title: PA14wt_24h 3

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: biol.replicate 2

hyb_protocol: 750 ng Cy3-labelled cRNA was fragmented and hybridized following Agilents instructions. After hybridization, microarrays were washed with GE Wash Buffer (Agilent).

scan_protocol: Slides were scanned with extended dynamic range (XDR) and 5 µm resolution (4x44K) using a G2565CA high-resolution laser microarray scanner (Agilent)

data_processing: Microarray image data were processed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol

organism: Danio rerio

source_name: total fish larvae

label_protocol: Cy3 labeled cRNA was prepared from 200ng total RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Wild type zebrafish (AB strain, https://zfin.org/action/genotype/view/ZDB-GENO-960809-7) were set up for mating overnight, in 3:2 ratios, females and males, respectively. Fertilized embryos from wildtype zebrafish AB strain were used for all experiments and kept in Embryo medium (E3, 5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4) in an incubator at 28ºC. At 1dpf, larvae were manually dechorionated under a stereomicroscope. At 2dpf, zebrafish larvae were divided randomly into the different experimental groups, at a density of 12 larvae per well of a 12 well plate (Corning) in 1.5mL of E3.

extract_protocol: After the desired exposure to diverse ligands, larvae were euthanized with Tricaine (MS-222, 300 µg/mL) and placed in Trizol for RNA isolation. RNA was isolated according the manufacturers instruction.

treatment_protocol: Three biological replicates of 12 larvae per condition were exposed to different conditions for 4 hours at 28 ºC: DMSO; DMSO + CH223191 (5mM); 3-o-C12-L-HSL (50mM); 3-o-C12-L-HSL (50mM) + CH223191 (5 mM ); 1-hydroxyphenazine (1-HP, 5mM); 1-HP (5mM) + CH223191(5mM) and 1-HP (5mM) + 3-o-C12-L-HSL (50mM).To mention, in experiments using the Aryl hydrocarbon Receptor inhibitor CH223191, larvae were pre-exposed to 5uM of the inhibitor for 2h prior to the start of the experiment and the inhibitor was kept during the experiment.

tag: tag

value: PA14 wildtype


title: DU145_si7DNAPK

status: Public on Oct 01 2019

type: RNA

city: San Francisco

first: vishal

last: kothari

state: California(CA)

address: HD300 1450 Third street, PO Box #3110

department: Radiation Oncology

country: USA

institute: university of California, San francisco

hyb_protocol: Following fragmentation, 3.7 ug of cDNA were hybridized for 20 hr at 48C on Human Gene ST 2.1 strip arrays using the Affymetrix Gene Atlas system.

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing: Data was analyzed using the oligo Bioconductor packages implemented in the R-statistical environment version 3.1.0. RMA was used to fit log2 transformed expression values.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: DU145 cells treated with DNAPK siRNA

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol from 400 ng total RNA (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2).

growth_protocol: Cell lines were grown in standard media (RPMI1640 for C42B, PC3 and DMEM for DU145 and VCaP cell line).

extract_protocol: RNA was extracted using TRIZOL reagent using manufecturer's protocol.

treatment_protocol: Cells were transfected with either non-targeting  siRNAs or with siRNAs targeting DNAPK. Cells were harvested 48 hours post transfection.

tag: cell line

tag: condition

value: DNAPK knockdown


title: PC3_si7DNAPK

source_name: PC3 cells treated with DNAPK siRNA


title: US-10024594.1.CBMRUANXX_8

type: SRA

city: Stanford

first: Erik

last: Ingelsson

state: California

address: 300 Pasteur Drive

institute: Stanford University

description:
barcode:
US-10024594
MaleHFDLivWT

library_source: transcriptomic

data_processing:
Alignment and quantification performed using STAR 2.5.3a
Genome_build: mm10
Supplementary_files_format_and_content: Raw gene expression counts

organism: Mus musculus

source_name: MaleHFDLivWT

extract_protocol:
RNA extraction protocol not provided.
RNA libraries were prepared for sequencing using standard protocols

tag: tissue

value: liver

tag: Sex

value: Male

tag: diet

value: HFD

tag: fam13a genotype

value: WT


title: PA14wt_24h 2

country: Germany

description: biol.replicate 2


title: PDAC_037

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

country: China

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2
mRNA and lncRNA annotated in GencodeV25 were quantified using featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: Blood extracellular vesicle

extract_protocol:
Plasma EV RNAs were extracted by exoRNeasy Serum/Plasma kit.
RNA libraries were prepared for sequencing using SMARTer® Stranded Total RNA-Seq Kit - Pico Input Mammalian

value: Plasma

tag: disease state

value: PDAC


title: VCaP_control

description: VCaP,siNTC

source_name: VCaP cells treated with non-targeting siRNA

value: VCaP

value: control


title: PDAC_041


title: T2_WT_I3

city: Irapuato

first: Manuel

last: Villalobos-Escobedo

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León Irapuato

department: Ingeniera Genetica

country: Mexico

institute: cinvestav

data_processing:
The sequences were mapped in the predicted transcripts in the genome of T. atroviride v2 from the JGI page (http://genome.jgi.doe.gov/Triat2/Triat2.home.html) using the Salmon software (Patro et al., 2017) and for A. thaliana, the version 10 of the genome obtained from TAIR was used for this mapping (https://www.arabidopsis.org/).
Differential expression analysis was done with the edgeR package (Robinson et al., 2010), using transcripts that at least had three counts per million in some library and a total of no less than 5 counts per million in all libraries. The counts matrix was normalized by trimmed mean of M-values method (TMM) (Robinson & Oshlack, 2010). The genes differentially expressed between the different conditions was determined using the method "Generalized linear model (GLM) likelihood radio test" (McCarthy et al., 2012). An FDR ≤ 0.05 was considered statistically significant in this analysis. A Fold-change =1 was put as a filter for differential genes.
Supplementary_files_format_and_content: counts

organism: Trichoderma atroviride

source_name: Trichoderma wild-type strain with Arabidopsis 3 dpi

growth_protocol:
The Arabidopsis seeds had previously been sterilized and subjected to a vernalization period of 2 days, at 4 ° C in darkness. Once seeded, they were sealed and incubated in a growth chamber at 24 °C, with a photoperiod of 16 h in constant light (200 μmolm2s-1) per 8 h in darkness. After four days 1x106 spores of the respective strains were inoculated 5 cm away from seedlings. At 3 and 5 days after the inoculation (dpi), both mycelium and roots were collected to obtain the RNA.
Trichoderma was grown in MS medium. The RNA of the fungus was extracted from the mycelium closest to the root of Arabidopsis at 3 dpi and at 5 dpi when there is already contact between the fungus and the plant. As a control of this experiment, the fungus was grown without the presence of Arabidopsis at 5 dpi.

extract_protocol:
The extraction of RNA from the mycelium of T. Atroviride and the root of the plant was also done with the TRIZOL protocol (INVITROGEN).
The cDNA synthesis was performed according to the TruSeq® RNA Sample Preparation v2 Guide protocol and the sequencing was done on the Illumina HiSeq 2000 platform, in a 2X100 format.

value: mycelium

tag: treatment

value: interaction with the plant

tag: replicates

value: biological replica 2


title: T2_WT_I5

source_name: Trichoderma wild-type strain with Arabidopsis 5 dpi


title: ni_24h 2

description: biol.replicate 1

value: non infected


title: PC3_control

source_name: PC3 cells treated with non-targeting siRNA


title: US-10024601.1.CBMRUANXX_6

description:
barcode:
US-10024601
MaleHFDLivKO

source_name: MaleHFDLivKO

value: KO


title: PDAC_036


title: DU145_control

source_name: DU145 cells treated with non-targeting siRNA


title: ni_24h 1

description: biol.replicate 1


title: PA14wt_24h 1

description: biol.replicate 2


title: ni_24h 3

description: biol.replicate 2


title: C4.2B_control

source_name: C42B cells treated with non-targeting siRNA


title: C4.2B_si7DNAPK

source_name: C42B cells treated with DNAPK siRNA


title: US-10024600.1.CBMRUANXX_6

description:
barcode:
US-10024600
MaleHFDLivKO


title: PA14wt_5h 3

description: biol.replicate 1


title: PDAC_035


title: US-10024595.1.CBMRUANXX_6

description:
barcode:
US-10024595
MaleHFDLivWT


title: T2_NR_I5

source_name: Trichoderma noxR mutant with Arabidopsis 5 dpi


title: PA14wt_5h 2

description: biol.replicate 1


title: PA14wt_5h 1

description: biol.replicate 1


title: PDAC_034


title: T2_NR_I3

source_name: Trichoderma noxR mutant with Arabidopsis 3 dpi


title: US-10024598.1.CBMRUANXX_6

description:
barcode:
US-10024598
MaleHFDLivKO


title: T1_WT_I5

value: biological replica 1


title: PDAC_033


title: T1_WT_I3


title: US-10024573.1.CBMRUANXX_3

description:
barcode:
US-10024573
MaleChowLivWT

source_name: MaleChowLivWT

value: Chow


title: ni_5h 3

description: biol.replicate 1


title: PDAC_032


title: US-10024572.1.CBMRUANXX_3

description:
barcode:
US-10024572
MaleChowLivWT


title: T1_NR_I5


title: US-10024571.1.CBMRUANXX_3

description:
barcode:
US-10024571
MaleChowLivWT


title: 72 h B NR rep1

city: Goettingen

first: Agnieszka

last: Zienkiewicz

address: Justus-von-Liebig Weg 11

department: Department of Plant Biochemistry

institute: University of Goettingen

description:
starvation_recovery_all_lfc1_cluster1.txt
starvation_recovery_all_lfc1_cluster2.txt
starvation_recovery_all_lfc1_cluster3.txt
starvation_recovery_all_lfc1_cluster4.txt

data_processing:
RNA-Seq reads were trimmed using Trimmomatic (v0.32) (Bolger et al. 2014, Bioinformatcs 30: 2114-2120.) with removal of leading and trailing low quality bases (below quality score 10 with a 4-base wide sliding window) as well as TruSeq Single End adaptors.
The resulting reads were aligned to the N. oceanica CCMP1779 genome assembly (GSE36959) (Vieler et al., 2012) using STAR (2.3.0e) (Dobin et al., 2013, Bioinformatics 29: 15-21) by only allowing unique mapping, a maximum of 4 mismatches per pair and a maximum intron length of 10,000 bp. The HTSeq (0.6.1) (Anders et al., 2015, Bioinformatics 21: 166-169.) was used to generate a count table for all genes using the exon as the feature type as well as the intersect-nonempty mode so that only reads that were completely aligned to two genes are considered ambiguous.
HTSeq count tables were used for differential expression analysis using DEseq2 (Love et al., 2014, Genome Biology 15: 550.). Differential gene expression was examined using DESeq2 (Love et al., 2014). A generalized linear model was fit, and we tested on condition (deprivation or recovery) and the time:condition interaction with log2-fold changes greater than 1. Significant differentially expressed genes with p-values less than 0.01 were identified after Benjamini-Hochberg (BH) multiple testing correction. Differentially expressed genes were clustered based on expression using K-means clustering (k = 4) with the Pearsons correlation distance metric within MeV (4.8.1) (Saeed et al., 2003, Biotechniques 34: 374-378.).

