title: colon_control_day14_rep8

city: Wageningen

first: Dirkjan

last: Schokker

department: Wageningen Livestock Research

institute: Wageningen UR

description: totalRNA scraping

hyb_protocol: The hybridization temperature is 65°C with rotation speed 10 rpm for 17 hours. After 17 hours the arrays are washed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling protocol from Agilent.

scan_protocol: The arrays where scanned using the DNA microarray scanner with SureScan High-Resolution Technology from Agilent Technologies. Agilent Scan Control with resolution of 5 µm, 16 bits and PMT of 100%. Feature extraction was performed using protocol 10.7.3.1 (v10.7) for 1 colour gene expression.

data_processing: The data were analysed by using R (v3.0.2) by executing different packages, including LIMMA (Gentleman et al., 2005) and arrayQualityMetrics (Kauffmann et al., 2009). The data were read in and background corrected (method=normexp and offset=1) with functions from the R package LIMMA (Gentleman et al., 2005) from Bioconductor (Gentleman et al., 2004). Quantile normalisation of the data was done between arrays. The duplicate probes mapping to the same gene were averaged (‘avereps’) and subsequently the lower percentile of probes were removed in a three-step procedure, 1) get the highest of the dark spots to get a base value, 2) multiply by 1.1, and 3) the gene/probe must be expressed in each of the samples in the experimental condition.

organism: Sus scrofa

source_name: colon, control, day14

label_protocol: Labelling of RNA was done as recommended by Agilent Technologies using the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling. The input was 10 ng of total RNA and 600 ng of labelled cRNA is used on the eight pack array. Hybridization was performed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling protocol from Agilent in the hybridization oven (G2545A hybridization Oven Agilent Technologies).

growth_protocol: All sows had at least 14 piglets born alive in their litter. Size of the litters was limited to 14 piglets by cross fostering piglets to other sows. Piglets were not given access to creep feed or a milk replacer during the lactation period.

extract_protocol: Total RNA was extracted from 50 to 100 mg jejunum or colon tissue. All samples were homogenised using the TisuPrep Homogenizer Omni TP TH220P) in TRizol reagent (Life Technologies) as recommended by the manufacturer with minor modifications. The homogenised tissue samples were dissolved in 5 ml of TRizol reagent. After centrifugation the supernatant was transferred to a fresh tube. Subsequently, Direct-zol™ RNA MiniPrep Kit by Zymo Research was used as described by the manufacturer. The RNA was quantified by absorbance measurements at 260 nm. Quality Control was performed by Agilent Bioanalyser.

treatment_protocol: The dietary intervention was administered from day 2 to 14 of age, piglets in each litter got twice a day an oral administration of either water (control, n=8) or 5 gram fructooligosaccharides (FOS) dissolved in water (FOS, n=6). Due to observed vomiting of the piglets in the first week, not quantitatively determined, the volume of oral administration was changed from day 7 onwards from 15 ml to 6 ml, which had no consequence on the dosage of FOS. The FOS preparations used for this experiment was Frutafit® TEX! (lcFOS) and Frutalose® OFP (scFOS) from SENSUS. Both FOS are from chicory and a polydispersed mixture of linear fructose polymers with mostly a terminal glucose unit, coupled by means of β(2-1) bonds. The number of units (degree of polymerization) can vary between 2-60 (lcFOS) or 3-10 (scFOS). The mixture used in this study was based upon the recommendation for use in babies (Boehm et al., 2003), being a 9:1 ratio, 90% scFOS and 10% lcFOS.

value: colon

tag: age (days)

value: control


title: Tfam (L/L, cre) rep3

status: Public on Jan 29 2018

type: SRA

city: Bentley

first: Irina

last: Kuznetsova

state: WA

address: Building 304, Kent Street

department: The Centre for Crop and Disease Management

country: Australia

institute: Curtin University

description:
55255 ko
gene_count_matrix_tfam_strain.csv
DESeq2_results_tfam_strain.csv

library_source: transcriptomic

data_processing:
HISAT2 version 2.0.4 (hisat2 -p 8 –dat) was used to perform alignment of paired-end reads to the Mus Musculus reference genome (GRCm38). The output files were sorted and indexed with SAMtools version 1.3.1
StringTie version 1.2.4  (stringtie -p 18 -e -B) was applied to estimate transcripts abundance
prepDE.py (http://ccb.jhu.edu/software/stringtie/dl/prepDE.py) Python version 2.7.6 was used to extract raw counts
DESeq2 R package version 3.3.2 was used for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: gene_count_matrix_tfam_strain.csv (Raw counts)
DESeq2_results_tfam_strain.csv (DESeq2 results)

molecule: total RNA

organism: Mus musculus

source_name: heart

growth_protocol: Total RNA isolated from hearts

extract_protocol: standard TruSeq library preparation

tag: strain background

tag: genotype/variation

value: Tfam (L/L, cre)

tag: age


title: colon_FOS_day14_rep4

type: RNA

address: Droevendaalsesteeg 1

country: Netherlands

description: totalRNA scraping

source_name: colon, FOS, day14

tag: tissue

tag: treatment

value: FOS


title: colon_FOS_day14_rep6

description: totalRNA scraping


title: colon_control_day14_rep3

description: totalRNA scraping


title: colon_FOS_day14_rep2

description: totalRNA scraping


title: colon_control_day14_rep4

description: totalRNA scraping


title: colon_control_day14_rep7

description: totalRNA scraping


title: colon_control_day14_rep1

description: totalRNA scraping


title: colon_control_day14_rep6

description: totalRNA scraping


title: jejunum_control_day25_rep5

description: totalRNA scraping

source_name: jejunum, control, day25

value: jejunum


title: colon_FOS_day14_rep1

description: totalRNA scraping


title: jejunum_FOS_day25_rep3

description: totalRNA scraping

source_name: jejunum, FOS, day25


title: colon_control_day14_rep2

description: totalRNA scraping


title: jejunum_FOS_day25_rep4

description: totalRNA scraping


title: jejunum_control_day25_rep6

description: totalRNA scraping


title: jejunum_FOS_day25_rep5

description: totalRNA scraping


title: jejunum_control_day25_rep7

description: totalRNA scraping


title: colon_FOS_day14_rep3

description: totalRNA scraping


title: colon_FOS_day14_rep5

description: totalRNA scraping


title: colon_control_day14_rep5

description: totalRNA scraping


title: jejunum_FOS_day25_rep2

description: totalRNA scraping


title: jejunum_FOS_day25_rep6

description: totalRNA scraping


title: jejunum_control_day25_rep8

description: totalRNA scraping


title: jejunum_FOS_day25_rep7

description: totalRNA scraping


title: jejunum_FOS_day14_rep6

description: totalRNA scraping

source_name: jejunum, FOS, day14


title: jejunum_FOS_day25_rep8

description: totalRNA scraping


title: jejunum_control_day25_rep2

description: totalRNA scraping


title: jejunum_control_day25_rep1

description: totalRNA scraping


title: jejunum_FOS_day14_rep5

description: totalRNA scraping


title: jejunum_FOS_day25_rep1

description: totalRNA scraping


title: jejunum_control_day14_rep6

description: totalRNA scraping

source_name: jejunum, control, day14


title: jejunum_control_day14_rep7

description: totalRNA scraping


title: jejunum_control_day14_rep8

description: totalRNA scraping


title: jejunum_FOS_day14_rep2

description: totalRNA scraping


title: jejunum_control_day25_rep3

description: totalRNA scraping


title: jejunum_control_day25_rep4

description: totalRNA scraping


title: jejunum_control_day14_rep5

description: totalRNA scraping


title: jejunum_control_day14_rep4

description: totalRNA scraping


title: jejunum_FOS_day14_rep4

description: totalRNA scraping


title: jejunum_control_day2_rep7

description: totalRNA scraping

source_name: jejunum, control, day2


title: jejunum_control_day2_rep6

description: totalRNA scraping


title: jejunum_control_day14_rep2

description: totalRNA scraping


title: RM_FSU_RNA1407-16_all_RNAseq

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

data_processing:
Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step.
Reads were mapped using STAR (2.4.1d).
Reads per gene were counted using featureCounts (1.4.6-p4).
Counts were normalized to RPKM values as described in Mortazavi et al. (2008).
Genome_build: genome: WBcel235, and respective gene annotation (WBcel235.84)
Supplementary_files_format_and_content: The Excel files include raw counts (sample_counts.xls) and RPKM values (sample_rpkms.xls) of all genes for each sample.

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans wildtype strain (N2) treated with T25B9.1 RNAi for  5 days after L4 larvae stage

extract_protocol:
Extraction was done as described in Baumgart et al. 2012. (PMID:22487494)
Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.

tag: strain

value: all

value: 5 days

tag: Sex

value: hermaphrodite

tag: perturbation

tag: genotype

value: wildtype


title: RM_FSU_RNA1407-23_all_RNAseq


title: jejunum_FOS_day14_rep1

description: totalRNA scraping


title: RM_FSU_RNA1407-19_all_RNAseq


title: RM_FSU_RNA1407-24_all_RNAseq


title: jejunum_control_day14_rep3

description: totalRNA scraping


title: jejunum_control_day14_rep1

description: totalRNA scraping


title: jejunum_control_day2_rep4

description: totalRNA scraping


title: jejunum_control_day2_rep1

description: totalRNA scraping


title: jejunum_control_day2_rep5

description: totalRNA scraping


title: jejunum_control_day2_rep3

description: totalRNA scraping


title: RM_FSU_RNA1407-20_all_RNAseq


title: jejunum_control_day2_rep2

description: totalRNA scraping


title: RM_FSU_RNA1407-15_all_RNAseq


title: Enterobacter C7-inoculated never ripe root under drought conditions, biological rep2

city: Granada

first: Pablo

last: Ibort Pereda

state: Granada

address: Profesor Albareda 1

department: Microbiología del Suelo y Sistemas Simbióticos

country: Spain

institute: Spanish National Research Council (EEZ-CSIC)

description:
Gene expression data from never ripe tomato roots inoculated with the PGPB strainEnterobacter C7 coming from plants grown under drought conditions.
NRC7D_2

hyb_protocol: After purification and fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Tomato Genome Array. Standard post-hybridization wash and double-stain protocols were used on an Affymetrix GeneChip fluidics station 450.

scan_protocol: GeneChips were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Data were analyzed with statistical tool LIMMA (Linear Models for Microarrays Analysis) by using affylmGUI in R software (v3.2.2 Open Source; http://www.r-project.org/).

label: biotin

organism: Solanum lycopersicum

source_name: Never ripe plants inoculated with Enterobacter C7 grown under drought conditions

label_protocol: Target complementary RNA (cRNA) labelled with biotin was prepared using the BioArray high-yield RNA transcript labeling kit (Enzo Biochem, New York).

growth_protocol: Seeds were sterilized (70% ethanol 5 min, 5% sodium hypochlorite 10 min and 3 washing steps with sterile water to remove any trace of chemicals), kept at 4ºC overnight and placed on sterile vermiculite at 25ºC until germination. Ten-days-old seedlings were transferred to 1 l plastic pots containing sterile peat moss:perlite (1:1, v:v, autoclaved twice at 120°C for 20 min). Plants were grown in a greenhouse under controlled conditions (18-24°C, 50-60% relative humidity, 16 h:8 h light (600 μmol m-2 s-1):dark).  All plants were grown for four weeks under well-watered conditions and the watering regime treatment was applied thereafter for other four weeks keeping half of the plants under well-watered conditions and the other half under drought conditions.

extract_protocol: Total RNA was isolated from root tissue from 3 different plants of each treatment (n=3) using RNeasy Plant Mini Kit (Qiagen Cat#74904, California, USA) according to instructions of manufacturer.

