title: RAL-832_brain_T=19h31m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_n_28245


title: ILN_MEF79_2_30

status: Public on Dec 10 2020

type: RNA

city: Cambridge

first: Suzanne

last: Szak

state: MA

address: 14 Cambridge Ctr

department: Drug Discovery

country: USA

institute: BiogenIdec, Inc.

hyb_protocol: The Mouse 430_2 GeneChip probe arrays were pre-hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocol. 15 ug of labeled cRNA was fragmented in 30 uL 1X fragmentation buffer 100 mM KOAc, 30 mM MgOAc at 95°C for 35 minutes. The fragmented labeled cRNA was resuspended in 300 uL 1X hybridization buffer containing 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween 20, 0.5 mg/mL Aceylated BSA, 0.1 mg/mL herring sperm DNA, control oligo B2, and control transcripts bioB 1.5 pM, bioC 5 pM, bioD 25 pM, and cre 100 pM, and hybridized to Genechip probe arrays according to manufacturer’s protocol (Affymetrix, Santa Clara, CA).

scan_protocol: The GeneChip probe arrays were scanned using GeneArray Scanner (Hewlett Packard, Corvallis, OR).

data_processing: CEL files were subjected to GC-content-based Robust Multi-array Average (GCRMA) normalization (version 2.20.0).  Expression levels were log (base 2) transformed.  All calculations and analyses were carried out using R (version 2.11.1) and Bioconductor computational tools.  Analyses were applied to discover genes that were differentially expressed between specific sets of tissue.  First, to identify differentially expressed genes between groups of samples, we applied the linear modeling approach (limma) to fit gene expression levels (log2 transformed) according to the defined groups of samples and Bayesian posterior error analysis (limma version 3.4.5).  Genes that exhibited a log-odds score greater than zero and fold change greater then 1.5 were considered significantly different.

label: Biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Five ug of purified total RNA was used in a 20 uL first strand reaction with 200U SuperScript II (Invitrogen, Carlsbad,CA) and 0.5ug (dT) T7primer[5’GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG(T)24] in 1X first strand buffer (Invitrogen Life Technologies, Carlsbad, CA) with a 42°C incubation for 1 hour. Second strand synthesis was carried out by the addition of 40 U E. coli DNA Polymerase, 2 U E. coli RNase H, 10 U E. coli DNA Ligase in 1X second strand buffer (Invitrogen Life Technologies, Carlsbad, CA) followed by incubation at 16°C for 2 hrs.  The second strand synthesis reaction was purified using the Genechip Sample Cleanup Module according to the manufacturer’s protocol (Affymetrix, Santa Clara, CA). The purified cDNA was amplified using BioArray high yield RNA transcription labeling kit (Enzo Life Sciences, Inc., Parmingdale, NY) according to manufacturer’s protocol to produce 70-120 ?g of biotin labeled cRNA (compliment RNA).

extract_protocol: Mice were sacrificed after specified time points and indicated organs were harvested for total RNA.

tag: strain

tag: tissue

value: Inguinal Lymph Node (ILN)


title: ILN_MEF79_2_29


title: RAL-857_brain_T=20h19m_Rep1

type: SRA

city: Lausanne

first: Bart

last: Deplancke

state: Vaud

address: EPFL-SV-IBI-UPDEPLA, Station 19

department: Biology

country: Switzerland

institute: École polytechnique fédérale de Lausanne (EPFL)

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_n_28252

library_source: transcriptomic

data_processing:
Multiple fastq files for each library were merged by samtools v1.3,
after which they were subjected to demultiplexing using BRB-seq tools v1.1.
Then samples were mapped to the reference genome using STAR v.2.5.0b in the alignReads mode with the following parameters: --outFilterScoreMinOverLread 0.20, --outFilterMatchNminOverLread 0.20, --outFilterMultimapNmax 1.
RefSeq Genes annotation track (UCSC, annotation database for dm3) was used to index the reference genome.
Samtools was used to remove reads with an insert size > 1kb.
Number of reads falling into each of the 16,995 genes was counted using the Python package HTSeq v0.6.1
Samples with < 300,000 reads assigned to the genes (no feature, ambiguous, low quality, not aligned or mapped to the multiple locations reads were not considered) were excluded from the analysis
Genes, expressed in less than 80% of the samples were removed from the analysis.
The count table was quantile normalized with the voom function from the limma v3.32.5 package.
Batch effects from different libraries were removed with ComBat from SVA v3.24.4 package.
Genome_build: dm3, UCSC, BDGP Release 5, Apr 2006
Supplementary_files_format_and_content: *.csv.gz with raw (integer) count values for each sample as well as quantile-normalized and batch corrected counts:
raw_counts_all_samples: raw (integer) counts for all samples
w1118_time_series_brain_norm: normalized by voom and batch corrected by Combat counts for brain samples of the reference w1118 time series
w1118_time_series_fatbody_norm: normalized by voom and batch corrected by Combat counts for fat body samples of the reference w1118 time series
w1118_time_series_gut_norm: normalized by voom and batch corrected by Combat counts for gut samples of the reference w1118 time series
w1118_time_series_malpighiantubules_norm: normalized by voom and batch corrected by Combat counts for malpighiantubules samples of the reference w1118 time series
w1118_time_series_all_DGRPs_brain_norm: normalized by voom and batch corrected by Combat counts for brain samples of the reference w1118 time series and all DGRP samples
w1118_time_series_all_DGRPs_fatbody_norm: normalized by voom and batch corrected by Combat counts for fat body samples of the reference w1118 time series and all DGRP samples
w1118_time_series_all_DGRPs_gut_norm: normalized by voom and batch corrected by Combat counts for gut samples of the reference w1118 time series and all DGRP samples
DGRP-796_time_series_brain_norm: normalized by voom and batch corrected by Combat counts for brain samples of the DGRP-796 time series
DGRP-796_time_series_gut_norm: normalized by voom and batch corrected by Combat counts for fat body samples of theDGRP-796 time series
w1118_and_DGRP-796_time_series_brain_norm: normalized by voom and batch corrected by Combat counts for brain samples of the reference w1118 time series and DGRP-796 time series
w1118_and_DGRP-796_time_series_gut_norm: normalized by voom and batch corrected by Combat counts for gut samples of the reference w1118 time series and DGRP-796 time series

organism: Drosophila melanogaster

growth_protocol: Flies were raised on standard food at 25 °C and under 12 hours light: 12 hours dark (LD) cycles.

extract_protocol:
Standart Trizol extraction was performed, followed by Direct-zol™-96 RNA Purification (Zymo Resaearch) RNA purification
BRB-seq libraries were prepared according to Alpern et al 2019

value: whole brain

tag: time of harvesting

tag: replicate

tag: library

tag: bloomington

tag: time series type

value: Single observation


title: ALUBIA CE3 #3

city: LAUSANNE

first: JOAQUIN

last: CLUA

address: BIOPHORE

department: DBMV

institute: UNIL

description: FPKM for ALUBIA genes.txt

data_processing:
Illumina reads were aligned to the P. vulgaris genome v2.1. using Tophat 2 (Kim et al., 2013)
Differential gene expression analysis of RNA-seq data was performed using Cufflinks pakage (Trapnell et al., 2012)
Genome_build: Phaseolus vulgaris genome v2.1 available at Phytozome (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Pvulgaris)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each P. vularis gene

molecule: polyA RNA

organism: Phaseolus vulgaris

source_name: Roots

growth_protocol: P. vulgaris seedlings were grown on acrylic boxes (17 cm x 22 cm x 4.5 cm) containing slanted agar-Fahraeus media and incubated for 7 days in a Persival Intellus Control System growth chamber at 25°C and 75% humidity with a long-day period (16-h-day/8-h-night cycle) and a photosynthetically active radiation of 200 μmol. s-1.cm-2 using mixed lighting containing four OSRAM cool daylight L36W/765 tubesand one OSRAM FLUORA L36W/77 tube.

extract_protocol:
RNA was extracted with Trizol following manufacture´s recommendations (Thermo Fisher). RNA quality was evaluated by capillary gel electrophoresis on an Agilent 2100 Bioanalyzer using the AgilentRNA6000 Pico kit.
Libraries were prepared using 3 µg of RNA and the Illumina TruSeq RNA Sample Preparation kit v2 following provider’s instructions. Superscript II (Invitrogen) reverse transcriptase was used for cDNA synthesis. PCR fragments were purified using AMPure XP beads (Beckman Coulter Genomics). Size of the synthesized fragments was verified in an Agilent 2100 Bioanalyzer using the DNA-1000 kit (Agilent). Libraries were multiplexed following Illumina recommendations for barcode compatibility.

treatment_protocol: After 7 days post germination roots were inoculated with 5 ml of Yeast Extract-Manitol (YEM) media as a control or with 5 ml of a suspension of strain SC15, CE3, 55N1 or 124N1 grown in YEM media until they reached an OD600=0.8

tag: agent

value: R. etli CE3

tag: cultivar

value: Alubia


title: ILN_MEF79_2_27


title: GC1_DP_G06.DecP.12_H.LZ

city: New York

first: Gabriel

last: Victora

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_G06

data_processing:
Raw fastq sequence files generated from Smartseq2 libraries were aligned to mouse genome (v. mm10) with the annotated transcriptome (v. gencode M22) using STAR (v. 2.6)(Dobin et al., 2013). Subsequently, genome-mapped BAM files were processed through RSEM (v. 1.3.1)(Li and Dewey, 2011) for gene quantification. The matrix of gene counts was then, used as input for analysis by the R package Seurat (v. 3.1.4.)(Stuart et al., 2019). Next, the dataset was corrected by using the regularized negative binomial regression (SCTransform) implemented by Seurat (Hafemeister and Satija, 2019). To control the dataset for unwanted sources of experimental variation, we fed the mitochondrial gene abundance and the experimental batches information into SCTransform. Additionally, cells containing more than 20% of sequence reads aligned to mitochondrial genes were excluded prior to normalization. Next, single cells were clustered and gene expression were evaluated with the Seurat workflow. Gene signature scoring was performed by using Seurat’s AddModuleScore function (See Supplemental Spreadsheet 1 for the complete list).
Genome_build: mm10
Supplementary_files_format_and_content: txt files contain raw, individual quantification matrices per experiment
Supplementary_files_format_and_content: tsv files contain metadata tables, umap/pca embeddings, and quality filtered raw and normalized quantification

