title: GC4_DZ_D05.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_D05


title: GC4_DZ_D02.DecP.30_H.DZ

status: Public on Dec 10 2020

type: SRA

city: New York

first: Gabriel

last: Victora

state: NY

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_D02

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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: ILN_6_DMF179_2_70

type: RNA

city: Cambridge

first: Suzanne

last: Szak

state: MA

address: 14 Cambridge Ctr

department: Drug Discovery

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

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_6_DMF179_2_68


title: ILN_6_DMF179_2_69


title: ILN_6_DMF179_2_67


title: RAL-642_gut_T=16h0m_Rep1

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_gut_norm.csv.gz
BRB6_Gut_n_28216

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 gut

tag: time of harvesting

tag: replicate

tag: library

tag: bloomington

tag: time series type

value: Single observation


title: ILN_6_DMF100_MEF79_2_90


title: RAL-595_gut_T=15h50m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28215


title: GC4_DZ_D01.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_D01


title: RAL-589_gut_T=15h40m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28213


title: ILN_6_DMF100_MEF79_2_89


title: ILN_6_DMF100_MEF79_2_87


title: ILN_6_DMF100_MEF79_2_88


title: ILN_6_DMF100_MEF79_2_86


title: GC4_DZ_C06.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_C06


title: ILN_6_DMF100_MEF79_2_83


title: ILN_6_DMF100_MEF79_2_84


title: GC4_DZ_C05.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_C05


title: ILN_6_DMF100_66


title: ILN_6_VEH_58


title: RAL-535_gut_T=15h12m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_28208


title: GC4_DZ_C03.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_C03


title: GC4_DZ_C02.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_C02


title: GC4_DZ_C04.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_C04


title: RAL-563_gut_T=15h21m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28211


title: RAL-584_gut_T=15h31m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_28212


title: ILN_6_DMF100_62


title: ILN_6_DMF100_61


title: ILN_6_DMF100_63


title: ILN_6_DMF100_60


title: GC4_DZ_B06.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_B06


title: ILN_6_DMF100_65


title: ILN_6_DMF100_64


title: Brain_12_VEH_8

value: Brain


title: ILN_6_DMF100_59


title: Brain_12_VEH_6


title: Brain_12_VEH_7


title: RAL-441_gut_T=14h4m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28198


title: GC4_DZ_B05.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_B05


title: RAL-502_gut_T=14h43m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28204


title: GC4_DZ_C01.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_C01


title: Brain_12_VEH_3


title: RAL-509_gut_T=15h2m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28206


title: GC4_DZ_B04.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_B04


title: RAL-796_gut_T=17h55m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28233


title: RAL-461_gut_T=14h24m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28200


title: Brain_12_VEH_2


title: RAL-440_gut_T=13h55m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_28197


title: GC4_DZ_B02.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_B02


title: GC4_DZ_B03.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_B03


title: RAL-426_gut_T=13h45m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28196


title: GC4_DZ_F02.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_F02


title: RAL-381_gut_T=12h57m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28188


title: Brain_12_VEH_4


title: Brain_12_NAIVE_43


title: RAL-373_gut_T=12h28m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28184


title: Brain_12_NAIVE_47


title: Brain_12_NAIVE_44


title: GC4_DZ_A06.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_A06


title: Brain_12_NAIVE_46


title: Brain_12_VEH_5


title: Brain_12_NAIVE_45


title: Brain_12_VEH_1


title: Brain_12_NAIVE_48


title: RAL-370_gut_T=12h9m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_28182


title: GC4_DZ_B01.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_B01


title: RAL-382_gut_T=13h7m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28189


title: GC4_DZ_A05.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_A05


title: RAL-386_gut_T=13h36m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28192


title: GC4_DZ_A04.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_A04


title: RAL-361_gut_T=12h0m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28180


title: Brain_12_MEF79_2_30


title: Brain_12_MEF79_2_32


title: Brain_12_NAIVE_41


title: Brain_12_NAIVE_42


title: Brain_12_MEF79_2_28


title: Brain_12_MEF79_2_29


title: Brain_12_MEF79_2_27


title: Brain_12_MEF79_2_25


title: GC4_DZ_A02.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_A02


title: RAL-352_gut_T=11h31m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28177


title: GC4_DZ_A03.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_A03


title: Brain_12_MEF79_2_31


title: GC3_DP_H08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_H08


title: RAL-359_gut_T=11h50m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28179


title: RAL-338_gut_T=11h2m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28173


title: RAL-340_gut_T=11h12m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28174


title: Brain_12_MEF79_2_26


title: GC3_DP_H07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_H07


title: GC3_DP_H06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_H06


title: GC4_DZ_A01.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_A01


title: Brain_12_DMF179_2_24


title: Brain_12_DMF179_2_23


title: RAL-332_gut_T=10h43m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28171


title: RAL-336_gut_T=10h52m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28172


title: Brain_12_DMF179_2_19


title: GC3_DP_H05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_H05


title: Brain_12_DMF179_2_21


title: Brain_12_DMF179_2_20


title: RAL-317_gut_T=10h24m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28167


title: Brain_12_DMF179_2_22


title: RAL-318_gut_T=10h33m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28168


title: Brain_12_DMF179_2_17


title: Brain_12_DMF100_MEF79_2_40


title: Brain_12_DMF100_MEF79_2_37


title: RAL-309_gut_T=10h14m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_28166


title: Brain_12_DMF100_MEF79_2_38


title: Brain_12_DMF179_2_18


title: GC3_DP_H04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_H04


title: GC3_DP_H03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_H03


title: RAL-287_gut_T=10h4m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28165


title: Brain_12_DMF100_MEF79_2_36


title: Brain_12_DMF100_MEF79_2_35


title: GC3_DP_G08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_G08


title: Brain_12_DMF100_9


title: GC3_DP_H01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_H01


title: Brain_12_DMF100_MEF79_2_34


title: Brain_12_DMF100_MEF79_2_33


title: Brain_12_DMF100_15_018


title: GC3_DP_H02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_H02


title: RAL-280_gut_T=9h55m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28164


title: GC3_DP_G05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_G05


title: RAL-228_gut_T=9h26m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28157


title: RAL-239_gut_T=9h45m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28161


title: GC3_DP_G07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_G07


title: Brain_12_DMF100_11


title: Brain_12_DMF100_13


title: Brain_12_DMF100_10


title: GC3_DP_G06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_G06


title: Brain_12_DMF100_14


title: Brain_12_DMF100_12


title: Brain_6_VEH_57


title: Brain_6_VEH_58


title: Brain_6_VEH_55


title: Brain_6_VEH_54


title: RAL-181_gut_T=8h57m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28151


title: Brain_6_VEH_53


title: RAL-109_gut_T=7h31m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28140


title: RAL-176_gut_T=8h38m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28149


title: Brain_6_VEH_52


title: GC3_DP_G03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_G03


title: RAL-158_gut_T=8h28m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28147


title: GC3_DP_G02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_G02


title: GC3_DP_F08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_F08


title: Brain_6_VEH_56


title: GC3_DP_G04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_G04


title: GC3_DP_G01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_G01


title: Brain_6_MEF79_2_81


title: Brain_6_MEF79_2_82


title: RAL-136_gut_T=7h50m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28142


title: RAL-105_gut_T=7h21m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28139


title: Brain_6_MEF79_2_79


title: GC3_DP_F06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_F06


title: RAL-101_gut_T=7h12m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28138


