snap-frozen primary tumor was pulverized using the T-prep method (Covaris, cat # 520097) on dry ice, followed by implementation of Agencourt RNAadvance (Beckman Coulter, cat # A32645) on a Biomek® FXP automation workstation (Beckman Coulter) to isolate RNA.
We used 150 ng RNA to prepare libraries with TruSeq Stranded Total RNA kits (Illumina, cat #RS-122-2301).


title: T3LL

description: TIGR4, Biological replicate 3


title: GT1A [S55]

description:
green light:dark, time point 1, replicate A
Sample name in processed data file:
S55

value: adult

tag: time point

tag: replicate

value: replicate A


title: GT1B [S56]

description:
green light:dark, time point 1, replicate B
Sample name in processed data file:
S56

value: time point 1


title: BT1D [S54]

description:
blue light:dark, time point 1, replicate D
Sample name in processed data file:
S54

value: blue light:dark

value: replicate D


title: PNET_11 RNA


title: PNET_10 RNA


title: T2LL

description: TIGR4, Biological replicate 2


title: TS1LL

description: TIGR4(SpnCI), Biological replicate 1


title: PNET_9 RNA


title: BT1C [S53]

description:
blue light:dark, time point 1, replicate C
Sample name in processed data file:
S53

value: replicate C


title: WT Replicate 2 T5

city: NEW YORK

middle: E.

last: Sause

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU School of Medicine

data_processing:
Raw reads were initially trimmed through the removal of Illumina adaptor sequences from 3' ends using cutadapt and by removing 3' end sequences if more than 20 bases with Q greater than or equal to 20 were present.
Paired end reads were mapped to the Staphylococcus aureus reference genome FPR3757 (NC_007793) using Bowtie2, and htseq-count was used to generate strand-specific count summaries.
Genome_build: NC_007793
Supplementary_files_format_and_content: log CPM normalized

organism: Staphylococcus aureus

source_name: Gram positive bacteria

growth_protocol: Overnight S. aureus strains were diluted 1:100 and grown at 37C in tryptic soy broth (TSB) for either 3 hours or 5 hours. Strains were incubated at a 45 degree angle while shaking at 180 RPM.

extract_protocol:
RNA was extracted using RNeasy kit (Qiagen)
Transcriptome sequencing (RNA-Seq) libraries were generated using an Illumina TruSeq Stranded Total RNA Library Prep kit, after ribodepletion was performed with an Epicenter Ribo-Zero Gold kit.

value: USA300 MRSA

tag: strain background

value: wild type


title: WT Replicate 1 T5

tag: genotype


title: BT1B [S52]

description:
blue light:dark, time point 1, replicate B
Sample name in processed data file:
S52

value: whole organism

value: replicate B


title: PP3 (RNA-Seq)

city: Nanjing

first: Shaowu

last: Yin

state: jiangsu

address: College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road,  210023, China.

institute: Nanjing Normal University

description: hybrid yellow catfish Huangyou-1 (P. fulvidraco ♀×P. vachelli ♂)

data_processing:
Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) including the Q20, Q30 and GC-content of the clean data.
All downstream analyses were based on clean data of high quality. De novo assembly of the transcriptome was performed with Trinity 2.4.0. Trinity groups transcripts into clusters based on shared sequence content.
Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene).
All assembled Unigenes were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/), Gene ontology (GO) (http://www.geneontology.org), SwissProt (http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.genome.jp/kegg/) and eggNOG (http://eggnogdb.embl.de/) databases using DIAMOND [3] with a threshold of E-value<0.00001.
Supplementary_files_format_and_content: TPMs

organism: Tachysurus fulvidraco x Tachysurus vachelli

source_name: liver

growth_protocol: Parental fish of P. fulvidraco and P. vachelli were obtained from Nanjing Fisheries Research Institute. Fish breeding and cultivation were performed at Nanjing Normal University at Jiangsu Province, China. Artificial fertilization of M ♀ × M ♂, F ♀ × F ♂, and F ♀ × M ♂ were conducted through manually abdominal compression for harvesting eggs from female and stripping sperm from male after hormone injections.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s protocol. The total RNA quantity and purity were analysed with Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
For nine cDNA library constructions (M1, M2, M3, F1, F2, F3, H1, H2 and H3), approximately 10 μg of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 2500 at the LC-BIO (Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: Obtained fertilized eggs (M, F, and H) were incubated at a water temperature of 28°C in flow-through water until hatching. Three lines were fed with live Artemia nauplii to satiation thrice-daily until the mouth gape sizes for all fish matched the size of the artificial compound feed. The feed was slightly over-supplied based on the previous consumption. 600 juvenile fish of M were averagely reared in 3 aquaria (200 individuals / 700 L of volume with bio-filtered water recirculation system) with same stocking density. The treatment procedure for F and H were also followed as the description of M.