source_name: Germinal Centers

extract_protocol:
Cell suspensions were resuspended in PBE and incubated on ice for 30 min with fluorescently-labeled antibodies (Table S2) along with 1 mg/mL of anti-CD16/32 (24G2, eBioscience). For detection of cells in early S of the cell cycle, we performed dual nucleotide pulse and staining as previously described (Gitlin et al., 2014). Briefly, mice were injected i.v. with 1 mg of EdU (A10044, Thermo Fisher Scientific) and one hour later with 2 mg of BrdU (B5002, Sigma). 30 min after the second injection, lymph nodes were harvested, and single cell suspensions were prepared. After cell surface receptor staining as described above, cells were fixed and permeabilized using BD Cytofix/Cytoperm™ fixation and permeabilization solution and BD Cytoperm Permeabilization Buffer PLUS, respectively. EdU and BrdU incorporation into DNA was assayed using the Click-iT Plus EdU Alexa Fluor 647 Flow Cytometry Assay Kit (Invitrogen) and FITC BrdU Flow Kit (BD), respectively. For single cell sorting, cells were stained as above and index-sorted directly into 96 well plates containing Buffer TCL (Qiagen) supplemented with 1% -mercaptoethanol using a BD FACS Aria II. Each plate contained all conditions assayed in each replicate. Cells were washed, filtered, and resuspended in PBE prior to analysis or sorting on BD FACS LSR II, FACS Symphony or FACS ARIA II cytometers. All data were analyzed using Flowjo software v.10.
Libraries were prepared as previously described (Trombetta et al., 2014). Briefly, nucleic acids were extracted from sorted single cell using RNAClean XP SPRI beads (Beckman Coulter), and RNA was hybridized first using RT primer (/5BiosG/AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN) then reverse-transcribed into cDNA using TSO primer (AAGCAGTGGTATCAACGCAGAGTACATrGrGrG) and RT maxima reverse transcriptase (Thermo Fisher Scientific). cDNA was amplified using ISPCR primer (AAGCAGTGGTATCAACGCAGAGT) and KAPA HiFi HotStart ReadyMix (Fisher Scientific), cleaned up using RNAClean XP SPRI beads three times, and tagmented using Nextera XT DNA Library Preparation Kit (Illumina). For each sequencing batch, up to four plates were barcoded at a time with Nextera XT Index Kit v2 Sets A-D (Illumina). Finally, dual-barcoded libraries were pooled and sequenced using Illumina Hiseq2500 (experiment 1)/Nextseq 550 (experiments 2-4) platform.
Smartseq2

tag: dec

tag: timepoint

tag: zone

tag: sequencing

tag: genotype


title: ALUBIA CE3 #1

description: FPKM for ALUBIA genes.txt


title: GC1_DP_G07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_G07


title: ILN_MEF79_2_28


title: ILN_MEF79_2_26


title: ALUBIA 55N1 #3

description: FPKM for ALUBIA genes.txt

value: R. etli 55N1


title: ALUBIA124N1 #3

description: FPKM for ALUBIA genes.txt

value: R. etli 124N1


title: GC1_DP_G04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_G04


title: ILN_Nav_40


title: GC1_DP_G05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_G05


title: GC1_DP_G03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_G03


title: RAL-810_brain_T=18h43m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_n_28239


title: GC1_DP_G08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_G08


title: GC1_DP_G02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_G02


title: RAL-796_brain_T=17h55m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28233


title: RAL-787_brain_T=17h36m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_n_28231


title: GC1_DP_G01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_G01


title: ALUBIA 124N1 #2

description: FPKM for ALUBIA genes.txt


title: RAL-802_brain_T=18h4m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28235


title: RAL-818_brain_T=18h52m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_n_28241


title: ILN_DMF100_MEF79_2_37


title: RAL-821_brain_T=19h12m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28243


title: ILN_DMF100_MEF79_2_39


title: ILN_MEF79_2_25


title: GC1_DP_F07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_F07


title: RAL-776_brain_T=17h16m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_n_28229


title: GC1_DP_F06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_F06


title: RAL-737_brain_T=16h48m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_n_28222


title: ILN_DMF100_MEF79_2_38


title: RAL-738_brain_T=16h57m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28223


title: ILN_DMF100_MEF79_2_35


title: ILN_DMF100_MEF79_2_36


title: GC1_DP_F08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_F08


title: ILN_DMF100_MEF79_2_33


title: GC1_DP_F05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_F05


title: RAL-589_brain_T=15h40m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28213


title: GC1_DP_F04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_F04


title: RAL-703_brain_T=16h19m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_n_28218


title: RAL-748_brain_T=17h7m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28224


title: GC1_DP_F02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_F02


title: RAL-721_brain_T=16h38m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_n_28220


title: ILN_DMF_179_2_24


title: RAL-642_brain_T=16h0m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_n_28216


title: RAL-584_brain_T=15h31m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_n_28212


title: GC1_DP_E08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_E08


title: RAL-508_brain_T=14h52m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_n_28205


title: GC1_DP_F01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_F01


title: GC1_DP_E07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_E07


title: ILN_DMF_179_2_19


title: GC1_DP_E06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_E06


title: RAL-441_brain_T=14h4m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28198


title: GC1_DP_F03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_F03


title: RAL-492_brain_T=14h33m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28203


title: ILN_DMF_179_2_17


title: ILN_DMF100_MEF79_2_32


title: RAL-461_brain_T=14h24m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_n_28200


title: GC1_DP_E05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_E05


title: ILN_DMF_179_2_18


title: ILN_DMF_179_2_21


title: GC1_DP_E04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_E04


title: RAL-426_brain_T=13h45m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_n_28196


title: RAL-385_brain_T=13h26m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_n_28191


title: ILN_DMF_100_9


title: ILN_DMF_100_15


title: ILN_DMF_100_13


title: GC1_DP_E03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_E03


title: ILN_DMF_179_2_20


title: ILN_DMF_100_16


title: RAL-382_brain_T=13h7m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28189


title: GC1_DP_D08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_D08


title: GC1_DP_D05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_D05


title: RAL-377_brain_T=12h48m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_n_28186


title: RAL-383_brain_T=13h16m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_n_28190


title: RAL-381_brain_T=12h57m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28188


title: GC1_DP_D06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_D06


title: GC1_DP_D07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_D07


title: RAL-370_brain_T=12h9m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_n_28182


title: ILN_DMF100_MEF79_2_34


title: GC1_DP_D04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_D04


title: GC1_DP_E02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_E02


title: RAL-352_brain_T=11h31m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_n_28177


title: RAL-371_brain_T=12h19m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_n_28183


title: GC1_DP_D02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_D02


title: RAL-340_brain_T=11h12m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_n_28174


title: RAL-361_brain_T=12h0m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_n_28180


title: GC1_DP_D03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_D03


title: ILN_DMF_100_14


title: GC1_DP_D01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_D01


title: RAL-338_brain_T=11h2m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_n_28173


title: GC1_DP_C08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_C08


title: ILN_DMF_100_12


title: Brain_VEH_6

value: Brain


title: ILN_DMF_100_10


title: Brain_VEH_8


title: Brain_VEH_3


title: Brain_VEH_4


title: ILN_DMF_100_11


title: RAL-318_brain_T=10h33m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_n_28168


title: Brain_VEH_5


title: GC1_DP_C06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_C06


title: RAL-336_brain_T=10h52m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28172


title: GC1_DP_C05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_C05


title: GC1_DP_C04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_C04


title: RAL-309_brain_T=10h14m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28166


title: Brain_VEH_7


title: GC1_DP_C07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_C07


title: GC1_DP_C03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_C03


title: RAL-317_brain_T=10h24m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_n_28167


title: Brain_VEH_2


title: GC1_DP_C02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_C02


title: Brain_Nav_46


title: Brain_Nav_47


title: Brain_VEH_1


title: Brain_Nav_43


title: Brain_Nav_45


title: Brain_Nav_44


title: RAL-280_brain_T=9h55m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28164


title: RAL-181_brain_T=8h57m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_n_28151


title: GC1_DP_B07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_B07


title: RAL-176_brain_T=8h38m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_n_28149


title: RAL-158_brain_T=8h28m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_n_28147


title: GC1_DP_B05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_B05


title: Brain_Nav_40


title: GC1_DP_B04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_B04


title: RAL-149_brain_T=8h19m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_n_28145


title: RAL-239_brain_T=9h45m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28161


title: GC1_DP_B03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_B03


title: Brain_Nav_42


title: RAL-138_brain_T=8h0m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28143


title: Brain_MEF79_2_29


title: P16: Fibroblasts from patient 02HNG

city: Evry

first: Nicolas

last: FORTUNEL

address: 2 Rue Gaston Cremieux

country: France

institute: CEA

data_processing:
Base Calling: Basecalls performed using CASAVA version 1.8;2
Read Quality: Quality of raw reads was assessed using FastQC quality control version 0.11.7  http://www.bioinformatics.babraham.ac.uk/projects/fastqc
Mapping: Primary assembly Homo sapiens genome sequence (release GRCh37.p87) (files Homo_sapiens.GRCh37.87.chr.cor.fa). High quality reads (fastq files) were mapped to this sequences using HISAT2.2.0.5
Gene filtering: genes with low expression (mean number of reads in the training set < 10) were filtering out
Normalization: For the quality control representations, the effective library sizes were first computed using function estimateSizeFactors from package DESeq2. The raw count values were then transformed using a regularized log (function rlogTransformation from package DESeq2 with parameter blind=TRUE).
Genome_build: GRCh37

organism: Homo sapiens

source_name: healthy adult skin

growth_protocol: Dermal fibroblast mass cultures were performed in plastic devices (Becton-Dickinson or Sarstedt), in DMEM-Glutamax medium supplemented with 10% FBS (  ) and 100 U/ml penicillin-streptomycin at the density of 500 to 1000 cells by cm2. Medium was renewed 3 times a week.When cultures reached 100% of confluence, medium was renewed and fibroblast cultures were stopped 24 hours after. RNA preparations were performed at a mean passage 8 in culture to avoid entering cell senescence. Some patient cells were studied at higher passage number , but not at higher number of population doublings, due to very slow growth of these cells.

extract_protocol:
Total RNA from cultures C1,C2, P1 to P16 was extracted with RNeasy Mini and Micro kits (Qiagen) and total RNA from cultures C3 to C8 was extracted with NucleoSpin RNA plus kit (Macherey – Nagel), followed by quality control using capillary electrophoresis (RNA 6000 Nano chips, Agilent).
Libraries were prepared according to Illumina's instructions with theTruSeq RNA Library Prep Kit v2. Briefly, total RNA (1µg) was purified and fragmented before first strand and second strand cDNA synthesis. Then ends are repaired and 3’ends adenylated before adapters ligation and PCR amplification. Libraries were then validated, normalized, and sequenced on Illumina HiSeq 1000 as short-insert paired-end libraries with read lengths 100 bp.

tag: cell type

value: dermal fibroblasts, untransformed cell strain

tag: biological samples

value: cancer patient


title: Brain_MEF79_2_31


title: Brain_MEF79_2_30


title: P15: Fibroblasts from patient COP053


title: GC1_DP_A07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_A07


title: GC1_DP_B08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_B08


title: RAL-217_brain_T=9h7m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28154


title: RAL-287_brain_T=10h4m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28165


title: GC1_DP_C01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_C01


title: RAL-237_brain_T=9h36m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28160


title: GC1_DP_B06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_B06


title: GC1_DP_A06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_A06


title: GC1_DP_A05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_A05


title: Brain_Nav_41


title: Brain_MEF79_2_25


title: Brain_MEF79_2_28


title: GC1_DP_B01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_B01


title: RAL-142_brain_T=8h9m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_n_28144