title: GC3_DP_F07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_F07


title: Brain_6_MEF79_2_77


title: Brain_6_MEF79_2_80


title: Brain_6_MEF79_2_76


title: Brain_6_VEH_51


title: GC3_DP_F05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_F05


title: Brain_6_MEF79_2_78


title: Brain_6_MEF79_2_75


title: Brain_6_DMF179_2_73


title: RAL-091_gut_T=7h2m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28136


title: RAL-088_gut_T=6h52m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28135


title: Brain_6_DMF179_2_71


title: Brain_6_DMF179_2_72


title: GC3_DP_F04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_F04


title: Brain_6_DMF179_2_74


title: Brain_6_DMF179_2_70


title: RAL-069_gut_T=6h24m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_28130


title: GC3_DP_F03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_F03


title: RAL-075_gut_T=6h33m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_28132


title: RAL-028_gut_T=5h36m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28124


title: Brain_6_DMF179_2_67


title: RAL-041_gut_T=5h55m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28126


title: GC3_DP_E08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_E08


title: GC3_DP_F02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_F02


title: RAL-045_gut_T=6h4m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28128


title: Brain_6_DMF179_2_69


title: Brain_6_DMF100_MEF79_2_88


title: Brain_6_DMF100_MEF79_2_90


title: Brain_6_DMF179_2_68


title: Brain_6_DMF100_MEF79_2_89


title: RAL-026_gut_T=5h26m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28123


title: GC3_DP_E06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_E06


title: GC3_DP_F01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_F01


title: GC3_DP_E05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_E05


title: GC3_DP_E04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_E04


title: Brain_6_DMF100_MEF79_2_87


title: Brain_6_DMF100_MEF79_2_86


title: RAL-714_gut_T=5h7m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_25745


title: Brain_6_DMF100_65


title: Brain_6_DMF100_MEF79_2_83


title: Brain_6_DMF100_63


title: Brain_6_DMF100_MEF79_2_84


title: RAL-021_gut_T=5h16m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28122


title: GC3_DP_E03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_E03


title: GC3_DP_E07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_E07


title: RAL-786_gut_T=4h28m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_25206


title: GC3_DP_E02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_E02


title: RAL-820_gut_T=4h38m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_25208


title: RAL-852_gut_T=4h48m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_25209


title: Brain_6_DMF100_60


title: RAL-774_gut_T=4h19m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_25205


title: GC3_DP_E01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_E01


title: WB_12_VEH_8

value: Whole Blood


title: RAL-732_gut_T=4h0m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_25203


title: RAL-707_gut_T=3h31m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_25200


title: Brain_6_DMF100_62


title: Brain_6_DMF100_MEF79_2_85


title: Brain_6_DMF100_64


title: Brain_6_DMF100_66


title: WB_12_VEH_7


title: WB_12_VEH_4


title: WB_12_VEH_2


title: Brain_6_DMF100_61


title: WB_12_VEH_1


title: GC3_DP_D08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_D08


title: Brain_6_DMF100_59


title: WB_12_VEH_5


title: WB_12_VEH_3


title: GC3_DP_D07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_D07


title: GC3_DP_D05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_D05


title: RAL-555_gut_T=3h21m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_25198


title: RAL-437_gut_T=3h2m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_25194


title: GC3_DP_D06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_D06


title: RAL-486_gut_T=3h12m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_25195


title: GC3_DP_D04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_D04


title: RAL-427_gut_T=2h52m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_25193


title: WB_12_MEF79_2_32


title: WB_12_MEF79_2_30


title: WB_12_MEF79_2_26


title: GC3_DP_D01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_D01


title: RAL-399_gut_T=2h43m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_25192


title: GC3_DP_D02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_D02


title: GC3_DP_C08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_C08


title: GC3_DP_D03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_D03


title: WB_12_NAIVE_44


title: WB_12_MEF79_2_31


title: WB_12_NAIVE_48


title: WB_12_NAIVE_46


title: WB_12_MEF79_2_28


title: RAL-362_gut_T=1h55m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_25187


title: RAL-379_gut_T=2h14m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_25189


title: WB_12_MEF79_2_25


title: WB_12_NAIVE_47


title: WB_12_NAIVE_45


title: GC3_DP_C07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_C07


title: WB_12_MEF79_2_27


title: GC3_DP_C06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_C06


title: WB_12_DMF179_2_19


title: WB_12_DMF179_2_18


title: RAL-380_gut_T=2h24m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_25190


title: WB_12_DMF179_2_23


title: WB_12_DMF179_2_17


title: RAL-357_gut_T=1h26m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_25184


title: GC3_DP_C04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_C04


title: RAL-315_gut_T=0h57m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_25181


title: RAL-313_gut_T=0h48m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_25180


title: RAL-360_gut_T=1h45m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_25186


title: WB_12_DMF100_MEF79_2_40


title: WB_12_DMF179_2_20


title: RAL-307_gut_T=0h38m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_25179


title: WB_12_DMF100_MEF79_2_37


title: WB_12_DMF100_MEF79_2_36


title: GC3_DP_C01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_C01


title: GC3_DP_C05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_C05


title: RAL-304_gut_T=0h28m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_25177


title: GC3_DP_C03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_C03


title: WB_12_DMF100_MEF79_2_38


title: GC3_DP_C02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_C02


title: WB_12_DMF100_MEF79_2_35


title: RAL-303_gut_T=0h19m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_25176


title: WB_12_DMF100_16


title: WB_12_DMF100_15


title: WB_12_DMF179_2_21


title: WB_12_DMF100_9


title: WB_12_DMF100_MEF79_2_33


title: RAL-208_gut_T=0h0m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_25174


title: GC3_DP_B06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_B06


title: WB_12_DMF100_MEF79_2_34


title: RAL-513_fatBody_T=23h50m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_29659

value: whole fat body


title: GC3_DP_B05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_B05


title: RAL-405_fatBody_T=23h31m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_29656


title: RAL-530_gut_T=0h0m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_29660


title: WB_12_DMF100_13


title: WB_12_DMF100_10


title: GC3_DP_B04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_B04


title: WB_12_DMF100_11


title: WB_6_VEH_56


title: WB_12_DMF100_12


title: WB_6_VEH_57


title: WB_6_VEH_54


title: GC3_DP_B08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_B08


title: WB_6_VEH_52


title: WB_6_MEF79_2_82


title: WB_12_DMF100_14


title: GC3_DP_B03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_B03


title: RAL-320_fatBody_T=23h21m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_29654


title: RAL-229_fatBody_T=23h12m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_29653


title: GC3_DP_B07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_B07


title: WB_6_VEH_53


title: GC3_DP_B02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_B02


title: RAL-040_fatBody_T=22h52m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_29651


title: WB_6_MEF79_2_78


title: WB_6_MEF79_2_79


title: RAL-409_fatBody_T=22h43m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28278


title: GC3_DP_A07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_A07


title: RAL-057_fatBody_T=23h2m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_29652


title: WB_6_MEF79_2_77


title: WB_6_MEF79_2_76


title: WB_6_VEH_51


title: GC3_DP_B01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_B01


title: RAL-913_fatBody_T=22h14m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28265


title: GC3_DP_A05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_A05


title: GC3_DP_A08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_A08


title: RAL-235_fatBody_T=22h33m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28275


title: WB_6_DMF179_2_73


title: WB_6_MEF79_2_80


title: WB_6_DMF179_2_71


title: RAL-911_fatBody_T=22h4m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28264


title: GC3_DP_A06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_A06


title: RAL-908_fatBody_T=21h55m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28263


title: GC3_DP_A04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_A04


title: RAL-907_fatBody_T=21h45m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28262