organism: Nannochloropsis oceanica

source_name: Nannochloropsis

growth_protocol: Nannochloropsis oceanica CCMP1779 cells were grown in F/2 medium (final concentrations in g/L-1:  NaH2PO4x1H2O 3.63x10-5 , Na2SiO3x9H2O 1.07x10-4, FeCl3x6 H2O 1x10-5, Na2EDTAx2H2O 1x10-5, CuSO4x5H2O 4x10-8, Na2MoO4x2 H2O 3x10-8, ZnSO4x7H2O 8 x10-8 , CoCl2x6H2O 5x10-8 MnCl2x4H2O 9x10-7, Vitamine B12 1x10-10,  Thiamine-HCl 3 x 10-7, Biotin 2 x10-9) under continuous light (85 μmol m-2 s-1 at 22°C with shaking at 105 rpm). For N deprivation experiments cells were washed twice with N-free F/2 medium then resuspended in N-free medium. For N resupply (NR) experiments, cells were grown in N-free medium for 72 h, than cells were harvested and resuspended in F/2 medium supplemented with N.

extract_protocol:
Cultured cells (50 ml per sample) were harvested for RNA isolation after N- or NR treatments at 6, 12, 24, 48 and 72 h. For each time point two biological replicates were harvested by centrifugation (4000 x g, 10 min, 22°C). Cells were flash-frozen in liquid N and ground  using TissueLyser II (Qiagen). RNA was extracted using the E.Z.N.A® Plant RNA kit (OMEGA) according to the manufacturer’s instructions. RNA quality was verified using the Bioanalyzer (Agilent). Single-end, 50 bp nucleotide sequences were acquired for each sample using an Illumina HiSeq 2500 (MSU-Research Technology Support Facility). RNA-Seq reads were trimmed using Trimmomatic (v0.32) (Bolger et al., 2014) with removal of leading and trailing low quality bases (below quality score 10 with a 4-base wide sliding window) as well as TruSeq Single End adaptors. The resulting reads were aligned to the N. oceanica CCMP1779 genome assembly (GSE36959) (Vieler et al., 2012) using STAR (2.3.0e) (Dobin et al., 2013) by only allowing unique mapping, a maximum of 4 mismatches per pair and a maximum intron length of 10,000 bp. The HTSeq (0.6.1) (Anders et al., 2015) was used to generate a count table for all genes using the exon as the feature type as well as the intersect-nonempty mode so that only reads that were completely aligned to two genes are considered ambiguous. HTSeq count tables were used for differential expression analysis using DEseq2 (Love et al., 2014). Differential gene expression was examined using DESeq2 (Love et al., 2014). A generalized linear model was fit, and we tested on condition (deprivation or recovery) and the time:condition interaction with log2-fold changes greater than 1. Significant differentially expressed genes with p-values less than 0.01 were identified after Benjamini-Hochberg (BH) multiple testing correction. Differentially expressed genes were clustered based on expression using K-means clustering (k = 4) with the Pearsons correlation distance metric within MeV (4.8.1) (Saeed et al., 2003).                                                              References:                                                                                Anders S, Pyl PT, Huber W (2015) HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics 31: 166-169    Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120    Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15: 550    Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J (2003) TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34: 374-378    Vieler A et al. (2012) Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779. PLoS Genet 8: e1003064
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: liquid cell culture

tag: time points

value: 72 h of N resupply (72 h NR) B

tag: genotype

value: wild type


title: 72 h B  rep 2


title: T1_NR_I3


title: 72 h A NR rep 2

value: 72 h of N resupply (72 h NR) A


title: PDAC_030


title: PDAC_029


title: PDAC_031


title: T2_NR_C5

source_name: Only Trichoderma noxR mutant 5 dpi (without Arabidopsis)


title: US-10024570.1.CBMRUANXX_3

description:
barcode:
US-10024570
MaleChowLivWT

value: liver

value: Male


title: 72 h A NR rep1


title: ni_5h 2

description: biol.replicate 1

source_name: total fish larvae


title: US-10024577.1.CBMRUANXX_3

description:
barcode:
US-10024577
MaleChowLivKO

source_name: MaleChowLivKO


title: US-10024599.1.CBMRUANXX_6

description:
barcode:
US-10024599
MaleHFDLivKO

value: HFD


title: ni_5h 1

description: biol.replicate 1


title: T1_WT_C5

source_name: Only Trichoderma wild-type strain 5 dpi (without Arabidopsis)


title: PDAC_028

source_name: Blood extracellular vesicle

value: Plasma

value: PDAC


title: 48 h B NR rep 2

value: 48 h of N resupply (48 h NR) B


title: US-10024576.1.CBMRUANXX_3

description:
barcode:
US-10024576
MaleChowLivKO


title: US-10024575.1.CBMRUANXX_3

description:
barcode:
US-10024575
MaleChowLivKO


title: T1_NR_C5

value: mycelium

value: control


title: 48 h A NR rep 2

value: 48 h of N resupply (48 h NR) A


title: PDAC_026


title: PDAC_027


title: 48 h B NR rep1


title: PDAC_025


title: US-10024574.1.CBMRUANXX_3

description:
barcode:
US-10024574
MaleChowLivKO


title: 24 h B NR rep1

value: 24 h of N resupply (24 h NR) B


title: WT_Rpb2_M

city: La Jolla

first: Christopher

middle: K

last: Glass

state: CA

address: 9500 Gilman Drive

department: School of Medicine

institute: University of California, San Diego

library_source: genomic

data_processing:
Preprocessing: FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. Bowtie2 with default parameters was used to map ChIP-seq experiments (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
H3K27ac and Rbp2 single was quantified by HOMER (Heinz et al., 2010) after IDR peak identification.
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated Homer annotation files /HOMER Peak files

molecule: genomic DNA

extract_protocol: ChIP-Seq sequencing libraries were prepared from recovered DNA by blunting, A-tailing, and adapter ligation using barcoded adapters (NextFlex, Bioo Scientific) as previously described (Heinz et al., 2010; Gosselin et al., 2014). Libraries were PCR-amplified for 12-15 cycles and size selected for fragments (225-400 bp) by gel extraction (10% TBE gels, Life Technologies EC62752BOX). Libraries were single-end sequenced for 51 cycles with an average sequence depth >20 million on an Illumina HiSeq 4000 or NextSeq 500 platform (Illumina, San Diego, CA) according to manufacturer’s instructions.

value: WT

tag: chip antibody

tag: gender

value: M


title: PDAC_024


title: PDAC_023


title: 48 h A NR rep1


title: PDAC_022


title: WT_Input_M


title: WT_Input_F

value: F


title: WT_Rpb2_F


title: 24 h A NR rep1

value: liquid cell culture

value: 24 h of N resupply (24 h NR) A


title: 24 h A NR rep 2

value: wild type


title: PDAC_021


title: WT_H3k27ac_M


title: PDAC_020


title: WT_H3k27ac_F


title: 24 h B NR rep 2


title: PDAC_019


title: HaCaT_control_harvested24h_rep3

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 20 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: HaCaT cells, no blue light irradiation, harvested 24h after irradiation

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

growth_protocol: HaCaT cells were cultured under standard conditions at 37°C with 5% CO2. They were cultured in Dulbecco´s modified Eagle´s medium (DMEM) high glucose containing 10% fetal bovine serum (FBS), 1mM sodium pyruvate and 100U/mL penicillin/streptomycin.

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

treatment_protocol: Lumileds LUXEON Rebel LXML-PR01-0275 were used (Koninklijke Philips N.V., Eindhoven/Netherlands) with an intensity of 23mW/cm2 at an irradiation distance of 55mm, beam divergence was ±15° and a peak wavelength of 453 nm (blue light).

tag: harvest time

tag: light

value: Control

tag: plate


title: HaCaT_7.5minblue_harvested24h_rep2

description: 10.35J/cm², 23mW/cm²

source_name: HaCaT cells, 7.5min blue light irradiation, harvested 24h after irradiation

value: Blue light 7.5min


title: HaCaT_7.5minblue_harvested24h_rep3

description: 10.35J/cm², 23mW/cm²


title: HaCaT_control_harvested24h_rep2


title: PDAC_018


title: HaCaT_7.5minblue_harvested24h_rep1

description: 10.35J/cm², 23mW/cm²


title: 12 h B NR rep1

value: 12 h of N resupply (12 h NR) B


title: 12 h A NR rep 2

value: 12 h of N resupply (12 h NR) A


title: PDAC_017

value: Plasma


title: 12 h A NR rep1


title: Cx3cr1KO_Input_M


title: PDAC_016

value: PDAC


title: HaCaT_control_harvested24h_rep1


title: HaCaT_control_harvested3h_rep3

source_name: HaCaT cells, no blue light irradiation, harvested 3h after irradiation


title: Cx3cr1KO_Input_F


title: PDAC_015


title: 6 h B NR rep1

value: 6 h of N resupply (6 h NR) B


title: 6 h B NR rep 2


title: HaCaT_control_harvested3h_rep2


title: 12 h B NR rep 2


title: Cx3cr1KO_H3k27ac_M


title: Cx3cr1KO_Rpb2_M


title: PDAC_014


title: HaCaT_7.5minblue_harvested3h_rep3

description: 10.35J/cm², 23mW/cm²

source_name: HaCaT cells, 7.5min blue light irradiation, harvested 3h after irradiation


title: Cx3cr1KO_H3k27ac_F


title: HaCaT_7.5minblue_harvested3h_rep2

description: 10.35J/cm², 23mW/cm²


title: 6 h A NR rep 2

value: 6 h of N resupply (6 h NR) A


title: Cx3cr1KO_Rpb2_F


title: Mouse hypothalamus KO3 (Drop-Seq)

city: Los Angeles

first: Douglas

last: Arneson

address: 2000 Terasaki Life Sciences Bldg 610 Charles E Young Drive East

department: Integrative Biology and Physiology

institute: UCLA

description: Sample 6

data_processing:
Base calls performed with bcl2fastq2.15.
Read 2 was aligned with Star v2.5.0c.
Each aligned read was tagged with its mate-pair UMI and cell barcode.
Each aligned exonic read was tagged with a gene name.
A digital gene expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes.
Samples 1-6 -- prepared from both WT and IDOL KO mouse hypothalami on multiple separate days -- were merged together into a single matrix. Merged DGE file from all 6 samples generated. Entries contain raw UMI counts.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Digital gene expression matrices (genes x cells). Compressed, flat text files with tab delimiters.

source_name: Mus musculus hypothalamus KO, 8 weeks

extract_protocol:
Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads. Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol.
Mouse hypothalamus was dissected and dissociated into single-cell suspension, followed by drop-seq library preparation. Libraries were prepared following the latest drop-seq protcol.

value: IDOL KO

value: hypothalamus

tag: age

value: 8 weeks

tag: barcode position

value: Bases 1 to 12 on R1

tag: umi position

value: Bases 13 to 20 on R1


title: 6 h A NR rep1

tag: tissue


title: PDAC_012


title: Mouse hypothalamus KO2 (Drop-Seq)

description: Sample 5


title: HaCaT_7.5minblue_harvested3h_rep1

description: 10.35J/cm², 23mW/cm²


title: PDAC_011


title: Mouse hypothalamus KO1 (Drop-Seq)

description: Sample 4


title: Mouse hypothalamus WT3 (Drop-Seq)

description: Sample 3

source_name: Mus musculus hypothalamus WT, 8 weeks

value: WT


title: PDAC_010


title: HaCaT_control_harvested3h_rep1


title: PDAC_009


title: Mouse hypothalamus WT2 (Drop-Seq)

description: Sample 2


title: 72 h B N- rep1

value: liquid cell culture

value: 72 h of N deprivation (72 h N-) B


title: 72 h A N- rep1

value: 72 h of N deprivation (72 h N-) A

value: wild type


title: 72 h A N- rep 2


title: HaCaT_control_harvested1h_rep3

source_name: HaCaT cells, no blue light irradiation, harvested 1h after irradiation

value: Control


title: PDAC_013


title: HaCaT_control_harvested1h_rep2


title: P17_retina_OIR+AFL_rep3

city: Cambridge

first: Jesus Eduardo

last: Rojo Arias

address: Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

description: SAMPLE 18

hyb_protocol: 5.5 ug of biotinylated and fragmented single-stranded cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Whole Transcriptome Arrays according to the GeneChip® WT PLUS Reagent Kit User Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
The scanned images were processed with the Transcriptome Analysis Console (TAC) Software (Affymetrix) using default parameters to obtain background subtracted and summarized probe sets.  The CDF MTA-1_0_na34-1-mm10 was used in the analysis.
The data were analyzed with the Agilent GeneSpring GX software version 13.0 using Affymetrix default analysis settings and GC-RMA. No baseline transformation was done. The file normalized_data_matrix.txt includes the GC-RMA values.