title: GC1_DP_B02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_B02


title: GC1_DP_A04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_A04


title: Brain_DMF100_MEF79_2_36


title: Brain_DMF100_MEF79_2_37


title: Brain_MEF79_2_27


title: GC1_DP_A03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_A03


title: GC1_DP_A02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_A02


title: P13: Fibroblasts from patient 27CLB


title: P12: Fibroblasts from patient 11CLB


title: P14: Fibroblasts from patient 07HM


title: Brain_DMF100_MEF79_2_34


title: Brain_DMF100_MEF79_2_33


title: P11: Fibroblasts from patient 01MTZ


title: Brain_DMF100_MEF79_2_35


title: Brain_DMF100_MEF79_2_39


title: Brain_MEF79_2_26


title: Brain_DMF_179_2_24


title: Brain_DMF100_MEF79_2_38


title: P9: Fibroblasts from patient 03JEM


title: P6: Fibroblasts from patient 04CLB


title: P10: Fibroblasts from patient 03CAV


title: P5: Fibroblasts from patient 19HM


title: GC1_DN_H11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_H11


title: GC1_DN_H10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_H10


title: GC1_DP_A01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_A01


title: P7: Fibroblasts from patient 03HM


title: GC1_DN_H09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_H09


title: P8: Fibroblasts from patient 08HM


title: P3: Fibroblasts from patient 29CLB


title: GC1_DP_E01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_E01


title: GC1_DN_G12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_G12


title: Brain_DMF_179_2_23


title: Brain_DMF_179_2_22


title: GC1_DN_H12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_H12


title: P4: Fibroblasts from patient 26CLB


title: Brain_DMF100_MEF79_2_32


title: GC1_DN_G11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_G11


title: Brain_DMF_179_2_21


title: GC1_DN_G10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_G10


title: P2: Fibroblasts from patient 23CLB


title: GC1_DN_G09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_G09


title: GC1_DN_F12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_F12


title: GC1_DN_F11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_F11


title: P1: Fibroblasts from patient 02JEM


title: Brain_DMF_179_2_19


title: Brain_DMF_179_2_20


title: C6: Human Normal Fibroblast 24517

value: healthy donor


title: C8: Human Normal Fibroblast 030317


title: C5: Human Normal Fibroblast 17517


title: C7: Human Normal Fibroblast 16617


title: Brain_DMF_179_2_17


title: GC1_DN_F09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_F09


title: C4: Human Normal Fibroblast 9517


title: GC1_DN_F10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_F10


title: GC1_DN_E12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_E12


title: C3: Human Normal Fibroblast 5517


title: Brain_DMF_100_9


title: C2: Human Normal Fibroblast HNF121


title: GC1_DN_E11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_E11


title: GC1_DN_E10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_E10


title: C1: Human Normal Fibroblast HNF116


title: GC1_DN_D12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_D12


title: Brain_DMF_100_16


title: GC1_DN_D11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_D11


title: GC1_DN_E09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_E09


title: Brain_DMF_100_15


title: Brain_DMF_179_2_18


title: Brain_DMF_100_14


title: Brain_DMF_100_11


title: Brain_DMF_100_13


title: Brain_DMF_100_10


title: GC1_DN_D10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_D10


title: Mock Dox 3

city: Philadelphia

first: Kristen

last: Lynch

state: Pennsylvania

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Molecular Biophysics

institute: University of Pennsylvania

data_processing:
fastq.gz reads trimmed with trim_galore to remove low-quality base calls and library adaptor sequences (reads <35nt discarded)
Reads were mapped to hg38 genome with STAR or Salmon.
For splicing analyses, reads mapped with STAR were quantified for alternative splicing with MAJIQ algorithm
For expression analyses, reads mapped with Salmon were quantified for transcript level counts.
Genome_build: hg38
Supplementary_files_format_and_content: quant.sf.txt files contain transcript counts

growth_protocol: Human lung adenocarcinoma epithelial cells (A549) were cultured in RPMI 1640 (Corning: 10-040-CV), 10% heat-inactivated FBS (Gibco: 16000-044), and 100 units/ml Pen/Strep antibiotics. All cells were maintained at 37C with 5% CO2. Cells were tested negative for mycoplasma. Cell lines were obtained and authenticated by ATCC (A549: CCL-185, MDCK: PTA-6500). A/Puerto Rico/8/1934 (PR8) and A/WSN/33 (WSN) strains were used as specified for individual experiments.

extract_protocol:
Total RNA isolated with RNA-bee (Tel-Test) protocol
TruSeq mRNA stranded library preparation

treatment_protocol: For infections, A549 cells were grown to 80% confluency, washed with PBS, and inoculated with viral titer diluted in PBS•BA (DPBS with Ca and Mg (Corning: 21-031-CV), 0.2% BSA (Lampire: 7500810), and 100 units ml−1 Pen/Strep antibiotics) for 1 h at room temperature (22˚C). Cells were then washed with PBS and incubated in Infection media (1X MEM, 0.2% BSA, 10 mM HEPES buffer, 0.12% NaHCO3, 100 units ml−1 Pen/Strep antibiotics) at 37˚C with 5% CO2 until desired time-point. At time-points, media was collected for plaque assay analyses. For protein and RNA analyses, wells were rinsed with PBS and either pelleted and lysed with RIPA buffer for Western blot analysis or RNA was extracted using RNA-Bee (amsbio: CS-501B). For knockdown of hnRNP K to test viral replication, A549 cells were treated with 50 nM siRNA (Dharmacon, SMARTpool, M-011692-00) as previously described 24. For RNA-Seq and validation experiments, hnRNP K was stably depleted from A549 cells using a lentiviral expressed doxycycline-inducible shRNA with sequence:  agcgGGACCTATTATTACTACACAATAGTGAAGCCACAGATGTATTGTGTAGTAATAATAGGTCC (target underlined)

tag: cell line

tag: experiment

value: shRNA Knockdown

tag: treatment

value: CTRL shRNA

tag: hours infected


title: WB_VEH_8

tag: strain

tag: tissue

value: Whole Blood


title: Mock Dox 2


title: GC1_DN_D09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_D09


title: GC1_DN_C12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_C12


title: hnRNP K knockdown 1

value: hnRNP K shRNA Knockdown


title: hnRNP K knockdown 2


title: Mock Dox 1


title: WB_VEH_5


title: WB_VEH_3


title: hnRNP K knockdown 3


title: WB_VEH_4


title: 12hr post infection 3

value: Flu Infection

value: Infected


title: 12hr post infection 2


title: GC1_DN_C09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_C09


title: GC1_DN_C10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_C10


title: GC1_DP_A08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_A08


title: GC1_DN_C11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_C11


title: WB_Nav_47


title: WB_VEH_6


title: WB_VEH_1


title: GC1_DN_B12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_B12


title: GC1_DN_B11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_B11


title: 6hr post infection 3


title: 6hr post infection 2


title: WB_VEH_2


title: WB_Nav_46


title: 6hr post infection 1


title: GC1_DN_B10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_B10


title: GC1_DN_B09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_B09


title: GC1_DN_A12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_A12


title: Mock infection 3

value: CTRL mock infection


title: Mock infection 2


title: Mock infection 1


title: GC1_DN_A11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_A11


title: GC1_DN_A09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_A09


title: A.thaliana_BG_rep3

city: Dublin

first: Samuel

middle: Patrick

last: Belton

state: Leinster

address: UCD, Belfield, Dublin 4

department: School of Biology and Environmental Science

country: Ireland

institute: University College Dublin

description:
s3BG
CM_vs_Control.genes.DEA.xls
genes.FPKM.annot.xls

data_processing:
Index-coded samples were clustered on a cBot Cluster Generation system using a PE Cluster Kit cBot-HS (Illumina) followed by paired-end sequencing on an IlluminaI platform.
FASTQ raw reads were filtered to remove adaptors, poly-N sequences and low-quality reads. Q20, Q30 and GC content were also calculated (Supplementary Table 6).
Using HISAT2 software, cleaned-up reads were mapped to the A. thaliana genome (TAIR10) before expressing read quantification as FPKM.
Differential expression of genes between treatments (n=3 biological replicates) was determined using the DESeq2 R package. The false discovery rate (FDR) was determined using the Benjamini and Hochberg procedure, after which genes with an adjusted P value (Padj) of 0.05 were considered to be differentially expressed.
Genome_build: TAIR10
Supplementary_files_format_and_content: file containing gene TAIR IDs, their FPKM values for each of 6 samples, gene annotation and gene description
Supplementary_files_format_and_content: file containing gene TAIR IDs, their read counts for each of 6 samples, gene annotation and gene description
Supplementary_files_format_and_content: file containing gene TAIR IDs, their mean read counts for treatment 1 (CM), their mean read counts for treatment 2 (BG), their change in expression (log2fold change, as calculated using the DESeq2 R package), the P-values for gene expression change, the adjusted P-values (calculated using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR)), gene name and gene description.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana undifferentiated cells from suspension cell culture

growth_protocol: Arabidopsis thaliana (var. Ler-0) suspension cell cultures were grown in liquid Murashige and Skoog (MS) containing 3% sucrose, 0.5 mg L-1 naphthaleneacetic acid (NAA) and 0.05 mg L-1 kinetin (pH adjusted to 5.8 using KOH). Cells were sub-cultured every 7 days by transferring 10 ml of mature cells into 90 ml of fresh growth medium. Cultures were grown at 21°C with shaking at 120 rpm for a photoperiod of 16 hours light (ca. 165 μmol m-2 sec-1 of cool white fluorescent light) and 8 hours darkness.

extract_protocol:
Cells (1 ml frozen aliquots) were pulverised into a powder by bead beating at 30 h/z for 1 min. Total RNA was then purified using an RNeasy® plant mini kit (Qiagen™; ref. 74904) according to manufacturer’s instructions
Library preparation and RNA-seq was performed by Novogene (Beijing, China). A total of 1 μg RNA was used as input material for library generation using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB USA), at which point index codes were added to each sample. mRNA was purified using magnetic beads harbouring poly-dT oligos. Fragmentation was performed using divalent cations in heated NEBNext First StrandSynthesis Reaction Buffer. First strand cDNA was synthesised using random hexamers and M-MuL MuLV Reverse Transcriptase. Second strand cDNA was synthesised using DNA Polymerase I (+RNase H). Blunt ends were generated via exonuclease/ polymerase activities. Next, 3’ DNA ends were adenylated before ligating an NEBNext hairpin loop adaptor for hybridization. Fragments of ca. 200 bp were preferentially selected for using an AMPure XP system (Beckman Coulter, Beverly, USA). Purified, adaptor-ligated fragments were treated with 3 µl of USER® Enzyme (NEB, USA) before selective PCR enrichment using Phusion® High-Fidelity DNA polymerase using Universal and index primers. Products were purified again using the AMPure XP system and library quality assessed using the 2100 BioAnalyzer® system.

treatment_protocol: 7-day-old Arabidopsis thaliana suspension cells were incubated with 20% v/v of Nostoc punctiforme-conditioned medium (CM). After 1 hour, 1 ml of cells was harvested by centrifugation and snap-frozen in liquid nitrogen ahead of RNA extraction. As a control treatment, 20% v/v of fresh N. punctiforme growth medium (BG) (growth medium in which no cells had been cultured) was instead used. N. punctiforme growth medium was liquid BG-11 (NH4).

tag: variety

value: Landsberg erecta (Ler-0).