title: WB_6_DMF179_2_67


title: WB_6_MEF79_2_81


title: WB_6_MEF79_2_75


title: WB_6_DMF179_2_69


title: GC3_DP_A03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_A03


title: RAL-897_fatBody_T=21h26m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28260


title: GC3_DP_A02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_A02


title: GC3_DN_H12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_H12


title: RAL-900_fatBody_T=21h36m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28261


title: RAL-892_fatBody_T=21h16m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28258


title: GC3_DP_A01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DP_A01


title: WB_6_DMF179_2_72


title: GC3_DN_H11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_H11


title: GC3_DN_H10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_H10


title: RAL-882_fatBody_T=20h48m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28255


title: RAL-890_fatBody_T=21h7m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28257


title: WB_6_DMF100_MEF79_2_90


title: WB_6_DMF100_MEF79_2_89


title: WB_6_DMF179_2_74


title: WB_6_DMF100_MEF79_2_84


title: WB_6_DMF179_2_68


title: WB_6_DMF100_MEF79_2_85


title: WB_6_DMF100_MEF79_2_86


title: WB_6_DMF100_MEF79_2_88


title: WB_6_DMF100_65


title: WB_6_DMF100_MEF79_2_83


title: WB_6_DMF100_64


title: GC3_DN_H09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_H09


title: WB_6_DMF100_66


title: WB_6_DMF100_61


title: GC3_DN_G11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_G11


title: WB_6_DMF100_62


title: WB_6_DMF100_MEF79_2_87


title: WB_6_DMF100_63


title: RAL-879_fatBody_T=20h38m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28254


title: GC3_DN_G12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_G12


title: RAL-857_fatBody_T=20h19m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28252


title: RAL-855_fatBody_T=20h9m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28251


title: GC3_DN_G10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_G10


title: GC3_DN_G09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_G09


title: GC3_DN_F12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_F12


title: Spleen_VEH_7

value: Spleen


title: WB_6_DMF100_60


title: Spleen_VEH_5


title: WB_12_DMF100_MEF79_2_39


title: Spleen_VEH_8


title: Spleen_VEH_6


title: Spleen_VEH_4


title: RAL-849_fatBody_T=19h50m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28248


title: RAL-837_fatBody_T=19h40m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28246


title: GC3_DN_F11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_F11


title: WB_6_DMF100_59


title: Spleen_VEH_3


title: GC3_DN_F09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_F09


title: RAL-822_fatBody_T=19h21m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28244


title: RAL-821_fatBody_T=19h12m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28243


title: Spleen_Nav_46


title: Spleen_Nav_45


title: Spleen_Nav_47


title: GC3_DN_E12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_E12


title: Spleen_VEH_2


title: Spleen_VEH_1


title: GC3_DN_E11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_E11


title: Spleen_Nav_40


title: Spleen_Nav_41


title: Spleen_Nav_43


title: Spleen_Nav_44


title: Spleen_MEF79_2_31


title: GC3_DN_E10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_E10


title: RAL-818_fatBody_T=18h52m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28241


title: RAL-819_fatBody_T=19h2m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28242


title: RAL-810_fatBody_T=18h43m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28239


title: RAL-853_fatBody_T=20h0m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28250


title: Spleen_MEF79_2_30


title: GC3_DN_E09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_E09


title: GC3_DN_D12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_D12


title: GC3_DN_F10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_F10


title: Spleen_MEF79_2_29


title: GC3_DN_D10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_D10


title: GC3_DN_D11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_D11


title: RAL-808_fatBody_T=18h33m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28238


title: Spleen_MEF79_2_28


title: Spleen_MEF79_2_26


title: Spleen_MEF79_2_27


title: Spleen_MEF79_2_25


title: Spleen_DMF100_MEF79_2_36


title: Spleen_DMF100_MEF79_2_38


title: Spleen_DMF100_MEF79_2_39


title: RAL-805_fatBody_T=18h24m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28237


title: GC3_DN_C12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_C12


title: RAL-796_fatBody_T=17h55m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28233


title: GC3_DN_C11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_C11


title: GC3_DN_D09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_D09


title: RAL-790_fatBody_T=17h45m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28232


title: RAL-787_fatBody_T=17h36m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28231


title: Spleen_DMF100_MEF79_2_35


title: Spleen_Nav_42


title: Spleen_DMF100_MEF79_2_32


title: Spleen_DMF100_MEF79_2_37


title: Spleen_DMF100_MEF79_2_33


title: Spleen_DMF100_MEF79_2_34


title: Spleen_DMF_179_2_22


title: Spleen_DMF_179_2_23


title: GC3_DN_C10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_C10


title: Spleen_DMF_179_2_24


title: RAL-802_fatBody_T=18h4m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28235


title: GC3_DN_C09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_C09


title: RAL-776_fatBody_T=17h16m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28229


title: Spleen_DMF_179_2_21


title: RAL-748_fatBody_T=17h7m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28224


title: RAL-737_fatBody_T=16h48m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28222


title: GC3_DN_B11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_B11


title: Spleen_DMF_179_2_19


title: GC3_DN_B12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_B12


title: Spleen_DMF_179_2_20


title: Spleen_DMF_179_2_18


title: Spleen_DMF_100_16


title: Spleen_DMF_100_15


title: Spleen_DMF_100_14


title: Spleen_DMF_179_2_17


title: Spleen_DMF_100_13


title: Spleen_DMF_100_9


title: GC3_DN_A11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_A11


title: RAL-642_fatBody_T=16h0m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28216


title: RAL-738_fatBody_T=16h57m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28223


title: GC3_DN_B09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_B09


title: RAL-716_fatBody_T=16h28m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28219


title: RAL-721_fatBody_T=16h38m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28220


title: RAL-703_fatBody_T=16h19m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28218


title: GC3_DN_A12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_A12


title: GC3_DN_A10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_A10


title: RAL-646_fatBody_T=16h9m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28217


title: Spleen_DMF_100_10


title: Spleen_DMF_100_12


title: RAL-595_fatBody_T=15h50m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28215


title: GC3_DN_B10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_B10


title: GC2_DP_H08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_H08


title: Spleen_DMF_100_11


title: MLN_VEH_6

value: Mesenteric Lymph Node (MLN)


title: MLN_VEH_4


title: MLN_VEH_5


title: MLN_VEH_7


title: MLN_VEH_3


title: MLN_VEH_8


title: RAL-563_fatBody_T=15h21m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28211


title: GC2_DP_H06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_H06


title: RAL-535_fatBody_T=15h12m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28208


title: GC2_DP_H05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_H05


title: GC2_DP_H07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_H07


title: MLN_Nav_45


title: MLN_Nav_46


title: MLN_VEH_1


title: MLN_VEH_2


title: MLN_Nav_47


title: MLN_Nav_42


title: RAL-832_fatBody_T=19h31m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28245


title: RAL-589_fatBody_T=15h40m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28213


title: GC2_DP_H02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_H02


title: RAL-509_fatBody_T=15h2m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28206


title: RAL-502_fatBody_T=14h43m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28204


title: MLN_MEF79_2_31


title: GC2_DP_H04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_H04


title: MLN_MEF79_2_30


title: MLN_Nav_40


title: MLN_Nav_41


title: MLN_MEF79_2_28


title: RAL-584_fatBody_T=15h31m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28212


title: MLN_Nav_44


title: MLN_MEF79_2_29


title: RAL-508_fatBody_T=14h52m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28205