treatment_protocol: Bacteria were grown in Luria broth (LB) medium with shaking (200 rpm) at 28ºC overnight. The culture optical density was measured at 600 nm (OD600), the cells were centrifuged (2655 g, 10 min) and the pellet was resuspended in sterile distilled water until OD600 = 1.5 corresponding to a cell density of 107 CFU ml-1. One ml of distilled water (control plants), or a bacterial suspension: Bm or C7 (inoculated plants) was added to each root seedling at transplantation.                                                                                Eight pots of 1 l containing the above mentioned substrate were watered until saturation and let them to drain for 24 hours. Pot weights (water-holding capacity of 100 %) were measured resulting in weight mean of 640.10 g. These pots were dried in a forced draught oven (70ºC, 7 days) and pot dry weights (water-holding capacity of 0 %) were determined again resulting in weight mean of 163.91 g. Thus, watering regime treatments were performed estimating the grams of water that one gram of substrate is able to contain by extrapolating water-holding capacity (WHC) to substrate weight (SW) in our experimental system and following the equation: SW = 4.7568*WHC + 163.91. All plants were grown for four weeks under well-watered conditions supplying water every two days in order to maintain constant soil water content close to 100 % WHC which corresponds to 640.10 g. Watering regime treatments was applied thereafter by watering plants up to water-holding capacity of 100 % (640.10 g) or 60 % (448.10 g) for well-watered and drought conditions, respectively.

value: Pearson cv. Never ripe mutation

tag: inoculated with

value: Enterobacter C7

tag: growth condition

value: drought conditions

value: 8 weeks post-inoculation

value: Roots


title: Bacillus megaterium-inoculated never ripe root under drought conditions, biological rep2

description:
Gene expression data from never ripe tomato roots inoculated with the PGPB strain Bacillus megaterium coming from plants grown under drought conditions.
NRBMD_2

source_name: Never ripe plants inoculated with Bacillus megaterium grown under drought conditions

value: Bacillus megaterium


title: Enterobacter C7-inoculated never ripe root under drought conditions, biological rep1

description:
Gene expression data from never ripe tomato roots inoculated with the PGPB strainEnterobacter C7 coming from plants grown under drought conditions.
NRC7D_1


title: Bacillus megaterium-inoculated never ripe root under drought conditions, biological rep3

description:
Gene expression data from never ripe tomato roots inoculated with the PGPB strain Bacillus megaterium coming from plants grown under drought conditions.
NRBMD_3


title: Bacillus megaterium-inoculated never ripe root under well-watered conditions, biological rep3

description:
Gene expression data from never ripe tomato roots inoculated with the PGPB strain Bacillus megaterium coming from plants grown under well-watered conditions.
NRBM_3

source_name: Never ripe plants inoculated with Bacillus megaterium grown under well-watered conditions

value: well-watered conditions


title: Ctrl3

city: Lausanne

first: Romano

last: Regazzi

address: Rue du Bugnon 9

department: Department of fundamental neurosciences

country: Switzerland

institute: University of Lausanne

description: Gene expression after 48 h of incubation

hyb_protocol: The labeled cRNAs were hybridized onto the Mouse Gene Expression Microarray v2 (4 x 44K, Agilent Technologies) based on the manufacturer’s standard protocols.

scan_protocol: Slides were scanned immediately after washing on the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

source_name: MIN6B1 cells, siGFP transfection, replicate 3

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent Cyanine-3 (cy3) cRNA using the manufacturer’s Agilent’s Quick Amp Labeling protocol.

extract_protocol: RNA was extracted using the miRNeasy kit (Qiagen), according to manufacturer guidelines.

treatment_protocol: MIN6B1 cells were incubated in culture medium (DMEM Glutamax medium supplemented with supplemented with 15 % fetal calf serum, 50 U/ml penicillin, 50 µg/ml streptomycin, and 70 µM β-mercaptoethanol) and cells were transfected with siGFP (Control) or circHIPK3 siRNA for 48 h with Lipofecatime RNAiMax.

value: MIN6B1 cells


title: Non-inoculated never ripe root under drought conditions, biological rep3

description:
Gene expression data from never ripe tomato roots non-inoculated with a plant growth-promotion bacteria (PGPB) coming from plants grown under drought conditions.
NRNOD_3

source_name: Never ripe plants non-inoculated grown under drought conditions

value: none (control)


title: Non-inoculated never ripe root under drought conditions, biological rep2

description:
Gene expression data from never ripe tomato roots non-inoculated with a plant growth-promotion bacteria (PGPB) coming from plants grown under drought conditions.
NRNOD_2


title: SH1

source_name: MIN6B1 cells, si circHIPK3 transfection, replicate 1


title: Bacillus megaterium-inoculated never ripe root under drought conditions, biological rep1

description:
Gene expression data from never ripe tomato roots inoculated with the PGPB strain Bacillus megaterium coming from plants grown under drought conditions.
NRBMD_1


title: WM983B_corin2_24h_rep2

city: Baltimore

first: Jay

middle: Hans

last: Kalin

state: MD

address: 725 N. Wolfe St., Hunterian 314

department: Pharmacology and Molecular Sciences

country: USA

institute: Johns Hopkins University

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Affiymetrix GeneChip scanner 3000 with G7 upgrade and default parameters (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA).

data_processing:
Affymetrix CEL files were extracted and their raw data RMA normalized with the Partek GS 6.6 platform.  The exons were summarized to create quantile-normalized log2 gene-level signal values, which were used in subsequent ANOVA analyses.
HuGene-2_0-st.pgf
HuGene-2_0-st-v1.na35.hg19.transcript.csv

organism: Homo sapiens

source_name: WM983B melanoma cells, 2.5 µM corin2 treated, 24 h

label_protocol: The Ambion Expression WT kit was used as described in the manufacturer's manual.

growth_protocol: WM983B melamona cells were cultured in DMEM supplemented with 10% FBS and 1% Penicillin/Streptomycin at 37 °C in a 5% CO2 atmosphere

extract_protocol: RNA was isolated from cells using an RNeasy Plus Mini kit available from Qiagen Inc. according to the manufacturer's instructions

treatment_protocol: 10 mM inhibitor stocks were prepared in DMSO, cells were treated with either 2.5 µM corin2, 2.5 µM MS-275, or a corresponding amount of DMSO for 24 h

tag: cell line

value: melanoma cell line WM983B

tag: agent

tag: dose


title: Enterobacter C7-inoculated never ripe root under well-watered conditions, biological rep2

description:
Gene expression data from never ripe tomato roots inoculated with the PGPB strainEnterobacter C7 coming from plants grown under well-watered conditions.
NRC7_2

source_name: Never ripe plants inoculated with Enterobacter C7 grown under well-watered conditions


title: SH3

source_name: MIN6B1 cells, si circHIPK3 transfection, replicate 3


title: SH2

source_name: MIN6B1 cells, si circHIPK3 transfection, replicate 2


title: Ctrl2

source_name: MIN6B1 cells, siGFP transfection, replicate 2


title: Non-inoculated never ripe root under well-watered conditions, biological rep3

description:
Gene expression data from never ripe tomato roots non-inoculated with a plant growth-promotion bacteria (PGPB) coming from plants grown under well-watered conditions.
NRNO_3

source_name: Never ripe plants non-inoculated grown under well-watered conditions


title: Enterobacter C7-inoculated never ripe root under drought conditions, biological rep3

description:
Gene expression data from never ripe tomato roots inoculated with the PGPB strainEnterobacter C7 coming from plants grown under drought conditions.
NRC7D_3


title: Non-inoculated never ripe root under drought conditions, biological rep1

description:
Gene expression data from never ripe tomato roots non-inoculated with a plant growth-promotion bacteria (PGPB) coming from plants grown under drought conditions.
NRNOD_1


title: Bacillus megaterium-inoculated never ripe root under well-watered conditions, biological rep2

description:
Gene expression data from never ripe tomato roots inoculated with the PGPB strain Bacillus megaterium coming from plants grown under well-watered conditions.
NRBM_2


title: Ctrl1

source_name: MIN6B1 cells, siGFP transfection, replicate 1


title: Enterobacter C7-inoculated never ripe root under well-watered conditions, biological rep1

description:
Gene expression data from never ripe tomato roots inoculated with the PGPB strainEnterobacter C7 coming from plants grown under well-watered conditions.
NRC7_1


title: WM983B_corin2_24h_rep3


title: WM983B_corin2_24h_rep1


title: Enterobacter C7-inoculated never ripe root under well-watered conditions, biological rep3

description:
Gene expression data from never ripe tomato roots inoculated with the PGPB strainEnterobacter C7 coming from plants grown under well-watered conditions.
NRC7_3


title: WM983B_MS-275_24h_rep3

source_name: WM983B melanoma cells, 2.5 µM MS-275 treated, 24 h


title: WM983B_MS-275_24h_rep1


title: Enterobacter C7-inoculated wild type root under drought conditions, biological rep3

description:
Gene expression data from wild type tomato roots inoculated with the PGPB strainEnterobacter C7 coming from plants grown under drought conditions.
WTC7D_3

source_name: Wild type plants inoculated with Enterobacter C7 grown under drought conditions

value: Pearson cv. Wild type


title: Enterobacter C7-inoculated wild type root under drought conditions, biological rep1

description:
Gene expression data from wild type tomato roots inoculated with the PGPB strainEnterobacter C7 coming from plants grown under drought conditions.
WTC7D_1


title: Bacillus megaterium-inoculated never ripe root under well-watered conditions, biological rep1

description:
Gene expression data from never ripe tomato roots inoculated with the PGPB strain Bacillus megaterium coming from plants grown under well-watered conditions.
NRBM_1


title: Enterobacter C7-inoculated wild type root under drought conditions, biological rep2

description:
Gene expression data from wild type tomato roots inoculated with the PGPB strainEnterobacter C7 coming from plants grown under drought conditions.
WTC7D_2


title: Non-inoculated never ripe root under well-watered conditions, biological rep1

description:
Gene expression data from never ripe tomato roots non-inoculated with a plant growth-promotion bacteria (PGPB) coming from plants grown under well-watered conditions.
NRNO_1


title: Normal colon organoids on differentiation medium STAR-

city: Hinxton

first: Rik

last: Lindeboom

address: Wellcome Trust Genome Campus

department: Cellular Genetics

country: United Kingdom

institute: Wellcome Sanger Institute

data_processing:
After trimming of barcodes, reads were aligned to the hg38 transcriptome annotation from UCSC with Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT2) version 2.0.4 with reporting alignments tailored for transcript assemblers enabled.
Alligned reads were counted per transcript with the htseq-count script in the HTSeq framework.
The rlogtransform function in DeSeq2 was used for noise stabilization of low expressed genes.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files with noise stabilized readcounts per gene

source_name: colon oganoids

growth_protocol: Healthy tissue-derived organoids were maintained as described previously (van de Wetering et al., 2015). The basic culture medium (WENR) contained advanced Dulbecco’s modified Eagles Medium/F12 supplemented with penicillin/streptomycin, 10mM HEPES and 1x Glutamax, 1x B27 [all from Life Technologies], and 1,25mM N-acetylcysteine [Sigma]), supplemented with 10mM Nicotinamide, 500nM A83-01, 3uM SB202190, 10μM Y-27632, 50ng/mL human recombinant EGF (Peprotech), Wnt3A (CM, 50% final volume), RSpondin-1 (CM, 20% final volume), and Noggin (CM, 10% final volume). The TPO-series were maintained as described previously (Drost et al., 2015).