tag: genome

value: 20% v/v fresh Nostoc punctiforme-growth medium (BG)


title: 12hr post infection 1


title: WB_Nav_41


title: A.thaliana_BG_rep2

description:
s2BG
CM_vs_Control.genes.DEA.xls
genes.FPKM.annot.xls


title: WB_Nav_40


title: WB_Nav_42


title: WB_MEF79_2_30


title: WB_MEF79_2_29


title: WB_MEF79_2_27


title: WB_MEF79_2_28


title: A.thaliana_BG_rep1

description:
s1BG
CM_vs_Control.genes.DEA.xls
genes.FPKM.annot.xls


title: A.thaliana_CM_rep2

description:
s2CM
CM_vs_Control.genes.DEA.xls
genes.FPKM.annot.xls

value: 20% v/v Nostoc punctiforme-conditioned medium (CM)


title: IP_B_SCR

city: Rome

first: Andrea

last: Cipriano

state: Italy

address: Piazzale Aldo Moro 5

department: Biologia e Biotecnologue C. Darwin

country: Italy

institute: La Sapienza

description: MATR3 IP in GAP-SCR treated Myotubes Replicate B

library_source: genomic

data_processing:
Base-Calling with Casava.
Quality trimming was performed using Trimmomatic software with parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:40.
Reads were aligned to mouse mm10 genome using Bowtie software with parameters --best --strata -m 1. PCR duplicates were removed using samtools rmdup.
For both GAP-SCR and GAP-1 experiments we used HOMER getDifferentialPeaksReplicates.pl program to call MATR3-enriched regions by comparing IP samples versus their corresponding Input samples (q-value < 0.1); to allow enriched regions with variable length we launched the program twice, once with -style histone parameter and the other with -region -size 260 parameter. MATR3-enriched regions obtained with both parameters were identified using Bedtools intersect; this list of overlapping regions was supplemented with regions obtained using only one of the two parameters.
IgG-enriched regions were called using HOMER findPeaks by comparing IgG samples with their corresponding Input samples with both -style histone and -region -size 260 parameters. IgG-enriched regions from both GAP-SCR and GAP-1 experiments were pooled together and used to filter off MATR3-enriched regions close to them using Bedtools window with parameters -v -w 500. This way we obtained two lists of MATR3-enriched regions, one for the GAP-SCR experiment and the other for the GAP-1 experiment.
Genome_build: mm10
Supplementary_files_format_and_content: BED files containing the genomic coordinates of Matrin 3 binding sites across the genome (mm10).

molecule: genomic DNA

growth_protocol: C2C12 murine myoblasts were  plated in grow medium (D-MEM 20% Fetal Bovine Serum (FBS)) at 40% of confluence and differentiated 24h after plating in differentiation medium  (D-MEM 0.5% FBS).

extract_protocol:
DM2 myotubes were crosslinked with 1% of Formaldehyde PBS for 10 minutes directly in the dish and che chromatin was collected and sonicated using Bioruprtor sonicator, and the ChIP experiments were performed according to manufacturer’s protocol (MAGnify ChIP, Life Technologies) and as previously described in Ballarino et al. 2018.
Ovation® Ultralow V2 DNA-Seq Library Preparation Kit (NuGEN, Redwood City, CA) was used for library preparation following the manufacturer’s instructions.  Immunoprecipitated DNA samples were quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA). Final libraries were checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and  Agilent Bioanalyzer DNA assay or Caliper (PerkinElmer, Waltham, MA). Libraries were then prepared for sequencing and sequenced on single-end 50 bp mode on HiSeq 2500 system with HiSeq v4 reagents.

treatment_protocol: pCharme RNAi experiments were performed with 75nM of LNA GapmeRs (Exiqon) using 3ul/ml of Transit-X2 (Mirus, Cat. N°. MIR 6000) as transfectant according to manufacturer’s specifications. Negative Control A (Euroclone) was used as negative (Scramble) control. Cells were transfected at  ̴ 80% confluence, for two overnights and collected 48h upon the induction of differentiation.

tag: chip antibody

value: MATR3 Bethyl Cat. N° A300-591A

tag: differentiation status

value: myotubes

tag: knockdown

value: control


title: A.thaliana_CM_rep3

description:
s3CM
CM_vs_Control.genes.DEA.xls
genes.FPKM.annot.xls


title: A.thaliana_CM_rep1

description:
s1CM
CM_vs_Control.genes.DEA.xls
genes.FPKM.annot.xls


title: GC1_DN_A10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DN_A10

tag: dec

tag: timepoint


title: WB_MEF79_2_25


title: IP_A_SCR

description: MATR3 IP in GAP-SCR treated Myotubes Replicate A


title: IgG_SCR

description: IgG from GAP-SCR treated Myotubes

value: Rabbit IgG from Magnify Chromatin Immunoprecipitation Kit (cat n 492024)


title: IP_A_GAP

description: MATR3 IP  in GAP-1 treated Replicate A

value: pCharme lncRNA


title: WB_DMF100_MEF79_2_38


title: IgG_GAP

description: IgG from GAP-1 treated Myotubes


title: IP_B_GAP

description: MATR3 IP in GAP1 treated Myotubes Replicate B


title: CECs_LPS_2Hr_2

city: Charlestown

first: Mahesh Chandra

last: Kodali

department: Neurology

institute: Massachusetts General Hospital / Harvard Medical School

description:
DESeq2_normalized_counts.txt
N23

data_processing:
Transcript abundance from RNA-seq reads was quantified using Salmon, and gene-level counts were obtained using tximport, against the C57BL/6J mouse genome annotation Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6), obtained from the National Center for Biotechnology Information. Subsequently, raw counts were processed with DESeq2 to determine differentially expressed genes.
salmon version 1.2.1
Genome_build: Mouse Build 38 patch release 6 (GRCm38.p6)
Supplementary_files_format_and_content: DESeq2 normalized count matrix

source_name: FACS sorted Cerebral Endothelial Cells (CECs)

extract_protocol:
RNA was extracted from mouse brain FACS sorted CECs and microglia after Buffer RLT Plus homogenization, and then using QIAGEN RNeasy plus micro Kit. Samples were initially DNAse treated with the GDNAse eliminator column, and finally eluted in in RNAse free water from Qiagen.
Isolated RNA sample quality was determined using High Sensitivity RNA Tapestation (Agilent Technologies Inc., California, USA) and concentration was measured using Qubit 2.0 RNA High Sensitivity assay (ThermoFisher, Massachusetts, USA). Libraries were then constructed following manufacturer’s instructions for SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio USA Inc., California, USA) followed by Nextera® XT DNA Library Prep Kit (Illumina, California, USA). Final library quantities were measured by KAPA SYBR® FAST qPCR and quality was assessed using TapeStation D1000 ScreenTape (Agilent Technologies, CA, USA). Resulting final library size was about 430bp with an insert size of about 200bp. Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed basing on QC values and sequencing was performed on an Illumina® HiSeq 4000 (Illumina, California, USA). The read length configuration was 150 PE for 40 M PE reads per sample (20M in each direction).

value: wild type

tag: gender

value: male

value: 10mg/kg LPS for 2 hours


title: CECs_LPS_2Hr_1

description:
DESeq2_normalized_counts.txt
N22

tag: genotype


title: CECs_LPS_2Hr_3

description:
DESeq2_normalized_counts.txt
N24


title: WB_DMF100_MEF79_2_37


title: WB_DMF100_MEF79_2_39


title: WB_DMF100_MEF79_2_35


title: INPUT_SCR

description: Input Chromatin from GAP-SCR treated Myotubes


title: WB_DMF100_MEF79_2_34


title: WB_DMF100_MEF79_2_36


title: INPUT_GAP

description: Input Chromatin from GAP-1 treated Myotubes


title: CECs_LPS_1Hr_3

description:
DESeq2_normalized_counts.txt
N21

value: 10mg/kg LPS for 1 hour


title: CECs_LPS_1Hr_1

description:
DESeq2_normalized_counts.txt
N19


title: CECs_LPS_30min_1

description:
DESeq2_normalized_counts.txt
N16

value: 10mg/kg LPS for 30 min


title: CECs_LPS_30min_2

description:
DESeq2_normalized_counts.txt
N17


title: CECs_PBS_Control_3

description:
DESeq2_normalized_counts.txt
N15

value: PBS


title: WB_DMF_179_2_22

value: Whole Blood


title: WB_DMF_179_2_24


title: CECs_LPS_1Hr_2

description:
DESeq2_normalized_counts.txt
N20


title: thymic epithelial tumor T012TA

city: rome

first: andrea

last: sacconi

address: via elio chianesi

institute: regina elena cancer institute

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix GeneChips 3000 Scanner according to the Affymetrix GeneChip WT labeling and hybridization user manual.

data_processing: Analyses were performed with Matlab. CEL files were read with celintensityread function included in MATLAB. We performed the background adjustment of Affymetrix microarray probe-level data using the Robust Multi-array Average (RMA) procedure. Data was quantile normalized and log2 transformed. Undetected probes as well as positive and negative controls were removed.

label: biotin

source_name: thymic epithelial tumor

label_protocol: 100 ng of total RNA was labeled using the WT Terminal Labeling Kit (Affymetrix) and hybridized on Affymetrix® Human Gene 2.0 ST Arrays 2.0 (Affymetrix, Santa Clara, California).

extract_protocol: Fresh frozen samples were homogenized by gentleMACSdissociator (Miltenyi Biotec,Bologna, Italy) in 700 μl of Qiazol (Qiagen, Chatsworth, CA) and RNA was extracted using the miRNAeasy® kit (Qiagen, Chatsworth, CA) following the manufacturer’s instructions.

value: thymic epithelial tumor


title: CECs_PBS_Control_2

description:
DESeq2_normalized_counts.txt
N14


title: thymic epithelial tumor T014T


title: CECs_PBS_Control_ 1

description:
DESeq2_normalized_counts.txt
N13


title: WB_DMF_179_2_23


title: WB_DMF_179_2_21


title: CECs_LPS_30min_3

description:
DESeq2_normalized_counts.txt
N18


title: WB_DMF_179_2_20


title: Microglia_LPS_2Hr_3

description:
DESeq2_normalized_counts.txt
N12

source_name: FACS sorted microglia


title: peritumoral thymic tissue 15803N

source_name: peritumoral thymic tissue

value: peritumoral thymic tissue


title: Microglia_LPS_2Hr_2

description:
DESeq2_normalized_counts.txt
N11


title: thymic epithelial tumor 15914B


title: WB_DMF_179_2_19


title: WB_DMF_179_2_17


title: Microglia_LPS_2Hr_1

description:
DESeq2_normalized_counts.txt
N10


title: thymic epithelial tumor 15711T


title: Thy2_ThemisKO

city: Singapore

first: Nicholas

last: Gascoigne

address: 1E Kent Ridge Road

department: Microbiology and Immunology

country: Singapore

institute: National University of Singapore

data_processing:
library strategy: targeted-RNAseq
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequences. The raw reads were mapped to the reference V, J and C genes of TCRa and assembled in order to extract specific gene regions CDR3 using Mixcr pipeline.
Genome_build: mm9
Supplementary_files_format_and_content: V,J segment usage and CDR3 peptide sequnces generated using Mixcr pipeline

source_name: sorted single positive  CD8 T thymocytes

extract_protocol:
TCRαβ libraries were generated from total RNA exctracted from sorted peripheral CD8 T cells and single positive CD8 thymocytes.
5' RACE TCR-targeted PCR

tag: strain background

tag: genotype/variation

tag: cell type

value: single positive thymocytes

tag: cell subset

value: TCRab+ CD8 T cells


title: WB_DMF_100_15


title: WB_DMF_100_9


title: peritumoral thymic tissue T012NA


title: thymic epithelial tumor 15636A


title: Thy2_ThemisWT


title: Thy1_ThemisKO


title: WB_DMF_100_14


title: peritumoral thymic tissue 15636N


title: Thy1_ThemisWT


title: WB_DMF_179_2_18


title: Microglia_LPS_1Hr_2

description:
DESeq2_normalized_counts.txt
N8

tag: treatment


title: WB_DMF_100_16


title: WB_DMF_100_12


title: Microglia_LPS_1Hr_3

description:
DESeq2_normalized_counts.txt
N9


title: LN1_ThemisKO

source_name: sorted CD8 T cells from lymph nodes

value: lymphocytes


title: thymic epithelial tumor 15104N


title: LN2_ThemisKO


title: Microglia_LPS_1Hr_1

description:
DESeq2_normalized_counts.txt
N7


title: WB_DMF_100_11


title: WB_DMF_100_10


title: Microglia_LPS_30min_3

description:
DESeq2_normalized_counts.txt
N6


title: Microglia_PBS_Control_2

description:
DESeq2_normalized_counts.txt
N2


title: PC3-EV, biological rep3

city: NanJing

first: Zhengdong

last: Zhang

address: 101 Longmian Avenue

department: Department of Environmental Genomics, School of Public Health

country: China

institute: Nanjing Medical University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. 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 data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily

source_name: advanced human prostate cancer cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: cell line

tag: vector

value: empty

value: prostate

tag: tumor stage

value: bone metastases


title: PC3-[gamma]2, biological rep3

source_name: Restoration of PPAR[gamma]2 action in PC3 cells

value: overexpresion of human PPAR[gamma]2

tag: tissue


title: LN2_ThemisWT


title: ELa3-6_MUT: irf6-/- zebrafish embryos rep 3

city: Boston

first: Eric

middle: Chienwei

last: Liao

state: Massachusetts

address: 185 Cambridge st czpn 4265

department: Center for Regenerative Medicine

institute: Massachusetts General Hospital

data_processing:
Base-calling was performed through the Casava v1.8.2 package followed by bcl2fastq v2.18 tool for the generation of fast files.
Reads were trimmed to remove Illumina adapter sequences and low quality sequence with Trimmomatic (v. 0.36).
Gene expression counts were extracted using featureCounts from the subread package (v 2.0) using Ensembl v91 gene annotations.
Differentially Expressed Genes were defined using the DESeq2 package in R,
Annotations for gene identifier (Ensembl ID) and Entrez ID were added to the dataset
Top DEGs were identified and filtered by taking DEGs with adjusted p-value (Benjamini-Hochberg) < 0.05 and absolute log2 fold-change >2, clustering for heatmap generation was performed with the hclust function in R
Genome_build: danRer10
Reads were aligned to danRer10 using STAR (v 2.7.1a) with custom built index based on Ensembl v91 gene annotations.
Supplementary_files_format_and_content: Text file containing count data from RNA-seq reads aligned to danRer10. File has tab delimited values corresponding to Gene ID (Ensembl), Chromosome, Read Start and Read End coordinates, and counts in each sample
Supplementary_files_format_and_content: Csv file containing DESeq2 output values including log2 fold-change, p value and adjusted p value, and added annotations.
Supplementary_files_format_and_content: Csv file containing list of filtered genes with a gene ID for each gene, normalized count data for each sample, and clusterid corresponding to cluster index assigned by hierarchical clustering

organism: Danio rerio

source_name: Full embryos

growth_protocol: Embryos were grown in E3 medium containing methylene blue at 28oC for the according to standard zebrafish protocols.

extract_protocol:
Embryo pools of roughly 50 embryos were dropped into trizol, homogenized, and RNA was isolated through phenol-chloroform extraction and ethanol precipitation. RNA was quantified using a Nanodrop 2500 and assessed for quality using Bioanalyzer 2100 RNA chips (Agilent). Samples with RIN numbers above 9 were selected for further processing into libraries.
Libraries were constructed using the NEBNext Ultra RNA Library preparation kit (E7530S) with poly(A) mRNA magnetic isolation module according to manufacturer instructions

value: whole embryos

tag: developmental stage

value: Oblong to sphere (4.5hpf)

tag: strain

value: Tubingen


title: Microglia_LPS_30min_1

description:
DESeq2_normalized_counts.txt
N4

value: wild type

value: male


title: Microglia_LPS_30min_2

description:
DESeq2_normalized_counts.txt
N5

value: 10mg/kg LPS for 30 min


title: LN1_ThemisWT


title: ELa3-5_MUT: irf6-/- zebrafish embryos rep 2


title: Va32_Thy1_ThemisWT

source_name: sorted Va2.3 positive single positive  CD8 T thymocytes

value: Va3,2 TCRab+ CD8 T cells


title: Microglia_PBS_Control_1

description:
DESeq2_normalized_counts.txt
N1

value: PBS


title: PC3-[gamma]2, biological rep1


title: PC3-[gamma]2, biological rep2


title: Seedling, in vivo nuclear mRNA-NAI treatment

city: Norwich

first: Yiliang

last: Ding

address: Colney lane

country: United Kingdom

institute: John Innes Centre

description:
in_vivo_SHAPE_reactivity_across_polyA_site.txt
in_vivo_SHAPE_reactivity_for_splicing_analysis.txt

data_processing:
Library strategy: SHAPE-MaP
The quality of raw reads was assessed by using FastQC (Ver. 0.11.5) and the low-quality reads were filtered out. The adapter trimming was performed by using Cutadapt (Ver.1.14).
Arabidopsis genome reference sequences were obtained from TAIR10 database (https://www.arabidopsis.org/). The genome index was built by Hisat2-build with GTF file containing the annotation of additional alternative splicing isoforms from AtRTD2 database. Sequencing reads were aligned onto genome sequence by using Hisat2 (Ver.2.1.0) with “--no-softclip, --no-mix, --reorder, -k 10” option. After the reads mapping, only uniquely mapped reads were retained for the following analysis.
Reverse transcription stop (RT-stop) were counted followed by SHAPE reactivity calculation and normalization by using customized perl scripts following previously published study.
Genome_build: Tair 10
Supplementary_files_format_and_content: SHAPE reactivity values. Tab-delimited text files with the first collumn denoted the gene id and start and stop genomic coordinate of the target regions.

molecule: nuclear RNA

source_name: Arabidopsis seedling

growth_protocol: Arabidopsis thaliana (Col-0) seeds were sterilized with 70% (v/v) ethanol and plated on half-strength Murashige and Skoog medium (1/2 MS). The plates were wrapped in foil and stratified at 4℃ for 3 days and then grown in growth chamber at 22℃ for 5 days

extract_protocol:
Briefly, Arabidopsis seedlings were chopped in the nuclei isolation buffer to release nucleus. The nuclei containing solution was then filtered by nylon mesh filter and the nuclei pellet was collected by centrifugation. The supernatant was obtained as the cytosolic fraction. Nuclear RNAs and cytosolic RNAs were extracted separately from the pellet and the supernatant by using RNeasy Plant Mini Kit (Qiagen). The intactness of isolated nuclei was examined under fluorescent microscopy after DAPI (4',6-diamidino-2-phenylindole) staining.
The genomic DNA was removed after RNA extraction using Turbo DNase Kit (Ambion). Ribosomal RNA (rRNA) depletion was performed by using ribo-zero magnetic kit (Illumina). The rRNA depleted RNAs were purified and recovered by using RNA clean and concentrator (Zymo research) after RNA fragmentation.  3′ dephosphorylation was performed by using T4 PNK enzyme (NEB) at 37 °C for 30 min. Next, 3′ adaptor (5′-/5rApp/AGATCGGAAGAGCACACGTCTG/3SpC3/-3′) was ligated to the RNAs at 25 °C for 1h using T4 RNA ligase 2 (NEB). The RNAs was then subjected for the reverse transcription using SuperScript III (Thermo Fisher Scientific) with reverse primer (5′-CAGACGTGTGCTCTTCCGATCT-3′). The synthesized first-strand cDNAs were purified by 10% TBE-Urea Gel (Thermo Fisher Scientific) followed by gel purification. Next, the 5’ adaptor ligation was performed by ligating the adaptor (5′-5Phos/AGATCGGAAGAGCGTCGTGTAGCTCTTCCGATCTNNNNNN/3SpC3-3′) to the purified cDNA using Quick T4 DNA ligase (NEB) at 20 °C for overnight. The ligated cDNAs were then purified by 10% TBE-Urea Gel (Thermo Fisher Scientific). The PCR reaction was performed using forward primer (5′-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′) and reverse primer (e.g. index 2) (5′-CAAG CAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3′, Supplementary Table 2) with 2X HiFi readymix (KAPA) followed by the agarose gel purification.

treatment_protocol:
Arabidopsis seedlings were completely covered in 20 ml SHAPE reaction buffer (100 mM KCl, 40 mM HEPES (pH 7.5) and 0.5 mM MgCl2) in 50 ml Falcon tubes. The NAI (2-methylnicotinic acid imidazolide) treatment was performed with a final concentration of 100 mM as previously reported. The (-)SHAPE treatment was performed by adding the same amount of anhydrous DMSO. The reaction was performed at 22°C for 15 min. Freshly prepared DTT (dithiothreitol) was added to a final concentration of 0.5 M to quench the reaction. The seedlings were then used for nuclei isolation and RNA extraction.
NAI treatment was applied on the whole seedlings

tag: development stage

value: 5 days

value: NAI

value: seedling

tag: fraction

value: in vivo nuclear mRNA


title: ELa3-4_MUT: irf6-/- zebrafish embryos rep 1


title: ELa3-3_WT: WT zebrafish embryos rep 3

value: WT


title: Seedling, in vivo nuclear mRNA-control

treatment_protocol:
Arabidopsis seedlings were completely covered in 20 ml SHAPE reaction buffer (100 mM KCl, 40 mM HEPES (pH 7.5) and 0.5 mM MgCl2) in 50 ml Falcon tubes. The NAI (2-methylnicotinic acid imidazolide) treatment was performed with a final concentration of 100 mM as previously reported. The (-)SHAPE treatment was performed by adding the same amount of anhydrous DMSO. The reaction was performed at 22°C for 15 min. Freshly prepared DTT (dithiothreitol) was added to a final concentration of 0.5 M to quench the reaction. The seedlings were then used for nuclei isolation and RNA extraction.
Whole seedlings with no NAI treatment as control.

value: No SHAPE reagent treatment


title: Va32_Thy2_ThemisKO

value: single positive thymocytes


title: Microglia_PBS_Control_3

description:
DESeq2_normalized_counts.txt
N3


title: Seedling, deproteinized nuclear mRNA-control

description:
deproteinized_SHAPE_reactivity_across_polyA_site.txt
deproteinized_SHAPE_reactivity_for_splicing_analysis.txt

treatment_protocol:
Arabidopsis seedlings were completely covered in 20 ml SHAPE reaction buffer (100 mM KCl, 40 mM HEPES (pH 7.5) and 0.5 mM MgCl2) in 50 ml Falcon tubes. The NAI (2-methylnicotinic acid imidazolide) treatment was performed with a final concentration of 100 mM as previously reported. The (-)SHAPE treatment was performed by adding the same amount of anhydrous DMSO. The reaction was performed at 22°C for 15 min. Freshly prepared DTT (dithiothreitol) was added to a final concentration of 0.5 M to quench the reaction. The seedlings were then used for nuclei isolation and RNA extraction.
After nucleus isolation, nucleus lysis and protein removal, no NAI treatment was applied.

value: No SHAPE reagent treatment, deproteinized

value: deproteinized nuclear mRNA


title: Va32_Thy1_ThemisKO


title: ELa3-2_WT: WT zebrafish embryos rep 2

value: whole embryos


title: PC3-EV, biological rep2

value: empty

value: prostate

value: bone metastases


title: Va32_LN1_ThemisWT

source_name: sorted Va2.3 positive CD8 T cells from lymph nodes

value: lymphocytes


title: Va32_LN2_ThemisKO


title: Va32_Thy2_ThemisWT


title: PC3-EV, biological rep1

value: male


title: D3TDP2

status: Public on Dec 09 2020

city: Stanford

first: Julien

last: Couthouis

state: CA

address: 279 Campus Dr

department: Genetics

institute: Stanford University

description:
72h TDP-43 treated replicate2
D3CON_vs_D3TDP-ExpDiff.csv
D3GFP_vs_D3TDP-ExpDiff.csv