value: juvenile fish

value: liver


title: WT Replicate 1 T3

tag: strain


title: Leaves from combined stress treated Col-0, biological rep 1


title: WT Replicate 2 T3


title: Leaves from mock treated gbf3 mutant, biological rep 2

description: Gene expression data of leaves from mock treated Atgbf3 plants

source_name: Leaves from mock treated gbf3 mutant

value: mock


title: Leaves from mock treated gbf3 mutant, biological rep 1


title: PP2 (RNA-Seq)


title: PNET_7 RNA


title: PNET_6 RNA

value: B


title: dpurR Replicate 2 T5

value: dpurR


title: PP1 (RNA-Seq)


title: Leaves from mock treated Col-0, biological rep 1

description: Gene expression data of leaves from mock treated Col-0 plants

source_name: Leaves from mock treated Col-0

value: Leaves


title: RT1D [S50]

description:
red light:dark, time point 1, replicate D
Sample name in processed data file:
S50

value: red light:dark


title: PP3 (miRNA-Seq)

data_processing:
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 21.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 21.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤20). (6) number of nucleotides in one bulge in mature region (≤8) (7) number of biased errors in one bulge in mature region (≤4) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤7) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: normalized_counts

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA libraries (M1, M2, M3, F1, F2, F3, H1, H2 and H3) according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.


title: dpurR Replicate 1 T5


title: PNET_5 RNA


title: PNET_3 RNA

value: A


title: RT1C [S49]

description:
red light:dark, time point 1, replicate C
Sample name in processed data file:
S49

value: adult


title: PP2 (miRNA-Seq)


title: dpurR Replicate 2 T3


title: RT1B [S48]

description:
red light:dark, time point 1, replicate B
Sample name in processed data file:
S48

value: time point 1


title: PP1 (miRNA-Seq)


title: RT1A [S47]

description:
red light:dark, time point 1, replicate A
Sample name in processed data file:
S47

value: replicate A


title: dpurR Replicate 1 T3


title: PNET_1 RNA


title: 016_Pds5_eco1_rad61_WCE

status: Public on Jun 11 2019

city: Oxford

first: Christophe

last: Chapard

address: South Parks road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
Library sequencing was carried out on the Ion Torrent Proton
The quality of the raw sequence data was examined using FastQC (Galaxy tool version 1.0.0) and trimming of reads was carried out using “trim sequences” (Galaxy tool version 1.0.0)
Any reads smaller than 50bp were removed using ‘Filter FASTQ’
The final reads were aligned to the Saccharomyces cerevisiae genome (sacCer3, SGD) or Candida glabrata genome (CBS138, genolevures) using Bowtie2 (Galaxy tool version 0.2) with the default (--sensitive) parameters
To generate an alignment in which all the sequences exclusively align to the Saccharomyces cerevisiae genome, the whole reads were first aligned to Candida glabrata genome and the unaligned reads were retrieved as a separate Fastq file. Subsequently, these unaligned reads were re-aligned to Saccharomyces cerevisiae genome and the resulting aligned BAM file therefore contained reads that were unique to Saccharomyces cerevisiae. A same strategy was used to generate alignments unique to Candida glabrata.
Genome_build: SacCer3 or Candida glabrata (ASM254v2)
Supplementary_files_format_and_content: bigwig files

organism: Saccharomyces cerevisiae

source_name: pds5-pk rad61 eco1(G211H) strain arrested in G1 with pheromone and released in nocodazole at 37C (K27341)

growth_protocol: Yeast cells were grown in YPD to reach a density of 0.3-0.6 OD600.