source_name: Retina, oxygen-induced retinopathy mouse treated with 25 mg per kg body weight AFL on P13 and P15

label_protocol: Biotinylated cDNA samples were prepared according to the GeneChip WT PLUS Reagent Kit (902280) protocol from 250 ng total RNA.

growth_protocol: Mice were housed in standard conditions. OIR mice were subjected to 75% oxygen from postnatal day 6 to postnatal day 11. OIR+AFL mice analyzed on postnatal day 14 were treated with Aflibercept at 25 mg per kg body weight on postnatal day 13. OIR+AFL mice analyzed on postnatal day 17 were treated with Aflibercept at 25 mg per kg body weight on postnatal days 13 and 15.

extract_protocol: Total RNA was isolated from whole retinas as follows. Mice were sacrificed either at P14 or P17 by an overdose of ketamine and xylazine (as before). Eyes were immediately removed from their orbits and retinal cups were promptly dissected in PBS at 37°C. After dissection, retinas of 2 normoxic, 2 OIR or 2 OIR+AFL mice were pooled together and warm PBS was replaced by 750 µl TRIzol (Thermo Fisher Scientific, MA, USA). Next, retinal tissues were disrupted by 10 rounds of aspiration/ejection through 18G and 23G needles and incubated at RT for 5 min. Thereafter, 150 µl chloroform (Merck, Darmstadt, Germany) were added, samples were vortexed at maximum speed for 15 seconds, incubated at RT for 15 min, and centrifuged at 12 000 g for 20 min at 4°C. After centrifugation, the aqueous phase was collected, 1.5 µl RNA-grade glycogen (Thermo Fisher Scientific, MA, USA) and 375 µl isopropanol (Merck, Darmstadt, Germany) were added. Samples were subsequently vortexed 15 seconds at maximum speed and centrifuged at 12000 g for 20 min at 4°C. The supernatant was discarded, and pellets were washed twice in 1 ml 75% ethanol in molecular biology-grade water, air-dried for 10-20 min and re-suspended in 20 µl RNAse-free water.

treatment_protocol: Aflibercept was administered to OIR mice intra-peritoneally at 25 mg per kg body weight on postnatal days 13 and 15.

value: Retina

tag: developmental stage

value: Postnatal day 17


title: HaCaT_7.5minblue_harvested1h_rep2

description: 10.35J/cm², 23mW/cm²

source_name: HaCaT cells, 7.5min blue light irradiation, harvested 1h after irradiation

value: Blue light 7.5min


title: HaCaT_7.5minblue_harvested1h_rep3

description: 10.35J/cm², 23mW/cm²


title: HaCaT_control_harvested1h_rep1


title: PDAC_007

value: Plasma

value: PDAC


title: 72 h B N- rep 2


title: Thymus_4_S32

city: Chicago

first: Nicolas

last: Chevrier

state: Illinois

address: 5640 South Ellis Avenue

department: Pritzker School of Molecular Engineering

institute: The University of Chicago

data_processing:
Fastq files were demultiplexed with custom codes and quality checked with FastQC.
Read mapping using STAR aligner with mm10 genome.
FeatureCounts was used to count mapped reads for each gene.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample.

source_name: Thymus

extract_protocol:
Upon thawing, tissues were lyzed in Trizol reagent and total RNA was extracted by phenol-chloroform extraction followed by purification with Dynabeads MyOne Silane beads (ThermoScientific, catalog # 37002D). Total RNAs were further purified by on-bead DNase I treatment followed by cleanup with 80% ethanol. RNA quality was verified using high sensitivity RNA screenTape assay (Agilent Technologies, catalog # 5067-5579) for tapestation analysis. RNA concentration was measured using the Quant-iT RiboGreen RNA Reagent (ThermoScientific, catalog # R11491).
For multiplex library construction, 100 ng of total RNA was used as a starting point for each sample. Total RNA was heat-fragmented to an average size of 500 bp fragments in the presence of 1X RT buffer and 1 pmole of barcoded oligo(dT) primers containing Illumina-compatible adaptor sequences (index 1, custom order from IDT). Resulting barcoded, cDNA:RNA samples were pooled using Zymo RNA clean & concentrator columns (>200nt protocol; Zymo Research, catalog # R1017) and RNA was hydrolyzed by adding to each 20 μl of RT reaction, 10 μl 0.5 M EDTA followed by 10 μl 1.0 M NaOH, and incubating at 65°C for 15 minutes (protocol from Oligo Clean & Concentrator manual, Zymo Research, catalog number D4060). Resulting single-stranded cDNA pools were flanked by Illumina-compatible adaptor sequences in their 3’ end using a ‘primer extension’ method with a custom oligonucleotide and DNA Pol I, Large Klenow Fragment exo minus (NEB, catalog # M0210L). cDNA pools flanked on both ends with illumina sequences were then amplified by PCR using primer to add illumina P5 adaptor containing a second index (index 2, custom order from IDT) and Q5 Hot Start High-Fidelity (NEB, catalog # M0494L), and sequenced on Illumina NexSeq500 machine.

value: 6 weeks old

tag: Sex

value: female

value: Thymus


title: P17_retina_OIR+AFL_rep1

description: SAMPLE 16


title: 48 h B N- rep1

value: 48 h of N deprivation (48 h N-) B


title: PDAC_006

tag: disease state


title: 48 h B N- rep 2


title: P17_retina_OIR_rep3

description: SAMPLE 15

source_name: Retina, oxygen-induced retinopathy mouse


title: 48 h A N- rep 2

source_name: Nannochloropsis

value: 48 h of N deprivation (48 h N-) A


title: HaCaT_7.5minblue_harvested1h_rep1

description: 10.35J/cm², 23mW/cm²


title: 48 h A N- rep1


title: PDAC_005


title: Thymus_2_S30


title: Thymus_3_S31


title: P17_retina_OIR+AFL_rep2

description: SAMPLE 17


title: P17_retina_OIR_rep1

description: SAMPLE 13


title: Thymus_1_S29


title: Mouse hypothalamus WT1 (Drop-Seq)

description: Sample 1

value: hypothalamus

value: 8 weeks

value: Bases 1 to 12 on R1

value: Bases 13 to 20 on R1


title: P17_retina_OIR_rep2

description: SAMPLE 14


title: PDAC_008


title: PDAC_003


title: 24 h B N- rep 2

value: liquid cell culture

value: 24 h of N deprivation (24 h N-) B


title: P17_retina_normoxia_rep3

description: SAMPLE 12

source_name: Retina, normoxic mouse


title: Spleen_4_S8

source_name: Spleen

value: Spleen


title: Spleen_3_S7


title: P17_retina_normoxia_rep2

description: SAMPLE 11

value: Retina


title: 24 h B N- rep1

value: wild type


title: PDAC_002


title: PDAC_001


title: 24 h A N- rep1

value: 24 h of N deprivation (24 h N-) A


title: Spleen_2_S6


title: Spleen_1_S5


title: P17_retina_normoxia_rep1

description: SAMPLE 10

value: Postnatal day 17


title: Colo320_G12V_Rep2

city: Rochester

first: Rentian

last: Wu

address: 200 1st Street SW

institute: Mayo Clinic

description:
Colo320_KRAS_RNAseq_DESeq2.txt
Colo320_KRAS_RNAseq_RPM.txt

data_processing:
Sequence reads from RNA-seq samples were aligned to human genome hg19 and gene annotation from Refseq gene using STAR v2.5.3 (Dobin et al., 2013). DESeq2 v1.14.1 (Love et al., 2014) was used to normalize gene read counts and calculate log2 fold change, p value and false discovery rate (FDR).
Reads from ChIP-seq were aligned to the human genome (hg19) using the Bowtie2 (Langmead and Salzberg, 2012). The H3K27ac peaks were identified using MACS2 (Zhang et al., 2008) using 0.01 as the cutoff FDR value.
Genome_build: hg19
Supplementary_files_format_and_content: bed file and txt file

source_name: Colo320 expressing KRAS G12V

growth_protocol: Cells were cultured in DMEM (Dulbecco’s Modified Eagle Medium) supplemented with 10% FBS (Sigma), 2 mM Glutamate (Gibco), penicillin and streptomycin (Millipore).  All cell lines were maintained at 37 °C in a humidified incubator with an atmosphere of 5% CO2.

extract_protocol:
The total RNA was extract using QIAGEN RNeasy Mini Kit. 5x106 active growing cultured cells were harvest, suspended in 10ml PBS, and cross-linked with 1% formaldehyde (final concentration) for 10 min, and quenched with 125 mM glycine for 5 min at room temperature, and washed twice with PBS. The pellets were resuspended in 100 μl cell lysis buffer (1% Triton-X, 0.1% Sodium-Deoxycholate, proteinase inhibitor, TE) and incubated on ice for 10 min. Lysates were diluted with 900 ul TE, and sonicated for 15 min (30 sec on / 30 sec off) using Bioruptor pico (Diagenode, Inc., Denville, NJ), and centrifuged at top speed for 10 min. The supernants were collected and the chromatin content was estimated by the Qubit assay (Invitrogen). The chromatin was then incubated with 2.5 μg of rabbit polyclonal anti-H3K27ac antibody (Abcam, D5E4, 1:5000) on a rocker overnight. Protein G-magnetic beads (30 μL, Invitrogen) were added for 4 hours incubation. The bedads were entensively washed with ChIP buffer (50 mM Tris-HCl, pH8.1, 10 mM EDTA, 100 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), high salt buffer (50 mM Tris-HCl, pH8.1, 10 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), LiCl buffer (10 mM Tris-HCl, pH8.0, 0.25 M LiCl2, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA), and TE buffer. Bound chromatin was eluted and reverse-crosslinked at 65 °C overnight. DNAs were purified using Min-Elute purification kit (QIAGEN, Valencia, CA) after the treatment of RNase A and proteinase K.
RNA library preparation and sequence were done through Novogene. ChIP-seq libraries were prepared from ChIP DNA using the NEBNext® Ultra™ II DNA Library Prep Kit (NEB). The ChIP-seq libraries were sequenced to 50 base pairs on an Illumina HiSeq 4000 using pair-end mode in the Mayo Clinic Center for Individualized Medicine Medical Genome Facility.