extract_protocol:
RNA from the FACS sorted organoids was extracted using the RNeasy RNA extraction kit (Qiagen) with DNAseI treatment.
A maximum of 250ng RNA per sample was used for ribosomal RNA depletion using the Ribo-Zero Gold rRNA removal kit (Illumina) followed by an ethanol precipitation. Afterwards the RNA was fragmented for 5 minutes at 95C using 5x fragmentation buffer (200mM tris-acetate, 500mM potassium acetate, 150mM magnesium acetate, pH 8.2). Ethanol precipitation was used to precipitate the fragmented RNA followed by first strand cDNA synthesis with Superscript III (Life Technologies) and second strand cDNA synthesis. Samples were purified using QIAquick MinElute columns (Qiagen) with ERC buffer. A maximum of 2ng cDNA per sample was used for library preparation using the Kapa Hyper Prep Kit (KAPA Biosystems). In short, end repair and A-tailing of the double stranded cDNA was done by incubating the cDNA with end repair and A-tailing buffer and enzyme mix followed by incubation at 20C for 30 minutes and 65C for 30 minutes. Afterwards, unique NEXTflex DNA barcodes (Bioo Scientific) were ligated to the samples by incubation with ligation buffer, DNA ligase, and the NEXTflex DNA barcode (14nM) for 15 minutes at 20C. The barcode ligated samples were purified using a 0.8x SPRI magnetic beads cleanup (Agencourt AMPure XP reagent). The purified samples were incubated for 15 minutes at 37C with USER enzyme (New England Biolabs) to digest the 2nd cDNA strand. Libraries were amplified by adding 2x KAPA HiFi Hotstart ReadyMix and 10x Library Amplification Primer Mix to the purified samples followed by PCR amplification (10 cycles). Amplified libraries were purified using QIAquick MinElute columns (Qiagen) followed by size selection of 300bp using E-Gel SizeSelect Agarose Gels 2% (Thermo Fisher Scientific). Size selected libraries were controlled for correct size selection using the BioAnalyzer (Agilent) and the concentration was measured using the KAPA Library Quantification Kit (KAPA Biosystems).

treatment_protocol: Organoids were harvested and trypsinized for 1-2 minutes at 37 ⁰C. Trypsin inhibitor in a 1:1 ratio with trypsin blocked the reaction. Cells were washed and spun down at 1200 RPM at 4 ⁰C. Next, the pellet was taken up into culture medium (human CRC or mouse intestinal organoid medium as described above, including 10μM Y-27632 and 2% Matrigel of the final volume) and passed through a 40μm filter. For xenotransplanted samples: Mice were sacrificed four months after transplantation with and the orthotopic tumors were carefully dissected. Tumors were minced in pieces of about 1-2 mm and digested in Collagenase Type II (Thermo Fisher Scientific) for 1h hour at 37 ⁰C while shaking. Next, cells were filtered through a 70 µm cell strainer, washed and spun down at 1200 RPM at 4 ⁰C. Finally, the pellet was collected into culture medium (human CRC as described above, including 10μM Y-27632). To label dead we incubated single cells with 3μM Draq7 (Cell Signaling) for 10 minutes. Viable cells were sorted using the Aria III (Becton Dickinson) and data was analyzed with FACS Diva software.

tag: facs sort

value: STAR negative

tag: cancer mutations

value: WT on differentiation medium

tag: organoid line

value: Normal human colon from patient tissue (P11N)

tag: xenotransplanted

value: no


title: Normal colon organoids on expansion medium STAR-

value: WT on expansion medium


title: Non-inoculated never ripe root under well-watered conditions, biological rep2

description:
Gene expression data from never ripe tomato roots non-inoculated with a plant growth-promotion bacteria (PGPB) coming from plants grown under well-watered conditions.
NRNO_2

tag: genotype/variation


title: WM983B_veh_24h_rep3

source_name: WM983B melanoma cells, vehicle treated, 24 h

value: vehicle

value: 0 µM


title: Normal colon organoids on differentiation medium STAR+

value: STAR positive


title: Bacillus megaterium-inoculated wild type root under drought conditions, biological rep1

description:
Gene expression data from wild type tomato roots inoculated with the PGPB strain Bacillus megaterium coming from plants grown under drought conditions.
WTBMD_1

source_name: Wild type plants inoculated with Bacillus megaterium grown under drought conditions

value: drought conditions

tag: age


title: WM983B_MS-275_24h_rep2


title: Bacillus megaterium-inoculated wild type root under drought conditions, biological rep3

description:
Gene expression data from wild type tomato roots inoculated with the PGPB strain Bacillus megaterium coming from plants grown under drought conditions.
WTBMD_3

value: 8 weeks post-inoculation

tag: tissue


title: WM983B_veh_24h_rep1


title: Bacillus megaterium-inoculated wild type root under drought conditions, biological rep2

description:
Gene expression data from wild type tomato roots inoculated with the PGPB strain Bacillus megaterium coming from plants grown under drought conditions.
WTBMD_2

value: Roots


title: BJ.RAS.gro.rep2.lane2

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

description: nascent RNA

data_processing:
Sequenced reads were aligned to the reference human genome (hg19) using bowtie2. Wig files contains genomic read coverage (merging the two lanes of the same sample). Separate files were created for the Crick and Watson strands
Genome_build: hg19
Supplementary_files_format_and_content: wig files for genomic read coverage

source_name: BJ

growth_protocol: BJ/ET/RasV12, TIG3/ET/RASV12, Ecopack 2 and HEK293-T cells were cultured in DMEM medium (Gibco), supplemented with 10% FCS (Hyclone), and 1% penicillin/streptomycin (Gibco).

extract_protocol:
5 × 106 nuclei were isolated and incubated 5 min at 30 °C with equal volume of reaction buffer (10 mM Tris-Cl pH 8.0, 5 mM MgCl2, 1 mM DTT, 300 mM KCL, 20 units of SUPERase In, 1% sarkosyl, 500 µM ATP, GTP and Br-UTP, 0.2 µM CTP+32P CTP) for the nuclear run-on. The reaction was stopped and total RNA was extracted with Trizol LS (Invitrogen) according to the manufacturer’s instructions. RNA was fragmented using fragmentation reagents (Ambion) and the reaction was purified through p-30 RNasefree spin column (BioRad). BrU-labeled RNA was immunoprecipitated with anti-BrdU agarose beads (Santa Cruz), washed one time in binding buffer, one time in low salt buffer (0.2× SSPE, 1 mM EDTA, 0.05% Tween-20), one time high-salt buffer (0.25× SSPE, 1 mM EDTA, 0.05% Tween-20, 137.5 mM NaCl) and two times in TET buffer (TE with 0.05% Tween-20). RNA was eluted with elution buffer (20 mM DTT, 300 mM NaCl, 5 mM Tris-Cl pH 7.5, 1 mM EDTA and 0.1% SDS) and isolated with Trizol LS. After the binding step, BrU-labeled RNA was treated with tobacco acid pyrophosphatase (TAP, Epicenter) to remove 5′-methyl guanosine cap, followed by T4 polynucleotide kinase (PNK; NEB) to remove 3′-phosphate group. BrU-containing RNA was treated with T4 PNK again at high pH in the presence of ATP to add 5′-phosphate group. The reaction was stopped and RNA was extracted with Trizol LS.
Sequencing libraries were prepared using TruSeq Small RNA kit (Illumina) following manufacturer’s instructions. Briefly, end-repaired RNA was ligated to RNA 3′ and 5′ adapters, followed by RT-PCR amplification. cDNA was purified using Agencourt AMPure XP (Beckman Coulter) and amplified by PCR for 12 cycles. Finally, amplicons were cleaned and size-selected using Agencourt AMPure XP (Beckman Coulter), quantified in a Bioanalyzer 2100 (Agilent), and sequenced in a HiSeq 2500 (Illumina)
GRO-seq

treatment_protocol: RAS_V12 was induced by treatment with 100 nM4-OHT (Sigma) 24h after seeded for 14days

tag: treatment


title: sox17-1.ESC.pool

city: Tallahassee

first: David

middle: M

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

description: 4C-seq profile of a pool of K3-EBNA1 cells transfected with sox17-1 E-BAC

library_source: genomic

data_processing:
Library strategy: 4C-seq
Reads were mapped to hg19 build using BWA.
Each profile was then normalized to RPM.
binned to 10kb windows
Genome_build: hg19

molecule: genomic DNA

source_name: K3 iPSC

growth_protocol: E-BAC transfected Human iPSCK3 were grown in Stem-  Pro (Thermo Fisher, A100701) culture media on Geltrex  (Thermo Fisher, A14133) coated dishes. Raji cells were maintained in RPMI media supplemented with 10% fetal bovine serum.

extract_protocol: 4C-seq was performed as previously described (27) with minor modifications. 10 million cells were fixed in 1% formaldehyde, and chromatin was digested using HindIII before proximity ligation, followed by DpnII after reverse crosslinking. 4C libraries were prepared using inverse-PCR primers that contain illumina adapters and anneal to the pBACe3.6 bacterial sequences (forward primer: 5’-ATAAACTACCGCATTAAAGC; reverse primer: 5’-GGAGCCACTATCGACTACGC). Libraries were sequenced with 3-7 million mappable reads using 50bp single-end sequencing with Illumina HiSeq 2500.

treatment_protocol: K3-EBNA1 were transfected with E-BACs.

tag: cell type

value: K3 iPSC

tag: transfection

value: sox17-1 E-BAC


title: TIG3.RAS.gro.lane2

description: nascent RNA


title: Enterobacter C7-inoculated wild type root under well-watered conditions, biological rep1

description:
Gene expression data from wild type tomato roots inoculated with the PGPB strainEnterobacter C7 coming from plants grown under well-watered conditions.
WTC7_1

source_name: Wild type plants inoculated with Enterobacter C7 grown under well-watered conditions

value: Enterobacter C7

value: well-watered conditions


title: TIG3.C.gro.lane1

description: nascent RNA


title: TIG3.RAS.gro.lane1

description: nascent RNA


title: BJ.RAS.gro.rep1.lane2

description: nascent RNA


title: Non-inoculated wild type root under drought conditions, biological rep1

description:
Gene expression data from wild type tomato roots non-inoculated with a plant growth-promotion bacteria (PGPB) coming from plants grown under drought conditions.
WTNOD_1

source_name: Wild type plants non-inoculated grown under drought conditions

value: none (control)


title: TIG3.C.gro.lane2

description: nascent RNA


title: BJ.C.gro.rep2.lane2

description: nascent RNA


title: Non-inoculated wild type root under drought conditions, biological rep2

description:
Gene expression data from wild type tomato roots non-inoculated with a plant growth-promotion bacteria (PGPB) coming from plants grown under drought conditions.
WTNOD_2

value: Pearson cv. Wild type


title: Non-inoculated wild type root under drought conditions, biological rep3

description:
Gene expression data from wild type tomato roots non-inoculated with a plant growth-promotion bacteria (PGPB) coming from plants grown under drought conditions.
WTNOD_3


title: BJ.C.gro.rep1.lane1

description: nascent RNA


title: BJ.C.gro.rep1.lane2

description: nascent RNA


title: Enterobacter C7-inoculated wild type root under well-watered conditions, biological rep2

description:
Gene expression data from wild type tomato roots inoculated with the PGPB strainEnterobacter C7 coming from plants grown under well-watered conditions.
WTC7_2


title: Bacillus megaterium-inoculated wild type root under well-watered conditions, biological rep3

description:
Gene expression data from wild type tomato roots inoculated with the PGPB strain Bacillus megaterium coming from plants grown under well-watered conditions.
WTBM_3

source_name: Wild type plants inoculated with Bacillus megaterium grown under well-watered conditions

value: Bacillus megaterium


title: Bacillus megaterium-inoculated wild type root under well-watered conditions, biological rep2

description:
Gene expression data from wild type tomato roots inoculated with the PGPB strain Bacillus megaterium coming from plants grown under well-watered conditions.
WTBM_2


title: BJ.C.gro.rep2.lane1

description: nascent RNA


title: Enterobacter C7-inoculated wild type root under well-watered conditions, biological rep3

description:
Gene expression data from wild type tomato roots inoculated with the PGPB strainEnterobacter C7 coming from plants grown under well-watered conditions.
WTC7_3


title: Non-inoculated wild type root under well-watered conditions, biological rep1

description:
Gene expression data from wild type tomato roots non-inoculated with a plant growth-promotion bacteria (PGPB) coming from plants grown under well-watered conditions.
WTNO_1

source_name: Wild type plants non-inoculated grown under well-watered conditions


title: WM983B_veh_24h_rep2

value: melanoma cell line WM983B


title: Bacillus megaterium-inoculated wild type root under well-watered conditions, biological rep1

description:
Gene expression data from wild type tomato roots inoculated with the PGPB strain Bacillus megaterium coming from plants grown under well-watered conditions.
WTBM_1


title: Non-inoculated wild type root under well-watered conditions, biological rep2

description:
Gene expression data from wild type tomato roots non-inoculated with a plant growth-promotion bacteria (PGPB) coming from plants grown under well-watered conditions.
WTNO_2


title: jejunum_FOS_day14_rep3

description: totalRNA scraping

source_name: jejunum, FOS, day14

value: jejunum

tag: age (days)

value: FOS


title: Non-inoculated wild type root under well-watered conditions, biological rep3

description:
Gene expression data from wild type tomato roots non-inoculated with a plant growth-promotion bacteria (PGPB) coming from plants grown under well-watered conditions.
WTNO_3


title: BJ.RAS.gro.rep2.lane1

description: nascent RNA


title: BJ.RAS.gro.rep1.lane1

description: nascent RNA


title: VIC_Tgfb3_2

city: Darlinghurst

first: Joshua

last: Ho

state: NSW

address: Lowy Packer Building

institute: Victor Chang Cardiac Research Institute

description: VIC treated with TGFB3

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: lumi R package using the log2 transformation and robust spline normalization.