extract_protocol:
To crosslink cells, 45ml of yeast culture was mixed with 4.2ml of fixation solution (50mM Tris-HCl pH 8.0, 100mM NaCl, 0.5mM EGTA, 1mM EDTA, 30% Formaldehyde) and incubated at 18°C for 30 minutes. The crosslinking reaction was quenched by incubating with 2ml of 2.5M Glycine for 5 min. Fixed cells were harvested, washed with ice-cold PBS and re-suspended in 1ml of ChIP lysis buffer (50mM Hepes-KOH pH 8.0, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1mM PMSF, Roche protease inhibitor). For each ChIP, 15 OD600 units of Saccharomyces cerevisiae cells mixed with 3 OD600 units of Candida glabrata cells were pelleted and re-suspended in 0.3ml of ChIP lysis buffer. Cells were mixed with glass beads and disrupted by FastPrep®-24 (MP Biomedicals, USA). The entire lysis was collected and sonicated at 4°C for 40 minutes using a Bioruptor (Diagenode, Belgium). The cell debris were removed by centrifugation and supernatants containing sheared chromatin with a size range from 100-800bp were adjusted to a final volume of 1ml with ChIP lysis buffer. Extracts were pre-cleared for 1 hour at 4°C with 30µl of Protein G Dynabeads (Invitrogen). 80µl of supernatant was taken as whole cell extract (W) and stored at -80°C. Five µg of anti-PK antibody (Bio-Rad) and 50 µl of Protein G Dynal beads (Invitrogen) was used for immunoprecipitation (6 hours-overnight, rotation at 4°C). The beads were subsequently washed for 5 minutes with the following buffers: 2Ã—ChIP lysis buffer; 3x ChIP high-salt lysis buffer (50mM Hepes-KOH pH 8.0, 500mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1mM PMSF); 2Ã—ChIP wash buffer (10mM Tris-HCl pH 8.0, 0.25M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1mM EDTA, 1mM PMSF) and 1x TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA, 50mM NaCl). The immunoprecipitated chromatin was eluted by incubation of beads with 120µl of TES buffer (50mM Tris-HCl pH 8.0; 10mM EDTA; 1% SDS) at 65°C for 15 minutes. The supernatants were collected and termed the IP sample. The whole cell extract sample (W) was mixed with 40µl of TES3 buffer (50mM Tris-HCl pH 8.0; 10mM EDTA; 3% SDS). Both samples were de-crosslinked at 65°C overnight. RNA was degraded by incubating with 2-µl of RNAse A (10mg/ml, Roche) at 37°C for 1 hour and protein was subsequently removed by incubation with 10µl of Proteinase K (18mg/ml, Roche) at 65°C for 2 hours. DNA was purified using ChIP DNA Clean & Concentrator kit (Zymo Research, USA).
NEBNext Fast DNA Library Prep set for Ion Torrent, E6270

treatment_protocol: arrest in G1 with pheromone and release in nocodazole at 37C

value: Saccharomyces cerevisiae cells

tag: sac_cer strain

tag: can_gla strain

tag: antibody

value: none (input)

value: pds5-pk rad61 eco1(G211H)


title: 013_Pds5_WT_WCE

source_name: pds5-pk wild type strain arrested in G1 with pheromone and released in nocodazole at 37C (K27339)

value: pds5-pk wild type


title: BT1A [S51]

description:
blue light:dark, time point 1, replicate A
Sample name in processed data file:
S51

extract_protocol:
Whole-organism RNA was extracted from animals (that were preserved in RNAlater and stored at -80) using Ambion RNAqueous extraction kit.
Libraries were prepared as in Meyer et al. (2011)

value: whole organism

value: blue light:dark


title: 014_Pds5_rad61_WCE

source_name: pds5-pk rad61 strain arrested in G1 with pheromone and released in nocodazole at 37C (K27342)

value: pds5-pk rad61


title: 012_Scc1_eco1_rad61_WCE

source_name: scc1-pk rad61 eco1(G211H) strain arrested in G1 with pheromone and released in nocodazole at 37C (K25298)

value: scc1-pk rad61 eco1(G211H)


title: Leaves from mock treated Col-0, biological rep 2

value: mock


title: 009_Scc1_WT_WCE

source_name: scc1-pk wild type strain arrested in G1 with pheromone and released in nocodazole at 37C (K14601)

value: scc1-pk wild type


title: 008_Pds5_eco1_rad61

value: anti-PK antibody (Bio-Rad)


title: 011_Scc1_eco1_WCE

source_name: scc1-pk eco1(G211H) strain arrested in G1 with pheromone and released in nocodazole at 37C (K16521)

value: scc1-pk eco1(G211H)


title: 006_Pds5_rad61


title: 005_Pds5_WT


title: 001_Scc1_WT


title: 002_Scc1_rad61

source_name: scc1-pk rad61 strain arrested in G1 with pheromone and released in nocodazole at 37C (K18704)

value: scc1-pk rad61


title: 010_Scc1_rad61_WCE


title: 004_Scc1_eco1_rad61


title: 015_Pds5_eco1_WCE

source_name: pds5-pk eco1(G211H) strain arrested in G1 with pheromone and released in nocodazole at 37C (K27340)

value: pds5-pk eco1(G211H)


title: 9444374158_R02C01

city: Newcastle upon Tyne

first: Ed

last: Schwalbe

address: Ellison Place

department: Applied Sciences

institute: Northumbria University

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 and Infinium MethylationEPIC Beadchips using standard Illumina protocol.