tag: cell type

value: Colo320 colon cancer cell

value: KRAS G12V


title: PDAC_004

value: Plasma

value: PDAC


title: 12 h B N- rep 2

value: 12 h of N deprivation (12 h N-) B


title: P14_retina_OIR+AFL_rep3

description: SAMPLE 9

source_name: Retina, oxygen-induced retinopathy mouse treated with 25 mg per kg body weight AFL on P13

value: Postnatal day 14


title: Skin_4_S56

source_name: Skin

value: 6 weeks old

value: female

value: Skin


title: 12 h B N- rep1


title: P14_retina_OIR+AFL_rep2

description: SAMPLE 8


title: 24 h A N- rep 2


title: Skin_3_S55


title: Colo320_WT_Rep2

source_name: Colo320 expressing KRAS WT

value: KRAS WT


title: P14_retina_OIR+AFL_rep1

description: SAMPLE 7


title: P14_retina_OIR_rep3

description: SAMPLE 6


title: Skin_2_S54


title: Colo320_Vector_Rep2

source_name: Colo320 expressing vector

value: Vector


title: P14_retina_OIR_rep2

description: SAMPLE 5


title: 12 h A N- rep 2

value: liquid cell culture

value: 12 h of N deprivation (12 h N-) A


title: Skin_1_S53


title: 12 h A N- rep1


title: 6 h B N- rep 2

value: 6 h of N deprivation (6 h N-) B


title: P14_retina_OIR_rep1

description: SAMPLE 4

value: Retina


title: K7174_Rep2

description:
K7174_RNAseq_DESeq2.txt
K7174_RNAseq_RPM.txt

value: HCT116 colon cancer cell

tag: treatment


title: Colo320_Vector_Rep1


title: 6 h B N- rep1

tag: strain

value: wild type


title: 6 h A N- rep 2

tag: time points

value: 6 h of N deprivation (6 h N-) A


title: SI_4_S52

source_name: Small Intestine

value: Small Intestine


title: Colo320_G12V_Rep1

value: Colo320 colon cancer cell

tag: genotype

value: KRAS G12V


title: SI_3_S51


title: P14_retina_normoxia_rep2

description: SAMPLE 2


title: 6 h A N- rep1


title: K7174_Rep1


title: SI_2_S50


title: P14_retina_normoxia_rep3

description: SAMPLE 3


title: SI_1_S49


title: DMSO_Rep2

value: DMSO


title: P14_retina_normoxia_rep1

description: SAMPLE 1

value: Postnatal day 14


title: Colo320_WT_Rep1


title: 0 h B rep2

value: start point of N deprivation (0 h) B


title: DMSO_Rep1


title: GATA1WT_Rep4

description:
GATA1KO_RNAseq_DESeq2.txt
GATA1KO_RNAseq_RPM.txt

source_name: GATA1 WT HCT116

value: GATA1 WT


title: 0 h B rep1


title: PBMC_4_S12

source_name: Whole blood

value: 6 weeks old

value: female

value: Whole blood


title: GATA1WT_Rep3


title: PBMC_3_S11


title: 0 h A rep2

value: liquid cell culture

value: start point of N deprivation (0 h) A


title: KO old, replicate 2

city: La Línea de la Concepción

first: Alejandro

last: Peralta-Garcia

state: Cádiz

address: Gabriel Miró 52 A

country: Spain

institute: Pablo de Olavide University

description:
NLRP3 knockout
Mouse_KO_Old-2

hyb_protocol: Following fragmentation, 5.2 µg of ss-cDNA were hybridized for 16 hr at 45C on GeneChipTM Mouse Transcriptome Array (MTA) 1.0. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression Analysis Technical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G and the images were acquired by Affymetrix GeneChip Command Console® (AGCC) Software.

data_processing: The .CEL files generated with AGCC software were processed and normalized into expression values using the SST (Signal Space transformation)-RMA (Robust Microarray Average) method by Expression Console (Affymetrix). The following gene level and alternative splicing analysis (ANOVA unpaired one-way) were performed using the Transcriptome Analysis Console (TAC) Software developed by Affymetrix.

source_name: Old knockout mouse

label_protocol: Total RNA from each sample (100 ng) was used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip WT PLUS Reagent Kit User Manual (Affymetrix).

growth_protocol: For all experiments, only male mice were used. Young and old C57/BL6/J and NLRP3−/− transgenic mice (C57BL/6J background), weighing 25-30 g were maintained on a regular 12 h light/dark cycle. All groups had ad libitum access to their prescribed diet and water throughout the whole study. Body weight and food intake were monitored weekly. Animal rooms were maintained at 20–22°C with 30–70% relative.

extract_protocol: RNeasy® Mini Kit from Qiagen was used for RNA extraction. It was performed according to manufacturer's protocol.

tag: strain/background

tag: genotype/variation

value: NLRP3 -/-

value: old (22 months)

value: male

value: cardiac


title: 0 h A rep1

value: wild type


title: KO old, replicate 3

description:
NLRP3 knockout
Mouse_KO_Old-3

tag: gender


title: KO old, replicate 1

description:
NLRP3 knockout
Mouse_KO_Old-1


title: GATA1WT_Rep2

value: HCT116 colon cancer cell


title: KO young, replicate 3

description:
NLRP3 knockout
Mouse_KO_Young-3

source_name: Young knockout mouse

value: young (3 months)


title: KO6

city: Baltimore

first: Mary

last: Armanios

state: MD

address: 401 North Broadway

institute: The Johns Hopkins University

data_processing:
Raw data were generated by NovaSeq6000 using NovaSeq Control Software v1.4. BCL files were demultiplexed and converted to compressed fastq with bcl2fastq2.20.0 (Illumina’s current demultiplexer).
Reads were trimmed to 100bp after FastQC (v. 0.10.0) quality checking
The reads were aligned to the mm10 genome using topHat2 v.2.1.0
The aligned reads were assembled with CLASS v.2.1.7 to create transcript models (transfrags).
Transfrags were merged using Cuffmerge (v.2.2.1) and mapped to GENECODE v.M17
FPKM were calculated with Cuffdiff2 v.2.2.1
FPKM values were log2 converted and quantile normalized with Partek GS 7.0
Genome_build: mm10
Supplementary_files_format_and_content: The tab-delimited text file (Cuffdiff_Annot_matrix.txt) provides the (Partek GS) Log2 quantile normalized FPKM values and annotations for all samples.

source_name: E12.5 Head

extract_protocol:
Whole heads were preserved in RNAlater, Millipore-Sigma, and then homogenized using the Bullet Blender (Zirconium oxide beads). Total RNA was prepared from this homogenate
Truseq Stranded mRNA Library preparation

value: embryonic head


title: PBMC_1_S9


title: PBMC_2_S10


title: GATA1WT_Rep1


title: KO5


title: KO4


title: mesLN_4_S16

source_name: mesenteric lymph node

value: mesenteric lymph node


title: mesLN_2_S14


title: mesLN_3_S15


title: GATA1KO_Rep3

source_name: GATA1 KO HCT116

value: GATA1 KO


title: GATA1KO_Rep4


title: WT old, replicate 3

source_name: Old wild type mouse


title: KO young, replicate 1

description:
NLRP3 knockout
Mouse_KO_Young-1


title: GATA1KO_Rep2


title: mesLN_1_S13


title: KO2


title: WT old, replicate 2


title: Lung_4_S24

source_name: Lung

value: Lung


title: GATA1KO_Rep1


title: WT old, replicate 1


title: HET5


title: Lung_3_S23


title: KO1


title: Lung_2_S22


title: HET3


title: HET4


title: WT young, replicate 3

source_name: Young wild type mouse


title: KO young, replicate 2

description:
NLRP3 knockout
Mouse_KO_Young-2


title: KO3


title: WT young, replicate 2


title: Lung_1_S21


title: WT5


title: Liver_4_S44

source_name: Liver

value: Liver


title: Liver_3_S43

value: 6 weeks old


title: WT4


title: WT3


title: WT1


title: WT2


title: Liver_1_S41

value: female


title: 09_ITD-3

city: Lyon

first: Fabien

last: Le Grand

address: 8 avenue Rockefeller

department: Melis

country: France

institute: Institut Neuromyogene

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® MouseGene2.0ST (Affymetrix) at 45°C for 17 hours.

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G. The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls.

data_processing:
Data were normalized using RMA algorithm in Bioconductor with the custom CDF vs 22. Statistical analysis ware carry out with the use of Partek® GS.
Fisrt, variations in gene expression were analyzed using unsupervised hierarchical clustering and PCA to assess data from technical biais and outlier samples. To find differentially expressed genes, we applied a one way ANOVA for each gene. Then, we used unadjusted p-value and fold changes to filter and select differentially expressed genes. Gene networks and canonical pathways representing key genes were identified using the curated Ingenuity Pathways Analysis ® (IPA) database.

source_name: Differentiating Primary Myoblasts treated with ITD

label_protocol: After purification according to Affymetrix protocol, 5.5ug of Sens Target DNA are fragmented and biotin labeled.

growth_protocol: satellite cells-derived myoblasts were cultured on collagen-coated dishes in Ham's-F10 nutrient mix supplemented with 20% FBS and 2.5ng/ul basic FGF

extract_protocol: The RNA from primary myoblasts were isolated using Direct-zol RNA Kit (Zymo Research) according to the manufacturer’s protocol. After validation of the RNA quality with Bioanalyzer 2100 (using Agilent RNA6000 nano chip kit), 100ng of total RNA is reverse transcribed following the GeneChip® WT Plus Reagent Kit (Affymetrix). Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA polymerase (all these steps are included in the WT cDNA synthesis and amplification kit of Affymetrix).

treatment_protocol: 24h-differentiating myoblasts were treated with 20ng/ml of TGFB1 or with ITD-1 at 5mM for 24h

tag: strain background

tag: tissue source

value: skeletal muscle

value: satellite cells-derived primary myoblasts

value: 5mM ITD-1 for 24h


title: WT young, replicate 1

tag: age


title: Kidney_3_S35

source_name: Kidney

value: Kidney


title: Kidney_2_S34


title: 04_TGFB1-1

source_name: Differentiating Primary Myoblasts treated with TGFB1

value: 20ng/ml of TGFB1 for 24hrs


title: Kidney_1_S33


title: Liver_2_S42


title: WT_NMS2: Wild type, nitrate, biological replicate 2

city: Seattle

first: Mitchell

middle: William

last: Pesesky

state: WA

address: 616 NE Northlake Place

institute: University of Washington

data_processing:
Alignment was performed using BWA version 0.7.12-r1044 using the BWA-MEM algorithm and default parameters.
The alignments were post-processed into sorted BAM files with SAMTools version 1.2-232-g87cdc4a.
Reads were attributed to open reading frames (ORFs) using the htseq-count tool from the ‘HTSeq’ framework version 0.6.1p1 in the ‘intersection-nonempty’ mode.
Differential abundance analysis was performed with DESeq2 1.2.10 using R 3.3.0.
Genome_build: NZ_JMLA01000000
Genome_build: NZ_JPOH01000000
Supplementary_files_format_and_content: *.txt files are two columns: locus tag (JGI) and read count. At the bottom of the file five lines of summary read alignment statistics are given.

organism: Methylobacter tundripaludum 21/22

source_name: exponential phase culture

growth_protocol: Starter cultures were grown to late logarithmic phase (OD600 ~ 0.8) and a 2% inoculum (v/v) was transferred into 50 mL NMS2 medium, under an atmosphere of 25% methane and 75% air.

extract_protocol:
Once samples reached OD600 ~ 0.6-0.7, 2.5 mL of a stop solution of 5% (v/v) phenol in ethanol was added to 22.5 mL of culture. Cells were pelleted for 15 min at 4°C, and resuspended in RNA extraction buffer (a 1:3 ratio of 5% cetrimonium brimide in 2.5 M NaCl to 0.1 M phosphate buffer at pH 5.8). An equal volume of phenol-chloroform-isoamyl alcohol (25:24:1 ratio) was added, and sodium dodecyl sulfate and N-lauroylsarcosine sodium salt were each added at 0.5% (v/v). Cells were lysed in a bead beater with 0.1-mm zirconia-silica beads (Biospec Products, Bartlesville, OK, USA) for 4 min, then centrifuged at 14,000 x g for 5 min. The aqueous fraction was then washed with chloroform-isoamyl alcohol (24:1 ratio), and the aqueous fraction from this wash was precipitated overnight with 150 mM sodium acetate (pH 5.5), 1.5 mM MgCl2, and 50% isopropanol at -80°C. Precipitated RNA was harvested at 14,000 x g for 30 min at 4°C, and treated with DNase I (Ambion, Foster City, CA, USA) before purification with the RNeasy minikit and on-column DNase (Qiagen, Hilden, Germany).
cDNA library preparation and RNA sequencing was performed by GENEWIZ using Illumina HiSeq 2x150 (pair ended) reads.