label: Biotin

source_name: human heart valve interstitial cells

label_protocol: cRNA was biotin-labeled by the Children's Hospital Boston Molecular Genetics Core Facility.

extract_protocol: Picopure RNA Isolation Kit including on column Dnase treatment

tag: cell-type

value: VIC

value: heart valve


title: VEC_Control_3

description: VEC without treatment

source_name: human heart valve endothelial cells

value: VEC

value: No


title: VEC_Bmp4_2

description: VEC treated with BMP4


title: VIC_Bmp4_3

description: VIC treated with BMP4


title: VEC_Tgfb3_3

description: VEC treated with TGFB3


title: VIC_Control_3

description: VIC without treatment


title: VEC_Bmp4_1

description: VEC treated with BMP4


title: VEC_Tgfb3_2

description: VEC treated with TGFB3


title: VIC_Tgfb3_3

description: VIC treated with TGFB3


title: VIC_Control_1

description: VIC without treatment


title: VEC_Tgfb3_1

description: VEC treated with TGFB3


title: VEC_Control_2

description: VEC without treatment


title: VIC_Control_2

description: VIC without treatment


title: VIC_Bmp4_2

description: VIC treated with BMP4


title: VIC_Bmp4_1

description: VIC treated with BMP4


title: VEC_Bmp4_3

description: VEC treated with BMP4


title: Aspergillus niger ΔxlnR mutant grown on D-xylose 2 hours, replicate 1

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

institute: Centre of fungal biodiversity

description:
Xyl-∆xlnR replicate 1
UU-A062.10 (ΔxlnR) cspA1, pyrA6, ΔargB, nicA1, leuA, pyrA6, ΔxlnR::pyrA+
Gene expression data from A. niger ΔxlnR mutant growing on D-xylose.

hyb_protocol: Following fragmentation, 10 µg of cRNA was hybridized to Affymetrix A. niger Genome GeneChips (GPL6758). GeneChips were washed and stained in an automated process.

scan_protocol: GeneChips were scanned.

data_processing: Microarray data was analyzed using the Bioconductor tool package version 2.8 (http://www.bioconductor.org/) together with house-made Perl (version .5.0) and Python (version 3.0) scripts. Probe intensities were normalized for background by the robust multi-array average (RMA) method using the R statistical language and environment. This method makes use of only perfect match (PM) probes. Normalization was processed by the quantiles algorithm. The median polish summary method was used to calculate the gene expression values.

organism: Aspergillus niger

label_protocol: Biotin-labeled antisense cRNA was produced from 2 µg of total RNA with the Eukaryotic One-Cycle Target Labeling kit (Affymetrix; www.affymetrix.com).

growth_protocol: A. niger N402 wild type was pre-cultured in 1 L Erlenmeyer flasks in 250 mL complete medium (CM) supplemented with 2% D-fructose. The pre-cultures were inoculated with 10e6 spores/mL and incubated at 250 rpm for 16 h at 30°C.

extract_protocol: RNA was extracted using TRIzol reagent (Invitrogen) and purified using TRIzol® Plus RNA Purification Kit (Sigma-Aldrich) according to the instructions of the manufacturer.

treatment_protocol: Mycelium was washed with MM and transferred for 2 h to 250 ml Erlenmeyer flasks containing 50 ml MM supplemented with 25 mM D-glucose, D-fructose, D-galactose, L-arabinose, D-xylose, D-mannose, D-galacturonic acid, L-rhamnose, Maltose, Sucrose, Ferulic acid or ferulic acid, or mixture of 25 mM L-rhamnose and 25 mM D-galacturonic acid, or 1% Inulin from chicory, Cellulose, Guar gum, Xyloglucan, Xylan (from beechwood), Polygalacturonic acid (from apples), Apple pectin, Galactan (from potato), Debranched 1,5-α-L-arabinan (from sugar beet), Rhamnogalacturonan I (from potato), Mannan (ivory nut), Citrus pulp, Sugar beet pulp or Soy bean hulls. The only exceptions were D-maltose cultures of N402 and ∆amyR strains that were incubated for 4 h. Mycelium was harvested by vacuum filtration, dried between towels and frozen in liquid nitrogen. While N402 liquid cultures were performed on all carbon sources listed before as well as on the mixture of L-rhamnose and D-galacturonic acid, the regulatory mutant strains ΔxlnR, ΔaraR, ΔamyR, ΔrhaR and ΔgalX were grown on D-xylose, L-arabinose, maltose, L-rhamnose and D-galactose, respectively, and L-rhamnose and D-galacturonic acid. All cultures were performed as biological duplicates.

tag: strain

tag: genotype

value: cspA1, pyrA6, <delta>argB, nicA1, leuA, pyrA6, <delta>xlnR::pyrA+

value: mycelium

value: 2 hours

tag: substrate

value: 25 mM D-xylose


title: Aspergillus niger wild type grown on sucrose 2 hours, replicate 2

description:
Suc-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on sucrose.

source_name: A. niger wild type growing on sucrose

value: cspA1 (wild type)

value: 25 mM sucrose


title: Aspergillus niger wild type grown on xyloglucan 2 hours, replicate 1

description:
XG-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on xyloglucan.

value: 1% xyloglucan


title: Aspergillus niger wild type grown on xyloglucan 2 hours, replicate 2

description:
XG-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on xyloglucan.


title: Normal colon organoids on expansion medium STAR+

value: STAR positive

value: WT on expansion medium

value: Normal human colon from patient tissue (P11N)

value: no


title: VIC_Tgfb3_1

description: VIC treated with TGFB3


title: Aspergillus niger ΔxlnR mutant grown on D-xylose 2 hours, replicate 2

description:
Xyl-∆xlnR replicate 2
UU-A062.10 (ΔxlnR) cspA1, pyrA6, ΔargB, nicA1, leuA, pyrA6, ΔxlnR::pyrA+
Gene expression data from A. niger ΔxlnR mutant growing on D-xylose.


title: Aspergillus niger wild type grown on sucrose 2 hours, replicate 1

description:
Suc-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on sucrose.


title: MVIC_MVP_4_Rep2

city: Memphis

first: Shannon

last: McKinney-Freeman

state: TN

address: 262 Danny Thomas Place

department: Hematology

institute: St. Jude Children's Research Hospital

hyb_protocol: Hybridized at 42ºC overnight using the HybBag mixing system with 1X OneArray Hybridization Buffer (Phalanx Biotech, Belmont, CA), 0.01 mg/ml sheared salmon sperm DNA (Promega, Madison, WI, USA), at a concentration of 0.025 mg/ml labeled target.

scan_protocol: Raw intensity signals for each microarray were captured using a Molecular Dynamics™ Axon 4100A scanner, measured using GenePixPro™ Software, and stored in GPR format.

data_processing: Raw intensities (exclude flagged and control data) were normalized with median scaling

source_name: Myxomatous Mitral Valve Tissue  (Posterior Leaflet)

label_protocol: RNA was converted to double-stranded cDNA and amplified using in vitro transcription that included amino-allyl UTP, and the RNA product was subsequently conjugated with Cy5™ NHS ester (GEH Life sciences).

extract_protocol:
P2 leaflets were collected in RNA later solution and kept frozen at -80C until analysis
Extraction of RNA was performed using the RNeasy Fibrous tissue kit(QIAGEN, Valencia, CA).

tag: disease state

value: MVP

value: Mitral Valve Tissue  (Posterior Leaflet)

tag: gender

value: Male


title: MVIC_MVP_3_Rep2


title: MVIC_MVP_4_Rep3


title: MVIC_MVP_3_Rep1


title: VEC_Control_1

description: VEC without treatment

value: heart valve


title: Aspergillus niger wild type grown on D-xylose 2 hours, replicate 1

description:
Xyl-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on D-xylose.

source_name: A. niger wild type growing on D-xylose


title: MVIC_MVP_4_Rep1


title: Aspergillus niger ΔRhaR mutant grown on L-rhamnose 2 hours, replicate 2

description:
Rha-∆rhaR replicate 2
FP-304 (ΔrhaR) cspA1, ΔkusA::amdS+, pyrA5, ΔrhaR::pyrA+
Gene expression data from A. niger ΔrhaR mutant growing on L-rhamnose.

value: cspA1, <delta>kusA::amdS+, pyrA5, <delta>rhaR::pyrA+

value: 25 mM L-rhamnose


title: Aspergillus niger wild type grown on D-xylose 2 hours, replicate 2

description:
Xyl-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on D-xylose.


title: Aspergillus niger ΔRhaR mutant grown on L-rhamnose 2 hours, replicate 1

description:
Rha-∆rhaR replicate 1
FP-304 (ΔrhaR) cspA1, ΔkusA::amdS+, pyrA5, ΔrhaR::pyrA+
Gene expression data from A. niger ΔrhaR mutant growing on L-rhamnose.


title: MVIC_Control_4_Rep2

source_name: Control Mitral Valve Tissue  (Posterior Leaflet)

value: control


title: MVIC_Control_3_Rep1


title: MVIC_Control_3_Rep2


title: MVIC_MVP_3_Rep3


title: MVIC_Control_4_Rep3


title: MVIC_MVP_2_Rep3


title: MVIC_MVP_2_Rep2


title: MVIC_MVP_1_Rep2


title: Aspergillus niger wild type grown on L-rhamnose 2 hours, replicate 1

description:
Rha-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on L-rhamnose.

value: mycelium


title: Aspergillus niger wild type grown on rhamnogalacturonan 2 hours, replicate 2

description:
RG-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on rhamnogalacturonan.

value: 2 hours

value: 1% rhamnogalacturonan


title: MVIC_Control_4_Rep1


title: MVIC_MVP_1_Rep3


title: MVIC_MVP_2_Rep1


title: MVIC_MVP_1_Rep1


title: Aspergillus niger wild type grown on L-rhamnose 2 hours, replicate 2

description:
Rha-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on L-rhamnose.

value: cspA1 (wild type)


title: mutant_serine_tRNA_LEU_rep1

city: Aveiro

first: Marisa

last: Reverendo

state: Aveiro

address: campus universitário de santiago

country: Portugal

institute: University of Aveiro

description: mutant tRNA gene expression

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Zebrafish (V2) Gene Expression Microarray, (G2519F) for 17 hours at 65°C in a rotating  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 Agilent DNA Microarray Scanner G2565AA  using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (Protocol GE1_105_Dec08 and Grid: 019161_D_20080131) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Danio rerio