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

source_name: Primary cortical neurons

growth_protocol: Primary mouse cortical neurons were dissociated into single-cell suspensions from E16.5 mouse cortices with a papain dissociation system (Worthington Biochemical Corporation). Neurons were seeded onto poly-L-lysine–coated plates (0.1% (wt/vol)) and grown in Neurobasal medium (Gibco) supplemented with B-27 serum-free supplement (Gibco), GlutaMAX, and penicillin–streptomycin (Gibco) in a humidified incubator at 37 °C, with 5% CO2. Neurons were cultured for 3 days to let their processes grow before treatment.

extract_protocol:
RNA extraction and isolation in RLT buffer of the QIAGEN RNeasy Plus Micro Kit (QIAGEN), according to the manufacturer’s protocol. In brief, cells were lysed, homogenized, and loaded on a genomic DNA (gDNA) eliminator column. After removal of genomic DNA, RNA was purified using RNeasy spin columns.
polyA enriched mRNA libraries (SureSelect Automated Strand-Specific RNA Library Prep, mRNA Library Prep for Illumina Paired-End Multiplexed Sequencing)

treatment_protocol: We transduced the neurons with lentiviruses expressing either a 50-repeat poly(PR) protein, (PR)50, TDP-43, or GFP as a negative control. Both (PR)50 and TDP-43 caused marked cell death and axonal degeneration 72h after transduction. (PR)50 and TDP-43 expressing neurons formed numerous tubulin bIII puncta, indicating that microtubules disassembled, and the axons underwent degeneration

value: Primary cortical neurons

tag: time


title: D3CON1

description:
72h control untreated replicate1
D3CON_vs_D3GFP-ExpDiff.csv
D3CON_vs_D3PR-ExpDiff.csv
D3CON_vs_D3TDP-ExpDiff.csv

value: Control


title: D3TDP1

description:
72h TDP-43 treated replicate1
D3CON_vs_D3TDP-ExpDiff.csv
D3GFP_vs_D3TDP-ExpDiff.csv


title: D3PR2

description:
72h (PR)50 treated replicate2
D3CON_vs_D3PR-ExpDiff.csv
D3GFP_vs_D3PR-ExpDiff.csv


title: D2GFP1

description:
48h GFP treated replicate1
D2CON_vs_D2GFP-ExpDiff.csv
D2GFP_vs_D2PR-ExpDiff.csv
D2GFP_vs_D2TDP-ExpDiff.csv

value: GFP


title: D2TDP2

description:
48h TDP-43 treated replicate2
D2CON_vs_D2TDP-ExpDiff.csv
D2GFP_vs_D2TDP-ExpDiff.csv


title: D3GFP2

description:
72h GFP treated replicate2
D3CON_vs_D3GFP-ExpDiff.csv
D3GFP_vs_D3PR-ExpDiff.csv
D3GFP_vs_D3TDP-ExpDiff.csv


title: D3GFP1

description:
72h GFP treated replicate1
D3CON_vs_D3GFP-ExpDiff.csv
D3GFP_vs_D3PR-ExpDiff.csv
D3GFP_vs_D3TDP-ExpDiff.csv


title: D2PR1

description:
48h (PR)50 treated replicate1
D2CON_vs_D2PR-ExpDiff.csv
D2GFP_vs_D2PR-ExpDiff.csv


title: D2GFP2

description:
48h GFP treated replicate2
D2CON_vs_D2GFP-ExpDiff.csv
D2GFP_vs_D2PR-ExpDiff.csv
D2GFP_vs_D2TDP-ExpDiff.csv


title: Va32_LN1_ThemisKO

value: Va3,2 TCRab+ CD8 T cells


title: D3PR1

description:
72h (PR)50 treated replicate1
D3CON_vs_D3PR-ExpDiff.csv
D3GFP_vs_D3PR-ExpDiff.csv


title: Va32_LN2_ThemisWT


title: D2TDP1

description:
48h TDP-43 treated replicate1
D2CON_vs_D2TDP-ExpDiff.csv
D2GFP_vs_D2TDP-ExpDiff.csv


title: D2PR2

description:
48h (PR)50 treated replicate2
D2CON_vs_D2PR-ExpDiff.csv
D2GFP_vs_D2PR-ExpDiff.csv


title: Seedling, deproteinized nuclear mRNA-NAI treatment

treatment_protocol:
Arabidopsis seedlings were completely covered in 20 ml SHAPE reaction buffer (100 mM KCl, 40 mM HEPES (pH 7.5) and 0.5 mM MgCl2) in 50 ml Falcon tubes. The NAI (2-methylnicotinic acid imidazolide) treatment was performed with a final concentration of 100 mM as previously reported. The (-)SHAPE treatment was performed by adding the same amount of anhydrous DMSO. The reaction was performed at 22°C for 15 min. Freshly prepared DTT (dithiothreitol) was added to a final concentration of 0.5 M to quench the reaction. The seedlings were then used for nuclei isolation and RNA extraction.
NAI treatment was applied after nucleus isolation, nucleus lysis and protein removal

value: 5 days

value: NAI, deproteinized

value: seedling


title: D2CON1

description:
48h control untreated replicate1
D2CON_vs_D2GFP-ExpDiff.csv
D2CON_vs_D2PR-ExpDiff.csv
D2CON_vs_D2TDP-ExpDiff.csv


title: D2CON2

description:
48h control untreated replicate2
D2CON_vs_D2GFP-ExpDiff.csv
D2CON_vs_D2PR-ExpDiff.csv
D2CON_vs_D2TDP-ExpDiff.csv


title: D1TDP2

description:
24h TDP-43 treated replicate2
D1CON_vs_D1TDP-ExpDiff.csv
D1GFP_vs_D1TDP-ExpDiff.csv


title: ELa3-1_WT: WT zebrafish embryos rep 1

value: Oblong to sphere (4.5hpf)

value: Tubingen

value: WT


title: D1TDP1

description:
24h TDP-43 treated replicate1
D1CON_vs_D1TDP-ExpDiff.csv
D1GFP_vs_D1TDP-ExpDiff.csv


title: D1GFP2

description:
24h GFP treated replicate2
D1CON_vs_D1GFP-ExpDiff.csv
D1GFP_vs_D1PR-ExpDiff.csv
D1GFP_vs_D1TDP-ExpDiff.csv


title: D1PR2

description:
24h (PR)50 treated replicate2
D1CON_vs_D1PR-ExpDiff.csv
D1GFP_vs_D1PR-ExpDiff.csv


title: D1PR1

description:
24h (PR)50 treated replicate1
D1CON_vs_D1PR-ExpDiff.csv
D1GFP_vs_D1PR-ExpDiff.csv


title: D3CON2

description:
72h control untreated replicate2
D3CON_vs_D3GFP-ExpDiff.csv
D3CON_vs_D3PR-ExpDiff.csv
D3CON_vs_D3TDP-ExpDiff.csv


title: D1CON1

description:
24h control untreated replicate1
D1CON_vs_D1GFP-ExpDiff.csv
D1CON_vs_D1PR-ExpDiff.csv
D1CON_vs_D1TDP-ExpDiff.csv


title: D1GFP1

description:
24h GFP treated replicate1
D1CON_vs_D1GFP-ExpDiff.csv
D1GFP_vs_D1PR-ExpDiff.csv
D1GFP_vs_D1TDP-ExpDiff.csv


title: D1CON2

description:
24h control untreated replicate2
D1CON_vs_D1GFP-ExpDiff.csv
D1CON_vs_D1PR-ExpDiff.csv
D1CON_vs_D1TDP-ExpDiff.csv


title: RNA-seq_BMDM KO LPS rep1

city: Chicago

first: Jie

last: Du

address: 900 E. 57th Street

institute: University of Chicago

description:
Sample 10
Yli-Du-12s-NT-10_S10

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 mm10 whole genome using STAR v2.6.1d.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: bone marrow-derived macrophage

growth_protocol: Bone marrows were isolated from C57BL/6 mice and then cultured in RPMI1640 medium with 30% L929 condition medium

extract_protocol:
BMDMs were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. SMARTer Stranded RNA-seq Kit (Cat#634836) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMDMs were treated by LPS or PBS for 6 hours

value: bone marrow

tag: age

value: post natal week 6

value: Mettl14 f/f; LysM-cre

value: bone marrow-derived macrophage

value: LPS


title: RNA-seq_BMDM KO LPS rep3

description:
Sample 12
Yli-Du-12s-NT-12_S12


title: RNA-seq_BMDM f/f LPS rep3

description:
Sample 9
Yli-Du-12s-NT-9_S9

value: Mettl14 f/f


title: RNA-seq_BMDM KO LPS rep2

description:
Sample 11
Yli-Du-12s-NT-11_S11


title: RNA-seq_BMDM f/f LPS rep1

description:
Sample 7
Yli-Du-12s-NT-7_S7


title: RNA-seq_BMDM KO PBS rep1

description:
Sample 4
Yli-Du-12s-NT-4_S4

value: PBS


title: RNA-seq_BMDM f/f PBS rep3

description:
Sample 3
Yli-Du-12s-NT-3_S3


title: RNA-seq_BMDM f/f PBS rep1

description:
Sample 1
Yli-Du-12s-NT-1_S1


title: RNA-seq_BMDM KO PBS rep3

description:
Sample 6
Yli-Du-12s-NT-6_S6


title: RNA-seq_BMDM KO PBS rep2

description:
Sample 5
Yli-Du-12s-NT-5_S5


title: RNA-seq_BMDM f/f PBS rep2

description:
Sample 2
Yli-Du-12s-NT-2_S2


title: BMDM f/f PBS  input

data_processing:
Sequencing raw data were preprocessed by trim_galore v0.6.5 and then mapped against mm10 reference genome by HISAT2 v2.1.0.
Peak calling was carried out using R package exomePeak.
Downstream analysis and visualization of data were accomplished using R v3.6.
Motif search was performed using HOMER v4.10.0.
The longest isoform was retained if a gene has more than one isoforms.
Genome_build: mm10
Supplementary_files_format_and_content: peak file

extract_protocol:
BMDMs were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. SMARTer Stranded RNA-seq Kit v2- Pico Input  Mammalian (Cat#634411) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: rip antibody

value: none (input)


title: BMDM KO LPS input

tag: genotype


title: BMDM f/f LPS input


title: BMDM KO PBS m6A rep1

value: anti-m6A (Synaptic Systems; Cat#:202003; RRID:AB_2279214)


title: BMDM f/f LPS m6A rep2


title: BMDM KO LPS m6A rep3


title: BMDM f/f PBS m6A rep3


title: BMDM KO LPS m6A rep2


title: BMDM f/f PBS m6A rep2


title: BMDM KO PBS m6A rep3


title: H3_RNA

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
QC was performed using FASTQC software (Andrews, 2010)
Reads were trimmed and aligned using the HISAT2 (Kim, 2015) program and count matrices were generated using the featureCounts function of the Subreads program (Shi W., 2013)
Differential expression was analyzed using the DESeq2 (Love MI, 2014) package and the following cutoffs were used for determining differentially regulated genes: |log2foldchange| > 0.38, p-value < 0.05.
Peaks for ChIP-seq data were called using MACS (Zhang Y, 2008)
Genome_build: mm10
Supplementary_files_format_and_content: Counts in tab delimited text file, peaks from MACS in tab delimited text file

source_name: nucleus accumbens

extract_protocol:
Chromatin was isolated as described previously (Cates et al., 2018) from frozen tissue, after fixation in 1% formaldehyde and quenching in 2M glycine. Fixed tissue punches were mechanically processed by being passed through a 22-guage needle 10 times. Cells were lysed for 15 minutes (5 mM PIPES pH 8, 85 mM KCl, 0.5% NP40, protease inhibitors), followed by a 10 minute nuclear lysis (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS, protease inhibitors).  Chromatin was sheared using a sonicator (Bioruptor, Diagenode) with 25 cyles of 30 seconds on/off. Sheared chromatin was centrigured at high speed and resuspended in RIPA buffer. Magnetic M-280 Dynabeads Sheep anti-Rabbit IgG (Thermofisher, cat #11202D) were conjugated to H3K79me2 antibody (Abcam, cat #ab3594) by rotation at 4C for 6 hours. Conjugated beads and chromatin were incubated together with rotation at 4C overnight. H3K79me2-associated DNA was washed in order with a low salt buffer (0.1% SDS, 1% Triton x100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl pH 8), a high salt buffer (0.1% SDS, 1% Triton x100, 2 mM EDTA, 500 mM NaCl, 20 mM Tris-HCl pH 8), a LiCl buffer (150 mM LiCl, 1% NP40, 1% NaDOC, 1 mM EDTA, 10 mM Tris-HCl pH 8), and TE + 50 mM NaCl. DNA was eluted in ChIP elution buffer (1% SDS, 100 mM NaHCO3) and de-crosslinked overnight at 65 degrees C. RNA from whole tissue was prepared using the RNeasy Mini Kit (Qiagen, cat #74104) and converted to cDNA using the iScript cDNA Synthesis Kit (Bio Rad, cat #1708890)
Sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit (NEB, cat #E7645) and sheared to an average size of 300-400 bp. Libraries were submitted to sequencing with Genewiz on an Illumina HISeq 4000 machine with a 2x150 bp paired-end read configuration to a minimum depth of 30M reads.