title: GC2_DP_H03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_H03


title: MLN_MEF79_2_25


title: MLN_MEF79_2_26


title: MLN_DMF100_MEF79_2_35


title: MLN_MEF79_2_27


title: RAL-492_fatBody_T=14h33m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28203


title: GC2_DP_G05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_G05


title: RAL-461_fatBody_T=14h24m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28200


title: MLN_DMF100_MEF79_2_38


title: GC2_DP_H01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_H01


title: MLN_DMF100_MEF79_2_36


title: RAL-386_fatBody_T=13h36m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28192


title: RAL-441_fatBody_T=14h4m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28198


title: GC2_DP_G08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_G08


title: GC2_DP_G04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_G04


title: MLN_DMF100_MEF79_2_32


title: GC2_DP_G06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_G06


title: RAL-443_fatBody_T=14h14m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28199


title: GC2_DP_G07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_G07


title: RAL-385_fatBody_T=13h26m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28191


title: GC3_DN_A09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC3_DN_A09


title: GC2_DP_G03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_G03


title: RAL-440_fatBody_T=13h55m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28197


title: MLN_DMF100_MEF79_2_34


title: MLN_DMF_179_2_24


title: MLN_DMF_179_2_22


title: MLN_DMF_179_2_19


title: MLN_DMF100_MEF79_2_33


title: MLN_DMF_179_2_18


title: MLN_DMF_179_2_23


title: MLN_DMF_179_2_20


title: MLN_DMF_179_2_21


title: GC2_DP_G02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_G02


title: MLN_DMF_179_2_17


title: MLN_DMF_100_9


title: GC2_DP_F08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_F08


title: RAL-381_fatBody_T=12h57m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28188


title: GC2_DP_F07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_F07


title: RAL-382_fatBody_T=13h7m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28189


title: MLN_DMF_100_16


title: RAL-373_fatBody_T=12h28m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28184


title: RAL-377_fatBody_T=12h48m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28186


title: RAL-383_fatBody_T=13h16m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28190


title: MLN_DMF_100_13


title: MLN_DMF_100_11


title: MLN_DMF_100_10


title: MLN_DMF_100_14


title: MLN_DMF_100_15


title: MLN_DMF_100_12


title: GC2_DP_F03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_F03


title: Kidney_VEH_6

value: Kidney


title: Kidney_VEH_3


title: GC2_DP_G01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_G01


title: Kidney_VEH_8


title: Kidney_VEH_4


title: Kidney_VEH_5


title: GC2_DP_F05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_F05


title: RAL-361_fatBody_T=12h0m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28180


title: RAL-371_fatBody_T=12h19m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28183


title: RAL-338_fatBody_T=11h2m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28173


title: GC2_DP_F06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_F06


title: RAL-340_fatBody_T=11h12m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28174


title: RAL-352_fatBody_T=11h31m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28177


title: Kidney_Nav_47_088


title: Kidney_Nav_46


title: Kidney_Nav_45


title: Kidney_VEH_1


title: Kidney_VEH_2


title: RAL-336_fatBody_T=10h52m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28172


title: GC2_DP_E08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_E08


title: GC2_DP_F02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_F02


title: GC2_DP_F01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_F01


title: GC2_DP_E07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_E07


title: GC2_DP_F04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_F04


title: GC2_DP_E06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_E06


title: Kidney_Nav_42


title: RAL-318_fatBody_T=10h33m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28168


title: RAL-317_fatBody_T=10h24m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28167


title: Kidney_Nav_43


title: RAL-332_fatBody_T=10h43m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28171


title: Kidney_Nav_44


title: GC2_DP_E04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_E04


title: RAL-309_fatBody_T=10h14m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28166


title: Kidney_Nav_41


title: Kidney_MEF79_2_28


title: Kidney_MEF79_2_30


title: Kidney_MEF79_2_29


title: GC2_DP_E03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_E03


title: Kidney_MEF79_2_31


title: Kidney_Nav_40


title: RAL-280_fatBody_T=9h55m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28164


title: Kidney_MEF79_2_27


title: GC2_DP_E01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_E01


title: RAL-237_fatBody_T=9h36m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28160


title: GC2_DP_E02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_E02


title: GC2_DP_D08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_D08


title: RAL-239_fatBody_T=9h45m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28161


title: GC2_DP_E05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_E05


title: Kidney_DMF100_MEF79_2_38


title: Kidney_MEF79_2_25


title: Kidney_DMF100_MEF79_2_39


title: Kidney_DMF100_MEF79_2_36


title: Kidney_MEF79_2_26


title: RAL-287_fatBody_T=10h4m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28165


title: RAL-228_fatBody_T=9h26m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28157


title: Kidney_DMF100_MEF79_2_37


title: GC2_DP_D07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_D07


title: GC2_DP_D06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_D06


title: Kidney_DMF100_MEF79_2_32


title: Kidney_DMF_179_2_24


title: Kidney_DMF100_MEF79_2_34


title: Kidney_DMF100_MEF79_2_35


title: RAL-217_fatBody_T=9h7m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28154


title: RAL-181_fatBody_T=8h57m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28151


title: GC2_DP_D05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_D05


title: GC2_DP_D04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_D04


title: RAL-176_fatBody_T=8h38m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28149


title: GC2_DP_D03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_D03


title: RAL-158_fatBody_T=8h28m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28147


title: RAL-149_fatBody_T=8h19m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28145


title: RAL-142_fatBody_T=8h9m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28144


title: GC2_DP_D02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_D02


title: GC2_DP_D01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_D01


title: Kidney_DMF_100_9


title: Kidney_DMF_179_2_20


title: Kidney_DMF_179_2_21


title: Kidney_DMF_179_2_19


title: Kidney_DMF_179_2_17


title: Kidney_DMF_100_16


title: GC2_DP_C07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_C07


title: Kidney_DMF_100_15


title: Kidney_DMF_179_2_23


title: Kidney_DMF_100_13


title: Kidney_DMF_179_2_18


title: RAL-138_fatBody_T=8h0m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28143


title: Kidney_DMF_100_12


title: RAL-136_fatBody_T=7h50m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28142


title: Kidney_DMF_100_14


title: RAL-109_fatBody_T=7h31m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28140


title: GC2_DP_C06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_C06


title: Kidney_DMF_179_2_22


title: RAL-101_fatBody_T=7h12m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28138


title: GC2_DP_C05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_C05


title: GC2_DP_C08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_C08


title: Kidney_DMF_100_11


title: RAL-091_fatBody_T=7h2m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28136


title: GC2_DP_C04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_C04


title: Kidney_DMF_100_10


title: Jejunum_VEH_7

value: Jejunum


title: RAL-083_fatBody_T=6h43m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28134


title: RAL-088_fatBody_T=6h52m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28135


title: Jejunum_VEH_6


title: GC2_DP_C02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_C02


title: GC2_DP_C03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_C03


title: GC2_DP_C01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_C01


title: RAL-059_fatBody_T=6h14m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28129


title: RAL-069_fatBody_T=6h24m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28130


title: Jejunum_VEH_8


title: RAL-045_fatBody_T=6h4m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28128


title: GC2_DP_B08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_B08


title: RAL-038_fatBody_T=5h45m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_28125


title: GC2_DP_B07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_B07


title: GC2_DP_B06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_B06


title: GC2_DP_B05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_B05


title: mRNA-seq_rep1

city: Beijing

first: Yan-Ming

last: Chen

address: Beichen West Rd.