treatment_protocol: Hcp mutant and wild type cells were grown under ‘high oxygen’ condition in either NMS or   AMS to OD600 of approximately 0.5, and these cells were used to inoculate replicate cultures and these were incubated as above, for another 24 hours, to OD600 of approximately 0.5. At this point, half of the samples were given the same methane/air atmosphere for one hour, after which these samples (the oxic samples) were collected. The second set of samples were given the atmosphere of methane/dinitrogen (25/75% V/V), to create hypoxic conditions, and samples were collected after 24 hours.

tag: growth conditions

value: nitrate

tag: replicate


title: 05_TGFB1-2


title: 08_ITD-2


title: 02_CTL-2

source_name: Differentiating Primary Myoblasts


title: 06_TGFB1-3


title: SCD5

city: Nanjing

first: Peng

last: Hua

state: Jiangsu

address: 101 Longmiandadao

department: State Key Laboratory of Reproductive Medicine and Offspring Health

institute: Nanjing Medical University

data_processing:
*I1_001.fastq.gz: contains the sample index.
*R1_001.fastq.gz: contains the cell barcode (first 16 nt) and UMI (next 10 nt).
*R2_001.fastq.gz: contains the RNA sequence.
Single-cell RNA sequencing libraries were prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10XGenomics, cat. no. 120237). 10,000 CD34+ cells from each donor were loaded on a GemCode Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell Gel Bead in emulsion (GEMs) respectively. Reverse transcription (RT) was performed according to the manufacturer's protocol (55 °C for 2 h then 85 °C for 5 min). After RT, GEMs were broken and the single-strand cDNA was purified with DynaBeads MyOne Silane Beads and SPRIselect Reagent (0.6 × SPRI). cDNA was amplified by PCR (98 °C for 3 min; 98 °C for 15 s; 67 °C for 20 s; and 72 °C for 1 min) for 14 cycles then 72 °C for 1 min. The amplified cDNA product was cleaned up using SPRIselect beads (0.6 × SPRI). The cDNA was enzymatically fragmented and end-repair, dA-tailing and adaptor ligation were performed. The patient samples were differentially indexed using Chromium i7 sample indexing. The barcoded and indexed libraries were quantified by quantitative PCR (KAPA Biosystems Library Quantification Kit for Illumina platforms, cat. no. KK4824) and normalised. The library pool was sequenced on an Illumina NovaSeq6000 (S2 kits, PE100bp) (Novogene). Approximately 3,000-5,000 cells were captured for each donor and at least 100,000 reads per cell were obtained (QC30 shown in supplemental Table 2).
The Cell Ranger Single-Cell Software (1.2.0, 10x Genomics) was used to perform sequencing data demultiplexing, barcode processing and gene counting against the reference genome (GRCh38-1.2.0).
Genome_build: GRCh38-1.2.0
Supplementary_files_format_and_content: tar archive containing genes.tsv, matrix.mtx, barcodes.tsv

source_name: sickle cell disease patient's bone marrow cells

growth_protocol: uncultured

treatment_protocol: no treatment

tag: individual

value: sickle cell disease patient

tag: tissue

value: bone marrow

value: CD34+ cells


title: SCD4

extract_protocol: Single-cell RNA sequencing libraries were prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10XGenomics, cat. no. 120237). 10,000 CD34+ cells from each donor were loaded on a GemCode Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell Gel Bead in emulsion (GEMs) respectively. Reverse transcription (RT) was performed according to the manufacturer's protocol (55 °C for 2 h then 85 °C for 5 min). After RT, GEMs were broken and the single-strand cDNA was purified with DynaBeads MyOne Silane Beads and SPRIselect Reagent (0.6 × SPRI). cDNA was amplified by PCR (98 °C for 3 min; 98 °C for 15 s; 67 °C for 20 s; and 72 °C for 1 min) for 14 cycles then 72 °C for 1 min. The amplified cDNA product was cleaned up using SPRIselect beads (0.6 × SPRI). The cDNA was enzymatically fragmented and end-repair, dA-tailing and adaptor ligation were performed. The patient samples were differentially indexed using Chromium i7 sample indexing. The barcoded and indexed libraries were quantified by quantitative PCR (KAPA Biosystems Library Quantification Kit for Illumina platforms, cat. no. KK4824) and normalised. The library pool was sequenced on an Illumina NovaSeq6000 (S2 kits, PE100bp) (Novogene). Approximately 3,000-5,000 cells were captured for each donor and at least 100,000 reads per cell were obtained (QC30 shown in supplemental Table 2).


title: WT_AMS2: Wild type, ammonia, biological replicate 2

value: wild type

value: ammonia


title: 01_CTL-1


title: hDPSCs_odontogenic differentiation_14day_rep2

city: Guangzhou

first: Zhao

last: Chen

state: Guangdong

address: Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China

department: Department of Stomatology

description: gene expression after 14 days odontogenic induction

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number 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 with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

label: Cyanine 3-pCp

source_name: human dental pulp stem cells, odontogenic differentiation, 14 day

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Isolated hDPSCs were cultured in Dulbecco modified Eagle medium (DMEM) (Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco, Grand Island, NY, USA) and 100 U/mL penicillin/streptomycin (HyClone, NY, USA), and maintained at 37 °C in a humidified atmosphere with 95% air and 5% CO2. Single cell suspension is obtained by filtering cells through a 70μm filter (BD Falcon, Franklin Lakes, NJ). Single-cell suspensions were inoculated into six-well plates at a density of 1×104 cells/well. The limited dilution techniques are used to obtain colonies of single cell origin

extract_protocol: According to the manufacturer’s protocol, total RNA was isolated from cultured cells with Trizol reagent (Thermo Fisher Scientific, Waltham, MA). The quantity and quality of RNA are determined by nano dropper ND-1000 (Nano Dropper Technology Company, Wilmington, DE) and Agilent 2100 Biological Analyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: hDPSCs at differentiated group were cultured with an odontogenic differentiation medium containing 50 mg/ml ascorbic acid, 100 nmol/L dexamethasone, and 10 mmol/L β-glycerolphosphate (Sigma, St Louis, MO, USA) for 14 days in 6-well plates.  hDPSCs at undifferentiated group were cultured in 10 % FBS in DMEM with no supplements.

tag: cell

value: hDPSCs


title: 07_ITD-1


title: hDPSCs_odontogenic differentiation_14day_rep3

institute: Nanfang Hospital, Southern Medical University


title: hDPSCs_odontogenic differentiation_14day_rep1


title: 03_CTL-3


title: Kidney_4_S36

tag: Sex


title: hDPSCs_cultured_14day_rep3

description: gene expression after 14 days cultured

source_name: human dental pulp stem cells, cultured, 14 day


title: 165_AMS2: Mutant (tundrinone), ammonia, biological replicate 2

value: tundrinone-


title: hDPSCs_cultured_14day_rep1

description: gene expression after 14 days cultured


title: hDPSCs_cultured_14day_rep2

description: gene expression after 14 days cultured


title: SCD3

tag: cell type


title: iLN_4_S40

source_name: Inguinal lymph node

value: Inguinal lymph node


title: iLN_3_S39


title: SCD2


title: 165_NMS2: Mutant (tundrinone), nitrate, biological replicate 2


title: iLN_2_S38


title: SCD1


title: 142_AMS2: Mutant (quorum sensing), ammonia, biological replicate 2

value: qs-


title: iLN_1_S37

value: 6 weeks old


title: C1

source_name: normal donor's bone marrow cells

value: normal donor

value: Lin-CD34+ cells


title: WT_NMS1: Wild type, nitrate, biological replicate 1


title: Heart_4_S28

source_name: Heart

value: female

value: Heart


title: BT3

source_name: Major Thalassemia patient's bone marrow cells

value: Major Thalassemia patient


title: WT_AMS1: Wild type, ammonia, biological replicate 1


title: BT2


hyb_protocol: The labeled cRNA over the procession of  inspissation and desiccation and then redissolved with water. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent Microarray Scanner (part number 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 with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, miRNAs that at least 1 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed miRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed miRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts.

label_protocol: Sample labeling and array hybridization were performed according to the Agilent miRNA Microarray Systemwith miRNA Complete Labeling and Hyb Kit protocol (Agilent Technology). Briefly, total miRNA from each sample was labeled with Cyanine 3-pCp under the action of T4 RNA ligase.


title: 142_NMS2: Mutant (quorum sensing), nitrate, biological replicate 2


title: Heart_1_S25


title: BT1


title: FRT_4_S64

source_name: female reproductive tract

value: female reproductive tract


title: BM4


title: 142_NMS1: Mutant (quorum sensing), nitrate, biological replicate 1

value: nitrate


title: 142_AMS1: Mutant (quorum sensing), ammonia, biological replicate 1


title: hDPSCs_cultured_14day_rep2

description: gene expression after 14 days cultured


title: hDPSCs_cultured_14day_rep3

description: gene expression after 14 days cultured


title: FRT_3_S63


title: NMS2: Wild type, nitrate, biological replicate 2

organism: Methylobacter tundripaludum 31/32


title: Heart_2_S26


title: BM2


title: 165_NMS1: Mutant (tundrinone), nitrate, biological replicate 1


title: hDPSCs_cultured_14day_rep1

description: gene expression after 14 days cultured


title: FRT_2_S62


title: NMS1: Wild type, nitrate, biological replicate 1


title: Heart_3_S27


title: AMS2: Wild type ammonia, biological replicate 2


title: BM1


title: FRT_1_S61


title: 165_AMS1: Mutant (tundrinone), ammonia, biological replicate 1


title: BM3


title: AMS1: Wild type ammonia, biological replicate 1


title: MUAL2: Mutant (hcp/hcr), ammonia, low oxygen, biological replicate 2

value: hcp/hcr-

value: ammonia, low oxygen


title: Conv9

city: Jouy en Josas, France

first: Unai

middle: Escribano

last: Vazquez

state: --- Sélectionner ---

address: Domaine de Vilvert Bat 440

department: MICALIS

institute: INRA

description: CV

data_processing:
The normalization and all the data analysis were performed according to the GenEx software (Multid Analyses).
For the normalization the Global normalization method of the expression of all genes was applied.
The GenNex software automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data. The deltadeltaCt values are not available.

label: FAM

source_name: Ileal mucosa

label_protocol: Gene expression analysis was performed with a customized TaqMan OpenArray Real-time PCR System (Life Technologies). The cDNA (10 μl) was mixed with the TaqMan OpenArray Real-Time PCR Master Mix and loaded onto the cards using the AccuFill™ System. The cards were cycled in an OpenArray NT Cycler System (Applied Biosystems).

extract_protocol: RNA isolation was carried out using the Ambion mirVana Kit (Life Technologies) according to the manufacturer’s recommendations. The RNA quality of all samples was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) with an average RNA integrity number superior to 9 on a scale of 0 to 10

tag: colonisation  status

value: CV

tag: group type

value: conventional

tag: colonisation


title: Conv8

description: CV


title: MUNL2: Mutant (hcp/hcr), nitrate, low oxygen, biological replicate 2

tag: genotype

value: nitrate, low oxygen


title: Colon_2_S18

source_name: Colon

tag: strain

value: Colon


title: Colon_1_S17


title: WTAL2: Wild-type, ammonia, low oxygen, biological replicate 2

value: wild type


title: Colon_3_S19


title: Brain_4_S60

source_name: Brain

value: Brain


title: Conv7

description: CV


title: Conv6

description: CV


title: WTNL2: Wild-type, nitrate, low oxygen, biological replicate 2


title: krill fished at 06:00, LD, biological replicate 1 (LD06-A2)