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.6 ug RNA using the Quick Amp Labeling 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.

growth_protocol: Zebrafish were maintained at 28ºC on a 14 h-light/10 h-dark cycle.

extract_protocol: Total RNA was extracted using Trizol® according to manufacturer´s instructions. Total RNA was treated with DNAseI to eliminated DNA contamination and RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Empty plasmid and plasmid containg the endogenous and mutant tRNAS were microinjected at 1-cell stage. Embryos were were maintained at 28ºC on a 14 h-light/10 h-dark cycle and collected at 24hpf.

value: 24hfp embryo


title: mutant_serine_tRNA_VAL_rep2

description: mutant tRNA gene expression


title: MVIC_Control_2_Rep3


title: MVIC_Control_1_Rep1


title: mutant_serine_tRNA_VAL_rep1

description: mutant tRNA gene expression


title: mutant_serine_tRNA_LEU_rep3

description: mutant tRNA gene expression


title: mutant_serine_tRNA_LEU_rep2

description: mutant tRNA gene expression


title: mutant_serine_tRNA_VAL_rep3

description: mutant tRNA gene expression


title: MVIC_Control_2_Rep2


title: MVIC_Control_3_Rep3


title: MVIC_Control_2_Rep1


title: MVIC_Control_1_Rep3


title: Aspergillus niger wild type grown on maltose 4 hours, replicate 2

description:
Mal-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on maltose.

source_name: A. niger wild type growing on maltose

value: 4 hours

value: 25 mM maltose


title: Aspergillus niger wild type grown on rhamnogalacturonan 2 hours, replicate 1

description:
RG-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on rhamnogalacturonan.


title: mutant_serine_tRNA_ALA_rep3

description: mutant tRNA gene expression


title: mutant_serine_tRNA_GLY_rep1

description: mutant tRNA gene expression


title: mutant_serine_tRNA_GLY_rep2

description: mutant tRNA gene expression


title: MVIC_Control_1_Rep2


title: mutant_serine_tRNA_GLY_rep3

description: mutant tRNA gene expression


title: PC3_PPARGW_E6

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with lumi in R.

source_name: pC3 cells, PPARD overexpression+GW501516

label_protocol: TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System (Epicentre).

growth_protocol: PC3 cell line was maintained in DMEM media supplemented with 10% (v/v) foetal bovine serum (FBS) and 1% (v/v) penicillin-streptomycin.

extract_protocol: RNA was extracted from cells with RNA isolation kit from Macherey-Nagel.

treatment_protocol: GW501516 (Enzo life sciences) was dissolved in DMSO and used at 0.1µM concentration.

tag: cell line

value: prostate cancer cell line

value: PPARD overexpression+GW501516


title: PC3_PPARV_E6

source_name: pC3 cells, PPARD overexpression

value: PPARD overexpression


title: mutant_serine_tRNA_ALA_rep2

description: mutant tRNA gene expression


title: Aspergillus niger wild type grown on maltose 4 hours, replicate 1

description:
Mal-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on maltose.


title: Aspergillus niger ΔamyR mutant grown on maltose 4 hours, replicate 2

description:
Mal-∆amyR replicate 2
UU-A101.1 (ΔamyR) cspA1, ΔargB, pyrA6, leuA1, nicA1, ΔamyR::argB+
Gene expression data from A. niger ΔamyR mutant growing on maltose.

value: cspA1, <delta>argB, pyrA6, leuA1, nicA1, <delta>amyR::argB+


title: Aspergillus niger wild type grown on galactan 2 hours, replicate 2

description:
GLN-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on galactan.

source_name: A. niger wild type growing on galactan

value: 1% galactan


title: Aspergillus niger wild type grown on inulin 2 hours, replicate 1

description:
Inu-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growint on inulin.

source_name: A. niger wild type growing on inulin

value: 1% inulin


title: 012T_miRNAseq_ctrl

city: Omaha,

first: Sowmya

middle: V

last: Yelamanchili

state: NE

address: 985800 Nebraska Medical Center - DRC 1 3008

department: Pharmacology and Experimental Neuroscience

institute: University of Nebraska Medical center

description: microRNA

data_processing:
Raw sequencing reads (40 nts) were obtained using Illumina’s Sequencing Control Studio software  version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's  Real-Time Analysis version 1.8.70 (RTA v1.8.70).
A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data  analysis
Genome_build: MMUL1.0
Standard Data Analysis: Obtaining Mappable Sequences from Raw Reads  After the raw sequence reads, or sequenced sequences (sequ seqs) were extracted from image data, a  series of digital filters (LC Sciences) were employed to remove various un-mappable sequencing  reads:  A: Generating Unique Families of Sequ Seqs by Sorting Raw Sequencing Reads  In this step, identical sequ seqs in the raw data file were clustered into unique families and the file  [Sample]_unique.fq was generated. An example of a typical entry of this file is shown below:  @5_18368  AGCAGAGTGGCGCAGCGGAAGCGTGCTGGGC  +  fffffefffffffffeeedeeeeceeefeee  B: Filtering Sequ Seqs  In this step, the “impurity” sequences due to sample preparation, sequencing chemistry and  processes, and the optical digital resolution of the sequencer detector were removed. Those  remaining sequ seqs (filtered sequ seqs with lengths between 15 and 32 bases) were grouped by  families (unique seqs), and stored in the file [Sample]_mappableReads.fq, and were used to map  with the reference database files.

organism: Macaca mulatta

source_name: Frozen brain

extract_protocol:
Previously dissected and frozen macaque brain tissue (weighing approximately 500 mg each) were dissected and treated with 20 units/ml papain (Worthington) in Hibernate A solution (5 ml/hemi-brain; BrainBits, Springfield, IL) and rocked for 15 min at 37° C. The brain tissue was gently homogenized in 10 ml/brain of cold Hibernate A solution. The brain homogenate was sequentially filtered through a 40 μm mesh filter (BD Biosciences), a 5 µm Filter (Pall Corporation) and a 0.2 μm syringe filter (Thermo Scientific). Exosomes were isolated from the filtrate as described previously. Briefly, the filtrate was sequentially centrifuged at 300 × g for 10 min at 4° C, 2000 × g for 10 min at 4° C, and 10,000 × g for 30 min at 4° C to discard cells, membranes, and debris. The supernatant was centrifuged at 100,000 × g for 60 min at 4° C to pellet exosomes. The exosome pellet was resuspended in 37 ml of cold PBS (Hyclone), and the exosome solution was centrifuged at 100,000 × g for 60 min at 4° C. The washed exosome pellet was resuspended in 2 mL of 0.95 M sucrose solution and inserted inside a sucrose step gradient column (six 2 ml steps starting from 2.0 M sucrose down to 0.25 M sucrose in 0.35 M increments, with the 0.95 M sucrose step containing the exosomes). The sucrose step gradient was centrifuged at 200,000 × g for 16 hr at 4° C. A 1 ml fraction was collected from the top of the gradient and discarded, and 6 mL of the gradient were collected in the exosome rich layers containing material with density higher then 1.07 (0.60 M sucrose layer) and lower than 1.17 (1.30 M sucrose layer) [28]. Pooled fractions were diluted to a volume 30 ml of cold PBS. 25 ml of this volume was taken for RNA extraction and 5 ml for Western blot studies. Sample volumes were brought up to appropriate volumes with cold PBS and centrifuged at 100,000 × g at 4° C for 60 min. PBS was pipetted off both pellets.
Using the RNA isolated from exosomes, a small RNA library was generated using the Illumina Truseq Small RNA Preparation kit following the manufacturer’s guidelines. The cDNA library was purified and used for cluster generation on Illumina’s Cluster Station and then sequenced on the Illumina GAIIx. Raw sequencing reads were obtained using Illumina’s Sequencing Control Studio software (version 2.8) following real-time sequencing image analysis and base-calling by Illumina's Real-Time Analysis (version 1.8.70). A pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis. Sequences were then mapped to miRbase (version 20.0) [54]. 636 unique sequences mapped to both Macaca mullata mirs in miRbase and the Macaca mullata genome.

value: ctrl - no infection

value: Exosomal isolate


title: 016T_miRNAseq_ctrl

description: microRNA


title: 011T_miRNAseq_ctrl

description: microRNA


title: endogenous_serine_tRNA_rep2

description: endogenous tRNA gene expression


title: Aspergillus niger wild type grown on inulin 2 hours, replicate 2

description:
Inu-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growint on inulin.


title: Aspergillus niger ΔamyR mutant grown on maltose 4 hours, replicate 1

description:
Mal-∆amyR replicate 1
UU-A101.1 (ΔamyR) cspA1, ΔargB, pyrA6, leuA1, nicA1, ΔamyR::argB+
Gene expression data from A. niger ΔamyR mutant growing on maltose.


title: PC3_BabeV_E6

source_name: pC3 cells, vehicle control

value: vehicle control


title: 013T_miRNAseq_SIV

description: microRNA

value: SIV


title: mutant_serine_tRNA_ALA_rep1

description: mutant tRNA gene expression


title: Aspergillus niger wild type grown on galactan 2 hours, replicate 1

description:
GLN-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on galactan.

value: mycelium


title: PC3_BabeV_E5


title: PC3_PPARGW_E4


title: PC3_PPARV_E5


title: PC3_PPARV_E4


title: PC3_PPARGW_E5


title: wild_type_rep2

description: wild type gene expression


title: 008T_miRNAseq_SIV

description: microRNA


title: empty_plasmid_rep2

description: empty plasmid gene expression


title: endogenous_serine_tRNA_rep1

description: endogenous tRNA gene expression


title: endogenous_serine_tRNA_rep3

description: endogenous tRNA gene expression


title: empty_plasmid_rep1

description: empty plasmid gene expression


title: 007T_miRNAseq_SIV

description: microRNA


title: wild_type_rep1

description: wild type gene expression


title: empty_plasmid_rep3

description: empty plasmid gene expression


title: 006T_miRNAseq_SIV

description: microRNA


title: 017T_miRNAseq_SIVE

description: microRNA

value: SIV + Encephalitis


title: 009T_miRNAseq_SIVE

description: microRNA


title: 004T_miRNAseq_SIVE

description: microRNA


title: 003T_miRNAseq_SIVE

description: microRNA


title: Aspergillus niger wild type grown on D-galacturonic acid 2 hours, replicate 2

description:
GalA-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on D-galacturonic acid.

value: 2 hours

value: 25 mM D-galacturonic acid


title: Aspergillus niger wild type grown on ferulic acid 2 hours, replicate 2

description:
FA-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on ferulic acid.

value: cspA1 (wild type)

value: 25 mM ferulic acid


title: Aspergillus niger wild type grown on Beech wood xylan 2 hours, replicate 1

description:
BWX-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on Beech wood xylan.

value: 1% Beech wood xylan


title: Aspergillus niger wild type grown on D-galacturonic acid plus L-rhamnose 2 hours, replicate 1

description:
GalA/Rha-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on D-galacturonic acid plus L-rhamnose.

value: 25 mM D-galacturonic acid plus L-rhamnose


title: Aspergillus niger ΔgalX mutant grown on D-galactose 2 hours, replicate 2

description:
Gal-∆galX replicate 2
FP-306 (ΔgalX) cspA1, ΔkusA::amdS+, pyrA5, ΔgalX::pyrA+
Gene expression data from A. niger ΔgalX mutant growing on D-galactose.

value: cspA1, <delta>kusA::amdS+, pyrA5, <delta>galX::pyrA+

value: 25 mM D-galactose


title: Aspergillus niger wild type grown on ferulic acid 2 hours, replicate 1

description:
FA-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on ferulic acid.