country: China

institute: Institute of Genetics and Developmental Biology Chinese Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence. The 3-nt random sequence at the 5'-end of each sequencing read was removed(, except for the two disome-seq-3AT libraries). The removed 3-nt sequence was added to the head of each read in the fastq format as the UMI, which can serve to remove PCR duplications generated during Illumina library preparation. The sequence identical to the 3'-sequencing adaptor (AGATCGGAAGAGCACACGTCT for read 1 in both disome-seq libraries and the disome-seq_negative_control; TGGAATTCTCGGGTGCCAAG for all eight monosome-seq and mRNA-seq libraries) was also trimmed in each read using cutadapt V1.16. The trimmed reads were mapped against rRNA with bowtie V1.2.2 with default parameters, and the mapped reads were filtered to avoid rRNA contamination. The rest reads were aligned against SGD R64-1-1 coding sequences with the --no-novel-juncs parameter using Tophat V2.1.1.
Genome_build: SGD R64-1-1
Supplementary_files_format_and_content: tab-delimited text files include read number for each Sample

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: The laboratory strain BY4742 (MATα his3Δ1 leu2Δ0 lys2Δ0 uraΔ0) was cultivated at 30ºC in the rich medium YPD (1% yeast extract, 2% peptone, and 2% dextrose).

extract_protocol:
Ribosomes were extracted with the polysome lysis buffer (PLB), which contained 200 mM Tris-HCl (pH 8.0), 200 mM KCl, 35 mM MgCl2, 1% (v/v) Triton X-100, 5 mM DTT, and 50 µg/mL cycloheximide.
50000 units (A260) of ribosome dissolved in the PLB buffer were treated with 750 U RNase I (Ambion, AM2294) at 25°C for 2 hours. Our pilot experiments, as well as previous studies, have shown that polysome profiling is not necessary as long as the digestion with RNase I is complete; rather, this step consumes a large amount of ribosome (especially disome) samples. The following-up computational analyses can help to tell if the RNA fragments being collected are largely protected by ribosomes: whether the fragments are restricted to the coding sequences, whether the fragments are enriched in certain sizes, and whether a 3-nt periodicity exists . Therefore, RNA was directly extracted from the enzyme reaction system with hot phenol and was separated on a 17% (w/v) 7 M urea denaturing polyacrylamide gel in a 0.5×Tris-borate-EDTA (TBE) electrophoresis buffer. RNA fragments with the length of 25-30 nts or 50-80 nts were extracted by gel crushing and further incubated with an RNA gel extraction buffer (300 mM NaOAc pH 5.2, 10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0) overnight. The purified extracted RNA fragments for monosome-seq, disomes-seq, and mRNA-seq were subjected to small RNA library construction for Illumina sequencing (Gnomegen, k02420). The 5′-RNA adaptor contained a 3-nt random sequence at the 3′-end to avoid biased ligation. Monosome and disome footprints were sequenced with single-end 50 and paired-end 100 modes on BGISEQ-500 (BGI Group), respectively. The lengths of RNA fragments protected by single ribosomes peaked at 28-nt, consistent with previous studies.

treatment_protocol: For experiments using the 3-AT treatment, the strain S288C was cultivated at 30ºC in the SC−His+3-AT medium (synthetic complete medium with histidine dropped-out and 100 mM 3-AT added)

tag: treatment

value: rich medium


title: RAL-129_fatBody_T=7h40m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28141


title: RAL-028_fatBody_T=5h36m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_28124


title: Jejunum_VEH_2


title: monosome-seq_rep2

data_processing:
Library strategy: Ribo-Seq (ribosome profiling)
Sequenced reads were trimmed for adaptor sequence. The 3-nt random sequence at the 5'-end of each sequencing read was removed(, except for the two disome-seq-3AT libraries). The removed 3-nt sequence was added to the head of each read in the fastq format as the UMI, which can serve to remove PCR duplications generated during Illumina library preparation. The sequence identical to the 3'-sequencing adaptor (AGATCGGAAGAGCACACGTCT for read 1 in both disome-seq libraries and the disome-seq_negative_control; TGGAATTCTCGGGTGCCAAG for all eight monosome-seq and mRNA-seq libraries) was also trimmed in each read using cutadapt V1.16. The trimmed reads were mapped against rRNA with bowtie V1.2.2 with default parameters, and the mapped reads were filtered to avoid rRNA contamination. The rest reads were aligned against SGD R64-1-1 coding sequences with the --no-novel-juncs parameter using Tophat V2.1.1.
Genome_build: SGD R64-1-1
Supplementary_files_format_and_content: tab-delimited text files include read number for each Sample


title: Jejunum_VEH_5


title: RAL-026_fatBody_T=5h26m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28123


title: monosome-seq_rep1


title: RAL-021_fatBody_T=5h16m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_28122


title: Jejunum_VEH_4


title: mRNA-seq_rep2


title: RAL-714_fatBody_T=5h7m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_25745


title: GC2_DP_B03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_B03


title: GC2_DP_B02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_B02


title: Jejunum_Nav_46


title: GC2_DP_B04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_B04


title: Jejunum_VEH_3


title: Jejunum_Nav_45


title: Jejunum_Nav_44


title: Jejunum_Nav_47


title: Jejunum_VEH_1


title: GC2_DP_A08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_A08


title: GC2_DP_B01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_B01


title: RAL-365_fatBody_T=4h57m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_25445


title: KO2

first: Qingyuan

last: Sun

state: Beijing

address: Beichen West Rd., Chaoyang

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

description: Bulk RNA-seq

data_processing:
All cDNA libraries were fragmented and then sequenced on Illumina HiSeq platform. After sequencing, the raw reads in the fastq format were first processed and the clean reads were obtained by removing adapter sequences and low-quality reads from raw data. Next, the clean reads were aligned to the reference genome (mm10) using TopHat . Based on the comparison results, the sequencing data were assembled by Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: gene counts

source_name: E5.5 Mettl14-/-embryos

extract_protocol:
RNA were prepared for sequencing
Four E5.5 embryos were subjected to RNA sequencing (RNASeq). RNA was isolated from single E5.5 embryo and amplified using Smart-Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories,Mountain View, CA, USA) and sequenced by Novogene Corporation (Haidian, Beijing, China). Then we identified the genotype of 4 embryos based on Mettl14 qPCR of parts of the returned amplified cDNA. Fortunately, 2 embryos were identified as Mettl142/2, while the other 2 embryos expressing Mettl14 mRNA were classified as the control group. Library construction was performed according to the manufacturer’s instructions (Illumina, San Diego, CA, USA). Libraries were sequenced on the Illumina HiSeq PE150.

treatment_protocol: Gene knockout

tag: strain bckground

tag: age

value: Embryonic day 5.5

tag: genotype/variation

value: E5.5 embryos


title: WT2

description: Bulk RNA-seq

source_name: E5.5 Mettl14+/+embryos


title: RAL-852_fatBody_T=4h48m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_25209


title: WT1

description: Bulk RNA-seq


title: GC2_DP_A07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_A07


title: GC2_DP_A06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_A06


title: Jejunum_Nav_41


title: Jejunum_MEF79_2_31


title: GC2_DP_A05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_A05


title: Jejunum_Nav_40


title: KO1

description: Bulk RNA-seq


title: RAL-786_fatBody_T=4h28m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_25206