tag: Sex

value: Male

tag: condition

value: ELS

tag: pulldown

value: Dot1l knockdown

value: nucleus accumbens


title: BMDM KO LPS m6A rep1

tag: cell type


title: BMDM KO PBS input

tag: treatment


title: BMDM KO PBS m6A rep2


title: BMDM f/f LPS m6A rep1


title: BMDM f/f LPS m6A rep3


title: G4_RNA

value: Standard

value: Dot1l overexpression


title: F4_RNA

value: GFP


title: G3_RNA


title: H1_RNA


title: BMDM f/f PBS  m6A rep1


title: E4_RNA


title: E1_RNA


title: D4_RNA


title: G2_RNA


title: H2_RNA


title: E2_RNA


title: G1_RNA


title: H4_RNA


title: F3_RNA


title: F2_RNA


title: D3_RNA


title: E3_RNA


title: F1_RNA


title: RNA-seq_BMDM f/f LPS rep2

description:
Sample 8
Yli-Du-12s-NT-8_S8


title: C3_RNA


title: D2_RNA


title: A3_RNA


title: D1_RNA


title: A2_RNA


title: H7: ms22_input

value: input


title: H3: ms2_input


title: D2: me10_input


title: D10: me20_input


title: C4_RNA


title: C9: ME3


title: D1: ME19


title: C1_RNA


title: B3_RNA


title: B4_RNA


title: C2_RNA


title: B2_RNA


title: B1_RNA


title: H5: ms18_input


title: A4_RNA


title: A1_RNA


title: D9: ME20


title: H9: ms6_input


title: C1: ME8


title: C10: me19_input


title: D7: ME22


title: C7: ME12


title: B3: ME9


title: C5: ME14


title: B4: me8_input


title: C4: me18_input


title: B9: MS21


title: C2: ms21_input


title: B10: me12_input


title: A9: MS6


title: A8: me9_input


title: B6: me22_input


title: B8: me14_input


title: B5: MS25


title: B7: MS22


title: A4: ms25_input


title: A10: ms17_input


title: A7: MS8


title: A1: MS2


title: B2: ms20_input


title: B1: MS20


title: C3: ME18


title: A2: ms8_input


title: SK_VD18_REP1

first: Sonia

last: Kupfer

state: IL

address: 900 East 57th Street, MB#9

department: Department of Medicine

data_processing:
ATAC-seq fastq reads aligned with bwa mem (v 0.7.17)
ATAC-seq read filtering performed with samtools (v 1.10)
ATAC-seq peak calling performed with MACS2 (v 2.1.0)
ATAC-seq differential peak calling performed with R packages DiffBind and edgeR
ATAC-seq motif enrichment and peak annotation performed with HOMER (v 4.11.1)
RNA-seq equence alignment and gene expression value estimation was performed using RSEM (v.1.3.1) using the STAR aligner in paired-end mode.
RNA-seq differential expression analysis was performed with the R package DESeq2
Genome_build: ATAC-seq and RNA-seq reads were aligned to reference sequence hs37d5
Supplementary_files_format_and_content: peak files are MACS2 outputted narrowPeak files for treated and untreated ATAC-seq samples at the two timepoints

source_name: colonic organoid

growth_protocol: Organoids were derived using a protocol adapted from Sato et al 2011

extract_protocol:
RNA-seq: mRNA was isolated from cells using the RNeasy® Plus Mini Kit (Qiagen) according to the manufacturer’s protocol. ATAC-seq: cells were  treated using the Omni-ATAC protocol with some modifications. Briefly, the cells were treated with lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and then suspended in the transposition reaction mix (50% TD Tagment DNA buffer, 5% TDE1 Tagment DNA Enzyme,33% PBS) for 30 minutes.
RNA-seq libraries were prepared using Illumina mRNA TruSeq kits as protocolled by Illumina. ATAC-seq ibraries were prepared using the Nextera Index kit (Illumina #15055289).

treatment_protocol: After 24 hours of culturing in the basal media, organoids were treated with either 100nM 1α,25(OH)2D3 or vehicle control (ethanol) for 4 and 18 hours (for ATAC-seq), or 6 or 24 hours (for RNA-seq).

value: organoid

value: rectosigmoid mucosa

value: vitamin D 18 hrs


title: SK_ETH4_REP1

value: ethanol control 4 hrs


title: SK_VD4_REP2

value: vitamin D 4 hrs


title: SK_ETH4_REP3


title: SK_VD4_REP1


title: SK_VD4_REP3


title: A6: me3_input


title: SK_ETH18_REP3

value: ethanol control 18 hrs


title: A3: MS18


title: SK_ETH18_REP1


title: SK_VD18_REP3


title: A5: MS17


title: Laser microdissection REF9

city: Indianapolis

first: Michael

middle: T

last: Eadon

state: IN

address: 950 W Walnut St

institute: Indiana University

data_processing:
For Illumina Sequencing data, FastQC for sequencing quality check
Adapter sequences (smart CDS) were removed
Reads were aligned to the human referece genome Hg38 using STAR-2.4.2b with parameters ajusted to short reads and Integrative Genomics Viewer (IGV) alignment.
Expression counts determined by subreads 1.5
Genes removed from analysis with 0 read counts across all specimens, total genes included 25,550.
Quantile normalization
Genome_build: Hg38
Supplementary_files_format_and_content: csv

source_name: Kidney

extract_protocol:
Kidney tissue was obtained from one of two sources. The first is a clinical kidney biopsy, placed in Michels solution and frozen on OCT within 24 h. The second is either a deceased donot nephrectomy or unaffected portion of a tumor nephrectomy. Approximately 1 million square microns of cross-sectional glomerular biopsy tissue was cut on a cryotome and placed in Arcturus Picopure extraction buffer. RNA was extracted according to the Arcturus protocol.
SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input
RNA sequencing on an Illumina HiSeq 4000, 100 millions input reads per sample

tag: disease

value: Reference

tag: tissue type

value: Nephrectomy

tag: storage

value: OCT at -80C


title: Laser microdissection ING2

value: Idiopathic Nodular Glomerulosclerosis

value: Biopsy


title: Laser microdissection ING3


title: Laser microdissection ING5


title: Laser microdissection ING1


title: Laser microdissection ING4


title: Laser microdissection REF6


title: Laser microdissection REF8


title: Laser microdissection REF7


title: Laser microdissection REF5


title: Laser microdissection REF4


title: Laser microdissection DIA18

value: Diabetic Nephropathy


title: Laser microdissection DIA16


title: Laser microdissection DIA12


title: Laser microdissection DIA17


title: Laser microdissection DIA8


title: Laser microdissection DIA9


title: Laser microdissection REF3


title: SK_ETH4_REP2

tag: tissue


title: Laser microdissection DIA6


title: Laser microdissection DIA2


title: Laser microdissection DIA3


title: Laser microdissection REF2


title: Laser microdissection REF1


title: SK_VD18_REP2


title: HCT116_MTAP_Wt AGI24512_2

city: Cambridge

first: Katya

last: Marjon

address: 88 Sidney Street

institute: Agios

data_processing:
Mapping and transcripts counting was done with Omicsoft (ArrayStudio, Qiagen)
DEXseq package was downloaded from Bioconductor
https://bioconductor.org/packages/release/bioc/html/DEXSeq.html
In house processing using R and Python
Scripts uploaded (DEXseq.R dexseq_count.py)
Genome_build: Omicsoft.Human.B36.3
Supplementary_files_format_and_content: Excel sheet

source_name: Horizon Discovery

growth_protocol: According to ATCC suggestion

extract_protocol:
poly-A enriched RNA extraction
Hiseq4000 (100PE) library construction protocol

treatment_protocol: Dosing as annotated in the figure legends

value: engineered colon cancer cell line

tag: cell line

value: WT


title: HCT116_MTAP_Wt DMSO_2

value: DMSO


title: HCT116_MTAP_Wt AGI24512_3


title: HCT116_MTAP_Wt DMSO_3


title: SK_ETH18_REP2


title: Laser microdissection DIA15


title: Laser microdissection DIA14


title: Laser microdissection DIA4


title: HCT116_MTAP_Null AGI24512_3

value: MTAP null


title: Laser microdissection DIA11


title: Laser microdissection DIA13


title: Laser microdissection DIA5


title: Laser microdissection DIA10


title: HCT116_MTAP_Null AGI24512_1


title: HLY-shATM 1

city: Baltimore

first: Heather

middle: Huot

last: Creasy

state: Maryland

address: 801 West Baltimore St

institute: Institute for Genome Sciences

data_processing:
Raw data were analyzed using the HISAT2 aligner with stand-specific settings  and Homo sapiens genomic reference sequence (Ensembl version GRCh38.96).
Differential gene expression was analyzed using the DESeq R package (Bioconductor) and the negative binomial model
Criteria for significant differences in gene expression were (1) false discovery rate (FDR) <0.05, (2) expression level >10th percentile, and (3) ≥ 2-fold change.
Genome_build: Homo sapiens (GRCh38)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: DLBCL cell line HLY

growth_protocol: DLBCL cell lines was grown in RPMI media with 10%FBS and P/S antibiotic

extract_protocol:
Polysomal rna was extracted using sucrose gradients columns
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells were clutured under regular culture conditions

value: DLBCL cell line HLY

tag: passages

tag: genotype/variation

value: expressing shATM lentivirus

tag: molecule

value: Polysomal RNA


title: HLY-shATM 2


title: HLY-shATM 3


title: HCT116_MTAP_Wt AGI24512_1


title: Laser microdissection DIA7


title: HCT116_MTAP_Null DMSO_3


title: HCT116_MTAP_Null DMSO_2


title: HCT116_MTAP_Null DMSO_1


title: HCT116_MTAP_Null AGI24512_2


title: Laser microdissection DIA1


title: HLY-NT 2

value: wild type ATM


title: HLY-NT 3


title: HLY-NT 1


title: HCT116_MTAP_Wt DMSO_1


title: whole_lung_control_rep7 [Tx_Batch2_S4]

city: Ann Arbor

first: Vibha

middle: N.

last: Lama

state: Michigan

address: 1150 W. Medical Center Drive

department: Internal Medicine

institute: University of Michigan

hyb_protocol: Following labeling procedure, 2.53 ug of cDNA were hybridized at 48C on a Mouse Gene 2.1 ST 16-Array Plate, and were washed and stained using the Affymetrix GeneTitan system [software version: 4.3.0.1592 (RAS) and 3.2.4.1515 (BOS)].

scan_protocol: Peg Arrays were scanned using the Affymetrix GeneTitan system [software version: 4.3.0.1592 (Batch 2) and 3.2.4.1515 (Batch 1)].

data_processing: The datasets were normalized using a robust multi-array average for each gene and analyzed using the oligo and limma packages of bioconductor implemented in the R statistical environment (ver.3.4.0). A weighted linear model designed for microarray analysis was fit to the data to compute differential expression statistics between allograft and isograft data for each time point for the RAS and BOS transplant models, with year of data collection included in the model to account for batch effects.