title: Aspergillus niger wild type grown on arabinose 2 hours, replicate 3

description:
Ara-wt replicate 3
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on arabinose.

source_name: A. niger wild type growing on arabinose

value: 25 mM arabinose


title: Aspergillus niger wild type grown on D-galacturonic acid plus L-rhamnose 2 hours, replicate 2

description:
GalA/Rha-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on D-galacturonic acid plus L-rhamnose.


title: Aspergillus niger wild type grown on D-galacturonic acid 2 hours, replicate 1

description:
GalA-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on D-galacturonic acid.


title: Aspergillus niger wild type grown on D-fructose 2 hours, replicate 1

description:
Frc-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on D-fructose.

value: 25 mM D-fructose


title: Aspergillus niger wild type grown on Beech wood xylan 2 hours, replicate 2

description:
BWX-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on Beech wood xylan.


title: Aspergillus niger wild type grown on cellulose 2 hours, replicate 1

description:
Cel-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on cellulose.

source_name: A. niger wild type growing on cellulose

value: 1% cellulose


title: Aspergillus niger wild type grown on D-fructose 2 hours, replicate 2

description:
Frc-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on D-fructose.


title: Aspergillus niger ΔgalX mutant grown on D-galactose 2 hours, replicate 1

description:
Gal-∆galX replicate 1
FP-306 (ΔgalX) cspA1, ΔkusA::amdS+, pyrA5, ΔgalX::pyrA+
Gene expression data from A. niger ΔgalX mutant growing on D-galactose.


title: Aspergillus niger wild type grown on cellulose 2 hours, replicate 2

description:
Cel-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on cellulose.


title: 45_BE2C_2

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Gene expression profiling in BE(2)-C, rep2

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized at 45C for 16 hr at 60RPM on GeneChip Arrays (PrimeView). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manurfacturer's instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Expression Console. A CDF containing the ERCC probes was provided by Affymetrix.

data_processing: A CDF provided by Affymetrix, which contained the ERCC probes (PrimeView_withERCC_binary.cdf) was used instead of the standard PrimeView cdf. The data were analyzed with Bioconductor using the MAS5 nomalization method. Then, these data were renormalized to the external spike-ins. See manuscript for additional details.

source_name: BE(2)-C_neuroblastoma cell line

label_protocol: Biotinylated aRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT Express Kit User Manual, 2009, Affymetrix).

growth_protocol: Neuroblastoma cell lines were cultured in DMEM supplemented with 10% FBS.

extract_protocol: Prior to RNA isolation, cell numbers were determined and total RNA isolation was performed using the miRvana miRNA total RNA isolation kit (ThermoFisher Scientific, AM1560) according to manufacturers instructions. Following isolation, RNA was digested with DNase (Ambion). During isolation, external RNA spike-ins (ERCC, Ambion) were added at the time of cell lysis.

value: neuroblastoma cell line


title: 48_KELLY_2

description: Gene expression profiling in KELLY, rep2

source_name: KELLY_neuroblastoma cell line

value: KELLY


title: GSH with ciprofloxacin (50 ng/ml) exposed culture, biological replicate 2

city: MUMBAI

first: Manish

last: Goswami

state: Maharashtra

address: Mod Labs, trombay

department: Molecular Biology Division

country: India

institute: Bhabha Atomic Research Centre

description:
GSH-Cip 2
Gene expression data from GSH with ciprofloxacin (50 ng/ml) exposed logarithmically growing MG1655 cells.

hyb_protocol: Fragmented, biotinylated cDNA generated using the GeneChip® IVT express kit was hybridized to Affymetrix GeneChip® E. coli genome 2.0 arrays for 16 h at 45°C and 60 r.p.m.

scan_protocol: Hybridized probe arrays were scanned on the GeneChip® Scanner 3000 7G to detect the patterns of hybridization.

data_processing: Original microarray data (CEL files) were preprocessed using RMA (Robust Multichip Average) algorithm in GeneSpring GX 12.0.

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

source_name: GSH with ciprofloxacin (50 ng/ml) exposed MG1655 culture

label_protocol: Total RNA was reverse transcribed, biotin labelled and purified using GeneChip® IVT express kit according to the manufacturer's instruction.

growth_protocol: Overnight grown E. coli were freshly diluted 1:100 in LB medium for collection of total RNA at mid-logarithmic stage (OD600 ~ 0.3-0.4).

extract_protocol: Total RNA was obtained using the RNeasy Protect Bacteria Mini kit (Qiagen) according to the manufacturer's instructions. The purity, concentration, and integrity of RNA were confirmed by Agilent Bioanalyzer 2100 and agarose gel electrophoresis.

treatment_protocol: E. coli cells were grown with three different conditions namely (i) with 10 mM GSH (ii) with 3 ng/ml ciprofloxacin (sub-inhibitory antibiotic concentration) and (iii) with 10 mM GSH and 50 ng/ml ciprofloxacin (inhibitory antibiotic concentration). Control cultures were grown in LB with no exogenous GSH or ciprofloxacin added.

value: wild type

tag: growth stage

value: logarithmic

value: glutathione (GSH) and ciprofloxacin


title: 46_BE2C_3

description: Gene expression profiling in BE(2)-C, rep3


title: GSH with ciprofloxacin (50 ng/ml) exposed culture, biological replicate 1

description:
GSH-Cip 1
Gene expression data from GSH with ciprofloxacin (50 ng/ml) exposed logarithmically growing MG1655 cells.


title: 49_KELLY_3

description: Gene expression profiling in KELLY, rep3


title: 47_KELLY_1

description: Gene expression profiling in KELLY, rep1


title: 44_BE2C_1

description: Gene expression profiling in BE(2)-C, rep1


title: Aspergillus niger ΔaraR mutant grown on L-arabinose 2 hours, replicate 2

description:
AraR-ara replicate 2
UU-A033.21 (ΔaraR) cspA1, pyrA6, nicA1, leuA1, ΔargB::pIM2101 ΔaraR::argB+
Gene expression data from A. niger ΔaraR mutant growing on L-arabinose.

value: cspA1, pyrA6, nicA1, leuA1, <delta>argB::pIM2101 <delta>araR::argB+

value: mycelium

value: 25 mM L-arabinose


title: Aspergillus niger wild type grown on arabinose 2 hours, replicate 2

description:
Ara-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on arabinose.

value: cspA1 (wild type)

value: 2 hours


title: 42_NGP_2

description: Gene expression profiling in NGP, rep2

source_name: NGP_neuroblastoma cell line

value: NGP


title: 43_NGP_3

description: Gene expression profiling in NGP, rep3


title: Aspergillus niger wild type grown on arabinose 2 hours, replicate 1

description:
Ara-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on arabinose.


title: Aspergillus niger wild type grown on Apple pectin 2 hours, replicate 2

description:
AP-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on Applepectin.

value: 1% Apple pectin


title: Aspergillus niger ΔaraR mutant grown on L-arabinose 2 hours, replicate 1

description:
Ara-∆araR replicate 1
UU-A033.21 (ΔaraR) cspA1, pyrA6, nicA1, leuA1, ΔargB::pIM2101 ΔaraR::argB+
Gene expression data from A. niger ΔaraR mutant growing on L-arabinose.


title: Ctrl3

description: Gene expression

hyb_protocol: The labeled cRNAs were hybridized onto the Human circRNA Array (6x7K, Arraystar) based on the manufacturer’s standard protocols.

scan_protocol: After washing, slides were scanned with the Axon GenePix 4000B Scanner.

data_processing:
GenePix Pro 6.0 software (Axon) was used to analyse acquired array images. Quantile normalization and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, genes that at least 1 out of 3 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.
GSE105096_Conservation_circRNAs_human_islet_array_vs._mouse_islet_RNA_seq.xlsx: The excel sheet consists of a computational comparison of the data obtained by the array of GSE105096 with data obtained by re-analysing RNA sequencing data from GSE92602. ^SAMPLE = GSM2817920
GenePix Pro 6.0 software (Axon) was used to analyse acquired array images. Quantile normalization and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, genes that at least 1 out of 3 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.
GSE105096_Conservation_circRNAs_human_islet_array_vs._mouse_islet_RNA_seq.xlsx: The excel sheet consists of a computational comparison of the data obtained by the array of GSE105096 with data obtained by re-analysing RNA sequencing data from GSE92602. ^SAMPLE = GSM2817921
GenePix Pro 6.0 software (Axon) was used to analyse acquired array images. Quantile normalization and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, genes that at least 1 out of 3 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.
GSE105096_Conservation_circRNAs_human_islet_array_vs._mouse_islet_RNA_seq.xlsx: The excel sheet consists of a computational comparison of the data obtained by the array of GSE105096 with data obtained by re-analysing RNA sequencing data from GSE92602.

source_name: Human islet cells, repliate 3

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen), according to manufacturer guidelines. RNA was depleted for linear RNA by RNase R treatment (Arraystar).

treatment_protocol: Human islet cells were incubated for 48 h in culture medium (CMRL medium supplemented with 10 % FCS, 100 U/ml Penicillin, 100 µg/ml Streptovidin, 2 mM L-Glutamine and 250 µM Hepes)

value: Pancreatic islet cells

tag: sample type

value: male, 20 years old, BMI 22.8

value: male

tag: bmi


title: Aspergillus niger wild type grown on Arabinan 2h, replicate 2

description:
Abn-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on Arabinan.

source_name: A. niger wild type growing on Arabinan

value: 1% Arabinan


title: Aspergillus niger wild type grown on Apple pectin 2 hours, replicate 1

description:
AP-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on Applepectin.


title: GSH exposed culture, biological replicate 2

description:
GSH 2
Gene expression data from GSH exposed logarithmically growing MG1655 cells.

source_name: GSH exposed MG1655 culture

tag: genotype/variation

value: glutathione (GSH)


title: 41_NGP_1

description: Gene expression profiling in NGP, rep1

value: neuroblastoma cell line


title: Ciprofloxacin (3 ng/ml) exposed culture, biological replicate 2

description:
Cip 2
Gene expression data from ciprofloxacin (3 ng/ml) exposed logarithmically growing MG1655 cells.

source_name: Ciprofloxacin (3 ng/ml) exposed MG1655 culture

value: ciprofloxacin


title: 39_SHS-Y5Y_2

description: Gene expression profiling in SHS-Y5Y, rep2

source_name: SHS-Y5Y_neuroblastoma cell line


title: Aspergillus niger wild type grown on Arabinan 2h, replicate 1

description:
Abn-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on Arabinan.

tag: age


title: 40_SHS-Y5Y_3

description: Gene expression profiling in SHS-Y5Y, rep3


title: GSH exposed culture, biological replicate 1

description:
GSH 1
Gene expression data from GSH exposed logarithmically growing MG1655 cells.

value: wild type


title: 38_SHS-Y5Y_1

description: Gene expression profiling in SHS-Y5Y, rep1


title: Ctrl2

description: Gene expression

data_processing: GenePix Pro 6.0 software (Axon) was used to analyse acquired array images. Quantile normalization and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, genes that at least 1 out of 3 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

source_name: Human islet cells, repliate 2

tag: tissue

value: female, 56 years old, BMI 23.8

value: female


title: Control culture, biological replicate 2

description:
Control 2
Gene expression data from control unexposed logarithmically growing MG1655 cells.

source_name: Control culture of MG1655

value: logarithmic

tag: treatment


title: PC3_BabeV_E4

tag: cell type

value: prostate cancer cell line

value: vehicle control


title: Control culture, biological replicate 1

description:
Control 1
Gene expression data from control unexposed logarithmically growing MG1655 cells.


title: Ctrl1

description: Gene expression

source_name: Human islet cells, repliate 1

value: female, 56 years old, BMI 19.7


title: 36_SKNAS_2

description: Gene expression profiling in SKNAS, rep2

source_name: SKNAS_neuroblastoma cell line

value: SK-N-AS


title: 35_SKNAS_1

description: Gene expression profiling in SKNAS, rep1


title: Ciprofloxacin (3 ng/ml) exposed culture, biological replicate 1

description:
Cip 1
Gene expression data from ciprofloxacin (3 ng/ml) exposed logarithmically growing MG1655 cells.