title: EloA_null_FB10_rep2

city: Boston

first: Manashree

last: Damle

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

description:
nascent RNA
FB10_RPKMs.txt

data_processing:
Library strategy: Bru-seq
Bru-seq: Reads were aligned using bowtie 2 v2.3.4.3
Bru-seq: Reads were separated by orientation using samtools
Bru-seq: Gene annotations were obtained from ncbi refseq
Bru-seq: Reads in genes were counted using featureCounts v1.6.1
Bru-seq: EdgeR was used for normalization
Bru-seq: Drosophila spike-ins were used to compare samples
Genome_build: mm10, dm3 (Bru-seq)
Cut-n-run: Reads were aligned to the mm10 genome using bowtie 2 v2.3.4.3
Cut-n-run: Peaks were called using SEACR
Genome_build: mm10 (Cut-n-run)
ChIP-seq: Reads were aligned to the mm10 genome using bowtie 2 v2.3.4.3
ChIP-seq: Peaks were called using Homer v4.10.3
Genome_build: mm10 (CHIP-seq)
Supplementary_files_format_and_content: Genome browser tracks were generated using Homer v4.10.3

source_name: embryonic stem cells

growth_protocol: Murine CCE28 cells (wild-type & ELoA null, Kind gift of Dr. Teijiro Aso at Kochi Medical School) were grown on 0.2% gelatin-coated 6-well plates seeded with irradiated or mitomycin C treated mouse embryonic fibroblast (MEF). ES cell medium contained: 1x DMEM knockOut medium, 15% hyclone FBS, 1x GlutaMAX, 1x NEAA, 1x pen/strep, 1-1.6x10e3 Units/ml of mLIF (Millipore), 55μM 2BME. Media was supplemented with 1µM and 3µM of PD0325901 and CHIR99021, respectively (2i). ES cells were depleted of MEF by plating the ES cell suspension at 37oC for 30min.

extract_protocol:
Bru-RNA enrichment:Mouse aBrdU antibody (SCBT, sc-32323) was coupled to Dynabeads M-280 Sheep Anti-Mouse IgG (11201D). 1ml of magnetic beads was washed 4 x with PBS-DEPC/0.1%BSA and 500ul of Ab  was incubated with 1ml of beads and yeast RNA (500ng/µl final concentration) for 2-3 hours at 4oC, washed 3x with PBS-DEPC/0.1%BSA/Tween 0.05%.The final volume was raised to 1ml. For enrichment of Bru-RNA, 25-50µg of total RNA (after preheating at 95oC and immediate cooling) was added to 50µl of Antibody-bound beads in 1 ml of PBS-DEPC/0.1%BSA/Tween 0.05% and incubated for 90 min at RT with a foil wrapped around the tube. Beads were washed 4x with PBS-DEPC/0.1%BSA/Tween 0.05%, 5-10min (last wash was done with Tween-free buffer). Enriched RNA was either eluted by addition of 25µl of DEPC-water and incubation at 95oC for 10min with occasional flicking/shaking, or Trizol extraction. The enriched RNA was depleted of ribosomal RNA and used for generation of RNA-seq library.
ChIP-seq: mESC were MEF depleted, crosslinked with 1% formaldehyde in PBS for 10min in conical tubes while gently rotating at RT and quenched by adding Glycine to a final concentration of 0.125M and left at RT for 5min on rotator. Crosslinked cells were spun down for 3min at 3500 rpm (2850 rcf) and lysed in cell lysis buffer  (50mM Tris PH 8.0, 50mM NaCl, 1mM EDTA, 5mM MgCl2, 0.25% NP-40, Roche complete EDTA-free protease inhibitor tablet(PI)* 0.2% PMSF* and 0.2% DTT*(*freshly-added)) at 2-2.5x10e7 cells/ml. Cells were left on ice for 10 min and dounced 10x using the tight pestle. Nuclei was spun down at 2850 rcf in 15ml conical tubes and the supernatnant was completely removed and nuclei was resuspended in sonication buffer (20mM Tris PH 8.0, 1% SDS, 2mM EDTA, 0.5mM EGTA, 0.5mM PMSF*, PI*(freshly added) at 5.0x10e7 nuclei/ml. Resuspended nuclei was left on ice for 10min and sonicated using the Bioruptor sonicator, at high setting 30’’ on 45’’ off twice for 15min. Water and ice was changed in between each sonication. IP was performed with 10 ul of  EloA R-19 antibody (SCBT, sc-1557), 1-2.5x10e6 nuclei were used per IP reaction, by adding 20-50 µl of sonicated chromatin to 1-1.25ml of IP buffer (20mM Tris PH 8.0, 0.5% Triton X-100, 150mM NaCl, 10% glycerol, 2mM EDTA) with the respective antibodies and after 4 hours of incubation protein A (40-50 µl) was added to the IP reaction and incubated for 4 more hours. Each wash was done on the rotator at RT for 5min as follows: x1 low salt wash (20mM Tris PH 7.8, 0.1% SDS, 1% Triton X-100, 2mM EDTA, 150mM NaCl), x3 high salt wash (20mM Tris PH 7.8, 0.1% SDS, 1% Triton X-100, 2mM EDTA, 500mM NaCl), x1 LiCl wash (20mM Tris PH 7.8, 1% NP-40, 1% NaDeoxycholate, 2mM EDTA, 250mM LiCl), x2 TE wash.Elution was done on the IPed samples in 2x250µl of elution buffer (1% SDS, 0.1M NaHCO3) on the rotator at RT. To the 500µl elution buffer, 20 µl of 5M NaCl was added and samples were incubated in a thrmomixer for 4hr-O/N at 65oC to reverse the crosslink (same was done for the Input material). Next, 15µl of 1M Tris PH 7.8, 1-2 µl glycoblue (Ambion) and 2 µl of proteinase K was added to the reaction mix and incubated at 65oC for 30-60min. DNA was extracted from the reversed crosslink material using phenol/chloroform extraction and EtOH precipitation.
Cut-and-run-seq:Mouse ES cells were crosslinked with 1% formaldehyde in PBS for 10 min and quenched with 0.125M glycine for 5min, cells were pelleted and washed once with PBS, spun down, resuspended in freezing media (DMEM, 10% DMSO), placed in a styrofoam container and frozen O/N (this step was included to minimize cell membrane rupture and DNA breakage). On the day of the experiment, crosslinked cells were thawed and washed once with PBS and twice in cut&run wash buffer (20 mM HEPES pH7.5, 150 mM NaCl, 0.1% Tween20, 0.1%BSA, 1 Roche complete EDTA-free protease inhibitor tablet/50ml), Tween20 was included in the wash buffer to minimize  concanavalin A magnetic bead aggregation in downstream steps. Next, 5x10e6 cells were resuspended in 950 μl of wash buffer. 50 μl of BioMag-Plus Concanavalin A beads (Polysciences Inc.) was also washed gently twice with binding buffer (20 mM HEPES pH 7.9, 1 mM CaCl2, 1mM MnCl2) and resuspended in binding buffer at the initial volume (50 μl). Concanavalin A beads (50μl) was added to 5x10e6 cells in 950 μl of wash buffer and incubated rotating for 15min at RT. The cells were divided into five 200ul aliquots for each antibody used (1x10e6 cells/antibody) and after removal of wash buffer, 50 μL of ice cold antibody buffer (wash buffer containing 0.05% Digitonin and 2mM EDTA) containing 0.5 μg of antibody was added to 1x10e6 bead-bound cell pellet and the mixture was gently resuspended by pipetting up and down 25 times . Resuspended beads were placed on a vortex at the lowest setting, and incubated at room temperature for 15 min. For the EloA cut&run experiment using goat anti EloA (SCBT, R-19), a bridging rabbit anti goat antibody was used for efficient binding to protein A. Cells were washed once after primary antibody incubation with 1ml of Digitonin buffer (Wash buffer containing 0.05% Digitonin) resuspended in 50 μl of digitonin buffer with 0.5 μg of rabbit anti goat IgG (rabbit anti-goat IgG (ab6697)). Left on the lowest setting of the vortex and incubated at RT for 15 min. Next, permeabilized, antibody-bound cells were washed once in digitonin buffer containing 1mM EDTA, and 50 μL of digitonin buffer containing Protein A-MNase (pA-MN) at a final concentration of 700ng/ml was added to the pellet, resuspended and incubated at room temperature for 15min. Cells were washed twice with digitonin buffer containing 1mM EDTA. Next, 150 μl of ice cold digitonin buffer was added to the pA-MN bound cells, resuspended and digested on ice (0 oC) for 30 min after addition of CaCl2 to a final concentration of 4 mM. Added 100ul of 2x stop buffer as described in (Skene et al, 2018), and incubated on thermomixer for 15min at 37oC to release the cleaved DNA fragments into solution. The mixture was spun down in a cold tabletop centrifuge at max speed for 5min, and 2ul of proteinase K was added to the supernatant eluate. The mixture was incubated at 65 oC for 4 hours and DNA was extracted by using ChIP DNA Clean & Concentrator (Zymo research).
Library constructing for sequencing was prepared as described elsewhere (Bowman et al., BMC Genomics 2013).