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

department: Biology

country: Italy

institute: University of Padova

description: Gene expression profiling of Antarctic krill in LD condition (LD06-A2)

hyb_protocol: 1.65 μg of labeled cRNA were used in each reaction and the hybridization was carried out at 65°C for 17 hours in an hybridization oven rotator (Agilent Technologies, Palo Alto, CA). The arrays were washed by Agilent Gene expression washing buffers and Stabilization and Drying Solution as suggest by the supplier.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) and Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

data_processing: Inter-array normalization of expression levels was performed with quantile to correct possible experimental distortions. A normalization function was applied to the expression data of all experiments and then values of spot replicates within arrays were averaged. Furthermore, Feature Extraction Software provided spot quality measures to evaluate the quality and the reliability of the hybridization. In particular, flag glsFound (set to 1 if the spot has an intensity value significantly different from the local background, 0 otherwise) was used to filter out unreliable probes: flag equal to 0 will be noted as not available (NA). So, in order to make more robust and unbiased statistical analyses, probes with a high proportion of null values were removed from the dataset. 26% of null was used as threshold in the filtering process, obtaining a total of 38,028 available krill transcripts.

organism: Euphausia superba

label_protocol: 800 ng of total RNA were labeled with “Agilent One-Color Microarray-Based Gene Expression protocol” according to the manufacturer’s instructions. The synthesized cDNA was transcribed into cRNA and labeled with Cy3-dCTP. Labeled cRNA was purified with RNeasy Mini columns (Qiagen, Valecia, CA). The quality of each cRNA sample was verified by total yield and specificity calculated with NanoDrop ND-1000 spectrophotometer measurements (Nanodrop, Wilmington, DE).

extract_protocol: For each sampling, five-seven animals were collected, and total RNA was extracted with TRIzol (Thermo Fisher) reagent according to the manufacter's instructions. All RNA samples were checked for quality by capillary electrophoresis (RNA 6000 Nano LabChip, Agilent Bioanalyzer 2100, Agilent Technologies).

treatment_protocol: Maintenance of krill and specimens collection were identical to what was described by Teschke et al. (2011). Briefly, two experimental tanks were exposed to a light:dark (LD) regime of 16 hours light and 8 hours darkness and constant darkness (DD) respectively. Prior to the collection of samples, all specimens, in both experimental tanks, were exposed for a period of 3–4 weeks to these conditions to provide a successful acclimatisation to the aquarium conditions. Krill were sampled at regular intervals (every three hours) over a full 24 hour cycle.

value: Head (including brain and compound eyes)


title: MUAH2: Mutant (hcp/hcr), ammonia, high oxygen, biological replicate 2

value: ammonia, high oxygen


title: krill fished at 03:00, LD, biological replicate 3 (LD03-C)

description: Gene expression profiling of Antarctic krill in LD condition (LD03-C)


title: Conv3

description: CV


title: Colon_4_S20

value: 6 weeks old


title: Brain_3_S59


title: krill fished at 06:00, LD, biological replicate 3 (LD06-C2)

description: Gene expression profiling of Antarctic krill in LD condition (LD06-C2)


title: krill fished at 06:00, LD, biological replicate 2 (LD06-B2)

description: Gene expression profiling of Antarctic krill in LD condition (LD06-B2)


title: krill fished at 03:00, LD, biological replicate 2 (LD03-B)

description: Gene expression profiling of Antarctic krill in LD condition (LD03-B)


title: Conv2

description: CV


title: MUNH2: Mutant (hcp/hcr), nitrate, high oxygen, biological replicate 2

value: nitrate, high oxygen


title: krill fished at 03:00, LD, biological replicate 1 (LD03-A)

description: Gene expression profiling of Antarctic krill in LD condition (LD03-A)


title: krill fished at 24:00, LD, biological replicate 3 (LD24-C)

description: Gene expression profiling of Antarctic krill in LD condition (LD24-C)


title: Brain_2_S58

value: female


title: krill fished at 24:00, LD, biological replicate 2 (LD24-B)

description: Gene expression profiling of Antarctic krill in LD condition (LD24-B)


title: Brain_1_S57


title: WTNH2: Wild-type, nitrate, high oxygen, biological replicate 2


title: WTAH2: Wild-type, ammonia, high oxygen, biological replicate 2


title: BM_4_S4

source_name: Bone marrow

value: Bone marrow


title: Conv4

description: CV


title: Conv10

description: CV


title: MUAL1: Mutant (hcp/hcr), ammonia, low oxygen, biological replicate 1


title: BM_3_S3


title: Ax33

description: Ax

value: germfree

value: control


title: Conv1

description: CV


title: MUNL1: Mutant (hcp/hcr), nitrate, low oxygen, biological replicate 1


title: BM_2_S2


title: BM_1_S1


title: WTNL1: Wild-type, nitrate, low oxygen, biological replicate 1


title: Ax32

description: Ax


title: Ax31

description: Ax


title: CTRL ASO 39708

city: Carlsbad

first: Sagar

middle: S

last: Damle

address: 2855 Gazelle Ct

department: Functional Genomics

institute: Ionis Pharmaceuticals

description:
CTRL ASO
CTRL ASO
nuclear RNA pulldown
PRO-seq exp #3

data_processing:
Libraries were sequenced on an illumin Nextseq 550 instrument and bascalls applied by bcl2fastq2 version 2.20.0
Reads were aligned to mouse genome build GRCm38 using STAR version 2.5.1b
Genome_build: GRCm38
Supplementary_files_format_and_content: bedgraph files contain genome coverages

source_name: MHT Cells

growth_protocol: MHT cell 90% DMEM, 10% Serum.

extract_protocol:
PRO-seq protocol is adjusted from Nat Protoc. 2016 Aug; 11(8):1455-76.
NEB ultra II for chromatin RNA-seq,

treatment_protocol: 5-10-5 MOE gapmer ASOs were applied to cell culture medium at different concentrations for 24 hrs (free uptake).

tag: treatment

value: CTRL ASO

tag: concentration

value: 10 uM

tag: duration

value: 24 hrs


title: Ax30

description: Ax


title: MUAH1: Mutant (hcp/hcr), ammonia, high oxygen, biological replicate 1

value: hcp/hcr-


title: krill fished at 24:00, LD, biological replicate 1 (LD24-A)

description: Gene expression profiling of Antarctic krill in LD condition (LD24-A)


title: krill fished at 21:00, LD, biological replicate 3 (LD21-C)

description: Gene expression profiling of Antarctic krill in LD condition (LD21-C)


title: Ax22

description: Ax


title: krill fished at 21:00, LD, biological replicate 2 (LD21-B)

description: Gene expression profiling of Antarctic krill in LD condition (LD21-B)


title: krill fished at 21:00, LD, biological replicate 1 (LD21-A)

description: Gene expression profiling of Antarctic krill in LD condition (LD21-A)


title: krill fished at 18:00, LD, biological replicate 2 (LD18-B)

description: Gene expression profiling of Antarctic krill in LD condition (LD18-B)


title: krill fished at 15:00, LD, biological replicate 3 (LD15-C)

description: Gene expression profiling of Antarctic krill in LD condition (LD15-C)


title: ATXN10 ExASO1 39707

description:
ATXN10 ExASO1
1273212
nuclear RNA pulldown
PRO-seq exp #3

value: ATXN10 ExASO1


title: MUNH1: Mutant (hcp/hcr), nitrate, high oxygen, biological replicate 1


title: krill fished at 18:00, LD, biological replicate 3 (LD18-C)

description: Gene expression profiling of Antarctic krill in LD condition (LD18-C)


title: ATXN10 InASO1 39706

description:
ATXN10 InASO1
1130580
nuclear RNA pulldown
PRO-seq exp #3

value: ATXN10 InASO1


title: NEDD4 ExASO3 30461

description:
NEDD4 ExASO3
1030642
nuclear RNA pulldown
PRO-seq exp #2

value: NEDD4 ExASO3


title: Ax20

description: Ax


title: WTAH1: Wild-type, ammonia, high oxygen, biological replicate 1

value: wild type


title: WTAL1: Wild-type, ammonia, low oxygen, biological replicate 1

value: ammonia, low oxygen


title: CTRL ASO 30460

description:
CTRL ASO
CTRL ASO
nuclear RNA pulldown
PRO-seq exp #2

value: 1 uM


title: Ax12

description: Ax


title: WTNH1: Wild-type, nitrate, high oxygen, biological replicate 1


title: krill fished at 15:00, LD, biological replicate 2 (LD15-B)

description: Gene expression profiling of Antarctic krill in LD condition (LD15-B)

value: Head (including brain and compound eyes)


title: Ax11

description: Ax


title: CtWT -Dox rep. #2

city: San Antonio

first: Yidong

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to C_parapsilosis/CDC317 or C_tropicalis/MYA3404 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: C. tropicalis MYA3404 or C. parapsilosis/CDC317 genome from Candida Genome Database
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

organism: Candida tropicalis

source_name: fungal cells

growth_protocol: C. parapsilosis wild-type (ELY70) and tetO-CpUME6 (ELY194) strains as well as C. tropicalis wild-type (ELY5) and tetO-CtUME6 (ELY184) strains have been previously described (Lackey, et al., Eukaryot. Cell 12(10):1356-1368 (2013)). Standard growth conditions for all strains were in yeast extract-peptone-dextrose (YEPD) at 30°C.

extract_protocol:
Total RNA was extracted using the hot acid phenol protocol (Ausubel, et al., Current Protocols in Molecular Biology, 1992)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For RNA preparation and cell fixing, strains were initially grown overnight at 30°C in 5 mL of YEPD in the presence (tetO-CpUME6 and tetO-CtUME6 strains) or absence (CpWT and CtWT strains) of 20 ug/mL Dox. Saturated overnight cultures were washed twice in ddH2O and resuspended in 5 mL ddH2O. Next, 10 uL of this cell suspension was diluted in 10 mL of ddH2O. For C. parapsilosis strains, either 1 mL or 2 mL of this diluted culture was used to inoculate 50 mL of synthetic complete (SC) medium in the presence and absence of 100 ng/mL Dox and cells were grown at 30°C for 36 hours prior to harvesting 1 mL for fixing and 5 mL for RNA preparation. For C. tropicalis strains, either 1 mL or 2 mL of the diluted culture was used to inoculate 50 mL of YEPD + 50% fetal bovine serum (FBS) (Atlanta Biologicals) in the presence and absence of 100 ng/mL Dox and cells were grown at 30°C for 24 hours prior to harvesting 1 mL for fixing and 5 mL for RNA preparation.