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

data_processing:
Arrays were imported and quality control performed using minfi.
Beta values - A correction for the type of material (FFPE/frozen) was performed by using the removeBatchEffect function of the limma package v.3.24.15. The log2-transformed intensities of the methylated and unmethylated signal were corrected individually. Beta-values were calculated from the retransformed intensities using an offset of 100 (as recommended by Illumina) and used for all downstream analyses.
GSE130051_beta_values.csv: Beta values; Rows are Samples, columns are ID_REFs.
GSE130051_transposed_beta_values.csv: Beta values; Rows are ID_REFs, columns are Samples.

source_name: medulloblastoma

label_protocol: Standard Illumina protocol.

extract_protocol: Genomic DNA was extracted and purified from medulloblastoma samples using standard extraction protocols.

tag: cohort

value: Previously unpublished - sample from St. Jude collection

value: Medulloblastoma

tag: subgroup

tag: subtype


title: 9610361022_R03C01


title: 003_Scc1_eco1


title: 200517420053_R03C01

value: MBNOS


title: 200514090108_R01C02


title: 200511460046_R01C01


title: 200400320088_R03C01


title: 200400320010_R05C02


title: 200400320010_R04C01


title: 200397860069_R04C01


title: 007_Pds5_eco1

value: Saccharomyces cerevisiae cells


title: 200397860069_R01C02


title: D2121/13: ASD patient

city: Olomouc

first: Zuzana

last: Čapková

state: Czech Republic

address: I.P. Pavlova 6

department: Department of Medical Genetics

country: Czech Republic

institute: University Hospital Olomouc

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: The array image was acquired using Affymetrix GeneChip® Command Console (version 4.0.0.1567G). Copy number values were extracted and converted from CEL files into CYCHP files using Chromosome Analysis Suite software (v.3.3.0.139) in default manner using CYTO2 algorythm v.s. 2.2.0. Reference file was CytoScan HD Array.na33.r2, ChAS Browser was NefAffx Build hg19 (20170803).

label: Biotin

source_name: Peripheral blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from mononuclear cell  of peripheral blood using saline method. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: diagnosis

value: autism spectrum disorders (ASD)

tag: gender

value: F

tag: facial dysmorphia

value: no


title: D254/14: ID patient

value: intellectual disabilities (ID)

value: M


title: D1365/13: ASD patient

value: yes


title: 200397860056_R03C01

tag: tissue


title: 200397860039_R01C01


title: 200397860023_R02C01


title: D1567/13: ID patient


title: 200397860003_R03C01


title: 200397540067_R06C01


title: 200397540067_R01C02


title: 200397860003_R05C01


title: 200397540001_R06C02


title: 200397540002_R01C02


title: 200406080086_R04C01


title: 200397540001_R03C02


title: 200394970024_R01C02


title: 200394870113_R04C01


title: 200379120124_R06C02


title: 200362700194_R04C01


title: 200379120101_R02C02


title: 200362700194_R03C02


title: 200362700194_R03C01


title: 200397860056_R04C01


title: 200362700174_R02C02


title: 200360420060_R05C01


title: 200360420062_R06C02


title: 200325530167_R01C01


title: 200360420060_R02C01


title: 200325530167_R02C02


title: 200360420061_R03C01


title: 200325530103_R04C02


title: 200325530103_R02C02


title: 200325530044_R03C01


title: 200325530024_R04C01


title: 9969477111_R03C02

value: Northcott et al. 2017 (PMID:28726821)


title: 9969477099_R05C02


title: 9969477111_R01C02


title: 200256300118_R06C02


title: 9969477099_R04C02


title: 200362700174_R06C01


title: 9969477090_R06C01


title: 9969477090_R05C01


title: 9969477090_R01C02


title: 9969477017_R01C02


title: 9969477061_R04C01


title: 9968646113_R04C01


title: 9968646113_R01C01


title: 9934987136_R05C02


title: 9934987115_R05C01


title: 9934987115_R04C02


title: 9934987115_R04C01


title: 9934987115_R03C02


title: 9934987115_R03C01


title: 9934987115_R02C02


title: 9934987115_R01C02


title: TS2LL

description: TIGR4(SpnCI), Biological replicate 2

tag: growth state

value: Late logarithmic

tag: temperature

value: 37 degreeC

tag: growth medium

value: Todd Hewitt Broth +lysed horse blood


title: 9934987105_R05C01


title: 9934987105_R04C02


title: 200325530023_R03C02


title: 9934987105_R04C01


title: 9969477111_R06C01


title: 9934987105_R03C01


title: 9934987115_R02C01


title: 9934987105_R02C01


title: 9934987105_R02C02


title: 9934987103_R06C02


title: 9934987103_R06C01


title: 9934987103_R04C02


title: 9934987103_R05C01


title: 9934987103_R02C02


title: 9934987103_R01C01


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