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

growth_protocol: Mice aged between 8 to 12 weeks, and weighing 24 to 30 g.

extract_protocol: Lung explants were homogenized in sterile phosphate buffered saline, and then total RNA was extracted using the Qiagen RNA isolation kit, followed by removal of DNA contamination. RNA quantitation, quality and integrity was determined using the nanospectrophotometer.

treatment_protocol: Batch 1 (B6D2F1/J into DBA/2J); Batch 2 (B6D2F1/J into C57BL6/J )

tag: donor strain

value: B6D2F1/J (H2-b/d) F1 lungs

tag: treatment/time point

value: whole lung homogenate


title: whole_lung_control_rep4 [Tx_Batch2_S1]


title: whole_lung_day40_rep2 [Tx_Batch2_S14]


title: whole_lung_control_rep5 [Tx_Batch2_S2]


title: whole_lung_day40_rep4 [Tx_Batch2_S16]


title: whole_lung_day40_rep3 [Tx_Batch2_S15]


title: whole_lung_day28_rep4 [Tx_Batch2_S12]


title: whole_lung_day40_rep3 [Tx_Batch1_S12]


title: whole_lung_day28_rep1 [Tx_Batch2_S9]


title: whole_lung_day28_rep3 [Tx_Batch2_S11]


title: whole_lung_day28_rep2 [Tx_Batch2_S10]


title: whole_lung_day14_rep2 [Tx_Batch1_S5]


title: whole_lung_day40_rep4 [Tx_Batch1_S13]


title: whole_lung_day40_rep1 [Tx_Batch1_S10]


title: whole_lung_control_rep2 [Tx_Batch1_S2]


title: whole_lung_day40_rep2 [Tx_Batch1_S11]


title: whole_lung_day14_rep4 [Tx_Batch2_S8]


title: whole_lung_control_rep1 [Tx_Batch1_S1]


title: whole_lung_day40_rep1 [Tx_Batch2_S13]


title: whole_lung_day28_rep2 [Tx_Batch1_S8]


title: whole_lung_day14_rep3 [Tx_Batch2_S7]


title: whole_lung_day14_rep2 [Tx_Batch2_S6]


title: whole_lung_day14_rep1 [Tx_Batch2_S5]


title: whole_lung_control_rep6 [Tx_Batch2_S3]


title: whole_lung_day28_rep3 [Tx_Batch1_S9]


title: HEK-293 transfected cells (pEGFP_rRIZ1) 2

city: Caserta

first: Monica

last: Rienzo

address: Viale  Lincoln

department: Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies

institute: University of Campania “Luigi Vanvitelli”

description: Biological replicate 2 of 3 HEK-293 cells overexpressing rat RIZ1

hyb_protocol: The hybridized microarrays were then washed according to manufacturer’s instructions, scanned after washing using an Agilent Microarray Scanner (G4845A) at 2μm resolution and 20-bit color-depth

scan_protocol: Images were quantified using Agilent Feature Extraction Software (10.5 Protocol GE2_105_Dec08).

data_processing: Raw data files (unedited)

source_name: HEK-293 transfected cells

label_protocol: Samples were processed according to Agilent Two-color Microarray Based Gene Expression Analysis (Low Input Quick Amp Labeling Kit protocol) by Agilent Spike-In Kit, according to the manufacturer’s instructions. The Agilent Two-Color Microarray-based Gene Expression Analysis uses Cyanine 3- and Cyanine 5-labeled targets to measure gene expression in experimental and control samples. Equal amounts of Cyanine 3-labeled (control samples) and Cyanine 5-labeled (experimental samples) cRNA from samples were simultaneously co-hybridized onto the arrayed oligonucleotides on the same Agilent 44k Whole Human Genome chip (Agilent Technologies, 4X44k format) slide at 65°C for 17 h using an Agilent Gene Expression Hybridization Kit in Agilent’s SureHyb Hybridization Chambers (G2545A)

growth_protocol: HEK-293 were maintained at 37 °C with 5% CO2 in humidified atmosphere in DMEM high glucose supplemented with 10% FCS, 1% Non-Essential Amino Acid (NEAA), and antibiotics (100 U/mL penicillin, 100 mg/mL streptomycin).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Cells were transfected with  plasmid DNAs using LipofectamineTM 2000 Reagent in OptiMem I Reduced Serum Medium (Life Technologies, Carlsbad, CA, USA) for 6h, following the manufacturer’s instructions.

tag: transfection

value: embryonic kidney

tag: age

value: Fetus


title: HEK-293 transfected cells (pEGFP_rRIZ1+hRIZ2) 3

description: Biological replicate 3 of 3 HEK-293 cells co-overexpressing rat RIZ1and human RIZ2


title: HEK-293 transfected cells (pEGFP_rRIZ1) 1

description: Biological replicate 1 of 3 HEK-293 cells overexpressing rat RIZ1


title: HEK-293 transfected cells (pEGFP_hRIZ2) 3

description: Biological replicate 3 of 3 HEK-293 cells overexpressing human RIZ2


title: HEK-293 transfected cells (pEGFP_rRIZ1) 3

description: Biological replicate 3 of 3 HEK-293 cells overexpressing rat RIZ1


title: HEK-293 transfected cells (pEGFP_rRIZ1+hRIZ2) 2

description: Biological replicate 2 of 3 HEK-293 cells co-overexpressing rat RIZ1and human RIZ2


title: HEK-293 transfected cells (pEGFP_rRIZ1+hRIZ2) 1

description: Biological replicate 1 of 3 HEK-293 cells co-overexpressing rat RIZ1and human RIZ2


title: HEK-293 transfected cells (pEGFP_hRIZ2) 1

description: Biological replicate 1 of 3HEK-293 cells overexpressing human RIZ2


title: whole_lung_day28_rep1 [Tx_Batch1_S7]


title: whole_lung_day14_rep3 [Tx_Batch1_S6]


title: Control (HEK-293 pEGFP_empty) 2

description: Biological replicate 2 of 3. Control  cells


title: whole_lung_control_rep3 [Tx_Batch1_S3]


title: Control (HEK-293 pEGFP_empty) 1

description: Biological replicate 1 of 3. Control  cells


title: whole_lung_day14_rep1 [Tx_Batch1_S4]


title: Control (HEK-293 pEGFP_empty) 3

description: Biological replicate 3 of 3. Control  cells


title: 252644011436: IFN Treated pig # 10_dpi-1_PBMC

city: toronto

first: Chandrika

last: Senthilkumaran

state: ON

address: 8, Wisteria RD

country: Canada

institute: Canadian food inspection agency

description: Gene expression in PBMC samples  before pre-treatment of IFN in pigs

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Porcine V2 arrays (G2519F-026440) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Microarray slides were scanned on Agilent high resolution C scanner (G2505C) and images processed using the Agilent Feature Extraction software. Quality of samples was analyzed using the ArrayQualityMetrics package and the data imported into GeneSpring 14.8 (Agilent) for further analysis.

data_processing: The data was normalized using a shift to the 75th percentile; thereafter the value was further transformed as log2

organism: Sus scrofa

source_name: PBMC samples before pre-treatment of IFN and (24 hrs) before innoculation of Ebola Kikwit from pig 10

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification.  Dye incorporation and cRNA yield were checked with the NanoDrop.

extract_protocol: Total RNA was extracted from PBMC and BALP pellets and the concentrations were determined using a NanoDrop (NanoDrop Technologies) and shipped to MOGENE LC, St. Louis, MO, USA for the microarray assay.

treatment_protocol: 7 pigs were randomly divided in 2 groups: A (4 pigs) and B (3 pigs). Animals in Group A (# 7, 8, 9, 10) were inoculated subcutaneously (SC) in the neck with 2x1010 pfu/2ml of Ad5-porIFNα. Animals in Group B (Control group #11, 17, 18) were SC inoculated with 2 ml of phosphate-buffered saline (PBS). One day later all pigs were oro-nasally inoculated with 106 pfu/2ml/pig of EBOV (0.5 ml per each nostril, 1ml orally). Arbitrarily, the day of inoculation (dpi) with EBOV was designated as 0 dpi. Clinical signs, behavioral changes and rectal temperature were recorded daily. Nasal washes, oral swabs and blood were collected for each pig the day of Ad5-porIFNα or PBS treatment (-1 dpi), and at 0, 3 and 5 or 6 dpi with EBOV. Blood was collected into BD vacutainer CPTTM cell preparation tubes (Becton Dickinson, New Jersey, USA), plasma and the peripheral blood mononuclear cells (PBMC) were separated according to the manufacturer’s protocol. PBMC pellets diluted four times with PBS

value: PBMC

tag: gender

value: Female

value: 6 weeks


title: 252644011438: IFN Treated pig # 10_dpi 6_BAP

description: Gene expression in Broncho alvelor pellet samples  6  days after innoculation of Ebola Kikwit in pig  pre-treated with IFN

source_name: Broncho alvelor pellet samples from 6  days after innoculation of Ebola Kikwit from pig 10

value: Broncho alvelor pellet


title: 252644011435: IFN Treated pig # 8_dpi 5_BAP

description: Gene expression in Broncho alvelor pellet samples  5  days after innoculation of Ebola Kikwit from pig pre-treated with IFN

source_name: Broncho alvelor pellet samples from 5  days after innoculation of Ebola Kikwit from pig 8


title: 252644011438: IFN Treated pig # 8_dpi 5_BAP

description: Gene expression in Broncho alvelor pellet samples  5  days after innoculation of Ebola Kikwit in pig  pre-treated with IFN


title: 252644011437: IFN Treated pig # 10_dpi 6_BAP


title: 252644011437: IFN Treated pig # 9_dpi3_PBMC

description: Gene expression in PBMC samples  3  days after innoculation of Ebola Kikwit in pig pre-treated with IFN

source_name: PBMC samples from 3  days after innoculation of Ebola Kikwit from pig 9

value: Male


title: 252644011438: control pig # 11_dpi 5_BAP

description: Gene expression in Broncho alvelor pellet samples  5  days after innoculation of Ebola Kikwit in pig not pre-treated with IFN

source_name: Broncho alvelor pellet samples from 5  days after innoculation of Ebola Kikwit from pig 11


title: 252644011437: IFN Treated pig # 7_dpi 5_BAP

source_name: Broncho alvelor pellet samples from 5  days after innoculation of Ebola Kikwit from pig 7


title: 252644011438: IFN Treated pig # 7_dpi 5_BAP