value: absence of Dox


title: CtWT +Dox rep. #2

value: Doxycycline, 100 ng/mL


title: Ax10

description: Ax


title: ATXN10 InASO1 30458

description:
ATXN10 InASO1
1130580
nuclear RNA pulldown
PRO-seq exp #2


title: krill fished at 15:00, LD, biological replicate 1 (LD15-A)

description: Gene expression profiling of Antarctic krill in LD condition (LD15-A)


title: CTRL ASO 27395

description:
CTRL ASO
CTRLASO
nuclear RNA pulldown
PRO-seq exp #1


title: ANC_N9I

description: Nissle

value: E. coli Nissle

value: mono-associated


title: NEDD4 ExASO1 27394

description:
NEDD4 ExASO1
1030522
nuclear RNA pulldown
PRO-seq exp #1

value: NEDD4 ExASO1


title: CtWT -Dox rep. #1


title: krill fished at 12:00, LD, biological replicate 3 (LD12-C)

description: Gene expression profiling of Antarctic krill in LD condition (LD12-C)


title: CtWT +Dox rep. #1


title: NEDD4 InASO2 27393

description:
NEDD4 InASO2
1046095
nuclear RNA pulldown
PRO-seq exp #1

value: NEDD4 InASO2


title: ANC_N8I

description: Nissle


title: tetO-CtUME6 -Dox rep. #2


title: CTRL ASO 31557

description:
CTRL ASO
CTRL
nuclear RNA
chromatin RNA-seq  exp #4

value: CTRL ASO


title: ANC_N7I

description: Nissle


title: ANC_N6I

description: Nissle


title: tetO-CtUME6 -Dox rep. #1


title: ATXN10 ExASO2 31552

description:
ATXN10 ExASO2
1130340
nuclear RNA
chromatin RNA-seq  exp #4

value: ATXN10 ExASO2

value: 20 uM


title: tetO-CtUME6 +Dox rep. #1


title: ANC_N4I

description: Nissle


title: ANC_N5I

description: Nissle


title: ANC_N3I

description: Nissle


title: krill fished at 09:00, LD, biological replicate 2 (LD09-B)

description: Gene expression profiling of Antarctic krill in LD condition (LD09-B)


title: krill fished at 09:00, LD, biological replicate 3 (LD09-C)

description: Gene expression profiling of Antarctic krill in LD condition (LD06-C)


title: krill fished at 18:00, LD, biological replicate 1 (LD18-A)

description: Gene expression profiling of Antarctic krill in LD condition (LD18-A)


title: ATXN10 InASO1 28290

description:
ATXN10 InASO1
1130580
nuclear RNA
chromatin RNA-seq  exp #3

value: 10 uM

value: 24 hrs


title: tetO-CtUME6 +Dox rep. #2


title: krill fished at 12:00, LD, biological replicate 2 (LD12-B)

description: Gene expression profiling of Antarctic krill in LD condition (LD12-B)


title: krill fished at 12:00, LD, biological replicate 1 (LD12-A)

description: Gene expression profiling of Antarctic krill in LD condition (LD12-A)


title: krill fished at 06:00, LD, biological replicate 3 (LD06-C1)

description: Gene expression profiling of Antarctic krill in LD condition (LD06-C1)


title: krill fished at 09:00, LD, biological replicate 1 (LD09-A)

description: Gene expression profiling of Antarctic krill in LD condition (LD09-A)


title: krill fished at 06:00, LD, biological replicate 2 (LD06-B1)

description: Gene expression profiling of Antarctic krill in LD condition (LD06-B1)


title: krill fished at 06:00, LD, biological replicate 1 (LD06-A1)

description: Gene expression profiling of Antarctic krill in LD condition (LD06-A1)


title: ANC_N2I

description: Nissle


title: ANC_N1I

description: Nissle


title: ANC_C9I

description: CEC

value: E. coli CEC


title: W46: chronic wound circRNA 5

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

country: Sweden

institute: Karolinska Institutet

description: circRNA expression data from chronic wound

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Quantile normalization was performed using the R software limma package. The circRNAs detected in more than 50% samples (determined by GeneSpring software) were retained for differential analysis. Differentially expressed circRNAs with statistical significance between two groups were identified through volcano plot filtering.

source_name: test

label_protocol: Total RNA was treated with RNAse R to enrich circRNA. The enriched circRNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primers according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

growth_protocol: Human skin wound biopsies

treatment_protocol: Chronic wounds biopsies (4 mm in diameter) were collected from the non-healing edges of DFUs. The acute wounds (4 mm in diameter) were surgically created on the skin of healthy volunteers and the wound-edge tissues (6 mm in diameter) were collected 7 days later.

value: chronic wound biopsy from diabetic foot ulcer

tag: gender

value: Female


title: CTRL ASO 28287

description:
CTRL ASO
CTRLASO
nuclear RNA
chromatin RNA-seq  exp #3


title: ATXN10 ExASO1 28286

description:
ATXN10 ExASO1
1273212
nuclear RNA
chromatin RNA-seq  exp #3

value: ATXN10 ExASO1


title: NEDD4 ExASO1 27391

description:
NEDD4 ExASO1
1030522
nuclear RNA
chromatin RNA-seq  exp #2


title: W28: chronic wound circRNA 4

tag: age


title: ANC_C7I

description: CEC


title: NEDD4 ExASO2 27390

description:
NEDD4 ExASO2
1265380
nuclear RNA
chromatin RNA-seq  exp #2

value: NEDD4 ExASO2


title: krill fished at 06:00, DD, biological replicate 3 (DD06-C2)

description: Gene expression profiling of Antarctic krill in DD condition (DD06-C2)

data_processing: Inter-array normalization of expression levels was performed with quantile to correct possible experimental distortions. A normalization function was applied to the expression data of all experiments and then values of spot replicates within arrays were averaged. Furthermore, Feature Extraction Software provided spot quality measures to evaluate the quality and the reliability of the hybridization. In particular, flag glsFound (set to 1 if the spot has an intensity value significantly different from the local background, 0 otherwise) was used to filter out unreliable probes: flag equal to 0 will be noted as not available (NA). So, in order to make more robust and unbiased statistical analyses, probes with a high proportion of null values were removed from the dataset. 26% of null was used as threshold in the filtering process, obtaining a total of 38,231 available krill transcripts.

value: Head (including brain and compound eyes)


title: NEDD4 ExASO3 27389

description:
NEDD4 ExASO3
1030642
nuclear RNA
chromatin RNA-seq  exp #2

value: NEDD4 ExASO3


title: ANC_C6I

description: CEC


title: krill fished at 06:00, DD, biological replicate 2 (DD06-B2)

description: Gene expression profiling of Antarctic krill in DD condition (DD06-B2)


title: krill fished at 06:00, DD, biological replicate 1 (DD06-A2)

description: Gene expression profiling of Antarctic krill in DD condition (DD06-A2)


title: ANC_C4I

description: CEC


title: W22: chronic wound circRNA 2

value: Male


title: ATXN10 InASO1 27387

description:
ATXN10 InASO1
1130580
nuclear RNA
chromatin RNA-seq  exp #2

value: ATXN10 InASO1


title: krill fished at 03:00, DD, biological replicate 3 (DD03-C)

description: Gene expression profiling of Antarctic krill in DD condition (DD03-C)


title: W23: chronic wound circRNA 3


title: NEDD4 InASO2 27392

description:
NEDD4 InASO2
1046095
nuclear RNA
chromatin RNA-seq  exp #2


title: krill fished at 03:00, DD, biological replicate 2 (DD03-B)

description: Gene expression profiling of Antarctic krill in DD condition (DD03-B)


title: ANC_C3I

description: CEC

value: mono-associated


title: krill fished at 03:00, DD, biological replicate 1 (DD03-A)

description: Gene expression profiling of Antarctic krill in DD condition (DD03-A)


title: ANC_C8I

description: CEC


title: NEDD4 InASO1 27386

description:
NEDD4 InASO1
1046011
nuclear RNA
chromatin RNA-seq  exp #2

value: NEDD4 InASO1


title: CTRL ASO 27385

description:
CTRL ASO
CTRL
nuclear RNA
chromatin RNA-seq  exp #2


title: C6_7: acute wound circRNA 4

description: circRNA expression data from acute wound

source_name: control

value: acute wound biopsy from healthy volunteer


title: ANC_C1I

description: CEC


title: PBS 27157

description:
PBS
PBS
nuclear RNA
chromatin RNA-seq  exp #1

value: PBS

value: 0 uM


title: krill fished at 24:00, DD, biological replicate 3 (DD24-C)

description: Gene expression profiling of Antarctic krill in DD condition (DD24-C)


title: NEDD4 ExASO3 27156

description:
NEDD4 ExASO3
1030642
nuclear RNA
chromatin RNA-seq  exp #1


title: 42 weeks of age biological replicate 3

city: Chengdu

first: Kequan

last: Li

state: Sichuan

address: 172 shun sheng road, zhengxing street, tianfu new district

institute: Sichuan Eagene Technology services co. LTD

data_processing:
The quality control of raw data were completed by removing low-quality reads, adaptor sequences, empty reads, reads with N sequences over 10% and rRNA reads.
Processed reads from each sample were mapped to the reference genome of chicken using Hisat, The mapped reads were assembled with Stringtie v1.3.3; and then the assembled transcripts were merged into consensus transcripts using custom Python scripts,the known transcripts were removed by blastx and HMMER
The Coding Potential Calculator (CPC) was applied to estimate the coding ability of the remaining transcripts, and transcripts with CPC score > 0 were filtered. Subsequently, transcripts with FPKM > 0 at least in one biological replicate were identified as lncRNAs. LncRNAs were initially classified as 2 major categories according to the lncRNA location with respect to mRNA (Protein Coding Genes) by FEELnc
The expression levels of the transcripts were expressed as FPKM (fragments per kilobase of transcript per million mapped reads) values of mRNA and lncRNA using the Cufflinks v2.2.1 and Stringtie v1.3.3, noting that a value of 1 was added to the FPKM value of each gene before log2 transformation to avoid infinite values. FPKM > 0.1 was used to filter the expressed mRNA. Pearson correlations were estimated across 8 developmental stages, hierarchical clustering was performed using MultiExperimentViewer (MeV version 4.9.0)
Differentially expressed mRNAs and lncRNAs were calculated by DESeq2 based on the reads count that produced from FPKM calculated by Stringtie v1.3.3. We used the analysis of variance (ANOVA) to do pair-wise comparisons between 2 adjacent time points. Genes and transcripts with the FC ≥ 2 or ≤ 0.5 plus the P-value ≤ 0.05 were identified to age-dependent genes.
We constructed a co-expression network using the Weighted Gene Co-expression Network Analysis (WGCNA) in the R package
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: tab-delimited text files include log2 (FPKM+1) values for each Sample

organism: Gallus gallus

source_name: liver

extract_protocol:
The total RNA was extracted using the TrIzol reagent (Life Technologies, Beijing, China) according to the manufacturer’s protocols. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: 42 weeks

tag: Stage

value: Adult and aged


title: ANC_C10I

description: CEC

value: E. coli CEC


title: NEDD4 ExASO1 27155

description:
NEDD4 ExASO1
1030522
nuclear RNA
chromatin RNA-seq  exp #1

value: NEDD4 ExASO1

value: 10 uM

value: 24 hrs


title: Nissle_S9

description: Nissle

data_processing:
The normalization and all the data analysis were performed according to the GenEx software (Multid Analyses).
For the normalization the Global normalization method of the expression of all genes was applied.
The GenNex software automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data. The deltadeltaCt values are not available.
Fold Change worksheet reports relative quantification of the expiremental group (CEC, Nissle or CV) to the control group (Ax: axenic/germfree), where Ax group has been used as a calibrator on the DeltadeltaCt calculation.

source_name: Colonic mucosa

extract_protocol: RNA isolation was carried out using the Ambion mirVana Kit (Life Technologies) according to the manufacturer’s recommendations. The RNA quality of all samples was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) with an average RNA integrity number superior to 9 on a scale of 0 to 10.