treatment_protocol:
Bru-seq: 5-BromoUridine (BrU) was added to CJ7 mES cells growing in plates at a final concentration of 2mM for 10min in 10mm plates. Media was aspirated off and RNA was extracted by addition of 4ml of Trizol. Flavopiridol (FP) treatment was carried out at a final concentration of 1uM for 1 hour. Plates were washed with warm PBS before addition of Bru-containing media for the indicated time points.
Experiments were carried out on de-MEFed mouse ES cells grown on feeder-free, 1% gelatinized 100mm tissue culture dishes. 5-Bromouridine (BrU) was added to cells at a final concentration of 2mM (from a100mM BrU stock) and incubated in the incubator for 10 min. Media was aspirated off and cells were lysed in 4ml of Trizol. 800µl of chloroform was next added to the lysed cells in 5ml epp tubes, vortexed and spun down at 5200 g for 15min. Equal volume of isopropanol was added to the aqueous phase, mixed, left at RT for 5-10 min and spun down at 4oC for 20min at max speed (14000 g) in a tabletop centrifuge to precipitate the RNA.  Resulting RNA pellet was washed twice with 70% EtOH, air dried and resuspended in 200-400 µl Nuclease-free water. The amount of RNA was quantified using Nanodrop, and a small fraction of the total RNA was run on agarose gel to determine the quality of purified total RNA.

value: EloA null

value: 60 min flavopiridol, 10 min Bromouridine

tag: cell type

value: embryonic stem cells


title: GC2_DP_A04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_A04

tag: dec


title: RAL-732_fatBody_T=4h0m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_25203


title: GC2_DP_A02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_A02

tag: timepoint


title: RAL-820_fatBody_T=4h38m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_25208


title: RAL-774_fatBody_T=4h19m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_25205


title: GC2_DP_A01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_A01

tag: zone


title: EloA_null_B10_rep2

description:
nascent RNA
B10_RPKMs.txt

value: 10 min Bromouridine


title: RAL-765_fatBody_T=4h9m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_25204


title: Jejunum_Nav_43


title: EloA_null_FB5_rep2

description:
nascent RNA
FB5_RPKMs.txt

value: 60 min flavopiridol, 5 min Bromouridine


title: Jejunum_MEF79_2_30


title: EloA_null_FB10_rep1

description:
nascent RNA
FB10_RPKMs.txt


title: WT_FB10_rep2

description:
nascent RNA
FB10_RPKMs.txt

value: wild type


title: EloA_null_B10_rep1

description:
nascent RNA
B10_RPKMs.txt


title: Jejunum_MEF79_2_29


title: Jejunum_MEF79_2_28


title: Jejunum_MEF79_2_26


title: Jejunum_MEF79_2_27


title: RAL-712_fatBody_T=3h40m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_25201

value: Single observation


title: Kidney_DMF100_MEF79_2_33


title: GC2_DN_H12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_H12

tag: sequencing


title: GC2_DP_A03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DP_A03

tag: genotype


title: EloA_null_FB5_rep1

description:
nascent RNA
FB5_RPKMs.txt


title: GC2_DN_H11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_H11


title: RAL-486_fatBody_T=3h12m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_25195

tag: strain


title: WT_FB10_rep1

description:
nascent RNA
FB10_RPKMs.txt


title: RAL-427_fatBody_T=2h52m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_25193

tag: tissue


title: GC2_DN_H10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_H10


title: RAL-399_fatBody_T=2h43m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_25192

tag: time of harvesting


title: RAL-707_fatBody_T=3h31m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_25200

tag: replicate


title: RAL-555_fatBody_T=3h21m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_25198

tag: library


title: GC2_DN_H09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_H09


title: Jejunum_DMF100_MEF79_2_39


title: WT_FB5_rep2

description:
nascent RNA
FB5_RPKMs.txt


title: Jejunum_DMF100_MEF79_2_38


title: Jejunum_MEF79_2_25


title: Jejunum_DMF100_MEF79_2_37


title: GC2_DN_G12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_G12


title: WT_FB5_rep1

description:
nascent RNA
FB5_RPKMs.txt


title: WT_B10_rep2

description:
nascent RNA
B10_RPKMs.txt


title: Jejunum_DMF100_MEF79_2_36


title: RAL-380_fatBody_T=2h24m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_25190

tag: bloomington


title: GC2_DN_G10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_G10


title: RAL-375_fatBody_T=2h4m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_25188

tag: time series type


title: Jejunum_DMF100_MEF79_2_35


title: RAL-362_fatBody_T=1h55m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_25187


title: WT_input_chipseq_rep2

library_source: genomic

data_processing:
Bru-seq: Reads were aligned using bowtie 2 v2.3.4.3
Bru-seq: Reads were separated by orientation using samtools
Bru-seq: Gene annotations were obtained from ncbi refseq
Bru-seq: Reads in genes were counted using featureCounts v1.6.1
Bru-seq: EdgeR was used for normalization
Bru-seq: Drosophila spike-ins were used to compare samples
Genome_build: mm10, dm3 (Bru-seq)
Cut-n-run: Reads were aligned to the mm10 genome using bowtie 2 v2.3.4.3
Cut-n-run: Peaks were called using SEACR
Genome_build: mm10 (Cut-n-run)
ChIP-seq: Reads were aligned to the mm10 genome using bowtie 2 v2.3.4.3
ChIP-seq: Peaks were called using Homer v4.10.3
Genome_build: mm10 (CHIP-seq)
Supplementary_files_format_and_content: Genome browser tracks were generated using Homer v4.10.3

molecule: genomic DNA


title: WT_B10_rep1

description:
nascent RNA
B10_RPKMs.txt

tag: treatment


title: GC2_DN_G11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_G11


title: WT_input_chipseq_rep1


title: GC2_DN_G09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_G09


title: GC2_DN_F12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_F12


title: EloA_null_EloA_chipseq_rep2

tag: chip antibody

value: EloA


title: GC2_DN_F11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_F11


title: Jejunum_DMF100_MEF79_2_34


title: RAL-357_fatBody_T=1h26m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_25184


title: RAL-360_fatBody_T=1h45m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_25186


title: RAL-379_fatBody_T=2h14m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_25189


title: GC2_DN_F10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_F10


title: GC2_DN_F09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_F09


title: WT_EloA_chipseq_rep2


title: WT_EloA_chipseq_rep1


title: RAL-335_fatBody_T=1h16m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_25183