title: 37_SKNAS_3

description: Gene expression profiling in SKNAS, rep3


title: NY2182_gene_expression

status: Public on Jan 28 2018

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Illumina beadarray Assay System Manual

data_processing: For each probe, replicated mesurements (beads) were averaged after removing outliers by Genome Studio software v.3 (Illumina). Data were were then normalized using cubic spline algorithm implemented in GenePattern Illumina normalizer module (www.broadinstitute.org/genepattern) after setting a floor value of 1.

extract_protocol: RNA was isolated using RNeasy kit (Qiagen) according to manufacturer’s protocol.

treatment_protocol: FFPE tissue sections (10 micron-thick) sliced from FFPE blocks

tag: patient id

tag: tumor or not (y/n)

value: Y


title: NY2203_gene_expression

scan_protocol: Refer to the Illumina beadarray Assay System Manual

data_processing: For each probe, replicated mesurements (beads) were averaged after removing outliers by Genome Studio software v.3 (Illumina). Data were were then normalized using qubic spline algorithm implemented in GenePattern Illumina normalizer module (www.broadinstitute.org/genepattern) after setting a floor value of 1.


title: NY2206_gene_expression

label_protocol: Refer to the Illumina beadarray Assay System Manual


title: NY2181_gene_expression


title: NY2189_gene_expression


title: NY2198_gene_expression


title: NY2202_gene_expression


title: NY2185_gene_expression


title: NY2190_gene_expression


title: NY2204_gene_expression

value: N


title: NY2196_gene_expression


title: NY2205_gene_expression


title: NY2186_gene_expression


title: NY2199_gene_expression


title: NY2176_gene_expression


title: NY2194_gene_expression


title: NY2187_gene_expression


title: NY2183_gene_expression


title: NY2200_gene_expression


title: NY2195_gene_expression


title: NY2201_gene_expression


title: NY2172_gene_expression


title: NY2177_gene_expression


title: NY2184_gene_expression


title: NY2175_gene_expression


title: NY2173_gene_expression


title: NY2174_gene_expression


title: NY2179_gene_expression


title: NY2188_gene_expression


title: NY2169_gene_expression


title: NY2167_gene_expression


title: NY2101_gene_expression


title: NY2134_gene_expression


title: NY2178_gene_expression


title: NY2168_gene_expression


title: NY2062_gene_expression


title: NY2087_gene_expression


title: NY2123_gene_expression


title: NY2007_gene_expression


title: NY2088_gene_expression


title: NY2171_gene_expression


title: NY2133_gene_expression


title: NY2132_gene_expression


title: NY2170_gene_expression


title: NY2102_gene_expression


title: NY2086_gene_expression


title: NY2100_gene_expression


title: NY2064_gene_expression


title: NY2063_gene_expression


title: NY2027_gene_expression


title: NY2028_gene_expression


title: NY2005_gene_expression


title: NY2029_gene_expression


title: NY2006_gene_expression


title: NY2199_copy_number

type: genomic

description: raw data sample ID: X56

data_processing: Log R Ratio and B Allele Frequency were directly retrieved from the final report generated by GenomeStudio (GSGT Version 1.9.4).

extract_protocol: DNA was isolated using QIAamp FFPE DNA kit (Qiagen) according to manufacturer’s protocol.


title: NY2198_copy_number

description: raw data sample ID: X55


title: NY2202_copy_number

description: raw data sample ID: X59


title: NY2204_copy_number

description: raw data sample ID: X61


title: NY2196_copy_number

description: raw data sample ID: X53


title: NY2205_copy_number

description: raw data sample ID: X62


title: NY2201_copy_number

description: raw data sample ID: X58


title: NY2174_copy_number

description: raw data sample ID: X35


title: NY2200_copy_number

description: raw data sample ID: X57


title: NY2184_copy_number

description: raw data sample ID: X45


title: NY2197_copy_number

description: raw data sample ID: X54


title: NY2180_copy_number

description: raw data sample ID: X41


title: NY2182_copy_number

description: raw data sample ID: X43


title: NY2195_copy_number

description: raw data sample ID: X52


title: NY2206_copy_number

description: raw data sample ID: X63


title: NY2187_copy_number

description: raw data sample ID: X47


title: NY2176_copy_number

description: raw data sample ID: X37


title: NY2189_copy_number

description: raw data sample ID: X49


title: NY2179_copy_number

description: raw data sample ID: X40


title: NY2177_copy_number

description: raw data sample ID: X38


title: NY2185_copy_number

description: raw data sample ID: X46


title: NY2173_copy_number

description: raw data sample ID: X34


title: NY2188_copy_number

description: raw data sample ID: X48


title: NY2175_copy_number

description: raw data sample ID: X36


title: NY2181_copy_number

description: raw data sample ID: X42


title: NY2190_copy_number

description: raw data sample ID: X50


title: NY2178_copy_number

description: raw data sample ID: X39


title: NY2203_copy_number

description: raw data sample ID: X60


title: NY2194_copy_number

description: raw data sample ID: X51


title: NY2183_copy_number

description: raw data sample ID: X44


title: NY2172_copy_number

description: raw data sample ID: X33


title: NY2100_copy_number

description: raw data sample ID: X17


title: NY2133_copy_number

description: raw data sample ID: X25


title: NY2170_copy_number

description: raw data sample ID: X31


title: NY2134_copy_number

description: raw data sample ID: X26


title: NY2102_copy_number

description: raw data sample ID: X19


title: NY2169_copy_number

description: raw data sample ID: X30


title: NY2088_copy_number

description: raw data sample ID: X16


title: NY2171_copy_number

description: raw data sample ID: X32


title: NY2064_copy_number

description: raw data sample ID: X13


title: TEBS-IPS-BipoFibr_F_Y-fMG02

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
library strategy: TEBS (Target enriched 'bisulfite-seq')
Basecalls performed using CASAVA
Targeted bisulfite sequencing (TEBS, aligent) data were mapped to mm9 (MGSCv37) by BSMAP2.9 with the parameters: “-m 17 -x 600 -p 6 -z 33 -f 5 -g 3 -r 0 -u -R”.
methylation level were calculated by methratio provided by BSMAP.
methratio results, beta-value of CG with at least 3 reads have been extracted and converted to bigwig for visualization.
Genome_build: mm9(MGSCv37)
Supplementary_files_format_and_content: bigwig

source_name: Cell Line

extract_protocol:
Genomic DNA was extracted using DNeasy Blood & Tissue kit (Qiagen, 69504) for each iPS cell lines. Then DNA was processed using the SureSelectXT Mouse Methyl-Seq Reagent kit (Agilent, 931052).
After capture, the bisulfite conversion of the eluted DNA was performed by EZ DNA Methylation-Gold kit (Zymo Research, D5005). Then the converted DNA was amplified using the PCR reagents from SureSelectXT Mouse Methyl-Seq Reagent kit (Agilent, 931052) according to the manufacturer’s recommendations.

value: iPSCs from fibroblast Bipolar cell MakeRetina fMG02

tag: molecule subtype

value: bisulfite treated genomic DNA


title: TEBS-IPS-Cone_M_N-rCh257.4

tag: strain

value: iPSCs from mature Cone cell CanNotMakeRetina rCh257.4


title: NY2029_copy_number

description: raw data sample ID: X10


title: TEBS-IPS-Amac_I_N-rG79.04

value: iPSCs from immature Amacrine cell CanNotMakeRetina rG79.04


title: TEBS-IPS-AmacFibr_F_Y-fG140.04

value: iPSCs from fibroblast Amacrine cell MakeRetina fG140.04


title: TEBS-IPS-AmacFibr_F_Y-fG140.03

value: iPSCs from fibroblast Amacrine cell MakeRetina fG140.03


title: TEBS-IPS-Cone_I_N-rCh209.04

value: iPSCs from immature Cone cell CanNotMakeRetina rCh209.04


title: NY2010_copy_number

description: raw data sample ID: X4


title: NY2013_copy_number

description: raw data sample ID: X7


title: TEBS-IPS-MullFibr_F_N-FCR02

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR02


title: TEBS-IPS-BipoFibr_F_Y-fMG03

value: iPSCs from fibroblast Bipolar cell MakeRetina fMG03


title: TEBS-IPS-Mull_M_N-rCr143.02

value: iPSCs from mature Muller cell CanNotMakeRetina rCr143.02


title: NY2167_copy_number

description: raw data sample ID: X28


title: TEBS-IPS-Bipo_I_N-rM0408

value: iPSCs from immature Bipolar cell CanNotMakeRetina rM0408


title: TEBS-IPS-MullFibr_F_N-FCR01

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR01


title: TEBS-IPS-RodFibr_F_Y-FNR07

value: iPSCs from fibroblast Rod cell MakeRetina FNR07


title: TEBS-IPS-Cone_M_Y-257.03

value: iPSCs from mature Cone cell MakeRetina 257.03


title: TEBS-IPS-Cone_I_Y-209.13

value: iPSCs from immature Cone cell MakeRetina 209.13


title: TEBS-IPS-Cone_I_Y-209.12

value: iPSCs from immature Cone cell MakeRetina 209.12


title: NY2011_copy_number

description: raw data sample ID: X5

value: Y


title: TEBS-IPS-Cone_I_Y-209.11

value: iPSCs from immature Cone cell MakeRetina 209.11


title: TEBS-IPS-Bipo_I_Y-208.04

value: iPSCs from immature Bipolar cell MakeRetina 208.04

value: bisulfite treated genomic DNA


title: TEBS-IPS-Mull_M_Y-rCr33.01

value: iPSCs from mature Muller cell MakeRetina rCr33.01


title: TEBS-IPS-Mull_M_Y-263.08

value: iPSCs from mature Muller cell MakeRetina 263.08


title: TEBS-IPS-Amac_M_Y-30.02

value: iPSCs from mature Amacrine cell MakeRetina 30.02


title: NY2125_copy_number

description: raw data sample ID: X22


title: TEBS-IPS-Mull_I_Y-207.11

value: iPSCs from immature Muller cell MakeRetina 207.11


title: TEBS-IPS-Bipo_I_Y-rM0401

value: iPSCs from immature Bipolar cell MakeRetina rM0401


title: NY2005_copy_number

description: raw data sample ID: X1

value: N


title: TEBS-IPS-Rod_I_Y-8602

value: iPSCs from immature Rod cell MakeRetina 8602


title: TEBS-mESC-Eb5_E_Y-Eb5

value: mouse embryonic stem cell Eb5


title: TEBS-IPS-Mull_M_Y-rCr33.04

value: iPSCs from mature Muller cell MakeRetina rCr33.04


title: NY2063_copy_number

description: raw data sample ID: X12


title: TEBS-IPS-Rod_S_N-SCN194

value: iPSCs from SCNT Rod cell SCN194


title: NY2101_copy_number

description: raw data sample ID: X18


title: TEBS-IPS-Rod_I_Y-8601

value: iPSCs from immature Rod cell MakeRetina 8601


title: TEBS-IPS-Bipo_I_Y-rM0405

value: iPSCs from immature Bipolar cell MakeRetina rM0405


title: TEBS-IPS-Bipo_I_Y-208.03

value: iPSCs from immature Bipolar cell MakeRetina 208.03


title: NY2086_copy_number

description: raw data sample ID: X14


title: NY2166_copy_number

description: raw data sample ID: X27


title: NY2132_copy_number

description: raw data sample ID: X24


title: NY2087_copy_number

description: raw data sample ID: X15

value: Y


title: NY2123_copy_number

description: raw data sample ID: X20


title: AtrxΔE2+5-ALA #2

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Quiagen).