value: E. coli Nissle

tag: colonisation days


title: 42 weeks of age biological replicate 2


title: NEDD4 InASO1 27153

description:
NEDD4 InASO1
1046011
nuclear RNA
chromatin RNA-seq  exp #1


title: ANC_C2I

description: CEC


title: Nissle_S8

description: Nissle


title: C3_7: acute wound circRNA 2

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


title: 5 weeks of age biological replicate 3

value: 5 weeks

value: Rapid growth


title: 42 weeks of age biological replicate 1


title: Nissle_S7

description: Nissle


title: NEDD4 InASO2 27152

description:
NEDD4 InASO2
1046095
nuclear RNA
chromatin RNA-seq  exp #1

value: NEDD4 InASO2


title: C1_7: acute wound circRNA 1

value: Male


title: W11: chronic wound circRNA 1

description: circRNA expression data from chronic wound

value: chronic wound biopsy from diabetic foot ulcer


title: Nissle_S6

description: Nissle

value: mono-associated


title: C4_7: acute wound circRNA 3

value: acute wound biopsy from healthy volunteer

value: Female


title: 5 weeks of age biological replicate 2


title: non-targeting ASO 27151

description:
non-targeting ASO
700465
nuclear RNA
chromatin RNA-seq  exp #1

value: non-targeting ASO


title: krill fished at 24:00, DD, biological replicate 1 (DD24-A)

description: Gene expression profiling of Antarctic krill in DD condition (DD24-A)

value: Head (including brain and compound eyes)


title: krill fished at 21:00, DD, biological replicate 2 (DD21-B)

description: Gene expression profiling of Antarctic krill in DD condition (DD21-B)


title: C7_7: acute wound circRNA 5


title: krill fished at 24:00, DD, biological replicate 2 (DD24-B)

description: Gene expression profiling of Antarctic krill in DD condition (DD24-B)


title: krill fished at 21:00, DD, biological replicate 1 (DD21-A)

description: Gene expression profiling of Antarctic krill in DD condition (DD21-A)


title: krill fished at 18:00, DD, biological replicate 3 (DD18-Pool)

description: Gene expression profiling of Antarctic krill in DD condition (DD18-Pool)


title: krill fished at 21:00, DD, biological replicate 3 (DD21-C)

description: Gene expression profiling of Antarctic krill in DD condition (DD21-C)


title: CTRL ASO 27150

description:
CTRL ASO
CTRL
nuclear RNA
chromatin RNA-seq  exp #1

value: CTRL ASO


title: krill fished at 18:00, DD, biological replicate 2 (DD18-C)

description: Gene expression profiling of Antarctic krill in DD condition (DD18-C)


title: 5 weeks of age biological replicate biological replicate 1

value: liver


title: krill fished at 18:00, DD, biological replicate 1 (DD18-B)

description: Gene expression profiling of Antarctic krill in DD condition (DD18-B)


title: Nissle_S4

description: Nissle


title: Nissle_S5

description: Nissle


title: embryonic day of 13 biological replicate 3

value: embryonic day of 13

value: Embryonic


title: embryonic day of 13 biological replicate 2


title: krill fished at 15:00, DD, biological replicate 3 (DD15-C)

description: Gene expression profiling of Antarctic krill in DD condition (DD15-C)


title: embryonic day of 13 biological replicate 1


title: BL-IVF rep3

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

description: a Day 7 IVF blastocyst

data_processing:
RNA-seq reads were mapped to the pig reference genome (Sscrofa11.1) using HISAT21 (version 2.0.4) with parameters “hisat2 --sensitive --no-discordant --no-mixed -I 1 -X 1000” and to the reference cDNA sequence using Bowtie22 with parameters “bowtie2 -q  --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200”.
Then the expression levels of each gene were calculated by the fragments per kilobase of exons per million fragments mapped (FPKM) using RSEM3 with parameters “rsem-calculate-expression --paired-end -p 8” based on the result of Bowtie2.
The final expression matrix was subjected to hierarchical clustering using R software.
Development stage (PE, PrE, TE, VE and EPI)-specific genes were selected to do the subsequent analyses. They were mapped to the final expression matrix to do the PCA and heatmap analysis with R software.
FPKMs of 13,825 protein coding genes detected by RNA-seq
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: tab-delimited Excel files include FPKM values for each sample

molecule: polyA RNA

organism: Sus scrofa

source_name: Embryonic cells

growth_protocol: Embryonic explants and XEN cells were cultured on a feeder layer of early passage (n=3) CF-1 mouse embryonic fibroblasts (MEF) cells mitotically inactivated by treatment with mitomycin-C (3 hr, 10 μg/mL). A day before seeding the embryos or XEN cells, the feeders were plated in MEF medium (high-glucose Dulbecco's modified Eagle medium, DMEM (Gibco, Grand Island, NY) supplemented with 10% (v/v) FBS (HyClone, Logan, UT)) on 0.1% (v/v) gelatin-coated four-well plates (Nunclon) at a density of 3-5 × 105 cells per cm2. At least 2 hr before the start of the experiment, the MEF medium was aspirated and replaced with ‘standard ES medium’ which included DMEM/ Nutrient Mixture Ham's F12 (DMEM/F-12, Gibco) supplemented with 15% ES-qualified fetal calf serum (FCS, HyClone), 1 mM sodium pyruvate, 2 mM L-glutamine, 100 units/mL penicillin-streptomycin, 0.1 mM 2-β-mercaptoethanol, 1% non-essential amino acids (NEAA) (all from Gibco), with various combination of growth factors; 10 ng/mL human recombinant leukemia inhibitory factor (hrLIF; Milipore, Bedford, MA) and 10 ng/mL human recombinant basic fibroblast growth factor (hrbFGF; R&D Systems, Minneapolis, MN). Other media combinations that were tested include RPMI 1640 or N2B27 serum free medium (1:1 ratio of DMEM/F12 and Neurobasal medium plus N2 and B27) (all from Gibco), with a com bination of LIF and/or bFGF, or 25 ng/mL human recombinant fibroblast growth factor 4 (hrFGF4; R&D Systems) and 1 μg/mL heparin. Following initial plating, attachment and outgrowth development, the medium was refreshed on d 3, followed by media exchange every 2 days. After 7-8 days of culture, the primary outgrowths were mechanically dissociated into small clumps, and transferred onto fresh feeders for passaging. The pXEN cells were cultured at 38.5°C in 5% O2 and 5% CO2, with the culture medium being refreshed every other day and passaged at 1:20 every 7-8 days. Cells were passaged as clumps by gentle pipetting following 10 min digestion with Accutase (Gibco).

extract_protocol:
For isolation of genomic DNA (gDNA) from cells and tissues, the QIAamp mini DNA Kit (Qiagen) was used according to the manufacturers’ instructions. Total RNA was isolated using Trizol plus RNeasy mini kit (Qiagen) and mRNA from individual blastocysts was extracted using the Dynabeads mRNA Direct Kit (Dynal Asa, Oslo, Norway).
Synthesis of cDNA was performed using a High Capacity cDNA Reverse transcription kit (Applied Biosystems; ABI, Foster City, CA) according to the manufacturers’ instructions. The QIAseq FX Single Cell RNA Library kit (Qiagen) was used for Illumina library preparation and transcriptomics analysis.

treatment_protocol: The pXEN cells were differentiated by means of embryoid body (EB) formation and treatment with small molecules and factors as previously described [#ref]. pXEN cells were dissociated as clumps, washed, and resuspended in medium (DMEM/F12 plus 15% FBS) as hanging drops on the lid of a 60mm dish, and cultured for 5 days, during which time spheroids were formed. To direct pXEN cells differentiation into either visceral endoderm (VE) or parietal endoderm (PE), accutase-dissociated single cells (2 x 105 cells per cm2) were seeded onto a laminin- or fibronectin-coated 6 well plate in N2B27 medium supplemented with the respective differentiation factors and/or chemicals. For example, for differentiation into VE, the cells were treated with CHIR99021(10 μM, stem cell biotech) and BMP4 (50 ng/mL, R&D) for activating Wnt/β-catenin pathway; for differentiation into PE, Folskolin (50 μM) and dbcAMP (1 mM) for activating the cyclic adenosine monophosphate (cAMP) signaling pathway were utilized; as per previous publications [#ref]. Differentiation medium was replaced every two days, and cells were processed for analysis on day 12.

tag: sample type

value: a Day 7 IVF blastocyst


title: Nissle_S2

description: Nissle


title: Nissle_S3

description: Nissle


title: ATXN10 InASO2 28288

description:
ATXN10 InASO2
1130658
nuclear RNA
chromatin RNA-seq  exp #3

value: ATXN10 InASO2

value: 10 uM

value: 24 hrs


title: BL-IVF rep2

description: a Day 7 IVF blastocyst


title: Nissle_S1

description: Nissle

value: E. coli Nissle


title: Nisle_S10

description: Nissle


title: BL-IVF rep1

description: a Day 7 IVF blastocyst


title: YS-D28 rep3

description: D28 Yolk Sac from AI

source_name: Yolk sac

value: D28 Yolk Sac from AI


title: CV_S9

description: CV

value: CV

value: conventional


title: CV_S8

description: CV


title: YS-D28 rep2

description: D28 Yolk Sac from AI


title: krill fished at 15:00, DD, biological replicate 2 (DD15-B)

description: Gene expression profiling of Antarctic krill in DD condition (DD15-B)

tag: tissue


title: krill fished at 12:00, DD, biological replicate 3 (DD12-C)

description: Gene expression profiling of Antarctic krill in DD condition (DD12-C)


title: Wildtype cell 3

city: Shanghai

first: Zhaoyuan

last: Fang

address: 320 Yueyang Road

institute: Chinese Academy of Sciences

description:
Wildtype cell 3
U87_NC_3

hyb_protocol: Agilent standard procedures and instructions

scan_protocol: Feature Extraction software, Agilent Technologies

data_processing: The raw signal data were processed, log transformed and quantile normalized (limma package).

source_name: Wildtype cells

extract_protocol:
Total RNA was isolated from 3 control and 3 AEP RNAi U87 cell lines.
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018 , Life technologies, Carlsbad, CA, US) & TAKARA RNAiso Plus#9109 following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

tag: cell line

value: control


title: CV_S7

description: CV


title: Wildtype cell 1

description:
Wildtype cell 1
U87_NC_1

label_protocol: Agilent standard procedures and instructions


title: YS-D28 rep1

description: D28 Yolk Sac from AI


title: krill fished at 12:00, DD, biological replicate 2 (DD12-B)

description: Gene expression profiling of Antarctic krill in DD condition (DD12-B)


title: Wildtype cell 2

description:
Wildtype cell 2
U87_NC_2


title: AEP knockdown cell 3

description:
AEP knockdown cell 3
U87_KD_3

source_name: AEP knockdown cells

value: AEP knockdown


title: krill fished at 12:00, DD, biological replicate 1 (DD12-A)

description: Gene expression profiling of Antarctic krill in DD condition (DD12-A)


title: CV_S5

description: CV


title: krill fished at 15:00, DD, biological replicate 1 (DD15-A)

description: Gene expression profiling of Antarctic krill in DD condition (DD15-A)


title: krill fished at 09:00, DD, biological replicate 3 (DD09-C)

description: Gene expression profiling of Antarctic krill in DD condition (DD06-C)


title: MCF10A cells, hG1a2

city: Graz

first: Wolfgang

last: Schreibmayer

state: Styria

address: Neue Stiftingtalstrasse 6/D04

department: Biophysics

country: Austria

institute: Medical University of Graz

data_processing:
Mapping to human Transcriptome reference (AmpliSeq_Transcriptome_21K.v1, Thermo Fisher) by TMAP
Count reads per Transcript
Write Excel xls
Supplementary_files_format_and_content: Count reads per Transcript

source_name: benign mammary epithelial cell line MCF10A

extract_protocol:
Cells were grown to 70% - 80% confluence, harvested by trypsinization and spun at 750 rpm for 3 minutes. RNA was isolated from cell-pellet using QIA shredder spin column and RNeasy Mini Kit according to manufacturer’s protocol.
10 ng of isolated RNA was heat inactivated for 10 min at 80 °C followed by cDNA Synthesis using the SuperScript ® VILO™ cDNA Synthesis Kit. DNA library was generated using the Ion AmpliSeq™Transcriptome Human Gene Expression Kit according to manufacturers’ instructions. Sequencing was performed on Ion S5 XL benchtop sequencer (Thermo Fisher Scientific) to a length of 200 base pairs. On average 8 million reads were sequenced per sample.

value: stably overexpressing KCNJ3 gene product (GIRK1)


title: AEP knockdown cell 2

description:
AEP knockdown cell 2
U87_KD_2