title: EloA_null_EloA_chipseq_rep1


title: Jejunum_DMF100_MEF79_2_32


title: Jejunum_DMF100_MEF79_2_33


title: Jejunum_DMF_179_2_22


title: Jejunum_DMF_179_2_24


title: RAL-324_fatBody_T=1h7m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_25182


title: RAL-315_fatBody_T=0h57m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB1_FB_n_25181


title: RAL-307_fatBody_T=0h38m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_25179


title: GC2_DN_E11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_E11


title: GC2_DN_E12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_E12


title: GC2_DN_E10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_E10


title: EloA_null_Ser2p_cutnrun_rep1

data_processing:
Library strategy: CUT&RUN
Bru-seq: Reads were aligned using bowtie 2 v2.3.4.3
Bru-seq: Reads were separated by orientation using samtools
Bru-seq: Gene annotations were obtained from ncbi refseq
Bru-seq: Reads in genes were counted using featureCounts v1.6.1
Bru-seq: EdgeR was used for normalization
Bru-seq: Drosophila spike-ins were used to compare samples
Genome_build: mm10, dm3 (Bru-seq)
Cut-n-run: Reads were aligned to the mm10 genome using bowtie 2 v2.3.4.3
Cut-n-run: Peaks were called using SEACR
Genome_build: mm10 (Cut-n-run)
ChIP-seq: Reads were aligned to the mm10 genome using bowtie 2 v2.3.4.3
ChIP-seq: Peaks were called using Homer v4.10.3
Genome_build: mm10 (CHIP-seq)
Supplementary_files_format_and_content: Genome browser tracks were generated using Homer v4.10.3


title: Jejunum_DMF_179_2_20


title: Jejunum_DMF_179_2_19


title: GC2_DN_D12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_D12


title: Jejunum_DMF_179_2_21


title: Jejunum_DMF_179_2_18


title: RAL-301_fatBody_T=0h9m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_25175


title: WT_Ser2p_cutnrun_rep1


title: GC2_DN_E09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_E09


title: RAL-303_fatBody_T=0h19m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_25176


title: Jejunum_DMF_179_2_17


title: WT_IgG_cutnrun_rep1

value: IgG


title: RAL-530_fatBody_T=0h0m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_n_29660

value: whole fat body


title: WT_IgG_cutnrun_rep2


title: Jejunum_DMF_100_9


title: RAL-208_fatBody_T=0h0m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_25174


title: GC2_DN_D11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_D11


title: EloA_null_Ser2p_cutnrun_rep2


title: EloA_null_EloA_cutnrun_rep2


title: GC2_DN_D10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_D10


title: GC2_DN_D09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_D09


title: EloA_null_EloA_cutnrun_rep1


title: RAL-513_brain_T=23h50m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_n_29659

value: whole brain


title: WT_EloA_cutnrun_rep2


title: Jejunum_DMF_100_14


title: Jejunum_DMF_100_16


title: WT_Ser2p_cutnrun_rep2


title: GC2_DN_C12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_C12


title: Jejunum_DMF_100_15


title: RAL-304_fatBody_T=0h28m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_n_25177


title: GC2_DN_C11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_C11


title: RAL-405_brain_T=23h31m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_n_29656


title: RAL-320_brain_T=23h21m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_n_29654


title: Jejunum_DMF_100_13


title: WT_EloA_cutnrun_rep1


title: NAG12 YEM #3

city: LAUSANNE

first: JOAQUIN

last: CLUA

address: BIOPHORE

department: DBMV

institute: UNIL

description: FPKM for NAG12 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

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 YEM

tag: cultivar


title: Jejunum_DMF_100_10


title: GC2_DN_C10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_C10


title: RAL-409_brain_T=22h43m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28278


title: GC2_DN_C09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_C09


title: RAL-040_brain_T=22h52m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_29651


title: NAG12 YEM #1

description: FPKM for NAG12 genes.txt


title: NAG12 YEM #2

description: FPKM for NAG12 genes.txt


title: GC2_DN_B12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_B12


title: ILN_VEH_8

value: Inguinal Lymph Node (ILN)


title: GC2_DN_B11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_B11


title: ILN_VEH_6


title: NAG12 SC15 #2

description: FPKM for NAG12 genes.txt

value: R. etli SC15


title: GC2_DN_B09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_B09


title: GC2_DN_B10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_B10


title: RAL-235_brain_T=22h33m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28275


title: RAL-085_brain_T=22h24m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_n_28274


title: ILN_VEH_4


title: ILN_VEH_5


title: NAG12 SC15 #1

description: FPKM for NAG12 genes.txt


title: RAL-229_brain_T=23h12m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_n_29653


title: RAL-913_brain_T=22h14m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_n_28265


title: GC2_DN_A12.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_A12


title: RAL-908_brain_T=21h55m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28263


title: GC2_DN_A11.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_A11


title: NAG12 CE3 #2

description: FPKM for NAG12 genes.txt

value: R. etli CE3


title: ILN_VEH_3


title: NAG12 SC15 #3

description: FPKM for NAG12 genes.txt


title: NAG12 CE3 #3

description: FPKM for NAG12 genes.txt


title: RAL-900_brain_T=21h36m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_n_28261


title: ILN_VEH_7


title: RAL-907_brain_T=21h45m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28262


title: GC2_DN_A09.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_A09


title: ILN_VEH_2


title: NAG12 55N1 #3

description: FPKM for NAG12 genes.txt

value: R. etli 55N1


title: GC2_DN_A10.DecN.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC2_DN_A10


title: NAG12 CE3 #1

description: FPKM for NAG12 genes.txt


title: ILN_VEH_1


title: RAL-897_brain_T=21h26m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_n_28260


title: ILN_Nav_47


title: RAL-892_brain_T=21h16m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28258


title: GC1_DP_H08.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_H08


title: ILN_Nav_46


title: RAL-890_brain_T=21h7m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_n_28257


title: GC1_DP_H06.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_H06


title: RAL-884_brain_T=20h57m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_n_28256


title: ILN_Nav_45


title: ILN_Nav_44


title: GC1_DP_H05.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_H05


title: RAL-879_brain_T=20h38m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_n_28254


title: RAL-855_brain_T=20h9m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28251


title: GC1_DP_H04.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_H04


title: NAG12 124N1 #1

description: FPKM for NAG12 genes.txt

value: R. etli 124N1


title: GC1_DP_H03.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_H03


title: NAG12 124N1 #3

description: FPKM for NAG12 genes.txt


title: NAG12 124N1 #2

description: FPKM for NAG12 genes.txt


title: NAG12 55N1 #1

description: FPKM for NAG12 genes.txt


title: ILN_Nav_41


title: NAG12 55N1 #2

description: FPKM for NAG12 genes.txt


title: RAL-853_brain_T=20h0m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_n_28250


title: ILN_Nav_42


title: GC1_DP_H02.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_H02


title: ALUBIA YEM #2

description: FPKM for ALUBIA genes.txt

value: Alubia


title: ILN_Nav_43


title: GC1_DP_H07.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_H07


title: GC1_DP_H01.DecP.12_H.LZ

description:
1dec_07082018-scRNAseq.txt.gz
GC1_DP_H01


title: ALUBIA SC15 #2

description: FPKM for ALUBIA genes.txt


title: ALUBIA YEM #1

description: FPKM for ALUBIA genes.txt


title: RAL-837_brain_T=19h40m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_n_28246


title: ALUBIA SC15 #1

description: FPKM for ALUBIA genes.txt