treatment_protocol: We administered 5-ALA (3mg/kg, p.o.) to AtrxΔE2 mice daily between post-natal day 30 to 90. WT, n=7 mice; AtrxΔE2, n=7 mice; 5-ALA treated AtrxΔE2, n=4 mice.

value: Atrx{delta}E2 mouse

tag: treated with

value: 5-ALA (3mg/kg, p.o.)

value: Hippocampus


title: Wild-type vs. AtrxΔE2

description: normalized log2 ratio (AtrxdE2/WT)

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: WT

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Qiagen).

treatment_protocol: We administered TMPyP4 (30mg/kg, i.p.) to AtrxΔE2 mice twice weekly between post-natal day 30 to 90.

value: wild type


title: NY2126_copy_number

description: raw data sample ID: X23


title: NY2007_copy_number

description: raw data sample ID: X3


title: TEBS-IPS-Rod_M_Y-7602

value: iPSCs from mature Rod cell MakeRetina 7602

value: bisulfite treated genomic DNA


title: AtrxΔE2 #2


title: AtrxΔE2+5-ALA #3


title: NY2027_copy_number

description: raw data sample ID: X8


title: NY2028_copy_number

description: raw data sample ID: X9


title: NY2124_copy_number

description: raw data sample ID: X21


title: NY2062_copy_number

description: raw data sample ID: X11


title: RNA-IPS-Mull_M_N-rCr33.05

data_processing:
Basecalls performed using CASAVA
Transcriptome sequencing data were mapped to the human genome mm9(MGSCv37) using in-house software StrongArm.
We required > 30% of exon have > 30x depth. And raw counts by HTSEQ(version 0.6.1p1) based on GENCODE annotation vM7 have been converted to FPKM.
For Differential Expression analysis, we used Voom packge(R 3.23, edgeR 3.12.1, limma 3.26.9) for statical tests.
Genome_build: mm9(MGSCv37)
Supplementary_files_format_and_content: tab-delimited text files include raw counts

extract_protocol:
RNA was extracted from each iPS cell lines by using RNeasy Plus Mini kit (Qiagen, 74134) or Direct-zol kit (Zymo Research, R2050).
Libraries were prepared from ~500 ng total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s directions (Illumina).

value: iPSCs from mature Muller cell CanNotMakeRetina rCr33.05


title: NY2012_copy_number

description: raw data sample ID: X6


title: RNA-IPS-RodFibr_F_Y-FNR07

value: iPSCs from fibroblast Rod cell MakeRetina FNR07


title: Wild-type vs. AtrxΔE2+TMPyP4

description: normalized log2 ratio (AtrxdE2+TMPyP4/WT)

value: TMPyP4 (30mg/kg, i.p.)


title: TEBS-IPS-Rod_M_Y-3302

value: iPSCs from mature Rod cell MakeRetina 3302


title: RNA-IPS-MullFibr_F_N-FCR03

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR03


title: RNA-IPS-Amac_I_Y-206.12

value: iPSCs from immature Amacrine cell MakeRetina 206.12


title: RNA-IPS-Amac_I_N-rG79.04

value: iPSCs from immature Amacrine cell CanNotMakeRetina rG79.04


title: RNA-IPS-Cone_I_N-rCh209.04

value: iPSCs from immature Cone cell CanNotMakeRetina rCh209.04


title: RNA-IPS-Mull_M_N-rCr143.02

value: iPSCs from mature Muller cell CanNotMakeRetina rCr143.02


title: RNA-IPS-MullFibr_F_N-FCR02

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR02


title: Wild-type #2


title: RNA-IPS-MullFibr_F_N-FCR01

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR01


title: NY2168_copy_number

description: raw data sample ID: X29

value: Y


title: AtrxΔE2+5-ALA #4

value: Atrx{delta}E2 mouse

value: 5-ALA (3mg/kg, p.o.)


title: RNA-IPS-Cone_I_Y-209.13

value: iPSCs from immature Cone cell MakeRetina 209.13


title: RNA-IPS-Cone_I_Y-209.12

value: iPSCs from immature Cone cell MakeRetina 209.12


title: NY2006_copy_number

description: raw data sample ID: X2


title: RNA-IPS-Amac_M_Y-30.02

value: iPSCs from mature Amacrine cell MakeRetina 30.02


title: RNA-IPS-Mull_M_Y-263.08

value: iPSCs from mature Muller cell MakeRetina 263.08


title: RNA-IPS-Mull_M_Y-Cr143.01

value: iPSCs from mature Muller cell MakeRetina Cr143.01


title: AtrxΔE2+5-ALA #1

value: Hippocampus


title: RNA-IPS-Mull_M_Y-rCr33.04

value: iPSCs from mature Muller cell MakeRetina rCr33.04


title: Wild-type #7

value: wild type


title: AtrxΔE2 #1


title: RNA-IPS-Mull_I_Y-207.11

value: iPSCs from immature Muller cell MakeRetina 207.11


title: AtrxΔE2 #7


title: RNA-IPS-Bipo_I_Y-rM0405

value: iPSCs from immature Bipolar cell MakeRetina rM0405


title: RNA-IPS-Bipo_I_Y-rM0401

value: iPSCs from immature Bipolar cell MakeRetina rM0401


title: AtrxΔE2 #5


title: AtrxΔE2 #4


title: INPUT-NRL-Rod_M_N-P21

data_processing:
Basecalls performed using CASAVA
BWA (version 0.5.9-r26-dev, default parameter) to align the ChIP-Seq reads to mouse genome mm9(MGSCv37 from Sanger), Picard(version 1.65(1160)) then have been used for marking duplicated reads. Then only non-duplicated reads with have been kept by samtools (parameter “-q 1 -F 1024” version 0.1.18 (r982:295)). We followed the ENCODE criterion to quality control (QC) the data that non-duplicated version of SPP (version 1.11) have been used to draw cross-correlation and calculated relative strand correlation value (RSC) under support of R (version 2.14.0) with packages caTools(version 1.17) and bitops(version 1.0-6) and estimated the fragment size.
We required > 10M unique mapped reads for point-source factor (H3K4me2/3, H3K9/14Ac, H3K27Ac, CTCF, RNAPolII, BRD4) and RSC > 1. We required 20M unique mapped reads for broad markers (H3K9me3, H3K27me3, H3K36me3). We required 10M unique mapped reads for INPUTs and RSC < 1. We noticed H3K4me1 is point-source factor in some stages while broad in other stages so we QC H3K4me1 as broad markers. Then upon manually inspection, the cross-correlation plot generated by SPP, the best fragment size estimated (the smallest fragment size estimated by SPP in all our cases) were used to extend each reads and generate bigwig file to view on IGV (version 2.3.40).
All profiles were manually inspected for clear peaks and good signal to noise separation. We followed ENCODE guideline for quality control.
We extended reads and generate the final bigwig track normalized to 30M reads for visualization.
Genome_build: mm9(MGSCv37)
Supplementary_files_format_and_content: bigwig

extract_protocol:
After removal of IRMEFs, iPS cells were collected after washing with PBS. Then cells were subjected to crosslinking in 1% formaldehyde (Thermo scientific, 28906) for 10 minutes at room temperature, followed by the addition of glycine at the final concentration of 0.125 M to quench the reaction. After centrifuge, cells were washed with cold PBS, counted and pelleted as 10 million cells for each nuclei preparation.
The nuclei were isolated and prepared for shearing using TruChIP chromatin shearing kit (Covaris, 520127) according to manufacturer’s protocol. After shearing, ChIP was performed using the iDeal ChIP-seq kit (Diagenode, C01010051). The antibodies used were: anti-H3K4me3 (Diagenode, C15410003-50), anti-H3K4me2 (Abcam, ab7766), anti-H3K4me1 (Abcam, ab8895), anti-H3K9/14ac (Diagenode, C15410200), anti-H3K27ac (Abcam, ab4729), anti-H3K36me3 (Active Motif, 61101), anti-H3K27me3 (Active Motif, 39155), and anti-CTCF (Active Motif, 61311). After de-crosslinking, DNA was extracted using MinElute PCR-purification kit (Qiagen, 28006) or Agencourt AMPure XP beads (Beckman Coulter, A63881) and subjected to library preparation using NEBNext ChIP-Seq Library Prep Master Mix Set for illumina (NEB, E6240L). The ChIP experiments and library preparation for antibodies including anti-RNA polymerase II (Abcam, ab5095), anti-Brd4 (Bethyl Laboratories, A301-985A) and anti-H3K9me3 (Active Motif, 39161), were performed by Active Motif.

tag: strain background

value: NRL-GFP sorted Rod cell postnatal day 21

tag: chip antibody

value: none (input)


title: RNA-IPS-Cone_M_N-rCh257.4

value: iPSCs from mature Cone cell CanNotMakeRetina rCh257.4


title: INPUT-IPS-Amac_I_N-rG79.04

value: iPSCs from immature Amacrine cell CanNotMakeRetina rG79.04


title: INPUT-IPS-Mull_M_N-rCr143.02

value: iPSCs from mature Muller cell CanNotMakeRetina rCr143.02


title: AtrxΔE2 #3

value: Atrx{delta}E2 mouse


title: AtrxΔE2 #6


title: RNA-IPS-AmacFibr_F_N-fG140.02

value: iPSCs from fibroblast Amacrine cell CanNotMakeRetina fG140.02


title: INPUT-IPS-Cone_I_N-rCh209.04

value: iPSCs from immature Cone cell CanNotMakeRetina rCh209.04


title: Wild-type #6


title: INPUT-IPS-MullFibr_F_N-FCR01

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR01


title: RNA-IPS-Mull_M_N-rCr263.4

value: iPSCs from mature Muller cell CanNotMakeRetina rCr263.4


title: INPUT-IPS-RodFibr_F_Y-FNR07

value: iPSCs from fibroblast Rod cell MakeRetina FNR07


title: RNA-IPS-Bipo_I_N-rM0408

value: iPSCs from immature Bipolar cell CanNotMakeRetina rM0408


title: Wild-type #4

value: Hippocampus


title: Wild-type #3

value: wild type


title: INPUT-IPS-Cone_I_Y-209.13

value: iPSCs from immature Cone cell MakeRetina 209.13


title: RNA-IPS-Mull_M_Y-rCr33.01

value: iPSCs from mature Muller cell MakeRetina rCr33.01


title: Wild-type #1


title: INPUT-IPS-Cone_I_Y-209.12

value: iPSCs from immature Cone cell MakeRetina 209.12


title: INPUT-IPS-Mull_M_Y-Cr143.01

value: iPSCs from mature Muller cell MakeRetina Cr143.01


title: INPUT-IPS-Mull_M_Y-263.08

value: iPSCs from mature Muller cell MakeRetina 263.08

value: none (input)


title: INPUT-IPS-Mull_M_Y-rCr33.01


title: INPUT-IPS-Amac_M_Y-30.02

value: iPSCs from mature Amacrine cell MakeRetina 30.02


title: RNA-IPS-Cone_M_Y-257.03

value: iPSCs from mature Cone cell MakeRetina 257.03


title: INPUT-IPS-Mull_I_Y-207.11

value: iPSCs from immature Muller cell MakeRetina 207.11


title: INPUT-IPS-Mull_M_N-rCr263.4


title: RNA-IPS-Cone_I_Y-209.11

value: iPSCs from immature Cone cell MakeRetina 209.11


title: RNAPolII-IPS-Amac_I_N-rG79.04

value: iPSCs from immature Amacrine cell CanNotMakeRetina rG79.04

value: RNAPolII (Abcam,ab5095)


title: RNAPolII-IPS-Cone_M_N-rCh257.4

value: iPSCs from mature Cone cell CanNotMakeRetina rCh257.4


title: RNA-IPS-Rod_I_Y-8602

value: iPSCs from immature Rod cell MakeRetina 8602


title: Wild-type #5